internal_name experiment_id method species GEO_ENA_Accession BioProject_Accession processed_ENCODE processed_3plex triplex_or_Hoogsteen_in_paper article_DOI author year available_bed_link experiment_specificity condition gencode_gene_name GenBank_ID author_lncRNA_name Ensembl_gene_ID notes
7SK 7SK-GSE69141 ChIRP-seq Human GSE69141 PRJNA284635 v1 v1 no 10.1038/nsmb.3176 Flynn 2016 download single_RNA H1 cell line RN7SK 7SK ENSG00000202198
Rn7sk Rn7sk-GSE69141 ChIRP-seq Mouse GSE69141 PRJNA284635 v1 v1 no 10.1038/nsmb.3176 Flynn 2016 download single_RNA mES cell line Rn7sk 7sk ENSMUSG00002076161
CDKN2B-AS1 CDKN2B-AS1-GSE162221 ChIRP-seq Human GSE162221 PRJNA681143 v1 v1 experimental 10.1093/nar/gkab245 Alfeghaly 2021 download single_RNA HEK293 cell line CDKN2B-AS1 ANRIL ENSG00000240498 low quality in replicate 2
AC087482.1 AC087482.1-GSE58989 ChIRP-seq Human GSE58989 PRJNA254057 v1 v1 computational 10.1093/hmg/ddv343 Merry 2015 download single_RNA HCT116 cell line AC087482.1 DACOR1 ENSG00000259347 triplex evidence in other papers (10.3390/ijms21030830)
Z85996.1 Z85996.1-GSE76418 ChIRP-seq Human GSE76418 PRJNA307254 v1 v1 no 10.1038/ng.3673 Schmitt 2016 download single_RNA U2OS cell line Z85996.1 DINO ENSG00000285244
Bloodlinc Bloodlinc-GSE97119 ChIRP-seq Mouse GSE97119 PRJNA380759 v1 v1 no 10.1016/j.celrep.2017.05.082 Alvarez-Dominguez 2017 download single_RNA MEL cell line Bloodlinc EC7 ENSMUSG00000087330
Eprn Eprn-GSE147208 ChIRP-seq Mouse GSE147208 PRJNA613423 v1 v1 computational 10.1093/nar/gkaa628 Zapparoli 2020 NA single_RNA NMuMG-EPR cell line Eprn Epr ENSMUSG00000113346
CPEB2-DT CPEB2-DT-GSE156121 ChIRP-seq Human GSE156121 PRJNA656806 v1 v1 no 10.1172/jci.insight.143289 Reddy 2021 download single_RNA THP1 cell line stably overexpressing DRAIR CPEB2-DT DRAIR ENSG00000247624
FA2H-2-MLKL FA2H-2-MLKL-NA ChIRP-seq Human NA NA no 10.1038/s41418-018-0235-z Guo 2019 NA single_RNA THP-1 cell line FA2H-2-MLKL no data available
MIR503HG MIR503HG-PRJEB34589 ChIRP-seq Human PRJEB34589 NA v1 v1 no 10.1172/JCI135439 Pachera 2020 NA single_RNA BJ5TA MIR503HG H19X ENSG00000223749
Gm18840 Gm18840-NA ChIRP-seq Mouse NA NA no 10.3389/fcell.2021.615950 Luo 2021 download single_RNA Gm18840-transduced HL-1 cell line Gm18840 Gm18840 ENSMUSG00000107568
Gm4665 Gm4665-GSE145189 ChIRP-seq Mouse GSE145189 PRJNA606277 v1 v1 no 10.1101/gr.264333.120 Li 2021 download single_RNA male germ cells Gm4665 Gm4665 ENSMUSG00000098127
9530018H14Rik@GLIAL 9530018H14Rik@GLIAL-GSE70986 ChIRP-seq Mouse GSE70986 PRJNA290073 v1 v1 no 10.1371/journal.pgen.1005680 Carlson 2015 download single_RNA Glial cell line 9530018H14Rik HOTCHON ENSMUSG00000102373
9530018H14Rik@LIMB 9530018H14Rik@LIMB-GSE70986 ChIRP-seq Mouse GSE70986 PRJNA290073 v1 v1 no 10.1371/journal.pgen.1005680 Carlson 2015 download single_RNA Limb Mesenchyme 9530018H14Rik HOTCHON ENSMUSG00000102373
HAND2-AS1 HAND2-AS1-GSE126122 ChIRP-seq Human GSE126122 PRJNA521057 v1 v1 no 10.15252/embj.2018101110 wang 2019 NA single_RNA Hepatocellular carcinoma cells HAND2-AS1 HAND2-AS1 ENSG00000237125
Hmrhl Hmrhl-NA ChIRP-seq Human NA NA computational 10.1093/narcan/zcab042 Choudhury 2021 download single_RNA K562 cell line Hmrhl
Lin28a Lin28a-GSE90574 ChIRP-seq Mouse GSE90574 PRJNA355091 v1 v1 no 10.7554/eLife.23468 Li 2017 download single_RNA mES cell line Lin28a Lin28a ENSMUSG00000050966
HOTAIR HOTAIR-GSE31332 ChIRP-seq Human GSE31332 PRJNA146003 v1 v1 experimental 10.1016/j.molcel.2011.08.027 Chu 2011 download single_RNA MDA-MB-231 cell line HOTAIR HOTAIR ENSG00000228630 triplex evidence in other papers (10.1093/nar/gkw802)
DT926623.1 DT926623.1-GSE66819 ChIRP-seq Mouse GSE66819 PRJNA278066 v1 v1 no 10.1016/j.stem.2015.02.002 Luo 2015 download single_RNA HPC5 cell line DT926623.1 lincHSC2
HOTTIP HOTTIP-GSE114981 ChIRP-seq Human GSE114981 PRJNA473439 v1 v1 no 10.1016/j.ccell.2019.10.011 Luo 2019 download single_RNA MOLM13 cell line HOTTIP HOTTIP ENSG00000243766
lncSmad7 lncSmad7-GSE174636 ChIRP-seq Mouse GSE174636 PRJNA730846 v1 v1 experimental doi.org/10.1093/nar/gkac083 Maldotti 2022 NA single_RNA mES cell line lncSmad7 lncSmad7 ENSMUSG00000025880
Linc-ASEN Linc-ASEN-GSE128396 ChIRP-seq Human GSE128396 PRJNA527315 no 10.1038/s41418-019-0467-6 Lee 2020 download single_RNA MCF7 cell line Linc-ASEN no input or negative control
LINC01667 LINC01667-NA ChIRP-seq Human NA NA no 10.3389/fonc.2021.650173 Zhang 2021 NA single_RNA HepG2 cell line LINC01667 the raw data supporting the conclusions of this article will be made available by the authors, without undue reservation, to any qualified researcher.
1200007C13Rik@4T1 1200007C13Rik@4T1-GSE142169 ChIRP-seq Mouse GSE142169 PRJNA596185 v1 v1 no 10.1038/s41467-020-20207 Chang 2020 download single_RNA 4T1 cell line 1200007C13Rik MaTAR25 ENSMUSG00000087684 the number of peaks provided by the authors is equal to the maximum number of rows in xls files
LINC01605 LINC01605-GSE112602 ChIRP-seq Human GSE112602 PRJNA448439 no 10.1038/s41598-018-25530-5 Forrest 2018 download single_RNA VACO 703 cell line LINC01605 lncDUSP ENSG00000253161 small number of reads in fastqs (3543)
MALAT1 MALAT1-GSE58444 CHART-seq Human GSE58444 PRJNA252626 v1 v1 no 10.1016/j.molcel.2014.07.012 West 2014 download single_RNA MCF7 cell line MALAT1 MALAT1 ENSG00000251562
MEG3 MEG3-PRJEB7307 ChOP-seq Human PRJEB7307 NA v1 v1 experimental 10.1038/ncomms8743 Mondal 2015 download single_RNA BT-549 cell line MEG3 MEG3 ENST00000451743
NEAT1 NEAT1-GSE58444 CHART-seq Human GSE58444 PRJNA252626 v1 v1 experimental 10.1016/j.molcel.2014.07.012 West 2014 download single_RNA MCF-7 cell line NEAT1 NEAT1 ENSG00000245532 triplex evidence in other papers (10.1093/nar/gky1305)
1200007C13Rik@NDL 1200007C13Rik@NDL-GSE142169 ChIRP-seq Mouse GSE142169 PRJNA596185 v1 v1 no 10.1038/s41467-020-20207 Chang 2020 download single_RNA NDL cell line 1200007C13Rik MaTAR25 ENSMUSG00000087684 the number of peaks provided by the authors is equal to the maximum number of rows in xls files
NFKBMARL-1 NFKBMARL-1-GSE167504 ChIRP-seq Human GSE167504 PRJNA704835 no 10.1038/s43587-021-00056-0 Cai 2021 download single_RNA IMR90 cell line NFKBMARL-1 unclear positive control, negative control and input definition
NRAD1 NRAD1-NA ChIRP-seq Human NA NA no 10.1038/s41418-019-0362-1 Vidovic 2020 NA single_RNA MDA-MB-468 cell line NRAD1 ENSG00000233725 no data available
Meg3 Meg3-GSE99798 ChIRP-seq Mouse GSE99798 PRJNA389664 v1 v1 experimental 10.1128/MCB.00278-17 Iyer 2017 download single_RNA MIN6-4N cell line Meg3 Meg3 ENSMUSG00000021268
AK156552.1 AK156552.1-GSE73805 ChIRP-seq Mouse GSE73805 PRJNA297950 v1 v1 poor 10.1016/j.celrep.2017.11.045 Wang 2018 download single_RNA mES cell line AK156552.1 Panct1
PCGEM1 PCGEM1-GSE47804 ChIRP-seq Human GSE47804 PRJNA207830 no 10.1038/nature12451 Yang 2013 download single_RNA LNCaP cell line PCGEM1 ENSG00000227418 no input or negative control
Rmrp Rmrp-GSE73912 ChIRP-seq Mouse GSE73912 PRJNA298543 no 10.1038/nature16193 Huang 2015 download single_RNA Rmrp RMRP ENSMUSG00000115420 Retracted article
AL109615.3 AL109615.3-GSE136185 CHART-seq Human GSE136185 PRJNA561525 v1 v1 no 10.1158/0008-5472.CAN-20-2612. Zagorac 2021 NA single_RNA MDA-MB-231 sphere-derived cell AL109615.3 SCIRT ENSG00000237686
AC018781.1 AC018781.1-GSE104479 ChIRP-seq Human GSE104479 PRJNA412810 v1 v1 no 10.1002/art.41200 Fan 2020 download single_RNA Jurkat cell line AC018781.1 SLEAR ENSG00000248599
SNHG11 SNHG11-NA ChIRP-seq Human NA NA no 10.1038/s41388-020-01512-8 Xu 2020 download single_RNA hypoxia-treated HCT-116 cell line SNHG11 ENSG00000174365 no data available
SRA1 SRA1-GSE58641 ChIRP-seq Human GSE58641 PRJNA253062 v1 v1 no 10.1371/journal.pgen.1005615 Wongtrakoongate 2015 download single_RNA NTERA2 pluripotent stem cell line SRA1 SRA ENSG00000213523
Tug1 Tug1-GSE77493 ChIRP-seq Mouse GSE77493 PRJNA310632 v1 v1 speculated 10.1172/JCI87927 Long 2016 download single_RNA Conditionally immortalized mouse podocytes Tug1 Tug1 ENSMUSG00000056579
ROX2 ROX2-GSE31332 ChIRP-seq Drosophila GSE31332 PRJNA146003 no 10.1016/j.molcel.2011.08.027 Chu 2011 download single_RNA S2 cell line ROX2
TERC TERC-GSE31332 ChIRP-seq Human GSE31332 PRJNA146003 v1 v1 experimental 10.1016/j.molcel.2011.08.027 Chu 2011 download single_RNA cell line V703 (Patient-derived colon cancer) TERC TERC ENSG00000277925 triplex evidence in other papers (10.1093/nar/gkz584)
Xist Xist-GSE137305 RAP-seq Mouse GSE137305 PRJNA565139 experimental 10.1126/science.1237973 Engreitz 2013 single_RNA ES cell line Xist Xist ENSMUSG00000086503 chrX only; triplex evidence in other papers (10.1186/s13100-019-0173-4)
GSE93281@Mouse GSE93281@Mouse-GSE93281 ChIRP-seq Mouse GSE93281 PRJNA360462 no 10.1093/nar/gkx055 Hu 2017 ERV-9 assoc. lncRNAs day 5 Tg mouse spleen NA
GSE93281@Human GSE93281@Human-GSE93281 ChIRP-seq Human GSE93281 PRJNA360462 no 10.1093/nar/gkx055 Hu 2017 ERV-9 assoc. lncRNAs day 13 erythroblast NA
GSE132192 GSE132192-GSE132192 RADICL-seq Mouse GSE132192 PRJNA546280 NA 10.1038/s41467-020-14337-6 Bonetti 2020 all_RNAs mES cell line NA
GSE82312@Drosophila GSE82312@Drosophila-GSE82312 GRID-seq Drosophila GSE82312 PRJNA324602 NA 10.1038/nbt.3968 Li 2017 all_RNAs S2 cell line NA
GSE82312@Human GSE82312@Human-GSE82312 GRID-seq Human GSE82312 PRJNA324602 NA 10.1038/nbt.3968 Li 2017 all_RNAs MDA-MB-231 breast cancer cell line (HTB-26, ATCC) NA
GSE82312@Mouse GSE82312@Mouse-GSE82312 GRID-seq Mouse GSE82312 PRJNA324602 NA 10.1038/nbt.3968 Li 2017 all_RNAs mES cell line NA
GSE92345@ES GSE92345@ES-GSE92345 MARGI-seq Human GSE92345 PRJNA357269 NA 10.1016/j.cub.2017.01.011 Sridhar 2017 all_RNAs ES cell line NA
GSE92345@H9 GSE92345@H9-GSE92345 MARGI-seq Human GSE92345 PRJNA357269 NA 10.1016/j.cub.2017.01.011 Sridhar 2017 all_RNAs H9 cell line NA
GSE97131 GSE97131-GSE97131 ChAR-seq Drosophila GSE97131 PRJNA380782 NA 10.7554/eLife.27024.001 Bell 2018 all_RNAs CME-W1-cl8+ cell line NA