title: P2.5_232

description:
Library name: P2_5_232
SMART-Seq2


title: USP39 (5116) eCLIP in K562 cells, INPUT replicate 2

status: Public on Apr 24 2026

type: SRA

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

country: USA

institute: UCSD

description:
Library name: USP39_K562_5116_INPUT_rep2
USP39_K562_5116.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for USP39, biological replicate 2

library_source: transcriptomic

data_processing:
Supplementary files format and content: Tab-delimited BED-like files containing reproducible enriched windows identified by eCLIP. Columns include: chromosome, start, end, feature type, enrichment odds ratio, p-value, FDR.
eCLIP data processing pipeline (Skipper v1.99.0)
Reads were trimmed, mapped to hg38 using STAR, deduplicated, and binding sites identified using beta-binomial model accounting for GC bias.
Reproducible enriched windows were identified at FDR < 0.2 across biological replicates.
Assembly: hg38
Supplementary files format and content: reproducible_enriched_windows.tsv.gz files contain reproducible enriched windows between two replicates (using uniquely mapped reads).
Supplementary files format and content: .bw files contain reads-per-million scaled read densities.
Library strategy: iCLIP

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Cells were UV crosslinked at 400 mJ/cm2, lysed, and treated with RNase I. Target RBP was immunoprecipitated with specific antibody. RNA was dephosphorylated, ligated to 3' RNA adaptor, and run on SDS-PAGE. Protein-RNA complexes were transferred to nitrocellulose membrane, excised, and treated with proteinase K.
RNA was reverse transcribed with AffinityScript (Agilent) and size-selected on TBE-Urea gel. 5' Illumina adaptor was ligated, and cDNA was PCR amplified. Libraries were sequenced on Illumina platforms. Detailed protocol in Van Nostrand et al., 2017, DOI: 10.1007/978-1-4939-7204-3_14.

tag: cell line

tag: treatment

value: USP39 (5116) eCLIP  INPUT


title: USP39 (5116) eCLIP in K562 cells, IP replicate 2

description:
Library name: USP39_K562_5116_IP_rep2
USP39_K562_5116.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for USP39, biological replicate 2

value: USP39 (5116) eCLIP  IP


title: P2.5_229

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

country: China

institute: Nanjing Medical University

description:
Library name: P2_5_229
SMART-Seq2

library_source: transcriptomic single cell

data_processing:
The RNA-seq data were first subjected to adaptor trimming and low-quality read filtering with flexbar (version 2.5).
The trimmed paired-end reads were then aligned to the human reference genome (mm10) by STAR (version 2.7.10b) under the parameters: -outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 6 --alignSJDBoverhangMin 1 --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonicalUnannotated.
HTSeq (v0.13.5) was employed for gene expression quantification.
RSEM (v1.3.3) was employed for gene expression normalization as FPKM
Assembly: mm10
Supplementary files format and content: gzipped tsv, FPKM values, gene expression levels
Supplementary files format and content: gzipped tsv, gene expression read counts

molecule: polyA RNA

organism: Mus musculus

source_name: female germ cell

extract_protocol:
Each sample is lysed using a 2 µL lysis buffer with 0.2% TritonX-100 and 40 U/mL Recombinant RNase Inhibitor, which disrupts cell membranes to release RNA and other cellular contents while preventing RNA degradation.
Transcriptome libraries were prepared following the Smart-seq2 protocol. Sequencing libraries were constructed by using KAPA HyperPlus Kit according to the manufacturer’s instructions.  All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 150-bp paired-end mode.

tag: cell type

value: female germ cell

tag: Stage


title: KHSRP (5001) eCLIP in K562 cells, IP replicate 1

description:
Library name: KHSRP_K562_5001_IP_rep1
KHSRP_K562_5001.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for KHSRP, biological replicate 1

value: KHSRP (5001) eCLIP  IP


title: AGO2 (4116) eCLIP in K562 cells, IP replicate 2

description:
Library name: AGO2_K562_4116_IP_rep2
eCLIP immunoprecipitation sample for AGO2, biological replicate 2


title: P2.5_230

description:
Library name: P2_5_230
SMART-Seq2


title: LARP1 (5110) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: LARP1_K562_5110_INPUT_rep2
LARP1_K562_5110.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for LARP1, biological replicate 2

value: LARP1 (5110) eCLIP  INPUT


title: P2.5_231

description:
Library name: P2_5_231
SMART-Seq2


title: AGO2 (4116) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: AGO2_K562_4116_INPUT_rep2
eCLIP size-matched input control for AGO2, biological replicate 2


title: LARP1 (5110) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: LARP1_K562_5110_INPUT_rep1
LARP1_K562_5110.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for LARP1, biological replicate 1


title: AGO2 (4116) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: AGO2_K562_4116_INPUT_rep1
eCLIP size-matched input control for AGO2, biological replicate 1


title: P2.5_228

description:
Library name: P2_5_228
SMART-Seq2


title: USP39 (5116) eCLIP in K562 cells, IP replicate 1

description:
Library name: USP39_K562_5116_IP_rep1
USP39_K562_5116.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for USP39, biological replicate 1


title: LARP1 (5110) eCLIP in K562 cells, IP replicate 1

description:
Library name: LARP1_K562_5110_IP_rep1
LARP1_K562_5110.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for LARP1, biological replicate 1

value: LARP1 (5110) eCLIP  IP


title: USP39 (5116) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: USP39_K562_5116_INPUT_rep1
USP39_K562_5116.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for USP39, biological replicate 1


title: YTHDF2 (5108) eCLIP in K562 cells, IP replicate 2

description:
Library name: YTHDF2_K562_5108_IP_rep2
YTHDF2_K562_5108.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for YTHDF2, biological replicate 2

value: YTHDF2 (5108) eCLIP  IP


title: YTHDF2 (5108) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: YTHDF2_K562_5108_INPUT_rep2
YTHDF2_K562_5108.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for YTHDF2, biological replicate 2

value: YTHDF2 (5108) eCLIP  INPUT


title: PABPC1 (5117) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: PABPC1_K562_5117_INPUT_rep2
PABPC1_K562_5117.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for PABPC1, biological replicate 2

value: PABPC1 (5117) eCLIP  INPUT


title: YTHDF2 (5108) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: YTHDF2_K562_5108_INPUT_rep1
YTHDF2_K562_5108.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for YTHDF2, biological replicate 1


title: P2.5_227

description:
Library name: P2_5_227
SMART-Seq2


title: APEX1 (4028) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: APEX1_K562_4028_INPUT_rep2
eCLIP size-matched input control for APEX1, biological replicate 2


title: YTHDF2 (5108) eCLIP in K562 cells, IP replicate 1

description:
Library name: YTHDF2_K562_5108_IP_rep1
YTHDF2_K562_5108.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for YTHDF2, biological replicate 1


title: P2.5_226

description:
Library name: P2_5_226
SMART-Seq2


title: PABPC1 (5117) eCLIP in K562 cells, IP replicate 2

description:
Library name: PABPC1_K562_5117_IP_rep2
PABPC1_K562_5117.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for PABPC1, biological replicate 2

value: PABPC1 (5117) eCLIP  IP


title: APEX1 (4028) eCLIP in K562 cells, IP replicate 2

description:
Library name: APEX1_K562_4028_IP_rep2
eCLIP immunoprecipitation sample for APEX1, biological replicate 2


title: PABPC1 (5117) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: PABPC1_K562_5117_INPUT_rep1
PABPC1_K562_5117.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for PABPC1, biological replicate 1


title: AGO2 (4116) eCLIP in K562 cells, IP replicate 1

description:
Library name: AGO2_K562_4116_IP_rep1
eCLIP immunoprecipitation sample for AGO2, biological replicate 1


title: P2.5_225

description:
Library name: P2_5_225
SMART-Seq2


title: MDA5 siRNA bio rep 3

city: Columbus

first: Laszlo

last: Farkas

state: OH

address: 473 W 12th Avenue

institute: The Ohio State University

description: Library name: MDA5 siRNA bio rep 3

data_processing:
Raw Data was analyzed using ROSALIND (https://rosalind.bio/) as published previously (ROSALIND, Inc., San Diego, CA). In brief, reads were trimmed using cutadapt. Quality scores were assessed using FastQC. Reads were aligned to the Homo sapiens genome build GRCh38 using STAR. Individual sample reads were quantified using Htseq and normalized via Relative Log Expression (RLE) using DESeq2 R library. Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RseQC. Deseq2 was also used to calculate fold changes and p-values and perform optional covariate correction.
Assembly: GRCh38
Supplementary files format and content: TXT files, raw counts and normalized counts

source_name: primary

growth_protocol: Human pulmonary artery endothelial cells were cultured in complete EGM-2MV media (Lonza CC-3162) in a cell culture incubator at 37°C with 5% CO2 and 100% humidity.

extract_protocol:
RNA was isolated using the Qiagen miRNAeasy mini kit (217084) according to the manufacturer's instructions, followed by DNAse digestion to remove potential genomic DNA contamination. DNAse I treatment was performed at 0.1 U/μl final activity for 15 min at room temperature, followed by the addition of 25 mM EDTA and incubation at 65˚C for 10 min to inactivate DNAse. Total mRNA concentrations were measured using Nanodrop (ThermoFisher Scientific).
RNA sequencing was performed by Novogene (Sacramento, CA). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms according to the effective library concentration and the amount of data.

treatment_protocol: primary pulmonary artery endothelial cells were transfected with siRNA targeting human MDA5 (IFIH1) or non-targeting control siRNA (IDT) at 50 nM  using GeneMute transfection reagent. After 16hours, the cell culture medium was changed, and mRNA was harvested 72h after transfection. siRNAs used: control siRNA (IDT, 51-01-14-04), MDA5 (IDT, 13.2).

tag: tissue

value: lung

value: pulmonary artery endothelial cells

value: MDA5 siRNA


title: APEX1 (4028) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: APEX1_K562_4028_INPUT_rep1
eCLIP size-matched input control for APEX1, biological replicate 1


title: PABPC1 (5117) eCLIP in K562 cells, IP replicate 1

description:
Library name: PABPC1_K562_5117_IP_rep1
PABPC1_K562_5117.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for PABPC1, biological replicate 1


title: MDA5 siRNA bio rep 2

description: Library name: MDA5 siRNA bio rep 2


title: P2.5_224

description:
Library name: P2_5_224
SMART-Seq2


title: P2.5_223

description:
Library name: P2_5_223
SMART-Seq2


title: P2.5_222

description:
Library name: P2_5_222
SMART-Seq2


title: APEX1 (4028) eCLIP in K562 cells, IP replicate 1

description:
Library name: APEX1_K562_4028_IP_rep1
eCLIP immunoprecipitation sample for APEX1, biological replicate 1


title: MDA5 siRNA bio rep 1

description: Library name: MDA5 siRNA bio rep 1


title: FXR1 (4036) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: FXR1_K562_4036_INPUT_rep2
eCLIP size-matched input control for FXR1, biological replicate 2


title: EIF2S1 (5130) eCLIP in K562 cells, IP replicate 2

description:
Library name: EIF2S1_K562_5130_IP_rep2
EIF2S1_K562_5130.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF2S1, biological replicate 2

value: EIF2S1 (5130) eCLIP  IP


title: EIF2S1 (5130) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: EIF2S1_K562_5130_INPUT_rep2
EIF2S1_K562_5130.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF2S1, biological replicate 2

value: EIF2S1 (5130) eCLIP  INPUT


title: control siRNA bio rep 2

description: Library name: non-targeting control (NTC) siRNA bio rep 2

value: control siRNA


title: EIF2S1 (5130) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: EIF2S1_K562_5130_INPUT_rep1
EIF2S1_K562_5130.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF2S1, biological replicate 1


title: FXR1 (4036) eCLIP in K562 cells, IP replicate 2

description:
Library name: FXR1_K562_4036_IP_rep2
eCLIP immunoprecipitation sample for FXR1, biological replicate 2


title: FXR1 (4036) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: FXR1_K562_4036_INPUT_rep1
eCLIP size-matched input control for FXR1, biological replicate 1


title: P2.5_220

description:
Library name: P2_5_220
SMART-Seq2


title: FXR1 (4036) eCLIP in K562 cells, IP replicate 1

description:
Library name: FXR1_K562_4036_IP_rep1
eCLIP immunoprecipitation sample for FXR1, biological replicate 1


title: EIF2S1 (5130) eCLIP in K562 cells, IP replicate 1

description:
Library name: EIF2S1_K562_5130_IP_rep1
EIF2S1_K562_5130.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF2S1, biological replicate 1


title: EIF1 (5134) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: EIF1_K562_5134_INPUT_rep2
EIF1_K562_5134.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF1, biological replicate 2

value: EIF1 (5134) eCLIP  INPUT


title: control siRNA bio rep 3

description: Library name: non-targeting control (NTC) siRNA bio rep 3


title: RAW_Rosi_CUTTag_H3K27ac_2

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

library_source: genomic

data_processing:
ChIP-seq raw files (fastq, paired-end) were aligned to the mm9 version of the mouse reference genome using Bowtie2 with default parameters. Peaks were called using HOMER. HOMER was then used to construct tag directories from the SAM files, remove duplicate reads, call peaks, annotate peaks, extract raw tag counts, and generate bed files. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are retained.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm9
Supplementary files format and content: Bedgraph files contain the gene expression tags counts and p-value.
Supplementary files format and content: The differential expression file was further provided(tab-delimited file).
The raw ATAC-seq files (fastq, paired-end) were aligned to the mouse reference genome version mm9 using Bowtie2 with default parameters. Peak calling was then performed using MACS2. HOMER was then used to create tag directories from the SAM files, eliminate duplicate reads, identify peaks, annotate peaks, extract raw tag counts, and generate bed files. Only peaks meeting the criteria of fold enrichment over input tag count and local tag count > 4 with a false discovery rate (FDR) < 0.001 (using default settings -F -L -C -fdr) were retained.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm9
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.
Cut&Tag raw files (fastq, paired-end) were aligned to the mouse reference genome (mm9) using Bowtie2 with default settings. Peak calling was performed using MACS2. HOMER was then used to construct tag directories from the SAM files, eliminate duplicate reads, call peaks, annotate peaks, extract raw tag counts, and generate bed files. Only peaks that met the criteria of fold enrichment over input tag count, local tag count > 4, and false discovery rate (fdr) < 0.001 (using default parameters -F -L -C -fdr) were retained.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm9
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.
Library strategy: Cut&Tag

molecule: genomic DNA

source_name: Ascites

growth_protocol: RAW264.7 cells were maintained normal 10% FBS DMEM medium.

extract_protocol:
The Cut and Tag Library preparation was performed through the manufacturer's introduction (Steven Henikoff lab,Bench top CUT&Tag V.3 ).
The Cut and Tag Library preparation was performed through the manufacturer's introduction (Steven Henikoff lab,Bench top CUT&Tag V.3 ).

treatment_protocol: RAW264.7 cells were treated  with or without Rosiglitazone (5uM),9-cis retinoic acid(RA,5uM) treatment for 3 hours.

value: Ascites

value: Macrophages

tag: strain

value: BALB/c

value: Rosiglitazone (Rosi)  treatment


title: P2.5_219

description:
Library name: P2_5_219
SMART-Seq2

value: female germ cell


title: P2.5_221

description:
Library name: P2_5_221
SMART-Seq2


title: FMRP (4030) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: FMRP_K562_4030_INPUT_rep2
eCLIP size-matched input control for FMRP, biological replicate 2


title: P2.5_218

description:
Library name: P2_5_218
SMART-Seq2


title: control siRNA bio rep 1

description: Library name: non-targeting control (NTC) siRNA bio rep 1


title: RAW_Rosi_CUTTag_H3K27ac_1


title: P2.5_217

description:
Library name: P2_5_217
SMART-Seq2


title: EIF1 (5134) eCLIP in K562 cells, IP replicate 2

description:
Library name: EIF1_K562_5134_IP_rep2
EIF1_K562_5134.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF1, biological replicate 2

value: EIF1 (5134) eCLIP  IP


title: EIF1 (5134) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: EIF1_K562_5134_INPUT_rep1
EIF1_K562_5134.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for EIF1, biological replicate 1


title: FMRP (4030) eCLIP in K562 cells, IP replicate 2

description:
Library name: FMRP_K562_4030_IP_rep2
eCLIP immunoprecipitation sample for FMRP, biological replicate 2


title: P2.5_215

description:
Library name: P2_5_215
SMART-Seq2


title: FMRP (4030) eCLIP in K562 cells, IP replicate 1

description:
Library name: FMRP_K562_4030_IP_rep1
eCLIP immunoprecipitation sample for FMRP, biological replicate 1


title: FMRP (4030) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: FMRP_K562_4030_INPUT_rep1
eCLIP size-matched input control for FMRP, biological replicate 1


title: P2.5_216

description:
Library name: P2_5_216
SMART-Seq2


title: CNOT3 (5133) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: CNOT3_K562_5133_INPUT_rep2
CNOT3_K562_5133.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for CNOT3, biological replicate 2

value: CNOT3 (5133) eCLIP  INPUT


title: RAW_CUTTag_H3K27ac_2

value: Control


title: P2.5_214

description:
Library name: P2_5_214
SMART-Seq2


title: RAW_RA_CUTTag_H3K27ac_1

value: Retinoic acid(RA) treatment


title: CNOT3 (5133) eCLIP in K562 cells, IP replicate 2

description:
Library name: CNOT3_K562_5133_IP_rep2
CNOT3_K562_5133.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for CNOT3, biological replicate 2

value: CNOT3 (5133) eCLIP  IP


title: RAW_RA_CUTTag_H3K27ac_2


title: RAW_CUTTag_H3K27ac_1


title: EIF1 (5134) eCLIP in K562 cells, IP replicate 1

description:
Library name: EIF1_K562_5134_IP_rep1
EIF1_K562_5134.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for EIF1, biological replicate 1


title: SF3A1 (4117) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: SF3A1_HepG2_4117_INPUT_rep2
eCLIP size-matched input control for SF3A1, biological replicate 2


title: CNOT3 (5133) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: CNOT3_K562_5133_INPUT_rep1
CNOT3_K562_5133.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for CNOT3, biological replicate 1


title: SF3A1 (4117) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: SF3A1_HepG2_4117_IP_rep2
eCLIP immunoprecipitation sample for SF3A1, biological replicate 2


title: P2.5_213

description:
Library name: P2_5_213
SMART-Seq2


title: HEK293T RNA-seq data Rep1

city: Denver

first: Gongyi

last: Zhang

state: CO

address: 1400 Jackson St

department: Immunology and Genomic Medicine

institute: National Jewish Health

description: Library name: Sample 55

data_processing:
RNA-seq: Data were analyzed by workflows on Basepair (hmps://www.basepairtech.com).
Assembly: Hg38
Supplementary files format and content: Bigwig

source_name: Human Kidney

growth_protocol: HEK293T cells were cultured in DMEM plus 10% FBS, 100 units/mL penicillin, and 100 μg/mL streptomycin in a humidified 37°C, 5% CO2 incubator.

extract_protocol:
RNA-seq:  For RNA, total RNA was purified with an RNeasy Mini kit (QIAGEN).
RNA-seq: mRNAs were isolated using NEBNext Poly(A) mRNA Magnetic isolation kit (NEW ENGLAND Biolabs). Libraries were prepared by using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB #E7530S/L (NEW ENGLAND Biolabs). The DNA library was validated using TapeStation (Agilent Technologies).

treatment_protocol: For RNA-seq:  no special treatment is applied

value: Human Kidney

value: Human embryonic kidney 293

tag: genotype

value: wt

value: Native control


title: SF3A1 (4117) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: SF3A1_HepG2_4117_INPUT_rep1
eCLIP size-matched input control for SF3A1, biological replicate 1


title: Hek293T RNA-seq data Rep2

description: Library name: Sample 56


title: CNOT3 (5133) eCLIP in K562 cells, IP replicate 1

description:
Library name: CNOT3_K562_5133_IP_rep1
CNOT3_K562_5133.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for CNOT3, biological replicate 1


title: CDK9 (5063) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: CDK9_HepG2_5063_INPUT_rep2
CDK9_HepG2_5063.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for CDK9, biological replicate 2

value: CDK9 (5063) eCLIP  INPUT


title: P2.5_212

description:
Library name: P2_5_212
SMART-Seq2


title: P2.5_211

description:
Library name: P2_5_211
SMART-Seq2


title: SF3A1 (4117) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: SF3A1_HepG2_4117_IP_rep1
eCLIP immunoprecipitation sample for SF3A1, biological replicate 1


title: PRPF39 (4114) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: PRPF39_HepG2_4114_INPUT_rep2
eCLIP size-matched input control for PRPF39, biological replicate 2


title: HEK293T Ser2ph-CTD of Pol II DRB withdraw 60 minutes rep 1

description: Library name: Sample 54

data_processing:
CUT&TAG-seq: Adapter sequences from reads were trimmed with fastp v0.20.0 and aligned to the GRCh38 human reference genome by bwa v0.7.12. Mitochondrial reads and duplicate reads were removed and the remaining reads were filtered to include only properly aligned pairs by sambamba v0.7.1. Peaks were called from the deduplicated bam files using macs2 with parameters -q 0.001 --keep-dup all -B --SPMR --nomodel –nolambda. Peaks were merged using bedtools v2.26.0  and intersected with refGene_hg38 gene models on the standard chromosomes.
Assembly: Hg38
Supplementary files format and content: Bigwig
Library strategy: CUT&Tag

extract_protocol:
CUT&TAG-seq: Split cells into 1 million cells per 10 cm dish one day before harvesting. Wash cells 2 times in PBS. Add 4 ml 0.1% formaldehyde in PBS into each dish. And incubate at room temperature for 2 minutes. Stop cross-linking by addition of 1.25 M glycine to twice the molar concentration of formaldehyde (e.g., 600 µL to 10 ml). Wash 2 times in PBS and harvest cells in PBS in conical centrifuge tubes (15 ml or 50 ml). Centrifuge 4 min 1300 x g at 4 °C and drain liquid by pouring off and inverting onto a paper towel for a few seconds. Resuspend in Wash buffer to a concentration of ~1 million cells per ml. Check nuclei using ViCell or cell counter slide.
CUT&TAG-seq:Libraries for CUT&TAG-seq were prepared following the protocol by Henikoff v3 (hmps://www.protocols.io/). Briefly, in a thin-wall 0.5 ml PCR tube, using a different barcode for each sample (Indexed primers described by Buenrostro, J.D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523:486 (2015)). Add 25 µL NEBNext HiFi 2x PCR Master mix. Mix, quickly spin, and place in Thermocycler. Begin the cycling program with a heated lid. Cycle 1: 72 °C for 5 min (gap filling), Cycle 2: 98 °C for 30 sec, Cycle 3: 98 °C for 10 sec, Cycle 4: 63 °C for 10 sec, Repeat Cycles 3-4 13 times, 72°C for 1 min and hold at 8 °C. The amplified libraries were purified, and size-selected, and the quality and quantity of libraries were assessed on the 4150 TapeStation System (Agilent, CA).

treatment_protocol: CUT&TAG-seq: HEK293T cells were not treated or treated with 100 µM DRB. Cells were harvested at  5, 15, and 30 minutes post-treatment, and following 30-minute DRB exposure, cells were washed and allowed to recover for 10, 30, or 60 minutes before harvesting.

value: DRB withdarw for 60 minutes

tag: cu&tag-seq antibodies

value: 3E10, Abcam cat.no.ab252855


title: CDK9 (5063) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: CDK9_HepG2_5063_IP_rep2
CDK9_HepG2_5063.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for CDK9, biological replicate 2

value: CDK9 (5063) eCLIP  IP


title: HEK293T Ser2ph-CTD of Pol II DRB withdraw 30 minutes rep 1

description: Library name: Sample 53

value: DRB withdraw for 30  minutes


title: P2.5_209

description:
Library name: P2_5_209
SMART-Seq2


title: PRPF39 (4114) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: PRPF39_HepG2_4114_IP_rep2
eCLIP immunoprecipitation sample for PRPF39, biological replicate 2


title: CDK9 (5063) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: CDK9_HepG2_5063_INPUT_rep1
CDK9_HepG2_5063.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for CDK9, biological replicate 1


title: PABPN1 (5062) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: PABPN1_HepG2_5062_INPUT_rep2
eCLIP size-matched input control for PABPN1, biological replicate 2

value: PABPN1 (5062) eCLIP  INPUT


title: P2.5_208

description:
Library name: P2_5_208
SMART-Seq2


title: HEK293T Ser2ph-CTD of Pol II DRB withdraw 10 minutes rep 1

description: Library name: Sample 52

value: DRB withdraw for 10 minutes


title: PRPF39 (4114) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: PRPF39_HepG2_4114_IP_rep1
eCLIP immunoprecipitation sample for PRPF39, biological replicate 1


title: HEK293T H4S1ph DRB withdraw 60 minutes rep 1

description: Library name: Sample 51

value: Abcam cat.no.ab177309


title: CDK9 (5063) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: CDK9_HepG2_5063_IP_rep1
CDK9_HepG2_5063.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for CDK9, biological replicate 1


title: P2.5_207

description:
Library name: P2_5_207
SMART-Seq2

value: female germ cell


title: P2.5_210

description:
Library name: P2_5_210
SMART-Seq2


title: HEK293T H4S1ph DRB withdraw 30 minutes rep 1

description: Library name: Sample 50


title: PRPF39 (4114) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: PRPF39_HepG2_4114_INPUT_rep1
eCLIP size-matched input control for PRPF39, biological replicate 1


title: HEK293T H4KS1ph DRB withdraw 10 minutes rep 1

description: Library name: Sample 49


title: GARS (4108) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: GARS_HepG2_4108_IP_rep2
eCLIP immunoprecipitation sample for GARS, biological replicate 2


title: P2.5_206

description:
Library name: P2_5_206
SMART-Seq2


title: GARS (4108) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: GARS_HepG2_4108_INPUT_rep2
eCLIP size-matched input control for GARS, biological replicate 2


title: PABPN1 (5062) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: PABPN1_HepG2_5062_IP_rep2
eCLIP immunoprecipitation sample for PABPN1, biological replicate 2

value: PABPN1 (5062) eCLIP  IP


title: P2.5_205

description:
Library name: P2_5_205
SMART-Seq2


title: HEK293T H3S10ph DRB withdraw 30 minutes rep 1

description: Library name: Sample 47

value: CMA311, a gift from Dr. Hiroshi Kimura’s group


title: SFPQ (5125) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: SFPQ_K562_5125_INPUT_rep2
SFPQ_K562_5125.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for SFPQ, biological replicate 2

value: SFPQ (5125) eCLIP  INPUT


title: HEK293T H3S10ph DRB withdraw 60 minutes rep 1

description: Library name: Sample 48


title: PABPN1 (5062) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: PABPN1_HepG2_5062_IP_rep1
eCLIP immunoprecipitation sample for PABPN1, biological replicate 1


title: P2.5_204

description:
Library name: P2_5_204
SMART-Seq2


title: HEK293T H4K12Ac DRB withdraw 60 minutes rep 1

description: Library name: Sample 45

value: Active Motif.cat.no.39165


title: GARS (4108) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: GARS_HepG2_4108_INPUT_rep1
eCLIP size-matched input control for GARS, biological replicate 1


title: GARS (4108) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: GARS_HepG2_4108_IP_rep1
eCLIP immunoprecipitation sample for GARS, biological replicate 1


title: SFPQ (5125) eCLIP in K562 cells, IP replicate 1

description:
Library name: SFPQ_K562_5125_IP_rep1
SFPQ_K562_5125.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for SFPQ, biological replicate 1

value: SFPQ (5125) eCLIP  IP


title: HEK293T H4K12Ac DRB withdraw 30 minutes rep 1

description: Library name: Sample 44

value: Human Kidney

value: Human embryonic kidney 293


title: PABPN1 (5062) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: PABPN1_HepG2_5062_INPUT_rep1
eCLIP size-matched input control for PABPN1, biological replicate 1


title: ELAVL1 (4083) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: ELAVL1_HepG2_4083_INPUT_rep1
eCLIP size-matched input control for ELAVL1, biological replicate 1


title: ELAVL1 (4083) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: ELAVL1_HepG2_4083_INPUT_rep2
eCLIP size-matched input control for ELAVL1, biological replicate 2


title: HEK293T H3KS10ph DRB withdraw 10 minutes rep 1

description: Library name: Sample 46

value: wt


title: P2.5_200

description:
Library name: P2_5_200
SMART-Seq2


title: P2.5_199

description:
Library name: P2_5_199
SMART-Seq2


title: P2.5_202

description:
Library name: P2_5_202
SMART-Seq2


title: SFPQ (5125) eCLIP in K562 cells, IP replicate 2

description:
Library name: SFPQ_K562_5125_IP_rep2
SFPQ_K562_5125.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for SFPQ, biological replicate 2


title: P2.5_203

description:
Library name: P2_5_203
SMART-Seq2


title: P2.5_201

description:
Library name: P2_5_201
SMART-Seq2


title: ELAVL1 (4083) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: ELAVL1_HepG2_4083_IP_rep2
eCLIP immunoprecipitation sample for ELAVL1, biological replicate 2


title: HEK293T H4K12Ac DRB withdraw 10 minutes rep 1

description: Library name: Sample 43


title: THOC4 (5123) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: THOC4_K562_5123_INPUT_rep1
THOC4_K562_5123.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for THOC4, biological replicate 1

value: THOC4 (5123) eCLIP  INPUT


title: APEX1 (4081) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: APEX1_HepG2_4081_IP_rep2
eCLIP immunoprecipitation sample for APEX1, biological replicate 2


title: ELAVL1 (4083) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: ELAVL1_HepG2_4083_IP_rep1
eCLIP immunoprecipitation sample for ELAVL1, biological replicate 1


title: HEK293T H3K9Ac DRB withdraw 60 minutes rep 1

description: Library name: Sample 42

value: DRB withdarw for 60 minutes

value: Active Motif. cat.no.61251


title: P2.5_198

description:
Library name: P2_5_198
SMART-Seq2


title: THOC4 (5123) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: THOC4_K562_5123_INPUT_rep2
THOC4_K562_5123.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for THOC4, biological replicate 2


title: SFPQ (5125) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: SFPQ_K562_5125_INPUT_rep1
SFPQ_K562_5125.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for SFPQ, biological replicate 1


title: THOC4 (5123) eCLIP in K562 cells, IP replicate 2

description:
Library name: THOC4_K562_5123_IP_rep2
THOC4_K562_5123.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for THOC4, biological replicate 2

value: THOC4 (5123) eCLIP  IP


title: APEX1 (4081) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: APEX1_HepG2_4081_INPUT_rep2
eCLIP size-matched input control for APEX1, biological replicate 2


title: HEK293T H3K9Ac DRB withdraw 30 minutes rep 1

description: Library name: Sample 41

value: DRB withdraw for 30  minutes


title: P2.5_195

description:
Library name: P2_5_195
SMART-Seq2


title: HEK293T Ser2ph-CTD of Pol II DRB  30 minutes rep 2

description: Library name: Sample 39

value: DRB treatment for 30  minutes

value: 3E10, Abcam cat.no.ab252855


title: P2.5_196

description:
Library name: P2_5_196
SMART-Seq2


title: P2.5_197

description:
Library name: P2_5_197
SMART-Seq2


title: EIF4E (4082) eCLIP in HepG2 cells, INPUT replicate 2

description:
Library name: EIF4E_HepG2_4082_INPUT_rep2
eCLIP size-matched input control for EIF4E, biological replicate 2


title: HEK293T Ser2ph-CTD of Pol II DRB 30 minutes rep 1

description: Library name: Sample 38


title: HEK293T H3K9Ac DRB withdraw 10 minutes rep 1

description: Library name: Sample 40

value: DRB withdraw for 10 minutes


title: P2.5_194

description:
Library name: P2_5_194
SMART-Seq2

value: female germ cell


title: NCBP1 (5121) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: NCBP1_K562_5121_INPUT_rep1
NCBP1_K562_5121.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for NCBP1, biological replicate 1

value: NCBP1 (5121) eCLIP  INPUT


title: APEX1 (4081) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: APEX1_HepG2_4081_IP_rep1
eCLIP immunoprecipitation sample for APEX1, biological replicate 1


title: NCBP1 (5121) eCLIP in K562 cells, IP replicate 2

description:
Library name: NCBP1_K562_5121_IP_rep2
NCBP1_K562_5121.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for NCBP1, biological replicate 2

value: NCBP1 (5121) eCLIP  IP


title: P2.5_193

description:
Library name: P2_5_193
SMART-Seq2


title: NCBP1 (5121) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: NCBP1_K562_5121_INPUT_rep2
NCBP1_K562_5121.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for NCBP1, biological replicate 2


title: THOC4 (5123) eCLIP in K562 cells, IP replicate 1

description:
Library name: THOC4_K562_5123_IP_rep1
THOC4_K562_5123.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for THOC4, biological replicate 1


title: P2.5_192

description:
Library name: P2_5_192
SMART-Seq2


title: HEK293T Ser2ph-CTD of Pol II DRB 15 minutes rep 2

description: Library name: Sample 37

value: DRB treatment for 15 minutes


title: APEX1 (4081) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: APEX1_HepG2_4081_INPUT_rep1
eCLIP size-matched input control for APEX1, biological replicate 1


title: EIF4E (4082) eCLIP in HepG2 cells, IP replicate 2

description:
Library name: EIF4E_HepG2_4082_IP_rep2
eCLIP immunoprecipitation sample for EIF4E, biological replicate 2


title: EIF4E (4082) eCLIP in HepG2 cells, INPUT replicate 1

description:
Library name: EIF4E_HepG2_4082_INPUT_rep1
eCLIP size-matched input control for EIF4E, biological replicate 1


title: HEK293T Ser2ph-CTD of Pol II DRB  5 minutes rep 2

description: Library name: Sample 35

value: DRB treatment for five minutes


title: HEK293T Ser2ph-CTD of Pol II DRB 15 minutes rep 1

description: Library name: Sample 36


title: NCBP1 (5121) eCLIP in K562 cells, IP replicate 1

description:
Library name: NCBP1_K562_5121_IP_rep1
NCBP1_K562_5121.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for NCBP1, biological replicate 1


title: P2.5_191

description:
Library name: P2_5_191
SMART-Seq2


title: BCAT2 (5120) eCLIP in K562 cells, IP replicate 2

description:
Library name: BCAT2_K562_5120_IP_rep2
BCAT2_K562_5120.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for BCAT2, biological replicate 2

value: BCAT2 (5120) eCLIP  IP


title: BCAT2 (5120) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: BCAT2_K562_5120_INPUT_rep2
BCAT2_K562_5120.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for BCAT2, biological replicate 2

value: BCAT2 (5120) eCLIP  INPUT


title: P2.5_190

description:
Library name: P2_5_190
SMART-Seq2


title: U2OS cytosolic condensates, PEG treatment, biol rep 3

city: Heidelberg

first: Alessia

last: Ruggieri

address: Im Neuenheimer Feld 344

department: Dpt. of Infectious Diseases, Molecular Virology

country: Germany

institute: Heidelberg University

description: Library name: U2OS_PEG_Rep3

data_processing:
Raw reads were trimmed to remove adapter sequences and low-quality bases using Trimmomatic v0.36.
Trimmed reads were aligned to the Homo sapiens GRCh38 reference genome using STAR aligner v2.5.2b.
Only uniquely aligned reads falling within annotated exons were retained using exon-based annotation and strand-specific settings.
Unique gene hit counts were generated using featureCounts from the Subread package v1.5.2.
Assembly: Homo sapiens, GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: U2OS wild type cells were cultured at 37°C and 5% CO2 in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% FCS, 1% non-essential amino acids, 100 U/ml penicillin, and 100 µg/ml streptomycin.

extract_protocol:
After treatment, samples were centrifuged at 14,000 g for 10 minutes at 4°C. Pellets were washed twice with 20 µl ice-cold PBS and resuspended in RNase-free water. Input samples containing U2OS cytosolic extracts were not pelleted. RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepared by using poly(A) selection for mRNA enrichment. Following fragmentation, cDNA was synthesized using random hexamer priming. Second-strand synthesis, 5′ end repair, dA-tailing, adaptor ligation, and PCR amplification were performed.

treatment_protocol: In vitro translation reactions with U2OS cytosolic extracts were performed with the following treatments for 2 hours at 37°C: 250 nM dsRNA, 1% PEG, 2 µg/ml silvestrol, untreated (mock).

value: osteosarcoma

value: wild type


title: EIF4E (4082) eCLIP in HepG2 cells, IP replicate 1

description:
Library name: EIF4E_HepG2_4082_IP_rep1
eCLIP immunoprecipitation sample for EIF4E, biological replicate 1


title: P2.5_189

description:
Library name: P2_5_189
SMART-Seq2


title: HEK293T Ser2ph-CTD of Pol II control rep 2

description: Library name: Sample 33

value: Human Kidney

value: Human embryonic kidney 293

value: wt

value: Native control


title: HEK293T Ser2ph-CTD of Pol II DRB 5 minutes rep 1

description: Library name: Sample 34


title: BCAT2 (5120) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: BCAT2_K562_5120_INPUT_rep1
BCAT2_K562_5120.reproducible_enriched_windows.tsv.gz
eCLIP size-matched input control for BCAT2, biological replicate 1


title: U2OS cytosolic condensates, PEG treatment, biol rep 2

description: Library name: U2OS_PEG_Rep2


title: U2OS cytosolic condensates, PEG treatment, biol rep 1

description: Library name: U2OS_PEG_Rep1


title: P2.5_188

description:
Library name: P2_5_188
SMART-Seq2


title: HEK293T Ser2ph-CTD of Pol II control rep 1

description: Library name: Sample 32


title: BCAT2 (5120) eCLIP in K562 cells, IP replicate 1

description:
Library name: BCAT2_K562_5120_IP_rep1
BCAT2_K562_5120.reproducible_enriched_windows.tsv.gz
eCLIP immunoprecipitation sample for BCAT2, biological replicate 1


title: P2.5_187

description:
Library name: P2_5_187
SMART-Seq2


title: U2OS cytosolic condensates, silvestrol treatment, biol rep 1

description: Library name: U2OS_Silvestrol_Rep1

value: silvestrol (2µg/ml, 2h)


title: TIAL1 (4221) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: TIAL1_K562_4221_INPUT_rep2
eCLIP size-matched input control for TIAL1, biological replicate 2


title: TIAL1 (4221) eCLIP in K562 cells, IP replicate 2

description:
Library name: TIAL1_K562_4221_IP_rep2
eCLIP immunoprecipitation sample for TIAL1, biological replicate 2


title: HEK293T H4S1ph  DRB 30 minutes rep 2

description: Library name: Sample 31

value: DRB treatment for 30  minutes

value: Abcam cat.no.ab177309


title: HEK293T H4S1ph DRB 15 minutes rep 2

description: Library name: Sample 29


title: U2OS cytosolic condensates, silvestrol treatment, biol rep 3

description: Library name: U2OS_Silvestrol_Rep3


title: HEK293T H4S1ph DRB 30 minutes rep 1

description: Library name: Sample 30


title: P2.5_186

description:
Library name: P2_5_186
SMART-Seq2


title: P2.5_185

description:
Library name: P2_5_185
SMART-Seq2


title: TIAL1 (4221) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: TIAL1_K562_4221_INPUT_rep1
eCLIP size-matched input control for TIAL1, biological replicate 1


title: U2OS cytosolic condensates, silvestrol treatment, biol rep 2

description: Library name: U2OS_Silvestrol_Rep2


title: P2.5_184

description:
Library name: P2_5_184
SMART-Seq2


title: TIAL1 (4221) eCLIP in K562 cells, IP replicate 1

description:
Library name: TIAL1_K562_4221_IP_rep1
eCLIP immunoprecipitation sample for TIAL1, biological replicate 1


title: U2OS cytosolic condensates, dsRNA treatment, biol rep 2

description: Library name: U2OS_dsRNA_Rep2

value: dsRNA (250 nM, 2h)


title: HEK293T H4S1ph DRB 5 minutes rep 1

description: Library name: Sample 26


title: HEK293T H4S1ph DRB  5 minutes rep 2

description: Library name: Sample 27


title: P2.5_183

description:
Library name: P2_5_183
SMART-Seq2

value: female germ cell


title: U2OS cytosolic condensates, dsRNA treatment, biol rep 3

description: Library name: U2OS_dsRNA_Rep3


title: U2OS cytosolic condensates, mock treatment, biol rep 3

description: Library name: U2OS_mock_Rep3

value: untreated


title: ELAC2 (4224) eCLIP in K562 cells, IP replicate 2

description:
Library name: ELAC2_K562_4224_IP_rep2
eCLIP immunoprecipitation sample for ELAC2, biological replicate 2


title: P2.5_182

description:
Library name: P2_5_182
SMART-Seq2


title: ELAC2 (4224) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: ELAC2_K562_4224_INPUT_rep2
eCLIP size-matched input control for ELAC2, biological replicate 2


title: U2OS cytosolic condensates, dsRNA treatment, biol rep 1

description: Library name: U2OS_dsRNA_Rep1


title: ELAC2 (4224) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: ELAC2_K562_4224_INPUT_rep1
eCLIP size-matched input control for ELAC2, biological replicate 1


title: HEK293T H4S1ph DRB 15 minutes rep 1

description: Library name: Sample 28


title: HEK293T H4S1ph control rep 2

description: Library name: Sample 25


title: P2.5_181

description:
Library name: P2_5_181
SMART-Seq2


title: HEK293T H4S1ph control rep 1

description: Library name: Sample 24


title: U2OS cytosolic condensates, mock treatment, biol rep 2

description: Library name: U2OS_mock_Rep2


title: ELAC2 (4224) eCLIP in K562 cells, IP replicate 1

description:
Library name: ELAC2_K562_4224_IP_rep1
eCLIP immunoprecipitation sample for ELAC2, biological replicate 1


title: U2OS cytosolic extract, input, biol rep 3

description: Library name: U2OS_Input_Rep3


title: P2.5_179

description:
Library name: P2_5_179
SMART-Seq2


title: EED (4223) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: EED_K562_4223_INPUT_rep2
eCLIP size-matched input control for EED, biological replicate 2


title: P2.5_180

description:
Library name: P2_5_180
SMART-Seq2


title: HEK293T H3S10ph DRB 30 minutes rep 1

description: Library name: Sample 22

value: CMA311, a gift from Dr. Hiroshi Kimura’s group


title: EED (4223) eCLIP in K562 cells, IP replicate 2

description:
Library name: EED_K562_4223_IP_rep2
eCLIP immunoprecipitation sample for EED, biological replicate 2


title: U2OS cytosolic condensates, mock treatment, biol rep 1

description: Library name: U2OS_mock_Rep1


title: P2.5_178

description:
Library name: P2_5_178
SMART-Seq2


title: HEK293T H3S10ph  DRB 30 minutes rep 2

description: Library name: Sample 23


title: U2OS cytosolic extract, input, biol rep 2

description: Library name: U2OS_Input_Rep2


title: P2.5_177

description:
Library name: P2_5_177
SMART-Seq2


title: U2OS cytosolic extract, input, biol rep 1

description: Library name: U2OS_Input_Rep1


title: P2.5_176

description:
Library name: P2_5_176
SMART-Seq2


title: EED (4223) eCLIP in K562 cells, IP replicate 1

description:
Library name: EED_K562_4223_IP_rep1
eCLIP immunoprecipitation sample for EED, biological replicate 1


title: HEK293T H3S10ph DRB  5 minutes rep 2

description: Library name: Sample 19


title: T47D Mutated (ESR1:Y537S) siRNAs Replicate 2

city: Miami

first: Rodrigo

last: Lucena Borges

state: Florida

address: 1501 NW 10th Avenue

department: Department of Human Genetics

institute: Sylvester Comprehensive Cancer Center

description: Library name: T47D_537_siNeg_rep2.fastq.gz

data_processing:
Hisat2 (https://daehwankimlab.github.io/hisat2/) was used to map RNAseq fastq files to hg19 followed by featureCounts v2.0.2 (https://pubmed.ncbi.nlm.nih.gov/24227677/) to calculate gene counts
Assembly: GRCh37
Supplementary files format and content: Tab-separated files of gene counts (raw counts)
Supplementary files format and content: RNA_counts_FM_5M_8M.tsv are counts from reprocessed data from GSE168644

source_name: Cell line

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations and split 1:3 every 3 days. Culture media: RPMI-1640(Lonza 12-167Q) supplemented with 10% FBS(Gemini 100-106), 1x penicillin/streptomycin(Thermo Fisher Scientific 15140-12, 10000U/mL), and 1x glutamax( Life Technologies 35050-061 ).

extract_protocol:
Total RNA was isolated from frozen cell pellets using the TRIzol reagent (Thermo Fisher Scientific cat# 15596018) according to manufacturer's instructions. RNA quantity and quality was measured on a nanodrop. 2 ug of RNA were treated using the TURBO DNA-free Kit (Thermo Fisher AM1907) to remove DNA contamination and later on DNAse and divalent cations from the sample. 1ug of the treated RNA was used for library preparation. Quality was checked using a Bioanalyzer
Library preparation was perfromed on Dnase-treated RNA using the Illumina TruSeq Stranded Total RNA Library Prep Gold (Illumina 20020598). TruSeq RNA UD Indexes (Illumina 20022371) were used for the adapter ligation step. Samples were normalized to a concentration of ranging from 100-250ng for input, and 1 ul of ERCC spike-in Mix 1 (Thermo Fisher 4456740) diluted 1:200 was added to the samples.

treatment_protocol: 5x105 T47D cells were seeded into 6-well plates in hormone deprived media one day before siRNA transfection and maintained in antibiotic-free culture medium. 25nM of siRNAs (Sigma-Aldrich #SIC007 for control, EHU001431 for KDM4C) were transfected using Lipofectamine RNAiMAX (Thermo Fisher Scientific #13778150) following the manufacturer’s instructions.

value: T47D ATCC HTB-113

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

value: Y537S Mutation in ESR1 and 25nM of siRNAs (Sigma-Aldrich #SIC007)


title: HEK293T H3S10ph DRB 15 minutes rep 2

description: Library name: Sample 21

value: DRB treatment for 15 minutes


title: T47D Mutated (ESR1:Y537S) siRNAs Replicate 1

description: Library name: T47D_537_siNeg_rep1.fastq.gz


title: P2.5_174

description:
Library name: P2_5_174
SMART-Seq2


title: EED (4223) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: EED_K562_4223_INPUT_rep1
eCLIP size-matched input control for EED, biological replicate 1


title: DDX1 (4231) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: DDX1_K562_4231_INPUT_rep2
eCLIP size-matched input control for DDX1, biological replicate 2


title: P2.5_175

description:
Library name: P2_5_175
SMART-Seq2


description: Library name: ESR1_Y537S_REP2

data_processing:
Paired-end Hi-C FASTQ reads for each of the different conditions: parental, primed, reprogrammed and T47DWT/Y537S (two replicates for each condition), were mapped to the reference genome (build hg19) using Juicer45. To normalize the number of Hi-C contact pairs, we downsampled each contact set to 322,339,000 by randomly keeping the same number of Hi-C contact pairs. Downsampled Hi-C contact pairs were used in downstream analysis, including the differential analysis between different conditions. The downsampled Hi-C contacts were converted to Hi-C contact matrices with different resolutions, including 1 Kb,10 Kb, 20 Kb, 40 Kb, 100 Kb, and 1 Mb, in a cool format using the software cooler46, which were further normalized using the “cooler balance” command. HiCRep47 was used to calculate the stratum-adjusted correlation coefficient (SCC) to assess the reproducibility of Hi-C data at various resolutions. The genome-wide SCC is the average value of SCCs for individual chromosomes
Assembly: hg19
Supplementary files format and content: Hi-C files

growth_protocol: T47D FM or parental: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations and split 1:3 every 3 days. Culture media: RPMI-1640(Lonza 12-167Q) supplemented with 10% FBS(Gemini 100-106), 1x penicillin/streptomycin(Thermo Fisher Scientific 15140-12, 10000U/mL), and 1x glutamax( Life Technologies 35050-061 ). T47D Primed or 6M CD44 sorted: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were culture in estrogen deprived conditions for 6 months. Cell expressing high levels of CD44 were sorted and kept in culture. Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and (Thermo Fisher Scientific 15140-12, 10000U/mL. T47D Reprogrammed or 9M : T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were culture in estrogen deprived conditions for 9 months. Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and Penicillyn/Streptomycin (Thermo Fisher Scientific 15140-12, 10000U/mL. T47D Y537S: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations and split 1:3 every 3 days. Culture media: RPMI-1640(Lonza 12-167Q) supplemented with 10% FBS(Gemini 100-106), 1x penicillin/streptomycin(Thermo Fisher Scientific 15140-12, 10000U/mL), and 1x glutamax( Life Technologies 35050-061 ).

extract_protocol:
genomic DNA was isolated according to Arima HiC kit (A510008) protocol
Arima HiC kit protocol followed by Library Preparation using NEBNext Ultra II DNA Library Prep Kit.

value: ESR1L:Y537S  Point mutation


title: DDX1 (4231) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: DDX1_K562_4231_INPUT_rep1
eCLIP size-matched input control for DDX1, biological replicate 1


description: Library name: ESR1_Y537S_REP1


title: HEK293T H3S10ph control rep 2

description: Library name: Sample 17


title: HEK293T H3S10ph DRB 15 minutes rep 1

description: Library name: Sample 20


title: DDX1 (4231) eCLIP in K562 cells, IP replicate 1

description:
Library name: DDX1_K562_4231_IP_rep1
eCLIP immunoprecipitation sample for DDX1, biological replicate 1


title: HEK293T H3S10ph DRB 5 minutes rep 1

description: Library name: Sample 18

value: DRB treatment for five minutes


title: DDX1 (4231) eCLIP in K562 cells, IP replicate 2

description:
Library name: DDX1_K562_4231_IP_rep2
eCLIP immunoprecipitation sample for DDX1, biological replicate 2


title: METTL1 (4225) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: METTL1_K562_4225_INPUT_rep2
eCLIP size-matched input control for METTL1, biological replicate 2


title: HEK293T H4K12Ac DRB 30 minutes rep 1

description: Library name: Sample 14

value: Human Kidney

value: Active Motif.cat.no.39165


title: Hi-C Reprogrammed Cells - Replicate 1

description: Library name: 9M_REP1

value: 9 months after E2 depletion


title: HEK293T H4K12Ac DRB 30 minutes rep 2

description: Library name: Sample 15

value: Human embryonic kidney 293

value: wt


title: P2.5_173

description:
Library name: P2_5_173
SMART-Seq2


title: P2.5_171

description:
Library name: P2_5_171
SMART-Seq2


title: P2.5_172

description:
Library name: P2_5_172
SMART-Seq2


title: HEK293T H4K12Ac DRB 15 minutes rep 2

description: Library name: Sample 13


title: Hi-C Primed Cells - Replicate 2

description: Library name: 6M_REP2

value: 6 months after E2 depletion


title: Hi-C Reprogrammed Cells - Replicate 2

description: Library name: 9M_REP2


title: HEK293T H4K12Ac DRB 15 minutes rep 1

description: Library name: Sample 12


title: HEK293T H3S10ph control rep 1

description: Library name: Sample 16

value: Native control


title: P2.5_169

description:
Library name: P2_5_169
SMART-Seq2


title: METTL1 (4225) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: METTL1_K562_4225_INPUT_rep1
eCLIP size-matched input control for METTL1, biological replicate 1


title: P2.5_167

description:
Library name: P2_5_167
SMART-Seq2


title: METTL1 (4225) eCLIP in K562 cells, IP replicate 2

description:
Library name: METTL1_K562_4225_IP_rep2
eCLIP immunoprecipitation sample for METTL1, biological replicate 2


title: HEK293T H4K12Ac DRB 5 minutes rep 1

description: Library name: Sample 11


title: METTL1 (4225) eCLIP in K562 cells, IP replicate 1

description:
Library name: METTL1_K562_4225_IP_rep1
eCLIP immunoprecipitation sample for METTL1, biological replicate 1


title: P2.5_168

description:
Library name: P2_5_168
SMART-Seq2


title: P2.5_166

description:
Library name: P2_5_166
SMART-Seq2


title: ADAT1 (4217) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: ADAT1_K562_4217_INPUT_rep2
eCLIP size-matched input control for ADAT1, biological replicate 2


title: P2.5_170

description:
Library name: P2_5_170
SMART-Seq2


title: Hi-C Parental Cells - Replicate 1

description: Library name: FM_REP1


title: HEK293T H4K12Ac control rep 2

description: Library name: Sample 10


title: Hi-C Parental Cells - Replicate 2

description: Library name: FM_REP2


title: Hi-C Primed Cells - Replicate 1

description: Library name: 6M_REP1


title: HEK293T H4K12Ac control rep 1

description: Library name: Sample 9


title: E2_SiKDM4C_IgG Replicate 2

description: Library name: E2_SiKDM4C_IgG Replicate 2

data_processing:
nf-core/cutandrun pipeline v3.2.2-g6e1125d  was used for read trimming, QC, alignment against hg19 for target reference and Escherichia_coli_K_12_MG1655 for spike-in reference and generation of normalized bigwigs. Default parameters were used except trim_nextseq : 30.
Assembly: hg19 for target samples; Escherichia coli K_12_MG1655 for spike-in
Supplementary files format and content: Bigwig files (average signal between replicates)
Library strategy: CUT&Run

growth_protocol: T47D SiC/siKDM4C HD T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were culture in estrogen deprived conditions for 3 days. Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and Penicillyn/Streptomycin(Thermo Fisher Scientific 15140-12, 10000U/mL) T47D SiC/siKDM4C E2 T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were culture in estrogen deprived conditions for 3 days. Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and Penicillyn/Streptomycin(Thermo Fisher Scientific 15140-12, 10000U/mL). Cells were stimulated with 10nM E2 for 8 hours.

extract_protocol:
CUT&RUN was performed with the CUTANATM ChIC/CUT&RUN kit according to the manufacturer’s protocol (EpiCypher, 14-1048).
CUTANATM Library Prep Kit Primer Set 2 (EpiCypher, 14-1002, lot: 23317004-01)

treatment_protocol: SiC : 25nM of siRNAs (Sigma-Aldrich #SIC007) were transfected using Lipofectamine RNAiMAX (Thermo Fisher Scientific #13778150) following the manufacturer’s instructions. SiKDM4C: 25nM of siRNAs (Sigma-Aldrich EHU001431) were transfected using Lipofectamine RNAiMAX (Thermo Fisher Scientific #13778150) following the manufacturer’s instructions.

tag: antibody

value: Anti-IgG (EpiCypher, 13-0042K)

value: Hormone deprived media (HD) for 3 days. Then 10nM E2 for 8h. Transfected with 25nM of siRNAs (Sigma-Aldrich EHU001431)


title: E2_SiKDM4C_IgG Replicate 1

description: Library name: E2_SiKDM4C_IgG Replicate 1


title: ADAT1 (4217) eCLIP in K562 cells, IP replicate 2

description:
Library name: ADAT1_K562_4217_IP_rep2
eCLIP immunoprecipitation sample for ADAT1, biological replicate 2


title: P2.5_164

description:
Library name: P2_5_164
SMART-Seq2

value: female germ cell


title: ADAT1 (4217) eCLIP in K562 cells, IP replicate 1

description:
Library name: ADAT1_K562_4217_IP_rep1
eCLIP immunoprecipitation sample for ADAT1, biological replicate 1


title: P2.5_165

description:
Library name: P2_5_165
SMART-Seq2


title: HEK293T H3K9Ac DRB 30 minutes rep 2

description: Library name: Sample 8

value: DRB treatment for 30  minutes

value: Active Motif. cat.no.61251


title: ADAT1 (4217) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: ADAT1_K562_4217_INPUT_rep1
eCLIP size-matched input control for ADAT1, biological replicate 1


title: SNRNP200 (4152) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: SNRNP200_K562_4152_INPUT_rep2
eCLIP size-matched input control for SNRNP200, biological replicate 2


title: HEK293T H3K9Ac DRB 15 minutes rep 2

description: Library name: Sample 6


title: E2_SiKDM4C_H3K27me3 Replicate 1

description: Library name: E2_SiKDM4C_H3K27me3 Replicate 1

value: T47D ATCC HTB-113

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

value: Anti-H3K27me3 (Active Motif, 39155)


title: HEK293T H3K9Ac DRB 30 minutes rep 1

description: Library name: Sample 7


title: P2.5_163

description:
Library name: P2_5_163
SMART-Seq2


title: SNRNP200 (4152) eCLIP in K562 cells, IP replicate 2

description:
Library name: SNRNP200_K562_4152_IP_rep2
eCLIP immunoprecipitation sample for SNRNP200, biological replicate 2


title: SNRNP200 (4152) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: SNRNP200_K562_4152_INPUT_rep1
eCLIP size-matched input control for SNRNP200, biological replicate 1


title: P2.5_161

description:
Library name: P2_5_161
SMART-Seq2


title: E2_SiKDM4C_H3K9me3 Replicate 1

description: Library name: E2_SiKDM4C_H3K9me3 Replicate 1

value: Anti-H3K9me3 (Abcam, ab4729)


title: HEK293T H3K9Ac DRB 15 minutes rep 1

description: Library name: Sample 5

value: DRB treatment for 15 minutes


title: E2_SiC_IgG Replicate 2

description: Library name: E2_SiC_IgG Replicate 2

value: Hormone deprived media (HD) for 3 days. Then 10nM E2 for 8h. Transfected with 25nM of siRNAs (Sigma-Aldrich SIC007)


title: E2_SiKDM4C_H3K27me3 Replicate 2

description: Library name: E2_SiKDM4C_H3K27me3 Replicate 2


title: HEK293T H3K9Ac DRB  5 minutes rep 2

description: Library name: Sample 4

value: Human Kidney

value: DRB treatment for five minutes


title: P2.5_162

description:
Library name: P2_5_162
SMART-Seq2


title: P2.5_159

description:
Library name: P2_5_159
SMART-Seq2


title: HEK293T H3K9Ac DRB 5 minutes rep 1

description: Library name: Sample 3

value: Human embryonic kidney 293


title: P2.5_160

description:
Library name: P2_5_160
SMART-Seq2


title: ADAR (4137) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: ADAR_K562_4137_INPUT_rep2
eCLIP size-matched input control for ADAR, biological replicate 2


title: SNRNP200 (4152) eCLIP in K562 cells, IP replicate 1

description:
Library name: SNRNP200_K562_4152_IP_rep1
eCLIP immunoprecipitation sample for SNRNP200, biological replicate 1


title: P2.5_157

description:
Library name: P2_5_157
SMART-Seq2


title: E2_SiC_H3K27me3 Replicate 2

description: Library name: E2_SiC_H3K27me3 Replicate 2


title: HEK293T H3K9Ac control rep 1

description: Library name: Sample 1

value: WT


title: HEK293T H3K9Ac control rep 2

description: Library name: Sample 2

value: wt


title: RNA from patient HTA3_80017, derived from LUAD (Stage 1A) [PCGA02_30017_6010003]

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Library name: PCGA02_30017_6010003

data_processing:
After sequencing, FASTQ files for each sample were aligned to hg38 using STAR.
After alignment of FASTQ files, RSEM was used to summarize gene and transcript counts.
Quality metrics were generated by STAR and RSeQC to evaluate sample quality.
Somalier was used to confirm relatedness among samples from the same patient.
Assembly: hg38
Supplementary files format and content: Processed data are stored as a count matrix in a TSV (tab-separated values) file.

source_name: Resected lung tissue

extract_protocol:
Formalin-fixed parrafin-embedded (FFPE) tissue was annotated for normal, tumor, and premalignant histology, and then laser capture microdissected. RNA was isolated from LCM FFPE samples using the Qiagen All-Prep FFPE kit.
Sequencing libraries were prepared with the Illumina TruSeq Paired-End Cluster Kit.
Total RNA sequencing was performed on an Illumina NextSeq 500 (generating paired-end 75-nucleotide reads), or on an Illumina NextSeq 2000 (generating paired-end 100-nucleotide reads).

value: Resected lung tissue

tag: htan id

tag: sample histology

value: ADC

tag: flow cells


title: E2_SiKDM4C_H3K9me3 Replicate 2

description: Library name: E2_SiKDM4C_H3K9me3 Replicate 2

value: Hormone deprived media (HD) for 3 days. Then 10nM E2 for 8h. Transfected with 25nM of siRNAs (Sigma-Aldrich EHU001431)


title: ADAR (4137) eCLIP in K562 cells, IP replicate 1

description:
Library name: ADAR_K562_4137_IP_rep1
eCLIP immunoprecipitation sample for ADAR, biological replicate 1


title: ADAR (4137) eCLIP in K562 cells, IP replicate 2

description:
Library name: ADAR_K562_4137_IP_rep2
eCLIP immunoprecipitation sample for ADAR, biological replicate 2


title: E2_SiC_IgG Replicate 1

description: Library name: E2_SiC_IgG Replicate 1

value: Anti-IgG (EpiCypher, 13-0042K)


title: E2_SiC_H3K9me3 Replicate 2

description: Library name: E2_SiC_H3K9me3 Replicate 2


title: RNA from patient HTA3_80017, derived from AIS/MIA [PCGA02_30017_6010002]

description: Library name: PCGA02_30017_6010002

value: AIS/MIA


title: P2.5_156

description:
Library name: P2_5_156
SMART-Seq2

value: female germ cell


title: P2.5_158

description:
Library name: P2_5_158
SMART-Seq2


title: P2.5_155

description:
Library name: P2_5_155
SMART-Seq2


title: E2_SiC_H3K27me3 Replicate 1

description: Library name: E2_SiC_H3K27me3 Replicate 1

value: T47D ATCC HTB-113


title: MFAP1 (4169) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: MFAP1_K562_4169_INPUT_rep2
eCLIP size-matched input control for MFAP1, biological replicate 2


title: E2_SiC_H3K9me3 Replicate 1

description: Library name: E2_SiC_H3K9me3 Replicate 1

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site


title: ADAR (4137) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: ADAR_K562_4137_INPUT_rep1
eCLIP size-matched input control for ADAR, biological replicate 1


title: RNA from patient HTA3_80017, derived from AAH [PCGA02_30017_6010001]

description: Library name: PCGA02_30017_6010001

value: AAH


title: P2.5_154

description:
Library name: P2_5_154
SMART-Seq2


title: RNA from patient HTA3_80016, derived from AAH #2 [PCGA02_30016_6010005]

description: Library name: PCGA02_30016_6010005

value: HJLGNBGXL


title: HD_SiKDM4C_IgG Replicate 2

description: Library name: HD_SiKDM4C_IgG Replicate 2

value: Hormone deprived media (HD) for 3 days. Transfected with 25nM of siRNAs (Sigma-Aldrich #EHU001431)


title: P2.5_153

description:
Library name: P2_5_153
SMART-Seq2


title: MFAP1 (4169) eCLIP in K562 cells, IP replicate 1

description:
Library name: MFAP1_K562_4169_IP_rep1
eCLIP immunoprecipitation sample for MFAP1, biological replicate 1


title: HD_SiKDM4C_IgG Replicate 1

description: Library name: HD_SiKDM4C_IgG Replicate 1


title: RNA from patient HTA3_80016, derived from AAH #1 [PCGA02_30016_6010004]

description: Library name: PCGA02_30016_6010004


title: MFAP1 (4169) eCLIP in K562 cells, IP replicate 2

description:
Library name: MFAP1_K562_4169_IP_rep2
eCLIP immunoprecipitation sample for MFAP1, biological replicate 2


title: RNA from patient HTA3_80016, derived from AIS/MIA [PCGA02_30016_6010003]

description: Library name: PCGA02_30016_6010003


title: RNA from patient HTA3_80016, derived from LUAD Region 2 (Stage 1A) [PCGA02_30016_6010006]

description: Library name: PCGA02_30016_6010006

value: HJMCCBGXL


title: P2.5_150

description:
Library name: P2_5_150
SMART-Seq2


title: P2.5_152

description:
Library name: P2_5_152
SMART-Seq2


title: RNA from patient HTA3_80016, derived from LUAD Region 1 (Stage 1A) [PCGA02_30016_6010002]

description: Library name: PCGA02_30016_6010002


title: EIF3A (4138) eCLIP in K562 cells, IP replicate 2

description:
Library name: EIF3A_K562_4138_IP_rep2
eCLIP immunoprecipitation sample for EIF3A, biological replicate 2


title: EIF3A (4138) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: EIF3A_K562_4138_INPUT_rep2
eCLIP size-matched input control for EIF3A, biological replicate 2


title: P2.5_151

description:
Library name: P2_5_151
SMART-Seq2


title: HD_SiKDM4C_H3K27me3 Replicate 2

description: Library name: HD_SiKDM4C_H3K27me3 Replicate 2

value: Anti-H3K27me3 (Active Motif, 39155)


title: MFAP1 (4169) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: MFAP1_K562_4169_INPUT_rep1
eCLIP size-matched input control for MFAP1, biological replicate 1


title: HD_SiKDM4C_H3K9me3 Replicate 1

description: Library name: HD_SiKDM4C_H3K9me3 Replicate 1

value: Anti-H3K9me3 (Abcam, ab4729)


title: HD_SiKDM4C_H3K27me3 Replicate 1

description: Library name: HD_SiKDM4C_H3K27me3 Replicate 1


title: RNA from patient HTA3_80016, derived from Normal [PCGA02_30016_6010001]

description: Library name: PCGA02_30016_6010001

value: N


title: EIF3A (4138) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: EIF3A_K562_4138_INPUT_rep1
eCLIP size-matched input control for EIF3A, biological replicate 1


title: P2.5_148

description:
Library name: P2_5_148
SMART-Seq2


title: HD_SiKDM4C_H3K9me3 Replicate 2

description: Library name: HD_SiKDM4C_H3K9me3 Replicate 2


title: P2.5_149

description:
Library name: P2_5_149
SMART-Seq2


title: EIF3A (4138) eCLIP in K562 cells, IP replicate 1

description:
Library name: EIF3A_K562_4138_IP_rep1
eCLIP immunoprecipitation sample for EIF3A, biological replicate 1


title: RNA from patient HTA3_80015, derived from AAH #2 [PCGA02_30015_6010004]

description: Library name: PCGA02_30015_6010004


title: MORC2 (4139) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: MORC2_K562_4139_INPUT_rep2
eCLIP size-matched input control for MORC2, biological replicate 2


title: RNA from patient HTA3_80015, derived from Normal [PCGA02_30015_6010003]

description: Library name: PCGA02_30015_6010003


title: P2.5_147

description:
Library name: P2_5_147
SMART-Seq2


title: HD_SiC_IgG Replicate 2

description: Library name: HD_SiC_IgG Replicate 2

value: Hormone deprived media (HD) for 3 days. Transfected with 25nM of siRNAs (Sigma-Aldrich #SIC007)


title: RNA from patient HTA3_80015, derived from LUAD (Stage IIA) [PCGA02_30015_6010002]

description: Library name: PCGA02_30015_6010002


title: HD_SiC_IgG Replicate 1

description: Library name: HD_SiC_IgG Replicate 1


title: MORC2 (4139) eCLIP in K562 cells, IP replicate 2

description:
Library name: MORC2_K562_4139_IP_rep2
eCLIP immunoprecipitation sample for MORC2, biological replicate 2


title: MORC2 (4139) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: MORC2_K562_4139_INPUT_rep1
eCLIP size-matched input control for MORC2, biological replicate 1


title: P2.5_145

description:
Library name: P2_5_145
SMART-Seq2


title: HD_SiC_H3K27me3 Replicate 2

description: Library name: HD_SiC_H3K27me3 Replicate 2


title: RNA from patient HTA3_80015, derived from AAH #1 [PCGA02_30015_6010001]

description: Library name: PCGA02_30015_6010001


title: P2.5_146

description:
Library name: P2_5_146
SMART-Seq2


title: P2.5_144

description:
Library name: P2_5_144
SMART-Seq2


title: MORC2 (4139) eCLIP in K562 cells, IP replicate 1

description:
Library name: MORC2_K562_4139_IP_rep1
eCLIP immunoprecipitation sample for MORC2, biological replicate 1


title: HD_SiC_H3K27me3 Replicate 1

description: Library name: HD_SiC_H3K27me3 Replicate 1


title: EIF6 (4222) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: EIF6_K562_4222_INPUT_rep2
eCLIP size-matched input control for EIF6, biological replicate 2


title: HD_SiC_H3K9me3 Replicate 1

description: Library name: HD_SiC_H3K9me3 Replicate 1


title: P2.5_143

description:
Library name: P2_5_143
SMART-Seq2


title: RNA from patient HTA3_80014, derived from LUAD (Stage 1A) [PCGA02_30014_6010007]

description: Library name: PCGA02_30014_6010007


title: RNA from patient HTA3_80014, derived from AAH #5 [PCGA02_30014_6010006]

description: Library name: PCGA02_30014_6010006


title: HD_SiC_H3K9me3 Replicate 2

description: Library name: HD_SiC_H3K9me3 Replicate 2


title: EIF6 (4222) eCLIP in K562 cells, IP replicate 2

description:
Library name: EIF6_K562_4222_IP_rep2
eCLIP immunoprecipitation sample for EIF6, biological replicate 2


title: RNA from patient HTA3_80014, derived from AAH #4 [PCGA02_30014_6010005]

description: Library name: PCGA02_30014_6010005


title: RNA from patient HTA3_80014, derived from Normal [PCGA02_30014_6010008]

description: Library name: PCGA02_30014_6010008


title: EIF6 (4222) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: EIF6_K562_4222_INPUT_rep1
eCLIP size-matched input control for EIF6, biological replicate 1


title: P2.5_141

description:
Library name: P2_5_141
SMART-Seq2


title: P2.5_142

description:
Library name: P2_5_142
SMART-Seq2


title: EIF6 (4222) eCLIP in K562 cells, IP replicate 1

description:
Library name: EIF6_K562_4222_IP_rep1
eCLIP immunoprecipitation sample for EIF6, biological replicate 1


title: Reprogrammed cells Replicate 2 (ChIP - Cohesin)

description: Library name: lted_9m_ctcf.fastq.gz

data_processing:
Single-end fastq files were processed using ENCODE ATAC-Seq pipeline v1.5.0 was used for read trimming, QC, alignment against hg19  and generation of bigwigs with default parameters
Single-end fastq files for CTCF and Cohesin were processed using ENCODE TF/Histone ChIP-Seq pipeline v1.5.0.
Inputs were used from GSE168644 ChIP-seq files
Assembly: hg19
Supplementary files format and content: Bigwigs of log2 of signal over input

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations and split 1:3 every 3 days. Culture media: RPMI-1640(Lonza 12-167Q) supplemented with 10% FBS(Gemini 100-106), 1x penicillin/streptomycin(Thermo Fisher Scientific 15140-12, 10000U/mL), and 1x glutamax( Life Technologies 35050-061).

extract_protocol:
Cells were grown to 80% confluence on 150cm plates and fixed with 11% solution containing formaldehyde (Thermo Fisher #28908), 50mM HEPES-KOH(pH 7.5), 100mM Nacl, 0.5M EDTA, 0.5M EGTA for 10 min. 1/20 of the plates volume equivalent of freshly prepared Glycine 2.5M(stock) was added to quench the reaction for 5min . The supernatant was aspirated, and the cells were washed twice with 5 ml PBS and harvested on ice using cell scrapers . Cells were pelleted at 2950 x g for 10 min at 4°C, washed 1x with 10 ml cold PBS, and pelleted once more. Cell pellets were flash freeze in liquid nitrogen and store at -80°C until processing day. Cell pellet collected from 6 plates of cells was resuspended in 5 ml of Lysis Buffer 1 (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), allowed to rotate for 10 min at 4°C, and pelleted at 2950 x g for 10 min at 4°C. Cells were then resuspended in 5 ml of Lysis Buffer 2 (10 mM Tris-HCL pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), allowed to rotate for 10 min at room temperature, and pelleted at 2950 x g for 10 min at 4°C. Cells were then resuspended in 3 ml of Lysis Buffer 3 (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and then transfer to 15ml sonication tubes (Diagenode cat# C01020031). Cells were sonicated on a Bioruptor Pico at 4°C for 20min of 30’’ ON-OFF cycles with 1.2 g of sonication beads. After sonication, samples were transferred to 2 separate 1.5 ml microtube and centrifuged at 20,000 x g for 15 minutes at 4°C. The supernatant was transferred to new 15 ml tubes. To check sonication efficiency, 50µl of sonicated samples was transferred to a new microtube with 50µl PBS and incubated at 65°C for 3hr on an Eppendorf Thermomixer shaking at 1000rpm to decrosslink. DNA was purified with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 50µl of H20. 1 ug of decrosslinked chromatin from each sample were run in a 1% agarose gel at 100V for 45min and imaged on a Bio-rad ChemiDoc XRS+. DNA concentration in the sonicated decrosslinked samples were measured via qubit, and this concentration was then used to estimate the concentration of chromatin in the un-decrosslinked samples. 5ug of Antibody (see Key Resources table for list of antibodies) along with 1ug of Spike-in antibodies (Active Motif 61686) were bound to 50 ul of Dynabeads Protein G (Thermo Fisher 10004D), previously washed with 1 ml of 0.5% BSA in 1x PBS three times, and rotated end-to-end overnight at 4°C (Eppendorf cat# 0030108051). After binding of the antibodies , beads were washed with 1 ml of 0.5% BSA in 1x PBS three times. 30ug of chromatin and 50 ng of Spike-in chromatin (Active Motif 53083) were added to 1.5ml LoBind tube (Eppendorf cat# 0030108051) containing pre-bound antibodies beads and brought up to 500µl final volume with Lysis Buffer and rotated end-to-end overnight at 4°C. 5 µl was removed as input material (1%) and placed in a separate microtube at 4°C completing the volume to 50uL with Lysis Buffer 3. Beads were washed 6 times with 1 ml Wash Buffer (50 mM Hepes-KOH, pH 7.6; 500 mM LiCl, 1 mM EDTA, 1% NP-40; 0.5% Na-Deoxycholate) and once with 1 ml TE containing 50 mM NaCl. Beads were dried after the last wash by removing as much TE as possible. 210 ul of Elution Buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA, 1% SDS) was added to each sample and 150 ul elution buffer were added to each input sample that was previously set aside. To elute immunocomplexes from beads, samples were incubated at 65°C for 15 minutes on an Eppendorf Thermomixer shaking at 1000rpm. Tubes were centrifuged for 3min at 960xg at RT and 200µl of supernatant was transferred to a new tube and reverse crosslinked overnight at 65°C. Next day, 200 ul of TE was added to each decrosslinked sample and input, and the samples were treated sequentially with 0.2 mg/ml RNAse A (Sigma R5503) at 37°C and 0.2 ug/ml Proteinase K (NEB P8107S) at 55°C for two hours each. DNA purification was performed with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 50µl of H2O and quantified by Qubit.
Immunoprecipitated DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs cat# 7370) following the manufacturer’s instructions.

value: 9 months after E2 depletion

value: CTCF


title: P2.5_140

description:
Library name: P2_5_140
SMART-Seq2


title: RNA from patient HTA3_80014, derived from AAH #7 [PCGA02_30014_6010010]

description: Library name: PCGA02_30014_6010010

value: Resected lung tissue

value: HFMTWBGXL


title: Parental Replicate 2 (ChIP - CTCF)

description: Library name: ctcf_rep2_wt2.fastq.gz


title: P2.5_139

description:
Library name: P2_5_139
SMART-Seq2


title: RNA from patient HTA3_80014, derived from AAH #3 [PCGA02_30014_6010004]

description: Library name: PCGA02_30014_6010004


title: Parental Replicate 1 (ChIP - CTCF)

description: Library name: ctcf_rep1_wt2.fastq.gz


title: RYBP (4140) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: RYBP_K562_4140_INPUT_rep2
eCLIP size-matched input control for RYBP, biological replicate 2


title: P2.5_138

description:
Library name: P2_5_138
SMART-Seq2


title: Reprogrammed cells Replicate 1 (ChIP - Cohesin)

description: Library name: lted_9m_cohesin.fastq.gz

value: Cohesin


title: RNA from patient HTA3_80014, derived from AIS/MIA [PCGA02_30014_6010003]

description: Library name: PCGA02_30014_6010003

value: AIS/MIA


title: RYBP (4140) eCLIP in K562 cells, IP replicate 2

description:
Library name: RYBP_K562_4140_IP_rep2
eCLIP immunoprecipitation sample for RYBP, biological replicate 2


title: Parental Replicate 2 (ChIP - Cohesin)

description: Library name: 02_cohesin_rep2_wt2.fastq.gz


title: RNA from patient HTA3_80014, derived from AAH #6 [PCGA02_30014_6010009]

description: Library name: PCGA02_30014_6010009


title: RYBP (4140) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: RYBP_K562_4140_INPUT_rep1
eCLIP size-matched input control for RYBP, biological replicate 1


title: RYBP (4140) eCLIP in K562 cells, IP replicate 1

description:
Library name: RYBP_K562_4140_IP_rep1
eCLIP immunoprecipitation sample for RYBP, biological replicate 1


title: P2.5_135

description:
Library name: P2_5_135
SMART-Seq2

value: female germ cell


title: RNA from patient HTA3_80014, derived from AAH #1 [PCGA02_30014_6010001]

description: Library name: PCGA02_30014_6010001


title: P2.5_134

description:
Library name: P2_5_134
SMART-Seq2


title: HEK293T Pro-seq DRB 30 minutes Rep1 with Spike

description:
Library name: Sample 59
The raw data will be available to public after publication

data_processing:
PRO-seq libraries were first trimmed using bbduk v38.05 (parameters: ktrim=r qtrim=rl trimq=9 k=21 mink=11 hdist=2 maq=10 minlen=20 tpe tbo). Reads were then mapped using Hisat2 v2.1.0 (parameters: --very-sensitive --no-spliced-alignment --rf). Resulting SAM files were then converted to BAM files using samtools view v1.8, then to normalized bigwig files using deepTools bamCoverage v3.5.4 (parameters: --ignoreDuplicates --normalizeUsing RPKM). Quality was assessed using FastQC v0.11.8 and MultiQC v1.8.
Assembly: Hg38
Supplementary files format and content: Bigwig
Library strategy: PRO-Seq

extract_protocol:
PRO-seq:Cell cultures were collected in 50 mL Falcon tubes and centrifuged in a fixed-angle rotor centrifuge at 600 x g, 4 °C for 5 minutes. The supernatant was removed, and ice-cold PBS (10 mL) was used to wash the pellet (wash repeated 3 times as above). The pellet was then resuspended in 10 mL ice-cold Lysis Buffer. The samples were then incubated for 10 minutes on ice. The samples were centrifuged in a fixed-angle rotor centrifuge at 1000 × g for 10 minutes at 4 °C in 50 mL Falcon tubes. The resulting supernatant was poured off, and the pellet was resuspended with 1 mL lysis buffer, using a wide-mouth P1000 pipette tip. The volume of the sample was brought to 10 mL with lysis buffer and centrifuged at 1000 x g, 4 °C, 5 minutes (wash repeated as above twice). Nuclei were then resuspended in 1 mL freezing buffer (50 mM Tris-HCl pH 8.3, 5 mM MgCl2, 40% Glycerol, 0.1 mM EDTA pH 8.0, brought to volume with 0.1% DEPC-treated DI-water) and transferred to a 1.7 mL Eppendorf tube. Nuclei were centrifuged at 1000 x g, 4 °C, 5 minutes, and the supernatant was removed by pipetting. The pellet was resuspended with 500 μL freezing buffer. The nuclei were again pelleted at 1000 x g, 4 °C, 5 minutes. The supernatant was removed, and the nuclei were resuspended in 110 μL freezing buffer and stored at -80 °C until library preparation.
PRO-seq libraries were generated using the qPRO protocol established by Judd et al., 2020. PRO-seq libraries were generated using the qPRO protocol established by Judd et al., 2020. A detailed step-by-step protocol is available at dx.doi.org/10.17504/protocols.io.57dg9i6. In short, ice-cold isolated nuclei were added to 37 °C 100 µl reaction buffer. The reaction was allowed to proceed for 10 minutes at 37 °C. RNA was extracted twice with Trizol, washed once with chloroform, and precipitated with 2.5 volumes of ice-cold ethanol and 1 µl GlycoBlue. The pellet was washed in 75% ethanol before resuspending in 30 µl of DEPC-treated water. The resulting RNA was denatured at 65 °C for 30 seconds and snap-cooled on ice. RNA was then fragmented by base hydrolysis in 0.2 N NaOH on ice for 10–12 min and neutralized by adding a 1× volume of 1 M Tris-HCl pH 6.8, and passed through a P-30 buffer exchange column. The 3’ adaptor (/5Phos/GAUCGUCGGACUGUAGAACUCUGAAC/3InvdT/) was ligated with T4 RNA Ligase 1. Biotin-labeled RNA was enriched with streptavidin beads, treated with T4 PNK and RppH for 5’ end repair, and ligated to a reverse 5’ RNA adaptor (5’ UGGAAUUCUCGGGUGCCAAGG). RNA was extracted from beads, and reverse transcribed using SuperScript III. The product was amplified using Phusion DNA polymerase and TruSeq Small RNA Library Preparation Kit barcoded primers. Then the library was size selected with 0.9X AMPure XP beads before being sequenced.

treatment_protocol: For PRO-seq: HEK293T cells were not treated or treated with 100 µM DRB. Cells were harvested at  5, 15, and 30 minutes post-treatment.

value: Human Kidney

value: Human embryonic kidney 293

value: wt

value: DRB treatment for 30  minutes


title: P2.5_137

description:
Library name: P2_5_137
SMART-Seq2


title: Parental Replicate 1 (ChIP - Cohesin)

description: Library name: 01_cohesin_rep1_wt2.fastq.gz

value: T47D ATCC HTB-113

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site


title: RNA from patient HTA3_80013, derived from AAH #3 [PCGA02_30013_6010006]

description: Library name: PCGA02_30013_6010006

value: AAH


title: RNA from patient HTA3_80014, derived from AAH #2 [PCGA02_30014_6010002]

description: Library name: PCGA02_30014_6010002


title: HEK293T Pro-seq DRB 5 minutes Rep1 with Spike

description:
Library name: Sample 57
The raw data will be available to public after publication

value: DRB treatment for 5 minutes


title: EXOSC10 (4161) eCLIP in K562 cells, IP replicate 2

description:
Library name: EXOSC10_K562_4161_IP_rep2
eCLIP immunoprecipitation sample for EXOSC10, biological replicate 2


title: HEK293T Pro-seq DRB 15 minutes Rep1 with Spike

description:
Library name: Sample 58
The raw data will be available to public after publication

value: DRB treatment for 15 minutes


title: EXOSC10 (4161) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: EXOSC10_K562_4161_INPUT_rep2
eCLIP size-matched input control for EXOSC10, biological replicate 2


title: RNA from patient HTA3_80013, derived from AAH #2 [PCGA02_30013_6010005]

description: Library name: PCGA02_30013_6010005


title: P2.5_136

description:
Library name: P2_5_136
SMART-Seq2


title: EXOSC10 (4161) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: EXOSC10_K562_4161_INPUT_rep1
eCLIP size-matched input control for EXOSC10, biological replicate 1


title: P2.5_132

description:
Library name: P2_5_132
SMART-Seq2


title: P2.5_133

description:
Library name: P2_5_133
SMART-Seq2


title: JUN gRNA vincristine 5

city: Bethesda

first: Claire

middle: E

last: LE PICHON

state: MD

address: 35A Convent Drive, 2D933

department: NICHD

institute: National Institutes of Health

description: Library name: Sample 61

data_processing:
Sequenced reads from all genotypes were trimmed to remove adaptor sequences using cutadapt v3.4 with the following parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 20 --minimum-length 25
Trimmed reads were aligned to GRCh38 human reference GENCODE release 28 using STAR 1-pass v2.7.8.a with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate.
Quantitation of aligned reads was performed using the featureCounts of the subread package v2.0.1 with annotation sourced from GRCh38 human reference GENCODE release 28 and the following parameters: -s2  -p
Assembly: GRCh38
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

source_name: "cortical", NGN2

extract_protocol:
For RNA extraction, 2.5 million neurons were pleated in 6 well plates (Thomas Scientific, #1198D71) and differentiated for 10-14 days. Neurons were treated with DMSO or 5 nM vincristine for 16 hours before RNA extraction. Neurons were washed once with PBS and harvested in 700 µL Qiazol (Qiagen, #79306) and immediately placed on ice. RNA extraction was performed using RNeasy Mini Kit (Qiagen, #74104) following the manufacturer’s instructions. Columns were treated with RNase-Free DNase (Qiagen, #79254), and RNA was eluted in 25 µL of RNAse free water. Eluted RNA was separated into two tubes, one containing 2 µL, subsequently used for quality control and the other used for RNAseq.
For RNA sequencing, 1-4 µg of total RNA samples were purified with PolyA extraction, and then purified mRNAs were constructed to RNA-Seq libraries with specific barcodes using Illumina TruSeq Stranded mRNA Library Prep Kit. All the RNA-Seq libraries were pooled together and sequenced using Illumina NovaSeq 6000 to generate approximately ~40 million 2x100 paired-end reads for each sample. The raw data were demultiplexed and analyzed further.

value: "cortical", NGN2

value: neuron

value: JUN gRNA

value: vincristine


title: EXOSC10 (4161) eCLIP in K562 cells, IP replicate 1

description:
Library name: EXOSC10_K562_4161_IP_rep1
eCLIP immunoprecipitation sample for EXOSC10, biological replicate 1


title: P2.5_131

description:
Library name: P2_5_131
SMART-Seq2


title: HEK293T Pro-seq control Rep1 with Spike

description:
Library name: Sample 56
The raw data will be available to public after publication

value: Native control


title: RNA from patient HTA3_80013, derived from Normal [PCGA02_30013_6010004]

description: Library name: PCGA02_30013_6010004

value: Resected lung tissue

value: N

value: HJMJGBGXL


title: DDX43 (4160) eCLIP in K562 cells, IP replicate 2

description:
Library name: DDX43_K562_4160_IP_rep2
eCLIP immunoprecipitation sample for DDX43, biological replicate 2


title: JUN gRNA vincristine 4

description: Library name: Sample 60


title: RNA from patient HTA3_80013, derived from AAH #1 [PCGA02_30013_6010003]

description: Library name: PCGA02_30013_6010003

value: HFMTWBGXL


title: RNA from patient HTA3_80013, derived from LUAD (Stage 1A) [PCGA02_30013_6010002]

description: Library name: PCGA02_30013_6010002

value: ADC


title: DDX43 (4160) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: DDX43_K562_4160_INPUT_rep2
eCLIP size-matched input control for DDX43, biological replicate 2


title: P2.5_130

description:
Library name: P2_5_130
SMART-Seq2

value: female germ cell


title: JUN gRNA vincristine 3

description: Library name: Sample 59


title: DDX43 (4160) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: DDX43_K562_4160_INPUT_rep1
eCLIP size-matched input control for DDX43, biological replicate 1


title: RNA from patient HTA3_80013, derived from AAH #1 [PCGA02_30013_6010001]

description: Library name: PCGA02_30013_6010001


title: JUN gRNA vincristine 2

description: Library name: Sample 58


title: JUN gRNA vincristine 1

description: Library name: Sample 57


title: P2.5_128

description:
Library name: P2_5_128
SMART-Seq2


title: DDX43 (4160) eCLIP in K562 cells, IP replicate 1

description:
Library name: DDX43_K562_4160_IP_rep1
eCLIP immunoprecipitation sample for DDX43, biological replicate 1


title: JUN gRNA untreated 4

description: Library name: Sample 55

value: untreated


title: RNA from patient HTA3_80012, derived from AAH #3 [PCGA02_30012_6010004]

description: Library name: PCGA02_30012_6010004


title: P2.5_129

description:
Library name: P2_5_129
SMART-Seq2


title: RNA from patient HTA3_80012, derived from AAH #1 [PCGA02_30012_6010002]

description: Library name: PCGA02_30012_6010002


title: SRSF9 (4132) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: SRSF9_K562_4132_INPUT_rep2
eCLIP size-matched input control for SRSF9, biological replicate 2


title: P2.5_125

description:
Library name: P2_5_125
SMART-Seq2


title: P2.5_127

description:
Library name: P2_5_127
SMART-Seq2


title: RNA from patient HTA3_80012, derived from AAH #2 [PCGA02_30012_6010003]

description: Library name: PCGA02_30012_6010003


title: P2.5_124

description:
Library name: P2_5_124
SMART-Seq2


title: RNA from patient HTA3_80012, derived from LUAD (Stage IA) [PCGA02_30012_6001001]

description: Library name: PCGA02_30012_6001001


title: SRSF9 (4132) eCLIP in K562 cells, IP replicate 1

description:
Library name: SRSF9_K562_4132_IP_rep1
eCLIP immunoprecipitation sample for SRSF9, biological replicate 1


title: JUN gRNA untreated 2

description: Library name: Sample 53


title: P2.5_126

description:
Library name: P2_5_126
SMART-Seq2


title: JUN gRNA untreated 5

description: Library name: Sample 56


title: JUN gRNA untreated 1

description: Library name: Sample 52


title: SNRPD3 (4155) eCLIP in K562 cells, IP replicate 2

description:
Library name: SNRPD3_K562_4155_IP_rep2
eCLIP immunoprecipitation sample for SNRPD3, biological replicate 2


title: SRSF9 (4132) eCLIP in K562 cells, IP replicate 2

description:
Library name: SRSF9_K562_4132_IP_rep2
eCLIP immunoprecipitation sample for SRSF9, biological replicate 2


title: SRSF9 (4132) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: SRSF9_K562_4132_INPUT_rep1
eCLIP size-matched input control for SRSF9, biological replicate 1


title: RNA from patient HTA3_80010, derived from AAH #2 [PCGA02_30010_6010007]

description: Library name: PCGA02_30010_6010007


title: JUN gRNA untreated 3

description: Library name: Sample 54


title: RNA from patient HTA3_80010, derived from AAH #3 [PCGA02_30010_6010010]

description: Library name: PCGA02_30010_6010010


title: SNRPD3 (4155) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: SNRPD3_K562_4155_INPUT_rep2
eCLIP size-matched input control for SNRPD3, biological replicate 2


title: P2.5_122

description:
Library name: P2_5_122
SMART-Seq2


title: P2.5_123

description:
Library name: P2_5_123
SMART-Seq2


title: RNA from patient HTA3_80009, derived from ADC [PCGA02_30009_6010003]

description: Library name: PCGA02_30009_6010003


title: SNRPD3 (4155) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: SNRPD3_K562_4155_INPUT_rep1
eCLIP size-matched input control for SNRPD3, biological replicate 1


title: RNA from patient HTA3_80010, derived from AAH #1 [PCGA02_30010_6010003]

description: Library name: PCGA02_30010_6010003

value: HJMCCBGXL


title: P2.5_120

description:
Library name: P2_5_120
SMART-Seq2


title: P2.5_119

description:
Library name: P2_5_119
SMART-Seq2


title: P2.5_118

description:
Library name: P2_5_118
SMART-Seq2


title: ATF2 gRNA vincristine 5

description: Library name: Sample 51

value: ATF2 gRNA


title: ATF2 gRNA vincristine 3

description: Library name: Sample 49


title: ATF2 gRNA vincristine 2

description: Library name: Sample 48


title: SNRPC (4164) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: SNRPC_K562_4164_INPUT_rep2
eCLIP size-matched input control for SNRPC, biological replicate 2


title: RNA from patient HTA3_80009, derived from AAH #1 [PCGA02_30009_6010001]

description: Library name: PCGA02_30009_6010001

value: AAH


title: ATF2 gRNA vincristine 4

description: Library name: Sample 50


title: P2.5_117

description:
Library name: P2_5_117
SMART-Seq2


title: RNA from patient HTA3_80008, derived from Normal [PCGA02_30008_6010002]

description: Library name: PCGA02_30008_6010002


title: RNA from patient HTA3_80008, derived from AAH #1 [PCGA02_30008_6010001]

description: Library name: PCGA02_30008_6010001


title: RNA from patient HTA3_80009, derived from AAH #2 [PCGA02_30009_6010002]

description: Library name: PCGA02_30009_6010002


title: P2.5_121

description:
Library name: P2_5_121
SMART-Seq2


title: CACTIN (4158) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: CACTIN_K562_4158_INPUT_rep2
eCLIP size-matched input control for CACTIN, biological replicate 2


title: SNRPC (4164) eCLIP in K562 cells, IP replicate 1

description:
Library name: SNRPC_K562_4164_IP_rep1
eCLIP immunoprecipitation sample for SNRPC, biological replicate 1


title: RNA from patient HTA3_80008, derived from ADC [PCGA02_30008_6002004]

description: Library name: PCGA02_30008_6002004


title: SNRPD3 (4155) eCLIP in K562 cells, IP replicate 1

description:
Library name: SNRPD3_K562_4155_IP_rep1
eCLIP immunoprecipitation sample for SNRPD3, biological replicate 1


title: ATF2 gRNA untreated 3

description: Library name: Sample 45


title: ATF2 gRNA untreated 4

description: Library name: Sample 46


title: RNA from patient HTA3_80008, derived from Normal [PCGA02_30008_6003005]

description: Library name: PCGA02_30008_6003005


title: CACTIN (4158) eCLIP in K562 cells, IP replicate 2

description:
Library name: CACTIN_K562_4158_IP_rep2
eCLIP immunoprecipitation sample for CACTIN, biological replicate 2


title: SNRPC (4164) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: SNRPC_K562_4164_INPUT_rep1
eCLIP size-matched input control for SNRPC, biological replicate 1


title: RNA from patient HTA2_90014, derived from LUAD Region 3 (Stage 1B) [HTA2_90014_6000104]

description: Library name: HTA2_90014_6000104


title: P2.5_115

description:
Library name: P2_5_115
SMART-Seq2


title: SNRPC (4164) eCLIP in K562 cells, IP replicate 2

description:
Library name: SNRPC_K562_4164_IP_rep2
eCLIP immunoprecipitation sample for SNRPC, biological replicate 2


title: P2.5_116

description:
Library name: P2_5_116
SMART-Seq2


title: ATF2 gRNA untreated 1

description: Library name: Sample 43


title: ATF2 gRNA untreated 5

description: Library name: Sample 47


title: ATF2 gRNA untreated 2

description: Library name: Sample 44


title: P2.5_114

description:
Library name: P2_5_114
SMART-Seq2


title: RNA from patient HTA2_90014, derived from LUAD Region 2 (Stage 1B) [HTA2_90014_6000102]

description: Library name: HTA2_90014_6000102


title: RNA from patient HTA2_90014, derived from Normal [HTA2_90014_6000103]

description: Library name: HTA2_90014_6000103


title: Control gRNA vincristine 4

description: Library name: Sample 41

value: Control gRNA


title: CACTIN (4158) eCLIP in K562 cells, INPUT replicate 1

description:
Library name: CACTIN_K562_4158_INPUT_rep1
eCLIP size-matched input control for CACTIN, biological replicate 1


title: Control gRNA vincristine 5

description: Library name: Sample 42


title: P2.5_113

description:
Library name: P2_5_113
SMART-Seq2


title: RNA from patient HTA2_90014, derived from LUAD Region 1 (Stage 1B) [HTA2_90014_6000101]

description: Library name: HTA2_90014_6000101


title: RNA from patient HTA2_90013, derived from LUAD Region 3 (Stage 1A) [HTA2_90013_6000104]

description: Library name: HTA2_90013_6000104


title: CACTIN (4158) eCLIP in K562 cells, IP replicate 1

description:
Library name: CACTIN_K562_4158_IP_rep1
eCLIP immunoprecipitation sample for CACTIN, biological replicate 1


title: P2.5_111

description:
Library name: P2_5_111
SMART-Seq2


title: RPS10 (4104) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: RPS10_K562_4104_INPUT_rep2
eCLIP size-matched input control for RPS10, biological replicate 2


title: Control gRNA vincristine 3

description: Library name: Sample 40


title: RNA from patient HTA2_90013, derived from Normal [HTA2_90013_6000103]

description: Library name: HTA2_90013_6000103


title: Control gRNA vincristine 1

description: Library name: Sample 38


title: P2.5_109

description:
Library name: P2_5_109
SMART-Seq2


title: RPS10 (4104) eCLIP in K562 cells, IP replicate 1

description:
Library name: RPS10_K562_4104_IP_rep1
eCLIP immunoprecipitation sample for RPS10, biological replicate 1


title: P2.5_112

description:
Library name: P2_5_112
SMART-Seq2


title: P2.5_110

description:
Library name: P2_5_110
SMART-Seq2


title: Control gRNA vincristine 2

description: Library name: Sample 39


title: P2.5_107

description:
Library name: P2_5_107
SMART-Seq2


title: RPS10 (4104) eCLIP in K562 cells, IP replicate 2

description:
Library name: RPS10_K562_4104_IP_rep2
eCLIP immunoprecipitation sample for RPS10, biological replicate 2


title: CXXC1 (4088) eCLIP in K562 cells, INPUT replicate 2

description:
Library name: CXXC1_K562_4088_INPUT_rep2
eCLIP size-matched input control for CXXC1, biological replicate 2


title: Control gRNA untreated 5

description: Library name: Sample 37


title: P2.5_108

description:
Library name: P2_5_108
SMART-Seq2


title: RNA from patient HTA2_90013, derived from LUAD Region 1 (Stage 1A) [HTA2_90013_6000101]

description: Library name: HTA2_90013_6000101