title: ChIP-Seq_OS-RC2_input_2

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

data_processing:
Fastq files were aligned to hg19 using Bowtie2.
ENCODE blacklisted regions were removed, reads were extended to a modal length of 250bp and duplicates were removed.
Genomewide coverage was determined in 10bp windows and normalized to counts/million uniquely mapped reads.
Genomewide coverage data was converted to BigWig format.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files display counts/million uniquely mapped reads in 10bp windows.

source_name: OS-RC-2 cell line

growth_protocol: Cells grown under standard tissue culture conditions in RPMI + 10% FBS.Cells grown under standard tissue culture conditions in RPMI + 10% FBS.

extract_protocol:
Cells were crosslinked in 1% formaldehyde for 10min at room temperature, followed by 5 min quenching with 0.125M glycine. Cells were washed twice with PBS, the supernatant was aspirated and cell pellets were frozen in liquid nitrogen and stored at -80°C. 100µl of Protein A/G magnetic beads (Thermo 26162) were blocked with 0.5% BSA in PBS, followed by incubation with the antibody. Cross-linked cells were resuspendend and sonicated in lysis buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 0.1% SDS, and 1% Triton X-100). Sonication was performed using Bioruptor (Diagenode) for 14 cycles (30’’ on/ 30’’ off) at max output to obtain fragments of 100-500bp. Sonicated lysates were cleared and incubated overnight at 4°C with antibody-bound magnetic beads. Beads were sequentially washed three times with low salt buffer (50mM HEPES pH7.5, 140mM NaCl, 1% Triton) and once with high salt buffer (50mM HEPES pH7.5, 500mM NaCl, 1% Triton). DNA was eluted in elution buffer (50mM NaHCO3, 1%SDS) and cross-links were reversed for 3h (65°C, 1000rpm shaking). DNA was purified using the QuickClean II PCR Extraction Kit (Genescript L00419-100) according to the manufacturer’s recommendations and eluted with 100µl H2O.
Purified ChIP DNA was used to prepare Illumina multiplexed sequencing libraries with the KAPA Hyper Prep Kit (KR0961) Illumina platforms sample preparation protocol (v1.14). Briefly, DNA was end-repaired and A-tailed to produce end-repaired, 5’-phosphorylated, 3’-dA-tailed, dsDNA fragments. These 3’-dA-tailed library fragments were then ligated with dsDNA adapters with 3’dTMP overhangs. After adapter ligation, libraries were size selected to 150-350bp using AMPure XP reagent (Agencourt A63880) according to the protocol recommendations. Size selected libraries were amplified for 15 cycles using the KAPA HiFi HotStart ReadyMix. PCR libraries were pooled in equimolar concentrations and sequenced.

tag: cell line type

value: renal cancer cell line

tag: treatment

tag: target molecule

value: na (input control)

tag: antibody


title: SEP_3

status: Public on Jun 12 2018

type: SRA

city: Uppsala

first: Gustav

last: Arvidsson

state: Uppsala

address: Husargatan 3

department: Department of Medical Sciences

country: Sweden

institute: Uppsala Universitet

description:
Sample_3B
hg19_count_table.csv, mm10_count_table.csv

library_source: transcriptomic

data_processing:
Short reads were indexed using the species-based short read separation software Xenome (v1.0.1) for human and mouse based on UCSC reference genomes as specified below.
Species-specific PE short reads of human and murine origin were aligned to reference genomes hg19 and mm10 respectively using the splice aware short read aligner Tophat2 (2.0.11) with Bowtie2 (v2.2.2) and Samtools (v0.1.19) using PE read input and default options
Species specific read pairs per feature were counted using summarizeOverlaps from the Bioconductor (v2.14) package GenomicAlignments (v1.0.6). Annotated genes were acquired through Bioconductor packages TxDb.Hsapiens.UCSC.hg19.knownGene (v2.14.0) and TxDb.Mmusculus.UCSC.mm10.knownGene (v2.14.0).
Data was pairwise interrogated for differentially expressed genes using the Bioconductor package Deseq (v1.16.0).
Genome_build: hg19 (GRCh37) and mm10 (GRCm38) were obtained from the UCSC Genome Browser FTP server
Supplementary_files_format_and_content: hg19_count_table.csv: RAW read count table per feature for all samples after species-based separation of reads of human origin and alignment to hg19
Supplementary_files_format_and_content: mm10_count_table.csv: RAW read count table per feature for all samples after species-based separation of reads of murine origin and alignment to mm10

molecule: polyA RNA

organism: Homo sapiens

source_name: -, Jeko-1

growth_protocol: MS-5 cells and Jeko-1 cells mono- or co-cultured in αMEM-glutamax (Gibco) supplemented with 10% H.I. FBS (Gibco), 2mM sodium pyruvate, 100U/mL penicillin and 100µg/mL streptomycin (Gibco). All cells were cultivated in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy (Qiagen) with QIAshredders following the protocol supplied by the manufacturer.
Libraries were constructed using Illumina Truseq 2.0 reagents according to manufacturers protocol, mRNA was purified by poly-T oligo-attached magnetic beads.

treatment_protocol: 5x10^5 MS-5 stromal cells were seeded 24h in advance to 10cm dishes (TPP) and 5x10^6 Jeko-1 cells were subsequently added. RNA was extracted following 24h of incubation at 37 degrees 5% CO2.

tag: cultivation

value: mono-cultured cell line

tag: cell type

value: mantle cell lymphoma cell line


title: SEP_1

description:
Sample_1B
hg19_count_table.csv, mm10_count_table.csv


title: SEP_4

description:
Sample_4B
hg19_count_table.csv, mm10_count_table.csv


title: ChIP-Seq_OS-RC2_input_1

library_source: genomic

molecule: genomic DNA

tag: cell line


title: HL-60_C/EBPβ_ChIP

city: shanghai

first: wang

last: yujie

state: Shanghai

address: Chi Feng road No:65

country: China

institute: Shanghai JiaYin Biological technology co., LTD

data_processing:
ChIP-seq reads were aligned to the hg19 reference genome using BWA(0.7.10)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 version 2.1.1 was used to call peaks with the sonicated input as a control and an initial threshold q-value of 0.01 as cutoff
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using MACS

growth_protocol: HL-60 were grown in DMEM supplemented with 10%FBS, at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: myeloblast

tag: gentoype/variation

value: C/EBPβ-overexpressed

tag: chip antibody

value: C/EBPβ (Santa Cruz, sc-150x)


title: ChIP-Seq_OS-RC2_HIF1B


title: ChIP-Seq_OS-RC2_H3K27ac_2

value: ab4729 (Abcam)


title: ChIP-Seq_OS-RC2_H3K27ac_1


title: ChIP-Seq_OS-LM1_input_1

source_name: OS-LM1 cell line


title: ChIP-Seq_OS-LM1_HIF1B


title: ChIP-Seq_OS-LM1_input_2


title: ChIP-Seq_OS-LM1_H3K27ac_2


title: ChIP-Seq_786-O_input_2

source_name: 786-O cell line


title: ChIP-Seq_OS-LM1_H3K27ac_1


title: ChIP-Seq_786-O_HIF1B


title: ChIP-Seq_786-O_H3K27ac_2


title: ChIP-Seq_786-O_H3K4me1_2

value: ab8895 (Abcam)


title: ChIP-Seq_786-O_H3K4me1_1


title: ChIP-Seq_786-M1A_input_2

source_name: 786-M1A cell line


title: ChIP-Seq_786-M1A_H3K4me1_2


title: ChIP-Seq_786-M1A_input_1


title: ChIP-Seq_786-O_H3K27ac_1


title: ChIP-Seq_786-M1A_p300

value: sc-585 (Santa Cruz)


title: ChIP-Seq_786-M1A_H3K4me1_1


title: ChIP-Seq_786-M1A_H3K27ac_2


title: ChIP-Seq_786-M1A_HIF1B


title: ChIP-Seq_786-M1A-iMAE-1.1_H3K27ac

value: CRISPRi – iMAE-1.1


title: ChIP-Seq_786-M1A-iMAE-126_H3K27ac

value: CRISPRi – iMAE-126


title: ChIP-Seq_786-M1A-Ctrl_H3K27ac

value: non-targeting CRISPRi


title: 32D_C/ebpβ_ChIP

data_processing:
ChIP-seq reads were aligned to the mm10 reference genome by Bowtie2 (version 2.1.0) with default parameter settings
Sam files were converted to Bam format using Samtools and used for peak calling
enriched binding regions were called with the sonicated input as a control using MACS1.4 at a p-value cut off of 1e-6 .
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using MACS1.4

organism: Mus musculus

source_name: 32D cells

growth_protocol: 32D cells were grown in RPMI 1640 medium with 2 mM L-glutamine adjusted to contain 1.5 g/L sodium bicarbonate, 4.5 g/L glucose, 10 mM HEPES, and 1.0 mM sodium pyruvate supplemented with: 10% heat-inactivated fetal bovine serum 10% mouse Interleukin-3 culture supplement , at 37 °C in a humidified atmosphere with 5% CO2

value: C/EBPÎ² (Santa Cruz, sc-150x)


title: ChIP-Seq_786-O_input_1


title: 32D_Jmjd3_ChIP

value: JMJD3 (Abcam, ab85392)


title: MS-5_2

description:
Sample_2A
hg19_count_table.csv, mm10_count_table.csv

value: bone marrow derived stromal cell line


title: RNA-Seq_OS-LM1_2

data_processing:
Fastq files were mapped to the human transcriptome using Bowtie2, relative gene expression was determined using RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: Gene level RSEM output files.

molecule: total RNA

growth_protocol: Cells grown under standard tissue culture conditions in RPMI + 10% FBS.

extract_protocol:
RNA was extracted from 80% confluent cells using the RNeasy Mini Kit (Qiagen 74104) following the manufacturer’s recommendations. RNA quality was assessed with the RNA Nano 6000 kit (Agilent 5067-1511) and Agilent Bionalyzer 2100 instrument.
Purified RNA (1µg) was used to prepare Illumina multiplexed sequencing libraries. Libraries were prepared following the KAPA Stranded mRNA-seq Kit (KR0960) Illumina platforms sample preparation protocol (v3.15). Briefly, poly(A) RNA was captured with magnetic oligo-dT beads and heat fragmented (94°C) to a size of 200-300bp. Fragmented RNA was used for 1st strand cDNA synthesis, generating cDNA-RNA hybrids which were used for 2nd strand synthesis and marking to obtain dscNDA marked with dUTP. Newly synthesized fragments were end-repaired and A-tailed to add dAMP to the 3’-end of dscDNA fragments. These 3’-dA-tailed library fragments were then ligated with 3’-dTMP adapters. After adapter ligation, libraries were cleaned up using the Agencourt AMPure XP reagent (A63880) according to manufacturer’s recommendations. Purified, adapter-ligated DNA was amplified for 15 cycles. PCR libraries were pooled in equimolar concentrations and sequenced.

value: OS-LM1 renal cancer cell line


title: RNA-Seq_OS-LM1_1


title: RNA-Seq_OS-RC2_TGL_1

value: OS-RC2 renal cancer cell line


title: MS-5_3

description:
Sample_3A
hg19_count_table.csv, mm10_count_table.csv


title: ChIP-Seq_786-M1A_H3K27ac_1

value: renal cancer cell line


title: MS-5_1

description:
Sample_1A
hg19_count_table.csv, mm10_count_table.csv

value: mono-cultured cell line


title: RNA-Seq_OS-RC2_TGL_2


title: JMJD3 KO_rep3

data_processing:
Basecalls performed using CASAVA version 1.8
Adapter sequences were removed by using SeqPrep, and then poor quality reads filtered by sickle(version 1.200) for quality control
Quality filtered reads were then mapped to GRCh38 using TopHat (v2.0.4)
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . RSEM was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
GO functional enrichment and KEGG pathway analysis were carried out by Goatools  and KOBAS
Genome_build: GRCh38
Supplementary_files_format_and_content: excel file of expression analysis result of  EdgeR and annotation

source_name: JMJD3 KO

growth_protocol: HL-60 were grown in DMEM supplemented with 10% FBS, at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: JMJD3 knockout


title: Parental_rep2

source_name: Parental

value: parental cells


title: Parental_rep1


title: HL60_JMJD3_rep3

tag: transduced with

value: JMJD3-expression vector


title: HL60_JMJD3_rep2


title: HL60_JMJD3_rep1


title: Parental_rep3


title: ChIP-Seq_786-O_p65_1

value: ab16502 (Abcam)


title: ChIP-Seq_786-O_input_3

value: na (input control)


title: ChIP-Seq_786-M1A_HIF2A

value: ab199 (Abcam)


title: ChIP-Seq_786-O_HIF2A


title: ChIP-Seq_786-M1A_p65_2


title: ChIP-Seq_786-M1A_p65_1


title: ChIP-Seq_786-M1A_input_3


title: ChIP-Seq_786-O_p65_2


title: HL60_Vector_rep2

value: control vector


title: HL60_Vector_rep1


title: MS-5_4

description:
Sample_4A
hg19_count_table.csv, mm10_count_table.csv


title: HiC_786-M1A_2

data_processing:
library strategy: HiC-seq
Reads were aligned to the hg19 human genome build using the HiC-Pro pipeline (PMID: 26619908). A HindIII restriction fragments map was created using the script provided by Hi-C-Pro (digest_genome.py) with the ligation site "A^AGCTT". The configuration file for the HiC-Pro run used this map as well as the following parameters: fragment size between 100 and 600bp (according to preliminary analysis), maximum number of iterations 200, filtering low count percentage 0.02, filtering high count percentage 0 and eps 0.1.
Multimapping, low quality and duplicate reads are removed according to the HiC-Pro pipeline, as well as Hi-C specific artefacts. Matrices of 20kb and 40kb resolutions were built from the filtered alignment and normalised using ICE, also as part of the HiC-Pro pipeline. TADbit (https://github.com/3DGenomes/TADbit) was used to call TADs from the 40kb raw matrices, while the ICE-normalised 20kb matrices were used for visualisation using HiC-Plotter.
Reads were aligned to the hg19 human genome build using the HiC-Pro pipeline (PMID: 26619908). A HindIII restriction fragments map was created using the script provided by Hi-C-Pro (digest_genome.py) with the ligation site "A^AGCTT". The configuration file for the HiC-Pro run used this map as well as the following parameters: fragment size between 100 and 600bp (according to preliminary analysis), maximum number of iterations 200, filtering low count percentage 0.02, filtering high count percentage 0 and eps 0.1.
Multimapping, low quality and duplicate reads are removed according to the HiC-Pro pipeline, as well as Hi-C specific artefacts. Matrices of 20kb and 40kb resolutions were built from the filtered alignment and normalised using ICE, also as part of the HiC-Pro pipeline. TADbit (https://github.com/3DGenomes/TADbit) was used to call TADs from the 40kb raw matrices, while the ICE-normalised 20kb matrices were used for visualisation using HiC-Plotter.
Genome_build: hg19
Supplementary_files_format_and_content: The chr2 interaction matrices are in the HiC-Pro format (for more information, check https://github.com/nservant/HiC-Pro) with a matrix file and a corresponding bed file for each resolution (20kb and 40kb) where the 20kb matrices are ICE-normalised and the 40kb ones are raw for TAD calling.

extract_protocol: In-nucleus Hi-C was performed on 20 million cells per cell line as previously described by Nagano, T. et al. (Genome Biol 16, 175, doi:10.1186/s13059-015-0753-7 (2015).) with only minor modifications: DNA extraction and all purifications were performed using Agencourt Ampure XP beads (Beckman Coulter) and ligations were performed in a volume of 1 ml.  Final libraries were amplified using 6 cycles of PCR and 2 samples pooled per sequencing lane.


title: HiC_786-O_2


title: JMJD3 KO_rep2


title: JMJD3 KO_rep1


title: ChIP-Seq_MDA-MB-231_H3K27ac

source_name: MDA-MB-231 cell line

value: breast cancer cell line

value: ab4729 (Abcam)


title: HiC_786-M1A_1


title: HiC_786-O_1


title: ChIP-Seq_786-M1A-iMAE-1.2_H3K27ac

value: CRISPRi – iMAE-1.2


title: ChIP-Seq_786-M2A_H3K27ac

source_name: 786-M2A cell line


title: ChIP-Seq_786-M2B_H3K27ac

source_name: 786-M2B cell line


title: RNA-Seq_786-O_2

value: 786-O renal cancer cell line


title: RNA-Seq_786-M1A_iMAE-126_1

value: 786-M1A renal cancer cell line

value: CRISPRi – iMAE-126


title: RNA-Seq_786-M1A_iMAE-126_2


title: RNA-Seq_786-O_1


title: ChIP-Seq_1833-BoM_H3K27ac

source_name: 1833-BoM cell line


title: HL60_Vector_rep3


title: RNA-Seq_786-M1A_iMAE-1.1_3

value: CRISPRi – iMAE-1.1


title: RNA-Seq_786-M1A_SC_6

value: non-targeting CRISPRi


title: RNA-Seq_786-M1A_iMAE-1.2_3


title: RNA-Seq_786-M1A_iMAE-1.2_1


title: RNA-Seq_786-M1A_iMAE-1.1_2


title: RNA-Seq_786-M1A_iMAE-1.2_4


title: RNA-Seq_786-M1A_iMAE-1.1_4


title: RNA-Seq_786-M1A_SC_5


title: RNA-Seq_786-M1A_SC_4


title: ChIP-Seq_786-M1A-iMAE-2_H3K27ac

value: renal cancer cell line

value: CRISPRi – iMAE-2


title: RNA-Seq_786-M1A_SC_2


title: RNA-Seq_786-M1A_2


title: ChIP-Seq_4175-LM2_H3K27ac

source_name: 4175-LM2 cell line


title: ChIP-Seq_786-M1A-SC_H3K27ac


title: RNA-Seq_786-M1A_1


title: MKN74_mir1271_RNAseq

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description:
MKN74
processed data file: RNAseq_FPKM.xlsx

data_processing:
RNA_seq;
Illumina Casava1.7 software used for basecalling.
mapped to hg19 whole genome using Tophat 2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a standard protocol. The rpkm values are on log2 scale.
miRNA-seq;
Illumina Casava1.7 software used for basecalling.
mapped to hg19 whole genome using Tophat 2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a standard protocol. The rpkm values are on log2 scale.
MBD_seq;
Base calling performed using CASAVA version 1.7
mapped to hg19 whole genome using bwa v.0.5.9
Methylation levels were called using pysam (-2 kb~500 bp from TSS). Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a standard protocol. The rpkm values are on log2 scale.
Genome_build: hg19
Supplementary_files_format_and_content:
RNA_seq; tab-delimited text files include FPKM values for each Sample
miRNA-seq; tab-delimited text files include RPKM values for each Sample
MBD_seq; bedgraph files were generated using homer

source_name: gastric cancer cell line

extract_protocol:
MBD2-immunoprecipitated chromatin fragments were extracted for MBD-seq. RNAs were isolated using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific)
We collected MBD2-immunoprecipitated chromatin fragments and genomic libraries were constructed using the TruSeq ChIP Sample Prep Kit (Illumina).RNAs were isolated using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific) and libraries were prepared using the Illumina TruSeq Small RNA Sample Prep Kit.

treatment_protocol: Synthetic mimic of mir-1271 were purchased from the Thermo Fisher Scientific. 2×105 cells onto a 6-well plate (SPL) were transfected with 100 pmoles of miRNA using Lipofectamine® RNAiMAX (Invitrogen).

tag: tissue/cell type

value: gastric cancer cell line

tag: transfected with

value: miR-1271 mimic

tag: molecular subtype

value: total RNA


title: RNA-Seq_786-M1A_iMAE-1.1_1


title: SNU484_MBDseq

value: genomic DNA


title: SNU601_mir1271_RNAseq

description:
SNU601
processed data file: RNAseq_FPKM.xlsx


title: RNA-Seq_786-M1A_SC_1


title: SNU601_control_RNAseq


title: RNA-Seq_786-M1A_iMAE-1.2_2


title: AGS_MBDseq

description: AGS

value: AGS


title: csc2_miRNAseq

description:
patient 2 gastric cancer stem cell
processed data file: miRNAseq_RPKM.xlsx

source_name: gastric cancer stem cell

tag: source subject id

value: gastric cancer (GC) patinet 2

value: gastric cancer stem cell

value: small RNA


title: MKN74_MBDseq


title: Normal3_miRNAseq

description:
patient 3 gastric normal tissue
processed data file: miRNAseq_RPKM.xlsx

source_name: gastric normal tissue

value: gastric cancer (GC) patinet 3

value: gastric normal tissue


title: Normal2_miRNAseq

description:
patient 2 gastric normal tissue
processed data file: miRNAseq_RPKM.xlsx


title: RNA-Seq_786-M1A_SC_3


title: mut rep 3

status: Public on Jun 11 2018

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

country: United Kingdom

institute: Cerevance ltd

description:
KO 3
SLX-12903.i703_i505.HHJT3BBXX.s_5

data_processing:
Star alignment
Htseq-count (quality filter "-q 20")
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Unnormalized raw count generated with htseq-count

extract_protocol:
manual dissection of epiblast/VE. Arcturus Pico Puro RNA isolation kit
SmartSeq2
1ng input followed by 15 cycles pre-amplification with polyA selection

tag: strain background

value: mixed

tag: genotype

value: Sox2Cre+/-; Oct4 fl/-

tag: tissue

value: embryo


title: MKN74_control_RNAseq


title: mut rep 1

description:
KO 1
SLX-12903.i701_i505.HHJT3BBXX.s_5


title: mut rep 2

description:
KO 2
SLX-12903.i702_i505.HHJT3BBXX.s_5


title: DMSO_1

city: Majadahonda

first: Maria

last: Barrero

state: Madrid

address: Crta. Majadahonda-Pozuelo KM 2.2

country: Spain

institute: ISCIII

data_processing:
RNA-seq processing:
RNA-seq analysis was performed with the nextpresso pipeline v1.4, using the following tools:
Read files were quality-checked with FastQC.
Reads were aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 2.2.1
Homo sapiens GRCh37/hg19 transcript annotations from the UCSC Genome Browser were used
Genome_build: GRCh37/hg19

source_name: K562 cells

growth_protocol: K562 cells wer grown in RPMI+10%FBS

extract_protocol:
Cells were trypsinized and total RNA was extracted using the RNeasy kit (Qiagen).
From1 µg of total RNA PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit. Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced for 50 bases in a single-read format (Illumina HiSeq 2000).

treatment_protocol: K562 cells were treated for 48 hours with with 200 nM JQ1, 5 µM CBP30 , 10 µM C646 or vehicle (DMSO). Two biological replicates were used per condition.

tag: treatment

value: DMSO


title: wt rep 2

description:
WT 8
SLX-12903.i703_i506.HHJT3BBXX.s_5

value: WT; Sox2Cre-/-; Oct4 fl/+


title: DMSO_2


title: C646_1


title: wt rep 1

description:
WT 7
SLX-12903.i702_i506.HHJT3BBXX.s_5


title: csc3_miRNAseq

description:
patient 3 gastric cancer stem cell
processed data file: miRNAseq_RPKM.xlsx


title: CBP30_1


title: C646_2


title: CBP30_2


title: JQ1_2


title: H7CD24P100

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

country: USA

institute: National Cancer Institute

data_processing:
Basecalling performed by RTA version 1.18.66.3
Demultiplexing performed by Bcl2fastq version 1.8.4
Adaptor trimming and quality control by Trimmomatic version 0.30
Read alignment performed by STAR version 2.5.1
Transcript quantification performed by RSEM version 1.2.22
Data normalized by median normalization
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file of RSEM values for each single cell

source_name: HuH-7 CD24 positive 100 cells pooled

growth_protocol: HuH-1 and HuH-7 were grown in DMEM medium plus 10% fetal bovine serum and 1% antibiotics. At 80% confluence, the cell were harvested for flow cytometry sorting

extract_protocol:
no RNA extraction step droplet-based single-cell RNA-seq (SMART-seq)
Cells were lysed in ice-cold lysis buffer. SMART-seq protolcol was performed on single or pooled sorted cells following the manufacturere's instructions with some modification. Briefly, whole transcriptome was amplified with the SMART-seq v4 Ultra Low Input RNA kit (Clonetech), purified (Beckman Coulter, A63881) and barcoded (Illumina, FC-131-1096). Finally, libraries were pooled and sequenced on Illumina Hiseq2500.

value: hepatcellular carcinoma

tag: cell surface marker

tag: cell number

tag: cell status

value: pooled


title: H7CD133P100

source_name: HuH-7 CD133 positive 100 cells pooled


title: H7CD24P10

source_name: HuH-7 CD24 positive 10 cells pooled


title: H7CD133SC13

source_name: HuH-7 CD133 positive single cell 13

value: single-cell


title: JQ1_1


title: H7CD133SC12

source_name: HuH-7 CD133 positive single cell 12


title: H7CD133SC11

source_name: HuH-7 CD133 positive single cell 11


title: H7CD133SC10

source_name: HuH-7 CD133 positive single cell 10


title: H7CD133SC8

source_name: HuH-7 CD133 positive single cell 8


title: H7CD133SC7

source_name: HuH-7 CD133 positive single cell 7


title: H7TPP100

source_name: HuH-7 triple positive 100 cells pooled

value: TriplePos


title: H7EPCAMP10

source_name: HuH-7 EPCAM positive 10 cells pooled

value: EPCAM


title: H7CD133SC6

source_name: HuH-7 CD133 positive single cell 6


title: H7CD133SC5

source_name: HuH-7 CD133 positive single cell 5


title: H7CD133SC9

source_name: HuH-7 CD133 positive single cell 9


title: H7CD133SC4

source_name: HuH-7 CD133 positive single cell 4


title: H7EPCAMP100

source_name: HuH-7 EPCAM positive 100 cells pooled


title: H7CD133P10

source_name: HuH-7 CD133 positive 10 cells pooled


title: H7CD24SC8

source_name: HuH-7 CD24 positive single cell 8


title: H7CD24SC3

source_name: HuH-7 CD24 positive single cell 3


title: H7CD24SC5

source_name: HuH-7 CD24 positive single cell 5


title: H7CD133SC1

source_name: HuH-7 CD133 positive single cell 1


title: H7CD24SC7

source_name: HuH-7 CD24 positive single cell 7


title: H7CD24SC4

source_name: HuH-7 CD24 positive single cell 4


title: H7CD133SC3

source_name: HuH-7 CD133 positive single cell 3


title: H7CD24SC6

source_name: HuH-7 CD24 positive single cell 6


title: H7CD133SC2

source_name: HuH-7 CD133 positive single cell 2


title: H7EPCAMSC12

source_name: HuH-7 EPCAM positive single cell 12


title: H7CD24SC2

source_name: HuH-7 CD24 positive single cell 2


title: H7EPCAMSC13

source_name: HuH-7 EPCAM positive single cell 13


title: H7CD24SC1

source_name: HuH-7 CD24 positive single cell 1


title: H7TPP10

source_name: HuH-7 triple positive 10 cells pooled


title: H7EPCAMSC11

source_name: HuH-7 EPCAM positive single cell 11


title: H7EPCAMSC10

source_name: HuH-7 EPCAM positive single cell 10


title: H7EPCAMSC9

source_name: HuH-7 EPCAM positive single cell 9


title: H7EPCAMSC8

source_name: HuH-7 EPCAM positive single cell 8


title: MEF_ChIPSeq_Co_Ing1_rep2

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

description: Sample 2

data_processing:
ChIP-Seq reads were quality assesed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The reads were aligned to the mm9 genome with Bowtie v.0.12.9 (http://bowtie.cbcb.umd.edu) with parameters: -m 1 --best --strata
Peak calling analysis of ING1 ChIP vs. Control ChIP was performed for each replicate with MACS v.1.4.2 (http://liulab.dfci.harvard.edu/MACS/index.html)
Genome_build: NCBIM37 (mm9)
Supplementary_files_format_and_content: bigWig coverage files created from mapped reads extended to 400bp average fragment size and RPKM-normalised using deepTools (http://deeptools.readthedocs.io/en/latest/index.html)

source_name: ChIP-Seq Control (Ing1) MEFs

growth_protocol: Mouse embryonic fibroblasts (MEFs) were isolated from  male, wildtype embryos (embryonic day E15.5) and cultured for 4 passages.

extract_protocol: ChIP was carried out essentially as described (Schäfer et al., 2013; doi: 10.1101/gad.186916.112) using rabbit a-HA antibody (Abcam, ab9110). ChIP-seq library preparation was performed using NuGEN´s Ovation Ultralow System V2 1-16 (2014), following the manufacturer’s recommendations. Libraries were prepared from 1 ng  ChIP-DNA and were amplified in 14 PCR cycles. Size selection (300-1550bp fragments) was performed using a XT DNA 750 chip (Perkin Elmer). Libraries were profiled in a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). ING1 libraries were pooled in equimolar ratio and sequenced on two HiSeq2500 lanes, rapid mode, single read for 68 cycles for read 1 plus 7 cycles for the index read.

treatment_protocol: Cells were electroporated in duplicates with either control plasmid or plasmid coding for human HA-tagged ING1b using a NeonTM Transfection System (Invitrogen) according to the manufacturer’s instructions, followed by 36h incubation.

value: Control

tag: cell type

value: Mouse Embryonic Fibroblasts (MEFs)


title: H7EPCAMSC7

source_name: HuH-7 EPCAM positive single cell 7

tag: cell line


title: MEF_ChIPSeq_Ing1_rep2

description: Sample 4

source_name: ChIP-Seq Ing1 MEFs


title: MEF_ChIPSeq_Ing1_rep1

description: Sample 3


title: MEF_ChIPSeq_Co_Ing1_rep1

description: Sample 1


title: H7EPCAMSC6

source_name: HuH-7 EPCAM positive single cell 6


title: H7EPCAMSC5

source_name: HuH-7 EPCAM positive single cell 5


title: H7EPCAMSC4

source_name: HuH-7 EPCAM positive single cell 4


title: MEF_ChIPSeq_Gadd45a_rep2

description: Sample 4

data_processing:
ChIP-Seq reads were quality assesed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The reads were aligned to the mm9 genome with Bowtie v.0.12.9 (http://bowtie.cbcb.umd.edu) with parameters: -m 1 --best --strata
Peak calling analysis of Gadd45a ChIP vs. Control ChIP was performed for each replicate with MACS v.1.4.2 (http://liulab.dfci.harvard.edu/MACS/index.html)
Genome_build: NCBIM37 (mm9)
Supplementary_files_format_and_content: bigWig coverage files created from mapped reads extended to 400bp average fragment size and RPKM-normalised using deepTools (http://deeptools.readthedocs.io/en/latest/index.html)

source_name: ChIP-Seq Gadd45a MEFs

growth_protocol: Mouse embryonic fibroblasts (MEF cells) were isolated from male, wildtype embryos (embryonic day E15.5) and cultured for 4 passages.

extract_protocol: ChIP was carried out essentially as described (Schäfer et al., 2013; doi: 10.1101/gad.186916.112) using rabbit a-HA antibody (Abcam, ab9110). ChIP-seq library preparation was performed using NuGEN´s Ovation Ultralow System V2 1-16 (2014), following the manufacturer’s recommendations. Libraries were prepared from 48 ng ChIP-DNA and were amplified in 9 PCR cycles. Double bead size selection with ratios of 0.65:1 and 0.85:1 (beads:DNA ratio) was performed to enrich the library for 230-730bp fragments using Agencourt AMPure XP (Beckman Coulter).  Libraries were profiled in a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). GADD45a libraries were pooled in equimolar ratio and sequenced on two HiSeq2500 lanes, rapid mode, single read for 68 cycles for read 1 plus 7 cycles for the index read.

treatment_protocol: Cells were electroporated in duplicates with either control plasmid or plasmid coding for human HA-tagged GADD45a using a NeonTM Transfection System (Invitrogen) according to the manufacturer’s instructions, followed by 36h incubation.


title: H7EPCAMSC3

source_name: HuH-7 EPCAM positive single cell 3


title: MEF_ChIPSeq_Gadd45a_rep1

description: Sample 3


title: MEF_ChIPSeq_Co_G45a_rep2

description: Sample 2

source_name: ChIP-Seq Control (Gadd45a) MEFs


title: H7EPCAMSC2

source_name: HuH-7 EPCAM positive single cell 2


title: H7EPCAMSC1

source_name: HuH-7 EPCAM positive single cell 1


title: H7TNSC11

source_name: HuH-7 triple negative single cell 11

value: TripleNeg


title: H7TNSC10

source_name: HuH-7 triple negative single cell 10


title: MEF_ChIPSeq_Co_G45a_rep1

description: Sample 1


title: Sox4_wt_No_treatment_HCC_1

city: Utrecht

first: Ana

last: Lourenço

address: Uppsalalaan 8

country: Netherlands

institute: UMC Utrecht

description:
anti-SOX4 ChIP-seq
SLX-8379A012

data_processing:
ChIP-sequencing reads were mapped with Bowtie 2.1.0 against the reference genome (hg19) using default settings (Langmead and Salzberg, 2012).
Peaks were called with HOMER software using the input as a control (Fold over local region=8, Fold over input=2) (Heinz et al., 2010).
Mapped fragments were extended according to the average fragment size and converted to TDF files, visualized with IGV tools v2.3.36 and represented as coverage normalized tracks (Robinson et al., 2011). SAMtools was used for manipulation of SAM and BAM files; manipulation of BED file format was performed with BEDtools (Li et al., 2009; Quinlan and Hall, 2010).
Motif discovery, peak annotation and generation of histograms were performed using HOMER software. For motif discovery the 200 bp sequence surrounding each peak was examined and motifs with length of 8, 10 and 12 nt were searched. Motifs were identified through de novo motif discovery.
Genome_build: hg19
Supplementary_files_format_and_content: Bam and Bigwig

growth_protocol: Cell lines were grown according to manufacture]s protocol

extract_protocol:
Crosslink was performed with disuccinimidyl glutarate (DSG) (Thermo Scientifis) for 45 minutes followed by 30 minutes incubation with formaldehyde 1%. The reaction was blocked with glycine 100 mM. Shearing was performed using Covaris S2 (Covaris, Woburn, MA) for 8 min at maximum intensity. The sonicated chromatin was incubated O/N at 4°C in presence of 15µl of anti-SOX4 (CS-129-100, Diagenode) or 2µg of anti-SMAD3 (ab28379, abcam) coupled to A/G sepharose beads (Santa Cruz Biotechnology).
Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA) was used for End-repair, A-tailing and ligation of sequence adaptors. Samples were amplified by PCR and the libraries were size-selected in the 200-500 bp range.

treatment_protocol: Doxycicline, TGF-β or both

value: human breast cell line

tag: immunoprecipitation

value: CS-129-100, Diagenode


title: Sox4_wt_TGFb_HCC_1

description:
anti-SOX4 ChIP-seq
SLX-8379A002


title: Smad3_wt_No_treatment_HCC_2

description:
anti-SMAD3 ChIP-seq
SLX-8379A018

value: ab28379, abcam


title: Smad3_wt_TGFb_HCC_1

description:
anti-SMAD3 ChIP-seq
SLX-8379A016


title: Input_HCC_wt

description:
input ChIP-seq
SLX-8376A002

value: Input


title: H7TNSC6

source_name: HuH-7 triple negative single cell 6


title: H7TNSC9

source_name: HuH-7 triple negative single cell 9


title: H7TNSC7

source_name: HuH-7 triple negative single cell 7


title: H7TNSC8

source_name: HuH-7 triple negative single cell 8


title: Smad3_wt_TGFb_HCC_2

description:
anti-SMAD3 ChIP-seq
SLX-8379A019


title: H7TNSC5

source_name: HuH-7 triple negative single cell 5


title: Smad3_wt_No_treatment_HCC_1

description:
anti-SMAD3 ChIP-seq
SLX-8379A015


title: H7TNSC4

source_name: HuH-7 triple negative single cell 4


title: Input_wt_231

description:
input ChIP-seq
SLX-8376A012


title: Sox4_wt_TGFb_231_1

description:
anti-SOX4 ChIP-seq
SLX-8379A006


title: H7TNSC3

source_name: HuH-7 triple negative single cell 3


title: H7TNSC2

source_name: HuH-7 triple negative single cell 2


title: Sox4_wt_No_treatment_231_1

description:
anti-SOX4 ChIP-seq
SLX-8379A004


title: Smad3_wt_TGFb_231_2

description:
anti-SMAD3 ChIP-seq
SLX-8379A014


title: H7TNSC1

source_name: HuH-7 triple negative single cell 1


title: H7TNSC12

source_name: HuH-7 triple negative single cell 12


title: Smad3_wt_TGFb_231_1

description:
anti-SMAD3 ChIP-seq
SLX-8379A007


title: Smad3_wt_No_treatment_231_2

description:
anti-SMAD3 ChIP-seq
SLX-8379A013


title: Smad3_wt_No_treatment_231_1

description:
anti-SMAD3 ChIP-seq
SLX-8379A005


title: H7TPSC8

source_name: HuH-7 triple positive single cell 8


title: H7TPSC7

source_name: HuH-7 triple positive single cell 7


title: HMECinput_S11.merged

description:
input ChIP-seq
HMECinputmerged.bam.sorted.bam

source_name: Immortalized human mammary epithelial cells

value: HMLE


title: HMECsSox4plusdoxplusTGF_S12.merged

description:
anti-SOX4 ChIP-seq
HMECsSox4plusdoxplusTGF_S12.merged.bam.sorted.bam

value: Immortalized human mammary epithelial cells


title: HMECsSox4mindoxplusTGF_S11.merged

description:
anti-SOX4 ChIP-seq
HMECsSox4mindoxplusTGF_S11.merged.bam.sorted.bam


title: H7TPSC5

source_name: HuH-7 triple positive single cell 5


title: H7TPSC3

source_name: HuH-7 triple positive single cell 3


title: HMECsSox4plusTGF_S9.merged

description:
anti-SOX4 ChIP-seq
HMECsSox4plusTGF_S9.merged.bam.sorted.bam


title: H7TPSC2

source_name: HuH-7 triple positive single cell 2


title: HMECsSmad3NT_S8.merged

description:
anti-SMAD3 ChIP-seq
HMECsSmad3NT_S8.merged.bam.sorted.bam


title: HMECsSox4NT_S7.merged

description:
anti-SOX4 ChIP-seq
HMECsSox4NT_S7.merged.bam.sorted.bam


title: HMECsSmad3plusdoxplusTGF_S4.merged

description:
anti-SMAD3 ChIP-seq
HMECsSmad3plusdoxplusTGF_S4.merged.bam.sorted.bam


title: H7TPSC1

source_name: HuH-7 triple positive single cell 1


title: HMECsSox4plusdox_S2.merged

description:
anti-SOX4 ChIP-seq
HMECsSox4plusdox_S2.merged.bam.sorted.bam


title: H1RDP100-2

source_name: HuH-1 random 100 cells pooled 2

value: Random


title: H1RDP100-4

source_name: HuH-1 random 100 cells pooled 4


title: H1RDP100-1

source_name: HuH-1 random 100 cells pooled 1


title: H1RDP100-3

source_name: HuH-1 random 100 cells pooled 3


title: H7TPSC9

source_name: HuH-7 triple positive single cell 9


title: H1CD133P100

source_name: HuH-1 CD133 positive 100 cells pooled


title: HMECsSox4mindox_S1.merged

description:
anti-SOX4 ChIP-seq
HMECsSox4mindox_S1.merged.bam.sorted.bam


title: HMECsSmad3mindoxplusTGF_S3.merged

description:
anti-SMAD3 ChIP-seq
HMECsSmad3mindoxplusTGF_S3.merged.bam.sorted.bam


title: H1CD24P100

source_name: HuH-1 CD24 positive 100 cells pooled


title: HMLE_SOX4 KD TGF_1

description:
Human mammary epithelial cells kindly provided by Prof. Dr. Weinberg
194treated1_0

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly) using TopHat v2.0.9 as previously described (Trapnell et al., 2012). Only uniquely mapped reads were selected for further analysis.
guide transcripts were assembled using CuffLinks v2.2.1. Reads were quartile normalized using the –library-norm-method quartile option.
Differential gene analysis was performed using CuffDiff.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing FPKM normalized values

source_name: HMLE_SOX4 KD TGF

extract_protocol:
total RNA-isolation with RNAeasy kit (Qiagen)
TruSeq stranded ribo-zero kit (Illumina)
Samples were sequenced on the NextSeq 500 (Illumina), SE75

treatment_protocol: Upon lentiviral transduction HMLEs were grown and expanded under puromycin selection before RNA-isolation (0.5 µg/mL)

value: Immortalized human mammary epithelail cells

tag: shRNA

value: targeting SOX4

tag: name and source shrna

value: TRCN0000018213, Sigma Aldrich, St. Louis, MS


title: HMLE_SOX4 KD TGF_2

description:
Human mammary epithelial cells kindly provided by Prof. Dr. Weinberg
194treated2_0

value: TRCN0000018213,Sigma Aldrich, St. Louis, MS


title: HMLE_SOX4 KD UNTR2

description:
Human mammary epithelial cells kindly provided by Prof. Dr. Weinberg
194untr2_0

source_name: HMLE_SOX4 KD UNTR


title: H1EPCAMP100

source_name: HuH-1 EPCAM positive 100 cells pooled

value: hepatcellular carcinoma

value: pooled


title: H7TPSC6

source_name: HuH-7 triple positive single cell 6

value: TriplePos

value: single-cell


title: HMLE_SCR TGF_2

description:
Human mammary epithelial cells kindly provided by Prof. Dr. Weinberg
scr2treated_0

source_name: HMLE_SCR TGF

value: scrambled

value: SHC002, Sigma Aldrich, St. Louis, MS


title: HMECsSmad3plusTGF_S10.merged

description:
anti-SMAD3 ChIP-seq
HMECsSmad3plusTGF_S10.merged.bam.sorted.bam

source_name: Immortalized human mammary epithelial cells


title: H1TPP100

source_name: HuH-1 triple positive 100 cells pooled


title: H1CD133P10

source_name: HuH-1 CD133 positive 10 cells pooled


title: IU9036_4-RNA-seq

city: Bloomington

first: Malcolm

last: Winkler

state: IN

address: 1001 E. Third Street

department: Biology

institute: Indiana University

data_processing:
Bases were called using bcl2fasta v2.16.0.10
Reads were quality and adapter trimmed using Trimmomatic v0.30 using default parameters, Illumina adapters, and a minimum read length of 50bps
Mapping was accomplished with bowtie2 version 2.1.0 by mapping to chromosome NC_008533 and the plasmid NC_005022
Differential gene expression was identified using the program DESeq with these non-default parameters: estimateDispersions was set to "blind" and the sharingMode as "fit-only"
Genome_build: NC_008533.1
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest including genes and intergenic regions for each fastq file; intergenic regions are identified as follows Inter.<molecule>.<strand>.<basepair_begin>.<basepair_end>

organism: Streptococcus pneumoniae

source_name: Exponentially grown cells

growth_protocol: Cultures of strains IU9036 (∆khpA) and IU1824 (parent) grown exponentially in BHI media at 37ºC to OD620 ≈0.15 to 0.2. Starter cultures were used to inoculate 30 mL cultures of BHI broth in 50 mL conical tubes.

extract_protocol:
RNA was extracted from 23 ml of exponentially growing culture (OD620 ≈ 0.15) using a FastRNA Pro Blue Kit (MP Bio) according to the manufacturer's guidelines. Briefly, cells were collected by centrifugation at 14, 500 xg for 5 min at 4°C. Cells were resuspended in 1 mL RNApro (MP Bio) and processed twice in a Fast-Prep 24 homogenizer (MP Bio) for 40 s at setting 6.0. Chloroform and 100% ethanol were used to extract and precipitate the RNA from the resulting lysate, and the miRNeasy minikit (Qiagen) with on-column DNase I treatments was used to purify RNA.
cDNA libraries were prepared from total RNA by the Center for Genomics and Bioinformatics at Indiana University in Bloomington, Indiana. The mRNA was enriched from 1 μg of total RNA using RiboZero™ rRNA Removal Kit (Bacteria) (EpiCentre, Inc.). rRNA-depleted mRNA samples were purified using RNeasy Minelute Cleanup Kit (Qiagen). Double-stranded cDNA synthesis was performed following ScriptSeq™ Complete Kit (Bacteria) Preparation guide (EpiCentre, Inc.) in accordance with the manufacturer's standard protocol. Entire resultant mRNA sample was fragmented using divalent cations via incubation for 5 min at 85°C. The first strand of cDNA was synthesized by reverse transcription using random-sequence primers containing a tagging sequence at their 5′ ends. Di-tagged cDNA was synthesized by random annealing of a terminal-Tagging Oligo to the 3′ end of the cDNA for extension of the cDNA by DNA polymerase. Di-tagged cDNA was purified using Agencourt AMPure® XP beads (Beckman Coulter) followed by PCR amplification for 15 cycles using Failsafe™ PCR enzyme and ScriptSeq™ Index PCR Primer set (EpiCentre, Inc.). This step generated the second strand of cDNA and completed the addition of Illumina adapter sequences incorporating a user-defined barcode. The amplified libraries were purified using Agencourt AMPure® XP beads. Quality and quantity were assessed using D1000 TapeStation (Agilent Technologies) and Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies), respectively. Sequencing was performed at the Greehey Children’s Cancer Research Institute Genome Sequencing Facility at the University of Texas Health Science Center at San Antonio, Texas. Cluster generation was performed using TruSeq PE Cluster Kit v3-cBot-HS (Illumina).
Single-end, 50 bp sequencing was performed using TruSeq SBS Kit v3-HS (Illumina) on a NextSeq 500 sequencer (Illumina). Image analysis, base calling, sequencing reads de-multiplexing were followed by default Illumina procedure.

tag: strain

tag: mutation

value: ∆cps rpsL1::∆khpA


title: IU9036_3-RNA-seq


title: HMLE_SCR UNTR2

description:
Human mammary epithelial cells kindly provided by Prof. Dr. Weinberg
scr2untr_0

source_name: HMLE_SCR UNTR


title: H1CD24P10

source_name: HuH-1 CD24 positive 10 cells pooled


title: IU9036_1-RNA-seq


title: H1EPCAMP10

source_name: HuH-1 EPCAM positive 10 cells pooled

value: EPCAM


title: IU1824_2-RNA-seq

value: ∆cps rpsL1


title: HMLE_SCR UNTR1

description:
Human mammary epithelial cells kindly provided by Prof. Dr. Weinberg
scr1untr_0


title: IU1824_4-RNA-seq


title: H1TPP10

source_name: HuH-1 triple positive 10 cells pooled


title: IU1824_1-RNA-seq


title: single cells from HuH-7 cells

description: droplet-based single-cell RNA-seq with unique molecular identifiers (UMIs).

data_processing:
Basecalling performed by RNA v. 1.12.4.2
Demultiplexing performed by Bcl2fastq v. 2.17
Alingment, tagging, gene and transcript counting performed by Cellranger v. 2.0.1
Data normalized by median normalization
Genome_build: hg19
Supplementary_files_format_and_content: Three filtered matrix files 1) sample barcodes (barcodes.tsv) 2) genes detected (genes.tsv) and 3) count matrix (matrix.mtx)

growth_protocol: Human liver cancer cell lines, HuH1 and HuH7 were routinely maintained in DMEM medium plus 10% fetal bovine serum and 1% antibotics. At 80% confluence, the cells were harvested and frozen in liquid nitrogen.

extract_protocol:
no extraction step
Chromium Single Cell platform from 10X Genomics was used to generate gene expression data from single cells. Briefly, frozen cells were thawed at 37°C, washed and were loaded onto the 10XGenomics Chromium Controller machine for Gel Beads-in-Emulsion (GEM) generation. Cells were lysed inside the cell-specific droplets and cDNA libraries were constructed. Illumina libraries were then prepared using the Chromium Single cell 3’ Reagent Kit (V1 chemistry) from 10X Genomics. All samples were pooled and sequenced.

treatment_protocol: For HuH1 and HuH7, at 80% confluence, the cells were harvested and frozen in liquid nitrogen. For primary HCC cells, they were dissociatd from HCC biopsy and frozen in liquid nitrogen.

value: random

value: hepatocellular carcinoma


title: H1CD133SC9

source_name: HuH-1 CD133 positive single cell 9


title: H1CD133SC7

source_name: HuH-1 CD133 positive single cell 7


title: H1CD133SC8

source_name: HuH-1 CD133 positive single cell 8


title: single cells from HuH-1 cells


title: H1CD133SC6

source_name: HuH-1 CD133 positive single cell 6


title: H1CD133SC4

source_name: HuH-1 CD133 positive single cell 4


title: H1CD133SC3

source_name: HuH-1 CD133 positive single cell 3


title: H1CD24SC6

source_name: HuH-1 CD24 positive single cell 6


title: H1CD133SC2

source_name: HuH-1 CD133 positive single cell 2


title: HMLE_SOX4 KD UNTR1

description:
Human mammary epithelial cells kindly provided by Prof. Dr. Weinberg
194untr1_0

source_name: HMLE_SOX4 KD UNTR

value: HMLE


title: H1CD133SC1

source_name: HuH-1 CD133 positive single cell 1


title: H7TPSC4

source_name: HuH-7 triple positive single cell 4


title: HMLE_SCR TGF_1

description:
Human mammary epithelial cells kindly provided by Prof. Dr. Weinberg
scr1treated_0

source_name: HMLE_SCR TGF


title: H1CD24SC3

source_name: HuH-1 CD24 positive single cell 3


title: H1CD24SC4

source_name: HuH-1 CD24 positive single cell 4


title: H1CD24SC5

source_name: HuH-1 CD24 positive single cell 5


title: AOMDSSCurcumin_1 [Bisulfite-seq]

city: Piscataway

first: Renyi

last: Wu

state: NJ

address: 160 Frelinghuysen road

department: Pharmacy School

institute: Rutgers University

data_processing:
Illumina standard procedure for basecalling.
The reads were aligned to the in silico bisulfite-converted mouse genome (mm9) with the Bismark (version 0.15.0) alignment algorithm.
After alignment, DMRfinder (version 0.1) was used to extract methylation counts and cluster CpG sites into differentially methylated regions (DMRs)
Each DMR contains at least five CpG sites. Methylation differences greater than 0.10 and with a p-value smaller than 0.05 were considered significant.
Genomic annotation was performed by ChIPseeker (version 1.10.3) in R (version 3.4.0)
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited tables of counts of methylation and unmethylation for each DMR (differentially methylated region).

source_name: colon epithelial cell

extract_protocol:
All the colons were flushed with ice-cold saline to remove feces and opened longitudinally on filter paper. The proximal segment and tumors of the right portion of the colon were removed, then colon epithelial cells were isolated from the remaining tissues using a scraping method as previously described. Briefly, the tissues were scraped using a glass slide on ice and the mucosal scrapings were resuspended in ice cold PBS. The remaining tissue after scraping was snap frozen and stored for further analyses. The epithelial preparations were centrifuged at low-speed (150x g) and washed with ice cold PBS twice to reduce blood cell contamination. Isolated epithelial cells were pelleted, snap frozen with dry ice, then store at -80°C for further analysis.
DNA libraries were prepared for sequencing using Agilent SureSelectXT Mouse Methyl-Seq system. (Catlog number 931052)

value: Colon

tag: age

value: 18 weeks

tag: group

value: AOM and DSS induced plus curcumin


title: H1CD24SC2

source_name: HuH-1 CD24 positive single cell 2


title: H1CD24SC1

source_name: HuH-1 CD24 positive single cell 1


title: AOMDSSCurcumin_0 [Bisulfite-seq]


title: AOMDSS_1 [Bisulfite-seq]

value: AOM and DSS induced


title: H1EPCAMSC5

source_name: HuH-1 EPCAM positive single cell 5


title: AOMDSS_0 [Bisulfite-seq]


title: H1EPCAMSC4

source_name: HuH-1 EPCAM positive single cell 4


title: H1CD133SC5

source_name: HuH-1 CD133 positive single cell 5


title: Control_0 [Bisulfite-seq]

value: control


title: H1EPCAMSC3

source_name: HuH-1 EPCAM positive single cell 3

value: hepatcellular carcinoma


title: H1EPCAMSC2

source_name: HuH-1 EPCAM positive single cell 2


title: Control_1 [Bisulfite-seq]


title: H1TNSC12

source_name: HuH-1 triple negative single cell 12

value: TripleNeg


title: H1TNSC11

source_name: HuH-1 triple negative single cell 11


title: AOMDSSCurcumin_0 [RNA-seq]

data_processing:
Illumina standard procedure for basecalling.
Reads were aligned to mm9 using tophat2 (Version 2.1.1, bowtie version 2.2.6) with default parameters.
Duplicates were removed with picard.
Reads overlapping gene features were counted by featureCounts (version 1.5.1).
Differential expression by DESeq2 (version 1.14.1) in R (version 3.4.0).
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited tables with FPKM values for each sample.

extract_protocol:
All the colons were flushed with ice-cold saline to remove feces and opened longitudinally on filter paper. The proximal segment and tumors of the right portion of the colon were removed, then colon epithelial cells were isolated from the remaining tissues using a scraping method as previously described. Briefly, the tissues were scraped using a glass slide on ice and the mucosal scrapings were resuspended in ice cold PBS. The remaining tissue after scraping was snap frozen and stored for further analyses. The epithelial preparations were centrifuged at low-speed (150x g) and washed with ice cold PBS twice to reduce blood cell contamination. Isolated epithelial cells were pelleted, snap frozen with dry ice, then store at -80°C for further analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: AOMDSS_3 [RNA-seq]


title: AOMDSS_2 [RNA-seq]


title: H1TNSC13

source_name: HuH-1 triple negative single cell 13


title: AOMDSSCurcumin_3 [RNA-seq]


title: AOMDSSCurcumin_1 [RNA-seq]


title: AOMDSSCurcumin_2 [RNA-seq]


title: H1TNSC10

source_name: HuH-1 triple negative single cell 10


title: H1TNSC8

source_name: HuH-1 triple negative single cell 8


title: H1TNSC9

source_name: HuH-1 triple negative single cell 9


title: H1TNSC7

source_name: HuH-1 triple negative single cell 7


title: Control_3 [RNA-seq]


title: AOMDSS_1 [RNA-seq]


title: H1TNSC6

source_name: HuH-1 triple negative single cell 6


title: AOMDSS_0 [RNA-seq]


title: H1TNSC5

source_name: HuH-1 triple negative single cell 5


title: Control_0 [RNA-seq]

source_name: colon epithelial cell


title: H1TNSC4

source_name: HuH-1 triple negative single cell 4


title: H1TNSC3

source_name: HuH-1 triple negative single cell 3


title: Control_2 [RNA-seq]


title: H1TNSC2

source_name: HuH-1 triple negative single cell 2


title: MEF_D6_Adipogenesis_RNASeq_DKO_rep3

data_processing:
RNA-Seq reads were quality assesed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The reads were aligned to the mm9 genome with TopHat v2.0.9 (https://ccb.jhu.edu/software/tophat) and Bowtie v.2.1.0 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) with a GTF annotation transcript file of Ensemble release 67 and additional parameter: -g 5
The mapped reads were summarized on gene level using htseq-count, HTSeq package v0.5.4 (http://www-huber.embl.de/HTSeq)
Differential expression analysis were performed using the R Bioconductor package DESeq (http://bioconductor.org/packages/release/bioc/html/DESeq.html)
Genome_build: NCBIM37 (mm9)
Supplementary_files_format_and_content: tab-delimited text file with summarised read counts per gene from htseq-count

source_name: MEF-to-Adipocyte differentiation day 6, Gadd45a-/- Ing1-/- (DKO) cells, replicate 3

growth_protocol: Gadd45a deficient mice (Hollander et al. 1999; doi:10.1038/13802) and Ing1 deficient mice (Kichina et al. 2006; doi:10.1038/sj.onc.1209118) were interbred to obtain single-mutant, Gadd45a-/-;Ing1-/- double-mutant (DKO) and  wildtype (WT) embryos. Mouse embryonic fibroblasts (MEFs) of the four genotypes were isolated from embryonic day E15.5 male embryos and cultured for 4 passages.

extract_protocol:
After 6 days of differentiation, total RNA was isolated using the RNeasy mini kit with on-column DNase digest (Qiagen) following the manufacturer's protocol, quantified with a Thermo NanoDrop and quality tested on Agilent Bioanalyzer.
NGS libraries were prepared from 280ng RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina) according to manufacturer’s recommendations and amplified in 12 PCR cycles. Libraries were profiled in a High Sensitivity DNA chip on a 2100 Bioanalyzer and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). The 12 libraries were pooled in equimolar ratio and sequenced in 7 lanes on a HiSeq 2000 Illumina sequencer, single read mode for 51 cycles plus 7 cycles for the index read.

treatment_protocol: Post-confluent MEFs were treated with with 0.5 mM 3-Isobutyl-1-methylxanthine, 1 μM Dexamethasone, 2µM Rosiglitazone and 10 µg/ml  Insulin. After 48h, differentiation was continued with culture medium supplemented with 10 mg/ml Insulin. Adipocyte differentiation medium was exchanged every two days.

tag: genotype/variation


title: Control_1 [RNA-seq]


title: MEF_CaptureC_DKO_rep1

description: Sample 10

data_processing:
Sample demultiplexing and FastQ file generation was performed using Illumina Conversion Software bcl2fastq v.2.18.
The raw data were processed following the standard workflow described in Davies et al. 2016 (doi:10.1038/nmeth.3664 and https://github.com/telenius/captureC/releases) in the following steps:
Read quality assessment with FastQC v.0.11.5 followed by adaptor trimming using Trim Galore v.0.4.1 (https://www.bioinformatics.babraham.ac.uk/projects/) with parameters: --stringency 3 --paired
Merging the paired-end reads into fragments using FLASH v.1.2.11 (https://sourceforge.net/projects/flashpage) with parameters: --interleaved-output -m 10 -M 150 -x 0.1 -t 1 -z
In silico DpnII restriction digest of the merged reads using the custom script dpnII2E.pl (https://github.com/telenius/captureC/releases)
Alignment of the digested reads to the mm9 genome with Bowtie v.1.1.2 (http://bowtie-bio.sourceforge.net/index.shtml) with parameters: -p 1 -m 2 -y --best --strata --chunkmbs 1024
Mapped data filtering, visualisation and interaction quantitation using the custom script CCanalyser3.pl (https://github.com/telenius/captureC/releases) with default parameters
Genome_build: NCBIM37 (mm9)
Supplementary_files_format_and_content: tarball containing 37 .gff files with Capture-C interaction counts, 37 smoothed .wig coverage files for browser visualisation and a .txt annotation file for the 37 captured genomic regions

source_name: Gadd45a/Ing1 double knockout (DKO) MEFs

growth_protocol: Gadd45a deficient mice (Hollander et al. 1999; doi:10.1038/13802) and Ing1 deficient mice (Kichina et al. 2006; doi:10.1038/sj.onc.1209118) were interbred to obtain single-mutant, Gadd45a-/-;Ing1-/- double-mutant (DKO) and  wildtype (WT) embryos.  Mouse embryonic fibroblasts (MEF cells) of the four genotypes were isolated from embryonic day E15.5 male embryos and cultured for 4 passages.

extract_protocol:
80% confluent MEF cultures were crosslinked, harvested and processed according to Davies et al. 2016 (doi:10.1038/nmeth.3664).
NG Capture-C libraries were prepared as described in Davies et al. 2016 (doi:10.1038/nmeth.3664) using a pool of 63 oligos targeting 37 capture regions.

tag: strain background

value: Mouse Embryonic Fibroblasts (MEFs)


title: H1TNSC1

source_name: HuH-1 triple negative single cell 1

value: single-cell


title: MEF_CaptureC_DKO_rep2

description: Sample 11


title: H1EPCAMSC1

source_name: HuH-1 EPCAM positive single cell 1


title: MEF_CaptureC_DKO_rep3

description: Sample 12


title: MEF_D6_Adipogenesis_RNASeq_DKO_rep1

source_name: MEF-to-Adipocyte differentiation day 6, Gadd45a-/- Ing1-/- (DKO) cells, replicate 1


title: MEF_CaptureC_Ing1-KO_rep3

description: Sample 9

source_name: Ing1 knockout MEFs


title: MEF_D6_Adipogenesis_RNASeq_DKO_rep2

source_name: MEF-to-Adipocyte differentiation day 6, Gadd45a-/- Ing1-/- (DKO) cells, replicate 2


title: MEF_CaptureC_Ing1-KO_rep1

description: Sample 7


title: MEF_D6_Adipogenesis_RNASeq_Ing1-KO_rep3

source_name: MEF-to-Adipocyte differentiation day 6, Ing1-/- cells, replicate 3


title: H1TPSC7

source_name: HuH-1 triple positive single cell 7

value: TriplePos


title: H1TPSC9

source_name: HuH-1 triple positive single cell 9


title: MEF_CaptureC_Ing1-KO_rep2

description: Sample 8


title: MEF_CaptureC_Gadd45a-KO_rep3

description: Sample 6

source_name: Gadd45a knockout MEFs


title: MEF_D6_Adipogenesis_RNASeq_Ing1-KO_rep1

source_name: MEF-to-Adipocyte differentiation day 6, Ing1-/- cells, replicate 1


title: MEF_CaptureC_Gadd45a-KO_rep2

description: Sample 5


title: MEF_D6_Adipogenesis_RNASeq_Ing1-KO_rep2

source_name: MEF-to-Adipocyte differentiation day 6, Ing1-/- cells, replicate 2


title: H1TPSC5

source_name: HuH-1 triple positive single cell 5


title: MEF_CaptureC_Gadd45a-KO_rep1

description: Sample 4


title: MEF_CaptureC_WT_rep3

description: Sample 3

source_name: Wildtype MEFs

value: Wildtype


title: H1TPSC3

source_name: HuH-1 triple positive single cell 3


title: MEF_D6_Adipogenesis_RNASeq_Gadd45a-KO_rep2

source_name: MEF-to-Adipocyte differentiation day 6, Gadd45a-/- cells, replicate 2


title: MEF_CaptureC_WT_rep2

description: Sample 2


title: MEF_D6_Adipogenesis_RNASeq_Gadd45a-KO_rep1

source_name: MEF-to-Adipocyte differentiation day 6, Gadd45a-/- cells, replicate 1


title: H1TPSC2

source_name: HuH-1 triple positive single cell 2


title: H1TPSC10

source_name: HuH-1 triple positive single cell 10


title: MEF_CaptureC_WT_rep1

description: Sample 1


title: H1TPSC8

source_name: HuH-1 triple positive single cell 8


title: MEF_D6_Adipogenesis_RNASeq_WT_rep2

source_name: MEF-to-Adipocyte differentiation day 6, wildtype cells, replicate 2


title: MEF_D6_Adipogenesis_RNASeq_WT_rep1

source_name: MEF-to-Adipocyte differentiation day 6, wildtype cells, replicate 1


title: tRF-3009_rep2

city: Charlottesville,

first: Anindya

last: Dutta

email: ad8q@virginia.edu, pk7z@virginia.edu

state: VA

address: Room no. 1232, Jordan Hall

department: MD-BIOC BC/Mole Genetics~School of medicine

institute: University of Virginia

data_processing: We received on an average 30 million 50 bases long paired end reads for each of the replicates and had two replicates for each condition.  The transcript (RefSeq genes) sequences for the genome build hg38 were downloaded from UCSC table browser on Dec 10, 2016 (http://genome.ucsc.edu). We used default parameters of Kallisto (Bray, Pimentel et al. 2016) to build an index for the above transcript sequence and then quantified abundances of the transcripts from the paired end RNAseq fastq reads (Bray, Pimentel et al. 2016). The DESeq2 (Love, Huber et al. 2014) package in R was used for differential expression analysis of the quantified data obtained from Kallisto. The normalized count data from DESeq2 was used for all other downstream analysis.

growth_protocol: complete medium

extract_protocol:
Total RNA was purified with Qiagen RNeasy kit
1 ug of total RNA from pcDNA3(empty vector), tRNA LeuAAG (tRF-3003) and tRNA LeuTAA (tRF-3009) overexpressing cells were used for library preparation. Libraries were prepared using NEBNext Ultra directional RNA library prep kit with NEBNext Poly(A) mRNA Magnetic Isolation Module for Illumina. The libraries were indexed using NEBNext Multiplex oligos for Illumina.

treatment_protocol: HEK293T cells were transfected with empty vector or tRNA expression plasmids 4 times in two days intervals.

tag: genotype

value: WT

tag: passage

tag: transfection


title: H1TPSC1

source_name: HuH-1 triple positive single cell 1

tag: tissue

tag: cell surface marker


title: MEF_WGBS_DKO

description: Sample 2

data_processing:
Bisulfite sequenced reads were quality assesed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The reads were aligned to the mm9 genome using Bismark v.0.9.0 (https://www.bioinformatics.babraham.ac.uk/projects/bismark/) with Bowtie v.0.12.9 (http://bowtie.cbcb.umd.edu) dependency with additional parameters for paired end reads: -n 3 -l 60 -e 200
Methylation calling was performed using the Bismark scripts "bismark_methylation_extractor" with parameters: -p --no_overlap --merge_non_CpG --ignore_r2 3 --bedGraph --counts and "bedGraph2cytosine" with default parameters
Genome_build: NCBIM37 (mm9)
Supplementary_files_format_and_content: tab-delimited text file with methylation calls for all CpG sites from Bismark (chromosome, position, strand, count_methylated, count_unmethylated, C-context, trinucleotide_context)

source_name: Bisulfite treated Gadd45a/Ing1 double knockout (DKO) MEFs

growth_protocol: Gadd45a deficient mice (Hollander et al. 1999; doi:10.1038/13802) and Ing1 deficient mice (Kichina et al. 2006; doi:10.1038/sj.onc.1209118) were interbred to obtain single-mutant, Gadd45a-/-;Ing1-/- double-mutant (DKO) and  wildtype (WT) embryos. Mouse embryonic fibroblasts (MEFs) were isolated from embryonic day E15.5 male embryos, either wild-type (WT) or Ing1/Gadd45a (double knockout, DKO), and cultured for 4 passages.

extract_protocol:
Genomic DNA from a wildtype and a Gadd45a-/-;Ing1-/- (DKO) MEF line was purified with a DNeasy Blood & Tissue kit (Qiagen) according to the manufacturer’s instructions.
Genomic DNA was fragmented with a Covaris S2 Ultrasonicator. For end repair of DNA fragments, the Paired End DNA Sample Prep kit (Illumina) was used. Adapter ligation was carried out with an Early Access Methylation Adapter Oligo kit (Illumina) and the Paired End DNA Sample Prep kit (Illumina). After size selection of fragments using the E-Gel electrophoresis system (Invitrogen), DNA was bisulfite converted with a EZ DNA Methylation kit (Zymo Research).


title: WT_rep2

value: control(empty vector)


title: tRF-3009_rep1


title: SKNO1-shCt-C

status: Public on Jun 10 2018

city: Miami

first: Stephen

last: Nimer

state: FL

address: 1120 NW 14th ST

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

data_processing:
Base calling using Illumina RTA 2.4.11
Reads mapped to GRCh38.p7 transcriptome using STAR v2.5.3 and RSEMv1.3.0 with default parameters.
Counts were estimated using using RSEM gene.results.
Genome_build: Ensembl 87: GRCh38.p7
Supplementary_files_format_and_content: Tab-delimited file contains aggragated raw RSEM expected gene level counts for all samples .

source_name: AML cell line

growth_protocol: According to provider's instructions (ATCC or DSMZ)

extract_protocol:
RNA was harvested using Trizol (Invitrogen #15596-026) and RNAeasy mini kit (Qiagen). Sequencing libraries were generated using Illumina TruSeq Total Stranded kit (RS-122-2201) with Ribo-Zero rRNA reduction per manufacturer's instructions.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Growth protocol conditions

value: AML

tag: virus

value: Lentiviral constitutive

tag: condition

value: shScramble

tag: media supplement

value: 10ng/mL GM-CSF supplement

tag: experiment

value: Replicate 3


title: HIV15.1

city: New York

first: Jeffrey

middle: Stuart

last: Berger

state: NY

address: 522 First Avenue

department: Cardiology

institute: NYU Langone Medical Center

data_processing:
Alignment against hg19 using Tophat2.1.1
Gene counting against hg19 reference gtf using HTSeq-count 0.6.1
Normalization of raw counts using DESeq2
Genome_build: hg19

source_name: Platelet

extract_protocol:
Platelets were subjected to negative selection based on magnetic cell sorting and RNA harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: HIV

tag: molecule

value: platelet RNA


title: WT_rep1

tag: cell type


title: HIV17.1


title: MEF_D6_Adipogenesis_RNASeq_Gadd45a-KO_rep3

source_name: MEF-to-Adipocyte differentiation day 6, Gadd45a-/- cells, replicate 3


title: THR67.1

value: healthy


title: MEF_WGBS_WT

description: Sample 1

source_name: Bisulfite treated Wildtype MEFs


title: SKNO1-sh55-C

tag: cell line

value: shCARM1 hairpin 1


title: SKNO1-shCt-B

value: Replicate 2


title: H1TPSC4

source_name: HuH-1 triple positive single cell 4

value: hepatcellular carcinoma

tag: cell number

tag: cell status


title: SKNO1-sh57-C

value: shCARM1 hairpin 2


title: SKNO1-sh57-B


title: SKNO1-sh55-B


title: THR66.1


title: HIV03.1


title: HIV04.1


title: SKNO1-shCt-A

value: Replicate 1


title: HIV12.1


title: MEF_D6_Adipogenesis_RNASeq_WT_rep3

source_name: MEF-to-Adipocyte differentiation day 6, wildtype cells, replicate 3

tag: genotype/variation


title: THR68.1


title: SKNO1-sh55-A


title: SKNO1-sh57-A


title: MV411-shCt-C


title: MV411-sh55-C


title: HIV10.1


title: MV411-sh57-C


title: MV411-shCt-B


title: siLacZ-449-Pol II ChIP-seq

city: Jerusalem

first: Eran

last: Rosenthal

address: Givat Ram

department: Computer Science

country: Israel

institute: Hebrew University

description: Pol II ChIP-Seq

data_processing:
All reads were aligned to the human reference genome (hg19, GRCh37) using the bowtie 2 aligner with default parameters (only setting –N 1)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig (bw) files contains aligned read for 4sUDRBseq with masked exons

source_name: Human cervical carcinoma, HeLa cell

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% bovine serum supplemented with antibiotics

extract_protocol:
4sU labled RNA was tagged with Biotion, and enriched with Streptavidin magnetic beads.  cDNA libraries were prepared with Illumina TruSeq RNA sample preparation v2 kit according to the manufacturer's instructions but without the polyA isolation stage
4sUDRBseq: cDNA libraries were prepared with Illumina TruSeq RNA sample preparation v2 kit according to the manufacturer’s instructions but without the polyA isolation stage

treatment_protocol: Cells were treated with DRB for 3hr and harvested after DRB removal. Cells were also labeld with 4sU for 12 min before harvested.

value: HeLa

value: siLacZ

tag: replicate


title: siRNF20-450-Pol II ChIP-seq

description: Pol II ChIP-Seq


title: MV411-sh57-B


title: siLacZ-450-Pol II ChIP-seq

description: Pol II ChIP-Seq


title: siRNF20-449-Pol II ChIP-seq

description: Pol II ChIP-Seq


title: siRNF20-12Min-385-4sUDRBseq

description: Nascent RNA labled with 4sU

tag: time

value: 12 minutes

tag: treatment

value: 3 h DRB, release - 12 min, 4sU - 12 min


title: MV411-sh55-B

value: AML


title: MV411-shCt-A

value: Lentiviral constitutive


title: siRNF20-NT-385-4sUDRBseq

description: Nascent RNA labled with 4sU

value: control

value: DRB - untreated, 4sU - 12 min


title: siRNF20-8Min-385-4sUDRBseq

description: Nascent RNA labled with 4sU

value: 8 minutes

value: 3 h DRB, release -  8 min, 4sU -12 min


title: H1TPSC6

source_name: HuH-1 triple positive single cell 6

value: TriplePos

value: single-cell


title: MV411-sh57-A


title: EP_3_B input (ATAC-seq)

city: Toronto

first: Rama

last: Khokha

state: ON

address: Princess Margaret Research Tower, 101 College Street

department: Medical Biophysics

country: Canada

institute: Princess Margaret Cancer Centre

description:
genomic DNA following transposase
input

data_processing:
Reads were filtered for quality and trimming using FASTX Toolkit 0.0.13.1
Filtered reads were aligned to the Mouse genome (mm10) using BWA(Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25:1754-1760). Duplicate reads were marked and removed using Picard (https://github.com/broadinstitute/picard). For comparisons the larger dataset was downsampled to match the size of smaller dataset using Picard (https://github.com/broadinstitute/picard).
Peaks were called using MACS2.0 (https://github.com/taoliu/MACS/)(Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS: Model-based analysis of ChIP-Seq (MACS). Genome biology 2008;9:R137)
Genome_build: mm10
Supplementary_files_format_and_content: Peak bed files were generated using MACS2.0 with default parameters. Bed files contain peak calls on merged reads using corresponding inputs as control.
Supplementary_files_format_and_content: bigWig file

source_name: Basal or myoepithelial mammary epithelial cells_input

growth_protocol: Primary luminal and basal mammary epithelial cells were FACS-purified from WT FVB mice.

extract_protocol:
Mammary glands were dissociated and cells purified using previously established protocols (PMID: 20445538). Lysates were extracted from sorted nuclei using a nuclei lysis buffer (according to ATAC-seq protocol from Buenrostro et al 2013). Transposase reaction was carried out following the protocol of the Nextera DNA library preparation kit (illumina).
Libraries were prepared using the NeBNext buffer and appropriate ATAC-seq libraries adaptors (Illumina, Buenrostro et al, 2013). The llibrary was size-selected using the DNA on a ChIP technology.

treatment_protocol: Prior to cell extraction mice were ovariectomized, allowed to recover for 1 week and treated with 17β-oestradiol + progesterone (EP) by slow-release pellet for 2 weeks.

tag: background strain

value: Wildtype FVB

tag: gender

value: Female

value: Mammary gland

tag: age

value: Adult (8-12 weeks)

tag: protocol

value: Ovariectomy + 2 weeks 17β-oestradiol + progesterone


title: siRNF20-12Min-384-4sUDRBseq

description: Nascent RNA labled with 4sU

value: HeLa

tag: condition


title: EP_2_L input (ATAC-seq)

description:
genomic DNA following transposase
input

source_name: Luminal mammary epithelial cells_input

tag: tissue


title: EP_3_L input (ATAC-seq)

description:
genomic DNA following transposase
input


title: EP_3_L (ATAC-seq)

description:
genomic DNA following transposase
replicate of EP_2_L
EP_2-3_L_peaks.narrowPeak
EP_2-3_L_treat_pileup.bigWig

source_name: Luminal mammary epithelial cells


title: siRNF20-8Min-384-4sUDRBseq

description: Nascent RNA labled with 4sU


title: Molm13-shCt-C

tag: virus

value: shScramble

tag: media supplement

tag: experiment

value: Replicate 3


title: siRNF20-0Min-384-4sUDRBseq

description: Nascent RNA labled with 4sU

value: 0 minutes

value: 3 h DRB, release - 0 min,4sU -12min


title: EP_3_B (ATAC-seq)

description:
genomic DNA following transposase
replicate of EP_2_B
EP_2-3_B_peaks.narrowPeak
EP_2-3_B_treat_pileup.bigWig

source_name: Basal or myoepithelial mammary epithelial cells


title: Molm13-sh57-C

tag: cell type

value: AML

value: Lentiviral constitutive

value: shCARM1 hairpin 2


title: siRNF20-0Min-385-4sUDRBseq

description: Nascent RNA labled with 4sU

tag: cell line


title: siRNF20-NT-384-4sUDRBseq

description: Nascent RNA labled with 4sU

value: control

value: DRB - untreated, 4sU - 12 min


title: Molm13-shCt-B

value: Replicate 2


title: siLacZ-12Min-384-4sUDRBseq

description: Nascent RNA labled with 4sU

value: 12 minutes

value: 3 h DRB, release - 12 min, 4sU - 12 min

value: siLacZ


title: MDCK STK11 Knockdown 2

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

description: Cell Line

data_processing:
Raw sequence reads were pseudo aligned to the Dog transcriptome CanFam3.1 (Ensembl Build 83) using Kallisto (Version 0.42.4, Bray et al. Nat. Biotechnology 2016) runing 100 bootstrap rounds.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: Tab-delimited text files per sample include effectice read counts and transcript per million (TPM) values for each transcript

organism: Canis lupus familiaris

source_name: Madin-Darby canine kidney (MDCK) cells

growth_protocol: Madin-Darby canine kidney (MDCK) cells were cultured using Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (Biochrome, Berlin, Germany) and 1% Penicillin-Streptomycin.

extract_protocol:
Total RNAs were extracted and purified from tetracycline-inducible Lkb1 knockdown MDCK cell line (2 independent experiments per condition), using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNAs quality was checked using a Fragment Analyzer™ (Advanced Analytical Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To generate tetracycline-inducible knockdown MDCK cell lines, MDCK-tTR-KRAB were transduced with shRNAs by the lentivirus-based transduction system (pLVTH) as previously described (Wiznerowicz et al. J virology 2003).

tag: strain

value: MDCK cell line

value: Kidney

tag: knockdown

value: plus tetracycline

value: replicate 2

value: adult epithelial kidney cell


title: siLacZ-12Min-385-4sUDRBseq

description: Nascent RNA labled with 4sU

value: HeLa


title: EP_2_B (ATAC-seq)

description:
genomic DNA following transposase
replicate of EP_3_B
EP_2-3_B_peaks.narrowPeak
EP_2-3_B_treat_pileup.bigWig

value: Wildtype FVB

value: Female

value: Mammary gland

value: Adult (8-12 weeks)

value: Ovariectomy + 2 weeks 17β-oestradiol + progesterone


title: Molm13-sh55-C

value: AML

value: Lentiviral constitutive

value: shCARM1 hairpin 1

value: Replicate 3


title: siRNF20-385-mRNA

description: mRNA for replicate 385, experiment siRNF20


title: Basal rep.2 (RRBS)

data_processing:
For each of the original 4 RRBS samples obtained from mice, the adapters from the raw data in FastQ format,  were trimmed using Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Samples were then aligned to the mice genome (version mm9) using Bismark which calls Bowtie and produces a SAM file containing the methylation calls in each aligned bisulfite sequencing read along with the genomic coordinate where each read starts.
Using Samtools, the SAM files were sorted, and then further processed using methylKit.
The function filterByCoverage() function was used to discard bases with coverage below 10X and bases with more than 99.9th percentile coverage in each sample to mitigate PCR bias.
Genome_build: mm9

extract_protocol:
Mammary glands were dissociated and cells extracted using previously established protocols (PMID: 20445538).
RRBS libaries were prepared as described previously (PMID: 21412275)

treatment_protocol: Prior to cell extraction mice were ovariectomised, allowed to recover for 1 week and treated with 17β-oestradiol + progesterone (EP) by slow-release pellet for 2 weeks.


title: Luminal rep.1 (RRBS)


title: Molm13-sh57-B

value: shCARM1 hairpin 2

value: Replicate 2


title: Luminal rep.2 (RRBS)


title: MV411-sh55-A

value: Replicate 1


title: EP_2_B input (ATAC-seq)

description:
genomic DNA following transposase
input


title: Basal rep.1 (RRBS)


title: siRNF20-384-mRNA

description: mRNA for replicate 384, experiment siRNF20


title: Molm13-sh57-A


title: Molm13-sh55-A


title: MLL-AF1p_MI-2-2_rep3

status: Public on Jun 09 2018

city: Gaithersburg

first: Jingya

state: Maryland

address: 1 Medimmune Way

data_processing:
Basecalls performed using CASAVA-1.8.2
Sequenced reads were aligned to the mm9 genome assembly using Bowtie v2.0.0.7 with default settings
RPKM (Reads per kilo base per million) were calculated using HTseq and  differentially expressed genes detected using EdgeR
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample

source_name: MLL-AF1p transformed leukemia cells

growth_protocol: MLL-AF9, MLL-AF6 and MLL-AF1P cells were cultured in IMDM medium (Life Technologies, Catalog # 12440-053)with 15% FBS (Stemcell Technologies, Catalog # 06200) and 1% penicillin/streptomycin

extract_protocol:
Total RNA was extracted from cells using RNeasy mini kit (Qiagen) according to manufacturer instructions. RNA was assessed for quality using the TapeStation (Agilent, Santa Clara, CA). Samples with RINs (RNA Integrity Numbers) of 8 or greater were prepped using the Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS-122-2001, RS-122-2002) (Illumina, San Diego, CA). Where 0.1-3ug of total RNA was converted to mRNA using a polyA purification.
The mRNA was fragmented and copied into first strand cDNA using reverse transcriptase and random primers.  The products were purified and enriched by PCR to create the final cDNA library. Final libraries were be checked for quality and quantity by TapeStation  (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (catalog # KK4835) (Kapa Biosystems,Wilmington MA).  They were clustered on the cBot (Illumina) and sequenced 4 samples per lane on a 50 cycle single end (100 cycle paired end run) on a HiSeq 2000 (Illumina) in High Output mode using version 3 reagents according to manufacturer’s protocols.

treatment_protocol: MLL-AF9, MLL-AF6 and MLL-AF1P cells were plated in 12-well plates at the initial concentration of 1 mln cells/ml and treated with 6 µM of MI-2-2 or DMSO, at final DMSO concentration of 0.25%, for 6 days. Media were changed at day three, with viable cell concentration restored to 1 mln cells/ml and compound or DMSO resupplied.

value: Mixed Lineage Leukemia (MLL)

tag: transformed construct


title: MLL-AF1p_MI-2-2_rep2


title: EP_2_L (ATAC-seq)

description:
genomic DNA following transposase
replicate of EP_3_L
EP_2-3_L_peaks.narrowPeak
EP_2-3_L_treat_pileup.bigWig


title: MLL-AF1p_MI-2-2_rep1


title: MLL-AF1p_DMSO_rep3


title: MLL-AF1p_DMSO_rep2


title: MLL-AF6_MI-2-2_rep3

source_name: MLL-AF6 transformed leukemia cells


title: MLL-AF6_MI-2-2_rep2


title: MLL-AF9_MI-2-2_rep3

source_name: MLL-AF9 transformed leukemia cells


title: MLL-AF9_MI-2-2_rep2


title: MLL-AF6_MI-2-2_rep1


title: MLL-AF9_DMSO_rep2


title: siLacZ-385-mRNA

description: mRNA for replicate 385, control

value: siLacZ

tag: replicate


title: Molm13-sh55-B


title: MLL-AF9_DMSO_rep1


title: MLL-AF6_DMSO_rep1


title: Molm13-shCt-A

value: shScramble


title: siLacZ-384-mRNA

description: mRNA for replicate 384, control


title: MLL-AF1p_DMSO_rep1


title: 758_INPUT

status: Public on Jun 08 2018

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Library strategy: eCLIP-seq
Takes output from raw files.  Run to trim off both 5’ and 3’ adapters on both reads. Command: quality-cutoff 6  -m 18  -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT  AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1. Run to trim off the 3’ adapters on read 2, to control for double ligation events. Command: cutadapt -f fastq --match-read-wildcards  --times 1  -e 0.1  -O 5  --quality-cutoff 6  -m 18  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2.  Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir /path/to/RepBase_human_database_file --genomeLoad LoadAndRemove  --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz --outSAMunmapped Within  --outFilterMultimapNmax 30  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam --outSAMattributes All  --readFilesCommand zcat  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam
Takes output from STAR rmRep.  Maps unique reads to the human genome.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir  /path/to/STAR_database_file --genomeLoad LoadAndRemove  --readFilesIn  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate1  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate2  --outSAMunmapped Within  --outFilterMultimapNmax 1  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --outSAMattributes All  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam
takes output from STAR genome mapping.  Custom random-mer-aware script for PCR duplicate removal. Command: barcode_collapse_pe.py  --bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --out_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  --metrics_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.metrics
Takes output from barcode collapse PE.  Sorts resulting bam file for use downstream.  Command: java  -Xmx2048m  -XX:+UseParallelOldGC  -XX:ParallelGCThreads=4  -XX:GCTimeLimit=50  -XX:GCHeapFreeLimit=10  -Djava.io.tmpdir=/full/path/to/files/.queue/tmp  -cp /path/to/gatk/dist/Queue.jar  net.sf.picard.sam.SortSam  INPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  TMP_DIR=/full/path/to/files/.queue/tmp  OUTPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  VALIDATION_STRINGENCY=SILENT  SO=coordinate  CREATE_INDEX=true
Takes output from sortSam, makes bam index for use downstream.  Command: samtools index  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam.bai
Takes inputs from multiple final bam files.  Merges the two technical replicates for further downstream analysis.  Command: samtools  merge  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.D08.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam
Takes output from sortSam, makes bam index for use downstream.  Command: samtools  index  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/CombinedID.merged.bam.bai
Takes output from sortSam.  Only outputs the second read in each pair for use with single stranded peak caller.  This is the final bam file to perform analysis on.  Command: samtools view -hb -f 128  /full/path/to/files/CombinedID.merged.bam  >  /full/path/to/files/CombinedID.merged.r2.bam
Takes results from samtools view.  Calls peaks on those files.  Command: clipper  -b /full/path/to/files/CombinedID.merged.r2.bam  -s hg19  -o /full/path/to/files/CombinedID.merged.r2.peaks.bed  --bonferroni  --superlocal  --threshold-method binomial  --save-pickle
Genome_build: hg19
Supplementary_files_format_and_content: bed format, contains clusters of predicted RBP binding

growth_protocol: HepG2 cells were grown under standard conditions (DMEM + 10% FBS + Pen/Strep (100U / mL)). K562 cells were grown in suspension in standard media (RPMI + 10% FBS + Pen/Strep (100U / mL)).

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes.
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB) (at this step, multiple replicates of the same RBP, or potentially RBPs of similar size and bound RNA amount, can be uniquely barcoded and pooled after ligation to simplify downstream steps - see Supplementary Fig. 2A). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

treatment_protocol: While plated, HepG2 cells were crosslinked with UV (254 nm, 400 mJ/cm2). HepG2 cells were then isolated with cell scrapers, pelleted at 200g, and snap frozen. K562 suspension cells were pelleted at 200g and resuspended in 1X PBS to 20 million cells per mL. 60 million cells in 3 mL were UV crosslinked (254 nm, 400 mJ/cm2) per 10 cm dish, pelleted, and snap frozen.

tag: barcodes

tag: antibody

tag: antibody catalog#

tag: antibody lot#


title: 759_INPUT


title: 757_INPUT


title: 756_INPUT


title: 749_INPUT


title: 760_INPUT


title: 751_INPUT


title: 720_INPUT


title: 718_INPUT


title: 728_INPUT


title: 725_INPUT


title: 715_INPUT


title: 710_INPUT

value: ADAR


title: MLL-AF9_MI-2-2_rep1


title: MLL-AF9_DMSO_rep3


title: MLL-AF6_DMSO_rep2


title: MLL-AF6_DMSO_rep3


title: 704_INPUT


title: 688_INPUT


title: 701_INPUT


title: 691_INPUT


title: 673_INPUT


title: 727_INPUT


title: 671_INPUT


title: 657_INPUT


title: 637_INPUT


title: 648_INPUT


title: 636_INPUT

value: AARS


title: 635_INPUT


title: 634_INPUT

value: CALR


title: 630_INPUT


title: 594_INPUT


title: 599_INPUT


title: 580_INPUT


title: 591_INPUT


title: 622_INPUT


title: 528_INPUT


title: 597_INPUT


title: 627_INPUT


title: 554_INPUT

value: PKM


title: 687_INPUT


title: 579_INPUT


title: 573_INPUT


title: 590_INPUT


title: 618_INPUT


title: 542_INPUT


title: 666_INPUT


title: 557_INPUT


title: 486x4000_INPUT

value: HNRNPR


title: 500_INPUT


title: 479_INPUT


title: 474_INPUT


title: 472_INPUT


title: 467_INPUT


title: 430_INPUT


title: 407_INPUT


title: 429_INPUT


title: 397_INPUT


title: 403x4000_INPUT


title: 328_INPUT


title: 356_INPUT


title: 290_INPUT


title: 327_INPUT


title: 386x4000_INPUT


title: 396_INPUT


title: 317_INPUT


title: 351_INPUT


title: 300_INPUT


title: 255_INPUT


title: 363x4000_INPUT


title: 323x4000_INPUT


title: 254_INPUT

value: BCCIP


title: 232_INPUT


title: 333x4000_INPUT


title: TPA-KO2

city: Madrid

first: Monica

last: Martinez-Fernandez

address: Avda Complutense 40

institute: CIEMAT

description: KOvsKOTPA.csv & TPAKOvsTPAWT.csv

data_processing:
Image analysis and per-cycle base calling was performed with Illumina Real Time Analysis software (RTA1.9).
Conversion to FASTQ read format was performed by CASAVA-1.8 (Illumina).
Sequence reads were analyzed using the bioconductor package "oneChannelGUI". Briefly, the package perfomes a  primary mapping with Bowtie/Picard. Then, the function miRNAs fq linker trimming removes the 5 and 3 prime end linkers. Finally, diferential expression was detected using edgeR and baySeq.
Genome_build: mm10
Supplementary_files_format_and_content: oneChannelGUI COMPARISON-RESULT files

source_name: Dorsal skin of adult male mouse pool

extract_protocol:
Total RNA was obtained using miRNeasy Mini kit (Quiagen, cat nº/ID 217004) following the manufacturer’s protocol
RNA samples were processed as described in the "TruSeq Small RNA Sample Preparation Guide" (Illumina part # 15004197 Rev. A of November 2010)

treatment_protocol: Dorsal skins were shaved and depilated 24 h before treatment with TPA (Sigma). TPA was applied topically twice (at days 1 and 3) and mice were sacrificed at day 4. In the control group, animals were treated with vehicle (acetone) only.

tag: agent

value: TPA

tag: genotype

value: TRa1-/-/TRb-/- double knockout


title: TPA-WT3

description: TPAKOvsTPAWT.csv & wt-wttpa.csv

value: wild-type TRa1+/+/TR<beta>+/+


title: 648_02


title: 648_01


title: 214_INPUT


title: 219_INPUT


title: 225_INPUT


title: 202_INPUT


title: 760_02


title: TPA-WT2

description: TPAKOvsTPAWT.csv & wt-wttpa.csv


title: 760_01


title: KO3

description: KOvsKOTPA.csv & nott-only1vs3-0.05.csv

value: acetone


title: 759_02


title: TPA-KO3

description: KOvsKOTPA.csv & TPAKOvsTPAWT.csv


title: KO1

description: KOvsKOTPA.csv & nott-only1vs3-0.05.csv


title: 758_01


title: 725_02


title: 751_01


title: 758_02


title: 757_02


title: 756_02


title: WT3

description: nott-only1vs3-0.05.csv & wt-wttpa.csv


title: WT1

description: nott-only1vs3-0.05.csv & wt-wttpa.csv


title: 728_02


title: 751_02


title: 759_01


title: 725_01


title: 756_01


title: 727_02


title: 749_02


title: 757_01


title: 728_01


title: 727_01


title: 688_02


title: 701_02


title: 710_02


title: 701_01


title: 688_01


title: 710_01


title: 687_02


title: 687_01


title: 671_02


title: 666_02


title: 671_01


title: 749_01


title: 720_02


title: 528_02


title: 666_01


title: 718_02


title: 718_01


title: 720_01


title: 704_02


title: 715_02


title: 528_01


title: 715_01


title: 635_02


title: 635_01


title: 636_02


title: 636_01


title: 704_01


title: TPA-WT1

description: TPAKOvsTPAWT.csv & wt-wttpa.csv


title: 634_01


title: 599_01


title: 597_01


title: 597_02


title: 691_02


title: 673_01


title: 673_02


title: 657_02


title: 657_01


title: 474_02


title: 573_01


title: 472_01


title: 472_02


title: 474_01


title: 403_02_4000


title: 637_01


title: 637_02


title: 634_02


title: 403_01_4000


title: 486_02_4000


title: 599_02


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title: 630_02


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title: 386_01_4000


title: 363_02_4000


title: 630_01


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title: 579_01


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title: 500_01


title: 627_02


title: 500_02


title: 618_02


title: 627_01


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title: 594_02


title: 591_02


title: 594_01


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title: 580_02


title: 590_01


title: 590_02


title: 323_02_4000


title: 323_01_4000


title: 333_02_4000


title: 333_01_4000


title: 591_01


title: 554_02


title: 557_01


title: 479_02


title: 554_01


title: 542_01


title: 542_02


title: 467_01


title: 430_01


title: 479_01


title: 351_01


title: 467_02


title: 407_02


title: 351_02


title: 622_02


title: 430_02


title: 396_02


title: 429_01


title: 396_01


title: 557_02


title: 407_01


title: 397_02


title: 290_02


title: 300_01


title: 429_02


title: 300_02


title: 397_01


title: 328_01


title: 356_02


title: 356_01


title: 327_02


title: 328_02


title: 327_01


title: 254_01


title: 254_02


title: 317_01


title: 255_02


title: 202_02


title: 255_01


title: 214_01


title: 234_01


title: 232_01


title: 219_02


title: 232_02


title: 219_01


title: 290_01


title: 202_01


title: 317_02


title: 225_01


title: 739_INPUT

value: CENPI


title: 724_INPUT


title: 721_INPUT


title: 669_INPUT


title: 662_INPUT


title: 616_INPUT


title: 611_INPUT


title: 609_INPUT


title: 598_INPUT


title: 541_INPUT


title: 547_INPUT


title: 536_INPUT


title: 534_INPUT


title: 535_INPUT


title: 523_INPUT


title: 225_02


title: 520_INPUT


title: 513_INPUT


title: 512_INPUT

value: NELFE


title: 674_INPUT


title: 706_INPUT


title: 498_INPUT


title: 499_INPUT


title: 463_INPUT


title: 485x4000_INPUT


title: 510_INPUT

value: POLK


title: 459_INPUT


title: 451x4000_INPUT


title: 555_INPUT


title: 299_INPUT

value: NONO


title: 355x4000_INPUT


title: 266_INPUT


title: 264_INPUT


title: 471_INPUT


title: 419_INPUT


title: 669_02


title: 739_02


title: 739_01


title: 662_02


title: 662_01


title: 706_02


title: 724_02


title: 496_INPUT

value: AATF


title: 724_01


title: 674_02


title: 674_01


title: 721_01


title: 609_02


title: 609_01


title: 555_02


title: 485_02_4000


title: 555_01


title: 485_01_4000


title: 616_01


title: 451_01_4000


title: 451_02_4000


title: 520_02


title: 520_01


title: 611_02


title: 523_01


title: 706_01


title: 721_02


title: 616_02


title: 534_01


title: 534_02


title: 547_02


title: 355_02_4000


title: 547_01


title: 541_01


title: 536_02


title: 536_01


title: 611_01


title: 535_01


title: 523_02


title: 513_01


title: 513_02


title: 510_02


title: 471_02


title: 471_01


title: 598_01


title: 355_01_4000


title: 459_02


title: 598_02


title: 512_02


title: 512_01


title: 499_02


title: 498_02


title: 499_01


title: 498_01


title: 541_02


title: 496_01


title: 419_01


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