title: WT 3h LPS RelA ChIP-seq


title: WT 8h LPS RelA ChIP-seq

status: Public on Jun 26 2018

type: SRA

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

country: USA

institute: NCI / NIH

library_source: genomic

data_processing:
Base-calling with Illumina run time analysis software 1.12.4.2
Alignment to mm9 using Casava Eland extended
Areas of enrichment were identified using DNase2Hotspots software(http://sorceforge.net/proujects/dnase2hotspots/) software with FDR 0%.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Values for tag densities were normalized to 10 million reads to adjust for differences in the sequencing depth between samples.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph, CSV

molecule: genomic DNA

organism: Mus musculus

source_name: Bone marrow derived macrophages

extract_protocol:
For the RelA and Ikaros ChIP, BMDMs were cross-linked with 1% formaldehyde for 10 min at room temperature. After cross-linking, chromatin was isolated from approximately 2 × 107 cells and processed as follows. The lysis buffer to shear the chromatin contained 0.5% SDS, 10 mM EDTA (pH 8), 50 mM tris-HCl (pH 8), and proteinase inhibitor cocktail. Sonication was performed with a Bioruptor Plus (Diagenode) at medium setting for a total time of 17 min for Ikaros ChIP, 20 min for RelA ChIP, using a 30 sec ON, 30 sec OFF cycle to shear the chromatin to generate DNA fragments with a size range of 200 to 600 base pairs. The sonicated mixture was centrifuged at 14,000 rpm for 10 min. The sheared chromatin samples were diluted 1:5 in dilution buffer [0.01% SDS, 1.1% Triton-X, 1.2 mM EDTA (pH 8), 20 mM tris-HCl (pH 8), 167 mM NaCl, and proteinase inhibitor cocktail]. For the RelA ChIP, 10 ml of a rabbit polyclonal anti-RelA antibody (ab7970, Abcam) was diluted in 1 ml immune complex buffer with Dynabeads protein A (Invitrogen). For the Ikaros ChIP, 10 ul of a goat polyclonal Ikaros antibody ((M-20), Santa Cruz)) was diluted in 1 ml immune complex buffer with Dynabeads protein G (Invitrogen). 200 mg chromatin DNA was immunoprecipitated with antibody-bead complexes at 4oC overnight. The chromatin-DNA complexes were washed with immune complex buffers (Low salt, High salt, LiCl and TE) and were eluted followed by reverse cross-linking (10 mM Tris-HCl, 300 mM NaCl, 55 mM EDTA, 0.5% SDS).
Sequencing libraries were generated using Illumina TruSeq V3 protocol and subjected to 51 bp single-end sequencing on an Illumina HiSeq2000.

treatment_protocol: Primary macrophages derived from bone marrow were stimulated with lipopolysaccharide for the indicated number of hours.

tag: strain background

tag: cell type

value: Bone marrow derived macrophages

tag: genotype/variation

value: wild type

tag: stimulated with

value: LPS for 8h

tag: chip antibody

value: RelA (ab7970, Abcam)


title: WT 4h LPS rep1

library_source: transcriptomic

data_processing:
The Illumina basecalling and read generation algorithm versions were RTA 1.12.4.2 and CASAVA-1.8.2.
Samples were demultiplexed allowing one mismatch on the barcode and each sample was separated in by the given six bait primers. Reads are filtered and trimmed based on the bait sequences
Samples were aligned to the reference human genome hg19 using TopHat v2.0.8 with -r 10 –mate-std-dev 200 options.
Gene model annotation for hg19 from Ensembl was provided to the aligner with the -G parameter.
Cufflinks v2.1.1 with hg19 UCSC genes from iGenomes was used to generate gene-level abundance estimates.
Genome_build: hg19
Supplementary_files_format_and_content: fpkm_tracking files contain Cufflinks output for gene expression

molecule: total RNA

source_name: Bone marrow derived macrophages_WT 4h LPS

extract_protocol: Extraction and library construction methods are described in the accompanying publication.

tag: strain

value: 10 ng/ml LPS for 4h


title: KO 2h LPS rep2

source_name: Bone marrow derived macrophages_KO 2h LPS

value: Ikzf KO

value: 10 ng/ml LPS for 2h


title: WT 2h LPS rep2

source_name: Bone marrow derived macrophages_WT 2h LPS


title: KO 10h LPS rep1

source_name: Bone marrow derived macrophages_KO 10h LPS

value: 10 ng/ml LPS for 10h


title: WT 10h LPS rep2

source_name: Bone marrow derived macrophages_WT 10h LPS


title: KO 4h LPS rep1

source_name: Bone marrow derived macrophages_KO 4h LPS


title: WT 8h LPS Ikaros ChIP-seq

value: Ikaros (M-20, Santa Cruz)


title: KO 4h LPS rep2


title: WT 0h LPS rep1

source_name: Bone marrow derived macrophages_WT 0h LPS

value: 10 ng/ml LPS for 0h


title: KO 2h LPS rep1


title: Scramble rep 1 PolII ChIP-seq

city: Davis

first: Frederic

last: Chedin

state: CA

address: 1 Shields Avenue

department: MCB

institute: UC Davis

description: wtA

data_processing:
DRIP-seq, DRIPc-seq, RNA-seq, RNA Pol II ChIP-seq: All fastq files were trimmed with fastq-mcf before mapping.
DRIP-seq, DRIPc-seq, and RNA Pol II ChIP-seq: Trimmed fastq reads were mapped to hg19 using Bowtie2.1.0. RNA Pol II ChIP-seq peak calling was performed using macs14 1.4.2. DRIP-seq and DRIPc-seq peak calling were performed using HMM as described in methods.
RNA-seq: Trimmed fastq reads were mapped to hg19 using TopHat 2.0.5. Count table was generated using htseq-count using the "-m intersection-nonempty" option.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig: binary of wiggle format, containing coordinate and aggregate signal of the data. tsv: RNA-seq count table as well as differential expression log2fold change and statistics, created by DESeq2

organism: Homo sapiens

source_name: Scramble, HEK293

extract_protocol:
Genomic DNA was extracted from HEK293 cells, sonicated and immunoprecipitated with antibody specific for RNA Polymerase II
standard illumina protocol

tag: cell line

value: Scramble control

tag: antibody

value: RNA Polymerase II


title: Top1 KD rep 1 RNA-seq

description:
kdA
RNA_DESeq2.tsv

source_name: Top1 KD, HEK293

extract_protocol:
Total RNA was extracted from HEK293 cells using Trizol for downstream processing with the Illumina Truseq kit.
Illumina TruSeq protocol

value: Top1 KD


title: WT 0h LPS RelA ChIP-seq

value: LPS for 0h


title: Top1 KD rep 2 RNA-seq

description:
kdB
RNA_DESeq2.tsv


title: Top1 KD rep 1 DRIPc-seq

description:
RNA/DNA hybrids
kdA

data_processing:
Library strategy: DRIPc-seq
DRIP-seq, DRIPc-seq, RNA-seq, RNA Pol II ChIP-seq: All fastq files were trimmed with fastq-mcf before mapping.
DRIP-seq, DRIPc-seq, and RNA Pol II ChIP-seq: Trimmed fastq reads were mapped to hg19 using Bowtie2.1.0. RNA Pol II ChIP-seq peak calling was performed using macs14 1.4.2. DRIP-seq and DRIPc-seq peak calling were performed using HMM as described in methods.
RNA-seq: Trimmed fastq reads were mapped to hg19 using TopHat 2.0.5. Count table was generated using htseq-count using the "-m intersection-nonempty" option.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig: binary of wiggle format, containing coordinate and aggregate signal of the data. tsv: RNA-seq count table as well as differential expression log2fold change and statistics, created by DESeq2

extract_protocol:
Genomic DNA was extracted from HEK293 cell lines and fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI. Monoclonal S9.6 antibody was used to enrich for RNA/DNA hybrids.
standard illumina protocol

value: Monoclonal S9.6


title: Scramble rep 1 RNA-seq

description:
wtA
RNA_DESeq2.tsv


title: Scramble rep 2 RNA-seq

description:
wtB
RNA_DESeq2.tsv


title: WT 2h LPS rep1


title: WT 10h LPS rep1


title: Scramble rep 2 PolII ChIP-seq

description: wtB


title: Top1 KD rep 1 PolII ChIP-seq

description: kdA


title: X12-M435-IM

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

data_processing:
cleaning .fastq files with fastq-mcf, quality control with fastQC
mapping to genome with Bowtie2 / TopHat2
count reads with htseq-count
call peaks with MACS2
normlization with deepTools
Genome_build: Mus musculus (mm10), Homo sapiens (GRCh37/hg19)
Supplementary_files_format_and_content: tab-delimited text files contain raw mRNA counts
Supplementary_files_format_and_content: narrowpeak / bed files with the called peaks (macs2)
Supplementary_files_format_and_content: bedgraph files with normalized signals

source_name: xenograft of patient sample

extract_protocol:
Maxwell 16 LEV simplyRNA Cells Kit according to manufacturers instructions (Promega)
all libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: xenograft of patient sample

tag: genotype

value: NUP214-ABL1 positive, TLX3 positive

tag: treatment

value: imatinib


title: X12-M436-DMSO

value: DMSO


title: Top1 KD rep 2 DRIPc-seq

description:
RNA/DNA hybrids
kdB


title: X12-M436-IM


title: X12-M435-DMSO


title: X12-M433-IM


title: X12-M434-IM


title: ALLSIL-DMSO-3

source_name: ALL-SIL cell line

value: ALL-SIL

value: NUP214-ABL1 positive, TLX1 positive


title: ALLSIL-IM-1


title: ALLSIL-IM-2


title: ALLSIL-IM-3


title: Top1 KD rep 2 PolII ChIP-seq

description: kdB


title: ALLSIL-DMSO-1


title: ALLSIL-DMSO-2


title: E13.5 Foxd1Cre;Smo(flox-) sample 1

city: Toronto

first: Norman

middle: D

last: Rosenblum

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

description:
MUT1
Processed data file: Unstr_DE_All_WT_vs_MUT_NormCounts.txt

data_processing:
Sequencing platform: Illumina HiSeq 2500, sequenced 1 lane.
Transcripts aligned to mouse genome (mm10) using TopHat version 2.0.12.
Subsequent analysis followed general pipeline provided by Anders et al., 2013, Nature Protocols, Volume 8 1765-1786: Number of alignments using HTSeq version used: 0.5.4, Analysis of differentially regulated genes was carried out using DESeq2 version 1.4.5.
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: Unstr_DE_All_WT_vs_MUT_NormCounts.txt: Tab-delimited text file includes RPKM values for each sample (samples in different columns); log2 fold change (WT compared to MUT).

source_name: E13.5 Foxd1Cre;Smo(flox/-) kidney tissue

growth_protocol: Foxd1Cre(Smo+/-) mice were mated with Smo(flox/flox) mice; embryonic days were timed by checking for a vaginal plug. Noon of the day of the plug was set to E0.5.

extract_protocol:
At E13.5, pregnant dams were sacrificed using CO2, kidneys were dissected from embryos, then RNA was isolated using the Qiagen RNeasy micro kit.
Library prep was done using Illumina TruSeq RNA library prep kit using poly(A) selection with oligodT beads, RNA quantified using Qubit RNA HS assay. 500 ng RNA was used as starting input.

tag: strain/background

value: C57BL/6 (mixed)

tag: developmental stage

value: kidney


title: TET1_KO_3_2

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

department: Bioinformatics

institute: Coriell Institute

data_processing:
Illumina HiSeq2500 single end sequencing
Sequenced reads were aligned to the hg19 genome assembly using the Star software suite
ht-seq-count  with default settings to generate counts of each gene
Cuffdiff to generate FPKM and fold change of each condition compared to control, we filtered for genes that had 0 reads across all samples
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are in excel format. The first column is gene name.  The next 12 columns are the FPKMs of the individual samples.

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium with 10% fetal bovine serum

extract_protocol:
RNA was isolated using Rneasy Plus Mini Kit (Qiagen)
Strand-specific RNA libraries were generated from 1μg of RNA using TruSeq stranded total RNA with Ribo-Zero Gold (Illumina)

treatment_protocol: gRNAs targeting 3 different TET1 exons were cloned into the Lenti CRISPR V2 plasmid.  gRNAs targeted exon 6 (KO-1), exon 3 (KO-2) and exon 11 (KO-3).  Lentiviruses were generated using HEK293T cells by transfecting with packaging plasmid (psPAX2, Addgene 12260), envelope plasmid (pMD2.G, Addgene 12259) and lenti-CRISPR V2 plasmid (Addgene 52961).  Cells were transfected using Lipofectamine 2000.  Viral supernatant was collected at 48 and 72 hours, filtered with 0.45µm membrane and incubated on MDA-MB-231 cells for 7 hours in the presence of polybrene (6µg/mL, Millipore).  We puromycin selected (1µg/mL) the cells for three days, followed by single cell cloning using serial dilution in 96 well plates.  After selection, cells were maintained in normal media supplemented with 0.25 µg/mL puromycin.

value: Triple negative breast cancer cell line

tag: age

value: adult

value: TET1 KO_3 (gRNA targeting exon 11)


title: X12-M433-DMSO


title: E13.5 Smo(flox/+) sample 4

description:
WT4
Processed data file: Unstr_DE_All_WT_vs_MUT_NormCounts.txt

source_name: E13.5 wildtype kidney tissue

value: Smo(flox/+)


title: TET1_KO_3_3


title: E13.5 Foxd1Cre;Smo(flox-) sample 2

description:
MUT2
Processed data file: Unstr_DE_All_WT_vs_MUT_NormCounts.txt


title: N658-BT

city: Santa Monica

first: Dave

last: Hoon

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

description: circulating tumor cells-enriched cells

data_processing:
Base calling and demultiplexing were processed using CASAVA version 1.8
Reads were mapped using the GENCODE release 19 reference using STAR version 2.4.2a
Read counts were generated using the quantMode GeneCounts option in STAR.

source_name: melanoma patients

extract_protocol:
Total RNA was extracted using in-house TRI Reagent.
mRNA libraries were constructed using Illumina TruSeq RNA Access Library Preparation kit, according to the manufacturer's recomendations (Illumina Inc).

value: circulating tumor cells-enriched cells


title: N661-BT

description: circulating tumor cells-enriched cells


title: X12-M434-DMSO


title: E13.5 Foxd1Cre;Smo(flox-) sample 4

description:
MUT4
Processed data file: Unstr_DE_All_WT_vs_MUT_NormCounts.txt


title: E13.5 Smo(flox/+) sample 3

description:
WT3
Processed data file: Unstr_DE_All_WT_vs_MUT_NormCounts.txt


title: TET1_KO_2_2

value: TET1 KO_2 (gRNA targeting exon 3)


title: TET1_KO_2_1


title: TET1_KO_1_3

value: TET1 KO_1 (gRNA targeting exon 6)


title: E13.5 Foxd1Cre;Smo(flox-) sample 3

description:
MUT3
Processed data file: Unstr_DE_All_WT_vs_MUT_NormCounts.txt


title: TET1_KO_2_3


title: TET1_KO_1_2


title: E13.5 Smo(flox/+) sample 1

description:
WT1
Processed data file: Unstr_DE_All_WT_vs_MUT_NormCounts.txt


title: E13.5 Smo(flox/+) sample 2

description:
WT2
Processed data file: Unstr_DE_All_WT_vs_MUT_NormCounts.txt


title: m41_DMSO

source_name: thymus

extract_protocol: all libraries were prepared for sequencing using standard Illumina protocols


title: N659-BT

description: circulating tumor cells-enriched cells


title: m44_DMSO


title: TET1_KO_1_1


title: m2_NA_TLX1


title: Empty Vector_3

value: Empty vector single clone 1


title: m3_NA_TLX1


title: Empty Vector_1


title: CD2Cre-NA-2

value: NUP214-ABL1 positive


title: Empty Vector_2


title: CD2Cre-NA-1


title: TET1_KO_3_1


title: Lck_TLX1

value: TLX1 positive


title: wt_thymus_4

value: wild type


title: wt_thymus_5


title: wt_thymus_1


title: wt_thymus_3


title: wt_thymus_2


title: m402_H3K27ac

description: H3K27ac histone marks in NUP214-ABL1 positive, TLX1 positive cells.

data_processing:
Library strategy: ChIPmentation
cleaning .fastq files with fastq-mcf, quality control with fastQC
mapping to genome with Bowtie2 / TopHat2
count reads with htseq-count
call peaks with MACS2
normlization with deepTools
Genome_build: Mus musculus (mm10), Homo sapiens (GRCh37/hg19)
Supplementary_files_format_and_content: tab-delimited text files contain raw mRNA counts
Supplementary_files_format_and_content: narrowpeak / bed files with the called peaks (macs2)
Supplementary_files_format_and_content: bedgraph files with normalized signals


title: CD4Cre-NA


title: T98G_lrna_b2

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description:
RIP-seq
RNA extracted with trizol (Invitrogen) was fragmented using RNA fragmentation kit(NEB __) and rRNA depleted using rRNA removal kit (Epicenter __). Libraries were then prepared using NEB-next small RNA library preparation kit (NEB ___).
Adaptors were trimmed using cutadapt. Reads were aligned to hg19 using Tophat. Reads mapping to genes were counted using feature counts. EZH2 enriched genes were determined using DESeq2.

data_processing:
Illumina CASAVA version 1.8 used for basecalling.
EZH2 enriched RIP-seq targets were identified by comparing EZH2 RIP-seq enriched genes with IgG IP and input using DESeq2. iCLIP peaks were called using pyicoclip and intersected with significant RIP-seq enriched full length transcripts. The transcripts common across both RIP-seq and iCLIP were identified as EZH2 full-length RNA targets.
EZH2 enriched small RNAs were identified by comparing read counts at exons in EZH2 IP to IgG IP and input using DESeq2. Exons significantly different by atleast 2 fold were considered EZH2 enriched. Peaks within enriched exons were further called using pyicoclip to identify EZH2 small RNA targets.
Differentially expressed genes in siRNA treated and control samples were determined using DESeq2.
Intron retention was calculated as the ratio of reads mapping to introns normalized by the average number of reads mapping to adjacent exons. Differential intron retention in response to EZH2 knockdown was calculated as the ratio of intron retention in siEZH2 and intron retention in siGFP. To reduce false positives, only introns or exons with more than 9 reads were used and introns showing less than 2-fold change in intron retentions were filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: bed

source_name: T98G cell line

growth_protocol: Cells were grown in EMEM with 10% FBS and maintained at 37oC and 5% Co2.

extract_protocol: Cells were incubated in hypotonic solution (10 mM KCL, 10 mM HEPES pH 7.5, 1.5 mM Mgcl2 and 2 mM DTT) for 5 mins and spun down by centrifugation. 1mg/ml digitonin (Cat #) was then added to the lysate resuspension and further incubated for 10 min with constant mixing. Cells were then mechanically lysed using dounce homogenizer (15 times) and spun down. Pelleted cells were then resuspended in NP40 lysis buffer (150 mM KCL, 50 mM hepes pH 7.5, 5 mM EDTA, 0.5 % IGEPAL and 2 mM DTT) and subjected to mild sonication (6 cycles, 10 sec on and 30 sec off). All the steps in this procedure were performed at 4oC.

treatment_protocol: No treatment

tag: cancer type

value: Immortalized GBM cell line

value: No Antibody


title: EZH2_iCLIP

description:
iCLIP
EZH2_full-length_RNA_targets_T98G
Libraries were constructed as previously published (PMID20601959).
Adaptors were trimmed using cutadapt. Reads were aligned to hg19 using Bowtie2. Reads mapping to genes were counted using feature counts. EZH2 enriched genes were determined using DESeq2.

extract_protocol: Cells were crosslinked with 0.15J/cm2 of UV254 using stratalinker 2400. Crosslinked cells were lysed using NP40 lysis buffer (50mM Tris, pH7.4; 100 mM Nacl; 1% Igepal CA-630; 0.1%SDS;0.5% sodium deoxycholate and protease inhibitor). Lysates were then treated with 200U/ml Turbo DNaseI and 20U/ml of RNaseI followed by incubation at 37C for 2 mins.

value: EZH2(Active motif, 39875 and Abcam 186006)


title: T98G_lRNA_ezh2_b2

value: EZH2(Active motif, 39875)


title: U87MG_siEZH2_b1

description:
RNA-seq
DESEq2_siezh2_siGFP_padj005.bed
RNA extracted with trizol (Invitrogen) was fragmented using RNA fragmentation kit(NEB __) and Poly-A tailed RNA were extracted using PolyA selection kit (Bioo __). Libraries were then prepared using NEB-next small RNA library preparation kit (NEB ___).
Adaptors were trimmed using cutadapt. Reads were aligned to hg19 using Tophat 2 v2.0.11 with parameters --b2-fast --library-type=fr-unstranded --no-novel-juncs --no-novel-indels --transcriptome-index. Reads mapping to genes were counted using feature counts. Differentially expressed genes were determined using DESeq2.

source_name: U87MG cell line

extract_protocol: Cells were grown in 6well plates and treated with Trizol (Invitrogen). RNA was harvested using manufacturers instructions.

treatment_protocol: siRNA for EZH2


title: U87MG_siEZH2_b2

description:
RNA-seq
EZH2_seRNA_proximal_retained_introns_U87MG
RNA extracted with trizol (Invitrogen) was fragmented using RNA fragmentation kit(NEB __) and Poly-A tailed RNA were extracted using PolyA selection kit (Bioo __). Libraries were then prepared using NEB-next small RNA library preparation kit (NEB ___).
Adaptors were trimmed using cutadapt. Reads were aligned to hg19 using Tophat 2 v2.0.11 with parameters --b2-fast --library-type=fr-unstranded --no-novel-juncs --no-novel-indels --transcriptome-index. Reads mapping to genes were counted using feature counts. Differentially expressed genes were determined using DESeq2.

treatment_protocol: siRNA for EZH3


title: T98G_lRNA_igg2_b2

value: IgG2a(Sigma Aldrich, M5409 )


title: T98G_lrna_b1


title: U87MG_siGFP_b2

description:
RNA-seq
RNA extracted with trizol (Invitrogen) was fragmented using RNA fragmentation kit(NEB __) and Poly-A tailed RNA were extracted using PolyA selection kit (Bioo __). Libraries were then prepared using NEB-next small RNA library preparation kit (NEB ___).
Adaptors were trimmed using cutadapt. Reads were aligned to hg19 using Tophat 2 v2.0.11 with parameters --b2-fast --library-type=fr-unstranded --no-novel-juncs --no-novel-indels --transcriptome-index. Reads mapping to genes were counted using feature counts. Differentially expressed genes were determined using DESeq2.

treatment_protocol: siRNA for GFP


title: T98G_lRNA_igg2_b1


title: U87MG_siGFP_b1


title: m402_p300

description: p300 binding in NUP214-ABL1 positive, TLX1 positive cells.

value: NUP214-ABL1 positive, TLX1 positive

value: p300 (Santa Cruz Biotechnology, SC-585X, AB_2616339)


title: T98G_lRNA_ezh2_b1


title: m402_BRD4

description: BRD4 binding in NUP214-ABL1 positive, TLX1 positive cells.


title: m402_H3K4me3

description: H3K4me3 histome marks in NUP214-ABL1 positive, TLX1 positive cells.

value: H3K4me3 (Cell Signaling Technology, 9751, AB_2616028)


title: U87MG_input_b2

description:
RIP-seq
Small RNA RIP-seq libraries were prepared using NEB-next small RNA library preparation kit (NEB ___). Following library preparation, 20-50 bases long products were size selected from 6% TBE gel as per manufacturer’s instructions.
Adaptors were trimmed using cutadapt. Reads were aligned to hg19 using BWA aligner. Reads mapping to exons were counted using bedtools. Differentially expressed exons were determined using DESeq2 and peaks were called using pyicoclip.


title: m402_STAT5_mix

description: STAT5 binding in NUP214-ABL1 positive, TLX1 positive cells.


title: U87MG_EZH2_b2


title: U87MG_input_b1


title: M403S-DMSO

source_name: spleen

value: spleen

value: DMSO


title: M403S-IM

value: imatinib


title: U87MG_igg2_b1


title: M402S-IM


title: U87MG_EZH2_b1

description:
RIP-seq
EZH2_small_RNA_targets_U87MG.bed
Small RNA RIP-seq libraries were prepared using NEB-next small RNA library preparation kit (NEB ___). Following library preparation, 20-50 bases long products were size selected from 6% TBE gel as per manufacturer’s instructions.
Adaptors were trimmed using cutadapt. Reads were aligned to hg19 using BWA aligner. Reads mapping to exons were counted using bedtools. Differentially expressed exons were determined using DESeq2 and peaks were called using pyicoclip.


title: T98G_input_b2

growth_protocol: Cells were grown in EMEM with 10% FBS. K562 cell line (ATCC-CCL-243) was grown in IMDM with 10% FBS. All cell lines were maintained at 37oC and 5% Co2.


title: M401S-IM


title: T98G_igg2_b2


title: M401S-DMSO


title: T98G_EZH2_b2


title: m337 - thymus

value: thymus


title: m336 - thymus


title: m339 - thymus


title: m413 -thymus


title: m340 - thymus


title: K562_EZH2

description:
RIP-seq
EZH2_small_RNA_targets_K562.bed
Small RNA RIP-seq libraries were prepared using NEB-next small RNA library preparation kit (NEB ___). Following library preparation, 20-50 bases long products were size selected from 6% TBE gel as per manufacturer’s instructions.
Adaptors were trimmed using cutadapt. Reads were aligned to hg19 using BWA aligner. Reads mapping to exons were counted using bedtools. Differentially expressed exons were determined using DESeq2 and peaks were called using pyicoclip.

source_name: K562 cell line

growth_protocol: K562 cell line (ATCC-CCL-243) was grown in IMDM with 10% FBS and maintained at 37oC and 5% Co2.

value: Immortalized CML cell line


title: T98G_EZH2_b1

description:
RIP-seq
EZH2_small_RNA_targets_T98G.bed
Small RNA RIP-seq libraries were prepared using NEB-next small RNA library preparation kit (NEB ___). Following library preparation, 20-50 bases long products were size selected from 6% TBE gel as per manufacturer’s instructions.
Adaptors were trimmed using cutadapt. Reads were aligned to hg19 using BWA aligner. Reads mapping to exons were counted using bedtools. Differentially expressed exons were determined using DESeq2 and peaks were called using pyicoclip.


title: m401_TLX1

description: TLX1 binding in NUP214-ABL1 positive, TLX1 positive cells.

value: TLX1 (Santa Cruz Biotechnology, sc-880, AB_2203789)


title: T98G_igg2_b1


title: U87MG_igg2_b2


title: m295 - PB

source_name: peripheral blood

value: peripheral blood


title: T98G_input_b1


title: m316 - thymus


title: m296 - PB


title: K562_igg

value: IgG2a(Sigma Aldrich, M5409)


title: K562_input


title: TLX1-3 - thymus

value: TLX1 positive


title: CD2Cre - NA - 2

value: NUP214-ABL1 positive


title: m1777-NA - thymus


title: CD2Cre - NA - 1


title: CD4Cre - NA


title: TLX1-2 - thymus


title: M402S-DMSO


title: wt-2 - thymus

value: wild type


title: wt-3 - thymus


title: wt-1 - thymus


title: AH74 Setd1b HOM (FD/FD; RC/+)

city: Dresden

first: Konstantinos

last: Anastassiadis

address: Tatzberg 47

department: Biotechnology Center

country: Germany

institute: Technische Universitaet Dresden

data_processing:
[basecalling] Basecalls were performed using Illumina bcl2fastq version 2.17.1.14.
[alignment] Reads were aligned to the mouse genome assembly (mm10) using GSNAP (2015-12-31; parameters: -d mm10 --gunzip –use-sarray=1 -B 5 -t 8 -N 1 -s EnsemblGene-81.ss.mm10.iit  -n 1 -A sam) with known splice sites from Ensembl (v81) as support.
[read counting] Uniquely aligned fragments and gene annotations from Ensembl (v81) were used for featureCounts (v1.5.0; parameters: -a EnsemblGene-81.mm10.TR.gtf -s 1 -o featureCounts.mm10.e81.csv -Q 1 -T 8) to obtain a table with read counts per gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited counts table from featureCounts (featureCounts.mm10.e81.csv.gz) with the following columns: Ensembl Gene ID, Chromosome, Gene Start, Gene End, Strand, Gene Length, then all sample counts; comments start with '#'

source_name: Setd1b HOM (FD/FD; RC/+)

extract_protocol:
Total RNA was isolated using the miRNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Eluted RNA was reverse-transcribed and amplified using the SMARTer Stranded Total RNA-seq Kit – Pico Input Mammalian (Takara) following manufacturer's protocol.

treatment_protocol: Mice were treated with 4.5 mg tamoxifen per mouse per day by gavage (4 days gavage - 3 days pause - 2 days gavage) and sacrificed 3 days after the last treatment. Bone marow cells were isolated, lineage-depleted and the LSK (Lin-, Sca+, Kit+) compartment was stained with fluorescently-labeled antibodies. On a FACSAria III cytometer the LSK compartment (on average 25 x 10^3 cells) was collected and stored at -80°C until further processing.

value: Bone marrow

value: Hematopoietic Stem and Progenitor cell (HSPC - LSK compartment)

value: 17 weeks

tag: Sex

value: male

value: Setd1b HOM (FD/FD; RC/+)

value: Tamoxifen


title: AI03 Setd1b HET (FD/+; RC/+)

source_name: Setd1b HET (FD/+; RC/+)

value: 16 weeks

value: Setd1b HET (FD/+; RC/+)


title: AI54 Setd1b HET (FD/+; RC/+)


title: Caco2/15 shNT cells, replicate 2

city: Sherbrooke

first: Francois

last: Boudreau

state: Quebec

address: 3201 rue Jean-Mignault

department: Anatomie et biologie cellulaire

institute: Université de Sherbrooke

data_processing:
Base-calling was performed using Illumina CASAVA pipeline. Trimming and clipping was done with Trimmomatic software.
Alignement was done with the combinaison of Tophat and Bowtie software using the 1000 Genome reference (b37)
Assembling of transcripts was done by Cufflinks program and reads count by HTSeq
Differential gene expression analysis was generated with DESeq and edgeR software.
Genome_build: b37
Supplementary_files_format_and_content: Tab-delimited txt files containing Gene or transcripts names, fold change, p-value and raw counts.

source_name: Caco2/15 cells

growth_protocol: Caco2/15 cells were cultured in DMEM media containing 10% FBS, 2 mM L-glutamine and 100 mM HEPES buffer.  Cells were cultivated at a maximum confluency of 80% to avoid initiation of differentiation.

extract_protocol:
Total RNA were extracted from cells using QIAGEN RNeasy mini kit.
Librairies were prepared using first strand TrueSeq mRNA protocol (Illumina) with 250 ng of total RNA.

treatment_protocol: Cells were seeded in 6-well plates to get an average confluency of 60% on the next day. They were then infected with 350 ul of lentiviruses (in 2 ml total media containing 4 ug/ml of hexadimethrine bromide) for 48 hours. Lentiviruses were removed by washing in PBS 1X and cells incubated in fresh media for another 24 hours. At that time, cells reached confluence.

value: Colorectal cancer cells

tag: culture status

value: 1 day post-confluence

tag: infection

value: Infected with control lentiviral shRNA (pLKO.1 SHC002, Sigma-Aldrich)


title: Caco2/15 shP2 cells, replicate 3

tag: cell type

value: Infected with lentiviral shRNA against HNF4alpha P2 isoforms


title: Caco2/15 shNT cells, replicate 3


title: Caco2/15 shP1 cells, replicate 2

value: Infected with lentiviral shRNA against HNF4alpha P1 isoforms


title: AI55 Setd1b HOM (FD/FD; RC/+)


title: Caco2/15 shP2 cells, replicate 2


title: Caco2/15 shP2 cells, replicate 1


title: Caco2/15 shP1 cells, replicate 3


title: Caco2/15 shNT cells, replicate 1


title: Caco2/15 shP1 cells, replicate 1


title: AI02 Setd1b HOM (FD/FD; RC/+)


title: Scramble DRIP-seq

description:
RNA/DNA hybrids
wtB

data_processing:
Library strategy: DRIP-seq
DRIP-seq, DRIPc-seq, RNA-seq, RNA Pol II ChIP-seq: All fastq files were trimmed with fastq-mcf before mapping.
DRIP-seq, DRIPc-seq, and RNA Pol II ChIP-seq: Trimmed fastq reads were mapped to hg19 using Bowtie2.1.0. RNA Pol II ChIP-seq peak calling was performed using macs14 1.4.2. DRIP-seq and DRIPc-seq peak calling were performed using HMM as described in methods.
RNA-seq: Trimmed fastq reads were mapped to hg19 using TopHat 2.0.5. Count table was generated using htseq-count using the "-m intersection-nonempty" option.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig: binary of wiggle format, containing coordinate and aggregate signal of the data. tsv: RNA-seq count table as well as differential expression log2fold change and statistics, created by DESeq2

tag: genotype/variation

value: Scramble control

value: Monoclonal S9.6


title: Top1 KD rep 2 DRIP-seq

description:
RNA/DNA hybrids
kdB

value: Top1 KD


title: ESP Biological Replicate 3

status: Public on Jun 25 2018

city: Dublin

first: Carsten

last: Kroeger

address: Moyne Institute of Preventive Medicine

department: Microbiology

country: Ireland

institute: Trinity College Dublin

data_processing:
Sequence reads were mapped to the Acinetobacter baumannii 17978-mff reference genome using bowtie2 with -local -verysensitive settings.
Genome_build: GenBank file: CP012004.1 [PMID:26170289]
Supplementary_files_format_and_content: .gr files are provided showing  mapped sequence reads after normalization. The number of mapped nucleotides for each position was divided by the number of uniquely mapped reads of the smallest library (ESP_2) and then multiplied by the number of reads for the library that was supposed to be normalised. Ready to load into Integrated Genome Browser (IGB). The file consists of two columns showing nucleotide position on the chromosome and number of reads mapped at each location. "Plus" and "Minus" refer to the two strands of the Acinetobacter chromosome

organism: Acinetobacter baumannii

source_name: RNA from bacteria

growth_protocol: Cells were grown overnight in 5 ml Lennox (L-) broth (10 g/L tryptone, 5 g/L yeast extract, 5 g/L NaCl) and diluted the next morning (1:1,000) in 250 ml flasks in 25 ml L-broth and grown at 37°C and 220 rpm. Early stationary phase (ESP) samples were collected when cultures reached OD600 2.0 in L-broth. Samples from the following growth conditions and environmental shocks were combined to create the “pool” sample: growth in L-broth until OD600 of 0.25, 0.75, 1.8, 2, 2.5 and 2.8 and growth for 16 h on an L-agar plate at 37°C. Environmental shocks were induced by the addition to an exponentially growing (OD600 0.3) culture for 10 minutes of 250 µl of a 1:100 dilution of disinfectant (Distel 'High Level Medical Surface Disinfectant', non-fragranced), hydrogen peroxide to a final concentration of 1 mM, ethanol to a final concentration (v/v) of 2%, kanamycin to a final concentration of 50 µg/ml, NaCl to a final concentration of 0.3 M or 2,2’-dipyridyl to a final concentration of 0.2 mM. Growth in M9 minimal medium containing 1 mM MgSO4, 0.1 mM CaCl2 and carbon source 31.2 mM fumarate, 33.3 mM xylose or pyruvate. Growth at 25 °C and temperature shift from 25 °C to 37 °C (10 min).

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) and contaminating DNA digested with DNase I
cDNA libraries of the three ESP biological replicates were constructed using the NEBNext™ Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions. cDNA libraries of the RNA pool and TEX_RNA pool samples were constructed by vertis Biotechnologie AG (Freising) using an in-house protocol. Total RNA (DNase I digested) was fragmented by ultrasound (4 pulses of 30s at 4°C). The to construct dRNA-seq libraries, one part of the fragmented RNA was first treated with T4 Polynucleotide Kinase (NEB). RNA fragments with monophosphorylated 5' ends were then degraded using Terminator Exonuclease (TEX, Epicentre). The remaining 5'PPP structures were finally converted into 5' monophosphate ends using RNA 5' Polyphosphatase (5'PP, Epicentre). The other part of the fragmented RNA was dephosphorylated with Antarctic Phosphatase (NEB) and re-phosphorylated with T4 Polynucleotide Kinase. Oligonucleotide adapters were ligated to the 5' and 3' ends of the RNA samples. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The resulting cDNAs were amplified with PCR using a high fidelity DNA polymerase. The number of cycles and the barcode sequences which are part to the 3' sequencing adapters. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. For Illumina sequencing, the samples were pooled in approximately equimolar amounts. An aliquot of the pool was analyzed by capillary electrophoresis.

tag: growth phase

value: early stationary phase (ESP)


title: ATACseq_humanPDX_AML_control

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 (v2.2.2) with default parameters.
To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads; bed files representing dynamic peaks under treatment vs control conditions

source_name: human MA9 leukemia

growth_protocol: In vitro transformed MLL-AF9 Lin-Sca-1+c-Kit+ bone marrow cells were cultured in IMDM supplemented with heat inactivated 10% fetal bovine serum, 50 U/mL penicillin/streptomycin and murine interleukin-3 (10 ng/mL), interleukin-6 (10 ng/mL) and stem cell factor (SCF) (20 ng/mL, all PeproTech).

extract_protocol:
Cell nuclei were fresh prepared from 50,000 cells as previously described (Buenrostro et al. 2013 Nature Methods).
ATAC-seq was performed as previously described (Buenrostro et al. 2013 Nature Methods). For each sample, cell nuclei were prepared from 50,000 cells, and incubated with 2.5 uL transposase (Illumina) in a 50 uL reaction for 30 min at 37°C. Following purification of transposase fragmented DNA, the library was amplified by PCR and subjected to high-throughput sequencing using Illumina HiSeq 2500 platform.

treatment_protocol: The irreversible LSD1 inhibitor GSK-LSD1 was solubilized in DMSO for in vitro assays and in sterile phosphate-buffered saline for in vivo experiments. The DOT1L inhibitor EPZ4777 was kindly provided by Epizyme and was solubilized in DMSO as the vehicle for all experiments.

value: MA9 leukemia xenograft

value: leukemia

value: MLL-AF9 fusion


title: ATACseq_humanPDX_AML_LSD1i

value: LSD1 inhibitor


title: mRNA-Seq_131_WT_MUC3615

city: Munich

first: Mareen

last: Engel

address: Kraepelinstr. 2-10

department: Stress Neurobiology and Neurogenetics

institute: Max-Planck-Institute of Psychiatry

data_processing:
Basecalls were performed and demultiplexed using bcl2fast2 v2.18.
Trimming, alignment and counting was performed using STAR.
DESeq2 was used to normalize and detect differentially expressed genes comparing CRFR1-cKO and CRFR1-WT mice.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated files include gene symbol and raw count value (raw_counts.csv) and differential expression analysis (DESeq2_DGE.csv)

source_name: cerebellum

extract_protocol:
Total RNA was isolated from freshly dissected cerebella using Trizol (Invitrogen, CA, USA) according to the manufacturer’s instructions after homogenization by a Bullet Blender (Next Advance) and followed by isopropanol precipitation. Residual genomic DNA was removed using the Turbo DNA-free kit (Ambion®,Invitrogen, CA, USA). RNA integrity and absence of DNA was confirmed by Bioanalyzer RNA Nano chips (Agilent, RIN > 9.3) and Qubit DNA High sensitivity kit, respectively.
Sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation HT Kit following the standard protocol starting from 4 μg of total RNA using 11 cycles of PCR amplification. Sequencing was performed on 2 lanes of an   Illumina HiSeq4000 (Illumina, CA, USA) multiplexing all samples.

value: cerebellum

value: WT


title: ESP Biological Replicate 1


title: mRNA-Seq_129_cKO_MUC3614

value: deltaalpha6-Cre Crfr1 knock-out


title: mRNA-Seq_127_WT_MUC3613


title: mRNA-Seq_125_WT_MUC3612


title: mRNA-Seq_119_cKO_MUC3609


title: mRNA-Seq_107_WT_MUC3607


title: Control DRIP-seq

description:
RNA/DNA hybrids
wtA

source_name: Control, HEK293

value: Control


title: Top1 KD rep 1 DRIP-seq

description:
RNA/DNA hybrids
kdA

source_name: Top1 KD, HEK293


title: mRNA-Seq_109_cKO_MU3608


title: mRNA-Seq_97_WT_MUC3603


title: mRNA-Seq_101_cKO_MUC3604


title: Water.Rep2

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
RNA-Seq sequencing reads were aligned to hg19 genome using Tophat v2.0.11 using parameters "--library-type fr-firststrand" and using known transcripts annotation from ensembl gene verion 70
Number of reads counts on exons were summarised using featureCounts function available in rsubread R package.
Genome_build: hg19
Supplementary_files_format_and_content: reads counts on genes

source_name: IMR90 ER:RAS

growth_protocol: IMR90 ER:RAS cells were grown in DMEM, 10% FBS, for 6 days and media change was performed at day 1 and 4

extract_protocol:
50μl of lysis buffer (prepared according to Smart-seq2 protocol) was used for each well (condition) of a 96-well plate to lyse approximately 6000 cells
2μl of the lysate was used for reverse transcription, pre-amplification and library preparation following the Smart-seq2 protocol which takes advantage of the Nextera XT index kit

treatment_protocol: To induce RAS expression and senescence, cells were treated with 100nM 4OHT

tag: imr90 passage

tag: days after 4oht induction

tag: state

value: senescent

tag: transfected

value: mock-transfected


title: Water.Rep1


title: p53.Rep3

value: siRNA Hs_TP53_3


title: p65.Rep3

value: siRNA Hs_RELA_7


title: p65.Rep2


title: p53.Rep1


title: p38.Rep3

value: siRNA Hs_MAPK14_12


title: AI56 Setd1b HET (FD/+; RC/+)

tag: strain

tag: tissue

value: Bone marrow

value: Hematopoietic Stem and Progenitor cell (HSPC - LSK compartment)

value: 16 weeks

value: male

value: Setd1b HET (FD/+; RC/+)

value: Tamoxifen


title: mRNA-Seq_121_WT_MUC3610

tag: genotype


title: p38.Rep1


title: p38.Rep2


title: p16.Rep3

value: siRNA Hs_CDKN2A_15


title: p16.Rep2


title: p16.Rep1


title: Noninduced.Rep3

value: proliferating


title: mRNA-Seq_103_cKO_MUC3605

value: cerebellum


title: Noninduced.Rep1


title: mRNA-Seq_105_cKO_MUC3606


title: Hs_UBE2V2_6.Rep2

value: siRNA Hs_UBE2V2_6


title: Hs_UBE2V2_6.Rep1


title: ESP Biological Replicate 2

value: early stationary phase (ESP)


title: p53.Rep2


title: p65.Rep1


title: Hs_UBE2V2_5.Rep3

value: siRNA Hs_UBE2V2_5


title: Hs_UBE2V2_5.Rep1

value: senescent


title: Hs_UBE2V2_5.Rep2


title: Hs_TMEM219_4.Rep2

value: siRNA Hs_TMEM219_4


title: Hs_TMEM219_4.Rep3


title: Hs_TMEM219_1.Rep3

value: siRNA Hs_TMEM219_1


title: Hs_TMEM219_4.Rep1


title: Hs_TMEM219_1.Rep1


title: Noninduced.Rep2

value: mock-transfected


title: Hs_SKP1A_9.Rep2

value: siRNA Hs_SKP1A_9


title: Hs_SKP1A_5.Rep3

value: siRNA Hs_SKP1A_5


title: Hs_SKP1A_9.Rep3


title: Hs_SKP1A_9.Rep1


title: Hs_SKP1A_5.Rep2


title: Hs_SHFM3_2.Rep1

value: siRNA Hs_SHFM3_2


title: Hs_SKP1A_5.Rep1


title: Hs_SHFM3_2.Rep3


title: Hs_SHFM3_1.Rep3

value: siRNA Hs_SHFM3_1


title: Hs_UBE2V2_6.Rep3


title: Hs_SHFM3_1.Rep2


title: Hs_SHFM3_1.Rep1


title: Hs_RNF6_8.Rep1

value: siRNA Hs_RNF6_8


title: Hs_RNF6_6.Rep3

value: siRNA Hs_RNF6_6


title: Hs_RNF6_8.Rep3


title: Hs_TMEM219_1.Rep2


title: Hs_PTPN14_6.Rep3

value: siRNA Hs_PTPN14_6


title: Hs_RNF6_6.Rep1


title: Hs_RNF6_6.Rep2


title: Hs_RNF6_8.Rep2


title: Hs_PTPN14_5.Rep3

value: siRNA Hs_PTPN14_5


title: Hs_PTPN14_6.Rep2


title: Hs_PTPN14_5.Rep1


title: Hs_PTPN14_5.Rep2


title: Hs_PTBP1_5.Rep2

value: siRNA Hs_PTBP1_5


title: Hs_PTBP1_2.Rep3

value: siRNA Hs_PTBP1_2


title: Hs_PTBP1_2.Rep1


title: Hs_PTBP1_2.Rep2


title: Water.Rep3


title: Hs_PROK2_2.Rep2

value: siRNA Hs_PROK2_2


title: Hs_PROK2_2.Rep3


title: Hs_PROK2_6.Rep1

value: siRNA Hs_PROK2_6


title: Hs_SHFM3_2.Rep2


title: Hs_PTBP1_5.Rep1


title: Hs_PROK2_2.Rep1


title: Hs_PROK2_6.Rep2


title: Hs_PPP1CB_7.Rep2

value: siRNA Hs_PPP1CB_7


title: Hs_PROK2_6.Rep3

value: senescent


title: Hs_PPP1CB_7.Rep3


title: Hs_PLCB1_6.Rep3

value: siRNA Hs_PLCB1_6


title: Hs_PTPN14_6.Rep1


title: Hs_PPP1CB_7.Rep1


title: Hs_PLCB1_6.Rep2


title: Hs_PPP1CB_6.Rep1

value: siRNA Hs_PPP1CB_6


title: Hs_PLCB1_6.Rep1


title: Hs_PPP1CB_6.Rep3


title: Hs_PPP1CB_6.Rep2


title: Hs_PTBP1_5.Rep3


title: Hs_PLCB1_4.Rep3

value: siRNA Hs_PLCB1_4


title: Hs_PEO1_3.Rep2

value: siRNA Hs_PEO1_3


title: Hs_PEO1_3.Rep3


title: Hs_PEO1_2.Rep3

value: siRNA Hs_PEO1_2


title: Hs_PEO1_3.Rep1


title: Hs_NRG1_9.Rep2

value: siRNA Hs_NRG1_9


title: Hs_PEO1_2.Rep1


title: Hs_NRG1_9.Rep1


title: Hs_NRG1_9.Rep3


title: Hs_PEO1_2.Rep2


title: Hs_PLCB1_4.Rep2


title: Hs_NRG1_10.Rep3

value: siRNA Hs_NRG1_10


title: Hs_NRG1_10.Rep1


title: Hs_MCFP_6.Rep2

value: siRNA Hs_MCFP_6


title: Hs_MCFP_6.Rep1


title: Hs_MCFP_3.Rep3

value: siRNA Hs_MCFP_3


title: Hs_MAP3K6_5.Rep2

value: siRNA Hs_MAP3K6_5


title: Hs_MCFP_3.Rep1


title: Hs_MCFP_3.Rep2


title: Hs_MAP3K6_11.Rep2

value: siRNA Hs_MAP3K6_11


title: Hs_MAP3K6_11.Rep3


title: Hs_MAP3K6_5.Rep3


title: Hs_LOC51136_7.Rep3

value: siRNA Hs_LOC51136_7


title: Hs_MAP3K6_11.Rep1


title: Hs_LOC51136_7.Rep1


title: Hs_PLCB1_4.Rep1


title: TLX1-1 - thymus

value: thymus

value: TLX1 positive


title: Hs_MAP3K6_5.Rep1


title: Hs_LOC51136_7.Rep2


title: Hs_MCFP_6.Rep3


title: Hs_LOC51136_4.Rep1

value: siRNA Hs_LOC51136_4


title: Hs_LOC51136_4.Rep3


title: Hs_LOC399818_2.Rep2

value: siRNA Hs_LOC399818_2


title: Hs_LOC399818_2.Rep3

value: senescent


title: Hs_LOC399818_5.Rep2

value: siRNA Hs_LOC399818_5


title: Hs_LOC399818_5.Rep1


title: Hs_LOC399818_5.Rep3


title: Hs_LOC399818_2.Rep1


title: Hs_LNX2_6.Rep3

value: siRNA Hs_LNX2_6


title: Hs_NRG1_10.Rep2


title: Hs_LNX2_6.Rep2


title: Hs_LNX2_5.Rep2

value: siRNA Hs_LNX2_5


title: Hs_LNX2_6.Rep1


title: Hs_KCNQ4_4.Rep1

value: siRNA Hs_KCNQ4_4


title: Hs_KCNQ4_1.Rep2

value: siRNA Hs_KCNQ4_1


title: Hs_KCNQ4_1.Rep3


title: Hs_KCNQ4_4.Rep3


title: Hs_KCNA5_6.Rep3

value: siRNA Hs_KCNA5_6


title: Hs_ITCH_5.Rep3

value: siRNA Hs_ITCH_5


title: Hs_KCNA5_5.Rep2

value: siRNA Hs_KCNA5_5


title: Hs_KCNQ4_1.Rep1


title: Hs_LOC51136_4.Rep2


title: Hs_KCNA5_5.Rep3


title: Hs_ITCH_5.Rep2


title: Hs_KCNA5_6.Rep1


title: Hs_KCNA5_6.Rep2


title: Hs_KCNA5_5.Rep1


title: Hs_LNX2_5.Rep3


title: Hs_ITCH_3.Rep2

value: siRNA Hs_ITCH_3


title: Hs_IL17RE_9.Rep3

value: siRNA Hs_IL17RE_9


title: Hs_IL17RE_1.Rep2

value: siRNA Hs_IL17RE_1


title: Hs_ITCH_3.Rep3


title: Hs_ITCH_3.Rep1


title: Hs_IL17RE_9.Rep2


title: Hs_IL17RE_9.Rep1


title: Hs_IL17RE_1.Rep3


title: Hs_IL15_3.Rep2

value: siRNA Hs_IL15_3


title: Hs_IL15_3.Rep1


title: Hs_IL15_2.Rep3

value: siRNA Hs_IL15_2


title: Hs_IL15_2.Rep2


title: Hs_IFNA17_6.Rep3

value: siRNA Hs_IFNA17_6


title: Hs_IFNA17_9.Rep3

value: siRNA Hs_IFNA17_9


title: Hs_KCNQ4_4.Rep2


title: Hs_IFNA17_9.Rep2


title: Hs_LNX2_5.Rep1


title: Hs_IFNA17_6.Rep2


title: Hs_IL15_2.Rep1


title: Hs_ITCH_5.Rep1


title: Hs_HSPC182_4.Rep3

value: siRNA Hs_HSPC182_4


title: Hs_IFNA17_6.Rep1

value: senescent


title: Hs_HSPC182_4.Rep2


title: Hs_HSPC182_4.Rep1


title: Hs_IL15_3.Rep3


title: Hs_HSPC182_2.Rep3

value: siRNA Hs_HSPC182_2


title: Hs_GPRC5D_6.Rep2

value: siRNA Hs_GPRC5D_6


title: Hs_IFNA17_9.Rep1


title: Hs_GPRC5D_6.Rep1


title: Hs_GPRC5D_5.Rep3

value: siRNA Hs_GPRC5D_5


title: Hs_IL17RE_1.Rep1


title: Hs_GPRC5D_5.Rep2


title: Hs_HSPC182_2.Rep1


title: Hs_GPRC5D_6.Rep3


title: Hs_ERCC3_4.Rep3

value: siRNA Hs_ERCC3_4


title: Hs_ERCC3_4.Rep2


title: Hs_ERCC3_1.Rep1

value: siRNA Hs_ERCC3_1


title: Hs_ERCC3_4.Rep1


title: Hs_EMR4_2.Rep3

value: siRNA Hs_EMR4_2


title: Hs_EMR4_3.Rep2

value: siRNA Hs_EMR4_3


title: Hs_EMR4_3.Rep3


title: Hs_EMR4_2.Rep2


title: Hs_EMR4_3.Rep1


title: Hs_ERCC3_1.Rep3


title: Hs_HSPC182_2.Rep2


title: Hs_DUSP11_5.Rep3

value: siRNA Hs_DUSP11_5


title: Hs_DUSP11_5.Rep2


title: Hs_EMR4_2.Rep1


title: Hs_DUSP11_10.Rep3

value: siRNA Hs_DUSP11_10


title: Hs_DUSP11_10.Rep2


title: Hs_DCAMKL3_5.Rep3

value: siRNA Hs_DCAMKL3_5


title: Hs_DCAMKL3_6.Rep3

value: siRNA Hs_DCAMKL3_6


title: Hs_DCAMKL3_5.Rep2


title: Hs_CTDSPL_8.Rep3

value: siRNA Hs_CTDSPL_8


title: Hs_DCAMKL3_6.Rep1


title: Hs_DCAMKL3_6.Rep2


title: Hs_GPRC5D_5.Rep1


title: Hs_DUSP11_5.Rep1


title: Hs_ERCC3_1.Rep2


title: Hs_CTDSPL_2.Rep2

value: siRNA Hs_CTDSPL_2


title: Hs_CTDSPL_8.Rep1


title: Hs_CTDSPL_2.Rep1


title: Hs_CCL23_5.Rep2

value: siRNA Hs_CCL23_5


title: Hs_CCL23_5.Rep1


title: Hs_CCL23_5.Rep3


title: Hs_CCL23_2.Rep1

value: siRNA Hs_CCL23_2


title: Hs_C20orf18_5.Rep2

value: siRNA Hs_C20orf18_5


title: Hs_CCL23_2.Rep3

value: senescent


title: Hs_C20orf18_5.Rep3


title: Hs_C20orf18_1.Rep3

value: siRNA Hs_C20orf18_1


title: Hs_C20orf18_1.Rep1


title: Hs_C20orf18_1.Rep2


title: Hs_BRD8_3.Rep3

value: siRNA Hs_BRD8_3


title: Hs_C20orf18_5.Rep1


title: Hs_CCL23_2.Rep2


title: Hs_DCAMKL3_5.Rep1


title: Hs_CTDSPL_8.Rep2


title: Hs_CTDSPL_2.Rep3


title: Hs_BRD8_3.Rep2


title: Hs_BRD8_12.Rep2

value: siRNA Hs_BRD8_12


title: Hs_BRD8_12.Rep1


title: Hs_BPIL1_4.Rep2

value: siRNA Hs_BPIL1_4


title: Hs_BPIL1_2.Rep3

value: siRNA Hs_BPIL1_2


title: Hs_BPIL1_2.Rep2


title: Hs_BPIL1_4.Rep3


title: Hs_BPIL1_2.Rep1


title: Hs_BRD8_12.Rep3


title: Hs_ASB15_2.Rep3

value: siRNA Hs_ASB15_2


title: Hs_DUSP11_10.Rep1


title: Hs_ASB15_2.Rep2


title: Hs_ASB15_1.Rep1

value: siRNA Hs_ASB15_1


title: Hs_ASB15_2.Rep1


title: Hs_ASB15_1.Rep2


title: Hs_ALOX5_4.Rep3

value: siRNA Hs_ALOX5_4


title: Hs_ALOX5_4.Rep2


title: Hs_ALOX5_4.Rep1


title: Hs_ALOX5_2.Rep2

value: siRNA Hs_ALOX5_2


title: Hs_ALOX5_2.Rep3


title: Hs_AKR1C1_8.Rep2

value: siRNA Hs_AKR1C1_8


title: Hs_ALOX5_2.Rep1


title: Hs_AKR1C1_1.Rep3

value: siRNA Hs_AKR1C1_1


title: Hs_AKR1C1_8.Rep1


title: Hs_BPIL1_4.Rep1


title: Hs_AKR1C1_8.Rep3


title: Hs_BRD8_3.Rep1


title: Hs_AKR1C1_1.Rep2


title: Hs_AKR1C1_1.Rep1


title: Hs_ABCD4_1.Rep1

value: siRNA Hs_ABCD4_1


title: Hs_ABCD4_1.Rep3


title: Extras8.Rep2

value: scramble siRNA (AllStars 1)


title: Hs_ABCD4_2.Rep1

value: siRNA Hs_ABCD4_2


title: Extras8.Rep3


title: Extras8.Rep1


title: Extras7.Rep3

value: GFP siRNA


title: Extras7.Rep2


title: Extras7.Rep1


title: Extras6.Rep3

value: scramble siRNA (AllStars Negative Control)


title: Extras6.Rep2

value: senescent


title: Extras6.Rep1


title: Extras4.Rep3

value: proliferating


title: Extras4.Rep2


title: Extras5.Rep1

value: mock-transfected


title: Extras5.Rep3


title: Extras4.Rep1


title: Hs_ABCD4_2.Rep2


title: Extras3.Rep3


title: Extras2.Rep2


title: Hs_ABCD4_2.Rep3


title: Extras3.Rep1


title: Hs_ASB15_1.Rep3


title: Extras2.Rep1


title: Extras1.Rep3


title: Hs_ABCD4_1.Rep2


title: Extras1.Rep2


title: Extras1.Rep1


title: CEBPb.Rep1

value: siRNA Hs_CEBPB_5


title: Allstars.Rep3


title: Allstars.Rep2


title: Allstars.Rep1


title: CEBPb.Rep2


title: si_PTBP1_5 + 4OHT Replicate 3

extract_protocol:
Cells were scraped and homogenised in TRIzol® RNA isolation reagent, mixed with Chloroform in a 5:1 ratio, centrifuged at 15,000 rpm for 30 min and after successful phase separation, the top clear RNA-containing phase was purified using the RNAeasy® Mini Kit (Qiagen)
Libraries were prepared according to Illumina's kit instructions (mRNA stranded library prep kit)

tag: transfection

value: siRNA targeting PTBP1


title: si_EXOC7_4 + 4OHT Replicate 3

value: different siRNA targeting EXOC7


title: si_EXOC7_3 + 4OHT Replicate 3

value: siRNA targeting EXOC7


title: Extras2.Rep3


title: Extras3.Rep2


title: si_PTBP1_5 + 4OHT Replicate 2


title: si_EXOC7_3 + 4OHT Replicate 2


title: si_Scramble + 4OHT Replicate 2

value: scramble siRNA


title: si_Scramble Replicate 3


title: si_PTBP1_5 + 4OHT Replicate 1


title: si_EXOC7_4 + 4OHT Replicate 2


title: si_EXOC7_4 + 4OHT Replicate 1


title: si_EXOC7_3 + 4OHT Replicate 1


title: si_Scramble Replicate 1


title: CEBPb.Rep3


title: si_Scramble + 4OHT Replicate 3


title: shPTBP1_53 + 4OHT Replicate 3

growth_protocol: IMR90 ER:RAS cells were grown in DMEM, 10% FBS, for 6 days and media change was performed at day 3

tag: transduction

value: pGIPZ-based shRNA targeting PTBP1


title: si_Scramble + 4OHT Replicate 1


title: shPTBP1_86 + 4OHT Replicate 3

value: different pGIPZ-based shRNA targeting PTBP1


title: Vector Replicate 3

value: empty pGIPz vector


title: shPTBP1_53 + 4OHT Replicate 2


title: shPTBP1_86 + 4OHT Replicate 2


title: Vector + 4OHT Replicate 2


title: shPTBP1_86 + 4OHT Replicate 1


title: shPTBP1_53 + 4OHT Replicate 1


title: Vector Replicate 1


title: Vector + 4OHT Replicate 3


title: si_Scramble Replicate 2


title: Zeb2-cKO-3

city: Cincinnati

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then filtered low quality reads by NGSQC
Filtered reads were mapped to mm10 whole genome using Tophat using default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression matrix file

extract_protocol:
Cerebellum were collected, flash frozen on dry ice, and total RNA was extracted using Trizol reagent
Libraries were prepared according to Illumina's instructions accompanying Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)

tag: age

value: Postnatal day 0

tag: geneotype

value: Zeb2 f/f; hGFAP-cre


title: Vector Replicate 2


title: ChIP_mouseMA9_PU1_control

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 (v2.2.2) with default parameters.
To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads

source_name: MA9-transformed mouse leukemia

extract_protocol: ChIP-seq libraries were constructed with the NEBNext ChIP-seq library prep kit following the manufacturer’s recommended protocol (New England Biolabs, Ipswich, MA, USA).

value: bone marrow

tag: cell markers

value: MLL-AF9 fusion

tag: chip antibody

value: anti-PU.1 (Santa Cruz, sc-352)

tag: treatment


title: Vector + 4OHT Replicate 1


title: ATACseq_mouseMA9_CebpaWT_control

tag: cell type

value: MLL-AF9 fusion; Cebpa WT


title: Control 3

value: Zeb2 f/+; hGFAP-cre


title: ATACseq_mouseMA9_CebpaKO_LSD1i

value: MLL-AF9 fusion; Cebpa KO

value: LSD1 inhibitor


title: ATACseq_mouseMA9_CebpaKO_control


title: ChIP_mouseMA9_PU1_LSD1i


title: Extras5.Rep2

value: senescent

value: mock-transfected


title: Zeb2-cKO-2

value: cerebellum


title: Control 1


title: Zeb2-cKO-1


title: TET_E2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
Raw sequence reads had the first 6 base pairs clipped off the 5' end to remove 6N random priming portion of the reads, and were also trimmed to remove both poor quality calls and adapters using Trim Galore (v0.4.1, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, parameters: --clip_r1 6, Cutadapt v1.8.1). Remaining sequences were then aligned to the mouse genome (build GRCm38) with Bismark (v0.14.5) in single-end mode (parameters: --non_directional). Methylation calls were extracted after duplicate sequences had been excluded.
Genome_build: GRCm38
Supplementary_files_format_and_content: The genome-wide CpG methylation report is tab-delimited, uses 1-based genomic coordinates and is in the following format: <chromosome>  <position>  <strand>  <count methylated>  <count non-methylated>  <C-context>  <trinucleotide context>

source_name: mouse embryonic stem cell

extract_protocol:
Cells were sorted into 2.5ul RLT plus lysis buffer (QIAGEN) containing SUPERase-In (Ambion).
scBS-seq libraries were prepared as previously described (Smallwood et al., Nature Methods 11, 817-820) but with the following modifications: bisulfite conversion was carried out using Imprint reagent (Sigma, MOD50), with desulphonation and purification using magnetic beads, following the manufacturers’ instructions but with half volumes. Primers for first and second strand synthesis contained a 3’ random hexamer instead of a nonamer and biotin capture of first strand synthesis products was omitted, substituting an extra AMPure XP (Beckman Coulter, A63881) purification between second strand synthesis and PCR amplification. In order to avoid potential batch effects which could mask subtle differences between samples all libraries were prepared in parallel with the pre-PCR purification steps carried out using a Bravo Workstation pipetting robot (Agilent Technologies).

tag: cell line

value: E14 embryonic stem cell

value: C57BL/6 wild-type


title: TET_F1


title: TET_F2

value: NanogGFP (TNGA) embryonic stem cell


title: Control 2


title: ChIP_mouseMA9_LSD1

value: anti-LSD1 (Abcam, ab17721)


title: ATACseq_mouseMA9_LSD1control


title: ChIP_mouseMA9_input


title: ChIP_mouseMA9_Cebpa_LSD1i

value: anti-Cebpa (Santa Cruz, sc-61)


title: ATACseq_mouseMA9_PU1UREKO_control

value: MLL-AF9 fusion; PU.1 URE KO


title: ATACseq_mouseMA9_PU1WT_control

value: MLL-AF9 fusion; PU.1 URE WT


title: ATACseq_mouseMA9_DOT1Lcontrol

value: bone marrow


title: ATACseq_mouseMA9_PU1UREKO_LSD1i


title: ATACseq_mouseMA9_PU1WT_LSD1i


title: ATACseq_mouseMA9_CebpaWT_LSD1i


title: ATACseq_mouseMA9_LSD1i

value: MLL-AF9 fusion


title: ATACseq_mouseMA9_DOT1Li

value: DOT1L inhibitor


title: ChIP_mouseMA9_Cebpa_control


title: TET_E1


title: TET_C3


title: TET_B3


title: TET_D2


title: TET_C2


title: TET_A3


title: TET_A2


title: TET_B2


title: TDG_F4


title: TDG_F5


title: TDG_H5


title: TDG_H4


title: TDG_E5


title: TDG_G4


title: TDG_D5


title: Cytosolic TNFα

city: Rehovot

first: Rivka

last: Dikstein

address: 2 Hertzl st.

country: Israel

institute: The Weizmann Institute of Science

data_processing:
Demultiplexing and base calling was done with CASAVA 1.8.2 (RTA 1.17.21.3).
Reads were aligned to the hg19 genome built using Tophat (v2.0.04) with an annotation file (refSeq from igenomes UCSC).
Raw gene read counts were calculated by HTSeq using refSeq gene annotations (igenomes).
Normalized gene counts were calculated with DESeq. Chromatin and cytosol samples were analysed separately.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file containing gene counts

source_name: HeLa_Cytosolic TNFα

growth_protocol: Hela cells were grown using standard growth conditions

extract_protocol:
Cells were separated into cytosol and chromatin fractions which were then subjected to RNA extraction and DNAseI tretment
Cytosolic and chromatin associated RNA samples were depleted of ribosomal RNA using Ribozero gold rRNA depletion kit (Epicentre). RNA was processed using the TruSeq RNA Sample Preparation Kit v2 protocol (Illumina)without poly A capturing. Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing of 4 samples on one lane. Paired-end 101 bp reads were sequenced on Illumina HiSeq 2500 rapid mode with cBot on HiSeq Rapid Flow Cell v1 HCS: 2.0.12.0.

treatment_protocol: HeLa cells were transfected with control Spt5 RNAi plasmids along with a plasmid direcing puromycin resistant gene. Transfected cells were selected with puromycin. 72 hours post transfection cell were trearted with TNFα for one hour.

value: HeLa

tag: genotype/variation

value: wild type (control)

tag: treated with

value: TNFα for 1 hr

tag: molecule subtype

value: cytoplasmic RNA


title: TDG_H6


title: TDG_C6


title: Chromatin TNFα

source_name: HeLa_Chromatin TNFα

value: Chromatin RNA


title: Cytosolic Spt5 KD TNFα

source_name: HeLa_Cytosolic Spt5 KD TNFα

value: Spt5 KD


title: Chromatin control

source_name: HeLa_Chromatin control


title: Cytosolic control

source_name: HeLa_Cytosolic control


title: Cytosolic Spt5 KD control

source_name: HeLa_Cytosolic Spt5 KD control


title: TDG_B6


title: TDG_C5


title: TDG_B5


title: EB_d3_F10


title: TDG_A6


title: EB_d3_F9


title: EB_d3_F12


title: TDG_A5


title: EB_d3_E9


title: EB_d3_F11


title: Chromatin Spt5 KD control

source_name: HeLa_Chromatin Spt5 KD control


title: Chromatin Spt5 KD TNFα

source_name: HeLa_Chromatin Spt5 KD TNFα


title: EB_d3_E5


title: EB_d3_E7


title: EB_d3_E10


title: EB_d3_F7


title: TDG_E4


title: EB_d3_D7


title: EB_d3_D8


title: TDG_G5


title: TET_H3


title: EB_d3_E12


title: TET_H2


title: TET_G2


title: EB_d1_F6


title: EB_d3_C12


title: EB_d3_D6


title: EB_d3_B7


title: EB_d1_F7


title: EB_d3_B9


title: EB_d3_C10


title: EB_d3_B10


title: EB_d3_D10


title: EB_d3_B8


title: EB_d1_F11


title: EB_d3_C5


title: EB_d1_F10


title: EB_d1_F8


title: EB_d3_B5


title: EB_d3_D5


title: EB_d1_E7


title: EB_d3_B6


title: EB_d1_D9


title: TET_G1


title: EB_d1_E12


title: EB_d1_D7


title: EB_d1_D12


title: EB_d1_E11


title: EB_d1_D10


title: EB_d1_C9


title: EB_d1_D11


title: TET_H1


title: EB_d1_C8


title: EB_d1_C7


title: EB_d1_B7


title: EB_d1_C10


title: DNMT_E7


title: DNMT_G8


title: DNMT_D7


title: EB_d1_B12


title: EB_d1_C5


title: DNMT_D8


title: DNMT_C7


title: DNMT_C8


title: EB_d1_B8


title: DNMT_H8


title: DNMT_H7


title: DNMT_F7


title: DNMT_F8


title: EB_d1_C6


title: DNMT_B8


title: EB_d1_B10


title: DNMT_A7


title: DNMT_B7


title: 2i_07hr30c

description: PBAT Bilsulfite-seq

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
Raw sequence reads were trimmed to remove both poor quality calls and adapters using Trim Galore (v0.4.1, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Cutadapt version 1.8.1, parameters: --paired). Trimmed reads were first aligned to the mouse genome in paired-end mode to be able to use overlapping parts of the reads only once while writing out unmapped singleton reads; in a second step remaining singleton reads were aligned in single-end mode. Alignments were carried out with Bismark v0.14.4 (Krueger and Andrews, 2011) with the following set of parameters: a) paired-end mode: --pbat; b) single-end mode for Read 1: --pbat; c) single-end mode for Read 2: defaults. Reads were then deduplicated with deduplicate_bismark selecting a random alignment for position that were covered more than once.
2i_release: CpG methylation calls were extracted from the deduplicated mapping output ignoring the first 6bp of each read to reduce the methylation bias typically observed in PBAT libraries using the Bismark methylation extractor (v0.14.4) with the following parameters: a) paired-end mode: --ignore 6 --ignore_r2 6; b) single-end mode: --ignore 6.
genome build: GRCm38
processed data files format and content: The genome-wide CpG methylation report is tab-delimited, uses 1-based genomic coordinates and is in the following format: <chromosome>  <position>  <strand>  <count methylated>  <count non-methylated>  <C-context>  <trinucleotide context>

growth_protocol: ESCs were cultured in serum/LIF or 2i conditions as described previously (Ficz et al., Cell Stem Cell 13, 351–359)

extract_protocol:
2i_release: Cells were lysed by RLT plus lysis buffer (Qiagen) containing 0.5mM 2-mercaptoethanol. Total nucleic acid was purified from the lysate with RNAdvance magnetic beads (Beckman Coulter, A32649) using a Bravo Workstation pipetting robot (Agilent Technologies).
BS-seq libraries were prepared from total nucleic acid using the bulk-cell method previously described (Smallwood et al., Nature Methods 11, 817-820) but with the following modifications: bisulfite conversion was carried out using the EZ Methylation Direct MagPrep kit (Zymo, D5044), with desulphonation and purification using magnetic beads, following the manufacturers’ instructions but with half volumes. Primers for first and second strand synthesis contained a 3’ random hexamer instead of a nonamer and biotin capture of first strand synthesis products was omitted, substituting an extra AMPure XP (Beckman Coulter, A63881) purification between second strand synthesis and PCR amplification. In order to avoid potential batch effects which could mask subtle differences between samples all libraries were prepared in parallel with the pre-PCR purification steps carried out using a Bravo Workstation pipetting robot (Agilent Technologies).


title: DNMT_E8


title: EB_d1_B11


title: 2i_07hr30a

description: PBAT Bilsulfite-seq


title: DNMT_A8


title: DNMT_G7


title: 2i_08hr30b

description: PBAT Bilsulfite-seq


title: 2i_08hr30c

description: PBAT Bilsulfite-seq


title: 2i_08hr30a

description: PBAT Bilsulfite-seq


title: 2i_06hr30c

description: PBAT Bilsulfite-seq


title: 2i_06hr30a

description: PBAT Bilsulfite-seq


title: 2i_06hr30b

description: PBAT Bilsulfite-seq


title: 2i_07hr30b

description: PBAT Bilsulfite-seq


title: 2i_04hr45a

description: PBAT Bilsulfite-seq


title: 2i_03hr30b

description: PBAT Bilsulfite-seq


title: 2i_05hr30a

description: PBAT Bilsulfite-seq


title: 2i_02hr00a

description: PBAT Bilsulfite-seq


title: 2i_05hr30c

description: PBAT Bilsulfite-seq


title: 2i_04hr00b

description: PBAT Bilsulfite-seq


title: 2i_02hr00b

description: PBAT Bilsulfite-seq


title: 2i_04hr45c

description: PBAT Bilsulfite-seq


title: 2i_01hr30c

description: PBAT Bilsulfite-seq


title: 2i_02hr30b

description: PBAT Bilsulfite-seq


title: 2i_03hr00a

description: PBAT Bilsulfite-seq


title: 2i_03hr00c

description: PBAT Bilsulfite-seq


title: 2i_04hr00c

description: PBAT Bilsulfite-seq


title: 2i_04hr45b

description: PBAT Bilsulfite-seq


title: 2i_04hr00a

description: PBAT Bilsulfite-seq


title: 2i_03hr00b

description: PBAT Bilsulfite-seq


title: 2i_02hr30a

description: PBAT Bilsulfite-seq


title: 2i_02hr30c

description: PBAT Bilsulfite-seq


title: 2i_03hr30c

description: PBAT Bilsulfite-seq


title: 2i_03hr30a

description: PBAT Bilsulfite-seq


title: 2i_05hr30b

description: PBAT Bilsulfite-seq


title: 2i_01hr30a

description: PBAT Bilsulfite-seq


title: 2i_01hr30b

description: PBAT Bilsulfite-seq


title: 2i_01hr00b

description: PBAT Bilsulfite-seq


title: 2i_01hr00c

description: PBAT Bilsulfite-seq


title: 2i_02hr00c

description: PBAT Bilsulfite-seq


title: 2i_00hr45c

description: PBAT Bilsulfite-seq


title: 2i_00hr45b

description: PBAT Bilsulfite-seq


title: 2i_00hr45a

description: PBAT Bilsulfite-seq


title: 2i_00hr00c

description: PBAT Bilsulfite-seq


title: RNA pool

tag: sample type

value: a pool of 16 different environmental conditions


title: 2i_01hr00a

description: PBAT Bilsulfite-seq

value: E14 embryonic stem cell


title: 2i_00hr00b

description: PBAT Bilsulfite-seq

value: C57BL/6 wild-type


title: 2i_00hr00a

description: PBAT Bilsulfite-seq


title: ASO_NC

status: Public on Jun 23 2018

city: Guangzhou

first: Lin

last: Gao

state: Guangdong province

address: No. 1023, South Shatai Road

department: School of Public Health

country: China

institute: Southern Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for poly-N or low-quality sequence.Reference genome and gene model annotation files were downloaded from genome website  (human assembly GRCh37/hg19 ) directly. Index of the reference genome was built using Bowtie v2.0.6 and  paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Genome_build: human assembly GRCh37/hg19
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: skin/epidermis

growth_protocol: A431 cells were cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum  and maintained at 37℃ with 5% CO2 in a humidified atmosphere.

extract_protocol:
Culture medium were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
1 μg of total RNA was subjected to library synthesis for sequencing using standard Illumina protocols

value: cutaneous squamous cell carcinoma cells (CSCC)

tag: source subject age

value: 85 years

value: negative control


title: M1_ASO_2

value: siRNA-induced gene knockdown of MALAT1


title: HEK Cell H4

status: Public on Jun 22 2018

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

institute: Ludwig-Maximilians University Munich

data_processing:
Fastq reads were processed with the zUMIs pipeline
cDNA reads were aligned to the Human Genome (hg38) with STAR 2.5.3
Quantification was done with ENSEMBL gene models (GRCh38.84)
Genome_build: hg38
Supplementary_files_format_and_content: cell (columns) and gene (rows) -wise UMI expression table

source_name: cell culture

extract_protocol:
Cells were FACS sorted into lysis buffer (1/500 Phusion HF reaction buffer)
Libraries were constructed according to the SCRB-seq protocol described in Ziegenhain et al., 2017


title: HEK Cell H12


title: HEK Cell G5


title: HEK Cell G10


title: HEK Cell H9


title: HEK Cell H8


title: HEK Cell H10


title: HEK Cell G6


title: HEK Cell H3


title: HEK Cell H5


title: HEK Cell G8


title: HEK Cell G3


title: HEK Cell H1


title: HEK Cell G9


title: HEK Cell G7


title: HEK Cell H11


title: HEK Cell G4


title: HEK Cell H2


title: HEK Cell G12


title: HEK Cell H7


title: HEK Cell G11


title: TEX_RNA_pool

source_name: RNA from bacteria

tag: strain


title: HEK Cell H6


title: HEK Cell G2


title: HEK Cell G1


title: HEK Cell F11


title: HEK Cell F9


title: HEK Cell F12


title: HEK Cell F7


title: HEK Cell F4


title: HEK Cell F10


title: HEK Cell F5


title: HEK Cell F6


title: HEK Cell E11


title: HEK Cell E9


title: HEK Cell E8


title: HEK Cell F1


title: HEK Cell E4


title: HEK Cell E2


title: HEK Cell E3


title: HEK Cell E1


title: HEK Cell E12


title: HEK Cell E10


title: HEK Cell F3


title: HEK Cell E7


title: HEK Cell D12


title: HEK Cell F8


title: HEK Cell E6


title: HEK Cell D11


title: Lean+Oligofructose (S39_R1)

city: Memphis

first: Jacquelyn

middle: A

last: Myers

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children’s Research Hospital

data_processing:
Raw reads were cleaned using Trimmomatic-0.32 with the following parameters: SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15
Reads were aligned to mm10 using STAR_2.4.2a and the following parameters: --twopassMode Basic --runMode alignReads --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read couts were generated using htseq-count v0.6.1 using the following parameters: -q -f bam -s no -r pos -i gene_name
Differential expression was performed using R3.3.0 and the DESeq2.1.12.3 package using default methods. The obese+oligofructose and obese+cellulose data were library size normalized together, independent of the additional samples.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: Raw count data are provided for each sample as individual .txt files.

molecule: polyA RNA

source_name: Lean+Oligofructose

extract_protocol: TruSeq stranded mRNA

treatment_protocol: At 5 weeks of age, mice were provided ad lib access to either a low-fat diet (Lean, 10% kcal from fat, Open Source Diets #D12450B) or high-fat diet (Obese, 60% kcal from fat, Open Source Diets #D12492).  At 17 weeks of age, mice were then offered ad lib access to Lean or Obese diet supplemented with either a control fiber (Cellulose, 10%w/w, JRS Pharma VIVAPURÒ) or prebiotic (Oligofructose, 10%w/w, Beneo-Orafti, Orafti P95)

tag: disease state

value: Lean

value: Oligofructose

tag: tissue

value: colon


title: Obese+Oligofructose (S45_R1)

source_name: Obese+Oligofructose

value: Obese


title: Obese+Oligofructose (S46_R1)


title: Obese+Oligofructose (S47_R1)


title: HEK Cell D10


title: HEK Cell E5


title: Lean+Oligofructose (S38_R1)


title: HEK Cell F2


title: HEK Cell D9


title: HEK Cell D8


title: HEK Cell D7


title: HEK Cell D5


title: HEK Cell D3


title: HEK Cell D4


title: Lean+Oligofructose (S37_R1)


title: Lean+Cellulose (S34_R1)

source_name: Lean+Cellulose

value: Cellulose


title: Lean+Cellulose (S35_R1)


title: HEK Cell D2


title: HEK Cell D1


title: Obese+Cellulose (S43_R1)

source_name: Obese+Cellulose


title: HEK Cell C12


title: HEK Cell D6


title: Obese+Cellulose (S41_R1)


title: HEK Cell C10


title: HEK Cell C11


title: HEK Cell C9


title: Lean+Cellulose (S33_R1)


title: Lean+Oligofructose (2051_d_colon_R_R1)


title: Obese+Cellulose (2061_d_colon_R1)


title: Lean+Cellulose (2041_d_colon_R1)


title: HEK Cell C6


title: HEK Cell C7


title: HEK Cell C8


title: HEK Cell C5


title: Obese+Cellulose (S42_R1)


title: Obese+Oligofructose (2071_d_colon_R1)


title: HEK Cell C4


title: 54411_Double_3

city: Ann Arbor

first: Qing

last: Li

state: Michigan

address: 109 Zina Pitcher Place, BSRB 1520

department: Internal Medicine

institute: University of Michigan

description: Total RNA after the removal of ribosomal RNA and mitochondrial RNA

data_processing:
Reads were created by CASAVA 1.8.2 from the HiSeq 2500, and these are all reads which pass filter.
Reads were filtered from the adapter sequences and were aligned to mm10 whole genome using TopHat2 (Ref 56) (Kim D et al, Genome Biol 2013;14:R36).
Gene annotation files inclue RefSeq (NCBI). Normalization of gene expression was done using EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes gene name and log2RPKM values for each sample. Sample ID and genotype are indicated in the name of each raw file.

source_name: SLAM hematopoietic stem cell (CD150+CD48-Lin-Sca1+cKit+)

extract_protocol:
SLAM-HSCs were FACS-sorted into TRIzol (Ambion). Total RNA was isolated using the AllPrep DNA/RNA kit from Qiagen (Valencia, CA) according to manufacturer’s instructions. Ribosomal RNA (rRNA) and mitochondrial RNA (mtRNA) was removed using the RiboGone-Mammalian kit (Takara 634847) according to manufacturer's instructions.
RNA-seq libraries were prepared using the SMARTer Stranded RNA-seq Kits (Takara 634837) according to the manufacturer's instructions.

value: Bone marrow

value: SLAM HSC

value: Postnatal week 10-12

tag: genotype


title: 54409_Tet2_3


title: 54410_Nras_3


title: HEK Cell C3


title: HEK Cell C2


title: HEK Cell C1


title: 54408_WT_3

value: wild type


title: HEK Cell B11


title: 54407_Double_2


title: 54406_Nras_2


title: HEK Cell B8


title: 54405_Tet2_2


title: HEK Cell B9


title: HEK Cell B7


title: 54403_Double_1


title: HEK Cell B5


title: HEK Cell B2


title: HEK Cell B1


title: 54401_Tet2_1


title: HEK Cell B10


title: 54402_Nras_1


title: HEK Cell B4


title: 54404_WT_2


title: HEK Cell B12


title: 54400_WT_1


title: HEK Cell B6


title: HEK Cell A12


title: HEK Cell B3


title: HEK Cell A9


title: HEK Cell A7


title: HEK Cell A8


title: HEK Cell A6


title: HEK Cell A10


title: HEK Cell A3


title: HEK Cell A11


title: HEK Cell A2


title: HEK Cell A1


title: TALE MO zebrafish 12hpf biological replicate2

city: Worcester

first: Franck

last: Ladam

state: Massachusetts

address: 364 plantation street , LRB 870D

department: Biochemistry and Molecular Pharmacology

institute: University of Massachusetts Medical School

description: Prep1 and Pbx2/4 morpholino injected (TALE MO) 12hpf zebrafish embryos, biological replicate 2

data_processing:
reads quality check with FastQC
alignment and read counts with RSEM_v1.2.28
Normalized abundance measurements and identification of differentially expressed genes with DESeq2
Genome_build: GRCz10/DanRer10 sept2014
Supplementary_files_format_and_content: .tsv containing read count tpm values from RSEM for each biological replicate and experimental condtion

organism: Danio rerio

source_name: total 12hpf zebrafish embryo

growth_protocol: zebrafish egg water maintained at 28°C

extract_protocol:
Total RNA extraction using the RNeasy kit (Qiagen) with on column DNAse treatment.
3ug of total RNA was used to construct RNA-seq libraries with the Illumina Truseq stranded mRNA library kit after PolyA+ RNA enrichment

treatment_protocol: Injection of

value: total 12hpf zebrafish embryo

value: Ekwill

tag: developmental stage

value: 12 hours post-fertilization (segmentation)


title: Control zebrafish 12hpf biological replicate2

description: control 12hpf zebrafish embryos, biological replicate 2


title: Control zebrafish 12hpf biological replicate3

description: control 12hpf zebrafish embryos, biological replicate 3


title: HEK Cell A4


title: Control zebrafish 6hpf biological replicate3

description: control 6hpf zebrafish embryos, biological replicate 3

source_name: total 6hpf zebrafish embryo

value: total 6hpf zebrafish embryo

value: 6 hours post-fertilization (gastrulation)


title: TALE MO zebrafish 6hpf biological replicate1

description: Prep1 and Pbx2/4 morpholino injected (TALE MO) 6hpf zebrafish embryos, biological replicate 1


title: TALE MO zebrafish 12hpf biological replicate3

description: Prep1 and Pbx2/4 morpholino injected (TALE MO) 12hpf zebrafish embryos, biological replicate 3


title: TALE MO zebrafish 6hpf biological replicate3

description: Prep1 and Pbx2/4 morpholino injected (TALE MO) 6hpf zebrafish embryos, biological replicate 3


title: Control zebrafish 6hpf biological replicate2

description: control 6hpf zebrafish embryos, biological replicate 2


title: WT AGO1-IP Rep1

city: Zürich

first: Alexis

last: Sarazin

address: Universitätstrasse 2

country: Switzerland

institute: ETH

data_processing:
Basecalling pipeline: HiSeq Control Software 2.2.58; RTA 1.18.64.0; CASAVA-1.8.2
FASTQ file generation and demultiplexing and adapter removal was done by Fasteris.
For each sample, fastq files from the 2 independant lanes were merged and small RNA reads were filtered to 18-35nt long reads for analysis. Reads with identical sequence were grouped using the processReads function from the ncPRO-seq pipeline and aligned against A.thaliana’s genome (TAIR10) using bowtie2.
Genome_build: TAIR10
Supplementary_files_format_and_content: For each sample, tab-delimited text files including distinct sequences and reads count values.

organism: Arabidopsis thaliana

source_name: seedlings, total RNA

growth_protocol: Plants were grown for 2 weeks on MS-agar plates 16h light/8h dark photoperiod (22°C/20°C).

extract_protocol:
Total-RNA samples were extracted from 2-week-old seedlings grown on MS-agar plates using TRI-reagent according to the manufacturer’s instruction. For AGO1-loaded small RNA samples, IP were performed from 300 mg of 2-week-old seedlings grown on MS-agar plates. AGO1-loaded small RNA were then extracted by adding TRI-reagent directly on the magnetic beads and extraction of RNA was then performed according to the manufacturer’s instruction.
Extracted RNA was processed into sequencing libraries using adapted Illumina protocols and sequenced at Fasteris (http://www.fasteris.com, Switzerland) using the Illumina HiSeq 2500 sequencer

tag: strain and genotype

value: Columbia-0 wild type

value: seedlings

tag: development stage


title: WT AGO1-IP Rep2


title: ago1-57 total Rep2

source_name: seedlings, Immunoprecipitated RNA

value: Columbia-0 AGO1sup19 mutant


title: ago1-57 AGO1-IP Rep1


title: ago1-57 AGO1-IP Rep2


title: ago1-57 total Rep1


title: Control zebrafish 6hpf biological replicate1

description: control 6hpf zebrafish embryos, biological replicate 1


title: HEK Cell A5


title: WT total Rep2


title: WT total Rep1


title: CS_ML3

city: Qingdao

last: Wang

state: Shandong

address: 106 Nanjing Road

institute: Yellow Sea Fisheries Research Institute, Chinese Academy Fishery Science

description: CS_ML RNA-seq

data_processing:
After filtering raw reads containing adapters, reads with more than 10% of unknown nucleotides and low quality reads, reads containing more than 50% of low quality bases (Q-value < 20), the datas were aligned with Bowtie2 and mapped to Cynolossus semilaevis genome via TopHat2 (version 2.0.3.12) for rRNA removal and gene annotation.
Then, transcript assemblies were conducted with Cuffinks and the reference annotation based transcripts (RABT) program to obtain a comprehensive set of transcripts.
To identify novel transcripts, the assembled transcripts were aligned to C. semilaevis genome and were divided into twelve categories using Cuffcompare. Genes with classcode “u”, lengths ≥ 200 bp, and exon numbers ≥ 2 were defined as novel genes, and were further annotated via alignment with the Nr and KEGG database.
Genome_build: Cynoglossus semilaevis genome  (assembly Cse_v1.0) https://www.ncbi.nlm.nih.gov/assembly/GCF_000523025.1/
Supplementary_files_format_and_content: Text file with FPKM and raw counts of genes for Cynoglossus semilaevis 24 libraries. A FASTA file with the novel transcript sequences is available on the series record.

organism: Cynoglossus semilaevis

source_name: the liver of male Cynoglossus semilaevis

extract_protocol:
To increase biological repeatability, every five tissues from males or females were firstly mixed as one sample, and three samples for each tissue were used for the following experiment. Thus, 24 samples named CSE_MB1-3, CSE_MP1-3, CSE_MG1-3, CSE_ML1-3, CSE_FB1-3, CSE_FP1-3, CSE_FG1-3, and CSE_FL1-3 were acquired and their total RNA was extracted via Trizol reagent (Invitrogen, USA) and measured with the Agilent 2100 RNA 6000 Nano kit (Agilent, USA) for quality control. Twenty-four cDNA libraries were constructed using 3 μg RNA (RIN > 7.0) from each sample by the conventional protocol, and the subsequent sequencing was carried with an Illumina HiseqTM 4000 by the Gene Denovo Biotechonolgy Co. (Guangzhou, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: age

value: two-year-old

tag: genetic sex

value: male


title: Control zebrafish 12hpf biological replicate1

description: control 12hpf zebrafish embryos, biological replicate 1


title: TALE MO zebrafish 6hpf biological replicate2

description: Prep1 and Pbx2/4 morpholino injected (TALE MO) 6hpf zebrafish embryos, biological replicate 2


title: CS_MB3

description: CS_MB RNA-seq

source_name: the brain of male Cynoglossus semilaevis

value: brain


title: CS_MG3

description: CS_MG RNA-seq

source_name: the gonad of male Cynoglossus semilaevis

value: gonad


title: CS_ML1

description: CS_ML RNA-seq


title: CS_MG1

description: CS_MG RNA-seq


title: CS_MB2

description: CS_MB RNA-seq


title: CS_ML2

description: CS_ML RNA-seq


title: CS_MP1

description: CS_MP RNA-seq

source_name: the pituitary of male Cynoglossus semilaevis

value: pituitary


title: CS_MB1

description: CS_MB RNA-seq


title: CS_MP2

description: CS_MP RNA-seq


title: CS_MP3

description: CS_MP RNA-seq


title: CS_FB1

description: CS_FB RNA-seq

source_name: the brain of female Cynoglossus semilaevis

value: female


title: CS_FL1

description: CS_FL RNA-seq

source_name: the liver of female Cynoglossus semilaevis


title: CS_FP3

description: CS_FP RNA-seq

source_name: the pituitary of female Cynoglossus semilaevis


title: CS_FG1

description: CS_FG RNA-seq

source_name: the gonad of female Cynoglossus semilaevis


title: CS_FL3

description: CS_FL RNA-seq


title: CS_FG2

description: CS_FG RNA-seq


title: CS_MG2

description: CS_MG RNA-seq


title: CS_FL2

description: CS_FL RNA-seq


title: CS_FB3

description: CS_FB RNA-seq


title: CS_FB2

description: CS_FB RNA-seq


title: CS_FP2

description: CS_FP RNA-seq


title: ViCHC198 treatment PRO_2_1

status: Public on Jun 21 2018

city: Barcelona

first: Guillaume

last: Filion

address: Dr. Aiguader 88

department: GRSCC

country: Spain

institute: CRG

description:
Immortalized human T lymphocyte Jurkat cell line
index: GCTA

data_processing:
Library strategy: B-HIVE
Sequences were manually demultiplexed with custom scripts. The used indices are specified in the last rows (index X) of the Sample section.
The barcode sequences in the construct are flanked by the Illumina adaptor and the T7 promoter sequence (TATAGTGAGTCGTATTAAAA). The promoter sequence was identified using Seeq (http://github.com/ezorita/seeq) allowing up to 2 mismatches.
Barcodes were clustered by sequence similarity using starcode and allowing up to 1 mismatch (http://github.com/gui11aume/starcode).
Genome_build: none
Supplementary_files_format_and_content: text file with barcode mRNA counts upon drug treatment

source_name: ViCHC198/GFP- PRO treatment

growth_protocol: Jurkat human T cells with latent HIV infections were grown in RPMI 1640 medium (gibco) supplemented with 10% fetal bovine serum (gibco), 1% Pen Strep (gibco) and 1% GlutaMAX (100x) (gibco) at 37℃ under a 95% air/5% CO2 atmosphere. Cells were split every 2 days with 1 to 5 dilution.

extract_protocol:
Total RNA from each infected cell pool treated by an indicated drug was extracted by the AllPrep DNA/RNA Mini Kit (Qiagen). Total RNA was further proceeded to purify mRNA by the Oligotex mRNA Mini Kit (Qiagen) to perform RT-PCR .
10 µL mRNA was reverse transcribed (ThermoScript RT-PCR System; Invitrogen, 11145-024) with the primer annealing downstream of the T7 promoter incorporated in the genome of HIV. PCR (Phusion polymerase reaction mix; Thermo Fisher Scientific, F530S) was performed with the primers annealing on the Illumina PE1.0 sequence and the T7 promoter in order to measure individual HIV expression. RNA libraries were pooled in the final concentration of 4 nM and sequenced 50 bp single read by the HiSeq2000.

treatment_protocol: Samples were treated indicated drugs for 24 hours before the extract protocol.

value: Jurkat

value: T lymphocyte

tag: duration of drug treatment (h)

tag: drug treatment

value: PRO


title: ViCHC198 treatment PRO_1_2

description:
Immortalized human T lymphocyte Jurkat cell line
index: TCAG

tag: cell line

tag: cell type


title: ViCHC198 treatment PRO_1_1

description:
Immortalized human T lymphocyte Jurkat cell line
index: GACT


title: ViCHC198 treatment PRO_2_2

description:
Immortalized human T lymphocyte Jurkat cell line
index: TCGA


title: ViCHC198 treatment SAHA_2_2

description:
Immortalized human T lymphocyte Jurkat cell line
index: GATC

source_name: ViCHC198/GFP- SAHA treatment

value: SAHA


title: ViCHC198 treatment SAHA_2_1

description:
Immortalized human T lymphocyte Jurkat cell line
index: CTAG


title: CS_FG3

description: CS_FG RNA-seq


title: CS_FP1

description: CS_FP RNA-seq


title: ViCHC198 treatment SAHA_1_2

description:
Immortalized human T lymphocyte Jurkat cell line
index: CGTA


title: ViCHC198 treatment TQ_2_2

description:
Immortalized human T lymphocyte Jurkat cell line
index: TACG

source_name: ViCHC198/GFP- TQ treatment

value: TQ


title: ViCHC198 treatment SAHA_1_1

description:
Immortalized human T lymphocyte Jurkat cell line
index: GCAT


title: ViCHC198 treatment TQ_1_1

description:
Immortalized human T lymphocyte Jurkat cell line
index: CAGT


title: ViCHC198 treatment MQ_2_1

description:
Immortalized human T lymphocyte Jurkat cell line
index: TAGC

source_name: ViCHC198/GFP- MQ treatment

value: MQ


title: ViCHC198 treatment MQ_1_1

description:
Immortalized human T lymphocyte Jurkat cell line
index: GTAC


title: ViCHC198 treatment DMSO_2_2

description:
Immortalized human T lymphocyte Jurkat cell line
index: ATGC

source_name: ViCHC198/GFP- DMSO treatment

value: none (DMSO)


title: B28_r2

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

description:
response to nerve repair
B28_1

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 50 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0.13 (--no-novel-juncs) was used to map reads to the mouse mm10 reference genome+transcriptome (UCSC).
cuffquant (--no-novel-juncs) was used to quantify transcripts based on the mouse mm10 reference genome+transcriptome (UCSC).
cuffdiff v2.2.1 was used to call differentially expressed genes based on the mouse mm10 reference genome+transcriptome (UCSC).
Genome_build: Mouse mm10 (UCSC)
Supplementary_files_format_and_content: Tab delimited text files including counts, FPKM values, and p-values generated from Cuffdiff2 when corrected for multiple hypothesis testing

source_name: macrophage

extract_protocol:
Macrophages were isolated from inert conduits 5, 14 and 28 days after sciatic transection by flow cytometry (Lin-F4/80+CD14+CD11b+CD16/32+). Total RNA was isolated with the Quick-RNA MicroPrep kit (Zymo Research).
RNA-seq libraries were prepared from 25 ng total RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

tag: time point


title: ViCHC198 treatment DMSO_1_1

description:
Immortalized human T lymphocyte Jurkat cell line
index: ACGT


title: ViCHC198 treatment DMSO_2_1

description:
Immortalized human T lymphocyte Jurkat cell line
index: CATG


title: ViCHC198 treatment DMSO_1_2

description:
Immortalized human T lymphocyte Jurkat cell line
index: ATCG


title: B14_r2

description:
response to nerve repair
B14_1


title: B28_r1

description:
response to nerve repair
B28_0


title: B05_r3

description:
response to nerve repair
B05_2


title: ViCHC198 treatment TQ_2_1

description:
Immortalized human T lymphocyte Jurkat cell line
index: CGAT


title: B14_r1

description:
response to nerve repair
B14_0


title: ViCHC198 treatment MQ_2_2

description:
Immortalized human T lymphocyte Jurkat cell line
index: TGCA


title: B05_r1

description:
response to nerve repair
B05_0


title: ViCHC198 treatment TQ_1_2

description:
Immortalized human T lymphocyte Jurkat cell line
index: AGTC


title: C57BL6.5xtetO_HoxC_tetREZH2_noDOX.H3K27Me3.iWTr_0hr

first: Danny

last: Reinberg

address: 522 First Avenue

institute: NYU School of Medicine

data_processing:
Bowtie2 v2.2.6 was used to align reads to reference genome with default parameters.
Aligned reads were normalized based on the mapped reads in spike-in Drosophila control.
BedGraph files were generated from the aligned reads using 'genomecov' function in bedtools v2.17.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated from BedGraph files using 'bedGraphToBigWig' function in USCS.

growth_protocol: E14Tga2 and C57BL/6 ESCs were grown in standard medium supplemented with LIF, 1 μM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 μM GSK3 inhibitor (CHIR99021, Stemgent).

extract_protocol:
Cells were fixed with 1% Formaldehyde. Nuclei was isolated and  chromatin was fragmented. Chromatin immunoprecipitation (ChIP) was performed and the libraries was prepared using the eluted DNA from ChIP.
Eluted DNA from ChIP was repaired to generate blunt 5' P ends using 'EndIT DNA End Repair kit' (Epicentre), 3' A overhang was generated using 'Klenow Fragment (3´→ 5´ exo-)' (NEB).  Illumina barcodes were ligated using 'Rapid T4 DNA Ligase' (Enzymatics). Next libraries were size selected using 'Ampure beads' (Beckman Coulter) .  After around 13 cycles of amplification, libraries were cleaned, quantified and pooled.

value: inducible WT EED rescue  0hr,  EZH2 is endogenously tagged with tetR

tag: chip antibody

value: H3K27Me3, Cell Signaling, #9733


title: C57BL6.5xtetO_HoxC_tetREZH2_withDOX.H3K27Me3.iWTr_24hr

value: inducible WT EED rescue  24hr,  EZH2 is endogenously tagged with tetR


title: C57BL6.36hr.KDM2B.iWTr

value: inducible WT EED rescue  36hr

value: Gift from Robert J. Klose


title: C57BL6.5xtetO_HoxC_tetREZH2_noDOX.H3K27Me3.iWTr_24hr


title: C57BL6.5xtetO_Desert_tetREZH2_noDOX.H3K27Me3.iWTr_0hr


title: C57BL6.5xtetO_Desert_tetREZH2_noDOX.H3K27Me3.iWTr_24hr


title: ViCHC198 treatment MQ_1_2

description:
Immortalized human T lymphocyte Jurkat cell line
index: AGCT


title: C57BL6.12hr.H3K27Me2.iMTr

value: inducible MT EED rescue  12hr

value: H3K27Me2, Cell Signaling, #9728


title: C57BL6.5xtetO_Desert_tetREZH2_withDOX.H3K27Me3.iWTr_24hr


title: C57BL6.24hr.H3K27Me2.iMTr

value: inducible MT EED rescue  24hr


title: C57BL6.36hr.H3K27Me2.iMTr

value: inducible MT EED rescue  36hr


title: C57BL6.0hr.SUZ12.iMTr

value: inducible MT EED rescue  0hr

value: SUZ12, Cell Signaling, #3737


title: E14Tga2.KO.SUZ12

value: EED KO


title: B05_r2

description:
response to nerve repair
B05_1


title: E14Tga2.Y365A.SUZ12

value: EED Y365A


title: E14Tga2.WT.SUZ12

value: EED WT