title: Control 3 (C3)

city: Frederick

first: Zhi-Ming

last: Zheng

state: Maryland

department: Center for Cancer Research

institute: National Cancer Institute

data_processing:
Samples were pooled and sequenced on single lane on HiSeq2500 with Illumina TruSeq V4 chemistry.
Basecalling was performed by RTA (version 1.18.64).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 1.8.4) allowing 1 mismatch.
Reads were filtered with a base call quality >94% of bases with Q30 and and above.
Trimming of adapters and low-quality bases was performed using Trimmomatic (version 0.35).
First pass alignment of reads to the mm10 reference genome was performed using STAR (version 2.4.2a) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMtype BAM Unsorted
Second pass alignment of reads to the mm10 reference genome was performed using STAR (version 2.4.2a) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMunmapped Within --outWigType None --outWigStrand Stranded --sjdbFileChrStartEnd /path/to/sjdbFile.txt --sjdbGTFfile /path/to/annotations.gtf --limitSjdbInsertNsj 4000000 --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate
Gene-level expression quantificiation was performed using subread (version 1.4.6).
Normalization and differential expression was performed using edgeR (version 3.12) and limma (version 3.26.3).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file is normalized differential expression output.

source_name: skin tissue from ear

growth_protocol: Immunodeficient BALB/c FoxN1nu/nu mice (Envigo, Indianapolis, IN) were housed in aseptic conditions in micro-isolator cages.

extract_protocol:
Total RNA was isolated using Tri-Pure Reagent (Roche).
TruSeq Stranded Total RNA Library Prep Kit with Mouse Ribo-Zero (RS-122-2201, Illumina)

treatment_protocol: The ears of 6-8 weeks old mice were scarified and wounded using 27-gauge needle before infection with 2x108 virus genome equivalent (VGE) of MmuPV1. Phosphate-buffered saline (PBS) was used for mock infection. The wart tissues were colected 6 months post infection.

tag: strain

value: BALB/c FoxN1nu/nu

tag: tissue

value: ear tissue from mock-infected control

tag: infection

value: Mock infection (no MmuPV1)


title: Control 1 (C1)

status: Public on Aug 30 2019

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus


title: Control 2 (C2)


title: WT_NC14_R3_B1_L1

city: Princeton

first: Amanda

last: Amodeo

state: NJ

address: Carl Ichan Laboratory, Washington Rd

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description: Single end 75bp reads

data_processing:
Raw sequencing reads were filtered by Illumina HiSeq Control Software and only the Pass-Filter reads were used for further analysis.
Sequenced raw reads were demultiplexed using fastq-multx (v 1.3.1) and trimmed using Trim Galore (v 0.5.0) default parameters.
Trimmed reads were mapped to the Drosophila melanogaster transcriptome (r6.19) and quantified using default parameters in Salmon (0.10.2).
Normalization and differnetial gene expression analysis were performed using DESeq2 (v 1.20.0) after collapsing the technical replicates (same library sequenced in different batches/ lanes).
Genome_build: Drosophila melanogaster Trranscriptome r6.19
Supplementary_files_format_and_content: Tab-delimited raw quantfication output from Salmon. Tab-delimited files for DESeq2 normalized gene counts as well as DE analysis outputs for each of the Slbp, abo pooled and abo timecourse experiments.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Single Embryo

growth_protocol: Drosophila stocks grown and embryos collected in 18°C (Slbp experiment) or 25°C  (abo experiment). Embryos staged and imaged at 22°C.

extract_protocol:
The appropriately staged embryos were placed into an RNase free tube, lysed with a sterile needle. Then 100 μl of lysis buffer (Applied Biosystems, KIT0214) was added, and embryos were flash-frozen in liquid nitrogen, then stored at -80°C
For the Slbp comparison: rRNA depletion was performed using the Ribo-Zero rRNA Removal (Human, Mouse, Rat) Kit (Illumina, MRZH11124) followed by converting the poly-A containing RNA transcripts to cDNA using oligo-dT adaptor and further amplified by PCR following the Smart-seq2 method (Picelli et al, 2014). Illumina sequencing libraries were made from the amplified cDNA samples using the Nextera DNA library prep kit (Illumina, FC-121-1031). For the abo single time point comparison: poly-A containing RNA transcripts were enriched using oligo-dT bead and further converted to cDNA and Illumina sequencing library using PrepX RNA-seq library kit on the automated Apollo 324 NGS Library Prep System (Wafergen Biosystems) following the manufacturer's protocol. For the abo timecourse comparison: poly-A containing RNA transcripts were converted to cDNA using oligo-dT adaptor and further amplified by PCR following the Smart-seq2 method (Picelli et al, 2014). Illumina sequencing libraries were made from the amplified cDNA samples using the Nextera DNA library prep kit (Illumina, FC-121-1031). The RNA-seq libraries were sequenced on Illumina HiSeq 2500 Rapid flow-cells as single-end 75nt reads, following the standard Illumina protocol.

tag: treatment

value: Wild-type

tag: developmental stage

tag: embryo/ biological replicate

value: Replicate 3

tag: sequencing batch/ lane/ technical replicate

value: abo timecourse experiment:Batch 1 Lane 1


title: WT_NC13_R3_B1_L1

description: Single end 75bp reads


title: Infected 1 (I1)

value: infected ear tissue without visible warts

value: MmupV1 infection


title: WT_NC14_R2_B1_L1

description: Single end 75bp reads

value: Replicate 2


title: Infected 3 (I3)


title: WT_NC13_R2_B1_L1

description: Single end 75bp reads


title: Tumor 3 (T3)

value: infected ear tissue with tumor


title: Infected 2 (I2)


title: Tumor 2 (T2)


title: WT_NC13_R1_B1_L1

description: Single end 75bp reads

value: Replicate 1


title: WT_NC12_R2_B1_L1

description: Single end 75bp reads


title: Tumor 1 (T1)


title: WT_NC12_R3_B1_L1

description: Single end 75bp reads


title: WT_NC11_R3_B1_L1

description: Single end 75bp reads


title: WT_NC11_R1_B1_L1

description: Single end 75bp reads


title: WT_NC12_R1_B1_L1

description: Single end 75bp reads


title: WT_NC10_R3_B1_L1

description: Single end 75bp reads


title: WT_NC10_R2_B1_L1

description: Single end 75bp reads


title: PBS_MG_C

city: New York

first: Lyden

middle: C

last: David

state: NY

address: 413 East 69th Street, Room BB1228

department: Cell and Developmental Biology

institute: Weill Cornell Medicine

description:
counts-mg-vst.csv
MG_LRT_DEGs.csv

data_processing:
FastQC v0.11.7 to assess sequence base quality, per-base sequence content, GC content, N content, and the sequence length distribution
Reads were subsequently trimmed using Trimmomatic v0.38, to remove Illumina adapters, leading and trailing bases with score ≤ 3, all bases after the sliding window average ≤ 15, and all edited reads ≤ 36 bp
Reads were aligned to Mus musculus annotation GRCm38.p6 using Salmon v0.10.0. Default parameters were used for building the index and for alignment.
DESeq2 v1.18.1 was used to assess differential gene expression using the likelihood ratio test, with the model ~ replicate + condition analyzed against the reduced model ~ replicate.
Variance Stabilized Transformed gene counts were used to identify outliers, using both Principal Component Analysis and sample clustering (using the euclidean distance metric and the complete clustering method).
Gene names were mapped to entrez gene identifiers using ensembl biomart, mouse version GRCm38.p6.
Genome_build: GRCm38.p6

source_name: Mus musculus brain slice FACS-sorted exosome-positive microglial cells

extract_protocol: For brain slices, the PC ring was removed and slices were PBS washed. Immunofluorescence was carried out in free-floating conditions using the same protocol for tissue sections. For invasion, fixed slices were washed in PBS, outer-ring regions were dissected out and tissue was embedded in OCT and frozen. Cryosections perpendicular to the plane of the slice were immunostained as for tissue sections.    Brain slices were pre-treated with PBS or PKH67-labelled exosomes (5 µg/slice) for two consecutive days, the outer-ring areas were dissected out and the PC ring removed. Tissue was washed with PBS before Dispase/Collagenase (Roche; Dispase II at 1 U/mL and Collagenase A at 2.5mg/mL final concentration) digestion for 15 minutes at 37ºC with agitation (70 RPM). Single-cell suspensions were obtained by pipetting and filtering through a 100µm cell strainer. Cells were washed with MACS buffer (PBS Ca2+/Mg2+ 224 -free, 1% Bovine Serum Albumin, 2mM EDTA), collected by centrifugation at 300xg, 5 min at 4ºC, and incubated with Myelin Removal Beads (Miltenyi). Myelin-free cells were resuspended in MACS buffer and incubated with fluorescently-labelled antibodies (Supplementary Table 3) for 30 min at 4ºC: CD45, CD31, CD11b, and CD49d. BrECs were defined as CD45- CD31+ and microglial cells as CD45+ CD11blow CD49dlow 228 (Supplementary Fig. 5h and references therein). Cells were washed with MACS buffer, filtered through a 40µm strainer and DAPI-stained. Unstained and single-stained cells/beads were used for cell sorter set-up. DAPI+ 231 dead cells were excluded. Sorting was performed on a FACS Aria (Becton Dickinson) and exosome positive BrECs and microglia cells were sorted into RLT buffer (Qiagen) with 2-Mercaptoethanol and frozen. Becton Dickinson Diva Software was used for cell sorting and data acquisition and TreeStar FlowJo 10.5.3 was used for data analysis.    RNA was extracted from cells using the RNeasy Micro kit (QIAGEN) and quantified using Qubit 2.0 Fluorometer (Life Technologies). RNA integrity was checked with TapeStation (Agilent Technologies).

treatment_protocol: Brain slices were pre-treated with PBS or PKH67-labelled exosomes (5 µg/slice) for two consecutive days, the outer-ring areas were dissected out and the PC ring removed. Tissue was washed with PBS before Dispase/Collagenase (Roche; Dispase II at 1 U/mL and Collagenase A at 2.5mg/mL final concentration) digestion for 15 minutes at 37ºC with agitation (70 RPM). Single-cell suspensions were obtained by pipetting and filtering through a 100µm cell strainer. Cells were washed with MACS buffer (PBS Ca2+/Mg2+ 224 -free, 1% Bovine Serum Albumin, 2mM EDTA), collected by centrifugation at 300xg, 5 min at 4ºC, and incubated with Myelin Removal Beads (Miltenyi). Myelin-free cells were resuspended in MACS buffer and incubated with fluorescently-labelled antibodies for 30 min at 4ºC: CD45, CD31, CD11b, and CD49d. BrECs were defined as CD45- CD31+ and microglial cells as CD45+ CD11blow CD49dlow 228 . Cells were washed with MACS buffer, filtered through a 40µm strainer and DAPI-stained. Unstained and single-stained cells/beads were used for cell sorter set-up. DAPI+ dead cells were excluded. Sorting was performed on a FACS Aria (Becton Dickinson) and exosome positive BrECs and microglia cells were sorted into RLT buffer (Qiagen) with 2-Mercaptoethanol and frozen. Becton Dickinson Diva Software was used for cell sorting and data acquisition and TreeStar FlowJo 10.5.3 was used for data analysis.

tag: organ

value: brain

tag: cell type

value: microglial cells

tag: condition

value: PBS


title: KO2_MG_A

description:
counts-mg-vst.csv
MG_LRT_DEGs.csv

value: knock out 2


title: PBS_MG_B

description:
counts-mg-vst.csv
MG_LRT_DEGs.csv


title: PBS_MG_A

description:
counts-mg-vst.csv
MG_LRT_DEGs.csv


title: KO2_MG_B

description:
counts-mg-vst.csv
MG_LRT_DEGs.csv


title: WT_NC14_R1_B1_L1

description: Single end 75bp reads


title: KO2_MG_C

description:
counts-mg-vst.csv
MG_LRT_DEGs.csv


title: KO1_MG_A

description:
counts-mg-vst.csv
MG_LRT_DEGs.csv

value: knock out 1


title: WT_NC0_R3_B1_L1

description: Single end 75bp reads

value: Unfertilized


title: WT_NC10_R1_B1_L1

description: Single end 75bp reads


title: WT_NC0_R2_B1_L1

description: Single end 75bp reads


title: KO1_MG_B

description:
counts-mg-vst.csv
MG_LRT_DEGs.csv


title: KO1_MG_C

description:
counts-mg-vst.csv
MG_LRT_DEGs.csv


title: WT_MG_B

description:
counts-mg-vst.csv
MG_LRT_DEGs.csv

value: wild type


title: WT_MG_A

description:
counts-mg-vst.csv
MG_LRT_DEGs.csv


title: ABO_NC14_R1_B1_L1

description: Single end 75bp reads

value: abo mutation; Histone overexpression


title: PBS_EC_A

description:
counts-ec-vst.csv
EC_LRT_DEGs.csv

source_name: Mus musculus brain slice FACS-sorted exosome-positive endothelial cells

value: endothelial cells


title: ABO_NC14_R3_B1_L1

description: Single end 75bp reads


title: ABO_NC13_R3_B1_L1

description: Single end 75bp reads


title: WT_NC0_R1_B1_L1

description: Single end 75bp reads

value: Wild-type


title: PBS_EC_B

description:
counts-ec-vst.csv
EC_LRT_DEGs.csv


title: PBS_EC_C

description:
counts-ec-vst.csv
EC_LRT_DEGs.csv


title: ABO_NC13_R2_B1_L1

description: Single end 75bp reads


title: ABO_NC13_R1_B1_L1

description: Single end 75bp reads


title: KO2_EC_A

description:
counts-ec-vst.csv
EC_LRT_DEGs.csv


title: KO2_EC_B

description:
counts-ec-vst.csv
EC_LRT_DEGs.csv


title: ABO_NC12_R1_B1_L1

description: Single end 75bp reads


title: KO1_EC_A

description:
counts-ec-vst.csv
EC_LRT_DEGs.csv


title: KO2_EC_C

description:
counts-ec-vst.csv
EC_LRT_DEGs.csv


title: ABO_NC12_R2_B1_L1

description: Single end 75bp reads


title: KO1_EC_B

description:
counts-ec-vst.csv
EC_LRT_DEGs.csv


title: ABO_NC12_R3_B1_L1

description: Single end 75bp reads

value: Replicate 3


title: KO1_EC_C

description:
counts-ec-vst.csv
EC_LRT_DEGs.csv


title: WT_EC_A

description:
counts-ec-vst.csv
EC_LRT_DEGs.csv


title: ABO_NC11_R2_B1_L1

description: Single end 75bp reads

value: abo timecourse experiment:Batch 1 Lane 1


title: ABO_NC10_R3_B1_L1

description: Single end 75bp reads


title: WT_MG_C

description:
counts-mg-vst.csv
MG_LRT_DEGs.csv


title: ABO_NC14_R2_B1_L1

description: Single end 75bp reads


title: WT_EC_C

description:
counts-ec-vst.csv
EC_LRT_DEGs.csv


title: WT_EC_B

description:
counts-ec-vst.csv
EC_LRT_DEGs.csv


title: ABO_NC10_R2_B1_L1

description: Single end 75bp reads


title: ABO_NC10_R1_B1_L1

description: Single end 75bp reads


title: WT_NC11_R2_B1_L1

description: Single end 75bp reads


title: ABO_NC0_R2_B1_L1

description: Single end 75bp reads


title: WT_NC14_Rep3_poold

description: Single end 75bp reads

source_name: 40 Pooled Embryos

value: abo pooled experiment:Single sequencing run


title: ABO_NC0_R1_B1_L1

description: Single end 75bp reads


title: Chr18+/- ncRNA-seq (smH3)

city: Bethesda

first: Heejin

last: Choi

address: 50 South drive, Building 50, Room 3131

institute: NIH

data_processing:
Raw sequence reads were trimmed with cutadapt 1.18 to remove any adapters while performing light quality trimming with parameters "-a ATCGGAAGAGC -A ATCGGAAGAGC -q 20 --minimum-length=25."
Sequencing library quality was assessed with fastqc v0.11.8 with default parameters and trimmed reads were mapped to the Mus musculus mm10 reference genome using hisat2 2.1.0 with default parameters. Multimapping reads were filtered using SAMtools 1.9. Uniquely aligned reads were then mapped to gene features using subread featureCounts v1.6.2 as a second strand library with parameters. "-t gene -g gene_id -f -p -B -P -C." Differential expression between groups of samples was tested using R version 3.5.1 (2018-07-02) with DESeq2 1.20.0. Transcript quantification was performed with salmon 0.11.3 with parameters "--gcBias --libType A --seqBias --threads 1."
piRNA annotations were derived from the Zamore lab. Transposon-mapping reads were aligned to repBase annotated regions, upbuilt from mm9 to mm10, using the software pipeline piPipes and bowtie2 2.2.5.
s1.txt and s2.txt files are paired-end sequencing results
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: HT Testis

extract_protocol:
Total RNA from testes samples was isolated using miRNAeasy Mini (Qiagen). The sequencing libraries were constructed from 100 ng – 1,000 ng of total RNA using the Illumina’s TruSeq Stranded Total RNA kit with Ribo-Zero following the manufacturer instruction. The fragment size of RNAseq libraries was verified using the Agilent 2100 Bioanalyzer (Agilent) and the concentrations were determined using Qubit instrument (LifeTech). The libraries were loaded onto the Illumina HiSeq 3000 for 2x50 bp paired end read sequencing. The fastq files were generated using the bcl2fastq software for further analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols. NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs) was used per the manufacturer’s instructions. In general, 1 mg total RNA was subjected to 3’ and 5’ adapter ligation, reverse transcribed, PCR amplified, followed by size selection with AMPure XP beads (Beckman Coulter) for deep sequencing .

treatment_protocol: Isolated testes total RNA was incubated with 5X borate buffer (148 mM borax, 148 mM boric acid, pH 8.6, Thermo Fisher Scientific), 10 min at room temperature for periodate reaction and β-elimination as well as freshly dissolved 200 mM NaIO4 (Thermo Fisher Scientific). To quench unreacted NaIO4,  glycerol (ThermoFisher Scientific) was added and incubated for 10 min at room temperature. After adding 1X borate buffer, RNA was precipitated with ethanol for 1 hr, at -80 °C. After centrifugation, the RNA was dissolved in 1X borax buffer (30 mM borax and 30mM boric acid, 17.5 mM NaOH, pH 9.5) and incubated for 90 min at 45 °C prior to addition 1X borate buffer and  glycogen. The RNA was precipitated with ethanol for 1 hr, at -80 °C, collected by centrifugation and dissolved in water. During β-elimination, periodate-reacted RNAs were shortened by 1 nt at the 3’ end with monophosphates and were unable to be amplified during library preparation. piRNAs, protected from β-elimination by 2’-O-methylation at 3’ end, were enriched in the non-coding RNA-seq libraries.

tag: genotype

value: HT control

tag: age

value: post natal day 28

value: testis


title: Chr18-/- ncRNA-seq (smK3)

source_name: KO Testis

value: KO


title: Chr18-/- ncRNA-seq (smK2)


title: Chr18-/- ncRNA-seq (smK1)


title: Chr18+/- ncRNA-seq (smH1)


title: Chr18+/- ncRNA-seq (smH2)


title: WT_NC14_Rep2_poold

description: Single end 75bp reads

value: Replicate 2


title: WT_NC14_Rep1_poold

description: Single end 75bp reads

value: Replicate 1


title: FVB4-FF

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
For scRNA-Seq, the Cell Ranger Single Cell Software Suite, version 1.3 was used for de-multiplexing, barcode ad UMI processing, and single-cell 3′ gene counting. Reads were mapped to the mm10 genome for FVB3 and FVB4 and to th Hg19 for the 3 Cell-line mixture
10xbulk and freash frozen mRNA-Seq libraries were aligned to the mouse mm10 and GRCh38 reference genome using the STAR aligner algorithm. Resulting BAM files were sorted and indexed using Samtools and QC was performed using Picard. Tran-script read counts were determined was performed using Salmon
Genome_build: mm10, hg19, GRCh38
Supplementary_files_format_and_content: Cell Ranger output

source_name: Normal adult Mammary Gland

growth_protocol: All cell lines were maintained independently in culture medium DMEM (Gibco) supplemented with 10% FBS (Millipore) and 1% penicillin-streptomycin (Gibco) and grown in incubators maintained at 37°C with 5% CO2

extract_protocol:
The FVB/NJ mammary glands were placed in 10 ml of a digestion medium con-taining EpiCultTM-B Mouse Medium Kit (#05610, StemCell Technologies), Col-lagenase/Hyaluronidase (#07912, StemCell Technologies) and 1% penicillin streptomycin (Gibco). The mammary gland was digested overnight in a thermocycler maintained at 37 C with continuous rotation. RNA was isolated from the cell-lines and the mammary glands using the RNeasy Mini Kit (#74104, Qiagen) according to manufacturer protocol.
scRNA-Seq libraries were prepared following the Single Cell 30 Reagent Kits v2 User Guide (Manual Part # CG00052 Rev A) using the following Single Cell 30 Reagent Kits v2: ChromiumTMSingle Cell 3' Library & Gel Bead Kit v2, PN-120237, Single Cell 3' Chip Kit v2 PN-120236, and i7 Multiplex Kit PN-120262 (10X Genomics). 10xBulk and Fresh frozen mRNA-Seq were made using total RNA and the Illu-mina TruSeq mRNA sample preparation kit.
scRNA-Seq Libraries were run on an Illumina HiSeq 4000 as 2 150 paired-end reads. 10x bulk andfresh frozen mRNA-Seq Paired end (2 50bp) sequencing was performed on the Illumina HiSeq 2000/2500 sequencer

tag: tag

value: 12 weeks old mouse mammary gland

value: Fresh frozen contralteral mammary gland for bulk mRNAseq

value: FVB/NJ mouse/ female


title: FVB3-FF


title: ABO_NC14_Rep2_poold

description: Single end 75bp reads


title: ABO_NC14_Rep3_poold

description: Single end 75bp reads


title: ABO_NC11_R3_B1_L1

description: Single end 75bp reads


title: FVB4-10xSS

value: Pooled cell suspensions for bulk mRNAseq


title: ABO_NC14_Rep1_poold

description: Single end 75bp reads


title: FVB3-10xSS


title: WT_NC14_R5_B2

description: Single end 75bp reads

value: Replicate 5

value: Slbp experiment:Batch 2


title: WT_NC14_R3_B2

description: Single end 75bp reads


title: WT_NC14_R2_B2

description: Single end 75bp reads


title: WT_NC14_R1_B2

description: Single end 75bp reads


title: ABO_NC11_R1_B1_L1

description: Single end 75bp reads

value: abo mutation; Histone overexpression


title: ESC_24hr_2_Input

city: Cambridge

first: Elena

last: Kingston

state: Massachusetts

address: Nine Cambridge Center

institute: Whitehead Institute MIT

data_processing:
Bases were called using the Illumina sequencing platform pipeline
Sequencing reads were trimmed at the 5' and 3' ends using fastx_trimmer and cutadapt
Trimmed reads were then filtered for quality with fastq_quality_filter
miRNA reads were called by string-matching the first 19 nucleotides of the filtered reads to a curated dictionary of miRNA sequences
Reads from EU libraries were normalized with the EU-containing quantitative standards (spike_22, spike_24, spike_26), and reads from input libraries were normalized with the sequencing quantitative standards (dme-miR-14_spike, xtr-miR-427_spike).
Genome_build: A miRNA dictionary curated by filtering miRbase_v21 miRNA annotations for all conserved or confidently annotated small RNA species (as annotated by TargetScanMouse, release 7.2)
Supplementary_files_format_and_content: All miRNA reads called for a given timecourse were merged into one table. These data have not yet been normalized.

source_name: Mouse embryonic stem cells

growth_protocol: MEFs were passaged every 2-3 days in DMEM with 10% FBS; mESCs were passaged every 2 days in DMEM/F12 media supplemented with B27, N2, MEM NEAA, BSA, GlutaMAX, BME, Pen/Strep, LIF, and the inhibotors PD0325901 and CHIR99021. All contact-inhibited MEF samples were maintained in a contact-inhibited state for 5 days prior to treatment initiation.

extract_protocol:
Cells were rinsed twice with PBS prior to the addition of Trizol. Following addition of the Trizol, cells were scraped off the plate and snap frozen. Total RNA was later extracted as per the manufacturer's protocols.
Libraries were generated as detailed at  http://bartellab.wi.mit.edu/protocols.html. Briefly, samples for library preparation were assembled by mixing either 2–5 μg of total RNA (input libraries) or the entire eluate from 5EU pulldown (EU libraries) with size-selection markers and quantitative sequencing standards. Size-selection markers were 18 and 32 nt 5'-end-labeled RNAs. Sequencing standards were added at a level of either 0.1 fmol per 1 μg total RNA (input libraries) or 2.5 amol per sample (EU libraries). Both 3' and 5' ligations were carried out with degenerate adaptors (each containing 4 random nucleotides) in the presence of 10% Polyethylene Glycol and 0.5 μL of Superasin with either T4 RNA-ligase 2, truncated K227Q or T4 RNA-ligase 1, respectively. Reverse transcription was with SuperScript III, and subsequent PCR amplification of the cDNA was with Phusion. Samples were sequenced on an Illumina HiSeq platform with 40 nt single-end reads.
RNA-seq samples were prepared using the NEXTflex Rapid Directional mRNA-seq Kit. Briefly, mRNAs were enriched from 10 µg total RNA with NEXTflex Poly(A) Beads. These species were then fragmented, synthesized into cDNA, ligated to adaptors, and PCR amplified as per the manufacturer’s protocol. Samples were then sequenced on an Illumina HiSeq platform with 40 nt single-end reads.

treatment_protocol: 5-ethynyluridine was added to the media to a final concentration of 400 uM (MEFs) or 125 uM (mESCs); cells were incubated with the 5EU for the times specified in their filenames.

tag: cell line

value: mESC line

tag: passages

value: input

tag: time


title: ESC_8hr_2_Input


title: ESC_2hr_2_Input


title: WT_NC13_R6_B2

description: Single end 75bp reads

value: Wild-type

value: Replicate 6


title: WT_NC13_R5_B2

description: Single end 75bp reads


title: ESC_4hr_2_Input


title: ESC_16hr_2_Input


title: ESC_16hr_2_EU


title: ESC_24hr_2_EU


title: ESC_8hr_2_EU


title: WT_NC13_R4_B2

description: Single end 75bp reads

value: Replicate 4


title: WT_NC13_R2_B2

description: Single end 75bp reads


title: WT_NC13_R1_B1

description: Single end 75bp reads

value: Slbp experiment:Batch 1


title: ESC_4hr_2_EU


title: ESC_2hr_2_EU


title: ESC_1hr_2_EU


title: WT_Pre9_R5_B2

description: Single end 75bp reads


title: WT_Pre9_R4_B2

description: Single end 75bp reads


title: WT_NC14_R4_B2

description: Single end 75bp reads


title: WT_NC13_R1_B2

description: Single end 75bp reads


title: WT_Pre9_R3_B2

description: Single end 75bp reads

value: Replicate 3


title: CIMEF_CyrKO_1wk_Input

source_name: Mouse embryonic fibroblasts

value: CIMEF

value: Embryo-derived fibroblasts


title: ESC_1hr_2_Input


title: CIMEF_CyrKO_72hr_Input


title: CIMEF_CyrKO_24hr_Input


title: WT_Pre9_R2_B2

description: Single end 75bp reads

value: Replicate 2


title: SLBP_NC13_R4_B2

description: Single end 75bp reads

value: Slbp RNAi; Histone knockdown


title: CIMEF_CyrKO_4hr_Input


title: CIMEF_CyrKO_2hr_Input


title: CIMEF_CyrKO_8hr_Input


title: SLBP_NC13_R2_B1

description: Single end 75bp reads


title: CIMEF_CyrKO_1wk_EU


title: CIMEF_CyrKO_24hr_EU


title: CIMEF_CyrKO_8hr_EU


title: CIMEF_CyrKO_4hr_EU


title: SLBP_NC13_R2_B2

description: Single end 75bp reads


title: SLBP_NC13_R1_B1

description: Single end 75bp reads

value: Replicate 1


title: SLBP_NC13_R1_B2

description: Single end 75bp reads


title: WT_NC13_R3_B2

description: Single end 75bp reads


title: CIMEF_CyrKO_2hr_EU


title: SLBP_Pre9_R4_B2

description: Single end 75bp reads


title: SLBP_Pre9_R3_B2

description: Single end 75bp reads


title: RNA_Olig2-GFP-_2

city: Cincinnati

first: Richard

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 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. Differential gene expression analysis was performed using Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: GFP- cells

extract_protocol:
GFP+ cells and GFP- cells from medulloblastoma tumor tissues of hGFAPcre;Ptchc/c;Olig2-GFP mice were sorted by fluorescence activated cell sorting (FACS). RNA of GFP+ cells and GFP- cells were extracted using RNeasy Micro Kit (Qiagen).
Libraries were prepared according to Illumina's instructions accompanying Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)

value: Postnatal day 15

tag: geneotype


title: RNA_Olig2-GFP-_1


title: RNA_Olig2-GFP-_3


title: SLBP_Pre9_R5_B2

description: Single end 75bp reads


title: SLBP_Pre9_R2_B2

description: Single end 75bp reads


title: WT_Pre9_R1_B2

description: Single end 75bp reads


title: SLBP_Pre9_R1_B2

description: Single end 75bp reads


title: SLBP_NC13_R3_B2

description: Single end 75bp reads


title: SLBP_NC13_R5_B2

description: Single end 75bp reads


title: RNA_Olig2-GFP+_3

source_name: GFP+ cells


title: RNA_Olig2-GFP+_1


title: CIMEF_CyrKO_72hr_EU

tag: strain


title: Control ChIP-seq from K562 (ENCLB659SFI)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR861LKS/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ZBTB40 tagged K562 cell line.
experiment encode accession: ENCSR861LKS
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-11-30
lab: Kevin White, UChicago
library encode accession: ENCLB659SFI
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting eGFP-ZBTB40

tag: antibody

value: Control

tag: line

value: cell line

tag: description

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZBTB40

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

value: adult

value: 53 year

tag: lab

value: Kevin White, UChicago

tag: passage number

tag: health state

value: chronic myelogenous leukemia (CML)

tag: link

value: ENCBS848PQJ at ENCODE; https://www.encodeproject.org/ENCBS848PQJ/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Control ChIP-seq from uterus (ENCLB910SBM)

description:
https://www.encodeproject.org/experiments/ENCSR859LXC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR859LXC
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB910SBM
size range: 200-600

source_name: Homo sapiens female adult (51 year) uterus tissue

value: uterus

value: tissue

tag: age

value: 51 year

value: Bradley Bernstein, Broad

value: ENCBS102SRR at ENCODE; https://www.encodeproject.org/ENCBS102SRR/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Drop_seq_P12

data_processing:
Illumina Casava software used for basecalling.
Drop-seq mapping and analysis procedure
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include expression value of each cell

source_name: medullablastoma tumor cells

extract_protocol:
Tumor tissues were digested by TrypLE added with collagenase type I, and single cell suspension was treated by Red Blood Cell Lysis Buffer, the sequencing followed Drop-seq protocols. Briefly, monodisperse droplets ∼1 nl in size were generated using the microfluidic device, in which barcoded microparticles, suspended in lysis buffer. As soon as droplet generation was complete, droplets were broken with perfluorooctanol in 30 ml of 6× SSC. The addition of a large aqueous volume to the droplets reduces hybridization events after droplet breakage. The beads were then washed and resuspended in a reverse transcriptase mix, followed by a treatment with exonuclease I to remove unextended primers, and PCR amplified.
The amplified cDNA was quantified on a BioAnalyzer High Sensitivity Chip (Agilent). cDNA size selection was performed to reduce reads that end up just giving PolyA tail sequences. The cDNA was then fragmented and amplified for sequencing with the Nextera XT DNA sample prep kit (Illumina) using custom primers that enabled the specific amplification of only the 3’ ends. The libraries were purified, quantified, and then sequenced on the Illumina Hiseq 2500.

value: Postnatal day 12

value: hGFAPcre;Ptchc/c


title: MB_Input

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 with the default configuration
Peak calling was performed using MACS (Model-based Analysis of ChIP-Seq) (http://liulab.dfci.harvard.edu/MACS) with a p value cut off of 1x e9.
Genome_build: mm10
Supplementary_files_format_and_content: bed files were generated using Macs14

source_name: Medulloblastoma tissue

extract_protocol:
Lysates were clarified from sonicated nuclei and proteine-DNA complexes were isolated with antibody.
Dissociated tissues were fixed for 15 min at room temperature with 1% formaldehyde-containing medium. Nuclei were isolated and sonicated in sonication buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA and protease inhibitor cocktail). Sonicated chromatin (~300 µg) was used for immunoprecipitation by incubation with appropriate antibodies (4 mg) overnight at 4°C. Ten percent of chromatin used for each ChIP reaction was kept as input DNA. Pre-rinsed magnetic protein A/G beads (50 ml) were added to each ChIP reaction and reactions were incubated for 1 hr at 4°C.The beads were then incubated in 200 ml elution buffer at 65°C for 20 min to elute immunoprecipitated materials. The ChIP-seq libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB catalogue number E6240L) and then run on the Illumina sequencer HiSeq 2500.


title: Control ChIP-seq from uterus (ENCLB080IBC)

description:
https://www.encodeproject.org/experiments/ENCSR859LXC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR859LXC
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB080IBC
size range: 200-600

value: Control

value: ENCBS443NGH at ENCODE; https://www.encodeproject.org/ENCBS443NGH/


title: CB_Input

source_name: Cerebellum


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB348QKR)

description:
https://www.encodeproject.org/experiments/ENCSR845BEG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR845BEG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545WFH
encode release date: 2018-12-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB348QKR
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) esophagus muscularis mucosa tissue

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis

value: female

value: ENCBS677JLV at ENCODE; https://www.encodeproject.org/ENCBS677JLV/


title: ChIP_MB_H3k27ac_repeat 2

value: H3k27ac (Abcam, ab4729)


title: ChIP_MB_Olig2_repeat 3

value: Olig2 (Millipore, ab9610)


title: ChIP_MB_Olig2_repeat 2


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB877RRK)

description:
https://www.encodeproject.org/experiments/ENCSR845BEG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR845BEG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545WFH
encode release date: 2018-12-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB877RRK
fragmentation methods: sonication (generic)
size range: 200-600

value: adult


title: Control ChIP-seq from tibial artery (ENCLB767OVM)

description:
https://www.encodeproject.org/experiments/ENCSR819JOI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR819JOI
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB767OVM
size range: 200-600

source_name: Homo sapiens male adult (54 years) tibial artery tissue

value: tibial artery

value: EnTEX:Artery - Tibial

value: male

value: 54 year

value: ENCBS736PQK at ENCODE; https://www.encodeproject.org/ENCBS736PQK/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Histone ChIP-seq from heart left ventricle (ENCLB865WMZ)

description:
https://www.encodeproject.org/experiments/ENCSR803MVC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR803MVC
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR178FVP
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB865WMZ
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) heart left ventricle tissue

value: heart left ventricle

value: tissue

value: EnTEX:Heart - Left Ventricle

value: 51 year

value: Bradley Bernstein, Broad

value: ENCBS684IAD at ENCODE; https://www.encodeproject.org/ENCBS684IAD/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: HA-DNMT3A2_ChIPseq_mESC_NSD1_KO

city: Santiago de Compostela

first: Carmen

last: Rivas

address: Avda Barcelona

department: CIMUS

country: Spain

institute: Universidad de Santiago de Compostela

description: According to manufacturer's protocol

data_processing:
Raw ChIP sequencing reads were aligned using BWA version 0.7.17 with default parameters
Raw RNA sequencing reads were aligned using STAR version 2.5.3a with default parameters
Raw reads from whole-genome bisulfite sequencing were aligned using BWA (version 0.6.1). Low-quality sequence at the 3′ ends were trimmed. After alignment, we filtered duplicated or poorly mapping reads (>2% mismatches or aberrant insert size). Samtools (version 0.1.18) in mpileup mode was applied to call CpG methylation. We filtered CpGs with less than 5x coverage, overlapping with SNPs from dbSNPs (build 137) or located within the ENCODE DAC blacklisted regions or Duke excluded regions.
Genome_build: hg19, mm10 and dm6 for human, mouse and drosophila data, respectively
Supplementary_files_format_and_content: bigWig

growth_protocol: Mouse embryonic stem cells were maintained on gelatin-coated plates in Knockout DMEM (Gibco) supplemented with 15% ES-cell-qualified FBS (Gemini), 0.1 mM 2-mercapoethanol, 2mM L-glutamine (Life technologies) and LIF.

extract_protocol:
To obtain a soluble chromatin extract, ~2x10^7 cells were resuspended in 1 mL LB1 (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x Complete protease inhibitor) and incubated rotating at 4°C for 10 min. Samples were centrifuged, resuspended in 1 mL LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x Compete protease inhibitor), and incubated rotating at 4°C for 10 min. Finally, samples were centrifuged, resuspended in 1 mL LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X-100, 1x Complete protease inhibitor), and homogenized by passing two times through a 27-gauge needle. Chromatin extracts were sonicated for 8 min (anti-HA ChIP) or 12 min (anti-histone PTM ChIP) using a Covaris E220 focused ultra-sonicator at peak power 140, duty factor 5, and cycles/burst 200. For histone PTM ChIP-Rx, after centrifugation soluble chromatin was spiked-in with soluble chromatin from Drosophila S2 cells that was similarly prepared and equivalent to 5-10% of the mouse/human cell chromatin. The lysates were incubated with 100 μl Pierce anti-HA beads (Themo Scientific, 88836) or with anti-H3K4me1 (Abcam, ab8895), anti-H3K9me3 (Abcam, ab8898), anti-H3K27ac (Active Motif, 39133), anti-H3K27me3 (Cell Signaling Tech, 9733), anti-H3K36me2 (Cell Signaling, 2901) or anti-H3K36me3 (Active Motif, 61101) antibody bound to 75 μl protein A or protein G Dnya1 magnetic beads (Invitrogen) and incubated overnight at 4°C with 5% kept as input DNA. Magnetic beads were washed with low salt buffer (150 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), high salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), LiCl buffer (150 mM LiCl; 0.5% Na deoxycholate; 0.1% SDS; 1% Nonidet P-40; 1 mM EDTA; 50 mM Tris-HCl) and TE buffer (1 mM EDTA; 10 mM Tris-HCl). For ChIP-seq, beads were resuspended in elution buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10mM EDTA, 200 mM NaCl) and incubated for 30 min at 65°C. After centrifugation the eluate was reverse cross-linked overnight at 65°C. The eluate was then treated with RNaseA for 1 hr at 37°C and with Proteinase K (Roche) for 1 hr at 55°C and DNA was recovered using Qiagen PCR purification kit.
KAPA Hyper Prep Kit

tag: chip antibody

value: HA (ThermoFisher, #88836)

value: ESC line V6.5 1A

tag: cell type

value: C57BL/6 x 129S4/SvJae F1 embryo-derived embryonic stem cells

tag: genotype

value: sgNsd1 line stably expressing FLAG-HA tagged DNMT3A2 WT


title: HA-DNMT3A2_ChIPseq_mESC_DNMT3A_KO

description: According to manufacturer's protocol

tag: cell line

value: sgDnmt3a line stably expressing FLAG-HA tagged DNMT3A2 WT


title: TF ChIP-seq from upper lobe of left lung (ENCLB327NNR)

description:
https://www.encodeproject.org/experiments/ENCSR799TJD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR799TJD
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR750DLX
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB327NNR
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) upper lobe of left lung tissue

value: CTCF

value: upper lobe of left lung

value: female

value: adult

value: ENCBS939RMD at ENCODE; https://www.encodeproject.org/ENCBS939RMD/


title: Histone ChIP-seq from heart left ventricle (ENCLB256GGB)

description:
https://www.encodeproject.org/experiments/ENCSR803MVC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR803MVC
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR178FVP
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB256GGB
fragmentation methods: sonication (generic)
size range: 200-600

value: heart left ventricle


title: TF ChIP-seq from upper lobe of left lung (ENCLB706UTK)

description:
https://www.encodeproject.org/experiments/ENCSR799TJD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR799TJD
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR750DLX
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB706UTK
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue


title: ESC_mRNA_2

data_processing:
Bases were called using the Illumina sequencing platform pipeline
Sequencing reads were trimmed at the 5' and 3' ends using fastx_trimmer and cutadapt
Trimmed reads were then filtered for quality with fastq_quality_filter
miRNA reads were called by string-matching the first 19 nucleotides of the filtered reads to a curated dictionary of miRNA sequences
Reads from EU libraries were normalized with the EU-containing quantitative standards (spike_22, spike_24, spike_26), and reads from input libraries were normalized with the sequencing quantitative standards (dme-miR-14_spike, xtr-miR-427_spike).
Genome_build: A miRNA dictionary curated by filtering miRbase_v21 miRNA annotations for all conserved or confidently annotated small RNA species (as annotated by TargetScanMouse, release 7.2)
Supplementary_files_format_and_content: All miRNA reads called for a given timecourse were merged into one table. These data have not yet been normalized.
Bases were called using the Illumina sequencing platform pipeline
Sequencing reads were aligned to the mouse genome with Star v. 2.4
Aligned reads were then assigned to genes based on annotations from Ensembl with htseq-count v0.9.1
Genome_build: mm10, Mus_musculus.GRCm38.94.gtf
Supplementary_files_format_and_content: Raw counts for aligned reads are shown for Ensembl genes; all 6 RNA-seq samples are merged into one file.

value: embryonic stem cells

tag: passages


title: HA-DNMT3A2_ChIPseq_mESC_Parental

description: According to manufacturer's protocol

value: Parental line stably expressing FLAG-HA tagged DNMT3A2 WT


title: RNA_Olig2-GFP+_2

value: Postnatal day 15

tag: geneotype


title: Histone ChIP-seq from heart left ventricle (ENCLB622JVK)

description:
https://www.encodeproject.org/experiments/ENCSR799KLF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR799KLF
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR178FVP
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB622JVK
fragmentation methods: sonication (generic)
size range: 200-600

tag: antibody

value: EnTEX:Heart - Left Ventricle

value: 51 year

value: Bradley Bernstein, Broad

value: ENCBS684IAD at ENCODE; https://www.encodeproject.org/ENCBS684IAD/


title: Histone ChIP-seq from heart left ventricle (ENCLB545GKJ)

description:
https://www.encodeproject.org/experiments/ENCSR799KLF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR799KLF
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR178FVP
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB545GKJ
fragmentation methods: sonication (generic)
size range: 200-600

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Control ChIP-seq from uterus (ENCLB596CQX)

description:
https://www.encodeproject.org/experiments/ENCSR859LXC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR859LXC
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB596CQX
size range: 200-600

value: Control

value: uterus

value: ENCBS102SRR at ENCODE; https://www.encodeproject.org/ENCBS102SRR/


title: DMEF_mRNA_2

tag: strain

value: DMEF

value: Embryo-derived fibroblasts


title: Control ChIP-seq from upper lobe of left lung (ENCLB393BYZ)

description:
https://www.encodeproject.org/experiments/ENCSR750DLX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR750DLX
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB393BYZ
size range: 200-600

value: upper lobe of left lung

tag: description

value: female

value: adult


title: ESC_mRNA_1


title: CIMEF_mRNA_1

value: CIMEF


title: DMEF_mRNA_1


title: Control ChIP-seq from upper lobe of left lung (ENCLB451EVE)

description:
https://www.encodeproject.org/experiments/ENCSR750DLX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR750DLX
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB451EVE
size range: 200-600

value: tissue

tag: biosample encode accession

value: ENCBS939RMD at ENCODE; https://www.encodeproject.org/ENCBS939RMD/


title: Control ChIP-seq from tibial artery (ENCLB283EFP)

description:
https://www.encodeproject.org/experiments/ENCSR819JOI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR819JOI
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB283EFP
size range: 200-600

value: tibial artery

value: EnTEX:Artery - Tibial

tag: Sex

value: male

value: 54 year

value: ENCBS646JZQ at ENCODE; https://www.encodeproject.org/ENCBS646JZQ/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: ESC_16hr_1_Input

value: embryonic stem cells

tag: treatment

value: input

tag: time


title: ESC_24hr_1_Input


title: Histone ChIP-seq from upper lobe of left lung (ENCLB934BAS)

description:
https://www.encodeproject.org/experiments/ENCSR706OFD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR706OFD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR750DLX
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB934BAS
fragmentation methods: sonication (generic)
size range: 200-600

tag: dev stage

value: 51 year

tag: lab

value: Bradley Bernstein, Broad

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: ESC_8hr_1_Input


title: CIMEF_mRNA_2

value: Embryo-derived fibroblasts


title: Control ChIP-seq from K562 (ENCLB827GLA)

description:
https://www.encodeproject.org/experiments/ENCSR745QMZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ZNF148 tagged K562 cell line.
experiment encode accession: ENCSR745QMZ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB827GLA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Homo sapiens K562 cell line stably expressing C-terminal eGFP-tagged eGFP-ZNF148

value: Control

tag: line

value: cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF148

value: female

value: 53 year

value: Kevin White, UChicago

tag: passage number

tag: health state

value: chronic myelogenous leukemia (CML)

tag: link

value: ENCBS091XYE at ENCODE; https://www.encodeproject.org/ENCBS091XYE/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: ChIP_CB_H3k27ac

value: Olig2 (Millipore, ab9610)


title: ESC_4hr_1_Input

tag: cell type


title: ESC_2hr_1_Input

tag: cell line


title: Histone ChIP-seq from heart left ventricle (ENCLB895CTS)

description:
https://www.encodeproject.org/experiments/ENCSR702OVJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR702OVJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR178FVP
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB895CTS
fragmentation methods: sonication (generic)
size range: 200-600

value: heart left ventricle

value: tissue

value: EnTEX:Heart - Left Ventricle

value: adult

tag: age

value: ENCBS684IAD at ENCODE; https://www.encodeproject.org/ENCBS684IAD/


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB155YDI)

description:
https://www.encodeproject.org/experiments/ENCSR701GIE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR701GIE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545WFH
encode release date: 2018-12-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB155YDI
fragmentation methods: sonication (generic)
size range: 200-600

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis

value: 51 year

value: Bradley Bernstein, Broad

value: ENCBS677JLV at ENCODE; https://www.encodeproject.org/ENCBS677JLV/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: ESC_1hr_1_Input

value: embryonic stem cells

tag: passages

value: input


title: Histone ChIP-seq from heart left ventricle (ENCLB679XVG)

description:
https://www.encodeproject.org/experiments/ENCSR702OVJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR702OVJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR178FVP
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB679XVG
fragmentation methods: sonication (generic)
size range: 200-600

tag: antibody

value: female


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB578KHJ)

description:
https://www.encodeproject.org/experiments/ENCSR701GIE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR701GIE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545WFH
encode release date: 2018-12-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB578KHJ
fragmentation methods: sonication (generic)
size range: 200-600


title: Histone ChIP-seq from upper lobe of left lung (ENCLB692ITP)

description:
https://www.encodeproject.org/experiments/ENCSR642DSR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR642DSR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR750DLX
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB692ITP
fragmentation methods: sonication (generic)
size range: 200-600

value: upper lobe of left lung

value: ENCBS939RMD at ENCODE; https://www.encodeproject.org/ENCBS939RMD/


title: ESC_8hr_1_EU

tag: strain


title: Histone ChIP-seq from upper lobe of left lung (ENCLB504ULQ)

description:
https://www.encodeproject.org/experiments/ENCSR623YMO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR623YMO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR750DLX
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB504ULQ
fragmentation methods: sonication (generic)
size range: 200-600

tag: description


title: Histone ChIP-seq from upper lobe of left lung (ENCLB468DDW)

description:
https://www.encodeproject.org/experiments/ENCSR642DSR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR642DSR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR750DLX
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB468DDW
fragmentation methods: sonication (generic)
size range: 200-600

tag: biosample encode accession


title: ESC_24hr_1_EU


title: Histone ChIP-seq from upper lobe of left lung (ENCLB246HWG)

description:
https://www.encodeproject.org/experiments/ENCSR623YMO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR623YMO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR750DLX
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB246HWG
fragmentation methods: sonication (generic)
size range: 200-600

tag: Sex


title: ESC_4hr_1_EU

tag: treatment


title: Histone ChIP-seq from upper lobe of left lung (ENCLB392GVP)

description:
https://www.encodeproject.org/experiments/ENCSR706OFD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR706OFD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR750DLX
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB392GVP
fragmentation methods: sonication (generic)
size range: 200-600


title: DMEF_72hr_2_Input

value: DMEF

value: Embryo-derived fibroblasts

tag: time


title: DMEF_8hr_2_Input


title: ESC_0hr_1_EU


title: ESC_1hr_1_EU


title: DMEF_24hr_2_Input


title: Control ChIP-seq from esophagus muscularis mucosa (ENCLB787CTY)

description:
https://www.encodeproject.org/experiments/ENCSR545WFH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR545WFH
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB787CTY
size range: 200-600

value: Control

value: tissue

tag: dev stage


title: DMEF_2hr_2_Input


title: DMEF_4hr_2_Input


title: DMEF_1hr_2_Input


title: H3K36me3_ChIPseq_mESC_NSD1_KO

description: According to manufacturer's protocol

organism:
Drosophila melanogaster
Mus musculus

source_name: Mouse embryonic stem cells & S2 cells

tag: chip antibody

value: ESC line V6.5 1A

value: C57BL/6 x 129S4/SvJae F1 embryo-derived embryonic stem cells

tag: genotype


title: Control ChIP-seq from esophagus muscularis mucosa (ENCLB584RBP)

description:
https://www.encodeproject.org/experiments/ENCSR545WFH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR545WFH
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB584RBP
size range: 200-600

value: esophagus muscularis mucosa

value: adult

tag: lab

value: ENCBS955ZON at ENCODE; https://www.encodeproject.org/ENCBS955ZON/


title: Control ChIP-seq from esophagus muscularis mucosa (ENCLB343UYI)

description:
https://www.encodeproject.org/experiments/ENCSR545WFH/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR545WFH
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB343UYI
size range: 200-600

value: EnTEX:Esophagus - Muscularis

value: 51 year

value: Bradley Bernstein, Broad


title: ESC_0hr_1_Input

value: embryonic stem cells


title: H3K36me3_ChIPseq_mESC_Parental

description: According to manufacturer's protocol

value: wild-type


title: ESC_16hr_1_EU


title: DMEF_24hr_1_Input

value: input


title: H3K36me2_ChIPseq_mESC_NSD1_KO

description: According to manufacturer's protocol

value: H3K36me2 (Cell Signaling Tech, #2901)


title: H3K36me2_ChIPseq_TKO

description: According to manufacturer's protocol

source_name: C3H10T1/2 cells & S2 cells

growth_protocol: C3H10T1/2 cells were cultured in Dulbecco's modified Eagles' medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, Sigma). Drosophila S2 cells were cultured in Schneider's Drosophila Medium (Invitrogen) containing 10% heat-inactivated FBS.

value: C3H embryo-derived mesenchymal progenitor cells

value: sgNsd1/Nsd2/Setd2 #1


title: DMEF_4hr_1_Input

value: DMEF

value: Embryo-derived fibroblasts


title: Control ChIP-seq from K562 (ENCLB819FVH)

description:
https://www.encodeproject.org/experiments/ENCSR529YPZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-VEZF1 tagged K562 cell line.
experiment encode accession: ENCSR529YPZ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-11-30
lab: Kevin White, UChicago
library encode accession: ENCLB819FVH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting eGFP-VEZF1

value: Control

tag: line

value: cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to VEZF1

value: female

value: 53 year

value: Kevin White, UChicago

tag: passage number

tag: health state

value: chronic myelogenous leukemia (CML)

value: ENCBS431ZXQ at ENCODE; https://www.encodeproject.org/ENCBS431ZXQ/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: DMEF_8hr_1_Input

tag: cell line

tag: cell type


title: MKO1420

city: LOS ANGELES

first: Xingxing

last: Kong

address: UCLA PEDIATRICS, 10833 LE CONTE AVE, CHS-MARION DAVIES CHILDREN CTR

institute: UCLA

data_processing:
The data was sequenced on HiSeq3000 usinga single-read 50bp read run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
The reads were mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
TMM (trimmed mean of M-values) was used to normalize the gene expression.  Mapping statistics were above average; between 58.43% and 80.68% of reads mapped to the transcriptome for any given sample.
Supplementary_files_format_and_content: tab-delimited text files include RSEM values for each Sample.

source_name: Skeletal muscle (Gastrocnemius)

extract_protocol:
Skeletal muscle was removed, flash frozen on liquid nitrogen, and RNA was harvested using RNA Sample Prep Kit.
Libraries for RNA-Seq were prepared with Kapa Stranded mRNA. The workflow consisted of mRNA enrichment, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification.

value: Male

tag: food

value: High fat diet

tag: tissue

value: Skeletal muscle (Gastrocnemius)

value: IRF4 knock out


title: MOE1536

tag: strain

value: IRF4 overexpression


title: Control ChIP-seq from esophagus muscularis mucosa (ENCLB739WYM)

description:
https://www.encodeproject.org/experiments/ENCSR545WFH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR545WFH
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB739WYM
size range: 200-600

tag: antibody

value: esophagus muscularis mucosa

value: tissue

tag: description

value: EnTEX:Esophagus - Muscularis

value: adult

tag: age

value: 51 year

value: Bradley Bernstein, Broad

tag: link

value: ENCBS677JLV at ENCODE; https://www.encodeproject.org/ENCBS677JLV/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: MKO1421

tag: Sex


title: ESC_2hr_1_EU

source_name: Mouse embryonic stem cells

value: embryonic stem cells

tag: passages

tag: treatment

tag: time


title: MOE1541

tag: genotype


title: DMEF_2hr_1_Input

source_name: Mouse embryonic fibroblasts

value: DMEF

value: Embryo-derived fibroblasts

value: input


title: DMEF_1hr_1_Input


title: Chr18-/- ssRNA-seq (HC3802-7)

source_name: KO Testis

value: KO

value: post natal day 28

value: testis


title: MKO1283

value: Male

value: High fat diet

value: Skeletal muscle (Gastrocnemius)

value: IRF4 knock out


title: Chr18-/- ssRNA-seq (HC3802-9)


title: DMEF_0hr_1_Input


title: Chr18+/- ssRNA-seq (HC3802-6)

source_name: HT Testis

value: HT control


title: Chr18-/- ssRNA-seq (HC3802-8)


title: Chr18+/- ssRNA-seq (HC3802-5)


title: Chr18+/- ssRNA-seq (HC3802-4)


title: Histone ChIP-seq from upper lobe of left lung (ENCLB585VMC)

description:
https://www.encodeproject.org/experiments/ENCSR453MUW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR453MUW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR750DLX
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB585VMC
fragmentation methods: sonication (generic)
size range: 200-600

value: upper lobe of left lung

value: tissue

tag: biosample encode accession

value: female

tag: dev stage

value: adult

tag: lab

value: ENCBS939RMD at ENCODE; https://www.encodeproject.org/ENCBS939RMD/


title: Chr18+/+ ssRNA-seq (HC3802-3)

source_name: WT Testis

value: WT control


title: MOE1579

value: IRF4 overexpression


title: Chr18+/+ ssRNA-seq (HC3802-2)


title: Histone ChIP-seq from upper lobe of left lung (ENCLB122HWS)

description:
https://www.encodeproject.org/experiments/ENCSR429VWL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR429VWL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR750DLX
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB122HWS
fragmentation methods: sonication (generic)
size range: 200-600

value: 51 year

value: Bradley Bernstein, Broad

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Chr18+/+ ssRNA-seq (HC3802-1)

value: post natal day 28


title: DMEF_72hr_1_Input

tag: cell line

value: DMEF

value: Embryo-derived fibroblasts

value: input


title: DMEF_8hr_2b_EU

description:
Resequencing of DMEF_8hr_2_EU to obtain greater sequencing depth
DMEF_EU_2.txt

tag: cell type


title: DMEF_4hr_2b_EU

description:
Resequencing of DMEF_4hr_2_EU to obtain greater sequencing depth
DMEF_EU_2.txt


title: DMEF_2hr_2b_EU

description:
Resequencing of DMEF_2hr_2_EU to obtain greater sequencing depth
DMEF_EU_2.txt


title: DMEF_72hr_2_EU


title: DMEF_8hr_2_EU


title: DMEF_24hr_2_EU


title: Histone ChIP-seq from upper lobe of left lung (ENCLB514ZGR)

description:
https://www.encodeproject.org/experiments/ENCSR453MUW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR453MUW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR750DLX
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB514ZGR
fragmentation methods: sonication (generic)
size range: 200-600


title: DMEF_4hr_2_EU


title: DMEF_2hr_2_EU


title: Histone ChIP-seq from upper lobe of left lung (ENCLB800GUF)

description:
https://www.encodeproject.org/experiments/ENCSR238WIK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR238WIK
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR750DLX
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB800GUF
fragmentation methods: sonication (generic)
size range: 200-600


title: Histone ChIP-seq from upper lobe of left lung (ENCLB062BUN)

description:
https://www.encodeproject.org/experiments/ENCSR238WIK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR238WIK
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR750DLX
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB062BUN
fragmentation methods: sonication (generic)
size range: 200-600


title: DMEF_1hr_2_EU


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB847DDD)

description:
https://www.encodeproject.org/experiments/ENCSR185JEP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR185JEP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR147KFH
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB847DDD
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) esophagus muscularis mucosa tissue

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis updated Feb 2019 with updated term name and ID from DCC.

value: male

value: 37 year

value: ENCBS884JOD at ENCODE; https://www.encodeproject.org/ENCBS884JOD/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: DMEF_72hr_2b_EU

description:
Resequencing of DMEF_72hr_2_EU to obtain greater sequencing depth
DMEF_EU_2.txt


title: Histone ChIP-seq from heart left ventricle (ENCLB013UTR)

description:
https://www.encodeproject.org/experiments/ENCSR181ATL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR181ATL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR178FVP
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB013UTR
fragmentation methods: sonication (generic)
size range: 200-600

value: heart left ventricle

value: tissue

value: EnTEX:Heart - Left Ventricle

value: female

value: adult

value: ENCBS684IAD at ENCODE; https://www.encodeproject.org/ENCBS684IAD/


title: Histone ChIP-seq from heart left ventricle (ENCLB008SDO)

description:
https://www.encodeproject.org/experiments/ENCSR181ATL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR181ATL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR178FVP
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB008SDO
fragmentation methods: sonication (generic)
size range: 200-600

value: 51 year

value: Bradley Bernstein, Broad

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: DMEF_8hr_1_EU

value: DMEF

value: Embryo-derived fibroblasts


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB367XLA)

description:
https://www.encodeproject.org/experiments/ENCSR185JEP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR185JEP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR147KFH
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB367XLA
fragmentation methods: sonication (generic)
size range: 200-600

value: esophagus muscularis mucosa


title: DMEF_24hr_1_EU


title: DMEF_24hr_2b_EU

description:
Resequencing of DMEF_24hr_2_EU to obtain greater sequencing depth
DMEF_EU_2.txt


title: Control ChIP-seq from heart left ventricle (ENCLB702RZR)

description:
https://www.encodeproject.org/experiments/ENCSR178FVP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR178FVP
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB702RZR
size range: 200-600

value: Control


title: Histone ChIP-seq from upper lobe of left lung (ENCLB263TZE)

description:
https://www.encodeproject.org/experiments/ENCSR429VWL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR429VWL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR750DLX
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB263TZE
fragmentation methods: sonication (generic)
size range: 200-600

value: upper lobe of left lung

value: ENCBS939RMD at ENCODE; https://www.encodeproject.org/ENCBS939RMD/


title: DMEF_4hr_1_EU


title: Control ChIP-seq from heart left ventricle (ENCLB173VED)

description:
https://www.encodeproject.org/experiments/ENCSR178FVP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR178FVP
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB173VED
size range: 200-600


title: DMEF_2hr_1_EU


title: DMEF_1hr_1_EU


title: Control ChIP-seq from esophagus squamous epithelium (ENCLB919BXX)

description:
https://www.encodeproject.org/experiments/ENCSR156WTZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR156WTZ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB919BXX
size range: 200-600

source_name: Homo sapiens male adult (37 years) esophagus squamous epithelium tissue

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa updated Feb 2019 with updated term name and ID from DCC.

value: male

value: 37 year

value: ENCBS608MZC at ENCODE; https://www.encodeproject.org/ENCBS608MZC/


title: Control ChIP-seq from esophagus squamous epithelium (ENCLB315WHE)

description:
https://www.encodeproject.org/experiments/ENCSR156WTZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR156WTZ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB315WHE
size range: 200-600

value: tissue

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: CIMEF_1wk_2_Input

value: CIMEF

value: input


title: CIMEF_72hr_2_Input


title: DMEF_72hr_1_EU


title: CIMEF_4hr_2_Input


title: Control ChIP-seq from esophagus muscularis mucosa (ENCLB243NUR)

description:
https://www.encodeproject.org/experiments/ENCSR147KFH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR147KFH
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB243NUR
size range: 200-600

value: EnTEX:Esophagus - Muscularis updated Feb 2019 with updated term name and ID from DCC.

value: adult

value: Bradley Bernstein, Broad

value: ENCBS884JOD at ENCODE; https://www.encodeproject.org/ENCBS884JOD/


title: Control ChIP-seq from esophagus muscularis mucosa (ENCLB615KHW)

description:
https://www.encodeproject.org/experiments/ENCSR147KFH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR147KFH
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB615KHW
size range: 200-600

value: esophagus muscularis mucosa


title: CIMEF_24hr_2_Input

value: Embryo-derived fibroblasts


title: CIMEF_2hr_2_Input


title: CIMEF_8hr_2_Input


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB934QGC)

description:
https://www.encodeproject.org/experiments/ENCSR143XNJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR143XNJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR156WTZ
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB934QGC
fragmentation methods: sonication (generic)
size range: 200-600


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB805GSB)

description:
https://www.encodeproject.org/experiments/ENCSR143XNJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR143XNJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR156WTZ
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB805GSB
fragmentation methods: sonication (generic)
size range: 200-600


title: CIMEF_1wk_1_Input


title: CIMEF_8hr_1_Input


title: CIMEF_4hr_1_Input


title: CIMEF_24hr_1_Input


title: CIMEF_1hr_2_Input


title: CIMEF_0hr_1_Input


title: CIMEF_1wk_2_EU


title: CIMEF_2hr_1_Input


title: 3 Cell-Line-mixture-Bulk

source_name: Human Cell-lines

tag: tag

value: MDA-MB-438, MCF7, Human dermal fibroblast (HF)

value: Ratios of mixing:MDA-MB-438:60%, MCF7:30%, HF:10%

value: Pooled cell suspensions for bulk mRNAseq


title: CIMEF_72hr_2_EU


title: Histone ChIP-seq from uterus (ENCLB774KVX)

description:
https://www.encodeproject.org/experiments/ENCSR124AZR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR124AZR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR859LXC
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB774KVX
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) uterus tissue

value: uterus

value: female

value: 51 year

value: ENCBS102SRR at ENCODE; https://www.encodeproject.org/ENCBS102SRR/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Histone ChIP-seq from uterus (ENCLB573KRA)

description:
https://www.encodeproject.org/experiments/ENCSR124AZR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR124AZR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR859LXC
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB573KRA
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue


title: CIMEF_1hr_1_Input

value: CIMEF


title: DMEF_0hr_1_EU

value: DMEF


title: miRNAseq in GBM tumor 4

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Reads were trimmed using cutadapt, mapped using Hisat2 and reads were counted using featureCounts.
miRNA reads were trimmed using cutadapt, mapped  against miRBase v21 and reads were counted using a custom script.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for RNA-seq and normalized counts for miRNA-seq.

source_name: miRNAseq in GBM tumor

growth_protocol: T98G cells (ATCC-CRL-1690) were grown in EMEM with 10% FBS. Cells were maintained at 37°C and 5% CO2.

extract_protocol:
RNA from T98G cells and primary tumor samples were extracted with TRIzol.
RNA-seq libraries were prepared using NEBNext small RNA library preparation kit (NEB E7330) .

treatment_protocol: For type I interferon treatment, cells were treated with universal type I IFN a (PBL assay science, 11200) at 100 U/ml final concentration for 6 hrs. For type II interferon treatment, cells were treated with IFN-γ (SRP3058) for 48 hr at 30 ng/ml final concentration.

tag: cancer type

value: Glioblastoma

tag: tissue

value: Bulk tumor tissue

tag: tissue source

value: Brain


title: CIMEF_24hr_2_EU

tag: strain


title: miRNAseq in GBM tumor 3


title: CIMEF_8hr_2_EU


title: miRNAseq in GBM tumor 2


title: CIMEF_4hr_2_EU


title: miRNAseq in GBM tumor 1


title: CIMEF_1hr_2_EU


title: IFN alpha/beta treated rep1

source_name: T98G_IFN alpha/beta treated

value: Universal Type I IFN alpha treatment


title: IFN alpha/beta treated rep2


title: CIMEF_2hr_2_EU


title: CIMEF_72hr_1_Input

value: input


title: CIMEF_72hr_1_EU

value: Embryo-derived fibroblasts


title: CIMEF_1wk_1_EU


title: TF ChIP-seq from HCT116 (ENCLB555ABX)

description:
https://www.encodeproject.org/experiments/ENCSR101FJM/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF274 HCT116 ChIP-Seq
experiment encode accession: ENCSR101FJM
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000EUX
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ABX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-500

source_name: Homo sapiens HCT116 cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5aaf2e58-de7c-451b-b6d7-747b82278bc3/@@download/attachment/Farnham_TF_ChIP_Library_Protocol_130201.docx.pdf

tag: antibody

tag: line

value: cell line

tag: description

value: colorectal carcinoma (PMID:7214343)

value: male

value: adult

tag: age

value: unknown

value: Peggy Farnham, USC

tag: health state

value: colorectal carcinoma

value: ENCBS476AAA at ENCODE; https://www.encodeproject.org/ENCBS476AAA/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: KMS11_DMSO treated

city: Kumamoto

first: Yutaka

last: Okuno

state: Kumamoto

address: 1-1-1 Honko, Chuo Ku

department: Department of Hematology

country: Japan

institute: Kumamoto university of Medicine

data_processing:
Biomedical Genomics Workbench
Raw data filtering:
Remove reads containing adapters
Remove reads containing N > 10% (N represents the base cannot be determined).
Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
supplemental file and content: fold-change

source_name: KMS11 myeloma cells

growth_protocol: RPMI-1640 medium containing 10% FBS

extract_protocol:
RNA was extracted and purified using Trizol reagent (Thermo Fisher Scientific) and an RNeasy Mini Kit (Qiagen).
mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic samples, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

tag: treatment

value: DMSO


title: KMS11_OSSL_325096 treated


title: CIMEF_24hr_1_EU

value: CIMEF

tag: passages

tag: time


title: TF ChIP-seq from HCT116 (ENCLB555ABW)

description:
https://www.encodeproject.org/experiments/ENCSR101FJM/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF274 HCT116 ChIP-Seq
experiment encode accession: ENCSR101FJM
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000EUX
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ABW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-500

tag: biosample encode accession

tag: Sex

tag: dev stage

tag: link

value: ENCBS475AAA at ENCODE; https://www.encodeproject.org/ENCBS475AAA/


title: TF ChIP-seq from HEK293 (ENCLB555ACB)

description:
https://www.encodeproject.org/experiments/ENCSR000FCI/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF274 HEK293 ChIP-Seq
experiment encode accession: ENCSR000FCI
assay title: TF ChIP-seq
possible controls: ENCSR000EVA
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ACB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-500

source_name: Homo sapiens HEK293 cell line

value: embryonic kidney, cells contain Adenovirus 5 DNA

value: female

value: embryonic

tag: lab

value: ENCBS480AAA at ENCODE; https://www.encodeproject.org/ENCBS480AAA/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: CIMEF_8hr_1_EU

tag: cell line

tag: cell type

value: Embryo-derived fibroblasts


title: TF ChIP-seq from HEK293 (ENCLB555ACA)

description:
https://www.encodeproject.org/experiments/ENCSR000FCI/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF274 HEK293 ChIP-Seq
experiment encode accession: ENCSR000FCI
assay title: TF ChIP-seq
possible controls: ENCSR000EVA
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ACA
fragmentation methods: sonication (Bioruptor generic)
size range: 200-500

value: cell line

value: ENCBS479AAA at ENCODE; https://www.encodeproject.org/ENCBS479AAA/


title: KMS12PE_DMSO treated

source_name: KMS12PE myeloma cells


title: Control ChIP-seq from skeletal muscle myoblast (ENCLB695AQV)

description:
https://www.encodeproject.org/experiments/ENCSR000ANN/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on human skeletal muscle myoblast
experiment encode accession: ENCSR000ANN
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695AQV
fragmentation methods: see document

source_name: Homo sapiens male adult (22 years) skeletal muscle myoblast primary cell

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f10bdd36-e370-4777-a7f3-83091c115749/@@download/attachment/wgEncodeBroadHistone.html.pdf

value: Control

value: skeletal muscle myoblast

value: primary cell

value: skeletal muscle myoblasts

value: male

value: adult

value: 22 year

value: Bradley Bernstein, Broad

value: ENCBS023XCT at ENCODE; https://www.encodeproject.org/ENCBS023XCT/

value: Derived from ENCODE donor ENCDO341XKY; https://www.encodeproject.org/ENCDO341XKY/


title: Akap11-KO_Day25

city: Hong Kong

first: Vincent Ka Fai

last: Cheng

state: -- select --

address: L202 lab block 21 Sassoon road Pokfulam Hong Kong

department: Pharmacology and Pharmacy

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Base calling was performed using Illumina’s RTA (Version 1.12.4.2).
Adapters of RNA-seq reads were trimmed.
The BAM files with coordinate-sorted alignments were imported to Cufflinks 2.2.1 to assemble and quantify the transcripts as fragments per kilobase per million aligned reads (FPKM).
Cuffdiff 2 was employed to perform differential expression analysis.
Genome_build: Genome Reference Consortium Mouse Build 38
Supplementary_files_format_and_content: tab-delimited text files include log2 foldchange value

growth_protocol: Cell were maintained in proliferation medium, α‐MEM (Gibco, Thermo Fisher Scientific, Waltham, MA, USA; catalog # 12571) containing 10% v/v fetal bovine serum (FBS), 100 units/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
Cell were washed with PBS and RNA was harvested using Trizol reagent.
100ng total RNA was used for library construction by KAPA Stranded mRNA-Seq Kit (Roche).

treatment_protocol: 50 µg/ml ascorbic acid and 5 mM β-glycerophosphate were added to the medium for osteogenic differentiation. Medium was changed every 3 days and cells were incubated at 37 °C in a 5% CO2 atmosphere.

tag: genotype


title: CIMEF_2hr_1_EU

tag: strain

value: CIMEF


title: CIMEF_4hr_1_EU


title: early-maturation embryo replicate 2_single-end (Run 1)

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Embryos from the seeds with 6 - 7 mm in length were hand-dissected and collected.

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads were quality-filtered and cleaned for adapter sequences using fastx-clipper from FASTX-Toolkit with default parameters.
Only paired-end fastq files were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie2 v2.3.4.1 with default paired-end parameters.
Mapped reads were quality filtered (q > 2) using samtools (samtools view -q 2).
ATAC-Seq Peaks were determined using the HOMER findPeaks package with the following parameters -minDist 150 -region. Peaks were processed using the pos2bed.pl from HOMER. Reproducible peaks were determined by peaks present in two biological replicates using Bedtools.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: tab-delimited text file of the genomic coordinates of reproducible peaks detected in both replicates

organism: Glycine max

source_name: Soybean early-maturation stage embryos

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010).

extract_protocol:
Transposase treatment using Illumina Nextra Kit was adapted from the published protocol (Buenrostro et al., Curr. Protoc. Mol. Biol. 2015) and performed on 50,000 nuclei, followed by iolation of transposase-fragmented DNAs using QIAGEN MinElute PCR purification kit.
Purified transposase-fragmented DNAs were converted to sequencing libraries through ten PCR cycles using customized indexed Nextera PCR primers, followed by purification of library fragments using QIAGEN MieElute PCR purification kit

treatment_protocol: Ealry-maturation embryos were hand-dissected and collected from the seeds with 6-7mm in length. Intact Nuclei were purifed using Percal gradient.

tag: cultivar

value: Williams 82

tag: developmental stage

value: early-maturation stage

tag: tissue

value: embryo


title: CIMEF_1hr_1_EU

value: Embryo-derived fibroblasts


title: early-maturation embryo replicate 2_paired-end (Run 2)


title: KMS12PE_OSSL_325096 treated


title: Control ChIP-seq from skeletal muscle myoblast (ENCLB695AQW)

description:
https://www.encodeproject.org/experiments/ENCSR000ANN/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on human skeletal muscle myoblast
experiment encode accession: ENCSR000ANN
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695AQW
fragmentation methods: see document

tag: antibody

tag: age

value: ENCBS914GNL at ENCODE; https://www.encodeproject.org/ENCBS914GNL/


title: Akap11-KO_Day7


title: Akap11-KO_Day16


title: Control ChIP-seq from HEK293 (ENCLB801JYR)

description:
https://www.encodeproject.org/experiments/ENCSR000EVA/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on human HEK293
experiment encode accession: ENCSR000EVA
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2011-10-29
lab: Peggy Farnham, USC
library encode accession: ENCLB801JYR
fragmentation methods: see document

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7e85e27a-1b03-493d-b73f-db4ce2246318/@@download/attachment/wgEncodeSydhHistone.release3.html.pdf, general protocol: https://www.encodeproject.org/documents/0612f0bf-3665-47f8-af5d-09aab3d4ca24/@@download/attachment/wgEncodeSydhTfbs.release3.html.pdf

tag: line

value: cell line

tag: description

value: embryonic kidney, cells contain Adenovirus 5 DNA

value: female

value: embryonic

value: unknown

value: Peggy Farnham, USC

tag: health state

value: ENCBS375ENC at ENCODE; https://www.encodeproject.org/ENCBS375ENC/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: early-maturation embryo replicate 1_paired-end (Run 2)


title: CIMEF_0hr_1_EU

tag: passages

tag: treatment

tag: time


title: early-maturation embryo replicate 1_single-end (Run 1)


title: RNA_GFAP_Ptch_Olig2_2

source_name: Medullobalstoma

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

value: Postnatal day 20

tag: geneotype

value: Ptchf/f; Olig2c/c; hGFAPcre


title: RNA_GFAP_Ptch_2

value: Ptchf/f; hGFAPcre


title: WT_Day16

value: WT


title: RNA_GFAP_Ptch_Olig2_1


title: arf7-hypocotyl-MOCK

city: Qingdao

first: feng

last: zhang

state: Shandong

address: 72 Binhai Road

country: China

institute: shandong university

data_processing:
The amplicons were purified and sequenced using an Illumina/Solexa Genome Analyzer (Beijing Genomics Institute, Shenzhen, China).
Raw reads were trimmed by removing low-quality and adaptor sequences, then aligned to the A. thaliana genome using SOAP2 software.
Transcript frequency was calculated using the reads per kilobase per million reads method.  The RPKM was calculated by the method of "Reads Per Kb per Million reads", the method was showed in the article of "Mortazavi, A., B. A. Williams, et al . (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 5(7): 621-8."  Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the P value and the false discovery rate (FDR) (Audic and Claverie, 1997).
Genome_build: TAIR10
Supplementary_files_format_and_content: text files with RPKM

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: The seedlings grew on 1/2 MS in dark  for 4 days with 500 nM auxinnaphthalene acetic acid (NAA) treatment or not. The hypocotyls of the seedlings were extracted for RNA sequencing.

extract_protocol:
Total RNA was isolated using a RNeasy Mini Kit (Qiagen).
First strand cDNA was generated using reverse transcriptase and random primers. The constructed cDNA libraries was qualified and quantified with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, and then sequenced via Illumina HiSeqTM 2000 or other sequencer when necessary at the Beijing Genomics Institute, Shenzhen, China.

tag: seedling age

value: Hypocotyls

value: arf7 T-DNA mutant


title: arf7-hypocotyl-NAA


title: Col-hypocotyl-NAA

value: wild type


title: Akap11-KO_Day0

tag: cell line


title: WT_Day0


title: RNA_GFAP_Ptch_1


title: RNA_Lats12cko_3

value: Postnatal day 18

value: Lats1/2f/f; Math1cre


title: Col-hypocotyl-MOCK


title: WGBS_mESC_NSD1_KO

data_processing:
Raw reads from whole-genome bisulfite sequencing were aligned using BWA (version 0.6.1). Low-quality sequence at the 3′ ends were trimmed. After alignment, we filtered duplicated or poorly mapping reads (>2% mismatches or aberrant insert size). Samtools (version 0.1.18) in mpileup mode was applied to call CpG methylation. We filtered CpGs with less than 5x coverage, overlapping with SNPs from dbSNPs (build 137) or located within the ENCODE DAC blacklisted regions or Duke excluded regions.
Genome_build: mm10
Supplementary_files_format_and_content: tdf

source_name: Mouse embryonic stem cells

extract_protocol:
DNA was extracted from flash frozen cell pelets of about 5 million cells using DNeasy Blood & Tissue Kit from QIAGEN Cat. #69506
NxSeq AmpFREE Low DNA Library Kit (Lucigen). Samples were then bisulfite converted using the EZ-DNA Methylation Gold Kit (Zymo Research). DNA was amplified by 9 cycles of PCR using the Kapa Hifi Uracil + DNA polymerase (KAPA Biosystems).

value: C57BL/6 x 129S4/SvJae

value: ESC line V6.5 1A

tag: cell type

value: C57BL/6 x 129S4/SvJae F1 embryo-derived embryonic stem cells


title: WT_Day25

tag: genotype


title: RNA_Lats12cko_2


title: WGBS_mESC_Parental

tag: strain

value: wild-type


title: RNA_Lats12cko_1


title: WGBS_NSD_1_2_DKO

data_processing:
Raw ChIP sequencing reads were aligned using BWA version 0.7.17 with default parameters. After alignment, we sorted the bam files using samtools, then igvtools was used to generate wig files (igvtools count -w 25 -e 200). Finally, bigWig files were obtained using wigToBigWig.
Raw RNA sequencing reads were aligned using STAR version 2.5.3a with default parameters. The bigWig files were generated similarly as ChIP-seq.
Raw reads from whole-genome bisulfite sequencing were aligned using BWA (version 0.6.1). Low-quality sequence at the 3′ ends were trimmed. After alignment, we filtered duplicated or poorly mapping reads (>2% mismatches or aberrant insert size). Samtools (version 0.1.18) in mpileup mode was applied to call CpG methylation. We used igvtools to generate the tdf files.
Genome_build: hg19, mm10 and dm6 for human, mouse and drosophila data, respectively
Supplementary_files_format_and_content: bigWig, tdf

source_name: C3H10T1/2 cells

growth_protocol: C3H10T1/2 cells were cultured in Dulbecco's modified Eagles' medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, Sigma).

extract_protocol: KAPA High Throughput Library Preparation Kit (KAPA Biosystems). Samples were then bisulfite converted using the EZ-DNA Methylation Gold Kit (Zymo Research). DNA was amplified by 9 cycles of PCR using the Kapa Hifi Uracil + DNA polymerase (KAPA Biosystems) according to the manufacturer’s protocol.

value: C3H embryo-derived mesenchymal progenitor cells

value: sgNSD1/2 #1


title: RNA_CB_3

source_name: cerebellum


title: WGBS_Parental


title: RNA_CB_1


title: RNA_CB_2