title: non-infected_rep5

city: Montpellier

first: Anne

last: Geiger

address: TA A-17 / G Campus international de Baillarguet

institute: IRD-CIRAD

description:
S001138-31242460_J40-10
Processed data file: subread-align_featureCounts_all.tab.txt
Processed data file: DESeq2_infectedvsnon-infected.complete.txt
Processed data file: edgeR_infectedvsnon-infected.complete.txt

data_processing:
Base calling: BaseSpace Onsite Operating Software, including the software Generatefastq, version 2.1; default parameters. Illumina Technical Support.
Quality check: FastQC, version v0.11.5; Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Mapping: Subread-align, version v1.5.0; Threads: 10; Phred offset: 33; All subreads: 10; Min read1 votes: 3; Min read2 votes: 1; Max fragment size: 2000; Min fragment size: 0; Allowed mismatch: 10 bases; Max indels: 5; # of Best mapping: 1; Unique mapping: no. Liao Y, Smyth GK and Shi W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research, 41(10):e108, 2013.
Feature count: Subread featureCounts, version v1.5.0; Annotations: Glossina-palpalis-IAEA_BASEFEATURES_GpapI1.1.gtf; Threads: 1; Strand specific: yes; Multimapping reads: not counted; Multi-overlapping reads: not counted; Read orientations: fr; Attribute type: gene_id; Feature type: transcript. Liao Y, Smyth GK and Shi W. featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30, 2014.
Differential expression: SARTools, version v1.3.2. H. Varet, L. Brillet-Guéguen, J.-Y. Coppee and M.-A. Dillies, SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data, PLoS One, 2016, doi: 10.1371/journal.pone.0157022
Differential expression: DESeq2, version 1.12.3; featuresToRemove: None; varInt: group; condRef: non-infected; batch: NULL; fitType: parametric; cooksCutoff: TRUE; independentFiltering: TRUE; alpha: 0.05; pAdjustMethod: BH; typeTrans: VST; locfunc: median. Michael I Love, Wolfgang Huber and Simon Anders (2014): Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biology.
Differential expression: edgeR, version 3.14.0; featuresToRemove: NULL; varInt: group; condRef: non-infected; batch: NULL; alpha: 0.05; pAdjustMethod: BH; cpmCutoff: 1; gene.selection: pairwise; normalizationMethod: TMM. Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140.
Identification of homologs from Glossina palpalis to Drosophila melanogaster: blastall, version 2.2.26; blastall -i genome/Glossina_palpalis/Glossina-palpalis-IAEA_PEPTIDES_GpapI1.1.fa \   -d genome/Drosophila_melanogaster/Drosophila_melanogaster.BDGP6.pep.all_blastdb_pT \   -M BLOSUM45 -p blastp -m 8 -e 1e-5 \   > genome/Glossina_palpalis/Glossina-palpalis-IAEA_PEPTIDES_GpapI1.1_blastp_hits.tsv \   2> genome/Glossina_palpalis/Glossina-palpalis-IAEA_PEPTIDES_GpapI1.1_blastp_hits.log . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Stephen F. Altschul Thomas L. Madden Alejandro A. Schäffer Jinghui Zhang Zheng Zhang Webb Miller David J. Lipman. Nucleic Acids Res (1997) 25 (17): 3389-3402. doi: 10.1093/nar/25.17.3389
Functional enrichment: DAVID (https://david.ncifcrf.gov/), version 42614; 1. Tool "Functional annotation"; 2. query: FLYBASE_GENE_ID of drosophila BBH for glossina differentially expressed genes (down or up treated separately); 3. background: FLYBASE_GENE_ID for all the BBH from glossina to drosophila. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protoc. 2009;4(1):44-57; Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009;37(1):1-13.
Genome_build: Glossina palpalis GpapI1 (vectorbase, June 2015 release, Glossina-palpalis-IAEA_SCAFFOLDS_GpapI1.fa; Glossina-palpalis-IAEA_BASEFEATURES_GpapI1.gff3; Glossina-palpalis-IAEA_BASEFEATURES_GpapI1.gtf; Drosophila_melanogaster.BDGP6.pep.all.fa; doi: 10.1093/nar/gku1117)
Genome_build: Drosophila melanogaster BDGP6 (ensemblgenomes 32, Drosophila_melanogaster.BDGP6.pep.all.fa, doi: 10.1093/nar/gkv1209)
Supplementary_files_format_and_content: subread-align_featureCounts_all.tab.txt: Tab-delimited text file includes feature counts for all aligned samples.
Supplementary_files_format_and_content: DESeq2_infectedvsnon-infected.complete.txt: Tab-delimited text file includes differentially-expressed genes found using DESeq2.
Supplementary_files_format_and_content: edgeR_infectedvsnon-infected.complete.txt: Tab-delimited text file includes differentially-expressed genes found using edgeR.

organism: Glossina palpalis

source_name: midgut, non-infected

growth_protocol: Tsetse flies were captured in south Cameroun using pyramidal traps (Lancien J., 1981) placed in suitable tsetse fly biotopes.

extract_protocol:
Total RNA were extracted from the midguts using Nucleospin TriPreps Kit of Macherrey Nagel.
TruSeq Stranded mRNA Library Prep Kit from Illumina with poly(A) selection.

treatment_protocol: The midguts were dissected according to the midgut dissection protocol developed by Penchenier and Itard (1981).

value: midgut

tag: infection


title: Osr1 GCE/+ Rep 1

status: Public on Jul 28 2017

type: SRA

city: Paris

first: Mickael

last: Orgeur

address: 25-28 rue du Docteur Roux

country: France

institute: Institut Pasteur

library_source: transcriptomic

data_processing:
Paired-end reads were mapped against the genome version mm9 of Mus musculus by using TopHat2 and the UCSC gene model annotation from iGenome as guide (default parameters, except for --mate-inner-dist 150 and --min-intron-length 50)
Aligned fragments (both reads from each pair correctly mapped) were counted at the gene level by using HTSeq-count (default parameters, except for --mode intersection-strict)
Differential expression analysis was carried out by using DESeq2 (alpha 0.05).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files containing the raw fragment counts for each gene feature for each replicate generated by HTSeq and used as input for DESeq2

molecule: total RNA

organism: Mus musculus

source_name: Mesenchymal cells

extract_protocol:
Limbs of E13.5 Osr1 GCE/+ and Osr1 GCE/GCE embryos were extracted, minced and digested by using a collagenase solution. Cell suspensions were stained with propidium iodine. GFP-expressing live cells were sorted by using a FACS Aria II and collected directly into RLT buffer for RNA extraction (RNeasy mini kit, Qiagen).
RNA libraries were prepared by using the TruSeq RNA Library Preparation Kit v2 according to Illumina's intructions and subjected to high-throughput sequencing by using the Illumina HiSeq 2500 technology. 65-75 million of 50-bp paired-end reads were generated with a mean insert size of 150 bp.

tag: strain

tag: tissue

value: limbs

tag: developmental stage

tag: genotype

value: Heterozygous


title: FN Treatment, 2

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

country: China

institute: Renji Hospital

data_processing:
Reads were mapped to the human genome (hg19) using TopHat v2.0.11 (http://tophat.cbcb.umd.edu) with the following default options with a TopHat transcript index built from Ensembl_GRCh37. Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file.
Genome_build: Ensembl_GRCh37(hg19)
Supplementary_files_format_and_content: count

organism: Homo sapiens

source_name: HT-29 cells

growth_protocol: The human colorectal cancer cells HT-29 were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
total RNA of HT-29 cells with different treatment was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cultured F.nucleatum was used to treat  the HT29 colorectal cancer cells, while the blank culture medium-teated HT29 CRC cells was used as negative controls.

tag: cell type

value: human colorectal cancer cells

tag: agent

value: F. nucleatum


title: ODS 2

city: Würzburg

first: Corinna

last: Rosenbaum

address: Röntgenring 11

department: Department of Tissue Engineering and Regenerative Medicine

country: Germany

institute: University Hospital Wuerzburg

data_processing:
Basecalls and demultiplexing were performed using CASAVA for HiSeq2500 sequencing. Each sample was previously splitted into four samples indicated by name affix 'gp 1-4'
Mapping was performed with TopHat2 (v2.0.5, default settings) against the human reference genome assembly "hg19" with the annotation from Gencode "v17".
Gene quantification was calculated with a python script, “rpkmforgenes.py” from the Sandberg Laboratory (http://sandberg.cmb.ki.se/rnaseq/) at readcount and RPKM level (=reads per kilobase of exon model per million mapped reads) according to Mortazavi et al. using uniquely mapped reads.
Differential gene expression profiling was carried out exclusively based on readcount quantification via the DESeq2 package developed for RNA sequencing data.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample.

source_name: Rectal wall

extract_protocol:
RNA was isolated from frozen whole rectal wall samples with the RNAeasy Mini Plus Kit (Qiagen, Hilden, Germany) and checked for quality and quantity with Agilent’s 2100 Bioanalyzer using the RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, USA).
cDNA libraries were prepared using Illumina’s TruSeqTM RNA Sample Preparation v2 protocol. Sequencing was performed using an Illumina HiSeqTM 2500. Quality and quantity was checked with Agilent's 2100 Bioanalyzer using DNA 1000 Kit.

tag: disease state

value: ODS

tag: gender

value: female

value: Rectal wall


title: non-infected_rep3

description:
S001136-31248330_J18-17
Processed data file: subread-align_featureCounts_all.tab.txt
Processed data file: DESeq2_infectedvsnon-infected.complete.txt
Processed data file: edgeR_infectedvsnon-infected.complete.txt


title: non-infected_rep1

description:
S001134-31243408_J16-16
Processed data file: subread-align_featureCounts_all.tab.txt
Processed data file: DESeq2_infectedvsnon-infected.complete.txt
Processed data file: edgeR_infectedvsnon-infected.complete.txt


title: non-infected_rep2

description:
S001135-31251333_J16-43
Processed data file: subread-align_featureCounts_all.tab.txt
Processed data file: DESeq2_infectedvsnon-infected.complete.txt
Processed data file: edgeR_infectedvsnon-infected.complete.txt


title: Invader 4 LTR ctrl standard

city: Vienna

first: Schaefer

last: Matthias

state: AT

address: Schwarzspanierstrasse 17-I

department: Cell and Developmental Biology

country: Austria

institute: Medical University Vienna, Center for Anatomy & Cell Biology

description:
PCR product from Invader 4 LTR
alignment to LTR sequence

library_source: genomic

data_processing:
Linkers and barcode sequences were extracted from the 454 output. Barcoded reads representing each genotype and experimental condition were binned (raw data files: barcode-separated reads) and mapped to an Invader 4 LTR sequence (FBgn0063427) using pairwise sequence alignment (processed data files: alignment to Inv4_LTR). C at positions of Cs in Invader4 LTR scored as 0 in sequencing reads while Ts at positions of Cs scored as 1 (processed data files: matrix score of methylation_output).
Genome_build: aligned to DM3 Invader 4 LTR sequence (FBgn0063427); sequence available on series record.
Supplementary_files_format_and_content: text file with aligned reads and text file with methylation score for each sample.  Methylation scoring card (0:methylated; 1: not methylated). Methylation scores are provided only for the Cs in the sequence.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: wild type; control, mixed adults, whole body

growth_protocol: Flies were cultured on standard fly food in a humidified incubator (60% humidity) at a 12/12 hour day-night light cycle

extract_protocol: Bisulfite conversion on 5 µg of genomic DNA was carried using the EpiTect Bisulfite Kit (Qiagen) according to the manufacturer’s instructions. 200 ng bisulfite-treated DNA was used as template in a first PCR reaction (35 cycles, annealing temperature= 50°C) to amplify regions in the canonical Invader4 LTR. Amplicons were gel-purified and 50 ng were used as template for a second PCR reaction (15 cycles, annealing temperature= 50°C) to re-amplify the amplicon and adding 454-sequencing adapters.

treatment_protocol: Adult flies were heat-shocked (37 C for one hour) in a water bath, followed by a recovery period of 5 hours at RT for heat shock samples, one and 3 days for recovery samples before extracting genomic DNA.

value: adults 3 days after hatching

value: mixed

value: whole body


title: Treated_24h_rep2

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

country: USA

institute: Michigan State University

data_processing:
Illumina bcl2fastq (v1.8.4) was used to de-multiplexe and converte reads to FASTQ format
Trimmomatic (v0.32) with a 4 bp sliding window, cutting when the read quality was below 15 (using the Phred33 quality scoring system) or read length was less than 36 bp.
Trimmed reads were then aligned to the M. tuberculosis H37Rv genome (assembly 19595v2) using Bowtie with the –S option to produce SAM files as output. Alignment quality control was performed using the HTSeq-qa function within the HTSeq software package. Further graphical quality control analyses were performed using the Qualimap software suite.
SAMtools was used to calculate coverage depth (>98% coverage acrosss the genome for all samples).
HTSeq software suite was used to analyze aligned and determin counts per gene feature in the M. tuberculosis H37Rv genome
Differential gene expression was calculated by normalizing the data utilizing the trimmed mean of M-values normalization method and filtering out genes that had <23 counts per million (CPM) within the edgeR package
R was used for statistical analysis and differential gene expression by fitting a negative binomial model to each set of conditions and testing for differences utilizing the DESeq package
Qualimap was used to analyze coverage against the reference genome, sequence depth and pearson's correlation coefficient between replicates
Genome_build: M. tuberculosis H37Rv genome (ASM19595v2)
Supplementary_files_format_and_content: Processed files are presented as .xlsx spreadsheets and represents the average of 2 biological replicates
Supplementary_files_format_and_content: Table_S1_2h: Normalized counts and differential expression 2B8 treated 2h
Supplementary_files_format_and_content: Table_S2_24h: Normalized counts and differential expression 2B8 treated 24h

organism: Mycobacterium tuberculosis

source_name: Bacterial cell

growth_protocol: M. tuberculosis H37Rv was cultured in 7H9 media to an OD600 of 0.4.

extract_protocol:
Cells were resuspended in trizol and disrupted using Zirconia beads (Biospec, Bartlesville, OK, USA) by beating six times for 30 sec and cooling on ice for one min in between. Beads were removed and chloroform was added to trizol (0.2:1, v/v). Samples were vortexed and centrifuged to extract solubilized RNA in the aqueous phase. To precipitate RNA, molecular grade 100% ethanol (Sigma-Aldrich Aldrich, USA) was added to the aqueous phase and incubated at -80⁰C overnight. The RNA was pelleted by centrifugation (×17,000g) at 4⁰C, for 15 min followed by washing with 75% ethanol. DNA contamination was removed by treating with 10 µL DNase1 (New England Biomed, Ipswich, MA, USA) at 37⁰C for 30 min. Then 100 µL of acid phenol (Sigma-Aldrich, USA) was added to the samples and vortexed. After centrifugation (×17,000g) for one min, the aqueous phase was collected and transferred to clean RNAse-free tubes, followed by the addition of 33 µL sodium acetate (Sigma-Aldrich, USA) and 250 µL of 100% ethanol. Samples were gently mixed by inverting and placed at -80⁰C overnight. Samples were centrifuged (×17,000g) for 15 min at 4⁰C to collect RNA pellets. Pellets were further washed with 80% ethanol. After ethanol removal, pellets were air-dried at room temperature for five min and reconstituted in 15 µL of RNAse-free water (Corning, USA).
Illumina Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) with the Epicentre Ribo-Zero Gram positive bacteria ribosomal RNA depletion (Illumina, USA).
The pool was loaded on one lane of a HiSeq Rapid Run flow cell (v1) and sequenced in a 1×50 bp single end (SE50) format using Rapid SBS reagents. Base calling was performed by Illumina Real Time Analysis (RTA, Illumina, USA) v1.18.61 and output of RTA was de-multiplexed and converted to FastQ format with Illumina Bcl2fastq v1.8.4 (Illumina, USA). To compensate for the low number of reads obtained for one sample, MiSeq (SE50) sequencing was performed with this one library. Reads from both the HiSeq and MiSeq runs were combined for that particular sample.

treatment_protocol: M. tuberculosis H37Rvtreated with 125 µM 2B8 for 2 and 24 h.  Following treatment, RNA was isolated from the bacterial cultures and used for RNA-seq. 2 Biological Replicates were performed.

tag: treatment

value: 125 microM 2B8

tag: time (hours)


title: Treated_24h_Rep1


title: WT_CLP_D1_rep1

city: Bethesda

first: Damian

last: Kovalovsky

address: 9000 Rockville Ave

institute: National Cancer Institute

description:
Transcriptome analysis of lymphoid progenitors in Zbtb1-deficient mice
WT5_CLP_D1

data_processing:
Basecalling with RTA v1.18.61
Demultiplexing with Bcl2fastq v1.8.4
Trimming with Trimmomatic v0.32
Mapping with STAR 2.4.0d
Read Count with htseq v0.6.1p1
Normalization and differential expression with DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text format; count data as content

source_name: Wild type CLP after culture

growth_protocol: Cells were analyzed ex-vivo (D0) or grown on OP9-DL1 cocultures plus IL-7 and Flt3L for 24hs (D1)

extract_protocol:
RNA was extracted from sorted cells using qiagen Rneasy micro kit  and cDNA amplified using SMARTer Ultra Low RNA-Seq System
Nextera XT DNA Sample Prep Kit FC-131-1096

treatment_protocol: D1: IL7 (1ng/ml) Flt2L (5ng/ml), D0: no treatment

value: wildtype

tag: background strain

value: common lymphoid progenitors

tag: co-culture treatment


title: non-infected_rep4

description:
S001137-31249354_J2-8
Processed data file: subread-align_featureCounts_all.tab.txt
Processed data file: DESeq2_infectedvsnon-infected.complete.txt
Processed data file: edgeR_infectedvsnon-infected.complete.txt


title: infected_rep5

description:
S001133-31241419_J16-51
Processed data file: subread-align_featureCounts_all.tab.txt
Processed data file: DESeq2_infectedvsnon-infected.complete.txt
Processed data file: edgeR_infectedvsnon-infected.complete.txt

source_name: midgut, infected

value: Trypanosoma congolense s.l.


title: infected_rep3

description:
S001131-31250350_J17-18
Processed data file: subread-align_featureCounts_all.tab.txt
Processed data file: DESeq2_infectedvsnon-infected.complete.txt
Processed data file: edgeR_infectedvsnon-infected.complete.txt


title: infected_rep1

description:
S001129-31254269_J26-1
Processed data file: subread-align_featureCounts_all.tab.txt
Processed data file: DESeq2_infectedvsnon-infected.complete.txt
Processed data file: edgeR_infectedvsnon-infected.complete.txt


title: infected_rep4

description:
S001132-31238395_J17-23
Processed data file: subread-align_featureCounts_all.tab.txt
Processed data file: DESeq2_infectedvsnon-infected.complete.txt
Processed data file: edgeR_infectedvsnon-infected.complete.txt


title: infected_rep2

description:
S001130-31254268_J20-10
Processed data file: subread-align_featureCounts_all.tab.txt
Processed data file: DESeq2_infectedvsnon-infected.complete.txt
Processed data file: edgeR_infectedvsnon-infected.complete.txt


title: Neat1 wt rep3

status: Public on Jul 27 2017

city: Stanford

first: Stephano

last: Spano Mello

state: CA

address: 269 Campus Drive

institute: Stanford University

data_processing:
Basecalls performed using CASAVA 1.8
STAR aligner was used for alignment to mouse genome version mm10
DESeq2 was used for statistical analysis and to generate a variance stabilized table of counts used for subsequent analysis
Genome_build: mm10
Supplementary_files_format_and_content: normalized abundance measurements

source_name: E1A;HRasV12-expressing MEFs_Neat1 WT

growth_protocol: DMEM with 10% FCS, for RNA-seq 1.5x 106 cells were plated on 10 cm dish

extract_protocol:
Total RNA was isolated using Qiagen's RNAeasy Micro Kit.
Illumina TruSeq Stranded RNA LT Kit (Cat#15032612) was used and 1 µg of total RNA was entered for the construction of sequencing libraries. The libraries were prepared using the manufacturer's standard protocol.

tag: strain background

tag: genotype/variation

value: wild-type

value: E1A;HRasV12-expressing mouse embryonic fibroblasts (MEFs)


title: Neat1 null rep2

source_name: E1A;HRasV12-expressing MEFs_Neat1-KO


title: Untreated_Rep1_A


title: Neat1 null rep3


title: Neat1 wt rep2


title: Treated_2h_Rep2


title: Neat1 wt rep4


title: Neat1 null rep1


title: Neat1 wt rep1


title: Neat1 null rep4


title: Untreated_Rep2


title: Untreated_Rep1_B


title: Treated_2h_Rep1


title: FN Treatment, 1


title: 1835_cortical_d41_1

city: Evanston

first: Winton

last: Moy

state: Illinois

address: 1001 University Place

department: Center Psychiatric Genetics

institute: Northshroe Univeristy Health Systems

description: cell culture duplicate

data_processing:
Library strategy: ATAC-Seq
Library strategy: ATAC-Seq
Illumina CASAVA v1.8 standard
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard.
Genome-wide read density was calculated as the number of insertions found within 150bp sliding window with 20 bp step size.
Peaks were called using the HOTSPOT v4 with FDR set to 0.05 and the default settings. The 50bp mappability files were downloaded from http://www.uwencode.org/proj/hotspot/.
Genome_build: hg19
Supplementary_files_format_and_content: The hotspot peaks are stored in a tab delimited bed file with column 1 indicating the chromosome column 2 and 3 indicate the start and end of the peak. The scores stored in the 5th columnare z-scores that are from the binomial model for scoring hotspots

source_name: Cortical neurons differentiated from iPSC

growth_protocol: For iPSC culture and cortical neuron differentiation, we have adopted the protocol (Shi et al., Nature Protocols, 2012) to our iPSCs growing In feeder-free medium (mTeSR). In brief, we plate 5 wells of iPSCs (on a 6-well plate) onto one well of Geltrax-coated 12-well plate in 800ul of mTeSR media, allowing cells to attach overnight and reaching 100% confluence 1 day after plating. For neural induction, we switched the cell culture media to neural induction media (NIM) containing 1uM of Dorsomorphin. After 10 days of neural induction when a homogeneous neuroepithelial layer is formed, we passaged the cells onto laminin-coated 35-mm dish and switched the cell culture media to Neural Maintenance Medium (NMM). Upon appearance of neural rosettes, we added 20ng/ml of FGF2 for 2-4 days to promote the expansion of neural stem cells (NSCs). At about day 20 after neural induction, we passaged the cells for the first NSC expansion (1: 3). After another round of NSC expansion at day 25, we passaged the NSC culture at ~day 30 using Accutase at a ratio of 1:4 onto laminin-coated 35-mm dish (for collecting cells later) and laminin-coated coverslips (for immunofluorescence staining). We continued the neural differentiation for the plated cells in NMM until the specified days to collect the cells.

extract_protocol:
For ATAC-seq, we harvested 50,000 cells (iPSCs, induced NSCs and neurons at days 27, 33 and 41 of neural induction) by centrifugation at 500g x 5 min at 4°C. We washed cells once with PBS buffer and resuspended  the cell pellet in 50 μL of cold lysis buffer (10 mM Tris-HCl, pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). We spinned down cell pellet, discarded the supernatant, and immediately continued to transposition reaction (keep the nuclei pellet on ice) in 50 μl transposition reaction mix. We incubated the transposition reaction at 37°C for 30 min, immediately followed by purification through a Qiagen MinElute Kit. We stored purified DNA at -20°C until library creating sequencing library.
The library was generated and sequenced at University of Minnesota Genomic Center. We have followed the protocol as previously described (Buenrostro et al., Nature Methods. doi:10.1038/nmeth.2688, 2013) except for using primers from the Illumina Nextera kit for PCR amplification of the transposed DNA fragments.

value: Cortical neurons at day 41 of neuronal differentiation

tag: Sex

tag: passage number


title: 1835_iPS2

description: iPSC cell culture duplicate

source_name: iPSC derived from fibroblast cells of GM01835 from Coriell Cell Repositories

value: iPSC


title: 1835_cortical_d33

description: day 33 culture; but was  considered as duplicate of day 30 because of high correlation with day 27 sample

source_name: Cortical neuron stem cells differentiated from iPSC

value: Cortical NSC/neurons at day 33 of neuronal  differentiation


title: 1835_cortical_d27

description: day 27 culture; but was  considered as duplicate of day 30 because of high correlation with day 33 sample

value: Cortical NSC/neurons at day 27 of neuronal differentiation


title: 1835_cortical_d41_2

description: cell culture duplicate


title: 1835_iPS1

description: iPSC cell culture duplicate


title: MCF10A TGFb esterified leucine batch6 RP

city: Amsterdam

first: Koos

last: Rooijers

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

description:
ribosome profiling
adapter sequence (3'): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG

data_processing:
Adapter sequences were trimmed from raw data using cutadapt 1.1 with parameters (--quality-base=33 -O 12 -m 20 -q 5). Reads without adapter sequence were discarded.
rRNA was filtered from data by alignment to transcript database compiled from Ensembl 37.65 (gene categories “rRNA”, “rRNA_pseudogene” and “Mt_rRNA”) using bowtie (v2.0.6) with parameters (--seed 42 --local) and retention of the unmapped reads.
Analogous to rRNA filtering, tRNA was filtered by alignment to a tRNA database compiled from the GtRNAdb (Chan and Lowe, NAR, 2009).
Reads not mapped in previous steps were used in final alignment using tophat (v2.0.7) with parameters (--seed 42 -n 2 -m 1 --no-novel-juncs --no-novel-indels --no-coverage-search --segment-length 25) to hg19 and transcripts defined by GENCODE v19/BASIC.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files were generated from alignment files output by tophat in the final alignment step, only using primary alignments and alignments with mapping quality >= 10. Scores indicate read coverage, normalized to reads per 10 million reads.

source_name: MCF10A cell line

growth_protocol: MCF10A-inducible RASV12 cells were cultured in DMEM/F12 1:1 medium supplemented with 5% horse serum, EGF (10 ng/ml), insulin (10 μg/ml), cholera toxin (100 ng/ml), and hydrocortisone (500 ng/ml) in 5% CO2 at 37°C.

extract_protocol:
Approximately 30e6 cells were treated with chloramphenicol (100μg/ml) for 15 minutes and cycloheximide (100μg/ml) for 5 minutes. Cells were lysed in buffer B (20 mM Tris-HCl, pH 7.8, 100mM KCl, 10mM MgCl2, 1% Triton X-100, 2mM DTT, 100 μg/ml chloramphenicol, 100 μg/ml cycloheximide, 1x Complete protease inhibitor). Lysates were centrifuged at 5000 rpm and the supernatant was treated with 2U/μl of RNase I (Ambion) for 40 minutes at room temperature. Lysates were fractionated on a linear sucrose gradient (7% - 47%) using the SW- 41Ti rotor at 36,000 rpm for 2hrs. Fractions enriched in mito-monosomes and cytosolic monosomes were identified by western blotting, pooled and treated with proteinase K (Roche) in 1% SDS. Released RPFs were purified using Trizol reagent (Invitrogen) following the manufacturer’s instructions.
RNA was gel-purified on a denaturing 10% polyacrylamide urea (7 M) gel. A section corresponding to 30-33 nucleotides was excised, eluted and ethanol precipitated. The resulting fragments were 3′-dephosphorylated using T4 polynucleotide kinase (New England Biolabs Inc. Beverly, MA, USA) for 6 h at 37°C in 2-(N-morpholino)ethanesulfonic acid (MES) buffer (100 mM MES-NaOH, pH 5.5, 10 mM MgCl2, 10 mM β-mercaptoethanol, 300 mM NaCl). 3′ adaptor was added with T4 RNA ligase 1 (New England Biolabs Inc. Beverly, MA, USA) for 2.5 h at 37°C. Ligation products were 5′-phosphorylated with T4 polynucleotide kinase for 30 min at 37°C. 5′ adaptor was added with T4 RNA ligase 1 for 18 h at 22°C.

treatment_protocol: Cells were treated with TGF-beta (10ng/ml) for 48 hrs. For rescue experiments, cells were treated with esterified Leucine (2.5 mM) for 18 hrs

tag: cell line


title: SUM159 batch3d leucine starvation 0.2x 24h RP

source_name: SUM159 cell line

growth_protocol: SUM159PT cells were cultured in DMEM/F12 1:1 medium supplemented with 5% FCS, insulin (5 μg/ml), and hydrocortisone (1ug/ml) in 5% CO2 at 37°C.

treatment_protocol: For Leucine starvation, cells were cultured in the same medium lacking Leucine for 12 and 24hrs.


title: SUM159 batch3d leucine starvation 0x 12h RP


title: MCF10A control batch6 RP


title: PHH 2

city: Bunkyo-ku

first: Taketomo

last: Kido

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

data_processing:
The mapping of the reads was performed using the STAR program and the quantification of genes and transcripts was done with the RSEM program.
Genome_build: hg38

source_name: Primary human hepatocyte

growth_protocol: hiPSC-derived LPCs, LSECs, and HSCs were plated onto collagen gel. Cells were cultured in DMEM/F12 supplemented with 10% FBS, penicillin-streptomycin-glutamine, ITS, N-2 supplement, MEM non-essential amino acids solution, L-glutamine, ascorbic acid (1 mM), nicotinamide (10 mM), N-acetylcysteine (0.2 mM), dexamethasone (1×10-7 M), Y27632 (5 mM), A83-01 (2.5 mM), HGF (20 ng/ml), EGF (10 ng/ml), and OSM (20 ng/ml) for 10 weeks.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacture’s protocol.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Kit.

value: hepatocyte


title: iPS-liver 1

source_name: hiPSC-derived liver model

value: hepatocyte, sinusoidal endothelial cell, and stellate cell


title: SUM159 batch3d control RP


title: iPS-LPC 1

source_name: hiPSC-derived liver progenitor cells

value: liver progenitor cell


title: iPS-LPC 2


title: iPS-liver 2


title: PHH 1


title: U2OS control batch7 RNAseq

data_processing:
(Ribosome profiling data only) Adapter sequences were trimmed from raw data using cutadapt 1.1 with parameters (--quality-base=33 -O 12 -m 20 -q 5). Reads without adapter sequence were discarded.
rRNA was filtered from data by alignment to transcript database compiled from Ensembl 37.65 (gene categories “rRNA”, “rRNA_pseudogene” and “Mt_rRNA”) using bowtie (v2.0.6) with parameters (--seed 42 --local) and retention of the unmapped reads.
Analogous to rRNA filtering, tRNA was filtered by alignment to a tRNA database compiled from the GtRNAdb (Chan and Lowe, NAR, 2009).
Reads not mapped in previous steps were used in final alignment using tophat (v2.0.6) with parameters (--seed 42 -n 2 -m 1 --no-novel-juncs --no-novel-indels --no-coverage-search --segment-length 25) to hg19 and transcripts defined by GENCODE v19/BASIC.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files were generated from alignment files output by tophat in the final alignment step, only using primary alignments and alignments with mapping quality >= 10. Scores indicate read coverage, normalized to reads per 10 million reads.

source_name: U2OS control batch7 RNAseq

growth_protocol: U2OS WII-I cells containing the doxycycline-inducible Myc (a gift from Martin Ellers) were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen). Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions.

treatment_protocol: For induction of Myc gene, U2OS WII-I cells were treated with doxycycline for 36 hours.


title: U2OS control batch6 RNAseq

source_name: U2OS control batch6 RNAseq


title: U2OS myc batch7 RP

source_name: U2OS myc batch7 RP


title: MCF10A SLC3A2 OE batch5 RP

source_name: MCF10A SLC3A2 OE batch5 RP

growth_protocol: MCF10A cells were cultured in DMEM/F12 1:1 medium supplemented with 5% horse serum, EGF (10 ng/ml), insulin (10 μg/ml), cholera toxin (100 ng/ml), and hydrocortisone (500 ng/ml) in 5% CO2 at 37°C.

treatment_protocol: SLC3A2 expression vector were kindly provided by Roy Zent. Stable expression clones were selected with blasticidin. For TGFβ1 treatment, MCF10a cells were treated with human recombinant TGFβ1 (10ng/ml) for 48 hours (R&D Systems).


title: MCF10A SLC3A2 OE TGFb batch5 RP

source_name: MCF10A SLC3A2 OE TGFb batch5 RP


title: U2OS control batch7 RP

source_name: U2OS control batch7 RP


title: MCF10A TGFb batch5 RP

source_name: MCF10A TGFb batch5 RP


title: MCF10A siSLC3A2 TGFb batch4 RNAseq

source_name: MCF10A siSLC3A2 TGFb batch4 RNAseq

treatment_protocol: MCF10A cells were transfected using Dharmafect I reagent (Dharmacon) following the manufacturer's instructions. For TGFβ1 treatment, MCF10a cells were treated with human recombinant TGFβ1 (10ng/ml) for 48 hours (R&D Systems).


title: MCF10A control batch5 RP

source_name: MCF10A control batch5 RP


title: U2OS control batch6 RP

source_name: U2OS control batch6 RP


title: MCF10A TGFb batch6 RP


title: MCF10A siCtrl batch4 RNAseq

source_name: MCF10A siCtrl batch4 RNAseq


title: MCF10A siSLC3A2 TGFb batch4 RP

source_name: MCF10A siSLC3A2 TGFb batch4 RP


title: MCF10A siCtrl TGFb batch4 RNAseq

source_name: MCF10A siCtrl TGFb batch4 RNAseq


title: MCF10A siSLC3A2 batch4 RP

source_name: MCF10A siSLC3A2 batch4 RP


title: MCF10A siSLC3A2 batch4 RNAseq

source_name: MCF10A siSLC3A2 batch4 RNAseq


title: U2OS myc batch7 RNAseq

source_name: U2OS myc batch7 RNAseq


title: U2OS myc batch6 RNAseq

source_name: U2OS myc batch6 RNAseq


title: MCF10A siCtrl TGFb batch4 RP

source_name: MCF10A siCtrl TGFb batch4 RP


title: MCF10A TGFb 1 batch2 RP

description:
ribosome profiling
adapter sequence (3'):TCGTATGCCGTCTTCTGCTTG

source_name: MCF10A TGFb 1 batch2 RP

treatment_protocol: For TGFβ1 treatment, MCF10a cells were treated with human recombinant TGFβ1 (10ng/ml) for 48 hours (R&D Systems).


title: MCF10A siCtrl batch4 RP

source_name: MCF10A siCtrl batch4 RP


title: MCF10A TGFb 2 batch1 RP

description:
ribosome profiling
adapter sequence (3'):TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG

source_name: MCF10A TGFb 2 batch1 RP


title: MCF10A control 1 batch2 RP

source_name: MCF10A control 1 batch2 RP


title: U2OS myc batch6 RP

source_name: U2OS myc batch6 RP


title: MCF10A control 2 batch1 RP

source_name: MCF10A control 2 batch1 RP


title: MCF10A TGFb 1 batch1 RNAseq

source_name: MCF10A TGFb 1 batch1 RNAseq


title: MCF10A control 1 batch1 RNAseq

source_name: MCF10A control 1 batch1 RNAseq


title: MCF10A control 1 batch1 RP

source_name: MCF10A control 1 batch1 RP


title: shRNA_SCR_RRBSseq

city: Augusta

first: Jan

last: van Riggelen

state: GA

address: 1410 Laney Walker Blvd.

institute: Augusta University

data_processing:
Sequencing was carried out on an Illumina HiSeq 3000.
Quality control of sequencing reads was performed using FastQC.
Adapter removal was performed using Trim Galore! v0.4.1.
Reads were then aligned to the reference genome using bismark v0.16.1, followed by methylation calling using the corresponding bismark functionality.
The comparative RRBS analysis was carried out using methylKit, based on reference genome mm9.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph represent the CpG methyaltion status

source_name: T-cell acute lymphoblastic leukemia_shRNA_SCR

extract_protocol:
Genomic DNA was extracted using the Macherey-Nagel NucleoSpin Tissue Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: T-cell

tag: strain

value: FVB/N

value: EuSR[gamma]-tTA;tet-o-MYC


title: shRNA_DNMT3B_RRBSseq

source_name: T-cell acute lymphoblastic leukemia_shRNA_DNMT3B


title: GRO Br Set8KO

city: Vassilika Vouton, Herakleion

first: Iannis

last: Talianidis

state: Crete

address: 100 N. Plastira Str

department: Institute of Molecular Biology and Biotechnology

country: Greece

institute: Foundation for Research and Technology - Hellas

data_processing:
Library strategy: GRO-Br-seq
Base calling was performed using software provided with the Ion Torrent Proton sequencer.
Sequenced reads were mapped to mm9 whole genome using, for RNA-Seq reads, tophat2 with default settings and using additional transcript annotation data for the mm9 genome from Illumina iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html). The reads which remained unmapped were submitted to a second round of mapping using Bowtie2 against mm9 with the --local and --very-sensitive options. For ChIP-Seq reads, Bowtie2 with default parameters was used. For GRO-Seq reads, Bowtie2 with standard parameters was used in two rounds: in the first mapping round, GRO-Seq samples were aligned against the Mus musculus clone RP23-225M6 45S pre-ribosomal RNA gene  to remove ribosomal RNA contamination which led to the removal of 3 to 10% of short reads. The remaining reads were aligned against the mm9 genome using again Bowtie2.
For RNA-Seq, reads overlapping the Ensembl build 67 mouse exons were counted and filtered for artifacts as follows: if an annotated gene had up to five exons, tag presence was required in at least two exons. If an annotated gene had E >5 exons, tag presence was required in at least E/5 exons. The final gene counts were calculated as the sums of their exonic reads. The counts table was normalized using DESeq normalization and analyzed for differential expression using DESeq and the Bioconductor package metaseqR. The final list of differentially expressed genes was derived by the genes demonstrating a binomial test p-value less than 0.05. ChIP-Seq data were processed using SICER for the detection of H4K20me1 enriched regions and MACS2 broad calling for Phf8 enriched regions.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited files containing DESeq normalized counts for each Ensembl gene for RNA-Seq data. Tab-delimited files containing raw read counts for each Ensembl gene for GRO-Seq data. BigWig signal files for ChIP-Seq data.

source_name: Liver

growth_protocol: Mice were maintained in grouped cages in a temperature controlled, pathogen-free facility on a 12-h light/dark cycle and fed by a standard chow diet (Altromin 1324; 19% protein, 5% fat) and water ad libitum.

extract_protocol: For library preparation of NRO samples, the Ion Total RNA-Seq Kit v2 for Whole Transcriptome Libraries protocol (ThermoFisher Scientific) was used. Two different sets of NRO samples were prepared:For GRO-EU-seq, liver nuclear RNA from EU-treated mice were prepared by Trizol extraction followed by biotinylation reaction and purification using Click-iT Nascent RNA Capture Kit (Thermo Fisher C10365). 1μl of RNaseIII enzyme and buffer was used to fragment the EU samples, prior to hybridization and ligation, for 2min at 37°C. The samples were further hybridized, ligated and reverse transcribed, according to protocol. GRO-BrU-seq, reactions in isolated liver nuclei were performed as described in (Fang et al., 2014; Cell, Vol 159: pp 1140-1152). After treatment with RppH and polynucleotide kinase, 10μl were directly hybridized with 4μl of Ion adaptor Mix V2 and 6μl hybridization solution, for 10’ at 65°C and 5’ at 30°C followed by ligation with 20μl ligation buffer and 4μl enzyme, for 70’ at 30°C. The samples were then reverse transcribed in a mixture containing 14μl of Ion RT Primer V2 and 8μl 10x Superscript III enzyme. The resulting cDNA from both BR and EU samples was purified with nucleic acid binding beads, eluted in 6μl  ddH2O and amplified according to protocol, in the presence of 45μl Platinum PCR Supermix High Fidelity, 1μl Ion Xpress RNA 3’ Barcode primer and 1μl Ion Xpress RNAseq BC Barcode primer 1-24. [94°C-2’/(97°C-20’’,50°C-30’’,68°C-30’’)*2cycles/(94°C-30’’,62°C-30’’,68°C-30’’)*16cycles/68°C-5’]. The amplified cDNAs were further purified with nucleic acid binding beads, eluted in 15μl ddH2O and their concentration measured in Agilent bioanalyzer. 40 pM of each library was templated using the Ion Chef instrument, loaded on a Ion P1 V3 chip and sequenced on Ion Proton sequencer.

treatment_protocol: Mice were left untreated, except for GRO-EU-seq experiments where mice received a single dose of 25mg /kg bodyweight Ethydyl-Uridine (EU) injection intraperitoneally 30 min before sacrifice. Livers were dissected and divided for the preparation of RNA and crosslinked chromatin or nuclei (for GRO-Br-seq).

value: F1 mice (C57Bl6/CBA)

tag: age

value: 45 days postnatal

tag: tissue

value: liver


title: GRO Eu Set8KO

data_processing:
Library strategy: GRO-Eu-seq
Base calling was performed using software provided with the Ion Torrent Proton sequencer.
Sequenced reads were mapped to mm9 whole genome using, for RNA-Seq reads, tophat2 with default settings and using additional transcript annotation data for the mm9 genome from Illumina iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html). The reads which remained unmapped were submitted to a second round of mapping using Bowtie2 against mm9 with the --local and --very-sensitive options. For ChIP-Seq reads, Bowtie2 with default parameters was used. For GRO-Seq reads, Bowtie2 with standard parameters was used in two rounds: in the first mapping round, GRO-Seq samples were aligned against the Mus musculus clone RP23-225M6 45S pre-ribosomal RNA gene  to remove ribosomal RNA contamination which led to the removal of 3 to 10% of short reads. The remaining reads were aligned against the mm9 genome using again Bowtie2.
For RNA-Seq, reads overlapping the Ensembl build 67 mouse exons were counted and filtered for artifacts as follows: if an annotated gene had up to five exons, tag presence was required in at least two exons. If an annotated gene had E >5 exons, tag presence was required in at least E/5 exons. The final gene counts were calculated as the sums of their exonic reads. The counts table was normalized using DESeq normalization and analyzed for differential expression using DESeq and the Bioconductor package metaseqR. The final list of differentially expressed genes was derived by the genes demonstrating a binomial test p-value less than 0.05. ChIP-Seq data were processed using SICER for the detection of H4K20me1 enriched regions and MACS2 broad calling for Phf8 enriched regions.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited files containing DESeq normalized counts for each Ensembl gene for RNA-Seq data. Tab-delimited files containing raw read counts for each Ensembl gene for GRO-Seq data. BigWig signal files for ChIP-Seq data.

tag: genotype


title: GRO Br WT

value: Wild type


title: SDS1 Input Set8KO replicate 1

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer.
Sequenced reads were mapped to mm9 whole genome using, for RNA-Seq reads, tophat2 with default settings and using additional transcript annotation data for the mm9 genome from Illumina iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html). The reads which remained unmapped were submitted to a second round of mapping using Bowtie2 against mm9 with the --local and --very-sensitive options. For ChIP-Seq reads, Bowtie2 with default parameters was used. For GRO-Seq reads, Bowtie2 with standard parameters was used in two rounds: in the first mapping round, GRO-Seq samples were aligned against the Mus musculus clone RP23-225M6 45S pre-ribosomal RNA gene  to remove ribosomal RNA contamination which led to the removal of 3 to 10% of short reads. The remaining reads were aligned against the mm9 genome using again Bowtie2.
For RNA-Seq, reads overlapping the Ensembl build 67 mouse exons were counted and filtered for artifacts as follows: if an annotated gene had up to five exons, tag presence was required in at least two exons. If an annotated gene had E >5 exons, tag presence was required in at least E/5 exons. The final gene counts were calculated as the sums of their exonic reads. The counts table was normalized using DESeq normalization and analyzed for differential expression using DESeq and the Bioconductor package metaseqR. The final list of differentially expressed genes was derived by the genes demonstrating a binomial test p-value less than 0.05. ChIP-Seq data were processed using SICER for the detection of H4K20me1 enriched regions and MACS2 broad calling for Phf8 enriched regions.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited files containing DESeq normalized counts for each Ensembl gene for RNA-Seq data. Tab-delimited files containing raw read counts for each Ensembl gene for GRO-Seq data. BigWig signal files for ChIP-Seq data.

extract_protocol:
For ChIP-seq, extracts from crosslinked liver tissues were immunoprecipitated by antibodies against RNA Pol-II (Euromedex IPB-7G5), Rabbit polyclonal anti-phospho Ser2-RNA Pol-II CTD (Abcam ab5095), Rabbit polyclonal anti-PHF8 (Abcam ab36068), H4K20Me1 (Abcam ab9051) as described in Sarris et al., 2016, Cancer Cell Vol: 14. pp 354-366).
About 10 ng of the immunoprecipitated DNA and input DNA was used for library preparation following the optimized workflow of Ion Proton system (Life Technologies). Briefly, ChIPseq DNA libraries were created using the Ion Plus Fragment Library Kit (ThermoFisher Scientific) protocol with the following modifications: approximately 2ng of sheared chromatin immunoprecipitated DNA was diluted with ddH2O in a final volume of 79μl. For DNA samples with undetected concentration the whole eluted volume was used (~25μl) and added to the required amount of ddH2O. DNA was End-repaired by the addition of 20μl of End-repair buffer and 1μl enzyme per sample followed by 30min incubation at RT. Samples were purified with Agencourt AMPure XP beads (Beckman Coulter) at a ratio of 1.8 and, after subsequent washes with 70%EtOH, were eluted in 40μl Low TE. Adaptors were then ligated to the DNA in the presence of 10μl ligase buffer and 2μl ligase enzyme. 1μl of universal IonXpress P1 adaptor was added in all samples with 1μl of barcoded IonXpress adaptor, 1-96. The reaction was diluted in ddH2O to a final volume of 100μl and incubated for 30min at RT. After a further purification with Agencourt AMPure XP beads at a ratio of 1.5, the  samples, eluted in 25μl of LowTE, were amplified using 100ul Platinum PCR Supermix High Fidelity and 5μl Library amplification primer mix. Each sample was divided into two 65μl reactions and amplified using the following thermal cycling protocol: 72°C-20’/95°C-5’/(97°C-15’’,60°C-15’’,70°C-1’)*17cycles/70°C-5’. The 2 reactions for each sample were mixed again and the samples were purified using a 2 step purification protocol. During the first step, Agencourt AMPure XP beads to sample ratio of 0.8 was used, to remove fragments of 400bp or more. The supernatant was used for a 2nd purification using Agencourt AMPure XP beads ratio of 0.5 and eluted in in 25μl ddH2O. The ChIP DNA libraries with a mean fragment length of 200bp were quantified on an Agilent bioanalyzer and 40pM of each library was templated using the Ion Chef instrument, loaded on a Ion P1 V3 chip and sequenced on an Ion Proton sequencer.


title: SDS1 Input WT replicate 2


title: GRO Eu WT


title: SDS1 Input WT replicate 1


title: SDS1 Set8KO WT PolII replicate 1


title: SDS1 Set8KO WT PolII replicate 2


title: SDS1 ChIP WT PolII replicate 2


title: Input Set8KO replicate 2


title: Input WT replicate 2


title: SDS1 ChIP WT PolII replicate 1


title: Input WT replicate 1


title: ChIP Set8KO Phf8 replicate 1


title: MCF10A TGFb 1 batch1 RP

source_name: MCF10A TGFb 1 batch1 RP


title: J-35 2i/L to S/L p30

city: Cambridge

first: Kendell

last: Clement

state: MA

address: 7 Divinity Ave.

institute: Harvard University

data_processing:
Sequencing reads were trimmed using timgalore, as well as NuGEN-provided script for diversity trimming and filtering.
Alignment: bisulfite-converted reads were aligned to a the mm9 genome using Bsmap version 2.89 with the following flags: -v 0.05 -s 16 -w 100 -S 1 -p 8 -u
Methylation calling: CpGs in the reference sequence were compared to the sequence in the aligned read. If bisulfite conversion (signifying an unmethylated cytosine) was detected, the read added to the unmethylated count for that CpG, otherwise, it added to the methylated count.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files contain the number of methylated and total reads for CpGs covered by RRBS with the columns: chromosome, start, end, number of reads methylated divided by number of reads seen, methylation percent/1000

source_name: ESC

extract_protocol: RRBS libraries were prepared using a commercial kit (Ovation RRBS Methyl-Seq System, NuGen, San Carlos, CA) following the manufacturer's protocol except that we pooled 12 individually barcoded reactions after the final repair step and performed the bisulfite conversion and library amplification as a pool. Libraries were sequenced on an Illumina HiSeq2500 high-output flowcell without a PhiX spike-in using Nugen's custom sequencing primer and standard Illumina sequencing primers to read the sample barcodes

treatment_protocol: generation protocol: J-34 ESCs at passage 4 were cultured in 2i/L for 16 passages and then switched back to S/L for 10 passages.

tag: cell type

value: J-34 ESCs

value: male


title: J-37 2i/L to S/L p30

treatment_protocol: generation protocol: J-37 ESCs at passage 4 were cultured in 2i/L for 16 passages and then switched back to S/L for 10 passages.

value: J-37 ESCs


title: J-37 2i/L to S/L p23

treatment_protocol: generation protocol: J-37 ESCs at passage 4 were cultured in 2i/L for 16 passages and then switched back to S/L for 3 passages.


title: ChIP WT Phf8 replicate 1


title: ChIP Serin2 Set8KO PolII replicate 2


title: ChIP Set8KO Phf8 replicate 2


title: ChIP WT Phf8 replicate 2


title: SDS1 Input Set8KO replicate 2


title: ChIP Set8KO H4K20me1 replicate 2


title: Input Set8KO replicate 1


title: J-35 PKCi/L p20

treatment_protocol: generation protocol: J-35 ESCs at passage 4 were cultured in PKCi/L for 16 passages.

value: J-35 ESCs


title: ChIP Set8KO H4K20me1 replicate 1


title: J-34 2i/L to S/L p23

treatment_protocol: generation protocol: J-34 ESCs at passage 4 were cultured in 2i/L for 16 passages and then switched back to S/L for 3 passages.


title: ChIP Serin2 WT PolII replicate 1


title: ChIP WT H4K20me1 replicate 2


title: ChIP WT H4K20me1 replicate 1


title: J-35 a2i/L p20

treatment_protocol: generation protocol: J-35 ESCs at passage 4 were cultured in a2i/L for 16 passages.


title: Set8KO replicate 3

molecule: polyA RNA

extract_protocol:
Approximately 20 µg of total RNAs were used for mRNA isolation using the Dynabeads® mRNA DIRECT™ Micro Kit (Life Technologies, Carlsbad, CA, USA)
For RNA-Seq experiments, the isolated mRNA was digested with RNaseIII, hybridized and ligated to Ion Adaptors, reverse transcribed, barcoded and amplified, using the Ion Total RNA-Seq Kit v2 (Life Technologies, Carlsbad, CA, USA). Samples were processed on an OneTouch 2 instrument and enriched on a One Touch ES station. Templating was performed using the Ion PI™ Template OT2 200 Kit (Life Technologies, Carlsbad, CA, USA) and sequencing with the Ion PI™ Sequencing 200 Kit on Ion Proton PI™ chips (Life Technologies, Carlsbad, CA, USA) according to commercially available protocols.


title: Set8KO replicate 1


title: Set8KO replicate 2


title: Wildtype replicate 3


title: Wildtype replicate 2


title: Wildtype replicate 1


title: J-35 2i/L to S/L p23

treatment_protocol: generation protocol: J-35 ESCs at passage 4 were cultured in 2i/L for 16 passages and then switched back to S/L for 3 passages.


title: ChIP Serin2 Set8KO PolII replicate 1


title: J-37 2i/L p20

treatment_protocol: generation protocol: J-37 ESCs at passage 4 were cultured in 2i/L for 16 passages.


title: LGMP_in_vivo_miR99_KD_2

city: NEW YORK

first: WENHUO

last: HU

email: huwenhuo@gmail.com, huw@mskcc.org

state: NEW YORK

address: 1275 YORK AVENUE

department: HOPP

institute: MEMORIAL SLOAN KETTERING CANCER CENTER

data_processing:
trim_glaie (trimming adaptor sequences)
STAR alignment to mm9
picard (remove duplicates)
htseq_count (read numbers for each gene)
DESEQ2 DEG analysis
Genome_build: mm9
Supplementary_files_format_and_content: HTSeq count file

source_name: FACS-sorted L-GMPs at time of death

growth_protocol: Primary L-GMP cells (GFP+ tdTom+ c-Kit+ Sca-1+ CD16/32+ CD34+) from Scr or miR-99 KD MLL-AF9 secondary recipients were FACS purified at the time of death

extract_protocol:
FACS-purified cells were lysed in Trizol LS, from which RNA extractions were performed.
Libraries were prepared using SMARTer amplification

tag: protocol

value: Primary leukemic stem cells


title: ChIP Serin2 WT PolII replicate 2


title: LGMP_in_vivo_Scr_2


title: LGMP_in_vivo_miR99_KD_1


title: LGMP_in_vivo_Scr_1


title: J-34 2i/L p20

treatment_protocol: generation protocol: J-34 ESCs at passage 4 were cultured in 2i/L for 16 passages.


title: J-35 2i/L p20

treatment_protocol: generation protocol: J-35 ESCs at passage 4 were cultured in 2i/L for 16 passages.


title: PPAR KO

first: Xing-Ming

last: Shi

address: 1120 15th Street

data_processing:
illumina HiSeq2000 (fastq.gz) had been mapped with Tophat (v2.0.5) against reference assembly UCSC mm9 downloaded from illumina iGenome.
Mapping files from Tophat (accepted_hits.bam) from each sample had  been input into cufflinks (v2.0.2), to locate genomic regions with expression under guide of  ‘genes.gtf’ ( annotation file from illumina iGnome). Information of expression were recorded in  ‘transcript.gtf’.
cufflinks.cuffmerge had been called to combine all ‘transcripts.gtf’ into a single ‘merged.gtf’.
Mapping files generated by Tophat were input into cufflinks.cuffdiff (v.2.0.2), to measure  expression level on regions (genes, transcripts, CDS, etc.) defined in ‘merged.gtf’.
Expression level were measured with FPKM (Fragments Per Kilobase per Million mapped),  which could be found in .fpkm_tracking files in cuffdiff folder. Statistical test on difference  between samples could be found in .diff files. qvalue  less than 0.05 is considered as statistically  significant.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample with column names of "tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status"

source_name: Bone marrow mesenchymal stem/progenitor cells (MSCs)

growth_protocol: DMEM supplemented with10% FBS

extract_protocol:
Total cellular RNAs were isolated using TRIzol reagent according to the manufacturer's instructions (Invitrogen Corp., Grand Island, NY, USA). The RNA samples were cleaned  up with the Qiagen RNeasy® Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone Marrow

value: PPAR KO


title: J-37 S/L p20

treatment_protocol: generation protocol: J-37 ESCs at passage 4 were cultured in S/L for 16 passages.


title: Stably_Engrafted_LSK_Scr_2

source_name: Stably Engrafted LSKs

growth_protocol: Stably engrafted GFP+ LSK (Lin-negative s-Kit+ Sca-1+) cells from mice transplanted with GFP+ miR-99 KD or Scr LT-HSCs were FACS sorted 3 months post-transplantation.

value: Primary stem and progenitor cells


title: Stably_Engrafted_LSK_miR99_KD_2


title: Stably_Engrafted_LSK_miR99_KD_1


title: J-34 S/L p20

treatment_protocol: generation protocol: J-34 ESCs at passage 4 were cultured in S/L for 16 passages.


title: J-35 S/L p20

treatment_protocol: generation protocol: J-35 ESCs at passage 4 were cultured in S/L for 16 passages.


title: LSK_miR99_KD_1_Day2_in_vitro

source_name: FACS sorted GFP+ cells 48hr post-transduction of LSKs

growth_protocol: Primary mouse LSK (Lin-negative c-Kit+ Sca-1+) cells were transduced with Scr or miR-99 KD lentiviral vectors. GFP+ cells were FACS purified 48hr after infection.


title: J-34 a2i/L p20

treatment_protocol: generation protocol: J-34 ESCs at passage 4 were cultured in a2i/L for 16 passages.


title: J-35 PKCi/L p10

treatment_protocol: generation protocol: J-35 ESCs at passage 4 were cultured in PKCi/L for 6 passages.


title: LSK_Ctrl_3_Day2_in_vitro


title: J-34 a2i/L p10

treatment_protocol: generation protocol: J-34 ESCs at passage 4 were cultured in a2i/L for 6 passages.


title: J-37 2i/L p10

treatment_protocol: generation protocol: J-37 ESCs at passage 4 were cultured in 2i/L for 6 passages.


title: J-34 PKCi/L p20

treatment_protocol: generation protocol: J-34 ESCs at passage 4 were cultured in PKCi/L for 16 passages.


title: LSK_Ctrl_1_Day2_in_vitro


title: J-35 2i/L p10

treatment_protocol: generation protocol: J-35 ESCs at passage 4 were cultured in 2i/L for 6 passages.


title: PPAR-f/f

value: mesenchymal stem/progenitor cells (MSCs)

value: PPAR-flox


title: QT7 2

city: Hamilton

first: Bradley

last: Doble

state: Ontario

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

description:
Clone B
Galaxy126-[CellXtype_WT_vs_QT7]
Galaxy122-[CellXtype_QKO_vs_QT7]
Galaxy124-[CellXtype_QT7_vs_QT7L1]

data_processing:
Illumina RTA (v1.18.64) was used for basecalling. Illumina bcl2fastq (v1.8.4) was used to generate the FASTQ files.
Sequenced reads were mapped to mm10 whole genome, using Star (v2.4.0f1) with the parameters:  -runMode alignReads  -outSAMunmapped Within -outSAMtype BAM SortedByCoordinate.
The public instance of Galaxy (usegalaxy.org) was used to run htseq-count (on BAM files provided by the McGill University and Génome Québec Innovation Centre (http://gqinnovationcenter.com/support/techSupport.aspx?l=e).  The following parameters were used: 1) GFF file - Mus Musculus GRCm38.84.gtf; 2) Mode - Intersection (strict); 3) Stranded - reverse; 4) Minimum alignment quality - 10; 5) Feature type - exon; 6) ID attribute - gene_id; 7) Additional BAM output - False; 7) Force sorting - False.
DEseq2 (v2.1.8.3) was then used to compare htseq-count data obtained for the various cell lines by using the following parameters: 1) factor name - cell type; 2) factor levels - WT, QKO, QT1 and QT3; 3) Visualising the analysis results - True; 4) Output all levels vs all levels of primary factor - True; 5) Fit type - parametric; 6) Turn off outliers replacement - True; 7) Turn off outliers filtering - True; 8) Turn off independent filtering - True.  The history for the Galaxy analyses can be obtained here: https://usegalaxy.org/u/braddoble/h/deseq2-qko-lines.
Genome_build: mm10
Supplementary_files_format_and_content: Tabular ht-seq files for each sample, are provided with ensembl ID and raw counts. Additionally, tabular DESeq2 files for each comparison, are provided with ensembl ID and normalized counts.

source_name: mouse embryonic stem cells

growth_protocol: Mouse ES cells were maintained for 48hr in standard mESC media (15% serum + LIF).

extract_protocol:
Total RNA was extracted with Invitrogens Purelink RNA Mini Kit, in accordance with the prescribed protocol provided with the kit. Quality Control was performed by running the samples on a Agilent Bioanalyzer 2100 using an RNA 6000 Nano chip.
Libraries were generated from 250 ng of total RNA using the Illumina TruSeq stranded mRNA Sample Preparation Kit, as per the manufacturer’s recommendations. Libraries were quantified using the Life Technologies Quant-iT™ PicoGreen® dsDNA Assay Kit and the Kapa Biosystems Illumina GA with Revised Primers-SYBR Fast Universal kit. Average size fragment was determined using a Perkin Elmer LabChip GX instrument.

tag: mouse es cell type

tag: mouse strain

tag: timepoint


title: QT7L1 2

description:
Clone B
Galaxy127-[CellXtype_WT_vs_QT7L1]
Galaxy123-[CellXtype_QKO_vs_QT7L1]
Galaxy124-[CellXtype_QT7_vs_QT7L1]


title: QT7 1

description:
Clone A
Galaxy126-[CellXtype_WT_vs_QT7]
Galaxy122-[CellXtype_QKO_vs_QT7]
Galaxy124-[CellXtype_QT7_vs_QT7L1]


title: QKO 1

description:
Clone A
Galaxy125-[CellXtype_WT_vs_QKO]
Galaxy122-[CellXtype_QKO_vs_QT7]
Galaxy123-[CellXtype_QKO_vs_QT7L1]


title: QT7L1 1

description:
Clone A
Galaxy127-[CellXtype_WT_vs_QT7L1]
Galaxy123-[CellXtype_QKO_vs_QT7L1]
Galaxy124-[CellXtype_QT7_vs_QT7L1]


title: WT 2

description:
Biological replicate 2
Galaxy125-[CellXtype_WT_vs_QKO]
Galaxy126-[CellXtype_WT_vs_QT7]
Galaxy127-[CellXtype_WT_vs_QT7L1]

value: WT


title: WT 1

description:
Biological replicate 1
Galaxy125-[CellXtype_WT_vs_QKO]
Galaxy126-[CellXtype_WT_vs_QT7]
Galaxy127-[CellXtype_WT_vs_QT7L1]


title: Stably_Engrafted_LSK_Scr_1


title: J-37 S/L p10

treatment_protocol: generation protocol: J-37 ESCs at passage 4 were cultured in S/L for 6 passages.


title: J-35 S/L p10

treatment_protocol: generation protocol: J-35 ESCs at passage 4 were cultured in S/L for 6 passages.


title: J37S_ESC_H2AX

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

data_processing:
The  output  sequencing  reads  were  filtered  and  pre-analyzed  with  Illumina  standard workflow. After filtration, the qualified tags (in fastq format) were aligned to the mouse genome (mm9) with bowtie2 (2.0.6). Reads mapped to sex chromosomes were discarded.
Then, these aligned reads were used for peak calling with the RSEG algorithm (0.4.8) with mode 3 to identify differential binding regions compared with J34 S/L samples. For cells cultured in 2i and then switched back to serum, the combination of all male S/L samples were used as control to reach a comparable throughput. The relative decreased regions were assigned to whole genome-wise 20kb windows to calculate a weighted average score and used for enumerating overlapping regions. Heatmap and unsupervised hierarchical clustering analysis were drawn in 500kb domains. GREAT was used to predicts the putative target genes and calculates statistical enrichments for associations between genomic regions and annotations.

growth_protocol: Male and female ESC lines were derived from blastocysts (129S6 X C57B6) as previously described53. For S/L culture, ESCs were cultured on irradiated MEF feeders in KO DMEM (Invitrogen) supplemented with 15% FBS (Hyclone), 1mM L- glutamine, 100 uM non-essential amino acids, 1X PenStrep, 0.1 mM beta-mercaptoethanol, and 103 IU LIF). For 2i/L culture, ESCs were cultured in a 1:1 mixture of DMEM/F12 and Neurobasal medias (Invitrogen) supplemented with N2 (Invitrogen), B27 (Invitrogen), 1X PenStrep, 103 IU LIF, 1 μM PD0325901, and 3 μM CHIR990216.

extract_protocol:
Native  Chromatin  immunoprecipitation  (N-ChIP)  assay  was  performed  as  previously described. Approximately 10  million  of  ESC s  were  used  for  each  ChIP  and massive  parallel  sequencing  (ChIP-Seq)  experiment.  In brief, chromatin  pellets  were  briefly digested  with  MNase  (New  England  BioLabs) and  the  mononucleosomes  were  monitored  by electrophoresis.5ug  anti-H2A.X antibodies (active motif 39689)were  used  per  ChIP experiment.
Libraries were prepared according to Illumina's standard protocol, with instructions accompanying the DNA Sample Kit

tag: antibody vendor

value: active motif

tag: antibody

tag: antibody cat#

tag: culturing condition

value: Serum/LIF


title: J-34 S/L p10

treatment_protocol: generation protocol: J-34 ESCs at passage 4 were cultured in S/L for 6 passages.


title: LSK_miR99_KD_2_Day2_in_vitro


title: J37i_ESC_H2AX


title: J35S_ESC_Input

value: No antibody


title: J35S_ESC_H2AX


title: J35i_ESC_Input


title: J35i_ESC_H2AX


title: J-34 2i/L p10

treatment_protocol: generation protocol: J-34 ESCs at passage 4 were cultured in 2i/L for 6 passages.


title: LSK_Ctrl_2_Day2_in_vitro


title: Wild-type keratinocytes

treatment_protocol: generation protocol: Neonatal mouse keratinocytes were isolated essentially as described (Lichti et al., 2008). The isolated keratinocytes were plated on a 25cm2 flask coated with conditioned media derived from a rat epithelial cell line (Riddelle et al., 1991) using proliferative media previously described to allow for the continual culture and passaging of mouse keratinocytes (Mou et al., 2016).

value: Neonatal mouse keratinocytes

value: female


title: 2i/L keratinocytes #1


title: J34S_ESC_H2AX


title: J-34 PD

treatment_protocol: generation protocol: J-34 ESCs were treated with PD for 6 passages.


title: J34i_ESC_H2AX


title: J-34 CHIR

treatment_protocol: generation protocol: J-34 ESCs were treated with CHIR for 6 passages.


title: J32XS_ESC_H2AX


title: MEK DKO

treatment_protocol: generation protocol: Mek1fl/fl;Mek2-/- MEFs were infected with a lentivirus constitutively expressing M2rtTA and a lentivirus containing a doxycycline-inducible polycistronic cassette encoding Oct4, Klf4, Sox2 and c-Myc. Infected MEFs were plated onto irradiated MEF feeders in complete S/L media supplemented daily with 2 μg/ml doxycycline until iPSC colonies emerged. Doxycycline-independent, clonal Mek1fl/fl;Mek2-/- iPSCs were picked, expanded, and electroporated with a plasmid expressing Cre recombinase to delete the floxed Mek1 allele. Resultant Mek1/2 double knock-out iPSCs were maintained on irradiated MEF feeders in S/L.

value: Mek1fl/fl;Mek2-/- MEFs


title: QKO 2

description:
Clone B
Galaxy125-[CellXtype_WT_vs_QKO]
Galaxy122-[CellXtype_QKO_vs_QT7]
Galaxy123-[CellXtype_QKO_vs_QT7L1]


title: J30XS_ESC_Input


title: H3K9me3_WT_SPY137_TSA removal 5 hr

city: Boston

first: Gloria

last: Jih

address: 240 Longwood Ave, LHRRB 517

department: Cell Biology

institute: Harvard Medical School

description: barcode sequence: ACTAACTGC

data_processing:
Raw reads were separated by barcode. Barcode sequence were removed from the reads and attached to the identifier. Reads were mapped using Bowtie's default parameters. Mapped reads were normalized to reads per million, tiled with igvtools, and visualized in Integrated Genome Viewer (IGV).
Genome_build: ASM294v2
Supplementary_files_format_and_content: Mapped reads were normalized to reads per million, tiled with igvtools for visualization in Integrated Genome Viewer (IGV).

organism: Schizosaccharomyces pombe

source_name: H3K9me3_WT_SPY137_TSA removal 5 hr

extract_protocol:
ChIP was performed as previously described (Yu et al., 2014). Conditions for fixation and immunoprecipitation (IP) are briefly described here. 50 ml cultures of cells were grown overnight (or 24 hours when 2.5 ug/ml tetracycline was added) in YES to an optical density (OD) of 2 and fixed as follows. For H3K9me2, H3K9me3, and Chp1 ChIP, cell were fixed with 1% formaldehyde for 15 min. For Swi6 and Flag-protein ChIP, we used a modified dual-crosslinking protocol in which cells were first incubated at 18 °C for two hours, resuspended in 5 ml of room temperature PBS, and fixed with 1.5 mM ethylene glycol bis-succinimidyl succinate (EGS, Thermo Scientific #21565) for 30 min, followed by addition of formaldehyde to 1% final concentration for another 30 min (Zeng et al., 2006). For Swi6 ChIP in Figure S4, the 2 hr incubation at 18 °C was omitted. For each IP, ~ 2 ug of antibody was pre-incubated with 30 ul of Invitrogen Dynabeads Protein A or Protein G: anti-H3K9me2 (Abcam 1220) with Protein A, anti-H3K4me3 (Millipore 04-745) with protein G, anti-H3K36me3 (Abcam 9050) with protein A, anti-H4K16ac (Active Motif 39167) with protein A, anti-Chp1 (Ab18191) with protein A, anti-Flag (Sigma F1804) with protein G, anti-Swi6 (rabbit polyclonal) with protein A, anti-RNA pol II 8WG16 (BioLegend MMS-126R-500) with protein A. For IP with H3K9me3 antibody, Dynabeads M-280 Streptavidin beads were first incubated with 1 ug of anti-H3K9me3 (Diagenode C15500003), followed by blocking with 5 uM biotin. Sheared chromatin lysate was added to the antibody-bead mixture and incubated for 2 hr at 4 °C on a rotating device.
Immunoprecipitated DNA was cleaned up using the Qiagen PCR Purification Kit after reversing cross-links, RNaseA, and proteinase K treatment. Immunoprecipitated DNA was eluted from column with the provided elution buffer (50 ul x 2), subjected to additional shearing in a Qsonica water bath sonicator at 20% amplitude for 15 minutes of total shearing time (each cycle is 15” on + 15” off), followed by vacuum centrifugation to reduce the volume to 30 ul. DNA concentration was measured using Qubit dsDNA HS Kit.1 to 10 ng of immunoprecipitated DNA was used for standard Illumina library construction using barcoded adapters and protocol described previously (Wong et al., 2013). Libraries were pooled and sequenced on the Illumina HiSeq2000 or 2500.

tag: media

value: YEA - TSA

value: H3K9me3 (Diagenode C15500003)


title: 2i/L keratinocytes #2

tag: Sex

value: male


title: Dnmt1-deficient ES cells mRNA

city: Athens

middle: J

last: Schmitz

address: B416 Davison Life Sciences

institute: University of Georgia

data_processing:
RNA-seq: Basecalls performed using bcl2fastq v1.8.4
RNA-seq: Adapter sequence removed using fastq-mcf
RNA-seq: Reads trimmed according to quality score using seqtk trimfq (-q 0.01)
RNA-seq: Reads mapped to mouse genome (mm10) with TopHat2 v2.0.10
RNA-seq: Transcripts assembled for wildtype, Drosha-/- and Dnmt1c/c datasets for each of the RNA types (short, long and mRNA) using Cufflinks v2.1.1 (default settings, -g gencode.vM3.annotation.gtf)
RNA-seq: Wildtype and Drosha-/- transcripts merged using Cuffmerge to obtain master transcriptomes for each pairwise comparison of gene expression, in each RNA type
RNA-seq: Differential gene expression analysis carried out using Cuffdiff (gencode.vM3.annotation.gtf, short RNA was masked using a gtf file containing gencode rRNAs, Mt_tRNAs, snRNAs, Mt_rRNAs and snoRNAs)
Genome_build: Mus musculus GRCm38 reference genome
Supplementary_files_format_and_content: tab delimited text file

source_name: Dnmt1-deficient ES cells

growth_protocol: MethylC-Seq: ES cells were cultured in ES cell media which consists of Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum, 100 IU/mL penicillin, 100mg/mL streptomycin, 2 mmol/L L-glutamine, MEM non-essential amino acids, 0.12 mmol/L β-mercaptoethanol, and leukemia inhibitory factor (LIF); RNA-seq: ES cells were cultured in ES cell media which consists of Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum, 100 IU/mL penicillin, 100mg/mL streptomycin, 2 mmol/L L-glutamine, MEM non-essential amino acids, 0.12 mmol/L β-mercaptoethanol, and leukemia inhibitory factor (LIF)

extract_protocol:
RNA-seq: Trizol Extracted total RNA was subsequently fractionated into long and short (using miRVana miRNA Isolation Kit) and mRNA (using Oligotext mRNA Mini Kit)
MethylC-Seq: Genomic DNA was prepared from fresh cell pellets using GeneJET Genomic DNA Purification Kit (ThermoScientific) according to the manufacturer’s protocol; RNA-seq: Libraries were constructed according to NEBNext Multiple Small RNA Library Prep Protocol (NEB)

tag: genotype/variation

value: embryonic stem cells (ES cells)

tag: molecule subtype

value: mRNA RNA


title: J37iS_ESC_H2AX

tag: strain

value: 2i/LIF then Serum/LIF


title: J30XS_ESC_H2AX


title: J34iS_ESC_H2AX


title: H3K9me3_WT_SPY137_TSA removal 7 hr

description: barcode sequence: CAGGAGGCG

source_name: H3K9me3_WT_SPY137_TSA removal 7 hr


title: IgG_Control

value: No antibody IgG control


title: H3K9me3_WT_SPY137_TSA removal 0 hr

description: barcode sequence: GGTCCTTGA

source_name: H3K9me3_WT_SPY137_TSA removal 0 hr


title: H3K9me3_WT_SPY137_TSA removal 3 hr

description: barcode sequence: TTGAGTGT

source_name: H3K9me3_WT_SPY137_TSA removal 3 hr


title: Dnmt1-deficient ES cells total RNA

value: Total RNA


title: J31XS_ESC_H2AX


title: H3K9me3_WT_SPY137_untreated

description: barcode sequence: AACACCTAC

value: YEA


title: Drosha-deficient ES cells short RNA

source_name: Drosha-deficient ES cells

value: Drosha-deficient

value: Short RNA


title: H3K9me2_WT_SPY137_TSA removal 7 hr

description: barcode sequence: CGGACGTGG

source_name: H3K9me2_WT_SPY137_TSA removal 7 hr

value: WT


title: Drosha-deficient ES cells total RNA


title: Drosha-deficient ES cells mRNA


title: H3K9me2_WT_SPY137_TSA removal 5 hr

description: barcode sequence: ATCCTATTC

source_name: H3K9me2_WT_SPY137_TSA removal 5 hr


title: ATAC_ILCP_rep2

city: Chicago

first: Aiping

last: Mao

state: IL

address: 929 East 57th street

department: Pathology

institute: University of Chicago

data_processing:
Base calling was performed using Illumina software pipeline
ATAC-seq and ChIP-seq reads were aligned to mm10 genome using bowtie with the following parameters: --sam --best -m 1 -n 2 --chunkmbs 300
Duplicate reads were removed using picard tools
Peaks were called using MACS
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated using HOMER
Supplementary_files_format_and_content: bed files contained the peaks called by MACS

extract_protocol: Illumina Nextra DNA prep kit (Part# FC-121-1030)

value: Bone marrow

value: ILCP

tag: antibodies


title: WT ES cells short RNA

source_name: WT ES cells

value: wild type


title: ATAC_ILCP_rep1

tag: tissue


title: H3K9me2_WT_SPY137_TSA removal 3 hr

description: barcode sequence: GTGGGATA

source_name: H3K9me2_WT_SPY137_TSA removal 3 hr

tag: genotype


title: WT ES cells mRNA

tag: cell type


title: H3K9me2_WT_SPY137_TSA removal 0 hr

description: barcode sequence: TAGCTAGTA

source_name: H3K9me2_WT_SPY137_TSA removal 0 hr


title: ATAC_CLP_rep3

value: CLP


title: WT ES cells total RNA


title: H3K9me2_WT_SPY137_untreated

description: barcode sequence: ACGTAGCTC


title: Flag_flag-clr4W31G_SPY5562

description: barcode sequence: CATTCCAAG

value: YES

value: Flag (Sigma F1804)


title: ATAC_NKT_rep1

value: Thymus

value: NKT


title: ATAC_CLP_rep1


title: 2i_S_ESCs_WGBS

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

data_processing:
Libraries were sequenced on the HiSeq2500 (2 X 101 bp or 2×100 bp paired-end reads, illumina)
Low quality bases and adapters in sequenced reads were trimmed with cutadapt-1.9.1
The trimmed reads were mapped to both B6 mouse genome (mm10) and MSM/ms mouse genome independently by Bismark software-v0.15.0 with bowtie2 (version 2.2.8) and default settings, and the reads mapped to the same chromosome and positions of both B6 and MSM/ms genomes with high mapping quality (MAPQ>=20) were used for further analysis. MSM/ms mouse genome were reconstructed from mm10 using the SNPs (NIG Mouse Genome Database (MSMv4HQ, http://molossinus.lab.nig.ac.jp/msmdb/index.jsp)). Chromosomes Y and M were ommited from MSM/ms genomes because of lack of the SNPs information.
For methyl-seq libraries, the B6-derived and MSM/ms-derived sequenced reads were selected based on the MSM/ms SNPs data which were not in CpG sites and the patterns of bisulfite conversion. Methylated cytosines were extracted from the reads by the Bismark methylation extractor with --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5 options. For methyl-seq libraries, only the original bottom (OB) data were used for analysis of methylation status and methylation percentages were represented at the sites which have equal or more than 5 read depth.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph colums: <chromosome> <start position> <end position> <methylation percentage>, *The coordinates are zero-based, half-open.

source_name: ES cells

extract_protocol:
PureLink Genomic DNA mini kit (invitrogen)
For methyl-seq library preparation, 3μg of genomic DNA was sheared by covaris. Libraries were constructed using SureSelectXT Mouse Methyl-Seq Reagent Kit (Agilent Technologies). Bisulfite treatment was perfomed by EZ DNA methylation-GOLD kit (ZYMO RESEARCH). For whole genome bisulfite sequencing library, 500ng of DNA was sheared by covaris and ligated with methylated adapters supplied by TruSeqTM DNA, Sample Prep Kit-v2 (Illumina). Subsequently, DNA was bisulfite-treated using EZ DNA Methylation-Gold KitTM according to the supplier’s instruction. Final library amplification was performed using Pfu Turbo Cx (Agilent Technologies). The libraries were then sequenced on HiSeq 2500 (2 X 101 bp paired-end reads, Illumina).

tag: passage

value: F1 (129X1/SvJ and MSM/Ms)

value: ES cells


title: S_ESC_36_female_WGBS

tag: gender

value: female


title: Flag_flag-clr4F449Y_SPY4642

description: barcode sequence: ATCGCCAGC


title: ATAC_CD4SP_rep2

value: CD4SP thymocyte


title: 2i_ESC_23_male_WGBS

value: male


title: 2i_ESC_15_female_WGBS


title: ATAC_NKT_rep2


title: ATAC_CD4SP_rep1


title: Flag_flag-clr4_SPY4636

description: barcode sequence: TGACGCAT


title: Flag_clr4F449Y flag-clr3_SPY5597

description: barcode sequence: TGATCCGA

source_name: Flag_clr4F449Y flag-clr3_SPY5597

value: clr4F449Y flag-clr3


title: MEFs_female_methylseq

source_name: MEFs

value: MEFs


title: Flag_clr4Δ flag-clr3_SPY5595

description: barcode sequence: GCAAGTAGA

source_name: Flag_clr4Δ flag-clr3_SPY5595

value: clr4_delta flag-clr3


title: J-37 2i/L to S/L p23

first: Konrad

last: Hochedlinger

address: 185 Cambridge St.

department: Molecular Biology

institute: Massachusetts General Hospital

description: J-37 2i/L to S/L p23

data_processing:
Quality Control: PICARD, Version: 1.100, CollectRnaSeqMetrics
Alignment: STAR version 2.3.0
Alignment manipulation: Samtools 0.1.18.0
Feature Counting: HTSeq version 0.6.0. Parameters: unstranded=TRUE, quality thresh=10, feature file=ftp://ftp.ensembl.org/pub/release-67/gtf/mus_musculus/Mus_musculus.NCBIM37.67.gtf.gz
Differential Expression: R library edgeR, version 3.8.6
Genome_build: mm9
Supplementary_files_format_and_content: Excel spreadsheet (CPM.all_samples.xlsx) provides counts per million (CPM) values for those genes with CPM >= 1 for at least two samples.

source_name: ESC

growth_protocol: The cells cultured in each condition were passaged onto MEF feeder layers in respective media every four days using trypsin.

extract_protocol:
Undifferentiated ESCs were sorted for SSEA1+ to control for the homogeneity of cells before RNA extraction using the phenol/chloroform protocol.
One microgram of total RNA from each sample was used as input for Illumina Ribo-Zero Kit, followed by NEBNext Ultra Directional RNA Library Prep Kit for Illumina.
Each paired-end library was prepared with an adaptor with unique index sequence. The size profiles of resulting libraries were than determined on the BioAnalyzer 2100 with Agilent High Sensitivity DNA kit, followed by quantification by qPCR on the Perkin Elmer 7500Fast with Kapa library quantification kit KK4824. These libraries were then pooled together at equal molar concentration and sequenced on an Illumina HiSeq 2000.

tag: generation protocol

value: J-37 ESCs at passage 4 were cultured in 2i/L for 16 passages and then switched back to S/L for 3 passages.


title: J-35 2i/L to S/L p23

description: J-35 2i/L to S/L p23

value: J-35 ESCs at passage 4 were cultured in 2i/L for 16 passages and then switched back to S/L for 3 passages.


title: Flag_WT flag-clr3_SPY5593

description: barcode sequence: CATTCCAAG

source_name: Flag_WT flag-clr3_SPY5593

value: WT flag-clr3


title: S_ESC_8_female_methylseq


title: ATAC_CLP_rep2

value: Bone marrow


title: Flag_clr4F449Y flag-chp2_SPY5382

description: barcode sequence: TAGCTAGTA

source_name: Flag_clr4F449Y flag-chp2_SPY5382

value: clr4F449Y flag-chp2


title: S_ESC_36_female_methylseq


title: Flag_clr4Δ flag-chp2_SPY5380

description: barcode sequence: CGAACTGTG

source_name: Flag_clr4Δ flag-chp2_SPY5380

value: clr4_delta flag-chp2

value: YES


title: 2i_MEFs_methylseq


title: Flag_WT flag-chp2_SPY5378

description: barcode sequence: ACGTAGCTC

source_name: Flag_WT flag-chp2_SPY5378

value: WT flag-chp2

value: Flag (Sigma F1804)


title: J-37 2i/L p20

description: J-37 2i/L p20

value: J-37 ESCs at passage 4 were cultured in 2i/L for 16 passages.


title: J-34 2i/L to S/L p23

description: J-34 2i/L to S/L p23

value: J-34 ESCs at passage 4 were cultured in 2i/L for 16 passages and then switched back to S/L for 3 passages.


title: MEFs_male_methylseq

value: F1 (129X1/SvJ and MSM/Ms)


title: Flag_untagged_SPY137

description: barcode sequence: ATCGCCAGC

value: untagged


title: Swi6_clr4F449Y_SPY4642

description: barcode sequence: GTTGTCCCA

value: Swi6 (Rabbit polyclonal)


title: J-37 S/L p20

description: J-37 S/L p20

value: J-37 ESCs at passage 4 were cultured in S/L for 16 passages.

value: male


title: J-34 2i/L p20

description: J-34 2i/L p20

value: J-34 ESCs at passage 4 were cultured in 2i/L for 16 passages.


title: J-35 S/L p20

description: J-35 S/L p20

value: J-35 ESCs at passage 4 were cultured in S/L for 16 passages.


title: J-35 2i/L p20

description: J-35 2i/L p20

value: J-35 ESCs at passage 4 were cultured in 2i/L for 16 passages.


title: Swi6_swi6Δ_SPY1098

description: barcode sequence: TGACGCAT


title: 2i_ESC_2_female_methylseq

value: ES cells

value: female


title: B6_129_22_p3_WGBS

data_processing:
Libraries were sequenced on the HiSeq2500 (2 X 101 bp or 2×100 bp paired-end reads, illumina) or Nextseq500 (75 bp, single read, illumina)
Low quality bases and adapters in sequenced reads were trimmed with cutadapt-1.9.1
For normal WGBS analysis, the trimmed reads were mapped to the mouse genome (mm10) by Bismark software-v0.15.0 with bowtie2 (version 2.2.8) and default settings, and the mapped reads with high mapping quality (MAPQ>=20) were used for extraction of methylated cytosines by the Bismark methylation extractor with --ignore 10 --ignore_3prime 5 options (single-end reads) or with --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5 options (paired-end reads).
For allelic methylation analysis, the trimmed reads were mapped to both B6 mouse genome (mm10) and MSM/ms mouse genome independently by Bismark software-v0.15.0 with bowtie2 (version 2.2.8) and default settings, and the reads mapped to the same chromosome and positions of both B6 and MSM/ms genomes with high mapping quality (MAPQ>=20) were used for further analysis. MSM/ms mouse genome were reconstructed from mm10 using the SNPs (NIG Mouse Genome Database (MSMv4HQ, http://molossinus.lab.nig.ac.jp/msmdb/index.jsp)). Chromosomes Y and M were ommited from MSM/ms genomes because of lack of the SNPs information.
For caluculation of allelic methylation levels, the B6-derived and MSM/ms-derived sequenced reads were selected based on the MSM/ms SNPs data which were not in CpG sites and the patterns of bisulfite conversion. Methylated cytosines were extracted from the reads by the Bismark methylation extractor with --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5 options. For allelic methylation analysis with methyl-seq libraries, only the original bottom (OB) data were used for analysis of methylation status and methylation percentages were represented at the sites which have equal or more than 5 read depth.
For RNA-seq analysis, the sequenced reads were mapped to the mouse reference genome (mm10) using tophat-2.1.0 11 with the GENCODE version M9 annotation gtf file and the aligner Bowtie2-2.2.5 6 after trimming adaptor sequences and low-quality bases by cutadapt-1.9.1 12. For allelic expression analysis of RNA-seq, the trimmed reads were also mapped to MSM genomes described as above, and the reads mapped to the same chromosome and positions of both B6 and MSM/Ms genomes with high mapping quality (MAPQ>=20) were used for further analyses. The expression level of each gene was calculated as reads per kilobase per million mapped reads (RPKM) by cufflinks-2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bedGraph colums: <chromosome> <start position> <end position> <methylation percentage>, *The coordinates are zero-based, half-open.

extract_protocol:
PureLink Genomic DNA mini kit (invitrogen) for genomic DNA and RNAeasy plus Mini Kit (QIAGEN) for RNA.
For methyl-seq library preparation, 3μg of genomic DNA was sheared by covaris. Libraries were constructed using SureSelectXT Mouse Methyl-Seq Reagent Kit (Agilent Technologies). Bisulfite treatment was perfomed by EZ DNA methylation-GOLD kit (ZYMO RESEARCH). For whole genome bisulfite sequencing library, 500ng of DNA was sheared by covaris and ligated with methylated adapters supplied by TruSeqTM DNA, Sample Prep Kit-v2 (Illumina). Subsequently, DNA was bisulfite-treated using EZ DNA Methylation-Gold KitTM according to the supplier’s instruction. Final library amplification was performed using Pfu Turbo Cx (Agilent Technologies). The libraries were then sequenced on HiSeq 2500 (2 X 101 bp paired-end reads, Illumina). To generate RNA-seq libraries, Truseq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier’s instruction.

value: F1 (129X1/SvJ and C57BL6)


title: J-34 S/L p20

description: J-34 S/L p20

value: J-34 ESCs at passage 4 were cultured in S/L for 16 passages.


title: 2i_S_ESCs_methylseq


title: Swi6_WT_SPY137

description: barcode sequence: ACTAACTGC

value: WT

value: YES


title: Pol2_swi6Δ chp2Δ_SPY5242

description: barcode sequence: GCAAGTAGA

source_name: Pol2_swi6Δ chp2Δ_SPY5242

value: swi6_delta chp2_delta

value: Pol2 (BioLegend MMS-126R-500)


title: Dnmt1-deficient ES cells short RNA

first: Robert

source_name: Dnmt1-deficient ES cells

value: embryonic stem cells (ES cells)

value: Short RNA


title: J-37 S/L+PD p7

description: J-37 S/L+PD p7

value: J-35 ESCs at passage 4 were cultured in S/L+PD for 3 passages.


title: B6_129_22_p2_WGBS


title: 2i_ESC_15_female_methylseq

value: F1 (129X1/SvJ and MSM/Ms)


title: J-34 S/L+PD p7

description: J-34 S/L+PD p7

value: J-34 ESCs at passage 4 were cultured in S/L+PD for 3 passages.


title: J-37 PKCi/L p10

description: J-37 PKCi/L p10

value: J-35 ESCs at passage 4 were cultured in PKCi/L for 6 passages.

value: male


title: Pol2_chp2Δ_SPY1368

description: barcode sequence: TATCTCCG


title: B6_129_16_p3_WGBS


title: B6_129_22_p1_WGBS


title: Pol2_swi6Δ_SPY1098

description: barcode sequence: ACAGTGCAC


title: 2i_ESC_23_male_methylseq


title: B6_129_16_p2_WGBS


title: J-34 PKCi/L p10

description: J-34 PKCi/L p10

value: J-34 ESCs at passage 4 were cultured in PKCi/L for 6 passages.


title: Swi6_clr4Δ_SPY815

description: barcode sequence: CAGGAGGCG

value: Swi6 (Rabbit polyclonal)


title: Pol2_clr4I418P_SPY6537

description: barcode sequence: AACACCTAC


title: ChIP_NKT_Input

extract_protocol: Illumina TruSeq DNA Sample Preparation Guide (Part# 15026486).

value: Thymus

value: NKT


title: Pol2_clr4F449Y_SPY4642

description: barcode sequence: GCGTTTCGA


title: Pol2_clr4Δ_SPY815

description: barcode sequence: ATCGCCAGC


title: J-34 a2i/L p10

description: J-34 a2i/L p10

value: J-34 ESCs at passage 4 were cultured in a2i/L for 6 passages.


title: B6_129_12_p3_WGBS

value: F1 (129X1/SvJ and C57BL6)

value: ES cells


title: B6_129_12_p2_WGBS


title: J-35 2i/L p10

description: J-35 2i/L p10

value: J-35 ESCs at passage 4 were cultured in 2i/L for 6 passages.


title: Pol2_WT_SPY137

description: barcode sequence: GTGGGATA

value: WT

value: YES


title: J-34 2i/L p10

description: J-34 2i/L p10

value: J-34 ESCs at passage 4 were cultured in 2i/L for 6 passages.


title: J-35 S/L p10

description: J-35 S/L p10

value: J-35 ESCs at passage 4 were cultured in S/L for 6 passages.


title: Chp1_chp1Δ_SPY2421

description: barcode sequence: TAGCTAGTA


title: B6_129_12_p1_WGBS


title: t2i_XX_1_p15_WGBS

value: female


title: t2i_XX_3_p15_WGBS


title: Chp1_clr4F449Y_SPY4642

description: barcode sequence: CGAACTGTG


title: Chp1_clr4Δ_SPY815

description: barcode sequence: ACGTAGCTC


title: Chp1_WT_SPY137

description: barcode sequence: TGATCCGA


title: TA3 Serum/Lif RNA-seq

city: Charlestown

first: Toshihiro

last: Shioda

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

data_processing:
Illumina NextSeq generated base call (.bcl) files. Sequence read files (.fastq.gz) were generated by Illumina BaseSpace web service.
Paired-end sequence reads (.fastq.gz) were aligned to the mouse GRCm38/mm10 reference genome sequence using the STAR aligner (ver. 2.4.2.a), generating the .bam format aligned reads files.
The aligned reads files (.bam) generated from the four lanes of the sequencer were merged, sorted and subjected to extraction of uniquely aligned reads, generating .merged.sorted.uniq.bam files.
The aligned unique reads files (.merged.sorted.uniq.bam) were directly visualized by the Integrative Genomics Viewer (ver. 2.3.25).
SNPs were recognized on the igv display, and their allelic biases were evaluated by counting allele-specific read numbers.
Because we are interested in allelic bias of mRNA expression for only a handful, predefined genes, we directly counted the uniquely aligned reads containing allele-discriminating SNPs in the .bam files using the igv.
Allelic_balance_GEO.xlsx contains allele-specific unique read counts determined by manual inspections of the .bam files using the igv.
Genome_build: GRMm38/mm10
Supplementary_files_format_and_content: Allelic_balance_GEO.xlsx

source_name: Induced pluripotent stem cells

growth_protocol: For S/L culture, iPSCs were cultured on irradiated MEF feeders in KO DMEM (Invitrogen) supplemented with 15% FBS (Hyclone), 1mM L-glutamine, 100 μM non-essential amino acids, 1X PenStrep, 0.1 mM beta-mercaptoethanol, and 103 IU LIF). For 2i/L culture, iPSCs were cultured in a 1:1 mixture of DMEM/F12 and Neurobasal media (Invitrogen) supplemented with N2 (Invitrogen), B27 (Invitrogen), 1X PenStrep, 103 IU LIF, 1 μM PD0325901, and 3 μM CHIR990216.

extract_protocol:
Undifferentiated iPSCs were sorted for SSEA1+ to control for the homogeneity of cells before RNA extraction using Dneasy Blood & Tissue Kit (Qiagen).
Total RNA samples (RIN > 9.4, 1 ug) were subjected to synthesis of ribosomal RNA-depleted, directional Illumina NextSeq deep sequencing libraries using the TruSeq Stranded Total RNA LT with Ribo-Zero Gold Set A (Illumina Cat# RS-122-2301) following the protocol provided by the manufacturer (Illumina Cat# RS-122-9008DOC, Part# 15031060 Rev. E).
Stranded (directional) RNA-seq. Paired-end (75 nt + 75 nt).

tag: growth protocol

value: Cultured in Serum/Lif

value: iPSC


title: B6_129_16_p1_WGBS


title: TA3 2i/Lif RNA-seq

value: Cultured in 2i/Lif


title: ChIP_NKT_Runx1

value: Abcam; ab23980


title: H4K16ac_WT_SPY137

description: barcode sequence: GAGTTAAC

value: H4K16ac (Active Motif 39167)


title: serum_ESC_46_XX_RNA-seq

description:
RNA-seq
serum-ESC #46 XX
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz

data_processing:
Libraries were sequenced on the HiSeq2500 (2 X 101 bp or 2×100 bp paired-end reads, illumina)
For RNA-seq analysis, the sequenced reads were mapped to the mouse reference genome (mm10) using tophat-2.1.0 11 with the GENCODE version M9 annotation gtf file and the aligner Bowtie2-2.2.5 6 after trimming adaptor sequences and low-quality bases by cutadapt-1.9.1 12. For allelic expression analysis of RNA-seq, the trimmed reads were also mapped to MSM genomes described as above, and the reads mapped to the same chromosome and positions of both B6 and MSM/Ms genomes with high mapping quality (MAPQ>=20) were used for further analyses. The expression level of each gene was calculated as reads per kilobase per million mapped reads (RPKM) by cufflinks-2.2.1
genome build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes RPKMs for each sample.

extract_protocol:
RNAeasy plus Mini Kit (QIAGEN) for RNA.
To generate RNA-seq libraries, Truseq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier’s instruction.


title: H3K36me3_clr4F449Y_SPY4642

description: barcode sequence: CCATACAC


title: J-35 a2i/L p10

description: J-35 a2i/L p10

value: J-35 ESCs at passage 4 were cultured in a2i/L for 6 passages.

value: male


title: H4K16ac_clr4Δ_SPY815

description: barcode sequence: GCAGCCTC


title: a2i_ESC_1_XY_RNA-seq

description:
RNA-seq
a2i-ESC #a1 XY
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: 02_2i_ESC_6_XY_RNA-seq

description:
RNA-seq
t2i-ESC #t6 XY
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: serum_ESC_16_XY_RNA-seq

description:
RNA-seq
serum-ESC #16 XY
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: serum_ESC_17_XX_RNA-seq

description:
RNA-seq
serum-ESC #17 XX
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: H3K36me3_clr4Δ_SPY815

description: barcode sequence: CTCTGTCT


title: 02_2i_ESC_2_XY_RNA-seq

description:
RNA-seq
t2i-ESC #t2 XY
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: a2i_ESC_3_XY_RNA-seq

description:
RNA-seq
a2i-ESC #a3 XY
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: c2i_ESC_6_XY_RNA-seq

description:
RNA-seq
2i-ESC #c6 XY
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: H4K16ac_clr4F449Y_SPY4642

description: barcode sequence: TCGCGTAC


title: serum_ESC_10_XY_RNA-seq

description:
RNA-seq
serum-ESC #10 XY
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: H3K36me3_WT_SPY137

description: barcode sequence: AGGTCAGT


title: H3K4me3_WT_SPY137

description: barcode sequence: TAGCTT

value: H3K4me3 (Millipore 04-745)


title: H3K4me3_clr4Δ_SPY815

description: barcode sequence: GGCTAC


title: H3K4me3_clr4F449Y_SPY4642

description: barcode sequence: CTTGTA


title: Chp1_clr4I418P_SPY6537

description: barcode sequence: ATCGCCAGC


title: H3K9me3_swi6Δ_SPY1098

description: barcode sequence: GGTCCTTGA

value: H3K9me3 (Diagenode C15500003)


title: J-34 S/L p10

description: J-34 S/L p10

value: J-34 ESCs at passage 4 were cultured in S/L for 6 passages.


title: H3K9me3_chp2Δ_SPY1368

description: barcode sequence: CCTTTACAG


title: H3K9me3_chp1Δ_SPY2421

description: barcode sequence: AACACCTAC


title: a2i_ESC_4_XX_RNA-seq

description:
RNA-seq
a2i-ESC #a4 XX
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz

value: F1 (129X1/SvJ and C57BL6)

value: ES cells


title: 0.2_2i_ESC_3_XX_RNA-seq

description:
RNA-seq
t2i-ESC #t3 XX
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: H3K9me3_clr4W31G_SPY5562

description: barcode sequence: TTGAGTGT


title: 0.2_2i_ESC_1_XX_RNA-seq

description:
RNA-seq
t2i-ESC #t1 XX
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: H3K9me3_clr4I418P_SPY6537

description: barcode sequence: GAGTTAAC


title: c2i_ESC_3_XX_RNA-seq

description:
RNA-seq
2i-ESC #c3 XX
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: H3K9me3_WT_SPY137

description: barcode sequence: CGCATTAA

value: WT


title: a2i_ESC_18_XX_RNA-seq

description:
RNA-seq
a2i-ESC #a18 XX
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: c2i_ESC_4_XX_RNA-seq

description:
RNA-seq
2i-ESC #c4 XX
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: c2i_ESC_2_XY_RNA-seq

description:
RNA-seq
2i-ESC #c2 XY
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: H3K9me2_SPY5244_tetracycline

description: barcode sequence: TATCTCCG

value: YES + 2.5 ug/mL tetracycline


title: 2i_ESC_23_XY_RNA-seq

description:
RNA-seq
2i-ESC #23 XY
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz

value: F1 (129X1/SvJ and MSM/Ms)


title: 2i_ESC_20_XY_RNA-seq

description:
RNA-seq
2i-ESC #20 XY
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: S_ESC_12_XY_RNA-seq

description:
RNA-seq
S-ESC #12 XY
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: 2i_S_ESC_15_XX_RNA-seq

description:
RNA-seq
2i-S-ESC #15 XX
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: H3K9me2_SPY6326_tetracycline

description: barcode sequence: TGAGAGTG


title: H3K9me2_SPY5245

description: barcode sequence: ACAGTGCAC

value: YES


title: H3K9me2_SPY5086_tetracycline

description: barcode sequence: CGGACGTGG


title: 2i_ESC_2_XX_RNA-seq

description:
RNA-seq
2i-ESC #2 XX
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz

value: female


title: H3K9me2_clr4I418P ago1Δ_SPY6529

description: barcode sequence: AGGTCAGT

source_name: H3K9me2_clr4I418P ago1Δ_SPY6529

value: clr4I418P ago1_delta


title: H3K9me2_SPY5086

description: barcode sequence: ATCCTATTC


title: S_ESC_8_XX_RNA-seq

description:
RNA-seq
S-ESC #8 XX
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz


title: H3K9me2_SPY6326

description: barcode sequence: GTGACTACA


title: MEF_4_XY_RNA-seq

description:
RNA-seq
MEF #4 XX
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz

value: MEFs


title: H3K9me2_SPY5245_tetracycline

description: barcode sequence: CACAGTTGG


title: H3K9me2_SPY5244

description: barcode sequence: GCGTTTCGA


title: H3K9me2_ago1Δ_SPY4710

description: barcode sequence: ACTTGA


title: MEF_2_XX_RNA-seq

description:
RNA-seq
MEF #2 XY
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz