title: 4T1_shCTRL_3

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

data_processing:
Base calling was done using Illumina software
Sequenced reads were mapped to MM10 version of mouse genome using RNA-STAR using parameters (outFilterMultimapNmax=10 and outFilterType="BySJout")
Counts are obtained using qcount in qusaR and CPM (counts per million) was computed for each sample
Genome_build: mm10
Supplementary_files_format_and_content: txt file and contains counts as CPM values for each sample

source_name: 4T1 cell line, Non-Targeting shCTRL vector

growth_protocol: 4T1 cell lines were grown in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum, 2mM Glutamine, 100μg/ml penicillin-streptomycin  at 37°C and 5% CO2 in a humidified incubator

extract_protocol:
Total RNA was isolated from 3 different cell lines in 3 replicates each using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction
RNA quality control was performed with Bioanalyzer 2100 (Agilent) using the Eukaryote Total RNA Nano analysis kit from Labgene and RNA concentration was measured by Quanti-iTTM RiboGreen RNA assay kit (Thermo Fisher Scientific). 200ng of RNA was utilized for library preparation with the TruSeq Stranded total RNA kit plus Ribozero Gold (Illumina). The library quality check was performed using the DNF-473-33 - SS NGS Fragment analysis kit (Advanced Analytical Technologies Inc).

treatment_protocol: Lentiviral plasmids containing shRNAs against murine MEK5 and ERK5 and the Non-Targeting shCTRL vector were used. To produce lentiviral particles, HEK293T cells were transfected with the shRNA containing plasmids, the helper vectors pMDL and pREV and the envelope encoding plasmid pVSV. Virus-containing supernatant was conditioned for 2 days. 4T1 cells were infected with the virus containing supernatant and 8mg/mL polybrene. Then infected cells were selected with 4μg/ml puromycin

value: breast cancer cells


title: 4T1_shMEK5-2_1

status: Public on May 17 2018

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: 4T1 cell line, shRNA against murine MEK5

tag: cell line

tag: cell type


title: 4T1_shCTRL_2


title: 4T1_shCTRL_1


title: 4T1_shMEK5-2_2


title: 4T1_shERK5-1_2

source_name: 4T1 cell line, shRNA against murine ERK5


title: Ovaries of Drosophila melanogaster strain w1118

city: Seoul

first: Jae Yun

last: Lim

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
BWA software was used for basecalling and genome alignment.
Sequenced reads were mapped to dmel_r5.42 using bwa with parameters aln -q 20 and paired-end results were generated by sampe option.
Reads within gene were counted by the HTSEQ package of Python.
Reads were normalized by DESeq package of R
Genome_build: dmel_r5.42
Supplementary_files_format_and_content: tab-delimited text files include gene id and DESeq norvalized values

organism: Drosophila melanogaster

source_name: Drosophila ovaries

growth_protocol: All flies were maintained at room temperature (24–26°C) on cornmeal-molasses medium.

extract_protocol: Illumina TruSeqTM RNA sample prep kit with standard low throughput (LT) protocol

tag: genotype/variation

value: strain w1118

tag: phenotype

value: white eye phenotype but generally considered as a wild type


title: 4T1_shERK5-1_1


title: 4T1_shERK5-1_3


title: SA33554

city: Houston

first: Jason

last: Shohet

state: TX

address: One Baylor Plaza

department: Pediatrics

country: USA

institute: Baylor College of Medicine

data_processing:
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were allowed.
The mapped reads were then assembled into transcripts with Cufflinks 2.0 and the UCSC RefSeq gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: UCSC mm10/NCBI 38
Supplementary_files_format_and_content: tab-delimited text file include normalized FPKM values for each Sample

organism: Homo sapiens

source_name: MYCN3 cells

growth_protocol: Human neuroblastoma cell line SHEP was stably transduced with Tet-inducible human MYCN gene and stable single clone was selected and named as MYCN3 (SHEP-MYCN-TET) and was routinely maintained and cultured.

extract_protocol:
RNA was extracted from neuroblastoma cells using Arcturus PicoPure RNA isolation kit (Applied Biosystems Inc., Carlsbad, CA) according to the manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The samples are: A) untreated, B) treated with nutlin3a for 8 h, C) treated with doxycycline for 16 h, D) treated with doxycycline for 16 h followed by nutlin3a for 8 h

value: MYCN3 (SHEP-MYCN-TET)

tag: protocol

value: nutlin3a for 8 h


title: No_Antibody_ChIPseq

city: Athens

first: Mark

middle: Daniel

last: Slayton

state: Ohio

address: 7 Depot Street

department: Biomedical Sciences

institute: Ohio University

library_source: genomic

data_processing:
Basecalling was performed during runs with built-in MiSeq Control software.
ChIP-seq reads were aligned to the custom reference genome (homo sapiens & human cytomegalovirus) in CLC Genomics Workbench 9.0 (QIAGEN)
Reads were trimmed and duplicate reads removed in CLC Genomics Workbench 9.0 (QIAGEN)
Peaks were called with two methods: Transcription Factor ChIP-seq module (Genomics Workbench) and by 125bp sliding window read count variance.  Both methods compared Myc-UL34-ChIP to Input reads.
Genome_build: GRCh39.p10 (Homo sapeins)
Genome_build: FJ527563.1 (Human cytomegalovirus)
Supplementary_files_format_and_content: tab delimited text files containing peak data from both methods
Supplementary_files_format_and_content: oriLyt region peaks

molecule: genomic DNA

source_name: HCMV infected human fibroblasts

growth_protocol: Primary human foreskin fibroblasts were routinely maintained in DMEM with streptomycin, penicillin, glutamine and 10% NuSerum.  For all experiments, passage number 5 or 6 were used.

extract_protocol:
ChIP was performed with the SimpleChIP Enzymatic Chromatin IP Kit w/ Magnetic Beads (Cell Signaling).  Protein-DNA complex were crosslinked, DNA was digested with MNase to yield 150-900bp fragments and Myc-UL34 bound DNA was isolated with antibody then purified.
Libraries were constructed with the TruSeq ChIP Sample Preparation Kit (Illumina).  Briefly, ChIP-enriched DNA were fragmented with Covaris Ultrasonicator and fragment sizes were confirmed on Agilent High Sensitivity DNA chip on an Agilent 2100 Bioanalyzer.  DNA ends were repaired to generate dsDNA moleculars and purified with Agencourt AMPure XP beads.  The repaired dsDNA were adenylated and adaptors for Illumina sequencing were added to the A-overhang prior to repeat purification with Agencourt AMPure XP beads.  Bead-purified samples were size selected on Pippen Prep targeting 150-350 bp.  The ligated library was enriched with 18 cycles of PCR and purified again with Agencourt AMPure XP beads.  Size distribution was confirmed again with Agilent Bioanalyzer; the exact quantification was performed with Kapa Biosystem Complete Kit (ROX Low) on a Stratagene Mx3000P Real Time PCR machine.  Enriched libraries were normalized and pooled in equimolar ratios, denatured and poolde with PhiX control (10%) prior to sequencing on an Illumina MiSeq with 2 x 75 Paired End v3 chemistry.

treatment_protocol: 7x106 cells were infected with Myc-UL34-AD169 at an MOI of 5 pfu/cell for one hour, then fresh media was applied.

value: Primary foreskin fibroblasts

tag: passages

tag: viral strain

tag: hours post infection

tag: chip antibody


title: Input_DNA


title: Myc-UL34_ChIPseq-2

value: Myc-tag (9B11) Mouse mAb #2276 (Cell Signaling)


title: Myc-UL34_ChIPseq-1


title: ChIP_KO

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.4
Reads were mapped to the reference genome using bowtie 0.12.7 with -m 1
Peaks were called using macs2 2.0.10.20130520 with standard parameters
Genome_build: GRCm38.80

source_name: adoptively transferred OT-1

extract_protocol:
OT-1 chromatin was sonicated and TOX-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions using the Truseq ChIP-seq protocol.

tag: genotype

value: Tox-deficient

tag: pathogen

value: LCMV-OVA

tag: strain

value: Rabbit anti-TOX1 antibody (Abcam ab155768, lot GR124281-8)


title: ChIP_WT

value: wild type


title: N2_J2IP-1

city: Boulder

first: Christopher

last: Link

state: Colorado

address: 1725 Pleasant st

department: Integrative Physiology

institute: University of Colorado Boulder

description:
total RNA (J2IP)
N2_HPL2_J2IP_DESeqresults.xlsx

data_processing:
Basecalls performed using CASAVA software from Illumina
Analysis of library complexity and per-base sequence quality (i.e. q > 30) was assessed using FastQC (v0.11.2) software. Low quality bases (q < 10) were trimmed from the 3’ end of reads.
Reads were aligned to the C. elegans WS220 genome using TopHat2 (v2.0.14) --b2-very-sensitive -i 30 -I 5000 --read-edit-dist 3 -N 3 - -read-realign-edit-dist 0 -p 10 --segment-length 25 --segment-mismatches 2 --no- coverage-search --min-coverage-intron 30 --max-coverage-intron 5000 --min-segment-intron 30 --max-segment-intron 5000
(RNAseq) For poly-A selected RNA-Seq reads, uniquely mapped reads were used as input to obtain gene counts using the WS220 annotation with Rsubread (v 1.18.0). Differential expression of genes was determined using DESeq2 (v1.14.1)
(ChIPseq) Reads were uniquely mapped to the WS220 genome with Bowtie1 allowing 2 mismatches in a 45bp seed. Total genomic DNA control libraries were processed and mapped in an identical manner. MACS version 1.4.2 (47) was used to identify significant peaks (p<0.05, FDR<10%) and total genomic sequencing of DNA from wild type and tdp-1(ok803) worms respectively were used as the control datasets to normalize HPL-2 ChIP-seq peaks. Diffbind (version 1.10.2) was used to call differentially represented peaks between wild type and tdp-1(ok803). HPL-2 ChIP-seq and respective total genomic sequencing for each sample was used for normalization. A p-value cut off of P<0.05 and FDR<10% was used.
Genome_build: ws220
Supplementary_files_format_and_content: (RNA-Seq) abundance measurements and differential expression of genes
(ChIPseq) bigwig files

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Worms were grown at on agarose plates and harvested as young adults

extract_protocol:
(RNAseq) Worms were broken by bead beating (Minibead Beater; Biospec Products) in homogenization buffer [10 mM KCl/1.5/1 mM DTT/10 mM Tris·HCl (pH 8.0)/50 mM Sucrose/0.05% Nonidet P-40/1 mM complete protease inhibitors (Sigma #P2714) at a 1:1 ratio of 0.1mm glass beads to packed worm volume for 3 cycles of 30 secs at 5,000 rpm. Extracts were used immediately for immunoprecipitations and equal concentration of extract as determined by protein quantification was added to each IP
(ChIPseq) All worms were maintained and grown on op50 seeded NGM plates and harvested in water. The worms were washed three times in water, and the bacteria were cleared by sucrose flotation. The worms were then frozen in liquid nitrogen and ground to a powder with a mortar and pestle. The resulting worm powder was transferred into cross-linking buffer (1 mM phenylmethylsulfonyl fluoride [PMSF], 1 mM EDTA, 1 mM EGTA, 1% formaldehyde, phosphate-buffered saline [PBS]) for 10 min at room temperature. The reaction was quenched for 5 min at room temperature by the addition of glycine to the mixture to a final concentration of 125 mM and sedimented at 4,000 × g. Pellets were washed three times with FA buffer plus 0.1% SDS (50 mM HEPES [pH 7.5], 1 mM EDTA, 1% Triton, 0.1% deoxycholic acid, 150 mM NaCl, 0.1% SDS) containing protease inhibitors. Each wash mixture was incubated for 5 min at 4°C and then sedimented at 4,000 × g. The pellets were then divided into 500-μl aliquots and stored at −80°C. Each aliquot was resuspended in 1.5 ml of FA buffer plus 0.3% SDS containing protease (Complete cocktail tablets, catalog number 11697498001; Roche) and phosphatase inhibitors (catalog number 786-450; GBiosciences). The samples were sonicated with a Virsonic digital 600 sonicator using a microtip (20 pulses of 11 s each at 30% amplitude with bursts of 0.9 s on and 0.5 s off) to generate DNA fragments of approximately 500 bp, as determined experimentally. Samples were sedimented at 13,000 × g for 15 min at 4°C, and the supernatant was transferred into a new tube, which was then diluted to 4.5 ml with FA buffer containing protein and phosphatase inhibitors.
Total RNA sequencing libraries was extracted from whole animals by TRIzol extraction. Genomic DNA was removed using TURBO DNase (Invitrogen). Poly-A selected, single-ended, 125 bp strand-specific libraries were prepared by the UCCC Genomics Core (Aurora, CO) using the TruSeq Stranded mRNA Library Prep Kit (Illumina). For the J2-IP analyses, RNA recovered by immunoprecipitation with the J2 antibody (three biologically independent lysates) of young adult worms as well as input material (as a loading control) was converted into strand‐specific total RNA libraries using V2 Scriptseq (Epicenter #SSV21106) kits following manufacturer's instructions, except reverse transcription was done with SuperScript III (Invitrogen #18080‐044) using incrementally increasing temperatures from 42 to 59°C to allow for transcription though structured RNAs. rRNA was not removed from J2‐IP RNA samples. Immunoprecipitated DNA from ChIP samples were converted into sequencing libraries using ChIP‐Seq DNA Sample Prep Kit (IP‐102– 1001). Cluster generation and sequencing were performed on the Illumina HiSeq 2500 platform. The reads were de-multiplexed and converted to FASTQ format using CASAVA software from Illumina.

treatment_protocol: hpl-2(tm1489)  and tdp-1(ok803) mutants strains were compared to WT (N2 Bristol) worms.

tag: Stage

value: young adult

value: N2 (Bristol)

tag: temperature

tag: ip antibody

value: J2 antibody, English & Scientific Consulting, Lot J2-1102 and J2-1103


title: N2_J2IP-2


title: Input_WT


title: N2_InputRNA


title: tdp-1(ok803)_genomic_control

description: Supplementary_files_format_and_content: Processed data file "ok803_genomic_control.bw" is an RPKM normalized bigwig


title: Ovaries of Drosophila melanogaster egg2138/Df(2R)Dll-Mp mutants

value: mutant (egg2138/Df(2R)Dll-Mp)

value: early premature stop codon (egg2138) and a deficiency for the gene region, Df(2R)Dll-Mp


title: Lm-OVA_CNS_d7_3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed to BCL files with the Illumina BaseCaller software and samples were demultiplexed to FASTQ files with CASAVA (version 1.8.2).
Sequences were aligned to the genome reference sequence of Mus Musculus (UCSC genome assembly version mm10). Alignment was performed using the STAR alignment software (Dobin et al., 2012; version 2.3.0e) allowing for 2 mismatches within 50 bases.
Conversion of resulting SAM files to sorted BAM files, filtering of unique hits and counting was conducted with SAMtools (Li et al., 2009, version 0.1.18) and HTSeq (Anders et al., 2014, version 0.6.1p1).
Data was preprocessed and analyzed in the R/Bioconductor environment (www.bioconductor.org) using the DESeq2 package (Love et al., 2014, version 1.8).
Candidate genes were filtered to a minimum of 2-fold change and FDR-corrected p-value < 0.05. Gene annotation was performed using Mus musculus entries from Ensembl (www.ensembl.org) via the biomaRt package (Durinck et al., 2005, version 2.18.0).
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: tab-delimited count files as obtained from HTSeq

source_name: adoptively transfered OT-1

extract_protocol:
Splenic and CNS-infiltrating OT-1 cells were FACS sorted with Aria II and RNA was harvested using Trizol reagent.
RNA-samples were prepared with the "TruSeq RNA Sample Prep Kit v2" according to the manufacturer's protocol (Illumina).

value: Lm-OVA

tag: day post infection


title: LCMV-OVA_CNS_d7_2


title: Lm-OVA_CNS_d7_2


title: Lm-OVA_Spleen_d7_3


title: Lm-OVA_CNS_d7_1


title: LCMV-OVA_CNS_d7_1


title: LCMV-OVA_CNS_d7_3


title: Lm-OVA_Spleen_d7_2


title: LCMV-OVA_Spleen_d7_3


title: Lm-OVA_Spleen_d3_3


title: LCMV-OVA_Spleen_d7_1


title: Lm-OVA_Spleen_d3_1


title: Lm-OVA_Spleen_d7_1


title: Lm-OVA_Spleen_d3_2


title: LCMV-OVA_Spleen_d3_3


title: LCMV-OVA_Spleen_d7_2


title: N2_J2IP-3


title: LCMV-OVA_Spleen_d3_2


title: Tox-deficient_3

extract_protocol:
CNS-infiltrating OT-1 cells were FACS sorted with Aria II and RNA was harvested using Trizol reagent.
RNA-samples were prepared with the "TruSeq RNA Sample Prep Kit v2" according to the manufacturer's protocol (Illumina).


title: LCMV-OVA_Spleen_d3_1


title: GATA2+/+ CD43+ hematopoietic progenitors no dox-treatment

city: Madison

first: Oleg

last: Moskvin

state: WI

address: 1220 Capitol Court

institute: University of Wisconsin-Madison

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 1 --seed-length 25 "
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files containing non-normalized "Expected Counts" and normalized "Transcripts Per Million" expression estimates calculated by RSEM.

source_name: genetically engineered h1ESCs-derived hemotopoietic progenitors

growth_protocol: Human embryonic stem cells (h1ESCs) including all of genetical engineered hESCs generated in this study were directed to differentiate towards hematopoietic progenitors on collagen IV-coated plate in xeno-free condition using stage-wise cytokine combinations as is described in Uenish et al. (25448067). For secondary differentiation, CD31+ cells at day 4 of differentiation were sorted using MACS and plated on collagen IV-coated plate in secondary differentiation media that is day 4 media with 50 ng/mL EGF, 50 ng/mL IGF-1, 50 ng/mL IGF-2.

extract_protocol:
RNAs were isolated using RNeasy Mini Kit (Qiagen) from cell population of interest
Samples were then prepared for sequencing using the Ligation Mediated Sequencing (LM-Seq) protocol

treatment_protocol: Most case doxycycline was added to differentiating cells at day 4 of differentiation for 24 hours. By changing differentiation media, doxycycline was withdrawn. For secondary differentiation with MACS-sorted CD31+ cells, doxycycline was added to the secondary differentiation media and next day media were changed.

tag: source cell type

value: genetically engineered human embryonic stem cells (h1ESCs)

value: hemotopoietic progenitors


title: GATA2+/+  VE+ hemogenic endothelial cells

source_name: genetically engineered h1ESCs-derived hemogenic endothelial progenitors

value: hemogenic endothelial progenitors


title: GATA2+/+ D4+1 VE+ hemogenic endothelial cells no dox-treatment

source_name: genetically engineered h1ESCs-derived endothelial cells

value: endothelial cells


title: Tox-deficient_2


title: GATA2+/+ D4+1 VE+ hemogenic endothelial cells dox-treatment D4+0 to D4+1

source_name: genetically engineered h1ESCs-derived GATA2-induced endothelial cells

value: GATA2-induced endothelial cells


title: GATA2-/- CD43+ hematopoietic progenitors no dox-treatment

source_name: genetically engineered GATA2-/- h1ESCs-derived hemotopoietic progenitors

value: genetically engineered GATA2-/- human embryonic stem cells (h1ESCs)


title: WT_3

source_name: adoptively transfered OT-1_WT


title: Tox-deficient_1


title: GATA2+/+ non-hemogenic endothelial cells no dox-treatment

source_name: genetically engineered h1ESCs-derived non-hemogenic endothelial cells

value: non-hemogenic endothelial cells


title: WT_2


title: WT_1


title: V481_lincDUSP KD_replicate 3

city: Cleveland

first: Ahmad

middle: M

last: Khalil

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University

description: Adult human

data_processing:
FastQC was used to assess the quality of the reads. Adapter sequences were removed using TrimGalore
Reads were aligned to the UCSC hg38 human genome using Bowtie2 and Tophat v2.1.1
Read counts were calculated using HTSeq with the conditions stranded=reverse, type=exon, and mode=union
Differential expression was analyzed using DESeq2
Genome_build: UCSC hg38
Supplementary_files_format_and_content: Excel files containing differentially expressed RNAs

source_name: Human colon cancer cell line

growth_protocol: cells were grown in media with 10% FBS

extract_protocol:
RNA was isolated using Qiagen RNA isolation kit
Total RNA (1ug) from each cell type was used to generate next generation RNA-seq libraries using Illumina TruSeq stranded library preparation kit per manufacturer’s protocol
100 bp paired-end, strand-specific

treatment_protocol: KD of lincDUSP was achieved using Gapmers. Control cells were treated with negative control Gapmers.

tag: tissue

value: Colon

tag: sample type

value: Tumor derived


title: GATA2-/- VE+ hemogenic endothelial cells

source_name: genetically engineered GATA2-/- h1ESCs-derived hemogenic endothelial progenitors

tag: cell type


title: V481_lincDUSP KD_replicate 2

description: Adult human


title: V481_negative control_replicate 2

description: Adult human


title: V481_negative control_replicate 1

description: Adult human


title: GATA2-/-  non-hemogenic endothelial cells no dox-treatment

source_name: genetically engineered GATA2-/- h1ESCs-derived non-hemogenic endothelial cells


title: V481_lincDUSP KD_replicate 1

description: Adult human


title: V703_lincDUSP KD, replicate 2

description: Adult human


title: V481_negative control_replicate 3

description: Adult human


title: V703_lincDUSP KD, replicate 3

description: Adult human


title: V703_lincDUSP KD, replicate 1

description: Adult human


title: V703, negative control, replicate 2

description: Adult human


title: V703, negative control, replicate 3

description: Adult human


title: V703, negative control, replicate 1

description: Adult human


title: GATA2-/- D4+1 VE+ hemogenic endothelial cells no dox-treatment

source_name: genetically engineered GATA2-/- h1ESCs-derived endothelial cells


title: GATA2-/- D4+1 VE+ hemogenic endothelial cells dox-treatment D4+0 to D4+1

source_name: genetically engineered GATA2-/- h1ESCs-derived GATA2-induced endothelial cells


title: PDL_1

status: Public on May 16 2018

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

description:
NSC-PDL-2DIV-1
mRNA
Processed data file: Complete_geneList.xlsx

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2.
Aligned to mm10 using STAR2.4.0.
Count read using HT-seq0.6.1 using mm10 RefSeq as reference.
Normalization (TMM) and differential expression analysis using EdgeR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Complete_geneList.xlsx: Excel file; TMM values are highlighted in yellow.

source_name: spinal cord, PDL

growth_protocol: Embryonic day 12 (E12) spinal cords from C57BL/6 mice were dissected in ice cold HBSS, digested in 0.25% Trypsin for 20 minutes at 37°C, washed 3 times with 10% FBS in Neurobasal medium (Life Technologies, Carlsbad, CA), triturated in 5 ml Neurobasal medium + B27 (Life Technologies, Carlsbad, CA), and plated in Neurobasal + B27. RNA was extracted after 2 days in culture and prepared for RNAseq.

extract_protocol:
Mouse E12 spinal cords were dissociated and plated in 6-well tissue culture treated plates (Thermo Scientific, Logan, UT) at 500,000 cells in 2 ml of media coated as described above: PDL, PDL & laminin, PDL & laminin & myelin, and PDL & myelin. In addition, wells coated with myelin without cells were collected to control for potential RNA presence in the myelin coating. Cells were cultured for 48 hours prior to RNA extraction. RNA was collected using Absolutely RNA Nanoprep Kit (Agilent, Santa Clara, CA) according to manufacturer’s instructions. N = 3 biological replicates per condition.
cDNA was generated using the TruSeq RNA vs library prep kit (Illumina). Paired-end libraries for multiplex sequencing were generated.

treatment_protocol: Plates were pre-coated with Poly-D-lysine hydrobromide (PDL, 20 μg/ml in water, Sigma-Aldrich, St. Louis, MO) overnight at room temperature, washed 3 times with sterile water and air-dried. Additionally, some wells were coated with wildtype myelin membranes at 10 μg/ml in PBS overnight at 4°C, and washed 3 times with PBS. Wells coated with laminin (1 μg/ml in PBS, Sigma-Aldrich, St. Louis, MO) were incubated for 4 hours at room temperature, washed 3 times with media and not dried before plating.

tag: strain/background

tag: genotype/variation

value: Wild type

tag: developmental stage

value: spinal cord

tag: condition

value: PDL


title: LAM_Mye_3

description:
NSC-L-My-2DIV-3
mRNA
Processed data file: Complete_geneList.xlsx

source_name: spinal cord, Laminin + Myelin

value: Laminin + Myelin


title: LAM_Mye_2

description:
NSC-L-My-2DIV-2
mRNA
Processed data file: Complete_geneList.xlsx


title: PDL_2

description:
NSC-PDL-2DIV-2
mRNA
Processed data file: Complete_geneList.xlsx


title: LAM_3

description:
NSC-Lam-2DIV-3
mRNA
Processed data file: Complete_geneList.xlsx

source_name: spinal cord, Laminin

value: Laminin


title: LAM_2

description:
NSC-Lam-2DIV-2
mRNA
Processed data file: Complete_geneList.xlsx


title: Mye_1

description:
NSC-My-2DIV-1
mRNA
Processed data file: Complete_geneList.xlsx

source_name: spinal cord, Myelin

value: Myelin


title: LAM_1

description:
NSC-Lam-2DIV-1
mRNA
Processed data file: Complete_geneList.xlsx


title: PDL_3

description:
NSC-PDL-2DIV-3
mRNA
Processed data file: Complete_geneList.xlsx


title: LAM_Mye_1

description:
NSC-L-My-2DIV-1
mRNA
Processed data file: Complete_geneList.xlsx


title: LT_High_Fat_diet_4048

city: Auburn

first: Michael

middle: W

last: Greene

state: AL

address: 260 Lem Morrison Dr

department: Nutrition

institute: Auburn University

data_processing:
Quality control checks on raw sequence data from each sample will be performed using FastQC (Babraham Bioinformatics, London, UK). Raw reads were mapped to the reference mouse genome mm9 using TopHat v2.0 (Langmead et al. 2009; Trapnell, Pachter, and Salzberg 2009) with two mismatches allowed and other default parameters.  The alignment metrics of the mapped reads was estimated using SAMtools  (Li et al. 2009). Aligned reads were then imported onto the commercial data analysis platform, Avadis NGS (Strand Scientifics, CA, USA). After quality inspection, the aligned reads were filtered on the basis of read quality metrics where reads with a base quality score less than 30, alignment score less than 95, and mapping quality less than 40 were removed. Remaining reads were then filtered on the basis of their read statistics, where missing mates, translocated, unaligned and flipped reads were removed. The reads list was then filtered to remove duplicates. Samples were grouped and quantification of transcript abundance was done on this final read list using Trimmed Means of M-values (TMM) (Robinson and Oshlack 2010) as the normalization method. Differential expression of genes was calculated on the basis of fold change (using default cut-off â‰¥ ±2.0) observed between defined conditions, and the p-value of the differentially expressed gene list was  estimated by z-score calculations using determined by Benjamini Hochberg FDR correction of 0.05 (Benjamini and Hochberg 1995).
Genome_build: mm9
Supplementary_files_format_and_content: excel file includes normalized expression values for each sample

source_name: Liver

extract_protocol:
Total RNA was harvested from frozen livers using a Qiagen RNAesy kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001). The concentration and integrity of the total RNA was estimated by Qubit® 2.0 Fluorometer (Invitrogen, Carlsbad, California), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively.
Five hundred ng of total RNA was required for proceeding to downstream RNA-seq applications. First, ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). The second strand synthesis was then performed using the NEBnext Second Strand synthesis module. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by A-tailing and custom adapter ligation. Post-ligated materials were individually barcoded with unique in-house Genomics Service Laboratory (GSL) primers and amplified through 12 cycles of PCR. Library quantity was assessed by Qubit 2.0 Fluorometer, and the library quality was estimated by utilizing a DNA 1000 chip on an Agilent 2100 Bioanalyzer. Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing (50 million, 100-bp paired-end reads) was on an Illumina HiSeq2500 sequencer (Illumina, Inc.).

treatment_protocol: Seven week old mice were placed on a standard chow diet or received a high-fat Western diet (HFWD) (Test Diets, Cat. #5TJN) containing ∼12% and 40% energy from fat, respectively, with or without sugar (42 g/L) added to the drinking water at a ratio of 55% fructose/45% sucrose (F/S). The composition of fat in the diets was 30% from lard, 30% from butterfat, and 30% from Crisco. Mice were euthanized by inhalation of CO2.  Liver was excised, weighed, flash frozen in liquid nitrogen, and stored at -80°C until used for RNA extraction.

tag: treatment

value: High fat Western diet


title: LT_High_Fat_diet_4049


title: LT_High_Fat_Sugar_diet_4038

value: High fat Western diet + liquid sugar


title: LT_High_Fat_Sugar_diet_4035


title: LT_Child_diet_4007

value: Chow diet


title: LT_Child_diet_4006


title: LT_High_Fat_diet_4019


title: LT_High_Fat_Sugar_diet_4039


title: LT_High_Fat_diet_4052


title: LT_Child_diet_4008


title: LT_High_Fat_Sugar_diet_4044


title: RNA-Seq_HUVEC_AdHIF2a_rep2

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

description:
batch_2
rRNA-depleted RNA

data_processing:
Libraries were sequenced for 75 cycles on an Illumina NextSeq 500 according to the manufacturer’s instructions.
Poor quality reads were filtered out (minimum 97% of bp over quality cutoff 10).
Reads were aligned to the hg19 genome using STAR.
Data analysis was performed using HOMER and the detailed instructions for analysis can be found at http://homer.salk.edu/homer/
The differential gene expression analysis was performed using edgeR and thresholds used were fold change > 2 and FDR < 0.1
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression values (raw reads) and UCSC Bedgraphs are provided.

source_name: overexpressing adenovirally delivered HIF2a

growth_protocol: HUVECs were cultured in Endothelial Cell Growth medium (EGM; Thermo Scientific) on fibronectin-gelatin coated surfaces (10 µg/ml, 0.05%; Sigma-Aldrich).

extract_protocol:
RNA was purified using RNeasy Mini Kit and rRNAs were depleted using  Ribo-Zero Gold Kit (Illumina)
Libraries were prepared at EMBL Genecore for strand specific RNA libraries

treatment_protocol: HUVECs were transduced with an MOI 20 of adenovirus preparations and grown for 48h before RNA extraction

value: Human umbilical vein endothelial cell


title: RNA-Seq_HUVEC_AdHIF1a_rep3

description:
batch_2
rRNA-depleted RNA

source_name: overexpressing adenovirally delivered HIF1a


title: RNA-Seq_HUVEC_AdHIF2a_rep3

description:
batch_2
rRNA-depleted RNA


title: LT_High_Fat_Sugar_diet_4053


title: RNA-Seq_HUVEC_AdHIF2a_rep1

description:
batch_2
rRNA-depleted RNA


title: LT_High_Fat_diet_4020


title: RNA-Seq_HUVEC_AdCMV_rep3

description:
batch_2
rRNA-depleted RNA

source_name: control


title: RNA-Seq_HUVEC_AdHIF1a_rep1

description:
batch_2
rRNA-depleted RNA


title: RNA-Seq_HUVEC_AdCMV_rep2

description:
batch_2
rRNA-depleted RNA


title: LT_Child_diet_4047


title: RNA-Seq_HUVEC_AdCMV_rep1

description:
batch_2
rRNA-depleted RNA


title: DKO_rep1_RNA-Seq

city: seattle

first: xueqiu

last: lin

state: wa

address: 1100 Fairview Ave N

institute: FRED HUTCHINSON CANCER CENTER

description:
DKO RNA-seq biological replicate1
WTvsDKO13_gene_exp.diff.gz

data_processing:
Reads were aligned with Tophat 2.0.10 to both refseq transcriptome and mm9 genome.
Differential gene expression between groups was assessed by Cufflinks / Cuffdiff 2.2.1.
Genome_build: mm9
Supplementary_files_format_and_content: gene_exp.diff is a tab separated text file of the Cuffdiff output for differential gene expression analysis of these groups: WTvs3aKO; WTvsTet1KO; WTvsDKO.

source_name: embryonic stem cells

growth_protocol: For the FLT3-ITD retroviral model, Sca1+ enriched Dnmt3a KO or WT murine bone marrow cells were transduced with retroviruses expressing MSCV-FLT3-ITD-IRES-GFP or MSCV-GFP transgenes and transplanted into lethally irradiated recipients by retro-orbital injections. Freshly sorted donor-derived mouse thymus and bone marrow cells (CD4+CD8+) from each genotype were collected from transplant recipients. For the Flt3-ITD knock-in model, bulk bone marrow cells were collected.

extract_protocol:
RNA was purified from 500,000 cells with RNeasy Plus Micro Kit (Qiagen, 74034).
RNA libraries were prepared from 1 μg total RNA using standard Illumina protocols.

value: Dnmt3a-/- and Tet1-/-


title: 3aKO Tet1_ChIPSeq

data_processing:
Raw reads treated by bisulfite were quality trimmed (Trimgalore), and uniquely mapped to the mm9 reference genome using BWA .
Chromatin marks were compared with Danpos2. Briefly, the experiments were input background-subtracted and normalized to the same read  depth.
Genome_build: mm9
Supplementary_files_format_and_content: The bigWig files were reads density, created from Danpos2 wiggle files. More information may be found in the Danpos2 documentation.

growth_protocol: ES cells were cultured on 0.1% gelatin-coated dishes in DMEM (Gibco, 11965-092) supplemented with 15% Fetal Bovine Serum (Foundation, 900-108), 1×Non-Essential Amino Acids (Gibco, 11140-050), 1×GlutaMAX (Gibco, 35050-061), 1 μM 2-Mercaptoethanol (Sigma, M7522), 1×Sodium pyruvate (Sigma, S8636), 1×Penicillin/Streptomycin (Gibco, 15140-122) and 1000 U/ml LIF (Millipore, ESG1106).

extract_protocol:
1×107 cells were fixed for 10 minutes with 1% formaldehyde, followed by chromatin extraction and sonication to generate 200-500bp fragments. The sheared chromatin was incubated overnight at 4°C with anti-Tet1 and Dynabeads Grotein A (Thermo Fisher, 10001D), or anti-Flag M2 and  Dynabeads Protein G (Thermo Fisher, 10003D). ChIP washes were performed in the following order: 1×low-salt buffer, 3×high-salt buffer, 2×LiCl buffer and 1×TE buffer. Cross-linking was reversed with the addition of elution buffer (20 mM Tris-HCl, pH7.5, 5 mM EDTA, 50 mM NaCl, 1% SDS, 50 μg/mL Proteinase K) to washed beads and incubation at 68°C with rotation for three hours. DNA was purified with MinElute PCR purification kit (Qiagen, 28004).
For ChIP-Seq, sequencing libraries were prepared using ThruPLEX DNA-seq 48D kit (Rubicon Genomics, R400406) following standard protocols.

tag: chip antibody


title: WT Tet1 Input DNA

tag: genotype

value: wild type


title: 3aKO Tet1_Flag_ChIPSeq

value: anit-Flag M2 (Sigma, F1804)


title: WT Tet1_Flag_ChIPSeq


title: WT Tet1_ChIPSeq


title: Tet1KO_rep1_RNA-Seq

description:
Tet1KO RNA-seq biological replicate1
WTvsTet1KO_gene_exp.diff.gz


title: 3aKO Tet1 Input DNA


title: Tet1KO_rep2_RNA-Seq

description:
Tet1KO RNA-seq biological replicate2
WTvsTet1KO_gene_exp.diff.gz


title: DKO_rep2_RNA-Seq

description:
DKO RNA-seq biological replicate2
WTvsDKO13_gene_exp.diff.gz


title: 3aKO_rep2_RNA-Seq

description:
3aKO RNA-seq biological replicate2
WTvs3aKO_gene_exp.diff.gz


title: WT_rep2_RNA-Seq

description: WT RNA-seq biological replicate2


title: DKO H3K4me3_ChIPSeq

description: DKO H3K4me3

extract_protocol:
2×106 cells were fixed for 10 minutes with 1% formaldehyde, followed by chromatin extraction and sonication to generate 200-500bp fragments. The sheared chromatin was incubated overnight at 4°C with H3K4me3 or H3K27me3 antibody. After incubation, 10 µl of Dynabeads Protein A magnetic beads previously washed in RIPA buffer was added, and samples were incubated for an additional 2 hours at 4°C. Bead-protein complexes were washed three times with RIPA buffer and twice with TE buffer. Genomic  DNA was eluted for 2 hours at 68°C in 100 µl of Complete Elution Buffer (20 mM Tris, pH7.5, 5 mM EDTA, 50 mM NaCl, 1% SDS, 50 µg/ml proteinase K) and purified with MinElute PCR purification kit (Qiagen, 28004).
For ChIP-Seq, sequencing libraries were prepared using ThruPLEX DNA-seq 48D kit (Rubicon Genomics, R400406) following standard protocols.

value: anti-H3K4me3 (Millipore, 07-473)


title: DKO H3K27me3_ChIPSeq

description: DKO H3K27me3

value: anti-H3K27me3 (Millipore, 07-449)


title: RNA-Seq_HUVEC_AdHIF1a_rep2

description:
batch_2
rRNA-depleted RNA


title: Tet1KO H3K27me3_ChIPSeq

description: Tet1KO H3K27me3


title: Tet1KO H3K4me3_ChIPSeq

description: Tet1KO H3K4me3


title: 3aKO H3K27me3_ChIPSeq

description: 3aKO H3K27me3


title: 3aKO H3K4me3_ChIPSeq

description: 3aKO H3K4me3


title: WT H3K27me3_ChIPSeq

description: WT H3K27me3


title: WT H3K4me3_ChIPSeq

description: WT H3K4me3


title: 3aKO CMS Input DNA

data_processing:
Raw reads treated by bisulfite were quality trimmed (Trimgalore), and uniquely mapped to the mm9 reference genome using BSMAP.
Chromatin marks were compared with Danpos2. Briefly, the experiments were input background-subtracted and normalized to the same read  depth.
Genome_build: mm9
Supplementary_files_format_and_content: The bigWig files were reads density, created from Danpos2 wiggle files. More information may be found in the Danpos2 documentation.

source_name: 3aKO CMS Input DNA

extract_protocol: none provided by the submitter


title: 3aKO CMS-seq r1

source_name: 3aKO CMS-seq r1

value: anti-CMS


title: WT CMS Input DNA

source_name: WT CMS Input DNA


title: WT CMS-seq r2

source_name: WT CMS-seq r2


title: Mye_3

description:
NSC-My-2DIV-3
mRNA
Processed data file: Complete_geneList.xlsx


title: WT_rep1_RNA-Seq

description: WT RNA-seq biological replicate1


title: 3aKO_rep1_RNA-Seq

description:
3aKO RNA-seq biological replicate1
WTvs3aKO_gene_exp.diff.gz


title: WT CMS-seq r1

source_name: WT CMS-seq r1


title: 2nd trimester human fetal testis PRDM1-ChIP-seq

city: Bozeman

first: Fang

last: Fang

state: Montana

address: CBB Room 103

department: Cell Biology

institute: Montana State University

data_processing:
sequence data processed by FASTQC/Galaxy
Aligment by Bowtie-illumina/Galaxy
Peak call by MACS2/Galaxy
BedGraph generated by MACS2
Motif detection by MEMEChIP
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph

source_name: Fetal testis

growth_protocol: H1 hESCs (WiCell) were maintained feeder-free on Matrigel (BD Biosciences)-coated plates. Briefly, all cultures were grown at 37 °C with 5% CO2 in mTeSR1 medium (STEMCELL Technologies).

extract_protocol:
Cells were lysed with 1% SDS Lysis Buffer (on ice, 5 min) and then centrifuged (2,000 rpm, 10 min). Remove supernatant as described above and resuspend samples in 0.1% SDS buffer with PIC (1ml 0.1%SDS buffer for every 100ul nuclear pellet). Samples were then sonicated with glass beads for 12 times (30 s pulses with 30 s break interval) using the Bioruptor water bath sonicator (Diagenode).
Libraries were prepared according to Illumina's instructions by Stanford genomic core facility

value: 2nd trimester human fetal testis

tag: antibody

value: anti-PRDM1 (C14A4, Cell Signaling Technology);


title: H1 OCT4-ChIP-seq

source_name: Embryonic stem cells

value: anti-OCT4 (sc-8628, Santa Cruz Biotechnology);


title: 2nd trimester human fetal testis PAX5-ChIP-seq

value: anti-PAX5 (sc-1974, Santa Cruz Biotechnology);


title: 1%H1 ESCs mixed with 99% fibroblast OCT4-ChIP-seq

source_name: Embryonic stem cells mixed with fibroblast cells

value: 1%H1 ESCs mixed with 99% fibroblast


title: 2nd trimester human fetal testis OCT4-ChIP-seq replicate1


title: ATAC kmt2a MO rep3

city: Shanghai

first: Yong

last: Zhang

address: No. 1239, Siping Road

country: China

institute: Tongji University

data_processing:
All sequenced reads were cut to 40 bp from the 3’ end and mapped to the zebrafish genome (zv9 assembly) using Bowtie (version 2.2.3) with default parameters.
The reads were then filtered as follows: only the reads that aligned concordantly to the nuclear DNA with MAPQ >= 30 were kept; the duplicate read pairs that aligned to the same location in the genome were collapsed into one; and one left read was randomly selected from the left read pair.
After calculating the correlation between samples, reads with fragment lengths <= 100 were regarded as open chromatin reads for the following analysis.
We combined replicates from each stage for the analysis.
Bigwig files were generated using genomeCoverageBed (version 2.20.1) and bedGraphToBigWig with normalization to 1 M reads.
Peak calling was using MACS (version 1.4.2 20120305) with parameters of -f BED –g 1.4e9  --keep-dup all --nomodel --shiftsize 25. Peak with P value <= 1e-10 and fold >= 10 were kept.
Genome_build: danRer7/zv9
Supplementary_files_format_and_content: Bigwig files were generated using genomeCoverageBed (version 2.20.1) and bedGraphToBigWig with normalization to 1 M reads. Scores represent the ATAC-seq signal.

organism: Danio rerio

source_name: embryos

growth_protocol: Zebrafish were maintained under standard condition. Embryos were collected at the 1-cell stage, synchronized and allowed to develop to the desired developmental stages at 28°C.

extract_protocol:
Each stage of embryos was harvested and washed 3 times with pre-iced PBS. Then embryos were re-suspended in cold lysis buffer (10mM Tris-HCL, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1%IGEPAL CA-630), and lysed by pipetting up and down 5-10 times using widen pipet, kept on iced for 5 minutes. The isolated nuclei were then pelleted and re-suspended in transposition reaction (25μl 2×TD Buffer, 2.5μl Tn5 transposes, 22.5 μl Nuclease Free H2O) for 30 minutes at 37℃, and then purified using Qiagen MinElute Kit.
PCR was performed to yield the libraries by adding different barcode, and the PCR conditions is as follows: 72℃ 5min, 98℃ 30s, 15 cycles of 98℃ 10s, 63℃ 30s, 72℃ 1min, and hold at 4℃. Then the libraries were purified with Agencourt AMPure XP beads

treatment_protocol: One nanoliter of morpholino solution was injected into embryos at the 1-cell stage. The concentration of morpholino for cxxc1b is 0.75pmol, kmt2a is 1.0pmol, pou5f3 is 0.05pmol, nanog is 0.05pmol and smarca4a is 0.25pmol. To rescue the loss-of-function phenotype, 100pg of pou5f3 and 100pg of nanog mRNA were injected either individually or together into morpholino injected embryos at 1-cell stage.

value: embryos

value: 3.7 hpf (oblong stage)

tag: genetic background

value: Tübingen

value: Morpholino against kmt2a


title: ATAC cxxc1b MO rep2

value: Morpholino against cxxc1b


title: ATAC cxxc1b MO rep3


title: ATAC kmt2a MO rep1


title: ATAC kmt2a MO rep2


title: 3aKO CMS-seq r2

source_name: 3aKO CMS-seq r2

tag: strain


title: ATAC cxxc1b MO rep1


title: ATAC smarca4a MO rep2

value: Morpholino against smarca4a


title: ATAC pou5f3 MO with mRNA rescue rep3

value: Morpholino against pou5f3 with mRNA rescue


title: ATAC smarca4a MO rep1


title: PTEN_p53_EP347

city: San Antonio

first: Zhenqing

last: Ye

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads aligned to mouse reference genome (mm10) using Tophat (v2.0.6) with parameters "-p 4 --keep-fasta-order --keep-tmp -z0 --no-coverage-search --bowtie1 --library-type fr-unstranded --max-multihits 20".
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragment falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
bigwig files were generated by RSeQC v2.6.4.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include "chrom", "st", "end"," mRNA_size"," strand"," fragment count"," FPM" and "FPKM" values for each Sample.

source_name: Prostate tissue

growth_protocol: Mice were handled according to approved Mayo Clinic IACUC protocols and were given access to food and water ad libitum

extract_protocol:
Tissue was  flash frozen on dry ice, and RNA was harvested using the RNease Plus Mini Kit (Qiagen). 200 ng high quality total RNA was used to generate the RNA sequencing library.
cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina indexed adapters were performed according to the TruSeq RNA Sample Prep Kit v2 (Illumina).

value: Prostate


title: PTEN_p53_EP284


title: PTEN_p53_ERG_EP94


title: PTEN_p53_ERG_GP323


title: PTEN_p53_ERG_FP12


title: PTEN_p53_EP254


title: ATAC pou5f3 MO with mRNA rescue rep2


title: 2nd trimester human fetal testis Input


title: ATAC pou5f3 MO with mRNA rescue rep1

treatment_protocol: One nanoliter of morpholino solution was injected into embryos at the 1-cell stage. The concentration of morpholino for cxxc1b is 0.75pmol, kmt2a is 1.0pmol, pou5f3 is 0.05pmol, nanog is 0.05pmol and smarca4a is 0.25pmol. To rescue the loss-of-function phenotype, 100pg of pou5f3 and 100pg of nanog mRNA were injected either individually or together into morpholino injected embryos at 1-cell stage


title: 3bKO_WGBS_r3

description:
bisulfite converted genomic DNA
3bKO WGBS biological replicate3
3bKO_WGBS_mcall_merge.G.bed.gz

data_processing:
Bisulfite-treated sequencing reads were be aligned to  the mm9 reference genome using BSMAP. Cytosine methylation ratios were calculated with MOABS.
Genome_build: mm9
Supplementary_files_format_and_content: text output of bsmap utility methratio.py; chromosome, coordinate (1-based), strand, sequence context (2nt upstream to 2nt downstream in Watson strand direction), methylation ratio, number of effective total C+T counts on this locus (strands combined), number of total C counts on this locus (strands combined), number of total C+T counts on this locus (strands combined), number of total G counts on this locus of reverse strand (value is NA), number of total G+A counts on this locus of reverse strand (value is NA), lower bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion, upper bound of 95% confidence interval

extract_protocol:
1 μg of genomic DNA was isolated from mESCs and fragmented using a Covaris sonication system (Covaris S2).
Following DNA fragmentation, libraries were constructed using the Illumina TruSeq DNA sample preparation kit. After ligation, libraries were treated with bisulfite using the EpiTect Bisulfite kit (Qiagen, 59104). Ligation efficiency was tested by PCR using TruSeq primers and Pfu Turbo Cx Hot-Start DNA polymerase (Stratagene, 600632). After determining the optimal number of PCR cycles for each sample, a large-scale PCR reaction (100 μl) was performed. PCR products were sequenced with Illumina HiSeq sequencing systems.
Whole Genome Bisulfite Sequencing


title: 3bKO_WGBS_r1

description:
bisulfite converted genomic DNA
3bKO WGBS biological replicate1
3bKO_WGBS_mcall_merge.G.bed.gz


title: 2nd trimester human fetal testis OCT4-ChIP-seq replicate2


title: 3aKO_WGBS_r3

description:
bisulfite converted genomic DNA
3aKO WGBS biological replicate3
3aKO_WGBS_mcall_merge.G.bed.gz


title: 3aKO_WGBS_r2

description:
bisulfite converted genomic DNA
3aKO WGBS biological replicate2
3aKO_WGBS_mcall_merge.G.bed.gz


title: WT_WGBS_r2

description:
bisulfite converted genomic DNA
WT WGBS biological replicate2
WT_WGBS_mcall_merge.G.bed.gz

value: wild type


title: WT_WGBS_r3

description:
bisulfite converted genomic DNA
WT WGBS biological replicate3
WT_WGBS_mcall_merge.G.bed.gz


title: ATAC nanog MO with mRNA rescue rep2

value: Morpholino against nanog with mRNA rescue


title: ATAC nanog MO with mRNA rescue rep1


title: ATAC nanog MO with mRNA rescue rep3


title: 3bKO_WGBS_r2

description:
bisulfite converted genomic DNA
3bKO WGBS biological replicate2
3bKO_WGBS_mcall_merge.G.bed.gz


title: 3aKO_WGBS_r1

description:
bisulfite converted genomic DNA
3aKO WGBS biological replicate1
3aKO_WGBS_mcall_merge.G.bed.gz


title: ATAC pou5f3 MO rep2

value: Morpholino against pou5f3


title: WT_WGBS_r1

description:
bisulfite converted genomic DNA
WT WGBS biological replicate1
WT_WGBS_mcall_merge.G.bed.gz


title: Tet1 KO Dnmt3a1 Input DNA_r2

description:
Tet1KO Input biological replicate2
Tet1KO_Dnmt3a1_BioChIPSeq_bgsub_nor.bw

data_processing:
Reads were mapped to the mouse genome mm9 using bowtie by allowing up to two mismatches and 100 alignments for a read.
The multi-reads were allocated with CSEM using Expectation-Maximization.
Dnmt3a1 occupancy was compared with Danpos2. Briefly, the experiments were input background-subtracted and normalized to the same read depth.
Genome_build: mm9
Supplementary_files_format_and_content: The bigWig files were reads density, created from Danpos2 wiggle files. More information may be found in the Danpos2 documentation.

extract_protocol:
5×106 cells were fixed for 10 minutes with 1% formaldehyde, followed by chromatin extraction and sonication to generate 200-500bp fragments. Ten percent of chromatin is kept as Input. Immunoprecipitation was performed overnight at 4°C using streptavidin-M280 (Thermo Fisher, 11205D) magnetic beads. ChIP washes were performed in the following order: 2% SDS, 1×high-salt buffer, 1×LiCl buffer, 1×TE buffer, 1×TE buffer 0.2% Triton X-100. Cross-linking was reversed with the addition of elution buffer (20 mM Tris-HCl, pH7.5, 5 mM EDTA, 50 mM NaCl, 1% SDS, 50 μg/mL Proteinase K) to washed beads and incubation at 68°C with rotation for three hours. DNA was purified with MinElute PCR purification kit (Qiagen, 28004).
For ChIP-Seq, sequencing libraries were prepared using ThruPLEX DNA-seq 48D kit (Rubicon Genomics, R400406) following standard protocols.

treatment_protocol: Biotinated Dnmt3a1 expression was induced by adding 2 μg/mL doxycycline in ES medium for 16 hours .


title: WT Dnmt3a1_BioChIPSeq_r2

description:
WT Dnmt3a1 BioChIPSeq biological replicate2
Tet1KO_Dnmt3a1_BioChIPSeq_bgsub_nor.bw

value: M-280 Streptavidin (Thermo Fisher, 11205D)


title: Tet1 KO Dnmt3a1_BioChIPSeq_r2

description:
Tet1KO Dnmt3a1 BioChIPSeq biological replicate2
Tet1KO_Dnmt3a1_BioChIPSeq_bgsub_nor.bw


title: WT Dnmt3a1 Input DNA_r2

description:
WT Input biological replicate2
Tet1KO_Dnmt3a1_BioChIPSeq_bgsub_nor.bw


title: ATAC nanog MO rep3

value: Morpholino against nanog


title: ATAC nanog MO rep1


title: ATAC nanog MO rep2


title: Tet1 KO Dnmt3a1 Input DNA_r1

description:
Tet1KO Input biological replicate1
WT_Dnmt3a1_BioChIPSeq_bgsub_nor.bw


title: ATAC control MO rep1

value: Control morpholino


title: Tet1 KO Dnmt3a1_BioChIPSeq_r1

description:
Tet1KO Dnmt3a1 BioChIPSeq biological replicate1
WT_Dnmt3a1_BioChIPSeq_bgsub_nor.bw


title: ATAC control MO rep3


title: ATAC dome rep2

value: 4.5 hpf (dome)

value: NO


title: WT Dnmt3a1 Input DNA_r1

description:
WT Input biological replicate1
WT_Dnmt3a1_BioChIPSeq_bgsub_nor.bw


title: ATAC dome rep3


title: ATAC pou5f3 MO rep3


title: ATAC pou5f3 MO rep1


title: Nrf2 KO 2

city: East Lansing

first: Karen

last: Liby

state: MI

address: 1355 Bogue Street

department: Pharmacology&Toxicology

institute: Michigan State University

data_processing:
After removal of adaptors and low quality reads, reads were mapped to the mm10 mouse reference genome using TopHat2
Reads that mapped to genes were counted and normalized to gene length, then reported in FPKM (Fragments Per Kilo bases per Million reads)
Routine identification of differentially expressed genes was performed using DESeq2
Supplementary_files_format_and_content: FPKM

source_name: Lung

extract_protocol:
Lung tumors were dissected and total RNA was extracted by Qiagen RNeasy Mini Kit.
RNA libraries for sequencing were prepared using standard Illumina protocols

treatment_protocol: Wildtype and Nrf2 knockout mice were injected with 2 or 4 doses of  vinyl carbamate (16 mg/kg) and lung tumors were dissected 40-44 weeks after initiation with carcinogen. Tumors were pooled (3-4 tumors/sample) prior to isolating total RNA

value: Balb/c

value: lung tumor


title: ATAC oblong rep3

value: embryos

value: 3.7 hpf (oblong stage)


title: WT 2


title: ATAC oblong rep2

value: Tübingen


title: ATAC control MO rep2


title: WT 1


title: ATAC 1k-cell rep1

value: 3 hpf (1k-cell stage)


title: ATAC 1k-cell rep2


title: ATAC 256-cell rep3

value: 2.5 hpf (256-cell stage)


title: WT Dnmt3a1_BioChIPSeq_r1

description:
WT Dnmt3a1 BioChIPSeq biological replicate1
WT_Dnmt3a1_BioChIPSeq_bgsub_nor.bw


title: ATAC 256-cell rep1


title: ATAC 256-cell rep2


title: ATAC 64-cell rep2

value: 2 hpf (64-cell stage)


title: ATAC 64-cell rep3


title: ATAC 64-cell rep1


title: Nrf2 KO 1


title: ATAC dome rep1


title: U87_DMSO_2h_rep3

status: Public on May 15 2018

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

data_processing:
Raw fastq files were pseudoaligned to Ensemble version 82 transcripts using Kallisto
Kallisto output files were later summarized into gene level abundance and counts using tximport Bioconductor package followed by DESeq2 to perform differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: abundance.tsv output from kallisto containing abundance in TPM and estimated fragment counts for all Ensemble 82 transcripts.

molecule: polyA RNA

growth_protocol: U87 cells were  cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. NNI24 tumor spheres were maintained in growth medium consisting of basic fibroblast growth factor (bFGF; 20 ng/ml), epidermal growth factor (EGF; 20 ng/ml), heparin (5 µg/ml), B27 supplement, and DMEM/F-12 Mixture (3:1) and subsequently expanded by mechanical trituration.

extract_protocol:
Total RNA was extracted by using RNeasy Kit (Qiagen).
Standard Illumina protocol

tag: cell line

value: U87 GBM

value: DMSO

tag: characterstics

value: Adherent culture


title: U87_DMSO_8h_rep3


title: U87_DMSO_24h_rep2


title: U87_DMSO_24h_rep3


title: U87_dBET6_500nM_8h_rep3


title: U87_dBET6_500nM_8h_rep2


title: U87_DMSO_2h_rep1


title: U87_DMSO_8h_rep1


title: U87_dBET6_500nM_2h_rep3


title: U87_DMSO_8h_rep2


title: U87_dBET6_500nM_2h_rep2


title: ATAC oblong rep1


title: ATAC 1k-cell rep3


title: U87_DMSO_2h_rep2


title: U87_DMSO_24h_rep1


title: U87_dBET6_500nM_2h_rep1


title: U87_dBET6_500nM_24h_rep3


title: U87_dBET6_500nM_24h_rep2


title: U87R_JQ1_1000nM_24h_rep2

source_name: U87-MG with Acquired Resistance to JQ1

value: U87-MG with Acquired Resistance to JQ1

value: U87 JQ1-resisitant Cells


title: NNI24_DMSO_24h_rep2

source_name: NNI24 Patient-derived GBM-propagating Cells

value: Gliomasphere


title: NNI24_dBET6_50nM_24h_rep2

value: NNI24 Patient-derived GBM-propagating Cells


title: NNI24_DMSO_24h_rep1


title: Mye_2

description:
NSC-My-2DIV-2
mRNA
Processed data file: Complete_geneList.xlsx

source_name: spinal cord, Myelin

value: Wild type

value: spinal cord

value: Myelin


title: U87R_JQ1_1000nM_24h_rep1


title: NNI24_dBET6_50nM_24h_rep1


title: U87_dBET6_500nM_8h_rep1


title: U87P_JQ1_1000nM_24h_rep2

value: U87 Parental Cells


title: U87P_JQ1_1000nM_24h_rep1


title: U87P_dBET6_1000nM_24h_rep1


title: U87P_dBET6_1000nM_24h_rep2


title: U87R_dBET6_1000nM_24h_rep1


title: U87R_dBET6_1000nM_24h_rep2


title: U87R_DMSO_24h_rep1


title: U87_dBET6_500nM_24h_rep1


title: U87P_DMSO_24h_rep2


title: U87P_DMSO_24h_rep1


title: U87_Input

data_processing:
Raw fastq files were aligned to human gneome using bowtie (VN:1.1.2) and duplicates were removed using picard. Alignent parameters and source code here: https://gist.github.com/PoisonAlien/f95e176ad9f2b07938bd36a37be32ebe
Peaks were called using MACS2 with parameters -g hs --keep-dup 1 --bdg --SPMR --nomodel --extsize 200 -q 0.01 Source code here: https://gist.github.com/PoisonAlien/aeb9506d4cab20cbe11accb19feb9240Peaks were called using MACS2 with parameters -g hs --keep-dup 1 --bdg --SPMR --nomodel --extsize 200 -q 0.01 Source code here: https://gist.github.com/PoisonAlien/aeb9506d4cab20cbe11accb19feb9240
Bedgraph files generated by MACS2 were converted to bigWig files using ucsc bedGraphToBigWig tool.
Genome_build: hg19
Supplementary_files_format_and_content: bw files indicating pileup signal normalized to Reads Per Million. NarrowPeak files indicating peaks detected by MACS2

growth_protocol: U87 cells were  cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Standard Illumina library preparation protocol

value: Mock

tag: antibody (catalog)


title: U87R_DMSO_24h_rep2


title: U87_BRD4_dBET6_500nM_24h

value: BRD4 (Bethyl, A301-985A)


title: U87_H3K27Ac

value: H3K27Ac (Actvemotif, 39133)

value: Not Applicable


title: U87_RNA-Pol2

value: RNA Pol2 (Santa Cruz, sc-899X)


title: U87_BRD3_dBET6_500nM_24h

value: BRD3 (Bethyl, A302-367A)


title: U87_H3K4Me3

value: U87 GBM

value: H3M4Me3 (Emdmillipore, 04-745)


title: U87_E2F1

value: E2F1 (Cell Signalling Technology, 3742S)


title: U87_BRD4_dBET6_500nM_2h


title: U87_BRD3_dBET6_500nM_2h


title: U87_BRD2_dBET6_500nM_2h

value: BRD2 (Proteintech, 22236-1-AP)


title: U87_BRD2_dBET6_500nM_24h


title: U87_BRD4


title: U87_BRD3


title: U87_BRD2


title: Tlr7-/- CL075/poly dT rep1

city: Taipei

first: Yi-Ping

last: Hsueh

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

data_processing:
Illumina bcl2fastq2.17 was used to generate fastqs from bcl files
Sequenced reads were trimmed for adaptor sequence,low quality sequences, then mapped to mm10 whole genome using CLC Genomics Workbench with parameters: mismatches=2, minimum fraction length =0.9, minimum fraction similarity=0.9, and maximum hits per read = 5.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using  CLC Genomics Workbench
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample .
Supplementary_files_format_and_content: Txt files include "Name"  "Chromosome"    "Region"        "TPM"   "RPKM"  "Total exon reads"

source_name: primary cultured neuron

growth_protocol: Mouse cortical and hippocampal mixed neurons were cultured in Neurobasal medium/DMEM (1:1) with B27 supplement

extract_protocol:
Total RNA was  using Trizol reagent according to the manufacturer’s instructions (Invitrogen).
2 ug of total RNA was used for RNA-seq library preparation using the TruSeq Stranded mRNA LT set A Sample Prep Kit.

treatment_protocol: WT neurons were treated with vehicle control, poly IC  and CL075, while Tlr7-/- neurons were treated with vehicle control and CL075/poly dT ( for 6hr

tag: day in vitro

value: Div 4

value: CL075/poly dT


title: Tlr7-/- CL075/poly dT rep3


title: Tlr7-/- CL075/poly dT rep2


title: U87_RNA-Pol2_dBET6_500nM_24h


title: Tlr7-/- ctrl rep3

value: vechicle


title: Tlr7-/- ctrl rep1


title: Tlr7-/- ctrl rep2


title: WT CL075 rep3

value: WT


title: WT CL075 rep1


title: WT CL075 rep2


title: RES lamb 4

city: León

first: Alba

middle: Santos

last: Baza

state: León

address: Finca Marzanas, Grulleros

department: Nutrición y Producción de Herbívoros

country: Spain

institute: Instituto de Ganadería de Montaña (CSIC)

data_processing:
Basecalls performed using bcl2fastq 1.8.4
BBDuk version 36.30 (BBMap tools) was applied to raw fastq files for quality trimming (Phred >= 10), filtering short reads (min length = 30) and removing adapter sequences
BBMap version 36.30 was used to map the trimmed reads onto the reference genome; parameters: "maxindel=200k ambig=random intronlen=20"
Bioconductor packages GenomicFeatures (v 1.24.5), GenomicAlignments (v 1.8.4) and the Oar_v4.0 annotation were used to calculate per gene read counts. Bioconductor package mygene was used to obtain the Entrez ID
Differential expression analysis was conducted with the bioconductor package DESeq2 (v 1.12.4).  TPM values were calculated according to Wagner et al. (2012; PMID 22872506) using DESeq2-normalized read counts
Genome_build: GCF_000298735.2_Oar_v4.0
Supplementary_files_format_and_content: The processed data file contains the results of the DESeq2 differential expression analysis, the TPM values for each sample/biological replicate and the Entrez annotation

organism: Ovis aries

source_name: Liver tissue

extract_protocol:
Liver samples stabilized in RNAlater were homogenized using RLT (Qiagen), Lysing Matrix D and a FastPrep-24 instrument (MP Biochemicals); RNA purification was performed with the  RNeasy Mini kit and RNase-Free DNase Set kit (Qiagen).
Poly(A)+ mRNA fraction was isolated from total RNA and cDNA libraries were obtained following Illumina´s recommendations. Briefly, poly(A)+ RNA was isolated on poly-T oligo-attached magnetic beads and chemically fragmented prior to reverse transcription and cDNA generation. The cDNA fragments then go through an end repair process, the addition  of a single ‘A’ base to the 3’ end and then ligation of the adapters. Finally, the products are purified and enriched with PCR to create the indexed final double stranded cDNA library. The quality of the libraries was analyzed in Bioanalyzer 2100, High Sensitivity assay; the quantity of the libraries was determined by real-time PCR in LightCycler 480 (Roche). The pool of the libraries was sequenced by paired-end sequencing (100 × 2) in an Illumina HiSeq 2500 instrument.

tag: tissue

value: Liver

tag: slaughter weight

value: 27 kg


title: RES lamb 3


title: RES lamb 2


title: WT polyIC rep3

value: poly IC


title: RES lamb 1


title: ADL lamb 4


title: WT polyIC rep2


title: WT ctrl rep1


title: WT ctrl rep2


title: ADL lamb 2


title: ADL lamb 3


title: WT polyIC rep1


title: WT ctrl rep3


title: ADL lamb 1


title: G9a.mut.7

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

data_processing:
RNA-seq reads were all trimmed to 40nt and then adapter- and quality-trimmed, and aligned with Tophat2 (Kim et al., 2013) against the mouse reference (GRCm38/mm10) genome. Read counts per ENSEMBL were obtained by featureCounts. Differential expression was evaluated with the DESeq2 package (Love et al., 2014).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Processed data files contain read counts per ENSEMBL transcript obtained by featureCounts

source_name: E2.5 8-cell stage embryo

growth_protocol: Timed natural matings were used for all experiments unless otherwise stated. Noon of the day when the vaginal plugs of mated females were identified was scored as E0.5. For Ehmt2 matings a published conditional allele was used (Sampath et al., 2007). To obtain Ehmt2Cntr or Ehmt2Mat embryos, Ehmt2F/+ Zp3-Cre+ve or Ehmt2F/- Zp3-Cre+ve females were used respectively (de Vries et al., 2000). Only morphologically normal 8-cell stage embryos were used for RNAseq analysis.

extract_protocol:
cDNA was prepared and amplified as earlier described (Tang et al., 2010). This strategy results in a 3'bias in sequencing.
Illumina libraries were prepared as published (Huang et al., 2017). cDNA were fragmented to ~200 bp with Focused-ultrasonicator (Covaris, Woburn, MA) and adaptor ligated libraries were generated using NEBNext II Ultra DNA library Prep Kit for illumina (New England Labs, Ipswich, MA). Single-end 50 bp sequencing was performed with HiSeq1500 (Illumina, San Diego, CA)

treatment_protocol: Zona pellucida was removed from oocytes and embryos prior to lysis.

tag: background

value: mixed background

tag: maternal genotype

value: Ehmt2 Maternal KO

tag: zygotic genotype


title: G9a.mut.4


title: G9a.mut.1


title: G9a.mut.3


title: G9a.mut.10


title: G9a.mut.8


title: G9a.mut.9


title: G9a.mut.5


title: G9a.cntr.10

value: Ehmt2 Maternal WT


title: G9a.cntr.8


title: G9a.cntr.9


title: G9a.cntr.2


title: G9a.cntr.4


title: G9a.cntr.3


title: G9a.cntr.6


title: G9a.cntr.7


title: G9a.cntr.5


title: Mbd1 KO 2 (FAIRE-Seq)

first: Xinyu

last: Zhao

address: 1500 HIGHLAND AVE, T513 Waisman Center

department: Department of Neuroscience

data_processing:
Reads were aligned to the mm9 genome with bowtie using the following command: bowtie -S -p 8 -v 2 -m 4 mm9 UWBC_Zhao_1_L000_R1_001.fastq UWBC_Zhao_1_L000_R1_001.sam
SAM files were converted to BAM files using the following command: samtools view -bS UWBC_Zhao_1_L000_R1_001.sam > UWBC_Zhao_1_L000_R1_001.bam
BAM files were sorted using the following command: samtools sort UWBC_Zhao_1_L000_R1_001.bam > UWBC_Zhao_1_L000_R1_001.sorted.bam
BAM file indices were generated using the following command: samtools index UWBC_Zhao_1_L000_R1_001.sorted.bam
MACS2 was used to call peaks using the following command: macs2 callpeak -t UWBC_Zhao_1_L000_R1_001.sorted.bam -n sample1 -f BAM -g mm
Genome_build: Pre-built mm9 indices were downloaded from the Johns Hopkins University's Center for Computational Biology (ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/)
Supplementary_files_format_and_content: The summit BED files contain genomic coordinates of FAIRE-seq peak summits.

source_name: Mbd1 KO

growth_protocol: All animal procedures were performed according to protocols approved by the University of Wisconsin-Madison Care and Use Committee. Mice were group housed up to 5 per cage with the same gender and maintained on a 12-h light/dark cycle with food and water available ad libitum. mice around 9 weeks old were used for Faire-Seq

extract_protocol:
The fixed dentate gyri from  were sonicated and then preceded to phenol chloroform extraction and the top layer was transferred to a new tube. TE buffer was then added to the old tube, followed by one more phenol chloroform extraction. The top layer was transferred and combined with the saved top layer, the combined top layers were then followed by two more rounds of phenol chloroform extraction. The purified DNA is FAIRE-seq DNA.
The FAIRE-seq libraries were constructed using Nugen Ovation ultralow system V2 Kit according to its manual. Single 50bp sequencing was performed, using an Illumina HiSeq2000 sequencer.

value: dentate gyrus

tag: genotype/variation


title: G9a.mut.6


title: G9a.mut.2


title: Mbd1 KO 1 (FAIRE-Seq)

value: Mbd1 KO


title: Input DNA 1 (ChIP-Seq)

description: FLAG tagged-Mbd1 mouse line

data_processing:
ChIP and input samples were aligned with bowtie (version 0.12.7) under the parameter setting (-k 1 -m 1 --best --strata –sam).
Peaks were called with R package mosaics (version 2.9.8, using the hmm mode) (Chung et al., 2014; Kuan et al., 2011) with parameters binSize=200, capping=0 for each replicate (Rep1 and Rep2) against their matched input controls at a false discovery rate of 0.2
The average fragment length parameters were computed using strand cross-correlation and set as 290, 270, 295, and 280 bps for Rep 1 ChIP and input and Rep2 ChIP and input samples, respectively. The rest of the mosaics parameters were set to their default values.
We also generated a pooled sample (Rep0) by simply concatenating the reads from the two replicates and called peaks for the combined sample under the same setting. The three peak sets were consolidated by taking the intersection of Rep1 and Rep2 peaks and intersecting these with the Rep0 peaks. The final peak boundaries for the intersection peaks were taken from Rep0 peaks.
We used logMinP >= -log10(0.05) and aveLog2Ratio >= log2(1.5) from the mosaics output to require minimum posterior probability of enrichment within a peak to be at least 0.95 and average normalized ChIP to input fold-change to be at least 1.5.
Genome_build: mm9
Supplementary_files_format_and_content: Peak file in text format

source_name: Dentate gyrus

growth_protocol: All animal procedures were performed according to protocols approved by the University of Wisconsin-Madison Care and Use Committee. Mice were group housed up to 5 per cage with the same gender and maintained on a 12-h light/dark cycle with food and water available ad libitum. mice around 9 weeks old were used for ChIP-Seq

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
Samples that met the Illumina sample input guidelines were prepared according the TruSeq¨ ChIP Sample Preparation kit (Illumina Inc., San Diego, California, USA) with minor modifications. Libraries were size selected for an average size of 350 bp using SPRI-based bead selection. Quality and quantity of the finished libraries were assessed using an Agilent DNA1000 chip and Qubit¨ dsDNA HS Assay Kit, respectively.   Libraries were standardized to 2_M.  Cluster generation was performed using standard Cluster Kits (v3) and the Illumina Cluster Station.  Single 100bp sequencing was performed, using standard SBS chemistry (v3) on an Illumina HiSeq2000 sequencer.  Images were analyzed using the standard Illumina Pipeline, version 1.8.2.


title: WT 1 (FAIRE-Seq)

source_name: WT


title: WT 2 (FAIRE-Seq)


title: G9a.cntr.1


title: Mbd1-ChIPSeq 2 (ChIP-Seq)

description: FLAG tagged-Mbd1 mouse line

value: anti-FLAG (Sigma, catalog# F1804)


title: Mbd1-ChIPSeq 1 (ChIP-Seq)

description: FLAG tagged-Mbd1 mouse line


title: Wildtype mouse 9055 (C57BL6J background)

city: Seattle

first: Brian

last: Iritani

state: WA

address: 1959 NE Pacific Street

department: Comparative Medicine

institute: University of Washington

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.2
Reads of low quality were filtered out prior to alignment to mm10 using TopHat v2.1.0.  Counts were generated from TopHat alignments at the gene-level  using “intersection-strict” overlap mode in HTSeq v0.6.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts generated at the gene-level by HTSeq-count v0.6.1

source_name: cortical kidney tissue

extract_protocol: RNA was purified from frozen kidney tissue with the use of RNeasy Mini Kit (Qiagen Valenica, CA). Total RNA integrity was checked using an Agilent 2200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA).

treatment_protocol: Kidney were flash frozen after isolation from mice

value: cortical kidney tissue


title: Fnip1 null mouse 8637 (C57BL6J background)


title: Wildtype mouse 9056 (C57BL6J background)


title: Trained; MeCP2-shRNA; rep4

city: Heidelberg

first: Ana

last: Oliveira

address: Im Neuenheimer Feld 364

department: Biology

institute: Heidelberg University

data_processing:
Illumina sequencing was performed using 2 x 150 bp paired-end reads in FastQ format with at least 30 million read pairs (+/-3%). Gene expression was analyzed using the Bowtie, TopHat, Cufflinks, Cuffmerge, Cuffdiff software suite. Mus musculus, mm10 / GRCm38, Ensembl reference genome was used for the alignment.
Illumina sequencing was performed by GATC Biotech, Constance, Germany
Genome_build: Mus musculus, mm10 / GRCm38, Ensembl reference genome
Supplementary_files_format_and_content: Excel files include average FPKM values per condition, comparative gene expression changes between two conditions (log2 fold change), uncorrected pvalue and FDR adjusted pvalue.

source_name: Dorsal hippocampus

extract_protocol:
Hippocampal tissue was dissected and frozen in RNAlater in dry ice. Rneasy kit (Qiagen) was used for RNA extraction and 1ug of total RNA was used for library preparation.
Librarires were prepared according to Illumina instructions (performed by GATC Biotech, Constance, Germany)

value: Dorsal hippocampus

tag: age

tag: environment

value: trained

value: MeCP2-specific shRNA


title: Fnip1 null mouse 9210 (C57BL6J background)


title: Fnip1 null mouse 9121 (C57BL6J background)


title: Old Mouse Number 4 in Hind Limb Unloading + Reloading Group

city: Orlando

first: Paul

last: Coen

state: FL

address: 301 East Princeton Street

department: Translational Research Institute for Metabolism and Diabetes

institute: Florida Hospital

description: Expression profiling analysis-Coen.xls

data_processing:
Reads from 36 samples (40 raw files) were mapped to mouse genome, mm10, using tophat 2.0.1 (https://ccb.jhu.edu/software/tophat/index.shtml), mapped reads were filtered based on the mapping quality. The overall mapping rates were about 90%. mRNA quantification and normalization was done using Partek Genomics Suite 6.6, annotation database using RefSeq Transcript 77 July 2016 . R package DeSeq (http://bioconductor.org/packages/release/bioc/html/DESeq.html) was used to analyze the differential expression of mRNAs.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Total RNA from Soleus muscle

growth_protocol: 6-month and 22-24 month old male C57BL/6J mice were obtained from the National Institute on Aging rodent colony (Charles River Laboratories, Madison, WI). Young and aged animals were divided into the following experimental groups: 10-day of hind limb unloading (UN), 10-day of hind limb unloading followed by 3 days of reloading recovery (RL), and control (CON). Mice were fed ad libitum with a standard chow diet (#2916, Harlan-Teklad, Houston, Tx) and water/hydrogel (ClearH2O, Westbrook, ME, US) and housed at 22C with a 12-h light/dark cycle.

extract_protocol:
Soleus were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The quality of Total RNA was assessed by the Agilent Bioanalyzer Nano chip (Agilent Technologies). 1ug of Total RNA was used as starting material to construct RNA Seq library using Illumina's Truseq Stranded Total RNA Library preparation kit as per the instructions. First the total RNA is Ribo depleted to remove rRNA from total RNA. The remaining non-rRNA is fragmented into small pieces using divalent cations under elevated temperature. Following fragmentation, the first strand cDNA were synthesized using random primers and followed by second strand synthesis using DNA Polymerase I. The cDNA is then ligated with index adapters for each sample followed by purification and then enriched with PCR to create the final library. The quality and quantity of the libraries were detected by Agilent Bioanalyzer and Kapa Biosystems qPCR.
The quality and quantity of the libraries were detected by Agilent Bioanalyzer and Kapa Biosystems qPCR. Multiplexed libraries are pooled and single-end 50-bp sequencing was performed on one flow-cell of an Illumina Hiseq 2500.

treatment_protocol: 1) hind limb unloaded for 10 days, 2) hind limb unloaded for 10 days and reloaded for 3 days, or 3) maintained under control conditions for 10 days.

value: Soleus

tag: sample group

value: old unloading + reloading


title: Old Mouse Number 1 in Hind Limb Unloading + Reloading Group

description: Expression profiling analysis-Coen.xls


title: Trained; MeCP2-shRNA; rep3


title: Old Mouse Number 3 in Hind Limb Unloading + Reloading Group

description: Expression profiling analysis-Coen.xls


title: Old Mouse Number 3 in Hind Limb Unloading Group

description: Expression profiling analysis-Coen.xls

value: old unloading


title: Old Mouse Number 5 in Hind Limb Unloading Group

description: Expression profiling analysis-Coen.xls


title: Trained; Control-shRNA; rep4

value: control shRNA


title: Trained; Control-shRNA; rep3


title: Trained; MeCP2-shRNA; rep1


title: Trained; MeCP2-shRNA; rep2


title: Old Mouse Number 4 in Hind Limb Unloading Group

description: Expression profiling analysis-Coen.xls


title: Old Mouse Number 2 in Hind Limb Unloading Group

description: Expression profiling analysis-Coen.xls


title: Trained; Control-shRNA; rep2


title: Input DNA 2 (ChIP-Seq)

city: Madison

institute: University of Wisconsin-Madison

description: FLAG tagged-Mbd1 mouse line

tag: chip antibody


title: Trained; Control-shRNA; rep1


title: Home cage; MeCP2-shRNA; rep3

value: home cage


title: Old Mouse Number 9 in Control Group

description: Expression profiling analysis-Coen.xls

value: old control


title: Home cage; MeCP2-shRNA; rep4


title: Old Mouse Number 8 in Control Group

description: Expression profiling analysis-Coen.xls


title: Old Mouse Number 1 in Hind Limb Unloading Group

description: Expression profiling analysis-Coen.xls


title: Home cage; MeCP2-shRNA; rep2


title: Old Mouse Number 7 in Control Group

description: Expression profiling analysis-Coen.xls


title: Old Mouse Number 6 in Hind Limb Unloading Group

description: Expression profiling analysis-Coen.xls


title: Home cage; MeCP2-shRNA; rep1


title: Home cage; Control-shRNA; rep4


title: Old Mouse Number 2 in Hind Limb Unloading + Reloading Group

description: Expression profiling analysis-Coen.xls


title: Home cage; Control-shRNA; rep3


title: Old Mouse Number 4 in Control Group

description: Expression profiling analysis-Coen.xls


title: Old Mouse Number 5 in Control Group

description: Expression profiling analysis-Coen.xls


title: Old Mouse Number 3 in Control Group

description: Expression profiling analysis-Coen.xls


title: Old Mouse Number 2 in Control Group

description: Expression profiling analysis-Coen.xls


title: Home cage; Control-shRNA; rep2


title: Home cage; Control-shRNA; rep1


title: Young (Adult) Mouse Number 4 in Hind Limb Unloading + Reloading Group

description: Expression profiling analysis-Coen.xls

value: young unloading + reloading


title: Young (Adult) Mouse Number 1 in Hind Limb Unloading + Reloading Group

description: Expression profiling analysis-Coen.xls


title: Young (Adult) Mouse Number 3 in Hind Limb Unloading Group

description: Expression profiling analysis-Coen.xls

value: young unloading


title: Old Mouse Number 1 in Control Group

description: Expression profiling analysis-Coen.xls


title: Young (Adult) Mouse Number 2 in Hind Limb Unloading Group

description: Expression profiling analysis-Coen.xls


title: Young (Adult) Mouse Number 4 in Hind Limb Unloading Group

description: Expression profiling analysis-Coen.xls


title: Young (Adult) Mouse Number 2 in Hind Limb Unloading + Reloading Group

description: Expression profiling analysis-Coen.xls


title: Young (Adult) Mouse Number 3 in Hind Limb Unloading + Reloading Group

description: Expression profiling analysis-Coen.xls


title: Young (Adult) Mouse Number 7 in Control Group

description: Expression profiling analysis-Coen.xls

value: young control


title: Young (Adult) Mouse Number 9 in Control Group

description: Expression profiling analysis-Coen.xls


title: Young (Adult) Mouse Number 6 in Control Group

description: Expression profiling analysis-Coen.xls


title: Young (Adult) Mouse Number 1 in Control Group

description: Expression profiling analysis-Coen.xls


title: Young (Adult) Mouse Number 3 in Control Group

description: Expression profiling analysis-Coen.xls


title: Young (Adult) Mouse Number 4 in Control Group

description: Expression profiling analysis-Coen.xls


title: Young (Adult) Mouse Number 5 in Control Group

description: Expression profiling analysis-Coen.xls


title: Young (Adult) Mouse Number 8 in Control Group

description: Expression profiling analysis-Coen.xls


title: Old Mouse Number 6 in Control Group

description: Expression profiling analysis-Coen.xls


title: Young (Adult) Mouse Number 1 in Hind Limb Unloading Group

description: Expression profiling analysis-Coen.xls


title: Dll4-Cas9-proT_PtengRNA_Tal1unstim_3

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

data_processing:
cleaning .fastq files with fastq-mcf, quality control with fastQC
mapping to genome with TopHat2
count reads with htseq-count
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files contain raw mRNA counts

growth_protocol: pro-T cells were grown in the presence of DL4, Scf and Il7

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

treatment_protocol: Prior to RNA extraction, cells were left unstimulated for 18h, followed by 8h stimulation with indicated cytokines

tag: cell type

value: Pro-T cells

tag: treatment

value: transduced with a Pten gRNA-GFP and TAL1-mCherry, unstimulated (no DL4, Scf or Il7)


title: Dll4-Cas9-proT_PtengRNA_Tal1unstim_2

tag: strain


title: Young (Adult) Mouse Number 2 in Control Group

description: Expression profiling analysis-Coen.xls


title: Dll4-Cas9-proT_PtengRNA_Tal1SCF_3

value: transduced with a Pten gRNA-GFP and TAL1-mCherry, Scf stimulated


title: Dll4-Cas9-proT_PtengRNA_Tal1unstim_1


title: Dll4-Cas9-proT_PtengRNA_2

source_name: Dll4-Cas9-proT_PtengRNA_Pro-T cells

value: transduced with a Pten gRNA-GFP, unstimulated (no DL4, Scf or Il7)


title: Dll4-Cas9-proT_PtengRNA_Tal1SCF_1


title: Dll4-Cas9-proT_PtengRNA_Tal1SCF_2


title: Dll4-Cas9-proT_PtengRNA_3


title: DL4+IL7_1

source_name: DL4+IL7_Pro-T cells

value: stimulated with DL4 and Il7


title: DL4_3

source_name: DL4_Pro-T cells

value: stimulated with DL4


title: Dll4-Cas9-proT_PtengRNA_1


title: IL7_2

source_name: IL7_Pro-T cells

value: stimulated with Il7


title: DL4+IL7_2


title: Dll4-Cas9-proT_GFPempty_3

source_name: Dll4-Cas9-proT_GFPempty_Pro-T cells

value: transduced with an empty MSCV_GFP vector, unstimulated (no DL4, Scf or Il7)


title: DL4+SCF+IL7_1

source_name: DL4+SCF+IL7_Pro-T cells

value: stimulated with DL4, Scf and Il7


title: DL4+SCF+IL7_2


title: unstimulated_1

source_name: unstimulated_Pro-T cells

value: unstimulated


title: DL4+SCF_3

source_name: DL4+SCF_Pro-T cells

value: stimulated with DL4 and Scf


title: SCF+IL7_1

source_name: SCF+IL7_Pro-T cells

value: stimulated with Scf+Il7


title: unstimulated_2


title: SCF+IL7_3


title: DL4+SCF+IL7_3


title: DL4+IL7_3


title: SCF+IL7_2


title: Dll4-Cas9-proT_GFPempty_1


title: DL4+SCF_2


title: Dll4-Cas9-proT_GFPempty_2


title: SCF_1

source_name: SCF_Pro-T cells

value: stimulated with Scf


title: DL4_1


title: IL7_3


title: DL4+SCF_1


title: IL7_1


title: unstimulated_3


title: SCF_2


title: DL4_2


title: cdc62_6N

city: Copenhagen N

first: Mengmeng

last: Sun

address: Ole Maaløes Vej 5

country: Denmark

institute: copenhagen university

data_processing:
Illumina Casava HiSeqX HD 3.4.0.38 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content sequence of the cleandata were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S.L. Salzberg, 2012)
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Differential expression analysis of two groups was performed using the DESeq R package (Wang et al., 2010). Corrected P-value of 0.005 and log2 (Fold change) of 1 were set as the threshold for significantly differential expression.
Genome_build: S. islandicus REY15A (accession no. NC_017276)

organism: Saccharolobus islandicus

source_name: cdc6-2 deletion mutant

growth_protocol: The genetic host S. islandicus strain E233S1 and ∆cdc6-2 were cultured at 78 °C in SCVU medium (basic salts and 0.2% sucrose, 0.2% Casamino acids, 1% vitamin solution, 20 μg/mL uracil).

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA, USA), NEBNext Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols. rRNA is removed using a specialized kit that leaves the mRNA. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter,Beverly, USA). Then 3 μl USER Enzyme (NEB，USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.

treatment_protocol: For NQO treatment, each strain was grown to an early exponential phase (A600=ca. 0.20) at which NQO was supplemented to a concentration of 2 µM. Aliquots without the drug were set as control. Incubation was then continued. Cell samples for RNA extraction were taken after 6 hours.

tag: genotype

value: cdc6-2 deletion mutant

tag: cell growth phase

value: log phase

tag: nqo treatment

value: YES


title: cdc6_2

value: NO


title: E233S_6N

source_name: wild type E233S1

value: wild type


title: Escherichia coli BW25113 (EF4 mutant) tetracycline treated replicate 2

status: Public on May 14 2018

city: Beijing

first: Bin

last: Liu

state: Beijing

address: Hai Dian

department: School of Life Sciences

institute: Tsinghua University

description:
Ribosome footprints
Processed data file: Processed_data_rpkm.xlsx
Processed data file: Processed_data_ratios.xlsx

data_processing:
Library strategy: Ribo-Seq
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BW25113 whole genome using bowtie v2.2.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: BW25113 (CP009273.1)
Supplementary_files_format_and_content: Processed_data_rpkm.xlsx: Excel file includes RPKM values for each Sample.
Supplementary_files_format_and_content: Processed_data_ratios.xlsx: Excel file includes mutant/WT log2 ratios.

organism: Escherichia coli BW25113

source_name: Mutant cells tetracycline treated

extract_protocol:
Ribosome footprints were extracted using RNeasy MiNi Kit according to the manual.
The libraries were prepared for sequencing using standard protocols.

tag: strain/background

value: EF4 mutant

value: Tetracycline


title: Escherichia coli BW25113 (EF4 mutant) tetracycline treated replicate 1


title: SCF_3

value: Pro-T cells


title: Escherichia coli BW25113 tetracycline treated replicate 1

source_name: WT cells tetracycline treated


title: Escherichia coli BW25113 replicate 1

source_name: WT cells non-treated


title: Escherichia coli BW25113 replicate 2


title: Escherichia coli BW25113 tetracycline treated replicate 2


title: set2_viewpoint_3_replicate_6

city: Utrecht

first: Geert

last: Geeven

state: Utrecht

address: Uppsalalaan 8

department: Biomedical Genomics

country: Netherlands

institute: Hubrecht Institute

data_processing:
Library strategy: 4C-seq
The initial step in the 4C-seq analysis is the alignment of the sequencing reads (starting from the first restriction enzyme DpnII motif GATC) using bowtie2 with default parameters. We use samtools to filter for mapped reads with a minimum mapping quality score of 1. Next we extract from the reference genome (mm9) all possible 4C capture sequences (in FASTA format) with the exact  same length as the observed 4C captures from the sequencing run. We map and filter these reference capture sequences with the same parameters as the observed 4C reads using bowtie2 and samtools. In subsequent analysis we only include the thus mappable 4C fragment ends.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated .txt files contain counts of reads at uniquely mappable 4C fragment ends on the cis chromosome, i.e. the chromosome on which the bait/viewpoint fragment is located.  Scores represent the number of reads mapping to a DpnII restriction fragment end.

source_name: embryonic stem cells

growth_protocol: E14 ES cells (IB10 cells) were cultured in BRL-conditioned Dulbecco’s Modified Eagle Medium (DMEM with High Glucose, GlutaMAX™, pyruvate; Life Technologies) supplemented with 10% fetal calf serum (FCS), non-essential amino acids (NEAA) (Life Technologies), 1000 U/ml leukemia inhibitory factor (LIF) and 2-mercaptoethanol. We isolated fetal livers from e14.5 embryos by dissection and obtained single cell suspensions by filtration through a cell strainer (BD biosciences).

extract_protocol:
The initial steps of the 4C procedure, as published before (van de Werken et al., 2012, Nature Methods (PMID 22961246)), remain unchanged.  Cells are cross-linked using 2% formaldehyde for 10 minutes at room temperature in PBS 10%FCS and nuclei are isolated, after which chromatin is digested with DpnII and subsequently ligated. After reversal of the cross-links, the DNA is purified and treated with the second restriction enzyme treatment (Csp6I). After a second re-ligation step, the sample is purified and a 4C PCR is performed. For mESCs we generated three biological replicates from individual dishes (~10x106 cells). For fetal livers, biological replicates were generated from individual embryos from a single pregnant mouse. We used barcoded primers to distinguish between replicates and tissues.
4C PCR

treatment_protocol: cells are cross linked using 2% formaldehyde for 10 minutes at room temperature in 10%FCS/PBS

value: embryonic stem cell

tag: tissue/cell line

value: cell line


title: set2_viewpoint_3_replicate_4


title: set2_viewpoint_3_replicate_5


title: set2_viewpoint_3_replicate_2


title: Escherichia coli BW25113 (EF4 mutant) replicate 2

source_name: Mutant cells non-treated


title: set2_viewpoint_2_replicate_6


title: set2_viewpoint_2_replicate_5


title: set2_viewpoint_2_replicate_4


title: set2_viewpoint_2_replicate_2


title: set2_viewpoint_2_replicate_3


title: set2_viewpoint_3_replicate_1


title: set2_viewpoint_1_replicate_3


title: set2_viewpoint_2_replicate_1


title: set2_viewpoint_1_replicate_5


title: set2_viewpoint_1_replicate_6


title: E233S


title: set2_viewpoint_1_replicate_2


title: set1_viewpoint_10_FL_replicate_3

source_name: fetal liver

tag: tissue

value: fetal liver

value: tissue


title: set2_viewpoint_1_replicate_1


title: Escherichia coli BW25113 (EF4 mutant) replicate 1


title: set1_viewpoint_10_FL_replicate_2


title: set2_viewpoint_1_replicate_4


title: set2_viewpoint_3_replicate_3


title: set1_viewpoint_10_ESC_replicate_2


title: set1_viewpoint_10_FL_replicate_1


title: set1_viewpoint_10_ESC_replicate_1


title: set1_viewpoint_9_FL_replicate_3


title: set1_viewpoint_8_ESC_replicate_1


title: set1_viewpoint_8_ESC_replicate_2


title: set1_viewpoint_8_FL_replicate_2


title: set1_viewpoint_8_ESC_replicate_3


title: set1_viewpoint_8_FL_replicate_3


title: set1_viewpoint_9_FL_replicate_1


title: set1_viewpoint_9_ESC_replicate_1


title: set1_viewpoint_7_FL_replicate_2


title: set1_viewpoint_9_ESC_replicate_3


title: set1_viewpoint_7_FL_replicate_3


title: set1_viewpoint_7_ESC_replicate_3


title: set1_viewpoint_7_ESC_replicate_1


title: set1_viewpoint_7_ESC_replicate_2


title: set1_viewpoint_8_FL_replicate_1


title: set1_viewpoint_6_FL_replicate_2


title: set1_viewpoint_7_FL_replicate_1


title: set1_viewpoint_6_FL_replicate_1


title: set1_viewpoint_6_FL_replicate_3


title: set1_viewpoint_6_ESC_replicate_3


title: set1_viewpoint_10_ESC_replicate_3


title: set1_viewpoint_9_FL_replicate_2


title: set1_viewpoint_6_ESC_replicate_1


title: set1_viewpoint_6_ESC_replicate_2


title: set1_viewpoint_9_ESC_replicate_2


title: set1_viewpoint_5_FL_replicate_3


title: set1_viewpoint_5_FL_replicate_2


title: set1_viewpoint_5_ESC_replicate_3


title: set1_viewpoint_5_ESC_replicate_2


title: set1_viewpoint_5_ESC_replicate_1


title: set1_viewpoint_5_FL_replicate_1


title: set1_viewpoint_4_FL_replicate_3


title: set1_viewpoint_4_FL_replicate_2


title: set1_viewpoint_3_FL_replicate_3


title: set1_viewpoint_4_FL_replicate_1


title: set1_viewpoint_4_ESC_replicate_3


title: set1_viewpoint_4_ESC_replicate_2


title: set1_viewpoint_3_FL_replicate_2


title: CE_mRNA_rep_3_5

city: New York

first: Itai

last: Yanai

address: 430 East 29th St., Office 510

department: Biochemistry and Molecular Pharmacology

institute: New York University, School of Medicine

data_processing:
Libraries were sequenced on the Illumina HiSeq2500, paired-end sequencing R1- 15bp, R2- 35bp, Index- 6bp
Filter barcode minimum quality of 10.
Demultiplexing using the CEL-Seq2 pipeline (Hashimshony, et a. 2016) of second mate, using first mate barcode, allowing no mismatches in barcode.
Using htseq-count, annotated mRNA were counted
Genome_build: WS230
Supplementary_files_format_and_content: expression matrix

source_name: C. elegans embryo_stage 5- 270 min

growth_protocol: C. elegans embryos were isolated from cut N2 adult worms using mouth pipette (Baugh et al. 2003) and staged at eight developmental time-points (60, 120, 180, 225, 270, 330, 410 and 500 minutes after the 4 cell stage).

extract_protocol:
From each sample, total RNA was extracted using TRIzol and eluted in 1.5ul of RNase-free water of which 0.5ul was used for the CEL-Seq protocol
CEL-Seq

treatment_protocol: 50 embryos were collected at each time-point, in triplicates.

tag: developmental stage

value: stage 5- 270 min

value: embryo


title: CE_mRNA_rep_2_8

source_name: C. elegans embryo_stage 8- 500 min

value: stage 8- 500 min


title: CE_mRNA_rep_3_3

source_name: C. elegans embryo_stage 3- 180 min

value: stage 3- 180 min


title: CE_mRNA_rep_3_6

source_name: C. elegans embryo_stage 6- 330 min

value: stage 6- 330 min


title: CE_mRNA_rep_3_1

source_name: C. elegans embryo_stage 1- 60 min

value: stage 1- 60 min


title: CE_mRNA_rep_3_7

source_name: C. elegans embryo_stage 7- 410 min

value: stage 7- 410 min


title: CE_mRNA_rep_3_2

source_name: C. elegans embryo_stage 2-120 min

value: stage 2-120 min


title: CE_mRNA_rep_3_8


title: set1_viewpoint_4_ESC_replicate_1


title: set1_viewpoint_3_FL_replicate_1


title: CE_mRNA_rep_2_7


title: set1_viewpoint_3_ESC_replicate_3


title: CE_mRNA_rep_2_5


title: set1_viewpoint_3_ESC_replicate_2


title: set1_viewpoint_3_ESC_replicate_1


title: CE_mRNA_rep_2_6


title: set1_viewpoint_2_FL_replicate_3


title: CE_mRNA_rep_2_4

source_name: C. elegans embryo_stage 4- 225 min

value: stage 4- 225 min


title: CE_mRNA_rep_2_2


title: CE_mRNA_rep_3_4


title: set1_viewpoint_2_FL_replicate_1


title: CE_mRNA_rep_2_3


title: CE_mRNA_rep_1_8


title: set1_viewpoint_2_ESC_replicate_3


title: set1_viewpoint_2_ESC_replicate_1


title: CE_mRNA_rep_1_6


title: CE_mRNA_rep_1_2


title: CE_mRNA_rep_1_4


title: CE_mRNA_rep_1_3


title: set1_viewpoint_1_ESC_replicate_3


title: set1_viewpoint_1_FL_replicate_2


title: set1_viewpoint_1_ESC_replicate_2


title: set1_viewpoint_1_ESC_replicate_1


title: CE_mRNA_rep_1_5