title: PT_2

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Basecalls performed using CASAVA
Sequenced reads were mapped to mm9 whole genome using tophat version 2.0.9 with parameters : -p 8 --splice-mismatches 1  --segment-mismatches 2
FPKM and differential expression were calculated using the Cufflinks suite version 2.1.1
To determine differential splicing events, MATS 3.0.8 beta was used counting junction reads and reads falling into the tested region within ENSEMBL v65 gene definitions. Splicing events were labelled significant if the sum of the reads supporting a specific event exceeded 10 reads, the p-value was lower than 0.05. All other parameters were left at the default value.
Genome_build: mm9
Supplementary_files_format_and_content: fpkm.txt tab-delimited text file includes FPKM values for WT and PT Samples

source_name: Bone marrow

growth_protocol: B cells were isolated from the bone marrow of pretumoral, 6 to 8-week old Eµ-myc;Prmt5F/FCreER mice (strain: C57BL/6 x 129S1/SvlmJ background). The cells were grown in the presence of 5 ng/ul IL-7.

extract_protocol:
RNA was isolated from cells using Trizol Reagent and Purelink RNA Mini Kit.  Illumina TruSeq RNA Sample Prep Kit v2(Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Paired-end RNA library was prepared according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.

treatment_protocol: Prmt5 was deleted by incubation with 50 nM 4-OHT for 24 h (EtOH was added to the controls), after which the EtOH or 4-OHT was washed off, and the cells were resuspended in fresh medium and incubated for an additional 5 days.

value: C57BL/6 x 129S1/SvlmJ

value: E-mu-myc;Prmt5F/FCreER transgenic

value: post natal 6-8 week old

value: B-Cells

tag: treatment protocol


title: PT_3

status: Public on May 19 2015

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: genotype/variation

tag: age

tag: cell type

value: Prmt5 was deleted by incubation with 50 nM 4-OHT


title: STT6027_LMS

city: Stanford

first: Xiangqian

last: Guo

state: CA

address: 300 Pasteur Dr.

department: Department of Pathology

country: USA

institute: Stanford University

description: Experiment type: 3SEQ

data_processing:
Sequenced Reads after filtered by quality, were re-filtered by fastx, and then were mapped to the transcriptome (refMrna, downloaded from the UCSC genome browser, www.genome.ucsc.edu/) by using SOAP2, allowing at most two mismatches
Total numbers of sequenced reads for each gene symbol from the transcriptome mapping were determined and were used to create the gene-expression profile matrix. The library size was then normalized to one million reads (TPM).
The sequencing depth for each library was determined with the estimation of library saturation for transcriptome detection, which showed that our sequencing depths were deep enough to detect almost all of the known mRNAs expressed.
The distances between sequencing reads and 3’end of mRNAs were measured to be around 100-200nt as we expected.
Genome_build: hg19
Supplementary_files_format_and_content: expressional matrix with sample by column and gene by row

organism: Homo sapiens

source_name: Leiomyosarcoma

extract_protocol:
Multiple 2mm-diameter cores were taken from diagnostic FFPE material for RNA isolation. Then, total RNA was extracted by using of RecoverAll Total Nucleic Acid Isolation Kit (Ambion).
Poly(A)+RNA was selected and enriched with oligo(dT) using the Oligotex mRNA mini Kit (Qiagen).  The Poly(A) RNA was heat sheared to 100~200nt fragments. The sheared RNA was then subjected to first and second strand cDNA synthesis, followed by additional steps of library construction as described previously [1-3]. The libraries were sent to the Stanford Genomic Center to be sequenced for the first 36bp at the 5’end of mRNA fragments with Illumina GA IIx machines.

treatment_protocol: Clinical tissue samples were formalin-fixed and paraffin-embedded (FFPE).

tag: tissue

value: Soft Tissue

tag: tissue archive method

value: FFPE

tag: subtypes

value: I


title: KO_cTEC_2

city: Montreal

first: Charles

last: St-Pierre

state: Quebec

address: 2950, Chemin de Polytechnique

department: Institute for Research in Immunology and Cancer

country: Canada

institute: Montreal University

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were trimmed for adaptor sequence and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

source_name: Thymic epithelial cells

extract_protocol:
Thymi were isolated and stromal cell enrichment was performed. Briefly, thymi were mecanically disrupted, digested and thymic stromal cells were sorted by multicolour flow cytometry.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Aire KO

value: cTEC

value: Thymus

value: 6-8 week old


title: PT_1


title: WT_mTEC_hi_2

value: wild type

value: mTEC


title: WT_cTEC_3


title: WT_mTEC_hi_1


title: KO_mTEC_hi_3


title: WT_2

value: incubation with EtOH (control)


title: KO_cTEC_1


title: WT_1


title: KO_mTEC_hi_1


title: WT_3


title: KO_mTEC_lo_2


title: Control_2_mRNA

status: Public on May 18 2015

city: Seoul

first: Gir Won

last: Lee

address: Sangdo-dong

country: South Korea

institute: Soongsil University

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence
Mapped to MG8 whole genome using Tophat version 2.0.8b with parameters -p 8 -r --mate-std-dev --read-realign-edit-dist 0 --GTF --min-intron-length --max-intron-length --no-discordant.
Transcripts were assembled and quantitated using Cufflinks version 2.1.1.
Genome_build: Magnaporthe oryzae 70-15 downloaded from Broad Institute (http://www.broadinstitute.org/)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for "Hypoxia" and "Normoxia" sample.

organism: Pyricularia oryzae

source_name: Normoxia Control

growth_protocol: 3 day culture in complete media (0.6% yeast extract, 0.6% casamino acid, 1% glucose)  with 150rpm shaking. Ttransfer mycelia to V8 agar plates after homogenization and rinsing. After three hours, the plates were divided into two treatment groups.

extract_protocol:
According to manufacturer's instructions using Easy-spin™ total RNA extraction kit (iNtRON Biotechnology, Seoul, Korea)
Libraries were constructed from mRNA using the Illumina TruSeq RNA sample preparation kit (FC-122-1001) following  manufacturer's protocols.

treatment_protocol: 21% and 1% Oxygen

value: mycelia


title: ChIP-Seq (input)

city: Bad Nauheim

first: Lei

last: Gu

state: MASSACHUSETTS

address: parkstreet 1

country: Germany

institute: Max Planck Institute for heart and lung research

description: input

library_source: genomic

data_processing:
mapping using bwa
peak calling using macs2
Genome_build: ce10

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: whole worm WT gDNA

growth_protocol: Mixed stage WT (N2) worms were grown at 20 degrees

extract_protocol:
Worms were washed several times with M9 buffer and snap frozen in liquid nitrogen. Pellets were sent to Umass Medical School Deep Sequencing Core for gDNA extraction and ChIP-Seq
Library was constructed by Umass Medical School Deep sequencing core

treatment_protocol: Worms were fed dam-dcm- bacteria

tag: antibody

value: none, input

tag: developmental stage

value: WT (N2) mixed stage worms


title: Control_3_mRNA


title: ChIP-Seq

description: 6mA enriched


title: KO_cTEC_3


title: Hypoxia_3_mRNA

source_name: Hypoxia


title: Control_1_mRNA


title: Hypoxia_1_mRNA


title: SeaUrchin_48hpf (13)

city: Seville

first: Carlos

last: Gómez

state: Seville

address: Crta Utrera  km 1

country: Spain

institute: Centro Andaluz de Biologia del Desarrollo

data_processing:
library strategy: 4C-Seq
Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the Mus musculus (mm9 assembly) , Danio rerio (danRer7 assembly) or S.purpuratus (StrPur4 assembly) genomes using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept. Reads located in fragments flanked by two restriction sites of the same enzyme, or in fragments smaller than 40 bp were filtered out
Mapped reads were then converted to reads-per-first-enzyme-fragment-end units, and smoothed using a 30 DpnII fragments mean running window algorithm.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: mm9/danRer7/StrPur4
Supplementary_files_format_and_content: bedGraph, they contain smoothed data of 4Cseq of  viewpoint that can be directly uploaded to UCSC for visualization.

organism: Strongylocentrotus purpuratus

source_name: 48hpf sea urchins embryos

growth_protocol: Embryos were raised at 12ºC untill they reached the desired developmental stage. They were cellularised before fixation.

extract_protocol:
Chromatin was extracted from single cells preparations from different samples. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.

treatment_protocol: No treatment

value: whole embryos


title: STT6791_LMS

description: Experiment type: 3SEQ

value: III


title: E33

city: Cambridge

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

description:
MS369_Tet+1
RNA-Seq followed by Nextera XT

data_processing:
Hiseq 2500 processing
Alignments done with Tophat v1.4.1 to hg19
Cufflinks v2.1.1 used to summarize expression with the --compatible-hits-norm option and the annotation file -G Homo_sapiens.GRCh37.74.gtf
Genome_build: hg19
Supplementary_files_format_and_content: gtf annotation file for cufflinks transcripts
Supplementary_files_format_and_content: tab-delimited text file with transcript ids described by bathomas_merged.gtf, gene symbol and 16 sample columns containing log2 RPKM values for each sample

source_name: CCR6+, CD4+ T cells from HLA-DR4+ MS patient, myelin tetramer positive

growth_protocol: CCR6+ memory CD4+ T cells from HLA-DR4+ healthy controls and HLA-DR4+ MS patients were amplified by PHA and IL-2 and stimulated by irradiated autologous monocytes and DR4 myelin peptides (MOG97-109 and PLP180-199). Cell proliferation was measured and two of the highest proliferated wells were picked for DR4 tetramers staining (MOG97-109-tetramers and PLP180-199-tetramers). Myelin tetramer+ and tetramer− cells were sorted into RNA lysis buffer for RNA sequencing.

extract_protocol:
RNA was extracted using the NucleoSpin RNA XS Kit (Macherey-Nagel, Bethlehem, PA) according to the manufacturers instructions.
cDNA synthesis and amplification were performed using SMARTer Ultra Low Input RNA for Illumina Sequencing High Volume Kit (Clontech, Mountain View, CA) according to the manufacturers instructions. The average number of cells used to isolate RNA was 3,000, which yielded >1ng input RNA. Paired-end sequencing libraries were prepared using the Nextera XT DNA sample Prep Kit (Illumina, SanDiego, CA) according to the manufacturers instructions.

treatment_protocol: Amplified T cell libraries assay were carried out as previous described (Geiger, 2009). Naïve, CCR6− and CCR6+ memory CD4+ T from paired MS patients and healthy controls were pre-sorted and cultured in 96-well round-bottom plates (Costar) at 2 × 103 cells per well in complete RPMI 1640 medium, and stimulated with 1 μg/ml PHA (Roche) and 20 U/ml IL-2 in the presence of irradiated (45Gy) allogeneic feeder cells (2×104/well). IL-2 was added on day 4, 7 and 10. Cultures were washed and split into two 96-well plates after 2-weeks of stimulation and expansion. Library screening was performed by culturing ~ 106 T cells/well with autologous monocytes (~105), which were either unpulsed or pulsed for 3 h with 10 μg/ml myelin peptide pools (MBP85-99, MOG222-241, PLP30-49, PLP129-148, MOG97-109, PLP180-199), or C. albicans (GREER). [3H] (Perkin Elmer) was added into the cultures 16 h before harvest. On day 5, cell proliferation was measured by 3H-thymidine incorporation on a scintillation beta-counter (Perkin Elmer). Culture supernatants were taken on day 7 for cytokine profiling as described below.

tag: diagnosis

value: Multiple Sclerosis

tag: cell population


title: E22

description:
MS181_Tet+2
RNA-Seq followed by Nextera XT

value: CCR6+, CD4+ T cells from HLA-DR4+ MS patient, myelin tetramer positive


title: LmjF_WT_DMOG_smallRNA

city: athens

first: robert

last: sabatini

state: GA

address: 120 Green street

department: Biochemistry and Molecular Biology

institute: University of Georgia

description: Small RNA

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the respective reference genomes (T. brucei 427 v6.0 and L. major v4.2) using bowtie-2 with default 'local-sensitive' mode and further processed using samtools. For the small RNA libraries, reads shorter than 18 bp were discarded before mapping.
To express the transcripts levels for individual genes, we determined the number of reads per kilobase per million reads (RPKM) using a protocol from Mortazavi et al. 2008. Briefly, we counted the number of reads mapped to all annotated transcriptomic features (e.g. mRNA) on the same strand (i.e. sense) and opposite strand (i.e. antisense). Both the sense and antisense read numbers were normalized by length of the feature (in kilobase) and the total number of reads (in millions) mapped to non-structural RNAs in the corresponding library (i.e. number of mappable reads excluding rRNA and tRNA reads).
Genome_build: Trypanosoma brucei 427 v6.0, Leishmania major v4.2
Supplementary_files_format_and_content: Wig files

organism: Leishmania major

source_name: WT parasite, DMOG

growth_protocol: Leishmania major Friedlin V1 cells were grown at 26°C in M199 medium supplemented with 40 mM 4-(2-hydroxyethyl)-1-piperazineethanesuphonic acid (HEPES) pH 7.4, 100 uM adenine , 1 µg mL-1 biotin, 10 µg mL-1 hemin , 2 µg mL-1 biopterin, 50 units/mL penicillin, 50 µg/mL streptomycin, and 10% (v/v) heat-inactivated fetal calf serum. Bloodstream form T. brucei cells were grown as described in Hirumi et al. (1980). Parasitology 80, 371–382. Cell density was determined by using a hemocytometer.

extract_protocol:
Small RNAs were isolated from T. brucei or L. major using Qiagen miRNeasy kit according to manufacturer's instructions. 5x10^7 cells were used per sample, and isolated at the log phase of parasite growth. Total RNA was isolated from log-phase T. brucei cultures using a Qiagen RNeasy kit according to the manufacturer’s instructions. 5x10^7 cells were used for each prep.
All four small RNA-seq libraries were prepared using approximately 250ng small RNA using the TruSeq small RNA kit (Illumina) according to the manufacturer's instructions with the following exception: the PCR amplification was performed for 12-16 cycles using the KAPA HiFi DNA polymerase (Kapabiosystems). The PCR product was purified and concentrated using AMPure XP beads (Beckman Coulter). Quality and concentration of all libraries was determined using a Bioanalyzer 2100 (Agilent) and high-throughput sequencing was performed on a HiSeq 2000 (Illumina). The two full-length RNA-seq libraries were constructed from approximately 1 µg of total RNA by Vertis Biotechnology AG. Briefly, total RNA was polyA-enriched using oligo(dT) chromatography and fragmented by ultrasound. Next, first strand cDNA was synthesized using N6 random primers followed by a strand-specific ligation of sequencing adapter to the 3' and 5' ends of the first stranded cDNA and PCR amplification of 10-20 cycles depending on the amount of starting material. High-throughput sequencing was performed on a HiSeq 2000 (Illumina).

treatment_protocol: DMOG treatment of cells was performed by supplementing media with 1mM DMOG for 5 days in T. brucei or at 5mM for 10 days in L. major.

tag: strain/background

value: Friedlin V1

value: WT

value: whole body

tag: lifestage

value: promastigote

tag: treatment

value: DMOG


title: SeaUrchin_48hpf (15)


title: SeaUrchin_48hpf (17)


title: LmjF_WT_DMSO_smallRNA

description: Small RNA

source_name: WT parasite, DMSO control

value: DMSO


title: E32

description:
MS369_Tet-2
RNA-Seq followed by Nextera XT

source_name: CCR6+, CD4+ T cells from HLA-DR4+ MS patient, myelin tetramer negative


title: E7

description:
MS266_Tet-1
RNA-Seq followed by Nextera XT

value: CCR6+, CD4+ T cells from HLA-DR4+ MS patient, myelin tetramer negative


title: SeaUrchin_48hpf (16)


title: E30

description:
MS358_Tet+2
RNA-Seq followed by Nextera XT


title: E26

description:
MS386_Tet-2
RNA-Seq followed by Nextera XT


title: E29

description:
MS358_Tet-2
RNA-Seq followed by Nextera XT


title: E8

description:
MS266_Tet+1
RNA-Seq followed by Nextera XT


title: E27

description:
MS386_Tet+1
RNA-Seq followed by Nextera XT


title: E21

description:
MS181_Tet-2
RNA-Seq followed by Nextera XT


title: E19

description:
HC4_Tet+1
RNA-Seq followed by Nextera XT

source_name: CCR6+, CD4+ T cells from HLA-DR4+ healthy control, myelin tetramer positive

value: Healthy


title: E14

description:
HC2_Tet+2
RNA-Seq followed by Nextera XT

value: CCR6+, CD4+ T cells from HLA-DR4+ healthy control, myelin tetramer positive


title: E17

description:
HC4_Tet-1
RNA-Seq followed by Nextera XT

source_name: CCR6+, CD4+ T cells from HLA-DR4+ healthy control, myelin tetramer negative


title: E6

description:
HC3_Tet+1
RNA-Seq followed by Nextera XT


title: Hypoxia_2_mRNA


title: E5

description:
HC3_Tet-1
RNA-Seq followed by Nextera XT

value: CCR6+, CD4+ T cells from HLA-DR4+ healthy control, myelin tetramer negative


title: E12

description:
HC2_Tet-1
RNA-Seq followed by Nextera XT


title: mRNA-seq 18h H. pylori rep2

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

institute: Max Planck Institute for Infection Biology

data_processing:
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 hg19  using TopHat2
expression levels of genes and expression changes were analyzed using the Cufflinks/Cummerbund pipeline
Genome_build: hg19
Supplementary_files_format_and_content: matrix table

molecule: polyA RNA

source_name: Gastric epithelial cells

growth_protocol: Gastric epithelial cells were cultured in propagation medium containing growth-factors

extract_protocol:
Qiagen-Allprep-Kit was used accroding to manufacturers instructions, including Qiagen DNAse-treatment
Illumina True-Seq RNA directional library

treatment_protocol: 2 h prior to infection of cells with the P12 strain of H. pylori, medium was replaced with RPMI-medium containing 0.1% FCS and infections were performed at an MOI of 25 for the indicated times.

value: primary short-term culture

tag: passage

value: H. pylori infection

tag: time


title: mRNA-seq non-infected rep2

value: non-infected


title: mRNA-seq 18h H. pylori rep1


title: mRNA-seq non-infected rep1


title: H2AXpS139-ChIP-seq 10 Gy IR rep2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
enirched regions were identified using HOMER (Heintz et al. 2010) with a window-size of 2500 bp and a minimal distance of 5000 bp
Genome_build: hg19
Supplementary_files_format_and_content: bed-files generated by HOMER's getPeaks tool using a window-size of 2.5kb and a minimal distance of 5kb

source_name: AGS cells

growth_protocol: AGS cells were routinely grown in RPMI containing 10% FCS and replated every 2-3 days at a ratio of 1:3

extract_protocol:
Chromatin was corsslinked for 10 min in 1% Formaldehyd, before nuclei were isolated and protein-DNA-complexes were purified with the antibody
Libraries were constructed with NuGEN Ovation Ultralow Multiplex System (Part no 0330, 0331); after end-repair, adapter-ligation and quality control all samples were sequenced on an Illumina HiSeq2500

treatment_protocol: 2 h prior to infection of AGS cells with the P12 strain of H. pylori, medium wsa replaced with RPMI-medium containing 0.1% FCS and infections were performed at an MOI of 50 for the indicated times. For irraditaion, the growth medium was replaced in a similar fashion, cells were irradiated for 11 min with a Cs-137 source (Gammacell 40 Exacotr; Nordion), corresponding to 10 Gy, followed by a 90 min recovery phase

value: gastric cancer cell line

tag: cell line

value: AGS

value: 10 Gy IR

tag: chip-antibody


title: H2AXpS139-ChIP-seq 10 Gy IR rep1


title: H2AXpS139-ChIP-seq 18 h H.pylori rep2


title: H2AXpS139-ChIP-seq 18 h H.pylori rep1


title: H2AXpS139-ChIP-seq 6 h H.pylori rep2

value: 6 h


title: Mouse_E14.5 (11)

source_name: E14.5 mouse embryos

growth_protocol: CBA/Ca×C57Bl/10 crosses. Embryos taken at 14.5dpc, taking the day in which the plug was found as 0.5dpc.

value: whole embryos


title: H2AXpS139-ChIP-seq 6 h H.pylori rep1


title: Mouse_E14.5 (10)


title: H2AXpS139-ChIP-seq non-infected rep1

value: control


title: H2AXpS139-ChIP-seq non-infected rep2


title: Mouse_E14.5 (9)


title: Mouse_E14.5 (8)


title: Mouse_E9.5 (6)

source_name: E9.5 mouse embryos

growth_protocol: CBA/Ca×C57Bl/10 crosses. Embryos taken at 9.5dpc, taking the day in which the plug was found as 0.5dpc.


title: Mouse_E14.5 (7)


title: Mouse_E14.5 (4)


title: Mouse_E14.5 (5)


title: Mouse_E9.5 (3)


title: Mouse_E14.5 (2)


title: Mouse_E14.5 (1)


title: Day 15 +Wnt, replicate2

city: Chuo-ku

first: Munazah

last: Andrabi

state: Kobe

address: 2-2-3 Minatojima-minamimachi

country: Japan

institute: RIKEN:Center for Developmental Biology

data_processing:
Basecalls were performed using illumina RTA  software (version 1.17.21.3) and reads were de-multiplexed using bcl2fastq ( version 1.8.4).
Quality check of the reads was performes using FastQC(version 0.10.1). Ascertaining the high quality of sequencing, reads were mappedto mm10 mouse genome assembly using Tophat (version 2.0.8b) with default parameter settings.
Number of reads originating from genes were quantified by cuffdiff program in Cufflinks package (version 2.1.1). These count values were subsequently used to test for differential expression using edgeR(version 3.2.4)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including normalized expression values for each sample

source_name: SFEBq derived  Retinal Pigmented Epithelium

growth_protocol: ES cell culture was performed using 2i conditioned media (3uM CHIR99201 and 1uM PD184352) in the presence of LIF and blasticidin. ES cells (Rx::GFP cells) were trypsinized and 3000 cells were reaggregated in 100uL differentiation media for each well of a 96-Well low-cell-adhesion plate with Lipidure Coat and incubated at 37C and 5% CO2. Defining trypsinization and reaggregation as Day 1, at Day 2 Matrigel was introduced to achieve a final Matrigel concentration of 4%. Aggregates were incubated at 37C and 5% CO2 until Day 10, when sample collection and Wnt/Fgf treatment began.

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen) using the company-provided protocol. SFEBq aggregates were resuspended in 700uL buffer RLT and spun through QIAshredder (Qiagen) prior to RNA extraction.
Libraries were prepared using 700ng of total RNA, according to the protocol of TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: At Day 10, GFP+ neural retina epithelium was explanted using forceps and either collected for RNA-seq analysis (NRE samples) or further cultured in retinal maturation media (RMM) containing Wnt/β-catenin signaling stimulating conditions (achieved via inhibition of GSK3 using 3uM CHIR99201 for the first 24 hours and then 1uM CHIR99201 thereafter) or Fgf-signaling stimulating conditions (5ng/mL human recombinant bFgf + 10% FBS) thus generating RPE and NR tissues, respectively. Media was exchanged with fresh media at days 11, 12, and 14. RPE and NR samples were collected in triplicate at Day 12 and Day 15.

tag: strain

value: EB5 Rx::GFP+/-


title: Mouse ChIP Exo

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description: chromatin for ChIP-Exo (no input sample)

data_processing:
Library strategy: ChIP-Exo
Reads were trimmed with Trimmomatic Version 0.32, parameters: ILLUMINACLIP:TruSeq3-SE.fa (or -PE.fa):2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:25
Trimmed reads were mapped to the mm9 or hg19 genomes with bwa mem version 0.7.10-r789.
Mapped reads were indexed and sorted with samtools 0.1.18.
Peaks were called with MACS2 (MACS2.1.0.20140616)
Genome_build: mm9 or hg19

source_name: 8w Mouse Testis

extract_protocol:
Testis samples were fixed with formaldehyde.
The ChIP libraries were made from the input and the material immuniprecipitated with the Dmrt1 antibody described in PMID 11040213.   Chromatin fragments were blunted with Lucigen DNA terminator enyme mix (Lucigen# 40035).  Blunted fragments were adenylated with Exo- Klenow (NEB #MO2125).  Illumina adapters (Illumina #100521) were diluted 1:50 and ligated to adenylated fragments with T4 ligase (NEB #NEB M0202T).  Products were amplified with 18 rounds of PCR using Phusion Polymerase (NEB M0530s) using barcoded oligonucleotides.  DNA fragments between 150 and 250 were purified by agarose gel electrophoresis. ChIP-Exo libraries were prepared as described in PMID: 22153082.

value: C57BL/6, Mixed

value: 8 weeks

value: Testes

value: dmrt1 Antibody (PMID:11040213)


title: Day 15 +Wnt, replicate3

value: SFEBq derived  Retinal Pigmented Epithelium


title: Day 15 +Fgf, replicate3

source_name: SFEBq derived Neural Retina

value: SFEBq derived Neural Retina


title: Day 15 +Wnt, replicate1


title: Day 15 +Fgf, replicate1


title: Day 12 +Wnt, replicate3


title: Day 12 +Fgf, replicate3


title: Day 12 +Wnt, replicate2


title: Mouse_E14.5 (12)


title: Day 12 +Fgf, replicate2


title: Day 10 Rx::GFP+, replicate3

source_name: SFEBq derived Neural Retina Epithelium

value: SFEBq derived Neural Retina Epithelium


title: Day 12 +Wnt, replicate1


title: Day 12 +Fgf, replicate1


title: Day 10 Rx::GFP+, replicate1


title: Day 10 Rx::GFP+, replicate2


title: Ho7L2

city: Brussels

first: Simon

middle: Lieven Imanuel Johannes

last: Denil

address: Laarbeeklaan 101

department: University Hospital Brussels

country: Belgium

institute: VUB/ULB

data_processing:
base-calling: all reads were acquired by using the Genome Analyzer Data Collection Software SCS version 2.6
alignment: Reads were mapped to the Oryza sativa subsp. Japonica reference genome (build MSU7.0) in two phases using TopHat version 1.3.1 and Cufflinks, version 1.0.3, a detailed description of the workflow and settings used in the data analysis can be found in the description of GEO-submission GSE35843
quantification: Expression was quantified per sample and per annotated or unannotated transcript as the sum of all reads mapped to the respective gene exons with a 16 base pair tolerance on either side to compensate for potential errors in the gene annotation.
Genome_build: MSU7
Supplementary_files_format_and_content: tab separated values, gene names (known and novel) with location information and number of reads per sample

organism: Oryza sativa Japonica Group

source_name: Shoots of Ho-infected plants, 7 days post infection, replicate 2

growth_protocol: Oryza sativa cv. ‘Nipponbare’ (GSOR-100, USDA) was germinated on wet filter paper for 6 days at 30°C and then transferred to SAP-substrate (Sand Absorbent Polymer; Reversat et al., 1999) and further grown at 26°C under a 16h/8h light-regime.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plant Mini Kit (Qiagen), with an additional sonication step after addition of buffer RLT. RNA integrity was checked using the Agilent BioAnalyzer 2100 (Agilent).
Approximately two microgram of total RNA was used for mRNA-Seq library construction according to the manufacturer’s recommendations (Illumina). We used the multiplexing sequencing adapters provided in the Multiplexing Sample Preparation Oligo Kit (Illumina). Size selection of the library was performed on a 2% agarose gel (Low Range Ultra Agarose, Biorad 161-3107). The denatured library was diluted to a final concentration of 6 pM and loaded on a paired-end read flow cell (TruSeq v5 kit, Illumina).

treatment_protocol: Hirschmanniella oryzae infected rice roots were collected in rice fields in Myanmar and sent to Ghent University by Zin Thu Zar Maung (Plant Protection Division, Yangon, Myanmar). The nematodes were extracted using a Baermann funnel. Five days after transplanting in SAP the plants were inoculated with 400 nematodes per plant or mock-inoculated with tap water. One day after inoculation the plants were transferred to a hydroponic culturing system with Hoagland solution (Reversat et al., 1999) to synchronize the infection process. Systemic shoots were collected 3 and 7 days post inoculation (dpi). At each time point, two independent biological replicates, containing a pool of 6 different plants, were taken for RNA-Sequencing. Similarly, shoot tissue of 2 independent biological replicates of uninfected plants was taken to be used as control.

tag: cultivar

value: Nipponbare (GSOR-100)

value: shoot

tag: agent

value: root rot nematode (H. oryzae)


title: Zebrafish_24hpf (63)

organism: Danio rerio

source_name: 24hpf zebrafish embryos

growth_protocol: Embryos were raised at 28ºC untill they reached the desired developmental stage. They were dechorionated with pronase before fixation.

tag: tissue


title: Ho7L1

source_name: Shoots of Ho-infected plants, 7 days post infection, replicate 1


title: Zebrafish_Dome (61)

source_name: Dome zebrafish embryos

value: Dome


title: Bl7L3

source_name: Shoots of uninfected plants, 7 days post infection, replicate 2


title: Ho3L3

source_name: Shoots of Ho-infected plants, 3 days post infection, replicate 2


title: Bl3L2

source_name: Shoots of uninfected plants, 3 days post infection, replicate 1


title: Day 15 +Fgf, replicate2


title: Ho3L1

source_name: Shoots of Ho-infected plants, 3 days post infection, replicate 1


title: Zebrafish_24hpf (62)


title: MCF10A_HC20_MYC-ER_ChIP-Seq

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

description: MCF10A cells were stably transduced with a lentivirus encoding MYC-ER.

data_processing:
Basecalling was performed with the RTA package within the Genome Analyzer Data Collection Software (SCS2.10).
Fastq files were generated by CASAVA, considering only high-quality sequences (PF-cluster).
Overall sequencing quality was checked with the FastQC script.
Reads were aligned to the human genome hg19 with BOWTIE v0.12.8 using default parameters.
Peaks were called with MACS-1.4.2 using default parameters and the input file as control.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: .wig files generated with MACS using a 10 bps resolution.

source_name: MCF10A MYC-ER cells, MYC-ER ChIP

growth_protocol: MCF10A cells were maintained in DMEM/F-12, supplemented with 5% horse serum, 100ug/ml EGF, 0.5ug/ml hydrocortisone, 10ug/ml insulin, 100ng/ml cholera toxin and 1% penicillin/streptomycin.

extract_protocol:
Cells were cross-linked with 1% formaldehyde. After a hypotonic lysis step, nuclei were resuspended in sonication buffer containing 0.1% SDS and 0.1% Na-deoxycholate and sonication was performed in a Branson sonifier. Anti-ER-a antibody (HC20; Santa Cruz, sc-543, lot# L1512) was coupled to Protein A-Dynabeads (Invitrogen). Bound chromatin was eluted with 1% SDS, and after decrosslinking, DNA was purified with phenol-chloroform.
ChIP DNA was end-repaired, A-tailed and ligated to Illumina adaptors using the NEBNext ChIP-Seq Sample Preparation Kit. After size selection on an agarose gel and purification with a Qiagen gel extraction kit, PCR-amplification was performed. Library quality was tested with an Experion DNA Chip (BioRad) and quantified using a picogreen assay.

treatment_protocol: MCF10A MYC-ER cells were treated with 100nM 4-OHT for 24h.

tag: stable expression

value: MYC-ER

tag: chip antibody

value: anti-ER-alpha (HC20)


title: Zebrafish_80%epiboly (60)

source_name: 80%epiboly zebrafish embryos


title: Zebrafish_24hpf (56)


title: Zebrafish_24hpf (55)


title: Zebrafish_24hpf (58)


title: Zebrafish_80%epiboly (54)


title: Zebrafish_24hpf (57)


title: Zebrafish_48hpf (51)

source_name: 48hpf zebrafish embryos


title: Zebrafish_80%epiboly (52)


title: Zebrafish_Dome (53)


title: MCF10A_Input_ChIP-Seq

source_name: MCF10A MYC-ER cells, input


title: Zebrafish_24hpf (50)


title: Zebrafish_24hpf (48)


title: Zebrafish_24hpf (49)


title: Bl7L1

source_name: Shoots of uninfected plants, 7 days post infection, replicate 1


title: Bl3L3

source_name: Shoots of uninfected plants, 3 days post infection, replicate 2


title: Zebrafish_80%epiboly (46)


title: Zebrafish_80%epiboly (45)


title: Zebrafish_24hpf (47)


title: Zebrafish_80%epiboly (41)


title: Zebrafish_24hpf (36)


title: Zebrafish_24hpf (44)


title: Zebrafish_48hpf (40)


title: Zebrafish_80%epiboly (37)


title: Zebrafish_24hpf (39)


title: Zebrafish_Dome (34)


title: Zebrafish_48hpf (59)


title: Zebrafish_80%epiboly (33)


title: Zebrafish_48hpf (32)


title: Zebrafish_24hpf (30)


title: Zebrafish_24hpf (31)


title: Zebrafish_24hpf (43)


title: HeLa-miR-603

city: shanghai

first: jin

last: fan

address: dongchuan Road

country: China

institute: novelbio informatics company

data_processing:
The raw reads ≥50 bp which passed filtering were used for mapping. We used the Masplicing as our RNA-seq data mapping analysis tool whose core program is Bowtie that can identify the exon-exon splicing immediately and accurately
We applied the EBseq to filter the differentially expressed genes for the case and control groups. After the statistical analysis, we selected the differentially expressed genes according to the FDR threshold (FDR < 0.05)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and count number for each Sample.

growth_protocol: Cells are growing for 24 hours and then are used for transfection.

extract_protocol:
Total RNA was extracted from each sample using TRIzol Reagent (Life technologies, USA) according to the proto- col from manufacturer. The concentration of each sample was measured by NanoDrop 2000 (Thermo Scientific, USA). The quality was assessed by the Agilent2200 (Agilent, USA).
The cDNA library was prepared using the Ion Total RNA-Seq Kit v2 (Lifetech, Carlsbad, CA, USA, Cat. No. 4479789) following the manufacturer’s instructions
Instrument model: ABI IonProton.

treatment_protocol: Cells are transfected with miR-603 negative control or miR-603 mimic for 48 hours.

value: HeLa cervical cancer cell line

tag: transfection

value: miR-603 mimic


title: Zebrafish_24hpf (35)

tag: developmental stage

value: whole embryos


title: HEK293-miR-603

value: HEK293 embryonic kidney cell line


title: Zebrafish_80%epiboly (28)


title: HEK293-Negative Control

source_name: HEK293-Negative Control

value: miR-603 negative control


title: HeLa-Negative Control

source_name: HeLa-Negative Control


title: Zebrafish_48hpf (27)


title: Zebrafish_24hpf (25)


title: Zebrafish_80%epiboly (24)


title: Zebrafish_Dome (29)


title: Zebrafish_24hpf (21)


title: Zebrafish_24hpf (38)


title: Zebrafish_24hpf (23)


title: Zebrafish_Dome (42)


title: Zebrafish_24hpf (20)


title: BRA_FLyB_Input

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

country: United Kingdom

institute: University of Cambridge

data_processing:
ChIP-seq reads aligned to hg19 using bowtie (version 0.12.7) with default parameters.
bigWig density profiles were created with in-house script incorporating UCSC's wigToBigWig utility.
Peaks were called using MACS.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig – read density profile, BED – peaks file

source_name: Mesoderm progenitors

growth_protocol: Undifferentiated human embryonic stem cells (H9 hESCs [WiCell, Madison, WI]) were routinely grown in a chemically defined medium (CDM) as previously described (Brons et al., Nature, 2007, 448: 191-195).

extract_protocol:
Chromatin immunoprecipitation was performed as previously described (Brown et al., 2011, Stem Cells, 29(8): 1176-1185), with minor modifications. Briefly, cell lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies.
Sequencing libraries were prepared using the ChIP-seq DNA sample kit (Illumina, IP-102-1001) with minor modifications and sequenced with a Genome Analyzer II (Illumina).

treatment_protocol: Cells were differentiated as previously described (Bernardo et al., 2011, Cell Stem Cell, 9:144-155). For differentiation into endoderm progenitors, H9 cells were grown for 36 hours in CMD-PVA supplemented with FGF2 (20 ng/ml), LY294002 (10 μM) and Activin A (100 ng/ml). For differentiation into mesoderm progenitors, H9 cells were grown for 36 hours in CMD-PVA supplemented with FGF2 (20 ng/ml), LY294002 (10 μM) and BMP4 (10 ng/ml). All cells were collected for ChIP after 36h of culture in differentiation media.

tag: cell type

value: hES-derived mesoderm progenitor cells

value: none (input)


title: BRA_FLyB_ChIPseq_SC

value: BRACHYURY (Santa Cruz, sc-20109)


title: morpholino control (miRNA-Seq)

city: Beijing

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

data_processing:
FASTX-Toolkit clipper was used to remove sequencing adapters.
The .fastq file was converted to a tab-delimited file which held only the unique sequence read and its corresponding number of copies.
The files were uploaded to DSAP (http://dsap.cgu.edu.tw/index.htm) for clustering of tags, classification of non-coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase database respectively.
The differential expressed miRNAs were detected by R package DEGseq using the output data of DSAP.
Genome_build: Zv9

source_name: embryo

growth_protocol: Zebrafish embryos were kept in a 28.5℃ incubator to 48hpf

extract_protocol:
Immediately after harvesting, 40-50 pooled embryos at 48 hpf from different experiment replicates were snap-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from the pooled embryos using TRIzol (Invitrogen) according to the manufacturer’s instructions.
small RNA libraries were constructed using the Illumina miRNA-Seq library preparation kit according to the manufacturer’s instructions.

treatment_protocol: Zebrafish embryos at the one-cell stage were injected with the MOs using an Microinjector (WPI SYS-PV830). Based on initial injection trials, 2-5 ng MO and control MO was chosen as the optimal concentration.

tag: genotype

value: control morpholino

value: embryo 48hpf


title: RPS24 MO (miRNA-Seq)

value: RPS24 morpholino knockdown


title: BRA_FLyA_Input

source_name: Endoderm progenitors

value: hES-derived endoderm progenitor cells


title: RPS24_MO

description: Sample 2

data_processing:
TopHat for mapping of Hiseq 2000 RNA-Seq data
Cufflinks for assembling transcripts, estimating their abundances, and testing for differential expression and regulation in RNA-Seq samples
Computation and visualization were achieved using the heatmap plus package in R.
IPA and the Gene Ontology for functional analysis of specific genes
Genome_build: Zv9
Supplementary_files_format_and_content: Tab-delimited .txt files report abundance measurements (FPKM).

extract_protocol:
Immediately after harvesting, 40-50 pooled embryos at 48 hpf from different experiment replicates were snap-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from the pooled embryos using TRIzol (Invitrogen) according to the manufacturer’s instructions.
mRNA libraries were constructed using the Illumina mRNA-Seq library preparation kit according to the manufacturer’s instructions.

value: embryo

tag: age

tag: genotype/variation


title: BRA_FLyB_ChIPseq_RD

value: BRACHYURY (R&D systems, AF2085)


title: Zebrafish_24hpf (19)

source_name: 24hpf zebrafish embryos


title: BRA_FLyA_ChIPseq_SC


title: BRA_FLyA_ChIPseq_RD


title: morpholino_control

description: Sample 1

value: control


title: Zebrafish_24hpf (26)


title: Zebrafish_24hpf (22)


title: MC3T3-E1 cells_day9_DNase-seq

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

description: Sample 2

data_processing:
Basecalls performed using CASAVA version 1.6
DNase-seq reads were aligned to the mm9 genome assembly using Bowtie (version 1.1.2) allowing up to 2 mismatches
Read densities and regions of statistically significant enrichment (“peaks”) were determined using F-seq v1.85 (Boyle et al., 2008) with default settings using mapped reads from combined technical duplicates.
Genome_build: mm9
Supplementary_files_format_and_content: The wig files were generated using align2rawsignal (wiggler) (Kundaje A., http://code.google.com/p/align2rawsignal/) with mapped reads from combined technical duplicates. wig files were converted to a bigwig format using wigToBigWig (version 4). The bed files report read densities and regions of statistically significant enrichment (“peaks”).

source_name: matrix-depositing MC3T3-E1 subclone 4 cells at day 9

growth_protocol: The calvaria-derived preosteoblast cell line MC3T3-E1 (Subclone 4) was obtained from ATCC and maintained in ascorbic acid-free alpha-MEM (Hyclone) supplemented with 10% fetal bovine serum (FBS; Hyclone), 2 mM L-glutamine, 100 U/ml of penicillin and 100 µg/ml streptomycin (Pen/Strep, Invitrogen). To induce osteogenic differentiation, complete alpha-MEM was supplemented with 280 μM ascorbic acid and 10 mM beta-glycerophosphate (Sigma Aldrich). Cells were maintained at 37C in a humidified 5% CO2 environment and media replaced every 2-3 days for the duration of all experiments.

extract_protocol: DNaseI treated chromatin was ligated to a custom designed 5'-adaptor that contains a MmeI restriction site and conjugated to Biotin.  Ligated products were treated with MmeI to generate 20-bp chromatin fragments representing DNase-hypersensitive tags.  These products were then ligated to a 3' barcoded adaptor.  Libraries were sequenced on either the Illumina Genome Analyzer II or a Hiseq1000 platforms.

treatment_protocol: Whole-cell nuclei were permeabilized with low concentration of detergent and subjected to a range of DNaseI concentrations (0.12U to 40U) per 132 uL to yield chromatin fragments between 1 Mb to 50 kb in length.

value: matrix-depositing osteoblast

tag: passages

value: p4 and p31

tag: dnase treatment


title: Tb_WT_DMSO_RNA-seq

description: PolyA-enriched RNA (mRNA)

organism: Trypanosoma brucei

source_name: WT parasite, DMSO control

tag: strain/background

value: 221a of strain 427

value: WT

value: whole body

tag: lifestage

value: bloodstream form

tag: treatment

value: DMSO


title: MC3T3-E1 cells_day28_DNase-seq

description: Sample 3

source_name: mineralizing MC3T3-E1 subclone 4 cells at day 28

tag: cell line

tag: time

value: mineralizing osteoblast

tag: strain


title: Tb_WT_DMOG_smallRNA

description: Small RNA

source_name: WT parasite, DMOG

tag: tissue

value: DMOG


title: Mouse Input replicate 2

data_processing:
Reads were trimmed with Trimmomatic Version 0.32, parameters: ILLUMINACLIP:TruSeq3-SE.fa (or -PE.fa):2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:25
Trimmed reads were mapped to the mm9 or hg19 genomes with bwa mem version 0.7.10-r789.
Mapped reads were indexed and sorted with samtools 0.1.18.
Peaks were called with MACS2 (MACS2.1.0.20140616)
Genome_build: mm9 or hg19

source_name: 8w Mouse Testis

value: C57BL/6, Mixed

value: 8 weeks

value: Testes

tag: antibody

value: none (input)


title: Mouse ChIP replicate 2

value: dmrt1 Antibody (PMID:11040213)


title: Tb_WT_DMSO_smallRNA

description: Small RNA


title: Mouse Input replicate 1


title: Mouse ChIP replicate 1


title: TSC1_GFP-

first: HyoJin

middle: Rosaria

last: Chiang

address: 265 Campus Dr.

institute: Stanford

data_processing:
Illumina Casava1.8.2 software used for basecalling.
51bps of a single end of paired-end sequencing runs were extracted. These reads and the reads from single end sequencing runs were aligned to hg19 genome without Y chromosome using Tophat v.2.0.9 with parameters --library-type fr-unstranded
RPKM was calculated using cufflinks v. 2.1.1 with bias correction for genome assembly hg19 without Y chromosome and unstranded library type selection
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text includes RPKM values for each sample

source_name: differentiated TSC1_c1 cells

extract_protocol:
Rneasy Plus Micro Kit (Qiagen)
Ovation RNA-seq System V2 (NuGEN Technologies)

tag: gfp reporter

value: GFP-

value: differentiated TSC1_c1 cells


title: TripleX_GFP+

source_name: differentiated TripleX cells

value: GFP+

value: differentiated TripleX cells


title: TripleX

source_name: iPSC derived from triple X female

value: iPSC derived from triple X female


title: TSC1_GFP+


title: TSC1_c2

source_name: iPSC derived from Turner syndrome patient


title: Control_GFP+

source_name: differentiated Control_c7 cells

value: differentiated Control_c7 cells


title: Control_c8

source_name: iPSC derived from female with normal fertility


title: Control_GFP-


title: Tb_WT_DMOG_RNA-seq

description: PolyA-enriched RNA (mRNA)

value: 221a of strain 427

value: WT


title: H9_GFP-

source_name: differentiated H9 cells

value: differentiated H9 cells


title: H9_GFP+


title: H9

source_name: stem cell

value: stem cell


title: Control_c7

value: iPSC derived from female with normal fertility


title: Brx-11_CL#15

status: Public on May 17 2015

city: Boston

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
Color space reads were aligned using tophat version 2.0.4 and bowtie1 version 0.12.7 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 knownGene table from genome.ucsc.edu.
Reads that did not align or aligned to multiple locations in the genome were discarded.
The hg19 table knownToLocusLink from genome.ucsc.edu was used to map, if possible, each aligned read to the gene who's exons the read had aligned to. The reads count for each gene was the number of reads that were so mapped to that gene.
The read count was divided by the total number of reads that were mapped to any gene and multiplied by one million to form the reads-per-million (rpm) count.
Genome_build: hg19
Supplementary_files_format_and_content: The readCounts.xls file gives the read counts described above for each sample (columns) and gene (rows). The file platform.xls gives the genes corresponding to the row IDs in readCounts.xls.

source_name: CTC cluster

extract_protocol:
We used the Cluster-Chip to capture CTC-clusters from the blood of a breast cancer patient with high CTC counts, released CTC-clusters in solution, stained them with TexasRed-conjugated antibodies against the leukocyte cell surface markers CD45, CD14 and CD16, and then isolated intact CTC-clusters individually using a micromanipulator. From a single time point, we retrieved 15 CTC-clusters. In addition, two leukocytes were isolated from the blood of a healthy donor using a micromanipulator, after enrichment of the mononuclear fraction using a BD Vacutainer CPT Cell Preparation Tube with Sodium Citrate and staining with the above leukocyte cell surface markers.
Libraries were constructed as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535). Briefly, to generate cDNA, samples were treated with reverse transcription master mix (0.05 uL RNase inhibitor, 0.07uL T4 gene 32 protein, and 0.33uL SuperScript III Reverse Transcriptase per 1X volume) and incubated on thermocycler at 50C for 30 minutes and 70C for 15 minutes. To remove free primer, 1.0uL of EXOSAP mix was added to each sample, which was incubated at 37C for 30 minutes and inactivated at 80C for 25 minutes. Next, a 3'-poly-A tail was added to the cDNA in each sample by incubating in master mix (0.6uL 10X PCR Buffer II, 0.36uL 25mM MgCl2, 0.18uL 100mM dATP, 0.3uL Terminal Transferase, 0.3uL RNase H, and 4.26uL H2O per 1X volume) at 37C for 15 minutes and inactivated at 70C for 10 minutes. A second strand cDNA was synthesis by dividing each sample into 4 and incubating in master mix (2.2uL 10X High Fidelity PCR Buffer, 1.76uL 2.5mM each dNTP, 0.066uL UP2 Primer at 100uM, 0.88uL 50mM MgSO4, 0.44uL Platinum Taq DNA Polymerase, and 13.654uL H2O per 1X volume) at 95C for 3 minutes, 50C for 2 minutes, and 72C for 10 minutes. DNA was sheared using a Covaris S2 system and then prepared for ABI 5500XL library construction with end polishing, size selection of 200-500 bp using AMPure XP, ABI barcode adaptor ligation, amplification and purification with AMPure XP, and then pooling of barcoded samples for emulsion PCR wiht template beads preparation.  Samples were then loaded per protocol on the ABI 5500XL.
RNA-Seq using oligo-dT cDNA synthesis and amplification of cDNA libraries using custom universal PCR primers

tag: patient


title: Healthy_donor_1

source_name: White blood cell

value: Healthy donor


title: Healthy_donor_2


title: Brx-11_CL#14


title: MC3T3-E1 cells_day0_DNase-seq

description: Sample 1

source_name: proliferating preosteoblast MC3T3-E1 subclone 4 cells at day 0

value: preosteoblast

value: p4 and p31


title: Brx-11_CL#13


title: Brx-11_CL#12


title: Brx-11_CL#10


title: Brx-11_CL#8


title: Brx-11_CL#6


title: Brx-11_CL#7


title: Brx-11_CL#11


title: Brx-11_CL#9


title: Brx-11_CL#5


title: Brx-11_CL#4


title: TSC1_c1

value: iPSC derived from Turner syndrome patient


title: input

city: Birmingham

first: keith

middle: e

last: giles

state: AL

address: 1825 University Blvd/ SHEL 706

department: Biochemistry & Molecular Genetics/ Stem Cell Institute

institute: University of Alabama at Birmingham

data_processing:
Illumina CASAVA version 1.8.2 software was used to create the fastq files from the bcl files for ChIP-seq.  bcl2fastq version 1.8.4 was used for RNA-seq.  ChIP fastq files were filtered using the fastx filter tool to have 80% of the reads with a Qual score of >= 20.  The remaining reads were collapsed using the collapser tool to eliminate all PCR duplicates.  The resulting FASTA file was aligned to hg18 using Bowtie2 under default conditions.  The aligned SAM files were converted to BAM using samtools then to BED format using BEDTools.  The aligned BED files from AGO2ChIPseqMilliporeRep1.fastq.gz and AGO2ChIPseqMilliporeRep2.fastq.gz were concatenated to create AGO2ChIPseqMilliporeRep1.bed.  Similarly, AGO2ChIPseqAbcamRep4.fastq.gz was combined with Rep5, to create AGO2ChIPseqAbcamRep3.bed.  The AGO2ChIPseqMilliporeRep3.fastq.gz was directly converted into Rep2 without concatenation.
RNA-seq datsets were aligned to hg18 using Tophat2 using default conditions.
For ChIP-seq peak-calling, MACS v. 1.0.1 was used by randomly selecting an equal number of lines from the Input file to match the corresponding AGO2ChIPseq bed file.  Peaks with FDR < 10% were analyzed further.
Determination of FPKM values from RNA-seq study was carried out using Cufflinks from UAB Galaxy instance.  The workflow was as follows: Tophat -> Cufflinks -> CuffMerge -> CuffDiff. All settings used were default settings.
Genome_build: hg18
Supplementary_files_format_and_content: Woolnough2015_MACS_Peaks.xls is the data output from MACS showing the called Peaks analyzed from the 3 replicates analyzed.  Woolnough2015_CuffDiff_RNAseq.xls is the cuffdiff output from our 2 RNA-seq replicates.  Input_subset_AGO2_rep1-3.bed represent the randomly selected input files in BED format, used to comapare with each  ChIP for Peak Calling.

source_name: chronic myelogenous leukemia cell line

growth_protocol: IMDM + 10% FCS + 2mM L-glutamine + 1% Penn/Strep

extract_protocol:
Formaldehyde cross-linked nuclei were sonicated and AGO2 was purified using indicated antibody and protein A beads.  Immunopurified DNA was reverse-cross-linked, phenol:chloroform extracted and ethanol precipitated
Library was constructed using Illuina Tru-seq branched adapters and subjected to 25 PCR cycles

treatment_protocol: untreated


title: IgG input

value: IgG


title: Brx-11_CL#2


title: Brx-11_CL#3


title: AGO2 ChIP-seq Abcam 57113 rep 5

tag: antibody vendor/catalog#

value: Abcam 57113


title: AGO2 ChIP-seq Millipore 04-642 rep 3

value: Millipore 04-642


title: mRNA-seq 293T shAGO2 rep 2

source_name: human embryonic kidney cell line transformed with SV40 T antigen

growth_protocol: HEK293T cultured in Dulbecco's Modified Eagle's  Medium supplemented with 10% fetal calf serum + 2mM L-glutamine + 1% Penicillin/Streptomycin.

extract_protocol:
RNA-seq: Trizol followed by 2 rounds of poly A selection with Poly A purist (ambion 1922).
Libraries were prepared by Illumina's Tru-seq Library Preparation Kit v2. with 15 cycles of PCR.  Paired-end sequencing was carried out on Hi-Seq 2000 (PE50 runs).

treatment_protocol: 293T cells were calfectin-transfected with lentiviral vector.

tag: lentivirus


title: AGO2 ChIP-seq Millipore 04-642 rep 1


title: AGO2 ChIP-seq Millipore 04-642 rep 2


title: mRNA-seq 293T shAGO2 rep 1


title: mRNA-seq 293T shMock rep 2

value: shMock


title: mRNA-seq 293T shMock rep 1

treatment_protocol: untreated 293T cells


title: DKO female NKT P1 1

city: Bethesda

first: Daniel

last: Northrup

state: MD

address: 9000 Rockville Pike Building 10 7B04

institute: NIH

description: DKO 2 female

data_processing:
Bowtie Allignment mm9
In house RPKM calculator.  This software combines all exons of each ensembl gene and then counts the reads that fall in these ranges. RPKM is calculated from tag count.
Excel was used to find genes with RPKM > 3 and
Genome_build: mm9
Supplementary_files_format_and_content: excel spread sheet, gene names and RPKM values

source_name: DKO female NKT P1

growth_protocol: Fresh

extract_protocol:
Used the protocol described in Nature Protocols, 5, 516-535
Indexed illumina sequencing kit

treatment_protocol: Sorted NKT P1 cells (CD1d-PBS-57 Tetramer +, CD24 -, NK1.1 -, CD44 -)

tag: strain background

value: mixed C57BL/6 and 129

value: UTX/JMJD3 DKO

tag: gender

value: female

value: thymus

tag: cell type

value: sorted NKT P1 cells (CD1d-PBS-57 Tetramer +, CD24 -, NK1.1 -, CD44 -)


title: DKO Male NKT P1

description: DKO Male

source_name: DKO Male NKT P1

tag: genotype/variation

value: male


title: DKO female NKT P1 2

description: DKO 2 female


title: WT female NKT P1 2

description: WT 2 female

source_name: WT female NKT P1

value: WT


title: WT female NKT P1 1

description: WT 1 female


title: N8 RNA-Seq

status: Public on May 16 2015

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

data_processing:
Reads obtained by NGS were mapped to the human genome with STAR 2.3.0e, using transcriptome annotations from Ensembl 73 as a reference.
Fragments Per Kilobase of an expressed transcript per Megabase of library size (FPKEM) were calculated using an in-house developed script. Counts of reads mapped to exons of each gene were normalized to a size of expressed and mappable portion of the gene and to a total number of reads in the sample. Mappable regions of genes were estimated using as a criteria existence of mapped reads in any of the analyzed samples.
Genome_build: GRCh37
Supplementary_files_format_and_content: shRNA counts are tab-delimited files with raw counts of sequencing reads mapped to each of shRNAs from the pool. Vcf file contains a list of annotated variants in VCF format version 4.1. Gene expression measurments files contains tab-delimited gene expression values in FPKM units

source_name: Hematopoietic stem/progenitor cells

growth_protocol: Primary cells from AML patients and CD34-selected (MACS Microbeads, Miltenyi Biotech) hematopoietic stem/progenitor cells (HSPC) derived from healthy donors underwent controlled rate freezing and were subsequently stored in the vapor phase of liquid nitrogen. Freshly thawed B- and T-lymphocyte-depleted (MACS Mircobeads, Miltenyi Biotech) leukemic or normal HSPC were used for experiments. All primary cells were grown in StemSpan SFEM with 2% FCS (both StemCell Technologies) supplemented with rhIL3, rhTPO, rhFLT3-ligand and rhSCF (all R&D Systems). Leukemic cell preparations contained less than 0.5 % lymphocytes while normal HSCs were >95% CD34+. All primary cells were obtained under protocols approved by the local Institutional Review Board and all donors had given written informed consent for the use of their cells for research purposes.

extract_protocol:
Total RNA was extracted from 10e6 cells with RNAeasy Mini kit from Qiagen.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: donor index

value: blood

value: Normal CD34+ HSPCs


title: N10 RNA-Seq


title: Brx-11_CL#1


title: N9 RNA-Seq


title: AML29 RNA-Seq

source_name: Leukemic blasts

tag: disease

value: AML

tag: fab-subtype

value: Leukemic blasts


title: AML2 RNA-Seq


title: AML26 RNA-Seq


title: H3K27ac Ileum WT Input

first: Boaz

middle: Eliezer

last: Aronson

state: Massachusetts

address: 300 Longwood Avenue

department: GI/Nutrition

institute: Children's Hospital Boston

data_processing:
50bp single-end reads performed on Illumina HiSeq2000
ChIP-seq read were aligned with ELAND tools, allowing 0-2 mismatches
Genome_build: mm9
Supplementary_files_format_and_content: BAM files; Contains data for processing through MACS peak calling

source_name: Ileal epithelial cells

extract_protocol:
6 week old adult mice were dissected. Jejunal and ileal epithelial cells were subsequently extracted by using the adjusted Weisser method  (Verzi et al. Dev Cell 2010 Nov 16;19(5):713-26.)
NEB Next kit

value: Ileal epithelial cells

value: Gata4FlapvCre-, C57BL/6

tag: developmental stage

value: Adult

tag: protocol used

value: ChIP protocol was used according to Verzi et al. (Dev Cell. 2010 Nov 16;19(5):713-26.)


title: AML2 exome sequencing

data_processing:
Library strategy: exome-seq
Reads obtained by NGS were aligned to the human genome (Ensembl 74, primary assembly GRCh37) using bwa mem version 0.7.5a.
Variant calling and filtering was performed using samtools and vcftools. Only reads with mapQ alignment score of at least 30 were analyzed. Additionally, all bases with quality score lower than 30 were ignored. Further variant annotation and effect prediction was done with programs from the SnpEff package, using Ensembl database release 74 as a source of SNP annotations. All variants annotated as frequent, known to have no health impact, located in intronic or intergenic regions, or not causing significant changes in protein sequences were discarded.
Genome_build: GRCh37
Supplementary_files_format_and_content: shRNA counts are tab-delimited files with raw counts of sequencing reads mapped to each of shRNAs from the pool. Vcf file contains a list of annotated variants in VCF format version 4.1. Gene expression measurments files contains tab-delimited gene expression values in FPKM units

extract_protocol:
Exome sequencing was carried out with 50 ng of genomic DNA, enriched for exonic sequences (Nextera Rapid Exome Kit, Illumina).
The library was prepared for sequencing using standard Illumina protocols.


title: AML2 shRNA screen (d0 post-transduction)

data_processing:
Reads obtained by NGS were trimmed on both ends to the final size of 46 bp and aligned to the library of all possible amplicons containing shRNA sequences using Bowtie (Version 1.0). For each read, all potential alignments were reported and only the shRNA sequence with the least amount of mismatches was used for the final read annotation. Ambiguous reads (i.e. mapping to more than one shRNA with the same number of mismatches) were discarded.
In order to normalize samples for differences in total read counts and possible amplification biases, we performed a loess regression of shRNAs fitting log2-transformed counts from “day 9” to the “day 0” sample. Residuals of the regression were considered estimates of shRNA abundance fold change, and converted into modified Z-scores, where median and median absolute deviation were used as measures of a central tendency and an amount of variation in the sample. All calculations were performed using functions implemented in R, version 3.0.
Genome_build: GRCh37
Supplementary_files_format_and_content: shRNA counts are tab-delimited files with raw counts of sequencing reads mapped to each of shRNAs from the pool. Vcf file contains a list of annotated variants in VCF format version 4.1. Gene expression measurments files contains tab-delimited gene expression values in FPKM units

extract_protocol:
Genomic DNA extraction was performed with DNeasy Kit from Qiagen.
The barcodes contained within the pro-viral inserts were amplified and appended with adapter sequences for next-generation-sequencing (NGS) using a two-step PCR approach (for details see http://www.broadinstitute.org/rnai/public/).

treatment_protocol: We transduced 12e7 cells overnight with SP1 of the TRC library16 (Sigma-Aldrich) at a multiplicity of infection (MOI) of 1.5 using retronectin-coated plates (Takara).

tag: days pt


title: H3K27ac ileum WT ChIP

tag: strain


title: AML24 RNA-Seq

tag: tissue


title: AML2 shRNA screen (d9 post-transduction)


title: H3K27ac Jejunum WT input

source_name: Jejunal epithelial cells

value: Jejunal epithelial cells


title: pepper_sRNA

city: SEOUL

first: Chanseok

last: Shin

address: Gwanak-gu Daehak-dong

institute: Seoul National University

description: Conserved microRNAs in pepper flower and root samples by high-throughput sequencing

data_processing: Illumina GA single read sequencing, 38 cycle. Removed adaptors. Sequences without adapters were discarded. Small RNA sequences that did not match tRNA and rRNA sequences were selected.

organism: Capsicum annuum

source_name: pepper flower and root

extract_protocol: Illumina Small RNA Sample Preparation Kit v1.

value: flower and root


title: WT Male NKT P1

description: WT Male

source_name: WT Male NKT P1

value: mixed C57BL/6 and 129


title: H3K27ac Jejunum G4KO ChIP

value: Gata4FlapvCre+, C57BL/6


title: Gata4IP

value: Gata4FlagBio, C57BL/6

value: BioChIPseq protocol was used according to He et al. (Curr Protoc Mol Biol. 2010 Oct;Chapter 21:Unit 21.20).


title: Gata4Input


title: NICDmyc_Input

city: San Francisco

first: Deepak

last: Srivastava

address: 1650 Owens St.

department: Gladstone Institute of Cardiovascular Disease

institute: J. David Gladstone Institutes

description: Input DNA

data_processing:
Tags were mapped back to the genome using the bowtie aligner
ChIP tag densities were calculated using bedops
Peaks in ChIP signal were identified using SPP
Genome feature enrichment analysis was implemented in perl and R, utilizing bedops in conjunction with Ensemble annotations
Genome_build: hg19
Supplementary_files_format_and_content: Processed data file includes chromosome, peak position, score and smoothed enrichemnt in tab delimited format .txt

source_name: aortic valve endothelial cells

growth_protocol: Cells were grown on plates coated with 10 mg/mL fibronectin from bovine plasma (Sigma, St Loius, MO) and grown in endothelial cell media (ECM)(Sciencell) at 5% CO2. Media was changed every other day and cells were passaged with 0.05% Trypsin EDTA when confluent.

extract_protocol:
DNA was isolated by phenol/chloroform/isoamylalcohol.
ChIPs were done in triplicate with Protein G magnetic beads and then pooled for subsequent ChIP-seq library preparation with the standard Illumina ChIP-seq library protocol.

treatment_protocol: Cells were infected with lentivirus encoding NOTCH1 intracellular domain fused to a myc tag. After 48-72 hours, cells were fixed, chromatin sheared and NICD-myc isolated with goat polyclonal to myc tag ChIP grade antibody (ab9132, Abcam, Cambridge, MA).

value: Primary aortic valve endothelial cells

tag: passage

tag: chip antibody


title: Control siRNA, No shear stress.

data_processing:
RNA-seq reads were aligned to the human hg19 genome using TopHat
TopHat was supplied with GTF-format annotation of known exon positions. Novel exon discovery was disallowed—only exons and splice junctions that were already present in the annotation were included. Duplicate reads (reads mapping to the exact same start / stop position) were removed using the Picard tool MarkDuplicates
Secondary mapping locations were discarded. For each read, only the top alignment was retained.
For paired-end reads, any "singleton" reads (where both ends did not map successfully) were discarded.
Cufflinks was used to obtain a reads-per-gene total and provide normalized expression levels, reported as RPKM (reads mapped to a gene per thousand bases of the gene, per million mapped reads)
Differentially expressed genes were identified using Cuffdiff, part of the Cufflinks suite. Only genes with RPKMs > 1 and CuffDiff output of “OK” were included in subsequent analysis
Genome_build: hg19
Supplementary_files_format_and_content: Processed Data file includes gene ID, gene short name, locus, FPKM and status for each condition in tab delimeted .txt file.

extract_protocol:
RNA was purified using trizol extraction followed by RNeasy MinElute Cleanup Kit with on column DNAse digestion (Qiagen, Valencia, CA).
Biological triplicates were pooled prior to library generation. 50 ng of RNA was used with the Ovation® RNA-Seq System (7100-08)(NuGEN, San Carlos, CA) and manufacturer’s protocol to synthesize and SPIA amplify cDNA, which was then sheared with a covaris S-series. After end repair, purification and P1 P2 adaptor ligation, templated beads were generated with the EZ beads system, and libraries where then paired end sequened (50bp forward, 35bp reverse) on a SOLiD4 DNA sequencing system (Life Technologies).

treatment_protocol:
siRNAs were delivered into endothelial cells using RNAiMax (Life Technologies, Carlsbad, CA). The siRNAs used were NOTCH1 siRNA (cat# 4392422 s963)and control scrambled siRNA (cat# 4390843) (Ambion/Life Technologies). Endothelial cell media was changed to optimem with no suplements (Gibco/Life Technologies), siRNA/RNAiMax was added for 4 hours. Then, the media was changed to full ECM and the cells were harvested for analysis 48 hours later.
Cells were cultured in “flow” or pulsatile shear stress conditions using microSlide I 0.8 Luer channel slides and flow kit (Ibidi, Verona, WI) and a L/S® Modular brushless digital dispensing drive peristaltic pump with 6-roller cartridge pump head (Cole Parmer, Vernon Hills, IL). Shear stress conditions were between 13 and 15 dynes/cm2.

tag: treatment

value: Control siRNA, No shear stress

tag: primary source

value: 55 yr old female (heart transplant pulmonary hypertension)


title: Control siRNA, 15 dynes/cm2 shear stress.


title: Rag1ko Brg1-sh 2

status: Public on May 15 2015

city: Freiburg

first: Claudia

last: Bossen

address: Breisacher Strasse 115

department: Center for Chronic Immunodeficiency

institute: University Hospital Freiburg (D)

description:
RNA-Seq
processed data file: Rag1ko_Brg1kd_vs_Rag1ko_ctrl.txt

data_processing:
RNA-Seq: Basecalls were performed using CASAVA. Alignment and trimming of reads was performed using the OSA algorithm against the mm10 mouse genome reference in Arraystudio (Omicsoft, http://bioinformatics.oxfordjournals.org/content/ early/2012/05/15/bioinformatics.bts294). RNA transcripts were quantified using RSEM methods as implemented in Arraystudio (http://deweylab.biostat.wisc.edu/rsem/; Omicsoft). Principal Component Analysis (PCA) was then performed to check for possible batch effects and outliers. Abundance values (counts) were normalized and compared between samples using DESeq (http://www-huber.embl.de/users/anders/DESeq/). Genome build: mm10. Outputs from DESeq are provided as supplementary files as a tab-delimited text file.
Genome_build: mm10
Supplementary_files_format_and_content: Outputs from DESeq are provided as supplementary files as a tab-delimited text file.

source_name: Cultured ProB

growth_protocol: B220+ cells from the bone marrow were cultured in vitro for 7 days in presence of IL7 and SCF

extract_protocol:
Total RNA was isolated using RNeasy Mini kit (Qiagen). RNA was treated with TURBO DNase (Life Technologies). mRNA was purified from total RNA using Dynabeads mRNA purification kit (Life Technologies).
cDNA was generated with the First-strand synthesis kit (Life Technologies) using a combination of random hexamers and oligo(dT) in presence of actinomycin D. Second-strand synthesis was performed with dUTP instead of dTTP. The ds-cDNA was sonicated to 200-400 bp using the S220 Focused-ultrasonicator (Covaris). Sonicated cDNA was ligated to adaptors (NEBNext primer kit). The resulting DNA was treated with uracil-N-glycolsylase prior to PCR amplification with the indexing primers (NEBNext primer kit). Following PCR, fragments were size-selected.

treatment_protocol: On day 3 and 4 of culture, cells were spin-infected with retroviral supernatant. Retroviral supernatant was obtained through 293T transfection by the calcium phosphate method with Ctrl-sh and Brg1-sh in conjunction with the packaging plasmid pCL-Eco. Two days post-infection, infected cells were enriched with hCD25 magnetic beads (Miltenyi biotech) on an autoMACS separator.

value: Rag1-/-_Brg1-knock down

value: Cultured pro-B cells


title: Rag1ko ctrl-sh 3


title: ProB_ko 2

description:
RNA-Seq
processed data file: ProB_Brg1ko_vs_ProB_ctrl.txt

treatment_protocol: For the last 60 hours, tamoxifen was added at 0.3µM

value: Brg1F/F x ER-Cre


title: Rag1ko ctrl-sh 2


title: ProB_ctrl 2

value: Brg1+/+ x ER-Cre


title: ProB_ko 1


title: Ikaros ChIP-Seq, proB cells

description: ChIP-Seq

data_processing:
ChIP-Seq: Basecalls were performed using CASAVA. Reads were aligned to mm9 using Bowtie with the parameter –m 1 (v0.12.7). Data was analyzed using HOMER (http://homer.salk.edu/homer). Genome build: mm9. Bedgraph files from pooled duplicates are provided as supplementary files.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files from pooled duplicates are provided as supplementary files.

extract_protocol:
Cells were fixed for 15 minutes in PBS 1.5mM Ethylene glycol-bis(succinic acid N-hydroxysuccinimide ester) (EGS), followed by 15 minutes with 1% formaldehyde. Formaldehyde was quenched for 10 minutes with 0.2M glycine. Cells were washed 2 times with PBS and pellets were frozen in liquid nitrogen. 30µl Protein G Dynabeads (Life Technologies) were blocked with 0.5% BSA (w/v) in PBS. Magnetic beads were bound with 6µg of indicated antibody. Crosslinked cells were lysed in lysis buffer 1 (50mM HEPES pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% TritonX-100) and washed with lysis buffer 2 (10mM Tris-HCl pH8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA). Cells were resuspended and sonicated in lysis buffer 3 (10mM Tris-HCl pH8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) for 10 cycles at 10 sec each on ice (20W) with 50 s on ice between cycles. Lysates were cleared by centrifugation and Triton X-100 was added at a final concentration of 1%. Lysates were then incubated overnight at 4°C with the previously prepared magnetic beads. Beads were washed once with RIPA (50mM Tris-HCl pH8.0, 150mM NaCl, 0.1% SDS, 0.1% Na-Deoxycholate, 1% Triton X-100, 1mM EDTA), once with RIPA 500 (50mM Tris-HCl pH8.0, 500mM NaCl, 0.1% SDS, 0.1% Na-Deoxycholate, 1% Triton X-100, 1mM EDTA), once with LiCl wash (10mM Tris-HCl pH8.0, 250mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1mM EDTA) and finally twice with TE (10mM Tris pH8.0, 1mM EDTA). Bound complexes were eluted from the beads in elution buffer (10mM Tris-HCl pH8.0, 0.5% SDS, 300mM NaCl, 5mM EDTA) for 30 min at 65 °C with shaking. Crosslinks were reversed overnight at 65°C. RNA and protein were digested in the supernatant using RNase A and Proteinase K and DNA was purified using ChIP DNA clean and concentrator columns (Zymoresearch).
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (minus exo) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina primers with the respective indexes for 18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size- selected from a 8% polyacrylamide gel.

tag: antibody

value: Ikaros (Ik-C, rabbit antibody (kind gift of S.Smale))


title: ProB_ctrl 1


title: Ikaros ChIP-Seq, preproB cells

description: ChIP-Seq

source_name: Cultured PreProB

growth_protocol: E2A-deficient multipotent progenitors were derived from E2A-deficient fetal liver and grown in the presence of IL7, SCF and FLT3L on sub-confluent S17 stromal cells

value: Cultured pre-pro-B cells


title: ATAC BLP ko 2

description:
ATAC-Seq
processed data file: BLP-ko-all.ucsc.bedGraph.gz
library strategy: ATAC-seq

data_processing:
ATAC-Seq: Basecalls were performed using CASAVA. Reads were aligned to mm9 using Bowtie with the parameter –m 1 (v0.12.7). Data was analyzed using HOMER (http://homer.salk.edu/homer). Tag directories were generated using parameter – tbp 1, which removed most of the reads arising from mitochondrial DNA. Genome build: mm9. Bedgraph files from pooled duplicates are provided as supplementary files.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files from pooled duplicates are provided as supplementary files.

source_name: Sorted BLP

extract_protocol:
25000 cells pelleted by centrifugation, nuclei were prepared prior to transposition
13 cycles of PCR using indexing primers from Nextera kit

value: mixed

value: Brg1F/F x IL7R-Cre

value: BLP (Lin-KitintFlt3+IL7R+Ly6D+)


title: ATAC ProB ko 2

description:
ATAC-Seq
processed data file: ProB-ko-all.ucsc.bedGraph.gz
library strategy: ATAC-seq

extract_protocol:
After Ficoll tratment, 50000 cells pelleted by centrifugation. Nuclei were prepared prior to transposition
12 cycles of PCR using indexing primers from Nextera kit


title: ATAC ProB ko 1


title: ATAC BLP Ctrl 2

description:
ATAC-Seq
processed data file: BLP-ctrl-all.ucsc.bedGraph.gz
library strategy: ATAC-seq

value: Brg1F/+ x IL7R-Cre


title: H3K27ac Jejunum WT ChIP

value: Jejunal epithelial cells

value: Gata4FlapvCre-, C57BL/6

value: Adult

value: ChIP protocol was used according to Verzi et al. (Dev Cell. 2010 Nov 16;19(5):713-26.)


title: ATAC ProB Ctrl 1

description:
ATAC-Seq
processed data file: ProB-ctrl-all.ucsc.bedGraph.gz
library strategy: ATAC-seq


title: ATAC ALP ko 2

description:
ATAC-Seq
processed data file: ALP-ko-all.ucsc.bedGraph.gz
library strategy: ATAC-seq

source_name: Sorted ALP

extract_protocol:
50000 cells pelleted by centrifugation, nuclei were prepared prior to transposition
12 cycles of PCR using indexing primers from Nextera kit

value: ALP (Lin-KitintFlt3+IL7R+Ly6D-)


title: NOTCH1 siRNA, 15 dynes/cm2 shear stress

value: NOTCH1 siRNA, 15 dynes/cm2 shear stress

value: Primary aortic valve endothelial cells


title: ATAC ALP Ctrl 2

description:
ATAC-Seq
processed data file: ALP-ctrl-all.ucsc.bedGraph.gz
library strategy: ATAC-seq


title: ATAC BLP ko 1

extract_protocol:
3500 cells pelleted by centrifugation, nuclei were prepared prior to transposition
16 cycles of PCR using indexing primers from Nextera kit


title: ATAC ALP ko 1

extract_protocol:
17000 cells pelleted by centrifugation, nuclei were prepared prior to transposition
14 cycles of PCR using indexing primers from Nextera kit


title: ATAC BLP Ctrl 1

extract_protocol:
5000 cells pelleted by centrifugation, nuclei were prepared prior to transposition
15 cycles of PCR using indexing primers from Nextera kit


title: NOTCH1 siRNA, No shear stress.

value: NOTCH1 siRNA, No shear stress

value: 55 yr old female (heart transplant pulmonary hypertension)


title: Rag1ko Brg1-sh 3

value: Rag1-/-_Brg1-knock down

value: Cultured pro-B cells


title: NICDmyc_ChIP

description: DNA pulled down with NOTCH1 intracellular domain

value: anti-myc tag (myc-Notch)

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #


title: ATAC ALP Ctrl 1

extract_protocol:
14000 cells pelleted by centrifugation, nuclei were prepared prior to transposition
14 cycles of PCR using indexing primers from Nextera kit

value: mixed

tag: cell type


title: AGO2 ChIP-seq Abcam 57113 rep 4

extract_protocol:
Formaldehyde cross-linked nuclei were sonicated and AGO2 was purified using indicated antibody and protein A beads.  Immunopurified DNA was reverse-cross-linked, phenol:chloroform extracted and ethanol precipitated
Library was constructed using Illuina Tru-seq branched adapters and subjected to 25 PCR cycles

tag: cell line

tag: antibody vendor/catalog#

value: Abcam 57113


title: ATAC ProB Ctrl 2

tag: genotype/variation

value: Brg1+/+ x ER-Cre


title: wild-type3

city: Raleigh

first: Nirav

middle: M

last: Amin

state: NC

address: 1060 William Moore Drive

department: Molecular Biomedical Sciences

institute: North Carolina State University

description: Sample 6

data_processing:
Fastq files were checked for quality with FASTQC 0.10.1
Fastq files were aligned to Mouse genome mm10 using TopHat (v2.0.8), with Bowtie  2.1.0.0 and processed into .bamfiles by TopHat using Samtools 0.1.19.0
Transcripts were counted and normalized using Cufflinks (v2.1.1)
Differential expression analysis was performed by Cufflinks using the cuffdiff option.
Genome_build: mm10
Supplementary_files_format_and_content: gene_exp.diff.txt contains the output from cuffdiff, sample 1: wild-type; sample 2: casz1 mutant, values indicate FPKM value for indicated gene and log2fold change from sample 1 to 2. test-stat and p-value as calculated by Cufflinks. Adjusted p-value (q-value) was determined by Cufflinks to determine significance at high stringency.

source_name: wild type_E10.5 heart

extract_protocol:
E10.5 hearts were harvested from pregnant mice individually and total RNA was extracted individually using standard Trizol extraction followed by DNaseI treatment and Rneasy (Qiagen) cleanup. Tissue was taken from non-cardiac source to determine genotypes for Casz1 and Nkx2-5 prior to RNA-seq library construction.
libraries were constructed by Vanderbilt University using standard Tru-Seq adaptors and Illumina library prep protocols

tag: strain background

value: wild type; Nkx2-5+/+,Casz1f/+

value: heart


title: wild-type2

description: Sample 5

tag: developmental stage


title: mutant2

description: Sample 3

source_name: casz1 mutant_E10.5 heart

value: conditional Casz1 knockout; Nkx2-5Cre/+,Casz1f/f


title: wild-type1

description: Sample 1


title: mutant1

description: Sample 2


title: parous luminal ductal

city: Cold Spring Harbor

first: Camila

last: dos Santos

state: NY

address: 1 Bungtown Road

department: Cancer Center

institute: Cold Spring Harbor Laboratory

data_processing:
Mapping and methylome construction were preformed with MethPipe (a pipeline for analyzing bisulfite sequencing data). The analysis steps were performed as described in MethPipe's manual (http://smithlabresearch.org/software/methpipe/).
Genome_build: mm9
Supplementary_files_format_and_content: The methcount files contain mammary methylation profiles. The detailed description of this file format can be found at the following website: http://smithlabresearch.org/software/methpipe/

source_name: Parous mammary cells

extract_protocol:
Cells were incubated with cell lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCL pH 8) and DNA purified with phenol/chorophorm/isoamilic alcohol
purified genomic DNA was fragmented, adenylated, and ligated to Illumina-compatible paired-end adaptors. Bisulfite conversion was performed using the EZ DNA Methylation Gold kit (Zymo) according the manufacturer’s instruction.
Bisulfite converted, adaptor-ligated fragments were PCR enriched and further utilized on pair-ended Illumina sequencing.

value: Balb/C

tag: gender

value: Female

value: Mammary gland

tag: compartment

value: Luminal

value: luminal ductal

tag: molecule subtype

value: Bisulfite converted genomic DNA


title: parous basal MaSC

tag: strain

tag: tissue

value: Basal

value: basal mammary stem cells


title: parous luminal progenitor

value: luminal progenitor


title: nulliparous estrogen progesterone

description: slow-release estrogen progesterone pellet (pseudo-pregnancy)

source_name: Nulliparous mammary cells

value: luminal total


title: parous luminal alveolar

value: luminal alveolar


title: Rag1ko Brg1-sh 1

value: Rag1-/-_Brg1-knock down

value: Cultured pro-B cells


title: nulliparous luminal progenitor


title: nulliparous luminal alveolar


title: nulliparous basal progenitor

value: basal progenitor


title: nulliparous luminal ductal


title: Brg1 ChIP-Seq, proB cells

description: ChIP-Seq

value: Brg1 (Millipore, catalog# 07-478, lot# DAM1776465)


title: Rag1ko ctrl-sh 1


title: nulliparous basal differentiated

value: basal differentiated


title: parous basal differentiated


title: Whole zebrafish embryo

city: Bitlhoven

first: Marja

last: Driessen

state: Utrecht

address: Antonie van Leeuwenhoeklaan 9

department: Laboratory for Health Protection Research

country: Netherlands

institute: National Institute of Public Health and the Environment (RIVM)

data_processing: Illumina Genome Analyzer pipeline. Genome_build: Ensemble, Zv8, Release 59, August 2010. Supplementary_files_format_and_content: RPKM

source_name: Whole zebrafish embryo

extract_protocol: Whole zebrafish embryo and adult zebrafish are exposed for 48 hours to human hepatotoxicants. Afterwards, the adult liver is dissected and snap frozen untill processed for RNA isolation. The whole zebrafish embryos are pooled, one sample consists of 15 embryos, and are also snap frozen untill processed for RNA isolation. For every sample RNA is isolated according to the protocol of de Jong et al (2009). and then equal amounts of every sample is pooled. The two pools (one for the adult zebrafish liver, the other for the whole zebrafish embryo) are sequenced.

treatment_protocol: Zebrafish are exposed for 48h to 9 known human hepatotoxicants, including paraquat, acetaminophen, thioacetamide, cyclosporine A, 17a-ethynylestradiol, chlorpromazine, amiodarone, tetracycline and valproic acid.

value: whole embryo

value: embryo


title: Adult zebrafish liver

source_name: Adult zebrafish liver

value: liver

value: adult

value: exposed for 48h to 9 known human hepatotoxicants, including paraquat, acetaminophen, thioacetamide, cyclosporine A, 17a-ethynylestradiol, chlorpromazine, amiodarone, tetracycline and valproic acid


title: mutant3

description: Sample 4

value: conditional Casz1 knockout; Nkx2-5Cre/+,Casz1f/f

value: heart


title: Input, proB cells

description: ChIP-Seq

value: none (input)


title: Modified ChIP against H3K27ac

city: Rotterdam

first: Raymond

middle: A

last: Poot

address: Wytemaweg 80

department: Cell Biology

institute: Erasmus MC

data_processing:
Filtering against low complexity reads using prinseq-lite using options -lc_method dust and -lc_treshhold 7
mapping reads using bowtie 0.12.7 the options -n 2 -l 36 -e 70 -k 1 --best
Picard-tools-1.81 MarkDuplicates was used to remove the duplicates from the sam/bam file
MACS 1.4.2 was used for generating wig file using default settings
Genome_build: mm9

growth_protocol: Mouse embryonic stem cell line CGR8 was grown on gelatin coated dishes without feeders. Cells were cultured in Glasgow minimal essential medium supplemented with leukemia inhibitory factor, 15% fetal bovine serum, 0.25% sodium bicarbonate, 1mM glutamine, 1mM sodium pyruvate, nonessential amino acids, 50 μM beta-mercaptoethanol, and penicillin-streptomycin

extract_protocol: For each histone modification ChIP, 300x10^6 ESCs were used. For chromatin preparation, cells were washed on plate three times with PBS and incubated with 2 mM Disuccinimidyl glutarate (DSG, Thermo Scientific) in PBS for 45 min at room temperature. Subsequently, ESCs were washed in PBS three times, 0.1 volume of 11% formaldehyde (Merck) in 50 mM Hepes-KOH pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA was added, mixed and incubated for 12 min at room temperature, washed two times in 4 °C PBS and collected by centrifugation. All subsequent steps were performed on ice with pre-cooled buffers. Cell lysis was performed as described43. In brief, cells were collected and resuspended in LB1 (50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100). After 10 minutes incubation, cells were pelleted by centrifugation and resuspended in LB2 (10 mM Tris-HCl, pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA). After 10 min incubation, cells were pelleted and resuspended in 3 ml freshly prepared LB3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine) and sonicated on a Soniprep 150 (MSE), 27 cycles 15 s on, 45 s off on amplitude 7. After sonication, enriched DNA fragment size was confirmed to be between 200 and 1000 bp.  300 x 106 ESCs yielded approximately 10 mg chromatin (as measured by DNA content). To prevent immunoglobin elution and subsequent interference with the mass spectrometry analysis, 50 µg antibodies were crosslinked to 500 µl Protein A magnetic bead solution (15 mg beads, Life Technologies) with Dimethyl Pimelimidate (Sigma). Cross-linked antibody-bead complexes were equilibrated in LB3 buffer and subsequently blocked with 0.5 mg/ml BSA (New England Biolabs) and 0.2 mg/ml sonicated salmon sperm DNA (Stratagene) for one hour. The antibody-bead mixture was rotated overnight with approximately 10 mg chromatin at 4°C. Beads were transferred to 1.5 ml no stick tubes (Alpha laboratories) and washed five times 5 minutes in RIPA buffer (50 mM Hepes-KOH pH 7.6, 500 mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate).  Beads were washed once with 1 ml T50E10N50. Beads were eluted in 210 ul elution buffer and incubated for 30 minutes at 65 °C. Beads were discarded and supernatant was  incubated for 8 hours at 65 °C for decrosslinking. Subsequently the DNA was purified by two rounds of phenol extraction. DNA pellet was resolved in 60 ul of water. The library was prepared according to the illumina protocol. Briefly 10 ng of DNA ChIP material was end-repaired, ligated to adapters, size selected on gel (200 bp +-25 bp range) and PCR amplified using Phusion polymerase with 30 seconds incubation at 98 ᴼC, 18 cycles of 10 second 98 ᴼC , 30 seconds 65 ᴼC, 30 seconds 72ᴼC. Followed with 5 minutes of final extension at 72 ᴼC. Cluster generation was performed using the illumina genome analyzer II platform. Step-by-step protocol was uploaded to http://www.nature.com/protocolexchange/.

treatment_protocol: wt

value: Embryonic Stem Cell

tag: chip antibody

value: H3K27ac (ab4729, Abcam)


title: Modified ChIP against H3K9me3

value: H3K9me3(ab8898, Abcam)


title: Modified ChIP against H3K4me3

value: H3K4me3 (ab8580, Abcam)


title: parous 12Mo post pregnancy

value: Balb/C

value: Female

value: Mammary gland

value: Luminal

value: luminal total

value: Bisulfite converted genomic DNA


title: parous basal progenitor

value: Basal

value: basal progenitor


title: BTP15 rep2

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequences were aligned to the M. tuberculosis H37Rv genome (NCBI accession NC_000962.2) using Bowtie2 with default parameters. Read count for all annotated features were obtained with htseq-count program. Regions where genes overlapped were excluded from counting. Reads spanning more than one feature were counted for each feature. Since the RNA library was strand-specific, the orientation of sequence reads had to correspond to the orientation of annotated features to be counted.
Analysis of differential gene expression was carried out using the DESeq package.
Genome_build: NC_000962.2
Supplementary_files_format_and_content: Read count per gene

organism: Mycobacterium tuberculosis

source_name: bacteria

growth_protocol: Bacteria were grown at 37°C in Sauton's media to exponential phase (OD600 of 0.6)

extract_protocol:
Bacteria were resuspended in 600 µl of Trizol and lysed in with 400 µl of glass beads in a bead beater. After spinning and recovery of the supernatant, 200 ul of chloroform were added. After shaking and spinning, the supernatant was purified using the RNeasy bench protocol. DNA was removed from RNA samples using Turbo DNA free (Ambion) by incubation at 37°C for 1 h. RNA integrity was assessed by agarose gel electrophoresis and absence of contaminating DNA was checked by lack of amplification products after 30 PCR cycles. Successful preparation of primary transcriptome was confirmed by lack of 23S/16S rRNA bands and presence of intact 5S rRNA  in agarose gels.
100 ng of total RNA were mixed with 5x Fragmentation buffer (Applied Biosystems), incubated for 4 minutes at 70°C and then transferred immediately on ice. RNA was purified using RNAClean XP beads (Beckman Coulter), according to the manufacturer’s recommendations, and subsequently treated with Antarctic phosphatase (New England Biolabs). RNA was then re-phosphorylated at the 5’-end with polynucleotide kinase (New England Biolabs) and purified with Qiagen RNeasy MinElute columns. In order to ensure strand-specificity, v1.5 sRNA adapters (Illumina) were ligated at the 5’- and 3’-ends using RNA ligase. Reverse transcription was carried out using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). Twelve cycles of PCR amplification using Phusion DNA polymerase were then performed and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer’s instructions. A small aliquot (2.5 ml) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer prior to sequencing on Illumina HiSeq 2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3.

treatment_protocol: 30 ml of bacterial suspension was pelleted, resuspended in fresh Sauton's media and compounds (Cpd7 or Cpd15) were added for 8 hours. Bacteria were then harvested by centrifugation.

tag: treatment

value: 5uM of BTP15


title: nulliparous basal MaSC

value: basal mammary stem cells


title: BBH7 rep2

value: 5uM of BBH7


title: BTP15 rep1


title: Control rep2

description: DMSOB

value: DMSO


title: BBH7 rep1


title: v5 control ChIP-seq in CGR8 Embryonic Stem Cells

data_processing:
Filtering against low complexity reads using prinseq-lite using options -lc_method dust and -lc_treshhold 7
mapping reads using bowtie 0.12.7 the options -n 2 -l 36 -e 70 -k 1 --best
Picard-tools-1.81 MarkDuplicates was used to remove the duplicates from the sam/bam file
MACS 1.4.2 was used for generating wig file and peak calling using options --no-model --shiftsize 75 --to-large
Genome_build: mm9
Supplementary_files_format_and_content: .wig files generated using MACS1.4

extract_protocol:
For each ChIP 100 million cells were used. As a control, CGR8 Embryonic Stem Cells expressing no V5 tag were used. Cells were cross-linked and washed twice with cold 1x PBS and collected by centrifugation. Cells were resuspended  in LB1 (50mM Hepes-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton-X-100 . After 10 minutes incubation, cells were pelleted by centrifugation and resuspended in LB2 (10 mM Tris-HCl, pH8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA. After 10 minutes incubation, cells were pelleted and resuspended in freshly prepared LB3 (10mM Tris-HCl pH8.0, 100mM NaCl, 1mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine and sonicated on a Soniprep 150(MSE). For quality control of the sonication, it was verified whether the DNA fragment size was between 100 and 1000bp. V5-Agarose beads were blocked 1 hr with 0.5 mg/ml BSA. The chromatin was incubated overnight with the blocked V5-Agarose beads. The following day the beads were washed 5 times with RIPA buffer and eluted with elution buffer 50mM Tris-HCl pH8.0 10mM EDTA and 1% SDS for 30 minutes. Samples were de-cross-linked overnight at 65 degrees celcius and treated the following day with proteinase K for one hour at 45 degrees celcius. DNA was extracted by phenol/chloroform/isoamyl extraction and precipitated with ethanol and resuspended in water.
The library was prepared according to the illumina protocol. Briefly 10 ng of DNA ChIP material was end-repaired, ligated to adapters, size selected on gel (200 bp +-25 bp range) and PCR amplified using Phusion polymerase with 30 seconds incubation at 98 ᴼC, 18 cycles of 10 second 98 ᴼC , 30 seconds 65 ᴼC, 30 seconds 72ᴼC. Followed with 5 minutes of final extension at 72 ᴼC.  Cluster generation was performed using the Illumina HiSeq 2000 platform.

treatment_protocol: The coding sequence of Dppa2 was amplified from mouse ES cell cDNA. The cDNA was cloned including a N-terminal V5-tag into a pPyCAG driven expression vector. CGR8 cells were transfected with lipofectamine 2000 and clones were selected by puromycin. Expression of stable clones was tested by Westernblot


title: v5-Dppa2 ChIP-seq in CGR8 Embryonic Stem Cells


title: Colony ID 24541

city: Baton Rouge

first: Brenda

last: Richards

state: LA

address: 6400 Perkins Rd.

department: Basic Science

institute: Pennington Biomedical Research Center

description: SAGE-Seq

data_processing:
XSQ files generated from 5500XL SOLiD sequencer were converted into CSFASTA and QUAL files using XSQ Tools.
Sequenced reads were aligned to the NCBI RefSeq reference sequence and
SAGE tags were counted using SOLiD SAGE Analysis Software v1.10
SAGE tag counts were normalized to reads per million (RPM) using R.
Values of RPM were expressed as binary logarithm values (log2 RPM).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: txt file; tag hits, i.e., successfully aligned reads, were normalized according to DESeq by estimating the size factor for each sample and dividing the sample counts by the corresponding size factor. File contains: symbol, id, geneID, chr, strand, transcStart, transEnd, baseMean, baseMeanA, baseMeanB, foldChange,log2FoldChange, pval, padj; and one column per individual mouse sample/ID.

source_name: Hypothalamus

growth_protocol: Not applicable

extract_protocol:
Total RNAs were isolated using the AllPrep RNA/Protein kit (Qiagen, Valencia, CA) and re-suspended in Nanopure water.
Serial analysis of gene expression (SAGE) library was constructed using a SOLiD SAGE kit (Life Technologies) according to manufacturer's instructions.

treatment_protocol: Not applicable

tag: study id

tag: colony id

tag: genotype across subcongenic segment

tag: 10 sum total kcal

tag: 10 sum carbohydrate/protein kcal