title: HumanBrain-5-hmC

status: Public on Jun 10 2015

first: Michael

last: Corley

address: 413 East 69th Street

department: Medicine, Division of Infectious Diseases

data_processing:
Torrent Suite v4.0 used to perform base calling.
Reads were trimmed for adapter sequence, poly-clonal, and low quality then aligned to the hg19 assembly using TMAP.
BAM files of mapped MeDIP-seq reads and IgG reads were used with MACS v2.
Genome_build: hg19
Supplementary_files_format_and_content: bed files of MACS peaks called

source_name: Postmortem Human Brain

growth_protocol: HCT116-WT and HCT116-DKO (DKO1 line) cells were generous gifts from Dr. B. Vogelstein (Johns Hopkins University). These cells were cultured in McCoy's 5A medium with 10% FBS.

extract_protocol:
Genomic DNA (1 μg) was isolated from cultured cells and postmortem brain tissue using  the AllPrep DNA/RNA kit (Qiagen) according to the manufacturer’s recommendations for  cells and tissues. DNA concentration was determined using the Qubit DNA Broad Range  fluorescence assay (Life Technologies) and Qubit Instrument (Life Technologies).
MeDIP-Seq libraries for Ion Torrent semiconductor sequencing on the Ion Torrent PGM  or Ion Torrent Proton instruments were generated using a modified protocol consisting of  Life Technologies’ Ion Plus Fragment Library kit (Catalog # 4471252) in combination  with a commercially available 5-methylcytosine (MagMeDIP Kit, Catalog # mc-magme-  048) or 5-hydroxymethylcytosine (5hmC Kit, Catalog # AF-110-0016)  immunoprecipitation kit (Diagenode). A nonspecific mouse IgG was used for an  immunoprecipitation reaction as a negative control. For both 5-mC and 5-hmC MeDIPSeq,  1 ug of DNA was sheared to a mean fragment size of 300 bp by sonication with the  Covaris M220 Focused-ultrasonicator instrument (Covaris) in a 50 μl microTUBE AFA  Fiber Screw-CAP (Covaris). Sonicated DNA was end-repaired, purified with Agencourt  AMPure XP reagent beads (Beckman Coulter), and ligated with Ion Torrent compatible  sequencing adapters following the standard Ion Plus Fragment Library Kit protocol.  Adapter-ligated DNA was purified using Agencourt AMPure XP reagent beads and  immunoprecipitated using either a 5-methylcytosine kit (MagMeDIP) or 5-  hydroxymethylcytosine (hMeDIP) MeDIP kit according to the manufacturer’s protocol.  Following either 5-mC or 5-hmC MeDIP, libraries were size-selected from 200-400 bp on  a 2% agarose E-gel (Invitrogen) and extracted using a MinElute Gel DNA extraction kit  (Qiagen) according to the manufacturer’s instructions. Libraries were then amplified at  18 cycles of PCR (95°C, 15 s; 58°C, 15 s; 70°C, 1 min), purified using MinElute columns  (Qiagen), and eluted in 16 μl EB (Qiagen). Libraries were assessed for quality and  concentration on an Agilent Bioanalyzer instrument. An aliquot of each library was used  to assess enrichment efficiency for control methylated DNA and hydroxymethylated DNA  compared to 10% input DNA.

value: brain

tag: region

value: subventricular zone

tag: medip antibody

value: 5-hmC (Diagenode, catalog# AF-110-0016, lot# 004)


title: ds066_293T_FOXM1_GTX_1

status: Public on Jun 11 2015

type: SRA

city: Cambridge

first: Giovanni

last: Marsico

address: Robinson Way

country: United Kingdom

institute: CRUK Cambridge Institute

description: experiment 1

library_source: genomic

data_processing:
fastq files were aligned to the reference genome using bowtie2
bam files from the alignment were cleaned (q > 10, no Encode balcklist) using samtools
peaks were called on the cleaned bam files using macs2 with the inputs from each respective experiment (see samples description) and defualt parameters
Genome_build: hg19
Supplementary_files_format_and_content: bed format; content is peaks called by macs

molecule: genomic DNA

organism: Homo sapiens

source_name: HEK293 Flp-In cells

growth_protocol: HEK293 Flp-In cells were obtained from Invitrogen (Life Technologies Ltd) and grown in Eagle's Minimum Essential Media (Invitrogen) supplemented with 10% tetracycline free fetal bovine serum (Clontech) and 100 μg/ml Zeocin (Invitrogen). The Flp-In cell line was first transfected with pcDNA6/TR (Invitrogen) and selected with 5 μg/ml Blasticidine (Sigma) to generate HEK293 TetR Flp-In cells. To generate the GFP-FOXM1 stable cells lines the TetR Flp-In cells were transfected with pcDNA5FRT containing an insert coding for either WT or DNA binding domain mutated (H287A or R286A) full length FOXM1B with an N-terminal EGFP tag and a control cell line expressing only EGFP was also generated. Insertion of the FOXM1 sequence occured following co-transfection of the pOG44 recombinase plasmid (Invitrogen) and positive cells were selected with 100 μg/ml hygromycin (Invitrogen) to generate GFP-FOXM1 HEK293TetR cells.

extract_protocol:
IP was carried out as described in Schmidt et al. (2009) (PMID 19275939). In brief, cells were cross-linked using 1% formaldehyde for 10 min at RT, reaction was quenched with 1/20th volume 2.5M Glycine and cell pellets were collected after scraping plates. Nuclear lysates were prepared by lysing with LB1 (50mM Hepes-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton-X plus PI) 10 min at 4°C and LB2 (10mM Tris-HCl, pH8.0, 200mM NaCl, 1mM EDTA, 0.5M EGTA plus PI) 5 min at 4°C, followed by sonication in LB3 (10mM Tris-HCl, pH8.0, 100mM NaCl, 1mM EDTA, 0.5M EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine plus PI) using a diagnode sonicator to give a fragment size of ~200-300bp. Sonicated lysate was combined with 100ul protein-A magnetic beads preloaded with either 10 ug anti-FOXM1 antibody (GeneTex (USA); cat no. GTX-1000276 and GTX102170) or 10 μl anti-GFP antibody (Abcam, Cambridge, UK; ab290) O/N at 4°C. Beads were washed X6 in RIPA buffer (50mM HEPES pH7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCl) and DNA was eluted for 16 hr at 65°C in elution buffer (50mM Tris-HCl, pH8.0, 10mM EDTA, 1% SDS). Extracted DNA was treated with RNase A for 30 min at 37°C, followed by Proteinase K for 1 hr at 55°C, and DNA was purified by phenol-chloroform extraction and quntified by bioanalyzer and quibit.
Illumina ChIP-seq kit sample prep kit was used to prepare duplicate/triplicate samples

treatment_protocol: Cells were plated in 4 x 150 cm2 dishes (1 x 10E7 per dish), cultured overnight, and treated with doxycycline (1 μg/ml) for 24 h prior to extraction .

tag: cell type

value: 293 Flp

tag: antibody


title: HCT116-DKO-IgG

city: New York

state: NY

country: USA

institute: Weill Cornell Medicine

source_name: HCT116 cells expressing hypomorphic DNMT1 and lack DNMT3b (HCT116-DKO)

tag: cell line

value: HCT116 colon cancer cells

tag: genotype/variation

value: DKO (expressing hypomorphic DNMT1 and lack DNMT3b)

value: IgG (Rat)(Diagenode, catalog# AF-110-0016, lot# 004)


title: HCT116-WT-IgG

source_name: HCT116 cells

value: WT


title: HCT116-DKO-5-mC-Proton

value: 5-mC (Diagenode, catalog# mc-magme-048, lot# D008)


title: HCT116-WT-5-mC-Proton


title: HumanBrain-5-mC

tag: tissue


title: sensitive control 2 replicate 3

city: Thiverval-Grignon

first: Sabine

last: Fillinger

department: UMR1290 BIOGER

country: France

institute: INRA

library_source: transcriptomic

data_processing:
primary bioinformatics analysis for quality metrics control  (Illumina pipeline vers. 1.9)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped then mapped to reference genes (Mgraminicolav2.FrozenGeneCatalog20080910.transcripts)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Mgraminicolav2.FrozenGeneCatalog20080910.transcripts
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

molecule: total RNA

organism: Zymoseptoria tritici

source_name: wheat

growth_protocol: strains were grown in liquid YPD during 60 h at 18°C and 140 rpm

extract_protocol:
RNA was extracted using the RNeasy plant mini kit (Qiagen) and verified on 2100 Bioanalyzer (Agilent)
library prep with  RNA Truseq Sample prep kit at sequencing provider IGA technologies, Udine, Italy

tag: strain

tag: fungicide-phenotype

value: sensitive


title: MDR6 strain replicate 3

value: 09-ASA-3a pz

value: TriR6 MDR


title: MDR6 strain replicate 1


title: MDR7 strain replicate 3

value: TriR7 MDR


title: sensitive control 2 replicate 1


title: MDR7 strain replicate 2


title: sensitive control 2 replicate 2


title: MDR7 strain replicate 1


title: HumanBrain-IgG


title: HCT116-DKO-5-mC-PGM


title: sensitive control 1 replicate 3


title: HCT116-WT-5-mC-PGM


title: Hybrid_control

city: London

first: Peter

middle: P

last: Cherepanov

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
Sequences were cropped to remove linker and viral portions
Cropped sequences were aligned to hg19 version of the human genome using BLAT with settings ‑stepSize=6, -minIdentity=97 and -maxIntron=0; the output was filtered to retain unique, high-quality matches starting with the first nucleotide downstream of the processed U5 sequence CAAAATTCCATGACA. To minimize cross-talk between datasets, only the integration sites observed more than once were retained in multiplexed barcoded samples.
The genomic coordinates were converted to the standard browser extensible data (BED) format, with each interval reporting the center dinucleotide of a PFV integration site.
Genome_build: hg19
Supplementary_files_format_and_content: The genomic coordinates were converted to the standard browser extensible data (BED) format, with each interval reporting the center dinucleotide of a PFV integration site.

growth_protocol:
HT1080 cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal calf serum in 5% CO2 humidified atmosphere.
PFV vectors were produced by co-transfection of HEK293T cells with pMD9 (GFP reporter PFV vector) and codon-optimized foamy virus GAG, POL and ENV packaging constructs. Mutations were introduced into POL expression construct (pcoP-POL). Viruses were concentrated by centrifugation of cell-free supernatants through 20% sucrose cushion and re-suspended in phosphate buffered saline for immediate use.

extract_protocol:
DNA from infected HT1080 cells was  extracted using Mammalian Genomic DNA miniprep kit (Sigma-Aldrich).
Genomic DNA, digested with BfaI, BanII and CviQI, was ligated to a linker made by annealing synthetic oligonucleotides 5´- TAGTCCCTTAAGCGGAG (with 3´ end blocked by an amino group modifier) and 5´-GTAATACGAC TCACTATAGG GCNNNNNCTC CGCTTAAGGGAC (the string of random nucleotides comprise a serial number, not relevant to this study). PFV U5 integration sites were PCR-amplified using primers 5´- CAAGCAGAAG ACGGCATACG AGATCGGTCT CGGCATTCCT GCTGAACCGCT CTTCCGATCT GTAATACGAC TCACTATAGGGC and 5´-GTGTGAACTA CACTTATCT TAAATGATG followed by a nested PCR with primers 5´- CAAGCAGAAG ACGGCATACG AGATCGGTCT CGGCATTCCT GCTGAACCG CTCTTCCGAT CTGTAATACG ACTCACTAT AGGGC and 5´- AATGATACGG CGACCACCGA GATCTACAC TCTTTCCCTA CACGACGCTC TTCCGATCTX XXXXCTTAAA TGATGTAACT CCTTAGGATA ATCAATATAC (the string of underlined nucleotides marked with “X” denotes the position of a 5-base index, which was unique for each integration site library analyzed).

treatment_protocol: HT0180 cells were infected with PFV vectors at a confluence of 20-30% and allowed to expand for 5-7 days to eliminate non-integrated viral DNA prior to genomic DNA isolation.

tag: pfv status

value: Hybrid control PFV vector


title: K168E

value: K168E PFV vector


title: Clone k20

city: Wuhan

first: wang

last: jue

address: Jiefang Avenue 1095

department: Hematology

country: China

institute: Huazhong University of Science and Technology, Tongji Hospital

data_processing:
Illumina RTA 1.13.48 and OLB-1.9.4 software used for basecalling.
As there are some adaptor sequences and/or low quality reads present in the raw reads, data filtering is carried out to obtain high quality reads as the clean reads (clean  data). The procedure include following steps:1. Remove reads with adaptor sequences.2. Remove reads in which the percentage of unknown bases (N) is greater than 10%.3. Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, we define this read as low quality, then mapped to hg19 reference gene using SOAPaligner/soap2 Version2.21t with parameters -m 0 -x 1000 -s 28 -l 32 -v 2 -r 2 .
The gene expression level is calculated by using RPKM( Mortazavi, A., B. A. Williams, et al . (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 5(7): 621-8.) method (Reads Per kb per Million reads)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include geneID,the number of reads that uniquely mapped to genes,gene length(bp),the percentage of gene covered by reads and RPKM values for each Sample

source_name: Leukemia cells

growth_protocol: The cells were cultured routinely in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) (Gibco) and were maintained in serial passage culture for 4 weeks prior to RNA-seq analysis

extract_protocol:
RNA was harvested using Trizol reagent. Illumina RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina Hiseq 2000 protocols

tag: genotype

value: FLT3 haplo-insufficiency


title: Hybrid_P135E_T240E

value: P135E/T240E hybrid PFV vector


title: Clone k324


title: sensitive control 1 replicate 1


title: BG E12.5 Input rep2

city: San Francisco

first: John

last: Rubenstein

state: CA

address: 1550 4th Street

department: Psychiatry

institute: UCSF

description: BG E12.5 InputChromatin rep2

data_processing:
Basecalls performed using standard Illumina pipeline
ChIP-seq reads were aligned to the mm9 genome assembly using BWA with the following call: bwa aln -t 6 -l 25  mm9 sample.fastq.gz
Peaks were called using MACS (version 1.4) incoporating matched input data with the following call: macs14 -t chip.bam --control=input.bam –name=chip_output --format=BAM --gsize=mm --tsize=50 --bw=300 --mfold=10,30 --nolambda --nomodel ---llocal=20000 --shiftsize=150 -p 0.00001
Peaks were filtered to remove regions where a significant proportion of the reads mapped within repetitive regions
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated by extending reads to 300bp and calculating the number of reads per 25bp bins across the genome; .bed files represent filtered peaks ranked by significance

organism: Mus musculus

source_name: Basal Ganglia and Septum

growth_protocol: Basal Ganglia and Septum were microdissected from CD-1 mice at E12.5.  Samples represent pooled tissues from multiple embryos/mice.

extract_protocol:
ChIP was performed using anti-OTX2 (R&D#AF1979) E12.5 CD1 GEs were fixed in 1.5% formaldehyde for 20 min. and neutralized with glycine. Fixed chromatin was lysed and sheared into 200-1000 bp fragments using a bioruptor (Diagenode). Immunoprecipitation (IP) reactions were performed in duplicates using Goat IgG as negative controls.A 3rd Replicate was performed omitting IgG as negative control. Precipitated fractions were purified using Dynabeads (Invitrogen).
Libraries were prepared using an Ovation Ultralow DR Multiplex System (Nugen), size selected in the range of 200-300 bp on a LabChip (Lifesciences), quality control tested on a Bioanalyzer (Agilent) and sequenced on a HiSeq (Illumina).
ChIP-seq (1x50bp reads, 6 samples/lane)

value: wildtype

tag: developmental stage

value: basal ganglia and septum

tag: chip antibody


title: BG E12.5 Otx2 rep3

description: BG E12.5 Otx2 ChIP-Seq rep3

value: anti-OTX2 (R&D, catalog# AF1979, lot# KNO0211051)


title: BG E12.5 Otx2 rep2

description: BG E12.5 Otx2 ChIP-Seq rep2


title: MDR6 strain replicate 2


title: BG E12.5 IgG rep1

description: BG E12.5 IgG negative control rep1

value: Normal Goat IgG (SC, catalog# 2028, lot# F1411)


title: WT

value: WT PFV vector


title: mESC_input

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

description: c-Jun was induced by dox for 36h, extracted DNA directly and performed sequencing

data_processing:
Use iIllumina Casava1.8 software for basecalling, trim adaptor and filter low-quality reads by bcl2fastq(v2.15.0.4)
Clean reads were mapped to mouse genome(mm9)  using bowtie2 (version 2.2.3).
Peaks calling using MACS(macs14 1.4.2), using input as control
Genome_build: mm9
Supplementary_files_format_and_content: peaks called by MACS in bed format

source_name: mouse embryonic stem cells(mESCs)

extract_protocol:
For c-Jun ChIP, ESCs were fixed with 1% formaldehyde for 15min and then followed by the reaction with 0.125M glycine. Cells were then lysed in ChIP- buffer A (50mM HEPAS-KOH, 140mM NaCl, 1mM EDTA (pH8.0), 10% glycerol, 0.5% NP-40, 0.25% Triton X-100  and 50mM Tris-HCl (pH8.0), and protease inhibitor cocktail for 10min at 4℃. Samples were centrifuged at 1400g for 5min at 4 ℃.Pellets were lysed in ChIP buffer B (1% SDS,50mM Tris-HCl (pH8.0),10mM EDTA and protease inhibitor cocktail) for 5min at  4℃. The DNA was fragmented to 100-500bp by sonication, and then centrifuged at 12000g for 2min. The supernatant was diluted with ChIP IP buffer (0.01%SDS, 1%TritonX-100, 2mM EDTA, 50 mM Tris-HCl (pH8.0), 150mM NaCl and protease inhibitor cocktail). Immunoprecipitation was preformed with 2μg rabbit anti-c-Jun antibody (ab31419) coupled to Dynabeads with proteinA /G overnight at 4 ℃. Beads were washed, eluted and reverse cross-linked. DNA was extracted by phenol/chloroform for sequencing.
The ChIP DNA library was constructed following the Illumina ChIP-seq library generation protocol. Briefly, 10ng ChIP DNA was blunt-ended, then a dA tail was added. Illumina genomic adapters with index sequence were ligated to the DNA. The Adaptor-ligated DNA was amplified by PCR for 18 cycles, the resulting DNA libraries were quantified and tested by qPCR with positive primers to assess the quality of the library. The DNA was diluted to 10nM before sequencing. Sequencing on a HiSeq2000 instrument was carried out by BGI (Shenzhen, China).

value: OG2 transgenetic mouse embryonic stem cells(OG3ES)

tag: passages

value: input


title: In vitro

source_name: deproteinized human genomic DNA

extract_protocol: Human genomic DNA reacted with PFV intasome was digested with NheI, AvrII, SpeI, and BanII and ligated to a linker made by annealing synthetic oligonucleotides 5´-CTAGGCAGCCCG (with 5’-phosphate modification and 3´ end blocked by an amino group modifier) and 5´-GTAATACGAC TCACTATAGG GCACGCGTGG TCGACGGCCC GGGCTGC. Integration sites were PCR-amplified using primers 5´- CAAGCAGAAG ACGGCATACG AGATCGGTCT CGGCATTCCT GCTGAACCGC TCTTCCGATC TGTAATACGA CTCACTATAG GGC and 5´- AATGATACGG CGACCACCGA GATCTACAC TCTTTCCCTA CACGACGCTC TTCCGATCTX XXXXCTTAAA TGATGTAACT CCTTAGGATA ATCAATATAC (the string of underlined nucleotides marked with “X” denotes the position of a 5-base index, which was unique for each integration site library analyzed).

treatment_protocol: To generate the reference dataset of  in vitro integration sites, 10 ug deproteinized human genomic DNA was incubated with 0.8 ug PFV intasome in 1 ml of 125 mM NaCl, 10 mM MgCl2, 2 mM DTT, 20 uM ZnCl2, 25 mM BisTris propane, pH 7.45 for 30 min at 37 oC.

value: purified recombinant intasome in vitro


title: K562_P30_rep1

city: Rome

first: Alessandro

last: Fatica

address: P.le Aldo Moro 5

department: Biology and Biotechnology "C. Darwin"

country: Italy

institute: Sapienza University of Rome

data_processing:
Basecalls performed using CASAVA version 1.4
Seq-reads were aligned to the hg19 human assembly using TopHat 2.0 with  parameters -p  -o  -G read-edit-dist 4 --read-gap-length 2 --read-mismatches 2 --read-realign-edit-dist 1 --library-type fr-firststrand --min-intron-length 50 --max-intron-length 300000
Transcripts were assembled with Cufllinks 2.2 using  Gencode v.19 with parameters -o output --frag-bias-correct dirhg19.fa --multi-read-correct -G dirgencode.v19.annotation.gtf  --compatible-hits-norm --library-type fr-firststrand --max-bundle-frags 500000 -p 8 -q
Diffreential expression was assessed using CuffDiff
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: K562  P30 cells

growth_protocol: K562 cell lines were cultured at 37°C under an atmosphere containing 5% CO2 in RPMI 1640 medium supplemented with 1x Penicillin/Streptomicin solution, 1x L-glutamine and 10% Fetal Bovine Serum.

extract_protocol:
RNA was prepared using the Rneasy kit (Qiiagen)
Libraries were prepared for sequencing using standard Illumina protocol accompanying TruSeq stranded mRNA sample prep kit  (RS-122-2101)

treatment_protocol: Doxycycline (Dox) were purchased from Sigma and utilized at a concentration of 200 ng/ml for 48 hours

value: leukemia cell line

tag: treatment

value: P30 induction


title: K562_CEBPA_rep1

source_name: K562 CEBPA cells

value: CEBPA induction


title: Spleen

city: Los Angeles

first: Dario

last: Boffelli

address: 700 N San Vicente Blvd

department: Pediatrics

institute: Cedars Sinai

description: size-selected small RNA

data_processing:
Basecalls performed using CASAVA version 1.8
The last 6 bases (Illumina indexes) were removed and added to the header line of the .fastq files.
Reads that did not pass Illumina quality control were filtered.
3' adapters were stripped using Cutadapt with the following parameters:  -a -e 0.25 -n 3 -O 1 -m 15
5' adapters were removed using Cutadapt with the following parameters:  -b -e 0.25 -n 3 -O 5  -m 15
Known ncRNAs were removed by aligning reads to non-coding RNA sequences using Bowtie with the following parameters:  -v3 -k1 --un
Remaining small RNAs were aligned to the mm9 genome using Bowtie with the following parameters:  -v1 -m1 --best -- strata
3' UTR clusters were generated by selecting  3' UTRs with at least 3 sense small RNAs and a minimum density of 7.5 reads per kilobase 3' UTR per million reads aligned.  Genes where the density of sense small RNAs in the 3' UTR was less than two fold that of the density in the coding region were removed.  We then set the cluster boundaries as the region of the largest 3' UTR isoform and extended the 3' boundary into intergenic sequence if there was at least 1 sense small RNA per 2 kb.
RNAs that intersected the 3' UTR clusters were isolated using BEDtools IntersectBed with the default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: bam – alignments of trimmed and filtered RNAs

source_name: WT spleen

extract_protocol:
Liver and spleen were removed, flash frozen in liquid nitrogen, and small RNA (10-200bp) was harvested using RNAzol RT reagent.  RNA were then run on a polyacrylamide gel, and RNA with size from ~24-31 nt was purified and used for the construction of sequencing libraries.
RNA libraries were prepared using the Illumina Small RNA v1.5 Sample Preparation kit.

value: spleen

value: adult


title: BG E12.5 Input rep3

description: BG E12.5 Input Chromatin rep3


title: MEF_Oct4

description: overexpressed Oct4 in MEF

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.
Transcripts per million(TPM) were calculated using RSEM(1.1.21) with parameters(-p 8 --estimated-rspd --no-bam-output).
Genome_build: mm9
Supplementary_files_format_and_content: TXT files including tau values for each RNA-seq samples, and TPM values are generated for all the samples.

source_name: mouse embryonic fibroblasts (MEFs)

extract_protocol:
Total RNA was extracted by Trizol-based protocol.
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.

value: OG2 transgenic mouse embryonic fibroblasts (MEFs)


title: Clone k114


title: reprogramming_c-JunDN_ChIPseq

description: MEF induced reprogramming  by Sox2, Klf4, c-Myc and c-JunDN, on day 3, extracted DNA, using c-JunDN antibody performed ChIPseq

value: c-Jun


title: KSM_with_Jdp2

description: transfect Jdp2 with  KSM, extracing RNA on Day 3


title: BG E12.5 IgG rep2

description: BG E12.5 IgG negative control rep2


title: sensitive control 1 replicate 2

value: sensitive


title: Liver

description: size-selected small RNA

source_name: WT liver

value: liver


title: 293Trex_USP7

city: New York City

first: Danny

last: Reinberg

state: New York

address: 522 First Avenue, 2nd floor Rm 211

institute: NYU School of Medicine / HHMI

data_processing:
mapped to hg19 with BOWTIE -m4 -v2
1nt resolution bedgraphs were generated with the BEDtools bamToBed and genomeCoverageBed utilities after extending each read to 200
coverage was normalized to FP10M (fragments per 10 million reads sequenced)
bigWig files were generated with bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: FP10M-normalized bigWig

growth_protocol: 293T-REx cells were grown in DMEM with 10% FBS, penicillin (100 IU/ml), streptomycin (100 mg/ml) and glutamine (300 mg/ml).

extract_protocol:
Cells were fixed in DMEM containing 10 mM Hepes, pH 7.6, 1% formaldehyde, 15 mM NaCl, 0.15 mM EDTA and 0.075 mM EGTA, for 10 min at room temperature. The reaction was quenched with 0.125 M glycine for 5 min at room temperature, cells were washed with PBS and lysed in 50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% Igepal CA630 and 0.25% Triton X-100. After centrifugation, isolated nuclei were washed once in 10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA, then resuspended in 10 mM Tris, pH 8.0, 1 mM EDTA, 0.5 mM EGTA and 0.5% N-Lauryl Sarcosine, and sonicated using a Diagenode Bioruptor to an average chromatin size of 200 bp.
Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with LigaFast (Promega, city, state #M8225). Fragments of 300±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530).

value: anti-USP7 (Bethyl, catalog# A300-033A)


title: Clone kw3

value: FLT3 wild type


title: MEF_Jdp2

description: overexpressed Jdp2 in MEF

value: overexpressed Jdp2 in MEF


title: MEF_c-JunDN

description: overexpressed c-JunDN in MEF

value: overexpressed c-JunDN in MEF


title: MEF_DR

description: overexpressed DR in MEF

value: overexpressed DR in MEF


title: Clone kw2


title: BG E12.5 Input rep1

description: BG E12.5 Input Chromatin rep1

value: wildtype

value: basal ganglia and septum


title: K562_CTR_rep2

source_name: K562 CTR cells

value: control


title: c-Jun_TetOn_36h_without_dox

description: c-Jun_TetOn_mESC, without dox induced as control

value: OG2 transgenetic mouse embryonic stem cells(OG2ES)


title: MEF

description: WT MEF

value: WT MEF


title: mESC_c-Jun_ChIPseq

description: c-Jun was induced by dox for 36h, using c-Jun antibody performed ChIP-seq

value: OG2 transgenetic mouse embryonic stem cells(OG3ES)


title: BG E12.5 Otx2 rep1

description: BG E12.5 Otx2 ChIP-Seq rep1

value: anti-OTX2 (R&D, catalog# AF1979, lot# KNO0211051)


title: SUM159-MDA453_H3K27me3_ChIPSeq

status: Public on Jun 09 2015

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Basecalls performed using the SOLiD4 Pipeline.
ChIP-seq reads were aligned to the hg18 (March, 2006) human genome assembly using bowtie version 0.12.7 with default configuration.
peaks were called using SICER version 1.03 with the following setting: Window size (200bp), Gap size (600bp), Other parameters (default).
Genome_build: hg18
Supplementary_files_format_and_content: Bed files were generated using SICER. Each raw represents each peak detected by SICER. Numbers in the fifth column represent enrichment scores calculated by SICER.

source_name: Breast cancer cells

extract_protocol: Following cell purification, cells were immediately cross-linked with formaldehyde (final concentration is 0.5%) at room temperature for 10 minutes. Cells were washed, lysed, and the DNA was fragmented with a Covaris S2 (Covaris). The fragmented DNA was incubated with a specific antibody for 8 hours. The immunoprecipitates were sequentially washed, reverse-crosslinked, and purified by AMPureXP Agencourt Bioscience). ChIP-ed DNA was end-repaired by END-It DNA End Repair Kit (Epicentre), and adaptor oligo (Life technologies) was ligated and subjected to PCR amplification (15 cycles) using specific primers provided by the Life technologies. The PCR product was purified with AMPureXP and the emulsion PCR performed according to the manufacturer's instructions and sequenced by SOLiD4 (Life technologies).

value: Heterofusion

tag: chip-antibody

tag: chip-antibody vendor

value: CST

tag: chip-antibody cat. #


title: GENEA020

first: Albert

last: Ruzo

address: 1230 York Avenue

department: Laboratory of Stem Cell Biology and Molecular Embryology

institute: The Rockefeller University

data_processing:
Reads aligned using Tophat2, providing it with gene annotations from UCSC hg19 assembly
Transcripts were assembled and quantified using Cufflinks, providing it with a reference for gene annotations from the UCSC hg19 assembly.
Genome_build: hg19
Supplementary_files_format_and_content: Cufflinks FPKM measurements

source_name: embryonic stem cells

growth_protocol: hESCs were maintained in MEF-conditioned medium in presence of 20ng/ml bFGF

extract_protocol:
QIAZOL and Rneasy purification columns (QIAGEN)
Illumina TruSeq RNA Sample Prep Kit v2

treatment_protocol: No treatment

value: human embryonic stem cells (hESCs)


title: Clone kw1


title: SUM159-21NT_H3K27me3_ChIPSeq


title: SpleenMiwi2KO

description: size-selected small RNA

source_name: MIWI2 KO spleen

value: spleen

value: adult


title: LiverMiwi2KO

description: size-selected small RNA

source_name: MIWI2 KO liver

value: liver


title: K562_P30_rep2

source_name: K562 P30 cells

value: leukemia cell line

value: P30 induction


title: RUES2


title: K562_CEBPA_rep2

value: CEBPA induction


title: SUM159-ZR75-1_H3K27me3_ChIPSeq


title: GENEA019


title: additional_ESC_H6

city: Barcelona

first: Lars

last: Velten

address: C. Dr. Aiguader 88, P05

department: Bioinformatics and Genomics

country: Spain

institute: CRG

description: Single Cell

data_processing:
Demultiplexed using batch and cell barcode (in fwd. and rev. read, respectively). Pyhton2.7/HTSeq
Trim off 8 bases of the reverse read (molecular barcode) and store with first read. Discard reverse read. Perl5
Trim off polyA from 3' end of forward read. Discard reads not ending in a poly A tail. Python2.7/HTSeq
Align reads to Mus Musculus genome GRCm38, to which ERCC spike in seqeunce has been appended. Gsnap
Filter out reads of non-unique alignment, low alignemt quality, alignment to A-rich genomic regions, A-rich reads. Python2.7/HTSeq
Count unique molecular barcodes aligning to different genomic features. Python2.7/HTSeq
Remove barcode counts stemming from similar molecular barcodes with a Hamming distance of less than 1. Perl5
Collapse putative polyadenylation sites stemming from genomic positions within 12bp distance. Perl5
For the summary files, 27 cells were removed because less than 1000 molecular barcodes were observed. R-3.0.2
Genome_build: Mus Musculus GRCm38 (ensembl version 38.73), with the sequences of the ERCC control RNA spike ins appended to it
Supplementary_files_format_and_content: isoforms.counts, comma-separated value files containing the ensembl gene ID of the closest genomic feature, the 3' alignment position (polyadenylation site), the Barcode Count, the Read Count, a brief description of the alignment site, the distance to the closest annotated transcript termination site

molecule: polyA RNA

source_name: Embryonic stem cells

extract_protocol:
Single cell RNA sequencing (no RNA extraction, FACS sorting into 0.6µL lysis buffer containing 10% NP-40)
Polyadenylation-site specific single cell transcriptome sequencing using the BATSeq protocol. (Velten et al., in preparation). The protocol is highly multiplexed and uses both batch and cell barcodes, which are given in the characteristics columns of the SAMPLES section. 4 independent sequencing runs were performed.

value: Embryonic Stem Cells

tag: growth medium

value: 10% FBS + 10ng/mL LIF

tag: cell cycle stage

tag: batch barcode

value: AAGCTA

tag: cell barcode

value: CATTCA


title: ZR75-1_H3K27me3_ChIPSeq

tag: cell line

tag: cell type

value: Luminal cells


title: K562_CTR_rep1

value: control


title: KSM_with_c-JunDN

description: transfect c-JunDN with  KSM, extracing RNA on Day 3

value: OG2 transgenic mouse embryonic fibroblasts (MEFs)

tag: strain

tag: genotype/variation


title: additional_ESC_H4

description: Single Cell

value: CGAAAC


title: additional_ESC_H3

description: Single Cell

value: TCGGGA


title: KSM_DR

description: transfect DR with  KSM, extracing RNA on Day 3


title: KSM_with_Oct4

description: transfect Oct4 with  KSM, extracing RNA on Day 3


title: additional_ESC_G5

description: Single Cell

value: TCCGTC


title: MEF_c-Jun

description: overexpressed c-Jun in MEF

value: overexpressed c-Jun in MEF


title: c-Jun_TetOn_36h_with_dox

description: c-Jun_TetOn_mESC, dox induced for 36h

value: OG2 transgenetic mouse embryonic stem cells(OG2ES)

value: c-Jun_TetOn_mESC, dox induced for 36h


title: additional_ESC_G3

description: Single Cell

value: CCACTC


title: additional_ESC_G4

description: Single Cell

value: GCTACC


title: mESC

description: WT OG2ES

value: WT OG2ES


title: MDA-MB-453_H3K27me3_ChIPSeq

value: CST


title: additional_ESC_G2

description: Single Cell

value: Embryonic Stem Cells

value: CTCTAC


title: 21NT_H3K27me3_ChIPSeq


title: CAL51-MCF7_H3K27me3_ChIPSeq

value: Heterofusion


title: additional_ESC_F1

description: Single Cell

value: 10% FBS + 10ng/mL LIF

value: AAGCTA

value: TTGCGG


title: additional_ESC_F4

description: Single Cell

value: ATTCCG


title: additional_ESC_F5

description: Single Cell

value: GTATAG


title: Bulk48ESCFCS

description: 48 cells pooled

value: ACATCG


title: CAL51_H3K27me3_ChIPSeq

value: Basal-like cells


title: additional_ESC_H1

description: Single Cell

value: TTCGAA


title: additional_ESC_H5

description: Single Cell

value: GAATGA


title: additional_ESC_D6

description: Single Cell

value: CGTGAT

value: CATTCA


title: additional_ESC_D4

description: Single Cell

value: CGAAAC


title: additional_ESC_D5

description: Single Cell


title: MDA-MB-231_H3K27me3_ChIPSeq

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: additional_ESC_C6

description: Single Cell

value: CTGATC


title: additional_ESC_F6

description: Single Cell

value: Embryonic Stem Cells

value: ATCGTG


title: additional_ESC_F3

description: Single Cell

value: TCTGAG


title: additional_ESC_E6

description: Single Cell

value: 10% FBS + 10ng/mL LIF

value: ATAGAT


title: additional_ESC_C4

description: Single Cell

value: GCTACC


title: additional_ESC_E5

description: Single Cell

value: AAGCTA

value: AGCGCT


title: additional_ESC_B3

description: Single Cell


title: additional_ESC_B1

description: Single Cell

value: TTGCGG


title: additional_ESC_A5

description: Single Cell


title: additional_ESC_A4

description: Single Cell

value: CACTGT


title: additional_ESC_A3

description: Single Cell

value: GGAACT


title: additional_ESC_H2

description: Single Cell

value: GCTGTA


title: additional_ESC_C1

description: Single Cell

value: CGTGAT

value: TGTGCC


title: additional_ESC_G6

description: Single Cell


title: 48_2i_1

description:
48 cells pooled
Sample 145

extract_protocol:
48 cells were sorted into Qiagen buffer RLT with beta-Mercaptoethanol and RNA was purified using a 1.8x Amoure bead cleanup
Polyadenylation-site specific single cell transcriptome sequencing using the BATSeq protocol which includes amplification of cDNA and polyadenylation site mapping

value: GCCTAA


title: NSC_H6

description:
Sample 144
Single Cell

data_processing:
Demultiplexed using batch and cell barcode (in fwd. and rev. read, respectively). Pyhton2.7/HTSeq
Trim off 8 bases of the reverse read (molecular barcode) and store with first read. Discard reverse read. Perl5
Trim off polyA from 3' end of forward read. Discard reads not ending in a poly A tail. Python2.7/HTSeq
Align reads to Mus musculus genome GRCm38 (ensembl version 38.73), with the sequences of the ERCC control RNA spike ins appended to it. Gsnap
Filter out reads of non-unique alignment, low alignemt quality, alignment to A-rich genomic regions, A-rich reads. Python2.7/HTSeq
Count unique molecular barcodes aligning to different genomic features. Python2.7/HTSeq
Remove barcode counts stemming from similar molecular barcodes with a Hamming distance of less than 1. Perl5
Collapse putative polyadenylation sites stemming from genomic positions within 12bp distance. Perl5
For the summary files, 27 cells were removed because less than 1000 molecular barcodes were observed. R-3.0.2
Genome_build: GRCm38
Supplementary_files_format_and_content: *isoforms.counts.gz: comma-separated value files containing the ensembl gene ID of the closest genomic feature, the 3' alignment position (polyadenylation site), the Barcode Count, the Read Count, a brief description of the alignment site, the distance to the closest annotated transcript termination site
Supplementary_files_format_and_content: TotalGeneCounts.csv contains total counts of molecular barcodes by gene (identified by ensembl gene ID, column 1) for 107 cells which pass the quality control criteria. (columns 2-108); includes some summarisation of the processed data files (removal of polyadenylation site information).
Supplementary_files_format_and_content: TotalIsoformCounts.csv contains molecular barcode and read counts (column 3+4) by gene (column 1), polyadenylation site in genomic coordinates (column 2), and Cell (column 7) for 107 cells which pass the quality control criteria. Additional information on distance to closest annotated transcript termination site (column 6) and a brief description of the alignment position (column 5) is also given.

source_name: Neural stem cells

extract_protocol:
Single cell RNA sequencing (no RNA extraction, FACS sorting into 0.6µL lysis buffer containing 10% NP-40)
Polyadenylation-site specific single cell transcriptome sequencing using the BATSeq protocol. (Velten et al., in preparation). The protocol is highly multiplexed and uses both batch and cell barcodes, which are given in the 'Characteristics' section. 4 independent sequencing runs were performed.

value: ES-derived neural progenitor cells

value: TGGTCA

value: TCGGGA


title: NSC_H5

description:
Sample 143
Single Cell


title: additional_ESC_F2

description: Single Cell

value: Embryonic Stem Cells

value: CGTACG


title: additional_ESC_G1

description: Single Cell

value: 10% FBS + 10ng/mL LIF


title: NSC_H4

description:
Sample 142
Single Cell

value: TTCGAA


title: additional_ESC_E4

description: Single Cell


title: NSC_H3

description:
Sample 141
Single Cell

value: CATTCA


title: NSC_H2

description:
Sample 140
Single Cell

value: GAATGA


title: additional_ESC_E3

description: Single Cell

value: AAGCTA


title: additional_ESC_E2

description: Single Cell

value: GAGAGT


title: additional_ESC_E1

description: Single Cell

value: AGTCTT


title: NSC_H1

description:
Sample 139
Single Cell

value: CGAAAC


title: NSC_G6

description:
Sample 138
Single Cell

value: CCACTC


title: NSC_G5

description:
Sample 137
Single Cell

value: CTCTAC


title: NSC_G4

description:
Sample 136
Single Cell

value: TGTGCC


title: additional_ESC_D2

description: Single Cell

value: CGTGAT

value: GCTGTA


title: additional_ESC_D3

description: Single Cell


title: additional_ESC_D1

description: Single Cell


title: additional_ESC_C5

description: Single Cell

value: TCCGTC


title: additional_ESC_C3

description: Single Cell


title: additional_ESC_C2

description: Single Cell


title: additional_ESC_B4

description: Single Cell

value: ATTCCG


title: NSC_G1

description:
Sample 133
Single Cell

value: ES-derived neural progenitor cells

value: TGGTCA

value: GCTACC


title: additional_ESC_B2

description: Single Cell

value: Embryonic Stem Cells

value: 10% FBS + 10ng/mL LIF

value: CGTACG


title: NSC_F4

description:
Sample 130
Single Cell

value: TTGCGG


title: NSC_F5

description:
Sample 131
Single Cell


title: NSC_F1

description:
Sample 127
Single Cell


title: additional_ESC_A6

description: Single Cell

value: ATAGAT


title: additional_ESC_A1

description: Single Cell

value: AGTCTT


title: additional_ESC_B6

description: Single Cell

value: ATCGTG


title: additional_ESC_A2

description: Single Cell

value: GAGAGT


title: 48_2i_2

description:
48 cells pooled
Sample 146


title: NSC_E6

description:
Sample 126
Single Cell

value: GGAACT


title: NSC_E3

description:
Sample 123
Single Cell


title: NSC_D6

description:
Sample 120
Single Cell

value: GCCTAA

value: TCGGGA


title: NSC_E1

description:
Sample 121
Single Cell

value: CACTGT


title: NSC_C6

description:
Sample 114
Single Cell

value: CCACTC


title: NSC_C4

description:
Sample 112
Single Cell

value: TGTGCC


title: NSC_G3

description:
Sample 135
Single Cell

value: ES-derived neural progenitor cells

value: CTGATC


title: NSC_F6

description:
Sample 132
Single Cell

value: TGGTCA

value: TCTGAG


title: NSC_G2

description:
Sample 134
Single Cell

value: TCCGTC


title: NSC_C1

description:
Sample 109
Single Cell

value: GCTACC


title: NSC_F2

description:
Sample 128
Single Cell

value: GTATAG


title: NSC_F3

description:
Sample 129
Single Cell


title: NSC_E5

description:
Sample 125
Single Cell


title: NSC_E4

description:
Sample 124
Single Cell


title: NSC_B6

description:
Sample 108
Single Cell


title: NSC_B4

description:
Sample 106
Single Cell

value: TTGCGG


title: NSC_B3

description:
Sample 105
Single Cell


title: NSC_B1

description:
Sample 103
Single Cell

value: ATTCCG


title: NSC_D2

description:
Sample 116
Single Cell

value: GAATGA


title: NSC_A6

description:
Sample 102
Single Cell


title: NSC_E2

description:
Sample 122
Single Cell

value: AGCGCT


title: NSC_D5

description:
Sample 119
Single Cell

value: GCTGTA


title: NSC_D4

description:
Sample 118
Single Cell

value: GCCTAA

value: TTCGAA


title: NSC_D3

description:
Sample 117
Single Cell

value: CATTCA


title: NSC_D1

description:
Sample 115
Single Cell

value: CGAAAC


title: ESC_H9

description:
Sample 96
Single Cell

value: Embryonic Stem Cells

value: 10% FBS + 10ng/mL LIF

value: ACATCG

value: TCGGGA


title: NSC_C5

description:
Sample 113
Single Cell

value: ES-derived neural progenitor cells

value: CTCTAC


title: ESC_H7

description:
Sample 94
Single Cell


title: ESC_H12

description:
Sample 93
Single Cell


title: NSC_B2

description:
Sample 104
Single Cell


title: NSC_A5

description:
Sample 101
Single Cell

value: GAGAGT


title: ESC_G12

description:
Sample 87
Single Cell

value: CTGATC


title: ESC_F8

description:
Sample 83
Single Cell

value: CGTACG


title: NSC_A4

description:
Sample 100
Single Cell

value: AGTCTT


title: ESC_F12

description:
Sample 81
Single Cell

value: ATCGTG


title: ESC_F11

description:
Sample 80
Single Cell

value: GTATAG


title: NSC_A3

description:
Sample 99
Single Cell

value: ATAGAT


title: ESC_E9

description:
Sample 78
Single Cell

value: GGAACT


title: ESC_F10

description:
Sample 79
Single Cell

value: ATTCCG


title: NSC_C3

description:
Sample 111
Single Cell

value: GCCTAA


title: NSC_A2

description:
Sample 98
Single Cell

value: AGCGCT


title: NSC_C2

description:
Sample 110
Single Cell

value: TCCGTC


title: NSC_A1

description:
Sample 97
Single Cell

value: CACTGT


title: NSC_B5

description:
Sample 107
Single Cell


title: ESC_H11

description:
Sample 92
Single Cell

value: Embryonic Stem Cells

value: 10% FBS + 10ng/mL LIF

value: ACATCG

value: GAATGA


title: ESC_E7

description:
Sample 76
Single Cell


title: ESC_H8

description:
Sample 95
Single Cell

value: GCTGTA


title: ESC_E12

description:
Sample 75
Single Cell


title: ESC_E10

description:
Sample 73
Single Cell


title: ESC_H10

description:
Sample 91
Single Cell

value: CGAAAC


title: ESC_G9

description:
Sample 90
Single Cell

value: CCACTC


title: ESC_G8

description:
Sample 89
Single Cell

value: CTCTAC


title: ESC_F7

description:
Sample 82
Single Cell

value: TTGCGG


title: ESC_G11

description:
Sample 86
Single Cell


title: ESC_F9

description:
Sample 84
Single Cell

value: TCTGAG


title: ESC_G7

description:
Sample 88
Single Cell

value: TGTGCC


title: ESC_G10

description:
Sample 85
Single Cell

value: GCTACC


title: ESC_E8

description:
Sample 77
Single Cell

value: GAGAGT


title: ESC_D11

description:
Sample 68
Single Cell

value: TACAAG


title: ESC_D7

description:
Sample 70
Single Cell

value: TTCGAA


title: ESC_C9

description:
Sample 66
Single Cell


title: ESC_C12

description:
Sample 63
Single Cell

value: CTGATC


title: ESC_C11

description:
Sample 62
Single Cell

value: TCCGTC


title: ESC_C7

description:
Sample 64
Single Cell

value: Embryonic Stem Cells


title: ESC_C10

description:
Sample 61
Single Cell

value: 10% FBS + 10ng/mL LIF


title: ESC_D9

description:
Sample 72
Single Cell

value: TCGGGA


title: ESC_E11

description:
Sample 74
Single Cell

value: ACATCG

value: AGCGCT


title: ESC_B9

description:
Sample 60
Single Cell


title: ESC_D8

description:
Sample 71
Single Cell

value: GCTGTA


title: ESC_B7

description:
Sample 58
Single Cell


title: ESC_B11

description:
Sample 56
Single Cell

value: GTATAG


title: ESC_D12

description:
Sample 69
Single Cell

value: CATTCA


title: ESC_D10

description:
Sample 67
Single Cell

value: CGAAAC


title: ESC_A8

description:
Sample 53
Single Cell


title: ESC_A7

description:
Sample 52
Single Cell

value: AGTCTT


title: ESC_C8

description:
Sample 65
Single Cell

value: CTCTAC


title: ESC_A10

description:
Sample 49
Single Cell

value: CACTGT


title: ESC_B8

description:
Sample 59
Single Cell

value: CGTACG


title: 2i_H4

description:
Sample 46
Single Cell

value: AAGCTA


title: ESC_B12

description:
Sample 57
Single Cell

value: TACAAG

value: ATCGTG


title: 2i_H5

description:
Sample 47
Single Cell


title: ESC_B10

description:
Sample 55
Single Cell

value: ATTCCG


title: 2i_H1

description:
Sample 43
Single Cell

value: Embryonic Stem Cells


title: ESC_A9

description:
Sample 54
Single Cell

value: 10% FBS + 10ng/mL LIF

value: GGAACT


title: 2i_G3

description:
Sample 39
Single Cell

value: CTGATC


title: 2i_G2

description:
Sample 38
Single Cell

value: TCCGTC


title: 2i_G1

description:
Sample 37
Single Cell

value: GCTACC


title: ESC_A11

description:
Sample 50
Single Cell

value: AGCGCT


title: 2i_F4

description:
Sample 34
Single Cell

value: TTGCGG


title: ESC_A12

description:
Sample 51
Single Cell

value: ATAGAT


title: 2i_H6

description:
Sample 48
Single Cell

value: TCGGGA


title: 2i_H3

description:
Sample 45
Single Cell

value: CATTCA


title: 2i_H2

description:
Sample 44
Single Cell

value: GAATGA


title: 2i_E3

description:
Sample 27
Single Cell


title: 2i_G6

description:
Sample 42
Single Cell

value: CCACTC


title: 2i_G5

description:
Sample 41
Single Cell

value: AAGCTA

value: CTCTAC


title: 2i_G4

description:
Sample 40
Single Cell

value: TGTGCC


title: 2i_F5

description:
Sample 35
Single Cell

value: CGTACG


title: 2i_F6

description:
Sample 36
Single Cell

value: Embryonic Stem Cells

value: TCTGAG


title: 2i_D1

description:
Sample 19
Single Cell

value: CGTGAT

value: CGAAAC


title: 2i_C5

description:
Sample 17
Single Cell


title: 2i_F3

description:
Sample 33
Single Cell

value: ATCGTG


title: 2i_F2

description:
Sample 32
Single Cell

value: GTATAG


title: additional_ESC_B5

description: Single Cell

value: 10% FBS + 10ng/mL LIF


title: 2i_F1

description:
Sample 31
Single Cell

value: ATTCCG


title: 2i_E4

description:
Sample 28
Single Cell

value: AGTCTT


title: 2i_E6

description:
Sample 30
Single Cell

value: GGAACT


title: 2i_D4

description:
Sample 22
Single Cell

value: TTCGAA


title: 2i_D5

description:
Sample 23
Single Cell

value: GCTGTA


title: 2i_E5

description:
Sample 29
Single Cell

value: GAGAGT


title: 2i_E2

description:
Sample 26
Single Cell

value: AAGCTA

value: AGCGCT


title: 2i_D6

description:
Sample 24
Single Cell

value: TCGGGA


title: 2i_B2

description:
Sample 8
Single Cell


title: 2i_E1

description:
Sample 25
Single Cell

value: CACTGT


title: 2i_D3

description:
Sample 21
Single Cell

value: Embryonic Stem Cells

value: CATTCA


title: 2i_B1

description:
Sample 7
Single Cell

value: CGTGAT


title: 2i_C4

description:
Sample 16
Single Cell

value: TGTGCC


title: 2i_C3

description:
Sample 15
Single Cell

value: CTGATC


title: 2i_A3

description:
Sample 3
Single Cell

value: ATAGAT


title: 2i_C2

description:
Sample 14
Single Cell

value: TCCGTC


title: 2i_B6

description:
Sample 12
Single Cell

value: TCTGAG


title: 2i_B4

description:
Sample 10
Single Cell

value: TTGCGG


title: 2i_A2

description:
Sample 2
Single Cell


title: 2i_A1

description:
Sample 1
Single Cell


title: 2i_B5

description:
Sample 11
Single Cell

value: CGTACG


title: Ribosome profiling rep2-SiControl-input-ribominus

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E. 57th. Street

department: Chemistry

institute: The University of Chicago

description:
rRNA removal RNA
C-Y1-Ribosome profiling.xlsx

data_processing:
General: Illumina Casava 1.8.2 software were used for basecalling.
General: Reads were aligned to the hg19 genome assembly using bowtie version 1.0 with at most 2 mismatch allowed -n 2 -g 1.
A: PAR-CLIP data were analyzed by PARalyzerv1.1 with default settings.
B and C: RIP and Ribosome profiling were mapped by Tophat version 2.0 and analyzed by DESeq to generate RPKM
All other following calculation steps were illustrated in processed files.
Genome_build: hg19
Supplementary_files_format_and_content: The results were organized in the Microsoft Excel format

source_name: HeLa cell

extract_protocol: NEBNext small RNA library prep set for Illumina (NEB)

value: HeLa

tag: cell treatment

value: 40nM siRNA knock-down for 48h

tag: sample treatment and extract

value: Extracy by trizol, then rRNA removal


title: 2i_D2

description:
Sample 20
Single Cell

value: GAATGA


title: Ribosome profiling rep2-SiControl-RPF

description:
Ribosome-bound mRNA
C-Y1-Ribosome profiling.xlsx

value: Isolate from surcrose gradient, recovered by trizol


title: Ribosome profiling rep2-SiYTHDF1_8-RPF


title: Ribosome profiling rep2-SiYTHDF1_8-input-ribominus


title: Ribosome profiling rep1-SiControl-input-ribominus

description:
rRNA removal mRNA
C-Y1-Ribosome profiling.xlsx

value: Extract by trizol, then rRNA removal


title: YTHDF1-RIP-input ribominus

description:
RNA after rRNA removal
B-Y1-RIP.xlsx

extract_protocol: Truseq stranded mRNA sample prepration kit (illumina)

value: over-express N-terminal flag-tagged YTHDF1 for 24h(0.75ug plasmid/mL)


title: 2i_A5

description:
Sample 5
Single Cell

value: Embryonic Stem Cells

value: GAGAGT


title: 2i_A4

description:
Sample 4
Single Cell

value: CGTGAT

value: AGTCTT


title: YTHDF1-PAR-CLIP-rep2

description:
small RNA fragments crosslinked with YTHDF1
A-Y1-PARCLIP.xlsx

extract_protocol: Truseq small RNA sample prepration kit (illumina)

value: over-express N-terminal flag-tagged YTHDF1 for 24h (0.75ug plasmid/mL)

value: fed with 4SU, UV crosslink, partial digested by RNase T1, anti-flag-beads IP


title: YTHDF1-RIP-input polyA

description:
Poly(A) selected mRNA
B-Y1-RIP.xlsx

value: Extract by trizol, then poly-dT beads pull-down


title: 2i_C6

description:
Sample 18
Single Cell

value: CCACTC


title: YTHDF1-PAR-CLIP-rep1


title: 2i_C1

description:
Sample 13
Single Cell

value: GCTACC


title: 2i_B3

description:
Sample 9
Single Cell

value: ATCGTG


title: Ribosome profiling rep1-SiYTHDF1_1-input-ribominus

value: HeLa


title: Ribosome profiling rep1-SiControl-RPF

value: 40nM siRNA knock-down for 48h


title: ZR75_RNAseq

data_processing:
Basecalls performed using CASAVA version 1.7 or 1.8.
RNA-Seq raw data was mapped by Tophat to hg19.
Genome_build: hg19
Supplementary_files_format_and_content: text file of normalized count data (FPKM). the file consists of following columns (tracking_id, class_code,nearest_ref_id, gene_id, gene_short_name, tss_id,locus, length, coverage, FPKM, FPKM_conf_lo, FPKM_conf_hi, FPKM_status)

extract_protocol: polyA RNA were purified using the MACS mRNA isolation kit (Miltenyi Biotec).  PolyA RNA was fragmented by RNA fragmentation reagent (Ambion), and subjected to first strand synthesis by using SupeScript II (Invitrogen) and random hexamer oligos. The second strand was synthesized, and then subjected to end repair, A-tailing, ligation of Illumia paired end adaptor. Following PCR amplification, the final library was purified with Ampure XP beads.

value: Luminal cells


title: 2i_A6

description:
Sample 6
Single Cell

value: GGAACT


title: SUM159MDA453_RNAseq

value: Heterofusion


title: SUM159ZR75_RNAseq


title: YTHDF1-RIP-IP-rep1

description:
RNA IP with YTHDF1
B-Y1-RIP.xlsx

value: anti-flag-beads IP


title: YTHDF1-RIP-IP-rep2

description:
RNA IP with YTHDF1
B-Y1-RIP.xlsx


title: Ribosome profiling rep1-SiYTHDF1_1-RPF

value: Isolate from surcrose gradient, recovered by trizol


title: MOPS-rich-CAM-1

city: La Jolla

first: Haythem

last: Latif

state: California

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive

institute: University of California San Diego

description: wild type, mid log, MOPS rich + 0.2% glucose, replicate 1

data_processing:
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for base calling and demultiplexing
fastq files were adaptor trimmed using cutadapt v1.3
bowtie v1.0.0 was used for aligning to the NC_000913.2 genome
Subsequent analysis was performed using custom scripts for calculating the center weighted value for each read mapping to the E. coli genome. Enclosed is a gff file containing the center weighted count for all positions and both strands.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: gff

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: Cells were grown aerobically at 37 °C in batch to early exponential phase on MOPS rich media supplemented with 02.% glucose.

extract_protocol:
Cells were lysed using repeated freeze thaws in a buffer that retained ribosome integrity and digested DNA. Monosomes were recovered using Sephacryl spin columns and total RNA was recovered using Qiagen's small Rneasy kit. rRNA was depleted using Epicentre's RiboZero kit.
After T4 PNK treatment, libraries were constructed using NEB's small RNA library construction kit. During the processes, tRNAs were eliminating using DNA oligos and a high temperature Rnase H.

treatment_protocol: Cells were treated chloramphenicol 2 min prior to harvest. Cells were then quickly centrifuged, reconstituted in lysis buffer and stored at -80 °C until the time of processing.

tag: genotype

value: wild type


title: MDA453_RNAseq


title: 21NT_RNAseq


title: MOPS-rich-CAM-2

description: wild type, mid log, MOPS rich + 0.2% glucose, replicate 2

source_name: Escherichia coli str. K-12 substr. MG1655


title: SUM159MDA231_RNAseq


title: CAL51_RNAseq

value: Basal-like cells


title: SUM159CAL51_RNAseq


title: SUM15921NT_RNAseq


title: CAL51MCF7_RNAseq


title: MDA-MB-231/MCF7_H3K27me3_ChIPSeq

data_processing:
Basecalls performed using the Illumina Genome Analyzer Pipeline.
ChIP-seq reads were aligned to the hg18 (March, 2006) human genome assembly using the Illumina Genome Analyzer Pipeline with default configuration. All reads that passed quality filtering and mapped with two or fewer mismatches were retained.
peaks were called using SICER version 1.03 with the following setting: Window size (200bp), Gap size (600bp), Other parameters (default).
Genome_build: hg18
Supplementary_files_format_and_content: Bed file format for aligned chip-seq reads. ChIP-seq reads were aligned to the hg18 (March, 2006) human genome assembly using the Illumina Genome Analyzer Pipeline with default configuration. All reads that passed quality filtering and mapped with two or fewer mismatches were retained.
Supplementary_files_format_and_content: Bed file format (with appendix .probscoreisland.bed) for ChIP-Seq peaks detected by SICER. Peaks were called using SICER version 1.03 with the following setting: Window size (200bp), Gap size (600bp), Other parameters (default). Each raw represents each peak detected by SICER. Each column represents chrom, start, end and enrichment_score calculated by SICER.

extract_protocol: Following cell purification, cells were immediately cross-linked with formaldehyde (final concentration is 0.5%) at room temperature for 10 minutes. Cells were washed, lysed, and sonicated using a Bioruptor (Diagenode). The sonicated lysates were incubated with a specific antibody for 8 hours. The immunoprecipitates were sequentially washed, reverse-crosslinked, and purified by phenol-chloroform extraction and ethanol precipitation. ChIP-ed DNA was end-repaired by END-It DNA End Repair Kit (Epicentre), and 'A' base was added to 3'-ends by Klenow fragment. 1:10 diluted Adaptor oligo mix (ChIP-Seq Sample Preparation Kit, Illumina) were ligated using T4 DNA ligase HC (Invitrogen), and subjected to PCR amplification (18 cycles) using specific primers provided in the kit (Illumina). Fragments ranging from 150-300 bp were isolated from 8% polyacrylamide gel, and then sequenced by Illumina Genome Analyzer.

tag: chip antibody

value: Millipore


title: Gallus gallus_CHL6_JIIT14DS1_HH40

city: Noida

first: vibha

last: rani

state: UP

address: A-10, sector 62

department: Biotechnology

country: India

institute: Jaypee Institute of Information Technology

description:
small RNA
CHL6

data_processing:
The sequence retrived after high throughput sequencing using illumina platform was further aligned with chicken genome  using TopHat alignment and cufflinks assembly
Small RNA's (piRNA, miRNA, miRNA like, snoRNAs and snRNAs)annotations using Software Rfam
Identification of known and novel miRNAs using miRBase 19.0v database
miRNA target prediction using Target scan 6.0v and miRanda
Expression analysis for known and novel miRNAs using RNA Express

organism: Gallus gallus

source_name: Heart _HH40

growth_protocol: Fertilized Gallus gallus chicken eggs were obtained from Hatcheries, Faridabad, Haryana, India. The eggs were incubated in an incubator at 37.5°C with more than 90% humidity and with rotations every 6 h. Chick embryos were collected at days four, six, eight, ten, twelve and fourteenth day of incubation [CHL1–CHL6] and selected to represent the embryonic developmental stages 24, 29, 34, 36, 38 and 40 respectively .

extract_protocol:
Total RNA was isolated from each six stage of developing chick heart and small RNA was isolated using Ambion mirVana miRNA Isolation Kit. The quality and Integrity of small RNA was checked by Agilent 2000 bioanalyzer. Small RNA cDNA was constructed for each six samples using ScriptSeq RNA-Seq Library Preparation Kit and libraries were constructed .
Total six cardiac heart libraries (CHL1 to CHL6) were prepared for deep sequencing and subsequent characterization. For that total RNA samples from each stage were prepared. The low-molecular- weight RNA was precipitated with PEG8000/NaCl. RNA was purified by polyacrylamide gel electrophoresis [PAGE] to elute molecules in the range of 18–30nt. The extracted RNAs were ligated to the 3′ adapter [TCGTATGCCGTCTTCTGCTTG]. The ligated RNAs from each library were eluted from 15% denatured polyacrylamide gel using 0.3N NaCl, followed by the ligation of 5′ adapter [GTTCAGAGTTCTACAGTCCGACGATC]. The samples were further used as templates for cDNA synthesis using small RNA v1.5 cDNA synthesis kit (illumine) by using primers complementary to 5’ and 3’ adapter sequences with 25 PCR cycles of 95°C for 30s, 50°C for 30s, and 72°C for 30s. The PCR products were extracted from the agarose gels using the Gel Extraction Kit [Qiagen]. For each heart developmental stage, equal quantities [20μg] of small RNA were submitted to Illumina Inc.for small RNA deep sequencing.

tag: tissue

value: heart

tag: developmental stage


title: ZR75_ChIPSeq_Input

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie2 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig format: refer to UCSC file format FAQ (http://www.genome.ucsc.edu/FAQ/FAQformat.html#format6.1)

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. ChIPseq libraries were prepared by following Rubicon Thruplex-FD kit. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by PAGE gel electrophoresis and purified.

tag: chip-antibody

value: Input


title: SUM159_MCF7_ChIPSeq_Input


title: T47D_ChIPSeq_Input


title: Gallus gallus_CHL5_JIIT12DS1_HH38

description:
small RNA
CHL5

source_name: Heart _HH38


title: SUM159_ZR75_ChIPSeq_Input


title: T-47D_H3K27me3_ChIPSeq


title: SUM159_T47D_ChIPSeq_Input


title: SUM159PT/MCF7_H3K27me3_ChIPSeq


title: Gallus gallus_CHL4_JIIT10DS1_HH36

description:
small RNA
CHL4

source_name: Heart _HH36


title: SUM159PT_H3K27me3_ChIPSeq


title: MDA231_MCF7_ChIPSeq_Input


title: SUM159_BT474_ChIPSeq_Input


title: MDA231_ChIPSeq_Input


title: MCF7_H3K27me3_ChIPSeq


title: SUM159PT/T-47D_H3K27me3_ChIPSeq


title: eTMgly3-glycerol-2

data_processing:
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing
bowtie2 v2.1.0 was used for alignment
cuffdiff v2.2.1 was used for normalization, FPKM determination, and differential expression analysis. Note that the wild type was processed with the glucose evolved cultures seperately from the processing done on glycerol adapted cultures.
Genome_build: NC_021214
Supplementary_files_format_and_content: .diff file from the cuffdiff package

organism: Thermotoga maritima MSB8

source_name: eTMgly3, mid log, glycerol minimal media, replicate 2

growth_protocol: Cells were grown anerobically at 80 °C in batch bioreactors with continuous pH control and 80% N2/20% CO2 gas sparging. The pH set point was set to 6.5.

extract_protocol:
Total RNA was isolated via enzymatic lysis followed by purification with Qiagen's Rneasy Kit with on column Dnase treatment.
Strand-specific paired-end librariries were constructed using the "dUTP" methods. Breifely, rRNA depletion was performed using Epicentre's RiboZero kit. Depleted RNA was then fragmented, primed with random hexamers, and reverse transcribed. Second strand synthesis was performed with incorporation of dUTPs instead of dTTPs. This creates a marker on the second strand for enzymatic degradation of this strand producing strand specific libraries. After second strand synthesis, end-repair, dA tailing, adaptor ligation, USER treatment and PCR enrichment were performed.

treatment_protocol: Total RNA was stabilized by harvesting cells in 10% v/v of 95% EtOH/5% Trizol solution. Cells were then centerifuged and stored at -80 °C until the time of RNA extraction.

tag: culture

value: glycerol-adapted culture,eTMgly3


title: BT-474_DGE

data_processing:
Reads were aligned to UCSC gene tracks using IndexDPgenomic (hg18). Reads aligning to ribosomal and mitochondrial transcripts were discarded. Aligned reads were normalized to reads per million for comparison. No length correction was performed.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include normalized count for each gene. Aligned reads were normalized to reads per million for comparison. No length correction was performed.

extract_protocol: PolyA+ RNA was extracted from breast cancer cells using a micro-MACS RNA purification kit (Miltenyi Biotec). Helicos DGE libraries were constructed following the manufacturer’s protocols. Briefly, 250ng of polyA RNA was converted to first strand cDNA molecules, and digested. The cDNA molecules were modified with PolyA tails of a controlled length and modified with a dideoxy nucleotide. The modified cDNA molecules were subjected to sequencing by the Helicos Heliscope system.


title: CAL51_ChIPSeq_Input


title: eTMgly2-glycerol-2

source_name: eTMgly2, mid log, glycerol minimal media, replicate 2

value: glycerol-adapted culture,eTMgly2


title: ZR75_ChIPSeq_H3K27Ac

value: H3K27Ac (Abcam, ab4729)


title: MCF7_ChIPSeq_Input


title: Gallus gallus_CHL2_JIIT6DS1_HH29

description:
small RNA
CHL2

source_name: Heart _HH29


title: Gallus gallus_CHL3_JIIT8DS1_HH34

description:
small RNA
CHL3

source_name: Heart _HH34


title: Gallus gallus_CHL1_JIIT4DS1_HH24

description:
small RNA
CHL1

source_name: Heart _HH24


title: MDA-MB-231_DGE

source_name: Breast cancer cells


title: eTMgly2-glycerol-1

source_name: eTMgly2, mid log, glycerol minimal media, replicate 1


title: CAL51_MCF7_ChIPSeq_Input


title: eTMgly3-glycerol-1

source_name: eTMgly3, mid log, glycerol minimal media, replicate 1


title: Hs578T_DGE


title: eTMgly1-glycerol-2

source_name: eTMgly1, mid log, glycerol minimal media, replicate 2

value: glycerol-adapted culture,eTMgly1


title: SUM159_ZR75_ChIPSeq_H3K27Ac


title: eTMgly1-glycerol-1

source_name: eTMgly1, mid log, glycerol minimal media, replicate 1


title: hda6-6 rep2  BS-seq

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

description: Bisulfite-treated genomic DNA

data_processing:
BS-Seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics) to TAIR8 chr1..5/C/M, allowing up to 2 mismatches and retaining only uniquely-mapping reads. Identical reads were collapsed into single reads. Only reference genome cytosines covered with at least 4 reads were considered for analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: Presented as a single base-pair resolution UCSC genome browser wiggle file for each nuclear genome (1-5), where column 1 is the genomic coordinate of the cytosine and column 2 is the methylation level #C/(#C+#T).
Supplementary_files_format_and_content: For each genotype, three wiggle files were generated. Where each file represents data of methylation levels in three sequence contexts (CG, CHG, CHH)

organism: Arabidopsis thaliana

source_name: 3wk-old leaf tissue

extract_protocol: Fragmented genomic DNA library as described in Cokus et al., Nature 2008, except directly with pre-methylated final adapters (see Feng et al., Methods Mol. Biol. 2011;733:223-38 for further information)

treatment_protocol: Genomic DNA was extracted using Qiagen DNeasy Mini Kit.

tag: ecotype

value: Columbia

value: leaf


title: eTMglc3-glucose-2

source_name: eTMglc3, mid log, glucose minimal media, replicate 2

value: glucose-evolved culture eTMglc3


title: T47D_ChIPSeq_H3K27Ac

value: Luminal cells


title: eTMglc3-glucose-1

source_name: eTMglc3, mid log, glucose minimal media, replicate 1


title: SUM159PT_BT-474_DGE


title: WT for hda6 BS-seq

description: Bisulfite-treated genomic DNA

value: Wild type


title: hda6-6 rep1 BS-seq

description: Bisulfite-treated genomic DNA


title: SUM159PT_DGE


title: SUM159PT_T-47D_DGE

value: Heterofusion


title: SUM159_BT474_ChIPSeq_H3K27Ac


title: eTMglc2-glucose-1

source_name: eTMglc2, mid log, glucose minimal media, replicate 1

value: glucose-evolved culture eTMglc2


title: eTMglc1-glucose-1

source_name: eTMglc1, mid log, glucose minimal media, replicate 1

value: glucose-evolved culture eTMglc1


title: Pre-dormancy stage 1 whole seed

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description:
Whole seeds 0.8 - 1.0 cm in length and have fresh weight between 150 - 260 mg were collected. The embryo starts to dry up and the seed coat is hard to peel off.
AA2

data_processing:
Basecalls performed using RTA version 1.12.4.2
Original data file from the Illumina sequencing pipeline.  Each lane of sequencing is attached as an individual compressed file.  The sequence data are in the QSEQ format
We aligned the raw reads to a pre-processed reference genome using BS Seeker [Chen et al. BMC Bioinformatics (2010)] allowing for two mismatches.  The pre-processed reference genome consisted of sequences from the soybean genome (Glyma version 1.0.1) [Schmutz et al. Nature (2010)] obtained from the Phytozome website (http://phytozome.net), soybean chloroplast genome (GenBank: DQ317523), lambda reference genome (GenBank: J02459), and Phi-X174 reference genome (GenBank: J02482).
Reads containing three consecutive methylation in the non-CG sites were removed, possibly representing non-converted cytosines (Cokus et al. Nature 2008). Clonal reads possibly arising during the PCR amplification step were collapsed into one read.
Methylation level of sampled cytosine was calculated as (methylated calls / (methylated calls + unmethylated calls)).
Genome_build: Glyma version 1.01
Supplementary_files_format_and_content: tab-delimited text file including methylation level of each sampled cytosine

organism: Glycine max

source_name: Soybean seeds containing cotyledon (COT) stage embryos

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010).  Whole seeds containing globular (GLOB) stage, cotyledon (COT), early- (EM), mid- (B1), and late- (AA1) maturation stage embryos were collected. Whole dry (DRY) seeds containing dormant embryos were also collected.  For seedlings, seeds were sown on soil and after six days after imbibition, the whole seedlings and the cotyledons of seedling were manually collected.

extract_protocol: Harvested seeds were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al.,  Plant Physiol.132. 27-35 (2003)).  Seed compartment was captured from ten-micron sections using a Leica LMD6000.  Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA).  Approximately 300 nanogram of genomic DNA was subjected to library preparation following the methods of Hsieh et al. (Hsieh T-F et al. 2009. Science 324:1451-1454) with modifications.  We spiked-in ~ three nanogram of unmethylated lambda DNA (Promega) to serve as a control for complete bisulfite conversion.  Adapter-ligated genomic DNA was subjected to two rounds of bisulfite (BS) treatment using the EpiTect kit (Qiagen, Valencia, CA).  BS-treated DNA was purified using AMpure XP beads (Beckman) and PCR-amplified for 10 cycles using ExTaq (EpiCentre) DNA polymerase.  PCR-amplified DNA fragments were size selected using the AMpure XP beads (Beckman).  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: cultivar

value: Williams 82

value: pre-dormancy stage 1 (PD1)


title: CAL51_MCF7_ChIPSeq_H3K27Ac


title: T-47D_DGE


title: Cotyledon of seedling biological replicate 3

description:
Cotyledons were carefully collected from seedlings six days after imbibition.
SDLG-COT

source_name: Soybean cotyledons of Seedling six days after imbibition

value: seedling cotyledons (SDLG-COT)


title: Seedling biological replicate 3

description:
Whole seedlings were collected six days after imbibition.
SDLG

source_name: Soybean seedling six days after imbibition

value: post-germination seedling (SDLG)


title: SUM159_T47D_ChIPSeq_H3K27Ac


title: Cotyledon of seedling biological replicate 2


title: Late-maturation stage whole seed biological replicate 2

description:
Whole seeds 1.2 - 1.5 cm in length and have a fresh weight between 230 - 350 mg were collected.  The entire embryo is yellow including the axis and cotyledons.
AA1

source_name: Soybean seeds containing late-maturation (LM) stage embryos

value: late-maturation stage (LM)


title: hda6-7  BS-seq

description: Bisulfite-treated genomic DNA


title: MCF7_DGE


title: SUM159PT_MCF7_DGE


title: SUM159_MCF7_ChIPSeq_H3K27Ac


title: CAL51_ChIPSeq_H3K27Ac

value: Basal-like cells


title: Nasonia_giraulti_24h_adult_female

status: Public on Jun 08 2015

city: Ithaca

first: Andrew

last: Clark

address: 227 Biotech Building

institute: Cornell University

description: Illumina WGBS-seq

data_processing:
Illumina CASAVA 1.7 software was used for HiSeq2000 basecalling for N.vit data and Illumina CASAVA 1.8.2 software was used for HiSeq2000 basecalling for N.gir data.
Illumina read QC was performed using FastQC software. Adapter containing reads were trimmed by Trimmomatic.
We built C->T converted reference genomes for both the Watson (+) and Crick (-) strand for Nasonia vitripennis reference genome, with all Cs in CpGs context remains Cs (meth_genome) and all CpG Cs converted to Ts (unmeth_genome).
Illumina sequencing reads were aligned to the converted genomes using BWA with a maximum of 4 mismatches for N.vit and 6 mismatches for N.gir. ~85% of all the reads were aligned to the converted genomes in both species and only ~65% uniquely mapped to the genome were kept for the methylation analysis. For uniquely mapped reads with indels, we queried the indel position against the indel database and unmatched spurious indels due to misalignment were excluded. In the end, 50-60% reads survived these QC filtering steps and they were summarized in a single BAM file for methylation analysis.
Of the 14,024,488 CpG sites in Nasonia haploid genome, we only included CpG sites covered by Illumina genome DNA sequencing data (on samples without bisulfite treatment) in our analysis. CpGs sites located in a potential repetitive region were also excluded. Base counts were summarized at 13,451,035 alignable CpGs in N.vit and 9,742,004 alignable CpGs in N.gir.
Genome_build: Nvit_1.0 scaffold
Supplementary_files_format_and_content: gzipped tab-delimited text file includes the C and T counts at alignable CpG positions in Nasonia vitripennis and Nasonia giraulti genome.

organism: Nasonia giraulti

source_name: 24h adult Nasonia giraulti female whole body

extract_protocol:
Genomic DNA samples were extracted from a pool of 50 adult whole-body samples 24 hour following eclosion from N.vit (strain AsymCX) and N.gir (strain R16A) males and females, using DNeasy Blood & Tissue Kit (Qiagen, CA).
Whole-genome bisulfite sequencing libraries were made according to the Illumina protocols (WGBS for Methylation Analysis Guide, Part# 15021861 Rev. A) with 15 ug of starting genomic DNA and Illumina TruSeq adapters.

value: 24-hour adult

value: whole body

tag: Sex

value: female


title: Nasonia_giraulti_24h_adult_male

description: Illumina WGBS-seq

source_name: 24h adult Nasonia giraulti male whole body

value: male


title: Nasonia_giraulti_24h_adult_male_replicate3

description: Illumina RNA-seq

data_processing:
Illumina CASAVA 1.8.2 software was used for basecalling.
Illumina reads QC was performed using FastQC software. Adapter containing reads were trimmed by Trimmomatic.
Illumina short reads were aligned to N.vit and N.gir reference genomes (v1.0) respectively using TopHat v2.0 and ~90% of them were uniquely mapped to the genome scaffolds. Counts of aligned reads in Nasonia OGS2 (official gene set 2) transcripts were summarized by Cufflinks v2.1.0 and reads mapped to multiple places in the genome were weighted by the “-u” parameter. We also summarized the counts from uniquely mapped reads only to eliminate the problems caused by paralogs to extremely highly expressed genes. By gene reads counts were summaried by two additional softwares, HTSeq and BEDTools. Read counts for only less than 30 genes disagree among all three and we manually corrected them. These read counts were fed into the edgeR package in Bioconductor. Normalization was performed and total expression level were calculated using edgeR.
Genome_build: Nvit_1.0 scaffold
Supplementary_files_format_and_content: Tab-delimited by gene read counts in Nasonia vitripennis and Nasonia giraulti adult male and female RNA-seq data for expressed nasonia OGS2 (official gene set 2) genes.

extract_protocol:
Total RNA samples were extracted from a pool of 10 adult whole-body samples 24 hour following eclosion from N.vit (strain AsymCX) and N.gir (strain R16A) males and females, using Qiagen RNeasy Plus mini kit (Qiagen, CA). Three independent batches biological replicates were performed and collected for each species and each sex.
RNA-Seq libraries were made from 2 ug total RNA input using TruSeq RNA Sample Preparation Kits v2 (Illumina Inc., CA)


title: SUM159_ChIPSeq_H3K27Ac

value: H3K27Ac (Abcam, ab4729)

tag: cell line


title: Seedling biological replicate 2


title: eTMglc2-glucose-2

source_name: eTMglc2, mid log, glucose minimal media, replicate 2


title: MDA231_ChIPSeq_H3K27Ac

source_name: Breast cancer cells

tag: cell type


title: MDA231_MCF7_ChIPSeq_H3K27Ac


title: TM-wt-glucose-2

source_name: wild type, mid log, glucose minimal media, replicate 2

tag: strain

value: wild type


title: eTMglc1-glucose-2

source_name: eTMglc1, mid log, glucose minimal media, replicate 2


title: MCF7_ChIPSeq_H3K27Ac

value: Luminal cells


title: Nasonia_giraulti_24h_adult_female_replicate3

description: Illumina RNA-seq


title: PhoB_deletion_mutant_sample1

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

country: Germany

institute: Technische Universität Braunschweig

description:
Custom strand-specific RNA-seq protocol.
PhoB mutant rep1.

data_processing:
Sequenced ChIP-seq reads were trimmed for adaptor sequence allowing for a minimal quality of 10 at their ends, then mapped to the UCBP-PA14 genome using bowtie v0.12.7 with default parameters.
RNA-seq reads were mapped to the UCBP-PA14 genome using the stampy aligner with default settings.
ChIP-seq peaks were called using the MACS algorithm with the following options: -g 5200000 –nomodel --shiftsize=30 -p 0.05
Differential expression was estimated using the DESeq R library.
For detection of differentially expressed genes, both replicates for each condition were used for testing for differential expression with DESeq. The ChIP-seq peaks were detected superposing the treated against the control sample.
Genome_build: ASM1462v1 (gi|116048575|ref|NC_008463.1|)
Supplementary_files_format_and_content: Artemis browser files containing the read pileup at each genomic position covered in the ChIP-seq experiments. File format: <genomic coordinate> <number of reads on + strand> <number of reads on - strand>.
Supplementary_files_format_and_content: Processed RNA-seq data includes the raw read counts for each gene.

organism: Pseudomonas aeruginosa UCBPP-PA14

source_name: UCBP-PA14 bacterial culture, PhoB mutant

growth_protocol: UCBP-PA14 strains in DeMoss minimal medium under low-phosphate conditions at 37°C and 180 r.p.m. until OD600=2.0.

extract_protocol:
Using RNeasy kit (Qiagen) plus Qiashredder columns.
Customized protocol (Dötsch et al., PloS ONE, 2012). Briefly, rRNA depletion using MICROBExpress kit with the Pseudomonas module (Ambion) and fragmentation by sonication using Covaris Adaptive Acoustics device (Covaris). Upon ligation of barcoded adapters, reverse transcription with SuperScript II kit (Invitrogen) followed. Amplification was done by PCR using Illumina platform compatible primers. Established cDNA library was normalized by double-strand-specific nuclease treatment (Evrogen) according to DSN Normalization Sample Preparation Guide from Illumina.

treatment_protocol: Cells from 3 pooled cultures were harvested by addition of the same volume of RNA-protect buffer (Qiagen) and centrifugation.

tag: strain/background

tag: genotype/variation

value: phoB deletion mutant


title: TctD_transposon_mutant_sample2

description:
Custom strand-specific RNA-seq protocol.
TctD mutant rep2.

source_name: UCBP-PA14 bacterial culture, TctD mutant

value: tctD transposon mutant


title: PA14_wildtype_sample2

description:
Custom strand-specific RNA-seq protocol.
Wild type rep2.

source_name: UCBP-PA14 bacterial culture, WT

value: WT


title: PhoB_control

description:
ChIP-seq using Illumina platform.
ChIP-seq control.

source_name: UCBP-PA14 bacterial culture, vector only, 6XHis ChIP

extract_protocol:
Polyhistidine-tagged sample was isolated by using anti-6XHis antibodies (Abcam, cat.# ab9108, lots GR67062-1 and GR76800-1) and magnetic beads coupled with protein-G (Invitrogen) on a rotator.
Immunoprecipitated DNA was linear amplified similar to the LinDA-ChIP-seq protocol published by Shankaranarayanan et al., Nature protocols, 2012. Library was constructed using the TruSeq DNA sample preparation kit according to the low-throughput protocol (Illumina).

treatment_protocol: DNA-protein crosslinking was performed by addition of formaldehyde to a final concentration of 0.5% for 5 minutes at ambient temperature. Reaction was quenched by addition of glycine to a final concentration of 137 mM. Cells were lysed in lysis buffer containing EDTA and lysozyme. Cells were disrupted and DNA was sheared by sonication.

value: WT (empty vector)

value: anti-6X His tag


title: PhoB_deletion_mutant_sample2

description:
Custom strand-specific RNA-seq protocol.
PhoB mutant rep2.


title: MDA-MB-231_MCF7_DGE

value: Heterofusion


title: Late-maturation stage whole seed biological replicate 3

value: Williams 82


title: Pre-dormancy stage 2 whole seed

description:
Whole seeds with fresh weight less than 150 mg were collected. The embryo is round and not totally dry.
AA3

source_name: Soybean seeds containing early maturation (EM) stage embryos

value: pre-dormancy stage 2 (PD2)


title: TM-wt-glucose-1

source_name: wild type, mid log, glucose minimal media, replicate 1


title: fetal_beta_6

city: Berkeley

first: Shaked

last: Afik

address: Stanley Hall

department: Computational Biology Graduate Group

institute: UC Berkeley

description: Sample 24

data_processing:
Bowtie 2 was used to remove reads aligning to rRNA sequences by allowing up to 1 mismatch with multiple mappers.
Remaining reads were aligned by RSEM to a human transcript reference file generated using UCSC RefSeq annotations downloaded May 10, 2014.  RSEM was then used to calculate total and normalized reads per gene using the following parameters, in addition to defaults: -n 2 for maximum number of mismatches, -e 70 for maximum sum of mismatch quality scores across the alignment, -l 25 for minimum read or insert length allowed, --chunkmbs 500 for memory allocated for best first alignment calculation, -p 4 for number of threads to use, and -m 200 for alignment suppression if > 200 valid alignments exist for a read.
Genome_build: hg19
Supplementary_files_format_and_content: rna.seq.tpm.xlsx includes normalized gene expression measurements (TPM) for each gene in each sample. The file was created using RSEM as described in the data processing step above.

source_name: fetal beta cells

growth_protocol: Adult human islets were obtained from the Integrated Islet Distribution Program (IIDP) or Prodo Laboratories, Inc. Fetal tissues (12-18 gestational weeks) were obtained from Advanced Bioscience Resources or StemExpress (some tissues were pooled). Pancreata were minced and incubated with Dispase for 10 min at 37°C. The tissue was gently disrupted using a blunt 14 gauge needle, incubated for another 30-40 min with digestion stopped (EDTA to 5mM).

extract_protocol:
Sorted adult cells were pelleted and digested using the Ambion RecoverAll Total Nucleic Acid Isolation Kit. RNA was quantified and analyzed for RNA Integrity Number (RIN) using the Agilent 2100 Bioanalyzer and 6000 Pico Chip. Sorted fetal cells were pelleted and resuspended in TE buffer containing 0.5% SDS and 0.8µl of 20 mg/ml Proteinase K (Roche). Cells were incubated at 65°C for 2 h and total RNA isolated using phenol/chloroform extraction, aqueous phase precipitation with isopropanol and columns (Qiagen).
For adult islet alpha and beta subsets (samples 1-3) and fetal b cell populations, up to 100 ng of RNA for each cell population was isolated. Libraries were constructed by RNA fragmentation, 1st and 2nd strand cDNA synthesis, adaptor ligation, amplification, library validation, and ribosomal RNA removal by double stranded nuclease digestion (Beijing Genomics Institute). Sequencing for adult and fetal was performed on the Illumina HiSeq 2000 and TruSeq platforms, respectively. Total RNA isolated from fetal a cell subsets (1 ng) and adult islet cell subsets (5 ng, samples 4-7) was processed using Nugen Ovation RNA-Seq System V2 and Ovation Ultralow DR Multiplex Systems 1-8. Quantitative and qualitative assessments of cDNA libraries were performed using an Agilent DNA 1000 chip. Libraries were sequenced using the Illumina HiSeq 2000, and 20 million clean reads were acquired/sample.

treatment_protocol: Adult Islet dissociation and intracellular antibody staining used a protocol with modifications included using TrypLE (Invitrogen) for dissociation, and incubating antibodies with RNasin for 30 min prior to adult tissue staining. Anti-insulin (Gallus Immunotech), anti-chicken allophycocyanin, (APC, Jackson ImmunoResearch), and Zenon (Invitrogen) conjugated anti-glucagon (Sigma-Aldrich) with Pacific Blue, and anti-somatostatin (LSBio) with Zenon AlexaFluor488 were used to stain b, a, and d cells, respectively. Fetal cells were filtered, washed twice with PBS containing 5 mM EDTA, fixed, and covered for 10 min with Fixation Permeabilization solution (BD Biosciences) with 20µl of RNAseOUT (Invitrogen) and 10µl RNA Later (Invitrogen) at 4°C. Fixed cells were washed twice with 1xBD Wash Buffer (BD Bioscience) with ultra-pure grade BSA (0.2%, Invitrogen), and RNAseOUT. Antibodies against insulin (Fitzgerald), glucagon (Sigma-Aldrich) and somatostatin (Genetex) were conjugated to Zenon Alexa Fluor 647, R-Phycoerythrin or Pacific Blue, respectively. Antibody cocktails (antibodies in 1xBD washing solution with 20µl RNaseOUT) were added to cells, and incubated at 4°C in the dark with gentle shaking for 25-30 min. Cells were washed twice with 1xBD wash buffer with 0.2% of BSA and RNaseOUT, once in PBS, and resuspended in PBS with RNaseOUT. Adult and fetal cell preparations were sorted using a BD Biosciences FACS Aria II (UMASS Medical School Flow Core Laboratory). Cells were sorted into PBS containing 0.5% BSA and RNasin (Promega). For adult tissues, the purified α and β cell positive populations were resorted and quantified to determine cell purity of each cell subset (>97% pure). RNA was extracted from enriched α, β, and δ fetal cell types and purity was assessed by qRT-PCR.

value: fetal (12-18 gestational weeks)

value: beta cells


title: Dry seed biological replicate 2

description:
Whole dry seeds
Dry

source_name: Dry soybean seeds

value: dormancy stage (DRY)


title: fetal_beta_4

description: Sample 22


title: fetal_alpha_5

description: Sample 18

source_name: fetal alpha cells

value: alpha cells


title: fetal_beta_1

description: Sample 19


title: fetal_alpha_2

description: Sample 15


title: fetal_alpha_1

description: Sample 14


title: PhoB_chip

description:
ChIP-seq using Illumina platform.
ChIP-seq treated.

source_name: UCBP-PA14 bacterial culture, polyhistidine-tagged phoB, 6XHis ChIP

value: WT overexpressing polyhistidine-tagged phoB


title: adult_alpha_7

description: Sample 13

source_name: adult alpha cells

value: adult


title: Nasonia_giraulti_24h_adult_female_replicate1

description: Illumina RNA-seq

source_name: 24h adult Nasonia giraulti female whole body

value: 24-hour adult

value: whole body

value: female


title: TctD_transposon_mutant_sample1

description:
Custom strand-specific RNA-seq protocol.
TctD mutant rep1.


title: Nasonia_giraulti_24h_adult_male_replicate2

description: Illumina RNA-seq

source_name: 24h adult Nasonia giraulti male whole body

value: male


title: PA14_wildtype_sample1

description:
Custom strand-specific RNA-seq protocol.
Wild type rep1.


title: adult_alpha_5

description: Sample 11


title: Nasonia_giraulti_24h_adult_male_replicate1

description: Illumina RNA-seq


title: adult_alpha_4

description: Sample 10


title: Nasonia_giraulti_24h_adult_female_replicate2

description: Illumina RNA-seq


title: fetal_beta_3

description: Sample 21


title: adult_beta_7

description: Sample 7

source_name: adult beta cells


title: fetal_beta_2

description: Sample 20


title: fetal_alpha_4

description: Sample 17


title: adult_beta_1

description: Sample 1


title: adult_beta_6

description: Sample 6


title: fetal_alpha_3

description: Sample 16


title: adult_alpha_6

description: Sample 12


title: fetal_beta_5

description: Sample 23


title: adult_beta_3

description: Sample 3


title: adult_alpha_1

description: Sample 8


title: Nasonia_vitripennis_24h_adult_male_replicate3

description: Illumina RNA-seq

organism: Nasonia vitripennis

source_name: 24h adult Nasonia vitripennis male whole body


title: input DNA

city: Houston

first: Toni-Ann

last: Mistretta

address: 1 Baylor Plaza, BCM 315

department: Pathology

institute: Baylor College of Medicine

data_processing:
Amplified DNAs (DNA libraries) were sequenced on the Illumina Genome Analyzer II.
Sequences (36 nt reads, single end) were aligned to the human genome (hg19) using the BWA algorithm
The resulting histograms (genomic “signal maps”) were stored in BAR (Binary Analysis Results) files
Peak locations were determined using the MACS algorithm with a cutoff of pvalue = 1e-7.
Genome_build: hg19
Supplementary_files_format_and_content: Binary Analysis Results and text files containing BAR file contents

source_name: HT29 cells

growth_protocol: Over night cultured HT-29 cells with DMEM (Lonza) containing 10% FCS (Lonza)

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer.  Lysates were sonicated and the DNA sheared to an average length of 300-500 bp.
ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3’ ends.  Illumina adaptors were added and the library was size-selected (175-225 bp) on an agarose gel. The adaptor-ligated libraries were amplified for 18 cycles. The resulting amplified DNAs were purified, quantified, and tested by QPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions.

value: Human colorectal cancer

value: none (input)


title: Nasonia_vitripennis_24h_adult_male_replicate2

description: Illumina RNA-seq


title: Nasonia_vitripennis_24h_adult_female_replicate3

description: Illumina RNA-seq

source_name: 24h adult Nasonia vitripennis female whole body


title: adult_alpha_3

description: Sample 9


title: Nasonia_vitripennis_24h_adult_female_replicate2

description: Illumina RNA-seq


title: adult_beta_2

description: Sample 2


title: Nasonia_vitripennis_24h_adult_male (HiSeq 2000)

description: Illumina WGBS-seq


title: IgGa

city: University of Helsinki

first: Henna

last: Heinonen

address: PO Box 63

country: Finland

institute: University of Helsinki

description: Chromatin IP against IgG

data_processing:
Alignment: Sequence reads were obtained, purity filtered using the Illumina Genome Analyzer Pipeline and mapped to the human (Feb, 2009) genomes using BOWTIE. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/). Two lanes for each HOXB7 replicate and four lanes of IgG were concataned before peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: Processed peak files in BED format

source_name: BT-474 cells

growth_protocol: DMEM medium of BT-474 was supplemented with 15% FBS, 1% 100 mM sodium pyruvate, 1 % 200 mM L-glutamine and 1% Pen-Strep (penicillin 10 000 U/ml, streptomycin 10 000 µg/ml).

extract_protocol: Lysates were clarified from sonicated nuclei and DNA-protein complexes were isolated with respective antibodies. 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 (3' to 5' exo minus) 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 DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: ChIP antibodies: HOXB7 (H0291, Sigma-Aldrich), anti-rabbit IgG (20009-5, Alpha Diagnostic International)

value: Breast cancer cells derived from ductal carcinoma

tag: passages

value: rIgG (20009-5, Alpha Diagnostic International)


title: IgGd

description: Chromatin IP against IgG


title: HOXB7_AF2b

description: Chromatin IP against HOXB7

value: HOXB7 (H0291, Sigma-Aldrich)


title: IgGc

description: Chromatin IP against IgG


title: IgGb

description: Chromatin IP against IgG


title: HOXB7_AF2a

description: Chromatin IP against HOXB7


title: Nasonia_vitripennis_24h_adult_male_replicate1

description: Illumina RNA-seq


title: HOXB7_AF1b

description: Chromatin IP against HOXB7


title: H3K27ac_pDC

city: St Louis

first: Gary

middle: E

last: Grajales-Reyes

state: Mo

address: Room 7766, CSRB

department: Immunology

institute: Washington University in St. Louis

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were alignted using Bowtie 1.0.1
Uniquely mapped reads were masked using samtools with blacklist of ENCODE project and RepeatMasker in the UCSC genome browser
Bedgraph were made using makeUCSCfile program of the Homer Software package
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph

source_name: Flt3L cultured dendritic cells

growth_protocol: Bone marrow was harvested with mortar and pestle. Afterlysing red blood cells, whole bone maroow was cultured in 100 ng/ml Flt3 ligand for 9 days.  CD24+DCs, CD172a+DCs and pDCs were sorted to >95% purity using by FACS AraFusion.  CD24 DCs: CD11c+ MHC II+ CD24+ CD172a- BST2- CD45RA-; CD172a DCs: CD11c+ MHC II+ CD24- CD172a+ BST2- CD45RA-, pDCs: BST2+ CD45RA+

extract_protocol:
For ChIP of p300, sorted cells were incubated in fresh media with Flt3L for 2 hours before crosslinking; for ChIP of IRF8, Batf3, H3K27ac, and H3K4me1, cells fixed before purification.  Cells were crosslinked with 1% formaldehyde, quenched with 1.25M Glycine, twice washed with PBS.  Chromatin was sonicated for shearing DNA size from 140 to 500 bp. Chromatin fragments were immunoprecipitated overnight at 4 °C with Dynabeads Protein A or G bound to anti-p300 (sc-585X, Santa Cruz Biotechnology), anti-IRF-8 (sc-6058x, Santa Cruz Biotechnology), or anti-Batf3, anti-H3K27ac (Ab 4729, Abcam) and H3K4me1 (Ab 8895, Abcam).  ChIPed DNA was eluted and reverse-crosslinked for 6 hr.  DNA was purified with phenol:chloroform extraction followed by ethanol precipitation.
Libraries for ChIP-seq were prepared using ThruPLEX-FD kit (Rubicon Genomics) and sequenced using Illumina HiSeq 2500 as single reads extending 50 bases.

value: pDC

tag: antibody vendor/catalog#

value: Ab 4729, Abcam


title: Input

value: whole cultured cells


title: H3K4me1_pDC

value: Ab 8895, Abcam


title: adult_beta_5

description: Sample 5

value: beta cells


title: p300_pDC

value: sc-585X, Santa Cruz Biotechnology


title: HOXB7_AF1a

description: Chromatin IP against HOXB7


title: SOX9_ChIPSeq

value: SOX9  (Millipore, AB5535)


title: Irf8_pDC

value: sc-6058x, Santa Cruz Biotechnology


title: p300_CD172DC


title: H3K27ac_CD172DC


title: adult_beta_4

description: Sample 4

value: adult


title: Batf3_CD172DC


title: Nasonia_vitripennis_24h_adult_female_replicate1

description: Illumina RNA-seq

value: 24-hour adult

value: whole body