title: XP13

city: Berkeley

first: António Pedro

last: Gonçalves

address: 341A Koshland Hall

department: Plant and Microbial Biology

institute: University of California, Berkeley

data_processing:
Illumina Casava1.8.0 software used for basecalling.
Reads were mapped to known transcripts with Tophat v2.0.4 (options: --GTF)
Fragments Per exon Kilobase per Megabase read (FPKM) were calculated with Cufflinks v2.0.2 (options: -u -b -G --compatible-hits-norm --max-bundle-frags=100000000)
Differential Expression was estimated with Cuffdiff (options: -u -N -b --compatible-hits-norm --max-bundle-frags=100000000)
Genome_build: OR74A version 10 (call 5) from the Broad Institute (n_crassa_or74a__transcripts_plus_mito_jan_2012)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

organism: Neurospora crassa

growth_protocol: Conidial suspensions were obtained and 1 x 106 cells/ml incubated in minimal medium for 6 hours (26ºC, 140 rpm, constant light).

extract_protocol:
Cells were harvested using 0.45 μm filters and immediately frozen in liquid nitrogen. Total RNA was isolated by the Trizol-Phenol-Chloroform method. After digestion of 25 μg RNA with TURBO DNAse (Life Technologies), mRNA was purified using Dynabeads oligo(dT) magnetic beads (Life Technologies). The mRNA was chemically fragmented using the Ambion RNA fragmentation kit (Life Technologies). First and second strand cDNA synthesis was achieved using appropriate kits (Life Technologies).
The illumina TruSeq kit was employed to generate the cDNA libraries with indexing adapters essentially following the manufacturer’s protocol. After purification of the libraries with AMPure XP beads (Roche), the quality of the libraries was analysed in a Agilent 2100 Bioanalyzer.

treatment_protocol: Addition of drug (or DMSO) and growth for 1 more hour.

value: Wild type

tag: agent

tag: growth stage

value: 6h+1h conidia culture


title: TX129

status: Public on Nov 25 2015

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: strain


title: Mfa132-2

city: Shanghai

first: Zilong

last: Qiu

address: No.320, Rd. Yueyang

country: China

institute: Chinese Academic of Science

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.1.6 mapping to reference genome
Counts counting
Genome_build: mfa5.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Macaca fascicularis

source_name: brain tissue of aborted newborn wild-type monkey

extract_protocol:
Total RNA was extracted from brain tissues of wild-type or MECP2 transgenic monkey by Trizol reagent (Invitrogen) separately.
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

tag: tissue

value: cortical region

tag: age

tag: genotype

value: wild-type


title: TX34


title: D1


title: Norm High Sensitive

city: Moscow

first: Alina

last: Artcibasova

address: Samory Mashela, 1

country: Russia

institute: Federal Research Center of Pediatric Hematology, Oncology and Immunology

data_processing:
FASTQ to FASTA conversion
The adapter sequence (5’-TGGAATTCTCGGGTGCCAAGG-3’) was clipped from the 3’-end of raw reads, and reads shorter than 16nt were discarded.
Remaining sequences were mapped to miRBase human microRNA reference using the short-read aligner Bowtie [19261174], up to two mismatches were allowed. The sequences that failed to map to the genome were mapped against the artificially introduced sequences. The multiplicity count of mapped sequences was normalized to the total number of reads that mapped to the genome.
Aligned reads were attributed to known microRNAs using processing with SAMTools
Prior analysis, quantile normalization was done for microarray gene expression data. AI and WI samples were treated as the "case" samples. Pre-experimental normal samples were used as the controls. The analysis was done separately for HCMV infection high and low sensitive cell cultures. The data were normalised using preprocessCore quantile normalisation in R.
Genome_build: miRBase human microRNAs
Supplementary_files_format_and_content: text file with mapped and normalized data for each sample

organism: Homo sapiens

source_name: human embryonic lung fibroblast (line HELF-977)

growth_protocol: The cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM, PanEco, Moscow, Russia) supplemented with 10% fetal bovine serum (FBS, PanEco), 2 mM L-glutamine and 50 ug/ml gentamicin at 37°C in 5% CO2. The cells were maintained by regular passages when confluence was reached. To obtain cells in G0 phase of cell cycle the cells of both lines were cultured in DMEM with 0.2% FBS for 48 hours.

extract_protocol:
Short RNA fractions were cloned from total RNA extracts. Non-coding RNAs within a 19–33 nt window were isolated from 12% polyacrylamide gels. 3’- and 5’-linkers were ligated, and products were reverse-transcribed using Superscript III (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols. Following PCR amplification, the libraries were sequenced using the Illumina GAIIx platform in accordance with Illumina protocols (Illumina, USA).

treatment_protocol: Cells HELF- 977 and HAF-1608 synchronized in G0 phase were infected with HCMV at multiplicity of infection of 3 or mock-infected. Viral inoculum was added to the cells and allowed to adsorb for 60 min at 37°C in 5% CO2. Then virus inoculum was removed and replaced with fresh medium.

tag: cell line

tag: sensitivity

value: High

value: embryonic lung fibroblast

tag: infection


title: Infected High Sensitive 3 hours after infection

value: HCMV at multiplicity of infection of 3


title: DMSO

description: wtDMSO

source_name: 6h+1h DMSO

value: DMSO


title: HeLa-Cas9

city: Toronto

first: Jason

last: Moffat

state: ON

address: 160 College St

department: CCBR

country: Canada

institute: University of Toronto

description: RNAseq of Cas9 knock-in

data_processing:
TopHat v2.0.13
command line:  tophat --transcriptome-index gencode.v19.annotation -T hg19 [fastq file]
Cufflinks v2.0.2
command ine:  cufflinks -G gencode.v19.annotation.gtf accepted_hits.bam
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet of log2(fpkm+0.01) for protein coding genes

source_name: HeLa

growth_protocol: HCT116 cells were maintained in McCoy’s 5A medium with L-glutamine (Life Technologies) supplemented with 10% FBS (Life Technologies) and 1% Penicillin/Streptomycin (Life Technologies). HeLa, DLD1, and hTERT RPE1 cells were maintained in DMEM with high glucose and pyruvate (Life Technologies) supplemented with 10% FBS (Life Technologies) and 1% Penicillin/Streptomycin (Life Technologies). The patient-derived GBM514 glioblastoma cell line was kindly provided by Peter Dirks’ laboratory at SickKids, Toronto. GBM cells were cultured as described in Pollard et al. 2009.

extract_protocol:
RNA was extracted from Cas9-expressing cell lines using TriReagent (Sigma) according to manufacturer's instructions
RNA sequencing libraries were prepared with Illumina TruSeq V2 RNA library preparation kit according to manufacturer's directions. Multiplexed libraries (HCT116 only) were sequenced on a single read High Output Illumina NextSeq500 flow cell (version 1 chemistry) with a read length of 61bp.

treatment_protocol: HCT116, HeLa, DLD1, hTERT RPE1 and GBM514 cells were infected with virus carrying the Cas9-2A-Blasticidin expressing cassette and infected cells were selected with blasticidin (5 ug/ml). After 10 days of selection, single cells were sorted onto 96-well plates with a BD FACS Aria IIu cell sorter at low pressure (20 PSI) using a 100 micron nozzle or by manual seeding of a single cell suspension at 0.6 cells/96 well plates. Independent clones were isolated and FLAG-Cas9 expression was determined using Western blot analysis.

tag: genotype/variation

value: Cas9 knock-in


title: shoot single-end

city: New York

first: Huan

last: Wang

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

description: directional single-end RNA-seq

data_processing:
After quality control analysis of raw sequencing datasets, RNA-seq sequences were aligned to the maize genome using TopHat. Then the mapped sequences of each sample were assembled by Cufflinks. Fragments per kilobase of exon per million fragments mapped of assembled transcripts (FPKM) were calculated and normalized using Cuffcompare and Cuffdiff with global normalization parameters.
Genome_build: Zea mays ssp. mays L., Maize Golden Path B73 RefGen_v2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all Samples

molecule: polyA RNA

organism: Zea mays subsp. mays

source_name: shoots

growth_protocol: Maize (Zea mays ssp. mays L.) B73 plants were grown in growth chamber of New York city at the Rockefeller University, and were harvested 14 days after germinationgermination. The shoot and root tissue were separately collected.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plant Mini kit. Total RNA was treated with Turbo DNase I (Life Technologies AM2238) according to product specification. DNase I treated RNA was then applied again to an RNeasy spin column with 0.5 volumes of ethanol, washed and eluted according to the manufacturer’s instructions.
Sequencing libraries were prepared using the Illumina Stranded mRNA sample Prep kit, set A (RS-122-2101, Illumina Inc.) according to the manufacturer's instructions.  The quality and size of cDNA libraries for sequencing were checked using the Agilent 2200 TapeStation system (Agilent Inc.). The libraries were sequenced for 100 cycles on HiseqTM 2500 (Illumina Inc.)

value: shoots

tag: developmental stage

value: sample harvested 14 days after germination


title: PARN_OE

city: Kansas City

first: Peter

last: Baumann

state: MO

institute: Stowers Institute for Medical Research

data_processing:
Library strategy: RLM-RACE-seq
Reads were filtered for non-hTR and hTR with sequencing error. Reads were kept if an exact match to at least 28 nucleotides of the 3' end of the hTR sequence was found.
Reads were binned and counted based on their hTR sequence. The counts were normalized to library size.
Supplementary_files_format_and_content: Percentages of hTR forms per sample.

molecule: genomic DNA

growth_protocol: HeLa cells were cultured in Dulbecco’s modified eagle medium (Life  Technologies 11995-065) containing 10% fetal bovine serum (Sigma) at 37°C, 5% CO2.

extract_protocol:
Cells were washed once with Dulbecco’s phosphate-buffered saline and  collected in Trizol reagent (Ambion, Life Technologies) according to manufacturer’s  instructions, followed by treatment with DNase I (New England Biolabs) at 37°C for 30  min. RNA was extracted with phenol/chloroform equilibrated with 50 mM NaOAc (pH  5.0) and ethanol precipitated.
Library preparation was modified from the protocol which published by Goldfard  and Cech (Goldfarb and Cech 2013). The samples were sequenced on the Illumina HiSeq using RapidSeq-100bp single-end  reads.

treatment_protocol: For siRNA knockdown,  cells were treated twice (two or three day interval) with 20 nM or 40 nM siRNA using  Dharmafect I (Dharmacon). For PARN overexpression, PARN-pCMV6-XL (Origene,  SC325208 ) was transfected into HeLa cells using Fugene HD (Promega) for 72 hours.

value: HeLa

tag: construct


title: Infected Low Sensitive 3 hours without infection

source_name: human adult skin fibroblasts (line HAF-1608)

value: Low

value: adult skin fibroblasts

value: mock


title: root single-end

description: directional single-end RNA-seq

source_name: roots

value: roots


title: AB395 [Sample 53]

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: single cell expression matrix include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: experimental_design.txt' associating each single cell with its amplification batch and index sorting readouts

organism: Mus musculus

source_name: Cebpa control

growth_protocol: 6 to 8 weeks-old mice housed at the Weizmann Institute animal facility (Samples 21-32 were 14 weeks old and housed at Biotech Research and Innovation Centre, Copenhagen)

extract_protocol:
Each mouse was euthanized and bone marrow harvested by crushing of the femur, tibia and ilia. Cell suspensions were cKit enriched with MACS magnetic beads.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation

treatment_protocol: For samples 21-22, 25-26, 31-32, mice were injected three times with 300 µg poly(I:C) three weeks before bone marrow harvest

value: C57BL/6 Cebpa(flox/flox)

tag: organ

value: bone marrow

tag: selection marker

value: Lin- cKit+ Sca1-

tag: treatment


title: AB396 [Sample 54]


title: siPARN

value: siPARN


title: AB394 [Sample 52]

value: C57BL/6 Cebpa(flox/flox)Mx1-Cre


title: Vector_PARN_OE


title: N131 Dnase1

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

description: Dnase-seq

library_source: genomic

data_processing:
Basecalls performed using RTA 1.7 or Illumina Casava1.7
DNase-seq reads were mapped to the mouse genome (mm9) using Bowtie2. The reads with MAPQ <=10 or redundant reads were removed from further analysis in each library.
We identified Dnase I hypersensitive sites in Enocode data and our small cell number Pico-seq data using MACS.
Genome_build: hg18
Supplementary_files_format_and_content: Bed: plan text file. Each line is one read. The six columns are chrom, start position, end position, length, alignment score and strand.

source_name: formalin-fixed paraffin-embedded tissue

growth_protocol: NIH/3T3 tet-on 3G cells (Clontech cat# 631197) were cultured in DMEM (Invitrogen cat# 10566-016) supplemented with 10% FBS ( Sigma cat# F4135-500ML) and 100U/ml Penicillin-Streptomycin (Invitrogen cat# 15140-122). Mouse ES cells were cultured as described in G. Hu et al. (Cell Stem Cell, 2013).

extract_protocol:
For DNase I digestion, 0.2 to 1 unit of Dnase I was added to the cells and incubated at 37°C for 5 minutes. The reaction was stopped by adding 80 ul of Stop Buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 0.15% SDS, 10mM EDTA), 1 ul of 20mg/ml Proteinase K and 5 ul of 6ng/ul circular carrier DNA. The mixture was incubated at 55°C for 1 hour and DNA purified by Phenol-chloroform extraction, followed by precipitation with ethanol in the presence of glycogen.
The library was prepared using Illumina kits as described G. Hu et al. (Nature immunology 2013). The libraries were amplified using a two-step method to preferentially amplify the small DNA fragments derived from the DNA hypersensitive sites and to reduce non-specific amplification of the carrier DNA. The first amplification was done with index primers with the PCR condition: 98°C, 10"; 67°C, 30"; 72°C, 30" for 6 cycles. The second amplification was done with the P5 and P7 primers with the condition: 98°C, 10"; 68°C, 30"; 72°C, 30" for 22 cycles. The fragments between 160bp to 300bp were isolated on E-gel and sequenced on Illumina HiSeq2000.

treatment_protocol: Single cell suspension after trypsinization was used for DAPI staining immediately before sorting by flow cytometry. Single live cells were sorted and deposited directly into each tubes of a PCR strip-tube, which containing 30 ul cell lysis buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% Triton X-100).

tag: patient

value: papillary thyroid carcinoma

tag: cell type

value: normal


title: TX87

value: Wild type

tag: agent

value: 6h+1h conidia culture


title: siZC3H18


title: AB392 [Sample 50]

source_name: Cebpa KO


title: Mfa132-1

value: cortical region

value: wild-type


title: AB390 [Sample 48]


title: AB389 [Sample 47]


title: siCBP80


title: AB388 [Sample 46]


title: AB391 [Sample 49]


title: AB387 [Sample 45]


title: siTRF4-2


title: siCtrl_CBCA


title: AB385 [Sample 43]


title: siMTR4


title: AB386 [Sample 44]


title: siCtrl_TRAMP


title: siCtrl_PARN


title: siZCCHC7


title: siRRP40


title: siCtrl_RRP6+DIS3


title: siRRP6+DIS3


title: siCtrl_RRP40


title: AB393 [Sample 51]


title: CMP_CD41_P

data_processing:
bcl2fastq/2.15.0.4
alignment using bowtiebowtie2/2.1.0 using default parameters
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: CMP CD41 neg

growth_protocol: 6 to 8 weeks-old mice housed at the Weizmann Institute animal facility

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Lara-Astiaso D, Weiner A, Lorenzo-Vivas E, Zaretsky I et al. Immunogenetics. Chromatin state dynamics during blood formation. Science 2014 Aug 22;345(6199):943-9. PMID: 25103404
indexing-first chromatin immunoprecipitation

treatment_protocol: no treatment

value: 6-8 wks

value: common myeloid progenitor (CMP)

tag: cell subtype

value: CMP CD41 neg

tag: chip antibody

value: K4me2 (Abcam-ab7766)


title: CMP_CD41_M

source_name: CMP CD41

tag: strain

tag: tissue

value: CMP CD41


title: siARS2

value: HeLa


title: CMP_MHCII

source_name: CMP Irf8-GFP+ MHCII+

tag: age

value: CMP Irf8-GFP+ MHCII+


title: AB328 [Sample 42]

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: CMP Flt3+ Csf1r+

tag: strain background

value: wild type

value: bone marrow

value: Lin- cKit+ Sca1- CD34+ FcgR(low) Flt3+ Csf1r+


title: siRRP40_rep1

state: Missouri

address: 1000 E 50th Street

institute: HHMI/Stowers Institute

data_processing:
RNAseq reads were aligned to the human genome (Ensembl, release 78) using TopHat v2.0.13. Parameters were -p 8 --no-novel-juncs --library-type fr-firststrand -g 20 --report-secondary-alignments
A custom script was used to count alignments that were single mapping, did not overlap multiple genic regions, and had a mapping quality greater than 10.
EdgeR was used to calculate differential expression.
Genome_build: hg38
Supplementary_files_format_and_content: Tables of differential expression from EdgeR

growth_protocol: Hela cells and Hela-S3 cells were cultured in DMEM (Life Technoloies #11995065) supplemented with 10% fetal bovine serum.

extract_protocol:
For RNAseq experiments, individual replicates were collected and extracted using the RNAqueous kit (Life Technologies #AM1912). DNAse digestion was performed twice, once in batch and once on the column, using the RNAeasy kit (Qiagen #74104).
RNA libraries were prepared for sequencing using standard ribo-depleted Illumina protocols.  We sequenced using the Illumina HiSeq, outputting single end, 50 bp, stranded RNAseq reads

value: 20nM Rrp40 siRNA - Dharmacon

tag: cell line


title: siRRP40_rep2


title: AB326 [Sample 40]

value: Lin- cKit+ Sca1- CD34+ FcgR(low) GFP+ MHCII+


title: AB327 [Sample 41]


title: siCtrl_siRrp40_rep3

value: 20nM Ctrl siRNA - Dharmacon


title: siCtrl_siRrp40_rep2


title: AB325 [Sample 39]


title: AB323 [Sample 37]


title: siCtrl_siRrp40_rep1


title: siRRP6/siDIS3_rep3

value: 20nM RRP6/ 20nM DIS3 siRNA - Dharmacon


title: AB322 [Sample 36]


title: CMP_Flt3

value: CMP Flt3+ Csf1r+


title: siRRP6/siDIS3_rep2


title: AB300 [Sample 34]


title: AB321 [Sample 35]


title: siRRP6/siDIS3_rep1


title: Flag-tagged Hfq

city: Toulouse

first: Bashir

last: Saadeh

address: 4 Rue Villaudric

country: France

institute: CNRS

description: Brucella suis 1330 with 3xFlag tagged Hfq

data_processing:
Quality check using FastQC
The low quality sequences (Phred score<28) were trimmed before downstream analyses. The remaining reads were mapped to two circular chromosomes of B. suis 1330 (NC_004310.3 and NC_004311.2) using the READemption pipeline v0.34 with the ‘-poly_a_clipping’ option.
Genome_build: NC_004310.3 and NC_004311.2
Supplementary_files_format_and_content: .gr (IGB) files
Supplementary_files_format_and_content: Chromosome 1 negative strand : B._suis_wt_CoIP_RNA_-ve_control.fa_in_NC_004310.fa.gr_normalized_by_4884700_multiplied_by_4430540.0_minus
Supplementary_files_format_and_content: Chromosome 1 positive strand  : B._suis_wt_CoIP_RNA_-ve_control.fa_in_NC_004310.fa.gr_normalized_by_4884700_multiplied_by_4430540.0_plus
Supplementary_files_format_and_content: Chromosome 2 negative strand  : B._suis_wt_CoIP_RNA_-ve_control.fa_in_NC_004311.fa.gr_normalized_by_4884700_multiplied_by_4430540.0_minus
Supplementary_files_format_and_content: Chromosome 2 positive strand  : B._suis_wt_CoIP_RNA_-ve_control.fa_in_NC_004311.fa.gr_normalized_by_4884700_multiplied_by_4430540.0_plus
Supplementary_files_format_and_content: Chromosome 1 negative strand  : B._suis_1330_3xFlag_CoIP_RNA.fa_in_NC_004310.fa.gr_normalized_by_4430540_multiplied_by_4430540.0_minus
Supplementary_files_format_and_content: Chromosome 1 positive strand  : B._suis_1330_3xFlag_CoIP_RNA.fa_in_NC_004310.fa.gr_normalized_by_4430540_multiplied_by_4430540.0_plus
Supplementary_files_format_and_content: Chromosome 2 negative strand  : B._suis_1330_3xFlag_CoIP_RNA.fa_in_NC_004311.fa.gr_normalized_by_4430540_multiplied_by_4430540.0_minus
Supplementary_files_format_and_content: Chromosome 2 positive strand  : B._suis_1330_3xFlag_CoIP_RNA.fa_in_NC_004311.fa.gr_normalized_by_4430540_multiplied_by_4430540.0_plus

organism: Brucella suis 1330

source_name: Flag-tagged Hfq

growth_protocol: Tryptic Soy Broth, 37 degrees celcius in shaking incubator

extract_protocol:
50OD total bacteria of each the sample and the negative control were harvested after growth to an OD of 1 and co-IP with anti-flag antibodies was performed. RNA-Protein pulldown was performed using sepharose beads coated with protein A. RNA was separated from protein using classic phenol/chloroform extraction,
poly(A) polymerase/TAP/oligo(dt) + M-MLV RT then barcoding and amplification

tag: antibody


title: AB299 [Sample 33]

tag: genotype/variation


title: siCtrl_siRRP6/siDIS3_rep3

value: 40nM Ctrl siRNA - Dharmacon


title: Negative control

description: Wild type brucella suis

source_name: Negative control


title: AB296 [Sample 32]

value: Lin- cKit+ Sca1-

tag: injected with

value: 300 µg poly(I:C) (3 times; 3 wks before bone marrow harvest)


title: shoot paired-end

description: non-directional paired-end RNA-seq

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plant Mini kit. Total RNA was treated with Turbo DNase I (Life Technologies AM2238) according to product specification. DNase I treated RNA was then applied again to an RNeasy spin column with 0.5 volumes of ethanol, washed and eluted according to the manufacturer’s instructions.
Sequencing libraries were prepared using the TruSeq RNA Sample Preparation Kits v2, set A (RS-122-2001, Illumina Inc.) according to the manufacturer's instructions.  The quality and size of cDNA libraries were checked using the Agilent 2200 TapeStation system (Agilent Inc.). The libraries were sequenced for 100 cycles (paired-end, PE) on HiseqTM 2000 (Illumina Inc.).

value: shoots

tag: developmental stage

value: sample harvested 14 days after germination


title: root paired-end

description: non-directional paired-end RNA-seq

value: roots


title: AB295 [Sample 31]


title: siCtrl_siRRP6/siDIS3_rep2


title: siCtrl_siRRP6/siDIS3_rep1


title: AB324 [Sample 38]


title: siDIS3_rep3

value: 20nM DIS3 siRNA - Dharmacon


title: AB292 [Sample 30]

source_name: Cebpe control

value: Cebpe+/+


title: AB291 [Sample 29]


title: AB288 [Sample 28]

source_name: Cebpe KO

value: Cebpe-/-


title: CMP_tripleneg

source_name: CMP Flt3- Csf1r- Irf8-GFP- MHCII-

value: 6-8 wks

value: common myeloid progenitor (CMP)

value: CMP Flt3- Csf1r- Irf8-GFP- MHCII-

value: K4me2 (Abcam-ab7766)


title: siDIS3_rep2

value: HeLa


title: siDIS3_rep1


title: siRRP6_rep3

value: 20nM RRP6 siRNA - Dharmacon


title: siRRP6_rep2


title: AB287 [Sample 27]

value: bone marrow


title: AB284 [Sample 26]

value: Cebpa(flox/flox)


title: GA6158 Single ES DNase1

description: Pico-Seq

data_processing:
Basecalls performed using RTA 1.7 or Illumina Casava1.7
DNase-seq reads were mapped to the mouse genome (mm9) using Bowtie2. The reads with MAPQ <=10 or redundant reads were removed from further analysis in each library.
We identified DNase I hypersensitive sites in ENCODE data and our small cell number Pico-Seq data using MACS. For the single cell Pico-Seq libraries, any mapped reads in the promoter or enhancer regions that identified in the cell population were treated as real signal, which indicated the promoter or enhancer is accessible in the cell.
Genome_build: mm9
Supplementary_files_format_and_content: Bed: plan text file. Each line is one read. The six columns are chrom, start position, end position, length, alignment score and strand.

source_name: Embryonic stem cells

extract_protocol:
For DNase I digestion, 0.2 to 1 unit of Dnase I was added to the cells and incubated at 37°C for 5 minutes. The reaction was stopped by adding 80 u of Stop Buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 0.15% SDS, 10mM EDTA), 1ul of 20mg/ml Proteinase K and 5ul of 6ng/l circular carrier DNA. The mixture was incubated at 55°C for 1 hour and DNA purified by Phenol-chloroform extraction, followed by precipitation with ethanol in the presence of glycogen.
The library was prepared using Illumina kits as described G. Hu et al. (Nature immunology 2013). The libraries were amplified using a two-step method to preferentially amplify the small DNA fragments derived from the DNA hypersensitive sites and to reduce non-specific amplification of the carrier DNA. The first amplification was done with index primers with the PCR condition: 98°C, 10”; 67°C, 30”; 72°C, 30” for 6 cycles. The second amplification was done with the P5 and P7 primers with the condition: 98°C, 10”; 68°C, 30”; 72°C, 30” for 22 cycles. The fragments between 160bp to 300bp were isolated on E-gel and sequenced on Illumina HiSeq2000.

treatment_protocol: Single cell suspension after trypsinization was used for DAPI staining immediately before sorting by flow cytometry. Single live cells were sorted and deposited directly into each tubes of a PCR strip-tube, which containing 30ul cell lysis buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% Triton X-100).

tag: cell number

value: Single cell


title: ChIP-Seq analysis for Input

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

description: Input sample was used for normalization.

data_processing:
For sequencing data alignment and analysis, the current assembly of mouse reference genome is missing the ribosomal rDNA repeats, of which there are approximately 400, located on chromosomes 12, 14 and 15. To compensate for this we utilized the procedure of Zentner et al (2011) and constructed a custom reference sequence that contained a non-masked rDNA repeat, taken from BK000964, which was added to the end of chromosome 12 of the MM9 assembly.
The analysis procedure involved the use of the SOAP2 program to map the reads to the constructed reference genome. Sequences with more than two mismatches were discarded from further analysis. The resulting individual sequences were remapped back to the annotated UCSC MM9 reference sequence which allows for the identification of peaks corresponding to the levels of association of the ChIP target with those loci.
Sequence data was filtered to obtain clean data which was then mapped to the reference genome. Only cleanly mapped sequences were used in further analysis.
The distribution of sequence hits along each chromosome is shown in the WIG file output.
Supplementary_files_format_and_content: WIG (Wiggle) format file, that allows the mapping of sequence hits to the reference genome, for example using the UCSC genomic browser.

source_name: Mouse embryonic fibroblasts, input

growth_protocol: Mouse embryonic fibroblasts cells were grown in DMEM medium (Gibco), supplemented with 10% foetal bovine serum (Gibco) and a 1% penicillin/streptomycin cocktail.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the indicated antibody.
5 ng of precipitated DNA was used to prepare sequencing libraries at the Bejing Genome Institute (Hong Kong) using the Illumina HiSeq 2000 platform. Briefly, ChIP DNA was fragmented to 100-500bp by sonication. DNA-end was repaired to overhang a 3’-dA, then adapters were ligated to the end DNA fragments. DNA fragments with proper size (usually 100-300bp, including adaptor sequence) were selected after PCR amplification. Finally we got qualified library for sequencing.

value: mouse embryonic fibroblasts

tag: passages


title: siRRP40_rep3

source_name: HeLa

tag: treatment

value: 20nM Rrp40 siRNA - Dharmacon


title: siRRP6_rep1


title: AB283 [Sample 25]

tag: selection marker

value: Lin- cKit+ Sca1-

value: 300 µg poly(I:C) (3 times; 3 wks before bone marrow harvest)


title: GA6152 Single ES DNase1

description: Pico-Seq


title: siCtrl_singleKD_rep3

value: 20nM Ctrl siRNA - Dharmacon


title: AB279 [Sample 23]


title: siCtrl_singleKD_rep2


title: siCtrl_singleKD_rep1


title: GA6146 Single ES DNase1

description: Pico-Seq


title: GA6151 Single ES DNase1

description: Pico-Seq


title: Spliceostatin A_rep3

value: SpliceostatinA - Yoshida Lab


title: Spliceostatin A_rep2


title: AB247 [Sample 22]


title: GA6142 Single ES DNase1

description: Pico-Seq


title: Spliceostatin A_rep1


title: AB235 [Sample 20]

value: wild type

value: Lin- cKit+ Sca1- CD34+ FcgR(low) Flt3+ Csf1r+


title: GA5841 Single ES DNase1

description: Pico-Seq


title: GA5837 Single ES DNase1

description: Pico-Seq


title: AB234 [Sample 19]


title: S2 paired-end

description: non-directional paired-end RNA-seq

data_processing:
After quality control analysis of raw sequencing datasets, RNA-seq sequences were aligned to the rice genome using TopHat. Then the mapped sequences of each sample were assembled by Cufflinks. Fragments per kilobase of exon per million fragments mapped of assembled transcripts (FPKM) were calculated and normalized using Cuffcompare and Cuffdiff with global normalization parameters.
Genome_build: Oryza sativa L. ssp. Japonica, MSU Rice Genome Annotation Project Release 7
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all Samples

organism: Oryza sativa Japonica Group

source_name: mature seeds

growth_protocol: Seeds from the cultivated rice subspecies Oryza sativa L. ssp. Japonica were grown in a greenhouse in Singapore. Flower buds were collected before flowering and flowers were collected at the flowering day. Flag leaves and roots were collected at the before- and after-flowering stage. The before-flowering sample was defined as a mixture of different stages in a period from panicle initiation to 1 day before flowering. The after-flowering sample was defined as a mixture of different stages after the flowering day. Milk grains and mature seeds were also collected.

value: mature seeds


title: GA6156 Single ES DNase1

description: Pico-Seq


title: Methanol_rep2

value: VWR #BDH1135-4LP


title: Methanol_rep3


title: AB280 [Sample 24]

value: Cebpe-/-


title: S1 paired-end

description: non-directional paired-end RNA-seq

source_name: milk grains

value: milk grains


title: GA5817 Single 3T3  cell #3 DNase1

description: scDNase-Seq

source_name: NIH/3T3 tet-on 3G cells

value: NIH/3T3 fibroblast cell line


title: AB212 [Sample 16]

source_name: Unsorted myeloid


title: AB213 [Sample 17]


title: R2 paired-end

description: non-directional paired-end RNA-seq

source_name: roots sampled after flowering

value: roots sampled after flowering


title: AB246 [Sample 21]

source_name: Cebpa KO

value: bone marrow


title: GA6143 Single ES DNase1

description: Pico-Seq


title: GA6164 Single ES DNase1

description:
Dnase-seq
ES DNase1

data_processing:
Basecalls performed using RTA 1.7 or Illumina Casava1.7
DNase-seq reads were mapped to the mouse genome (mm9) using Bowtie2. The reads with MAPQ <=10 or redundant reads were removed from further analysis in each library.
We identified Dnase I hypersensitive sites in Enocode data and our small cell number Pico-seq data using MACS.
Genome_build: mm9
Supplementary_files_format_and_content: Bed: plan text file. Each line is one read. The six columns are chrom, start position, end position, length, alignment score and strand.

extract_protocol:
For DNase I digestion, 0.2 to 1 unit of Dnase I was added to the cells and incubated at 37°C for 5 minutes. The reaction was stopped by adding 80 ul of Stop Buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 0.15% SDS, 10mM EDTA), 1 ul of 20mg/ml Proteinase K and 5 ul of 6ng/ul circular carrier DNA. The mixture was incubated at 55°C for 1 hour and DNA purified by Phenol-chloroform extraction, followed by precipitation with ethanol in the presence of glycogen.
The library was prepared using Illumina kits as described G. Hu et al. (Nature immunology 2013). The libraries were amplified using a two-step method to preferentially amplify the small DNA fragments derived from the DNA hypersensitive sites and to reduce non-specific amplification of the carrier DNA. The first amplification was done with index primers with the PCR condition: 98°C, 10"; 67°C, 30"; 72°C, 30" for 6 cycles. The second amplification was done with the P5 and P7 primers with the condition: 98°C, 10"; 68°C, 30"; 72°C, 30" for 22 cycles. The fragments between 160bp to 300bp were isolated on E-gel and sequenced on Illumina HiSeq2000.

treatment_protocol: Single cell suspension after trypsinization was used for DAPI staining immediately before sorting by flow cytometry. Single live cells were sorted and deposited directly into each tubes of a PCR strip-tube, which containing 30 ul cell lysis buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% Triton X-100).


title: AB211 [Sample 15]


title: R1 paired-end

description: non-directional paired-end RNA-seq

source_name: roots sampled before flowering

value: roots sampled before flowering


title: Isoginkgetin_rep2

value: Isoginkgetin - EMD Millipore Chemicals # CAS548-19-6

value: HeLa


title: L2 paired-end

description: non-directional paired-end RNA-seq

source_name: leaves sampled after flowering

value: leaves sampled after flowering


title: AB210 [Sample 14]

value: Lin- cKit+ Sca1-


title: Isoginkgetin_rep1


title: GA5842 Single ES DNase1

description:
Dnase-seq
ES DNase1

value: Single cell


title: AB214 [Sample 18]


title: GA5843 Single ES DNase1

description:
Dnase-seq
ES DNase1


title: AB209 [Sample 13]


title: L1 paired-end

description: non-directional paired-end RNA-seq

source_name: leaves sampled before flowering

value: leaves sampled before flowering


title: AB208 [Sample 12]


title: F2 paired-end

description: non-directional paired-end RNA-seq

source_name: flowers

value: flowers


title: DMSO_rep2

value: DMSO - Sigma #D2438


title: DMSO_rep3


title: GA5838 Single ES DNase1

description:
Dnase-seq
ES DNase1


title: F1 paired-end

description: non-directional paired-end RNA-seq

source_name: flower buds

value: flower buds


title: Methanol_rep1


title: AB206 [Sample 10]

value: wild type


title: GA6147 10 ES DNase1

description:
Dnase-seq
10 ES DNase1

value: 10 cells


title: Isoginkgetin_rep3


title: GA6162 Single ES DNase1

description:
Dnase-seq
ES DNase1


title: GA6141 10 ES DNase1

description:
Dnase-seq
10 ES DNase1


title: BNL CL.2_IgG_ChIP-seq

first: Fang

address: NO. 800 Xiangyin Road

department: Medical Genetics

institute: Second Military Medical University

description: genomic DNA

data_processing:
Data Cleaning: filter the low Quality Reads and Adapter Sequence
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie with following setting:-v 2 ,-l 28
Remove Duplication reads
peaks were called using MACS version 1.4 with following setting :Pvalue=1e-5,MFOLD=10,30,SMALLLOCAL=1000,LARGELOCAL=10000.
Genome_build: mm9
Supplementary_files_format_and_content: wig file generated by MACS,and the scores mean the density of reads

source_name: Fetal liver

growth_protocol: The BNL CL.2 cells were cultured in Minimum Essential Medium (Gibco-BRL) with 10% fetal bovine serum (Gibco-BRL). The cells were maintained in a humidified incubator at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
Libraries were prepared according to Illumina's instructions accompanying the chip-DNA Sample Kit (TruSeq® chip DNA LT Sample Prep Kit). 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 (32 to 52 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 15 cycles and library fragments of ~260 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.

value: BNL CL.2

tag: cell type

value: fetal liver cells

value: rabbit immunoglobulin G (IgG)


title: AB205 [Sample 9]


title: GA6169 1K ES DNase1

description:
Dnase-seq
1K ES DNase1

value: 1K cells


title: Cold_rep4

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Sequencing reads were aligned to the mouse reference genome (version mm9) using STAR (Dobin et al. 2013, Bioinformatics; 29(1):15-21) with default parameters.
The number of exon reads for all RefSeq genes were counted using iRNA-seq (Madsen et al. 2015, Nucleic Acids Res.;43(6):e40) only keeping the longest RefSeq transcripts for further analyzes.
The resulting count matrix was analysed with EdgeR (Robinson et al. 2010. Bioinformatics; 26(1):139-40), and HTSFilter (Rau et al., 2013, Bioinformatics; 29(17):2146-52) was applied to filter out genes with low, constant levels of expression in the two conditions. Differential expression was determined using a cut-off significance level of FDR<0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files containing non-normalized tag counts for each sample (output from iRNA-seq) and differential expression analyzed for included genes (output from EdgeR)

growth_protocol: Prior to the experiment, all mice were single-housed at 22°C under standard laboratory conditions including 12h light/dark cycle with free access to water and food (chow, Altromin 1324, Brogaarden, Denmark)

extract_protocol:
Interscapular brown adipose tissues were isolated, and snap frozen in liquid nitrogen. Total RNA was harvested using Isol-RNA lysis reagent (5 PRIME) and the integrity of the RNA was confirmed using a Bioanalyzer 2100 (Agilent Technologies).
4 ug of total RNA from iBAT was polyA-selected, and subsequently subjected to fragmentation and cDNA-synthesis using the TruSeq RNA Sample Prep kit v2 (Illumina). cDNA-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: 5 mice were kept room temperature (22°C) and 5 mice were exposed to cold (4°C) for 3 days.

value: 8 weeks

tag: gender

value: Male

value: interscapular brown adipose tissue

value: room temperature (4°C)


title: GA6167 1K ES DNase1

description:
Dnase-seq
1K ES DNase1


title: AB204 [Sample 8]

value: bone marrow


title: Cold_rep5


title: BNL CL.2_hnRNP U_ChIP-seq

description: genomic DNA

value: anti-hnRNP U(Abcam)


title: Cold_rep3


title: GA5862 Single 3T3  cell #2 DNase1

description:
scDnase-seq
3T3 DNase1

value: NIH/3T3 fibroblast

value: Single cell


title: Cold_rep2


title: AB176 [Sample 6]

value: Lin- cKit+ Sca1-


title: GA5859 Single 3T3  cell #5 DNase1

description:
scDnase-seq
3T3 DNase1


title: AB207 [Sample 11]


title: AB175 [Sample 5]


title: DMSO_rep1

value: DMSO - Sigma #D2438

value: HeLa


title: GA5856 Single 3T3  cell #4 DNase1

description:
scDnase-seq
3T3 DNase1


title: AB174 [Sample 4]

value: wild type


title: Control_rep4

value: room temperature (22°C)


title: Control_rep5


title: AB173 [Sample 3]


title: Control_rep3


title: Control_rep2


title: AB168 [Sample 2]

source_name: CMP CD41

value: Lin- cKit+ Sca1- CD34+ FcgR(low) CD41+


title: GA5748 10K 3T3 DNase1

description:
Dnase-seq
10K 3T3 DNase1

value: 10K cells


title: Control_rep1


title: GA5763 1K 3T3 DNase1

description:
Dnase-seq
1K 3T3 DNase1


title: SHC-04W-ACC-5

status: Public on Nov 24 2015

city: Gottingen

first: Ramon

last: Oliveira Vidal

address: Grisebachstraße 5

department: Bioinformatics

country: Germany

institute: DZNE

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the mm10 genome assembly using STAR aligner version 2.3.0e_r291 with default options
Unmapped reads were removed using samtools -F 4 option
Genome_build: mm10
Supplementary_files_format_and_content: Read counts for all genes and all exons (Ensembl annotation v72) were obtained using FeaturesCount. DEGs were calculated using DESEQ2 and DEE were calculated using DEXSEQ

source_name: Anterior Cingulate Cortex

growth_protocol: 3 months-old male C56BL/6 mice, individually housed in standard conditions.

extract_protocol:
Total RNA was extracted using Tri Reagent (Sigma).
Libraries were prepared using the TruSeq RNA Sample Preparation v2 kit (Illumina).

treatment_protocol: Mice were subjected to contextual fear conditioning. One group (5 mice) was exposed to a new context and then received a 0,7 mA electric footshock (CS), one group was exposed only to the new context (C) and naive mice (N) were used as control. The mice were sacrificed either 1h or 4 weeks after the training. Two brain regions were studied : the hippocampal CA1 and the Anterior Cingulate cortex (ACC).

value: 3 months old

tag: Sex

value: male

tag: condition

value: shock 4w


title: SHC-04W-ACC-2

tag: strain


title: SHC-04W-ACC-3


title: SHC-04W-ACC-1


title: AB203 [Sample 7]

tag: tissue


title: SHC-04W-ACC-4

tag: age


title: SHC-01H-CA1-4

source_name: hippocampal CA1

value: shock 1h


title: SHC-01H-CA1-1


title: Cold_rep1

value: 8 weeks

value: Male

value: interscapular brown adipose tissue


title: SHC-01H-CA1-3


title: GA5861 Single 3T3 cell #1 DNase1

description:
scDnase-seq
3T3 DNase1


title: CON-04W-ACC-4

value: context 4w


title: SHC-01H-CA1-2


title: GA5767 100 3T3 DNase1

description:
Dnase-seq
100 3T3 DNase1

value: NIH/3T3 fibroblast

value: 100 cells


title: AB167 [Sample 1]

tag: strain background

value: bone marrow


title: CON-04W-ACC-3


title: CON-01H-CA1-5

value: context 1h


title: CON-04W-ACC-1


title: CON-01H-CA1-3


title: NAI-00H-CA1-4

value: naive


title: CON-01H-CA1-2


title: NAI-00H-CA1-5


title: NAI-00H-CA1-3


title: NAI-00H-CA1-1


title: CON-01H-CA1-1


title: NAI-00H-ACC-5


title: NAI-00H-ACC-4


title: NAI-00H-ACC-3


title: CON-04W-ACC-5


title: NAI-00H-ACC-1


title: SHC-04W-CA1-NON-MC-2

data_processing:
Basecalls performed using CASAVA version 1.8.2
MeDIP-seq reads were aligned to the mm10 genome assembly using Bowtie version v2.0.2 allowing for 2 mismatches using seed alignment.
Unmapped reads were removed using samtools -F 4 option
High quality uniquely and multi-mapped reads were obtained by filtering out reads with low quality (MAPQ != {0, 2, 3, 4})
Genome_build: mm10
Supplementary_files_format_and_content: The high quality uniquely and multi-mapped reads BAM files were converted into WIG and BigWig files using the function ‘MEDIPS.exportWIG’ from the R package MEDIPS (version 1.16.0) with a window of 50bp and RPM normalization.

extract_protocol:
The tissue were fixed and the nuclei were isolated and stained with NeuN antibody to be FACS sorted into neuronal and non-neuronal populations. Genomic DNA was extracted and MeDIP-seq was performed.
After DNA shearing, Illumina-compatible adapters were ligated (NEB E6240) and an IP using 5mC antibody (Eurogentech BI-MECY-0100) was conducted. The IPed DNA was amplified by PCR and sequenced on Illumina Hiseq 2000.

treatment_protocol: Mice were subjected to contextual fear conditioning. One group (20 mice x 2 replicates) was exposed to a new context and then received a 0,7 mA electric footshock (CS), one group was exposed only to the new context (C) and naive mice (N) were used as control. The mice were sacrificed either 1h or 4 weeks after the training. Two brain regions were studied : the hippocampal CA1 and the Anterior Cingulate cortex (ACC).

value: non neuron


title: SHC-04W-CA1-NON-MC-1


title: SHC-04W-CA1-NEU-MC-2

value: neuron


title: SHC-04W-ACC-NON-MC-2

source_name: Anterior Cingulate cortex


title: SHC-04W-ACC-NEU-MC-2


title: CON-01H-CA1-4


title: SHC-04W-ACC-NON-MC-1


title: SHC-04W-CA1-NEU-MC-1


title: SHC-04W-ACC-NEU-MC-1


title: SHC-01H-CA1-NEU-MC-2


title: SHC-01H-CA1-NON-MC-1


title: CON-04W-ACC-2


title: SHC-01H-CA1-NEU-MC-1


title: NAI-00H-ACC-2


title: SHC-01H-ACC-NON-MC-1


title: SHC-01H-ACC-NEU-MC-1


title: NAI-00H-CA1-2


title: SHC-01H-ACC-NON-MC-2


title: NAI-00H-CA1-NON-MC-1


title: NAI-00H-CA1-NON-MC-2


title: NAI-00H-CA1-NEU-MC-2


title: NAI-00H-ACC-NON-MC-1


title: NAI-00H-CA1-NEU-MC-1


title: NAI-00H-ACC-NON-MC-2


title: NAI-00H-ACC-NEU-MC-1


title: NAI-00H-ACC-NEU-MC-2


title: SHC-01H-CA1-NON-MC-2


title: CON-04W-CA1-NON-MC-1


title: CON-04W-CA1-NON-MC-2


title: CON-04W-ACC-NON-MC-2


title: CON-04W-CA1-NEU-MC-2


title: CON-04W-CA1-NEU-MC-1


title: CON-04W-ACC-NEU-MC-2


title: CON-04W-ACC-NON-MC-1


title: CON-01H-CA1-NON-MC-2


title: CON-01H-CA1-NON-MC-1


title: SHC-01H-ACC-NEU-MC-2


title: CON-01H-CA1-NEU-MC-2


title: CON-04W-ACC-NEU-MC-1


title: CON-01H-ACC-NON-MC-2


title: CON-01H-ACC-NON-MC-1


title: SHC-01H-CA1-NEU-H3-2

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie version v2.0.2 allowing for 2 mismatches using seed alignment.
Unmapped reads were removed using samtools -F 4 option
High quality uniquely and multi-mapped reads were obtained by filtering out reads with low quality (MAPQ != {0, 2, 3, 4})
Genome_build: mm10
Supplementary_files_format_and_content: The high quality uniquely and multi-mapped reads BAM files were converted into WIG and BigWig files using the function ‘MEDIPS.exportWIG’ from the R package MEDIPS (version 1.16.0) with a window of 50bp and RPM normalization.

extract_protocol:
The tissue were fixed and the nuclei were isolated and stained with NeuN antibody to be FACS sorted into neuronal and non-neuronal populations. Chromatin was sheared and ChIP-seq was performed using the following antibodies : H3 Abcam  ab1791; H3K4me1 Abcam ab8895; H3K4me3 Abcam ab8580; H3K27ac Abcam ab4729; H3K9ac Millipore 07-352; H3K79me3 Abcam ab2621; H3K27me3 Millipore CS200603.
Libraries were constructed from ChIPed DNA using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, H3K9ac) or MicroPlex Kit (Diagenode, all other marks).

tag: antibody vendor/catalog

value: Abcam ab1791


title: CON-01H-ACC-NEU-MC-1


title: SHC-01H-CA1-NEU-H3-1

tag: antibody


title: SHC-01H-CA1-NON-H3-1


title: SHC-01H-CA1-NON-H3-2


title: CON-01H-ACC-NEU-MC-2


title: NAI-00H-CA1-NON-H3-2


title: NAI-00H-CA1-NEU-H3-2


title: NAI-00H-ACC-NON-H3-1


title: CON-01H-CA1-NON-H3-2


title: NAI-00H-ACC-NEU-H3-1


title: NAI-00H-ACC-NON-H3-2


title: CON-01H-CA1-NEU-H3-2


title: NAI-00H-ACC-NEU-H3-2


title: SHC-01H-CA1-NON-H3K27AC-2

value: Abcam ab4729


title: SHC-01H-CA1-NON-H3K27AC-1

value: 3 months old


title: SHC-01H-CA1-NEU-H3K27AC-2

value: male


title: CON-01H-CA1-NEU-MC-1


title: SHC-01H-CA1-NEU-H3K27AC-1


title: NAI-00H-ACC-NON-H3K27AC-1


title: NAI-00H-CA1-NEU-H3K27AC-1


title: NAI-00H-CA1-NON-H3K27AC-2


title: NAI-00H-CA1-NON-H3K27AC-1


title: NAI-00H-ACC-NON-H3K27AC-2


title: NAI-00H-CA1-NEU-H3K27AC-2


title: NAI-00H-CA1-NON-H3-1


title: NAI-00H-ACC-NEU-H3K27AC-2


title: NAI-00H-ACC-NEU-H3K27AC-1


title: CON-01H-CA1-NEU-H3K27AC-2


title: NAI-00H-CA1-NEU-H3-1


title: CON-01H-CA1-NON-H3K27AC-2


title: SHC-01H-CA1-NON-H3K27ME3-2

value: Millipore CS200603


title: CON-01H-CA1-NON-H3K27AC-1


title: CON-01H-CA1-NEU-H3K27AC-1


title: SHC-01H-CA1-NON-H3K27ME3-1

value: shock 1h


title: CON-01H-CA1-NON-H3-1


title: SHC-01H-CA1-NEU-H3K27ME3-2


title: SHC-01H-CA1-NEU-H3K27ME3-1


title: NAI-00H-CA1-NON-H3K27ME3-2


title: CON-01H-CA1-NEU-H3-1


title: NAI-00H-ACC-NON-H3K27ME3-2


title: NAI-00H-CA1-NON-H3K27ME3-1


title: NAI-00H-CA1-NEU-H3K27ME3-2


title: NAI-00H-ACC-NON-H3K27ME3-1


title: NAI-00H-ACC-NEU-H3K27ME3-2


title: NAI-00H-ACC-NEU-H3K27ME3-1


title: CON-01H-CA1-NEU-H3K27ME3-2


title: CON-01H-CA1-NON-H3K27ME3-2


title: SHC-01H-CA1-NEU-H3K4ME1-2

value: Abcam ab8895


title: CON-01H-CA1-NEU-H3K27ME3-1


title: SHC-01H-CA1-NEU-H3K4ME1-1


title: SHC-01H-CA1-NON-H3K4ME1-2


title: NAI-00H-CA1-NON-H3K4ME1-1


title: NAI-00H-CA1-NON-H3K4ME1-2


title: NAI-00H-ACC-NON-H3K4ME1-2


title: NAI-00H-CA1-NEU-H3K4ME1-2


title: SHC-01H-CA1-NON-H3K4ME1-1


title: CON-01H-CA1-NON-H3K4ME1-2


title: CON-01H-CA1-NON-H3K4ME1-1


title: CON-01H-CA1-NON-H3K27ME3-1


title: NAI-00H-CA1-NEU-H3K4ME1-1


title: NAI-00H-ACC-NEU-H3K4ME1-1


title: CON-01H-CA1-NEU-H3K4ME1-2


title: NAI-00H-ACC-NON-H3K4ME1-1


title: CON-01H-CA1-NEU-H3K4ME1-1


title: NAI-00H-CA1-NON-H3K4ME3-2

value: Abcam ab8580


title: SHC-01H-CA1-NON-H3K4ME3-1


title: NAI-00H-ACC-NEU-H3K4ME1-2


title: NAI-00H-CA1-NEU-H3K27ME3-1


title: SHC-01H-CA1-NEU-H3K4ME3-2


title: SHC-01H-CA1-NON-H3K4ME3-2


title: NAI-00H-CA1-NON-H3K4ME3-1


title: NAI-00H-CA1-NEU-H3K4ME3-2


title: NAI-00H-CA1-NEU-H3K4ME3-1


title: NAI-00H-ACC-NON-H3K4ME3-1


title: NAI-00H-ACC-NEU-H3K4ME3-2


title: NAI-00H-ACC-NON-H3K4ME3-2


title: CON-01H-CA1-NEU-H3K4ME3-2


title: NAI-00H-ACC-NEU-H3K4ME3-1


title: NAI-00H-CA1-NON-H3K79ME3-2

value: Abcam ab2621


title: SHC-01H-CA1-NEU-H3K4ME3-1


title: SHC-01H-CA1-NEU-H3K79ME3-2


title: NAI-00H-ACC-NON-H3K79ME3-1


title: SHC-01H-CA1-NON-H3K79ME3-1


title: NAI-00H-CA1-NEU-H3K79ME3-2


title: CON-01H-CA1-NEU-H3K4ME3-1


title: SHC-01H-CA1-NON-H3K79ME3-2


title: NAI-00H-CA1-NEU-H3K79ME3-1


title: CON-01H-CA1-NON-H3K79ME3-1


title: NAI-00H-ACC-NEU-H3K79ME3-1


title: NAI-00H-ACC-NON-H3K79ME3-2


title: CON-01H-CA1-NON-H3K79ME3-2


title: NAI-00H-ACC-NEU-H3K79ME3-2


title: CON-01H-CA1-NEU-H3K79ME3-1


title: CON-01H-CA1-NEU-H3K79ME3-2


title: SHC-01H-CA1-NEU-H3K9AC-1

value: Millipore 07-352


title: CON-01H-CA1-NON-H3K4ME3-1


title: NAI-00H-CA1-NON-H3K9AC-2


title: SHC-01H-CA1-NON-H3K9AC-1


title: CON-01H-CA1-NON-H3K4ME3-2


title: SHC-01H-CA1-NEU-H3K9AC-2


title: NAI-00H-CA1-NON-H3K9AC-1


title: NAI-00H-CA1-NON-H3K79ME3-1


title: CON-01H-CA1-NON-H3K9AC-2


title: NAI-00H-CA1-NEU-H3K9AC-2


title: SHC-01H-CA1-NEU-H3K79ME3-1


title: CON-01H-CA1-NON-H3K9AC-1


title: CON-01H-CA1-NEU-H3K9AC-2


title: CON-01H-CA1-NEU-H3K9AC-1


title: NAI-00H-CA1-NEU-H3K9AC-1


title: MCF7 polysomal RNA-seq, replicate #2

city: Geneva

first: Joseph

last: Curran

address: 1 rue Michel Servet

department: Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva Medical School

description:
mammary gland, breast; derived from metastatic site: pleural effusion
processed data file: cuffdiff2_polysomal_RefSeq.tar.gz
processed data file: cuffdiff2_polysomal_Ensembl.tar.gz

data_processing:
conversion to Phred+33 representation with SeqIO command from Biopython library
trim of reads with Phred score less than 20 with "fastq_trimmer_by_quality.py" from FASTX toolkit with parameters -f illumina -s 1 -t 1 -e 3 -a min -x 0 -k - c '>=' -q 20
Read alignment with Tophat, version 2.08b to RefSeq transcriptome. Parameters used -r 90 -M --mate-std-dev 30 --solexa1.3-quals --library-type fr-unstranded –no-noveljuncs
Differential expression analysis with Cuffdiff of both polysomal and total RNAseq, version 2.1 with parameters --compatible-hits-norm -u -b
Genome_build: hg19
Supplementary_files_format_and_content: The results of differential gene and promoter expression analysis  produced with Cuffdiff for total and polysomal RNAseq experiments with alignment to RefSeq and Ensembl catalogue igenomes (igenomes archive-2013-03-06-12-22-32).

growth_protocol: MCF10A (ATCC, CRL-10317) cells were cultured in Dulbecco’s modified Eagle’s medium F12 (DMEM; Invitrogen) supplemented with 5% horse serum (Brunschwig), 1% penicillin/streptomycin (Gibco), in the presence of EGF (10µg/ml), dexamethazone (1µM) and insulin (5µg/ml) in a humidified atmosphere containing 5% CO2. MCF7 (ATCC, HTB-22)  cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Sigma) supplemented with 10% fetal calf serum (Brunschwig), 1% penicillin/streptomycin (Gibco), in presence of insulin (10µg/ml) and estradiol (0.5nM) in a humidified atmosphere containing 5% CO2.

extract_protocol:
RNA was extracted using the Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
For deep-sequencing we employed the Illumina mRNA-seq Sample Prep protocol (Cat # RS-930-1001) using oligo(dT) enriched RNA. Sequences were generated on an Illumina GAII, using 75 bps paired end reads

tag: cell line

tag: sample molecule

value: polysomal RNA

value: epithelial


title: MCF10A polysomal RNA-seq, replicate #1

description:
mammary gland; breast
processed data file: cuffdiff2_polysomal_RefSeq.tar.gz
processed data file: cuffdiff2_polysomal_Ensembl.tar.gz


title: MCF10A polysomal RNA-seq, replicate #2


title: MCF10A polysomal RNA-seq, replicate #3


title: MCF7 polysomal RNA-seq, replicate #3


title: MCF10A total RNA-seq, replicate #3

description:
mammary gland; breast
processed data file: cuffdiff2_total_RefSeq.tar.gz
processed data file: cuffdiff2_total_Ensembl.tar.gz

value: total RNA


title: SiR4ET (miRNA)

city: Rochester

first: Xuewei

address: 200 1st street

institute: Mayo Clinic

description: VDR knockdown_ethanol

data_processing:
Base calling by CASAVA
Alignment by Bowtie
miRNA count by miRDeep2
Genome_build: hg19
Supplementary_files_format_and_content: .txt file for miRNA count

source_name: skeletal muscle cells

growth_protocol: In brief, human skeletal muscle cells were seeded in 6-well trays and grown to 50-60% confluence in growth medium.

extract_protocol:
RNA was prepared using RNA/protein spin columns (Clontech).  Lysis solution was added to cells which were lysed by passage successively through 21 and 27 gauge needles.  Individual lysates were applied to RNA spin columns, and RNAs were eluted into nuclease-free water.  Before library construction, RNA quality was assessed.
We synthesized miRNA libraries from 1,25(OH)2D3 or vehicle treated cells using total RNA samples and a NEBNext® Multiplex Small RNA Kit (New England BioLabs).  Adaptors were ligated to the 3’ ends of the small non-coding RNAs present in 500 ng of total RNA.  A complementary primer was annealed to the 3’ adaptor sequences followed by ligation of a 5’ RNA adaptor.  A cDNA library was created by reverse transcriptase (Superscript III; Invitrogen) of the adaptor-ligated and annealed small RNA population.  The library was enriched by 15 cycles of PCR employing a common 5’ primer and a 3’ primer containing one of eight index primers (3’ adaptor complement; Index sequences equivalent to Illumina TruSeq Small RNA sequences).  The PCR products were subsequently purified.  The libraries were assessed for miRNA products by Agilent Bioanalyzer DNA 1000 (Santa Clara, CA) analysis.  The 130-160 bp region was quantitated to determine equimolar amounts of vehicle and 1,25(OH)2D3-treated sample libraries to pool.  The pooled small RNA libraries were fractionated to extract a miRNA-enriched sample via 3% Pippin Prep (Sage Science) gel cassettes.  The recovered fraction was purified and reconstituted in 10 mcL nuclease-free dH2O.  Pooled miRNA fractions were assessed by a second Agilent DNA 1000 assay.  A predominant peak at 140-150bp indicated that the miRNA-modification and size selection steps were performed as expected.  The final concentration of each library pool was determined.
Libraries were loaded onto single end flow cells at concentrations of 8-10 pM to generate cluster densities of 700,000/mm2 following Illumina’s standard protocol using the Illumina cBot cluster kit version 3.  The flow cells were sequenced as two reads: read 1- 51 cycles using the Small RNA Sequencing Primer and an Index read to demultiplex the samples.  Libraries were sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 3 and SCS version 1.4.8 data collection software.  Base-calling was performed using Illumina’s RTA version 1.12.4.2.

treatment_protocol: Human skeletal muscle cells were transfected with VDR siRNA or scrambled siRNA.  48 hr following transfection, 1α,25(OH)2D3) at 10-8M in ethanol or an equivalent volume of vehicle was added to primary cultures of human skeletal muscle cells 48 hours and 24 hours prior to isolation of RNA.

value: primary culture of skeletal muscle cells

tag: transfection

value: VDR knockdown

tag: agent

value: ethanol


title: MCF7 polysomal RNA-seq, replicate #1


title: SiR4VD (miRNA)

description: VDR knockdown_1,25(OH)2D3 treatment


title: MCF7 total RNA-seq, replicate #3

description:
mammary gland, breast; derived from metastatic site: pleural effusion
processed data file: cuffdiff2_total_RefSeq.tar.gz
processed data file: cuffdiff2_total_Ensembl.tar.gz


title: SiR3VD (miRNA)

description: VDR knockdown_1,25(OH)2D3 treatment


title: MCF10A total RNA-seq, replicate #1

description:
mammary gland; breast;
processed data file: cuffdiff2_total_RefSeq.tar.gz
processed data file: cuffdiff2_total_Ensembl.tar.gz


title: MCF7 total RNA-seq, replicate #2


title: SiR2ET (miRNA)

description: VDR knockdown_ethanol


title: SiR1ET (miRNA)

description: VDR knockdown_ethanol


title: SiR3ET (miRNA)

description: VDR knockdown_ethanol


title: NEG4VD (miRNA)

description: baseline_1,25(OH)2D3 treatment

value: baseline


title: NEG1VD (miRNA)

description: baseline_1,25(OH)2D3 treatment


title: NEG2ET (miRNA)


title: NEG1ET (miRNA)


title: MCF7 total RNA-seq, replicate #1


title: SiR1VD (miRNA)

description: VDR knockdown_1,25(OH)2D3 treatment


title: MCF10A total RNA-seq, replicate #2


title: NEG2VD (miRNA)

description: baseline_1,25(OH)2D3 treatment


title: NEG4ET (miRNA)


title: NEG3ET (miRNA)


title: SiR4VD (mRNA)

data_processing:
Base calling by CASAVA
Alignment by Tophat2
Gene count by HT-Seq
Normalization by edgeR
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts and normalized counts for all samples

source_name: VDR knockdown_1,25(OH)2D3 treatment

extract_protocol:
RNA was prepared using RNA/protein spin columns (Clontech, Mountain View, CA).  Lysis solution was added to cells in 6-well plates and cells were solubilized by passage of tissue successively through 21 and 27 gauge needles.  Individual cell lysates were applied to RNA spin columns for purification.  RNAs eluted into nuclease-free water were quantitated by UV spectroscopy, quality assessed by 260nm/280nm ratio then frozen at -80 0C.  Before library construction, RNA quality was assessed by capillary electrophoresis against a known size standard.
Poly-A containing mRNA was purified using poly-T oligo attached magnetic beads. The purified mRNA was fragmented and ethanol precipitated. The RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis was performed using DNA polymerase I and RNase H. The cDNA was purified ends were repaired and phosphorylated using Klenow, T4 polymerase, and T4 polynucleotide kinase, after which an “A” base was added to the 3’ ends of double-stranded DNA using Klenow exo- (3’ to 5’ exo minus).  Paired end DNA adaptors (Illumina) with a single “T” base overhang at the 3’ end were ligated. DNA fragments of approximately 250-300 bp were purified on, and excised from agarose gels.  The adapter-modified DNA fragments were enriched by PCR using primers PE 1.0 and PE 2.0 (Illumina). The concentration and size distribution of the libraries was determined on an Agilent Bioanalyzer DNA 1000 chip.
mRNA libraries were loaded onto Illumina TruSeq v3 paired end flow cells at concentrations of 9 pM to generate cluster densities of 600,000-800,000/mm2 following Illumina’s standard protocol using the Illumina cBot and TruSeq Rapid Paired end cluster kit version 3.  The flow cells were sequenced as 51 X 2 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 3 and HiSeq data collection version 2.0.12.0 software. Base-calling is performed using Illumina’s RTA version 1.17.21.3.

treatment_protocol: Cells were transfected with VDR siRNA or scrambled siRNA.  48 hr following transfection, 1α,25(OH)2D3) at 10-8M in ethanol or an equivalent volume of vehicle was added to primary cultures of human skeletal muscle cells 48 hours and 24 hours prior to isolation of RNA.

value: skeletal muscle cells

tag: transfected with

value: VDR siRNA

tag: treated with

value: 1,25(OH)2D3 treatment


title: SiR4ET (mRNA)

source_name: VDR knockdown_ethanol


title: SiR2VD (mRNA)


title: SiR2ET (mRNA)


title: SiR3VD (mRNA)


title: SiR3ET (mRNA)


title: SiR1VD (mRNA)


title: NEG4ET (mRNA)

value: scrambled siRNA


title: NEG3VD (mRNA)

source_name: baseline_1,25(OH)2D3 treatment


title: SiR1ET (mRNA)


title: NEG4VD (mRNA)


title: SiR2VD (miRNA)

description: VDR knockdown_1,25(OH)2D3 treatment


title: NEG3ET (mRNA)


title: NEG2VD (mRNA)


title: NEG2ET (mRNA)


title: NEG1ET (mRNA)


title: NEG1VD (mRNA)


title: SHC-01H-CA1-NON-H3K9AC-2

value: 3 months old

value: male

value: non neuron


title: NEG3VD (miRNA)

description: baseline_1,25(OH)2D3 treatment


title: M180 r2

city: Valencia

first: Sonia

last: Tarazona

address: Eduardo Primo de Yúfera

country: Spain

institute: Centro de Investigación Príncipe Felipe

data_processing:
FastQC tool was used to check the quality of the sequencing reads.
TopHat software was used to map the reads to the A. fumigatus reference genome (strain Af293, version 14) downloaded from EnsemblFungi website.
htseq-count tool was used in order to obtain the number of reads mapped to annotated genes.
Counts were normalized to RPKM values and ASCA method was used to remove the batch effect from the data
The NOISeq method was applied on the batch-corrected data to compute differential expression.
Genome_build: Af293
Supplementary_files_format_and_content: text file including RPKM values

organism: Aspergillus fumigatus

source_name: Mycelium

growth_protocol: A. fumigatus was grown 16 h in minimal medium, harvested and pooled.

extract_protocol:
A. fumigatus mycelia was disrupted by grinding with liquid nitrogen, and total RNA was extracted with RNeasy plant (Qiagen, Germany)
RNA libraries were prepared for sequencing by GATC Biotech (Konstanz, Germany). using two different methods. For replicate 1, the time point pre, B30 and B180 the SMART protocol was used and for r1 M30 and M180 and all r2 time points the TrueSeq protocol was used. Paired end sequencing (Read length 100 bp) was carried out on Illumina HiSeq 2000 by GATC Biotech.

treatment_protocol: Mycelia were split in tubes with convenient media (Blood or Minimal) or directly frozen in liquid nitrogen (pre). There are 2 biological replicates per condition (experiments Blood5 and Blood7 1, from different blood extractions). They were several times inverted and incubated on a rotator at 37°C for 15, 30, 60, 90, 180 min followed by harvesting and shock freezing in liquid nitrogen.

value: Mycelium

tag: growth condition

value: Minimal Medium

tag: experiment


title: B30 r2

value: Human Blood


title: B180 r2


title: M180 r1


title: pre r2

value: Pre


title: M30 r1


title: M30 r2


title: B180 r1


title: B30 r1


title: pre r1


title: Promoter Capture Hi-C, Jurkat T lymphocyte cells, replicate one & two

city: Manchester

first: Paul

last: Martin

state: Greater Manchester

address: Oxford Road

department: Centre for Genetics and Genomics Versus Arthritis

country: United Kingdom

institute: Univeristy of Manchester

description: This Sample represents 2 replicates

data_processing:
Library strategy: Hi-C
Casava software (v1.8, Illumina) was used to make base calls.
reads failing Illumina filters were removed before further analysis
Sequences were output in FASTQ format, poor quality reads truncated or removed as necessary, using Trimmomatic version 0.3023, and subsequently mapped to the human reference genome (GRCh37/hg19) and filtered to remove experimental artefacts using the Hi-C User Pipeline (HiCUP, http://www.bioinformatics.babraham.ac.uk/projects/hicup/).
Off-target di-tags, where neither end mapped to a targeted fragment, were removed from the final data sets using a combination of BEDTools and command line tools.
Genome_build: hg19
Supplementary_files_format_and_content: BEDPE files include on-target read counts
Supplementary_files_format_and_content: BED files include capture bait coordinates (region_baits_coordinates.bed.gz & promoter_baits_coordinates.bed.gz)

source_name: Jurkat T lymphocyte cells

growth_protocol: Jurkat cells were cultured in RPMI 1640/20 mM L-glutamine supplemented with 10% fetal bovine serum in 25cm2 vented culture flasks at 37C/5% CO2

extract_protocol:
Cells were thawed on ice and re-suspended in 50ml freshly prepared ice-cold lysis buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% Igepal CA-630, one protease inhibitor cocktail tablet). Routinely, two pellets from each cell line were re-suspended and combined in 7ml complete lysis buffer to give ~50-60million cells. Cells were lysed on ice for a total of 30 min, with 2x10 strokes of a Dounce homogeniser with a 5 minute break between Douncing. Following lysis, the nuclei were pelleted and washed with 1.25xNEB Buffer 2 then re-suspended in 1.25xNEB Buffer 2 to make aliquots of 5-6million cells for digestion. Following lysis, Hi-C libraries were digested using HindIII then prepared as described in van Berkum et al with modifications described in Dryden et al.
Pre-Capture amplification was performed with 8 cycles of PCR on multiple parallel reactions from Hi-C libraries immobilised on Streptavidin beads which were pooled post-PCR and SPRI bead purified. The final library was re-suspended in 30µl TLE and the quality and quantity assessed by Bioanalyzer and qPCR. Hi-C samples corresponding to 750ng were concentrated in a Speedvac then re-suspended in 3.4μl water. Hybridisation of SureSelect custom promoter and region capture libraries to Hi-C libraries was carried out using Agilent SureSelectXT reagents and protocols. Post-capture amplification was carried out using 6 cycles of PCR from streptavidin beads in multiple parallel reactions, then pooled and purified using SPRI beads.

treatment_protocol: Cells were fixed in 2% formaldehyde for 10 minutes at room temperature, followed by the addition of cold 1M glycine to a final concentration of 0.125M for 5 minutes at room temperature, then by 15 minutes on ice.

value: Jurkat

tag: restriction enzyme

value: HindIII


title: Region Capture Hi-C, Jurkat T lymphocyte cells, replicate one & two

description: This Sample represents 2 replicates


title: Promoter Capture Hi-C, GM12878 Lymphoblastoid cells, replicate one & two

description: This Sample represents 2 replicates

source_name: GM12878 Lymphoblastoid cells

growth_protocol: GM12878 cells were cultured in RPMI 1640/20 mM L-glutamine supplemented with 15% fetal bovine serum in 25cm2 vented culture flasks at 37C/5% CO2


title: IA_8_2

status: Public on Nov 23 2015

city: Champaign

first: Chia-Ching

last: Chu

state: IL

address: 1910 Griffith Drive

institute: University of Illinois at Urbana Champaign

description: wild-type Diabrotica virgifera virgifera adults from Ames, Iowa fed on soybean foliage (Glycine max ‘Williams 82’) for 8 hours

data_processing:
FASTQ files were generated and demultiplexed using Casava 1.8.2
Reads were mapped using the assembled and annotated non-redundant WCR gut transcriptome using Bowtie 2.0.2
The output SAM file was parsed to find unique alignments, then converted to BAM format and sorted using SAMtools 0.1.18
Supplementary_files_format_and_content: gene counts

organism: Diabrotica virgifera virgifera

source_name: digestive tract

growth_protocol: Insects were sampled from corn fields and maintained on corn ear diets in the laboratory

extract_protocol:
Complete intestinal tracts were removed using forceps, soaked in 50 uL of RNAlater (Ambion, Inc.) and stored (within the solution) at -80°C until use. Total RNA was extracted from these samples using the E.Z.N.A. Total RNA Kit I (Omega Bio-Tek; including DNase treatments). Rootworm populations were grouped into three phenotypic groups based on the documented range where RR-WCR have been reported and previous phenotypic characterization on these populations. The Higginsville (Missouri) and Concord (Nebraska) populations were grouped as WT populations, while the Urbana, Minonk and Shabbona populations from Illinois were classified as RR populations. An additional wild-type population from Ames, Iowa that exhibited a slightly elevated tolerance of soybean diet (yet lower than RR populations) in a previous study was sequenced separately. For each dietary treatment, RNA samples from populations within each “phenotype” were pooled (at equal mass; resulting a "sequencing sample"). For example, one RNA sample from Higginsville WCR fed with corn diets was pooled with another from Concord WCR fed with the same corn diet, resulting an independent “pooled WT x corn” sample. Two biological replicates of such sequencing samples from nine “phenotype x diet” treatments (eighteen in total) were included in this study.
RNA-seq libraries were prepared with Illumina's TruSeq RNA Sample Prep kit. Both single and paired-end sequencing were used in this study. For single-end reads, the libraries were quantitated by qPCR, and sequenced on two lanes for 101 cycles on an Illumina HiSeq2000 (Illumina, Inc.) using V3 SBS sequencing chemistry. For paired-end reads, the same libraries were sequenced on one lane for 101 cycles from each end.

treatment_protocol: Western corn rootworm (WCR) adults from each population were caged on soybean plants for 8 or 36 h, or offered a corn ear diet (under 24°C, 70–90% RH, 14:10 [L:D] photoperiod). Prior to soybean dietary treatments, insects were starved for 48 h (with water access) to promote soybean feeding. Two independent replicates of gut samples were collected for each “population x diet” treatment; each biological replicate was pooled with complete intestinal tracts from five beetles.

tag: developmental stage

value: adult stage

tag: isolate

value: wild-type from Iowa

tag: diet

value: soybean (8 h)


title: IA_36_2

description: wild-type Diabrotica virgifera virgifera adults from Ames, Iowa fed on soybean foliage (Glycine max ‘Williams 82’) for 36 hours

value: soybean (36 h)


title: IA_36_1


title: Region Capture Hi-C, GM12878 Lymphoblastoid cells, replicate one & two

description: This Sample represents 2 replicates


title: RR_8_2

description: rotation-resistant Diabrotica virgifera virgifera adults from Urbana, Minonk, and Shabbona (Illinois) fed on soybean foliage (Glycine max ‘Williams 82’) for 8 hours

value: rotation-resistant


title: RR_8_1


title: IA_8_1


title: IA_0_2

description: wild-type Diabrotica virgifera virgifera adults from Ames, Iowa fed on corn ears (Zea mays ‘Sugar Buns’)

value: corn


title: WT_36_2

description: wild-type Diabrotica virgifera virgifera adults from Concord, Nebraska and Higginsville Missouri fed on soybean foliage (Glycine max ‘Williams 82’) for 36 hours

value: wild-type


title: PMC42ET-9d-C_S78

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

data_processing:
Alignment to hg19 using Bismark (v0.90), mismatch=0, seed sequence=28
bismark_methylation_extractor on alignment files
Methpat processing of bismark_methylation_extractor output
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file containing amplicon of interest, DNA methylation pattern in strings of 0 and 1, and counts of patterns. (0 unmethylated, 1 methylated)

source_name: Human Cell Line

extract_protocol:
Phenol-Chloroform, Ethanol Precipitation
Tagged Bisuflite PCR Primers, PCR amplification
Index Barcoding as per Illumina protocol

tag: type

value: Breast cancer cell line

tag: treatment

value: control


title: PMC42LA-9d-C_S73


title: PMC42ET-9d-EGF_S79

value: EGF


title: PMC42ET-72h-EGF_S77


title: WT_36_1


title: WT_8_1

description: wild-type Diabrotica virgifera virgifera adults from Concord, Nebraska and Higginsville Missouri fed on soybean foliage (Glycine max ‘Williams 82’) for 8 hours


title: PMC42LA-72h-C_S71


title: LA-S2-3-9_S88


title: WT_8_2


title: WT_0_2

description: wild-type Diabrotica virgifera virgifera adults from Concord, Nebraska and Higginsville Missouri fed on corn ears (Zea mays ‘Sugar Buns’)


title: RR_36_2

description: rotation-resistant Diabrotica virgifera virgifera adults from Urbana, Minonk, and Shabbona (Illinois) fed on soybean foliage (Glycine max ‘Williams 82’) for 36 hours


title: RR_36_1


title: LA-C3-3-9_S86


title: ET-S2-3-9_S84


title: LA-C1-3-9_S85


title: PMC42LA-72h-EGF_S72


title: RR_0_1

description: rotation-resistant Diabrotica virgifera virgifera adults from Urbana, Minonk, and Shabbona (Illinois) fed on corn ears (Zea mays ‘Sugar Buns’)


title: RR_0_2


title: 468-S1-3-9_S91


title: PMC42LA-9d-EGF_S74


title: PMC42LA-9d-TGFb_S75

value: TGF


title: Sample 26

source_name: Primary human sample

value: Primary human sample


title: Sample 29


title: PMC42ET-9d-TGFb_S80


title: Sample 23


title: IA_0_1


title: LA-S1-3-9_S87


title: WT_0_1


title: ET-S1-3-9_S83


title: PMC42ET-72-C_S76


title: ET-C1-3-9_S81


title: Sample 16


title: ET-C2-3-9_S82


title: 468-S2-3-9_S92


title: Sample 12


title: Sample 11


title: 468-C2-3-9_S90


title: Sample 25


title: Sample 27


title: 468-C1-3-9_S89


title: Sample 28


title: Sample 21


title: Sample 19


title: Sample 18


title: Sample 17


title: Sample 3


title: Sample 4


title: Sample 1


title: Sample 13


title: Sample 14


title: Sample 15


title: Sample 24


title: Sample 22


title: OVCAR8

description: Cancer cell line

source_name: Cell Line


title: SKNAS

description: Neuroblastoma cancer cell line

value: SKNAS (ATCC CRL2137)


title: Sample 9


title: Sample 20


title: Sample 8


title: Sample 7


title: JWL

description: Normal lymphoblast cell line

value: JWL


title: Sample 5


title: U231

description: Cancer cell line


title: Sample 2


title: HTB22-Col

description: MCF7 breast cancer cell line

value: HTB22-Col (ATCC HTB22)


title: NCCIT

description: Embryonic carcinoma cell line

value: NCCIT (ATCC CRL-2073)


title: 207_R3

city: Shanghai

first: Han

last: Xiao

address: 300 Fenglin Rd

department: National Key Laboratory of Plant Molecular Genetics

institute: Shanghai Institutes for Biological Sciences

description: RNAi line 207

data_processing:
Reads were mapped to tomato genome using Tophat program v.1.3.2 (Trapnell et al. 2009). Then the transcripts were assembled using cufflinks based on transcripts predicted in SL2.40 assembly from SGN (Trapnell et al. 2010).The expression values of the transcripts were calculated in fragments per kilobase of transcript per million mapped reads (FPKM) (Mortazavi et al. 2008).
Genome_build: Tomato genome assembly SL2.40 from SGN (Sol Genomics Network: solgenomics.net)
the values of columns B-G in 'cds_exp_diff_2D.txt' are FPKM calculated by Cufflinks.

organism: Solanum pimpinellifolium

source_name: 2 dpa fruits,replicate 3

growth_protocol: Tomato plants including the transgenic lines were grown in phytotron under the condition of temperature at 20-25 °C and humidity of 70-80%, illuminated for 16 hours daily by light of 150 mE·m–2·s–1 from metal halide and high pressure sodium lamps. Plants were fertilized weekly with all-purpose fertilizer and watered as needed.

extract_protocol:
Total RNA was extracted by Trizol reagent (InvitroGen) from shoot tips including one small visible leaf were collected from one and half month old plants.
Libraries were constructed with Illumina TruSeq Stranded mRNA LT kit

treatment_protocol: 2 dpa fruits were from hand-pollinated flowers.

tag: strain

tag: genotype

value: transgenic, line 207

tag: age

value: two-months old


title: Sample 6


title: 207N_R3

description: nontransgenic sibling

value: wild type


title: 207N_R2

description: nontransgenic sibling

source_name: 2 dpa fruits,replicate 2


title: MCF7

description: Breast cancer cell line

tag: cell line

value: MCF7 (ATCC HTB22)


title: Sample 10


title: HELA

description: Cancer cell line

value: HELA (ATCC CCL-2)


title: 207N_R1

description: nontransgenic sibling

source_name: 2 dpa fruits,replicate 1


title: MB231BAG

description: Breast cancer cell line

value: MB231BAG (ATCC HTB-26)


title: NALM6

description: Leukaemia cell line

value: NALM6 (ACC 128)


title: 9A-Whole-Blood

source_name: Blood

tag: tissue

value: Whole blood sample from individual 9A


title: LS174T

description: Cancer cell line


title: EKVX

description: Cancer cell line

value: EKVX


title: HT1080

description: Cancer cell line

value: HT1080 (ATCC CCL121)


title: K562

description: CML cancer cell line


title: HEPG2

description: Liver cancer cell line

value: HEPG2 (ATCC HB-8065)


title: 9A-CD33

source_name: Bone marrow

value: Normal Fluorescent Activated Cell Sorted (FACS) CD33 positive bone marrow cells from individual 9A


title: DG75

description: Lymphoblast cancer cell line

value: DG75 (ATCC CRL-2625)


title: 207_R1

description: RNAi line 207


title: CaCo

description: Caco2 Colon cancer cell line

value: Caco-2 (ATCC HTB37)


title: BRL

description: Normal lymphoblast cell line

value: BRL


title: 6C-CD34

tag: sample type

value: Normal Fluorescent Activated Cell Sorted (FACS) CD34 positive bone marrow cells from individual 6C


title: 910046

source_name: Fibroblast

value: Normal fibroblast cell line


title: 207_R2

description: RNAi line 207

value: transgenic, line 207


title: 6-MDA453

value: MDA-MB-453 metastatic breast cancer cell line. ATCC HTB-131


title: 9A-CD45

value: Normal Fluorescent Activated Cell Sorted (FACS) CD45 positive bone marrow cells from individual 9A


title: 9A-CD34

value: Normal Fluorescent Activated Cell Sorted (FACS) CD34 positive bone marrow cells from individual 9A


title: 9A-CD19

value: Normal Fluorescent Activated Cell Sorted (FACS) CD19 positive bone marrow cells from individual 9A


title: 293

value: HEK-293 embryonic kidney cell line. ATCC CRL1573


title: 6C-CD45

value: Normal Fluorescent Activated Cell Sorted (FACS) CD45 positive bone marrow cells from individual 6C


title: 12A-CD45

value: Normal Fluorescent Activated Cell Sorted (FACS) CD45 positive bone marrow cells from individual 12A


title: 12A-CD19

value: Normal Fluorescent Activated Cell Sorted (FACS) CD19 positive bone marrow cells from individual 12A


title: 12A-CD34

value: Normal Fluorescent Activated Cell Sorted (FACS) CD34 positive bone marrow cells from individual 12A


title: 40424


title: 12A-CD33

value: Normal Fluorescent Activated Cell Sorted (FACS) CD33 positive bone marrow cells from individual 12A


title: H3K4me3_Trim33-/-_24h

city: Fontenay aux roses

first: federica

last: ferri

address: 18 route du panorama

institute: cea

data_processing:
Illumina Casava software used for basecalling.
Sequence reads were mapped to reference genome mm9/NCBI37 using Bowtie v0.12.7 with the following parameters -m 1 --strata --best.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)

source_name: bone marrow derived macrophages

growth_protocol: Bone marrow cells were cultured in IMDM supplemented with 10% FCS (Invitrogen) 10μM thioglycerol (Sigma) and 25ng/ml mouse CSF1 (Milteny Biotech).

extract_protocol: ChIP-seq libraries were prepared using ChIP-Seq Sample Prep Kit (#IP-102-1001, Illumina) following the manufacturer's protocol with some modifications. Briefly, 10 ng of ChIP enriched DNA or control DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 14 cycles; 5 min at 72°C) and then purified using Agencourt AMPure XP beads (#A63881, Beckman). DNA library size selection was performed by excising the 250-350 bp fragments from a 2% agarose gel followed by purification using a QIAquick Gel Extraction Kit (#28906, Qiagen).

treatment_protocol: On day 7, macrophages were treated for 4h, 12h and 24h  with 100ng/ml LPS (Sigma) in IMDM supplemented with 2.5% FCS. Cells were cross-linked with 1% formaldehyde for 10 min at 37°C, lysed in SDS lysis buffer [50 mM Tris pH8, 10 mM EDTA, 1% SDS, protease inhibitor cocktail (Roche)] and sonicated (cycle conditions: 15sec ON/30sec OFF, 15 min; Bioruptor, Diagenode) to obtain DNA fragments with an average length of 200-600 bp. Supernatant was diluted 10 times in IP dilution buffer [16.7 mM Tris pH8, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X100, 0.01% SDS, protease inhibitor cocktail (Roche)] and immunoprecipitations were performed using 5μg of specific antibodies. Immunoprecipitated chromatin was collected using protein A agarose/Salmon Sperm DNA beads (Millipore) and, after washing and elution, reverse cross- linking was carried out with 0.2M NaCl at 65°C overnight. The chromatin was then digested by 20 μg of Proteinase K (Invitrogen) for 1h at 45°C and isolated by phenol- chloroform extraction.

tag: cell type

value: bone marrow derived macrophages

tag: chip antibody


title: H3K4me3_Trim33-/-_4h


title: H3K4me3_WT_24h

value: wild type


title: H3K4me3_Trim33-/-_0h


title: H3K4me3_Trim33-/-_12h


title: TRIM33_macrophage_24h


title: H3K4me3_WT_12h


title: H3K4me3_WT_4h


title: TRIM33_RAW

source_name: RAW

value: macrophage ce line

value: BALB/c


title: RNA from A549 cell, 12 hrs

city: Riverside

first: Weifeng

last: Gu

state: California

address: 900 University Ave

department: Molecular, Cell and Systems Biology

institute: University of California at Riverside

description:
5' barcode CCTT
A549 cell, 12 hrs

data_processing:
Library strategy: CAP-Seq
The original reads are grouped according to the barcodes, and debarcoded.
The first 40 nt of each read was extracted and mapped to human genome and annotations, and the unmatched reads were obtained
A unmatched read was split into two halves: the first 20 nt and the last 20nt. The last 20 nt was mapped to influenza genome, and the match was extended using the sequence from the first 20nt with match bonus +1 and penalty -3. The extension with the best score was chosen, and the leftover of the first 20 nt was considered as the sequence snatched by the virus.
Human transcription start sites were defined using the CapSeq data. The snatched sequences were mapped to the transcription start site regions.
Genome_build: Ensembl GRCh37 release 71
Supplementary_files_format_and_content: tabbed txt file containing the first 40 nt of each read used for the analysis

source_name: A549 cell, 12 hrs

growth_protocol: A549 cells (American Type Culture Collection, ATCC) were seeded at 2.5 x 105 cells per well (0.5 ml per well) in a 24-well plate in F-12K medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37°C overnight. Influenza A Brisbane/59/2007 (H1N1), originally obtained from NIH Biodefense and Emerging Infections Research Resources Repository, NIAID, NIH (NR-12282; lot 58550257), was propagated in Madin-Darby canine kidney cells (ATCC) for three passages. Virus was added to A549 cells at a multiplicity of infection of 1 in 100 ul of influenza virus growth medium [DMEM with 100 U/ml penicillin, 100 mg/ml streptomycin, 7.5% bovine serum albumin, and 0.2 mg/ml TPCK-treated-trypsin (Sigma)]. After incubation at 37°C for 1 h, cells were washed once with Hank’s Balanced Salt Solution and 500 ul of influenza virus growth medium was added to each well. Cells were again incubated at 37°C and at 24 h following infection, supernatants from four wells were pooled together and cells were harvested in TRIzol reagent. Minimal cytopathic effect was observed in A549 cells post-infection. The experiment was repeated once with cells collected at 12 h post-infection instead of 24 h.

extract_protocol:
RNAs were extracted with TRIzol
The capped RNAs were enriched by terminator exonuclease from 1-2 ug of total RNA, decapped, 5' ligated with a barcoded linker and 3' random-primed. A detailed procol can be downloaded from the supplementary information in Cell, Volume 151, Issue 7, 21 December 2012, Pages 1488–1500
5' RNA ligation and 3' random priming

treatment_protocol: The A549 cells are infected with influenza virus for 12 and 24 hrs.


title: RNA from A549 cell, infected by influenza virus A for 12 hrs

description:
5' barcode CAGT
A549 cell, infected by influenza virsu A for 12 hrs


title: RNA from A549 cell, infected by influenza virus A for 24 hrs

description:
5' barcode ATCA
A549 cell, infected by influenza virsu A for 24 hrs


title: RNA from A549 cell, 24 hrs

description:
5' barcode CAGT
A549 cell, 24 hrs

source_name: A549 cell, 24 hrs


title: H3K4me3_WT_0h


title: 6C-CD33

value: Normal Fluorescent Activated Cell Sorted (FACS) CD33 positive bone marrow cells from individual 6C


title: 6C-CD19

value: Normal Fluorescent Activated Cell Sorted (FACS) CD19 positive bone marrow cells from individual 6C


title: CHL-1 untreated

city: Stanford

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

data_processing:
Library strategy: Ribosome profiling
Adaptor sequence was trimmed from reads, rRNA reads were removed using Bowtie2 and Non-rRNA reads were then mapped to hg19 using Tophat2
Ribosome binding for Refseq mRNAs was derived by converting genome-mapped reads to transcriptome mapped reads in a tab format using the refseq transcriptome (UCSC genome browser) as a reference
Genome_build: hg19
Supplementary_files_format_and_content: Average ribosome-binding density for size-normalized refseq transcripts was calculated for each sample. Average Graphs showing ribosome binding distributions - Transcript base read density was calculated from transcriptome-guided, genome-mapped reads by using a script that quantifies the number of reads at each base for each refseq transcript (from a bedGraph file). For refseq transcripts, the total number of reads at each base was calculated. The average number of reads at each base was then calculated for all refseq transcripts. To facilitate clear comparisons between treatment conditions, each sample was normalized using the median average read value for refseq transcripts. That is, for each treatment condition, the average number of reads at each base was divided by the median of the average reads for all transcripts. These normalized read density values were visualized using Prism 6.0 (Graphpad Software Inc.). Pausing Index calculation - We calculated the pausing index for transcripts with a ribosome binding density of >15rpkm. This ensured that transcripts included in the analysis were at least moderately expressed. To calculate the pausing index we calculated the sum of base reads over the first and last 10 codons. Dividing the 5’PI/3’PI yielded the pausing index score.

source_name: CHL-1 melanoma cells

growth_protocol: CHL-1 cells were cultured in DMEM, 10%FBS,

extract_protocol:
Cells were washed with ice-cold PBS, lysed on ice with cyclohexamide-containing buffer
Sequencing library was prepared as described in Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc. 2012, 7(8):1534-50

treatment_protocol: To induce ribosomal stress were treated with a combination of the amino acid analog L-azetidine-2-carboxylic-acid (AZC, 10mM) and proteasome inhibitor MG132 (20uM) for 20 minutes

value: melanoma cell line


title: CHL-1 + CRISPR

value: CRISPR SNORD50A/B


title: CHL-1 + CRISPR rRNA removed

value: CRISPR SNORD50A/B - rRNA removed


title: CHL-1 untreated - rRNA removed

value: CHL-1 rRNA removed


title: 10mM AZC + MG132

value: 10mM AZC + MG132


title: GA7622-Gata3 KO2-NKp46+ ILC3

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Basecalls performed using CASAVA 1.0
Sequence reads were mapped to the mouse (mm9) genomes with bowtie2 (2.2.2) with default settings. We kept one hit if multiple reads were mapped to the same position for each RNA-Seq libraries.
For each RNA-Seq sample, gene expression was quantified by RPKM with in-house script and RefSeq gene annotation. For each ChIP-Seq data, a BEDGraph file was generated to visuliaze the read density, with a bin size of 200 bps; the number of reads per bin is normalized against total read number and bin size.
Genome_build: mm9
Supplementary_files_format_and_content: rpkm: plan text file. Columns from left to right denote RefSeq ID, RPKM, gene transcript size, number of read mapped to exons, a combination of RefSeq ID, gene symbol, etc, and reserved column for future development.
Supplementary_files_format_and_content: bedGraph txt: Columns from left to right denote chromsome, bin start position, bin ending position, normalized read density.

source_name: type 3 Innate lympoid cells (ILC3s)

growth_protocol: For in vitro cultured Th2 cells,  naïve CD4+ T cells from C57BL/6 mice were sorted and differentiated to Th2 cells with T cell depleted splenic antigen presenting cells plus anti-CD3, anti-CD28, IL-4, anti-IFN-gamma, anti-IL-12, IL-2 for three days, and rested with IL-2 for additional two days or more. The differentiation was repeated for three rounds,

extract_protocol:
For total ILC3 RNA-Seq, live Lineage-CD127+Thy1highKLRG-1- cells were sorted from siLP of Gata3fl/fl and Gata3ΔILC3 mice by FACSAria.  Total RNA was purified by QIAzol lysis reagent and miRNeasy Micro Kit (Qiagen). 10-20 ng of total RNA was amplified with the Ovation RNA-Seq System V2 (NuGEN).   For ILC3 subsets RNA-Seq, indicated ILC3 subsets were sorted based on RORgt-E2-Crimson, Tbet-ZsGreen reporters and CCR6, NKp46 staining. Library prepare refer to the protocol above.  For ChIP-Seq, live Lineage-CD127+Thy1highKLRG-1-NK1.1- ILC3s were sorted from siLP of Rag1-/- mice, live Lineage-CD127+Thy1+KLRG-1+ ILC2s were sorted from mesenteric lymph nodes of IL-25-injected Rag1-/- mice, and Th2 cells were prepared from three round differentiated naïve CD4+ T cells as previous described. Cells were cross-linked with 1% formaldehyde for 10 min.
For RNA-Seq, the double-stranded cDNA was sonicated (30” on and 30” off for 20 cycles) to an average size of 200 bp by Bioruptor Pico (Diagenode). Indexed sequencing libraries were then generated using 250 ng sonicated cDNA with the KAPA LTP Library Preparation Kit (KAPABiosystems) according to the manufacture’s protocol with minor modifications. Multiplex sequencing reads of 50 bp were generated by the NHLBI DNA Sequencing and Computational Biology Core.  For ChIP-Seq,  chromatin was prepared by sonication with Bioruptor Pico (30” on and 30” off for 9 cycles) and immunoprecipitated with anti-GATA3 (L50-823) and anti-mouse IgG-coated magnetic beads using iDeal ChIP-Seq Kit for transcription factors (Diagenode). ChIPed DNA was made into an indexed library and sequenced as described above for RNA-Seq.

tag: genotype/variation

value: Gata3 KO

tag: in vivo treatment

value: isolated from small intestine lamina propria

tag: in vitro treatment


title: GA7626-ILC3 GATA3 ChIP

value: Rag1 KO

tag: antibody


title: GA7625-ILC3 GATA3 ChIP input

value: anti-mouse IgG


title: GA7618-WT2-NKp46+ ILC3

value: wildtype


title: GA7627-ILC2 GATA3 ChIP

source_name: type 2 Innate lympoid cells (ILC2s)

value: three IL-25 injections then isolated from mesenteric lymph nodes


title: GA7628-Th2 GATA3 ChIP

source_name: type 2 T helper cells (Th2s)

value: three rounds in vitro differentiated Th2 cells


title: GA7621-Gata3 KO2-CCR6+ ILC3


title: GA7614-Gata3 KO1-NKp46+ ILC3


title: GA7613-Gata3 KO1-CCR6+ ILC3


title: GA6451-ILC3-Gata3 KO2

value: C57BL/6 Gata3fl/fl-Rorc(gt)-Cre


title: GA7610-WT1-NKp46+ ILC3


title: GA7617-WT2-CCR6+ ILC3


title: GA6450-ILC3-Gata3 KO1


title: GA6449-ILC3-WT2


title: GA7609-WT1-CCR6+ ILC3


title: GA6448-ILC3-WT1


title: Pou3f1_ChIPD2.fastq

city: Guangzhou

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

department: Guangzhou Institutes of Biomedicine and Health

institute: Chinese Academy of Sciences

data_processing:
Raw reads were mapped to mm9 with TopHat version 1.4.1
FPKM for each gene as expression value was assigned by cufflinks version 1.3.0
Cuffdiff was used to identify differentially expressed genes
ChIP-seq reads were aligned with SOAP version 2.20 to the mouse genome build mm9
findPeaks software of Homer was used to identify Oct6 binding peaks with 4 fold more normalized tags in experiment group than control
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, bed file includes the tag density

source_name: Embryonic stem cell

growth_protocol: Mouse embryonic stem cells(mESCs) (R1 and R1/E) were maintained on a layer of mitomycin C-treated mouse embryonic fibroblast feeder cells in standard medium supplemented with 1,000 U/mL mouse leukemia inhibitory factor (LIF). Unbiased ESC differentiation in serum-containing medium was performed as described previously (Zhang, T., et al.,2013)

extract_protocol:
For ChIP-seq, cell lysates were clarified from sonicated nuclei and Pou3f1-DNA complexes were precipitated with Pou3f1 antibody (Santa Cruz, sc-11661, Lot# C2012), then genomic DNA was recoveried and purified for subsequent library construction.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Differentiation cells with or without Pou3f1 overexpression

value: Pou3f1-overexpressing ESC

tag: time

value: ESC neural differentiation day2


title: 10mM AZC + MG132 - rRNA removed

value: 10mM AZC + MG132 - rRNA removed