title: Stallion sperm transcriptome 1

city: College Station

first: Pranab

middle: Jyoti

last: Das

state: TX

address: Room 314B Bldg. 1197

department: Department of Veterinary Integrative BioSciences

institute: Texas A&M University

data_processing:
The 50 bp single-end SOLiD raw reads were directly aligned with the horse reference sequence EcuCab2 using ABI aligner software (NovoalignCS version 1.00.09, novocraft.com) which uses multiple indexes in the reference genome, identifies candidate alignment locations for each primary read, and allows completion of the alignment.
The single highest-scoring alignment for each raw read was mapped. Alignments in repetitive sequences were discarded by removing reads with multiple similarly scoring alignments (non-unique matches).
Sequence alignment and alignment clustering to define expressed loci and perform linear normalization across the two sperm RNA samples was carried out with a software package EXP (Cofactor Genomics).
Gene expression level or average coverage (AC) was calculated by normalizing each sample to the fewest reads and directly comparing different loci. Expression level of a transcript was estimated from the number of reads that mapped to that transcript.
The variability present in sequencing depths in different samples was taken care of by the use of two biological replicates. Sequencing depth at each locus and differences in gene expression (AC) between the two sperm samples were calculated using log (base2) ratio, thus showing the association between the two samples.
Genome_build: EcuCab2
Supplementary_files_format_and_content: tab-delimited text files include chromosomal location of 19,257 RNA Seq tag combining two biological replicate with their expression value (Average Coverage), Average coverage≥1

organism: Equus caballus

source_name: Stallion Spermatozoa

extract_protocol: Total RNA was isolated from sperm with TRIzol reagent (Invitrogen). Total RNA from the sperm of reproductively normal stallions was used for next generation sequencing (NGS) on the ABI SOLiD platform. THE TOTAL 500 ng of total RNA was directly used for SOLiD single-end RNA sequencing fragment library construction according to the ABI protocol

treatment_protocol: Fresh sperm ejaculates from reproductively normal stallions were collected using an artificial vagina. The ejaculates were first evaluated for sperm concentration, motility characteristics and morphological features, followed by purification from somatic cells and immature sperm by EquiPure™ (Nidacon International, Sweden) discontinuous gradient centrifugation.

tag: fertility stutus

value: Normal fertile male

tag: tissue

value: Sperm


title: RN2/shRnf20.3595

status: Public on Feb 19 2013

type: SRA

city: Cold Spring Harbor

first: Shinpei

last: Kawaoka

address: 1 Bungtown road

country: USA

institute: Cold Spring Harbor Laboratory

library_source: transcriptomic

data_processing:
FastaX-trimmer was used for removing adaptor sequences
The trimmed reads were mapped to mouse genome (mm9) using bowtie
Cufflinks software was used to compare gene expression profiles between shRen.713-treated cells and shRNF20 shRNAs-treated cells
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

molecule: total RNA

organism: Mus musculus

growth_protocol: The Tet-on-competent leukemia cells (RN2) were cultured in RPMI1640 media supplemented with 10%FBS and 1%P/S

extract_protocol:
Total RNAs were extracted using Trizol reagent.
"Not so random" primer-based RNA-seq libraries were constructed as described previously (Armour et al. 2009 Nature Methods)

treatment_protocol: RN2 cells harboring a Doxyclycline-inducible shRNA (shRen.713/shRNF20.3277/shRNF20.3595) were treated with doxycycline for 4 days and harvested.

tag: cell type

value: Acute myeloid leukemia

tag: strain

tag: cell line


title: wild type_reps1-3

city: Honolulu

first: Yangrae

last: Cho

state: HI

address: 3190 Maile Way, St John 317

department: Plant and Environmental Protection Sciences

institute: University of Hawaii at Manoa

description: biological replicates 1-3

data_processing:
Sequence tags were mapped to the genome sequence of A. brassicicola using the programs TopHat 1.3.1 [69] and Bowtie 0.12.7 [70].  Default settings were used, except the segment length was set at 25 nucleotides and the number of allowed segment mismatches was set at 1 nucleotide.  Additionally, intron length was designated as a minimum of 10 nucleotides and a maximum of 400 nucleotides.  The program Cuffdiff, version 1.0.3, which is part of Cufflinks [71], was used to identify reads overlapping with previously predicted genes.  The expression levels of each predicted gene were determined and normalized by the mapped Fragments Per Kilobase of exon model per Million (FPKM).  Differentially expressed genes between the wild type and the mutant were determined by comparing FPKMs from three biological replicates for both the wild type and the mutant.  We also applied a cutoff of at least a two-fold change in expression value for differential expression. The bias correction method was used while running Cuffdiff [72].  Custom scripts were written in Python to analyze the data.
Processed data linked as supplementary files on Series record.
Genome_build: version 1; http://jgi.doe.gov/Abrassicicola
Supplementary_files_format_and_content: Processed data files describing proteinId, gene name, expression value of WT, expression value of Δamr1, fold-change, significant difference below P-value 0.05, biological sample that show higher expreesion, PFAM annotation, and GO annotation.

organism: Alternaria brassicicola

source_name: mixture of pathogen and host

growth_protocol: All host plant, Brassica oleracea were grown under 14 hours light 10 hour dark cycle.  Both wild type and Δamr1-4 mutant were grown on PDA plates for 7 days before conidium harvest

extract_protocol: Libaray was constructed with TruSeq (Illumina kit) with mRNA enriched with Agencourt AMPureXP (Beckman Coulter)

treatment_protocol: Conidia were harvested and washed three times with water.  2,000 conidia in 10ul water were inoculated.

tag: genotype/variation

value: wild type

tag: host plant

value: Brassica oleracea

tag: plant cultivar

value: Early green cabbage

value: saprophytic mycellia on necrotized host leaves


title: DR1-sta

status: Public on Feb 16 2013

city: Seoul

first: Jisun

last: Kim

address: Anam-Dong, Sungbuk-Gu

department: Environmental Science and Ecological Engineering

country: South Korea

institute: Korea university

data_processing:
Base-calling: CASAVA v1.6
Alignment: CLC Genomics Workbench 4.5
Generation of normalized abundance measurement: CLC Genomics Workbench 4.5
Genome_build: ASM19679v1; Acinetobacter oleivorans DR1 chromosome, complete genome RefSeq (NC_014259.1)
Supplementary_files_format_and_content: text files containing normalized abundance measurements (including RPKMs)

organism: Acinetobacter oleivorans DR1

source_name: control (stationary)

extract_protocol: Total RNA was isolated from 5 ml of stationary cells, using the RNeasy Mini kit (QIAGEN, USA), according to the manufacturer’s instructions. The RNA was subjected to a subtractive Hyb-based rRNA removal process using the MICROBExpress Bacterial mRNA Enrichment Kit (Ambion). RNA sequencing was performed using the Illumina Genome Analyzer IIx to generate single-ended 36-bp reads.

tag: genotype

value: Wild type

tag: growth phase

value: stationary


title: Ring1b_Kdm2bKD

status: Public on Feb 20 2013

city: Boston

first: Li

last: Shen

address: 200 Longwood Ave

institute: HHMI/Boston Children's Hospital/Harvard Medical School

library_source: genomic

data_processing:
Basecalls were performed using CASAVA version v.1.8.2
Sequenced reads were de-multiplexed, trimmed and mapped to mm8 whole genome using bowtie v0.12.7
Peak calling were performed using MACS 1.4.1, meanwhile, wiggle files were generated
Genome_build: mm8
Supplementary_files_format_and_content: wiggle files (scores represent tag numbers per 10 million reads)

molecule: genomic DNA

source_name: Kdm2b knockdown mouse ES cells

growth_protocol: E14 mESCs are cultured on the 0.1% gelatin coated plates in the DMEM medium (Sigma) supplemented with 100U/ml penicillin/streptomycin, 15% fetal bovine serum (Sigma), 1x nonessential amino acid, 1x sodium pyruvate, 1x GlutaMax, 1x beta-mercaptoethanol (Invitrogen) and 1000 units/ml leukemia inhibitory factor (ESGRO, EMD Millipore).

extract_protocol: Libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (NEB) following manufacture's instructions.

treatment_protocol: Around 1x10^5 ES cells/well in 24-well plates are infected with lentiviral vectors at 10 MOI. 48 hours after transduction, puromycin (2ug/ml) is added to the medium for selecting transduced cells.

tag: chip antibody

tag: antibody manufacturer

value: Cell signaling Technology

tag: antibody catalog number

tag: antibody lot number

value: inbred 129

value: embryonbic stem cells

value: Kdm2b knockdown


title: RN2/shRen.713


title: Δamr1-4_reps1-3

description: biological replicates 1-3

value: Δamr1-4 mutant


title: ΔaqsR-sta

source_name: aqsR mutant (stationary)

value: aqsR mutant type


title: input genomic DNA_brain

status: Public on Feb 15 2013

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

description: Brains were collected from female F1 hybrid (BL6/spretus) carring an Xist mutation (B6.Cg-Xist<tm5Sado>) and thus having complete skewing of inactivation of the spretus X chromosome.

data_processing:
Basecalls performed using CASAVA version 1.4
A pseudo-spretus genome was assembled by replacing available SNPs between C57BL/6J and M. spretus (Sanger Center) into the BL6 reference genome. Reads were aligned to the C57BL/6J reference sequence (mm9, UCSC) and to the pseudo-spretus genome separately using BWA (Burrows-Wheeler Aligner).
Only high-quality uniquely-mapped reads were used for assignment to each haploid genome based on available SNPs.
PolII-S5p peak regions in brain were selected using all uniquely mapped reads by both CisGenome (FDR=1e-5 as the cutoff) and MACS (Model-based Analysis of ChIP-Seq) (p=1e-5 as the cutoff).
The SNP-associated read counts were used to assess average allelic enrichment at the 5’ end and 3’ end of genes.
Genome_build: mm9

organism: Mus musculus x Mus spretus

source_name: Mouse adult hybrid brain

extract_protocol:
ChIP was performed using fixed chromatin from mouse brain or cell lines. DNA from ChIP pull-down chromatin fractions were de-crosslinked and purified using QIAquick PCR purification kit. Genomic DNA was prepared from an aliquot of the same batch of nuclei from F1 brain
Sequencing libraries were prepared each from four pooled independent PolII-S5p ChIP samples from Patski cells or from Xist mutant F1 brain, using the Illumina seq sample prep kit. Size selection of the library was done by gel excision and purification of DNA in the 200-600bp range. Control sequencing library was prepared from genomic DNA prepared from F1 brain.

value: Adult whole brain


title: PolII-S5p_brain_ChIPSeq

value: PolII-S5p, Abcam ab5131


title: H14

city: Dublin

first: Sarah

last: Connell

address: College Green

country: Ireland

institute: Trinity College Dublin

data_processing:
Reads were clipped by 4 bp at the 3' end and aligned with bowtie v0.10.1, allowing 3 mismatches per read.
The number of counts falling on each gene model was determined with Erange v3.3.
Genome_build: Gallus_gallus-2.1 at http://www.ncbi.nlm.nih.gov/assembly/GCF_000002315.2/
Supplementary_files_format_and_content: Tab-separated text file of raw counts per gene for each individual

organism: Gallus gallus

source_name: C. jejuni-susceptible_high colonization

extract_protocol:
Total RNA was extracted with Trizol using the Qiagen RNeasy Lipid purification kit
Libraries were prepared according to instruction in the Illumina protocol Part # 1004898 Rev. A September 2008. Poly-A mRNA was first isolated from total RNA using oligodT beads. The mRNA was then fragmented using divalent cations at 94°C. mRNA was converted to cDNA, blunt-ended at both ends using T4 DNA polymerase and Klenow DNA polymerase. A single A base was then added to the 3′ end to prepare for ligation to adapter sequence. cDNA templates were then size-selected by visualization and excision from agarose gel and purified. The resulting cDNA fragments were PCR-amplified and sequenced generating 40-bp reads using the Illumina Genome Analyzer.

tag: breed

value: Barred Rock chickens

tag: c. jejuni-susceptibility

value: susceptible

tag: caecal colonization level

value: high-colonized

value: whole caecum


title: H11


title: H13


title: H12


title: Kdm2b_Kdm2bKD

description: Kdm2b ChIP-seq was done by Flag antibody because we knocked in a Flag tag upstream of Kdm2b gene.

value: Flag

value: Sigma


title: C. elegans_degradome_02.14.2008

city: SEOUL

first: Chanseok

last: Shin

address: Gwanak-gu Daehak-dong

institute: Seoul National University

data_processing:
7.6 million of 20-nt tags from wild-type adult cleavage libraries were mapped to the C. elegans genome (ce6), requiring a perfect match.
For tags mapped to at most 10 genomic loci, the final tag number was normalized with the loci number.
Of genome-mapping tags, ~70% mapped to exons of annotated genes (RefSeq with new 3′UTR annotations), including rRNAs, ~25% mapped to intergenic regions, ~3% mapped to intronic regions of genes, and 0.5% mapped antisense to annotated genes.
Genome_build: C. elegans genome (ce6)

organism: Caenorhabditis elegans

source_name: Whole organ

extract_protocol:
Worms were harvested at the appropriate stage, washed twice with M9 buffer, and frozen in liquid nitrogen. Total RNA was extracted using Tri-Reagent (Ambion), which was further purified with phenol:chloroform followed by precipitation with ethanol.
Poly(A) RNA was enriched from wild-type adult C. elegans total RNA using the Oligotex mRNA kit (QIAGEN). A custom 5' RNA adapter containing a MmeI recognition site was ligated to the poly(A) RNA possessing a 5'-monophosphate, by T4 RNA ligase, and the ligated products were reverse transcribed. This cDNA was amplified and then digested with restriction enzyme MmeI, which cleaves 20 nts 3’ of the recognition site. This MmeI digested product was ligated to a 3’ double strand adaptor, amplified by PCR, gel-purified and submitted for Illumina sequencing.

value: Wild-type (N2)

tag: developmental stage

value: Adult stage


title: H4

tag: tissue


title: H10


title: H2


title: Stallion sperm transcriptome 2

tag: fertility stutus

value: Normal fertile male

value: Sperm


title: H9


title: H7


title: H6


title: H3


title: H1


title: H8


title: L14

source_name: C. jejuni-resistant_no colonization

value: resistant

value: nil-colonized


title: L12


title: THP1 RNA-seq HG

city: Duarte

first: Nancy

last: Chen

state: CA

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

description: glucose treatment 25 mM

data_processing:
OLB 1.8 was used for base-calling.
Align to an hg18 genome assembly using bowtie with --best option.
Expression levels of Refseq transcripts were summarized by Partek® Genomic Suite (version 6.5 beta, Partek Inc., St. Louis, MO) including raw reads# and RPKM reads# for each Refseq transcripts in hg18.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited data containing refseq gene symbol with its total reads# and PRKM normalized reads# at gene level

organism: Homo sapiens

source_name: THP1 cells High glucose

growth_protocol: RPMI 1640 medium

extract_protocol:
TRIZOL RNA Isolation Protocol
PolyA RNA was depleted of rRNA using RiboMinus kits (Invitrogen)

treatment_protocol: 25 mM glucose for 72 hours

tag: cell type

tag: glucose

value: High 25 mM


title: L11


title: L8


title: L10


title: THP1 RNA-seq NG

description: No Treatment

source_name: THP1 cells Normal glucose

value: Normal 5 mM


title: L13


title: L9


title: L7


title: L6


title: Ezh2_Ctrl

source_name: Control mouse ES cells

value: Cell signaling Technology

tag: strain

value: inbred 129

tag: cell line

value: embryonbic stem cells

value: Control


title: L5

value: Barred Rock chickens


title: L3


title: L2


title: L4


title: L1


title: HeLa siALKB5 RNASeq

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

description: knock down ALKBH5

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 and mm9 whole genome using tophat with -n 2 -g 1
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cuffdiff
Genome_build: hg19,mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: HeLa cells

extract_protocol: RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total

tag: passages

value: HeLa

tag: treatment


title: mouse wt RNASeq

description: wild-type

source_name: testicular cells

tag: genetic background

tag: age

value: 12 weeks

value: testicular cells

tag: genotype

value: wt


title: RNA-Seq Cultured white pre-adipocytes

city: Cambridge

first: Cole

last: Trapnell

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing: All files were mapped against mm9 using TopHat 1.1.0 and mm9 transcripts were quantified using Cufflinks 0.9.3.

source_name: Cultured white pre-adipocytes

growth_protocol: Interscapular brown adipose tissues, epididymal fat pads and subcutaneous fat pad are harvested from five 8-week old male mice. Fat tissues are minced, digested in collagenase, and fractioned by centrifugation.  Adpocytes are collected from the top layer.    Brown pre-adipocytes are isolated from interscapular brown fat and white pre-adipocytes are isolated from subcutaneous fat pat from young mice (2 week old). After collagenase digestion and fractionation, pre-adipocytes,enriched in bottom stromal vascular fraction (VSC)s, are resuspended and cultured to confluence in DMEM supplemented with 10% New-born Bovine Serum.  The cells arethen exposed to differentiation medium: 10%FBS DMEM, Insulin 850nM (Sigma), Dexamethasone 0.5uM (Sigma), IBMX 250uM (Sigma), Rosiglitazone 1uM (Cayman Chemical) (brown adipocyte cultures, T3 1nM and Indomethacin 125nM were also added into the medium). After 2 days, cells are incubated in culture medium containing insulin 160nM (supplemented with T3 for brown adipocyte cultures) for another 2 days, and then are switched to 10% FBS DMEM

extract_protocol: Total RNAs are extracted using the Qiagen MiRNAEasy kit and 10ug of total RNAs for each sample is used to prepare mRNA-seq libraries according to manufacturer's instruction (Illumina). These libraries were sequenced to produce 36bp single end reads.

value: Cultured white pre-adipocytes


title: RNA-Seq Primary white adipocytes

source_name: Primary white adipocytes

value: Primary white adipocytes


title: RNA-Seq Cultured brown pre-adipocytes

source_name: Cultured brown pre-adipocytes

value: Cultured brown pre-adipocytes


title: HeLa siControl RNASeq

description: knock down control

value: siControl


title: RNA-Seq Primary brown adipocytes

value: Primary brown adipocytes


title: RNA-Seq Cultured white adipocytes

source_name: Cultured white adipocytes

value: Cultured white adipocytes


title: PolII-S5p_Patski_ChIPSeq

description: The Patski fibroblast line was originally derived from BL6/spretus hybrid embryonic kidney and has the inactive X from BL6

source_name: Patski cells

value: Fibroblasts derived from hybrid embryonic kidney

tag: chip antibody

value: PolII-S5p, Abcam ab5131


title: mouse ALKBH5 KO RNASeq

description: ALKBH5 knock out

value: ALKBH5 KO


title: RNA-Seq Cultured brown adipocytes

source_name: Cultured brown adipocytes

value: Cultured brown adipocytes


title: HSC_young_500_reconst_3

status: Public on Feb 14 2013

first: Isabel

last: Beerman

address: 200 Longwood Ave, WAB 156

institute: Boston Childrens Hospital

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9) using MAQ bisulfite alignment mode.
Aligned bam files were processed using custom software (PMID: 20852634).
Genome_build: mm9
Supplementary_files_format_and_content: bed file columns: chrom, chromstart, chromend,'number methylated cytosines/number total cytosines',score,strand

source_name: bone marrow

extract_protocol:
Please see Gu et al., 2011 (PMID: 21412275) and Smith et al., 2012 (PMID: 22456710)
RRBS was performed according to a previously published protocol (Smith et al., 2009 PMID: 19442738) with some optimizations for small cell numbers (Gu et al., 2010, PMID: 20062050)

value: hematopoietic stem cell

value: 500 young HSCs transplanted

tag: replicate

value: Rep 1


title: HSC_young_4x5FU_1

value: 3.5 months + 6 months

value: 4 doses of 5-FU


title: HSC_young_2x5FU_2

value: 2 doses of 5-FU

value: Rep 2


title: HSC_young_4x5FU_2


title: HSC_young_50_reconst_3

value: 50 young HSCs transplanted


title: HSC_young_10_reconst_3

value: 10 young HSCs transplanted

value: Rep 3


title: HSC_young_2x5FU_3


title: HSC_young_2x5FU_1


title: HSC_young_2

value: 3.5 months


title: HSC_young_10_reconst_1


title: HSC_young_10_reconst_2


title: HSC_young_1


title: HSC_old_50_reconst_4

value: 50 old HSCs transplanted


title: HSC_fetal_2

source_name: fetal liver


title: H5

tag: breed

value: Barred Rock chickens

value: susceptible

value: high-colonized

value: whole caecum


title: HSC_young_0x5FU_3

value: 0 doses of 5-FU


title: HSC_young_0x5FU_2

value: hematopoietic stem cell


title: HSC_young_0x5FU_1


title: HSC_old_500_reconst_3

value: 500 old HSCs transplanted


title: mBS62

city: Los Angeles

first: John

last: Vincent

address: 621 Charles E Young Dr. S

department: MCDB

institute: UCLA

data_processing:
BS-seq reads were aligned to the mm9 genome assembly using BS Seeker, allowing up to 10 mismatches.
Alignments with three consecutive methylated non-CG sites are removed.
If multiple alignments mapped to the same location only one is kept.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data (CGmap) is in text format.  column 1=chromosome id (see mouse_mm9_chr_name_id.txt); column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.

source_name: iPGCs

growth_protocol: ESCs were cultured under standard conditions in LIF on feeders.  iPGCs were generated via ESC differentiation for 6 days following selection of SSEA1+/cKitbright cells by FACS.  Indicated viruses were transduced into ESCs prior to embryoid body differentiation.

extract_protocol:
Genomic DNA was isolated via Zymo gDNA Mini Prep columns and subjected to sonication.
Briefly, sonicated DNA was end repaired with T4/Klenow DNA polymerases and T4 polynucleotide kinase, adenylated, and ligated to pre-methylated single end Illumina Adapters with T4 DNA ligase. Following purification and size selection (150-300bp), samples were bisulfite converted with CpG Genome Kit (Millipore).  Libraries were then subjected to one round of PCR amplification (15 cycles)

tag: lentivirus

value: shRNA against Tet1

value: iPGCs


title: mBS61

value: control shRNA lentivirus


title: mBS64


title: mBS60r


title: mBS56

value: wild type

value: no virus


title: HSC_old_500_reconst_1

value: Rep 1


title: HSC_old_500_reconst_2

value: Rep 2


title: HSC_old_10_reconst_3

value: 10 old HSCs transplanted


title: HSC_old_10_reconst_2


title: newly-transcribed RNA 1-2hpi

city: Munich

first: Lukas

last: Windhager

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität Munich

data_processing:
ALIGNMENT: Reads were aligned in a 4-step process using the Bowtie alignment program. First, all reads were aligned to mouse transcripts (Ensembl version 63). Remaining unaligned reads were aligned to the mouse genome (mm9, NCBI Build 37). Then, remaining reads were aligned to MCMV coding sequences and finally to the full MCMV genomic sequence. Reads with ambiguous base calls, non-unique alignment positions or more than 4 mismatches were discarded.
WIG: Wiggle files were created for the virus genome using all aligned reads.
RPKM: RPKM values were calculated for MCMV genes. Therefore, all reads aligning to a gene were summed and normalized. The length of the sequence covered by the gene was used for length normalization. The total number of reads aligned to mouse exons (Ensembl version 63) and virus genes was used for sample normalization.
Genome Build:
897_+_strand.wig: BAC-derived MCMV Smith strain
897_-_strand.wig: BAC-derived MCMV Smith strain
897.rpkm: BAC-derived MCMV Smith strain

source_name: NIH-3T3 fibroblasts

growth_protocol: Murine NIH-3T3 fibroblasts were cultured in DMEM supplemented with 5% fetal calf serum

extract_protocol: RNA was subjected to WTAK library construction to generate transcriptomic fragment libraries (50 bp, SOLiD™ (Life Technologies, Foster City, CA, USA) Total RNA-Seq Kit V3) that preserve strandedness information of the reads. Molecular barcoding was used in order to pool several libraries in a single sequencing reaction according to the manunfacturer´s protocol. Sequencing was performed using the SOLiDTM 3 system (Life Technologies). Potential sequencing errors were corrected using the SOLiD Accuracy Enhancement Tool (solidsoftwaretools.com/gt/project/saet).

treatment_protocol: Cells were seeded overnight to 80% confluence followed by infection with BAC-derived MCMV Smith strain. Infection was performed at a MOI of 10 using centrifugal enhancement (30 min, 2000 rpm) or a MOI of 0.5. The time point after centrifugation was marked as time point 0 min in all kinetics. RNA labeling was started by adding 200 µM 4-thiouridine (4sU, Sigma) to culture media for 1 h at different times of infection. At the end of labeling total cellular RNA was isolated using Trizol reagent (Invitrogen). Biotinylation and purification of 4sU-tagged RNA (newly transcribed RNA) as well as the dot blot analysis were performed as described previously (Dölken et al., RNA, 2008)

value: fibroblasts

tag: infected with

value: BAC-derived MCMV (murine cytomegalovirus) Smith strain

tag: hours past infection

tag: rna type

value: newly-transcribed RNA


title: newly-transcribed RNA 5-6hpi

data_processing:
ALIGNMENT: Reads were aligned in a 4-step process using the Bowtie alignment program. First, all reads were aligned to mouse transcripts (Ensembl version 63). Remaining unaligned reads were aligned to the mouse genome (mm9, NCBI Build 37). Then, remaining reads were aligned to MCMV coding sequences and finally to the full MCMV genomic sequence. Reads with ambiguous base calls, non-unique alignment positions or more than 4 mismatches were discarded.
WIG: Wiggle files were created for the virus genome using all aligned reads.
RPKM: RPKM values were calculated for MCMV genes. Therefore, all reads aligning to a gene were summed and normalized. The length of the sequence covered by the gene was used for length normalization. The total number of reads aligned to mouse exons (Ensembl version 63) and virus genes was used for sample normalization.
Genome Build:
898_+_strand.wig: BAC-derived MCMV Smith strain
898_-_strand.wig: BAC-derived MCMV Smith strain
898.rpkm: BAC-derived MCMV Smith strain


title: HSC_old_3

value: 25 months


title: newly-transcribed RNA mock

data_processing:
ALIGNMENT: Reads were aligned in a 4-step process using the Bowtie alignment program. First, all reads were aligned to mouse transcripts (Ensembl version 63). Remaining unaligned reads were aligned to the mouse genome (mm9, NCBI Build 37). Then, remaining reads were aligned to MCMV coding sequences and finally to the full MCMV genomic sequence. Reads with ambiguous base calls, non-unique alignment positions or more than 4 mismatches were discarded.
WIG: Wiggle files were created for the virus genome using all aligned reads.
RPKM: RPKM values were calculated for MCMV genes. Therefore, all reads aligning to a gene were summed and normalized. The length of the sequence covered by the gene was used for length normalization. The total number of reads aligned to mouse exons (Ensembl version 63) and virus genes was used for sample normalization.
Genome Build:
896_+_strand.wig: BAC-derived MCMV Smith strain
896_-_strand.wig: BAC-derived MCMV Smith strain
896.rpkm: BAC-derived MCMV Smith strain

value: none (mock)

value: mock


title: mBS65


title: HSC_old_4


title: HSC_fetal_3


title: pre-existing RNA 25hpi

data_processing:
ALIGNMENT: Reads were aligned in a 4-step process using the Bowtie alignment program. First, all reads were aligned to mouse transcripts (Ensembl version 63). Remaining unaligned reads were aligned to the mouse genome (mm9, NCBI Build 37). Then, remaining reads were aligned to MCMV coding sequences and finally to the full MCMV genomic sequence. Reads with ambiguous base calls, non-unique alignment positions or more than 4 mismatches were discarded.
WIG: Wiggle files were created for the virus genome using all aligned reads.
RPKM: RPKM values were calculated for MCMV genes. Therefore, all reads aligning to a gene were summed and normalized. The length of the sequence covered by the gene was used for length normalization. The total number of reads aligned to mouse exons (Ensembl version 63) and virus genes was used for sample normalization.
Genome Build:
894_+_strand.wig: BAC-derived MCMV Smith strain
894_-_strand.wig: BAC-derived MCMV Smith strain
894.rpkm: BAC-derived MCMV Smith strain

value: pre-existing RNA


title: mBS63


title: newly-transcribed RNA 47-48hpi

data_processing:
ALIGNMENT: Reads were aligned in a 4-step process using the Bowtie alignment program. First, all reads were aligned to mouse transcripts (Ensembl version 63). Remaining unaligned reads were aligned to the mouse genome (mm9, NCBI Build 37). Then, remaining reads were aligned to MCMV coding sequences and finally to the full MCMV genomic sequence. Reads with ambiguous base calls, non-unique alignment positions or more than 4 mismatches were discarded.
WIG: Wiggle files were created for the virus genome using all aligned reads.
RPKM: RPKM values were calculated for MCMV genes. Therefore, all reads aligning to a gene were summed and normalized. The length of the sequence covered by the gene was used for length normalization. The total number of reads aligned to mouse exons (Ensembl version 63) and virus genes was used for sample normalization.
Genome Build:
902_+_strand.wig: BAC-derived MCMV Smith strain
902_-_strand.wig: BAC-derived MCMV Smith strain
902.rpkm: BAC-derived MCMV Smith strain


title: newly-transcribed RNA 18-19hpi

data_processing:
ALIGNMENT: Reads were aligned in a 4-step process using the Bowtie alignment program. First, all reads were aligned to mouse transcripts (Ensembl version 63). Remaining unaligned reads were aligned to the mouse genome (mm9, NCBI Build 37). Then, remaining reads were aligned to MCMV coding sequences and finally to the full MCMV genomic sequence. Reads with ambiguous base calls, non-unique alignment positions or more than 4 mismatches were discarded.
WIG: Wiggle files were created for the virus genome using all aligned reads.
RPKM: RPKM values were calculated for MCMV genes. Therefore, all reads aligning to a gene were summed and normalized. The length of the sequence covered by the gene was used for length normalization. The total number of reads aligned to mouse exons (Ensembl version 63) and virus genes was used for sample normalization.
Genome Build:
900_+_strand.wig: BAC-derived MCMV Smith strain
900_-_strand.wig: BAC-derived MCMV Smith strain
900.rpkm: BAC-derived MCMV Smith strain


title: newly-transcribed RNA 12-13hpi

data_processing:
ALIGNMENT: Reads were aligned in a 4-step process using the Bowtie alignment program. First, all reads were aligned to mouse transcripts (Ensembl version 63). Remaining unaligned reads were aligned to the mouse genome (mm9, NCBI Build 37). Then, remaining reads were aligned to MCMV coding sequences and finally to the full MCMV genomic sequence. Reads with ambiguous base calls, non-unique alignment positions or more than 4 mismatches were discarded.
WIG: Wiggle files were created for the virus genome using all aligned reads.
RPKM: RPKM values were calculated for MCMV genes. Therefore, all reads aligning to a gene were summed and normalized. The length of the sequence covered by the gene was used for length normalization. The total number of reads aligned to mouse exons (Ensembl version 63) and virus genes was used for sample normalization.
Genome Build:
899_+_strand.wig: BAC-derived MCMV Smith strain
899_-_strand.wig: BAC-derived MCMV Smith strain
899.rpkm: BAC-derived MCMV Smith strain


title: newly-transcribed RNA 24-25hpi

data_processing:
ALIGNMENT: Reads were aligned in a 4-step process using the Bowtie alignment program. First, all reads were aligned to mouse transcripts (Ensembl version 63). Remaining unaligned reads were aligned to the mouse genome (mm9, NCBI Build 37). Then, remaining reads were aligned to MCMV coding sequences and finally to the full MCMV genomic sequence. Reads with ambiguous base calls, non-unique alignment positions or more than 4 mismatches were discarded.
WIG: Wiggle files were created for the virus genome using all aligned reads.
RPKM: RPKM values were calculated for MCMV genes. Therefore, all reads aligning to a gene were summed and normalized. The length of the sequence covered by the gene was used for length normalization. The total number of reads aligned to mouse exons (Ensembl version 63) and virus genes was used for sample normalization.
Genome Build:
901_+_strand.wig: BAC-derived MCMV Smith strain
901_-_strand.wig: BAC-derived MCMV Smith strain
901.rpkm: BAC-derived MCMV Smith strain


title: pre-existing RNA mock

data_processing:
ALIGNMENT: Reads were aligned in a 4-step process using the Bowtie alignment program. First, all reads were aligned to mouse transcripts (Ensembl version 63). Remaining unaligned reads were aligned to the mouse genome (mm9, NCBI Build 37). Then, remaining reads were aligned to MCMV coding sequences and finally to the full MCMV genomic sequence. Reads with ambiguous base calls, non-unique alignment positions or more than 4 mismatches were discarded.
WIG: Wiggle files were created for the virus genome using all aligned reads.
RPKM: RPKM values were calculated for MCMV genes. Therefore, all reads aligning to a gene were summed and normalized. The length of the sequence covered by the gene was used for length normalization. The total number of reads aligned to mouse exons (Ensembl version 63) and virus genes was used for sample normalization.
Genome Build:
893_+_strand.wig: BAC-derived MCMV Smith strain
893_-_strand.wig: BAC-derived MCMV Smith strain
893.rpkm: BAC-derived MCMV Smith strain


title: total RNA 48hpi

data_processing:
ALIGNMENT: Reads were aligned in a 4-step process using the Bowtie alignment program. First, all reads were aligned to mouse transcripts (Ensembl version 63). Remaining unaligned reads were aligned to the mouse genome (mm9, NCBI Build 37). Then, remaining reads were aligned to MCMV coding sequences and finally to the full MCMV genomic sequence. Reads with ambiguous base calls, non-unique alignment positions or more than 4 mismatches were discarded.
WIG: Wiggle files were created for the virus genome using all aligned reads.
RPKM: RPKM values were calculated for MCMV genes. Therefore, all reads aligning to a gene were summed and normalized. The length of the sequence covered by the gene was used for length normalization. The total number of reads aligned to mouse exons (Ensembl version 63) and virus genes was used for sample normalization.
Genome Build:
892_+_strand.wig: BAC-derived MCMV Smith strain
892_-_strand.wig: BAC-derived MCMV Smith strain
892.rpkm: BAC-derived MCMV Smith strain

value: total RNA


title: total RNA 25hpi

data_processing:
ALIGNMENT: Reads were aligned in a 4-step process using the Bowtie alignment program. First, all reads were aligned to mouse transcripts (Ensembl version 63). Remaining unaligned reads were aligned to the mouse genome (mm9, NCBI Build 37). Then, remaining reads were aligned to MCMV coding sequences and finally to the full MCMV genomic sequence. Reads with ambiguous base calls, non-unique alignment positions or more than 4 mismatches were discarded.
WIG: Wiggle files were created for the virus genome using all aligned reads.
RPKM: RPKM values were calculated for MCMV genes. Therefore, all reads aligning to a gene were summed and normalized. The length of the sequence covered by the gene was used for length normalization. The total number of reads aligned to mouse exons (Ensembl version 63) and virus genes was used for sample normalization.
Genome Build:
891_+_strand.wig: BAC-derived MCMV Smith strain
891_-_strand.wig: BAC-derived MCMV Smith strain
891.rpkm: BAC-derived MCMV Smith strain


title: WT + NO rep2

city: New York

first: Ivan

last: Gusarov

state: NY

address: 450E 29th street

department: Biochemistry

institute: NYU School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then run through the tophat (version 2.0.2) / cufflinks (version 2.0.5) pipeline against Ensembl WS220 C.elegans genome assembly with the default parameters.
CummeRbund package version 2.0.0 with R version 2.15.2 were used for the analysis and visualization of the differential gene expression results.
Genome_build: WS220 (Ensembl release 66)
Supplementary_files_format_and_content: tab-delimited text file that includes FPKM values for each Sample and differential expression test statistics.

source_name: whole organism

growth_protocol: C.elegans were grown on NGM plates seeded with E.coli OP50 at 20oC

extract_protocol:
C.elegans mixed with Trizol reagents were flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Synchronized stage L4 C.elegans were treated with 1mM MAHMA NONOate, let recover for 4 hours at 20oC and then total RNA isolated.

tag: genotype/variation

value: WT

tag: agent

value: NO


title: WT + NO rep1


title: pre-existing RNA 48hpi

data_processing:
ALIGNMENT: Reads were aligned in a 4-step process using the Bowtie alignment program. First, all reads were aligned to mouse transcripts (Ensembl version 63). Remaining unaligned reads were aligned to the mouse genome (mm9, NCBI Build 37). Then, remaining reads were aligned to MCMV coding sequences and finally to the full MCMV genomic sequence. Reads with ambiguous base calls, non-unique alignment positions or more than 4 mismatches were discarded.
WIG: Wiggle files were created for the virus genome using all aligned reads.
RPKM: RPKM values were calculated for MCMV genes. Therefore, all reads aligning to a gene were summed and normalized. The length of the sequence covered by the gene was used for length normalization. The total number of reads aligned to mouse exons (Ensembl version 63) and virus genes was used for sample normalization.
Genome Build:
895_+_strand.wig: BAC-derived MCMV Smith strain
895_-_strand.wig: BAC-derived MCMV Smith strain
895.rpkm: BAC-derived MCMV Smith strain

tag: cell type


title: mBS57

source_name: ESCs- V6.5

value: ESCs- V6.5


title: Input

first: Sebastian

last: Pott

state: Il

address: 920 58th Street

department: Human Genetics

description: ChIP

data_processing:
The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, hg18) using Eland software with maximal 2 mis-matches.
Peak detection was performed using CCAT ( Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics. 2010 May 1;26(9):1199-204.) in region mode for H3K122ac  and otherwise default setttings except for fragment length which was set to the empirically determined length of 170bp. The sequence tag density generated from the input library was used as background.
BedGraph files were prepared from BED files of aligned sequencing reads using genomecoverage with the –bg option. Libraries are scaled to 10M reads (-scale).
Genome_build: hg18
Supplementary_files_format_and_content: bedGraph files contain normalized signal intensities for specified genomic intervals, files can be displayed in UCSC genome browser hg18; peak files contain locations of peaks and an associated score, file is in bed format.

growth_protocol: Cells were grown in DMEM supplemented with 10% FCS and L-glutamine

extract_protocol: For ChIP-Seq of H3K122ac, H3K27ac, H2A.Z and H2A.Zac, chromatin was prepared by micrococcal nuclease digestion of crosslinked MCF-7 nuclei. For a typical experiment 3-6*10^7 MCF-7 cells were harvested, washed in PBS, resuspended in cold buffer I (300mM sucrose, 60mM KCl, 15mM NaCl, 5mM MgCl, 0.1mM EDTA pH 8.0, 15mM Tris pH 7.5, 1x protease inhibitors (Roche), 10mM sodium butyrate, 1mM DTT) at a density of 1.5x10^7 cells/ml. Cell suspension was mixed under gentle vortexing with the same volume of cold buffer II (as buffer I but with 0.5% NP-40) and incubated on ice for 10min to lyse the cell membrane. 8ml of a 40% sucrose cushion was prepared (buffer III: 1.2M sucrose, 60mM KCl, 15mM NaCl, 5mM MgCl, 0.1mM EDTA pH 8.0, 15mM Tris pH 7.5, 1x protease inhibitors, 10mM sodium butyrate, 1mM DTT) and a maximum of 3*10^7 cells were loaded onto one cushion. The released nuclei were separated from the cyctoplasm by centrifugation at 10,000rpm for 20min in a HB4 swing bucket rotor (Beckman) at 4°C.  MCF-7 cell nuclei were resuspendend in Mnase digestion buffer (320mM sucrose, 4mM MgCl2, 1mM CaCl2, 50mM Tris pH 7.5, 0.2mM AEBSF, 10mM sodium butyrate) with 0.2% formaldehyde and crosslinked at RT for 5min under constant agitation. The fixation was quenched by adding glycine to a final concentration of 25mM for 5min on a rolling wheel. Crosslinked nuclei were washed with Mnase digestion buffer once, pelleted again and resuspendend in Mnase digestion buffer with 60U/ml Mnase (Fermentas) and digested to >90% mononucleosomes at 37°C for 15min. Digestion was stopped by addition of 10mM EDTA final concentration and transferred to ice. After 15min on ice the samples were centrifuged at 10,000rpm for 10min and the supernatant containing the nucleosomes saved. 80µg of nucleosomes were diluted 1:10 in incubation buffer (50mM Tris pH 7.5, 75mM NaCl, 5mM EDTA pH 8.0, 0.1% NP40, 1x protease inhibitor, 10mM NaBut) and centrifuged at 13,000 rpm for 10min to remove any precipitant. Soluble nucleosomes were incubated with respective antibodies pre-bound to Dynabeads protein A (Invitrogen) at 4°C o/n. The immunocomplexes were collected in a magnetic rack and washed 1x in low salt buffer (50mM Tris pH 7.5, 150mM NaCl, 5mM EDTA pH 8.0, 1% Triton-X100, 0.5% NP-40) and 5x in high salt buffer (50mM Tris pH 7.5, 450mM NaCl, 5mM EDTA pH 8.0, 1% Triton-X100, 0.5% NP-40). After a final wash in TE buffer the immunocomplexes were eluted with 200µl N-ChIP elution buffer (incubation buffer with 1% SDS) in a thermoshaker at 30°C, 900rpm for 30min. The eluates were subsequently digested eith RNAse (Roche) and Proteinase K (Roche) and the DNA purified with the Qiaquick PCR purification Kit (Qiagen), according to the manufacturers instructions, and eluted in 80µl TE buffer. For Illumina sequencing the DNA from three individual immunoprecipitations was pooled. ChIP-Seq libraries were prepared according to manufacturer’s protocols and sequenced with Illumina GAII.

treatment_protocol: cells were kept for 3 days in phenol-red free DMEM supplemented with 5% charcoal-dextran treated FCS and L-glutamine

value: breast cancer cells


title: WT rep2

value: control


title: H2A.Zac

description: ChIP

value: Anti-Histone H2A.Z (acetyl K4 + K7 + K11)

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: mBS48

value: wild type

value: no virus


title: H2A.Z

description: ChIP

tag: cell line

value: Anti-Histone H2A.Z

value: Millipore


title: H3K27ac_ChIP

description: ChIP

value: Anti-Histone H3 (acetyl K27)


title: STAT5B_ChIPSeq

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: Chromatin IP against STAT5B

data_processing: Alignment: Sequence reads were obtained and mapped to the mouse (Febrary, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.

source_name: Dendritic Cell in Spleen

growth_protocol: Dendritic cells were isolated from mouse spleen and maintained in growth medium (RPMI-1640 with 10% FBS, 200μM L-glutamine, 10 I.U./ml penicillin, 10μg/ml streptomycin and 55μM 2-mercaptoethanol)

extract_protocol: After cytokine treatment, the cells were fixed with 1% formaldehyde at 37°C for 10 min. Chromatin from 5 × 107 cells was sonicated for 20 cycles of 12 sec on/48 sec off, into 200-500 bp fragments, the DNA ends were repaired using polynucleotide kinase and Klenow enzyme and then treated with Taq polymerase to generate a protruding 3’ “A” nucleotide. A pair of Solexa PE adaptors (Illumina) was ligated and the DNA amplified using the adaptor primers (PE 1.0 and 2.0, Illumina) for 19 cycles. DNA fragments of approximately 250-450 bp were purified from agarose gels and used directly for cluster generation and sequencing using the Solexa 1G Genome Analyzer according to the manufacturer’s protocols.

treatment_protocol: Dendritic cells were rested in 37°C for 1 hour then treated with IL-21 and/or GM-CSF for 2 hours

tag: antibody

value: R&D systems, anti-stat 5B serum PA-ST5B

value: Dendritic Cell

tag: strain

tag: treatment


title: IL21+GMCSF_STAT3_ChIPSeq

description: Chromatin IP against IL21+GMCSF STAT3

value: Invtrogen, monoclonal antibody ST3-5G7

value: IL-21 and GM-CSF


title: IL21_STAT3_ChIPSeq

description: Chromatin IP against IL21 STAT3


title: Input_ 266.6

city: Copenhagen N

first: Anne

last: Grapin-Botton

address: Blegdamsvej3 B

department: DanStem

country: Denmark

institute: University of Copenhagen

description: Input Chromatin

data_processing: Alignment: Data were processed with the Illumina Pipeline Software v1.60. Sequence reads were  mapped to the mouse (NCBI37/mm9) genomes with the Eland program allowing for up to two mismatches. Downstream analysis was carried out with ChIP-Seq tools at http://ccg.vital-it.ch/chipseq/. Alignment Score was 88.79+/-0.61 with a % Error Rate of 0.23+/-0.02.

source_name: 266.6 Pancreatic Cells

growth_protocol: 266.6 cells, a pancreatic cell line which expresses many of the same  genes as an E10.5 dorsal pancreas, were cultured in DMEM 4.5g/L glucose and 10%FCS on 10cm plates coated with 0.1% pig skin gelatin . They were split twice a week with 0.25% trypsin, 0.03% EDTA.

extract_protocol: Two Ptf1a/266.6 chromatin IPs were combined and gel purified. Fragments between 100 and 400bp were isolated and quantified using the Qubit fluorometer (Invitrogen). The ChIP-Seq Sample Preparation Kit (Illumina No. IP-102-1001) was used according to the protocol supplied with the reagents and  5ng of ChIP sample

treatment_protocol: Cells 90% confluent (~20 million cells/ 10cm plate 10-15 plates) were crosslinked with DMEM/1% formaldehyde for 10 minutes. After glycine neutralization and 2X PBS washes, cells were collected from plates by scraping. Cell pellets were stored  at -80°C. Chromatin from isolated nuclei was fragmented to between 100 -500 bp and used for ChIP.

value: C57BL/6 X SJL

value: pancreatic

tag: passage


title: Ptf1a_ChIPSeq_266.6

description: Chromatin IP against Ptf1a

tag: chip antibody

value: Ptf1a  (Beta Cell Biology Consortium)


title: IL21+GMCSF_STAT5B_ChIPSeq

description: Chromatin IP against IL21+GMCSF STAT5B


title: mBS47

data_processing:
BS-seq reads were aligned to the mm9 genome assembly using BS Seeker, allowing up to 10 mismatches.
Alignments with three consecutive methylated non-CG sites are removed.
If multiple alignments mapped to the same location only one is kept.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data (CGmap) is in text format.  column 1=chromosome id (see mouse_mm9_chr_name_id.txt); column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.

tag: genotype

value: No virus


title: GMCSF_STAT5B_ChIPSeq

description: Chromatin IP against GMCSF STAT5B


title: mBS49


title: ChipSeq for Suz12

status: Public on Feb 13 2013

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
Chromatin IP against Suz12
cell number: 30 million

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 1 -m 1 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended by MACS and allocated into 50bp bins

source_name: Embryonic stem cells

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: antibody vendor and catalog number

value: Abcam AB12073

tag: background strain


title: ChipSeq for H3K4

description:
Chromatin IP against H3K4 (10^7)
cell number: 10 million

value: Abcam AB8580


title: ChIP-Seq for Cdk9 in mES cells

description: ChIP-Seq for Cdk9

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 350bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: Santa Cruz SC-8338,SC-484


title: mBS44

tag: lentivirus

value: No Virus


title: C2C12 WCE

description: WCE for C2C12 myotubes

source_name: myotubes

growth_protocol: C2C12 myoblasts were grown under typical C2C12 myoblast conditions.  Myotube formation was induced for 48 hours in 2% horse serum and 1x selenium, transferrin and insulin.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. 1x10^8 cells were sonicated at 21 watts in 20 second pulses for 3 min of sonication time. Half of the cell lysate was used for immunoprecipitation. The chromatin extracts containing DNA fragments with an average size of 500 bp were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: None WCE


title: p300_ChIP

description: CHIP

data_processing:
The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, hg18) using Eland software with maximal 2 mis-matches.
Peak detection was performed using CCAT ( Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics. 2010 May 1;26(9):1199-204.) in Peak mode and otherwise default settting . The sequence tag density generated from the input library was used as background.
BedGraph files were prepared from BED files of aligned sequencing reads using genomecoverage with the –bg option. Libraries are scaled to 10M reads (-scale).
Genome_build: hg18
Supplementary_files_format_and_content: bedGraph files contain normalized signal intensities for specified genomic intervals, files can be displayed in UCSC genome browser hg18; peak files contain locations of peaks and an associated score, file is in bed format

extract_protocol: MCF-7 cells were grown to 80–90% confluency and fixed by adding formaldehyde (Sigma) to 1% final concentration for 10min at RT. Fixation was quenched by addition of 125mM glycine final concentration. The cells were washed twice with ice cold PBS and collected by scraping in PBS supplemented with 1x protease inhibitors and 10mM NaBut. Cells were pelleted and resuspendend in 1.2ml RIPA lysis buffer (50mM Tris-HCl pH 8.0, 150mM NaCl, 2mM EDTA pH 8.0, 0.1% SDS, 1% NP-40 (Roche) 0.5% sodium deoxycholate, 1x protease inhibitors and 10mM NaBut) for 1.5*10^7 cells and incubated on ice for 10min. The lysates were sonicated with a Bioruptor (Diagenode) to an average size of ~300–800 bp. The sonicated samples were centrifuged at 17,000g for 10min and the supernatant, containing the soluble chromatin, was flash- frozen in liquid N2 and stored at -80°C after taking 50µl of chromatin as input to determine the concentration of chromatin. The 50µl input material was mixed with 127µl 1.6x elution buffer (160mM NaHCO3, 1.6% SDS), supplemented with 1µl RNAse (Roche) and incubated at 37°C for 1h. Next, 20µg proteinase K (Roche) and 20µl of 5M NaCl were added and incubated at 65°C for at least 5h to reverse the crosslinking. DNA was purified with the Qiaquick PCR purification Kit (Qiagen) and eluted in 100µl. p300 ChIP an equivalent to 250µg DNA was used. Prior to immunoprecipitation the chromatin was diluted 1:5 with dilution buffer (20mM Tris pH 8.0, 150mM NaCl, 2mM EDTA pH 8.0, 1% Triton X-100, 1x protease inhibitors and 10mM NaBut) and pre-cleared with 20µl washed protein A sepharose beads (Amersham), 1.5µg sonciated salmon sperm DNA (Sigma) and 4µg BSA (NEB) per IP. The pre-cleared chromatin was incubated with p300 antibody overnight at 4°C. Next day 20µl of 50% protein A slurry blocked with sonicated salmon sperm DNA and BSA was added to collect the immunocomplexes for 2h at 4°C. The bound immunocomplexes were washed once with dilution buffer and five times with LiCl buffer (500mM LiCl, 50mM HEPES, pH 8.0, 1mM EDTA pH 8.0, 1% NP-40, 0.7% sodium deoxycholate) for 10min. After a final wash in TE buffer the beads were resuspended in 180µl freshly prepared 1.1x elution buffer (110mM NaHCO3, 1.1% SDS) and the immunocomplexes eluted by incubation at 30°C. The eluates were de-crosslinked and purified as described for the input (see above). ChIP-Seq libraries were prepared according to manufacturer’s protocols and sequenced with Illumina GAII.

treatment_protocol: before harvesting cells were kept for 3 days in phenol-red free DMEM supplemented with 5% charcoal-dextran treated FCS and L-glutamine

value: breast cancer cells

value: p300 Antibody (C-20)

value: Santa Cruz

tag: chip antibody lot #


title: RNA-seq_HeLa_siZNF143

city: Strasbourg

first: PHILIPPE

last: CARBON

address: 15 rue René Descartes

department: UPR9002 ARN du CNRS

country: France

institute: IBMC

data_processing:
Basecalls performed using Illumina CASAVA version 1.7 or v1.8
RNA-seq reads were aligned to hg19 genome using TopHat v2.0.3 software
RNA-seq mRNA abundance mesurement (FPKM) was performed with Cufflinks RNA-Seq analysis tools
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM for the RNA-seq assembled transcripts (Reference Refseq Genes)

source_name: immortalized cervical cancer derived cell line

extract_protocol: Total RNA was extracted with TRI-REAGENTM (Euromedex) following the manufacturer protocol for RNA isolation. mRNA was purified from total RNA using oligo-dT magnetic beads. RNA-seq libraries preparation was performed using illumina TruSeq RNA Sample Preparation kit according to manufacturer protocol.

value: HeLa

value: Transfected siRNA ZNF143


title: Input_control (for p300)

description: ChIP

source_name: MCF7_Input_control (for p300)


title: total RNA mock

data_processing:
ALIGNMENT: Reads were aligned in a 4-step process using the Bowtie alignment program. First, all reads were aligned to mouse transcripts (Ensembl version 63). Remaining unaligned reads were aligned to the mouse genome (mm9, NCBI Build 37). Then, remaining reads were aligned to MCMV coding sequences and finally to the full MCMV genomic sequence. Reads with ambiguous base calls, non-unique alignment positions or more than 4 mismatches were discarded.
WIG: Wiggle files were created for the virus genome using all aligned reads.
RPKM: RPKM values were calculated for MCMV genes. Therefore, all reads aligning to a gene were summed and normalized. The length of the sequence covered by the gene was used for length normalization. The total number of reads aligned to mouse exons (Ensembl version 63) and virus genes was used for sample normalization.
Genome Build:
890_+_strand.wig: BAC-derived MCMV Smith strain
890_-_strand.wig: BAC-derived MCMV Smith strain
890.rpkm: BAC-derived MCMV Smith strain

value: fibroblasts

tag: infected with

value: none (mock)

tag: hours past infection

value: mock

tag: rna type

value: total RNA


title: RNA-seq_HeLa_Control

value: Transfected siRNA control


title: ChIP-seq_ZNF76_FLP76_T4

data_processing:
Basecalls performed using Illumina CASAVA version 1.7 or v1.8
ChIP-seq reads were aligned to the hg19 or mm9 genome using Illumina software ELAND or Bowtie v0.12.7.
ChIP-seq peak calling was performed using MACS v1.4
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: Wig files were generated using MACS v1.4 (10bps resolution).

source_name: derived from HEK293, human embryonic kidney cells

extract_protocol: ChIP assays were performed essentially as previously described (Myslinski et al. 2006) with 1-4x107 cells. The chromatin was sonicated to an average of 200bp using a BioruptorTM UCD-200 (Diagenode) at Maximum power level for 30 minutes (pulses of 30 seconds with 30 seconds breaks). The immunoprecipitation step was performed with 5µg of specific antibodies. DNA purification steps were done using the MinElute PCR purification kit (Qiagen, cat. No. 28004) or using the classical phenol/chloroform extraction protocol. ChIP-seq library preparation was performed using illumina TruSeq DNA Sample Prep Kits according to manufacturer protocol.

tag: cell line specificity

value: HEK293-T-Rex inducible cell line expressing ZNF76

value: 4h Induction with 1µg/mL ofdoxycycline

value: ZNF76, mouse monoclonal (Santa Cruz Biotechnology, cat. #sc-81147)


title: WT rep1

tag: genotype/variation

value: WT

tag: age

tag: agent

value: control


title: RNA-seq_FLP143_T0

tag: cell line

value: HEK293-T-Rex inducible cell line expressing ZNF143

value: 0h Induction with 1µg/mL ofdoxycycline


title: H3K122Ac_ChIP

description: ChIP

tag: cell type

value: breast cancer cells

value: Anti-Histone H3 (acetyl K122)

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: ChIP-seq_ZNF143_FLP143HA_T4

value: HEK293-T-Rex inducible cell line expressing ZNF143-HA

tag: treatment

tag: chip antibody

value: HA, 12CA5 antibody, (Roche Applied Science)


title: RNA-seq_FLP143_T24

value: 24h Induction with 1µg/mL ofdoxycycline


title: ChIP-seq_ZNF143_FLP143HA_T0


title: ChIP-seq_ZNF143_HPB-ALL

source_name: T-cell acute lymphoblastic leukemia cells

value: HPB-ALL

value: ZNF143, rabbit polyclonal raised against a C-terminal epitope of ZNF143 (Myslinski et al JBC 2006)


title: ChIP-seq_ZNF143_293T-rex


title: ChIP-seq_ZNF143_HeLa_rep2

value: HeLa S3


title: Cdk8_mES_r2_ChipSeq

description: Chromatin IP against Cdk8_mES_r2

tag: antibody vendor and catalog number

value: Santa Cruz SC-1521


title: ChIP-seq_ZNF143_HeLa_rep1


title: ChIP-seq_ICN1_HPB-ALL

value: ICN1, rabbit polyclonal raised against amino acids 2278 to 2470 of human Notch1 (Wang et al PNAS 2010)


title: ChIP-Seq_WCE

description: Chromatin IP against WCE in V6.5 ESCs

value: Input INPUT

tag: background strain


title: INPUT_HPB-ALL

value: NONE, INPUT


title: STAT3_control_ChIPSeq

description: Chromatin IP against STAT3 control

tag: antibody

value: Invtrogen, monoclonal antibody ST3-5G7

value: Dendritic Cell

tag: strain


title: ChIP-seq_ZFP143_3T3

source_name: Mouse embryonic fibroblast cell line

value: NIH 3T3


title: ChIP-seq_ZFP143_Fibro

value: MEF-like


title: ChIP-Seq_Nanog_V65

description: Chromatin IP against NANOG in v6.5

growth_protocol: V6.5 embryonic stem cells V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

value: Nanog

value: Bethyl A300-397A


title: ChIP-seq_ZFP143_mESC

source_name: Mouse Embryonic Stem cells

value: mESC J1


title: ChIP-Seq_Oct4_V65

description: Chromatin IP against OCT4 in v6.5 ESCs

value: Santa Cruz SC-8628X


title: activatedB_wt_RNASeq

status: Public on Feb 12 2013

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

data_processing:
Basecalling: Illumina RTA 1.9.35
RNA-Seq reads were aligned using tophat requiring unique alignment
Uniquely aligned reads in ChIP-seq dataset were analyzed by SICER using an expectation value E of 0.05 in a random background model
alignment: aligned against mm9 with  tophat 1.3.2 using known splice sites from RefSeq
Wiggle files for pol2 were generated using 50nt binned raw read densities limiting to a max. redundancy of 5, scaled in RPKM
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cuffdiff software
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM

source_name: in vitro activated B cells

growth_protocol: B lymphocytes were stimulated with LPS and IL4 and incubated for 72h

extract_protocol:
RNA was prepared using Illumina's protocol.
Libraries were prepared according to Illumina's instructions

value: Splenocyte (B lymphocytes)

tag: genotype

value: Trp53bp1+/+ Aicda+/+


title: activatedB_53BP1mm_RNASeq

value: Trp53bp1-/- Aicda-/-


title: activatedB_53BP1mm_polII_chip

data_processing:
Basecalling: Illumina RTA 1.9.35
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie requiring unique alignment (-m 1)
Uniquely aligned reads in ChIP-seq dataset were analyzed by SICER using an expectation value E of 0.05 in a random background model
alignment: aligned against mm9 with bowtie 0.12.8 (--best --all --strata -m1 -n2 -l36)
Wiggle files for pol2 were generated using 50nt binned raw read densities limiting to a max. redundancy of 5, scaled in RPKM
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cuffdiff software
Genome_build: mm9
Supplementary_files_format_and_content: wig

extract_protocol:
ChIP-Seq was performed as described. In brief, cells were fixed with 1% paraformaldehyde at 37°C for 10 minutes followed by sonication. Chromatin fragments were then immunoprecipitated with antibodies specific for serine 5-phosphorylated RNA Polymerase II (Abcam).
Libraries were prepared according to Illumina's instructions


title: ChIP-Seq_Sox2_V65

description: Chromatin IP against SOX2 in v6.5

value: R&D Systems MAB2018


title: EGFPFL pro-siRNA, repeats 1 and 2

first: Linfeng

last: Huang

state: Massachusetts

address: 200 Longwood Avenue

department: PCMM

institute: Boston Children's Hospital

description:
mRNA-seq for EGFPFL pro-siRNA treated cells.
This Sample represents 2 replicates.
Directional RNA-seq.

data_processing:
Standard Illumina GA II.
Tophat and Cufflinks software suites were used to analyze the RNA deep sequencing data according to Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7, 562-578 (2012) (PMID 22383036).
Genome_build: Human GRCh37/hg19 and EGFP sequence.
Supplementary_files_format_and_content: Output files were generated by the Cuffdiff program within the Cufflinks software suite.
Supplementary_files_format_and_content: EGFPFL-hg19EGFP-gene_exp-diff.txt: Comparing gene expression changes of EGFPFL pro-siRNA with control siRNA.
Supplementary_files_format_and_content: EGFPFL-lnc-diff.txt: Comparing lncRNA expression changes of EGFPFL pro-siRNA with control siRNA.

source_name: HeLa-d1EGFP, EGFPFL pro-siRNA

growth_protocol: Cells were grown in DMEM medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions. rRNA was depleted using the Ribo-Zero rRNA Removal Kit (Epicentre).
Libraries were prepared according to New England Biolab's (NEB's) instructions accompanying the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7530).

treatment_protocol: siRNA transfections were performed using Lipofectamine 2000 following the manufacturer's protocol. Briefly, cells were plated in 24-well plates (1×10^5 per well) and the transfection complex (containing 1.0 ml Lipofectamine 2000 and siRNAs) was added directly to the medium. RNA samples were isolated from cells 24 hr post-transfection.

value: derived from HeLa cells

tag: sirna

value: EGFPFL pro-siRNA


title: activatedB_wt_polII_chip

value: serine 5-phosphorylated RNA Polymerase II (Abcam)


title: Negative control siRNA, repeats 1 and 2

description:
mRNA-seq for control siRNA treated cells.
This Sample represents 2 replicates.
Directional RNA-seq.

data_processing:
Standard Illumina GA II.
Tophat and Cufflinks software suites were used to analyze the RNA deep sequencing data according to Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7, 562-578 (2012) (PMID 22383036).
Genome_build: Human GRCh37/hg19 and EGFP sequence.
Supplementary_files_format_and_content: Output files were generated by the Cuffdiff program within the Cufflinks software suite.

source_name: HeLa-d1EGFP, control siRNA

value: control siRNA


title: EGFP siRNA, repeats 1 and 2

description:
mRNA-seq for EGFP siRNA treated cells.
This Sample represents 2 replicates.
Directional RNA-seq.

data_processing:
Standard Illumina GA II.
Tophat and Cufflinks software suites were used to analyze the RNA deep sequencing data according to Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7, 562-578 (2012) (PMID 22383036).
Genome_build: Human GRCh37/hg19 and EGFP sequence.
Supplementary_files_format_and_content: Output files were generated by the Cuffdiff program within the Cufflinks software suite.
Supplementary_files_format_and_content: EGFPsiRNA-hg19EGFP-gene_exp-diff.txt: Comparing gene expression changes of EGFP siRNA with control siRNA.
Supplementary_files_format_and_content: EGFPsiRNA-lnc-diff.txt: Comparing lncRNA expression changes of EGFP siRNA with control siRNA.

source_name: HeLa-d1EGFP, EGFP siRNA

value: EGFP siRNA


title: EGFP100 pro-siRNA, repeats 1 and 2

description:
mRNA-seq for EGFP100 pro-siRNA treated cells.
This Sample represents 2 replicates.
Directional RNA-seq.

data_processing:
Standard Illumina GA II.
Tophat and Cufflinks software suites were used to analyze the RNA deep sequencing data according to Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7, 562-578 (2012) (PMID 22383036).
Genome_build: Human GRCh37/hg19 and EGFP sequence.
Supplementary_files_format_and_content: Output files were generated by the Cuffdiff program within the Cufflinks software suite.
Supplementary_files_format_and_content: EGFP100-hg19EGFP-gene_exp-diff.txt: Comparing gene expression changes of EGFP100 pro-siRNA with control siRNA.
Supplementary_files_format_and_content: EGFP100-lnc-diff.txt: Comparing lncRNA expression changes of EGFP100 pro-siRNA with control siRNA.

source_name: HeLa-d1EGFP, EGFP100 pro-siRNA

value: EGFP100 pro-siRNA


title: WTN_WTG_7D_2 [sandwich]

status: Public on Feb 11 2013

first: Sean

last: O'Keeffe

address: 701 West 168th Street

institute: Columbia University

description: processed data file: sandwich.txt

data_processing:
bowtie aligned with following parameters: -X 20000 -k 2 -m 2 -q -p 8' & for single ends (Sandwich) are '-k 2 -m 200 --best --strata -q -p 8
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM abundance measurements (RPKM's were normalized as reads per kilobase per million using a method defined by Mortazavi et al. Nat Methods, 5(7):621-628)) values for each Sample

source_name: Sandwich

extract_protocol:
RNA was extracted using a combination of Trizol (Invitrogen) and RNeasy columns (Qiagen).
Libraries were prepared using either standard protocols from Illumina or the Nextera transposase-mediated method (Gertz J, et al. 2012) and sequenced using the Illumina platform.

tag: timepoint

tag: rnaextractedfrom

value: Neuron

tag: sandwich type

value: WT neurons; WT glia


title: WTN_WTG_7D_1 [sandwich]

description: processed data file: sandwich.txt

tag: genotype/variation


title: WTN_WTG_3D_1 [sandwich]

description: processed data file: sandwich.txt


title: WTN_MTG_7D_2 [sandwich]

description: processed data file: sandwich.txt

value: WT neurons; SOD1_G93A mutant glia


title: WTN_WTG_14D_1 [sandwich]

description: processed data file: sandwich.txt


title: ChIP-seq_ZNF143_K562

source_name: chronic myelogenous leukemia cells

value: ZNF143, rabbit polyclonal raised against a C-terminal epitope of ZNF143 (Myslinski et al JBC 2006)


title: WTN_MTG_7D_1 [sandwich]

description: processed data file: sandwich.txt


title: WTN_MTG_3D_2 [sandwich]

description: processed data file: sandwich.txt


title: WTN_MTG_3D_1 [sandwich]

description: processed data file: sandwich.txt


title: WTG_WTN_7D_2 [sandwich]

description: processed data file: sandwich.txt

value: Glia

value: WT glia; WT neurons


title: WTN_MTG_14D_2 [sandwich]

description: processed data file: sandwich.txt


title: WTN_MTG_14D_1 [sandwich]

description: processed data file: sandwich.txt


title: WTG_WTN_7D_1 [sandwich]

description: processed data file: sandwich.txt


title: WTG_WTN_3D_2 [sandwich]

description: processed data file: sandwich.txt


title: WTG_WTN_3D_1 [sandwich]

description: processed data file: sandwich.txt


title: WTG_WTN_14D_1 [sandwich]

description: processed data file: sandwich.txt


title: WTG_MTN_3D_2 [sandwich]

description: processed data file: sandwich.txt

value: WT glia; SOD1_G93A mutant neurons


title: WTG_MTN_7D_2 [sandwich]

description: processed data file: sandwich.txt


title: WTG_WTN_14D_2 [sandwich]

description: processed data file: sandwich.txt


title: WTN_WTG_14D_2 [sandwich]

description: processed data file: sandwich.txt


title: WTG_MTN_14D_1 [sandwich]

description: processed data file: sandwich.txt


title: MTN_WTG_14D_1 [sandwich]

description: processed data file: sandwich.txt

value: SOD1_G93A mutant neurons; WT glia


title: MTN_WTG_3D_1 [sandwich]

description: processed data file: sandwich.txt


title: WTG_MTN_14D_2 [sandwich]

description: processed data file: sandwich.txt


title: MTN_MTG_7D_2 [sandwich]

description: processed data file: sandwich.txt

value: SOD1_G93A mutant neurons; SOD1_G93A mutant glia


title: MTN_WTG_7D_2 [sandwich]

description: processed data file: sandwich.txt


title: MTN_MTG_7D_1 [sandwich]

description: processed data file: sandwich.txt


title: MTN_MTG_3D_2 [sandwich]

description: processed data file: sandwich.txt


title: MTN_MTG_14D_2 [sandwich]

description: processed data file: sandwich.txt


title: MTG_WTN_7D_2 [sandwich]

description: processed data file: sandwich.txt

value: SOD1_G93A mutant glia; WT neurons


title: MTN_MTG_3D_1 [sandwich]

description: processed data file: sandwich.txt


title: MTG_WTN_14D_2 [sandwich]

description: processed data file: sandwich.txt


title: MTG_WTN_14D_1 [sandwich]

description: processed data file: sandwich.txt


title: MTG_WTN_3D_1 [sandwich]

description: processed data file: sandwich.txt


title: MTG_WTN_7D_1 [sandwich]

description: processed data file: sandwich.txt


title: MTG_MTN_7D_1 [sandwich]

description: processed data file: sandwich.txt

value: SOD1_G93A mutant glia; SOD1_G93A mutant neurons


title: MTG_MTN_7D_2 [sandwich]

description: processed data file: sandwich.txt


title: MTG_WTN_3D_2 [sandwich]

description: processed data file: sandwich.txt


title: MTG_MTN_3D_2 [sandwich]

description: processed data file: sandwich.txt


title: Ovary shWhite Rep2

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

description: RNA-Seq experiment

data_processing:
base-calling: Casava1.8
ChIP-seq alignment: Bowtie 0.12.7
RNA-seq alignment: TopHat 1.4.1
bedGraph track generation: custom-written python script
Genome_build: dm3
Supplementary_files_format_and_content: read coverage, normalized to RPM (Read Per Million)

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Ovary shWhite_RNA-Seq

growth_protocol: Flies were kept at 24C and aged 3-5 days, at least 2 of which were on yeast, before dissection.

extract_protocol:
RNA-seq libraries were built from polyA-selected RNA from fly ovaries following standard protocols using Ribozol for extraction of total RNA, phenol-chloroform and choloroform extraction, and the Invitrogen Dynabeads kit for polyA selection.
ChIP-Seq: Libraries were prepared using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina, and NEBNext Multiplex Oligos for Illumina. Size selection was performed using Agencourt AMPure XP beads (Beckman Coulter) according to the manufacturer’s inscrution followed by DNA purification using the Zimo Research DNA Clean & Concentrator-5 kit.
RNA-Seq: Libraries were prepared by the Millard and Muriel Jacobs Genetics and Genomics Laboratory.

tag: strain background (bloomington stock number)

value: shWhite:BL33623, nos-gal4:BL4937

value: shWhite x nos-gal4; control knockdown of a protein irrelevant to the system we studied (White)

tag: tissue

value: Ovaries


title: Ovary shPiwi Rep1

description: RNA-Seq experiment

source_name: ovary shPiwi_RNA-Seq

value: shPiwi:BL33724, nos-gal4:BL4937

value: shPiwi x nos-gal4; Piwi knockdown


title: WTG_MTN_7D_1 [sandwich]

description: processed data file: sandwich.txt


title: Ovary shPiwi Rep2

description: RNA-Seq experiment


title: Ovary shWhite Rep1

description: RNA-Seq experiment

source_name: ovary shWhite_RNA-Seq


title: MTG_MTN_3D_1 [sandwich]

description: processed data file: sandwich.txt


title: MTG_MTN_14D_2 [sandwich]

description: processed data file: sandwich.txt


title: MTG_MTN_14D_1 [sandwich]

description: processed data file: sandwich.txt


title: Ovary

description: RNA-Seq experiment

source_name: ovary WT_RNA-Seq

value: 146-sequencing strain wild type


title: Dox

city: Oxford

first: Carme

last: Camps

address: Roosevelt Drive

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics/ U. of Oxford

description: Sample 3

data_processing:
Two lanes of single-end sequencing reads of 36bp were generated from each of the three libraries in a GAII Illumina Genome Analyser. The sequencing reads for each sample were combined and trimmed from the adaptor using the FASTQ/A Clipper from the FASTX tool kit (http://hannonlab.cshl.edu/fastx_toolkit/). Only reads with a length greater than 16 bases were selected for mapping.
Bowtie (version 0.12.7) (http://bowtie-bio.sourceforge.net/index.shtml) was used to align the selected reads to the miRNA mature sequences for Mus musculus included in the mature.fa file from miRBase (version 18) (http://www.mirbase.org/). In order to allow only perfect matches, the default parameters were used except for the following: “—seedmms  0  --seedlen 60 --maqerr 10 -m 2000000 -k 2000000”. Reads mapping to a unique position were assigned to the particular miRNA. Reads mapping to several positions were assigned to the miRNA with the same length whenever possible or to the miRNA with the closest length. In case that more than one miRNA fulfilled this requirement the read was then assigned to each of these miRNAs.
Reads resulting unmmaped to mature forms were subsequently aligned to the miRNA precursor sequences for Mus musculus included in the hairpin.fa from miRBase (version 18) by using the same parameters described before. In order to assign the aligned reads to mature forms produced from the matching precursor, the coordinates for all mature forms derived from the 5p and the 3p arms of all miRNA precursors were determined as follows: mature forms for Mus musculus extracted from the mature.fa file from miRBase (version 18) were mapped to the precursor sequences (Mus musculus haipin.fa, miRBase, version 18) using Bowtie and the same parameters described previously. These coordinates were used to assign the reads mapped to precursors to the corresponding mature form derived from these precursors. In order for a read to be assigned to a certain mature form, total or partial overlap to the specified coordinates was required. Under these conditions, reads mapping to one position were assigned to the respective mature miRNA. Since some mature forms can be produced from more than one precursor, reads mapping across all precursors were identified and assigned only once to the corresponding mature miRNA. For any remaining reads mapping to several positions in the hairpin.fa, all positions were accepted.
We only considered a miRNA to be expressed if 10 or more reads were found across all 3 samples.
Genome_build: miRBase (mouse, version 18)
Supplementary_files_format_and_content: Tab-delimited text files include reads normalized to the total number of reads for the respective sample and multiplied by 1,000,000 in order to scale the values to the range of "reads per million".

source_name: TAG 1 ES_Dox

growth_protocol: ES cells were were maintained in DMEM (Invitrogen) containing 15% Foetal Bovine Serum (FBS) (Source Bioscience) and Leukemia Inhibitory Factor (LIF) (homemade), 2 mM L-Glutamine, 1% Penicillin-Streptomycin, 0.1 nM b-Mercaptoethanol at 37°C in a 5% CO2 humidified incubator

extract_protocol: Total RNA containing the short RNA fraction was isolated using the miRVana miRNA isolation kit (Ambion). Libraries were prepared according to the Illumina small RNA preparation protocol v1.0. The 20-30 nucleotide fraction was isolated from 10µg of total RNA after being run in a 15% Urea-TBE gel (Invitogen) for 1h. The RNA contained on the excised gel bands was eluted on 300μl of 0.3M NaCl solution during 4h at RT and constant rotation. The elute was separated from the gel debris through a Spin-X-column (Fisher) and RNA was precipitated by adding 750μl of 100% ethanol and 3μl of glycogen (Ambion) (1mg/ml) and incubating it for 30min at -80˚C. The precipitated RNA was centrifuged at 14K rpm for 25 min at 4˚C, washed with 75% ethanol and resuspended on 5.7μl of RNAse free water. A 5’ adaptor was ligated to the RNA in a reaction containing the full amount of RNA recovered from last step, 1.3μl of SRA 5’ adaptor (Illumina), 1μl T4 RNA ligase (10U/μl) (Promega), 1 μl 10X T4 RNA ligase (Promega) and 1 μl RNAseOUT (Invitrogen). The reaction was incubated at 20˚C in a thermal cycler for 6h. The resulting product was run on a 15% Urea-TBE gel (Invitrogen) and the band corresponding to 40-60 nucleotides was excised. The 5’ ligated RNA was eluted and precipitated as described before and finally resuspended in 6.4 μl of RNAse free water. A 3’ adaptor was added to these molecules in a reaction containing the entire 5’ ligated RNA recovered from last step, 0.6 μl of SRA 3’ adaptor v 1.0 (Illumina), 1μl T4 RNA ligase (10U/μl) (Promega), 1 μl 10X T4 RNA ligase (Promega) and 1 μl RNAseOUT (Invitrogen). The reaction was incubated at 20˚C in a thermal cycler for 6h. The product obtained was run on a 10% Urea-TBE gel (Invitrogen) and the band corresponding to 70-90 nucleotides was excised. The 5’ and 3’ ligated RNA was eluted and precipitated as described before and finally resuspended in 4.5 μl of RNAse free water. In order to synthesize single stranded DNA from this material, 0.5 μl of SRA RT-primer (Illumina) were added to it and the mixture was incubated at 65˚C for 10 min. This was complemented with 2 μl of 5X first strand buffer, 1 μl 100mM DTT, 0.5 μl RNAseOUT (all from Superscript II reverse transcription kit (Invitrogen)) and 0.5 μl 12.5mM dNTP mix (BioLine) and incubated at 48˚C for 3 min. After adding 1 μl of Superscript II retrotranscriptase (Invitrogen), the reaction was incubated at 44˚C for 1h. A PCR reaction was then set up with the resultant product and 0.5µl GX1 primer, 0.5µl GX2 primer (both from Illumina), 0.5µl 25mM dNTP mix (Bioline), 10µl 5X cloned Phu buffer, 0.5µl Phu polymerase (both from NEB) and 28µl RNAse free water. The cycling conditions were as follows: 1 cycle of 98˚C for 30 sec; 15 cycles of 98˚C for 10 sec, 60˚C for 30 sec and 72˚C for 15 sec; 1 cycle of 72˚C for 10 min. The PCR product was purified by running it on a 10% TBE-PAGE gel for 35 min. The band around 90bp was excised and eluted on 100µl of 1X Elution buffer 2 (NEB) for 2h at RT and at constant rotation. The elute was separated from the gel debris through a Spin-X-column (Fisher) and DNA was precipitated by adding 1μl of glycogen (1mg/ml) (Ambion), 10ul 3M sodium acetate (Ambion) and 325μl of -20˚C100% ethanol and  centrifuging at 14K rpm for 20 min. After a wash with 70% ethanol, the DNA was vacuum dried and resuspended in 10µl of water.

treatment_protocol: RNA was extracted from mouse ES cells which were either untreated (control sample), treated for 16 hrs with 30 µM SB-431541 (SB sample), or for 16 hrs 30 µM SB followed by 12 hrs 1 µg/µl Dox (Dox sample)

tag: cell type

value: TAG 1 ES cells

tag: treated with

value: Dox treated (P-Smad2/3 induced)

tag: molecule subtype

value: Total RNA containing short RNA fraction


title: Ovary shWhite Rep2 PolII Input

description: ChIP-Seq Input experiment

source_name: ovary shWhite PolII Input

extract_protocol:
Piwi ChIP was done using 200 pairs of ovaries per IP conditions. For RNA polymerase II standard ChIP protocol was used with 1% PFA crosslinking at RT for 10 minutes followed by quenching with glycine (final concentration 25mM) for 5min at RT, and then washed 3 times in PBS. Nuclei were isolated by light douncing in Farnham Buffer (5mM HEPES pH8.0; 85mM KCl; 0.5% NP-40/Igepal; NaCl Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM) and centrifugation of intact nuceli. Nuclei were resuspended and dounced in RIPA Buffer (20mM Tris pH7.4; 150mM; 1% NP-40/Igepal; 0.5% Sodium Deoxycholate; 0.1% SDS; Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM) prior to sonication. Sonicaton was performed at 4C using a Bioruptor from Diagenode on Medium power for 20 cycles (30sec ON, 30sec OFF). Samples are then centrifuged and the supernatant was pre-cleared for 2h at 4C using Dynabeads Protein G (Invitrogen). For RNAse treatment samples were incubated with 1µl of RNAse A (10mg/ml) during pre-clearing and all samples incubated 2h at RT. Antibodies were conjugated to Dynabeads Protein G for 2h at 4C and then added to the precleared supernatant and incubated for 2h at 4C. Beads were then washed 5 times at 4C using LiCl IP Buffer (10mM Tris ph7.5; 500mM LiCL; 1% NP-40/Igepal; 1% Sodium Deoxycholate), then rinsed in TE and finally resuspended in Proteinase K Buffer (200mM Tris ph7.4; 25mM EDTA; 300mM NaCL; 2% SDS) with 100µg of proteinase K. Samples were incubated 3h at 55C then overnight at 65C. DNA was extracted following standard phenol-chlorophorm extraction.
ChIP-Seq: Libraries were prepared using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina, and NEBNext Multiplex Oligos for Illumina. Size selection was performed using Agencourt AMPure XP beads (Beckman Coulter) according to the manufacturer’s inscrution followed by DNA purification using the Zimo Research DNA Clean & Concentrator-5 kit.
RNA-Seq: Libraries were prepared by the Millard and Muriel Jacobs Genetics and Genomics Laboratory.


title: Ovary shWhite Rep2 PolII

description: ChIP-Seq experiment

source_name: ovary shWhite PolII

tag: chip-seq antibody

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S) antibody [clone 4H8]

tag: chip-seq antibody vendor

value: Abcam

tag: chip-seq antibody cat. #


title: Ovary shWhite Rep2 H3K9me3

description: ChIP-Seq experiment

source_name: ovary shWhite H3K9me3


title: Ovary shWhite Rep2 Input H3K9me3

description: ChIP-Seq Input experiment

source_name: ovary shWhite Input H3K9me3


title: Ovary shPiwi Rep2 PolII Input

description: ChIP-Seq Input experiment

source_name: ovary shPiwi PolII Input


title: MTN_MTG_14D_1 [sandwich]

description: processed data file: sandwich.txt

value: Neuron


title: Ovary shPiwi Rep2 H3K9me3 Input

description: ChIP-Seq Input experiment

source_name: ovary shPiwi H3K9me3 Input


title: Ovary shPiwi Rep2 H3K9me3

description: ChIP-Seq experiment

source_name: ovary shPiwi H3K9me3

value: Anti-Histone H3 (tri methyl K9) antibody

tag: chip-seq antibody lot #


title: Ovary shPiwi Rep2 PolII

description: ChIP-Seq experiment

source_name: ovary shPiwi PolII


title: Ovary shWhite Rep1 PolII

description: ChIP-Seq experiment


title: Control

description: Sample 1

source_name: TAG 1 ES_Control


title: Ovary shWhite Rep1 H3K9me3

description: ChIP-Seq experiment


title: Ovary shPiwi Rep1 PolII

description: ChIP-Seq experiment


title: Ovary shWhite Rep1 Input

description: ChIP-Seq Input experiment

source_name: ovary shWhite Input


title: Ovary shPiwi Rep1 Input

description: ChIP-Seq Input experiment

source_name: ovary shPiwi Input


title: 8wk_WT_M [spinal cord]

description: processed data file: spinalCord.txt

source_name: Spinal Cord

extract_protocol:
Two hundred and fifty microliters of chloroform per 1 mL of Trizol was added to each tube. Tubes were then vortexed at maximum speed for 15 sec, incubated at room temperature for 2-3 min, and centrifuged at 12,000 x g for 15 min at 4 °C. The aqueous phase was transferred to new tubes, to which an equal volume of 70% ethanol was slowly added with frequent mixing. This mixture was then applied to an RNeasy column (Qiagen), which was then washed and from which RNA was eluted according to the manufacturer’s instructions. RNA was eluted in a final volume of 32 uL.
Libraries were prepared using either standard protocols from Illumina or the Nextera transposase-mediated method (Gertz J, et al. 2012) and sequenced using the Illumina platform.

tag: gender

value: M

value: Spinal Cord

value: WT


title: Ovary shPiwi Rep1 H3K9me3

description: ChIP-Seq experiment


title: 8wk_WT_F [spinal cord]

description: processed data file: spinalCord.txt

value: F


title: 8wk_MT_M [spinal cord]

description: processed data file: spinalCord.txt

value: SOD1_G93A mutant


title: 4wk_WT_F [spinal cord]

description: processed data file: spinalCord.txt


title: 8wk_MT_F [spinal cord]

description: processed data file: spinalCord.txt


title: 4wk_WT_M [spinal cord]

description: processed data file: spinalCord.txt


title: 4wk_MT_M [spinal cord]

description: processed data file: spinalCord.txt


title: 4wk_MT_F [spinal cord]

description: processed data file: spinalCord.txt


title: SB

description: Sample 2

source_name: TAG 1 ES_SB

value: SB-431541 treated (P-Smad2/3 repressed)


title: 17wk_MT_F [spinal cord]

description: processed data file: spinalCord.txt


title: 17wk_WT_F [spinal cord]

description: processed data file: spinalCord.txt


title: 12wk_WT_F [spinal cord]

description: processed data file: spinalCord.txt


title: 17wk_MT_M [spinal cord]

description: processed data file: spinalCord.txt


title: 12wk_WT_M [spinal cord]

description: processed data file: spinalCord.txt


title: 12wk_MT_M [spinal cord]

description: processed data file: spinalCord.txt


title: 12wk_MT_F [spinal cord]

description: processed data file: spinalCord.txt


title: Embryonic1

status: Public on Feb 10 2013

first: J Raphael

last: Gibbs

address: 35 Convent Drive, Bldg 35/1A1015, MSC3707

department: Computational Biology Core

institute: National Institutue on Aging, NIH

data_processing:
Basecalls performed using CASAVA version 1.7.1
alignment: tophat (v1.0.13) and bowtie (v0.12.7.0)
read counts: HT-SEQ (0.5.3p3)
normalization and differential expression: DE-SEQ (v1.6.1)
variant base calls: SAMtools pileup (samtools-0.1.7a)
Genome_build: mm9
Supplementary_files_format_and_content: variance stabalized quantified data, DE-Seq normalized values

source_name: cerebral cortex

extract_protocol: trizol extraction for RNA standard illumina RS-100-0801  mRNA-Seq 8 sample prep kit

tag: strain

tag: age

value: cerebral cortex


title: Adult3

value: Adult


title: Embryonic3


title: Adult1


title: Embryonic4


title: SRT1_MH

city: Wuhan

first: zhong

last: xiaochao

address: 狮子山街1号

country: China

institute: National center of plant gene research（Wu han）

description: OsSRT1 antibody was prepared by immunizing rabbits with E.coli produced OsSRT1 protein

data_processing:
Alignment: Sequence reads were obtained and mapped to the rice genomes (MSU6.0) using MAQ software with defaulted parameters. All reads mapping with two or fewer mismatches were retained.
peaks were called using MACS version 1.4 with the default parameters and LARGELOCAL(5000).
Peaks in gene body and upstream and downstream 2Kb were identified as the histone modification or OsSRT1 binding.
Genome_build: MSU6.0
Supplementary_files_format_and_content: wig files were generated using MACS version 1.4; Scores represent tag density.
Supplementary_files_format_and_content: TXT files contained H3K9ac modificated genes and OsSRT1 bound genes ; Scores represent tags within modification or binding peak

organism: Oryza sativa

source_name: seedling

growth_protocol: Rice seedlings were grown under the conditions (14h light/10h dark at 25°C-28°C) in 1/2 Murashige and Skoog medium 11 days

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 DNA Sample Kit (Part# 0801-0303). 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 ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: line

value: 11 days seedling

tag: chip antibody


title: ChIP-seq input nos-GAL4->piwi

status: Public on Feb 09 2013

city: Cold Spring Harbor

first: Nikolay

middle: V

last: Rozhkov

email: nik.rozhkov@gmail.com, rozhkov@cshl.edu

address: 1 Bungtown Rd.

institute: CSHL

data_processing:
Reads were aligned to consensus drosphila transposon sequences (v9.4.1 available from flybase.org) using bowtie2 (version 2.0.0-beta7) and the following parameters: -p2 -k 10 -N1
Reads were separately aligned to the dm3 genome using bowtie2 and the same parameters
For ChIPseq libraries, peaks were identified using SICER (version 1.1) and the following parameters: redundancy threshold =1, fragment size = 250, window size = 500, gap size = 500, FDR = 0.05, effective genome size = 0.72
Genome_build: dm3

source_name: ChIP-seq input nos-GAL4->piwi

growth_protocol: flies were kept at 25 degrees

extract_protocol:
ChIP-seq: chromatin from 50 ovaries was fragmented on Bioruptor during 14 min (2 cycles, 7 min each), an aliquot was kept as "input", the rest was used for ChIP with H3K9me-ab. The detailed protocols can be found in the Rozhkov et al, 2013
The detailed methods described in the Rozhkov et al. 2013

treatment_protocol: ovaries were dissected on ice

value: ovaries

value: 3-5 days

value: none (input)


title: 17wk_WT_M [spinal cord]

description: processed data file: spinalCord.txt

tag: timepoint

tag: rnaextractedfrom


title: H3K9ac_MH

value: H3K9ac (Millipore, 07-325, lot DAM1813175)


title: ChIP-seq H3K9me3 Tj-GAL4->piwi

source_name: ChIP-seq H3K9me3 Tj-GAL4->piwi

value: H3K9me3 (Abcam, ab8898)


title: ChIP-seq H3K9me3 nos-GAL4->piwi

source_name: ChIP-seq H3K9me3 nos-GAL4->piwi


title: ChIP-seq H3K9me3 nos-GAL4->white

source_name: ChIP-seq H3K9me3 nos-GAL4->white


title: ChIP-seq input Tj-GAL4->white

source_name: ChIP-seq input Tj-GAL4->white


title: ChIP-seq input nos-GAL4->white

source_name: ChIP-seq input nos-GAL4->white


title: ChIP-seq input Tj-GAL4->piwi

source_name: ChIP-seq input Tj-GAL4->piwi


title: ChIP-seq H3K9me3 Tj-GAL4->white

source_name: ChIP-seq H3K9me3 Tj-GAL4->white


title: RNA-seq nos-GAL4->piwi

data_processing:
Reads were aligned to consensus drosphila transposon sequences (v9.4.1 available from flybase.org) using bowtie2 (version 2.0.0-beta7) and the following parameters: -p2 -k 10 -N1
Reads were separately aligned to the dm3 genome using bowtie2 and the same parameters
For RNAseq libraries, genomic alignments to dm3 were performed with tophat (v2.0.5) using the following parameters: --segment-length 18 -p 10 --library-type fr-firststrand
For RNAseq and GROseq libraries, differential expression was performed with DESeq (release 1.10.1) with the following parameters: method='pooled',sharingMode="maximum",fitType="local"
Genome_build: dm3

source_name: RNA-seq nos-GAL4->piwi

extract_protocol:
RNA-seq: libraries were constructed from 150ng of total RNA using Encore Complete RNA-seq kit (NuGen)
RNA-seq - using Encore Complete RNA-seq kit (NuGen)
The detailed methods described in the Rozhkov et al. 2013


title: Liver High androstenone rep 5

city: Bonn

first: Sudeeep

last: Sahadevan

state: NRW

address: Endenicher Allee 15

department: Institute of Animal Science

institute: University of Bonn

description: Sample B10

data_processing:
Base calling performed using Illumina Casava 1.7
The raw reads were trimmed for adapter sequences and mapped to sscrofa9 refseq and mRNA sequences and sscrofa9 whole genome using bwa using the default parameteres.
Raw read counts were calculated from the annotated files using samtools using default parameters for sscrofa9 refseq and mrna mapppings using the default parameters.
Genome_build: Sscrofa9 (NCBI)
Supplementary_files_format_and_content: tab limited text file include raw read count for each sample

organism: Sus scrofa

source_name: Liver High androstenone

extract_protocol:
Testis and liver were frozen in liquid nitrogen immediately after slaughter and stored at -80°C until used for RNA extraction. RNA was harvested using RNeasy Mini Kit according to manufacturer’s recommendations (Qiagen).
Full-length cDNA was obtained from 1 μg of RNA, with the SMART cDNA Library Construction Kit (Clontech, USA), according to the manufacturer's instructions. Libraries of amplified RNA for each sample were prepared following the Illumina mRNA-Seq protocol.
The library preparations were sequenced on an Illumina HiSeq 2000 as single-reads to 100 bp using 1 lane per sample on the same flow-cell (first sequencing run) at GATC Biotech AG (Konstanz, Germany).

tag: breed

value: Duroc x F2 cross. F2 was created by crossing F1 animals (Leicoma x German Landrace). Large White pig

value: liver

value: 116 day old


title: Embryonic2


title: Liver High androstenone rep 2

description: Sample B7


title: H3K9ac_srt1-RNAi


title: RNA-seq Tj-GAL4->white

source_name: RNA-seq Tj-GAL4->white


title: RNA-seq Tj-GAL4->piwi

source_name: RNA-seq Tj-GAL4->piwi


title: Liver High androstenone rep 3

description: Sample B8


title: Adult2


title: Liver High androstenone rep 1

description: Sample B6


title: Liver High androstenone rep 4

description: Sample B9