title: E93-44hAPF-FAIRE-Rep2

status: Public on Jun 06 2017

city: Chapel Hill

first: Spencer

middle: L

last: Nystrom

state: NC

address: 250 Bell Tower Drive

department: Curriculum in Genetics and Molecular Biology

institute: UNC-Chapel Hill

description:
E93-44hAPF-FAIRE-Rep2
E93_44hAPF_RepPooled_PCRDupsRemoved_peaks.txt
E93_44hAPF_FAIRE_merge_Rep12_bs10_e125_1x_znorm.bw
Barcode: GAACT

data_processing:
RNAseq - Sequenced reads were mapped to the dm3 whole genome using Tophat2 v2.1.0., supplementing a dm3 version transcript annotation file and using library-type fr-firststrand
RNAseq – The resulting bam file was indexed and sorted using samtools v1.2
RNAseq – htseq-count v0.6.1 was used to count reads mapping to genes, using the parameters -s reverse -a 10 -t exon -i gene_name -f bam -r pos
RNAseq – FPKMs were calculated from the resulting count files using EdgeR
FAIREseq – Sequenced reads were mapped ot the dm3 whole genome using bowtie2 v2.2.8, using seed 123
FAIREseq – the resulting bam file was indexed and sorted using samtools v1.3.1, and all reads with a mapq score less than 5 were removed setting -bq 5
FAIREseq – the resulting bam file was indexed and sorted using samtools v1.3.1
FAIREseq – PCR duplicates were marked in the resulting sorted, indexed sam file using Picard v2.2.4 MarkDuplicates
FAIREseq – PCR duplicates were removed with samtools v1.3.1 by removing all reads marked with the PCR duplicates bit flag (samtools view -bF 0x400)
FAIREseq – The resulting bam file was indexed and further filtered to include only reads mapping to chr2L, chr2R, chr3L, chr3R, chr4, and chrX (no Y, U, or heterochromatic regions)
FAIREseq – the resulting bam file was indexed and converted to a bed file with bedtools v2.25.0
FAIREseq – bigwigs normalized to reads per genomic content (RPGC) were generated from the resulting bedfile using Deeptools v2.24.0 bamCoverage setting: --normalizeTo1x 121400000 –binSize 10 -e 125 –outFileFormat bedgraph
FAIREseq – bigwigs were Z-normalized using standard deviations and means for each chromosome arm
FAIREseq – peak calls were generated by pooling the bedfiles for each replicate which were then input to MACS2 (v 2015-06-03) using -g dm, --nomodel, --extsize 125, --seed 123
ChIPseq – Sequenced reads were mapped ot the dm3 whole genome using bowtie2 v2.2.8, using seed 123
ChIPseq – the resulting bam file was indexed and sorted using samtools v1.3.1, and all reads with a mapq score less than 5 were removed setting -bq 5
ChIPseq – the resulting bam file was indexed and sorted using samtools v1.3.1
ChIPseq – PCR duplicates were marked in the resulting sorted, indexed sam file using Picard v2.2.4 MarkDuplicates
ChIPseq – PCR duplicates were removed with samtools v1.3.1 by removing all reads marked with the PCR duplicates bit flag (samtools view -bF 0x400)
ChIPseq – The resulting bam file was indexed and further filtered to include only reads mapping to chr2L, chr2R, chr3L, chr3R, chr4, and chrX (no Y, U, or heterochromatic regions)
ChIPseq – the resulting bam file was indexed and converted to a bed file with bedtools v2.25.0
ChIPseq – bigwigs normalized to reads per genomic content (RPGC) were generated from the resulting bedfile using Deeptools v2.24.0 bamCoverage setting: --normalizeTo1x 121400000 –binSize 10 -e 125 –outFileFormat bedgraph
ChIPseq – bigwigs were Z-normalized using standard deviations and means for each chromosome arm
ChIPseq – peak calls were generated by pooling the bedfiles for each replicate which were then input to MACS2 (v 2015-06-03) using -g dm, --nomodel, --extsize 125, --seed 123
MACS2 peak calls were all normalized to Control_GenomicDNA_UMR_sorted_PCRDupsRemoved.bed
Genome_build: dm3
Supplementary_files_format_and_content: RNAseq – a single matrix table in the form of a xls file contains FPKMs for genes at all the timepoints
Supplementary_files_format_and_content: FAIREseq – Z-normalized bigwig files generated from the pooled datasets used to generate peakCalls
Supplementary_files_format_and_content: FAIREseq – txt files containing output from MACS2 peak calls on pooled datasets
Supplementary_files_format_and_content: ChIPseq – txt files containing output from MACS2 peak calls on pooled datasets

source_name: 44hAPF wings

extract_protocol:
A minimum of 40 wings were dissected from staged female flies in 1x PBS and transferred to ice for subsequent processing. 6 rounds of bead beating (1 minute beating, 2 minutes resting) were performed on dissected tissue. Lysate was sonicated with a Branson sonifier to a fragment size range of 500 bp – 2kb. Soluble chromatin fraction was isolated by centrifugation at 15,000 RCF x 5’ at 4C. Soluble chromatin fraction was phenol-chloroform extracted. Isolated FAIRE-enriched DNA was used for library prep.
Rubicon Thruplex DNA-seq kit

value: wing

tag: developmental stage

tag: genotype

tag: biological replicate number


title: GH infusion_14d male liver pool 2_polyA-selected_G96_M6

status: Public on Jul 14 2017

type: SRA

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

country: USA

institute: Boston University

description: poly-A selected RNA, unstranded library

library_source: transcriptomic

data_processing:
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) RNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene. Primary RNA transcripts (hnRNA) were quantified by counting reads that map to the intersection of all intronic sequences across all isoforms of a given gene; this counting thus excludes sequence reads that map to an exonic region of at least one isoform of the gene.
Differential expression analysis for RefSeq genes was conducted using edgeR (Robinson, 2010, Bioinformatics),
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file containing normalized read counts and differential expression results comparing cGH-treated male mouse livers to sham-treated male mouse livers; The raw sequencing data for the sham-treated controls is found in GEO series GSE66140, samples GSM1612771, GSM1612772, and GSM1612773.

molecule: total RNA

organism: Mus musculus

source_name: liver tissue

extract_protocol:
RNA was extracted from flash fozen mouse liver using Trizol per the manufacturer's instructions.
RNA was polyA-selected and sequencing libraries were prepared using the Illumina TruSeq RNA library preparation kit (Illumina, cat# RS-122-2001), according to the manufacturer's instructions.

treatment_protocol: Male CD1 mice, 8–9 weeks of age, were purchased from Charles River Laboratories  (Crl:CD1(ICR)). Alzet osmotic pumps (model 1007D) were filled with recombinant rat GH and were implanted subcutaneously under ketamine and xylazine anesthesia. GH was infused at a rate of 25 ng/g body weight/h for either 10 h or 14 d.

tag: strain

value: Crl:CD1(ICR) (Charles River, strain code #022)

tag: treatment

value: Continuous GH 14 days

tag: Sex

value: Male

tag: age

value: 8-9 weeks


title: EA0898_NRAIA

status: Public on Apr 03 2018

type: RNA

city: Newcastle upon Tyne

first: Arthur

last: Pratt

address: Framlington Place

department: Faculty of Medical Sciences

country: United Kingdom

institute: Newcastle University

hyb_protocol: cRNA was hybridized to the Illumina WG6 (version 4) BeadChip (Illumina, San Diego, following the manufacturer’s protocol.

scan_protocol: Illumina BeadArray Reader as per Illumina protocol.

data_processing: Normalisation of component dataset[s] (which, in some cases included raw data extracted from Pratt AG et al 2012; GEO accession GSE20098) was first carried out by robust spline normalisation (RSN) , and variance stability transformation (VST) (Du P et al 2008 Bioinformatics; Lin SM et al 2008 Nucleic Acids Res). Unique IDs for defined analyses are listed in relevant manuscript text. Where required data were merged using InSilicoMerging Bioconductor package (Taminau J et al 2012 BMC Bioinformatics), and batch correction was carried out by linear modelling Batch correction was carried out by linear modelling  (Ritchie ME et al 2015 Nucleic Acids Res).

label: biotin

organism: Homo sapiens

source_name: NRAIA_Blood CD4+ T Cells

label_protocol: 50ng RNA was reverse transcribed into cRNA, and biotin-UTP labeled, using the Illumina TotalPrep RNA Amplification Kit (Ambion, Texas).

extract_protocol: Monocytes were first depleted by immunorosetting (Rosettesep Human Monocyte depletion cocktail, Stemcell Technologies Inc., Vancouver, non-RA inflammatory arthritisanada), and remaining cells underwent positive selection using Easisep whole blood CD4+ positive selection kit reagents in conjunction with the Robosep automated cell separator (Stemcell). CD4+ T-cell purity was determined using standard flow cytometry techniques; FITC-conjugated anti-CD4 and PE-conjugated anti-CD14 antibodies were used (Beckton Dickinson, New Jersey, USA). RNA was immediately extracted from CD4+ T-cell isolates using RNeasy MINI kits (Qiagen GmbH, Germany), incorporating an “on-column” DNA digestion step.

treatment_protocol: Between 0900 and 1200hrs during the clinic appointment, 15ml peripheral whole blood was drawn into EDTA tubes (Greiner Bio-One, ACPA- RAustria) and stored at room temperature for a maximum of 4 hours before processing.

tag: gender

value: F

tag: age (yrs)

tag: diagnostic category

value: Non-RA inflammatory arthritis (NRAIA) - includes Code A 4-11)

tag: tissue

value: peripheral blood

tag: cell type

value: CD4+ T-cell


title: E93-mimic-ChIP-Rep2

description:
E93-mimic-ChIP-Rep2
E93-mimic-ChIP-Rep12-Pooled_peaks.txt
E93mimic_ChIP_merge_Rep12_bs10_e125_1x_znorm.bw
Barcode: CTTGTA

library_source: genomic

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: 24hAPF wings

extract_protocol:
700+ Wings were manually dissected from 24hAPF male and female E93 protein trap flies. Wings were fixed in batches of 20 in 4% paraformaldehyde, 50mM HEPES, 100mM NaCl, 1mM EDTA, 0.5mM EGTA for 20-minutes at room temperature, followed by quenching with 125mM glycine in 1x PBS, 0.01% Triton. Fixed wings were Dounce homogenized in 10mM HEPES, 10mM EDTA, 0.5mM EGTA, 0.25% Triton, 1mM PMSF. Nuclei were pelleted at 4,500xg for 20-minutes, and re-suspended in 10mM HEPES, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.01% Triton, 1mM PMSF. After nutating at 4C for 10-minutes, nuclei were pelleted again and re-suspended in 140mM NaCl, 10mM HEPES, 1mM EDTA, 0.5mM EGTA, 1mM PMSF, 0.1% SDS, followed by sonication on ice with a Branson Sonifier until average chromatin fragment size was 200bp. The soluble chromatin fraction was used for ChIP. Briefly, extracts were pre-cleared with protein-A dynabeads for 2 hours at 4C, and cleared extracts were incubated with 5µg of rabbit anti-GFP antibody (Abcam cat# ab290) overnight at 4C. Bead pulldown was performed for 3-hours the following day. Antibody-bead complexes were washed successively, and then eluted with 1% SDS, 250mM NaCl, 10mM Tris, 1mM EDTA. Samples were treated with RNase A and proteinase K, heated overnight at 65C to reverse crosslinks, and purified DNA was recovered by phenol-chloroform/ethanol precipitation.
Rubicon Thruplex DNA-seq kit

value: yw/+; + ; Mi{MIC}Eip93F/+

tag: chip antibody

value: anti-GFP antibody (Abcam, cat# ab290, lot# GR278480-1)


title: E93-3LW-FAIRE-Rep1

description:
E93-3LW-FAIRE-Rep1
E93_3LW_RepPooled_PCRDupsRemoved_peaks.txt
E93_3LW_FAIRE_POOL_Rep12_bs10_e125_1x_znorm.bw
Barcode: AGTCT

source_name: 3LW wing imaginal discs


title: E93-24hAPF-FAIRE-Rep1

description:
E93-24hAPF-FAIRE-Rep1
E93_24hAPF_RepPooled_PCRDupsRemoved_peaks.txt
E93_24hAPF_FAIRE_merge_Rep12_bs10_e125_1x_znorm.bw
Barcode: TCCAT


title: E93-24hAPF-FAIRE-Rep2

description:
E93-24hAPF-FAIRE-Rep2
E93_24hAPF_RepPooled_PCRDupsRemoved_peaks.txt
E93_24hAPF_FAIRE_merge_Rep12_bs10_e125_1x_znorm.bw
Barcode: TGGTA


title: E93-mimic-ChIP-Rep1

description:
E93-mimic-ChIP-Rep1
E93-mimic-ChIP-Rep12-Pooled_peaks.txt
E93mimic_ChIP_merge_Rep12_bs10_e125_1x_znorm.bw
Barcode: GGCTAC


title: EA0878_NRAIA


title: E93-3LW-FAIRE-Rep2

description:
E93-3LW-FAIRE-Rep2
E93_3LW_RepPooled_PCRDupsRemoved_peaks.txt
E93_3LW_FAIRE_POOL_Rep12_bs10_e125_1x_znorm.bw
Barcode: AACGC


title: GH infusion_10h male liver pool 2_polyA-selected_G96_M4

description: poly-A selected RNA, unstranded library

value: Continuous GH 10 hours


title: EA0929_ACPAnRA

source_name: ACPAnRA_Blood CD4+ T Cells

value: ACPA-neg RA


title: EA0854_ACPApRA

source_name: ACPApRA_Blood CD4+ T Cells

value: M

value: ACPA-pos RA


title: E93-44hAPF-FAIRE-Rep1

description:
E93-44hAPF-FAIRE-Rep1
E93_44hAPF_RepPooled_PCRDupsRemoved_peaks.txt
E93_44hAPF_FAIRE_merge_Rep12_bs10_e125_1x_znorm.bw
Barcode: CGAAG


title: EA0845_NRAIA


title: EA0882_ACPApRA


title: EA0810_ACPApRA


title: EA0809_NRAIA


title: GH infusion_10h male liver pool 1_polyA-selected_G96_M3

description: poly-A selected RNA, unstranded library


title: ChIPseq.HumanPRDM9_HA.antiH3K4me3.ProtocolC.Rep2

status: Public on May 31 2017

city: Berkeley

first: Nicolas

last: Altemose

state: CA

address: 327 Stanley Hall

department: Bioengineering

institute: University of California, Berkeley

description:
Uniquely Mapped Fragments: 54451480
Multiplex Group: 3

data_processing:
ChIP-seq: Reads were aligned to hg19 using BWA (v0.7.0-r313, option -q 10) followed by Stampy (v1.0.23_(r2059), option --bamkeepgoodreads). PCR duplicates, reads not mapped in a proper pair, reads with an insert size larger than 10 kb, and read pairs for which neither read had a mapping quality score greater than 0 were removed using samtools (v0.1.19-44428cd). For samples with only one replicate, fragments were split at random into two equally-sized pseudo-replicates. Fragment coverage from each replicate was then computed at each position in the genome using in-house code and the samtools (v0.1.19-44428cd) and bedtools (v2.23.0, genomecov -d) packages. Peaks were called using a custom peak calling algorithm (described in Gupta-Hinch et al. 2014). Enrichments and p-values are reported for the base with the maximum likelihood value within each peak region.
ATAC-seq: Reads were mapped to hs37d5 using BWA (v0.7.0-r313) followed by Stampy (v1.0.23_(r2059), with option --bamkeepgoodreads). PCR duplicates, mtDNA-mapped reads, reads not mapped in a proper pair, reads with mapping quality equal to 0, and pairs with an insert size larger than 2 kb were removed using samtools (v0.1.19-44428cd). Fragments were split by size into inter-nucleosome (51-100 bp) and mono-nucleosome fragments (180-247 bp), and the position of the central base in each fragment was reported.
RNA-seq: We created a custom reference sequence by merging the hs37d5 reference with the construct and vector sequences transfected into our cells. Data were analyzed using the Tuxedo software package. Reads were mapped and processed using TopHat (version 2.0.13, options --mate-inner-dist=250 --mate-std-dev 80 --transcriptome-index=Ensembl.GRCh37.genes.gtf); followed by Cufflinks, CuffQuant, and CuffDiff (version 2.2.1); then analyzed using CummeRbund.
Genome_build: hg19 (ChIP-seq), hs37d5 (ATAC-seq), hs37d5+ (RNA-seq)
Supplementary_files_format_and_content: bedgraph files contain fragment coverage data for each base across the 22 autosomes and X chromosome. For ChIP-seq samples, these values were used as inputs for de novo peak calling and force-calling. ChIP-seq peak call files are in tab-delimited text format, with one peak per rown and column headers indicating the contents of each column. For ATAC-seq samples, fragment coverage data were split into subsets representing internucleosome fragments (51-100 bp long) and mononucleosome fragments (180-247 bp long), and only the position of the central base of each fragment is reported. For RNA-seq samples, the final CuffDiff output file (tab-delimited diff format) is provided.

source_name: HEK293T cells

growth_protocol: Cells were grown in DMEM media (Sigma D6546) supplemented with 10% FBS (Sigma F7524), 1X L-Glutamine (Sigma G7513), and 1X penicillin/streptomycin (Sigma P0781) in flasks or plates at 37C with 5% CO2. Confluent cells were split 1:10 and passaged for no longer than one month before transfection.

extract_protocol:
ChIP was performed as described in Gupta-Hinch et al. 2014, with modifications. Crosslinking was performed in 1% formaldehyde for 5 minutes. Input chromatin was "pre-cleared" to remove chromatin bound non-specifically by the beads. For each sample, 50 ul of equilibrated magnetic beads were resuspended in 100 ul PBS/BSA and added to the chromatin samples for pre-clearing for two hours at 4C with rotation. Beads were removed, and 100 ul of pre-cleared chromatin was set aside for the input control. 5 ul ChIP-grade rabbit polyclonal antibody was added to the remaining pre-cleared chromatin and incubated overnight at 4C with rotation. 50 ul beads were washed and resuspended as before, then incubated with the chromatin samples for two hours at 4C with rotation. After washing and decrosslinking, samples were further incubated with 80 ug RNAse A at 37C for 60 minutes and then with 80 ug Proteinase K at 55C for 90 minutes.
Libraries were prepared for sequencing using standard Illumina protocols by the Oxford Genomics Centre.

treatment_protocol: 15 million cells were seeded in 30 ml growth medium in a T175 cell culture flask. The following morning, cells were transfected by mixing 30 ug total construct DNA into 800 ul OPTI-MEM (Life Technologies 31985062), then carefully adding 90 ul FuGENE-HD Transfection Reagent and flicking to mix, incubating at room temperature for 15 minutes, and then adding the mixture dropwise to each dish while swirling gently to mix.

tag: cell line

value: HEK293T (ATCC CRL-3216)

tag: transfected with

value: H3K4me3 (Abcam ab8580)


title: ChIPseq.ChimpPRDM9_V5.antiV5.ProtocolC

description:
Uniquely Mapped Fragments: 44594666
Multiplex Group: 3


title: ChIPseq.Untransfected.antiH3K4me3.Rep2.ProtocolC

description:
Uniquely Mapped Fragments: 60883503
Multiplex Group: 3


title: ChIPseq.Untransfected.antiH3K4me3.Rep1.ProtocolC

description:
Uniquely Mapped Fragments: 57205316
Multiplex Group: 3


title: ChIPseq.HumanPRDM9_HA.antiH3K36me3.ProtocolC

description:
Uniquely Mapped Fragments: 59690192
Multiplex Group: 3


title: ChIPseq.Untransfected.antiH3K36me3.ProtocolC

description:
Uniquely Mapped Fragments: 52368417
Multiplex Group: 3


title: ChIPseq.HumanPRDM9_HA.antiH3K4me3.ProtocolC.Rep1

description:
Uniquely Mapped Fragments: 52439279
Multiplex Group: 3


title: ChIPseq.HumanPRDM9_V5.antiV5.ProtocolC

description:
Uniquely Mapped Fragments: 38717735
Multiplex Group: 3


title: ChIPseq.HumanPRDM9_HA.antiHA.ProtocolC

description:
Uniquely Mapped Fragments: 39385214
Multiplex Group: 3


title: DU145-miR-875-5p rep 2

status: Public on Jun 01 2017

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

description: DU145 cells transfected with miR-875-5p synthetic mimic

hyb_protocol: Standard Illumina DASL hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were log2 transformed and normalized with robust spline normalization using the lumi package from Bioconductor.

source_name: prostate cancer cells

label_protocol: Biotinylated cRNA was prepared with the TotalPrep Amplification kit (Ambion) for Illumina arrays

growth_protocol: DU145 cells were maintained at 37°C/5% CO2 in RPMI medium supplemented with 10% fetal bovine serum

extract_protocol: Trizol (Invitrogen/Life Technologies) according to the manufacturer's protocol

treatment_protocol: Transfection of Ambion® Pre-miR™ miRNA Precursors (Life Technologies) at 20 nM final concentration using Lipofectamine reagent.


title: DRIP_replicate_2

city: Beijing

first: li

last: kuan

address: zhongguancun

country: China

institute: Tsinghua University

description: DNA:RNA hybird

data_processing:
Library strategy: DRIP-seq
Illumina Casava software used for basecalling.
DRIP-seq reads were aligned to the TAIR10 genome using bwa version 0.7.12.
peaks were called using MACS2
read coverage normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC))
Genome_build: TAIR10
Supplementary_files_format_and_content: wR-loops: R-loop formation with RNA corresponded to Watson DNA;cR-loops: R-loop formation with RNA corresponded to Crick DNA

organism: Arabidopsis thaliana

source_name: 12-day-old seedlings

extract_protocol:
Nuclei were isolated from 12-day-old Arabidopsis Col-0 seedling, followed by SDS/proteinase K treatment at 37°C overnight. Genome DNA was extracted by the phenol-chloroform method and precipitated with isopropanol. DNA fragmentation was performed overnight using endonucleases (SspI, EcoRI, HindIII, DdeI, MspI, and RsaI); the negative control was treated with RNase H (New England Biolabs) overnight. DRIP was performed as described in Ginno et al., 2012 and Sun et al., 2013. Briefly, 4ug of DNA was bound with 10 ug of S9.6 antibody in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4˚C. 50 ul Protein G sepharose beads were added for 4 hours. Bound beads were washed 4 times in binding buffer and elution was performed in elution buffer (50 mM Tris pH 8, 10 mM EDTA, 0.5% SDS, Proteinase K) for 45 min at 55˚C. DNA was purified and sonoicated to 150 bp fragments .
The first adapter was ligated to the 3’ end of the ssDNA using Adaptase (Swift Biosciences) via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified.

value: Wild type

tag: ecotype

value: Columbia

value: seedlings


title: RNase H_DRIP_replicate_1

description:
DNA:RNA hybird
RNase H is a kind of non-sequence-specific endonuclease enzymes that catalyze the cleavage of RNA in an RNA:DNA hybird. RNase H treated samples were considered as negetive controls, in which the DRIP signal were much lower than untreated samples.


title: DU145-miR-875-5p rep 3


title: DRIP_replicate_1

description: DNA:RNA hybird


title: 48_L1.N701_502

status: Public on Apr 26 2017

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

data_processing:
Raw read data was aligned against mouse transcriptome (MouseEnsembl release 61) using Bowtie2 (Langmead and Salzberg, 2012). Splice junctions were defined as available in Ensembl v75. Read mappings were then mapped to genes and transcripts based on the transcript models annotated in Ensembl v75 using in-house tools and, again using in-house software, RPKM values were computed as described previously (Mortazavi et al., 2008).
Genome_build: MouseEnsembl release 61
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: MMTV-PyMT mammary tumors

extract_protocol:
Cell sorting was performed using FACS Aria II apparatus (BD). Each cell population (n=4) was isolated from an independent tumor. Typically, 2x104 to 2x105 cells were obtained for each cell population. Sorted cell populations were immediately homogenized in 700 µl Qiazol reagent (Qiagen). 140 µl of chloroform was added to the homogenate and the mixture centrifuged at 16,000 x g for 5 min at 4°C in Phase Lock Tubes (Qiagen). RNA was subsequently extracted from the aqueous phase using the RNeasy Micro kit (Qiagen) according to manufacturer’s instructions. Genomic DNA was removed using the RNase free DNase set (Qiagen) during the extraction. RNA was quality controlled on Agilent Eukaryote Total RNA pico chips (Agilent Technologies). High quality RNA (RIN >7) was obtained for all samples. SMARTer ultra low RNA kit for Illumina sequencing (Clontech) was used to prepare and amplify cDNA from 520 pg of total RNA according to manufacturer’s instructions.
Then, 1 ng of amplified cDNA was subjected to Nextera XT library preparation (Illumina) according to manufacturer’s instructions. Sequencing libraries were quantified using the Kapa Library Quantification kit (Kapa Biosystems) and quality controlled by capillary electrophoresis on a Bioanalyzer using High Sensitivity chips (Agilent Technologies). Libraries were sequenced on a HiSeq2500 sequencer (Illumina) for 2 x 50 cycles using version 4 cluster generation kits and version 4 sequencing reagents (Illumina).

treatment_protocol: When tumors reached a size of 300 mm3, mice were injected i.p with the following moAbs: mouse IgG1 (clone MOPC-21, 500 μg) + rat IgG2a (clone 2A3, 100 μg), designated as “IgG”; or anti-VEGFA/ANGPT2 (A2V, 500 μg) + rat IgG2a (clone 2A3, 100 μg), designated “A2V”.  Five days later, mice were euthanized and tumors harvested and prepared for fluorescence-activated cell sorting (FACS).

value: CD4+ cells

value: IgG


title: Input

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to the TAIR10 genome using bwa version 0.7.12.
Read coverage normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC))
Genome_build: TAIR10
Supplementary_files_format_and_content: Input_Watson: Watson strand of input DNA; Input_Crick: Crick strand of input DNA


title: 47_L1.N711

value: CD8+ cells


title: ChIPseq.Untransfected.Input.ProtocolC

description:
Input coverage was combined (Human + Untransfected) for all Protocol C peak calls
Uniquely Mapped Fragments: 56445392
Multiplex Group: 3


title: DU145-mock rep 1

description: DU145 cells transfected with a mock molecule

value: mock


title: DU145-miR-875-5p rep 1


title: DU145-mock rep 3


title: DU145-mock rep 2


title: 62_L4

value: Macrophages


title: ChIPseq.HumanPRDM9_HA.Input.ProtocolC

description:
Input coverage was combined (Human + Untransfected) for all Protocol C peak calls
Uniquely Mapped Fragments: 53219513
Multiplex Group: 3


title: 46_L1.N710


title: EA0969_NRAIA

value: F

value: Non-RA inflammatory arthritis (NRAIA) - includes Code A 4-11)

value: peripheral blood

value: CD4+ T-cell


title: EA0973_NRAIA


title: ChIPseq.ChimpPRDM9_HA.antiHA.ProtocolC

description:
Uniquely Mapped Fragments: 36662728
Multiplex Group: 3


title: RNase H_DRIP_replicate_2


title: 50_L1.N702


title: 31_L1.N707


title: 18_L2


title: 32_L1.N708


title: 30_L1.N706


title: 2_L2


title: 35_L1.N711


title: 45_L1.N709

value: CD31+ cells


title: 16_L1.N704


title: 4_L3


title: 51_L1.N703


title: 33_L1.N709


title: 64_L1.N703


title: 3_L1.N703


title: 20_L2


title: 15_L1.N703


title: 17_L1


title: 29_L1.N705


title: 1_L1


title: 34_L1.N710


title: 14_L1.N702


title: 13_L1.N701


title: 63_L5


title: 19_L1


title: 36_L1.N712


title: 61_L1.N712


title: 52_L1.N704


title: EA0996_ACPAnRA

value: ACPA-neg RA


title: EA0813_UA

source_name: UA_Blood CD4+ T Cells

value: Undifferentiated arthritis


title: PCa_CC8

status: Public on Mar 09 2017

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

description: Prostate adenocarcinoma from Caucasian men.

hyb_protocol: Samples were hybridized to oligonucleotide glass arrays with sequences representing probes for 866 human and 89 human viral miRNAs from the Sanger miRBase (release 12.0) (Human miRNA Microarray V3, Agilent Technologies). After 20 hours, slides were washed and scanned.

scan_protocol: Slides were scanned with the dual-laser Agilent scanner G2505B.

data_processing: The LIMMA (LInear Models for Microarray Analysis) package was used to analyze miRNA expression profiles in normal prostates and prostate cancer tissues. Raw intensity values were background subtracted (method = subtract with an offset of 20) and normalized using the quantile method. Duplicated probes were averaged.

source_name: Prostate cancer

label_protocol: MiRNA expression profiling was carried out using the one-colour labelling method. Labelling, hybridization, washing and slide scanning were performed following the manufacturer's protocol (Agilent Technologies). Briefly, 100 ng of total RNA were dephosphorylated and denaturated; then a ligation and labeling step with Cy3 was performed.

extract_protocol: Total RNA was isolated following standard TriReagent protocol (Sigma-Aldrich) and DNase treatment was performed (TURBO DNase-free, Life Technologies). Total RNA quality and quantity were checked by means of Bioanalyzer (Agilent Technologies) and NanoDrop ND-1000 Spectrophotometer (Thermo Scientific), respectively.

value: prostate adenocarcinoma

value: male

tag: population

value: Caucasian


title: PCa_CC75


title: PCa_Z56


title: PCa_CC62


title: PCa_L16


title: PCa_Z59


title: PCa_L12


title: PCa_P55


title: PCa_K6


title: PCa_CC41


title: PCa_Y50


title: PCa_Z55


title: PCa_Y48


title: PCa_G65


title: PCa_G70


title: PCa_M26


title: PCa_F51


title: PCa_X40


title: PCa_Y44


title: PCa_P60


title: PCa_Q70


title: PCa_W25


title: PCa_W28


title: PCa_V18


title: 49_L1.N701


title: PCa_H75


title: PCa_CC35


title: PCa_CC3


title: PCa_P57


title: PCa_CC17


title: PCa_B17


title: PCa_B12


title: PCa_C25


title: PCa_BB5


title: PCa_C27


title: PCa_AA97


title: PCa_AA90


title: PCa_B11


title: PCa_CC87


title: PCa_CC91


title: PCa_AA69


title: GHE2100 [expression]

status: Public on Jan 30 2017

city: Rouen

first: Sydney

last: Dubois

address: Rue d'Amiens

country: France

institute: Centre Henri Becquerel

description:
Characteristics definitions:
ID: sample ID
AGE: age at diagnosis
SEX: male (M) or female (F)
TREATMENT: treatment line used
IPI: calculated IPI
Age_Adjusted_IPI: calculated age-adjusted IPI
PFS_TIME: duration of progression free survival (PFS) in months
CENS_PFS: coded as 0 if PFS event, 1 if not
OS_TIME: duration of overall survival (OS) in months
CENS_OS: coded as 0 if OS event, 1 if not
COO: cell of origin according to Affymetrix GeneChip arrays as described in methods

hyb_protocol: Hybridization of cRNA on Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays was performed by Expression Analysis, Inc.

scan_protocol: GeneChips were scanned with the GeneChip Scanner 3000 (Affymetrix). Images were analyzed with the Gene Chip® Operating Software (GCOS) 1.4

data_processing: The data were analyzed with GeneSpring software (Agilent Technologies) using default settings and the RMA normalization and summarization algorithm.

source_name: DLBCL tumor biopsy

label_protocol: Biotinylated cRNA was prepared by Expression Analysis, Inc. (Durham, NC).

extract_protocol: Total RNA was isolated with the miRNeasy mini kit (Qiagen).

tag: ID

tag: diagnosis

value: DLBCL

value: FEMALE

tag: Stage

value: STAGE 3

tag: ipi

tag: coo

value: Other


title: GHE2084 [expression]

tag: Sex

value: MALE

value: STAGE 4

tag: treatment


title: GHE2109 [expression]

tag: age


title: GHE2127 [expression]

value: R-ACVBP+Conso

value: ABC


title: GHE2026 [expression]


title: GHE2023 [expression]

value: GC


title: GHE2017 [expression]


title: GHE2036 [expression]


title: GHE2096 [expression]

value: STAGE 2


title: GHE2119 [expression]


title: GHE2005 [expression]


title: GHE2132 [expression]


title: GHE2003 [expression]


title: GHE1560 [expression]


title: GHE2037 [expression]


title: GHE2012 [expression]


title: GHE2030 [expression]


title: GHE2106 [expression]


title: GHE2019 [expression]


title: GHE2121 [expression]


title: GHE2002 [expression]


title: GHE1554 [expression]


title: GHE1498 [expression]


title: GHE2098 [expression]


title: GHE1450 [expression]


title: GHE1558 [expression]


title: GHE1521 [expression]


title: GHE1440 [expression]


title: GHE1537 [expression]


title: GHE1553 [expression]


title: GHE1536 [expression]


title: GHE1437 [expression]


title: GHE1438 [expression]


title: GHE1393 [expression]


title: GHE1413 [expression]


title: GHE1424 [expression]


title: GHE1392 [expression]


title: GHE1409 [expression]


title: GHE1423 [expression]


title: GHE1379 [expression]


title: GHE1390 [expression]

value: PMBL


title: GHE1352 [expression]

value: STAGE 1


title: GHE1360 [expression]


title: GHE1353 [expression]


title: GHE1369 [expression]


title: GHE1373 [expression]


title: GHE1385 [expression]

value: ACVBP


title: GHE1311 [expression]


title: GHE1374 [expression]


title: GHE1380 [expression]


title: GHE1287 [expression]


title: GHE1209 [expression]


title: GHE1302 [expression]


title: GHE1104 [expression]


title: GHE1189 [expression]


title: GHE1349 [expression]


title: GHE1192 [expression]


title: GHE1099 [expression]


title: GHE1376 [expression]


title: GHE1069 [expression]


title: GHE1229 [expression]


title: GHE1225 [expression]


title: GHE1222 [expression]


title: GHE1071 [expression]


title: GHE1066 [expression]


title: GHE1046 [expression]


title: GHE1036 [expression]


title: GHE1034 [expression]


title: GHE1053 [expression]


title: GHE0993 [expression]


title: GHE1017 [expression]


title: GHE1028 [expression]


title: GHE1023 [expression]


title: GHE1009 [expression]


title: GHE0992 [expression]


title: GHE0982 [expression]


title: GHE0978 [expression]


title: GHE0986 [expression]


title: GHE0984 [expression]


title: GHE0925 [expression]


title: GHE0997 [expression]


title: GHE1018 [expression]


title: GHE0976 [expression]


title: GHE0923 [expression]


title: GHE0885 [expression]


title: GHE0908 [expression]


title: GHE0988 [expression]


title: GHE0865 [expression]


title: GHE0877 [expression]


title: GHE0873 [expression]


title: GHE0883 [expression]


title: GHE0955 [expression]


title: GHE0909 [expression]


title: GHE0857 [expression]


title: GHE0856 [expression]


title: GHE0849 [expression]


title: GHE0860 [expression]


title: GHE0822 [expression]


title: GHE0834 [expression]


title: GHE0808 [expression]


title: GHE0853 [expression]


title: GHE0807 [expression]


title: GHE0837 [expression]


title: GHE0842 [expression]


title: GHE0733 [expression]


title: GHE0745 [expression]


title: GHE0708 [expression]


title: GHE0809 [expression]


title: GHE0776 [expression]


title: GHE0777 [expression]


title: GHE0810 [expression]


title: GHE0705 [expression]


title: GHE0771 [expression]


title: GHE0811 [expression]


title: GHE0852 [expression]


title: GHE0743 [expression]


title: GHE0717 [expression]

value: R-ACVBP+ASCT


title: GHE0701 [expression]


title: GHE0714 [expression]


title: GHE0721 [expression]


title: GHE0693 [expression]


title: GHE0690 [expression]


title: GHE1035 [expression]


title: GHE0635 [expression]


title: GHE0632 [expression]


title: GHE0689 [expression]


title: GHE0645 [expression]


title: GHE0629 [expression]


title: GHE0623 [expression]


title: GHE0614 [expression]


title: GHE0624 [expression]


title: GHE0622 [expression]


title: GHE0563 [expression]


title: GHE0602 [expression]


title: GHE0615 [expression]


title: GHE0659 [expression]


title: GHE0562 [expression]


title: GHE0515 [expression]


title: GHE0522 [expression]


title: GHE0605 [expression]


title: GHE0604 [expression]


title: GHE0547 [expression]


title: GHE0519 [expression]


title: GHE0535 [expression]


title: GHE0609 [expression]


title: GHE0512 [expression]


title: GHE0534 [expression]


title: GHE0507 [expression]


title: GHE0523 [expression]


title: GHE0501 [expression]


title: GHE0536 [expression]


title: GHE0491 [expression]


title: GHE0470 [expression]


title: GHE0495 [expression]


title: GHE0685 [expression]


title: GHE0440 [expression]


title: GHE0446 [expression]


title: GHE0459 [expression]


title: GHE0463 [expression]


title: GHE0506 [expression]


title: GHE0429 [expression]


title: GHE0436 [expression]


title: GHE0426 [expression]


title: GHE0430 [expression]


title: GHE0423 [expression]


title: GHE0469 [expression]


title: GHE0454 [expression]


title: GHE0427 [expression]


title: GHE0414 [expression]


title: GHE0400 [expression]


title: GHE0395 [expression]


title: GHE0352 [expression]


title: GHE0393 [expression]


title: GHE0375 [expression]


title: GHE0368 [expression]


title: GHE0855 [expression]


title: GHE0397 [expression]


title: GHE0300 [expression]


title: GHE0356 [expression]


title: GHE0294 [expression]


title: GHE0371 [expression]


title: GHE0292 [expression]


title: GHE0415 [expression]


title: GHE0258 [expression]


title: GHE0242 [expression]


title: GHE0275 [expression]


title: GHE0262 [expression]


title: GHE0241 [expression]


title: GHE0219 [expression]


title: GHE0176 [expression]


title: GHE0229 [expression]


title: GHE0206 [expression]


title: GHE0169 [expression]


title: GHE0236 [expression]


title: GHE0216 [expression]


title: GHE0218 [expression]


title: GHE0228 [expression]


title: GHE0202 [expression]


title: GHE0197 [expression]


title: GHE0140 [expression]


title: GHE0194 [expression]


title: GHE0150 [expression]


title: GHE0057 [expression]


title: GHE0047 [expression]


title: GHE0134 [expression]


title: GHE0052 [expression]


title: GHE0024 [expression]


title: GHE0114 [expression]


title: GHE0092 [expression]


title: GHE0049 [expression]


title: GHE0050 [expression]


title: GHE0358 [expression]


title: GHE0016 [expression]


title: GHE0034 [expression]


title: GHE0061 [expression]


title: GHE0002 [expression]


title: GHE0015 [expression]


title: GHE0006 [expression]


title: GHE0001 [expression]


title: GHE0028 [expression]


title: GHE0025 [expression]


title: GHE0004 [expression]


title: control biological rep6

status: Public on Jul 01 2016

city: Baltimore

first: Susan

middle: G

last: Dorsey

address: 655 West Lombard Street

department: Pain and Translational Symptom Science

institute: University of Maryland Baltimore

description:
CTRL_Pos-6UP
gene expression data

hyb_protocol: cRNA hybridization per Affymetrix standard protocol

scan_protocol: Gene arrays were scanned on Affymetrix platform

data_processing: The data were normalized using gcrma R package (v.2.20.0) from Bioconductor.

source_name: control_muscle biopsy

label_protocol: Biotinylated cRNA prepared, hybridized, and scanned using Affymetrix standard protocol from 1ug RNA

growth_protocol: biopsy sample in clinic

extract_protocol: Trizol extraction of total RNA per manufacturer

tag: sample type

value: CONTROL

value: unknown

value: skeletal muscle


title: control biological rep3

description:
CTRL_Pos-3UP
gene expression data


title: control biological rep1

description:
CTRL_Pos-1UP
gene expression data


title: control biological rep4

description:
CTRL_Pos-4UP
gene expression data


title: control biological rep5

description:
CTRL_Pos-5UP
gene expression data


title: EN-5

status: Public on Jun 01 2016

city: Bethesda

first: Frederic

last: Barr

state: MD

address: 10 Center Drive, Rm 3B55

institute: National Cancer Institute

hyb_protocol: Sample hydridization wa perfromed for 16 hours according to standard Affymetrix protocols

scan_protocol: Samples were scanned using an Affymetrix GeneChip Scanner

data_processing: Analysis was performed in R with the oligo package, RMA was used for normalization

source_name: Rhabdomyosarcoma

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols

growth_protocol: human fusion-postive and fusion-negative rhabdomyosarcoma tissue samples

extract_protocol: Total RNA extracted using RNA STAT-60 in accordance with manufacturer's instructions

treatment_protocol: human surgical specimens, frozen

value: Rhabdomyosarcoma

tag: pax-foxo1 fusion status

value: Fusion-Negative


title: B9

tag: tissue

value: PAX3-FOXO1 Fusion-Positive


title: EN-9


title: B7


title: B6


title: EN-4


title: B5


title: B40


title: EN-3


title: EN-11


title: B36


title: B42


title: B35


title: B38


title: B39


title: EN-10


title: GHE0293 [expression]

value: DLBCL

value: Other


title: B32


title: B30


title: B8


title: B4


title: B41


title: B34


title: B37


title: B31


title: B33


title: B3


title: B26


title: B28


title: B27


title: B29


title: B23

value: PAX7-FOXO1 Fusion-Positive


title: B25


title: B20


title: B21


title: B24


title: B22


title: B18


title: B2


title: B16


title: B17


title: B19


title: B14


title: B13


title: B11


title: B12


title: B15


title: A7-1


title: A3-8


title: B1


title: A3-9


title: A3-5


title: A7-2


title: B10


title: A3-6


title: A3-4


title: A3-14


title: A3-11


title: Tanja_Waldmann_7.4_(HG-U133_Plus_2)

status: Public on Jul 21 2015

city: Cologne

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

country: Germany

institute: University of Cologne

hyb_protocol: 12.5µg of fragmented aRNA was hybridized to the Human Genome U133 plus 2.0 microarrays in the Genechip Hybridisation Oven-645 (Affymetrix, United Kingdom) for 16 h at 45º C.

scan_protocol: Arrays were washed and stained with phycoerythrin with Fluidics Station 450 and scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions

data_processing: The quality control (QC) matrices were confirmed with expression console software (Affymertix, USA) and Partek genomics suite version 6.6 (Partek Inc.St.Louis,USA). QC passed CEL files were further analyzed using Partek genomics suite version 6.6. All CEL files were RMA background corrected, quantile normalized and all probe sets were summarized using median polish algorithm.

source_name: hESCs_phenylmercuric acetate_6 days

label_protocol: 100ng total RNA was used for aRNA amplification with GeneChip® 3’ IVT Express Kit (Affymetrix, United Kingdom) according to the manufacturer’s instructions. After 16 h of biotinylated in vitro transcription, aRNA was purified using magnetic beads and 15µg of purified aRNA was fragmented with fragmentation buffer

growth_protocol: According to Krug AK et al. (2013) Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach. Arch Toxicol 87(1):123-43).

extract_protocol: Total RNA from 6 days differentiated hESCs in the presence and absence of benchmark concentration (BMC) of toxicants has  been isolated with  Trizol reagent (Invitrogen) and purified with the RNeasy Plus kit from Qiagen

treatment_protocol: H9 hESCs were differentiated for 6 days in the presence and absence of the toxicants into neuroepithelia progenitors (NEP)  (Krug AK et al. (2013) Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach. Arch Toxicol 87(1):123-43).

tag: gender

value: female

tag: cell type

value: human embryonic stem cells

tag: incubated or treated with

value: phenylmercuric acetate for 6 days

tag: cell status

value: differentiated state


title: Tanja_Waldmann_8.4_(HG-U133_Plus_2)

value: 4-chloromercuribenzoic acid for 6 days


title: Tanja_Waldmann_8.1_(HG-U133_Plus_2)


title: Tanja_Waldmann_8.3_(HG-U133_Plus_2)


title: Tanja_Waldmann_3.3_(HG-U133_Plus_2)

source_name: hESCs_panobinostat_6 days

value: panobinostat for 6 days


title: Tanja_Waldmann_3.2_(HG-U133_Plus_2)


title: Tanja_Waldmann_7.3_(HG-U133_Plus_2)


title: Tanja_Waldmann_7.2_(HG-U133_Plus_2)


title: EN-6


title: Tanja_Waldmann_5.2_(HG-U133_Plus_2)

source_name: hESCs_entinostat_6 days

value: entinostat for 6 days


title: Tanja_Waldmann_8.2_(HG-U133_Plus_2)


title: Tanja_Waldmann_7.1_(HG-U133_Plus_2)


title: Tanja_Waldmann_4.1_(HG-U133_Plus_2)

source_name: hESCs_HgBr2_6 days

value: HgBr2 for 6 days


title: Tanja_Waldmann_6.2_(HG-U133_Plus_2)

source_name: hESCs_culturing medium_6 days

value: culturing medium for 6 days


title: Tanja_Waldmann_5.3_(HG-U133_Plus_2)


title: Tanja_Waldmann_3.1_(HG-U133_Plus_2)


title: Tanja_Waldmann_1.4_(HG-U133_Plus_2)

source_name: hESCs_belinostat_6 days

value: belinostat for 6 days


title: Tanja_Waldmann_4.4_(HG-U133_Plus_2)


title: Tanja_Waldmann_1.3_(HG-U133_Plus_2)


title: Tanja_Waldmann_4.2_(HG-U133_Plus_2)


title: Tanja_Waldmann_4.3_(HG-U133_Plus_2)


title: Tanja_Waldmann_5.1_(HG-U133_Plus_2)


title: Tanja_Waldmann_6.1_(HG-U133_Plus_2)


title: Tanja_Waldmann_5.4_(HG-U133_Plus_2)


title: Tanja_Waldmann_1.1_(HG-U133_Plus_2)


title: Tanja_Waldmann_3.4_(HG-U133_Plus_2)


title: Tanja_Waldmann_6.4_(HG-U133_Plus_2)


title: Tanja_Waldmann_1.2_(HG-U133_Plus_2)


title: control biological rep2

description:
CTRL_Pos-2UP
gene expression data

value: CONTROL

value: unknown

value: skeletal muscle


title: Tanja_Waldmann_6.3_(HG-U133_Plus_2)


title: Tanja_Waldmann_2.2_(HG-U133_Plus_2)


title: Tanja_Waldmann_2.3_(HG-U133_Plus_2)


title: UKN1_77_biom_A_HgCl2_D12_21

source_name: hESCs_HgCl2_6 days

value: HgCl2 for 6 days


title: UKN1_70_biom_A_Thim_D12_18

source_name: hESCs_thimerosal_6 days

value: thimerosal for 6 days


title: UKN1_72_biom_A_Thim_D12_20


title: UKN1_59_biom_A_untr_D12_19


title: UKN1_76_biom_A_HgCl2_D12_20


title: UKN1_52_biom_A_VPA_D12_09

source_name: hESCs_valproic acid_6 days

value: valproic acid for 6 days


title: UKN1_65_biom_A_DMSO(SAHA solvent)_D12_21

source_name: hESCs_DMSO (suberanilohydroxamic acid solvent) as a vehicle_6 days

value: DMSO (suberanilohydroxamic acid solvent) as a vehicle for 6 days


title: UKN1_58_biom_A_untr_D12_18

value: female


title: Tanja_Waldmann_2.4_(HG-U133_Plus_2)

value: human embryonic stem cells


title: UKN1_51_biom_A_VPA_D12_08


title: UKN1_74_biom_A_HgCl2_D12_18


title: UKN1_69_biom_A_SAHA_D12_21

source_name: hESCs_suberanilohydroxamic acid_6 days

value: suberanilohydroxamic acid for 6 days


title: UKN1_62_biom_A_DMSO(SAHA solvent)_D12_18

value: differentiated state


title: UKN1_63_biom_A_DMSO(SAHA solvent)_D12_19


title: UKN1_66_biom_A_SAHA_D12_18


title: UKN1_64_biom_A_DMSO(SAHA solvent)_D12_20


title: UKN1_60_biom_A_untr_D12_20


title: UKN1_53_biom_A_VPA_D12_10


title: UKN1_71_biom_A_Thim_D12_19


title: UKN1_50_biom_A_VPA_D12_07


title: Tanja_Waldmann_2.1_(HG-U133_Plus_2)


title: UKN1_61_biom_A_untr_D12_21


title: UKN1_68_biom_A_SAHA_D12_20


title: UKN1_67_biom_A_SAHA_D12_19


title: UKN1_75_biom_A_HgCl2_D12_19


title: UKN1_73_biom_A_Thim_D12_21


title: UKN1_49_biom_A_untr_D12_10


title: UKN1_48_biom_A_untr_D12_09


title: UKN1_46_biom_A_untr_D12_07


title: UKN1_44_biom_A_untr_D11_24


title: UKN1_45_biom_A_untr_D11_25


title: UKN1_47_biom_A_untr_D12_08


title: Prdm1/Blimp-1 mutant anti-Irf-1 ChIP2

status: Public on Jul 10 2015

city: Oxford

first: Arne

middle: Wyndham

last: Mould

state: Oxfordshire

address: Warneford Hospital

department: Psychiatry

institute: Oxford University

description: processed data file: VCBH_IRF1_ChIP.wig.gz

data_processing:
ChIP-seq reads were mapped to mm9 using Stampy with default parameters
Peaks were called using MACS1.4.2 with default parameters with .wig files generated for data visualization.
Genome_build: mm9
Supplementary_files_format_and_content: Tar archives containing .wig files for data visualization of all ChIP experiments and associated input samples.  Biological replicates are merged into single files for each condition.

source_name: Prdm1/Blimp-1 mutant anti-Irf-1 ChIP

extract_protocol:
Lysates were precleared with Protein G Dynabeads. Complexes were then isolated with 10µg anti-GFP monoclonal antibody (Invitrogen A11120, clone 3E6, IgG2a), polyclonal rabbit anti-Irf1 antibody (M-20, Santa Cruz, SC-640) or control rabbit IgG (Santa Cruz sc-2027, Mouse IgG) linked to Protein G Dynabeads.
Sequencing libraries were then prepared using the Illumina ChIP-seq DNA Sample Prep Kit. Libraries were size selected at ~200bp and four libraries were multiplexed per lane on a HiSeq 2000.

tag: strain background

tag: developmental stage

tag: genotype/variation

value: Prdm1/Blimp-1 mutant

value: small intestine

tag: chip antibody

value: polyclonal rabbit anti-Irf1 antibody (M-20)

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: Prdm1/Blimp-1 mutant anti-Irf-1 input2

description: processed data file: VCBH_IRF1_input.wig.gz

source_name: Prdm1/Blimp-1 mutant anti-Irf-1 input


title: Prdm1/Blimp-1 mutant anti-Irf-1 input1


title: UKN1_17_biom_A_TSA_D11_22

source_name: hESCs_trichostatin-A_6 days

value: trichostatin-A  for 6 days


title: UKN1_16_biom_A_TSA_D11_21


title: UKN1_43_biom_A_untr_D11_23

value: culturing medium for 6 days


title: UKN1_29_biom_A_DMSO(TSA solvent)_D11_24

source_name: hESCs_DMSO (trichostatin-A solvent) as a vehicle_6 days

value: DMSO (trichostatin-A solvent) as a vehicle for 6 days


title: UKN1_19_biom_A_TSA_D11_24


title: wild type anti-Irf-1 input1

description: processed data file: WT_input.wig.gz

source_name: wild type anti-Irf-1 input

value: wild type


title: wild type anti-Irf-1 input2

description: processed data file: WT_input.wig.gz


title: UKN1_30_biom_A_DMSO(TSA solvent)_D11_25


title: UKN1_18_biom_A_TSA_D11_23


title: UKN1_3_biom_A_MeHg_D11_23

source_name: hESCs_MeHg_6 days

value: MeHg  for 6 days


title: UKN1_11_biom_A_EtOH(MeHg solvent)_D11_21

source_name: hESCs_ethanol (MeHg solvent) as a vehicle_6 days

value: ethanol (MeHg solvent) as a vehicle for 6 days


title: UKN1_2_biom_A_MeHg_D11_22


title: wild type IgG ChIP2

description: processed data file: WT_IgG_ChIP.wig.gz

source_name: wild type IgG ChIP

value: control rabbit IgG


title: UKN1_13_biom_A_EtOH(MeHg solvent)_D11_23


title: UKN1_27_biom_A_DMSO(TSA solvent)_D11_22


title: UKN1_28_biom_A_DMSO(TSA solvent)_D11_23


title: UKN1_42_biom_A_untr_D11_22


title: UKN1_12_biom_A_EtOH(MeHg solvent)_D11_22


title: UKN1_26_biom_A_DMSO(TSA solvent)_D11_21


title: UKN1_20_biom_A_TSA_D11_25


title: UKN1_5_biom_A_MeHg_D11_25


title: UKN1_14_biom_A_EtOH(MeHg solvent)_D11_24


title: UKN1_41_biom_A_untr_D11_21


title: UKN1_1_biom_A_MeHg_D11_21


title: UKN1_15_biom_A_EtOH(MeHg solvent)_D11_25


title: UKN1_4_biom_A_MeHg_D11_24


title: wild type IgG ChIP1

description: processed data file: WT_IgG_ChIP.wig.gz


title: wild type anti-Irf-1 ChIP2

description: processed data file: WT_IRF1_ChIP.wig.gz

source_name: wild type anti-Irf-1 ChIP


title: wild type anti-Irf-1 ChIP1


title: anti-Blimp-1-eGFP input1

description: processed data file: BEG_GFP_input.wig.gz

source_name: anti-Blimp-1-eGFP input

value: expressing Blimp-1-eGFP fusion protein


title: anti-Blimp-1-eGFP ChIP2

description: processed data file: BEG_GFP_ChIP.wig.gz

source_name: anti-Blimp-1-eGFP ChIP

value: GFP Tag Antibody (3E6)

value: Invitrogen


title: anti-Blimp-1-eGFP input2


title: anti-Blimp-1-eGFP ChIP1


title: wild type anti-GFP ChIP

description: processed data file: WT_GFP_ChIP.wig.gz

source_name: wild type anti-GFP ChIP


title: genomic_input_OregonR

status: Public on Nov 07 2013

first: Daniel

middle: J

last: McKay

address: 3344 Genome Sciences Building

department: Biology, Genetics

institute: The University of North Carolina at Chapel Hill

description:
Input
genomic_input_OregonR

data_processing:
Basecalls performed with CASAVA version 1.7
FAIRE-seq GAII reads were filtered with Tagdust, and aligned to the Drosophila reference genome (version dm3) using Bowtie (version 0.12.3) with up to four possible alignments (m), and up to two mismatches in the seed (n) permitted.
FAIRE-seq HiSeq reads were first filtered with Tagdust. The first 8 bases were trimmed with fastx_trimmer to remove the internal Index. The last 6 bases were trimmed with fastx_trimmer to make HiSeq reads equivalent in length to GAII reads. Trimmed reads were aligned to the Drosophila reference genome (version dm3) using Bowtie (version 0.12.3) with up to four possible alignments (m), and up to two mismatches in the seed (n) permitted.
FAIRE-seq signal files were generated by extending each read to a total of 110bp, and the number of reads overlapping each base in the genome was counted.
FAIRE data were normalized by subtracting Input signal from FAIRE at each base, and z-scores were generated using the mean and standard deviation for each chromosome arm.
FAIRE peaks were called using MACS2 with Input as control, a shift size of 125bp, and a q-value cutoff of 1.00e-2.
RNA-seq GAII reads were filtered with Tagdust, and aligned to the Drosophila reference genome (version dm3) using TopHat (version 1.1.4) and default parameters.
RNA-seq HiSeq reads were first filtered with Tagdust. The first 8 bases were trimmed with fastx_trimmer to remove the internal index. The last 6 bases were trimmed with fastx_trimmer to make HiSeq reads equivalent in length to GAII reads. Trimmed reads were aligned to the Drosophila reference genome (version dm3) using TopHat (version 1.1.4) and default parameters.
Genome_build: dm3
Supplementary_files_format_and_content: FAIRE processed data files are in wig format, and contain Input-subtracted FAIRE z-scores, smoothed with a 200bp sliding window average and 10bp step size.
Supplementary_files_format_and_content: RNA processed data files are matrices of gene names with their associated FPKM values calculated with Cuffdiff from the Tophat-aligned reads and using a RefSeq genome annotation file.

source_name: adult female virgins

extract_protocol: 1-100ng DNA was prepared for sequencing on an Illumina GAII or HiSeq 2000 machine at the UNC High-Throughput Sequencing Facility.

tag: strain

value: OregonR

value: adult

value: whole adult


title: wild type anti-GFP input

description: processed data file: WT_GFP_input.wig.gz

source_name: wild type anti-GFP input


title: Liver Met, biological rep2

status: Public on Apr 22 2014

city: Barcelona

first: Xabier

last: Garcia-Albeniz

address: Baldiri Reixac 10

country: Spain

institute: IRB Barcelona

hyb_protocol: Hybridization of the samples to HG1.0ST gene expression chip (Affymetrix) were performed by Functional Genomics Core Facility of IRB, Barcelona using standard methodology

scan_protocol: Gene chips were scanned using GeneChip Scanner 3000 from affymetrix

data_processing: Data analysis was performed using R (Bioconductor). Quantile normalization and RMA summarization were used to obtain probeset level expression estimates as implemented in the “oligo” package of Bioconductor. In order to prevent non-specific or miss-targeted probesets to bias the gene level expression estimates, for each gene we selected the 50% of the probesets with highest inter-quartile range across all samples and obtained a gene level expression estimate via median polish, in a fashion analogous to RMA

source_name: Liver metastasis derivative

label_protocol: Labeling of the samples to HG1.0ST gene expression chip (Affymetrix) were performed by Functional Genomics Core Facility of IRB, Barcelona using standard methodology

growth_protocol: cells were maintained in 5% CO2 at 37oC in DMEM medium (Gibco) supplemented with 5% fetal bovine serum (FBS) (Biological Industries), Glutamine 0.29 mg/ml (Biological Industries), Penicillin 100 U/ml (Biological Industries) and Streptomycin 0.1 mg/ml (Biological Industries)

extract_protocol: RNA was extracted from cells using RNeasy mini kit (Qiagen)

value: balb/c

tag: cell line

value: liver metastasis


title: Parental, biological rep4

source_name: Parental

value: parental


title: Liver Met, biological rep3


title: Parental, biological rep3


title: Parental, biological rep1


title: Skeletal muscle 5 (set B)

status: Public on Dec 01 2011

city: Helsinki

first: Suvi

last: Savola

address: Haartmaninkatu 3

department: Pathology

country: Finland

institute: University of Helsinki

description: Skeletal muscle 5

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA extracted using standard Trizol protocol, followed by Qiagen RNeasy column clean-up

tag: diagnosis

value: normal

value: skeletal muscle


title: skeletal muscle, Normal 5

status: Public on Nov 01 2012

city: Gaithersburg

first: Wei

last: Zhu

state: Md

address: One MedImmune Way

department: Translational Sciences

institute: MedImmune

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HGU133 Plus 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using fRMA normalization.

source_name: Quadriceps

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Open muscle biopsies was performed at the time of a diagnostic biopsy  and immediately frozen in liquid nitrogen.  RNA was extracted from muscle biopsies using the mirVana miRNA Isolation kit (Applied Biosystems/Ambion, Austin, TX).

tag: age (y)

value: F

tag: disease state

value: Normal

value: Quadriceps


title: Skeletal muscle 10 (set B)

description: Skeletal muscle 10


title: Liver Met, biological rep1

tag: sample type


title: skeletal muscle, Normal 4

source_name: Biceps

value: M

tag: tissue

value: Biceps


title: skeletal muscle, Normal 1

tag: gender


title: Skeletal muscle 3 (set B)

description: Skeletal muscle 3


title: skeletal muscle, Normal 3


title: skeletal muscle, Normal 2


title: Parental, biological rep2


title: Skeletal muscle 4 (set B)

description: Skeletal muscle 4


title: HCV infected liver _Fibrosis Stage 0_pool1

status: Public on Nov 01 2007

city: Riyadh

first: Saira

last: Khalid

address: Amr Ibn Alaas street

country: Saudi Arabia

institute: King Saud University

description: Experiment ID: Rag208 HG U133Plus 2.0

hyb_protocol: The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChipTM arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B2 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99o C for 5 min followed by incubation at 45o C for 5 min before injecting the sample into the GeneChipTM. Then the hybridization was done at 45oC for 16 h with mixing on a rotisserie at 60 rpm.  After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR). The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated by both gel electrophoresis and hybridization (fraction of the sample) onto test-3 microarray as a measure of quality control before hybridizing onto the Affymetrix Gene Expression Arrays.

scan_protocol: Probe arrays were scanned in the Affymetrix GeneChipTM system confocal scanner by using Affymetrix GeneChipTM Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.

data_processing: The CEL files generated by Gene Chip Operating Software (GCOS) were uploaded to Genespring GX software. Gene expression measures were computed using the Robust Multi-chip average method (RMA) that includes background correction, probe-level quantile normalization and calculation of expression measures.

label: Biotin

source_name: Pooled early fibrosis Stage 0 of chronic HCV infected liver

label_protocol: 50ng of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChipTM System (Santa Clara, CA) at the Microarray Facilities, Mayo Foundation General Clinic Research (Rochester, MN). Double stranded cDNA was then purified by phase lock gel (Eppendorf, Westbury, NY) with phenol/chloroform extraction. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).

extract_protocol: Total RNA was isolated from frozen liver tissues using TRIzol reagent (Invitrogen, MD) and purified using affinity resin column (Rneasy Qiagen, Chatsworth, CA). Equal amounts of total RNA from 4 individuals with fibrosis stage 0 were pooled. The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: Tissue

value: Liver biopsy tissue

tag: Disease stage

value: A pooled RNA sample from 4 liver tissues with chronic hepatitis C, fibrosis stage 0, grade of inflammation 0-1.


title: Skeletal muscle 2 (set B)

description: Skeletal muscle 2


title: S110_sarcoma

status: Public on Jun 27 2010

city: Bordeaux

first: fred

last: chibon

address: 229 cours de l'argonne

institute: Institut Bergonie

hyb_protocol: Samples were then analyzed on Human Genome U133 Plus 2.0 array (Affymetrix®), according to the manufacturer’s procedures.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: All microarray data were simultaneously normalized using the GCRMA algorithm.

source_name: Extremities

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA were extracted from frozen tumor samples with TRIzol reagent (Life Technologies, Inc.) and purified using the RNeasy® Min Elute TM Cleanup Kit (Qiagen) according to the manufacturer’s procedures. RNA quality was checked on an Agilent 2100 bioanalyzer (Agilent Technologies).

treatment_protocol: RNA was extracted from frozen tissue of the untreated primary tumor.

value: Extremities sarcoma

value: RMS PLEOMORPHE


title: S16_sarcoma


title: S127_sarcoma

source_name: Trunk wall

value: Trunk wall sarcoma


title: HCV infected liver_Advance Fibrosis pool

description: Experiment ID: Rag210 HG U133Plus 2.0

source_name: Pooled advance fibrosis stage III-IV chronic HCV infected liver

value: Liver tissues

tag: Disease state

value: A pooled RNA sample from 4 liver tissues with chronic hepatitis C fibrosis stage III and IV, grade of inflammation III-IV

tag: Male to female ratio


title: S136_sarcoma


title: S64_sarcoma


title: S49_sarcoma


title: S48_sarcoma


title: Non-viral hepatic liver_pool1

description: Experiment ID: Rag209 HG U133Plus 2.0

source_name: Pooled Non-viral hepatitis

value: A pooled RNA sample from 3 liver tissues with non-viral hepatitis fibrosis stage 3, grade of inflammation II


title: S101_sarcoma


title: Prdm1/Blimp-1 mutant anti-Irf-1 ChIP1

source_name: Prdm1/Blimp-1 mutant anti-Irf-1 ChIP

tag: strain background

tag: developmental stage

value: Prdm1/Blimp-1 mutant

value: small intestine

value: polyclonal rabbit anti-Irf1 antibody (M-20)

value: Santa Cruz