title: collagenous fibroma (STT5993_FC)

description: Experiment type: 3SEQ


title: dermatofibrosarcoma protuberans (STT5638_DFSP)

status: Public on Nov 21 2013

type: SRA

city: Stanford

first: Xiangqian

last: Guo

state: CA

address: 300 Pasteur Dr.

department: Department of Pathology

country: USA

institute: Stanford University

description: Experiment type: 3SEQ

library_source: transcriptomic

data_processing:
Sequenced Reads after filtered by quality, were re-filtered by fastx, and then were mapped to the transcriptome (refMrna, downloaded from the UCSC genome browser, www.genome.ucsc.edu/) by using SOAP2, allowing at most two mismatches
Total numbers of sequenced reads for each gene symbol from the transcriptome mapping were determined and were used to create the gene-expression profile matrix. The library size was then normalized to one million reads (TPM).
The sequencing depth for each library was determined with the estimation of library saturation for transcriptome detection, which showed that our sequencing depths were deep enough to detect almost all of the known mRNAs expressed.
The distances between sequencing reads and 3’end of mRNAs were measured to be around 100-200nt as we expected.
Genome_build: hg19
Supplementary_files_format_and_content: 10groups.fibrous.tumor.transcriptome_RPM_round.txt expressional matrix with sample by column and gene by row (linked as supplementary file on Series record).

molecule: total RNA

organism: Homo sapiens

source_name: DFSP

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

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

tag: tissue

value: Soft Tissue

tag: tissue archive method

value: FFPE

tag: stromal signature

value: DFSP signature

tag: prognosis

value: UNCLEAR


title: dermatofibrosarcoma protuberans (STT6081_DFSP)

description: Experiment type: 3SEQ


title: dermatofibrosarcoma protuberans (STT5647_DFSP)

description: Experiment type: 3SEQ


title: dermatofibrosarcoma protuberans (STT6082_DFSP)

description: Experiment type: 3SEQ


title: solitary fibrous tumor (STT4711_SFT)

description: Experiment type: 3SEQ

source_name: SFT

value: SFT signature


title: solitary fibrous tumor (STT3524_SFT)

description: Experiment type: 3SEQ


title: solitary fibrous tumor (STT2162_SFT)

description: Experiment type: 3SEQ


title: palmar fibromatosis (STT5773_PF)

description: Experiment type: 3SEQ

source_name: PF

value: PF signature


title: desmoid type fibromatosis (STT5779_DTF)

description: Experiment type: 3SEQ

source_name: DTF

value: DTF(3SEQ) signature


title: desmoid type fibromatosis (STT5768_DTF)

description: Experiment type: 3SEQ


title: desmoid type fibromatosis (STT5766_DTF)

description: Experiment type: 3SEQ


title: desmoid type fibromatosis (STT5764_DTF)

description: Experiment type: 3SEQ


title: desmoid type fibromatosis (STT5629_DTF)

description: Experiment type: 3SEQ


title: HCT15 parental cells

status: Public on Nov 20 2013

city: Taipei

first: Wei-Lun

last: Hwang

address: No.155, Sec.2, Linong Street

department: Department of Biotechnology and Laboratory Science in Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

description: HCT15 parental cells

data_processing:
3’ adaptors of the FASTQ raw data were trimmed, and trimmed data were collapsed by the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit).
For all datasets, reads that shorter than 17 nt or longer than 30 nt were filtered out.
Genome_build: hg19

source_name: colon cancer cells

growth_protocol: Cells were cultured under RPMI (10%FBS, 1% penicillin-streptomycine). Atmosphere: air, 95%; carbon dioxide (CO2), 5%. Temperature, 37.0°C

extract_protocol: TruSeq Small RNA Sample Prep Kit (Cat# RS-200-0012) was used with 1 ug of total RNA for the construction of sequencing libraries

tag: cell line


title: desmoid type fibromatosis (STT5634_DTF)

description: Experiment type: 3SEQ


title: hESCs transfected with LIN-41 #1 siRNA - replicate 2

city: San Francisco

first: Kathleen

middle: A

last: Worringer

address: 1650 Owens St.

institute: Gladstone Institutes

data_processing:
Input sequences were 100bp paired end ("100PE") human samples. The actual mRNA fragment size was given as 410bp. (210 + 100 + 100 -- this is the "--mate-inner-dist" option in the Tophat alignment command below -- it's 85 plus the length of the two pairs).
Alignment of reads -> genome was done with Tophat 2.0.6. Exact alignment parameters: tophat --mate-inner-dist=210 --no-discordant --no-mixed --GTF=Homo_sapiens.GRCh37.56.chr.gtf  --no-novel-juncs --min-anchor=5 --segment-length=25 --no-coverage-search --segment-mismatches=2 --splice-mismatches=2 --microexon-search --num-threads=6 hg19
Duplicate reads (likely to be PCR duplicates) were removed with the program "MarkDuplicates," part of the Picard suite. Web site: http://picard.sourceforge.net/
Differential expression P-values were computed using the DefinedRegionDifferentialSeq program, part of the USeq package. Web site: http://useq.sourceforge.net/
Genome_build: hg19 annotation from Ensembl, build #56
Supplementary_files_format_and_content: Excel format, contains annotation, raw counts and FPKM for all samples, stats

source_name: human embryonic stem cell 1

growth_protocol: hESCs were split the day prior to transfection in the presence of Rock inhibitor in mTESR medium on matrigel.

extract_protocol:
RNA was isolated using Trizol and purified over an Rneasy micro column (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected using lipofectamine RNAimax with 50nM siRNAs, in the presence of Rock inhibitor. Medium (without Rock inhibitor) was changed every 24 hours thereafter. At 72 hours, total RNA was collected.

tag: cell type

value: pluripotent human embryonic stem cells (hESCs)

tag: transfection

value: LIN-41 siRNA #1


title: hESCs transfected with LIN-41 #2 siRNA - replicate 3

value: LIN-41 siRNA #2


title: hESCs transfected with LIN-41 #1 siRNA - replicate 1


title: small RNAs from Taenia multiceps

status: Public on Nov 22 2013

city: Ya'an

first: Guangyou

last: Yang

address: Xinkang Road 46*

department: Department of Parasitology

country: China

institute: Sichuan Agricultural University

data_processing:
Firstly, the data is processed by the following steps: (1) Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table). (2) Getting rid of reads with 5' primer contaminants. (3) Getting rid of reads without 3' primer. (4) Getting rid of reads without the insert tag. (5) Getting rid of reads with poly A. (6) Getting rid of reads shorter than 18nt. (7) Summarize the length distribution of the clean reads. Secondly, map the small RNA tags to the Brugia malayi genome by SOAP to analyze their expression and distribution on the genome. Thirdly, align small RNA tags to the miRNA precursor/mature miRNA of all animals in miRBase17.0. Show the sequence and count of miRNA families(no specific species) which can be found in the samples. Align small RNA tags to repeat associated RNA to find matched tags in the sample. Annotate the small RNA tags with sequences from Rfam and get rid of matched tags from unannotated tags. Finally, summarize all alignments and annotation before.
Tm.unique_counts.txt contains the length of the sequence (nt) information along with SEQUENCE, COUNT.

organism: Taenia multiceps

source_name: whole body

extract_protocol: RNA fragments of 18-44 bases long were isolated and purified from 10 μg total RNA using a Novex 15% TBE-Urea gel. The 5’ and 3’ adaptors (Illumina) were  added to the ends of fragments. Reverse transcription PCR (RT-PCR) was performed using a RT-PCR kit (Invitrogen).The fragments were purified using a 6% TBE PAGE gel

treatment_protocol: liquid nitrogen and stored at -80ºC

tag: development stage

value: adult stage

tag: Sex

value: hermaphrodite

value: whole body


title: hESCs transfected with LIN-41 #2 siRNA - replicate 2


title: hESCs transfected with LIN-41 #2 siRNA - replicate 1


title: HT29 spheres cells

description: HT29 spheres cells (sphere-derived cancer stem cells)

growth_protocol: Cells were cultured in tumor sphere medium composed of DMEM-F12 with N2 Plus Supplement, 10 ng/ml recombinant bFGF , 10 ng/ml EGF  and 1% penicillin-streptomycine for enriching spheroid cells.


title: HT29 parental cells

description: HT29 parental cells

growth_protocol: Cells were cultured under DMEM (10%FBS, 1% penicillin-streptomycine). Atmosphere: air, 95%; carbon dioxide (CO2), 5%. Temperature, 37.0°C


title: hESCs transfected with control siRNA - replicate 3

value: control


title: hESCs transfected with control siRNA - replicate 2


title: hESCs transfected with control siRNA - replicate 1


title: desmoid type fibromatosis (STT5646_DTF)

description: Experiment type: 3SEQ


title: hESCs transfected with LIN-41 #1 siRNA - replicate 3


title: HCT15 spheres cells

description: HCT15 spheres cells (sphere-derived cancer stem cells)


title: Hdac6KD_p400ChIP

city: Singapore

first: Benson

last: Chen

address: 60 Biopolis Street, Genome, #04-01

department: Genome Institute of Singapore

country: Singapore

institute: A*STAR

description:
Sample 2
wildtype/ Hdac6

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Barcode sequences were trimmed and ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie allowing at most one mismatch in every alignment.
For multimappers, only one alignment was chosen randomly by the -M 1 parameter setting.
Each aligned location was extended downstream to a length of 300 bp. Any extension that exceeded the end of the chromosome was clipped. The extended mapped locations overlapping with simple repeats annotated by RepBase were removed.
For each remaining read along with its occurrence, we calculated the relative distance to the nearest TSS and for each TSS tallied the sum of read occurrence from its upstream 2000 bp to downstream 2000 bp. The occurrences were normalized and binned in 20 bp intervals.
Genome_build: mm9
Supplementary_files_format_and_content: The aggregation signals around each TSS (+/- 2000bp) are tabulated in flat format (*.txt)

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: Feeder-free growth on gelatin coated dishes in standatd ES medium: KO DMEM + 10% FBS, glutamine, LIF, non-essential amino acids, beta-mercaptoethanol.

extract_protocol:
Cells from ~80 % confluent 10 cm dishes were crosslinked by adding fixation solution (1% formaldehyde, 0.1M NaCl, 1mM EDTA, 50mM HEPES⋅KOH pH 7.6) for 10 minutes at room temperature. Crosslinking was quenched with 125mM Glycine for 5 minutes. Cells were washed twice with cold PBS containing protease inhibitors (Roche), and pelleted at 1000g for 5 minutes at 4°C. Cell pellets were either flash frozen in liquid nitrogen and stored at -80°C or immediately sonicated. Pellets were resuspended in Lysis buffer 1 (50mM HEPES⋅KOH pH 7.6, 140mM NaCl, 1mM EDTA, 10% (v/v) Glycerol, 0.5% NP-40, 0.25% Triton X-100) including protease inhibitors and incubated for 10 minutes at 4°C. After centrifugation at 1350g for 5 minutes, pellets were resuspended in Lysis buffer 2 (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) containing protease inhibitors and incubated for another 10 minutes at 4°C. Pellets were collected after centrifugation at 1350g for 5 minutes and resuspended in Lysis buffer 2 for sonication. Samples were transferred into 15 ml tubes (Falcon) and sonicated in a Bioruptor set to high for 2 cycles (10 minutes for one cycle with 30 sec on/ 30 sec off). The supernatants were collected after a 13000 rpm spin for 10 minutes at 4°C. 50μl Protein G Magnetic beads (NEB) were washed twice with PBS with 5mg/ml BSA and 10μg of anti-Flag M2 antibody (Sigma) coupled in 500μl PBS with 5mg/ml BSA overnight at 4°C. Immunoprecipitation was performed with antibody-coupled beads and sonicated supernatants in ChIP buffer (20mM Tris-HCl pH8.0, 150mM NaCl, 2mM EDTA, 1% Triton X-100) overnight at 4°C. Magnetic beads were washed twice with ChIP buffer, once with ChIP buffer including 500mM NaCl, 4 times with RIPA buffer (10mM Tris-HCl pH8.0, 0.25M LiCl, 1mM EDTA, 0.5% NP-40, 0.5% Na⋅Deoxycholate), and once with TE buffer (pH 8.0). Chromatin was eluted twice from washed beads by adding elution buffer (20mM Tris-HCl pH8.0, 100mM NaCl, 20mM EDTA, 1% SDS) and incubating for 15 minutes at 65°C. The crosslinking was reversed at 65°C for 6hr and RNase A (Sigma) was added for 1hr at 37°C followed by proteinase K (Ambion) treatment overnight at 50°C. ChIP-enriched DNA was purified using Phenol/Chloroform/Isoamyl alcohol extractions in phase-lock tubes.
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with Phusion polymerase using 16 cycles of PCR before size selection of 200-300 bp fragments on a 2% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing (50 bp) was performed on an Illumina HiSeq2000.

treatment_protocol: In one 10 cm2 dish, 1X10^6 cells were infected with 30 ul of concentrated lentivirus. After 12-15 hours, the media was replaced and cells were cultured until 72 hours post-infection.

tag: genotype/variation

tag: chip antibody


title: Tip60KD_Hdac6ChIP

data_processing:
Basecalls performed using CASAVA version 1.8.2
Barcode sequences were trimmed and ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie allowing at most one mismatch in every alignment.
For multimappers, only one alignment was chosen randomly by the -M 1 parameter setting.
Each aligned location was extended downstream to a length of 150 bp. Any extension that exceeded the end of the chromosome was clipped. The extended mapped locations overlapping with simple repeats annotated by RepBase were removed.
For each remaining read along with its occurrence, we calculated the relative distance to the nearest TSS and for each TSS tallied the sum of read occurrence from its upstream 2000 bp to downstream 2000 bp. The occurrences were normalized and binned in 20 bp intervals.
Genome_build: mm9
Supplementary_files_format_and_content: The aggregation signals around each TSS (+/- 2000bp) are tabulated in flat format (*.txt). The occurrences were normalized and binned in 20 bp intervals.

value: Hdac6-H3F/ Hdac6KD

value: Flag-M2 (Sigma, F1804)


title: GFPKD_p400ChIP

description:
Sample 1
wildtype/ GFPKD

value: GFPKD


title: ZNF

city: Lausanne

first: Marion

last: LELEU

address: Station 15

country: Switzerland

institute: EPFL

description:
Primer name: ZNF107_4c_seq_F
Sequence: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTTGCAACAGAAGGAAATACCAAC
Primer name: ZNF107_4C_seq_R
Sequence: CAAGCAGAAGACGGCATACGATCTCTCATTCCCCTTCCATC

data_processing:
Reads were normalized to the total number of reads. Smoothed data were obtained by applying a running mean algorithm with 19 fragments per window.As the data from the three replicated viewpoints were strongly correlated,  we used the average of each fragments for these experiments.
We used a domainogram algorithm to detect significantly interacting regions without imposing a fixed window size as suggested in [de Wit et al, Global chromatin domain organization of the Drosophila genome, PLoS Genet. 2008 Mar 28;4(3)]. The positive signals were ranked per chromosome and Bricks (Blocks of Regulators In Chromosomal Kontext) were called based on a FDR threshold of 0.1 for “short-range” interactions, defined as interactions within 2.5 Mb up- and downstream of GBAS and MDH2, the first and last viewpoint, respectively (HSA7 coordinates: 53,532,296-78,116,172; about 25 Mb around the WBSCR). Genomic space outside of these borders was called the “long-range” region. As interactions in this long-range region are more subject to random interactions, we used a more stringent FDR threshold of 0.001. To determine differentially interacting regions between the WBS and Ctrl cells, we first computed the log2 ratio of WBS over Ctrl of the smoothed profile corrected data and selected ratio Bricks (as described above) that were specific to either WBS or Ctrl.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files: The 2 "smoothed" files correspond to smoothed data for 2 conditions (WT and WBS), while file "ratios_selectedBricks.bedGraph" is a list of significantly interacting regions obtained as described above.

source_name: EBV transformed mononuclear cells from peripheral blood

growth_protocol: Lymphoblastoid cell lines were grown in RPMI1640 medium supplemented with 10% FCS and 1% PS

extract_protocol:
50 million exponentially growing cells were harvested and crosslinked with 1% formaldehyde, lysed and cut with the restriction enzyme BglII. After ligation and reversal of the crosslinks, the DNA was purified to obtain the 3C library. This 3C library was further digested with NlaIII and circularized to obtain a 4C library. The inverse PCR primers to make the 4C-seq templates were designed to contain the Illumina adaptor tails, as well as the bait-specific sequences for each of the six loci we interrogated. 4C libraries were multiplexed (three samples per mulitplex), libraries were prepared according to Illumina's instructions for ChIP-seq but without size selection and sequenced on Illumina GAIIxl (76-mer single end tags)
Instrument model: Illumina GAIIxl
library_strategy: 4C-seq

value: Lymphoblastoid cells

tag: control lymphoblastoid cell line id

tag: wbs lymphoblastoid cell line id

tag: interrogated locus

value: ZNF


title: GFPKD_Hdac6ChIP

value: Hdac6-H3F/ GFPKD


title: AcH3_Butyrate (S01037)

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 2.1.0 with default parameters.
Reads of control experiment were normalized using total reads of the experiment (read per million reads per kilobase genome) and those of treated cells were normalized using internal control (5 positions from Rpl13a).
Wiggle files were generated using our in-house program with window size 50bp and cutoff value 5 reads per window.
TDF files were converted from wiggle files using IGVTools version 2.2.1.
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle files and TDF files containing identical summary data (ie, histone acetylation).

source_name: Naïve T cells

growth_protocol: Naïve T cells were isolated from spleen and were cultured in the presence of TCR signaling, IL-2, TGF-beta and in the presence or absene of Butyrate.

extract_protocol:
Sheared chromatin DNA was extracted using Magnify ChIP kit and Covaris S220 accroding to manufacture's procedure followed by precipitation of chromatin-DNA complex
Libraries were prepared according to NEB's instructions accompanying the NEBNext® Ultra DNA Library Prep kit for Illumina.  Adapter ligated DNA was PCR amplified with Illumina primers for 18 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hi-Seq 1000 following the manufacturer's protocols.

treatment_protocol: 10 ng/mL IL-2, 0.2 ng/mL TGF-beta, and 0.1 mM Butyrate

tag: strain

tag: marker

value: Naive T cells

tag: culture conditions

value: Treg-inducing condition

tag: agent

value: Butyrate

tag: antibody


title: Hdac6KD_Tip60ChIP

value: Tip60-H3F/ Hdac6KD


title: WT_Differentiated_ChIPSeq

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Botwie2 (version 2.0.5) with default parameters.
peaks were called using MACS2 (version 2.0.10) with default parameters
Genome_build: mm9 (NCBI version 37.2)
Supplementary_files_format_and_content: Wiggle

source_name: Embryonic stem cells

growth_protocol: Differentiating embryonic stem cells are cultured on a gelatin-coated 100-mm dish with 10% serum for 2 days in the presence of 10 nM retinoic acid. Undifferentiated embryonic stem cells are maintained in the presence of KSR (15%), LIF (1,000U), serum (1%).

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.

treatment_protocol: DRB is used last 16 hours before harvesting the cells if necessary.

value: Wild type

tag: treatment

value: Retinoic acid treatment for 2 days

tag: drb treatment

value: no

value: in house antibody


title: WT_Undifferentiated_ChIPSeq

value: Undifferentiated


title: AcH3_Control (S01035)

value: Control


title: H3K36me3_Ash1l ∆SET_DRB(-)_ChIPSeq S00942

value: Ash1l delta-SET

value: Abcam (ab9050)


title: collagenous fibroma (STT5772_FC)

description: Experiment type: 3SEQ

source_name: FC

tag: tissue

value: Soft Tissue

tag: tissue archive method

value: FFPE

tag: stromal signature

value: FC signature

tag: prognosis

value: UNCLEAR


title: H3K36me3_WT_DRB(+)_ChIPSeq S00940

value: yes, last 16 hours


title: H3K36me2_Ash1l ∆SET_DRB(+)_ChIPSeq S00914

value: Abcam (ab9049)


title: Untag_FlagChIP

tag: cell type

value: WT

value: Flag-M2 (Sigma, F1804)


title: H3K36me2_WT_DRB(-)_ChIPSeq S00941

tag: genotype/variation


title: H3K36me3_WT_DRB(-)_ChIPSeq S00944


title: deltaSET_Differentiated

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to mm9 genome using tophat2 (version 2.0.6) with default parameters.
Aligned reads were assigned to genes and counted using cufflinks version  2.1.1) with default parameters and annotation file of mouse Entrez genes.
Genome_build: mm9 (NCBI version 37.2)
Supplementary_files_format_and_content: FPKM (cufflinks output, tab-separated values)

extract_protocol:
Total RNA was harvested using Isogen II reagent (Nippongene). The total RNA was further treated with DNase I and purified by aid of RNeasy Mini Kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ash1l deltaSET


title: H3K36me2_Ash1l ∆SET_DRB(-)_ChIPSeq S00916


title: H3K36me2_WT_DRB(+)_ChIPSeq S00939

value: Wild type


title: WT_Differentiated

value: Retinoic acid treatment for 2 days


title: SH_2_reads

status: Public on Nov 19 2013

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University Colege Dublin Conway Institute

description:
DESeq_WN_v_SH.txt
DESeq_WH_v_SH.txt

data_processing:
basecalling with CASAVA v1.8
fastq files were demultiplexed using the three barcodes (AGCTAT, CGATCT, GCTAGT) Hiseq2000 libraries were received demultiplexed
demultiplexed fastq files were aligned to the Y. lipolytica genome using TopHat 2.0.6, discarding reads that map to two or more regions and allowing one mismatch per aligned read
BAM files were converted into SAM files using SAMtools. Total counts for annotated features were calculated using HtSeq-count. These counts were used as input for DESeq. Normalization and differential gene expression comparisons were carried out using DESeq
Supplementary_files_format_and_content: 4 files normalized using DESeq for 1) wildtype normoxia vs wildtype hypoxia 2) wildtype normoxia vs upc2 deletion hypoxia 3) wildtype normoxia vs sre1 deletion hypoxia and 4) wildtype hypoxia vs sre1 deletion hypoxia

molecule: polyA RNA

organism: Yarrowia lipolytica

source_name: Strain SMY5

growth_protocol: Cells were grown overnight from single colonies in 5 ml YPD (1% Yeast Extract, 2% Peptone, 2% Glucose; FormediumTM) at 28°C . They were diluted in 50 ml fresh YPD to an A600 of 0.2, and grown to an A600 of 1 at 21% or 1% oxygen.

extract_protocol: mRNA purified from total RNA using oligo dT Dynabeads (Invitrogen) was fragmented to an average size of 200 nucleotides by a 5 minute heat treatment (70°C) with a buffered zinc solution (Fragmentation Reagent, Ambion). Fragmentation of mRNA was stopped using an EDTA based Stop buffer (Ambion). Fragmented mRNA was incubated with 3 μg Random Hexamer Primers at 65°C for 5 min. First strand cDNA synthesis was carried out using 1 x First Strand Buffer (Invitrogen), 10 mM DTT, 500 μM dNTP mix (Invitrogen), 20 Units RNaseOUT and 200 units SuperScriptTM II Reverse Transcriptase (Invitrogen). For strand-specific library generation, unincorporated dNTPs were subsequently removed using G-50 Micro Columns (GE Healthcare). Second strand cDNA was generated using 1x Second Strand Buffer, 300 μM dNTP mix, 2 units RNaseH, 50 units DNA Polymerase I (NEB), while a 300 μM dUTP mix was used instead of a dNTP mix for the generation of a strand specific library. This material was used for library preparation. For strand-specific libraries, DNA fragments were blunted in an End Repair reaction using T4 DNA Polymerase, Klenow DNA Polymerase and T4 Polynucleotide Kinase, after which a single ‘A’ base was added to the 3’ end using dATP and Klenow Exo Fragment. To allow multiplexing of samples 6-nt barcoded Illumina compatible adapters (AGCTAT, CGATCT, GCTAGT) were ligated to the ends of the DNA fragments, in place of the commercially supplied adapters (PMID:18794863). Fragments of approximately 200-250 base pairs were purified from a 2% Agarose Gel. The second strand containing uridine was removed by treatment with 1 unit Uracil N-glycosylase (UNG) in TE Buffer at 37°C for 15 min. In all cases, purified adapter ligated DNA templates were then amplified through PCR enrichment, using PCR primers (Illumina), a dNTP mix, Phusion Polymerase (NEB) and 13 cycles of PCR. All libraries were quantified using a Qubit® Fluorometer (Invitrogen) and assessed on a 2% agarose gel. Four libraries were generated by GATC and sequenced on an Illumina HiSeq2000

tag: growth condition

value: 1% Oxygen

tag: genotype

value: SRE1 deletion


title: UH_3_reads

source_name: Strain SMY2

value: UPC2 deletion


title: UH_1_reads


title: UH_2_reads


title: WT_Undifferentiated

value: KSR+LIF


title: sRNAs from SINV-infected VERO cells

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

country: France

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

description:
Small RNA profiling
Sample 4
-

data_processing:
Base calling were performed using CASAVA v.1.6.0 (samples 1 to 4) and v.1.8.2 (samples 5 to 10)
Sequencing reads were preprocessed using the Dustmasker program and FASTX-Toolkit to filter out low complexity sequences and to remove instances of the 3' adaptor respectively. If needed, degenerate bases incorporated during the new library preparation protocol were also trimmed. For siCtl and siRNAseL libraries, we also eliminated reads corresponding to the siRNA sequences.
Remaining reads of at least 15 nt in length were then mapped simultaneously to the human and SINV genomes using Bowtie 0.12.7. Up to 2 mismatches in total with no more than 1 mismatch in the first 15 nucleotides of each read were permitted. In addition, only alignments from the lowest mismatch-stratum were recorded and reads that could map to more than 50 loci were discarded.
For each source library, small RNAs deriving solely from SINV, in either sense or antisense orientation, were computationally extracted and profiled based on their length distribution and their coverage distribution along the viral genome.
Genome_build: GRCh37/hg19 + NC_001547.1
Processed data files format and content: .bed is an alignment file of only the viral reads for each library (Reference, Begin [0-based offset], End [1-based offset], Name [=raw readcount], Score [=raw readcount], Strand)
Processed data files format and content: Summary.txt (linked as a supplementary file on the Series record) is a tab-delimited file with a detailed description of all the alignments + sequences obtained in the 10 libraries (Length, Sequence, Raw readcount in each of the 10 libraries, Reference, Begin [1-based offset], End [1-based offset], Strand, Mismatch number, Mismatch description [position_in_the_read : base_in_the_reference > base_in_the_read])

organism: Chlorocebus aethiops

source_name: SINV-infected VERO cells

growth_protocol: HEK293 and VERO cells were maintained in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere of 5% CO2 at 37°C. Cells were infected with SINV at MOI 0.01. Samples were harvested at 16 hours post-infection (hpi).

extract_protocol:
RNA was extracted from non-infected and infected cells using Tri-reagent (Ambion) as per manufacturer’s instructions.
Small RNA libraries were prepared from 10 or 20 μg of total RNA as previously described (Pfeffer, S. 2007. Identification of virally encoded microRNAs. Methods Enzymol. 427:51-63), except that PCR products were not concatemerized but directly sent for large-scale sequencing. Libraries from samples 5 to 10 were generated using the same protocol except that degenerate 5' and 3' adapters were used to limit ligation biases.

tag: host cell line

value: VERO

tag: viral infection of host cell line

value: Sindbis virus

tag: viral infection conditions


title: GFPKD_Tip60ChIP

value: Tip60-H3F/ GFPKD

tag: chip antibody


title: sRNAs from non-infected VERO cells

description:
Small RNA profiling
Sample 3
-

source_name: non-infected VERO cells

value: non-infected


title: WH_3_reads

description:
DESeq_WN_v_WH.txt
DESeq_WH_v_SH.txt

source_name: Strain JMY2900

value: Wildtype


title: WH_2_reads

description:
DESeq_WN_v_WH.txt
DESeq_WH_v_SH.txt


title: WH_1_reads

description:
DESeq_WN_v_WH.txt
DESeq_WH_v_SH.txt


title: WN_2_reads

description:
DESeq_WN_v_WH.txt
DESeq_WN_v_UH.txt
DESeq_WN_v_SH.txt

value: 21% Oxygen


title: WH_5_reads

description:
DESeq_WN_v_WH.txt
DESeq_WH_v_SH.txt


title: H3K36me3_Ash1l ∆SET_DRB(+)_ChIPSeq S00915

tag: strain

value: Ash1l delta-SET

value: yes, last 16 hours

value: Abcam (ab9050)


title: WH_4_reads

description:
DESeq_WN_v_WH.txt
DESeq_WH_v_SH.txt


title: WN_4_reads


title: WN_3_reads


title: sRNAs from siRNaseL transfected and SINV-infected HEK293 cells

description:
Small RNA profiling
Sample 6
siRNaseL transfection was performed before infection and total RNA extraction

tag: transfection of host cell line

value: siRNaseL


title: deltaSET_Undifferentiated

value: Ash1l deltaSET


title: sRNAs from siCtl transfected and SINV-infected HEK293 cells

description:
Small RNA profiling
Sample 5
siCtl transfection was performed before infection and total RNA extraction

value: siCtl


title: sRNAs from SINV-infected HEK293 cells, treated with NaIO4

description:
Small RNA profiling
Sample 10
Extracted total RNA was treated with NaIO4 before cloning and sequencing

tag: naio4 treatment

value: yes


title: sRNAs from SINV-infected HEK293 cells, non-treated with NaIO4

description:
Small RNA profiling
Sample 9
-

value: no


title: sRNAs from non-infected HEK293 cells, non-treated with NaIO4

description:
Small RNA profiling
Sample 7
-


title: SH_1_reads

description:
DESeq_WN_v_SH.txt
DESeq_WH_v_SH.txt

source_name: Strain SMY8

value: 1% Oxygen

value: SRE1 deletion


title: sRNAs from non-infected HEK293 cells, treated with NaIO4

description:
Small RNA profiling
Sample 8
Extracted total RNA was treated with NaIO4 before cloning and sequencing


title: ChIPSeq_PolII_E12.5_distalforelimb

city: Montreal

first: Soizik

last: Berlivet

state: Quebec

address: 110, avenue des Pins Ouest

country: Canada

institute: Institut de Recherches Cliniques de Montreal

data_processing:
Sequence reads were trimmed for adapter sequences.
The trimmed reads were mapped to the mouse mm9 genome assembly with Bowtie using the --best parameters.
To identify the highly significant RNAP2 and Med12 peaks, we used the MACS 1.4.1 peak finder with the following parameters: --format SAM --wig --bw 250 --mfold 7,30 --pvalue 1e-5 -g mm
Genome_build: mm9

source_name: distal forelimb

growth_protocol: Normal mouse gestation to day E12.5

extract_protocol:
Distal forelimbs were collected in 1X PBS containing 10% FBS and the samples were incubated with collagenase  to obtain single-cell suspensions  The cells were then fixed with 1% formaldehyde at room temperature. Crosslinking was stopped with glycine. Cell pellets were flash frozen on dry ice. Cells were sonicated to obtain fragments with average sizes ranging between 100-600 bp. Protein G Dynal Beads (Invitrogen) were incubated 8 hours at 4°C with antibodies.  The chromatin was then incubated with the beads overnight. Immunoprecipitated complexes were sequentially washed.  The protein/DNA complexes were eluted in an SDS buffer (1% SDS, 50 mM Tris (pH 8.0), 10 mM EDTA).  Crosslinks were reversed. Samples were treated with RNAseA and then with Proteinase K.  Finally, the DNA was purified on QIAquick columns (Qiagen).
Libraries were prepared according to Illumina's instructions

treatment_protocol: Pregnant mothers were euthanized and embryos were removed and placed in cold PBS. Distal forelimbs were collected with forcepts.

tag: developmental stage

tag: chip-antibody

value: PolII (Abcam, ab5131, lot GR37362-1)


title: ChIPSeq_Med12_E12.5_distalforelimb


title: ChIPSeq_Input_E12.5_distalforelimb


title: sRNAs from SINV-infected HEK293 cells

description:
Small RNA profiling
Sample 2
-

source_name: SINV-infected HEK293 cells


title: sRNAs from non-infected HEK293 cells

description:
Small RNA profiling
Sample 1
-

source_name: non-infected HEK293 cells


title: WN_1_reads


title: EBF null total RNA-seq

city: Baltimore

first: Karen

last: Reddy

state: MD

address: 855 North Wolfe Street

department: Center for Epigenetics/Biological Chemistry

institute: Johns Hopkins University

description: Sample 1

data_processing:
Read cleaning: Raw reads were cleaned by 'Fastq quality trimmer by sliding window' to trim both ends of the reads examining a window size of 3 nucleotides, with a step size of 1 nucleotide, requiring 'aggregates' (windows) to meet a mean quality score greater than 20.0 for inclusion in the 'cleaned' data sets
Alignment: Cleaned reads were aligned to the mouse reference genome (mm9) with TopHat (v1.5) using strand-specific parameters.
Abundance measurments: Transcript abundance (measured as fragments per kilobase per million reads, FPKM) and differential expression estimates were generated by running Cuffdiff2.1.1 on the aligned reads using the protein-coding genes of RefSeq as the reference
Analysis platform: All RNA-seq analysis was performed on Galaxy Cloudman using AWS.
Comprehensive integrated multi-omics data can be found at: https://usegalaxy.org/u/thereddylab/p/prediction-of-gene-activity-based-on-an-integrative-multi-omics-analysis
Genome_build: mm9
Supplementary_files_format_and_content: Transcript abundance for all RefSeq genes generated by Cuffdiff 2.1.1 are provided as Cuffdiff "transcript FPKM tracking" and "transcript differential expression testing" files.

source_name: EBF null pre-pro-B cell

growth_protocol: Ebf1 -/- pre-pro-B cells and Rag2 -/- pro-B cells were cultured on OP-9 stromal cells in Opti-MEM, supplemented with 5% defined FBS (HyClone SH30070.03), 2 mM glutamine, 1% penicillin/streptomycin, beta-mercaptoethanol (1:1000 dilution) and cytokines [pre-pro-B cells: Il-7 (5 ng/mL; Cell Signalling 5217SC ), Scf (10ng/mL; Cell Signaling Technology 5223SC), Flt3l (10ng/mL; R&D systems 427-FL-025); pro-B cells: Il-7 (5 ng/mL)] under standard tissue culture conditions. Cells were harvested by washing media over stromal cells to liberate B cells, which were then placed in a fresh tissue culture flask to allow residual stromal cells to attach to the culture vessel for 30 minutes under standard tissue culture conditions, after which B cells in suspension were removed and washed three times in cold phosphate buffered saline (pH 7.4) before downstream analysis.

extract_protocol:
Total RNA was extracted from Ebf1 -/- pre-pro-B cells and Rag2 -/- pro-B cells by TRIzol, then subject to DNAse digestion to remove residual DNA and cleaned over a RNeasy (Qiagen 74104) column using the manufacturer's 'cleanup protocol' to remove contaminants and deplete RNAs <200 nt. RNA quality was assessed by RNA 6000 nano total RNA (Agilent 5067-1511) analysis on a 2100 Bioanalyzer (Agilent G2938C); all samples had RIN (RNA integrity number) scores = 9.9.
RNA samples were depleted of mature ribosomal RNA (rRNA) transcripts with RiboZERO (Epicentre RZH1064) per the manufacturer's recommendation, using 2 μg of RNA as input. RNA depleted of rRNA was converted to indexed, strand-specific RNA sequencing libraries using the ScriptSeqv2 system (Epicentre SSV21106) following the manufacturer's recommendation, using 50 ng of rRNA-depleted RNA as input.
RNA-seq libraries were sequenced on a HiSeq 2000 (Illumina SY-401-1001) to a read depth of ~90,000,000 single end 97 bp reads per sample.

tag: strain background

value: Ebf1 -/- pre-pro-B cells


title: S353_RFPminus_3

status: Public on Nov 18 2013

city: Dresden

first: Federico

last: Calegari

address: Fetscherstr. 105

department: Center for Molecular and Cellular Bioengineering (CMCB)

country: Germany

institute: TU Dresden

description: Strand-specific RNA-Seq

data_processing:
Basecalling: Illumina CASAVA-1.8.0
Read Alignment: BWA VN:0.5.9-r32-MPI-patch2 against mm9 transcriptome (with exon-exon junction library based on Ensembl Gene v. 61 annotation)
Counts per feature: Reads per gene were computed using bedtools version 2.11, based on Ensembl Gene v. 61 annotation (intersectBed -f 0.55 for non-split reads, -f 1 for split reads - falling on exon-exon junctions).
Read count normalization: The raw read counts (absolute number of reads) were normalized with the DESeq R package (v.1.8.1).
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited file with sample size normalized counts per gene (rows) and sample (columns)

source_name: Lateral cortex of the brain

extract_protocol:
E14.5 Btg2GFP/Tubb3GFP cortices were dissociated using the papain-based neural dissociation kit (Miltenyi Biotec) after removal of meninges and ganglionic eminences. FACS was performed at 4˚C in the 4-way purity mode with a flow rate of 20 μl/min using side and forward scatter light to eliminate debris and aggregates and gating established for green (488 nm) and red (561 nm) fluorescence. About 1x106 sorted cells from >3 embryos from different litters were immediately lysed in μMACS™ mRNA Isolation Kit and lysates cleaned on LysateClear Colums (Miltenyi) resulting in ca. 1 µg of poly-A RNAs with a integrity number >9.2
Library preparation and enrichment was performed using 15 µl Sera-Mag Oligo(dT) beads (Thermo Scientific) in 50 µl 10 mM Tris-HCl. Samples were treated with 1U Turbo DNAse (Ambion) and purified with Agencourt RNAclean XP beads. Eluted mRNA (18 µl) was chemically fragmented with NEBNext-Mg RNA Fragmentation Module (New England Biolabs), re-purified with RNAclean XP beads and eluted in 13,5 µl nuclease-free water. First strand cDNA synthesis was performed using 0.15 µg/µl Random Primers (New England Biolabs), 1x First Strand Synthesis Reaction Buffer (New England Biolabs), 10 U/uL Superscript II (Invitrogen) with an initial hybridization for 5 min at 65°C with mRNA and primers followed by incubation at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. After purification with Agencourt Ampure XP-beads (Beckman Coulter), second strand synthesis was performed using the Second Strand Synthesis module (New England Biolabs) replacing the 2nd strand synthesis buffer with a NTP-free buffer and adding equimolar 2.5 mM of d-nucleotides. Incubation for 2.5 h at 16°C was followed by Ampure XP beads purification as described above. End-Repair was done with the NEBnext End Repair Module (New England Biolabs) followed by XP beads purification and A-Tailing using the NEBnext dA-Tailing Module. Adaptors were ligated  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3') using 1x NEBnext Quick Ligation Buffer (New England Biolabs), 0.3 uM DNA Adaptors, 1 uL Quick T4 DNA Ligase (New England Biolabs) in 50 µl. XP beads purification was followed by dUTP cleavage with 1 U USER enzyme mix (New England Biolabs) per sample and direct enrichment using the PCR Enrich Adaptor Ligated cDNA Library module (New England Biolabs) with indexed primers.

value: Embryonic day 14.5

value: Proliferating Progenitors_Btg2 negative


title: adipocyte_PPARg_ChIP-seq

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

country: Finland

institute: university of eastern finland

description: Samples collected from the SGBS cell line. The PPARg, CEBPa and LXR samples were collected from the same chromatin lysate.

data_processing:
Raw reads were first quality controlled using the FASTQ software v.0.10.0
All reads that were detected as read artifacts or that had low quality base pair calling were removed and read stacks collapsed using the FASTX software v.0.0.13 (minimum quality score of phred 10 across the read length was required).
The reads that passed the quality control steps were aligned to the hg19 human genome using the Bowtie software v0.1.25 (one mismatch allowed, maximum three locations in the genome from which the highest quality match was reported).
All histone data was analyzed using the EpiChIP software v.0.9.7, where the H3K4me3 signal was quantified from -750 to +1250 region centered at Refseq TSS coordinates. This region was detected to have the highest signal by window analysis.
Transcription factor peak detection was performed using the QuEST software v.2.4. run in the advanced mode without FDR analysis with defaults settings applied except for the mappable genome fraction (set to 0.88) and enrichment (ChIP enrichment set to 15 and ChIP to background enrichment to 2.5).
The final peak lists were filtered to remove peaks with log10Qvalue less than 3
Genome_build: hg19
Supplementary_files_format_and_content: The wig files represent the genome-wide normalized combined density profile. Combined density profile represents enrichment in the data. It is calculated after applying kernel density estimation to both strands and adding obtained values after the peak shift correction.

source_name: SGBS cell line undergoing differentiation for 10 days

growth_protocol: SGBS cells were cultured in Dulbecco's modified Eagle's medium (DMEM)/Nutrient Mix F12 (Gibco) containing 8 mg/l biotin, 4 mg/l pantothenate, 0.1 mg/mg streptomycin and 100 U/ml penicillin (OF medium) supplemented with 10% FBS in a humidified 95%air/5%CO2 incubator. The cells were seeded into culture medium flasks or plates, which were coated with a solution of 10 microL/ml fibronectin and 0.05% gelatine in phosphate-buffered saline. Confluent cells were cultured in serum-free OF medium for 2 days followed by stimulation to differentiate with OF media supplemented with 0.01 mg/ml human transferrin, 200 nM T3, 100 nM cortisol, 20 nM insulin, 500 microM IBMX and 100 nM rosiglitazone (Cayman Chemicals). After day 4, the differentiating cells were kept in OF media supplemented with 0.01 mg/ml human transferrin, 100 nM cortisol and 20 nM insulin.

extract_protocol:
Nuclear proteins were cross-linked to DNA by adding formaldehyde directly to the medium to a final concentration of 1% for 8 min at room temperature. Cross-linking was stopped by adding glycine to a final concentration of 0.125 M and incubating for 5 min at room temperature on a rocking platform. The medium was removed and the cells were washed twice with ice-cold PBS. The cells were then collected in lysis buffer (1% SDS, 10 mM EDTA, protease inhibitors, 50 mM Tris-HCl, pH 8.1) and the lysates were sonicated by a Bioruptor UCD-200 (Diagenode, Liege, Belgium) to result in DNA fragments of 200 to 500 bp in length. Cellular debris was removed by centrifugation and the lysates were diluted 1:10 in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl, protease inhibitors, 16.7 mM Tris-HCl, pH 8.1). Chromatin solutions were incubated overnight at 4C with rotation with antibodies. The immuno-complexes were collected with 20 ul of MagnaChIP protein A beads (Millipore) for 1 h at 4C with rotation. Non-specific background was removed by incubating the MagnaChIP protein A beads overnight at 4C with rotation in the presence of BSA (250 ug/ml). The beads were washed sequentially for 3 min by rotation with 1 ml of the following buffers: low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl, pH 8.1), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl, 20 mM Tris-HCl, pH 8.1) and LiCl wash buffer (0.25 M LiCl, 1% Nonidet P-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.1). Finally, the beads were washed twice with 1 ml TE buffer (1 mM EDTA, 10 mM Tris-HCl, pH 8.1). The immuno-complexes were then eluted by adding 500 ul of elution buffer (25 mM Tris-HCl, pH 7.5, 10 mM EDTA, 0.5% SDS) and incubating for 30 min on rotation. The cross-linking was reversed and the remaining proteins were digested by adding 2.5 ul of proteinase K (Fermentas) to a final concentration of 80 ug/ml and incubating overnight at 65C. The DNA was recovered by phenol/chloroform/isoamyl alcohol (25:24:1) extractions and precipitated with 0.1 volume of 3 M sodium acetate, pH 5.2, and 2 volumes of ethanol using glycogen as carrier. Immunoprecipitated chromatin DNA was then used as a template for real-time quantitative PCR or for library preparation and sequencing (performed at EMBL Core facility, Heidelberg, Germany).
Libraries were prepared according to Illumina's instructions

treatment_protocol: See growth protocol for induction of differentiation.

value: adipocyte

value: PPARg (mixture of 0.5 ul per IP of sc-7196x, Santa Cruz Biotechnologies, and 5 ul per IP of 101700, Cayman)


title: adipocyte_LXR_ChIP-seq

value: LXR (antibody from Dr. Eckardt Treuter, Karolinska Institute)


title: preadipocyte_H3K4me3_ChIP-seq

source_name: Confluent preadipocyte SGBS cell line

value: preadipocyte

value: H3K4me3 (17-614, Millipore)


title: adipocyte_CEBPa_ChIP-seq

value: CEBPa (sc-61, Santa Cruz Biotechnologies)


title: adipocyte_H3K4me3_ChIP-seq


title: S355_GFPplus_3

description: Strand-specific RNA-Seq

value: Neurons_Tubb3 positive


title: S354_RFPplus_3

description: Strand-specific RNA-Seq


title: S334_RFPminus_2

description: Strand-specific RNA-Seq


title: S336_GFPplus_2

description: Strand-specific RNA-Seq


title: S335_RFPplus_2

description: Strand-specific RNA-Seq


title: S167_RFPplus_1

description: Strand-specific RNA-Seq


title: S168_GFPplus_1

description: Strand-specific RNA-Seq


title: adipocyte_InputCtrl_ChIP-seq


title: S166_RFPminus_1

description: Strand-specific RNA-Seq


title: RNA in MEFs derived from TgOG2 (mother) X JF1 (father) cross

city: Duarte

first: Xiwei

last: Wu

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

institute: Beckman Research Institute

description: OG2XJF1 (OXJ) MEFs

data_processing:
library strategy: Strand-specific RNA-Seq
Illumina Casava 1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v1.2.0 with default settings.
The coverage by aligned reads on forward and reverse strand on a selection of imprinted and control regions were calculated.
FDD 3.0 format containing the average coverage of bases within defined regions by the aligned reads.
Genome_build: mm9
Supplementary_files_format_and_content: GFF coverage file for each sample with forward and reverse strand on a selection of known imprinted and control regions.

source_name: 13.5 dpc mouse embryo

growth_protocol: in vivo

extract_protocol:
RNA was isolated using RNA-Bee (AMS Biotechnology). DNAseI digestion was applied to remove DNA contamination. 10 μg total RNA was treated with the Ribominus kit (Life Technologies) to remove ribosomal RNA contamination. The amount of RNA was monitored using a Nanodrop spectrophotometer followed by a quality check using the Bioanalyzer.
First-strand synthesis was done using Superscript II reverse transcriptase, dNTPs and the Illumina RNA seq library preparation kit. The enzyme was inactivated and the dNTPs were removed. To enable strand-specific analysis, the second strand cDNA was labeled with dUTP before ligating the adapter. The second strand was synthesized using E. coli DNA polymerase I and dATP, dGTP, dCTP, dUTP nucleotides in the presence of E. coli ligase and RNase H. Ends were repaired using “End It Enzyme mix”, and dATP 3’ overhangs were created using Klenow exo- and then R2 adapters were ligated to the double stranded cDNA fragments. The second strand was degraded using USER™ (Uracil-Specific Excision Reagent) enzyme complex. Only the first strand was used as PCR template for paired-end deep sequencing. The read1 sequences (F2R1 or R1F2) represent the antisense strand and the read 2 (F1R2 or R2F1) sequences represent the sense strand of the RNA. The single stranded cDNA containing the adapter was amplified by PCR using two different index primers. Reads resulting from the JXO cross MEF started with the sequence ACTTGA and reads resulting from the OXJ cross MEF started with the sequence CCGTCC. The two MEF samples were sequenced on half a lane each of the Illumina sequencer.

value: TgOG2 (mother) X JF1 (father) cross

tag: gender

value: female

value: mouse embryo fibroblast

tag: age

value: 13.5 dpc at derivation of MEF


title: Runx3_CD8+T_CHIP_H3K4me1_IP2

city: Rehovot

first: Joseph

last: Lotem

department: Molecular genetics

country: Israel

institute: Weizmann institute of science

description: second IP experiment of H3K4me1

data_processing:
GAPipeline1.4.0: Runx3_CD8+T_CHIP_Runx3_IP1.1.fastq, Runx3_CD8+ T_CHIP_NIS1.fastq, Runx3_CD8+T_CHIP_H3K4me1_IP1.fastq; CASAVA 1.6: Runx3_CD8+T_CHIP_Runx3_IP1.2.fastq;  CASAVA 1.7: Runx3_CD8+T_CHIP_Runx3_IP2.1.fastq, Runx3_CD8+T_CHIP_H3K4me1_IP2.fastqRunx3_CD8+T_CHIP_NIS2.fastq, Runx3_CD8+T_CHIP_NIS2.fastq
For data analysis ~30 million Runx3, H3K4me1 and NIS IP short read (40-42bp) sequences were aligned uniquely to the mouse genome (mm9) using ELAND. Peaks of enriched Runx3 or H3K4me1 regions were detected using the uniquely aligned sequences (sorted file) of merged biological replicates of IP versus the NIS,  using MACS1.4.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files containing peaks detected by MACS1.4 done by scaling to small

source_name: Splenic CD8+ T cells

growth_protocol: Two biological replicate ChIP-Seq experiments were conducted for detection of Runx3-bound genomic regions and H3K4me1-marked regions using in-house anti Runx3 Ab and monoclonal anti-H3K4me1 Ab, rspectively, with 30 million splenic CD8+ T cells isolated by positive selection on anti-CD8 magnetic beads (BD Biosciences) >95% purity. Isolated CD8+ T cells were fixed and frozen at  -80°C.

extract_protocol:
Isolated cells were fixed in 1% formaldehyde and sonicated to yield DNA fragments of ~300bp. For immunoprecipitation, 48ul of anti-Runx3 Ab, anti-H3K4me1 or NIS were added to 12 mL of diluted, fragmented chromatin. DNA was purified using QIAquick spin columns (QIAGEN).
For ChIP-seq analysis, ChIP-seq libraries were prepared using the ChIP-Seq sample preparation kit (IP-102-1001, illumina) according to the manufactures instructions. Illumina sequencing was performed using Illumina genome analyzer IIx according to the manufactures instructions by loading 15 pM of denatured library template onto separate lanes of a flow cell. Sequencing short reads (40-42 bp) were aligned to the mouse genome (mmp9) using the ELAND program (Illumina).

value: Splenic CD8+ T cells

tag: passages

value: Collected from 18 mice. Cells were freshly isolated, fixed and frozen at -80°C.

value: ICR

value: Monoclonal anti-H3K4me1


title: RNA in MEFs derived from JF1 (mother) X TgOG2 (father) cross

description: JF1XOG2 (JXO) MEFs

value: JF1 (mother) X TgOG2 (father) cross

tag: cell type


title: Runx3_CD8+T_CHIP_H3K4me1_IP1

description: first IP experiment of H3K4me1


title: Runx3_CD8+T_CHIP_Runx3_IP2

description: second IP experiment of Runx3

value: Runx3 poly clonal home made


title: Runx3_CD8+ T_CHIP_NIS1

description: first IP experiment of NIS

value: Non-immune rabbit serum


title: Runx3_CD8+ T_CHIP_NIS2

description: second IP experiment of NIS


title: Rag null total RNA-seq

description: Sample 2

source_name: Rag null pro-B cell

value: Rag2 -/- pro-B cells


title: Runx3_CD8+T_CHIP_Runx3_IP1 file 2

description: first IP experiment of Runx3


title: Runx3_CD8+T_CHIP_Runx3_IP1 file 1

description: first IP experiment of Runx3


title: Runx3_IL2NK_CHIP_H3K4me1_IP

description: first IP experiement of H3K4me1

data_processing:
GAPipeline1.3.2: Runx3_IL-2NK_CHIP_Runx3_IP1.fastq, Runx3_IL-2NK_CHIP_NIS1.fastq; GAPipeline1.4.0: Runx3_IL-2NK_CHIP_Runx3_IP2.fastq, Runx3_IL-2NK_CHIP_NIS2.fastq, Runx3_IL-2NK_CHIP_H3K4me1_IP.fastq.
For data analysis 18.8, 11.5 and 11.2 million  Runx3, H3K4me1 and NIS IP short read (40 bp) sequences were aligned uniquely to the mouse genome (mm9) using ELAND. Peaks of enriched Runx3 or H3K4me1 regions were detected using the uniquely aligned sequences (sorted file) of merged biological replicates of IP versus the NIS,  using MACS1.4.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files containing peaks detected by MACS1.4 done by scaling to small

source_name: Splenic NK cells

growth_protocol: Two biological replicate ChIP-Seq experiments for detection of Runx3-bound genomic regions and one ChIP-Seq experiment for detection of H3K4me1-marked regions were conducted using in-house anti Runx3 Ab and monoclonal anti-H3K4me1 Ab, rspectively, with 40 million cultured splenic NK cells. NK cells were isolated by negative  selection using NK cell isolation kit (R&D) and cultured for 7 days with 1000u/ml human recombinant IL-2 (Beit Haemek, Israel). Cultured NK cells were all NKp46+ and were fixed and frozen at  -80°C.

extract_protocol:
Cultured NK cells were fixed in 1% formaldehyde and sonicated to yield DNA fragments of ~300bp. For immunoprecipitation, 48ul of anti-Runx3 Ab, anti-H3K4me1 or NIS were added to 12 mL of diluted, fragmented chromatin. DNA was purified using QIAquick spin columns (QIAGEN).
For ChIP-seq analysis, ChIP-seq libraries were prepared using the ChIP-Seq sample preparation kit (IP-102-1001, illumina) according to the manufactures instructions. Illumina sequencing was performed using Illumina genome analyzer IIx according to the manufactures instructions by loading 15 pmoles of denatured library template onto separate lanes of a flow cell. Sequencing short reads (40 bp) were aligned to the mouse genome (mmp9) using the ELAND program (Illumina).

value: Splenic NK cells

value: Cells were cultured for 7 days with IL-2, fixed and frozen at -80°C.


title: Runx3_IL2NK_CHIP_NIS2

description: second IP experiement of NIS


title: Runx3_IL2NK_CHIP_NIS1

description: first IP experiement of NIS


title: Runx3_IL2NK_CHIP_Runx3_IP1

description: first IP experiement of Runx3


title: Runx3_IL2NK_CHIP_Runx3_IP2

description: second IP experiement of Runx3


title: Runx3_IL2CD8+T_CHIP_H3K4me1_IP

description: first IP experiment of H3K4me1

data_processing:
GAPipeline1.3.2: Runx3_IL-2CD8+T_CHIP_Runx3_IP1.fastq, Runx3_IL-2CD8+ T_CHIP_Runx3_IP2.fastq, Runx3_IL-2CD8+ T_CHIP_NIS1.fastq, Runx3_IL-2CD8+T_CHIP_NIS2.fastq; GAPipeline1.4.0: Runx3_CD8+T_CHIP_H3K4me1_IP1.fastq
For data analysis 7.6, 6.2 and 12.5 million Runx3, H3K4me1 and NIS IP short read (38-40bp) sequences, respectively, were aligned uniquely to the mouse genome (mm9) using ELAND. Peaks of enriched Runx3 or H3K4me1 regions were detected using the uniquely aligned sequences (sorted file) of merged biological replicates of IP versus the NIS,  using MACS1.4.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files containing peaks detected by MACS1.4 done by scaling to small

growth_protocol: Two biological replicate ChIP-Seq experiments were conducted for detection of Runx3-bound genomic regions and H3K4me1-marked regions using in-house anti Runx3 Ab and monoclonal anti-H3K4me1 Ab, rspectively, with splenic CD8+ T cells isolated by positive selection on anti-CD8 magnetic beads (BD Biosciences) >95% purity. Isolated CD8+ T cells were TCR-activated for 2 days on anti-CD3e coated plates with soluble anti-CD28 as published (Cruz-Guilloty et al., J Exp Med 206: 51-59, 2009) and then cultured for 4 additional days in the presence of 100u/ml recombinant human IL-2 (Beit Haemek, Israel). Cultured cells were then fixed and frozen at -80°C.

extract_protocol:
Isolated cells were fixed in 1% formaldehyde and sonicated to yield DNA fragments of ~300bp. For immunoprecipitation, 48ul of anti-Runx3 Ab, anti-H3K4me1 or NIS were added to 12 mL of diluted, fragmented chromatin. DNA was purified using QIAquick spin columns (QIAGEN).
For ChIP-seq analysis, ChIP-seq libraries were prepared using the ChIP-Seq sample preparation kit (IP-102-1001, illumina) according to the manufactures instructions. Illumina sequencing was performed using Illumina genome analyzer IIx according to the manufactures instructions by loading 15 pmoles of denatured library template onto separate lanes of a flow cell. Sequencing short reads (40-42 bp) were aligned to the mouse genome (mmp9) using the ELAND program (Illumina).

value: After culture with IL-2 cells were fixed and frozen at -80°C.


title: Runx3_NK_CHIP_NIS

description: first IP experiment of NIS

data_processing:
CASAVA 1.7
For data analysis 25-30 million Runx3, H3K4me1 and NIS IP short read (40 bp) sequences were aligned uniquely to the mouse genome (mm9) using ELAND. Peaks of enriched Runx3 or H3K4me1 regions were detected using the uniquely aligned sequences (sorted file) of merged biological replicates of IP versus the NIS,  using MACS1.4.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files containing peaks detected by MACS1.4 done by scaling to small

growth_protocol: ChIP-Seq experiments for detection of Runx3-bound genomic regions and H3K4me1-marked regions were conducted using in-house anti Runx3 Ab and monoclonal anti-H3K4me1 Ab, rspectively, with 40 million freshly isolated (resting) splenic NK cells isolated by negative selection using NK cell isolation kit (R&D) and sorting for NKp46+ cells. Isolated NK cells were fixed and frozen at  -80°C.

extract_protocol:
Isolated cells were fixed in 1% formaldehyde and sonicated to yield DNA fragments of ~300bp. For immunoprecipitation, 48ul of anti-Runx3 Ab, anti-H3K4me1 or NIS were added to 12 mL of diluted, fragmented chromatin. DNA was purified using QIAquick spin columns (QIAGEN).
For ChIP-seq analysis, ChIP-seq libraries were prepared using the ChIP-Seq sample preparation kit (IP-102-1001, illumina) according to the manufactures instructions. Illumina sequencing was performed using Illumina genome analyzer IIx according to the manufactures instructions by loading 15 pmoles of denatured library template onto separate lanes of a flow cell. Sequencing short reads (40 bp) were aligned to the mouse genome (mmp9) using the ELAND program (Illumina).

value: Cells were freshly isolated, fixed and frozen at -80°C.


title: Runx3_IL2CD8+ T_CHIP_NIS2

description: second IP experiment of NIS


title: Runx3_IL2CD8+T_CHIP_Runx3_IP1

description: first IP experiment of Runx3


title: Runx3_IL2CD8+T_CHIP_Runx3_IP2

description: second IP experiment of Runx3


title: Runx3_NK_CHIP_H3K4me1_IP

description: first IP experiment of H3K4me1


title: MG_Male_12

status: Public on Nov 17 2013

city: Ann Arbor

first: Jung

last: Kim

state: MI

address: 1400 E. Medical Center Drive

institute: University of Michigan

description: CpG enriched DNA library

data_processing:
The raw sequencing image data obtained by Illumina GAIIx using 80 cycles of single ends were analyzed by the Illumina analysis pipeline.
Around 30 million reads per sample (ranging between 27 to 37 million reads) were obtained, and 12 bp-long adapter sequences were trimmed for each sample. Approximately 70% of these were mapped uniquely to the mouse mm9 reference genome using Burrows-Wheeler Aligner (BWA) tool.
We adopted a tiered-based profiling pipeline to identify regions of altered methylation (RAMs) by examining the locus-specific genome-wide methylation patterns associated with BPA exposure levels. We scanned the entire genome using a window size of 100bp with a 50bp moving shift, which accounts for over 53 million windows for each sample. The genomic regions containing at least 10 reads in 25% of the samples (~ 4 million windows) were then subjected to edgeR analysis, which we used to test for differences in each exposure group.
The edgeR analysis using R software was run using the glmFit function, which uses a negative binomial generated linear model, and identified the regions with differential methylation in three different comparisons; the methylation levels from the control group (n=4) against the 50 µg BPA/kg diet group (Ctr vs. UG, n = 4), control group against 50 mg BPA/kg diet group (Ctr vs. MG, n = 4), and 50 µg BPA/kg diet group against 50 mg BPA/kg diet group (UG vs. MG).
Using MACS chip-seq tool (v1.4.0), the wig type files are generated for visualization.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files generated from MACS peak tool showing methylation reads pileup

source_name: Mouse Liver

growth_protocol: Mice were obtained from a colony that has been maintained with sibling mating and forced heterozygosity for the viable yellow agouti (Avy) and non-agouti (a) alleles for over 220 generations, resulting in a genetically invariant background. Wild-type a/a dams were housed in polycarbonate-free cages with ad libitum access to diet and BPA-free water.

extract_protocol:
Total genomic DNA was isolated from liver tissue using buffer ATL, proteinase K, and RNase A (Qiagen Inc., Valencia, CA), followed by phenol-chloroform extraction and ethanol precipitation. DNA quality and concentration was assessed using a ND1000 spectrophotometer (NanoDrop Technology, Wilmington, DL).
MethylPlex library synthesis and GC-enrichment service was obtained through a commercial service at Rubicon Genomics Inc., Ann Arbor, MI.  Briefly, fifty nanograms of genomic DNA were digested with a proprietary cocktail of methylation-sensitive restriction enzymes and then amplified by PCR with universal primers to create a MethylPlex library that is enriched for methylated DNA.  MethylPlex DNA was then subjected to additional enzymatic treatment to deplete all non-GC-rich DNA sequences, purified and amplified in a second round of PCR. After purification, amplification adaptors were removed by a restriction enzyme digest, and the purified products were directly incorporated into the Illumina genomic DNA sequencing sample preparation kit procedure (Illumina Inc., San Diego, CA) at the end repair step, skipping the nebulization process.  An adenine base was then added to the purified end repaired products using Klenow exo (3’ to 5’ exo minus) enzyme.  The reaction product was purified, ligated to Illumina adaptors with DNA ligase and resolved on a 2% agarose gel.  Gel pieces were excised at 400 base pair positions, and the DNA was extracted using Qiagen gel extraction kit (Qiagen Inc., Valencia, CA).  The purified MethylPlex library was analyzed by Bioanalyzer (Agilent Technologies, San Diego, CA) before subjecting it to flow cell generation, where 10 nM of library was used to prepare flowcells with approximately 30,000 clusters per lane, with the sequencing performed by the  University of Michigan DNA Sequencing Core.

treatment_protocol: To avoid effects associated with parity, virgin wild-type a/a dams, 6 weeks of age, were randomly assigned to one of three phytoestrogen free AIN-93G diets (diet 95092 with 7% corn oil substituted for 7% soybean oil; Harlan Teklad, Madison, WI): 1) standard diet; 2) standard diet supplemented with 50 µg BPA/kg diet; or 3) standard diet supplemented with 50 mg BPA/kg diet. All diet ingredients were supplied by Harlan Teklad except BPA, which was supplied by NTP (National Toxicology Program, Durham NC). Wild-type a/a dams were provided with their respective diet two weeks prior to mating with 8-week-old Avy/a males and housed in polycarbonate-free cages with ad libitum access to diet and BPA-free water. The dams remained on the assigned diets throughout pregnancy and lactation, after which offspring were sacrificed at post-natal day 22 (PND22). For this study, liver DNA from a subset of a/a wild-type animals was analyzed for full methylome characteristics: 1) standard diet (Ctr, n = 4 offspring); 2) 50 µg BPA/kg diet (UG, n = 4 offspring); 3) 50 mg BPA/kg diet (MG, n = 4 offspring).

tag: levels of exposure

value: 50 mg BPA/kg

value: Male

tag: origin

value: liver tissue from post-natal day 22 mouse


title: MG_Female_10

description: CpG enriched DNA library

value: Female


title: UG_Male_8

description: CpG enriched DNA library

value: 50 ug BPA/kg


title: MG_Female_11

description: CpG enriched DNA library


title: CTR_Female_2

description: CpG enriched DNA library

value: control


title: CTR_Male_3

description: CpG enriched DNA library


title: CTR_Male_4

description: CpG enriched DNA library


title: UG_Male_7

description: CpG enriched DNA library


title: UG_Female_6

description: CpG enriched DNA library


title: CTR_Female_1

description: CpG enriched DNA library


title: UG_Female_5

description: CpG enriched DNA library


title: Runx3_IL2CD8+ T_CHIP_NIS1

description: first IP experiment of NIS

value: Splenic CD8+ T cells


title: Bcells_18hEstradiol_ChIPseq_Cebpa

city: Houston

first: Bruno

last: Di Stefano

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: Sample 2

data_processing:
Basecalls: Images obtained from high throughput sequencing were processed using the Illumina pipeline to generate raw sequence files
Reads alignement: performed with bowtie v2.1.0 (option: -–very-sensitive, other default), on mm9
Filtering: Reads were filter to keep only reads that map, with a quality score (from bowtie2) higher than 10 (samtools -F4 -q10), that map only a unique position (removing reads with tag "XS:i:", using grep -v) and remove duplicates that match the same position (samtools rmdup)
Peak calling: performed with HOMER v4.3 (option: -style factor, other default), using Bcell untreated as control dataset
Genome_build: mm9
Supplementary_files_format_and_content: BED file (chromosome, start, strand, name, score, strand=+)

source_name: primary Bcell after 18h treatment of estradiol

growth_protocol: ESCs and iPSCs were cultured on mitomycin C treated MEF feeder cells in KO-DMEM (Invitrogen) supplemented withL-glutamine, penicillin/streptomycin, nonessential amino acids, β-mercaptoethanol, 1,000 U/ml LIF (ESC medium) and 15% fetal bovine serum (FBS, Invitrogen). MEF cultures were established by trypsin digestion of mouse embryos (embryonic day 13.5) and the resulting cells cultured in DMEM supplemented with 10% FBS, L-glutamine and penicillin/streptomycin. CD19+ pro-B and pre-B cells were isolated from bone marrow using monoclonal antibodies to CD19 (1D3), obtained from BD Pharmingen, using MACS (Miltenyi Biotech). After isolation B cells were grown in RPMI medium supplemented with 10% FBS and IL-7. cell reprogramming experiments were conducted in gelatinized plates seeded with a feeder layer of the OP9 stromal cell line, using ESC medium supplemented with 2μg/ml of doxycycline and 15% FBS. For the reprogramming of B cells, IL-4 (10ng/ml), IL-7 (10ng/ml) and IL-15 (2ng/ml) were added to the medium.

extract_protocol:
ChIP experiments were performed as described previously (van Oevelen et al, 2008, PMID:20956564).
DNA libraries of C/EBPa enriched chromatin fragments were prepared using Illumina's reagents and instructions.

treatment_protocol: Cells were trypsinized and FACS-sorted to remove feeder and dead cells

value: primary B cells

tag: treatment

value: Estradiol for 18h

value: anti-Cebpa (Santa Cruz, catalog:sc-61, lot:k1009)


title: Bcells_untreated_ChIPseq_Cebpa

description: Sample 1

source_name: primary Bcells untreated

value: untreated


title: Bcells_untreated_RNAseq

description: Sample 1

data_processing:
Basecalls: performed with Illumina's CASAVA-1.8.2 software
Reads alignement: performed with STAR v2.3.0.1 (option: outFilterMismatchNmax 2, outFilterMultimapNmax 1)
Reads counting: performed with Htseq count (option: mode union, stranded, features exons, attribute gene_id) on Refseq mm9 annotation
Filtering: genes for which no reads were counted in both conditions were removed before normalisation
Normalization: performed with Deseq (option: method blind, sharingMode fit-only, fitType local)
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated file. Col1=gene Name; Col2=normalized reads count

extract_protocol:
RNA isolation was done with the miRNeasy Mini kit
Libraries was prepared with the Truseq stranded mRNA protocol, with an insert size of 200 to 400bp.


title: Bcells_18hEstradiol_RNAseq

description: Sample 2


title: P18

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.7 with default parameters. All 36-bp-long reads were mapped to the reference human genome sequence, hg18, using Illumina’s ELAND aligner with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser
Genome_build: hg18
Supplementary_files_format_and_content: wiggle track raw reads counts (bigWig files) and peak files (*wgl.bed files)

growth_protocol: OCI-Ly7 were grown in medium containing 90% Iscove’s (Cellgro, Manassas, VA), 10% fetal bovine serum (Gemini, Irvine,CA), and 1% penicillin/streptomycin (Invitrogen, Carlsbad, CA)

extract_protocol:
ChIP protocol: OCI-Ly7 cells were fixed with 1% formaldehyde, lysed and sonicated to generate fragments less than 500bp. Sonicated lysates were incubated with antibodies overnight and after increasing stringency washes immunocomplexes were recovered and DNA was isolated.
Genomic DNA-fragment libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions (Illumina, CA). Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs into phosphorylated blunt ends with the use of T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. Illumina single-end adapters were ligated to the ends of the DNA fragments. Ligation products were purified on a 2% agarose gel with a size selection of 200-300bp. Fifteen PCR cycles were performed with Illumina genomic DNA primers that anneal to the ends of the adapters. The purified PCR-amplified fragment libraries were quantified with the use of the PicoGreen dsDNA Quantitation Assay with the Qubit Fluorometer (Invitrogen, CA). The size range of libraries was validated on the Agilent Technologies 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent, CA).

value: OCI-Ly7 lymphoma cells

value: P18 (MAFK)

tag: chip antibody host/amount

value: Rabbit poly/5ug

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: Runx3_NK_CHIP_Runx3_IP

description: first IP experiment of Runx3

value: Splenic NK cells

value: ICR

tag: chip antibody

value: Runx3 poly clonal home made


title: MG_Female_9

description: CpG enriched DNA library

value: 50 mg BPA/kg


title: Ctrl_H3K27me3

status: Public on Nov 16 2013

first: Alexandre

last: Reymond

address: Dorigny

department: CIG

institute: UNIL

data_processing:
alignment: Sequence reads were obtained and mapped to the human genome hg19 using Bowtie version 0.12.6; reads  with two or fewer mismatches were retained. Only a single tag was retained from identical sequences.
regions: The identification of ChIP-enriched regions was performed using SICER version 1.1 with two libraries (SICER-df-rb.sh) and the following parameters: window size 200bp, gap size 400bp, for H4K20me1 and gap size 600bp for H3K27me3, and E-value 100.

source_name: EBV transformed mononuclear cells from perypherial blood

growth_protocol: Lymphoblastoid cell lines were grown in RPMI1640 medium suplemented with 10% FCS and 1% PS

extract_protocol: Cross-linking was performed by adding 0.5% formaldehyde directly to the growth medium and incubating 5 minutes in room temperature. Cells were lysed in lysis buffer (1% SDS, 50mM Tris-HCl pH 8.1, 10mM EDTA) and the chromatin was sheared using Bioruptor (Diagenode) ? 45 minutes, medium power settings, 30? on ? 30? off cycles. Chromatin was diluted 10 fold in ChIP dilution buffer (0.01% SDS, 1.1% Triton X100, 1.2mM EDTA, 16.7mM Tris-HCl pH 8.1, 167mM NaCl) and subsequently immuno-precipitated. 1 million cells were used per ChIP. The histone-antibody complexes were collected using magnetic beads (Invitrogen). Next, beads were washed 2 times with dialysis buffer

value: Lymphoblastoid cells

tag: cell line id

value: H3K27me3 [Millipore 07-449]


title: WBRdupS_H3K27me3

extract_protocol: Cross-linking was performed by adding 0.5% formaldehyde directly to the growth medium and incubating 5 minutes in room temperature. Cells were lysed in lysis buffer (1% SDS, 50mM Tris-HCl pH 8.1, 10mM EDTA) and the chromatin was sheared using Bioruptor (Diagenode) ? 45 minutes, medium power settings, 30? on ? 30? off cycles. Chromatin was diluted 10 fold in ChIP dilution buffer (0.01% SDS, 1.1% Triton X100, 1.2mM EDTA, 16.7mM Tris-HCl pH 8.1, 167mM NaCl) and subsequently immuno-precipitated. 1 million cells were used per ChIP. The histone-antibody complexes were collected using magnetic beads (Invitrogen). Next, beads were washed 2 times with dialysis buffer (2mM EDTA, 50mM Tris-HCl pH 8.0, 0.2% sarcosyl) and 4 times with wash buffer (100mM Tris-HCl pH 9.0, 500mM LiCl, 1% NP40, 1% sodium deoxycholate). DNA was eluted and than purified using DNA purification kit (Qiagen). Concentration was measured with Qubit (Invitrogen) and 10ng of each sample was used for library preparation. Libraries were prepared according to Illumina's protocol and were sequenced with Illumina GAIIx (two lanes per library)

value: AUBLA


title: DGS_H3K27me3


title: SMS_H3K27me3


title: WBS_H4K20me1

value: H4K20me1 [Abcam ab9051]


title: WBRdupS_H4K20me1


title: DGS_H4K20me1


title: wt_hsc_l4 RNA-Seq

first: Margaret

last: Goodell

address: One Baylor Plaza, N1030

description: technical replicate of biological replicate 1

data_processing:
RUM to make alignments; Customized script to count fragments on gene; DESEQ to do differential expression test;
Genome_build: mm9
Supplementary_files_format_and_content: Tab separated text file for gene's count and fpkm for each sample; TXT file for two sample comparison testing if a gene is differentially expressed;

source_name: wild type Hematopoietic Stem Cells

growth_protocol: Freshly sorted wild type and Dnmt3a-KO mouse HSCs (SP-KSL-CD150+)

extract_protocol:
Extract RNA using Qiagen Rneasy Micro kit.
Tru-Seq RNA sample prep kit

treatment_protocol: PolyA selection

tag: strain

tag: genotype/variation

value: wild type

value: Murine bone marrow derived primary HSCs

tag: cell surface marker


title: wt_hsc_l3 RNA-Seq


title: wt_hsc_l2 RNA-Seq


title: wt_hsc_l1 RNA-Seq


title: m12_b1 Bisulfite-Seq

data_processing:
use moabs to process bisulfite treated data
Genome_build: mm9
Supplementary_files_format_and_content: text; chromosome, start, end, methylation ratio, total reads, methylated reads, strand, next nucletide of cytosine, plus_strand, total reads from plus strand, methylated reads from plus strand, minus strand, total reads from minus strand, methylated reads from minus strand

source_name: 12 month Hematopoietic Stem Cells

growth_protocol: Freshly sorted 12 month wild type (Mx1-cre-;Dnmt3afl/fl) and knockout (Mx1-cre+;Dnmt3a-/-) mouse HSCs (SP-KSL-CD150+)

extract_protocol:
Extract genomic DNA using Invitrogen PureLink Genomic DNA kits
Tru-Seq DNA sample prep kit

treatment_protocol: Adapter-ligated fragments were treated with sodium bisulfite (Qiagen)


title: m12_b3 Bisulfite-Seq

description: technical replicate of biological replicate 2


title: m12_b2l4 Bisulfite-Seq


title: m12_b2l2 Bisulfite-Seq


title: m12_b2l1 Bisulfite-Seq


title: m12_b2l3 Bisulfite-Seq


title: m12_b4l1 Bisulfite-Seq


title: m12_b4l2 Bisulfite-Seq


title: WBS_H3K27me3


title: ko3a_b1 Bisulfite-Seq

source_name: Dnmt3a knockout Hematopoietic Stem Cells


title: ko3a_b2l2 Bisulfite-Seq


title: ko3a_b2l4 Bisulfite-Seq


title: ko3a_b5 Bisulfite-Seq


title: ko3a_b2l3 Bisulfite-Seq


title: ko3a_b2l1 Bisulfite-Seq


title: Ctrl_H4K20me1


title: ko3a_b7l1 Bisulfite-Seq


title: SMS_H4K20me1


title: MDA-MB-LM2

status: Public on Nov 15 2013

city: New York

first: Dingcheng

last: Gao

state: NY

address: 1300 York Ave

department: CT Surgery

institute: Weill Cornell Medical College

description: miRNA-seq

data_processing:
Delete linker sequence using in-house perl script
Match with miRNA database using in-house perl script
Data normalization using in-house perl script
fold calculation (MDA/MCF7)

source_name: Breast

extract_protocol:
Trizol extraction
Illumina library kit

tag: cell line

value: human breast cancer cell line


title: MCF7

description: miRNA-seq


title: MCF10A

description: miRNA-seq


title: MDA-MB-231

description: miRNA-seq


title: pol2ser5p_30_illumina

city: Austin

first: Vishy

last: Iyer

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the sacCer3 genome assembly using BWA (Version: 0.5.9-r16) with default options
Non-uniquely mapped reads were filtered out in order to remove the reads with low mapping quality
Reads that mapped onto rRNA were filtered out
Genome_build: sacCer3
Supplementary_files_format_and_content: Wig format

organism: Saccharomyces cerevisiae

source_name: Wild type yeast cells

growth_protocol: Normal growth conditions were 30°C in YPD media with shaking at 250 rpm. Yeast cells were grown to mid-log phase (O.D 600 nm of 0.6 to 0.8), and fixed with formaldehyde. For heat shock, mid-log phase yeast cells were collected and re-suspended in pre-warmed 39°C YPD media, then incubated for 15 min at 39°C.

extract_protocol:
Cross-linked chromatins were sheared using a sonicator, and immunoprecipitated using the following beads or anti-body: IgG Sepharose 6 Fast Flow (GE Healthcare Life Sciences) to pull-down all TAP-tagged proteins used in this study, anti-Myc conjugated agarose bead (Sigma Aldrich, cat.# E6654) to pull-down Swi6 in the SWI6-13XMyc strains, and RNAPII Ser5P antibody (Abcam, cat.# ab5131) to pull-down active RNAPII. Mock ChIP DNA was prepared by immunoprecipitation with IgG Sepharose in the wild type strain with no TAP-tagged protein expression. Input DNA was prepared in parallel with the SWI6-TAP ChIP sample but leaving out the immunoprecipitation step.
The NEB ChIP-seq library preparation for Illumina (New England BioLabs) and the SOLiD V3 barcoded fragment library preparation protocol (Applied Biosystems) were used to sequence the samples using Illumina HiSeq 2000 and SOLiD V4, respectively

treatment_protocol: For rapamycin treatment, either DMSO or rapamycin was added to mid-log phase yeast cells and incubated for 30 min at 30°C. Since DMSO is a solvent for rapamycin, control and rapamycin-added cells were treated with DMSO and rapamycin to be a final concentration of 0.1% and 100 nM, respectively

value: RNAPII Ser5P antibody

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #

value: Wild type yeast cells

tag: temperature


title: pol2ser5p_rap_illumina

value: rapamycin


title: pol2ser5p_DMSO_illumina

value: DMSO


title: hsf1_39_illumina

source_name: HSF1 TAP-tagged yeast cells

value: IgG

value: GE Healthcare Life Sciences

value: HSF1 TAP-tagged yeast cells


title: ko3a_b7l2 Bisulfite-Seq


title: tup1_rap_illumina

source_name: TUP1 TAP-tagged yeast cells

value: TUP1 TAP-tagged yeast cells


title: hsf1_30_illumina


title: rsc2_DMSO_illumina

source_name: RSC2 TAP-tagged yeast cells

value: RSC2 TAP-tagged yeast cells


title: rsc2_rap_illumina2


title: swi6_39_illumina

source_name: SWI6 TAP-tagged yeast cells

value: SWI6 TAP-tagged yeast cells


title: rsc2_rap_illumina


title: tup1_DMSO_illumina


title: mock_39_illumina


title: swi6_DMSO_illumina


title: swi6_30_illumina


title: rsc2_DMSO_illumina2


title: input_DMSO_illumina

value: input DNA


title: mnn10_DMSO_solid

source_name: MNN10 TAP-tagged yeast cells

value: MNN10 TAP-tagged yeast cells


title: tup1_rap_solid


title: mock_DMSO_illumina


title: tup1_DMSO_solid


title: Ptf1aCre;Kras,Brg1-/- s.c. PDA

status: Public on Nov 14 2013

city: San Francisco

first: Nilotpal

last: Roy

address: 513 Parnassus Ave.

department: Diabetes Center

data_processing:
RTA 1.12.4 and CASAVA 1.7
Sequenced reads were trimmed by 5bp to account for low qualities and mapped to mm9 whole genome using tophat v1.3.1
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a Samtools v0.1.13 and a mm9 gene annotation. All isoforms of a gene were combined for a per gene read count.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: subcutaneous PDA

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed on a RNA bioanalyser.

value: mixed background

tag: genotype

value: subcutaneous pancreatic ductal adenocarcinoma


title: mock_DMSO_solid

tag: cell type


title: Ptf1a;Kras;p53+/- s.c. PDA


title: pol2ser5p_39_illumina


title: Spike_infected_stage 3 (2011S3)

city: Wuhan

first: Chao

middle: Jin

last: Quan

state: Hubei

address: Bayi Road,Wuchang

department: College of Life Sciences

institute: Wuhan University

data_processing:
Illumina BCL Converter(BclConverter-1.9.0-11-03-08)software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference database (merged by integrating indica rice genome into japonica rice full-length cDNAs from the KOME with 95% threshold value) using SOAPaligner/soap2 V2.21t with parameters -m 0 -x 1000 -s 28 -l 32 -v 2 -r 2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Poisson distribution model was used to identify differentially expressed genes between  two samples(Referring to "The significance of digital gene expression profiles" from Audic S. et al.).In short, denote the number of unambiguous clean tags from gene A as x, given every gene's expression occupies only a small part of the library, p(x) will closely  follow the Poisson distribution.
Expression pattern analysis of differentially expressed genes using Cluster with parameters -g 7 -e 7 -m a
Reference sequence then mapped to NR( from NCBI) using Blast v2.2.23 with parameters -p blastx -e 1e-5 -m 7, then mapped to GeneOntology  using BLAST2GO v2.3.5 - 16.03.2009. And then, mapped to KEGG PATHWAY database using Blast v2.2.23 with parameters -o blastx -e 1e-5 -m 8.
Using hypergeometric test to find significantly enriched GO terms in differentially expressed genes comparing to the genome background.
Pathway enrichment analysis identifies significantly enriched metabolic pathways or signal transduction pathways in differentially expressed genes comparing with the whole genome background using hypergeometric test.
Genome_build: Reference database was merged by integrating indica rice genome into japonica rice full-length cDNAs from the KOME with 95% threshold value
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa Indica Group

source_name: the booting rice panicle

growth_protocol: Rice cultivar 9311 was grown in a glasshouse with an air temperature range of 28-31℃ and above 80% humidity under natural daylight at booting stage.

extract_protocol: Total RNA was extracted from frozen samples using standard protocols (Trizol) and then treated with DNase to remove potential genomic DNA contamination according to the manufactures’s protocols. Sample quality and concentration were evaluated using Qubit fluorometer (Invitrogen, CA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA). mRNA was isolated from total RNA by binding the mRNA to a magnetic oligo（dT）bead, and break down it about 200nt by adding fragmentation buffer. Then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via Illumina HiSeq™ 2000.

treatment_protocol: At booting stage, each panicle was injected 2 ml 10^6/ml spore suspension ( 10^6/ml ) at 4:00-6:00, PM. Control was injiected with water. Each infected and control stages spikes were collected at 6 dpi.

tag: cultivar

tag: tissue

value: spike

tag: disease stage

value: stage 3

tag: infection

value: Ustilaginoidea virens


title: Spike_infected_stage 2 (2011S2)

value: stage 2


title: Spike_control (2011CK)

value: control


title: Spike infected stage 2

data_processing: Alignment: Sequence reads were obtained and mapped to the refence database (merged by integrating indica rice genome into japonica rice full-length cDNAs from the KOME with 95% threshold value) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.

source_name: Spike infected stage 2

growth_protocol: Rice cultivar 9311 was grown  in a glasshouse with an air temperature range of 28-31â and above 80% humidity under natural daylight at booting stage.

extract_protocol: Total RNA was extracted from frozen samples using standard protocols (Trizol) and then treated with DNase to remove potential genomic DNA contamination according to the manufacturesâs protocols. Sample quality and concentration were evaluated using Qubit fluorometer (Invitrogen, CA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA). mRNA was isolated from total RNA by binding the mRNA to a magnetic oligoï¼dTï¼bead, and break down it about 200nt by adding fragmentation buffer. Then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via Illumina HiSeqâ¢ 2000.

value: Oryza sativa indica


title: Spike infected stage 1

source_name: Spike infected stage 1

value: stage 1


title: Spike_infected_stage 1 (2011S1)


title: Spike control

source_name: Spike control

value: uninfected


title: Bxa26_CpG_stimulated

status: Public on Nov 13 2013

city: Edinburgh

first: Musa

last: Hassan

state: Scotland

address: Easter Bush

department: Roslin

country: United Kingdom

institute: University of Edinburgh

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were mapped to mm9 whole genome using Tophat 2.0.4 with the following parameters --min-anchor-length 4  --splice-mismatches 0 --min-intron-length 50 --max-intron-length 1000000   --no-novel-juncs --no-novel-indels --library-type fr-unstranded
Gene expression was calculated as Fragments per Kilobase of modeled exon per Million mapped reads (FPKM) using Cufflinks v2.0.0.
Genome_build: mm9
Supplementary_files_format_and_content: excel files include FPKM values for each Sample

source_name: BMDM

growth_protocol: Bone marrow cells were cultured in cell culture medium conditioned with 20% L929 for 7 days before havensting and freezing in liquid nitrogen until use. Cell were pre-plated in the same L929 conditioned medium overnight prior to stimulation or infection.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Total RNA (Qiagen RNeasy Plus kit) was isolated from the non-stimulated cells (plated overnight), stimulated and infected cells and the integrity, size, and concentration of RNA checked (Agilent 2100 Bioanalyser). The mRNA was then purified by polyA-tail enrichment (Dynabeads mRNA Purification Kit; Invitrogen), fragmented into 200╨400 base-pair, and reverse transcribed into cDNA before Illumina sequencing adapters were added to each end. Libraries were barcoded, multiplexed into 4 samples per sequencing lane in the Illumina HiSeq 2000

treatment_protocol: BMDMs were left unstimulated, stimulated with IFN/TNF, or CpG for 18 hrs or infected for 8 hrs.

value: BMDM

tag: age

value: 10 weeks

value: wild type

tag: treatment

value: stimulated with CpG for 18 hrs


title: Spike infected stage 3

source_name: Spike infected stage 3


title: mock_30_illumina

tag: chip antibody

value: IgG

value: GE Healthcare Life Sciences

value: Wild type yeast cells


title: Bxa24_CpG_stimulated


title: Bxa25_CpG_stimulated


title: Bxa14_CpG_stimulated


title: Bxa12_CpG_stimulated


title: Bxa13_CpG_stimulated


title: Bxa8_CpG_stimulated


title: Bxa11_CpG_stimulated


title: Bxa2_CpG_stimulated


title: Axb24_CpG_stimulated


title: Bxa4_CpG_stimulated


title: Tel Bulge_Nfatc1_ChIPSeq

first: Brice

last: Keyes

address: 1230 York Ave, Box 300

institute: The Rockefeller University

description: Chromatin IP against Nfatc1

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9, build 37) using the Bowtie program (Version 0.1.2.7). Unique reads mapped to a single genomic location (allowing two mismatches) were kept for peak identification.
Peak detection was performed with the software SPP (Version 1.7).
wig files created using IGVtools with 25bp windows with 200 bp extension to reads.
Genome_build: mm9
Supplementary_files_format_and_content: wig files; enrichment values in 25bp windows

source_name: Mouse back skins

growth_protocol: HFSCs were FACS-purifed from the telogen back skins of indicated ages of mice

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 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 25 cycles and library fragments of 150-300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No treatment

value: Telogen quiescent hair follicle stem cells

tag: Sex

value: Female

tag: sorting markers

value: integrin α6 and CD34

value: NFATc1 (Abcam, ab2796)


title: Axb19_CpG_stimulated

tag: strain


title: Axb13_CpG_stimulated


title: Axb15_CpG_stimulated


title: Axb12_CpG_stimulated


title: Axb10_CpG_stimulated


title: Axb8_CpG_stimulated


title: Axb6_CpG_stimulated


title: Axb4_CpG_stimulated


title: Axb5_CpG_stimulated


title: B6_CpG_stimulated


title: Bxa7_CpG_stimulated


title: Bxa26_Infected

value: infected with type II (Pru A7) for 8 hrs


title: Bxa25_Infected


title: AJ_CpG_stimulated

value: AJ


title: Bxa14_Infected


title: Bxa24_Infected


title: Bxa16_Infected


title: Axb23_CpG_stimulated


title: Bxa13_Infected


title: Bxa7_Infected


title: Bxa11_Infected


title: Bxa8_Infected


title: Bxa2_Infected


title: Bxa1_Infected


title: Axb19_Infected


title: Axb2_CpG_stimulated


title: Axb23_Infected


title: Axb1_CpG_stimulated


title: Axb15_Infected


title: Axb12_Infected


title: Axb13_Infected


title: Bxa1_CpG_stimulated


title: Axb10_Infected


title: Axb5_Infected


title: Axb6_Infected


title: Axb4_Infected


title: Bxa12_Infected


title: Axb2_Infected


title: Bxa16_CpG_stimulated


title: B6_Infected


title: Axb1_Infected


title: Bxa4_Infected


title: Bxa26_IFN/TNF_stimulated

value: stimulated with IFN/TNF


title: Bxa24_IFN/TNF_stimulated


title: Bxa25_IFN/TNF_stimulated


title: Bxa16_IFN/TNF_stimulated


title: Bxa13_IFN/TNF_stimulated


title: Bxa12_IFN/TNF_stimulated


title: AJ_Infected


title: Axb24_Infected


title: Bxa7_IFN/TNF_stimulated


title: Bxa2_IFN/TNF_stimulated


title: Bxa14_IFN/TNF_stimulated


title: Axb24_IFN/TNF_stimulated


title: Bxa4_IFN/TNF_stimulated


title: Bxa8_IFN/TNF_stimulated


title: Axb23_IFN/TNF_stimulated


title: Axb19_IFN/TNF_stimulated


title: Bxa1_IFN/TNF_stimulated


title: Axb13_IFN/TNF_stimulated


title: Axb12_IFN/TNF_stimulated


title: Axb10_IFN/TNF_stimulated


title: Axb15_IFN/TNF_stimulated


title: Axb6_IFN/TNF_stimulated


title: Axb4_IFN/TNF_stimulated


title: Axb2_IFN/TNF_stimulated


title: Axb5_IFN/TNF_stimulated


title: Axb1_IFN/TNF_stimulated


title: Bxa11_IFN/TNF_stimulated


title: Bxa26_Non_Stimulated


title: Bxa25_Non_Stimulated


title: AJ_IFN/TNF_stimulated


title: Bxa14_Non_Stimulated


title: Bxa16_Non_Stimulated


title: Bxa13_Non_Stimulated


title: Bxa8_Non_Stimulated


title: Bxa11_Non_Stimulated


title: Bxa7_Non_Stimulated


title: Axb24_Non_Stimulated


title: Bxa2_Non_Stimulated


title: Axb19_Non_Stimulated


title: Axb8_IFN/TNF_stimulated


title: Axb15_Non_Stimulated


title: Axb23_Non_Stimulated


title: Axb12_Non_Stimulated


title: Bxa1_Non_Stimulated


title: Axb10_Non_Stimulated


title: Axb6_Non_Stimulated


title: Axb13_Non_Stimulated


title: Axb5_Non_Stimulated


title: Axb8_Non_Stimulated


title: Axb4_Non_Stimulated


title: Axb1_Non_Stimulated


title: Bxa24_Non_Stimulated


title: B6_IFN/TNF_stimulated


title: AJ_Non_Stimulated


title: Bxa12_Non_Stimulated


title: Axb2_Non_Stimulated


title: B6_Non_Stimulated