title: Mrk-0 (6937)


title: LI-OF-065 (630)

status: Public on Jul 14 2016

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Methylated cytosine calls were made using the pipeline described in Lister et al. Human DNA methylomes at base resolution show widespread epigenomic differences. 2009. Nature
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab separated file of methylated cytosine positions

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations.
Approximately one to three micrograms of genomic DNA was sonicated to ~100 bp using the Covaris S2 System using the following parameters: cycle number = 6, duty cycle = 20%, intensity = 5, cycles/burst = 200 and time = 60 seconds. Sonicated DNA was purified using Qiagen DNeasy minielute columns (Qiagen). Each sequencing library was constructed similar to genomic DNA libraries except the ligation was performed with methylated adapters provided by Illumina. Ligation products were purified with AMPure XP beads (Beckman) at a ratio of 1.8X of beads to sample. Up to 450 ng of ligated DNA was bisulfite treated using the MethylCode Kit (Invitrogen, Carlsbad, CA) following the manufacturer’s guidelines and then PCR amplified using Pfu Cx Turbo (Agilent, Santa Clara, CA) using the following PCR conditions (2 minutes at 95C, 4 cycles of 15 seconds at 98C, 30 seconds at 60C, 4 minutes at 72C and 10 minutes at 72C).

tag: cultivar

tag: ecotype id

tag: tissue

value: leaf


title: ZdrI 2-9 (6434)

value: ZdrI 2-9


title: TDr-18 (6203)


title: TOM 07 (6241)

value: TOM 07


title: TFA 08 (6218)

value: TFA 08


title: TDr-9 (6195)


title: TDr-16 (6201)


title: TAA 14 (6163)

value: TAA 14


title: T960 (6148)


title: TAA 17 (6166)

value: TAA 17


title: TDr-13 (6198)


title: TAD 01 (6169)

value: TAD 01


title: TAL 03 (6177)

value: TAL 03


title: TAD 06 (6174)

value: TAD 06


title: T880 (6140)


title: T930 (6145)


title: TGR 01 (6220)

value: TGR 01


title: T860 (6138)


title: Kz-13 (6830)


title: TV-22 (6268)


title: T800 (6133)


title: T850 (6137)


title: Sr:3 (6086)


title: T470 (6107)


title: T530 (6111)


title: T1090 (6099)


title: T460 (6106)


title: T480 (6108)


title: OMo1-7 (6073)


title: TAD 03 (6171)

value: TAD 03


title: Gro-3 (6025)


title: Nyl-2 (6064)


title: Fja1-2 (6019)


title: TAA 04 (6154)

value: TAA 04


title: Lis-3 (6041)


title: Hov3-5 (6038)


title: Eden-1 (6009)


title: Hov1-10 (6035)


title: Fly2-2 (6024)


title: DraIV 3-7 (5921)

value: DraIV 3-7


title: DraIV 2-9 (5907)

value: DraIV 2-9


title: Fja1-5 (6020)


title: DraIV 1-11 (5893)

value: DraIV 1-11


title: Eds-9 (6017)


title: DraIV 5-12 (5950)

value: DraIV 5-12


title: DraIV 6-13 (5984)

value: DraIV 6-13


title: Dra-3 (5860)

value: leaf


title: UKID96 (5800)


title: Set-1 (5772)


title: Cnt-1 (5726)


title: Mc-1 (5757)


title: DraIV 6-22 (5993)

value: DraIV 6-22


title: Bor-1 (5837)


title: Bra-1 (5717)


title: UKNW06-481 (5644)


title: UKNW06-003 (5353)


title: UKSE06-533 (5276)


title: UKSE06-432 (5210)


title: UKSE06-470 (5236)


title: UKSE06-639 (5349)


title: UKSE06-491 (5249)


title: DraIV 1-8 (5890)

value: DraIV 1-8


title: UKSE06-252 (5104)


title: UKSE06-325 (5151)


title: BRR60 (506)


title: UKSE06-118 (5023)


title: UKSW06-360 (4958)


title: UKSW06-333 (4931)


title: Doubravnik7 (410)


title: Zdarec3 (403)


title: UKSW06-207 (4807)


title: UKSW06-285 (4884)


title: UKNW06-403 (5577)


title: TOU-A1-89 (351)


title: Ste-40 (2317)


title: PYL-6 (265)


title: Sna-1 (5778)


title: SLSP-35 (2278)


title: MNF-Pin-39 (2016)


title: Pent-23 (2202)


title: MNF-Riv-21 (1890)


title: TOU-A1-88 (350)


title: Mdn-1 (1829)


title: MNF-Che-2 (1925)


title: MAR2-3 (159)


title: Ale-Stenar-64-24 (1002)


title: Brosarp-34-145 (1066)


title: MNF-Jac-12 (1954)


title: Aledal-6-49 (1158)


title: Tnz-1 (10024)


title: Bg-5 (10026)


title: Draha2 (424)


title: Uk-3 (10022)


title: Strand-1 (10023)


title: Hl-0 (10021)


title: Jl-2 (10020)


title: Petro-1 (10017)


title: Dobra-1 (10018)


title: Wiz.Female_Het2.E13.5Brain.RNAseq

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

country: Australia

institute: SAiGENCI

library_source: transcriptomic

data_processing:
For ChIP-seq, sequenced reads were provided by the sequencing service provider (Active Motif) in a .fastq.gz format. Reads were mapped to the mouse mm10 genome by the service provider, using the BWA program using default settings.
For ChIP-seq, peak calling was done by the service provider (Active Motif) using MACS2 (Version  2.1.0) by first filtering out duplicate reads then using default parameters and the following options -s 75 --bw 200 -m 10 30 –p 0.0000001. Peaks were considered significant if they had a p value of equal or less than 1E-20
For RNA-seq, sequenced reads were provided by the sequencing service provider (Australian Genome Research Facility) in a .fastq.gz format. Reads were mapped to the mouse mm10 genome using the program Tophat (version 2.0.11) with the following parameters: -I 100000 --library-type=fr-unstranded --read-edit-dist 3 --no-coverage-search --read-mismatches 3
For RNA-seq, read counts for gene exons were extracted using the program htseq-count (version 0.6.1) with the options -s no -m intersection-strict. Normalization and differnetial gene expression was assessed using the R-package DEseq, with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: For processed ChIP-seq data, Bigwig format files showing the mapped read density across the genome. For processed RNA-seq data, tab-delimited text files include raw read counts for each of the samples

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Brains were dissected from embryos into 1xPBS and flash frozen on dry ice, RNA was harvested using Trizol reagent. Libraries were constructed using the illumina TruSeq RNA Sample Preparation kit (cat Num RS-122-2201).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: FVB

value: Embryonic Whole Brain

tag: age

value: 13.5 days post coitum

tag: genotype

value: Wiz MommeD30/+


title: Ara-1 (10015)


title: Xan-1 (10014)


title: Wiz.Female_Het1.E13.5Brain.RNAseq


title: Wiz.Male_Het3.E13.5Brain.RNAseq


title: Wiz.Female_WT2.E13.5Brain.RNAseq

value: Wiz +/+


title: Wiz.Female_WT1.E13.5Brain.RNAseq


title: Rod-17-319 (1435)


title: Wiz.Male_WT3.E13.5Brain.RNAseq


title: Lerik1-3 (10013)


title: Wiz.Male_WT2.E13.5Brain.RNAseq


title: Yeg-1 (10011)


title: Wiz.Male_Het2.E13.5Brain.RNAseq


title: Wiz.Male_WT1.E13.5Brain.RNAseq


title: Sij-4 (10010)


title: Wiz.Male_Het1.E13.5Brain.RNAseq


title: Sij-2 (10009)


title: Wiz.Het2.Cerebellum.RNAseq

extract_protocol:
Cerebellum were removed from mice and flash frozen on dry ice, RNA was harvested using Trizol reagent. Libraries were constructed using the illumina TruSeq RNA Sample Preparation kit (cat Num RS-122-2201).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cerebellum

value: 56 days post partum


title: Wiz.Het1.Cerebellum.RNAseq


title: Wiz.WT3.Cerebellum.RNAseq


title: Del-10 (10016)


title: Kastel-1 (10006)


title: Bolin-1 (10004)


title: Wiz.WT2.Cerebellum.RNAseq


title: Wiz.WT1.Cerebellum.RNAseq


title: Gr-1 (430)


title: TueV-13 (10001)


title: TKS120 Thy-sonic Satb1-IVB-L smoothed-peaks

city: San Francisco

first: Hunter

last: Richards

address: 513 Parnassus Ave., HSW 863

department: Orofacial Sciences

institute: UCSF

description: 6XHis-tagged, full-length Satb1 protein

data_processing:
Raw ChIP-seq data was aligned to mouse genome release mm9 using bowtie v1.0.0 with the following parameters set: --chunkmbs 1024 --best --strata -n 3 -m 1
Candidate peaks were called using MACS (v1.4.3) using default settings.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: bigWig tracks of coverage profiles were generated using the wigToBigWig utility from UCSC. The bigWig track of MACS peaks was created using a custom Perl script.

source_name: purified DNA

growth_protocol: E14 cells were maintained in ES medium (knock-out DMEM, 20% fetal bovine serum, 55 µM mercaptoethanol, 1 mM sodium pyruvate, 2 mM glutamine, 0.1 mM nonessential amino acids, and 1000 U/ml mouse LIF), on tissue culture plates coated with 0.1% gelatin, in 6% CO2 at 37°C.

extract_protocol:
Cells for ChIP were crosslinked in 1% formaldehyde for 15 min at room temperature, followed by quenching of the formaldehyde in 0.125 M glycine for 5 min. After washing the cells with PBS, they were scraped in cell lysis buffer (4% SDS, 50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 100 mM NaCl, 1 mM PMSF) containing protease inhibitor (Roche). The cell lysate was incubated for 30 min at room temperature, and the crude extract was loaded on top of 8 M urea followed by ultracentrifugation overnight. The pure chromatin pellets were collected in dialysis buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 0.5 mM EGTA, 5% glycerol 0.1% Triton X-100), and dialyzed for 16 hrs at 4°C. Chromatin recovered from dialysis was fragmented to 300–800 bp by restriction enzyme digestion followed by sonication in a Bioruptor (Diagenode, high power, 30 sec on and 30 sec off for 15 cycles) in sonication buffer (0.1% SDS and 0.1% DOC in dialysis buffer). To separate insoluble components, we centrifuged the samples at 13,000 rpm for 5 min at 4°C and recovered the supernatant and pellet separately. The pellets were dissolved in sonication buffer, sonicated again for 15 cycles in a Bioruptor on high power, and centrifuged at 13,000 rpm for 10 min at 4°C. The supernatant was combined with the previous one, and a reverse-crosslinked aliquot was examined for chromatin shearing efficiency on a Bioanalyzer 2100 (Agilent Technologies Inc.). Reverse crosslinking of chromatin was done at 55°C overnight in buffer containing 1% SDS, 200 mM NaCl, 10 mM EDTA and 200 µg/ml proteinase K followed by incubation with 100 µg/ml RNase A at 37°C for 1 hr. DNA was recovered by using QIAquick PCR purification kit (Qiagen).
DNA from ChIP and input chromatin fractions were sheared to an average size of approximately 300 bp using a Bioruptor UCD-200 (Diagenode) and verified on a Bioanalyzer 2100 (Agilent). For each ChIP-seq experiment, we used a custom library construction protocol. Briefly per library, ChIP DNA fragments were end-repaired and ligated to indexed sequencing adapters and amplified with 15 rounds of PCR. The amplified library was selected for fragments over 200 bp in length using Agencourt AMPureXP or SPRI beads.

tag: cell type

value: thymocytes

tag: genotype/variation

tag: passage/age

value: 2 week old mouse

tag: chip antibody

value: (in vitro pulldown, w/ Ni-NTA beads)


title: m39 total RNA

city: Pittsburgh

first: Miler

middle: T

last: Lee

state: PA

address: 4249 Fifth Ave.

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
Base calls were performed using Illumina Pipeline 1.3.
Sequencing reads were aligned non-strand specifically to the zebrafish GRCz10 genome using Tophat v2.0.13 with Bowtie v2.2.3.0, guided by splice junctions defined by cDNA-to-genomic alignments from NCBI Release 104.
Transcriptional units were defined separately for each sample using Cufflinks v2.2.1, and the resulting transcript GTF files were combined between samples (WT and m39) and reconciled with NCBI gene annotations using cuffmerge.
Read counts per gene for each sample were calculated using the Bedtools v2.21.0 intersect command between the alignment BAM file and the exons defined above.  Only reads with a MAPQ score > 0 aligning at least 5 nt of an exon were counted.
Genome_build: GRCz10
Supplementary_files_format_and_content: Reads-per-million (RPM) counts tables for gene units defined by Cufflinks (one for polyA, one for total RNA); GTF files of gene units generated by Cufflinks (one for polyA, one for total RNA)

molecule: total RNA

organism: Danio rerio

source_name: Whole embryos_m39_total_RNA

growth_protocol: Embryos were raised according to standard protocols at 28°C and in egg water

extract_protocol:
RNA was extracted using Trizol Reagent on whole embryos
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AB

tag: Stage

value: 90% epiboly to Tailbud

value: whole embryo


title: TKS185 E14-shTip5 H3K27ac coverage

source_name: Tip5-knockdown E14 cells

value: mouse embryonic cell line E14

value: passage 3 post-transfection

value: H3K27ac (AbCam, ab4729)


title: TKS120 Thy-sonic input coverage


title: WT total RNA

source_name: Whole embryos_WT_total_RNA

value: wildtype


title: TKS185 E14-shTip5 Jarid2 coverage

value: Jarid2 (AbCam, ab48137)


title: TKS161 E14-shTip5 H3K27me3 coverage

value: H3K27me3 (Millipore, 07-449)


title: TKS185 E14-shTip5 input coverage


title: Wiz.Het3.Cerebellum.RNAseq

value: FVB


title: TKS161 E14-shTip5 Suz12 coverage

value: Suz12 (Millipore, 17-661)


title: m39 poly(A)+

source_name: Whole embryos_m39_polyA+RNA


title: WT poly(A)+

source_name: Whole embryos_WT_polyA+RNA


title: TKS184 E14 H3K27ac coverage

source_name: wild-type E14 cells

value: wild type


title: TKS184 E14 Jarid2 coverage


title: A549_TMPyP4(2.0μM)-treated

city: Guangzhou

first: Yong

last: Zhao

state: Guangdong

address: No. 135, Xingang Xi Road

country: China

institute: Sun Yat-Sen University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were filtered those adaptor contaminated, unpaired, contains N , and  then mapped to hg19 whole genome using tophat 2.0.2 with default parameters
Reads count were calculated by htseq-count(Htseq Frame work v 0.6.0) with parameters  -s no
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell C, Nat. Biotechnol. 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragment 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.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample (each column represents sample's expression for genes showing abundance in all samples)

organism: Homo sapiens

source_name: human alveolar adenocarcinoma (A549) cells

extract_protocol:
Total RNA was extracted using the Trizol reagent (Takara). A total of 3 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using a NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturer’s recommendations.

tag: cell line

tag: gene treatment

tag: dose

tag: gene expression

value: stable cell line


title: TKS161 E14-shTip5 input coverage


title: TKS184 E14 H3K27me3 coverage


title: TKS169 E14 Suz12 coverage


title: TKS184 E14 input coverage


title: TKS169 E14 input coverage


title: Col-0 (6909)

data_processing:
Base calling was done by RTA version 1.17.20 and 1.18.61. Base call files (bcl) were converted by fastq by CASAVA version 1.8.2.
Sequenced reads were trimmed for adaptor sequence.  Read mapping and counting were performed by the rmake pipeline version 1.0c (http://physiology.med.cornell.edu/faculty/mason/lab/r-make/; Sheng Li, Nat Biot 2014).
Reads were mapped to TAIR10 genome assemly and TAIR10 gene models using the STAR aligner version 2.4.2a with parameters "--runThreadN 11 --outFilterMultimapNmax 1 --readFilesCommand zcat --outSAMunmapped Within --outStd SAM".  STAR index were generated from TAIR10 genome sequences and TAIR10 gene model GTF file and paramter "--ajdbOverhang 99".  Only read1 of the PE reads from HiSeq 4000 were mapped.
Read counts on genes for individual accessions were quantified by the count program in rmake.
To generate the gene by accession expression matrix (supplementary file), raw read counts were first quantile-normalized, then normalized by the RUVg functon in the R package RUVseq version 1.5.0, using a set of 21 reference genes from Wang et al. (Scientific Reports 2014; doi:10.1038/srep06781) with parameter k=4.
Genome_build: TAIR10
Supplementary_files_format_and_content: one tab-delimited text files of raw read counts for each sample

source_name: rosette leaves

growth_protocol: Plants were grown in long-day growth chamber at 22 degree celsius.

extract_protocol:
Total RNA was extracted from frozen leave tissue from 10 rosettes just before bolting, using the RNeasy Mini Kit according to protocol (QIAGEN).
The mRNA libraries were constructed using the TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) using 1 - 4 µg total RNA, according to manufacturer's instructions with modifications to confer strand specificity. The mRNA was purified using the RNA Purifications Beads as per Illumina protocol instructions. The mRNA was incubated in the Elute, Prime, Fragment Mix at 94˚C for 8 min. After first strand synthesis (as per Illumina protocol instructions), the product was purified using RNAClean XP beads (Beckman, Brea, CA) as per manufacturer's instructions and eluted in 18 µL nuclease free water. Second strand synthesis was performed by adding the RNAClean XP purified product to 2.5 µL 10x NEB Buffer 2 (New England Biolabs, Ipswich, MA), 2 µL dUTP mix (10mM dATPs, 10mM dGTPs, 10mM dCTPs, and 20mM dUTPs), 0.5 µL RNAse H (2 U/µL), 1 µL DNA Polymerase I (E. coli) (New England Biolabs), and 1 µL DTT (100 mM). The 25 µL mixture was incubated at 16˚C for 2.5 hours. The addition of a 3’ A base and Adapter ligation was performed per Ilumina protocol instructions. The purified ligation products were incubated with 2 µL Uracil DNA Glycosylase (Fermentas) before PCR amplification (also done per Illumina protocol specifications 12 cycles). The reaction products were purified using AMPure XP beads according to manufacturer’s specifications. RNA-seq libraries were sequenced using the Illumina HiSeq 2500 (Illumina) with SE 1X100 Single index read or on HiSeq 4000 with 2X150 PE reads.

tag: developmental stage

value: before bolting

tag: light condition

value: long day

value: leaf


title: AMSC_19_proliferating

status: Public on Jul 13 2016

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 12.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

growth_protocol: AMSCs were routinely passaged in growth media consisting of Advanced MEM with 5% platelet lysate (Mill Creek Life Sciences), 2 mM L-glutamine (Invitrogen) and antibiotics (100 U/ml penicillin, 100 g/ml streptomycin) and were plated at 3,000cells/cm2 in T-175 flasks.

extract_protocol:
Proliferating and confluent AMSCs were harvested using the miRNeasy Mini Kit (Qiagen) according to the manufacturers' protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were actively proliferating for three days in culture and reached confluence on the fourth day of culture

value: Adipose-derived Mesenchymal Stromal Cell


title: AMSC_19_confluent


title: AMSC_4_proliferating


title: AMSC_3_proliferating


title: TKS191 E14 Tip5 coverage and smoothed-peaks

description: Two different processed data outputs: the coverage file is just the ChIP-seq read-pileups (which does not consider  the input control data); the smoothed-peaks file is the peaks as called by the peak-caller (which does factor the input control into the calculations of what is are the "true" peaks) which was converted to a height-accurate  peaks-only file.

value: Tip5 (Diagenode, CS-090-100)


title: AMSC_1_confluent


title: AMSC_1_proliferating


title: ChIP-seq BRG1 T30

city: Barcelona

first: François

last: Le Dily

address: Dr. Aiguader, 88

country: Spain

institute: CRG-Centre for Genomic Regulation

description: Chromatin immunoprecipitation (ChIP) against BRG1 30 minutes after treatment with R5020 (synthetic analog of the progesterone)

data_processing:
ChIP-Seq Single-end reads were processed by aligning to the reference human genome (GRCh37/hg19) using Bowtie v1.0.0. ChIP-seq signals were summed in windows of 100 Kb. Summed reads were normalised for sequencing depth and divided by the corresponding signal obtained for an input DNA of T47D cells to determine the normalised signal over input enrichment/depletion. Homer (Hypergeometric Optimization of Motif EnRichment) v4.3 was used to find regions of significance enrichment using an input as a control.
genome build: hg19
processed data files format and content: ChIP-seq data files are peak results “TSV” files with genomic coordinates of peaks

source_name: Breast cancer cells

growth_protocol: Grow breast cancer T47D cells in RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100 mg/ml streptomycin. For the experiments, cells were plated in RPMI medium without phenol red supplemented with 10% dextran-coated charcoal treated FBS (DCC/FBS) and 48 h later medium was replaced by fresh medium without serum. After one over night in serum-free conditions, cells were incubated with R5020 (10 nM) for different times at 37ºC.

extract_protocol:
ChIP-seq and Mnase-seq experiments were performed according to Vicent et al., Methods Mol Biol. 2014;1204:1-14.  Book “Steroid receptors: Methods and protocols”, Humana press (Springer, U.S.A.) Progesterone receptor interaction with chromatin
We have used the NEBNext Ultra DNA Library Prep kit for Illumina (Ref.:#7370), with amplification by Real Time PCR (light cycler) to determine the optimal number of cycles to amplify the library

tag: small interfering knock-down

tag: time after r5020

value: 30 minutes

value: anti_BRG1  Abcam ab110641 [EPNCIR111A]


title: RNA-seq T6

description: 6 hours after treatment with R5020 (synthetic analog of the progesterone)

data_processing:
RNA-Seq Paired-end reads were mapped using GEM mRNA Mapping Pipeline (v1.7) using last Gencode Annotation version 18, which followed specific steps: 1) Map reads to genome reference index (including chromosme 1 to X) with maximum mismatch ratio of 0.06 and base quality threshold of 26. 2) Map reads to a transcriptome index generated from previous reference index using same options as step 1. 3) Create de-novo trasncriptome index and map again the reads to this index using maximum mismatch ratio of 0.04, minimmum split size of 15 bp and maximmum of 500000 bp. 4) Map reads again to de-novo transcriptome index created using same options as step 1. 5) Merge mappings created and pair alignments using with base quality threshold of 26 and maximmum insertion size of 500000 bp. As a result BAM alignment files were obtained and used to generate strand-specific genome-wide normalized profiles using RSeQC3 software. Exon quantifications summarized by per-genes for expression level determination were obtained either as raw read counts and reads per kilobase per milion mapped reads (RPKM) using Flux Capacitor.
genome build: hg19
processed data files format and content: RNA-Seq data file is a “TSV” table which summarizes read counts per genes.

growth_protocol: Grow breast cancer T47D cells in RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100 mg/ml streptomycin.

extract_protocol:
RNA Isolation, Rneasy Mini Kit Qiagen.
We have used the Illumina Truseq Stranded mRNA Sample Prep Kit (RS-122-2101).

treatment_protocol: For the experiments, cells were plated in RPMI medium without phenol red supplemented with 10% dextran-coated charcoal treated FBS (DCC/FBS) and 48 h later medium was replaced by fresh medium without serum. After one over night in serum-free conditions, cells were incubated with R5020 (10 nM) for different times at 37ºC.

value: 6 hours


title: AMSC_4_confluent


title: AMSC_3_confluent


title: RNA-seq T0

description: before treatment with R5020 (synthetic analog of the progesterone)

value: 0 hours


title: TKS191 E14 input coverage

value: mouse embryonic cell line E14

value: passage 3 post-transfection


title: RNA-seq si-control T6 rep2

description: control of the small interfering (si) knock-down 6 hours after treatment with R5020 (synthenic analog of the progesterone) (replicate #2)

data_processing:
RNA-seq reads were trimmed using Trimmomatic to remove sequencing adapters with parameters: sequencing type=PE, seedMismatches=2, palindromeClipThreshold=30, simpleClipThreshold=12, minAdapterLength=1, keepBothReads=True, minQual=3, minLength=36 (all other parameters as default). Trimmed reads were aligned to hg19 using STAR with parameters: outFilterType "BySJout", outFilterMultimapNmax 20, alignSJoverhangMin 8, alignSJDBoverhangMin 1, outFilterMismatchNmax 999, outFilterMismatchNoverLmax 0.04, alignIntronMin 20, alignIntronMax 1000000, alignMatesGapMax 1000000 (all other parameters as default). Gene expression was measured as per-gene read counts using featureCounts treating reads as reversely stranded (all other parameters as default).
genome build: hg19
processed data files format and content: txt files with gene raw read counts (featureCounts standard output format)

value: si-control


title: RNA-seq si-control T6 rep1

description: control of the small interfering (si) knock-down 6 hours after treatment with R5020 (synthenic analog of the progesterone) (replicate #1)


title: ChIP-seq BRG1 T0

description: Chromatin immunoprecipitation (ChIP) against BRG1 before treatment with R5020 (synthetic analog of the progesterone)


title: RNA-seq si-control T0 rep1

description: control of the small interfering (si) knock-down before treatment with R5020 (synthenic analog of the progesterone) (replicate #1)


title: RNA-seq si-BRG1 T6 rep1

description: small interfering (si) knock-down of BRG1 6 hours after treatment with R5020 (synthetic analog of the progesterone) (replicate #1)


title: RNA-seq si-BRG1 T6 rep2

description: small interfering (si) knock-down of BRG1 6 hours after treatment with R5020 (synthetic analog of the progesterone) (replicate #2)


title: THP1_PMA-VDR input

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description: input DANN

data_processing:
Alignment: Sequence reads were obtained and mapped to the human genome (hg19) using Bowtie.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS II) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Alignment to hg19 using Bowtie v1.0 with the following parameters: -n 1 -k 1 -m 1 -l 28 -t -q --best
Peak discovery using MACS2 with the following parameters: -m 5 50 --bw 300
Visualization as tdf in Integrative Genomics Viewer via conversions from sam to sorted bam (using samtools) and then to tdf (using igvtools).
Genome_build: hg19
Supplementary_files_format_and_content: bed and peak bed files

source_name: THP-1 cells, differentiated to M2-type macrophages

growth_protocol: THP-1 human monocytic leukemia cells were grown in RPMI 1640 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and the cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol: Standard protocol as suggested by the manufacturer for ChIP-seq libraries as utilized at the EMBL Gene Core in Heidelberg, Germany

treatment_protocol: For differentiation into macrophages the cells were incubated for 3 days with 20 nM PMA. After differentiation, cells were either treated with 100 nM of the natural VDR ligand 1,25D (Sigma-Aldrich) or unstimulated

tag: treatment

tag: treatment time

tag: antibody


title: RNA-seq si-BRG1 T0 rep1

description: small interfering (si) knock-down of BRG1 before treatment with R5020 (synthetic analog of the progesterone) (replicate #1)


title: RNA-seq si-BRG1 T0 rep2

description: small interfering (si) knock-down of BRG1 before treatment with R5020 (synthetic analog of the progesterone) (replicate #2)


title: THP1_PMA-VDR unstim

description: Chromatin IP against VDR

value: unstimulated

value: VDR


title: THP1_PMA-VDR 2 h 1,25D

description: Chromatin IP against VDR

value: 2 h


title: THP1_PMA-VDR 1 h 1,25D

description: Chromatin IP against VDR

value: 1 h


title: RNA-seq si-FOXA1 T6 rep2

description: small interfering (si) knock-down of FOXA1 6 hours after treatment with R5020 (synthetic analog of the progesterone) (replicate #2)


title: RNA-seq si-FOXA1 T0 rep1

description: small interfering (si) knock-down of FOXA1 before treatment with R5020 (synthetic analog of the progesterone) (replicate #1)


title: RNA-seq si-CBX3 T6 rep2

description: small interfering (si) knock-down of CBX3 6 hour after treatment with R5020 (synthetic analog of the progesterone) (replicate #2)


title: RNA-seq si-FOXA1 T0 rep2

description: small interfering (si) knock-down of FOXA1 before treatment with R5020 (synthetic analog of the progesterone) (replicate #2)


title: RNA-seq si-CBX3 T6 rep1

description: small interfering (si) knock-down of CBX3 6 hour after treatment with R5020 (synthetic analog of the progesterone) (replicate #1)


title: RNA-seq si-CBX3 T0 rep2

description: small interfering (si) knock-down of CBX3 before treatment with R5020 (synthetic analog of the progesterone) (replicate #2)


title: RNA-seq si-control T0 rep2

description: control of the small interfering (si) knock-down before treatment with R5020 (synthenic analog of the progesterone) (replicate #2)


title: RNA-seq si-FOXA1 T6 rep1

description: small interfering (si) knock-down of FOXA1 6 hours after treatment with R5020 (synthetic analog of the progesterone) (replicate #1)


title: LVNC proband hiPSC-CMs at 2 weeks #2

city: stanford

first: Kazuki

last: Kodo

address: campus street

institute: Stanford

data_processing:
Paired-end fastq sequence reads from each sample were assembled against hg19 using the Tophat v2.0.6  with the Illumina-supplied hg19 gene-model annotation file ( gtf annotation).
The expression level (FPKM) was estimated by Cufflinks.
Cuffdiff was used to call differentially expressed genes with false discovery rate less than 0.05. Cuffdiff was run against the UCSC iGenomes GTF file from Illumina.
Subsequent to determining which genes were differentially expressed, FPKM was used for ﬁltering, and visualization purposes.
Genome_build: hg19

source_name: cardiomyocytes

growth_protocol: hiPSCs were grown to 90% confluence and differentiated subsequently into beating cardiomyocytes using a small molecule-based monolayer method adapted after4 and described in detail previously.3 10 days after cardiac differentiation, hiPSC-CM monolayers were purified using non-glucose culture medium containing RPMI-1640 without glucose (Life technologies) and B27 supplement (Life technologies). Non-glucose culture medium was changed every two days and after 5 days, hiPSC-CMs were dissociated using TripleE (10 min), washed and plated onto matrigel-coated plates in culture medium with glucose.

extract_protocol:
Total RNA was extracted and quantified using miRNeasy Kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s protocol. An additional DNAseI digestion step was performed to ensure that the samples were not contaminated with genomic DNA. Following the Qiagen RNA sample preparation protocol, 10 ug of total RNA was used to generate index-tagged paired-end cDNA libraries.5 Briefly, mRNAs were purified by polyA enrichment procedure using Dynal Oligo(dT) beads (Life technologies).
mRNA fragmentation was performed using RNA Fragmentation Reagents (Life technologies) with incubation at 70oC for 1 min to obtain 200-300b fragments. cDNA was generated using SuperScript Double-Stranded cDNA Synthesis Kit (Life technologies). Illumina sequencing adapters were ligated to cDNA using LigaFast (Promega) and PE Adapter Oligo Mix (Illumina, San Diego, CA). PCR was performed on the adapter-ligated cDNA with 2X Phusion DNA polymerase Master Mix (New England Biolabs, Ipswich, MA) using the following conditions: denaturation 98°C for 30 seconds, followed by 15 cycles of denaturation 98°C for 10 seconds, annealing 65°C for 30 seconds, and extension 72°C for 30 seconds, ending with an extension at 72°C for 5 min. After cDNA libraries were generated using the sample preparation kit, quality of the libraries was checked using Bioanalyzer (Agilent Technologies).

treatment_protocol: hiPSC-CMs were cultured in RPMI with B27 supplement and 2% FBS 2 days before experiment to accelerate the proliferation.

value: induced pluripotent stem cell derived cardiomyocytes

tag: passages

tag: genotype

tag: cardiac phenotype

value: severe LVNC


title: LVNC proband hiPSC-CMs at 2 weeks #1

tag: cell type


title: NZB:C57 Heart rep3

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

institute: CNIC

data_processing:
Illumina RTA software v 1.13.48.0
Illumina2bam v:0.03
SamToFastq.jar v1.86
Reads were pre-processed with Cutadapt 1.2.1, To remove TruSeq adaptor.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build GRCm38.v70) And genome, Using RSEM v1.2.3 and Bowtie2 v2.0.6.
Data were normalized using TMM with the Bioconductor package EdgeR
Data were batch corrected with Bioconductor package ComBat.R
Differential expression were tested using GLM with the Bioconductor package EdgeR
Genome_build: GRCm38.v70
Supplementary_files_format_and_content: matrix_table.txt file contains ENSEMBL gene Ids, TMM-Normalized counts per million for each sample.

source_name: Heart

growth_protocol: Conplastic strains were obtained after 10 generations of backcrossing to create a new line harboring the nuclear genome of one strain and the mtDNA of another (C57BL/6 and NZB were purchased from Harlan Laboratories).

extract_protocol:
Twelve 10-week-old males per genotype were killed by cervical decapitation and liver (median lobe) and heart (left ventricle) tissues were dissected and immediately frozen in liquid nitrogen. Total RNA was extracted with QIAzol Lysis Reagent and then purified on RNeasy spin columns (Qiagen). RNA integrity (RNA Integrity Score ≥ 7.9) and quantity were determined on the Agilent 2100 Bioanalyzer. RNA samples from different animals were mixed in equal proportion at four samples per pool, and three pools per genotype were analyzed in the Illumina Genome Analyzer IIx.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: NZB

tag: mitochondria

tag: tissue

value: heart

tag: gender

value: male

tag: age

value: 10 weeks old


title: mild DCM hiPSC-CMs at 2 weeks #1

value: asymptomatic DCM


title: NZB:C57 Liver rep1

source_name: Liver

value: liver


title: NZB:NZB Heart rep3


title: NZB:C57 Liver rep2


title: NZB:C57 Liver rep3


title: LVNC sibling1 hiPSC-CMs at 2 weeks #1

value: asymptomatic LVNC


title: NZB:C57 Heart rep1


title: NZB:C57 Heart rep2


title: NZB:NZB Liver rep2


title: BL/6J:NZB Heart mix3


title: NZB:NZB Heart rep2


title: BL/6J:NZB Liver mix1


title: BL/6J:NZB Liver mix3


title: BL/6J:NZB Heart mix2


title: NZB:NZB Liver rep1


title: NZB:NZB Liver rep3


title: BL/6J:C57 Heart mix2


title: BL/6J:NZB Heart mix1


title: BL/6J:C57 Heart mix1


title: BL/6J:C57 Liver mix3


title: BL/6J:C57 Heart mix3


title: BL/6J:NZB Liver mix2


title: BL/6J:C57 Liver mix1


title: NZB:NZB Heart rep1


title: BL/6J:C57 Liver mix2


title: coPu1n_K4me3.3

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
ChIPed DNA
Single-end protocol (read2 used to read molecule barcodes only).

data_processing:
bcl2fastq/2.15.0.4
Alignment using bowtie2/2.1.0 using default parameters.
PCR duplications were removed using picard-tools (v1.108). In case of paired-end samples, if single-end protocol was used, a short read in R2 was used as a UMI.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigWig, bedGraph

source_name: Bone marrow-derived dendritic cells, Pu.1 and H3K4me3 ChIPs

growth_protocol: Total bone marrow was isolated and cells were plated in RPMI medium + 10% FBS and 20 ng/mL GMCSF and grown for 8 days.

extract_protocol:
Revert crosslinking and purify ChIPed DNA with AMPure beads.
High-throughput reChIP, developed from the iChIP protocol (Lara-Astiaso, Weiner et al. Science 2014 [PMID 25103404]).

tag: strain/background

value: Bone marrow-derived dendritic cells

tag: sample type

value: primary culture

tag: chip antibody1

value: Pu.1 (Santa Cruz sc-352)

tag: chip antibody2

value: H3K4me3 (Millipore 07-473)


title: coPu1n_K4me3.1


title: coPu1n_K4me3.2


title: coPu1n_K27ac.2

source_name: Bone marrow-derived dendritic cells, Pu.1 and H3K27ac ChIPs

value: H3K27ac (Abcam ab4729)


title: coPu1_K4me3.2


title: coPu1n_K27ac.3


title: coPu1_K4me3.3


title: coPu1n_H3.2

source_name: Bone marrow-derived dendritic cells, Pu.1 and H3 ChIPs

value: H3 (Abcam ab1791)


title: coPu1n_K4me2.2

source_name: Bone marrow-derived dendritic cells, Pu.1 and H3K4me2 ChIPs

value: H3K4me2 (Abcam ab32356)


title: coPu1n_H3.1


title: coCebpb_K4me3.3

source_name: Bone marrow-derived dendritic cells, Cebpb and H3K4me3 ChIPs

value: Cebpb (Santa Cruz sc-150)


title: coPu1_K27ac.1


title: coPu1_K27ac.2


title: coPu1_H3.3


title: coPu1n_K27ac.1


title: coCebpb_K4me2.3

source_name: Bone marrow-derived dendritic cells, Cebpb and H3K4me2 ChIPs


title: coPu1_K4me2.3


title: coPu1n_K4me2.1


title: coPu1_K4me3.1


title: coPu1_K27ac.3


title: coPu1n_H3.3


title: coPu1n_K4me2.3


title: coCebpb_K4me2.1


title: coPu1_K4me2.2


title: coPu1_H3.2


title: coCebpb_K4me2.4


title: coPu1_H3.1


title: coCebpb_K4me3.1


title: coCebpb_K27ac.4

source_name: Bone marrow-derived dendritic cells, Cebpb and H3K27ac ChIPs


title: coCebpb_K4me2.2


title: coCebpb_K4me3.2


title: coCebpb_K27ac.3


title: coPu1_K4me2.1


title: coCebpb_K4me3.4


title: coCebpb_H3.4

source_name: Bone marrow-derived dendritic cells, Cebpb and H3 ChIPs


title: coCebpb_K27ac.2


title: coCebpb_K27ac.1


title: coCebpb_H3.3


title: coCTCF_K4me3.3

source_name: Bone marrow-derived dendritic cells, CTCF and H3K4me3 ChIPs

value: CTCF (Upstate 07-729)


title: coCTCF_K4me2.4

source_name: Bone marrow-derived dendritic cells, CTCF and H3K4me2 ChIPs


title: coCTCF_K4me3.4


title: coCTCF_K4me2.2


title: coCTCF_K4me2.1


title: coCebpb_H3.1


title: coCTCF_K4me3.2


title: coCebpb_H3.2


title: coCTCF_K4me3.1


title: coCTCF_K4me2.3


title: coCTCF_K27ac.1

source_name: Bone marrow-derived dendritic cells, CTCF and H3K27ac ChIPs


title: coCTCF_K27ac.3


title: coK27me3M-K4me3M-Es2i_1

description: ChIPed DNA

source_name: B6 X BCA F1 ESC line - Addgene 52382, H3K27me3 and H3K4me3 ChIPs

value: B6 X BCA F1

value: Embryonic stem cell line

value: cell line

value: H3K27me3 (Millipore 07-449)


title: coCTCF_H3.4

source_name: Bone marrow-derived dendritic cells, CTCF and H3 ChIPs


title: coK27ac-K4me3m-Es2i_1

description: ChIPed DNA

source_name: B6 X BCA F1 ESC line - Addgene 52382, H3K27ac and H3K4me3 ChIPs


title: coK27me3M-K4me3M-EsLlif_1

description: ChIPed DNA


title: coCTCF_H3.3


title: coCTCF_K27ac.4


title: coCTCF_H3.2


title: coK27me3M-K4me3M-EsLlif_2

description: ChIPed DNA


title: coK27ac-K4me3m-EsLlif_2

description: ChIPed DNA


title: coCTCF_H3.1


title: coCTCF_K27ac.2


title: coK27ac-K4me3m-Es2i_2

description: ChIPed DNA


title: coK27ac-K4me3m-EsLlif_1

description: ChIPed DNA


title: coChIP5_H4K8ac_H3K4me3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H4K8ac and H3K4me3 ChIPs

value: H4K8ac (Millipore 07-328)


title: coChIP5_H4K8ac_H3K4me3.1

description: ChIPed DNA


title: coChIP5_H4K8ac_H3K4me1.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H4K8ac and H3K4me1 ChIPs

value: H3K4me1 (Abcam ab8895)


title: coChIP5_H4K8ac_H3K4me2.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H4K8ac and H3K4me2 ChIPs


title: coChIP5_H4K8ac_H3K4me2.1

description: ChIPed DNA


title: coChIP5_H4K8ac_H3K27ac.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H4K8ac and H3K27ac ChIPs


title: coChIP5_H4K5ac_H3K4me3.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H4K5ac and H3K4me3 ChIPs

value: H4K5ac (Millipore 07-327)


title: coChIP5_H4K5ac_H3K4me2.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H4K5ac and H3K4me2 ChIPs


title: coChIP5_H4K8ac_H3K4me1.2

description: ChIPed DNA


title: coK27me3M-K4me3M-Es2i_2

description: ChIPed DNA


title: coChIP5_H4K5ac_H3K4me2.2

description: ChIPed DNA


title: coChIP5_H4K5ac_H3K4me3.2

description: ChIPed DNA


title: coChIP5_H4K8ac_H3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H4K8ac and H3 ChIPs


title: coChIP5_H4K20me3_H3K4me2.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K20me3 and H3K4me2 ChIPs

value: H3K20me3 (Abcam ab9053)


title: coChIP5_H4K20me3_H3K4me2.2

description: ChIPed DNA

value: Bone marrow-derived dendritic cells


title: coChIP5_H4K20me3_H3K4me3.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K20me3 and H3K4me3 ChIPs

value: primary culture


title: coChIP5_H4K5ac_H3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H4K5ac and H3 ChIPs


title: coChIP5_H4K5ac_H3K4me1.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H4K5ac and H3K4me1 ChIPs


title: coChIP5_H4K5ac_H3.1

description: ChIPed DNA


title: coChIP5_H4K20me3_H3K4me3.2

description: ChIPed DNA


title: coChIP5_H4K5ac_H3K27ac.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H4K5ac and H3K27ac ChIPs


title: coChIP5_H4K5ac_H3K27ac.1

description: ChIPed DNA


title: coChIP5_H4K20me3_H3K27ac.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K20me3 and H3K27ac ChIPs


title: coChIP5_H4K20me3_H3K4me1.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K20me3 and H3K4me1 ChIPs


title: coChIP5_H4K20me3_H3K27ac.1

description: ChIPed DNA


title: coChIP5_H4K20me3_H3K4me1.2

description: ChIPed DNA


title: coChIP5_H4K8ac_H3K27ac.1

description: ChIPed DNA


title: coChIP5_H4K20me3_H3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K20me3 and H3 ChIPs


title: coChIP5_H4K8ac_H3.1

description: ChIPed DNA


title: coChIP5_H4K12ac_H3K4me3.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H4K12ac and H3K4me3 ChIPs

value: H4K12ac (Millipore 07-595)


title: coChIP5_H4K5ac_H3K4me1.1

description: ChIPed DNA


title: coChIP5_H4K20me3_H3.1

description: ChIPed DNA


title: coChIP5_H4K12ac_H3K4me2.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H4K12ac and H3K4me2 ChIPs


title: coChIP5_H4K12ac_H3K4me2.1

description: ChIPed DNA


title: coChIP5_H4K12ac_H3K4me1.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H4K12ac and H3K4me1 ChIPs


title: coChIP5_H4K12ac_H3K4me3.2

description: ChIPed DNA

value: H3K4me3 (Millipore 07-473)


title: coChIP5_H4K12ac_H3K27ac.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H4K12ac and H3K27ac ChIPs

value: H3K27ac (Abcam ab4729)


title: coChIP5_H4K12ac_H3K27ac.1

description: ChIPed DNA


title: coChIP5_H4K12ac_H3.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H4K12ac and H3 ChIPs

value: H3 (Abcam ab1791)


title: coChIP5_H4K12ac_H3.2

description: ChIPed DNA


title: coChIP5_H3K9me3_H3K4me3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9me3 and H3K4me3 ChIPs

value: H3K9me3 (Abcam ab8898)


title: coChIP5_H3K9me3_H3K4me2.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9me3 and H3K4me2 ChIPs

value: H3K4me2 (Abcam ab32356)


title: coChIP5_H3K9me3_H3.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9me3 and H3 ChIPs


title: coChIP5_H3K9me3_H3.2

description: ChIPed DNA


title: coChIP5_H3K9me3_H3K27ac.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9me3 and H3K27ac ChIPs


title: coChIP5_H3K9me3_H3K4me1.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9me3 and H3K4me1 ChIPs


title: coChIP5_H3K9me1_H3K4me2.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9me1 and H3K4me2 ChIPs

value: H3K9me1 (Abcam ab8896)


title: coChIP5_H3K9me3_H3K4me2.1

description: ChIPed DNA


title: coChIP5_H3K9me1_H3K4me2.1

description: ChIPed DNA


title: coChIP5_H3K9me3_H3K4me1.2

description: ChIPed DNA


title: coChIP5_H3K9me1_H3K4me1.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9me1 and H3K4me1 ChIPs


title: coChIP5_H3K9me3_H3K27ac.1

description: ChIPed DNA


title: coChIP5_H3K9me1_H3K4me3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9me1 and H3K4me3 ChIPs


title: coChIP5_H3K9me1_H3K4me1.2

description: ChIPed DNA


title: coChIP5_H3K9me1_H3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9me1 and H3 ChIPs


title: coChIP5_H3K9me1_H3.1

description: ChIPed DNA


title: coChIP5_H3K9me1_H3K27ac.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9me1 and H3K27ac ChIPs


title: coChIP5_H3K9ac_H3K4me3.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9ac and H3K4me3 ChIPs

value: H3K9ac (Abcam ab4441)


title: coChIP5_H3K9ac_H3K4me2.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9ac and H3K4me2 ChIPs


title: coChIP5_H3K9ac_H3K4me1.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9ac and H3K4me1 ChIPs


title: coChIP5_H3K9me1_H3K27ac.1

description: ChIPed DNA


title: coChIP5_H3K9me3_H3K4me3.1

description: ChIPed DNA


title: coChIP5_H4K12ac_H3K4me1.1

description: ChIPed DNA


title: coChIP5_H3K9ac_H3K27ac.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9ac and H3K27ac ChIPs


title: coChIP5_H3K9ac_H3K27ac.1

description: ChIPed DNA


title: coChIP5_H3K9ac_H3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9ac and H3 ChIPs


title: coChIP5_H3K9ac_H3.1

description: ChIPed DNA


title: coChIP5_H3K9me1_H3K4me3.1

description: ChIPed DNA


title: coChIP5_H3K4me1_H3K4me2.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4me1 and H3K4me2 ChIPs


title: coChIP5_H3K4me1_H3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4me1 and H3 ChIPs


title: coChIP5_H3K4me1_H3K27ac.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4me1 and H3K27ac ChIPs


title: coChIP5_H3K4me1_H3K4me3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4me1 and H3K4me3 ChIPs


title: coChIP5_H3K4me1_H3K27ac.1

description: ChIPed DNA


title: coChIP5_H3K4me1_H3.1

description: ChIPed DNA


title: coChIP5_H3K4me1_H3K4me3.1

description: ChIPed DNA


title: coChIP5_H3K4me1_H3K4me1.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4me1 and H3K4me1 ChIPs


title: coChIP5_H3K4me1_H3K4me1.1

description: ChIPed DNA


title: coChIP5_H3K4me1_H3K4me2.1

description: ChIPed DNA


title: coChIP5_H3K4ac_H3K4me3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4ac and H3K4me3 ChIPs

value: H3K4ac (Abcam EPR16596)


title: coChIP5_H3K4ac_H3K4me3.1

description: ChIPed DNA


title: coChIP5_H3K9ac_H3K4me2.1

description: ChIPed DNA


title: coChIP5_H3K9ac_H3K4me1.2

description: ChIPed DNA


title: coChIP5_H3K4ac_H3K4me2.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4ac and H3K4me2 ChIPs


title: coChIP5_H3K9ac_H3K4me3.2

description: ChIPed DNA


title: coChIP5_H3K4ac_H3K4me2.1

description: ChIPed DNA


title: coChIP5_H3K4ac_H3K4me1.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4ac and H3K4me1 ChIPs


title: coChIP5_H3K4ac_H3K27ac.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4ac and H3K27ac ChIPs


title: coChIP5_H3K4ac_H3K4me1.2

description: ChIPed DNA


title: coChIP5_H3K4ac_H3.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4ac and H3 ChIPs


title: coChIP5_H3K36me3_H3K4me3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K36me3 and H3K4me3 ChIPs

value: H3K36me3 (Abcam ab9050)


title: coChIP5_H3K36me3_H3K4me3.1

description: ChIPed DNA


title: coChIP5_H3K4ac_H3K27ac.2

description: ChIPed DNA


title: coChIP5_H3K36me3_H3K4me1.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K36me3 and H3K4me1 ChIPs


title: coChIP5_H3K36me3_H3K4me2.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K36me3 and H3K4me2 ChIPs


title: coChIP5_H3K36me3_H3K4me1.1

description: ChIPed DNA


title: coChIP5_H3K36me3_H3K27ac.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K36me3 and H3K27ac ChIPs


title: coChIP5_H3K36me3_H3K27ac.1

description: ChIPed DNA


title: coChIP5_H3K36me2_H3K4me2.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K36me2 and H3K4me2 ChIPs

value: H3K36me2 (Abcam ab9049)


title: coChIP5_H3K36me2_H3K4me3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K36me2 and H3K4me3 ChIPs


title: coChIP5_H3K36me2_H3K27ac.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K36me2 and H3K27ac ChIPs


title: coChIP5_H3K36me2_H3K27ac.2

description: ChIPed DNA


title: coChIP5_H3K36me2_H3K4me1.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K36me2 and H3K4me1 ChIPs


title: coChIP5_H3K36me2_H3K4me3.1

description: ChIPed DNA


title: coChIP5_H3K36me2_H3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K36me2 and H3 ChIPs


title: coChIP5_H3K36me2_H3.1

description: ChIPed DNA


title: coChIP5_H3K27me3_H3K4me3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27me3 and H3K4me3 ChIPs

value: H3K27me3 (Millipore 07-449)


title: coChIP5_H3K27me3_H3K4me2.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27me3 and H3K4me2 ChIPs


title: coChIP5_H3K27me3_H3K4me1.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27me3 and H3K4me1 ChIPs

value: H3K4me1 (Abcam ab8895)


title: coChIP5_H3K27me3_H3K4me3.1

description: ChIPed DNA


title: coChIP5_H3K36me3_H3.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K36me3 and H3 ChIPs


title: coChIP5_H3K36me3_H3K4me2.2

description: ChIPed DNA


title: coChIP5_H3K36me3_H3.2

description: ChIPed DNA


title: coChIP5_H3K36me2_H3K4me1.1

description: ChIPed DNA


title: coChIP5_H3K27me3_H3K27ac.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27me3 and H3K27ac ChIPs


title: coChIP5_H3K27me3_H3K4me2.1

description: ChIPed DNA


title: coChIP5_H3K27ac_H3K4me3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27ac and H3K4me3 ChIPs


title: coChIP5_H3K27me3_H3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27me3 and H3 ChIPs


title: coChIP5_H3K4ac_H3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4ac and H3 ChIPs


title: coChIP5_H3K27ac_H3K4me3.1

description: ChIPed DNA


title: coChIP5_H3K27me3_H3.1

description: ChIPed DNA


title: coChIP5_H3K27ac_H3K4me2.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27ac and H3K4me2 ChIPs


title: coChIP5_H3K27ac_H3K4me1.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27ac and H3K4me1 ChIPs


title: coChIP5_H3K36me2_H3K4me2.1

description: ChIPed DNA


title: coChIP5_H3K27ac_H3K4me1.1

description: ChIPed DNA


title: coChIP5_H3K27ac_H3K27ac.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27ac and H3K27ac ChIPs


title: coChIP5_H3K18ac_H3K4me3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K18ac and H3K4me3 ChIPs

value: H3K18ac (Abcam ab1191)


title: coChIP5_H3K27ac_H3.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27ac and H3 ChIPs


title: coChIP5_H3K18ac_H3K4me2.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K18ac and H3K4me2 ChIPs


title: coChIP5_H3K18ac_H3K4me1.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K18ac and H3K4me1 ChIPs


title: coChIP5_H3K27ac_H3.1

description: ChIPed DNA


title: coChIP5_H3K27me3_H3K4me1.1

description: ChIPed DNA


title: coChIP5_H3K18ac_H3K4me2.2

description: ChIPed DNA


title: coChIP5_H3K27ac_H3K27ac.2

description: ChIPed DNA


title: coChIP5_H3K18ac_H3.1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K18ac and H3 ChIPs


title: coChIP5_H3K18ac_H3.2

description: ChIPed DNA


title: coChIP5_H3K27me3_H3K27ac.2

description: ChIPed DNA


title: coChIP5_H3K18ac_H3K4me1.2

description: ChIPed DNA


title: coChIP5_H3K18ac_H3K27ac.2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K18ac and H3K27ac ChIPs


title: coChIP5_H3K18ac_H3K4me3.1

description: ChIPed DNA


title: coChIP3-K9ac-K4me2_2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9ac and H3K4me2 ChIPs


title: coChIP3-K4me3-K4me2_2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4me3 and H3K4me2 ChIPs


title: coChIP3-K9me3-K4me2_3

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9me3 and H3K4me2 ChIPs


title: coChIP5_H3K27ac_H3K4me2.2

description: ChIPed DNA


title: coChIP3-K9me3-K4me2_1

description: ChIPed DNA


title: coChIP3-K9ac-K4me2_3

description: ChIPed DNA


title: coChIP3-K9me3-K4me2_2

description: ChIPed DNA


title: coChIP3-K4me3-K4me2_3

description: ChIPed DNA


title: coChIP5_H3K18ac_H3K27ac.1

description: ChIPed DNA


title: coChIP3-K4me2-K4me2_2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4me2 and H3K4me2 ChIPs


title: coChIP3-K9ac-K4me2_1

description: ChIPed DNA


title: coChIP3-K4me3-K4me2_1

description: ChIPed DNA


title: coChIP3-K4me2-K4me2_1

description: ChIPed DNA


title: coChIP3-K4me1-K4me2_3

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4me1 and H3K4me2 ChIPs


title: coChIP3-K4me1-K4me2_2

description: ChIPed DNA


title: coChIP3-K27ac-K4me2_2

description: ChIPed DNA


title: coChIP3-K27me3-K4me2_1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27me3 and H3K4me2 ChIPs


title: coChIP3-K18ac-K4me2_2

description: ChIPed DNA


title: coChIP3-K4me1-K4me2_1

description: ChIPed DNA


title: coChIP3-K27me3-K4me2_2

description: ChIPed DNA


title: coChIP3-K18ac-K4me2_3

description: ChIPed DNA


title: coChIP3-K9me3-K27me3_3

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9me3 and H3K27me3 ChIPs


title: coChIP3-K9me3-K27me3_1

description: ChIPed DNA


title: coChIP3-K18ac-K4me2_1

description: ChIPed DNA


title: coChIP3-K27me3-K4me2_3

description: ChIPed DNA


title: coChIP3-K4me3-K27me3_1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4me3 and H3K27me3 ChIPs


title: coChIP3-K9ac-K27me3_1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9ac and H3K27me3 ChIPs


title: coChIP3-K9me3-K27me3_2

description: ChIPed DNA


title: coChIP3-K4me3-K27me3_2

description: ChIPed DNA


title: coChIP3-K27ac-K4me2_1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27ac and H3K4me2 ChIPs


title: coChIP3-K9ac-K27me3_2

description: ChIPed DNA


title: coChIP3-K27ac-K4me2_3

description: ChIPed DNA


title: coChIP3-K4me2-K4me2_3

description: ChIPed DNA


title: coChIP3-K4me2-K27me3_1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4me2 and H3K27me3 ChIPs


title: coChIP3-K9ac-K27me3_3

description: ChIPed DNA


title: coChIP3-K4me3-K27me3_3

description: ChIPed DNA


title: coChIP3-K4me1-K27me3_2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4me1 and H3K27me3 ChIPs


title: coChIP3-K4me1-K27me3_3

description: ChIPed DNA


title: Bacillus thuringiensis transcriptomics CT-43(4CG1)

city: Oak Ridge

first: Steven

last: Brown

state: TN

address: 1 Bethel valley road

institute: ORNL

description: The SRA accession SRX532039 contains 16 runs (SRR) that include libraries made from bacteria grown with media from two lots and collected on various dates. The file "GEO_data key.xlsx"  available on the series record contains the key to the medium lot and collection date for each SRR id.

data_processing:
Illumina HiSeq 2000 software Casava v1.8 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence and then mapped to respective whole reference genomes of strains CT-43 and ATCC 10792 using CLC Genomics Workbench 7.0.4 (CLCBio)
Differenential gene expression was calculated using DESeq2 (Love, M.I. et al., Genome Biol, 2014).
The comparisons were performed within strain but across different media lots or collection dates.
Genome_build: CT-43 and ATCC 10792
Supplementary_files_format_and_content: excel (.xlsx) differential gene expression data (results DESeq2)

organism: Bacillus thuringiensis

growth_protocol: Single colonies from plates were picked for both the strains and inoculated into 5mL of Luria Bertani (LB) broth overnight (30o C, 200 rpm). A 1 mL aliquot from this culture was used to inoculate a 200mL LB broth. This was grown for 3 hrs at 30o C and 200 rpm (New Brunswick Scientific, Innova 4430).

extract_protocol:
The pellet from each sample was resuspended in ~3mLs of TRIzol.  The TRIzol cell mixture was added to tubes containing 800mg of 0.1mm glass beads (Biospec products Inc.) and cells were lysed by bead beating on a Precelly 24 (Bertin Technologies, Montigny-le-Bretonneux, France) (3X20 sec, 6,500 rpm).  Chloroform was added, mixed by vortexing and the mixture was centrifuged at 20,817 x g (Centrifuge 5417R, Eppendorf) for 15 min at 4oC.  The aqueous phase was collected and mixed with ethanol and purified on an RNeasy column (Qiagen) following the manufacturer’s protocol using the optional on column DNaseI treatment. Ribosomal RNA was depleted from the samples using a Ribo-Zero rRNA removal kit for Gram-Positive bacteria (Epicentre) following the manufacturer’s recommendations.
cDNA libraries were prepared and barcoded using a ScriptSeq v2 RNA-Seq Library preparation kit (Epicentre) following the manufacturer’s recommendations.

treatment_protocol: The cells were harvested from different media lots used and  on four different dates, in their mid-log phase from a 40 mL aliquot of this culture by centrifugation (Sorvall, Evolution RC) at 7,649 x g at 4o C for 5min. The pellet was frozen in liquid nitrogen for 10min followed by storage at -800 C until further use.


title: coChIP3-K4me2-K27me3_2

description: ChIPed DNA


title: coChIP3-K27me3-K27me3-3

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27me3 and H3K27me3 ChIPs


title: coChIP3-K4me1-K27me3_1

description: ChIPed DNA


title: coChIP3-K4me2-K27me3_3

description: ChIPed DNA


title: coChIP3-K9me3-K27ac_3

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9me3 and H3K27ac ChIPs


title: coChIP3-K18ac-K27me3_2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K18ac and H3K27me3 ChIPs


title: coChIP3-K9me3-K27ac_1

description: ChIPed DNA


title: coChIP3-K27ac-K27me3_3

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27ac and H3K27me3 ChIPs


title: coChIP3-K27ac-K27me3_2

description: ChIPed DNA


title: coChIP3-K27me3-K27me3-2

description: ChIPed DNA


title: coChIP3-K18ac-K27me3_1

description: ChIPed DNA


title: Bacillus thuringiensis transcriptomics ATCC 10792

description: The SRA accession SRX533541 contains 16 runs (SRR) that include libraries made from bacteria grown with media from two lots and collected on various dates. The file "GEO_data key.xlsx"  available on the series record contains the key to the medium lot and collection date for each SRR id.


title: coChIP3-K27ac-K27me3_1

description: ChIPed DNA


title: coChIP3-K27me3-K27me3-1

description: ChIPed DNA


title: coChIP3-K4me3-K27ac_3

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4me3 and H3K27ac ChIPs


title: coChIP3-K9ac-K27ac_2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K9ac and H3K27ac ChIPs


title: coChIP3-K18ac-K27me3_3

description: ChIPed DNA


title: coChIP3-K9me3-K27ac_2

description: ChIPed DNA


title: coChIP3-K9ac-K27ac_1

description: ChIPed DNA


title: coChIP3-K4me2-K27ac_1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4me2 and H3K27ac ChIPs


title: coChIP3-K4me2-K27ac_2

description: ChIPed DNA


title: coChIP3-K27me3-K27ac_2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27me3 and H3K27ac ChIPs


title: coChIP3-K27me3-K27ac_3

description: ChIPed DNA


title: coChIP3-K9ac-K27ac_3

description: ChIPed DNA


title: coChIP3-K4me1-K27ac_3

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4me1 and H3K27ac ChIPs


title: coChIP3-K27ac-K27ac_3

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27ac and H3K27ac ChIPs


title: coChIP3-K27ac-K27ac_2

description: ChIPed DNA


title: coChIP3-K4me2-K27ac_3

description: ChIPed DNA


title: coChIP3-K27me3-K27ac_1

description: ChIPed DNA


title: coChIP3-K4me1-K27ac_1

description: ChIPed DNA


title: coChIP3-K4me3-K27ac_1

description: ChIPed DNA


title: coChIP3-K18ac-K27ac_3

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K18ac and H3K27ac ChIPs


title: coChIP3-K4me1-K27ac_2

description: ChIPed DNA


title: coChIP3-K4me3-K4me3_1

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4me3 and H3K4me3 ChIPs


title: coChIP3-K4me2-K4me3_2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4me2 and H3K4me3 ChIPs


title: coChIP3-K18ac-K27ac_2

description: ChIPed DNA


title: coChIP3-K27ac-K27ac_1

description: ChIPed DNA


title: coChIP3-K4me3-K27ac_2

description: ChIPed DNA


title: coChIP3-K18ac-K27ac_1

description: ChIPed DNA


title: coChIP3-K27me3-K4me3_2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27me3 and H3K4me3 ChIPs


title: coChIP3-K4me3-K4me3_3

description: ChIPed DNA


title: coChIP3-K4me1-K4me3_2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K4me1 and H3K4me3 ChIPs


title: coChIP3-K4me1-K4me3_3

description: ChIPed DNA


title: coChIP3-K27ac-K4me3_3

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K27ac and H3K4me3 ChIPs


title: coChIP3-K4me2-K4me3_3

description: ChIPed DNA


title: coChIP3-K18ac-K4me3_2

description: ChIPed DNA

source_name: Bone marrow-derived dendritic cells, H3K18ac and H3K4me3 ChIPs


title: coChIP3-K4me3-K4me3_2

description: ChIPed DNA


title: coChIP6_Lung_27me3_4me1_2

source_name: Lung, H3K27me3 and H3K4me1 ChIPs

value: Lung

value: Adult


title: coChIP3-K27ac-K4me3_2

description: ChIPed DNA

value: Bone marrow-derived dendritic cells

value: primary culture


title: coChIP6_Liver_27me3_4me3_2

source_name: Liver, H3K27me3 and H3K4me3 ChIPs

value: Liver

value: H3K4me3 (Millipore 07-473)


title: coChIP3-K4me2-K4me3_1

description: ChIPed DNA


title: coChIP3-K27me3-K4me3_3

description: ChIPed DNA


title: coChIP6_Lung_27me3_4me3_2

source_name: Lung, H3K27me3 and H3K4me3 ChIPs


title: coChIP3-K27me3-K4me3_1

description: ChIPed DNA


title: coChIP6_Liver_27me3_4me1_2

source_name: Liver, H3K27me3 and H3K4me1 ChIPs


title: coChIP3-K18ac-K4me3_3

description: ChIPed DNA


title: coChIP6_Kidney_27me3_4me3_2

source_name: Kidney, H3K27me3 and H3K4me3 ChIPs

value: Kidney


title: coChIP6_Kidney_27me3_4me1_2

source_name: Kidney, H3K27me3 and H3K4me1 ChIPs


title: coChIP6_Brain_27me3_4me3_2

source_name: Brain, H3K27me3 and H3K4me3 ChIPs

value: Brain


title: coChIP6_Lung_27me3_4me1_1


title: coChIP3-K4me1-K4me3_1

description: ChIPed DNA


title: coChIP3-K18ac-K4me3_1

description: ChIPed DNA


title: coChIP3-K27ac-K4me3_1

description: ChIPed DNA

value: H3K27ac (Abcam ab4729)


title: coChIP6_Lung_27me3_4me3_1


title: coChIP6_Liver_27me3_4me1_1


title: coChIP6_Kidney_27me3_4me1_1


title: coChIP6_Liver_27me3_4me3_1


title: brain_E11.5 (Sample 91)

description:
processed data file: Timeline.xlsx
day11.5_brain_2
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
alignment: bowtie2 with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna mm9 -d <List of tag dir> -count 3utr -condenseGenes -strand + -norm 1e7
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

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

extract_protocol:
Cells were FACS sorted into lysis buffer and RNA was processed from the lysates
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
3' RNA-seq for digital gene expression quantitation

treatment_protocol: 5 mg/kg poly I:C to pregnant females at embryonic day 12.5 or 14.5

value: CX3CR1-GFP+ C57BL/6J

tag: selection marker

tag: developmental stage


title: coChIP6_Kidney_27me3_4me3_1


title: coChIP6_Brain_27me3_4me1_1

source_name: Brain, H3K27me3 and H3K4me1 ChIPs


title: coChIP6_Brain_27me3_4me1_2


title: AB444 (Sample 17)

description: Raw data files were processed as single-end files since the read2 (mate) files contained only cell and molecule barcodes. This information is appended to the fastq entry header.

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

growth_protocol: Mice housed at the Weizmann Institute animal facility

extract_protocol:
Each mouse was euthanized and brain or Yolk sac was extracted for proccessing
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation

treatment_protocol: no treatment

value: brain

value: adult


title: coChIP6_Brain_27me3_4me3_1


title: brain_E11.5 (Sample 90)

description:
processed data file: Timeline.xlsx
day11.5_brain_1
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

tag: treatment


title: AB441 (Sample 14)

value: embryonic day 18.5


title: AB439 (Sample 12)


title: AB445 (Sample 18)


title: AB442 (Sample 15)


title: AB440 (Sample 13)


title: AB437 (Sample 10)


title: AB438 (Sample 11)


title: AB443 (Sample 16)


title: AB434 (Sample 7)

value: yolk sac

value: embryonic day 12.5


title: AB400 (Sample 6)


title: AB435 (Sample 8)


title: AB399 (Sample 5)


title: AB398 (Sample 4)


title: Adult microglia k4me2

description: Sample 1

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

source_name: Adult microglia k4me2

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

value: Adult microglia

tag: chip antibody


title: E12.5 microglia ATAC

description:
Sample 7
Library strategy: ATAC-seq

source_name: E12.5 microglia B ATAC

value: E12.5 microglia


title: Pre-microglia k4me2

description: Sample 3

source_name: Pre-microglia k4me2

value: Pre-microglia


title: E12.5 microglia k4me2

description: Sample 2

source_name: E12.5 microglia k4me2


title: E12.5 YS progenitors ATAC

description:
Sample 8
Library strategy: ATAC-seq

source_name: E12.5 US progenitors ATAC

value: E12.5 YS progenitors


title: Adult microglia ATAC

description:
Sample 5
Library strategy: ATAC-seq

source_name: Adult microglia ATAC


title: AB335 (Sample 1)


title: AB436 (Sample 9)


title: Mafb_ctrl_5wk (Sample 80)

description:
processed data file: MafbKO.xlsx
5wk_ctrl_WT3.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

tag: genotype/variation

value: Mafb ctrl


title: Mafb_KO_Newborn (Sample 89)

description:
processed data file: MafbKO.xlsx
D4_Mafb_KO_6.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

value: Mafb KO

value: newborn


title: Mafb_KO_Newborn (Sample 84)

description:
processed data file: MafbKO.xlsx
C5_Mafb_KO_3.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Mafb_ctrl_5wk (Sample 79)

description:
processed data file: MafbKO.xlsx
5wk_ctrl_WT2.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Mafb_KO_Newborn (Sample 81)

description:
processed data file: MafbKO.xlsx
A3_Mafb_KO_1.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Mafb_KO_Newborn (Sample 85)

description:
processed data file: MafbKO.xlsx
C6_Mafb_KO_4.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Mafb_ctrl_Newborn (Sample 88)

description:
processed data file: MafbKO.xlsx
D3_WT_control_3.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Mafb_KO_Newborn (Sample 82)

description:
processed data file: MafbKO.xlsx
A7_Mafb_KO_2.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Mafb_KO_5wk (Sample 76)

description:
processed data file: MafbKO.xlsx
5wk_Mafb_KO2.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Mafb_KO_Newborn (Sample 87)

description:
processed data file: MafbKO.xlsx
D2_Mafb_KO_5.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Mafb_KO_5wk (Sample 77)

description:
processed data file: MafbKO.xlsx
5wk_Mafb_KO3.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Brain_GFctrl_8wk (Sample 74)

description:
processed data file: GermFree.xlsx
ctrl_c57_8_wk_2.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

value: GF ctrl


title: Brain_GFctrl_8wk (Sample 73)

description:
processed data file: GermFree.xlsx
ctrl_c57_8_wk_1.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Mafb_KO_5wk (Sample 75)

description:
processed data file: MafbKO.xlsx
5wk_Mafb_KO1.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: AB397 (Sample 3)


title: AB336 (Sample 2)


title: Brain_GFctrl_4wk (Sample 72)

description:
processed data file: GermFree.xlsx
ctrl_c57_4_wk_2.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Pre-microglia ATAC

description:
Sample 6
Library strategy: ATAC-seq

source_name: Pre-microglia ATAC


title: E12.5 YS progenitors k4me2

description: Sample 4

source_name: E12.5 YS progenitors k4me2


title: Mafb_ctrl_Newborn (Sample 86)

description:
processed data file: MafbKO.xlsx
D1_WT_control_2.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Brain_GF_Newborn (Sample 67)

description:
processed data file: GermFree.xlsx
NB_GF_3.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

value: GF Newborn


title: Brain_GFctrl_Newborn (Sample 70)

description:
processed data file: GermFree.xlsx
NB_ctrl_3.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

value: Brain


title: Brain_GFctrl_Newborn (Sample 69)

description:
processed data file: GermFree.xlsx
NB_ctrl_2.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Mafb_ctrl_5wk (Sample 78)

description:
processed data file: MafbKO.xlsx
5wk_ctrl_WT1.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Brain_GFctrl_4wk (Sample 71)

description:
processed data file: GermFree.xlsx
ctrl_c57_4_wk_1.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Mafb_ctrl_Newborn (Sample 83)

description:
processed data file: MafbKO.xlsx
C2_WT_control_1.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Brain_GF_Newborn (Sample 66)

description:
processed data file: GermFree.xlsx
NB_GF_2.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Brain_GFctrl_6wk (Sample 54)

description:
processed data file: GermFree.xlsx
GF_ctrl_6wk_female_3.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Brain_GF_6wk (Sample 60)

description:
processed data file: GermFree.xlsx
GF_mice_6wk_female_5.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

value: GF 6wk


title: Brain_GFctrl_6wk (Sample 55)

description:
processed data file: GermFree.xlsx
GF_ctrl_6wk_female_4.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Brain_GF_6wk (Sample 58)

description:
processed data file: GermFree.xlsx
GF_mice_6wk_female_3.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Brain_GFctrl_Newborn (Sample 68)

description:
processed data file: GermFree.xlsx
NB_ctrl_1.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Brain_GF_6wk (Sample 59)

description:
processed data file: GermFree.xlsx
GF_mice_6wk_female_4.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Brain_GF_8wk (Sample 63)

description:
processed data file: GermFree.xlsx
Germ_free_8_wk_1.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

value: GF 8wk


title: Brain_GF_8wk (Sample 64)

description:
processed data file: GermFree.xlsx
Germ_free_8_wk_2.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Brain_GF_6wk (Sample 56)

description:
processed data file: GermFree.xlsx
GF_mice_6wk_female_1.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Brain_GF_6wk (Sample 57)

description:
processed data file: GermFree.xlsx
GF_mice_6wk_female_2.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Brain_GFctrl_6wk (Sample 53)

description:
processed data file: GermFree.xlsx
GF_ctrl_6wk_female_2.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Brain_GF_4wk (Sample 62)

description:
processed data file: GermFree.xlsx
Germ_free_4_wk_2.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

value: GF 4wk


title: Brain_GF_Newborn (Sample 65)

description:
processed data file: GermFree.xlsx
NB_GF_1.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Brain_GF_4wk (Sample 61)

description:
processed data file: GermFree.xlsx
Germ_free_4_wk_1.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: Brain_GFctrl_6wk (Sample 52)

description:
processed data file: GermFree.xlsx
GF_ctrl_6wk_female_1.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: 10% RWC

city: Beijing

first: Lihong

last: Xiao

address: No.105 North Road of West 3rd-ring Road.Haidian District

institute: Capital Normal University

data_processing:
Basecalls performed using the Illumina GA Pipeline.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity (unknown bases are less than 10%) or low-quality sequence (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read), then mapped to Bhy_V1.0 (unpublished) whole genome using SOAPaligner/soap2.
The conversion rate would be calculated when we got the alignment information of whole-genome base (qmap).
Clean data were mapped to reference genome when we made sure the data quantity of clean data was qualified. After quality test, the uniquely mapped data were used to get methylation information of cytosine in whole genome after we made sure that the alignment result was qualified. Later, we used the cytosine information for standard bioinformatics analysis and personalized bioinformatics analysis.
Genome_build: Bhy_V1.0
Supplementary_files_format_and_content: excel files include annotation, methylation level and methylation changes of each differentially methylated genes.

organism: Dorcoceras hygrometricum

source_name: 10% RWC

extract_protocol:
DNA extracted from hydrated, moderate dehydration (70% RWC) and desiccated (10% RWC) leaf tissues of resurrection plant species B. hygrometrica.
Fragment genome DNA to 100-300bp by Sonication, and then DNA-end repair , 3’-dA overhang and ligation of methylated sequencing adaptors are conducted. Bisulfite treatment by ZYMO EZ DNA Methylation-Gold kit. Desalting, size selection, PCR amplification and size selection again. Qualified library for sequencing.

treatment_protocol: Plants growing in pots were subjected to hydrated, dehydtrating to 70% RWC and to 10% RWC.

tag: growth condition

value: 10% RWC

value: leaf


title: 70% RWC

source_name: 70% RWC

value: 70% RWC


title: HD

source_name: HD

value: HD


title: E.14.5_Poly.IC_injected_4wk (Sample 51)

description:
processed data file: PolyIC.xlsx
Poly_i_c_day_14_m2_4wk_6.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

value: poly i:c injection E14.5


title: E.14.5_Poly.IC_injected_4wk (Sample 49)

description:
processed data file: PolyIC.xlsx
Poly_i_c_day_14_m2_4wk_4.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: E.14.5_Poly.IC_injected_4wk (Sample 50)

description:
processed data file: PolyIC.xlsx
Poly_i_c_day_14_m2_4wk_5.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: E.14.5_Poly.IC_injected_4wk (Sample 48)

description:
processed data file: PolyIC.xlsx
Poly_i_c_day_14_m2_4wk_3.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: E.14.5_Poly.IC_injected_4wk (Sample 46)

description:
processed data file: PolyIC.xlsx
Poly_i_c_day_14_m2_4wk_1.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: distal cell 7

city: Boston

first: Peter

last: Kharchenko

state: MA

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

data_processing:
reads were aligned against mm9 annotations (NCBI37.61) using tophat 1.2.0 with default settings
FPKM values were estimated using cufflinks 1.3.0 with default settings
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files, as written out by cufflinks

source_name: HSPC-distal cell from col2.3GFP mouse

growth_protocol: Newborn col2.3GFP animals were injected with DiI-labeled LKS CD34-Flk2- adult bone marrow cells, as described below, and sacrificed 48 hours after transplantation.

extract_protocol:
Femurs were dissected, embedded in 10% low melting temperature agarose (Lonza) and sectioned at 100 _ using a vibratome (Leica). Single OLC harvesting was performed using a physiology microscope BX51 (Olympus) equipped with filters to detect GFP and DiI fluorescence, DIC optics, micromanipulators (Eppendorff), real-time imaging camera, peristaltic pump, in-line heater, perfusion chamber (Harvard Apparatus) and SAS Air Syringe (Research Instruments). Sections were pre-screened for the presence of rare GFP-labeled OLCs located next to single DiI-positive transplanted HSCPs, which were found in 1-2 out of 15 sections per animal.  Once a target proximal OLC was identified, the section was rotated so that the target was directly opposite the aspiration pipette (Humagen) and secured against the bottom of the perfusion chamber using a horizontal portion of the holding pipette (Humagen). With the aspiration pipette just above the target, the section was perfused with warm (37C) cell dissociation solution (Liberase TM, Roche) for 8-10 minutes while the target cell was visually monitored. Then, applying positive pressure from the micropipette using Air Syringe, hematopoietic cells surrounding the target OLC were dislodged to create a 20-30 _ clearing. Finally, the aspiration pipette was lowered onto the target OLC, the cell was gently detached from the endosteal surface and aspirated. The presence of GFP fluorescence in the aspirated cell inside the aspiration pipette was confirmed, the contents of the pipette was ejected into a PCR tube with the lysis buffer for the single cell RNA-Seq protocol, and frozen immediately at -80C.
Reverse transcription, cDNA amplification, library preparation and SOLiD RNA-Seq were performed as described in Tang, F. et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 6, 377-82 (2009)

value: distal


title: distal cell 6


title: distal cell 8


title: E.14.5_Poly.IC_injected_4wk (Sample 45)

description:
processed data file: PolyIC.xlsx
Poly_i_c_day_14_m1_4wk_6.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: E.14.5_Poly.IC_injected_4wk (Sample 43)

description:
processed data file: PolyIC.xlsx
Poly_i_c_day_14_m1_4wk_4.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: E.14.5_Poly.IC_injected_4wk (Sample 41)

description:
processed data file: PolyIC.xlsx
Poly_i_c_day_14_m1_4wk_2.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: E.14.5_Poly.IC_injected_4wk (Sample 42)

description:
processed data file: PolyIC.xlsx
Poly_i_c_day_14_m1_4wk_3.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: E.14.5_Poly.IC_injected_4wk (Sample 47)

description:
processed data file: PolyIC.xlsx
Poly_i_c_day_14_m2_4wk_2.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: E.14.5_Poly.IC_injected_4wk (Sample 40)

description:
processed data file: PolyIC.xlsx
Poly_i_c_day_14_m1_4wk_1.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: E.14.5_Poly.IC_injected_4wk (Sample 44)

description:
processed data file: PolyIC.xlsx
Poly_i_c_day_14_m1_4wk_5.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: proximal cell 8

source_name: HSPC-proximal cell from col2.3GFP mouse

value: proximal


title: distal cell 1


title: distal cell 4


title: distal cell 3


title: E.12.5_Poly.IC_injected_newborn (Sample 38)

description:
processed data file: PolyIC.xlsx
Poly_i_c_E12.5_NB4.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

value: poly i:c injection E12.5


title: proximal cell 7


title: proximal cell 3


title: proximal cell 5


title: proximal cell 4


title: E.12.5_Poly.IC_injected_newborn (Sample 37)

description:
processed data file: PolyIC.xlsx
Poly_i_c_E12.5_NB3.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: proximal cell 6


title: proximal cell 2


title: E.12.5_Poly.IC_injected_newborn (Sample 36)

description:
processed data file: PolyIC.xlsx
Poly_i_c_E12.5_NB2.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: distal cell 5


title: Fru_DHA_hypothalamus_rep2

city: Los Angeles

first: Xia

last: Yang

address: 2000 Terasaki Life Sciences Bldg, 610 Charles E. Young Drive East

department: IBP

institute: UCLA

description: processed data file: Hypothalamus_fpkm_processed.txt

data_processing:
Paired-end RNA-Seq reads were analyzed using the Tuxedo tool package comprised of Tophat/Bowtie, Cufflinks, and Cuffdiff. Specifically, we used TopHat2/Bowtie2 which allows alignment across splice junctions to map reads to the rat genome (UCSC assembly 5.0) and to discover transcript splice sites. Cufflinks were then used to assemble the aligned reads onto transcripts, and Cuffdiff was used to compare the aligned reads between different treatment groups to identify genes and gene transcripts that are differentially expressed. Multiple hypothesis testing was corrected using the Benjamini-Hochberg method to estimate false discover rate (FDR).
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and status ("FAIL","HIGHDATA","LOWDATA","OK",etc.) for each sample

organism: Rattus norvegicus

extract_protocol:
Total RNA was extracted with Qiagen AllPrep DNA/RNA Mini Kit. Quantity and quality of RNA were checked using Nanodrop (Thermo Fisher Scientific, MA, USA), Bioanalyzer (Agilent Technologies, CA, USA) and Qubit RNA assay (Life Technologies, NY, USA).
The RNA-Seq libraries were prepared followed the standard Illumina protocol (http://support.illumina.com/sequencing/documentation.ilmn). Briefly, about 1,000 ng total RNA was first enriched for mRNA by poly-A selection, then fragmented, and reverse transcribed using random hexamer-primers to generate first-strand cDNA. Second-strand cDNA was then generated using RNase H and DNA polymerase. Fragments of 200-400 bp in size were next enriched through PCR and multiplex barcodes were also added. Sequencing was performed on HiSeq 2000 (Illumina Inc, CA, USA). Data quality check was done on Sequencing Analysis Viewer and demultiplexing was performed with CASAVA 1.8.2 (Illumina Inc, CA, USA).

value: Sprague Dawley

value: male

tag: fed with

value: fructose and DHA for 6 wks

value: hypothalamus


title: distal cell 2

tag: cell type


title: E.12.5_Poly.IC_injected_newborn (Sample 35)

description:
processed data file: PolyIC.xlsx
Poly_i_c_E12.5_NB1.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

tag: strain

value: newborn


title: Fru_DHA_hypothalamus_rep1


title: E.12.5_Poly.IC_injected_newborn (Sample 39)

description:
processed data file: PolyIC.xlsx
Poly_i_c_E12.5_NB5.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

value: Brain


title: input DNA

city: Ithaca

first: Wojciech

last: Pawlowski

state: NY

address: Bradfield Hall, Room 403

department: Plant Breeding and Genetics

institute: Cornell University

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the B73 reference genome sequence (release AGPv2) using the Burrows-Wheeler Aligner (BWA)
Data were filtered base on unique mapping
peak calling using MACS with parameter bandwidth 800
bed file were used to calculated ratio of nucleasome occupancy
Ratio calculated by treatment divided by control from peak regions
Genome_build: B73 (release AGPv2)
Supplementary_files_format_and_content: [.bed] reports peaks, counts, ratios of nucleasome occupancy

organism: Zea mays

source_name: Flower

extract_protocol: Nuclei were prepared as described in the ChIP protocol except that EDTA was omitted from buffers.  Nuclei pellet was resuspended in 500 μl Digestion Buffer (50 mM Tris-HCl pH8.0, 5 mM CaCl2, 0.1 mM PMSF, 1 µg/ml cOmplete Protease Inhibitor Cocktail (Roche, Penzberg, Germany)). Samples were sonicated for 5 second and treated with 0.02 U /µl of micrococcal nuclease (NEB, Ipswich, MA, USA) for 10 min at room temperature.  The reaction was stopped with 10 mM EDTA and DNA was prepared as in the ChIP protocol.  The purified DNA was separated in a 2% agarose gel and fragments ~150 bp in size were recovered.  Approximately 100 ng of mononucleosome DNA was used for Illumina library construction.  As a control, randomly fragmented chromatin was prepared by sonication to produce 200 - 500 bp fragments.

tag: inbred line


title: Fru_DHA_hippocampus_rep4

description: processed data file: Hippocampus_fpkm_processed.txt

tag: tissue

value: hippocampus


title: Fru_DHA_hypothalamus_rep4

tag: gender


title: E.14.5_PBS_injected_4wk (Sample 33)

description:
processed data file: PolyIC.xlsx
PBS_d14_4wk_3.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

value: PBS injection E14.5


title: Fru_DHA_hippocampus_rep2


title: Fru_DHA_hippocampus_rep3


title: E.14.5_Poly.IC_injected_newborn (Sample 32)

description:
processed data file: PolyIC.xlsx
NB_poly_i_c__inj_e14_2.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: E.14.5_PBS_injected_newborn (Sample 30)

description:
processed data file: PolyIC.xlsx
NB_PBS_inj_e14_2.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: proximal cell 1


title: Fru_DHA_hippocampus_rep1


title: yolk_E13.5 (Sample 27)

description:
processed data file: Timeline.xlsx
ys_13.5_dispo_1.2
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.

value: CX3CR1-GFP+ C57BL/6J

value: Yolk sac


title: E.14.5_PBS_injected_4wk (Sample 34)

description:
processed data file: PolyIC.xlsx
PBS_d14_4wk_4.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: E.14.5_Poly.IC_injected_newborn (Sample 31)

description:
processed data file: PolyIC.xlsx
NB_poly_i_c__inj_e14_1.M
Fastq files contain only read1. read2 used to read sample barcodes and UMI only. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.


title: rat hypothalamus Fru_rep4

description: replicate 4

data_processing:
We tested data qualities by using Principal Component Analysis, hierarchical cluster analysis and variances test, and excluded one of the samples (Hypo_Fru_rep4) as an outlier.
Paired-end RNA-Seq reads were analyzed using the Tuxedo tool package comprised of Tophat/Bowtie, Cufflinks, and Cuffdiff. Specifically, we used TopHat2/Bowtie2 which allows alignment across splice junctions to map reads to the rat genome (UCSC assembly 5.0) and to discover transcript splice sites. Cufflinks were then used to assemble the aligned reads onto transcripts, and Cuffdiff was used to compare the aligned reads between different treatment groups to identify genes and gene transcripts that are differentially expressed. Multiple hypothesis testing was corrected using the Benjamini-Hochberg method to estimate false discover rate (FDR).
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and status ("FAIL","HIGHDATA","LOWDATA","OK",etc.) for each sample

source_name: rat hypothalamus

value: fructose