title: Mecp2_ko_p50_IP


title: Untreated 2 SMAD2 ChIP

status: Public on Dec 31 2016

type: SRA

city: London

first: Caroline

middle: S

last: Hill

address: 1 Midland Road

department: Developmental Signalling

country: United Kingdom

institute: Francis Crick Institute

description:
processed data file: Untr_S2_ChIP_4_1.bedGraph
processed data file: Untr_S2_ChIP_4_1.bed
processed data file: Untreated_SMAD2_peaks_2.txt

library_source: genomic

data_processing:
The raw reads were aligned to the mouse mm10 genome assembly using BWA 0.6.2r126 (Li and Durbin, 2009), with a maximum mismatch threshold of 2 permissible within a seed length of 51 bp. All other parameters were kept as default
To identify regions enriched with reads when compared to an input control we used MACS (Zhang et al., 2008) (q-value 0.05). Peaks were annotated in terms of distance to nearest gene (user-defined) using ChIPPeakAnno (Bioconductor)
genome build: mm10
processed data files format and content: Bed files are those generated by MACS and contain information for all peaks called for a given ChIP vs input comparison. bedGraph files derived from the original BAM alignment files.  Tab-delimited text files contain detailed annotation information for all MACS-called peaks, including: chr start-end, peak width, strand, peak summit, peak MACS fold enrichment score, MACS logged p-value, nearest feature (gene), distance to feature, gene feature details in terms of entrezid, symbol, genename, chr location, igv

molecule: genomic DNA

organism: Mus musculus

source_name: p19 cells

growth_protocol: DMEM + 10 % FCS

extract_protocol:
Samples for ChIP-seq with the corresponding inputs were prepared by crosslinking in 1% formaldehyde for 10 minutes at RT, cytoplasmic lysis, sonication of nuclei to shear the DNA to 100-500 bp, followed by incubation with anti-SMAD2 antibody overnight. pre-blocked protein A dynabeads (invitrogen) were added for 4 hours, followed by washing, DNA elution, reversal of crosslinks and proteinase K digestion. Resulting enriched ChIP DNA was cleaned up using Qiagen PCR purification kit. Corresponding input chromatin was processed alongside at the same time.
Following end repair, poly-A-tailing and adapter ligation, Illumina TruSeq ChIP sample preparation kits were used to generate the libraries. The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix (Kapa Biosystems, Cape Town, South Africa).  The PCR was run before gel isolation using the Invitrogen SizeSelect E-gel system (SizeSelect gel protocol, Thermo Fisher Scientific).  Post PCR we used AMPure XP beads (AMPure bead protocol, Beckman Coulter, Inc.) at a 1:1 ratio to maintain size integrity. Samples were multiplexed and 51-bp single end reads were generated on an Illumina HiSeq 2500.

treatment_protocol: either none (untreated); or pre-treatment with 10 μM SB-431542 overnight + washout using PBS (3x), followed by replacement of fresh media containing 20 ng/ml Activin or 10 μM SB-431542 for the indicated times

tag: cell type

value: Embryonic teratoma

tag: cell line

tag: signal inhibition pretreatment

tag: ligand treatment

tag: chip antibody

value: SMAD2 (Cell signaling 5339)


title: 8 hr Activin 2 SMAD2 ChIP

description:
processed data file: Act8_S2_ChIP_4_1.bedGraph
processed data file: Act8_S2_ChIP_4_1.bed
processed data file: 8hrActivin_SMAD2_peaks_2.txt

value: 10 μM SB-431542 overnight + washout

value: 8 hr 20ng/ml Activin A


title: SB-431542 2 SMAD2 ChIP

description:
processed data file: SB_S2_ChIP_4_1.bedGraph
processed data file: SB_S2_ChIP_4_1.bed

value: 10 μM SB-431542 overnight

value: 1 hr Media replacement containing 10 μM SB-431542


title: 1 hr Activin 2 SMAD2 ChIP

description:
processed data file: Act1_S2_ChIP_4_1.bedGraph
processed data file: Act1_S2_ChIP_4_1.bed
processed data file: 1hrActivin_SMAD2_peaks_2.txt

value: 1 hr 20ng/ml Activin A


title: Mecp2_ko_p56_IP

city: Boston

first: Hao

last: Wu

state: Massachusetts

address: 149G Warren Alpert Building, 200 Longwood Avenue

department: Genetics

country: USA

institute: Harvard Medical School/HHMI

description:
Ribosome-associating mRNA
DESeq2_htseq-counts_wt.vs.ko.txt

library_source: transcriptomic

data_processing:
Sequencing reads (51bp, single-end) were first mapped to the Mus musculus primary assembly reference genome (Gencode GRCm38/release M6) using STAR-2.4.2a. Uniquely mapped reads that overlapped with exons of known protein coding genes were counted using htseq-count python script. Differential expression was calculated using DESeq2 (Love et al., 2014), and P-values were adjusted for multiple testing using the Benjamini-Hochberg procedure.
Genome_build: GRCm38/release M6
Supplementary_files_format_and_content: tab-delimited text files include DESeq2-normalized count values (dervied from htseq-count script) for each sample.

molecule: total RNA

source_name: Hippocampus

growth_protocol: Mecp2 KO mice (Mecp2 tm1.1bird from The Jackson Laboratory, 003890) and WT littermates were maintained on C57/Bl6 background by breeding Mecp2 -/+ females with WT males from Charles Rivers.The Cck-bacTRAP GM39) line was provided by Dr. Nathaniel Heintz at the Rockefeller University.  In this mouse, EGFP fused to the ribosomal protein L10a was inserted in the bacterial artificial chromosome (BAC) in such a way that expression was driven by the cholecystokinin (Cck) promoter. All experiments were performed on littermate WT and Mecp2 KO mice, with the experimenter blinded to genotype.

extract_protocol:
Translating mRNAs were immunoprecipitated from acutely dissected hippocampal tissue and purified as previously described (Heiman et al., 2008, Heiman et al., 2014). RNA samples were analyzed with Bioanalyzer (Agilent) to confirm RNA integrity (RIN>7). RNA concentrations were determined by Quant-it Ribogreen RNA assay (Life Technologies).
Purified RNA (1~1.5 ng) was converted to cDNAs with Ovation RNA-seq V2 system (NuGEN). 500 ng cDNAs from each sample were fragmented to around 200bp size using a Covaris S2 ultrasonicator. Fragmented cDNA (100 ng) was end-repaired, dA-tailed and ligated to adaptors using the NEBNext Ultra DNA library prep kit (New England Biolabs). Sequencing libraries were prepared using the KAPA HiFi Hotstart Ready Mix PCR Kit (Kapa biosystems) and NEBNext Multiplex Oligos for Illumina (Index Primers Set1 and 2).  Library quality was examined by Qubit dsDNA HS Assay Kit (Life Technologies) and Bioanalyzer using High Sensitivity DNA kit (Agilent).  Final concentrations of sequencing libraries were quantified by qPCR using KAPA Library Quantification Kit (Kapa biosystems). TRAP-seq libraries were sequenced on a HiSeq 2500 or a NextSeq 500 sequencer (Illumina).

treatment_protocol: Chronic CTEP treatment (0.4 mg/kg) was administered via subcutaneous injection (for mice younger than P30) or oral gavage (for mice older than P30) once every 48 hr. This dose was chosen after a pilot study revealed that the dose of 2 mg/kg used in previous studies in fragile X (Michalon et al., 2012) and 16p11.2 microdeletion (Tian et al., 2015) mouse models caused significant weight loss in the Mecp2 mice.

tag: age of animal

value: postnatal day 56

tag: cell-type

value: Hippocampal CA1 neurons (Cck-EGFP-L10a)

tag: drug treatment

value: no

tag: strain


title: Ets1_KO_Rep2

city: Buffalo

first: Lee Ann

last: Sinha

state: NY

address: 701 Ellicott St

department: Biochemistry

institute: University at Buffalo

data_processing:
Reads were mapped to mouse transcriptome (mm9 assembly) using Tophat2 version 2.0.13
The aligned reads were assembled and mapped to the mm9 transcriptome.
Cuffdiff was used to calculate differential gene expression and derive FPKM (Fragments per kilobase of transcript per million mapped reads) values
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited files include FPKM values for each sample

source_name: Spleen

extract_protocol:
Quiescent follicular B cells were sorted out from splenocytes and RNA was harvested using Trizol reagent and purified by Direct-zol RNA Miniprep kit
1 μg of total RNA was used to construct the libraries using Illumina TruSeq RNA Sample Prep Kit

value: Quiescent follicular B cell

tag: genotype


title: 1 hr Activin 2 input ChIP

description: processed data file: 1hrActivin_input_4_1.bedGraph

value: 1 hr 20 ng/ml Activin A


title: Untreated 2 input ChIP

description: processed data file: Untr_input_4_1.bedGraph


title: Mecp2_ko_p60_Veh_IP

description:
Ribosome-associating mRNA
DESeq2_htseq-counts_Veh.vs.CTEP.txt

value: postnatal day 60

value: Vehicle


title: Mecp2_ko_p60_CTEP_IP

value: CTEP


title: Mecp2_ko_p37_IP

value: postnatal day 37


title: Mecp2_wt_p37_IP

description:
Ribosome-associating mRNA
DESeq2_htseq-counts_IP.vs.input.txt, DESeq2_htseq-counts_wt.vs.ko.txt


title: SB-431542 1 SMAD2 ChIP

description:
processed data file: SB_Smad2_5339_2_1.bedGraph
processed data file: SB_5339.bed


title: Beads control 1 ChIP

description: processed data file: Beads_control_2_1.bedGraph

value: Invitrogen prot A dynabeads


title: 1 hr Activin 1 SMAD2 ChIP

description:
processed data file: Activin_1hr_Smad2_5339_2_1.bedGraph
processed data file: Activin_1hr_5339.bed
processed data file: 1hrActivin_SMAD2_peaks_1.txt

value: Embryonic teratoma


title: SB-431542 2 input ChIP

description: processed data file: SB_input_4_1.bedGraph


title: Untreated 1 SMAD2 ChIP

description:
processed data file: Untreated_Smad2_5339_2_1.bedGraph
processed data file: Untreated_5339.bed
processed data file: Untreated_SMAD2_peaks_1.txt

value: SMAD2 (Cell signaling 5339)


title: 8 hr Activin 1 SMAD2 ChIP

description:
processed data file: Activin_8hr_Smad2_5339_2_1.bedGraph
processed data file: Activin_8hr_5339.bed
processed data file: 8hrActivin_SMAD2_peaks_1.txt

value: 10 μM SB-431542 overnight + washout

value: 8 hr 20 ng/ml Activin A


title: Untreated 1 input ChIP

description: processed data file: input_Untreated_2_1.bedGraph


title: 1 hr Activin 1 input ChIP

description: processed data file: input_Activin_1hr_2_1.bedGraph


title: 8 hr Activin 1 Emetine RNAseq

description:
processed data file: RNAseq_reads_RPKM_logFC_emetine.txt
processed data file: RNASeq.rawcountsPerGene.allSamples.csv

data_processing:
The 101 bp single-end read data were aligned to the mm10 version of the mouse genome using Tophat2 (Kim et al., 2013). A transcriptome guide file derived from the knownGene annotation table available from the University of California, Santa Cruz (UCSC) Genome Bioinformatics site was provided to focus alignments towards characterized transcripts. Non-unique alignments were removed prior to further analysis.
The data were quantified at the gene level by counting reads aligning within each gene's exon structure. Reads partially aligning outside exon boundaries were excluded from the quantification using the summarizeOverlaps function from the GenomicAlignments Bioconductor library with mode="IntersectionStrict" (Huber et al., 2015).
genome build: mm10
processed data files format and content: RNAseq_reads_RPKM_logFC*: tab-delimited text files include normalised read counts for each sample, as well as FPKM values for each of the replicates. In addition, columns containing log2FC relative to SB-431542, with corresponding (adjusted) p-values are provided
processed data files format and content: RNASeq.rawcountsPerGene.allSamples.csv, a tab-delimited text file contains raw read counts per gene.

extract_protocol:
All RNA-seq experiments were performed in duplicate. Total RNA was prepared using Trizol followed by a clean up with an RNeasy kit (Qiagen). The quality of the RNA was assessed using a Bioanalyzer (Agilent).
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina). 101 bp single end reads were generated using an Illumina HiSeq 2500.

value: 8 hr 20 ng/ml Activin A + 10 μM emetine


title: SB-431542 1 input ChIP

description: processed data file: input_SB_2_1.bedGraph

value: 10 μM SB-431542 overnight

value: 1 hr Media replacement containing 10 μM SB-431542


title: Beads control 2 ChIP

description: processed data file: Beads_ChIP_4_1.bedGraph


title: 8 hr Activin 1 CHX RNAseq

description:
processed data file: RNAseq_reads_RPKM_logFC_CHX.txt
processed data file: RNASeq.rawcountsPerGene.allSamples.csv

value: 8 hr 20 ng/ml Activin A  + 5 ng/ml Cycloheximide


title: 1 hr Activin 1 CHX RNAseq

value: 1 hr 20 ng/ml Activin A   + 5 ng/ml Cycloheximide


title: SB-431542 2 CHX RNAseq

value: 1 hr Media replacement containing 10 μM SB-431542  + 5 ng/ml Cycloheximide


title: SB-431542 1 CHX RNAseq

value: 1 hr Media replacement containing 10 μM SB-431542 + 5 ng/ml Cycloheximide


title: 8 hr Activin 1 input ChIP

description: processed data file: input_Activin_8hr_2_1.bedGraph


title: 1 hr Activin 1 Emetine RNAseq

value: 1 hr 20 ng/ml Activin A  + 10 μM emetine


title: Untreated 2 RNAseq

description:
processed data file: RNAseq_reads_RPKM_logFC_ctrl.txt
processed data file: RNASeq.rawcountsPerGene.allSamples.csv


title: 8 hr Activin 2 Emetine RNAseq


title: Untreated 1 RNAseq


title: 1 hr Activin 2 Emetine RNAseq

value: 1 hr 20 ng/ml Activin A + 10 μM emetine


title: 1 hr Activin 2 CHX RNAseq

value: 1 hr 20 ng/ml Activin A  + 5 ng/ml Cycloheximide


title: SB-431542 1 Emetine RNAseq

value: 1 hr Media replacement containing 10 μM SB-431542 + 10 μM emetine


title: 8 hr Activin 1 RNAseq


title: 8 hr Activin 2 RNAseq


title: 1 hr Activin 1 RNAseq

value: 1 hr 20 ng/ml Activin A


title: SB-431542 1 RNAseq


title: 8 hr Activin 2 CHX RNAseq


title: SB-431542 2 Emetine RNAseq


title: Gfi1 36N_H3K9ac_ChIP-Seq

city: Essen

first: Cyrus

last: Khandanpour

address: Hufelandstr. 55

country: Germany

institute: Universitätsklinikum Essen

data_processing:
Basecalls were performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm10 genome assembly using STAR version 2.5.0c with the following configurations: STAR --genomeDir /path/... --runThreadN 12 --readFilesIn /path/. Sample_1a_R1.fastq,Sample_1b_R1.fastq,Sample_1c_R1.fastq,Sample_1d_R1.fastq --outFileNamePrefix Gfi1_36X --sjdbGTFfile /path/to/ann.gtf --outSAMtype BAM Unsorted SortedByCoordinate --alignIntronMax 1
BAM-file indexes were generated using samtools
BAM files were analyzed using SeqMonk V 0.32.1 and peak-probes were defined using the MACS algorithm, probes were quantitated in log-format and normalized to total read counts, annotated with closest genes and exported as txt-files
Subsequently, H3K9ac probe-levels were analyzed by ALtAnalyze V2.0 (default parameters but: data type: Other ID; platform: Ensembl; process expression file; greater 1.5-fold enrichment) and GSEA (default parameters but: collapse to symbols;  1000 permutations; permutation type: gene_set; Collapsing mode for probe sets ==> 1 gene: Median of probes).
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheet with annotated probes, closest genes, probe-levels

source_name: leukemic spleen cells

extract_protocol:
the spleens were isolated from NUP98/HOXD13 mice carrying either the human GFI136S or the human GFI136N cDNA. The spleens were homogenised and ery lysis was performed. 3x10^7 cells were fixed with 0.4% formaldehyde and sonicated for 20 min. Histone-DNA antibody were isolated with antibody
Libraries were prepared using the NEBNext® UltraTM DNA Library Prep Kit for Illumina®. Samples were pooled after quality check.

value: Gfi1 36N/N-Nup98/HoxD13

tag: tissue

value: spleen

tag: chip-antibody

value: H3K9ac, Active Motif, Cat#  39917, Lot# 23913004


title: SB-431542 2 RNAseq

value: Embryonic teratoma


title: Gfi1 36S_H3K9ac_ChIP-Seq

value: Gfi1 36S/S-Nup98/HoxD13


title: 1 hr Activin 2 RNAseq

value: 10 μM SB-431542 overnight + washout


title: Input Histone Activin 8h ChipSeq biological replicate 2

description: ChIP antibody: none

data_processing:
Raw reads were aligned to the mouse mm10 genome assembly using BWA 0.6.2r126 (Li and Durbin, 2009), with a maximum mismatch threshold of 2 permissible within a seed length of 51 bp. All other parameters were kept as default.
Alignments were post-processed with picard-tools 1.107 for the removal of reads that could have arisen from PCR duplication (http://sourceforge.net/projects/picard/).
DiffReps 1.55.4 (Shen et al. 2013) was used to determine sites of differential enrichment of Pol II (either phosphorylated on Ser2 or Ser5 of the CTD) at each time point relative to SB-431542. For each ChIP-seq experiment, replicate samples for each time point were compared to the SB-431542 sample. The corresponding input samples were also provided to DiffReps for background noise estimation. The "--nsd" and "--frag" parameters were set to "broad" and "200", respectively, and all other parameters were kept as default.
Genome_build: mm10
Supplementary_files_format_and_content: Unnormalised bedgraph files were generated from deduplicated bam files using bedtools 2.25 genomeCoverageBed with default parameters. Bedgraph files for H3 ChIP samples represent the merged coverage from technical replicates.
Supplementary_files_format_and_content: Differential sites generated by diffReps 1.55.4 are provided in ".tsv" format. See https://github.com/shenlab-sinai/diffreps for file format and field information.

source_name: P19 cells

extract_protocol: Following end repair, poly-A-tailing and adapter ligation, Illumina TruSeq ChIP sample preparation kits were used to generate the libraries. The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix (Kapa Biosystems, Cape Town, South Africa).  The PCR was run before gel isolation using the Invitrogen SizeSelect E-gel system (SizeSelect gel protocol, Thermo Fisher Scientific).  Post PCR we used AMPure XP beads (AMPure bead protocol, Beckman Coulter, Inc.) at a 1:1 ratio to maintain size integrity. Samples were multiplexed and 51-bp single end reads were generated on an Illumina HiSeq 2500.

treatment_protocol: Either none (untreated); or pre-treatment with 10 μM SB-431542 overnight + washout using PBS (3x), followed by replacement of fresh media containing 20 ng/ml Activin or 10 μM SB-431542 for the indicated times.

value: embryonic teratoma


title: Input Histone Activin 4h ChipSeq biological replicate 2

description: ChIP antibody: none


title: Input Histone Activin 4h ChipSeq biological replicate 1

description: ChIP antibody: none


title: Input Histone Activin 1h ChipSeq biological replicate 2

description: ChIP antibody: none


title: Input Histone Untreated ChipSeq biological replicate 2

description: ChIP antibody: none


title: Input Histone SB-431542 ChipSeq biological replicate 1

description: ChIP antibody: none


title: Input Histone Untreated ChipSeq biological replicate 1

description: ChIP antibody: none


title: Input PolII Activin 8h ChipSeq biological replicate 2

description: ChIP antibody: none


title: Input Histone SB-431542 ChipSeq biological replicate 2

description: ChIP antibody: none


title: Input PolII Activin 8h ChipSeq biological replicate 1

description: ChIP antibody: none


title: Input PolII Activin 4h ChipSeq biological replicate 2

description: ChIP antibody: none


title: Input Histone Activin 8h ChipSeq biological replicate 1

description: ChIP antibody: none


title: Input Histone Activin 1h ChipSeq biological replicate 1

description: ChIP antibody: none


title: Input PolII SB-431542 ChipSeq biological replicate 2

description: ChIP antibody: none


title: Input PolII Activin 4h ChipSeq biological replicate 1

description: ChIP antibody: none


title: Input PolII Activin 1h ChipSeq biological replicate 2

description: ChIP antibody: none


title: Input PolII SB-431542 ChipSeq biological replicate 1

description: ChIP antibody: none


title: Input PolII Activin 1h ChipSeq biological replicate 1

description: ChIP antibody: none


title: Input PolII Untreated ChipSeq biological replicate 1

description: ChIP antibody: none


title: H3 Activin 8h ChipSeq biological replicate 2 techical replicates 1 and 2

description: ChIP antibody: Abcam Ab1791


title: Input PolII Untreated ChipSeq biological replicate 2

description: ChIP antibody: none


title: H3 SB-431542 ChipSeq biological replicate 2 techical replicates 1 and 2

description: ChIP antibody: Abcam Ab1791


title: H3 Activin 4h ChipSeq biological replicate 1 techical replicates 1 and 2

description: ChIP antibody: Abcam Ab1791


title: H3 Activin 4h ChipSeq biological replicate 2 techical replicates 1 and 2

description: ChIP antibody: Abcam Ab1791


title: H3 Untreated ChipSeq biological replicate 2 techical replicates 1 and 2

description: ChIP antibody: Abcam Ab1791


title: H3 Activin 1h ChipSeq biological replicate 2 techical replicates 1 and 2

description: ChIP antibody: Abcam Ab1791


title: H3 Activin 1h ChipSeq biological replicate 1 techical replicates 1 and 2

description: ChIP antibody: Abcam Ab1791


title: H3 Activin 8h ChipSeq biological replicate 1 techical replicates 1 and 2

description: ChIP antibody: Abcam Ab1791


title: 8 hr Activin 2 input ChIP

description: processed data file: 8hrActivin_input_4_1.bedGraph

value: 8 hr 20 ng/ml Activin A


title: H3 Untreated ChipSeq biological replicate 1 techical replicates 1 and 2

description: ChIP antibody: Abcam Ab1791


title: H3K9ac Activin 4h ChipSeq biological replicate 1

description: ChIP antibody: Abcam Ab4441


title: H3 SB-431542 ChipSeq biological replicate 1 techical replicates 1 and 2

description: ChIP antibody: Abcam Ab1791


title: H3K27ac Activin 4h ChipSeq biological replicate 1

description: ChIP antibody: Abcam Ab4729


title: H3K9ac Activin 8h ChipSeq biological replicate 2

description: ChIP antibody: Abcam Ab4441


title: H3K27ac Untreated ChipSeq biological replicate 1

description: ChIP antibody: Abcam Ab4729


title: PolII Serine5 Activin 8h ChipSeq biological replicate 2

description:
ChIP antibody: Diagenode C15200005
processed data file: POLII_SER5_SBvsACT_8H.tsv.gz


title: H3K9ac Activin 4h ChipSeq biological replicate 2

description: ChIP antibody: Abcam Ab4441


title: H3K27ac SB-431542 ChipSeq biological replicate 1

description: ChIP antibody: Abcam Ab4729


title: H3K9ac Activin 1h ChipSeq biological replicate 2

description: ChIP antibody: Abcam Ab4441


title: H3K9ac Activin 1h ChipSeq biological replicate 1

description: ChIP antibody: Abcam Ab4441


title: H3K9ac SB-431542 ChipSeq biological replicate 2

description: ChIP antibody: Abcam Ab4441


title: H3K9ac Activin 8h ChipSeq biological replicate 1

description: ChIP antibody: Abcam Ab4441


title: H3K9ac Untreated ChipSeq biological replicate 2

description: ChIP antibody: Abcam Ab4441


title: H3K9ac SB-431542 ChipSeq biological replicate 1

description: ChIP antibody: Abcam Ab4441


title: H3K27ac Activin 8h ChipSeq biological replicate 2

description: ChIP antibody: Abcam Ab4729


title: H3K9ac Untreated ChipSeq biological replicate 1

description: ChIP antibody: Abcam Ab4441


title: PolII Serine5 Activin 1h ChipSeq biological replicate 2

description:
ChIP antibody: Diagenode C15200005
processed data file: POLII_SER5_SBvsACT_1H.tsv.gz


title: PolII Serine5 SB-431542 ChipSeq biological replicate 2

description: ChIP antibody: Diagenode C15200005


title: H3K27ac Activin 8h ChipSeq biological replicate 1

description: ChIP antibody: Abcam Ab4729


title: H3K27ac Activin 4h ChipSeq biological replicate 2

description: ChIP antibody: Abcam Ab4729


title: H3K27ac Activin 1h ChipSeq biological replicate 2

description: ChIP antibody: Abcam Ab4729


title: H3K27ac Activin 1h ChipSeq biological replicate 1

description: ChIP antibody: Abcam Ab4729


title: H3K27ac SB-431542 ChipSeq biological replicate 2

description: ChIP antibody: Abcam Ab4729


title: PolII Serine5 Untreated ChipSeq biological replicate 1

description:
ChIP antibody: Diagenode C15200005
processed data file: POLII_SER5_SBvsUNT.tsv.gz


title: PolII Serine2 Activin 8h ChipSeq biological replicate 1

description:
ChIP antibody: Diagenode C15200005
processed data file: POLII_SER2_SBvsACT_8H.tsv.gz


title: PolII Serine5 Activin 8h ChipSeq biological replicate 1


title: H3K27ac Untreated ChipSeq biological replicate 2

description: ChIP antibody: Abcam Ab4729


title: PolII Serine2 Activin 1h ChipSeq biological replicate 1

description:
ChIP antibody: Diagenode C15200005
processed data file: POLII_SER2_SBvsACT_1H.tsv.gz


title: PolII Serine2 Activin 4h ChipSeq biological replicate 1

description:
ChIP antibody: Diagenode C15200005
processed data file: POLII_SER2_SBvsACT_4H.tsv.gz


title: PolII Serine2 Activin 1h ChipSeq biological replicate 2


title: PolII Serine5 Activin 4h ChipSeq biological replicate 1

description:
ChIP antibody: Diagenode C15200005
processed data file: POLII_SER5_SBvsACT_4H.tsv.gz


title: PolII Serine5 Untreated ChipSeq biological replicate 2


title: PolII Serine5 SB-431542 ChipSeq biological replicate 1

description: ChIP antibody: Diagenode C15200005


title: PolII Serine5 Activin 4h ChipSeq biological replicate 2


title: PolII Serine2 Activin 4h ChipSeq biological replicate 2


title: PolII Serine2 SB-431542 ChipSeq biological replicate 2

description: ChIP antibody: Diagenode C15200005


title: PolII Serine2 SB-431542 ChipSeq biological replicate 1

description: ChIP antibody: Diagenode C15200005


title: PolII Serine2 Activin 8h ChipSeq biological replicate 2


title: PolII Serine2 Untreated ChipSeq biological replicate 1

description:
ChIP antibody: Diagenode C15200005
processed data file: POLII_SER2_SBvsUNT.tsv.gz


title: PolII Serine5 Activin 1h ChipSeq biological replicate 1


title: Liver_2_ZT20

city: Lausanne

first: Jonathan

middle: Aryeh

last: Sobel

state: Vaud

address: EPFL SV IBI-SV UPNAE AAB 0 36 (Batiment AAB) Station 15

department: School of Life Sciences

country: Switzerland

institute: EPFL

data_processing:
RNA-seq mapping was performed with the STAR mapping protocol (Dobin et al. Bioinformatics 2013)
bam2wig.py at http://rseqc.sourceforge.net/
wigToBigWig
To assess gene expression in NIH3T3 fibroblasts along the circadian cycle, we performed an RNA Seq experiment in synchronized cells, extracting RNA in duplicates every 4h for 48h (16h after Dex - 64h after Dex, 26 samples in total). We assessed quality and quantity of the samples using a NanoDrop (Thermo Fisher) and reverse transcribed 1  g of each RNA sample into cDNA (SuperScript II, Life Technologies) to perform qPCR on known rhythmic genes (Dbp, Bmal1) in order to check for phase and amplitude of circadian rhythms (see supplementary figure 1B). Values were determined as fold change compared to Gapdh housekeeping control and the mean of each cycle was set to 1. Samples were then submitted to the Lausanne Genomics Facility (University of Lausanne) for whole RNA single read Truseq Stranded RNA sequencing. Fastq sequence reads were mapped against the mm9 mouse genome using RNA-Star (Dobin et al., 2013) with default parameters. Reads per kilo base per million (RPKM) were computed using custom perl. For each gene (Ensembl annotation, (Curwen et al., 2004)), all reads overlapping an exon of the different transcripts of the gene are counted, but each read is only counted once. Selection is based upon unique mapping and strand selectivity (reads need to map to the same strand as the gene). The length of the gene is computed as the mean length of the different transcripts
Mouse liver RNA-seq data was generated from RNA samples provided by Fr  d  ric Gachon (University of Lausanne) from previously published work (Jouffe et al, 2013). The RNA was isolated through hybridization of poly(A) regions on magnetic beads. Isolated RNA was fragmented and cDNA was synthesized with random primers. Sequencing of these non-strand-specific 100-bp paired-end reads was performed with an Illumina HiSeq 2500 machine at the Lausanne Genomic Technologies Facility for two replicates. RNA-seq mapping was performed with the STAR mapping protocol using default options for the mm9 (NCBI37) genome. Quality control of the samples was performed and validated with Bioanalyzer assays and the FastQC read quality analysis package.
Genome_build: mm9
Supplementary_files_format_and_content: WIG and BigWig standard

source_name: Liver

growth_protocol:
NIH3T3 fibroblasts and undifferentiated 3T3-L1 cells were kept in DMEM high glucose medium (Life Technologies) supplemented with 1%  Penicilling/Streptomycin/Glutamate (PGS; Sigma Aldrich) solution and 10% fetal calf serum (FCS, Sigma Aldrich). They were split using trypsin (Tryple Express, Life Technologies) as detaching and dissociation agent as necessary depending on experimental conditions or when reaching confluency. For transient tranfection, cells were transfected with 2µg of DNA per 35mm dish using Fugene HD (Promega) or Lipfectamine 2000 (Life Technologies) reagent following supplier's instructions. For synchronization with dexamethasone (Dex; Sigma Aldrich), cells were incubated for 30 minutes with 100 nM Dex solution (stock 100µM in ethanol), then washed once with PBS and supplied with fresh medium. Stable Zeb1 knockdown cells were obtained by lentiviral transduction using MISSION shRNAs (Sigma Aldrich) TRCN0000235850,
All animal studies were conducted in accordance with our regional committee for ethics in animal experimentation and the regulations of the veterinary office of the Canton of Vaud. C57Bl/6J mice were purchased from Janvier (Le Genest) or Charles River Laboratory. In all experiments, male mice between 10 and 12 wk of age are used. Unless noted otherwise, mice were maintained under standard animal housing conditions, with free access to food and water and in 12-h light/12-h dark cycles. However, for all experiments, animals were fed only at night during 4 d before the experiment to reduce effects of feeding rhythm.

extract_protocol:
RNA preparation using the Ambion PureLink RNA Mini Kit (Life Technologies)
Briefly, fractions were precipitated by the addition of three volumes of ethanol and kept overnight at 280uC. After 30 min of centrifugation at 5,200 g, RNAs were extracted from the non- soluble fraction by classical protocol. Liver RNAs were extracted and analysed by real-time quantitative RT-PCR, mostly as previously described(Jouffe et al 2013). Briefly, 0.5 mg of liver RNA was reverse transcribed using random hexamers and SuperScript II reverse transcriptase (Life Technol- ogies). The cDNAs equivalent to 20 ng of RNA were PCR amplified in triplicate in an ABI PRISM 7700 Sequence Detection System (Applied Biosystem) using the TaqMan or the SYBR Green technologies
Illumina TruSeq RNA
Libraries for ultra-high throughput sequencing were prepared with the RNA-seq sample kit (Illumina) as recommended by the manufacturer.

treatment_protocol:
Dexamethasone synchronization for 3T3 Cells
Livers were homogenized in lysis buffer containing 20 mM HEPES (pH 7.6), 250 mM NaCl, 10 mM MgCl2, 10 mM DTT, 20 mg/ml cycloheximid, 10 U/ml RNase inhibitor, and a protease inhibitor cocktail containing 0.5 mM PMSF, 10 mg/ml Aprotinin, 0.7 mg/ml Pepstatin A, and 0.7 mg/ml Leupeptin.

value: liver

tag: age

tag: light/dark cycle

tag: water/food access


title: Liver_2_ZT18


title: Liver_2_ZT22


title: Liver_2_ZT02


title: Liver_2_ZT06


title: Liver_2_ZT08


title: Liver_2_ZT10


title: Liver_2_ZT04


title: Liver_2_ZT00


title: Liver_1_ZT20


title: Liver_1_ZT18


title: PolII Serine2 Untreated ChipSeq biological replicate 2


title: Liver_1_ZT16


title: Liver_1_ZT14


title: Liver_1_ZT12


title: Liver_1_ZT10


title: Liver_2_ZT14


title: Liver_2_ZT12


title: Liver_1_ZT08


title: Liver_1_ZT04


title: Liver_2_ZT16


title: Liver_1_ZT02


title: Liver_1_ZT22


title: H3K27ac ZT 26 WT

description: Chromatin

data_processing:
All alignments were performed using the BBCF HTSstation (available at http://htsstation.epfl.ch , David et al., 2014).
Peak calling was done using ChIP-peak (Schmid CD, Bucher P. 2010, Ambrosini G., Dreos R. and Bucher P. IWBBIO 2014, Available: http://ccg.vital-it.ch/chipseq/chip_peak.php) on DNase signal using all ZT concatenated with the following parameters: cutoff=100,vicinity=400,window size=600, threshold=1000. A peak calling was done as well specifically for ZT6 in the WT and in the Bmal1KO context with the following parameters: cutoff=100,vicinity=1000,window size=600, threshold=200. Detected peaks were quantified using the DNase and PolII signal with a window of +/-300 bp around peak center and using the H3K27ac with a window of +/-1kb peak center for each time point and in each context.
Wig files were generated using bam2wig (see David et al., 2014) and were normalized according to the number mapped reads divided by 10e7. DNase I signal is represented using the first position of the reads considered as the cutting position and without strand shifting. Pol II and H3K27ac are represented using the whole read length and a shift of respectively 80bp and 90bp for PolII and H3K27ac.
DNase hypersensitive sites footprints were detected using Wellington algorithm (Piper et al. 2013) with the following parameters: -sh 20,36,5 -fdr 0.05
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Processed data files contain the normalized signal for each mark at each time point in BigWig format. In addition, the DNaseI hypersensitive peaks detected by the peak calling tool are provided in BigBed format. The footprints detected by Wellington algorithm are provided in BigWig format where the footprint score is reproted in negative scale (see Piper 2013). A table of quantile-normalized quantification of each mark at each time point and in WT and Bmal1KO context is provided in text format.

source_name: Liver, WT, ZT 26, H3K27ac ChIP

growth_protocol: C57/BL6 male, 12- to 14-wk-old (at time of sacrifice) mice were housed in a 12 h light/12 h dark (LD) regimen for 2 wk with water and food available ad libitum. They were then phase-entrained to a 12 h/12 h LD regimen with water ad libitum but food access between ZT12 and ZT24 for 7 d (ZT, Zeitgeber time; ZT0 is defined as the time when the lights are turned on and ZT12 as the time when lights are turned off). At each ZT2, ZT06, ZT10, ZT14, ZT18, ZT22, and ZT26, five mice were anesthetized with isoflurane and decapitated. The livers were perfused with 2 ml of PBS through the spleen and immediately collected. A small piece of liver tissue (approx. 100 mg) was snap-frozen in liquid nitrogen and kept at -80°C for RNA extraction. The remaining liver tissue was immediately homogenized in PBS containing 1% formaldehyde for chromatin preparation. All animal care and handling was performed according to the State of Geneva's law for animal protection.

extract_protocol:
ChIP-seq H3K27ac protocol: ChIPs were performed according to the method described by Reddy et al. (2009) with a few modifications. The 100 ul chromatin aliquots were used for each IP and diluted with 900 ul of RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS in PBS at pH 7.4) and added to dynal magnetic beads conjugated with (sheep anti-mouse IgG Dynabeads, Invitrogen, Cat no: 110-31) pre-treated with 3 ul of polyclonal antibody for H3K27ac (Active Motif, Cat no: 39135) for immunoprecipitation of specific complexes. The samples were incubated overnight at 4°C on rotator, then magnetic beads washed 7 times with lithiumchloride wash buffer (100mM Tris at pH 7.5, 500mM LiCl, 1% NP-40 and 1% sodiumdeoxycholate) and finally once with 1X TE buffer (10mM Tris-HCl at pH 7.5, 0.1mM Na2EDTA). The chromatin complex was eluted using elution buffer (1% SDS, 0.1M NaHCO3) for 1 h at 65°C using eppendorf thermo-mixer. The chromatin was then de-crosslinked overnight at 65°C and ChIP DNA purified using Qiagen PCR purification kit and eluted in 50 ul of elution buffer. For qPCR reaction, 1.5 ul of 1/10 diluted ChIP DNA is used.
Libraries for ultra-high-throughput sequencing were prepared with the ChIP-Seq DNA sample kit (Illumina) as recommended by the manufacturer.

tag: strain/background

tag: genotype/variation

value: WT

tag: gender

value: male

tag: feeding

value: night-restricted feeding

tag: time point

value: ZT 26

tag: technique

value: H3K27ac ChIP-seq


title: H3K27ac ZT 26 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 26, H3K27ac ChIP

value: Bmal1 KO

tag: chip antibody


title: H3K27ac ZT 10 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 10, H3K27ac ChIP

value: ZT 10


title: H3K27ac ZT 14 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 14, H3K27ac ChIP

value: ZT 14


title: H3K27ac ZT 22 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 22, H3K27ac ChIP

value: ZT 22


title: H3K27ac ZT 14 WT

description: Chromatin

source_name: Liver, WT, ZT 14, H3K27ac ChIP


title: H3K27ac ZT 18 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 18, H3K27ac ChIP

value: ZT 18


title: H3K27ac ZT 18 WT

description: Chromatin

source_name: Liver, WT, ZT 18, H3K27ac ChIP


title: H3K27ac ZT 6 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 6, H3K27ac ChIP

value: ZT 6


title: H3K27ac ZT 2 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 2, H3K27ac ChIP

value: ZT 2


title: Liver_1_ZT06


title: H3K27ac ZT 10 WT

description: Chromatin

source_name: Liver, WT, ZT 10, H3K27ac ChIP


title: H3K27ac ZT 22 WT

description: Chromatin

source_name: Liver, WT, ZT 22, H3K27ac ChIP


title: H3K27ac ZT 6 WT

description: Chromatin

source_name: Liver, WT, ZT 6, H3K27ac ChIP


title: H3K27ac ZT 2 WT

description: Chromatin

source_name: Liver, WT, ZT 2, H3K27ac ChIP


title: PolII ZT 26 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 26, PolII ChIP

extract_protocol:
ChIP-seq PolII protocol: Perfused livers were processed for chromatin preparation as described in Ripperger JA, Schibler U (2006). The chromatin samples from the five mice were then pooled, frozen in liquid nitrogen, and stored at -80°C. For the ChIP experiments, the following antibody was used: anti-RPB2 (Santa Cruz Biotechnology, sc-673-18). To determine the optimal amounts of antibody, we performed pilot ChIP assays and determined the enrichment for a set of promoters by real-time qPCR according to Ripperger JA, Schibler U (2006). A total of 1 ml of each chromatin suspension (containing about 60 µg of DNA) was incubated with 10 µg of anti-RPB2 in buffer A (20 mM Tris/HCl (pH 7.5), 150 mM NaCl, 2 mM EDTA) overnight at 4°C on a rotating wheel. Ten µl of protein A bead suspension (25% slurry in buffer A), pre-blocked with 10 µg/ml of salmon sperm DNA and BSA at 4°C overnight, was then added and the incubation was continued for 1 h at room temperature on a rotating wheel. The beads were then washed with dialysis buffer and ChIP wash buffer as described in O'Geen H, Nicolet CM, Blahnik K, Green R, Farnham PJ (2006). Protein-DNA complexes were eluted from the beads, de-cross-linked, and treated with RNase A and, subsequently, with proteinase K, as described in O'Geen H, Nicolet CM, Blahnik K, Green R, Farnham PJ (2006). The DNA concentration was determined by fluorometry on the Qubit system (Invitrogen). A total of 10-12 ng DNA were used for the preparation of the library.
Libraries for ultra-high-throughput sequencing were prepared with the ChIP-Seq DNA sample kit (Illumina) as recommended by the manufacturer.

value: PolII ChIP-seq

value: anti-PolII


title: PolII ZT 18 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 18, PolII ChIP


title: PolII ZT 10 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 10, PolII ChIP


title: PolII ZT 14 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 14, PolII ChIP


title: PolII ZT 2 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 2, PolII ChIP


title: PolII ZT 26 WT

description: Chromatin

source_name: Liver, WT, ZT 26, PolII ChIP


title: PolII ZT 18 WT

description: Chromatin

source_name: Liver, WT, ZT 18, PolII ChIP


title: PolII ZT 22 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 22, PolII ChIP


title: PolII ZT 22 WT

description: Chromatin

source_name: Liver, WT, ZT 22, PolII ChIP


title: PolII ZT 6 WT

description: Chromatin

source_name: Liver, WT, ZT 6, PolII ChIP


title: PolII ZT 10 WT

description: Chromatin

source_name: Liver, WT, ZT 10, PolII ChIP


title: PolII ZT 14 WT

description: Chromatin

source_name: Liver, WT, ZT 14, PolII ChIP


title: Liver_1_ZT00

source_name: Liver


title: PolII ZT 2 WT

description: Chromatin

source_name: Liver, WT, ZT 2, PolII ChIP


title: DNase ZT 26 WT

description: Chromatin

source_name: Liver, WT, ZT 26, DNase

extract_protocol:
DNase1-seq protocol: Mouse liver nuclei were prepared as described in (Tian and Schibler 1991). Freshly prepared nuclei were suspended in ice-cold Ψ-buffer (11 mM KPO4 pH 7.4, 108 mM KCl, 22 mM NaCl, 5mM MgCl, 1 mM CaCl2, 1 mM DTT) and pelleted. 5x10^6 nuclei were suspended in 200 μl of Ψ-buffer supplemented with 0.2% of NP40 and 1 u/ml of DNaseI (DPFF Worthington Biochemical Corporation). DNase1 digestion was performed for 6 minutes in room temperature and the reaction was stopped by adding 200 μl of lysis buffer (50mM Tris-HCl pH 8, 20 mM EDTA, 1% SDS, 200 μg/ml proteinaseK). Protease digestion was performed overnight at 55 oC. RNaseA (100 μg/ml) was then added and samples were incubated at 37 oC for an hour. DNA was then extracted twice with phenol-chloroform and precipitated with isopropanol in the presence of 0.5 M NaCl. DNAs were dissolved in 5 mM Tris-HCl pH 8. DNAs from 4 animals were pooled and 75 μg of DNA was loaded on 11 ml 10%-50% sucrose gradient in STE buffer (1M NaCl, 20 mM Tris-HCl pH 8, 5 mM EDTA) and centrifuged at 30000 rpm for 16 hours at 20 oC (SW 40 Ti rotor, Beckman Coulter Inc). The sucrose gradients were then fractionated and DNA was precipitated by two volumes of ethanol in the presence of 5 μg of glycogen. Fractions containing DNA sized around 300bp were pooled and used for Illumina library preparation.
Libraries for ultra-high-throughput sequencing were prepared with the ChIP-Seq DNA sample kit (Illumina) as recommended by the manufacturer.

value: ad libitum

value: DNase-seq


title: DNase ZT 6 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 6, DNase

value: liver


title: DNase ZT 22 WT

description: Chromatin

source_name: Liver, WT, ZT 22, DNase

value: WT


title: PolII ZT 6 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 6, PolII ChIP

value: male


title: DNase ZT 10 WT

description: Chromatin

source_name: Liver, WT, ZT 10, DNase


title: Rkk15_Nx_BG505

city: La Jolla

first: Shane

last: Crotty

state: CA

address: 9420 Athena Cir

department: Division of Vaccine Discovery

institute: La Jolla Institute for Allergy and Immunology

description: Microscaled (SmartSeq2) cDNA amplification - RNA seq

data_processing:
Bulk RNA-seq data was mapped against the human hg19 reference using TopHat43 (v1.4.1., --library-type fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site. Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id)
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements as a matrix table

molecule: polyA RNA

organism: Macaca mulatta

source_name: Blood PBMCs

extract_protocol:
Cells were sorted directly into Trizol LS buffer by Flow cytometry. Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012)
Purified total RNA (5 ng) was amplified following the smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).

treatment_protocol: Cells were stimulated with BG505 Env antigen (protein and overlapping peptides) for 18 h at 37 C.

tag: animal

value: Blood PBMCs

tag: cell type

value: CD4+CD45RA-CD25+OX40+ T cells

tag: stimulation

value: BG505 SOSIP.v5.2 protein and peptides

tag: neutralization group

value: Low


title: DNase ZT 18 WT

description: Chromatin

source_name: Liver, WT, ZT 18, DNase


title: Rop15Nx_BG505

value: High


title: RUj15_BG505_2_N705S504


title: DNase ZT 6 WT

description: Chromatin

source_name: Liver, WT, ZT 6, DNase


title: Rjm15_BG505_N703S507


title: DNase ZT 2 WT

description: Chromatin

source_name: Liver, WT, ZT 2, DNase


title: RJm15_BG505_2_N705S503


title: DNase ZT 14 WT

description: Chromatin

source_name: Liver, WT, ZT 14, DNase

value: ZT 14


title: RUj15_BG505_N703S508


title: 99_BG505_N703S506


title: RKJ15_wk18_BG505


title: 209_BG505_N702S506


title: RKK_BG505_N702S503


title: 157_BG505_N702S504


title: RDl15_BG505_N701S508


title: 209_NS_N701S507

value: CD4+CD45RA-T cells


title: Rkm15_BG505_N702S502


title: 204_NS_N701S506


title: RKK_NS_N701S504


title: ROP15_BG505_N702S517


title: 157_NS_N701S505


title: RKM15_NS_N701S503


title: ROP15_NS_N701S502


title: RDl15_NS_N701S517


title: 99_12_BG505_2_N705S502


title: 204_BG505_N702S505


title: T01-axenic

first: Adam

last: Dobson

address: Gower Street

department: GEE

institute: University College London

data_processing:
QC: Libraries were inspected for quality using FastQC (0.11.3)
Alignment: Libraries were aligned using TopHat2 (2.0.14)
Read counting: Reads were enumerated using HTSeq (0.6.1)
Genome_build: dm6
Supplementary_files_format_and_content: text files with read counts.

organism: Drosophila melanogaster

source_name: Whole fly

growth_protocol: Drosophila melanogaster lines were reared on a yeast-glucose diet (10% yeast (MP Biomedicals), 10% glucose (Sigma), 1.2% agar (Apex), 0.04% phosphoric acid (Sigma), and 0.42% propionic acid (Sigma)).

extract_protocol:
On dry ice (-80°C), replicate vials were pooled and male flies sorted into chilled sterile microcentrifuge tubes containing 110 ml of 1.4 mm lysing matrix (MP Biomedicals), 500 ml buffer RLT (Qiagen), and 5 ml b-mercaptoethanol. Flies were immediately homogenised at 4.0 m/s for 30 s on a Fastprep-24 (MP Biomedicals) and frozen at -80°C. RNA was isolated using the RNeasy mini kit (Qiagen)
TruSeq RNA Sample Prep Kit v2 – Set A (Illumina RS-122-2001). The samples were sequenced (50 bp single end reads) on the Illumina HiSeq 2500 platform in multiplexed pools of 6 samples per lane.

treatment_protocol: To produce gnotobiotic and axenic flies, eggs were collected within 20 h of laying, washed for 5 min in 0.6% sodium hypochlorite, rinsed with sterile water, and transferred aseptically to 7.5 ml sterile yeast-glucose diet. Axenic flies were not manipulated further, and gnotobiotic flies were created by immediately inoculating the transferred eggs with 50 ml 108 colony forming units (CFU) ml-1, comprising 5 species in equal proportions: Acetobacter pomorum DmCS_004, A. tropicalis DmCS_006, Lactobacillus brevis DmCS_003, L. fructivorans DmCS_002 and L. plantarum DmCS_001.  To generate the bacterial inoculum, monocultures were grown overnight 30°C on modified MRS medium [12], with or without shaking for Acetobacter and Lactobacillus species, respectively.  After one wash in mMRS, the density of each bacterial culture was determined by OD600 [12], normalized to 108 CFU ml-1, and the five cultures were combined in equal ratios.

value: whole fly

tag: strain

tag: Sex

tag: microbiome status

value: axenic


title: T01-gnotobiotic

tag: tissue

value: gnotobiotic


title: T05-axenic


title: B17-axenic


title: B10-axenic


title: T29A-axenic


title: B04-axenic


title: B17-gnotobiotic


title: T05-gnotobiotic


title: I38-gnotobiotic


title: DOA10 delete 30hrs

city: Jerusalem

first: Nir

last: Friedman

address: Givat Ram

department: School of Engineering

country: Israel

institute: The Hebrew University of Jerusalem

description: plasmid insert sequence

data_processing:
Illumina bcl2fastq to extract read pairs
Filter read pairs, retaining only ones that contained the flanking signature sequences from the plasmid, and if the sequence frame relative to the URA was positively identified
Reads were aligned to the yeast genome using bowtie2
Fragments were counted to bins according to their frame relative to the URA protein, and their sequence.
Genome_build: sacCer3
Supplementary_files_format_and_content: CSV file describing the location of the fragement, and their counts in each of the libraries

organism: Saccharomyces cerevisiae

extract_protocol:
Plasmids were purified from yeast pellets equivalent to 10OD using AccuPrep Plasmid MiniPrep DNA Extraction Kit (Bioneer; Republic of Korea).
Sequencing Library preparation consisted of two amplification steps. The first step (18 cycles) was performed using primers flanking the peptide, with overhangs complementary to Illumina adapters. A primer mix was used to increase library complexity for downstream NGS step. The second step was performed with the standard N-series Illumina barcoded adapters (12 cycles). Sequences were size selected to 200-800bp using Ampure XP beads for next generation sequencing (Agencourt). Instrument models used: Illumina MiSeq and Illumina NextSeq 500.

tag: plasmid type

value: cytosolic

tag: genetic background


title: B04-gnotobiotic


title: B10-gnotobiotic


title: I34-gnotobiotic


title: I38-axenic


title: I34-axenic


title: I16-axenic


title: ZW184-axenic


title: I16-gnotobiotic


title: RAL_555-gnotobiotic


title: N15-gnotobiotic


title: RAL_555-axenic


title: N15-axenic


title: T29A-gnotobiotic


title: CantonS-axenic

value: Canton-S


title: N04-gnotobiotic


title: CantonS-gnotobiotic


title: 211_11_BG505_N703S505


title: N01-gnotobiotic


title: N04-axenic


title: N01-axenic


title: RAL_42-gnotobiotic


title: RAL_318-gnotobiotic


title: RAL_318-axenic


title: RAL_42-axenic


title: RAL_306-gnotobiotic


title: CC/SS heatshocked sample 3

city: Wien

first: Fumiyo

last: Ikeda

address: Dr. Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology

description: Sample 12

data_processing:
Base calling was done following the HiSeq2500 instrument manufacturer's base calling software.
Reads were aligned against the Drosophila melanogaster reference genome (UCSC dm3 release) using STAR version 2.4.0d
After alignment reads were associated with known genes based on annotations derived from UCSC and number of reads aligned with each gene was counted using Htseq tool version 0.5.4p3.
Data were normalized using TMM normalization method of the edgeR R/Bioconductor package (R version 3.2.0, Biocunductor version 3.1)
For statistical testing data were log transformed using voom approach in the limma package.
Genome_build: UCSC dm3 release
Supplementary_files_format_and_content: [.txt] tab delimited text file including count values for each sample

source_name: Whole body

growth_protocol: Fly cultures and crosses were carried out on normal growth medium at 25 °C

extract_protocol:
Total RNA was isolated using TRIzol and contaminating DNA digested by TURBO DNA-free Kit (Thermo Fisher Scientific)
poly(A) enrichment (NEB, Ipswich, MA)

treatment_protocol: Heat stress was given by submerging the flies in 37 C water bath for 1 hr

tag: age

value: Day 2-5

value: CC/SS

tag: treatment

value: Heatshocked at 37C for 1 hr


title: w- heatshocked sample 3

description: Sample 10

tag: genotype/variation

value: w-


title: ZW184-gnotobiotic

value: male


title: CC/SS untreated sample 2

description: Sample 7

value: Untreated


title: CC/SS heatshocked sample 1

description: Sample 4


title: RAL_306-axenic


title: w- untreated sample 3

description: Sample 9


title: CC/SS untreated sample 1

description: Sample 3


title: CC/SS untreated sample 3

description: Sample 11


title: w- untreated sample 2

description: Sample 5


title: 28993_Mi

description: E. coli pricked (recovery 2 h)

data_processing:
Base calling was done following the HiSeq2500 instrument manufacturer's base calling software.
Reads were aligned against the Drosophila melanogaster reference genome (UCSC dm3 release) using TopHat version 2.0.9 or STAR version 2.4.0d
After alignment reads were associated with known genes based on annotations derived from UCSC and number of reads aligned with each gene was counted using Htseq tool version 0.5.4p3.
Data were normalized using TMM normalisation method of the edgeR R/Bioconductor package (R version 3.2.0, Biocunductor version 3.1)
For statistical testing data were log transformed using voom approach in the limma package.
Genome_build: UCSC dm3 release
Supplementary_files_format_and_content: tab delimited text file including count values for each sample

source_name: Mi-el w- E. coli pricked sample 1

treatment_protocol: Septic injury using Gram-negative E. coli DH5α bacteria and incubated at 25 °C for 2 h

value: Male

tag: genotype

value: Mi-el

value: Whole body


title: 28995_Mi

description: E. coli pricked (recovery 2 h)

source_name: Mi-el w- E. coli pricked sample 3


title: 28992_delRing2

description: E. coli pricked (recovery 2 h)

source_name: delR2 w- E. coli pricked sample 3


title: w- heatshocked sample 1

description: Sample 2


title: w- untreated sample 1

description: Sample 1


title: 28991_delRing2

description: E. coli pricked (recovery 2 h)

source_name: delR2 w- E. coli pricked sample 2


title: w- heatshocked sample 2

description: Sample 6


title: 28989_CS

description: E. coli pricked (recovery 2 h)

source_name: CC/SS w- E. coli pricked sample 3


title: 28990_delRing2

description: E. coli pricked (recovery 2 h)

source_name: delR2 w- E. coli pricked sample 1


title: CC/SS heatshocked sample 2

description: Sample 8


title: 28985_W1118

description: E. coli pricked (recovery 2 h)

source_name: w- E. coli pricked sample 2


title: 28988_CS

description: E. coli pricked (recovery 2 h)

source_name: CC/SS w- E. coli pricked sample 2


title: 28984_W1118

description: E. coli pricked (recovery 2 h)

source_name: w- E. coli pricked sample 1


title: 23937_delRing2

description: Control pricked

source_name: delR2 control pricked sample 2


title: 28987_CS

description: E. coli pricked (recovery 2 h)

source_name: CC/SS w- E. coli pricked sample 1


title: 23938_delRing2

description: Control pricked

source_name: delR2 control pricked sample 3


title: 23933_CS

description: Control pricked

source_name: CC/SS control pricked sample 1


title: 23935_CS

description: Control pricked

source_name: CC/SS control pricked sample 3


title: 23936_delRing2

description: Control pricked

source_name: delR2 control pricked sample 1


title: 28986_W1118

description: E. coli pricked (recovery 2 h)

source_name: w- E. coli pricked sample 3


title: 23934_CS

description: Control pricked

source_name: CC/SS control pricked sample 2


title: 23930_W1118

description: Control pricked

source_name: w- control pricked sample 1


title: 23939_Mi

description: Control pricked

source_name: Mi-el control pricked sample 1


title: HEK293T_clone1_SC_average_10

city: HOUSTON

first: Kuanwei

last: Sheng

state: TX

address: ONE BAYLOR PALAZA

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
The raw sequencing data was trimmed using skewer package.
The reads were mapped to the transcriptome using TOPHAT
A Python program using HT-seq package was written to analyze the barcode information
Genome_build: Hg19
Supplementary_files_format_and_content: txt files include the read count and barcode count for exon-based and intron-based analyses

organism: Homo sapiens

source_name: HET239T_pool-and-split averaged single cell

growth_protocol: HEK293T cells were grown in DMEM/High Glucose medium (ThermoFisher Scientific) with 10% FBS (Life Technologies) and 1% Penicillin-Streptomycin (Life Technologies). Cells were passed every 2-3 days.

extract_protocol: cDNA libraries were prepared for sequencing using standard Illumina Truseq protocols

tag: cell line


title: 23931_W1118

description: Control pricked

source_name: w- control pricked sample 2


title: HEK293T_clone1_SC_average_8


title: HEK293T_clone1_SC_average_6


title: HEK293T_clone1_SC_average_9


title: HEK293T_clone1_SC_average_5


title: HEK293T_clone1_SC_average_2


title: HEK293T_clone1_SC38

source_name: HEK293T single cell


title: HEK293T_clone1_SC_average_3


title: HEK293T_clone1_SC37


title: HEK293T_clone1_SC_average_1


title: 23940_Mi

description: Control pricked

source_name: Mi-el control pricked sample 2


title: HEK293T_clone1_SC36


title: HEK293T_clone1_SC_average_7


title: HEK293T_clone1_SC35


title: HEK293T_clone1_SC_average_4


title: 28994_Mi

description: E. coli pricked (recovery 2 h)

source_name: Mi-el w- E. coli pricked sample 2


title: 23941_Mi

description: Control pricked

source_name: Mi-el control pricked sample 3


title: 23932_W1118

description: Control pricked

source_name: w- control pricked sample 3


title: HEK293T_clone1_SC34


title: HEK293T_clone1_SC33


title: HEK293T_clone1_SC32


title: HEK293T_clone1_SC31


title: HEK293T_clone1_SC30


title: hot_replicate_2

city: Bandar Sunway

first: Huan You

last: Gan

state: Selangor

address: Jalan Lagoon Selatan

country: Malaysia

institute: Monash University Malaysia

description:
isolated sRNA
S3

data_processing: Base calling was performed by the Illumina Real Time Analysis (RTA) 1.18.54 software launched by the Miseq Control Software (2.4.1.3). Raw fastq reads were imported into the UEA sRNA workbench 3.2 and trimmed for adaptor sequences followed by filtering of low complexity sequences, sequences below 8nt, sequences above 35nt, sequences that match known transfer RNAs and sequences that match known ribosomal RNAs. The miRProf tool was used to align the filtered sequences to the mirBase 21 dataset of mature miRNAs in the plant category. Parameters were set to allow 0 mismatches, disallow overhangs, keep only best matches, disallow grouping variants, organisms, mature and star sequences. Normalised expression values were calculated by multiplying the raw number of reads matching an miRNA by a million divided by the total number of filtered reads in the sample. The rice miRNAs predicted targets and the description of the targets were found using the web software psRNAtarget and accessed through this web address (http://plantgrn.noble.org/psRNATarget/). miRNA sequences in fasta format were uploaded and Oryza Sativa (rice), transcript, MSU Rice Genome Annotation, version 7 was selected for target search.  Other parameters were maximum expection (3.0); Length of complementarity scoring (hspsize) (20); # of top target genes for each small RNA (200); Target accessibility - allowed maximum energy to unpair the target site (UPE)( 25.0) ;Flanking length around target site for target accessibility analysis (17  bp in upstream /  13 bp in downstream);Range of central mismatch leading to translational inhibition (9 - 11 nt). Genome Build: miRBase 21. Supplementary_files_format_and_content: abundance

organism: Oryza sativa

source_name: National Institute of Agricultural Research, Japan

growth_protocol: A total of 40 Kasalath seeds were used; 5 Kasalath seeds were placed in damp tissue with no media, in labelled petri dishes. 4 petri dishes were placed in the lab at 25 °C and were covered with a small cardboard box and the 4 petri dishes were placed in the Binder Cooled Incubator (Model KB23) where the temperature was set at 35°C and remained constant throughout the experiment. Tissues in petri dishes were dampened with tap water until the 8th day.

extract_protocol:
The mirVana™ miRNA Isolation Kit was used to extract the total RNA and isolate the sRNA from germinating seeds
Libraries were constructed using the NEBNext® Small RNA Library Prep Set for Illumina® kit according to the manufacturer's instructions. Size selection was performed using AMPure XP Beads (E7330)

value: germinating seeds

tag: developmental stage

value: 5 days after germination

tag: cultivar

value: Kasalath


title: hot_replicate_3

description:
isolated sRNA
S4


title: hot_replicate_1

description:
isolated sRNA
S2


title: normal_replicate_3

description:
isolated sRNA
L4


title: normal_replicate_2

description:
isolated sRNA
L3


title: normal_replicate_1

description:
isolated sRNA
L2


title: RAD21_ChIP_Replicate2

city: Berlin

first: Daniel

middle: Murad

last: Ibrahim

state: Berlin

address: Augustenburger Platz 1

department: Center for Regenerative Therapies

institute: Berlin Institute of Health

description:
RAD21.bw
RAD21_peaks.bed

data_processing:
Reads were filtered by quality using FASTX Toolkit 0.0.13 (-q 28 -p 50 -v -o X -Q 33)
Samples were aligned to the Galgal4 genome using BWA 0.5.9 for Illumina  (-n 0 -n 0.04 -o 1 -e -1 -d 16 -i 5 -l-1 -k 2 -M 3 -O 11 -E 4)
Lines were selected with the following pattern: XT:A:U|^@SQ|^@PG
sam files were converted to bam with the samtools version 0.1.18
bam files were merged with Picard 1.56 (beta) version and peaks were called on the pooled bam files using MACS2 (2.0.10.20120913) with the p-value cut off at 1e-1, tag size 50 and the rest of the default options. Afterwards the peaks were ranked according to the p-value and only the reproducible peaks from the list were seleced. Finally the peaks were filtered to discard the peaks located on mitochondrial or random chromosomes. IDR pipeline was used to determine the number of reproducible peaks for every sample which was done as in: Kundaje et al., 2012 ( https://sites.google.com/site/anshulkundaje/projects/idr )
Genome_build: Galgal4
Supplementary_files_format_and_content: bed files are produced as described above. Shared peaks are considered shared only is the summits are at the most 200bp away or closer. Bigwig files are normalised reads per milion and are extended 150bp. Bigwig files were generated using the samtools and bedtools.
Supplementary_files_format_and_content: CTCF_peaks.bed: HOX-CTCF co-bound peaks

organism: Gallus gallus

source_name: Chicken Micromass primary cells

growth_protocol: MSCs were isolated from the HH24 chicken limb buds, infected with an RCASBP(A) or (B) virus carrying the transgene on interest. Afterwards cells were cultured for 6 days with the DMEM:HAM F11 media (supplemented with 10% Fetal Bovine Serum, 0,2% Chicken Serum, 1% Penicilin-Streptomicin and 1% L-glutamine).

extract_protocol:
Nuclei were isolated with three different lysis buffers as in Lee et al., 2006 and sonicated in the lysis buffer 3 until the chromatin was disrupted to the size between 200 and 300bp.
Libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix for Illumina (New England Biolabs), fragments between 300-450bp were selected and sequenced on a Illumina HiSeq 1500 using Illumina TruSeq v3 chemistry.

treatment_protocol: Cells were infected with RCASBP viruses carrying different transgenes.

value: MSCs derived from embryonal HH25 limb bud

tag: infection

value: HA-CTCF

tag: days in culture

value: 6 days

tag: antibody

value: RAD21 (abcam Rat polyclonal; #ab992; Lot GR214359-1)


title: RAD21_ChIP_Replicate1

description:
RAD21.bw
RAD21_peaks.bed

tag: cell type


title: HEK293T_clone1_SC28


title: CTCF_Input_Replicate1


title: CTCF_Input_Replicate2


title: HEK293T_clone1_SC26


title: CTCF_ChIP_Replicate2

description:
CTCF.bw
CTCF_peaks.bed


title: CTCF_ChIP_Replicate1

description:
CTCF.bw
CTCF_peaks.bed


title: HEK293T_clone1_SC25


title: HEK293T_clone1_SC24


title: HEK293T_clone1_SC23


title: HEK293T_clone1_SC22


title: HOXD13_ChIP_Replicate2

description:
HOXD13.bw
HOXD13_peaks.bed
HOXD13-CTCF_peaks.bed

value: FLAG (Sigma Mouse monoclonal M2; F3165)


title: HEK293T_clone1_SC21


title: HOXD13_Input_Replicate1


title: HOXD12_Input_Replicate2


title: HEK293T_clone1_SC20


title: HOXD13_ChIP_Replicate1


title: HEK293T_clone1_SC27


title: HOXD12_ChIP_Replicate1

description:
HOXD12.bw
HOXD12_peaks.bed
HOXD12-CTCF_peaks.bed


title: HEK293T_clone1_SC19


title: HEK293T_clone1_SC17


title: HEK293T_clone1_SC29


title: HEK293T_clone1_SC16


title: HEK293T_clone1_SC15


title: HOXD11_Input_Replicate1


title: HOXD11_Input_Replicate2


title: HOXD13_Input_Replicate2


title: HEK293T_clone1_SC12


title: HOXD11_ChIP_Replicate1

description:
HOXD11.bw
HOXD11_peaks.bed
HOXD11-CTCF_peaks.bed


title: HOXD11_ChIP_Replicate2


title: HEK293T_clone1_SC14


title: HOXD10_Input_Replicate1


title: HOXD10_Input_Replicate2


title: HEK293T_clone1_SC11


title: HEK293T_clone1_SC10


title: HOXD10_ChIP_Replicate2

description:
HOXD10.bw
HOXD10_peaks.bed
HOXD10-CTCF_peaks.bed


title: HEK293T_clone1_SC9


title: HOXD12_Input_Replicate1


title: HEK293T_clone1_SC7


title: HOXD9_Input_Replicate1


title: HEK293T_clone1_SC18


title: HEK293T_clone1_SC6


title: HOXD9_ChIP_Replicate2

description:
HOXD9.bw
HOXD9_peaks.bed
HOXD9-CTCF_peaks.bed


title: HOXD12_ChIP_Replicate2


title: HEK293T_clone1_SC8


title: HOXD9_ChIP_Replicate1


title: HEK293T_clone1_SC5


title: HOXA13_Input_Replicate1


title: HOXA11_Input_Replicate2


title: HEK293T_clone1_SC3


title: HEK293T_clone1_SC1


title: HEK293T_clone1_SC13


title: HOXA11_Input_Replicate1


title: DSN_HEK293T_sc_5

data_processing:
The raw sequencing data was trimmed using skewer package.
The reads were mapped to the transcriptome using TOPHAT
A Python program using HT-seq package was written to analyze the barcode information
Genome_build: Hg19
Supplementary_files_format_and_content: dat files include the read count and barcode count for exon-based and intron-based analyses

source_name: HEK293T cell line

growth_protocol:
HEK293T cells were grown in DMEM/High Glucose medium (ThermoFisher Scientific) with 10% FBS (Life Technologies) and 1% Penicillin-Streptomycin (Life Technologies). Cells were passed every 2-3 days.
MCF10A cells were grown in DMEM/F12 medium with 5% Horse Serum, 20ng/ml EGF, 100ng/ml Cholera Toxin, 10ug/ml Insulin, 500ng/ml Hydrocortisone, and 1% Penicillin Streptomycin.

tag: sample type

value: single cell


title: HEK293T_clone1_SC2


title: HOXA11_ChIP_Replicate2

description:
HOXA11.bw
HOXA11_peaks.bed
HOXA11-CTCF_peaks.bed


title: HOXA10_Input_Replicate2


title: HOXD10_ChIP_Replicate1


title: HOXA11_ChIP_Replicate1


title: HOXD9_Input_Replicate2


title: HOXA10_Input_Replicate1


title: DSN_HEK293T_sc_2


title: DSN_HEK293T_sc_1


title: DSN_HEK293T_sc_4


title: DSN_HEK293T_sc_3


title: HOXA10_ChIP_Replicate1

description:
HOXA10.bw
HOXA10_peaks.bed
HOXA10-CTCF_peaks.bed


title: avervaged_onefifth_MCF10A_ERCC_spiked_5

source_name: MCF10A cell line + ERCC spike-in

value: pool-and-split averaged single cell


title: avervaged_onefifth_MCF10A_ERCC_spiked_4


title: HOXA9_Input_Replicate1


title: HOXA9_Input_Replicate2


title: HEK293T_clone1_SC4


title: HOXA10_ChIP_Replicate2


title: HOXA13_ChIP_Replicate1

description:
HOXA13.bw
HOXA13_peaks.bed
HOXA13-CTCF_peaks.bed


title: HOXA9_ChIP_Replicate1

description:
HOXA9.bw
HOXA9_peaks.bed
HOXA9-CTCF_peaks.bed


title: avervaged_onefifth_MCF10A_ERCC_spiked_6


title: HOXD13_RNA_Replicate2

data_processing:
The reads were aligned using the STAR mapper (Dobin et al. 2012) splice junctions based on RefSeq/ENSEMBL gene annotations; options: ‐‐alignIntronMin 20 ‐‐alignIntronMax 500000 --outFilterMultimapNmax 5 ‐‐outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.1).
The annotation used was a merged from RefSeq (galGal4) and ENSEMBL (release 75) gene annotation.
DEseq2 was used to generate Log2 fold changes as in Love et al. 2014.
Genome_build: Galgal4
Supplementary_files_format_and_content: bigwig files contain normalized (RPM) genome browser tracks for each replicate RNA-seq experiment
Supplementary_files_format_and_content: The tab delimited txt file contains read counts for each gene (RefSeq/ENSEMBL annotation) and each replicate experiment in the table used as input for DEseq2

extract_protocol:
Cells were separated from the ChIP sample prior to fixation an mRNA was extracted with the Rnaeasy (QIAGEN) kit according to the manufacturer's instructions.
mRNA was purified with the NEBNext Poly(A) mRNA Magnetic Isolation Module from 500g of total RNA. RNA-seq libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina according with a size selection was performed between 300-450bp. Libraries were sequenced on a a Illumina HiSeq 1500 using Illumina TruSeq v3 chemistry (single-read, 50 cycle).


title: Ctrl_RNA_Replicate2


title: Ctrl_RNA_Replicate1


title: HOXA9_ChIP_Replicate2


title: HOXD13_RNA_Replicate1


title: avervaged_onefifth_MCF10A_ERCC_spiked_1


title: avervaged_onefifth_MCF10A_ERCC_spiked_2


title: HOXD12_RNA_Replicate2


title: MCF10A_averaged_sc_6

source_name: MCF10A cell line


title: MCF10A_averaged_sc_4


title: HOXD11_RNA_Replicate2


title: HOXD12_RNA_Replicate1


title: MCF10A_averaged_sc_1


title: MCF10A_averaged_sc_5


title: MCF10A_sc_6


title: HOXD11_RNA_Replicate1


title: MCF10A_averaged_sc_2


title: avervaged_onefifth_MCF10A_ERCC_spiked_3


title: MCF10A_sc_5


title: HOXD9_RNA_Replicate2


title: HOXD10_RNA_Replicate1


title: MCF10A_sc_2


title: MCF10A_sc_3


title: MCF10A_sc_1


title: HOXD9_RNA_Replicate1


title: HOXA13_RNA_Replicate2


title: HEK293T_sc_10


title: HOXA11_RNA_Replicate2


title: HEK293T_sc_9


title: HOXA11_RNA_Replicate1


title: HEK293T_sc_8


title: MCF10A_averaged_sc_3


title: MCF10A_sc_4


title: HEK293T_sc_7


title: HEK293T_sc_4


title: HOXA10_RNA_Replicate1


title: HEK293T_sc_5


title: HEK293T_sc_6


title: HEK293T_sc_3


title: HEK293T_sc_2


title: HOXA9_RNA_Replicate1


title: HEK293T_sc_1


title: HOXD10_RNA_Replicate2


title: Donor11_RESTV_1D_LPS_6H

city: New York

first: Angela

last: Rasmussen

department: Center for Infection and Immunity

institute: Columbia University

data_processing:
On-instrument base-calling with Illumina NextSeq 500 NCS v1.3 software/Real Time Analysis v2
Raw reads (76 bp) had their adapter sequences removed. General quality control of the raw reads was performed using FastQC. Ribosomal RNA reads were removed via mapping by Bowtie (v2.1.0) using an index of human, mouse, and rat rRNA sequences. An average of ~10% of all reads were identified as rRNA and removed from downstream analysis.  Viral reads mapping to either EBOV or RESTV genomes were also removed. Reads were then mapped against a human reference genome (hg19, build GRCh37, from the UCSC genome browser using STAR (v2.4.0h1). Quantitative gene counts were produced from this alignment using the python package HT-Seq utilizing the human annotation associated with the genome.
Prior to differential analysis expression, genes with no counts were removed and counts across samples were normalized using the weighted trimmed mean of M-values. Remaining genes without at least three samples with counts were additionally removed leaving 14,288 genes with an average of ~10M reads per samples. Normalization and differential expression analysis were carried out using R (v3.1.3) and software package edgeR (v3.10.2). Differentially expressed genes were determined between treatments relative to time-matched and donor-matched samples using a generalized linear model implemented in edgeR. Cutoff for differential gene expression were defined as an absolute fold change of 2 and a p-value of ≤ 0.05 after false-discovery rate adjustment using the Benjamini-Hochberg multiple testing correction.
Supplementary_files_format_and_content: tab-delimited text (normalized matrix), comma separated values (differentially expressed genes)

source_name: primary monocyte-derived macrophages

growth_protocol: Virus stocks were propagated in VeroE6 cells and purified by ultracentrifugation through a 20% sucrose cushion. Monocyte-derived macrophages were generated by Ficoll separation and CD14 enrichment, and allowed to adhere for 1 hr. Cells were incubated for 6-8 days in RPMI 1640 with 5% human AB serum to ensure differentiation into macrophages.

extract_protocol:
Total RNA from 1.5x106 (6-well format) or 3x105 (24-well format) MDM was isolated at the indicated time points using TRIzol Reagent (Invitrogen) according to the manufacturer's protocol. RNA concentration was determined using the NanoDrop 1000 Spectrophotometer (Thermo Scientific).
Libraries for mRNA sequencing were constructed using the Kapa Stranded mRNA-Seq Kit (Kapa Biosystems) according to the manufacturer's guidelines. Libraries were quality controlled and quantified using the BioAnalzyer 2100 (Agilent Technologies, Inc) and QuBit (Invitrogen) systems. The libraries were clonally amplified and sequenced on an Illumina NextSeq 500 to achieve a target density of approximately 200K-220K clusters/mm2 on the flow cell with dual indexed paired end sequencing at a 76 bp length using NextSeq 500 NCS v1.3 software.

treatment_protocol: Differentiated monocyte-derived macrophages were infected with EBOV or RESTV at MOI=5-7. Mock-treated cells were treated with culture medium containing no virus. LPS-treated cells were pre-treated with 10 ug/mL LPS for 3 hours, followed by treatment with 1 ng/mL LPS in the culture medium.

value: RESTV/LPS

tag: hours post-infection

tag: donor


title: Donor11_EBOV_1D_LPS_6H

value: EBOV/LPS


title: Donor11_EBOV_2D

value: EBOV


title: Donor11_RESTV_1D

value: RESTV


title: Donor11_LPS1D

value: LPS


title: Donor11_EBOV_1D


title: Donor11_MOCK_1D

value: mock


title: HOXA10_RNA_Replicate2


title: Donor11_EBOV_6H


title: Donor11_LPS-1D_6H


title: Donor11_MOCK-1D_6H


title: HOXA9_RNA_Replicate2


title: Donor10_RESTV-1D_LPS 6H


title: Donor11_RESTV_2D


title: Donor10_EBOV-2D


title: Donor10_MOCK-2D


title: Donor10_LPS-2D


title: Donor10_LPS-1D


title: Donor10_RESTV-2D


title: Donor10_EBOV-1D


title: Donor10_MOCK-1D


title: Donor10_LPS-6H


title: Donor11_MOCK_2D


title: C2-1

city: Baltimore

first: Dimitrios

last: Avramopoulos

state: Maryland

address: 733 North Broadway

department: Genetic Medicine

institute: Johns Hopkins University

data_processing:
Forward and reverse raw reads separated by 12 barcodes were received from our core facility
Analysis was performed using the Tuxedo suite of programs including tophat for read mapping, cufflinks for transcript assembly and cuffdiff for transcript abundance comparisons
Following the Tuxedo pipeline the output was further processed using the R Bioconductor package CummeRbund
Genome_build: GRCh37/hg19

source_name: Human embryonic Kidney derived cell line

growth_protocol: human embryonic kidney cell line (HEK293; ATCC #CRL-1573) was cultured using standard protocols. Cells were maintained in Dulbecco’s Modified Eagle Medium (Invitrogen #11965-084) with 10% fetal bovine serum (Sigma #12003C).

extract_protocol:
RNeasy Mini Kit (Qiagen #74104).
RiboMinus™ technology (ThermoFisher Scientific) was used to deplete ribosomal RNA. Illumina’s TruSeq RNA v2 protocol was used to generate libraries

treatment_protocol: no treatment

tag: modifications

value: CRISPR/Cas9 targetted - unmodified

tag: dinucleotide length


title: Donor9_EBOV-1D_LPS-6H


title: Donor9_RESTV-1D_LPS-6H


title: Donor11_LPS_2D


title: Donor9_RESTV-2D


title: C1-4

value: Human embryonic Kidney derived cell line

value: CRISPR/Cas9 targetted - modified


title: Donor11_RESTV_6H


title: C1-3


title: Donor10_EBOV-1D_LPS 6H


title: C1-0


title: Donor9_LPS2D


title: Donor9_MOCK_2D


title: Donor10_EBOV-6H


title: Donor10_MOCK-6H


title: Donor10_RESTV-6H


title: Donor9_EBOV_1D


title: DAC+Depsi_3 (MCF7)

city: Philadelphia

first: Takahiro

last: Sato

state: PA

address: 3307 North Broad Street

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

description:
derived from metastatic site: pleural effusion
Each sample was run on two separate lanes on the HiSeq2500 generating two fastq files. The two files were merged for final analysis.

data_processing:
Illumina HiSeq2500 single end sequencing
tophat2 --sensitive alignment of the reads in two fastq files from each sample to hg19, generating one BAM file per sample
ht-seq-count  with default settings to generate counts of each gene
edgeR to generate RPKM and fold change of each condition compared to control, only keep genes with at least one read in one of the samples
export fold change of each inhibitor vs. control into a text file, then import all the fold changes into one excel file
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are in excel format. The first 30 columns are the RPKMs of the individual samples. The following columns are the fold change and FDR of the triplicates of each condition compared against the triplicates of control samples

source_name: MCF7 breast cancer cell line

growth_protocol: MCF7 cell line was cultured in DMEM medium with 10% fetal bovine serum

extract_protocol:
RNA was isolated using Rneasy Mini Kit (Qiagen)
Strand-specific RNA libraries were generated from 1μg of RNA using TruSeq stranded total RNA with Ribo-Zero Gold (Illumina)

treatment_protocol: Cells were treated daily with 100nM decitabine (5-aza-CdR, Sigma), 10uM S2101 (Millipore), 1uM UNC0638 (Sigma), and 1uM GSK343 (Sigma) for 96 hours, or 20nM depsipeptide (Romidepsin, Sigma) was added for 24 hours

tag: tissue

value: mammary gland, breast

value: breast cancer cell line MCF7

tag: er status

value: positive

value: DAC+Depsi

tag: gender

value: female


title: Donor10_RESTV-1D

tag: treatment


title: Depsi_3 (MCF7)

value: Depsi


title: DAC+GSK343_3 (MCF7)


title: Donor9_LPS_1D


title: Donor9_MOCK_1D


title: GSK343_3 (MCF7)


title: Donor9_RESTV_6H


title: Donor9_LPS_6H


title: Donor9_EBOV_6H


title: S2101_3 (MCF7)


title: DAC_3 (MCF7)

value: DAC


title: DAC+S2101_3 (MCF7)


title: Donor9_MOCK_6H


title: TCP_rep2

city: Naples

first: Stefano

last: Amente

address: via pansini, 5

department: Department of  Molecular Medicine and Medical Biotechnologies

country: Italy

institute: University of Naples "FEDERICO II"

data_processing:
Raw sequences files (-fastaq files) were aligned to the human genome (h19 version)
gene-level quantification was performed using R-SEM and UCSC annotation
Subsequently, data were normalized with VOOM method
differential expression evaluated with limma Bioconductor packages
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] tab-delimited text files report FKPMs

source_name: TCP

growth_protocol: SHEP Tet-21/N cells were cultured in Dulbecco’s modified Eagle’s Medium (DMEM) supplemented with antibiotics, 10% fetal calf serum.

extract_protocol:
RNA was prepared from Tet-21N cells treated with TCP or with siLSD1 and control untreated cells using EuroGold Trifast (EuroClone).
RNA-seq libraries (two biological replicas for each sample) were generated using TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s recommendation.

treatment_protocol: Were indicated, cells were treated with TCP (1mM, Enzo Life Sciences) or with siRNA against LSD1 (100nM, Dharmacon)

value: SHEP Tet-21/N neuroblastoma cell line

tag: protocol

value: LSD1 inhibitor, TCP (tranylcypromine)


title: Donor9_EBOV-2D


title: Donor9_RESTV_1D


title: TCP_rep1

tag: cell line


title: DAC+Depsi_2 (MCF7)


title: Depsi_2 (MCF7)


title: UNC0638_3 (MCF7)


title: siLSD1_rep2

value: LSD1 Knock-Down


title: siLSD1_rep1


title: CRT_rep2

source_name: CRT

value: untreated


title: GSK343_2 (MCF7)


title: Cntrl_3 (MCF7)

value: Cntrl


title: DAC+UNC0638_3 (MCF7)


title: UNC0638_2 (MCF7)


title: DAC+S2101_2 (MCF7)


title: HEK293T_averaged_sc_8

value: pool-and-split averaged single cell


title: HEK293T_averaged_sc_10


title: DAC_2 (MCF7)


title: HEK293T_averaged_sc_6


title: HEK293T_averaged_sc_7


title: HEK293T_averaged_sc_5


title: Cntrl_2 (MCF7)


title: HEK293T_averaged_sc_4


title: Depsi (MCF7)


title: HEK293T_averaged_sc_3


title: DAC+GSK343 (MCF7)


title: GSK343 (MCF7)


title: HEK293T_averaged_sc_1


title: DAC+UNC0638 (MCF7)


title: CRT_rep1


title: DAC+UNC0638_2 (MCF7)


title: DAC+S2101 (MCF7)


title: S2101_2 (MCF7)


title: C1-2


title: S2101 (MCF7)


title: Cntrl (MCF7)


title: HEK293T_averaged_sc_9


title: DAC+Depsi_3 (YB5)

description:
96h_DAC+_24h_20nM_Depsi_2 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression

data_processing:
Illumina HiSeq2500 single end sequencing
tophat2 --sensitive alignment of the reads in fastq files to hg19 and generating BAM files
ht-seq-count  with default settings to generate counts of each gene
edgeR to generate RPKM and fold change of each condition compared to control, only keep genes with at least one read in one of the samples
export fold change of each inhibitor vs. control into a text file, then import all the fold changes into one excel file
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are in excel format. The first 30 columns are the RPKMs of the individual samples. The following columns are the fold change, p-value, and FDR of the triplicates of each condition compared against the triplicates of control samples

source_name: YB5 colon cancer cell line

growth_protocol: YB5 cell line was cultured in L-15 medium with 10% fetal bovine serum

value: colon cancer cell line YB5

value: colorectal adenocarcinoma

tag: dukes' type

value: C

tag: grade

value: IV


title: Depsi_3 (YB5)

description:
20nM_Depsi_24h_2 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: DAC+GSK343_3 (YB5)

description:
DAC+_1uM_GSK343_2 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: DAC+UNC0638_3 (YB5)

description:
DAC+_1uM_UNC0638_2 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: DAC+S2101_3 (YB5)

description:
DAC+_10uM_S2101_2 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: S2101_3 (YB5)

description:
10uM_S2101_2 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: UNC0638_3 (YB5)

description:
1uM_UNC0638_2 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: Cntrl_3 (YB5)

description:
Cntrl_2 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: DAC+Depsi_2 (YB5)

description:
96h_DAC+_24h_20nM_Depsi_1 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: DAC+Depsi (MCF7)

value: mammary gland, breast


title: HEK293T_averaged_sc_2


title: Depsi_2 (YB5)

description:
20nM_Depsi_24h_1 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: DAC+GSK343_2 (YB5)

description:
DAC+_1uM_GSK343_1 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: GSK343_2 (YB5)

description:
1uM_GSK343_1 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: DAC_3 (YB5)

description:
100nM_DAC_2 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: DAC+UNC0638_2 (YB5)

description:
DAC+_1uM_UNC0638_1 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: UNC0638 (MCF7)

value: breast cancer cell line MCF7


title: DAC+S2101_2 (YB5)

description:
DAC+_10uM_S2101_1 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: DAC+Depsi (YB5)

description:
96h_DAC+_24h_20nM_Depsi_0 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: DAC_2 (YB5)

description:
100nM_DAC_1 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: Cntrl_2 (YB5)

description:
Cntrl_1 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: Depsi (YB5)

description:
20nM_Depsi_24h_0 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: UNC0638 (YB5)

description:
1uM_UNC0638_0 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: GSK343 (YB5)

description:
1uM_GSK343_0 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: DAC+GSK343 (YB5)

description:
DAC+_1uM_GSK343_0 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: DAC+S2101 (YB5)

description:
DAC+_10uM_S2101_0 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: DAC+UNC0638 (YB5)

description:
DAC+_1uM_UNC0638_0 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: S2101 (YB5)

description:
10uM_S2101_0 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: Cntrl (YB5)

description:
Cntrl_0 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: S2101_2 (YB5)

description:
10uM_S2101_1 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: RNA-Seq_NON_ALL06_IN_TCM_IFNG

first: Alessandro

last: Sette

address: 9420 Athena Circle

description:
PolyAtail selected messenger RNA
Smart seq 2 cDNA amplification

data_processing:
Illumina filtering
Alignment with TopHat
DUST scores were calculated with PRINSEQ Lite (v 0.20.3)
Low-complexity reads (DUST > 4) were removed from the BAM files
Generation of SAM files with SAMtools
Obtention of read counts with htseq-count using "union" option
Removing absent features (zero counts in all samples)
Raw counts were imported to R/Bioconductor package DESeq2 to identify differentially expressed genes among samples
DESeq2 normalizes counts by dividing each column of the count table (samples) by the size factor of this column. The size factor is calculated by dividing the samples by geometric means of the genes.
P-values for differential expression are calculated using binomial test for differences between the base means of two conditions.
These p-values are then adjusted for multiple test correction using Benjamini Hochberg algorithm to control the false discovery rate.
We considered genes differentially expressed between two groups of samples when the DESeq2 analysis resulted in an adjusted P-value of <0.05 and the fold-change in gene expression was 2-fold.
Genome_build: UCSC hg19

source_name: Blood PBMCs

growth_protocol: Cells were cultured for less than 18 hours in RPMI1640 supplemented with 5% human AB serum in 24 well plates at a density of 4x106/ml and incubated at 37˚C

extract_protocol:
IFNγ or IL5 cytokine producing cells were captured using a cytokine secretion assay according to manufacturers’ instructions  (Miltenyi Biotech, Germany). Briefly cells were harvested, washed and labeled with 20 μl of anti-IFNγ/CD45- or anti-IL5/CD45- antibody conjugates (Miltenyi Biotech). After cytokine capture, cells were stained with 20 μl/107 cells of PE-labeled detection antibody and co-stained with a combination of antibodies (Anti-CD3, -CD4, -CD45RA and –CCR7) to allow further separation of cells into effector memory (TEM; CD45RA-CCR7-), and central memory (TCM; CD45RA-CCR7+)  by FACS sorting (FACS ARIA BD-Bioscience). Cells were sorted directly in 750ul Trizol LS. To maximize the cell lysis, samples were votexed every 5 minutes for 15 seconds.Total RNA was purified from the different sorted populations using a miRNAeasy kit (Qiagen, USA) as described as recommended by manufacturer. Purified total RNA (0.2–5ng) was amplified following the smart-seq2 protocol (Picelli et al. Nature methods, Vol10 (11), pp1096-98).
1 ng of amplified cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina, San Diego, USA).
Single-end 50bp length reads RNA-seq using the HiSeq2500 sequencer (Illumina, San Diego, USA)

treatment_protocol: 4 million/ml PBMCs from 5 allergic and 6 non-allergic individuals were stimulated in vitro for 3 hours with 2.5 μg/ml of a Tymothy Grass Allergen immunodominant peptides pool (see paper).

value: IFNg secreting central memory CD4 Tcells - CD3+ CD4+ CD45RA- CCR7+ IFNG+

tag: patient phenotype

value: Timothy Grass Non Allergic

tag: seasonality

value: Blood draw during of Timothy Grass pollen season


title: RNA-Seq_NON_ALL06_IN_TCM_NEG

value: Central memory CD4 Tcells - CD3+ CD4+ CD45RA- CCR7+ IFNG+


title: RNA-Seq_NON_ALL06_IN_TCM_IL5

value: IL5 secreting central memory CD4 Tcells - CD3+ CD4+ CD45RA- CCR7+ IFNG+


title: RNA-Seq_NON_ALL06_IN_TEM_IL5

value: IL5 secreting memory effector CD4 Tcells - CD3+ CD4+ CD45RA- CCR7- IFNG+


title: RNA-Seq_NON_ALL06_IN_TEM_IFNG

value: IFNg secreting memory effector CD4 Tcells - CD3+ CD4+ CD45RA- CCR7- IFNG+


title: RNA-Seq_ALL05_IN_TCM_IFNG

value: Timothy Grass  Allergic


title: GSK343_3 (YB5)

description:
1uM_GSK343_2 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression

value: female


title: UNC0638_2 (YB5)

description:
1uM_UNC0638_1 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression


title: RNA-Seq_NON_ALL06_IN_TEM_NEG

value: Memory effector CD4 Tcells - CD3+ CD4+ CD45RA- CCR7- IFNG+


title: DAC (YB5)

description:
100nM_DAC_0 in YB5 RNA-seq Summary Table.xlsx
YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression

value: DAC


title: RNA-Seq_ALL05_IN_TCM_IL5


title: RNA-Seq_NON_ALL05_OUT_TCM_IFNG

value: Blood draw out of Timothy Grass pollen season


title: RNA-Seq_ALL05_IN_TEM_IFNG


title: RNA-Seq_NON_ALL05_OUT_TEM_IFNG


title: RNA-Seq_ALL05_IN_TEM_IL5


title: RNA-Seq_NON_ALL05_OUT_TEM_IL5


title: RNA-Seq_NON_ALL05_OUT_TEM_NEG


title: RNA-Seq_NON_ALL05_OUT_TCM_NEG


title: RNA-Seq_NON_ALL04_OUT_TCM_IFNG


title: RNA-Seq_NON_ALL04_OUT_TCM_IL5


title: RNA-Seq_NON_ALL04_OUT_TEM_IL5


title: RNA-Seq_ALL04_IN_TCM_IFNG


title: RNA-Seq_ALL04_IN_TCM_IL5


title: RNA-Seq_NON_ALL04_OUT_TEM_IFNG


title: DAC (MCF7)

description:
derived from metastatic site: pleural effusion
Each sample was run on two separate lanes on the HiSeq2500 generating two fastq files. The two files were merged for final analysis.

value: positive


title: RNA-Seq_ALL04_IN_TEM_IL5


title: RNA-Seq_ALL04_IN_TCM_NEG


title: RNA-Seq_ALL03_OUT_TCM_IFNG


title: RNA-Seq_ALL04_IN_TEM_NEG


title: RNA-Seq_NON_ALL05_OUT_TCM_IL5


title: RNA-Seq_ALL03_OUT_TEM_IFNG


title: RNA-Seq_ALL03_OUT_TCM_IL5


title: RNA-Seq_ALL03_OUT_TEM_IL5


title: RNA-Seq_ALL03_OUT_TCM_NEG


title: RNA-Seq_ALL03_OUT_TEM_NEG


title: RNA-Seq_ALL01_IN_TEM_IL5

value: Timothy Grass Allergic


title: HOXA13_RNA_Replicate1

value: MSCs derived from embryonal HH25 limb bud

tag: infection

tag: days in culture

value: 6 days


title: RNA-Seq_ALL01_IN_TEM_NEG

tag: cell type


title: RNA-Seq_ALL01_OUT_TCM_IFNG


title: RNA-Seq_ALL04_IN_TEM_IFNG


title: RNA-Seq_ALL02_OUT_TEM_IL5


title: RNA-Seq_ALL02_OUT_TCM_IL5


title: RNA-Seq_ALL02_OUT_TCM_IFNG


title: RNA-Seq_ALL01_OUT_TEM_IFNG


title: RNA-Seq_ALL02_OUT_TEM_IFNG


title: RNA-Seq_ALL02_IN_TCM_IL5


title: RNA-Seq_ALL02_IN_TCM_IFNG


title: RNA-Seq_ALL02_IN_TEM_IL5


title: RNA-Seq_NON_ALL01_OUT_TEM_IFNG


title: RNA-Seq_ALL02_IN_TEM_IFNG


title: RNA-Seq_NON_ALL01_OUT_TCM_IFNG


title: RNA-Seq_NON_ALL01_OUT_TCM_IL5


title: RNA-Seq_ALL01_IN_TCM_NEG


title: RNA-Seq_NON_ALL01_IN_TEM_IFNG


title: RNA-Seq_NON_ALL01_IN_TCM_IFNG


title: RNA-Seq_NON_ALL01_OUT_TEM_IL5


title: RNA-Seq_NON_ALL01_IN_TCM_IL5


title: RNA-Seq_NON_ALL01_IN_TEM_IL5


title: RNA-Seq_NON_ALL02_OUT_TCM_IFNG


title: RNA-Seq_NON_ALL02_OUT_TEM_IFNG


title: RNA-Seq_ALL01_OUT_TCM_IL5


title: RNA-Seq_NON_ALL02_OUT_TCM_IL5


title: RNA-Seq_NON_ALL02_OUT_TEM_IL5


title: RNA-Seq_NON_ALL02_IN_TCM_IFNG


title: RNA-Seq_NON_ALL02_IN_TEM_IL5


title: RNA-Seq_NON_ALL03_OUT_TCM_IFNG


title: RNA-Seq_NON_ALL03_OUT_TEM_IFNG


title: RNA-Seq_ALL01_OUT_TEM_IL5


title: RNA-Seq_NON_ALL03_OUT_TCM_IL5


title: RNA-Seq_NON_ALL03_OUT_TEM_IL5


title: RNA-Seq_NON_ALL03_IN_TCM_IFNG


title: RNA-Seq_NON_ALL03_IN_TCM_IL5


title: RNA-Seq_NON_ALL03_IN_TEM_IFNG


title: RNA-Seq_ALL01_OUT_TCM_NEG

value: central memory CD4 Tcells - CD3+ CD4+ CD45RA- CCR7+ IFNG+


title: RNA-Seq_ALL01_IN_TEM_IFNG


title: RNA-Seq_ALL01_IN_TCM_IFNG

value: IFNg secreting central memory CD4 Tcells - CD3+ CD4+ CD45RA- CCR7+ IFNG+


title: RNA-Seq_ALL01_IN_TCM_IL5


title: RNA-Seq_NON_ALL02_IN_TEM_IFNG

value: Timothy Grass Non Allergic


title: 004 normal skin tissues of  rattus RNA-Seq

city: Shanghai

first: Tienan

last: Feng

state: Shanghai

address: Siping Road No. 1239

country: China

institute: Tongji University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with fastx_toolkits 0.0.12, then mapped to rn6 whole genome using tophat 2.1.0 with default parameters
FPKM value were calculated using Cufflinks tool v2.1.1
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Rattus norvegicus

source_name: skin tissues

growth_protocol: SD rats grown in normal condition

extract_protocol:
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 45 Gy electron beam

tag: strain

value: SD

tag: condition

value: normal


title: 005 normal skin tissues of  rattus RNA-Seq


title: 006 normal skin tissues of  rattus RNA-Seq


title: RNA-Seq_NON_ALL02_IN_TCM_IL5

value: IL5 secreting central memory CD4 Tcells - CD3+ CD4+ CD45RA- CCR7+ IFNG+

value: Blood draw during of Timothy Grass pollen season


title: Low CO2 Rep 3

city: shanghai

first: Ming

middle: Ju

last: Lu

state: shanghai

address: 320 Yueyang Road, Xuhui Area, Shanghai, China

department: Partner Institute for Computational Biology, Shanghai Institutes for Biologic Sciences, CAS

institute: Shanghai Institutes for Biological Sciences, CAS

data_processing:
filter low quality reads  using FastQC, and trim the remained using fastx_trimmer. Both used the default parameters.
mapping treamed reads to CDNA dataset of Arabidopsis thaliana using Tophat in default parameters
Calculate the transcript RPKM values appling Cufflinks
Differential exprssed genes were determined using Cuffdif with Pvalue<=0.05
Supplementary_files_format_and_content: xls file containing RPKM of mean value from three replicates for both normal CO2 and Low CO2

organism: Arabidopsis thaliana

source_name: Whole Leaf

growth_protocol: Arabidopsis thaliana Columbia-0 (Col-0) seeds were imbibed in 0.1% (w/v) agar solution and kept at 4°C. After two days, seeds were transferred to pots with Pindstrup soil containing in a growth chamber (NC-350HC-LC, Nihonika, Japan). Two CO2 levels, i.e. 100 ppm and 380 ppm, were used during the growth. Plants were grown under long-day growth conditions (i.e. 16/8h day/night duration), at 21°C and 70% relative humidity. After four weeks, leaf samples were collected and stored at -80°C for RNA isolation

extract_protocol:
Total RNA was isolated using Ambion RNA isolation kit (PureLink® RNA Mini Kit) following instructions provided with the kit
The cDNA libraries were constructed following Illumina TruSeqTM RNA sample preparation version 2 guide (catalog # RS-930–1021)

tag: ecotype

value: Columbia

tag: genotype

value: Wild type

value: Leaf


title: Low CO2 Rep 1

treatment_protocol: Two CO2 levels, i.e. 100 ppm and 380 ppm, were used during the growth

tag: tissue


title: Normal CO2 Rep 1


title: Low CO2 Rep 2


title: 003 skin tissues of rattus RNA-Seq

value: irradiated


title: Normal CO2 Rep 3


title: Normal CO2 Rep 2


title: 002 skin tissues of rattus RNA-Seq


title: 001 skin tissues of rattus RNA-Seq