title: QR6

city: jinan

first: juren

last: zhang

address: shanda nanlv 27

institute: shandong university

data_processing:
The small RNA digitalization analysis based on HiSeq high-throughput sequencing takes the SBS-sequencing by synthesis. Then the 50nt sequence tags from HiSeq sequencing will go through the data cleaning first, which includes getting rid of the low quality tags and several kinds of contaminants from the 50nt tags.
Length distribution of clean tags are then summarized. Afterwards, the standard bioinformatics analysis will annotate the clean tags into different categories and take those which can not be annotated to any category to predict the novel miRNA and base edit of potential known miRNA.
Compare the known miRNA expression between two samples to find out the differentially expressed miRNA.
(1)Normalize the expression of miRNA in two samples (control and treatment) to get the expression of transcript per million (TPM).       Normalization formula: Normalized expression = Actual miRNA count/Total count of clean reads*1000000
(2)Calculate fold-change and P-value from the normalized expression. Then generate the log2ratio plot and scatter plot.
Genome_build: n/a
Supplementary_files_format_and_content: raw counts

growth_protocol: Seeds of the maize inbred line Q319 were surface sterilized and held at 28°C in darkness. Seedlings (4 days old) were transferred to a sufficient phosphate (SP, 1,000 μM KH2PO4) solution (Ca(NO3)2.4H2O 2 mM, NH4NO3 1.25 mM, KCl 0.1 mM, K2SO4 0.65 mM, MgSO4 0.65 mM, H3BO3 10.0 mM, (NH4)6Mo7O24 0.5 mM, MnSO4 1.0 mM, CuSO4.5H2O 0.1 mM, ZnSO4.7H2O 1.0 mM, Fe-EDTA 0.1 mM), allowed to grow for 4 days (plants with 2–3 leaves).

extract_protocol:
The roots and leaves were then harvested at 0, 1, 2, 4, 8 days and 8 days and cultured in SP solution (as a normal growth control) for small RNA analysis. The samples were frozen in liquid nitrogen immediately and stored at -80℃ for further analysis. Each biological repeat contains segments from 15~20 plants. Total RNA was extracted as previously described in Molecular Cloning (Sambrook and Russell David, 1989) and was then subjected to two additional chloroform washes prior to nucleic acid precipitation.
The small RNA digitalization analysis based on HiSeq high-throughput sequencing takes the SBS-sequencing by synthesis.

treatment_protocol: After 2-3 days of re-culturing in SP nutrient solutions, half of the seedlings were transplanted into a low phosphate (LP, same composition as the SP solution, except that 5 μM KH2PO4 and 1 mM KH2PO4 were replaced with 1 mM KCl) nutrient solution. The plants were grown under a 32°C/25°C (day/night) temperature regime at a photon flux density (PFD) of 700 μmol m-2 s-1 with a 14 h/10 h light/dark cycle in a greenhouse with approximately 65% relative humidity.

tag: tissue

value: Maize root at 4-leaf stage

value: low phospahte treat for 8 day


title: IPSDM M1 rep4

status: Public on Jul 08 2015

type: SRA

city: New York

first: Chenyi

last: Xue

state: NY

country: USA

institute: Columbia University

description: Sample 18

library_source: transcriptomic

data_processing:
Base calling was done by RTA v1.13.48.0
Sequence reads were aligned to hg19 genome using STAR with default options.
Alignment was filtered using the following specifications: 1) the mapping quality score of each read is ≥ 30, 2) reads from the same pair were mapped to the same chromosome with expected orientations and mapping distance between the read pair was < 500,000 bp, 3) read was uniquely mapped
Fragments Per Kilobase of exon per Million reads mapped (FPKM) was estimated by Cufflinks 2.1.1. Differential expression was tested by Cuffdiff with options "-u --max-bundle-frags 50000000 --library-type fr-firststrand". Annotation from RefSeq genes and the stringent set of lincRNAs from Cabili et al. 2011 was provided.
Genome_build: hg19
Supplementary_files_format_and_content: DIFF files were obtained from Cuffdiff output.Tab-delimited text file include normalized FPKM values from HMDM, IPSDM and iPSC samples
HMDM_MAC_M1_gene_exp.diff contains differential expression result from HMDM and M1-HMDM. sample_1 = HMDM, sample_2 = M1-HMDM
HMDM_MAC_M2_gene_exp.diff contains differential expression result from HMDM and M2-HMDM. sample_1 = HMDM, sample_2 = M2-HMDM
HMDM_M1_M2_gene_exp.diff contains differential expression result from M1-HMDM and M2-HMDM. sample_1 = M1-HMDM, sample_2 = M2-HMDM
IPSDM_M1_M2_gene_exp.diff contains differential expression result from M1-IPSDM and M2-IPSDM. sample_1 = M1-IPSDM, sample_2 = M2-IPSDM
IPSDM_MAC_M1_gene_exp.diff contains differential expression result from IPSDM and M1-IPSDM. sample_1 = IPSDM, sample_2 = M1-IPSDM
IPSDM_MAC_M2_gene_exp.diff contains differential expression result from IPSDM and M2-IPSDM. sample_1 = IPSDM, sample_2 = M2-IPSDM
HMDM_IPSDM_gene_exp.diff contains differential expression result from HMDM and IPSDM. sample_1 = HMDM, sample_2 = IPSDM
iPS_IPSDM_gene_exp.diff contains differential expression result from iPSC and IPSDM. sample_1 = iPSC, sample_2 = IPSDM
HMDM_IPS_IPSDM.norm.expr.txt contains normalized FPKM from all samples

molecule: polyA RNA

organism: Homo sapiens

source_name: Macrophage

growth_protocol: iPSC lines were maintained in hESC media consisting of Dulbecco modified Eagle medium/F12 (50:50; Life Technologies, Grand Island, NY) supplemented with 20% knockout serum replacement, 100 μM nonessential amino acids, 50 U/ml penicillin, 50 μg/ml streptomycin (Life Technologies), 10−4 M β-mercaptoethanol (Sigma-Aldrich, St. Louis, MO), and 10 ng/ml human basic fibroblast growth factor (bFGF) on irradiated mouse embryonic feeder cells (MEF, GlobalStem, Rockville, MD). PBMC were cultured in 20% FBS/RPMI with 100 ng/ml human M-CSF (Peprotech, Rocky Hill, NJ) for 7 days to induce differentiation to macrophages. iPSC were differentiated to macrophages according to established protocols and maintained in 20% FBS/RPMI with 100 ng/ml human M-CSF.

extract_protocol:
RNA samples were extracted using All Prep DNA/RNA/miRNA Universal Kit (Qiagen, Valencia, CA). Extracted RNA samples underwent quality control (QC) assessment using the Agilent Bioanalyzer (Agilent, Santa Clara, CA)
With a minimum of 300 ng input RNA, we generated first-strand cDNA using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis using RNase H and DNA polymerase, and ligation of sequencing adapters using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA). Fragments of ~350 bp were selected by gel electrophoresis. To minimize lane and batch effects in RNA-Seq experiments, barcoded libraries were mixed and pooled in equimolar (2 nmol/L) amounts and diluted to 4 pmol/L for cluster formation on a single flow cell lane, followed by 100 bp paired-end sequencing on Illumina’s HiSeq 2000.

tag: cell type

value: M1-polarized IPSDM


title: IPSDM M1 rep2

description: Sample 16


title: QR4

country: China

molecule: total RNA

organism: Zea mays

value: Maize root at 3-leaf stage

tag: treatment

value: low phospahte treat for 2 day


title: QR5

value: low phospahte treat for 4 day


title: IPSDM M2 rep4

description: Sample 22

value: M2-polarized IPSDM


title: IPSDM MAC rep4

description: Sample 14

value: iPSC derived macrophage (IPSDM)


title: QR3

value: low phospahte treat for 1 day


title: QR1

value: low phospahte treat for 0 day


title: IPSDM MAC rep3

description: Sample 13


title: IPSDM MAC rep2

description: Sample 12


title: QL6

value: Maize leaf at 4-leaf stage


title: QL5

value: Maize leaf at 3-leaf stage


title: IPSDM MAC rep1

description: Sample 11


title: QL4


title: QL3


title: iPS rep2

description: Sample 8

source_name: Induced pluripotent stem cell

value: Induced pluripotent stem cell (iPSC)


title: IPSDM M1 rep3

description: Sample 17


title: HMDM M2 rep2

description: Sample 6

value: M2-polarized HMDM


title: IPSDM M1 rep1

description: Sample 15


title: iPS rep3

description: Sample 9


title: Q319L_8d_CK_2


title: iPS rep4

description: Sample 10


title: QL1


title: iPS rep1

description: Sample 7


title: Q319R_8d_CK_2


title: Q319R_8d_CK_1


title: HMDM M1 rep1

description: Sample 3

value: M1-polarized HMDM


title: HMDM M1 rep2

description: Sample 4


title: Q319R_0d_CK_1


title: Q319L_0d_CK_2


title: HMDM MAC rep2

description: Sample 2

value: PBMC derived macrophage (HMDM)


title: HMDM MAC rep1

description: Sample 1


title: Q319L_8d_CK_1


title: Q319R_0d_CK_2


title: Q319L_0d_CK_1


title: MII15

city: Davis

first: James

middle: Lee

last: Chitwood

state: CA

address: 1 Shields Avenue

department: Animal Science

institute: University of California, Davis

data_processing:
Illumina fastq sequences were imported and processed in CLC Genomics Workbench.
Trimming was performed by removing 2 bp from the 5' end of every sequence.
Bovine Ensembl UMD 3.1.68 was used for determing expression values during RNA-seq analysis in CLC Genomics Workbench.
An extended annotation was generated using sample reads and the Transcript Discovery tool, and RNA-seq analysis was performed again.
Differential gene expression was determined using default parameters in the DESeq package in R.
Genome_build: Augmented Ensembl UMD 3.1.68 (provided in supplementary files)
Supplementary_files_format_and_content: Expression values in RPKM for all samples and the extended genome annotation used for RNA-seq analysis.

organism: Bos taurus

source_name: In vitro matured oocytes

growth_protocol: Abbatoir-derived bovine ovaries were aspirated to collect cumulus-oocyte-complexes. GV samples were collected at aspiration while MII oocytes were matured in vitro for 24 hours.

extract_protocol:
RNA was extracted from invidual oocytes using the Clontech SMARTer Ultralow RNA Kit for Illumina Sequencing and cDNA synthesized/amplified immediately. Amplified cDNA was used with the Illumina DNA kit to make sequencing libraries.
Illumina protocols were followed to synthesize indexed libraries SR50 sequencing. Only adapter concentration was adjusted for each sample based on cDNA input: (GV14 1:30, GV15 1:10, GV15c 1:10, MII14 1:30, MII14c 1:50, MII15 1:50)

tag: Stage

value: metaphase II ooyctes


title: GV15c

value: germinal vesicle


title: GV15


title: GV14


title: MII14


title: HMDM M2 rep1

description: Sample 5


title: ZT16-24h_Control-R3

status: Public on Jul 07 2015

city: Londrina

first: Alexandre

middle: Lima

last: Nepomuceno

state: Paraná

address: Rodovia Carlos João Strass, s/n Acesso Orlando Amaral

country: Brazil

institute: Embrapa Soja

description: processed data file: DEGs_ZT16-24h.txt

data_processing:
Base calling of the raw data was performed with parsing reads according to the respective barcodes and trimmed to remove adaptors and primer sequencing
Trimmed sequences were aligned with the soybean genome Glyma v1.1 using the BWA method. As mapping included both unique and multiple reads, we counted these two types differentially: unique reads were counted as a whole count, whereas multiple reads were counted proportionally for each location they were mapped to (up to five sites) when none of the adjacent unique reads appeared. Multiple reads mapped next to a set of unique reads mapped in one location were counted fully to that site. From this alignment, sequences were mapped on exons, introns, and intergenic regions, which were characterized as sequences outside of any annotated gene. The remaining unmapped reads were then aligned to a spliced reference created using all possible combinations of known exons to generate putative splice junction sites based on the annotation described above.
Reads per Mapped Million (RPM) was calculated by taking the count value and dividing it by the number of millions of mapped reads and the Reads Per Kilobase per Million (RPKM), which was calculated by taking the RPM value and dividing it by the kilobase length of the longest transcript for each gene.
A pairwise comparison between the control and water deficit treatment using all three libraries was performed using the edgeR statistical test. Normalization was performed by dividing values of gene expression under water deficit and control conditions. We combined the statistical test with the multiple-hypothesis-testing correction method of Benjamini and Hochberg, which calculates the False Discovery Rate (FDR), to qualify statistically significant, differentially expressed genes by avoiding inflation of type-1 errors. Differential gene expression was considered significant at an adjusted p-value ≤ 0.01, and down- and up-regulation was established in the range of ≤ -2 to ≥ 2 fold-change (fc), respectively.
Genome_build: Glyma v1.1
Supplementary_files_format_and_content: tab-delimited text files show the differentially expressed genes (DEGs) for each Sample. RPKM data for all genes in each sample are available on the series record.

organism: Glycine max

growth_protocol: Soybean plants from cultivar BR16 were cultivated until the V1 developmental stage in a growth chamber under controlled  conditions. Seeds were germinated in SuperSoil® (Scotts Miracle-Gro Company, Marysville, Ohio) at a temperature of 28/20°C (day/night, respectively), relative humidity of 80%, and photoperiod of 14 h day (under 500 μmol m-2 s-1 of white light)/10 h night. The experimental design was completely randomized and included two treatments (control and water deficit), six time points, and six biological replicates for each treatment/time point.

extract_protocol:
Total RNA was extracted from leaves using the RNA Plant Reagent® (Ambion) and treated with DNAse (Invitrogen). Following analysis of RNA quality and integrity in a Bioanalyzer (Agilent) (RIN ≥ 8.0), equimolar quantities of purified total RNA samples from each of two biological replicates were pooled into one template for library synthesis.
For each time period and treatment were synthesized three independent libraries using the Ovation RNA-Seq® (NuGEN Technologies) method, which is suitable to use with the Illumina platform. Approximately 150 ng of total RNA was mixed with the selected primers to synthesize the first strand of the cDNA using a reverse transcription polymerase. The second strand was synthesized using a single primer for reverse transcription and incorporation of analog nucleotides, followed by RNA strand degradation. Double-stranded DNA was fragmented by sonication to a median size of 200 bp and purified with the Agencourt RNAClean XP system (Beckman Coulter) using magnetic beads. Fragment ends were repaired to produce blunt ends and ligated to a pair of double-stranded fragments containing nucleotide analog-tagged adaptors. Strand selection eliminated sequences with the nucleotide analog (insert or insert + adaptor), thereby creating a sequence library with a single insert orientation. Sequences containing both adaptors were amplified using forward and reverse primers for 15 cycles, resulting in a specific-strand, rRNA-depleted cDNA library. Following qualitative and quantitative analysis using a Bioanalyzer, libraries were used to produce clusters for a 2 x 50 bp paired end-sequencing run.

treatment_protocol: Soybean field capacity was determined using the gravimetric humidity method to establish the percentage of water in the soil. We previously estimated the water volume needed to reach a 100% soil field capacity by weighting the pots daily to calculate the ratio between its fresh and dry weight. We established a 70% soil field capacity to grow all plants during 14 days. At the 15th day irrigation was suspended to initiate the water deficit treatment: control plants were maintained at 70% and the stressed-plants were monitored periodically until soil field capacity reach 30%, approximately (3 days after starting the stress treatment). At this condition, leaves were sampled in six time-points with consecutive 4-h intervals. Plants’ harvesting initiated at 8:00 h am (ZT0) and followed as: 12 h am/ZT4, midday; 16 h/ZT8, late day; 20 h/ZT12, dusk (transition light-dark); 24 h/ZT16, midnight; and 4 h/ZT20, pre-dawn. By convention, Zeitgeber time (ZT times) was used to indicate when light period started (ZT0) and to associate the six time-points to the respective time of day. Leaves were collected, immediately frozen in liquid nitrogen and stored at -80°C.

value: leaves

tag: developmental stage

tag: cultivar


title: ZT20-4h_Stress-R1

description: processed data file: DEGs_ZT20-4h.txt


title: ZT20-4h_Stress-R2

description: processed data file: DEGs_ZT20-4h.txt


title: ZT20-4h_Stress-R3

description: processed data file: DEGs_ZT20-4h.txt


title: ZT20-4h_Control-R2

description: processed data file: DEGs_ZT20-4h.txt


title: ZT12-20h_Control-R2

description: processed data file: DEGs_ZT12-20h.txt


title: ZT12-20h_Stress-R3

description: processed data file: DEGs_ZT12-20h.txt


title: ZT16-24h_Stressl-R3

description: processed data file: DEGs_ZT16-24h.txt


title: ZT20-4h_Control-R3

description: processed data file: DEGs_ZT20-4h.txt


title: ZT16-24h_Control-R2

description: processed data file: DEGs_ZT16-24h.txt


title: ZT12-20h_Control-R1

description: processed data file: DEGs_ZT12-20h.txt


title: ZT16-24h_Control-R1

description: processed data file: DEGs_ZT16-24h.txt


title: MII14c


title: ZT8-16h_Control-R2

description: processed data file: DEGs_ZT8-16h.txt


title: ZT8-16h_Control-R3

description: processed data file: DEGs_ZT8-16h.txt


title: ZT12-20h_Control-R3

description: processed data file: DEGs_ZT12-20h.txt


title: ZT12-20h_Stress-R1

description: processed data file: DEGs_ZT12-20h.txt


title: ZT20-4h_Control-R1

description: processed data file: DEGs_ZT20-4h.txt


title: ZT8-16h_Stress-R3

description: processed data file: DEGs_ZT8-16h.txt


title: ZT8-16h_Control-R1

description: processed data file: DEGs_ZT8-16h.txt


title: ZT8-16h_Stress-R2

description: processed data file: DEGs_ZT8-16h.txt


title: ZT16-24h_Stressl-R2

description: processed data file: DEGs_ZT16-24h.txt


title: ZT16-24h_Stressl-R1

description: processed data file: DEGs_ZT16-24h.txt


title: ZT8-16h_Stress-R1

description: processed data file: DEGs_ZT8-16h.txt


title: ZT4-12h_Control-R2

description: processed data file: DEGs_ZT4-12h.txt


title: ZT4-12h_Stress-R3

description: processed data file: DEGs_ZT4-12h.txt


title: ZT4-12h_Control-R3

description: processed data file: DEGs_ZT4-12h.txt


title: ZT4-12h_Stress-R2

description: processed data file: DEGs_ZT4-12h.txt


title: ZT4-12h_Stress-R1

description: processed data file: DEGs_ZT4-12h.txt


title: ZT0-8h_Control-R2

description: processed data file: DEGs_ZT0-8h.txt


title: ZT0-8h_Stress-R3

description: processed data file: DEGs_ZT0-8h.txt

data_processing:
Base calling of the raw data was performed with parsing reads according to the respective barcodes and trimmed to remove adaptors and primer sequencing
Trimmed sequences were aligned with the soybean genome Glyma v1.1 using the BWA method. As mapping included both unique and multiple reads, we counted these two types differentially: unique reads were counted as a whole count, whereas multiple reads were counted proportionally for each location they were mapped toRPK (up to five sites) when none of the adjacent unique reads appeared. Multiple reads mapped next to a set of unique reads mapped in one location were counted fully to that site. From this alignment, sequences were mapped on exons, introns, and intergenic regions, which were characterized as sequences outside of any annotated gene. The remaining unmapped reads were then aligned to a spliced reference created using all possible combinations of known exons to generate putative splice junction sites based on the annotation described above.
Reads per Mapped Million (RPM) was calculated by taking the count value and dividing it by the number of millions of mapped reads and the Reads Per Kilobase per Million (RPKM), which was calculated by taking the RPM value and dividing it by the kilobase length of the longest transcript for each gene.
A pairwise comparison between the control and water deficit treatment using all three libraries was performed using the edgeR statistical test. Normalization was performed by dividing values of gene expression under water deficit and control conditions. We combined the statistical test with the multiple-hypothesis-testing correction method of Benjamini and Hochberg, which calculates the False Discovery Rate (FDR), to qualify statistically significant, differentially expressed genes by avoiding inflation of type-1 errors. Differential gene expression was considered significant at an adjusted p-value ≤ 0.01, and down- and up-regulation was established in the range of ≤ -2 to ≥ 2 fold-change (fc), respectively.
Genome_build: Glyma v1.1
Supplementary_files_format_and_content: tab-delimited text files show the differentially expressed genes (DEGs) for each Sample. RPKM data for all genes in each sample are available on the series record.


title: ZT0-8h_Control-R3

description: processed data file: DEGs_ZT0-8h.txt


title: EV + 4OHT Rep3

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description: Expression profile of senescent cells (EV + 4OHT)

data_processing:
RNA-Seq reads were aligned to human genome hg19 using Tophat verion 2.0.8 in strand specific mode. Gene annotations were obtained from Ensembl gene version 72. FPKM values were computed using R script
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: IRM90 ER:RAS

growth_protocol: IRM90 ER:RAS were grown in DMEM 10% FBS for 7 days. Media was changed at Day 4

extract_protocol: Libraries were prepared according to Illumina's kit instructions (mRNA stranded library prep kit)

treatment_protocol: To induce RAS expression, cells were treated with 4OHT [100nM]

tag: cell line

tag: days after 4oht induction

tag: passage

value: senescent cells


title: ZFP36L1mut +4OHT Rep3

description: Expression profile of senescent cells expressing ZFP36L1mut

value: senescent cells expressing ZFP36L1mut


title: RNASeq DC +LPS+IL21 4h

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: pretreated with IL21 for 1h followed by LPS 4h

data_processing:
Sequenced reads (50 bp, single end) were mapped to the mouse genome (NCBI37/mm9, July 2007) using Bowtie 0.12.9, and only the reads that mapped on exons of each RefSeq gene were measured and normalized using reads per kilobase per million mapped reads (RPKM). The analyses of differential gene expression were performed using the R package edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: RPKM

organism: Mus musculus

source_name: Splenic conventional dendritic Cells

growth_protocol: Mouse spleens were injected with 1 ml of 1 mg/ml collagenase D and 20 g/ml DNase I (Roche), cut and incubated in collagenase solution at 37C for 20 min. After passage through a cell strainer, red blood cells were lysed using ACK lysis buffer, and remaining cells incubated with Fc block (BD Biosciences) at 4C for 10 min. CD11c+ cells were positively selected with CD11c microbeads (Miltenyi Biotec). Purity of CD11c+ DCs was 93-95%.

extract_protocol: Total RNA was isolated, and 5 μg per sample were used for mRNA purification using Dynal oligo(dT) beads (Invitrogen). Double-stranded cDNA was synthesized with random hexamer primers, SuperScript II, DNA polymerase I, and T4 DNA polymerase (Invitrogen) and fragmented by Bioraptor. After end repair (Epicentre DNA END-Repair kit) and the addition of an “A” nucleotide to the 3’ ends with Taq DNA polymerase, two mixed Solexa adaptors (Illumina) were ligated to DNA ends using T4 DNA ligase (New England Biolabs). 250-500 bp fragments were isolated on 2% E-Gels (Invitrogen) and amplified for 18 cycles using PE 1.0 and 2.0 primers (Illumina) and Phusion High Fidelity PCR Master Mix (New England Biolabs). PCR products were run on a gel, and 250-500 bp fragments were purified. Final PCR products were sequenced on an Illumina HiSeq 2000 platform.

treatment_protocol: For ChIP-Seq analysis, DCs were rested 1 h and treated with IL-21 for 1 h; CD4+ T cells were pre-activated with 5 μg/ml plate-bound anti-CD3 + 2 μg/ml soluble anti-CD28 for 3 days, washed, rested for 16 h, and treated with IL-21 for 1 h. For RNA-Seq analysis, total mouse splenic CD4+ T cells were pre-activated with plate-bound anti-CD3 + anti-CD28 for 3 days, washed and rested overnight, and not stimulated or stimulated with IL-21 for 4 h. For determining the effect of IL-21, IL-10, or LPS alone, cDCs isolated from spleens were rested 1 h, then stimulated with 100 ng ml-1 of IL-21, IL-10 or LPS for 4 h. For determining the effect of IL-21 or IL-10 on the LPS-stimulated gene regulation, cDCs were stimulated with LPS for 4 h, with or without pre-treatment of IL-21 or IL-10 1 h prior LPS stimulation.

tag: strain

value: Spleen

tag: protocol


title: RNASeq DC +IL10 4h

description: treated with IL10 for 4h

value: treated with IL10 for 4h


title: ZT0-8h_Stress-R2

description: processed data file: DEGs_ZT0-8h.txt


title: ZT0-8h_Stress-R1

description: processed data file: DEGs_ZT0-8h.txt


title: ZT0-8h_Control-R1

description: processed data file: DEGs_ZT0-8h.txt


title: ZFP36L1wt +4OHT Rep3

description: Expression profile of senescent cells expressing ZFP36L1wt

value: senescent cells expressing ZFP36L1wt


title: ZFP36L1mut +4OHT Rep2


title: ZFP36L1wt +4OHT Rep2


title: RNASeq DC +LPS 4h

description: treated with LPS for 4h

value: treated with LPS for 4h


title: RNASeq DC +LPS+IL10 4h

description: pretreated with IL10 for 1h followed by LPS 4h


title: ZT4-12h_Control-R1

description: processed data file: DEGs_ZT4-12h.txt


title: ZFP36L1mut +4OHT Rep1


title: RNASeq DC untreated

description: untreated

value: untreated


title: ZFP36L1wt +4OHT Rep1


title: P60 Male F1r sample 6

city: Cambridge

first: Nimrod

middle: Daniel

last: Rubinstein

state: MA

address: 16 Divinity Avenue

department: Molecular and Cellular Biology

institute: Harvard University

description:
MF1r6_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv

data_processing:
Quality and adapter trimming was performed using the Trim Galore  utility (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore) with stringency level 3.
Each C57Bl/6J×Cast/EiJ hybrid RNA-seq sequenced library was mapped to the  C57Bl/6J, Cast/EiJ diploid genome and transcriptome splice junctions using STAR RNA-seq  aligner (Dobin et al., 2013) allowing a maximum of three mismatches.
Cutom code was used to transfor bam files from C57Bl/6J×Cast/EiJ genomic coordinates to C57Bl/6J×Cast/EiJ transcriptomic coordinates where reads not mapping to any transcript were removed.
Transcript expression levels were estimated using MMSEQ (Turro et al., 2011).
Trannscripts with considerable read-sharing were collapsed as described in the manuscript.
FPKM units were converted to TPM units and an the low expression cutoff was empirically determined as described in the manuscript
Genome_build: C57Bl/6J and Cast/EiJ single nucleotide polymorphisms and indels (obtained from the Mouse Genome Project: ftp://ftpmouse.  sanger.ac.uk/REL-1303-SNPs_Indels-GRCm38) were incorporated into the Mus musculus GRCm38 reference genome sequence to obtain a C57Bl/6J, Cast/EiJ diploid genome.
Supplementary_files_format_and_content:

MF.A.P8.P60.allele.csv: A table which rows are autosomal transcript IDs and columns are for each sample: (1) MMSEQ's posterior mean of log(paternal TPM), (2) MMSEQ's posterior variance of log(paternal TPM), (3) MMSEQ's posterior mean of log(maternal TPM), (4) MMSEQ's posterior variance of log(maternal TPM), (5) MMSEQ's posterior mean of log(paternal TPM) - log(maternal TPM), (6) MMSEQ's posterior variance of log(paternal TPM) - log(maternal TPM)

F.X.P8.P60.allele.csv: A table which rows are X-linked transcript IDs and columns are for each female sample: (1) MMSEQ's posterior mean of log(paternal TPM), (2) MMSEQ's posterior variance of log(paternal TPM), (3) MMSEQ's posterior mean of log(maternal TPM), (4) MMSEQ's posterior variance of log(maternal TPM), (5) MMSEQ's posterior mean of log(paternal TPM) - log(maternal TPM), (6) MMSEQ's posterior variance of log(paternal TPM) - log(maternal TPM)

gencode.vM2.annotation.2wayconspseudos.knownGene.retro.fnRDB.C57.CAST.gtf.gz: A GTF file of the  C57Bl/6k, Cast/Eij diploid transcriptome which was used to quantify expression from the F1 hybrids used in this study  reference genome sequence to obtain a C57Bl/6J, Cast/EiJ diploid genome.

Supplementary_File_1.xlsx: An excel file which contains the results of inferring parentally biased expression for either both P8 and P60 age groups together or each age group separately, for autosomes, and X chromosome

source_name: P60 Male F1r cerebellum

growth_protocol: F1 hybrids were generated by reciprocally crossing C57Bl/6J and Cast/EiJ mouse strains

extract_protocol:
RNA was isolated from tissues of interest using the Trizol reagent (Life Technologies) according   to the manufacturer instructions and further purified using DNase I digestion and the RNeasy kit  (Qiagen).
3ug of  total RNA were used for preparing libraries according to the Illumina Tru-Seq RNA sample preparation   protocol. Average fragment size of 250 bp was selected
Each RNA-seq library was sequenced on an individual HiSeq200 lane generating 59bp single-end reads

treatment_protocol: Animals were kept in standard housing conditions at room temperature and on a reverse 12-h light/dark cycle. Food and water were available ad libitum.

value: Cast/EiJxC57Bl/6J hybrid

tag: gender

value: male

value: postnatal day 60

value: cerebellum


title: P60 Male F1r sample 5

description:
MF1r5_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: EV + 4OHT Rep1


title: P60 Male F1r sample 4

description:
MF1r4_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: EV - 4OHT Rep3

description: Expression profile of Non-senescent cells (EV - 4OHT)

value: Non-senescent cells


title: EV + 4OHT Rep2


title: P60 Male F1r sample 3

description:
MF1r3_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: EV - 4OHT Rep1


title: RNASeq DC +IL21 4h

description: treated with IL21 for 4h

value: treated with IL21 for 4h


title: P60 Male F1r sample 2

description:
MF1r2_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: EV - 4OHT Rep2


title: P60 Female F1r sample 5

description:
FF1r5_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv

source_name: P60 Female F1r cerebellum

value: female


title: P60 Female F1r sample 3

description:
FF1r3_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P60 Female F1r sample 2

description:
FF1r2_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P60 Male F1r sample 1

description:
MF1r1_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P60 Male F1i sample 6

description:
MF1i6_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv

source_name: P60 Male F1i cerebellum

value: C57Bl/6JxCast/EiJ hybrid


title: P60 Male F1i sample 2

description:
MF1i2_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P60 Male F1i sample 1

description:
MF1i1_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: ZT12-20h_Stress-R2

description: processed data file: DEGs_ZT12-20h.txt


title: P60 Female F1r sample 1

description:
FF1r1_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P60 Female F1r sample 6

description:
FF1r6_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P60 Female F1i sample 4

description:
FF1i4_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv

source_name: P60 Female F1i cerebellum


title: P60 Male F1i sample 5

description:
MF1i5_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P60 Female F1i sample 5

description:
FF1i5_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P60 Female F1r sample 4

description:
FF1r4_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P60 Female F1i sample 6

description:
FF1i6_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P60 Female F1i sample 2

description:
FF1i2_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P60 Female F1i sample 1

description:
FF1i1_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P8 Male F1r sample 6

description:
MF1r6_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv

source_name: P8 Male F1r cerebellum

value: postnatal day 8


title: P8 Male F1r sample 4

description:
MF1r4_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P8 Male F1r sample 3

description:
MF1r3_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P8 Male F1r sample 2

description:
MF1r2_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P8 Male F1r sample 1

description:
MF1r1_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P60 Male F1i sample 3

description:
MF1i3_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P60 Male F1i sample 4

description:
MF1i4_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P8 Female F1r sample 6

description:
FF1r6_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv

source_name: P8 Female F1r cerebellum


title: P8 Female F1r sample 3

description:
FF1r3_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P8 Female F1r sample 4

description:
FF1r4_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P8 Female F1r sample 5

description:
FF1r5_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P8 Female F1r sample 2

description:
FF1r2_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P8 Female F1r sample 1

description:
FF1r1_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P8 Male F1i sample 6

description:
MF1i6_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv

source_name: P8 Male F1i cerebellum


title: P8 Male F1i sample 2

description:
MF1i2_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P8 Male F1i sample 5

description:
MF1i5_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P8 Female F1i sample 3

description:
FF1i3_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv

source_name: P8 Female F1i cerebellum


title: P8 Male F1i sample 3

description:
MF1i3_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P8 Female F1i sample 4

description:
FF1i4_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P8 Female F1i sample 6

description:
FF1i6_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P8 Female F1i sample 2

description:
FF1i2_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: WT DC T +IL21 STAT3

description: ChIP against STAT3

library_source: genomic

data_processing:
For ChIP-Seq and RNA-Seq, Basecalls performed using CASAVA 1.8
Raw reads were aligned to the mm9 genome assembly using Bowtie 0.12.9
Aligned reads are converted to BED format and removed redundancies using unpublished python and perl scripts
For ChIP-Seq, peaks are called using MACS 1.4.2 and visualized using IGV browser
Genome_build: mm9
Supplementary_files_format_and_content: BED files are generated using CASAVA pipeline 1.8 and unpublished python scripts; txt files containing abundance measurements

molecule: genomic DNA

growth_protocol: Mouse spleens were injected with 1 ml of 1 mg/ml collagenase D and 20 μg/ml DNase I (Roche), cut and incubated in collagenase solution at 37C for 20 min. After passage through a cell strainer, red blood cells were lysed using ACK lysis buffer, and remaining cells incubated with Fc block (BD Biosciences) at 4C for 10 min. CD11c+ cells were positively selected with CD11c microbeads (Miltenyi Biotec). Purity of CD11c+ DCs was 93-95%.

extract_protocol:
Chromatin from 2 × 107 cells was sonicated for 20 cycles of 12 sec on/48 sec off, into 200-500 bp fragments, DNA ends were repaired using polynucleotide kinase and Klenow enzyme, and treated with Taq polymerase to generate a protruding 3’ “A” nucleotide. DNA fragments of ~250-450 bp were purified from agarose gels and used for cluster generation and sequencing. Various Antibodies against STAT3, IRF4, H3K4me1, H3K4me3, H3K27me3, H3K27ac were used.
PCR products were barcoded (indexed) and sequenced on Illumina HiSeq 2000 platform or on Illumina Genome Analyzer II.

treatment_protocol: DCs were rested 1 h and treated with IL-21 for 1 h; CD4+ T cells were pre-activated with 5 μg/ml plate-bound anti-CD3 + 2 μg/ml soluble anti-CD28 for 3 days, washed, rested for 16 h, and treated with IL-21 for 1h (for ChIP-Seq) or 4h (for RNA-Seq).

value: Splenic conventional dendritic Cells

tag: treated with

value: IL-21 for 1h

tag: chip antibody

tag: chip antibody vendor

value: Invitrogen

tag: chip antibody cat.#


title: P8 Male F1r sample 5

description:
MF1r5_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P8 Female F1i sample 1

description:
FF1i1_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: RNASeq CD4 T +IL21 4h Rep2

description: treated with IL-21 for 4h

source_name: Pre-activated CD4+ T cells

value: Spleen

value: Pre-activated CD4+ T cells

value: IL-21 for 4h


title: P60 Female F1i sample 3

description:
FF1i3_P60
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: RNASeq CD4 T untreated Rep2

description: untreated

value: none (untreated)


title: RNASeq CD4 T +IL21 4h Rep1

description: treated with IL-21 for 4h


title: WT DC T -IL21 STAT3

description: ChIP against STAT3


title: RNASeq CD4 T untreated Rep1

description: untreated


title: WT DC +IL21 H3K27ac

description: ChIP against H3K27ac

value: Abcam


title: WT DC +IL21 H3K4me1

description: ChIP against H3K4me1


title: WT DC -IL21 H3K4me1

description: ChIP against H3K4me1


title: P8 Male F1i sample 4

description:
MF1i4_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: P8 Female F1i sample 5

description:
FF1i5_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv


title: WT DC -IL21 H3K4me3

description: ChIP against H3K4me3

value: Millipore


title: WT DC +IL21 H3K27me3

description: ChIP against H3K27me3


title: WT DC -IL21 H3K27me3

description: ChIP against H3K27me3


title: WT DC -IL21 H3K27ac

description: ChIP against H3K27ac


title: WT CD4 T -IL21 H3K27ac

description: ChIP against H3K27ac


title: WT CD4 T +IL21 H3K4me1

description: ChIP against H3K4me1


title: WT CD4 T +IL21 H3K27ac

description: ChIP against H3K27ac


title: WT DC +IL21 H3K4me3

description: ChIP against H3K4me3


title: WT CD4 T -IL21 H3K4me1

description: ChIP against H3K4me1


title: WT CD4 T +IL21 STAT3

description: ChIP against STAT3


title: WT CD4 T +IL21 H3K27me3

description: ChIP against H3K27me3


title: WT CD4 T -IL21 STAT3

description: ChIP against STAT3


title: WT CD4 T +IL21 H3K4me3

description: ChIP against H3K4me3


title: H3K4me3_ChIPSeq

city: Konstanz

first: Claudius

middle: F

last: Kratochwil

address: Universitaetsstr. 10

department: Biology

country: Germany

institute: University of Konstanz

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied.
Reads were aligned to the anchored Oreochromis niloticus genome Orenil1.1 (Brawand et al. 2014). Read mapping was performed using CLC Genomics Workbench 7.0.3 using standard setting of the Map Reads to Reference Package (no masking, mismatch cost 2, insertion cost 3, deletion cost 3, length fraction 0.5, similarity fraction 0.8).
Chip-Seq peaks were detected using the and ChIP-Seq Analysis package with standard settings (Window Size 250, Maximum False discovery rate (FDR) 5%, shift reads based on fragment length 250, with and without boundary refinement, filter peaks on probability of identical locations on forward and reverse reads (Wilcoxon p-value 0.0001)
Genome_build: Orenil1.1
Supplementary_files_format_and_content: bed files were generated using CLC Genomics Workbench 7.0.3 and contain H3K4me3 ChIP-seq peaks

organism: Oreochromis niloticus

source_name: Adult fin tissue

extract_protocol:
Tilapia fin tissue was dissected, immediately frozen on dry ice, and stored at _80¡C. ChIP-seq was performed based on Active Motif's HistonePath method (Active Motif) as previously described (Ramagopalan et al. 2010). The frozen tissue was crushed in liquid nitrogen and fixed in PBS + 1% formaldehyde at room temperature for 10 minutes. Fixation was stopped by the addition of 0.125 M glycine (final concentration), and the fin pieces were washed 2x in PBS and 1x in deoxycholate sonication buffer. Lysates were sonicated with a microtip in order to shear the DNA to an average length of 300-500 bp. Lysates were cleared by centrifugation and stored at -80¡C. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by phenol/chloroform extraction and ethanol precipitation. Purified DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield.
For each ChIP reaction, 15 µg of chromatin was pre-cleared with protein A agarose beads (Invitrogen). ChIP reactions were set up using pre-cleared chromatin and antibody H3K4me3 (Active Motif, cat. 39159, Lot# 4) and incubated overnight at 4¡C. Protein A agarose beads were added and incubation at 4¡C was continued for another 3 h. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase treatment and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 ¡C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
ChIP DNA was prepared for amplification by converting overhangs into phosphorylated blunt ends and the addition of an adenine to the 3'-ends. Illumina genomic adapters were ligated and the sample was size-fractionated (200-300 bp) on an agarose gel. After a final PCR amplification step (18 cycles), the resulting DNA libraries were quantified and sequenced on Illumina MiSeq. Sequences (50 nt reads, single end).

tag: body part

value: anal fin

tag: age

value: adult

tag: antibody


title: In vitro 2

status: Public on Jul 06 2015

first: Michał

last: Pasternak

state: - None -

address: Francis Crick Avenue

institute: MRC Laboratory of Molecular Biology

data_processing:
Illumina OLB(off-line Basecaller) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bwa with parameters GenomeBwaOptions_PE = -o 1 -e 63 -i 90 -L -k 2 -l 31 -t 4 -q 10
The mapped read counts for each gene were normalized for RNA length and for the total read number in each lane using the fragments per kilobase per million (FPKM) method.We used a strict algorithm to identify differentially expressed genes (DEGs) based on comparing the in vitro with in vivo group to generate the DEGs.
Genome_build: mm9
Supplementary_files_format_and_content: excel file includes mean signal for in vitro group and in vivo group with statistics and gene annotation.

source_name: Oocytes grown in vitro

growth_protocol: Ovaries were dissected from two to five 10-12 day old (C57BL x CBA) F1 females. To obtain individual follicles, the ovaries were incubated in modified MEM-alpha medium optimized for in vitro culture of follicles (MEM-alpha (Gibco 12000-014) supplemented with 0.026M NaHCO3 (Sigma), 5678U/100 ml Penicillin G (Sigma) and 8265U/100ml Streptomycin (Sigma), 1x ITS (Insulin/Transferrin/Selenium Solution; Sigma; Stock is 100x), 5% FBS (Fetal Bovine Serum; Gibco 16000044) and 0.01 µg/ml FSH (Follicle Stimulating Hormone; National Hormone and Peptide Program, NDDK-oFSH-20) that was supplemented with 2 mg/ml collagenase (Roche) for about 30-40 minutes total. During incubation with collagenase, the ovaries were pipetted up and down every 10 minutes to facilitate dissociation and then washed through several droplets of follicle culture medium without collagenase and were cultured at 37°C in 5% CO2 on membrane inserts in 6 well or 12 well culture dishes filled with follicle culture medium (see above).

extract_protocol:
NucleoSpin RNA XS (Macherey-Nagel)
A cDNA library was prepared using SMARTer® Ultra™Low Input RNA for Sequencing (Clonetech Laboratories) and the samples were processed by BGI Tech Solutions. The cDNA product was synthesized and amplified using SMARTer PCR cDNA Synthesis Kit (Clontech) from the total RNA (10 ng) of sample. The cDNA was fragment by Covaris E210 (Covaris) and the median insert length was about 200bp.

value: (C57BL x CBA) F1

tag: tissue

value: Oocyte (GV)


title: In vivo 2

source_name: Oocytes obtained directly from adult mice

growth_protocol: Oocytes obtained directly from adult (C57BL x CBA) F1 females (7-11 weeks old) in M2 medium supplemented in dbcAMP by punctuation of ovaries with a needle.


title: In vivo 3


title: In vitro 3


title: Transcriptome of control of C. albicans

city: Guangzhou

first: Wenru

address: No.100, Xianliezhong Road

institute: Institute of Microbiology, Guangdong Academy of Sciences

description: ck

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Candida albicans WO-1 whole genome using Tophat2 v2.0.10 with parameters --read_mismatches 2 --read_gap_length 2 --read_edit_dist 2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Candida albicans WO-1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and counts for each Sample

organism: Candida albicans

source_name: control

extract_protocol:
Cells of C. albicans were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2  (Cat#RS-122-2002) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treament

value: control


title: Transcriptome of garlic oil-treated C. albicans

description: sample 1

source_name: garlic oil-treated

value: garlic oil


title: In vitro 1


title: P8 Male F1i sample 1

description:
MF1i1_P8
processed data files: MF.A.P8.P60.allele.csv,F.X.P8.P60.allele.csv

value: C57Bl/6JxCast/EiJ hybrid

value: male

tag: developmental stage

value: cerebellum


title: GATA2_GMP_KO_1

first: Sarah

last: Bettigole

address: 1300 York Avenue, E907

institute: Weill Cornell Medical College

data_processing:
Illumina's CASAVA1.8.2 software was used for basecalling
The reads that passed illumina's quality/purity filter were aligned to the mouse genome (Illumina iGenomes mm9 build) using STAR aligner (version 2.3.0) with default parameters.
The resulting SAM alignment files were then converted to the BAM file format, sorted and indexed using SAMtools (version 0.1.14).
The HTSeq python package (Anders S, Pyl PT, and Huber W. 2014. Bioinformatics) was used to summarize the aligned sequence reads into counts by feature using the "union" setting.
The DESeq bioconductor package was used to statistically analyze raw count data from HTSeq for differential expression (Anders S, Huber W.. 2010. Genome Biology)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw count values

source_name: GATA2-transduced GMP (48 hrs)

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq sample preparation kit (IP-202-1012) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

tag: growth protocol

value: FACS purified, transduced, resorted and cultured for 48 hrs

tag: library construction

value: SMARTer UltraTMLow Input RNA Kit, then TruSeq sample preparation kit IP-202-1012


title: GATA2_GMP_WT_3

value: wild type


title: GATA2_GMP_WT_2


title: GATA2_GMP_KO_2


title: GATA2_GMP_WT_1


title: GATA2_GMP_KO_3


title: WT CD4 T -IL21 H3K27me3

description: ChIP against H3K27me3

value: Spleen

tag: cell type

value: Pre-activated CD4+ T cells


title: GMP_KO_2

source_name: GMP

tag: strain

value: None, sorted into Trizol

value: TruSeq sample preparation kit IP-202-1012


title: GMP_KO_3


title: GMP_WT_3


title: WT CD4 T -IL21 H3K4me3

description: ChIP against H3K4me3

value: none (untreated)

value: Millipore


title: In vivo 1


title: GMP_KO_1


title: HiCap_replicate2_mESC

city: Stockholm

first: Ilgar

last: Abdullayev

address: Nobels väg 3

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

description:
HiCap_rep2_promoter-enhancer.gff
Hi-C coupled with sequence capture, biological replicate 2

data_processing:
Mapping of reads. Paired-end sequences were aligned to the mouse genome (build mm9) through the tool HiCUP (Babraham Bioinformatics). We then used custom scripts to pair the independently mapped sequence ends and we indexed each sequence pair to their corresponding MboI restriction fragment.
Calling of interactions. We called significant interactions for all promoter containing restriction fragments. To this end, aligned pairs of which at least one mate mapping on a promoter were selected. Promoter regions were defined as 1000 bases downstream and 3000 bases upstream of transcription start site. The extension allowed mappings involving the directly surrounding fragment of the promoter-anchored fragment to be incorporated into analyses, as restriction cut efficiency was only 71%. Nonetheless, in 77% of interactions detected in first HiCap replicate and 92% of interactions detected in the second HiCap replicate, all reads mapped to sequence capture probes. We collected all paired sequences with one end originating from a promoter region and the other end at least 1000 bp away from the promoter region. Next we counted the occurrence of interactions to all MboI restriction fragments in the genome from each captured promoter region. Read pairs with the exact same mapping positions were discarded (to remove any potential effect from PCR duplicates). The same procedure was applied to the negative control regions to obtain read pairs for interactions that were later used as background interaction probabilities. We binned all negative control interactions distances (bin size of 1kb) and calculated the average and standard deviation of the number of interactions found per fragment for negative control regions (discarding fragments with zero interactions from the calculations). These background probabilities of interactions were then used to assess whether each promoter-anchored interaction was significant in each biological replicate independently, using a Z-test. We adjusted the P-values, to account for the multiple tests performed, using the Benjamini-Hochberg procedure and we required a significant interaction to have adjusted P-values below 0.2 in both biological replicates, resulting in an effective adjusted P-value threshold of 0.04 since interactions were required to be present in both biological replicates. Additionally, we required at least 4 supporting read pairs in each biological replicate. Promoter-promoter interactions were called similarly, but requiring that both ends of the paired reads aligned within the annotated promoter regions.
Using significant promoter-enhancer interactions (read threshold 3) we generated a GFF files (for biological replicates separately and for replicated interactions between them) for visualization in Genome Browser.
Genome_build: mm9
Supplementary_files_format_and_content: GFF

source_name: Embryonic stem cells

growth_protocol: Mouse  embryonic stem cells (line R1) were obtained from Janet Rossant’s lab (Toronto, Canada). Cells were maintained on 0.1% gelatin-coated dishes in Dulbecco modified Eagle medium (DMEM) supplemented with 10% fetal calf serum (FCS), 0.1 mM non- essential amino acids, 0.3 mg/ml L-glutamine, 1 mM pyruvate (Invitrogen), 1000 U/ml murine LIF (Chemicon International ESGRO), and were kept in a 5% CO2 atmosphere at 37 °C. The medium of undifferentiated cells was changed daily.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes, lysed and nuclei were isolated. Isolated nuclei were digested with 4-cutter FastDigest MboI (Thermo Scientific, 1µl/µg DNA) for 4 hours at 37 °C. The ends of digested material were filled with biotinylated dATP, dGTP, dCTP and dTTP using Klenow fragment (Fermentas, 0.1 U per 1 µg DNA).  Klenow was deactivated using 0.01 M EDTA at incubating 75 °C for 15 minutes. Then the material was diluted to 3.5 ng/µl and ligated using T4 DNA Ligase (Promega). The crosslinking was reversed by adding Proteinase K and incubating overnight at 65 °C. The proteins were removed and DNA was purified using phenol-chloroform followed by ethanol precipitation. Biotinylated but unligated ends were removed using T4 DNA polymerase by incubating at 12 °C for 15 minutes. The material was fragmented to 300-600 bases by sonication. The fragment ends were repaired and A-tailed. Then the biotinylated fragments were bound to streptavidin beads and unbound fragments were washed away. Sequencing adapters were then ligated to the fragments bound to beads. The material was amplified 6-9 cycles while bound to beads to obtain sufficient amount for sequence capture. Original biotinylated material was removed, supernatant was hybridized to sequence capture probe set according to manufacturer’s instructions (Roche Nimblegen Inc.). Hybridized material was washed according to manufacturer’s instructions and amplified with PCR for 3-6 cycles. Hybridization of the probes to the Hi-C material was done exactly according to the manufacturer’s instructions (Roche Nimblegen Inc).
Libraries were prepared for sequencing using Illumina TruSeq protocol

tag: cell line


title: CaptureC_replicate2_mESC

description: 3C coupled with sequence capture, biological replicate 2


title: HiCap_replicate1_mESC

description:
HiCap_rep1_promoter-enhancer.gff
Hi-C coupled with sequence capture, biological replicate 1


title: GMP_WT_2


title: GMP_WT_1


title: mESC

description: Mouse embryonic stem cell RNA-seq from R1 cell line

data_processing:
Reads were aligned to mouse genome (mm9 assembly) and a comprehensive collection of splice junctions (Wang, E. T., 2008) using bowtie (version 0.12.7). Expression levels were estimated as reads per kilobase of gene model and million uniquely mapped reads (RPKMs) using Rpkmforgenes (Ramsköld, D., 2009), where only uniquely mappable positions were included in the gene model length.
Mappability was determined using MULTo (Storvall, H., 2013) and gene models were based on RefSeq annotation downloaded from the UCSC genome browser on 31 July 2011
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text

extract_protocol:
Total RNA was extracted using standard Qiagen kits.
RNA library was prepared for sequencing using Illumina mRNA-seq protocol


title: RPED_P4_D32

city: Santa Barbara

first: Monte

middle: J.

last: Radeke

address: Neuroscience Research Institiute

department: Neuroscience Research Institute

institute: University of California, Santa Barbara

data_processing:
Base-calling was carried out using Torrent Suite 4.4 and default parameters
Read alignment was accomplished using a 2-stage pipeline. The ten 5-prime bases from each sequence were trimmed using FASTX Trimmer 0.0.14. Sequences with a remaining length of  50 bases or greater were then aligned to the human genome (hg38 + 45S-RNA and 5S-RNA bait sequences) using TopHat 2.0.12 (Bowtie2 2.2.3) and settings optimized for variable read-length Ion Torrent sequences: read-mismatches = 4, read-gap-length = 4, read-edit-dist = 8, max-multihits =1, b2-i = S,1,1.15, b2-rdg = 5,2. Any unmapped sequences were passed to TMAP 3.4.1 and aligned using 5-prime and 3-prime soft-clipping (g = 0). The resulting TopHat and TMAP alignments were merged into a single alignment file and any sequences mapping to the 45S or 5S RNA bait sequences were deleted.
Gene-level RNA quantification was determined using Partek Genomics Suite 6.6 and the hg38 RefSeq Transcript annotation (10/17/2014). Only reads aligned to exons were considered in the determination of the number of reads per gene. In the case where there were two sequencing runs for the same condition (RPEC_P0_D32) the alignments results were combined prior to quantification. Any fractional read count values were rounded to the nearest integer.
Protein coding RNA gene level results were normalized using the trimmed mean of the M-values (TMM) method of Robinson and Oshlack [Genome Biology 2010, 11:R25] as implemented by “edgeR”. Using the raw integer read counts for protein coding genes (HUGO Gene Nomenclature Database, 4/13/2015) as input, the normalization factor (norm.factor) and  total number of mRNAs reads for each sample (lib.size) were determined.  The final processed normalized data for each gene is expressed as reads per million aligned reads (RPM) where RPM = (raw read count * 1 x 106) /(norm.factor * lib.size) .
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text; Annotations, mRNA  gene-level raw read counts (Reads) and TMM-normalized read counts per million mRNA alignments (RPM) for all protein coding genes

source_name: Fetal RPE-Donor "D"

growth_protocol: RPE cells were isolated from fetal donor eyes (Advanced Biosciences Resources, Alameda, CA USA) according to the methods of Hu and Bok [Mol. Vis. 2001, 7:14-19; Methods Mol. Biol. 2010, 652:55-73]. Beyond the initial isolation, all cell culture was carried out using a base medium described by Maminiskis [Invest. Ophthalmol. Vis. Sci.2006, 47:3612-3624]. For 2-3 days post-plating the medium included 15% heat inactivated fetal calf serum. Thereafter, it was reduced to 5%. To generate a working cell bank, primary fetal RPE stocks were expanded approximately 10-fold and these working stocks were designated Passage 0. For routine serial passage, cells were harvested using trypsin digestion and plated at 4,000 cells/cm2. At approximately 80% confluence (every 3-5 days depending on passage number) the cells were enzymatically harvested and re-seeded at 4,000 cells/cm2. To determine the extent to which inhibition of TGF signaling restores the capacity to acquire a prototypical RPE phenotype in late passage cells, Passage 4 cells were plated at 80,000 cells/cm2 and maintained in medium supplemented with 500 nM A-83-01 for 32 day and compared with differentiated Passage 0 and undifferentiated, untreated Passage 4 cultures. Cultures were carried out on laminin-coated porous supports (mouse laminin, Life Technologies, Grand Island, NY USA; Millicell-HA Culture Inserts, EMD Millipore Inc., Billerica, MA USA) or laminin-coated tissue culture plastic as indicated. All cultures were fed every 2-4 days by complete exchange of the medium.

extract_protocol:
Total RNA was purified using miRNeasy mini-preps (Qiagen Inc., Valencia, CA USA)
PolyA RNA was purified from 1 microgram of total RNA using the Magnetic mRNA Isolation Kit (New England Biolabs, Inc ., Ipswitch MA USA) and mRNA-Seq libraries were constructed using the  Ion Total RNA-Seq Kit v2 (Life Technologies, Inc., Grand Island NY USA).

tag: donor id

tag: plating density

tag: passage number

tag: culture time

value: 32 Days

tag: treatment

tag: substrate

value: TC Plastic


title: RPEA_P4_D32_A83

source_name: Fetal RPE-Donor "A"


title: RPEC_P4_D32

source_name: Fetal RPE-Donor "C"


title: RPEB_P4_D32_A83

source_name: Fetal RPE-Donor "B"


title: RPEC_P0_D32_1

value: Microporous support


title: RPEB_P4_D32


title: RPEA_P0_D32


title: RPEB_P0_D32


title: CaptureC_replicate1_mESC

description: 3C coupled with sequence capture, biological replicate 1


title: WT Input

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: RIP-RNA

data_processing:
Sequencing reads from CLIP-seq and RIP-seq libraries were first trimmed of polyA tails, adapters, and low quality ends using cutadapt with parameters --match-read-wildcards --times 2 -e 0 -O 5 --quality-cutoff' 6 -m 18 -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b TGGAATTCTCGGGTGCCAAGG -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT.
Reads were then mapped against a database of repetitive elements derived from RepBase18.05. Bowtie version 1.0.0 with parameters -S -q -p 16 -e 100 -l 20 was used to align reads against an index generated from Repbase sequences (Langmead et al., 2009).
Reads not mapped to Repbase sequences were aligned to the hg19 human genome (UCSC assembly) using STAR (Dobin et al., 2013) version 2.3.0e with parameters --outSAMunmapped Within –outFilterMultimapNmax 1 –outFilterMultimapScoreRange 1.
RPKMs for each gene annotated in gencode v17 were calculated from RIP-seq data using custom scripts
Genome_build: hg19
Supplementary_files_format_and_content: rpkm files, contains RPKMs for each sample

source_name: FLP-in 293 cells

growth_protocol: Human FLP-In 293 cells were acquired from Invitrogen and grown according to the manufacturer instructions. Open reading frames for expression of UPF1_WT_FLAG, UPF1_DEAA_FLAG, UPF1_KA_FLAG, and FLAG were cloned into the pcDNA5/FRT (Invitrogen) backbone. Cells were transfected and selected with hygromycin. Stable cell lines were generated according to the manufacturer instructions.

extract_protocol:
Two confluent 10cm dishes of cells were lysed in isotonic lysis buffer (per sample).
Extracts were immunoprecipated with M2 FLAG magnetic beads (Sigma).  Anti-FLAG immunoprecipitated RNA was extracted with Trizol (Invitrogen) and made into a library using the Illumina TruSeq stranded total RNA library prep kit with Ribo-Zero Gold

value: HEK 293 FRT

value: Anti-FLAG IP RNA


title: D2d5_1

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

data_processing:
The mouse reference genome (GRCm38/mm10) was downloaded from ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/chromosomes/. Sequencing reads (XSQ format) from C57BL/6J samples were aligned to the C57BL/6J reference genome using the Whole Transcriptome mapping module of the LifeScope 2.5.1 software (http://www.lifetechnologies.com/lifescope). Similarly, sequencing reads from DBA/2J samples were aligned to the enhanced DBA/2J genome that was generated by substituting ~4.5 million DBA/2J SNPs in the reference genome. Filter reference containing polyA, polyC, polyG, polyT, rRNAs, tRNAs, as well as adaptor, barcode, and primer sequences was used to remove non-mRNAs reads prior to the mapping. We used the mouse RefSeq transcript annotation downloaded from UCSC genome browser (www.genome.ucsc.edu) to generate a junction reference library containing a list of exon-exon pairs. Reads were aligned against both the reference genome and the junction library. Reads that could not be mapped were realigned against the H1N1 viral contigs. Reads with minimum mapping quality of 10 were used to generate raw counts to be used for downstream differential and correlation analysis.
DESeq2 statistical package was used to normalize and log transform raw read counts producing ‘normalized expression counts’. The ‘normalized expression counts’ were then used for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts

source_name: lungs

extract_protocol: 20µg of total RNA was enriched for poly A+ RNA using one cycle of the Poly A Purist Kit from Ambion according to manufacturer’s standard protocol. The resulting enriched RNA samples were then analyzed on an Agilent Bioanalyzer to determine   the remaining amount of rRNA in the samples. If the amount was higher than 5%, samples were subjected to another cycle of Poly A enrichment.  100ng of the poly A+ enriched RNA was then used to prepare libraries for sequencing using the AB Library Builder™ Whole Transcriptome Core Kit for 5500 Genetic Analysis Systems on a Library Builder system. Libraries were amplified for 15 cycles before 5500 Wildfire primers were added using five cycles of fusion primer amplification as directed in the 5500 Wildfire manual. Before sequencing, small aliquots of libraries were pooled and sequenced on an Ion Torrent PGM 314 chip after additional amplification with PGM fusion primers. The library pools were quantified by Real-Time PCR and immobilized on flowcells for the SOLiD 5500 Wildfire instrument (Applied Biosystems) and sequenced (50bp reads). The average number of reads per sample was 29.5. One sample had high number of reads (230 million) and the others on average had 23 million reads.

treatment_protocol: Mice were sacrificed and entire lungs were extracted from both mouse strains on days 1, 3 and 5 after infection. For mock-treated animals, mice were sacrificed at days 1 and 3 post treatment. In addition, lungs from C57BL/6J mice were also collected on days 8 and 14. For every treatment and day post infection (p.i.) 4-5 mice were prepared. The lungs were immediately transferred to RNAlater solution (Qiagen), kept at 4°C for one day and subsequently stored at -20°C. RNA was isolated using Qiagen Midi Kit as described previously (Alberts et al., 2010). RNA quality was controlled on a 2100 Bioanalyzer Instrument (Agilent). All RNA samples had a RIN of ≥9.7. Three independent biological replicates were selected for each time point for subsequent RNA sequencing.

value: lungs

tag: infection

value: influenza

tag: time

value: 5 d


title: D2d3_1

tag: tissue

value: 3 d


title: D2d3_3


title: D2d5_3


title: D2d1_2

value: 1 d


title: K498A IP

description: RIP-RNA

tag: antibody


title: D2d1_1


title: D2md3_3

value: mock

value: control


title: D2d1_3


title: RPEC_P0_D32_2


title: RPEC_P4_D32_A83


title: WT IP

description: RIP-RNA


title: D2d5_2


title: D2md1_3


title: D2d3_2


title: D2md1_2


title: D2md1_1


title: DEAA IP

description: RIP-RNA


title: K498A CLIP rep2

description:
Crosslinked Anit-FLAG IP RNA
K498A.bam

data_processing:
Sequencing reads from CLIP-seq and RIP-seq libraries were first trimmed of polyA tails, adapters, and low quality ends using cutadapt with parameters --match-read-wildcards --times 2 -e 0 -O 5 --quality-cutoff' 6 -m 18 -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b TGGAATTCTCGGGTGCCAAGG -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT.
Reads were then mapped against a database of repetitive elements derived from RepBase18.05. Bowtie version 1.0.0 with parameters -S -q -p 16 -e 100 -l 20 was used to align reads against an index generated from Repbase sequences (Langmead et al., 2009).
Reads not mapped to Repbase sequences were aligned to the hg19 human genome (UCSC assembly) using STAR (Dobin et al., 2013) version 2.3.0e with parameters --outSAMunmapped Within –outFilterMultimapNmax 1 –outFilterMultimapScoreRange 1.
Reads that were PCR replicates were removed from each CLIP-seq library using a custom script. Briefly one read was kept at each nucleotide position when more than one read’s 5' end was mapped
Clusters were then assigned using the CLIPper software with parameters --bonferroni --superlocal --threshold- software (Lovci et al., 2013).
Genome_build: hg19
conclusions discussed in the associated manuscript are based on the BAM files

extract_protocol:
Two confluent 10cm dishes of cells were lysed in isotonic lysis buffer (per sample). Extracts were immunoprecipated with M2 FLAG magnetic beads (Sigma)
Samples 1-3: Anti-FLAG immunoprecipitated RNA was fragmented and made into a library according to a custom CLIP-seq library generation protocol. Described in (Yeo et al., 2009)

treatment_protocol: Samples were crosslinked with 4000 mW/cm2 258nm UV light

tag: sample type

value: CLIP-RNA


title: K498A Input

description: RIP-RNA


title: Flag Input

description: RIP-RNA


title: B6d14_1


title: D2md3_1


title: DEAA Input

description: RIP-RNA


title: B6d14_3


title: WT CLIP rep2

description:
Crosslinked Anit-FLAG IP RNA
WT.bam


title: B6d14_2


title: Flag IP

description: RIP-RNA


title: D2md3_2


title: B6d8_2

value: 8 d


title: B6d3_3


title: K498A CLIP rep1

description:
Crosslinked Anit-FLAG IP RNA
K498A.bam


title: B6d8_3


title: B6d1_3


title: B6d3_1


title: DEAA CLIP rep2

description:
Crosslinked Anit-FLAG IP RNA
DEAA.bam


title: WT CLIP rep1

description:
Crosslinked Anit-FLAG IP RNA
WT.bam

extract_protocol:
Two confluent 10cm dishes of cells were lysed in isotonic lysis buffer (per sample). Extracts were immunoprecipated with M2 FLAG magnetic beads (Sigma)
Samples 1-3: Anti-FLAG immunoprecipitated RNA was fragmented and made into a library according to a custom CLIP-seq library generation protocol. Described in (Yeo et. al., 2009)


title: B6d8_1


title: DEAA CLIP rep1

description:
Crosslinked Anit-FLAG IP RNA
DEAA.bam


title: B6d1_2


title: B6d3_2


title: B6d5_1


title: B6d5_2


title: B6d1_1


title: B6md1_2


title: B6md3_2


title: B6md1_1


title: B6md1_3


title: B6d5_3


title: BaAQ_3

city: Corvallis

first: Christopher

middle: Michael

last: Sullivan

state: OR

address: Sinnhuber Aquatic Research Laboratory, 28645 East HWY 34

department: Environmental & Molecular Toxicology

institute: Oregon State University

data_processing:
Illumina Casava 1.8 software was used for basecalling
Sequence reads were trimmed for adapters and filtered to exclude low quality reads. Quality was assessed using FastQC and second read sequences were trimmed to 24 bp to exclude a low quality sequence region.
Reads were mapped to Danio rerio genome Zv9.70 using TopHat 2 with the following parameters: --library-type fr-unstranded --no-mixed -r 200 --mate-std-dev 150 -i 50 -I 10000
Read counts per gene were calculated using htseq-count with the following parameters: -m intersection-nonempty --stranded=no
Count data were normalized and statistically tested for differential gene expression in EdgeR
Genome_build: Zv9.70
Supplementary_files_format_and_content: Tab delimited text file includes Ensembl Gene ID and raw count data for each gene in all samples

organism: Danio rerio

source_name: whole embryos (20)

growth_protocol: Zebrafish embryos were collected from group spawns on three separate days and visually examined for viability before exposure at 6 hours post fertilization

extract_protocol:
Whole embryos were homogenized with a bullet blender and total RNA was extracted with RNAzol. RNA integrity was assessed with an Agilent Bioanalyzer (RIN for all samples >9). Sequencing libraries were constructed from poly-A selected mRNA using ScriptSeq Index primers (Set 1, cat. no. RSBC10948) and ScriptSeq v2 library preparation kit
Sequencing libraries were constructed according to standard ScriptSeq protocols

treatment_protocol: Embryos were batch-exposed in vials (20 embryos in 2 mL) to 10 μM 1,9-benz-10-anthrone, 10 μM benzanthracene-7,12-dione or 1% DMSO control from 6-48 hpf on a rocker at 37°C in the dark. The vial is the sample unit, three independent biological replicate samples were collected for each exposure condition.

value: whole embryo

tag: age

value: 48 hours post fertilization

value: wild-type 5D

tag: vehicle

value: 1% DMSO

tag: exposure


title: BaAQ_1


title: BEZO_3


title: BEZO_2


title: BEZO_1


title: Ste12-myc_3

city: San Francisco

first: Trevor

last: Sorrells

department: Biochemistry and Biophysics

institute: University of California, San Francisco

data_processing:
Quality analysis was performed using FastQC
Files were indexed and aligned to the K. lactis genome using bowtie2
Files were converted to .bam format using samtools
Peak separation distance was determined using the binding.characteristics function in the SPP package in R
Peaks were called using macs2
Genome_build: The K. lactis genome was downloaded from the Yeast Gene Order Browser in August 2014
Supplementary_files_format_and_content: bedGraph files were converted from bam files using the script genomeCoverageBed

organism: Kluyveromyces lactis

source_name: a cell

growth_protocol: Cells were grown overnight for 14 h in YEPD, washed, then resuspended to OD=0.25 in phosphate starvation SD media for 2 hours, then induced with K. lactis alpha factor for 2 hours

extract_protocol:
Cells were lysed with glass bead vortexing, sonicated for 3 15-minute cycles, and immunoprecipitated at 4˚C overnight
Libraries were prepared using the NEBNext ChIP-Seq library prep kit for Illumina (New England Biolabs)

tag: media condition

value: phosphate-starvation

tag: chip antibody

value: human c-myc


title: Control_3

tag: strain

value: Control


title: B6md3_3


title: second round replicate 3

status: Public on Jul 05 2015

city: El Paso

first: Haoquan

last: wu

state: Texas

address: 5001 El Paso Dr

department: Biomedical Scienes

institute: Texas Tech Health Sciences Center El Paso

data_processing:
Fastq quality filter by fastq_illumina_filter
Trimed the sequences missing 3' adaptor
Trimed the sequences missing 5' adaptor
Trimed the sequences that is shorter than 15bp
Trimed the sequences contains "N"
Merged reads
Removed the reads with <5 copies
Reads align to gRNA
Supplementary_files_format_and_content: table containing the raw read counts and sequences for each sample

source_name: 293FT cell

growth_protocol: 293 FT cell was cultured in DMEM with 10% FBS and 1X PS.

extract_protocol:
Genomic DNA was extracted from the surviving cells using DNeasy Blood and Tissue Kit (QIAGEN)
The library construction follows Illumina’s TruSeq method. Briefly, sgRNA sequences were amplified by nested PCR with the first pair of primers, GATAGGCTTGGATTTCTATAAG (forward) and CTGCTGGAATCTCGTGAAG (reverse), followed by amplification with the second pair of primers, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNCTTGGAGAAAAGCCTTGTT (forward) and CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCGCTATTTCTAGCTCTAAAAC (reverse, where XXXXXX indicates index sequences). The indexes for first round screen are: replicate1: CAGATC; replicate2: TGCTCA; replicate3: CAGTAG. For the second round screen, the indexes are: replicate1: GCTGAT; replicate2: CTGAGT; replicate3: TCGACT.

treatment_protocol: 293FT cells were infected with lentivirus expressing a certain sgRNA at MOI 0.05. After 72h culture, the cells were then sorted on a FACSAria II cell sorter, and it was confirmed that >90% of the sorted cells were GFP-positive. Approximately 5x106 cells were recovered, which was expanded to 2x107 cells.   Cells (2x107) harboring the sgRNA library were transfected with the pX261–dU6 plasmid using Lipofectamine 2000 (Life Technologies), according to the manufacturer’s instructions. The transfected cells were infected with the WNV-B956 strain at MOI=2 and incubated for 12 days.

tag: cell line

value: HEK 293FT


title: second round replicate 1


title: first round replicate 1


title: SrtC2

status: Public on Jul 04 2015

city: Portland

first: Qingshuo

last: Zhang

address: 3181 SW Sam Jackson Park Road

department: Department of Pediatrics

institute: Oregon Health & Science University

data_processing:
Standard Illumina Cassava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to the mouse reference genome (version mm9) using Bowtie short read aligner software.
Data analysis was performed using Poisson Seq algorithms.
Data-mining and pathway analysis were carried out with the MetaCore integrated software suite (Thomson Reuters, New York, USA).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized tag counts for each Sample

source_name: cKit+ Sca1+ Lin- cells

extract_protocol:
Trizol followed by RNAeasy kit and mRNA purification with Dynabeads Oligo (dT)25
Libraries were prepared according to Illumina's instructions accompanying TruSeq RNA Sample Prep Kit. (Part#RS-122-2001)

treatment_protocol: One month-old wild-type mice were given either SRT3025 diet or placebo for 3 months. The SRT3025 diet was made by mixing SRT3025 (provided by Sirtris, a GSK company, Cambridge, MA, USA) with common rodent diet at 3.18g/kg diet (Research Diets Inc., New Brunswick, NJ, USA).

value: 4 month

tag: gender

value: female

tag: genotype

value: wild-type

tag: drug treatment

value: palcebo


title: BaAQ_2


title: Ste12-myc_2


title: Control_1


title: Control_2


title: Ste12 untagged control


title: Ste12-myc_1


title: SrtA2


title: FLT3_WT4_DNAse-Seq

status: Public on Jul 03 2015

city: Freiburg

first: Pierre

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

data_processing:
Base-calling (Illumina)
DNAse-seq reads were aligned to the hg18 genome assembly using Bowtie 1.00 to SAM output using --all --best --strata --v 2 -m 1 -S
Fragments were extended using an R pipeline described in Koch, Fenouil, Gut et al. Nat Struct Mol Biol 2011.
Fixed-step 10bp wig files were generated using an R pipeline described in Koch, Fenouil, Gut et al. Nat Struct Mol Biol 2011
Peaks were called using CoCAS (Benoukraf et al. Bioinformatics 2009)
Genome_build: hg18
Supplementary_files_format_and_content: Fragments were extended using an R pipeline described in Koch, Fenouil, Gut et al. Nat Struct Mol Biol 2011. Fixed-step 10bp wig files were generated using an R pipeline described in Koch, Fenouil, Gut et al. Nat Struct Mol Biol 2011. Peaks were called using CoCAS (Benoukraf et al. Bioinformatics 2009)

source_name: FLT3 wild type AML patient sample

growth_protocol: Patient and donor samples were obtained either from blood or bone marrow. Lymphoprep extraction of leukocytes was performed following 30 min no brake centrifugation. Enrichment for CD34 and CD117 were checked via FACS analysis. For CD14 samples, enricment for CD14 was controlled by FACS analysis. Where available, purification was performed using MACS columns following anti-CD34 bead conjugation to samples (anti-CD14 for CD14 samles).

extract_protocol:
Phenol-chloroform
Libraries of DNA fragments from chromatin immunoprecipitation or DNase I treatment were prepared from approximately 10 ng of DNA. Firstly, overhangs were repaired by treatment of sample material with T4 DNA polymerase, T4 PNK and Klenow DNA polymerase (all enzymes obtained from New England Biolabs UK) in a reaction also containing 50 mM Tris-HCl,10 mM MgCl2, 10 mM Dithiothreitol, 0.4 mM dNTPs and 1 mM ATP. Samples were purified after each step using Qiagen MinElute columns (according to the manufacturer’s guidelines). Adenosine bases were added to 3’ ends of fragments using Klenow Fragment (3´- 5´ exo-minus), allowing for subsequent ligation of adapter oligonucleotides (Illumina part #1000521) using Quick T4 DNA ligase. After a further column clean up to remove excess adaptors, fragments were amplified in an 18 cycle PCR reaction using adapter-specific primers (sequences 5’- CAAGCAGAAGACGGCATACGAGCTCTTCCGATC*T and 5’-AATGATACGGCGACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T).  The libraries were purified and adapter dimers removed by running PCR products on 2% agarose gels and excising gel slices corresponding to fragments approximately 200-300 bp in size, which were then extracted using the Qiagen gel extraction kit. Libraries were validated using quantitative PCR for known targets, and quality assessed by running 1 μl each sample on an Agilent Technologies 2100 Bioanalyser. Once prepared, DNA libraries were subject to massively parallel DNA sequencing on an Illumina Genome Analyzer. ETO, RUNX1, C/EBPα, PU.1, LMO2 ChIP and Kasumi-1 DNase I libraries were sequenced employing the Illumina Genome Analyzer GAIIx, by using 36 base pair single end reads.

treatment_protocol: To perform DNaseI accessibility assays with patient and donor samples, the optimal cell number and DNaseI (DPFF DNaseI, Worthington Biochemical Corporation) concentration was titrated for each sample. The DNA digestion extent was comparable in all the generated samples as measured by RT-PCR (5). Briefly, nuclei were isolated from 1-5 x 106 cells by detergent lysis and immediately digested for 3 min at 22 °C with DNaseI at 1-10 U/ml in a 1 mM CaCl2 supplemented buffer. Nuclear proteins were digested with 1 mg/ml Proteinase K overnight at 37 °C

tag: dnasei origin

value: Worthington


title: FLT3_WT2_DNAse-Seq


title: second round replicate 2


title: CD34_PBSC_Runx1_ChIP-Seq

source_name: CD34+ PBSC from donor

growth_protocol: Patient and donor samples were obtained either from blood or bone marrow. Lymphoprep extraction of leukocytes was performed following 30 min no brake centrifugation. Enrichment for CD34 and CD117 were checked via FACS analysis. For CD14 samples, enrichment for CD14 was controlled by FACS analysis. Where available, purification was performed using MACS columns following anti-CD34 bead conjugation to samples (anti-CD14 for CD14 samples).

treatment_protocol: Cells were resuspended in 10 ml of growing medium, and cross-linked with 1% formaldehyde (Pierce) for 10 min at RT. The cross-linking reaction was stopped by adding glycine to a final concentration of 0.4 M, followed by two washes with ice–cold PBS. Cells were resuspended in 10 ml of ice-cold ChIP buffer A (10 mM HEPES pH 8.0, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100, proteinase inhibitor cocktail (Roche UK, Burgess Hill, UK) and 0.1 mM PMSF), incubated for 10 min at 4°C with rotation, and centrifuged 5 min at 500 x g at 4 °C. The pellet was resuspended in 10 ml of ice–cold ChIP buffer B (10 mM HEPES pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.01% Triton X-100, protease inhibitor cocktail and 0.1 mM PMSF), incubated for 10 min at 4 °C with rotation and centrifuged for 5 min at 500 x g at 4 °C. Cells were resuspended in 600 μl of ice-cold ChIP lysis buffer (25 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.25% SDS, protease inhibitor cocktail and 0.1 mM PMSF), incubated 10 min on ice and sonicated at 5 °C using a Bioruptor™ (Diagenode, Liege, Belgium) to generate fragments an average length of 400-500 bp (10 min with 30 s “ON” and “OFF” cycles, power setting high). The lysates were centrifuged for 5 min at 16,000 x g at 4 °C and the supernatants were diluted with two volumes of ice-cold ChIP dilution buffer (25 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 7.5% glycerol, protease inhibitor cocktail and 0.1 mM PMSF). For each IP, 15 μl of Dynabeads® protein G were pre–incubated with 50 μg BSA and 2 μg antibody against RUNX1 (Abcam, ab23980) for 2 h at 4 °C with rotation. The blocked antibody-bound protein G mix was added to 20–25 μg chromatin in a total volume of 500 μl diluted ChIP lysis buffer and incubated for 2 h at 4°C with rotation. After magnetic separation the beads were washed once with 1 ml wash buffer 1 (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), twice with 1 ml wash buffer 2 (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with 1 ml LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxycholate) and twice with 1 ml TE/NaCl buffer (10 mM Tris-HCl pH 8.0, 50 mM NaCl, 1 mM EDTA). For each wash the beads were mixed with ice-cold washing buffers for 10 min at 4 °C. The immunoprecipitated DNA was eluted two times with 50 μl ChIP elution buffer (100 mM NaHCO3, 1% SDS) for 15 min at RT with shaking. At this step the input control (1% of the starting material) was included in the experimental procedure after first adjusting the final volume to 100 μl with ChIP elution buffer. The eluted DNA was incubated overnight at 65 °C in the presence of 50 μg proteinase K. The DNA was finally purified using Agencourt AMPure (Beckman Coulter) magnetic beads according to the manufacturer’s instructions, eluted with 50 μl x TE.

tag: cell type

value: PBSC

tag: antibody manufacturer and catalog number

value: Abcam; ab23980


title: CD14_PBSC_DNAse-Seq

source_name: CD14+ PBSC from donor


title: B6md3_1

value: lungs

tag: infection

value: mock

tag: time

value: control


title: first round replicate 3


title: H3K27me3_ChIP_rep2

first: Laura

middle: L

last: Baxter

address: 35A Convent Drive

department: NHGRI

description:
immortalized melanocyte cell line
input sample = GSM1713771

data_processing:
ChIP-Seq peaks for each experimental replicate were called independently using the Model-based Analysis for ChIP-Seq (MACS v1.4.2) algorithm by applying default settings and a significance p-value threshold of 1.00e-05, except for H3K27me3 where the broad peak parameters were applied as follows: macs14 -t chip.bam -c input.bam -name = chip_output -format = BAM -gsize = mm -tsize = 50 -bw = 300 -mfold = 10,30 -nolambda -nomodel -shiftsize = 150 --pvalue=1.00e-05.
Only ChIP-Seq profiles that showed reproducible overlap between both experimental samples were used for downstream analyses.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS and scores represent tag pileup over each position; text files contain MACS output with called peak coordinates and scores.

source_name: melan-Ink4a-Arf-1 (melan-a)

growth_protocol: According to guidelines from Bennett et al. 1987 (PMID 3102392), cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum (Gibco), 200 nM 12-O-tetradecanoylphorbol 13-acetate (Sigma-Aldrich, St Louis, MO, USA) and 200 pM cholera toxin (Sigma- Aldrich, St Louis, MO, USA) at 37°C in humidified air with 10% CO2.

extract_protocol:
Approximately 2 x 10^7 cells were harvested and crosslinked at room temperature with 1% formaldehyde for 10 minutes. Crosslinking reaction was quenched with the addition of glycine to a final concentration of 125 mM for at least 15 minutes. Crosslinked cells were lysed on ice using 1 ml low-salt ChIP buffer (150 mM NaCl, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.5% NP-40, 1.0%Triton X-100) and sonicated using a Qsonica Sonicator Q500 (Newtown, CT 0647) with the following settings: 90% amplitude; 30 seconds on/30 seconds off cycles; total sonication time of 35 minutes. Sonicated samples were centrifuged and the soluble chromatin (supernatant) was used for chromatin immunoprecipiation reactions. Briefly, 200 µl of lysate (~ 2 x 106 cells) was incubated with each  antibody and immunoprecipitated chromatin was recovered using recombinant protein G beads or magnetic Dynabeads® (Invitrogen). ChIP samples were reverse crosslinked and DNA was purified using the phenol-chloroform extraction method.
Aliquots of input (total genome) and ChIP DNA obtained from two independent experiments per antibody were used for ChIP library construction and high-throughput sequencing, per Illumina protocols.

tag: source

value: Normal embryonic skin

tag: genotype/variation

value: Cdkn2a tm1RDp/tm1RDp mice

tag: developmental stage

value: embryo

tag: tissue

value: skin

value: melanocyte

value: H3K27me3 (ab6002; Abcam)


title: FLT3_ITD3_DNAse-Seq

source_name: FLT3-ITD AML patient sample


title: FLT3_ITD4_DNAse-Seq


title: H3K27me3_ChIP_rep1


title: SrtC3

tag: age


title: SL_15_4002

city: Albuquerque

first: Raymond

middle: J

last: Langley

state: New Mexico

address: 2425 Ridgecrest Dr

department: immunology

institute: LRRI

description: Low Dose Challenge

data_processing:
Illumina Casava software used for basecalling.
Bowtie (v.0.12.8) was used to build index files from the macaque genome (Ensembl release 69)
The macaque gene transfer format (GTF) file used for alignments was downloaded from Ensembl (ftp://ftp.ensembl.org/pub/release-69/gtf/macaca_mulatta)
Alignments were performed with TopHat (v.2.0.6)
The binary alignment map (BAM) files from TopHat served as input files for the coverageBed command in the BEDTools program (v.2.17.0). A gene-level browser extensible data (BED) file, which defined the start and stop positions of all annotated macaque genes, was downloaded using the Ensembl BioMart tool (http://www.ensembl.org/biomart/martview/).
The coverageBed function assigned reads in the BAM file to genes as defined by the BED file, resulting in an output of counts data representing the number of RNA sequencing reads per gene.
Genome_build: Ensembl release 69
Supplementary_files_format_and_content: Text file with the raw counts data normalized as reads/million total reads

organism: Macaca fascicularis

source_name: Whole lung RNA, Low Dose Challenge

extract_protocol:
Trizol
Truseq RNA with Ribozero rRNA depletion

value: lung


title: Setdb1_Δ/Δ_RNA-seq

city: Saint Louis

first: Patrick

last: Collins

state: MO

address: 1217 Oakleaf dr

department: Pathology and Immunology

institute: Washington University

data_processing:
RNA-Seq data were aligned to the transcriptome and reference genome (mm10) using TopHat 2.0.9
RPKM values of ERV families was obtained using RSeQC
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using bedTools; Scores represent total reads

source_name: bone marrow

growth_protocol: Murine bone marrow-derived pro-B cells were isolated and purified by FACS. Cells were then clutured for four days in media containing 5 ng/µl of IL-7 (Invitrogen, PMC0075).

extract_protocol:
RNA was extracted and purified from day four cultures using QIAGEN Rneasy kits, followed by ribodepletion (Ribo-Zero, Epicentre).
Libraries were prepared using TruSeq RNA Sample kits with indexed adaptors (Illumina). Libraries pooled from two samples were subjected to 101 bp paired-end sequencing using an Illumina HiSeq2000 (San Diego CA, USA)

value: IL-7 Cultured pro-B cell

value: Δ/Δ


title: SrtC1

value: 4 month

value: female

value: wild-type


title: SrtA3


title: H3K27ac_ChIP_rep1

institute: NIH

value: H3K27ac (ab4729; Abcam)


title: first round replicate 2

value: HEK 293FT


title: SrtA1


title: ITD4_Runx1_ChIP-Seq

value: AML

tag: antibody

value: Abcam; ab23980


title: FLT3_WT5_DNAse-Seq

value: Worthington


title: SL_14_4001

description: Low Dose Challenge


title: SL_13_3002

description: Low Dose Challenge


title: SL_12_3001

description: Low Dose Challenge


title: SL_11_2002

description: Low Dose Challenge


title: FLT3_WT3_DNAse-Seq


title: SD_18_67431

description: Sepsi-induced Death

source_name: Whole lung RNA, Sepsis-induced Death


title: SD_17_2704

description: Sepsi-induced Death


title: H3K27ac_ChIP_rep2

value: Normal embryonic skin

tag: chip antibody


title: Laublab_BglII_HiC_NA1000_IsceI_site_33kb_from_oriC_IsceI_enzyme_induced

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

institute: John Innes Centre

data_processing:
library strategy: chromosome conformation capture coupled with deep sequencing (Hi-C)
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
We mapped reads in each FASTQ file back to the genome of Caulobacter CB15N (NA1000) independently by Bowtie version 2. All the processing steps afterwards were performed using public-availabe scripts as reported previously in Le et al., 2013 (PMID: 24158908) and in Imakaev et al., 2012 (PMID: 22941365)
Genome_build: NC_011916.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices.

organism: Caulobacter vibrioides NA1000

source_name: C. crecentus_vanillate

growth_protocol: Caulobacter crescentus were grown as described previously in Skerker et al., 2005 (PMID: 16176121). When appropriate, media were supplemented with antibiotics at the following concentrations (liquid/solid media) [ug/ml]): chloramphenicol (1/2), kanamycin (5/25), oxytetracycline (1/2), spectinomycin (25/100). Synchronizations were performed on mid-exponential phase cells using Percoll (GE Healthcare) and density gradient centrifugation as described previously in Jones et al., 2001 (PMID: 11283290).

extract_protocol:
Hi-C experiments were performed using BglII restriction enzyme according to previous publications (Le et al., 2013 PMID: 24158908)
Standard library construction for Illumina Hiseq2000 sequencing platform

treatment_protocol: Caulobacter cells were depleted of DnaA for 1.5 h before synchronization. Swarmer cells were then released into DnaA depleting conditions (without IPTG) and double-strand breaks were induced for 1 h by the addition of 500 μM vanillate.

value: G1-arrested cells

value: IsceI site 33kb from oriC  and Isce-encoding gene at van locus

tag: restriction enzyme

value: BglII


title: FLT3_ITD2_lane3_DNAse-Seq

description: H17606_sorted_from_ordered_tag_gff_bin1_bin10.wig


title: MV4/11_siMM_cFos_ChIP-Seq

source_name: FLT3-ITD AML cell line

growth_protocol: Patient and donor samples were obtained either from blood or bone marrow.  Lymphoprep extraction of leukocytes was performed following 30 min no brake centrifugation. Enrichment for CD34 and CD117 were checked via FACS analysis. For CD14 samples, enricment for CD14 was controlled by FACS analysis. Where available, purification was performed using MACS columns following anti-CD34 bead conjugation to samples (anti-CD14 for CD14 samles).

extract_protocol:
Phenol-chloroform
Libraries of DNA fragments from chromatin immunoprecipitation or DNase I treatment were prepared from approximately 10 ng of DNA. Firstly, overhangs were repaired by treatment of sample material with T4 DNA polymerase, T4 PNK and Klenow DNA polymerase (all enzymes obtained from New England Biolabs UK) in a reaction also containing 50 mM Tris-HCl,10 mM MgCl2, 10 mM Dithiothreitol, 0.4 mM dNTPs and 1 mM ATP. Samples were purified after each step using Qiagen MinElute columns (according to the manufacturer’s guidelines). Adenosine bases were added to 3’ ends of fragments using Klenow Fragment (3´- 5´ exo-minus), allowing for subsequent ligation of adapter oligonucleotides (Illumina part #1000521) using Quick T4 DNA ligase. After a further column clean up to remove excess adaptors, fragments were amplified in an 18 cycle PCR reaction using adapter-specific primers (sequences 5’- CAAGCAGAAGACGGCATACGAGCTCTTCCGATC*T and 5’-AATGATACGGCGACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T).  The libraries were purified and adapter dimers removed by running PCR products on 2% agarose gels and excising gel slices corresponding to fragments approximately 200-300 bp in size, which were then extracted using the Qiagen gel extraction kit. Libraries were validated using quantitative PCR for known targets, and quality assessed by running 1 μl each sample on an Agilent Technologies 2100 Bioanalyser. Once prepared, DNA libraries were subject to massively parallel DNA sequencing on an Illumina Genome Analyzer.

value: anti-cFos

value: Santa Cruz Biotechnology; sc-253

tag: cell line


title: SH_16_F6645

description: High Dose Challenge

source_name: Whole lung RNA, High Dose Challenge

value: lung


title: MV4/11_STAT5_ChIP-Seq

value: Santa Cruz Biotechnology; sc-835


title: SL_9_1002

description: Low Dose Challenge


title: FLT3_ITD1_lane2_DNAse-Seq

description: SN513_R302_MERGED_J15668_sorted_from_ordered_tag_gff_bin1_bin10.wig


title: H3K27_ChIP_input

description:
This input sample was used in the analysis of all H3K27 ChIP samples in this study: GSM1713769, GSM1713770, GSM1713772, GSM1713773
immortalized melanocyte cell line

value: Cdkn2a tm1RDp/tm1RDp mice

value: embryo

value: skin

value: melanocyte


title: FLT3_ITD1_lane3_DNAse-Seq


title: FLT3_WT1_DNAse-Seq


title: MV4/11_siFLT3_cFos_ChIP-Seq


title: CON_7_EOEO2

description: Baseline Control

source_name: Whole lung RNA, Baseline Control


title: SL_8_1001

description: Low Dose Challenge


title: CD34_PBSC_DNAse-Seq


title: Setdb1_C/C_RNA-seq

value: IL-7 Cultured pro-B cell

value: C/C


title: SL_10_2001

description: Low Dose Challenge


title: FLT3_ITD1_lane1_DNAse-Seq


title: FLT3_ITD2_lane1_DNAse-Seq


title: FLT3_ITD5_lane1_DNAse-Seq

description: r63_b_190_ATCACG_L003_L004_R1_001_treat_afterfiting_all_fixed.wig


title: FLT3_ITD5_lane2_DNAse-Seq


title: CON_6_F6F5C

description: Baseline Control


title: SD_5_1045C

description: Sepsi-induced Death


title: SH_4_B4470

description: High Dose Challenge


title: SD_3_B7800

description: Sepsis-induced Death


title: SH_1_10737

description: High Dose Challenge


title: SH_2_3075F

description: High Dose Challenge


title: FLT3_WT8_DNAse-Seq


title: Multiple 8-oxoG challenge - 120 min

city: Galveston

first: Istvan

last: Boldogh

address: 301 UNIVERSITY BLVD.

department: Microbiology & Immunology

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

description: Sample 8

data_processing:
Base call conversion to sequence reads was done with Casava-1.8.2 software (Illumina).
Sequence data were analyzed with the Bowtie 2
Splice junction mapping was performed with TopHat
Assembly and estimation of abundance was perforemed with GFOLD
Genome_build: mm10
Supplementary_files_format_and_content: Sample*RPKM.txt tab-delimited text file includes RPKM values for the Sample.

source_name: Lung

extract_protocol:
Total RNA was extracted with RNeasy Mini Kit (Qiagen) followed by DNase I treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Balb/cJ

value: Lung

tag: gender

value: female

value: wild type

tag: treatment

value: multiple 8-oxoG challenge

value: 120 min

tag: type of sample

value: Test


title: SOX10_ChIP_input

city: Bethesda

description: immortalized melanocyte cell line

value: Normal embryonic skin

tag: cell type


title: SOX10_ChIP_rep2

description: immortalized melanocyte cell line

value: SOX10 (sc-17342X; Santa Cruz Biotechnology)