title: A4

city: Nanjing

first: Lingfei

last: Shangguan

state: Jiangsu

address: 1 Weigang Rd

department: Horticultural Department

institute: Nanjing Agri. University

description: processed data file: A4_A2.xls, A4_A3.xls

data_processing:
Fastx-toolkit for data clean
The DGE-pro (http://www.genomics.jhu.edu/software/EDGE/index.shtml) programs provides RPKM values within a 95% confidence interval. Differential expression was analyzed and calculated according to the count values of each transcript in the two libraries using edgeR (the Empirical analysis of Digital Gene Expression in R) software.
“FDR < 0.001” and“|log2 fold-change (log2FC)| ≥1” were used as the thresholds for judging significant difference in transcript expression. Transcripts with |log2FC| <1 were supposed have no change in expression levels.
Genome_build: Plant ensembl, vitis vinifera, IGGP_12x (http://plants.ensembl.org/Vitis_vinifera/Info/Index)
Supplementary_files_format_and_content: xls, gene expression analysis

organism: Vitis vinifera

source_name: Grapevine fruit at 90 DAF

growth_protocol: Berries from Cv. Summer Black (hybrid of V. vinifera and V. labrusca) were sampled at the fruit expanding (40 days after flowering), véraison (65 days after flowering), and ripe (90 days after flowering), stages throughout the growing season.

extract_protocol:
Total RNA was extracted from selected berry samples with three replicates of each growth stage were extracted by using Trizol reagent (Invitrogen, Carlsbad, CA, USA)
library construction with the Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) as directed in manufacturer’s protocol.

treatment_protocol: Additionally, in order to investigate a demonstrative biological selection of transcripts at specific growth stage, RNA for Illumina sequencing was filtered from tissues comprised of three biological replicated for each growth stage.

value: Grapevine fruit

value: at 90 DAF


title: input_for_BRG1_ChIP-seq_TA1del_Rep1

status: Public on Jan 27 2016

type: SRA

city: Research Triangle Park

first: Paul

middle: A

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

country: USA

institute: NIEHS

library_source: genomic

data_processing:
Reads were filtered based on a mean base quality score >20. Reads were mapped to hg19 genome using Bowtie 0.12.8
For ATAC-seq data processing, we performed Trim Galore! to remove adapter sequence contamination. The offset parameters suggested by Buenrostro et al were applied to each mapped read.
Peak calling was performed with HOMER v4.1 at default parameters.  Peaks were then adjusted to 200-mers centered on the midpoint of the HOMER calls.
Duplicate reads were removed using MarkDuplicates.jar from picard-tools-1.107 package.
All paired-end reads were converted to a single fragment.  After normalization within each data set, bigWig files were generated to visualize the genomic coverage.
For RNA-seq data processing, read counts per gene per sample were collected by HTSeq-Count.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, bed

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Cells were grown on 15 cm plats in high glucose DMEM medium with 10% FBS

extract_protocol: Libraries were prepared according to Illumina or BIOO SCIENTIFIC instruction. ATAC-seq libraries were prepared by following the original protocol (Buenrostro et al., 2013) with several modifications (as described above)

treatment_protocol:
ChIP-Seq: Cells were lysed with Tris-HCl pH 8.0 based buffer with appropriate concentration of SDS. Chromatin fragmentation was performed by sonication with Bioruptor or Covaris. DNA was precipitated with antibody against each target protein.
MNase-seq: Cells were treated with a hypotonic buffer. Isolated nuclei were digested with MNase. DNA Mononucleosomal DNA was extracted by using a ZYMO RESEARCH cleanup column and QIAGEN Gel extraction kit.
ATAC-seq: Cells were treated with CSK buffer (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.1% Triton X-100), and then chromatin tagmentation was performed by Tn5 transposase (5 µl in 25 µl total reaction, Nextera DNA Library Preparation Kit from Illumina).

tag: genotype/variation

value: Ty1-TA1del expressed

tag: passages

tag: antibody


title: A3

country: China

description: processed data file: A3_A2.xls, A4_A3.xls

library_source: transcriptomic

molecule: total RNA

source_name: Grapevine fruit at 65 DAF

tag: tissue

tag: age

value: at 65 DAF


title: HCC gDNA Input

city: Worcester

first: Brian

middle: C

last: Lewis

state: Massachusetts

address: 364 Plantation Street; LRB 521

department: PGFE

institute: University of Massachusetts Medical School

description:
library DNA with no IP
fastq file 1 = rep1
fastq file 2 = rep1_2
fastq file 3 = rep2

data_processing:
Sequence reads obtained and mapped to mm9 genome using Illumina Genome Analyzer Pipeline
Reads uniquely mapped with 2 or fewer mismatches were retained for peak detection
Peak detection was performed with MACS 1.3.6 algorithm (http://liulab.dfci.harvard.edu/MACS/)
Default MACS settings EXCEPT: --shiftsize=80 --oldfdr  --gsize=2500000000 --tsize=76 --bw=150 --mfold=10
KLF6 IP peaks were determined using Input dataset as control
Genome_build: mm9
Supplementary_files_format_and_content: Peak sites, annotated; Files are located at series level

organism: Mus musculus

source_name: HCC cell line

growth_protocol: HCC cells are grown in DMEM medium with 10%FBS

extract_protocol:
Cells were crosslinked and chromatin immunoprecipitation was performed with a V5 antibody; the control is the isolated DNA without the IP performed
libarary constructed following Illumina Sample Prep guide.

treatment_protocol: HCC cells were transfected with a plasmid containing full length KLF6 in frame with a V5 tag

tag: cell type

value: hepatocellular carcinoma


title: KLF6 ChIP DNA

description:
library DNA from V5-KLF6 IP
fastq file 1 = rep1
fastq file 2 = rep1_2
fastq file 3 = rep2


title: CHIPSEQ_mCN_SMCX_KO_H3K4me1_rep2

city: Ann Arbor

first: Saurabh

last: Agarwal

state: Michigan

address: 1241 E. Catherine St. 5815 Medical Science II

department: Human Genetics

institute: University of Michigan

description: ChIP-DNA

data_processing:
Following sequencing cluster imaging, base calling were conducted using the Illumina pipeline.
ChIP-Seq and Input reads were mapped to mm9 using bowtie v 0.12.8
Genome_build: mm9

source_name: E16.5 mouse embryonic cortex

growth_protocol: Cortices from E16.5 male mouse embryos were collected in HHGN dissection solution (Hanks' Balanced Salt Solution supplemented with 2.5 mM Hepes, 35 mM Glucose, 4 mM sodium bicarbonate). Cortices were incubated with 0.1% trypsin (Life Technologies) in HHGN for 20 min. at room temperature, quenched in Neurobasal media (Life Technologies) containing 10% fetal bovine serum (FBS), and triturated in Neurobasal media containing 0.01 mg/ml DNaseI.  Dissociated cells were suspended in Neurobasal media supplemented with 1x B27 solution (Life Technologies), 1x penicillin-streptomycin , 0.5 mM L-glutamine, and 25 mM 2-mercaptoethanol. Cells from one cortex were plated in a 10-cm tissue culture dish treated with 50 mg/ml Poly-D-lysine hydrobromide (Sigma, MW 30,000-70,000). Cultured are maintained in humidified incubators with 5% CO2 at 37°C. Half of culture media was replaced with new culture media every 3 days in vitro (DIV), and cells were harvested on 9 or 10 DIV.

extract_protocol:
Chromatin was immunoprecipitated (overnight, 4°C) with beads and antibody (H3K4me3 Millipore CMA304; H3K4me1 Diagenode pAb-037-050). After immunoprecipitation, beads were washed as described previously. Immune complexes were eluted from beads (65°C, 5 min; and room temperature, 15 min) with 50 mM Tris-HCl pH 8.0, 1 mM EDTA and 1% SDS. Elution was repeated and eluates pooled. Reverse cross-linking was carried out (16h, 65°C) with addition of NaCl and RNase A. EDTA was increased to 5 mM and samples were incubated with 200 μg/ml proteinase K (2h, 50°C). DNA was recovered by phenol-chloroform extraction and ethanol precipitation, and quantifed by Qubit (Life Technologies).
ChIP-Seq libraries were prepared through standard Illumina's procedure for library-preparation using NEBNext library reagents.
ChIP-seq libraries were prepared from 10 ng DNA using NEBNext DNA library preparation reagents (E6000) and the protocol and reagent concentrations described in the Illumina Multiplex ChIP-seq DNA sample Prep Kit. Libraries were indexed using a single indexed PCR primer. After PCR amplification, 300-600 bp DNA fragments were selected on an agarose gel. Libraries were quantified by Qubit (Invitrogen), and library size was assessed by Bioanalyzer (Agilent). Libraries were sequenced using a HiSeq 2000 (Illumina) to generate 50 base single-end reads. ChIP-seq libraries were generated from two biological repeats per antibody, and matched Input samples.

treatment_protocol: Chromatin preparation was performed as described in8 with some modifications. Cortical neurons were fixed in 1% formaldehyde (10 min for histone modifications, 20 mins for Kdm5c, RT). Fixation was stopped by addition of Glycine to 0.125M (5 min, RT). Cells were washed in cold PBS, before “swelling” buffer (25 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCl and 0.1% NP-40) was added to lyse the cells (10 min, 4°C). After resuspension in “sonication” buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and 0.1% SDS), nuclei were sonicated using a Misonix 3000 (Amplitude 60; 25 cycles; 15s ‘on’, 45s ‘off’; 4°C). The resulting material was centrifuged twice (10 min, 4°C) at 14,000 rpm. Swelling and sonication buffers were supplemented with 5 mM NaF, 1 mM PMSF, and protease inhibitor cocktail (Roche). Magnetic beads (Protein G dynabeads, Invitrogen) were washed with sonication buffer before use.

tag: genotype

value: SMCX KO male

tag: culture

value: 10 Days in vitro

value: embryonic cortex

tag: gender

value: male

tag: developmental stage


title: A2

description: processed data file: A3_A2.xls, A4_A2.xls

source_name: Grapevine fruit at 40 DAF

value: at 40 DAF


title: CHIPSEQ_mCN_SMCX_KO_H3K4me1_rep1

description: ChIP-DNA


title: input_for_BRG1_ChIP-seq_GATA3_Rep1

value: Ty1-GATA3 expressed


title: input_for_BRG1_ChIP-seq_GATA3_Rep2


title: input_for_BRG1_ChIP-seq_control_Rep2

value: Control cells (vector control)


title: input_for_BRG1_ChIP-seq_GATA3_Rep3


title: input_for_BRG1_ChIP-seq_control_Rep3


title: BRG1_ChIP-seq_TA1del_Rep1


title: BRG1_ChIP-seq_TA1del_Rep3


title: BRG1_ChIP-seq_GATA3_Rep3


title: BRG1_ChIP-seq_TA1del_Rep2


title: input_for_BRG1_ChIP-seq_control_Rep1


title: BRG1_ChIP-seq_control_Rep1

description: BRG1.ChIP-seq.Controlcells.merged.bigWig


title: BRG1_ChIP-seq_control_Rep3


title: Input_for_Ty1_ChIP-seq_GATA3_Rep1


title: Input_for_Ty1_ChIP-seq_TA1del_Rep1


title: Ty1_ChIP-seq_TA1del_Rep2

description:
Ty1.ChIP-seq.TA1delcells.merged.bigWig
TA1del.homer.peak.bed

value: anti-Ty1 (Menafra et al., 2014)


title: BRG1_ChIP-seq_GATA3_Rep2


title: Ty1_ChIP-seq_GATA3_Rep2


title: Ty1_ChIP-seq_TA1del_Rep1


title: Input_for_Ty1_ChIP-seq_TA1del_Rep2


title: Input_for_Ty1_ChIP-seq_GATA3_Rep2


title: MNase-seq_TA1del_Rep3


title: Ty1_ChIP-seq_GATA3_Rep1


title: MNase-seq_TA1del_Rep1


title: MNase-seq_GATA3_Rep2


title: BRG1_ChIP-seq_GATA3_Rep1


title: MNase-seq_control_Rep3


title: Input_for_H3K4me1_and_H3K27ac_ChIP-seq_TA1del_Rep2


title: MNase-seq_control_Rep1


title: BRG1_ChIP-seq_control_Rep2


title: Input_for_H3K4me1_and_H3K27ac_ChIP-seq_GATA3_Rep2


title: Input_for_H3K4me1_and_H3K27ac_ChIP-seq_control_Rep1


title: Input_for_H3K4me1_and_H3K27ac_ChIP-seq_control_Rep2


title: MNase-seq_GATA3_Rep1


title: H3K27ac_ChIP-seq_TA1del_Rep2

description: H3K27ac.ChIP-seq.TA1delcells.merged.bigWig

value: anti-H3K27ac (ab4729)


title: Input_for_H3K4me1_and_H3K27ac_ChIP-seq_GATA3_Rep1


title: H3K27ac_ChIP-seq_GATA3_Rep2

description: H3K27ac.ChIP-seq.GATA3cells.merged.bigWig


title: H3K4me1_ChIP-seq_TA1del_Rep1

description: H3K4me1.ChIP-seq.TA1delcells.merged.bigWig

value: anti-H3K4me1 (ab8895)


title: H3K4me1_ChIP-seq_control_Rep1

description: H3K4me1.ChIP-seq.Controlcells.merged.bigWig


title: H3K4me1_ChIP-seq_TA1del_Rep2


title: H3K27ac_ChIP-seq_control_Rep2

description: H3K27ac.ChIP-seq.Controlcells.merged.bigWig


title: H3K27ac_ChIP-seq_control_Rep1


title: MNase-seq_TA1del_Rep2


title: H3K4me1_ChIP-seq_GATA3_Rep2

description: H3K4me1.ChIP-seq.GATA3cells.merged.bigWig


title: H3K4me1_ChIP-seq_control_Rep2


title: H3K27ac_ChIP-seq_GATA3_Rep1


title: ATAC-seq_TA1del_Rep3

data_processing:
Library strategy: ATAC-Seq
Reads were filtered based on a mean base quality score >20. Reads were mapped to hg19 genome using Bowtie 0.12.8
For ATAC-seq data processing, we performed Trim Galore! to remove adapter sequence contamination. The offset parameters suggested by Buenrostro et al were applied to each mapped read.
Peak calling was performed with HOMER v4.1 at default parameters.  Peaks were then adjusted to 200-mers centered on the midpoint of the HOMER calls.
Duplicate reads were removed using MarkDuplicates.jar from picard-tools-1.107 package.
All paired-end reads were converted to a single fragment.  After normalization within each data set, bigWig files were generated to visualize the genomic coverage.
For RNA-seq data processing, read counts per gene per sample were collected by HTSeq-Count.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, bed

value: Ty1-GATA3(126-444) truncation mutant (TA1del) expressed


title: ATAC-seq_TA1del_Rep2


title: MNase-seq_GATA3_Rep3


title: MNase-seq_control_Rep2


title: Input_for_H3K4me1_and_H3K27ac_ChIP-seq_TA1del_Rep1


title: ATAC-seq_GATA3_Rep3

value: GATA3 expressed


title: ATAC-seq_GATA3_Rep2


title: ATAC-seq_control_Rep3

description: ATAC-seq.Controlcells.merged.bigWig

value: Control cells (GFP expressed)


title: H3K27ac_ChIP-seq_TA1del_Rep1


title: ATAC-seq_GATA3_Rep1


title: ATAC-seq_control_Rep1

description: ATAC-seq.Controlcells.merged.bigWig


title: ATAC-seq_control_Rep2

description: ATAC-seq.Controlcells.merged.bigWig


title: Input_for_GATA3_ChIP-seq_PE_37C_Rep2


title: H3K4me1_ChIP-seq_GATA3_Rep1


title: Input_MVEH8

city: Innsbruck

first: Jose Miguel

last: Ramos Pittol

address: Innrain 80-82

department: Institute of Biochemistry

country: Austria

institute: University of Innsbruck

data_processing:
Sequencing reads were mapped against the reference genome (mm9 assembly, NCBI37) using BWA package ( mem –t 7 –c 100 –M –R ).
Peaks were called using MACS 1.4 package (p 4, nomodel, nolambda, shiftsize=150) with each respective input as background
Wig files were constructed with custom perl script counts on extended reads on 50bp intervals
Genome_build: mm9
Supplementary_files_format_and_content: .wig.gz WIG files, scores represent read counts over 50bp intervals
Supplementary_files_format_and_content: .bed.gz Peak and Summit Intervals

source_name: Liver tissue

extract_protocol:
Lysates were clarified from sonicated nuclei foxated with Formaldehyde/DSG, and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to the instructions accompanyindg the SOLiD ChIP-seq kit for library preparation. Libraries were sequenced on the SOLiD 5500 WG following the manufacturer's protocols.

treatment_protocol: Male mice were treated daily by oral gavage for 7 days with OCA/INT-747 (10mg/kg/day) or vehicle (1% methyl cellulose).

tag: chip antibody

tag: treatment

value: vehicle (1% methyl cellulose)

tag: strain


title: FXRChIP_MVEH9

value: FXR (SantaCruz, sc-13063)


title: Input_MVEH9


title: Input_for_GATA3_ChIP-seq_PE_37C_Rep1


title: Input_MINT4

value: OCA (10mg/kg/day)


title: Input_for_GATA3_ChIP-seq_PE_Rep2


title: FXRChIP_MINT5


title: Input_for_GATA3_ChIP-seq_PE_Rep1


title: ATAC-seq_TA1del_Rep1


title: BG879 rep. 2

city: New York

first: David

middle: H

last: Bechhofer

state: NY

address: One Gustave L. Levy Place, Box 1603

department: Department of Pharmacology and Systems Therapeutics

institute: Icahn School of Medicine at Mount Sinai

description:
Regular RNA-seq
processed data file: expression.txt

data_processing:
Base-calling was performed by Illumina CASAVA software.
Reads from fastq files were aligned to Bacillus subtilis genome by Bowtie 2 with --local option.
SAMtools and BEDtools were used to count reads mapped to specific genes for regular RNA-seq. Gene annotation reference was obtained from NCBI database. Homemade Python scripts were used to count read coverage at each base and to pick the peaks with >100 reads per position and >25nt in length for PARE experiments.
For regular RNA-seq, homemade Python script was used to normalize and compare the read abundance (reads/base) of each transcript as described in a previous study (Liu, B., et al. 2014 PMID: 25099370).
For PARE, homemade Python script was used to calculate an RR ratio for each peak found in BG880, which is the ratio of read coverage in the specific peak region in BG880 and BG879 normalized by the expression data of this region from regular RNA-seq (peak_100_RR.txt)
Genome_build: NC_000964.3
Supplementary_files_format_and_content: Tab-delimited txt files contain peaks (peaks_10_BG*.txt) or read abundance for genes (expression.txt)

organism: Bacillus subtilis

growth_protocol: The cells were cultured in LB medium at 37°C until mid-log phase.

extract_protocol:
Total RNA was extracted with hot phenol method, and ribosomal RNA was removed with Ribo-Zero rRNA Removal Kit for bacteria
For regular RNA-seq, Libraries were constructed according to the standard Illumina RNA-seq protocol. For PARE, equal amounts of samples were used to construct the PARE libraries using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (Set 1). The manufacturer’s protocol was modified so that 5ʹ monophosphorylated ends that result from endonuclease cleavage or pyrophosphohydrolase activity were preferentially selected. Briefly, after 3ʹ SR Adaptor ligation, reverse transcriptase (RT) primer hybridization, and 5ʹ SR Adaptor ligation – performed as per the manufacturer’s protocol – the reaction mixture volume was brought to 100 μl and samples were cleaned up with the RNeasy MinElute Cleanup Kit (Qiagen). 12 μl of RNA was recovered following the manufacturer’s protocol. The RNA was fragmented using the NEBNext® Magnesium RNA Fragmentation Module at 94°C for 4 minutes, and 2 μl of stop solution was added. After a second RNeasy MinElute cleanup, half of the RNA (6 μl) was again ligated to the 3ʹ SR Adaptor. Thus, after magnesium fragmentation only RNAs that retained their 5ʹ SR Adaptor (and original 5’ monophosphate) would undergo subsequent RT and PCR amplification. After addition of the RT primer, the reaction volume was adjusted to 30 μl and RT/PCR amplification reactions were performed as per the manufacturer’s protocol, using barcoded primers. One tenth of the PCR reaction was run on a 1.5% agarose gel to visualize the library, which consisted of cDNA ranging from 50 to ~500 nts. 20 μl of the cDNA library were prepared for Illumina sequencing using a 1.5X volume of Agencourt AMPure XP Beads (Beckman Coulter), according to the manufacturer’s instructions. The procedure was repeated twice, and the sample was eluted in a final volume of 20 µl.

tag: genotype (on ribonucleases)

value: ΔrnjA::spec Δrnc::ery

tag: growth condition

value: 37°C LB medium to mid-log phase

tag: molecule subtype

value: Total RNA with rRNA removed


title: Input_for_GATA3_ChIP-seq_SE_rep2


title: FXRChIP_MINT4


title: GATA3_ChIP-seq_PE_37C_Rep1

description: GATA3.ChIP-seq.GATA3cells.37degrees.merged.bigWig

value: GATA3 serum (Adomas et al, 2014)


title: BG879 rep. 1


title: GATA3_ChIP-seq_PE_37C_Rep2


title: GATA3_ChIP-seq_PE_Rep2

description: GATA3.ChIP-seq.GATA3cells.onice.merged.bigWig


title: BG880 rep. 2


title: Input_for_GATA3_ChIP-seq_SE_rep1


title: BG880 rep. 1


title: GATA3_ChIP-seq_SE_rep2


title: GATA3_ChIP-seq_SE_rep1


title: Input_MINT5

value: male


title: GATA3_ChIP-seq_PE_Rep1


title: Colo741_Input

status: Public on Jan 26 2016

city: South San Francisco

first: Florian

last: Gnad

address: 1 DNA Way

institute: Genentech

description: Input

data_processing:
Reads were aligned to the human genome (hg19) using the BWA algorithm (default settings).
Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis.
For Brd4 ChIP-seq, samples were normalized using Drosophila chromatin spike-in. Briefly, normalization was performed by equalizing the Drosophila tag counts across all samples so that the final tag counts were based off of the sample containing the lowest number of Drosophila tags. Then the human tags counts for all samples were proportionally scaled based on the ratios used to adjust the drosophila tag counts. Scaling to the target tag number was performed by randomly removing excess tags. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome to generate bigWig files.
For H3K27ac ChIP-seq, samples were normalized by random downsampling to a specific number of total reads and bedgraph files were generated using Bedtools (default settings).
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files, bigWig files

source_name: COLO 741

growth_protocol: Cell lines were grown at 37 degrees celsius and crosslinked for ChIP during logarithmic growth phase.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes (Brd4 ChIP) or 5 minutes (H3K27ac ChIP). DNA was sonicated to an average length of 200 - 500 bp. IP and Input DNA was reverse crosslinked and purified for library preparation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.

tag: cimp status

value: CIMP (-)

tag: cell line

value: COLO 741


title: Colo741_Brd4

description: Brd4 ChIP


title: LS180_Brd4

description: Brd4 ChIP


title: LS180_H3K27ac

description: H3K27ac ChIP


title: Colo741_H3K27ac

description: H3K27ac ChIP


title: Colo320_Input_Brd4

description: Input for Brd4 ChIP-seq

source_name: COLO 320

value: COLO 320


title: Colo320_Brd4

description: Brd4 ChIP


title: Sw480_Brd4

description: Brd4 ChIP


title: Sw480_Input_Brd4

description: Input for Brd4 ChIP-seq


title: HCT15_Brd4

description: Brd4 ChIP

value: CIMP (+)


title: Colo205_Brd4

description: Brd4 ChIP

source_name: COLO 205

value: COLO 205


title: LS180_Input

description: Input


title: Colo205_Input_Brd4

description: Input for Brd4 ChIP-seq


title: HCT15_Input_Brd4

description: Input for Brd4 ChIP-seq


title: HCT116_Input_Brd4

description: Input for Brd4 ChIP-seq

source_name: HCT 116

value: HCT 116


title: HT29_Brd4

description: Brd4 ChIP


title: HCT116_Brd4

description: Brd4 ChIP


title: HT29_Input_Brd4

description: Input for Brd4 ChIP-seq


title: Chd4 knockdown pol II ChIP-exo replicate 1

city: Gif-sur-Yvette

first: Matthieu

last: GERARD

address: SBIGeM bldg 142

country: France

institute: CEA

description: library strategy: ChIP-exo

data_processing:
Basecalls was performed using Bcl2FastQ version 2.16.0. Sequenced reads were masked for low-quality sequence, then mapped to mm9 whole genome using bwa mem 0.7.9a with the default parameters
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using WigMaker 3 with default parameters; Scores represent the maximum number of reads overlapping in a 25 bp bin
Supplementary_files_format_and_content: BIGWIG files were generated with UCSC tools (v4) using WigToBigWig program

source_name: Chd4 knockdown pol II ChIP-exo, ESC

growth_protocol: Embryonic stem cells were cultured at 37°C, 5% CO2, on mitomycin C-inactivated mouse embryonic fibroblasts, in DMEM (Sigma) with 15% foetal bovine serum and leukemia inhibitory factor (LIF).

extract_protocol:
ChIP-exo using an antibody anti-RNA polymerase II: The immunoprecipitation step was performed using antibodies against Pol II (sc-899, Santa Cruz Biotechnology) attached to magnetic beads, followed by DNA polishing, A-tailing, Illumina adaptor ligation (ExA2), and lambda and recJ exonuclease digestion on the beads.
After elution, a primer was annealed to EXA2 and extended with phi29 DNA polymerase, then A-tailed. A second Illumina adaptor was then ligated, and the products PCR-amplified and gel-purified.

treatment_protocol: described in the SAMPLES section (experimental conditions)

value: 46C (129/Ola strain)

value: ESC line 46C

tag: transfection

value: shRNA vector targeting Chd4, replicate 1

value: Pol II Antibody (N-20) (Santa Cruz Biotechnology, catalog# sc-899, lot# A2014)


title: Brg1 knockdown pol II ChIP-exo replicate 2

description: library strategy: ChIP-exo

source_name: Brg1 knockdown pol II ChIP-exo, ESC

value: shRNA vector targeting Brg1, replicate 2


title: Brg1 knockdown pol II ChIP-exo replicate 1

description: library strategy: ChIP-exo

value: shRNA vector targeting Brg1, replicate 1


title: Chd4 knockdown pol II ChIP-exo replicate 2

description: library strategy: ChIP-exo

value: shRNA vector targeting Chd4, replicate 2


title: Control pol II ChIP-exo replicate 1

description: library strategy: ChIP-exo

source_name: Control pol II ChIP-exo, ESC

value: control shRNA vector, replicate 1


title: Control pol II ChIP-exo replicate 2

description: library strategy: ChIP-exo

value: control shRNA vector, replicate 2


title: Ep400 knockdown pol II ChIP-exo replicate 1

description: library strategy: ChIP-exo

source_name: Ep400 knockdown pol II ChIP-exo, ESC

value: shRNA vector targeting Ep400, replicate 1


title: Ep400 knockdown pol II ChIP-exo replicate 2

description: library strategy: ChIP-exo

value: shRNA vector targeting Ep400, replicate 2


title: COLO320JQ1 3

description:
COLO320JQ1
SAM20050169

data_processing:
Alignment with GSNAP version ‘2012-01-11' -M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap
Differential gene expression analysis using Deseq and Limma
Genome_build: NCBIM37
Supplementary_files_format_and_content: FASTQ to BAM

growth_protocol: Cell lines were grown at 37 degrees celsius and harvested for RNA extraction during logarithmic growth phase.

extract_protocol:
RNA was extracted using RNA-easy mini kit.  On column DNAse digestion was performed.
TruSeq RNA Sample Preparation kit

treatment_protocol: Cells were treated for 24 hours with DMSO or 0.5 uM JQ1 in triplicate.


title: 2D rep 1

first: Indika

last: Rajapakse

state: MI

address: 1600 Huron Parkway, NCRC Building 520, Rm. 3392

department: Department of Computational Medicine & Bioinformatics

data_processing:
Library strategy: 4C-Seq
Paired-end reads were mapped to HG19 using Bowtie2, with default parameter settings and the “–very-sensitive- local” preset option.
HOMER (http:// homer.salk.edu/homer/interactions/) was used to develop the contact matrix with “makeTagDirectory” with the –tbp 1setting, and with “analyzeHi-C” with the “-raw” and “-res 1000000” settings to produce the raw contact matrix at 1 MB resolution or and “-res 1000000” for the 100 kb contact matrix.
Genome_build: hg19
Supplementary_files_format_and_content: each text file has a raw Hi-C matrix at 100 kb resolution for the indicated sample.

source_name: fibroblast

growth_protocol: Human foreskin fibroblasts from a normal karyotyped male individual (Cat # CRL-2522, ATCC) were propagated in growth medium, composed of MEM medium (cat # 11095–098, Life Technologies), 10% fetal bovine serum (FBS, cat # 10082–147), 1 X non-essential amino acids (NEAA, cat # 11140–050, Life Technologies), and 1 X antibiotic/antimycotic (cat # 15240–062, Life Technologies).

extract_protocol:
The methods for Hi-C library construction were adopted from (Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. Hi-C: a comprehensive technique to capture the conformation of genomes. Methods 2012). For each Hi-C library, ~20*106 cells were resuspended in 1 mL ice-cold lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 0.2% Igpel, 10 mL protease inhibitor cocktail) and incubated on ice for 15 min. Cells were homogenized on ice. Cells were collected by spinning for 5 minutes at 2,000 xg, then washed twice in 500 mL of ice cold 1x NEB buffer 2. Cells were distributed between 4 centrifuge tubes. Chromatins in each tube were digested with 400u of restriction enzyme HindIII in 1x NEB buffer 2 at 37 C overnight on a spin wheel. After HindIII digestion, restriction site overhanging ends were filled and labeled with biotin with DNA polymerase I large (Klenow) fragments in a reaction containing dATP, dGTP, dTTP, and biotin-14-dCTP in each of the 4 Hind III digestion tube. DNA fragments labeled biotin-14-dCTP from each of the 4 tubes were ligated at 16 C for 4 hours in an 8.23 mL reaction containing 1x ligation buffer, 1% Triton X-100, 1 mg/ml Bovine serum albumin (BSA),10 mM ATP, and 50u T4 DNA ligase . Reverse cross-linking started with 50 ml of 10 mg/ml proteinase K added to each tube and incubated at 65 C for 4 hours. Then, another 50 ml of proteinase K were added to each tube and continued incubating at 65 C overnight. Next, DNA was extracted with saturated phenolchloroform (1:1) and desalted by using AMICON! Ultra Centrifugal Filter with 1 x TE buffer. The final volume of desalted DNA was adjusted to 100 mL in 1 x TE buffer. Removal of Biotin from un-ligated ends was carried out in 8 individual reactions each of 50 mL containing 5 mg of Hi-C 405 DNA, 1 mg/ml BSA,1X NEB buffer 2, 25 nM dATP, 25 nM dGTP, and 15u T4 DNA polymerase at 20 C for 4 hours. The Hi-C DNA was then pooled in a single tube, purified with single phenol extraction, and precipitated by ethanol. The DNA was re-dissolved in 105 ml of water, and transferred to a microTUBE AFA tube.
DNA fragmentation was performed in a Sonicator. The DNA fragments of 200 – 400 bp were recovered with Agencourt AMPure XP mixture. DNA fragment ends were repaired in a 70 mL reaction containing 1X ligation buffer, 0.25 mM of dNTP mixture, 7.5 u of T4 DNA polymerase, 25u of T4 polynucleotide kinase, 2.5u of DNA polymerase I large fragment at 20 C for 30 min. The reaction was purified with a MinElute column. The DNA was eluted in 32 mL of elusion buffer for A-tailing, which was performed in a 50 mL reaction containing 5 mg DNA, 1X NEB buffer 2, 0.2 mM dATP, 15u Klenow fragment. The reaction was incubated at 37 C for 30 min, then at 65 C for 20 min. For Streptavidin pull-down, the biotinylated Hi-C products were mixed with MyOne C1 streptavidin bead solution. Non-specifically binding DNA was removed by washing with 1X binding buffer (5 mM Tris-HCl (pH8.0), 0.5 mM EDTA, and 435 1 M NaCl, then with 1X T4 Ligation buffer). The DNA-bound beads were resuspended in 38.75 ml of 1 X ligation buffer for adapter ligation. Illumina adapter ligation was performed in a 50 mL reaction by adding to the DNA-bound beads suspension of 1X T4 ligation buffer, 90 pM of Illumina paired end adapter, 3u of T4 DNA ligase. The reaction was incubated at room temperature for 2 hours. The beads were reclaimed, and the supernatant discarded. The beads were washed twice in Tween Wash Buffer (5 mM Tris-HCl pH8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween 20), once in 1X binding buffer (5 mM Tris-HCl (pH8.0), 0.5 mM EDTA, and 1 M NaCl, and twice in 1 X NEB buffer 2. After the last wash, the beads were resuspended in 20 ml of 1X NEB buffer 2. The Hi-C DNA sample was amplified by 15 PCR cycles for Illumina HiSeq sequencing. Each PCR reaction in 25 ml, 1.5 ml of Bead-bound Hi-C DNA, 0.35 ml of PE primer 1.0, 0.35 ml of PE primer 2.0, 0.2 ml of 25 mM dNTP, 2.5 ml of 10X PfuUltra buffer, 19.6 ml of H2O, and 0.5 ml of PfuUltra Fusion DNA polymerase. The PCR cycling parameters were 98 C for 30 seconds, followed by 15 cycles at 98 C for 10 seconds, 65 C for 30 seconds, and 72 C for 30 seconds, and a final extension at 72 C for 7 minutes. PCR products pooled from the supernatant of multiple reactions were subjected to AMpure XP beads purification to remove primer dimers. Each Hi-C library that passed the QC procedure was then sequenced in a single lane of a flow cell on a HiSeq 2000 sequencer to generate paired-end sequence reads at 100 bases per end read.

treatment_protocol:
Fibroblasts were synchronized to G0/G1
with serum-free MEM supplemented with 1X NEAA and 1X Antibiotic/antimycomic for 48 hours. Synchronized cells were dissociated with 0.25% trypsin to suspend for replating. For 2D monolayer cultures, 4*106 cells were plated in each 150 mm dish. For 3D cultures, 0.5*106 cells were plated in each well of a 96-well PERFECTA3D Hanging Drop Plate (3D Biomatrix). All cultures were incubated for 48 hours in growth medium at 37 C with 5% CO2. Approximately 20*106 cells grown in 2D were cross linked with 1% formaldehyde in serum free-medium for 15 min at room temperature, and then quenched with glycine to a final concentration of 0.128 M. Spheroids were harvested in serum-free medium, and crosslinked with 2% formaldehyde for 30 min at room temperature. The cross linking reaction was quenched with the glycine to a final concentration of 0.128 M. Cross linked cells were flash frozen in liquid nitrogen then stored at 80 C until the construction of Hi-C libraries.

value: ATCC CRL-2522

tag: passages

tag: culture type


title: 2D rep 2


title: COLO320JQ1 2

description:
COLO320JQ1
SAM20050168


title: COLO320JQ1 1

description:
COLO320JQ1
SAM20050167


title: 3D rep 1

value: 3D hanging drop spheriods


title: 3D rep 2


title: COLO320DMSO 3

description:
COLO320DMSO
SAM20050166

value: DMSO

value: COLO 320


title: HCT15JQ1 3

description:
HCT15JQ1
SAM20050163


title: COLO320DMSO 2

description:
COLO320DMSO
SAM20050165


title: HCT15JQ1 2

description:
HCT15JQ1
SAM20050162


title: HCT15DMSO 3

description:
HCT15DMSO
SAM20050160


title: COLO205JQ1 2

description:
COLO205JQ1
SAM20050156

value: COLO 205


title: HCT15DMSO 2

description:
HCT15DMSO
SAM20050159


title: COLO205DMSO 2

description:
COLO205DMSO
SAM20050153


title: COLO320DMSO 1

description:
COLO320DMSO
SAM20050164


title: COLO205DMSO 3

description:
COLO205DMSO
SAM20050154


title: HCT15DMSO 1

description:
HCT15DMSO
SAM20050158


title: HCT15JQ1 1

description:
HCT15JQ1
SAM20050161


title: COLO205DMSO 1

description:
COLO205DMSO
SAM20050152


title: COLO205JQ1 3

description:
COLO205JQ1
SAM20050157


title: HT29JQ1 3

description:
HT29JQ1
SAM20050151


title: COLO205JQ1 1

description:
COLO205JQ1
SAM20050155


title: HT29DMSO 2

description:
HT29DMSO
SAM20050147


title: SW480JQ1 3

description:
SW480JQ1
SAM20050145


title: HT29JQ1 1

description:
HT29JQ1
SAM20050149


title: HT29DMSO 1

description:
HT29DMSO
SAM20050146


title: SW480JQ1 2

description:
SW480JQ1
SAM20050144


title: SW480JQ1 1

description:
SW480JQ1
SAM20050143


title: SW480DMSO 2

description:
SW480DMSO
SAM20050141


title: SW480DMSO 3

description:
SW480DMSO
SAM20050142


title: HCT116JQ1 1

description:
HCT116JQ1
SAM20050137

value: HCT 116


title: SW480DMSO 1

description:
SW480DMSO
SAM20050140


title: HCT116JQ1 2

description:
HCT116JQ1
SAM20050138


title: HCT116DMSO 2

description:
HCT116DMSO
SAM20050135


title: HT-29 shBRD4.8 2

description:
SAM19833508
HT-29 shBRD4.8

treatment_protocol: Cells were treated for 3.5 days with 0.5 ug/ml doxycycline to induce shRNA expression.  Samples were harvested in triplicate.

value: shRNA BRD4 (8)


title: HT-29 shBRD4.7 3

description:
SAM19833506
HT-29 shBRD4.7

value: shRNA BRD4 (7)


title: HCT116DMSO 1

description:
HCT116DMSO
SAM20050134


title: HT-29 shBRD4.8 1

description:
SAM19833507
HT-29 shBRD4.8


title: HT-29 NTC 3

description:
SAM19833500
HT-29 NTC

value: NTC


title: HT-29 shBRD4.7 2

description:
SAM19833505
HT-29 shBRD4.7


title: HCT116 shBRD4.8 3

description:
SAM19833497
HCT116 shBRD4.8


title: HT-29 shBRD4.7 1

description:
SAM19833504
HT-29 shBRD4.7


title: HT29JQ1 2

description:
HT29JQ1
SAM20050150


title: HCT116 shBRD4.7 3

description:
SAM19833494
HCT116 shBRD4.7


title: HCT116 shBRD4.8 1

description:
SAM19833495
HCT116 shBRD4.8


title: HCT116 shBRD4.7 2

description:
SAM19833493
HCT116 shBRD4.7


title: HCT116JQ1 3

description:
HCT116JQ1
SAM20050139


title: HCT116 NTC 3

description:
SAM19833488
HCT116 NTC


title: HT-29 NTC 2

description:
SAM19833499
HT-29 NTC


title: HCT116 NTC 1

description:
SAM19833486
HCT116 NTC


title: HT29DMSO 3

description:
HT29DMSO
SAM20050148


title: HCT116DMSO 3

description:
HCT116DMSO
SAM20050136


title: HCT116 shBRD4.7 1

description:
SAM19833492
HCT116 shBRD4.7


title: HT-29 shBRD4.8 3

description:
SAM19833509
HT-29 shBRD4.8


title: Control ChIP-Seq replicate 1

data_processing:
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity/low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.7 with parameters  -a -m1 --best --strata -v2 p3
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using WigMaker 3 with default parameters; Scores represent the maximum number of reads overlapping in a 25 bp bin

source_name: embryonic stem cells

extract_protocol:
Formaldehyde-fixed chromatin was digested by MNase to release individual nucleosomes
Libraries were prepared according to the Illumina ChIP-seq protocol. Following end-repair and adapter ligation, fragments were size-selected on an agarose gel to purify genomic DNA fragments between 140 and 180 bp. Purified fragments were next amplified before clustering and single-read sequencing

value: 46C (129/Ola strain)

value: untagged cells

tag: chip antibodies

value: sequential ChIP whith HA and FLAG antibodies


title: Chd9 ChIP-Seq replicate 2

value: TAP-tag introduced by homologous recombination at the gene encoding Chd9


title: FAIRE-seq replicate 1


title: Chd9 ChIP-Seq replicate 1


title: Ep400 ChIP-Seq replicate 2

value: TAP-tag introduced by homologous recombination at the gene encoding Ep400


title: Ep400 ChIP-Seq replicate 1


title: Chd4 ChIP-Seq replicate 1

value: TAP-tag introduced by homologous recombination at the gene encoding Chd4


title: Chd4 ChIP-Seq replicate 2


title: HCT116 shBRD4.8 2

description:
SAM19833496
HCT116 shBRD4.8


title: Chd8 ChIP-Seq replicate 1

value: TAP-tag introduced by homologous recombination at the gene encoding Chd8


title: HCT116 NTC 2

description:
SAM19833487
HCT116 NTC


title: RNA-seq Control 2

city: Madison

first: Reid

last: Alisch

state: Wisconsin

address: 6001 Research Park Blvd

institute: University of Wisconsin-Madison

data_processing:
In order to elucidate differences in gene expression, we employed the Tuxedo Suite for RNA-seq analysis (Trapnell et al., 2012). Each testing condition contained three samples each that contributed > 80 million reads with seed lengths of 101 bps per condition. Exon–intron splice-junctions were found using TopHat (v1.0.12) with all parameters set to default, with the exception of the following: the addition of a reference gene model annotation (obtained through the Illumina iGenomes website (https://support.illumina.com/sequencing/sequencing_software/igenome.html); the anchor length was reduced to 6 bp, and the minimum intron length was raised to 70 bp (Trapnell et al., 2009 and Shi et al., 2014). This analysis produced > 90,000 splice junctions and > 100 million alignments per condition with an average read depth of 2384.
Aligned RNA-seq reads accepted by our TopHat parameters were then assembled into a set of transcripts and their relative abundances estimated using Cufflinks (v2.1.1) (Trapnell et al., 2010). All parameters were set to default, except that the reads were quantitated against a reference gene model annotation instead of attempting to find novel transcripts. These testing parameters produced > 30,000 full transcripts per testing condition. Assembled transcriptomes were then merged into one, along with a reference gene model annotation, using Cuffmerge (Trapnell et al., 2012). This produced a “master” transcriptome with 23,861 known annotated genes. Finally, to find significant differential gene expression between our two working conditions, accepted aligned reads for each condition were quantitated against our produced “master” transcriptome using Cuffdiff (v2.1.1) with all parameters set to default (Trapnell et al., 2013).
Genome_build: mm9

source_name: Hippocampus

growth_protocol: Mice were purchased from the Jackson laboratories (Bar Harbor, ME) and maintained on C57BL/6J background. The mice were housed under uniform conditions in a pathogen-free mouse facility with a 12-hour light/dark cycle. Food and water were available ad libitum. All experiments were approved by the University of Wisconsin — Madison Institutional Animal Care and Use Committee (M02529).

extract_protocol:
Approximately 100 ng of total RNA was used for sequence library construction following instructions of NuGen mRNA sample prep kit (cat# 0348). In brief, total RNA was copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. These cDNA fragments went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. These products were gel purified and enriched with PCR to create the final cDNA libraries.
The library constructs were run on the bioanalyzer to verify the size and concentration before sequencing on the Illumina HiSeq2500 machine where 100-cycle paired-end sequencing was performed by the University of Wisconsin Biotechnology Center. In total, three libraries (N = 2 genomes/library, except N = 1 for one library; the same mice and combinations that were used to generate the 5hmC data) were sequenced for each experimental condition.

treatment_protocol: On the day of the experiment seven-week old male C57BL/6 mice were randomly divided into experimental or control (naïve) groups (N = 6 and 5 per group, respectively). At the same time that the experimental mice were taken from the cage to begin the stress paradigm, the naïve mice also were taken from the cage for brief anesthesia (isoflurane) prior to sacrifice and tissue dissection. Following a published acute stress paradigm that resulted in alterations in histone modifications and gene expression ( Gray et al., 2014 and Hunter et al., 2009), the experimental mice were restrained for 30 min (2 h after lights-on) using a 50 ml conical vial and then individually housed in a clean cage for 1 h. Following this recovery period, experimental animals received brief anesthesia (isoflurane) prior to sacrifice and tissue dissection.

tag: age

value: Postnatal day 28

tag: Sex

value: Male

tag: treatment group


title: Chd6 ChIP-Seq replicate 2

value: TAP-tag introduced by homologous recombination at the gene encoding Chd6


title: RNA-seq Control 1


title: RNA-seq Experimental 3

value: stress paradigm


title: RNA-seq Control 3


title: HT-29 NTC 1

description:
SAM19833498
HT-29 NTC


title: RNA-seq Experimental 1


title: 5hmC-Control 1

description: 5-hydroxymethylcytosine enriched genomic DNA

data_processing:
Alignment of sequence data was described previously (Szulwach et al., 2011). Briefly, FastQ files from each sequenced library were separately aligned to mouse NCBI37v1/mm9 references using Bowtie 0.12.9. Each uniquely mapped read (.bed files), with no more than two mismatches in the first 25 bp, was concatenated to separately achieve experimental and control 5hmC peaks of sequence reads. The MACS software was used to identify peaks of 5hmC content using the default parameters, except for the following: effective genome size = 2.7 × 10; tag size = 85; band width = 300; P-value cutoff = 1e − 5 (Zhang Y et al., 2008).
Data processing of mapped reads was conducted in R using the Bioconductor GenomicRanges and edgeR packages (Robinson, 2010 and Lawrence et al., 2013). Read data from individual genomes were converted to GRangesObjects and were extended to 275 bp, which is roughly the average fragment length. Peaks under one condition (e.g., control) were defined as the regions that overlap with the peaks from at least two of the biological replicates under the same condition. The total peaks of both control and experimental groups were pooled together as the candidates for differentially hydroxymethylated regions (DhMRs). EdgeR was then used to perform differential enrichment analysis and a negative binomial distribution was used to determine the P-value for each candidate region. Multiple testing was corrected for using a Benjamini and Hochberg false discovery rate (FDR). The candidate regions with a FDR P-value < 0.05 were labeled as DhMRs.
DhMR annotation to each chromosome, gene (within 10 kb), and genomic structure was performed on nebula.curie.fr. A Manhattan plot was generated using a modified function of the qqman package. DhMRs were then labeled as either hyper or hypo based on the average log fold-changes in normalized read depth between the two groups (calculated by edgeR). A DhMR was hyper if the experimental group has higher average normalized read depth than the control group, otherwise hypo. There were no cases where the two groups had exactly the same average normalized depth.
Genome_build: mm9

extract_protocol:
Whole brains were extracted and immediately flash frozen in 2-methylbutane and dry ice. Whole hippocampal tissue was excised by micropunch (− 0.95 to − 3.79 mm posterior to bregma) and approximately 30 mg of tissue was homogenized with glass beads (Sigma) and DNA and RNA were extracted using AllPrep DNA/RNA mini kit (Qiagen).
Chemical labeling-based 5hmC enrichment was described previously ( Song et al., 2011 and Papale et al., 2015). Briefly, a total of 10 μg of pooled hippocampal DNA (N = 2 mice for all enrichments, except N = 1 for one of the enrichment) was sonicated to 300 bp and incubated for 1 h at 37 °C in the following labeling reaction: 1.5 μl of N3-UDPG (2 mM); 1.5 μl β of -GT (60 μM); and 3 μl of 10 × β-GT buffer, in a total of 30 μl. Biotin was added and the reaction was incubated at 37 °C for 2 h prior to capture on streptavidin-coupled Dynabeads (Invitrogen, 65001). Enriched DNA was released from the beads during a 2-hour incubation at room temperature with 100 mM DTT (Invitrogen, 15508013), which was removed using a Bio-Rad column (Bio-Rad, 732–6227). Capture efficiency was approximately 5–7% for each sample.
5hmC-enriched libraries were generated using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina sequencing, according to the manufacturer's protocol. Briefly,5hmC-enriched DNA fragments were purified after the adapter ligation step using AMPure XP beads (Agencourt A63880). An Agilent 2100 BioAnalyzer was used to quantify the amplified library DNA and 20 pM of diluted libraries (N = 6) were used in each lane for sequencing, which yielded approximately 25 to 35 million uniquely mapped 50 bp reads from each library. 50-Cycle single-end sequencing was performed by Beckman Coulter Genomics. Image processing and sequence extraction were done using the standard Illumina Pipeline.


title: Chd6 ChIP-Seq replicate 1


title: Chd2 ChIP-Seq replicate 1

value: TAP-tag introduced by homologous recombination at the gene encoding Chd2


title: 5hmC-Experimental 2


title: Chd2 ChIP-Seq replicate 2


title: Female neuron 7 months PS2APP SAM19447894

first: Brad

last: Friedman

state: CA

department: Bioinformatics

institute: Genentech, Inc.

data_processing: Reads were aligned to the NCBIM37 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from sorted brain cells

extract_protocol: Cells were centrifuged at 2,600 rcf for 7 minutes (neurons) or 6,600 rcf for 7 minutes (other cell types) and the supernatant was discarded. RNA was extracted from the cell pellet using Qiagen RNeasy Plus Micro kit in a final volume of 25 μl. We typically obtained 200-300 ng RNA from neurons, 10-20 ng from microglia, and 2-5 ng from astrocytes. RNA quality was quantified using the Bioanalyzer.

tag: animalid

tag: cell type

value: neuron

value: 7 months

tag: genotype


title: Smarca4 ChIP-Seq replicate 1

value: TAP-tag introduced by homologous recombination at the gene encoding Smarca4


title: 5hmC-Control 3


title: Female neuron 13 months non-Tg SAM19447904

value: 13 months

value: non-Tg


title: RNA-seq Experimental 2


title: 5hmC-Control 2


title: arp5d

city: Stanford

first: Devin

middle: Aalpoel

last: King

address: 371 Serra Mall

department: Biology

institute: Stanford University

description: biological replicates 1 and 2

data_processing:
Reads mapped to sacCer3 using Tophat2
Expression was quantified according to FPKM using cuffdiff (--no-novel-juncs) as described in Trapnell et al., 2012 ('Quantification of reference annotation only' protocol)
Expression values and significance results were accessed using cummeRbund
Genome_build: sacCer3
Supplementary_files_format_and_content: .txt file with matrix of expression values in FPKM

molecule: polyA RNA

organism: Saccharomyces cerevisiae

growth_protocol: Yeast were grown to mid-log-phase in rich medium at 30C. (Asynchronous culture).

extract_protocol:
Poly(A) mRNA enrichment was performed on RNA extracted via the Illumina TruSeq RNA sample preparation v2 low-throughput protocol
Sequencing performed at the Stanford Center for Genomics and Personalized Medicine on an Illumina HiSeq2000 Platform.

tag: genotype/variation

value: BY4741 arp5::LEU2

tag: growt protocol

value: liquid yeast culture


title: 5hmC-Experimental 1

tag: strain


title: 5hmC-Experimental 3


title: WT

description: biological replicates 1 and 2

source_name: WT

value: MATa his31 leu20 met150 ura30


title: Female microglia 13 months non-Tg SAM18605027

value: microglia


title: Female astrocyte 13 months PS2APP SAM18605039

value: astrocyte


title: Female microglia 7 months PS2APP SAM18605003


title: Female neuron 7 months PS2APP SAM19447897


title: Female microglia 7 months non-Tg SAM18604999


title: Female neuron 7 months non-Tg SAM18605017


title: Male astrocyte 13 months PS2APP SAM18605038


title: ies6d

description: biological replicates 1 and 2

value: BY4741 ies6::LEU2


title: Chd1 ChIP-Seq replicate 1

value: 46C (129/Ola strain)

value: TAP-tag introduced by homologous recombination at the gene encoding Chd1

value: sequential ChIP whith HA and FLAG antibodies


title: Female astrocyte 7 months PS2APP SAM18605012


title: Female astrocyte 7 months non-Tg SAM18605009


title: Female microglia 7 months non-Tg SAM18605000


title: Female neuron 7 months non-Tg SAM18605020


title: Female neuron 13 months non-Tg SAM19447907


title: ino80d

description: biological replicates 1 and 2


title: Female neuron 7 months non-Tg SAM18605021


title: arp8d

description: biological replicates 1 and 2

value: BY4741 arp8::LEU2


title: Male neuron 13 months PS2APP SAM19447901


title: Female astrocyte 7 months PS2APP SAM18605013


title: Female astrocyte 13 months non-Tg SAM18605036


title: Female microglia 7 months non-Tg SAM18604997


title: Female microglia 13 months non-Tg SAM18605025


title: Female microglia 13 months PS2APP SAM18605028


title: Male astrocyte 13 months non-Tg SAM18605033


title: Male neuron 13 months PS2APP SAM19447898


title: Female neuron 7 months non-Tg SAM18605018


title: Female neuron 13 months non-Tg SAM19447905


title: Female microglia 7 months PS2APP SAM18605004


title: Female microglia 7 months PS2APP SAM18605005


title: Female microglia 7 months non-Tg SAM18605001


title: Male microglia 13 months non-Tg SAM18605023


title: Female microglia 13 months PS2APP SAM18605030


title: Female astrocyte 13 months non-Tg SAM18605037


title: Female neuron 13 months PS2APP SAM19447902


title: Dcr2 RNAi sm RNA-seq rep3

city: St. Louis

first: Mindy

last: Steiniger

address: 1 University Blvd.

institute: University of Missouri-St. Louis

description: rRNA depleted Small RNA

data_processing:
All adapter sequences were trimmed and the libraries cleaned using Cutadapt (MARTIN 2011).We aggressively trimmed the siRNA reads to 25 nts from the 5’ end following adapter removal to filter remaining rRNAs, snoRNAs, snRNAs and tRNAs out of the data set before mapping. All data sets were mapped using the RNA-seq Unified Mapper (RUM) (GRANT et al. 2011). The NEB kit used to prepare the RNA-seq samples produces libraries with high directionality and RUM utilized this feature to strand specifically map the RNA-seq reads. RUM separated unique and non-uniquely mapping sequences into separate output files that could be further analyzed. The UCSC genome browser (www.genome.ucsc.edu) was used to visualize the non-uniquely mapping bedgraph output files.
Genome_build: dm3
Supplementary_files_format_and_content: Text files with normalized readcounts unique and non-unique RNA-seq and small RNA-seq reads.

organism: Drosophila melanogaster

source_name: tissue culture cells

growth_protocol: Dmel-2 cells were grown in Sf-900 serum free media.

extract_protocol:
Total RNA from 8 x 106 Drosophila Dmel-2 tissue culture cells was isolated using QIAzol Lysis Reagent (Qiagen). Total RNA was fractionated into large (>200 nts) and small (<200 nts) fractions using RNeasy Mini spin columns and RNeasy MinElute spin columns, respectively (Qiagen). DNA was removed from the large fraction by on-column DNase digestion (Qiagen). 28S, 18S and 5S rRNAs were depleted from 5 µg of each large RNA fraction using the Ribo-Zero Magnetic Kit (Epicentre). 2S rRNA was depleted from the small RNA fraction according to Seitz et al.  (SEITZ et al. 2008) with the following modifications. 0.1 nMoles 2S rRNA complementary oligo were bound to 500 µg streptavidin beads in 1 mL 0.5x SSC for one hour at 4oC. The beads were then washed 5X in 0.5X SSC followed by 5 minute incubation at 65oC to remove secondary structure. 2 µg of the small RNA fraction were diluted to 12.5 ng/µl and 160 µl were added to the bead slurry.
RNA-seq libraries were prepared in triplicate from 35 ng of the rRNA-depleted large RNA fraction using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). smRNA-seq libraries were prepared in triplicate from ~475 ng of the 2S rRNA-depleted small RNA fraction using the NEBNext Small RNA Library Prep Set for Illumina (NEB).

treatment_protocol: RNAi was performed as described (Sullivan, et. al., Mol. Cell, 2009)


title: Female neuron 7 months PS2APP SAM19447896


title: Dcr2 RNAi sm RNA-seq rep2

description: rRNA depleted Small RNA


title: Female neuron 7 months non-Tg SAM19447892


title: Female neuron 13 months PS2APP SAM19447900


title: Female microglia 13 months PS2APP SAM18605029


title: Female microglia 7 months PS2APP SAM18605002


title: Dcr2 RNAi sm RNA-seq rep1

description: rRNA depleted Small RNA


title: Female astrocyte 7 months non-Tg SAM18605007


title: Female neuron 7 months non-Tg SAM18605022


title: Male astrocyte 13 months PS2APP SAM18605041


title: Female microglia 13 months PS2APP SAM18605032


title: LacZ RNAi sm RNA-seq rep3

description: rRNA depleted Small RNA


title: Female microglia 7 months PS2APP SAM18605006


title: Female microglia 13 months non-Tg SAM18605026


title: Female astrocyte 7 months non-Tg SAM18605010


title: LacZ RNAi sm RNA-seq rep2

description: rRNA depleted Small RNA


title: Female astrocyte 13 months non-Tg SAM18605034


title: Female astrocyte 13 months non-Tg SAM18605035


title: LacZ RNAi sm RNA-seq rep1

description: rRNA depleted Small RNA


title: Female microglia 7 months non-Tg SAM18604998


title: Female astrocyte 7 months non-Tg SAM18605011


title: Female neuron 13 months PS2APP SAM19447899


title: Female neuron 7 months PS2APP SAM19447893


title: Female astrocyte 7 months PS2APP SAM18605016


title: Male neuron 13 months non-Tg SAM19447903


title: Female astrocyte 7 months PS2APP SAM18605015


title: Female neuron 7 months PS2APP SAM19447895


title: Female astrocyte 13 months PS2APP SAM18605040


title: Male microglia 13 months PS2APP SAM18605031


title: Female astrocyte 7 months non-Tg SAM18605008


title: Female astrocyte 7 months PS2APP SAM18605014


title: Female neuron 13 months non-Tg SAM19447906


title: Female neuron 7 months non-Tg SAM18605019


title: 13 months Non-Tg SAM24295810

data_processing:
Reads were aligned to the NCBIM37 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.
Supplementary_files_format_and_content: Entrez Gene ID an nRPKM

source_name: RNA from whole cortex

extract_protocol: Hemicortices were rapidly frozen on dry ice and stored until a full collection was obtained. RNA was extracted using the RNeasy Lipid Tissue extraction kit with on-column DNase digestion (Qiagen). Quality and quantity of total RNA samples were determined using ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent), respectively.

value: Non-Tg


title: 7 months PS2APP SAM24295813


title: 7 months Non-Tg SAM24295828


title: 7 months PS2APP SAM24295815


title: 7 months Non-Tg SAM24295826


title: 13 months Non-Tg SAM24295811


title: 7 months Non-Tg SAM24295812


title: 13 months Non-Tg SAM24295819


title: 13 months PS2APP SAM24295809


title: 7 months PS2APP SAM24295817


title: 13 months PS2APP SAM24295818


title: 7 months PS2APP SAM24295829


title: 7 months Non-Tg SAM24295814


title: 13 months PS2APP SAM24295806


title: 7 months PS2APP SAM24295825


title: 7 months Non-Tg SAM24295824


title: 7 months Non-Tg SAM24295816


title: 7 months PS2APP SAM24295827


title: 13 months PS2APP SAM24295808


title: 13 months Non-Tg SAM24295820


title: 13 months PS2APP SAM24295807


title: 13 months PS2APP SAM24295822


title: Female microglia 13 months non-Tg SAM18605024


title: S - starvation conditions

city: Pretoria

first: Stanford

last: Kwenda

state: Gauteng

address: Lunnon Road, Hilcrest

department: Microbiology and Plant Pathology Forestry and Agricultural Biotechnology Institute (FABI)

country: South Africa

institute: University of Pretoria

description: HI

data_processing:
Clean pair-end reads were quality checked using FASTQC:Read QC and trimmed using Trim sequences implemented within the Galaxy software
Quality trimmed reads were mapped to the P. atrosepticum SCRI1043 genome using Bowtie2
The mapped reads in SAM format were converted to sorted and indexed BAM files using SAMtools version 0.1.18.20. Each BAM file was split into two separate forward and reverse strand alignments using SAMtools to obtain transcriptional direction. And the Artemis genome browser used for visualization and manual identification of small RNA trasncripts.
Read counts of the identified sRNAs were used as input for the sRNA differential expression analysis using edgeR. sRNA transcripts were considered differentially expressed provided that the p-value was < 0.05 and q-value < 0.1.
Genome_build: ASM1160v1 (NC_004547.2)
Supplementary_files_format_and_content: Read counts of the identified sRNAs. Read counts were used as input for the sRNA differential expression analysis using edgeR.

organism: Pectobacterium atrosepticum SCRI1043

source_name: cultured cells

growth_protocol: The cultures with inoculation titer of 2–3 x 106 CFU per ml were grown in Luria-Bertani medium, with aeration (200 r.p.m.) at 28 °C for 16 hours (growth-promoting conditions). Aliquots of these cultures were used for total RNA extraction. The remaining cells were transferred (after double wash) to carbon and phosphorus deficient AB medium containing 1 g l-1 NH4Cl; 0.62 g l-1 MgSO4 x 7H2O; 0.15 g l-1 KCl; 0.013 g l-1 CaCl2 x 2H2O and 0.005 g l-1 FeSO4 x 7H2O, pH 7.5 and incubated under starvation conditions with initial cell density of 5.4 x 108 ± 6.1 x 107 CFU per ml in glass vials without aeration at 28 °C.

extract_protocol:
Total RNA was isolated from bacterial cells using the RNeasy Protect Bacteria Mini Kit (Qiagen, USA), according to the manufacturer’s instructions. Contaminating DNA was removed from the samples by DNAse (Qiagen) treatment. RNA was quantified using a Qubit fluorometer (Invitrogen, USA).
Library construction and strand-specific sequencing were carried out at the Beijing Genomics Institute (BGI-Shenzhen, China; http://www.genomics.cn/en/index), following the manufacturer’s protocols. Briefly, the rRNA was depleted from 1 microgram of total RNA using the Ribo-Zero Magnetic Gold Kit (Epicenter). TruSeq RNA Sample Prep Kit v2 (Illumina) was used for library construction. RNA was fragmented into small pieces using Elute Prime Fragment Mix. First-strand cDNA was synthesized with First Strand Master Mix and Super Script II (Invitrogen) reverse transcription (25°C for 10 min; 42°C for 50 min; 70°C for 15 min). After product purification (Agencourt RNAClean XP Beads, AGENCOURT) the second-strand cDNA library was synthesized using Second Strand Master Mix and dATP, dGTP, dCTP, dUTP mix (1 hour at 16°C). Purified fragmented cDNA was end repaired (30 min at 30°C) and purified with AMPureXP Beads (AGENCOURT). Addition of the poly (A) tail was done with A-tailing Mix (30 min at 37°C) prior to ligating sequencing adapters (10 min at 30°C). The second-strand cDNA was degraded using the Uracil-N-Glycosylase (UNG) enzyme (10 min at 37°C) and the product purified by AMPureXP Beads (AGENCOURT). Several rounds of PCR amplification with PCR Primer Cocktail were performed to enrich the cDNA fragments and the PCR products were purified with AMPureXP Beads (AGENCOURT). Sequencing was performed using the Illumina HiSeqTM 2000 platform with pair-end 90 base reads.

tag: growth conditions

value: S (carbon and phosphorus deficient AB medium)

tag: incubation time

value: 24 hours


title: 13 months Non-Tg SAM24295821


title: sample 27 - neuron - vehicle

data_processing:
Reads were aligned to the NCBIM37 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript.
Supplementary files include Entrez Gene IDs, adjusted RPKM and counts.

tag: tissue

value: brain

value: neuron

tag: treatment

value: vehicle


title: sample 26 - neuron - lps

value: lps


title: G - growth-promoting

description: KI

value: G (Nutrient-rich (Luria-Bertani) medium)

value: 16 hours


title: sample 20 - astrocyte - lps


title: sample 28 - astrocyte - lps


title: sample 19 - microglia - lps


title: sample 25 - neuron - lps


title: 13 months PS2APP SAM24295823

value: 13 months


title: sample 24 - microglia - lps

value: microglia


title: sample 23 - microglia - vehicle


title: Dcr2 RNAi RNA-seq rep2

description: rRNA depleted Large RNA

tag: cell line


title: Dcr2 RNAi RNA-seq rep3

description: rRNA depleted Large RNA


title: sample 18 - neuron - lps


title: Dcr2 RNAi RNA-seq rep1

description: rRNA depleted Large RNA


title: sample 15 - astrocyte - vehicle

value: astrocyte


title: LacZ RNAi RNA-seq rep2

description: rRNA depleted Large RNA


title: LacZ RNAi RNA-seq rep1

description: rRNA depleted Large RNA


title: sample 13 - neuron - vehicle


title: sample 17 - microglia - lps


title: sample 16 - astrocyte - lps


title: sample 12 - astrocyte - vehicle


title: LacZ RNAi RNA-seq rep3

description: rRNA depleted Large RNA


title: 3%O2_30 min

city: Beijing

first: Fanglei

last: Zuo

address: No. 17 Qinghua East Road, Haidian District

institute: China Agricultural University

data_processing:
Base-calling performed using SOLiD 4 System SETS software
All sequenced reads were aligned to the genome of B. longum BBMN68 using SOLiD Corona Lite software v4.2
We used a recursive strategy to improve the usable sequenced reads information as follows: 50 mers reads were firstly mapped to the genome with ≤ 5 color-space mismatches and unmapped reads were progressively trimmed off 5 bases from the 3’ end once, then the trimmed reads were mapped to the genome again until a match was found
All those uniquely mapped reads were used to calculate the RPKM values (reads per kilobase of exon per million mapped sequenced reads) of genes, which indicated the normalized gene expression level
Differentially expressed genes (DEGs) from different samples were identified according to an R package DEGseq (http://waprna.big.ac.cn/rnaseq/function/degseq.jsp)
Genome_build: NCBI assembly accession number CP002286
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each gene of sample

organism: Bifidobacterium longum

growth_protocol: B. longum BBMN68 were cultivated under standard anaerobic conditions in MRS broth (Oxoid) at 37°C in infusion vials purged with a gas mixture of 10% (v/v) H2, 10% CO2, and 80% N2

extract_protocol:
Total RNA isolation was carried out using TRIzol reagent (Invitrogen) as the manufacturer’s instructions, and purified using a RiboMinus Kit (Invitrogen) to eliminate ribosomal RNA
The RNA-seq library was constructed using a total RNA-Seq Kit (Applied Biosystems) for SOLiD method according to manufacturer’s introductions

treatment_protocol: Exponential-phase culture of B. longum BBMN68 was subjected to static headspace oxygen treatment by injection of O2 into the vial headspace. The MRS broth and headspace were kept at a 1:1 (v/v) ratio. The two oxidative-stress treatments consisted of exposing B. longum BBMN68 grown in MRS broth with no L-cysteine HCl to 3% O2 for 30 min and 60 min, respectively.

tag: stress treatment

value: 3% oxygen for 30 min


title: control

source_name: Bifidobacterium longum_control


title: sample 21 - neuron - vehicle


title: sample 11 - astrocyte - vehicle


title: sample 22 - neuron - lps


title: sample 14 - microglia - vehicle


title: RNA-seq embryonic stem cells

value: 46C (129/Ola strain)

value: untagged cells


title: Control ChIP-Seq replicate 2

value: sequential ChIP whith HA and FLAG antibodies


title: sample 6 - astrocyte - lps


title: sample 10 - microglia - vehicle


title: sample 7 - microglia - lps


title: sample 9 - neuron - vehicle


title: sample 8 - neuron - vehicle


title: Chd1 ChIP-Seq replicate 2

value: TAP-tag introduced by homologous recombination at the gene encoding Chd1


title: sample 5 - astrocyte - vehicle


title: sample 4 - microglia - vehicle


title: sample 3 - microglia - vehicle


title: Chd8 ChIP-Seq replicate 2

value: TAP-tag introduced by homologous recombination at the gene encoding Chd8


title: Smarca4 ChIP-Seq replicate 2

value: TAP-tag introduced by homologous recombination at the gene encoding Smarca4


title: sample 2 - neuron - lps


title: 3%O2_60 min

value: 3% oxygen for 60 min


title: sample 1 - microglia - lps

value: brain


title: Colo320_H3K27ac

description: H3K27ac ChIP

tag: cimp status

value: CIMP (-)

tag: chip antibody

value: COLO 320


title: Control ATAC-seq replicate 4

description: library strategy: ATAC-seq

data_processing:
Basecalling was performed with RTA 1.18.64. Bcl conversions into Fastq and demultiplexing were performed using bcl2fastq version 1.8.3, Sequenced reads were trimmed for adaptor sequence and masked for low-complexity/low-quality sequence with Trimmomatic 0.32, then mapped to mm9 whole genome using bowtie v0.12.7 with parameters -a -m1 --best --strata -v2 p3
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using WigMaker 3 with default parameters; Scores represent the maximum number of reads overlapping in a 25 bp bin
Supplementary_files_format_and_content: BIGWIG files were generated with UCSC tools (v4) using WigToBigWig program

source_name: Control ATAC-seq, ESC

extract_protocol:
50,000 cells were collected, washed with cold PBS and resuspended in 50ul of ES buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2). Permeabilized cells were resuspended in 50 ul Transposase reaction (1X Tagmentation buffer, 1.0-1.5 ul Tn5 transposase enzyme (Illumina)) and incubated for 30min at 37°C. Subsequent steps of the protocol were performed as described in PMID: 24097267.
Transposed DNA was subjected to several round of amplification with Ad2 primer pairs (the reverse primer contains the index allowing subsequent multiplexing. Oligonucleotide sequences are available in PMID: 24097267). Libraries were next purified using a Qiagen MinElute kit and Ampure XP magnetic beads (1:1.6 ratio) to remove remaining non ligated adapters.

value: ESC line 46C

tag: transfection

value: control shRNA vector, 48h timepoint, replicate 2


title: Colo320_Input_H3K27ac

description: Input for H3K27ac ChIP-seq

source_name: COLO 320


title: Sw480_Input_H3K27ac

description: Input for H3K27ac ChIP-seq


title: Control ATAC-seq replicate 3

description: library strategy: ATAC-seq

value: control shRNA vector, 48h timepoint, replicate 1


title: Brg1 knockdown ATAC-seq replicate 2

description: library strategy: ATAC-seq

source_name: Brg1 knockdown ATAC-seq, ESC

value: shRNA vector targeting Brg1, 48h timepoint, replicate 2


title: HCT15_H3K27ac

description: H3K27ac ChIP

value: CIMP (+)


title: Chd4 knockdown ATAC-seq replicate 2

description: library strategy: ATAC-seq

source_name: Chd4 knockdown ATAC-seq, ESC

value: shRNA vector targeting Chd4, 30h timepoint, replicate 2


title: Colo205_H3K27ac

description: H3K27ac ChIP

source_name: COLO 205

value: COLO 205


title: Sw480_H3K27ac

description: H3K27ac ChIP


title: Ep400 knockdown ATAC-seq replicate 1

description: library strategy: ATAC-seq

source_name: Ep400 knockdown ATAC-seq, ESC

value: 46C (129/Ola strain)

value: shRNA vector targeting Ep400, 30h timepoint, replicate 1


title: HT29_H3K27ac

description: H3K27ac ChIP


title: Ep400 knockdown ATAC-seq replicate 2

description: library strategy: ATAC-seq

value: shRNA vector targeting Ep400, 30h timepoint, replicate 2


title: HCT116_Input_H3K27ac

description: Input for H3K27ac ChIP-seq

source_name: HCT 116

value: HCT 116


title: Chd4 knockdown ATAC-seq replicate 1

description: library strategy: ATAC-seq

value: shRNA vector targeting Chd4, 30h timepoint, replicate 1


title: Control ATAC-seq replicate 1

description: library strategy: ATAC-seq

value: control shRNA vector, 30h timepoint, replicate 1


title: Control ATAC-seq replicate 2

description: library strategy: ATAC-seq

value: control shRNA vector, 30h timepoint, replicate 2


title: HT29_Input_H3K27ac

description: Input for H3K27ac ChIP-seq


title: Mouse NPCs bc14 (NP Tot)

city: Singapore

first: Vivek

last: Tanavde

state: Singapore

address: 30 Biopolis Street, #07-01, Matrix

department: Genome and Gene Expression Data Analysis Division

country: Singapore

institute: Bioinformatics Institute, A*STAR, Singapore

description:
NP Unfractionated Total RNA.
Processed data file: Unscaled-RPKM-data.xlsx

data_processing:
Alignment of the reads to Mus musculus genome was done using LifeScopeTM.
The bam files comprising of the alignments were then imported into Partek Genomics Suite. The allocation of the reads to each transcript was done through Partek using the Expectation Maximisation algorithm.
RPKM normalised reads were further scaled using scaling factors calculated from the polyA spike in RNAs.
The scaled normalised reads were converted into percentage of reads in each group, where the sum of each group was 100%.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Unscaled-RPKM-data.xlsx: Unscaled normalised values for all samples.
Supplementary_files_format_and_content: Scaled-data.xlsx: Scaled normalised and scaled percentage values for samples (1 to 8).

source_name: SOX1-GFP NPCs, unfractionated

growth_protocol: ESCs were cultured on 0.1% gelatin in DMEM (GIBCO) supplemented with 15% fetal bovine serum (FBS) (GIBCO), 0.2 mM β-mercaptoethanol, 2 mM L-glutamine (GIBCO), 13 MEM nonessential amino acids (GIBCO), and LIF.

extract_protocol:
Cytoplasmic mRNAs were separated on 10-50% sucrose gradients and fractionated into 12 fractions. Fractions were pooled corresponding to non-translated, low translation and high translation fractions. The bottom of the gradient was collected as fraction 12.
Total RNA was treated with Ribominus kit (Life Technologies) as per manufacturer's instructions. Ambion SOLiD kit was utilized with protocol 4452437 (Revision B) opting for initial fragmentation using RNase III. After size-selection of the cDNA on Agencourt SPRI beads (as described), barcoding primers were used to amplify the libraries in a 14-cycle PCR reaction. No product was seen if reverse transcriptase was omitted in the reverse transcription step. Amplified libraries were checked for yield and quality on an Agilent Bioanalyzer chip and processed for SOLiD sequencing by the Biomolecular Resource Facility, Australian National University.

treatment_protocol: For NPC differentiation, Sox1-GFP ESCs were plated at low density and grown in N2B27 media for 6 days.

tag: originating cell line

value: NPCs differentiated from ESCs

tag: rna fraction

value: unfractionated


title: Mouse NPCs bc12 (NP4)

description:
NP Fraction 12.
Processed data file: Unscaled-RPKM-data.xlsx
Processed data file: Scaled-data.xlsx

source_name: SOX1-GFP NPCs, fraction 12

value: fraction 12


title: HCT15_Input_H3K27ac

description: Input for H3K27ac ChIP-seq


title: H2O2-21-3d-Replicate 1

city: Tuxedo

first: Suresh

last: Cuddapah

state: New York

address: 57 Old Forge Road

department: Environmental Sciecne

institute: New York University Langone Medical center

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-Seq data analysis was performed using Biowardrobe experimental management system. Breifly Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37/hg19 whole genome using STAR version 2.4.oj using default parameters; multi hits removed
Gene expression levels were quantified as reads per kilobase of exon per million fragments mapped (RPKM) using Biowardrobe algorithm
Differential gene expression was calculated using DESeq2
More information on Biowardrobe suite can be found at https://www.biowardrobe.com/
Genome_build: Feb. 2009 (GRCh37/hg19)
Supplementary_files_format_and_content: csv file include RPKM values for each Sample

source_name: Bronchial epithelial cell

growth_protocol: Immortalized human bronchial epithelial cells (BEAS-2B) were cultured as previously reported in Dulbecco’s modified Eagle’s medium (DMEM) (Cellgro), supplemented with 1% (vol/vol) penicillin–streptomycin and 10% (vol/vol) FBS (Atlanta Biologicals) at 37 °C. For 21% O2 cultures, the cells were incubated in a standard incubator (NuAire NU-8700 AutoFlow water jacketed CO2 incubator).

extract_protocol:
Total RNA was isolated from cells cultured at different O2 levels using RNeasy kit (Qiagen)
RNASeq libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit (RS-122-2002), according to the manufacturer’s instructions.

treatment_protocol: The cells cultured at 10% O2 were incubated in Panasonic MCO-5M-PA O2/CO2 incubator equipped with zirconia sensor and automatic O2 cylinder switch over system for constant moitoring and maintanence of O2 levels. CO2 levels were maintained at 5% in both the conditions. The cells and the media were pre-equilibriated at 10% O2 for 24 hrs before the start of each experiment. The cells were cultured at 10% O2 and 21% O2 for 3 days (acute) and 3 weeks (chronic). For H2O2 exposure, BEAS-2B cells were treated with 150 µM H2O2 for 3 days.

tag: experiment

value: BEAS2B cells

value: 150 uM H2O2 added and then cultured at 21% O2 tension in vitro for 3 days


title: H2O2-10-3d-Replicate 2

tag: cell type

value: 150 uM H2O2 added and then cultured at 10 % O2 tension in vitro for 3 days


title: H2O2-21-3d-Replicate 2


title: Mouse NPCs bc11 (NP3)

description:
NP High Translation Polysomal RNA Fractions 9-11.
Processed data file: Unscaled-RPKM-data.xlsx
Processed data file: Scaled-data.xlsx

source_name: SOX1-GFP NPCs, high translation polysomal

value: high translation polysomal (fractions 9-11)


title: H2O2-10-3d-Replicate 1


title: Brg1 knockdown ATAC-seq replicate 1

description: library strategy: ATAC-seq

value: ESC line 46C

value: shRNA vector targeting Brg1, 48h timepoint, replicate 1


title: control-10-3-weeks-Replicate 2

value: 10 % O2 tension in vitro for 3 weeks


title: Mouse NPCs bc10 (NP2)

description:
NP Low Translation Polysomal RNA Fractions 6-8.
Processed data file: Unscaled-RPKM-data.xlsx
Processed data file: Scaled-data.xlsx

source_name: SOX1-GFP NPCs, low translation polysomal

value: low translation polysomal (fractions 6-8)


title: Colo205_Input_H3K27ac

description: Input for H3K27ac ChIP-seq

data_processing:
Reads were aligned to the human genome (hg19) using the BWA algorithm (default settings).
Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis.
For Brd4 ChIP-seq, samples were normalized using Drosophila chromatin spike-in. Briefly, normalization was performed by equalizing the Drosophila tag counts across all samples so that the final tag counts were based off of the sample containing the lowest number of Drosophila tags. Then the human tags counts for all samples were proportionally scaled based on the ratios used to adjust the drosophila tag counts. Scaling to the target tag number was performed by randomly removing excess tags. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome to generate bigWig files.
For H3K27ac ChIP-seq, samples were normalized by random downsampling to a specific number of total reads and bedgraph files were generated using Bedtools (default settings).
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files, bigWig files

value: CIMP (+)

value: COLO 205


title: Ep400 knockdown MNase-seq replicate 2

description: MNase-seq

source_name: Ep400 knockdown MNase-seq, ESC

extract_protocol:
1 million cells were fixed 10 min in culture medium containing 1% formaldehyde and ollected in 15 mM Tris-HCl PH7.5, 0.3 M sucrose, 60 mM KCl, 15 mM NaCl, 5mM MgCl2, 0.1 mM EGTA, 0.4% Igepal CA-630 (Sigma). We next added 2 mM CaCl2 and 4 units of MNase, and incubated 10 min at 37°C. MNase digestion was stopped by adding 10 mM EDTA (final concentration), and storing on ice. Cells were then disrupted by 15 passages through a 25G needle, followed by a 10 min centrifugation at 18,000 g. The supernatant was collected and incubated 1h at 65°C with 15 mg of RNase A. We next added 10 mg of proteinase K, adjusted each sample to 0.1% SDS (final concentration) and incubated 2 h at 55°C. NaCl concentration was then adjusted to 200 mM and the samples were incubated overnight at 65°C for crosslink reversal. DNA was purified from each sample by phenol-chloroform extraction followed by ethanol precipitation.
20 ng of purified DNA was used for library preparation according to manufacturer's instructions, using Ultralow ovation library system, Nugen. Following end-repair and adapter ligation, fragments were size-selected onto an agarose gel in order to purify genomic DNA fragments between ~ 60 and 220 bp.

value: 46C (129/Ola strain)

value: shRNA vector targeting Ep400, replicate 2


title: Mouse NPCs bc09 (NP1)

description:
NP Monosome RNA Fractions 1-5.
Processed data file: Unscaled-RPKM-data.xlsx
Processed data file: Scaled-data.xlsx

source_name: SOX1-GFP NPCs, monosome

value: monosome (fractions 1-5)


title: WL_D1.fq.gz

first: Bo

last: Zhang

address: No. 2 Yuanmingyuan West Road, College Animal Science & Technology, China Agriculture University, Beijing

data_processing:
Libraries were constructed and sequenced by Illumina Hiseq 2000 according to the manufacturer’s instructions
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the fourth release of the chicken reference genome(G. gallus) using BWA
In RNA-Seq analysis, the number of reads per kb of transcript per million mapped reads (RPKM) was used to calculate the levels of gene expression.
Genome_build: Gallus gallus
Supplementary_files_format_and_content: text file with RPKM data

organism: Gallus gallus

source_name: White leghom_embryonic heart

extract_protocol:
Total RNA was isolated from heart tissues with TRIzol according to the manufacturer’s instructions.
RNA sequencing libraries were prepared using the Illumina mRNA-Seq Prep Kit

value: Embryonic heart

tag: age

value: 16 d after incubation

tag: breed

value: White leghom


title: CH1.fq.gz

source_name: Chahua chicken_embryonic heart

value: Chahua


title: WL_D2.fq.gz


title: control-10-3-weeks-Replicate 1

value: BEAS2B cells


title: HCT116_H3K27ac

description: H3K27ac ChIP

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes (Brd4 ChIP) or 5 minutes (H3K27ac ChIP). DNA was sonicated to an average length of 200 - 500 bp. IP and Input DNA was reverse crosslinked and purified for library preparation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.

value: HCT 116


title: Ep400 knockdown MNase-seq replicate 1

description: MNase-seq

value: shRNA vector targeting Ep400, replicate 1


title: Mouse ESCs bc07 (E3)

description:
ES High Translation Polysomal RNA Fractions 9-11.
Processed data file: Unscaled-RPKM-data.xlsx
Processed data file: Scaled-data.xlsx

source_name: SOX1-GFP ESCs, high translation polysomal

tag: genotype/variation

value: ESC

value: high translation polysomal (fractions 9-11)


title: Mouse ESCs bc08 (E4)

description:
ES Fraction 12.
Processed data file: Unscaled-RPKM-data.xlsx
Processed data file: Scaled-data.xlsx

source_name: SOX1-GFP ESCs, fraction 12

value: fraction 12


title: control-21-Replicate 2

value: 21% O2 tension in vitro for 3 days


title: Control MNase-seq replicate 2

description: MNase-seq

source_name: Control MNase-seq, ESC

tag: strain

value: ESC line 46C

value: control shRNA vector, replicate 2


title: Mouse ESCs bc13 (E Tot)

description:
ES Unfractionated Total RNA.
Processed data file: Unscaled-RPKM-data.xlsx

source_name: SOX1-GFP ESCs, unfractionated

value: unfractionated


title: Control MNase-seq replicate 1

description: MNase-seq

value: 46C (129/Ola strain)

value: control shRNA vector, replicate 1


title: LWC1.fq.gz

source_name: Lhasa White_embryonic heart

value: Lhasa White


title: LWC2.fq.gz

value: Embryonic heart


title: TC2.fq.gz

source_name: Linzhi Tibetan chicken_embryonic heart

value: 16 d after incubation

value: Linzhi Tibetan


title: control-21-Replicate 1


title: control-10-3d-Replicate 2

value: 10 % O2 tension in vitro for 3 days


title: FAIRE-seq replicate 3

source_name: embryonic stem cells

value: untagged cells


title: TC1.fq.gz


title: CH2.fq.gz

value: Chahua


title: FAIRE-seq replicate 2


title: Mouse ESCs bc05 (E1)

description:
ES Monosome RNA Fractions 1-5.
Processed data file: Unscaled-RPKM-data.xlsx
Processed data file: Scaled-data.xlsx

source_name: SOX1-GFP ESCs, monosome

value: monosome (fractions 1-5)


title: control-10-3d-Replicate 1

value: BEAS2B cells


title: STT6076_PVNS

status: Public on Jan 25 2016

first: Xiangqian

last: Guo

address: 300 Pasteur Dr.

department: Department of Pathology

description: Experiment type: 3SEQ

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

source_name: PVNS

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

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

value: soft tissue sarcoma

tag: tissue subtype

value: PVNS

tag: tissue archive method

value: FFPE

tag: source

value: Stanford Surgical


title: STT3705_SS

description: Experiment type: 3SEQ

source_name: SS

tag: tissue

value: SS


title: STT5532_SS

description: Experiment type: 3SEQ


title: STT5533_SS

description: Experiment type: 3SEQ


title: STT6079_TGCT

description: Experiment type: 3SEQ

source_name: TGCT

value: TGCT


title: STT6074_PVNS

description: Experiment type: 3SEQ


title: STT5523_EWS

description: Experiment type: 3SEQ

source_name: EWS

value: EWS


title: STT5600_EWS

description: Experiment type: 3SEQ


title: STT5598_EWS

description: Experiment type: 3SEQ


title: STT5592_EMC

description: Experiment type: 3SEQ

source_name: EMC

value: EMC


title: STT5522_EWS

description: Experiment type: 3SEQ


title: STT5526_EMC

description: Experiment type: 3SEQ


title: STT5525_EMC

description: Experiment type: 3SEQ


title: Mouse ESCs bc06 (E2)

description:
ES Low Translation Polysomal RNA Fractions 6-8.
Processed data file: Unscaled-RPKM-data.xlsx
Processed data file: Scaled-data.xlsx

source_name: SOX1-GFP ESCs, low translation polysomal

value: ESC

value: low translation polysomal (fractions 6-8)


title: STT5595_MLPS

description: Experiment type: 3SEQ

source_name: MLPS

value: MLPS


title: STT5596_MLPS

description: Experiment type: 3SEQ


title: STT5591_MLPS

description: Experiment type: 3SEQ


title: STT5590_MLPS

description: Experiment type: 3SEQ


title: STT5531_MLPS

description: Experiment type: 3SEQ


title: STT5517_DDLPS

description: Experiment type: 3SEQ

source_name: DDLPS

value: DDLPS


title: STT6075_PVNS

description: Experiment type: 3SEQ


title: STT5870_ESS

description: Experiment type: 3SEQ

source_name: ESS

value: ESS


title: STT5518_DDLPS

description: Experiment type: 3SEQ


title: STT5534_DDLPS

description: Experiment type: 3SEQ


title: STT5868_ESS

description: Experiment type: 3SEQ


title: STT5867_ESS

description: Experiment type: 3SEQ


title: STT5869_ESS

description: Experiment type: 3SEQ


title: STT6080_TGCT

description: Experiment type: 3SEQ


title: STT5776_ESS

description: Experiment type: 3SEQ


title: STT5774_ESS

description: Experiment type: 3SEQ


title: STT5866_ESS

description: Experiment type: 3SEQ


title: STT5864_ESS

description: Experiment type: 3SEQ


title: STT5775_ESS

description: Experiment type: 3SEQ


title: STT5865_ESS

description: Experiment type: 3SEQ


title: STT5527_EMC

description: Experiment type: 3SEQ


title: STT5967_GIST_WT

description: Experiment type: 3SEQ

source_name: GIST WT

value: GIST WT


title: STT5521_ESS

description: Experiment type: 3SEQ


title: STT5966_GIST_WT

description: Experiment type: 3SEQ


title: STT5520_ESS

description: Experiment type: 3SEQ


title: STT5543_ESS

description: Experiment type: 3SEQ


title: STT5963_GIST_WT

description: Experiment type: 3SEQ


title: STT5965_GIST_WT

description: Experiment type: 3SEQ


title: STT5519_ESS

description: Experiment type: 3SEQ


title: STT5962_GIST_WT

description: Experiment type: 3SEQ


title: Sample 64

city: Tjelle

first: Tina

middle: Sorensen

last: Dalgaard

address: Blichers Allé 20

department: Department of Animal Science

country: Denmark

institute: Aarhus University

data_processing:
Initial control quality was assessed by the FastQC software version 0.11.3
Raw reads were than trimmed for low quality bases using the Trimmomatic tool version 0.32 applying minimum Phred quality score >10 averaged across the sliding window of five bases. Furthermore, all reads with the length below 40 bp were removed.The following settings for Trimmomatic were used:SLIDING WINDOW:5:10 MINLEN:40
The trimmed reads were mapped to the Gallus gallus reference genome (Gallus_gallus-4.0, release 80 ) using a spliced aligner TopHat2 version 2.014. The Gallus gallus gene annotation used for mapping was retrieved from Ensembl database version 80 (www.ensembl.org). The mapping quality was assessed using a set of Python scripts within the RSeQC toolkit.
Gene count estimation was performed using the HTSeq-count tool in ‘union’ mode. The HTSeq-count is a Python script within the HTSeq framework, version 0.7.1, which is an open source toolkit that allows the input of raw counts from aligned reads to be annotated with gene names based on genomic features.
The read counts obtained were used to estimate gene expression and identify differentially expressed (DE) genes. This was achieved using Bioconductor package edgeR version 3.10.0 and limma version 3.24.5 following a previously described protocol Anders et al. 2013 (Nature Protocols)
Genome_build: Gallus_gallus-4.0, release 80
Supplementary_files_format_and_content: tab-delimited text files include raw gene count values for Sample

source_name: L10L_6 wks old_infected bird_spleen

extract_protocol:
Tissue samples were homogenized on a TissueLyzer LT (Qiagen, Hilden, Germany). Total RNA was extracted with the Qiagen RNAeasy Kit (Catalog ID 74104, Qiagen, Venlo, Netherlands) according to the manufacturer’s instructions. The quality of the 64 total RNA samples was verified using a 2200 TapeStation RNA Screen Tape device (Agilent, Santa Clara, CA, USA) and the concentration ascertained using an ND-1000 spectrophotometer (NanoDrop, Wilmington, DE). Libraries were prepared with the Illumina TruseqRNA sample prep kit (Catalog ID FC-122-1001, Illumina, San Diego, USA) following the manufacturer’s protocol and evaluated with the Agilent Tape Station 2200. Libraries were quantified by Picogreen and then normalized to 10 nM as recommended by Illumina for cluster generation on the Hiseq2000. Equimolar amounts of each library were mixed before NaOH denaturation. The Illumina Truseq PE cluster kit v3 (Catalog ID PE-401-3001) was used to generate clusters on the grafted Illumina Flowcell and the hybridized libraries were sequenced on six lines of a Flowcell on the Hiseq2000 with 100 cycles of a paired-end sequencing module using the Truseq SBS kit v3 (Catalog ID FC-401-3001).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: chicken line

value: low serum concentration of mannose-binding lectin (MBL)

tag: time point

value: 6 weeks old (3 wks post infection)

value: spleen


title: Sample 62


title: Sample 63


title: STT5959_GIST_WT

description: Experiment type: 3SEQ

value: soft tissue sarcoma


title: Sample 59


title: Sample 58


title: Sample 61


title: Sample 57


title: Sample 60


title: Sample 56

source_name: L10L_6 wks old_uninfected bird_spleen


title: Sample 54


title: STT6078_TGCT

description: Experiment type: 3SEQ


title: Sample 53


title: Sample 55


title: Sample 49


title: Sample 51


title: Sample 50


title: Sample 52


title: T. brucei H3V-KO + DMOG rep 3

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
adapter and quality trimming: Trimmomatic v0.32 using TruSeq3 adapters, removing leading and trailing bases with quality less than 15, and removing reads with average quality less than 20 and reads shorter than 50 bp; quality based on Phred 33 scores
alignment: Bowtie2 v2.2.3 using sensitive local alignment mode
sorting: Samtools v1.2 using default parameters
expression level of replicates: Cuffnorm (from Cufflinks v2.2.1) using the reference annotation and library type fr-firststrand; replicates were considered individual samples
expression level of condition: Cuffdiff (from Cufflinks v2.2.1) using reference annotation and library type fr-firststrand; the three replicates combined were considered a sample
Genome_build: Trypanosoma brucei Lister 427 (v9.0 from TriTrypDB.org)
Supplementary_files_format_and_content: Column 1=gene: Gene name, as identified by the T. bruce Lister427 annotation
Supplementary_files_format_and_content: Column 2=locus: chromosome with start and stop positions for the gene
Supplementary_files_format_and_content: Column 3=replicate_FPKM: Cuffnorm estimated FPKM value for the specific replicate.  FPKM stands for fragments per kilobases per million reads and is used to determine a geneâs expression level
Supplementary_files_format_and_content: Column 4=condition_FPKM: Cuffdiff estimated FPKM value for the condition (WT vs H3VKO, with or without DMOG) estimated by combining data from replicates .  FPKM stands for fragments per kilobases per million reads and is used to determine a geneâs expression level

organism: Trypanosoma brucei

source_name: H3VKO parasite

growth_protocol: Bloodstream form T. brucei cells were grown as described in Hirumi et al. (1980).  Parasitology 80, 371–382.

extract_protocol:
Total RNA was isolated from log phase T. brucei cultures using Trizol, according to the manufacturer’s instructions. 5x107 cells were used for each prep.
RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity.

treatment_protocol: DMOG treatment of cells was performed by supplementing media with 1mM DMOG for 5 days in T. brucei

tag: strain, lifestage

value: 221a of strain 427

tag: lifestage

value: bloodstream form

tag: genotype

value: H3V KO


title: Sample 47

source_name: L10L_4 wks old_infected bird_spleen

value: 4 weeks old (1 wk post infection)


title: T. brucei H3V-KO rep 3


title: T. brucei H3V-KO + DMOG rep 1


title: Sample 48


title: Sample 44


title: T. brucei H3V-KO + DMOG rep 2


title: Sample 43


title: Sample 41


title: T. brucei H3V-KO rep 2


title: T. brucei H3V-KO rep 1


title: Sample 40

source_name: L10L_4 wks old_uninfected bird_spleen


title: T. brucei WT + DMOG rep 3

source_name: WT parasite

value: wild type


title: Sample 38


title: T. brucei WT + DMOG rep 2


title: Sample 37


title: Sample 36


title: T. brucei WT + DMOG rep 1


title: Sample 35


title: Sample 33


title: T. brucei WT rep 3


title: Sample 32

source_name: L10H_6 wks old_infected bird_spleen

value: high serum concentration of mannose-binding lectin (MBL)

tag: infected with

value: infectious bronchitis virus (IBV) at age of 3 wks


title: T. brucei WT rep 2


title: Sample 28


title: Sample 45


title: Sample 29


title: Sample 42


title: Sample 26


title: Sample 27


title: T. brucei WT rep 1


title: Sample 39


title: Sample 24

source_name: L10H_6 wks old_uninfected bird_spleen

value: none (uninfected control)


title: para-carcinoma nasal tissues from goat 2

city: Yaan

first: Yan

middle: Qi

last: gui

address: Xin kang road no.48

department: College of Veterinary Medicine

institute: Sichuan Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to capra hircus whole genome using bowtie v0.12.2 with parameters -q -p 4 -n 1-e 100--best --strata
Number of reads mapping to each kown and novel predicted miRNA was counted and TPM (numbers of each miRNA matched to total reads)/number total reads(M)) was calculated.

organism: Capra hircus

source_name: nose

extract_protocol:
tumor tissue or para-carcinoma tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.The 18-30nt fraction of total RNA was excised and purified following 155 Tris-Borate-EDTA denaturing polyacrylamide gel electrophoresis.Before RT-PCR, 5'adaptor and 3'adptor were respectively ligated using T4 RNAligase.Finally,  Illumina TruSeq SmallRNA Sample Prep Kit Set D(Cat#RS-200-0048) was used for the construction of sequencing libraries.
SmallRNA libraries were prepared for sequencing using standard Illumina protocols

value: Nanjiang yellow goat

tag: tissues

value: nose

tag: tissues status

value: para-carcinoma tissues


title: Sample 21


title: para-carcinoma nasal tissuesfrom goat 3


title: enzootic nasal adenocarcinoma from goat 3

value: tumor tissue


title: Sample 22


title: Sample 34


title: enzootic nasal adenocarcinoma from goat 2

value: tumor tissues


title: Sample 20


title: Sample 19


title: Sample 17


title: Sample 18


title: para-carcinoma nasal tissues from goat 1


title: enzootic nasal adenocarcinoma from goat 1


title: Sample 31


title: Sample 16

source_name: L10H_4 wks old_infected bird_spleen


title: Sample 30


title: Sample 15