title: RNAseq_Day_7_1

first: Aarthi

last: Ramakrishnan

state: New York

department: Neuroscience

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIPseq: For H3K4me3, H3K4me3Q5ser and Taf3 ChIP-seq in RN46A-B14 cells, raw sequencing reads were aligned to the rat genome (rn6) using default settings of Bowtiev2.2.0. Only uniquely mapped reads were retained. Alignments were filtered using SAMtoolsv0.1.19 to remove duplicated reads. Peak-calling–normalized to respective inputs–was performed using MACSv2.1.150 with default settings and filtered for FDR < 0.05 and fold change > 1.2; the window size was set as 300 bp.  Raw sequencing reads from mouse brains (H3K4me3 vs. H3K4me3Q5ser) were aligned to the mouse genome (mm10) using default settings of HISATv0.1.6b. Only uniquely mapped reads were retained. Alignments were filtered using SAMtoolsv0.1.19 to remove duplicate reads, and peak-calling–normalized to respective inputs–was performed using MACSv2.1.1 with default settings and filtered for FDR < 0.05 and fold change > 1.2. Raw sequencing reads from human PSCs vs. ¬5-HT neurons (H3K4me3Q5ser) were aligned to the human genome (hg38) using default settings of HISAT2v2.1.0. Again, only uniquely mapped reads were retained. Alignments were filtered using SAMtoolsv1.8 to remove duplicated reads, and peak-calling–normalized to respective inputs–was performed using MACSv2.1.1 with default settings and filtered for FDR < 0.05 and fold change > 1.2.
RNAseq: Raw sequencing reads from RN46A-B14 cells were mapped to rn6 using TopHat2v2.1.051. Counts of reads mapping to genes were obtained using HTSeq-count against Ensembl v81 annotation. Differential expression analysis was done using the DESeq2 package52 (v1.6.3) at an FDR cutoff of 0.05. Raw RNA-seq reads obtained from mouse brains were mapped to mm10 using HISAT v0.1.6b. StringTie v1.2.1 was used to obtain gene-level FPKM values against Ensembl v84. Raw RNA-seq reads obtained from human cells were mapped to the human genome (hg38) using HISAT2v2.1.0. Counts of reads mapping to genes were obtained using HTSeq-count against Ensembl v90 annotation. Differential expression analysis was done using the DESeq2 package (v1.6.3), again with a FDR<0.05 cutoff.
Genome_build: rn6, mm10, hg38
Supplementary_files_format_and_content: Peaks called using MACS and annotated using region_analysis in tab delimited text file. Counts in tab delimited text files generated using HTSeq-count against Ensembl v81 annotation; Tab delimited text files include gene level FPKM values for each sample obtained using StringTiev1.2.1 against Ensembl v84 annotation

source_name: Serotonergic cells

growth_protocol: For RN46A-B14 cell differentiation, a modified version of published protocols was used. Briefly, RN46A-B14 cells were cultured and maintained in DMEM with 10% FBS, 1% Pen/Strep and 250 ug/ml Geneticin at 33°C with 5% CO2 on 10 cm cell culture dishes. The day before differentiation, cell culture dishes were coated with 6 ml of a matrigel/DMEM mixture for 1 hr at RT. After matrigel polymerization, 0.7-0.8 x 10^6 cells were seeded onto each plate with 10 ml regular growth media. Plates were then incubated at 33°C overnight allowing the cells to adhere to the plate. On the day of differentiation, regular growth media was removed from plates and 10 ml of differentiation media (1% Pen/Strep, 1% B-27 supplement, 0.1% Insulin, 0.1% apotransferrin, 0.1% putrescine, in B16 Base media) was added to each plate. Cells were then incubated at 39°C with 5% CO2, 95% humidity for three days. On the fourth day, differentiation media was changed conditionally at a 1:1 ratio. Differentiated RN46A-B14 cells were collected on the sixth day with 0.05% trypsin by centrifugation, washed several times and then reconstituted in DPBS on ice. Induced pluripotent stem cells were derived from human fibroblasts and cultured on Matrigel-coated plastic plates using a modified recipe of mTeSR1 medium (Stemcell Technologies). Briefly, hPSCs were maintained as colonies and passaged by mechanical and enzymatic dissociation (Dispase). Cells were cultured for 1 week with daily media changes prior to harvesting. Serotonergic neurons were generated using a modified version of a previously described method24. Briefly, floating embyroid bodies (EBs) were generated by mechanical and enzymatic (collagenase) dissociation of hPSC colonies. EBs were cultured for one week with DMEM/F12-Glutamax:Neurobasal (1:1) including: N2, B27 supplements, 1x non essential amino acids, SB431542 (2 μM), DMH-1 (2 μM) and CHIR99021 (1.4µM) (Serotonergic medium). EBs were plated onto to poly-ornithine/laminin (Sigma)-coated plastic plates in Serotonergic medium with the addition of Sonic hedgehog protein (Shh, 500 ng/ml) for another week. Rosette-forming EBs and derived neural precursor cells were selected and cultured as monolayers in Serotonergic medium containing Shh (500 ng/ml) and FGF-4 (10 ng/ml), and were then maintained at high densities. Serotonergic neurons were derived by culturing for an additional 3 weeks at lower densities in serotonergic differentiation medium comprised of a base of Neurobasal medium containing GDNF (10 ng/ml), BDNF (10 ng/ml) (Peprotech), dibutyrl-cyclicAMP (1 mM, Sigma), ascorbic acid (200 nM, Sigma), laminin (1 μg/ml), DAPT (2.5 µM) and TGF-beta3 (1 ng/ml). Medium was changed every other day for 3 weeks before cells were harvested for further processing. All protocols were performed in accordance with the Salk Institute’s IRB.

extract_protocol:
Cell pellets (>10 x 10^6/n) and brain tissues were crosslinked and quenched. Samples were washed thoroughly before being subjected to lysis and sonication. Samples were then incubated with specific antibodies (7.5 μg/sample) bound to M-280 Dynabeads on a rotator at 4°C overnight. The following day, immunoprecipitates were washed, eluted and reverse crosslinked. Following RNA and protein digestion, DNA fragments were purified using a Qiagen PCR purification kit.
RNA and ChIP libraries were prepared for sequencing using standard Illumina protocols

tag: cell/region

value: RN46A-B14 cells

tag: chip antibody

tag: differentiation status

value: Differentiated


title: RNAseq_Day_0_3

status: Public on Dec 18 2018

type: SRA

city: New York

address: 1425 Madison Avenue

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

molecule: total RNA

organism: Rattus norvegicus

value: Undifferentiated


title: RNAseq_Day_7_2


title: RNAseq_Day_7_3


title: RNAseq_Day_0_2


title: Fibroblast Non_CD sample 29 from patient 15

status: Public on Dec 19 2018

city: Amsterdam

first: Peter

last: Henneman

state: Noord Holland

address: Meibergdreef 9

department: Clinical Genetics

country: Netherlands

institute: Academic Medical Center Amsterdam

data_processing:
Sequenced checked for quality using FastQC (v1.10.1) after which reads were mapped to hg19 whole genome using STAR v2.5 at default settings and converted into binary files using SAMtools (v1.2)
Binary files were imported in R (v3.3.2) after which the reads were counted and annotated according to the Ensembl Gene ID using GenomicAlignments (v1.10)
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated text files including raw counts per sample

organism: Homo sapiens

source_name: patient 15

growth_protocol: After 24 hours of culturing, fibroblast cells were adhered to the culture plates and the RPMI medium was refreshed to wash away debris, dead cells and non-adherent cells. After cells reached a minimum of 80% confluency, they were washed with HBSS (Lonza BioWhittaker, Switzerland) and then detached from the culture plates through a ten-minute trypsin wash (10x diluted in HBSS) at 37°C. The fibroblasts were then first plated in T25 flasks after which samples in later passages were transferred to T75 flasks (VWR, Pennsylvania, USA; Tissue Culture Flasks 25 cm2 & 75 cm2) to allow for further expansion. During passages 1 through 5, cells have been harvested for downstream DNA and RNA analysis. For RNA isolation were stored in RNAlater (Thermo Fisher Scientific, Waltham, Massachusetts, USA) at 4°C overnight after which the samples were transferred to -80°C as per manufacturer’s protocol.

extract_protocol:
RNA was isolated from the fibroblasts using the RNAeasy mini kit (Qiagen)
The NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs) was used for mRNA isolation, cDNA generation and sequencing adapter ligation.  Performed on an Illumina NextSeq500 at a coverage of 10M reads per sample. The preparation and sequencing of the RNA was performed at GenomeScan B.V. in Leiden, the Netherlands.

treatment_protocol: Mucosal samples were thoroughly washed in repeated cycles of ice-cold phosphate buffered saline (PBS) supplemented with 1% penicillin/streptomycin and 40 μg/mlL G418 (PGA). The mucosa was then finely cut and placed in full-grown RMPI 1640 culture medium (Invitrogen) supplemented with 1.5 mg/mL collagenase A (Roche, Germany) and minced using the Gentlemacs Dissociator (Miltenyi Biotec, Leiden, the Netherlands). After 60 minutes of incubation at 37 °C, the Gentlemacs Dissociator was used a second time for further dissociation. Cells were transferred to tubes and washed extensively with PGA after which the cells were plated and cultured at 37°C in RMPI 1640 with 10% FCS, 1% penicillin/streptomycin, 1% L-glutamin, G418 (40 μg/mlL; Lonza, Leusden, the Netherlands) and amphotericin B (0.025 μg/mL; Gibco, Rockford, IL).

tag: gender

value: F

tag: disease state

value: Non_Crohn’s disease

tag: disease stage

tag: montreal score

tag: age

tag: passage

tag: sampleID

tag: thiopurine usage

value: No

tag: atnf usage

tag: cell type

value: ileal fibroblast


title: RNAseq_Day_0_1


title: ChIPseq_H3K4me3Q5ser_Day_7_2

library_source: genomic

molecule: genomic DNA

value: H3K4me3Q5ser (Millipore 4491a; Lot#RA1608107)


title: ChIPseq_H3K4me3Q5ser_Day_7_3


title: Fibroblast NINF sample 19 from patient 11

source_name: patient 11

value: Crohn’s disease

value: non-inflamed

value: Yes


title: ChIPseq_H3K4me3Q5ser_Day_0_1


title: ChIPseq_H3K4me3Q5ser_Day_0_3


title: ChIPseq_H3K4me3_Day_7_3


title: ChIPseq_H3K4me3_Day_7_2


title: ChIPseq_H3K4me3_Day_0_3


title: S433WT3Gut

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
Sequence reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped read pairs (fragments) were retained.
Genewise counts were obtained using featureCounts. Fragments overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped fragments) value of 1 or greater in at least two libraries. The Ig genes, pseudo genes, gene models, genes not on the primary assemblies of the chromosomes, genes not having official symbols and ribosomal RNA genes were also removed from the analysis.
Counts were converted to log2 counts per thousand bases per million fragments (log2 FPKM), quantile normalized and precision weighted with the ‘voom’ function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.1 (adjusted globally) or less and had an expression change of two folds or greater.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file 'Supp_Raw_Counts.txt' includes raw read counts for genes in each library.

organism: Mus musculus

source_name: WT_Gut Rep3

growth_protocol: Treg cells were sorted as CD4+ TCRb+ YFP+ cells from gut or spleen

extract_protocol:
RNA purification was performed following the manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

tag: strain

tag: tissue

value: gut (colon plus small intestine)

value: Treg

tag: genotype

value: WT (Foxp3Cre-YFP)


title: ChIPseq_H3K4me3_Day_0_2


title: ChIPseq_Input_Day_7_3

value: Input


title: ChIPseq_H3K4me3_Day_0_1


title: ChIPseq_H3K4me3_Day_7_1


title: ChIPseq_Input_Day_0_3


title: Muscle FED ZT20 Replicate 5

city: Irvine

first: Christophe

middle: Nicolas

last: Magnan

state: CA

address: Institute for Genomics and Bioinformatics 236, Info & Computer Science Building 2

institute: University of California, Irvine

description:
RNAseq_expression_results.xlsx
EISA_exonic_expression_results.xlsx
EISA_intronic_expression_results.xlsx

data_processing:
Basecalling performed using RTA version 1.18.64
Demultiplexing performed using CASAVA version 1.8.2
Alignment to reference assembly mm10 and known splice junctions extracted from the RefSeq database performed using ELAND v2e (Illumina)
Mapping results filtering performed using in-house tools
Read counting for each gene and normalization to RPKM values performed using in-house tools
Exon Intron Split Analysis (EISA) implemented in-house following the protocol reported in Gaidatzis et al., Nat. Biotech., 2015
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression results (RPKM values) of the standard RNAseq analysis are reported in the Excel file RNAseq_expression_results.xlsx for all 72 replicates. Exonic and intronic expression results (RPKM values) resulting from the EISA analysis described in Gaidatzis et al., Nat. Biotech., 2015, are reported in the Excel files EISA_exonic_expression_results.xlsx and EISA_intronic_expression_results.xlsx respectively for all 72 replicates.

source_name: Gastrocnemius Muscle

extract_protocol:
Total RNA was extracted from liver and skeletal muscle with TRIzol (Invitrogen), followed by precipitation with isopropanol and ethanol.
RNA libraries for each group were prepared as described in the TruSeq RNA Sample Preparation v2 Guide (Illumina).

value: 8 weeks

tag: timepoint/condition

value: ZT20 ad libitum normal chow feeding


title: ChIPseq_Input_Day_0_2

tag: cell/region

value: RN46A-B14 cells


title: ChIPseq_Input_Day_0_1

tag: chip antibody


title: Muscle FED ZT20 Replicate 2


title: Muscle FED ZT16 Replicate 1

value: ZT16 ad libitum normal chow feeding


title: Muscle FED ZT12 Replicate 5

value: ZT12 ad libitum normal chow feeding


title: Muscle FED ZT16 Replicate 4


title: Muscle FED ZT12 Replicate 1


title: Muscle FED ZT16 Replicate 5


title: Muscle FED ZT20 Replicate 1


title: Muscle FED ZT12 Replicate 3


title: 6w.M.HF6

city: Seongnam-si

first: Nayoung

last: Kim

state: Gyeonggi-do

address: 82 Gumi-ro, 173 Beon-gil, Bundang-gu

department: Department of Internal Medicine

country: South Korea

institute: Seoul National University Bundang Hospital

data_processing:
Assembly Program: FLASH (Fast Length Adjustment of SHort reads) (1.2.11).
Pre-processing & clustering by CD-HIT-OTU. Short reads were filtered out and extra long tails were trimmed. Filtered reads were clustered at 100% identity using CD-HIT-DUP. Chimeric reads were identified. Secondary clusters were recruited into primary clusters. Noise sequences in clusters of size below 3 were removed. Remaining representative reads from non-chimeric clusters were clustered using a greedy algorithm into OTUs at a user-specified OTU cutoff (97% ID at species level).
Taxonomic assignment by QIIME.  Representative sequences were used from each OTU to assign taxonomy. Phylogenetic trees were contructed from aligned and filtered representative sequences of OTUs. Publication-quality graphic results were produced through statistical analysis and visualization.
Diversity analysis by QIIME. Alpha and beta diversity were analyzed by QIIME.
Genome_build: RDP release11 and NCBI 16S
Supplementary_files_format_and_content: tab-delimited text files include ‘microbial phylotypes classification’ for each sample

organism: rat gut metagenome

growth_protocol: Specific-pathogen-free male and female Fisher-344 rats (6-weeks and 2-years old) were used (Orient, Seoul, Korea). The rats were bred under a specific-pathogen-free condition, at 23℃ and a 12:12-hour light-dark cycles. They were provided with unrestricted access to food and water. This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of South Korea.

extract_protocol:
Stool samples were collected and subjected to bacterial genomic DNA (gDNA) extraction using a QIAamp stool DNA extraction kits (Qiagen) following the manufacturer’s protocol.
PCR amplification was performed using primers targeting the V3 to V4 regions of the 16S rRNA gene with extracted DNA. For bacterial amplification, barcoded primer of 341F (5’-TCGTCGGCAGCGTC-AGATGTGTATAAGAGACAG-CCTACGGGNGGCWGCAG-3’; underlined sequence indicates the target region primer) and 805R (5’-GTCTCGTGGGCTCGG-AGATGTGTATAAGAGACAG-GACTACHVGGGTATCTAATCC-3’; underlined sequence indicates the target region primer).
Pyrosequencing (Illumina Miseq system; Macrogen, Inc., Seoul, Korea)

treatment_protocol: Rats were divided into groups that were given different commercial diets: control diets and high fat diets. Rats in high-fat diet group were ad libitum fed with high fat diets comprising 60 % kcal from fat (Research Diets, Inc., NJ, USA) for 8 weeks.

value: Fisher 344

value: 6 weeks

tag: Sex

value: male

tag: diet

value: high fat (HF)

value: stool

tag: molecule subtype

value: microbial DNA


title: ChIPseq_H3K4me3Q5ser_Day_7_1

value: H3K4me3Q5ser (Millipore 4491a; Lot#RA1608107)

tag: differentiation status

value: Differentiated


title: Muscle FED ZT08 Replicate 5

value: ZT08 ad libitum normal chow feeding


title: ChIPseq_H3K4me3Q5ser_Day_0_2

value: Undifferentiated


title: 6w.M.HF3


title: 6w.M.HF5


title: 6w.M.HF1


title: 6w.M.HF4


title: ChIPseq_Input_Day_7_1


title: 6w.M.HF2


title: Muscle FED ZT08 Replicate 3


title: 6w.M.C3

value: control chow


title: 6w.M.C2


title: Muscle FED ZT04 Replicate 3

value: ZT04 ad libitum normal chow feeding


title: 6w.M.C6


title: Muscle FED ZT08 Replicate 2

value: 8 weeks


title: 6w.M.C1


title: 6w.F.HF6

value: female


title: 6w.M.C5


title: 6w.M.C4


title: Muscle FED ZT04 Replicate 1


title: Muscle FED ZT04 Replicate 5


title: 6w.F.HF5


title: Muscle FED ZT00 Replicate 3

value: ZT00 ad libitum normal chow feeding


title: 6w.F.C6


title: 6w.F.HF1


title: 6w.F.HF2


title: Muscle FED ZT00 Replicate 5


title: 6w.F.C5


title: Muscle FAST ZT20 Replicate 5

value: ZT20 after 24-hr fasting


title: 6w.F.HF4


title: 6w.F.HF3


title: Muscle FAST ZT20 Replicate 1


title: Muscle FED ZT00 Replicate 4


title: 2yr.M.HF5

value: 2 years


title: 6w.F.C2

value: Fisher 344


title: 2yr.M.HF3


title: 2yr.M.C5


title: 2yr.M.HF1


title: 6w.F.C4

value: 6 weeks


title: 2yr.M.HF2

value: male


title: 2yr.M.C4


title: Muscle FAST ZT16 Replicate 1

value: ZT16 after 24-hr fasting


title: 6w.F.C3

value: stool


title: Muscle FAST ZT20 Replicate 2


title: ChIPseq_Input_Day_7_2

value: RN46A-B14 cells

value: Input


title: Muscle FAST ZT16 Replicate 5


title: Muscle FAST ZT16 Replicate 2


title: Muscle FAST ZT12 Replicate 5

value: ZT12 after 24-hr fasting


title: 2yr.M.C3

value: microbial DNA


title: Muscle FAST ZT12 Replicate 2


title: 2yr.M.C2


title: 2yr.F.HF4

value: high fat (HF)


title: 2yr.M.C1

value: control chow


title: 2yr.F.HF3


title: 2yr.F.HF2


title: Muscle FAST ZT08 Replicate 5

value: ZT08 after 24-hr fasting


title: 6w.F.C1


title: 2yr.F.HF5


title: Muscle FAST ZT08 Replicate 3

value: 8 weeks


title: 2yr.F.C1

value: female


title: Muscle FAST ZT04 Replicate 5

value: ZT04 after 24-hr fasting


title: Muscle FAST ZT12 Replicate 3


title: 2yr.F.C5


title: 2yr.F.C3


title: Muscle FAST ZT04 Replicate 4


title: Muscle FAST ZT04 Replicate 2


title: Muscle FAST ZT00 Replicate 3

value: ZT00 after 24-hr fasting


title: Muscle FAST ZT00 Replicate 1


title: 2yr.F.C2

value: 2 years


title: Liver FED ZT20 Replicate 5

source_name: Liver

value: ZT20 ad libitum normal chow feeding


title: Muscle FAST ZT00 Replicate 5


title: Muscle FAST ZT08 Replicate 4


title: 2yr.F.C4

value: Fisher 344


title: Liver FED ZT20 Replicate 4


title: Liver FED ZT20 Replicate 1


title: Liver FED ZT16 Replicate 3

value: ZT16 ad libitum normal chow feeding


title: 2yr.F.HF1


title: Liver FED ZT12 Replicate 3

value: ZT12 ad libitum normal chow feeding


title: Liver FED ZT08 Replicate 3

value: ZT08 ad libitum normal chow feeding


title: Liver FED ZT12 Replicate 4


title: Liver FED ZT04 Replicate 4

value: ZT04 ad libitum normal chow feeding


title: Liver FED ZT08 Replicate 5


title: Liver FED ZT00 Replicate 3

value: ZT00 ad libitum normal chow feeding


title: Liver FED ZT16 Replicate 1


title: Liver FED ZT04 Replicate 5


title: Liver FAST ZT20 Replicate 4

value: ZT20 after 24-hr fasting


title: Liver FED ZT08 Replicate 1


title: Liver FED ZT12 Replicate 5


title: Liver FED ZT04 Replicate 2


title: Liver FAST ZT12 Replicate 4

value: ZT12 after 24-hr fasting


title: Liver FAST ZT16 Replicate 5

value: ZT16 after 24-hr fasting


title: Liver FAST ZT16 Replicate 3


title: Liver FED ZT00 Replicate 1


title: Liver FAST ZT20 Replicate 5


title: Liver FAST ZT04 Replicate 4


title: Liver FED ZT16 Replicate 2


title: Liver FAST ZT12 Replicate 5


title: Liver FED ZT00 Replicate 5


title: Liver FAST ZT20 Replicate 1


title: Liver FAST ZT08 Replicate 3


title: Liver FAST ZT16 Replicate 4


title: Liver FAST ZT04 Replicate 3


title: Liver FAST ZT12 Replicate 2


title: Liver FAST ZT08 Replicate 1


title: Liver FAST ZT00 Replicate 4


title: Liver FAST ZT00 Replicate 5


title: 5456_NAcc_neg (ATAC-Seq)

status: Public on Dec 17 2018

city: Baltimore

first: Andrew

middle: P.

last: Feinberg

state: MD

address: 855 N. Wolfe St

institute: Johns Hopkins University School of Medicine

data_processing:
We trimmed reads of their adapter sequences using trimadap (v0.1) with the following parameters: trimadap-mt -3 CTGTCTCTTATACACATCTCCGAGCCCACGAGA ${READ1}; trimadap-mt -3 CTGTCTCTTATACACATCTGACGCTGCCGACGA ${READ2}. We then aligned these trimmed reads to the hg19 build of the human genome (including autosomes, sex chromosomes, mitochondrial sequence, unplaced sequence, and unlocalized sequence) using Bowtie214 (v2.2.5) with alignment parameters: bowtie2 -X 2000 --local --dovetail. Potential PCR duplicate reads were marked using MarkDuplicates from the Picard library (v2.2.1).
Peaks were called using MACS (v2.1.0) on a metasample formed by combining all non-duplicate-marked reads with a mapping quality > 30 from the 22 samples: macs2 callpeaks --nomodel --nolambda --call-summits -t ${BAMS[@]}. We excluded those peaks overlapping the ENCODE mappability consensus blacklist regions (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) and the blacklist for ATAC-seq created by Buenrostro et al. (https://sites.google.com/site/atacseqpublic/atac-seq-analysis-methods/mitochondrialblacklists-1). We extended +/- 250 bp from the summit of peak and merged overlapping peaks to form our initial set of peaks.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: Matrix of read count data for each genome location for all samples.

source_name: NeuN negative nuclei sorted from nucleus accumbens (NAcc)

extract_protocol: Nextera DNA library prep kit (cat #:FC-121-1031, Illumina)

treatment_protocol: ATAC-seq was performed as described in Buenrostro et al. 2015 using 100,000 neuronal and non-neuronal nuclei isolated from nucleus accumbens and prefrontal cortex (BA9) tissues (for samples with "_pos" or "_neg" at end of sample ID) and sorted via FACS based on NeuN staining as in Montano et al. 2013.

value: NeuN neg

value: nucleus accumbens (NAcc)

tag: individual id


title: 5540_BA9_neg (ATAC-Seq)

source_name: NeuN negative nuclei sorted from prefrontal cortex (BA9)

value: prefrontal cortex (BA9)


title: 5343_BA9_neg (ATAC-Seq)


title: 5343_NAcc_pos (ATAC-Seq)

source_name: NeuN positive nuclei sorted from nucleus accumbens (NAcc)

value: NeuN pos


title: Liver FAST ZT00 Replicate 1

tag: age

value: 8 weeks


title: Liver FAST ZT08 Replicate 2

value: ZT08 after 24-hr fasting


title: 5404_BA9_pos (ATAC-Seq)

source_name: NeuN positive nuclei sorted from prefrontal cortex (BA9)


title: 5347_BA9_pos (ATAC-Seq)


title: 5347_NAcc_pos (ATAC-Seq)


title: 5358_NAcc_pos (ATAC-Seq)


title: 5540_NAcc_neg (ATAC-Seq)


title: 5540_NAcc_pos (ATAC-Seq)


title: 5456_BA9_pos (ATAC-Seq)


title: 5404_BA9_neg (ATAC-Seq)


title: 5456_BA9_neg (ATAC-Seq)


title: 5358_NAcc_neg (ATAC-Seq)


title: 5358_BA9_neg (ATAC-Seq)


title: 5343_BA9_pos (ATAC-Seq)


title: 5540_BA9_pos (ATAC-Seq)


title: Liver FAST ZT04 Replicate 1

value: ZT04 after 24-hr fasting


title: 5347_NAcc_neg (RNA-Seq)

data_processing:
We trimmed the first 3 bp of read1, which were derived from template switching oligos and not the cDNA of interest, using seqtk (https://github.com/lh3/seqtk; v1.2-r94) with the following parameters: seqtk trimfq -b 3 ${READ1}. We then quasi-mapped these trimmed reads to a FASTA file of protein-coding and lncRNA genes from GENCODE v19 (http://www.gencodegenes.org/releases/19.html) and performed transcript-level quantification using Salmon (v0.7.2).
We used tximport (v1.2.0) to compute normalized gene-level counts from the transcript-level abundance estimates (scaling these using the average transcript length over samples and the library size). Only autosomal genes with at least 1 cpm in at least 4 libraries (the size of the smallest group of samples) were retained for downstream analysis.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: Matrix of gene-level read counts for each gene from all samples.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini kit (cat#: 74104 )
SMARTer Stranded Total RNA-Seq Kit – Pico Input Mammalian

treatment_protocol: RNA was extracted from neuronal and non-neuronal nuclei isolated from nucleus accumbens or prefrontal cortex (BA9) tissues (for samples with "_pos" or "_neg" at end of sample ID) and sorted via FACS based on NeuN staining as in Montano et al. 2013.


title: 5347_BA9_pos (RNA-Seq)


title: 5404_BA9_pos (RNA-Seq)


title: 5358_BA9_pos (RNA-Seq)


title: 5404_BA9_neg (RNA-Seq)


title: 5343_BA9_neg (RNA-Seq)


title: 5456_BA9_pos (RNA-Seq)


title: 5343_BA9_pos (RNA-Seq)


title: 5347_BA9_neg (ATAC-Seq)


title: 5347_NAcc_pos (RNA-Seq)


title: 5347_BA9_neg (RNA-Seq)


title: 5347_NAcc_neg (ATAC-Seq)


title: 5343_NAcc_neg (RNA-Seq)


title: 5343_NAcc_neg (ATAC-Seq)


title: 5358_NAcc_pos (RNA-Seq)


title: 5343_NAcc_pos (RNA-Seq)


title: ChIP_LM3_H3K36me3 Rep2

city: Shanghai

first: Jin

last: Li

state: Shanghai

address: 130 Dong-An Road

department: Institutes of Biomedical Sciences (IBS)

country: China

institute: Fudan University

data_processing:
ChIP-seq: We firstly filtered out low quality reads. The remaining reads were aligned to human reference genome (hg19) with Bowtie (version 1.0.0). The alignment was unique mapping and allowed up to 2 mismatches. Peaks were identified with the MACS (version14) with default parameters and --nomodel
RNA-seq: We firstly filtered out low quality reads. Then mRNA-seq reads were aligned to hg19 with TopHat2 (v2.0.12) with default parameters. The mapped reads were further analyzed by Cufflinks (v2.2.1) with default parameters to call FPKM of genes.
Methylation by GPS: We firstly filtered out low quality reads. Read2 were aligned onto reference genome (hg19) using Bowtie2 (v2.2.3) with default parameters except "-k 20". We used the Smith-Waterman algorithm to map the Read1 to the reference target sequence that is located within 1kb of opposite strand of downstream of the Read2. Cytosines which are covered by no less than 5 reads are used for methylation analysis.
Methylation by WGBS: We firstly filtered out low quality reads. Read1 and Read2 were aligned onto reference genome (hg19) using BSMAP with default parameters except -v 3 -g 1. Cytosines which are covered by no less than 5 reads are used for methylation analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include methylation level/ChIP peak loci/ gene FPKM values for each Sample

source_name: hepatoma cell line

growth_protocol: Cell lines were cultured at 37˚C in 5% CO2 in high-glucose DMEM (Hyclone, USA) supplemented with 10% fetal bovine serum (Hyclone, USA), and collected under standard culture protocols.

extract_protocol:
Methylation: Genomic DNA from tissues and cell lines was extracted using QIAamp DNA Mini Kit (Qiagen, 51306, Valencia, CA). 3μg genomic DNA was fragmented into 300-500bp by sonication. ChIP:Approximate 300 ug fixed chromatin and 5 ug antibody were used for each ChIP pull-down. RNA-seq: We extracted approximate 6 micrograms of total RNA, removed ribosomal RNA (rRNA) according to the manufacturer’s instructions with minor modifications.
Libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: liver

value: H3K4me3 (human, Abcam, ab8580)


title: 5456_NAcc_neg (RNA-Seq)


title: 5456_BA9_neg (RNA-Seq)


title: 5540_NAcc_neg (RNA-Seq)


title: 5628_NAcc (bisulfite-Seq)

data_processing:
WGBS raw sequencing reads were trimmed using Trim Galore! (v0.4.0) and aligned using Bismark (v0.14.3) against human genome version hg19/GRCh37. Bismark's bismark_methylation_extractor was used to call CpG methylation and the output was read into bsseq (v1.10.0) for analysis using the BSmooth method (Hansen et al 2012).
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: The "M" and "Cov" matrices for all sorted and intact tissue samples are provided as text files. "M" matrix contains the number of reads supporting methylation at each CpG for each sample while the "Cov" matrix contains the number of reads covering each CpG for each sample.

source_name: nucleus accumbens (NAcc) tissue

extract_protocol:
Genomic DNA was extracted using the Epicentre MasterPure DNA Purification Kit (cat#: MCD85201)
NEBNext Ultra DNA library Prep kit for Illumina followed by size selection (300-400bp), bisulfite conversion with EZ DNA Methylation-Gold kit (cat#:D5005,Zymo), and amplification using Kapa hifi Uracil+ (cat#:KK282, Kapa Biosystems).

treatment_protocol: DNA was extracted from intact brain tissues or neuronal and non-neuronal nuclei isolated from brain tissues (for samples with "_pos" or "_neg" at end of sample ID) and sorted via FACS based on NeuN staining as in Montano et al. 2013.

value: bulk tissue


title: 5540_BA9_neg (RNA-Seq)


title: ChIP_LM3_H3K4me3 Rep2

value: H3K36me3 (human, Abcam, ab9050)


title: 5628_BA24 (bisulfite-Seq)

source_name: anterior cingulate cortex (BA24) tissue

value: anterior cingulate cortex (BA24)


title: ChIP_97L_H3K27ac Rep2

value: H3K27Ac (human, Abcam, ab4729)


title: 5569_HC (bisulfite-Seq)

source_name: hippocampus (HC) tissue

value: hippocampus (HC)


title: RNA_97L Rep2


title: ChIP_LM3_H3K27ac Rep2


title: 5570_BA24 (bisulfite-Seq)


title: 5552_HC (bisulfite-Seq)


title: 5552_BA24 (bisulfite-Seq)


title: 5552_BA9 (bisulfite-Seq)

source_name: prefrontal cortex (BA9) tissue


title: 5540_BA9 (bisulfite-Seq)


title: 5570_HC (bisulfite-Seq)


title: ChIP_97L_H3K4me3 Rep2


title: 5628_HC (bisulfite-Seq)


title: 5456_NAcc_pos (RNA-Seq)


title: 5540_BA9_pos (RNA-Seq)


title: ChIP_97L_H3K36me3 Rep2


title: 5404_NAcc (bisulfite-Seq)


title: 5570_BA9 (bisulfite-Seq)


title: 5358_BA9 (bisulfite-Seq)


title: 5284_HC (bisulfite-Seq)


title: 5250_BA9 (bisulfite-Seq)


title: 5569_BA9 (bisulfite-Seq)


title: 5248_BA9 (bisulfite-Seq)


title: 5404_BA24 (bisulfite-Seq)


title: 5628_BA9 (bisulfite-Seq)


title: 5358_NAcc (bisulfite-Seq)


title: 5284_NAcc (bisulfite-Seq)


title: 5628_NAcc_neg (bisulfite-Seq)


title: 5628_HC_pos (bisulfite-Seq)

source_name: NeuN positive nuclei sorted from hippocampus (HC)


title: 5250_NAcc (bisulfite-Seq)


title: 5086_NAcc (bisulfite-Seq)


title: 5628_HC_neg (bisulfite-Seq)

source_name: NeuN negative nuclei sorted from hippocampus (HC)


title: 5628_BA24_pos (bisulfite-Seq)

source_name: NeuN positive nuclei sorted from anterior cingulate cortex (BA24)


title: 5628_BA24_neg (bisulfite-Seq)

source_name: NeuN negative nuclei sorted from anterior cingulate cortex (BA24)


title: 5570_NAcc_pos (bisulfite-Seq)


title: 5570_HC_pos (bisulfite-Seq)


title: 5570_NAcc_neg (bisulfite-Seq)


title: 5248_HC (bisulfite-Seq)


title: 5250_BA24 (bisulfite-Seq)


title: 5628_NAcc_pos (bisulfite-Seq)


title: 5085_NAcc (bisulfite-Seq)


title: 5570_BA24_pos (bisulfite-Seq)


title: 5569_NAcc_neg (bisulfite-Seq)


title: 5628_BA9_pos (bisulfite-Seq)


title: 5086_BA9 (bisulfite-Seq)


title: 5569_HC_pos (bisulfite-Seq)


title: 5570_HC_neg (bisulfite-Seq)


title: 5628_BA9_neg (bisulfite-Seq)


title: 5552_HC_pos (bisulfite-Seq)


title: 5570_BA9_pos (bisulfite-Seq)


title: 5552_NAcc_pos (bisulfite-Seq)


title: 5552_HC_neg (bisulfite-Seq)


title: 5569_BA9_neg (bisulfite-Seq)


title: 5552_BA24_neg (bisulfite-Seq)


title: 5569_NAcc_pos (bisulfite-Seq)


title: 5569_BA9_pos (bisulfite-Seq)


title: 5540_NAcc_pos (RNA-Seq)


title: 5284_BA24_pos (bisulfite-Seq)


title: 5248_NAcc_pos (bisulfite-Seq)


title: 5569_BA24_pos (bisulfite-Seq)


title: 5248_NAcc_neg (bisulfite-Seq)


title: 5552_BA9_pos (bisulfite-Seq)


title: 5552_BA9_neg (bisulfite-Seq)


title: 5284_NAcc_pos (bisulfite-Seq)


title: 5284_HC_pos (bisulfite-Seq)


title: 5570_BA9_neg (bisulfite-Seq)


title: 5284_BA9_neg (bisulfite-Seq)


title: 5248_BA9_neg (bisulfite-Seq)


title: 5248_HC_pos (bisulfite-Seq)


title: 5248_BA24_neg (bisulfite-Seq)


title: 5284_HC_neg (bisulfite-Seq)


title: 5569_HC_neg (bisulfite-Seq)


title: 5552_NAcc_neg (bisulfite-Seq)


title: 5248_HC_neg (bisulfite-Seq)


title: 5569_BA24_neg (bisulfite-Seq)


title: 5248_BA9_pos (bisulfite-Seq)


title: RNA_Liver

data_processing:
ChIP-seq: We firstly filtered out low quality reads. The remaining reads were aligned to human reference genome (hg19) with Bowtie (version 1.0.0). The alignment was unique mapping and allowed up to 2 mismatches. Peaks were identified with the MACS (version14) with default parameters and --nomodel
RNA-seq: We firstly filtered out low quality reads. Then mRNA-seq reads were aligned to hg19 with TopHat2 (v2.0.12) with default parameters. The mapped reads were further analyzed by Cufflinks (v2.2.1) with default parameters to call FPKM of genes.
Methylation sequencing: We firstly filtered out low quality reads. Read2 were aligned onto reference genome (hg19) using Bowtie2 (v2.2.3) with default parameters except '-k 20'. We used the Smith-Waterman algorithm to map the Read1 to the reference target sequence that is located within 1kb of opposite strand of downstream of the Read2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include methylation level/ChIP peak loci/ gene FPKM values for each Sample

source_name: liver

extract_protocol:
Methylation: Genomic DNA from tissues and cell lines was extracted using QIAamp DNA Mini Kit (Qiagen, 51306, Valencia, CA). 3μg genomic DNA was fragmented into 300-500bp by sonication. ChIP:Approximate 300 ug fixed chromatin and 5 ug antibody were used for each ChIP pull-down. RNA-seq: We extracted approximate 6 micrograms of total RNA, removed ribosomal RNA (rRNA) according to the manufacturer’s instructions with minor modifications.
Libraries were prepared for sequencing using standard Illumina protocols
DNA Methylation sequencing, ChIP-seq and RNA-seq

value: normal liver cells


title: 5248_BA24_pos (bisulfite-Seq)


title: 5284_NAcc_neg (bisulfite-Seq)


title: ChIP_LM3_H3K4me3 Rep1


title: RNA_97L Rep1


title: Hdac7_Th17

status: Public on Dec 16 2018

first: Rajal

last: Sharma

state: NY

address: 1425 Madison Ave., Room 16-52

institute: ISMMS

data_processing:
Basecalls performed using CASAVA version 1.4
Read sequences were filtered by FASTX ( -q 20 -p 90 )
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2
Peaks were called using MACS with Input as control with the following setting: pvalue cutoff (1.00e-05), model fold (10, 30).
Genome_build: mm9
Supplementary_files_format_and_content: Wig files generated by computing feature density over a 5 bp window across the genome. http://genome.ucsc.edu/goldenPath/help/wiggle.html

source_name: primary T cells

growth_protocol: CD4+ T cells were purified from spleen. Naïve T cells were activated with plate bound anti-CD3 and anti-CD28 plus IL6(20ng/mL), TGFb(2.5ng/mL) . The cells were cultured for 48h to 72h before harvesting for further analysis.

extract_protocol:
Whole cell lysates were sonicated and protein-DNA complexes were isolated with antibodies.
ChIP-DNA was end repaired with T4 DNA polymerase and polynucleotide kinase. An A-base was added to the end-repaired DNA fragments. Solexa adaptors were ligated to the ChIP DNA fragments and 200-300bp size fractions were excised from 2% agarose gel stained with GelStar. Adaptor-modified fragments were enriched by 16 cycles of PCR amplification. The DNA library prep was validated in Bioanalyzer for quantity and size.

value: primary T cells

tag: antibody

value: Santa Cruz sc-11421


title: Hdac4_Th17

value: Bethyl A303-467A


title: ChIP_97L_H3K27ac Rep1


title: ChIP_LM3_H3K36me3 Rep1


title: ChIP_LM3_H3K27ac Rep1


title: E.coli wt II

status: Public on Dec 15 2018

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

country: Germany

institute: Helmholtz Centre for Infection Research

data_processing:
library quality assessment using FastQC
alignment vs. reference genome using Bowtie2 (V2.2.3) with default parametrization
read count quantification using htseq-count (http://www.huber.embl.de/users/anders/HTSeq)
Detection of differentially expressed genes using DeSEQ2 with raw count data using a beta prior and disabled Cook distance cutoff filter
Genome_build: E.coli strain E2348/69 (Acc.: chr: FM180568.1, plasmid pE2348-2: FM18070.1, plasmid pMAR2: FM180569.1)
Supplementary_files_format_and_content: htseqcounts*.tab files: CSV format with raw read counts per gene; des2rlog*.tab files: CSV format with DESeq2 rlog transformed read counts per gene; DESeq2_genes_diffexp*.xls: MS Excel files with differentially expressed genes

organism: Escherichia coli

source_name: cell pellet

growth_protocol: Overnight cultures of EPEC strains grown in SOB medium were used to inoculate 150 ml of modified M9 medium (MgSO4 1 mM, CaCl2 0.6 mM, FeSO4*7H2O 12.5 µM, NH4Cl 1 mM, Fe(NO3)3*9H2O, NaCl 100 mM, KCl 5 mM, NaH2PO4*H2O 1 mM, Na2HPO4  33 mM, KH2PO4 22 mM) supplemented with 0.2 % glucose (w/v) and 0.05 % (w/v) casamino acids at a start OD600 of 0.05. Bacterial cells were grown until an OD600 of 1 was reached at 37°C, 160 rpm.

extract_protocol:
Total RNA was isolated from bacterial cell pellet.
QC of total RNAs. Isolation of mRNA using Ribo-Zero Removal Kits (Bacteria). Library preparation from the isolated mRNA using ScriptSeq v2 RNA-Seq Library Preparation Kit. Sequencing of the libraries on HiSeq2500.

value: wild type


title: 5284_BA9_pos (bisulfite-Seq)

value: prefrontal cortex (BA9)


title: ChIP_97L_H3K4me3 Rep1


title: Rongchang_B_mRNA_hippocampus_iron dextran

city: Chongqing

first: Ling

last: Gan

address: 160#Xue Yuan Road,RongchangCounty

department: 1The Department of Veterinary Medicine

institute: Southwest University

description:
Rongchang_B1_mRNA
Rongchang_B2_mRNA

data_processing:
Raw reads were discarded if containing more than 2 unknown (N) bases or if too short (less than 20 nt), with the remaining reads processed by clipping the adaptors and removing low quality bases to get clean reads. Cutadapt（ https://pypi.python.org/pypi/cutadapt/1.2.1）was used to discard sequence adaptor, prinseq（http://prinseq.sourceforge.net/）was applied to control quality and blast+ （http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download）was used to conducted blast analysis.
clean reads were aligned to the reference genome by TopHat (Trapnell et al., 2009). Based on gene annotation, aligned reads with more than one genomic location were discarded to eliminate location ambiguity. RNA-seq reads were analyzed on the basis of the coverage length of the transcriptional units. The expressed level of gene is reckoned using  FPKM（Mortazavi et al., 2008）.
Genome_build: Sscrofa10.2/susScr3
Supplementary_files_format_and_content: expressed_genes_FPKM.txt

organism: Sus scrofa

source_name: hippocampus induced by iron dextran

extract_protocol:
The hippocampus from Rongchang pig (Sus Scrofa) in the control and iron dextran treatment were collected, and immediately frozen in liquid nitrogen, and stored in -80°C until use. The total RNA was extracted using RNAiso plus in accordance with the manufacturers’ instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Rongchang

tag: developmental stage

value: piglet

value: wide type

tag: agent

value: iron dextran

value: hippocampus


title: Rongchang_A_mRNA_hippocampus

description:
Rongchang_A1_mRNA
Rongchang_A2_mRNA

source_name: hippocampus

value: control


title: E.coli wt III

tag: strain


title: RNA_LM3

tag: tissue

value: liver


title: ChIP_97L_H3K36me3 Rep1

value: H3K4me3 (human, Abcam, ab8580)


title: E.coli csrA knockout II

tag: genotype

value: csrA knockout


title: E.coli csrA knockout I


title: E.coli wt I


title: E.coli csrA knockout III


title: Hdac1_Th17

tag: cell type

value: Bethyl A300-713A


title: Rongchang_3_miRNA

status: Public on Dec 14 2018

data_processing:
Cutadapt-1.2.2 and mass fraction pretreatment method were used to obtain clean reads of raw reads.
The clean reads were screened against the GenBank non-coding RNA database (http://blast.ncbi.nlm.nih.gov/) and the Rfam database (http://pfam.janelia.org/) to remove non-coding RNA (such as rRNA, scRNA, tRNA, snRNA, snoRNA, and other ncRNA).
the remaining reads were aligned against the known pig miRNA precursors and mature miRNAs were deposited in the miRBase 21.0 to identify the pig known miRNAs.
all unique candidate sequences were re-queried against known animal mature miRNAs (from the miRBase database) by using BLASTn software to further identify of conserved pig miRNAs. Subsequently, sequences between 18 nt and 30 nt were aligned against raw sequence data by miRDeep2 software with the default parameter to confirm the novel miRNAs.
Genome_build: (SGSC Sscrofa10.2/ susScr3)  was used for our  analysis

source_name: ventral hippocampus induced by oxidative stress

extract_protocol:
The ventral hippocampus and dorsal hippocampus were isolated separately from the Rongchang piglets in the control group and oxidative stress group and mixed as a sample, respectively, and immediately frozen in liquid nitrogen, and stored in -80°C until use. The total RNA  was extracted using using TRIZOL reagent in accordance with the manufacturers’ instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Eight purebred newborn Rongchang piglets (4 females and 4 males) coming from the same litter with the similar weight, physiology, health status, were randomly divided into the control group (n=4) and oxidative stress group (n=4) with the same sex ratio. The piglets in the oxidative stress group were intra-muscularly injected with 200 mg iron dextran on day 3 and 4 post-partum to induce oxidative stress

value: Rongchang piglets

tag: genotype/variation

tag: injected with

value: ventral hippocampus

value: small RNA(< 200 nt)


title: Rongchang_1_miRNA

source_name: ventral hippocampus

value: none (control)


title: Rongchang_4_miRNA

source_name: dorsal hippocampus induced by oxidative stress

value: 200 mg iron dextran on day 3 and 4 post-partum

value: dorsal hippocampus


title: Input_Th17

value: primary T cells


title: 5358_BA9_pos (ATAC-Seq)

source_name: NeuN positive nuclei sorted from prefrontal cortex (BA9)

value: NeuN pos

value: prefrontal cortex (BA9)


title: Rongchang_2_miRNA

source_name: dorsal hippocampus

value: wide type


title: DHTtreated_ERG_ChIAPET

city: Singapore

first: Edwin

last: Cheung

state: Singapore

address: Genome Institute of Singapore 60 Biopolis Street, Genome, #02-01

department: Cancer Biology and Pharmacology

country: Singapore

institute: Genome Institute of Singapore

description: ERG ChIA-PET after DHT treatment. CHV031M_L1.cluster.pet2+.txt is a file storing all the AR mediated chromatin interaction with PET count>=2. And CHV031M_L1.peak.bed is a bed file storing the AR binding site locations estimated from self-ligation pet.

data_processing:
Alignment: For ChIA-PET, GRO-seq, we use program called BATMIS - Basic Alignment Tool for Mismatches http://code.google.com/p/batmis/. For G-PET, sequence tags were uniquely mapped to the human reference sequence (NCBI Build 37) allowing 2 mismatches. For RNA-PET, we use the RNA alignment program TopHat. For G-PET, sequence tags were mapped to the human reference sequence (NCBI Build 37) allowing 2 color code mismatches and paired using SOLiD System Analysis Pipeline Tool, Corona Lite (Applied Biosystems).
Interaction cluster calling: ChIA-PET data was processed with ChIA-PET Tool software: Li, G., Fullwood, M.J., Xu, H., Mulawadi, F.H., Velkov, S., Vega, V., Ariyaratne, P.N., Mohamed, Y.B., Ooi, H.S., Tennakoon, C., Wei, C.L., Ruan, Y. and Sung, W.K. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol, 11 (2). R22
Peak calling: ChIA-PET data was processed with ChIA-PET Tool software: Li, G., Fullwood, M.J., Xu, H., Mulawadi, F.H., Velkov, S., Vega, V., Ariyaratne, P.N., Mohamed, Y.B., Ooi, H.S., Tennakoon, C., Wei, C.L., Ruan, Y. and Sung, W.K. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol, 11 (2). R22
Coverage data: use bedtool "genomeCoverageBed" with the alignment data
SV calling: Detect all Structural Variations (deletions, inversions, insertions, tandem and translocations) for each library using SVGenModule program.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bed.gz: peak
Supplementary_files_format_and_content: bedpe.gz: chromatin interaction
Supplementary_files_format_and_content: bedgraph.gz: RNA-seq coverage
Supplementary_files_format_and_content: pet2+.txt: chromatin interaction
Supplementary_files_format_and_content: xls: structure variation

source_name: VCaP cells, DHT 2hr, ERG ChIP

growth_protocol: VCaP cells were seeded in DMEM supplemented with 10% fetal bovine serum (FBS), sodium pyruvate, sodium bicarbonate and penicillin:streptomycin solution for 3 days. Prior to ETOH/DHT stimulation, VCaP cells were washed and the medium was replaced with phenol red-free DMEM supplemented with 10% charcoal stripped fetal bovine serum (CDFBS), sodium pyruvate, sodium bicarbonate and penicillin:streptomycin solution to starve the cells for 24 hours.

extract_protocol:
ChIA-PET: ChIP Chromatin was divided into two aliquots and each aliquot was ligated with two different barcoded biotinylated half-linkers (linker A or linker B) that contain a flanking MmeI site using T4 DNA ligase. These chromatins ligated with different linkers were pooled and molecular circularization/ligation was carried out in extremely dilute condition. After ligation, DNA was purified and digested with MmeI.
The biotinylated PETs purified on Streptavidin Dynabeads were ligated with a sequencing adapter by T4 DNA ligase (RT for 16h with rotation). The nick on one strand of the DNA at the ligation site was subsequently repaired by incubation with E. coli DNA polymerase I at RT for 2h, followed by 18-20 rounds of PCR. This PCR product was used as the template for Illumina GAIIx 2x36 bp pair end sequencing.

treatment_protocol: Hormone-deprived VCaP cells were treated with 100nM DHT for 2 hours.

value: VCaP

value: prostate cancer cell line

tag: treatment

value: DHT for 2hrs

tag: chip antibody

value: anti-ERG (vendor:Santa Cruz; catalog number:sc-353; lot#:I2509)


title: 6h_RNA_SEQ

description: RNA-seq at 6 hours after DHT treatment.

source_name: VCaP cells, DHT 6hr

extract_protocol:
RNA was harvested using Trizol reagent (Sigma) and purified according to the manufacturer's protocol in the PureLink RNA Mini Kit (Invitrogen).
Sequencing adaptors were ligated to the PET constructs, which were then amplified by PCR and sequenced by the Illumina platform.

treatment_protocol: Hormone-deprived VCaP cells were treated with ETOH/10nM DHT for the indicated time points.

value: DHT for 6hrs


title: DHTtreated_AR_ChIAPET

description: AR ChIA-PET after DHT treatment. CHV029M_L1.cluster.pet2+.txt is a file storing all the AR mediated chromatin interaction with PET count>=2. And CHV029M_L1.peak.bed is a bed file storing the AR binding site locations estimated from self-ligation pet.

source_name: VCaP cells, DHT 2hr, AR ChIP

value: anti-AR (vendor:Santa Cruz; catalog number:sc-815x; lot#:D1709)


title: 2h_GRO_seq

description: GRO-seq after DHT treatment. "XXX.plusgraph" is the bedgraph file for the groseq coverage of forward strand. "XXX.minusgraph" is the bedgraph file for the groseq coverage of reverse strand.

source_name: VCaP cells, DHT 2hr

extract_protocol:
Nuclei were isolated from VCaP cells with or without DHT treatment.
GRO-seq libraries were prepared from 10 million cells based on previously published protocols (Core et al., 2008). After harvesting the cells, RNA polymerases were allowed to run-on for 5 minutes at 30C (~100bp) in the presence of sarkosyl and BrUTP. The RNA was then base hydrolyzed, end-repaired and immunopurified with anti-BrdUTP-coated agarose beads thrice. The affinity-enriched RNAs are then reverse transcribed, amplified, and PAGE purified for deep sequencing on the Illumina Genome Analyzer and HiSeq 2000.

treatment_protocol: Hormone-deprived VCaP cells were treated with 100nM DHT for the indicated time points.


title: 24h_RNA_SEQ

description: RNA-seq at 24 hours after DHT treatment.

source_name: VCaP cells, DHT 24h

value: DHT for 24hrs


title: 0h_RNA_SEQ

description: RNA-seq before DHT treatment.

source_name: VCaP cells, untreated


title: 0h_GRO_seq

description: GRO-seq before DHT treatment. "XXX.plusgraph" is the bedgraph file for the groseq coverage of forward strand. "XXX.minusgraph" is the bedgraph file for the groseq coverage of reverse strand.


title: carrier_sample_5529

city: Los Angeles

first: Grace

last: Xiao

address: 610 Charles E. Young Drive S

department: UCLA Department of Integrative Biology and Physiology

institute: UCLA

description: carrier definition: sample derived from Fragile X Carrier

data_processing:
Map fastq reads with HISAT2 hisat2 -q --phred64 -x grch37_tran/genome_tran  --no-unal --reorder --no-mixed
Extract uniquely mapped reads from SAM files
Remap unmapped reads with hyperediting pipeline. In brief, convert all adenosines to guanosines and align to modified hg19 genome where adenosines are also substituted by guanosines.
Obtain uniquely mapped reads pairs from hyperediting pipeline and combine with uniquely mapped reads from first round of read mapping
Identify RNA-DNA differences between mapped reads and hg19 reference genome.
Apply log-likelihood test to determine whether RDD is likely resulted from sequencing error (Bahn et. al. PMID: 21960545)
Apply posterior filters to remove RDD sites that are likely caused by technical artifats (Bahn et. al. PMID: 21960545 and Lee et. al. PMID: 23598527)
Retain only highly prevalent editing sites. In particular, filter for editing sites that for at least 5 people have at least 5 total reads of which 2 reads are edited
Also quantify gene expression as RPKM values over the exon union of ENSEMBL transcripts in hg19.
Genome_build: hg19
Supplementary_files_format_and_content: gene expression (RPKM)

molecule: polyA RNA

source_name: human frontal cortex

extract_protocol:
Total RNA was extracted using TRIzol from frozen tissues
RNA-Seq libraries were prepared using NEBNext Poly (A) mRNA magnetic isolation module (NEB, E7490) followed by NEBNext Ultra Directional RNA library prep kit for Illumina according to manufacturer’s instruction.

value: Brain

tag: library

value: polyA-selected


title: carrier_sample_5212


title: FMR_Rep2_Input

data_processing:
Takes output from raw files.  Run to trim off both 5’ and 3’ adapters on both reads. Command: quality-cutoff 6  -m 18  -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT  AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1. Run to trim off the 3’ adapters on read 2, to control for double ligation events. Command: cutadapt -f fastq --match-read-wildcards  --times 1  -e 0.1  -O 5  --quality-cutoff 6  -m 18  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2.  Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir /path/to/RepBase_human_database_file --genomeLoad LoadAndRemove  --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz --outSAMunmapped Within  --outFilterMultimapNmax 30  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam --outSAMattributes All  --readFilesCommand zcat  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam
Takes output from STAR rmRep.  Maps unique reads to the human genome.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir  /path/to/STAR_database_file --genomeLoad LoadAndRemove  --readFilesIn  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate1  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate2  --outSAMunmapped Within  --outFilterMultimapNmax 1  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --outSAMattributes All  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam
takes output from STAR genome mapping.  Custom random-mer-aware script for PCR duplicate removal. Command: barcode_collapse_pe.py  --bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --out_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  --metrics_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.metrics
Takes output from barcode collapse PE.  Sorts resulting bam file for use downstream.  Command: java  -Xmx2048m  -XX:+UseParallelOldGC  -XX:ParallelGCThreads=4  -XX:GCTimeLimit=50  -XX:GCHeapFreeLimit=10  -Djava.io.tmpdir=/full/path/to/files/.queue/tmp  -cp /path/to/gatk/dist/Queue.jar  net.sf.picard.sam.SortSam  INPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  TMP_DIR=/full/path/to/files/.queue/tmp  OUTPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  VALIDATION_STRINGENCY=SILENT  SO=coordinate  CREATE_INDEX=true
Takes output from sortSam, makes bam index for use downstream.  Command: samtools index  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam.bai
Takes inputs from multiple final bam files.  Merges the two technical replicates for further downstream analysis.  Command: samtools  merge  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.D08.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam
Takes output from sortSam, makes bam index for use downstream.  Command: samtools  index  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/CombinedID.merged.bam.bai
Takes output from sortSam.  Only outputs the second read in each pair for use with single stranded peak caller.  This is the final bam file to perform analysis on.  Command: samtools view -hb -f 128  /full/path/to/files/CombinedID.merged.bam  >  /full/path/to/files/CombinedID.merged.r2.bam
Takes results from samtools view.  Calls peaks on those files.  Command: clipper  -b /full/path/to/files/CombinedID.merged.r2.bam  -s hg19  -o /full/path/to/files/CombinedID.merged.r2.peaks.bed  --bonferroni  --superlocal  --threshold-method binomial  --save-pickle
Genome_build: hg19
Supplementary_files_format_and_content: bed format, contains clusters of predicted RBP binding

source_name: human brain

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes.
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

treatment_protocol: Flash-frozen brain tissue was cryo-ground in pestles pre-chilled with liquid nitrogen, spread out in standard tissue culture plates pre-chilled to -80 C, and UV crosslinked twice at 254 nM (400 mJ/cm2). 50 mg of crosslinked tissue was then used for each eCLIP experiment.

tag: barcodes

tag: antibody manufacturer

value: MBL

tag: antibody catalog #

tag: antibody lot#

value: antibody lot#:001

tag: rnase i fragmentation condition


title: FXR_Rep1

tag: antibody

value: Bethyl


title: FMR_Rep2


title: FMR_Rep1


title: NusA (1_195)

city: San Francisco

first: Anton

last: Ogorodnikov

address: 513 Parnassuss Ave

department: Rheumatology

institute: UCSF

description:
NusA
1_195
1_198_siRNAs.txt.gz

data_processing:
TREND annotation and neuroblastoma analysis: 3′READS was carried out as previously described (Hoque et al., 2013, PMID 23241633).
TREND annotation and neuroblastoma analysis: Reads were mapped to human genome hg38 using bowtie2
TREND annotation and neuroblastoma analysis: reads arising from internal priming were excluded as previously described (Hoque et al., 2013, PMID 23241633)
Applied to neuroblastoma analysis only: reads were normalized as reads per million. Number of counts per each TREND isoform was performed with genomeCoverageBed (bedtools v2.26.0)
Applied to neuroblastoma analysis only: bigwig files were constructed using bedGraphToBigWig v 4
TREND annotation: Filtered poly(A) site-supporting (PASS) reads were used to construct peaks using the Cufflinks ver. 2.1.1
TREND annotation: reads association with genes was done applying BEDOPS v2.4.25 (closest-features) using UCSC codinf and non-coding genes assembly
TRENDseq: Raw reads were demultiplexed, trimmed and filtered using Cel-Seq protocol (Hashimshony et al., 2012, PMID 22939981).
TRENDseq: Mapping to the human genome (hg38): bowtie2 "--no-unal" option
TRENDseq: Number of reads associated with each TREND-isoform was calculated using HTSeq (htseq-count command, intersection-strict option).
Genome_build: hg38
Supplementary_files_format_and_content: 1_198_siRNAs.txt.gz - HTSeq (htseq count output) - number of reads assigned to each TREND-isoform (chromosome_coordinate) for every knockdown variant (columns). For 198 siRNA variants
Supplementary_files_format_and_content: 2_bioReps_and_dual.txt.gz - HTSeq (htseq count output) - number of reads assigned to each TREND-isoform (chromosome_coordinate) for every knockdown variant (columns). For biological replicates and dual depletions
Supplementary_files_format_and_content: 3_PCF11reps.txt.gz - HTSeq (htseq count output) - number of reads assigned to each TREND-isoform (chromosome_coordinate) for every knockdown variant (columns). Additional PCF11 replicates
Supplementary_files_format_and_content: 4_01_BE2C_Control_3READS.bw.gz - bigwig file of TREND isoforms for control sample of neuroblastoma differentiation. Two files - for sense (positive) and antisense (negative) DNA strands
Supplementary_files_format_and_content: 4_02_BE2C_ATRA_3READS_neg.bw.gz - bigwig file of TREND isoforms for ATRA-treated sample of neuroblastoma differentiation. Two files - for sense (positive) and antisense (negative) DNA strands

source_name: BE(2)-C neuroblastoma cell line

growth_protocol: BE(2)-C cells were propagated in monolayer culture in DMEM medium with 10% FBS.

extract_protocol:
Total RNA was extracted from cells using PeqGold TriFast (VWR).
Libraries were prepared according to TRENDseq protocol
Small RNA TruSeq

treatment_protocol: For siRNA transfection master mix included RotiFect RNAi Lipo (Roth, 2 µl per 1 ml of total transfection volume) and siRNA (50 nM final) mixed in OptiMEM (ThermoFisher Scientific) 20% of final volume according to the manufacturer's instruction.

tag: origin

value: neuroblastoma, derived from metastatic site:bone marrow

value: siRNA transfection

tag: cell line

tag: data type


title: FXR_Rep2_Input

tag: tissue


title: FXR_Rep2


title: fragileX_sample_5746

description: fragileX definition: sample derived from patient diagnosed with Fragile X Syndrome


title: FXR_Rep1_Input


title: BE2C_ATRA_3'READS (4_02)

description:
BE2C_ATRA_3'READS
4_02

value: 5 µM ATRA treatment


title: BE2C_Control_3'READS (4_01)

description:
BE2C_Control_3'READS
4_01

value: DMSO control


title: mock.2.7 (1_198)

description:
mock.2.7
1_198
1_198_siRNAs.txt.gz


title: TERT (1_181)

description:
TERT
1_181
1_198_siRNAs.txt.gz


title: AGO2 (1_184)

description:
AGO2
1_184
1_198_siRNAs.txt.gz


title: DICER1 (1_182)

description:
DICER1
1_182
1_198_siRNAs.txt.gz


title: MAPK8 (1_186)

description:
MAPK8
1_186
1_198_siRNAs.txt.gz


title: mock.1.7 (1_197)

description:
mock.1.7
1_197
1_198_siRNAs.txt.gz


title: IFIT3 (1_194)

description:
IFIT3
1_194
1_198_siRNAs.txt.gz


title: Luciferase.7 (1_196)

description:
Luciferase.7
1_196
1_198_siRNAs.txt.gz


title: XRCC5 (1_179)

description:
XRCC5
1_179
1_198_siRNAs.txt.gz


title: PRKDC (1_178)

description:
PRKDC
1_178
1_198_siRNAs.txt.gz


title: MAPK1 (1_188)

description:
MAPK1
1_188
1_198_siRNAs.txt.gz


title: PPP1R10 (1_192)

description:
PPP1R10
1_192
1_198_siRNAs.txt.gz


title: IFIT1 (1_193)

description:
IFIT1
1_193
1_198_siRNAs.txt.gz


title: fragileX_sample_5319


title: PPP1CA (1_190)

description:
PPP1CA
1_190
1_198_siRNAs.txt.gz


title: FMR_Rep1_Input


title: TARBP2 (1_183)

description:
TARBP2
1_183
1_198_siRNAs.txt.gz


title: ELAVL1 (1_175)

description:
ELAVL1
1_175
1_198_siRNAs.txt.gz


title: CASP3 (1_177)

description:
CASP3
1_177
1_198_siRNAs.txt.gz


title: XRCC6 (1_180)

description:
XRCC6
1_180
1_198_siRNAs.txt.gz


title: mock.2.6 (1_173)

description:
mock.2.6
1_173
1_198_siRNAs.txt.gz


title: S96

city: Bar Harbor

first: Catherine

middle: C

last: Kaczorowski

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
Bowtie 1.1.2 alignment (bowtie -q -p 8 -a --best --strata --sam -v 3)
EMASE 0.10.16 for abundance measurements
Genome_build: mm10
Supplementary_files_format_and_content: Process data is provided in the form of a .csv spreadsheet where columns correspond to unique samples and rows correspond to normalized counts (normalized to tpm, or transcripts per milion) for either genes or isoforms

source_name: Hippocampus

growth_protocol: Animals were fear conditioning at either 6 or 14 months. Immediately following contextual fear memory testing, mice were euthanized by isoflurane, decapitated, and brains were immediately harvested. Hippocampus was freshly dissected, snap frozen in liquid nitrogen, and stored at -80 until RNA extraction

extract_protocol:
RNEasy mini kit (QIAGEN) on QIACUBE (QIAGEN)
RNA was isolated on a Qiacube using the RNeasy mini kit (Qiagen) and treated with Dnase to remove contaminating DNA. RNA quality was confirmed using a BioAnalyzer (Agilent Technologies). All samples had RNA Integrity Numbers (RIN values) > 8.0. Sequencing libraries were prepared from 1 µg RNA with the Truseq Stranded mRNA Sample Preparation Kit (Illumina Inc) following the manufacturer’s protocol. Final PCR-enriched fragments were validated on a 2200 Tapestation Instrument using the D1000 ScreenTape (Agilent Technologies) and quantified by qPCR using a Universal Library Quantification Kit (Kapa Biosystems) on the QuantStudio 6 Flex (ThermoFisher Scientific). Final library pools were sequenced by 75bp paired-end sequencing on a HiSeq2500 (Illumina Inc).

treatment_protocol: Hippocampus was dissected from fresh tissue, snap frozen in liquid nitrogen, and stored at -80 until RNA extraction

value: Hippocampus

tag: Sex

value: Male

tag: age

tag: bxd strain

tag: genotype

value: Ntg


title: BCL2 (1_176)

description:
BCL2
1_176
1_198_siRNAs.txt.gz

tag: treatment


title: mock.1.6 (1_172)

description:
mock.1.6
1_172
1_198_siRNAs.txt.gz


title: PPP1CB (1_191)

description:
PPP1CB
1_191
1_198_siRNAs.txt.gz


title: TIAL1 (1_174)

description:
TIAL1
1_174
1_198_siRNAs.txt.gz


title: MAPK3 (1_189)

description:
MAPK3
1_189
1_198_siRNAs.txt.gz


title: MAPK9 (1_187)

description:
MAPK9
1_187
1_198_siRNAs.txt.gz


title: Luciferase.6 (1_171)

description:
Luciferase.6
1_171
1_198_siRNAs.txt.gz


title: S77


title: XPO4 (1_169)

description:
XPO4
1_169
1_198_siRNAs.txt.gz


title: TIA1 (1_170)

description:
TIA1
1_170
1_198_siRNAs.txt.gz


title: S84


title: S56


title: S82


title: TP53 (1_165)

description:
TP53
1_165
1_198_siRNAs.txt.gz


title: CDKN2A (1_166)

description:
CDKN2A
1_166
1_198_siRNAs.txt.gz


title: CDKN2D (1_167)

description:
CDKN2D
1_167
1_198_siRNAs.txt.gz


title: MAPK14 (1_185)

description:
MAPK14
1_185
1_198_siRNAs.txt.gz


title: DDX20 (1_168)

description:
DDX20
1_168
1_198_siRNAs.txt.gz


title: S51


title: S50


title: S91


title: S47


title: BTG2 (1_164)

description:
BTG2
1_164
1_198_siRNAs.txt.gz


title: S22


title: PCNA (1_161)

description:
PCNA
1_161
1_198_siRNAs.txt.gz


title: RPA3 (1_160)

description:
RPA3
1_160
1_198_siRNAs.txt.gz


title: S166


title: S37


title: RPA1 (1_159)

description:
RPA1
1_159
1_198_siRNAs.txt.gz


title: CHD2 (1_158)

description:
CHD2
1_158
1_198_siRNAs.txt.gz


title: CCNB1 (1_163)

description:
CCNB1
1_163
1_198_siRNAs.txt.gz


title: S3


title: S26


title: S153


title: S17


title: S149


title: CHD1 (1_157)

description:
CHD1
1_157
1_198_siRNAs.txt.gz


title: S162


title: S140


title: SUPT16H (1_156)

description:
SUPT16H
1_156
1_198_siRNAs.txt.gz


title: SMARCA4 (1_155)

description:
SMARCA4
1_155
1_198_siRNAs.txt.gz


title: SETD1B (1_152)

description:
SETD1B
1_152
1_198_siRNAs.txt.gz


title: CDK2 (1_162)

description:
CDK2
1_162
1_198_siRNAs.txt.gz


title: S132

value: female


title: S130


title: SLBP (1_150)

description:
SLBP
1_150
1_198_siRNAs.txt.gz


title: S147


title: SETD1A (1_151)

description:
SETD1A
1_151
1_198_siRNAs.txt.gz


title: KAT2B (1_154)

description:
KAT2B
1_154
1_198_siRNAs.txt.gz


title: SETD2 (1_153)

description:
SETD2
1_153
1_198_siRNAs.txt.gz


title: S133


title: S13


title: S109


title: Luciferase.5 (1_146)

description:
Luciferase.5
1_146
1_198_siRNAs.txt.gz


title: TUT1 (1_145)

description:
TUT1
1_145
1_198_siRNAs.txt.gz


title: PARN (1_149)

description:
PARN
1_149
1_198_siRNAs.txt.gz


title: S11


title: TRDMT1 (1_142)

description:
TRDMT1
1_142
1_198_siRNAs.txt.gz


title: S93

value: Female


title: S89


title: DNMT1 (1_141)

description:
DNMT1
1_141
1_198_siRNAs.txt.gz


title: mock.2.5 (1_148)

description:
mock.2.5
1_148
1_198_siRNAs.txt.gz


title: mock.1.5 (1_147)

description:
mock.1.5
1_147
1_198_siRNAs.txt.gz


title: DNMT3B (1_144)

description:
DNMT3B
1_144
1_198_siRNAs.txt.gz


title: S106


title: S79


title: S103


title: S108


title: CIRBP (1_140)

description:
CIRBP
1_140
1_198_siRNAs.txt.gz


title: S100


title: S70


title: S80


title: EIF4A1 (1_136)

description:
EIF4A1
1_136
1_198_siRNAs.txt.gz


title: DNMT3A (1_143)

description:
DNMT3A
1_143
1_198_siRNAs.txt.gz


title: EIF4E (1_137)

description:
EIF4E
1_137
1_198_siRNAs.txt.gz


title: S71


title: EIF4G1 (1_138)

description:
EIF4G1
1_138
1_198_siRNAs.txt.gz


title: S75


title: S65


title: EIF3C (1_135)

description:
EIF3C
1_135
1_198_siRNAs.txt.gz


title: S64


title: KHSRP (1_132)

description:
KHSRP
1_132
1_198_siRNAs.txt.gz


title: RBM7 (1_131)

description:
RBM7
1_131
1_198_siRNAs.txt.gz


title: EIF2A (1_134)

description:
EIF2A
1_134
1_198_siRNAs.txt.gz


title: S5


title: S57


title: NCBP1 (1_130)

description:
NCBP1
1_130
1_198_siRNAs.txt.gz


title: S46


title: S43


title: FUBP3 (1_133)

description:
FUBP3
1_133
1_198_siRNAs.txt.gz


title: ExosC6 (1_125)

description:
ExosC6
1_125
1_198_siRNAs.txt.gz


title: DCP2 (1_127)

description:
DCP2
1_127
1_198_siRNAs.txt.gz


title: S25


title: S63


title: S49


title: S62


title: IGF2BP1 (1_129)

description:
IGF2BP1
1_129
1_198_siRNAs.txt.gz


title: S24


title: GNB2L1 (1_139)

description:
GNB2L1
1_139
1_198_siRNAs.txt.gz


title: mock.1.4 (1_122)

description:
mock.1.4
1_122
1_198_siRNAs.txt.gz


title: ZFP36 (1_128)

description:
ZFP36
1_128
1_198_siRNAs.txt.gz


title: S23


title: S40


title: S18


title: SKIV2L (1_124)

description:
SKIV2L
1_124
1_198_siRNAs.txt.gz


title: S33


title: S14


title: EXOSC10 (1_119)

description:
EXOSC10
1_119
1_198_siRNAs.txt.gz


title: S27


title: DCP1A (1_126)

description:
DCP1A
1_126
1_198_siRNAs.txt.gz


title: DIS3 (1_117)

description:
DIS3
1_117
1_198_siRNAs.txt.gz


title: mock.2.4 (1_123)

description:
mock.2.4
1_123
1_198_siRNAs.txt.gz


title: CNOT7 (1_115)

description:
CNOT7
1_115
1_198_siRNAs.txt.gz


title: Luciferase.4 (1_121)

description:
Luciferase.4
1_121
1_198_siRNAs.txt.gz


title: CNOT2 (1_114)

description:
CNOT2
1_114
1_198_siRNAs.txt.gz


title: XRN1 (1_113)

description:
XRN1
1_113
1_198_siRNAs.txt.gz


title: S129


title: S163


title: SMG6 (1_112)

description:
SMG6
1_112
1_198_siRNAs.txt.gz


title: ALYREF (1_111)

description:
ALYREF
1_111
1_198_siRNAs.txt.gz


title: S124


title: S127


title: DIS3L (1_118)

description:
DIS3L
1_118
1_198_siRNAs.txt.gz


title: RNPS1 (1_109)

description:
RNPS1
1_109
1_198_siRNAs.txt.gz


title: SKIV2L2 (1_120)

description:
SKIV2L2
1_120
1_198_siRNAs.txt.gz


title: S107


title: S105


title: S144


title: S98


title: UPF2 (1_106)

description:
UPF2
1_106
1_198_siRNAs.txt.gz


title: S9


title: TNRC6A (1_116)

description:
TNRC6A
1_116
1_198_siRNAs.txt.gz


title: UPF3A (1_107)

description:
UPF3A
1_107
1_198_siRNAs.txt.gz


title: CASC3 (1_110)

description:
CASC3
1_110
1_198_siRNAs.txt.gz


title: UPF3B (1_108)

description:
UPF3B
1_108
1_198_siRNAs.txt.gz


title: S122


title: S95


title: S83


title: S85


title: RBM5 (1_103)

description:
RBM5
1_103
1_198_siRNAs.txt.gz


title: SRSF3 (1_101)

description:
SRSF3
1_101
1_198_siRNAs.txt.gz


title: SRSF4 (1_102)

description:
SRSF4
1_102
1_198_siRNAs.txt.gz


title: S8


title: UPF1 (1_105)

description:
UPF1
1_105
1_198_siRNAs.txt.gz


title: Nova2 (1_104)

description:
Nova2
1_104
1_198_siRNAs.txt.gz


title: CDC40 (1_100)

description:
CDC40
1_100
1_198_siRNAs.txt.gz


title: S60


title: S97


title: SRRM2 (1_099)

description:
SRRM2
1_099
1_198_siRNAs.txt.gz


title: S44


title: S41


title: mock.2.3 (1_098)

description:
mock.2.3
1_098
1_198_siRNAs.txt.gz


title: SRRM1 (1_095)

description:
SRRM1
1_095
1_198_siRNAs.txt.gz


title: mock.1.3 (1_097)

description:
mock.1.3
1_097
1_198_siRNAs.txt.gz


title: Luciferase.3 (1_096)

description:
Luciferase.3
1_096
1_198_siRNAs.txt.gz


title: S53


title: S4


title: S21


title: S81


title: S10


title: S28


title: S38


title: S36


title: S2


title: SNRPA1 (1_091)

description:
SNRPA1
1_091
1_198_siRNAs.txt.gz


title: DDX23 (1_092)

description:
DDX23
1_092
1_198_siRNAs.txt.gz


title: SF3A1 (1_094)

description:
SF3A1
1_094
1_198_siRNAs.txt.gz


title: S68


title: SNRNP70  (1_090)

description:
SNRNP70
1_090
1_198_siRNAs.txt.gz


title: S20


title: S165


title: S19


title: SCAF1 (1_088)

description:
SCAF1
1_088
1_198_siRNAs.txt.gz


title: SNRNP48 (1_093)

description:
SNRNP48
1_093
1_198_siRNAs.txt.gz


title: S164


title: S16


title: CTDP1 (1_087)

description:
CTDP1
1_087
1_198_siRNAs.txt.gz


title: S158


title: PIN1 (1_086)

description:
PIN1
1_086
1_198_siRNAs.txt.gz


title: S154


title: S155


title: S148


title: S152


title: CDK9 (1_084)

description:
CDK9
1_084
1_198_siRNAs.txt.gz


title: CDK7 (1_083)

description:
CDK7
1_083
1_198_siRNAs.txt.gz


title: CDK8 (1_082)

description:
CDK8
1_082
1_198_siRNAs.txt.gz


title: S145


title: S15


title: NRF1 (1_079)

description:
NRF1
1_079
1_198_siRNAs.txt.gz


title: RBL2 (1_081)

description:
RBL2
1_081
1_198_siRNAs.txt.gz


title: E2F4 (1_080)

description:
E2F4
1_080
1_198_siRNAs.txt.gz


title: XRN2 (1_078)

description:
XRN2
1_078
1_198_siRNAs.txt.gz


title: S160


title: GTF2I (1_076)

description:
GTF2I
1_076
1_198_siRNAs.txt.gz


title: S128


title: S120


title: MEF2D (1_077)

description:
MEF2D
1_077
1_198_siRNAs.txt.gz


title: S111


title: mock.1.2 (1_073)

description:
mock.1.2
1_073
1_198_siRNAs.txt.gz


title: POLR2J (1_075)

description:
POLR2J
1_075
1_198_siRNAs.txt.gz


title: NRD1 (1_089)

description:
NRD1
1_089
1_198_siRNAs.txt.gz


title: S110


title: SSU72 (1_085)

description:
SSU72
1_085
1_198_siRNAs.txt.gz


title: S99


title: Luciferase.2 (1_072)

description:
Luciferase.2
1_072
1_198_siRNAs.txt.gz


title: S114


title: POLR2E (1_071)

description:
POLR2E
1_071
1_198_siRNAs.txt.gz


title: S94


title: mock.2.2 (1_074)

description:
mock.2.2
1_074
1_198_siRNAs.txt.gz


title: S136


title: S92


title: POLR2C (1_070)

description:
POLR2C
1_070
1_198_siRNAs.txt.gz


title: POLR2B (1_069)

description:
POLR2B
1_069
1_198_siRNAs.txt.gz


title: S87


title: CTCF (1_066)

description:
CTCF
1_066
1_198_siRNAs.txt.gz


title: MYC (1_067)

description:
MYC
1_067
1_198_siRNAs.txt.gz


title: S90


title: S118


title: S76


title: YBX1 (1_065)

description:
YBX1
1_065
1_198_siRNAs.txt.gz


title: S74


title: S73


title: WDR61 (1_062)

description:
WDR61
1_062
1_198_siRNAs.txt.gz


title: S78


title: CTR9 (1_061)

description:
CTR9
1_061
1_198_siRNAs.txt.gz


title: S69


title: S67


title: S61


title: S66


title: TBP (1_063)

description:
TBP
1_063
1_198_siRNAs.txt.gz


title: S58


title: LEO1 (1_060)

description:
LEO1
1_060
1_198_siRNAs.txt.gz


title: CDC73 (1_059)

description:
CDC73
1_059
1_198_siRNAs.txt.gz


title: POLR2A (1_068)

description:
POLR2A
1_068
1_198_siRNAs.txt.gz


title: MORF4 (1_056)

description:
MORF4
1_056
1_198_siRNAs.txt.gz


title: S42


title: S39


title: DDX42 (1_057)

description:
DDX42
1_057
1_198_siRNAs.txt.gz


title: S34


title: S31


title: TTF2 (1_064)

description:
TTF2
1_064
1_198_siRNAs.txt.gz


title: S167


title: RBBP6 (1_053)

description:
RBBP6
1_053
1_198_siRNAs.txt.gz


title: S32


title: TTC37 (1_054)

description:
TTC37
1_054
1_198_siRNAs.txt.gz


title: SETX (1_055)

description:
SETX
1_055
1_198_siRNAs.txt.gz


title: CPEB1 (1_050)

description:
CPEB1
1_050
1_198_siRNAs.txt.gz


title: S157


title: S142


title: S161


title: mock.2.1 (1_049)

description:
mock.2.1
1_049
1_198_siRNAs.txt.gz


title: S139


title: WDR33 (1_052)

description:
WDR33
1_052
1_198_siRNAs.txt.gz


title: S12


title: PAF1 (1_058)

description:
PAF1
1_058
1_198_siRNAs.txt.gz


title: Luciferase.1 (1_047)

description:
Luciferase.1
1_047
1_198_siRNAs.txt.gz


title: S138


title: S134


title: S112


title: ZCCHC8 (1_044)

description:
ZCCHC8
1_044
1_198_siRNAs.txt.gz


title: S102


title: CSTF2T (1_051)

description:
CSTF2T
1_051
1_198_siRNAs.txt.gz


title: SF1 (1_043)

description:
SF1
1_043
1_198_siRNAs.txt.gz


title: S101


title: DDX39B (1_042)

description:
DDX39B
1_042
1_198_siRNAs.txt.gz


title: SND1 (1_045)

description:
SND1
1_045
1_198_siRNAs.txt.gz


title: SRSF1 (1_040)

description:
SRSF1
1_040
1_198_siRNAs.txt.gz


title: SNRPA (1_038)

description:
SNRPA
1_038
1_198_siRNAs.txt.gz


title: RNA-seq_clf-50swn-1_ABA_0uM_4d

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

data_processing:
The sequencing reads were cleaned, including removing bases with low quality score (<20) and irregular GC content based on FastQC, cutting sequencing adaptor followed by filtering short reads.
The cleaned reads were mapped to Arabidopsis thaliana genome (TAIR10) using BOWTIE2.0 for DNA sequencing and TOPHATv2.0.8 for RNA sequencing, both with default settings.
The duplicated reads were removed, and only alignments with MAPQ score > 20 were kept for further analysis.
For ChIP-seq, SICER_V1.1 was used to identify read enriched regions (peaks) and MAnorm was applied to characterize the change of genome-wide H3K27me3 profile. For RNA-seq, HTSeq-count was used to preprocess the RNA-seq alignments and deseq was used to detect the differentially expressed genes.
Genome_build: TAIR10
Supplementary_files_format_and_content: In ChIP-seq, peak files was provided; In RNA-seq, read counts for genes (TAIR10) was provided.

organism: Arabidopsis thaliana

source_name: 10-d old seedlings treated with 0 μM ABA for 4 days

growth_protocol: Arabidopsis thaliana seedlings were grown on 1/2 Murashige and Skoog (MS) medium without sucrose (2% agar, PH 5.8) under LDs conditions

extract_protocol:
Chromatin or RNA was extracted from the treated seedlings, using standard protocols.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 3000 following the manufacturer’s instructions (Illumina).

treatment_protocol: 10-d old seedlings were transferred onto 1/2 Murashige and Skoog (MS) medium containing 50 μM ABA or 100 μM ABA for certain time.

tag: ecotype

value: Ws

value: the aerial parts of seedlings

value: control

tag: dose

value: 0 μM

tag: time

value: 4 days


title: RNA-seq_swn-1_ABA_0uM_4d


title: SF3B1 (1_039)

description:
SF3B1
1_039
1_198_siRNAs.txt.gz


title: RNA-seq_clf-50_ABA_0uM_4d


title: mock.1.1 (1_048)

description:
mock.1.1
1_048
1_198_siRNAs.txt.gz


title: SYMPK (1_041)

description:
SYMPK
1_041
1_198_siRNAs.txt.gz


title: RNA-seq_WT_ABA_0uM_4d

value: WT


title: SFPQ (1_037)

description:
SFPQ
1_037
1_198_siRNAs.txt.gz


title: NONO (1_036)

description:
NONO
1_036
1_198_siRNAs.txt.gz


title: RNA-seq_clf-50swn-1_ABA_100uM_4d_rep2

source_name: 10-d old seedlings treated with 100 μM ABA for 4 days

value: ABA


title: HNRNPH3 (1_035)

description:
HNRNPH3
1_035
1_198_siRNAs.txt.gz


title: S104


title: HNRNPH2 (1_034)

description:
HNRNPH2
1_034
1_198_siRNAs.txt.gz


title: HNRNPH1 (1_033)

description:
HNRNPH1
1_033
1_198_siRNAs.txt.gz


title: RNA-seq_clf-50swn-1_ABA_100uM_5h

source_name: 10-d old seedlings treated with 100 μM ABA for 5 hours

value: 5 hours


title: RNA-seq_clf-50swn-1_(Ctrl)

source_name: 10-d old seedlings treated with 0 μM ABA for 5 hours


title: HNRNPF (1_032)

description:
HNRNPF
1_032
1_198_siRNAs.txt.gz

value: neuroblastoma, derived from metastatic site:bone marrow


title: RNA-seq_clf-50swn-1_ABA_100uM_4d_rep1


title: HNRNPA2B1 (1_031)

description:
HNRNPA2B1
1_031
1_198_siRNAs.txt.gz

value: siRNA transfection


title: RNA-seq_WT_ABA_100uM_4d_rep1


title: PTBP1 (1_030)

description:
PTBP1
1_030
1_198_siRNAs.txt.gz


title: RNA-seq_WT_(Ctrl)


title: H3K27me3_ABA_100uM_4d

tag: chip antibody

value: H3K27me3 (Upstate, USA, Cat. 07–449)


title: RNA-seq_WT_ABA_100uM_5h


title: H3K27me3_ABA_0uM_4d_(Ctrl_for_100uM_4d)


title: U2AF1 (1_028)

description:
U2AF1
1_028
1_198_siRNAs.txt.gz


title: PABPC4 (1_026)

description:
PABPC4
1_026
1_198_siRNAs.txt.gz


title: JUP (1_046)

description:
JUP
1_046
1_198_siRNAs.txt.gz


title: H3K27me3_ABA_0uM_4d_(Ctrl_for_50uM_4d)


title: H3K27me3_ABA_50uM_4d

source_name: 10-d old seedlings treated with 50 μM ABA for 4 days

value: 50 μM


title: H3K27me3_ABA_50uM_5h_rep2

source_name: 10-d old seedlings treated with 50 μM ABA for 5 hours


title: Luciferase (1_023)

description:
Luciferase
1_023
1_198_siRNAs.txt.gz


title: H3K27me3_ABA_50uM_5h_rep1


title: PAPD7 (1_021)

description:
PAPD7
1_021
1_198_siRNAs.txt.gz


title: H3K27me3_ABA_0uM_5h_(Ctrl_for_50uM_5h)_rep2


title: PAPD5 (1_020)

description:
PAPD5
1_020
1_198_siRNAs.txt.gz


title: PAPD4 (1_019)

description:
PAPD4
1_019
1_198_siRNAs.txt.gz


title: PAPOLG (1_018)

description:
PAPOLG
1_018
1_198_siRNAs.txt.gz


title: RNA-seq_WT_ABA_100uM_4d_rep2


title: CLP1 (1_016)

description:
CLP1
1_016
1_198_siRNAs.txt.gz


title: U2AF2 (1_029)

description:
U2AF2
1_029
1_198_siRNAs.txt.gz


title: PAPOLA (1_017)

description:
PAPOLA
1_017
1_198_siRNAs.txt.gz


title: mock.1 (1_024)

description:
mock.1
1_024
1_198_siRNAs.txt.gz


title: AHCYL1 (1_014)

description:
AHCYL1
1_014
1_198_siRNAs.txt.gz


title: BARD1 (1_013)

description:
BARD1
1_013
1_198_siRNAs.txt.gz


title: mock.2 (1_025)

description:
mock.2
1_025
1_198_siRNAs.txt.gz


title: PABPN1 (1_027)

description:
PABPN1
1_027
1_198_siRNAs.txt.gz


title: PCF11 (1_015)

description:
PCF11
1_015
1_198_siRNAs.txt.gz


title: CPSF7 (1_012)

description:
CPSF7
1_012
1_198_siRNAs.txt.gz


title: CSTF2 (1_008)

description:
CSTF2
1_008
1_198_siRNAs.txt.gz


title: CSTF3 (1_009)

description:
CSTF3
1_009
1_198_siRNAs.txt.gz


title: NUDT21 (1_010)

description:
NUDT21
1_010
1_198_siRNAs.txt.gz


title: PABPC1 (1_022)

description:
PABPC1
1_022
1_198_siRNAs.txt.gz


title: FIP1L1 (1_006)

description:
FIP1L1
1_006
1_198_siRNAs.txt.gz


title: CSTF1 (1_007)

description:
CSTF1
1_007
1_198_siRNAs.txt.gz


title: GPET_VCaP_rep1_rep2

description:
Genome Pair-End Sequence with 10k insert size, replicates 1 and 2.
This Sample represents 2 replicates.

extract_protocol:
Genomic DNA was hydrosheared, EcoP15I recognition sites were methylated and EcoP15I CAP adaptors were ligated to the ends of DNA fragments.
The methylated DNA constructs were separated on agarose gel and 10 Kb sized fragments were selected for ligation resulting in circularized products where 5' and 3' ends of 10 Kb fragments were connected by an internal biotinylated adaptor with two flanking non-methylated EcoP15I CAP adaptors. Constructs were digested by methylation sensitive EcoP15I to release 5' and 3' paired-end tag (PET) constructs.

treatment_protocol: No treatment.

value: VCaP

tag: cell type

value: prostate cancer cell line


title: H3K27me3_ABA_0uM_5h_(Ctrl_for_50uM_5h)_rep1


title: CPSF2 (1_002)

description:
CPSF2
1_002
1_198_siRNAs.txt.gz


title: CPSF3L (1_004)

description:
CPSF3L
1_004
1_198_siRNAs.txt.gz


title: CPSF3 (1_003)

description:
CPSF3
1_003
1_198_siRNAs.txt.gz


title: wr3 (wntlof)

city: Saint Louis

first: Bo

last: Zhang

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Aligned to mus musculus reference build ensembl R76
alinged reads were counted using the featureCounts Subreads package
Differential expression analysis was performed from counts file using edgeR
Genome_build: mus musculus reference build ensembl R76
Supplementary_files_format_and_content: .txt files of  featureCounts and differential expression analysis

source_name: right ventricle

extract_protocol:
RNA was isolated from ventricle using Trizol.
RNA libraries were made using Illumina protocols

value: heart

value: adult

value: wnt lof


title: wl3 (wntlof)

source_name: left ventricle


title: CPSF4 (1_005)

description:
CPSF4
1_005
1_198_siRNAs.txt.gz


title: wr1 (wntlof)


title: wl2 (wntlof)


title: mock.2 (3_05)

description:
mock.2
3_05
3_PCF11reps.txt.gz


title: wr2 (wntlof)


title: CPSF6 (1_011)

description:
CPSF6
1_011
1_198_siRNAs.txt.gz


title: cr3 (wntlof)


title: cr2 (wntlof)


title: cr1 (wntlof)


title: wl1 (wntlof)


title: cl3 (wntlof)


title: cl2 (wntlof)


title: Luciferase (3_04)

description:
Luciferase
3_04
3_PCF11reps.txt.gz


title: 6m (wntgof)

source_name: ventricles

extract_protocol:
RNA was isolated from using Trizol.
RNA libraries were made using Illumina protocols

value: embryonic day 12.5

value: wnt gof


title: 5m (wntgof)


title: PCF11_3 (3_03)

description:
PCF11_3
3_03
3_PCF11reps.txt.gz


title: PCF11_2 (3_02)

description:
PCF11_2
3_02
3_PCF11reps.txt.gz


title: cl1 (wntlof)

value: control


title: PCF11_1 (3_01)

description:
PCF11_1
3_01
3_PCF11reps.txt.gz


title: 4m (wntgof)


title: mock.1 (2_13)

description:
mock.1
2_13
2_bioReps_and_dual.txt.gz


title: 3m (wntgof)


title: Luciferase (2_12)

description:
Luciferase
2_12
2_bioReps_and_dual.txt.gz


title: CPSF1 (1_001)

description:
CPSF1
1_001
1_198_siRNAs.txt.gz


title: 1m (wntgof)


title: PCF11+CPSF4 (2_10)

description:
PCF11+CPSF4
2_10
2_bioReps_and_dual.txt.gz

value: dual siRNA transfection


title: PCF11+SRSF3 (2_11)

description:
PCF11+SRSF3
2_11
2_bioReps_and_dual.txt.gz


title: 6c (wntgof)


title: 2m (wntgof)


title: PCF11+CPSF1 (2_09)

description:
PCF11+CPSF1
2_09
2_bioReps_and_dual.txt.gz


title: PCF11+CSTF3 (2_08)

description:
PCF11+CSTF3
2_08
2_bioReps_and_dual.txt.gz


title: 4c (wntgof)


title: 3c (wntgof)


title: SRSF3 (2_06)

description:
SRSF3
2_06
2_bioReps_and_dual.txt.gz


title: 2c (wntgof)


title: CPSF1 (2_04)

description:
CPSF1
2_04
2_bioReps_and_dual.txt.gz


title: CPSF4 (2_05)

description:
CPSF4
2_05
2_bioReps_and_dual.txt.gz


title: CSTF3 (2_03)

description:
CSTF3
2_03
2_bioReps_and_dual.txt.gz


title: 5c (wntgof)


title: 1c (wntgof)


title: PCF11+CPSF6 (2_07)

description:
PCF11+CPSF6
2_07
2_bioReps_and_dual.txt.gz


title: PCF11 (2_02)

description:
PCF11
2_02
2_bioReps_and_dual.txt.gz


title: CPSF6 (2_01)

description:
CPSF6
2_01
2_bioReps_and_dual.txt.gz


title: WGS7_rep2

city: Brisbane

first: Carlos

middle: Horacio

last: Luna Flores

state: QLD

address: Cnr College Rd and Cooper Rd

institute: AIBN

data_processing:
The samples were sequenced using the illumina platform 100 bp PE.
Tophat, Cufflinks, and CuffDiff were used to align the RNAseq reads against the reference genome P. acidipropionici ATCC 55737, normalize and annotate the transcripts, and evaluate the differential expression, respectively .
Genome_build: Propionibacterium acidipropionici ATCC 55737
Supplementary_files_format_and_content: tab-delimeted cuffdiff output file. The file content differential expression results. The data was normalized in FPKM.

organism: Acidipropionibacterium acidipropionici

source_name: Genome shuffling

growth_protocol: The culture media (PAM) for pre-inoculum consisted of, yeast extract (10 g/L), trypticase soy (5 g/L), K2HPO4 (0.05 g/L), MnSO4 (0.05 g/L), and sucrose (40 g/L). Sucrose (80 g/L) was added to perform fermentations in instrumented fermenters. Fermentations were performed using 2L Applikon fermenters with a working volume of 1 L.  Fermenters were equipped with probes and controllers for pH, dissolved oxygen, temperature, and agitation.  The agitation rate was controlled with two Rushton impellers at 300 rpm. The pH was controlled at 6.5 using 10 M NaOH.  The temperature of the culture was maintained at 32 oC using an electric jacket. Before inoculation, the fermenters were sparged with N2 for at least 15 minutes. A constant top N2 flow was kept for the entire fermentation at a flow rate of 0.3 L/min. Cultures were activated under sterile conditions in a 1.5 mL Eppendorf tubes containing one mL of PAM media inoculated with 0.8% (v/v) of a glycerol stock.  Inoculums were grown for 24 hours at 32 oC. Cultures were transferred into a 15 mL Falcon tube containing 14 mL of PAM media and allowed to grow for 24 hours.  5% (vol/vol) of this culture was used to inoculate 250 mL serum bottles containing 100 mL of PAM media and allowed to grow for an additional 24 hours. Cells from the serum bottles in mid-exponential phase fermenters at an initial A600 of 0.3.

extract_protocol:
Cells sampled at a mid-exponential phase of instrumented fermenters were used for RNA extraction. Briefly, 50 ODs were harvested and centrifuged at 4000g for 10 min at room temperature. The supernatant was removed, and five mL of RNA later reagent was added to the pellet. After 8-24 h of incubation at 4 oC, the RNA later was removed by centrifugation and the pellet stored at -80 oC for further use. RNeasy® Mini Kit (Qiagen) was used to extract the RNA and the RNA Clean and Concentrator-25 Kit (Zymo) to clean it. Next, the RNA was enriched depleting the ribosomal RNA with the Ribbo-Zero Magnetic Kit (Illumina). The samples were cleaned and concentrated with the RNA Clean and Concentrator-5 Kit (Zymo). The quality of the RNA was evaluated by a Bioanalyzer.
Illumina standard protocols

tag: strain

tag: genotype/variation

value: Genome shuffling recombinant


title: WGS7_rep1


title: ATCC55737_rep1

source_name: Corn

value: Wild Type


title: PI3K_engineered_rep1

status: Public on Dec 13 2018

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

data_processing:
Illumina NextSeq 500 / Illumina Four-Channel SBS Sequencing  for base calling
Quality control tests for the mapped reads were performed using the FASTQC software (www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads were aligned to the GRCh37/hg19 human genes by using Tophat2 v2 (Kim et al., 2013) with standard parameters. Quality control tests for the aligned reads and for the replicate consistency were performed by using the qualimap v2.2 (Garcia-Alcalde et al., 2012) and the SARTools (Hugo Varet, 2015) pipelines.
Gene level reads(counts) were computed using the Feature Counts method implemented in the Bioconductor v3.2 RSubread package (Liao et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include reads(counts) values for each sample.

source_name: SK-N-BE(2)-C neuroblastoma cell line

extract_protocol:
RNA was extracted from cells with the RNeasy Kit and on-column DNA digestion (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols
Strand-specific mRNA seq libraries were pooled and sequenced on a NextSeq500 instrument with single-end 75bp reads to a depth of 30-40M reads/sample.

tag: status

value: PI3K engineered

value: vehicle


title: PI3K_engineered_rep2


title: GFP_control_rep3

value: GFP control


title: GFP_control_rep2


title: Resistant_JQ1_treated_rep2

value: resistant


title: Resistant_JQ1_treated_rep1


title: Resistant_JQ1_treated_rep3


title: Naïve_JQ1_treated_rep3

value: naive


title: Resistant_vehicle_treated_rep3


title: Naïve_JQ1_treated_rep2


title: Naïve_JQ1_treated_rep1


title: Resistant_vehicle_treated_rep1


title: Naive_vehicle_treated_rep3


title: Naïve_vehicle_treated_rep1


title: Naive_vehicle_treated_rep2


title: ChIP-seq_H3K27Ac_resistant_JQ1_treated

data_processing:
Basecalls performed using Illumina NextSeq500.
ChIP-seq data sets were aligned using bwa-0.7.15, parameters: bwa mem -M -t 8,  to the build version NCBI37/hg19 of the human genome.
Quality control tests were performed based on the FastQC v.0.11.2 software (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and by using the ChIPQC library available from Bioconductor v3.2. Duplicates were filtered out.
The peaks for H3K27Ac were identified using MACS v1.4.3 with the cut-off 1e-05 for the P-value. The peaks were annotated by using the Annotate Peaks function available in the Homer v4.7 package.
Genome_build: NCBI37/hg19
Supplementary_files_format_and_content: Bigwig files were generated using the bamCompare module available from the DeepTools v2.2.3 software. Scores represent the normalized H3K27Ac signal with background input subtracted in  Reads Per Kilobase per Million reads per 20 bp bin.

growth_protocol: Neuroblastoma cells were plated in 15 cm dishes and grown to 70-80% confluence.

extract_protocol:
Cells were harvested, washed twice in ice cold PBS with protease inhibitors and then lysed in 50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS supplemented with protease inhibitors (Roche). Chromatin was sheared to ~250 bp fragments using the Covaris ultra-sonication. The sonicated lysate was then diluted with ChIP dilution buffer (16.7 mM Tris-HCl pH 8.1, 16.7 mM NaCl, 1.2 mM EDTA, 1.1% Triton-X100, 0.01% SDS).  Subsequently, 2.5% of the lysate was removed as the input control.  The remaining lysate was incubated over night at 4°C with 3 µg of H3K27Ac antibody (ab4729, Abcam). The precipitated lysate was then incubated with protein A/G sepharose beads (Pierce, catalog #20423) for 2 hours and then washed sequentially in ice cold low salt buffer (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton-X100, 0.1% SDS), high salt buffer (20 mM Tris-HCl pH 8.1, 2 mM EDTA, 500 mM NaCl, 1% Triton-X100, 0.1% SDS), LiCl buffer (10 mM Tris-HCl pH 8.1, 0.25 M LiCl, 1 mM EDTA, 1% deoxycholic acid, 1% IGEPAL CA-630) and TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA).  Samples were incubated at 65°C overnight with elution buffer (0.1 M NaHCO3, 1% SDS) supplemented with 0.2M NaCl to reverse crosslinking.
ChIP libraries were prepared using the Rubicon Genomics Thruplex DNA-seq prep kit optimized for low input samples.

treatment_protocol: Cells were crosslinked with 1% formaldehyde in cell culture media for 6 minutes and then quenched with 0.125 M glycine for 5 minutes.


title: ChIP-seq_H3K27Ac_naive_vehicle_treated


title: ChIP-seq_Input_naive_JQ1_treated

value: Input


title: ATCC55737_rep2


title: ChIP-seq_H3K27Ac_naive_JQ1_treated


title: ChIP-seq_Input_naive_vehicle_treated


title: ChIP-seq_Input_resistant_JQ1_treated


title: ChIP-seq_Input_resistant_vehicle_treated


title: Aneuploid population A2 from a-selection rep 1

status: Public on Dec 12 2018

first: Hung-Ji

last: Tsai

state: Maryland

address: 855 N Wolfe Street

department: Cell Biology

institute: Johns Hopkins University

description:
Processed data file: AneuSeq_GEO_RawCounts.xlsx
Processed data file: AneuSeq_GEO_DESeq.xlsx

data_processing:
Illumina RTA version 2.4.11 was used for base calling. Demultiplexing was done with Bcl2fastq 2.17.1.14.
Sequenced reads were checked for read quality using FastQC v.0.11.5, trimmed for adaptor sequence, then mapped to S288c whole genome using HISAT2 v2.0.5 with default parameters.
Read counts were extracted using HTSeq v.0.6.1p1 and significant differentially expressed genes were determined using DESeq2 v.1.14.1.
Genome_build: S288c R64-2-1
Supplementary_files_format_and_content: Excel files with gene-wise raw read counts and log2 fold change in aneuploid populations with respect to euploid populations.
Supplementary_files_format_and_content: AneuSeq_GEO_RawCounts.xlsx: Raw read counts by gene for all samples.
Supplementary_files_format_and_content: AneuSeq_GEO_DESeq.xlsx: Gene expression fold change.

organism: Saccharomyces cerevisiae

growth_protocol: YPD rich media overnight, followed by 4 hour refresh in YPD at 23 degree in 96 deep well plate format.

extract_protocol:
Master Pure Yeast RNA extraction kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: aneuploid


title: Aneuploid population A3 from a-selection rep 2


title: Aneuploid population A3 from a-selection rep 3


title: Aneuploid population A2 from a-selection rep 3


title: Aneuploid population A1 from a-selection rep 3


title: Aneuploid population A3 from a-selection rep 1


title: PI3K_engineered_rep3


title: Resistant_vehicle_treated_rep2


title: Euploid population from a-selection rep 3

source_name: Euploid population from a-selection

value: euploid


title: Aneuploid population A1 from a-selection rep 1


title: Euploid population from a-selection rep 2


title: Aneuploid population A2 from a-selection rep 2


title: Aneuploid population A1 from a-selection rep 2


title: ChIP-seq_H3K27Ac_resistant_vehicle_treated


title: Euploid population from a-selection rep 1


title: Aneuploid population T1 from tetrad dissection rep 3