title: Plasma_Cisplatin_D4_3

first: Pooja

last: Shah

address: 40 Landsdowne Street

institute: Takeda Pharmaceuticals

data_processing:
OSA v4 (http://omicsoft.com/osa) was used to align the reads to the rat genome (Rnor_5.0) and to MiRBase (v.21) [44] allowing for two mismatches and excluding any reads that aligned to greater than 10 genomic locations
Expression levels were quantified by counting the number of reads aligned to mature miRNA region
Genome_build: rat genome (Rnor_5.0)
Supplementary_files_format_and_content: excel file includes miRNA count data for each sample

organism: Rattus norvegicus

extract_protocol:
Total RNA was isolated from plasma or urine by Asuragen following a proprietary small-scale  biofluid RNA isolation procedure. Samples were eluted in 20 μL of water to 10 urine equivalents  (UE) or plasma equivalents (PE) per μL
Isolation of miRNA from 50 μ tissue samples used a lysis buffer (RLT [Qiagen] + 1% β  mercaptoethanol) and a rotor-stator homogenizer
A TruSeq Small RNA Library Kit (Illumina) was used for library construction of rat miRNA
Sequencing was performed on the GAIIx (Illumina) at 36 base pair read length and targeting 12 million reads per sample

treatment_protocol: Eight rats each  received one of the following: (1) a 5 ml intravenous administration of 2 or 5 mg/kg cisplatin or  vehicle (0.9% sterile saline); (2) a 10 ml oral gavage of 400 or 1250 mg/kg APAP or vehicle  (0.5% methylcellulose); or (3) a 10 ml oral gavage of 250 or 1500 mg/kg CCL4 or vehicle (corn  oil). Cisplatin was purchased from Teva Pharmaceuticals while both APAP and CCL4 were  purchased from Sigma-Aldrich. Four animals from each group were euthanized 24 hours post  dose and the remaining four animals were euthanized at 72 hours post dose. Animals first  received intramuscular injection of an anesthetic cocktail (ketamine HCl [75 mg/kg], xylazine  [2.5 mg/kg] and acepromazine [2.5 mg/kg]) and exsanguinations were performed in accordance  with accepted American Veterinary Medical Association guidelines.

value: Plasma

value: Sprague-Dawley

value: Cisplatin

tag: dosage

value: 5 mg/kg

tag: regimen

value: IV; once

tag: time point

tag: prep type

value: Qiagen RNeasy_96

tag: Sex

value: Male

tag: age

tag: age unit

value: Weeks


title: Plasma_Cisplatin_D4_2

status: Public on Jun 01 2016

type: SRA

city: Cambridge

state: MA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: strain

tag: treatment


title: Plasma_vehicle (0.9% Sterile Saline)_D4_3

value: vehicle (0.9% Sterile Saline)

value: 0 mg/kg


title: Plasma_vehicle (0.9% Sterile Saline)_D4_1


title: Plasma_Cisplatin_D4_1


title: Plasma_vehicle (0.9% Sterile Saline)_D4_2


title: Plasma_CCl4 (Carbon Tetrachloride)_D2_3

value: CCl4 (Carbon Tetrachloride)

value: PO; once


title: Plasma_CCl4 (Carbon Tetrachloride)_D2_1


title: Plasma_vehicle (Corn Oil)_D2_3

value: vehicle (Corn Oil)


title: Plasmid_replicate_4_7.5k_Pool

city: Bar Harbor

first: Ryan

last: Tewhey

state: ME

address: 600 Main Street

institute: Jackson Laboratory

description:
7.5k Oligo Pool
barcode count data
fastq of 3' UTR barcode and residual 5' flanking sequencing

library_source: genomic

data_processing:
Library strategy: MPRA
Perfect UTR barcode matches were asigned to their respective oligo. Counts for all barcodes asigned to an oligo were summed.
Genome_build: hg19

molecule: genomic DNA

organism: synthetic construct

source_name: plasmid DNA

growth_protocol: 24 hour growth post-transfection

extract_protocol:
Qiagen Rneasy followed by hybridization pulldown of the GFP transcript.
Illumina Custom Paired-end (TruSeq)

tag: cell line

value: Plasmid DNA


title: Plasmid_replicate_2_7.5k_Pool


title: Plasma_APAP (Acetaminophen)_D2_1

value: APAP (Acetaminophen)


title: Plasma_vehicle (0.5% methylcellulose)_D2_3

value: vehicle (0.5% methylcellulose)


title: Plasmid_replicate_1_7.5k_Pool


title: Plasma_CCl4 (Carbon Tetrachloride)_D2_2


title: Urine_Cisplatin_D4_2

value: Urine


title: Plasma_vehicle (0.5% methylcellulose)_D2_1

value: Plasma


title: Plasma_vehicle (Corn Oil)_D2_2

value: Sprague-Dawley


title: Plasma_APAP (Acetaminophen)_D2_2


title: Urine_vehicle (0.9% Sterile Saline)_D4_1


title: Plasma_APAP (Acetaminophen)_D2_3


title: Urine_CCl4 (Carbon Tetrachloride)_D2_2


title: Plasma_vehicle (0.5% methylcellulose)_D2_2


title: Urine_Cisplatin_D4_3

value: Cisplatin


title: Urine_vehicle (Corn Oil)_D2_2


title: Urine_APAP (Acetaminophen)_D2_3


title: Urine_vehicle (0.5% methylcellulose)_D2_1


title: Liver_CCl4 (Carbon Tetrachloride)_D2_3

value: Liver


title: Urine_Cisplatin_D4_1

value: IV; once


title: Urine_vehicle (0.5% methylcellulose)_D2_2

value: Qiagen RNeasy_96


title: Urine_vehicle (0.9% Sterile Saline)_D4_3

value: Male


title: Urine_vehicle (0.9% Sterile Saline)_D4_2

value: Weeks


title: Liver_vehicle (Corn Oil)_D2_2


title: Liver_vehicle (Corn Oil)_D2_3


title: Urine_CCl4 (Carbon Tetrachloride)_D2_3


title: Urine_vehicle (Corn Oil)_D2_1


title: Urine_APAP (Acetaminophen)_D2_1


title: Urine_CCl4 (Carbon Tetrachloride)_D2_1


title: Kidney_vehicle (0.9% Sterile Saline)_D4_3

value: Kidney

value: vehicle (0.9% Sterile Saline)


title: Plasma_vehicle (Corn Oil)_D2_1

value: 0 mg/kg


title: Kidney_vehicle (0.9% Sterile Saline)_D4_1


title: Urine_vehicle (Corn Oil)_D2_3

value: PO; once


title: BS2980 cancer Trop2+ CD49f Hi

city: Los Angeles

first: Bryan

last: Smith

state: CA

address: MRL 5-720, 675 Charles E. Young Drive South

department: Microbiology, Immunology, and Molecular Genetics

institute: UCLA

description: Sample 14

data_processing:
Illumina CASAVA 1.8.2 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reads were mapped to UCSC hg19 using MapSplice 2.1.8 software.
Gene expression was quantified using RSEM 1.2.25 and quantile normalized.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes normalized RSEM quantification for each Sample

organism: Homo sapiens

source_name: prostate

extract_protocol:
Total RNA was isolated from human prostate basal (Trop2+ CD49f Hi) and luminal (Trop2+ CD49f Lo) populations using the RNeasy Mini kit (QIAGEN). Samples with a RNA integrity number (RIN) > 8 were used for construction of RNA-seq libraries.
RNA-seq libraries were constructed using the Ovation RNA-seq V2 (Nugen) and PrepX ILM DNA (IntegenX) kits.

tag: patient

tag: tissue type

value: cancer

tag: cell type

value: basal

tag: cell population

value: Trop2+ CD49f Hi


title: BS2980 cancer Trop2+ CD49f Lo

description: Sample 15

value: luminal

value: Trop2+ CD49f Lo


title: BS3337 benign Trop2+ CD49f Hi

description: Sample 16

value: benign


title: Urine_APAP (Acetaminophen)_D2_2

value: Urine

value: Sprague-Dawley

value: APAP (Acetaminophen)


title: Urine_vehicle (0.5% methylcellulose)_D2_3

value: vehicle (0.5% methylcellulose)


title: Liver_CCl4 (Carbon Tetrachloride)_D2_2

value: Liver

value: CCl4 (Carbon Tetrachloride)

value: Qiagen RNeasy_96


title: Kidney_Cisplatin_D4_2

value: Kidney

value: Cisplatin

value: 5 mg/kg

value: IV; once

value: Male

value: Weeks


title: Liver_vehicle (Corn Oil)_D2_1

value: vehicle (Corn Oil)

value: 0 mg/kg

value: PO; once


title: Liver_vehicle (0.5% methylcellulose)_D2_1


title: Kidney_Cisplatin_D4_3


title: BS3337 cancer Trop2+ CD49f Hi

description: Sample 18

value: cancer

value: basal

value: Trop2+ CD49f Hi


title: Liver_APAP (Acetaminophen)_D2_1

value: Sprague-Dawley

value: APAP (Acetaminophen)


title: Liver_APAP (Acetaminophen)_D2_2

value: Liver


title: Liver_APAP (Acetaminophen)_D2_3


title: Liver_CCl4 (Carbon Tetrachloride)_D2_1

value: CCl4 (Carbon Tetrachloride)


title: BS2506 benign Trop2+ CD49f Hi

description: Sample 7

value: benign


title: BS2340 benign Trop2+ CD49f Hi

description: Sample 4


title: Liver_vehicle (0.5% methylcellulose)_D2_3

value: vehicle (0.5% methylcellulose)

value: Qiagen RNeasy_96


title: Liver_vehicle (0.5% methylcellulose)_D2_2


title: Kidney_Cisplatin_D4_1

value: Kidney

value: Cisplatin

value: 5 mg/kg


title: Kidney_vehicle (0.9% Sterile Saline)_D4_2

value: vehicle (0.9% Sterile Saline)

value: IV; once

value: Male

value: Weeks


title: SU484-pHSC

first: Jason

middle: Daniel

last: Buenrostro

address: 415 Main Street

institute: Broad Institute

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh37/hg19) using STAR using standard input parameters. Aligned reads were filtered for those reads that map uniquely to non-mitochondrial regions.
Duplicate reads (artifacts from amplification) were removed using PICARD MarkDuplicates.
Processed BAM files were analyzed for transcript counts using HTseq against the UCSC refGene transcriptome. Transcript counts were processed using DESeq2, normalizing for both library size and transcript GC content using Conditional Quantile Normalization (Hansen et al., 2012).
Genome_build: hg19
Supplementary_files_format_and_content: Count file is a tab-delimited text file where rows represent unique genes and columns represent unique samples.

source_name: pHSC

extract_protocol:
RNA was isolated from 1,000-100,000 FACS-purified cells using the Qiagen RNeasy Plus Micro Kit
5 ul of total RNA (300 pg – 80 ng) was used as input into the NuGen Ovation V2 cDNA synthesis kit. SPIA-amplified cDNA was sheared using a Covaris S2 sonicator as follows: 10% duty cycle, 5 intensity, 100 cycles/burst, 5 minutes, 120 ul volume. Sheared cDNA was purified and size selected using Ampure XP beads at a 0.9:1 beads:sample ratio. After cleanup, Illumina TruSeq adapters were ligated onto the cDNA using the NEB Next Ultra library prep kit per manufacturer instructions

value: acute myeloid leukemia, pre-leukemic hematopoietic stem cell

tag: donorid

tag: sample type

value: primary human leukemia cell from cryopreserved sample


title: shCac_D, repl 1

city: Lausanne

first: Mauro

last: Delorenzi

address: Génopode Building, Quartier Sorge

country: Switzerland

institute: Swiss Institute of Bioinformatics

data_processing:
CASAVA pipeline v 1.8.2 was used for base-calling
The reads were quality trimmed with sickle [Joshi NA, Fass JN. (2011). Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files [Software]. Available at https://github.com/najoshi/sickle.] using parameters -q 20 -l 20
The reads were aligned to the human genome build hg19 using RUM v 1.0.9 [Grant et al (2011): Comparative analysis of RNA-seq alignment algorithms and the RNA-seq unified mapper (RUM). Bioinformatics 27(18):2518-2528].
The featurequant2geneprofiles.pl script provided with RUM was used to generate FPKM estimates for each intron, exon and gene in the built-in annotation, using only uniquely mapping reads.
Genome_build: hg19
Supplementary_files_format_and_content: GQY2025_expression.min: text file with FPKM estimates from featurequant2geneprofiles.pl for each intron, exon and gene in the built-in annotation. Columns: feature ID, location, shCtrl repl 1, shCtrl repl 2, shCac_C repl 1, shCac_C repl 2, shCac_D repl 1, shCac_D repl 2

source_name: shCac_D, repl 1

growth_protocol: U2OS cells were grown in a high glucose D-MEM (Invitrogen) medium supplemented with 10% TET-free FBS (Pan Bio Tech) and 100 U/ml Penicillin-Streptomycin (Sigma-Aldrich) in an atmosphere containing 6% CO2 at 37°C

extract_protocol:
Total RNA was isolated using the TRIzol reagent (Invitrogen) according to manufacturer's instructions,
Roughly 5 µg of isolated RNA was sent to Fasteris SA (Plan-les-Ouates, CH) for high-throughput RNA sequencing using Illumina technology. The sequencing was performed with a single-end protocol providing reads of 100 bp.

treatment_protocol: U2OS cells were transfected at 60% confluency with shRNA plasmids using Lipofectamine 2000 (Invitrogen) according to manufacturer's instructions.

value: Human osteosarcoma U2OS cells

value: shRNA transfection

tag: time


title: BS2916 cancer Trop2+ CD49f Lo

description: Sample 20

value: cancer

value: luminal

value: Trop2+ CD49f Lo


title: shCtrl, repl 1

source_name: shCtrl, repl 1


title: BS3337 cancer Trop2+ CD49f Lo

description: Sample 19


title: shCtrl, repl 2

source_name: shCtrl, repl 2


title: BS3337 benign Trop2+ CD49f Lo

description: Sample 17

value: benign


title: GEN 3h BIO2

city: Kgs. Lyngby

first: Gitte

middle: M.

last: Knudsen

state: Not applicable

address: Matematiktorvet, Bldg 301

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

description: mRNA and sRNAs

data_processing:
The RNA seq data was analyzed using the CLC genomics workbench software (CLC Aarhus, version 6.0). Quality and quantity of RNA sequence data was evaluated by the number of reads, GC%, PHRED-score, nucleotide contribution, quality distribution and enriched 5mers sequences. All reads were trimmed, removing the 15 first nucleotides from the 5´end due to non-normal nucleotide distribution. Subsequently, reads were sorted according to their respective adaptor sequences and individually aligned to the reference genome. Reads Per Kilobase per Million (RPKM) was used as expression value. Quality control of the transcriptomic data was evaluated by hierarchal clustering and principal component analysis. The gene expression profiles of biological replicates were paired and compared between treated and control samples within the same time point. Baggerlys test was used to evaluate statistically significant gene expression differences with a statistical filter of fold changes above 2, P-value < 0.05 and a false discovery rate (FDR) of < 0.05
Genome_build: L. monocytogenes EGD-e reference genome (NC_003210.1)
Supplementary_files_format_and_content: xslx files including total gene reads, RPKM values etc. for each sample

organism: Listeria monocytogenes

source_name: Listeria monocytogenes_GEN_3h

growth_protocol: To obtain balanced growth, an overnight culture of Listeria monocytogenes EGD was diluted 10^9-fold in 5 ml BHI and grown for 16h at 37˚C at 250 rpm. This culture was used for inoculation of 50 ml prewarmed BHI to OD600 = 0.01 and grown at 37˚C with 250 rpm to OD600 = 0.1. The culture was split in five by diluting 8 ml culture with 42 ml pre-warmed BHI broth and incubated again. At OD600 = 0.1, equal volumes of antibiotic or MQ water were added to each flask to obtain final concentrations of 0.03 µg/ml ampicillin, 0.035 µg/ml tetracycline, 0.3 µg/ml gentamicin or 0.2 µg/ml co-trimoxazole. Samples for gene expression and bacterial counts were taken at time zero of supernatant addition for the MQ control and at 3h for all samples, with two independent biological replicates.

extract_protocol:
Samples for RNA sequencing were harvested from antibiotic-exposed and control cells at 0h and 3h and were quenched for 30 min in ice-cold 2% phenol, 38% ethanol, 62% water, to stabilise RNA (Eriksson et al., 2003). Cells were pelleted by centrifugation and stored at -80°C until total RNA extraction using Trizol (Invitrogen) according to Gomez-Lozano et al. (2012). Quantity and quality of the purified total RNA was evaluated by Nanodrop and Agilent 2100 Bioanalyzer using the RNA 6000 Nano kit. To reduce the amount of rRNA reads for the RNA sequencing, we isolated mRNA from good quality total RNA (RIN 9.8-10) using the MICROBExpress kit (Ambion #AM1905) according to the manufacture’s protocol. Depletion of the 16S and 23S was verified on a RNA 6000 Nanochip (2100 Bioanalyser, Agilent) and quantity was measured using a Qubit RNA assay (Invitrogen).
Libraries for RNA Seq were prepared using the TruSeq RNA Sample preparation Kit v2 (set A: RS-122-2001 and set B: RS-122-2002) according to the manufactures protocol. In brief, cDNA was generated from 325 ng mRNA, which was mixed with 13 µl Elute, Prime and Fragment mix and fragmented to approximately 180 bp. Specific adaptors were ligated to each of the 20 samples. The library was validated by measuring quantity with the Qubit dsDNA BR assay kit and quality with the Agilent 2100 Bioanalyzer on DNA-1000 chip. Due to a peak at 1500 bp, an E-gel size select (Invitrogen G6610-02) was performed to isolate the cDNA sequences of 200-400 bp. Lastly, each library was normalized to 10 nM and pooled yielding a final concentration of 10.3 nM with an average base pair size of 270.

value: EGD

value: 0.3 µg/ml gentamicin at time 3h


title: BS2980 benign Trop2+ CD49f Lo

description: Sample 13


title: BS2980 benign Trop2+ CD49f Hi

description: Sample 12

value: basal

value: Trop2+ CD49f Hi


title: BS2771 cancer Trop2+ CD49f Lo

description: Sample 11


title: BS2506 benign Trop2+ CD49f Lo

description: Sample 8


title: BS2553 cancer Trop2+ CD49f Lo

description: Sample 10


title: BS2553 cancer Trop2+ CD49f Hi

description: Sample 9


title: BS2340 cancer Trop2+ CD49f Hi

description: Sample 6


title: SU484-Blast

source_name: Blast

value: acute myeloid leukemia, blast cell


title: BS2339 cancer Trop2+ CD49f Hi

description: Sample 3


title: BS2340 benign Trop2+ CD49f Lo

description: Sample 5


title: SU070-pHSC


title: SU209-Blast


title: BS2339 benign Trop2+ CD49f Lo

description: Sample 2


title: BS2339 benign Trop2+ CD49f Hi

description: Sample 1


title: MQ 3h BIO3

description: mRNA and sRNAs

source_name: Listeria monocytogenes_MQ_3h

value: MQ water at time 3h


title: shCac_C, repl 2

source_name: shCac_C, repl 2


title: shCac_C, repl 1

source_name: shCac_C, repl 1


title: SU351-Blast


title: GEN 3h BIO3

description: mRNA and sRNAs


title: SU048-pHSC


title: SU351-pHSC


title: TET 3h BIO3

description: mRNA and sRNAs

source_name: Listeria monocytogenes_TET_3h

value: 0.035 µg/ml tetracycline at time 3h


title: SXT 3h BIO3

description: mRNA and sRNAs

source_name: Listeria monocytogenes_SXT_3h

value: 0.2 µg/ml co-trimoxazole at time 3h


title: SXT 3h BIO2

description: mRNA and sRNAs


title: osm-9_200mM_NaCl_4

city: Orono

first: Benjamin

middle: L

last: King

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

data_processing:
Reads were aligned to genome build WS235 using Tophat 1.4.1.
Mapped reads were analyzed using Cufflinks 2.0.1 and Ensembl version 71 annotation.
Read counts per gene were analyzed using R/edgeR 3.2.4.
Genome_build: Genome build WS235; Ensembl version 71 annotation.
Supplementary_files_format_and_content: Tab-delimited text file with read counts per gene per sample. Columns are Cufflinks transcript ID, Ensembl gene symbol, Ensembl gene ID, Ensembl transcript IDs (comma-separated), followed by counts per sample.

organism: Caenorhabditis elegans

growth_protocol: Worms were cultured at 20 °C using standard methods (Brenner S. The genetics of Caenorhabditis elegans. Genetics 1974 77:71-94).

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA).
PolyA+ TruSeq RNA sequencing libraries were prepared for sequencing using standard Illumina protocols (Illumina, Inc., San Diego, CA).

treatment_protocol: Hypertonic agar plates were generated by adding NaCl to standard nematode growth medium.

tag: developmental stage


title: MQ 0h BIO3

description: mRNA and sRNAs

source_name: Listeria monocytogenes_MQ_0h

value: MQ water at time 0h


title: shCac_D, repl 2

source_name: shCac_D, repl 2


title: MDA231_CD3-CD28_SP

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

description:
MDAS328_RNA-seq
Transcriptome analysis by RNA-seq

data_processing:
TopHat 2.0.8b. was used for mapping sequence reads to the human genome (hg19) with the parameter for Illumina stranded sequencing (--library-type fr-firststrand).
BedTools 2.16.2 and bedGraphToBigWig generated stranded binary wiggle files after in-house scripts split reads mapped to each strand.
FeatureCounts 1.4.6 was used to compute the number of reads mapped to each gene and transcript.
DESeq 1.10.1 was used for differential expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet contains FPKM values for each transcript in all samples.

source_name: MDA-MB-231 cell line

growth_protocol: Blood samples from healthy donors were purchased from a local blood bank. Peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll-Paque (GE Healthcare) density gradient separation. To activate T cells, a total of 3 million PBMCs were treated with immobilized anti-CD3 and soluble anti-CD28 antibodies (eBioscience) in 1ml of RPMI-1640 media supplemented with 10% FBS. After 48 hrs, PBMCs and the conditioned-media were harvested. PBMCs were transferred into 0.4µm Transwell Insert (Corning) and placed into 6-well plates with pre-seeded MDA-MB-231 and MCF7 cells, respectively. MDA-MB-231 or MCF7 cells were co-cultured with PBMCs alone or the conditioned-media or a combination of both for 24 hrs, and then harvested for further analysis. Control experiments were performed in the same manner except that isotype control antibodies were used.

extract_protocol:
RNA was extracted using Qiagen Qiazal reagents
Libraries for stranded mRNA sequencing were prepared using KAPA Stranded mRNAseq Kit Illumina platform (Kapa Biosystems) following manufacturer’s instructions.

treatment_protocol: No treatment invovled.

tag: cell types

value: Breast Cancer Cell line, ER(-)

tag: tumorgenecity

value: Tumor

value: CD3-CD28 SP


title: TET 3h BIO2

description: mRNA and sRNAs


title: osm-9_200mM_NaCl_2


title: SU209-pHSC

value: acute myeloid leukemia, pre-leukemic hematopoietic stem cell

value: primary human leukemia cell from cryopreserved sample


title: AMP 3h BIO2

description: mRNA and sRNAs

source_name: Listeria monocytogenes_AMP_3h

value: 0.03 µg/ml ampicillin at time 3h


title: SU070-Blast


title: MQ 3h BIO2

description: mRNA and sRNAs


title: AMP 3h BIO3

description: mRNA and sRNAs


title: MCF7_CD3-CD28_SP

description:
MCF7S328_RNA-seq
Transcriptome analysis by RNA-seq

source_name: MCF7 Cell line

value: Breast Cancer Cell line, ER(+)


title: MCF7_Isotype_PBMC+SP

description:
MCF7PS_RNA-seq
Transcriptome analysis by RNA-seq

value: Isotype PBMC+SP


title: osm-9_51mM_NaCl_4


title: osm-9_51mM_NaCl_1


title: N2_200mM_NaCl_1


title: osm-9_51mM_NaCl_2


title: N2_51mM_NaCl_2


title: MDA231_Isotype_SP

description:
MDAS_RNA-seq
Transcriptome analysis by RNA-seq

value: Isotype SP


title: SU048-Blast


title: MDA231_CD3-CD28_PBMC+SP

description:
MDAPS328_RNA-seq
Transcriptome analysis by RNA-seq

value: CD3-CD28 PBMC+SP


title: MQ 0h BIO2

description: mRNA and sRNAs

value: EGD


title: MDA231_CD3-CD28_PBMC

description:
MDAP328_RNA-seq
Transcriptome analysis by RNA-seq

value: CD3-CD28 PBMC


title: osm-9_200mM_NaCl_1


title: N2_51mM_NaCl_1


title: MCF7_Isotype_SP

description:
MCF7S_RNA-seq
Transcriptome analysis by RNA-seq


title: osm-9_200mM_NaCl_3


title: MDA231_Isotype_PBMC

description:
MDAP_RNA-seq
Transcriptome analysis by RNA-seq

value: Isotype PBMC


title: MDA231_Isotype_PBMC+SP

description:
MDAPS_RNA-seq
Transcriptome analysis by RNA-seq


title: osm-9_51mM_NaCl_3


title: 5131-Memory-T336

city: New York

middle: Conrad

last: Thompson

state: NY

address: 1 Gustave L. Levy Place

department: Charles Bronfman Institute for Personalized Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
We used Casava 1.8.2 (Illumina) to demultiplex and process the raw reads into fastq files.
RNA-seq reads in FASTQ files were aligned to hg19 using Tophat 2.0.0
Reads were assigned to annotated genes and counted using the "summarizeOverlaps" function from the GenomicRanges Bioconductor package in "IntersectionNotEmpty" mode (TODO cite GenomicRanges: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118 ). Overlaps were computed to features of type "exon" with a Parent feature has type "mRNA" (excluding "ncRNA" in particular), grouped by gene ID (the Parent property of the mRNA feature to which each exon belongs).
Read counts were normalized to CPM using a non-standard application of the TMM method from the edgeR package (see article text)
Gene CPM values were normalized for gene length by dividing by the length in kb of the longest transcript isoform for each gene to produce fragments per kilobase per million reads (FPKM) values
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files (with column names in first line) with metadata columns Entrez Gene ID, Gene Symbol, Gene Name, Unigene, Ensembl, Refseq, UCSC known gene, and Uniprot, followed by the transcript length used for FPKM calculations, and finally the three data columns raw count, normalized CPM, and normalized FPKM.

source_name: Memory CD4 T-cells

growth_protocol: CD4 T cells were cultured in RPMI 1640 (Mediatech, #SH30027.07) supplemented with 100 U/ml Penicillin, 100 g/ml Streptomycin and 10% FBS at 37 °C and 5% CO2.  T cells were activated with DynaBead Human T-Activator CD3/CD28 (Invitrogen, #111.32D) for 24 and 120 h.  Cells maintained in culture out to 2 weeks received 30 U/mL of human recombinant IL-2 (NIH repository) beginning at day 5 after activation.

extract_protocol:
Cells harvested for RNA (5 x 106 cells) were washed 3 times in 1 mL of PBS without calcium and magnesium (Corning, #21-040-CV), flash frozen in liquid nitrogen, and stored at -80°C until RNA purification.  RNA for RNA-Seq was isolated from purified cells using an All Prep kit (QIAGEN, #80004) following the manufacturer’s instructions (www.qiagen.com).
For RNA-Seq, purified total RNA was converted to cDNA using the Ovation RNA-Seq system (NuGEN) followed by S1 endonuclease digestion (Promega, M5761) as previously described (Head et al, 2011).  Digested cDNA libraries were then end-repaired and A-tailed.  Indexed adapters were ligated, and ligation product was purified on Agencourt AMPure XP beads (Beckman Coulter Genomics, #A83880) followed by size selection from 2% agarose.  Purified product was amplified with 15 cycles of PCR followed by size selection from 2% agarose. Libraries were assessed on an Agilent Bioanalyzer using a DNA chip and quantitated using the Quant-iT ds DNA BR Assay kit (Invitrogen, #Q32853) and a Qubit Fluorimeter (Invitrogen).  Cluster generation and sequencing on an Illumina HiSeq system was conducted directly with purified libraries following manufacturer’s instructions (www.illumina.com).  100 bp single-end reads were generated for naïve and memory CD4 T cells from 4 donors with 2 samples per lane.

value: Memory

tag: activated

value: TRUE

tag: days after activation

tag: donor id

tag: technical batch


title: MCF7_CD3-CD28_PBMC

description:
MCF7P328_RNA-seq
Transcriptome analysis by RNA-seq


title: 5053-Memory-T336


title: 5291-Memory-T120


title: N2_200mM_NaCl_2

tag: strain


title: 5291-Memory-T336


title: MCF7_Isotype_PBMC

description:
MCF7P_RNA-seq
Transcriptome analysis by RNA-seq

tag: treatment


title: MCF7_CD3-CD28_PBMC+SP

description:
MCF7PS328_RNA-seq
Transcriptome analysis by RNA-seq

tag: cell line


title: 4659-Memory-T336


title: 5291-Memory-T24


title: 5053-Memory-T24


title: 4659-Memory-T120


title: 5053-Memory-T120


title: 5131-Memory-T0

value: FALSE


title: 5291-Memory-T0


title: 4659-Memory-T24


title: 5131-Memory-T120


title: 5053-Memory-T0


title: 5131-Memory-T24


title: 4659-Memory-T0


title: 5053-Naive-T336

source_name: Naive CD4 T-cells

value: Naive


title: 5291-Naive-T24


title: 4659-Naive-T336


title: 5291-Naive-T336


title: 5131-Naive-T336


title: 5291-Naive-T120


title: 5131-Naive-T120


title: 5053-Naive-T24


title: 5131-Naive-T0


title: 5053-Naive-T120


title: 5053-Naive-T0


title: 4659-Naive-T24


title: 4659-Naive-T120


title: 5131-Naive-T24


title: H3K27me3-Memory-D5-Donor5291

description:
H3K27me3.Memory.D5_peaks_IDR_filtered.bb
H3K27me3_peaks_IDR_filtered.bb
H3K27me3.Memory.D5_normalized_cpm_pileup.bw

data_processing:
We used Casava 1.8.2 (Illumina) to demultiplex and process the raw reads into fastq files.
Reads in FASTQ files were aligned to hg19 using bowtie2 version 2.1.0
Peaks were called for each sample against all input reads using macs2 2.1.0.20141030, which also produced coverage depth tracks
Consensus peaks were determined using the IDR method for each condition and overall
Coverage depth tracks were normalized using the method of Lun & Smyth 2014
Reads were assigned to annotated gene promoters and counted using the "featureCounts" function from the Rsubread Bioconductor package
Genome_build: hg19
Supplementary_files_format_and_content: BigWig of sample coverage depth in raw counts
Supplementary_files_format_and_content: BigWig of sample coverage depth in normalized CPM
Supplementary_files_format_and_content: BigBed of consensus peaks for each treatment group
Supplementary_files_format_and_content: BigBed of consensus peaks for all samples
Supplementary_files_format_and_content: GFF3 of promoter counts, CPM, and FPKM (1kb radius about TSS)
Supplementary_files_format_and_content: GFF3 of promoter counts, CPM, and FPKM (2.5kb radius about TSS)

extract_protocol:
3 x 107 cells were fixed for 10 min in cell culture medium with 1% formaldehyde at room temperature.  Fixation was quenched with 10% glycine for 5 min at room temperature.  Cell pellets were flash frozen in liquid nitrogen and stored at -80°C until chromatin isolation.  Chromatin was isolated from cell pellets using the ChIP-It Express Enzymatic Shearing Kit (Active Motif, #53035) per the manufacturer’s instructions (www.activemotif.com).  For immunoprecipitation, 7.5 μg of chromatin was diluted in a total of 1 mL of low salt wash buffer (0.1% SDS, 1.0% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl) with protease inhibitor cocktail and pre-cleared with 30 μL of Dynal Protein G magnetic beads (Invitrogen, #10004D) for 2 h at room temperature with rotation.  20 μL of pre-cleared chromatin was saved for input analysis and stored at -80°C.  Remaining chromatin was incubated with 2 μL of anti-H3K4me2 antibody (Millipore, #07-030) or 4 μL of anti-H3K4me3 antibody (Millipore, #07-473) overnight at 4°C with rotation.  30 μL of Dynal Protein G beads were added to each ChIP and incubated at 4°C with rotation for 2 h.  Beads were washed three times in low salt wash buffer and then 2 times with high salt wash buffer (0.1% SDS, 1.0% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl) with 5 min of rotation at 4°C for each wash.  Beads were resuspended in 150 μL of elution buffer (1% SDS, 0.1M NaHCO3) and incubated in a thermomixer at 65°C for 30 minutes at 1,200 rpm to reverse cross-linking.  2 μL of Proteinase K (Invitrogen, #AM2546) was added to each sample, and 6 μL of 5 M NaCl was added for a total concentration of 200 mM.  Samples were then incubated in a thermomixer at 65°C overnight at 1,200 rpm.  Eluted samples were removed from the beads and purified using the Qiaquick PCR purification kit (QIAGEN, #28104) per the manufacturer’s instructions (www.qiagen.com).
For ChIP-Seq, 10 ng of purified DNA from individual chromatin IPs were end repaired and A-tailed.  Indexed adapters were ligated, and ligation product was purified on Agencourt Ampure XP beads and processed followed by size selection from 2% agarose.  Purified product was amplified with 15 cycles of PCR followed by size selection from 2% agarose. Libraries were assessed on an Agilent Bioanalyzer using a DNA chip and quantitated using the Quant-iT ds DNA BR Assay kit (Invitrogen, #Q32853) and a Qubit Fluorimeter (Invitrogen).  Cluster generation and sequencing on an Illumina HiSeq system was conducted directly with purified libraries following manufacturer’s instructions (www.illumina.com).  100 bp single-end reads were generated for naïve and memory CD4 T cells from 4 donors with 2 samples per lane.

tag: chip antibody


title: H3K27me3-Naive-D0-Donor5131

description:
H3K27me3.Naive.D0_peaks_IDR_filtered.bb
H3K27me3_peaks_IDR_filtered.bb
H3K27me3.Naive.D0_normalized_cpm_pileup.bw


title: H3K27me3-Memory-D0-Donor5131

description:
H3K27me3.Memory.D0_peaks_IDR_filtered.bb
H3K27me3_peaks_IDR_filtered.bb
H3K27me3.Memory.D0_normalized_cpm_pileup.bw


title: H3K27me3-Naive-D14-Donor5053

description:
H3K27me3.Naive.D14_peaks_IDR_filtered.bb
H3K27me3_peaks_IDR_filtered.bb
H3K27me3.Naive.D14_normalized_cpm_pileup.bw


title: H3K27me3-Naive-D5-Donor5053

description:
H3K27me3.Naive.D5_peaks_IDR_filtered.bb
H3K27me3_peaks_IDR_filtered.bb
H3K27me3.Naive.D5_normalized_cpm_pileup.bw


title: 5291-Naive-T0


title: 4659-Naive-T0


title: H3K27me3-Naive-D14-Donor5291


title: H3K27me3-Naive-D5-Donor5291


title: H3K27me3-Naive-D14-Donor4659


title: H3K27me3-Memory-D5-Donor4659


title: H3K27me3-Naive-D5-Donor5131


title: input-Memory-D14-Donor5131

value: input


title: H3K27me3-Memory-D0-Donor4659


title: H3K27me3-Memory-D14-Donor5131

description:
H3K27me3.Memory.D14_peaks_IDR_filtered.bb
H3K27me3_peaks_IDR_filtered.bb
H3K27me3.Memory.D14_normalized_cpm_pileup.bw


title: H3K27me3-Memory-D14-Donor5291


title: input-Naive-D14-Donor5291


title: H3K27me3-Naive-D0-Donor4659


title: H3K27me3-Naive-D14-Donor5131


title: H3K27me3-Memory-D5-Donor5131


title: H3K27me3-Naive-D0-Donor5053


title: input-Memory-D14-Donor5053


title: H3K27me3-Memory-D5-Donor5053


title: H3K27me3-Memory-D0-Donor5053


title: input-Naive-D14-Donor4659


title: H3K4me2-Naive-D14-Donor5291

description:
H3K4me2.Naive.D14_peaks_IDR_filtered.bb
H3K4me2_peaks_IDR_filtered.bb
H3K4me2.Naive.D14_normalized_cpm_pileup.bw


title: H3K27me3-Naive-D0-Donor5291


title: input-Naive-D14-Donor5131


title: H3K27me3-Naive-D5-Donor4659


title: H3K27me3-Memory-D0-Donor5291


title: H3K27me3-Memory-D14-Donor4659


title: input-Memory-D14-Donor5291


title: H3K4me3-Memory-D14-Donor5131

description:
H3K4me3.Memory.D14_peaks_IDR_filtered.bb
H3K4me3_peaks_IDR_filtered.bb
H3K4me3.Memory.D14_normalized_cpm_pileup.bw


title: H3K4me3-Naive-D14-Donor5131

description:
H3K4me3.Naive.D14_peaks_IDR_filtered.bb
H3K4me3_peaks_IDR_filtered.bb
H3K4me3.Naive.D14_normalized_cpm_pileup.bw


title: H3K4me3-Memory-D14-Donor5053


title: H3K4me2-Naive-D14-Donor4659


title: input-Naive-D14-Donor5053


title: input-Memory-D14-Donor4659


title: H3K4me3-Naive-D14-Donor5291


title: H3K27me3-Naive-D1-Donor5291

description:
H3K27me3.Naive.D1_peaks_IDR_filtered.bb
H3K27me3_peaks_IDR_filtered.bb
H3K27me3.Naive.D1_normalized_cpm_pileup.bw


title: input-Naive-D1-Donor5131


title: H3K4me2-Naive-D1-Donor5131

description:
H3K4me2.Naive.D1_peaks_IDR_filtered.bb
H3K4me2_peaks_IDR_filtered.bb
H3K4me2.Naive.D1_normalized_cpm_pileup.bw


title: H3K27me3-Naive-D1-Donor5131


title: H3K4me3-Memory-D14-Donor5291


title: input-Memory-D1-Donor5131


title: H3K4me3-Memory-D1-Donor5131

description:
H3K4me3.Memory.D1_peaks_IDR_filtered.bb
H3K4me3_peaks_IDR_filtered.bb
H3K4me3.Memory.D1_normalized_cpm_pileup.bw


title: H3K4me2-Memory-D14-Donor5291

description:
H3K4me2.Memory.D14_peaks_IDR_filtered.bb
H3K4me2_peaks_IDR_filtered.bb
H3K4me2.Memory.D14_normalized_cpm_pileup.bw


title: H3K27me3-Memory-D1-Donor5131

description:
H3K27me3.Memory.D1_peaks_IDR_filtered.bb
H3K27me3_peaks_IDR_filtered.bb
H3K27me3.Memory.D1_normalized_cpm_pileup.bw


title: H3K4me3-Memory-D14-Donor4659


title: H3K4me2-Naive-D1-Donor5291


title: H3K4me2-Naive-D14-Donor5131


title: H3K4me3-Naive-D14-Donor5053


title: H3K4me2-Naive-D14-Donor5053


title: H3K4me2-Memory-D14-Donor5053


title: H3K4me3-Naive-D14-Donor4659


title: H3K27me3-Naive-D1-Donor5053


title: input-Naive-D1-Donor5291


title: input-Memory-D1-Donor5291


title: H3K4me3-Memory-D1-Donor5291


title: H3K4me2-Memory-D1-Donor5291

description:
H3K4me2.Memory.D1_peaks_IDR_filtered.bb
H3K4me2_peaks_IDR_filtered.bb
H3K4me2.Memory.D1_normalized_cpm_pileup.bw


title: H3K4me2-Memory-D14-Donor4659


title: input-Naive-D1-Donor4659


title: H3K4me3-Naive-D1-Donor4659

description:
H3K4me3.Naive.D1_peaks_IDR_filtered.bb
H3K4me3_peaks_IDR_filtered.bb
H3K4me3.Naive.D1_normalized_cpm_pileup.bw


title: H3K27me3-Memory-D1-Donor5291


title: H3K27me3-Naive-D1-Donor4659


title: H3K4me3-Naive-D1-Donor5131


title: input-Memory-D1-Donor4659


title: H3K4me2-Naive-D1-Donor5053


title: H3K4me2-Memory-D1-Donor5131


title: H3K4me3-Naive-D1-Donor5053


title: input-Naive-D1-Donor5053


title: input-Naive-D5-Donor5291


title: input-Naive-D0-Donor5131


title: input-Naive-D5-Donor5131


title: H3K4me2-Memory-D1-Donor5053


title: input-Memory-D5-Donor5131


title: input-Naive-D5-Donor5053


title: H3K27me3-Memory-D1-Donor5053


title: H3K4me3-Memory-D1-Donor5053


title: input-Naive-D0-Donor5053


title: H3K4me3-Naive-D1-Donor5291


title: H3K4me2-Naive-D1-Donor4659


title: input-Naive-D5-Donor4659


title: input-Memory-D5-Donor5291


title: H3K4me2-Memory-D1-Donor4659


title: H3K4me3-Memory-D1-Donor4659


title: H3K27me3-Memory-D1-Donor4659


title: input-Memory-D0-Donor5291


title: input-Memory-D1-Donor5053


title: input-Naive-D0-Donor5291


title: input-Memory-D0-Donor5131


title: input-Memory-D5-Donor5053


title: H3K4me2-Memory-D14-Donor5131


title: input-Memory-D5-Donor4659


title: input-Naive-D0-Donor4659


title: H3K4me3-Naive-D5-Donor5291

description:
H3K4me3.Naive.D5_peaks_IDR_filtered.bb
H3K4me3_peaks_IDR_filtered.bb
H3K4me3.Naive.D5_normalized_cpm_pileup.bw


title: H3K4me2-Naive-D0-Donor5291

description:
H3K4me2.Naive.D0_peaks_IDR_filtered.bb
H3K4me2_peaks_IDR_filtered.bb
H3K4me2.Naive.D0_normalized_cpm_pileup.bw


title: H3K4me3-Naive-D0-Donor5291

description:
H3K4me3.Naive.D0_peaks_IDR_filtered.bb
H3K4me3_peaks_IDR_filtered.bb
H3K4me3.Naive.D0_normalized_cpm_pileup.bw


title: H3K4me3-Memory-D5-Donor5291

description:
H3K4me3.Memory.D5_peaks_IDR_filtered.bb
H3K4me3_peaks_IDR_filtered.bb
H3K4me3.Memory.D5_normalized_cpm_pileup.bw


title: H3K4me3-Memory-D0-Donor5291

description:
H3K4me3.Memory.D0_peaks_IDR_filtered.bb
H3K4me3_peaks_IDR_filtered.bb
H3K4me3.Memory.D0_normalized_cpm_pileup.bw


title: H3K4me2-Naive-D5-Donor5131

description:
H3K4me2.Naive.D5_peaks_IDR_filtered.bb
H3K4me2_peaks_IDR_filtered.bb
H3K4me2.Naive.D5_normalized_cpm_pileup.bw


title: H3K4me2-Memory-D5-Donor5291

description:
H3K4me2.Memory.D5_peaks_IDR_filtered.bb
H3K4me2_peaks_IDR_filtered.bb
H3K4me2.Memory.D5_normalized_cpm_pileup.bw


title: input-Memory-D0-Donor5053


title: H3K4me3-Naive-D5-Donor5131


title: H3K4me3-Naive-D0-Donor5131


title: H3K4me2-Naive-D0-Donor5131


title: H3K4me3-Memory-D5-Donor5131


title: H3K4me3-Memory-D0-Donor5131


title: H3K4me2-Memory-D5-Donor5131


title: H3K4me2-Memory-D0-Donor5291

description:
H3K4me2.Memory.D0_peaks_IDR_filtered.bb
H3K4me2_peaks_IDR_filtered.bb
H3K4me2.Memory.D0_normalized_cpm_pileup.bw


title: H3K4me3-Naive-D5-Donor5053


title: input-Memory-D0-Donor4659


title: H3K4me2-Memory-D0-Donor5131


title: H3K4me2-Naive-D5-Donor5291


title: H3K4me2-Memory-D0-Donor5053


title: H3K4me3-Naive-D5-Donor4659


title: H3K4me3-Memory-D5-Donor5053


title: H3K4me2-Naive-D5-Donor5053


title: H3K4me3-Naive-D0-Donor4659


title: H3K4me2-Naive-D0-Donor5053


title: H3K4me2-Memory-D5-Donor5053


title: H3K4me3-Memory-D0-Donor5053


title: H3K4me2-Naive-D0-Donor4659


title: H3K4me2-Memory-D5-Donor4659


title: H3K4me3-Memory-D5-Donor4659


title: H3K4me2-Memory-D0-Donor4659


title: R1 RUNX1 overexpressing

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description: lentiviral vector expressing RUNX1 & GFP

data_processing:
Sequence images were transformed with Illumina BaseCaller software to bcl files, which were demultiplexed to fastq files with CASAVA (version 1.8.2).
Molecule abundances for all RNA species and differentially expressed small RNA molecules were identified using the OASIS platform (Pubmed ID 25701573) with standard parameters. For annotation, OASIS used mirBase release 21 (2014) in addition to other resources.
Genome_build: hg19
Supplementary_files_format_and_content: Flat file with abundance measurements

source_name: K562 cells_RUNX1_overexpression

growth_protocol: K562 cells were grown in RPMI medium containing 1% Pen/Strep and 10% FCS

extract_protocol:
Total RNA was harvested from transduced K562 cells after 10 days in culture using Trizol reagent. Qiagen miRNeasy Kit (Cat#217004) was used with 1 ug of total RNA for the construction of sequencing libraries.
Library preparation for small RNA-Seq was performed using the TruSeq Small RNA Sample Preparation Kit from Illumina (catalog RS-200-0012) starting from 1000 ng of total RNA.

treatment_protocol: K562 cells were transduced with lentiviral vectors SIEW as empty control expressing GFP only or SIEW RUNX1 overexpressing human RUNX1 and GFP.


title: R3 RUNX1 overexpressing


title: MI

city: Ipswich

first: Barton

last: Slatko

state: Massachusetts

address: 240 County Road

institute: New England Biolabs

data_processing:
Sequenced reads were mapped to the genome using TopHat v1.4.1 with parameters -g 40.
Fragments Per Kilobase of Million mapped reads (FPKM) were calculated using Cufflinks v1.3.0.
Cufflinks assemblies were merged using Cuffmerge v1.0.0.
Cuffdiff v1.3.0 was used for differential expression testing with parameter --FDR FLOAT 0.01.
Genome_build: nDi.2.2
Supplementary_files_format_and_content: text files include FPKM values for each Sample

organism: Dirofilaria immitis

source_name: Male Intestine

extract_protocol:
Tissues were dissected, flash frozen on dry ice and RNA was harvested using Trizol reagent. New England Biolabs NEBNext® mRNA Library Prep Master Mix Set for Illumina® (Cat. # E6110) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TRS

tag: endosymbiont

value: Wolbachia

tag: tissue

value: Intestine

tag: gender

value: male


title: H3K4me3-Memory-D0-Donor4659

tag: cell type


title: MT

source_name: Male Testis

value: Testis


title: D

city: Beijing

first: Xiaoyang

last: Qi

address: haidian area,zhongguancun south street

country: China

institute: Chinese Academy of Agricultural Sciences

description: Coccinella septempunctata L.

data_processing:
Illumina Casava1.8 software used for basecalling.
The clean reads were filtered to remove reads with adaptors, low-quality reads (ratio of greater than 20 bases, less than 50%), and reads showing an N ratio (unknown sequences) greater than 5% using the FastX program (version 0.0.13)
The RPKM (reads per kb per million reads) method was used to calculate the expression counts of the unigenes. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Tcas_3.0.   Coccinella septempunctata L. assembly_sequence.fa is linked as a supplementary file on the Series record.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Coccinella septempunctata

source_name: adult

growth_protocol: Non-diapause and diapause-terminated female insects were reared at 24±1°C, with a RH of 70±10% and a 16:8 h light: dark (L: D) photoperiod. Female adults in diapause were reared at 18±1°C at an RH of 70±10% and a 10:14-h (L:D) photoperiod.

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Non-diapause and diapause-terminated female insects were collected after oviposition. Diapause female insects were collected after diapause 30days.

value: adult

tag: diapause state

value: diapause

tag: age

value: diapause day 30


title: MBW2

source_name: Male Body Wall

value: Body Wall


title: R2 RUNX1 overexpressing


title: ND

description: Coccinella septempunctata L.

tag: developmental stage

value: non-diapause

value: post natal day 1 (after oviposition)


title: H3K4me3-Naive-D0-Donor5053


title: FU2

source_name: Female Uterus

value: Uterus

value: female


title: S3 empty vector control

description: empty lentiviral vector expressing GFP

source_name: K562 cells_control


title: MBW1


title: S2 empty vector control

description: empty lentiviral vector expressing GFP


title: FH2

source_name: Female Head

value: Head


title: S1 empty vector control

description: empty lentiviral vector expressing GFP


title: H3K4me2-Naive-D5-Donor4659

value: TRUE


title: FU1


title: FI2

source_name: Female Intestine


title: FH1


title: DT

description: Coccinella septempunctata L.

value: diapause terminated


title: FBW2

source_name: Female Body Wall


title: Colxhalleri Standard biological replicate 3

city: Cologne

first: Fei

last: He

address: Zuelpicher Str. 47 B

department: Botanical Institute

institute: University of Cologne

description: replicate 3

data_processing:
FastX-toolkit was used for sequence trimming and filtering. Reads were mapping to the concatenation of the A. thaliana Col-0 reference genome (TAIR10, www.arabidopsis.org) and the A. lyrata MN47 reference genome (Araly1,(Nordberg et al. 2014) using tophat2 with -p 5, -N 5, --read-edit-dist 5 --read-gap-length 5. Uniquely and high-quality mapping reads were selected by "samtools view -q 10". Gene expression difference was computed by DESeq2. ASE analysis were calculated by the allele ratios, which fully decribed in the paper.
Supplementary_files_format_and_content: allele-specific levels of expression

organism: Arabidopsis thaliana x Arabidopsis halleri

source_name: Rossete

growth_protocol: A.thalianaxA.lyrata and A.thalianaxA.halleri F1 hybrids were germinated and grown on germination medium (GM) containing Murashige and Skoog salts, 1% sucrose, and 0.8% agar. The plants were stratified for 5 days at 4°C, and then grown for 4 weeks in a growth chamber at 22°C under 16 h light/8 h dark.

extract_protocol:
Total RNA was extracted from whole aerial part of one hybrid individual in 1 mL of TRIZOL Reagent (Thermo Fisher Scientific). DNA was cleaned up using the DNA-free kit (Thermo Fisher Scientific). RNA quality and quantity was examined with the Bioanalyzer 2100 (Agilent) and Qubit® 2.0 Fluorometer (Thermo Fisher Scientific). Two micrograms of Total RNA were used for library preparation.
The library preparation followed the TruSeq® RNA Sample Preparation v2 Guide (Illumina).

treatment_protocol: For dehydration, plants were removed from the agar and dehydrated in plastic dishes for 1 hour at 22°C under dim light (0.7±0.8 mmol sec±1 m±2). For cold exposure, plants were grown under dim light(0.7±0.8 mmol sec±1 m±2) at 4°C for 1 hour. Leaf samples of plants growing in non-stressful conditions (standard treatment) were collected on 4 week-old plants grown at 22°C. Each sample was prepared for 3 biological replicates in one week intervals.  prepared for 3 biological replicates in one week intervals.

value: 4 weeks

value: Standard growth condition

tag: ecotype


title: FBW1

value: TRS

value: Wolbachia


title: Colxhalleri Standard biological replicate 1

description: replicate 1


title: Colxhalleri Dehydration biological replicate 2

description: replicate 2

value: 1 hour dehydration at 22°C


title: Colxhalleri Dehydration biological replicate 3

description: replicate 3


title: Colxhalleri Cold biological replicate 2

description: replicate 2

value: 4°C for 1 hour


title: ColxMN47 Standard biological replicate 3

description: replicate 3

organism: Arabidopsis thaliana x Arabidopsis lyrata


title: ColxMN47 Dehydration biological replicate 3

description: replicate 3


title: ColxMN47 Standard biological replicate 2

description: replicate 2


title: Colxhalleri Dehydration biological replicate 1

description: replicate 1


title: Colxhalleri Cold biological replicate 3

description: replicate 3


title: ColxMN47 Cold biological replicate 2

description: replicate 2


title: Treatment_8

city: Zürich

first: Marc

last: Stevens

address: Winterthurerstrasse 272

department: Vetsuisse

institute: University of Zurich

data_processing:
Illumina raw data reads (100 bp) were separated by barcode and mapped against the genome of M. ruminantium DSM 1093 (GenBank accession no. CP001719) using CLC Genomics Workbench 6.5.1 (http://www.clcbio.com), applying the default settings. Maximum allowance of mismatches was set at 2, minimum length fraction at 0.9 and minimum similarity fraction at 0.8. Theprocessed data provided are the total counts per gene, not normalized against gene length or library size.
Genome_build: CP001719
Supplementary_files_format_and_content: The processed data files contain a table with in the first column the locus_tag of the gene as it is stored in NCBI Genbank (<locus_tag>), and in the second column the total counts resulting from the RNA mapping (<Total gene reads>).

organism: Methanobrevibacter ruminantium

source_name: M. ruminantium M1 DSM 1093 mono culture

growth_protocol: A pure culture of M. ruminantium (strain M1, DSM 1093) was obtained from the “Deutsche Sammlung von Mikroorganismen und Zellkulturen,” Braunschweig, Germany. It was anaerobically cultivated in 50 mL of modified methanobacterium medium (DSMZ No.1523) in 116 mL bottles under a CO2/H2 (0.2:0.8) atmosphere at 150 kPa and at 39°C in an incubation shaker as described previously. Growth of the cultures was monitored by recording CH4 formation and optical density at 600 nm (OD600). Lauric acid (C12) (≥97% purity) was obtained from Sigma-Aldrich (Buchs, Switzerland), and a stock solution with a concentration of 200 mg/mL was prepared by dissolving the C12 in sterile dimethyl sulfoxide (DMSO) (Sigma-Aldrich) and stored at room temperature (RT) for one week in darkness before supplementation. Nine bottles of 45 mL of pre-warmed anaerobic medium were inoculated with 5 mL of growing culture in its exponential phase (inoculation culture OD600 = approx. 0.64). The CH4 formation rate (µmol/mL/h) was determined at 24, 48, and 60 hours after inoculation and calculated from bottle head space gas volume and the amount of CH4 produced as described in with modification due to different headspace gas volume. The headspace gas initially present in the bottles filled with 100 kPa was calculated as 6.26 mmol.

extract_protocol:
Total RNA was isolated according to the modified Chomczynski and Sacchi protocol (1987) by using TRIzol ® Reagent (Life Technologies, USA). Briefly, frozen cell pellets from each sample were grounded with a sterile pre-chilled (4°C) mortar and pestle under liquid N2. TRIzol was added immediately to the grounded samples before they were thawed. The mixtures were transferred to sterile tubes and incubated at RT for 5 min. Chloroform with 1/5 volume of TRIzol was then added, vigorously mixed and incubated for further 2-3 min. The samples were centrifuged (12,000 × g, 15 min, 4°C) and the aqueous phases were collected. In order to remove any residual organic solvents from the samples, one additional chloroform extraction with half volume of the aqueous phase was performed. The incubation and centrifugation was repeated under the same conditions as described above. In order to precipitate RNA from the collected aqueous phases, isopropanol was added in the ½ volume and the mixtures were incubated at RT for 10 min. The precipitated RNAs were pelleted by centrifugation (12,000 × g, 10 min, 4°C), washed with 75% (v/v) ethanol, air-dried and re-suspended in RNase-free water. In order to remove genomic DNA from total RNA samples, they were further DNase-digested using RNase-Free DNase Set (Qiagen, Germany) according to the manufacturer’s instructions. After enzymatic treatment, RNA samples were purified by following subsequent steps: a) addition of the ½ volume of chloroform-IisoamylalcohlAA; b) centrifugation (12,000 × g, 5 min, 4°C); c) collection of the supernatant into the new tubes, d) addition of the 1/10 volume of sodium acetate (3M, pH 5.5) and 3 volumes of ice cold 100% (v/v) ethanol; e) overnight incubation in -20°C for RNA precipitation; f) centrifugation (12,000 × g, 15 min, 4°C), removal of supernatant and washing the RNA pellet with 75% (v/v) ethanol; g) centrifugation (12,000 × g, 15 min, 4°C); h) removal of supernatant and air-drying of RNA pellet; h) resuspension of RNA pellet in 50 µl of RNase-free water.
RNA-sequencing was performed on an Illumina HiSeq 2500 sequencer (Illumina Inc., California, USA) at the Functional Genomics Center Zurich (FGCZ). Libraries were prepared using the Ribo-Zero™ rRNA Removal Kit (Bacteria) (http://www.illumina.com/products/ribo-zero-rrna-removal-bacteria.html, Epicentre an Illumina company, San Diego, USA), followed by the TruSeq Stranded total RNA Sample Prep Kit (Illumina) according to the manufacturer’s protocol. The libraries were qualitatively and quantitatively checked using a Qubit® (1.0) Fluorometer (Life Technologies Europe BV, Zug, Switzerland) and a Bioanalyzer 2100 (Agilent, Basel, Switzerland) and were subsequently normalized at 10 nM in Tris-Cl (10mM, pH 8.5) containing 0.1 % Tween20. Cluster generation was performed using the TruSeq SR Cluster Kit v4-cBot-HS (Illumina) using 8 pM of pooled normalized libraries on the cBOT and stranded sequencing of 125 bp was done using the TruSeq SBS Kit v4-HS (Illumina).

treatment_protocol: After 60 hours of incubation, when cells reached the mid-exponential-phase, three bottles were supplemented with 0.1 mL of the C12 stock solution to reach a final concentration of 0.4 mg C12/mL (treatment group), three bottles were supplemented with 0.1 mL of DMSO (final concentration of DMSO: 0.2 %) (control group), and three bottles received no supplement (blank group). The concentration of C12 was chosen based on a pre-test and was in a range where most cells remained alive but where CH4 formation was inhibited (data not shown). After 1 h of incubation, CH4- formation rates were determined, and the survival rate of M. ruminantium was detected by using the LIVE/DEAD BacLight Bacterial Viability Kit for microscopy and quantitative assays as in our previous study (Kit L7012; Invitrogen GmbH, Darmstadt, Germany). In total, nine samples of each 50 mL of culture were anaerobically collected at 4°C after centrifugation at 5,000 × g for 6 min. Cell pellets were immediately frozen in liquid N2 and then stored at -80°C until RNA extraction.

tag: culture

value: mono

tag: culture suplemmentation

value: Lauric acid in DMSO


title: Treatment_9


title: Colxhalleri Standard biological replicate 2

description: replicate 2


title: ColxMN47 Cold biological replicate 3

description: replicate 3


title: FI1

value: Intestine


title: Treatment_7


title: FSONTC

city: Bogota

first: Silvia

last: Restrepo

state: Bogota

address: Carrera Primera #18A-12,

department: Biology

country: Colombia

institute: Universidad de los Andes

data_processing:
FOX reads were aligned to the Fusarium oxysporum reference genome using TopHat 2.0.14
FSO reads were aligned to the Fusarium solani reference genome using TopHat 2.0.14
Reads were assembled using cufflinks 2.2.0
Transcripts were merged to obtain a transcriptome assembly for each species
Nomalized counts were obtained via FPKM normalizetion in cufflinks 2.2.0
Differential expression was calculated using edgeR package in R
Genome_build: ASM14995v2 for Fusarium oxysporum (http://www.ncbi.nlm.nih.gov/assembly/GCA_000149955.2/);  v2.0 for Fusarium solani (http://www.ncbi.nlm.nih.gov/assembly/GCF_000151355.1/)
Supplementary_files_format_and_content: [.tsv] Normalized counts files were generated in tabular format

organism: Fusarium solani

source_name: fungi

growth_protocol: Strains were grown on Potato Dextrose Agar (PDA) at 25 °C for 10 days. Cultures were flooded in a sterile saline solution and filtered to remove cellular and mycelial clumps. The conidial suspensions were adjusted to the desired concentration of 105 conidia ml-1 using a hemocytometer. Viability of the   inoculum was determined by serial plating onto PDA

extract_protocol:
Mycelia was collected by filtration and macerated in liquid nitrogen using a mortar and pestle. Total RNA was extracted using the Hot Acidic Phenol method (Krieg, 1996)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A suspension of 105 conidia ml-1 were inoculated in 50 ml of Yeast Peptone Glucose broth (YPG) and incubated at 25°C for 7 days with agitation at 150 rpm (Wang et al., 2010). Mycelia were collected by filtration and incubated in fresh YPG broth supplemented with sublethal concentrations of antifungals, which corresponded to half of the Minimum Inhibitory Concentration (MIC) of AMB and PSC in each case, Negative controls (NTC) contained dimethyl-sulfoxide (DMSO) at a final concentration of 1%. Samples were incubated for 48 hours under the same incubation conditions mentioned previously.

tag: protocol

value: mycelium exposed to 48 hours to dimethyl-sulfoxide

value: mycelium


title: FSOPSC

value: mycelium exposed to 48 hours to posaconazole


title: ColxMN47 Cold biological replicate 1

description: replicate 1


title: FOXNTC

organism: Fusarium oxysporum


title: Control_4

value: DMSO


title: Control_5


title: Control_6


title: ColxMN47 Standard biological replicate 1

description: replicate 1


title: Blank_3

value: non


title: Colxhalleri Cold biological replicate 1

description: replicate 1


title: FOXPSC


title: Blank_1


title: ColxMN47 Dehydration biological replicate 2

description: replicate 2


title: Blank_2


title: FOXAMB

value: mycelium exposed to 48 hours to amphotericine


title: ColxMN47 Dehydration biological replicate 1

description: replicate 1


title: Ct_1313_Δ2031-4

status: Public on May 31 2016

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

data_processing:
Demultiplexing and file conversion performed by bcl2fastq version bcl2fastq-1.8.3
RNAseq reads were aligned to the C. thermocellum DSM1313 (NC_017304.1) genome assembly using Fastq files imported into the CLCBio RNA-sequencing pipeline. Default settings were used for mismatch, insertion, and deletion costs.
Total gene counts from the CLCBio mapping (DESeq_input.txt) were used for DESeq2 analysis to normalise and determine significant gene expression differences (DE_results.xlsx)
Supplementary_files_format_and_content: Tab deliminated file includes read counts for each gene across the 8 samples used in this study

organism: Acetivibrio thermocellus DSM 1313

source_name: Clostridium thermocellum_1313 culture

growth_protocol: Strains were grown to mid-exponential phase (OD ~ 0.33) in sealed, N2 sparged 162 ml serum bottles containing 50 ml MTC (initial pH of 7.2) supplemented with 4.5 g/l cellobiose

extract_protocol:
Cells  pelleted from a 50 mL sample resuspended in 1 mL of TRIzol (Invitrogen, CA), throughly mixed and then refrozen.  The frozen TRIzol cell suspension was used for cell lysis by bead beating with 0.8 g of 0.1mm glass beads (Biospec Products) with 3 X 20 s bead beating treatments at 6,500 rpm in a Precellys 24 high-throughput tissue homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France). The RNA from each cell lysate was purified and DNaseI treated using the Qiagen RNeasy kit. The RNA quantity and quality assessed by Nanodrop and Bioanalyzer respectively. Purified RNA was depleted of rRNA using the Ribo-Zero rRNA Removal kit for Gram Positive Bacteria (Epicentre/Illumina). The sample was then concentrated with RNA Clean & Concentrate-5 (Zymo Research, CA) following the manufacturer’s protocol.
Depleted RNA was used as the starting material for the Epicentre ScriptSeq™ mRNA-Seq Library preparation kit (Illumina compatible) utilising Epicentres Fail Safe PCR Enzyme mix (Epicentre, WI) and following the manufacturer’s protocol. cDNA, tagged with ScriptSeq adaptors (1-12), was eluted with 20 µl of Buffer EB provided in the Min-Elute PCR purification kit (Qiagen) according to the ScriptSeq™ mRNA-Seq Library preparation kit protocol. Twelve PCR cycles were used during library amplification and samples were purified using Agencourt AmPureXP magnetic beads (Beckman Coulter, IN )  and eluted with 20 µl of buffer EB. The final mRNA Seq library was quantified with a Qubit Fluorometer (Invitrogen, CA) and library quality was assessed with an Agilent Bioanalyzer DNA Chip (Agilent, CA). Samples were pooled and the concentration determined.  Pools of barcoded samples were sent to Hudson Alpha for SR50 sequencing run on an Illumina Hiseq 2500 platform.

tag: genotype

value: delta 2031


title: Ct_1313_Δ2031-3


title: Ct_1313_WT (Δhpt)-3

value: wild type delta hpt


title: KO

first: Xiaopeng

last: Ma

state: Outside US and Canada

address: HaiDian district

institute: Tsinghua Univeristy

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using tophat2 version 2.0.3 with the default parameters
HTseq was used for calculating raw read counts of every gene with parameter of --type="exon" --idattr="gene_id" --mode="union"  --stranded=no
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw reads count of each gene for all samples

organism: Mus musculus

source_name: Treg cells

growth_protocol: Treg cells were sorted from peripheral lymphoid organ of indicated mice by FACS

extract_protocol:
Total RNA was extracted with Trizol reagents, mRNA was isolated using Dynabeads mRNA DIRECT MicroKit (cat no.61021)
TruePrep Minus DNA Sample Prep Kit(1ng DNA),Vazyme,Code: S503-01-A

value: lymph nodes and spleen

tag: age of mice

tag: genotype/variation

value: Ubc9 wild type mouse


title: WT

tag: strain


title: nmt1-SEB1

city: Newark

first: Bin

last: Tian

state: NEW JERSEY

address: 205 South Orange Ave., CC-F1230

department: Department of Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers University

data_processing:
The details of the method was described previously (Hoque, et al., 2014). Briefly, the 3'-adapter sequence was first removed (using fastx_clipper -a TGGAATT). Reads were mapped to the Pombe genome (ASM294v2.20) using Bowtie2 (local mode). 5' four random nucleotides were removed before mapping using "-5 4" parameter in bowtie2. Reads with a mapping quality score (MAPQ) ≥10 were selected for further analysis. Reads with ≥2 non-genomic As after alignment were called polyA site supporting (PASS) reads.
All PASS reads mapped to the 3’-most exons of a gene were used to calculate the expression level of the gene, shown as the reads per million total PASS reads (RPM) value.
Genome_build: Pombe(ASM294v2.20)
Supplementary_files_format_and_content: tab delimited file containing information of Chr., Strand, pA coordinates, read number of pAs in different samples

organism: Schizosaccharomyces pombe

source_name: knock out SEB1 (minimal media + thiamine)

extract_protocol:
Library construction protocol is explained in Hoque et al (2014) Methods  Mol Biol.
All PASS reads mapped to the 3’-most exons of a gene were used to calculate the expression level of the gene, shown as the reads per million total PASS reads (RPM) value.

value: SEB1 KO


title: DNaseSeq_WT_L1_rep1

city: Bethesda

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

description: ChIP-seq

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using the Bowtie aligner (Langmead et al., Nature method, 2012)
DNase-seq reads were aligned to the mm9 genome assembly using the Bowtie aligner (Langmead et al., Nature method, 2012)
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: BedGraph files can be used to check ChIP-seq peaks through the UCSC genome browser.
Supplementary_files_format_and_content: DNase-seq: BedGraph files can be used to check DNase-seq peaks through the UCSC genome browser.

source_name: Mammary

growth_protocol: C57BL/6 mice were purchased from Charles River. Wap-delE1a, -delE1b, -delE1c, -delE2, -delE3, -delE1a_delE2, -delE2_delE3 and -delE1a_delE2_delE3  were inter-bred to maintain homozygosity. Genotyping was confirmed by PCR followed by the DNA sequencing using genomic DNAs from a tail snip. All animals were handled and housed in accordance with the guidelines of the National Institute of Diabetes, Digestive and Kidney Diseases Animal Care and Use Committee.

extract_protocol:
DNase-seq: L1 mammary gland was isolated and snap frozen in liquid nitrogen. Frozen tissue was grinded into powder and homogenized with buffer A (15 mM Tris–HCl pH 8.0, 15 mM NaCl, 60 mM KCl, 1 mM EDTA, 0.5 mM EGTA, 0.15 mM Spermine, 0.5 mM Spermidine, 0.5 mM DTT, 1 mM PMSF with proteinase inhibitors). After cells were lysed in buffer A supplemented with 0.2% NP40, nuclei were collected, counted and re-suspended in DNase buffer. 10 U DNase I (New England Biolab) was used to digest 10 million nuclei at 37◦C for 5 min followed by proteinase K digestion.  Genomic DNA was then purified. Approximately, 50–100 bp DNA fragments were selected for further library construction and sequencing.
Libraries were prepared for sequencing using standard Illumina protocols.

value: Mammary gland

tag: state

value: lactation day 1

value: wild type


title: MBD-IN

city: Birmingham

first: Jeremy

middle: Jason

last: Day

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: UAB

description: Input

data_processing:
Raw single-end sequenced reads (as fastq format) underwent quality control (FASTQC) in Galaxy.
Low-quality reads were filtered with the FASTX toolkit in Galaxy ("filter by quality"), with a quality cutoff of 20 and a minimum percentage of 90.
High-quality reads were aligned to the rat genome (rn5) in Galaxy using Bowtie.
Genome-aligned sequenced reads for each sample were examined using SeqMonk (Babraham institute), using Ensembl v. 70 gene and feature annotations. Due to library size, reads were extended by 250 bp to recapitulate the ~300bp fragment size average. For each sample, gene and promoter (+/-2.5kb from TSS) methylation were determined by computing the reads per million mapped reads (RPM) from MBD-IP samples.
Genome_build: Rnor_5.0 (rn5)
Supplementary_files_format_and_content: Matrix with RPM values for each sample (columns) and each gene (rows). The first row contains column identifiers. The first column contains RefSeq gene names. Promoter and gene body RPM estimates are provided in separate files.

source_name: Cortical neuronal culture, input

growth_protocol: Neurons were removed from cortical tissue at embryonic day 18, and maintained in vitro for 11 days prior to experimental treatment. Each culture well contained ~250,000 cells.

extract_protocol:
Genomic DNA was extracted, RNase-treated, and purified (DNeasy Blood and Tissue Kit, Qiagen). 2µg of total DNA was sonicated to 200-400bp and prepared for MBD-based methylated DNA capture (MethylMiner Kit, Life Technologies). MBD-IP and Input samples underwent library construction and whole-genome sequencing.
DNA sequencing was performed at Hudson Alpha using NEBNext reagents (New England Biolabs) according to manufacturer's recommendations with minor modifications (including the use of custom library adapters and indexes). DNA libraries were quantified with the Kapa Library Quant Kit (Kapa Biosystems), and underwent sequencing (25M total 50 bp single-end reads) on an Illumina sequencing platform (HiSeq 2000). We sequenced two biological replicates, as well as an input (non-IP) control for normalization.

treatment_protocol: Neurons were not treated prior to DNA extraction.

tag: strain/background

value: Sprague-Dawley

value: cortical neuronal culture

value: embryonic day 18, 11 DIV

tag: treatment

value: untreated (media alone)

tag: mbd-capture

value: no


title: Ct_1313_WT (Δhpt)-2


title: Ct_1313_Δ2031-2


title: Ct_1313_WT (Δhpt)-1


title: Wild-type

source_name: Wild-type (minimal media + thiamine)


title: ChIPSeq_Wap-delE1c_L1_ELF5_rep1

description: ChIP-seq

extract_protocol:
Frozen-stored mammary tissues from L1 and p13 were broken into powder with mortar and pestle. Nuclei were extracted in Farnham lysis buffer (5mM PIPES pH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitors). Mammary epithelial cells were isolated from fresh L1 and p13 mammary tissues. Antibodies against STAT5A (Santa Cruz, sc-1081), GR (Thermo Scientific, PA1-511A), MED1 (Bethyl laboratory, A300-793A), H3K27ac (Abcam, Ab4729), NFIB (Santa Cruz, sc-5567), ELF5 (Santa Cruz, sc-9645), RNA Pol II (Abcam, Ab5408) and H3K4me3 (Milllipore, 17-614) were used for ChIP.
Libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

tag: chip antibody

value: ELF5 (Santa Cruz, sc-9645)


title: ChIPSeq_Wap-delE1b_L1_NFIB

description: ChIP-seq

value: NFIB (Santa Cruz, sc-5567)


title: ChIPSeq_Wap-delE1c_L1_ELF5_rep2

description: ChIP-seq


title: Ct_1313_WT (Δhpt)-4


title: ChIPSeq_Wap-delE3_L1_H3K27ac_rep2

description: ChIP-seq

value: H3K27ac (Abcam, ab4729)


title: ChIPSeq_Wap-delE1c_L1_NFIB

description: ChIP-seq


title: FSOAMB

value: mycelium exposed to 48 hours to amphotericine

value: mycelium


title: ecT1

description: non-polyA RNA

data_processing:
Raw paired-end sequenced reads (as fastq format) underwent quality control (FASTQC) in Galaxy.
Low quality reads were filtered with the FASTX toolkit in Galaxy ("filter by quality"), with a quality cutoff of 20 and a minimun percentage of 90.
High-quality reads were aligned to the rat genome (rn5) in Galaxy using Tophat v1.4.0 (with custom settings –p 8 –r 175).
Genome-aligned sequenced reads for each sample were examined using SeqMonk (Babraham institute), using Ensemble v. 70 gene and feature annotations. For each sample, gene/transcript expression levels were determined by computing the fragments per kilobase of exon per million mapped reads (FPKM). For PolyA- RNA-seq, estimates of pre-TSS (1kb upstream of TSS), intronic, and post-TES (2kb downstream of TES) were also quantified for comparison.
Gene expression differences between groups (i.e., untreated versus KCl) were calculated in SeqMonk using all replicates for each group. Statistical significance was assessed using Student's t-tests and an false-discovery rate of 0.05.
Genome_build: rn5
Supplementary_files_format_and_content: Matrix with FPKM values for each sample (Columns) and each gene (rows). The first row contains column identifiers. The first column contains Refseq gene names or Region IDs.

source_name: Cortical neuronal culture

extract_protocol:
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 2µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 9.5) and library construction for polyA+ or polyA- RNA sequencing. For PolyA- RNA, an additional step (removal of ribosomal RNA with NEBNext rRNA depletion kit) occured prior to adapter ligation.
Directional polyA+ and polyA- RNA llibraries were constructed at HudsonAlpha Genomic Services Lab using NEBNext reagents (New England Biolabs) according to manufacturer's recommendations with minor modifications (including the use of custom library adapters and indexes). RNA libraries were quantified (Kapa Library Quant Kit, Kapa Biosystems), and underwent sequencing (25M total 50bp paired-end reads) on an Illumina sequencing platform (HiSeq2000).

treatment_protocol: Neurons were treated as described with 25mM KCl or 1uM TTX for 1hr. Media was removed and RNA was extracted immediately following treatment.

value: Embryonic day 18, 11 DIV

value: 1hr 1uM TTX inactivation


title: ecK2

description: non-polyA RNA

value: 1hr 25mM KCl stimulation


title: DNaseSeq_WT_L1_rep2

description: ChIP-seq


title: ChIPSeq_Wap-delE3_L1_STAT5A_rep2

description: ChIP-seq

value: STAT5A (Santa Cruz, sc-1081)


title: ChIPSeq_Wap-delE2_L1_H3K27ac_rep1

description: ChIP-seq

value: Mammary gland


title: ecV1

description: non-polyA RNA

value: Untreated (media alone)


title: ChIPSeq_Wap-delE2_L1_GR

description: ChIP-seq

value: lactation day 1

value: GR (Thermo Scientific, PA1-511A)


title: V2

description: polyA RNA

value: Sprague-Dawley


title: V1

description: polyA RNA


title: ChIPSeq_Wap-delE2_L1_STAT5A_rep1

description: ChIP-seq


title: MBD-2

source_name: Cortical neuronal culture, MBD precipitated

tag: cell type

value: cortical neuronal culture

value: embryonic day 18, 11 DIV

value: yes


title: MBD-1

tag: age

value: untreated (media alone)


title: ChIPSeq_Wap-delE1c_L1_H3K27ac

description: ChIP-seq


title: ecT2

description: non-polyA RNA


title: AGO2 IP

first: Xiuying

last: Liu

address: Yard 28, Science Park Road, Changping District

institute: Changping Laboratory

description: AGO2 IP

data_processing:
Mapping with Bowtie version 1.1.2
Generate bigwig file with RseQC v2.3.7
bigwig files are UCSC specified, which can be visualized in IGV (Integrative Genomics Viewer) browser (http://www.broadinstitute.org/igv/)
Genome_build: TAIR10
Supplementary_files_format_and_content: Bigwig (.bw) files are from bam files by bam2wig.py (from RSeQC software), which can be visualized in IGV browser and contain the loci information for each read.

organism: Arabidopsis thaliana

growth_protocol: Surface sterilized seeds were plated in MS media + 1% Sucrose, and grown under long day conditions (16h light/8h dark) for 8 days.

extract_protocol:
The plants were collected in liquid nitrogen, ground with morthat and pestle, and RNA extracted in TRIZOL and sequentially purified with phenol:chloroform:isoamylalcohol(25:24:1) and chloroform followed by Ethanol precipitation.
small RNA construction following the protocol previously described by Hafner et al. 2008 Methods 44, 3-12.

treatment_protocol: MS liquid media + 1% Sucrose for mock treatment and MS liquid media + 1% Sucrose + 150 mM NaCl for salt stress treatment

value: Columbia

value: 8 days old

tag: treated with

value: MS + 1% Sucrose (mock)

value: whole seedlings


title: T2

description: polyA RNA

value: Embryonic day 18, 11 DIV


title: ChIPSeq_Wap-delE1b_L1_ELF5

description: ChIP-seq

value: ELF5 (Santa Cruz, sc-9645)


title: ChIPSeq_Wap-delE1c_L1_GR

description: ChIP-seq


title: T1

description: polyA RNA

value: 1hr 1uM TTX inactivation


title: Ct_1313_Δ2031-1

value: delta 2031


title: AGO3 IP

description: AGO3 IP

tag: ecotype


title: K2

description: polyA RNA

value: 1hr 25mM KCl stimulation


title: ChIPSeq_Wap-delE3_L1_H3K27ac_rep1

description: ChIP-seq

value: Mammary gland

value: H3K27ac (Abcam, ab4729)


title: ChIPSeq_Wap-delE3_L1_GR

description: ChIP-seq

value: lactation day 1

value: GR (Thermo Scientific, PA1-511A)


title: Total

description: Total

value: WT


title: ecK1

description: non-polyA RNA

value: Sprague-Dawley


title: K1

description: polyA RNA


title: ChIPSeq_Wap-delE3_L1_STAT5A_rep1

description: ChIP-seq

value: STAT5A (Santa Cruz, sc-1081)


title: ChIPSeq_Wap-delE2_L1_H3K27ac_rep2

description: ChIP-seq


title: ChIPSeq_Wap-delE1b_L1_GR

description: ChIP-seq


title: ChIPSeq_Wap-delE1a_L1_H3K27ac_rep2

description: ChIP-seq


title: ChIPSeq_Wap-delE1a_L1_STAT5A_rep2

description: ChIP-seq


title: ChIPSeq_Wap-delE1a_L1_STAT5A_rep1

description: ChIP-seq


title: ChIPSeq_WT_L1_MECs_H3K4me3

description: ChIP-seq

value: Mammary epithelial cells

value: wild type

value: H3K4me3 (Millipore, 17-614)


title: AGO2 IP Salt

description: AGO2 IP Salt

value: Columbia

value: 8 days old

value: MS + 1% Sucrose + 150 mM NaCl (salt stress)


title: ChIPSeq_Wap-delE2_L1_STAT5A_rep2

description: ChIP-seq


title: AGO3 IP Salt rp2

description: AGO3 IP Salt rp2

value: whole seedlings


title: ChIPSeq_WT_p13_NFIB_rep2

description: ChIP-seq

value: pregnancy day 13

value: NFIB (Santa Cruz, sc-5567)


title: ChIPSeq_WT_p13_ELF5_rep2

description: ChIP-seq

value: ELF5 (Santa Cruz, sc-9645)


title: ecV2

description: non-polyA RNA

value: Embryonic day 18, 11 DIV

value: Untreated (media alone)


title: ChIPSeq_Wap-delE1c_L1_STAT5A_rep2

description: ChIP-seq

value: Mammary gland

value: lactation day 1


title: ChIPSeq_WT_p13_NFIB_rep1

description: ChIP-seq


title: SFB-UHRF2 ChIP-seq

city: Hangzhou

first: Lin-Yu

last: Lu

state: Zhejiang

address: 268 Kaixuan Road, North Central Building, Room 536

institute: Zhejiang University

data_processing:
The 50 bp single-ended short reads were aligned to the human reference genome hg19 using Bowtie 2 (version 2.1.0) using default parameters.
To determine peaks, Model-Based Analysis of ChIP-Seq (MACS, version 1.4.0) was used with default parameters and pvalue cutoff of 1e-8.
HOMER (Hypergeometric Optimization of Motif EnRichmert) Suite (v4.7) was applied to annotate the significant peak regions.
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated by MACS (vision 1.4.0) using default parameters. The last column represents -10*log(pvalue) value for each peak.

source_name: embryonic kideny

growth_protocol: 293T cells stably expressing SFB-tagged UHRF2 or ZNF618 were cultured in DMEM supplemented with 10% FBS

extract_protocol:
ChIP was performed using ChIP assay kit (Millipore) following manufacturer's instructions,except that S-protein beads (Millipore, 69704) were used to pull down SFB-tagged proteins and to replace protein A beads. 2x107 cells were used for each IP.
The DNA after ChIP was decrosslinked,end processed using Quick Blunting Kit and dA-Tailing Module, and ligated to Illumina-compatible adaptors. The DNA was then amplified by PCR using barcode-containing primers.

tag: cell line

tag: expression

value: SFB-tagged UHRF2


title: ChIPSeq_Wap-delE1c_L1_STAT5A_rep1

description: ChIP-seq


title: ChIPSeq_Wap-delE1b_L1_H3K27ac_rep2

description: ChIP-seq

value: H3K27ac (Abcam, ab4729)


title: ChIPSeq_WT_p13_H3K27ac_rep2

description: ChIP-seq


title: Total Salt

description: Total Salt

value: WT


title: ChIPSeq_WT_p13_GR_rep1

description: ChIP-seq

value: GR (Thermo Scientific, PA1-511A)


title: ChIPSeq_Wap-delE1b_L1_H3K27ac_rep1

description: ChIP-seq


title: ChIPSeq_Wap-delE1a_L1_H3K27ac_rep1

description: ChIP-seq


title: AGO3 IP Salt rp1

description: AGO3 IP Salt rp1


title: SFB-ZNF618 ChIP-seq

value: SFB-tagged ZNF618


title: ChIPSeq_Wap-delE1b_L1_STAT5A_rep1

description: ChIP-seq

value: STAT5A (Santa Cruz, sc-1081)


title: ChIPSeq_WT_L1_RNAPolII_rep2

description: ChIP-seq

value: wild type

value: RNA Pol II (Abcam, ab5408)


title: ChIPSeq_Wap-delE1a_L1_GR

description: ChIP-seq


title: ChIPSeq_WT_p13_STAT5A_rep2

description: ChIP-seq


title: ChIPSeq_WT_p13_MECs_H3K4me3

description: ChIP-seq

value: Mammary epithelial cells

value: H3K4me3 (Millipore, 17-614)


title: ChIPSeq_WT_p13_ELF5_rep1

description: ChIP-seq

value: pregnancy day 13


title: ChIPSeq_Wap-delE1b_L1_STAT5A_rep2

description: ChIP-seq


title: ChIPSeq_WT_p13_GR_rep2

description: ChIP-seq


title: ChIPSeq_WT_p13_H3K27ac_rep1

description: ChIP-seq


title: ChIPSeq_WT_L1_NFIB_rep2

description: ChIP-seq

value: NFIB (Santa Cruz, sc-5567)


title: ChIPSeq_WT_L1_NFIB_rep1

description: ChIP-seq


title: ChIPSeq_WT_L1_RNAPolII_rep1

description: ChIP-seq


title: ChIPSeq_WT_p13_H3K4me3

description: ChIP-seq


title: ChIPSeq_WT_L1_GR_rep2

description: ChIP-seq


title: ChIPSeq_WT_L1_H3K27ac_rep2

description: ChIP-seq


title: ChIPSeq_WT_L1_MED1_rep2

description: ChIP-seq

value: MED1 (Bethyl lab, A300-793A)


title: ChIPSeq_WT_L1_MED1_rep1

description: ChIP-seq


title: ChIPSeq_WT_L1_ELF5_rep2

description: ChIP-seq

value: ELF5 (Santa Cruz, sc-9645)


title: ChIPSeq_WT_p13_STAT5A_rep1

description: ChIP-seq


title: brain_WT_Z3

city: Cambridge

first: Dario

last: Beraldi

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute

data_processing:
Raw sequence reads were trimmed to remove poor quality reads, adapter contamination, and the first 6 base pairs, using Trim Galore http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Trimmed sequencing reads were aligned to mouse genome assembly NCBIM37 (mm9) using Bowtie2. Peaks were called in the SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) using the MACS peak caller, with a p-value cutoff of 1x10-5 and a fragment size of 200 base pairs
Genome_build: NCBIM37
Supplementary_files_format_and_content: Bed files of positions of 5fC peaks.

source_name: hindbrain

extract_protocol:
Embryonic tissues were lysed in RLT plus buffer (Qiagen), homogenised via centrifugation through a QIAshreddred column (Qiagen) at full speed for two minutes in a microcentrifuge. DNA and RNA were isolated using AllPrep DNA/RNA kit (Qiagen) following the manufacturer’s instructions.
Sequencing libraries were generated using the NEBNext library preparation modules. 16 cycles of PCR amplification were performed with the Illumina PCR Master Mix and PCR Primer Cocktail. Prior to sequencing, libraries were quantified by qPCR (KAPA Biosystems) and their fragment size profile analysed by TapeStation (Agilent). Sequencing was performed on an Illumina Nextseq 500, run in paired-end mode with 100 read cycles.

value: wild-type

value: Z


title: ChIPSeq_WT_L1_STAT5A_rep2

description: ChIP-seq

value: Mammary gland

value: lactation day 1


title: ChIPSeq_WT_L1_STAT5A_rep1

description: ChIP-seq


title: ChIPSeq_WT_L1_H3K27ac_rep1

description: ChIP-seq

value: H3K27ac (Abcam, ab4729)


title: brain_WT_Q3

value: Q


title: brain_WT_2A8

value: A


title: brain_KO_Q2

value: knock-out


title: brain_WT_O3

value: O


title: FBXL10 T/T female 2

city: St. Louis

first: John

middle: R.

last: Edwards

state: MO

address: 660 S. Euclid Ave, Campus Box 8220

department: Center for Pharmacogenomics

institute: Washington University School of Medicine

description: processed data file: female_edgeR.diff.gz

data_processing:
RNA-seq reads were mapped to the mouse genome (mm9) using TopHat (v1.4.1). Mapped reads were assigned to annotated genes using htseq-count (v 0.5.3p9). Differential expression was assessed via edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited file of EdgeR results, including log-fold change and cpm values for each sample.

molecule: polyA RNA

source_name: Whole embryo

growth_protocol: The FBXL10 Trap mutation (FBXL10 T/T) was backcrossed to the C57BL6/J genetic background for more than ten generations. Trap/Trap embryos and wild type litter-mates were analyzed. The sex of each embryo was determined by PCR detection of Sry gene using genomic DNA extracted form the yolk sac.  Total RNA was extracted from whole embryos (yolk sac excluded) dissected at embryonic day e9.5.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Life technologies), treated with DNase I (Roche) and then purified using the RNeasy Mini Kit (Qiagen). RNA integrity number (RIN) was measured using a 2100 Bioanalyzer (Agilent Technologies).
Purified RNA with RIN greater than 8 served for preparation of poly(A)+ RNA Seq libraries using the mRNA-Seq Sample Preparation Kit (Illumina).

value: embryo

tag: gender

value: female

tag: developmental stage

value: Fbxl10 T/T


title: FBXL10 T/T male 2

description: processed data file: male_edgeR.diff.gz

value: male

tag: genotype


title: FBXL10 T/T male 1

description: processed data file: male_edgeR.diff.gz


title: brain_KO_Z1


title: ChIPSeq_WT_L1_ELF5_rep1

description: ChIP-seq

value: wild type


title: FBXL10 T/T female 1


title: brain_KO_2A2


title: WT female 2

value: WT


title: WT female 1


title: WT male 2

description: processed data file: male_edgeR.diff.gz


title: brain_KO_O4


title: ChIPSeq_WT_L1_GR_rep1

description: ChIP-seq

value: GR (Thermo Scientific, PA1-511A)


title: WT male 1

description: processed data file: male_edgeR.diff.gz


title: DNaseSeq_Wap-delE1c_L1

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using the Bowtie aligner (Langmead et al., Genome Biology, 2009)
DNase-seq reads were aligned to the mm9 genome assembly using the Bowtie aligner (Langmead et al.,  Genome Biology, 2009)
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: BedGraph files can be used to check ChIP-seq peaks through the UCSC genome browser.
Supplementary_files_format_and_content: DNase-seq: BedGraph files can be used to check DNase-seq peaks through the UCSC genome browser.


title: DNaseSeq_Wap-delE1a_L1


title: ChIPSeq_WT_L1_H3K4me3

extract_protocol:
Frozen-stored mammary tissues from L1 and p13 were broken into powder with mortar and pestle. Nuclei were extracted in Farnham lysis buffer (5mM PIPES pH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitors). Antibodies against STAT5A (Santa Cruz, sc-1081), GR (Thermo Scientific, PA1-511A), MED1 (Bethyl laboratory, A300-793A), H3K27ac (Abcam, Ab4729), NFIB (Santa Cruz, sc-5567), ELF5 (Santa Cruz, sc-9645), and H3K4me3 (Milllipore, 17-614) were used for ChIP.
Libraries were prepared for sequencing using standard Illumina protocols.

value: H3K4me3 (Millipore, 17-614)


title: ChIPSeq_WT_p13_MED1

value: pregnancy day 13

value: MED1 (Bethyl lab, A300-793A)


title: UDP4823 Control

first: Barbara

last: Pusey

state: MD

address: 50 Center Drive

department: Undiagnosed Diseases Program

institute: NHGRI

data_processing:
Illumina Casava1.8 software used for basecalling.
Transcriptome fastq reads (phred33-scaled) were mapped onto the human genome assembly hg19 using the Bowtie2 in the TopHat2 (v.2.0.3). Pre-computed human reference sequence (NBCI Build 37; hg19) Bowtie2 index files were used as the index files for read mapping. The UCSC known gene splice junction library (GTF file) was used for splice-read mapping; in addition the fusion-search parameter switch was turned on to enable gene-fusion derived transcript discovery
Transcript assembly, abundance estimates and differential expression analyses were performed using Cufflinks2 (v2.2.1) and Cuffdiff2 (v2.2.1)
Differential gene expression comparisons were run without biological replicates; therefore biological sample gene variance could not be estimated. Differential expression was calculated as fold-changes in gene expression (measured as fragments per kilobase mapped (FPKM)). Pseudo-count of FPKM 1 was added to all FPKM values to minimize inflation of differential gene expression log-likelihood ratios (base 10).
Local neighborhood gene-differential analysis was performed at chromosomal breakpoint junctions, using the Pearson-correlation coefficient to detect anti-correlated gene expression signature deviation from expectation
The Pearson correlation coefficient of gene expression on chromosomes 14 and 18 was calculated using all-possible pairs (N2) resulting from a window of 3 genes to derive matrix M. M is symmetric; therefore, correlation values Mi,j=Mj,i. Values in M range from -1 to +1, where -1 occurs when gene expression values are anti-correlated and +1 when their expression patterns are correlated.
The comparison is between two conditions A, and B; A is the normal control fibroblast gene expression data, and B is individual II-1 fibroblast gene expression data. Values for gene expression are FPKM values derived from RNASeq data. A window was defined as adjacent genes along the same chromosome. All genes in a window were treated as a vector, and the correlation coefficient was calculated
Genome_build: hg19
Supplementary_files_format_and_content: tsv files containing gene expression data from cuffdiff output, as well as differential gene expression comparison between two conditions
Supplementary_files_format_and_content: modified cuffdiff output with isoform status=[broken,intact] column for TCF4
Supplementary_files_format_and_content: Transcript isoform statuses
Supplementary_files_format_and_content: archive of cuffdiff output and filtered output with removal of random and chrUn
Supplementary_files_format_and_content: Archive of network and differential analysis
Supplementary_files_format_and_content: Tophat fusions output for UDP4637

source_name: Fibroblasts; Cultured Skin

extract_protocol:
Poly-A selected RNA-seq libraries were constructed from 1 µg mRNA using the Illumina TruSeq RNA Sample Prep Kits, version 2. The resulting cDNA was fragmented using a Covaris E210.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin fibroblasts

value: Control Tissue


title: ChIPSeq_WT_p13_ELF5

value: Mammary gland

value: ELF5 (Santa Cruz, sc-9645)


title: EB_het

city: Chongqing

first: Ting

middle: huan

last: zhang

address: Rongchang

institute: Chongqing Academy of Animal Science

data_processing:
Illumina Casava1.8 software used for basecalling.
Clean reads were aligned to the reference genome using TopHat (ver. 2.0.7).
RPKM values (reads per kilobase of exon model per million mapped reads) were calculated to measure the expression level of genes.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: RPKM

organism: Sus scrofa

source_name: inner ear stria vascularis tissue

extract_protocol:
Stria vascularis  were dissected from the lateral walls of the cochlea in Ambion RNAlater Stabilization Solution (Cat#AM7021),  and RNA was harvested using Qiagen RNeasy Micro Kit (Cat#74004).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: MITF R/r

value: inner ear stria vascularis


title: EB_hom

value: MITF r/r


title: shLuc+LPS-rep1

city: Boston

first: Evan

last: Rosen

address: 3 Blackfan Cir

department: Endocrinology

institute: Beth Israel Deconess Medical Center

data_processing:
Data analysis was carried out using the following standard software: (1) Base-calling - Illumina RTA 1.18.61. (2) De-multiplexing - bcl2fastq v2.17.1.14.
(3) Alignment - TopHat v2.0.14 (with parameters -M --GTF mm9.gtf –mate-inner-dist fragment_size). (4) Filtering reads for duplicates and low quality reads – Picard 2.2.4 and samtools 0.1.19.
(4) Assignment of reads to genes – featureCounts 1.4.6 with no overlaps. A meta-annotation that excluded transcript overlaps and derived from mm9 was used. Genes included in that meta-annotation are described in as part of raw_counts.txt.
(5) Differential expression analysis – edgeR; standard approach to pair-wise comparisons with no confounding factors as described in the manual.
Genome_build: mm9
Supplementary_files_format_and_content: File raw_counts.txt contains gene descriptions (lists of non-overlapping exons assigned to appropriate UCSC IDs) and corresponding raw counts in all 18 experiments.

source_name: 3T3-L1 adipocytes

growth_protocol: DMEM + 10%FBS + Pen/Strep, 5% CO2, 37°C

extract_protocol:
RNA was isolated using Trizol reagent and Qiagen RNEasy kit. mRNA was extracted from 70ng total RNA using Ribo-zero magnetic gold kit following manufacturer's protocol.
RNA libraries were constructed using the TruSeq RNA Sample Prep Kit v2 (cat# RS-122-2001)

treatment_protocol: Overexpression or knockdown of IRF3 was achieved with lentivirus transduction in mature 3T3-L1 adipocytes for 6 days. 3T3-L1 adipocytes with IRF3 knockdown were further treated with LPS for another 6 days followed by media change containing LPS every other day.

value: Differentiated 3T3-L1 adipocytes

tag: passage

tag: sample type

value: Control for Irf3 knockdown treated with LPS


title: UDP4637 Experiment

value: Mutant Copy


title: shLuc+LPS-rep3


title: Ecoli_O01-T02

city: Tianjin

first: Du

last: Wen

address: Tianjin Economic and Technological Development 13th street NO.29

institute: Tianjin University  of Science and Technology

data_processing:
The sequencing of the two samples was performed on an IlluminaHiSeq2500 system
Q20, Q30，GC-content of the reads was calculated and get clean reads according to remove the primers and connector or filter the inferior quantify reads
The clean reads was mapped to the reference genome of E.coli K12 on NCBI and get mapped reads with Bowtie2 software
Screen out the differentially expressed gene using DEseq
the sequences were aligned using BLASTX (E-value≤10−5)against the following public  databases
Supplementary_files_format_and_content: All_gene_rpkm files include RPKM values for each Sample; All_gene_counts T01_vs_T02 include counts values for each Sample. KEGG include KEGG values for two Sample T01_vs_T02 include annotation values for each Sample.

organism: Escherichia coli

source_name: bacterium at late-logarithmic growth

growth_protocol: 37℃，200rpm，The middle and late period of logarithm

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA) from E.coli strain cells according to the manufacturer’s instructions
RNA-seq libraries were created using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB,CA,USA) according to the manufacturer’s protocols.

treatment_protocol: centrifugate the bacterial fluid for 13000g with 2min and remove the supernatant

tag: strain

tag: time

tag: color

value: red


title: Ecoli_O01-T01

source_name: bacterium at mid-logarithmic growth


title: shIrf3-rep3

value: Knockdown of Irf3


title: shLuc-rep1

value: Control for Irf3 knockdown


title: shIrf3+LPS-rep3

value: Knockdown of Irf3 treated with LPS


title: UDP4637 Control

tag: tissue


title: shLuc-rep2


title: shLuc-rep3


title: shIrf3+LPS-rep1


title: EGFP-rep3

value: Control for overexression of Irf3


title: shIrf3+LPS-rep2


title: EGFP-rep1


title: shIrf3-rep2


title: DNaseSeq_Wap-delE3_L1

tag: state

value: lactation day 1


title: EGFP-rep2

tag: cell type


title: 2D-rep3

value: Overexpression of Irf3


title: shIrf3-rep1


title: 2D-rep1


title: shLuc+LPS-rep2


title: liver_KO_i1

source_name: liver

value: knock-out


title: liver_WT_i6

value: wild-type


title: liver_WT_i9


title: 2D-rep2


title: liver_KO_i5


title: heart_WT_i6

source_name: heart


title: heart_KO_i1


title: heart_WT_i9


title: carcass_WT_i6

source_name: carcass


title: carcass_KO_i1


title: heart_KO_i5


title: ago4-1;PAGO4-FM-AGO3

description:
4F3
Bisulfite conversion with EpiTect Kit (Qiagen)

data_processing:
Reads alignment with Bismark version 0.14.3
Deduplicate for alignment results
Extract methylation information with bismark_methylation_extractor
Generated wig files through swDMR version 1.0.0
wig files are UCSC specified, which can be visualized in IGV (Integrative Genomics Viewer) browser (http://www.broadinstitute.org/igv/)
Genome_build: TAIR10
Supplementary_files_format_and_content: Wig files in AGOs_BS-Seq folder are DMRs fragment loci on genome, containing Chromosome  Start End information.

source_name: 4-week plants

growth_protocol: Surface sterilized seeds were plated in MS media + 1% Sucrose, and grown under short day conditions (16h dark/8h light) for 11 days.

extract_protocol:
The plants were collected in liquid nitrogen, ground with morthat and pestle, and DNA extracted in CTAB, Rnase treated and purified with phenol:chloroform followed by Ethanol precipitation.
Bisulfite conversion with EpiTect Kit (Qiagen); Approximately 1 ug of genomic DNA were used to generate libraries using premethylated adapters (NEXTFlex Bisulfite-Seq Adapters, Bioo Scientific #511911). The adaptor-ligated fragments were purified by QIAQuick column (QIAGEN) and bisulfite converted using the EpiTect Kit (Qiagen) following the manufacturer’s instructions. The converted DNA was later enriched by 15 cycles of PCR using the Pfu Turbo Cx Polymerase (Agilent), using the specific primers provided by Bios Scientific for enrichment. The library was finally purified with Agencourt AMPure XP beads (Beckman Coulter) according to manufacturer’s instruction.

value: Landsberg erecta

tag: age

value: 4 weeks old

value: aerial part


title: carcass_KO_i5


title: ago4-1;PAGO4-FM-AGO4

description:
4F4
Bisulfite conversion with EpiTect Kit (Qiagen)


title: pp_nic4

status: Public on May 30 2016

city: New Haven

first: Marina

last: Picciotto

state: CT

address: 301 Cedar Street Congess place/YPI 4th floor

department: Psychiatry

institute: Yale University

description: processed data file: prepost_EdgeR_processed_counts.txt

data_processing:
Sequences were called from image files with the Illumina Genome Analyzer Pipeline (GApipeline) and aligned to the reference genome (UCSC mm9) using Extended Eland in the GApipeline.
The uniquely aligned reads by ELAND pipeline were considered in calling peaks. To eliminate noise and account for unequal total numbers, we used a defined analysis model (Model-based Analysis of ChIP-Seq, MACS) with default parameters to find peaks, which were called “peaks” of H3K4me3.
For comparison analysis, a customized genomic interval file was created for EdgeR  analysis.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include EdgeR processed pseudo count for each sample.

source_name: Pre and postnatal nicotine received

growth_protocol: NIH Guide for Care and Use of Laboratory Animals. C57BL/6J mice (Jackson Laboratories, Bar Harbor, ME) used in the developmental nicotine exposure studies acclimated for 1 week, had ad libitum food and water and a 12-h light–dark cycle (lights on at 7AM).

extract_protocol:
Mouse tissue samples (50 mg) were cut into slices less than 1 mm in thickness, and fixed in 3 ml of 1% formaldehyde/PBS solution. the tissue samples were homogenized in a glass-Teflon homogenizer. Following homogenization, chromatin was isolated using the Magna ChIP G kit (Millipore, Temecula, CA) according to the Millipore protocol. Cells were lysed in Cell Lysis Buffer in the presence of protease inhibitor cocktail.
Sample preparation and sequencing on the Genome Analyzer (Illumina, San Diego, CA) were carried out according to the Illumina protocols with some modifications. Briefly, the double stranded cDNA and ChIP-enriched genomic DNA were treated with T4 DNA polymerase and the Klenow fragment for end repair. The 5’ ends of the DNA fragments were then phosphorylated by T4 polynucleotide kinase, and an adenosine base was added to the 3’ end of the fragments by Klenow (3’-5’ exo). A universal adaptor was then added to both ends of the DNA fragments by A-T ligation. Following 18 cycles of PCR with the Phusion DNA polymerase, the DNA library was then purified on a 2% agarose gel, and fragments of 170 – 300 base-pair in size were recovered. Around 15 ng of the DNA library was then used for cluster generation on a grafted GAII Flow Cell, and then sequenced on the Genome Analyzer for 36 cycles using the “Sequencing-by-synthesis” method.

treatment_protocol: Saccharin or Nicotine soultion delivered to pregnant mice from the conception. Nicotine and saccharin water weaned from offspring 21 day old. The animal let live undisturbed by 90 day old

value: brain

tag: tissue compartment

value: cerebral cortex

value: 3 month old

tag: chip antibody

value: H3K4me3 (Millipore, 06-598, lot JBC940052)