title: vehicle_rep3

city: Gainesville

first: Xiefan

last: Fang

state: Florida

address: 1200 Newell Drive, ARB R1-148

department: Pediatrics

institute: University of Florida

data_processing:
The fastq files generated from RNA-Seq were uploaded to the UF Research Computing Galaxy instance developed by the University of Florida. The data were cleaned with the following steps: removed sequencing artifacts, trimmed 5’ or 3’ ends with low scores, removed adaptor contamination, and filtered low quality reads by the FastQC program. The remaining high quality RNA-Seq reads were mapped to the mouse genome (mm10) with the Tophat2 tool. Counting of RNA-Seq reads were performed with HTSeq, with Ensembl Mus_GRCm38.79.gtf as the reference annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each gene annotated to Ensembl Mus_GRCm38.79.gtf.

source_name: Left ventricle

extract_protocol:
Total RNA was isolated from the left ventricles of male one-year-old mice treated with vehicle or 20 mg/kg caffeine during E6.5-10.5, using the RNeasy Plus Mini kit (Qiagen). mRNA was isolated from total RNA using NEXTflex™ Poly(A) Beads (Bioo Scientific, Austin, TX, USA). The mRNA was quantitated using the Qubit RNA assay and Qubit 2.0 Flourometer (Thermo Fisher Scientific, Waltham, MA, USA), as well as a 2200 TapeStation (Pico mRNA; Agilent Technologies, Santa Clara, CA, USA).
Sequencing libraries were prepared with the NEBNext® mRNA Library Prep Master Mix Set for Illumina (NEB, Ipswich, MA, USA). Briefly, purified mRNA (50-250 ng) was fragmented to ~200 nucleotide mRNA prior to generating first and second strand cDNA. The resulting cDNA was prepared for sequencing by blunt end repair, dA-tailing, adaptor ligation using the NEBNext Multiplex Oligos for Illumina (NEB), size selection using Agencourt AMPure XP Beads (Beckman Coulter, Brea, CA, USA), and PCR enrichment of adaptor ligated cDNA. Library quality was assessed using the Agilent 2200 TapeStation (high sensitivity DNA assay). The concentration of each library was quantitated by a KAPA Library Quantification kit (Illumina platforms; Kapa Biosystems, Woburn, MA, USA) on a GeneAmp 7300 Real Time PCR (Thermo Fisher Scientific).

treatment_protocol: Pregnant CD-1 mice were treated with vehicle (normal saline) or 20 mg/kg caffeine via i.p. injection once daily during embryonic day (E) 6.5-9.5 (n=3 per treatment). Pups were born and raised to one year of age.

tag: tissue

value: left ventricle

tag: developmental stage

value: one year old male

value: vehicle


title: Untreated RNA rep2

status: Public on Feb 09 2017

type: SRA

city: Boston

first: Bruce

last: Horwitz

state: MA

address: 77 Ave Louis Pasteur

department: Pathology

country: USA

institute: Brigham and Women's Hospital

description: Untreated

library_source: transcriptomic

data_processing:
Trim_galore
Rbowtie
QuasR qCount
DESeq
Genome_build: mm10
Supplementary_files_format_and_content: csv of normalized expression values

molecule: total RNA

organism: Mus musculus

source_name: Bone Marrow Derived Macrophages

growth_protocol: Bone marrow precursors were grown in M-CSF conditioned media containing FBS for 5 days prior to stimulation

extract_protocol:
Cells were rinsed in PBS and lysed in TRIzol, RNA was purified with qiagen RNeasy Columns
NEB next ribomal depletion followed by NEB Directional RNA Library Prep Kit

treatment_protocol: Untreated, LPS (1ng/mL)  for 195min, LPS and IL-10 (1ng/mL) for 195min (c10), LPS for 195min and IL-10 for the last 30min of the stimulation (a10)

tag: genotype

tag: strain

tag: cell type

value: Bone Marrow Derived Macrophage


title: caffeine_rep1

molecule: polyA RNA

tag: treatment

value: 20 mg/kg caffeine


title: caffeine_rep3


title: vehicle_rep2


title: Stressed male 2 (SM2) miRNA

city: New York

first: Eddie

last: Loh

address: 1425 Madison Avenue

department: Department of Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
miRNA-Seq
SM2
Processed data file: small_RNA_raw_counts.txt

data_processing:
miRNA-seq: Raw sequencing reads were processed by fastx trimmer to remove the 3' adaptor sequence, and sequences shorter than 16 nucleotides were subsequently discarded. Sequencing quality was assessed by FastQC. Reads were aligned to the mm9 mouse genome using Bowtie short read aligner and quantified against mature miRBase release 21 annotation using the HT-Seq Python package.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with tabulated read counts for all samples and genes/miRNAs.

source_name: nucleus accumbens, male, stressed

extract_protocol:
Small RNA-Seq libraries were generated from enriched small RNA fractions (<200 bp) according to the instructions of the Scriptminer Small RNA-Seq Library Preparation Kit (Epicentre, Madison, WI) with modifications as described in Dias et al. (Nature, 2014).
14-gauge ventral striatum punches were collected from each animal and flash frozen on dry ice. RNA was isolated using homogenization in Qiazol (Qiagen, Hilden, Germany) followed by chloroform layer separation. Bilateral NAc punches from 5 animals (10 NAc punches) were pooled for each library at the point of homogenization. The aqueous RNA layer was further processed via miRNeasy mini kit (Qiagen, Hilden, Germany) to yield separate fractions enriched for small RNA (<200 bp; for small RNA sequencing) and large RNA (>200 bp; for mRNA sequencing).

treatment_protocol: Male and female mice were exposed to Subchronic Variable Stress (SCVS).

tag: strain/background

value: nucleus accumbens

tag: Sex

value: male

tag: age

value: 9 weeks

value: subchronic variable stress (SCVS)


title: caffeine_rep2


title: Stressed male 1 (SM1) miRNA

description:
miRNA-Seq
SM1
Processed data file: small_RNA_raw_counts.txt


title: Stressed male 3 (SM3) miRNA

description:
miRNA-Seq
SM3
Processed data file: small_RNA_raw_counts.txt


title: Stressed female 3 (SF3) miRNA

description:
miRNA-Seq
SF3
Processed data file: small_RNA_raw_counts.txt

source_name: nucleus accumbens, female, stressed

value: female


title: Stressed female 2 (SF2) miRNA

description:
miRNA-Seq
SF2
Processed data file: small_RNA_raw_counts.txt


title: Nonstressed male 2 (NSM2) miRNA

description:
miRNA-Seq
NSM2
Processed data file: small_RNA_raw_counts.txt

source_name: nucleus accumbens, male, nonstressed

value: nonstressed


title: vehicle_rep1


title: Stressed female 1 (SF1) miRNA

description:
miRNA-Seq
SF1
Processed data file: small_RNA_raw_counts.txt


title: 195minLPS+c10 Rep2

description: 195min LPS + IL-10 (c10)


title: Nonstressed female 3 (NSF3) miRNA

description:
miRNA-Seq
NSF3
Processed data file: small_RNA_raw_counts.txt

source_name: nucleus accumbens, female, nonstressed


title: Nonstressed female 1 (NSF1) miRNA

description:
miRNA-Seq
NSF1
Processed data file: small_RNA_raw_counts.txt


title: Nonstressed female 2 (NSF2) miRNA

description:
miRNA-Seq
NSF2
Processed data file: small_RNA_raw_counts.txt


title: RatID_10_HIP_TRM_mRNA

city: Kuopio

first: Anssi

last: Lipponen

address: Neulaniementie 2

department: A. I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

description:
Hippocampus_DEseq2_raw_counts.txt
Identical  (raw file) to GSM1943622

data_processing:
Base calling were performed with OLBv1.8 software.
Reads were aligned to the rat genome (Rnor_5.0) using Spliced Transcripts Alignment to a Reference (STAR) (version 2.3.0e_r291).
Differentially expressing genes were identified with DEseq2 R-package (R version 3.1.0).
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: Tab-delimited raw count matrices

organism: Rattus norvegicus

source_name: dorsal hippocampus, TBI

growth_protocol: Adult male Sprague-Dawley (Harlan, Netherlands) weight 330-371g at a time of traumatic brain injury were housed in a controlled enviroment (21-23 °C, 12h dark/light cycle, 50-60% relative humidity) with drinking and feeding ad libitum.

extract_protocol:
Tissue was collected at 3 months after TBI. For tissue collection rats were anesthetized with isoflurane and decapitated. The brain was removed from skull, flushed with 0.9% cold sodium chloride, and two 2-mm-thick coronal slices (between -2.2 to -6.2 from the bregma) were cut with a slicing matrix. Perilesional cortex, thalamus, and dentate gyrus (including CA3c-b) were dissected under the magnifying glass on top of the light table.  Samples were stored at -80oC until RNA extraction.
Total RNA extraction were done by using the DNaesy Blood & Tissue kit (Qiagen #69504), followed by DNase digestion. RNA quality was verified on the Shimadzu MultiNA capillary electrophoresis system (Shimadzu). Poly-A mRNA was isolated with Dynabead Oligo(dT) enrichment (Invitrogen). Sequencing libraries were prepared using the NEBNext® mRNA Library Prep Reagent Set for Illumina® (New England Biolabs). Libraries were quantified on MultiNA system and sequenced at a concentration of 13 pM on the Genome Analyzer IIx (Illumina Inc, CA, USA) using the TruSeq version 5 cluster kit (cBot) and SBS kit (36 cycles).

treatment_protocol: The induction of TBI was done according the lateral fluid precussion (LFP) described by McIntosh et al. (1989) and Kharatishvili  et al. (2006). Animals were anesthezied with an intraperitoneal (i.p.) injection of a solution (6 ml/kg) containing sodium pentobarbital (58 mg/kg), chloral hydrate (60 mg/kg), magnesium sulphate (127.2 mg/kg), propylene glycol (42.8%) and absolute ethanol (11.6%) and placed in a Kopf stereotactic frame (David Kopf Instruments, Tujunga, CA, USA). The skull was exposed with a midline skin incision followed by extraction of the periosteum. The left temporal muscle was detached from the lateral ridge and then a circular craniectomy (diameter 5mm) was performed over the left parietal lobe midway between lambda and bregma keeping the dura mater intact. The edges of craniectomy were sealed with a modified LuerLock cap that was filled with saline while the calvaria was covered with dental acrylate (Selectaplus CN, Dentsply DeTrey GmbH, Dreieich, Germany). Lateral FPI was induced 90 min after the administration of anaesthesia by connecting the rat to a fluid-precussion device (AmScien Instruments, Richmond, VA, USA) via a female Luer-Lock fitting. In this study the main of the impact was 3.32 +/- 0.01 atm. Control animals received anaesthesia and all surgical procedures but without lateral FPI.

value: Sprague-Dawley

tag: gender

value: Male

value: dorsal hippocampus

value: TBI


title: RatID_8_HIP_TRM_mRNA

description:
Hippocampus_DEseq2_raw_counts.txt
Identical  (raw file) to GSM1943620


title: Stressed male 3 (SM3) mRNA

description:
mRNA
SM3
Processed data file: mRNA_raw_counts.txt

data_processing:
mRNA-seq: Raw sequencing reads were aligned to the Ensembl Mus musculus NCBIM37 version 67 reference genome using TopHat2. Individual gene counts for each sample were obtained using the HTSeq Python package.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with tabulated read counts for all samples and genes/miRNAs.

extract_protocol:
RNA-Seq libraries were generated from large RNA fractions (>200 bp) with RIN values > 8.8. RNA (1 ug) was used for mRNA library construction according to the standard protocol of the TruSeq RNA Library Preparation Kit v2 (Illumina, San Diego, CA).
14-gauge ventral striatum punches were collected from each animal and flash frozen on dry ice. RNA was isolated using homogenization in Qiazol (Qiagen, Hilden, Germany) followed by chloroform layer separation. Bilateral NAc punches from 5 animals (10 NAc punches) were pooled for each library at the point of homogenization. The aqueous RNA layer was further processed via miRNeasy mini kit (Qiagen, Hilden, Germany) to yield separate fractions enriched for small RNA (<200 bp; for small RNA sequencing) and large RNA (>200 bp; for mRNA sequencing).


title: RatID_7_HIP_TRM_mRNA

description:
Hippocampus_DEseq2_raw_counts.txt
Identical  (raw file) to GSM1943619


title: Strain LF82 at 2h replicate C

city: Stony Brook

first: Yuanhao

last: Zhang

address: AMS Department,Stony Brook University

department: Applied Mathematics and Statistics

institute: Stony Brook University

data_processing:
Raw sequences were filtered to remove human sequence contamination, remove short reads (< 50 bp), depleted of duplicate reads, and quality trimmed using Trimmomatic (v 0.32).  rRNA sequences were identified and culled using SortMe RNA (v1.9)
Raw sequence reads for LF82 and HS were mapped to NCBI reference genomes NC_011993 and NC_009800, respectively  using the Burroughs Wheeler aligner (BWA)
Counts for each annotated genomic loci were determined by HTseq-count (version 0.6.1)
Genome_build: genomes NC_011993 and NC_009800
Supplementary_files_format_and_content: txt, raw count for each sample

organism: Escherichia coli LF82

source_name: cell

growth_protocol: Triplicate Luria broth cultures (37o C) of LF82 and HS were grown with continuous shaking for 2 hours (exponential phase) and 24 h without shaking (stationary phase).

extract_protocol:
Total RNA was extracted from the cells using the RiboPure Bacteria kit (Life Technologies Corp. Carlsbad, CA), following the manufacturer’s protocol.
Two micrograms of RNA was depleted of ribosomal RNA using the RiboMinus Transcriptome Isolation Kit (Life Technologies Corp. Carlsbad, CA).  These samples were then used as a template for strand-specific cDNA synthesis

tag: time point

tag: growth phase

value: exponential


title: RatID_9_HIP_TRM_mRNA

description:
Hippocampus_DEseq2_raw_counts.txt
Identical  (raw file) to GSM1943621


title: Strain LF82 at 24h replicate C

value: stationary


title: Strain LF82 at 24h replicate B


title: Stressed male 2 (SM2) mRNA

description:
mRNA
SM2
Processed data file: mRNA_raw_counts.txt


title: Stressed male 1 (SM1) mRNA

description:
mRNA
SM1
Processed data file: mRNA_raw_counts.txt


title: RatID_4_HIP_SHM_mRNA

description:
Hippocampus_DEseq2_raw_counts.txt
Identical  (raw file) to GSM1943616

source_name: dorsal hippocampus, sham operated

value: sham operated


title: Stressed female 2 (SF2) mRNA

description:
mRNA
SF2
Processed data file: mRNA_raw_counts.txt


title: Strain LF82 at 2h replicate B


title: Nonstressed male 3 (NSM3) mRNA

description:
mRNA
NSM3
Processed data file: mRNA_raw_counts.txt


title: Stressed female 1 (SF1) mRNA

description:
mRNA
SF1
Processed data file: mRNA_raw_counts.txt


title: Nonstressed male 3 (NSM3) miRNA

description:
miRNA-Seq
NSM3
Processed data file: small_RNA_raw_counts.txt


title: Strain LF82 at 24h replicate A


title: BMA02-T3C8

city: Cleveland

first: Jonathan

middle: D

last: Kenyon

state: OH

address: 2103 Cornell

institute: Case Western Reserve University

description: bisulfite modified PCR amplified genomic DNA

library_source: genomic

data_processing:
version 2.6 of gsRunProcessor
doValleyFilterTrimBack>true<
vfBadFlowThreshold>4<
vfLastFlowToTest>320<
vfMaxFailedPercent>100<
vfTrimBackMinimumLength>84<
vfTrimBackScaleFactor>0.7<
if test="Run.Flow.CycleCount > 299"><vfTrimBackScaleFactor>2.2</vfTrimBackScaleFactor>
vfScanLimit>4096</vfScanLimit
computeUopt>false</computeUopt><scaleMultimers>false</scaleMultimers>
doQScoreTrim>true<
errorQscoreWindowTrim>0.010</
QScoreTrimNukeWindowSize>40<
QScoreTrimBackScaleFactor>0.9<
if test="starts-with(InstrumentModel,'GSJUNIOR_A')"><QScoreTrimBackScaleFactor>1.2</
if test="Run.Flow.CycleCount > 299"><QScoreTrimBackScaleFactor>1.5</
enable>true</enable><options>--fna --qual --454BaseCallerMetrics.txt --454BaseCallerMetrics.csv --454RuntimeMetricsAll.txt --454RuntimeMetricsAll.csv --454QualityFilterMetrics.txt --454QualityFilterMetrics.csv --454AllControlMetrics.txt --454AllControlMetrics.csv
sequence reads were next screened by barcode and compared to a hypothetical bisulfite modified 100% unmethylated sequence. All sequences with less than 70% homology to the hypothetical sequence were discarded.
Each CpG within sequence reads was then scored 0 for unmethylated or 1 for methylated. Frequency of methylation at each CpG was next calculated for each sample.
Supplementary_files_format_and_content: .tab processed files are the sequence reads obtained for each barcode from the raw data and screened (70% cutoff) for homology to a theoretical 100% bisulfite (BS) converted sequence of the hMLH1 promoter PCR amplification products from the given primers in the spreadsheet. The first column contains the unique sequence read name (G6ZBNM301CO5B5 for instance) which was generated by the run and plate location. The second column are the sequence reads with the barcodes trimmed (this was done to facilitate the 70% homology screen).
Supplementary_files_format_and_content: .csv files contain the CpG methylation scoring and frequencies. Three regions of the hMLH1 gene were amplified and sequenced (fragments were named A, B, C). The first row is a header, subsequent rows contain sequence read specific data. The first column of these files is the sequence read name, followed by the read length, then several columns of scores (1 = methylated or 0 = unmethylated) for each CpG within the amplified product, the next column shows the aveidentity (% sequence homology to hypothetical BS converted), and the last column is the sequence of bases observed at the CpG sites for that sequence read (A;A;R;A.... etc. for instance indicates the third CpG site was methyated).

molecule: genomic DNA

organism: Homo sapiens

source_name: A single colony forming unit grown from human bone marrow aspirate donation

extract_protocol:
DNA from individual CFU, CD34+, or RKO cells was harvested by Qiagen genomic DNA kit. DNA was next bisulfite modified and PCR amplified with forward oligonucleotides MLH1-AF (5' [Linker/spacer][barcode]actcaaaatcctctaccttataatatc 3'),  MLH1-BF (5' [Linker/spacer][barcode]acaaaccaaacacaaaaccccat 3'), MLH1-CF (5' [Linker/spacer][barcode] tcacctcaacaaaaacacacaaac 3') when [linker/spacer]= (5' CGTATCGCCTCCCTCGCGCCATCAG 3') and [barcode] was sample specific. Negative oligonucleotides used were: MLH1-AR (5'[Linker/spacer][barcode]ttaaaagaagtaagatggaag 3'),  MLH1-BR (5' [Linker/spacer][barcode]tttagttaataggagtagagatg 3'), MLH1-CR (5' [Linker/spacer][barcode]GTTAAATTTTTTAATTTTGTGGGTTGTTGGG 3') when [linker/spacer]= (5' CTATGCGCCTTGCCAGCCCGCTCAG 3') and [barcode] was sample specific.
Amplified products were run on an 1.5% agarose gel and appropriate sized bands excized. DNA fragments were purified from gel fragments and submitted for 454 sequencing. In parallel 1/2 of each sample was processed for RNA extracts. Total RNA was generated for each sample and used as the template for cDNA synthesis by a single cycle of reverse transcriptase activity followed by RNA digestion. Expression of the human gene hMLH1 (in parallel with human beta actin as a control) was next assessed for each cDNA sample generated by QRT-PCR on an Applied biosystems RT-PCR 7500 fast machine. Threshold values were automatically generated according to the manufacturers protocol. Gene expression for hMLH1 (scored as 1) was considered observed if amplification products broke threshold for both hMLH1 and beta actin. However, loss of hMLH1 (scored as 0) gene expression was defined as the observation of detectable amplification products for beta actin but not hMLH1

tag: donor number

tag: donorid

tag: donor age

value: hematiopoietic progenitor

tag: hmlh1 expression

tag: barcode

value: TACAGGTTT


title: RatID_6_HIP_TRM_mRNA

description:
Hippocampus_DEseq2_raw_counts.txt
Identical  (raw file) to GSM1943618

tag: tissue


title: Nonstressed male 2 (NSM2) mRNA

description:
mRNA
NSM2
Processed data file: mRNA_raw_counts.txt


title: Nonstressed male 1 (NSM1) mRNA

description:
mRNA
NSM1
Processed data file: mRNA_raw_counts.txt


title: Stressed female 3 (SF3) mRNA

description:
mRNA
SF3
Processed data file: mRNA_raw_counts.txt


title: RatID_3_HIP_SHM_mRNA

description:
Hippocampus_DEseq2_raw_counts.txt
Identical  (raw file) to GSM1943615


title: Nonstressed male 1 (NSM1) miRNA

description:
miRNA-Seq
NSM1
Processed data file: small_RNA_raw_counts.txt


title: Strain LF82 at 2h replicate A


title: Nonstressed female 2 (NSF2) mRNA

description:
mRNA
NSF2
Processed data file: mRNA_raw_counts.txt


title: Nonstressed female 3 (NSF3) mRNA

description:
mRNA
NSF3
Processed data file: mRNA_raw_counts.txt


title: Untreated RNA rep1

description: Untreated

value: Bone Marrow Derived Macrophage


title: RatID_1_HIP_SHM_mRNA

description:
Hippocampus_DEseq2_raw_counts.txt
Identical  (raw file) to GSM1943613


title: B. gymnorrhiza leaf rep2

city: Guangzhou

first: Ming

last: Wen

address: No. 135, Xingang Xi Road

department: Life Science

country: China

institute: Sun Yat-sen University

description: small RNAs

data_processing:
Sequenced reads were trimmed for adaptor sequence, and removing low-quality reads
Genome_build: Populus trichocarpa v1.1
Supplementary_files_format_and_content: fasta file with cleaned small RNA reads

organism: Bruguiera gymnorhiza

source_name: Bruguiera gymnorrhiza leaf

growth_protocol: Plant material from K. candel and B. gymnorrhiza was collected from a field at Dongzhai Harbor, Hainan, China.

extract_protocol:
Tissue samples of leaves and flower buds were harvested and immediately stored in RNAlater (Applied Biosystems/Ambion, Austin, TX, USA) until further processing according to the manufacturer’s instructions. Total RNA was extracted using a modified CTAB method and evaluated with a Agilent 21100 Bioanalyzer.
Small RNA libraries were prepared using standard protocols of the Illumina Small RNA Sample Prep kit

value: leaf


title: Nonstressed female 1 (NSF1) mRNA

description:
mRNA
NSF1
Processed data file: mRNA_raw_counts.txt

value: nucleus accumbens


title: RatID_10_CX_TRM_mRNA

source_name: Perilesional cortex, TBI

value: perilesional cortex


title: YY56_3

first: fanwei

last: dai

state: Guangdong

address: The Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mulberry transcriptome (NCBI accession no. SRP026705)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: The transcript identifiers in rpkm files are public database IDs of MorusDB (http://morus.swu.edu.cn/morusdb/), referenced in the two following papers: 1) Draft Genome Sequence of the Mulberry Tree Morus notabilis. Nat Commun, 2013, 4:2445. and 2) MorusDB: a resource for mulberry genomics and genome biology. DATABASE, 2014, doi:10.1093/database/bau054
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Morus alba var. atropurpurea

source_name: Leaf

extract_protocol:
Leaves were collected and flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ploidy type

value: Autotetraploid


title: 2_p140_Set-C

city: Dresden

first: Francis

last: Stewart

address: Tatzberg 47-49

country: Germany

institute: BIOTEChnology Center TU Dresden

data_processing:
alignment against mm10 with GSNAP (2014-10-14)
generation of counts table using featureCounts (version 1.4.4), Ensembl Gene annotation version 69
Differential gene expression analysis with DESeq2 R package (version 1.3.79)
Genome_build: mm10
Supplementary_files_format_and_content: files with counts per gene and differentially expressed genes

source_name: MII oocytes

growth_protocol: in vivo / none

extract_protocol:
For single oocyte RNA profiling Setd1bGdf9cKO and control mice were superovulated and four oocytes collected for each genotype. Cells were lysed, RNA reverse transcribed and amplified according to the protocol of SMARTer Ultra Low RNA Kit for Illumina Sequencing (vers. 1, Clontech).
Samples were subjected to NEBNext Ultra DNA library preparation for Illumina using indexed adaptors (NEB). Resulting libraries were pooled in equimolar quantities for 75-bp single-read sequencing on Illumina HiSeq 2000, resulting in about 20 (16-23) million reads per sample.

value: oocyte

tag: genotype/variation

value: Control


title: 4_p140_Set-C


title: RatID_8_CX_TRM_mRNA

tag: strain


title: YY56_2

department: The Sericulture and Agri-Food Research Institute

institute: Guangdong Academy of Agricultural Sciences


title: RatID_9_CX_TRM_mRNA


title: 3_p140_Set-K

tag: cell type

value: Knock Out


title: 3_p140_Set-C


title: 4_p140_Set-K


title: 1_p140_Set-C


title: RatID_6_CX_TRM_mRNA

value: Sprague-Dawley

tag: treatment


title: 1_p140_Set-K


title: RatID_2_HIP_SHM_mRNA

description:
Hippocampus_DEseq2_raw_counts.txt
Identical  (raw file) to GSM1943614

value: Male


title: CUMS 2 PFC Illumina Hiseq miRNA

city: Beijing

first: Ke

last: Ma

state: Beijing

address: 15 Datun road,Chaoyang Strict,Beijing, China

department: Diseases Epigenetics

institute: Institute of biophysics, chinese academy of science

data_processing:
49 nt-sequence tags from Hiseq sequencing were initially processed to remove adaptor sequences, low-quality reads and contaminants for the credible clean reads. To remove reads from ncRNA (noncoding RNA), such as rRNAs (ribosomal RNAs), tRNAs (transfer RNAs), snRNAs (small nuclear RNAs), snoRNAs (small nucleolar RNAs) and repeat RNA, we aligned the reads to Genbank database and Rfam database with blast or bowtie softwares.
All of the high-quality clean reads ranging from 18-25 nt were matched to the known miRNA precursor of corresponding species in miRBase to obtain the miRNA count. The detailed criteria include: 1) align the tags to miRNA precursor in miRBase with no mismatch, 2) based on the first criteria, the tags align to the mature miRNA in miRBase with at least 16 nt overlap allowing offsets.
Those miRNAs satisfied with these criteria would be counted to get the expression of identified miRNAs. The remained reads without any annotation were used to predict potential novel miRNAs and its stem loop structure by Miredp based on the references
We used DESeq software algorithm that was based on negative binomial distribution and biology duplicate samples to compare the known or novel miRNA expression in control versus depression groups. The criteria for assigning signiﬁcance included that P-value was less than 0.05 and the fold-change was larger than 1.5.
Gene targets of differentially expressed miRNAs were predicted with four miRNA target prediction softwares, such as Targetscan, PITA, RNA22 and miRDB. To eliminate bias caused by a single database prediction, the genes predicted by more than two softwares were chosen for further analysis.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Differential expression file containing : id,baseMean,baseMeanA,baseMeanB,foldChange,log2FoldChange,pval,padj

source_name: medial prefrontal cortices

extract_protocol:
Twenty-four hours after the mice were surely tested to demonstrate CUMS-induced depression-like behaviors, these depression-like mice and controls were anesthetized by using Isoflurane and decapitated by guillotine. Both sides of the medial prefrontal cortex were quickly isolated and dissected on the ice-cold glass slides. These cortical tissues were placed into the frozen vials that contained RNAlater RNA Stabilization Reagent (QIAGEN, Germany) at 4°C and stored at -80°C for subsequent analysis. Total RNAs from the tissue of medial prefrontal cortex in each mouse were isolated with TRIzol Reagent (Life Technologies, Carlsbad, CA, USA) based on the manufacturer instruction. Total RNA samples placed in the dried ice were delivered to Beijing Genomics Institute (BGI), China for sequencing analysis. RNA samples were done with quality-control by BGI staff using Agilent 2100 Bioanalyzer (Agilent Technologies, USA) with RNA 6000 nano Reagents Port 1. The concentration of total RNA, the value of RNA integrity number (RIN) and the ratio of 28S to 18S ribosomal RNA were measured. The samples with total RNA amount larger than 10 μg, the concentration larger than 200 ng/μl, the RIN larger than 8, and the ratio of 28S to 18S larger than 1.0 were selected for the construction of transcriptome and small RNA libraries, respectively.
miRNA sequencing library was constructed from those total RNAs, in which low molecular weight RNAs (18-30 nt) were isolated by polyacrylamide gel electrophoresis. 5ˊ-RNA adapter was ligated to RNAs with T4 RNA ligase. The ligated RNA was size-fractionated and 36-50 nucleotide fractions were excised. 3ˊ-RNA adapter was subsequently ligated to the precipitated RNA by using T4 RNA ligase. The ligated RNAs were size-fractionated and the 62-75 nucleotide fraction (small RNA+adaptors) was excised. Small RNAs ligated with adaptors were subjected to RT-PCR to produce sufficient templates for sequencing. PCR products were purified and collected by gel purification and ready for high-throughput sequencing.

treatment_protocol: chronic unpredictable mild stress (CUMS)-induced depression

value: prefrontal cortices


title: RatID_5_CX_SHM_mRNA

source_name: Perilesional cortex, sham operated


title: YY56_1


title: Control 2 PFC Illumina Hiseq miRNA


title: B. gymnorrhiza leaf rep1

description: small RNAs


title: CUMS 2 PFC Illumina Hiseq mRNA

data_processing:
Bioinformatics analysis of transcriptome: The original image data was transferred into sequence data by base calling, which were defined as raw data or raw reads. DynamicTrim Perl script implemented in SolexaQA package was performed to control the quality of raw sequencing data based on the following criteria.
1) Remove reads with adapters. 2) Remove reads in that unknown bases were more than 10%. 3) Remove with 50% of the bases with low quality score (PHRED score 5).
After filtering, the remained reads were called as "clean reads" and then mapped to mouse genome reference sequence (UCSC mm10) by using TopHat v1.0.12 which incorporated Bowtie v0.11.3 software to perform the alignments.
For the alignment and mapping, the maximum of allowable mismatch was set to 3 for each read.
The sole reads uniquely aligned to the genes were used to calculate the gene expression level. Reads per kilo-base per million reads (RPKM) were used for gene expression and genes with low expression level (RPKM< 0.5) were removed for further analysis.
Differentially expressed genes (DEGs) were detected by NOIseq package.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Differential expression file containing: GeneID,geneLength,Means-Ctl,Means-CUMS,log2Ratio(CUMS/Ctl),Up-Down-Regulation(CUMS/Ctl),Probability,Symbol,Description,KEGG Orthology,GO Component,GO Function,GO Process,Blast nr

extract_protocol:
Twenty-four hours after the mice were surely tested to demonstrate CUMS-induced depression-like behaviors, these depression-like mice and controls were anesthetized by using Isoflurane and decapitated by guillotine. Both sides of the medial prefrontal cortex were quickly isolated and dissected on the ice-cold glass slides. These cortical tissues were placed into the frozen vials that contained RNAlater RNA Stabilization Reagent (QIAGEN, Germany) at 4°C and stored at -80°C for subsequent analysis. Total RNAs from the tissue of medial prefrontal cortex in each mouse were isolated with TRIzol Reagent (Life Technologies, Carlsbad, CA, USA) based on the manufacturer instruction. Total RNA samples placed in the dried ice were delivered to Beijing Genomics Institute (BGI), China for sequencing analysis. RNA samples were done with quality-control by BGI staff using Agilent 2100 Bioanalyzer (Agilent Technologies, USA) with RNA 6000 nano Reagents Port 1. The concentration of total RNA, the value of RNA integrity number (RIN) and the ratio of 28S to 18S ribosomal RNA were measured. The samples with total RNA amount larger than 10 μg, the concentration larger than 200 ng/μl, the RIN larger than 8, and the ratio of 28S to 18S larger than 1.0 were selected for the construction of transcriptome and small RNA libraries, respectively.
mRNAs were extracted from total RNA by oligo(dT) beads. mRNAs were randomly sheared into 200 bp fragments that were reversely transcribed into complementary DNA (cDNAs) by random oligonucleotides. Upon end repair, these synthesized cDNAs were purified by using QiaQuick PCR extraction kit and ligated by sequencing adaptors. After the amplification with Illumina PCR Primer Cocktail within 15 cycles of PCR reaction, these cDNAs were size-selected and purified by agarose gel electrophoresis. cDNAs with sizes between 200 and 300 bp were selected for library construction.


title: TL_2

value: Diploid


title: TL_3


title: 2_p140_Set-K


title: B. gymnorrhiza flower rep1

description: small RNAs

source_name: Bruguiera gymnorrhiza flower

value: flower buds


title: Control 1 PFC Illumina Hiseq mRNA


title: TL_1


title: CUMS 1 PFC Illumina Hiseq mRNA


title: RatID_3_CX_SHM_mRNA


title: HiSeq_RRBS

city: Royal Parade

first: Andrew

last: Keniry

state: Victoria

department: Molecular Medicine

country: Australia

institute: The Waler and Eliza Hall Institute of Medical Research

description: Bisulfite treated genomic DNA

data_processing:
For HiSeq200: Illumina Casava1.7 software used for basecalling.
For NextSeq500: Base calling and quality scoring: Real-Time Analysis v2.4.6,  FASTQ file generation and de-multiplexing: bcl2fastq conversion software v2.15.0.4
Trimming of adapters and low quality base calls was performed with trim_galore
Trimmed reads were then filtered for true RRBS reads (which contain an MspI cut site at the 5’ end of both read 1 and read 2) with trimRRBSdiversityAdaptCustomers.py (NuGEN)
To eliminate potential mapping bias between the alleles, sequencing reads were aligned to a bisulfite converted custom version of the mouse genome (mm10), where SNPs that exist between Mus musculus domesticus and Mus musculus castaneus have been N-masked, using bismark.
Methylation bias in the reads was determined using the bismark_methylation_extractor using the --mbias_only option, and methylation calls were made, excluding the 13 5’ bases of reads due to mbias, using bismark_methylation_extractor.
NOTE: For processing of the NextSeq sample, 6bp were removed from the 5' end of R2 to improve mapping, as discussed in the paper. The methylation calls provided here were produced using this method.
Genome_build: mm10
Supplementary_files_format_and_content: Text file containing methylation calls for each SNP.  Produced by the bismark_methylation_extractor.
Columns:
(1) seq-ID
(2) methylation state
(3) chromosome
(4) start position (= end position)
(5) methylation call
A more detailed description of the Bismark methylation extractor output can be found at:  http://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_User_Guide.pdf.

source_name: E9.5 whole embryo

extract_protocol:
Pregnant females were sacrificed at E9.5 by CO2 asphyxiation and the embryos dissected from deciduae in PBS. Embryo samples were snap frozen in buffer RLT plus (Qiagen) and DNA was later extracted with the AllPrep DNA/RNA Mini Kit (Qiagen) using the manufacturer’s instructions. DNA was treated with RNase A then purified through the DNA Clean and Concentrator column (Zymo).
RRBS libraries were made from 100 ng of purified DNA using the Ovation RRBS Methyl-Seq System (NuGEN), according to the manufacturers recommendations, which includes use of the Qiagen Epitect kit for bisulfite conversion.

value: C57BL/6 x castaneous

value: whole embryo


title: B. gymnorrhiza flower rep2

description: small RNAs


title: RatID_2_CX_SHM_mRNA

value: sham operated


title: RatID_1_CX_SHM_mRNA


title: CUMS 1 PFC Illumina Hiseq miRNA


title: Cells infected with Mutant Reovirus, replicate 1

city: Sherbrooke

first: Martin

last: Bisaillon

state: Québec

address: 3201 rue Jean-Mignault

department: Biochimie

country: Canada

institute: Université de Sherbrooke

description: Technical replicate (1/3)

data_processing:
Sequence reads were aligned on a transcriptome reference sequence database (UCSCGene MM10) using Bowtie aligner and associated gene isoforms quantified in transcript-per-million (TPM) using RSEM for each sequenced sample.  Alternative splicing events were automatically detected and quantified using the percent-spliced-in (PSI, Ψ) metric based on isoform expression TPM for the long (L) and the short (S) forms.
Welch's t-test (Student's t-test with unequal sample sizes and unequal variances) was calculated through the GSL library (http://www.gnu.org/software/gsl/) integrated to Perl system analysis for gene expression and alternative splicing data.  Also, false discovery rate were calculated with the Q-value package in R (https://cran.r-project.org/src/contrib/Archive/qvalue/) based on Storey et al.
Genome_build: mm10
Supplementary_files_format_and_content: excel files for gene expression data and alternative splicing comparison between infected and control cells

source_name: L929 cell line

growth_protocol: grown in minimal Eagle medium (Wisent) containing 5% fetal bovine serum, cells passaged as recommended by ATCC

extract_protocol:
Total RNA was extracted with Trizol® as recommended by the manufacturer (Life Technologies).
Messenger RNAs were isolated from 5 ug total RNA using New England Biolabs magnetic mRNA isolation kit (S1550S), as per manufacturer's protocol, and then eluted in 25 ul. Quality and quantity assessments were performed on Agilent Nano Chip (Catatalog number 5067-1511). The RNA-seq library was then built using Illumina SSV21106 kit from 9 ul isolated mRNA. Library quality was assessed using Agilent DNA HS Chip (Catatalog number 5067-4626). Library quantification was performed by qPCR following Illumina Kappa library quantification protocol. Reovirus-infected and mock libraries were multiplexed and sequencing was done in triplicate. Pooled libraries were sequenced at 100bp paired-end reads using Illumina HiSeq 2000 at McGill University and Génome Québec Innovation Centre Sequencing Service.

treatment_protocol: L929 cells were plated at a density of 7X10E4 cells per square centimeter the day before infection at a MOI of 50 TCID 50 units per cell using standard procedures with T3D-S mutant reovirus (more sensitive to interferon).  Cells were collected 14 hrs post-infection, at which time visible cytopathic effect was still minimal.

tag: cell line

value: C3H/An mouse conjunctive tissue (fibroblasts)


title: Cells infected with Mutant Reovirus, replicate 2

description: Technical replicate (2/3)


title: Cells infected with Reovirus, replicate 3

description: Technical replicate (3/3)

treatment_protocol: L929 cells were plated at a density of 7X10E4 cells per square centimeter the day before infection at a MOI of 50 TCID 50 units per cell using standard procedures with T3D-S reovirus strain.  Cells were collected 14 hrs post-infection, at which time visible cytopathic effect was still minimal.


title: Cells infected with Mutant Reovirus, replicate 3

description: Technical replicate (3/3)


title: Control 2 PFC Illumina Hiseq mRNA


title: Cells infected with Reovirus, replicate 2

description: Technical replicate (2/3)


title: Cells infected with Reovirus, replicate 1

description: Technical replicate (1/3)


title: Mock Cells, Replicate 3

description: Technical replicate (3/3)


title: Mock Cells, Replicate 1

description: Technical replicate (1/3)


title: RatID_7_CX_TRM_mRNA

value: TBI


title: Mock Cells, Replicate 2

description: Technical replicate (2/3)


title: RatID_4_CX_SHM_mRNA


title: Control 1 PFC Illumina Hiseq miRNA


title: RatID_5_HIP_SHM_mRNA

description:
Hippocampus_DEseq2_raw_counts.txt
Identical  (raw file) to GSM1943617

value: dorsal hippocampus


title: KPC pancreatic fibroblasts, biological replicate 1

city: Columbus

first: Jason

middle: R

last: Pitarresi

state: Ohio

address: 460 W. 12th Ave

institute: Ohio State University Medical Center

data_processing:
fastqc (v0.10.1): from visual inspection of fastqc results, determined that the first 13 bases across reads were of consistently lower quality across samples than the rest of the reads.
fastx_trimmer (fastx_toolkit v0.0.13): removed first 13 bases from all reads
fastq_quality_filter (fastx_toolkit v0.0.13): filtered out reads with more than 10% of bases having read quality less than 20
Tophat (v2.0.3): reads aligned to mm10
Sort reads: samtools (v0.1.18)
coverageBed: GRCm38 gene position bed file from UCSC genome browser
Genome_build: mm10
Supplementary_files_format_and_content: txt file with chromosome location, gene symbol, number of reads, number of bases in the gene that had non-zero coverage, and the fraction of the bases in the gene covered by the reads for that sample.

source_name: Pancreatic fibroblasts

growth_protocol: Fibroblasts were cultured using a modified protocol for gravity separation.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Poly-A containing mRNA molecules was purified from total RNA (0.6 µg; RIN >7) using poly-T oligo-attached magnetic beads from TruSeq RNA Sample Prep Kit v2 (Illumina; RS-122-2001). Subsequent library construction of the RNA-seq library according to the manufacturer's instructions. Libraries were prepared with 13 cycles of PCR. Sequencing was performed using the single-read 50bp approach on HiSeq 2000 high output mode.

treatment_protocol: Fibroblasts  were grown in 10% FBS DMEM in a 37° incubator with 7% CO2

value: pancreas

value: mixed

value: KPC


title: KPC pancreatic fibroblasts, biological replicate 2


title: wild type pancreatic fibroblasts, biological replicate 1

value: wild type


title: wild-type replicate2

first: Chunsheng

last: Han

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

data_processing:
RNA-seq reads generated from each sample were aligned to the mouse genome (UCSC mm9) with Tophat-2.0.6.
Mapped reads were subsequently assembled into transcripts guided by reference annotation (mm9, USCS gene annotation) with Cufflink-2.0.2.
Differential gene and expression analysis was conducted by using cuffdiff.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: bigWig files were generated using bam2wig; The bigWig format is for display of dense, continuous data that will be displayed in the Genome Browser as a graph

source_name: testes

extract_protocol:
Total RNA was extracted from 24-day-old or adult mouse testes by using Trizol according to the standard protocol (Invitrogen). DNA contaminants were eliminated by RNase-free DNase treatment. Then the RNA samples were subjected to RNA sequencing following manufacturer’s recommendations (Novogene) using Illumina Hiseq 2000 instrument.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To identify RFX2-dependent genes during spermatogenesis, we carried out RNA-seq analysis using 24-day-old wild-type and mutant testes samples. We chose P24 samples because spermiogenesis in mutants was normal before this time point while massive round spermatids detached from the tubules thereafter. RNAs were isolated from the total testicular cells.

value: DBA

value: male

tag: development stage

tag: genotype


title: wild-type replicate1

tag: gender


title: wild type pancreatic fibroblasts, biological replicate 2


title: rfx2 knockout replicate2


title: Wildtype

city: Bundoora

first: Harald

last: Oey

state: Vic

address: Kingsbury Drive

department: Genetics

institute: La Trobe University

data_processing:
3' ends were trimmed for low quality bases using trim_seq with the settings --trim=right -l 3 -m 15 (www.biopieces.org)
Reads were mapped to the mouse genome (build mm9) using Bismark and Bowtie2 with the options --bowtie2 -N 1 -D 100 -R 10 --maxins 300
Libraries were equalized by subsampling based on mapped read counts, PCR duplicates removed using deduplicate_bismark and filtered to only include reads with mapping quality >= 38.
CpG methylation values were extracted using bismark_methylation_extractor with the options --ignore_r2 2 --counts --paired-end --no_overlap --merge_non_CpG
CpG methylation values were merged into a single value per CpG and CpGs with < 8 reads covering the CpG or with uneven coverage (lower coverage sample < 60% of readcount for the higher coverage sample) were discarded.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files contain CpG methylation scores for sites with at least 8 sequencing reads covering the CpG and with similar covarage across both samples

source_name: Sperm

extract_protocol:
Sperm was extracted from cauda epididymis and vas deferens into Dulbecco’s Modified Eagle Medium (DMEM). The extract was washed in PBS and contaminating somatic cells removed by resuspension in distilled water for osmotic lysis followed by incubation for 20 min on ice in somatic cell lysis buffer (0.1% SDS, 0.5% Triton-X). Genomic DNA was isolated using the DNeasy Blood & Tissue Kit (Qiagen).
Total genomic DNA was treated with sodium bisulfite to convert unmethylated cytosines, fragmented to ~200bp and ligated to paired-end sequencing adapters

value: FVB/N

value: Wildtype


title: rfx2 knockout replicate1


title: GFP-Bcl2-2

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

data_processing:
Fastq data files were aligned to the mouse Mm10 Ensembl genome with Novoalign read aligner version 2.08.02
Novoaligned sam files were parsed into binary point data files and differentially expressed genes identified using the RNASeq application from USeq software version 8.4.1
RNASeq application calculates fraction of reads that are exonic, intronic and intergenic and makes normalized read data tracks (FPKM) from the point data for visualization in the Integrated Genome Browser
RNASeq application runs DefinedRegionsDifferentialSeq for calculating differential expression using Anders DESeq negative binomial statistics and Benjamini and Hochberg mulitple testing correction
Genome_build: Ensembl Mus musculus Mm10
Supplementary_files_format_and_content: Data table with Ensembl IDs, chromosome coordinates, individual sample raw read counts, FPKM counts, Log2 ratio and false discovery rate

source_name: Liver

extract_protocol:
Total RNA extracted using TRIzol (Invitrogen) and on column DNAse digestion using Direct-zol RNA kit (Zymo Research)
Illumina TruSeq Standed Total RNA Sample Prep with Ribo-Zero

tag: Sex

tag: age

value: 8 weeks

tag: gene delivery


title: GFP-Bcl2-4


title: GFP-Bcl2-3


title: GFP-Bcl2-5


title: KO-DG astrocytes

city: Shanghai

first: Yezheng

last: Tao

address: No.130, Dong An Road

institute: IOBS, Fudan University

description: PCR amplified cDNA library

data_processing:
Base calling was performed by Wuxi Apptec.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 by TopHat v1.4.0 with  -p 8  -a 8 -m 2 -i 30 -I 500000 -g 20 -G /galaxy-repl/main/files/006/992/dataset_6992006.dat --library-type fr-unstranded --max-insertion-length 3 --max-deletion-length 3 --coverage-search --min-coverage-intron 10 --max-coverage-intr.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: annotated FPKM files in excel format for each Sample

source_name: astrocytes

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

treatment_protocol: WT and β-arr1-/- mice were sacrificed. DG astrocytes (1×10^6 cells) were cultured and transferred into Trizol.

value: dentate gyrus

value: Beta-arr1 knockout


title: GFP-Bcl2-1


title: GFP-Ctrl-2

value: GFP


title: dMCs_P2_r2

first: Yunfei

last: Zheng

address: 22 Zhongguancun Avenue South, Haidian District

department: Oral and Maxillofacial Surgery

institute: Peking University School and Hospital of Stomatology

description:
extracting RNA of the second passage cells
prcessed_dMCs_p2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Transcripts per million(TPM) were calculated using RSEM(1.1.21) with parameters(-p 8 --estimated-rspd --no-bam-output).
Genome_build: mm10
Supplementary_files_format_and_content: TXT files including tau values for each RNA-seq samples, and TPM values are generated for all the samples.

source_name: mouse dental mesenchymal cells

extract_protocol:
Total RNA was extracted using the RNeasy® Mini Kit
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.

value: ICR mouse embyonic dental mesenchymal cells

tag: passage

value: ICR


title: dMCs_P2_r1


title: dMCs_P1_r2

description:
extracting RNA of the first passage cells
prcessed_dMCs_p1


title: dMCs_P0_r1

description:
extracting RNA after isolation
prcessed_dMCs_p0


title: K. candel leaf rep2

description: small RNAs

organism: Kandelia candel

source_name: Kandelia candel leaf

value: leaf


title: dMCs_P0_r2


title: K. candel flower rep1

description: small RNAs

source_name: Kandelia candel flower

value: flower buds


title: MommeD13 heterozygote

value: MommeD13 heterozygote


title: K. candel leaf rep1

description: small RNAs


title: Ovary small RNA (Zonza)

city: Oxford

first: Peter

middle: W. H.

last: Holland

address: South Parks Road

department: Department of Zoology

country: United Kingdom

institute: University of Oxford

description: Small RNA

data_processing:
(Small RNA) - Bowtie index created for each of the Cameraria ohridella and Pararge aegeria genome assemblies
(Small RNA) - miRDeep2 "mapper.pl" script used to parse fastq to fasta, clip adapters, remove entries with non-canonical letters, collapse reads and map reads to bowtie index
(Small RNA) - Size selection done on collapsed reads to exclude sequences outside the range of 18-24 nt
(Small RNA) - miRDeep2 "mirdeep2.pl" script used to predict miRNA hairpins based on processed small RNA reads
(Small RNA) - Predicted hairpins filtered based on structure and free energy as well as comparisons to existing miRNA data
(Total RNA) - First 16 bases clipped from all reads
(Total RNA) - Assembly using Trinity (version: trinityrnaseq_r20140717)
(Total RNA) - Transcriptome assembly annotation using BLAST2GO, BLASTn and tBLASTn
Genome_build: Pararge aegeria genome assembly available in the Oxford Research Data Archive (doi 10.5287/bodleiandury.3)
Supplementary_files_format_and_content: Tab-delimited text files indicating each predicted miRNA precursor sequence as well as sequence and read counts for each of its mature products

organism: Pararge aegeria

source_name: Pararge aegeria ovary (Zonza)

extract_protocol:
TRIzol extraction followed by DNase I digestion
Library construction performed by the Beijing Genomics Institute

tag: sample type

value: Laboratory-reared population

value: ovary


title: Ovary RNA (Zonza)

description:
Total RNA
Pae_combined_transcriptome.fasta
Combined_transcriptome_annotation.txt
Raw data pooled with sample 1 for transcriptome assembly


title: K. candel flower rep2

description: small RNAs


title: 24Bm

first: Jin

last: Xu

address: Yuanmingyuan western road No.2

institute: China Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
All trimmed sequences in length of 18-30nt were aligned with BBSV and satellite RNA genome and allowed three-mismatched reads were used for all further analysis.
Genome_build: BBSV genome (JN635330.1), satellite RNA genome (NC_006460.1), miRbase 21 database
Supplementary_files_format_and_content: processed data_files_format_and_content: small RNA sequences and their read numbers

organism: Nicotiana benthamiana

source_name: leaves

growth_protocol: N. benthamiana plants were grown in a growth chamber with a 16-h-light/8-h-dark cycle at 25ºC.

extract_protocol:
Three systemic leaves were harvested at 12 dpi. Total RNA was harvested using Trizol reagent. Small RNA libraries were generated following the manufacturer’s protocol (Illumina, California, USA).
Small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Three leaves of N. benthamiana, typically at the four-leaf stage in 1-month-old, were used for inoculation, 4 plants for each experiment. BBSV alone or with its associated sat-RNA were inoculated to plants. After inoculation, plants were grown at 18ºC and 25ºC conditions.

tag: growth temperature

tag: inoculum

value: BBSV


title: 24Bm+Sat

value: BBSV with satellite RNA


title: Ovary small RNA (St Hubert)

description: Small RNA

source_name: Pararge aegeria ovary (St Hubert)

tag: tissue


title: 24Mock

value: Buffer


title: GFP-Ctrl-3

value: male


title: 18Bm+Sat


title: Ovary RNA (St Hubert)

description:
Total RNA
Pae_combined_transcriptome.fasta
Combined_transcriptome_annotation.txt
Raw data pooled with sample 2 for transcriptome assembly


title: WT-DG astrocytes

description: PCR amplified cDNA library

value: wildtype


title: GFP-Ctrl-1


title: dMCs_P1_r1


title: 18Bm


title: Strain HS at 24h replicate B

data_processing:
Raw sequences were filtered to remove human sequence contamination, remove short reads (< 50 bp), depleted of duplicate reads, and quality trimmed using Trimmomatic (v 0.32).  rRNA sequences were identified and culled using SortMe RNA (v1.9)
Raw sequence reads for LF82 and HS were mapped to NCBI reference genomes NC_011993 and NC_009800, respectively  using the Burroughs Wheeler aligner (BWA)
Counts for each annotated genomic loci were determined by HTseq-count (version 0.6.1)
Genome_build: genomes NC_011993 and NC_009800
Supplementary_files_format_and_content: txt, raw count for each sample

organism: Escherichia coli HS

source_name: cell

extract_protocol:
Total RNA was extracted from the cells using the RiboPure Bacteria kit (Life Technologies Corp. Carlsbad, CA), following the manufacturer’s protocol.
Two micrograms of RNA was depleted of ribosomal RNA using the RiboMinus Transcriptome Isolation Kit (Life Technologies Corp. Carlsbad, CA).  These samples were then used as a template for strand-specific cDNA synthesis

value: HS

tag: time point

tag: growth phase

value: stationary


title: Strain HS at 24h replicate C

tag: strain


title: Strain HS at 2h replicate C

value: exponential


title: Strain HS at 24h replicate A


title: Strain HS at 2h replicate A


title: mRNAs from Burkholderia glumae BICL39 after 12hrs in LB Liquid culture

city: Seoul

first: Ingyu

last: Hwang

address: Kwanak Gu Daehak Dong

department: Agricultural Biotechnology

country: South Korea

institute: Seoul National University

data_processing:
BWA software was used for basecalling and genome alignment.
Sequenced reads were mapped to Burkholderia glumae BGR1 genome using bwa with parameters aln -q 20 and samse
Reads of mRNAs were counted by manual Python script.
Genome_build: Burkholderia_glumae_BGR1_uid59397
Supplementary_files_format_and_content: tab-delimited text files include gene information and hit-normalized raw counts, RPKM values for each Sample …

organism: Burkholderia glumae BGR1

source_name: Bacteria culture

growth_protocol: Each Baterial strain was grown for 12 hrs in LB liquid.

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer's protocol.
Illumina TruSeqTM RNA sample prep kit with standard low throughput (LT) protocol

value: isocitrate lyase (bglu_1g12420) mutant BICL39


title: mRNAs from Burkholderia glumae wild type  BGR1 after 12hrs in LB Liquid culture

value: wild type BGR1


title: Population STARR-seq Rep 1

first: Timothy

middle: E

last: Reddy

address: 101 Science Dr. RM 2383

institute: Duke University

data_processing:
Library strategy: STARR-Seq
bowtie2-build haplotype.fasta haplotypes
bowtie2 -N 0 --mp 100 --rdg 100,100 --rfg 100,100 -x haplotypes -1 Read1.fastq -2 Read2.fastq
filtering: discard any variant with read counts less than 1
significance evaluation: Fisher's Exact Test was applied to RNA vs. DNA read counts for reference vs. alternate haplotypes; P-values were adjusted via multiple hypothesis correction to control for False Discovery Rate (FDR) via procedure p.adjust() in R.
Genome_build: hg19

source_name: hepatocellular carcinoma

growth_protocol: HepG2 cells were obtained through the Duke University Cell Culture Facilities and were maintained in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was purified via RNA midi prep (Qiagen) including DNAse I treatment steps. 70 ug of RNA total RNA was used as input for poly-a selection and ribosomal RNA depletion using the dynabead OligoDT mRNA purificatin kit (invitrogen). RNA was treated with turbo DNAse (invitrogen) then repurified using a a RNAeasy colum (Qiagen).
cDNA was generated using SuperScript III reverse transcriptase using a reporter gene specific primer that bound the transcript generated from the plamsid. Libraries were constructed in two rounds. cDNA generated from spliced mRNA was amplified using a splice specific PCR primer. Then sequencing libraries were amplified from the reporter cDNA as per methods section.
library strategy: self-transcribing active regulatory region sequencing (STARR-seq)

treatment_protocol: Cells were transfected with reporter vectors using Fugene HD (promega) at a 5:1 Fugene to DNA ratio

tag: cell type

tag: passages

tag: days post transfection


title: H1-GATA2-/- HE rep1

first: qianyu

last: chen

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: hg19
Supplementary_files_format_and_content: TPM

source_name: Hemogenic endothelium

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: ES derived Hemogenic endothelium


title: H1-GATA2-/- HPC rep1

source_name: Hematopoietic progenitor cells

value: ES derived Hematopoietic progenitor cells

tag: genotype


title: Control_HSC3_RNA-Seq

city: Bethesda

first: Aniket

last: Gore

state: MD

address: Bldg 6B center drive

institute: National Institute of child health and human development

data_processing:
Illumina software for base calling
reads trimmed using trimmomatc and aligned using TOPHAT
differential RNA expression calculated using cufflinks and using ANOVA from PARTEK genomic suite
Genome_build: Zv9
Supplementary_files_format_and_content: BAM

organism: Danio rerio

source_name: control morpholino injected embryos

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

value: Ek

value: hematopoietic stem and progenitor cells (HSPCs)


title: Population STARR-seq Input Plasmid Library

source_name: Input Plasmid Library


title: HSC_Mutant_RNA-Seq

source_name: dnmt3bb.1 morpholino injected embryos


title: Strain HS at 2h replicate B

first: Yuanhao

last: Zhang

address: AMS Department,Stony Brook University

institute: Stony Brook University


title: H1 HPC rep1


title: Population STARR-seq Rep 3


title: HSC_Control_RNA-Seq


title: mRNAs from Burkholderia glumae BICL39C after 12hrs in LB Liquid culture

value: complemented strain BICL39C of isocirate lyase mutant


title: Population STARR-seq Rep 2


title: H1-GATA2-/- HE rep2


title: H1 HE rep2


title: H1-GATA2-/- rep1

source_name: Embryonic stem cells

value: Embryonic stem cells


title: H1 HPC rep2


title: H1 HE rep1


title: H1 rep2


title: Mutant_HSC2_RNA-Seq


title: 18Mock


title: H1 rep1


title: H1-GATA2-/- rep2


title: input DNA

city: Nagoya

first: Kunio

last: Ihara

state: Aichi

address: Furo-cho 1, Chikusa-ku

department: Center for Gene Research

country: Japan

institute: Nagoya University

data_processing:
Basecalls and alignment on dm 3 were performed using CLCbio with default configurations
The read with lower mapping quality than 8 was eliminated.
The peaks were called by comparing ChIP DNA with input DNA, using PICS on Strand NGS with a default setting except for the following parameters; for PICS, 120 bp as an average fragment length, 10 bp as a minimum distance between forward and reverse reads, 200 bp as a minimum distance between forward and reverse reads, 100 bp as a window width, with 5% false discovery rate.
The peaks were called by comparing ChIP DNA with input DNA, using ERD on Strand NGS, 2 as an enrichment factor, 100 bp as a window size, 10 bp as a window slide size, 100 bp as a minimum region size.
Overlapping peaks called by PICS and ERD were determined as peaks.
When trained flies and naïve flies were compared, the read counts were obtained in the 1 kb window covering entire genome and analyzed by DESeq2, to determine the region enriched with CREB/CRTC in a specific group of samples. The region with increased or decreased CREB/CRTC binding were determined if the region were defined by the CREB/CRTC binding sites in the above criteria.
Genome_build: dm3
Supplementary_files_format_and_content: txt files were generated using Strand NGS and DESeq2; score and FDR determined by PICS, and adjusted p value and fold change determined by DESeq2
Supplementary_files_format_and_content: CREB CRTC binding analyzed by DESeq2.txt: txt showing statistically alteration in CREB/CRTC binding on three replicates
Supplementary_files_format_and_content: CREB sites.txt: txt showing CREB binding sites (determined by peak calling at least in 2 samples out of 3 biological replicates)
Supplementary_files_format_and_content: CRTC sites.txt: txt showing CRTC binding sites (determined by peak calling at least in 2 samples out of 3 biological replicates)

organism: Drosophila melanogaster

source_name: mushroom body

growth_protocol: Flies were raised under a 12 h:12 h, light:dark cycle, at 23℃ and 60% humidity.

extract_protocol:
Heads were collected and homogenized in crosslinking buffer. The nuclei were dissolved in extraction buffer, sonicated to dissociate the individual nuclei, and precipitated with ANTI-FLAG M2 Affinity Gel. The precipitates were rinsed 4 times in extraction buffer, with 5 min nutation at 4℃ between washes, and subjected to ChIP analysis. The purified mushroom body nuclei were sonicated, resulting in fragmentation of DNA ranging from 100 bp to 500 bp. The extracts were centrifuged to remove insoluble materials including the M2 Affinity Gel, and the supernatants were used for immunoprecipitation with specific antibodies.
The ChIP DNA samples prepared were used to prepare a library for Miseq, according to the manufacturer’s instructions.

treatment_protocol: Flies were subjected to spaced trained in which an odor is paired with electrical shocks.

tag: chip antibody

tag: treatment

value: naïve


title: CRTC_ChIPSeq spaced 3

value: anti-CRTC (lab made antibodies)

value: spaced trained 1d


title: H1-GATA2-/- HPC rep2


title: CRTC_ChIPSeq spaced 2


title: CRTC_ChIPSeq naïve 2


title: CRTC_ChIPSeq naïve 1


title: CREB_ChIPSeq spaced 2

value: anti-CREB (lab made antibodies)


title: CREB_ChIPSeq naïve 2


title: CREB_ChIPSeq naïve 1


title: CREB_ChIPSeq spaced 3


title: CRTC_ChIPSeq spaced 1


title: LsoB male polyA RNA

city: College Station

first: Cecilia

last: Tamborindeguy

address: Heep Center

institute: Texas A&M University

description: processed data file: LsoBmale.xlsx

data_processing:
SCS 2.8/RTA 1.8... real time basecalling, resulting in .cif, .pos, .bcl files.
BclConverter-1.7.1 (setupBclToQseq.py)...  bcl conversion producing qseq.txt files
demultiplex.pl (packaged with CASAVA-1.7.0)... separating out the barcodes
GERALD.pl (packaged with CASAVA-1.7.0)... converting to .fastq format
CLC genomics Workbench 6 for mapping and RPKM values
Genome_build: Candidatus Liberibacter solanacearum NC_014774.1
Supplementary_files_format_and_content: excel files include RPKM values Lso genes

organism: Candidatus Liberibacter solanacearum

source_name: Bactericera cockerelli, 1-day old adult

growth_protocol: Insects were maintained in tomato plants at room temperature and photoperiod of 12:12 (L:D)

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen), rRNA was removed using RNA depletion using RiboMinus Transcriptome Isolation kit (Life Technologies) and polyA RNA was purified using Dynabeads mRNA Purification kit  (Life Technologies)
The library from the polyA purified RNA was prepared using the RNA-TruSeq Library kit (Illumina) and the library from the depleted RNA was prepared using ScriptSeq RNA (Epicenter Biotechnologies).

treatment_protocol: Insects were 1 day old adult, and were sexed under the microscope

tag: psyllid sex

value: male

tag: psyllid vector

value: Bactericera cockerelli

tag: haplotype

value: B

tag: rna prep

value: polyA


title: LsoA male polyA RNA

description: processed data file: LsoAmale.xlsx

value: A


title: LsoB male depleted RNA

description: processed data file: LsoBmale.xlsx

value: depleted total RNA


title: CREB_ChIPSeq spaced 1


title: H3K9Ac_ChIPSeq spaced 2

city: Sai Kung

first: Yukinori

last: Hirano

address: Clear water bay

department: LIFS

country: Hong Kong

institute: The Hong Kong University of Science and Technology

description:
H3K9Ac increased sites.txt
all peak H3K9Ac.txt

data_processing:
Basecalls and alignment on dm 3 were performed using Lifescope with default configurations
The read with lower mapping quality than 8 was eliminated.
The peaks were called by comparing ChIP DNA with input DNA, using PICS on Strand NGS with a default setting except for the following parameters; for PICS, 120 bp as an average fragment length, 10 bp as a minimum distance between forward and reverse reads, 200 bp as a minimum distance between forward and reverse reads, 100 bp as a window width, with 5% false discovery rate.
The peaks were called by comparing ChIP DNA with input DNA, using ERD on Strand NGS, 2 as an enrichment factor, 100 bp as a window size, 10 bp as a window slide size, 100 bp as a minimum region size.
Overlapping peaks called by PICS and ERD were determined as peaks.
When trained flies and naïve flies were compared, the read counts in the individual peaks were statistically analyzed as follows. First, the centers of the H3K9Ac and H4K16Ac peaks were first extracted and then used to create neighboring 400 bp windows. The mapped reads were counted in these 400 bp windows for each biological replicate of ChIP-seq analysis. The counted read numbers in individual regions were normalized by elav for H3K9Ac ChIP-seq, and gapdh2 for H4K16Ac ChIP. The normalized read numbers in individual windows obtained from the spaced trained flies and the naïve flies were analyzed by Student’s t test (p < 0.05). Standard deviations of the normalized read numbers in individual windows from 3 replicates of naïve flies were 0.07 in H3K9Ac-ChIP-seq and 0.10 in H4K16Ac-ChIP-seq. Significantly increased peaks showing a more than 1.2-fold increase (>2SD) were determined as sites with an increase in H3K9Ac or H4K16Ac.
Genome_build: dm3 (BDGP R5)
Supplementary_files_format_and_content: txt files were generated using Strand NGS; FDR determined by PICS and fold increase determined by ERD were shown. Increase in histone acetylation was determined using three replicates of each naïve and trained flies, and the mean, SD and p value by student t test were shown.
Supplementary_files_format_and_content: all peak H3K9Ac.txt [txt showing all H3K9 peaks from 3 replicates of spaced trained samples (determined by overlaps between PICS and ERD)]
Supplementary_files_format_and_content: all peak H4K16Ac.txt [txt showing all H4K16 peaks from 3 replicates of spaced trained samples (determined by overlaps between PICS and ERD)]
Supplementary_files_format_and_content: H3K9Ac increased sites.txt [txt showing statistically increased sites in H3K9Ac based on three replicates]
Supplementary_files_format_and_content: H4K16Ac increased sites.txt [txt showing statistically increased sites in H4K16Ac based on three replicates]
Supplementary_files_format_and_content: CREB sites.txt [txt showing CREB binding sites (determined by overlaps between PICS and ERD)]
Supplementary_files_format_and_content: CRTC sites.txt [txt showing CRTC binding sites (determined by overlaps between PICS and ERD)]

extract_protocol:
Heads were collected and homogenized in crosslinking buffer. The nuclei were dissolved in extraction buffer, sonicated to dissociate the individual nuclei, and precipitated with ANTI-FLAG M2 Affinity Gel. The precipitates were rinsed 4 times in extraction buffer, with 5 min nutation at 4℃ between washes, and subjected to ChIP analysis. The purified mushroom body nuclei were sonicated, resulting in fragmentation of DNA ranging from 100 bp to 500 bp. The extracts were centrifuged to remove insoluble materials including the M2 Affinity Gel, and the supernatants were used for immunoprecipitation with specific antibodies.
The ChIP DNA samples prepared were used to prepare a library for SOLiD5500, according to the manufacturer’s instructions.

value: anti-H3K9Ac (catalog# ab4441, Abcam, lot# 2455632)


title: H4K16Ac_ChIPSeq naïve 3

description:
H4K16Ac increased sites.txt
all peak H4K16Ac.txt

value: anti-H4K16Ac (07-329, Merck Millipore, lot# DAM1780380)


title: LsoA male depleted RNA

description: processed data file: LsoAmale.xlsx


title: H4K16Ac_ChIPSeq naïve 2


title: H3K9Ac_ChIPSeq spaced 3


title: H3K9Ac_ChIPSeq naïve 2


title: H4K16Ac_ChIPSeq spaced 1


title: H3K9Ac_ChIPSeq naïve 1


title: H4K16Ac_ChIPSeq spaced 3


title: H4K16Ac_ChIPSeq naïve 1


title: LsoB female polyA RNA

description: processed data file: LsoBfemale.xlsx

value: female


title: H4K16Ac_ChIPSeq spaced 2


title: H3K9Ac_ChIPSeq naïve 3


title: CRTC_ChIPSeq naïve 3


title: LsoA female depleted RNA

description: processed data file: LsoAfemale.xlsx


title: LsoB female depleted RNA

description: processed data file: LsoBfemale.xlsx


title: H3K9Ac_ChIPSeq spaced 1


title: CREB_ChIPSeq naïve 3


title: 2014.SB.M.N100.3

city: Villenave d'Ornon

first: Pierre

last: Helwi

address: 210 chemin de Leysotte

country: France

institute: Bordeaux University

description: Processed data file: 2014_SB.rpkm

data_processing:
Image analysis and base calling were performed using RTA 1.18.61 and CASAVA 1.8.2.
Reads were mapped onto the 12X assembly of the Vitis vinifera genome using TopHat v2.0.10 and bowtie2 v2.1.0.
Gene expression was quantified from uniquely aligned reads using HTSeq v0.5.4p3 with the intersection_nonempty mode and CRIBI V1 gene annotations (http://genomes.cribi.unipd.it/DATA/GFF/V1.tar.gz). RPKM were then computed from these quantification results.
Genome_build: 12X Vitis vinifera genome (http://genomes.cribi.unipd.it/DATA/GENOME_12X/Genome12X.tar.gz)
Supplementary_files_format_and_content: *.rpkm: One tab-delimited text file per year, containing RPKM for each sample.

organism: Vitis vinifera

source_name: Grape berry, soil N100, v+35, 2014

extract_protocol:
Total RNAs were extracted according to the procedure of Reid et al. (Reid, Olsson, Schlosser, Peng, & Lund, BMC Plant Biol. 2006; 6:27) from 1 g of grounded frozen berries. Traces of genomic DNA were removed by a DNase I treatment (Ambion TURBO DNA-free DNase, Life Technologies).
Libraries of template molecules suitable for high-throughput DNA sequencing were created using "TruSeq™ RNA Sample Preparation v2 Kit" (Illumina Inc.). Briefly, mRNA was purified using poly-T oligo-attached magnetic beads and fragmented using divalent cations at 94°C for 8 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers, then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The double-stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double-stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C). Then surplus PCR primers were removed by purification using AMPure XP beads (Agencourt Biosciences Corporation). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent). The libraries were loaded in the flow cell at 7pM concentration and clusters were generated in the Cbot.

treatment_protocol: Nitrogen was added to the soil in 2 applications (bud break and flowering) to Sauvignon blanc vines. Berries were sampled at 2 stages ((v+28) and (v+35)) and frozen immediately in liquid nitrogen, grounded and stored at -80C.

tag: cultivar

value: Sauvignon blanc

value: Whole berry

tag: Stage

value: 35 days after mid-veraison (v+35)

tag: year

tag: modality

value: Soil N100


title: 2014.SB.M.N100.1

description: Processed data file: 2014_SB.rpkm

tag: tissue


title: 2014.SB.M.T.3

description: Processed data file: 2014_SB.rpkm

source_name: Grape berry, control, v+35, 2014

value: Control


title: 2014.SB.M.T.1

description: Processed data file: 2014_SB.rpkm


title: 2014.SB.M.N100.2

description: Processed data file: 2014_SB.rpkm


title: 2014.SB.MM.N100.2

description: Processed data file: 2014_SB.rpkm

source_name: Grape berry, soil N100, v+28, 2014

value: 28 days after mid-veraison (v+28)


title: 2014.SB.MM.T.3

description: Processed data file: 2014_SB.rpkm

source_name: Grape berry, control, v+28, 2014


title: 2014.SB.MM.N100.3

description: Processed data file: 2014_SB.rpkm


title: 2014.SB.M.T.2

description: Processed data file: 2014_SB.rpkm


title: 2014.SB.MM.N100.1

description: Processed data file: 2014_SB.rpkm


title: LsoA female polyA RNA

description: processed data file: LsoAfemale.xlsx


title: 2013.SB.M.N100.3

description: Processed data file: 2013_SB.rpkm

source_name: Grape berry, soil N100, v+35, 2013


title: 2013.SB.M.N100.2

description: Processed data file: 2013_SB.rpkm


title: 2014.SB.MM.T.1

description: Processed data file: 2014_SB.rpkm


title: 2013.SB.M.T.1

description: Processed data file: 2013_SB.rpkm

source_name: Grape berry, control, v+35, 2013


title: 2013.SB.M.T.3

description: Processed data file: 2013_SB.rpkm


title: 2014.SB.MM.T.2

description: Processed data file: 2014_SB.rpkm


title: 2013.SB.MM.T.2

description: Processed data file: 2013_SB.rpkm

source_name: Grape berry, control, v+28, 2013


title: 2013.SB.M.N100.1

description: Processed data file: 2013_SB.rpkm


title: 2013.SB.MM.N100.2

description: Processed data file: 2013_SB.rpkm

source_name: Grape berry, soil N100, v+28, 2013


title: 2013.SB.MM.T.1

description: Processed data file: 2013_SB.rpkm


title: 2013.SB.MM.N100.3

description: Processed data file: 2013_SB.rpkm


title: 2013.SB.MM.T.3

description: Processed data file: 2013_SB.rpkm


title: Δxyr1 Glucose 1

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

data_processing:
Illumina HiseqTM 2000 technology was used to perform sequencing, resulting in 147 million and  187 million 100 bp paired-end reads for parental (QM9414) and mutant (Δxyr1) strains, respectively. Quality-filtered reads were mapped to the Trichoderma reesei 2.0 reference genome, available at JGI Genome Portal (http://genome.jgi-psf.org/Trire2/Trire2.home.html), using the TopHat2 v2.0.4  aligner (Kim et al, 2013), allowing two mismatches and only unique alignments. After alignment, Samtools version 0.1.19 (Li et al., 2009) was used to process the alignments files which were visualized using the Integrative Genomics Viewer (Thorvaldsdottir et al., 2012). HTSeq version 0.6.0. was used to count reads over Trichoderma reesei transcripts. Bioconductor DESeq2 package version 1.6.3  (Love et al, 2014) was employed to differential expression analysis, using two-fold change, i.e., log2 fold change ≥ 1 or ≤ -1 and adjusted p-value ≤ 0.05 as thresholds.
Genome_build:v2.0
Supplementary_files_format_and_content: Tab-delimited text files containing gene expression information expressed as normalized abundance counts and as log2 Fold change between indicated samples and the respective p-value calculated by DESeq2.

organism: Trichoderma reesei

source_name: mycelia

growth_protocol: Wild-type strain was grown in MEX medium at 28°C for 7-10 days for complete sporulation. For gene expression assays, a spore suspension containing approximately 107 cells mL-1 was inoculated into 200 mL of Mandels-Andreotti medium (Schmollet al. 2009) containing 1% (w/v) of cellulose, or 2% (w/v) of glucose, or 1 mM of sophorose, as the carbon source.

extract_protocol:
Total RNA was extracted using the TRIzol kit (Invitrogen) according to manufacture's instructions.
RNA-seq libraries were prepared for sequencing using Illumina TruSeq RNA Sample Prep Kit.

value: Mutant

value: mycelia

tag: carbon source

value: 2% of glucose


title: Δxyr1 Sophorose 3

value: 1mM of sophorose


title: Δxyr1 Sophorose 2


title: Δxyr1 Cellulose 3

value: 1% (w/v) of cellulose


title: Δxyr1 Glucose 2


title: Δxyr1 Cellulose 2


title: Δxyr1 Glucose 3


title: 2013.SB.M.T.2

description: Processed data file: 2013_SB.rpkm


title: Δxyr1 Cellulose 1


title: Zhewan1-10

city: Hangzhou

last: Liu

address: No.198, Shiqiao Road, Jianggan District

data_processing:
The raw reads were first filtered by removing the adapter sequences and the low quality sequences, which included the reads with the N percentage (i.e., the percentage of nucleotides in a read that could not be sequenced) that was over 5% and the ones that contained more than 20% of the nucleotides in the read with a Q-value ≤ 10. The Q-value represented the sequencing quality of the related nucleotides. The clean reads were used in the de novo assembly of the transcriptomes. The RNA-Seq data were de novo assembled using the Trinity assembly program (Grabherr et al., 2011).
The function of the unigenes was annotated by BLASTing with an E-value threshold of 10-5 to protein databases that included the NCBI non-redundant (nr) database, the Swiss-Prot protein database, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and the Clusters of Orthologous Groups of proteins (COG) database. The proteins with the highest sequence similarity were retrieved for the analyses. The KEGG produced an annotation of the metabolic pathways, while the COG matched each annotated sequence to an ancient conserved domain, which represented the primary phylogenetic lineages of the pea. Based on the nr annotation, 6 top-hit species were identified, and the Gene Ontology (GO) classifications were obtained with Blast2GO.
The alignment software, bowtie 0.12.8, was used to map the reads back to the transcriptome. Then, the number of mapped clean reads for each unigene was counted and normalized into a RPKM value (Reads Per kb per Million reads), which is widely used to calculate the unigene expression (Mortazavi et al., 2008). To detect differentially expressed genes, statistical analyses among libraries were performed following the formula as described (Shen et al., 2012), where FDR (false discovery rate) were used to determine the threshold the P value in multiple tests and analyses using the q-value package (Benjamini et al., 2001). In our work, the differentially expressed unigenes between two samples were screened with the threshold of FDR ≤ 0.001 and the absolute value of log2Ratio ≥ 1. Furthermore, the GO classifications and the KEGG pathway enrichments were compared between up-regulated and down-regulated  unigenes.
Supplementary_files_format_and_content: [Expression_data_differential_analysis.xlsx] expression data of genes and differential analysis results, and function of interest of some unique genes
Supplementary_files_format_and_content: [Transcript_expression_total.txt] expression data for all Unigenes
Supplementary_files_format_and_content: Trinity_uniq.fasta is linked as a supplementary file on the Series record.

organism: Lathyrus oleraceus

source_name: seed

growth_protocol: The vegetable pea cultivar ‘Zhewan 1’ and the grain pea cultivar ‘Zhongwan 6’ were grown in the field of the Vegetable Research Institute, Zhejiang Academy of Agricultural Sciences. In Figure 1, the different developmental stages of the seeds of these two pea cultivars are shown. The pea pods were collected at different developmental stages (10, 15, 20, 25, and 30 days after pollination [DAP]). To control for the effect of biological variation, the materials that were collected for each sample were composed of large amounts from many individuals. The seeds from different plants were pooled together as one biological sample and three biological replicates were collected for each sample. The samples were frozen in liquid nitrogen immediately and stored at -80oC until further use.

extract_protocol:
Total RNA was extracted using the TRIzol Reagent. The mRNA was isolated using oligo (dT)-attached magnetic beads. The four libraries were sequenced using IlluminaHiSeqTM 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Zhewan 1

tag: seed type

value: vegatable pea

tag: harvest stage

value: 10 days after pollination


title: Zhongwan6-10

institute: Zhejiang Academy of Agricultural Sciences

value: Zhongwan 6

value: grain pea


title: Zhongwan6-25

value: 25 days after pollination


title: Zhewan1-25

value: vegetable pea


title: scribKD+Tet Exp3 Rep2

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

data_processing:
fastq file processed by filering out low quality reads (<Q20) and llow quality bases (<Q20) with sickle. Adaptors were removed with cutadapt 1.0.
RNA-seq data have been aligned to C.familaris genome using TopHat 2.0.6
RPKMs were generated using custom scripts
Genome_build: C.familiaris 3.1
Supplementary_files_format_and_content: RPKMs in tsv format

organism: Canis lupus familiaris

source_name: MDCK-II cells

growth_protocol: MDCK-II scribKD cells were plated at 1,300,000 cells/10 cm plate. The cells were cultured in 10 ml DMEM + 10% tetracycline-free FBS.

extract_protocol:
67 hours after plating, RNA was harvested using Trizol reagent
Libraries were prepared from 1 µg RNA using TrueSeq RNA sample preparation V2 kit according to the manufacturers instructions

treatment_protocol: Where specified, 10 µg/ml tetracycline (Tet) was added at the time of plating. Medium +/- Tet was changed one day after plating

tag: cell type

value: Madin-Darby Canine Kidney Epithelial Cells

tag: phenotype/variation

value: scribble knock-down (scribKD+Tet)


title: scribKD-Tet Exp3 Rep2

value: wild-type scribble expression (scribKD-Tet)


title: 2013.SB.MM.N100.1

description: Processed data file: 2013_SB.rpkm

value: Sauvignon blanc

value: Whole berry

value: Soil N100


title: scribKD-Tet Exp3 Rep1


title: t4

city: Minneapolis

first: Kristi

middle: L

last: Frank

state: MN

address: 420 Delaware St SE, MMC196

department: Dept. of Microbiology

institute: University of Minnesota

description:
Sample 2: r1t4
Sample 4: r2t4
RNA treated with Dnase to remove contaminating DNA, MICROBEnrich to deplete eukaryotic RNA, and MICROBExpress to deplete bacterial rRNA

data_processing:
Base call files were generated with Illumina Real Time Analysis software.
Primary analysis and de-multiplexing were performed with CASAVA (version 1.8.2, Illumina) to generate FASTQ files for each sample.
All data analysis was carried out using the Galaxy server maintained by the Minnesota Supercomputing Institute at the University of Minnesota.  De-multiplexed FASTQ files were assessed for quality, prepared for trimming, and trimmed using FastQC, FASTQ Groomer, and FASTQ Trimmer, respectively
The trimmed paired end reads in separate files were joined with FASTQ interlacer and further processed in FASTQ de-interlacer.
The left and right de-interlaced files for each sequenced sample were aligned using Bowtie for Illumina, and the resulting SAM output files were sorted with SortSAM.
Transcript abundance for each sample was carried out with Cufflinks using the OG1RF genome for reference annotation.
The Cufflinks assemblies of the biological replicates for each time point were merged with Cuffmerge
Cuffcompare and Cuffdiff were then used to analyze the Cuffmerge output files for statically significant differences in gene expression between the subdermal chamber inocula and 4 hours post-inoculation samples
Genome_build: ASM17257v2 (CP002621)
Supplementary_files_format_and_content: Tab-delimited .txt file with FPKM values, fold-change, and statistical analysis results

organism: Enterococcus faecalis

source_name: subdermal chamber aspirate, four hours after inoculation

growth_protocol: E. faecalis OG1RF(pCF10) was inoculated into 10-25 ml BH medium and incubated for ~15-16 hours, then diluted 1:5 into 25-50 ml of fresh BH medium and incubated for 2 more hours.  Bacteria were harvested by centrifugation for 15-20 min at 6000 rpm in a Beckman JA-17 rotor at 4°C.  Pellets were resuspended to an optical density at a wavelength of 600 nm of ~1.7-1.8 in KPBS.  Aliquots of the prepared inoculum were  processed in RNAprotect Bacteria Reagent.

extract_protocol:
Frozen pellets were thawed, resuspended in 0.4 ml of RNase-free TE containing 50 mg/ml lysozyme and 1000 U/ml mutanolysin, homogenized using a hand-held motorized homogenizer with RNase-free pellet pestles (Fisher Scientific, Pittsburgh, PA), and incubated for 10 min at 37°C.  Each sample was then split in half and extracted in duplicate with the RNeasy Mini Kit (Qiagen Inc.) according to the manufacturer’s instructions with an added homogenization step using the QIAshredder (Qiagen Inc.) immediately after the addition of Buffer RLT.  RNA was eluted from each column with two 30 μl volumes of RNase-free water, and total RNA from duplicate extractions of each sample were pooled together.  All OG1RF(pCF10) RNA eluates obtained from a single rabbit were further pooled.Contaminating DNA was removed using a TURBO DNA-free kit (Ambion, Austin, TX) following the rigorous protocol as directed by the manufacturer. DNase-treated RNA was ethanol precipitated in the presence of a glycogen carrier and resuspended in RNase-free TE.  RNA harvested from rabbits was first treated with MICROBEnrich (Ambion) followed by MICROBExpress (Ambion), according to the manufacturer’s instructions, to deplete eukaryotic RNA and bacterial rRNA, respectively.  RNA from the infection inoculum was treated with MICROBExpress only.
Library creation and sequencing were performed by the University of Minnesota Genomics Center.  Indexed libraries were created using the TruSeq RNA Sample Preparation Kit v2 (Illumina, Inc., San Diego, CA) according to the manufacturer’s instructions.  Indexed libraries were size selected to 320 bp +/- 5% using a LabChip XT instrument (Perkin Elmer, Waltham, MA).  Prepared libraries were hybridized to paired end flow cells, clonally amplified on an Illumina cBot, and sequenced using Illumina SBS chemistry in a 100 bp paired end run on an Illumina HiSeq 2000 instrument.

treatment_protocol: Two ml of serous fluid were aspirated from the subdermal chamber and were replaced with 2 ml of prepared inoculum. At 4 hours post-inoculation, 25-28 ml of aspirate was collected, immediately added to twice the volume of RNAprotect Bacteria Reagent, and processed according to the manufacturer's directions.  Cells were condensed into twelve pellets.

tag: strain

tag: growth medium

value: serous fluid in implanted rabbit subdermal chamber

tag: biological replicates

value: 1 and 2


title: scribKD+Tet Exp3 Rep1


title: US2

city: Yangling District

first: Lei

state: Province, State or Region

address: No.22 Xinong Road,  Yangling District

department: College of Animal Science and Technology

institute: Northwest A&F University

data_processing:
Single-end sequencing (36 bp) on an Illumina Hiseq2500 (Illumina, San Diego, USA)
The raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and then the dataset was further processed with an in-house program (ACGT101-miR, LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA and snoRNA) and repeats.
Unique sequences 18-26 nt in length were mapped to specific species precursors in miRBase 20.0 (ftp://mirbase.org/pub/mirbase/CURRENT/) by BLAST search to identify known miRNAs
Genome_build: CHIR_1.0
Supplementary_files_format_and_content: Text files include results of expression and difference expression of miRNA in two samples

organism: Capra hircus

source_name: receptive endometrium

growth_protocol: A total of 20 healthy 24-month-old multiparous dairy goats (Xinong Saanen) were induced to estrous synchronization for this study. The first day of mating was considered to be Day 0 of pregnancy. Gestational days 5 and 15 were important time points for the embryo implantation in goats [38]. The experimental goats were observed 3 times daily to ascertained estrous sign and mated naturally twice in estrus. And then the goats were euthanized when the goats lost consciousness caused by intravenous injection of barbiturate (30mg/kg) at gestational day 5 (pre-receptive endometrium) and gestational day 15 (receptive endometrium).

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 (Agilent, CA, USA) and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number> 7.0. Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA). And then we performed the single-end sequencing (36 bp) on an Illumina Hiseq2500 (Illumina, San Diego, USA) at the LC-BIO (Hangzhou, China) following the vendor’s recommended protocol.
miRNA libraries were prepared for sequencing using standard Illumina protocols

value: endometrium

value: Xinong Saanen

tag: receptivity status

value: receptive

tag: gestation day

value: at gestational day 15

tag: age

value: 24 months


title: 62T

city: Busan

first: LEE

middle: SEONG

last: HYUK

address: Haeyang-ro

department: Department of Marine Biotechnology

institute: Korea Institute of Ocean Science and Technology

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Trimmomatic 0.32 as default parameter, then mapped to mm8 whole genome using bowtie v 2.2.4 with parameters -t --very-sensitive
Differential expression profiles were calculated by edgeR and DESeq
Genome_build: PRJNA59043 (2013-06-10)
Supplementary_files_format_and_content: Excel file includes differential expression profiles and locus tags for genes of T. onnurineus NA1

organism: Thermococcus onnurineus NA1

source_name: RNA from Archaeal cells

extract_protocol:
After cell harvest, RNA samples were prepared using TRIzol reagent. Genomic DNA was eliminated by DNaseI treatment.
To remove rRNA in total RNA, Ribo-Zero rRNA Removal Kits (Human/Mouse/Rat) (MRZH-11124, Epicentre, USA) was used. Illumina Stranded TruSeq Total RNA Sample Prep Kit (Cat#FC-122-2201) was used with 1 ug of rRNA depleted RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: media

value: MM1-CO (CO-supplied media)

tag: growth phase

value: exponential phase


title: 156T


title: 12T


title: 32T


title: 102T


title: 2T


title: Δxyr1 Sophorose 1

tag: genotype

value: Mutant

value: mycelia

value: 1mM of sophorose


title: 122T


title: US1

source_name: pre-receptive endometrium

value: pre-receptive

value: at gestational day 5


title: IFC rep3

city: zhengzhou

first: hongping

last: li

institute: Henan Agricultural University

organism: Zea mays

source_name: maize ovary

growth_protocol: Zea mays L. (maize) inbred Yu-A474 plants were grown at a research farm of Henan Agricultural University, Henan Province, China (34º53´N, 113 º35´E, 94 m altitude) under non-stress conditions during June-October 2014.

extract_protocol:
The ovaries were isolated by removing the glumes, lemma, and palea and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Under non-stress conditions.

tag: developmental state

value: before pollination

value: ovary

value: IFC mutant


title: WT rep3

value: wild type


title: WT rep2


title: 6h_RNA

city: Wuhan

first: Wang

last: Min

address: No.1,Shizishan Street

institute: Huazhong Agricultural University

data_processing:
Illumina base-calling Software 1.7 use for basecalling
Clean reads were obtained after removing reads of low quality, adaptors or reads with >5% unknown nucleotides. The reference sequences were obtained by de novo assembling the pooled-1_RNA and pooled-2_RNA raw files using Trinity software.
Reads alignment software was SOAPaligner/soap2 2.20. The read counts were normalized as RPKM (reads per kilobase per million mapped reads) values in regard of the differing library sizes and the length of the transcripts.Differentially expressed genes (DEGs) from different samples were identified using the R package. The criteria applied to determine significant DEGs included a false discovery rate (FDR) smaller than 10−3 and log2-fold change be equal or greater than 1. In pooled_RNA.txt, we have used the algorithm of FPKM (fragments per kilobase of exon per million fragments mapped) to calculate the estimate the gene expression level, because we did this based on the pair-end read.
genome build: Sequences in the pooled-Unigene.fa provided in processed data file files were used for read alignment.
processed data files format and content: The processed data file of pooled-Unigene.fa is in FASTA format with sequence ID and sequence size, this data was used as reference sequence and obtained by de novo assembly. The processed data file of pooled_RNA.txt is in tab-delimited text file include reference sequence ID,length and annotation. The processed data files of 0h_RNA.map.txt, 6h_RNA.map.txt,24h_RNA.map.txt and 72h_RNA.map.txt were also in tab-delimited text files includ RPKM values for each samples.

organism: Citrus trifoliata

source_name: leaf

growth_protocol: grown under field conditions

extract_protocol:
Total RNA was extracted with RNAiso Plus (TaKaRa, Dalian, China) according to the manufacturer's instructions.
The cDNA library was constructed using mRNA-Seq assay according to the instructions. In brief, poly(A) mRNA was enriched from 20 μg of total RNA using oligo(dT) magnetic beads, and cut into short fragments (200-700 bp) with fragmentation buffer. The short mRNA fragments were synthesized into double-strand cDNA using random hexamer primers, and purified with QiaQuick PCR Purification Kit (Qiagen, CA, USA). Then cDNA was washed with EB buffer for end repairing and poly(A) addition. Illumina paired-end sequencing adapters were then ligated to the ends of the 3’-adenylated cDNA fragments. Agarose gel electrophoresis was carried out so as to select fragments with suitable size that was enriched by PCR amplification to construct the cDNA library. The library was sequenced by BGI (Shenzhen, China) on Illumina HiSeqTM 2000 platform for 5 gigabase in-depth sequencing.

treatment_protocol: Three-month-old trifoliate orange (Poncirus trifoliata (L.) Raf.) seedlings were collected from an experimental nursery at Huazhong Agricultural University. After a full wash, the plants were incubated in glass beakers filled with tap water and kept for 5 d at 25°C in a growth chamber. In order to enrich stress-responsive genes, the seedlings were treated with different stresses, including cold, salt, and drought. For cold treatment, the plants were placed at 4°C; the leaves were harvested at indicated time points (0, 6, 24, and 72 h). Salinity treatment was applied by placing the seedlings in 200 mM NaCl solution for same time schedule as cold. For drought treatment, the seedlings were placed on filter papers and dehydrated at ambient environment; the whole plants were sampled at 0, 0.5, 3, and 6 h.  These tissues were immediately frozen in liquid nitrogen after sampling and stored at -80 °C until use for further analysis.

value: leaf

tag: developmental stage

value: Three-month-old trifoliate orange seedlings

tag: stress

value: cold

tag: time point (h)


title: WT rep1

tag: tissue


title: 0h_RNA


title: 24h_RNA


title: 72h_RNA