title: Cortex, control group, rep4

description: Gene expression of control group


title: MCF7 SIX1 overexpressing cells treated by 1 µM 8430 replicate 3

status: Public on May 30 2020

type: SRA

city: Aurora

first: Heide

last: Ford

state: CO

department: Pharmacology

country: USA

institute: University of Colorado Anschutz Medical Campus

description:
MCF7_SIX1_8430_HTSeq_counts.txt
MCF7_SIX1_8430_HTSeq_RPKM.txt

library_source: transcriptomic

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the HiSeq 4000 RTA software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
FASTQC (v0.11.5) was used to assess sequence data quality.
fastq files from 2 separate lanes were merged for each sample to obtain sufficient read depth.
Low quality bases (Q <10) were trimmed from the 3' end of reads and short reads (<30 nt after trimming) and adaptor sequences were removed using the fastqc-mcf(v1.04) tool from EAutils.
FastQ Screen (v0.9.1) was used to check for common sequencing contaminants
Alignment to the Human reference genome (GRCh37/hg19) was carried out using TopHat2 (v2.0.13, --b2-sensitive --keep-fasta-order --no-coverage-search --max-multihits 10 --library-type fr-firststrand) and Bowtie2 (v2.2.3.0) with the UCSC hg19 GTF annotation file provided in the iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Aligned reads were then filtered to remove low quality mapped reads (MAPQ < 10) using SAMtools (v1.3.1)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Quality assessment of final mapped reads was performed using RSeQC (v2.6.4)
Raw gene-level count data was generated using HTSeq (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon –idattr=gene_id --mode=intersection-nonempty) using the GTF provided in the UCSC hg19-based igenomes bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Genome_build: GRCh37/hg19; Bowtie2 index and GTF from iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Supplementary_files_format_and_content: Tab delimited text files containing raw gene-level counts for each sample

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: MCF7 cells were grown in DMEM with 10% Fetal bovine serum, 1% Pen/Strep, and 2mM L-glutamine

extract_protocol:
Total RNA was isolated from MCF7 using Direct-zol RNA Miniprep Kit (Zymo Research R2052)
Strand-specific poly(A)+-enriched mRNA (Illumina TruSEQ mRNA)

treatment_protocol: MCF7 cells were treated by either DMSO or compound 8430 at 1 or 10 µM

tag: disease state

value: Mammary gland adenocarcinoma

tag: treatment

tag: genotype/variation

value: SIX1 overexpressing


title: MCF7 SIX1 overexpressing cells treated by DMSO replicate 3

value: DMSO


title: Cortex, control group, rep2

type: RNA

city: Fontenay-aux-Roses

first: Maâmar

last: Souidi

address: 31 Avenue de la Division Leclerc

country: France

institute: IRSN

description: Gene expression of control group

hyb_protocol: One-color microarray protocol from Agilent

scan_protocol: The raw fluorescence signals were scanned with Agilent Technologies scanner G2505C

data_processing: FeatureExtractor spot analysis software 10.7.3.1

molecule: total RNA

organism: Rattus norvegicus

source_name: cortex control

treatment_protocol: Tissue was instantly deep-frozen in liquid nitrogen and then stored at -80°C until RNA isolation. Total RNA was extracted from both tissues, thyroid and cortex respectively, using mirVana™ Isolation Kit (ThermoFisher Scientific, France) according to the manufacturer’s protocol.  RNA quality control was performed using the kit RNA 6000 nano (Agilent Technologies, Waldbronn, Germany) on an Agilent 2100 Bioanalyzer System (Agilent Technologies, Waldbronn, Germany). Quality of RNA was defined by a 260/280 absorbance ratio> 1.8; a 260/230 ratio > 1.5 and a RIN value > 7.5 were desired.

tag: strain

value: Wistar

tag: tissue

value: Cortex cerebellum

tag: gender

value: male

value: control group


title: Cortex, control group, rep1

description: Gene expression of control group

label_protocol: One-color microarray protocol from Agilent

extract_protocol: Total RNA was extracted from both tissues, thyroid and cortex respectively, using mirVana™ Isolation Kit (ThermoFisher Scientific, France)


title: MCF7 SIX1 overexpressing cells treated by DMSO replicate 2


title: D4_Ctr_input [ChIP-seq]

city: Wuhan

first: Jing-Jing

last: Zhang

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

country: China

institute: Huazhong Agricultural University

library_source: genomic

data_processing:
Paired-end reads for ChIP-seq were aligned to the mouse mm10 genome using Bowtie2 with the ‘‘-X 2000’’ options.
The Picard was used to remove PCR duplicates and Samtools was used to remove low quality reads (MAPQ < 30).
The MACS2 software calls the ChIP-seq peak with default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files were generated using deepTools.

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic Stem Cells (ESCs)

growth_protocol: ESCs were routinely cultivated on mitotically inactivated mouse embryonic fibroblasts (MEFs) in Knockout DMEM supplemented with 20% Knockout Serum Replacement, 1× Glutamine Max, 1× NEAA, 1× Pen/Strep, 0.1 mM 2-mercaptoethanol, 1000 U ml-1 LIF, 1 μM PD0325901 and 3 μM CHIR99021. MEFs were grown in DMEM high glucose supplemented with 15% FBS and 1× Pen/Strep.

extract_protocol: ChIP was performed as described previously (Liu et al., 2015).

treatment_protocol: The EpiLCs induction were performed by seeding 1.0×10e5 ESCs into a well of a 12-well plate coated with 16.7 mg/ml human plasma fibronectin in N2B27 medium containing 20 ng/ml Activin A, 12 ng/ml bFGF, and 20% KSR. The culture medium was changed every day.

tag: cell line

value: Control

value: ESC to EpiLC transition

tag: time point

tag: chip antibody


title: D4_Ctr_H3K4me3 [ChIP-seq]


title: PrES_rep4

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

description:
PrES #8-2 P12
rpkm_pres_rev.tsv

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Sequences were aligned and counted using Kallito (version 0.44) and RefSeq mRNA database.
Genome_build: mm10
Supplementary_files_format_and_content: Read counts in plain text

source_name: PrES

growth_protocol: Derivation and maintenance of PrES cells. CD1-Tg(CAG-EGFP) female × CD1-Tg(CAG-EGFP) male and PWK female (BRC, RIKEN) × C57BL6N (Charles River) male F1 (PBF1) blastocysts were collected at E3.5 by flushing the uterus. CD1-Tg(CAG-EGFP) mice were kindly gifted from Prof. T. Wakayama (Yamanashi university). Each blastocyst was transferred to one well of a 48-well MMC-treated MEF feeder plate in PrESCM: StemFit® Basic02, 1 × penicillin-streptomycin (Thermo Fisher Scientific), 10 μM CHIR99021 (Reprocell), 50 ng/ml human FGF4 (Sigma), 1 ng/ml heparin (Sigma), 25 ng/ml human PDGF-AA (R&D). Embryos were cultured in PrES medium for over 5 days until they formed outgrowths. The outgrowth was dissociated with 1 × TrypLE™ Select (Thermo Fisher Scientific) and transferred into a new 48-well MEF feeder plate. After 5-7 days, PrES cell colonies rezched 50-80% confluence, cells were passaged into 12-well MEF feeder plate, then expanded into 6-well plate. PrES cells were frozen down in Cellbanker® 1plus (Zenoaq) and stored in -150°C ultra deep freezer (Panasonic). The use of serum free cryoprotectant significantly reduced cell viability. Other growth factors used were 103U/ml ESGRO LIF (Merck), 20 ng/ml human Activin A (R&D), 100 ng/ml mouse Cripto (R&D), 20 ng/ml human BMP4 (R&D), 100 ng/ml mouse Nodal (R&D). Other chemical compounds used were 10 μM XAV939 (Merck), 1 μM PD0325901 (Reprocell),   Derivation and maintenance of XEN cells. XEN cells were derived according to a standard protocol16 with minor modifications. CD1-Tg(CAG-EGFP) female × CD1-Tg(CAG-EGFP) male blastocysts were collected at E3.5. Each blastocyst was transferred to one well of a 48-well MEF feeder plate in serum-containing ES medium: RPMI1640 (Thermo Fisher Scientific), 20% fetal bovine serum (FBS, biosera), 1 × penicillin-streptomycin (Thermo Fisher Scientific), 1 × non-essential amino acids (NEAA, Thermo Fisher Scientific), 0.1 mM β-mercaptoethanol (β-ME, Sigma), 103U/ml ESGRO LIF on MEF feeder plate. Embryos were cultured for over 7 days until they formed outgrowths. The outgrowth was removed by pipetting and remaining adherent cells were continuously cultured for another 7 days. The proliferated cells were dissociated with 0.05% trypsin-EDTA (Thermo Fisher Scientific) and transferred into a new 48-well MEF feeder plate, then expanded into 6-well plate. XEN cells were frozen down in Cellbanker® 1plus (Zenoaq) and stored in -150°C ultra deep freezer (Panasonic). Removal of the primary outgrowth was not necessary when CHIR99021 (3 μM) was added.  ES cells and TS cells. C57B6N × 129X1 F1 (#1M, #6M) ES cells were cultured in standard ES medium: Neurobasal:DMEMF12(1:1), 0.5 × N2 supplement (Thermo Fisher Scientific), 0.5 × B27 supplement (Thermo Fisher Scientific), 0.15 mM 1-thioglycerol (Sigma), 0.05% bovine serum alubumin (BSA, Sigma), 1 × glutamine-penicillin-streptomycin (Thermo Fisher Scientific), 3 μM CHIR99021, 1 μM PD0325901, 103U/ml ESGRO LIF on gelatin-coated dish or in serum/2iL ES medium: RPMI1640, 20% FBS, 1 × NEAA, 0.1 mM β-mercaptoethanol, 1 × penicillin-streptomycin, 3 μM CHIR99021, 1 μM PD0325901, and 103U/ml ESGRO LIF on MEF feeder dish. CD1 × CD1 TS cells (#1-4M, #2-2M, #8M, #2-3F, #2-4F, #1F) were cultured in 70% RPMI1640/20% FBS (MEF conditioned), 30% RPMI1640/20% FBS, 1 × NEAA, 0.1 mM β-mercaptoethanol, 1 × penicillin-streptomycin, 50 ng/ml human FGF4, 10 μg/ml heparin, 10 μM XAV939 on MEF feeder dish.

extract_protocol: RNA-seq library preparation, sequencing, and data analysis. Total RNA was extracted using a RNeasy kit (Qiagen), and then RNA-seq libraries were generated using a NEBNext Ultra II RNA library prep kit (Illumina, E7770L) following the instructions. Libraries were evaluated using the Agilent 2200 TapeStation and quantified with the Library Quantification Kits (TaKaRa, #638324).

tag: stem cell

value: PrES


title: PrES_rep5

description:
PrES #8-3 P12
rpkm_pres_rev.tsv


title: Wt Exp#1

city: Cincinnati

first: Mark

middle: Jordan

last: Althoff

state: OH

address: 3333 Burnett Avenue

department: Experimental Hematology and Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description: Wt hematopoietic stem cells isolated from mice at 1 week post Cre induction, Exp#1

data_processing:
Reads were aligned with TopHat software, using  mm10 as the reference genome and Reads Per Kilobase of transcript per Million mapped reads (RPKM) as output.
RPKM were log2-transformed and baselined to the median expression of the average of each class of samples.
Analysis of differential gene expression and gene ontology (GO) pathway analyses using Altanalyze software v2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files

source_name: Bone Marrow

extract_protocol:
Total RNA was extracted from sorted hematopoietic stem cells derived from Mx1Cre;Wt or ScribbleΔ/Δ, TazΔ/Δ;Yap1Δ/Δ and ScribbleΔ/Δ;Taz Δ/Δ;Yap1Δ/Δ mice one week following polyinositide/cytidine (polyI:C) administration and gene deletion using RNeasy Mini Kit (QIAGEN).
The initial amplification step was performed with the Ovation RNA-Seq System v2 (Tecan Genomics) and the cDNA concentration and size were measured using the Qubit dsDNA BR assay and a DNA 1000 Chip, respectively. The subsequent libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies). Briefly, 1ng of cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Amplicon Tagment Mix), incubating at 55C for 10 min. NT Buffer was then added to neutralize the samples. Libraries were prepared by PCR with the Nextera PCR Master Mix, and 2 Nextera Indexes (N7XX, and N5XX) according to the following program: one cycle of 72C for 3min, one cycle of 98C for 30s, 12 cycles of 95C for 10s, 55C for 30s, and 72C for 1min, and one cycle of 72C for 5min.

treatment_protocol: Induction of Cre recombinase expression in inducible transgenic animals was achieved by 6 injections of polyinositide/cytidine (polyI:C) at an intraperitoneal dose of 10 mg/kg every other day in Mx1-CreTg/- animal.

value: hematopoietic stem cells

tag: genotype

value: Wild type


title: D4_Ctr_H3K4me1 [ChIP-seq]


title: PrES_rep3

description:
PrES #8-1 P12
rpkm_pres_rev.tsv


title: Thyroid, control group, rep7

source_name: thyroid control group

value: Thyroid


title: Thyroid, control group, rep6


title: MCF7 control cells treated by DMSO replicate 2

value: control


title: Thyroid, control group, rep5


title: Thyroid, control group, rep3


title: Thyroid, control group, rep4


title: MCF7 SIX1 overexpressing cells treated by DMSO replicate 1


title: PrES_rep2

description:
PrES CD-1 #6-5 M C10F4HPDGF
rpkm_pres_rev.tsv


title: MCF7 control cells treated by DMSO replicate 1


title: PrES_rep6

description:
PrES #5-3 P38
rpkm_pres_rev.tsv


title: D2_KO_Nanog [ChIP-seq]

value: Atg7 KO

value: Nanog


title: D2_KO_input [ChIP-seq]


title: MCF7 control cells treated by DMSO replicate 3


title: D4_Ctr_H3K27ac [ChIP-seq]


title: PrES_rep1

description:
PrES CD-1 #5-3 M C10F4HPDGF
rpkm_pres_rev.tsv


title: ES #6 M NB/L2i gelatin

description:
ES #6 M NB/L2i gelatin
rnaseq.counts.txt

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Sequences were aligned and counted using Kallito (version 0.44) and RefSeq mRNA database.
Genome_build: mm19
Supplementary_files_format_and_content: Read counts in plain text

source_name: cultured cell

extract_protocol:
RNA-seq library preparation, sequencing, and data analysis. Total RNA was extracted using a RNeasy kit (Qiagen)
RNA-seq libraries were generated using a NEBNext Ultra II RNA library prep kit (Illumina, E7770L) following the instructions. Libraries were evaluated using the Agilent 2200 TapeStation and quantified with the Library Quantification Kits (TaKaRa, #638324).

value: ES


title: ES #1 M NB/L2i gelatin

description:
ES #1 M NB/L2i gelatin
rnaseq.counts.txt


title: Thyroid, control group, rep2


title: D2_Ctr_Nanog [ChIP-seq]


title: D2_Ctr_input [ChIP-seq]


title: Thyroid, control group, rep1


title: Gill of salmon infected with pox virus, mid stage, fish 8 [M8]

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol for 4x44k microarrays

scan_protocol: Arrays were scanned with Agilent microarray scanner

data_processing: Global normalization was performed by equalizing the mean intensities of all microarrays. The individual values for each feature were divided to the mean value of all samples and expression ratios (ER) were calculated. Log2-ER were normalized with the locally weighted non-linear regression (Lowess)

organism: Salmo salar

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon was grown in tanks at aquaculture research station

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

tag: sample group

value: salmon infected with pox virus

tag: disease stage

value: mid stage

value: Gill


title: XEN #4 Basic02 Wnt3a MEF

description:
XEN #4 Basic02 Wnt3a MEF
rnaseq.counts.txt

value: XEN


title: XEN #3 Basic02 Wnt3a MEF

description:
XEN #3 Basic02 Wnt3a MEF
rnaseq.counts.txt


title: PDLIM51d_3

city: Chengdu

first: HAORONG

last: HE

state: Sichuan

address: No. 211 Huimin Road

department: Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province

institute: Sichuan Agricultural University

data_processing:
In this project, Oligo (dT) magnetic beads are used to enrich mRNA with polyA structure in total RNA, and the RNA is interrupted to 200-300bp fragments by ion interruption. Choose a fragment with a length of 200-300bp because the length of the linker is fixed. Using RNA as a template, the first strand of cDNA was synthesized with a 6-base random primer and reverse transcriptase, and the second strand cDNA was synthesized using the first strand cDNA as a template.
After the library construction is completed, PCR amplification is used to enrich the library fragments, and then library selection is performed according to the fragment size, and the library size is 300-400 bp. Then, the Agilent 2100 Bioanalyzer was used for quality inspection of the library, and then the total concentration of the library and the effective concentration of the library were tested. Then, according to the effective concentration of the library and the amount of data required by the library, the libraries containing different Index sequences are mixed in proportion. The mixed library is uniformly diluted to 2nM, and is denatured by alkali to form a single-stranded library.
The data source of the reference genome is the Ensembl database (http://www.ensembl.org/). Genome information used in this project: Genome: Gallus_gallus. Gallus_gallus-5.0.dna.toplevel.fa; Genebuild by: Ensembl; Database version: 90; Base Pairs: 1,230,258,557.
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM values for every gene and every sample

organism: Gallus gallus

source_name: Skeletal muscle satellite cells

extract_protocol:
Chicken skeletal muscle satellite cells undergo different treatments (si-PDLIM3, si-PDLIM5, si-LMO7, negative control), then after RNA extraction, purification, and library construction, the second generation sequencing technology (NGS) is used, based on Illumina HiSeq Sequencing platform, paired-end (PE) sequencing of these libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skeletal muscle

tag: cell type

value: Primary satellite cells


title: PrES_rep7

description:
PrES #7-2 P41
rpkm_pres_rev.tsv


title: PDLIM51d_1


title: PDLIM51d_2


title: Gill of salmon infected with pox virus, mid stage, fish 7 [M7]


title: PrES -> XEN PWKB6NF1 #2F CHIR

description:
PrES -> XEN PWKB6NF1 #2F CHIR
rnaseq.counts.txt


title: Gill of salmon infected with pox virus, mid stage, fish 6 [M6]


title: PrES -> XEN PWKB6NF1 #1F CHIR

description:
PrES -> XEN PWKB6NF1 #1F CHIR
rnaseq.counts.txt


title: Gill of salmon infected with pox virus, mid stage, fish 5 [M5]


title: Thyroid, KI-treated group, rep4

source_name: thyroid potasiium iodide group

value: Wistar

value: male

value: KI-treated group


title: PDLIM32d_3


title: Thyroid, KI-treated group, rep2


title: Thyroid, KI-treated group, rep6


title: PDLIM32d_2


title: Gill of salmon infected with pox virus, mid stage, fish 3 [M3]


title: Gill of salmon infected with pox virus, mid stage, fish 4 [M4]


title: ES #6 M FBS/L2i MEF

description:
ES #6 M FBS/L2i MEF
rnaseq.counts.txt

source_name: ES cell


title: T4

city: nancy

first: Olivier

last: Joubert

address: 2 allée guinier

department: Dpt 4

institute: Université de lorraine

description: Gene expression in NR8383 cells after 4 h in presence of CNT NM401 exposure (0.17 µg/mL)

hyb_protocol: Six hundred ng of CTP-Cy3-labelled cRNA were fragmented at 60°C for 30 min in a reaction volume of 25 µL following the manufacturer’s instructions. 25 µL of 2 x Agilent hybridization buffer were added to the fragmentation mixture and cRNA were hybridized to SurePrint G3 Rat GE v2 8x60K (Agilent) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1TM and 1 min with 37°C GE Wash buffer 2TM (Agilent).

scan_protocol: Slides were scanned immediately after washing using Agilent DNA Microarray Scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing: The scanned images were analyzed by Feature Extraction version 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 074036_D_F_20150914 ) to subtract background and to obtain spatially detrended processed signal intensities. Features flagged in Feature Extraction as Non-uniform outliers Feature were excluded.

source_name: NR8383, 4 h, 0.17 µg/mL of CNT NM401, replicate 4

label_protocol: CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent) according to manufacturer's instructions, followed by chromatographic purification (RNeasy Mini kit, QIAGEN). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (specific activity > 10 pmol Cy3 / µg cRNA, BioSpec-nano, Shimadzu) and by electrophoresis (Agilent 2100 Bioanalyzer).

growth_protocol: NR8383 cell line provides a homogenous source of alveolar macrophages, they were established from normal rat by lung lavage and was obtained from American Type Culture Collection (ATCC® CRL-2192™, Manassas, VA, USA). Cells, with a 50% adherent and 50% floating cell phenotype, were grown in DMEM medium supplemented with 15 % of heat-inactivated fetal bovine serum, 2mM L-glutamine, as well as 100 U/mL of penicillin, 100 µg/mL of streptomycin and 0.25 µg/mL of amphotericin B (all from Sigma Aldrich). Cells were incubated at 37°C in an atmosphere composed of 95 % air, 5 % CO2 and medium are changed every 2-3 days.

extract_protocol: The quality of the RNA extracted by RNA-Solv Reagent (Omega Bio-tek, USA) was determined by spectrophotometry (A260nm/A280nm, A260nm/A230nm > 1.8, BioSpec-nano, Shimadzu) and by capillary electrophoresis using RNA 6000 Nano® (RIN > 7.5, Agilent 2100 Bioanalyzer, Santa Clara, CA, USA).

treatment_protocol: Cell were seeded in Petri dishes at a density of 3 x 105 cells / mL. Cells were then incubated without (control) or with multi-walled carbon nanotubes (NM401) (0.17 µg/mL) for 4 h in absence of fetal bovine serum.

value: lung


title: T2

source_name: NR8383, 4 h, 0.17 µg/mL of CNT NM401, replicate 2


title: T3

source_name: NR8383, 4 h, 0.17 µg/mL of CNT NM401, replicate 3


title: ES #1 M FBS/L2i MEF

description:
ES #1 M FBS/L2i MEF
rnaseq.counts.txt


title: Thyroid, KI-treated group, rep1


title: Gill of salmon infected with pox virus, mid stage, fish 1 [M1]


title: Gill of salmon infected with pox virus, mid stage, fish 2 [M2]


title: KR_TS_008: secondary LMP1-Lymphoma 35

city: Berlin

first: Thomas

last: Sommermann

address: Robert-Rossle-Str. 10

country: Germany

institute: Max Delbruck Center for Molecular Medicine

data_processing:
Library strategy: Exome-Seq
Paired-end reads from each lane were mapped to the reference genome using bwa mem
PCR duplicates were marked using picard-tools-1.141
Read groups were added using picard-tools-1.141
Reads were realigned locally around indels using GATK v3.4
Paired-end information was fixed using picard-tools-1.141
Quality scores were recalibrated using GATK v3.4
Reads from different lanes for the same samples were merged to single bam files using GATK v3.4
Mutations were called using MuTect 1.1.7 with dbSNPv137 input
Genome_build: mm10
Supplementary_files_format_and_content: VCF files of mutation calls

source_name: liver/spleen

growth_protocol: ex vivo

extract_protocol: FACS-sorted cells were pelleted and gDNA was extracted using a Nucleopspin tissue kit (Macherey-Nagel)

tag: hspc donor

tag: secondary host

tag: secondary host strain

value: secondary LMP1-expressing mouse B cell lymphoma

tag: facs-sort

value: CD19+,humanCD2+(marker LMP1-TG)

value: liver/spleen


title: Thyroid, KI-treated group, rep5

value: Thyroid

tag: treatment


title: NC2d_3

value: negative control


title: PDLIM32d_1


title: TS CD-1 #2-3 F CM/F4HX MEF

description:
TS CD-1 #2-3 F CM/F4HX MEF
rnaseq.counts.txt

source_name: TS cell

value: TS


title: TS CD-1 #2-4 F CM/F4HX MEF

description:
TS CD-1 #2-4 F CM/F4HX MEF
rnaseq.counts.txt


title: NC2d_1


title: Gill of salmon infected with pox virus, late stage, fish 3 [L3]

value: late stage


title: C4

description: Gene expression in NR8383 cells after 4 h in absence of CNT NM401 exposure (0 µg/mL)

source_name: NR8383, 4 h, 0 µg/mL of CNT NM401, replicate 4


title: TS CD-1 #1 F CM/F4HX MEF

description:
TS CD-1 #1 F CM/F4HX MEF
rnaseq.counts.txt


title: NC1d_3


title: C3

source_name: NR8383, 4 h, 0 µg/mL of CNT NM401, replicate 3


title: XEN #1 Basic02 Wnt3a MEF

description:
XEN #1 Basic02 Wnt3a MEF
rnaseq.counts.txt


title: TS CD-1 #2-2 M CM/F4HX MEF

description:
TS CD-1 #2-2 M CM/F4HX MEF
rnaseq.counts.txt


title: T1

source_name: NR8383, 4 h, 0.17 µg/mL of CNT NM401, replicate 1


title: Gill of salmon infected with pox virus, late stage, fish 2 [L2]

value: salmon infected with pox virus


title: Gill of salmon infected with pox virus, late stage, fish 1 [L1]


title: Cortex, KI-treated group, rep3

description: Gene expression of treated group

source_name: cortex potasium iodide

value: Cortex cerebellum


title: C2

source_name: NR8383, 4 h, 0 µg/mL of CNT NM401, replicate 2


title: NC1d_2


title: C1

source_name: NR8383, 4 h, 0 µg/mL of CNT NM401, replicate 1


title: Gill of salmon infected with pox virus, early stage, fish 4 [E4]

value: early stage

value: Gill


title: NC1d_1

value: Skeletal muscle


title: TS CD-1 #1-4 M CM/F4HX MEF

description:
TS CD-1 #1-4 M CM/F4HX MEF
rnaseq.counts.txt


title: TS CD-1 #8 M CM/F4HX MEF

description:
TS CD-1 #8 M CM/F4HX MEF
rnaseq.counts.txt


title: LMO72d_3

value: Primary satellite cells


title: KR_TS_016: secondary LMP1-Lymphoma 47

type: genomic

hyb_protocol: according to the manufacturer's protocol

data_processing: The raw data text files were imported into R and analyzed as described in (Wilke et al., 2018). In brief, log-2 ratios were built from background corrected Cy3 and Cy5 signals and corrected for spatial artefacts before median normalization using the Bioconductor MANOR package (Neuvial et al., 2006). Median normalized log-2 ratios were subjected to copy number segmentation and calling using functions implemented in the Bioconductor CGHcall package (van de Wiel et al., 2007)  before summarization to copy number regions using the CGHregions package

source_name: germline

label_protocol: 250ng of genomic DNA of tumor and tail-DNA of donor animal were labelled with Cy3-dCTP and Cy5-dCTP, respectively using the Cytag kit (Enzo Lörrach, Germany). The labelled nucleotides were purified using Microcon xym-30 columns (Merck, Darmstadt, Germany)

value: embryo

tag: number hspc donor

value: humanCD2+(marker LMP1-transgene)


title: XEN CD-1 #2F LIF

description:
XEN CD-1 #2F LIF
rnaseq.counts.txt

source_name: XEN cell

value: XEN


title: KR_TS_015: secondary LMP1-Lymphoma 46

scan_protocol: according to the manufacturer's protocol

tag: strain


title: Gill of salmon infected with pox virus, early stage, fish 3 [E3]

tag: tissue


title: Gill of salmon infected with pox virus, early stage, fish 2 [E2]


title: KR_TS_014: secondary LMP1-Lymphoma 45


title: LMO72d_1


title: KR_TS_013: secondary LMP1-Lymphoma 43


title: XEN CD-1 #1M LIF

description:
XEN CD-1 #1M LIF
rnaseq.counts.txt


title: KR_TS_017: secondary LMP1-Lymphoma 48


title: Gill of controi salmon, fish 4 [C4]

source_name: Gill of controi salmon

value: controi salmon


title: NC2d_2

source_name: Skeletal muscle satellite cells


title: PrES CD-1 #7-3 M

description:
PrES CD-1 #7-3 M
rnaseq.counts.txt

source_name: PrES

value: PrES


title: KR_TS_010: secondary LMP1-Lymphoma 37

value: secondary LMP1-expressing mouse B cell lymphoma


title: XEN CD-1 #1M LIF/CHIR

description:
XEN CD-1 #1M LIF/CHIR
rnaseq.counts.txt


title: Gill of salmon infected with pox virus, late stage, fish 4 [L4]


title: PrES CD-1 #7-4 M

description:
PrES CD-1 #7-4 M
rnaseq.counts.txt


title: KR_TS_012: secondary LMP1-Lymphoma 40

value: liver/spleen


title: KR_TS_011: secondary LMP1-Lymphoma 39


title: Gill of salmon infected with pox virus, early stage, fish 1 [E1]


title: Gill of controi salmon, fish 3 [C3]


title: KR_TS_009: secondary LMP1-Lymphoma 36


title: Gill of controi salmon, fish 2 [C2]


title: PrES PWKB6NF1 #1 F

description:
PrES PWKB6NF1 #1 F
rnaseq.counts.txt


title: KR_TS_007: secondary LMP1-Lymphoma 32


title: LMO72d_2


title: Gill of controi salmon, fish 1 [C1]


title: WT_1

city: Adelaide

first: Stephen

middle: Martin

last: Pederson

state: SA

address: North Terrace

department: Biological Sciences

country: Australia

institute: University of Adelaide

description: A

data_processing:
Base calling was performed with CASAVA
Reads were trimmed using AdapterRemoval v2.2.1 setting a minimum quality of 30 and a minimum length of 35.
Trimmed reads were aligned to the Danio rerio genome Ensembl Release 94 (GRCz11) using STAR v2.5.3a.
featureCounts was used to count the aligned reads assigned to each gene, specifying that only unique alignments which strictly overlapped exonic regions were counted.
Genome_build: GRCz11
Supplementary_files_format_and_content: An output file was generated from FeatureCounts containing the gene counts of all samples.

organism: Danio rerio

source_name: Clutch of larvae

growth_protocol: The larvae were raised in E3 medium for 2 days.

extract_protocol:
Total RNA was extracted from pooled larvae using the mirVanaTM miRNA isolation Kit (Ambion, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA).  DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA-freeTM Kit (Ambion, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA). RNA was stabilised using RNAstable (Biomatrica) to prevent degradation of samples prior to RNA sequencing.
Strand-specific, poly-A library preparation was performed by Novogene

value: wild type

tag: developmental stage

value: larvae

tag: age

value: 2 days post-fertilization


title: WT_4

description: L


title: WT_3

description: G


title: fmr1_4


title: WT_2

description: D


title: fmr1_3


title: KR_TS_006: secondary LMP1-Lymphoma 31


title: PrES CD-1 #7-1 M

description:
PrES CD-1 #7-1 M
rnaseq.counts.txt


title: PrES CD-1 #7-2 M

description:
PrES CD-1 #7-2 M
rnaseq.counts.txt


title: XEN CD-1 #2F LIF/CHIR

description:
XEN CD-1 #2F LIF/CHIR
rnaseq.counts.txt


title: fmr1_1


title: PrES PWKB6NF1 #2 F

description:
PrES PWKB6NF1 #2 F
rnaseq.counts.txt


title: fmr1_2


title: KR_TS_008: secondary LMP1-Lymphoma 35


title: wild type d8_rep1 [R8_1]

status: Public on May 29 2020

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

institute: Ludwig-Maximilians-Universität München

data_processing:
Illumina Casava1.4 software used for basecalling.
fastq files were demultiplexed by clipping a leading 4-base barcode sequence from the start of read1
Reads were mapped by TopHat and count file was calculated by Htseq-count script from the DESeq software suite
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Derivative cardiac culture

growth_protocol: All cells were cultured at 37°C in a humidi- fied atmosphere containing 5% CO2. ESCs were cultured in ESC medium, consisting of Dulbecco’s modified Eagle’s medium GlutaMaxI, 15% (v/v) ES cell qualified fetal calf serum (SLI Ltd.), 1% (v/v) nonessential amino acids, 1% (v/v) Pen/Strep, 100 mM 2-mercaptoethanol, and 1,000 U/mL 1eukemia inhibitory factor (LIF, ESGRO; Chemicon/Milli- pore). Medium was changed daily on mouse ESC cultures and every 2 days during differentiation.

extract_protocol:
Cells from a 6cm culture dish were harvested by re-suspension in 500mL TRIzol (Invitrogen), and total RNA was extracted with the TRIzol method following the manufacturer’s protocol. RNA was quality controlled by the nanodrop and bioanalyzer. High-quality RNA (RIN > 9 and 260/230 > 2; 260/280 > 1.8) was converted to cDNA.
RNA-Seq libraries were prepared with NUGEN Ovation and Encore kits according to manufacturer's protocols

treatment_protocol: In vitro cardiac differentiation: For cardiac differentiation, embryoid bodies (EBs) were generated by the hanging-drop (HD) method as previously

tag: strain background

tag: genotype/variation

value: ES-derived cardiac cultures


title: wild type d14_rep1  [R14_1]


title: wild type d8_rep2 [R8_2]


title: wild type d14_rep2 [R14_2]


title: Rybp null mutant d14_rep1 [D14_1]

value: Rybp null mutant


title: Rybp null mutant d14_rep2 [D14_2]


title: Rybp null mutant d8_rep2 [D8_2]


title: Rybp null mutant d8_rep1 [D8_1]


title: T175

first: Roland

last: Kappler

address: Lindwurmstr. 2a

department: Pediatric Surgery

institute: University Munich

data_processing:
The STAR aligner (v 2.4.2a) (Dobin et al., 2013) with modified parameter settings (--twopassMode=Basic) was used for split-read alignment against the human genome assembly hg19 and UCSC knownGene annotation.
Quantification of the number of mapped reads of each gene was performed using htseq-counts (v0.6.0) (Anders et al., 2015)
Differential expression analysis was done using DESeq2 (v 1.24.0) (Love et al., 2014)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene (rows) and every sample (columns)

source_name: Hepatoblastoma

extract_protocol:
Liver samples were removed and cryopreserved in liquid nitrogen; RNA was harvested using Trizol reagent; Illumina TruSeq Non-stranded RNA v2 Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: hepatoblastoma patient

value: liver

tag: tissue type

value: Hepatoblastoma

tag: metastasis

value: No


title: T843


title: N794

source_name: Normal liver

value: Normal liver


title: T254


title: T253

source_name: Hepatoblastoma with metastasis

value: Yes


title: T667


title: N843


title: T690


title: T528


title: T734


title: T794


title: T744


title: N690


title: TC_10wkHFD_Saline_rep5_6_7_8

city: Reading

first: Wouter

last: Eilers

address: Whiteknights Campus

country: United Kingdom

institute: University of Reading

description: The sample is a mixture of equal amounts of muscle RNA extract from animal 5, 6, 7 & 8 of the Saline condition

hyb_protocol: Samples were hybridized to Affymetrix Mouse 430_2 GeneChips as per manufacturer’s guidelines (Nugen Technologies Inc and ThermoFisher Scientific)

scan_protocol: Affymetric GeneChips were scanned using an Affymetrix Scanner 3000 with 7G upgrade and image was processed as per manufacturer's AGCC software

data_processing: Raw intensity data were processed with the RMA algorithm with quantile normalisation using the Affymetrix Expression Console software

label: Biotin

source_name: Tibialis cranialis muscle + Saline, replicate 5-8

label_protocol: Labelled extracts were prepared from total RNA samples using the Nugen Ovation V2 system followed by Nugen Encore Biotin Labelling Kit (Nugen Technologies Inc, as per manufacturer’s instructions).

growth_protocol: Male C57Bl/6 mice (n=8) were switched from regular chow to a high fat diet (HFD) at 8 weeks of age

extract_protocol: Total RNA was extracted using Tri-reagent (Sigma Aldrich) according to the manufacturer's instructions

treatment_protocol: 4 Weeks after onset of the high fat diet, mice were given an intramuscular injection of AAV8 Promyo into one Tibialis Cranialis muscle, while the contralateral muscle was injected with saline. Mice were kept for 10 weeks post-injection before collecting the injected muscles.

value: saline

tag: Sex

value: Male

value: 22 weeks

value: Skeletal muscle


title: wild type  d0 [R0]

source_name: Embryonic Strem (ES) cell

tag: cell type

value: ES cell


title: T227


title: TC_10wkHFD_ProMyo_rep1_2_3_4

description: The sample is a mixture of equal amounts of muscle RNA extract from animal 1, 2, 3 & 4 of the AAV8 ProMyo condition

source_name: Tibialis cranialis muscle + AAV8 ProMyo, replicate 1-4

value: AAV8 ProMyo


title: Rybp null mutant d0 [D0]

source_name: Embryonic Stem (ES) cell


title: N744


title: N734


title: N667


title: N528


title: N227


title: N175


title: N254


title: N253


title: Thyroid, KI-treated group, rep3

source_name: thyroid potasiium iodide group

value: Wistar

value: Thyroid

tag: gender

value: male

value: KI-treated group


title: TC_10wkHFD_ProMyo_rep5_6_7_8

description: The sample is a mixture of equal amounts of muscle RNA extract from animal 5, 6, 7 & 8 of the AAV8 ProMyo condition

source_name: Tibialis cranialis muscle + AAV8 ProMyo, replicate 5-8


title: RNA180116RH_240_S31

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

description:
S240
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

data_processing:
FastQC was used for checking the quality of the raw sequence data.
Sequence data were then aligned using Spliced Transcripts Alignment to a Reference (STAR; Dobin et al., 2013), allowing for a maximum of 3 mismatches per 100 bp read. For all samples, > 85% of the reads uniquely aligned.
Reads were mapped to known genomic features to generate counts at the gene level using FeatureCounts (Liao et al., 2014). Raw read counts by gene obtained with featureCounts from the package SubRead --> # Program:featureCounts v1.6.0; Command: featureCounts -g gene_id -s 2 -T 16 -a ./Mus_musculus.GRCm38.78.gtf -o ./RNA180129RH_featureCounts_results_with_EnsemblID.txt *.bam
Gene expression data were imported into R and an upper-quartile normalization was performed using DESeq2 in Bioconductor (Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550 (2014)). Inclusion in the network analysis required a gene read density threshold of an average of greater than 1 count per million (CPM).
Network connectivity for coexpression and cosplicing were calculated as described elsewhere (Iancu et al., 2015; Colville et al. 2017; 2018).
Genome_build: Mus musculus (mm10/GRCm38)
Supplementary_files_format_and_content: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv: Raw counts in comma-separated text format where each column provides read counts for each sample and each line provides the gene's Ensembl ID.

source_name: Dissected Tissue (Brain) - Central Nucleus of the Amygdala

growth_protocol: One male and one female were randomly chosen from each of the 48 families for testing. An additional 12 males and 12 females were randomly chosen such that there were no more than 3 animals from any family. Thus, a total of 120 animals entered the phenotyping protocol; 114 finished (there was some loss due mostly to drinking tubes leaking).

extract_protocol:
Brains were removed from euthanized mice and immediately frozen on dry ice. Ninety-six samples balanced for sex, family and preference quartile were chosen for dissection. Our previous studies empirically established that in order to construct co-expression networks of high quality (see below), sample sizes of ~ 30 to 40 are required; given our previous observation of sex-specific transcriptional effects associated with excessive ethanol consumption and the long-established observation that female mice have a higher preference than male mice, sufficient animals were funneled through dissection, RNA extraction and RNA-Seq to analyze the male and female data separately.
Frozen brains were sliced in 25 micron coronal sections on a cryostat (Leica Biosystems CM1800, Buffalo Grove, IL) at -13°C; slices containing the amygdala were mounted on PEN slides (Thermo Fisher Scientific, Waltham, MA). Mounted slices were lightly thionin stained under RNase-free conditions and dehydrated in increasing concentrations of ethanol diluted in RNase-free water (50%, 70%, 95%, & 100%) for 30 seconds each and then air-dried. The CeA was dissected bilaterally on a Leica LMD-6000 using known anatomical landmarks. Dissected tissue was processed with the Arcturus Picopure kit (Thermo Fisher Scientific) yielding on average 200ng of total RNA. RNA quality was assessed using the Caliper Labchip GX and RNA Quality Scores (RQS). Only samples with RQS scores of > 7 and > 100 ng of total RNA were used for library formation.
Library formation (polyA+, stranded) and sequencing were all performed according to Illumina’s specifications at the OHSU Massively Parallel Sequencing Shared Resource. Eighty-four samples were sequenced. Libraries were multiplexed 6 per lane, balanced for sex, family and preference quartile, yielding approximately 25 to 30 million total reads per sample. In some lanes, there were only 5 samples.

treatment_protocol: Median age for both males and females was 15 weeks at the initiation of ethanol preference testing. Prior to beginning the trial, animals were individually housed for 1 week in cages of the same type as during rearing. At the end of the 1 week period, filter tops were removed from the cages to allow placement of two water-filled glass graduated cylinders fitted with rubber stoppers and stainless steel sipper tubes, introduced for a 4-day period. On day 5, one of the tubes was replaced with a 5% (v/v) ethanol solution, diluted with tap water from 100% ethanol (Fisher BioReagents, Waltham, MA). The side containing the ethanol solution was switched every 2 days across a 4-day period. On day 9, the ethanol concentration was increased to 10% for 4 days of acclimation to the 10% concentration. The 3-month ethanol trial then began, during which mice had access to water and 10% ethanol. The amounts of ethanol and water consumed were measured daily, and animals were weighed weekly. At the end of the 3 month (week 13) trial, all mice were euthanized between 10 AM and 2 PM; ethanol was available until the time of euthanasia. Animals were euthanized in four passes; thus, the ethanol trial lasted for 90-93 days. The key behavioral outcome measure was ethanol preference calculated as ml consumed from the ethanol tube divided by total ml consumed from both tubes.

value: Amygdala

value: Female

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_238_S29

description:
S238
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10


title: RNA180116RH_239_S30

description:
S239
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_234_S25

description:
S234
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_232_S23

description:
S232
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_222_S15

description:
S222
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_223_S16

description:
S223
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_224_S17

description:
S224
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_235_S26

description:
S235
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_226_S19

description:
S226
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: TC_10wkHFD_Saline_rep1_2_3_4

description: The sample is a mixture of equal amounts of muscle RNA extract from animal 1, 2, 3 & 4 of the Saline condition

source_name: Tibialis cranialis muscle + Saline, replicate 1-4

tag: treatment

tag: strain

tag: age


title: RNA180116RH_236_S27

description:
S236
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5

tag: cweek 6

tag: cweek 7

tag: cweek 8


title: RNA180116RH_233_S24

description:
S233
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 9

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_220_S13

description:
S220
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_225_S18

description:
S225
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_228_S21

description:
S228
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_221_S14

description:
S221
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_218_S12

description:
S218
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_216_S10

description:
S216
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_217_S11

description:
S217
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_214_S8_

description:
S214
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_211_S7_

description:
S211
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_230_S22

description:
S230
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_227_S20

description:
S227
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_237_S28

description:
S237
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_208_S4_

description:
S208
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_207_S3_

description:
S207
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_206_S2_

description:
S206
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_204_S1_

description:
S204
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_198_S41

description:
S198
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_203_S44

description:
S203
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_200_S42

description:
S200
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_215_S9_

description:
S215
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_209_S5_

description:
S209
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_194_S38

description:
S194
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_193_S39

description:
S193
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_195_S40

description:
S195
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_181_S29

description:
S181
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_191_S37

description:
S191
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_179_S28

description:
S179
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_178_S27

description:
S178
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_210_S6_

description:
S210
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_177_S38

description:
S177
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_187_S34

description:
S187
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_183_S30

description:
S183
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_184_S31

description:
S184
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_185_S32

description:
S185
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_188_S35

description:
S188
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_174_S36

description:
S174
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_173_S35

description:
S173
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_176_S37

description:
S176
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_172_S34

description:
S172
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_169_S33

description:
S169
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_168_S32

description:
S168
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_167_S31

description:
S167
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_166_S30

description:
S166
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_189_S36

description:
S189
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_165_S29

description:
S165
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_186_S33

description:
S186
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_164_S28

description:
S164
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_162_S27

description:
S162
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_159_S25

description:
S159
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_161_S26

description:
S161
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_158_S24

description:
S158
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_156_S22

description:
S156
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_153_S36

description:
S153
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_157_S23

description:
S157
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_155_S21

description:
S155
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_151_S35

description:
S151
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_145_S32

description:
S145
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_142_S30

description:
S142
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_146_S33

description:
S146
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_140_S29

description:
S140
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_149_S34

description:
S149
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_136_S27

description:
S136
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_134_S26

description:
S134
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_131_S24

description:
S131
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_133_S25

description:
S133
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_130_S23

description:
S130
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: RNA180116RH_138_S28

description:
S138
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5


title: RNA180116RH_128_S21

description:
S128
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 6

tag: cweek 7

tag: cweek 8

tag: cweek 9


title: RNA180116RH_129_S22

description:
S129
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: Control (77)

city: Houston

first: Chung-Yang

last: Kao

state: Texas

address: One Baylor Plaza

department: Molecular & Cellular Biology

institute: Baylor College of Medicine

data_processing:
EA/Q2 Solutions in-house developed RNAv9 pipeline which uses a variety of internally developed and open source programs available at https://github.com/ExpressionAnalysis/ea-utils/.
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: Ventral midbrain

extract_protocol:
Ventral midbrain tissues were removed, flash frozen on dry ice, and RNA samples were extracted and converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: Dopaminergic neurons

tag: age

value: 2 months old

tag: strain

value: Incipient congenic C57BL/6


title: RNA180116RH_126_S19

description:
S126
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5

tag: cweek 6

tag: cweek 7

tag: cweek 8


title: OE (78)

tag: cell type

tag: age


title: W D14 _rep2

city: Macao

first: Renhe

last: Xu

address: Avenida de Universidade  Taipa

department: Faculty of Health Sciences

institute: University of Macao

description: Mus musculus

data_processing:
Paired-end sequencing was performed on the Illumina HiSeq2500 platform
We applied FastQC for a standard quality control of our 100-bp length, paired-end RNA-seq data generated by Illumina HiSeq2500, tested both the raw sequence data, and trimmed sequence data.
Trimmomatic was used to trim the adaptor, and discarded low quality reads and the reads with length less then 36 bp. After trimming, we reserved the paired reads and abandoned unpaired reads for next step analysis. Then cleaned reads (paired reads) were submitted to the tuxedo pipeline.
Tophat2 internally called bowtie2 to map raw reads against the human genome hg38 and mouse genome mm10 with 2 mismatches allowed
Cufflinks were applied to generate the Fragments Per Kilobase Million (FPKM) value for each gene, based on the hg38 or mm10 gene annotation GTF file of University of California Santa Cruz. Human and mouse genome sequences, annotation files, and genome indexes were downloaded from iGenome
Genome_build: human genome hg38 and mouse genome mm10
The RNA-seq data was statically analyzed with R. One-way ANOVA test and fold change were used to identify DEG. We downloaded all the gene sets used for function/pathway enrichment from Gene Set Enrichment Analysis of the Broad Institute, and elucidated the hypergeometric distribution to determine P values of each enriched pathway. The R package “gplots” and “ggpubr” were used to prepare all figures.
Supplementary_files_format_and_content: FPKM

source_name: D14 Wounded skin with vehicle treatment_replicate2

growth_protocol: EMSC were generated by inducing hESC to differentiate into MSC using the method we reported previously. EMSC were cultured in high-glucose Dulebcco’s modified Eagle’s medium supplemented with 20% fetal bovine serum at 37.0℃ in 5% CO2 incubator, and passaged every 5-7 days. MSC between passages 6-10 were used for all experiments. For spheroid formation, MSC were split and seeded on adhesion substrates by using handing drop method at a density of 2.5×104 cells/drop as we recently reported 15, and the MSC in the handing drop formed spheroids within 2-day culture. Either MSC spheroids or cells dissociated from MSC in monolayer were harvested for transplantation.

extract_protocol:
Mice were sacrificed at designated time points, skin samples including the wound and 2 mm of the surrounding skin were harvested using an 8-mm biopsy punch, and three wounds were pooled per group. The tissues were sliced into small pieces and homogenized with a pestle. Skin fragments were added into a lysis buffer provided by QIAGEN RNeasy kit to isolate total RNA according to the manufacturer’s instructions.
The integrity and quality of samples were verified using the Nano RNA Bioanalyzer Assay (Agilent Technologies). Samples with RNA integrity number larger than 9 were used for Next Generation Sequencing library preparation using the NEB Ultra Directional RNA Library Preparation Kit.

treatment_protocol: The excisional wound splinting model was generated as reported. For the EMSCSp group, around 40 spheres equivalent of 1×106 EMSC were directly dropped onto the surface of each wound right after the wounding. For the EMSCDiss group, EMSCDiss at 0.7×106 cells in 100 l PBS (70% of the total cell dose) per wound were evenly injected into the dermis in four spots around the wound, and 0.3×106 EMSCDiss (30% of the total cell dose) mixed with 30-l Matrigel were dropped onto the surface of the wound. For the vehicle control group, 100-l PBS alone per wound was evenly injected around the wound, and 30-l Matrigel was dropped onto the surface of the wound as above.

tag: strain

value: NOD/SCID


title: W D14 _rep1

description: Mus musculus

source_name: D14 Wounded skin with vehicle treatment_replicate1


title: W D3_rep1

source_name: D3 Wounded skin with vehicle treatment_replicate1


title: RNA180116RH_143_S31

description:
S143
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: Sex

tag: pweek 7

tag: pweek 8

tag: pweek 9

tag: pweek 10

tag: pweek 11

tag: pweek 12

tag: pweek 13

tag: cweek 1

tag: cweek 9

tag: cweek 10

tag: cweek 11

tag: cweek 12

tag: cweek 13


title: W D7_rep2

description: Mus musculus

source_name: D7 Wounded skin with vehicle treatment_replicate2


title: W D7_rep1

description: Mus musculus

source_name: D7 Wounded skin with vehicle treatment_replicate1


title: W D3_rep2

source_name: D3 Wounded skin with vehicle treatment_replicate2


title: W0

source_name: D0 Wounded skin without treatment


title: mTS knocked-down Tead4 Set2

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

description: from whole cell lysate

data_processing:
base calling was performed using Illumina’s Real Time Analysis (RTA) software
Sequence reads were mapped to the mouse reference genome (GRCm38) using STAR with default parameters
Transcript abundance estimates were generated using Cufflinks and differential gene expression calculated using Cuffdiff with default parameters.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files of FPKM values for each Sample

source_name: Cell-line

growth_protocol: Mouse TS cells were routinely cultured under stem condition utilising standard protocol consists of 20% FBS in the presence of FGF4 & heparin (1 microgram/ml) in a base media, RPMI1640

extract_protocol:
Total RNA from the whole cell-extract was isolated using RNeasy Mini Kit (#74104) from Qiagen per the manufacturer’s protocol.  RNA concentrations were quantified using a NanoDrop Spectrophotometer at a  wavelength of 260nm. Integrity of the total RNA samples was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA) and the samples with RNA integrity values above 7.0 were used for the sequencing experiments.
Total RNA was used to construct RNA-seq libraries using the Illumina TruSeq RNA Sample Preparation Kit v3 according to manufacturer's instructions

treatment_protocol: Lentiviral (consists of either scramble or targeted shRNA against Tead4) transduced cells were selected with 1.5 microgram/ml puromycin for a week and then passaged atleast once before harvested for total RNA

tag: cell type

value: Mouse Trophoblast Stem Cells (mTS)

tag: shRNA


title: mTS (Scramble) Set2

description: from whole cell lysate

value: scramble


title: mTS knocked-down Tead4 Set1

description: from whole cell lysate


title: mTS (Scramble) Set1

description: from whole cell lysate


title: RNA180116RH_127_S20

description:
S127
pweek=preference ratio (number of ethanol mls divided by the number of total mls (the two bottles of ethanol and water)); cweek=g/kg of ethanol consumed (based on mls, body weight and the specific gravity of ethanol).
processed data file: RNA180116RH_mm10_gene_featcnt_reads_not_normalized.csv

tag: tissue

tag: pweek 1

tag: pweek 2

tag: pweek 3

tag: pweek 4

tag: pweek 5

tag: pweek 6

tag: cweek 2

tag: cweek 3

tag: cweek 4

tag: cweek 5

tag: cweek 6

tag: cweek 7

tag: cweek 8


title: Sox9EGFP high_1

city: Atlanta

first: Adam

middle: D

last: Gracz

state: GA

address: 615 Michael St. NE

department: Medicine

institute: Emory University

description:
High_MsA
Normalized_counts.csv

data_processing:
salmon indoex -t gencode.V24.transcripts.fa
salmon quant --seqBias --gcBias --validateMappings
DESeq2 1.26.0
Genome_build: mm10
Supplementary_files_format_and_content: .txt; normalized counts

source_name: primary dissociated liver cells

growth_protocol: Mice were fasted for 16hr prior to isolating cells

extract_protocol:
RNA was isolated per manufacturer protocol using the RNAqueous Micro Kit (Ambion). Total RNA was treated with DNAse for 30min
Libraries were constructed using the SMARTer Stranded Total RNA Pico Kit v2 (Takara), following manufacturer protocol.

treatment_protocol: Livers were digested to single cells and isolated into GFPneg, GFPsublow, GFPlow, and GFPhigh populations by FACS on a Sony SH800 cell sorter. 12,000 cells per population were collected directly into RNA lysis buffer

tag: transgene

tag: strain


title: Sox9EGFP high_3

description:
High_883
Normalized_counts.csv


title: Sox9EGFP high_2

description:
High_881
Normalized_counts.csv


title: Sox9EGFP low_2

description:
Low_881
Normalized_counts.csv


title: Sox9EGFP neg_2

description:
Neg_881
Normalized_counts.csv


title: Sox9EGFP low_3

description:
Low_883
Normalized_counts.csv


title: Sox9EGFP neg_1

description:
Neg_MsA
Normalized_counts.csv


title: Sox9EGFP sub_2

description:
SL_881
Normalized_counts.csv


title: Sox9EGFP sub_3

description:
SL_883
Normalized_counts.csv


title: Sox9EGFP low_1

description:
Low_MsA
Normalized_counts.csv


title: PC9_63-ExpSample

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415 Curie Boulevard

institute: University of Pennsylvania

description:
meltedData_PC9.tsv
full_PC9.csv

data_processing:
bcl2fastq conversion performed on BaseSpace using Illumina's default generate fastq workflow
Aligned to hg19 using STAR version 2.3.0e with default parameters
Filtered uniquely mapped reads using ngsutils/bamutils
Sorted using samtools-0.1.19
enumerated read counts per gene using HTseq-0.6.1 in union mode
filtered protein-coding genes then normalized by sequencing depth and gene length using custom R script
Genome_build: aligned to hg19, ensembl GRCh37.75 gtf used for gene annotations
Supplementary_files_format_and_content: tsv files contain gene level RNA-seq counts generated using HTSeq with GRCh37.75 gene annotations. csv files contain RPM, RPKM, and TPM normalized counts for protein coding genes used in subsequent variability analyses.

source_name: PC-9 NSCLC

growth_protocol: Grown in TU2% media

extract_protocol:
RNA extracted from 100,000-200,000 cells using miRNAeasy RNA extraction kit according to manufacturer's protocol (Qiagen 217004). Polyadenylated RNA was then purified using NEBNext Poly(A) Magnetic Isolation Module (NEB E7490L)
NEBNext Ultra RNA sequencing library prep kit for Illumina (NEB E7530L )
mRNA-seq, random hexamer primed RT, unstranded.

tag: treatment

tag: cell type

value: MemorySeq subclone


title: PC9_9-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_62-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_64-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_65-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_60-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_57-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_58-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: Sox9EGFP neg_3

description:
Neg_883
Normalized_counts.csv


title: PC9_56-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_59-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_51-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_52-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_50-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_49-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_47-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: Sox9EGFP sub_1

description:
SL_MsA
Normalized_counts.csv


title: PC9_41-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_44-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_38-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_43-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_4-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_33-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_35-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_46-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_6-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_3-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_30-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_28-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_25-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_29-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_48-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_11-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_12-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_14-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_15-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_19-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_10-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv