title: d20Beta2

city: San Francisco

first: Gopika

last: Nair

state: CA

address: 513 Parnassus Ave, HSW1119

department: Diabetes Center

institute: UCSF

data_processing:
Base-calling performed using Illumina Hiseq 4000 Control and Real-Time analysis software
Read qualities were assessed by FASTQC tool on Galaxy.
Reads were then mapped to the human genome (hg38) using TopHat version 2.1.0 [52] using the corresponding sample’s mean inner distance between mate pairs, library-type fr-firststrand for strand determination leaving other parameters default.
The tuxedo suite tools were used for further analysis: rRNA and tRNA reads were masked during transcript assembly using Cufflinks and differential expression analysis was performed using Cuffdiff.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Human Stem cell-derived beta cells

extract_protocol:
Total RNA was isolated from GFP-high cells FACS sorted from d27 eBCs, NECs and d20 immature clusters; and β-cells sorted from adult human islets using RNeasy Micro kits (Qiagen). RNA isolated from sorted cells was further concentrated employing RNA Clean & Concentrator (Zymo research).
rRNA was depleted by RiboGone (Clontech), and 325-350bp sized strand-specific cDNA libraries were prepared using the SMARTer Stranded Total RNA Sample Prep Kit – Low Input Mammalian Kit (Clontech).

value: Pancreatic Beta cells

tag: in vitro/in vivo

value: In vitro

tag: differentiation day


title: 6hpf_repeat1 [H6_1]

status: Public on Feb 01 2019

type: SRA

city: Shanghai

first: XiaoYuan

last: Zhang

address: 320 Yueyang road

country: China

institute: Shanghai Institute of Biochemistry and Cell Biology,CAS

library_source: transcriptomic

data_processing:
Raw reads were pre-processed by Trimmomatic
Reads were mapped to danRer10 using HISAT2 version 2.0.5
Gene expression quantification was done by StringTie version 1.3.3 with annotation file(Danio_rerio.GRCz10.89.gtf) downloaded from Ensembl.
A Python script prepDE.py(http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#deseq) was used to calculate gene read count.
Genome_build: danRer10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Danio rerio

extract_protocol:
PGCs were picked out by green fluoresence
RNA-seq library was constructed with NexteraXT kits by Smart-Seq2.

tag: strain

value: AB

tag: developmental stage

value: 6hpf (shield stage)

tag: tissue

value: gonad

tag: cell type

value: primordial germ cells (PGCs)


title: K8

first: zhongzhong

last: ji

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

institute: SJTU CHINA

data_processing:
Raw reads were first cleaned by removing adaptor sequences, low quality sequences (Sanger base quality < 20), and reads with unknown nucleotides larger than 10%. The TopHat-Cufflinks- Cuffmerge-Cuffdiff pipeline was used to analyze the clean data with default parameters .
The clean reads were mapped to the mouse GRCm38  reference genome using TopHat v2.0.13 . Cufflinks v2.2.0 was used to construct, identify, and estimate the abundance from TopHat alignment results. The parameter Fragment Per Kilobase of transcript per Million fragments mapped (FPKM) was used to quantify the abundance of assembled transcripts.
Cufflinks results for all samples were used to merge the assemblies by Cuffmerge v1.0.0 . Cuffdiff v2.2.0 was used to re-estimate the abundance of transcripts. Expression levels were measured using the FPKM method, and the distribution of gene expression was analyzed. Statistical comparison of the DEGs between two groups of samples was also performed using Cuffdiff v2.2.0.
To assess the significance of differential gene expression, the threshold of q-value was set at 0.05, and the absolute value of log2 ratios (fold change between two groups of samples) at 1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited Excel files include RPKM values for all Sample

organism: Mus musculus

source_name: DN3 thymocytes

growth_protocol: Mice were kept in SPF mouse facility with normal food and water, and 12 hours day and 12 hours night cycle.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen, USA)  according to the manufacturer's instructions, and was then treated with RNase-free DNase I (TaKaRa, China) to remove genomic DNA contamination.
Sequencing libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's recommendations, and index codes were added to attribute sequences to each sample.

treatment_protocol: 8-10 weeks mice thymus were isolated and staning cell surface marker CD44 CD25 CD4 CD8, then sorted the DN3 thymocytes(CD44- CD25+ CD4- CD8-)

value: DN3 thymocytes

value: thymus

tag: genotype/variation


title: d20Beta1

country: USA

organism: Homo sapiens


title: K7


title: NECBeta2


title: NECBeta1


title: illium control 17-1442I

type: RNA

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

description: Gene expression data from illium control 17-1442I

hyb_protocol: Mucosal cells, scraped from the jejunum and ileum segments, were homogenized with TriReagent and RNA was purified with Directzol RNA mini prep columns (Zymo Research Co., Irvine CA).  RNA was quantified with a Nanodrop ND 1000 spectrophotometer (Thermo Scientific, Wilmington, DE) and samples were shipped frozen to the University of Virginia for RNA quality and DNA microarray analyses in the Biomolecular Analysis Core facility. RNA quality was assessed with an Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA) and only samples with a RIN greater than 8.7 were used for microarray analysis.  Some tissue samples had to be re-extracted to recover RNA with a RIN > 8.7. Microarray analysis using the chicken genome 1.0 array (Affymetrix, Santa Clara, CA) was performed on the d10 samples (total of 50 samples: 5 treatments, 2 segments, 5 replicates).

data_processing: Data extraction, QC, and RMA normalization were performed with BioConductor software. Probes were annotated using the Bioconductor GeoQuery package. Differential expression was assessed with moderated ANOVA, using the BioConductor limma package; false discovery rate (FDR) estimates were calculated using the Benjamini-Hochberg method.

label: biotin

organism: Gallus gallus

source_name: chicken illium

growth_protocol: Day of hatch Cobb 500 male broilers were obtained from the Cobb hatchery in Wadesboro, NC and transported to the Virginia Tech Poultry Research Center.  125 chicks were weighed, wing-banded and placed in a room with adjoining floor pens (25/pen), separated by wire fencing. Broilers were individually weighed weekly (d7, d14, d21, and d28) to assess growth rates and not to generate statistically significant production data.

treatment_protocol: There were 5 experimental groups. Control group (T1) was provided feed without supplement and was compared to four treatment groups provided feed with either purified LPC, isolated from lysolecithin by column chromatography, (T2, T3) or lysolecithin (T4, T5), each at two different application levels.  T2 (LPC-low) contained 9.5 g/T of LPC supplemented as 500 g/T of purified LPC plus carrier.  T3 (LPC-high) contained 19 g/T of LPC supplemented as 1,000 g/T of purified LPC plus carrier. T4 (lysolecithin-low) contained 9.5 g/T of LPC supplemented as 250 g/T of lysolecithin. T5 (lysolecithin-high) contained 19 g/T of LPC supplemented as 500 g/T of lysolecithin. Lysoforte (as 50% w/w lysolecithin on carrier) and purified LPC were provided by Kemin Industries Inc., Des Moines, Iowa, USA. Pure LPC was applied to a carrier prior to mixing with feed to ensure homogeneous distribution within the feed.

value: illium

tag: treatment

value: control

tag: batch


title: illium lpc 500 21-1452I

description: Gene expression data from illium lpc 500 21-1452I

scan_protocol: Mucosal cells, scraped from the jejunum and ileum segments, were homogenized with TriReagent and RNA was purified with Directzol RNA mini prep columns (Zymo Research Co., Irvine CA).  RNA was quantified with a Nanodrop ND 1000 spectrophotometer (Thermo Scientific, Wilmington, DE) and samples were shipped frozen to the University of Virginia for RNA quality and DNA microarray analyses in the Biomolecular Analysis Core facility. RNA quality was assessed with an Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA) and only samples with a RIN greater than 8.7 were used for microarray analysis.  Some tissue samples had to be re-extracted to recover RNA with a RIN > 8.7. Microarray analysis using the chicken genome 1.0 array (Affymetrix, Santa Clara, CA) was performed on the d10 samples (total of 50 samples: 5 treatments, 2 segments, 5 replicates).

value: lpc 500


title: mononuclear blood cell_AHR antagonist_AML16626_1_24h

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

hyb_protocol: In accordance with manufacturer's protocols

scan_protocol: GeneChips were scanned using  Affymetrix® Scanner 3000 7G.

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm and baseline transformation to the median of all samples using GeneSpring GX software.

source_name: mononuclear blood cell_AHR antagonist_24h

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.

treatment_protocol: AML mononuclear cells were placed in serum-free media (StemSpan #09600, StemCell Technologies) supplemented with stem cell factor (100 ng/mL), FLT3 ligand (100 ng/mL) and thrombopoietin (20 ng/mL) at a density of 250,000 cells/mL, and treated with DMSO vehicle control or PD-AHA (1microM) for 24 hours in an incubator (37oC, 5% CO2).

value: peripheral blood

value: AML mononuclear cells

tag: treated with

value: AHR antagonist PD-AHA (1microM) for 24hr


title: jejunum control 19-1442J

description: Gene expression data from jejunum control 19-1442J

source_name: chicken jejunum

label_protocol: Mucosal cells, scraped from the jejunum and ileum segments, were homogenized with TriReagent and RNA was purified with Directzol RNA mini prep columns (Zymo Research Co., Irvine CA).  RNA was quantified with a Nanodrop ND 1000 spectrophotometer (Thermo Scientific, Wilmington, DE) and samples were shipped frozen to the University of Virginia for RNA quality and DNA microarray analyses in the Biomolecular Analysis Core facility. RNA quality was assessed with an Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA) and only samples with a RIN greater than 8.7 were used for microarray analysis.  Some tissue samples had to be re-extracted to recover RNA with a RIN > 8.7. Microarray analysis using the chicken genome 1.0 array (Affymetrix, Santa Clara, CA) was performed on the d10 samples (total of 50 samples: 5 treatments, 2 segments, 5 replicates).

value: jejunum


title: mononuclear blood cell_AHR antagonist_AML15331_24h

label_protocol: In accordance with manufacturer's protocols

value: bone marrow


title: C9


title: mononuclear blood cell_AHR antagonist_AML16626_24h


title: mononuclear blood cell_AHR antagonist_AML14366_24h


title: mononuclear blood cell_AHR antagonist_AML14170_24h


title: eBCBeta2


title: illium control 18-1512I

description: Gene expression data from illium control 18-1512I

extract_protocol: Mucosal cells, scraped from the jejunum and ileum segments, were homogenized with TriReagent and RNA was purified with Directzol RNA mini prep columns (Zymo Research Co., Irvine CA).  RNA was quantified with a Nanodrop ND 1000 spectrophotometer (Thermo Scientific, Wilmington, DE) and samples were shipped frozen to the University of Virginia for RNA quality and DNA microarray analyses in the Biomolecular Analysis Core facility. RNA quality was assessed with an Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA) and only samples with a RIN greater than 8.7 were used for microarray analysis.  Some tissue samples had to be re-extracted to recover RNA with a RIN > 8.7. Microarray analysis using the chicken genome 1.0 array (Affymetrix, Santa Clara, CA) was performed on the d10 samples (total of 50 samples: 5 treatments, 2 segments, 5 replicates).


title: jejunum control 20-1512J

description: Gene expression data from jejunum control 20-1512J


title: C5


title: mononuclear blood cell_AHR antagonist_AML18947_24h


title: eBCBeta1


title: K4


title: mononuclear blood cell_AHR antagonist_AML14362_24h


title: jejunum lysoforte 1000 16-1448J

description: Gene expression data from jejunum lysoforte 1000 16-1448J

value: lysoforte 1000


title: illium lysoforte 1000 15-1448I

description: Gene expression data from illium lysoforte 1000 15-1448I


title: mononuclear blood cell_DMSO_AML18947_24h

source_name: mononuclear blood cell_DMSO_24h

value: DMSO (vehicle) for 24hr


title: C3


title: jejunum lysoforte 500 14-1526J

description: Gene expression data from jejunum lysoforte 500 14-1526J

value: lysoforte 500


title: jejunum lysoforte 500 13-1435J

description: Gene expression data from jejunum lysoforte 500 13-1435J


title: skin_AGEP_rep8

city: Zurich

first: Emmanuel

last: Contassot

address: Gloriastrasse 31

department: Dematology

country: Switzerland

institute: University Hospital

description:
AGEP skin biopsy patient 8
Gene expression data from 6mm punch skin biopsy from adult AGEP patient

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Exon 1.0 ST.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Limma of Bioconductor using Affymetrix default analysis settings and global scaling as normalization method.

source_name: adult, 6 mm punch skin biopsy during the acute phase

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: not applicable

extract_protocol: Total RNAs were isolated from AGEP, MPR and healthy skin biopsies, as well as from keratinocytes and PBMC using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions

treatment_protocol: not applicable

value: skin biopsy

tag: adverse drug reaction

value: AGEP

tag: age

value: adult


title: XP-B/CS+XPB/GFP cell replicate 1-RNAseq

city: Illkirch

first: Frederic

last: Coin

address: 1, rue laurent fries

department: Functional Genomics and Cancer

country: France

institute: IGBMC

data_processing: Reads were mapped onto the hg19 assembly of the human genome. Read counting was performed with HOMER v4.8.3(65) and expression was estimated with EdgeR. Genome ontology was performed with The Database for Annotation and Integrated Discovery (DAVID) v6.7 (https://david.ncifcrf.gov).

source_name: Fibroblasts from XP-B/CS patients

extract_protocol:
GenElute Mammalian Total RNA Miniprep Kit (Sigma)
TruSeq Stranded mRNA Sample Preparation Kit following guide instructions and subsequently analyzed on an Illumina Hiseq 4000 as single-end 50 base reads following Illumina’s instructions

tag: mutation

value: ERCC3 c.296T>C mutant, pPhe99Ser (RefSeq accession number NM_000122.1)

value: wild-type XPB tagged with GFP


title: illium lysoforte 500 12-1526I

description: Gene expression data from illium lysoforte 500 12-1526I


title: skin_AGEP_rep7

description:
AGEP skin biopsy patient 7
Gene expression data from 6mm punch skin biopsy from adult AGEP patient


title: mononuclear blood cell_DMSO_AML15331_24h


title: illium lysoforte 500 11-1435I

description: Gene expression data from illium lysoforte 500 11-1435I


title: skin_AGEP_rep6

description:
AGEP skin biopsy patient 6
Gene expression data from 6mm punch skin biopsy from adult AGEP patient


title: illium lpc 1000 08-1514I

description: Gene expression data from illium lpc 1000 08-1514I


title: mononuclear blood cell_DMSO_AML14366_24h


title: treated3

city: Madrid

first: Monica

last: Martinez-Fernandez

address: Avda Complutense 40

country: Spain

institute: CIEMAT

hyb_protocol: Following fragmentation, 5,5 ug of fragmented and labeled ss-DNA were hybridized for 16 hr at 45ºC at 60 rpm on Hybridization Oven 640 de Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 7G de Affymetrix

data_processing: Expression data were normalized, background-and batch corrected using the Guanine Cytosine Count Normalization (GCCN) and Signal Space Transformation (SST), and prior to summarizing using the Robust Multi-Array Average (RMA) algorithm implemented in the Affymetrix Expression Console software. In order to combine the different microarray data sets, possible batch effects were corrected by using the Bioconductor Combat package in R environment (Johnson et al., 2007)

source_name: Bladder, adeno-cre inoculated, CM272+CDDP treated

label_protocol: cRNA is converted to biotinylated sense-strand DNA prepared according to the standard Affymetrix protocol from 12 ngs total RNA (GeneChip Whole Trasncript WT Expression Arrays, Affymetrix).

extract_protocol: Extraction of total RNA was performed using miRNeasy FFPE kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: To induce tumor formation, mice were inoculated in the bladder with an adenovirus coding for Cre recombinase. To study the potential activity of CM272+CDDP treatment in BC management, mice were treated daily with CM272(5mg/kg/day) intraperitoneally for 30 days plus a once per week 6 mg/kg dose of CDDP.

tag: background strain

value: FVB/N

tag: genotype

value: Rbf/f, Ptenf/f, Tp53f/f, p107-/-

value: bladder


title: jejunum lpc 1000 09-1459J

description: Gene expression data from jejunum lpc 1000 09-1459J


title: mononuclear blood cell_DMSO_AML16626_24h


title: illium lpc 1000 07-1459I

description: Gene expression data from illium lpc 1000 07-1459I

value: illium


title: skin_AGEP_rep3

description:
AGEP skin biopsy patient 3
Gene expression data from 6mm punch skin biopsy from adult AGEP patient


title: skin_AGEP_rep4

description:
AGEP skin biopsy patient 4
Gene expression data from 6mm punch skin biopsy from adult AGEP patient


title: mononuclear blood cell_DMSO_AML16626_1_24h

value: peripheral blood


title: skin_AGEP_rep5

description:
AGEP skin biopsy patient 5
Gene expression data from 6mm punch skin biopsy from adult AGEP patient


title: mononuclear blood cell_DMSO_AML14362_24h

value: AML mononuclear cells


title: HDF-2

city: Houston

first: Malgorzata

last: Borowiak

address: 1 Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: 600ng of the labeled cRNA were fragmented. Approximately 480ng of fragmented cRNA samples were loaded onto each of the Human G3 v2 8x60K Agilent Expression arrays. The arrays were hybridized in an Agilent Hybridization Chamber for 17h at 65°C with rotation at 10rpm.

scan_protocol: the slides were scanned with the Agilent Scanner (G2565BA) using Scanner Version C and Scan Control software version A.8.3.1.

data_processing: Data extraction and quality assessment of the microarray data was completed using Agilent Feature Extraction Software Version 11.0.1.1.

source_name: Adult human dermal fibroblast

label_protocol: The cDNA product was transcribed using T7 RNA Polymerase, producing cyanine-3-labeled cRNA.

growth_protocol: To derive M-E cells, we obtained human fetal pancreas, duodenum, and spleen, from 9.1 to 20.1 weeks after fertilization, in accordance with Institutional Review Board guidelines. Each tissue was chopped into approximately 4mm3 cubes. Samples were transferred to 6-well plates and kept at 37°C for 10 min to allow attachment of the tissue to the plate surface. Then, DMEM: F12- media (+10% FBS, 1×penicillin– streptomycin, 1×Glutamax (all Invitrogen)) was added. Over the subsequent 2 weeks, media was changed every other day, and wells were monitored for outgrowth of M-E cells. Once 50% confluent, the cubes were removed and M-E cells were trypsinized using 0.25% trypsin-EDTA and expanded until passage 3.

extract_protocol: RNA was isolated using TRIzol (Thermo Fisher Scientific) and extracted according to the manufacturer’s protocol. DNAase (Qiagen) treatment was performed before cDNA synthesis to remove genomic DNA contamination

treatment_protocol: No treatment

value: Skin

tag: Stage

value: Adult


title: mononuclear blood cell_DMSO_AML14170_24h


title: Metastasis4

source_name: Metastasis

value: metastatic tumor


title: METtreated

source_name: Metastasis-CM272+CDDP treated mouse


title: jejunum lpc 500 06-1478J

description: Gene expression data from jejunum lpc 500 06-1478J

value: jejunum

value: lpc 500


title: treated2


title: jejunum lpc 1000 10-1514J

description: Gene expression data from jejunum lpc 1000 10-1514J


title: treated1


title: Metastasis3


title: HDF-1


title: skin_AGEP_rep2

description:
AGEP skin biopsy patient 2
Gene expression data from 6mm punch skin biopsy from adult AGEP patient


title: skin_AGEP_rep1

description:
AGEP skin biopsy patient 1
Gene expression data from 6mm punch skin biopsy from adult AGEP patient


title: Wk20.1-3

source_name: human Wk20.1 upper GI tract, mesenchymal and endothelial cells

value: Upper GI tract

value: Week 20.1


title: E13.5_1

city: Tokyo

first: Kazushige

last: Shiraishi

address: 7-3-1, Hongo, Bunkyo-ku

department: Graduate School of Medicine

country: Japan

institute: The University of Tokyo

data_processing:
Adapter trimming and quality filtering of sequencing data were performed by Trimommatic-0.33 and PRINSEQ-0.20.4. Trimmed reads were mapped to the Refseq mm10 by using Bowtie2-2.2.5. Reads that were not mapped to NlaIII sites were removed, and quantified tag numbers of each gene as the expression level of each gene.
Total tag number was adjusted to 1 million tags, and between-sample normalization was performed by using R-3.4.0 and TCC package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized tag-count values for each sample

molecule: polyA RNA

source_name: Lung epithelial cells

extract_protocol:
Epithelial cells from various developmental stages (E13.5, E15.5, E18.5, P14, and P56) were isolated from C57BL/6 mice. Lungs were cut into small pieces and digested enzymatically using collagenase (Wako, Osaka, Japan), Dispase II (Roche, Basel, Switzerland), and DNase I (Sigma-Aldrich, St Louis, MO) for 60 min at 37°C. Single-cell suspended lung cells were first stained with anti-mouse CD31, CD45, Ter119, CD146, and Epcam antibodies. Cells were next stained with Streptavidin-APC, followed by anti-APC microbeads (Miltenyi). Labeled cells were magnetically depleted. Finally, lineage (CD31, CD45, Ter119, and CD146)– propidium iodide– Epcam+ live epithelial cells were sorted with a MoFlo Astrios flow cytometer (Beckman Coulter).
polyA RNAs were isolated and amplified from donor epithelial cells according to the protocol described in (Huang H, Nucleic Actd Res, 2014) with some modifications. 3'SAGE-seq libraries were constructed according to the protocol described in (Matsumura H, Methods Mol Biol, 2012) with some modifications. Sequencing was performed by using Ion Hi-Q Chef Kit, Ion PI v3 Chip Kit and Ion Proton Sequencer (Thermo Fisher Scientific) according to the manufacture’s instructions except the input library concentration (100 pM) and cycle number (200).

value: lineage (CD31, CD45, CD146 and Ter119) negative, Epcam positive epithelial cells

value: lung

value: Embryonic day 13.5


title: skin_MPR_rep6

description:
MPR skin biopsy patient 6
Gene expression data from 6mm punch skin biopsy from adult MPR patient

value: skin biopsy

value: MPR

value: adult


title: Wk20.1-2


title: skin_MPR_rep5

description:
MPR skin biopsy patient 5
Gene expression data from 6mm punch skin biopsy from adult MPR patient


title: skin_MPR_rep4

description:
MPR skin biopsy patient 4
Gene expression data from 6mm punch skin biopsy from adult MPR patient


title: jejunum control 04-1482J

description: Gene expression data from jejunum control 04-1482J

value: control


title: tumor7

source_name: Bladder, adeno-cre inoculated

value: FVB/N

value: Rbf/f, Ptenf/f, Tp53f/f, p107-/-

value: bladder tumor


title: illium lpc 500 05-1478I

description: Gene expression data from illium lpc 500 05-1478I

value: illium


title: Metastasis2


title: Wk20.1-1


title: Wk17.5h-2

source_name: human Wk17.5 head of pancreas, mesenchymal and endothelial cells


title: skin_MPR_rep3

description:
MPR skin biopsy patient 3
Gene expression data from 6mm punch skin biopsy from adult MPR patient


title: skin_MPR_rep2

description:
MPR skin biopsy patient 2
Gene expression data from 6mm punch skin biopsy from adult MPR patient


title: acidosis human brain pericytes replicate 2

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: Biological replicate 2 of 2. Brain pericytes were exposed to pH 6.5 medium for 24 hours.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: B.Control 2

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Human brain microvascular pericytes, initiated from normal brain cortical tissues, were purchased from Cell Systems Corporation. The cells were cultured using a CS-C complete medium kit (Cell Systems) at 37°C in 5% CO2 in a humidified incubator.

extract_protocol: Total RNAs from pericytes were collected by RNeasy mini kit with the RNase-free DNase set (QIAGEN).

treatment_protocol: The subconfluent pericytes were exposed to 1% oxygen for 24 hours or acidic-culture medium (pH 6.5) for 24 hours at 37°C in 5% CO2 in a humidified incubator.

value: brain pericytes

tag: passage


title: acidosis human brain pericytes replicate 1

description: Biological replicate 1 of 2. Brain pericytes were exposed to pH 6.5 medium for 24 hours.


title: Wk17.5h-3


title: Day0_Replicate2

city: Seattle

first: Elaine

middle: M.

last: Faustman

state: WA

address: 4225 Roosevelt Way NE, #100

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: gene expression in differentiating human neural progenitor cells in vitro

hyb_protocol: Purified RNA samples were then hybridized to Affymetrix Human 2.0 microarrays to measure global gene expression in each sample.

scan_protocol: Fragmented/Labeled DNA was combined with Hybridization cocktail 99C for 5 minutes according to Affymetrix hybridization kit protocol, then injected onto Affymetrix GeneChip Human Gene 2.0 ST array and incubated 16-18 hours 45C at 60rpm.

data_processing: Microarray CEL files were analyzed using R with the library packages, limma, oligo, NBclist, annotate and pd.hugene.1.0.st.v1.  Probe features were normalized with the rma() function. The getNetAffx() function was used to annotate probe features. Fitting of the expression values for replicates was performed by the lmFit() function.

source_name: human neural progenitor cells in differentiation conditions 0 days

label_protocol: Fragmented ssDNA was incubated with Affymetrix DNA Labeling Reagent 37°C 1 hour according to kit protocol

growth_protocol: Commercially available human neural progenitor cells (hNPCs) from ArunA Biomedical were expanded 8-10 passages in ENStem-A neural expansion medium (Millipore). At passages 8-10, cells were plated at a density of (200,000 cells/ml) in 35mm dishes coated in Matrigel (BD Biosciences) diluted 1:200 in DMEM/F-12.

extract_protocol: RNA from differentiating hNPC plates was harvested in Trizol 0, 1, 3, 7, 14, and 21 days following initiation of differentiation. RNA was then isolated using an RNA isolation kit (Ambion/mirVAna) according to kit protocol and samples were further purified with a cleanup kit (Qiagen) according to kit protocol. Expression data reflects replicate samples from 3 independent cell preparations.

treatment_protocol: Cells were allowed to attach and proliferate for 24 hours after plating, then medium was replaced with Hyclone neuronal differentiation medium (Thermo Scientific) in the absence of growth factor to initiate differentiation. Cells were maintained in differentiation conditions for up to 21 days, with half of the medium refreshed every two days.

value: hNPCs derived from WA09 hESCs , maintained in differentiation conditions


title: illium control 01-1417I

description: Gene expression data from illium control 01-1417I


title: illium control 02-1482I

description: Gene expression data from illium control 02-1482I


title: Mineral_wounding_3

city: Helsinki

first: Tommaso

last: Raffaello

address: Latokartanonkaari 7 PO Box 27

department: Forest Sciences

country: Finland

institute: University of Helsinki

hyb_protocol: Hybridization by NimbleGen Company.

scan_protocol: Scanning by NimbleGen Company.

data_processing: Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA). For information on RMA, see Biostatistics 2003 Apr; 4(2): 249-264.

organism: Pinus sylvestris

source_name: tree stem_wounding in mineral soil

label_protocol: Labelling by NimbleGen Company

growth_protocol: The sample plots were located in Lakkasuo, Orivesi (61°47’ N; 24° 18’ E; 150 m asl). Naturally regenerated mature Scots pine (Pinus sylvestris) trees were growing in mineral soil (dryish heath, Vaccinium vitis-idaea type), pristine mire (tall-sedge pine fen), and in drained peatland (Vaccinium vitis-idaea type II, drained counterpart of the pristine mire). Inoculations were conducted in the beginning of June 2010, and samples were harvested in the end of September 2010. Trees were cut down, and sample pieces close to the points of inoculation were cut out, and transported for storage at +4°C for 2 days, after which the samples were transported and stored at -20°C. Control samples were excised from untreated trees as 8 mm diameter core samples containing both the phloem and sapwood. Control samples were stored on dry ice after excision, and later stored at -20°C.

extract_protocol: 1. Grind plant tissue in liquid nitrogen.  2. Transfer 2.0 g of the ground sample to a sterile 50 ml tube.   3. Heat Extraction buffer to 65ºC and add 2-Mercaptoethanol (final concentration 2%). Mix by inversion.  4. To each tissue sample, add 8 ml of extraction buffer. Vortex well. Incubate for 40 min at 65ºC, and vortex briefly every 10 minutes.   5. Add equal volume of chloroform:isoamyl alcohol (24:1). Mix by inversion and centrifuge at 8000 rpm for 30 min at 25ºC.   6. Collect the upper (aqueous) phase to a sterile 15 ml tube. Add equal volume of chloroform:isoamyl alcohol (24:1). Mix by inversion and centrifuge at 8000 rpm for 30 min at 25ºC. Repeat if the aqueous phase is very cloudy.  7. Transfer aqueous phase to a new sterile tube. Add 1/4 volume of 10M LiCl and mix by inversion. Precipitate RNA overnight at 4ºC. Centrifuge at 12 000 rpm for 40 min.  8. Pipet out the supernatant and dry the pellet briefly. Dissolve the pellet in 500 µl SSTE and transfer into a sterile 1.5 ml tube.  9. Add an equal volume of chloroform:isoamyl alcohol. Mix by inversion and centrifuge at 13000rpm for 30 min at 25ºC.  10. Transfer aqueous phase to a new 1.5 ml tube. Add 2 volumes of cold absolute ethanol. Mix by inversion. Precipitate at -20ºC for at least 2 hours. Centrifuge at 13000rpm for 30 minutes.   11. Pipet out the supernatant. Wash the pellet by adding approximately 100 μl cold 70% ethanol. Centrifuge at 7500 rpm for 10 min.  12. Carefully pipet out the supernatant and dry the pellet in the sterile hood. Re-suspend the pellet in DEPC-treated water.    EXTRACTION BUFFER    2% CTAB  2% Polyvinylpyrrolidone (PVP) K-30  2% 2-Mercaptoethanol  100 mM Tris-HCl  25 mM EDTA   2 M NaCl  DEPC-treated water     SSTE BUFFER    1 M NaCl  0.5% SDS  10 mM Tris-HCl  1 mM EDTA  DEPC-treated water

treatment_protocol: The sample trees were inoculated either with sterile pine wood dowels (wounding), or with dowels pre-colonized by Heterobasidion annosum (infection). Autoclaved sterile dowels of Scots pine wood (diameter 10 mm) were placed on a two-week-old malt agar culture of H. annosum (homokaryotic isolate 03005 Kirkkonummi (Porkkala), courtesy of K. Korhonen, Finland) in Petri dishes incubated at room temperature in darkness for three weeks. Infected trees were inoculated with the pre-colonized dowels and wounded trees with the sterile dowels. Three inoculations were done in the stem and three in the roots of each tree in June 2010. On each site, 10 trees representing different genotypes were designated for both treatments. Stem inoculations were made at 50 cm, 100 cm and 150 cm height above the root neck. In the roots, inoculations were placed at least 15 cm apart. After four months, the samples were harvested by falling the trees and by cutting the roots with chainsaw. Periderm tissues were removed with a knife and an axe, after which the length and width of the necrotic lesions formed in the phloem and xylem were measured. Phloem tissues were harvested from each inoculation using a knife and a chisel. After harvesting, the tissue samples were stored at -20ºC. Phloem tissue from unwounded tree served as a control. Phloem samples were frozen in liquid nitrogen, ground to a powder using IKA® A11 basic analytical mill (IKA Werke) and stored at -80 ºC for further processing. RNA was extracted from the samples as described elsewhere (Chang et al. 1993). One microgram of total RNA from phloem in one stem inoculation was pooled into each RNA sample from infected, wounded and control sample trees.

tag: sample id

tag: inoculated with

value: sterile pine wood dowels (wounding)

tag: field/growth condition

value: mineral soil

tag: time point

value: 4 months after the inoculations

value: tree stem


title: tumor5

tag: tissue


title: tumor4


title: tumor6


title: PANC1DMSO_1

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to hg19 genome using STAR
read counting
Genome_build: hg19
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: PANC1 cell lines treated with DMSO for 6hr

growth_protocol: BxPC3, MiaPaCa-2 and PANC1 cells were cultured in F12 medium (containing 10% FBS, 5 mM β-glycerophosphate (Sigma, G9422), 50 ug/ml L-ascorbic acid (Sigma, A5960) and 1% penicillin/streptomycin, 6 × 10^5 cells were seeded into a well of 6-well-plate and treated with DMSO or THZ1 for 6hr.

extract_protocol:
Cells were harvest, and total RNA was extracted and ERCC spike-in controls were added according to kit guidelines (Thermo 4456740).
Libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina) according to the manufacturer's instructions.

tag: cell line

tag: cell type

value: human PDAC cell line

tag: tumor

value: Pancreatic Ductal Adenocarcinoma


title: Wk17.5h-1

value: Upper GI tract


title: PANC1DMSO_2


title: skin_healthy_rep6

description:
healthy skin biopsy donor 6
Gene expression data from plastic surgery specimen from aldut donor

source_name: adult, plastic surgery specimen

value: skin biopsy

value: healthy


title: skin_healthy_rep7

description:
healthy skin biopsy donor 7
Gene expression data from plastic surgery specimen from aldut donor

value: adult


title: skin_MPR_rep1

description:
MPR skin biopsy patient 1
Gene expression data from 6mm punch skin biopsy from adult MPR patient

value: MPR


title: Mineral_wounding_2


title: Miapaca2DMSO_3

source_name: MiaPaCa-2 cell lines treated with DMSO for 6hr


title: skin_healthy_rep5

description:
healthy skin biopsy donor 5
Gene expression data from plastic surgery specimen from aldut donor


title: Mineral_wounding_1


title: hypoxia human brain pericytes replicate 1

description: Biological replicate 1 of 2. Brain pericytes were exposed to 1% hypoxia for 24 hours.

source_name: A.Control 1

source_name: C.hypoxia 1


title: PANC1DMSO_3


title: hypoxia human brain pericytes replicate 2

description: Biological replicate 2 of 2. Brain pericytes were exposed to 1% hypoxia for 24 hours.

source_name: D.hypoxia 2


title: Mineral_infection_susceptible_2

source_name: tree stem_infected in mineral soil

value: dowels pre-colonized by Heterobasidion annosum (infection)

tag: responses to pathogen infection

value: susceptible


title: Mineral_infection_susceptible_3


title: control6

source_name: Bladder

value: FVB/N

value: Rbf/f, Ptenf/f, Tp53f/f, p107-/-

value: bladder


title: control5


title: control4


title: control1


title: control2


title: skin_healthy_rep3

description:
healthy skin biopsy donor 3
Gene expression data from plastic surgery specimen from aldut donor


title: skin_healthy_rep4

description:
healthy skin biopsy donor 4
Gene expression data from plastic surgery specimen from aldut donor


title: Miapaca2DMSO_1


title: BxPC3DMSO_3

source_name: BxPC3 cell lines treated with DMSO for 6hr


title: Untreated

city: Baltimore

first: Allen

middle: R

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: mRNA: ribosome footprints

data_processing:
Library strategy: Ribo-seq
Reads with N bases or Phred < 10 were dropped. The linker sequence was trimmed and reads mapping to rRNA or tRNA sequences were discarded. The remaining reads were mapped to the E. coli K-12 MG1655 genome version 3 with bowtie allowing two mismatches.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: WIG files of ribosome occupancy, assigned to the 3'-end of reads, normalized by the total number of reads in the library.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Cell cultures

growth_protocol: 150 mL cultures were grown in MOPS complete synthetic media to mid-log phase and harvested by filtration.

extract_protocol:
Cell pellets were cryogenically pulverized in a Spex 6870 freezer mill; 5 cycles of 1 min at 5 Hz with 1 min cooling. The lysis buffer contained 1 M NaCl to arrest translation. Lysates were clarified and ribosomes were pelleted prior to digestion of mRNA with MNase. After digestion, 70S monosomes were purified over a sucrose gradient.
Ribosome footprints and total RNA fragments were PAGE purified, ligated to a linker using RNA ligase T2, converted to DNA using RT, circularized, and PCR amplified.

treatment_protocol: Cell cultures were untreated or treated with Onc112.

tag: drug treatment


title: Onc112_treated

description: mRNA: ribosome footprints

value: 50 uM Onc112 for 10 min


title: Mineral_infection_resistant_2

value: resistant


title: Mineral_infection_resistant_3

value: mineral soil


title: BxPC3DMSO_2


title: BxPC3DMSO_1


title: PANC1THZ1_3

source_name: PANC1 cell lines treated with THZ1(100nM) for 6hr


title: skin_healthy_rep1

description:
healthy skin biopsy donor 1
Gene expression data from plastic surgery specimen from aldut donor

tag: adverse drug reaction


title: Miapaca2DMSO_2


title: Mineral_infection_susceptible_1

value: 4 months after the inoculations


title: tumor3

value: bladder tumor


title: PANC1THZ1_2

value: human PDAC cell line


title: Mineral_control_2

source_name: tree stem_control in mineral soil

value: none (untreated control)

value: tree stem


title: Mineral_infection_resistant_1


title: tumor1

source_name: Bladder, adeno-cre inoculated


title: tumor2


title: Mineral_control_3


title: Miapaca2THZ1_2

source_name: MiaPaCa-2 cell lines treated with THZ1(100nM) for 6hr

value: Pancreatic Ductal Adenocarcinoma


title: Miapaca2THZ1_3


title: skin_healthy_rep2

description:
healthy skin biopsy donor 2
Gene expression data from plastic surgery specimen from aldut donor

value: skin biopsy

value: healthy

tag: age


title: Miapaca2THZ1_1


title: BxPC3THZ1_3

source_name: BxPC3 cell lines treated with THZ1(100nM) for 6hr


title: BxPC3THZ1_2


title: PANC1THZ1_1


title: Drained_wounding_3

source_name: tree stem_wounding in drained soil

label_protocol: Labelling by NimbleGen Company.

growth_protocol: The sample plots were located in Lakkasuo, Orivesi (61°47’ N; 24° 18’ E; 150 m asl). Naturally regenerated mature Scots pine (Pinus sylvestris) trees representing random genotypes were growing in drained peatland (Vaccinium vitis-idaea type II, yield corresponding to Vaccinium type (VT) forest on mineral soil). Inoculations were conducted in the beginning of June 2010, and samples were harvested in the end of September 2010 (4 months after inoculation). Trees were cut down, and sample pieces close to the points of inoculation were cut out, and transported for storage at +4°C for 2 days, after which the samples were transported and stored at -20°C. Control samples were excised from untreated trees as 8 mm diameter core samples containing both the phloem and sapwood. Control samples were stored on dry ice after excision, and later stored at -20°C.

extract_protocol:
1. Grind plant tissue in liquid nitrogen.
2. Transfer 2.0 g of the ground sample to a sterile 50 ml tube.
3. Heat Extraction buffer to 65ºC and add 2-Mercaptoethanol (final concentration 2%). Mix by inversion.
4. To each tissue sample, add 8 ml of extraction buffer. Vortex well. Incubate for 40 min at 65ºC, and vortex briefly every 10 minutes.
5. Add equal volume of chloroform:isoamyl alcohol (24:1). Mix by inversion and centrifuge at 8000 rpm for 30 min at 25ºC.
6. Collect the upper (aqueous) phase to a sterile 15 ml tube. Add equal volume of chloroform:isoamyl alcohol (24:1). Mix by inversion and centrifuge at 8000 rpm for 30 min at 25ºC. Repeat if the aqueous phase is very cloudy.
7. Transfer aqueous phase to a new sterile tube. Add 1/4 volume of 10M LiCl and mix by inversion. Precipitate RNA overnight at 4ºC. Centrifuge at 12 000 rpm for 40 min.
8. Pipet out the supernatant and dry the pellet briefly. Dissolve the pellet in 500 µl SSTE and transfer into a sterile 1.5 ml tube.
9. Add an equal volume of chloroform:isoamyl alcohol. Mix by inversion and centrifuge at 13000rpm for 30 min at 25ºC.
10. Transfer aqueous phase to a new 1.5 ml tube. Add 2 volumes of cold absolute ethanol. Mix by inversion. Precipitate at -20ºC for at least 2 hours. Centrifuge at 13000rpm for 30 minutes.
11. Pipet out the supernatant. Wash the pellet by adding approximately 100 μl cold 70% ethanol. Centrifuge at 7500 rpm for 10 min.
12. Carefully pipet out the supernatant and dry the pellet in the sterile hood. Re-suspend the pellet in DEPC-treated water.

EXTRACTION BUFFER
2% CTAB
2% Polyvinylpyrrolidone (PVP) K-30
2% 2-Mercaptoethanol
100 mM Tris-HCl
25 mM EDTA
2 M NaCl
DEPC-treated water

SSTE BUFFER
1 M NaCl
0.5% SDS
10 mM Tris-HCl
1 mM EDTA
DEPC-treated water

treatment_protocol: The sample trees were inoculated either with sterile pine wood dowels (wounding), or with dowels pre-colonized by Heterobasidion annosum (infection). Autoclaved sterile dowels of Scots pine wood (diameter 10 mm) were placed on a two-week-old malt agar culture of H. annosum (homokaryotic isolate 03005 Kirkkonummi (Porkkala), courtesy of K. Korhonen, Finland) in Petri dishes incubated at room temperature in darkness for three weeks. Infected trees were inoculated with the pre-colonized dowels and wounded trees with the sterile dowels. Three inoculations were done in the stem and three in the roots of each tree in June 2010. Ten trees representing random genotypes were designated for both treatments. Stem inoculations were made at 50 cm, 100 cm and 150 cm height above the root neck. In the roots, the inoculations were placed at least 15 cm apart. After four months, the samples were harvested by falling the trees and by cutting the roots with chainsaw. Periderm tissues were removed with a knife and an axe, after which the length and width of the necrotic lesions formed in the phloem and xylem were measured. Phloem tissues were harvested from each inoculation using a knife and a chisel. After harvesting, the tissue samples were stored at -20ºC. Phloem tissue from unwounded tree served as a control. Phloem samples were frozen in liquid nitrogen, ground to powder using IKA® A11 basic analytical mill (IKA Werke) and stored at -80 ºC for further processing. RNA was extracted from the samples as described elsewhere (Chang et al. 1993). One microgram of total RNA from phloem in one stem inoculation was pooled into each RNA sample from infected, wounded and control sample trees.

value: sterile pine wood dowels (wounding)

tag: responses to pathogen infection:

value: drained peatland


title: BxPC3THZ1_1


title: Mineral_control_1


title: Drained_infection_susceptible_3

source_name: tree stem_infected in drained soil

value: dowels pre-colonized by Heterobasidion annosum (infection)

value: susceptible


title: Drained_infection_susceptible_2


title: Drained_wounding_2


title: Drained_wounding_1


title: Mutant untreated [E2-U]

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression after 5 hours

hyb_protocol: The  labeled cRNA sample was fragmented at 60 º C and hybridized on to a Genotypic designed Candida albicans Microarray Geneexpression 8X15k arrays(AMADID No: 26377) .Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327).

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Images were quantified using Feature Extraction software Version 11.5.1.1 of Agilent. Feature extracted raw data was analyzed using GeneSpring GX Version  software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Candida albicans

source_name: Cellular extract, 5 hrs

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps was carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Overnight grown primary culture in YEPD media at 30ºC and 220 rpm sub-cultured into fresh YEPD media with starting O.D 600 of 0.3. Secondary culture was grown for 5 hours before harvesting the cells.

extract_protocol: Total RNA, isolated using the RNeasymini kit (Qiagen), was treated with DNase I (Thermo Scientific) to remove contaminating DNA according to the manufacturer’s protocol.

treatment_protocol: Secondary culture was treated with 4.7μM  tunicamycin for 2 hours when the cells attained an O.D 600 of  1.

tag: genotype/variation

value: ifu5delta/delta mutant

tag: agent


title: Drained_infection_susceptible_1


title: Drained_infection_resistant_2


title: Drained_infection_resistant_3


title: jejunum control 03-1417J

description: Gene expression data from jejunum control 03-1417J

source_name: chicken jejunum

value: jejunum

tag: treatment

value: control

tag: batch


title: D. half #3 st12

city: Los Angeles

first: Edward

middle: M

last: De Robertis

address: 615 Charles E. Young Drive South

department: Biological chemistry

institute: HHMI/UCLA

description:
Dorsal half embryo cut at stage 8 and cultured until stage 12.
D. half #3 st12

data_processing:
After sequencing, adaptors were first trimmed from the RNA reads and RNA reads of low quality filtered. The clean RNA reads were mapped using Tophat (Version 2.09, default parameters) against the Xenopus laevis JGI9.1 (Xenbase) transcript sequences.
Transcripts counts were normalized using DESeq package in R . RPKM (Reads Per Kilobase per Million mapped reads) for transcripts was calculated in R.
Human gene names were assigned to transcripts using an annotation file obtained by blasting the JGI9.1 peptide sequences to human reference protein sequences.
Genome_build: Xenopus Laevis J-strain Version 9.1
Supplementary_files_format_and_content: Excel tables that include RPKM and fold induction values of genes for each sample

organism: Xenopus laevis

source_name: embryo

growth_protocol: The embryos were cultured in 0.1x Marc's Modified Ringers (MMR) and staged according to Nieuwkoop and Faber (1967).

extract_protocol:
RNA  was isolated with an Absolutely RNA miniprep Kit (Agilent).
Libraries were constructed with the Illumina TruSeq RNA Library Preparation Kit V2 according to manufacturer’s protocol. Briefly, 1 µg total RNA  was used for input RNA. Then mRNA was purified through polyA+ selection. After fragmentation of the mRNA, first strand and second strand synthesis, double strand cDNA (ds cDNA) was obtained. The ds cDNA was then further processed for A-tailing, end repair and ligation of appropriate adaptors. Finally, the ds cDNA with adaptors was amplified by PCR to generate libraries. After measurement of the length and concentration of the libraries by Bioanalyser and Qubit, the libraries were sent for sequencing on Illumina Hi-Seq 2000 using standard methods to generate 100-bp single end reads by the Broad Stem Cell Research Center at UCLA.

treatment_protocol: Left, right, dorsal and ventral halves embryos were cut at stage 8 in 1x Barth’s solution and cultured to stage 10.5 or stage 12 in 0.3 x Barth's solution.

tag: strain

value: Nasco

value: dorsal half embryo

tag: developmental stage


title: R. half#3 st12

description:
Right half embryo cut at stage 8 and cultured until stage 12.
R. half#3 st12

value: right half embryo


title: V. half#3 st12

description:
Ventral half embryo cut at stage 8 and cultured until stage 12.
V. half#3 st12

value: ventral half embryo


title: Metastasis1

source_name: Metastasis

tag: background strain

value: FVB/N

tag: genotype

value: Rbf/f, Ptenf/f, Tp53f/f, p107-/-

value: metastatic tumor


title: Mutant untreated [E1-U]

description: Gene expression after 5 hours


title: Drained_infection_resistant_1

tag: sample id

tag: inoculated with

value: resistant

tag: field/growth condition

tag: time point

value: 4 months after the inoculations

tag: tissue

value: tree stem


title: Wild type untreated [A2-U1]

description: Gene expression after 5 hours

value: Wild type


title: Tendon 4

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using FASTQC software (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The paired end reads were processed using Kallisto 0.42.4
Transcript counts were generated using Kallisto 0.42.4
Genome_build: Oryctolagus_cuniculus.OryCun2.0
Supplementary_files_format_and_content: tab-delimited text files include estimated counts for each transcript per sample

organism: Oryctolagus cuniculus

source_name: whole semitendinosus autografts

extract_protocol:
Frozen tendon biopsies were removed from -80° C and kept in liquid nitrogen at all times during processing. Individually, tendons were ground into a fine powder using a mortar and pestle set on dry ice while re-applying liquid nitrogen as needed (approximately every 30 seconds). Powder was then transferred to a sterile 1.5ml Eppendorf tube and 700µl of TRI Reagent (Zymogen Research) was added. Total mRNA was extracted using a Zymogen Research Direct-zol RNA Kit (Zymogen Research) and quantified using the NanoDrop 2000 spectrophotometer (Thermo Fischer Scientific, Wilmington, Delaware)
RNA integrity was assessed using the Agilent Bioanalyzer DNA 1000 chip (Invitrogen, Carlsbad, CA). Only samples with an RNA Integrity Number (RIN) and DV200 score greater than our Sequencing Core's minimum cutoff (RIN >6 and DV200 > 50%) were used for sequencing. In brief, library preparation was performed using the TruSeq RNA library preparation kit (Illumina, San Diego, CA). Polyadenylated mRNAs were selected using oligo dT magnetic beads. TruSeq Kits were used for indexing to permit multiplex sample loading on the flow cells.

treatment_protocol: Under sterile conditions, rabbit semitendinosus autografts were harvested employing a midline incision centered over the anterior aspect of the knee. A medial flap was developed along the fascial plane of the patellar tendon by exposure of the medial collateral ligament (MCL). Subsequently, a transverse incision was made in the muscular fascia just posterior and medial to the MCL and the medial edge of the quadriceps was lifted to expose the semitendinosus. The distal insertion of the tendon was released and retracted to allow for mobilization of the tendon to its proximal aspect.  Thereafter, the proximal aspect of the tendon was divided, providing 3-4 cm of tendon autograft for subsequent reconstruction.  For samples to be used for RNA sequencing, muscle was debrided from the tendon surface employing gentle perpendicular sweeps of a clean scalpel blade.   Thereafter, tendon was rinsed in sterile PBS and frozen at -80° C until mRNA isolation and sequencing.

value: Semitendinosus

value: 193 days

tag: Sex

value: Female


title: Drained_control_3

source_name: tree stem_control in drained soil

value: none (untreated control)

value: drained peatland


title: Drained_control_2


title: L. half#3 st12

description:
Left half embryo cut at stage 8 and cultured until stage 12.
L. half#3 st12

value: left half embryo


title: Drained_control_1


title: Wild type untreated [A1-U1]

description: Gene expression after 5 hours


title: cALD_8

type: genomic

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

institute: IDIBELL

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Genome Studio V2011.2
Unmethylated and methylated signal intensities in Series supplementary file

label: Cy3, Cy5

molecule: genomic DNA

source_name: Cerebrum_Frontal Cortex

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

value: Cerebrum_Frontal Cortex

value: cerebrum frontal cortex

tag: disease state

value: cALD

value: child

tag: race

value: Caucasian

tag: gender

value: Male


title: cAMN_4

value: cAMN

value: adult


title: cAMN_9


title: cAMN_8


title: cAMN_5


title: Control#3 st12

description:
whole embryo; control for L. half#3 st12, R. half#3 st12, D. half#3 st12 and V. half#3 st12.
Control#3 st12

value: Nasco

value: whole embryo


title: V. half#2 st12

description:
Ventral half embryo cut at stage 8 and cultured until stage 12.
V. half#2 st12

value: ventral half embryo


title: cALD_7


title: Tendon 1

value: Semitendinosus

tag: age


title: Tendon 3

value: 193 days


title: Tendon 2

value: Female


title: cAMN_3


title: P56_2

source_name: Lung epithelial cells

tag: cell type

value: lineage (CD31, CD45, CD146 and Ter119) negative, Epcam positive epithelial cells

value: lung

value: Postnatal day 56


title: cAMN_6

value: Cerebrum_Frontal Cortex


title: D. half #2 st12

description:
Dorsal half embryo cut at stage 8 and cultured until stage 12.
D. half #2 st12

value: dorsal half embryo


title: R. half#2 st12

description:
Right half embryo cut at stage 8 and cultured until stage 12.
R. half#2 st12

value: right half embryo


title: P56_1


title: P14_1

value: Postnatal day 14


title: L. half#2 st12

description:
Left half embryo cut at stage 8 and cultured until stage 12.
L. half#2 st12

value: left half embryo


title: cAMN_7

value: cerebrum frontal cortex

value: Caucasian

value: Male


title: Control#2 st12

description:
whole embryo; control for L. half#2 st12, R. half#2 st12, D. half#2 st12 and V. half#2 st12.
Control#2 st12

value: Nasco


title: cAMN_1

value: cAMN

value: adult


title: E18.5_2

value: Embryonic day 18.5


title: V. half#1 st12

description:
Ventral half embryo cut at stage 8 and cultured until stage 12.
V. half#1 st12

value: ventral half embryo


title: E18.5_1


title: D. half #1 st12

description:
Dorsal half embryo cut at stage 8 and cultured until stage 12.
D. half #1 st12


title: E15.5_1

value: Embryonic day 15.5


title: cAMN_2


title: cALD_5

value: cALD

value: child


title: L. half#1 st12

description:
Left half embryo cut at stage 8 and cultured until stage 12.
L. half#1 st12


title: cALD_6


title: R. half#1 st12

description:
Right half embryo cut at stage 8 and cultured until stage 12.
R. half#1 st12


title: Control#1 st12

description:
whole embryo; control for L. half#1 st12, R. half#1 st12, D. half#1 st12 and V. half#1 st12.
Control#1 st12

value: whole embryo


title: V. half#3 st10.5

description:
Ventral half embryo cut at stage 8 and cultured until stage 10.5.
V. half#3 st10.5


title: cALD_3

value: Cerebrum_Frontal Cortex


title: D. half #3 st10.5

description:
Dorsal half embryo cut at stage 8 and cultured until stage 10.5.
D. half #3 st10.5

value: dorsal half embryo


title: cALD_2


title: R. half#3 st10.5

description:
Right half embryo cut at stage 8 and cultured until stage 10.5.
R. half#3 st10.5

value: right half embryo


title: L. half#3 st10.5

description:
Left half embryo cut at stage 8 and cultured until stage 10.5.
L. half#3 st10.5


title: cALD_4


title: myometrium_mifepristone_rep 6

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

description: pregnant, term no labor, explant, 9 hours

hyb_protocol: Standard NASC hybridization protocol

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: The raw CEL files were normalized using the RMA background correction with quantile normalization, log base 2 transformation and mean probe-set summarization with adjustment for GC content. Differentially expressed genes (DEG) were identified by a two-way ANOVA, and p-values were adjusted using the FDR (false-discovery rate) method to correct for multiple comparisons. DEG were considered significant if p-value was £ 0.05 at a fold change (FC) of < -2 and > 2 with FDR <0.5.

source_name: myometrium, mifepristone

label_protocol: Total RNA according to the standard Affymetrix protocol (WT Expression Kit User Manual, 2010, Affymetrix).

growth_protocol: Tissue was dissected into 3x3x3mm3explants and plated immediately as per treatment protocol

extract_protocol: Trizol extraction of total RNA was performed using a Trizol® Plus RNA Purification kit (Thermo Fisher Scientific, Ambion, Abgene Ltd., West Sussex, UK)

treatment_protocol: Tissue were cultured for a period of 9 hours in DMEM supplemented with penicillin/streptomycin. Ethanol vehicle or 1µM mifepristone were added immediately.

value: myometrium


title: myometrium_vehicle_rep 6

source_name: myometrium, vehicle


title: myometrium_mifepristone_rep 5


title: Control#3 st10.5

description:
whole embryo; control for L. half#3 st10.5, R. half#3 st10.5, D. half#3 st10.5 and V. half#3 st10.5.
Control#3 st10.5


title: myometrium_vehicle_rep 4


title: myometrium_mifepristone_rep 3


title: myometrium_vehicle_rep 5


title: V. half#2 st10.5

description:
Ventral half embryo cut at stage 8 and cultured until stage 10.5.
V. half#2 st10.5


title: myometrium_mifepristone_rep 4


title: Control Adult_7

value: control


title: myometrium_vehicle_rep 3


title: cALD_1

value: cerebrum frontal cortex


title: Control Adult_5

value: Caucasian


title: Control Adult_6

value: Male


title: D. half #2 st10.5

description:
Dorsal half embryo cut at stage 8 and cultured until stage 10.5.
D. half #2 st10.5

value: Nasco


title: myometrium_mifepristone_rep 2


title: L. half#2 st10.5

description:
Left half embryo cut at stage 8 and cultured until stage 10.5.
L. half#2 st10.5

value: left half embryo


title: R. half#2 st10.5

description:
Right half embryo cut at stage 8 and cultured until stage 10.5.
R. half#2 st10.5


title: Control Adult_8

value: adult


title: Control Adult_9


title: Control#2 st10.5

description:
whole embryo; control for L. half#2 st10.5, R. half#2 st10.5, D. half#2 st10.5 and V. half#2 st10.5.
Control#2 st10.5


title: G-123

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

institute: INRA

hyb_protocol: 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array. Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing.

scan_protocol: Scan was performed with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3 μm and 20 bits).

data_processing: Data were then obtained with the Agilent Feature Extraction software (10.7.3.1) according to the appropriate GE protocol (GE1_107_Sep09) and imported into GeneSpring GX software (Agilent Technologies) for analysis.

source_name: Good quality fish egg - Clutch N°123

label_protocol: Zebrafish gene expression profiling was conducted using an Agilent 8x60K high-density oligonucleotide microarray. Labeling and hybridization steps were performed  following the Agilent “One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp labeling)” protocol. Briefly, for each sample, 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>825 ng cRNA) and specific activity (> 6 pmol of Cy3 per μg of cRNA) of Cy3-cRNA produced were checked with the NanoDrop ND1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA).

growth_protocol: Wildtype zebrafish (Danio rerio) of the AB strain were maintained at 25°C in a central filtration recirculating system with a 12 hr light/dark cycle. Individual couple pairing was performed by placing a male and a female  overnight in a tank with a partition for separation, and in the morning, the divider was removed after which the female released her eggs to be fertilized by the male.

extract_protocol: Total RNA of the pooled clutches was extracted using TRI reagent according to the manufacturer's protocol, and RNA quality and purity were assessed using the Agilent Nano RNA 6000 assay kit and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). All samples were confirmed to have an RIN (RNA integrity number) of 9-10 which are generally accepted as reflecting very good quality RNA.

treatment_protocol: One hundred and thirty-six clutches of fertilized zebrafish eggs at the one-cell stage from 58 families were harvested and divided into two parts. One part was flash-frozen in TRI reagent (Sigma-Aldrich, St. Louis, MO) and stored at -80°C for molecular biology analyses. The other part was cultured in modified Yamamoto's embryo solution and monitored for up to 48 hours, and the number of survivors was counted at 8, 24, and 48 hpf. Good quality eggs were defined as embryos that had a very high survival rate (>93%) at 48 hpf and bad quality eggs were those that suffered a very low survival rate (<38%) at 48 hpf.

value: Good quality fish egg


title: myometrium_vehicle_rep 2


title: G-135

source_name: Good quality fish egg - Clutch N°135


title: Control Adult_3

value: cerebrum occipital


title: myometrium_vehicle_rep 1


title: G-74

source_name: Good quality fish egg - Clutch N°74


title: Control Adult_1


title: V. half#1 st10.5

description:
Ventral half embryo cut at stage 8 and cultured until stage 10.5.
V. half#1 st10.5

value: ventral half embryo


title: D. half #1 st10.5

description:
Dorsal half embryo cut at stage 8 and cultured until stage 10.5.
D. half #1 st10.5


title: myometrium_mifepristone_rep 1


title: L. half#1 st10.5

description:
Left half embryo cut at stage 8 and cultured until stage 10.5.
L. half#1 st10.5


title: Control#1 st10.5

description:
whole embryo; control for L. half#1 st10.5, R. half#1 st10.5, D. half#1 st10.5 and V. half#1 st10.5.
Control#1 st10.5


title: Control Adult_2


title: Control Child_6


title: NE_of_Cau_with_BE#06

city: Ann Arbor

first: Derek

middle: John

last: Nancarrow

state: MI

address: 1500 E. Medical Center Dr.

department: Department of Surgery

institute: University of Michigan

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 20 hr at 48C on GeneChip Human Gene 2.1 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: Data was analyzed with R/Bioconductor software, normalized using RMA and log2-transformed. Analyses were restricted to the 24,909 coding and non-coding genes (probesets) for which both HUGO Gene Nomenclature Committee (HGNC) approved gene symbol and Entrez Gene ID annotation details were available.  We used a one-way analysis of variance (ANOVA) model across the four sample groups, but compared pairs of tissue groups by both  ANOVA and fold change in order to chose genes for further study.

source_name: specimen of normal esophageal squamous mucosa collected from subject diagnosed with esophageal adenocarcinoma

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (WT Expression Kit User Manual, 2010, Affymetrix).

extract_protocol: Total RNAs from primary tissues were isolated using Trizol reagent from Invitrogen and the RNeasy mini kit from QIAGEN following the manufacturers' instructions.

treatment_protocol: Samples were immediately fresh frozen in liquid nitrogen and stored at -80C until use

tag: subject group

value: American Caucasian with BE

tag: age (yr)

value: male

tag: racial group

value: American Caucasian

tag: smoking status

value: Former smoker

tag: gastroesophageal reflux disease (gerd) status

value: GERD

tag: bmi

tag: barrett's esophagus (be) pathology status

value: No BE noted

tag: clinical diagnosis

value: EAC

value: normal esophageal squamous


title: R. half#1 st10.5

description:
Right half embryo cut at stage 8 and cultured until stage 10.5.
R. half#1 st10.5

tag: strain

value: right half embryo

tag: developmental stage


title: NE_of_Cau_with_BE#05

tag: tissue


title: NE_of_Cau_with_BE#07

source_name: specimen of normal esophageal squamous mucosa collected from subject diagnosed with Barrett's esophagus and esophageal adenocarcinoma

value: female

value: BE noted

value: BE/EAC


title: G-67

source_name: Good quality fish egg - Clutch N°67


title: 3D-HEP-IND

city: Palo Alto

first: Weng Chuan

last: Peng

address: 265 Campus Drive

department: Developmental Biology

institute: Stanford University

data_processing:
The Cell Ranger Software (Version 2.1.1) was used to perform sample de-multiplexing, barcode processing and 3’ UMI counting.
Genome_build: mm10
Supplementary_files_format_and_content: mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample

source_name: Hepatocytes

growth_protocol: Mouse primary hepatocytes were embedded in growth-factor reduced (GFR) matrigel (BD) and cultured in William E medium containing 1 % (v/v) Glutamax, 1 % (v/v) Non-Essential Amino Acids, 1 % (v/v) penicillin/streptomycin, 0.2 % (v/v) normocin, 2 % (v/v) B27, 1 % (v/v) N2 supplement, 100 mM nicotinamide, 1.25 mM N-acetylcysteine, 10 uM Y27632, 1 uM A83-01. Expansion (EXP) medium also contained 3 uM CHIR99021, 25 ng/mL EGF, 50 ng/mL HGF and 100 ng/mL TNFa, while induction (IND) medium contained 25 ng/mL EGF, 50 ng/mL HGF and 3 uM dexamethasone.

extract_protocol:
10x Genomics single cell protocol (chromium system)
transcriptomic

value: Liver

tag: media

value: induction


title: G-68

source_name: Good quality fish egg - Clutch N°68

value: Good quality fish egg


title: 3D-HEP-EXP

value: expansion


title: NE_of_Cau_with_BE#08


title: Control Child_4

value: Cerebrum_Frontal Cortex

value: cerebrum frontal cortex

tag: disease state

value: control

value: child

value: Caucasian

value: Male


title: G-65

source_name: Good quality fish egg - Clutch N°65


title: G-66

source_name: Good quality fish egg - Clutch N°66


title: NE_of_Cau_with_BE#04

value: American Caucasian with BE

value: male

value: American Caucasian

value: Former smoker

value: No GERD

value: No BE noted


title: NE_of_Cau_with_BE#03

value: female

value: GERD

value: BE noted

value: BE/EAC

value: normal esophageal squamous


title: Control Child_8

value: Cerebrum_Frontal Cortex

tag: race


title: Control Child_3

value: cerebrum frontal cortex

tag: gender


title: G-54

source_name: Good quality fish egg - Clutch N°54

value: Good quality fish egg


title: NE_of_Cau_with_BE#01

value: Never smoked


title: Control Child_1

value: control

value: child

value: Caucasian


title: G-64

source_name: Good quality fish egg - Clutch N°64


title: G-51

source_name: Good quality fish egg - Clutch N°51


title: Control Child_5

source_name: Cerebrum_Frontal Cortex

value: Male


title: Control Child_2


title: PrefrontalCortex_A11-4

city: Pasadena

first: Gil

last: Sharon

address: 1200 E California Blvd

institute: California Institute of Technology

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B443_PFC

data_processing:
Demulitplexed fastq files were mapped to the mouse reference genome assembly (GRCm38/mm11) using STAR with Gencode M11 annotations
Quality control was performed using PicardTools (CollectAlignmnetSummaryMetrics, CollectRnaSeqMetrics, CollectGcBiasMetrics, CollectInsertSizeMetrics, MarkDuplicates)
Gene expression was quantified using featureCounts
Alternative splicing was analyzed using rMATS
Genome_build: GRCm38/mm11

source_name: PrefrontalCortex_ASD 11

growth_protocol: Mice were anestetized using 5% isoflurane for 30 seconds and euthanized by cervical dislocation. Brains were dissected and the striatum and prefrontal cortex were collected into RNALater and frozen to -80C

extract_protocol:
Approximately 30 mg of frozen brain tissue was then pulverized and RNA was extracted using Qiagen miRNeasy kits according to the manufacturer’s protocol
For each sample, RNA integrity number (RIN) values were quantified using an Agilent Bioanalyzer. RNA sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep kits using polyA selection (Illumina). Libraries were barcoded and randomly pooled in sets of 24.

tag: strain background

tag: mouse status

value: colonized with Human feces (ASD)

tag: age

tag: Sex

value: male

value: macro-dissected prefrontal cortex


title: PrefrontalCortex_A3-4

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B442_PFC

source_name: PrefrontalCortex_ASD 3


title: PrefrontalCortex_C1-4

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B440_PFC

source_name: PrefrontalCortex_control 1

value: colonized with Human feces (Control)


title: PrefrontalCortex_A24-4

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B441_PFC

source_name: PrefrontalCortex_ASD 24


title: Control Child_7


title: PrefrontalCortex_A17-4

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B438_PFC

source_name: PrefrontalCortex_ASD 17


title: PrefrontalCortex_A9-4

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B439_PFC

source_name: PrefrontalCortex_ASD 9


title: PrefrontalCortex_C4-4

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B437_PFC

source_name: PrefrontalCortex_control 4


title: PrefrontalCortex_A11-3

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B435_PFC


title: PrefrontalCortex_N5-7

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B436_PFC

source_name: PrefrontalCortex_control 5


title: NE_of_Cau_control#11

source_name: specimen of normal esophageal squamous mucosa collected from subject with neither Barrett's esophagus nor esophageal adenocarcinoma

tag: subject group

value: American Caucasian control

tag: age (yr)

tag: racial group

value: American Caucasian

value: Former smoker

value: No BE noted


title: NE_of_Cau_control#12

tag: smoking status

tag: gastroesophageal reflux disease (gerd) status

value: No GERD

tag: bmi

value: normal esophageal squamous


title: G-24

source_name: Good quality fish egg - Clutch N°24


title: NE_of_Cau_with_BE#02

source_name: specimen of normal esophageal squamous mucosa collected from subject diagnosed with Barrett's esophagus and esophageal adenocarcinoma

value: American Caucasian with BE

value: GERD

tag: barrett's esophagus (be) pathology status

value: BE noted

tag: clinical diagnosis

value: BE/EAC


title: Control Adult_4

tag: tissue

value: Cerebrum_Frontal Cortex

value: cerebrum frontal cortex

value: control

tag: developmental stage

value: adult


title: G-22

source_name: Good quality fish egg - Clutch N°22

value: Good quality fish egg


title: G-2

source_name: Good quality fish egg - Clutch N°2


title: NE_of_Cau_control#09

value: male

value: Current smoker


title: G-12

source_name: Good quality fish egg - Clutch N°12


title: NE_of_Cau_control#05

value: American Caucasian control


title: G-43

source_name: Good quality fish egg - Clutch N°43


title: G-15

source_name: Good quality fish egg - Clutch N°15


title: NE_of_Cau_control#06

value: American Caucasian


title: PrefrontalCortex_A3-3

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B433_PFC

value: colonized with Human feces (ASD)

value: macro-dissected prefrontal cortex


title: PrefrontalCortex_A24-3

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B432_PFC


title: NE_of_Cau_control#08

value: No BE noted


title: NE_of_Cau_control#07

value: Former smoker

value: normal esophageal squamous


title: NE_of_Cau_control#10

value: GERD


title: B-119

source_name: Bad quality fish egg - Clutch N°119

value: Bad quality fish egg


title: PrefrontalCortex_N5-3

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B434_PFC

value: colonized with Human feces (Control)


title: PrefrontalCortex_C1-3

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B431_PFC


title: B-124

source_name: Bad quality fish egg - Clutch N°16


title: B-115

source_name: Bad quality fish egg - Clutch N°115


title: PrefrontalCortex_A9-3

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B430_PFC


title: NE_of_Cau_control#03

value: No GERD


title: NE_of_Cau_control#04


title: NE_of_Cau_control#02

value: Never smoked


title: PrefrontalCortex_C4-3

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B428_PFC


title: PrefrontalCortex_A17-3

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B429_PFC


title: PrefrontalCortex_A11-2

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B426_PFC

source_name: PrefrontalCortex_ASD 11


title: PrefrontalCortex_N5-6

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B427_PFC


title: B-73

source_name: Bad quality fish egg - Clutch N°73


title: NE_of_Cau_control#01


title: NE_of_AA_control#12

value: African American control

value: African American


title: NE_of_AA_control#11


title: PrefrontalCortex_N5-2

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B425_PFC


title: NE_of_AA_control#10


title: B-58

source_name: Bad quality fish egg - Clutch N°58


title: B-109

source_name: Bad quality fish egg - Clutch N°109


title: B-86

source_name: Bad quality fish egg - Clutch N°86


title: B-57

source_name: Bad quality fish egg - Clutch N°57


title: B-34

source_name: Bad quality fish egg - Clutch N°34


title: PrefrontalCortex_A3-2

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B424_PFC

source_name: PrefrontalCortex_ASD 3


title: PrefrontalCortex_A24-2

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B423_PFC

source_name: PrefrontalCortex_ASD 24


title: B-10

source_name: Bad quality fish egg - Clutch N°10


title: NE_of_AA_control#08

source_name: specimen of normal esophageal squamous mucosa collected from subject with neither Barrett's esophagus nor esophageal adenocarcinoma


title: NE_of_AA_control#05


title: NE_of_AA_control#07


title: NE_of_AA_control#06


title: B-8

source_name: Bad quality fish egg - Clutch N°8


title: PrefrontalCortex_C1-2

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B422_PFC

source_name: PrefrontalCortex_control 1


title: B-29

source_name: Bad quality fish egg - Clutch N°29


title: B-55

source_name: Bad quality fish egg - Clutch N°55


title: NE_of_AA_control#04


title: PrefrontalCortex_A9-2

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B421_PFC

source_name: PrefrontalCortex_ASD 9


title: NE_of_AA_control#09


title: B-32

source_name: Bad quality fish egg - Clutch N°32


title: B-4

source_name: Bad quality fish egg - Clutch N°4


title: MIX-AN Biological Repeat-2

city: Stellenbosch

first: Kirti

last: Shekhawat

address: Alexander Street

country: South Africa

institute: IWBT

description:
L._thermotolerans_with_MIX_FPKM.txt
S._cerevisiae_with_MIX_FPKM.txt
Sc-plus-Lt-AN-R2_S10

data_processing:
NS2500 next generation sequencing platform
The reads were aligned to the reference genomes with Tophat v2.0.13. The obtained bam files were further converted in to gff files to analyse the data further. The number of reads in the alignments that overlap with gene features were counted with feature Counts 1.4.6. The following parameters were chosen: -Q 0 –s 0 –t exon –g gene_id.
Gene expression levels were normalized using fragments per kilobase of exon per million mapped reads (FPKM). A negative binomial generalized linear model (GLM) was fitted against the normalized counts using the EdgeR 3.4.0 package of Bioconductor. The differential expression was tested with a GLM likelihood ratio test, also implemented in the EdgeR package. The resulting p-values were corrected for multiple testing with Benjamini-Hochberg to control the false discovery rate (FDR)
Genome_build: S. cerevisia S288C for S. cerevisiae reference genome and Lachancea thermotolerans cbs 6340 for Lachancea thermotolerans
Supplementary_files_format_and_content: Text files include FPKM values of L. thermotolerans and S. cerevisiae single fermentations with their mixed fermentations

organism:
Saccharomyces cerevisiae
Lachancea thermotolerans

source_name: Lachancea thermotolerans and Saccharomyces cerevisiae Yeast Cells

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

tag: strain

value: S. cerevisiae Cross evolution-285 and L. thermotolerans IWBT-Y1240

tag: genotype

value: Wine Yeast

tag: treatment

value: Anaerobic

tag: cell type

value: Yeast cells


title: MIX-AN Biological Repeat-1

description:
L._thermotolerans_with_MIX_FPKM.txt
S._cerevisiae_with_MIX_FPKM.txt
Sc-plus-Lt-AN-R1_S9


title: MIX-AR Biological Repeat-2

description:
L._thermotolerans_with_MIX_FPKM.txt
S._cerevisiae_with_MIX_FPKM.txt
Sc-plus-Lt-R2-AR_S12

value: Aerobic


title: PrefrontalCortex_A17-2

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B420_PFC

source_name: PrefrontalCortex_ASD 17

tag: strain background

tag: mouse status

value: colonized with Human feces (ASD)

value: male


title: Lachancea thermotolerans-AR Biological Repeat-2

description:
L._thermotolerans_with_MIX_FPKM.txt
Lt-R2-AR-S6

organism: Lachancea thermotolerans

source_name: Lachancea thermotolerans Yeast Cells

value: L. thermotolerans IWBT-Y1240


title: PrefrontalCortex_C4-2

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B419_PFC

source_name: PrefrontalCortex_control 4

tag: age

tag: Sex

value: macro-dissected prefrontal cortex


title: NE_of_AA_control#03

tag: subject group

tag: age (yr)

tag: gender

value: Former smoker

value: No BE noted

value: normal esophageal squamous


title: PrefrontalCortex_A11-1

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B417_PFC

source_name: PrefrontalCortex_ASD 11


title: MIX-AR Biological Repeat-1

description:
L._thermotolerans_with_MIX_FPKM.txt
S._cerevisiae_with_MIX_FPKM.txt
Sc-plus-Lt-AR-R1_S11


title: NE_of_AA_with_BE#06

source_name: specimen of normal esophageal squamous mucosa collected from subject diagnosed with Barrett's esophagus without dysplasia

value: African American with BE

tag: racial group

tag: smoking status

tag: gastroesophageal reflux disease (gerd) status

value: GERD

value: BE noted

value: BE-no dysplasia


title: NE_of_AA_control#01

value: African American control

value: African American

value: No GERD

tag: bmi

tag: barrett's esophagus (be) pathology status

tag: clinical diagnosis


title: NE_of_AA_with_BE#07

source_name: specimen of normal esophageal squamous mucosa collected from subject diagnosed with Barrett's esophagus and esophageal adenocarcinoma

value: Current smoker

value: BE/EAC

tag: tissue


title: Lachancea thermotolerans-AR Biological Repeat-1

description:
L._thermotolerans_with_MIX_FPKM.txt
Lt-R1-AR-S5

tag: strain

tag: genotype

value: Wine Yeast

value: Aerobic

value: Yeast cells


title: PrefrontalCortex_N5-1

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B416_PFC

source_name: PrefrontalCortex_control 5

value: colonized with Human feces (Control)

value: male


title: PrefrontalCortex_A3-1

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B415_PFC

source_name: PrefrontalCortex_ASD 3

value: colonized with Human feces (ASD)

value: macro-dissected prefrontal cortex


title: PrefrontalCortex_C1-1

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B413_PFC


title: PrefrontalCortex_A9-1

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B412_PFC


title: PrefrontalCortex_A17-1

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B411_PFC


title: atf-7(qd22qd130) PA14 2

city: Cambridge

first: Dennis

last: Kim

state: MA

address: 31 Ames Street

institute: MIT

data_processing:
Base-calling was performed using Illumina's NextSeq control software, RTA 2.4.11
Quality control: Reads were aligned against C. elegans (ws206) using bwa aln/ sampe v. 0.7.16a-r1181 with flags –t 16 –f and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5’ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using dedicated perl scripts and bedtools v. 2.25.0.64.
RNA-Seq mapping and quantitation: Reads were aligned against wbps9/ws258  annotation using STAR v. 2.5.3a with flags -runThreadN 16 --runMode alignReads  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM with --genomeDir pointing to a 75nt-junction wbps9/ws258 STAR suffix array.
Gene expression was quantitated using RSEM v. 1.3.0 with the following flags for all libraries: rsem-calculate-expression --calc-pme --alignments -p 8  --forward-prob 0 against an annotation matching the STAR SA reference. Posterior mean estimates (pme) of counts and estimated RPKM were retrieved.
Genome_build: ws258(wbps9) annotation
Supplementary_files_format_and_content: txt file with, for each gene and each sample, gene length, effective gene length, and posterior mean estimates of read counts (from RSEM).

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Animals were synchronized by bleach prep. Arrested L1s dropped onto agar plates seeded with OP50 and grown at 20 degrees C until the L4 larval stage.

extract_protocol:
After 3 washes in M9 buffer, TRIzol Reagent (Invitrogen) was added to worm pellets and flash frozen in liquid nitrogen. After an additional round of freeze-thaw, RNA was isolated using the Direct-zol RNA MiniPrep kit (Zymo Research)
Libraries prepped using Kapa mRNA Hyperprep kit. Paired end reads sequenced on Illumina NextSeq500 sequencer, with v2 high-output chemistry.

treatment_protocol: L4 animals were washed to agar plates seeded with non-pathogenic (OP50) or pathogenic (PA14) bacteria for a period of 4 hours at 25 degrees C before RNA was harvested

value: whole animal

tag: bacterial exposure

tag: exposure length

value: 4 hours


title: NE_of_AA_control#02

source_name: specimen of normal esophageal squamous mucosa collected from subject with neither Barrett's esophagus nor esophageal adenocarcinoma

value: No BE noted

value: normal esophageal squamous


title: PrefrontalCortex_C4-1

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B410_PFC

tag: strain background

tag: mouse status


title: atf-7(qd22qd130) OP50 3

tag: age


title: B-1

source_name: Bad quality fish egg - Clutch N°1

value: Bad quality fish egg


title: Lachancea thermotolerans-AN Biological Repeat-2

description:
L._thermotolerans_with_MIX_FPKM.txt
Lt-R2-AN_S2

value: L. thermotolerans IWBT-Y1240

tag: treatment

value: Anaerobic

tag: cell type


title: PrefrontalCortex_N5-4

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B409_PFC

tag: Sex


title: Lachancea thermotolerans-AN Biological Repeat-1

description:
L._thermotolerans_with_MIX_FPKM.txt
Lt-R1-AN-S1


title: PrefrontalCortex_A24-1

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B414_PFC

source_name: PrefrontalCortex_ASD 24


title: Striatum_A11-4

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B478_STRIATUM

source_name: Striatum_ASD 11

value: macro-dissected Striatum


title: Striatum_A3-4

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B477_STRIATUM

source_name: Striatum_ASD 3


title: atf-7(qd22qd130) PA14 1


title: atf-7(qd22qd130) OP50 2


title: NE_of_AA_with_BE#05

tag: subject group

value: African American with BE

tag: age (yr)

tag: gender

value: female

tag: racial group

value: African American

value: Never smoked

value: GERD

value: BE noted

value: BE-no dysplasia


title: NE_of_AA_with_BE#04

value: male

tag: smoking status

value: Current smoker

tag: gastroesophageal reflux disease (gerd) status

tag: bmi

tag: barrett's esophagus (be) pathology status


title: NE_of_AA_with_BE#03

tag: clinical diagnosis

tag: tissue


title: NE_of_AA_with_BE#02

source_name: specimen of normal esophageal squamous mucosa collected from subject diagnosed with Barrett's esophagus with high grade dysplasia

value: Former smoker

value: BE-HGD


title: Developing Seed, 16DAF, lowGI (GQ01795)

city: Los Banos

last: Sreenivasulu

address: Metro Manila

country: Philippines

institute: IRRI

description: Gene expression of developing seed at 16 DAF(Days after fertilization)

hyb_protocol: Microarray hybridization was conducted in a SureHyb chamber assembly using the large-volume Hi-RPM Gene Expression Hybridization Kit. Hybridization was done in a hybridization oven set at 60°C rotating at 10 rpm for exactly 17 hours.

scan_protocol: Microarray slides with an ozone barrier slide cover were read by an Agilent SureScan microarray scanner controlled by Scan Control software using a scan resolution of 3 µm double pass. Raw data were generated from the TIFF file using Agilent Feature Extraction software. The quality of the data was judged per batch using the PDF QC report and as a group using QC Validation software.

data_processing:
The data were normalized using GeneSpring GX (Agilent, Santa Clara, CA) following the quantile normalization algorithm.
Differentially expressed genes (DEGs) between high GI vs intermediate GI and Intermediate vs Low GI was done.The Limma R package is used following the empirical Bayes method.The p-values adjustment method used was either Bonferroni.The top-ranked genes were selected having an p-value below 0.05 and fold change above ±1.

organism: Oryza sativa Indica Group

source_name: Developing seed,16(DAF)

label_protocol: Labelling was done using One-Color Microarray-Based Gene Expression Analysis protocol using a custom 8 x 60K microarray slide for rice (Agilent, Germany). cDNA synthesis and cRNA labelling were done using a single-color Low Input Quick Amp Labeling Kit following manufacturer's protocol.

growth_protocol: The rice accessions were grown during the 2015 dry season at IRRI using a phytotron glasshouse maintained with ambient light, 29°C/21°C day/night temperature, and 75-85% relative humidity. Soil preparation, fertilizer regime, pesticide application, and glasshouse maintenance were as previously described (Jagadish et al., 2011).

extract_protocol: Total RNA was extracted in a 2.0-mL RNAse-free tube from 200 mg pulverized seeds using 750 uL RNA extraction buffer (100 mM Tris-HCl pH 8.0, 150 mM LiCl, 50 mM EDTA and 1.5% SDS plus 1.5% β-mercaptoehanol freshly added before use) and 500 uL phenol:chloroform:isoamyl (25:24:1). RNA was precipitated from the supernatant at -20°C overnight using 700 µL isopropanol and 400 µL 1.2 M NaCl in a fresh 2-mL microfuge tube. The RNA pellet was re-suspended in 450 µL RLT buffer (Qiagen) with 10% β-mercaptoethanol and further purified using Qiagen RNeasy Plant Mini Kit based on the manufacturer’s recommendation (Qiagen, Germany). Purified total RNA extract was treated with RNAse-free DNAse (Qiagen, Germany) to ensure that no residual genomic DNA were present in the sample

treatment_protocol: No treatment was done. All rice lines were grown under optimum conditions as described in growth protocol. This is to catch any inherent transcriptomic variation within each accession.

value: Developing Seed

tag: type

value: GQ01795, lowGI


title: Striatum_A24-4

description:
processed data file:
RNAseq_featureCounts.csv.gz
sumstats_featureCounts.csv.gz
splicing_MATS_A3SS.csv.gz
splicing_MATS_A5SS.csv.gz
splicing_MATS_MXE.csv.gz
splicing_MATS_RI.csv.gz
splicing_MATS_SE.csv.gz
processed data column: B476_STRIATUM

source_name: Striatum_ASD 24

tag: strain background

value: colonized with Human feces (ASD)


title: Developing Seed, 16DAF, lowGI (GQ02497)

value: GQ02497, lowGI


title: Developing Seed, 16DAF, lowGI (GQ02522)

value: GQ02522, lowGI


title: pmk-1(km25) OP50 3

value: whole animal

tag: genotype

tag: bacterial exposure

tag: exposure length

value: 4 hours


title: Developing Seed, 16DAF, intermediateGI (GQ01818)

value: GQ01818, intermediateGI


title: NE_of_AA_with_BE#01

source_name: specimen of normal esophageal squamous mucosa collected from subject diagnosed with Barrett's esophagus with low grade dysplasia

value: African American with BE

value: female

value: African American

value: BE-LGD

value: normal esophageal squamous


title: Developing Seed, 16DAF, intermediateGI (GQ02364)

value: GQ02364, intermediateGI


title: Developing Seed, 16DAF, intermediateGI (GQ01908)

value: GQ01908, intermediateGI