hyb_protocol: cRNA targets were hybridized on high-density oligonucleotide gene chips (Affymetrix Human Genome U133 Plus 2.0 GeneChip arrays) according to the Affymetrix Eukaryotic Target  hybridization manual. The gene chips were washed and stained using the Affymetrix Fluidics Station 450/250 and Genechip Operating Software

scan_protocol: Chips were scanned by means of an Affymetrix GeneArray scanner

data_processing: The Affymetrix CEL files were imported into R v2.15.0 [24] using the “affy” library within BioConductor (v2.9). Probesets were reannotated to EntrezGene genes using the BrainArray custom CDF v15.0 annotations. The quality of the arrays was assessed through box plots, fitPLM, NUSE, RLE, clustering/heat maps, PCA and correlation plots. No technically deviating arrays were detected. Probeset intensities were normalized using the RMA algorithm. For detecting differentially expressed genes, the “limma” library was used to construct a linear model containing coefficients for all factor combinations. The resulting p-values were FWER-corrected using the False Discovery Rate (FDR) approach.

source_name: RNA from human primary hepatocytes

label_protocol: cDNA was prepared using the Affymetrix One-Cycle cDNA synthesis kit (Affymetrix, Santa Clara). cDNA synthesis and labeling was performed according to the manufacturer’s  rocedures. Subsequent labeling of the samples was conducted by synthesis of Biotin-labeled complementary RNA (cRNA) using the GeneChip IVT labeling kit (Affymetrix). Purified cRNA was quantified using a spectrophotometer, and unfragmented samples were checked on the Bioanalyzer. Subsequently, cRNA samples were fragmented for target preparation according to the Affymetrix manual and checked on the Bioanalyzer.Samples were stored at  20 C until ready to perform hybridization.

value: Primary human hepatocytes

tag: treatment

value: exposed to 1% ethanol for 5 days daily and subsequently to 3 days medium


title: Primary human hepatocyte 5 days 15 mM valproic acid and 3 days medium replicate 1

status: Public on Dec 15 2017

type: RNA

city: Maastricht

first: Simone

middle: G

last: van Breda

state: Limburg

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

label: Biotin

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cryopreserved primary human hepatocytes (PHH) and culture media were purchased from Life Technologies (Bleiswijk, The Netherlands), unless otherwise stated.PHH were cultured in pre-coated multi-well plates in a 2-layer collagen sandwich.PHH were thawed for 1 min at 37°C. Three vials (one per donor) were poured in 50 ml Thawing Medium (CHRM CM7000) and centrifuged at 4°C for 10 min at 100g. The cell pellet was dissolved in plating medium (CM9000) at a concentration of 1*10E6 cells/ml. After seeding, PHH were incubated in the pre-coated multi-well plates for 4 hours at 37°C. Next, debris was removed by shaking and washing the cells twice with Williams’ Medium E medium. Subsequently, PHH were covered by a collagen layer (containing DMEM, NaOH and rat tail Collagen type 1 (BD biosciences, Breda, The Netherlands)), incubated for 30 min at 37°C, and covered with incubation medium (CM600, CM4000).

extract_protocol: At the end of treatment, medium was removed and PHH were harvested in Qiazol (Qiagen). Total RNA was isolated using a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and followed by DNase I (Qiagen) treatment.

treatment_protocol: PHH were exposed to 15 mM of VPA in a 24 hour repeat-dose testing regime. Medium was changed daily thereby providing a new dose of VPA to the PHH each day. A bi-phasic treatment regime was applied, combining a 5-day VPA exposure with a subsequent 3-days washout period during which the PHH were exposed to medium only. 1% Ethanol was used as solvent control.

tag: cell type

value: exposed to 15 mM valproic acid for 5 days daily and subsequently to 3 days medium


title: Primary human hepatocyte 8 days control replicate 2


title: Primary human hepatocyte 5 days 15 mM valproic acid and 3 days medium replicate 2


title: Primary human hepatocyte 5 days control replicate 3

value: exposed to 1% ethanol for 5 days daily


title: LCTraf2DNIkB repl1

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

country: USA

institute: Eli Lilly and Company

description: 6120 -  536P LCTraf2DNIkB

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Standard Illumina BeadStudio plugin to GenomeStudio.

label: biotin

organism: Mus musculus

source_name: Myh6-TRAF2LC/Myh6-IκBαΔN double transgenic mice

label_protocol: Standard Illumina protocol

extract_protocol: Total RNA was extracted from hearts using the RNEasy Fibrous Tissue Midi kit (Qiagen, Valencia, CA), according to the manufacturer’s instructions.

tag: tissue

value: heart left ventricle

tag: gender

value: male

tag: genotype

value: Myh6-TRAF2LC/Myh6-IkappaBalphadeltaN double transgenic mice


title: Primary human hepatocyte 5 days 15 mM valproic acid replicate 2

value: exposed to 15 mM valproic acid for 5 days daily


title: LCTraf2DNIkB repl3

description: 6131 -  673P LCTraf2DNIkB


title: DNIkB repl1

description: 6125 -  621P DNIkB

source_name: mice overexpressing a mutated IκBα (IκBαΔN) under the control of the Myh6 promoter (Myh6-IκBαΔN)

value: mice overexpressing a mutated IkappaBalpha (IkappaBalphadeltaN) under the control of the Myh6 promoter (Myh6-IkappaBalphadeltaN)


title: Primary human hepatocyte 5 days 15 mM valproic acid and 3 days medium replicate 3


title: LCTraf2 repl1

description: 6123 -  622P LCTraf2

source_name: mice over expressing TRAF2 under the control of the Myh6 promoter (Myh6-TRAF2LC)


title: Normal mucosa tissue 6

status: Public on Dec 14 2017

city: Guangzhou

first: Yan

last: Zhang

state: Guangdong

address: 1838 north guangzhou avenue

country: China

institute: southern medical university, nanfang hospital

description: Total circular RNA was spotted on 5396 spots. 3071 spots were eliminated from the whole spot data.

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software..

source_name: Normal mucosa tissue 6

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000.

value: gastric mucosa tissue

tag: status after 1 years

value: Recurrence-free


title: Normal mucosa tissue 5

source_name: Normal mucosa tissue 5


title: LCTraf2 repl2

description: 6129 -  665P LCTraf2

value: mice over expressing TRAF2 under the control of the Myh6 promoter (Myh6-TRAF2LC)


title: LCTraf2DNIkB repl2

description: 6130 -  669P LCTraf2DNIkB


title: littermate control repl4

description: 6135 -  535P LM

source_name: Littermate control

value: Littermate control


title: Primary human hepatocyte 5 days 15 mM valproic acid replicate 3


title: DNIkB repl2

description: 6126 -  537P DNIkB


title: DNIkB repl3

description: 6127 -  538P DNIkB


title: Primary human hepatocyte 8 days control replicate 1


title: Primary human hepatocyte 5 days control replicate 2


title: Primary human hepatocyte 5 days 15 mM valproic acid replicate 1


title: Primary human hepatocyte 5 days control replicate 1


title: DNIkB repl4

description: 6134 -  623P DNIkB


title: LCTraf2DNIkB repl4

description: 6133 -  668P LCTraf2DNIkB


title: LCTraf2 repl3

description: 6132 -  675P LCTraf2


title: littermate control repl3

description: 6128 -  663P LM


title: littermate control repl1

description: 6121 -  617P LM


title: LCTraf2 repl4

description: 6155 -  618P LCTraf2


title: littermate control repl2

description: 6124 -  624P LM


title: Normal mucosa tissue 4

source_name: Normal mucosa tissue 4


title: Normal mucosa tissue 1

source_name: Normal mucosa tissue 1

value: Recurrence


title: Tumour tissue 6

source_name: Tumour tissue 6

value: primary gastric cancer


title: Normal mucosa tissue 3

source_name: Normal mucosa tissue 3


title: Normal mucosa tissue 2

source_name: Normal mucosa tissue 2


title: Tumour tissue 5

source_name: Tumour tissue 5


title: CTS_149

type: SRA

city: Oxford

first: Georgios

last: Baskozos

address: Level 6, West Wing, John Radcliffe Hospital

department: NDCN

country: United Kingdom

institute: Oxford University

library_source: transcriptomic

data_processing:
Sequencing, base calling, demultiplexing and QC using Illumina HiSeq4000 analysis software version HD 3.4.0.38
Demux of files and FastQ preparation by BcltoFastq 2.17.1.14
Reads were mapped to GRCh38 human genome (Homo_sapiens.GRCh38.dna.primary_assembly.fa, Homo_sapiens.GRCh38.88.chr.gtf) using STAR aligner
BAM files were merged across sequencing lanes and sorted using SAMtools
Features were counted using HTSeq with the intersection not empty strategy
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV file ens_genes_toc.csv includes read-pairs counts calculated using HTSeq.

molecule: polyA RNA

source_name: Tenosynovium sourced during CTS decompression surgery

extract_protocol:
Specimens were immersed in RNAlaterTM Stabilization Solution (Thermo Fisher Scientific) and stored at -80°C. RNA was extracted using a combination of the phenol extraction and column purification. Briefly, samples were homogenised in Trizol (Invitrogen), mixed with chloroform and centrifuged in order to collect the aqueous liquid phase. This solution was placed on High Pure RNA Isolation Kit (Roche) columns and subjected to multiple washes to purify the RNA sample, as per the manufacturers instructions.
Library preparation was polyA enriched and directional, using Illumina TruSeq Stranded mRNA and standard universal Illumina multiplexing adapters: 5' P-GATCGGAAGAGCACACGTCT and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT. The poly-A selected RNA was converted to cDNA using the strand-specific (deoxy-UTP strand-marking protocol) dUTP (Borodina et al., 2011) protocol. Amplification was performed by unique dual indexing using indexing primers described elsewhere71. Sequencing was performed using HiSeq4000 with 75bp read length and paired end reads. Healthy skin samples and CTS tenosynovium samples were extracted and sequenced using the same protocol but in different library batches.    Oxford Genomics produced FastQ sequencing files which encode quality metrics following the Sanger standard, i.e. Sanger qualities, using the standard Phred score (Ewing and Green, 1998). All sequencing lanes gave high yield, consistent GC content, consistent and expected sequence insert between the paired-end adapters and high quality base calling.  Individuals were multiplexed in lanes.

treatment_protocol: We collected tenosynovium from 41 patients from the PiNS cohort during their carpal tunnel decompression surgery. We also collected skin samples for 6 individuals recruited as helathy controls for the PiNS cohort.

tag: genome build

tag: condition

value: CTS


title: CTS_131


title: CTS_45

source_name: Skin sample from healthy individual

value: Healthy controls


title: CTS_155


title: CTS_148


title: CTS_143


title: CTS_70


title: CTS_48


title: CTS_132


title: CTS_40


title: CTS_63


title: CTS_133


title: CTS_145


title: CTS_141


title: Tumour tissue 3

source_name: Tumour tissue 3


title: CTS_147


title: CTS_159


title: CTS_130


title: Tumour tissue 4

source_name: Tumour tissue 4


title: CTS_142


title: Tumour tissue 2

source_name: Tumour tissue 2


title: CTS_203


title: CTS_77


title: CTS_128


title: Tumour tissue 1

source_name: Tumour tissue 1


title: CTS_202


title: CTS_146


title: CTS_193


title: CTS_182


title: CTS_199


title: CTS_198


title: CTS_188


title: CTS_187


title: CTS_200


title: CTS_195


title: CTS_186


title: CTS_151


title: CTS_181


title: CTS_194


title: CTS_197


title: CTS_176


title: CTS_177


title: CTS_175


title: CTS_170


title: CTS_178


title: CTS_168


title: CTS_166


title: CTS_164


title: CTS_160


title: HF_with_deband_repl3

description:
7989 - R_52
heart after TAC+MI at 0 wk and TAC removal at 2 wk, harvest at 6 wk, repl 3

data_processing: Standard Illumina BeadStudio plugin to GenomeStudio. Average normalization was applied to signal values.

label_protocol: Standard Illumina label protocol

extract_protocol: RNA was extracted from flash-frozen cardiac left ventricle sections using an Ika Turrax homogenizer and Trizol as per the manufacturer's directions.

tag: strain

value: female

tag: age

value: 13 wk


title: HF_with_sham_deband_repl6

description:
7982 - HF_23
heart after TAC+MI at 0 wk and sham surgery at 2 wk, harvest at 6 wk, repl 6


title: CTS_162


title: HF_with_sham_deband_repl2

description:
7983 - HF_34
heart after TAC+MI at 0 wk and sham surgery at 2 wk, harvest at 6 wk, repl 2


title: HF_with_sham_deband_repl4

description:
7984 - HF_40
heart after TAC+MI at 0 wk and sham surgery at 2 wk, harvest at 6 wk, repl 4


title: sham_surgeries_repl3

description:
7976 - SM_58
heart after sham surgeries at 0 wk and 2 wk, harvest at 6 wk, repl 3


title: HF_with_sham_deband_repl1

description:
7985 - HF_56
heart after TAC+MI at 0 wk and sham surgery at 2 wk, harvest at 6 wk, repl 1


title: HF_with_deband_repl4

description:
7990 - R_53
heart after TAC+MI at 0 wk and TAC removal at 2 wk, harvest at 6 wk, repl 4


title: HF_with_deband_repl2

description:
7991 - R_54
heart after TAC+MI at 0 wk and TAC removal at 2 wk, harvest at 6 wk, repl 2


title: HF_with_sham_deband_repl5

description:
7986 - HF_63
heart after TAC+MI at 0 wk and sham surgery at 2 wk, harvest at 6 wk, repl 5


title: sham_surgeries_repl6

description:
7979 - SM_66
heart after sham surgeries at 0 wk and 2 wk, harvest at 6 wk, repl 6


title: HF_with_sham_deband_repl3

description:
7981 - HF_19
heart after TAC+MI at 0 wk and sham surgery at 2 wk, harvest at 6 wk, repl 3


title: HF_with_deband_repl5

description:
7987 - R_1
heart after TAC+MI at 0 wk and TAC removal at 2 wk, harvest at 6 wk, repl 5


title: HF_with_deband_repl6

description:
7992 - R_55
heart after TAC+MI at 0 wk and TAC removal at 2 wk, harvest at 6 wk, repl 6


title: HF_with_deband_repl1

description:
7988 - R_22
heart after TAC+MI at 0 wk and TAC removal at 2 wk, harvest at 6 wk, repl 1


title: sham_surgeries_repl5

description:
7975 - SM_57
heart after sham surgeries at 0 wk and 2 wk, harvest at 6 wk, repl 5


title: KO rep1

city: Stockholm

first: kun

last: wang

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

country: Sweden

institute: Stockholms Universitet

data_processing:
Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite
Sequence reads were first trimmed to remove sequencing adaptors by cutadapt 1.9.1 and reads shorter than 20 nt were discarded.
Processed  reads were then mapped to the Sulfolobus acidocaldarius DSM639 genome (NC_007181.1) with Tophat 2.0.12 with parameters: “--no-novel-juncs --no-discordant and --no-mixed --max-multihits 1"
Read counts for each gene was obtained by featureCounts function in subread R package, only the genes having at least one count in all samples were used for  differential gene expression analysis with DESeq2
Genome_build: Sulfolobus acidocaldarius DSM639 genome (NC_007181.1)
Supplementary_files_format_and_content: raw counts of sequencing reads
Supplementary_files_format_and_content: DEseq2 output file

organism: Sulfolobus acidocaldarius DSM 639

source_name: cell

growth_protocol: Sulfolobus acidocaldarius strains MW001 and its derivates were cultivated in Brock basal salts medium supplemented with 0.2 (w/v)% sucrose, 0.2 (w/v)% NZamine and 10 ug ml-1 uracil at 80 Celsius degree and pH 2.

extract_protocol:
Total RNA samples were extracted by miRNeasy Mini Kit (Qiagen)
sequencing libraries were prepared with TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s protocol (#15031047,rev E) with the exception that no polyA selection was performed.
Paired-end (2×125 bp) RNA sequencing was performed using a Hiseq2500 system (Illumina)

treatment_protocol: cells were pelleted from WT and KO cultures in early exponential growth phase at an OD600 between 0.2 and 0.3.

value: saci_1107 knock out


title: sham_surgeries_repl2

description:
7980 - SM_67
heart after sham surgeries at 0 wk and 2 wk, harvest at 6 wk, repl 2


title: KO rep2


title: WT rep2

value: wild type


title: WT rep1


title: CTS_169


title: sham_surgeries_repl1

description:
7977 - SM_61
heart after sham surgeries at 0 wk and 2 wk, harvest at 6 wk, repl 1

value: heart left ventricle


title: sham_surgeries_repl4

description:
7978 - SM_65
heart after sham surgeries at 0 wk and 2 wk, harvest at 6 wk, repl 4


title: EV_Ctrl_rep3_RNAseq

status: Public on Dec 13 2017

city: Freiburg

first: Ritwick

last: Sawarkar

address: 51 Stubeweg

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
RNA-seq reads were trimmed and mapped to Ensembl annotation release 78 with TopHat2
Unique reads were counted with featureCounts and DESeq2 was used for differential gene expression analysis.
Genome_build: Hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample, differential gene expression analysis

growth_protocol: Human HEK293T cells were cultured in Dulbecco's Modified Eagle's medium (DMEM; Biochrom) supplemented with 10% FBS (Gibco), 1% Penicillin-streptomycin (Gibco) and 1% L-glutamine (Gibco) at 37C in an atmosphere of 5% CO2.

extract_protocol:
RNA was extracted in using the RNA Clean & Concentrator kit (Zymo Research, cat. no. R1013) according to the manufacturer’s protocol.
TruSeq Stranded mRNA library prep kit (Illumina cat. no. RS-122-2101)

treatment_protocol: HEK293T cells were transfected with a total of 1ug in 6-well plates using FuGene 6 tranfection reagent (Promega) following the manufacturer's protocol.

tag: cell line

tag: genotype/variation

value: control


title: ERbeta_rep1_RNAseq

source_name: ERbeta

value: ERbeta expression


title: ERbeta_rep3_RNAseq


title: EV_Ctrl_rep2_RNAseq


title: resident_microglia_GFP_22

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyi Biotec GmbH

hyb_protocol: Cy3 labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (8x60K, Design ID 028005) using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: ischemic brain tissue, 30min MCAo, 7d reperfusion

label_protocol: 250 ng of each of the amplified cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Samples were derived from bone marrow chimeric mice which had been subjected to 30 minutes focal brain ischemia followed by 7 days of reperfusion

extract_protocol: RNA was extracted using the NucleoSpin® RNA kit (Macherey & Nagel) following manufacturer's instructions. SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

treatment_protocol: No specific treatment

tag: animal (individual)

value: D

tag: fluorescence sorting marker

value: GFP +

value: resident microglia


title: 9082853 [LUM0455]

city: Leiden

first: Lodewijk

last: Toonen

address: einthovenweg 20

department: human genetics

institute: LUMC

data_processing:
Primary processing and base calling was performed with Illumina’s HCS and RTA. Demultiplexing and generation of FASTQ files was done with Illumina scripts (bcl2fastq v1.8).
Analysis of sequencing data was performed using the BIOPET Gentrap in-house pipeline (http://biopet-docs.readthedocs.io/en/v0.7.0/pipelines/gentrap/) The fastqc toolkit (v0.11.2) was used to evaluate sequencing quality (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Sickle (v1.33 with default settings) and Cutadapt (v1.10, with default settings except for “-m 20”) were used to clean up reads.
Cleaned reads were aligned to the mouse reference genome build 10 (GRCm38/mm10) using STAR aligner version 2.3.0e
The non-default settings used by STAR are “--outFilterMultimapNmax 1 –outFilterMismatchNmax 10 –outSJfilterReads Unique”.
Gene raw read counts are generated using HTSeq (v0.6.1) with the Refseq gene annotation extracted from UCSC on 11-09-2015. The non-default settings used by HTSeq are “--format bam –stranded no”. Gene expression analysis was performed using edgeR (v 3.14.0). The normalization was performed using the trimmed mean of M-values (TMM) normalization method.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited file (Counts_min4cpm.tab.gz) include CPM values for each Sample. Only genes exceeding 4 counts per million (CPM) across all samples are listed.

source_name: striatum

growth_protocol: MJD84.2 transgenic SCA3 mice and wild-type C57BL/6 mice were obtained from Jackson Laboratories (Bar Harbor, Maine, USA) and bred at the Leiden University Medical Center. Only male mice were used. Mice were group housed in individually ventilated cages with food and drinking water available ad libitum. Mice were aged to 17.5 months of age.

extract_protocol:
Brains were isolated directly after sacrifice and brainstem, cerebellum, cortex and striatum were dissected and snapfrozen in liquid nitrogen. Approximately 30mg of tissue was used for RNA isolation, using Trizol and the PureLink RNA mini column kit (Thermo Fisher Scientific) according to manufacturers instruction. RNA was treated with DNAse to remove contamination of genomic DNA. Isolated RNA was shipped to DeCode Genetics (Reykjavik, Iceland) for RNA sequencing.
quality of RNA was assessed with the LabChip GX using the 96-well RNA kit (Perkin Elmer). Approximately 1 µg of total RNA was used as starting material, and the average RIN values were 7.7. Non strand-specific sample preparation was performed using the TruSeq Poly-A v2 kit (Illumina, San Diego, USA) following manufacturer’s instructions. In brief, mRNA was captured using magnetic poly-T oligo-attached magnetic beads, RNA molecules were fragmented, and cDNA synthesis was performed using SuperScript II (Invitrogen, Carlsbad CA, USA) with random hexamer primers. Subsequently, 2nd strand cDNA synthesis was performed in conjunction with RNAse-H treatment. End repair was performed to generate blunt ends and 3′ adenylation was performed, followed by ligation of indexing adapters to the ds-cDNA. PCR was performed to amplify the fragments. Quality of sequencing libraries was determined through pool sequencing on a MiSeq instrument (Illumina) to assess insert size, sample diversity and optimize cluster densities. Pooled samples (4 samples/pool) were clustered on paired-end (PE) flowcells (1 pool per lane) using a cBot instrument (Illumina). The sequencing was performed using a HiSeq 2500 with v4 SBS sequencing kits (read lengths 2x125 cycles).

treatment_protocol: Mice were not treated in this study, but aged naturally to 17.5 months of age. All mice were exposed to behavioral tests (beamwalk and rotarod) at 4, 6, 7.5, 9 and 12 months of age, but the ataxic phenotype was not detected in the SCA3 mice.

tag: age in weeks

tag: bodyweight

tag: rin value

value: striatum

value: SCA3 transgenic


title: invading_macrophages_RFP_11

value: B

value: RFP +

value: invading macrophages


title: 9083514 [LUM0461]

source_name: brainstem

value: brainstem


title: 9082853 [LUM0456]

source_name: cortex

value: cortex


title: 9083513 [LUM0458]

source_name: cerebellum

value: cerebellum


title: invading_macrophages_RFP_17


title: resident_microglia_GFP_10


title: 9083513 [LUM0457]


title: resident_microglia_GFP_16

value: C


title: 9083513 [LUM0460]


title: invading_macrophages_RFP_07

value: A


title: 9083515 [LUM0468]


title: 9083515 [LUM0467]


title: 9083515 [LUM0466]


title: 9083514 [LUM0464]


title: 9083515 [LUM0465]


title: 9082853 [LUM0453]


title: 7267056 [LUM0452]


title: 7267056 [LUM0451]


title: 7267056 [LUM0450]


title: 9083514 [LUM0462]


title: invading_macrophages_RFP_13


title: 9083514 [LUM0463]


title: resident_microglia_GFP_06


title: 9082853 [LUM0454]


title: Kidney_1doseCis

city: New Haven

first: Robert

last: Safirstein

state: Connecticut

address: 333 Cedar Street

department: Internal Medicine (Nephrology)

institute: Yale University School of Medicine

description:
sample represents mean of 3 mice
Raw data column IDs: WK2_H004, WK2_H005, WK2_H006

hyb_protocol: 5μg of Cy5-labeled aRNA was hybridized according to the Phalanx OneArray Plus protocol

scan_protocol: Agilent 0.1 XDR Protocol

data_processing: Signal segmented (GPR) files were loaded into Rosetta Resolver® System (Rosetta Biosoftware) to process data analysis. The following data processing was performed: Rosetta profile error model calculation, squeeze replicated probes, normalize intensities (median scaling without flagged and control data), Pearson's correlation coefficient, and merge technical replicate data.

source_name: Kidney, 15mg/kg dose cisplatin

label_protocol: Target preparation was performed using an Eberwine-based amplification method with Amino allyl MessageAmpII aRNA Amplification kit (Ambion, AM1753) to generate amino-allyl antisense RNA (aa-aRNA). Labeled aRNA coupled with NHS-CyDye was prepared and purified prior to hybridiczation.

growth_protocol: Tissue was harvested from mice and stored at -80C prior to RNA extraction.

extract_protocol: RNA was extracted using the RNeasy® kit from QiaGen according to the manufacturer's protocol.

treatment_protocol: Mice received an intraperitoneal injection of either a single dose of saline (control), a single dose (15mg/kg) of cisplatin, or two doses (15mg/kg) of cisplatin administered two weeks apart.

value: 8-10 weeks

value: Kidney


title: 7267056 [LUM0449]


title: Kidney_Control

description:
sample represents mean of 3 mice
Raw data column IDs: WK0_H001,WK0_H002,WK0_H003

source_name: Kidney, saline


title: 7267054 [LUM0448]


title: Kidney_2doseCis

description:
sample represents mean of 3 mice
Raw data column IDs: WK4_H007,WK4_H008, WK4_H009

source_name: Kidney, two 15mg/kg doses of cisplatin administed 2 weeks apart


title: 9083375 [LUM0444]

value: wildtype


title: 9083373 [LUM0438]


title: 9083373 [LUM0437]


title: 7267054 [LUM0447]


title: 9083375 [LUM0442]


title: 9083375 [LUM0443]


title: 9083371 [LUM0431]


title: 7267054 [LUM0446]


title: 7267054 [LUM0445]


title: 9083373 [LUM0439]


title: 9083371 [LUM0429]


title: 9083373 [LUM0440]


title: 9083375 [LUM0441]


title: 9083371 [LUM0430]


title: 9082857 [LUM0428]


title: 9082857 [LUM0426]


title: 9082857 [LUM0427]


title: 9083371 [LUM0432]


title: 7267059 [LUM0422]


title: 7267059 [LUM0421]


title: 9082857 [LUM0425]


title: 7267059 [LUM0423]


title: 9083372 [LUM0436]


title: 9083372 [LUM0434]


title: 9083372 [LUM0435]


title: 9083372 [LUM0433]


title: 7267058 [LUM0417]


title: 7267055 [LUM0415]


title: 7267055 [LUM0416]


title: 7267058 [LUM0419]


title: BCGiv_Mtb_input_rep3

city: Chicago

first: Luis

last: Barreiro

state: Illinois

address: 900 E 57th Street

institute: University of Chicago

library_source: genomic

data_processing:
Adapter sequences and low quality score bases (Phred score < 20) were first removed from reads.
Trimmed reads were mapped to the mouse genome reference sequence (GRCm38/mm10) and non-uniquely mapped reads and PCR duplicates were removed.
Peaks were first called on ChIP-seq samples (using respective input IPs as a control) using the MACS2 software suite (Zhang et al., 2008) with the added parameters “g mm -q 0.05 -keep-dup all”. For comparison between samples, all peaks from each sample were merged to provide one set of combined peaks. For quantification of the combined peaks, we used the bamutils count command from NGSUtils (Breese and Liu, 2013) to count the number of overlapping reads for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include read count, CPM and RPKM values for each sample.

molecule: genomic DNA

source_name: Bone marrow-derived macrophages

growth_protocol: Six- to ten-week old C57BL/6J, Rag1-/-, Ccr2-/-, and CD45.1+ B6 mice were purchased from Jackson Laboratories or bred at the RI-MUHC, Montreal, QC,Canada. All experiments were performed with male mice, except parabiosis, which was performed on female mice. All animal studies were conducted in accordance with the guidelines of and approved by the Animal Research Ethics Board of McGill University (project ID: 5860). Throughout the paper, mice were intravenously (iv) or subcutaneously (sc) vaccinated with 1x106 single-suspended BCG in 100µl PBS, unless otherwise indicated. Image stream analyses were used to identify what cells in the BM were infected with BCG. For the Mtb challenges, mice were either infected with ~50 CFU of Mtb H37Rv in a nose-only aerosol exposure unit (Intox), or with ~1000 CFU Mtb H37Rv via intratracheal instillation. BMDMs were derived as described previously (Coulombe et al., 2014).

extract_protocol:
DNA was extracted using the PureGene DNA extraction kit (Gentra Systems).
Samples from BCGvaccinated and non-vaccinated, Mtb-infected and non-infected BMDMs were crosslinked with 37% w/v formaldehyde for 20 minutes at RT and immediately quenched for 5 minutes with 1M Glycine at RT. The formaldehyde fixed samples were then sonicated to 150500 bp using an E220 sonicator (Covaris), and subsequently ChIP-DNA was prepared using a manual chromatin immunoprecipitation method with AntibodiesAntigen incubation for 18 hours, followed by bead incubation for 150 minutes, and 7 5minute washing steps. Approximately 1x106 cells were used for each ChIP and ~50,000 cells for the input. The following antibodies were used: H3K4me1 (Company: CST, Cat. No.: 5326P, Lot No.: 1), H3K4me3 (Thermo Fisher Scientific, MA5-11199), H3K27ac (Abcam, Ab4729, Lot No.: GR2005631). ChIP and Input libraries were prepared using the MicroPlex Library Preparation Kit v2 (C05010013, Diagenode), with alterations including: PCR enrichment (9 to 18 cycles) prior to size selection, and use of Ampure beads for size selection (250-350 bp).

treatment_protocol: BMDMs (1x10^6 cells) were seeded in 6-well plates supplemented with RPMI without penicillin/streptomycin (1 ml), and incubated overnight at 37°C with 5% CO2. Next day, cells were infected with H37Rv (MOI 1), unless otherwise indicated. Cells were incubated for 4 hours at 37°C with 5% CO2. Subsequently, cells were washed 3x with sterile PBS, and then were supplemented with RPMI without penicillin/streptomycin. CFUs were enumerated at 4 hours, day 3 and day 5 post infection.

tag: histone mark

value: Input

tag: treatment

value: BCG iv

tag: infection

value: Mtb

tag: mouse id


title: PBSiv_NI_input_rep2

value: PBS iv

value: Non Infected


title: PBSiv_Mtb_input_rep2


title: 7267055 [LUM0413]

tag: tissue


title: PBSiv_NI_input_rep3


title: BCGiv_NI_input_rep3


title: 7267058 [LUM0420]


title: 7267055 [LUM0414]


title: BCGiv_NI_input_rep2


title: in vivo induced neuron 2

city: Columbus

first: Sashwati

last: Roy

state: OH

department: Surgery

institute: Ohio State University

description: murine transcriptome array (MTA 1.0)

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/ml), BioArray Eukaryotic Hybridization Controls (Affymetrix). Heat 65°C for 5 mins, 99°C for 5 mins, 45°C for 5 mins, centrifuge top speed for 5 mins. Hybridize 16hours at 45°C at 60rpm. Fluidics washing is  FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G using AGCC (Affymetrix GeneChip Command Console)

data_processing: For gene expression analysis, arrays were normalized using RMA16 algorithm in Expression Console and analysed using Genespring GX (Agilent, Santa Clara CA). Additional processing of data was performed using dChip® software (Harvard University)

source_name: in vivo induced neuron

label_protocol: Samples were enzymatically fragmented and biotinylated using the Bioarray Highyield RNA Transcript Labeling Kit (Affymetrix)

growth_protocol: induced neueon cultures were maintained in polylysine-coated plates with DMEM/F12/N2 media supplemented with 10 ng/ml of FGF. Cells were incubated at 37 C under a humidified atmosphere with 5% CO2.

extract_protocol: Extraction of total RNA was performed using PicoPure isolation kit according to the manufacturer's instructions.

treatment_protocol: In vitro cultures of iNs were prepared for comparison purposes via non-viral, electroporation-based transfection of ABM into mouse fibroblasts. Laser capture microdissection was used to prepare tissue isolates enriched for induced neurons (iNs) from mouse skin transfected with Ascl1, Brn2 and Myt1l (ABM)

tag: cell type

value: neuron


title: in vivo induced neuron 1

description: murine transcriptome array (MTA 1.0)


title: in vitro induced neuron 3

description: murine transcriptome array (MTA 1.0)

source_name: in vitro induced neuron


title: BCGiv_Mtb_input_rep2


title: PBSiv_NI_input_rep1


title: in vitro induced neuron 2

description: murine transcriptome array (MTA 1.0)


title: in vivo induced neuron 3

description: murine transcriptome array (MTA 1.0)


title: in vitro induced neuron 4

description: murine transcriptome array (MTA 1.0)


title: BCGiv_NI_input_rep1


title: BCGiv_Mtb_input_rep1


title: in vitro induced neuron 1

description: murine transcriptome array (MTA 1.0)


title: YF-17D virus NS4B-214 epitope specific human memory CD8 T cells F02

city: Atlanta

first: Rama

middle: S

last: Akondy

state: GA

address: 1462 CLifton Rd

department: Emory Vaccine Center

institute: Emory University

description:
CD3+CD8+ T cells isolated from donors using the YF-NS4B214 tetramers 5 to 8 months after the donors were vaccinated with YF-17D.
Set3MemoryF02

hyb_protocol: After hybridization on Affymetrix Human Genome U133 Plus 2.0 Arrays [HG-U133_Plus_2] or HGU133 A arrays (for set3 only) for 16 h at 45 °C and 60 r.p.m. in a Hybridization Oven 640 (Affymetrix), slides were washed and stained with a Fluidics Station 450 (Affymetrix).

scan_protocol: Scanning was performed on a seventh-generation GeneChip Scanner 3000 (Affymetrix).

data_processing: Scanning was performed on a seventh-generation GeneChip Scanner 3000 (Affymetrix), and Affymetrix GCOS software was used to perform image analysis and generate raw intensity data. Normalization and summarization was done using RMA in the Genespring GS 11 software.

source_name: Human PBMCs isolated from whole blood (Donor E07)

label_protocol: Two-round in vitro transcription amplification and labeling was performed starting with 50ng intact, uncontaminated total RNA per sample, following the Affymetrix protocol.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.Since cell numbers were small, the manufacturer's protocol including glycogen as a carrier was used.

tag: donor

value: T lymphocytes isolated from PBMC

value: 18-45 years


title: YF-17D virus NS4B-214 epitope specific human memory CD8 T cells E06

description:
CD3+CD8+ T cells isolated from donors using the YF-NS4B214 tetramers 5 to 8 months after the donors were vaccinated with YF-17D.
Set3MemoryE06

source_name: Human PBMCs isolated from whole blood (Donor H01)


title: YF-17D virus NS4B-214 epitope specific human memory CD8 T cells H09

description:
CD3+CD8+ T cells isolated from donors using the YF-NS4B214 tetramers 5 to 8 months after the donors were vaccinated with YF-17D.
Set3MemoryH09

source_name: Human PBMCs isolated from whole blood (Donor KER)

value: KER


title: YF-17D virus NS4B-214 epitope specific human memory CD8 T cells G08

description:
CD3+CD8+ T cells isolated from donors using the YF-NS4B214 tetramers 5 to 8 months after the donors were vaccinated with YF-17D.
Set3MemoryG08


title: YF-17D virus NS4B-214 epitope specific human memory CD8 T cells B03

description:
CD3+CD8+ T cells isolated from donors using the YF-NS4B214 tetramers 5 to 8 months after the donors were vaccinated with YF-17D.
Set3MemoryB03

source_name: Human PBMCs isolated from whole blood (Donor F06)


title: Human Naïve CD8 T cells G06

description:
Naïve CD3+ CD8+ T cells isolated by their CCR7+ CD45RA+ phenotype.
Set3NaiveG06


title: Human Naïve CD8 T cells D04

description:
Naïve CD3+ CD8+ T cells isolated by their CCR7+ CD45RA+ phenotype.
Set3NaiveD04

source_name: Human PBMCs isolated from whole blood (Donor F01)


title: Human Naïve CD8 T cells C09

description:
Naïve CD3+ CD8+ T cells isolated by their CCR7+ CD45RA+ phenotype.
Set3NaiveC09


title: YF-17D virus NS4B-214 epitope specific human memory CD8 T cells A09

description:
CD3+CD8+ T cells isolated from donors using the YF-NS4B214 tetramers 5 to 8 months after the donors were vaccinated with YF-17D.
Set3MemoryA09


title: YF-17D virus NS4B-214 epitope specific human effector CD8 T cells A08

description:
CD3+CD8+ T cells isolated from donors using the YF-NS4B214 tetramers 14 or 15 days after the donors were vaccinated with YF-17D.
Set2EffectorA08

source_name: Human PBMCs isolated from whole blood (Donor BLS)

value: BLS


title: YF-17D virus NS4B-214 epitope specific human effector CD8 T cells A07

description:
CD3+CD8+ T cells isolated from donors using the YF-NS4B214 tetramers 14 or 15 days after the donors were vaccinated with YF-17D.
Set2EffectorA07

source_name: Human PBMCs isolated from whole blood (Donor EEB)

value: EEB


title: YF-17D virus NS4B-214 epitope specific human effector CD8 T cells A06

description:
CD3+CD8+ T cells isolated from donors using the YF-NS4B214 tetramers 14 or 15 days after the donors were vaccinated with YF-17D.
Set2EffectorA06

source_name: Human PBMCs isolated from whole blood (Donor MRR)

value: MRR


title: YF-17D virus NS4B-214 epitope specific human effector CD8 T cells A05

description:
CD3+CD8+ T cells isolated from donors using the YF-NS4B214 tetramers 14 or 15 days after the donors were vaccinated with YF-17D.
Set2EffectorA05

source_name: Human PBMCs isolated from whole blood (Donor BAW)

value: BAW


title: Human Naïve CD8 T cells A03

description:
Naïve CD3+ CD8+ T cells isolated by their CCR7+ CD45RA+ phenotype.
Set2NaiveA03


title: YF-17D virus specific human effector CD8 T cells 9

description: Activated HLA-DR+ CD38+ CD3+ CD8+ T cells isolated from donors15 days after vaccination with YF-17D.

hyb_protocol: After hybridization on Affymetrix Human Genome U133 Plus 2.0 Arrays [HG-U133_Plus_2] for 16 h at 45 °C and 60 r.p.m. in a Hybridization Oven 640 (Affymetrix), slides were washed and stained with a Fluidics Station 450 (Affymetrix).

data_processing:
Affymetrix GCOS software was used to perform image analysis and generate raw intensity data.Normalization and summarization was done using fRMA (Biostatistics. 2010 Apr;11(2):242-53) (NaiveCD8 1-4) or RMA (NaiveCD8 5-9 and effector CD8 1-9).
The software used for fRMA was R (the R project for statistical computing). The RMA intensities are centered because they were generated in GeneSpring GX 11.0 using the guided workflow which uses a Baseline transformation (BT), a row-wise transformation where for a given row, you compute the median and subtract that median value from all the observations of that row. This transformation is done for better visualization of the data.

source_name: Human PBMCs isolated from whole blood (Donor 1909)

value: In vivo activated T lymphocytes (effector CD8 T cells) isolated from PBMC

tag: t-cell phenotype

value: HLA-DR+CD38+ CD3+CD8+


title: YF-17D virus specific human effector CD8 T cells 3

source_name: Human PBMCs isolated from whole blood (Donor 1911)


title: YF-17D virus specific human effector CD8 T cells 8

source_name: Human PBMCs isolated from whole blood (Donor 1908)


title: Human Naïve CD8 T cells A02

description:
Naïve CD3+ CD8+ T cells isolated by their CCR7+ CD45RA+ phenotype.
Set2NaiveA02


title: YF-17D virus specific human effector CD8 T cells 5

source_name: Human PBMCs isolated from whole blood (Donor 1915)


title: Human Naïve CD8 T cells A01

description:
Naïve CD3+ CD8+ T cells isolated by their CCR7+ CD45RA+ phenotype.
Set2NaiveA01


title: Human Naïve CD8 T cells 8

description: Naïve CD3+ CD8+ T cells isolated by their CCR7+ CD45RA+ phenotype.

value: T lymphocytes (naïve CD8 T cells) isolated from PBMC

value: CD45RA+ CCR7+ CD3+ CD8+


title: YF-17D virus specific human effector CD8 T cells 7

source_name: Human PBMCs isolated from whole blood (Donor 1907)


title: Human Naïve CD8 T cells 9


title: YF-17D virus specific human effector CD8 T cells 1

source_name: Human PBMCs isolated from whole blood (Donor 1901)


title: Human Naïve CD8 T cells 5


title: YF-17D virus specific human effector CD8 T cells 6

source_name: Human PBMCs isolated from whole blood (Donor 1904)


title: YF-17D virus specific human effector CD8 T cells 2

source_name: Human PBMCs isolated from whole blood (Donor 1906)


title: Human Naïve CD8 T cells 6


title: scalp_healthy_rep12

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays (8x60K v2, Design ID 039494) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

source_name: scalp biopsie

label_protocol: 100 ng total RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: ex vivo biopsies

extract_protocol: Human total RNA was isolated from the tissue samples with the use of Trizol (Sigma-Aldrich).

treatment_protocol: No treatment

tag: disease state

value: healthy control


title: scalp_healthy_rep10


title: scalp_healthy_rep13


title: Human Naïve CD8 T cells 7

tag: age


title: scalp_healthy_rep11


title: YF-17D virus specific human effector CD8 T cells 4

source_name: Human PBMCs isolated from whole blood (Donor 1914)


title: Human Naïve CD8 T cells 4


title: scalp_healthy_rep14


title: Human Naïve CD8 T cells 3


title: Human Naïve CD8 T cells 1


title: Human Naïve CD8T cells 2


title: scalp_healthy_rep9


title: scalp_healthy_rep5


title: scalp_healthy_rep6


title: scalp_healthy_rep7


title: scalp_healthy_rep3


title: scalp_healthy_rep8


title: scalp_healthy_rep2


title: scalp_alopecia_rep13

value: alopecia


title: scalp_alopecia_rep10


title: scalp_healthy_rep4


title: scalp_alopecia_rep11


title: scalp_alopecia_rep8


title: scalp_alopecia_rep6


title: scalp_alopecia_rep5


title: scalp_alopecia_rep7


title: scalp_alopecia_rep4


title: scalp_alopecia_rep3


title: scalp_healthy_rep1


title: scalp_alopecia_rep1


title: scalp_alopecia_rep9


title: scalp_alopecia_rep14


title: scalp_alopecia_rep12


title: scalp_alopecia_rep2


title: SMA Raphe_cells_#1

status: Public on Dec 12 2017

city: New York

first: George

middle: Z

last: Mentis

state: NY

address: 630 W 168th Street

department: Dept of Pathology&Cell Biology

institute: Columbia University

description:
SMA Raphe_cells_#1
5512953011_D

data_processing:
Raw data was translated into intensities with Illumina Genome Studio. Intensities were normalized with Lumi using the variance stabilizing transformation (VST) method followed by Robust Spline Normalization.
probes were included if their probability of detection was less than or equal to 0.05.

source_name: Brain Stem

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total cellular RNA was isolated using Absolutely RNA Nanoprep Kit (Stratagene).cDNA amplification  and performed with WT-Ovation Pico RNA Amplification System (NuGen).

tag: strain

value: FVB

value: Brain Stem

tag: group (tissue subtype)

value: Raphe cells


title: WT Raphe_cells_#1

description:
WT Raphe_cells_#1
5512953011_A


title: WT Raphe_cells_#3

description:
WT Raphe_cells_#3
5512953011_C


title: SMA Raphe_cells_#2

description:
SMA Raphe_cells_#2
5512953011_E


title: WT P4_DRG_#3

description:
WT DRG_#3
5512953012_C

source_name: Dorsal Root Ganglion

value: Dorsal Root Ganglion


title: SMA P4_DRG_#2

description:
SMA DRG_#2
5512953012_E


title: SMA Raphe_cells_#3

description:
SMA Raphe_cells_#3
5512953011_F


title: SMA P4_DRG_#3

description:
SMA DRG_#3
5512953012_F


title: WT P4_DRG_#2

description:
WT DRG_#2
5512953012_B


title: WT Raphe_cells_#2

description:
WT Raphe_cells_#2
5512953011_B


title: Subject8_Rep2_Visit1-Metformin_Adipose

city: Bronx

first: Ameya

last: Kulkarni

state: New York

address: 1301 Morris Park Ave, Price 253

department: Institute for Clinical and Translational Research

institute: Albert Einstein College of Medicine

data_processing:
Raw sequence reads preprocessed through WASP 3.0 (McLellan et al, 2012) and FASTQC (v0.11.5) was used for quality control.
FASTQ files were trimmed for adapter sequences using TrimGalore!
RSEM (RNA Sequencing by Expectation Maximization) algorithm (v1.2.25) in conjunction with STAR aligner (v2.4.2a) was used to quantify gene expression levels. Raw reads were mapped to GRCh38 build of the reference human genome with transcript annotations downloaded from GENCODE (gencode.v27.primary_assembly.annotation.gtf)
All statistical analyses for gene expression data were carried out using the R statistical software (v3.4.0)
Genes with a CPM value of <1 in two or more libraries were filtered for low expression
Raw gene count matrix (See Processed Data file matrix) obtained from RSEM was exported to edgeR (v3.18.1) for differential expression analysis
Genome_build: Human Genome GRCh38 (Downloaded from GENCODE Release 27)
Supplementary_files_format_and_content: tab-delimited text file containing raw counts for each sample (obtained from RSEM)

extract_protocol:
Following the skeletal muscle and subcutaneous adipose biopsies, the tissues were immediately homogenized in Trizol and stored in -80 C for subsequent mRNA extraction. The total RNA was extracted using QIAGEN's RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject id

tag: drug

value: Metformin

tag: crossover visit

value: Abdominal subcutaneous adipose


title: Subject12_Rep1_Visit1-Metformin_Adipose


title: Subject9_Rep1_Visit2-Metformin_Adipose


title: Subject10_Rep1_Visit2-Metformin_Adipose


title: Subject10_Rep2_Visit2-Metformin_Adipose


title: Subject13_Rep1_Visit1-Metformin_Adipose


title: Subject13_Rep2_Visit1-Metformin_Adipose


title: Subject11_Rep1_Visit1-Metformin_Adipose


title: Subject14_Rep3_Visit2-Metformin_Adipose


title: Subject14_Rep1_Visit2-Metformin_Adipose


title: Subject7_Rep2_Visit2-Metformin_Adipose


title: Subject7_Rep1_Visit2-Metformin_Adipose


title: Subject5_Rep3_Visit2-Metformin_Adipose


title: Subject11_Rep2_Visit1-Metformin_Adipose


title: Subject14_Rep2_Visit2-Metformin_Adipose


title: Subject6_Rep1_Visit2-Metformin_Adipose


title: SMA P4_DRG_#1

description:
SMA DRG_#1
5512953012_D


title: WT P4_DRG_#1

description:
WT DRG_#1
5512953012_A


title: Subject4_Rep1_Visit1-Metformin_Adipose


title: Subject5_Rep2_Visit2-Metformin_Adipose


title: Subject8_Rep1_Visit1-Metformin_Adipose


title: Subject1_Rep1_Visit1_Metformin_Adipose


title: Subject13_Rep1_Visit2_Placebo_Adipose

value: Placebo


title: Subject5_Rep1_Visit2-Metformin_Adipose


title: Subject3_Rep3_Visit2-Metformin_Adipose


title: Subject2_Rep1_Visit1_Metformin_Adipose


title: Subject3_Rep2_Visit2-Metformin_Adipose


title: Subject4_Rep2_Visit1-Metformin_Adipose


title: Subject7_Rep1_Visit1-Placebo_Adipose


title: Subject6_Rep2_Visit1-Placebo_Adipose


title: Subject10_Rep1_Visit1_Placebo_Adipose


title: Subject11_Rep1_Visit2_Placebo_Adipose


title: Subject12_Rep1_Visit2_Placebo_Adipose


title: Subject8_Rep1_Visit2_Placebo_Adipose


title: Subject9_Rep1_Visit1_Placebo_Adipose


title: Subject6_Rep3_Visit1-Placebo_Adipose


title: Subject6_Rep1_Visit1-Placebo_Adipose


title: Subject5_Rep1_Visit1-Placebo_Adipose


title: Subject4_Rep1_Visit2-Placebo_Adipose


title: Subject7_Rep2_Visit1-Placebo_Adipose


title: Subject14_Rep1_Visit1_Placebo_Adipose


title: Subject3_Rep1_Visit1-Placebo_Adipose


title: Subject13_Rep4_Visit1-Metformin_Muscle

value: Vastus lateralis muscle


title: Subject2_Rep1_Visit2_Placebo_Adipose


title: Subject1_Rep1_Visit2_Placebo_Adipose


title: Subject14_Rep1_Visit2-Metformin_Muscle


title: Subject3_Rep1_Visit2-Metformin_Adipose


title: Subject13_Rep3_Visit1-Metformin_Muscle


title: Subject13_Rep2_Visit1-Metformin_Muscle


title: Subject13_Rep1_Visit1-Metformin_Muscle


title: Subject12_Rep2_Visit1-Metformin_Muscle


title: Subject11_Rep4_Visit1-Metformin_Muscle


title: Subject11_Rep3_Visit1-Metformin_Muscle


title: Subject12_Rep4_Visit1-Metformin_Muscle


title: Subject11_Rep1_Visit1-Metformin_Muscle


title: Subject12_Rep3_Visit1-Metformin_Muscle


title: Subject9_Rep2_Visit2-Metformin_Muscle


title: Subject9_Rep1_Visit2-Metformin_Muscle


title: Subject7_Rep1_Visit2-Metformin_Muscle


title: Subject7_Rep3_Visit2-Metformin_Muscle


title: Subject8_Rep1_Visit1-Metformin_Muscle


title: Subject6_Rep2_Visit2-Metformin_Muscle


title: Subject3_Rep1_Visit2-Metformin_Muscle


title: Subject6_Rep3_Visit2-Metformin_Muscle


title: Subject5_Rep1_Visit2-Metformin_Muscle


title: Subject7_Rep2_Visit2-Metformin_Muscle


title: Subject10_Rep2_Visit2-Metformin_Muscle


title: Subject12_Rep1_Visit1-Metformin_Muscle


title: Subject4_Rep1_Visit1-Metformin_Muscle


title: Subject3_Rep2_Visit2-Metformin_Muscle


title: Subject11_Rep2_Visit1-Metformin_Muscle


title: Subject6_Rep1_Visit2-Metformin_Muscle


title: Subject2_Rep1_Visit1-Metformin_Muscle


title: Subject10_Rep1_Visit2-Metformin_Muscle


title: Subject13_Rep2_Visit2-Placebo_Muscle


title: Subject7_Rep4_Visit2-Metformin_Muscle


title: Subject14_Rep1_Visit1-Placebo_Muscle


title: Subject14_Rep2_Visit1-Placebo_Muscle


title: Subject12_Rep2_Visit2-Placebo_Muscle


title: Subject13_Rep1_Visit2-Placebo_Muscle


title: Subject12_Rep4_Visit2-Placebo_Muscle


title: Subject12_Rep3_Visit2-Placebo_Muscle


title: Subject11_Rep2_Visit2-Placebo_Muscle


title: Subject10_Rep1_Visit1-Placebo_Muscle


title: Subject9_Rep2_Visit1-Placebo_Muscle


title: Subject9_Rep1_Visit1-Placebo_Muscle


title: Subject12_Rep1_Visit2-Placebo_Muscle


title: Subject11_Rep1_Visit2-Placebo_Muscle


title: Subject7_Rep2_Visit1-Placebo_Muscle


title: Subject6_Rep1_Visit1-Placebo_Muscle


title: Subject4_Rep1_Visit2-Placebo_Muscle


title: Subject1_Rep1_Visit2-Placebo_Muscle


title: Subject5_Rep1_Visit1-Placebo_Muscle


title: Subject1_Rep2_Visit2-Placebo_Muscle


title: Subject2_Rep1_Visit 2 -Placebo_Muscle

source_name: visit2 -Placebo_Muscle


title: Subject3_Rep2_Visit1-Placebo_Muscle


title: NP-HF (#11976)

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

data_processing:
The raw sequences (fastq) were subjected to adapter removal and quality trimming using fqtrim (https://ccb.jhu.edu/software/fqtrim/).
The quality reads were then mapped to the bovine reference genome UMD3.1 using Hisat2 mapper (https://ccb.jhu.edu/software/hisat2/) .
To produce a global gene annotation file (GTF) for comprehensive quantification of gene expressions across the samples, the sorted binary alignment maps of sequence reads from each sample were assembled to generate transcriptomes those were then merged, along with the gene annotations from reference genome assembly.
The transcript assembly step was accomplished using the software ‘Stringtie’ (https://ccb.jhu.edu/software/stringtie/) .
The merged global transcriptome was then used in Stringtie to quantify transcript abundance of each sample. Differential expression analysis between sample groups were performed by robustly fitting the expression data to a weighted generalized linear model using edgeR robust.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab-limited text file of read count data.

organism: Bos taurus

extract_protocol:
Total RNA from the endometrium samples was extracted using the Isol-RNA Lysis Reagent (5Prime, Hamburg, Germany). Total RNA from the conceptuses was extracted using the AllPrep DNA/RNA/Protein Mini kit (Qiagen, Valencia, CA).
RNA library preparation and sequencing was conducted by the University of Missouri DNA Core facility. Libraries were constructed following the manufacturer’s protocol with reagents supplied in Illumina’s TruSeq mRNA stranded sample preparation kit.

tag: breed

value: Heifer cow

tag: fertility

value: High-fertile

tag: pregnancy

value: Non-pregnant

value: Endometrium

tag: hf conceptus size


title: P-HF (#11985)

value: Pregnant


title: NP-SF (#11975)

value: Sub-fertile


title: NP-IF (#11986)

value: Infertile


title: P-HF (#11971)


title: Subject7_Rep1_Visit1-Placebo_Muscle


title: P-HF (#11965)


title: NP-SF (#11926)


title: NP-HF (#11912)


title: NP-SF (#11952)


title: P-SF (#11910)


title: Subject10_Rep2_Visit1-Placebo_Muscle


title: Subject4_Rep2_Visit2-Placebo_Muscle


title: NP-IF (#11882)


title: P-HF (#11820)


title: NP-IF (#11861)


title: NP-IF (#11860)


title: Subject3_Rep1_Visit1-Placebo_Muscle


title: P-SF (#11755)


title: NP-HF (#11814)


title: Subject1_Rep1_Visit1-Metformin_Muscle


title: P-HF (#11811)


title: NP-IF (#11807)


title: NP-SF (#11698)


title: P-SF (#11748)


title: P-SF (#11690)


title: NP-HF (#11672)


title: 985_1.3cm_CONCEPTUS_HF

value: Conceptus

value: Short


title: 753_1.2cm_CONCEPTUS_HF


title: 753_1.5cm_CONCEPTUS_HF


title: NP-HF (#11704)


title: 971_2.8cm_CONCEPTUS_HF


title: 981_CONCEPTUS_HF

value: Long


title: 985_11.7_CONCEPTUS_HF


title: 971_17cm_CONCEPTUS_HF


title: 965_CONCEPTUS_HF


title: 969_CONCEPTUS_HF


title: 962_CONCEPTUS_HF


title: P-SF (#11949)


title: 825_9cm_CONCEPTUS_HF


title: 811_CONCEPTUS_HF


title: 825_3.4_Short_HF


title: 894_6.9_Short_HF


title: 700_Short_HF


title: 894_10.4cm_CONCEPTUS_HF


title: NP-SF (#11734)


title: 903_1.7cm_CONCEPTUS_SF


title: 910_2cm_CONCEPTUS_SF


title: 690_4cm_CONCEPTUS_SF


title: 778_4cm_CONCEPTUS_SF


title: 755_4cm_CONCEPTUS_SF


title: 755_13.5cm_CONCEPTUS_SF


title: 748_CONCEPTUS_SF


title: 690_5cm_CONCEPTUS_SF


title: Hepatocyte_no treatment_rep2

status: Public on Dec 11 2017

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: miRNA expression data from nontreated hepatocytes

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: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

organism: Rattus norvegicus

source_name: Primary hepatocytes

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: Hepatocytes and LSECs were isolated from Sprague-Dawley rat livers.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

value: Sprague-Dawley

value: 10 weeks

value: Primary hepatocytes


title: LSEC_no treatment_rep2

description: miRNA expression data from nontreated LSECs

source_name: Primary liver sinusoidal endothelial cells


title: LSEC_no treatment_rep1

value: Primary liver sinusoidal endothelial cells


title: 725_12cm_CONCEPTUS_HF


title: Hepatocyte_no treatment_rep1


title: 778_7cm_CONCEPTUS_SF


title: distal_ileumGG_10^9-administered_rep3

status: Public on Dec 10 2017

city: Tsukuba

first: Chise

last: Suzuki

state: Ibaraki

address: 2 Ikenodai

department: Animal Products Res. Division

institute: NARO Institute of Livestock and Grassland Science

description: Gene expression data from distal  ileum ofGG(10^9) administered mouse

hyb_protocol: Fragmented cRNA was hybridised to mouse 430 2.0 arrays (Affymetrix) during 16 h at 45°C.

scan_protocol: After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner; Affymetrix) with the GeneChip Operation Software Ver. 1.4 (Affymetrix).

data_processing: The microarray data were analyzed using R. Affymetrix CEL files were quantified by the RMA summarization.

source_name: distal ileumGG 10^9-administered rep3

label_protocol: cRNA was prepared using the Affymetrix One-cycle Target Labeling and Control Reagents kit, using 5 micro g total RNA as starting material. In vitro transcription, biotinylation of cRNA and fragmentation of biotinylated cRNA were carried out using IVT labeling kit.

growth_protocol: Mice were allowed free access to water and the basic feed (AIN93G) during 1 week housing period and during 2 weeks administration.

extract_protocol: After 3 hr fasting, ileum were taken and immediately kept in RNAlater (Qiagen). RNA was prepared by RNeasy kit (Qiagen).

treatment_protocol: 0.2 ml sample were administered using an intragastric stainless-steel feeding tube for 2 weeks.

value: distal ileum adjacent to cecum


title: distal_ileumGG_10^9-administered_rep5

source_name: distal ileumGG 10^9-administered rep5


title: 782_1.5cm_CONCEPTUS_SF


title: distal_ileumGG_10^9-administered_rep2

source_name: distal ileumGG 10^9-administered rep2


title: distal_ileumGG_10^9-administered_rep1

source_name: distal ileumGG 10^9-administered rep1


title: distal_ileumGG_10^8-administered_rep1

description: Gene expression data from distal  ileum ofGG(10^8) administered mouse

source_name: distal ileumGG 10^8-administered rep1


title: distal_ileumGG_10^8-administered_rep4

source_name: distal ileumGG 10^8-administered rep4


title: distal_ileumGG_10^7-administered_rep2

description: Gene expression data from distal  ileum ofGG(10^7) administered mouse

source_name: distal ileumGG 10^7-administered rep2


title: distal_ileum_C59_10^9-administered_rep3

description: Gene expression data from distal  ileum of C59(10^9) administered mouse

source_name: distal ileum C59 10^9-administered rep3


title: distal_ileum_C59_10^9-administered_rep2

source_name: distal ileum C59 10^9-administered rep2


title: distal_ileum_C59_10^8-administered_rep5

description: Gene expression data from distal  ileum of C59(10^8) administered mouse

source_name: distal ileum C59 10^8-administered rep5


title: distal_ileumGG_10^7-administered_rep3

source_name: distal ileumGG 10^7-administered rep3


title: distal_ileumGG_10^8-administered_rep3

source_name: distal ileumGG 10^8-administered rep3


title: distal_ileum_C59_10^7-administered_rep5

description: Gene expression data from distal  ileum of C59(10^7) administered mouse

source_name: distal ileum C59 10^7-administered rep5


title: distal_ileum_C59_10^9-administered_rep4

source_name: distal ileum C59 10^9-administered rep4


title: distal_ileumGG_10^9-administered_rep4

source_name: distal ileumGG 10^9-administered rep4


title: distal_ileum_C59_10^9-administered_rep5

source_name: distal ileum C59 10^9-administered rep5


title: distal_ileumGG_10^8-administered_rep5

source_name: distal ileumGG 10^8-administered rep5


title: distal_ileumGG_10^8-administered_rep2

source_name: distal ileumGG 10^8-administered rep2


title: distal_ileum_C59_10^8-administered_rep4

source_name: distal ileum C59 10^8-administered rep4


title: distal_ileum_C59_10^9-administered_rep1

source_name: distal ileum C59 10^9-administered rep1


title: distal_ileumGG_10^7-administered_rep5

source_name: distal ileumGG 10^7-administered rep5


title: Subject2_Rep2_Visit1-Metformin_Muscle

value: Metformin


title: distal_ileumGG_10^7-administered_rep4

source_name: distal ileumGG 10^7-administered rep4


title: distal_ileum_C59_10^8-administered_rep1

source_name: distal ileum C59 10^8-administered rep1


title: distal_ileum_C59_10^8-administered_rep2

source_name: distal ileum C59 10^8-administered rep2


title: distal_ileum_C59_10^8-administered_rep3

source_name: distal ileum C59 10^8-administered rep3


title: distal_ileum_PBS-administered_rep2

description: Gene expression data from distal  ileum of control mouse

source_name: distal ileum PBS-administered rep2


title: distal_ileum_C59_10^7-administered_rep4

source_name: distal ileum C59 10^7-administered rep4


title: distal_ileum_C59_10^7-administered_rep2

source_name: distal ileum C59 10^7-administered rep2


title: distal_ileum_PBS-administered_rep4

source_name: distal ileum PBS-administered rep4


title: distal_ileum_PBS-administered_rep5

source_name: distal ileum PBS-administered rep5


title: distal_ileum_C59_10^7-administered_rep1

source_name: distal ileum C59 10^7-administered rep1


title: distal_ileum_C59_10^7-administered_rep3

source_name: distal ileum C59 10^7-administered rep3


title: upper ileum GG--administered rep1

description: Gene expression data from upper ileum of GG-administered mouse

source_name: upper ileum of GG-administered mouse

value: Balb/c

tag: gender

value: male

value: 7 weeks

value: upper ileum including duodenum

tag: treatment group

value: GG-administered


title: distal_ileum_PBS-administered_rep3

source_name: distal ileum PBS-administered rep3

tag: tissue


title: upper ileum GG--administered rep4


title: distal_ileum_PBS-administered_rep1

source_name: distal ileum PBS-administered rep1


title: upper ileum GG--administered rep5


title: upper ileum GG--administered rep3


title: upper ileum C59-administered rep4

description: Gene expression data from upper ileum of C59-administered mouse

source_name: upper ileum of C59-administered mouse


title: Non-regenerating_MOON266

city: London

first: Lawrence

middle: DF

last: Moon

address: 16 - 18 Newcomen Street

department: Wolfson Centre for Age-Related Diseases

institute: King's College London

description: Identification of genes associated with axotomy or regeneration in the CNS.

hyb_protocol: Standard Affymetrix procedure for fragmentation and hybridization

scan_protocol: Standard GCOS scanning, GeneChip Scanner 3000

data_processing: GCOS, scaled to 200

source_name: Laser captured spinal cord neurons

label_protocol: Three round Eberwine amplification, proprietary modified Message Amp using BioArray High Yield labeling kit (Enzo) in last round.

extract_protocol: PicoPure (version C), Arcturus

treatment_protocol: Cut 10um transverse cryosections of unfixed spinal cord, dehydrate, laser capture

tag: Adult female Fischer 344


title: Regenerating_MOON266


title: upper ileum control rep5

description: Gene expression data from upper ileum of control mouse

source_name: upper ileum of control mouse

value: control


title: Traced_MM19


title: upper ileum control rep3


title: upper ileum control rep4


title: upper ileum control rep2


title: upper ileum GG--administered rep2


title: upper ileum control rep1


title: Regenerating_MOON265


title: Non-regenerating_MOON265


title: Traced_MM18


title: distal_ileumGG_10^7-administered_rep1

source_name: distal ileumGG 10^7-administered rep1


title: Non-regenerating_MM17


title: upper ileum C59-administered rep5


title: Traced_MM15 high yield replicate


title: Regenerating_MM16


title: Lower_ileum_GG--administered_rep3

description: Gene expression data from lower ileum of GG-administered mouse

source_name: lower ileum of GG-administered mouse

value: lower ileum adjacent to cecum


title: upper ileum C59-administered rep1


title: upper ileum C59-administered rep2


title: upper ileum C59-administered rep3


title: Non-regenerating_MM16


title: Lower_ileum_GG--administered_rep5


title: Lower_ileum_GG--administered_rep1


title: Lower_ileum_control_rep5

description: Gene expression data from lower ileum of control mouse

source_name: lower ileum of control mouse


title: Lower_ileum_control_rep2


title: Non-regenerating_MM11

source_name: Laser captured spinal cord neuron

tag: Fischer 344, adult female


title: Regenerating_MM14


title: Regenerating_MM13


title: Lower_ileum_GG--administered_rep2


title: Lower_ileum_GG--administered_rep4


title: Lower_ileum_control_rep4


title: Non-regenerating_MM14


title: Lower_ileum_control_rep1


title: Regenerating_MM17


title: Lower_ileum_C59-administered_rep4

description: Gene expression data from lower ileum of C59-administered mouse

source_name: lower ileum of C59-administered mouse


title: Lower_ileum_C59-administered_rep1


title: Non-regenerating_MM13


title: Lower_ileum_C59-administered_rep5


title: Lower_ileum_C59-administered_rep2


title: H9_DP197PR01: Pancreatic islet sample from partially pancreatectomized patient

status: Public on Dec 09 2017

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

hyb_protocol: 3.75µg cDNA per sample were hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips (Affymetrix) for 16-18 hours at 45°C and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix). The array was subsequently washed and stained with a fluidics station (GeneChip® Fluidics Station 450, Affymetrix) following the EukGe_WSv4_450 fluidics protocol for eukaryotic 3´-expression arrays.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Primary data analysis was performed with Affymetrix software GeneChip Operating System (GCOS) v1.4. Transcriptomic data were summarized and normalized with the Robust Multichip Analysis (RMA) using a software package (Array Studio; Omicsoft Corp., Cary, NC, USA). Batch correction of microarray data was performed using the R/Bioconductor package ComBat (Johnson et al., 2007).

Differential expression analysis comparing T2D and ND in OD or PPP cohorts:
Empirical Bayes moderated t statistics and corresponding p-values were computed using the Limma package in R correcting for age and sex covariates. P values were adjusted for multiple comparisons using the Benjamini Hochberg procedure.

source_name: Pancreatic islet sample by laser capture microdissection

label_protocol: 10 - 25 ng total RNA was amplified using the Ovation RNA Amplification System V2 and subsequently labelled with Biotin using the Encore™ Biotin Module following the manufacturer's instructions (NuGEN Technologies, San Carlos, CA, USA).

extract_protocol: Pancreatic islets within resected pancreas specimens were isolated by laser capture microdissection with Zeiss Palm MicroBeam system

tag: age (years)

tag: gender (m/f)

value: F

tag: body mass index (bmi)

tag: fasting glucose (mmol/l)

tag: diabetes status (nd (non-diabetic), t2d (type 2 diabetic), igt (impaired glucose tolerance, t3cd (type 3 diabetic))

tag: batch


title: Lower_ileum_control_rep3

tag: strain

tag: age


title: Lower_ileum_C59-administered_rep3


title: H9_DP194PR01: Pancreatic islet sample from partially pancreatectomized patient

value: M


title: H9_DP173PR01: Pancreatic islet sample from partially pancreatectomized patient

value: ND


title: H9_DP138PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP161PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP179PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP108PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP185PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP180PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP170PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP109PR02: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP187PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP125PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP177PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP169PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP105PR02: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP107PR02: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP104PR03: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP081PR02: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP118PR02: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP068PR01: Pancreatic islet sample from partially pancreatectomized patient


title: Regenerating_MM11


title: H9_DP075PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP132PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP074PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H8_DP111PR02: Pancreatic islet sample from partially pancreatectomized patient


title: H8_DP059PR02: Pancreatic islet sample from partially pancreatectomized patient


title: H8_DP116PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H8_DP066PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H7_DP143PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H8_DP083PR03: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP063PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP123PR01: Pancreatic islet sample from partially pancreatectomized patient

value: IGT


title: H8_DP057PR02: Pancreatic islet sample from partially pancreatectomized patient


title: H8_DP053PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H7_DP157PR02: Pancreatic islet sample from partially pancreatectomized patient


title: H7_DP072PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H7_DP090PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H7_DP071PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H7_DP095PR05: Pancreatic islet sample from partially pancreatectomized patient


title: H7_DP150PR02: Pancreatic islet sample from partially pancreatectomized patient


title: H6_DP110PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H6_DP124PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H6_DP093PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H7_DP065PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H6_DP126PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H7_DP043PR02: Pancreatic islet sample from partially pancreatectomized patient


title: H8_DP054PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H6_DP082PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H6_DP139PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H6_DP129PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H6_DP073PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H6_DP062PR02: Pancreatic islet sample from partially pancreatectomized patient


title: H7_DP005PR02: Pancreatic islet sample from partially pancreatectomized patient


title: H4_DP103PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H4_DP088PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H4_DP099PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H4_DP070PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H4_DP069PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H4_DP061PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H9_DP080PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H4_DP048PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H4_DP086PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H4_DP058PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H4_DP089PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H3_DP055PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H4_DP097PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H3_DP049PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H3_DP045PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H4_DP060PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H3_DP046PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H4_DP051PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H3_DP056PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H4_DP079PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H3_DP067PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H3_DP047PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H3_DP041PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H3_DP038PR01-2: Pancreatic islet sample from partially pancreatectomized patient


title: H3_DP033PR01-2: Pancreatic islet sample from partially pancreatectomized patient


title: H3_DP064PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H3_DP028PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H2_DP042PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H2_DP019PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H3_DP022PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H2_DP021PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H3_DP024PR01-2: Pancreatic islet sample from partially pancreatectomized patient


title: H2_DP013PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H1_DP008PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H2_DP023PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H3_DP027PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H1_DP012PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H2_DP034PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H1_DP017PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H1_DP002PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H2_DP040PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H1_DP010PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H8_PO880IR01: Pancreatic islet sample from organ donor

source_name: Pancreatic islet sample from cultured islets

extract_protocol: Groups of 100-120 islets were hand-picked, rinsed in sterile PBS (Sigma-Aldrich) and centrifuged at 3,000 x g for 5 min; the supernatant was disposed and 100 μl of extraction buffer (PicoPure RNA Isolation Kit, Life Technologies, Foster City, California) was added. Samples were incubated at 42 °C for 30 min, centrifuged at 3,000 x g for 2 min, and the supernatant collected and stored at -80°C until the isolation procedure. RNA isolation was performed according to the protocol provided by the manufacturer. Briefly, 100 μl of 70% ethanol were added to the cell extract, the mixture was added to the purification columns, washed and DNase treatment performed by incubation with 40 μl of DNase I solution (RNase-Free DNase Set, Qiagen GmbH, Hilden, Germany) for 15 min. Two additional washing steps were performed and RNA was eluted in 30 μl of elution buffer. RNA concentration and purity were evaluated using NanoDrop 2000c spectrophotometer (Thermo Scientific, Wilmington, DE); quality was evaluated using the Agilent 2100 Bioanalyzer system and the Agilent RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA).

tag: icu (intensive care unit) glycemia (mmol/l)

tag: diabetes status (nd (non-diabetic), t2d (type 2 diabetic))


title: H1_DP003PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H2_DP025PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H1_DP007PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H2_DP039PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H8_PO876IR01: Pancreatic islet sample from organ donor


title: H8_PO879IR01: Pancreatic islet sample from organ donor


title: H1_DP011PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H1_DP030PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H8_PO872IR01: Pancreatic islet sample from organ donor


title: H8_DP087PR03: Pancreatic islet sample from partially pancreatectomized patient


title: H8_PO869IR01: Pancreatic islet sample from organ donor


title: H8_PO871IR01: Pancreatic islet sample from organ donor


title: H8_PO860IR01: Pancreatic islet sample from organ donor


title: H8_PO865IR01: Pancreatic islet sample from organ donor


title: H8_PO855IR01: Pancreatic islet sample from organ donor


title: H6_PO946IR01: Pancreatic islet sample from organ donor


title: H8_PO856IR01: Pancreatic islet sample from organ donor


title: H5_PO914IR01: Pancreatic islet sample from organ donor


title: H8_PO853IR01: Pancreatic islet sample from organ donor


title: H8_PO851IR01: Pancreatic islet sample from organ donor


title: H6_PO944IR01: Pancreatic islet sample from organ donor


title: H5_PO907IR01: Pancreatic islet sample from organ donor


title: H5_PO905IR01: Pancreatic islet sample from organ donor


title: H5_PO897IR01: Pancreatic islet sample from organ donor


title: H5_PO916IR01: Pancreatic islet sample from organ donor


title: H5_PO903IR01: Pancreatic islet sample from organ donor


title: H5_PO900IR01: Pancreatic islet sample from organ donor


title: H8_PO846IR01: Pancreatic islet sample from organ donor


title: H5_PO901IR01: Pancreatic islet sample from organ donor


title: H8_PO854IR01: Pancreatic islet sample from organ donor


title: H8_PO849IR01: Pancreatic islet sample from organ donor


title: H6_PO937IR01: Pancreatic islet sample from organ donor


title: H5_PO902IR01: Pancreatic islet sample from organ donor


title: H5_PO918IR01: Pancreatic islet sample from organ donor


title: H5_PO908IR01: Pancreatic islet sample from organ donor


title: H5_PO906IR01: Pancreatic islet sample from organ donor


title: H5_PO909IR01: Pancreatic islet sample from organ donor


title: H5_PO891IR01: Pancreatic islet sample from organ donor


title: H5_PO888IR01: Pancreatic islet sample from organ donor


title: H5_PO887IR01: Pancreatic islet sample from organ donor


title: H5_PO884IR01: Pancreatic islet sample from organ donor


title: H5_PO889IR01: Pancreatic islet sample from organ donor


title: H4_DP102PR01: Pancreatic islet sample from partially pancreatectomized patient


title: H5_LO379IR01: Pancreatic islet sample from organ donor


title: H5_LO378IR01: Pancreatic islet sample from organ donor


title: H5_PO882IR01: Pancreatic islet sample from organ donor


title: H5_LO372IR01: Pancreatic islet sample from organ donor


title: H5_LO373IR01: Pancreatic islet sample from organ donor


title: H5_LO371IR01: Pancreatic islet sample from organ donor


title: H5_LO365IR01: Pancreatic islet sample from organ donor


title: H5_LO377IR01: Pancreatic islet sample from organ donor


title: H5_LO368IR01: Pancreatic islet sample from organ donor


title: H5_LO363IR01: Pancreatic islet sample from organ donor


title: H5_LO364IR01: Pancreatic islet sample from organ donor


title: H5_LO355IR01: Pancreatic islet sample from organ donor


title: H5_LO367IR01: Pancreatic islet sample from organ donor


title: H5_LO359IR01: Pancreatic islet sample from organ donor


title: H5_LO361IR01: Pancreatic islet sample from organ donor


title: H5_PO886IR01: Pancreatic islet sample from organ donor


title: H5_LO358IR01: Pancreatic islet sample from organ donor


title: H3_PO842IR01: Pancreatic islet sample from organ donor


title: H5_LO362IR01: Pancreatic islet sample from organ donor


title: H3_PO841IR01: Pancreatic islet sample from organ donor


title: H5_LO356IR01: Pancreatic islet sample from organ donor


title: H5_LO375IR01: Pancreatic islet sample from organ donor


title: H3_PO831IR01: Pancreatic islet sample from organ donor


title: H3_PO845IR01: Pancreatic islet sample from organ donor


title: H3_PO844IR01: Pancreatic islet sample from organ donor


title: H5_LO354IR01: Pancreatic islet sample from organ donor


title: H3_PO836IR01: Pancreatic islet sample from organ donor


title: H2_PO818IR01: Pancreatic islet sample from organ donor


title: H3_PO819IR01: Pancreatic islet sample from organ donor


title: H3_PO826IR01: Pancreatic islet sample from organ donor


title: H3_PO837IR01: Pancreatic islet sample from organ donor


title: H3_PO820IR01: Pancreatic islet sample from organ donor


title: H2_PO814IR01: Pancreatic islet sample from organ donor


title: H3_PO828IR01: Pancreatic islet sample from organ donor


title: H3_PO825IR01: Pancreatic islet sample from organ donor


title: H2_PO812IR01: Pancreatic islet sample from organ donor


title: H2_PO810IR01: Pancreatic islet sample from organ donor


title: H2_PO800IR01: Pancreatic islet sample from organ donor


title: H1_PO798IR01: Pancreatic islet sample from organ donor


title: H2_PO815IR01: Pancreatic islet sample from organ donor


title: H1_PO796IR01: Pancreatic islet sample from organ donor


title: H2_PO817IR01: Pancreatic islet sample from organ donor


title: H3_PO827IR01: Pancreatic islet sample from organ donor


title: H1_PO797IR01: Pancreatic islet sample from organ donor


title: H5_LO352IR01: Pancreatic islet sample from organ donor


title: H3_PO821IR01-m: Pancreatic islet sample from organ donor


title: H1_PO781IR01: Pancreatic islet sample from organ donor


title: H1_PO791IR01: Pancreatic islet sample from organ donor


title: H1_PO780IR01: Pancreatic islet sample from organ donor


title: H1_PO778IR01: Pancreatic islet sample from organ donor


title: H2_PO804IR01: Pancreatic islet sample from organ donor


title: H1_PO783IR01: Pancreatic islet sample from organ donor


title: H1_PO772IR01: Pancreatic islet sample from organ donor


title: H1_PO784IR01: Pancreatic islet sample from organ donor


title: H1_PO775IR01: Pancreatic islet sample from organ donor


title: H5_LO353IR01: Pancreatic islet sample from organ donor


title: H1_PO771IR01: Pancreatic islet sample from organ donor


title: H1_PO770IR01: Pancreatic islet sample from organ donor


title: H1_PO767IR01: Pancreatic islet sample from organ donor


title: H1_PO782IR01: Pancreatic islet sample from organ donor


title: H3_PO840IR01: Pancreatic islet sample from organ donor


title: H1_PO755IR01: Pancreatic islet sample from organ donor


title: H2_PO813IR01: Pancreatic islet sample from organ donor


title: CVL_110ksn_442_Wk5

city: Baltimore

first: Kenneth

last: Witwer

state: MD

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

description: Total RNA was reverse-transcribed, pre-amplified with feature-specific primers, and loaded onto custom OpenArrays by liquid handling robot in the Johns Hopkins University DNA Analysis Facility. Quantitative real-time PCR was performed for 220 features.

data_processing: Cq data were processed using ExpressionSuite (Applied Biosystems/Thermo Fisher), Microsoft Excel, and R/Bioconductor. Cqs>30 with amplification score > 1.15 were retained for further analysis. U6 data were not used. Normalization was performed to the geometric mean of ten abundant miRNAs (let-7b, miR-21, miR-27a, miR-28-3p, miR-29a, miR-30b, miR-92a, miR-197, miR-200c, and miR-320). Missing values indicate wells that did not amplify or did not satisfy the amplification score criterion (raw data).

label: none (TaqMan probe label: FAM)

organism: Macaca mulatta

extract_protocol:
Total RNA was obtained from ultracentrifugation-processed fractions of cervicovaginal lavage using the mirVana total RNA isolation procedure; purity and concentration were assessed by NanoDrop. As quality control, expression levels of several small RNAs including snRNA U6, miR-16, miR-223, and the spiked-in cel-miR-39 were assessed by stem-loop reverse transcription/hydrolysis probe qPCR assays.
RT and pre-amp protocol: 100 ng total RNA per sample was reverse-transcribed using Megaplex primers, set A (Applied Biosystems). cDNA was pre-amplified for twelve cycles with Mexaplex Pre-Amp primers, set A (Applied Biosystems), then diluted to 100 ul. Manufacturer's protocol was followed throughout.
qRT-PCR protocol: Pre-amplified cDNA was loaded onto custom TLDA cards. qRT-PCR was performed on an ABI 7800 instrument (Thermo Fisher) per manufacturer's recommendations.
data collection protocol: SDS software (Thermo Fisher) was used to collect Cq data.

value: cervicovaginal lavage

tag: siv status

tag: collection time

value: Week 5

tag: uc fraction

value: 110,000 xg supernant


title: CVL_110ksn_442_Wk4

value: Week 4


title: CVL_110ksn_439_Wk4


title: CVL_110ksn_439_Wk3

value: Week 3


title: CVL_110ksn_442_Wk1

value: Week 1


title: CVL_110ksn_442_Wk3


title: CVL_110ksn_442_Wk2

value: Week 2


title: CVL_110ksn_439_Wk1


title: CVL_110ksn_439_Wk2


title: CVL_110ksn_437_Wk4


title: H1_PO761IR01: Pancreatic islet sample from organ donor


title: H1_PO764IR01: Pancreatic islet sample from organ donor


title: CVL_110ksn_439_Wk5


title: CVL_110ksn_437_Wk2


title: CVL_110ksn_437_Wk1


title: CVL_110ksn_436_Wk5


title: CVL_110ksn_436_Wk4


title: CVL_110ksn_436_Wk2


title: CVL_110ksn_43K_Wk3

value: Uninfected


title: CVL_110ksn_43K_Wk2


title: CVL_110ksn_436_Wk3


title: CVL_110ksn_43K_Wk5


title: CVL_110ksn_43K_Wk4


title: CVL_110ksn_436_Wk1


title: CVL_110ksn_437_Wk5


title: CVL_110kp_442_Wk5

value: 110,000 xg pellet


title: CVL_110ksn_43K_Wk1


title: CVL_110kp_439_Wk5


title: CVL_110kp_442_Wk4


title: CVL_110kp_437_Wk4


title: CVL_110kp_439_Wk3


title: CVL_110kp_436_Wk3


title: CVL_110kp_439_Wk4


title: CVL_110kp_437_Wk5


title: CVL_110kp_442_Wk1


title: CVL_110kp_437_Wk1


title: CVL_110kp_437_Wk2


title: CVL_110kp_439_Wk2


title: CVL_110kp_436_Wk4


title: CVL_110kp_436_Wk5


title: CVL_110kp_439_Wk1


title: CVL_110kp_437_Wk3


title: CVL_110kp_436_Wk2


title: CVL_110kp_436_Wk1


title: CVL_110kp_43K_Wk5


title: CVL_110kp_442_Wk2


title: CVL_110kp_43K_Wk4


title: CVL_110kp_43K_Wk1


title: CVL_110kp_442_Wk3


title: CVL_110kp_43K_Wk2


title: CVL_110kp_43K_Wk3


title: CVL_110kp_1H_Wk5


title: CVL_110kp_1H_Wk2


title: CVL_110kp_1H_Wk4


title: CVL_110kp_1H_Wk1


title: CVL_10kp_442_Wk5

value: 10,000 xg pellet


title: CVL_10kp_442_Wk3


title: CVL_10kp_442_Wk2


title: CVL_10kp_442_Wk1


title: CVL_10kp_442_Wk4


title: CVL_10kp_437_Wk5


title: CVL_10kp_439_Wk5


title: CVL_10kp_439_Wk4


title: CVL_10kp_439_Wk3


title: CVL_10kp_439_Wk2


title: CVL_10kp_436_Wk4


title: CVL_10kp_439_Wk1


title: CVL_10kp_436_Wk5


title: CVL_10kp_437_Wk1


title: CVL_10kp_436_Wk3


title: CVL_10kp_437_Wk4


title: CVL_10kp_437_Wk2


title: CVL_10kp_436_Wk1


title: CVL_10kp_43K_Wk5


title: CVL_10kp_43K_Wk4


title: CVL_10kp_43K_Wk3


title: CVL_10kp_43K_Wk2


title: CVL_10kp_437_Wk3


title: CVL_10kp_43K_Wk1


title: CVL_10kp_436_Wk2


title: H2_PO809IR01: Pancreatic islet sample from organ donor


title: SPN-EC, biological rep2

status: Public on Dec 08 2017

first: Jiajing

last: Qiu

address: 1468 Madison Ave, ANBG bldg 24-10

department: Hematology/Oncology Department of Medicine

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from normal human splenic vascular endothelial cells

hyb_protocol: aRNAs were hybridized to Affymetrix human genome U133 Plus 2.0 array.

scan_protocol: GeneChip Scanner 3000

data_processing: GeneChip Command Console software

source_name: human normal spleen vascular endothelial cells

label_protocol: biotin labeled aRNA was synthesized using MessageAmpTM II aRNA Amplificaiton Kit (Ambion)

growth_protocol: Fresly processed human spleen specimens

extract_protocol: Total RNA was individually extracted from 0.5-1x105 freshly isolated viable SLCs or splenic vascular ECs using RNeasy Micro Kit (Qiagen). In vitro RNA amplification was performed using MessageAmpTM II aRNA Amplificaiton Kit (Ambion)

treatment_protocol: Minced fresh spleen specimens were digested with Collagenase B / Dispase II. CD45 cells were immunomegnetically depleted and the remaining RBCs were lysed from the harvested single cell suspensions.  Viable CD34- CD8a+ CD31+ CD3- CD45- SLCs and CD34+ CD8a- CD31+ CD3- CD45- splenic vascular ECs were isolated using Flow cytometric sorting.

value: spleen

tag: cell type

tag: cell phenotype


title: SPN-SLC, biological rep3

description: Gene expression data from normal human splenic littoral cells

source_name: human normal spleen littoral cells

tag: tissue

value: human normal spleen littoral cells


title: SPN-EC, biological rep1

value: human normal spleen vascular endothelial cells


title: SPN-SLC, biological rep1


title: SPN-SLC, biological rep2


title: Male of wild-type N2, fed biological rep3

status: Public on Dec 07 2017

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

description: Gene expression data from adult worms after the completion of development

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: Images from scanned chips were processed by using the default settings of the AGCC viewer. The Affymetrix output (CEL files) was imported into GeneSpring GX 12.0 (Agilent Technologies) microarray analysis software for the statistical analysis and presentation of the expression profiles. The CEL files were individually scaled to a median target signal of 500. The probe intensities, expression signals and fold changes of all genes (probe sets) were calculated using MAS5 implemented in GeneSpring software.

organism: Caenorhabditis elegans

source_name: Males ad libitum fed

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3' IVT Express kit mannual, Affymetrix). IVT incubation time was 16 hours.

growth_protocol: Synchronized wild-type N2 worms were grown on NGM plates at  20 C. At the young adult stage, males were separated from hermaphrodites by filtration through a 37 mm nylon mesh.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions with a minor modification (the addition of sterilized glass beads for homogenization). The extracted RNA was purified and treated with DNase using an RNeasy Mini Kit (Qiagen)

treatment_protocol: At the young adult stage, worms were transferred to NGM plats containing 200 ug/ml of 5’fluoro-2’deoxyuridine (FUdR) to prevent progenies from hatching. At day 2 of adulthood, worms were devided into 2 groups, fed and fasting. In the fed group, worms were allowed to feed ad libitum for 2 days. In the fasting group, worms were placed on NGM plates withour food and subjected to 48 hours of fasting.

tag: genetic background

tag: genotype

value: wild type

value: Whole body

value: Day 4 of adulthood

tag: gender

value: male

tag: treatment

value: fed ad libitum


title: Hermaphrodite of wild-type N2, fed biological rep2

source_name: Hermaphrodites ad libitum fed

value: Hermaphrodite


title: Male of wild-type N2, fed biological rep2


title: MCF7 Cells treated with DAC+455 Replicate 1

first: Benjamin

last: Leadem

address: 1650 Orleans St. Suite 541

institute: Johns Hopkins University

description: Biological replicate 1 of 3

hyb_protocol: standard as recommended by Agilent

scan_protocol: standard as recommended by Agilent standard as recommended by Agilent

data_processing: Data were normalized using loess and aquantile methods as described in the Bioconductor limma package.

source_name: MCF7 cells treated with DAC+455

label_protocol: standard as recommended by Agilent

growth_protocol: standard as recommended by ATCC

extract_protocol: Total RNA extracted using Qiagen RNeasy following manufacturer's instructions

tag: cell line

value: MCF7 adenocarcinoma cells

value: day 3

value: breast

source_name: MCF7 cells Mock Treatment

value: Breast


title: Hermaphrodite of wild-type N2, fed biological rep1


title: Male of wild-type N2, fasting biological rep3

source_name: Males subjected to 48 hors of fasting, beginning at day 2 of adulthood

value: fasted


title: Hermaphrodite of wild-type N2, fasting biological rep2

source_name: Hermaphrodites subjected to 48 hors of fasting, beginning at day 2 of adulthood


title: TET-ON_PROTOCOL_EOMES_KO_/_TET-ON_hESCs_d6

city: Münster

first: Boris

last: Greber

address: Von-Esmarch-Str. 54

institute: Max Planck Institute for Molecular Biomedicine

description:
EOMES KO / TET-ON hESCs, TET-ON protocol day 6
SAMPLE 23

hyb_protocol: 18 hours according to manufacturer's instructions (Illumina)

scan_protocol: Default settings on a HiScan SQ (Illumina)

data_processing: Cubic spline normalization with background subtration in GenomeStudio (Illumina)

source_name: differentiated cell line

label_protocol: Illumina TotalPrep RNA Amplification Kit (Thermo); 14h of in-vitro transcription

growth_protocol: Undifferentiated hESCs (HuES6 background) were grown to full confluency in chemically defined FTDA medium. Differentiation was initiated after - or concomitant with - replating cells at 1 M or 500,000 cells per well in Matrigel-coated 24-well plates.

extract_protocol: Qiagen RNeasy columns with on-column DNA-digestion. Three independent experiments were carried out for each series. RNA was then pooled from these replicates to be processed for microarray sample preparation.

treatment_protocol: Series 1 and 2 (standard cardiac induction protocol): d0 cells = confluent undifferentiated WT or EOMES knockout cells before replating. Replating medium used on d0 (500,000 cells per 24-well): KO-DMEM / ITS / PenStrep / 10 µM Rock Inhibitor Y27632 / 20 ng/ml FGF2 / 1 µM CHIR99021 / 0.75 ng/ml BMP4. Day 1 medium: KO-DMEM / Transferrin-Selenium / PenStrep / 250 µM phospho-ascorbate. Day 2 and 3: Same medium + 2 µM IWP2. Day 4 onwards: Same as on day 1. Volume of medium: 2 ml per well throughout. Series 3 (TET-ON protocol): Cells replated at 1 M per 24-well in FTA medium + 10µM Rock Inhibitor Y27632. Day 0 medium: KO-DMEM / ITS / PenStrep / 0.25 µg/ml doxycycline (DOX) - no signaling factors added. Day 1 medium: KO-DMEM / Transferrin-Selenium / 250 µM phospho-ascorbate / PenStrep / 0.25 µg/ml DOX. Day 2: Same medium + 0.5 µM C59. Day 3: Same, but with C59 only (no DOX). Hence after: Plain KO-DMEM / Transferrin-Selenium / phospho-ascorbate / PenStrep.

value: Human ES cells (line HuES6)

tag: genotype/variation

tag: protocol

value: TET-ON protocol

tag: time

value: day 6


title: Male of wild-type N2, fasting biological rep1

tag: age


title: TET-ON_PROTOCOL_EOMES_KO_/_TET-ON_hESCs_d7

description:
EOMES KO / TET-ON hESCs, TET-ON protocol day 7
SAMPLE 24

value: day 7


title: MCF7 Cells treated with DAC+455 Replicate 2

description: Biological replicate 2 of 3

tag: strain


title: Hermaphrodite of wild-type N2, fasting biological rep1


title: Hermaphrodite of wild-type N2, fed biological rep3


title: Male of wild-type N2, fasting biological rep2


title: Male of wild-type N2, fed biological rep1


title: Hermaphrodite of wild-type N2, fasting biological rep3


title: MCF7 Cells treated with DAC+455 Replicate 3

description: Biological replicate 3 of 3


title: TET-ON_PROTOCOL_EOMES_KO_/_TET-ON_hESCs_d5

description:
EOMES KO / TET-ON hESCs, TET-ON protocol day 5
SAMPLE 22

value: day 5


title: SPN-EC, biological rep3

value: spleen

value: human normal spleen vascular endothelial cells


title: MCF7 Cells treated with DAC+203 Replicate 2

description: Biological replicate 2 of 3

source_name: MCF7 cells treated with DAC+203


title: TET-ON_PROTOCOL_EOMES_KO_/_TET-ON_hESCs_d4

description:
EOMES KO / TET-ON hESCs, TET-ON protocol day 4
SAMPLE 21

value: day 4


title: MCF7 Cells treated with DAC+203 Replicate 3

description: Biological replicate 3 of 3


title: H1_PO765IR01: Pancreatic islet sample from organ donor

tag: age (years)

tag: gender (m/f)

value: F

tag: body mass index (bmi)

tag: icu (intensive care unit) glycemia (mmol/l)

tag: diabetes status (nd (non-diabetic), t2d (type 2 diabetic))

value: ND

tag: batch


title: CVL_110ksn_437_Wk3

tag: tissue

value: cervicovaginal lavage

tag: siv status

tag: collection time

value: Week 3

tag: uc fraction

value: 110,000 xg supernant


title: MCF7 Cells treated with DAC+203 Replicate 1

description: Biological replicate 1 of 3

value: MCF7 adenocarcinoma cells

value: day 3