title: mouse embryo Sox4_Sox11_control E14.5 brain, biological replicate 2

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

description: Gene expression data from E14.5 mouse brain (Sox4_Sox11_control).

hyb_protocol: Following fragmentation, labeled aRNA was hybridized for 16h on a mouse genome 430 2.0 array. Hybridization, washing and staining of the arrays were done according to the standard Affymetrix GeneChip protocol (Version2).

scan_protocol: GeneChips were scanned using GC Scanner 3000 with G7 update.

data_processing: The data were analyzed with Affymetrix Microarray Suite algorithm version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization procedure.

label: Biotin

source_name: mouse brain E14.5 (conditional Sox4, conditonal Sox11)

label_protocol: Biotinylated aRNA was prepared in the amplification step using the GeneChip 3’ IVT Express Kit starting with 100ng total RNA.

extract_protocol: Trizol extraction of total RNA from whole mouse brains at E14.5 was performed according to the manufacturer's protocol.  DNAseI was added to remove contaminating DNA and samples were cleaned up using the RNeasy Mini Kit according to Quiagen's instructions.

value: mixed 129SvJ/C57Bl/6J background

value: embryo E14.5

value: whole brain

tag: genotype

value: Sox4 flox/flox; Sox11 flox/flox


title: mouse embryo Sox4_Sox11_ dko E14.5 brain, biological replicate 1

status: Public on May 10 2018

type: RNA

country: Germany

description: Gene expression data from E14.5 mouse brain (Sox4_Sox11_dko).

molecule: total RNA

organism: Mus musculus

source_name: mouse brain E14.5 (Brn4::Cre, conditional Sox4, conditonal Sox11)

tag: strain

tag: developmental stage

tag: tissue

value: Brn4::Cre, Sox4 flox/flox, Sox11 flox/flox


title: genomic DNA from PL72 IUGR placenta

status: Public on May 11 2018

type: genomic

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
R version 3.2.5
The matrix_signal_Wilson_PEIUGR.csv contains Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted by standard salt method and purified using Qiagen DNeasy Kit according to standard instructions

tag: subject id

tag: pathology group

value: IUGR

tag: fetal sex

value: FEMALE

tag: gestational age

tag: sample tissue

value: Chorionic Villi

tag: 450k plate

tag: 450k sentrix_id

tag: 450k sentrix_position


title: mouse embryo Sox4_Sox11_ dko E14.5 brain, biological replicate 2


title: chicken embryo HH11, neural tube electroporated with pSuper-neo-GFP-Sox4-shRNA + pSuper-neo-GFP-Sox11-shRNA

description: Gene expression data from GFP+ cells from chicken embryo neural tube HH11 electroporated with siRNAs against Sox4 and Sox11.

hyb_protocol: Following fragmentation, labeled aRNA was hybridized for 16h on a chicken array. Hybridization, washing and staining of the arrays were done according to the standard Affymetrix GeneChip protocol (Version2).

organism: Gallus gallus

source_name: GFP+cells from chicken embryo HH11

extract_protocol: Trizol extraction of total RNA from GFP-positive sorted cells was performed according to the manufacturer's protocol.  DNAseI was added to remove contaminating DNA and samples were cleaned up using the RNeasy Mini Kit according to Quiagen's instructions.

treatment_protocol: Chicken embryos were electroporated on both sites with pSuper-neo-GFP plasmids at HH9 and kept for two days at 37.5°C before they were sacrificed at HH11. Neural tube tissue was prepared and dissociated to a single cell solution that underwent GFP-directed FACS.

value: embryo HH11

value: GFP+, FACS-sorted neural tube cells

tag: genotype/variation

value: Sox4Sox11 knockdown


title: genomic DNA from PM67 EOPE placenta

value: EOPE

value: MALE


title: genomic DNA from PM15 EOPE  placenta


title: Corneal tissue Con_48

type: SRA

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

description:
counts_table.txt
Con_48

library_source: transcriptomic

data_processing:
RNA samples were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina,USA) according to the manufacturer’s instructions. One μg of total RNA was used as input to the Ribozero rRNA-depletion step of the assay. The adapter-ligated cDNA was enriched using 12 cycles of PCR. The libraries were sequenced on a NextSeq500 (Illumina) using a 75bp paired end read high output v2 run. This produced between 27 M and 60 M paired end reads per sample
The samples were processed in 2 batches each with the same number of KC (n=5 per batch) and control subjects (n=5 per batch). We mapped the 75 nucleotide reads to the human genome (GRCh38) using TopHat2 (v 2.0.4) 56, calling the Bowtie aligner (v 2-2.0.0-beta7) 57, allowing up to 2 bp mismatches per read (default position)
HTSeq-count (Python package HTSeq, python v 2.7.3) was used to generate counts of reads uniquely mapped to known and annotated genes using the Ensembl annotation file GRCh38.79.gtf (mode=union, –t = exon, –i = gene_name). The number of uniquely mapped reads varied between 41-50 million per sample in the first batch and 18-32 million per sample in the second batch
The count table of uniquely mapped reads was then used and differential expression was tested using the Bioconductor packages, edgeR (v3.16.0) and DESeq2 (v1.14.0).
Genome_build: Ensembl Home sapiens genome (GRCh38)
Supplementary_files_format_and_content: Tab-delimited text file with read count for each sample.

source_name: Corneal tissue 48

extract_protocol:
RNeasy mini kit (Qiagen) was used to extract the RNA from tissues, following the manufacturer’s instruction with minor modifications. Briefly, RNALater was carefully removed from Eppendorf tubes containing tissues, and 300 μL of RLT containing 2-mercaptoethanol in a 100:1 ratio was added to each tube and the tubes were vortexed until the tissues were dissolved. Equal portions of 70% ethanol (300 μL) were added to each tube, vortexed, and centrifuged at 12,000xg for 20s at room temperature (RT). The cartridge was washed wash buffer I (700 μL) at 12,000g for 20s followed by two more wash with wash buffer II (500 μL) at 12,000g for 15s. The cartridge was dried at 12,000xg for 1min at RT and 30μL of RNase-Free water was added to center of the cartridge and incubated at RT for 2min. Purified RNA was eluted by centrifuging at 20,000xg for 2min at RT and then stored at -80 °C for further use.
mRNA libraries  were prepared at the Ramaciotti Centre for Genomics (UNSW University of New South Wales, Australia). The Illumina TruSeq Stranded mRNA Prep Kit was used. AllRNA-Seq libraries  were sequenced  using the Illumina NextSeq 500. R1.fastq and R2.fastq files were produced for each sample.

tag: individual

value: Control, myopia patient

value: Corneal tissue

tag: batch

tag: Sex

value: Male


title: Corneal tissue Con_51

description:
counts_table.txt
Con_51

source_name: Corneal tissue 51

value: Female


title: Corneal tissue Con_55

description:
counts_table.txt
Con_55

source_name: Corneal tissue 55


title: Corneal tissue Con_49

description:
counts_table.txt
Con_49

source_name: Corneal tissue 49


title: mouse embryo Sox4_Sox11_control E14.5 brain, biological replicate 1

value: mixed 129SvJ/C57Bl/6J background


title: Corneal tissue Con_S2

description:
counts_table.txt
Con_S2

source_name: Corneal tissue S2


title: genomic DNA from PM21 EOPE placenta


title: Corneal tissue Con_43

description:
counts_table.txt
Con_43

source_name: Corneal tissue 43


title: LPS_Vehicle_3

city: Cambridge MA

first: Jie

last: Quan

address: 1 Portland St

country: USA

institute: Pfizer

data_processing:
Illumina NextSeq sequencing data was processed and demultiplexed by bcl2fastq2-v2.15.0.4.
Sequence reads were mapped to mm10 using STAR_2.5.2a.
STAR "--quantMode TranscriptomeSAM GeneCounts" used for read counting.
Genome_build: mm10
Supplementary_files_format_and_content: A tab-delimited text file includes gene-level read counts for each sample.

molecule: polyA RNA

source_name: Isolated Neurovasculature

extract_protocol:
Brains were removed and flash frozen in liquid nitrogen and then were transferred into RNA-later-ICE Frozen Tissue Transition Solution (Life Technologies AM7030) in stored for 24 hours at -20 ⁰C. Brain vasculature was then isolated as previously described [Bales KR et al. Brain 2016, 139(Pt2):563-577] with the addition of two extra washes in sucrose buffer to remove remaining traces of myelin. Total RNA was purified using Qiagen RNeasy kits.
Stranded cDNA libraries were prepared from 50 ng RNA using TruSeq Stranded mRNA NeoPrep kits (Illumina).

treatment_protocol: Male CD1 mice aged 8-10 weeks were intraperitoneal injected with 3mg/kg of salmonella enterica typhimurium (Sigma L2262) at 0, 6 and 24 hours. For the pharmacology studies mice were dosed with 10 mg/kg subcutaneous CPD-4645 in a vehicle of 5:5:90 DMSO:Cremophor:Saline 30 minutes post each LPS dose. Mice were euthanized at 28 hours after the first LPS injection.

value: Neurovasculature

tag: agent


title: LPS_Vehicle_2


title: LPS_CPD4645_3


title: Sham_Vehicle_4


title: LPS_CPD4645_2


title: LPS_Vehicle_5


title: LPS_CPD4645_4


title: LPS_Vehicle_4


title: LPS_CPD4645_1


title: LPS_Vehicle_1


title: Sham_Vehicle_1


title: Sham_Vehicle_3


title: chicken embryo HH11, neural tube electroporated with pSuper-neo-GFP

description: Gene expression data from GFP+ cells from chicken embryo neural tube HH11.

value: control


title: MHb-d-1

city: La Jolla

first: Kristin

last: Baldwin

state: California

address: 10550 North Torrey Pines Road

department: Department of Neuroscience

institute: The Scripps Research Institute

description:
High intensity Tac2-Cre-positive habenula cells
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Adapters and low quality bases were removed using Trimmomatic (v0.32, ILLUMINACLIP: TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3), reads were then aligned using STAR and counts were generated using HTSeq. Mm10 did not include Ascl5, therefore, we added it to the reference GTF file in HTSeq
Raw and vsd-normalized count tables were generated using the R package, 'DESeq2'.
Genome_build: mm10
Supplementary_files_format_and_content: Raw and vsd-normalized counts are supplied as tab-delimited text files for all bulk RNA-Seq samples.

source_name: Habenula

growth_protocol: For reprogramming of induced neurons, transcription factors were induced 48 hours post-lentivral infection, by adding DMEM+10% FBS media (MEF media) supplemented with 5 μM doxycycline (Sigma). Four days after initiating induction with doxycycline, MEF media was replaced with N3 media as published in Vierbuchen, et al. (2010) but using N2 supplement (Gibco) in replacement of some individual components.  Eight days post-induction, doxycycline was withdrawn.  10 days post-induction, media was switched to neural maintenance media, which consisted of a 1:1 mix of N3 media and Neurobasal (Invitrogen) supplemented with B27 (minus vitamin A, Gibco) and bFGF (10 ng/ml) (N3/NB media).

extract_protocol:
Direct-zol RNA MiniPrep Kit (Zymo Rsearch)
Clontech SMARTER Ultra Low Input RNA for Sequencing -v3

tag: cell type

value: Neural cells

tag: day post-induction

tag: age

tag: purfication method

value: FACS

tag: rna input amount

value: 7 ng


title: N3O4_single_cells

description:
Read1 (26bp) and Read2 (98bp) with a single index (8bp)
FourTFpairs_withTFnames_10x_singlecell.txt
N/A

data_processing:
Samples were de-multiplexed, aligned and analyzed using 10X Genomics CellRanger (ver.1.3.1) pipeline with default parameters. This pipeline implements STAR as an alignment tool.
Multiple libraries were aggregated using the ‘cellranger aggr --normalized=mapped (default)’ command where mapped reads are sub-sampled so that each iN combination would have the same effective sequencing depth.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized log2 UMI tables are supplied as tab-delimited text files for all single-cell RNA-Seq samples.

source_name: Embryonic fibroblast (E13.5)

extract_protocol:
10x Genomics ChromiumTM Single Cell 3’ V2 Reagent Kit
10x Genomics ChromiumTM Single Cell 3’ V2 Reagent Kit

value: TauEGFP-positive induced neurons

tag: strain

value: TauEGFP

tag: reprogramming factors

value: Neurog3, Pou5f1


title: N3P1_single_cells

description:
Read1 (26bp) and Read2 (98bp) with a single index (8bp)
Supplemental_FiveTFpairs_10x_singlecell.txt
N/A

value: Pooled TauEGFP-positive and negative cells

value: Neurog3, Pou1f1


title: MHb-v-1

description:
Low intensity Tac2-Cre-positive habenula cells
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: N3-O4-1

description:
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: 10 ng


title: N1B3a_single_cells

value: Neurog1, Pou4f1


title: MHb-v-2


title: genomic DNA from PL131 EOPE  placenta

tag: subject id

tag: pathology group

value: EOPE

tag: fetal sex

value: FEMALE

tag: gestational age

value: Chorionic Villi


title: N3B4_single_cells

value: Neurog3, Pou3f4


title: OB-MT-3

description:
Pcdh21-positive Mitral and Tufted cells
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

source_name: Olfactory bulb


title: Sham_Vehicle_2

tag: tissue


title: genomic DNA from PL130 EOPE placenta

value: MALE

tag: sample tissue

tag: 450k plate

tag: 450k sentrix_id

tag: 450k sentrix_position


title: OB-MT-2


title: OB-MT-1


title: OB-GC-2

description:
Pcdh21-negative olfactory bulb cells
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: OB-GC-3


title: HIP-2

description:
Tac2-Cre-positive hippocampal cells
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

source_name: Hippocampus

value: 5 ng


title: A2NR1_single_cells

value: Ascl2, Nr4a2


title: CTX-2

description:
High intensity TauEGFP-positive cortical cells
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

source_name: Cortex

value: Neural cells


title: HIP-1

value: FACS


title: CTX-1


title: CER-1

description:
High intensity TauEGFP-positive cerebellar cells
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

source_name: Cerebellum


title: CER-2


title: DRG-2

description:
TauEGFP-positive dorsal root ganglion cells
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

source_name: Dorsal root ganglion


title: A2-B3a-2

value: Ascl2, Pou4f1


title: DRG-1


title: MHb-d-2

value: 7 ng


title: Brain-2

description:
RNA from Clontech SMARTER Ultra Low Input RNA for Sequencing -HV
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

source_name: Whole brain

value: WT BALB/c


title: ND2-B3c-1

value: TauEGFP-positive induced neurons

value: TauEGFP

value: NeuroD2, Pou4f3


title: Brain-1

value: 10 ng


title: ND2-B3c-2

value: 2 ng


title: N3-P1-1

value: Neurog3, Pou1f1


title: N3-P1-2


title: N3-O4-2

description:
alternate id: N3-O4-6
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Neurog3, Pou5f1


title: N3-B4-2

description:
alternate id: N3-B4-4
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: OB-GC-1


title: N3-B4-1

description:
alternate id: N3-B4-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: X3-5

city: Wuhan

first: Chuan

last: Liu

state: Hubei

address: Luojiashan

department: College of Life Sciences

country: China

institute: Wuhan University

data_processing:
RNA-Seq reads were aligned to the Nipponbare (IRGSP-1.0)  genome assembly using TopHat2
The "FPKM" and "CPM" was calculated according to Cuffdiff in the Cufflinks software
Genome_build: Nipponbare (IRGSP-1.0)
Supplementary_files_format_and_content: ".xls" files include "FPKM" and "Normalized (CPM)" for each sample

organism: Oryza sativa Indica Group

source_name: The uppermost fully expanded leaves

growth_protocol: natural long-day conditions

extract_protocol:
Total RNA was isolated from each leaf sample with aTRIzol reagent (Invitrogen, Carlsbad,CA, USA) according to the manufacturer's instructions. The total RNA was treated with RNase-free DNase I (New England Biolabs, Ipswich, MA, USA) to eliminate genomic DNA contamination.
The cDNA library was constructed according to the protocol that is provided with the NEBNext Ultra RNA Library Prep Kit for Illumina, NEB #E7530 (New England Biolabs, Inc.).

tag: developmental stage

value: 45 days seedlings

tag: sampling time

tag: genotype/variation

value: OsPRR37 overexpression in Guangluai4


title: X2-5


title: X3-2


title: X2-6


title: X3-4


title: X3-1


title: X2-4


title: X3-3


title: X2-3


title: N3-B3c-2

description:
alternate id: N3-B3c-3
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

tag: cell type

tag: day post-induction

tag: age

value: Neurog3, Pou4f3


title: N3-B3b-2

description:
alternate id: N3-B3b-5
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

tag: strain

tag: purfication method

tag: rna input amount

value: Neurog3, Pou4f2


title: N3-B3a-2

description:
alternate id: N3-B3a-6
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

tag: reprogramming factors

value: Neurog3, Pou4f1


title: X2-1


title: X1-6


title: N3-B3b-1

description:
alternate id: N3-B3b-5-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: X1-5


title: X3-6


title: N3-B3a-1

description:
alternate id: N3-B3a-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: X1-4


title: X1-3


title: N3-B2-2

description:
alternate id: N3-B2-4
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Neurog3, Pou3f2


title: N2-P1-2

description:
alternate id: N2-P1-5
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: FACS

value: Neurog2, Pou1f1


title: N2-P1-1

description:
alternate id: N2-P1-5-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: X1-1


title: G3-6


title: G3-4


title: N3-B3c-1

description:
alternate id: N3-B3c-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: G3-3


title: N2-B3a-2

description:
alternate id: N2-B3a-3
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Neurog2, Pou4f1


title: N2-B3c-2

description:
alternate id: N2-B3c-6
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Neurog2, Pou4f3


title: N2-B3a-1

description:
alternate id: N2-B3a-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: TauEGFP-positive induced neurons


title: G3-5


title: N2-B3c-1

description:
alternate id: N2-B3c-6-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: TauEGFP


title: N2-B3b-2

description:
alternate id: N2-B3b-6
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: 5 ng

value: Neurog2, Pou4f2


title: N2-B3b-1

description:
alternate id: N2-B3b-5
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: 10 ng


title: X2-2


title: N2-B2-2

description:
alternate id: N2-B2-5
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Neurog2, Pou3f2


title: G2-6


title: G3-1


title: G2-5


title: Cre-negative control iPSC-2

city: Clayton

first: Minna-Liisa

last: Anko

state: VIC

address: 15 Innovation Walk

department: Department of Anatomy and Developmental Biology

institute: Monash University

data_processing:
Paired-end RNA-seq reads aligned to the mm10 reference genome using STAR (v2.5.2) with default parameters
For alternative splicing analysis (MISO), the iPS-1 and iPS-2 control replicates were merged using samtools-merge (Samtools v1.2); producing a combined alignment for the control condition.
Differential splicing analysis was done using MISO v0.5.4 (LINK1; in a relaxed configuration where filter_results = False) and the mm10 alternative event annotation (version 2; LINK2). For each AS event type, the treatment replicates were compared to the combined control (using miso_compare).
Differential gene expression (DEG) was analysed using R with voom/limma to generate a CSV file that was uploaded to degust (https://drpowell.github.io/degust/).
Genome_build: mm10
Supplementary_files_format_and_content: .csv file containing log-fold chang, p-value, FDR and read counts for DEGs;  MISO output as .xlsx file containing each AS type in separate sheet

source_name: iPSC

growth_protocol: iPSCs were maintained on irradiated MEF feeder cells in iPSC medium without penicillin/streptomycin (KnockOut DMEM, 15% FBS, 2mM Glutamax, 1mM MEM non-essential amino acids, 1000U/ml Leukemia Inhibitory Factor (LIF), 1uM beta-mercaptoethanol). MEFs were depleted before iPSC collection for analysis.

extract_protocol:
RNA extraction was performed using TriReagent (Sigma)
The sequencing libraries were generated using Illumina TruSeq poly-A selection with strand specific chemistry.
75 bp paired-end seqeuncing using Illumina NextSeq550 High output mode and v2 chemistry (Illumina protocol 15046563 v02)

treatment_protocol: SRSF3 depletion was induced by 5uM 4-hydroxy-tamoxifen (4-OHT) for 24h.

tag: cre- or cre+

value: Cre-negative

value: iPSC

tag: genotype

value: control


title: Cre-negative control iPSC-1


title: Cre-positive SRSF3-KO-2

value: Cre-positive

value: SRSF3 knockout


title: Cre-positive SRSF3-KO-1


title: N2-B2-1

description:
alternate id: N2-B2-5-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: N1-P1-2

description:
alternate id: N1-P1-5
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Neurog1, Pou1f1


title: G2-4

value: 45 days seedlings


title: N3-B2-1

description:
alternate id: N3-B2-3
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: FACS

value: Neurog3, Pou3f2


title: X1-2

value: OsPRR37 overexpression in Guangluai4


title: G2-3


title: G2-2


title: N1-B3c-2

description:
alternate id: N1-B3c-6
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Neurog1, Pou4f3


title: G3-2


title: N1-B3c-1

description:
alternate id: N1-B3c-6-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: TauEGFP-positive induced neurons


title: N1-B3b-1

description:
alternate id: N1-B3b-5-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: TauEGFP

value: Neurog1, Pou4f2


title: N1-B3b-2

description:
alternate id: N1-B3b-5
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: G2-1


title: G1-5


title: N1-B3a-2

description:
alternate id: N1-B3a-3
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Neurog1, Pou4f1


title: G1-6


title: G1-4


title: G1-3


title: N1-B3a-1

description:
alternate id: N1-B3a-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: 10 ng


title: N1-P1-1

description:
alternate id: N1-P1-5-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: G1-1


title: N1-B2-1

description:
alternate id: N1-B2-5-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Neurog1, Pou3f2


title: N1-B2-2

description:
alternate id: N1-B2-5
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: G1-2


title: N1-B1-1

description:
alternate id: N1-B1-5
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Neurog1, Pou3f3


title: N1-B1-2

description:
alternate id: N1-B1-6
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: 5 ng


title: MEFs-2

description:
alternate id: MEFs-sorted-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Embryonic fibroblasts


title: Exp_4

city: Rochester

first: John

middle: Andrew

last: Smestad

state: Minnesota

address: 200 1st St. SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v2.2.3
Fragments Per Kilobase Million (FPKM) were calculated using systemPipeR
Genome_build: mm9

source_name: immortalized mouse embryonic fibroblast cell line

growth_protocol: Cells grown in DMEM (low glucose) containing 10% FBS at 37 degrees Celsius in 5% CO2.

extract_protocol:
Cells harvested by trypsinization.  Total RNA isolated from cells using Qiagen Rneasy Micro Kit.
Standard TruSeq v2 for mRNA

treatment_protocol: Gene rearrangement induced by adding doxycycline to media at 1 microgram/mL final concentration.

tag: line

tag: category

value: experimental


title: Exp_1


title: Exp_8


title: Exp_16


title: Exp_3


title: Ctl_2

value: control


title: Exp_7


title: MEFs-1

description:
alternate id: MEFs-sorted-1
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: Atoh1-B3c-2

description:
alternate id: Atoh1-B3c-6
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Atoh1, Pou4f3


title: Atoh1-B3c-1

description:
alternate id: Atoh1-B3c-6-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: A5-B3c-2

description:
alternate id: A5-B3c-6
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Ascl5, Pou4f3


title: A5-B3c-1

description:
alternate id: A5-B3c-5
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: FACS


title: A2-P1-2

description:
alternate id: A2-P1-6
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Ascl2, Pou5f1


title: Ctl_1


title: A2-P1-1

description:
alternate id: A2-P1-6-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: A2-Nurr1-1

description:
alternate id: A2-Nurr1-5
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Ascl2, Nr4a2


title: input

city: Salt Lake City

first: Kathleen

last: Clark

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

library_source: genomic

data_processing:
Reads aligned to genome version hg19 using Novoalign v.3.08.02
Peak calling performed with MACS2 using presets, comparing input and FLAG ChIP reads for each cell line.
Sorted BAM files were generated from the Novoalign output SAM files using Samtools v. 1.5
Bigwig files were generated from the sorted BAM files using DeeTools
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig

source_name: RWPE1-FLAG-ERG and RWPE1-FLAG-EHF

growth_protocol: Early passage RWPE1 cells were infected with retrovirus expressing either FLAG-ERG or FLAG-EHF and selected with hygromycin for 2 weeks. Cells were expanded in multiple 150 mm dishes and harvested for ChIPseq

extract_protocol:
Lysates were clarified from sonicated nuclei and taggedprotein-DNA complexes were isolated with anti-FLAG antibody.
Libraries were prepared for combined input for RWPE1-FLAG-ERG and RWPE1-FLAG-EHF, as well as ChIP DNA from FLAG immunoprecipitations form each cell line using NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina.

treatment_protocol: nearly confluent 150 mm dishes were treated with 1% formaldehyde, and harvested in Farnham lysis buffer and a crude nuclear pellet collected after centrifugation.

tag: cell line

value: normal prostate epithelial cells

tag: infection

value: retrovirus expressing FLAG-ERG and FLAG-EHF

tag: chip antibody


title: A2-Nurr1-2

description:
alternate id: A2-Nurr1-6
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: TauEGFP-positive induced neurons

value: TauEGFP


title: A2-B3c-1

description:
alternate id: A2-B3c-5
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Ascl2, Pou4f3


title: A2-B3c-2

description:
alternate id: A2-B3c-6
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: 10 ng


title: FLAG-EHF_ChIPSeq

value: retrovirus expressing FLAG-EHF

value: anti-FLAG antibody


title: A2-B3b-2

description:
alternate id: A2-B3b-3
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Ascl2, Pou4f2


title: FLAG-ERG_ChIPSeq

value: retrovirus expressing FLAG-ERG


title: A2-B3b-1

description:
alternate id: A2-B3b-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: A2-B3a-1

description:
alternate id: A2-B3a-4-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Ascl2, Pou4f1


title: A2-B2-1

description:
alternate id: A2-B2-5-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Ascl2, Pou3f2


title: A2-B2-2

description:
alternate id: A2-B2-5
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: GM19144 ribosome protected fragments

city: Chicago

first: Sidney

last: Wang

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

data_processing:
Sequencing image analysis and basecalling were performed using CASAVA version 1.7.0
Raw data provided are fastq files after the following processing. FASTX-Toolkit were used to clip the adaptor sequence and trim the 5' most base for each read. Reads that are shorter than 22-nt or that are mapped to rRNA, tRNA, snoRNA using bowtie were removed from the file.
For the supplement count-table, processed reads are then map to human genome (hg19) or chimpanzee genome (PanTro3) or rhesus macaque gemome (rheMac2) respectively using BWA. Uniquely mapped reads are used to intersect with orthologous gene annotations using BEDTools to get read count per gene for each individual.
Genome_build: hg19 or PanTro3 or rheMac2
Supplementary_files_format_and_content: Processed data file contains read count per orthologous gene for each individual. It is organized with one individual per column and one gene per row. The first two columns are ENSG ID and gene length.

molecule: cytoplasmic RNA

source_name: HapMap

growth_protocol: Cells were cultured at 37 degree Celsius and 5% CO2 in RPMI 1640 (supplemented with 2mM L-glutamine and 15% fetal bovine serum)

extract_protocol:
Ribosome footprint profiling experiments were performed using ARTseqTM Ribosome Profiling kit for mammalian cells (RPHMR12126) following vendor’s instructions. Cell lysates were prepared from flash frozen pellets of 30 to 50 million live cells by repeat pipetting in 1 ml cold lysis buffer. Sephacryl S400 spin column (GE; 27-5140-01) was used for monosome isolation. For rRNA depletion, Ribo-Zero Magnetic Kit (Epicentre; MRZH11124) was used.
Ribosome footprint cDNA libraries were PCR amplified (12 to 15 thermo-cycles) and barcoded using ScriptMiner Index PCR Primers (Epicentre; SMIP2124). Indexed libraries were pooled to sequence on an Illumina HiSeq 2500.

tag: gender

value: Male

value: Lymphoblastoid Cell Line

tag: enrichment type

value: ribosome protected fragments


title: PHx_n_1071: PHx-12h-Pparafl/fl

city: Beijing

first: Guomin

last: Xie

address: fengtai youanmen

institute: University

description: Gene expression data from Pparafl/fl mice liver at 12 hours after PHx operation

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mice Gene 2.0. GeneChip were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7 G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Mice liver from Pparafl/fl mice at 12 hour after PHx operation

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

growth_protocol: At 12 to 24 hours after PHx, the mice liver decelop marked steatosis, therefore, the time point of 12 hour after PHx was choosen for perform microarry analysis.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The WT (Pparafl/fl) mice and hepatocyte-specific PPARα disruption (Ppara△Hep) mice were performed PHx or Sham operation, and the liver tissue were harvested at 12 hour after PHx.

tag: tissue

value: Liver

tag: genotype/variation

value: Pparafl/fl


title: PHx_n_1072: PHx-12h-Pparafl/fl


title: PHx_p_1044: PHx-12h-Ppara△Hep mice liver

description: Gene expression data from Ppara△Hep mice liver at 12 hours after PHx operation

source_name: Mice liver from Ppara△Hep mice at 12 hour after PHx operation

value: Ppara△Hep


title: PHx_n_1043: PHx-12h-Pparafl/fl


title: PHx_p_1074: PHx-12h-Ppara△Hep mice liver


title: GM19137 ribosome protected fragments

value: Female

tag: cell type


title: con_n_1052: Sham-12h-Pparafl/fl

description: Gene expression data from Pparafl/fl mice liver at 12 hours after sham operation

source_name: Mice liver from Pparafl/fl mice at 12 hour after sham operation


title: con_p_1054: Sham-12h-Ppara△Hep mice liver

description: Gene expression data from Ppara△Hep mice liver at 12 hours after sham operation

source_name: Mice liver from Ppara△Hep mice at 12 hour after sham operation


title: con_n_1055: Sham-12h-Pparafl/fl


title: con_p_1056: Sham-12h-Ppara△Hep mice liver


title: PHx_p_1045: PHx-12h-Ppara△Hep mice liver


title: PHx_n_1064: PHx-12h-Pparafl/fl


title: PHx_p_1073: PHx-12h-Ppara△Hep mice liver


title: con_p_1053: Sham-12h-Ppara△Hep mice liver


title: A1-B4-2

description:
alternate id: A1-B4-4
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: TauEGFP-positive induced neurons

tag: day post-induction

tag: age

value: FACS

value: Ascl1, Pou3f4


title: A1-O4-1

description:
alternate id: A1-O4-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

tag: strain

value: TauEGFP

tag: purfication method

value: 10 ng

value: Ascl1, Pou5f1


title: A1-Nurr1-2

description:
alternate id: A1-Nurr1-6
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

tag: rna input amount

tag: reprogramming factors

value: Ascl1, Nr4a2


title: A1-P1-2

description:
alternate id: A1-P1-4
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Ascl1, Pou1f1


title: con_p_1062: Sham-12h-Ppara△Hep mice liver


title: con_n_1063: Sham-12h-Pparafl/fl


title: con_n_1061: Sham-12h-Pparafl/fl


title: A1-O4-2

description:
alternate id: A1-O4-4
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: A1-B3c-2

description:
alternate id: A1-B3c-3
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Ascl1, Pou4f3


title: A1-Nurr1-1

description:
alternate id: A1-Nurr1-6-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: GM19127 ribosome protected fragments


title: A1-B4-1

description:
alternate id: A1-B4-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: A1-P1-1

description:
alternate id: A1-P1-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: A1-B3c-1

description:
alternate id: A1-B3c-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: LuCaP 170 2 organoids G8 2

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

description:
200627820019_R08C02
LuCaP170.2-G8-Rep2

hyb_protocol: SDNA from each sample was quality checked using an Agilent TapeStation 2200 and PicoGreen Assay, and an aliquot of 200 ng of DNA was fragmented and prepared into libraries for hybridization to Illumina OmniExpress BeadChip Arrays at the National Cancer Institute, Cancer Genomics Research Laboratory.

scan_protocol: Samples were scanned using an iScan system.

data_processing:
Data was clustered against a panel of normal provided by Illumina using GenomeStudio (Illumina) and exported for analyses in Nexus Copy Number version 8 (BioDiscovery)  used for calling somatic copy number alterations.
the 'SomaticCopyNumber.seg' contains the log2 copy number values generated from probe medians derived by Nexus Copy Number,  for each segment of the genome.

label: Allele-specific single base extension of the primer incorporates a biotin nucleotide or a dinitrophenyl labeled nucleotide. C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled.

source_name: LuCaP 170 2 organoids G8

label_protocol: Samples were labeled using Infinium probe designs.

growth_protocol: LuCaP tumors were grown in mice or as organoids.

extract_protocol: Genomic DNA was extracted from fresh frozen PDX tissue and from fresh organoids, using a Qiagen AllPrep DNA/RNA Mini Kit.

treatment_protocol: Organoids were passaged.

tag: subject id

value: LuCaP 170.2

value: male

value: PDX-derived organoid

tag: generation

tag: replicate


title: LuCaP 170 2 organoids G2 2

description:
200627820019_R04C02
LuCaP170.2-G2-Rep2

source_name: LuCaP 170 2 organoids G2


title: LuCaP 170 2 organoids G8 1

description:
200627820019_R06C02
LuCaP170.2-G8-Rep1


title: A1-B3b-2

description:
alternate id: A1-B3b-5
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

source_name: Embryonic fibroblast (E13.5)

value: Ascl1, Pou4f2


title: A1-B3b-1

description:
alternate id: A1-B3b-5-2
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: LuCaP 170 2 organoids G2 1

description:
200627820019_R02C02
LuCaP170.2-G2-Rep1


title: LuCaP 170 2 PDX tissue 2

description:
200627820019_R11C02
LuCaP170.2-PDX-Rep2

source_name: LuCaP 170 2 PDX tissue

value: LuCaP tumor-derived xenografts (PDXs)


title: A1-B3a-2

description:
alternate id: A1-B3a-6
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Ascl1, Pou4f1


title: A1-B3a-1

description:
alternate id: A1-B3a-4
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt


title: LuCaP 170 2 PDX tissue 1

description:
200627820019_R09C02
LuCaP170.2-PDX-Rep1


title: LuCaP 167 organoids G8 2

description:
200627820019_R03C02
LuCaP167-G8-Rep2

source_name: LuCaP 167 organoids G8

value: LuCaP 167


title: A1-B2-1

description:
alternate id: A1-B2-3
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: Ascl1, Pou3f2


title: SERa+3

city: Genova

first: Sara

last: Stigliani

address: largo R Benzi 10

country: Italy

institute: IRCCS AOU San Martino-IST

hyb_protocol: hybridization was performed in Agilent Oven for 17 hours at 65°C 10 rpm.

scan_protocol: After washing and scanning using Agilent Scanner G2505C, data were extracted using Feature Extraction software v10.7, protocol GE1_1100_Jul11.

data_processing: Tab-delimited text files containing FE results were acquired and analyzed in R v3.1.3 software environment (www.r-project.org) using the limma package v3.22.7 (Smyth 2005). To perform a quantitative analysis, only spots with positive signal minus background (“gBGSubSignal” FE field name) were used in the following analysis as “detected” spots. In each two-groups comparison, probes with less than 75% of detected spots across all arrays in one of the two groups were removed from the analysis. Similarly, arrays with a number of detected spots smaller than a predefined cutoff (equal to the average number of detected spots minus two times the standard deviation across all arrays) were removed. Background corrected intensities (gBGSubSignal) of duplicate spots on each array were averaged. Data were then log2-transformed and normalized for between-array comparison using scale normalization (Yang 2002; Yang 2003). Differential expression analysis between groups was carried out using Student's t-test (unpaired, two-tailed, unequal variance). Probes with False Discovery Rate (FDR) < 0.1 (Benjamini 1995) and fold-change between the two groups larger than 3 were selected as differentially expressed genes.

source_name: pool of 8 oocytes

label_protocol: Five ng of total RNA were amplified using Ovation Pico WTA System V2 (NuGEN Technologies, San Carlos, CA) then labelled according to Agilent Enzymatic Labelling Kit, 3 ug was hybridized to Human GE 4x44K v2 Microarray Kit (Agilent Technologies) containing probes for 41,000 human transcripts

extract_protocol: Total RNA was extracted from each pool of 8-10 oocytes using the miRNeasy Micro kit (Qiagen, Helden, Germany), according to the manufacturer’s procedure. Quantification and quality control of total RNA were performed by RNA 6000 Pico kit on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: sample type

value: oocytes presenting SERa

value: female


title: A1-B2-2

description:
alternate id: A1-B2-4
bulk_rawcounts_iNscreen.txt
bulk_normcounts_iNscreen.txt

value: TauEGFP-positive induced neurons

value: FACS


title: SERa-1

source_name: pool of 10 oocytes

value: normal oocytes


title: SERa-3


title: Root tip after Al treatment C0, biological repeat 3(T3)

city: Hangzhou

first: Gezi

last: Li

address: #866,Yuhangtang Road

institute: Zhejiang University

description:
Gene expression data after Al treatment.
R6W_T_4_NS

hyb_protocol: The labeling, hybridization and scanning steps were carried out at a core facility. 10 ug of cRNA were hybridized for 16 hr at 45C.  GeneChips were washed and stained in the Affymetrix The labeling, hybridization and scanning steps were carried out at a core facility. Fluidics Station 450.

scan_protocol: The labeling, hybridization and scanning steps were carried out at a core facility. GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.  Please note that the values in the sample tables differ from those in the CHP files.  The CHP files are also provided in text format for convenience.

organism: Oryza sativa

source_name: Japonica rice

label_protocol: The labeling, hybridization and scanning steps were carried out at a core facility. 6 ug total RNA were prepared for biotinylated cRNA according to the standard Affymetrix protocol(Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seeds were soaked and germinated in water at room temperature (25-26°C) for 1-2 d and then transferred to a net floating on a 0.5 mM CaCl2 solution.

extract_protocol: Total RNA was isolated using TRIZOL Reagent (Life Technologies, Carlsbad, CA), and purified using an RNeasy mini kit and RNase-Free DNase Set (QIAGEN, GmBH, Germany), according to the standard protocols.

treatment_protocol: 5-d-old seedlings were exposed to a 0.5 mM CaCl2 solution containing 50 μM Al (pH 4.5) for 6 h, and then root tips were calculated and Al contents in root tips (0-1 cm) were selected for next experiment

tag: cultivar

value: Japonica

value: root tip


title: SERa-2


title: SERa+1


title: Root tip after Al treatment C0, biological repeat 2(T2)

description:
Gene expression data after Al treatment.
R6W_T_3_NS


title: Root tip after Al treatment, biological repeat 1(T1)

description:
Gene expression data after Al treatment.
R6W_T_2_NS


title: LuCaP 167 organoids G8 1

description:
200627820019_R01C02
LuCaP167-G8-Rep1


title: Root tip before Al treatment, biological repeat 1(C1)

description:
Gene expression data before Al treatment.
R6W_C_1_NS


title: Root tip before Al treatment  C0, biological repeat 3(C3)

description:
Gene expression data before Al treatment.
R6W_C_3_NS


title: SERa+2


title: 6 Gy X-ray irradiated gastric tissue-3

city: suzhou

first: zhang

middle: shu

last: yu

state: Jinagsu

address: 199 Ren'ai Rd

department: Radiation Medicine

institute: soochow University

description: 6 Gy X-ray irradiated gastric tissue-3. The mouse was sacrificed 7 days after irradiation and gastric tissues were collected. RNA was extracted and quantified. mRNA and lncRNA profilings of each groups were analyzed by microarray.

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression（4*180K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 14.8(Agilent). Probe that at least 1 out of 2 groups flagged as Detected were maintained.

source_name: 6 Gy X-ray irradiated gastric tissue-3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: C57 mice were housed in a pathogen-free environment at the facilities of Medical School of Soochow University. Animals were anesthetized with an intraperitoneal injection of ketamine (75 mg/kg) and xylazine (10 mg/kg) (Sigma).

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: The stomach of C57 mice were exposed to 0, 6 and 12 Gy X-ray irradiation at a dose rate of 2 Gy/min. The mice were sacrificed 7 days after irradiation and gastric tissues were collected.

tag: treatment

value: 6 Gy X-ray irradiated


title: 6 Gy X-ray irradiated gastric tissue-2

description: 6 Gy X-ray irradiated gastric tissue-2. The mouse was sacrificed 7 days after irradiation and gastric tissues were collected. RNA was extracted and quantified. mRNA and lncRNA profilings of each groups were analyzed by microarray.

source_name: 6 Gy X-ray irradiated gastric tissue-2


title: Mock irradiated gastric tissue-1

description: Mock irradiated gastric tissue-1. The mouse was sacrificed 7 days after irradiation and gastric tissues were collected. RNA was extracted and quantified. mRNA and lncRNA profilings of each groups were analyzed by microarray.

source_name: Mock irradiated gastric tissue-1

value: Mock irradiated


title: LuCaP 167 organoids G2 1

description:
200627820019_R10C01
LuCaP167-G2-Rep1

source_name: LuCaP 167 organoids G2

tag: gender


title: Root tip before Al treatment, biological repeat 2(C2)

description:
Gene expression data before Al treatment.
R6W_C_2_NS


title: LuCaP 167 PDX tissue 2

description:
200627820019_R08C01
LuCaP167-PDX-Rep2

source_name: LuCaP 167 PDX tissue


title: Mock irradiated gastric tissue-3

description: Mock irradiated gastric tissue-3. The mouse was sacrificed 7 days after irradiation and gastric tissues were collected. RNA was extracted and quantified. mRNA and lncRNA profilings of each groups were analyzed by microarray.

source_name: Mock irradiated gastric tissue-3


title: LuCaP 167 PDX tissue 1

description:
200627820019_R06C01
LuCaP167-PDX-Rep1


title: Mock irradiated gastric tissue-2

description: Mock irradiated gastric tissue-2. Themouse was sacrificed 7 days after irradiation and gastric tissues were collected. RNA was extracted and quantified. mRNA and lncRNA profilings of each groups were analyzed by microarray.

source_name: Mock irradiated gastric tissue-2


title: LuCaP 167 organoids G2 2

description:
200627820019_R12C01
LuCaP167-G2-Rep2


title: Hepatocyte_5hmDIP

status: Public on May 09 2018

city: Philadelphia

first: Klaus

middle: H

last: Kaestner

state: PA

address: University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard

department: Department of Genetics and Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine

institute: University of Pennsylvania

data_processing:
Read alignment (genome build mm9) and extraction of single-base resolution methylation levels were carried out by BSMAP v2.74 [Xi, 2009 #5747] using the following commands:
bsmap -a sample_R1_val_1.fq.gz -b sample_R2_val_2.fq.gz -d mm9_AllGenome.fa -o bam_file -R -D C-CGG
python methratio.py -i “no-action” -p -g -z -o sample_trim_galore_mm9.fa.meth -d mm9_AllGenome.fa bam_file
Percent methylation was calculated for one-hundred-base pair tiles with a minimum coverage of 10 CpGs.
Genome_build: mm9

source_name: Hepatocyte

extract_protocol: DNA was isolated from hepatocytes harvested from 20 day-old mice and sheared with the M220 Focused-ultrasonicatorTM (Covaris) using snap-cap tubes. Libraries were generated using NEBNext Ultra DNA Library Prep Kit (NEB E7645). Library DNA was denatured in 95C for 10 min. Denatured DNA was precipitate with 5hmc Ab (active motif 55010) and sequenced (50 bp single-end) on Next-seq (Illumina).

value: wild type

value: Hepatocyte


title: Liver_atac_wt_rep1

data_processing:
Atac-seq 75 PE sequences were obtained from NEXTSEQ. Sequences were trimmed with cutadapt v.1.15 and aligned with bowtie2 v 2.2.4. Duplicated sequences were removed with samtools rmdup mitochondrial DNA was removed as well and then peak files were generated  by Homer (findPeaks, factor style).
Genome_build: mm9

source_name: Liver

extract_protocol: The ATAC-Seq protocol was carried out on WT or Tet2/3 DKO hepatocytes with the following modifications. Nuclei were washed with 150 μl of cold PBS, pelleted at 2,000 g at 4°C for 5 min, resuspended in 150 μl of cold lysis buffer and then re-pelleted for 2,000g at 4°C for 10 min. Nuclei were re-suspended in 150 μl of transposition reaction mix and incubated at 37 C for 30 min. DNA was isolated (Qiagen MinElute Reaction Cleanup Kit) and subjected to PCR amplification to make the library as described[Buenrostro, 2013 #6098]. Magnetic beads (AMPure XP) were used to purify an ATAC-Seq library as described (Ackermann AM et al.), followed by quality control with a high-sensitivity DNA bioanalysis chip (Agilent), quantification with KAPA (Illumina) and QuBit. The libraries were sequenced (75 bp paired-end) on Next-Seq (Illumina).

value: Liver


title: Liver_atac_ko_rep1

value: TET2 and TET 3 was deleted after birth in hepatocytes


title: Liver_atac_ko_rep2


title: Liver_atac_wt_rep2


title: RNA-seq of mesenchymal stromal/stem cells (MSC) LPS treated for 6 hrs

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

institute: University of Ulm

data_processing:
Demultiplexing of raw reads were done using standard Illumina protocol
Demultiplexed fastq reads alignment using Tophat2 using Bowtie2 index
cufflinks based transcripts assembly
cuffdiff based differential gene expression
Genome_build: h38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: mesenchymal stromal/stem cells (MSC)

extract_protocol:
Total RNA was isolated from the MSCs and rRNA was removed using ribozero gold (Illumina). The rRNA depleted RNA was used for library preparation using TruSeq Directional RNAseq kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MSCs were treated with 100 ng of lipopolysaccharide (LPS) for 0 hrs, 6 hrs and 24 hrs

value: LPS treated for 6 hrs


title: RNA-seq of mesenchymal stromal/stem cells (MSC) LPS treated for 24 hrs

value: LPS treated for 24 hrs


title: TC1

city: Shanghai

first: Xueqing

last: Geng

state: Shanghai

address: Dongchuan Road 800#

department: School of Agriculture and Biology

institute: Shanghai JiaoTong University

data_processing:
Illumina Casava1.7 software used for basecalling.
High-quality reads were obtained from raw RNA-seq data after the removal of adapter sequences, 5′ and 3′ ends, low-quality bases (Q < 20), and < 25 bp reads.
Selected reads were assembled using Trinity (Trinity Software, Plymouth, NH, USA; http://trinitynaseq.sf.net) and clustered with TGICL Clustering tools (Institute for Genomic Research, Rockville, MD, USA).
Reads Per Kilobase per Million mapped reads (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Tribolium castaneum (Tcas3.26)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Tribolium castaneum

source_name: red flour beetle

growth_protocol: Full-grown late-instar larvae (≥ 5 mm in length, 20 days from oviposition) were used in this research.

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

treatment_protocol: For the hypoxia/hypercapnia treatment, 20 naked last-instar larvae were placed together in a 1-L glass bottle with whole-grain flour with 5% (w/v) yeast. Septum bottles with larvae were connected to the outlet of pressure gauges of gas cylinders via plastic tubing. Premixed gas (2% oxygen + 18% carbon dioxide + 80% nitrogen; Hesheng Specialty Gases, Shanghai, China) was delivered to the bottles for 9 s at 70 kPa as measured by a manometer and controlled by a regulator. Then the bottles were immediately tightly sealed with a rubber septum.

value: 20 days from oviposition

tag: genotype


title: TC2


title: RNA-seq of mesenchymal stromal/stem cells (MSC) Control

value: control


title: pooled samples from 11 patients with adenocarcinoma confirmed by histology. The median age of patients was 47.

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 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.

source_name: cervical tissues

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

extract_protocol:
A cotton swab was used to collect the cervical mucus. Each cotton swab was soaked in 900 µL of QIAzol Lysis Reagent. Total RNA was extracted with the miRNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany).
A total of 2 micro gram of extracted total RNA from the pooled samples in each disease category was prepared and 250 ng of this was labelled with a 3D-Gene miRNA labelling kit (Toray) followed by hybridizing onto 3D-Gene Human miRNA Oligo chips (Toray).

tag: histology

value: adenocarcinoma

tag: median age

tag: tissue

value: cervical tissues


title: GLD2KO1

city: Worcester

first: Dr Yvonne

last: Edwards

state: MA

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

data_processing:
The fastq reads were demultiplexed using the fastx barcode_splitter of the FASTX-toolkit (v0.0.14) (http://hannonlab.cshl.edu/fastx_toolkit/index.html) allowing 1-bp mismatch in the barcode (that is 4 bp long).
Poor quality reads and the barcodes were trimmed out using Trimmomatic (v0.32) (Bolger et al. 2014).
Adapter sequence and reads <12 bp were removed using Cutadapt (v1.3) (http://cutadapt.readthedocs.org/en/stable/guide.html).
The preprocessing step resulted in 12 fastq sequences, each ranging between 3.0 and 5.3 million; and the sequence length distribution peaks between 21 and 23 bp, indicative of miRNA enrichment
The 12 preprocessed fastq sequences were used as input for the mirDeep2 analysis.   The Mapper processes raw reads including mapping the processed reads to the reference genome. (b) The Quantifier module sums up read counts for known miRNA. In this analysis, the mouse genome (Ensembl GRCm38) and mirBase annotation (version 21) are used.
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: excel spreadsheet - gene expression (raw read counts) for miRNAs

source_name: hippocampus

growth_protocol: 3-months old wild-type Gld2 KO male mice on C57BL/6 backgrounds (Nakanishi T et al 2007; Biochem Biophys Res Commun 364: 14–19) from littermates derived from Gld2 heterozygous matings

extract_protocol:
Total RNA was TRIzol extracted from the hippocampi.
RNA was resolved by gel electrophoresis and the species migrating with a size of 28–32 bases was excised and used for cDNA library construction, as described by Gu et al. (2009). The barcoded samples were sequenced on an Illumina Hi-Seq 2500 instrument.

value: 3 months old

value: male


title: pooled samples from 19 patients with squamous cell carinoma confirmed by histology. The median age of patients was 56.

description: A total of 2 micro gram of extracted total RNA from the pooled samples in each disease category was prepared and 250 ng of this was labelled with a 3D-Gene miRNA labelling kit (Toray) followed by hybridizing onto 3D-Gene Human miRNA Oligo chips (Toray).

value: squamous cell carinoma


title: pooled samples from 11 patients with CIN1 confirmed by histology. The median age of patients was 37.


title: GLD2KO2


title: GLD2KO6


title: GLD2KO3


title: GLD2KO4


title: WT6


title: pooled samples from 16 patients with normal confirmed by histology. The median age of patients was 38.

value: normal


title: pooled samples from 29 patients with CIN3 confirmed by histology. The median age of patients was 34.


title: M_Liver_Corn oil

city: Tainan

first: Bu-Miin

last: Huang

address: No. 1, University Rd.

department: Cell Biology and Anatomy

country: Taiwan

institute: National Cheng Kung University

description: Gene expression after 3-week corn oil exposure (Vehicle Control)

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing:
Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.
Raw signal data was normalized by quantile normalization for differential expressed genes discovering.For functional assay, we provied enrichment test for differential expressed genes (For mostmodel organisms). Welgen Biotech used clusterProfiler for enrichment test for gene ontology (GO) and pathway (KEGG).

source_name: Corn oil ip injection, 5 days/week for 3 weeks (Vehicle Control)

label_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

extract_protocol: In each group, pooled RNA was prepared by mixing the same amount total RNA from livers of 5 mice. 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

treatment_protocol: 6-week old C57BL/6 mice were intraperitoneal injected with Aristolochic acid typ I at a dose of 5 mg/kg/day (for female mice) and 2 mg/kg/day (for male mice).

value: Male

value: 6 weeks


title: WT1


title: 12 Gy X-ray irradiated gastric tissue-2

description: 12 Gy X-ray irradiated gastric tissue-2. The mouse was sacrificed 7 days after irradiation and gastric tissues were collected. RNA was extracted and quantified. mRNA and lncRNA profilings of each groups were analyzed by microarray.

source_name: 12 Gy X-ray irradiated gastric tissue-2

value: 12 Gy X-ray irradiated


title: 6 Gy X-ray irradiated gastric tissue-1

description: 6 Gy X-ray irradiated gastric tissue-1. The mouse was sacrificed 7 days after irradiation and gastric tissues were collected. RNA was extracted and quantified. mRNA and lncRNA profilings of each groups were analyzed by microarray.

source_name: 6 Gy X-ray irradiated gastric tissue-1

value: 6 Gy X-ray irradiated


title: WT2

value: wild type


title: M_Liver_AAI_2

description: Gene expression after 3-week 2 mg/kg/day AAI exposure

source_name: 2 mg/kg/day AAI ip injected, 5 days/week for 3 weeks

value: Liver


title: WT4


title: F_Liver_AAI_5

description: Gene expression after 3-week 5 mg/kg/day AAI exposure

source_name: 5 mg/kg/day AAI ip injected, 5 days/week for 3 weeks

value: Female


title: 12 Gy X-ray irradiated gastric tissue-3

description: 12 Gy X-ray irradiated gastric tissue-3. The mouse was sacrificed 7 days after irradiation and gastric tissues were collected. RNA was extracted and quantified. mRNA and lncRNA profilings of each groups were analyzed by microarray.

source_name: 12 Gy X-ray irradiated gastric tissue-3


title: GLD2KO5


title: 12 Gy X-ray irradiated gastric tissue-1

description: 12 Gy X-ray irradiated gastric tissue-1 The mouse was sacrificed 7 days after irradiation and gastric tissues were collected. RNA was extracted and quantified. mRNA and lncRNA profilings of each groups were analyzed by microarray.

source_name: 12 Gy X-ray irradiated gastric tissue-1


title: stromal sample treated with vehicle (DMSO) 3

city: Milan

first: Linda

last: Pattini

address: piazza Leonardo da Vinci, 32

department: Department of Electronics, Information and Bioengineering

institute: Politecnico di Milano

data_processing:
raw sequences were filtered for good quality scores using FastQC software.
Sequences obtained were aligned to the Mouse genome (mm10 release) using STAR aligner (version 2.3.0e_r291)
Only uniquely mapped reads were used to estimate gene counts using the reported Ensembl gene annotations (v85) using Rsubread Bioconductor package.
Count data were normalized using the “weighted trimmed mean of M-values”. Differential analysis was performed by Limma
Genome_build: GRCm38
Supplementary_files_format_and_content: teb-delimited file; log ratio, nominal and adjusted p-values provided

source_name: stromal cells of the lymphoid microenvironment

growth_protocol: Cells were cultured in DMEM supplemented with 10% fetal bovine serum and antibiotics.

extract_protocol:
RNeasy Mini kit (Qiagen) was used to extract RNA from cells. cRNA preparation and amplification was performed using Illumina® TotalPrep™ RNA Amplification Kit, according to the manufacturer's instructions.
Reverse transcription of total RNA was performed with the ImProm-II Reverse Transcription System kit with random primers (Promega). qPCRs were performed using Universal Probe Library system (Roche) on a LightCycler480 (Roche).

treatment_protocol: Stroma was treated with BMS493 or vehicle (DMSO) for 48hrs.

tag: cell line

value: mSSC-YFP

tag: cell type

value: spleen stromal cells


title: stromal sample treated with BMS493 2

description: stromal sample treated with BMS493


title: F_Liver_Corn oil

source_name: Corn oil ip injected, 5 days/week for 3 weeks (Vehicle Control)

tag: strain

tag: age


title: stromal sample treated with vehicle (DMSO) 2


title: Hepatocyte_RRBS_Insulin_recepetor_ko_3

data_processing:
DNA methylation was analyzed by using one-hundred-base pair paired-end sequencing reads from RRBS that were trimmed and quality filtered by trim galore software (v0.3.3) using default parameters for RRBS with the following command:
Genome_build: mm9

extract_protocol: DNA was isolated from mouse hepatocytes or from snap-frozen mouse tissues and incubated in lysis buffer (25 mM Tris-HCl (pH  8), 2 mM EDTA, 0.2% SDS, 200 mM NaCl) supplemented with 300 μg/ml proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation. RRBS libraries were prepared as described (Boyle, 2012) and run on Hiseq 2500 (Illumina) using 100 bp paired-end sequencing.

tag: genotype/variation

value: Insulin receptor was deleted after birth in hepatocytes

value: Hepatocyte


title: WT P2 rep.1

city: Barcelona

first: Mario

last: Notari

address: Hospital Duran i Reynals Gran Via de l'Hospitalet, 199-203

country: Spain

institute: Center of Regenerative Medicine in Barcelona (CMRB)

data_processing:
Illumina HiSeq2500 software used for base calling
Quality of the reads was verified using FastQC v0.11.21 software. Then, the reads were mapped to Mus musculus reference genome vGRCm38 2, using tophat v2.0.143 software.
Following mapping, the transcript and normalization counts were performed using cuffdiff v2.2.1 4 software. The differential expression analysis of normalized counts was performed using cummeRbund v2.12 5 software, a widely used R v3.2 package which works together with the cuffdiff software; the applied threshold on the parameter alpha in the function getSig of the package was <= 0.05.
Genome_build: vGRCm38 2
Supplementary_files_format_and_content: Excel file with FPKM

source_name: heart ventricular tissue

extract_protocol:
Total RNA was extracted from only the ventricles of P1 (n=3) or P2 (n=3) hearts using Quiazol lysis reagent (Quiagen) and RNAeasy extraction kit (Qiagen) according to manufacturer's instructions. Polyadenylated RNA was isolated from 1 µg of total RNA using Dynabeads mRNA purification kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

value: 2-day old


title: WT P1 rep.2

value: 1-day old


title: WT5

value: 3 months old

value: male


title: WT P2 rep.2


title: WT P1 rep.3


title: WT P2 rep.3


title: stromal sample treated with vehicle (DMSO) 1


title: WT3


title: WT P1 rep.1


title: stromal sample treated with BMS493 1

description: stromal sample treated with BMS493


title: Hepatocyte_RRBS_Insulin_recepetor_ko_2


title: stromal sample treated with BMS493 3

description: stromal sample treated with BMS493


title: Hepatocyte_RRBS_Insulin_recepetor_ko_1


title: stromal sample treated with BMS493 4

description: stromal sample treated with BMS493


title: Liver_HNF6_ChIP_ko_rep2

data_processing:
ChIP-Seq 50 bp single-end reads were obtained from Hiseq 2500. Sequences were trimmed with cutadapt v.1.15 and aligned with bowtie2 v 2.2.4.  and analyzed by Homer (findPeaks, histone style) and heatmaps were prepared by Deeptools (computeMatrix). ChIP-Seq distribution was generated by Homer (annotatePeaks.pl).
Genome_build: mm9

extract_protocol: Chromatin was fixed and sheared with the M220 Focused-ultrasonicator™ (Covaris®) using the microTube snap-cap. The chromatin was then immunoprecipitated with HNF6 (Santa Cruz, sc-13050) antibodies. Libraries were generated using the Truseq DNA nano Preparation Kit (Illumina).

value: TET2 and TET 3 was deleted after birth in hepatocytes


title: Liver_HNF6_ChIP_wt_rep2


title: Liver_HNF6_ChIP_ko_rep1


title: Liver_HNF6_ChIP_wt_rep1


title: P10_crypt_rep1

city: Durham

first: Terry

last: Lechler

state: NC

institute: Duke University

data_processing:
HiSeq Control Software used for basecalling
Sequenced reads were trimmed for adapter sequences and low-quality reads using Trim Galore, followed by alignment to the mm9 reference genome using STAR using the following parameters: --outFilterMultimapNmax 1,--alignSJoverhangMin 500
The number of reads counted for each gene was calculated using HTSeq
Genome_build: mm9
Supplementary_files_format_and_content: .txt files containing HT-seq counts for each gene in each sample.

source_name: CD1 P10 medial small intestine - CD44+//Epcam+ cells

extract_protocol:
Medial small intestines were flushed with cold HBSS, and epithelium was isolated by incubating in EDTA for 20 min.  Cells were FACS sorted based on Epcam and CD44 staining, and cell pellet was frozen at -80 until RNA extraction. Total RNA was extracted and DNAseI treated using Qiagen RNeasy Mini kit according to the manufacturer's protocol. Quality control was evaluated by Qubit and 2100 Bioanalyzer.
poly(A)-mRNA libraries were constructed using the KAPA stranded mRNA-seq kit.

value: medial small intestinal epithelium

tag: developmental stage

value: Postnatal day 10

tag: cell population

value: Crypt


title: P10_villus_rep3

source_name: CD1 P10 medial small intestine - CD44-//Epcam+ cells

value: Villus


title: P10_villus_rep2


title: P10_crypt_rep3


title: P10_crypt_rep2


title: P6_crypt_rep3

source_name: CD1 P6 medial small intestine - CD44+//Epcam+ cells

value: Postnatal day 6


title: P6_villus_rep1

source_name: CD1 P6 medial small intestine - CD44-/Epcam+ cells


title: P6_villus_rep2

source_name: CD1 P6 medial small intestine - CD44-//Epcam+ cells


title: P6_crypt_rep2


title: P6_crypt_rep1


title: P10_villus_rep1


title: P3_crypt_rep2

source_name: CD1 P3 medial small intestine - CD44+//Epcam+ cells

value: Postnatal day 3


title: P0_villus_rep3

source_name: CD1 P0 medial small intestine - CD44-//Epcam+ cells

value: Postnatal day 0


title: P3_crypt_rep1


title: P3_villus_rep2

source_name: CD1 P3 medial small intestine - CD44-//Epcam+ cells


title: P3_crypt_rep3


title: P0_villus_rep2


title: P0_villus_rep1


title: P0_crypt_rep2

source_name: CD1 P0 medial small intestine - CD44+//Epcam+ cells


title: P3_villus_rep1


title: P0_crypt_rep1


title: P0_crypt_rep3


title: Bhlhe40_WT_Th1_ChIPseq

city: St. Louis

first: Maxim

last: Artyomov

state: MO

address: 425 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

data_processing:
ChIP-Seq reads were aligned to mm10 genome assembly using Bowtie v1.1.1 (-m 1 -v 3 --best --strata)
peaks were called using MACS v1.4 (macs14 -t WT -c KO -f BAM -g mm -n WTvsKO -p 0.00001) with corresponding Bhlhe40 KO sample used as an Input
Genome_build: mm10
Supplementary_files_format_and_content: peaks were annotated using R package ChIPseeker v1.14.1
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage tool from DeepTools v2.5.3. (--normalizeTo1x 2620345972 --ignoreForNormalization chrM)

source_name: In vitro TH1-polarized CD4+ T cells

growth_protocol: To generate in vitro-polarized TH1 cells, naïve splenic CD4+ T cells (Stemcell Technologies Easysep Mouse Naive CD4+ T Cell Isolation kit, typical purity ~90–96%) were cultured in IMDM with plate-bound anti-CD3 (2 μg/ml, clone 145-2C11, BioLegend) and anti-CD28 antibodies (2 μg/ml, clone 37.51, BioLegend) in the presence of IL-12 (10 ng/ml, Biolegend) and anti-IL-4 (20 ug/ml, Leinco).  Cultures were split on day 3 and used for ChIP-Seq on day 4.

extract_protocol:
Stimulated cells were fixed for 10 minutes at room temperature with 1% paraformaldehyde with shaking. Cross-linked chromatin was fragmented by sonication and then immunoprecipitated with polyclonal rabbit anti-Bhlhe40 antibody (Novus Biologicals NB100-1800, Lot A or Lot C1). After immunoprecipitation, DNA was purified by the GenElute PCR clean-up kit (Sigma).
Standard ChIP library prep for Illumina sequencing

value: CD4+ T cell

value: WT

tag: chip antibody

value: anti-Bhlhe40 (Novus Biologicals NB100-1800, Lot C1)

value: 50ng/mL PMA, 1uM Ionomycin for 1.5 hours


title: Bhlhe40_KO_GM_ChIPseq

source_name: GM-CSF-cultured bone marrow derived cells

growth_protocol: Bone marrow cells were isolated from femurs and tibias of mice and treated with ACK lysis buffer (0.15 M NH4Cl, 10 mM KHCO3, 0.1 mM EDTA) to lyse red blood cells. To generate GM-CSF-cultured bone marrow-derived dendritic cells and macrophages, bone marrow cells were cultured in complete RPMI (10% heat-inactivated FBS+ 2 mM L-glutamine+ 1X Penicillin/Streptomycin + 55μM β-mercaptoethanol) in 6-well plates with the addition of 20 ng/ml GM-CSF (PeproTech). Cells were incubated at 37°C in 8% CO2 for 8-9 days. At the end of the cultures, cells were harvested, counted, and adjusted to the desired cell concentrations.

value: Macrophage, DC, granulocyte mix

value: KO (Bhlhe40-/-)

value: anti-Bhlhe40 (Novus Biologicals NB100-1800, Lot A)

value: 10ug/mL heat-killed Mtb for 4 hours


title: Bhlhe40_KO_Th1_ChIPseq


title: Bhlhe40_WT_GM_ChIPseq


title: P3_villus_rep3

source_name: CD1 P3 medial small intestine - CD44-/Epcam+ cells


title: stromal sample treated with vehicle (DMSO) 4

value: mSSC-YFP

value: spleen stromal cells


title: colon, control diet, age 28 months, rep17*

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: same as GSM2691558

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.42.0).

source_name: scraping from colonic mucosa and submucosa, control diet, age 28 months

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: The design of the study and experimental procedures have been described in detail previously (PMID: 25504628).  Briefly, male C57BL/6J mice (age: 7 weeks) were purchased from Janvier (Cedex, France) and were housed in pairs of two in the light and temperature (20C)-controlled animal facility of Wageningen University (12-hour light/dark cycle, lights on at 04.00). The mice received standard AIN-93G (Research Diet Services, Wijk bij Duurstede, The Netherlands) for 2 weeks upon arrival. At the age of 9 weeks, mice were individually housed and randomized to different dietary regimens. For the current analyses, we only considered mice that were lifelong fed ad libitum a semi-synthetic control diet consisting of 10E% of fat (C; control). Mice were sacrificed at 6, 12, 24 or 28 months of age.

extract_protocol: Total RNA was isolated from the scrapings using TRIzol Reagent according to the manufacturer’s instructions (Invitrogen, Breda, The Netherlands). Isolated RNA was purified using RNeasy Micro columns (Qiagen, Venlo, The Netherlands) and total RNA yield (Nanodrop ND-1000, Nanodrop Products, Maarssen, The Netherlands) and RNA integrity (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) were assessed. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Prior to sacrifice, each mouse was first fasted for 4 hours after which they received an intragastric gavage of 400ul of 0.5% carboxymethyl cellulose, then fasted again for another 6 hours. During the sacrifice, after sedation with a mixture of isoflurane (1.5%), nitrous oxide (70%) and oxygen (30%), colon tissue was removed, whereafter the mucosa and submucosa was scraped-off, snap-frozen and stored at -80C until further analysis.

tag: Sex

value: male

tag: mouseid

tag: diet group

value: C

tag: diet (full name)

value: control

tag: age at sacrifice (months)

tag: mouse number

value: colon


title: colon, control diet, age 28 months, rep01*

description: same as GSM2691554


title: colon, control diet, age 24 months, rep09

source_name: scraping from colonic mucosa and submucosa, control diet, age 24 months


title: colon, control diet, age 12 months, rep05

source_name: scraping from colonic mucosa and submucosa, control diet, age 12 months


title: colon, control diet, age 28 months, rep09*

description: same as GSM2691557


title: colon, control diet, age 12 months, rep13


title: colon, control diet, age 24 months, rep07


title: colon, control diet, age 24 months, rep13


title: colon, control diet, age 24 months, rep05


title: colon, control diet, age 12 months, rep11


title: colon, control diet, age 28 months, rep03*

description: same as GSM2691555


title: colon, control diet, age 12 months, rep09


title: Patient 38: high PARP and platinum-sensitive

city: Tampere

first: Mauro

last: Scaravilli

address: Arvo Ylpön katu 34 D253

department: BioMediTech

country: Finland

institute: University of Tampere

description: Patient 38 vs. reference

hyb_protocol: The labeled RNA was purified using Quiagen Rneasy mini spin columns and quantified using NanoDrop UV-VIS Spectrophotometer ver. The hybridization was performed in Agilent 2X GE Hybridization Buffer HI-RPM according to Agilent guidelines in Agilent hybridization oven at 65 degrees C 10rpm for 19 hours.

scan_protocol: Scanned on Agilent scanner G2565CA. Images were quantified using Agilent Feature Extraction ver. 11.0.1.1

data_processing: Data were quantile normalized and probe sets were summarized by a probe with the highest average expression.

source_name: ovarian cancer

label_protocol: 100ng of total RNA were labeled using the Agilent Low Input Quick Amp labeling kit according to the manufacturer’s protocol

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: The tumor samples were collected at surgery and fresh-frozen. They were stored in liquid nitrogen prior to RNA collection.

tag: platinum sensitivity

value: sensitive

source_name: Human Universal Reference Ovary RNA

tag: sample type

value: reference


title: colon, control diet, age 12 months, rep01

tag: tissue


title: Patient 33: high PARP and platinum-sensitive

description: Patient 33 vs. reference


title: colon, control diet, age 24 months, rep03


title: colon, control diet, age 12 months, rep03


title: colon, control diet, age 28 months, rep05*

description: same as GSM2691556


title: Patient 75:  low PARP and platinum-resistant

description: Patient 75 vs. reference

value: resistant


title: colon, control diet, age 24 months, rep11


title: Patient 12: high PARP and platinum-sensitive

description: Patient 12 vs. reference


title: colon, control diet, age 24 months, rep01


title: colon, control diet, age 12 months, rep07


title: Patient 37: high PARP and platinum-sensitive

description: Patient 37 vs. reference


title: colon, control diet, age 6 months, rep11*

description: same as GSM2691552

source_name: scraping from colonic mucosa and submucosa, control diet, age 6 months


title: Patient 81: high PARP and platinum-sensitive

description: Patient 81 vs. reference


title: Patient 9: high PARP and platinum-sensitive

description: Patient 9 vs. reference


title: Patient 42:  low PARP and platinum-resistant

description: Patient 42 vs. reference


title: colon, control diet, age 6 months, rep09*

description: same as GSM2691551


title: colon, control diet, age 6 months, rep07*

description: same as GSM2691550


title: colon, control diet, age 6 months, rep03*

description: same as GSM2691549


title: Patient 36: low PARP and platinum-resistant

description: Patient 36 vs. reference


title: Patient 51:  low PARP and platinum-resistant

description: Patient 51 vs. reference


title: Liver_ID_lbw_mock

description:
G067_E09_15_D2_9_INT_MOCK.CEL
Liver, mouse fed according to intermittent diet regimen, low body weight group, vehicle-only [0.5% carboxymethyl cellulose (CMC)].

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.26.0).

source_name: Liver, intermittent diet regimen, low body weight group, vehicle only

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Mice arrived at the age of 7 weeks and received a semi-synthetic diet (AIN-93G) for a 2-week acclimatization period. At the age of 9 weeks, dietary intervention was started and the mice were sacrificed at the age of 12 months.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Prior to sacrifice, each mouse was first fasted for 4 hours after which they received an intragastric gavage of either solvent (0.5% carboxymethyl cellulose) or WY14,643 dispersed in solvent (160 mg WY14,643/kg body weight), then fasted again for another 6 hours. ID mice were sacrificed in their ad libitum MF feeding week. Mice were paired per dietary intervention group according to body weight at sacrifice, so that vehicle and WY14,643 treatment were provided to mice with similar body weight. After sedation with a mixture of isoflurane (1.5%), nitrous oxide (70%) and oxygen (30%), liver tissue was snap-frozen and stored at -80C until further analysis.

tag: strain/background

value: 12 months

value: liver

value: intermittent diet (ID)

tag: treatment

value: vehicle (CMC)

value: low


title: Patient 76:  low PARP and platinum-resistant

description: Patient 76 vs. reference


title: colon, control diet, age 28 months, rep19*

description: same as GSM2691539

tag: strain


title: Patient 31: low PARP and platinum-resistant

description: Patient 31 vs. reference


title: Liver_CR_lbw_Wy

description:
G067_D09_12_B2_14_CR_WY.CEL
Liver, mouse subjected to calorie restriction (30%), low body weight group, WY-treatment [160 mg WY14,643 per kg body weight dissolved in 0.5% carboxymethyl cellulose (CMC)].

source_name: Liver, calorie restriction (30%), low body weight group, WY treatment

tag: age

value: caloric restriction, 30% (CR)


title: Liver_CR_lbw_mock

description:
G067_D07_11_B2_13_CR_MOCK.CEL
Liver, mouse subjected to calorie restriction (30%), low body weight group, vehicle-only [0.5% carboxymethyl cellulose (CMC)].

source_name: Liver, calorie restriction (30%), low body weight group, vehicle only


title: Liver_MF_lbw_Wy

description:
G067_E07_14_C2_10_MF_WY.CEL
Liver, mouse fed the medium fat diet [25energy%], low body weight group, WY-treatment [160 mg WY14,643 per kg body weight dissolved in 0.5% carboxymethyl cellulose (CMC)].

source_name: Liver, medium fat diet (25% energy), low body weight group, WY treatment

value: medium fat (25energy%) (MF)


title: Liver_ID_lbw_Wy

description:
G067_F05_16_D2_10_INT_WY.CEL
Liver, mouse fed according to intermittent diet regimen, low body weight group, WY-treatment [160 mg WY14,643 per kg body weight dissolved in 0.5% carboxymethyl cellulose (CMC)].

source_name: Liver, intermittent diet regimen, low body weight group, WY treatment


title: Liver_ID_hbw_mock

description:
G073_G05_07_D2_13_INT_MOCK.CEL
Liver, mouse fed according to intermittent diet regimen, high body weight group, vehicle-only [0.5% carboxymethyl cellulose (CMC)].

source_name: Liver, intermittent diet regimen, high body weight group, vehicle only

value: high


title: Liver_Control_lbw_Wy

description:
G067_D05_10_A2_8_CTRL_WY.CEL
Liver, mouse fed the AIN-93W [control] diet, low body weight group, WY-treatment [160 mg WY14,643 per kg body weight dissolved in 0.5% carboxymethyl cellulose (CMC)].

source_name: Liver, AIN 93W (control) diet, low body weight group, WY treatment

value: AIN-93W (control)


title: Liver_ID_hbw_Wy

description:
G073_G07_08_D2_2_INT_WY.CEL
Liver, mouse fed according to intermittent diet regimen, high body weight group, WY-treatment [160 mg WY14,643 per kg body weight dissolved in 0.5% carboxymethyl cellulose (CMC)].

source_name: Liver, intermittent diet regimen, high body weight group, WY treatment


title: Liver_MF_lbw_mock

description:
G067_E05_13_C2_9_MF_MOCK.CEL
Liver, mouse fed the medium fat diet [25energy%], low body weight group, vehicle-only [0.5% carboxymethyl cellulose (CMC)].

source_name: Liver, medium fat diet (25% energy), low body weight group, vehicle only


title: Liver_Control_lbw_mock

description:
G067_C09_09_A2_7_CTRL_MOCK.CEL
Liver, mouse fed the AIN-93W [control] diet, low body weight group, vehicle-only [0.5% carboxymethyl cellulose (CMC)].

source_name: Liver, AIN 93W (control) diet, low body weight group, vehicle only


title: 203_knockout_mock_infected_rep1

city: Beijing

first: Sen

last: Zhang

address: East Street of Fengtai

institute: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology

description: Gene expression after 48h in mock-infected microRNA-203 knockout A549 cells

hyb_protocol: Array hybridization was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 5mm, 5mm scanning mode is single pass, Dye channel is set to Green and Green PMT is XDR Hi 100% and XDR Lo 10%)

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software. Open the Agilent Feature Extraction (FE) software. Add the images (.tif) to be extracted to the FE Project. Set FE Project Properties. Check the Extraction Set Configuration. Save the FE Project (.fep) by selecting File > Save As and browse for desired location. Select Project > Start Extracting and export data to txt.

source_name: microRNA-203 knockout A549 cells, mock-infected, 48h, replicate 1

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442).The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000 Spectrophotometer.

growth_protocol: A549 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and maintained at 37℃ in a 5% CO2 incubator.

extract_protocol: Lyse cells directly in 24-well plates by adding 1 ml of TRIzol Reagent, and passing the cell lysate several times through a pipette. Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C. Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C.At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C. At last RNA samples were cleaned up by RNasey Mini Kit (Qiagen) and quantified using a NanoDrop ND-1000 spectrophotometer.

treatment_protocol: Cells were infected with H5N1 virus at a multiplicity of infection (MOI) of 2 in DMEM medium supplemented with 2% FBS for 48h. Mock groups were treated with PBS under similar conditions for 48h. And uninfected groups were treated with nothing and cells were cultured in DMEM containing 10% FBS for 48h.

tag: cell type

tag: genotype/variation

value: microRNA-203 knockout

value: 48h in mock-infected


title: 203_knockout_infected_rep1

description: Gene expression after 48h in H5N1 infected microRNA-203 knockout A549 cells

source_name: microRNA-203 knockout A549 cells, infected with H5N1, 48h, replicate 1

value: 48h in H5N1 infected


title: Liver_MF_hbw_mock

description:
G067_B07_05_C2_13_MF_MOCK.CEL
Liver, mouse fed the medium fat diet [25energy%], high body weight group, vehicle-only [0.5% carboxymethyl cellulose (CMC)].

source_name: Liver, medium fat diet (25% energy), high body weight group, vehicle only

value: male


title: colon, control diet, age 24 months, rep15

source_name: scraping from colonic mucosa and submucosa, control diet, age 24 months

value: C

value: control

value: colon


title: Liver_CR_hbw_Wy

description:
G067_B05_04_B2_2_CR_WY.CEL
Liver, mouse subjected to calorie restriction (30%), high body weight group, WY-treatment [160 mg WY14,643 per kg body weight dissolved in 0.5% carboxymethyl cellulose (CMC)].

source_name: Liver, calorie restriction (30%), high body weight group, WY treatment


title: 203_knockout_uninfected_rep1

description: Gene expression after 48h in uninfected microRNA-203 knockout A549 cells

source_name: microRNA-203 knockout A549 cells, uninfected, 48h, replicate 1

value: 48h in uninfected


title: wt_A549_infected_rep1

description: Gene expression after 48h in H5N1 infected wild-type A549 cells

source_name: wild-type A549 cells, infected with H5N1, 48h, replicate 1

value: wild type


title: Liver_CR_hbw_mock

description:
G067_A09_03_B2_1_CR_MOCK.CEL
Liver, mouse subjected to calorie restriction (30%), high body weight group, vehicle-only [0.5% carboxymethyl cellulose (CMC)].

source_name: Liver, calorie restriction (30%), high body weight group, vehicle only

value: 12 months

value: liver


title: wt_A549_mock_infected_rep1

description: Gene expression after 48h in mock-infected wild-type A549 cells

source_name: wild-type A549 cells, mock-infected, 48h, replicate 1


title: colon, control diet, age 28 months, rep21*

description: same as GSM2691540

source_name: scraping from colonic mucosa and submucosa, control diet, age 28 months


title: Liver_MF_hbw_Wy

description:
G067_B09_06_C2_14_MF_WY.CEL
Liver, mouse fed the medium fat diet [25energy%], high body weight group, WY-treatment [160 mg WY14,643 per kg body weight dissolved in 0.5% carboxymethyl cellulose (CMC)].

source_name: Liver, medium fat diet (25% energy), high body weight group, WY treatment


title: Liver_Control_hbw_Wy

description:
G067_A07_02_A2_10_CTRL_WY.CEL
Liver, mouse fed the AIN-93W [control] diet, high body weight group, WY-treatment [160 mg WY14,643 per kg body weight dissolved in 0.5% carboxymethyl cellulose (CMC)].

source_name: Liver, AIN 93W (control) diet, high body weight group, WY treatment


title: Liver_Control_hbw_mock

description:
G067_A05_01_A2_9_CTRL_MOCK.CEL
Liver, mouse fed the AIN-93W [control] diet, high body weight group, vehicle-only [0.5% carboxymethyl cellulose (CMC)].

source_name: Liver, AIN 93W (control) diet, high body weight group, vehicle only

value: vehicle (CMC)


title: wt_A549_uninfected_rep1

description: Gene expression after 48h in uninfected wild-type A549 cells

source_name: wild-type A549 cells, uninfected, 48h, replicate 1


title: SKOv3ip1 replicate 1

city: Chicago

first: Andras

last: Ladanyi

address: 820 S. Wood St.

department: OB/GYN

institute: UIC

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Probe-level raw expression data were processed by Illumina Genome Studio v2011.1. Average signal intensities were background-subtracted, log2 transformed, and Quantile-normalized.

source_name: SKOV3ip1 ovarian cancer cells

label_protocol: Biotinylated cRNA were prepared with the Ambion Total Prep Kit.

growth_protocol: SKOV3ip1 cells were grown to near confluency in full growth media (10% fetal bovine serum) in 10cm dishes

extract_protocol: RNA was extracted using Qiagen RNeasy Mini kit using manufacturer's recommended protocol. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Control cells were maintained in DMEM/F12 medium containing 0.1% BSA for 16hrs and total RNA were extracted. Treated cells were incubated with freshly extracted mature omental adicpoytes in in DMEM/F12 medium containing 0.1% BSA media. After 16 hrs of co-culture adicpoytes were washed away with sterile PBS and total RNA was extracted.

tag: co-culture


title: BXPC-3 cont-3

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

institute: MDACC

description:
SAMPLE21
Cell 21

data_processing:
Genome Studio 5.0
rank invariant normalization

source_name: BXPC-3 cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Pancreas cancer cell lines were cultured and subjected to various exosomes based treatments.

extract_protocol: RNA was extracted with Trizol reagent,Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: The cells were harvested (untreated control 'cont') for RNA extraction, or treated for 3 hours with various exosomes preparations. The exosomes were collected from BJ human foreskin fibroblast culture supernatant without further processing (control exosomes or 'CE'), or engineered to contain scrambled siRNA ('scr') or KRASG12D siRNA ('iExo). Two or three distinct wells of cells were evaluated per treatment condition and assigned a well number (well -1, -2 or 3).

tag: cell line

value: BXPC-3 cells

value: untreated control

tag: well


title: SKOv3ip1 replicate 2


title: SKOv3ip1  + HPA replicate 2

value: human primary adipocytes


title: CytoplasmicRNA_IPPK-siRNA_2

city: Kyoto City

first: Masumi

last: Okamura

state: Kyoto Prefecture

address: Kitashirakawa Oiwakechou

institute: Kyoto University

hyb_protocol: Hybridization were performed using Agilent’s Low Input Quick Amp WT Labeling kit, one-color (Agilent Technology, USA), according to the manufacturer’s instructions.

scan_protocol: The microarrays were scaned in the Agilent G2505 DNA Microarray Scanner equipment (Agilent).

data_processing: The raw data of gene expression was normalized LOESS regression via R software

source_name: Cytoplasmic RNA, IPPK-siRNA, replicate 2

label_protocol: Labeling  were performed using Agilent’s Low Input Quick Amp WT Labeling kit, one-color (Agilent Technology, USA), according to the manufacturer’s instructions.

growth_protocol: U2OS cells were grown in Dulbecco's modified Eagle medium containing 10% fatal bovine serum.

extract_protocol: Cytoplasmic RNA was extracted with Sepasol RNA I Super G solution according to manufacture's instruction following to the separation of cytosolic fraction by using lysis buffer (20 mM Tris-HCl pH, 8.0, 200 mM NaCl, 1 mM MgCl2, 1 % NP40).

treatment_protocol: 20nM of siRNA was transfected with Lipofectamine2000 according to manufacture's instruction.

tag: sirna

value: IPPK

tag: rna fraction

value: cytoplasmic


title: CytoplasmicRNA_IPPK-siRNA_1

source_name: Cytoplasmic RNA, IPPK-siRNA, replicate 1


title: SKOv3ip1  + HPA replicate 1


title: CytoplasmicRNA_GLE1-siRNA_2

source_name: Cytoplasmic RNA, GLE1-siRNA, replicate 2


title: CytoplasmicRNA_IPPK-siRNA_3

source_name: Cytoplasmic RNA, IPPK-siRNA, replicate 3


title: BXPC-3 iEXO-1

description:
SAMPLE16
Cell 16

value: KRASG12D siRNA containing exosomes


title: BXPC-3 CE-2

description:
SAMPLE14
Cell 14

value: control exosomes


title: CytoplasmicRNA_GLE1-siRNA_3

source_name: Cytoplasmic RNA, GLE1-siRNA, replicate 3


title: BXPC-3 scr-3

description:
SAMPLE12
Cell 12

value: scramble siRNA containing exosomes


title: BXPC-3 cont-2

description:
SAMPLE20
Cell 20


title: BXPC-3 CE-3

description:
SAMPLE15
Cell 15


title: BXPC-3 CE-1

description:
SAMPLE13
Cell 13


title: BXPC-3 iEXO-2

description:
SAMPLE17
Cell 17


title: BXPC-3 cont-1

description:
SAMPLE19
Cell 19


title: CytoplasmicRNA_GLE1-siRNA_1

source_name: Cytoplasmic RNA, GLE1-siRNA, replicate 1


title: CytoplasmicRNA_DBP5-siRNA_2

source_name: Cytoplasmic RNA, DBP5-siRNA, replicate 2


title: CytoplasmicRNA_DBP5-siRNA_1

source_name: Cytoplasmic RNA, DBP5-siRNA, replicate 1


title: Panc-1 cont-3

description:
SAMPLE9
Cell 9

source_name: Panc-1 cells

value: Panc-1 cells


title: BXPC-3 iEXO-3

description:
SAMPLE18
Cell 18


title: BXPC-3 scr-2

description:
SAMPLE11
Cell 11