title: IL27Ra_repB3

city: Aurora

first: Ross

middle: M.

last: Kedl

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

data_processing:
FASTQ files were generated from BCL files using Illumina bcl2fastq converter (version 2.17) without adapter trimming.
Nextera TruSight adapters were trimmed with skewer (version 0.2.2).
Trimmed reads were mapped with the STAR aligner (version 2.4.1d) to the GRCm38 assembly of the mouse genome using gene using gene annotations from Ensembl version 84.
Reads mapping to each gene of the Ensembl 84 annotation were counted with the featureCounts program from the Subread software package (v1.5.1).
Statistical comparisons were conducted using the DESeq2 package (version 1.14.1) for the R statistical software (version 3.3.2).
Genome_build: GRCm38 (incl. “random” contigs)
Supplementary_files_format_and_content: counts per gene (Ensembl 84 mouse annotation) for each sample (gzipped output from featureCounts program)

source_name: IL-27R-/- OT1 T cell

growth_protocol: naïve Tg T cells transferred into naïve B6 recipients

extract_protocol:
3 days after immunization, spleens were harvested, CD8+ T cells isolated by magnetic column negative selection, CD451+CD8+ T cells isolated by flow sorting (<98% purity), and total RNA extracted using the Qiagen RNeasy Micro Kit (catalog # 74004) following the manufacturer's instructions.
A Clontech SMARTer® Ultra™ Low Input RNA Kit for Sequencing – v4 (Mountain View, CA, USA) and Nextera XT (San Diego, CA, USA) kit were used for construct libraries from isolated total RNA. Briefly, library construction started from 2 ng of total RNA, followed by SMARTer 1st strand cDNA synthesis, full length dscDNA amplification by LD-PCR, followed by purification and validation. After that, the samples were taken to the Nextera XT protocol where the sample is simultaneously fragmented and tagged with adapters followed by a limited cycle PCR that adds indexes. Once validated, the libraries were sequenced as barcoded-pooled samples on an Illumina HiSeq 2500 (San Diego, CA, USA) in the NJH Genomics Facility.

treatment_protocol: IP immunization with 100 µg ovalbumin (LPS free), 40 µg polyIC (GE technologies), and 40 µg anti-CD40 antibody FGK4.5.

tag: cell

value: CD8+ T cell

tag: developmental stage

value: day 3 post immunization


title: IL27Ra_repB2

status: Public on Sep 01 2018

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: genotype/variation


title: IL27Ra_repA1


title: WT_repB3

source_name: WT OT1 T cell

value: wild type


title: IL27Ra_repA3


title: WT_repB2


title: WT_repB1


title: WT_repA2


title: IL27Ra_repB1


title: KO 2

city: Birmingham

first: Adrie

middle: JC

last: Steyn

state: AL

address: 308, BBRB

department: Microbiology

institute: University of Alabama at Birmingham

description:
All Samples genes FPKM and normalized counts values.xlsx
AS7

data_processing:
Sequencing of mRNA was performed on the Illumina HiSeq2500.  Briefly, the quality of the total RNA was assessed using the Agilent 2100 Bioanalyzer followed by 2 rounds of poly A+ selection and conversion to cDNA. A TruSeq library generation kit was used as per the manufacturer’s instructions (Illumina, San Diego, CA). Library construction consisted of random fragmentation of the polyA mRNA, followed by cDNA production using random primers.  The ends of the cDNA were repaired, A-tailed and adaptors ligated for indexing (up to 12 different barcodes per lane) during the sequencing runs. The cDNA libraries were quantitated using qPCR in a Roche Light Cycler 480 with the Kapa Biosystems kit for library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation. Clusters were generated to yield approximately 725K-825K clusters/mm2. Cluster density and quality were determined during the run after the first base addition parameters were assessed. Performed paired end 2 x 50 bp sequencing runs to align the cDNA sequences to the reference genome.
TopHat was used to align the raw RNA-Seq fastq reads to the mouse mm10 genome using the short-read aligner Bowtie (1, 2). TopHat also analyzes the mapping results to identify splice junctions between exons. Cufflinks uses the aligned reads from TopHat to assemble transcripts, estimate their abundances and test for differential expression and regulation (3). Cuffmerge merges the assembled transcripts to a reference annotation and is capable of tracking Cufflinks transcripts across multiple experiments. Finally, Cuffdiff finds significant changes in transcript expression, splicing and promoter use. Genes that meet desired criteria (i.e. fold change ≥ ± 2.0 and q value < 0.05) were further analyzed using Ingenuity’s Pathway Analysis tool.
References: 1) Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7(3):562-78.; 2) Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq.Bioinformatics. 2009;25(9):1105-11; 3) Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511-5
Genome_build: mm10
Supplementary_files_format_and_content: RPKM  and normalized values for each sample

source_name: Lungs

extract_protocol:
Lungs were removed from Mtb infected mice at 9 weeks post infection, Stored in RNA later at -80. RNA was iolated using RNeasy Plus Mini Kit  (Cat No./ID: 74134) as per manufacturing recommendations. We was used 200 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mtb infected of Fth+/+ and Fth-/- mice

tag: genotype

value: Fth-/-

tag: tissue

value: Lungs

tag: infection

value: Mtb

tag: time

value: 9 weeks post-infection


title: KO 3

description:
All Samples genes FPKM and normalized counts values.xlsx
AS10


title: WT 3

description:
All Samples genes FPKM and normalized counts values.xlsx
AS4

value: Fth+/+


title: KO 1

description:
All Samples genes FPKM and normalized counts values.xlsx
AS6


title: Gonadal tdTomato- GFP+ cells from gonadal WAT

city: Durham

first: Rana

middle: K

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

data_processing:
Data was analyzed using Cell Ranger (v2.1.0) to perform demultiplexing, aligning reads, filtering, clustering, and gene expression analyses, using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files contain the barcodes, matrix, and genes.

source_name: gonadal white adipose tissue

extract_protocol:
The cells were isolated from gonadal WAT as previously described (Hepler et al. Elife 2017).
The library was generated according to manufacturer's instructions (10X Genomics).

tag: age

value: 8 weeks old

value: MuralChaser mice

value: gonadal white adipose tissue

tag: cell type

value: tdTomato- GFP+ cells


title: WT 1

description:
All Samples genes FPKM and normalized counts values.xlsx
AS2


title: MP-RNA19

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

description: Table_HTseq_Pronier_12samples_rawcounts.txt

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human genome assembly mm9 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with un-normalized read counts over all genes.

source_name: myeloid progenitors

growth_protocol: Freshly dissected femurs and tibias were isolated from Mx+ Wt1+/+ and Mx+ Wt1fl/+ mice. Bone marrow was spun at 8.000 rpm by centrifugation at 4°C into PBS supplemented with 0.2% Bovine Serum Albumin (PBS+BSA), and red blood cells were lysed in ammonium chloride-potassium bicarbonate lysis buffer for 10 min on ice. After centrifugation, cells were resuspended in PBS+BSA, passed through a cell strainer, and counted. Single live, Lineage-Sca1-c-Kit+ (LK); myeloid progenitors (MP) were sorted into PBS. Total RNA was extracted from MP-sorted bone marrow by DNA/RNA preparation kit (Qiagen) and their quality was assessed on TapeStation 2200, Agilent technologies.

extract_protocol: Libraries were prepared according to Lexogen 3' mRNA-seq Sample Preparation Kit

tag: age/condition

value: young acute

value: WT1 het


title: MP-RNA29

value: WT1 control


title: MP-RNA18


title: MP-RNA20


title: MP-RNA21


title: MP-RNA30


title: MP-RNA5

value: old chronic


title: MP-RNA3


title: MP-RNA2


title: MP-RNA1


title: MP-RNA4


title: MP-RNA6


title: WT 2

description:
All Samples genes FPKM and normalized counts values.xlsx
AS3


title: PCOS 154A

type: RNA

city: Rotterdam

first: Arne

last: IJpma

address: Dr. Molewaterplein 50

department: Bioinformatics

country: Netherlands

institute: Erasmus MC

description: Gene expression data from ovary biopt material

hyb_protocol: Hybridization was performed according to Affymetrix protocols.

scan_protocol: Chips were scanned on an Affymetrix Scanner according to the manufacturers protocol.

data_processing: The data were analyzed with Partek Genomics Suite version 6.6 using GCRMA with default settings and quantile normalization method. The data is log2 transformed.

label: biotin

organism: Homo sapiens

source_name: PCOS, ovary sample

label_protocol: cRNA was biotin-labeled.

growth_protocol: All tissue samples were snap frozen in liquid nitrogen immediately after collection.

extract_protocol: Total RNA was extracted from Ovary biopsies using TRIZOL reagent (Invitrogen, Breda, The Netherlands) as per manufacturer's instructions.  After Trizol purification, RNA was repurified using  the Rneasy Mini Kit (Qiagen, Venlo., The Netherlands) according to manufacturer's instructions.  Total RNA was quantified by OD260/OD280 measurement and with RiboGreen RNA Quantitation Kit (Moleular Probes, Leiden, The Netherlands). RNA quality was assessed on a 6000 nanochip using Agilent 2100 bioanalyzer (Agilent Technologys, Waldbronn, Germany).

treatment_protocol: There was no treatment on the tissues.

tag: gender

value: female

tag: disease state

value: PCOS

value: ovary


title: TSX 367A

source_name: TSX, ovary sample

tag: gender history

value: female to male transsexual


title: PCOS 153A


title: TSX 359A


title: TSX 362A


title: TSX 365A


title: PCOS 151A


title: PCOS 349A


title: PCOS 149A


title: TSX 350A


title: TSX 371A


title: TSX 351A


title: TGFb1 24h #5

city: Rostock

first: Björn

last: Spittau

address: Gertrudenstraße 9

department: Institute of Anaomy

country: Germany

institute: University of Rostock

hyb_protocol: Labeled fragments were hybridised to the arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 640.

scan_protocol: The arrays were scanned after washing and staining using the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software Version 3.0. Genedata Expressionist software was further used for data analysis.

data_processing: CEL files were imported into the Refiner (Version 6.1) module of Expressionist where GC background subtraction was performed using antigenomic background probes. Quantile normalisation and probe summarisation was performed with the Bioconductor RMA condensing algorithm as implemented in Refiner1. Differentially expressed genes between the groups were identifed and the paired Bayes T-test (CyberT)2 with the Bayes Confidence Estimate Value set to 10 and a window size of 101 genes as well as 100 % valid values in each group was used (Analyst module, version 2.2.6b). Benjamini-Hochberg q-value was calculated3 in order to control the false discovery rate. We then used the 2 groups paired activity of Analyst to calculate the paired Effect size score between the experimental groups. Only genes from the categories main and unmapped (see Affymetrix transcript annotation NA32) were included in the analysis.

source_name: microglia from 14 day old mixed cultes after shake off

label_protocol: dUTP was incorporated into the cDNA, and after hydrolysis of the cRNA with RNAse H, cDNA was purified and fragmented using Uracil-DNA Glycosylase (UDG) and human apurinic/apyrimidinic Endonuclease 1 (APE1). cDNA fragments were labeled at their 3' end with biotin using Terminal Deoxynucleotidyl Transferase (TdT).

growth_protocol: Microglia were prepared using the shake-off-method from mixed glia cultures obtained from P0/P1 pups of C57BL/6 mice. Cultures were maintained with DMEM/F12 medium contains 10 % FCS and antibiotics

extract_protocol: RNA was extracted using TRIzol reagent. Integrity of RNA was analysed by capillary electrophoresis using a 2100 Bioanalyzer (Agilent Technologies, CA). Samples with an RNA integrity number (RIN) between 8.6 and 10 (mean 9.45) were further processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay as described by the manufacturer. 500 ng of total RNA were reverse transcribed with (N6)-random primers coupled to a T7 RNA Polymerase promotor sequence. After second-strand synthesis, double-stranded cDNAs were amplified overnight by in-vitro-transcription using T7 RNA Polymerase. cRNA was purified and used as template for a second cycle of reverse transcription with (N6) random primers.

treatment_protocol: Microglia were treated recombinant human TGFb1 (Peprotech) at a final concentration of 5ng/ml  for 24 h under serum-free conditions.

value: primary mciroglia

tag: agent

value: wildtype


title: PCOS 152A


title: TSX 354A


title: TSX 361A


title: control 24h #4


title: WT3NewbornL

city: Boston

first: Mary

middle: Frances

last: Lopez

state: Massachusetts

address: 3 blackfan circle, center for life sciences-16

department: Encrocrinology

institute: Boston Children's Hospital

description: SAMPLE 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

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

extract_protocol: Total RNA was isolated using an Rneasy kit (Qiagen) according to manufacturer’s recommendations.  The integrity of RNA was analyzed on an Agilent Bioanalyzer 2100 .  The purity of RNA was tested and the yield of RNA was determined using NanoDrop 1000 spectrophotometer.

tag: strain background

value: mixed 129/ c57Bl/6

value: wild type

value: newborn

value: liver


title: KO3NewbornL

description: SAMPLE 6

value: Igf2 KO


title: mZFY2

city: Bar Harbor

first: Petko

last: Petkov

state: Maine

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

library_source: genomic

data_processing:
Sequence reads were trimmed using trimmomative version 0.32
ChIP-Seq reads were aligned to the GRC38m/mm10 or GRC38h/hg38 genome assembly or using BWA v0.7.9a
Potential PCR duplicates were removed from alignments using Samtools v0.1.19
Alignments were filtered for highest mapping quality score with no indels
Blacklist peaks were found in input/control samples utilizing custom code and filtered from Chip-Seq samples
Genome_build: GRC38m/mm10
Genome_build: GRC38h/hg38
Supplementary_files_format_and_content: Peaks were called utilizing MACS v1.4.2
Supplementary_files_format_and_content: Motif data was generated using Meme v4.9.0.3

molecule: genomic DNA

source_name: mouse genomic DNA

extract_protocol:
phenol-chlorophorm
Illumina  Nextera DNA

value: spleen

value: 3 months


title: control 24h #5


title: TSX 356A


title: TSX 368A


title: KO2NewbornL

description: SAMPLE 5


title: WT2NewbornL

description: SAMPLE 2


title: KO1NewbornL

description: SAMPLE 4


title: mouse control

description: mouse control


title: mCTCF

description: mCTCF


title: TSX 373A


title: mZFY1


title: control 24h #3


title: TGFb1 24h #3


title: control 24h #2


title: TGFb1 24h #2


title: yXD100-IP2

city: East Lansing

first: Min-Hao

last: Kuo

state: MI

address: Room401, 603 Wilson Road

department: Biochemistry and Molecular Biology

institute: Michigan State University

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA)v1.18.61 and output of RTA was demultiplexed and converted to FastQ by Illumina Bcl2fastq v1.8.4.
ChIP-seq reads were aligned to the Saccer 3.0 genome assembly using Bowtie with "-m 1" setting
The aligned reads were further analyzed by using Homer
Genome_build: Saccer 3.0
Supplementary_files_format_and_content: bedGraph

organism: Saccharomyces cerevisiae

source_name: G2M arrested cells

growth_protocol: All strains were grown in YPD medium to early Log phase (~ 1 OD600/mL).

extract_protocol:
The cells were disrupted by using the beadbeater from BioSpec. Extracted chromatins were then sonicated  and subjected to ChIP assay.
Libraries were prepared using standard  Illumina protocol

treatment_protocol: All cells were treated with 35 µg/mL Benomyl for 2.5 hours before fixed by formaldehyde.

tag: chip antibody

value: anti c-Myc (Roche)

tag: epitode tag


title: TGFb1 24h #4


title: LNCaP, replicate1

city: Darlinghurst

first: Timothy

middle: John

last: Peters

state: NSW

address: 384 Victoria St

department: Immunology

country: Australia

institute: Garvan Institute of Medical Research

description:
Cancer
LNCaP.1

data_processing:
Mean target gene signals were normalised to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The 'averaged_normalized.txt' reports normalised mean signal (against housekeeping gene ALAS1).
All deltadeltaCt based fold-change calculations were performed in the R statistical package.
the 'fold_change.txt' reports test/control (i.e., LNCaP/PrEC) ratios.
Please note that sample data table contains raw Ct values

label: SYBR Green

source_name: LNCaP

label_protocol: cDNA was synthesised from 1ug total RNA using Superscript 3 Reverse Transcriptase (Life Technologies) and Quantitative real-time PCR performed using an Applied Biosciences 7900HT following the Manufacturer’s instructions. Primers were obtained from Integrated DNA Technologies.

extract_protocol: Total RNA was extracted with Trizol.

value: androgen-sensitive human prostate adenocarcinoma


title: LNCaP, replicate2

description:
Cancer
LNCaP.2


title: ABCI20_total_rep1

city: Wageningen

first: Leónie

last: Bentsink

address: Droevendaalsesteeg 1

institute: Wageningen University

hyb_protocol: GeneChip® 3' IVT Express kit (cat. # 901229) was used for hybridization, washing and staining of the cartridges.

scan_protocol: Scanning of the arrays was performed using the Affymetrix 3000G scanner.

data_processing: The GeneChip data were analyzed using the R statistical programming environment and Bioconductor packages. The data were normalized using the RMA algorithm. The P values were adjusted for multiple testing with the Benjamini and Hochberg method to control for false positives.

organism: Arabidopsis thaliana

label_protocol: RNA was processed and cRNA synthesized according to the 3’ GeneChips OneCycle kit.

growth_protocol: For the transcriptome and  transcriptome analyses abci20 and Col-0 were grown in a randomized complete block design with three replicates. Each replicate consisted of a bulk of eight plants. The precise growth conditions used were described by (El-Lithy et al., Genetics, 2006).

extract_protocol: The total RNA and polysomal RNA were purified with TriPure Isolation Reagent (Roche, Basel, Switzerland), further purified using RNeasy Mini spin columns (Qiagen, Hilden, Germany) and dissolved in RNase-free H2O for further analyses.

treatment_protocol: RNA was extracted from freshly harvested, dry seeds of three biological replicates of each genotype.

tag: ecotype

value: abci20 mutant

value: seed

tag: rna fraction

value: Total RNA


title: yXD100-IP1

tag: strain


title: TGFb1 24h #1

tag: genotype/variation


title: WT1NewbornL

description: SAMPLE 1

tag: tissue


title: yXD100-IP3


title: yMK1141-Input3


title: LNCaP, replicate3

description:
Cancer
LNCaP.3


title: control 24h #1


title: yMK1141-Input2


title: PrEC, replicate2

description:
Control
PrEC.2

source_name: PrEC

value: prostate epithelial cells


title: PrEC, replicate3

description:
Control
PrEC.3


title: PrEC, replicate1

description:
Control
PrEC.1


title: yMK1141-Input1


title: yJL346-IP3

value: 3F10 (Roche)


title: bamRNAi2

city: Albany

first: Prashanth

last: Rangan

state: NY

address: 1400 Washington

department: Biological Sciences

institute: RNA Institute

data_processing:
Sequenced reads were aligned to the D. melanogaster genome (UCSC dm6) using HISAT2 (version 2.1.0) with the RefSeq annotated transcripts as a guide.
Raw counts were generated using featureCounts (version 1.6.0.4)
Differential gene expression was assayed by edgeR (version 3.16.5), using a false discovery rate of (FDR) of 0.05, and genes with 3-fold or higher were considered significant.
Genome_build: UCSC dm6

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Ovaries from UAS-Dcr2;nosGAL4>bam RNAi and UAS-Dcr2;nosGAL4>Nipped_A RNAi flies were dissected in 1x PBS.

extract_protocol:
RNA was isolated using TRIzol (Invitrogen, 15596026), treated with DNase (TURBO DNA-free Kit, Life Technologies, AM1907), and then run on a 1% agarose gel to check integrity of the RNA. To generate mRNA-enriched libraries total RNA was treated with poly(A)tail selection beads and then following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08), except RNA was fragmented for 13 minutes.
Following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08), except RNA was fragmented for 13 minutes

value: ovaries

value: dissected 2-3 days post-eclosion

value: UAS-Dcr2;nosGAL4>bam RNAi


title: yJL346-IP2


title: bamRNAi1


title: Nipped_ARNAi2

value: UAS-Dcr2;nosGAL4>Nipped_A RNAi


title: Nipped_ARNAi1


title: yJL345-IP2


title: yJL345-IP1


title: G12-CBS_HP strain induced with methanol for 24 h_rep1

city: Nanning

first: Xiulin

last: Qin

state: Guangxi

address: 100 Daxue Road

department: College of Life Science and Technology

country: China

institute: Guangxi university

description: This sample is of engineered strain G12-CBS, which was grown in BSM medium, induced with methanol for 24 h without L-Met feeding. It is the first of three engineered strain G12-CBS biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

data_processing: Scanned images were extracted and normalized using NimbleScan software (version 2.5) through quantile normalization and the Robust Multichip Average (RMA) algorithm. All gene level files were then imported into Agilent GeneSpring GX software (version 11.5.1) for subsequent normalization by the quantile method and further analysis, including hierarchical clustering. Genes that at least 2 out of 12 samples have values greater than or equal to lower cut-off: 100.0 (All Targets Value) were chosen for data analysis.

organism: Komagataella phaffii GS115

source_name: GS115 harboring recombinant methionine adenosyltransferase (MAT) gene DS56 and the weak promoter G12 to downregulate CYS4 gene, S-

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
Pichia pastoris strains GS115/3.5K, GS115/DS56 and G12-CBS were grown in BSM medium (1.82% K2SO4, 0.093% CaSO4, 2.68% H3PO4 (85%), 1.49% MgSO4•7H2O, 0.413% KOH, 4% glycerol), induced with methanol for 72 h, and supplied with L-Met after methanol induction for 24 h to promote SAM synthesis.
Pichia pastoris strainG12-CBS was grown in BSM medium induced with methanol for 24 h without L-Met feeding.

extract_protocol: Total RNA was extracted using the RNAeasy Kit (Qiagen, Valencia, CA, USA). The RNA quality and concentration were measured by NanoDrop ND-1000 and standard denaturing agarose gel electrophoresis.

tag: phenotype

value: SAM low-producing


title: G12-CBS_HP strain induced with methanol for 24 h_rep2

description: This sample is of engineered strain G12-CBS, which was grown in BSM medium, induced with methanol for 24  h without L-Met feeding. It is the second of three engineered strain G12-CBS biological replicates used in this experiment, each from separate cultures.


title: G12-CBS_HP strain induced with methanol for 24 h_rep3

description: This sample is of engineered strain G12-CBS, which was grown in BSM medium, induced with methanol for 24  h without L-Met feeding. It is the third of three engineered strain G12-CBS biological replicates used in this experiment, each from separate cultures.


title: G12-CBS_HP strain induced with methanol for 72 h_rep3

description: This sample is of engineered strain G12-CBS, which was grown in BSM medium, induced with methanol for 72 h, and supplied with L-Met 24 h after methanol induction to promote SAM synthesis. It is the third of three engineered strain G12-CBS biological replicates used in this experiment, each from separate cultures.

source_name: GS115 harboring recombinant methionine adenosyltransferase (MAT) gene DS56 and the weak promoter G12 to downregulate CYS4 gene

value: SAM high-producing


title: G12-CBS_HP strain induced with methanol for 72 h_rep2

description: This sample is of engineered strain G12-CBS, which was grown in BSM medium, induced with methanol for 72 h, and supplied with L-Met 24 h after methanol induction to promote SAM synthesis. It is the second of three engineered strain G12-CBS biological replicates used in this experiment, each from separate cultures.


title: yJL346-IP1


title: G12-CBS_HP strain induced with methanol for 72 h_rep1

description: This sample is of engineered strain G12-CBS, which was grown in BSM medium, induced with methanol for 72 h, and supplied with L-Met 24 h after methanol induction to promote SAM synthesis. It is the first of three engineered strain G12-CBS biological replicates used in this experiment, each from separate cultures.


title: Wheat_imbibition_24hr_1

city: Tokyo

first: Tomoko

last: TAMURA

address: 1-1-1 Sakuragaoka Setagaya-ku

department: Nutritional Science and Food Safety

country: Japan

institute: Tokyo University of Agriculture

description: Gene expression after 16hr imbibed seed

hyb_protocol: Cy3-labeled cRNA (1.65 μg) was fragmented to an average size of about 50–100 nucleotides and then hybridized for 17 h at 65°C to an wheat oligonucleotide microarray slide. 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: Scanned in Cy3 channel with the Agilent DNA Microarray Scanner (Agilent) ) using one color scan setting for 4x44k array slides.

data_processing: Signal intensity per spot was generated from the scanned image with Agilent scan control 8.0 software according to Agilent Technologies standard operation procedures. Spots that did not pass quality control procedures were flagged as Not Detected. The scanned images were analyzed using Genespring GX 11.5 software (Agilent Technologies) as follows: (i) genes that were undetected in at least seven of eight samples were excluded; (ii) threshold raw signals were set to unify; and (iii) 75th percentile normalization was applied.

organism: Triticum aestivum

source_name: 7 embryos from 24hr-imbibed seeds-1

label_protocol: Total RNA (200 ng) of 0-, 16-, and 24-h imbibed samples were amplified and transcribed into fluorescent cRNA using the Low Input Quick Amp Labeling kit (One-color) (Agilent Technologies, CA, USA).

growth_protocol: Dry seeds of Triticum aestivum ‘Norin61’ were soaked in 1% hypochlorous acid and then rinsed in water; they were then placed on moistened absorbent cotton in the dark at 25°C.

extract_protocol: Total RNA was extracted from seven wheat embryos using Qiagen RNeasy Plant Mini kit (Qiagen, Tokyo, Japan). DNA was removed with DNase I, and the RNA was purified using the kit. RNA quality and quantity were verified with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and NanoDrop ND-2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol: For the 8-h imbibition, seeds that had absorbed less than 0.04 g of water were excluded from the analysis. For the 16-, 24-h imbibition conditions, seeds with a radicle length of less than 3 or 7mm, respectively, were excluded. A total of 21 seeds at each imbibition stage were collected, trichotomized, and stored at −80°C until use.

tag: cultivar

value: embryo


title: yJL324-IP2


title: yJL345-IP3


title: Wheat_imbibition_16hr_2

description: Gene expression after 8hr imbibed seed

source_name: 7 embryos from 16hr-imbibed seeds-2


title: Wheat_imbibition_16hr_1

description: Gene expression after 8hr imbibed seed

source_name: 7 embryos from 16hr-imbibed seeds-1


title: yJL324-IP1


title: Wheat_dryseed_2

description: Gene expression after 0hr imbibed seed

source_name: 7 embryos from dryseeds-2


title: GS115/DS56_HP strain induced with methanol for 72 h_rep2

description: This sample is of engineered strain GS115/DS56, which was grown in BSM medium, induced with methanol for 72 h, and supplied with L-Met 24 h after methanol induction to promote SAM synthesis. It is the second of three engineered strain GS115/DS56 biological replicates used in this experiment, each from separate cultures.

source_name: GS115 harboring recombinant methionine adenosyltransferase (MAT) gene DS56


title: GS115/DS56_HP strain induced with methanol for 72 h_rep1

description: This sample is of engineered strain GS115/DS56, which was grown in BSM medium, induced with methanol for 72 h, and supplied with L-Met 24 h after methanol induction to promote SAM synthesis. It is the first of three engineered strain GS115/DS56 biological replicates used in this experiment, each from separate cultures.


title: Wheat_imbibition_24hr_3

description: Gene expression after 16hr imbibed seed

source_name: 7 embryos from 24hr-imbibed seeds-3


title: yJL322-IP2


title: Mybx1_6-hpf

city: Beijing

first: Jiawei

last: Sun

address: Medical Science Building, Tsinghua University

institute: School of Life Sciences, Tsinghua University

data_processing:
Raw reads of fastq format were processed using customerized perl scripts.
Index of the reference genome was built using Bowtie v2.2.3 and reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads mapped to each gene. FPKM was then calculated based on the length of the gene and mapped reads count.
Genome_build: GRCz10
Supplementary_files_format_and_content: Txt files with FPKM values.

organism: Danio rerio

source_name: embryos

extract_protocol:
Total RNA was extraxted using Trizol reagent, DNase I-treated and further purified with RNeasy columns.
The Ribo-zero kit was used to eliminate ribosomal RNA. Libraries were generated using NEBNext RNA Library Prep Kit for Illumina sequencing.

value: embryos

tag: genotype

value: Mybx1 mutant


title: Wheat_imbibition_24hr_2

description: Gene expression after 16hr imbibed seed

source_name: 7 embryos from 24hr-imbibed seeds-2


title: GS115/3.5K_LP strain induced with methanol for 72 h_rep3

description: This sample is of control strain  GS115/3.5K, , which was grown in expression medium (BSM), induced with methanol for 72 h, and supplied with L-Met 24 h after methanol induction. It is the third of three control strain biological replicates used in this experiment, each from separate cultures.

source_name: GS115 integrated with  the empty vector pPIC3.5K


title: Mybx1_0-hpf


title: yJL322-IP1


title: Wheat_imbibition_16hr_3

description: Gene expression after 8hr imbibed seed

source_name: 7 embryos from 16hr-imbibed seeds-3


title: GS115/3.5K_LP strain induced with methanol for 72 h_rep1

description: This sample is of control strain  GS115/3.5K, , which was grown in expression medium (BSM), induced with methanol for 72 h, and supplied with L-Met 24 h after methanol induction. It is the first of three control strain biological replicates used in this experiment, each from separate cultures.


title: GS115/3.5K_LP strain induced with methanol for 72 h_rep2

description: This sample is of control strain  GS115/3.5K, , which was grown in expression medium (BSM), induced with methanol for 72 h, and supplied with L-Met 24 h after methanol induction. It is the second of three control strain biological replicates used in this experiment, each from separate cultures.


title: WT_0-hpf

value: wild-type


title: Wheat_dryseed_1

description: Gene expression after 0hr imbibed seed

source_name: 7 embryos from dryseeds-1


title: SBMK_Y_AB3171

city: Bethesda

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

data_processing:
Illumina RTA 1.8 and bcl2fastq 2.19 for fastq generation
Quality trim and alignment using CLC genomics workbench v11.0.1
expression defined as total of exon-mapped reads per gene (reads with more than 10 equivalent alignments were ignored)
upper quartile normalization of inflated log2 read count
Genome_build: hg38

source_name: keratinocytes isolated using the suction blister method

growth_protocol: To characterize the effect of Y-27632 on the expression profile of SBK, we incubated cells starting from isolation in the presence (+Y) or absence (-Y) of the inhibitor in the co-culture feeder system described early in the methods. After removal of the feeder cells with Versene, RNA from  SBK at passage 4 and 5 for the +Y group and 4, 5, and 6 or the -Y group was isolated using the RNeasy kit (Qiagen).  To compare the differential transcriptional response to cytokine treatment between early and late keratinocytes passaged with Y-27632 we adapted the IL-17 + IFN- stimulation conditions described previously [26] with some modifications. Two types of media were used:  SFM (+), which contains SFM medium (Gibco) with 10 ng/mL EGF (Gibco), 50 µg/mL Bovine Pituitary Extract (Gibco), 1X primocin, and 10 µM Y-27632; or SFM(-), which only has SFM medium with 50 µg/mL Bovine Pituitary Extract and 1X primocin. We took early (pass 4) and late (pass 12) keratinocytes out of culture and seeded them into a 24 well cell culture plate with 1 mL of SFM(+) at a density of 2X105 cells/well and incubated 37° C and 5% CO2 for 24 hours.  The next day, cells were washed 3X with PBS and 1 mL of SFM(-) was added.  Cells were incubated at 37°C and 5% CO2 for 24 hours.  The next day, cells were washed with PBS, and 400 µL of SFM(-) was added containing 10 ng/mL of IL-17A (R&D Systems), IFN-γ (R&D Systems), or 0.1% BSA in PBS for the no treatment control. Cells were incubated at 37°C and 5% CO2 for 48 hours, after which RNA was isolated using the RNeasy kit (Qiagen). N=2 early and late pass patient cell lines were tested, with two technical replicates for each condition

extract_protocol:
RNeasy kit (Qiagen).
TrueSeq stranded mRNA by NeoPrep

treatment_protocol: cells grown with ROCK inhibitor Y-27632, stimulated with IL17 + IFNg, or untreated (NT) as described under "growth protocol)

tag: subject

value: primary human keratinocytes

tag: passage

value: Early

tag: passage number

tag: treatment

tag: growth media

value: F-medium


title: SBMK_NT_AB3172

value: NT


title: SBMK_NT_AB3168


title: SBMK_Y_AB3173


title: SBMK_NT_AB2887

value: Late

value: serum free media (experimental media)


title: SBMK_NT_AB2883


title: SBMK_NT_AB2886


title: WT_6-hpf


title: SBMK_NT_AB2871


title: SBMK_NT_AB2882


title: SBMK_NT_AB2870


title: SBMK_NT_AB2867


title: SBMK_NT_AB3170


title: SBMK_IL17IFNG_AB2889


title: SBMK_IL17IFNG_AB2888


title: SBMK_IL17IFNG_AB2885


title: SBMK_NT_AB2866


title: GS115/DS56_HP strain induced with methanol for 72 h_rep3

description: This sample is of engineered strain GS115/DS56, which was grown in BSM medium, induced with methanol for for 72 h, and supplied with L-Met 24 h after methanol induction to promote SAM synthesis. It is the third of three engineered strain GS115/DS56 biological replicates used in this experiment, each from separate cultures.


title: RIF patient_rep1

city: shanghai

first: Mingjie

last: Wang

address: 197 Ruijin Er Road

institute: Ruijin Hospital,Shanghai Jiaotong University,School of Medicine

description:
RIF-1
Gene expression of endometrial tissue from RIF patient 1

hyb_protocol: After fragmentation, 10 ug of RNA were hybridized for 16 hr at 45C on Affymetrix PrimeView Human Gene Expression Array. Chips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: All raw data were manipulated in R version 3.3.1 Background adjusted and normalizaed using R package affy utilizing the RMA algorithm, missing values were evaluate using package impute.

source_name: Endometrial tissue from RIF patient

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA extracted using Trizol following the manufacture's instructions.

tag: subject status

value: recurrent implantation failure (RIF) patient

tag: gender

value: Female

tag: age

value: Endometrial tissue

tag: sampling time

value: day 7 after oocyte recovery


title: SBMK_IL17IFNG_AB2869


title: SBMK_IL17IFNG_AB2868


title: RIF patient_rep3

description:
RIF-3
Gene expression of endometrial tissue from RIF patient 3


title: RIF patient_rep2

description:
RIF-2
Gene expression of endometrial tissue from RIF patient 2


title: Healthy control_rep3

description:
Control-3
Gene expression of endometrial tissue from health control subject 3

source_name: Endometrial tissue from health control subject

value: health control

value: day LH + 7


title: PC3_EX1_tRNA-41326582 REP2

city: Leicestershire

first: Victoria

last: James

address: Sutton Bonington Campus

country: United Kingdom

institute: University of Nottingham

description:
total RNA
PC3_EX2.htseq.count.txt

data_processing:
Reads were trimmed with cutadapat (v1.6)
microRNAs were mapped using Shrimp and a custom constructed database of mature and hairpin miRNA sequences (Genecode V24) and counts called
mRNAs were mapped using Homo_sapiens.GRCh38.87.gtf (SAM tools) and counts performed using HTSeq
Genome_build: Homo sapiens GRCh38.87
Supplementary_files_format_and_content: txt files are supplied with the counts per miRNA or gene

source_name: PC3 Human Prostate Cancer Cell Line Vesicles

growth_protocol: Prostate cancer PC3 cells were obtained from ECACC (Culture Collections, Salisbury, UK) and cultured in Dulbecco’s modified medium (DMEM) (#D5796, Sigma, Dorset, UK) supplemented with 10% FBS (#B9433, Sigma), 50 U mL-1 penicillin and 50µg mL-1 streptomycin (#15140122, Gibco, Loughborough, UK).

extract_protocol:
Vesicles isolated using  qEV columns (Izon Science, Oxford,UK) and RNA extracted using Qiagen miRNAEasy kit following manufacturers protocol
the Truseq small RNA library (#RS-200-0012, Illumina, Essex, UK), Truseq Stranded RNA library (#20020597, Illumina) - standard manufactureres protocols used.

tag: cell line

tag: cell type

value: Prostate Cancer

tag: cell compartment

value: extracellular vesicles


title: VJ-PC3-EX2-smRNA-41336463 REP2

description:
microRNA
Counts-shrimp.txt


title: PC3_EX1_tRNA-41337446 REP1

description:
total RNA
PC3_EX1.htseq.count.txt


title: VJ-PC3-EX1-smRNA-41326587 REP1

description:
microRNA
Counts-shrimp.txt


title: Hippocampus TBI 24hr post injury, rep2

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Rat Genome microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

organism: Rattus norvegicus

source_name: Hippocampus TBI 24hr post injury, rep2

label_protocol: Labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the Total RNA sample.  Briefly, Total RNA was reverse transcribed after priming with a DNA oligonucleotide containing the T7 RNA polymerase promoter 5’ to a d(T)24 sequence.  After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase.  The quantity and quality of the cRNA was assayed by spectrophotometry and on the Agilent Bioanalyzer.

growth_protocol: Rats were prepared for fluid percussion traumatic brain injury or sham injury (Naive rats had no anesthesia and were not handled in any way and gene expression in their brains serve as baseline data) and sacrificed 24 hr, 2 week, 3 month, 6 month and 1 year post-injury, hippocampi and cortex were obtained, and stored in RNA later.

extract_protocol: RNA was extracted and purified using Ribopure (Ambion) RNA isolation.  Quality and quantity of the Total RNA sample was assessed using an Agilent Bioanalyzer with the RNA6000 Nano Lab Chip (Agilent Technologies; Santa Clara, CA).

treatment_protocol: Moderate Fluid percussion injury (TBI), sham and Naive at various time points (24hr, 2 week,3,6 and 12 month)

tag: strain

value: Sprague-Dawley


title: Hippocampus TBI 24hr post injury, rep3

source_name: Hippocampus TBI 24hr post injury, rep3


title: Healthy control_rep2

description:
Control-2
Gene expression of endometrial tissue from health control subject 2

tag: tissue


title: Hippocampus TBI 24hr post injury, rep1

source_name: Hippocampus TBI 24hr post injury, rep1


title: 2B4cDNANC

city: Peking

first: wang

middle: li

last: yong

state: Peking

address: No 10 xi tou tiao, you an gate

department: medical school

institute: Capital Medical University

description: SAMPLE 7

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were normalised using quantile normalisation with AffymetrixGUI in R

source_name: low metastatic human prostate epithelial cell line

label_protocol: Cye labeled cRNA were prepared with the Ambion MessageAmp kit for Affymetrix arrays

growth_protocol: The highly metastatic human prostate epithelial cell line PC-3M-1E8 (1E8) and the low metastatic line PC-3M-2B4 (2B4) were grown in RPMI 1640 medium (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, 100 units/mL penicillin, and 2.0 mM glutamine in a humidified incubator with 5% CO2 and 95% air at 37°C.

extract_protocol: RNA was extracted with trizol, followed by clean-up and DNase I treatment with Ambian RNA Isolation kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were transiently co-transfected with LMNA plasmid, control plasmid, shRNA plasmid or control plasmid, using Lipofectamine 2000

tag: transiently transfected with

value: LMNA control plasmid


title: Healthy control_rep1

description:
Control-1
Gene expression of endometrial tissue from health control subject 1


title: A375 EGR1 ChIP

first: Carl

last: Novina

state: MA

address: 450 Brookline Ave

department: Cancer Immunology

institute: Dana-Farber Cancer Institute

description: ChIP performed with Cell Signaling EGR1 (44D5)

data_processing:
75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) were mapped to the genome using the BWA algorithm with default settings. Only reads that pass Illumina’s purity filter,  align with no more than 2 mismatches, and map uniquely to the genome are used in the  subsequent analysis.
Read tags were extended in silico (using Active Motif software) at their 3´- ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp). To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.
Peak calling, to identify intervals with local enrichment in reads, was performed using MACS (Zhang et al., 2008). MACS default cutoff p-value is 1e-7 for narrow peaks and 1e-1 for broad peaks. Peak filtering was performed by removing false ChIP-Seq peaks as defined within the ENCODE blacklist.
Genome_build: hg19
Supplementary_files_format_and_content: Binary files showing the fragment density for 32-nt bins along the genome ("signal map")

source_name: cell culture

growth_protocol: A375 cells were maintained in DMEM without glutamine (Invitrogen), supplemented with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with Cell Signaling EGR1 (44D5) antibody.
Libraries were prepared by Active Motif.

treatment_protocol: Following growth for 48 hours post-seeding, cells were crosslinked in 1% formaldehyde for 15 min, and the reaction was quenched by addition of 0.125 M glycine.

value: skin

tag: tumor stage

value: malignant melanoma

tag: chip antibody

value: anti-EGR1 (Cell Signaling, 44D5)


title: 2B4cDNA

description: SAMPLE 8

value: low metastatic human prostate epithelial cell line

value: LMNA plasmid


title: Normal Differentiated Mesodermal Cells (NDMCs) type 2, biological rep1 [exon]

description: Global gene expression measured in NDMC2.

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol at the Ramachiotti Center for Gene Function Analysis, UNSW, Australia.

scan_protocol: Human Transciptome arrays were scanned using a GC3000 scanner at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Kensington, NSW, Australia), according to the manufacturers instructions.

data_processing: The data were RMA normalized Using Expression Console (from Affymetrix and the library files on the Affymetrix website). rma-alt-splice.summary.txt.

source_name: Normal Differentiated Mesodermal Cells type 2 (NDMC2) , biological rep1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol at the Ramachiotti Center for Gene Function Analysis, UNSW, Australia.

growth_protocol: Tissue was collected from the site of surgical incision and a sample snap frozen in liquid nitrogen.  Samples of each tissue were weighed and minced with surgical scissors.

extract_protocol: Total RNA was extracted from NDMC samples following the RNeasy Lipid Tissue Mini Kit (Qiagen, Cat#74804). The protocol was followed exactly except that homogenisation used  the probe tissue ruptor for NDMCs, and on-column DNase digestion was carried out. RNA quality and quantity were determined on the Agilent Bioanalyser.

treatment_protocol: For each gram of minced tissue, 2 mL of HEPES buffer containing 1.25 mg/ mL of Collagenase I (Sigma Aldrich, CAT#C6885-1G) was added. This was incubated for 30 – 45 min at 37ºC before being diluted 1:9 with additional HEPES buffer. The mixture was passed through a 250 micron mesh before being centrifuged at 300 rcf for 6 minutes at room temperature. The top layer was removed and the NDMCs collected for snap-freezing in liquid nitrogen.

tag: ID


title: 2B4siRNA

description: SAMPLE X

value: LMNA shRNA plasmid


title: Input DNA_for_EGR

value: none (input)


title: 2B4Nc.siRNA

description: SAMPLE 9

value: LMNA shRNA control plasmid


title: SBMK_IL17IFNG_AB2872

tag: subject

value: primary human keratinocytes

tag: passage

value: Late

value: serum free media (experimental media)


title: Hippocampus Sham 24hr post injury, rep2

source_name: Hippocampus Sham 24hr post injury, rep2


title: ChIP-seq_A375 with SLNCR1

description: ChIP performed with Santa Cruz anti-AR antibody H-280

growth_protocol: A375 cells were maintained in phenol-red-free DMEM without glutamine (Invitrogen), supplemented with 5% charcoal-stripped FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with Santa Cruz AR (H-280) antibody.
Libraries were prepared by Active Motif.

treatment_protocol: Cells were transfected with pcDNA3.1(-) empty vector control, or vector expressing SLNCR1 24 hours post-seeding using Lipofectamine 2000.  (Invitrogen). Cells were crosslinked in 1% formaldehyde for 15 min 48 hour post-transfection, and the reaction was quenched by addition of 0.125 M glycine.

tag: genotype/variation

value: SLNCR1 expressing

value: anti-AR (Santa Cruz H-280)


title: Input DNA_for_AR

value: empty vector


title: 2B4MOCK

description: SAMPLE 6

value: none (mock control)


title: PrEC, untreated [exon-level]

data_processing: The data were RMA normalized Using Expression Console (from Affymetrix and the library files on the Affymetrix website). The analyses details/parameters are included in the readme.txt.

source_name: normal prostate epithelial cells (PrEC)

growth_protocol: LNCaP cells were grown at 37ºC with 5% CO2 in T medium with 10% fetal calf serum. PrEC cells were grown at 37ºC with 5% CO2 in PREGM media (Cambrex).

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

treatment_protocol: Untreated.

value: PrEC


title: Normal Differentiated Mesodermal Cells (NDMCs) type 2, biological rep3 [exon]

source_name: Normal Differentiated Mesodermal Cells type 2 (NDMC2), biological rep3

growth_protocol: Tissue was collected from the site of surgical incision and a sample snap frozen in liquid nitrogen. Samples of each tissue were weighed and minced with surgical scissors.

extract_protocol: Total RNA was extracted from NDMC samples following the RNeasy Lipid Tissue Mini Kit (Qiagen, Cat#74804). The protocol was followed exactly except that homogenisation used the probe tissue ruptor for NDMCs, and on-column DNase digestion was carried out. RNA quality and quantity were determined on the Agilent Bioanalyser.

value: Female


title: Normal Differentiated Mesodermal Cells (NDMCs) type 1, biological rep3 [exon]

description: Global gene expression measured in NDMC1.

source_name: Normal Differentiated Mesodermal Cells type 1 (NDMC1), biological rep3


title: Hippocampus TBI 3mo post injury, rep4

source_name: Hippocampus TBI 3mo post injury, rep4

value: Sprague-Dawley


title: 1E8siRNA

description: SAMPLE 5

source_name: highly metastatic human prostate epithelial cell line


title: Hippocampus Sham 24hr post injury, rep1

source_name: Hippocampus Sham 24hr post injury, rep1


title: Normal Differentiated Mesodermal Cells (NDMCs) type 2, biological rep2 [exon]

source_name: Normal Differentiated Mesodermal Cells type 2 (NDMC2), biological rep2


title: LNCaP, untreated [exon-level]

source_name: androgen-sensitive human prostate adenocarcinoma (LNCaP)

value: LNCaP


title: Normal Differentiated Mesodermal Cells (NDMCs) type 1, biological rep2 [exon]

source_name: Normal Differentiated Mesodermal Cells type 1 (NDMC1), biological rep2


title: Normal Differentiated Mesodermal Cells (NDMCs) type 1, biological rep2 [gene]

data_processing: The data were RMA normalized Using Expression Console (from Affymetrix and the library files on the Affymetrix website). rma-gene-full.summary.txt.


title: Normal Differentiated Mesodermal Cells (NDMCs) type 2, biological rep2 [gene]


title: Normal Differentiated Mesodermal Cells (NDMCs) type 1, biological rep1 [exon]

source_name: Normal Differentiated Mesodermal Cells type 1 (NDMC1) , biological rep1


title: Hippocampus TBI 3mo post injury, rep3

source_name: Hippocampus TBI 3mo post injury, rep3


title: Hippocampus TBI 3mo post injury, rep2

source_name: Hippocampus TBI 3mo post injury, rep2


title: Normal Differentiated Mesodermal Cells (NDMCs) type 1, biological rep1 [gene]

source_name: Normal Differentiated Mesodermal Cells type 1 (NDMC1), biological rep1


title: Normal Differentiated Mesodermal Cells (NDMCs) type 1, biological rep3 [gene]


title: Normal Differentiated Mesodermal Cells (NDMCs) type 2, biological rep3 [gene]


title: 1E8Nc.siRNA

description: SAMPLE 4

value: highly metastatic human prostate epithelial cell line


title: 1E8cDNA

description: SAMPLE 3


title: SBMK_IL17IFNG_AB2873

source_name: keratinocytes isolated using the suction blister method

tag: passage number

tag: treatment

tag: growth media


title: 1E8MOCK

description: SAMPLE 1


title: SBMK_IL17IFNG_AB2884

value: Early


title: PrEC, untreated [gene-level]


title: LNCaP, untreated [gene-level]


title: 1E8cDNANC

description: SAMPLE 2

value: LMNA control plasmid


title: Normal Differentiated Mesodermal Cells (NDMCs) type 2, biological rep1 [gene]

source_name: Normal Differentiated Mesodermal Cells type 2 (NDMC2), biological rep1

tag: gender


title: Hippocampus TBI 3mo post injury, rep1

source_name: Hippocampus TBI 3mo post injury, rep1


title: Hippocampus Sham 3mo post injury, rep4

source_name: Hippocampus Sham 3mo post injury, rep4


title: NDMC2_3

scan_protocol: HuGene2.0st arrays were scanned using a GC3000 scanner at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Kensington, NSW, Australia), according to the manufacturers instructions.

data_processing: The data were RMA normalized using R function oligo::rma().

source_name: Normal Differentiated Mesodermal Cells (NDMCs) type 2, biological rep3

extract_protocol: Total RNA was extracted from NDMC samples following the RNeasy Lipid Tissue Mini Kit (Qiagen, Cat#74804). The protocol was followed exactly except that homogenization used the probe tissue ruptor for NDMCs, and on-column DNase digestion was carried out. RNA quality and quantity were determined on the Agilent Bioanalyser.

tag: tissue origin

value: Normal Differentiated Mesodermal Cells

value: NDMC type 2


title: Hippocampus Sham 3mo post injury, rep2

source_name: Hippocampus Sham 3mo post injury, rep2


title: Hippocampus Sham 3mo post injury, rep3

source_name: Hippocampus Sham 3mo post injury, rep3


title: NDMC1_3

source_name: Normal Differentiated Mesodermal Cells (NDMCs) type 1, biological rep3

value: NDMC type 1


title: US45103089_253949440417_S01_GE1_1100_83K_1_1

city: Genova

first: Lorenzo

last: Ferrando

address: Viale Benedetto XV

department: Department of Internal Medicine

country: Italy

institute: University of Genoa

description: Gene Expression after capecitabine and radiotherapy cycle of 8 weeks

hyb_protocol: Agilent SurePrint G3 Human Gene Expression v2 8x60K Microarray.

scan_protocol: Slides were scanned (Agilent SureScan Microarray Scanner) immediately after washing procedure according to the precedure outlined in Agilent one-color Microarray-based gene expression analysis manual.

data_processing: The scanned images were analyzed with Feature Extraction Software v10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: FFPE

label_protocol: Agilent SureTag Labeling kit (Agilent Technologies, Palo Alto, CA, USA), enzymatically label 1.8 µg of amplified cDNA with Cyanine 3-dUTP for 2 hours at 37°C

extract_protocol: RNA extraction

treatment_protocol: chemoradiation therapy, a combination of capecitabine (825 mg/m2) and radiations (50.4 Gy) provided in 28 fractions in 12 weeks. Clinical staging was accomplished using two physical examinations, endoscopic ultrasound (EUS) and nuclear magnetic resonance (NMR) before the administration of the neoadjuvant treatment. After 8 weeks from the completion of neoadjuvant therapy, surgery was performed

value: Tumor Sample, advanced rectal adenocarcinoma

tag: age at surgery

tag: dworak tumor regression grade

value: M


title: Hippocampus Naive 3mo, rep4

source_name: Hippocampus Naive 3mo, rep4


title: US45103089_253949440417_S01_GE1_1100_86K_2_3

value: F


title: NDMC2_1

source_name: Normal Differentiated Mesodermal Cells (NDMCs) type 2, biological rep1

tag: cell type


title: NDMC1_2

source_name: Normal Differentiated Mesodermal Cells (NDMCs) type 1, biological rep2


title: US45103089_253949440417_S01_GE1_1100_81K_1_3


title: NDMC2_2

source_name: Normal Differentiated Mesodermal Cells (NDMCs) type 2, biological rep2


title: US45103089_253949440417_S01_GE1_1100_67K_2_1


title: Hippocampus Naive 3mo, rep3

source_name: Hippocampus Naive 3mo, rep3

tag: strain


title: Hippocampus Sham 3mo post injury, rep1

source_name: Hippocampus Sham 3mo post injury, rep1


title: NDMC1_1

source_name: Normal Differentiated Mesodermal Cells (NDMCs) type 1, biological rep1


title: US45103089_253949440416_S01_GE1_1100_88K_2_1

tag: tissue


title: US45103089_253949425628_S02_GE1_1100_22K_1_4


title: US45103089_253949425628_S02_GE1_1100_18K_2_1


title: Hippocampus Naive 3mo, rep1

source_name: Hippocampus Naive 3mo, rep1


title: ChIP-seq_A375 with empty vector

source_name: cell culture

tag: cell line

value: skin

value: malignant melanoma


title: hCTB 2_T15h_24h_BDE_47

city: SAN FRANCISCO

first: Joshua

middle: F

last: Robinson

state: CA

address: 513 Parnassus Ave HSE16

department: Obstretrics, Gynecology and Reproductive Sciences

institute: University of California, San Francisco

description: Sample processing and hybridization was performed by the UCSF Gladstone Institute (Winn et al., 2007)

hyb_protocol: Labeled cRNA was purified with an RNeasy column (QIAGEN). Quality was evaluated by using the Agilent Bioanalyzer 2100 system. cRNA was fragmented at 94 C for 35 min.

scan_protocol: Hybridized with 15ug of cRNA and then washed, stained, and imaged at the Gladstone Genomics Core Facility by using standard Affymetrix protocols.

data_processing: Affymetrix CEL files were processed using the Affymetrix Expression Console and Transcriptome Analysis Console (TAC) software packages. Raw values were normalized via the Robust Multi-array Average (RMA) algorithm.

label: Biotin

source_name: primary villous cytotrophoblast (2nd trimester)

label_protocol: Hybridization and labeling was accomplished by using the protocol devised by the UCSF Gladstone Genomics Core Facility. Double-stranded cDNAs were generated from total RNA samples by using SuperScript II reverse transcriptase (Invitrogen) and a T7-oligo primer (QIAGEN). Biotin-labeled cRNA was synthesized by in vitro transcription using an Enzo Bioassay RNA labeling kit (Enzo Diagnostics).

growth_protocol: As described  (Robinson et al., 2017), cytotrophoblasts (CTBs) were isolated from 2nd trimester human placentas. CTBs were cultured at a density of 500,000 CTBs/well in 1.5 ml medium containing DME/H-21, 2% Nutridoma (Roche), 1% sodium pyruvate (Sigma), 1% Hepes buffer (Invitrogen), 1% glutamate plus (Atlanta Biologicals), and 1% penicillin/streptomycin (Invitrogen) on Matrigel substrate.

extract_protocol: Immediately following a 24h exposure duration, CTBs were washed once with PBS and RLT Lysis Buffer (Qiagen) was directly added to the culture dish well. The lysate was collected and stored at -80oC. We isolated and purified RNA using the RNeasy Micro Kit (Qiagen). The RNA concentration and quality were estimated (Absorbance 260nm/280nm = 1.9 - 2.1) by using a Nanodrop spectrometer (Thermo Scientific) and the Agilent RNA 6000 Nano LabChip Kit and Bioanalyzer 2100 system (RIN ≥ 9).

treatment_protocol: Cells were incubated at 37oC in 5% CO2/ 95% air. Following attachment (t=3h) or the next morning (t=15h), fresh media was supplied and CTBs were exposed to vehicle control (0.1% DMSO) or 1µM BDE-47.

tag: age

tag: exposure

tag: exposure duration


title: hCTB 3_T15h_24h_BDE_47


title: US45103089_253949425627_S01_GE1_1100_78K_1_2


title: Hippocampus Naive 3mo, rep2

source_name: Hippocampus Naive 3mo, rep2


title: US45103089_253949425626_S02_GE1_1100_1K_2_4


title: hCTB 1_T15h_24h_BDE_47


title: US45103089_253949425626_S02_GE1_1100_49K_1_3


title: hCTB 3_T3h_24h_vehicle


title: hCTB 3_T3h_24h_BDE_47


title: hCTB 2_T3h_24h_BDE_47


title: hCTB 2_T3h_24h_vehicle


title: hCTB 1_T3h_24h_vehicle


title: hCTB 1_T3h_24h_BDE_47


title: US45103089_253949417626_S01_GE1_1100_38K_2_2


title: US45103089_253949425626_S01_GE1_1100_46K_1_1


title: hCTB 2_T15h_24h_vehicle


title: Time Point 28d Dose 0mg/m3 (C-7)

city: Ottawa

first: Andrew

last: Williams

address: 50 Colombine Dr

country: Canada

institute: Health Canada

hyb_protocol: An equimolar amount of UMRR cRNA was mixed with each experimental cRNA and was hybridized to Agilent SurePrint G3 Rat 8 × 60K microarrays (Agilent Technologies. Inc). Hybridization was conducted for 17 hours at 65oC.

scan_protocol: After washing, microarray slides were scanned in a Scanned on an Agilent G2565AA scanner (Agilent). Data was retrieved using the Feature Extraction 10.7.3 software (Agilent). Data analysis is described below.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

source_name: Time Point 28d Dose 0mg/m3

label_protocol: In brief, 200 ng of total RNA per individual rat lung sample or Universal Mouse Reference RNA UMRR (Agilent Technologies) was used to synthesise labelled cDNAs and cRNAs using the Linear Amplification Kit (Agilent Technologies). T7 RNA polymerase-transcribed cRNA from experimental samples were labelled with Cyanine-5 and UMRR was labelled with Cyanine-3.

growth_protocol: The animal exposure was performed as described in Gosens et al. (2016). In brief, adult male (8 week-old) Wistar Unilever outbred rats (strain HsdCpb:WU) were obtained from Harlan (Netherlands). Rats (332 ± 22 g) were acclimatized for two weeks in Macrolon type IV cages (2-5 individuals per cage) with food and water supplied ad libitum before the exposure. The experiments were conducted at the National Institute for Public Health (RIVM) at Bilthoven, The Netherlands, under permit number 201300190. Experimental procedures complied with the European directive on the protection of animals for scientific purposes (Directive 2010/63/EU).

extract_protocol: Total RNA was extracted from individual rat lung samples from each treatment group using the AllPrep DNA/RNA Mini kit for animal tissue (Qiagen), following the manufacturer’s instructions. Total RNA was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific), and RNA quality and integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies). All samples showed RNA integrity numbers (RIN) above 7. Details of the microarray procedures can be found in Halappanavar et al. (2015).

treatment_protocol: This is a short-term inhalation study (STIS). It was conducted according to the OECD Test Guideline 403 for Acute Inhalation Toxicity Test number 403 using the C × T protocol considering a 6-h exposure equivalent per day (the maximum recommended). In brief, rats were exposed by inhalation (nose-only) to the 6-hour equivalent doses of 3.3 and 13.2 mg NPs / m3. Control animals were exposed to air only. Exposure was conducted over 5 consecutive days. Lung tissues were collected on day 1 after the last exposure (referred to as T6) and on day 22 after the last exposure (referred to as T28). Each treatment group consisted of minimum of 5 animals.

value: CuO NPs

tag: sampleID

tag: time point

value: 28 days

tag: dose

value: lung

value: male

tag: developmental stage

value: adult

source_name: Universal  Rat Reference RNA

tag: reference composition

value: 14 rat cell lines


title: hCTB 1_T15h_24h_vehicle


title: Time Point 6d Dose 3.3mg/m3 (L-50)

source_name: Time Point 6d Dose 3.3mg/m3

tag: treatment

value: 6 days


title: PrEC, biological rep3

description:
Gene expression data from PrEC cell line.
PrEC_rep3

hyb_protocol: Samples were hybridised on Affymetrix HuGene 2.0ST arrays at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Kensington, NSW, Australia), according to the manufacturers instructions.

scan_protocol: GeneChips were scanned using a GC3000 scanner at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Kensington, NSW, Australia), according to the manufacturers instructions.

data_processing: Affymetrix CEL files were RMA normalised using the rma function as implemented in the R package oligo version (1.28.2).

source_name: PrEC untreated

label_protocol: Total RNA was fragmented and biotin labeled at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Kensington, NSW, Australia), according to the manufacturers instructions.

extract_protocol: Total input RNA was isolated as per the manufacturers instructions (Millipore, Cat# 17-700). Briefly, Cells were harvested at 80-90% confluency. After two ice-cold PBS washes, cells were scraped and collected by centrifugation at 1500 rpm for 5 minutes at 4C. The pellet was resuspended in an equal volume of lysis buffer and incubated on ice for 5 mins before being frozen at -80C to complete the lysis process. The lysate was thawed quickly and centrifuged at 14,000 rpm for 10 mins at 4C. 100ul of the supernatant was added to 900ul of buffer. 10 ul was removed as input RNA. The RNA was diluted with 107 ul wash buffer, 15ul of 10% SDS, and 18 ul proteinase K to a total volume of 150 ul. After incubation at 55 C for 30 mins with shaking to digest the protein, centrifuge briefly, and transfer supernatant into new tube. 250 ul wash buffer was added to each tube. Phenol:chloroform:isoamyl alcohol extraction was performed with an equal volume, followed by chloroform extraction, and the RNA was precipitated by adding 50 ul of Salt Solution I, 15 ul of Salt Solution II, 5 ul of Precipitate Enhancer and 850 ul of absolute ethanol and stored at -80C overnight. After centrifugation at 14,000 rpm for 30 mins at 4C, the pellet was washed once with 80% ethanol, before being re-suspended in 10-20 ul RNase-free water. RNA quality was assessed by RIN using a RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100 (Agilent Technologies).

value: PrEC

value: prostate epithelial cells


title: LNCaP, biological rep3

description:
Gene expression data from LNCaP cell line.
LNCaP_rep3

source_name: LNCaP untreated

extract_protocol: Total input RNA was isolated as per the manufacturers instructions (Millipore, Cat# 17-700). Briefly, Cells were harvested at 80-90% confluency. After two ice-cold PBS washes, cells were scraped and collected by centrifugation at 1500 rpm for 5 minutes at 4C. The pellet was resuspended in an equal volume of lysis buffer and incubated on ice for 5 mins before being frozen at -80 C to complete the lysis process. The lysate was thawed quickly and centrifuged at 14,000 rpm for 10 mins at 4C. 100ul of the supernatant was added to 900ul of buffer. 10 ul was removed as input RNA. The RNA was diluted with 107 ul wash buffer, 15ul of 10% SDS, and 18 ul proteinase K to a total volume of 150 ul. After incubation at 55 C for 30 mins with shaking to digest the protein, centrifuge briefly, and transfer supernatant into new tube. 250 ul wash buffer was added to each tube. Phenol:chloroform:isoamyl alcohol extraction was performed with an equal volume, followed by chloroform extraction, and the RNA was precipitated by adding 50 ul of Salt Solution I, 15 ul of Salt Solution II, 5 ul of Precipitate Enhancer and 850 ul of absolute ethanol and stored at -80C overnight. After centrifugation at 14,000 rpm for 30 mins at 4C, the pellet was washed once with 80% ethanol, before being re-suspended in 10-20 ul RNase-free water. RNA quality was assessed by RIN using a RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100 (Agilent Technologies).

value: LNCaP

value: androgen-sensitive human prostate adenocarcinoma


title: LNCaP, biological rep2

description:
Gene expression data from LNCaP cell line.
LNCaP_rep2


title: RNAseq of developing sino-atrial node

city: Boston

first: Jonathan

last: Seidman

address: 77 ave louis pasteur

institute: Harvard Medical School

description: SAN

data_processing:
Fastq sequence was aligned to the chicken genome Galgal3 using the Bowtie aligner as called by Tophat
RPKM were calculated as described in https://doi.org/10.1002/0471142727.mb0412s94
Genome_build: Galgal3
Supplementary_files_format_and_content: text file includes normalized and raw read count.

organism: Gallus gallus

source_name: embryo pacemaker region

growth_protocol: Chick embryos were havested at the indicated HH stage (HH st), dissected and pooled

extract_protocol:
RNA was extracted by the trisol method and polyA mRNA was selected for library construction
Libraries were constructed as described in Christodoulou et al., PMID 24509080; RNAseq libraries were paired end sequenced (36 bp) on Illumina HiSeq 2000

value: embryo

value: embryo pacemaker region


title: RNAseq of apex of embryonic ventricle

description: Vent

source_name: apex of common cardiac ventricle

value: apex of common cardiac ventricle


title: RNAseq of posterior lateral mesoderm HH st8

description: Post

source_name: posterior lateral mesoderm

value: posterior lateral mesoderm


title: Time Point 6d Dose 13.2mg/m3 (H-77)

source_name: Time Point 6d Dose 13.2mg/m3

tag: gender


title: Time Point 28d Dose 0mg/m3 (C-10)


title: Time Point 28d Dose 3.3mg/m3 (L-56)

source_name: Time Point 28d Dose 3.3mg/m3


title: PrEC, biological rep1

description:
Gene expression data from PrEC cell line.
PrEC_rep1


title: RNAseq of pacemaker progenitor field HH st 8

description: PMF

source_name: pacemaker progenitor field

value: pacemaker progenitor field


title: RNAseq of HH st17-18 atrioventricular junction

description: AVJ

source_name: atrio-ventricular junction HH st 17-18

value: atrio-ventricular junction HH st 17-18


title: RNAseq of left component of embryonic atrial

description: At

source_name: left embryonic atria

value: left embryonic atria


title: hCTB 3_T15h_24h_vehicle


title: RNAseq of anterior lateral plate mesoderm HH st 8

description: ant

source_name: anterior plate mesoderm HH st 8

value: anterior plate mesoderm HH st 8


title: RNAseq of lateral plate mesoderm corresponding to the left side of the embryo

description: Left

source_name: Left side of HH st 8 embryo lateral plate mesoderm


title: US45103089_253949417626_S01_GE1_1100_10K_1_3

source_name: FFPE

value: Tumor Sample, advanced rectal adenocarcinoma

value: M


title: Time Point 6d Dose 0mg/m3 (C-3)

source_name: Time Point 6d Dose 0mg/m3

value: CuO NPs

value: lung

value: male

value: adult


title: US45103089_253949417625_S01_GE1_1100_34K_1_2

value: F


title: PrEC, biological rep2

description:
Gene expression data from PrEC cell line.
PrEC_rep2

value: PrEC

value: prostate epithelial cells


title: Time Point 28d Dose 13.2mg/m3 (H-80)

source_name: Time Point 28d Dose 13.2mg/m3

value: 28 days

value: 14 rat cell lines


title: Time Point 6d Dose 13.2mg/m3 (H-75)

value: 6 days

source_name: Universal  Rat Reference RNA


title: LNCaP, biological rep1

description:
Gene expression data from LNCaP cell line.
LNCaP_rep1

value: LNCaP

value: androgen-sensitive human prostate adenocarcinoma


title: US45103089_253949417625_S01_GE1_1100_36K_2_2


title: Time Point 28d Dose 13.2mg/m3 (H-82)


title: Cre/+ TAM (P098_16_1504_579)

city: Rostock

first: Björn

last: Spittau

address: Gertrudenstraße 9

institute: University of Rostock

hyb_protocol: Samples were hybridized to an Affymetrix Mouse Gene 2.0 ST Array Plate. For hybridization, washing, staining and scanning an Affymetrix GeneTitan system, controlled by the Affymetrix GeneChip Command Console software v4.2, was used

scan_protocol: Sample processing was performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de).

data_processing: Differential Gene Expression Analyses were performed using DAVID.

source_name: Cre/+ TAM

label_protocol: 0.4 and 2.5 ng of total RNA was reverse transcribed into double-stranded cDNA in a two-step process, introducing a SPIA tag sequence. Bead purified cDNA was amplified by a SPIA amplification reaction followed by an additional bead purification. 3.0 µg of SPIA cDNA was fragmented, terminally biotin-labeled.

growth_protocol: Mice were deeply anaesthetised by an intraperitoneal injection of Ketamin (75 mg/kg) and Rompun (5.8 mg/kg) and perfused with ice-cold PBS. The brains were removed from the skulls and meninges were removed by rolling over absorbent paper. Brains were collected in cold dissection buffer, homogenised with a glass homogeniser and filtered through 75 μm cell strainers. Cells were washed with 30 ml HBSS and centrifuged 12 min, 300 g, 4 °C. For density gradient centrifugation, the pellet was re-suspended in 5 ml 37 % Percoll (P1644, Sigma Aldrich) in PBS, underlayed with 4 ml 70 % Percoll and overlayed with 4 ml 30 % Percoll in a 15 ml Falcon Tube. The gradient was centrifuged for 40 min, 600 g, 15 °C, without breaks. Afterwards, the cell layer was transferred to PBS + 1 % FCS and centrifuged for 5 min, 200 g, 4 °C.

extract_protocol: Microglia were sorted as CD11b+/CD45low cells using the BD Cell Sorter FACS Aria Fusion and the BD Cell Sorter FACS Aria III. RNA of microglia was isolated using PicoPure™ RNA Isolation Kit (KIT0202, Arcturus) according to manufacturer’s protocol.

treatment_protocol: For induction of Cre recombinase activity, 6-8-week-old Cx3cr1CreERT2 mice were treated with 8 mg tamoxifen (TAM, T5648, Sigma-Aldrich, Germany) solved in 200 µl corn oil (C8267, Sigma) injected subcutaneously and intraperitoneally at two time points 48 h apart. For all experiments, littermates carrying the respective loxP-flanked alleles but lacking expression of Cre recombinase (+/+ TAM) or not receiving tamoxifen (cre/+ OIL) were used as controls.

tag: genotype

value: Cre/+

tag: injection

value: TAM

value: adult microglia 4 weeks after injections


title: Cre/+ TAM (P098_19_1504_583)


title: US45103089_253949417613_S01_GE1_1100_30K_1_2

value: Tumor Sample, advanced rectal adenocarcinoma

tag: age at surgery

tag: dworak tumor regression grade


title: Time Point 6d Dose 3.3mg/m3 (L-51)

source_name: Time Point 6d Dose 3.3mg/m3

tag: strain


title: Cre/+ TAM (P098_14_1504_577)

tag: cell type


title: wt TAM (P098_15_1504_578)

source_name: wt TAM

value: wt


title: wt TAM (P098_17_1504_580)


title: Time Point 6d Dose 3.3mg/m3 (L-49)

value: CuO NPs

tag: tissue


title: Cre/+ TAM (P098_18_1504_581)


title: US45103089_253949417613_S01_GE1_1100_60K_2_1


title: US45103089_253949417602_S02_GE1_1100_51K1_1_1

value: M


title: Time Point 6d Dose 0mg/m3 (C-4)

value: lung

value: male


title: US45103089_253949417608_S01_GE1_1100_32K_1_4


title: US45103089_253949417596_S02_GE1_1100_31K_1_3

value: F


title: wt TAM (P098_11_1504-504 neg)


title: wt TAM (P098_10_1504_539)


title: US45103089_253949417607_S01_GE1_1100_25K_1_1


title: wt TAM (P098_13_1504_576)


title: Cre/+ TAM (P098_09_1504_538)


title: Time Point 28d Dose 13.2mg/m3 (H-83)

value: adult


title: Cre/+ OIL (P098_08_1504_530)

source_name: Cre/+ OIL

value: OIL


title: wt TAM (P098_06_1504_527)


title: Time Point 28d Dose 3.3mg/m3 (L-52)

value: 28 days


title: Time Point 28d Dose 3.3mg/m3 (L-55)

value: 14 rat cell lines


title: US45103089_253949417596_S01_GE1_1100_76K_2_2


title: Time Point 28d Dose 13.2mg/m3 (H-84)


title: Time Point 6d Dose 13.2mg/m3 (H-79)

value: 6 days


title: Cre/+ OIL (P098_05_1504_506_neg)


title: Male_Nr1d1 knockdown_biological rep4

city: Madison

first: Stephen

middle: Coull

last: Gammie

state: WI

address: 430 Lincoln Drive

department: Zoology

institute: University of Wisconsin

description: Gene expression data from Nr1d1 knockdown males

hyb_protocol: Fragmented and labeled ss-cDNA targets were hybridized with the arrays at 45°C for 16 hours.

scan_protocol: Arrays were scanned on an Affymetrix GC3000 G7 Scanner. Data were extracted and processed from scans using Affymetrix Command Console v. 3.1.1.1229.

data_processing: Raw array data were normalized and summarized using Affymetrix ® Transcriptome Analysis Console (TAC) software.

source_name: adult male_nucleus accumbens

label_protocol: cDNA for array hybridization was synthesized from 150 ng of total RNA using a GeneChip WT Plus Kit (Thermo Fisher Scientific Inc, CA, USA) according to the manufacturer’s specifications.

growth_protocol: The strain of mice used was C57BL/6J purchased from The Jackson Laboratory. Mice were approximately 15 weeks old at time of tissue collection.

extract_protocol: Total RNA was extracted using the Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio-Rad, Hercules, CA, USA).

treatment_protocol: Tissue was collected approximately 5 weeks following injection into nuclues accumbens of AAV with shRNA for Nr1d1 or scrambled control.  On postpartum day 0, pups were culled, if necessary, to standardize litter size to 11. Tissue was collected on postpartum day 7.  On postpartum day 0, pups were culled, if necessary, to standardize litter size to 11. Tissue was collected on postpartum day 7.

value: microdissected nucleus accumbens

tag: Sex

value: Nr1d1 knockdown

tag: age

value: 15 weeks


title: US45103089_253949417584_S01_GE1_1100_62K_1_1


title: US45103089_253949417580_S02_GE1_1100_56K_1_4


title: Cre/+ OIL (P098_04_1504_495_neg)

value: Cre/+


title: Male_Nr1d1 knockdown_biological rep5


title: Male_Nr1d1 knockdown_biological rep3


title: Male_Nr1d1 knockdown_biological rep1


title: US45103089_253949417584_S02_GE1_1100_57K_2_2


title: Male_Nr1d1 knockdown_biological rep6


title: US45103089_253949417585_S01_GE1_1100_58K_1_1


title: US45103089_253949417580_S02_GE1_1100_71K_2_2


title: Time Point 28d Dose 0mg/m3 (C-9)

source_name: Time Point 28d Dose 0mg/m3


title: US45103089_253949417585_S01_GE1_1100_33K_2_2


title: Male_Nr1d1 knockdown_biological rep2


title: Male_Control_biological rep6

description: Gene expression data from control males

value: control


title: Male_Control_biological rep5

description: Gene expression data from control males


title: Time Point 6d Dose 13.2mg/m3 (H-78)

source_name: Time Point 6d Dose 13.2mg/m3


title: Male_Control_biological rep4

description: Gene expression data from control males


title: Cre/+ TAM (P098_07_1504_529)

value: TAM

value: adult microglia 4 weeks after injections


title: Male_Control_biological rep3

description: Gene expression data from control males


title: Time Point 28d Dose 0mg/m3 (C-6)

value: CuO NPs


title: US45103089_253949417580_S01_GE1_1100_69K_1_1

value: Tumor Sample, advanced rectal adenocarcinoma


title: Time Point 6d Dose 0mg/m3 (C-2)

value: lung


title: Time Point 6d Dose 3.3mg/m3 (L-47)

value: male


title: siUSP342

city: Chengdu

first: Quan

last: Yuan

state: Sichuan

address: 14 Third section, Renmin Nan Road

institute: West China Hospital of Stomatology, Sichuan University

data_processing:
Illumina Casava1.8 software used for basecalling.
The reads were aligned to hg19 genome using Tophat.
Analysis of RNA-seq data was done using Cufflinks with Refseq mRNAs to guide assembly and the cummeRbund package in R
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized abundance measurements,

growth_protocol: α-MEM (Gibco) supplemented with 10% fetal bovine serum (Gibco),100 units/ml penicillin (Gibco) and 100 μg/ml streptomycin (Gibco)

extract_protocol:
Total RNAs were harvested using an RNeasy mini kit (Qiagen).
Libraries were prepared using the Illumina TrueSeq mRNA sample preparation kit according to manufacturer’s instruction

treatment_protocol: Human MSCs were treated with USP34 or control siRNAs and cultured in osteogenic induction medium for 2 days prior to RNA isolation

value: bone marrow

value: mesenchymal stem cells (MSCs)

tag: genotype/variation

value: USP34 siRNA


title: US45103089_253949417580_S01_GE1_1100_21K_2_3

value: F


title: siUSP341


title: siCTRL2

value: Control


title: siCTRL1


title: Male_Control_biological rep2

description: Gene expression data from control males


title: Female_Nr1d1 knockdown_biological rep4

description: Gene expression data from Nr1d1 knockdown females

source_name: adult female_nucleus accumbens

value: female


title: Female_Nr1d1 knockdown_biological rep5

value: microdissected nucleus accumbens


title: Time Point 6d Dose 13.2mg/m3 (H-76)

tag: sampleID

value: 6 days

value: adult

value: 14 rat cell lines


title: Female_Nr1d1 knockdown_biological rep3

value: Nr1d1 knockdown

value: 15 weeks


title: Female_Control_biological rep5

description: Gene expression data from control females

value: control


title: Female_Nr1d1 knockdown_biological rep6


title: Time Point 28d Dose 0mg/m3 (C-8)

value: CuO NPs

tag: time point

value: 28 days


title: Female_Nr1d1 knockdown_biological rep2


title: TSX 373B

city: Rotterdam

first: Arne

last: IJpma

address: Dr. Molewaterplein 50

institute: Erasmus MC

description: Gene expression data from ovary biopt material

scan_protocol: Chips were scanned on an Affymetrix Scanner according to the manufacturers protocol.

data_processing: The data were analyzed with Partek Genomics Suite version 6.6 using GCRMA with default settings and quantile normalization method. The data is log2 transformed.

source_name: TSX, ovary sample

label_protocol: cRNA was biotin-labeled.

growth_protocol: All tissue samples were snap frozen in liquid nitrogen immediately after collection.

extract_protocol: Total RNA was extracted from Ovary biopsies using TRIZOL reagent (Invitrogen, Breda, The Netherlands) as per manufacturer's instructions.  After Trizol purification, RNA was repurified using  the Rneasy Mini Kit (Qiagen, Venlo., The Netherlands) according to manufacturer's instructions.  Total RNA was quantified by OD260/OD280 measurement and with RiboGreen RNA Quantitation Kit (Moleular Probes, Leiden, The Netherlands). RNA quality was assessed on a 6000 nanochip using Agilent 2100 bioanalyzer (Agilent Technologys, Waldbronn, Germany).

treatment_protocol: There was no treatment on the tissues.

tag: gender history

value: female to male transsexual

value: ovary


title: Female_Nr1d1 knockdown_biological rep1


title: Time Point 28d Dose 3.3mg/m3 (L-54)

source_name: Time Point 28d Dose 3.3mg/m3

tag: dose

value: lung

value: male

tag: developmental stage


title: Male_Control_biological rep1

description: Gene expression data from control males


title: TSX 371B


title: Time Point 28d Dose 3.3mg/m3 (L-53)

tag: treatment

tag: reference composition


title: Time Point 6d Dose 0mg/m3 (C-1)

tag: gender


title: Time Point 28d Dose 13.2mg/m3 (H-81)


title: Time Point 6d Dose 0mg/m3 (C-5)


title: Female_Control_biological rep2

tag: genotype


title: TSX 368B


title: Female_Control_biological rep3


title: PAX5B3

city: Toulouse

first: Eric

last: DELABESSE

address: 1 avenue Irène Joliot-Curie

country: France

institute: Institut Universitaire de Cancérologie de Toulouse, site Oncopôle CHU de Toulouse

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
Probe-signal intensities were normalized and summarized by the Robust Multiarray Average (RMA) method using Affymetrix’s Expression Console software.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MoGene-2_0-st
program-name = Expression Console
program-version = 1.2.0.20

source_name: PAX5B cDNA EGFP transduction of Pax5-/- pro-B cells

label_protocol: RNA samples were purified and prepared according to the manufacturer's protocol with the Affymetrix's GeneChip Whole Transcript Sense Target Labeling Assay Kit

growth_protocol: The in vitro pro-B cell differentiation/proliferation protocol used was adapted from Rolink et al. [Rolink, A. G. 2004. B-cell development and pre-B-1 cell plasticity in vitro. Methods Mol Biol 271: 271-281]. The pro-B Pax5-/- cells were isolated from Pax5-/- embryo fetal liver liver at E17.5 and cocultivated with irradiated (30 Gy) OP9-derived stromal cells in 24-well plates in Iscove’s Modified Dulbecco’s Medium (IMDM; Gibco), supplemented with 5% Fetal Bovine Serum (FBS) (Stemcell Technologies), 2ng/ml murine IL7 (Peprotech), 0.05 mM β-mercaptoethanol (Sigma-Aldrich), 2mM L-glutamine (Invitrogen), penicillin (100 units/ml) and streptomycin (100 units/ml). Experiments were performed after an initial pro-B cell expansion on irradiated OP9 cells in the presence of 2ng/ml IL7. Every 3 days, pro-B cells were harvested and propagated on fresh OP9 stromal cells.  Full-length human PAX5A and PAX5B cDNA were amplified, sequenced and inserted into the retroviral vector pMSCV-IRES-EGFP (MIE), a bicistronic vector allowing the expression of EGFP under the control of the long terminal repeat (LTR) promoter. Retroviral supernatants were produced by Phoenix retrovirus producer line (Orbigen) using Lipofectamine 2000 (Invitrogen) reagent for transfection and proceeding according to the manufacturer’s instructions. After overnight incubation of the transfection mix, cells were treated with 10mM sodium butyrate (Millipore) and washed with PBS before pro-B cell medium was added. Viral supernatants were harvested after 24h of incubation at 32°C, passed on a 0.45µm filter, aliquoted and frozen at -80°C.  The pro-B cells, cultured on irradiated OP9 cells in the presence of 2ng/ml of IL7, are infected during exponential growth. Retroviral supernatant was diluted 1:3, supplemented with 4µg/ml polybrene (Sigma) and 2ng/ml of IL7 (Peprotech); spinoculation was performed at 1000xg at 32°C for 90 min. After centrifugation, 1ml of fresh medium supplemented with IL7 was added and the cells were incubated overnight at 37°C. After infected pro-B cell expansion for few days, cells were washed out of IL-7 and plated in IMDM, 5% FCS, 0.05mM β-mercaptoethanol and 2mM L-glutamine on irradiated OP9-derived stromal cells with or without IL7.   After 5 days in culture with 2ng/ml of IL7, infected cells were sorted according to their positivity for GFP fluorescence with a FACSAria II (BD Biosciences) cell sorter.

extract_protocol: Total RNA from GFPpos sorted pro-B infected cells were extracted using the Trizol method according to manufacturer’s instruction (Invitrogen). RNA quality was assessed using the RNA 6000 Nano Assay on the Agilent 2400 Bioanalyser (Agilent Technologies, Massy, FRANCE).

value: Pax5-/- pro-B cells

tag: transduced with

value: PAX5B cDNA EGFP

value: Blood B-cells


title: TSX 367B

hyb_protocol: Hybridization was performed according to Affymetrix protocols.


title: PAX5B2


title: Time Point 6d Dose 3.3mg/m3 (L-48)


title: PAX5B1


title: TSX 356B


title: Female_Control_biological rep4

value: female


title: TSX 362B


title: TSX 365B


title: MIE2

source_name: Empty EGFP vector (MIE) transduction of Pax5-/- pro-B cells

value: Empty EGFP vector (MIE)


title: TSX 354B


title: PAX5A2

source_name: PAX5A cDNA EGFP transduction of Pax5-/- pro-B cells

value: PAX5A cDNA EGFP


title: Female_Control_biological rep1

value: microdissected nucleus accumbens


title: TSX 351B


title: PAX5A3


title: APPKO DIV7-3: Cortical neurons APP-/- DIV7, biological rep 3

city: Brussels

first: Pascal

last: Kienlen-Campard

address: Avenue E. Mounier 53

department: Institute of NeuroScience

country: Belgium

institute: Université Catholique de Louvain

description: Gene expression data from  APP-/- primary cortical neurons after 7 days of in vitro culture

hyb_protocol: Following fragmentation and labeling, 5,2ug of ss-DNA were hybridized for 16 hr at 45C GeneChip®Mouse Transcriptome 1.0 Array. GeneChips were washed and stained using FS450_0001 protocol in the Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned using the GeneChip™ scanner 3000 7G

data_processing: Raw data were preprocessed and normalized with the Robust Multi-array Average (RMA)(Irizarry et al., 2003) method with R/Bioconductor

source_name: Primary cortical neurons after 7 days in vitro culture

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip WT PLUS reagent kit) from 250ng of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary cultures of cortical neurons were prepared from E18 mouse embryos. Briefly, cortices were dissected and dissociated in HBSS without calcium and magnesium. HBSS (with calcium and magnesium) was added and the mixture centrifuged on Fetal Bovine Serum (FBS) for 10min at 1000xg to pellet cells. Cells were plated at 200.000 cells/cm² in culture dishes pre-treated with 10µg/ml of poly-L-lysine in phosphate buffered saline (PBS) and cultured for 3 or 7 days in vitro in Neurobasal® medium supplemented with 2% v/v B-27® supplement medium, 1mM L-glutamine and penicillin-streptomycin (50U/ml -50µg/ml each) at 37°C, 5% CO2 and humidified atmosphere. Half of the medium was renewed every 2-3 days. Otherwise, embryonic cortices subjected to microarray (E18) were directly frozen in liquid nitrogen and kept at -80°C before RNA extraction.

value: Cortex

value: APP-/-

value: E18 + cultured for 7 days in vitro

tag: date of sample processing


title: TSX 361B


title: MIE1


title: TSX 359B


title: TSX 350B


title: PAX5A1


title: eli1 +glc rep1

city: Guelph

first: Malcolm

last: Campbell

state: Ontario

address: 50 Stone Road East

institute: University of Guelph

data_processing:
Base-calling: Off-Line Base Caller OLB-1.9.4
Alignment: Tophat 2.0.8b; Bowtie2
Quality control: Samstat
Expression analysis: Cufflinks
Differential expression analysis: Cuffdiff
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample

source_name: 4-day-old seedlings

growth_protocol: Seedlings were grown in MS growth medium in the dark at 21 degrees Celsius for 4 days, in 24-well microtitre plates, following a 3-day cold stratification period at 4 degrees Celsius and a 6-hour exposure to light.

extract_protocol:
The extraction was done using NucleoSpin® RNA Plant Mini Spin Kits with on-column rDNase treatment.
The library was constructed using NEBNext® mRNA Library Prep Reagent Set for Illumina® following the protocol in the product manual.

treatment_protocol: Samples of each genotype were grown with no treatment or with 1% m/v glucose.

tag: background ecotype

value: ectopic lignification1-1

value: seedling

value: 4 days post germination

value: 1% glucose


title: WT DIV7-3: Cortical neurons APP+/+ DIV7, biological rep 3

description: Gene expression data from  APP+/+ primary cortical neurons after 7 days of in vitro culture

value: APP+/+


title: APPKO DIV3-2: Cortical neurons APP-/- DIV3, biological rep 2

description: Gene expression data from  APP-/- primary cortical neurons after 3 days of in vitro culture

source_name: Primary cortical neurons after 3 days in vitro culture

value: E18 + cultured for 3 days in vitro


title: eli1 +glc rep2


title: PCOS 349B

source_name: PCOS, ovary sample

tag: disease state

value: PCOS

value: ovary


title: APPKO DIV3-1: Cortical neurons APP-/- DIV3, biological rep 1

tag: tissue


title: APPKO DIV7-1: Cortical neurons APP-/- DIV7, biological rep 1


title: WT DIV7-2: Cortical neurons APP+/+ DIV7, biological rep 2


title: APPKO DIV7-2: Cortical neurons APP-/- DIV7, biological rep 2


title: WT DIV7-1: Cortical neurons APP+/+ DIV7, biological rep 1


title: APPKO DIV3-3: Cortical neurons APP-/- DIV3, biological rep 3


title: WT DIV3-3: Cortical neurons APP+/+ DIV3, biological rep 3

description: Gene expression data from  APP+/+ primary cortical neurons after 3 days of in vitro culture


title: PCOS 154B


title: WT +glc rep1

value: Wild type


title: eli1 -glc rep2


title: eli1 -glc rep1


title: WT +glc rep2


title: WT -glc rep1


title: WT -glc rep2


title: PCOS 149B


title: PCOS 153B


title: PCOS 152B


title: WT DIV3-2: Cortical neurons APP+/+ DIV3, biological rep 2


title: Col0_RT_TSS-Seq_rep2

city: Frederiksberg C

first: Maxim

last: Ivanov

address: Thorvaldsensvej 40

department: Dept. of Plant and Environmental Sciences

country: Denmark

institute: University of Copenhagen

data_processing:
Library strategy: TSS-Seq
Illumina Casava v1.7 software was used for basecalling.
TSS-Seq: 1) Adapter trimming (Trim Galore v0.4.3; --adapter "ATCTCGTATGCCG"); 2) Trim UMI barcodes (8 nt; UMI-Tools extract); 3) Alignment (STAR v2.5.2b; --outSAMmultNmax 1 --alignEndsType Extend5pOfRead1); 4) Sort BAM files (Samtools v1.3.1); 5) Remove reads aligned to rRNA, tRNA, snRNA or snoRNA loci (BEDTools v2.17.0); 6) Remove reads with MAPQ < 10 (Samtools v1.3.1); 7) Deduplication (UMI-Tools dedup); 8) Make stranded bedGraph files from the 5' bases (BEDTools genomecov; -bg -5 -strand + / -); 9) Remove singletons (awk) and convert to Bigwig (kentUtils bedGraphToBigWig). See the full pipeline in https://github.com/Maxim-Ivanov/Nielsen_et_al_2018/01-Alignment_of_5Cap-Seq_data.sh
Genome_build: TAIR10
Supplementary_files_format_and_content: Bigwig files show sequencing coverage with single base resolution (no signal smoothing or transformation were applied).

source_name: Whole seedlings

growth_protocol: The Arabidopsis seedlings were grown on plates (1/2 Murashige and Skoog medium, 1% sucrose, 0.5% Microagar) with a 16h light/8h dark cycle at 22°C.

extract_protocol:
Total RNA was isolated from 14 day old seedlings using QIAgen Plant RNeasy Mini Kit following manufacturer’s instructions
Libraries were prepared as described in Pelechano et al. Nat Protoc. 2016 Feb 11(2):359-76; PMID: 26820793.

treatment_protocol: For cold treatment, seedlings were grown in control conditions for 10 days and subsequently transferred to 4°C for 3 hours and sampled.

value: Whole seedlings

tag: ecotype

value: Columbia (Col-0)

tag: cold treatment

value: No

value: 14 day

tag: protocol

value: TSS-Seq


title: Col0_cold_TSS-Seq_rep2

value: Yes

tag: age


title: WT DIV3-1: Cortical neurons APP+/+ DIV3, biological rep 1

value: Cortex


title: Col0_cold_TSS-Seq_rep1


title: APPKO E18-3: Embryo cortex APP-/- E18, biological rep 3

description: Gene expression data from an APP-/- embryonic cortex at E18

source_name: Embryonic cortex at E18 developmental stage

value: APP-/-

value: Embryo at E18


title: WT E18-2: Embryo cortex APP+/+ E18, biological rep 2

description: Gene expression data from an APP+/+ embryonic cortex at E18


title: Col0_RT_TSS-Seq_rep1


title: APPKO E18-1: Embryo cortex APP-/- E18, biological rep 1


title: APPKO E18-2: Embryo cortex APP-/- E18, biological rep 2


title: WT E18-3: Embryo cortex APP+/+ E18, biological rep 3


title: GATA2R396Q rep3

data_processing:
Probe-signal intensities were normalized and summarized using the robust multiarray average (RMA) method with the Affymetrix’s Expression Console software.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0

source_name: GATA2R396Q cDNA EGFP transduction of murine hematopoietic stem cells

label_protocol: RNA samples were purified and prepared according to the manufacturer's protocol using the Affymetrix's GeneChip Whole Transcript Sense Target Labeling Assay Kit (Affymetrix) and hybridized on Affymetrix GeneChip Mouse Exon 1.0 ST arrays.

growth_protocol: C57BL/6 8-week female were treated with 5-fluorouracil (5-FU) at 150mg/kg 6 days prior to bone marrow cell harvesting. Bone marrow cells from C57BL/6 8-week female mice were sorted according to stem cell surface markers (Lin-Sca+Kit+) using autoMACS (Miltenyi Biotec, Bergisch Gladbach, Germany).

extract_protocol: Total RNA was extracted using Rneasy plus MiniKit (Qiagen) and its quality was assessed with the RNA Screen Tape on Agilent 2200 Tapestation Bioanalyzer (Agilent Technologies).

treatment_protocol: The bone marrow cells were infected with MIE, WT and R396Q retroviral particles. One hundred thousand cells per condition were infected twice with retroviral vector-based particles by centrifugation at 3,000xg for 2 hours at 32°C with 2µg Polybrene (Hexadimethrine bromide, 400µg/uL) on 2 consecutive days. GFP-positive cells were sorted after 72h of culture.

tag: strain

value: Blood

tag: cell type

value: HSC

value: GATA2 R396Q


title: GATA2R396Q rep2


title: WT E18-1: Embryo cortex APP+/+ E18, biological rep 1

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

value: APP+/+