title: HFD + Inulin Propionate and -butyrate_cecum_3

value: 20 weeks


title: UNC_TGS_BC_227

status: Public on Oct 01 2018

type: SRA

city: Chapel Hill

first: Zhiyuan

last: Hu

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

country: USA

institute: University of North Carolina at Chapel Hill

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_227

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling and sequencing data were demultiplexed based on dual indexes.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, demultiplexed and then only read 1 in each sample were mapped to known Targeted regions of human genomes for counts using R package "ShortRead".
Raw counts of all samples were imported to edgeR for normalization by the size of the transcripts and by the size of the library and then calculation of CPM per sample as a gene expression matrix
Gene expression CPM dataset were median-centered and column-standardized using DWD
DWD dataset were used for iRDM data analysis including subtype classification, iRDM risks,  immunity scores, and proliferation scores.
Genome_build: hg19
Supplementary_files_format_and_content: csv files were generated including raw counts and normalized gene expression data

molecule: total RNA

organism: Homo sapiens

source_name: Breast cancer

extract_protocol:
FFPE tissues total RNA extraction was routinely performed using Roche FFPE RNA extraction kit according to the manufacturer’s protocol.
The Illumina TruSeq Targeted RNA expression kit was used to build libraries of the targeted 72-genes. To synthesize cDNA, 200 to 800 nanograms of purified FFPE RNA in a total volume of 3 µl was mixed with 4.0 µl RCS1, 2.0 µl ProtoScrip II Reverse Transcriptase, 1.0 µl 10mM DTT at 42OC for 30 min and 94OC for 10 min. The cDNA was hybridized with custom oligo pools in a thermal cycler programed to gradually decrease temperature from 70 OC to 30 OC in 30 minutes. The RNA/Oligo hybrid products were washed, extended and ligated. The ligated DNA was amplified by DNA polymerase on the thermal cycler with 35 PCR cycles of 98 OC for 30 seconds, 62 OC for 30 seconds and 72 OC for 60 seconds. The PCR products were purified with AMPure XP beads and eluted in 15 µl of buffer, measured using Agilent Bioanalyzer2100 and DNA1000 chips, pooled with equal amounts of DNA from each sample’s library, and finally diluted to 4 nM, denatured, and loaded to Nextseq500 according to the manufacturer’s protocol.
Libraries were multiplexed and sequenced on Illumina Nextseq500  to generate 75bp single read R1.

tag: gender

value: female

tag: dmfs time

tag: dmfs event

tag: sample type

value: Solid tumor

tag: irdm subtype

value: Immuno

tag: pam50 subtype

value: LumA

tag: immunity group

value: istrong

tag: proliferation group

value: low

tag: er status rna

value: ER+

tag: pr status rna

value: PR-


title: UNC_TGS_BC_204

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_204

value: Normal


title: UNC_TGS_BC_211

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_211

value: PR+


title: UNC_TGS_BC_205

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_205

value: Basal

value: iweak

value: high


title: UNC_TGS_BC_203

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_203


title: UNC_TGS_BC_202

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_202


title: UNC_TGS_BC_201

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_201

value: Mixed


title: UNC_TGS_BC_200

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_200


title: UNC_TGS_BC_20

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_20


title: UNC_TGS_BC_1m

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_1m

value: LumB


title: UNC_TGS_BC_199

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_199


title: UNC_TGS_BC_198

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_198


title: UNC_TGS_BC_197

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_197


title: WT_mk49 (rna-seq)

city: New Brunswick

first: SAURABH

middle: V

last: LADDHA

state: NEW JERSEY

address: 195 Little Albany Street

department: Center for Systems and Computational Biology

institute: Rutgers Cancer Institute of New Jersey

description: 2 x 76 paired end sequence reads

data_processing:
Raw fastq files were probed for sequencing quality control using FastQC. Sequencing reads were mapped to human transcripts corresponding to Genepattern genome (hg19 version) GTF annotations using RSEM with default parameters. RSEM package was used to prepare the reference genome with given GTF and calculated expression from mapped BAM files. STAR aligner was used to map reads in RSEM algorithm. Transcripts mapped data were normalized to TPM (Transcript Per Million) from RSEM and log2 transformed (Supplementary file). This log2 (x+1) TPM normalized values were used for all downstream analysis.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: log2 (x+1) TPM normalized values for each sample using RSEM and STAR

source_name: WT PanNET for ATRX / DAXX and MEN1

extract_protocol:
Total RNA was extracted with TRIzol reagent following the recommendations of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Pancreatic Neuroendocrine Tumors

tag: genotype

value: WT PanNET for ATRX / DAXX and MEN1

tag: tumor in specimen

value: Pancreas

tag: pannet subtype

value: A-D-M WT PanNETs

tag: phenotype

value: Well Differentiated PanNETs

tag: cell type

value: pancreatic neuroendocrine Islet cells


title: rabbit_liver_adult_male2

city: Cambridge

first: Francesco Nicola

last: Carelli

address: Henry Wellcome Building of Cancer and Developmental Biology,  Tennis Court Road

country: United Kingdom

institute: University of Cambridge

description: sample id: 3029sTS

data_processing:
RNA-seq reads were aligned to the assembled genomes of their corresponding species using STAR (version 2.2.1) using the 2-pass mapping mode and standard settings.
Aligned reads from all replicates of each organ were used to reconstruct transcripts through a genome-guided de novo transcriptome assembly using StringTie (version 1.3.4d) with the following parameters: -j 5 –g 50.
Assembled transcripts from each organ were then merged using Cuffmerge to define a unique set of transcripts. Expression levels (measured in FPKM) of the assembled transcripts were calculated with Cuffnorm (version 2.2.1) with --library-norm-method classic-fpkm.
Genome_build: human: hg38; macaque: rheMac8; marmoset: calJac3; mouse: mm10; rat: rn6; rabbit: oryCun2
Supplementary_files_format_and_content: *sample_name*.Signal.UniqueMultiple.str*N*.out.bw: STAR-generated bigWig tracks of the RPM-normalized read coverage from each sample. Files represent reads mapped on the forward (N=1) or reverse (N=2) strand.

molecule: polyA RNA

organism: Oryctolagus cuniculus

source_name: Adult liver

extract_protocol:
QIAGEN RNeasy Kit
Single-end strand-specific RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA LT kit according to manufacturer instructions. Libraries were sequenced using the Illumina HiSeq 2500.

value: liver

tag: Sex

value: male

tag: developmenta stage

value: adult


title: rabbit_liver_adult_female

description: sample id: 3015sTS

value: female


title: UNC_TGS_BC_196

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_196

tag: gender

tag: dmfs time

value: Solid tumor

value: Immuno

value: low

value: ER+


title: rabbit_liver_adult_female2

description: sample id: 3081sTS


title: WT_mk39 (rna-seq)

description: 2 x 76 paired end sequence reads


title: rabbit_liver_adult_male1

description: sample id: 3079sTS


title: UNC_TGS_BC_195

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_195

tag: dmfs event

tag: sample type

value: iweak

value: high

value: PR+


title: rabbit_kidney_adult_female2

description: sample id: 3023sTS

source_name: Adult kidney

value: kidney


title: WT_mk21 (rna-seq)

description: 2 x 76 paired end sequence reads

value: Pancreatic Neuroendocrine Tumors

value: WT PanNET for ATRX / DAXX and MEN1


title: rabbit_kidney_adult_female1

description: sample id: 3014sTS


title: UNC_TGS_BC_192

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_192

tag: irdm subtype

value: LumA

tag: pam50 subtype


title: rabbit_kidney_adult_male2

description: sample id: 3028sTS


title: WT_mk19 (rna-seq)

description: 2 x 76 paired end sequence reads

value: Pancreas

value: A-D-M WT PanNETs

value: Well Differentiated PanNETs


title: rabbit_kidney_adult_male1

description: sample id: 3047sTS

value: male


title: HFD + Inulin Propionate and -butyrate_cecum_2

type: RNA

city: Aberdeen

first: Claus

last: Mayer

address: Greenburn Road

institute: Biomathematics & Statistics Scotland

hyb_protocol: Labelled cRNA was hybridized using the Hi-RPM Gene Expression Hybridization Kit (cat no: 5188-5242), rotating at 65°C degrees for 17 hours. Washing was conducted using the Gene Expression Wash Buffer Kit (Cat no: 5188-5327)

scan_protocol: SureScan High Resolution Scanner (Agilent Technologies).

data_processing: The raw one-channel data (only Cy3 was used in this experiment) were normalised by the cyclicloess method within the Bioconductor library limma. This normalisation was applied to the Caecum and Liver data seperately.

organism: Mus musculus

source_name: cecum inulin propionate and -butyrate esters 8 weeks

label_protocol: Low Input Quick Amp Labeling Kit (Cat no: 5190-2305) using 100ng total RNA and a two step labelling process to generate cyanine 3-labeled cRNA for oligo microarrays. Steps include converting mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT, followed by amplifying sample using T7 RNA Polymerase, resulting in labelled anti-sense cRNA.

extract_protocol: RNA was extracted from 20 mg cecum (n = 6) using an RNeasy Mini Kit (Qiagen, Crawley, UK) incorporating DNase digestion, followed by quantification using a NanoDrop Spectrophotometer (NanoDrop Technologies). Quality was assessed using an Agilent Bioanalyser (Agilent Technologies).

treatment_protocol: Following 8 weeks consuming the experimental diets mice were killed under terminal anaesthesia. Cecal contents were removed and weighed. Cecum were weighed, frozen on dry ice and stored at -80°C prior to RNA extraction.

tag: strain

value: cecum

tag: age

value: 20 weeks


title: HFD + Inulin Propionate and -butyrate_cecum_1


title: HFD + inulin_cecum_5

source_name: cecum inulin 8 weeks


title: HFD + inulin_cecum_6


title: WT_mk27 (rna-seq)

description: 2 x 76 paired end sequence reads

value: pancreatic neuroendocrine Islet cells


title: WT_mk16 (rna-seq)

description: 2 x 76 paired end sequence reads


title: HFD + inulin_cecum_4


title: HFD_cecum_6

source_name: cecum high fat diet 8 weeks


title: HFD_cecum_4


title: UNC_TGS_BC_194

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_194

value: female

value: Solid tumor

value: LumB

tag: immunity group

value: istrong

tag: proliferation group

tag: er status rna

tag: pr status rna

value: PR-


title: Kidney_age_2-month_rep1

city: Dongguan

first: Shun

last: Xu

address: Xin Cheng Avenue 1#, Songshan Lake

country: China

institute: Guangdong Medical University

description: gene expression in 2-month old mouse kidney

hyb_protocol: the labeled cDNA was hybridized to the Agilent mRNA Array designed with eight identical arrays per slide (8 × 60K format), with each array containing probes interrogating about 39,430 Entrez Gene RNAs according to the manufacturer’s recommendations.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: The mRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V12 (Agilent).

source_name: C57BL/6 mouse, Kidney, 2-month, replicate 1

label_protocol: The obtained cDNA products were labeled by Klenow enzyme labeling strategy. Briefly, the cDNA was mixed with  random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, Klenow buffer, dNTP, Cy3-dCTP (GE Healthcare), and Klenow enzyme was added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer.

extract_protocol: Total RNA was extracted from mouse kidney by using  the Trizol reagent (Invitrogen) according to manufacter’s protocol. The purity and concentration of RNA were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000). RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

tag: tissue

value: 2 month


title: HFD + inulin_cecum_1


title: Kidney_age_2-month_rep3

source_name: C57BL/6 mouse, Kidney, 2-month, replicate 3

value: kidney


title: rabbit_heart_adult_female1

description: sample id: 3085sTS

source_name: Adult heart

value: heart

value: adult


title: HFD_cecum_2


title: HFD_cecum_3


title: HFD + inulin_cecum_2


title: HFD + inulin_cecum_3


title: rabbit_heart_adult_male2

description: sample id: 3027sTS


title: HFD_cecum_5


title: UNC_TGS_BC_191

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_191

value: Basal

value: iweak

value: high

value: ER-


title: WT_mk15 (rna-seq)

description: 2 x 76 paired end sequence reads

value: Pancreatic Neuroendocrine Tumors

tag: genotype

value: WT PanNET for ATRX / DAXX and MEN1

tag: tumor in specimen

value: Pancreas

tag: pannet subtype

value: A-D-M WT PanNETs

tag: phenotype

value: Well Differentiated PanNETs


title: UNC_TGS_BC_189

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_189

tag: gender

value: female

value: Solid tumor

value: LumA

value: low

value: ER+

value: PR+


title: Kidney_age_20-month_rep1

description: gene expression in 20-month old mouse kidney

source_name: C57BL/6 mouse, Kidney, 20-month, replicate 1

value: kidney

value: male

value: 20 month


title: Kidney_age_20-month_rep2

source_name: C57BL/6 mouse, Kidney, 20-month, replicate 2


title: Kidney_age_20-month_rep3

source_name: C57BL/6 mouse, Kidney, 20-month, replicate 3


title: WT_mk13 (rna-seq)

description: 2 x 76 paired end sequence reads

tag: cell type

value: pancreatic neuroendocrine Islet cells


title: HFD_cecum_1

value: cecum

tag: Sex

value: 20 weeks


title: Kidney_age_2-month_rep2

source_name: C57BL/6 mouse, Kidney, 2-month, replicate 2

value: 2 month


title: UNC_TGS_BC_188

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_188

tag: dmfs time

tag: dmfs event

tag: sample type

value: Normal

value: istrong

value: ER-


title: WT_ls65 (rna-seq)

description: 2 x 76 paired end sequence reads

value: Pancreatic Neuroendocrine Tumors

value: WT PanNET for ATRX / DAXX and MEN1

value: Pancreas

value: A-D-M WT PanNETs

value: Well Differentiated PanNETs


title: rabbit_heart_adult_male1

description: sample id: 3019sTS

value: heart

tag: developmenta stage

value: adult


title: WT_LS39 (rna-seq)

description: 2 x 76 paired end sequence reads


title: rabbit_brain_adult_female2

description: sample id: 3021sTS

source_name: Adult brain

value: brain

value: female


title: UNC_TGS_BC_186

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_186

value: Solid tumor

tag: irdm subtype

value: Immuno

tag: pam50 subtype

value: Mixed

value: low

value: PR-


title: UNC_TGS_BC_190

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_190

tag: immunity group

tag: proliferation group

value: ER+

value: PR+


title: UNC_TGS_BC_187

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_187

value: Basal

value: istrong

value: high

tag: er status rna

tag: pr status rna


title: WT_LS35 (rna-seq)

description: 2 x 76 paired end sequence reads

tag: tissue

value: Pancreatic Neuroendocrine Tumors

tag: genotype

value: WT PanNET for ATRX / DAXX and MEN1

value: Liver

value: pancreatic neuroendocrine Islet cells


title: UNC_TGS_BC_185

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_185

value: LumB


title: rabbit_brain_adult_male2

description: sample id: 3025sTS

value: brain

value: male

value: adult


title: WT_LS27 (rna-seq)

description: 2 x 76 paired end sequence reads

tag: tumor in specimen

value: Pancreas

tag: pannet subtype

value: A-D-M WT PanNETs

value: Well Differentiated PanNETs


title: UNC_TGS_BC_183

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_183

tag: gender

value: female

value: Solid tumor

value: Immuno

value: low


title: rabbit_brain_adult_female1

description: sample id: 3011sTS


title: WT_mk8 (rna-seq)

description: 2 x 76 paired end sequence reads

tag: phenotype

tag: cell type


title: rabbit_brain_adult_male1

description: sample id: 3017sTS

tag: Sex


title: UNC_TGS_BC_182

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_182

tag: dmfs time

tag: dmfs event

value: Basal

value: iweak

value: ER+

value: PR-


title: WT_mk50 (rna-seq)

description: 2 x 76 paired end sequence reads

value: Pancreatic Neuroendocrine Tumors

value: WT PanNET for ATRX / DAXX and MEN1


title: UNC_TGS_BC_180

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_180

tag: sample type

value: Mixed

value: high

value: PR+


title: AM1_mk36 (rna-seq)

description: 2 x 76 paired end sequence reads

source_name: ATRX and MEN1 mutated PanNET

value: ATRX and MEN1

value: A-D-M Mutant PanNETs

value: pancreatic neuroendocrine Islet cells


title: UNC_TGS_BC_181

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_181

tag: irdm subtype


title: D6 PGCLC from CRISPR screen 1

city: Rome

first: Jamie

last: Hackett

address: via Ramarini 32

department: Epigenetics & Neurobiology

country: Italy

institute: European Molecular Biology Laboratory (EMBL)

description: PGCLC infected with the CRISPR library were collected at day6 of differentiation from EpiLC with BMP4, BMP8b, SCF, EGF, LIF; replicate 1

data_processing:
RNA-seq reads were quality-trimmed and aligned to mm10 with TopHat2 version: 2.0.13
Differentially expressed genes were called using DESeq2
Datastore analysis was performed with SeqMonk version: 1.36
CRISPR libraries were processed using MaGECK software version 1.5.2
Genome_build: mm10
Supplementary_files_format_and_content: Fastq raw read files

source_name: PGCLC

growth_protocol: Stella-GFP; Esg1-tdTomato (SGET) embryonic stem cells (ESC) were maintained and differentiated into epiblast-like cells (EpiLC) and primordial germ cell-like cells (PGCLC). For EpiLC, ESC were transferred to a well of a 12-well plate coated with human plasma fibronectin (Merck Millipore; 16.7 mg/ml) in N2B27 medium containing Activin A (20 ng/ml), bFGF (12 ng/ml) and knockout serum replacement (KSR; 1 %) for 42hrs. Purified EpiLC were seeded in ultra-low cell binding U-bottom 96-well plates (Nunc; 3x10e3 cells per well) in GK15 medium (GMEM, 15% KSR, NEAA, 1 mM sodium pyruvate, 0.1 mM β-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin, and 2 mM L-glutamine) supplemented with cytokines: BMP4 (500 ng/ml), LIF (1000 U/ml), SCF (100 ng/ml), BMP8a (500 ng/ml), and EGF (50 ng/ml) and collected on day2 or day6 of differentiation.

extract_protocol:
For fluorescence-activated cell sorting (FACS), cultured cells or embryoids were dissociated into single cells with TrypLE, and suspended in phosphate buffered saline (PBS) with 0.5% BSA or 3% FBS. Filtered cell suspensions were subsequently sorted using a Sony SH800Z or a MoFlow high-speed cell sorter (Beckman Coulter) or analysed with BD LSRFortessa X-20 (BD Biosciences). For exit from pluripotency analyses, cells were sorted/analysed based on absence or presence of Stella-GFP expression, whilst maintaining Esg1-tdTomato activitaion (SG+/-ET+). For PGCLC, cells were sorted/analysed based on Stella-GFP re-activation coupled with low Esg1-tdTomato. The threshold(s) levels for sorting was set and normalised based on expression levels in pre-optimised SGET ESC. A negative population of ESC without any fluorescence was used to set absolute thresholds. Forward and side scatters were used to gate for the cell population and doublets. For each sort the maximum number of cells was collected.
Sample1-36: For RNA-seq of Nr5a2-/-, Zfp296-/- and matched WT control cell lines, 100 ng of total RNA from triplicate biological independent experiments was used as inputs for the NEBNext Ultra RNA library Prep Kit for Illumina (NEB), with the library generated as per manufacturer’s instructions. During the final PCR amplification stage, 15 cycles of amplifications were performed to generate the adaptor ligated, fragmented cDNA for sequencing. Samples were assessed using the High Sensitivity D1000 ScreenTape assay (Agilent) to ensure the library did not contain primer-dimer contamination after last round of AMPure beads cleaning. The Qubit dsDNA HS assay kit (ThermoFisher Scientific) and the NEBNext Library Quant Kit for Illumina was used to accurately quantify the concentration of each library preparation. Samples were multiplexed with 12 indexes per lane and a total of 2 lanes of sequencing on Illumina HiSeq4000, single-end 50bp with an average depth of approximately 20 million reads per sample. Sample 37-42: ESC, EpiLC, or day 6 PGCLC (from the CRISPR screen) were dissociated into single cell solutions with TrypLE and sorted with a Sony SH800Z or a MoFlow high-speed cell sorter (Beckman Coulter) based on appropriate Stella-GFP and Esg1-tdTomato expression. Samples were sorted into 150ul of extraction buffer from the PicoPure RNA isolation kit (Life Technologies) and rapidly frozen on dry ice or liquid nitrogen. Total RNA was subsequently extracted using the PicoPure RNA isolation Kit, including a 15 minute on-column DNaseI digestion. RNA integrity number was assessed with RNA HS ScreenTape (Agilent), and all samples confirmed to have a RIN >8.5. For RNA-seq from CRISPR screen samples, 50 ng of total RNA was used as input for the Ovation RNA-seq System v2 (Nugen) as per manufacturer’s instructions. Amplified double-stranded (ds) cDNA was diluted into EDTA-low TE (Agilent) and sheared into ~230bp in length using S220 Focused-Ultrasonicator (Covaris) using settings: duty factor 10%, cycle burst 200, intensity 5, temp at 4°C and treatment time of 5 minutes per sample.  A high Sensitivity D1000 ScreenTape assay (Agilent) was used to assess the efficiency of library fragmentation. Fragmented ds-cDNA was concentrated with Qiagen Reaction Clean Up kit (MiniElute) and 1μg of the fragmented ds-cDNA used as input for the library preparation using Encore Rapid DR Multiplex Library System (Nugen). This kit ligated the adaptors to repaired-end ds-cDNA without amplification, which eliminated biases introduced during PCR amplification. The KAPA Library Quantification Kit (Kapa bioscience) was used to quantify the concentration of each adaptor-ligated libraries prior to multiplexing. The ESC, EpiLC and PGCLC RNA sequencing libraries were generated in parallel for each replicate, and the biological replicates were generated on independent occasions. Samples were multiplexed and sequenced with Illumina HiSeq1500, single-end 50bp read length with a minimum depth of approximately 15 million reads per sample.  Sample43-52: To quantify the relative frequencies of integrated gRNAs during the CRISPR screen in each population during cell fate transitions, genomic DNA was isolated from day 12 ESC post-lentiviral transduction, from SG–ET+ and SG+ET+ EpiLC populations at 42hr, and from SG+ETlow PGCLCs from day 6 embryoids, in biological duplicate using the DNeasy Blood & Tissue kit (Qiagen). Purified genomic DNA was used as template for custom primers that specifically amplify the gRNA region, and include overhanging Illumina adaptors and indexes to allow deep sequencing and multiplexing, respectively (synthesised as Ultramers from IDT) (see oligo tables). Prior to PCR, genomic DNA was sonicated with a Biorupter (Diagenode) for 15 seconds on ‘LOW’ power to improve efficiency of amplification. gRNA sequences were amplified in multiple PCR reactions to enable all isolated DNA to be utilised, each with NEBNext Q5 HotStart HiFi PCR Master Mix (NEB), 0.2 uM of universal forward primer (mix of staggers), 0.2 uM of indexed reverse primer and genomic DNA (~650 ng / 50 ul rxn). For amplification from the plasmid vector, 15 ng was used as template for replicate amplifications. The following cycling conditions were used: 95°C for 2 minutes, then between 21-26 cycles of (98°C for 20 seconds, 62°C for 20 seconds and 72°C for 20 seconds) followed by 72°C for 1 minute and hold at 4°C. The number of cycles was optimised for the point at which PCR products can be first visualised on an agarose gel. The PCR reaction was subsequently purified with AMPure XP beads (Beckman Coulter) using double size selection to remove primer dimers and genomic DNA. Briefly, 0.55x of AMPure beads were added to PCR reaction (1x) and incubated for 5 minutes at room temperature. The supernatant was collected; the beads contained the unwanted larger fragments and were discarded. An additional 0.3x of AMPure beads was subsequently added to the supernatant (1x) and incubated for 5 minutes at room temperature. The supernatant was removed and beads washed twice with 200 ul of 80% EtOH, air dried for 5 minutes and DNA was eluted from AMPure beads with EDTA-low TE buffer. The concentration of adaptor ligated gRNA amplicons was measured with the Qubit DNA Assay kit (ThermoFisher Scientific) and the fragment distribution determined with an Agilent D1000 ScreenTape System (Agilent Technologies). Libraries were subsequently multiplexed and sequenced with an Illumina HiSeq 1500 using single-end 50bp reads. As the sequences for all samples were identical up to the gRNA region, these types of low complexity libraries can produce low quality data. To counteract this, forward staggered primers were introduced at equal ratios during PCR amplification, generating offset reads. In addition, libraries were sequenced with 4 dark cycles and low density (70%) clustering.
Sample 1-42: RNA-seq; Sample 43-52: amplicon

tag: strain

value: mixed B6CBA background

tag: fluorescent reporter

value: Stella-GFP; Esg1-tdTomato

tag: facs

value: GFP+; Tomato_low


title: D6 PGCLC from CRISPR screen 2

description: PGCLC infected with the CRISPR library were collected at day6 of differentiation from EpiLC with BMP4, BMP8b, SCF, EGF, LIF; replicate 2


title: UNC_TGS_BC_18

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_18

source_name: Breast cancer

value: female

value: Solid tumor

value: Normal

tag: pam50 subtype

tag: immunity group

tag: proliferation group

tag: er status rna


title: DM1_ls7 (rna-seq)

description: 2 x 76 paired end sequence reads

source_name: DAXX and MEN1 mutated PanNET

tag: tissue

tag: genotype

value: DAXX and MEN1

tag: tumor in specimen

value: Pancreas

value: Well Differentiated PanNETs


title: UNC_TGS_BC_179

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_179

tag: gender

value: LumB

value: iweak

value: ER+

tag: pr status rna


title: ESC from CRISPR screen 2

description: SGET ESC infected with the CRISPR library; replicate 2

source_name: ESC

value: GFP+; Tomato+


title: AM1_mk53 (rna-seq)

description: 2 x 76 paired end sequence reads

value: Pancreatic Neuroendocrine Tumors

value: Liver

tag: pannet subtype

tag: phenotype

tag: cell type


title: ESC from CRISPR screen 1

description: SGET ESC infected with the CRISPR library; replicate 1


title: UNC_TGS_BC_176

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_176

tag: dmfs time

tag: dmfs event

tag: sample type

value: LumA

value: istrong

value: low

value: PR+


title: UNC_TGS_BC_174

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_174

tag: irdm subtype

value: high


title: UNC_TGS_BC_173

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_173

value: female

value: Mixed


title: DM1_mk44 (rna-seq)

description: 2 x 76 paired end sequence reads

value: A-D-M Mutant PanNETs

value: pancreatic neuroendocrine Islet cells


title: UNC_TGS_BC_172

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_172

value: Solid tumor


title: WT2 sRNA <100: Infected human red blood cells with Plasmodium falciparum

city: Berlin

first: Christian

last: Schmitz-Linneweber

address: Granseer Str. 7

department: Faculty of Life Sciences

country: Germany

institute: Humboldt University Berlin

data_processing:
MiSeq Control Software v 2.4
Sequence trimming was done with CutAdapt
Trimmed sequences were mapped to the Plasmodium falciparum organellar genomes (NCBI apicoplast: DQ642846.1 and mitochondria: DQ642845.1) using Bowtie (version 1.1.1)  with the following parameters –a –best –strata –v 2
Genome_build: NCBI apicoplast: DQ642846.1 and mitochondria: DQ642845.1;
Supplementary_files_format_and_content: Strand-specific bigwig files were generated using deepTools 3.1.2

organism: Plasmodium falciparum

growth_protocol: Plasmodium falciparum NF54 cells were grown in unsynchronized cultures and split every 2-3 days.

extract_protocol:
Parasites were extracted from infected red blood cells using saponin lysis. After centrifugation and washing Parasites were disrupted using a cell disruption bomb (25 minutes at 1750 psi) in order to release intact organelles. After removal of debris through centrifugation the organelles were pelleted via centrifugation (20 min at 23.000 x g) and resuspended in TriZol.  RNA was extracted with the standard TriZol method.
Library was constructed as described in NEBNext Multiplex Small RNA Library Prep

tag: strain

value: wild type

tag: developmental stage

value: asexual stages

tag: molecule subtype

value: organelle enriched RNA


title: DM1_mk45 (rna-seq)

description: 2 x 76 paired end sequence reads

value: DAXX and MEN1

value: Pancreas

value: Well Differentiated PanNETs


title: UNC_TGS_BC_171

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_171

value: Basal

tag: pam50 subtype

tag: immunity group

value: iweak

tag: proliferation group

value: ER-

value: PR-


title: D_mk51 (rna-seq)

description: 2 x 76 paired end sequence reads

source_name: DAXX mutated PanNET

tag: tissue

value: Pancreatic Neuroendocrine Tumors

tag: genotype

value: DAXX

value: Liver


title: UNC_TGS_BC_170

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_170

tag: gender

value: female

value: LumA

value: istrong

value: low

tag: er status rna

value: ER+

value: PR+


title: EpiLC from CRISPR screen 2

description: EpiLC infected with the CRISPR library were collected at day2 of differentiation from ESC with ActA and bFGF; replicate 2

source_name: EpiLC

value: mixed B6CBA background

tag: fluorescent reporter

value: Stella-GFP; Esg1-tdTomato

tag: facs

value: GFP-; Tomato+


title: A_mk4 (rna-seq)

description: 2 x 76 paired end sequence reads

source_name: ATRX mutated PanNET

value: ATRX

tag: tumor in specimen

value: Pancreas

tag: pannet subtype

value: A-D-M Mutant PanNETs

tag: phenotype

value: Well Differentiated PanNETs

tag: cell type

value: pancreatic neuroendocrine Islet cells


title: EpiLC from CRISPR screen 1

description: EpiLC infected with the CRISPR library were collected at day2 of differentiation from ESC with ActA and bFGF; replicate 1


title: DM1_mk17 (rna-seq)

description: 2 x 76 paired end sequence reads

value: Pancreatic Neuroendocrine Tumors

value: DAXX and MEN1


title: UNC_TGS_BC_17

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_17

tag: dmfs time

tag: dmfs event

tag: sample type

value: Solid tumor

tag: irdm subtype

value: Immuno

value: high

value: ER-

tag: pr status rna


title: A_mk47 (rna-seq)

description: 2 x 76 paired end sequence reads


title: UNC_TGS_BC_169

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_169

value: female

tag: pam50 subtype

value: Basal

tag: immunity group

value: istrong


title: DM1_mk52 (rna-seq)

description: 2 x 76 paired end sequence reads

tag: tissue


title: UNC_TGS_BC_168

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_168

value: LumA

value: iweak

tag: proliferation group

value: low

value: ER+

value: PR+


title: D_mk42 (rna-seq)

description: 2 x 76 paired end sequence reads

tag: genotype

value: DAXX

value: Liver

value: A-D-M Mutant PanNETs


title: D_mk9 (rna-seq)

description: 2 x 76 paired end sequence reads

value: Pancreatic Neuroendocrine Tumors

value: Pancreas

value: Well Differentiated PanNETs

value: pancreatic neuroendocrine Islet cells


title: D_mk34 (rna-seq)

description: 2 x 76 paired end sequence reads


title: UNC_TGS_BC_166

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_166

tag: gender

value: Solid tumor

tag: er status rna

value: PR-


title: D_mk26 (rna-seq)

description: 2 x 76 paired end sequence reads


title: UNC_TGS_BC_165

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_165

value: female

value: Immuno

value: Mixed


title: D_mk18 (rna-seq)

description: 2 x 76 paired end sequence reads


title: UNC_TGS_BC_164

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_164

value: Basal

value: istrong

value: ER-


title: A_mk12 (rna-seq)

description: 2 x 76 paired end sequence reads

value: ATRX

value: Lymph Node


title: A_mk11 (rna-seq)

description: 2 x 76 paired end sequence reads


title: Human primary placenta (#3) trophoblast cells, 5 days following seeding, repeat 2

city: Rehovot

first: Valery

last: Krizhanovsky

address: Herzel 234

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: Expression data of  human placental trophoblasts cells in cultures, 5 days following seeding

hyb_protocol: cDNA was prepared, labeled, and hybridized to Affymetrix GeneChip PrimeView, Human Gene Expression Array, according to standard manufacturer protocols.

scan_protocol: Hybridized chips were stained, washed, and scanned with the Affymetrix GeneChip 3000 7G Plus scanner and converted to cell intensity files by Affymetrix Expression Console SoftwareTM.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. Data analysis (processing of raw data, clustering was carried out using Coupled Two-Way Clustering (CTWC) algorithm (http://www.pnas.org/content/97/22/12079) . Gene Set Enrichment Analysis tool (GSEA- http://broadinstitute.org/gsea)  was applied using annotations from KEGG (Subramanian et al., 2005) to determine whether predefined gene sets showed enrichment in late trophoblast cultures (day 5) compared to early cultures (day2). The raw probe intensities were adjusted according to the numbers of G and C bases in the probe sequence before any probe correction. Preprocessing was performed with the Robust Microarray Averaging algorithm (Irizarry, Hobbs et al., 2003). Genes expressed below background levels (log 1.5 intensity of 6.9) in all examined conditions were excluded from further analyses.

label: biotin

source_name: Human primary trophoblast cells, derived from placenta #3

growth_protocol: Human placental villous tissues (30 g) were isolated from human term placentas after delivery by an established method that is based on percoll gradient centrifugation (Kliman et al., 1986). Isolated trophoblasts were then cultured in DMEM supplemented with 2 mM L-glutamine, 100 units/ml of penicillin, 100 µg/ml of streptomycin, and 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was extracted from isolated placental trophoblast cells in culture, on days 1.5, 2, 3, and 5 following seeding, using an RNeasy Mini Kit (QIAGEN). RNA purity was assessed with an ND-1000 NanoDrop Spectrophotometer (Peqlab Biotechnologie) and BioAnalyzer 2100 system (Agilent Technologies).

treatment_protocol: Human primary trophoblast cells were seeded in 6 well plates and cultured with DMEM )supplemented with 2 mM L-glutamine, 100 units/ml of penicillin, 100 µg/ml of streptomycin, and 10% fetal bovine serum (FBS)), for 1.5, 2, 3 and 5 days, after which total RNA was extracted.

tag: time

value: 5 days following seeding

value: Human placenta trophoblast cells

tag: developmental stage

value: third trimester post partum


title: Human primary placenta (#3) trophoblast cells, 3 days following seeding, repeat 2

description: Expression data of  human placental trophoblasts cells in cultures, 3 days following seeding

label_protocol: cDNA was prepared, labeled, and hybridized to Affymetrix GeneChip PrimeView, Human Gene Expression Array, according to standard manufacturer protocols.

value: 3 days following seeding


title: UNC_TGS_BC_161

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_161

value: LumA

value: iweak

value: low

value: ER+

value: PR+


title: D_LS21 (rna-seq)

description: 2 x 76 paired end sequence reads

value: Pancreatic Neuroendocrine Tumors

value: DAXX

tag: tumor in specimen

value: Pancreas

tag: pannet subtype

value: A-D-M Mutant PanNETs

value: Well Differentiated PanNETs

value: pancreatic neuroendocrine Islet cells


title: Human primary placenta (#3) trophoblast cells, 1.5 days following seeding, repeat 2

description: Expression data of  human placental trophoblasts cells in cultures, 1.5 days following seeding

value: 1.5 days following seeding

value: female


title: UNC_TGS_BC_160

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_160

value: Solid tumor

value: Basal

value: high

value: ER-

value: PR-


title: Human primary placenta (#1) trophoblast cells, 3 days following seeding, repeat 1

source_name: Human primary trophoblast cells, derived from placenta #1

value: 3 days following seeding

value: Human placenta trophoblast cells

value: third trimester post partum


title: Human primary placenta (#1) trophoblast cells, 5 days following seeding, repeat 1

value: 5 days following seeding


title: UNC_TGS_BC_157

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_157

value: Normal

value: LumA

value: iweak

value: low

value: ER+

value: PR+


title: UNC_TGS_BC_163

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_163

value: istrong


title: UNC_TGS_BC_162

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_162

value: female


title: UNC_TGS_BC_156

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_156

value: Solid tumor


title: U87-129-2

city: Houston

first: Yubin

last: Zhou

state: TX

address: 2121 W Holcombe Blvd

department: Institute of Biosciences and Technology

institute: Texas A&M University

data_processing:
RNA-seq data were aligned to hg19 human reference genome using Tophat2 v2.0.12. The abundance of genes was quantified by Cufflinks v2.2.1. Differential expression data produced by cuffdiff.
Genome_build: hg19
Supplementary_files_format_and_content: Comma separated value file containing log2FoldChange and statistics for difference of each gene between control and experiment group

source_name: U87 cells

growth_protocol: U87 cells were  were cultured in Dulbecco's modified eagle's medium (DMEM) supplemented with 10% FBS in 5% CO2 at 37oC.

extract_protocol:
RNA was extracted using Total RNA was isolated with a RNeasy kit (Qiagen).
One microgram of total RNA was isolated and selected twice with Ambion MicroPoly(A)Purist Kit. cDNA conversion and library preparation were performed by using NEB RNA-seq library prep kit.

treatment_protocol: U87 cells were treated with 5 μM YZ129 for 24 h at 37 oC with 5% CO2 and DMSO was used as the control group

tag: treatment

value: treatment with drug YZ129

tag: cell line

tag: cell type

value: glioblastoma


title: Human primary placenta (#3) trophoblast cells, 2 days following seeding, repeat 2

description: Expression data of  human placental trophoblasts cells in cultures, 2 days following seeding

value: 2 days following seeding


title: Kidney_age_20-month_rep3

description: miRNA expression in 20-month old mouse kidney

hyb_protocol: The labeled miRNA was hybridized to the Agilent miRNA microarray designed with eight identical arrays per slide (8 × 60K format), with each array containing probes interrogating 1247 mouse miRNAs from the Sanger database (Version 19.0) according to the manufacturer’s protocol

data_processing: The miRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V12 (Agilent Technologie).

label_protocol: 100 ng purified RNA was dephosphorylated and ligated with pCp-Cy3 using the Agilent miRNA labeling reagent according to the manufacturer's instructions.

extract_protocol: Total RNA containing small RNA was extracted from mouse kidney by using  the Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA) according to manufacter’s protocol. The purity and concentration of RNA were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000). RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

value: kidney

value: male

tag: age

value: 20 month


title: UNC_TGS_BC_155

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_155

tag: dmfs time

tag: dmfs event

tag: sample type

tag: irdm subtype

value: high

value: ER-


title: U87-DMSO-2

value: Control


title: M1_LS1 (rna-seq)

description: 2 x 76 paired end sequence reads

source_name: MEN1 mutated PanNET

tag: tissue

value: Pancreatic Neuroendocrine Tumors

value: Pancreas

value: A-D-M Mutant PanNETs

tag: phenotype

value: Well Differentiated PanNETs

value: pancreatic neuroendocrine Islet cells


title: Human primary placenta (#1) trophoblast cells, 2 days following seeding, repeat 1

value: Human placenta trophoblast cells

value: third trimester post partum


title: Kidney_age_20-month_rep2


title: Kidney_age_20-month_rep1

source_name: C57BL/6 mouse, Kidney, 20-month, replicate 1


title: U87-DMSO-1


title: UNC_TGS_BC_151

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_151

value: female

value: Solid tumor

value: LumA

tag: pam50 subtype

tag: immunity group

value: iweak

tag: proliferation group

value: low

value: ER+

tag: pr status rna

value: PR+


title: UNC_TGS_BC_152

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_152

tag: gender

value: istrong

tag: er status rna


title: U87-129-1

value: treatment with drug YZ129

value: glioblastoma


title: Kidney_age_2-month_rep2

description: miRNA expression in 2-month old mouse kidney

value: kidney

value: male

value: 2 month


title: UNC_TGS_BC_15

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_15

value: Basal

value: high


title: Human primary placenta (#1) trophoblast cells, 1.5 days following seeding, repeat 1

tag: time

value: 1.5 days following seeding

value: Human placenta trophoblast cells

tag: developmental stage


title: Kidney_age_2-month_rep1

source_name: C57BL/6 mouse, Kidney, 2-month, replicate 1


title: Baso IL-2 rep 1

city: Xuzhou

first: Hui

last: Wang

state: Jiangsu

address: 209 Tongshan Rd

institute: Xuzhou Medical University

hyb_protocol: 600 ng of Cy3-labelled cRNA  from each sample was hybridized to Agilent SurePrint G3 Human Gene Expression 8×60K V2 microarray  according to the manufacturer's instructions

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw data were Quantile normalized using R.

source_name: Basophils, IL-2 rep 1, 24h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng total RNA using using the Agilent One-Color Microarray-Based Exon Analysis (Low Input Quick Amp Labeling) kit (Agilent Technologies, Palo Alto, Calif, USA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Purified basophils were cultured in RPMI 1640 medium supplemented with 2 mM L-glutamine, 10% heat-inactivated FCS, and 50 ug/mL gentamicin.  For gene expression microarray analysis, purified basophils at a density of 2×105 cells/well in a 96-well plate were cultured either with or without human IL-2 (10 ng/mL) (n = 3) for 24 hours.

extract_protocol: Total RNA was extracted using a miRneasy Mini Kit (Qiagen, Valencia, CA, USA).

value: whole blood

value: basophils


title: Baso IL-2 rep 2

source_name: Basophils, IL-2 rep 2, 24h


title: UNC_TGS_BC_149

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_149

value: female

value: Solid tumor

value: Normal


title: Baso IL-2 rep 3

source_name: Basophils, IL-2 rep 3, 24h


title: Baso Control rep 3

source_name: Basophils, control rep 3, 24h


title: UNC_TGS_BC_14m

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_14m

value: iweak

value: ER-

value: PR-


title: UNC_TGS_BC_145

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_145

value: low

value: ER+

value: PR+


title: UNC_TGS_BC_148

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_148

value: LumA


title: UNC_TGS_BC_153

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_153

value: istrong


title: Baso Control rep 1

source_name: Basophils, control rep 1, 24h

value: male


title: UNC_TGS_BC_141

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_141

source_name: Breast cancer

value: LumB

value: high


title: BSGX001-thi2-2

city: Qingdao

first: Yu

last: Shen

state: Shandong

address: binhai road 72

department: Microbiology and Biotechnology Institute

institute: Shandong University

data_processing:
Raw reads was produced by Illumina HiSeqTM 2000.
Raw reads was subjected to quality control (QC).
After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences.
The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio.
If alignment result passes QC, we will proceed with downstream analysis including gene and isoform expression,deep analysis based on gene expression(PCA/correlation/screening differentially expressed genes and so on),exon expression, gene structure,refinement, alternative splicing, novel transcript prediction and annotation, SNP detection, Indel detection, gene fusion. Deep analysis based on DEGs,including Gene Ontology (GO) enrichment analysis,Pathway enrichment analysis, cluster analysis, protein-protein interaction network analysis and finding transcriptor were performed.
We define "dirty" raw reads as reads which contain the sequence of adapter, high content of unknown bases and low quality reads. They need to be removed before data analysis. Filtering steps are as follows to make clean data:
1) Remove reads with adapters;
2) Remove reads in which unknown bases are more than 10%;
3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 10).
Genome_build: R64
Supplementary_files_format_and_content: text files with FPKM and DESeq output

organism: Saccharomyces cerevisiae

source_name: BSGX001 (thi2Δ),derived from CEN.PK 113-5D

growth_protocol: The fermentation media were Yeast Nitrogen Base (YNB) medium (1.7 g/L yeast nitrogen base (Sangon, China), 5 g/L ammonium sulfate (Sangon, China) ) supplemented with 20 g/L glucose and 20 g/L xylose as carbon source. The fermentation was performed at 30 °C and a stirring speed of 200 rpm.

extract_protocol:
The cells in each samples were collected by centrifuging at 5000 rpm, 4°C, for 5 minutes. Then the pellets were rapidly freezed in liquid nitrogen and stored at −80°C. UNIQ-10 Trizol RNA Purification Kit (Sangon Biotech, China) was used to extract total RNA.
The total RNA was extracted and fragmented, the DNA was digested with DNase I, enriching the eukaryotic mRNA with the magnetic beads with Oligo (dT) (if it is a prokaryote, then remove the rRNA from the reagent into the next). Add interrupting agent in Thermomixer to break the mRNA into short fragments. The cDNA is synthesized using the short fragments mRNA as template, then the two-stranded cDNA was synthesized by make two chain synthesis reaction system, the Short fragments are purified and resolved by the kit, the 3 'end of cDNA is connected with the base "A" and is connected with the connector, then suitable fragments were selected and the PCR amplification is performed. The constructed library is analyzed with the Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System,then sequenced using Illumina HiSeqTM 2000.

treatment_protocol: The samples taken at 20h in glucose-xylose co-fermentation were samples of GX stage.

tag: strain

value: BSGX001 (thi2delta),derived from CEN.PK 113-5D

tag: genotype

value: Ru-XI, XK, gre3::PPP, cox4delta, thi2delta, adaptive evolution in xylose

tag: Stage

value: GX stage


title: UNC_TGS_BC_142

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_142

value: female

tag: dmfs time


title: BSGX001-thi2-1


title: BSGX001-thi2-3


title: BSGX001-1-3

source_name: BSGX001,derived from CEN.PK 113-5D

value: BSGX001,derived from CEN.PK 113-5D

value: Ru-XI, XK, gre3::PPP, cox4delta, adaptive evolution in xylose


title: UNC_TGS_BC_140

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_140

tag: dmfs event

value: Solid tumor

value: Basal


title: Baso Control rep 2

source_name: Basophils, control rep 2, 24h

value: whole blood

tag: cell type

value: basophils


title: UNC_TGS_BC_139

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_139

tag: sample type

tag: irdm subtype

value: ER+

value: PR-


title: BSGX001-1-2


title: UNC_TGS_BC_150

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_150

value: ER-


title: Kidney_age_2-month_rep3

source_name: C57BL/6 mouse, Kidney, 2-month, replicate 3

tag: tissue

value: kidney

tag: age

value: 2 month


title: BSGX001-1-1


title: UNC_TGS_BC_138

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_138

value: LumB

tag: pam50 subtype

tag: immunity group

value: istrong

value: low

value: PR+


title: UNC_TGS_BC_136

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_136

value: Immuno

value: Mixed

tag: proliferation group

tag: pr status rna


title: UNC_TGS_BC_14

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_14

tag: gender

value: female

value: iweak

value: high

tag: er status rna


title: UNC_TGS_BC_143

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_143

value: Solid tumor

value: LumA


title: UNC_TGS_BC_132

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_132


title: UNC_TGS_BC_13

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_13


title: UNC_TGS_BC_133

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_133


title: UNC_TGS_BC_128

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_128


title: UNC_TGS_BC_127

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_127


title: UNC_TGS_BC_126

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_126


title: UNC_TGS_BC_123

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_123


title: UNC_TGS_BC_125

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_125


title: UNC_TGS_BC_120

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_120


title: UNC_TGS_BC_12

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_12


title: UNC_TGS_BC_11m

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_11m

value: Basal


title: 16C cells, biological rep2

city: Ghent

first: Lieven

last: De Veylder

state: Flanders

address: Technologiepark 927

department: VIB-UGent Center for Plant Systems Biology

country: Belgium

institute: University of Ghent

description: Expression data from YFP nuclei with DNA content 16C

hyb_protocol: A mixture of purified and fragmented biotinylated cRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix ATH1 Genome array followed by staining and washing in a GeneChip® fluidics station 450  (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: The raw endoploidy-specific microarray data was preprocessed using the Robust Multichip Average (RMA) normalization approach (background correction, quantile normalization and summarization) implemented in the Bioconductor R package, version 2.5.

organism: Arabidopsis thaliana

source_name: Roots of pCO2:YFP-H2B

label_protocol: Per sample, an amount of 45 to 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted and amplified to antisense cRNA in a first cycle in vitrotranscription reaction. Next, the cRNA was converted to double stranded cDNA in a second cycle reverse transcription reaction. Finally, the sample was converted and amplified to antisense cRNA and labeled with biotin in a second cycle in vitro transcription reaction. All steps were carried out according to the manufacturers protocol (Affymetrix).

growth_protocol: 5 day old roots of pCO2:YFP-H2B (Col-0 ecotype) plants were grown under continuous light conditions at 22-23°C

extract_protocol: The nuclear RNA was extracted from each nuclear DNA content population (2C, 4C, 8C, and 16C, approximately 0.2 ml [200,000 nuclei]/0.95 ml RLT) using the Qiagen RNeasy kit according to the manufacturer’s instructions. RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent).

treatment_protocol: Roots were excised just below hypocotyl region. Samples of combined root material (10 g fresh weight) were collected in a glass petri dish and chopped with slicing action after adding 10 ml nuclear isolation buffer (45 mM MgCl2, 30 mM sodium citrate (trisodium), 20 mM MOPS (3-LN-morpholino propane sulfonate), pH adjusted to 7.0). The solution was collected into a 15-ml tube and centrifuged at 2500 rpm in a Sorvall swinging bucket AH-3000 at 4°C for 8 min. The pellet was drained to about 0.5 ml and resuspended in nuclear isolation buffer to 4 ml, then transferred to a 30-μm strainer in a 5-ml tube and DAPI was added (20 μl/ml 0.1 mg/ml stock). Biparametric sorting was then done based on YFP fluorescence and nuclear DNA content. Sorting of isolated nuclei was done using a Dako-Cytomation MoFlo flow cytometer/cell sorter.

value: Root Cortex

tag: ecotype

value: 5day old

tag: ploidy


title: UNC_TGS_BC_115

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_115

value: ER+


title: 16C cells, biological rep1


title: UNC_TGS_BC_113

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_113

value: Normal


title: UNC_TGS_BC_117

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_117


title: 16C cells, biological rep3


title: 8C cells, biological rep1

description: Expression data from YFP nuclei with DNA content 8C


title: UNC_TGS_BC_112

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_112


title: 4C cells, biological rep3

description: Expression data from YFP nuclei with DNA content 4C


title: 8C cells, biological rep2


title: UNC_TGS_BC_122

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_122


title: UNC_TGS_BC_111

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_111


title: 2C cells, biological rep2

description: Expression data from YFP nuclei with DNA content 2C


title: 4C cells, biological rep2


title: 4C cells, biological rep1


title: 8C cells, biological rep3


title: sample48: A549 GDC-0973

city: South San Francisco

first: Christiaan

middle: Nicolaas

last: Klijn

state: CA

address: 1 DNA Way

department: Bioinformatics and Computational Biology

country: Netherlands

institute: Genentech

data_processing: Reads were aligned to the GRCh37 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: cell line

extract_protocol: Cells were centrifuged at 2,600 rcf for 7 minutes (neurons) or 6,600 rcf for 7 minutes (other cell types) and the supernatant was discarded. RNA was extracted from the cell pellet using Qiagen RNeasy Plus Micro kit in a final volume of 25 μl. We typically obtained 200-300 ng RNA from neurons, 10-20 ng from microglia, and 2-5 ng from astrocytes. RNA quality was quantified using the Bioanalyzer.

tag: cell line

tag: treatment


title: 2C cells, biological rep3


title: UNC_TGS_BC_100

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_100

tag: dmfs time


title: UNC_TGS_BC_107

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_107

tag: dmfs event

value: ER-

value: PR-


title: UNC_TGS_BC_101

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_101


title: UNC_TGS_BC_102

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_102

value: LumB


title: UNC_TGS_BC_105

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_105

value: istrong

value: low


title: sample47: NCI-H1792 DMSO, 0.2%


title: UNC_TGS_BC_10

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_10

value: Immuno


title: sample46: NCI-H2122 AZ638


title: 2C cells, biological rep1


title: UNC_TGS_BC_0614_R1

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_0614_R1


title: UNC_TGS_BC_0614

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_0614


title: UNC_TGS_BC_0612

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_0612

value: PR+


title: UNC_TGS_BC_0612_R1

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_0612_R1

value: female


title: UNC_TGS_BC_0604_R1

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_0604_R1


title: sample41: NCI-H1792 AZ638


title: sample45: NCI-H2122 GDC-0973


title: sample43: NCI-H727 GDC-0973


title: sample44: NCI-H1792 GDC-0973


title: sample42: A549 AZ638


title: UNC_TGS_BC_0604

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_0604


title: sample40: A549 DMSO, 0.2%


title: Control_Placenta Sample_100

type: genomic

city: Toronto

first: Rosanna

last: Weksberg

state: Ontario

address: 555 University Ave.

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

description: Genomic DNA extracted from placenta had DNA methylation measured using the HumanMethylation 450K  array (Illumina)

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

scan_protocol: Using an Illumina HiScan

data_processing: Using an Illumina HiScan

label: Cy3 and Cy5

molecule: genomic DNA

source_name: placenta

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from placenta samples using DNEasy (Qiagen) chemistry and columns. No modification was made to the manufacturer's specifications.

tag: outlier

value: Y

value: M

tag: art treatment


title: UNC_TGS_BC_0552_R1

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_0552_R1

tag: sample type

value: Solid tumor

tag: irdm subtype

value: iweak

value: high


title: sample39: NCI-H727 AZ638


title: UNC_TGS_BC_0552

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_0552

value: Basal


title: sample38: NCI-H2122 AZ638


title: Control_Placenta Sample_5

value: N

value: F


title: Control_Placenta Sample_57


title: Control_Placenta Sample_52


title: sample35: NCI-H727 AZ638


title: sample36: NCI-H2122 GDC-0973


title: ARSB-siRNA transfected Human Pulmonary Artery Endothelial Cells Replicate 4

city: Gliwice

first: Magdalena

last: Olbryt

address: Wybrzerze AK 15

department: Center for Translational Research and Molecular Biology of Cancer

country: Poland

institute: Cancer Center and Institute of Oncology

description:
raw data file: US11193903_253949439077_S01-2_GE2_1200_Jun14_2_4.txt
HPAEC_ARSB_4

hyb_protocol: Hybrydization and washing  was done according to Agilent protocol

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1).

data_processing: R Software (version 3.1.1) and limma package was used for LOWESS and aquantile normalization.

source_name: ARSB-siRNA transfected HPAEC

label_protocol: 90ng of total RNA and Low Input Quick Amp Labeling Kit (Agilent) was used. The RNA labeling was done according to manufactrer's protocol.

growth_protocol: Human HPAEC and PASM cells  grown in a SmGM-2 medium (Lonza, Basel, Switzerland) with 5% FBS or EGM-2 medium (Lonza, Basel, Switzerland) with 13% FBS, respectively, under standard conditions.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)  following manufacturer's instructions

value: HPAEC (CC-2530, Lonza)

tag: cell type

tag: transfected with

value: ARSB-siRNA


title: Control_Placenta Sample_10


title: sample37: NCI-H2122 DMSO, 0.2%


title: Control_Placenta Sample_27


title: Control_Placenta Sample_46


title: Control_Placenta Sample_36


title: sample34: NCI-H2122 DMSO, 0.2%


title: ARSB-siRNA transfected Human Pulmonary Artery Endothelial Cells Replicate 2

description:
raw data file: US11193903_253949439077_S01-2_GE2_1200_Jun14_2_2.txt
HPAEC_ARSB_2


title: ARSB-siRNA transfected Human Pulmonary Artery Endothelial Cells Replicate 3

description:
raw data file: US11193903_253949439077_S01-2_GE2_1200_Jun14_2_3.txt
HPAEC_ARSB_3


title: Control_Placenta Sample_71


title: UNC_TGS_BC_118

description:
FFPE RNA
Targeted RNA-seq
UNC_TGS_BC_118

tag: pam50 subtype

tag: immunity group

value: ER-

value: PR-


title: ARSB-siRNA transfected Human Pulmonary Artery Endothelial Cells Replicate 1

description:
raw data file: US11193903_253949439077_S01-2_GE2_1200_Jun14_2_1.txt
HPAEC_ARSB_1


title: sample33: NCI-H2122 AZ628 + GDC-0973


title: Control_Placenta Sample_53


title: Control_Placenta Sample_16


title: Control_Placenta Sample_58


title: sample32: NCI-H1792 AZ638


title: control (non-transfected) Human Pulmonary Artery Endothelial Cells Replicate 2

description:
raw data file: US11193903_253949439077_S01-2_GE2_1200_Jun14_2_2.txt
HPAEC_NT_2

source_name: control (non-transfected) HPAEC

value: none (non-transfected control)


title: Control_Placenta Sample_75


title: Control_Placenta Sample_77


title: sample30: A549 AZ628 + GDC-0973


title: control (non-transfected) Human Pulmonary Artery Endothelial Cells Replicate 4

description:
raw data file: US11193903_253949439077_S01-2_GE2_1200_Jun14_2_4.txt
HPAEC_NT_4


title: Control_Placenta Sample_54


title: Control_Placenta Sample_6


title: Control_Placenta Sample_39


title: Control_Placenta Sample_7


title: Control_Placenta Sample_31


title: sample28: NCI-H1792 DMSO, 0.2%


title: Control_Placenta Sample_55


title: Control_Placenta Sample_25


title: sample27: NCI-H727 AZ638


title: Control_Placenta Sample_19


title: Control_Placenta Sample_78


title: control (non-transfected) Human Pulmonary Artery Endothelial Cells Replicate 3

description:
raw data file: US11193903_253949439077_S01-2_GE2_1200_Jun14_2_3.txt
HPAEC_NT_3


title: sample29: NCI-H727 GDC-0973


title: sample26: NCI-H2122 AZ638


title: Control_Placenta Sample_33


title: sample25: A549 AZ628 + GDC-0973


title: Control_Placenta Sample_40


title: sample24: NCI-H727 DMSO, 0.2%


title: Control_Placenta Sample_72


title: Control_Placenta Sample_73


title: ARSB-siRNA transfected Pulmonary Artery Smooth Muscle Cells Replicate 2

description:
raw data file: US11193903_253949439077_S01-2_GE2_1200_Jun14_1_4.txt
PASM_ARSB_2

source_name: ARSB-siRNA transfected PASMC

value: PASMC (CC-2581, Lonza)

value: Pulmonary Artery Smooth Muscle Cells


title: sample23: A549 GDC-0973


title: iEkappa-/- pre-B cells gDNA #2

city: La Jolla

first: Salvatore

last: Loguercio

state: California

address: 10550 North Torrey Pines Rd

department: MB

institute: TSRI

description: iEk-/- pre-B cells gDNA biological replicate #2

library_source: genomic

data_processing:
Library strategy: VDJ-seq
Demultiplexed paired-end reads were adapter trimmed and quality filtered (Phred>20) using TrimGalore (max of 50 bases trimmed from 3’ end of read, if more bases trimmed from either read then both reads of the pair were thrown out).
Paired-end reads were then merged using pandaseq using default settings. VJ gene calling was performed on merged reads using Abstar (https://github.com/briney/abstar) with a custom version of the minimal output setting, appending Vk gene length in the output.
In addition, a Vk gene reference file was custom made for C57BL/6 (*01 alleles) and each Vk gene was cross-referenced to the mouse genome build mm9 on UCSC genome browser.
Abstar output was processed with a custom R pipeline (https://github.com/salvatoreloguercio/RepSeqPipe) which computed Vk or Jk gene usage statistics. The cutoff for Vk gene assignment was a minimum read length of 150 bp and a minimum of 95% sequence identity. Reads passing this filter were then deduplicated based on the six random adapter nucleotides (gDNA and RNA) and in the case of gDNA, samples were additionally deduplicated based on the starting position of the Vk gene read which are random due to shearing. Reads that contained the same start site (for gDNA) and random 6Ns were presumed to have originated from the same fragment and only counted once. For gDNA, reads needed further processing to deal with Jk PCR primer cross-amplification in order to accurately re-assign Jk gene calling. gDNA reads were re-assigned to their proper Jk gene based on the sequence upstream of each Jk primer. This did not include the most Vk proximal nucleotide of the Jk exon to allow for potential VkJk junctional loss. One pre-B cell gDNA library was prepped using a second set of Jk PCR primers located further downstream of the original Jk primers (closer to the biotin). Since these Jk primers were further away from the VkJk junction, we excluded the 6 most Vk proximal nucleotides from the Jk exon in Jk gene identification.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel spreadsheet with normalized read counts / percent read counts for 140 Vk genes.
Supplementary_files_format_and_content: Columns: 1) Vk gene name; 2) total.occurrences: # total reads; 3) X..total.occurrences: % total reads; 4) v_genes_prod: # productive reads; 5) prod_total: % productive reads within total reads; 6) prod_prod: % productive reads within all productive reads; 7) v_genes_nonprod: # non-productive reads; 8) nonprod_total: % non-productive reads within total reads; 9) nonprod_nonprod: % non-productive reads within all non-productive reads

source_name: iEkappa-/- C57BL/6 pre-B cells

extract_protocol:
Mouse bone marrow cells were enriched for CD19+ B cells using Miltenyi CD19 microbeads (mouse).  CD19+ B cells were sorted to either small pre-B cells (CD2+, CD43-) or pro-B cells (CD2-, CD43+).
For gDNA, sonicated fragments were end repaired, A-tailed and adapter ligated.  Jk gene biotinyated primer extension products were pulled out with streptaviding.  Sequential PCRs added index, barcode and flow cell binding sequences.  The last PCR utilized NEBNext Dual indexing primers.  For RNA, cDNA was made using Transcriptor high-fidelity reverse transcriptase (Roche).  RNA was degraded and ligated to bridge adapters.  Sequential PCRs were employed as in gDNA.

tag: strain

tag: tissue

value: Bone marrow

tag: genotype

value: iEkappa-/- C57BL/6


title: control (non-transfected) Human Pulmonary Artery Endothelial Cells Replicate 1

description:
raw data file: US11193903_253949439077_S01-2_GE2_1200_Jun14_2_1.txt
HPAEC_NT_1


title: sample22: NCI-H727 AZ628 + GDC-0973


title: sample21: NCI-H727 DMSO, 0.2%


title: control (non-transfected) Pulmonary Artery Smooth Muscle Cells Replicate 4

description:
raw data file: US11193903_253949439077_S01-2_GE2_1200_Jun14_1_3.txt
PASM_NT_4

source_name: control (non-transfected) PASMC


title: ARSB-siRNA transfected Pulmonary Artery Smooth Muscle Cells Replicate 1

description:
raw data file: US11193903_253949439077_S01-2_GE2_1200_Jun14_1_1.txt
PASM_ARSB_1


title: sample31: NCI-H727 DMSO, 0.2%


title: JEG3_b5_3

city: Maplewood

first: Nick

last: Illsley

state: NJ

address: Richmond Ave

institute: Placental Research Group LLC

data_processing:
Normalization was performed using the geometric mean of one or more housekeeping genes selected from ACTB, B2M, GAPDH, HPRT1 and RPLP0 (no significant difference between control & test, p < 0.05, t test).
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_HKG − Ct_Target)].
Fold change calculations performed using 2^deltadeltaCt. Fold Change file reports test/control ratios.

label: SYBR Green

source_name: JEG3 choriocarcinoma cells

label_protocol: Samples were analyzed using the Epithelial-Mesenchymal Transition (EMT) RT2 Profile PCR Array (Cat. #PAHS-090Z, Qiagen) using an ABI 7900 HT Fast Real-Time PCR System (Applied Biosystems, Foster City, CA) under cycling conditions recommended for the PCR Array.

growth_protocol: BeWo or JEG3 cells cultured in DMEM/F12 containing 10% FBS.

extract_protocol: RNA was extracted using an miRNeasy Mini Kit (Invitrogen) according to the manufacturer's instructions. cDNA was transcribed from 200 ng of RNA using an RT2 Superscript III Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: Cells transduced with empty vector or ZEB2oe vector for 24 hr; both vectors contain puromycin resistance and GFP genes. After 72 hr, 4 µg/mL puromycin added to culture medium. Stable clones obtained from highest GFP expressing cells, selected by flow cytometry.

value: Lentiviral transduction with ZEB2oe vector/clonal selection


title: ARSB-siRNA transfected Pulmonary Artery Smooth Muscle Cells Replicate 3

description:
raw data file: US11193903_253949439077_S01-2_GE2_1200_Jun14_1_2.txt
PASM_ARSB_3


title: iEkappa-/- pre-B cells gDNA #1

description: iEk-/- pre-B cells gDNA biological replicate #1


title: control (non-transfected) Pulmonary Artery Smooth Muscle Cells Replicate 3

description:
raw data file: US11193903_253949439077_S01-2_GE2_1200_Jun14_1_2.txt
PASM_NT_3


title: Control_Placenta Sample_8

description: Genomic DNA extracted from placenta had DNA methylation measured using the HumanMethylation 450K  array (Illumina)

tag: gender

value: M


title: WT pro-B cells RNA #2

description: WT pro-B cells RNA biological replicate #2

source_name: C57BL/6 pro-B cells

extract_protocol:
Mouse bone marrow cells were enriched for CD19+ B cells using Miltenyi CD19 microbeads (mouse).  CD19+ B cells were sorted to either small pre-B cells (CD2+, CD43-) or pro-B cells (CD2-, CD43+).
For gDNA, sonicated fragments were end repaired, A-tailed and adapter ligated.  J𝛋 gene biotinyated primer extension products were pulled out with streptaviding.  Sequential PCRs added index, barcode and flow cell binding sequences.  The last PCR utilized NEBNext Dual indexing primers.  For RNA, cDNA was made using Transcriptor high-fidelity reverse transcriptase (Roche).  RNA was degraded and ligated to bridge adapters.  Sequential PCRs were employed as in gDNA.

value: WT C57BL/6


title: Control_Placenta Sample_32


title: JEG3_b5_2


title: control (non-transfected) Pulmonary Artery Smooth Muscle Cells Replicate 2

description:
raw data file: US11193903_253949439077_S01-2_GE2_1200_Jun14_1_4.txt
PASM_NT_2


title: WT pro-B cells RNA #1

description: WT pro-B cells RNA biological replicate #1


title: ARSB-siRNA transfected Pulmonary Artery Smooth Muscle Cells Replicate 4

description:
raw data file: US11193903_253949439077_S01-2_GE2_1200_Jun14_1_3.txt
PASM_ARSB_4


title: control (non-transfected) Pulmonary Artery Smooth Muscle Cells Replicate 1

description:
raw data file: US11193903_253949439077_S01-2_GE2_1200_Jun14_1_1.txt
PASM_NT_1


title: Control_Placenta Sample_76


title: JEG3_b5_1


title: sample19: A549 AZ628 + GDC-0973


title: sample20: NCI-H1792 AZ628 + GDC-0973


title: WT pro-B cells gDNA #2

description: WT pro-B cells gDNA biological replicate #2


title: Control_Placenta Sample_29


title: JEG3_a7_3


title: sample18: NCI-H1792 AZ638


title: sample17: NCI-H1792 GDC-0973


title: JEG3_a7_2


title: sample16: A549 DMSO, 0.2%


title: Control_Placenta Sample_34


title: WT pro-B cells gDNA #1

description: WT pro-B cells gDNA biological replicate #1


title: WT pre-B cells RNA #3

description: WT pre-B cells RNA biological replicate #3

source_name: C57BL/6 pre-B cells


title: Control_Placenta Sample_30


title: JEG3_a7_1


title: WT pre-B cells RNA #2

description: WT pre-B cells RNA biological replicate #2


title: sample14: NCI-H2122 GDC-0973


title: WT pre-B cells RNA #1

description: WT pre-B cells RNA biological replicate #1


title: JEG3_ev_3

description: JEG3 Control

value: Lentiviral transduction with empty vector


title: JEG3_ev_2

description: JEG3 Control


title: WT pre-B cells gDNA #3

description: WT pre-B cells gDNA biological replicate #3


title: sample15: NCI-H1792 GDC-0973


title: sample13: NCI-H1792 DMSO, 0.2%


title: Control_Placenta Sample_3


title: Control_Placenta Sample_80


title: JEG3_ev_1

description: JEG3 Control


title: Control_Placenta Sample_35


title: Control_Placenta Sample_94


title: WT pre-B cells gDNA #2

description: WT pre-B cells gDNA biological replicate #2


title: sample12: NCI-H2122 AZ628 + GDC-0973


title: WT pre-B cells gDNA #1

description: WT pre-B cells gDNA biological replicate #1


title: BeWo_f11_3

source_name: BeWo choriocarcinoma cells

value: BeWo


title: BeWo_f11_2


title: sample11: NCI-H1792 AZ628 + GDC-0973


title: Control_Placenta Sample_81

value: Y


title: sample10: NCI-H727 AZ628 + GDC-0973


title: Control_Placenta Sample_91

value: N


title: BeWo_f11_1


title: sample9: A549 AZ638


title: sample8: NCI-H2122 AZ628 + GDC-0973


title: BeWo_c6_3


title: BeWo_c6_2


title: Control_Placenta Sample_79


title: sample7: NCI-H2122 DMSO, 0.2%


title: BeWo_c6_1


title: BeWo_ev_3

description: BeWo Control


title: sample6: A549 GDC-0973


title: Control_Placenta Sample_88

value: F


title: EMT6_i-MG1_R2

city: Ottawa

first: Adrian

last: Pelin

address: 501 Smyth Rd.

institute: Ottawa Hospital Research Institute

description: Gene expression from EMT6 cells infected with irradiated Maraba MG-1 virus

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

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

growth_protocol: Cell grown in 10% FBS, virus grown in Vero cells

extract_protocol: RNA was extracted using the RNeasy RNA extraction kit (Qiagen).

treatment_protocol: Treatment done at MOI 3

value: in-vitro cells


title: sample5: A549 DMSO, 0.2%


title: BeWo_ev_2

description: BeWo Control


title: sample4: NCI-H727 GDC-0973


title: EMT6_i-MG1_R1

source_name: EMT6 cells infected with irradiated Maraba MG-1 virus


title: EMT6_MG1_R2

description: Gene expression from EMT6 cells infected with Maraba MG-1 virus


title: EMT6_MG1_R1

source_name: EMT6 cells infected with Maraba MG-1 virus


title: EMT6_NV_R2

description: Gene expression from EMT6 cells

source_name: EMT6 cells


title: Control_Placenta Sample_83


title: ART_Placenta Sample_90

value: in vivo


title: Control_Placenta Sample_105


title: ART_Placenta Sample_45


title: Control_Placenta Sample_101


title: sample3: NCI-H1792 AZ628 + GDC-0973


title: ART_Placenta Sample_60


title: BeWo_ev_1

description: BeWo Control


title: smr1-pSMR1-GFP2

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

institute: VIB

data_processing:
Illumina CASAVA software used for basecalling.
Paired-end reads were trimmed for adaptor sequences and aligned to the TAIR10 transcriptome using Salmon v0.7.2.
Transcript quantification was also performed by Salmon v0.7.2.
Genome_build: Arabidopsis TAIR10 coding sequences
Supplementary_files_format_and_content: tab-delimited text files generated from Salmon quantification, contain length of transcript in nucleotides, computed effective length, transcripts per million (TPM) and number of reads.

source_name: sorted pSMR1-GFP positive nuclei from smr1

growth_protocol: Approximately 10,000 seeds of Col-O and smr1 plants holding the SMR1:GUS-GFP construct were sown on top of nylon mesh on squared plates holding 1% agar and ½ MS medium. Plants were grown for five days.

extract_protocol:
0,5cm root tips were isolated, protoplasted and filtered. 120000 GFP-positive nuclei were sorted directly into RLT buffer (QIAGEN) containing b-mercaptoethanol and immediately freezed into liquid nitrogen. RNA was extracted using QIAGEN RNeasy Micro Kit.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047).

value: roots

tag: strain/line

value: smr1 pSMR1-GFP


title: smr1-pSMR1-GFP4


title: 4T1_MG1_R1

description: Gene expression from 4T1 cells infected with Maraba MG-1 virus


title: EMT6_NV_R1

description: Gene expression from EMT6 cells


title: 4T1_MG1_R2

source_name: 4T1 cells infected with Maraba MG-1 virus


title: pSMR1-GFP4

source_name: sorted pSMR1-GFP positive nuclei from Col-0


title: ART_Placenta Sample_51

description: Genomic DNA extracted from placenta had DNA methylation measured using the HumanMethylation 450K  array (Illumina)


title: 4T1_i-MG1_R2

description: Gene expression from 4T1 cells infected with irradiated Maraba MG-1 virus


title: sample2: A549 AZ638

source_name: cell line

tag: cell line


title: 4T1_i-MG1_R1

description: Gene expression from

source_name: 4T1 cells infected with irradiated Maraba MG-1 virus


title: sample1: NCI-H727 AZ628 + GDC-0973

tag: treatment


title: smr1-pSMR1-GFP1


title: pSMR1-GFP2


title: ART_Placenta Sample_48

source_name: placenta


title: 4T1_NV_R1

description: Gene expression from 4T1 cells

source_name: 4T1 cells


title: 4T1_NV_R2

description: Gene expression from 4T1 cells


title: ART_Placenta Sample_49


title: ART_Placenta Sample_24


title: pl-cre_3

city: St. Louis

first: Joel

middle: D

last: Schilling

state: MO

address: 660 S. Euclid Ave

department: Internal Medicine

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq 2.0
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart.  RPKM calculated from gene counts with standard RPKM transformation with custom R scripting.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted tex format

growth_protocol: thioglycolate peritoneal macrophages were islated day 4 after TG injection and plated.  The next day the cells were stimulated as described below.

extract_protocol:
RNA was extraced using Ambion column kits.
Clonetech SMARTer v1

treatment_protocol: Cre (WT) or PPARg KO macrophages were treated with BSA-PBS and palm-LPS (doses above) for 8h

value: palmitate


title: pl-ppar_1


title: pl-ppar_3


title: pl-ppar_2


title: ART_Placenta Sample_50

value: in vitro


title: ART_Placenta Sample_65


title: ART_Placenta Sample_28


title: MEF_t=30

city: Edinburgh

first: Tom

middle: C

last: Freeman

address: Easter Bush Campus, Midlothian

department: Genetics and Genomics

institute: Roslin Institute

description:
MEF, 30 h
Gene expression data of MEF in synchronous late proliferation

hyb_protocol: Samples were hybridized to Mouse Gene 2.0 ST Arrays

scan_protocol: Arrays were scanned using the GeneAtlas system

data_processing: Data were pre-processed with Bioconductor package oligo. After QC data was RMA normalised.

source_name: MEF late proliferation

label_protocol: fragmented cDNA was labeled  by TdT DNA labelling reagent using GeneChip® WT Terminal Labelling Kit (Affymetrix, Buckinghamshire, UK) according to manufacturer’s instructions

growth_protocol: Mouse embryonic fibroblasts (MEF) were plated on 175 cm2 tissue culture flasks (Thermo Fisher, Perth, UK) at density of 6x103 cells/cm2. Cells were cultured in DMEM (Sigma-Aldrich, Missouri, US) with 10% (v/v) foetal calf serum (FCS) (GE Healthcare, Little Chalfont, UK) and antibiotics (25 U/ml penicillin and 25 µg/ml streptomycin (Life technologies, Paisley, UK).

extract_protocol: total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Manchester, UK) according to manufacturer’s instructions

treatment_protocol: Starvation-induced synchronisation was achieved by replacing full medium with DMEM containing 0.5% FCS for 48 h. After this time, medium was replaced with DMEM containing 10% FCS promoting the synchronised entry of the MEF back into the cell cycle.

value: Mouse embryonic fibroblasts (MEF)

tag: age

value: early passage MEF


title: bp-ppar_3

value: vehicle


title: MEF_t=28

description:
MEF, 28 h
Gene expression data of MEF in synchronous late proliferation


title: ART_Placenta Sample_14


title: MEF_t=24a

description:
MEF, 24 h, biological replica 1
Gene expression data of MEF in synchronous late proliferation


title: pl-cre_1


title: pl-cre_2


title: ART_Placenta Sample_18


title: bp-ppar_2


title: ART_Placenta Sample_12


title: ART_Placenta Sample_42


title: bp-ppar_1


title: MEF_t=24b

description:
MEF, 24 h, biological replica 2
Gene expression data of MEF in synchronous late proliferation


title: ART_Placenta Sample_74


title: MEF_t=20

description:
MEF, 20 h
Gene expression data of MEF in synchronous late proliferation


title: ART_Placenta Sample_21


title: bp-cre_3


title: MEF_t=22

description:
MEF, 22 h
Gene expression data of MEF in synchronous late proliferation


title: MEF_t=26

description:
MEF, 26 h
Gene expression data of MEF in synchronous late proliferation


title: MEF_t=18a

description:
MEF, 18 h, biological replica 1
Gene expression data of MEF in synchronous late proliferation


title: bp-cre_2


title: ART_Placenta Sample_62


title: MEF_t=18b

description:
MEF, 18 h, biological replica 2
Gene expression data of MEF in synchronous late proliferation


title: 564017A12 - 35S_AO2_26 vs CTRL_3

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Study of the biosynthesis of NAD in Arabidopsis. Involvment of L-Aspartate oxidase gene using T-DNA mutant (SAIL1145_B10) and overexpressor lines (promotor 35S, vector PCW162) at the same developmental stage (12 leaves)

hyb_protocol: CTRL_3 Cy5 / 35S_AO2_26 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: rosette - 1-Growth conditions (1-2-3-4); Media: Soil; hygrometry: 65%; Temperature: 20C; Light: 8 hours - 100 umol quanta m-2 s-1

treatment_protocol: no treatment

tag: arabidopsis thaliana (columbia)  -  dev.stage (boyes et al. plant cell 2001)

tag: arabidopsis thaliana (columbia)  mutant (35s

value: :AO) -  dev.stage (Boyes et al. Plant Cell 2001):boyes:1.12


title: ART_Placenta Sample_67

tag: outlier

tag: art treatment


title: bp-cre_1


title: ART_Placenta Sample_11


title: 564017A08 - 35S_AO1_14 vs CTRL_3

hyb_protocol: CTRL_3 Cy5 / 35S_AO1_14 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: MEF_t=14

description:
MEF, 14 h
Gene expression data of MEF in synchronous mid proliferation

source_name: MEF mid proliferation


title: MEF_t=16

description:
MEF, 16 h
Gene expression data of MEF in synchronous mid proliferation


title: 564017A09 - CTRL_1 vs 35S_AO2_23

hyb_protocol: 35S_AO2_23 Cy5 / CTRL_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 564017A10 - 35S_AO2_23 vs CTRL_1

hyb_protocol: CTRL_1 Cy5 / 35S_AO2_23 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: ART_Placenta Sample_15


title: LW50_WT_C

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

institute: Institute of Clinical Molecular Biology

data_processing:
Sequence reads from epithelial crypt were trimmed for adapters using the software cutadapt (version 1.5)
Sequence reads from tumor and normal tissues were trimmed for adapters using the software Trimmomatic (version 0.36)
Sequence reads from intestinal organoids were trimmed for adapters using the software cutadapt (version 1.9)
All filtered reads were mapped to the GRCm38 reference using the software tophat (version 2.0.14)
Expression counts of genes were estimated using htseq
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files with expression counts  for each sample

source_name: intestinal organoid

extract_protocol:
I) Epithelial crypts from H2Bflox/flox and H2BdIEC and ii) tumor tissue and surrounding unaffected tissue of H2B/p53flox/flox and H2B/p53dIEC mice and iii) intestinal organoids were harvested freshly. To isolate total RNA from animal tissue for RNA sequencing, the RNeasy Mini Kit from Qiagen (Hilden, Germany) was used according to supplier’s instructions including a QIAshredder column from Qiagen.
Individual strand-specific sequencing libraries were prepared with the TruSeq stranded mRNA kit (Illumina) from 500 ng total RNA.

value: intestinal organoid


title: 564017A11 - CTRL_3 vs 35S_AO2_26

hyb_protocol: 35S_AO2_26 Cy5 / CTRL_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: ART_Placenta Sample_23

value: M


title: MEF_t=12a

description:
MEF, 12 h, biological replica 1
Gene expression data of MEF in synchronous mid proliferation


title: LW50_WT_A


title: MEF_t=12b

description:
MEF, 12 h, biological replica 2
Gene expression data of MEF in synchronous mid proliferation


title: MEF_t=10

description:
MEF, 10 h
Gene expression data of MEF in synchronous mid proliferation


title: 564017A06 - 35S_AO1_11 vs CTRL_1

hyb_protocol: CTRL_1 Cy5 / 35S_AO1_11 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: ART_Placenta Sample_61

description: Genomic DNA extracted from placenta had DNA methylation measured using the HumanMethylation 450K  array (Illumina)


title: LW50_WT_B


title: H2Bp53DKO_3


title: 564017A07 - CTRL_3 vs 35S_AO1_14

hyb_protocol: 35S_AO1_14 Cy5 / CTRL_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: ART_Placenta Sample_47


title: MEF_t=08

description:
MEF, 8 h
Gene expression data of MEF in synchronous mid proliferation


title: ART_Placenta Sample_59


title: H2Bp53DKO_1


title: 564017A04 - mAO_3 vs CTRL_3

hyb_protocol: CTRL_3 Cy5 / mAO_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)

tag: arabidopsis thaliana (columbia)  mutant (sail_1145_b10) -  dev.stage (boyes et al. plant cell 2001)


title: 564017A05 - CTRL_1 vs 35S_AO1_11

hyb_protocol: 35S_AO1_11 Cy5 / CTRL_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: LW50_H2BKO_B


title: ART_Placenta Sample_43


title: MEF_t=04

description:
MEF,4 h
Gene expression data of MEF in synchronous early proliferation

source_name: MEF early proliferation


title: MEF_t=06

description:
MEF, 6 h
Gene expression data of MEF in synchronous early proliferation


title: 564017A03 - CTRL_3 vs mAO_3

hyb_protocol: mAO_3 Cy5 / CTRL_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: MEF_t=01

description:
MEF, 1 h
Gene expression data of MEF in synchronous early proliferation


title: 564017A02 - mAO_1 vs CTRL_1

hyb_protocol: CTRL_1 Cy5 / mAO_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: LW50_H2BKO_A


title: MEF_t=02

description:
MEF, 2 h
Gene expression data of MEF in synchronous early proliferation


title: 1321_SI_nonTumor

source_name: adjacent normal tissue

value: adjacent normal tissue


title: MEF_t=0b

description:
MEF, 0 h, biological replica 2
Gene expression data of MEF in a quiescent state

source_name: MEF quiescent


title: 1320_SI_nonTumor


title: ART_Placenta Sample_66


title: ART_Placenta Sample_44


title: 564017A01 - CTRL_1 vs mAO_1

hyb_protocol: mAO_1 Cy5 / CTRL_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: MEF_t=0a

description:
MEF, 0 h, biological replica 1
Gene expression data of MEF in a quiescent state


title: MEF_t =0.5

description:
MEF, 0.5 h
Gene expression data of MEF in synchronous early proliferation


title: ART_Placenta Sample_70


title: ART_Placenta Sample_20


title: MEF_ctrl.b

description:
MEF, unsynchronised, biological replica 2
Gene expression data of MEF unsynchronised

source_name: MEF unsynchronised


title: LW50_H2BKO_C


title: ART_Placenta Sample_98


title: ART_Placenta Sample_22


title: 1315_SI_nonTumor


title: MEF_ctrl.a

description:
MEF, unsynchronised, biological replica 1
Gene expression data of MEF unsynchronised


title: 1319_SI_Tumor

source_name: tumor tissue

value: tumor tissue


title: ART_Placenta Sample_64


title: TAOK3 KO rep3

city: Montreal

first: Joao Vitor

middle: Silva

last: Ormonde

state: QC

address: 1160 Pine Avenue West, Room 603

institute: McGill University

hyb_protocol: Thermo Fischer Scientific HuGene2.0-st

scan_protocol: The data from the probe cell intensities was normalized by using the software Expression Console v1.4.1(Thermo Fischer Scientific)

data_processing: Transcriptome Analysis Console v3.0 (Thermo Fischer Scientific)

source_name: Jurkat T cells

growth_protocol: Normal RPMI-suplemented (R10) medium

extract_protocol: Affinity collumn chromatography

tag: genotype/variation

value: TAOK3 KO


title: 1319_SI_nonTumor


title: TAOK3 KO rep2


title: ART_Placenta Sample_104

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

value: N


title: ART_Placenta Sample_1

value: F


title: TAOK3 KO rep1


title: 1322_SI_nonTumor


title: ART_Placenta Sample_93

value: Y


title: 1323_SI_Tumor


title: NHDF_24 h (set2)

description:
NHDF, 24 h
Gene expression data of NHDF in synchronous late proliferation

hyb_protocol: Samples were hybridized on Affymetrix Human Gene 1.1-ST Array Strips. Hybridization, wash and staining was done using the GeneAtlas System with the GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips (Affymetrix)

scan_protocol: Arrays were scanned using the Imaging station as part of the GeneAtlas system (Affymetrix).

data_processing: Data were pre-processed with Bioconductor package oligo. After QC data was RMA normalised.  This dataset was combined with Data Set 1 before downstream analysis. After merging the datasets, average intensities differences were adjusted with the batch correction algorithm ComBat.

source_name: NHDF late proliferation

growth_protocol: Primary human dermal fibroblasts (NHDF) isolated from neonate foreskins (gifted by Dr Finn Grey, University of Edinburgh, UK) were plated on 175 cm2 tissue culture flasks (Thermo Fisher, Perth, UK) at density of 6x103 cells/cm2. Cells were cultured in DMEM (Sigma-Aldrich, Missouri, US) with 10% (v/v) foetal calf serum (FCS) (GE Healthcare, Little Chalfont, UK) and antibiotics (25 U/ml penicillin and 25 µg/ml streptomycin (Life technologies, Paisley, UK).

treatment_protocol: Starvation-induced synchronisation was achieved by replacing full medium with DMEM containing 0.5% FCS for 48 h. After this time, medium was replaced with DMEM containing 10% FCS promoting the synchronised entry of the NHDF back into the cell cycle.

value: Primary human fibroblasts (NHDF)

value: early passage NHDF


title: ART_Placenta Sample_85

value: in vivo


title: 1323_SI_nonTumor


title: Jurkat WT rep3

value: wild type


title: NHDF_22 h (set2)

description:
NHDF, 22 h
Gene expression data of NHDF in synchronous late proliferation


title: ART_Placenta Sample_106

value: in vitro


title: Jurkat WT rep2


title: Jurkat WT rep1


title: H2Bp53DKO_2


title: 1316_SI_nonTumor


title: 1349_SI_Tumor


title: ART_Placenta Sample_84


title: ART_Placenta Sample_102


title: NHDF_20 h (set2)

description:
NHDF, 20 h
Gene expression data of NHDF in synchronous late proliferation


title: 1349_SI_nonTumor


title: KA_182_SI_Crypt_981

source_name: epithelial crypt

value: epithelial crypt

tag: mouse age

value: 52 weeks

value: H2B flox/flox


title: ART_Placenta Sample_99


title: KA_182_SI_Crypt_979


title: NHDF_18 h (set2)

description:
NHDF, 18 h
Gene expression data of NHDF in synchronous late proliferation


title: 1322_SI_Tumor


title: ART_Placenta Sample_96


title: NHDF_16 h (set2)

description:
NHDF, 16 h
Gene expression data of NHDF in synchronous late proliferation


title: KA_182_SI_Crypt_978


title: HIV low_ANA_9- 1w

city: Charleston

first: Zhenwu

last: Luo

state: SC

address: 173 Ashley Ave

department: Immunology & Microbiology

institute: Medical University of South Carolina

description: Gene expression data from low ANA

hyb_protocol: Affymetrix Human GeneChip U133 Plus 2.0 Array was used for RNA hybridization and labeling assay

scan_protocol: not provided.

data_processing: Biological profiles of distinct genes were analyzed and clustered using iPathway

source_name: Purified human B cells

label_protocol: total RNA were sent to do the gene expression microarray

growth_protocol: B cells were purified from fresh isolated PBMC

extract_protocol: RNeasy Micro kit

tag: diagnosis

value: HIV+

value: blood

tag: cell type

value: Purified human B cells

value: Female

tag: ana level

value: low

tag: weeks after influenza vaccination


title: NHDF_10 h (set2)

description:
NHDF, 10 h
Gene expression data of NHDF in synchronous mid proliferation

source_name: NHDF mid proliferation

tag: tissue


title: HIV low_ANA_8- 0w

description: Gene expression data from low ANA

tag: gender


title: HIV low_ANA_9- 0w

description: Gene expression data from low ANA


title: HIV low_ANA_7- 1w

description: Gene expression data from low ANA

value: Male


title: HIV low_ANA_7- 0w

description: Gene expression data from low ANA


title: NHDF_14 h (set2)

description:
NHDF, 14 h
Gene expression data of NHDF in synchronous mid proliferation


title: KA_182_SI_Crypt_976

tag: genotype

tag: strain


title: ART_Placenta Sample_97

description: Genomic DNA extracted from placenta had DNA methylation measured using the HumanMethylation 450K  array (Illumina)

value: N

value: M


title: HIV low_ANA_8- 1w

description: Gene expression data from low ANA


title: KA_182_SI_Crypt_975


title: NHDF_12 h (set2)

description:
NHDF, 12 h
Gene expression data of NHDF in synchronous mid proliferation


title: NHDF_8 h (set2)

description:
NHDF, 8 h
Gene expression data of NHDF in synchronous mid proliferation


title: HIV low_ANA_6- 1w

description: Gene expression data from low ANA


title: NHDF_6 h (set2)

description:
NHDF, 6 h
Gene expression data of NHDF in synchronous mid proliferation


title: ART_Placenta Sample_103


title: WT_mk49_methylation

city: New Brunswick

first: SAURABH

last: LADDHA

address: 195 Little Albany Street

institute: Rutgers Cancer Institute of New Jersey

description: DNA CpG Methylation profile for Human PanNETs

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

data_processing:
All IDAT files were processed in R using ChAMP package with QC,  normalization (FunctionNormalization) and Differentially methylated probes
Normalized data using FunctionNormalization method within ChAMP package and obtained Beta values for all quality passed probe

label: Cy3, Cy5

source_name: WT PanNET for ATRX / DAXX and MEN1

extract_protocol: Genomic DNA was extracted and purified from PanNET samples using Qiagen DNeasy Kit according to standard instructions

value: Pancreatic neuroendocrine tumors (PanNETs)

value: WT for ATRX/DAXX/MEN1

tag: pannet subtype

value: A-D-M WT PanNETs


title: ART_Placenta Sample_86

value: F


title: KA_182_SI_Crypt_972


title: KA_182_SI_Crypt_971


title: WT_mk8_methylation


title: HIV low_ANA_6- 0w

description: Gene expression data from low ANA

tag: age


title: HIV low_ANA_5- 1w

description: Gene expression data from low ANA


title: KA_182_SI_Crypt_970


title: NHDF_4 h (set2)

description:
NHDF, 4 h
Gene expression data of NHDF in synchronous early proliferation

source_name: NHDF early proliferation

value: Primary human fibroblasts (NHDF)

value: early passage NHDF


title: NHDF_1 h (set2)

description:
NHDF, 1 h
Gene expression data of NHDF in synchronous early proliferation


title: NHDF_2 h (set2)

description:
NHDF, 2 h
Gene expression data of NHDF in synchronous early proliferation


title: HIV low_ANA_4- 0w

description: Gene expression data from low ANA


title: NHDF_0 h (set2)

description:
NHDF, 0 h
Gene expression data of NHDF in a quiescent state

source_name: NHDF quiescent


title: NHDF_unsynch_Rep2 (set2)

description:
NHDF, unsynchronised, technical replica 2
Gene expression data of NHDF unsynchronised

source_name: NHDF unsynchronised


title: WT_mk15_methylation


title: HIV low_ANA_5- 0w

description: Gene expression data from low ANA


title: NHDF_unsynch_Rep1 (set2)

description:
NHDF, unsynchronised, technical replica 1
Gene expression data of NHDF unsynchronised


title: HIV low_ANA_2- 1w

description: Gene expression data from low ANA


title: WT_mk39_methylation


title: HIV low_ANA_4- 1w

description: Gene expression data from low ANA


title: WT_mk19_methylation


title: WT_mk50_methylation


title: HIV low_ANA_3- 1w

description: Gene expression data from low ANA


title: WT_mk21_methylation


title: WT_LS65_methylation


title: WT_mk27_methylation


title: HIV low_ANA_3- 0w

description: Gene expression data from low ANA


title: WT_mk13_methylation


title: HIV high_ANA_5- 1w

description: Gene expression data from high ANA

value: high


title: WT_LS35_methylation