title: monocultured HMVEC at time 24 hr, biological replicate 5

description: Gene expression array


title: monocultured SAEC DM control, biological replicate 4

status: Public on Apr 12 2019

type: RNA

city: Morgatown

first: Nancy

middle: Lan

last: Guo

state: WV

address: 2816 Health Sciences Center

department: Occupational and Environmental Health Sciences

country: USA

institute: West Virginia University

description: Gene expression array

hyb_protocol: Following purification of labeled cRNAs, 825 ng of Cy3- and Cy5-labeled cRNAs were combined and hybridized for 17 h at 65°C in an Agilent hybridization oven.

scan_protocol: Microarrays were then washed and scanned using an Agilent DNA Microarray Scanner.

data_processing:
In vitro microarray data were exported using Feature Extraction v10 as tab-delimited text files after background subtraction, log transformation, and lowess normalization and reported as log or relative expression of sample compared to universal reference. Data were read from each file into R using a custom script (Guo et al. 2012).
For each array, values for control spots, spots which were saturated on either channel, spots which were reported by Feature Extraction as non-uniform outliers on either channel, and spots which were not well above background on at least one channel were considered unreliable and/or uninformative and replaced by “NA”. Values were collated into a single table, and probes for which fewer than 10 present values were available were removed. For probes spotted multiple times on the array, values were averaged across replicate probes. Missing data were imputed using the K-means nearest neighbor algorithm as implemented by the impute.knn function in the impute R package from Bioconductor.

molecule: total RNA

organism: Homo sapiens

label_protocol: Total RNA (250 ng) was used for labeling using a QuickAmp labeling kit (Agilent). Extracted RNA was labeled with cyanine (Cy)-3-CTP (PerkinElmer, Waltham, MA) and reference RNA with (Cy)-5-CTP.

growth_protocol: SAEC were a kind gift from Dr. Tom K. Hei (Columbia University, New York, NY) (Piao et al. 2005). SAEC were cultured in serum free complete SAGM medium supplemented with various growth factors supplied by the manufacturer (Lonza Walkersville, Inc., Walkersville, MD). HMVEC were a kind gift from Dr. Rong Shao (Biomedical Research Institute, Baystate Medical Center/University of Massachusetts, Amherst, Springfield, MA) (Shao and Guo 2004). HMVEC were cultured in endothelial basal medium-2 (EBM-2) (Lonza) and supplemented with 10% fetal bovine serum (Atlanta Biological, Lawrenceville, GA), 100 U/mL penicillin and 10 ug/mL streptomycin (Lonza), 0.01 ug/mL epidermal growth factor (Sigma), and 1 ug/mL hydrocortisone (Sigma). All cells were maintained in an incubator at 37°C with 5% CO2.

extract_protocol: Total RNA was isolated from SAEC and HMVEC using RNAprotect Cell Reagent and an RNeasy Mini Kit from Qiagen according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA concentrations were determined using a NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE), and RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: To prepare cocultures, inserts were removed from 100 mm polycarbonate Transwell (Corning, Tewksbury, MA) dishes and hydrated in SAEC complete media in a companion 100 mm dish for at least 1 hour. HMVEC were plated at 1,000,000 cells in the bottom of each Transwell dish (growth area: 55 cm2) and allowed to adhere for at least 1 h without the apical chamber insert. Inserts were returned to the Transwell after hydration, and 1,000,000 SAEC were plated onto the Transwell insert (growth area: 44 cm2). Cells were maintained in 15 mL of complete EBM-2 media in the basolateral chamber and 10 mL of complete SAEC media in the apical chamber.

tag: cell type

value: monocultured SAEC DM control

tag: biological replicate

source_name: reference RNA

tag: reference

value: reference RNA


title: Breast tumour T22

type: genomic

city: Gothenburg

first: Jana

last: Biermann

address: Medicinaregatan 1F

country: Sweden

institute: University of Gothenburg

description: Human breast tumour

hyb_protocol: Probes annealing and ligation on tumour DNA, amplification by PCR, probes digestion and DNA hybridization on each array were performed according to the manufacturer's instructions.

scan_protocol: Hybridized probes were captured by streptavidinphycoerythrin conjugates using Fluidics Station 450 and arrays were scanned using GeneChip Scanner 3000 7G.

data_processing:
CEL files were processed using the Chromosome Analysis Suite (ChAS; v.3.3.0.139) to produce OSCHP files. Weighted log2 ratios and B allele frequencies generated by ChAS were processed by the ‘copynumber’ R-package (v.1.22.0) to obtain allele-specific segmentation into regions of constantcopy numbers using Piecewise Constant Fitting.
Excel metadata file, CEL files, OSCHP files, copy number data

label: Biotin

molecule: genomic DNA

source_name: Human breast tumour

label_protocol: Performed according to manufacturer's protocols.

growth_protocol: All samples were formalin-fixed paraffin-embedded (FFPE) tumours.

extract_protocol: Tumour tissues were sectioned and tumour DNA was extracted using the AllPrep DNA/RNA FFPE kit (Qiagen) with overnight Proteinase K treatment. The DNA concentration was determined with the Qubit Fluorometer.

tag: gender

value: Female


title: D1 sgDnmt1 Rep2

type: SRA

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

library_source: transcriptomic

data_processing:
Genes expression :Raw reads were first trimmed using Trimmomatic (v.0.36). Illumina sequence adaptors were removed, the leading and tailing low-quality base-pairs (less than 3) were trimmed, and a 4-bp sliding window was used to scan the reads and trim when the window mean quality dropped below 15. Only reads with more than 50-bp were kept. The resulting reads were mapped to the mm10 genome using STAR 33 (v.2.5.2b) with the following parameters: --outSAMtype BAM SortedByCoordinate –outSAMunmapped Within –outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --quantMode TranscriptomeSAM GeneCounts. The generated gene expression count files generated by STAR were then used for estimating gene expression.
Repeats expression :Multi-mapped reads and reads mapping to intronic or intergenic regions were extracted and then mapped to the repeats pseudo-genome. First, the TagReadWithGeneExon command of the dropseq tools was used to tag the reads into utr, coding, intergenic and intronic reads using the bam tag “XF”. Multi-mapped reads, intergenic and intronic reads were extracted and mapped to the repeats pseudo-genome using STAR. The STAR read counts were used as an estimate of repeats expression.
Analysis: For each sample, the genes and repeats expression matrices were merged together and then the “Trimmed Mean of M-values” normalization (TMM) method from the R/Bioconductor package edgeR package was used to calculate the normalized expression
Genome_build: mm10
Supplementary_files_format_and_content: tab

organism: Mus musculus

source_name: D1 sgDnmt1

growth_protocol: ES-E14TG2a cells were cultured with medium consisted of DMEM (Gibco, Cat. # 11995) with 15% FBS (Sigma, Cat. #F6178), 1000 U/ml mouse leukemia inhibitory factor (Millipore, Cat. #ESG1107), 0.1 mM non-essential amino acids (Gibco, Cat. # 11140), 0.1mM β-mercaptoethanol (Gibco, Cat. # 21986023), 1 mM Glutamine-max (Gibco, Cat. # 25030), 1 mM sodium pyruvate (Gibco, Cat. # 11360)) and penicillin/streptomycin (100 U/ml) (Gibco, Cat, #15140).

extract_protocol:
Cellular RNA and DNA was harvested using Qiagen Allprep RNA/DNA mini kit (Qiagen, Cat 80204).
The bulk RNA-seq library was prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, Cat E7420S). Drop-seq was performed as described in "Chen, R., Wu, X., Jiang, L. & Zhang, Y. Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity. Cell Rep 18, 3227-3241 (2017)." RRBS: DNA (1 ng) with 0.5% nonmethylated λ DNA spike-in was digested by MspI for 3.5 hours. DNA was then end-repaired, dA-tailed, and ligated with methylated adaptors. Bisulfite conversion was carried out using an EpiTect fast bisulfite conversion kit (Qiagen) according to the manufacturer’s instructions. Bisulfite-converted DNA was then amplified with five PCR cycles to obtain the final library.

treatment_protocol: Doxycycline is added to induce Dux transgene. CRISPR knockdown is performed as described in "Shalem O*, Sanjana NE*, Hartenian E, Shi X, Scott DA, Mikkelsen T, Heckl D, Ebert BL, Root DE,Doench JG, Zhang F (2014). Science, 343, 83-7. DOI: 10.1126/science.1247005".

tag: strain

tag: cell line

value: embryonic stem cell

tag: dux induction

value: Yes


title: sgGFP control for D1 sgDnmt1 experiment Rep1

source_name: sgGFP control for D1 sgDnmt1 experiment


title: Breast tumour T17

description: Human breast tumour


title: Breast tumour T19

description: Human breast tumour


title: Breast tumour T18

description: Human breast tumour


title: monocultured HMVEC at time 6 hr, biological replicate 6

description: Gene expression array

value: monocultured HMVEC

tag: time point

value: 6 hr


title: Breast tumour T2

description: Human breast tumour


title: monocultured HMVEC at time 6 hr, biological replicate 5

description: Gene expression array


title: Breast tumour T21

description: Human breast tumour


title: monocultured HMVEC at time 6 hr, biological replicate 3

description: Gene expression array


title: monocultured HMVEC at time 24 hr, biological replicate 1

description: Gene expression array

value: 24 hr


title: monocultured HMVEC at time 6 hr, biological replicate 2

description: Gene expression array


title: monocultured HMVEC at time 24 hr, biological replicate 2

description: Gene expression array


title: monocultured HMVEC DM control, biological replicate 6

description: Gene expression array

value: monocultured HMVEC DM control


title: monocultured HMVEC DM control, biological replicate 3

description: Gene expression array


title: monocultured HMVEC at time 6 hr, biological replicate 1

description: Gene expression array


title: monocultured HMVEC at time 6 hr, biological replicate 4

description: Gene expression array


title: Breast tumour T13

description: Human breast tumour


title: Breast tumour T115

description: Human breast tumour


title: D1 sgDnmt1 Rep1


title: Breast tumour T111

description: Human breast tumour


title: Breast tumour T113

description: Human breast tumour


title: sgGFP control for D0 sgDnmt1 experiment Rep2

source_name: sgGFP control for D0 sgDnmt1 experiment

value: No


title: Breast tumour T116

description: Human breast tumour


title: sgGFP control for D0 sgDnmt1 experiment Rep1


title: D0 sgDnmt1 Rep2

source_name: D0 sgDnmt1


title: D0 sgDnmt1 Rep1


title: T_60_2

city: Göttingen

first: Livia

last: Caizzi

address: Am Fassberg 11

department: Molecular Biology

country: Germany

institute: Max Planck Institute For Biophysical Chemistry

data_processing:
TTseq read alignment and counting. Paired-end 150 bp reads with additional 6 bp of barcodes were obtained for each sample. Reads were aligned using STAR version 2.5.0a (Dobin et al., 2013) in single pass mode. The genome Index was built against the full GENCODE version 24 annotation and the hg38 (GRCh38) genome assembly (Human Genome Reference Consortium) using 150 bp overhang size.  Additional specified parameters were alignSJDBoverhangMin 2, chimSegmentMin 15, chimScoreMin 15, chimScoreSeparation 10, and chimJunctionOverhangMin 15. The aligned reads were filtered for duplicates using Picard tools version 2.5.0 (https://broadinstitute.github.io/picard/) using the option MarkDuplicates REMOVE_DUPLICATES=true. In average, each TT-seq sample yielded about 250 M reads and each RNA-seq sample about 55 M reads.  For each sample, ~90% of the reads could be uniquely mapped to the reference genome. The duplication ratio was estimated to 55% by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Intron annotation and counting. Using custom scripts, all split reads (containing N stretches in Cigar string) were extracted to create a database of potential introns (~341k). The obtained introns were classified relative to annotated introns and genetic elements from the GENCODE annotation (version 24 obtained from (https://www.gencodegenes.org/releases/24.html). For each intron three characteristic counts were calculated: The numbers of reads starting in the upstream exon and extending into the intron (‘donor’), the number of reads starting in the intron and extending into the downstream exon (‘acceptor’), and all split reads matching the introns coordinates (‘junction’). The reads were filtered using a bam quality score of 255. Reads having secondary alignment flag were discarded.
Sample normalization and cross-contamination. To estimate the sample normalization factors F_j that account for variations in sequencing depth as well as the overall newly synthesized RNA fraction and the fraction of cross-contamination χ_j  of non-labeled reads in the TT-seq data, we modeled the expectation of counts E_ij of spike-in i in sample j using a statistical model similar to the one of (Schwalb et al. 2016). We assumed read count data to follow a negative binomial distribution with a common dispersion parameter for all data. The model parameters and the dispersion parameter were fitted as generalized linear model using maximum likelihood.
Determination of major isoforms. We applied the software Salmon (Patro et al., 2017) (index kmer size = 31) to all RNA-seq samples and mapped them against the full transcriptome of the GENCODE (Ver. 24) annotation. For each gene, we selected the isoform with the maximum mean TPM value across all RNA-seq samples as the major isoform.
Comparison of 4sU-seq and TT-seq.Alignment, counting and estimation of normalization factors / cross-contamination of RNA-seq data sets of (Schwalb et al., 2016) was done as described before for our data. Counts for 4sU-seq and TT-seq was normalized using (K_(i,j) ) ̂=K_(i,j)/F_j -(χ_j K_(i,RNA-Seq))/F_(RNA-Seq) , where i denotes the split / unsplit reads for each intron of the major transcripts and i is the sample (4sU- / TT-seq and replicate). Both replicates were pooled together.
Genome_build: hg38 (GRCh38) genome assembly (Human Genome Reference Consortium)
Supplementary_files_format_and_content: tsv file containing junction reads count table

source_name: K562_4sU (Carbosynth) labeling for 60min

growth_protocol: Human K562 erythroleukemia cells were obtained from DSMZ (Cat.# ACC-10) and grown in antibiotic-free RPMI 1640 medium supplemented with 10 % heat-inactivated fetal bovine serum and 2 mM GlutaMAX at 37 °C and 5% CO2. Cells were routinely verified to be free of mycoplasma contamination. K562 cells were authenticated at the DSMZ Identification Service according to standards for STR profiling (ASN-0002).

extract_protocol:
Ovation Universal RNA-Seq System (NuGEN)
TT-seq, RNA-seq (Schwalb et al., 2016)

treatment_protocol: Cells were exposed to 500 µM of 4-thiouracil (4sU, Carbosynth) for 2, 5, 10, 15, 20, 30, 60 min at 37 °C and 5 % CO2. 2.5 x 10^7 cells from two biological replicates were used for each time point.

value: erythroleukemia cells

tag: treatment

value: 500 µM 4-thiouracil (4sU, Carbosynth) for 60min

tag: method protocol

value: RNA-seq

tag: replicate

value: replicate 2

tag: molecule subtype

value: Total fragmented RNA


title: monocultured SAEC at time 24 hr, biological replicate 4

description: Gene expression array

value: monocultured SAEC


title: monocultured HMVEC DM control, biological replicate 4

description: Gene expression array


title: monocultured HMVEC DM control, biological replicate 5

description: Gene expression array


title: cocultured SAEC at time 24 hr, biological replicate 6

description: Gene expression array

value: cocultured SAEC


title: cocultured SAEC at time 24 hr, biological replicate 3

description: Gene expression array


title: cocultured SAEC at time 6 hr, biological replicate 6

description: Gene expression array


title: T_60_1

value: replicate 1


title: sgGFP control for D1 sgMyc experiment Rep2

source_name: sgGFP control for D1 sgMyc experiment


title: D1 sgMyc Rep2

source_name: D1 sgMyc


title: monocultured HMVEC DM control, biological replicate 1

description: Gene expression array

value: reference RNA


title: cocultured SAEC at time 24 hr, biological replicate 1

description: Gene expression array


title: monocultured HMVEC DM control, biological replicate 2

description: Gene expression array


title: cocultured SAEC at time 24 hr, biological replicate 2

description: Gene expression array


title: cocultured SAEC at time 6 hr, biological replicate 4

description: Gene expression array


title: sgGFP control for D1 sgMyc experiment Rep1


title: Breast tumour T106

description: Human breast tumour

value: Female


title: Breast tumour T108

description: Human breast tumour


title: D1 sgMyc Rep1

value: embryonic stem cell


title: T_30_2

source_name: K562_4sU (Carbosynth) labeling for 30min

value: 500 µM 4-thiouracil (4sU, Carbosynth) for 30min


title: cocultured SAEC at time 24 hr, biological replicate 5

description: Gene expression array


title: cocultured SAEC at time 6 hr, biological replicate 5

description: Gene expression array


title: cocultured SAEC at time 6 hr, biological replicate 2

description: Gene expression array


title: T_30_1


title: cocultured SAEC at time 24 hr, biological replicate 4

description: Gene expression array


title: D0 sgMyc Rep1

source_name: D0 sgMyc


title: sgGFP control for D0 sgMyc experiment Rep2

source_name: sgGFP control for D0 sgMyc experiment


title: D0 sgMyc Rep2


title: cocultured SAEC at time 6 hr, biological replicate 3

description: Gene expression array


title: Breast tumour T1

description: Human breast tumour


title: sgGFP control for D1 sgDnmt1 experiment Rep2

value: Yes


title: Breast tumour T101

description: Human breast tumour


title: cocultured SAEC at time 6 hr, biological replicate 1

description: Gene expression array

value: 6 hr


title: Breast tumour T105

description: Human breast tumour


title: T_15_2

source_name: K562_4sU (Carbosynth) labeling for 15min

value: 500 µM 4-thiouracil (4sU, Carbosynth) for 15min


title: cocultured SAEC DM control, biological replicate 5

description: Gene expression array

value: cocultured SAEC DM control


title: T_20_1

source_name: K562_4sU (Carbosynth) labeling for 20min

value: 500 µM 4-thiouracil (4sU, Carbosynth) for 20min


title: sgGFP control for D0 sgMyc experiment Rep1

value: No


title: T_20_2

value: erythroleukemia cells


title: T_10_2

source_name: K562_4sU (Carbosynth) labeling for 10min

value: 500 µM 4-thiouracil (4sU, Carbosynth) for 10min

value: RNA-seq


title: T_15_1

value: Total fragmented RNA


title: D1 2C+ cells Rep1

source_name: D1 2C+ cells


title: D1 2C+ cells Rep2


title: T_10_1


title: D1 2C- cells Rep2

source_name: D1 2C- cells


title: T_05_2

source_name: K562_4sU (Carbosynth) labeling for 5min

value: 500 µM 4-thiouracil (4sU, Carbosynth) for 5min

value: replicate 2


title: cocultured SAEC DM control, biological replicate 4

description: Gene expression array

source_name: reference RNA


title: cocultured SAEC DM control, biological replicate 3

description: Gene expression array


title: cocultured HMVEC at time 24 hr, biological replicate 4

description: Gene expression array

value: cocultured HMVEC

value: 24 hr


title: T_02_2

source_name: K562_4sU (Carbosynth) labeling for 2min

value: 500 µM 4-thiouracil (4sU, Carbosynth) for 2min


title: cocultured SAEC DM control, biological replicate 6

description: Gene expression array

value: reference RNA


title: D0 2C- cells Rep2

source_name: D0 2C- cells

value: embryonic stem cell


title: D0 2C- cells Rep1


title: D1 2C- cells Rep1

value: Yes


title: cocultured HMVEC at time 24 hr, biological replicate 5

description: Gene expression array


title: cocultured HMVEC at time 24 hr, biological replicate 3

description: Gene expression array


title: cocultured HMVEC at time 24 hr, biological replicate 1

description: Gene expression array


title: cocultured SAEC DM control, biological replicate 1

description: Gene expression array


title: T_02_1

value: replicate 1


title: cocultured HMVEC at time 24 hr, biological replicate 2

description: Gene expression array


title: T_05_1


title: cocultured HMVEC at time 6 hr, biological replicate 6

description: Gene expression array

value: 6 hr


title: L_60_2

value: 500 µM 4-thiouracil (4sU, Carbosynth) for 60min

value: TT-seq (Schwalb et al., 2016)

value: 4sU-labeled RNA


title: cocultured SAEC DM control, biological replicate 2

description: Gene expression array

value: cocultured SAEC DM control


title: cocultured HMVEC at time 6 hr, biological replicate 5

description: Gene expression array


title: cocultured HMVEC at time 6 hr, biological replicate 4

description: Gene expression array


title: cocultured HMVEC at time 6 hr, biological replicate 3

description: Gene expression array


title: cocultured HMVEC DM control, biological replicate 4

description: Gene expression array

value: cocultured HMVEC DM control


title: cocultured HMVEC at time 24 hr, biological replicate 6

description: Gene expression array


title: cocultured HMVEC at time 6 hr, biological replicate 2

description: Gene expression array


title: cocultured HMVEC DM control, biological replicate 5

description: Gene expression array


title: cocultured HMVEC at time 6 hr, biological replicate 1

description: Gene expression array


title: cocultured HMVEC DM control, biological replicate 6

description: Gene expression array


title: cocultured HMVEC DM control, biological replicate 3

description: Gene expression array


title: cocultured HMVEC DM control, biological replicate 2

description: Gene expression array


title: 24-3: 229R_rep3

city: Harbin

first: Wu

last: Pengfei

state: Hei Longjiang

address: No.246, Xuefu Road, Nangang District

department: Department of Neurosurgery, The Second Affiliated Hospital

country: China

institute: Harbin medical university

description: lncRNA expression in temozolomide-resistant glioblastoma cell

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: 229R, replicate 3

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM)/F12 with 10% fetal bovine serum (Gibco, USA) and at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: LN229 cells were seeded in 96 well plates with 6000 per hole and the half maximal inhibitory concentration (IC50) of TMZ was determined. Then, TMZ was added to the cell culture medium with IC50 1/50 concentration (0.83±0.26μM) to culture LN229 cells in 6 well plates. After cells grew stably, the drug dose was increased in multiples. Each dose was maintained for 15 days to the end of the fifth month. Induced TMZ-resistant cells were named as 229R.

tag: tissue

value: Glioblastoma cell

value: Temozolomide-resistant LN229


title: Input_KO_2

city: Houston

first: Daisuke

last: Nakada

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

library_source: genomic

data_processing:
Basecalling was performed using Illumina’s CASAVA software.
Reads were trimmed for quality using Trimmomatic (v 0.36).
Trimmed reads were mapped to mm10 using Bowtie2 (version 2.2.6).
CPM normalized coverage of mapped reads was computed, and bedGraph files generated, using BedTools (genomecov; version 2.26.0).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.CPM.bedgraph: bedGraphs containing CPM normalized reads.

source_name: Bmi1-deficient MSC cells

extract_protocol:
10,000 Bmi1-deficient MSCs and Control MSCs were sorted and treated with MNase, histone-DNA complexes were isolated with antibody.
ChIP DNA were purified for end repair, adaptor ligation and amplification using a NEB Ultra II library preparation kit following the manufacturer’s protocols (New England Biolabs, Ipswich, MA).

treatment_protocol: To study the role of Bmi1 in MSC function, we conditionally deleted Bmi1 in MSCs using Prx1-Cre. MSCs from Prx1-Cre; Bmi1fl/fl mice and control mice (Bmi1fl/fl) were sorted for ChIP-seq experiments.

tag: strain/background

tag: genotype/variation

value: Bmi1-deficient (Prx1-Cre; Bmi1fl/fl)

value: Bone marrow mesenchymal stromal cells

tag: chip antibody


title: Input_WT_1

source_name: Ctrl MSC Cells

value: Control (Bmi1fl/fl)


title: L_30_2

value: erythroleukemia cells

value: 500 µM 4-thiouracil (4sU, Carbosynth) for 30min

value: replicate 2


title: H3K27me3_KO_3


title: L_60_1

source_name: K562_4sU (Carbosynth) labeling for 60min


title: L_30_1


title: Input_KO_1


title: L_20_1

value: 500 µM 4-thiouracil (4sU, Carbosynth) for 20min


title: Input_WT_3


title: H3K27me3_KO_1


title: H3K27me3_KO_2


title: Input_WT_2


title: Input_KO_3


title: H3K27me3_WT_3


title: H3K27me3_WT_2


title: L_15_2

value: 500 µM 4-thiouracil (4sU, Carbosynth) for 15min


title: H2Aubi_KO_3


title: L_15_1

value: replicate 1


title: H3K27me3_WT_1


title: L_20_2


title: cfDNA19

city: NanJing

first: Jian

last: Wu

state: Jiangsu

address: Sipailou 2#, Sipailou 2#

institute: Southeast University

data_processing:
Library strategy: SALP-seq
The raw reads data were separated according to the barcode using a homemade Perl scripts.
The constant sequence (19 bp) and barcode (6 bp) sequences were removed from the 5ʹ end of the pair-end sequencing reads 2 then mapped to human genome (hg19) using Bowtie2 (version 2.2.6).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

source_name: Cell free DNA

extract_protocol:
The plasma was separated from whole blood, then cell free DNA was isolated with the Plasma Circulating DNA Kit (TIANGEN, DP339).
The denatured cell free DNA was ligated with variant single strand adaptors. Then elongated, purified with Ampure XP beads and ligated with barcoded T overhanging adaptors. After purified with Ampure XP beads, amplification was performed with Illumina compatible primers.

value: blood

tag: tissue compartment

value: plasma

tag: sequenced molecule

value: Cell free DNA

tag: condition

value: Healthy people


title: cfDNA20


title: cfDNA18


title: H2Aubi_KO_2

tag: cell type


title: H2Aubi_KO_1


title: 24-2: 229R_rep2

source_name: 229R, replicate 2


title: cocultured HMVEC DM control, biological replicate 1

description: Gene expression array

tag: biological replicate

tag: reference

value: reference RNA


title: H2Aubi_WT_3


title: L_10_2

tag: cell line

value: 500 µM 4-thiouracil (4sU, Carbosynth) for 10min

value: TT-seq (Schwalb et al., 2016)

value: 4sU-labeled RNA


title: cfDNA17


title: L_10_1


title: 24-1: 229R_rep1

source_name: 229R, replicate 1

value: Glioblastoma cell

value: Temozolomide-resistant LN229


title: 03-2: LN229_rep2

description: lncRNA expression in parental glioblastoma cell

source_name: LN229, replicate 2

value: Parental LN229


title: H2Aubi_WT_2

value: Control (Bmi1fl/fl)

value: Bone marrow mesenchymal stromal cells


title: cfDNA16

value: Esophageal cancer patient post-operation


title: 03-3: LN229_rep3

source_name: LN229, replicate 3


title: L_05_2

value: erythroleukemia cells

value: 500 µM 4-thiouracil (4sU, Carbosynth) for 5min

value: replicate 2


title: H2Aubi_WT_1


title: cfDNA15

value: blood


title: 03-1: LN229_rep1

source_name: LN229, replicate 1


title: L_05_1

value: replicate 1


title: cfDNA14

value: plasma

value: Cell free DNA


title: L_02_2

value: 500 µM 4-thiouracil (4sU, Carbosynth) for 2min


title: KO_MSC_3

description: processed data file: ReadCounts_FPKM_Symbol.csv

data_processing:
Basecalling was performed using Illumina’s CASAVA software.
Reads were quality trimmed using Trimmomatic (v 0.36).
Trimmed reads were mapped to mm10 using STAR (v2.5.1a).
FPKM matrix was generated using DESeq2 (version 1.18.1), from gene counts calculated using SummarizeOverlaps (Bioconductor package: GenomicRanges; version 1.30.3) with the UCSC knownGenes table (2018-04-11) as the reference annotation.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: ReadCounts_FPKM_Symbol.csv: Comma-delimited file containing FPKM values.

extract_protocol:
Cell were sorted into Trizol and RNA were extracted using RNeasy MiniElute Cleanup kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions.
cDNA libraries were generated using the Smart-seq2 protocol as described previously. Sequencing libraries were generated from 250 pg of amplified cDNA using Nextera XT kit according to the manufacturer's instructions. Barcoded libraries were purified and sequenced on a HiSeq2500 platform.

treatment_protocol: Bmi1-deficient MSCs and Control MSCs were isolated from Prx1-Cre; Bmi1fl/fl mice and control mice (Bmi1fl/fl).

value: Bmi1-deficient (Prx1-Cre; Bmi1fl/fl)


title: cfDNA13


title: PeriparturientNeu,C+7, rep3

city: Greensboro

first: Mulumebet

last: Worku

state: North Carolina

address: 1601 E market Street

department: Animal Sciences

institute: North Carolina Agricultural and Technical State University

description:
NeuC+7_003
Gene expression seven days post-calving cow neutrophils

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Bos taurus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA isolation was done using trizol according to manufacturer’s instruction (Ambion®). The appropriate precautions were used to avoid RNase contamination throughout in the entire procedure. Half (0.5) mL of 100% of isopropanol was added to each tube 114 containing the homogenized cell pellets in the TRIzol® Reagent and incubated at room temperature for 10 minutes. It was then centrifuged at 12,000× g for 10 minutes at 4 °C. Supernatant was removed from the tube leaving only the RNA pellet. The pellet was washed with 1 mL of 75% ethanol. The sample was vortexed briefly, and centrifuged at 7500×g for 5 minutes at 4°C. Supernatant was discarded and washed. RNA pellet was air dried for 10 minutes. The RNA pellet was resuspended in 30 µl RNase free water by passing the solution up and down several times through a pipette tip. RNA was stored at –80 °C. RNA concentration was measured using a Nano-Drop ND-1000 spectrophotometer (Nano-Drop Technologies). The purity of RNA (A260/A280) for all samples was above 1.80. The quality of RNA was evaluated using the Agilent Bioanalyzer system (Agilent 2100 Bioanalyzer, Agilent Technologies). The average RNA integrity number (RIN) value for samples was 9.0 ± 0.5

tag: breed

value: Holstein Friesian

tag: Sex

value: female

tag: status

value: periparturient cows

value: 7 d relative to actual calving date

value: Blood sampled from the jugular vein

value: Neutrophils


title: PeriparturientNeu,C+7, rep4

description:
NeuC+7_004
Gene expression seven days post-calving cow neutrophils

tag: time point


title: cfDNA12


title: L_02_1

tag: treatment

tag: method protocol

value: TT-seq (Schwalb et al., 2016)

tag: replicate

value: 4sU-labeled RNA


title: C9-6

city: Manchester

first: Huw

middle: Batten

last: Thomas

state: Greater Manchester

address: Dover Street

department: Biological Sciences

country: United Kingdom

institute: University of Manchester

data_processing:
Low quality bases and adpeter sequences were trimmed using Trimmomatic
Reads aligned to GRCh38 genome or transcriptome (Gencode v28 human gene annotation) using single pass mode of STAR aligner (v2.5.3a)
Differential expressio analysis was conducted using Bioconductor DESeq2 v1.20.0 using default parameters
rMATS v.4.0.2 was used to identify mis-splicing events filtering for events with a p-value <0.05 and FDR < 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited file of read counts in all samples and rMATS txt output files

source_name: HEK-293 cell line

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS @37°C +5% CO2

extract_protocol:
Total RNA was extracted using TRI-Reagent(r) and purified using Rneasy column purification kit (Qiagen), including a Dnase digestion step.
Libraries were constructed using standard illumina protocols

treatment_protocol: Cells were edited  using the D10A cas9 nickase mutant in a CRISPR cas9 genome editing strategy targeting EFTUD2 exon 4

value: CRISPR knock-down


title: cfDNA11

tag: tissue

value: Esophageal cancer patient pre-operation


title: KO_MSC_1

tag: strain/background

tag: genotype/variation

value: Bone marrow mesenchymal stromal cells


title: PeriparturientNeu,C+7, rep2

description:
NeuC+7_002
Gene expression seven days post-calving cow neutrophils


title: Ctrl_MSC_3

value: Control (Bmi1fl/fl)


title: PeriparturientNeu,C-14, rep4

description:
NeuC-14_004
Gene expression fourteen days pre-calving cow neutrophils

value: -14 d relative to expected calving date


title: PeriparturientNeu,C+7, rep1

description:
NeuC+7_001
Gene expression seven days post-calving cow neutrophils


title: C9-5


title: PeriparturientNeu,C-14, rep3

description:
NeuC-14_003
Gene expression fourteen days pre-calving cow neutrophils


title: KO_MSC_2


title: PeriparturientNeu,C-14, rep2

description:
NeuC-14_002
Gene expression fourteen days pre-calving cow neutrophils


title: Ctrl_MSC_2


title: C9-4


title: cfDNA10

value: blood

tag: tissue compartment

value: plasma


title: cfDNA9

tag: sequenced molecule

value: Cell free DNA


title: C9-3


title: Ctrl_MSC_1


title: cfDNA8

tag: condition


title: C9-1


title: cfDNA6


title: cfDNA5


title: WT-5

value: wild type


title: cfDNA4


title: H3K27me3_scRNAseq_HBCx-22-TamR

city: Paris

first: Kevin

last: Grosselin

address: 10 rue Vauquelin

department: CBI

country: France

institute: ESPCI Paris

data_processing:
scRNA-seq: Single-cell sequencing files were processed using the Cell Ranger Single Cell Software Suite (v1.3.1) to perform quality control, sample de-multiplexing, barcode processing, and single-cell 3′ gene counting. Samples were first demultiplexed and then aligned to the UCSC mouse (mm10) and human (hg19) transcriptome and genome using "cellranger mkfastq" with default parameters. UMI were counted using "cellrangercount".
Genome_build: mm10, hg19
Supplementary_files_format_and_content: tab-delimited text files include read count for each cell in genes (scRNA-seq, TAR of MTX and TSV) or genomic bins (scChIP-seq)

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

growth_protocol: Female Swiss nude mice were purchased from Charles River Laboratories and maintained under specific pathogen-free conditions. Their care and housing were in accordance with institutional guidelines and the rules of the French Ethics Committee (project authorization no. 02163.02). A PDX model of luminal breast cancer (HBCx-22) was previously established at Institut Curie from untreated early-stage luminal breast cancer with informed consent from the patient (Cottu et al, Breast Cancer Research Treatment, 2012). Acquisition of a resistant phenotype for a derivative of HBCx-22, HBCx-22-TamR, was previously established and maintained as previously described in Cottu et al, Clinical Cancer Research 2014. A PDX from a residual triple negative breast cancer post neo-adjuvant chemotherapy (HBCx-95) was previously established at Institut Curie with informed consent from the patient (Marangoni et al, Clinical Cancer Research, 2018). HBCx-95 xenografts were treated with Capecitabine (Xeloda, Roche Laboratories) orally at a dose of 540 mg/kg/day, 5 days a week for 6 weeks. Relative tumor volumes (RTV, mm^3) were calculated as previously described (Marangoni et al, Clinical Cancer Research, 2007). Mice with recurrent tumors were treated for a second round of Capecitabine when PDX reached a volume of over 200 mm^3. Mouse which did not respond to Capecitabine and PDX specimen was extracted at 1100mm^3 and tagged as HBCx-95-CapaR.

extract_protocol:
Prior scChIP-seq and  scRNA-seq, PDX were digested at 37°C for 2h with a cocktail of Collagenase I (Roche, # 11088793001) and Hyaluronidase (Sigma, # H3506) as previously described (Petit et al, Lab Investigation 2013). Cells were further individualized at 37°C using a cocktail of 0.25% trypsin/Versen (ThermoFisher Scientific, #15040-033), Dispase II (Sigma, # D4693) and Dnase I (Roche, # 11284932001). Red Blood Cell lysis buffer (ThermoFisher Scientific, # 00-4333-57) was then added to degrade red blood cells. To increase the viability of the cell suspension, we removed dead cells using a Dead Cell Removal kit (Miltenyi Biotec). Cells were re-suspended in PBS/0.04% BSA (ThermoFisher Scientific, # AM2616).
scRNA-seq libraries were prepared with Chromium Single cell 3' reagent v2 kit according to manufacturer's recommendations (10X Genomics).

value: mouse PDX human tumor


title: WT-4


title: H3K27me3_scRNAseq_HBCx-22

description: scRNA-seq libraries were prepared with Chromium Single cell 3' reagent v2 kit according to manufacturer's recommendations (10X Genomics).


title: WT-3


title: cfDNA2


title: WT-2


title: H3K27me3_scRNAseq_HBCx-95-CapaR


title: H3K27me3_scRNAseq_HBCx-95


title: cfDNA7


title: cfDNA1


title: siELIT-1 #3_TGF-β(+)

city: Hamamatsu

first: Satoshi

last: Sakai

state: Shizuoka

address: 1-20-1 Handayama, Higashi-ku

department: Virology and Parasitology

country: Japan

institute: Hamamatsu University School of Medicine

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: siELIT-1, #3, TGF-β treatment for 48h

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum and penicillin/streptomycin.

extract_protocol: The total RNA was isolated from cells using RNeasy Mini kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Huh7 cells were transfected with siRNAs (siCtrl #2 scramble, #3 scramble, siELIT-1 #2, or siELIT-1 #3). At 24 h after the first  transfection, cells were transfected with siRNAs, again. At 6 h after the second transfection, cells were  treated with or without 10 ng/mL TGF-βfor 48 h.

tag: derived tissue

value: Liver Carcinoma

tag: transfection

value: siELIT-1 #3

value: TGF-β(+)


title: C9-2


title: cfDNA3


title: siCtrl (#3 Scramble)_TGF-β(+)

source_name: siCtrl, #3_Scramble, TGF-β treatment for 48h

value: siCtrl (#3 Scramble)


title: WT-6


title: siCtrl (#2 Scramble)_TGF-β(+)

source_name: siCtrl, #2_Scramble, TGF-β treatment for 48h

value: siCtrl (#2 Scramble)


title: siELIT-1 #2_TGF-β(+)

source_name: siELIT-1, #2, TGF-β treatment for 48h

value: siELIT-1 #2


title: C2_S50_L004

status: Public on Apr 11 2019

city: Lincoln

first: Kyle

last: Harrison

state: Nebraska

address: 1700 E Campus Mall

department: Entomology

institute: USDA-ARS

data_processing:
Libraries were multiplexed and sequenced on the Illumina PE HiSeq 2500 v4 platform. Sequence cluster identification, quality prefiltering, base calling, and uncertainty assessment were done in real time using Illumina’s HCS 2.2.38 and RTA 1.18.61 software with default parameter settings.
Reads were mapped with TopHat 2.2.1 to the S. lycopersicum genome (vSL3.0) and the vITAG3.20 annotation. Libraries were normalized by hits to known transcripts in the vITAG3.20 S. lycopersicum annotation.
Expression levels of control and psyllid-primed samples were compared using Cuffdiff2 with a Benjamini–Hochberg false discovery rate correction for calculating adjusted q-values.
Genome_build: S. lycopersicum genome (vSL3.0) and the vITAG3.20
Supplementary_files_format_and_content: Tab-delimited txt file containing gene fpkm and DEG q-values (Jone  is J1-2_S53_L004 and J1-3_S54_L004)

organism: Solanum lycopersicum

source_name: Control tomato

growth_protocol: Lso-negative tomato psyllids were maintained on tomato plants under a 16:8 h (Light:Dark) photoperiod at room temperature (24±2°C). The absence of Lso in these psyllid colonies was tested monthly and confirmed using diagnostic PCRs.

extract_protocol:
Seven days after infestation, caged tomato leaves were removed with a sterile razor blade. Three weeks later, the top-most, fully-developed leaf was taken from each plant and immediately flash-frozen in liquid nitrogen. Total RNA extraction was performed using the Plant RNeasy Mini Kit following the manufacturer’s protocol.
For transcriptomic sequencing, libraries were developed using the TruSeq RNA Library Prep Kit v2 following the manufacturer’s protocol.
Sequence cluster identification, quality prefiltering, base calling, and uncertainty assessment were done in real time using Illumina’s HCS 2.2.38 and RTA 1.18.61 software with default parameter settings.

treatment_protocol: Psyllid infestation of tomato plants was performed when plants were six weeks old. Leaves branching below the apical meristem were caged with a small mesh bag (amazon.com). The bag either had no psyllids (control plants) or three adult male psyllids (psyllid-primed plants). There were five plants in each treatment.

value: Control

value: leaf

tag: age

value: 21 days after infestation


title: J1-3_S54_L004

source_name: Psyllid-primed tomato

value: Psyllid-primed


title: J1-2_S53_L004


title: E6_2

city: Haikou

first: Feng

last: Pang

address: Renmin Road 58

institute: Hainan University

data_processing:
Single-end sequencing on Illumina HiSeq 2500
ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Differential expression of miRNAs based on normalized deep-sequencing counts was analyzed by selectively using, Student t test . The significance threshold was set to be 0.01 and 0.05 in each test

source_name: NIH/3T3 cells expressing BPV-13 E6

extract_protocol:
Animal Tissue RNA Purification Kit (Product #TRK-1002; LC Sciences, Hangzhou, China).
TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA)

value: embryo

tag: cell line

value: NIH/3T3 cells expressing BPV-13 E6

tag: cell passages

tag: cell type

value: fibroblast


title: E6_3


title: siCtrl (#2 Scramble)_TGF-β(-)

source_name: siCtrl, #2_Scramble, without TGF-β treatment

value: TGF-β(-)


title: E6_1


title: Bj35

first: Tatsuya

last: Ohhata

address: Higashi-ku Handayama 1-20-1

department: Department of Molecular Biology

source_name: HBV genome (Bj35) containing vector, transfectant

treatment_protocol: HBV-replicating cells were prepared as follows; Huh7 cells were transfected with the each episomal HBV expression vectors, where the 1.24-fold HBV genome was inserted into pEBMulti-Puro, followed by maintaining in the medium in the presence of 5 μg/mL puromycin for 14 days.

value: HBV genome (Bj35) containing vector


title: PeriparturientNeu,C-14, rep1

description:
NeuC-14_001
Gene expression fourteen days pre-calving cow neutrophils

tag: breed

value: Holstein Friesian

tag: Sex

value: female

tag: status

value: periparturient cows

value: -14 d relative to expected calving date

value: Blood sampled from the jugular vein

value: Neutrophils


title: Ae

source_name: HBV genome (Ae) containing vector, transfectant

value: HBV genome (Ae) containing vector

value: Liver Carcinoma


title: Bj56

source_name: HBV genome (Bj56) containing vector, transfectant

value: HBV genome (Bj56) containing vector


title: NH_GFP_3

source_name: NIH/3T3 cells expressing GFP

value: NIH/3T3 cells expressing GFP


title: pEB_1

source_name: Empty vector transfectant, replicate1

value: Empty vector


title: WT-1

value: wild type


title: NH_GFP_2

value: embryo


title: C1_S49_L004

tag: treatment

value: Control

value: leaf

value: 21 days after infestation


title: pEB_2

source_name: Empty vector transfectant, replicate2


title: Gfap-2_66

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

description:
hGFAP-2_1/hGFAP-2_67(total 61)
hGFAP-gfp c1 P3-P6 expression profile.txt.gz

data_processing:
Fastq files were mapped to Mouse Genome(mm10) and generate TPM/FPKM/Counts value by RSEM using default settings
Tab-delimited table of TPM from RSEM in each cell

source_name: cerebral cortex

extract_protocol: GFP+ single cells were prepared using the C1 Single-Cell Auto Prep System (Fluidigm) according to the manufacturer’s instructions

treatment_protocol: P1-P6 GFP+ pups are euthanized one the ice, decapitated, and the brain was immediately removed and submerged in fresh ice-cold HBSS-HEPES(catalog), cortices were carefully dissected and minced by blade. The tissue pieces were incubated with 3 ml of TrypLE 5X solution(catalog) for 10 min in 37 incubator following by gentle trituration through Pasteur pipettes with polished tip for ten times, filtered the suspension by 40mm strainer, centrifuge at 1300rpm to get the single cell pellet. Collect the GFP+ alive cell by excluding the population of GFP- and 7-AAD+ (catalog) death cells performed on MoFloXDP (Beckman Coulter).

tag: genotype

value: hGFAP normal

tag: developmental stage

tag: strain

value: hGFAP-gfp


title: Gfap-2_67

treatment_protocol: P1-P6 GFP+ pups are euthanized one the ice, decapitated, and the brain was immediately removed and submerged in fresh ice-cold HBSS-HEPES(catalog), cortices were carefully dissected and minced by blade. The tissue pieces were incubated with 3 ml of TrypLE


title: Gfap-2_61


title: Gfap-2_64


title: Gfap-2_7


title: Gfap-2_59


title: Gfap-2_58


title: Gfap-2_65


title: Gfap-2_9


title: Gfap-2_62


title: Gfap-2_63


title: Gfap-2_60


title: Gfap-2_8


title: Gfap-2_6


title: NH_GFP_1

tag: tissue

value: fibroblast


title: Gfap-2_56


title: Gfap-2_55


title: Gfap-2_54


title: Gfap-2_51


title: Gfap-2_50


title: Gfap-2_48


title: Gfap-2_5


title: Gfap-2_46


title: Gfap-2_49


title: Gfap-2_47


title: Gfap-2_45


title: Gfap-2_41


title: Gfap-2_43


title: Gfap-2_40


title: Gfap-2_4


title: Gfap-2_39


title: Gfap-2_35


title: Gfap-2_53


title: Gfap-2_34


title: Gfap-2_28


title: Gfap-2_32


title: Gfap-2_3


title: Gfap-2_24


title: Gfap-2_31


title: Gfap-2_26


title: Gfap-2_25


title: Gfap-2_38


title: Gfap-2_37


title: Gfap-2_33


title: Gfap-2_2


title: Gfap-2_21


title: Gfap-2_18


title: Gfap-2_44


title: Gfap-2_17


title: Gfap-2_16


title: Gfap-2_19


title: Gfap-2_14


title: Gfap-2_27


title: Gfap-2_36


title: Gfap-2_13


title: Gfap-2_23


title: Gfap-2_11


title: Gfap-2_12


title: Gfap-2_20


title: Gfap-2_22


title: Gfap_9

description:
hGFAP_1/hGFAP_59(total 49)
hGFAP-gfp c1 P3-P6 expression profile.txt.gz


title: Gfap_60


title: Gfap_55


title: Gfap_50


title: Gfap_52


title: Gfap_56


title: Gfap_8


title: Gfap_6


title: Gfap_61


title: Gfap_7


title: Gfap_48


title: Gfap_47


title: Gfap-2_10


title: Gfap_53


title: Gfap_5


title: Gfap_45


title: Gfap_51


title: Gfap_57


title: Gfap_49


title: Gfap_43


title: Gfap-2_1


title: Gfap_40


title: Gfap_39


title: Gfap_32


title: Gfap_3


title: Gfap_36


title: Gfap_44


title: Gfap_31


title: Gfap_34


title: Gfap_33


title: Gfap_35


title: Gfap_24


title: Gfap_21


title: Gfap_18


title: Gfap_27


title: Gfap_14


title: Gfap_2


title: Gfap_17


title: Gfap_15


title: Gfap_16


title: Gfap_4


title: Gfap_10


title: Gfap_1


title: Gfap_26


title: Gfap_20


title: Pdgfra-2_9

description:
Pdgfra-2_1/Pdgfra-2_60 (total 60)
PDGFRa-gfp c1 P3-P6 expression profile.txt.gz

value: PDGFRa normal


title: Pdgfra-2_59


title: Pdgfra-2_7


title: Gfap_22


title: Gfap_29


title: Pdgfra-2_8


title: Gfap_23


title: Pdgfra-2_55


title: Pdgfra-2_6


title: Pdgfra-2_51


title: Pdgfra-2_53


title: Pdgfra-2_60


title: Pdgfra-2_54


title: Pdgfra-2_56


title: Pdgfra-2_58


title: Pdgfra-2_57


title: Pdgfra-2_52


title: Pdgfra-2_49


title: Pdgfra-2_5


title: Pdgfra-2_50


title: Pdgfra-2_48


title: Pdgfra-2_46


title: Pdgfra-2_47


title: Pdgfra-2_45


title: Pdgfra-2_44


title: Gfap_19


title: Pdgfra-2_43


title: Pdgfra-2_42


title: Pdgfra-2_41


title: Pdgfra-2_40


title: Pdgfra-2_38


title: Pdgfra-2_4


title: Pdgfra-2_39


title: Pdgfra-2_37


title: Pdgfra-2_33


title: Pdgfra-2_36


title: Pdgfra-2_31


title: Pdgfra-2_35


title: Pdgfra-2_29


title: Pdgfra-2_27


title: Pdgfra-2_34


title: Pdgfra-2_28


title: Pdgfra-2_26


title: Pdgfra-2_32


title: Pdgfra-2_3


title: Pdgfra-2_25


title: Pdgfra-2_24


title: Pdgfra-2_30


title: Pdgfra-2_23


title: Pdgfra-2_21


title: Pdgfra-2_20


title: Pdgfra-2_22


title: Pdgfra-2_2


title: Pdgfra-2_19


title: Pdgfra-2_18


title: Pdgfra-2_15


title: Pdgfra-2_14


title: Pdgfra-2_16


title: Pdgfra-2_17


title: Pdgfra-2_13


title: Pdgfra-2_12


title: Pdgfra-2_11


title: Pdgfra-2_10


title: Pdgfra_7

description:
Pdgfra_1/Pdgfra_60 (total 53)
PDGFRa-gfp c1 P3-P6 expression profile.txt.gz


title: Pdgfra-2_1


title: Pdgfra_56


title: Pdgfra_8


title: Pdgfra_57


title: Pdgfra_58


title: Pdgfra_9


title: Pdgfra_59


title: Pdgfra_48


title: Pdgfra_60


title: Pdgfra_6


title: Pdgfra_46


title: Pdgfra_43


title: Pdgfra_5


title: Pdgfra_44


title: Gfap_13


title: Pdgfra_47


title: Pdgfra_40


title: Pdgfra_4


title: Pdgfra_35


title: Pdgfra_36


title: Pdgfra_37


title: Pdgfra_42


title: Pdgfra_39


title: Pdgfra_34


title: Pdgfra_32


title: Pdgfra_45


title: Pdgfra_29


title: Pdgfra_33


title: Pdgfra_24


title: Pdgfra_27


title: Pdgfra_30


title: Pdgfra_2


title: Pdgfra_3


title: Pdgfra_18


title: Pdgfra_28


title: Pdgfra_31


title: Pdgfra_19


title: Pdgfra_41


title: Pdgfra_15


title: Pdgfra_23


title: Pdgfra_26


title: Pdgfra_17


title: Pdgfra_16


title: Pdgfra_12


title: Pdgfra_11


title: Pdgfra_25


title: Pdgfra_21


title: Pdgfra_13


title: Pdgfra_10


title: Pdgfra_1


title: Pdgfra_20


title: Pdgfra_14


title: P5-6 hGFAP-GFP

description: total 2000

data_processing:
library strategy: Drop-seq
Raw sequence data was first filtered to remove all read pairs with a barcode base quality of less than 10. The second read (50 or 60 bp) was then trimmed at the 5’ end to remove any TSO adapter sequence,  and at the 3’ end to remove polyA tails of length 6 or greater.
Then aligned reads to mm10 reference by STAR with default settings.
Uniquely mapped reads were grouped by cell barcode. To digitally count gene transcripts, a list of UMIs in each gene, within each cell, was assembled, and UMIs within ED = 1 were merged together. The total number of distinct UMI sequences was counted, and this number was reported as the number of transcripts of that gene for a given cell.
Normalize total number of detected UMIs from each gene in each cell to 10,000
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited table of normalized UMIs

extract_protocol:
For single cell RNA-seq of tumor cells, the tumor tissues were digested by TryplE with collagenase Ⅰ, and single cell suspension was treated by Red Blood Cell Lysis Buffer (Sigma, 11814389001). Cells from tumor tissues at dpi 25 were sequenced by drop-seq.
Libraries were prepared with Drop-seq protocol

tag: genotype/variataion

value: hGFAP normal; hGFAP-gfp

value: cerebral cortex


title: Pdgfra_22


title: P1-3 PDGFRa-GFP

description: total 3184

value: PDGFRa normal; PDGFRa-gfp


title: Pdgfra_38


title: 7584088_0_Post whole blood draw, T0, Post-injection

city: Cleveland

first: Mark

middle: R

last: Chance

address: 10900 Euclid Ave

institute: Case Western Reserve University School of Medicine

hyb_protocol: 2 ug of biotin labeled sscDNA probe were hybridized to Affymetrix GeneChip HT HG-U133+ PM plate arrays with modified conditions as described in Allaire et al[PMID:23289891].

scan_protocol: The processed GeneChip plate arrays were scanned using GeneTitan scanner (Affymetrix, Santa Clara, CA).

data_processing: The data were analyzed with the R Bioconductor affy package using RMA normalization.

label: biotin

source_name: Whole blood

label_protocol: Automated sample amplifications and biotin labelings were carried out using the NuGEN Ovation RNA Amplification system V2 (Cat # 3100), Ovation WB reagent (Cat # 1300) and Encore Biotin module (Cat # 4200) (NuGEN Technologies, Inc, San Carlos, CA) according to manufacturer’s recommendations using an Arrayplex automated liquid handler (Beckman Coulter, Indianapolis, IN).

extract_protocol: RNA extractions were completed on Arrayplex (Beckman Coulter, Indianapolis, IN) using Agencourt RNAdvance Blood kit (Part number A35604) according to the manufacturer’s specifications.

treatment_protocol: Subjects were injected with intramuscular IFN-β1a (Avonex®) precisely 12 hours before blood was drawn.

tag: time point

tag: response

value: Indeterminate

tag: ms type

value: CIS

tag: gender

value: M

tag: race

value: White


title: 7584080_0_Post whole blood draw, T0, Post-injection

value: RR

tag: age

value: F


title: 7584088_6_Post whole blood draw, T6, Post-injection


title: 7584083_0_Post whole blood draw, T0, Post-injection


title: 7584083_6_Post whole blood draw, T6, Post-injection


title: 7584084_0_Post whole blood draw, T0, Post-injection


title: 7584080_6_Post whole blood draw, T6, Post-injection


title: 7584071_0_Post whole blood draw, T0, Post-injection


title: 7584071_6_Post whole blood draw, T6, Post-injection


title: 7584060_6_Post whole blood draw, T6, Post-injection

value: Good


title: 7584066_0_Post whole blood draw, T0, Post-injection

value: Poor


title: 7584064_0_Post whole blood draw, T0, Post-injection


title: 7584057_6_Post whole blood draw, T6, Post-injection

value: Hispanic


title: 7584066_6_Post whole blood draw, T6, Post-injection


title: 7584052_6_Post whole blood draw, T6, Post-injection


title: 7584056_0_Post whole blood draw, T0, Post-injection


title: 7584057_0_Post whole blood draw, T0, Post-injection


title: 7584056_6_Post whole blood draw, T6, Post-injection


title: 7584042_6_Post whole blood draw, T6, Post-injection


title: 7584065_6_Post whole blood draw, T6, Post-injection


title: 7584060_0_Post whole blood draw, T0, Post-injection


title: Gfap_12


title: 7584052_0_Post whole blood draw, T0, Post-injection


title: 7584053_0_Post whole blood draw, T0, Post-injection


title: 7584084_6_Post whole blood draw, T6, Post-injection


title: 7584012_6_Post whole blood draw, T6, Post-injection


title: 7584064_6_Post whole blood draw, T6, Post-injection


title: 7584042_0_Post whole blood draw, T0, Post-injection


title: 7584003_6_Post whole blood draw, T6, Post-injection


title: 7584015_6_Post whole blood draw, T6, Post-injection


title: 7584009_6_Post whole blood draw, T6, Post-injection


title: 7584003_0_Post whole blood draw, T0, Post-injection


title: 7584009_0_Post whole blood draw, T0, Post-injection


title: 7584099_0_Post whole blood draw, T0, Post-injection


title: 7584011_6_Post whole blood draw, T6, Post-injection


title: 7584010_6_Post whole blood draw, T6, Post-injection


title: 7584010_0_Post whole blood draw, T0, Post-injection


title: 7584092_0_Post whole blood draw, T0, Post-injection


title: 7584095_6_Post whole blood draw, T6, Post-injection


title: 7584092_6_Post whole blood draw, T6, Post-injection


title: 7584002_6_Post whole blood draw, T6, Post-injection

value: Black


title: 7584096_0_Post whole blood draw, T0, Post-injection


title: 7584090_0_Post whole blood draw, T0, Post-injection


title: 7584065_0_Post whole blood draw, T0, Post-injection


title: 7584002_0_Post whole blood draw, T0, Post-injection


title: 7584015_0_Post whole blood draw, T0, Post-injection


title: 7584011_0_Post whole blood draw, T0, Post-injection


title: 7584012_0_Post whole blood draw, T0, Post-injection


title: 7584099_6_Post whole blood draw, T6, Post-injection


title: 7584053_6_Post whole blood draw, T6, Post-injection


title: 7584096_6_Post whole blood draw, T6, Post-injection


title: 7584095_0_Post whole blood draw, T0, Post-injection


title: 7584090_6_Post whole blood draw, T6, Post-injection


title: 7584085_0_Post whole blood draw, T0, Post-injection


title: 7584048_6_Post whole blood draw, T6, Post-injection


title: 7584085_6_Post whole blood draw, T6, Post-injection


title: 7584049_6_Post whole blood draw, T6, Post-injection


title: 7584072_6_Post whole blood draw, T6, Post-injection


title: 7584074_6_Post whole blood draw, T6, Post-injection


title: 7584046_0_Post whole blood draw, T0, Post-injection


title: 7584067_6_Post whole blood draw, T6, Post-injection


title: 7584041_0_Post whole blood draw, T0, Post-injection


title: 7584072_0_Post whole blood draw, T0, Post-injection


title: 7584021_0_Post whole blood draw, T0, Post-injection


title: 7584039_0_Post whole blood draw, T0, Post-injection


title: 7584074_0_Post whole blood draw, T0, Post-injection


title: 7584049_0_Post whole blood draw, T0, Post-injection


title: 7584067_0_Post whole blood draw, T0, Post-injection


title: 7584046_6_Post whole blood draw, T6, Post-injection


title: 7584039_6_Post whole blood draw, T6, Post-injection


title: 7584048_0_Post whole blood draw, T0, Post-injection


title: 7584032_0_Post whole blood draw, T0, Post-injection


title: 7584020_6_Post whole blood draw, T6, Post-injection


title: 7584038_6_Post whole blood draw, T6, Post-injection


title: 7584032_6_Post whole blood draw, T6, Post-injection


title: 7584041_6_Post whole blood draw, T6, Post-injection


title: 7584018_0_Post whole blood draw, T0, Post-injection


title: 7584038_0_Post whole blood draw, T0, Post-injection


title: 7584021_6_Post whole blood draw, T6, Post-injection


title: 7584020_0_Post whole blood draw, T0, Post-injection


title: 7584025_0_Post whole blood draw, T0, Post-injection


title: 7584025_6_Post whole blood draw, T6, Post-injection


title: 7584018_6_Post whole blood draw, T6, Post-injection


title: 7584098_0_Post whole blood draw, T0, Post-injection


title: 7584087_6_Post whole blood draw, T6, Post-injection


title: 7584082_6_Post whole blood draw, T6, Post-injection


title: 7584091_6_Post whole blood draw, T6, Post-injection


title: 7584087_0_Post whole blood draw, T0, Post-injection


title: 7584079_0_Post whole blood draw, T0, Post-injection


title: 7584008_0_Post whole blood draw, T0, Post-injection


title: 7584091_0_Post whole blood draw, T0, Post-injection


title: 7584097_6_Post whole blood draw, T6, Post-injection


title: 7584098_6_Post whole blood draw, T6, Post-injection


title: 7584097_0_Post whole blood draw, T0, Post-injection


title: 7584081_6_Post whole blood draw, T6, Post-injection


title: 7584094_0_Post whole blood draw, T0, Post-injection


title: 7584082_0_Post whole blood draw, T0, Post-injection


title: 7584078_0_Post whole blood draw, T0, Post-injection


title: 7584008_6_Post whole blood draw, T6, Post-injection


title: 7584094_6_Post whole blood draw, T6, Post-injection


title: 7584077_0_Post whole blood draw, T0, Post-injection


title: 7584081_0_Post whole blood draw, T0, Post-injection


title: 7584079_6_Post whole blood draw, T6, Post-injection


title: 7584076_0_Post whole blood draw, T0, Post-injection


title: 7584077_6_Post whole blood draw, T6, Post-injection


title: 7584078_6_Post whole blood draw, T6, Post-injection


title: 7584073_0_Post whole blood draw, T0, Post-injection


title: 7584073_6_Post whole blood draw, T6, Post-injection


title: 7584070_0_Post whole blood draw, T0, Post-injection


title: 7584069_6_Post whole blood draw, T6, Post-injection


title: 7584070_6_Post whole blood draw, T6, Post-injection


title: 7584069_0_Post whole blood draw, T0, Post-injection


title: 7584076_6_Post whole blood draw, T6, Post-injection


title: 7584068_6_Post whole blood draw, T6, Post-injection


title: 7584058_6_Post whole blood draw, T6, Post-injection


title: 7584061_0_Post whole blood draw, T0, Post-injection


title: 7584059_0_Post whole blood draw, T0, Post-injection


title: 7584051_6_Post whole blood draw, T6, Post-injection


title: 7584068_0_Post whole blood draw, T0, Post-injection


title: 7584051_0_Post whole blood draw, T0, Post-injection


title: 7584062_0_Post whole blood draw, T0, Post-injection


title: 7584061_6_Post whole blood draw, T6, Post-injection


title: 7584045_6_Post whole blood draw, T6, Post-injection


title: 7584062_6_Post whole blood draw, T6, Post-injection


title: 7584043_6_Post whole blood draw, T6, Post-injection


title: 7584050_6_Post whole blood draw, T6, Post-injection


title: 7584059_6_Post whole blood draw, T6, Post-injection


title: 7584050_0_Post whole blood draw, T0, Post-injection


title: 7584047_0_Post whole blood draw, T0, Post-injection


title: 7584044_6_Post whole blood draw, T6, Post-injection


title: 7584058_0_Post whole blood draw, T0, Post-injection


title: 7584036_6_Post whole blood draw, T6, Post-injection


title: 7584044_0_Post whole blood draw, T0, Post-injection


title: 7584034_0_Post whole blood draw, T0, Post-injection


title: 7584043_0_Post whole blood draw, T0, Post-injection


title: 7584034_6_Post whole blood draw, T6, Post-injection


title: 7584036_0_Post whole blood draw, T0, Post-injection


title: 7584035_0_Post whole blood draw, T0, Post-injection


title: 7584035_6_Post whole blood draw, T6, Post-injection


title: 7584047_6_Post whole blood draw, T6, Post-injection


title: 7584040_0_Post whole blood draw, T0, Post-injection


title: 7584040_6_Post whole blood draw, T6, Post-injection


title: 7584033_6_Post whole blood draw, T6, Post-injection


title: 7584033_0_Post whole blood draw, T0, Post-injection


title: 7584031_0_Post whole blood draw, T0, Post-injection


title: 7584024_0_Post whole blood draw, T0, Post-injection


title: 7584029_0_Post whole blood draw, T0, Post-injection


title: 7584031_6_Post whole blood draw, T6, Post-injection


title: 7584014_6_Post whole blood draw, T6, Post-injection


title: 7584019_0_Post whole blood draw, T0, Post-injection


title: 7584023_6_Post whole blood draw, T6, Post-injection


title: 7584019_6_Post whole blood draw, T6, Post-injection


title: 7584016_6_Post whole blood draw, T6, Post-injection


title: 7584024_6_Post whole blood draw, T6, Post-injection


title: 7584006_0_Post whole blood draw, T0, Post-injection


title: 7584017_6_Post whole blood draw, T6, Post-injection


title: 7584017_0_Post whole blood draw, T0, Post-injection


title: 7584005_6_Post whole blood draw, T6, Post-injection


title: 7584001_0_Post whole blood draw, T0, Post-injection


title: 7584023_0_Post whole blood draw, T0, Post-injection


title: 7584014_0_Post whole blood draw, T0, Post-injection


title: 7584016_0_Post whole blood draw, T0, Post-injection


title: 7584004_0_Post whole blood draw, T0, Post-injection


title: 7584007_0_Post whole blood draw, T0, Post-injection


title: 7584005_0_Post whole blood draw, T0, Post-injection


title: 7584029_6_Post whole blood draw, T6, Post-injection


title: 7584088_6_Pre whole blood draw, T6, Pre-injection


title: 7584007_6_Post whole blood draw, T6, Post-injection


title: 7584084_6_Pre whole blood draw, T6, Pre-injection


title: 7584006_6_Post whole blood draw, T6, Post-injection


title: 7584004_6_Post whole blood draw, T6, Post-injection


title: 7584088_0_Pre whole blood draw, T0, Pre-injection


title: 7584001_6_Post whole blood draw, T6, Post-injection


title: 7584071_0_Pre whole blood draw, T0, Pre-injection


title: 7584066_0_Pre whole blood draw, T0, Pre-injection


title: 7584084_0_Pre whole blood draw, T0, Pre-injection


title: 7584066_6_Pre whole blood draw, T6, Pre-injection


title: 7584080_0_Pre whole blood draw, T0, Pre-injection


title: 7584080_6_Pre whole blood draw, T6, Pre-injection


title: 7584057_6_Pre whole blood draw, T6, Pre-injection


title: 7584083_0_Pre whole blood draw, T0, Pre-injection


title: 7584065_6_Pre whole blood draw, T6, Pre-injection


title: 7584056_6_Pre whole blood draw, T6, Pre-injection


title: 7584053_0_Pre whole blood draw, T0, Pre-injection


title: 7584052_0_Pre whole blood draw, T0, Pre-injection


title: 7584064_6_Pre whole blood draw, T6, Pre-injection


title: 7584057_0_Pre whole blood draw, T0, Pre-injection


title: 7584060_0_Pre whole blood draw, T0, Pre-injection


title: 7584042_0_Pre whole blood draw, T0, Pre-injection


title: 7584011_6_Pre whole blood draw, T6, Pre-injection


title: 7584012_0_Pre whole blood draw, T0, Pre-injection


title: 7584065_0_Pre whole blood draw, T0, Pre-injection


title: 7584083_6_Pre whole blood draw, T6, Pre-injection


title: 7584015_0_Pre whole blood draw, T0, Pre-injection


title: 7584015_6_Pre whole blood draw, T6, Pre-injection


title: 7584064_0_Pre whole blood draw, T0, Pre-injection


title: 7584012_6_Pre whole blood draw, T6, Pre-injection


title: 7584056_0_Pre whole blood draw, T0, Pre-injection


title: 7584042_6_Pre whole blood draw, T6, Pre-injection


title: 7584052_6_Pre whole blood draw, T6, Pre-injection


title: 7584071_6_Pre whole blood draw, T6, Pre-injection


title: 7584010_0_Pre whole blood draw, T0, Pre-injection


title: 7584003_0_Pre whole blood draw, T0, Pre-injection


title: 7584011_0_Pre whole blood draw, T0, Pre-injection


title: 7584010_6_Pre whole blood draw, T6, Pre-injection


title: 7584009_0_Pre whole blood draw, T0, Pre-injection


title: 7584002_0_Pre whole blood draw, T0, Pre-injection


title: 7584002_6_Pre whole blood draw, T6, Pre-injection


title: 7584003_6_Pre whole blood draw, T6, Pre-injection


title: 7584099_0_Pre whole blood draw, T0, Pre-injection


title: 7584092_0_Pre whole blood draw, T0, Pre-injection


title: 7584099_6_Pre whole blood draw, T6, Pre-injection


title: 7584095_0_Pre whole blood draw, T0, Pre-injection


title: 7584095_6_Pre whole blood draw, T6, Pre-injection


title: 7584090_0_Pre whole blood draw, T0, Pre-injection


title: 7584096_6_Pre whole blood draw, T6, Pre-injection


title: 7584092_6_Pre whole blood draw, T6, Pre-injection


title: 7584096_0_Pre whole blood draw, T0, Pre-injection


title: 7584090_6_Pre whole blood draw, T6, Pre-injection


title: 7584009_6_Pre whole blood draw, T6, Pre-injection


title: 7584085_0_Pre whole blood draw, T0, Pre-injection


title: 7584074_0_Pre whole blood draw, T0, Pre-injection


title: 7584067_6_Pre whole blood draw, T6, Pre-injection


title: 7584085_6_Pre whole blood draw, T6, Pre-injection


title: 7584074_6_Pre whole blood draw, T6, Pre-injection


title: 7584067_0_Pre whole blood draw, T0, Pre-injection


title: 7584072_6_Pre whole blood draw, T6, Pre-injection


title: 7584072_0_Pre whole blood draw, T0, Pre-injection


title: 7584053_6_Pre whole blood draw, T6, Pre-injection


title: 7584048_0_Pre whole blood draw, T0, Pre-injection


title: 7584038_0_Pre whole blood draw, T0, Pre-injection


title: 7584046_0_Pre whole blood draw, T0, Pre-injection


title: 7584038_6_Pre whole blood draw, T6, Pre-injection


title: 7584049_0_Pre whole blood draw, T0, Pre-injection


title: 7584041_6_Pre whole blood draw, T6, Pre-injection


title: 7584046_6_Pre whole blood draw, T6, Pre-injection


title: 7584049_6_Pre whole blood draw, T6, Pre-injection


title: 7584039_0_Pre whole blood draw, T0, Pre-injection


title: 7584025_6_Pre whole blood draw, T6, Pre-injection


title: 7584041_0_Pre whole blood draw, T0, Pre-injection


title: 7584032_6_Pre whole blood draw, T6, Pre-injection


title: 7584039_6_Pre whole blood draw, T6, Pre-injection


title: 7584032_0_Pre whole blood draw, T0, Pre-injection


title: 7584048_6_Pre whole blood draw, T6, Pre-injection


title: 7584025_0_Pre whole blood draw, T0, Pre-injection


title: 7584020_6_Pre whole blood draw, T6, Pre-injection


title: 7584021_6_Pre whole blood draw, T6, Pre-injection


title: 7584020_0_Pre whole blood draw, T0, Pre-injection


title: 7584021_0_Pre whole blood draw, T0, Pre-injection


title: Head-HFD-3#

city: hangzhou

first: Rui

last: Huang

address: Yu-hang-tang road 866

institute: Zhejiang University

description: high fat food diet

data_processing:
Raw reads were removed adapter contaminants (length < 37 bp) and low-quality bases (N > 10%) to get clean reads.
Index of reference genome was built using Drosophila melanogaster genome (r3). Hisat was used to align clean reads to the fly transcriptome.
Genome_build: Drosophila melanogaster genome (r3)
Supplementary_files_format_and_content: FPKM was used to quantify gene expression for each sample

organism: Drosophila melanogaster

source_name: Head

growth_protocol: Flies were cultured in normal food or high fat diet for 5d.

extract_protocol:
The total RNA was harvested using Trizol reagent, subjected to poly(A) mRNA isolation, cDNA synthesization, library preparation (NEBNext Ultra RNA Library Prep Kit for Illumina, NEB, NEB)
RNA libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: The heads were harvest directly.

value: Oregon-R

value: WT


title: Head-HFD-1#

description: high fat food diet


title: Head-ND-3#

description: normal food diet


title: Head-HFD-2#

description: high fat food diet


title: Head-ND-2#

description: normal food diet


title: 7584008_6_Pre whole blood draw, T6, Pre-injection


title: Head-ND-1#

description: normal food diet


title: AKHR neuron-3#

description: AKHR producing neuron

source_name: neuron

growth_protocol: Flies containing containing cells labeled by mCD8GFP driven from nSyb-AD-AKHR-BD GAL4 lines were cultured in normal food for 5d.

extract_protocol:
The cDNA were sequenced using a modified SMART-seq2 protocol.
The amplified cDNA were sonicated to ~250 bp fragments by the Covaris S2 system and then subjected to end-repair, dA-tail, adaptor ligation, and 12 cycles of PCR amplification using the library preparation kit (NEBNext Ultra II DNA Library Prep Kit, NEB).
single cell RNA-seq

treatment_protocol: After brain dissection, GFP labeled single cells were pooled in situ.

value: AKHR neuron


title: 7584097_6_Pre whole blood draw, T6, Pre-injection


title: 7584018_6_Pre whole blood draw, T6, Pre-injection


title: 7584060_6_Pre whole blood draw, T6, Pre-injection


title: AKHR neuron-2#

description: AKHR producing neuron


title: 7584098_6_Pre whole blood draw, T6, Pre-injection


title: 7584008_0_Pre whole blood draw, T0, Pre-injection


title: 7584018_0_Pre whole blood draw, T0, Pre-injection


title: 7584087_6_Pre whole blood draw, T6, Pre-injection


title: 7584082_6_Pre whole blood draw, T6, Pre-injection


title: 7584081_0_Pre whole blood draw, T0, Pre-injection


title: AKHR neuron-1#

description: AKHR producing neuron


title: 7584079_6_Pre whole blood draw, T6, Pre-injection


title: 7584094_6_Pre whole blood draw, T6, Pre-injection


title: 7584098_0_Pre whole blood draw, T0, Pre-injection


title: met-1_mes-4_rep2

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
The RNA-seq data were mapped to the c.elegans genome (ce10) with the R package QuasR (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html) using the included spliced alignment algorithm SpliceMap. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce10",splicedAlignment=TRUE)". Gene expression was quantified by counting the number of reads that started within any of the exons belonging to a particular gene (WormBase, WS220). The command used to create the count table was qCount(proj,exons,orientation="same"). To compensate for differences in the read depths of the various libraries, each library was normalized to a total of 31.1M reads which represents the average library size. Log2 expression levels were calculated after adding a pseudocount of 8 (y=log2(x+8). This was done to minimize the large differences in expression that would otherwise be caused by genes with small number of counts.
Genome_build: ce10

organism: Caenorhabditis elegans

growth_protocol: 2000 L1 larvae obtained by synchronization after hypochlorite treatment were seeded on RNAi plates with a diameter of 15 cm and 6-fold concentrated bacteria. For each condition, 5 RNAi plates were seeded. After about 60-65 hours at 20°C, plates were washed off with M9 to collect gravid adults and hypochlorite treat them to extract embryos which were let hatch in M9 for 18 hrs and then refed for 2 hrs and 30 min with the corresponding RNAi bacteria

extract_protocol:
L1s were lysed in 750μl Trizol® and snap-frozen in liquid nitrogen. After freeze cracking of the samples by 6 subsequent transfers from liquid nitrogen to 42°C, samples were let vigorously shake 15 min at RT. Total RNA was purified using RNeasy kit (QIAGEN), including DNase treatment.
RNA-seq libraries were obtained using the Illumina ScriptSeq Complete Gold kit according to manufacturer’s guide, starting with 5µg of total RNA as input

treatment_protocol: RNAi bacteria feeding as described above

value: L1 larvae

tag: RNAi


title: 7584087_0_Pre whole blood draw, T0, Pre-injection


title: 7584091_6_Pre whole blood draw, T6, Pre-injection


title: 7584091_0_Pre whole blood draw, T0, Pre-injection


title: 7584081_6_Pre whole blood draw, T6, Pre-injection


title: 7584094_0_Pre whole blood draw, T0, Pre-injection


title: 7584079_0_Pre whole blood draw, T0, Pre-injection


title: 7584082_0_Pre whole blood draw, T0, Pre-injection


title: WT_L4440_rep2

value: wild type


title: WT_L4440_rep1


title: mrg-1_rep3

data_processing:
The RNA-seq data were mapped to the c.elegans genome (ce10) with the R package QuasR (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html) using the included spliced alignment algorithm SpliceMap. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce10",splicedAlignment=TRUE)". Gene expression was quantified by counting the number of reads that started within any of the exons belonging to a particular gene (WormBase, WS220). The command used to create the count table was qCount(proj,exons) which does not consider the strand of the reads (unstranded protocol). To compensate for differences in the read depths of the various libraries, each library was normalized to a total of 24.8M reads which represents the average library size. Log2 expression levels were calculated after adding a pseudocount of 8 (y=log2(x+8). This was done to minimize the large differences in expression that would otherwise be caused by genes with small number of counts.
Genome_build: ce10

growth_protocol: worms were expanded by hand picking to select worms carrying the balancer for mrg-1 mutants. 2000-4000 (depending on the replica) non rollers of F1 gravid adults, homozygous for mrg-1 mutation, were hand-picked and hypochlorite treated to collect embryos. For control N2, an equivalent number of gravid adults were washed off from plates and hypochlorite treated. Eggs were let hatch in M9 for 18 hrs and then refed for 2 hrs and 30 min

extract_protocol:
L1s were lysed in XB buffer from ARCTURUS® PicoPure® RNA Isolation Kit (Thermo Fisher), incubated 30 min at 42°C and snap-frozen in liquid nitrogen. After freeze cracking of the samples by 6 subsequent transfers from liquid nitrogen to 42°C, samples were let vigorously shake 10 min at RT and 10 min at 42°C. Next, RNA was extracted following the manufacturer’s instructions, including an on column DNAse digestion
NGS libraries were prepared from 2 ng of input RNA, using the Total RNA-Seq NuGen Ovation v2 kit in combination with the Illumina TruSeq DNA Nano kit, according to manufacturer’s guides


title: 7584097_0_Pre whole blood draw, T0, Pre-injection


title: mrg-1_rep2


title: mrg-1_rep1


title: 7584078_6_Pre whole blood draw, T6, Pre-injection


title: WT_rep2


title: WT_rep1


title: WT_rep3


title: 96plexHMEC_tech.rep_Lane4_MULTI

city: San Francisco

first: Christopher

middle: S

last: McGinnis

state: CA

address: 600 16th Street

department: Pharmaceutical Chemistry

institute: University of California, San Francisco

description:
MULTI-seq barcode DNA
processed data files:
HMEC_techrep_MULTI_matrix.csv

data_processing:
FASTQ files were generated directly from Illumina BCL files using Illumina bcl2fastq version 2.19
Gene-barcode matrices were determined using 10X Genomics Cellranger version 2.2 with default parameters (cellranger count).
Read-depth normalization was performed (when appropriate) using 10X Genomics CellRanger version 2.2 with default parameters (cellranger aggr).
Low-quality cell barcodes were excluded as described in the paper.
MULTI-seq barcode alignment and sample classification results were performed using the deMULTIplex R package (https://github.com/chris-mcginnis-ucsf/MULTI-seq)
Genome_build: hg19 (Samples 1-3, 6-12), concatenated mm10-hg19 (Sample 13-14), concatenated mm10-hg19 pre-mRNA (Sample 4-5)
Supplementary_files_format_and_content: Expression Libraries: gene-cell matrices are provided in the format produced by CellRanger. The matrix itself is in matrix market exchange format, with the column (cell barcodes) and row (gene identities) labels given in TSV format as described in the cellranger documentation. MULTI-seq Libraries: MULTI-seq barcode-cell matrices are provided in CSV format.

source_name: HMEC

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium instrument. Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev C.
Library preparation was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev C and using a custom MULTI-seq library preparation protocol.

tag: cell type

value: HMEC

tag: multi-seq reagent

value: LMO


title: 96plexHMEC_tech.rep_Lane3_MULTI


title: 96plexHMEC_tech.rep_Lane2_MULTI


title: 96plexHMEC_tech.rep_Lane1_MULTI


title: 7584077_6_Pre whole blood draw, T6, Pre-injection

value: Indeterminate


title: 96plexHMEC_original_Lane3_MULTI

description:
MULTI-seq barcode DNA
processed data files:
HMEC_orig_MULTI_matrix.csv


title: 96plexHMEC_original_Lane2_MULTI


title: 96plexHMEC_original_Lane1_MULTI


title: POC_scRNAseq_CMO_MULTI

description:
MULTI-seq barcode DNA
processed data files:
POC_MULTI_matrix.csv

value: mixture of HEK and HMECS

value: CMO


title: 7584077_0_Pre whole blood draw, T0, Pre-injection

value: M

value: White


title: 7584076_0_Pre whole blood draw, T0, Pre-injection

value: CIS

value: F


title: 7584073_6_Pre whole blood draw, T6, Pre-injection


title: 7584070_0_Pre whole blood draw, T0, Pre-injection

value: Poor

value: RR


title: 7584078_0_Pre whole blood draw, T0, Pre-injection


title: POC_scRNAseq_CMO

description:
polyA RNA
processed data files:
POC_barcodes.tsv
POC_genes.tsv
POC_matrix.mtx


title: POC_scRNAseq_LMO_MULTI


title: 7584073_0_Pre whole blood draw, T0, Pre-injection


title: POC_scRNAseq_UNLABELED


title: 7584069_0_Pre whole blood draw, T0, Pre-injection


title: 7584069_6_Pre whole blood draw, T6, Pre-injection


title: 7584061_0_Pre whole blood draw, T0, Pre-injection

value: Good


title: 7584059_6_Pre whole blood draw, T6, Pre-injection


title: 7584068_6_Pre whole blood draw, T6, Pre-injection


title: 7584070_6_Pre whole blood draw, T6, Pre-injection


title: 7584061_6_Pre whole blood draw, T6, Pre-injection


title: 7584076_6_Pre whole blood draw, T6, Pre-injection


title: DM11-4A3-Δ/Δ

city: Nijmegen

first: Remco

last: van Cruchten

address: Geert Grooteplein Zuid 26-28

department: Cell Biology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

description:
repeat_vs_noRepeat.A3SS.GeneDiffSplice.xls
repeat_vs_noRepeat.DEseq2_Method.GeneDiffExp.xls
repeat_vs_noRepeat.RI.GeneDiffSplice.xls
repeat_vs_noRepeat.MXE.GeneDiffSplice.xls
repeat_vs_noRepeat.A5SS.GeneDiffSplice.xls
repeat_vs_noRepeat.SE.GeneDiffSplice.xls
all.gene.fpkm

data_processing:
Clean reads were mapped to the hg38 genome assembly using HISAT v0.1.6-beta and transcripts were reconstructed using StringTie v.1.0.4
rMATS v3.0.9 was used for quantification of differential splicing.
For quantification of total expression levels RSEM v1.2.12 was used after merging reads for transcripts with an identical reference transcript with BowTie2 v2.2.5, and compared using DEseq2
Genome_build: hg38
Supplementary_files_format_and_content: Processed data files are in .xls format and contain rMATS v3.0.9 and DEseq2 output, comparing DM11_par, 4F9, EA11 and EA7 (‘repeat’) with 1E6, 3E3, 3B11 and 4A3 (‘noRepeat’)

source_name: cultured myoblasts

growth_protocol: Human myoblasts were cultured in a 1:1 mix of Skeletal Muscle Cell Growth Medium and F=1- Nutrient mix supplemented with 15% (v/v) Hyclone fetal bovine serum and 1% glutamax on culture dishes coated with 0.1% gelatin at 7.5% CO2 and 37°C.

extract_protocol:
Aurum total RNA Mini Kit (Bio-Rad)
Libraries were prepared using the Unstranded TruSeq mRNA kit from Illumina and ~40 million 100-bp paired end reads were obtained using the Hiseq4000 platform (all performed by Beijing Genomic Institute in Hong Kong)

treatment_protocol: CRISPR-Cas9 was applied for excision of the CTG repeat in the 3’ UTR of the dystrophia myotonica protein kinase (DMPK) gene

value: human immortalized myoblast line

tag: ctg repeat size dmpk gene

tag: underwent crispr procedure or not

value: Underwent CRISPR procedure


title: 7584068_0_Pre whole blood draw, T0, Pre-injection


title: 7584062_6_Pre whole blood draw, T6, Pre-injection


title: POC_scRNAseq_LMO


title: 7584058_6_Pre whole blood draw, T6, Pre-injection


title: DM11-3B11-Δ/Δ


title: DM11-3E3-Δ/Δ


title: 7584059_0_Pre whole blood draw, T0, Pre-injection


title: 7584062_0_Pre whole blood draw, T0, Pre-injection


title: DM11-1E6-13/Δ


title: DM11-EA7-13/2600


title: DM11-4F9-13/2600


title: DM11-EA11-13/2600


title: DM11-parental-13/2600

value: Did not undergo CRISPR procedure


title: SU353_LSC_96

city: Stanford

first: Howard

middle: Y.

last: Chang

state: CALIFORNIA

address: 269 Campus Drive, CCSR 2130

institute: Stanford

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters.
Paired-end reads were aligned to hg19 using bwa. Duplicates were removed using PICARD tools
Reads were subsequently filtered for alignment quality  and were required to be properly paired.
Genome_build: hg19
Supplementary_files_format_and_content: reads count. The last number in the column header refers to the cell number. E.g. singles-SU353-Blast-160205-1 = SU353_Blasts_1

source_name: LSC

extract_protocol:
Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips. Cells were permeabilized and accessible fragments were captured using 20 µL of Tn5 transposition mix (1.5x TD buffer, 1.5 µL transposease (Nextera DNA Sample Prep Kit, Illumina), 1x C1 Loading Reagent with low salt (Fluidigm), and 0.15% NP40) at 30 minutes at 37°C.
In a 96-well plate, 10 µL of harvested libraries were amplified in 50 µL PCR for an additional 14 cycles (1.25 µM custom Nextera dual-index PCR primers  in 1x NEBnext High-Fidelity PCR Master using the following PCR conditions: 72°C for 5min; 98°C for 30 s;  Mix)  using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. The PCR products were pooled creating a final volume of ~4.8 mL.  The pooled library was purified on a single MinElute PCR purification column (Qiagen) yielding libraries  at an approximate concentration of ~1 µM. Libraries were quantified using qPCR prior to sequencing.

tag: patient id

tag: patient diagnosis

value: acute myeloid leukemia

value: LSC


title: SU353_LSC_95


title: SU353_LSC_9


title: SU353_LSC_94


title: SU353_LSC_93


title: SU353_LSC_92


title: 7584051_6_Pre whole blood draw, T6, Pre-injection


title: 7584058_0_Pre whole blood draw, T0, Pre-injection


title: 7584051_0_Pre whole blood draw, T0, Pre-injection


title: SU353_LSC_91


title: 7584050_6_Pre whole blood draw, T6, Pre-injection


title: SU353_LSC_90


title: 7584047_6_Pre whole blood draw, T6, Pre-injection


title: 7584045_6_Pre whole blood draw, T6, Pre-injection


title: 7584050_0_Pre whole blood draw, T0, Pre-injection


title: SU353_LSC_89


title: 7584044_6_Pre whole blood draw, T6, Pre-injection


title: SU353_LSC_8


title: 7584047_0_Pre whole blood draw, T0, Pre-injection


title: 7584044_0_Pre whole blood draw, T0, Pre-injection


title: 7584040_0_Pre whole blood draw, T0, Pre-injection

value: Black


title: 7584035_6_Pre whole blood draw, T6, Pre-injection


title: 7584043_6_Pre whole blood draw, T6, Pre-injection


title: 7584045_0_Pre whole blood draw, T0, Pre-injection


title: 7584040_6_Pre whole blood draw, T6, Pre-injection


title: 7584043_0_Pre whole blood draw, T0, Pre-injection


title: 7584036_6_Pre whole blood draw, T6, Pre-injection


title: 7584035_0_Pre whole blood draw, T0, Pre-injection


title: SU353_LSC_86


title: SU353_LSC_88


title: 7584036_0_Pre whole blood draw, T0, Pre-injection


title: met-1_mes-4_rep1

tag: developmental stage

value: L1 larvae

tag: genotype


title: SU353_LSC_85


title: SU353_LSC_84


title: SU353_LSC_82


title: SU353_LSC_80


title: SU353_LSC_83


title: SU353_LSC_81


title: SU353_LSC_79


title: SU353_LSC_87


title: SU353_LSC_76


title: SU353_LSC_75


title: SU353_LSC_74


title: 7584031_0_Pre whole blood draw, T0, Pre-injection

value: Indeterminate


title: 7584034_6_Pre whole blood draw, T6, Pre-injection


title: SU353_LSC_72


title: SU353_LSC_73


title: SU353_LSC_7


title: 7584029_6_Pre whole blood draw, T6, Pre-injection


title: SU353_LSC_71


title: SU353_LSC_78


title: 7584033_6_Pre whole blood draw, T6, Pre-injection


title: 7584024_0_Pre whole blood draw, T0, Pre-injection


title: 7584024_6_Pre whole blood draw, T6, Pre-injection


title: 7584033_0_Pre whole blood draw, T0, Pre-injection


title: 7584031_6_Pre whole blood draw, T6, Pre-injection


title: 7584034_0_Pre whole blood draw, T0, Pre-injection


title: 7584023_0_Pre whole blood draw, T0, Pre-injection


title: SU353_LSC_77


title: 7584029_0_Pre whole blood draw, T0, Pre-injection


title: 7584019_0_Pre whole blood draw, T0, Pre-injection


title: 7584023_6_Pre whole blood draw, T6, Pre-injection


title: 7584019_6_Pre whole blood draw, T6, Pre-injection


title: 7584017_0_Pre whole blood draw, T0, Pre-injection


title: 7584016_6_Pre whole blood draw, T6, Pre-injection


title: 7584017_6_Pre whole blood draw, T6, Pre-injection


title: 7584014_0_Pre whole blood draw, T0, Pre-injection


title: SU353_LSC_6


title: 7584016_0_Pre whole blood draw, T0, Pre-injection


title: SU353_LSC_70


title: SU353_LSC_67


title: 7584014_6_Pre whole blood draw, T6, Pre-injection


title: SU353_LSC_68


title: SU353_LSC_64


title: SU353_LSC_63


title: SU353_LSC_62


title: SU353_LSC_69


title: SU353_LSC_65


title: SU353_LSC_5


title: SU353_LSC_66


title: SU353_LSC_58


title: SU353_LSC_59


title: SU353_LSC_57


title: SU353_LSC_55


title: 7584006_0_Pre whole blood draw, T0, Pre-injection


title: 7584006_6_Pre whole blood draw, T6, Pre-injection


title: 7584001_6_Pre whole blood draw, T6, Pre-injection


title: 7584007_6_Pre whole blood draw, T6, Pre-injection


title: 7584004_6_Pre whole blood draw, T6, Pre-injection


title: 7584004_0_Pre whole blood draw, T0, Pre-injection


title: SU353_LSC_61


title: 7584001_0_Pre whole blood draw, T0, Pre-injection


title: 7584005_0_Pre whole blood draw, T0, Pre-injection


title: 7584005_6_Pre whole blood draw, T6, Pre-injection


title: Sham-Ctr-003

city: Munich

first: Yiming

last: Wang

state: Bavaria

department: Department of Urology

institute: Ludwig-Maximilans University

description: gene expression of sham operated rat prostate tissue

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. Labeled cRNA was fragmented and diluted with GE Hybridization buffer.

scan_protocol: The hybridized arrays were scanned with the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

organism: Rattus norvegicus

source_name: sham operated, vehicle treated, sample 3

label_protocol: Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

extract_protocol: total RNA

tag: tissue

value: prostate

tag: protocol

value: sham operated, vehicle treated

value: male


title: Sham-Ctr-002

source_name: sham operated, vehicle treated, sample 2


title: BPH-Ghr-002

description: gene expression of 4w androgen-induced and ghrelin treated rat prostate tissue

source_name: BPH-induced, ghrelin treated, sample 2

value: BPH-induced, ghrelin treated


title: BPH-Ghr-003

source_name: BPH-induced, ghrelin treated, sample 3


title: Sham-Ctr-001

source_name: sham operated, vehicle treated, sample 1


title: 7584007_0_Pre whole blood draw, T0, Pre-injection

tag: time point


title: SU353_LSC_60


title: SU353_LSC_54


title: SU353_LSC_53


title: BPH-Ghr-001

source_name: BPH-induced, ghrelin treated, sample 1


title: SU353_LSC_51


title: SU353_LSC_52


title: SU353_LSC_56


title: ESCs_E8_48hr_rep3

city: Ottawa

first: William

last: Stanford

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Reads per KNOWN gene were counted with featureCounts (Rsubread version) using the GENCODE v23 GTF gene annotations.
DESeq2 (version) analysis was performed for 24hr and 48hr samples with replicates, against t0 replicates, for KNOWN GENCODE v23 genes. Each comparison is represented by three data columns: log2 fold change, p-value, and FDR.
Genome_build: hg38 (GENCODE v23)
Supplementary_files_format_and_content: Both the read counts per gene and DESeq2 analyses files are tab delimited tex files, with the relevant data described by column headers.

growth_protocol: hESCs were maintained in E8 media on Matrigel, passaged with EDTA.

extract_protocol:
Macherey-Nagel Nucleospin kit
Illumina TruSeq mRNA

treatment_protocol: Single-cell seeding differentiation in E8, E6 or E6 with 40 ng/mL BMP4 and Activin A (BA)

tag: cell line

value: Human embryonic stem cells

tag: agent

tag: time


title: ESCs_E6_48hr_rep2


title: ESCs_E6_48hr_rep3


title: BPH-Ctr-002

description: gene expression of 4w androgen-induced rat prostate tissue

source_name: BPH-induced, vehicle treated, sample 2

value: BPH-induced, vehicle treated

tag: gender


title: BPH-Ctr-001

source_name: BPH-induced, vehicle treated, sample 1


title: ESCs_BA_48hr_rep2

value: E6 with 40 ng/mL BMP4 and Activin A (BA)


title: ESCs_BA_24hr_rep3


title: BPH-Ctr-003

source_name: BPH-induced, vehicle treated, sample 3


title: SU353_LSC_48


title: ESCs_BA_48hr_rep3


title: ESCs_BA_24hr_rep2


title: SU353_LSC_47


title: SU353_LSC_49


title: SU353_LSC_4


title: SU353_LSC_45


title: SU353_LSC_44


title: SU353_LSC_46


title: ESCs_t0_rep3

value: control


title: SU353_LSC_42


title: SU353_LSC_43


title: ESCs_t0_rep2


title: SU353_LSC_40


title: SU353_LSC_41


title: ESCs_E6_24hr


title: ESCs_E6_48hr_rep1


title: ESCs_E6_42hr


title: ESCs_E6_30hr


title: SU353_LSC_50


title: ESCs_E6_36hr


title: SU353_LSC_3


title: SU353_LSC_39


title: ESCs_E6_18hr


title: ESCs_E8_48hr_rep2


title: SU353_LSC_38


title: ESCs_E6_6hr


title: SU353_LSC_36


title: SU353_LSC_37


title: ESCs_E8_48hr_rep1


title: SU353_LSC_35


title: ESCs_E8_36hr


title: ESCs_E8_42hr


title: SU353_LSC_34


title: SU353_LSC_32


title: ESCs_E8_30hr


title: SU353_LSC_33


title: SU353_LSC_30


title: ESCs_E8_12hr


title: ESCs_E8_24hr


title: SU353_LSC_2


title: ESCs_E8_6hr


title: ESCs_BA_42hr


title: ESCs_BA_36hr


title: SU353_LSC_27


title: SU353_LSC_28


title: ESCs_BA_48hr_rep1


title: SU353_LSC_29


title: SU353_LSC_26


title: SU353_LSC_25


title: ESCs_BA_30hr


title: ESCs_E6_12hr


title: ESCs_BA_24hr_rep1


title: SU353_LSC_24


title: SU353_LSC_23


title: ESCs_BA_18hr


title: SU353_LSC_22


title: ESCs_t0_rep1


title: ESCs_BA_6hr


title: ESCs_BA_12hr


title: SU353_LSC_21


title: SU353_LSC_20


title: ESCs_E8_18hr


title: SU353_LSC_1


title: SU353_LSC_31


title: 28_TNF_4h [RNA-Seq]

city: Tokyo

first: Yoshiki

last: Higashijima

address: 1-5-45 Yushima, Bunkyo

department: Medical Research Institute

institute: Tokyo Medical and Dental University

description: Gene expression data of human endothelial cells through TNF-induced inflammatory signaling

data_processing:
Illumina CASAVA1.8.2 software used for basecalling and demultiplexing.
Sequence reads (36-bp single read) were aligned to the human reference genome (GRCh37/hg19) with Tophat (version: 2.1.1) with following parameters: the mismatch to the reference genome should be supported by at least 2 reads, the lengths of insertions and deletions should be supported by at least 3bp.
The mapped sequence reads were extended to 500 bp and converted to the continuous signal data in wig format.  Wig files were converted to bigwig files using UCSC wigToBigWig program.
Genome_build: human NCBI genome build 37 (hg19)
Supplementary_files_format_and_content: bigwig

source_name: human umblical vein endothelial cells

growth_protocol: HUVECs were purchased from Lonza Japan Ltd. (Tokyo, Japan) and cultured and passaged every 2 or 3 days in EBM-2 complete medium composed of EBM-2 Basal Medium (Lonza) supplemented with EGM-2 SingleQuot Kit Suppl. & Growth Factors (Lonza) and 3% fetal bovine serum (FBS) (Thermo Fisher Scientific, Waltham, MA). We sub-cultured HUVECs when they reached 80 to 90% confluence to avoid excessive floaters. HUVECs were used within passage 4 to 7 for all experiments in this work. Human monocyte cell line U937 was purchased from JCRB Cell Bank (Osaka, Japan) and grown and passaged every 2 or 3 days in RPMI1640 (Thermo Fisher Scientific) supplemented with 1% penicillin/streptomycin (Wako, Osaka, Japan) and 10% FBS. All cells were cultured at 37 ºC and 5% CO2 in a humidified incubator.

extract_protocol:
Total RNA including miRNA was isolated from HUVECs using miRNeasy micro Kit (Qiagen, Hilden, Germany) with DNase digestion step according to the manufactures’ instructions.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Cells were incubated with a mixture of 100 nM siRNA and Lipofectamine RNAiMax (Thermo Fisher Scientific, Waltham, MA). 80-90% confluent HUVECs plates were washed with PBS once and then serum starved in EBM-2 Basal Medium containing 0.5% FBS for 16 hrs. HUVECs were stimulated with or without 10 ng/ml TNF-α (Peprotech, Rocky Hill, NJ) for indicated periods thereafter.

tag: conditions

value: TNF

tag: donor

value: pooled from multiple donors

tag: passages


title: 29_TNF_24h [RNA-Seq]