title: Fibroblasts, DS2

status: Public on Nov 30 2020

type: RNA

city: Rio de Janeiro

first: Vanessa

last: Rizzo

state: Rio de Janeiro

address: Cezar Zama St. 185

department: Biomedical Research Institute

country: Brazil

institute: Marcilio Dias Naval Hospital

description:
Test
SAMPLE 5

data_processing:
To determine the cycle threshold (CT), the following parameters were used for both groups in the Rotor-Gene Q Series Software version 2.3.1 (build 49): ignore first 3 cycles; threshould 0.02024; eliminate cycles before 4.95. No outlier identification was used. CT values were exported to an Excel file (.xlsx format) to create a table of CT values. This table was then uploaded on data analysis web portal at http://www.qiagen.com/geneglobe. Samples were assigned to controls and test groups. The selected CT Cut-Off was 36. After calculating the arithmetic mean of the CTs for each gene (among samples from the same group), the CT values of the test group were normalized based on an automatic selection of the panel of reference genes, considering those present at baseline concentrations both in the control and test group.   The data analysis web portal calculated fold change/ regulation using ΔΔCT method, in which ΔCT is calculated between gene of interest and an average of reference genes (HKG, housekeeping), followed by Δ-ΔCT calculations [ΔCT (test group) - ΔCT (control group)]. Fold change is then calculated using 2^ (-ΔΔCT) formula, as described by Livak and Schimittgen. The p values are calculated based on a Student’s t-test of the replicate 2^(-ΔCT) values for each gene in the control group and treatment groups.
The  web portal at http://www.qiagen.com/geneglobe computed normalized signal for all genes, excepted (CT>36): Actc1, Cdh1, Col5a1, Ctsl, Itgb3, Tgfb1, Timp1 and Gusb. These genes appeared only in test groups arrays. The following genes were not expressed in both groups: Acta2, Il10, Il2, Itga6, Itgb5, Pdgfa, Serpine1 and Tnf. In test group there were 48 genes up and 14 genes downregulated at day 1 post-wounding, under 50µg/mL DS treatment, as compared to control group.

label: SYBR Green

molecule: total RNA

organism: Mus musculus

source_name: Fibroblasts 24h DS treatement

label_protocol: The samples were incubated with 10µL of the enzyme reverse transcriptase present in the RT2 First Strand Kit (cat. nº. 330401, Qiagen). The tubes, with a final volume of 20µL, were homogenized and then incubated at 42°C for 15min (Rotor gene 5 PLEX Qiagen), the reaction being subsequently interrupted at 95°C for 5 min. 91µL of RNase free water was added to each reaction tube and stored at -20ºC until use.

growth_protocol: 2x10e5 cells were incubated in DMEM culture containing 10% fetal bovine serum and 1% solution antibiotic - antimycotic. The culture medium was changed every three days and fibroblast cultures were kept in incubator in an atmosphere of 5% CO2 until the experimental tests are carried out.

extract_protocol: These cells and those of the control group (without treatment) had their total RNA extracted with RNEasy Plus Mini Kit (cat. nº. 74104, Qiagen). For each group, about 1x10e5 cells were resuspended in DMEM culture medium and subjected to centrifugation at 14000rpm for 5min. After dispensing the supernatant, 350µL of buffer containing guanidine thiocyanate was added to the precipitate and vortexed for 30s, and then transferred to an extraction microcolumn to eliminate genomic DNA (gDNA). The samples were centrifuged for 30s at 14000rpm, and the resulting supernatant was collected and an equal volume (350µL) of 70% ethanol was added. The samples were vigorously homogenized and transferred to microtubes containing silica columns and submitted to a new centrifugation for 15s at 14000rpm. After discarding the supernatant, for washing the columns, 700µL of washing buffer was added, followed by 15s of centrifugation at 14000 rpm. A second stage of washing the columns was performed with 500µL of buffer under the same centrifugation conditions, and then repeated with the same volume of buffer at the same speed, but for 2min. An extra spin was performed at maximum speed for 60s to ensure better drying of the columns. At the end, the total RNA was eluted from the columns in 50µL of ultrapure water RNAse and DNAse free, by means of centrifugation at 14000 rpm for 60s. All purified RNA samples were immediately frozen at -80ºC for later use.   The purification yield was measured by spectrophotometry using the Qiaxpert nucleic acid quantifier (Qiagen), where the RNA concentrations obtained were evaluated and the degree of purity was estimated, considering the absorbance ratios measured at 260nm and 280nm, which should be equal to or greater than 1.75. For the following tests, samples considered to be pure were selected, which presented an optical density between 1.8 to 2.0. An additional step was performed with DNAse treatment to eliminate the remaining gDNA (starting from 583.2ng nucleic acid in a final volume of 10µL, for all samples). This gDNA elimination mix was incubated for 5min at 42°C and subsequently subjected to an ice bath for 1min.

treatment_protocol: After healing teste and the cells reached about 80% confluence (24h later), the culture medium was replaced by serial dilutions of treatment with DS (2.4 dermatan sulfate)  in concentrations of 1000, 500, 250, 100, 50, 20 and 10µg/mL and the cells were incubated for 72h.

tag: strain

tag: cell type

value: Primary cultures of fibroblasts from neonate mice between 3rd and 5th passages culture 2x10e5 cells

tag: treatment

value: DS


title: Fibroblasts, DS3

description:
Test
SAMPLE 6


title: Fibroblasts, Control3

description:
Control
SAMPLE 3

source_name: Fibroblasts untreated

value: control


title: Fibroblasts, DS1

description:
Test
SAMPLE 4


title: Fibroblasts, Control2

description:
Control
SAMPLE 2


title: Fibroblasts, Control1

description:
Control
SAMPLE 1


title: U937 lot2 untreated

type: SRA

city: Itabashi-ku

first: Kensuke

last: Ohse

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

library_source: transcriptomic

data_processing:
Torrent suite software (version5.0.5) were used for basecalling and creation of fastq file.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by Torrent suite software (version 5.0.5).
Sequence reads were mapped by HISAT2 version 2.1.0 (Kim et al., 2015) against GRCh.38 p13 release version 33.
Mapped reads were assembled and merged by StringTie version 2.1.1 (Pertea et al., 2015).
Merged transcript count data were normalized by TCC version 1.26.0 (Sun et al., 2013).
Genome_build: GRCh.38 p13 release version 33
Supplementary_files_format_and_content: Matrix table of raw gene reads counts is "gene_count_re.tsv".
Supplementary_files_format_and_content: "tcc_result_gene.txt" is the tab-delimited text files include normalized read counts.

organism: Homo sapiens

source_name: U937 cells

growth_protocol: U937 cells were maintained in RPMI1640 Medium (Thermo Fisher Scientific) supplemented with 10 % (v/v) fetal bovine serum and 1 % Penicillin-Streptomycin (Thermo Fisher Scientific). Cells were cultured at 37 °C in 5% CO2.

extract_protocol:
Cells were washed by PBS(-) and peletted by centrifugation. Total RNA were extracted by RNeasy Plus Mini Kit (QIAGEN) and polyA(+) RNA were concentrated by Dynabeas mRNA DIRECT Micro kit (Thermo fisher scientific).
Whole transcriptome library was prepared by Ion Total RNA-Seq Kit for the AB Library builder System (Thermo fisher Scientific) and whole transcriptome library was amplified and barcoded by IonXpress RNA-Seq Barcode 1-16 Kit (Thermo Fisher Scientific).

treatment_protocol: For the differentiation to macrophage-like cells, cells were cultured onto the culture dish at 6 x 104 cells /cm2 in 10 nM PMA for 72 hours.

value: without PMA for 72 hours

tag: cell line


title: U937 lot2 PMA

value: with PMA for 72 hours


title: U937 lot1 PMA


title: U937 lot1 untreated


title: Cont-5_Mock_83707

city: Vienna

first: Martin

middle: Alejandro

last: Darino

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute of Molecular Plant Biology

description: rlogtransformedGeneCounts.csv

data_processing:
We removed adapter sequences and performed quality trimming using Trimmomatic
Reads were mapped to the reference genome using STAR, version 2.7.0e, with the parameter  out FilterMismatchNoverLmax 0.05
We input the bam files to R 3.5.1 using the package Rsamtools
We removed low-expressed genes and analyzed 28843 for differential expression using DESeq2, after performing regularized log transformation
We compared the induced Jsi1-mCherry lines with control mCherry lines with and without β-estradiol treatment and kept genes with log fold change (FC) ˃ 1.5 and adjusted P value < 0.05
Genome_build: We obtained the genome annotation from Araport11 and gene models and read counts per gene were obtained with the packages Genomic Features and Genomic Alignments, respectively
Supplementary_files_format_and_content: rlog read count values for all samples produced with DESeq2, in . csv format

organism: Arabidopsis thaliana

source_name: plant seedlings

growth_protocol: Arabidopsis seeds from the lines were sown on a nylon mesh with 100 µm pores (SEFAR®) placed over square plates containing 1% agar, ½ MS salts (Duchefa), 1% (w/v) sucrose, 0.05% (w/v) MES (pH 5.7 with NaOH). Arabidopsis plants were grown vertically in growth chamber (16/8 hr light/dark cycle, 21°C, light intensity 50 ɥmol/m2/sec) for 7 days

extract_protocol:
Total RNA extraction of each replicate was performed using the RNeasy Plant kit (QIAGEN). mRNA from each replicate was isolated via Poly(A) RNA Selection kit (Lexogen) using 1 µg of total RNA.
Libraries were prepared using the NEBNext® UltraTM II RNA library Prep Kit for Illumina and Index primers from NEBNext Multiplex Oligos for Illumina (New England BioLabs) following manufacturer’s instructions.
Sequencing was performed on an Illumina Hiseq2500 machine with single-end 50-bp reads

treatment_protocol: Nylon mesh with the Arabidopsis seedlings was transferred to square plates with the same media described above but containing 5 µM β-estradiol and grown vertically in the same growth chamber for 6 hr. Approximately 30 mg of seedlings were transferred to a 2 ml Eppendorf tube, shock frozen in liquid nitrogen, and stored at -80°C

tag: plant stage

value: Seven days old seedlings

tag: ecotype

tag: genotype/variation

value: mCherry


title: Cont-7_Mock_83709

description: rlogtransformedGeneCounts.csv


title: Cont-6_Mock_83708

description: rlogtransformedGeneCounts.csv


title: Donor 2 (B5)

city: Miami

first: Charles

last: Dimitroff

state: Florida

address: AHC2, Rm 678

department: Translational Medicine

country: USA

institute: Herbert Wertheim College of Medicine, Florida International University

data_processing:
For library preparation, libraries were prepared using Roche Kapa mRNA HyperPrep sample preparation kits from 100ng of purified total RNA according to the manufacturer’s protocol.  The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with single-end 75bp reads.  For RNAseq analysis, sequenced reads were aligned to the UCSC hg19 reference genome assembly and gene counts were quantified using STAR (v2.5.1b) (55). Differential gene expression testing was performed by DESeq2 (v1.10.1) (56) and normalized read counts (FPKM) were calculated using cufflinks (v2.2.1) (57). RNA-seq analysis was performed using the VIPER snakemake pipeline (58).
For RNAseq analysis, sequenced reads were aligned to the UCSC hg19 reference genome assembly and gene counts were quantified using STAR (v2.5.1b) (55). Differential gene expression testing was performed by DESeq2 (v1.10.1) (56) and normalized read counts (FPKM) were calculated using cufflinks (v2.2.1) (57). RNA-seq analysis was performed using the VIPER snakemake pipeline (58).
Genome_build: hg19

source_name: tonsillar mononuclear cells

growth_protocol: Resting human naïve B cell isolates were treated with 50mM lactose on ice for 30 min, washed twice with media and then incubated overnight in 24-well plates using RPMI-1640/10% FCS/2mM L-glutamine, 1,000 Units/ml penicillin/streptomycin.  There were four treatment groups included in the overnight cultures:  1.) Buffer alone, 2.) 1µg/ml rhGal-9 (R&D Systems), 3.) 1µg/ml rhGal-9 + 50mM lactose and 4.) 50mM lactose alone.  After 16hrs, cultured cells were harvested and subjected to a Dead Cell Removal kit (Miltenyi Biotec) prior to staining for flow cytometric analysis and isolating RNA using RNeasy Plus Mini kits (Qiagen, Hilden, Germany).  RNA samples were submitted to the Dana-Farber Cancer Institute Molecular Biology Core Facilities (Boston, MA) for RNA-seq analysis.

extract_protocol:
After 16hrs, cultured cells were harvested and subjected to a Dead Cell Removal kit (Miltenyi Biotec) prior to staining for flow cytometric analysis and isolating RNA using RNeasy Plus Mini kits (Qiagen, Hilden, Germany).  RNA samples were submitted to the Dana-Farber Cancer Institute Molecular Biology Core Facilities (Boston, MA) for RNA-seq analysis.
For library preparation, libraries were prepared using Roche Kapa mRNA HyperPrep sample preparation kits from 100ng of purified total RNA according to the manufacturer’s protocol.  The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with single-end 75bp reads.  For RNAseq analysis, sequenced reads were aligned to the UCSC hg19 reference genome assembly and gene counts were quantified using STAR (v2.5.1b) (55). Differential gene expression testing was performed by DESeq2 (v1.10.1) (56) and normalized read counts (FPKM) were calculated using cufflinks (v2.2.1) (57). RNA-seq analysis was performed using the VIPER snakemake pipeline (58).
Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with single-end 75bp reads.  For RNAseq analysis, sequenced reads were aligned to the UCSC hg19 reference genome assembly and gene counts were quantified using STAR (v2.5.1b) (55). Differential gene expression testing was performed by DESeq2 (v1.10.1) (56) and normalized read counts (FPKM) were calculated using cufflinks (v2.2.1) (57). RNA-seq analysis was performed using the VIPER snakemake pipeline (58).

value: MACS-sorted human naive B cells

value: Treated with Lactose alone


title: Donor 2 (B2)

treatment_protocol: There were four treatment groups included in the overnight cultures:  1.) Buffer alone, 2.) 1µg/ml rhGal-9 (R&D Systems), 3.) 1µg/ml rhGal-9 + 50mM lactose and 4.) 50mM lactose alone.

value: Treated with Buffer alone


title: Donor 2 (B3)

value: Treated with Gal-9


title: Donor 1 (A3)


title: Donor 1 (A5)


title: Donor 1 (A4)

value: Treated with Gal-9 and Lactose


title: Donor 1 (A2)


title: Donor 2 (B4)


title: Eff2-4_B-est_83700

description: rlogtransformedGeneCounts.csv


title: Eff1-4_B-est_83694

description: rlogtransformedGeneCounts.csv


title: Eff2-2_B-est_83698

description: rlogtransformedGeneCounts.csv


title: Cont-4_B-est_83706

description: rlogtransformedGeneCounts.csv


title: Cont-3_B-est_83705

description: rlogtransformedGeneCounts.csv


title: Eff2-3_B-est_83699

description: rlogtransformedGeneCounts.csv


title: Cont-2_B-est_83704

description: rlogtransformedGeneCounts.csv


title: Eff1-3_B-est_83693

description: rlogtransformedGeneCounts.csv


title: Eff1-2_B-est_83692

description: rlogtransformedGeneCounts.csv


title: day4+BS1_2_BS1 treatment

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

data_processing:
Quality of reads was assessed using fastq.
adapter sequences were trimmed off using cutapt
read alignment to miRBase mature miRNA sequences and hairpin sequences, sorting, filtering and counting was conducted using mirPro.
read counts of mature sequences were imported into R before processing using functions of the DESeq2 package
Genome_build: miRBase release 22, human sequences
Supplementary_files_format_and_content: csv file with raw read counts of all samples

source_name: cultured cells

growth_protocol: HepaRG were differentiated by incubating them in grownth medium for one week after seeding and differentiation medium for 2 more weeks (i.e. growth medium + 1.8% DMSO).

extract_protocol:
At given timepoints, total RNA was extracted using the Monarch total RNA mini kit (New England Biolabs) according to manufacturer's recommendations
RNA libraries were prepared for sequencing using NEBNext small RNA sequencing protocol

treatment_protocol: Differentiated HepaRG were treated for 2 or for days with 0.5 µg/mL BS1 (lymphotoxin beta receptor agonizing antibody). Medium was changed after 2 days for the 4 days treatment group.

tag: tissue

value: liver

value: BS1 treatment


title: day4-BS1_3_no treatment

value: no treatment


title: day4+BS1_3_BS1 treatment


title: day4+BS1_4_BS1 treatment


title: day4-BS1_2_no treatment


title: day4-BS1_1_no treatment


title: day2-BS1_1_no treatment


title: day2+BS1_4_BS1 treatment


title: day2-BS1_2_no treatment


title: day2+BS1_2_BS1 treatment


title: day2+BS1_3_BS1 treatment


title: day2-BS1_4_no treatment


title: fSHAPE-eCLIP vitro Input rep2

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description:
processed data file:
fshapeclip_maps.tar.gz
vivo_reproducible_peaks.hg38.bed
vitro_reproducible_peaks.hg38.bed

data_processing:
library strategy: footprinting and selective 2’-hydroxyl acylation analyzed by primer extension (fSHAPE)
SHAPE libraries as follows:
Full code at https://github.com/meracorley/fSHAPE
zcat "$file".fastq.gz | umi_tools extract --bc-pattern=NNNNCCCCNNNNN > "$file".umi.fastq
cutadapt -a AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --minimum-length=23 --overlap=5 -o "$file".trim.fastq "$file".umi.fastq
STAR --runThreadN 8 --genomeDir /projects/ps-yeolab4/genomes/GRCh38/star/ --readFilesIn "$file".trim.fastq --outFileNamePrefix "$file" --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate
umitools dedup -I "$file"Aligned.sortedByCoord.out.bam --spliced-is-unique -S "$file".dedup.bam
Total coverage (bedtools genomecov -split -strand + -dz; bedtools genomecov -split -strand - -dz) and 5' end coverage (bedtools genomecov -5 -strand + -dz; bedtools genomecov -5 -strand - -dz) summed at each position in the transcriptome with de-duplicated reads.
For each human transcript with read coverage, (5'end coverage / total read coverage) calculated at each position and normalized between -protein and +protein SHAPE libraries to calculate "fSHAPE reactivity" at each nucleotide in *maps.tar.gz files. -protein SHAPE libraries normalized against untreated SHAPE libraries to produce "in vitro icSHAPE reactivity" at each nucleotide in *vitro_icshape.tar.gz files. +protein SHAPE libraries normalized against untreated SHAPE libraries to produce "in vivo icSHAPE reactivity" at each nucleotide in *vivo_icshape.tar.gz files.

SHAPE-eCLIP and fSHAPE-eCLIP libraries as follows:
Full code at https://github.com/meracorley/f-SHAPE-eCLIP
eCLIP pipeline (reads mapped with bowtie and STAR, de-duplicated, peaks called for regions with read pileup in IP samples relative to Input)
Total coverage and mutation counts summed at each position in the transcriptome with de-duplicated reads.
For each human transcript with read coverage, (mutation coverage / total read coverage) calculated at each position and normalized between -protein and +protein libraries, or treated and untreated libraries, to calculate "fSHAPE" or "SHAPE" reactivity at each nucleotide in fshape_clip_maps.tar.gz and *shapeclip_maps.tar.gz files.
Genome_build: Hg38 for icSHAPE and fSHAPE, Hg19 for SHAPE-eCLIP and fSHAPE-eCLIP
Supplementary_files_format_and_content: Tab-delimited .map files for multiple human transcripts: Nucleotide number in transcript, Average SHAPE or fSHAPE reactivity, Standard deviation, Base. Tab-delimited .rx files for multiple human transcripts: SHAPE or fSHAPE reactivity rep1, SHAPE or fSHAPE reactivity rep2.

source_name: fSHAPE-eCLIP vitro Input

growth_protocol: Cells grown to 80-90% confluency in appropriate media, spun down, washed in 1X phosphate buffered saline (PBS) and resuspended in media.

extract_protocol:
RNA in fSHAPE samples was Trizol extracted and column purified. eCLIP samples were lysed (eCLIP lysis buffer), immunoprecipitated (IP samples only), Dnase treated, and column purified to select for RNA.
fSHAPE libraries were contsructed from polyA selected RNA treated by NAI-N3 either in vivo or in vitro. SHAPE-eCLIP libraries were constructured from RNA immunoprecipiated by SLBP anitbody, treated with DMS/NAI in vivo or left untreated. fSHAPE-eCLIP libraries were constructed from RNA immunoprecipiated by SLBP antibody, treated with NAI in vivo or in vitro.

treatment_protocol: Cells either treated with appropriate RNA probing reagent (NAI-N3, DMS, or NAI) or left untreated. "In vitro" samples were not treated with RNA probing reagent until after RNA extraction.

tag: rna probing reagent

value: 2-methylnicotinic acid imidazolide (NAI)

tag: rna state when probed

value: in vitro

tag: eclip antibody


title: fSHAPE-eCLIP vitro IP rep2

source_name: fSHAPE-eCLIP vitro IP

value: SLBP (MBLI RN045P Lot#001)


title: fSHAPE-eCLIP vivo Input rep2

source_name: fSHAPE-eCLIP vivo Input

value: in vivo


title: HepG2 untreated rep2

description:
processed data file:
hepg2_vitro_icshape.tar.gz
hepg2_vivo_icshape.tar.gz

molecule: polyA RNA

source_name: HepG2 untreated


title: HeLa untreated rep2

description:
processed data file:
hela_vitro_icshape.tar.gz
hela_vivo_icshape.tar.gz

source_name: HeLa untreated

value: HeLa


title: fSHAPE-eCLIP vivo IP rep1

source_name: fSHAPE-eCLIP vivo IP


title: HepG2 untreated rep1


title: HeLa untreated rep1


title: K562 untreated rep2

description:
processed data file:
k562_vitro_icshape.tar.gz
k562_vivo_icshape.tar.gz

source_name: K562 untreated


title: fSHAPE-eCLIP vitro IP rep1


title: fSHAPE-eCLIP vitro Input rep1


title: K562 untreated rep1


title: fSHAPE-eCLIP vivo IP rep2


title: fSHAPE-eCLIP vivo Input rep1


title: SHAPE-eCLIP NAI IP rep2

description:
processed data file:
nai_shapeclip_maps.tar.gz
nonai_reproducible_peaks.hg38.bed

source_name: SHAPE-eCLIP NAI IP


title: HepG2 fSHAPE vivo rep1

description:
processed data file:
hepg2maps.tar.gz

source_name: HepG2 fSHAPE vivo


title: HepG2 fSHAPE vitro rep1

description:
processed data file:
hepg2maps.tar.gz

source_name: HepG2 fSHAPE vitro


title: SHAPE-eCLIP noNAI Input rep2

source_name: SHAPE-eCLIP noNAI Input


title: SHAPE-eCLIP noDMS Input rep2

description:
processed data file:
dms_shapeclip_maps.tar.gz
nodms_reproducible_peaks.hg38.bed

source_name: SHAPE-eCLIP noDMS Input


title: HeLa fSHAPE vitro rep2

description:
processed data file:
helamaps.tar.gz

source_name: HeLa fSHAPE vitro


title: HeLa fSHAPE vivo rep2

description:
processed data file:
helamaps.tar.gz

source_name: HeLa fSHAPE vivo


title: HeLa fSHAPE vivo rep1

description:
processed data file:
helamaps.tar.gz


title: SHAPE-eCLIP NAI IP rep1


title: SHAPE-eCLIP noNAI IP rep1

source_name: SHAPE-eCLIP noNAI IP


title: SHAPE-eCLIP DMS Input rep2

source_name: SHAPE-eCLIP DMS Input

value: dimethyl sulfate (DMS)


title: HepG2 fSHAPE vitro rep2

description:
processed data file:
hepg2maps.tar.gz


title: HepG2 fSHAPE vivo rep2

description:
processed data file:
hepg2maps.tar.gz


title: SHAPE-eCLIP noNAI IP rep2


title: SHAPE-eCLIP noDMS IP rep1

source_name: SHAPE-eCLIP noDMS IP


title: HeLa fSHAPE vitro rep1

description:
processed data file:
helamaps.tar.gz


title: SHAPE-eCLIP noNAI Input rep1


title: K562 fSHAPE vitro rep2

description:
processed data file:
k562maps.tar.gz

source_name: K562 fSHAPE vitro


title: SHAPE-eCLIP DMS IP rep2

source_name: SHAPE-eCLIP DMS IP


title: SHAPE-eCLIP noDMS Input rep1


title: SHAPE-eCLIP noDMS IP rep2


title: SHAPE-eCLIP DMS IP rep1


title: SHAPE-eCLIP DMS Input rep1


title: K562 fSHAPE vivo rep2

description:
processed data file:
k562maps.tar.gz

source_name: K562 fSHAPE vivo


title: K562 fSHAPE vivo rep1

description:
processed data file:
k562maps.tar.gz


title: K562 fSHAPE vitro rep1

description:
processed data file:
k562maps.tar.gz


title: TNF&IFN, 1h, rep2

city: New York

first: Elena

last: Zaslavsky

state: NY

address: 1 Gustave L Levy Pl

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Fragmented cRNA was hybridized to Affymetrix HU133plus2 Gene Chip Arrays

scan_protocol: Gene expression was assayed using broad human genome specific HG-U133_Plus_2 GeneChip expression probe arrays (Affymetrix)

data_processing: Affymetrix microarray data were normalized using gcRMA.

label: biotin

source_name: human moDC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Monocyte-derived DCs were obtained from healthy human blood donors following a standard protocol described elsewhere (Hartmann et al., 2017).

extract_protocol: RNA was extracted with the RNeasy plus kit (Qiagen) following the manufacturer’s instructions

treatment_protocol: IFNβ and TNFα treatments IFNβ (PBL InterferonSource) was added at a concentration of 2000 U/ml and TNFα (Symansis) at a concentration of 1.3 ng/ml to the DC culture. Incubation time varied

tag: agent

value: TNF and IFN

tag: time point


title: TNF, 2.5h, rep3

value: TNF


title: TNF, 1h, rep1


title: TNF, 1h, rep3


title: TNF&IFN, 2.5h, rep1


title: TNF&IFN, 2.5h, rep3


title: IFN, 2.5h, rep2

value: IFN


title: CONTROL, rep2

value: CONTROL


title: ApcΔ716 mouse polyp #3

type: genomic

city: Kobe

first: Yuko

last: Kiyosue

address: 2-2-3 Minatojima-Minamimachi, Chuo-ku

institute: RIKEN Center for Biosystems Dynamics Research

description: Independent polyp #3

hyb_protocol: Manufacterer's protocol.

scan_protocol: Slides were scanned using an Agilent SureScan Microarray Scanner.

data_processing: The results were analysed using the Agilent Genomic Workbench 7.0 software.

molecule: genomic DNA

source_name: ApcΔ716 mouse small intestine

label_protocol: Manufacterer's protocol. Dye-swap replication experiments were performed.

growth_protocol: Samples from independent intestinal polyps from ApcΔ716 KO mouse models were frozen and kept in -80 degree.

extract_protocol: Normal small intestinal tissues and small intestinal polyps were excised and DNA was extracted using  a DNeasy Blood & Tissue Kit (Qiagen).

tag: tumor mode

value: ApcΔ716 KO mouse

tag: age

value: 16 weeks

value: Small intestine, normal control

tag: background

source_name: ApcΔ716 mouse intestinal polyp

tag: mouse strain

value: ApcΔ716 mouse

value: Small intestine, polyp


title: UBLCP1 siRNA_rep1

city: Toyama

first: Yutaka

last: Hirose

state: Toyama

address: 2630 Sugitani

department: Graduate School of Medicine and Pharmaceutical Sciences

institute: University of Toyama

description: HeLa S3 cells transfected with UBLCP1 siRNA

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite

source_name: UBLCP1 siRNA, HeLa S3

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).

growth_protocol: HeLa S3 cells were cultured in DMEM medium supplemented with 10% calf serum at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA was extracted using a NucleoSpin column kit (TAKARA) and treated with DNase I (Promega) for 15 min at room temperature to remove residual genomic DNA. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies), producing RIN values between 9.5 and 10.

treatment_protocol: HeLa S3 cells were seeded on 6-well plates at 1.0 × 10^5 cell/well and cultured at 37°C 24 h before transfection. Cells were transfected with either negative control siRNA or siRNA specific to human UBLCP1 gene using Lipofectamine RNAi MAX (ThermoFisher) and further cultured for 72 h at 37°C.

value: human cervical cancer cell line HeLa S3

value: UBLCP1 knockdown


title: IFN, 1h, rep1


title: IFN, 2.5h, rep1


title: ApcΔ716 mouse polyp #2

description: Independent polyp #2


title: TNF, 2.5h, rep1


title: negative control siRNA_rep2

description: HeLa S3 cells transfected with negative control siRNA

source_name: negative control siRNA, HeLa S3

value: control


title: CONTROL, rep3


title: IFN, 2.5h, rep3


title: UBLCP1 siRNA_rep2


title: IFN, 1h, rep3


title: TNF&IFN, 1h, rep1


title: TNF&IFN, 2.5h, rep2


title: TNF, 2.5h, rep2


title: ApcΔ716 mouse polyp #1_dye swap

description: Dye-swap of AD0108_Set01

source_name: ApcΔ716 mouse normal small intestine


title: negative control siRNA_rep1


title: M18

city: Atlanta

first: Muralidhar

last: Padala

state: GA

address: 380B Northyards Blvd NW

institute: Emory University

description: 40wk post op MR surgery

data_processing:
Partek Flow, version rn6 rat reference genome, was used to map reads.
Mapped reads were quantified using the RefSeq transcripts 2019-02-02 annotation, using the Partek E/M method using GSA to compare each experimental group against Sham
Data were filtered using the following specifications: p≤0.05 and 2 ≤ fold change ≤ -2.
Functional enrichment analysis was performed using Protein Analysis Through Evolutionary Relationships (PANTHER version 15), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, to identify molecular and biochemical pathways
Genome_build: rn6
Supplementary_files_format_and_content: The processed data files is a text file (.txt) and contain normalized counts for each feature for each individual sample

organism: Rattus norvegicus

source_name: Myocardium

extract_protocol:
Myocardial tissue was section, snap frozen in liquid nitrogen and stored at -80 degress celcius. RNA was harvested using the miRNeasy mini kit. RNA sequencing was performed using the Illumina platform (Novogene).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rats were subjected to MR surgery (left thoracotomy and perforation of the mitral leaflet to create MR) or Sham surgery (mitral leaflet was not perforated) and followed until 2, 10, 20, or 40 weeks

tag: strain

value: Sprague-Dawley

value: 40wk post op

tag: protocol

value: MR surgery


title: CONTROL, rep1


title: M19

description: 40wk post op MR surgery


title: TNF&IFN, 1h, rep3


title: M20

description: 40wk post op MR surgery


title: M17

description: 40wk post op MR surgery


title: ApcΔ716 mouse polyp #3_dye swap

description: Dye-swap of AD0108_Set03


title: ApcΔ716 mouse polyp #2_dye swap

description: Dye-swap of AD0108_Set02


title: IFN, 1h, rep2


title: M10

description: 10wk post op MR surgery

value: 10wk post op


title: M11

description: 20wk post op MR surgery

value: 20wk post op


title: M9

description: 10wk post op MR surgery


title: M14

description: 20wk post op MR surgery


title: M16

description: 40wk post op MR surgery


title: M6

description: 10wk post op MR surgery


title: M15

description: 20wk post op MR surgery


title: M4

description: 2wk post op MR surgery

value: 2wk post op


title: LCMV D8_Tfh-2

city: Newark

first: Jason

last: Weinstein

state: NJ

address: New Jersey Medical School Cancer Center 205 South Orange Ave

department: Center for Immunity and Inflmmation

institute: Rutgers New Jersey Medical School

description:
LCMV D8_Tfh-2
processed data file: diffexpr-results_geneIDLCMV.csv
WT3

data_processing:
Base calling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and Alignment (Cutadapt v2.5, STAR vSTAR_2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Genome_build: Genome_build: GRCm38
Supplementary_files_format_and_content: Comma delimited file (csv) for differential gene expression counts via DESeq2.

source_name: Spleen

extract_protocol:
RNA was extracted using the RNAeasy plus mini kit (Qiagen)
Paired end strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols

tag: infected with

value: LCMV

tag: timepoint

value: Day 8 post infection

tag: cell type

value: Sorted Tfh cells (CD4+CD44+GITR-PSGL-1loCXCR5hiPD-1hi)


title: M12

description: 20wk post op MR surgery


title: LCMV D8_Tfh-1

description:
LCMV D8_Tfh-1
processed data file: diffexpr-results_geneIDLCMV.csv
WT2


title: S5

description: 2wk post op Sham surgery

value: Sham surgery


title: M7

description: 10wk post op MR surgery


title: TNF, 1h, rep2

value: TNF


title: 7M_Tfh-1

description:
7M_Tfh-1
processed data file: diffexpr-results_geneID7M.csv
8M-1Tfh

value: 7 month


title: S1

description: 2wk post op Sham surgery


title: S3

description: 2wk post op Sham surgery


title: M13

description: 20wk post op MR surgery


title: 4M_Tfh-1

description:
4M_Tfh-1
processed data file: diffexpr-results_geneID4M.csv
4M-1Tfh

value: 4 month


title: S2

description: 2wk post op Sham surgery


title: M5

description: 2wk post op MR surgery


title: 2M_Tfh-2

description:
2M_Tfh-2
processed data file: diffexpr-results_geneID2M.csv
2M-2Tfh

value: 2 month


title: M3

description: 2wk post op MR surgery


title: Naïve_2

description:
Naïve_2
processed data file: All
2M-2naiv

value: naive CD4 T cells


title: M1

description: 2wk post op MR surgery


title: Naïve_1

description:
Naïve_1
processed data file: All
2M-1naiv


title: V537

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

data_processing:
Paired-end sequencing reads were aligned to mouse genome GRCm38.95 using STAR aligner (Dobin et al., 2013)
FeatureCounts (Liao et al., 2014) was then used to assign reads to genes for quantifying gene expression levels based on GENCODE (Frankish et al., 2019) release M20
Limma was applied to the normalized expression levels to identify DEGs between Crym OE and GFP in males and in females, as well as DEGs between male GFP vs. female GFP, and male Crym OE vs. female Crym OE
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Brain

extract_protocol:
RNA was isolated as described previously (Walker et al., 2018) using RNAeasy Mini Kit (Qiagen, Fredrick, MD) with a modified protocol from the manufacturer allowing for the separation and purification of small RNAs from total RNA. Briefly, after cell lysis and extraction with QIAzol (Qiagen, Fredrick, MD), small RNAs were collected in the flow-through and purified using the RNeasy MinElute spin columns and total RNA was purified using RNeasy Mini spin columns. Samples were treated with DNAse to rid them of genomic DNA and run on nanodrop and an Agilent Bioanalyzer 2100 to confirm RNA purity, integrity and concentration.
Libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit protocol (Illumina, San Diego, CA). Briefly, poly A selection and fragmentation of 300 ng of RNA was performed, and the resulting RNA was converted to cDNA with random hexamers. Adapters were ligated and samples were size-selected with AMPur XP beads (Beckman Coulter, Brea, CA). Barcode bases (6 bp) were introduced at one end of the adaptors during PCR amplification steps. Library size and concentration were assessed using Tape Station (Life Technologies, Grand Island, NY) before sequencing. Libraries were pooled for multiplexing (pool of 21 samples) and sequenced on a HighSeq2500 System using V4 chemistry with 50 base pair single-end reads at UCLA Neuroscience Genomics core. Each pool was sequenced 3 times with the goal of obtaining ~30 million reads per sample.

tag: region

value: VTA

tag: Sex

value: M

tag: housing

value: G

tag: treatment (mg/kg cocaine)

tag: acute/chronic

value: CHR


title: V563

value: F

value: SI


title: V567


title: V565


title: V571


title: V536


title: S4

description: 2wk post op Sham surgery

value: Sprague-Dawley


title: 7M_Tfh-2

description:
7M_Tfh-2
processed data file: diffexpr-results_geneID7M.csv
8M-2Tfh


title: V525


title: V521


title: V524


title: V514


title: V511


title: V1238


title: V1239


title: Control MSN40 Rep 1 [MSN40_05S_1_R1]

first: Ravi

last: Iyengar

address: 1425 Madison Avenue, Room 12-70C

department: Pharmacological Sciences

data_processing:
The data processing pipeline consists of the following three steps:
First of all, use the script Build-Genome-Index.GEO.sh to generate a set of index files with a read length of 100 bp for the UCSC human genome reference library (version hg38) used by the STAR alignment program.
Secondly, launch the script Align-RNAseq-Reads.GEO.sh that uses the STAR aligner to align the 100-bp sequence reads contained in the FASTQ-format sequence data files (obtained from high-throughput random-primed mRNA-sequencing assays) to the reference library and generate the BAM-format alignment result files that contain the sequence reads tagged with alignment information, one alignment file for each sample.
Lastly, run the script Count-RNAseq-Reads.GEO.sh that uses the featureCounts program from the Subread software to assign the tagged sequence reads contained in the alignment files to corresponding genes annotated in the reference library and then create a read counts table that contains the number of sequence reads uniquely mapped to each reference gene in rows and for every sequenced sample in columns.
Genome_build: UCSC human genome referece library (version hg38)
Supplementary_files_format_and_content: Gene-Read-Counts.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence reads for 80 iPSC samples
Supplementary_files_format_and_content: Program-Source-Codes.tar.gz: a compressed file containing the source codes for sequence alignment, feature counts, and differential comparison.

source_name: Control MSN40

growth_protocol: Cultured under growth conditions with mTeSR1 Basal Medium  (see the Section 8. Splitting/expansion of induced pluripotent stem cells (MEF/feeder-free) of the SOP document DToxS SOP CE-7.0 Reprogramming Human Fibroblasts to Human Induced Pluripotent Stem.pdf)

extract_protocol:
Total RNA was isolated using Trizol (see the SOP document DToxS SOP A-1.0 Total RNA Isolation.pdf)
Library was prepared using 500 ng of total RNA enriched for mRNA using polyA beads and the TruSeq RNA Library Prep Kit (Illumina, Cat: RS-122-2001) per manufacturer’s instructions

tag: source tissue/cell type

value: skin/primary dermal fibroblasts

value: induced pluripotent stem cell

tag: passage number

tag: sample id

tag: rna amount (ng)

tag: nanodrop 260/280

tag: rna conc (ng/ul)

tag: rna volume (ul)

tag: h2o volume (ul)


title: Control MSN39 Rep 1 [MSN39_04S_1_R1]

source_name: Control MSN39


title: Control MSN40 Rep 2 [MSN40_05S_2_R1]


title: Control MSN38 Rep 2 [MSN38_04S_2_R1]

source_name: Control MSN38


title: V579


title: V1237


title: V1236


title: Control MSN39 Rep 2 [MSN39_04S_2_R1]


title: V1235


title: Control MSN38 Rep 1 [MSN38_04S_1_R1]


title: V1233


title: V1232


title: Control MSN36 Rep 2 [MSN36_06S_2_R1]

source_name: Control MSN36


title: Control MSN36 Rep 1 [MSN36_06S_1_R1]


title: Control MSN37 Rep 2 [MSN37_01S_2_R1]

source_name: Control MSN37


title: V1227


title: V1228


title: V1226


title: Control MSN35 Rep 1 [MSN35_05S_1_R1]

source_name: Control MSN35


title: Control MSN35 Rep 2 [MSN35_05S_2_R1]


title: Control MSN34 Rep 2 [MSN34_05S_2_R1]

source_name: Control MSN34


title: Control MSN34 Rep 1 [MSN34_05S_1_R1]


title: V1224


title: V1223


title: Control MSN33 Rep 1 [MSN33_04S_1_R1]

source_name: Control MSN33


title: V1234


title: V1221


title: Control MSN32 Rep 2 [MSN32_04S_2_R1]

source_name: Control MSN32


title: Control MSN33 Rep 2 [MSN33_04S_2_R1]


title: V1222


title: V1220


title: V1216


title: V1230


title: V1215


title: Control MSN31 Rep 1 [MSN31_01S_1_R1]

source_name: Control MSN31


title: Control MSN37 Rep 1 [MSN37_01S_1_R1]


title: Control MSN31 Rep 2 [MSN31_01S_2_R1]


title: Control MSN30 Rep 2 [MSN30_01S_2_R1]

source_name: Control MSN30


title: V1206


title: V1205


title: Control MSN29 Rep 2 [MSN29_03S_2_R1]

source_name: Control MSN29


title: V1210


title: Control MSN29 Rep 1 [MSN29_03S_1_R1]


title: V1202


title: Control MSN28 Rep 1 [MSN28_05S_1_R1]

source_name: Control MSN28


title: Control MSN27 Rep 2 [MSN27_03S_2_R1]

source_name: Control MSN27


title: Control MSN27 Rep 1 [MSN27_03S_1_R1]


title: V1175

value: A


title: V1176


title: V1178


title: Control MSN28 Rep 2 [MSN28_05S_2_R1]


title: Control MSN26 Rep 2 [MSN26_01S_2_R1]

source_name: Control MSN26


title: V1173


title: Control MSN26 Rep 1 [MSN26_01S_1_R1]


title: Control MSN32 Rep 1 [MSN32_04S_1_R1]


title: Control MSN25 Rep 1 [MSN25_09S_1_R1]

source_name: Control MSN25


title: V1170

source_name: Brain


title: V1171


title: Control MSN25 Rep 2 [MSN25_09S_2_R1]


title: Control MSN30 Rep 1 [MSN30_01S_1_R1]


title: V1158


title: Control MSN24 Rep 2 [MSN24_06S_2_R1]

source_name: Control MSN24


title: Control MSN24 Rep 1 [MSN24_06S_1_R1]


title: V1200


title: V1156


title: Control MSN23 Rep 2 [MSN23_01S_2_R1]

source_name: Control MSN23


title: V1155


title: V1177


title: Control MSN23 Rep 1 [MSN23_01S_1_R1]


title: Control MSN22 Rep 2 [MSN22_04S_2_R1]

source_name: Control MSN22


title: V1152


title: Control MSN22 Rep 1 [MSN22_04S_1_R1]


title: Control MSN21 Rep 2 [MSN21_08S_2_R1]

source_name: Control MSN21


title: V1145


title: V1147


title: Control MSN20 Rep 2 [MSN20_06S_2_R1]

source_name: Control MSN20


title: V1146


title: V1140


title: Control MSN21 Rep 1 [MSN21_08S_1_R1]


title: Control MSN19 Rep 2 [MSN19_07S_2_R1]

source_name: Control MSN19


title: V1141


title: Control MSN19 Rep 1 [MSN19_07S_1_R1]


title: V1127


title: Control MSN18 Rep 2 [MSN18_03S_2_R1]

source_name: Control MSN18


title: Control MSN20 Rep 1 [MSN20_06S_1_R1]


title: V1125


title: V1204


title: V1121


title: V1120


title: Control MSN17 Rep 1 [MSN17_07S_1_R1]

source_name: Control MSN17


title: Control MSN18 Rep 1 [MSN18_03S_1_R1]


title: V1112


title: Control MSN17 Rep 2 [MSN17_07S_2_R1]


title: V1150


title: Control MSN16 Rep 2 [MSN16_04S_2_R1]

source_name: Control MSN16


title: V1143


title: V1109


title: V1102


title: V1107


title: V1101


title: Control MSN15 Rep 1 [MSN15_31S_1_R1]

source_name: Control MSN15


title: Control MSN15 Rep 2 [MSN15_31S_2_R1]


title: ApcΔ716 mouse polyp #1

description: Independent polyp #1

source_name: ApcΔ716 mouse small intestine

tag: tumor mode

value: ApcΔ716 KO mouse

tag: age

value: 16 weeks

tag: tissue

value: Small intestine, normal control

tag: background

source_name: ApcΔ716 mouse intestinal polyp

tag: mouse strain

value: ApcΔ716 mouse

value: Small intestine, polyp


title: Control MSN14 Rep 2 [MSN14_06S_2_R1]

source_name: Control MSN14

tag: cell type


title: Control MSN13 Rep 2 [MSN13_03S_2_R1]

source_name: Control MSN13


title: Control MSN13 Rep 1 [MSN13_03S_1_R1]


title: Control MSN14 Rep 1 [MSN14_06S_1_R1]


title: V1095

tag: region

tag: Sex

tag: housing


title: V1094

tag: treatment (mg/kg cocaine)

tag: acute/chronic


title: Control MSN12 Rep 1 [MSN12_04S_1_R1]

source_name: Control MSN12

tag: source tissue/cell type

tag: passage number

tag: sample id


title: V1111


title: V1097


title: V1087


title: Control MSN12 Rep 2 [MSN12_04S_2_R1]

tag: rna amount (ng)

tag: nanodrop 260/280

tag: rna conc (ng/ul)


title: Control MSN16 Rep 1 [MSN16_04S_1_R1]

tag: rna volume (ul)

tag: h2o volume (ul)


title: V1086


title: V1093


title: Control MSN11 Rep 1 [MSN11_05S_1_R1]

source_name: Control MSN11


title: Control MSN11 Rep 2 [MSN11_05S_2_R1]


title: V1104

source_name: Brain


title: Control MSN10 Rep 1 [MSN10_07S_1_R1]

source_name: Control MSN10


title: Control MSN10 Rep 2 [MSN10_07S_2_R1]


title: V1090


title: V1085


title: Control MSN09 Rep 2 [MSN09_02S_2_R1]

source_name: Control MSN09


title: M8

description: 10wk post op MR surgery

source_name: Myocardium

tag: strain

tag: time point

value: 10wk post op

tag: protocol

value: MR surgery


title: V1084

value: VTA


title: Control MSN09 Rep 1 [MSN09_02S_1_R1]

tag: cell type


title: V1083

tag: region


title: Control MSN08 Rep 1 [MSN08_06S_1_R1]

source_name: Control MSN08


title: Control MSN07 Rep 2 [MSN07_07S_2_R1]

source_name: Control MSN07


title: 4M_Tfh-2

description:
4M_Tfh-2
processed data file: diffexpr-results_geneID4M.csv
4M-2Tfh

source_name: Spleen

tag: infected with

tag: timepoint

value: 4 month

value: Sorted Tfh cells (CD4+CD44+GITR-PSGL-1loCXCR5hiPD-1hi)


title: V1075

tag: Sex

value: M

tag: housing

tag: treatment (mg/kg cocaine)

value: CHR


title: Control MSN08 Rep 2 [MSN08_06S_2_R1]

tag: source tissue/cell type

tag: passage number


title: V1077

value: SI

tag: acute/chronic


title: V1074

value: F


title: V1071


title: V1070


title: Control MSN06 Rep 2 [MSN06_07R_2_R1]

source_name: Control MSN06

value: skin/primary dermal fibroblasts

tag: sample id

tag: rna amount (ng)

tag: nanodrop 260/280


title: V1067

value: G


title: Control MSN07 Rep 1 [MSN07_07S_1_R1]

value: induced pluripotent stem cell

tag: rna conc (ng/ul)

tag: rna volume (ul)

tag: h2o volume (ul)


title: 2M_Tfh-1

description:
2M_Tfh-1
processed data file: diffexpr-results_geneID2M.csv
2-1Tfh

tag: strain

value: 2 month


title: V1066


title: Control MSN05 Rep 2 [MSN05_01R_2_R1]

source_name: Control MSN05

tag: cell type


title: Control MSN05 Rep 1 [MSN05_01R_1_R1]


title: Control MSN04 Rep 2 [MSN04_05S_2_R1]

source_name: Control MSN04


title: Control MSN04 Rep 1 [MSN04_05S_1_R1]


title: Control MSN03 Rep 2 [MSN03_05S_2_R1]

source_name: Control MSN03


title: V1062

tag: region


title: V1060


title: Control MSN03 Rep 1 [MSN03_05S_1_R1]


title: Control MSN02 Rep 2 [MSN02_01S_2_R1]

source_name: Control MSN02


title: V1046

value: A


title: V1063


title: V1047


title: Control MSN02 Rep 1 [MSN02_01S_1_R1]


title: Control MSN01 Rep 2 [MSN01_02S_2_R1]

source_name: Control MSN01


title: V1044


title: V1045


title: Control MSN01 Rep 1 [MSN01_02S_1_R1]


title: Control MSN06 Rep 1 [MSN06_07R_1_R1]


title: V1040


title: V1041


title: V1037


title: V1038


title: V1036


title: V1033


title: V1034


title: V1032


title: V1065


title: V1035


title: V1030


title: V1031


title: MAND2

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

data_processing:
The libraries were sequenced as paired-end, 50 base read length on an Illumina HiSeq 2500 (Illumina Inc.) with an average read count of 21-28 million reads per sample.
Initial base calling and quality filtering of the mRNA-Seq reads generated with the Illumina analysis pipeline (fastQ format) was performed using the FastxToolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and adapters trimmed using CutAdapt (https://code.google.com/p/cutadapt/).
Reads that mapped to the human mitochondrial genome or to Phix were removed using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml).
Reads were mapped (tophat v2.0.13; http://ccb.jhu.edu/software/tophat/index.shtml) to the reference genome (from Ensembl, v78; http://www.ensembl.org/index.html) Homo_sapiens.GRCh38.dna.primary_assembly.fa using Homo_sapiens.GRCh38.78.gtf as annotation.
Tests for differential expression were made using cuffdiff v2.2.1.

source_name: NPC obtained from iPSC that were generated from primary skin fibroblasts of MAND

growth_protocol: Human iPSC and NPC were cultured in six-well tissue culture plates (Thermo Scientific) coated with Matrigel (BD Bioscience) under an atmosphere of 5 % CO2/air at 37°C in mTeSR1 medium (STEMCELL Technologies). Cells were passaged every 5–6 days.

extract_protocol:
RNA was isolated from control and patient NPC lines using RNeasy Plus Mini Kits (QIAGEN) according to manufacturer’s instructions.
Libraries were constructed following the Illumina’s protocol with reagents supplied in Illumina’s TruSeq mRNA stranded sample preparation kit.

treatment_protocol: Directed differentiation of iPSC to NPC was accomplished with STEMdiff Neural System (STEMCELL Technologies) in monolayer culture protocol.

value: Neural progenitor cells

tag: diagnosis

value: MBD5-Associated Neurodevelopmental Disorder (MAND)


title: MAND3


title: V1017


title: V1016


title: V1048


title: MAND1


title: V1015


title: CTR4

source_name: NPC obtained from iPSC that were generated from primary skin fibroblasts of non-complicated

value: control


title: V1014


title: CTR1


title: V1011


title: CTR3


title: V1008


title: V1007


title: V1006


title: V1005


title: CTR2

source_name: NPC obtained from iPSC that were generated from umbilical cord cells of non-complicated


title: V1002


title: GD2-B7H3_1

city: Los angeles

first: Xiangming

last: Ding

state: California

address: 4650 Sunset Blvd

institute: CHLA

data_processing:
Cutadapt software (cutadapt v1.16) was used to remove the reads contained adaptor contamination.
Reads were mapped to human hg38 genome using the hisat2 and featurecount was used to calculate the count of each gene in each sample
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CAR-T cells

growth_protocol: CAR-T cells were geenrated using lentiviruses. T cells were co-cultured with CHLA255 neuroblastoma cell line for 48 hours in T cell media.

extract_protocol:
qiagene RNA extraction kit was used to extract the RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GD2-B7H3 SynNotch gated CAR-T cells versus conventional B7H3 CAR-T cells are being used to co-culture with neuroblastoma tumor cell line.

value: T cell

tag: treatment


title: V1000

source_name: Brain

tag: Sex


title: B7H3_3


title: B7H3_1


title: GD2-B7H3_2


title: B7H3_2


title: P563

value: PFC

tag: housing


title: P537

tag: treatment (mg/kg cocaine)


title: P536


title: P524


title: P571


title: P525


title: SAMD9_E1136Q rep 3

city: Memphis

first: Jeffery

last: Klco

state: Tennessee

address: 262 Danny Thomas Place, D4047B

department: Pathology

institute: St Jude Children's Research Hospital

data_processing:
200207_A00239_0357_BH5MJ5DSXY v3.4.4 and bcl2fastq 2.20.0 to make basecalling
200207_A00239_0359_BH5MJ5DSXY v3.4.4 and bcl2fastq 2.20.0 to make basecalling
RNA reads were mapped using our in house pipeline StrongARM.
Reads from aligned bam files were assigned to genes and counted using HTSeq with the GENCODE human release 19 gene annotation. Log2 CPM (counts per million) values were used for differential gene expression analysis. A cut-off of 10 CPM was used as the threshold to define "expressed" genes. We first determined the number of samples in the smallest group among all groups being compared as N. For a gene to be considered as expressed, we required that at least N samples should have >=10 CPM.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix txt file for log2 CPM(counts per million) values for genes defined as "expressed".

source_name: cord blood-derived CD34+ cells

growth_protocol: Human cord blood-derived CD34+cells (Lonza, Switzerland) were cultured in expansion medium containing StemSpan SFEM-II (StemCell Technologies, Canada) enriched with human cytokines (PeproTech, NJ) including interleukin-6 (100ng/ml), Fms-like tyrosine kinase-3 ligand (FLT3-L, 100ng/ml), Stem Cell Factor (SCF, 100ng/ml), Thrombopoietin (100ng/ml), 1uM Stem Regenin-1 and 35nM UM171 (StemCell Technologies, Canada).

extract_protocol:
Total RNA was extracted using quick-RNA Microprep kit (Zymo Research, CA).
RNA-sequencing was performed using TruSeq Stranded Total RNA library kit (Illumina, CA)

treatment_protocol: hCD34+ cells were resuspended in 2X of their appropriate media supplemented with 1ug/ml polybrene (2.5x10^5 cells/well). Cells were transduced with equal volume of the concentrated lentiviral particles by spinfection at 2000xg/90min/30C followed by overnight incubation at 37C.

tag: time

value: 24hr post Lentivirus transduction

tag: genotype/variation


title: SAMD9_E1136Q rep 2


title: P514

tag: acute/chronic


title: SAMD9_E1136Q rep 1


title: HEK293T tRNA; AlkB WT + D135S; bio rep 1

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description: fastq files are paired-end demultiplexed

data_processing:
Paired-end reads were merged with BBMap v38.26
de-duplication with BBMap v38.26 and trimming UMI using the cutadapt command
sorting based on internal barcodes using the grep command
quality control using the fastq_quality_trimmer command of FASTX Toolkit with the option '-t 20 -l 22' to select for reads with quality higher than 20 and length longer than 22 nt.
Genome_build: non-redundant GtRNAdb hg19
alignment to genome using bowtie2
converting sam files to bam files using samtools v0.1.18
sorting bam files using samtools v0.1.18
base-calling using the bam-readcount command
calling mutations using a custom python script
mutation rates for the most abundant gene of each tRNA isodecoder from different samples were analyzed using an in-house R script
Supplementary_files_format_and_content: .txt; columns from left to right are "chr", "position", "base", "base_sum", "unknown", "A", "C", "G", "T", "N", "X"
Supplementary_files_format_and_content: .csv; for files ending with '.mut.csv', columns from left to right are "mutation type", "base_sum", "A", "T", "C", "G", "chromosome","position", "mutation rate", "base -3 location", "base -2 location", "base -1 location", "base current location", "base +1 location", "base +2 location", "base +3 location"
Supplementary_files_format_and_content: .csv; position, mutation rates

growth_protocol: HEK293T cells were cultured with complete DMEM medium under standard conditions. Briefly, HEK293T cells were grown in Hyclone DMEM medium (GE Healthcare Life Sciences, SH30022.01) with 10% FBS and 1% Pen-Strep (Penicillin-Streptomycin) to 80% confluency and passaged. Cells were collected and total RNA was extracted using TRIzol (ThermoFisher, 15596026) by following the manufacturer’s protocol when cells reached 80-90% confluency.

extract_protocol:
Nucleic acid was extracted with Trizol and isolated with Zymo Oligo clean and concentrator columns
RNA was deacylated then ligated to a 3’ adaptor with a barcode. Barcoded samples were pooled after ligation, then treated with AlkB demethylase where indicated. Next samples were used in reverse transcription with SuperScrip IV followed by RNaseH digest. Next a second libation was done with a UMI-bearing adaptor and the products were used as input for PCR application.

treatment_protocol: AlkB enzyme treatments were done as previously described (PMID: 26214130). Briefly, after adaptor ligation, 1 ug of total RNA was treated with 20 uM of AlkB and 20 uM of AlkB mutant when indicated. The reaction buffer contained 300 mM KCl, 2 mM MgCl2, 50 μM of (NH4)2Fe(SO4)2·6H2O, 300 μM 2-ketoglutarate (2-KG), 2 mM L-ascorbic acid, 50 μg/ml BSA, 50 mM MES buffer (pH 5.0). Reaction was incubated for 2 h at room temperature and quenched by the addition of 5 mM EDTA.

tag: cell line

tag: enzyme treatment

value: AlkB + AlkBD135S

tag: barcode

value: barcode, 3nt, bc9


title: HEK293T tRNA; AlkB WT; bio rep 1

value: AlkB

value: barcode, 3nt, bc8


title: HEK293T tRNA; no enzyme; bio rep 1

value: barcode, 3nt, bc7


title: V1003

value: VTA

value: F


title: HEK293T tRNA; AlkB WT + D135T; bio rep 1

value: AlkB + AlkBD135T

value: barcode, 3nt, bc10


title: SAMD9 rep 3


title: P1239

value: M

value: SI

value: CHR


title: SAMD9 rep 2


title: P565


title: P1238


title: SAMD9 rep 1


title: P1237


title: P1236


title: P1235


title: SAMD9L_H880Q rep 3


title: P1234


title: SAMD9L rep 3


title: P1232


title: SAMD9L rep 1


title: P1230


title: P1229

value: G


title: P521


title: P511


title: CL20c rep 3


title: P1228


title: SAMD9L_H880Q rep 1


title: P1224


title: P1227


title: CL20c rep 2


title: P1222


title: SAMD9L rep 2


title: Ribo_Plus_1

city: Rochester

first: Jin Sung

last: Jang

state: MN

address: 200 First St SW

institute: Mayo Clinic

description:
2nd set_Gene_counts.txt
Ribo_Plus_1

data_processing:
The STAR (2.6.1d) aligner was used to perform alignment of reads to the hg38. After alignment, the final BAM files were quantified using Partek E/M algorithm by Ensembl annotations (Ensembl Transcripts release 92).
Genome_build: hg38, Ensembl Transcripts release 92
Supplementary_files_format_and_content: tab-delimited text files and gene counts & transcripts counts

source_name: Whole blood

extract_protocol:
RNA was PAXgene RNA extraction kit (Qiagen)
1 ug of total RNA from each sample was used. The RNA-Seq libraries were generated using TruSeq Stranded mRNA Library Prep kit (Illumina, CA).

treatment_protocol: A total of 1 μg of each RNA sample was processed by four different kits to remove the globin gene (GLOBINClear Kit, NEBgr: NEBNext® Globin & rRNA Depletion Kit (NEBgr), RZr: Ribo-Zero Plus rRNA Depletion Kit (RZr), GZr: Globin-Zero Gold rRNA Removal Kit (GZr)).

value: Pooled-Ribo-Zero Plus rRNA Depletion


title: Ribo_Plus_2

description:
2nd set_Gene_counts.txt
Ribo_Plus_2


title: CL20c rep 1


title: Ribo-Zero_2

description:
2nd set_Gene_counts.txt
Ribo_Zero_2

value: Pooled-Globin-Zero Gold rRNA Removal


title: SAMD9L_H880Q rep 2


title: P1221

value: PFC


title: Pool GLB2

description:
2nd set_Gene_counts.txt
GLB2

value: Pooled-GLOBINClear


title: P1220


title: P1226


title: Pool GLB1

description:
2nd set_Gene_counts.txt
GLB1


title: GZr3

description:
1st set_Gene_counts.txt
PaxgeneRNA_S6-2

value: Globin-Zero Gold rRNA Removal


title: P1215


title: P1216


title: GZr2

description:
1st set_Gene_counts.txt
PaxgeneRNA_S5-2


title: P1206


title: GZr1

description:
1st set_Gene_counts.txt
PaxgeneRNA_S4-2


title: P1205


title: RZr3

description:
1st set_Gene_counts.txt
PaxgeneRNA_S6-1

value: Ribo-Zero Plus rRNA Depletion


title: P1204


title: RZr1

description:
1st set_Gene_counts.txt
PaxgeneRNA_S4-1


title: P1200


title: NEBGr3

description:
1st set_Gene_counts.txt
PaxgeneRNA_S3-2

value: NEBNext® Globin & rRNA Depletion


title: P1178

value: A


title: NEBGr2

description:
1st set_Gene_counts.txt
PaxgeneRNA_S2-2


title: GLB3

description:
1st set_Gene_counts.txt
PaxgeneRNA_S3-1

value: GLOBINClear


title: GLB1

description:
1st set_Gene_counts.txt
PaxgeneRNA_S1-1


title: P1176


title: NEBGr1

description:
1st set_Gene_counts.txt
PaxgeneRNA_S1-2


title: P1170


title: P1171


title: P1210


title: P1173


title: P1158


title: P1155


title: P1156


title: GLB2

description:
1st set_Gene_counts.txt
PaxgeneRNA_S2-1


title: P1152


title: P1202


title: GBM002_cC08_p58_SerDif_RNA

city: Montreal

first: Carol

last: Chen

state: QC

address: 1001 Decarie Boulevard, Rm E01.4380

department: Human Genetics

country: Canada

institute: Research Institute of McGill University Hospital Centre

data_processing: Datasets were processed using the ChIP-seq or RNA-seq module of GenPipes (Bourgey, 2019). Briefly, raw reads are trimmed using Trimmomatic to remove adaptor and sequencing-primer associated reads, then aligned to hg19 using bwa-mem for ChIP-seq, and STAR for RNA-seq using default parameters. PCR duplicate reads as defined by reads with identical mapping coordinates are then collapsed by Picard to produce uniquely aligned reads. Reads were then filtered for mapping quality of > 5. For SE75 ChIP datasets, reads were extended by 250bp. Wiggle tracks depicting coverage are then generated using uniquely aligned reads. Analysis of Hi-C generated libraries and downloaded files was performed using Juicer and the associated Juicer Tools (Durand et al. 2016). Contact maps were generated using Juicer with the following parameters: -s DpnII -g hg19. Map resolution was determined by using Juicer’s “calculate_map_resolution.sh” script. Hi-C contact maps and associated annotations were visualized using Juicebox (Durand et al. 2016)

source_name: patient-derived glioma cell line

growth_protocol: Tumor-derived cell lines HSJD-GBM002 were cultured in NeuroCult NS-A proliferation media (StemCell Technologies) supplemented with bFGF (10 ng/mL), rhEGF (20 ng/mL), and heparin (0.0002%) (StemCell Technologies) and on plates coated with poly-L-ornithine (0.01%) (Sigma) and laminin (0.01 mg/mL) (Sigma). KNS-42 and PS10-801 cell lines were cultured in DMEM containing 4.5 g/L glucose, L-glutamine, phenol red, and 10% FBS (Wisent). All lines were tested monthly for mycoplasma contamination (MycoAlert Mycoplasma Detection kit by Lonza), and STR fingerprinting was regularly performed.

extract_protocol:
For ChIP-seq, cells were fixed with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at -80°C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 60 cycles, 10s on 20s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and before ChIP reaction ~5% of sonicated drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing (see below). ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. 25ul Protein A beads were washed and then incubated with 6ug of H3K27ac antibody (Diagenode, C15410196), and 2 million cells of sonicated cell lysate combined with protease inhibitors for 10 hr, followed by 20 min wash cycle with provided wash buffers. Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail (Life Technologies) at 65°C for 30 min followed by 2ul Proteinase K (Thermo Fisher Scientific) at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol. For RNA-seq, total RNA was extracted from cell pellets and mouse tumors using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to instructions from the manufacturer. Library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts. Paired-end sequencing was performed on the Illumina HiSeq 2500/4000 platform. For Hi-C, libraries were generated from 5 million cultured G34 glioblastoma cell lines KNS-42, HSJD-GBM002 and PS10-801 as described in (Rao et al., 2014) with minor modifications. Briefly, in situ Hi-C consists of 7 steps: (1) crosslinking cells with formaldehyde, (2) digesting the DNA using a 4-cutter restriction enzyme (e.g., DpnII) within intact permeabilized nuclei, (3) filling in, biotinylating the resulting 5′-overhangs and ligating the blunt ends, (4) shearing the DNA, (5) pulling down the biotinylated ligation junctions with streptavidin beads, (6) library amplification and (7) analyzing these fragments using paired end sequencing. As quality control (QC) steps, we checked for efficient sonication with an agarose DNA gel and for appropriate size selection using the Agilent Bioanalyzer on final amplified libraries. For the final QC, we performed superficial sequencing on the Illumina Hiseq 2500 (~30M reads/sample) to assess quality of the libraries using percent of reads passing filter, percent of chimeric reads, and percent of forward-reverse pairs.  125bp paired-end sequencing was performed on the Illumina HiSeq 4000.
For ChIP-seq, library preparation was carried out using Kapa HTP Illumina library preparation reagents. Briefly, 25ul of ChIP sample was incubated with 45ul end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50ul buffer enzyme mix for 30°C 30 min, followed by PEG/NaCl purification. Adaptor ligation: bead bound sample was incubated with 45ul buffer enzyme mix and 5ul of different TruSeq DNA adapters (Illumina) for each sample, for 20°C 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. Size selection was performed after PCR using a 0.6x/0.8x ratio of Ampure XP beads (double size selection) set to collect 250-450bp fragments. Single-end or paired-end 50bp sequencing was performed on the Illumina HiSeq 4000 or NovaSeq 6000 platform.
For RNA-seq, RNA-seq library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts, paired-end sequencing (100 bp) was performed on the Illumina HiSeq 4000 platform.

treatment_protocol:
CRISPR-Cas9 editing of HSJD-GBM002 cell line was performed by designing a synthetic ALT-R crRNA (IDT) guide targeting the H3F3A G34R mutation. Nucleofection was performed using program A-023 on the Amaxa Nucleofector 2b (Lonza) device, following manufacturer’s instructions to introduce crRNA, tracrRNA and recombinant Alt-R S.p. Cas9 Nuclease V3. Single cell clones were isolated by limiting dilution, expanded and screened for editing events at the target locus by Sanger sequencing and confirmed through targeted deep sequencing using Illumina MiSeq.
For IUE - the piggyBac donor and helper vector system (CAG-PBase, PBCAG-GFP) was used to transduce NPCs in utero as described previously (Chen and LoTurco, 2012). Two ATRX shRNA vectors, cDNA encoding murine Pdgfra and cDNA encoding C-terminal HA-tagged Drosophila His3.3A (highly conserved orthology of mammalian H3f3a) were cloned into the PBCAG-GFP vector to generate shAtrx-PdgfraWT-H3f3aWT constructs, previously described in Pathania et al., 2017. CRISPR/Cas9 pX330 vectors containing Trp53-targeted gRNA were similarly used. G34R and PdgfraD842V mutants were generated using Quikchange Lightning site-directed mutagenesis (Agilent). In utero electroporation was performed using sterile technique on isoflurane/oxygen-anesthetized pregnant females at E13.5 (cortex), and ex vivo isolation of NPCs were as described in Panathia et al. 2017.

tag: tissue

value: patient-derived glioma cell line

tag: genotype

tag: cell line name

tag: clone name

tag: passage

tag: media

value: serum


title: GBM002_cF06_p64_SerDif_RNA


title: RZr2

description:
1st set_Gene_counts.txt
PaxgeneRNA_S5-1


title: P1150

tag: region

value: F


title: GBM002_cC08_p54_stem_RNA

value: stem


title: P1147

value: M


title: GBM002_cA10_p58_SerDif_RNA


title: GBM002_cA09_p58_SerDif_RNA


title: GBM002_cA09_p58_stem_RNA


title: P1177

value: SI


title: GBM002_cA10_p58_stem_RNA


title: P1143


title: P1140


title: P1141


title: GBM002_cF06_p64_stem_RNA


title: HSJD-GBM002_C08_p56_stem_RNA


title: HSJD-GBM002_A09_p59_stem_RNA


title: P1127


title: HSJD-GBM002_A10_p59_stem_RNA


title: P1125


title: P1126


title: HSJD-GBM002_F06_p56_stem_RNA


title: P1120


title: P1121


title: P1114


title: HSJD-GBM002_A09_p58_stem_RNA


title: HSJD-GBM002_A10_p58_stem_RNA


title: HSJD-GBM002_C08_p54_stem_RNA


title: HSJD-GBM002_F06_p55_stem_RNA


title: KNS-42_RNA

value: parental


title: P1107

value: G


title: HSJD-GBM002_RNA


title: P1111


title: P1112


title: PS10-801_CL_RNA


title: PS10-801_C13_RNA


title: PS10-801_Hi-C

library_source: genomic


title: P1145


title: P1104


title: P1102


title: HSJD-GBM002_Hi-C


title: KNS-42_Hi-C


title: P1097

value: CHR


title: KNS42p15_cells_ChIP1_CTCF_1

tag: chip antigen

value: CTCF


title: P1094

value: PFC

tag: Sex


title: P1095

tag: housing


title: TAD_rep3

city: Guangzhou

first: jie

last: sun

state: Gongdong

address: 1838 North Guangzhou Avenue

department: Department of Cardiology

country: China

institute: Nanfang Hospital, Southern Medical University

description:
LncRNA_rpkm.txt
mRNA_rpkm.txt
AD3

data_processing:
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis.The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads.2) Remove the low-quality  reads.3) Remove reads whose number of N bases accounting for more than 5 %.
Bowtie2  v2.2.3 was used  for  building  the  genome  index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM could eliminate the effect of sequencing depth and gene length on gene expression levels and the data could be compared between each other directly.
Genome_build: ftp://ftp.ensembl.org/pub/release-83/fasta/homo_sapiens
Supplementary_files_format_and_content: RPKMs

source_name: Aortic dissection

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3ug of total RNA for the Construction of sequencing
RNA libraries were prepared for sequencing using standard lllumina protocols

tag: gender

value: male

tag: age

value: Aortic specimen from TAD patient


title: P1093

tag: treatment (mg/kg cocaine)


title: P1109

tag: acute/chronic


title: TAD_rep1

description:
LncRNA_rpkm.txt
mRNA_rpkm.txt
AD1


title: P1087


title: control_rep3

description:
LncRNA_rpkm.txt
mRNA_rpkm.txt
CN3

source_name: thoracic aorta

value: Normal thoracic aorta


title: control_rep2

description:
LncRNA_rpkm.txt
mRNA_rpkm.txt
CN2


title: P1086


title: P1090


title: TAD_rep2

description:
LncRNA_rpkm.txt
mRNA_rpkm.txt
AD2


title: control_rep1

description:
LncRNA_rpkm.txt
mRNA_rpkm.txt
CN1


title: P1085


title: P1077


title: GD2-B7H3_3

tag: cell type

value: T cell

tag: treatment


title: P1084


title: P1101

value: A


title: P1076


title: P1075


title: PS10801p17_cells_ChIP1_CTCF_1


title: P1074


title: C2KO_Single muslce fiber [s740-7]

city: Cincinnati

first: Taejeong

last: Song

state: OH

address: 231 Albert Sabin Way, CVC Building Room 4978

department: Internal Medicine

institute: University of Cincinnati

description: run0299_lane9_indexN719-S511=740-7~mouse10_align

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were checked using FASTQC (v0.11.2)
Paired-end reads were aligned with HISAT2 (v2.0.5) with a strandedness option (RF).
Genes were counted using featureCounts (v1.5.2)
Genome_build: mm10
Supplementary_files_format_and_content: Read counts

source_name: C2KO_Single muslce fiber

extract_protocol:
Whole EDL muscles were carefully dissected from 2 to 3-month-old WT (n=3) and C2-/- (n=2) mice and incubated in 0.5% collagenase (Roche, 11088807001) for 90min at 37oC. Next, EDL muscles were transferred to DMEM containing 10% horse serum, and muscle fibers were released by repeated trituration using a glass pipette under a dissection microscope. An intact single fiber was selected and washed with fresh DMEM twice, followed by a final rinse with sterile PBS.
The single muscle fiber was lysed in 20uL of extraction buffer, and total RNA was isolated by column purification as directed by the manufacturer (PicoPure RNA Isolation Kit, KIT0204, Applied Biosystems). The quality of the isolated RNA was checked by the Agilent 2100 Bioanalyzer using the RNA 6000 Pico Assay.

tag: strain background

value: FVB/N

tag: genotype/variation

value: Extensor Digitorum Longus (EDL) muscle

tag: tissue type

value: single muslce fiber


title: C2KO_Single muslce fiber [s740-3]

description: run0296_lane9_indexN728-S506=740-3~mouse10_align

tag: tissue


title: C2KO_Single muslce fiber [s740-6]

description: run0299_lane9_indexN718-S510=740-6~mouse10_align


title: C2KO_Single muslce fiber [s740-5]

description: run0299_lane9_indexN716-S508=740-5~mouse10_align


title: C2KO_Single muslce fiber [s740-2]

description: run0296_lane9_indexN727-S505=740-2~mouse10_align


title: P1071

value: F


title: P1070


title: C2KO_Single muslce fiber [s740-4]

description: run0296_lane9_indexN729-S507=740-4~mouse10_align


title: P1066


title: C2KO_Single muslce fiber [s740-1]

description: run0092_lane9_indexN729-S506=740-1~mouse10_align


title: P1067


title: C2KO_Single muslce fiber [s740-8]

description: run0299_lane9_indexN720-S502=740-8~mouse10_align


title: C2KO_Single muslce fiber [s740-13]

description: run0299_lane9_indexN722-S505=740-13~mouse10_align


title: P1062


title: P1063


title: P1060


title: C2KO_Single muslce fiber [s2445-7]

description: run0299_lane9_indexN729-S502=2445-7~mouse10_align


title: C2KO_Single muslce fiber [s740-12]

description: run0299_lane9_indexN721-S503=740-12~mouse10_align


title: C2KO_Single muslce fiber [s2445-6]

description: run0299_lane9_indexN728-S511=2445-6~mouse10_align


title: P1047


title: C2KO_Single muslce fiber [s2445-8]

description: run0299_lane9_indexN716-S505=2445-8~mouse10_align


title: C2KO_Single muslce fiber [s2445-4]

description: run0299_lane9_indexN726-S508=2445-4~mouse10_align


title: P1046


title: P1045


title: C2KO_Single muslce fiber [s2445-2]

description: run0299_lane9_indexN724-S507=2445-2~mouse10_align


title: C2KO_Single muslce fiber [s2445-1]

description: run0299_lane9_indexN723-S506=2445-1~mouse10_align


title: P1040


title: P1041


title: C2KO_Single muslce fiber [s2445-13]

description: run0299_lane9_indexN720-S508=2445-13~mouse10_align


title: C2KO_Single muslce fiber [s2445-12]

description: run0299_lane9_indexN719-S507=2445-12~mouse10_align


title: P1038


title: P1037


title: C2KO_Single muslce fiber [s2445-11]

description: run0299_lane9_indexN718-S506=2445-11~mouse10_align


title: WT_Single muslce fiber [s87]

description: run0092_lane9_indexN728-S505=87~mouse10_align

source_name: WT_Single muslce fiber

value: WT


title: P1036

value: M


title: P1035

value: SI


title: WT_Single muslce fiber [s84]

description: run0092_lane9_indexN727-S503=84~mouse10_align


title: P1048


title: WT_Single muslce fiber [s83]

description: run0092_lane9_indexN726-S502=83~mouse10_align


title: WT_Single muslce fiber [s81_17723]

description: run2869_lane12_indexN708-S507=TJ-81_17723~mouse10_align


title: P1034


title: C2KO_Single muslce fiber [s2445-5]

description: run0299_lane9_indexN727-S510=2445-5~mouse10_align


title: P1033


title: WT_Single muslce fiber [s82_17724]

description: run2869_lane12_indexN710-S508=TJ-82_17724~mouse10_align


title: P1032


title: WT_Single muslce fiber [s79_17721]

description: run2869_lane12_indexN706-S505=TJ-79_17721~mouse10_align


title: WT_Single muslce fiber [s78_17720]

description: run2869_lane12_indexN705-S504=TJ-78_17720~mouse10_align


title: P1044


title: P1018


title: WT_Single muslce fiber [s77_17719]

description: run2869_lane12_indexN704-S503=TJ-77_17719~mouse10_align


title: P1030


title: WT_Single muslce fiber [s76_17718]

description: run2869_lane12_indexN703-S502=TJ-76_17718~mouse10_align


title: WT_Single muslce fiber [s63]

description: run0092_lane9_indexN724-S511=63~mouse10_align


title: P1015


title: WT_Single muslce fiber [s6_17673]

description: run2868_lane12_indexN701-S505=TJ-6_17673~mouse10_align


title: P1016


title: P1014


title: P1013


title: P1007


title: WT_Single muslce fiber [s59_17717]

description: run2869_lane12_indexN702-S517=TJ-59_17717~mouse10_align


title: WT_Single muslce fiber [s58_17716]

description: run2869_lane12_indexN701-S508=TJ-58_17716~mouse10_align


title: WT_Single muslce fiber [s57_17715]

description: run2869_lane12_indexN712-S507=TJ-57_17715~mouse10_align


title: WT_Single muslce fiber [s55_17714]

description: run2868_lane12_indexN711-S506=TJ-55_17714~mouse10_align


title: P1006


title: P1008


title: WT_Single muslce fiber [s54_17697]

description: run2868_lane12_indexN708-S504=TJ-54_17697~mouse10_align


title: P1017


title: P1005


title: WT_Single muslce fiber [s80_17722]

description: run2869_lane12_indexN707-S506=TJ-80_17722~mouse10_align


title: WT_Single muslce fiber [s50]

description: run0092_lane9_indexN721-S507=50~mouse10_align


title: Ribo-Zero_1

description:
2nd set_Gene_counts.txt
Ribo_Zero_1

value: Pooled-Globin-Zero Gold rRNA Removal


title: N579

value: Nac

value: G


title: WT_Single muslce fiber [s5_17691]

description: run2868_lane12_indexN702-S506=TJ-5_17691~mouse10_align


title: N577

value: CHR


title: WT_Single muslce fiber [s39_17694]

description: run2868_lane12_indexN705-S517=TJ-39_17694~mouse10_align


title: P1000

value: PFC


title: P1011


title: WT_Single muslce fiber [s61]

description: run0092_lane9_indexN722-S508=61~mouse10_align


title: P1003


title: N571


title: WT_Single muslce fiber [s38_17693]

description: run2868_lane12_indexN704-S508=TJ-38_17693~mouse10_align


title: N567


title: WT_Single muslce fiber [s2_17672]

description: run2868_lane12_indexN712-S504=TJ-2_17672~mouse10_align


title: N537


title: WT_Single muslce fiber [s51_17696]

description: run2868_lane12_indexN707-S503=TJ-51_17696~mouse10_align


title: WT_Single muslce fiber [s42_17695]

description: run2868_lane12_indexN706-S502=TJ-42_17695~mouse10_align


title: mIUE_G34R-WT_6_H3K27me3

source_name: neural progenitor cells

value: neural progenitor cells

tag: genotype

value: H3f3a(G34R), Pdgfra(WT), Atrx(shRNA), Tp53(sgRNA)


title: N525


title: mIUE_EV-WT_4_H3K27me3

value: H3f3a(EV), Pdgfra(WT), Atrx(shRNA), Tp53(sgRNA)


title: N524


title: WT_Single muslce fiber [s62]

description: run0092_lane9_indexN723-S510=62~mouse10_align


title: N514


title: N536


title: N1238


title: mIUE_EV-WT_4_H3K36me3


title: mIUE_EV-WT_7_H3K36me3


title: N1239


title: mIUE_G34R-WT_6_H3K36me3


title: N1237


title: WT_Single muslce fiber [s35_17692]

description: run2868_lane12_indexN711-S517=TJ-35_17692~mouse10_align


title: N1235


title: N1236


title: N1234


title: N1233


title: N565


title: mIUE_G34R-WT_7_H3K36me3


title: mIUE_EV-WT_10_H3K36me3


title: mIUE_G34R-WT_7_H3K27ac


title: N1232


title: mIUE_EV-WT_7_H3K27ac


title: mIUE_G34R-WT_4_H3K27ac


title: N1231


title: P1002


title: mIUE_G34R-WT_7_H3K27me3


title: mIUE_G34R-WT_6_H3K27ac


title: mIUE_EV-WT_10_H3K27ac


title: N1229


title: N1228


title: N1227


title: N1226


title: mIUE_EV-WT_10_H3K27me3


title: N1224


title: mIUE_EV-WT_7_H3K27me3


title: mIUE_EV-WT_4_Input

value: Input


title: mIUE_G34R-WT_4_Input


title: mIUE_EV-WT_4_H3K27ac


title: mIUE_G34R-WT_4_H3K27me3


title: N1222


title: N1223


title: mIUE_EV-WT_7_Input


title: N1220


title: mIUE_G34R-WT_7_Input


title: N1216


title: mIUE_EV-WT_10_Input


title: mIUE_G34R-WT_6_RNA


title: mIUE_G34R-WT_6_Input


title: N1215


title: N1210


title: mIUE_EV-WT_7_RNA


title: N1205


title: mIUE_G34R-WT_4_H3K36me3


title: N1230


title: mIUE_EV-WT_10_RNA


title: mIUE_G34R-WT_4_RNA


title: N1204


title: N1202


title: mIUE_EV-WT_4_RNA


title: N1178

value: A


title: N1200


title: mIUE_G34R-WT_7_RNA


title: N1177


title: pgcs_180410_O_E13

city: Geneve

first: Chloe

last: MAYERE

address: Michel Servet, 1

country: Switzerland

institute: UNIGE

description:
Ovary fetal germ cells 13.5 days development
raw_counts_matrix_pgcs_no_adrenal.csv.gz
raw_counts_matrix_pgcs_no_adrenal_unspliced.csv.gz
raw_counts_matrix_pgcs_gonad_adrenal.csv.gz

data_processing:
Demultiplexing, alignment, barcode filtering and UMI counting were performed with the Cell Ranger v2.1 pipeline (10x Genomics).
For cell-associated barcode selection, we computed the knee point and the inflection point of the ranked barcodes distribution plot. The local minimum between these points on the density curve (density base R function, bw=500, n=4096) of the UMI number per barcode was detected using the quantmod package. This local minimum was used as a threshold for cell-associated barcode selections. When no local minimum could be detected between the two points, the nearest local minimum was used.
Germ cells were selected with a louvain clustering approach. To cluster cells we first selected all genes detected in more than 50 cells, and performed ICA (n_comps=100, Seurat) on log normalized values. Clustering was performed using Scanpy louvain method with resolution 1.  Germ cells were identified using 10 well known fetal germ cells markers.
Selected germ cells barcodes were extracted and reads associated to these barcode were extracted from RAW bams using samtools (Version 1.8)
Spliced and unspliced counts matrix were genrated using Velocyto.py (version 0.17.8) script with bam as input and default parameters
Genome_build: Gencode GRCm38.p5   in which the eGFP (NC_011521.1) combined with the bovine GH 3′-splice/polyadenylation signals (Stallings et al., 2002) (NM_180996.1) sequences have been added.
Supplementary_files_format_and_content: CSV Raw spliced reads counts matrix of the germ cells only dataset.
Supplementary_files_format_and_content: CSV Raw unspliced reads counts matrix of the germ cells only dataset.
Supplementary_files_format_and_content: CSV Raw spliced reads counts matrix of the germ cells only dataset.

source_name: Fetal Ovary

growth_protocol: CD-1 female mice were bred with heterozygous Tg(Nr5a1-GFP) transgenic male mice. Adult females were time-mated and checked for the presence of vaginal plugs the next morning (E0.5). E10.5 (8±2 tail somites (ts)), E11.5 (19±4 ts), E12.5, E13.5, E16.5 and E18.5

extract_protocol:
Urogenital ridges and adrenal glands were enzymatically dissociated at 37ºC for 20 and 40 minutes, respectively, using the Papain dissociation system (Worthington #LK003150). Cells were resuspended in DMEM 2%FBS, filtered through a 70 μm cell strainer and stained with the dead cell marker Draq7™ (Beckman Coulter, #B25595). Viable single cells were collected on a BD FACS Aria II by excluding debris (side scatter vs. forward scatter), dead cells (side scatter vs. Draq7 staining), and doublets (height vs. width). Testes and ovaries (from E12.5 to E16.5) were enzymatically dissociated at 37ºC during 15 minutes in Trypsin-EDTA 0.05% (Gibco #25300054), resuspended in DMEM 2%FBS and filtered through a 70 μm cell strainer. After counting, 3000 to 7000 single cells were loaded on a 10x Chromium instrument (10x Genomics).
Single-cell RNA-Seq libraries were prepared using the Chromium Single Cell 3′ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Each condition (organ, sex and developmental stage) was performed in two biological independent replicates. Library quantification was performed using the Qubit fluorometric assay with dsDNA HS Assay Kit (Invitrogen). Library quality assessment was performed using a Bioanalyzer Agilent 2100 with a High Sensitivity DNA chip (Agilent Genomics). Libraries were diluted, pooled and sequenced on an Illumina HiSeq4000 using paired-end 26 + 98 bp as the sequencing mode. Libraries were sequenced at a targeted depth of 100 000 to 150 000 total reads per cell. Sequencing was performed at the Health 2030 Genome Center, Geneva.

tag: developmental stage

value: Female

tag: strain

tag: transgene

value: Germ cell


title: pgcs_180305_AGM_E16

description:
Adrenal ectopic fetal germ cells 16.5 days development
raw_counts_matrix_pgcs_gonad_adrenal.csv.gz

source_name: Fetal Adrenal

value: Male


title: N1176

tag: region


title: pgcs_180425_AGM_E12

description:
Adrenal ectopic fetal germ cells 12.5 days development
raw_counts_matrix_pgcs_gonad_adrenal.csv.gz

tag: Sex


title: pgcs_180227_AGM_E18

description:
Adrenal ectopic fetal germ cells 18.5 days development
raw_counts_matrix_pgcs_gonad_adrenal.csv.gz


title: N1173

value: F

tag: housing


title: pgcs_180222_O_E13


title: N1206


title: N1170


title: pgcs_170830_AGPF_E10

description:
Adreno Gonadal primordium fetal germ cells 10.5 days development female
raw_counts_matrix_pgcs_no_adrenal.csv.gz
raw_counts_matrix_pgcs_no_adrenal_unspliced.csv.gz
raw_counts_matrix_pgcs_gonad_adrenal.csv.gz

source_name: Adreno Gonadal Primordium


title: N1156


title: pgcs_170830_AGPM_E10

description:
Adreno Gonadal primordium fetal germ cells 10.5 days development male
raw_counts_matrix_pgcs_no_adrenal.csv.gz
raw_counts_matrix_pgcs_no_adrenal_unspliced.csv.gz
raw_counts_matrix_pgcs_gonad_adrenal.csv.gz


title: N1175


title: pgcs_170828_AGPF_E10


title: N1155


title: pgcs_170823_AGPM_E11

description:
Adreno Gonadal primordium fetal germ cells 11.5 days development male
raw_counts_matrix_pgcs_no_adrenal.csv.gz
raw_counts_matrix_pgcs_no_adrenal_unspliced.csv.gz
raw_counts_matrix_pgcs_gonad_adrenal.csv.gz


title: N1154


title: pgcs_170823_AGPF_E11

description:
Adreno Gonadal primordium fetal germ cells 11.5 days development female
raw_counts_matrix_pgcs_no_adrenal.csv.gz
raw_counts_matrix_pgcs_no_adrenal_unspliced.csv.gz
raw_counts_matrix_pgcs_gonad_adrenal.csv.gz


title: N1150


title: pgcs_170816_T_E12

description:
Testis fetal germ cells 12.5 days development
raw_counts_matrix_pgcs_no_adrenal.csv.gz
raw_counts_matrix_pgcs_no_adrenal_unspliced.csv.gz
raw_counts_matrix_pgcs_gonad_adrenal.csv.gz

source_name: Fetal Testis


title: N1152


title: N1146


title: pgcs_170816_O_E12

description:
Ovary fetal germ cells 12.5 days development
raw_counts_matrix_pgcs_no_adrenal.csv.gz
raw_counts_matrix_pgcs_no_adrenal_unspliced.csv.gz
raw_counts_matrix_pgcs_gonad_adrenal.csv.gz


title: N1145


title: pgcs_170823_AGM_E18


title: N1143


title: pgcs_170816_AGM_E12


title: pgcs_170814_AGPM_E11


title: pgcs_170814_AGPF_E11


title: N1158


title: N1126


title: pgcs_170828_AGPM_E10


title: N1125


title: pgcs_170807_AGM_E16


title: N1141


title: pgcs_170802_T_E13

description:
Testis fetal germ cells 13.5 days development
raw_counts_matrix_pgcs_no_adrenal.csv.gz
raw_counts_matrix_pgcs_no_adrenal_unspliced.csv.gz
raw_counts_matrix_pgcs_gonad_adrenal.csv.gz


title: pgcs_170726_T_E13


title: pgcs_170802_AGM_E13

description:
Adrenal ectopic fetal germ cells 13.5 days development
raw_counts_matrix_pgcs_gonad_adrenal.csv.gz


title: N1120


title: N1121


title: pgcs_170724_T_E12


title: N1127


title: pgcs_170724_O_E12


title: N1112


title: N1109


title: pgcs_170726_AGM_E13


title: N1104


title: N1107


title: pgcs_170316_T_E16

description:
Testis fetal germ cells 16.5 days development
raw_counts_matrix_pgcs_no_adrenal.csv.gz
raw_counts_matrix_pgcs_no_adrenal_unspliced.csv.gz
raw_counts_matrix_pgcs_gonad_adrenal.csv.gz


title: pgcs_170712_T_E16


title: pgcs_170712_O_E16

description:
Ovary fetal germ cells 16.5 days development
raw_counts_matrix_pgcs_no_adrenal.csv.gz
raw_counts_matrix_pgcs_no_adrenal_unspliced.csv.gz
raw_counts_matrix_pgcs_gonad_adrenal.csv.gz


title: N1102


title: pgcs_170313_O_E16


title: N1101


title: N1098


title: N1140


title: N1097


title: N1095


title: E3.75_WT_03_06_A_EPI

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

country: United Kingdom

institute: Cerevance ltd

description:
ICM
ICM from E3.5 mouse embryos

data_processing:
STAR alignment (ensembl 87)
--sjdbOverhang 149 --twopassMode Basic -–seedSearchStartLmax 10 --outFilterMismatchNoverLmax 0.3 --outFilterMismatchNmax 10 --outFilterMultimapNmax 100 --alignSJoverhangMin 12 --outSJfilterOverhangMin 30 10 10 10 --sjdbScore 1 --clip3pAdapterSeq
htseq-count
-s no -a 20 -m intersection-nonempty
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: ICM from E3.5 mouse embryos

extract_protocol: none provided by the submitter

tag: sample type

value: EPI

value: Stat3 +/+


title: E3.75_WT_03_05_A_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: E3.75_WT_03_08_A_PrE

description:
ICM
ICM from E3.5 mouse embryos

value: PrE


title: E3.75_WT_03_07_A_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: N1094

value: SI


title: E3.75_WT_03_03_A_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: N1090

value: Nac


title: N1093


title: UTUC-32T

city: Houston

first: Hui

last: Yao

state: TX

address: 1515 Holcombe Blvd.

department: Bioinformatics and Computational Biology

institute: MD Anderson Cancer Center

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

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: genomic DNA from upper-tract urothelium

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from upper-tract urothelial carcinomas samples and normal adjacent tissues using DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer’s instructions.

tag: gender

value: M

value: upper-tract urothelium

tag: disease state

value: cancer


title: UTUC-37T


title: UTUC-35T


title: UTUC-41T


title: UTUC-36T


title: UTUC-39T


title: UTUC-42T


title: UTUC-38T


title: UTUC-31T


title: UTUC-34T


title: N1087

value: G

tag: treatment (mg/kg cocaine)

tag: acute/chronic

value: CHR


title: UTUC-30T


title: UTUC-33T


title: E3.75_WT_03_01_A_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: UTUC-43T


title: N1086


title: E3.75_WT_02_16_C_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: UTUC-29T


title: UTUC-28T


title: UTUC-27T


title: N1083


title: UTUC-26T


title: E3.75_WT_02_15_C_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: UTUC-25T


title: E3.75_WT_03_04_A_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: UTUC-22T


title: E3.75_WT_02_14_C_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: N1076


title: E3.75_WT_03_02_A_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: UTUC-21T


title: E3.75_WT_02_13_C_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: UTUC-19T


title: UTUC-15T


title: UTUC-16N

value: normal


title: N1074


title: UTUC-18T


title: N1071


title: UTUC-17T


title: UTUC-14T


title: N1070


title: E3.75_WT_02_11_C_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: UTUC-16T


title: UTUC-12T


title: UTUC-13T


title: N1085


title: UTUC-12N


title: N1067


title: E3.75_WT_02_08_C_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: E3.75_WT_02_09_C_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: UTUC-09T


title: N1066


title: E3.75_WT_02_07_C_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: N1075


title: UTUC-08T


title: E3.75_WT_02_12_C_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: UTUC-09N


title: UTUC-07N


title: E3.75_WT_02_10_C_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: CpG sample 3 miRNA

city: Basseterre

first: Felix

last: Toka

address: West Farm

department: Biomedical Sciences

country: Dominica

institute: Ross University School of Veterinary Medicine

description:
CpG sample 3
CpG_Expt33_GATCAG

data_processing:
The 9 libraries were quantitated by qPCR, pooled in equimolar amounts and sequenced on one lane for 51 cycles from one end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1.
Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina) with -ml 10 option , which trims off adaptors and removes sequences less than 10 nt
Reads 17nt or longer were used to find known and novel miRNAs using miRDeep2 (Friedlander et al. 2012; Nucleic Acids Res, 40(1), 37-52. doi:10.1093/nar/gkr688) using mature and precursor sequences from miRBase release 21 for Bos taurus, Capra hircus and Ovis aries and also and the B. taurus reference genome (release UMD_3.1.1, NCBI Assembly ID GCF_000003055.6)
The resulting novel and known miRNA predictions from miRDeep2 were then checked for overlapping predicted regions.  Any scores from predicted regions with an overlap were compared, and the region with the highest overall score in the comparison was retained to break the tie.  These results were combined with the miRBase bovine-specific miRNAs that miRDeep2 reported as not being found in the reference genome.
Adapter-trimmed reads were initially de-replicated per sample, retaining counts and sample ID information in the sequence header.  Per-sample de-replicated reads were then concatenated and aligned using Novoalign 3.06.03 (using the miRNA mode) to the miRDeep2 predicted mature and hairpin sequences for B. taurus.  The final sorted alignments (now containing read IDs that have the sample and count) were then parsed by a simple script to generate accurate miRNA counts.
Data from counts mapping uniquely to mature miRNAs had the lowest level of ambiguity; these were used in downstream gene expression analyses.
Genome_build: NCBI UMD_3.1.1
Supplementary_files_format_and_content: counts

organism: Bos taurus

source_name: bovine macrophage cell line

growth_protocol: BoMac cells were routinely cultured in IMDM medium supplemented with fetal bovine serum, antibiotic-antimycotic, non-essential amino acids, vitamins and beta 2 mercaptoethanol. Cells were subcultured every 3 days.

extract_protocol:
total RNA was extracted with the Qiagen miRNeasy kit according to the manufacturers' instructions.
small RNA libraries were prepared using the TruSeq Small RNA Sample Prep kit (Illumina).

treatment_protocol: BoMac cells were plated into 6-well plates at least 24 h before treatment. CpG or pI:C was later added at 50 ug/ml and 10 ug/ml, respectively. Cells were then incubated for 6 h and thereafter harvested for RNA isolation.

tag: cell line

value: BoMac

tag: cell type

value: peripheral blood monocyte

tag: treatment

value: CpG

tag: replicate


title: CpG sample 2 miRNA

description:
CpG sample 2
CpG_Expt22_ACTTGA


title: E3.75_WT_02_03_C_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: N1062

city: New York

institute: Icahn School of Medicine at Mount Sinai


title: E3.75_WT_02_02_C_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: E3.75_WT_02_01_C_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: N1063


title: E3.75_WT_02_04_C_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: UTUC-05T

tag: tissue


title: UTUC-06N


title: UTUC-06T


title: CpG sample 1 miRNA

description:
CpG sample 1
CpG_Expt11_CAGATC


title: UTUC-04T


title: pl_C sample 3 miRNA

description:
pl_C sample 3
pI_C_Expt33_GCCAAT


title: UTUC-04N


title: E3.75_WT_01_08_C_EPI

description:
ICM
ICM from E3.5 mouse embryos

tag: genotype


title: E3.75_WT_01_07_C_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: N1047

value: A


title: N1048


title: N1065


title: UTUC-03T


title: pl_C sample 2 miRNA

description:
pl_C sample 2
pI_C_Expt22_ACAGTG


title: UTUC-3N


title: N1045


title: pl_C sample 1 miRNA

description:
pl_C sample 1
pI_C_Expt11_TGACCA


title: E3.75_WT_01_06_C_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: N1060


title: Control sample 3 miRNA

description:
Control sample 3
Control_Expt33_TTAGGC

value: Control


title: N1044

value: F


title: UTUC-2N


title: N1043


title: Control sample 1 miRNA

description:
Control sample 1
Control_Expt11_ATCACG


title: Control sample 2 miRNA

description:
Control sample 2
Control_Expt22_CGATGT


title: E3.75_WT_01_04_C_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: E3.75_WT_01_02_C_EPI

description:
ICM
ICM from E3.5 mouse embryos

value: EPI


title: UTUC-2T


title: N1037


title: N1036


title: E3.75_MUT_05_08_A_PrE

description:
ICM
ICM from E3.5 mouse embryos

value: Stat3 -/-


title: N1035


title: N1038


title: E3.75_MUT_05_06_A_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: E3.75_MUT_05_07_A_PrE

description:
ICM
ICM from E3.5 mouse embryos

value: PrE


title: E3.75_MUT_05_05_A_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: N1046


title: N1034

value: SI


title: N1033

value: Nac


title: E3.75_MUT_05_04_A_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: N1032


title: N1030


title: N1018

value: M


title: E3.75_MUT_05_02_A_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: N1017


title: E3.75_WT_01_05_C_EPI

description:
ICM
ICM from E3.5 mouse embryos

value: Stat3 +/+


title: E3.75_MUT_04_08_A_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: E3.75_MUT_04_07_A_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: E3.75_WT_01_01_C_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: N1015


title: E3.75_MUT_04_06_A_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: N1016


title: N1014


title: E3.75_MUT_04_04_A_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: E3.75_MUT_04_05_A_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: N1011


title: N1007


title: E3.75_MUT_04_02_A_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: E3.75_MUT_05_03_A_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: E3.75_MUT_04_01_A_PrE

description:
ICM
ICM from E3.5 mouse embryos