title: C. elegans RDE-3 Δ169-end #1

source_name: C. elegans RDE-3 Δ169-end #1

value: C. elegans RDE-3 Δ169-end


title: C. elegans RDE-3b #5

status: Public on Dec 08 2018

type: SRA

city: Madison

first: Melanie

last: Preston

state: WI

address: 433 Babcock Dr

department: Biochemistry

country: USA

institute: University of Wisconsin-Madison

library_source: transcriptomic

data_processing:
Illumina Casava1.9 software used for basecalling
Use custom Python script (extract tails.py) to identify unique tails added to tRNA reporter from every .fastq file in a directory.
Use custom Python script (analyzeTails.py) to compile nucleotide composition of tails added to tRNA reporter at each tail length and normalize to dataset size
Use custom Perl script to calculate the total percent of each nucleotide in added tails
Genome_build: N/A
Supplementary_files_format_and_content: txt file contains columns of sequence of the end of the reporter tRNA, tail sequence, and # times observed

molecule: total RNA

organism: Saccharomyces cerevisiae BY4741

source_name: C. elegans RDE-3b #5

growth_protocol: BY4741 yeast were co-transformed using standard methods with a plasmid expressing the reporter tRNA and a plasmid expressing the rNTase of interest, or vector controls, and selected on synthetic yeast medium lacking uracil and leucine (SD-Ura-Leu).  Cultures were inoculated with single colonies, grown to saturation, and then diluted to 0.1 OD600/mL and grown to log phase (0.8-1 OD600/mL).  Cells were spun down in pellets of 25 OD600 (approximately 5 x 108 cells) and stored at -80°C until RNA extraction

extract_protocol:
RNA was extracted from 25 OD of yeast corresponding to each sample by modification of a previously described method.  Briefly, to each sample, 0.5 g of 0.5 mm acid washed beads (Sigma-Aldrich), 0.5 mL of RNA ISO buffer (500 mM NaCl, 200 mM Tris-Cl pH 7.5, 10 mM EDTA, 1 % SDS) and 0.5 mL of phenol-chloroform-isoamyl alcohol pH 6.7 (PCA, Fisher Scientific) was added.  Samples were lysed with 10 cycles that each consisted of vortexing for 20 seconds and incubation on ice for 30 seconds.  1.5 volumes (relative to starting amount of ISO Buffer) of RNA ISO Buffer and of PCA were added, and samples were centrifuged at 4°C to separate phases. The aqueous layer was transferred to a pre-spun phase-lock gel (heavy) tube (5PRIME/Quantabio); an equal volume of PCA was added and mixed prior to centrifugation at room temperature to separate phases.  The aqueous layer was transferred to 2 new tubes for ethanol precipitation with 2 volumes of 100% ethanol followed incubation at -80°C for 1 hour to overnight. Precipitated RNA was pelleted by centrifugation at 4°C.  Each pellet was dissolved in 25 μL nuclease-free water and combined into 1 tube per sample.  Co-purifying DNA was digested with 20 U of Turbo DNase (Invitrogen) at 37°C for 4 hours, and RNA was cleaned up with the GeneJET RNA Purification Kit (Thermo Scientific), and eluted with 50 μL of DEPC-treated water.
Total RNA (100 ng) was ligated with 20 pmol of a 5ʹ adenylated primer containing a 7-nucleotide random DNA sequence (random heptamer), Illumina TruSeq adapter sequence and a 3ʹ dideoxycytidine (5ʹ-A(pp) NNNNNNN TGGAATTCTCGGGTGCCAAGG ddC-3ʹ) using 200 U of T4 RNA ligase 2, truncated KQ (New England BioLabs) in a 20μL reaction with 16°C overnight incubation.  This ligation added the random heptamer and Illumina TruSeq adapter sequence to the 3ʹ end of the RNAs in the sample.  Half of the ligation reaction (10 μL) was reverse transcribed using 5 pmol of Illumina RNA RT primer (5ʹ-GCCTTGGCACCCGAGAATTCCA-3ʹ) and ImProm-II Reverse Transcriptase (Promega Corporation) with 1.5 mM MgCl2 and 0.5 mM dNTPs, according to manufacturer’s instructions.  Samples were then PCR-amplified with a forward primer consisting of Illumina-specific sequences and sequence (underlined),  specific to the tRNA reporter   (5ʹ-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATCGAGGATCACCCATGTCGCAG-3ʹ) and a reverse Illumina RNA PCR Primer with various indices used for multiplexing, using GoTaq Green PCR Master Mix (Promega Corporation). PCR products were run on an 8% polyacrylamide 8M urea gel and gel extracted. Resulting samples for each sequencing run were combined in equimolar amounts and run on an Illumina HiSeq2000 or HiSeq2500 (2x50 bp or 2x100 bp), to produce approximately 1 x 106 reads per sample.

tag: rntase expressed

value: C. elegans RDE-3b

tag: trna reporter expressed

value: S. cerevisiae tRNASer(IGA) with MS2 stem loop


title: C. elegans RDE-3 Δ164-end #1

source_name: C. elegans RDE-3 Δ164-end #1

value: C. elegans RDE-3 Δ164-end


title: C. elegans RDE-3 Δ169-end #2

source_name: C. elegans RDE-3 Δ169-end #2


title: C. elegans RDE-3b #3

source_name: C. elegans RDE-3b #3


title: C. elegans ZK863.4 #1

source_name: C. elegans ZK863.4 #1

value: C. elegans ZK863.4


title: C. elegans RDE-3 Δ113-221 #3

source_name: C. elegans RDE-3 Δ113-221 #3

value: C. elegans RDE-3 Δ113-221


title: C. elegans RDE-3 Δ113-221 #2

source_name: C. elegans RDE-3 Δ113-221 #2


title: C. elegans RDE-3b DADA #1

source_name: C. elegans RDE-3b DADA #1

value: C. elegans RDE-3b DADA


title: C. elegans RDE-3b DADA #2

source_name: C. elegans RDE-3b DADA #2


title: C. elegans RDE-3 Δ164-end #2

source_name: C. elegans RDE-3 Δ164-end #2


title: C. elegans RDE-3b #4

source_name: C. elegans RDE-3b #4


title: C. elegans RDE-3 G366R #6

source_name: C. elegans RDE-3 G366R #6

value: C. elegans RDE-3 G366R


title: C. elegans RDE-3 G366R #4

source_name: C. elegans RDE-3 G366R #4


title: C. elegans RDE-3 G366R #5

source_name: C. elegans RDE-3 G366R #5


title: C. elegans RDE-3 G93E #2

source_name: C. elegans RDE-3 G93E #2

value: C. elegans RDE-3 G93E


title: C. elegans RDE-3 G93E #1

source_name: C. elegans RDE-3 G93E #1


title: tRNA reporter only #2

source_name: tRNA reporter only #2

value: Empty vector


title: C. elegans RDE-3 G366R #3

source_name: C. elegans RDE-3 G366R #3


title: C. elegans RDE-3 G366R #2

source_name: C. elegans RDE-3 G366R #2


title: C. elegans RDE-3 G366R #1

source_name: C. elegans RDE-3 G366R #1


title: C. elegans RDE-3 D189N #2

source_name: C. elegans RDE-3 D189N #2

value: C. elegans RDE-3 D189N


title: C. elegans RDE-3b #2

source_name: C. elegans RDE-3b #2


title: C. elegans RDE-3b #1

source_name: C. elegans RDE-3b #1


title: C. elegans RDE-3 Δ113-221 #1

source_name: C. elegans RDE-3 Δ113-221 #1


title: C. elegans RDE-3a DADA #4

source_name: C. elegans RDE-3a DADA #4

value: C. elegans RDE-3a DADA


title: C. elegans RDE-3a DADA #2

source_name: C. elegans RDE-3a DADA #2


title: C. elegans RDE-3a DADA #3

source_name: C. elegans RDE-3a DADA #3


title: C. elegans RDE-3a #4

source_name: C. elegans RDE-3a #4

value: C. elegans RDE-3a


title: C. elegans RDE-3a #2

source_name: C. elegans RDE-3a #2


title: C. elegans RDE-3a #1

source_name: C. elegans RDE-3a #1


title: C. elegans RDE-3 D189N #1

source_name: C. elegans RDE-3 D189N #1


title: C. elegans PUP-3 #1

source_name: C. elegans PUP-3 #1

value: C. elegans PUP-3


title: C. elegans PUP-2

source_name: C. elegans PUP-2

value: C. elegans PUP-2


title: C. elegans RDE-3a #3

source_name: C. elegans RDE-3a #3


title: C. elegans PUP-3 #2

source_name: C. elegans PUP-3 #2


title: C. elegans RDE-3a #6

source_name: C. elegans RDE-3a #6


title: C. elegans PUP-1 #1

source_name: C. elegans PUP-1 #1

value: C. elegans PUP-1


title: A549_NOCT_KO4

city: Princeton

first: Alexei

last: Korennykh

state: New Jersey

address: 216 Shultz Laboratory

department: Molecular Biology

institute: Princeton University

data_processing:
Reads were split by barcodes and assigned to the respective samples
Reads were mapped to HG19 using TopHat 2 set to map first stranded reads with default parameters
Exon reads were counted using HTseq-count in union mode
Genome_build: HG19
Supplementary_files_format_and_content: Excel sheet with exon counts

molecule: polyA RNA

organism: Homo sapiens

source_name: Lung carcinoma epithelium

growth_protocol: Grown in RMPI supplemented with 10% FBS

extract_protocol:
At the endpoint, media was aspirated and cells were lysed in 300 uL RLT buffer (RNeasy extraction kit, Qiagen) containing 1% BME and total RNA was extracted. RNA integrity was verified by an RNA 6000 Nano Chip, using BioAnalyzer and 2100 Expert software (Agilent Technologies).
The mRNA was enriched by oligo-dT pulldown from total RNA, followed by fragmentation, adapter ligation, PCR amplification, and finally sequencing on Illumina HiSeq 2000 platform.

treatment_protocol: Cells were seeded in 6-well plates and collected at 70% confluency.

tag: cell line

tag: genotype/variation

value: Nocturnin knockout A549


title: C. elegans HPO-31 #1

source_name: C. elegans HPO-31 #1

value: C. elegans HPO-31


title: A549_NOCT_KO5


title: C. elegans PUP-1 #2

source_name: C. elegans PUP-1 #2


title: C. elegans HPO-31 #2

source_name: C. elegans HPO-31 #2


title: A549_WT1

value: WT A549


title: C. elegans GLD-4 #1

source_name: C. elegans GLD-4 #1

value: C. elegans GLD-4

value: S. cerevisiae tRNASer(IGA) with MS2 stem loop


title: C. elegans RDE-3a DADA #1

source_name: C. elegans RDE-3a DADA #1


title: C. elegans RDE-3a #5

source_name: C. elegans RDE-3a #5


title: C. elegans RDE-3a #8

source_name: C. elegans RDE-3a #8


title: C. elegans RDE-3a #7

source_name: C. elegans RDE-3a #7


title: C. elegans GLD-4 #2

source_name: C. elegans GLD-4 #2


title: C. elegans GLD-2

source_name: C. elegans GLD-2

value: C. elegans GLD-2


title: C. elegans F43H9.3 #1

source_name: C. elegans F43H9.3 #1

value: C. elegans F43H9.3


title: C. elegans F43H9.3 #4

source_name: C. elegans F43H9.3 #4


title: RNA-Seq HeLa FLDD 1h TNF Repl2

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

country: Germany

institute: Philipps University of Marburg

data_processing: RNA-Seq data were aligned to hg38 or mm10 using RNA STAR using a gffread filtered gencode annotation file. Normalized reads were obtained using cufflinks.

source_name: HeLa

growth_protocol: HeLa and MEF cells were cultured in DMEM (Life Technologies) supplemented with FCS and Penicillin/Streptomycin.

extract_protocol:
For RNA-Seq cells were harvested and total RNA was isolated using the NucleoSpin RNA Kit (Macherey-Nagel).  For ChIP-Seq samples were crosslinked using Formaldehyde, Sonicated and chromatin was extracted using the p65 Antibody. DNA was purified NucleoSpin Gel and PCR Clean UP Kit with buffer NTB (Macherey-Nagel).
RNA-Seq libraries were prepared from total RNA using the TruSeq Stranded total RNA LT kit (Illumina). ChIP-Seq libraries were prepared from purified ChIP DNA with the Microplex Library Preparation Kit (Diagenode)

treatment_protocol: HeLa cells and MEFs were stimulated with TNFα (20 ng/ml) for 60 min

tag: tissue

value: HeLa cells

value: p65 KO, FLDD p65 rescue

tag: tnf stimulation

value: 1h TNF


title: C. elegans F43H9.3 #3

source_name: C. elegans F43H9.3 #3


title: C. elegans F43H9.3 #2

source_name: C. elegans F43H9.3 #2


title: A549_WT2


title: C. elegans F43E2.1 #2

source_name: C. elegans F43E2.1 #2

value: C. elegans F43E2.1


title: C. elegans F43E2.1 #3

source_name: C. elegans F43E2.1 #3


title: RNA-Seq HeLa FLDD 0h TNF Repl2

value: 0h TNF


title: C. elegans GLD-4 #3

source_name: C. elegans GLD-4 #3


title: RNA-Seq HeLa E39I 1h TNF Repl2

value: p65 KO, E39I p65 rescue


title: C. elegans F43E2.1 #1

source_name: C. elegans F43E2.1 #1


title: RNA-Seq HeLa E39I 0h TNF Repl2


title: RNA-Seq HeLa wt 1h TNF Repl2

value: p65 KO, wt p65 rescue


title: G-CSF 1

type: RNA

city: Frankfurt

first: Darja

last: Karpova

address: Sandhofstrasse 1

department: Cell Therapeutics

institute: German Red Cross Blood Donor Service

description: gene expression of G-CSF mobilized LSK

hyb_protocol: The balanced aRNAs were suspended in Agilent 2X Gene Expression buffer (55ul), Agilent 10X Blocking agent (11ul), and Kreablock (6ul).  The hybridization solutions were applied to Agilent Mouse v2 4x44K microarrays (G4846A-026655).  Hybridization was carried out at 65C for 20 hours.  Washing procedures were carried out according to Agilent gene expression protocols.

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence, according to manufacturer's specifications.

data_processing: Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies).

organism: Mus musculus

source_name: PB LSK, G-CSF, 9 injections

label_protocol: cDNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics).  Per reaction, 3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy5/DY-ULS (2ul).  The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes.  Labeled cDNA was purified with Qiagen PCR purification columns according to manufacturer’s protocol.  cDNAs were quantitated on a Nanodrop spectrophotometer. Detailed protocol can be found at http://www.kreatech.com/fileadmin/user_upload/Documenten/PDF/12_man_EA-021-022-023__D0.6.pdf

growth_protocol: HSCs harvested directly from mouse by flow cytometry

extract_protocol: RNA was prepared using the NucleoSpin® RNA XS Isolation kit (Macherey-Nagel, Bethlehem, PA, USA) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA transcripts were first amplified by WTA2 kit (Sigma Aldrich).  2ng of total RNA (14ul) was amplified according to manufacturer’s protocol.  http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Bulletin/wta2bul.pdf

treatment_protocol: HSCs from control mice or after 2 or 5 days of G-CSF treatment or 14 days after POL5551 infusion start

tag: strain background

tag: gender

value: male

tag: treatment

value: G-CSF (5 days)

value: peripheral blood

tag: cell type

value: LSK cells (HSPC)


title: G-CSF 2

description: gene expression of G-CSF mobilized LSK


title: CWHM-823+tGro-b 3

description: gene expression of CWHM-823+tGro-b mobilized LSK

source_name: PB LSK, CWHM-823+tGrob-b injection


title: AMD3100 2

description: gene expression of AMD3100 mobilized LSK

source_name: PB LSK, AMD3100 injection


title: C. elegans F31C3.2 #5

source_name: C. elegans F31C3.2 #5

value: C. elegans F31C3.2


title: AMD3100 3


title: CWHM-823+tGro-b 1


title: soxEb_3

city: Hangzhou

first: Yanmei

last: Tao

state: Zhejiang

address: 16 Xuelin Street, Xiasha

country: China

institute: Hangzhou Normal University

description: mutant 6

data_processing:
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon paired-end reads of bp length. This yielded gigabases (Gb) of sequence. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed .After that, a total of G bp of cleaned ,paired-end reads were produced.
We aligned reads of each sample to the Mus Musculus reference genome database ftp://ftp.ensembl.org/pub/release-88/gtf/mus_musculus (v88) and reference mRNA database ftp://ftp.ensembl.org/pub/release-88/gtf/mus_musculus (v88) using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome or mRNA.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the ﬁnal transcriptome was generated, StringTie was used to estimate the expression level for mRNAs by calculating FPKM (Fragments Per Kilobase of exon model per Million mapped reads).
Genome_build: v88
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: subcortical white matter tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature.
The cleaved RNA fragments were reverse-transcribed with Random Hexamers to create the cDNA library, and then synthesized the second strands with addition of buffer, dNTPs, RNaseH and DNA polymerase to be double-stranded DNA. Double-stranded DNA fragments with overhangs were repaired to have blunt ends by Klenow DNA polymerase and T4 DNA polymerase and then added A-overhang as well as adapters before purified by AMPure XP beads. Purified DNA fragments were amplified by PCR before purification again to generate the final library for sequencing. The paired-end sequencing was performed on an Illumina Hiseq4000 following the vendor’s recommended protocol and generated reads of 2x150bp (150 PE)

tag: genotype

tag: age

value: Doxycyclline from P21-P30

value: subcortical white matter tissue


title: treEb_2

description: littermate control to mutant 5


title: treEb_3

description: littermate control to mutant 6


title: treEb_1

description: littermate control to mutant 4


title: RNA-Seq HeLa wt 0h TNF Repl2


title: C. elegans F31C3.2 #4

source_name: C. elegans F31C3.2 #4

value: S. cerevisiae tRNASer(IGA) with MS2 stem loop


title: RNA-Seq HeLa ev 1h TNF Repl2

value: p65 KO, empty vector rescue


title: G-CSF 3

description: gene expression of G-CSF mobilized LSK


title: C. elegans F31C3.2 #3

source_name: C. elegans F31C3.2 #3


title: soxEb_1

description: mutant 4


title: CWHM-823+tGro-b 2


title: treEG_3

description: littermate control to mutant 3

value: TRE-dnEGFR

value: Doxycyclline from P21-P35


title: soxEb_2

description: mutant 5


title: C. elegans F31C3.2 #2

source_name: C. elegans F31C3.2 #2


title: RNA-Seq HeLa ev 0h TNF Repl2

value: HeLa cells


title: ctr BM 2

description: gene expression of steady state BM resident LSK

source_name: BM LSK, PBS injection

value: PBS

value: bone marrow


title: ctr BM 3


title: ctr BM 1


title: C. elegans F31C3.2 #1

source_name: C. elegans F31C3.2 #1


title: treEG_2

description: littermate control to mutant 2


title: treEG_1

description: littermate control to mutant 1


title: RNA-Seq HeLa FLDD 1h TNF Repl1

source_name: HeLa

value: p65 KO, FLDD p65 rescue

value: 1h TNF


title: C. elegans C53A5.16 #2

source_name: C. elegans C53A5.16 #2

value: C. elegans C53A5.16


title: RNA-Seq HeLa Ctr 1h TNF Repl2

value: Control cells


title: C. elegans C53A5.16 #4

source_name: C. elegans C53A5.16 #4


title: RNA-Seq HeLa FLDD 0h TNF Repl1

value: 0h TNF


title: soxEG_2

description: mutant 2


title: soxEG_3

description: mutant 3


title: RNA-Seq HeLa Ctr 0h TNF Repl2


title: AMD3100 1

value: male

value: peripheral blood


title: RNA-Seq HeLa E39I 1h TNF Repl1

value: p65 KO, E39I p65 rescue


title: C. elegans C53A5.16 #1

source_name: C. elegans C53A5.16 #1


title: soxEG_1

description: mutant 1


title: C. elegans C53A5.16 #3

source_name: C. elegans C53A5.16 #3


title: RNA-Seq HeLa E39I 0h TNF Repl1


title: C. albicans TRF4 #2

source_name: C. albicans TRF4 #2

value: C. albicans TRF4


title: nhr68_B12-PA_rep2

city: Worcester

first: Amy

last: Holdorf

state: MA

address: 368 Plantation St.

department: Program in Systems Biology

institute: Univesity of Massachusetts Medical School

data_processing:
BGI Bioinformatics Pipeline
Remove reads with adaptors, remove reads in which unknown bases are more than 10%, remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5), store clean reads as FASTQ format.
Use Bowtie2 to map clean reads to reference gene and use HISAT to reference genome.
Genes expression level is quantified by a software package called RSEM.
Use EBSeq to find differentially expressed genes between samples.
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Animals were grown on NGM-agar without vitamin B12 and synchronized for two generations by L1 arrest in M9 buffer for 18 hours post-treatment with buffered bleach.

extract_protocol:
Approximately 3000 L4 stage animals were harvested and washed three times in M9 buffer for each condition. Total RNA was isolated using Trizol (Invitrogen) followed by DNase I (NEB) treatment and cleanup using Direct-zol RNA Mini Prep kit (Zymo Research).
Libraries were prepared by BGI using their standard protocols.

treatment_protocol: Doubly synchronized animals were grown on NGM-agar alone, or on NGM-agar supplemented with either 20 nM vitamin B12 or 20 nM vitamin B12 and 40 mM propionate until the L4 stage.

tag: strain

tag: allele

tag: developmental stage

tag: agent

value: 20 nM vitamin B12 and 40 mM propionate

value: nhr-68 deletion


title: nhr68_B12-PA_rep1


title: HSF_rF1M-RGA_miRNA_4

city: Montreal

first: Dieter

middle: P.

last: Reinhardt

state: Quebec

address: 3640 University Street

country: Canada

institute: McGill University

description: miRNA

hyb_protocol: The target was hybridized on GeneChip® miRNA3.0 Array (Affymetrix) and incubated at 480C in the Genechip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (Affymetrix) using Affymetrix Hybridization Wash and Stain kit according to the manufacturer’s instructions (Affymetrix). The microarrays were finally scanned on a GeneChip® scanner 3000 (Affymetrix).

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G with the Affymetrix GeneChip Command Consol Scan Control 4.0.0.1567.

data_processing: The quality control of the data were processed using ExpressionConsole  build 1.3.1.187.

label: biotin

source_name: human skin fibrobasts

label_protocol: Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).  A tailing reaction followed by ligation of the biotinylated signal molecule to the target RNA sample was done from 1 µg of total RNA using the Affymetrix FlashTag™ Biotin HSR Labeling Kit according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA). An ELOSA QC Assay was done to confirm that the labeling kit performed appropriately.

growth_protocol: HSFs were seeded on the coated plates in DMEM supplemented with 10% v/v fetal bovine serum, 100 µg/mL penicillin, 100 µg/mL streptomycin, and 2 mM glutamine at 37°C in a 5% CO2 atmosphere.

extract_protocol: Total RNA extraction was performed using the miRNeasy Mini Kit (Qiagen, cat. no. 217004) according to the manufacturer’s instructions.

treatment_protocol: Cell culture plates were coated with the fibrillin-1 fragments rF1M-WT and rF1M-RGA at a concentration of 25 µg/mL in TBS overnight. 1,000,000 HSFs in serum-free media were seeded on the coated plates.  The cells were cultured for 24 h.

tag: fibrillin fragment


title: HSF_rF1M-RGA_miRNA_3

description: miRNA


title: C. albicans RPN1 #2

source_name: C. albicans RPN1 #2

tag: rntase expressed

value: C. albicans RPN1

value: S. cerevisiae tRNASer(IGA) with MS2 stem loop


title: C. albicans TRF4 #1

source_name: C. albicans TRF4 #1

tag: trna reporter expressed


title: RNA-Seq HeLa wt 0h TNF Repl1

value: p65 KO, wt p65 rescue


title: HSF_rF1M-RGA_miRNA_1

description: miRNA


title: HSF_rF1M-RGA_miRNA_2

description: miRNA


title: nhr68_B12_rep2

value: 20 nM vitamin B12


title: nhr68_B12_rep1


title: HSF_rF1M-WT_miRNA_1

description: miRNA


title: nhr68_OP50_rep2


title: HSF_rF1M-WT_miRNA_2

description: miRNA


title: C. albicans CR_03940W_A #2

source_name: C. albicans CR_03940W_A #2

value: C. albicans CR_03940W_A


title: RNA-Seq HeLa ev 1h TNF Repl1

value: HeLa cells

value: p65 KO, empty vector rescue


title: C. albicans CR_03940W_A #1

source_name: C. albicans CR_03940W_A #1


title: HSF_rF1M-WT_miRNA_3

description: miRNA


title: C. albicans CCA1

source_name: C. albicans CCA1

value: C. albicans CCA1


title: nhr10_B12-PA_rep2

value: nhr-10 deletion


title: HSF_rF1M-WT_miRNA_4

description: miRNA


title: C. albicans RPN1 #1

source_name: C. albicans RPN1 #1


title: RNA-Seq HeLa wt 1h TNF Repl1

value: 1h TNF


title: RNA-Seq HeLa Ctr 1h TNF Repl1

value: Control cells


title: RNA-Seq HeLa Ctr 0h TNF Repl1

value: 0h TNF


title: nhr68_OP50_rep1


title: RNA-Seq HeLa ev 0h TNF Repl1


title: HSF_rF1M-RGA_4

description: mRNA

hyb_protocol: After fragmentation and labeling, 3.5µg DNA target was hybridized on GeneChip® Human Gene 2.0 ST  (Affymetrix) and incubated at 450C in the Genechip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (Affymetrix) using Affymetrix Hybridization Wash and Stain kit according to the manufacturer’s instructions (Affymetrix). The microarrays were finally scanned on a GeneChip® scanner 3000 (Affymetrix).

label_protocol: Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).  Sense-strand cDNA was synthesized from 100 ng of total RNA, and fragmentation and labeling were performed to produce ss DNA with the Affymetrix GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (Affymetrix).


title: HSF_rF1M-RGA_2

description: mRNA


title: ChIP-Seq p65 HeLa FLDD 1h TNF

library_source: genomic

data_processing:
ChIP-Seq data were aligned to human genome hg19 and hg38 using bowtie 1.0 with n = 1 and m = 3 as parameter
Bigwig files were created using Galaxy/Cistrome or Galaxy/deepTools, duplicated tags were ignored

molecule: genomic DNA

value: p65 KO, FLDD p65 rescue

tag: chip antibody

value: p65 (C-20); Santa Cruz sc-372


title: HSF_rF1M-WT_4

description: mRNA


title: HSF_rF1M-RGA_3

description: mRNA


title: nhr10_B12-PA_rep1

tag: genotype/variation


title: A. nidulans cutB #3

source_name: A. nidulans cutB #3

value: A. nidulans cutB


title: C. albicans C3_02760C_A

source_name: C. albicans C3_02760C_A

value: C. albicans C3_02760C_A


title: ChIP-Seq p65 HeLa FLDD 0h TNF

tag: tissue


title: nhr10_B12_rep1


title: A. nidulans cutB #2

source_name: A. nidulans cutB #2


title: nhr10_B12_rep2


title: HSF_rF1M-RGA_1

description: mRNA


title: A. nidulans cutB #1

source_name: A. nidulans cutB #1


title: nhr10_OP50_rep2


title: A. nidulans cutA #3

source_name: A. nidulans cutA #3

value: A. nidulans cutA


title: ChIP-Seq p65 HeLa WT 1h TNF

source_name: HeLa

tag: tnf stimulation


title: ChIP-Seq p65 HeLa E39I 0h TNF

value: p65 KO, E39I p65 rescue


title: A. nidulans cutA #2

source_name: A. nidulans cutA #2

value: S. cerevisiae tRNASer(IGA) with MS2 stem loop


title: HSF_rF1M-WT_3

description: mRNA


title: ChIP-Seq p65 HeLa WT 0h TNF

value: p65 KO, wt p65 rescue


title: nhr10_OP50_rep1


title: ChIP-Seq p65 HeLa ev 1h TNF


title: N2_B12-PA_rep1

value: wild type

value: 20 nM vitamin B12 and 40 mM propionate


title: A. nidulans cutA #1

source_name: A. nidulans cutA #1


title: N2_B12_rep2

value: 20 nM vitamin B12


title: ChIP-Seq p65 HeLa Control 1h TNF

value: HeLa cells


title: N2_B12-PA_rep2


title: ChIP-Seq p65 HeLa ev 0h TNF

value: p65 KO, empty vector rescue


title: ChIP-Seq p65 HeLa E39I 1h TNF


title: ChIP-Seq p65 HeLa Control 0h TNF


title: HSF_rF1M-WT_2

description: mRNA


title: N2_OP50_rep1


title: N2_OP50_rep2


title: N2_B12_rep1


title: wt43

status: Public on Dec 07 2018

city: Indianapolis

first: Yupeng

last: Li

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

data_processing:
RNAseq data were subjected to a QC pipeline developed at Eli Lilly and Company. Briefly, base quality/base composition, heterologous organism contamination, adapter content, mapping rate/mapped read counts, 3’ bias, template length, and rRNA/mitochondrial content were checked. Four samples, WT-4m-3, rTg4510-4m-3, WT-8m-4, and rTg4510-8m-4, were excluded from further analysis due to failed RNAseq QC assessment.
To map reads to genes and obtain gene level expression measures, RNAseq data were subjected to a “rollup” pipeline developed at Eli Lilly and Company. The following rules were applied for the rollup: (1) Exon reads of multiple assays from the same libraries were summed; (2) Exons were excluded if more than 80% of samples have less than 10 counts; (3) Robust gene level signals across exons of a gene were determined by a robust linear model and were output for each library and each gene; (4) Mean signal of log2 transformed gene level across all samples were median normalized.
Genome_build: GRCm38
Supplementary_files_format_and_content: a single csv files that includes log2 expression value of each sample. Gene IDs are NCBI's ENTREZ Gene IDs.

source_name: microglia

extract_protocol:
Microglia were isolated using CD11b MicroBeads methods. Total RNA were isolated and sent to Cofactor Genomics (St. Louis, USA) for RNA deep sequencing. RNA samples were first examined using Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) for purity and quality. RNAs were reverse transcribed to cDNA using Ovation RNA-Seq System Version 2 (NuGEN, San Carlos, CA) according to the manufacturer’s protocol.
The resulting cDNAs were then sheared using a focused ultrasonicator (Covaris Inc., Woburn, MA, USA) and the libraries were prepared using the Kapa LTP Library Preparation Kit (Illumina, San Diego, CA, USA)

value: microglia

value: Wild-type

value: 8 months

tag: Sex

value: female


title: wt42


title: wt32

value: 6 months


title: wt44


title: wt22

value: 4 months


title: wt24


title: wt34


title: wt33


title: wt14

value: 2 months


title: wt41


title: wt23


title: wt21


title: wt13


title: HepG2_9A KD hairpin 34_3999545105_E

city: Amsterdam

first: Sander

last: Meisner

state: NH

address: Meibergdreef 69-71

department: Tytgat institute

country: Netherlands

institute: AMC

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: hairpin 34 replicate 1

label_protocol: Biotinylated cRNA were prepared with the Invitrogen Totalprep RNA amplification kit

extract_protocol: RNA was isolated using the isolate II RNA mini kit (Bioline). 150ng RNA was labelled with cRNA labeling kit for Illumina bid array (Ambion) and hybridized with Ref8v3 BeadArray (Illumina).

treatment_protocol: Human hepatoma (HepG2) cells were transduced with lentiviral constructs containing short hairpin for ATP9A gene. 72 hours after the transduction total RNA was isolated and gene expression profiling was done.

tag: cell line

value: Human hepatoma cell line

value: hairpin 34


title: HepG2_SHC_3999545105_A

source_name: short hairpin control

value: short hairpin control


title: HSF_rF1M-WT_1

description: mRNA

source_name: human skin fibrobasts


title: HepG2_SHC_3999545105_B


title: HepG2_SHC_3999545105_G


title: NSTEMI_3, blood

city: Beijing

first: Yan

address: An Zhen Road 2, An Ding Men Wai Street, Chaoyang District

institute: Beijing Institute of Heart, Lung and Blood Vessel Diseases

description: total RNA isolated from whole blood

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Probe Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were subjected to background adjustment, quantile normalization and log2 transformation with Robust Multiarray Average (RMA) using Transcriptome Analysis Console software.

source_name: Peripheral venous blood

label_protocol: Biotinylated cRNA is synthesized and amplified by in vitro Transcription (IVT) of the double-stranded cDNA template using T7 RNA polymerase.

extract_protocol: Extracting RNA from whole blood collected in Tempus blood RNA tubes using centrifugation based elution, and isolation of total RNA using mirVana PARIS Kit was performed according to the manufacturer's instructions.

tag: disease state

value: acute myocardial infarction (AMI)

tag: gender

value: Female

value: peripheral venous blood


title: NSTEMI_1, blood

description: total RNA isolated from whole blood

value: Male


title: wt11

tag: cell type

tag: genotype


title: HepG2_9A KD hairpin 34_3999545105_F


title: HepG2_9A KD hairpin 33_3999545105_C

source_name: hairpin 33 replicate 1

value: hairpin 33


title: HepG2_9A KD hairpin 33_3999545105_D


title: TG44

value: Transgenic

tag: strain

tag: age


title: wt31


title: NSTEMI_2, blood

description: total RNA isolated from whole blood


title: TG43


title: NSTEMI_4, blood

description: total RNA isolated from whole blood


title: TG42


title: TG32


title: TG24


title: TG12


title: TG41


title: TG34


title: TG14


title: TG22


title: TG21


title: TG33


title: TG31


title: TG23


title: wt12


title: TG11


title: TG13


title: WT male

city: Ariel

first: Elad

last: Lax

address: 65 Ramat HaGolan st.

country: Israel

institute: Ariel University

data_processing:
Sequences were aligned to the mm9 mouse reference genome using Bsmap v2.89
Output data were strand-sorted, filtered, and deduplicated with Picard tools
Methylation levels and coverage levels were extracted with methratio.py command in Bsmap
Differential methylation cytosines were analyzed with methylKit R package (FDR<0.05)
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

source_name: Frontal cortex

extract_protocol:
mice were sacrificed, the brains were rapidly removed, frontal cortices were isolated, flesh frozen and stored at -80°C for later analysis. DNA was sonicated, GR-antibody was used for immunprecipitaion, followed by DNA cleaning and bisulphite conversion
DNA libraries were prepared for sequencing using standard Illumina protocols

value: Frontal cortex

value: male

value: wild type


title: GR-i male

value: glucocorticoid receptor-impaired (GR-i)


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) liver, 12 Month DKO_12M_2

city: SAN DIEGO

first: gaowei

last: wang

state: CALIFORNIA

address: 3393 Lebon DR, APT 202

institute: University of California San Diego

data_processing:
Raw data quality control using QCfastq
Sequenced reads were mapped to mm9 whole genome using star
Fragments Per Kilobase Million(FPKM) were calculated using cuffdiff
Genome_build: mm9
Supplementary_files_format_and_content: csv files include FPKM value of genes for each sample

source_name: Liver

extract_protocol:
Samples were removed, flash frozen on dry ice, and RNA was harvested. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: wide type control, hepatocyte-specific shp2 deletion mice, hepatocyte-specific pten deletion mice, and hepatocyte-specific shp2 and pten double deletion mice

tag: genetic background

value: Liver

value: 12 month old

value: hepatocyte-specific deletion of Shp2 and Pten, shp2-/- and pten-/-


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) tumor liver, 12 Month DKO_12M_T_1

value: 12 month old, tumour


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) tumor liver, 7 Month DKO_7M_T_1

value: 7 month old, tumour


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) tumor liver, 7 Month DKO_7M_T_0


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) liver, 12 Month DKO_12M_0


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) liver, 7 Month DKO_7M_2

value: 7 month old


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) liver, 12 Month DKO_12M_1


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) tumor liver, 12 Month DKO_12M_T_2


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) liver, 7 Month DKO_7M_1


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) liver, 7 Month DKO_7M_0


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) liver, 2 Month DKO_2M_2

value: 2 month old


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) liver, 2 Month DKO_2M_1


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) liver, 1 Month DKO_1M_1

value: 1 month old


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) liver, 1 Month DKO_1M_2


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) liver, 1 Month DKO_1M_0


title: PKO (hepatocyte-specific deletion of Pten) tumor liver, 16 Month PKO_16M_HCC_3

value: 16 month old, tumour

value: hepatocyte-specific deletion of Pten, pten-/-


title: PKO (hepatocyte-specific deletion of Pten) tumor liver, 16 Month PKO_16M_HCC_1


title: PKO (hepatocyte-specific deletion of Pten) tumor liver, 16 Month PKO_16M_HCC_4


title: PKO (hepatocyte-specific deletion of Pten) tumor liver, 16 Month PKO_16M_HCC_2


title: PKO (hepatocyte-specific deletion of Pten) tumorliver, 16 Month PKO_16M_HCC_0


title: PKO (hepatocyte-specific deletion of Pten) tumor liver, 16 Month PKO_16M_HCA_3


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) tumor liver, 7 Month DKO_7M_T_2


title: PKO (hepatocyte-specific deletion of Pten) tumor liver, 16 Month PKO_16M_HCA_1


title: PKO (hepatocyte-specific deletion of Pten) tumor liver, 16 Month PKO_16M_HCA_0


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) tumor liver, 12 Month DKO_12M_T_0


title: PKO (hepatocyte-specific deletion of Pten) tumor liver, 12 Month PKO_12M_T_2


title: PKO (hepatocyte-specific deletion of Pten) tumor liver, 12 Month PKO_12M_T_0


title: PKO (hepatocyte-specific deletion of Pten) liver, 12 Month PKO_12M_1


title: PKO (hepatocyte-specific deletion of Pten) liver, 9 Month PKO_9M_2

value: 9 month old


title: PKO (hepatocyte-specific deletion of Pten) tumor liver, 12 Month PKO_12M_T_1


title: PKO (hepatocyte-specific deletion of Pten) liver, 9 Month PKO_9M_1


title: PKO (hepatocyte-specific deletion of Pten) liver, 9 Month PKO_9M_0


title: PKO (hepatocyte-specific deletion of Pten) liver, 12 Month PKO_12M_0


title: PKO (hepatocyte-specific deletion of Pten) liver, 7 Month PKO_7M_2_1


title: PKO (hepatocyte-specific deletion of Pten) liver, 12 Month PKO_12M_2


title: PKO (hepatocyte-specific deletion of Pten) liver, 7 Month PKO_7M_2_2


title: DKO (hepatocyte-specific deletion of Shp2 and Pten) liver, 2 Month DKO_2M_0


title: PKO (hepatocyte-specific deletion of Pten) liver, 7 Month PKO_7M_2_0


title: PKO (hepatocyte-specific deletion of Pten) liver, 7 Month PKO_7M_2


title: PKO (hepatocyte-specific deletion of Pten) tumor liver, 16 Month PKO_16M_HCA_2


title: PKO (hepatocyte-specific deletion of Pten) liver, 5 Month PKO_5M_2

value: 5 month old


title: PKO (hepatocyte-specific deletion of Pten) liver, 7 Month PKO_7M_0


title: PKO (hepatocyte-specific deletion of Pten) liver, 7 Month PKO_7M_1


title: PKO (hepatocyte-specific deletion of Pten) liver, 5 Month PKO_5M_1


title: PKO (hepatocyte-specific deletion of Pten) liver, 5 Month PKO_5M_0


title: PKO (hepatocyte-specific deletion of Pten) liver, 3 Month PKO_3M_2

value: 3 month old


title: PKO (hepatocyte-specific deletion of Pten) liver, 3 Month PKO_3M_1


title: PKO (hepatocyte-specific deletion of Pten) liver, 4 Month PKO_4M_0

value: 4 month old


title: PKO (hepatocyte-specific deletion of Pten) liver, 2 Month PKO_2M_2


title: PKO (hepatocyte-specific deletion of Pten) liver, 4 Month PKO_4M_2


title: PKO (hepatocyte-specific deletion of Pten) liver, 4 Month PKO_4M_1


title: PKO (hepatocyte-specific deletion of Pten) liver, 1 Month PKO_1M_2


title: PKO (hepatocyte-specific deletion of Pten) liver, 2 Month PKO_2M_0


title: PKO (hepatocyte-specific deletion of Pten) liver, 1 Month PKO_1M_1


title: PKO (hepatocyte-specific deletion of Pten) liver, 1 Month PKO_1M_0


title: SKO (hepatocyte-specific deletion of Shp2) liver, 12 Month SKO_12M_2

value: hepatocyte-specific deletion of Shp2, shp2-/-


title: Genomic DNA from ependymoma cell line_5

type: genomic

city: Nottingham

first: Hazel

middle: Anne

last: Rogers

address: Medical School

department: Clinical Sciences

country: United Kingdom

institute: University of Nottingham

hyb_protocol: Hybridization protocol was performed according to Illumina manufacturers protocol

scan_protocol: Scanning protocol was performed according to Illumina manufacturers protocol

data_processing: Data analysis was performed using the open source statistical programming language R (R Core Team, 2014; http://www.R-project.org/). Raw data files were processed using the Bioconductor package minfi (Version 3.6; Aryee et al., 2014 (PMID 24478339). The function 'preprocessIllumina' was used to perform same preprocessing steps as Illumina's GenomeStudio software.

label: Cy5 and Cy3

source_name: Cultured human ependymoma cells

label_protocol: Labeling was performed according to Illumina manufacturers protocol

extract_protocol: DNA was extracted from samples according to (Rogers et al 2012). Cells were lysed then DNA extracted using phenol chloroform extraction followed by isopropanol precipitation.

tag: cell line id

tag: tumour

value: Ependymoma

tag: location

value: Posterior fossa

tag: c11orf95-rela fusion positive

value: No


title: Genomic DNA from ependymoma cell line_4


title: SKO (hepatocyte-specific deletion of Shp2) liver, 12 Month SKO_12M_1

value: Liver

value: 12 month old


title: SKO (hepatocyte-specific deletion of Shp2) liver, 12 Month SKO_12M_0


title: SKO (hepatocyte-specific deletion of Shp2) liver, 7 Month SKO_7M_2


title: 97F

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Illumina protocol

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

data_processing:
GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, colour-correction)
Unmethylated and methylated signal intensities

source_name: buccal swab genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using Simhelix Buccal Swab DNA Isolation Kits (Cell Projects, Harrietsham, Kent, England). DNA was extracted using DNAeasy DNA extraction kit (Qiagen, Valencia, CA, USA).

tag: minority

tag: income

tag: adversity

tag: education

tag: genetic ancestry

tag: twin pairs


title: SKO (hepatocyte-specific deletion of Shp2) liver, 7 Month SKO_7M_0

tag: tissue


title: Genomic DNA from ependymoma cell line_6


title: 91M

tag: gender


title: Genomic DNA from ependymoma cell line_3

value: Supratentorial

value: Yes


title: Genomic DNA from ependymoma cell line_2


title: PKO (hepatocyte-specific deletion of Pten) liver, 3 Month PKO_3M_0


title: 94M


title: 98M


title: 96M


title: SKO (hepatocyte-specific deletion of Shp2) liver, 2 Month SKO_2M_1


title: 95


title: SKO (hepatocyte-specific deletion of Shp2) liver, 2 Month SKO_2M_2


title: 88M


title: SKO (hepatocyte-specific deletion of Shp2) liver, 1Month SKO_1M_2


title: PKO (hepatocyte-specific deletion of Pten) liver, 2 Month PKO_2M_1


title: SKO (hepatocyte-specific deletion of Shp2) liver, 2 Month SKO_2M_0


title: SKO (hepatocyte-specific deletion of Shp2) liver, 7 Month SKO_7M_1

value: 7 month old


title: Genomic DNA from ependymoma cell line_1


title: 86F


title: 99F


title: 90M


title: 89M


title: 85M


title: SKO (hepatocyte-specific deletion of Shp2) liver, 1Month SKO_1M_1


title: 9F


title: 93M


title: 87F


title: SKO (hepatocyte-specific deletion of Shp2) liver, 1Month SKO_1M_0


title: WT liver, 16 Month WT_16M_2

value: 16 month old

value: wild type


title: WT liver, 16 Month WT_16M_0


title: WT liver, 12 Month WT_12M_2


title: 80M


title: 84F


title: 82F


title: 83M


title: WT liver, 12 Month WT_12M_1


title: WT liver, 16 Month WT_16M_1


title: WT liver, 12 Month WT_12M_0


title: 92


title: WT liver, 9 Month WT_9M_1


title: WT liver, 7 Month WT_7M_2_2


title: 8M


title: 79M


title: WT liver, 7 Month WT_7M_2_1


title: 78F


title: WT liver, 7 Month WT_7M_2


title: WT liver, 9 Month WT_9M_0


title: WT liver, 7 Month WT_7M_0


title: WT liver, 7 Month WT_7M_2_0


title: WT liver, 5 Month WT_5M_2


title: WT liver, 5 Month WT_5M_1


title: 7M


title: 77M


title: 81M


title: WT liver, 4 Month WT_4M_1


title: WT liver, 5 Month WT_5M_0


title: WT liver, 4 Month WT_4M_2


title: WT liver, 9 Month WT_9M_2


title: WT liver, 4 Month WT_4M_0


title: WT liver, 3 Month WT_3M_2


title: WT liver, 3 Month WT_3M_1


title: 75M


title: WT liver, 3 Month WT_3M_0


title: WT liver, 7 Month WT_7M_1


title: WT liver, 2 Month WT_2M_2

value: 2 month old


title: 70F


title: WT liver, 2 Month WT_2M_0


title: 73M


title: 72


title: 76F


title: WT liver, 2 Month WT_2M_1


title: 62M


title: WT liver, 1 Month WT_1M_2

value: 1 month old


title: 71F


title: 68F


title: 65F


title: 74F


title: 59M


title: foxd3over_INJ1

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

institute: MRC Weatherall Institute of Molecular Medicine

description:
Wild-type
processed data: kmeans_35653000_Cl3.1_Cluster4.bed
processed data: kmeans_35653000_Cl3.1_Cluster5_7_9.bed
processed data: kmeans_44515950_ChIP_Cluster1_2_3_4_6_8.bed

data_processing:
ChIP-seq and ATAC-seq reads were mapped using bowtie (v.1.0.0)
ChIP-seq and ATAC-seq: duplicates were removed using MarkDuplicates (picard-tools/1.83)
Input reads were normalised to the same number of ChIP reads by random down-sampling using samtools/1.1
ChIP peak calling was performed using Homer (v.4.7) findPeaks script using -size 200-minDist 1500 parameters.
ATAC-seq: All samples were randomly down-sampled to the lowest-read containing sample (10,443,726) using samtools/1.1.
ATAC-seq: control tripilactes were merged and experimental triplicate BAM files were merged and sorted using samtools/1.1
ATAC-seq:k-means clustering of ATAC-seq signal was carried out using SeqMINER software as described (Ye et al., 2011), using 3.1 enhancer cluster ATAC-seq peaks and all pulled foxd3 Biotin-ChIP peaks as references for clustering.
RNA-seq reads were mapped using STAR (v.2.4.2a)
Genome_build: danRer10

organism: Danio rerio

extract_protocol:
Foxd3 overexpression ATAC-seq: 50 epiboly embryos were dissected to obtain cells that do not express foxd3 intrinsically; cells were dissociated with 0.05% trypsin to a single cell suspension, centrifuged and re-suspended in Hanks buffer. Cells were lysed and tagmented using Nextera DNA kit (Illumina FC-121-1030 ) for 15 minutes at 37C.
ATAC libraries: Tagmented DNA was amplifed using NEB Next High-Fidelity 2X PCR Master Mix for 15 cycles.

value: Wild-type

value: Embryo

tag: development stage

value: 50% epiboly

tag: cell type

value: Half embryo (intrinsic foxd3+ cells removed)

value: Dissecction

tag: treatment

value: foxd3 mRNA inejction at 1 cell stage

tag: amplification

tag: assay

value: ATAC-seq


title: WT liver, 1 Month WT_1M_1

tag: genetic background

tag: age

tag: genotype


title: 57M


title: foxd3over_INJ2

tag: strain

value: NEB Next High-Fidelity 2X PCR Master Mix


title: foxd3over_CTL3

value: Not injected


title: 5F

tag: minority


title: foxd3over_INJ3


title: 61M

tag: income


title: 55M

tag: adversity


title: foxd3over_CTL1


title: 56M

tag: education


title: 67M

tag: genetic ancestry


title: 63F

tag: twin pairs


title: PDGFR Ribonuclear Protein_shortRNA

city: Boston

first: Aron

last: Gyuris

address: 330 Brookline Avenue

department: Genetics

institute: Beth Israel Deaconess Medical Center

description:
smallRNA_cluster_raw_counts
smallRNA_cluster_norm_counts
smallRNA_miRNA_raw_counts
smallRNA_miRNA_norm_counts
smallRNA_tRNA_raw_counts
smallRNA_yRNA_raw_counts

data_processing:
Sequenced reads for both small RNA-Seq and long RNA-Seq were analyzed using bcbio-nextgen (https://github.com/bcbio/bcbio-nextgen)
Alignments were checked for evenness of coverage, rRNA content, genomic context of alignments (for example, alignments in known transcripts and introns), complexity and other quality checks using a combination of FastQC, Qualimap {Garcia-Alcalde, 2012 #100}, MultiQC {Ewels, 2016 #98} and custom code within the bcbio-nextgen pipeline.
In parallel, Transcripts Per Million (TPM) measurements per isoform were generated by quasialignment using Salmon {Patro, 2017 #105}. Differential expression at the gene level was called with DESeq2 {Love, 2014 #101}, preferring to use counts per gene estimated from the Salmon quasialignments by tximport {Soneson, 2015 #107}.
The DEGreport Bioconductor package was used for QC and clustering analysis (10.18129/B9.bioc.DEGreport).
For the small RNA library trimmed reads were aligned to miRBase v21 with seqbuster {Pantano, 2010 #104} and to the Mus musculus genome (version mm10) using STAR {Dobin, 2013 #97}.
seqcluster {Pantano, 2011 #103} was used to classify small RNA reads into rRNA, miRNA, repeats, genes, tRNAs and others from the UCSC annotation {Mangan, 2014 #102} and the isomiRs Bioconductor package {Ramos, 2017 #106} to get normalized expression values.
Genome_build: mm10, augmented with transcript information from Ensembl release GRCm38.84 using STAR. miRBase v21 for miRNA
Supplementary_files_format_and_content: csv files contain raw reads or normalized values (DESeq2 {Love, 2014 #101} using counts per gene estimated from the Salmon quasi-alignments by tximport) for all fractions

source_name: GBM Tumor-derived Cell Line

growth_protocol: Mouse GBM derived primary cell lines were maintained by plating 1 x 10^6 cells in a 15 cm dish, grown in DMEM (Corning) supplemented with 10%  FBS and p/s and  passaged every 3 days

extract_protocol:
Conditioned media was centrifuged at 300 x g for 10 minutes, then 2000 x g for 15 minutes. The cleared conditioned media was then passed sequentially through a series of syringe filters with decreasing pore size, 2 µm (Whatman), 0.8 µm (Millipore), 0.22 µm (Millipore), and 0.02 µm (Whatman) and the flow-through media cleared of EVs by filtration was further concentrated using a size-exclusion spin column centrifuged for 1 hour at 4200 x g using a 3 kDa size-exclusion spin column (Amicon, Millipore). This serial filtration series isolated small microvesicles (0.22 µm), exosomes (0.02 µm) and RNP complexes (3 kDa) respectively. Captured vesicles were lysed on the filter and total RNA was extracted using the miRCURY™ RNA Isolation Kit – Cell & Plant(Exiqon).
RNA was rRNA-depleted using the Ribo-Zero rRNA Removal Kits (Illumina, CA) and one quarter was fragmented to 100–500 nt using the 5× First-Strand Buffer (Clontech, CA) and used in the SMARTer Stranded RNA-Seq Kit (Clontech) to generate the long RNA library.  The remaining rRNA-depleted samples were used in the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) to generate the small RNA library.  The libraries were sequenced on HiSeq 2000 (Illumina) with single read 50 cycles at the Beijing Genomics Institute (BGI, China).

treatment_protocol: One day after passage, prior to EV collection, media was changed to DMEM (Corning) supplemented with 0.1%  FBS and p/s for 16 hours, then changed again and media was conditioned for 24 hours

tag: passage

tag: rna source

value: Vesicle-depleted conditioned media concentrated with 3 kDa size-exclusion column

value: hPDGFR-A overexpressed, p53-null


title: 64M

tag: gender


title: 14ss Input

description: 2 trangenic alleles: foxd3 BAC driving Avi-tagged foxd3 and ubiqutously-driven biotin ligase

source_name: 14ss Input

extract_protocol:
Biotin ChIP-seq: Cells were dissociated and crosslinked, and nuclei were expulsed using glass dounce tissue grinders, nuclei were lysed in SDS lysis buffer, material was sonicated, biotinylated foxd3 bound to DNA was extracted using streptavidin beads (Dynabeads M-280).
ChIP libraries were prepared using MicropPlex Library Preparation v1 or v2 kit (Diagenode) (75% epiboly - 13, 1-2ss - 12 cycles, 5-6ss - 12 cycles, BirA-only - 10 cycles, 14ss - 10 cycles of amplification)

tag: tissue

tag: development stage

value: 14 somites

tag: cell type

value: Neural crest (foxd3 cells)

value: In vivo Biotinylated foxd3

value: Input

value: Diagenode MicroPlex LibraryPrep

value: ChIP-seq


title: 54M


title: 52F


title: 14ss ChIP

source_name: 14ss ChIP

tag: treatment

value: ChIP

tag: amplification

tag: assay


title: PDGFR Ribonuclear Protein_longRNA

description:
longRNA_rna_raw_counts
longRNA_rna_norm_counts
longRNA_rna_norm_remove_rRNA_counts
longRNA_rnatx_raw_counts
longRNA_rnatx_norm_counts

tag: genotype


title: 66M

tag: age


title: 6M

tag: minority


title: 58M

tag: income


title: PDGFR Exosome_shortRNA

value: Extracellular vesicles from conditioned media captured on 0.02 µm filter


title: 49F

tag: adversity


title: 5-6ss Input

source_name: 5-6ss Input

tag: strain

value: Embryo

value: 5-6 somites


title: 5-6ss ChIP

source_name: 5-6ss ChIP


title: 50

tag: education

tag: genetic ancestry


title: 4M

tag: twin pairs


title: PDGFR Exosome_longRNA

tag: passage

tag: rna source


title: 1-2ss Input

source_name: 1-2ss Input

tag: tissue

value: 1-2 somites


title: 1-2ss ChIP

source_name: 1-2ss ChIP

tag: development stage


title: PDGFR Small Microvesicle_shortRNA

value: Extracellular vesicles from conditioned media captured on 0.22 µm filter


title: Control - BirA-Input

source_name: Control - BirA-Input

tag: cell type

value: CTL input


title: 48M

tag: gender


title: 75% epiboly Input

source_name: 75% epiboly Input

value: 75% epiboly

tag: treatment

tag: amplification


title: PDGFR Small Microvesicle_longRNA

tag: genotype


title: Control - BirA-ChIP

source_name: Control - BirA-ChIP

value: CTL ChIP

tag: assay


title: 47F

tag: age

tag: minority


title: 75% epiboly ChIP

source_name: 75% epiboly ChIP


title: 69M

tag: income

tag: adversity


title: ATACseq_NCC_Citrine-Cherry_2

data_processing:
ChIP-seq, Biotin-ChIP-seq, and ATAC-seq reads were trimmed for quality using sickle (v 1.33) and mapped using bowtie (v.1.0.0). Smoothened bigWig files were generated using a enhanced Perl script courtesy of Jim Hughes.
RNA-seq reads were mapped using STAR (v.2.4.2a)
Genome_build: danRer10

source_name: Citrine reporter and Cherry reporter expressing cells from 5-6ss embryos

extract_protocol:
FACS sorted cells were washed with PBS and stored at -80C in lysis buffer. RNA was extracted using Ambion RNAqueous Micro Total RNA isolation kit (AM1931), checked on Bioanalyser, samples with RIN >7 were used to prepare cDNA using Takara Clontech SmartSeq2 V4 kit (634889).
Sequencing libraries were prepared using Illumina Nextera XT library preparation kit (FC-131-1024).
For ATAC-seq, FACS sorted cells were lysed (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal) and tagmented using Nextera DNA kit (Illumina FC-121-1030 ) for 30 minutes at 37C. Tagmented DNA was ampli ed using NEB Next High-Fidelity 2X PCR Master Mix for 11 cycles. Tagmentation e fficiency was assessed using Agilent Tapestation. ATAC-Rx was carried as previously described (Orlando et al., 2014), and as described above with the addition of 50% extra Drosophila S2 cells. ATAC-seq libraries were sequenced using paired-end 40 bp run using Illumina NextSeq500 platform.

tag: strain

value: ATAC-seq

value: FACS


title: ATACseq_Rx_NCC_Citrine-Cherry

source_name: Citrine reporter and Cherry reporter expressing cells from 5-6ss embryos piked with S2 cell Drosophila genomic DNA

value: ATAC-seq Rx


title: ATACseq_NCC_Citrine-Cherry_1

value: Citrine reporter and Cherry reporter expressing cells from 5-6ss embryos


title: PDGFR Cell_shortRNA

value: GBM Tumor-derived Cell Line

value: hPDGFR-A overexpressed, p53-null


title: PDGFR Cell_longRNA


title: ATACseq_Rx_NCC_Citrine

source_name: Citrine reporter expressing cells from 5-6ss embryos spiked with S2 cell Drosophila genomic DNA


title: ATACseq_NCC_Citrine_1

source_name: Citrine reporter expressing cells from 5-6ss embryos


title: ATACseq_NCC_Citrine_2

value: Citrine reporter expressing cells from 5-6ss embryos


title: EGFR Ribonuclear Protein_shortRNA

value: Vesicle-depleted conditioned media concentrated with 3 kDa size-exclusion column


title: 53F

tag: education

tag: genetic ancestry


title: ATACseq_BudStage_Head_Citrine_2

source_name: Citrine reporter expressing cells from 1ss embryos


title: EGFR Exosome_shortRNA

tag: passage


title: ATACseq_BudStage_Head_Citrine_1

value: Citrine reporter expressing cells from 1ss embryos


title: foxd3over_CTL2

value: Wild-type

value: 50% epiboly

value: Half embryo (intrinsic foxd3+ cells removed)

value: Dissecction

value: Not injected

value: NEB Next High-Fidelity 2X PCR Master Mix


title: ATACseq_Epiboly_Citrine-Cherry_2

source_name: Citrine reporter and Cherry reporter expressing cells from 75% Epiboly stage embryos

value: 75% Epiboly


title: ATACseq_BudStage_Head_Citrine-Cherry_1

source_name: Citrine reporter and Cherry reporter expressing cells from 1ss stage embryos


title: EGFR Ribonuclear Protein_longRNA

source_name: GBM Tumor-derived Cell Line

tag: rna source


title: ATACseq_Epiboly_Citrine_1

source_name: Citrine reporter expressing cells from 75% Epiboly stage embryos

tag: tissue


title: ATACseq_Epiboly_Citrine_2

value: Citrine reporter expressing cells from 75% Epiboly stage embryos


title: EGFR Exosome_longRNA

value: Extracellular vesicles from conditioned media captured on 0.02 µm filter


title: EGFR Small Microvesicle_shortRNA

value: Extracellular vesicles from conditioned media captured on 0.22 µm filter


title: RNAseq_NCC14-16ss_Negatives2

source_name: Cells not expressing Citrine reporter and cells not expressing Cherry reporter from 14-16ss embryos

extract_protocol:
FACS sorted cells were washed with PBS and stored at -80C in lysis buffer. RNA was extracted using Ambion RNAqueous Micro Total RNA isolation kit (AM1931), checked on Bioanalyser, samples with RIN >7 were used to prepare cDNA using Takara Clontech SmartSeq2 V4 kit (634889).
Sequencing libraries were prepared using Illumina Nextera XT library preparation kit (FC-131-1024).
RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non-directional sequencing libraries after polyA-selection of RNA transcripts (NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEB) were built using NEBnext Ultra RNA library kit for Illumina (NEB). Following ribodepletion using Ribo-ZeroTM Magnetic Kit (Epicentre), directional RNA-seq libraries were constructed using Stranded RNA-Seq Library Preparation Kit (KAPABiosystems).

value: RNA-seq

value: FACS


title: 44F

source_name: buccal swab genomic DNA

tag: twin pairs


title: WT liver, 1 Month WT_1M_0

source_name: Liver

tag: genetic background

value: Liver

value: 1 month old

value: wild type


title: 46F

tag: gender


title: EGFR Small Microvesicle_longRNA


title: ATACseq_Epiboly_Citrine-Cherry_1

value: Citrine reporter and Cherry reporter expressing cells from 75% Epiboly stage embryos

value: ATAC-seq


title: 45F


title: RNAseq_NCC14-16ss_Citrine-Cherry_2

source_name: Citrine reporter and Cherry reporter expressing cells from 14-16ss embryos


title: RNAseq_NCC14-16ss_Citrine-Cherry_1

value: Citrine reporter and Cherry reporter expressing cells from 14-16ss embryos


title: 42M


title: 41M


title: 43F


title: EGFR Cell_shortRNA

value: GBM Tumor-derived Cell Line


title: RNAseq_NCC14-16ss_Citrine_1

source_name: Citrine reporter expressing cells from 14-16ss embryos


title: RNAseq_NCC14-16ss_Citrine_2

value: Citrine reporter expressing cells from 14-16ss embryos


title: RNAseq_NCC5-6ss_Negatives2

source_name: Cells not expressing Citrine reporter and cells not expressing Cherry reporter from 5-6ss embryos


title: RNAseq_Epiboly_Negatives2

source_name: Cells not expressing Citrine reporter and cells not expressing Cherry reporter from 75% Epiboly stage embryos


title: EGFR Cell_longRNA


title: RNAseq_NCC5-6ss_Negatives1

value: Cells not expressing Citrine reporter and cells not expressing Cherry reporter from 5-6ss embryos


title: RNAseq_Epiboly_Citriine-Cherry_2


title: RNAseq_NCC14-16ss_Negatives1

value: Cells not expressing Citrine reporter and cells not expressing Cherry reporter from 14-16ss embryos


title: RNAseq_Epiboly_Negatives1

value: Cells not expressing Citrine reporter and cells not expressing Cherry reporter from 75% Epiboly stage embryos


title: RNAseq_Epiboly_Citriine-Cherry_1

value: 75% Epiboly


title: 39M


title: 40


title: RNAseq_Epiboly_Citrine_1

value: Citrine reporter expressing cells from 75% Epiboly stage embryos


title: PAO1 PA1438 (MmnS) L172P_2

city: Emeryville

first: Charles

last: Dean

state: CA

address: 5300 Chiron Way

institute: Novartis Institutes for Biomedical Research

data_processing:
Basecalls were performed by MiSeq Control Center Software (MCS) version 2.6 followed by bcl2fastq to convert to fastq files.
Counts were generated by the Salmon quasi-mapping algorithm (version 0.9.1) with the following parameters: -l A --gcBias
Differential expression was calculated by DESeq2 (version 1.16.1), giving as input counts output by Salmon (filtering genes that had counts fewer than 10 across all conditions) with an alpha of .05.
Genome_build: PA01 RefSeq NC_002516.2 (assembly GCF_000006765.1). The file PA01_gene_transcripts.fa includes the gene ID in the processed data files and its associated Refseq and a gene name.
Supplementary_files_format_and_content: One set of files are the counts generated by Salmon; there are 6 files, one for each of the three replicates for the two samples. A final CSV file is also available with a list of log-2 fold changes for each gene, sorted by corrected p-values output by DESeq2.

organism: Pseudomonas aeruginosa

source_name: PA1438 (MmnS)

growth_protocol: Confluent P. aeruginosa bacterial growth was harvested from a Mueller-Hinton agar plate,  diluted to an OD600 of 0.05 in cation-adjusted Mueller-Hinton broth, and incubated at 37°C with shaking until the OD600 was  0.5 to 0.6.

extract_protocol:
RNA isolation done as described in https://doi.org/10.1038/srep41114.
rRNA was depleted using an Illumina Ribo-Zero rRNA removal kit (Bacteria; Illumina, San Diego, CA). RNA-seq libraries were constructed with a ScriptSeq RNA-seq library preparation kit (Illumina), pooled, and size selected (375 to 475 bp) with a Pippin Prep system (Sage Science, Beverley, MA). ; Libraries were sequenced on an Illumina MiSeq with 150 cycles kit (2 x 75 paired-end reads, single index) following the manufacturer’s instructions

treatment_protocol: P. aeruginosa PAO1 parent compared to PAO1 PA1438 (MmnS) L172P variant

value: PA1438 (MmnS)


title: PAO1 PA1438 (MmnS) L172P_1


title: PAO1 PA1438 (MmnS) L172P_3


title: PAO1 wild type_3

source_name: wildtype

value: wildtype


title: RNAseq_Epiboly_Citrine_2

value: RNA-seq


title: 37M


title: 36M


title: 3n


title: 38M


title: 35F


title: 12h_C3

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description: Gene expression of  mouse cecum tissues isolated 12 h after cauterization

hyb_protocol: After fragmentation of complementary RNA, microarray studies were performed using an Agilent SurePrint G3 Mouse GE v2 8x60K Microarray Kit)

scan_protocol: The arrays were scanned using an Agilent SureScan G4900DA (Agilent Technologies)

data_processing: Data analysis was performed with GeneSpring GX 14.9 (Agilent Technologies). Signal intensities for each probe were normalized to the 75th percentile without baseline transformation.

source_name: 12 h after cauterization

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent Technologies) according to the manufacturer's instructions

extract_protocol: Total RNA was isolated from mouse cecum tissues at 3 h, 12 h and 72 h after cauterization and the sham operation with the RNeasy Plus Mini Kit (Qiagen)

value: Male

tag: treatment

value: 12 h after cauterization

value: cecum


title: 3d_D1

description: Gene expression of  mouse cecum tissues isolated 72 h after cauterization

source_name: 72 h after cauterization

value: 72 h after cauterization


title: PAO1 wild type_1


title: 3d_D2


title: 12h_C2


title: 33


title: 12h_C1


title: 3h_B2

description: Gene expression of  mouse cecum tissues isolated 3 h after cauterization

source_name: 3 h after cauterization

value: 3 h after cauterization


title: 31


title: 3h_B3


title: 29F


title: PAO1 wild type_2


title: 34n


title: 3h_B1


title: B_clone_8

city: Montpellier

first: romain

last: forey

address: 142 avenue de la Cardonille

country: France

institute: IGH

data_processing:
RNA-seq read pairs were mapped to the reference human GRCh37 genome using the STAR aligner
Statistical analyses were performed with R (v3.2.3) and R packages developed by BioConductor project
The expression level of each gene was summarized and normalized using DESeq2 R/Bioconductor package
Differential expression analysis was performed using SAM multiclass analysis (samr package)
Genes with a fold change > 1.5 and a false discovery rate (FDR) < 0.05 were considered as significantly differentially expressed
Genome_build: GRCh37
Supplementary_files_format_and_content: expression level of each gene

source_name: BJ Ras clone 6 RNA-seq

extract_protocol:
Total RNA was obtained using a QIAGEN kit
RNA sequencing (RNA-seq) libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit
Paired-end RNA-seq was performed with an Illumina NextSeq sequencing instrument (Helixio, France)

tag: cell type

value: Immortalized BJ-hTERT cells


title: A_clone_8


title: Ctl_A3

description: Gene expression of sham control mouse cecum tissues

source_name: sham control

value: sham control


title: Ctl_A2


title: B_clone_5

source_name: BJ Ras clone 5 RNA-seq


title: 3d_D3


title: B_clone_4

source_name: BJ Ras clone 4 RNA-seq


title: A_clone_5


title: 51F


title: A_clone_4


title: 30M


title: Ctl_A1


title: B_BJ_ras

source_name: BJ Ras RNA-seq


title: B_BJ

source_name: BJ RNA-seq


title: A_BJ_ras


title: 24F

source_name: buccal swab genomic DNA


title: 23F


title: 2M


title: AB4933

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: Meta data file associating each single cell with its amplification batch

growth_protocol: patients BM was taken from bed-side aspirates, and control donors BM was taken from the proximal femur during hip replacement surgery

extract_protocol:
BM mononuclear cells were separated by Ficoll gradient density centrifugation, filtered and stained with Flow cytometry antibodies.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: treated patients were treated with bortezomib-baesd induction regimen and autologous stem transplant after high dose melphalan conditioning

tag: organ

value: Bone Marrow

tag: selection marker

value: treated

tag: group

value: patient with plasma cell neoplasms


title: AB4932


title: AB4934


title: 25M

tag: age

tag: minority


title: A_BJ


title: AB4930


title: AB4931


title: Thy_Vγ6

city: Hamburg

first: Immo

last: Prinz

address: Falkenried 94

department: Institute of Systems Immunology

institute: University medical center Hamburg Eppendorf

data_processing:
Sequencing libraries were demultiplexed to individual fastq files, than Cellranger v2.0 (10xGenomics) was used for alignment, annotation, and generation of barcode-gene matrices. Fastq files were mapped to the reference mouse genome mm10 (UCSC). Data from ambient RNA was trimmed based on nUMI-barcode saturation curve.
The R package Seurat v2.3 was used under R 3.5 for further data trimming, unsupervised clustering, and visualization(Butler et al., 2018). Briefly, to remove cells with poor quality, doublets and stressed cells, genes expressed on less than 10 cells and cells that have a gene number lower 400 or higher than 2500 were removed. Mitochondrial gene ratio was calculated to filter out cells with more than 8% mitochondrial genes(Ilicic et al., 2016). Next, the function ‘NormalizeData’ was used to normalize for differences on sequencing depth across single cells. Cell cycle score and cell phase were assigned to every single cell by the function ‘CellCycleScoring’ according to a gene list of known cell cycle markers (Kowalczyk et al., 2015). To reduce confounders, UMI number, percentage of mitochondrial genes and cell cycle scores were regressed out by the function ‘ScaleData’. Highly variable genes (hvg) were defined by ‘FindVariableGenes’ and used as input for principle component analysis (PCA). Using the PCElbowplot, we determined principle components (PCs)1 - 17 as statistically significant PCs which explained the most variance. Based on significant PCs and setting resolution = 0.4, unsupervised graph-based clustering was performed by ‘FindCluster’. Cells are embedded by tSNE plot. We executed ‘FindAllMarkers’ to identify differentially expressed genes (DEGs) among all genes, surface markers (Gene ontology ID: GO:0009986), or transcription factors (Riken Transcription Factor Database) by using wilcoxon rank sum test. We defined DEGs as average log2-fold change (logFC) ≥ 0.5, expressed in minimal percentage cells in at least 1 test group (min.pct) ≥ 20%, and adjust p-value ≤ 0.01.
For integrated analysis libraries of Vγ6pos /Vγ4neg thymus, Vγ6pos skin and Vγ6pos pLN samples were aggregated together and normalized by ‘cellranger aggr’ command provided by cellranger.
To further explorer Vγ6+ T cells, clusters with IL-17 committed gene signatures (Cd44+ Il23r+ Ccr2+ Cd27-) were subdivided as Vγ6+ T cell dataset, than we scaled and clustered this dataset as above.
To compare the transcriptome of skin Vγ4+ and Vγ6+ T cells, datasets of these two were integrated following the integrated analysis protocol from Seurat (Butler et al., 2018). Briefly, the top 1500 hvg from either were selected for canonical correlation analysis (CCA) by ‘RunCCA’ function in Seurat, which identified shared sources of variation across Vγ4 and Vγ6 datasets and combine them into one. CC1 – 10 were chosen for aligning into an integrated low-dimensional space (CCA.aligned). Based on CCA.aligned, we performed ‘FindCluster’ as above by a resolution = 0.6, then visualized the dataset by tSNE-map. DEGs were identified by ‘FindAllMarkers’ as above.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz
Supplementary_files_format_and_content: genes.tsv.gz
Supplementary_files_format_and_content: matrix.mtx.gz

source_name: Vγ6 γδ T cells

extract_protocol:
After euthanasia, ears, thymi and peripheral lymph nodes (pLN; including superficial cervical, axillary, brachial and inguinal) were collected.    To isolate lymphocytes from ear skin, ears were split into dorsal and ventral layers, cut into small pieces, and digested in RPMI media supplemented with (2 mg/ml) collagenase IV (Worthington) and (187.5 µg/ml) DNaseI (Roche) for 75 minutes at 37°C under 1400 rpm of shaking. The digestion was terminated by 5mM EDTA. Digested ears repeatedly went through an 18G needle for further dissociating tissue structure and releasing cells. Subsequently cells were filtered (100 μM cell strainer (Falcon) and facilitated to density gradient centrifugation using 40% and 70% Percoll solutions. For downstream applications cells were re-suspended in MACS buffer (PBS with 3% FCS and 4mM EDTA).  Single cell suspensions from thymus and peripheral lymph nodes were obtained by filtering organs through nylon gaze. To enrich thymus samples γδ T cells, CD4+ and CD8+ T cells were depleted. For flow cytometric cell sorting of Vγ6+ T cells and subsequent single-cell RNA-seq library generation, CD4+ and/or CD8+ thymus cells were lysed via incubation with monoclonal anti-CD4 and anti-CD8β IgM (homemade), DNaseI (Roche) and Standard Rabbit Complement (Cedaralane) at 37°C for 30 minutes. Next, thymus cells were retrieved via density gradient centrifugation using Lympholyte M (Cederlane).
FACS-Aria II (BD Bioscience) was used for cell sorting of indicated cell populations into PBS/4mM EDTA/5%FCS. Sorted Vγ4+  and Vγ6+  γδTcells were diluted to ≤ 1000 cells/μL. Single cell sequencing libraries were generated using the Chromium™ Single Cell 3’ reagent kits v2 according to the manufactures protocol (10xGenomics). Indexed libraries were pooled, and paired-end sequencing was performed by Hiseq4000 (Illumina).

value: Thymus

value: 8 weeks


title: 26n

tag: income

tag: adversity


title: pLN_Vγ6

tag: strain

value: peripheral lymph node


title: 21M

tag: education

tag: genetic ancestry


title: AB4929


title: 28F


title: 22M


title: AB4748

value: untreated


title: Skin_Vγ4

source_name: Vγ4 γδ T cells

value: Ear skin


title: Bulk

city: Minneapolis

first: Timothy

middle: Kaehler

last: Starr

state: MN

address: 420 Delaware St SE

department: Ob-Gyn & Women's Health

institute: University of Minnesota

data_processing:
Fastq files were processed using RNASeq by Expectation Maximum (RSEM) version 1.2.21
Sequences were mapped to human genome GRCh38
Gene Transcript File (GTF) was downloaded from Ensembl: Homo_sapiens_GRCh38_81
RSEM Reference preparation: rsem-prepare-reference --bowtie2 --gtf ~/genome_data/hg38/Homo_sapiens_GRCh38_81.gtf ~/genome_data/hg38 hg38
RSEM Expression calculation: rsem-calculate-expression --paired-end --bowtie2 --bowtie2-mismatch-rate 0 --estimate-rspd /R1.fastq /R2.fastq hg38 sample_id
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data file is data.txt and contains a matrix of genes x cells containing Transcripts Per Million counts

source_name: High Grade Serous Ovarian Cancer

growth_protocol: Cells were not cultured

extract_protocol:
RNA extraction and barcoded cDNA generation was performed per Fluidigm protocol PN 100-7168 using Clontech cDNA and Nextera XT library reagents
Barcoded cDNA was sequenced in a single lane of an Illumina HiSeq 2500 flow cell using rapid chemistry and 100 bp paired end sequencing

treatment_protocol: Samples were dissociated using the Miltenyi Tumor Dissociation Kit and GentleMACs Dissociater (Miltenyi Biotec, Inc.). Red blood cells were lysed using Red Blood Cell Lysis buffer (Roche). Cells were fluorescently labelled using an antibody ccocktail containing antibodies to CD3, CD14, CD19, CD20 and CD56 (BioLegend, San Diego). Cells were flow sorted into negative (91%) and positive (9%) populations by flow cytometry. The negative population was subjected to single cell capture using the Fluidigm C1 chips following manufacturer's protocol

tag: cell count

value: Single Cell


title: Skin_Vγ6

tag: tissue


title: 1F

tag: twin pairs


title: 20M


title: 2_C95


title: 2_C89


title: 192M


title: AB4747


title: 2_C87


title: AB4738


title: AB4746


title: AB4737


title: 19M


title: AB4739


title: 2_C86


title: AB4736

value: control donor


title: 2_C76


title: 2_C79


title: AB4733


title: 2_C75


title: AB4732


title: AB4735


title: 2_C74


title: 2_C73


title: AB4730


title: 191M


title: 18F


title: 190F


title: 189F


title: 2_C72


title: AB4726


title: 2_C71


title: 187F


title: AB4724


title: 186


title: 2_C69


title: AB4652


title: 2_C70


title: AB4653


title: 2_C67


title: 188M


title: AB4625


title: 2_C66


title: 181M


title: AB4731


title: AB4623


title: 2_C63


title: 17M


title: 180


title: AB4622


title: 179F


title: 2_C62


title: AB4621


title: 2_C61


title: 182F


title: 185M


title: 175F


title: 176F


title: 171F


title: 2_C60


title: AB4620


title: AB4619


title: 183M


title: 170M


title: AB4618


title: AB4624


title: 16M


title: AB4616


title: 2_C57


title: 174F


title: 2_C56


title: AB4615


title: 2_C55


title: 166F


title: 2_C59


title: AB4538


title: 173F


title: 2_C53


title: AB4537


title: 168M


title: 2_C51


title: 164M


title: 169F


title: AB4536


title: 2_C50


title: 2_C49


title: 163F


title: AB4535


title: 2_C42


title: 161F


title: AB4534


title: 2_C58


title: 2_C41


title: AB4471


title: 160F


title: 2_C34


title: 2_C29


title: AB4470


title: AB4469


title: 15M


title: 2_C27


title: 158F


title: 2_C26


title: AB4467


title: AB4617


title: 2_C64


title: 159F


title: AB4468


title: AB4466


title: AB4472


title: 157F


title: 156F


title: 155F


title: 2_C24


title: 2_C22


title: 2_C21


title: AB4261


title: AB4260


title: 153F


title: 2_C20


title: 162F


title: AB4262


title: 2_C23


title: 2_C19


title: AB4257


title: AB4256


title: 152F


title: AB4255


title: 150M


title: 149F


title: 2_C16


title: 2_C25


title: 2_C15


title: 14F


title: 146M


title: AB3546


title: 2_C13


title: 2_C10


title: AB3547


title: AB3474


title: 2_C07


title: 147F


title: AB3549


title: 145F


title: 148F


title: 143F


title: 2_C18


title: 2_C14


title: AB4254


title: 13M


title: 2_C06


title: 2_C05


title: AB3472


title: AB3471


title: 2_C04


title: 135M


title: AB3470


title: 2_C03


title: 134


title: 142F


title: AB3473


title: 141M


title: 144F


title: 140M


title: 138F


title: 2_C02


title: AB3463


title: 2_C01


title: 1_C93


title: AB3462


title: 1_C81


title: AB3548


title: 130F


title: 136


title: AB3461


title: 1_C75


title: AB3454


title: AB3469


title: 1_C67


title: 133F


title: AB3453


title: 132M


title: AB3464


title: 1_C65


title: 12M


title: AB3452


title: 1_C61


title: 129M


title: AB3451


title: 1_C59


title: 1_C51


title: 1_C55


title: 1_C48


title: AB3450


title: AB3449


title: AB3337


title: 1_C49


title: 131F


title: AB3324


title: 1_C44


title: AB3326


title: 1_C43


title: 128F


title: 127M


title: AB3195


title: 1_C42


title: AB3194


title: 1_C41


title: AB3325


title: AB3193


title: AB3187


title: 1_C38


title: 1_C40


title: 122F


title: AB3186


title: 121


title: AB3185


title: AB3179


title: 1_C34


title: 1_C36


title: AB3178


title: 125M


title: 1_C31


title: 124M


title: 1_C37


title: AB3144


title: 123F


title: 1_C30


title: AB3143


title: 1_C29


title: AB3066


title: 11F


title: 120


title: 1_C27


title: AB3065


title: AB3062


title: 119F


title: 1_C22


title: 1_C20


title: AB3061


title: AB3060


title: 1_C23


title: M. tuberculosis H37Rv, delta espL replicate 2

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

data_processing:
Reads were adapter- and quality-trimmed with Trimmomatic v0.33 and mapped onto the M. tuberculosis H37Rv reference genome (RefSeq NC_000962.3) using Bowtie2 v2.2.5.
Counting reads over features was done with featureCounts from the Subread package v1.4.6.
DESeq2 was used to infer differentially expressed genes.
Genome_build: NC_000962.3

organism: Mycobacterium tuberculosis

source_name: cell culture

growth_protocol: Mycobacterium tuberculosis strains were grown at 37°C in 7H9 medium (Difco) supplemented with 0.2% glycerol, 0.05% Tween 80 and 10% albumin-dextrose-catalase (ADC, Middlebrook) or on 7H10 plates supplemented with 0.5% glycerol and 10% oleic acid-albumin-dextrose-catalase (OADC, Middlebrook).

extract_protocol:
Total mRNA was extracted with 300 μl of chloroform : isoamyl alcohol (24:1) and precipitated at −20°C overnight with isopropyl alcohol prior to washing with 70% EtOH, then dried and resuspended in 40 μl DEPC‐treated water. RQ1 RNase‐Free DNase (Promega) and TURBO DNase (Ambion) were used to remove contaminating DNA, as recommended by the manufacturers. DNase treatment was followed by RNA purification using one volume of phenol : chloroform : isoamyl‐alcohol (25:24:1) and precipitation using 0.1 volume of 3 M sodium acetate (pH = 5.2) and 0.7 volume of isopropanol. RNA was resuspended in DEPC‐treated water and stored at −80°C. Integrity of RNA was checked by agarose gel electrophoresis, the amount and purity of RNA were assessed using a Nanodrop instrument.
RNA-seq libraries were prepared from 1 g of total RNA. The RNA samples were depleted of r-RNAs with the Illumina Ribo-Zero rRNA Removal Kit (Gram-Positive Bacteria) then used to generate sequencing libraries with the Illumina TruSeq Stranded mRNA reagents, omitting the polyA selection step (Illumina, San Diego, California, USA). Cluster generation was performed with the resulting libraries using the Illumina TruSeq SR Cluster Kit v4 reagents and sequenced on the Illumina HiSeq 2500 using TruSeq SBS Kit v4 reagents.

treatment_protocol: No treatment was perfomed.


title: 1_C19


title: 1_C18


title: SAMPLE 1_HepG2_DMSO_24h

first: kun

last: luo

state: Beijing

address: Haidian district

institute: Tsinghua university

description: gene expression after 24 hours DMSO treatment

hyb_protocol: Hybridization was performed by an Agilent SurePrint G3 Human Gene Expression v3 8x60K Microarray Kit using the One-Color gene expression system (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned on the Agilent DNA Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides

data_processing: Microarray data were extracted with Feature Extraction Software version 10.7 (Agilent Technologies) and processed using GeneSpring GX software 'Percentile 75'   parameter, log2 transformation.

source_name: HepG2 cell line, 2ul, 24 hours

label_protocol: cRNA was labelled with cyanine-3 (Cy3) for hybridization in an Agilent platform, according to the manufacturer’s instructions.

growth_protocol: HepG2 cells  were maintained in high-glucose Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, and 100 mg/mL streptomycin at 37°C in a humidified incubator under 5% carbon dioxide.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. RNA quality control was performed in a 2100 Bioanalyzer (Agilent Technologies). In all cases, RNA integrity number was above 8.

treatment_protocol: HepG2 cells were treated with white tea extract(200 μg/mL) or DMSO(1‰) for 24 hours.

tag: cell line

value: 2μl DMSO (1‰) for 24hrs


title: AB3058


title: M. tuberculosis H37Rv, delta espL replicate 1


title: M. tuberculosis H37Rv, replicate 2


title: 113M

tag: gender


title: AB3057

tag: treatment


title: 1_C17


title: 1_C16


title: SAMPLE 2_HepG2_WTE_24h

description: gene expression after 24 hours WTE treatment

source_name: HepG2 cell line, 2ul (100ug/ml), 24 hours

value: 2μl white tea extract (200 μg/mL) for 24hrs


title: AB3059


title: 114F


title: M. tuberculosis H37Rv, replicate 1


title: 107F


title: 1_C15


title: 115F


title: scRNA_seq_FoxD3_Citrine_94

source_name: Citrine reporter expressing cells from 5-6ss embryos

extract_protocol:
FACS sorted cells were washed with PBS and stored at -80C in lysis buffer. RNA was extracted using Ambion RNAqueous Micro Total RNA isolation kit (AM1931), checked on Bioanalyser, samples with RIN >7 were used to prepare cDNA using Takara Clontech SmartSeq2 V4 kit (634889).
Sequencing libraries were prepared using Illumina Nextera XT library preparation kit (FC-131-1024).
For scRNA.seq, individual cells were collected by FACS, cDNA was obtained and sequencing libraries as previously described (Picelli et al., 2014). Libraries were sequenced using 50 bp single end reads for 96 cells. 4x10E7 dilution of ERCC spike in control was used.

tag: assay

value: scRNA-seq

value: FACS


title: 1_C09


title: AB3054

tag: organ


title: AB3000

tag: selection marker


title: 1_C08


title: 109


title: scRNA_seq_FoxD3_Citrine_92

value: Citrine reporter expressing cells from 5-6ss embryos


title: AB2969

tag: group


title: 118M

tag: age


title: 112F

tag: minority


title: 117rF

tag: income


title: 116

tag: adversity


title: 106F


title: 104


title: 10


title: scRNA_seq_FoxD3_Citrine_91

tag: strain


title: 103F

tag: education


title: 100

tag: genetic ancestry


title: AB2964


title: 1_C02

tag: cell count


title: 110F


title: 1_C01


title: scRNA_seq_FoxD3_Citrine_89

tag: tissue


title: 101M

tag: twin pairs


title: AB2959


title: 105M


title: scRNA_seq_FoxD3_Citrine_88


title: AB2963


title: 108M


title: AB2958


title: scRNA_seq_FoxD3_Citrine_90


title: 111M


title: 16U T8 r2

city: London

first: Christopher

middle: Raja Socrates

last: Banerji

address: New Hunts House

department: Randall Division of Cell and Molecular Biophysics

institute: King's College London

data_processing:
Raw reads were trimmed using trim-galore, utilising cutadapt14 (v0.4.0) to remove the Illumina Sequencing Adapter (AGATCGGAAGAGC) at the 3' end. Additionally, 12 bases were also trimmed from the 5' end of the reads since they showed a biased distribution. Reads were mapped to the human transcriptome using the human genome sequence GRCh38 and v82 gene annotations downloaded from Ensembl. Mapping was performed using tophat 15 (v2.1.0) and bowtie 16 (v1.1.0), enabling the fr-firststrand option of tophat to restrict mapping to the sense strand of the transcript. Reads were assigned to genes using the featureCounts program 17 (v1.5.0), counting fragments and ignoring multi-mapping reads, and restricted to the sense strand.
Genome_build: GRCh38
Supplementary_files_format_and_content: Read count files for each batch
Supplementary_files_format_and_content: 12_16_gene_counts.csv
Supplementary_files_format_and_content: 54a5_a10_2_gene_counts.csv
Supplementary_files_format_and_content: 5412_546_gene_counts.csv

source_name: Immortalised Human Myoblasts

growth_protocol: Myoblasts were plated at 312,000 cells per well in 12 well plates and cultured for 48 hours in cultured in Skeletal Muscle Cell Growth Medium (Promocel) supplemented with 20% foetal bovine serum, 50ug/ml Fetuin (bovine), 10ng/ml Epidermal Growth Factor (recombinant human), 1ng/ml Basic Fibroblast Growth Factor (recombinant human), 10ug/ml Insulin (recombinant human), 0.4ug/ml Dexamethasone and 50 ug/ml Gentamycin, at 37oC under 5% CO2. Confluent cells were washed with PBS and induced to differentiate in DMEM gluatamax supplemented with 1/1000 insulin + 1/1000 gentamycin at 37oC under 5% CO2.

extract_protocol:
RNA was isolated at 8 time points: T1: 0 mins (confluent proliferating myoblasts); T2: 440 mins (54-6 alignment), T3: 530 mins (54-12 alignment), T4: 1355 mins (54-6 initiation of fusion), T5: 1505 mins (54-12 initiation of fusion), T6: 1860 mins (54-6 myotube formation), T7: 2165 mins (54-12 myotube formation) and T8: 5040 mins (myotube maturation) using miRNeasy kit (Qiagen, Manchester, UK) including DNase digestion from each cell line in triplicate. RNA quality/concentration were checked by LabChip Bioanalyzer (RIN>8.0) and Nanodrop.
RNA-seq libraries were prepared using the Agilent sureselect stranded RNAseq protocol, which allows polyA selection but was modified to work with ribodepletion. Libraries were sequenced on an Illumina HiSeq2500.

tag: pathology

value: Control

value: F

tag: batch


title: 102F

tag: gender


title: scRNA_seq_FoxD3_Citrine_87

tag: assay


title: AB2957

tag: organ

value: Bone Marrow

tag: treatment


title: 16U T8 r3


title: scRNA_seq_FoxD3_Citrine_86


title: AB2956

tag: selection marker

tag: group


title: 16U T8 r1


title: 16A T8 r3

value: FSHD


title: AB3055

value: patient with plasma cell neoplasms


title: scRNA_seq_FoxD3_Citrine_85


title: 1_C03


title: AB2955


title: 16A T8 r2


title: AB2952


title: 16A T8 r1


title: scRNA_seq_FoxD3_Citrine_84


title: AB2951


title: scRNA_seq_FoxD3_Citrine_82


title: scRNA_seq_FoxD3_Citrine_93


title: 12U T8 r3

value: M


title: AB2950


title: 12U T8 r1


title: scRNA_seq_FoxD3_Citrine_80


title: 12U T8 r2


title: AB2947


title: AB2948


title: 12A T8 r3


title: 12A T8 r2


title: 12A T8 r1


title: scRNA_seq_FoxD3_Citrine_78


title: AB2944


title: 54-A5 T8 r3


title: scRNA_seq_FoxD3_Citrine_76


title: scRNA_seq_FoxD3_Citrine_83


title: AB2943


title: AB2835


title: scRNA_seq_FoxD3_Citrine_79


title: 54-A5 T8 r2


title: scRNA_seq_FoxD3_Citrine_74


title: scRNA_seq_FoxD3_Citrine_75


title: 54-A5 T8 r1


title: AB2702


title: 54-A10 T8 r3


title: scRNA_seq_FoxD3_Citrine_73


title: AB2945


title: AB2701


title: scRNA_seq_FoxD3_Citrine_81


title: 54-A10 T8 r2


title: scRNA_seq_FoxD3_Citrine_77


title: AB2700


title: AB2697


title: AB2696


title: 54-2 T8 r3


title: 54-A10 T8 r1


title: scRNA_seq_FoxD3_Citrine_69


title: AB2562


title: scRNA_seq_FoxD3_Citrine_70


title: scRNA_seq_FoxD3_Citrine_71


title: 54-2 T8 r2


title: 54-2 T8 r1


title: scRNA_seq_FoxD3_Citrine_68


title: AB2561


title: scRNA_seq_FoxD3_Citrine_67


title: AB2829


title: 54-6 T8 r2


title: scRNA_seq_FoxD3_Citrine_66


title: 54-6 T8 r1


title: scRNA_seq_FoxD3_Citrine_72


title: AB2313


title: scRNA_seq_FoxD3_Citrine_64


title: scRNA_seq_FoxD3_Citrine_63


title: AB2312


title: AB2306


title: AB2307


title: 54-6 T7 r2


title: 54-6 T7 r3


title: scRNA_seq_FoxD3_Citrine_62


title: AB2303


title: 54-6 T6 r2


title: 54-6 T6 r3


title: scRNA_seq_FoxD3_Citrine_60


title: 54-6 T7 r1


title: 54-6 T8 r3


title: scRNA_seq_FoxD3_Citrine_61


title: AB2301


title: 54-6 T6 r1


title: AB2314


title: scRNA_seq_FoxD3_Citrine_59


title: 54-6 T5 r3


title: scRNA_seq_FoxD3_Citrine_58


title: AB2149


title: 54-6 T5 r2


title: scRNA_seq_FoxD3_Citrine_65


title: scRNA_seq_FoxD3_Citrine_57


title: AB2138


title: 54-6 T5 r1


title: AB2137


title: 54-6 T4 r3


title: scRNA_seq_FoxD3_Citrine_55


title: AB2302


title: AB2136


title: scRNA_seq_FoxD3_Citrine_54


title: scRNA_seq_FoxD3_Citrine_53


title: 54-6 T4 r1


title: 54-6 T4 r2


title: 54-6 T3 r3


title: 54-6 T3 r2


title: scRNA_seq_FoxD3_Citrine_51


title: scRNA_seq_FoxD3_Citrine_52


title: AB2150


title: scRNA_seq_FoxD3_Citrine_50


title: RNAseq_Ybx1sh1_1

city: München

first: Ashokkumar

last: Jayavelu

address: Am Klopferspitz 18

institute: Dept Proteomics and Signal Transduction, MaxPlanck Institute of Biochemistry

data_processing:
Sequencing reads were filtered, trimmed and then mapped to the Ensembl gene annotation and the mouse genome assembly GRCm38 using STAR aligner  with ENCODE settings in two-pass mode considering splice junctions across all samples in the second mapping step
Gene counts were quantified using featureCounts
differential expression calculated with the limma-voom pipeline
Gene and transcript expression levels were quantified using RSEM
Event level differential splicing was calculated with the EventPointer package
Genome_build: mm9

source_name: BaF3 Jak2V617F_Ybx1sh1

growth_protocol: Cells were grown in RPMI1640 containing 10% FBS and 1mM Sodium pyruvate

extract_protocol:
NucleoSpin RNA Kit according to the Manufacturer’s protocol (Macherey Nagel)
NEBNext Poly(A) mRNA Magnetic Isolation Module
Samples were sequenced on Illumina Nexseq500 and multiplexed reads were demultiplexed on the basis of their barcodes

tag: cell line/type

value: proBcells derived BaF3 cells

tag: genotype/variation


title: RNAseq_Ybx1sh1_2


title: scRNA_seq_FoxD3_Citrine_49


title: RNAseq_Ybx1sh2_1

source_name: BaF3 Jak2V617F_Ybx1sh2


title: RNAseq_shNT control_3

source_name: BaF3 Jak2V617F_shNT control

value: shNT control


title: RNAseq_shNT control_4


title: 54-6 T2 r3


title: 54-6 T2 r2


title: scRNA_seq_FoxD3_Citrine_56


title: scRNA_seq_FoxD3_Citrine_48


title: RNAseq_shNT control_2


title: RNAseq_Ybx1sh2_2


title: RNAseq_shNT control_1


title: scRNA_seq_FoxD3_Citrine_47


title: 54-12 T8 r3


title: 54-12 T8 r2


title: scRNA_seq_FoxD3_Citrine_45


title: 54-12 T7 r3


title: 54-12 T8 r1


title: 54-12 T7 r2


title: Ki67_neonate1_bulk RNA

city: Würzburg

first: Kai

last: Kretzschmar

address: Josef-Schneider-Str. 2

institute: University Hospital Würzburg

description:
Neonatal murine hearts
barcode file: CEL-Seq2_UMI8_barcodes.csv

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: coutb files contain UMI barcode normalised abundance counts

source_name: Extracted RNA from Ki67-RFP+ cells of hearts of neonatal Ki67TagRFP mice, replicate 1

extract_protocol:
Live single cells were sorted in 384- well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

tag: strain background

tag: timepoint

value: neonate

value: Heart


title: scRNA_seq_FoxD3_Citrine_43

tag: strain


title: PDC_S3

city: Cantanhede

first: Andreia

last: Gomes

address: Parque Tecnológico de Cantanhede, Núcleo 4, lote 8

department: CNC

country: Portugal

institute: Universidade de Coimbra

description: MHC-IIIntSiglecH+Bst2+ B220+

data_processing:
bcl2fastq2 v2.20 was used to convert BCL files generated by Illumina NextSeq to standard FASTQ file formats
Alignment to GRCm38.p5 was done using STAR v2.5.3a with default settings except for the following ones: --sjdbOverhang 74 --quantMode GeneCounts.
The resulting gene counts were further processed and normalised using DESeq2 R package v1.20.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: raw counts

source_name: plasmacytoid dendritic cell

growth_protocol: MEFs were cultured in gelatin-coated plates in DMEM+10%FBS. After co-transduction with lentiviral particles encoding PU.1, IRF8, and BATF3 and M2RTTA, MEFs were cultured in the presence of Doxycycline (1 µg/mL) – day 0.

extract_protocol:
Total RNA was extracted with TRIzol. cDNA was generated with the SMARTSeq v4 Ultra low input RNA kit (Takara).
Library preparation was performed using the Nextera XT DNA library preparation kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: Cells were sorted by FACS.

tag: cell type

value: plasmacytoid dendritic cell

tag: genotype

value: wildtype


title: scRNA_seq_FoxD3_Citrine_42

tag: tissue


title: Ki67_neonate2_bulk RNA

source_name: Extracted RNA from Ki67-RFP+ cells of hearts of neonatal Ki67TagRFP mice, replicate 2


title: 54-6 T3 r1


title: 54-12 T7 r1


title: PDC_S2

description: MHC-IIIntSiglecH+Bst2+ B220+


title: CDC2_S3

description: CD11c+ MHC-II+ CD11b+

source_name: splenic dendritic cell type 2

value: splenic dendritic cell type 2


title: scRNA_seq_FoxD3_Citrine_41


title: scRNA_seq_FoxD3_Citrine_40


title: PDC_S1

description: MHC-IIIntSiglecH+Bst2+ B220+


title: CDC2_S4

description: CD11c+ MHC-II+ CD11b+


title: 54-12 T6 r2


title: 54-12 T6 r3


title: scRNA_seq_FoxD3_Citrine_39


title: 54-6 T2 r1


title: scRNA_seq_FoxD3_Citrine_46


title: CDC2_S2

description: CD11c+ MHC-II+ CD11b+


title: 54-12 T5 r3


title: CDC2_S1

description: CD11c+ MHC-II+ CD11b+


title: scRNA_seq_FoxD3_Citrine_38


title: scRNA_seq_FoxD3_Citrine_37


title: scRNA_seq_FoxD3_Citrine_44


title: CDC1_S4

description: CD11c+ MHC-II+ CD8a+

source_name: splenic dendritic cell type 1

value: splenic dendritic cell type 1


title: 54-12 T5 r2


title: scRNA_seq_FoxD3_Citrine_36

value: scRNA-seq


title: CDC1_S2

description: CD11c+ MHC-II+ CD8a+


title: 54-12 T5 r1


title: scRNA_seq_FoxD3_Citrine_35

value: FACS


title: CDC1_S1

description: CD11c+ MHC-II+ CD8a+


title: CDC1_S3

description: CD11c+ MHC-II+ CD8a+


title: 54-12 T4 r3


title: 54-12 T4 r2


title: scRNA_seq_FoxD3_Citrine_34

value: Citrine reporter expressing cells from 5-6ss embryos