title: gDNA_acf_rep1

growth_protocol: Drosophila embryo extract was prepared from preblastoderm embryos 0-90 min AEL according to (Becker and Wu, Mol Cell Biol, 1992) with the following modifications: After collection, the embryos were dechorionated in 200 ml embryo wash buffer (0.7% NaCl, 0.04% Triton X-100) and 60 ml 13% sodium hypochlorite (VWR) for 3 min at room temperature while stirring. Embryos were rinsed for 5 min with cold water and transferred into a glass cylinder with embryo wash buffer. After settling of the embryos, the buffer was decanted and the embryos were washed first in 0.7% NaCl and then in extract buffer (10 mM HEPES, pH7.6, 10 mM KCI, 1.5 mM MgCl2, 0.5mM EGTA, 10% glycerol, 10 mM 3-glycerophosphate; 1 mM DTT, protease inhibitors added freshly before use: 0.2 mM PMSF, 1 mM Aprotinin, 1 mM Leupeptin, 1 mM Pepstatin). After the last wash, embryo wash buffer was decanted and embryos were homogenized with one stroke at 3000 rpm and 10 strokes at 1500 rpm using a homgenplus homogenizer  (Schuett-Biotec). The homogenate was adjusted to a final MgCl2 concentration of 5 mM and centrifuged for 15 min at 27000 g at 4°C. The white lipid layer was discarded and the supernatant was centrifuged for 2 h at 245420 g at 4°C. The clear supernatant was aspirated with a needle, leaving the lipid layer and pelleted nuclei in the tube. Genomic DNA was purified from Drosophila BG3-c2 cells with the Blood & Cell Culture Midi Kit (Qiagen). 1 μg of genomic or plasmid DNA were added to 60 μl Drosophila embryo extract supplied with 10 mM 3-glycerophosphate and an ATP-regenerating buffer (3 mM ATP, 30 mM creatine phosphate, 10 μg/ml creatine kinase, 3 mM MgCl2, 1 mM DTT) and filled up to a total volume of 120 μl with EX50 buffer (10 mM HEPES, pH 7.6, 50 mM KCI, 1.5 mM MgCl2, 0.5 mM EGTA, 10% glycerol, 10 mM 3-glycerophosphate; 1 mM DTT, 0.2 mM PMSF, 1 mM Aprotinin, 1 mM Leupeptin, 1 mM Pepstatin). Chromatin was assembled at 26°C for 6 h.


title: EaHy_2

status: Public on Aug 10 2018

type: SRA

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

country: USA

institute: Boston Children's Hospital

description: rRNA depleted RNA

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to hg19 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: hg19
Supplementary_files_format_and_content: excel files include RPKM values for each Sample ...

molecule: total RNA

organism: Homo sapiens

source_name: Endothelial cell line

growth_protocol: U937 and EaHy cells were cultured in RPMI media with Pen/Strep and heat inactivated FBS.

extract_protocol:
5 million cells were collected in duplicate and RNA was isolated by Qiagen RNeasy Plus Kit.
Ribosomal RNA was depleted using the RiboGone H/M/R kit from Illumina. Enriched mRNA was then applied to library preparation according to manufacturer’s protocol (NEBNext Ultra). After repeated quality control for average DNA input size of 300 bp, the samples were sequenced on a HiSeq Illumina sequencer with 2x100bp paired-end reads.

tag: cell line

value: EaHy


title: gDNA_salt

city: Planegg-Martinsried

first: Sandro

last: Baldi

address: Großhaderner Strasse 9

department: BMC Molecular Biology

country: Germany

institute: LMU Munich

library_source: genomic

data_processing:
mapping of Illumina reads: bowtie 1.1.1, default settings
In R with libraries "ShortRead", "rtracklayer": Nucleosoome dyad coverage vectors were obtained by size-selecting fragments of length >=120 and <=200 bp and resizing their length to 50 bp fixed at the fragment center. Genome coverage of nucleosome dyads was exported to .bedgraph file.
Genome_build: dm3
Supplementary_files_format_and_content: .bedgraph files containing nucleosome dyad coverages

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: in vitro assembled chromatin on genomic DNA

growth_protocol: A 100 ml assembly reaction containing 10 mg genomic DNA, ~10 mg purified Drosophila histone octamers (exact amount optimized by titration), 20 mg BSA, 0.1% Igepal CA-630, 10 mM Tris pH 7.6, 2 M NaCl, 1 mM EDTA were prepared and transferred to a dialysis cup (Slide-A-Lyzer; MWCO 3500, Thermo Fisher).  The dialysis cup was then floated in a big beaker containing 300 ml high salt buffer (10 mM Tris-HCl pH 7.6, 2 M NaCl, 1 mM EDTA pH 8.0, 0.05% Igepal CA-630, 0.1% 2-mercaptoethanol). NaCl concentration in the beaker was decreased constantly at room temperature over night by pumping 3 l of low salt buffer (10 mM Tris pH 7.6, 50 mM NaCl, 1 mM EDTA, 0.05% Igepal CA-630, 0.01% 2-mercaptoethanol) into the beaker with a peristaltic pump (Minipulse evolution, Gilson, mode 8.4 rpm). After the entire low salt buffer had been transferred, the dialysis cup was dialyzed another 2 h at room temperature against fresh low salt buffer. The quality of nucleosome assembly was assessed by limited MNase digestion.

extract_protocol:
1.5 mM f.c. CaCl2 and 1.4 x 10-3 U MNase were added to digest the chromatin at 30°C for 15 min. After quenching the reaction with 10 mM f.c. EDTA, samples were treated with 20 RNase mg A for 30 min. Proteins were digested overnight after adding 16 ml 2% SDS and 100 mg Proteinase K and incubating at 37°C. The DNA was purified with the GenElute PCR clean-up kit (Sigma-Aldrich).
Libraries were prepared using the MicroPlex Library Preparation kit (Diagenode). PCR amplification was monitored by quantifying amplified libraries.

tag: tissue

value: chromatin assembled with Drosophila preblastoderm extract

tag: genotype/variation

tag: molecule

value: mononucleosomal DNA


title: gDNA_wt_rep2

value: OregonR 0-2 h embryos


title: gDNA_wt_rep3


title: PC3M_1

description: rRNA depleted RNA

source_name: Prostate cancer cell line

growth_protocol: PC3M-LN4 cells were cultured in RPMI media with Pen/Strep, heat inactivated FBS, and L-glutamine.


title: Ef-rpoN-mut rep1 [V583-RpoN-3rd]

type: RNA

city: Miami

first: Vijayalakshmi

middle: S

last: Iyer

state: Florida

address: 1600 NW 10th Avenue, RMSB 2048

institute: University of Miami, Miller School of Medicine

hyb_protocol: Affymetrix protocol carried out by the University of Iowa core facility

data_processing: RMA analysis performed using an online interface at the University of Oklahoma Bioinformatics Core Facility: http://www.ou.edu/microarray/

label: Biotin

organism: Enterococcus faecalis V583

source_name: Colony biofilm cells

label_protocol: Biotinylated cDNA were prepared using methods adapted from: Ramsey MM, Whiteley M: Pseudomonas aeruginosa attachment and biofilm development in dynamic environments. Mol Microbiol 2004, 53(4):1075-1087

extract_protocol: RNABee using manufacturers instructions. See methods of associated paper for details.

tag: genotype

value: rpoN deletion


title: Ef-rpoN-mut+complement rpoN rep2 [RpoN-Complement v wt]

scan_protocol: Affymetrix protocol carried out by the University of Iowa core facility

value: rpoN deletion+ plasmid rpoN complement


title: Ef wild-type rep1 [V583-RpoN-3rd]

value: wildtype


title: Ef wild-type rep2 [RpoN-Complement v wt]


title: gDNA_wt_rep1


title: Ef wild-type rep1 [RpoN-Complement v wt]


title: BG3_GST

source_name: larval L3, central nervous system

growth_protocol: BG3-c2 cells were cultured at 26°C in Schneider’s Drosophila Medium (Gibco) including 10% fetal calf serum (FCS), Penicillin-Streptomycin and 10 µg/ml human insulin.

extract_protocol:
9 x 106 cells per condition were washed in 10 ml cold PBS and resuspended in 1 ml TM2 buffer (10 mM Tris-HCl pH 7.5, 2 mM MgCl2, 1 mM PMSF). The cells were incubated 1 min on ice and NP-40 added to 1.5 %, gently vortexed, and again incubated on ice for 10 min for lysis and release of the nuclei. After a 10 min centrifugation at 93 x g and 4°C the nuclei were resuspended in 600 ml of TM2 buffer with 2 mM CaCl2 and distributed into three 200 ml aliquots. Those were treated with 2.3/5.9/11.7 x 10-3 units of MNase for 20 min at 37°C. The reaction was then quenched by adding 5 ml 0.5 M EDTA and 100 mg RNase A, followed by a 20 min incubation at 37°C. Proteins were digested away at 50°C for 2 h after the addition of 12 ml 10% SDS and 200 mg Proteinase K. The DNA was then purified by Phenol/Chloroform extraction, precipitated in 2.5 V EtOH, 1/10 V NaOAC 3M and 20 mg glycogen and run on a 1.2% agarose gel in 0.5x TAE buffer. The samples with the best digestion degree (predominantly nucleosomes, achieved with 11.7 x 10-3 U of MNase) were chosen and the mononucleosomal bands cut out and purified (NucleoSpin Gel and PCR Clean-up, Macherey-Nagel). The purified DNA was then used for Next-Generation-Sequencing library preparation.
Libraries were prepared on 10 ng of DNA with the iDeal library preparation kit (Diagenode). PCR amplification was monitored by quantifying amplified libraries.

treatment_protocol: For knockdown of su(Hw) and CG7372 two different dsRNAs per gene were simultaneously used. For each knockdown condition, 1.5 x 107 cells were resuspended in 4 ml medium (containing antibiotics and insulin but no FCS), seeded in T-75 flask, and incubated with 100 mg (GST, su(Hw), CG7372) of in vitro transcribed dsRNA (MEGAscript T7 Transcription Kit). After gentle shaking for 45 min at room temperature, 16 ml of medium (+FCS/+antibiotics/+insulin) was added to the cells. After 5 days cells were treated again with dsRNA in the same manner, but this time two T-75 flasks per condition were seeded. After 5 more days, the cells were harvested.

value: BG3-c2 cells

value: RNAi:control dsRNA (GST)


title: Ef-rpoN-mut rep2 [V583-RpoN-3rd]


title: Ef wild-type rep2 [V583-RpoN-3rd]


title: Ef-rpoN-mut+complement rpoN rep1 [RpoN-Complement v wt]


title: tum11-mut

city: London

first: Philip

last: East

state: London

address: 1 Midland Road, London

department: Bioinformatics

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Basecalls were performed using bcl2fastq v2.19
Sequence reads were trimmed for adapter and low quality bases using cutadapt-1.9.1
Reads were aligned to the mouse genome GRCm38 from Ensembl using STAR-2.5.2a
Gene-level quantifications were generated using RSEM-1.2.31 against mouse annotation release 86 from Ensembl
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text output files from RSEM

organism: Mus musculus

source_name: whole tumour lysate

growth_protocol: Animals were euthanised by cervical dislocation and tumours harvested. The epidermis was dissected off and a piece of central homogenous tumour tissue weighing approximately 50 mg was isolated, snap-frozen in liquid N2 and stored at -80 °C.

extract_protocol:
Tissue was taken from -80 C and placed onto dry ice, prior to lysis by submersion in RLT buffer (Qiagen), directly followed by homogenisation in a microcentrifuge tube using a pestle at room temperature. Total RNA was isolated using the RNeasy Mini Kit (Qiagen).
mRNA libraries were prepared with the KAPA mRNA Hyper Prep kit (Roche Applied Science) and sequenced as 9-plex pools on the HiSeq 4000 (Roche Applied Science) and sequenced as 9-plex pools on the HiSeq 4000 (Illumina).

treatment_protocol: After tumour induction by topical 4OH-tamoxifen, mice were left untreated.

value: Rac1 P29S/wt

tag: strain

tag: group

value: mut


title: BG3_su(Hw)

description:
primer pair 1: TAATACGACTCACTATAGGGGAGGT TGTACCAGTGGCGTT/TAATACGACTCACTATAGGGCGGCTACCGT AGTCAAGCTC
primer pair 2: TAATACGACTCACTATAGGGAACTG TGGCCACGACCTAAC/TAATACGACTCACTATAGGGTGTGCGGTAA TTGTACGCAT

value: RNAi:su(Hw) dsRNA


title: gDNA_acf_rep2

value: Acf1C 0-2 h embryos


title: KO_ST2_rep1

city: Shanghai

first: Yu

last: Xu

address: 320 Yueyang Road

country: China

institute: Shanghai Institue of Biochemistry and Cell Biology

data_processing:
After quality filteration and removing the sequencing adapters with Trimmomatic (version 0.36), the RNA-seq reads were aligned to mouse genome (mm10) using HISAT2, and only reads hitting no more than 2 genomic loci were used to quantify gene expressions with StringTie.
The gtf file of mouse genes was downloaded from GENCODE (vM12).
The gene expressions were normalized as FPKM.
The fold change and p-value of all the detected genes were estimated by Ballgown.

source_name: thymus

extract_protocol:
All the RNA was extracted using Trizol reagent, purified and checked for integrity using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Libraries were generated for sequencing using the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Illumina).
RNA libraries were prepared for sequencing using standard illumina protocols

tag: cell type

value: Med23-deficient iNKT

tag: developmental stage

value: thymus


title: KO_ST2_rep2


title: KO_ST2_rep3


title: tum10-mut


title: tum7-mut


title: tum9-mut


title: tum8-mut


title: tum12-mut


title: A11V111_Wk19

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Reads were aligned to an assembly of Indian Rhesus macaque (Macaca mulatta) (MacaM_Rhesus_Genome_v7.fasta) using STAR software (v2.5.2b)
Insert size was estimated with Picard Tools v1.74
Transcripts were annotated using the UNMC rhesus annotation v 7.6.8
unsorted bam files were sorted and indexed using samtools and converted to HTSeq-count format.
Estimates of gene-wise and isoform-wise expression levels for individual genes were performed using the R package DESeq2 with R version 3.3.3.
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: PBMC

growth_protocol: PBMC were isolated using ficoll

extract_protocol:
After thaw and wash, PBMC pellets were resuspended in RNAzolRT prior to RNA extraction. Purified RNA was used for transcriptome analysis. Polyadenylated transcripts were purified on oligo-dT magnetic beads, fragmented, reverse transcribed using random hexamers and incorporated into barcoded cDNA libraries based on the Illumina TruSeq platform.
Modified Illumina TruSeq. Illumina-ready libraries were sequenced by 2x75 paired-end reads on a HiSeq 4000.

treatment_protocol: Samples for RNA extraction were resuspended in 10% DMSO-FBS and store in liquid nitrogen until use

tag: donor id

tag: time point

tag: art-treatment

tag: ifn-1ant treatment

value: Placebo


title: tum5-wt

value: Rac1 wt/wt

value: wt


title: tum6-wt


title: tum4-wt


title: tum3-wt


title: tum2-wt


title: mut-melan-12.1

data_processing:
Basecalls were performed using bcl2fastq v2.19 (bcl2fastq v1.8.4 for sample X1510he00_1_1)
Sequence reads were trimmed for adapter and low quality bases using cutadapt-1.9.1
Reads were aligned to the mouse genome GRCm38 from Ensembl using STAR-2.5.2a
Gene-level quantifications were generated using RSEM-1.2.31 against mouse annotation release 86 from Ensembl
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text output files from RSEM

source_name: melanocytes

growth_protocol: Cells were cultured in in RPMI with 10% FCS and the mitogen 12-O-tetradecanoylphorbol-13-acetate (TPA) at 200 nM in 5% CO2. Twenty-four hours before lysis, monolayers were washed once with PBS and medium was changed to medium lacking TPA.

extract_protocol:
Cells were lysed and total RNA was isolated using the RNeasy Mini Kit (Qiagen). The experiment was performed three times on a different day to obtain three independent replicates. RNA integrity was verified using the RNA 6000 Nano Kit in combination with the 2100 Bioanalyzer (both from Agilent).
mRNA libraries were prepared with the KAPA mRNA Hyper Prep kit (Roche Applied Science) and sequenced as 9-plex pools on the HiSeq 4000 (Roche Applied Science) and sequenced as 9-plex pools on the HiSeq 4000 (Illumina).

treatment_protocol: Cells were left untreated.


title: tum1-wt


title: WCE_Ser5P-Ser2P_mut-dhp1_MM+thiamine_SI_exp4

city: Sherbrooke

first: Pierre-Étienne

last: Jacques

state: Quebec

address: 2500 Boulevard de l'Université

department: Biologie

country: Canada

institute: Université de Sherbrooke

description: with spike-in

data_processing:
Briefly, the raw reads were trimmed using Trimmomatic version 0.32 (Bolger et al. 2014) with param ILLUMINACLIP:2:30:15 LEADING:30 TRAILING:30 MINLEN:23, and quality inspection was conducted using FastQC version 0.11.4 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Considering that most of the samples were generated from chromatin contain exogenous spiked-in from S. cerevisiae, the trimmed reads from all datasets were aligned using BWA version 0.7.12-r1039 (Li and Durbin 2010) with the algorithm mem or aln depending on the read length (above or below 70 nt) and default parameters, onto a concatenated reference genome containing both the sequences of the S. pombe ASM294v2 and S. cerevisiae sacCer3 assemblies, inpired by others (Orlando et al. 2014). Note that <0.28 % of reads coming from samples without spike-in were aligning to the S. cerevisiae genome. Note that no filtering on mapQ was performed in order to avoid discarding the signal at regions of the genome that are duplicated (BWA is randomly assigning the reads).
Signal density files in BedGraph format were then generated using BEDTools genomecov version 2.17 (Quinlan and Hall 2010) with default parameters, then converted in uniform 10 nt bins WIG files for further normalisation steps (inspired by the script bedgraph_to_wig.py [https://gist.github.com/svigneau/8846527]).
Each signal density file of the datasets without spike-in was scaled such that the total sum of the signal over the S. pombe genome is equivalent to 1M reads of 100 nt, then the signal of the input dataset was subtracted from its corresponding IP dataset to generate the “scl-Ctrl” files.
The normalization of the datasets with spike-in was inpired by the method of presented by Orlando et al. (Orlando et al. 2014). For each dataset, the sum of the signal coming from the reads aligned to the S. cerevisiae genome was first scaled to the equivalent of 1M mapped reads of 100 nt, and the same scaling factor was applied to the signal coming from the reads aligned to the S. pombe genome to generate the “normSI” files. For the datasets generated in a WT and mutant strains, the S. pombe signal was next scaled to a total signal equivalent to 1M mapped reads of 100 nt and the same scaling factor was applied to the corresponding mutant dataset to generate the “Spknorm” files. The signal of the input dataset was then subtracted from its corresponding IP to generate the final “Spknorm-Ctrl” files used in downstream analyses.
The normalized WIG files were then encoded in bigWig format using the Kent utilities (Kent et al. 2010). Visual inspection of the data was performed using an AssemblyHub on the UCSC Genome Browser (Casper et al. 2018) (https://genome.ucsc.edu/cgi-bin/hgHubConnect?hubUrl=https://datahub-i8kms5wt.udes.genap.ca/CTD_sno_pombe/hub.txt&hgHub_do_firstDb=on&hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on).
Genome_build: ASM294v2-SacCer3
Supplementary_files_format_and_content: IP: bigwig files of the normalized IP signal after substraction of the WCE signal; WCE: bigwig files of the normalized WCE signal

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

growth_protocol: Cells were routinely grown at 30°C in Edinburgh minimal media (EMM) or in yeast extract medium (YES) supplemented with adenine, uracil, histidine and leucine.

extract_protocol:
ChIP-seq experiments of total RNAPII and phospho-CTD modifications in wild-type and dhp1-depleted cells were performed with a spike-in adjustment procedure that allows a quantitative comparison between independent strains or conditions (Orlando et al. 2014). Chromatin preparations of S. pombe FBY1995 (Rpb3-HA; WT) and FBY2016 (Rpb3-HA; Pnmt-dhp1) strains and S. cerevisiae FBY2064 strain (reference strain containing a copy of HA-tagged histone H2B) were done as a regular ChIP, except that chromatin extracts have been frozen in liquid nitrogen and stored at -80°C before affinity purifications. For Tyr1-P, Ser2-P, Ser5-P, Ser7-P, and 8WG16 IPs, a S. pombe/S. cerevisiae chromatin ratio of 0.9:0.1 was used, whereas a chromatin ratio of 0.995:0.005 was used for Rpb3/H2B-HA purifications. Following combination of S. pombe/S. cerevisiae chromatin extracts, ChIP assays were performed as described above using antibody-coated beads. ChIP-seq profiles of total RNAPII from WT and ysh1-AA strains were also performed with a spike-in adjustment (ratio S. pombe/S. cerevisiae of 0.9:0.1) using extracts from S. pombe that were previously grown in EMM leu- and treated for 4 hours with 2.5 μg/ml of rapamycin.
DNA librairies for ChIP-seq experiments were prepared as described previously (Lemay et al. 2016) using either the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina kit (New England BioLabs) or the SPARK DNA Sample Prep Kit Illumina Platform (Enzymatics) according to the manufacturer’s instructions.

treatment_protocol: Conditional strains, in which the genomic copy of the essential genes pcf11, dhp1 and seb1 are expressed from the thiamine-sensitive nmt promoter (Pnmt), were repressed by the addition of 60 μM of thiamine in the EMM media for 12-15 hours as previously described (Lemay et al. 2014; Lemay et al. 2016). Depletion of nuclear Ysh1 was done by an anchor-away strategy (Ding et al. 2014). Briefly, wild-type (WT) and Ysh1- FRB-GFP (ysh1-AA) strains were grown in EMM without leucine and rapamycin was added at a final concentration of 2.5 μg/ml for 4h. Cells were collected at OD 600nm of ∼0.5-0.8.

tag: pombe strain

tag: chip antibody

tag: chip target

value: WCE

value: h? ade6-M21? leu1-32 ura4-D18 his3-D1 Rpb3-3HA::kanMX6 P81nmt-dhp1::kanMX6

tag: growth media

value: EMM media (MM) + thiamine


title: mut-melan-12.6


title: mut-melan-9


title: wt-melan-8


title: WCE_Ser5P-Ser2P_WT_MM+thiamine_SI_exp4

description: with spike-in

value: h+ ade6-M216 leu1-32 ura4-D18 his3-D1 Rpb3-3HA::kanMX6


title: IP_Tyr1P_WT_MM+thiamine_SI_exp4

description: with spike-in

value: clone 3D12, Active Motif, 61383


title: WCE_Rpb1-Ser7P-Tyr1P_WT_MM+thiamine_SI_exp4

description: with spike-in


title: WCE_Rpb1-Ser7P-Tyr1P_mut-dhp1_MM+thiamine_SI_exp4

description: with spike-in


title: IP_Tyr1P_mut-dhp1_MM+thiamine_SI_exp4

description: with spike-in


title: wt-melan-7


title: wt-melan-a


title: Trunk neural crest cells rep3

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

description: Differentiated H9:SOX10 hPSCs

hyb_protocol: 5.2µg of fragmented and biotinylated DNA molecules were applied to the Human Clariom D GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: Scanned on an Affymetrix® GeneChip Scanner 3000 according to manufacturer's protocols

data_processing: Data were analysed using the Affymetrix TAC software

label: biotin

source_name: hPSCs differentiated into the different anterior posterior populations at different time points as stated.

label_protocol: Biotinylation of sense DNA fragments carried out according to Affymetrix protocol

extract_protocol: Direct-zol™ RNA MiniPrep (Zymo Research) was used for RNA extraction according to manufacturers' instructions

treatment_protocol: H9:SOX10 hPSCs were differentiated into neural crest cells and samples taken along timepoints of differentiation corresponding to neural plate border progenitor cell state or migratory neural crest cells. We utilised protocols to generate cells along the anterior posterior axis. First using all-trans retinoic acid, to mimic previous protocols to posteriorise cranial neural crest cells (CD6 for cranial and VD6 for RA patterned cells). We also compared these to neural crest cells derived from Neuromesodermal progenitors, that are present in the primitive streak and give rise to the posterior neural and mesodermal tissues. We compared these populations (TD6- trunk neural plate border cells; TD9- trunk migratory neural crest cells) to determine which showed more posterior gene expression patterns and assess determine any novel markers of hPSC derived neural crest cell populations.

tag: patient group

value: Trunk neural crest cells


title: HCT116_WT_WGBS

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

institute: Memorial University of Newfoundland

data_processing:
Raw datasets underwent read quality check by FastQC, as well as quality and adapter trimming using Trim Galore.
Short reads in high quality were aligned to hg38 with Bismark using Bowtie2 and the default parameters
Methylation states in CpG context were extracted by Bismark methylation extractor module
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph of CpG beta scores (methylation scores)

source_name: HCT116 cell lines

growth_protocol: HCT116 cells were grown in RPMI 1640 medium with 10% FBS.

extract_protocol:
The DNA was extracted using Qiagen DNeasy Blood & Tissue Kits.
After samples DNA testing, negative control DNAs were added into the initial DNA pool, and then fragmented into a 200-300bp range using Covaris S220. Next, terminal repairing, A-ligation, methylation sequencing adapters ligation were performed to DNA fragments. Then, DNA fragments undergone a bisulfite treatment using the EZ DNA Methylation Gold Kit from Zymo Research. Library concentration was firstly quantified by Qubit 2.0, and then is diluted to 1 ng/ul before an insert size verification using the Agilent Bioanalyzer 2100 and followed by Q-PCR. Finally, the library was paired-end sequenced using the Illumina HiSeq 4000.

treatment_protocol: No treatment

tag: tissue

value: colon

tag: cell line


title: IP_Ser2P_mut-dhp1_MM+thiamine_SI_exp4

description: with spike-in

value: Abcam, ab5095


title: IP_Ser2P_WT_MM+thiamine_SI_exp4

description: with spike-in


title: Trunk neural crest cells rep2

description: Differentiated H9:SOX10 hPSCs


title: Trunk neural crest precursors rep2

description: Differentiated H9:SOX10 hPSCs

value: Trunk neural crest precursors


title: Trunk neural crest cells rep1

description: Differentiated H9:SOX10 hPSCs


title: RA patterned neural crest cells rep3

description: Differentiated H9:SOX10 hPSCs

value: RA patterned neural crest cells


title: Trunk neural crest precursors rep1

description: Differentiated H9:SOX10 hPSCs


title: RA patterned neural crest cells rep2

description: Differentiated H9:SOX10 hPSCs


title: IP_Ser7P_WT_MM+thiamine_SI_exp4

description: with spike-in

value: clone 4E12, EMD Millipore, 04-1570


title: WCE_Rpb1_mut-sen1-dbl8_RM_exp1

description: without spike-in

organism: Schizosaccharomyces pombe

value: h? ade6-M21? leu1-32 ura4-D18 his3-D1 dbl8::kanMX6 sen1::natMX6

value: YES media (RM)


title: IP_Rpb1_mut-sen1-dbl8_RM_exp1

description: without spike-in

value: clone 8WG16; Convance, MMS-126R


title: IP_Ser5P_WT_MM+thiamine_SI_exp4

description: with spike-in

value: Abcam, ab5131


title: RA patterned neural crest cells rep1

description: Differentiated H9:SOX10 hPSCs


title: IP_Rpb1_mut-dbl8_RM_exp1

description: without spike-in

value: h? ade6-M21? leu1-32 ura4-D18 his3-D1 dbl8::kanMX6


title: Trunk neural crest precursors rep3

description: Differentiated H9:SOX10 hPSCs


title: IP_Ser5P_mut-dhp1_MM+thiamine_SI_exp4

description: with spike-in


title: WCE_Rpb1_mut-sen1_RM_exp1

description: without spike-in

value: h? ade6-M21? leu1-32 ura4-D18 his3-D1 sen1::kanMX6


title: IP_Ser7P_mut-dhp1_MM+thiamine_SI_exp4

description: with spike-in


title: IP_Rpb1_mut-sen1_RM_exp1

description: without spike-in


title: IP_Rpb1_WT_MM+thiamine_SI_exp4

description: with spike-in


title: Neuromesodermal progenitors rep3

description: Differentiated H9:SOX10 hPSCs

value: Neuromesodermal progenitors


title: WCE_Rpb1_mut-dbl8_RM_exp1

description: without spike-in

value: WCE


title: R-3 (OD600 0.5)

city: Kuala Lumpur

first: Jia-Yi

last: Tan

address: University of Malaya

country: Malaysia

institute: University of Malaya

data_processing:
Rockhopper (assembly and generation of raw counts)
DESeq (differential expression, graphical visualization)
Genome_build: NZ_CP009706
Supplementary_files_format_and_content: tab-delimited text file includes raw counts, normalized counts and expression for each sample

organism: Hafnia alvei

source_name: R, fish paste

growth_protocol: LBB, 30°C, OD 0.5

extract_protocol:
RNA extraction: QIAamp RNA mini kit, RNAProtect
ScriptSeq

treatment_protocol: Replacement knockout of quorum sensing genes


title: Neuromesodermal progenitors rep1

description: Differentiated H9:SOX10 hPSCs


title: Cranial neural crest cells rep3

description: Differentiated H9:SOX10 hPSCs

value: Cranial neural crest cells


title: Neuromesodermal progenitors rep2

description: Differentiated H9:SOX10 hPSCs


title: Cranial neural crest cells rep2

description: Differentiated H9:SOX10 hPSCs


title: R-2 (OD600 0.5)


title: Cranial neural crest precursors rep2

description: Differentiated H9:SOX10 hPSCs

value: Cranial neural crest precursors


title: IP_Rpb3_mut-dhp1_MM+thiamine_SI_exp3

description: with spike-in

value: h? ade6-M21? leu1-32 ura4-D18 his3-D1 Rpb3-3HA::kanMX6 P81nmt-dhp1::kanMX6

value: EMM media (MM) + thiamine


title: R-1 (OD600 0.5)


title: Cranial neural crest cells rep1

description: Differentiated H9:SOX10 hPSCs


title: WCE_Rpb3_mut-dhp1_MM+thiamine_SI_exp3

description: with spike-in


title: I-3 (OD600 0.5)

source_name: I, fish paste


title: I-2 (OD600 0.5)


title: WCE_Rpb3_WT_MM+thiamine_SI_exp3

description: with spike-in

value: h+ ade6-M216 leu1-32 ura4-D18 his3-D1 Rpb3-3HA::kanMX6


title: WCE_Rpb1_WT_RM_exp1

description: without spike-in


title: Cranial neural crest precursors rep1

description: Differentiated H9:SOX10 hPSCs


title: IP_Rpb1_WT_RM_exp1

description: without spike-in


title: IP_Rpb1_mut-nab3_RM_exp1

description: without spike-in

value: h? ade6-M21? leu1-32 ura4-D18 his3-D1 nab3::kanMX6


title: I-1 (OD600 0.5)


title: WCE_Rpb1_mut-nab3_RM_exp1

description: without spike-in


title: WT-3 (OD600 0.5)

source_name: WT, fish paste

value: Wild type


title: WCE_Rpb1_mut-ysh1_MM+rapamycin_SI_exp5

description: with spike-in

value: h-  ade6-M210 leu1-32 ura4-D18 torSE::kanMX6 fkh1::URA+ leu1-32::(nmt1-rpl13-2FKBP12-leu1+) Ysh1-FRB-GFP::natMX6

value: EMM media (MM) leu- + rapamycin


title: WCE_Rpb1_mut-dhp1_MM+thiamine_SI_exp3

description: with spike-in


title: IP_Rpb1_mut-ysh1_MM+rapamycin_SI_exp5

description: with spike-in


title: HUASMC, Control, Rep2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Human arterial smooth muscle cells (HUASMCs) transfected with siGENOME Non-Targeting siRNA as controls

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-1_0-type from Affymetrix. A Custom CDF Version 21 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: HUASMCs transfected with siGENOME Non-Targeting siRNA

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

growth_protocol: Human arterial smooth muscle cells (HUASMCs) were freshly isolated from individual umbilical cords and grown on collagen I-bonded BioFlex® plates (Flexcell International) and exposed to biomechanical stretch (13%, 0.5 Hz) for 24 hours.

extract_protocol: RNA was isolated and processed for DNA microarray analysis according to manufacturers’ instructions

treatment_protocol: HUASMCs were transfected with short interfering RNA directed against NFAT5 (5’-CCA GTT CCT ACA ATG ATA A-3’).

tag: treatment

value: control


title: HUASMC, Control, Rep3


title: Human Embryonic Stem Cells rep3

description: Differentiated H9:SOX10 hPSCs

value: Human Embryonic Stem Cells


title: HUASMC, Control, Rep1


title: Human Embryonic Stem Cells rep2

description: Differentiated H9:SOX10 hPSCs


title: Human Embryonic Stem Cells rep1

description: Differentiated H9:SOX10 hPSCs


title: WT-2 (OD600 0.5)

tag: genotype


title: IP_Rpb3_WT_MM+thiamine_SI_exp3

description: with spike-in


title: WCE_Rpb1_WT_MM+rapamycin_SI_exp5

description: with spike-in

value: h-  ade6-M210 leu1-32 ura4-D18 torSE::kanMX6 fkh1::URA+ leu1-32::(nmt1-rpl13-2FKBP12-leu1+)


title: IP_Rpb1_WT_MM+thiamine_SI_exp3

description: with spike-in

value: clone 8WG16; Convance, MMS-126R


title: IP_Rpb1_mut-dhp1_MM+thiamine_SI_exp3

description: with spike-in


title: 1346 [ATAC-seq]

status: Public on Aug 09 2018

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

description: ATACseq

data_processing:
Alignment and quantification. We used the ENCODE ATAC-seq pipeline to perform alignment and peak calling(https://github.com/kundajelab/atac_dnase_pipelines){Sloan:2016hy}. FASTQ files were trimmed with Cutadapt v1.9{Martin:2011va} and aligned with Bowtie2 v2.2.6{Langmead:2012jh}. MACS2 v2.0.8 {Zhang:2008gm} was used to call peaks with default parameters. Irreproducible Discovery Rate (IDR){Li:2011gg} analyses were performed based on pseudo-replicates (subsample of reads) with a cutoff of 0.1 to output an IDR call set, which was used for downstream analysis. We used WASP {vandeGeijn:2014wg} to filter out reads that are prone to mapping bias.
Genome_build: hg19

source_name: coronary artery smooth muscle cell

growth_protocol: Sample acquisition and cell culture. A total of 8 primary human coronary artery smooth muscle cell (HCASMC) lines collected from donor hearts were purchased from PromoCell (catalog # C-12511, n = 19), Cell Applications (catalog # 350-05a, n = 25), Lonza (catalog # CC-2583, n = 3), Lifeline Cell Technology (catalog # FC-0031, n = 3), and ATCC (catalog # PCS-100-021, n = 2). All lines were stained with smooth muscle alpha actin to check for smooth muscle content and all lines tested negative for mycoplasma (Table S1).

extract_protocol: Library preparation and sequencing. ATAC-seq was used to assess chromatin accessibility with slight modifications to the published protocol {Buenrostro:2015be}. Approximately 5e4 fresh cells were collected at 500 g, washed in PBS, and nuclei extracted with cold lysis buffer. Pellets were subjected to transposition containing Tn5 transposases (Illumina) at 37 °C for 30 min, followed by purification using the DNA Clean-up and Concentration kit (Zymo). Libraries were PCR amplified using Nextera barcodes, with the total # of cycles empirically determined using SYBR qPCR. Amplified libraries were purified and quantified using bioanalyzer, nanodrop and qPCR (KAPA) analysis. Libraries were multiplexed and 2x75 bp sequencing was performed using an Illumina NextSeq 500.

treatment_protocol: All cell lines were cultured in smooth muscle growth medium (Lonza catalog # CC-3182) supplemented with hEGF, insulin, hFGF-b, and 5% FBS, according to Lonza instructions. All HCASMC lines were expanded to passage 5-6 prior to extraction.

tag: sample type

value: cell culture


title: TAC+PDE9A-I 6 (mRNA-seq)

city: Baltimore

first: Kristen

last: Kokkonen-Simon

state: Maryland

address: 720 Rutland Ave, Ross 858

department: Medicine

institute: Johns Hopkins University

description: 676_TAC+PDE9AI 6

data_processing:
Illumina CASAVA 1.8.4 was used for BCL to FASTQ file conversion and for base-calling using default parameters
RNA-seq reads were trimmed and mapped to the Ensembl mouse reference genome (mm10) using HISAT2 version 2.0.5
Transcript counts were quantified using RSEM v1.3.0 with default parameters
Bioconductor's DESeq2 1.18.1 was used for differential expression analysis of RNA count data
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain transcripts-per-million (TPM) normalized counts of mRNAs

source_name: Left ventricle myocardium

extract_protocol:
Left ventricle myocardium was collected and flash-frozen in liquid nitrogen. Total RNA was extracted using Qiazol and Qiagen's miRNeasy kit according to manufacturer protocol, and samples were run on an Agilent Bioanalyzer to evaluate RIN score prior to library construction
Sequencing libraries were constructed using the Illumina TruSeq Stranded Total RNA sample preparation kit (with barcodes) and 500 ng of total RNA

treatment_protocol: Mice subjected to sham or TAC (cardiac pressure-overload) surgeries were treated with either a PDE5A or PDE9A inhibitor for 4 weeks, with treatment initiated 1 week after surgery.

tag: strain

value: Left ventricle myocardium

tag: surgery

value: TAC (cardiac-pressure-overload)

tag: drug treatment

tag: sample id

value: Ear tag #676


title: 2305 [ATAC-seq]

description: ATACseq


title: 2356 [ATAC-seq]

description: ATACseq


title: 2989 [ATAC-seq]

description: ATACseq


title: 200212 [ATAC-seq]

description: ATACseq


title: 2510 [ATAC-seq]

description: ATACseq


title: 1508 [ATAC-seq]

description: ATACseq


title: WT-1 (OD600 0.5)


title: TAC+PDE9A-I 5 (mRNA-seq)

description: 542_TAC+PDE9AI 5

value: Ear tag #542


title: TAC+PDE9A-I 4 (mRNA-seq)

description: 531_TAC+PDE9AI 4

value: Ear tag #531


title: HUASMC with NFAT5, Rep3

description: Human arterial smooth muscle cells (HUASMCs) transfected with siRNA against NFAT5

source_name: HUASMCs transfected with siRNA against NFAT5


title: TAC+PDE9A-I 3 (mRNA-seq)

description: 529_TAC+PDE9AI 3

value: Ear tag #529


title: HUASMC with NFAT5, Rep2


title: 9070202

data_processing:
Alignment and quantification of transcriptomic and epigenomic features. De-multiplexed FASTQ files were mapped with STAR version 2.4.0i in 2-pass mode{Dobin:2013fg} over the hg19 reference genome. Prior to expression quantification, we filtered our reads prone to mapping bias using WASP {vandeGeijn:2014wg}. Total read counts and RPKM were calculated with RNA-SeQC v1.1.8{Deluca:2012dp} using default parameters with additional flags “-n 1000 -noDoC -strictMode” over GENCODE v19 reference. Allele-specific read counts were generated with the createASVCF module in RASQUAL{Kumasaka:2016fn}. We quantified intron excision levels using LeafCutter intron-spanning reads{Li:2016wz}. In brief, we converted bam files to splice junction files using the bam2junc.sh script, and defined intron clusters using leafcutter_cluster.py with default parameters, which requires at least 30 reads supporting each intron and allows intron to have a maximum size of 100kb. We used the ENCODE ATAC-seq pipeline to perform alignment and peak calling(https://github.com/kundajelab/atac_dnase_pipelines){Sloan:2016hy}. FASTQ files were trimmed with Cutadapt v1.9{Martin:2011va} and aligned with Bowtie2 v2.2.6{Langmead:2012jh}. MACS2 v2.0.8 {Zhang:2008gm} was used to call peaks with default parameters. Irreproducible Discovery Rate (IDR){Li:2011gg} analyses were performed based on pseudo-replicates (subsample of reads) with a cutoff of 0.1 to output an IDR call set, which was used for downstream analysis. We used WASP {vandeGeijn:2014wg} to filter out reads that are prone to mapping bias.
Genome_build: hg19

growth_protocol: Sample acquisition and cell culture. A total of 52 primary human coronary artery smooth muscle cell (HCASMC) lines collected from donor hearts were purchased from PromoCell (catalog # C-12511, n = 19), Cell Applications (catalog # 350-05a, n = 25), Lonza (catalog # CC-2583, n = 3), Lifeline Cell Technology (catalog # FC-0031, n = 3), and ATCC (catalog # PCS-100-021, n = 2). All lines were stained with smooth muscle alpha actin to check for smooth muscle content and all lines tested negative for mycoplasma (Table S1).

extract_protocol: Library preparation and sequencing. RNA was extracted using Qiagen miRNeasy Mini Prep Kit (catalog # 74106). Quality of RNA was assessed on the Agilent 2100 Bioanalyzer. Samples with RIN greater than or equal to 8 were sent to the Next-Generation Sequencing Core at the Perelman School of Medicine at the University of Pennsylvania. Libraries were made using Illumina TruSeq Stranded Total RNA Library Prep Kit (catalog # 20020597) and sequenced using 125bp paired-end on HiSeq 2500 Platform. We used ATAC-seq to assess chromatin accessibility with slight modifications to the published protocol {Buenrostro:2015be}. Approximately 5e4 fresh cells were collected at 500 g, washed in PBS, and nuclei extracted with cold lysis buffer. Pellets were subjected to transposition containing Tn5 transposases (Illumina) at 37 °C for 30 min, followed by purification using the DNA Clean-up and Concentration kit (Zymo). Libraries were PCR amplified using Nextera barcodes, with the total # of cycles empirically determined using SYBR qPCR. Amplified libraries were purified and quantified using bioanalyzer, nanodrop and qPCR (KAPA) analysis. Libraries were multiplexed and 2x75 bp sequencing was performed using an Illumina NextSeq 500.


title: TAC+PDE9A-I 2 (mRNA-seq)

description: 528_TAC+PDE9AI 2

value: Ear tag #528


title: 1522 [ATAC-seq]

description: ATACseq


title: TAC+PDE5A-I 5 (mRNA-seq)

description: 697_TAC+PDE5AI 5

value: Sildenafil (PDE5A-I)

value: Ear tag #697


title: TAC+PDE9A-I 1 (mRNA-seq)

description: 151_TAC+PDE9AI 1

value: Ear tag #151


title: WCE_Rpb1_WT_MM+thiamine_SI_exp3

description: with spike-in

value: WCE

value: h+ ade6-M216 leu1-32 ura4-D18 his3-D1 Rpb3-3HA::kanMX6

value: EMM media (MM) + thiamine


title: TAC+PDE5A-I 2 (mRNA-seq)

description: 536_TAC+PDE5AI 2

value: Ear tag #536


title: TAC+PDE5A-I 3 (mRNA-seq)

description: 627_TAC+PDE5AI 3

value: Ear tag #627


title: TAC 3 (mRNA-seq)

description: 541_TAC 3

value: Ear tag #541


title: HUASMC with NFAT5, Rep1


title: Sham 4 (mRNA-seq)

description: 606_sham 4

value: Sham

value: Ear tag #606


title: TAC 2 (mRNA-seq)

description: 157_TAC 2

value: Left ventricle myocardium

value: TAC (cardiac-pressure-overload)

value: Ear tag #157


title: TAC+PDE5A-I 1 (mRNA-seq)

description: 533_TAC+PDE5AI 1

value: Ear tag #533


title: IP_Rpb1_WT_MM+rapamycin_SI_exp5

description: with spike-in

value: clone 8WG16; Convance, MMS-126R

value: h-  ade6-M210 leu1-32 ura4-D18 torSE::kanMX6 fkh1::URA+ leu1-32::(nmt1-rpl13-2FKBP12-leu1+)

value: EMM media (MM) leu- + rapamycin


title: Sham 5 (mRNA-seq)

description: 608_sham 5

value: Ear tag #608


title: Sham 2 (mRNA-seq)

description: 175_sham 2

value: Ear tag #175


title: TAC+PDE5A-I 4 (mRNA-seq)

description: 647_TAC+PDE5AI 4

value: Sildenafil (PDE5A-I)

value: Ear tag #647


title: Sham 1 (mRNA-seq)

description: 165_sham 1

value: Ear tag #165


title: Sham 3 (mRNA-seq)

description: 189_sham 3

value: Ear tag #189


title: TAC 5 (mRNA-seq)

description: 631_TAC 5

value: Ear tag #631


title: TAC 1 (mRNA-seq)

description: 156_TAC 1

value: Ear tag #156


title: TAC+PDE9A-I 6 (miRNA-seq)

data_processing:
Illumina CASAVA 1.8.4 was used for BCL to FASTQ file conversion and for base-calling using default parameters.
miRge v1.0 was used for initial data analysis and microRNA counting and reads-per-million generation (Baras et al, PLOS One, 2015). miRge uses Cutadapt 1.8 for sequence read filtering and adapter trimming, and Bowtie 1.1.1 for read alignment. miRBase release version 21 was used for reference sequences for alignment.
After count data was generated, Microsoft Excel was used to remove all microRNAs for which less than 50% of mice had read counts.
Bioconductor's DESeq 1.26.0 was used for differential expression analysis of microRNA count data, using the "pooled" method for estimating dispersions.
Genome_build: miRBase release version 21
Supplementary_files_format_and_content: Processed data files contain raw counts of microRNAs generated by the miRge program

extract_protocol:
Left ventricle myocardium was collected and flash-frozen in liquid nitrogen. Total RNA was extracted using Qiazol and Qiagen's miRNeasy kit according to manufacturer protocol, and samples were run on an Agilent Bioanalyzer to evaluate RIN score prior to library construction
Sequencing libraries were constructed using the Illumina TruSeq Small RNA Sample Prep Kit (with barcodes) and 500 ng of total RNA

value: Ear tag #676


title: TAC 4 (mRNA-seq)

description: 612_TAC 4

value: Ear tag #612


title: TAC+PDE9A-I 5 (miRNA-seq)

value: Left ventricle myocardium

value: Ear tag #542


title: TAC+PDE9A-I 3 (miRNA-seq)

value: TAC (cardiac-pressure-overload)

value: Ear tag #529


title: TAC+PDE9A-I 2 (miRNA-seq)

value: Ear tag #528


title: TAC+PDE9A-I 4 (miRNA-seq)

value: Ear tag #531


title: TAC+PDE9A-I 1 (miRNA-seq)

value: Ear tag #151


title: TAC+PDE5A-I 3 (miRNA-seq)

value: Ear tag #627


title: TAC+PDE5A-I 4 (miRNA-seq)


title: TAC 5 (miRNA-seq)


title: TAC 4 (miRNA-seq)


title: TAC+PDE5A-I 5 (miRNA-seq)

value: Ear tag #697


title: TAC+PDE5A-I 2 (miRNA-seq)

value: Sildenafil (PDE5A-I)

value: Ear tag #536


title: Sham 5 (miRNA-seq)

value: Sham

value: Ear tag #608


title: Sham 2 (miRNA-seq)

value: Ear tag #175


title: TAC 1 (miRNA-seq)

value: Ear tag #156


title: KO: myoFoxf1 KO

city: Cincinnati

first: Yan

state: Ohio

address: 3333 Burnet Avenue

department: Pulmonary Biology

institute: Cicinnati children's Hospital Medical Center

description: fibroblasts isolated from myoFoxf1 KO mouse lungs

data_processing:
RNA from fibroblasts isolated from bleomycin-treated Foxf1fl/fl and myoFoxf1 KO mouse lungs were used for RNA-seq analysis.
RNeasy Mini kit (Qiagen) was used to isolate total RNA from total lung lysates or isolated fibroblast populations. mRNAs of specific genes were analyzed by qRT–PCR using the StepOnePlus Real-Time PCR system (Applied Biosystems)
Next-generation sequencing of equimolar pools of cDNA libraries was performed using a single read 75 rapid flow cell on a HiSeq 2500 sequencing platform (Illumina), generating greater than 20 million raw reads per sample.
The raw sequenced reads were aligned from FASTQ files to the mouse genome build GRCm38/mm10 and the UCSC reference transcriptome (http://ccb.jhu.edu/software/tophat/index.shtml) using “Cufflinks” .
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheet including Reads and FPKM expression

source_name: Lung Fibroblast cells

growth_protocol: Foxf1fl/fl mouse line was generated as 129/C57Bl/6 hybrids and bred into the C57Bl/6 mouse background. Foxf1fl/fl mice were bred with αSMA-Cre-ERT2  mice to generate αSMA-Cre-ERT2/ Foxf1fl/fl (abbreviated as myoFoxf1 KO) mice. Single transgenic Foxf1fl/fl littermates were used as controls.  ROSA26R(mTmG/mTmG) mice (Jackson Lab) were crossed with αSMA-Cre-ERT2  mice to generate ROSA26R(mTmG/+);αSMA-Cre-ERT2 (abbreviated as mTmG; αSMA-CreERT2 ) mice

extract_protocol:
Quantification of lung collagen content was performed using the Sircol collagen assay (Biocolor, Carrickfergus, UK) and the Hydroxyproline assay kit (Sigma) following manufacturer's protocol.
Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina).

treatment_protocol: For bleomycin-induced fibrosis studies, mice were administered 1 U/kg or 2 U/kg of bleomycin sulfate (EMD Biosciences) intratracheally one time per week for two, three or four weeks. Transgenic mice were given Tam (40 mg/Kg; Sigma) by intraperitoneal injection on days 2, 3, and 4 after bleomycin treatment. Mice were harvested one week after final bleomycin treatment.

value: lung


title: TAC 2 (miRNA-seq)

value: Ear tag #157


title: CON: bleomycin-treated Foxf1fl/fl

description: fibroblasts isolated from bleomycin-treated Foxf1fl/fl mouse lungs


title: Sham 4 (miRNA-seq)

value: Left ventricle myocardium

value: Ear tag #606


title: Sham 3 (miRNA-seq)

value: Ear tag #189


title: IP_Rpb1_mut-dhp1_MM+thiamine_SI_exp4

description: with spike-in

value: clone 8WG16; Convance, MMS-126R

value: h? ade6-M21? leu1-32 ura4-D18 his3-D1 Rpb3-3HA::kanMX6 P81nmt-dhp1::kanMX6

value: EMM media (MM) + thiamine


title: Sham 1 (miRNA-seq)

value: Ear tag #165


title: S471: cell 435

city: Cambridge

first: Orr

last: Ashenberg

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

description: Full-length RNAseq (SMART-Seq2) reads

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie mapping to UCSC mm10 mouse transcriptome
RSEM v1.2.8
Supplementary_files_format_and_content: cell.annotations.csv: cell sample annotation table; For each cell (row): cell name, sample number in plate, tetramer sorting condition, cluster number, cell type, number of genes
Supplementary_files_format_and_content: tpm.csv: Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each cell (columns)

source_name: pancreatic islets

extract_protocol:
Mouse pancreatic tissue was digested by collagenase, and islets were isolated and dissociated into single cells. Beta-cell-specific CD4 T cells were single-cell sorted by FACS based on tetramer labeling.
Full length RNAseq (SMART-Seq2) libraries sequenced with 50bp and 25bp paired end reads on an Illumina NextSeq 500.

tag: sample

tag: tetramer sort

value: Ins

tag: cell type

value: T follicular helper cell

tag: cluster


title: S477: cell 441

description: Full-length RNAseq (SMART-Seq2) reads


title: S476: cell 440

description: Full-length RNAseq (SMART-Seq2) reads

value: Activated CD4 T cell


title: S470: cell 434

description: Full-length RNAseq (SMART-Seq2) reads

value: Treg cell


title: S474: cell 438

description: Full-length RNAseq (SMART-Seq2) reads


title: S473: cell 437

description: Full-length RNAseq (SMART-Seq2) reads


title: TAC+PDE5A-I 1 (miRNA-seq)

value: TAC (cardiac-pressure-overload)

value: Sildenafil (PDE5A-I)

value: Ear tag #533


title: S475: cell 439

description: Full-length RNAseq (SMART-Seq2) reads


title: S463: cell 427

description: Full-length RNAseq (SMART-Seq2) reads

value: Dividing CD4 T cell


title: S465: cell 429

description: Full-length RNAseq (SMART-Seq2) reads


title: S472: cell 436

description: Full-length RNAseq (SMART-Seq2) reads

value: B cell


title: S467: cell 431

description: Full-length RNAseq (SMART-Seq2) reads


title: S460: cell 424

description: Full-length RNAseq (SMART-Seq2) reads


title: TAC 3 (miRNA-seq)

value: Ear tag #541


title: S459: cell 423

description: Full-length RNAseq (SMART-Seq2) reads


title: S466: cell 430

description: Full-length RNAseq (SMART-Seq2) reads


title: S455: cell 419

description: Full-length RNAseq (SMART-Seq2) reads


title: S468: cell 432

description: Full-length RNAseq (SMART-Seq2) reads


title: S454: cell 418

description: Full-length RNAseq (SMART-Seq2) reads


title: S464: cell 428

description: Full-length RNAseq (SMART-Seq2) reads


title: S462: cell 426

description: Full-length RNAseq (SMART-Seq2) reads


title: 4797P

first: Caitlin

middle: E

last: Dunn

department: Division of Human Genetics

institute: Cincinnati Children's Hospital Medical Center

description:
PlacentaTPM_by_gene
4797P

data_processing:
Reads were trimmed using Trimmomatic and aligned using the HiSat2 aligner.
Transcript counting and quantification was done using kallisto.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

molecule: polyA RNA

source_name: placenta

extract_protocol:
RNA was extracted with the TRIzol reagent (ThermoFisher Scientific). All samples had RQN >7 measured on an Advanced Analytical Fragment Analyzer.
PolyA stranded RNA-seq was performed on an Illumina HiSeq machine using a paired-end approach with 75 bp reads, generating approximately 30 million paired reads per sample.

treatment_protocol: Male mice were housed with females overnight to determine time of conception.  Pregnant female mice were sacrificed on the designated day of gestation and tissues were harvested and flash frozen in liquid nitrogen.

value: Mixed C57BL/6 and FVB


title: 4567P

description:
PlacentaTPM_by_gene
4567P


title: 4629P

description:
PlacentaTPM_by_gene
4629P


title: S461: cell 425

description: Full-length RNAseq (SMART-Seq2) reads


title: S458: cell 422

description: Full-length RNAseq (SMART-Seq2) reads


title: 4568P

description:
PlacentaTPM_by_gene
4568P


title: S457: cell 421

description: Full-length RNAseq (SMART-Seq2) reads


title: S456: cell 420

description: Full-length RNAseq (SMART-Seq2) reads


title: S449: cell 413

description: Full-length RNAseq (SMART-Seq2) reads


title: 4417P

description:
PlacentaTPM_by_gene
4417P


title: S453: cell 417

description: Full-length RNAseq (SMART-Seq2) reads


title: S452: cell 416

description: Full-length RNAseq (SMART-Seq2) reads


title: 4398AP

description:
PlacentaTPM_by_gene
4398AP

value: nontransgenic


title: 4797U

description:
UterusTPM_by_gene
4797U

source_name: uterus


title: S469: cell 433

description: Full-length RNAseq (SMART-Seq2) reads


title: S448: cell 412

description: Full-length RNAseq (SMART-Seq2) reads


title: 4568U

description:
UterusTPM_by_gene
4568U


title: S451: cell 415

description: Full-length RNAseq (SMART-Seq2) reads


title: S450: cell 414

description: Full-length RNAseq (SMART-Seq2) reads


title: S445: cell 409

description: Full-length RNAseq (SMART-Seq2) reads


title: 4759P

description:
PlacentaTPM_by_gene
4759P


title: S446: cell 410

description: Full-length RNAseq (SMART-Seq2) reads


title: 4629U

description:
UterusTPM_by_gene
4629U


title: 4567U

description:
UterusTPM_by_gene
4567U


title: 4414P

description:
PlacentaTPM_by_gene
4414P


title: 4667P

description:
PlacentaTPM_by_gene
4667P


title: S447: cell 411

description: Full-length RNAseq (SMART-Seq2) reads


title: 4429P

description:
PlacentaTPM_by_gene
4429P


title: S444: cell 408

description: Full-length RNAseq (SMART-Seq2) reads


title: 4757U

description:
UterusTPM_by_gene
4757U


title: S439: cell 403

description: Full-length RNAseq (SMART-Seq2) reads


title: 4429U

description:
UterusTPM_by_gene
4429U


title: S443: cell 407

description: Full-length RNAseq (SMART-Seq2) reads


title: Id1 WT-Normal (N)_C

city: Frederick

first: Jack

last: Chen

state: MD

address: SAIC-Frederick Miller Dr

institute: NIH

data_processing:
Illumina HiSeq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse mm10 genome using bowtie2 with default parameters.
Reads were counted by featurecount and then Reads per Megabase of library size (CPM) were generated and normalized by the limmaVoom pipeline.
Genome_build: mouse mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

source_name: Hematopoietic Stem Cells

extract_protocol:
RNA was isolated from FACS purified Id1+/+ and Id1-/- HSCs isolated from primary recipient mice 4 weeks after transplantation of Lin- Id1-/- and Id1+/+ BMCs.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone Marrow

tag: time

value: 4 weeks post BMT

value: Normal (N)

value: Hematopoietic Stem Cells


title: S442: cell 406

description: Full-length RNAseq (SMART-Seq2) reads


title: 4417U

description:
UterusTPM_by_gene
4417U


title: 4640U

description:
UterusTPM_by_gene
4640U


title: 4478U

description:
UterusTPM_by_gene
4478U


title: 4398BU

description:
UterusTPM_by_gene
4398BU


title: S438: cell 402

description: Full-length RNAseq (SMART-Seq2) reads


title: Id1 WT-Normal (N)_B


title: S440: cell 404

description: Full-length RNAseq (SMART-Seq2) reads


title: S437: cell 401

description: Full-length RNAseq (SMART-Seq2) reads


title: Id1 KO-Normal (N)_C


title: S436: cell 400

description: Full-length RNAseq (SMART-Seq2) reads


title: S433: cell 397

description: Full-length RNAseq (SMART-Seq2) reads


title: Id1 WT-Stressed (S)_B

value: Stressed (S)


title: S432: cell 396

description: Full-length RNAseq (SMART-Seq2) reads

value: Ins


title: S435: cell 399

description: Full-length RNAseq (SMART-Seq2) reads


title: S434: cell 398

description: Full-length RNAseq (SMART-Seq2) reads


title: Id1 WT-Normal (N)_A


title: S441: cell 405

description: Full-length RNAseq (SMART-Seq2) reads


title: Id1 WT-Stressed (S)_A


title: S430: cell 394

description: Full-length RNAseq (SMART-Seq2) reads


title: S429: cell 393

description: Full-length RNAseq (SMART-Seq2) reads


title: Id1 KO-Normal (N)_B


title: S426: cell 390

description: Full-length RNAseq (SMART-Seq2) reads


title: S431: cell 395

description: Full-length RNAseq (SMART-Seq2) reads


title: S424: cell 388

description: Full-length RNAseq (SMART-Seq2) reads


title: Id1 KO-Normal (N)_A


title: S425: cell 389

description: Full-length RNAseq (SMART-Seq2) reads


title: Id1 KO-Stressed (S)_B


title: S428: cell 392

description: Full-length RNAseq (SMART-Seq2) reads

value: T follicular helper cell


title: S423: cell 387

description: Full-length RNAseq (SMART-Seq2) reads


title: Id1 KO-Stressed (S)_A


title: S419: cell 383

description: Full-length RNAseq (SMART-Seq2) reads


title: S421: cell 385

description: Full-length RNAseq (SMART-Seq2) reads


title: S420: cell 384

description: Full-length RNAseq (SMART-Seq2) reads


title: S418: cell 382

description: Full-length RNAseq (SMART-Seq2) reads


title: S417: cell 381

description: Full-length RNAseq (SMART-Seq2) reads


title: S416: cell 380

description: Full-length RNAseq (SMART-Seq2) reads


title: S415: cell 379

description: Full-length RNAseq (SMART-Seq2) reads


title: S414: cell 378

description: Full-length RNAseq (SMART-Seq2) reads


title: S413: cell 377

description: Full-length RNAseq (SMART-Seq2) reads


title: S427: cell 391

description: Full-length RNAseq (SMART-Seq2) reads


title: S412: cell 376

description: Full-length RNAseq (SMART-Seq2) reads


title: S422: cell 386

description: Full-length RNAseq (SMART-Seq2) reads


title: S409: cell 373

description: Full-length RNAseq (SMART-Seq2) reads


title: S408: cell 372

description: Full-length RNAseq (SMART-Seq2) reads


title: DMSO_H661

city: Dallas

first: Elizabeth

last: McMillan

state: Tx

address: 6000 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw intensitity values were background corrected and quantile normalized using the lumi package in R.

label_protocol: Standard Illumina label protocol

extract_protocol: Total RNA was harvested using the miRNeasy Qiagen kit according to the manufacturer's instructions.

value: Non-small cell lung cancer cell line H661

tag: phenotype

value: DMSO treated


title: SW151511_H661

value: SW151511 treated, 24 hours


title: DMSO_H2122

value: Non-small cell lung cancer cell line H2122


title: DMSO_H596

value: Non-small cell lung cancer cell line H596


title: S410: cell 374

description: Full-length RNAseq (SMART-Seq2) reads

value: Treg cell


title: DMSO_HCC366

value: Non-small cell lung cancer cell line HCC366


title: SW151511_H2122


title: S407: cell 371

description: Full-length RNAseq (SMART-Seq2) reads


title: S406: cell 370

description: Full-length RNAseq (SMART-Seq2) reads

value: Dividing CD4 T cell


title: S405: cell 369

description: Full-length RNAseq (SMART-Seq2) reads

value: Activated CD4 T cell


title: S404: cell 368

description: Full-length RNAseq (SMART-Seq2) reads


title: S411: cell 375

description: Full-length RNAseq (SMART-Seq2) reads


title: fibroblast_ileum_inflamed_patientnumber23

city: Amsterdam

first: Jessica

middle: Rebecca

last: de Bruyn

address: Meibergdreef 69

department: Gastroenterology and Hepatology

country: Netherlands

institute: Academic Medical Center

description: Sample name: 3999185025_L

data_processing: Data were normalized using Genome studio software (Illumina)

source_name: intestinal fibroblast

label_protocol: RNA was labelled using cRNA labelling kit for Illumina Arrays (Ambion)

growth_protocol: Fibroblasts were isolated from human intestine using collagenase digestion, and placed into cell culture untill confluency was reached

extract_protocol: RNA from primary cells at Passage 1 was isolated using the RNAeasy mini kit (Qiagen)

treatment_protocol: Full-grown cell culture medium (RPMI) was refreshed 2x/week

tag: disease

value: Crohn's disease

value: ileum

value: fibroblast

value: inflamed

tag: patient number

tag: gender

value: female

tag: age at time of surgery (years)


title: SW151511_HCC366

tag: cell line

tag: treatment


title: fibroblast_ileum_stenotic_patientnumber17

description: Sample name: 3999185025_H

tag: tissue

value: stenotic


title: S402: cell 366

description: Full-length RNAseq (SMART-Seq2) reads

value: Ins


title: S403: cell 367

description: Full-length RNAseq (SMART-Seq2) reads

value: T follicular helper cell


title: fibroblast_ileum_normal_patientnumber47

description: Sample name: 3999185025_K

value: normal


title: fibroblast_ileum_stenotic_patientnumber50

description: Sample name: 3999185025_J

value: male


title: fibroblast_ileum_inflamed_patientnumber47

description: Sample name: 3999185025_I


title: S400: cell 364

description: Full-length RNAseq (SMART-Seq2) reads


title: S399: cell 363

description: Full-length RNAseq (SMART-Seq2) reads


title: S397: cell 361

description: Full-length RNAseq (SMART-Seq2) reads


title: S396: cell 360

description: Full-length RNAseq (SMART-Seq2) reads


title: S401: cell 365

description: Full-length RNAseq (SMART-Seq2) reads


title: fibroblast_ileum_normal_patientnumber50

description: Sample name: 3999185025_F


title: S395: cell 359

description: Full-length RNAseq (SMART-Seq2) reads


title: fibroblast_ileum_inflamed_patientnumber13

description: Sample name: 3999185025_G


title: SW151511_H596

value: SW151511 treated, 24 hours


title: fibroblast_ileum_normal_patientnumber25

description: Sample name: 3999185025_E


title: fibroblast_ileum_inflamed_patientnumber41

description: Sample name: 3999185019_J


title: S394: cell 358

description: Full-length RNAseq (SMART-Seq2) reads


title: fibroblast_ileum_normal_patientnumber41

description: Sample name: 3999185019_I


title: S398: cell 362

description: Full-length RNAseq (SMART-Seq2) reads


title: fibroblast_ileum_stenotic_patientnumber23

description: Sample name: 3999185025_D


title: fibroblast_ileum_stenotic_patientnumber13

description: Sample name: 3999185025_C


title: S390: cell 355

description: Full-length RNAseq (SMART-Seq2) reads


title: fibroblast_ileum_normal_patientnumber46

description: Sample name: 3999185019_H


title: S389: cell 354

description: Full-length RNAseq (SMART-Seq2) reads

value: B cell


title: fibroblast_ileum_normal_patientnumber23

description: Sample name: 3999185025_B


title: fibroblast_ileum_stenotic_patientnumber47

description: Sample name: 3999185019_L


title: S388: cell 353

description: Full-length RNAseq (SMART-Seq2) reads


title: fibroblast_ileum_normal_patientnumber13

description: Sample name: 3999185019_F


title: fibroblast_ileum_stenotic_patientnumber41

description: Sample name: 3999185019_K


title: fibroblast_ileum_inflamed_patientnumber17

description: Sample name: 3999185019_D


title: fibroblast_ileum_stenotic_patientnumber25

description: Sample name: 3999185025_A


title: fibroblast_ileum_normal_patientnumber17

description: Sample name: 3999185019_C


title: S387: cell 352

description: Full-length RNAseq (SMART-Seq2) reads


title: fibroblast_ileum_inflamed_patientnumber46

description: Sample name: 3999185019_B


title: fibroblast_ileum_inflamed_patientnumber25

description: Sample name: 3999185019_G


title: S392: cell 356

description: Full-length RNAseq (SMART-Seq2) reads


title: S393: cell 357

description: Full-length RNAseq (SMART-Seq2) reads


title: S384: cell 349

description: Full-length RNAseq (SMART-Seq2) reads


title: S383: cell 348

description: Full-length RNAseq (SMART-Seq2) reads


title: S385: cell 350

description: Full-length RNAseq (SMART-Seq2) reads


title: fibroblast_ileum_stenotic_patientnumber46

description: Sample name: 3999185019_A


title: fibroblast_ileum_inflamed_patientnumber50

description: Sample name: 3999185019_E


title: S380: cell 347

description: Full-length RNAseq (SMART-Seq2) reads


title: S386: cell 351

description: Full-length RNAseq (SMART-Seq2) reads


title: S377: cell 345

description: Full-length RNAseq (SMART-Seq2) reads


title: S376: cell 344

description: Full-length RNAseq (SMART-Seq2) reads


title: S375: cell 343

description: Full-length RNAseq (SMART-Seq2) reads


title: S373: cell 341

description: Full-length RNAseq (SMART-Seq2) reads


title: S374: cell 342

description: Full-length RNAseq (SMART-Seq2) reads


title: S371: cell 339

description: Full-length RNAseq (SMART-Seq2) reads


title: S372: cell 340

description: Full-length RNAseq (SMART-Seq2) reads


title: S370: cell 338

description: Full-length RNAseq (SMART-Seq2) reads


title: S369: cell 337

description: Full-length RNAseq (SMART-Seq2) reads


title: S368: cell 336

description: Full-length RNAseq (SMART-Seq2) reads


title: S367: cell 335

description: Full-length RNAseq (SMART-Seq2) reads


title: S378: cell 346

description: Full-length RNAseq (SMART-Seq2) reads


title: 3446A

first: Michael

last: Levin

address: South Kensington Campus

department: Paediatrics

institute: Imperial College London

hyb_protocol: Standard Illumina hybridisation protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using RSN, after background subtraction. The software used for data normalization was 'R' Language and Environment for Statistical Computing (R) 3.2.2

source_name: Whole Blood from patient with Kawasaki Disease

label_protocol: Standard Illumina TotalPrep RNA Amplification kits (Applied Biosystems).

extract_protocol: Standard PAXgene® blood RNA extraction kit protocol (Qiagen).

tag: category

value: Kawasaki Disease

tag: dataset

value: validation - acute

value: Female


title: 3393A

value: Male


title: 3204C

value: validation - conv


title: 3443A


title: 3410A


title: 3301C


title: 3405A


title: 3392A


title: S366: cell 334

description: Full-length RNAseq (SMART-Seq2) reads

value: Dividing CD4 T cell


title: 3363A


title: 3389A


title: 3421A


title: 3395A


title: S365: cell 333

description: Full-length RNAseq (SMART-Seq2) reads


title: S364: cell 332

description: Full-length RNAseq (SMART-Seq2) reads


title: S363: cell 331

description: Full-length RNAseq (SMART-Seq2) reads

value: Treg cell


title: S362: cell 330

description: Full-length RNAseq (SMART-Seq2) reads


title: S360: cell 328

description: Full-length RNAseq (SMART-Seq2) reads


title: 3390A


title: 3341A


title: S359: cell 327

description: Full-length RNAseq (SMART-Seq2) reads


title: S357: cell 325

description: Full-length RNAseq (SMART-Seq2) reads


title: 3339A


title: 3295A


title: 3355A


title: 3288A


title: 3296A


title: 3301A


title: 3343A


title: S356: cell 324

description: Full-length RNAseq (SMART-Seq2) reads


title: 3272A


title: 3244A


title: S355: cell 323

description: Full-length RNAseq (SMART-Seq2) reads


title: 3256A


title: S352: cell 320

description: Full-length RNAseq (SMART-Seq2) reads


title: S351: cell 319

description: Full-length RNAseq (SMART-Seq2) reads


title: S354: cell 322

description: Full-length RNAseq (SMART-Seq2) reads


title: 3237A


title: S353: cell 321

description: Full-length RNAseq (SMART-Seq2) reads


title: 3227A


title: 3220A


title: 3225A


title: 3204A


title: S348: cell 316

description: Full-length RNAseq (SMART-Seq2) reads


title: S350: cell 318

description: Full-length RNAseq (SMART-Seq2) reads


title: 3236A


title: 3214A


title: S347: cell 315

description: Full-length RNAseq (SMART-Seq2) reads


title: 3200A


title: S346: cell 314

description: Full-length RNAseq (SMART-Seq2) reads


title: S349: cell 317

description: Full-length RNAseq (SMART-Seq2) reads


title: 3180A


title: S345: cell 313

description: Full-length RNAseq (SMART-Seq2) reads

value: Activated CD4 T cell


title: 3192A


title: S344: cell 312

description: Full-length RNAseq (SMART-Seq2) reads


title: S343: cell 311

description: Full-length RNAseq (SMART-Seq2) reads


title: S342: cell 310

description: Full-length RNAseq (SMART-Seq2) reads


title: S338: cell 306

description: Full-length RNAseq (SMART-Seq2) reads


title: 3202A


title: S340: cell 308

description: Full-length RNAseq (SMART-Seq2) reads


title: S336: cell 304

description: Full-length RNAseq (SMART-Seq2) reads


title: S339: cell 307

description: Full-length RNAseq (SMART-Seq2) reads


title: 3170A


title: 3145A


title: 3147A


title: 3141A


title: 3162A


title: 3110A


title: S337: cell 305

description: Full-length RNAseq (SMART-Seq2) reads


title: 3127A


title: 3140A


title: 3068A


title: S334: cell 302

description: Full-length RNAseq (SMART-Seq2) reads


title: S335: cell 303

description: Full-length RNAseq (SMART-Seq2) reads


title: S341: cell 309

description: Full-length RNAseq (SMART-Seq2) reads


title: 3106A


title: S333: cell 301

description: Full-length RNAseq (SMART-Seq2) reads


title: S332: cell 300

description: Full-length RNAseq (SMART-Seq2) reads


title: 3084A


title: S330: cell 298

description: Full-length RNAseq (SMART-Seq2) reads


title: 3440A


title: S331: cell 299

description: Full-length RNAseq (SMART-Seq2) reads


title: 3440C


title: 3442C


title: 3430A


title: 3442A


title: 3423A


title: 3423C


title: S329: cell 297

description: Full-length RNAseq (SMART-Seq2) reads


title: 3411A


title: S325: cell 293

description: Full-length RNAseq (SMART-Seq2) reads


title: S323: cell 291

description: Full-length RNAseq (SMART-Seq2) reads


title: S322: cell 290

description: Full-length RNAseq (SMART-Seq2) reads


title: S328: cell 296

description: Full-length RNAseq (SMART-Seq2) reads


title: S327: cell 295

description: Full-length RNAseq (SMART-Seq2) reads


title: S324: cell 292

description: Full-length RNAseq (SMART-Seq2) reads


title: S326: cell 294

description: Full-length RNAseq (SMART-Seq2) reads


title: 3360A


title: Cranial neural crest precursors rep3

description: Differentiated H9:SOX10 hPSCs

tag: patient group

value: Cranial neural crest precursors


title: 3411C


title: S321: cell 289

description: Full-length RNAseq (SMART-Seq2) reads


title: 3406C


title: 3407C


title: S320: cell 288

description: Full-length RNAseq (SMART-Seq2) reads


title: 3403C


title: S319: cell 287

description: Full-length RNAseq (SMART-Seq2) reads


title: 3402A


title: S318: cell 286

description: Full-length RNAseq (SMART-Seq2) reads


title: S315: cell 283

description: Full-length RNAseq (SMART-Seq2) reads


title: 3407A


title: 3406A


title: S317: cell 285

description: Full-length RNAseq (SMART-Seq2) reads


title: S358: cell 326

description: Full-length RNAseq (SMART-Seq2) reads


title: 3397C


title: 3403A


title: 3400C


title: 3397A


title: S316: cell 284

description: Full-length RNAseq (SMART-Seq2) reads


title: S311: cell 279

description: Full-length RNAseq (SMART-Seq2) reads


title: S312: cell 280

description: Full-length RNAseq (SMART-Seq2) reads


title: S313: cell 281

description: Full-length RNAseq (SMART-Seq2) reads


title: S314: cell 282

description: Full-length RNAseq (SMART-Seq2) reads


title: S310: cell 278

description: Full-length RNAseq (SMART-Seq2) reads


title: 3394C


title: S361: cell 329

description: Full-length RNAseq (SMART-Seq2) reads


title: 3366C


title: 3386A


title: S308: cell 276

description: Full-length RNAseq (SMART-Seq2) reads


title: S307: cell 275

description: Full-length RNAseq (SMART-Seq2) reads


title: 3366A


title: S309: cell 277

description: Full-length RNAseq (SMART-Seq2) reads


title: 3394A


title: S305: cell 273

description: Full-length RNAseq (SMART-Seq2) reads


title: 3368C


title: S303: cell 271

description: Full-length RNAseq (SMART-Seq2) reads


title: 3365C


title: 3361C


title: 3362A


title: S302: cell 270

description: Full-length RNAseq (SMART-Seq2) reads


title: S301: cell 269

description: Full-length RNAseq (SMART-Seq2) reads


title: S306: cell 274

description: Full-length RNAseq (SMART-Seq2) reads


title: S300: cell 268

description: Full-length RNAseq (SMART-Seq2) reads


title: 3361A


title: 3350A


title: 3356C


title: S298: cell 266

description: Full-length RNAseq (SMART-Seq2) reads


title: 3356A


title: S299: cell 267

description: Full-length RNAseq (SMART-Seq2) reads


title: S304: cell 272

description: Full-length RNAseq (SMART-Seq2) reads


title: S297: cell 265

description: Full-length RNAseq (SMART-Seq2) reads


title: S296: cell 264

description: Full-length RNAseq (SMART-Seq2) reads


title: S294: cell 262

description: Full-length RNAseq (SMART-Seq2) reads


title: S295: cell 263

description: Full-length RNAseq (SMART-Seq2) reads


title: S292: cell 260

description: Full-length RNAseq (SMART-Seq2) reads


title: 3327A


title: 3334A


title: 3332A


title: S293: cell 261

description: Full-length RNAseq (SMART-Seq2) reads


title: 3345A


title: 3350C


title: 3345C


title: 3332C


title: 3334C


title: 3326C


title: S289: cell 257

description: Full-length RNAseq (SMART-Seq2) reads


title: S291: cell 259

description: Full-length RNAseq (SMART-Seq2) reads


title: 3326A


title: S288: cell 256

description: Full-length RNAseq (SMART-Seq2) reads

value: HIP


title: S290: cell 258

description: Full-length RNAseq (SMART-Seq2) reads


title: S284: cell 252

description: Full-length RNAseq (SMART-Seq2) reads


title: S285: cell 253

description: Full-length RNAseq (SMART-Seq2) reads


title: 3327C


title: S287: cell 255

description: Full-length RNAseq (SMART-Seq2) reads


title: S286: cell 254

description: Full-length RNAseq (SMART-Seq2) reads


title: S282: cell 250

description: Full-length RNAseq (SMART-Seq2) reads


title: S283: cell 251

description: Full-length RNAseq (SMART-Seq2) reads


title: S281: cell 249

description: Full-length RNAseq (SMART-Seq2) reads


title: S280: cell 248

description: Full-length RNAseq (SMART-Seq2) reads


title: 3314A


title: S278: cell 246

description: Full-length RNAseq (SMART-Seq2) reads


title: 3308C


title: S279: cell 247

description: Full-length RNAseq (SMART-Seq2) reads


title: 3304C


title: S277: cell 245

description: Full-length RNAseq (SMART-Seq2) reads


title: 3314C


title: 3313A


title: 3313C


title: 3316A


title: 3306C


title: S274: cell 242

description: Full-length RNAseq (SMART-Seq2) reads


title: 3308A


title: 3310A


title: 3297A


title: 3306A


title: S275: cell 243

description: Full-length RNAseq (SMART-Seq2) reads


title: 3304A


title: 3294C


title: 3290A


title: 3287A


title: S272: cell 240

description: Full-length RNAseq (SMART-Seq2) reads


title: 3294A


title: 3293A


title: 3287C


title: S269: cell 237

description: Full-length RNAseq (SMART-Seq2) reads


title: 3297C


title: S270: cell 238

description: Full-length RNAseq (SMART-Seq2) reads


title: S273: cell 241

description: Full-length RNAseq (SMART-Seq2) reads


title: 3284A


title: S271: cell 239

description: Full-length RNAseq (SMART-Seq2) reads


title: S267: cell 235

description: Full-length RNAseq (SMART-Seq2) reads


title: S266: cell 234

description: Full-length RNAseq (SMART-Seq2) reads


title: S276: cell 244

description: Full-length RNAseq (SMART-Seq2) reads


title: S268: cell 236

description: Full-length RNAseq (SMART-Seq2) reads


title: S265: cell 233

description: Full-length RNAseq (SMART-Seq2) reads


title: S264: cell 232

description: Full-length RNAseq (SMART-Seq2) reads


title: S262: cell 230

description: Full-length RNAseq (SMART-Seq2) reads


title: S263: cell 231

description: Full-length RNAseq (SMART-Seq2) reads


title: 3283C


title: 3270A


title: 3266C


title: S261: cell 229

description: Full-length RNAseq (SMART-Seq2) reads


title: 3263A


title: 3283A


title: 3263C


title: 3262C


title: S257: cell 225

description: Full-length RNAseq (SMART-Seq2) reads


title: 3270C


title: S255: cell 223

description: Full-length RNAseq (SMART-Seq2) reads


title: S256: cell 224

description: Full-length RNAseq (SMART-Seq2) reads


title: 3261C


title: S253: cell 221

description: Full-length RNAseq (SMART-Seq2) reads


title: S259: cell 227

description: Full-length RNAseq (SMART-Seq2) reads


title: S254: cell 222

description: Full-length RNAseq (SMART-Seq2) reads


title: S260: cell 228

description: Full-length RNAseq (SMART-Seq2) reads


title: S258: cell 226

description: Full-length RNAseq (SMART-Seq2) reads


title: S251: cell 219

description: Full-length RNAseq (SMART-Seq2) reads


title: S252: cell 220

description: Full-length RNAseq (SMART-Seq2) reads


title: 3255A


title: S247: cell 215

description: Full-length RNAseq (SMART-Seq2) reads


title: 3262A


title: 3258C


title: 3246A


title: 3246C


title: S250: cell 218

description: Full-length RNAseq (SMART-Seq2) reads


title: S245: cell 213

description: Full-length RNAseq (SMART-Seq2) reads


title: 3261A


title: S246: cell 214

description: Full-length RNAseq (SMART-Seq2) reads


title: 3253A


title: 3235A


title: 3211C


title: 3235C


title: 3259A


title: 3228C


title: 3228A


title: S242: cell 210

description: Full-length RNAseq (SMART-Seq2) reads


title: S249: cell 217

description: Full-length RNAseq (SMART-Seq2) reads


title: S248: cell 216

description: Full-length RNAseq (SMART-Seq2) reads


title: S244: cell 212

description: Full-length RNAseq (SMART-Seq2) reads


title: 3211A


title: 3189A


title: S240: cell 208

description: Full-length RNAseq (SMART-Seq2) reads


title: S239: cell 207

description: Full-length RNAseq (SMART-Seq2) reads


title: 3208A


title: 3205A


title: 3190C


title: 3184C


title: S236: cell 204

description: Full-length RNAseq (SMART-Seq2) reads


title: S243: cell 211

description: Full-length RNAseq (SMART-Seq2) reads


title: 3190A


title: S234: cell 202

description: Full-length RNAseq (SMART-Seq2) reads


title: 3188C


title: 3188A


title: S237: cell 205

description: Full-length RNAseq (SMART-Seq2) reads


title: S238: cell 206

description: Full-length RNAseq (SMART-Seq2) reads


title: S235: cell 203

description: Full-length RNAseq (SMART-Seq2) reads


title: S232: cell 200

description: Full-length RNAseq (SMART-Seq2) reads


title: S231: cell 199

description: Full-length RNAseq (SMART-Seq2) reads


title: S230: cell 198

description: Full-length RNAseq (SMART-Seq2) reads


title: 3175C


title: 3174A


title: 3182C


title: 3182A


title: 3177A


title: 3164A


title: S227: cell 195

description: Full-length RNAseq (SMART-Seq2) reads


title: 3172A


title: S228: cell 196

description: Full-length RNAseq (SMART-Seq2) reads


title: S226: cell 194

description: Full-length RNAseq (SMART-Seq2) reads


title: S225: cell 193

description: Full-length RNAseq (SMART-Seq2) reads


title: S224: cell 192

description: Full-length RNAseq (SMART-Seq2) reads


title: 3251A


title: S233: cell 201

description: Full-length RNAseq (SMART-Seq2) reads


title: S223: cell 191

description: Full-length RNAseq (SMART-Seq2) reads


title: 3157C


title: S229: cell 197

description: Full-length RNAseq (SMART-Seq2) reads


title: 3133A


title: 3149A


title: 3150C


title: S221: cell 189

description: Full-length RNAseq (SMART-Seq2) reads


title: 3123C


title: S222: cell 190

description: Full-length RNAseq (SMART-Seq2) reads


title: 3123A


title: S220: cell 188

description: Full-length RNAseq (SMART-Seq2) reads


title: S217: cell 185

description: Full-length RNAseq (SMART-Seq2) reads


title: S218: cell 186

description: Full-length RNAseq (SMART-Seq2) reads


title: S216: cell 184

description: Full-length RNAseq (SMART-Seq2) reads


title: S215: cell 183

description: Full-length RNAseq (SMART-Seq2) reads


title: 3121C


title: 3119A


title: 3121A


title: 3118C


title: 3118A


title: 3115C


title: 3119C


title: S214: cell 182

description: Full-length RNAseq (SMART-Seq2) reads


title: S211: cell 179

description: Full-length RNAseq (SMART-Seq2) reads


title: S219: cell 187

description: Full-length RNAseq (SMART-Seq2) reads


title: S213: cell 181

description: Full-length RNAseq (SMART-Seq2) reads


title: S209: cell 177

description: Full-length RNAseq (SMART-Seq2) reads


title: S208: cell 176

description: Full-length RNAseq (SMART-Seq2) reads


title: S207: cell 175

description: Full-length RNAseq (SMART-Seq2) reads


title: 3109C


title: 3100A


title: 3102A


title: 3098A


title: S206: cell 174

description: Full-length RNAseq (SMART-Seq2) reads


title: 3102C


title: S205: cell 173

description: Full-length RNAseq (SMART-Seq2) reads


title: 3100C


title: 3096A


title: S204: cell 172

description: Full-length RNAseq (SMART-Seq2) reads


title: S212: cell 180

description: Full-length RNAseq (SMART-Seq2) reads


title: S210: cell 178

description: Full-length RNAseq (SMART-Seq2) reads


title: S203: cell 171

description: Full-length RNAseq (SMART-Seq2) reads


title: S202: cell 170

description: Full-length RNAseq (SMART-Seq2) reads


title: 3098C


title: 3096C


title: 3082A


title: 3081A


title: 3078A


title: 3095A


title: 3089A


title: 3081C


title: S198: cell 166

description: Full-length RNAseq (SMART-Seq2) reads


title: S199: cell 167

description: Full-length RNAseq (SMART-Seq2) reads


title: S201: cell 169

description: Full-length RNAseq (SMART-Seq2) reads


title: S194: cell 162

description: Full-length RNAseq (SMART-Seq2) reads


title: 3089C


title: S196: cell 164

description: Full-length RNAseq (SMART-Seq2) reads


title: S197: cell 165

description: Full-length RNAseq (SMART-Seq2) reads


title: 3074C


title: 3078C


title: S195: cell 163

description: Full-length RNAseq (SMART-Seq2) reads


title: S180: cell 160

description: Full-length RNAseq (SMART-Seq2) reads


title: S168: cell 159

description: Full-length RNAseq (SMART-Seq2) reads


title: S167: cell 158

description: Full-length RNAseq (SMART-Seq2) reads


title: 3074A


title: 3073A


title: 3073C


title: S166: cell 157

description: Full-length RNAseq (SMART-Seq2) reads


title: 3072A


title: 3067C


title: 3064C


title: 3067A


title: 3064A


title: 3059A


title: S163: cell 154

description: Full-length RNAseq (SMART-Seq2) reads


title: S165: cell 156

description: Full-length RNAseq (SMART-Seq2) reads


title: S193: cell 161

description: Full-length RNAseq (SMART-Seq2) reads


title: S162: cell 153

description: Full-length RNAseq (SMART-Seq2) reads


title: 3058C


title: S161: cell 152

description: Full-length RNAseq (SMART-Seq2) reads


title: S160: cell 151

description: Full-length RNAseq (SMART-Seq2) reads


title: 3059C


title: 3063C


title: 3054C


title: 3058A


title: 3054A


title: 3049C


title: 3047C


title: 3063A


title: S156: cell 147

description: Full-length RNAseq (SMART-Seq2) reads


title: S154: cell 145

description: Full-length RNAseq (SMART-Seq2) reads


title: S155: cell 146

description: Full-length RNAseq (SMART-Seq2) reads


title: S158: cell 149

description: Full-length RNAseq (SMART-Seq2) reads


title: S159: cell 150

description: Full-length RNAseq (SMART-Seq2) reads


title: S200: cell 168

description: Full-length RNAseq (SMART-Seq2) reads


title: S152: cell 143

description: Full-length RNAseq (SMART-Seq2) reads


title: S151: cell 142

description: Full-length RNAseq (SMART-Seq2) reads


title: S157: cell 148

description: Full-length RNAseq (SMART-Seq2) reads


title: 3040A


title: 3046A


title: 3037C


title: 3038C


title: 3040C


title: 3174C


title: S149: cell 140

description: Full-length RNAseq (SMART-Seq2) reads


title: 3043A


title: 3049A


title: 3047A


title: S147: cell 138

description: Full-length RNAseq (SMART-Seq2) reads


title: S146: cell 137

description: Full-length RNAseq (SMART-Seq2) reads


title: S148: cell 139

description: Full-length RNAseq (SMART-Seq2) reads


title: S144: cell 135

description: Full-length RNAseq (SMART-Seq2) reads


title: 3034C


title: S145: cell 136

description: Full-length RNAseq (SMART-Seq2) reads


title: S150: cell 141

description: Full-length RNAseq (SMART-Seq2) reads


title: 3034A


title: 3037A


title: S143: cell 134

description: Full-length RNAseq (SMART-Seq2) reads


title: S141: cell 132

description: Full-length RNAseq (SMART-Seq2) reads


title: S142: cell 133

description: Full-length RNAseq (SMART-Seq2) reads


title: 3033C


title: 3029A


title: 3028A


title: 3033A


title: S139: cell 130

description: Full-length RNAseq (SMART-Seq2) reads


title: S137: cell 128

description: Full-length RNAseq (SMART-Seq2) reads


title: 3028C


title: 3020C


title: 3026C


title: 3026A


title: S136: cell 127

description: Full-length RNAseq (SMART-Seq2) reads


title: 3020A


title: 3019A


title: 3016C


title: 3065C


title: 3019C


title: S133: cell 124

description: Full-length RNAseq (SMART-Seq2) reads


title: S132: cell 123

description: Full-length RNAseq (SMART-Seq2) reads


title: S140: cell 131

description: Full-length RNAseq (SMART-Seq2) reads


title: S134: cell 125

description: Full-length RNAseq (SMART-Seq2) reads


title: S138: cell 129

description: Full-length RNAseq (SMART-Seq2) reads


title: S135: cell 126

description: Full-length RNAseq (SMART-Seq2) reads


title: S131: cell 122

description: Full-length RNAseq (SMART-Seq2) reads


title: 3016A


title: 3014A


title: S129: cell 120

description: Full-length RNAseq (SMART-Seq2) reads


title: S130: cell 121

description: Full-length RNAseq (SMART-Seq2) reads


title: 3007C


title: 3012C


title: S128: cell 119

description: Full-length RNAseq (SMART-Seq2) reads


title: S241: cell 209

description: Full-length RNAseq (SMART-Seq2) reads


title: S126: cell 117

description: Full-length RNAseq (SMART-Seq2) reads


title: 3007A


title: 3006C


title: S122: cell 114

description: Full-length RNAseq (SMART-Seq2) reads


title: S123: cell 115

description: Full-length RNAseq (SMART-Seq2) reads


title: 3005A


title: 3006A


title: S120: cell 112

description: Full-length RNAseq (SMART-Seq2) reads


title: 3004A


title: S127: cell 118

description: Full-length RNAseq (SMART-Seq2) reads


title: S117: cell 109

description: Full-length RNAseq (SMART-Seq2) reads


title: S124: cell 116

description: Full-length RNAseq (SMART-Seq2) reads


title: S119: cell 111

description: Full-length RNAseq (SMART-Seq2) reads


title: S118: cell 110

description: Full-length RNAseq (SMART-Seq2) reads


title: S121: cell 113

description: Full-length RNAseq (SMART-Seq2) reads


title: S114: cell 106

description: Full-length RNAseq (SMART-Seq2) reads


title: S113: cell 105

description: Full-length RNAseq (SMART-Seq2) reads


title: S112: cell 104

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_96

source_name: Whole Blood from patient with infection of uncertain bacterial or viral aetiology

value: Uncertain

value: Discovery


title: S111: cell 103

description: Full-length RNAseq (SMART-Seq2) reads

value: Ins

value: T follicular helper cell


title: Unknown_92


title: Unknown_88


title: Unknown_90


title: Unknown_94


title: Unknown_93


title: Unknown_86


title: Unknown_91


title: Unknown_89


title: Unknown_87


title: Unknown_95


title: S116: cell 108

description: Full-length RNAseq (SMART-Seq2) reads


title: S115: cell 107

description: Full-length RNAseq (SMART-Seq2) reads


title: S110: cell 102

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_85


title: S109: cell 101

description: Full-length RNAseq (SMART-Seq2) reads


title: S164: cell 155

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_84


title: Unknown_82


title: S108: cell 100

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_83


title: Unknown_81


title: S107: cell 99

description: Full-length RNAseq (SMART-Seq2) reads


title: S106: cell 98

description: Full-length RNAseq (SMART-Seq2) reads


title: S104: cell 96

description: Full-length RNAseq (SMART-Seq2) reads


title: S105: cell 97

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_79


title: Unknown_78


title: Unknown_80


title: Unknown_77


title: Unknown_76


title: S103: cell 95

description: Full-length RNAseq (SMART-Seq2) reads


title: S102: cell 94

description: Full-length RNAseq (SMART-Seq2) reads


title: S101: cell 93

description: Full-length RNAseq (SMART-Seq2) reads


title: S153: cell 144

description: Full-length RNAseq (SMART-Seq2) reads


title: S100: cell 92

description: Full-length RNAseq (SMART-Seq2) reads


title: S99: cell 91

description: Full-length RNAseq (SMART-Seq2) reads


title: S98: cell 90

description: Full-length RNAseq (SMART-Seq2) reads


title: S93: cell 87

description: Full-length RNAseq (SMART-Seq2) reads


title: S97: cell 89

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_74


title: S94: cell 88

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_75


title: Unknown_73


title: S92: cell 86

description: Full-length RNAseq (SMART-Seq2) reads


title: S91: cell 85

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_72


title: S89: cell 83

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_70


title: Unknown_69


title: S88: cell 82

description: Full-length RNAseq (SMART-Seq2) reads


title: S87: cell 81

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_65


title: S86: cell 80

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_71


title: Unknown_64


title: S82: cell 79

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_63


title: S81: cell 78

description: Full-length RNAseq (SMART-Seq2) reads


title: S78: cell 76

description: Full-length RNAseq (SMART-Seq2) reads


title: S79: cell 77

description: Full-length RNAseq (SMART-Seq2) reads


title: S90: cell 84

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_62


title: Unknown_60


title: Unknown_61


title: Unknown_59


title: Unknown_57


title: S77: cell 75

description: Full-length RNAseq (SMART-Seq2) reads


title: S75: cell 74

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_56


title: S74: cell 73

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_55


title: Unknown_53


title: S70: cell 70

description: Full-length RNAseq (SMART-Seq2) reads


title: S72: cell 71

description: Full-length RNAseq (SMART-Seq2) reads


title: S69: cell 69

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_58


title: Unknown_52


title: S67: cell 67

description: Full-length RNAseq (SMART-Seq2) reads


title: S66: cell 66

description: Full-length RNAseq (SMART-Seq2) reads


title: S68: cell 68

description: Full-length RNAseq (SMART-Seq2) reads


title: S65: cell 65

description: Full-length RNAseq (SMART-Seq2) reads


title: S64: cell 64

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_67


title: S63: cell 63

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_51


title: Unknown_49


title: Unknown_54


title: Unknown_46


title: Unknown_44


title: S62: cell 62

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_43


title: Unknown_48


title: S61: cell 61

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_50


title: Unknown_47


title: Unknown_45


title: Unknown_42


title: S60: cell 60

description: Full-length RNAseq (SMART-Seq2) reads


title: S59: cell 59

description: Full-length RNAseq (SMART-Seq2) reads


title: S57: cell 57

description: Full-length RNAseq (SMART-Seq2) reads


title: S56: cell 56

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_40


title: Unknown_38


title: S73: cell 72

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_41


title: Unknown_39


title: S53: cell 53

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_36


title: S54: cell 54

description: Full-length RNAseq (SMART-Seq2) reads


title: S52: cell 52

description: Full-length RNAseq (SMART-Seq2) reads


title: S58: cell 58

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_34


title: S50: cell 50

description: Full-length RNAseq (SMART-Seq2) reads


title: S49: cell 49

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_32


title: S55: cell 55

description: Full-length RNAseq (SMART-Seq2) reads


title: S48: cell 48

description: Full-length RNAseq (SMART-Seq2) reads


title: S47: cell 47

description: Full-length RNAseq (SMART-Seq2) reads


title: S51: cell 51

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_37


title: Unknown_35


title: Unknown_30


title: Unknown_28


title: S46: cell 46

description: Full-length RNAseq (SMART-Seq2) reads


title: S45: cell 45

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_33


title: Unknown_25


title: Unknown_29


title: Unknown_26


title: Unknown_24


title: Unknown_27


title: Unknown_31


title: S44: cell 44

description: Full-length RNAseq (SMART-Seq2) reads


title: S43: cell 43

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_22


title: S41: cell 41

description: Full-length RNAseq (SMART-Seq2) reads


title: S42: cell 42

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_23


title: S39: cell 39

description: Full-length RNAseq (SMART-Seq2) reads


title: S38: cell 38

description: Full-length RNAseq (SMART-Seq2) reads


title: S37: cell 37

description: Full-length RNAseq (SMART-Seq2) reads


title: S36: cell 36

description: Full-length RNAseq (SMART-Seq2) reads


title: S40: cell 40

description: Full-length RNAseq (SMART-Seq2) reads


title: S34: cell 34

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_18


title: Unknown_16


title: Unknown_66


title: S32: cell 32

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_68


title: Unknown_21


title: S29: cell 29

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_14


title: S30: cell 30

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_19


title: S33: cell 33

description: Full-length RNAseq (SMART-Seq2) reads


title: S31: cell 31

description: Full-length RNAseq (SMART-Seq2) reads


title: S35: cell 35

description: Full-length RNAseq (SMART-Seq2) reads


title: S27: cell 27

description: Full-length RNAseq (SMART-Seq2) reads


title: S26: cell 26

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_15


title: Unknown_20


title: Unknown_17


title: Unknown_12


title: Unknown_13


title: Unknown_10


title: Unknown_09


title: Unknown_11


title: S25: cell 25

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_04


title: S24: cell 24

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_06


title: Unknown_08


title: S28: cell 28

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_07


title: S22: cell 22

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_05


title: S20: cell 20

description: Full-length RNAseq (SMART-Seq2) reads


title: S17: cell 17

description: Full-length RNAseq (SMART-Seq2) reads


title: S19: cell 19

description: Full-length RNAseq (SMART-Seq2) reads


title: S18: cell 18

description: Full-length RNAseq (SMART-Seq2) reads


title: S16: cell 16

description: Full-length RNAseq (SMART-Seq2) reads


title: S23: cell 23

description: Full-length RNAseq (SMART-Seq2) reads


title: S15: cell 15

description: Full-length RNAseq (SMART-Seq2) reads


title: S21: cell 21

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_02


title: S14: cell 14

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_03


title: S13: cell 13

description: Full-length RNAseq (SMART-Seq2) reads


title: Unknown_01


title: Kawasaki_75

source_name: Whole Blood from patient with KD

value: KD


title: S11: cell 11

description: Full-length RNAseq (SMART-Seq2) reads


title: S12: cell 12

description: Full-length RNAseq (SMART-Seq2) reads


title: Kawasaki_73


title: S10: cell 10

description: Full-length RNAseq (SMART-Seq2) reads


title: Kawasaki_74


title: Kawasaki_72


title: Kawasaki_77


title: Kawasaki_78


title: S9: cell 9

description: Full-length RNAseq (SMART-Seq2) reads


title: S8: cell 8

description: Full-length RNAseq (SMART-Seq2) reads


title: Kawasaki_71


title: Kawasaki_76


title: S6: cell 6

description: Full-length RNAseq (SMART-Seq2) reads


title: Kawasaki_70


title: Kawasaki_68


title: S5: cell 5

description: Full-length RNAseq (SMART-Seq2) reads


title: S4: cell 4

description: Full-length RNAseq (SMART-Seq2) reads


title: Kawasaki_66


title: S3: cell 3

description: Full-length RNAseq (SMART-Seq2) reads


title: Kawasaki_64


title: Kawasaki_69


title: S2: cell 2

description: Full-length RNAseq (SMART-Seq2) reads


title: Kawasaki_63


title: Kawasaki_67


title: Kawasaki_61


title: S7: cell 7

description: Full-length RNAseq (SMART-Seq2) reads


title: Kawasaki_65


title: Kawasaki_60


title: S1: cell 1

description: Full-length RNAseq (SMART-Seq2) reads