title: SM_STG2_T2_4

value: Sierra Mixe

value: aerial root

value: stage 2

value: 2 hours after rain event


title: HLA-B27-positive acute anterior uveitis [SystUviAU017]

status: Public on Jan 29 2022

type: SRA

city: Utrecht

first: Jonas

last: Kuiper

address: Heidelberglaan 100

department: Ophthalmology

country: Netherlands

institute: Universitair Medisch Centrum Utrecht

description: RNA sequencing

library_source: transcriptomic

data_processing:
FastQC for quality check
STAR aligner for genome indexing and alignment of reads
Htseq to generate count data
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: .count data in processed folder present in Uveitis_Replication directory. Contains the read counts generated using Htseq count (python) module.

molecule: total RNA

organism: Homo sapiens

source_name: HLA-B27-positive acute anterior uveitis

extract_protocol: Nitrogen-stored PBMCs were thawed and subjected to cDC2 purification by flow cytometry and subjected to RNA-sequencing by NextSeq.

tag: disease status

value: Active uveitis, without systemic inflammatory disease, systemic treatment free

tag: Sex

value: F

tag: cell type

value: PBMC

tag: cell population

value: HLA-DR+ Lin-(CD19-CD3-CD14-) CD1c+ cDC2s


title: HLA-B27-positive acute anterior uveitis [SystUviAU011]

description: RNA sequencing


title: scATAC-F

city: New York

first: Shan

last: Jiang

department: Taub Institute for Research on Alzheimer’s Disease and the Aging Brain

country: USA

institute: Columbia University Irving Medical Center

description: single nuclear ATAC-seq

library_source: genomic

data_processing:
Paired-end sequencing reads were processed using cellranger-atac v1.2.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts from filtered cells

molecule: genomic DNA

extract_protocol:
snATAC-seq libraries were generated from frozen human cortical brain tissue using six different experimental conditions: 1spin/FANS/DAPI: 1x ultracentrifugation spin followed by FANS sorting with DAPI; 1spin/FANS/7aad: 1x ultracentrifugation spin followed by FANS sorting with 7aad; 1spin/FANS/scatter: 1x ultracentrifugation spin followed by FANS sorting by scatter (i.e. in the absence of a fluorescent dye); 2spins/no FANS: 2x ultracentrifugation spins without FANS; 2spins/FANS/DAPI: 2x ultracentrifugation spins followed by FANS sorting with DAPI; and 2spins/FANS/scatter: 2x ultracentrifugation spin followed by FANS sorting by scatter
Nuclei were hash tagged and partitioned using 10x Genomics B chips. Libraries were generated according to 10x Genomics recommendations via Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (PN-1000075)

tag: diagnosis

value: control

tag: tissue type

value: frozen brain

value: nuclei


title: ASCL1 4h

city: Bellinzona

first: Federico

last: Costanzo

address: Via Vela 6

country: Switzerland

institute: Institute of Oncology Research IOR

data_processing:
Processed using nf-core ChipSeq pipeline v1.0.0
Alingment with  BWA v0.7.17-r1188
peaks called with MACS2 v2.1.2 narrowpeak default
bigWig  generated with bedtools bedgraphTobigWig
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: ChIP material from SCLC samples treated 0 or 4h with a dna binding drug

growth_protocol: All cell lines were cultured in the medium and conditions recommended by the supplier and supplemented with 10%FBS, 2nmol/L L-glutamine, and penicillin-streptomycin mix (Sigma).

extract_protocol: none provided by the submitter

treatment_protocol: DMS53 cells were seeded in 15 cm dishes and grown to subconfluency before treatment with 50nM Lurbinectedin.

tag: chip antibody

tag: treatment

value: treated with biotinilated PM01183 50nM for 4 hours


title: SM_STG2_T2_3

city: Madison

first: Vania

last: Pankievicz

state: WI

address: 1550 Linder Dr.

department: Bacteriology

institute: University of Wiscosin - Madison

data_processing:
Pseudo sequence alignment, Kallisto (Kallisto-0.42.3).
100 bootstraps with four threads.
RStudio was used to run R-package sleuth and perform subsequent differential gene expression analysis.
Transcript abundance - Sleuth (version 0.30.0).
Differentially expressed genes (DEGs) between two groups accessed using a Wald test.
Differentially expressed genes FDR < 0.05.
Cut-off was set to a TPM (transcripts per million) expression value of 1.
Genome_build: Zea_mays.B73_RefGen_v4.cdna
Supplementary_files_format_and_content: Tar archives include abundance.h5 and abundance.tsv files; estimated counts and TPM values for each target transcript.

molecule: polyA RNA

organism: Zea mays

source_name: aerial root

growth_protocol: Sierra Mixe and B73 maize growing in a high ceiling room (14/10h light/dark cycles and 25/17º C and 85%/90% relative humidity).

extract_protocol:
The total RNA present in secreted mucilage was extracted using PureLink® RNA Mini Kit (Ambion) and treated with DNase (Ambion®) following the manufacturer’s instructions. A nanodrop spectrophotometer and Agilent Bioanalyzer’s electrophoresis on-chip were used to check RNA quantity and purity.
Libraries for sequencing were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina®) and sequenced in next-generation sequencing platform HiSeq 2500 system (Illumina®) using the TruSeq SBS Kit v3-HS (pair-end 100).

treatment_protocol: Rain events twice a week to trigger mucilage production. Stage 1 Sierra Mixe aerial roots, stage 2 Sierra Mixe aerial roots, and stage 1 B73 aerial roots were collected before a rain event and then 2 and 24 hours after a rain event. After excision, the roots were individually snap-frozen in liquid nitrogen and then stored.

tag: cultivar

tag: tissue

tag: Stage


title: HLA-B27-positive acute anterior uveitis [SystUviAU010]

description: RNA sequencing


title: scATAC-E

description: single nuclear ATAC-seq


title: SM_STG2_T2_2


title: Pol II 0h

value: RNAPOL II

value: untreated


title: EPZ5676 treated ALDH1- _rep3

city: Miami

first: Derek

last: Van Booven

state: FL

address: 1501 NW 10th Ave

institute: University of Miami

data_processing:
Trim_Galore used for adapter trimming
STAR aligner and quantification against GENCODE v19 build
Genome_build: hg19
Supplementary_files_format_and_content: complete_matrix.txt contains raw counts for all samples

source_name: MDA-MB-468 Triple negative breast cancer cells

growth_protocol: Cells were grown in DMEM media with 10% FBS, 1% Glutamine and 1% Penicillin-Streptomycin.

extract_protocol:
Total RNA was extracted from the sorted populations using TRIzol reagent and RNA quality was assayed by Nanodrop and Bioanalyzer
Three biological replicates with good quality RNA with RNA integrity number (RIN) >9, were used to make cDNA libraries. Libraries were constructed from 2µg total RNA using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, E7765S) following the manufacturer’s protocol. Quality of the libraries was verified using fragment analyzer

treatment_protocol: Cells were treated with either DMSO as control or DOT1L inhibitor EPZ5676 (0.5µM) for 10 days before sorting into ALDH1+ and ALDH1- cell populations. There biological replicates were performed

value: Human breast cancer cell

value: 10 days EPZ5676 treatment

tag: cell line


title: Biotin 0h

value: Biotin


title: scATAC-D

description: single nuclear ATAC-seq

source_name: 2spins/no FANS


title: SM_STG2_T2_1

value: Sierra Mixe


title: EPZ5676 treated ALDH1- _rep2


title: scATAC-C

description: single nuclear ATAC-seq


title: ASCL1 0h


title: SM_STG2_T0_4

value: aerial root

value: no water


title: input 0h


title: scATAC-B

description: single nuclear ATAC-seq


title: NeuroD1 4h


title: EPZ5676 treated ALDH1+ _rep3


title: SM_STG2_T0_3

value: stage 2


title: EPZ5676 treated ALDH1- _rep1


title: NeuroD1 0h


title: NCIH510A ASCL1 T3

data_processing:
Processed using nf-core RNA-Seq pipeline v1.3.3
Alingment with  HISAT 2.1.0
Read count with Subread featureCounts v1.6.4
DEG analisyed with Deseq2 from featurecounts matrix
FPKM calculated with Stringtie 1.3.5
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cell line

extract_protocol:
none provided by the submitter
RNA-seq polyA

value: siRNA ASCL1


title: SM_STG2_T0_2


title: RNA_seq_SingleCell_zsGreen_Day6

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

data_processing:
The 10X Genomics Cell Ranger pipeline (version 3.1.0) was used to perform sample demultiplexing, alignment to the mm10 mouse reference genome or hg38 human reference genome and the reporter sequences (mCherry or mCherry and zsGreenDR), barcode/UMI processing, and gene counting for each cell.
Genome_build: mm10 or hg38
Supplementary_files_format_and_content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI couns for each sample

source_name: pancreatic islet cells

extract_protocol:
Mouse isolated islets and human cadaveric islets were dissociated by agitation for 5 min at 37°C in dispersion solution. Dead cells with positive DAPI staining were removed by FACS, and cells were loaded into the 10x Genomics Chromium system.
ScRNA-seq libraries were prepared using the Single Cell 3’ Reagent Kits (version 3.1; 10X Genomics). Libraries were then sequenced on a NovaSeq 6000 (Illumina) with paired-end sequencing.

tag: transfection

value: zsGreen

tag: gender

value: male

tag: age

value: twenties


title: EPZ5676 treated ALDH1+ _rep1


title: SM_STG2_T0_1


title: NCIH510A ASCL1 T2


title: DMSO treated ALDH1- _rep3

value: 10 days DMSO treatment


title: SM_STG1_T24_4

value: stage 1

value: 24 hours after rain event


title: RNA_seq_SingleCell_mMycl_Dox2_Day6

value: mMycl


title: SM_STG2_T24_3


title: RNA_seq_SingleCell_hMYCL_Dox2_Day6

value: hMYCL


title: NCIH510A ASCL1 T1

value: treated with biotinilated PM01183 50nM for 4 hours


title: SM_STG1_T24_3


title: DMSO treated ALDH1- _rep2

value: Human breast cancer cell


title: NCIH510 ASCL1 C3

value: untreated


title: SM_STG1_T24_2


title: DMSO treated ALDH1- _rep1


title: C22_RFP_rep3

city: Providence

first: William

last: Fairbrother

state: RI

address: 70 Ship St, Box G

department: Molecular Biology, Cell Biology and Biochemistry

institute: Brown University

data_processing:
Reads originating from lariats were identified in the sequenced reads using an implementation of the branchpoint detection algorithm described in Pineda and Bradley (2018)
Genome_build: hg19
Supplementary_files_format_and_content: BED - each mapped lariat read is listed with the start and end coordinates being the 5' splice site and branchpoint (or vice versa if the the lariat maps to the negative strand); additionally, the read ID, inferred branchpoint nucleotide, and nearest 3' splice site are listed in the name field

source_name: HEK293T cells

growth_protocol: DMEM media +10% FBS with 1% pen-strep, 5% CO2, 37 deg. C

extract_protocol:
Trizol
Illumina with rRNA depletion

value: transfected with RFP expression vector

tag: genotype

value: DBR1 -


title: NCIH510 ASCL1 C2


title: C22_RFP_rep2


title: SM_STG1_T24_1

value: Sierra Mixe

value: aerial root


title: NCIH510A ASCL1 C1


title: C22_RFP_rep1


title: DMSO treated ALDH1+ _rep2


title: DMSO treated ALDH1+ _rep3


title: SM_STG1_T2_4

value: 2 hours after rain event


title: NCIH82 NEUROD1 T3

value: siRNA NEUROD1


title: C22_lipofectamine_rep3

value: treated with lipofectamine


title: scATAC-A

description: single nuclear ATAC-seq

value: control

value: frozen brain

value: nuclei


title: EPZ5676 treated ALDH1+ _rep2

value: 10 days EPZ5676 treatment


title: DMSO treated ALDH1+ _rep1

value: 10 days DMSO treatment


title: NCIH82 NEUROD1 T2


title: SM_STG1_T2_3

value: stage 1


title: SM_STG1_T2_2


title: C22_lipofectamine_rep2


title: NCIH82 NEUROD1 T1


title: C22_lipofectamine_rep1


title: SM_STG1_T2_1


title: NCIH82 NEUROD1 C2


title: SM_STG1_T0_2

value: no water


title: C22_DBR1_rep3

value: transfected with DBR1 expression vector


title: OES5R-A

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

data_processing:
Raw reads were quality assessed and low quality reads and contaminating adapter sequences removed
The resultant quality controlled fastq files were aligned to the Ensembl annoted Human genome (GRCh38.83) using STAR
Gene expression was quantified using FeatureCounts
Genome_build: GRCh38.83
Supplementary_files_format_and_content: Tab delimited text file contain gene expression in counts

source_name: Esophageal cancer specimen OES5R

growth_protocol: The full method for the establishment of close-to-patient esophageal cancer cells using a feeder layer method and subsequent growth with a stromal component in the 3D-tumor growth assay to form cancer cell clusters, which can then undergo clinically relevant ex vivo pharmacological assessment, has been described in detail (PMID: 27736801)

extract_protocol:
PolyA enrichment
Illumina

treatment_protocol: Three esophageal cancer specimens were isolated (samples OES4R-A, OES7R-A, and OES5R-A) and grown on fibroblast feeder layers (samples OES4R-B, OES7R-B, and OES5R-B) and then grown in 3D-tumour growth assays in combination with mesenchymal stem cells (samples OES4R-C, OES7R-C, and OES5R-C) or in the absence of mesenchymal stem cells (samples OES4R-D, OES7R-D, and OES5R-D).

value: esophageal cancer


title: OES5R-C

source_name: Sample OES5R cells grown in 3D with MSC


title: OES5R-D


title: OES5R-B

source_name: Sample OES5R feeder layer


title: NCIH82 NEUROD1 C1

value: untreated


title: C22_DBR1_rep2


title: NCIH82 NEUROD1 C3


title: SM_STG1_T0_4


title: SM_STG1_T0_1


title: C22_DBR1_rep1


title: OES7R-D

source_name: Sample OES7R cells grown in 3D with MSC


title: DMS53 siScrambled T2

value: siRNA Scrambled

value: treated with biotinilated PM01183 50nM for 4 hours


title: B73_STG1_T24_4

value: 24 hours after rain event


title: OES7R-C


title: DMS53 siScrambled T1


title: OES7R-B

source_name: Sample OES7R feeder layer


title: B73_STG1_T24_3

value: aerial root


title: DMS53 siNEUROD1 T2


title: HEK293T_wildtype_rep2

value: wild type


title: B73_STG1_T24_2


title: HEK293T_wildtype_rep1


title: DMS53 siNEUROD1 T1

value: siRNA NEUROD1


title: OES7R-A

source_name: Esophageal cancer specimen OES7R


title: B73_STG1_T24_1


title: DMS53 siASCL1 T2

value: siRNA ASCL1


title: OES4R-D


title: RNA-seq:cMyc48hLiver_ex3

data_processing:
The sequenced reads were mapped to the mm10 mouse reference genome using STAR version 2.7.8a with the GENCODE vM25 annotation gtf file after trimming adaptor sequences and low-quality bases by cutadapt-3.0. The uniquely mapped reads were summarized at the gene level using HTSeq-count v 0.11.2, with the GENCODE vM25 annotation file and expression values were calculated as TPM by using DESeq2 v1.30.0.
Supplementary_files_format_and_content: Matrix

organism: Mus musculus

source_name: Liver

extract_protocol:
RNAeasy plus Mini Kit (QIAGEN) for RNA.
RNA-seq libraries were generated using the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB)

value: Liver

tag: strain


title: OES4R-C


title: DMS53 siASCL1 T1


title: RNA-seq:cMyc48hLiver_ex1


title: DMS53 siScrambled C2


title: B73_STG1_T2_3

value: 2 hours after rain event


title: OES4R-B


title: RNA-seq:Mycl48hLiver_ex3


title: B73_STG1_T2_2


title: ATAQ-PM1183 R2

data_processing:
Processed using nf-core ataqSeq pipeline v1.0.0
Alingment with  BWA v0.7.17-r1188
peaks called with MACS2 v2.1.2 narrowpeak default
bigWig  generated with bedtools bedgraphTobigWig
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: ATAQ-Seq material from SCLC samples treated 0 or 4h with a dna binding drug


title: B73_STG1_T2_1


title: OES4R-A


title: DMS53 siScrambled C1


title: DMS53 siNEUROD1 C2


title: RNA-seq:Mycl48hLiver_ex2


title: HEK293T_wildtype_rep3


title: RNA-seq:Mycl48hLiver_ex1


title: DMS53 siNEUROD1 C1


title: B73_STG1_T0_4


title: RNA-seq:MyclNoDoxLiver_ex3


title: DMS53 siASCL1 C2


title: ATAQ-Control R2


title: B73_STG1_T0_3


title: RNA-seq:MyclNoDoxLiver_ex2


title: B73_STG1_T0_2


title: ATAQ-Control R1


title: DMS53 siASCL1 C1


title: RNA-seq:cMyc48hLiver_ex2


title: B73_STG1_T0_1


title: B73_STG1_T2_4


title: Patient 4 pretreatment biopsy [NS_CancerImmune_V1.1]

status: Public on Jan 28 2022

type: RNA

city: Houston

first: David

middle: S

last: Hong

state: Texas

address: Room FC8.3050, 1400 Holcombe Blvd.

department: Department of Investigational Cancer Therapeutics

institute: University of Texas M.D. Anderson Cancer Center

description:
100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes
07670151C

hyb_protocol: 65°C for 16-24 hours. Details are in user manual for nCounter Gene Expression CodeSet RNA hybridization protocol (Nanostring)

scan_protocol: nCounter® FLEX Analysis System (following the manufacturer's protocol)

data_processing:
Raw counts were exported using nSolver® Analysis Software (Nanostring) and analysed using custom R scripts (R v3.6.3). Background gene count levels were determined for each sample using mean plus two standard deviations of the included negative control counts. For data normalization, background-subtracted counts were then scaled using geometric means of 27 of 30 housekeeping genes shared between the two gene panels (excluding GPATHC3, CC2D1B and ZKSCAN5), with expected value set to 444.
Counts - number of molecules detected per 100 ng of total RNA

label: 6x fluorescent marker barcode

source_name: Primary Urothelial cancer

label_protocol: Detailed in user manual for nCounter Gene Expression CodeSet RNA hybridization protocol (Nanostring)

extract_protocol: Tumor tissue was macro-dissected from 4 μm sections of FFPE tissues and total RNA was extracted using the High Pure RNA FFPE Micro Kit (Roche), following the manufacturer’s protocol.

tag: timepoint

value: Baseline

tag: dose, bln cells

tag: cohort

tag: best overall response

value: Stable Disease


title: Patient 3 pretreatment biopsy [NS_CancerImmune_V1.1]

description:
100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes
07670118C

source_name: Metastatic Melanoma cancer

value: Progressive Disease


title: Patient 1 pretreatment biopsy [NS_CancerImmune_V1.1]

description:
100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes
2186

source_name: Metastatic Head&Neck cancer


title: Patient 2 pretreatment biopsy [NS_CancerImmune_V1.1]

description:
100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes
2185

value: Not Evaluable


title: Patient 10 pretreatment biopsy [NS_CancerImmune_V1.1]

description:
100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes
08950279C

source_name: Metastatic Urothelial cancer


title: Patient 7 pretreatment biopsy [NS_CancerImmune_V1.1]

description:
100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes
19_0055

source_name: Primary Head&Neck cancer


title: Patient 8 pretreatment biopsy [NS_CancerImmune_V1.1]

description:
100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes
07670152C


title: ATAQ-PM1183 R1

tag: cell type


title: RNA-seq:MyclNoDoxLiver_ex1


title: Patient 9 pretreatment biopsy [NS_CancerImmune_V1.1]

description:
100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes
08950277C

value: Screening


title: Patient 6 pretreatment biopsy [NS_CancerImmune_V1.1]

description:
100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes
19_0053


title: NF_11

city: Philadelphia

first: Benjamin

last: Prosser

state: PA

address: 700 CRB, 415 Curie Blvd

department: Physiology

institute: University of Pennsylvania

description: total RNA from post-mortem non-failing non-LVH patient's heart tissue

hyb_protocol: NanoString probes were hybridized as per the manufacturer's protocol.

data_processing: The geometric means of the positive control values were used to threshold followed by data normalization using the geometric means of the three housekeeping genes (GAPDH, Rpl4, Tbp).

label: Nanostring Label

source_name: heart tissue

label_protocol: NanoString probes were labelled as per the manufacturer's protocol.

extract_protocol: total RNA was extracted from ~10mg of heart tissue using TRIzol as per the manufacturer's protocol

tag: status

value: Normal

tag: etiology

value: Female

tag: race

value: Caucasian


title: NF_12

value: Male


title: NF_9

value: AA


title: NF_8


title: NF_10


title: NF_7


title: NF_5


title: NF_6


title: NF_4


title: Plasmaexosome_AIS [AIS_010]

city: Chengdu

first: Kejie

last: Chen

state: Sichuan

address: 783#, Xindu Avenue

country: China

institute: Chengdu Medical College

description: circRNA profile of plasma exosome

hyb_protocol: Each slide was hybridized with 1.65 μg Cy3-labeled cRNA using a Gene Expression Hybridization Kit (Agilent Technologies, Santa Clara, CA, US). After 17 hours of hybridization, the slides were washed with the Gene Expression Wash Buffer Kit (Agilent Technologies, Santa Clara, CA, US).

scan_protocol: These slides were scanned by an Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA, US).

data_processing: Data were extracted with Feature Extraction software10.7 (Agilent Technologies, Santa Clara, CA, US).Raw data were normalized by Quantile algorithm, R package “limma”. Genes with a fold change of at least 2 were selected for further analysis.

source_name: Plasma exosome, AIS patient

label_protocol: Total RNAs were incubated with RNase R to eliminate linear RNAs. The enriched circRNAs were amplified and transcribed into fluorescent complementary RNA (cRNA) by the Low Input Quick Amp WT Labeling Kit (Agilent Technologies, Santa Clara, CA, US). Labeled cRNA was purified with the RNeasy mini kit (QIAGEN, GmBH, Germany).

extract_protocol: Total RNA of plasma exosomes was extracted by exoRNeasy Serum/Plasma Maxi kit (77064, Qiagen Sciences Inc, Germany) following the manufacturer’s recommendation.

tag: subject status

value: AIS patient

value: male

tag: sample type

value: Plasma exosome


title: Plasmaexosome_CON [CON_010]

description: circRNA profile of plasma exosome

source_name: Plasma exosome, Control

value: Control


title: Plasmaexosome_CON [CON_008]

description: circRNA profile of plasma exosome


title: Plasmaexosome_AIS [AIS_007]

description: circRNA profile of plasma exosome


title: Plasmaexosome_CON [CON_005]

description: circRNA profile of plasma exosome

value: female


title: NF_3


title: HCM_12

description: total RNA from post-mortem heart failure patient's heart tissue

value: Heart failure

value: Hypertrophic cardiomyopathy


title: HCM_11


title: NF_1


title: Plasmaexosome_CON [CON_007]

description: circRNA profile of plasma exosome


title: HCM_10


title: Plasmaexosome_CON [CON_009]

description: circRNA profile of plasma exosome


title: NF_2


title: Plasmaexosome_AIS [AIS_006]

description: circRNA profile of plasma exosome


title: HCM_9

value: Indian


title: HCM_8


title: Plasmaexosome_CON [CON_004]

description: circRNA profile of plasma exosome


title: Plasmaexosome_CON [CON_006]

description: circRNA profile of plasma exosome


title: Plasmaexosome_AIS [AIS_005]

description: circRNA profile of plasma exosome


title: HCM_7


title: HCM_6


title: Plasmaexosome_AIS [AIS_008]

description: circRNA profile of plasma exosome


title: Plasmaexosome_CON [CON_001]

description: circRNA profile of plasma exosome


title: Plasmaexosome_AIS [AIS_004]

description: circRNA profile of plasma exosome


title: Plasmaexosome_CON [CON_002]

description: circRNA profile of plasma exosome


title: Plasmaexosome_AIS [AIS_001]

description: circRNA profile of plasma exosome


title: Plasmaexosome_AIS [AIS_009]

description: circRNA profile of plasma exosome


title: HCM_5


title: Plasmaexosome_CON [CON_003]

description: circRNA profile of plasma exosome


title: Plasmaexosome_AIS [AIS_003]

description: circRNA profile of plasma exosome


title: Plasmaexosome_AIS [AIS_002]

description: circRNA profile of plasma exosome


title: HCM_4


title: DCM_11

value: Dilated cardiomyopathy

value: Unknown


title: HCM_2


title: DCM_7


title: DCM_4


title: DCM_6


title: DCM_9


title: DCM_8


title: DCM_2


title: DCM_3


title: DCM_5


title: DCM_10


title: dppa3-cre_Smarcb1_tumor2

city: Münster

first: Kornelius

last: Kerl

address: Albert-Schweitzer-Campus 1

department: Department of Pediatric Hematology and Oncology

country: Germany

institute: University Children's Hospital Münster

data_processing:
After explorative quality control with FastQC (v0.11.9) and MultiQC (v1.11), we used STAR (v2.7.9a) for alignment of the samples to the mouse reference genome (downloaded from Ensembl, release 104). Default parameters were used.
Further analyses were performed in R. We employed the function featureCounts from the package Rsubread (v2.0.1) to count mapped reads and generate gene expression matrices.
Genome_build: GRCm39
Supplementary_files_format_and_content: raw_gene_counts_matrix.txt contains tab-separated raw counts for each gene and each sample

source_name: murine tumor

extract_protocol:
Fresh tumor tissues were isolated and fresh frozen. Total RNA was isolated using RNeasy mini Kit (Qiagen) as specified by the manufacturer.
For library construction we used the NEBNext Poly(A) mRNA Magnetic Isolation Module followed by NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina

tag: tissue

value: murine tumor

tag: localization

value: Extracranial

tag: localization details

value: facial, maxillar

tag: tumor classification

value: MYC


title: DCM_1

tag: gender

value: Female

value: Caucasian


title: dppa3-cre_Smarcb1_tumor1

value: Intracranial

value: Trigeminal nerve


title: HCM_1


title: P11056_2096

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

data_processing:
Libraries were sequenced in Hiseq 2500 with a 50-8-8-50 read set-up and a minimum of 25000 read pairs per cell.
Reads were trimmed and aligned to mm10 reference assembly using Bowtie2. Reads were called individually for each sample using MACS2. Called peaks were merged using bedtools mergedbed. Fragment files and counts were obtained using the individual bam files as input for ChromVar R package, Resulting on 1029 cells.
ATAC signal was binarized and convert to gene activity score over 500bp promoters regions, then integrated using Seurat2 to scRNA-seq (Falcao, van Bruggen wt al. 2018) to assign cell identities “Predicted_celltypes”.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data as R object from Seurat package, includes scATAC fragments counts as “gene activity” over promoter region in the RNA assay. Integrated assay includes integration with scRNA-seq Falcao, van Bruggen et al. 2018.

source_name: Ctr

growth_protocol: For the induction of EAE, the mouse model of MS, animals were injected subcutaneously with an emulsion of MOG35-55 peptide in complete Freud’s adjuvant (CFA; EK-2110 kit from Hooke Laboratories) followed by intraperitoneal injection with pertussis toxin in PBS (200 ng per animal) on the day of immunization and with 24 hours delay (according to manufacturer’s instructions). Control animals underwent the same treatment, but CFA without MOG35-55 peptide (CK-2110 kit from Hooke Laboratories) was used instead. Spinal cord and brains were collected at the peak of the disease when clinical score 3 has been reached, which corresponds to limp tail and complete paralysis of hind legs. Animals that did not reach this clinical score were not analyzed in this study.

extract_protocol:
Immediately after dissociation, cells were fixed in 1% formaldehyde (28906, ThermoFisher Scientific) for 10 minutes and quenched with glycine (125 mM) for 5 minutes at room temperature and then washed and stored in 0.5% BSA in PBS with 0.1% sodium azide at 4°C until further processing. The cells were counted and aliquots of 500.000 cells were centrifuged for 10 minutes at 1000xg and room temperature. Cells were resuspended in lysis buffer (containing 0.05% IGEPAL (CA-630), 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) and incubated for 5 minutes at room temperature. After a 20-minute centrifugation at 1000xg at room temperature, the cells were incubated with anti-GFP antibody (FITC, 1:100, Ab6662, Abcam) and DAPI (0.5 ug/ml) in PBS containing 5% BSA for 20 minutes at room temperature. The cells were centrifuged for 10 minutes at 1000xg and resuspended in tagmentation mix (dH2O, 2x TD buffer (Wang et al., 2013) and Tn5 enzyme (Picelli et al., 2014)) and incubated for 30 minutes at 37°C. For both lysis and tagmentation buffers the volume was scaled up to match the number of cells (50 ul per 50.000 cells). Tagmentation reaction was stopped by addition of 40 mM EDTA. Cells were then centrifuged for 10 minutes at 1000xg and room temperature and resuspended in PBS + 0.5% BSA. Sox10 GFP+/DAPI+ cells were sorted on an Influx (BD Biosciences) in reverse crosslinking buffer (Chen et al., 2018) with single cells in each well of 96 well plates. Also Sox10 GFP-/DAPI+ cells were sorted as a negative control for the OL lineage. The plates were incubated overnight at 65°C ending with 10 minutes at 80°C the next day. PCR master mixes (NEBNext High fidelity, M0541S, NEB) containing unique barcoding primers per well were dispensed on top of the reverse crosslinking buffer and DNA was amplified with the following cycling conditions: 72°C for 5 min, 98°C for 30s; 20 cycles at 98°C for 10s, 63°C for 30s and 72°C for 1 min. PCR products were purified with the MinElute purification kit (Qiagen) and then PAGE purified to remove adapter dimers. Three EAE and two CFA-control animals were used for independent replicates. Libraries were sequenced on an Illumina Hiseq 2500 with a 50-8-8-50 read set-up and a minimum of 25 000 read pairs per cell.
scATACseq (PI-ATAC Chen et al., 2018)

treatment_protocol: Mice were sacrificed with a ketaminol/xylazine intraperitoneal injection followed by intracardiac perfusion with PBS where after brain and spinal cords were collected and dissociated using the adult brain dissociation kit (130-107-677, Miltenyi) following manufacturer’s instructions including myelin debris removal, but excluding the red blood cell removal step.

value: brain

value: SoxGFP


title: HCM_3

value: Male


title: P11056_2097


title: P11056_2095


title: P11056_2094


title: P11056_2091


title: P11056_2089


title: P11056_2088


title: P11056_2087


title: P11056_2093


title: P11056_2084


title: P11056_2085


title: P11056_2090


title: P11056_2083


title: P11056_2082


title: P11056_2081


title: P11056_2078


title: P11056_2075


title: P11056_2076


title: P11056_2074


title: P11056_2077


title: P11056_2079


title: P11056_2080


title: P11056_2073


title: P11056_2072


title: P11056_2070


title: P11056_2071


title: P11056_2069


title: P11056_2067


title: P11056_2065


title: P11056_2068


title: P11056_2063


title: P11056_2061


title: P11056_2064


title: P11056_2086


title: P11056_2092


title: P11056_2060


title: P11056_2058


title: P11056_2057


title: P11056_2059


title: P11056_2056


title: P11056_2054


title: P11056_2055


title: P11056_2052


title: P11056_2049


title: P11056_2048


title: P11056_2047


title: P11056_2053


title: P11056_2051


title: P11056_2045


title: P11056_2043


title: P11056_2044


title: P11056_2035


title: P11056_2039


title: P11056_2040


title: P11056_2032


title: P11056_2041


title: P11056_2042


title: P11056_2046


title: P11056_2062


title: P11056_2034


title: P11056_2037


title: P11056_2036


title: P11056_2033


title: P11056_2066


title: P11056_2031


title: P11056_2050


title: P11056_2029


title: P11056_2028


title: P11056_2027


title: P11056_2026


title: P11056_2025


title: WT2M2

city: Shanghai

first: Wei

last: Zhou

address: N0.280 South Chongqing Road

institute: Shanghai Jiao Tong University

data_processing:
Raw sequencing data generated from Illumina HiSeq 4000 that pass the Illumina chastity filter are used for  following analysis.
Trimmed reads (trimmed 5’, 3’-adaptor bases) are aligned to reference genome. Based on  alignment statistical analysis (mapping ratio, rRNA/mtRNA content, fragment sequence bias), we determine  whether the results can be used for subsequent data analysis.
The expression profiling, differentially expressed genes and differentially expressed transcripts are calculated. The novel genes and transcripts are also  predicted. Principal Component Analysis (PCA), Correlation Analysis, Hierarchical Clustering, Gene Ontology  (GO), Pathway Analysis, scatter plots and volcano plots are performed for the differentially expressed genes in  R or Python environment for statistical computing and graphics.
Supplementary_files_format_and_content: tab-delimited Excel files include FPKM values for each Sample

source_name: Macrophage

growth_protocol: Macrophages(BMDMs) isolated from mice were differentiated for 7 d in the presence of recombinant mouse macrophage colony-stimulating factor (M-CSF; 20 ng/ml) in complete medium RPMI-1640 medium containing 10 mM glucose, 2 mM L-glutamine, 100 units/ml of penicillin-streptomycin and 10% FBS).

extract_protocol:
Macrophages were removed from dish, flash frozen on dry ice, and RNA was harvested using Trizol reagent.Samples were quantified on a NanoDrop ND-1000 instrument. Agarose electrophoresis was used to check the integrality of total RNA samples. 1 _x0018_ 2 _x0016_g total RNA of each sample was taken for RNA-seq library preparation.  Briefly, mRNA was isolated from total RNA with NEBNext® Poly(A) mRNA Magnetic Isolation Module.  Alternatively, rRNA is removed from the total RNA with a RiboZero Magnetic Gold Kit; The enriched mRNA  or rRNA depleted RNA was used for RNA-seq library preparation using KAPA Stranded RNA-Seq Library  Prep Kit (Illumina).
RNA-seq library preparation using KAPA Stranded RNA-Seq Library  Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library  strand-specific.
The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute  quantification qPCR method. To sequence the libraries on the Illumina HiSeq 4000 instrument, the barcoded  libraries were mixed, denatured to single stranded DNA in NaOH, captured on Illumina flow cell, amplified  in situ, and subsequently sequenced for 150 cycles for both ends on Illumina HiSeq instrument

treatment_protocol: Macrophages were cultured for 7 days, and then washed and stimulated with IL-4 (20 ng/ml; PeproTech) for 24hrs for M2 polarization (Murray et al., 2014).

value: Macrophage

tag: age

value: post natal 8 weeks

tag: genotype

value: wild type

tag: treatment


title: P11056_2023


title: P11056_2022


title: P11056_2021


title: P11056_2038


title: P11056_2020


title: P11056_2019


title: P11056_2030


title: P11056_2018


title: P11056_2017


title: P11056_2016


title: P11056_2014


title: P11056_2015


title: P11056_2008


title: P11056_2009


title: P11056_2010


title: P11056_2013


title: P11056_2011


title: P11056_2007


title: P11056_2003


title: P11056_2005


title: P11056_2002


title: P11056_2000


title: P11056_2004


title: P11056_1998


title: P11056_1997


title: P11056_1995


title: P11056_2024


title: P11056_1994


title: P11056_1993


title: P11056_1992


title: P11056_1990


title: P11056_1991


title: P11056_1989


title: P11056_1988


title: P11056_1987


title: P11056_1986


title: P11056_1985


title: P11056_2012


title: P11056_1982


title: P11056_1983


title: P11056_2001


title: P11056_1980


title: P11056_1975


title: P11056_1978


title: P11056_1976


title: P11056_1971


title: P11056_1981


title: P11056_1972


title: P11056_1969


title: P11056_1977


title: P11056_2006


title: P11056_1984


title: P11056_1974


title: P11056_1973


title: P11056_1999


title: P11056_1967


title: P11056_1970


title: P11056_1996


title: P11056_1965


title: P11056_1966


title: P11056_1968


title: P11056_1964


title: P11056_1963


title: P11056_1962


title: P11056_1961


title: P11056_1960

source_name: EAE


title: P11056_1959


title: P11056_1958


title: P11056_1957


title: P11056_1956


title: P11056_1979


title: P11056_1952


title: P11056_1950


title: P11056_1953


title: P11056_1954


title: P11056_1951


title: P11056_1949


title: P11056_1947


title: P11056_1948


title: P11056_1946


title: P11056_1943


title: P11056_1941


title: P11056_1945


title: P11056_1942


title: P11056_1938


title: P11056_1939


title: P11056_1940


title: P11056_1937


title: P11056_1936


title: P11056_1935


title: P11056_1934


title: P11056_1933


title: P11056_1932


title: P11056_1931


title: P11056_1930


title: P11056_1928


title: P11056_1929


title: P11056_1926


title: P11056_1927


title: P11056_1955


title: P11056_1924


title: P11056_1923


title: P11056_1921


title: P11056_1922


title: P11056_1920


title: P11056_1944


title: P11056_1918


title: P11056_1919


title: P11056_1917


title: P11056_1914


title: P11056_1916


title: P11056_1911


title: P11056_1910


title: P11056_1908


title: P11056_1912


title: P11056_1909


title: P11056_1906


title: P11056_1907


title: P11056_1905


title: P11056_1913


title: P11056_1904


title: P11056_1902


title: P11056_1903


title: P11056_1901


title: P11056_1897


title: P11056_1899


title: P11056_1896


title: P11056_1925


title: P11056_1895


title: P11056_1894


title: P11056_1898


title: P11056_1900


title: P11056_1892


title: P11056_1888


title: P11056_1889


title: P11056_1891


title: P11056_1915


title: P11056_1887


title: P11056_1885


title: P11056_1879


title: P11056_1878


title: P11056_1882


title: P11056_1884


title: P11056_1881


title: P11056_1876


title: P11056_1880


title: P11056_1883


title: P11056_1877


title: P11056_1874


title: P11056_1875


title: P11056_1873


title: P11056_1872


title: P11056_1869


title: P11056_1871


title: P11056_1868


title: P11056_1893


title: P11056_1865


title: P11056_1864


title: P11056_1866


title: P11056_1862


title: P11056_1863


title: P11056_1861


title: P11056_1890


title: P11056_1859


title: P11056_1860


title: P11056_1886


title: P11056_1858


title: P11056_1854


title: P11056_1857


title: P11056_1856


title: P11056_1853


title: P11056_1850


title: P11056_1851


title: P11056_1848


title: P11056_1849


title: P11056_1847


title: P11056_1846


title: P11056_1845


title: P11056_1843


title: P11056_1844


title: P11056_1842


title: P11056_1870


title: P11056_1867


title: P11056_1841


title: P11056_1840


title: P11056_1838


title: P11056_1839


title: P11056_1832


title: P11056_1834


title: P11056_1837


title: P11056_1836


title: P11056_1835


title: P11056_1831


title: P11056_1830


title: P11056_1829


title: P11056_1827


title: P11056_1828


title: P11056_1855


title: P11056_1826


title: P11056_1825


title: P11056_1824


title: P11056_1852


title: P11056_1822


title: P11056_1821


title: P11056_1820


title: P11056_1818


title: P11056_1819


title: P11056_1816


title: P11056_1817


title: P11056_1815


title: P11056_1814


title: P11056_1813


title: P11056_1812


title: P11056_1811


title: P11056_1810


title: P11056_1809


title: P11056_1808


title: P11056_1833


title: P11056_1807


title: P11056_1805


title: P11056_1804


title: P11056_1806


title: P11056_1802


title: P11056_1803


title: P11056_1796


title: P11056_1797


title: P11056_1798


title: P11056_1799


title: P11056_1795


title: P11056_1794


title: P11056_1793


title: P11056_1792


title: P11056_1791


title: P11056_1823


title: P11056_1790


title: P11056_1789


title: P11056_1788


title: P11056_1787


title: P11056_1786


title: P11056_1784


title: P11056_1785


title: P11056_1782


title: P11056_1783


title: P11056_1777


title: P11056_1776


title: P11056_1780


title: P11056_1781


title: P11056_1779


title: P11056_1778


title: P11056_1775


title: P11056_1774


title: P11056_1801


title: P11056_1773


title: P11056_1771


title: P11056_1769


title: P11056_1770


title: P11056_1768


title: P11056_1800


title: P11056_1766


title: P11056_1763


title: P11056_1764


title: P11056_1767


title: P11056_1761


title: P11056_1759


title: P11056_1758


title: P11056_1762


title: P11056_1756


title: P11056_1755


title: P11056_1760


title: P11056_1753


title: P11056_1757


title: P11056_1754


title: P11056_1749


title: P11056_1750


title: P11056_1751


title: P11056_1752


title: P11056_1748


title: P11056_1745


title: P11056_1744


title: P11056_1772


title: P11056_1747


title: P11056_1746


title: P11056_1741


title: P11056_1743


title: P11056_1740


title: P11056_1739


title: P11056_1742


title: P11056_1738


title: P11056_1737


title: P11056_1765


title: P11056_1736


title: P11056_1735


title: P11056_1732


title: P11056_1733


title: P11056_1731


title: P11056_1730


title: P11056_1728


title: P11056_1725


title: P11056_1727


title: P11056_1721


title: P11056_1723


title: P11056_1724


title: P11056_1722


title: P11056_1718


title: P11056_1715


title: P11056_1717


title: P11056_1711


title: P11056_1716


title: P11056_1710


title: P11056_1712


title: P11056_1706


title: P11056_1708


title: P11056_1707


title: P11056_1719


title: P11056_1709


title: P11056_1704


title: P11056_1705


title: P11056_1734


title: P11056_1703


title: P11056_1702


title: P11056_1701


title: P11056_1700


title: P11056_1729


title: P11056_1726


title: P11056_1698


title: P11056_1699


title: P11056_1697


title: P11056_1695


title: P11056_1696


title: P11056_1694


title: P11056_1693


title: P11056_1720


title: P11056_1714


title: P11056_1713


title: P11056_1690


title: P11056_1689


title: P11056_1691


title: P11056_1688


title: P11056_1686


title: P11056_1687


title: P11056_1678


title: P11056_1685


title: P11056_1679


title: P11056_1681


title: P11056_1680


title: P11056_1683


title: P11056_1684


title: P11056_1677


title: P11056_1676


title: P11056_1675


title: P11056_1674


title: P11056_1673


title: P11056_1672

value: non-GFP


title: P11056_1670


title: P11056_1668


title: P11056_1669


title: P11056_1667


title: P11056_1665


title: P11056_1664


title: P11056_1663


title: P11056_1692


title: P11056_1682


title: P11056_1662


title: P11056_1660


title: P11056_1654


title: P11056_1659


title: P11056_1655


title: P11056_1651


title: P11056_1653


title: P11056_1650


title: P11056_1656


title: P11056_1657


title: P11056_1648


title: P11056_1646


title: P11056_1647


title: P11056_1649


title: P11056_1644


title: P11056_1643


title: P11056_1642


title: P11056_1645


title: P11056_1671


title: P11056_1639


title: P11056_1641


title: P11056_1640


title: P11056_1666


title: P11056_1638


title: P11056_1637


title: P11056_1636


title: P11056_1635


title: P11056_1634


title: P11056_1633


title: P11056_1632


title: P11056_1631


title: P11056_1661


title: P11056_1630


title: P11056_1629


title: P11056_1658


title: P11056_1627


title: P11056_1626


title: P11056_1625


title: P11056_1624


title: P11056_1628


title: P11056_1652


title: P11056_1623


title: P11056_1622


title: P11056_1616


title: P11056_1617


title: P11056_1618


title: P11056_1619


title: P11056_1615


title: P11056_1614


title: P11056_1613


title: P11056_1612


title: P11056_1611


title: P11056_1610


title: P11056_1609


title: P11056_1608


title: P11056_1607


title: P11056_1606


title: P11056_1605


title: P11056_1601


title: P11056_1602


title: P11056_1603


title: P11056_1604


title: P11056_1600


title: P11056_1599


title: P11056_1598


title: P11056_1594


title: P11056_1596


title: P11056_1595


title: P11056_1597


title: P11056_1593


title: P11056_1621


title: P11056_1620


title: P11056_1591


title: P11056_1585


title: P11056_1588


title: P11056_1586


title: P11056_1587


title: P11056_1590


title: P11056_1584


title: P11056_1583


title: P11056_1582


title: P11056_1581


title: P11056_1580


title: P11056_1579


title: P11056_1578


title: P11056_1576


title: P11056_1577


title: P11056_1574


title: P11056_1575


title: P11056_1573


title: P11056_1572


title: P11056_1571


title: P11056_1570


title: P11056_1569


title: P11056_1567


title: P11056_1566


title: P11056_1592


title: P11056_1564


title: P11056_1565


title: P11056_1563


title: P11056_1559


title: P11056_1558


title: P11056_1589


title: P11056_1562


title: P11056_1555


title: P11056_1557


title: P11056_1556


title: P11056_1554


title: P11056_1553


title: P11056_1552


title: P11056_1551


title: P11056_1550


title: P11056_1549


title: P11056_1548


title: P11056_1547


title: P11056_1546


title: P11056_1544


title: P11056_1545


title: P11056_1543


title: P11056_1541


title: P11056_1538


title: P11056_1539


title: P11056_1537


title: P11056_1568


title: P11056_1534


title: P11056_1535


title: P11056_1532


title: P11056_1533


title: P11056_1561


title: P11056_1531


title: P11056_1536


title: P11056_1530


title: P11056_1560


title: P11056_1528


title: P11056_1529


title: P11056_1527


title: P11056_1526


title: P11056_1525


title: P11056_1524


title: P11056_1522


title: P11056_1523


title: P11056_1520


title: P11056_1521


title: P11056_1519


title: P11056_1518


title: P11056_1516


title: P11056_1515


title: P11056_1514


title: P11056_1512


title: P11056_1511


title: P11056_1542


title: P11056_1540


title: P11056_1509


title: P11056_1508


title: P11056_1506


title: P11056_1505


title: P11056_1504


title: P11056_1503


title: P11056_1507


title: P11056_1500


title: P11056_1501


title: P11056_1499


title: P11056_1502


title: P11056_1498


title: P11056_1497


title: P11056_1496


title: P11056_1494


title: P11056_1495


title: P11056_1492


title: P11056_1493


title: P11056_1490


title: P11056_1488


title: P11056_1489


title: P11056_1486


title: P11056_1487


title: P11056_1517


title: P11056_1485


title: P11056_1483


title: P11056_1513


title: P11056_1481


title: P11056_1480


title: P11056_1510


title: P11056_1479


title: P11056_1478


title: P11056_1477


title: P11056_1476


title: P11056_1475


title: P11056_1474


title: P11056_1473


title: P11056_1472


title: P11056_1471


title: P11056_1484


title: P11056_1470


title: P11056_1482


title: P11056_1468


title: P11056_1465


title: P11056_1464


title: P11056_1466


title: P11056_1463


title: P11056_1491


title: P11056_1461


title: P11056_1462


title: P11056_1460


title: P11056_1459


title: P11056_1458


title: P11056_1457


title: P11056_1456


title: P11056_1454


title: P11056_1455


title: P11056_1453


title: P11056_1452


title: P11056_1450


title: P11056_1451


title: P11056_1449


title: P11056_1448


title: P11056_1446


title: P11056_1447


title: P11056_1444


title: P11056_1445


title: P11056_1443


title: P11056_1442


title: P11056_1441


title: P11056_1436


title: P11056_1438


title: P11056_1437


title: P11056_1467


title: P11056_1435


title: P11056_1434


title: P11056_1430


title: P11056_1431


title: P11056_1439


title: P11056_1469


title: P11056_1432


title: P11056_1429


title: P11056_1428


title: P11056_1427


title: P11056_1426


title: P11056_1425


title: P11056_1424


title: P11056_1423


title: P11056_1422


title: P11056_1420


title: P11056_1421


title: P11056_1419


title: P11056_1418


title: P11056_1416


title: P11056_1417


title: P11056_1415


title: P11056_1414


title: P11056_1413


title: P11056_1440


title: P11056_1412


title: P11056_1407


title: P11056_1411


title: P11056_1409


title: P11056_1408


title: P11056_1406


title: P11056_1404


title: P11056_1433


title: P11056_1405


title: P11056_1402


title: P11056_1403


title: P11056_1401


title: P11056_1400


title: P11056_1396


title: P11056_1397


title: P11056_1399


title: P11056_1398


title: P11056_1390


title: P11056_1389


title: P11056_1387


title: P11056_1388


title: P11056_1386


title: P11056_1385


title: P11056_1383


title: P11056_1379


title: P11056_1380


title: P11056_1382


title: P11056_1384


title: P11056_1381


title: P11056_1378


title: P11056_1377


title: P11056_1375


title: P11056_1410


title: P11056_1373


title: P11056_1374


title: P11056_1376


title: P11056_1371


title: P11056_1372


title: P11056_1368


title: P11056_1367


title: P11056_1369


title: P11056_1370


title: P11056_1366


title: P11056_1395


title: P11056_1394


title: P11056_1392


title: P11056_1393


title: P11056_1364


title: P11056_1391


title: P11056_1365


title: P11056_1362


title: P11056_1361


title: P11056_1360


title: THLE2 cells - V600E mutant BRAF plasmid rep2

city: Little Rock

first: Christopher

middle: Paul

last: Wardell

state: AR

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

data_processing:
Basecalling performed by Beijing Genomics DNB-seq G400 sequencer
Reads aligned with STAR version 2.7.3a_2020-01-23 to reference genome GRCh38 with parameters: --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMunmapped Within --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonical --alignIntronMax 200000 --alignMatesGapMax 200000 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 0 --chimScoreDropMax 20 --chimScoreSeparation 10
Featurecounts created using featureCounts from subread version 2.0 against GENCODE v34 and parameters -T 20 -p
Differentially expressed transcripts were determined using DESeq2 with a false discovery rate (FDR) of 0.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files containing feature counts for every transcript per sample

source_name: THLE-2 cells

extract_protocol:
NucleoSpin RNA extraction kit
DNB-Seq standardized library construction was performed by Beijing Genomics using their proprietary technology

tag: cell line

value: Hepatocytes

value: Liver

tag: genotype/variation

value: V600E mutant BRAF plasmid


title: THLE2 cells - empty plasmid rep1

value: empty plasmid


title: THLE2 cells - V600E mutant BRAF plasmid rep1


title: P11056_1359


title: THLE2 cells - wildtype BRAF plasmid rep2

value: wildtype BRAF plasmid


title: P11056_1358


title: THLE2 cells - wildtype BRAF plasmid rep1


title: P11056_1356


title: P11056_1357


title: mTEC AB0 1

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

description: pool of 5-10 mice of 4-6 weeks

data_processing:
Basecalling was performed using bcl2fastq version 2.20.0.
Reads were trimmed for low-quality ends with TrimGalore and transcript abundance was estimated with Kallisto v0.43 using the mm10 reference transcriptome.
Kallisto counts were normalized by the regularized log (rlog) transformation using the DeSeq2 R Package.
Genome_build: mm10
Supplementary_files_format_and_content: Abundance.txt: transcript abundances estimated with Kallisto. rlog_normData.txt: tab-delimited text files with rlog normalized values for each sample.

source_name: medullary thymic epithelial cells (mTECs)

extract_protocol:
RNA was extracted with with RNeasy microkit (QIAGEN, Hilden, Germany)
Poly-A enriched libraries were generated with the Takara SMART-Seq v4 Ultra low input RNA Kit

value: thymus

value: A[beta] 0/0


title: mTEC AB0 2

description: pool of 5-10 mice of 4-6 weeks


title: mTEC AB0 3

description: pool of 5-10 mice of 4-6 weeks


title: P11056_1355


title: mTEC WT 3

description: pool of 5-10 mice of 4-6 weeks

value: wild-type


title: P11056_1354


title: P11056_1353


title: cTEC AB0 3

description: pool of 5-10 mice of 4-6 weeks

source_name: cortical thymic epithelial cells (cTECs)


title: P11056_1351


title: mTEC WT 1

description: pool of 5-10 mice of 4-6 weeks


title: P11056_1350


title: cTEC AB0 2

description: pool of 5-10 mice of 4-6 weeks


title: cTEC AB0 1

description: pool of 5-10 mice of 4-6 weeks


title: P11056_1349


title: P11056_1348


title: THLE2 cells - empty plasmid rep2


title: P11056_1363


title: cTEC WT 3

description: pool of 5-10 mice of 4-6 weeks


title: P11056_1347


title: cTEC WT 2

description: pool of 5-10 mice of 4-6 weeks


title: cTEC WT 1

description: pool of 5-10 mice of 4-6 weeks


title: Tub4

city: Palo Alto

first: Jamie

middle: O.

last: Brett

state: CA

address: 3801 Miranda Avenue, Building 100, Room E4-216

department: Neurology and Neurological Sciences

institute: Stanford University

data_processing:
RNA-Seq reads were processed with trim_galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore) for quality and adapter removal. Reads were then mapped to the mouse genome (mm10) with Ensembl transcript annotations using STAR (Dobin et al. 2013). Uniquely mapping exonic reads were summarized over genes with the featureCounts module of Subread (Liao et al. 2014). Counts were analyzed using edgeR (Robinson et al. 2010), normalizing with the Trimmed Mean of M-values (TMM) method. Genes that did not have at least 0.5 FPKM in at least 2 samples were filtered from the processed data file as non-expressed/noise.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited .txt file containing TMM-normalized FPKMs

source_name: Skeletal muscle stem cells

growth_protocol: For samples where MuSCs were grown in culture, cells were grown in Ham's F-10 media containing 10% horse serum, 100 U/mL penicillin, and 100 mcg/mL streptomycin on plastic tissue-culture plates coated with 25 mcg/mL ECM

extract_protocol:
FACS-isolated MuSCs or MuSCs grown ex vivo for 24h in the presence of either DMSO or TubA were snap-frozen. Total RNA was extracted using the RNeasy Micro Plus Kit (Qiagen) according to manufacturer’s instructions.
Reverse transcription was performed with 5 ng RNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara). The cDNA was then sheared with a Covaris S2 ultrasonicator. Library constructions were performed using the Ovation Ultralow Multiplex system (NuGEN). Libraries underwent paired-end 150-bp sequencing at Novogene with an Illumina HiSeq 2000 to a depth of 20-40 million reads.

treatment_protocol: TubA treatment was Tubastatin A (Cayman Chemical) dissolved in DMSO at 40 µM. Vehicle treatment was an equal volume of DMSO.

value: Skeletal muscle stem cells

tag: time ex vivo

value: TubA

tag: strain

value: male


title: Tub3


title: Tub2


title: P11056_1343

tag: cell type


title: P11056_1342


title: P11056_1341


title: Tub1


title: FI3

value: vehicle


title: P11056_1340


title: FI2


title: P11056_1339


title: mTEC WT 2

description: pool of 5-10 mice of 4-6 weeks


title: Veh3


title: P11056_1337


title: Veh2


title: FI1


title: Veh1


title: P11056_1338


title: P11056_1352


title: P11056_1336


title: P11056_1334


title: P11056_1333


title: P11056_1335


title: P11056_1332


title: P11056_1330


title: P11056_1329


title: P11056_1327


title: P11056_1346


title: P11056_1345


title: P11056_1326


title: P11056_1328


title: P11056_1325


title: P11056_1344


title: P11056_1324


title: P11056_1322


title: P11056_1323


title: P11056_1320


title: P11056_1321


title: 5_60T

city: Columbus

first: Erin

last: Gloag

state: Ohio

address: 460 W. 12th Ave

department: Microbial  Infection and Immunity

institute: The Ohio State Univerisity

data_processing:
HiSeq 4000 sequencing was performed, generating approximately 300 million total paired end 300 bp reads from the 15 total samples, with a mean quality score of 37.4.
Reads were aligned to the reference PAO1 genome using Rockhopper
Rockhopper: https://cs.wellesley.edu/~btjaden/Rockhopper/
Genome_build: PAO1 reference genome GenBank: AE004091.2
Supplementary_files_format_and_content: Text files comparing time points 10, 15, 30, 45 and 60 to the 5 min time point. Operon, transcript and summary outputs

organism: Pseudomonas aeruginosa PAO1

source_name: Bacterial

growth_protocol: Logarithmic phase bacterial culture in LB with optical density 600 (OD600) of 0.5 was inoculated in an Ibidi μ-Slide. At the indicated time from 5 - 60 min post-attachment, the channel was rinsed twice in PBS to remove non-adherent cells

extract_protocol:
200μL of Trizol was added to the channel. Trizol was collected and stored at -80°C for RNA isolation. Following a 5 min incubation at room temperature, 0.2 mL of chloroform was added and the samples were shaken vigorously for 1 min. Phases were separated by centrifugation (12,000 g, 5 min, 4°C) and the aqueous phase was combined with 0.6 mL of 70% ethanol and transferred to an RNeasy mini column (Qiagen). RNA was purified as per manufactures protocols
Libraries were constructed using the ScriptSeq Complete Kit (Illumina) following the Bacteria-Low Input protocol.

tag: time point


title: P11056_1319


title: P11056_1318


title: 5_45T


title: 5_15T


title: 5_30T


title: P11056_1316


title: P11056_1317


title: 5_10T


title: 5T


title: P11056_1314


title: P11056_1315


title: P11056_1313


title: RNA Amputation 7dpa-2

city: New York

first: Jingli

last: Cao

state: NY

department: Cell & Developmental Biology

institute: Weill Cornell Medical College

description: 7 days after heart apex amputation injury, replicate 2

data_processing:
Illumina Casava 1.8 software was used for basecalling.
Reads were trimmed for adaptors using flexbar
Sequences were aligned to the zebrafish genome (danRer10) using TopHat2
Transcript expressions were quantified using HTseq
Genome_build: DanRer10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: zebrafish epicardial cell

growth_protocol: Zebrafih were maintained in standard conditions

extract_protocol:
RNA was extracted using Qiagen RNeasy Plus Micro Kit following the manual
Libraries were made using Clontech SMARTer Ultra Low Input mRNA amplification and KAPA Hyper Prep Kit following the manual

treatment_protocol: Heart apex amputation injury

value: EK

value: heart epicardium

tag: protocol

value: heart apex amputation injury

value: 6 month

value: 7 days


title: P11056_1311


title: P11056_1310


title: RNA Amputation 7dpa-1

description: 7 days after heart apex amputation injury, replicate 1


title: P11056_1331


title: P11056_1309


title: P11056_1308


title: RNA Amputation 3dpa-2

description: 3 days after heart apex amputation injury, replicate 2

value: 3 days


title: P11056_1307


title: RNA Amputation 3dpa-1

description: 3 days after heart apex amputation injury, replicate 1


title: P11056_1305


title: P11056_1304


title: RNA Uninjured-2

description: non treated control, replicate 2

value: non treated


title: P11056_1303


title: P11056_1302


title: P11056_1300


title: P11056_1301


title: P11056_1299


title: RNA Uninjured-1

description: non treated control, replicate 1


title: P11056_1298


title: P11056_1297


title: P11056_1296


title: Deprivated-316-L-LGN

city: GuangZhou

first: Zhongshu

last: Tang

state: Guangdong

address: 54 South Xianlie Road

institute: Sun Yat-sen University

description: Only the left LGN of  monocular deprivated Macaca Fascicularis was sequencing owing to the low quality of the right LGN examined  using Agilent Bioanalyzer 2100

data_processing:
lllumina GA Pipeline v1.5 software used for basecalling.
Reads were further filtered by fastp(version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
Alignment with reference genome: an index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISA T2 (version 2.1.0) with “-rna-strandness RF” and other parameters set as a default.
Transcripts Reconstruction: the reconstruction of transcripts was carried out with software Stringtie(version 1.3.4), which together with HISA T2, allow biologists to identify new genes and new splice variants of known ones.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: NC_022273.1 Chromosome 2 Reference Macaca_fascicularis_5.0 Primary Assembly
Supplementary_files_format_and_content: "xlsx" excel files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw mRNA transcript counts for every mRNA transcript and every sample

organism: Macaca fascicularis

source_name: LGN

extract_protocol:
LGN of  Macaca Fascicularis were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Then we used Agilent Bioanalyzer 2100 to test the quality of RNA. We used  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The left eye of deprivated group was sutured by surgery from 1 month old to 3 month old.

tag: tissues

value: LGN

value: 3 months old

value: monocular visual deprivation of left eye


title: Control-331-R-LGN

description: We mixed the left LGN and the right LGN of control group of Macaca Fascicularis together for RNA sequencing

value: untreated


title: P11056_1294


title: P11056_1295


title: Control-317-L-LGN


title: P11056_1293


title: P11056_1292


title: Control-307-R-LGN


title: P11056_1312


title: P11056_1289


title: P11056_1291


title: P11056_1288


title: P11056_1290


title: 12W-5 mRNA

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

institute: 6/5000 Shandong Agricultural University

description:
12W-5
Goat kid

data_processing:
Paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq6000 (2 × 150bp read length)
The raw paired-end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Clean reads were separately aligned to the goat (Capra_hircus) reference genome (ARS1) with orientation mode using HIASAT (https://ccb.jhu.edu/software/hisat2/index.shtml) software. The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) in a reference-based approach.
The expression level of each transcript was calculated according to fragments per kilobases per million reads (FPKM) method.
Genome_build: ARS1
Supplementary_files_format_and_content: Tab-delimited text files include gene FPKM values for each Sample

organism: Capra hircus

source_name: Goat kid

extract_protocol:
Liver tissue were quickly collected after slaughter, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeqTM stranded total RNA Kit(San Diego, CA)  was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 12 weeks of age

value: liver


title: P11056_1286


title: P11056_1287


title: 12W-3 mRNA

description:
12W-3
Goat kid


title: P11056_1285


title: P11056_1306


title: 12W-2 mRNA

description:
12W-2
Goat kid


title: P11056_1283


title: P11056_1282


title: 12W-1 mRNA

description:
12W-1
Goat kid


title: Amputation 7dpa-4

description: 7 days after heart apex amputation injury, replicate 4

data_processing:
Illumina Casava 1.8 software was used for basecalling.
Reads were trimmed for adaptors using Cutadapt
Trimmed reads were alignned to the DanRer10 genome using Bowtie with parameters “-n 2 -m 4”
Reads mapped to mitochondrial DNA were removed and alignments were filtered for PCR artifacts
Peaks were called using MACS2 with parameters “-q 0.01 --nomodel --shift -100 --ext 200 --bdg”
Genome_build: DanRer10
Supplementary_files_format_and_content: bigWig files were generated using wigToBigWig with standard settings.

extract_protocol:
Extraction and library making was done as described (reference: PMID: 24097267)
Library making was done as described (reference: PMID: 24097267)


title: Amputation 7dpa-3

description: 7 days after heart apex amputation injury, replicate 3


title: P11056_1281


title: Amputation 7dpa-2

value: 7 days after heart apex amputation injury


title: P11056_1280


title: P11056_1279


title: 8W-5 mRNA

description:
8W-5
Goat kid

value: 8 weeks of age


title: P11056_1278


title: Deprivated-326-L-LGN


title: P11056_1277


title: 8W-4 mRNA

description:
8W-4
Goat kid


title: Amputation 3dpa-4

description: 3 days after heart apex amputation injury, replicate 4


title: P11056_1276


title: 8W-2 mRNA

description:
8W-2
Goat kid


title: P11056_1274


title: P11056_1275


title: 8W-1 mRNA

description:
8W-1
Goat kid


title: P11056_1272


title: 12W-4 mRNA

description:
12W-4
Goat kid


title: P11056_1271


title: 8W-3 mRNA

description:
8W-3
Goat kid


title: Amputation 3dpa-2

value: 3 days after heart apex amputation injury


title: Amputation 3dpa-3

description: 3 days after heart apex amputation injury, replicate 3


title: P11056_1270


title: Uninjured-4

description: non treated control, replicate 4

value: non treated control


title: 4W-5 mRNA

description:
4W-5
Goat kid

value: 4 weeks of age


title: Amputation 3dpa-1

value: EK

value: heart epicardium


title: 4W-4 mRNA

description:
4W-4
Goat kid


title: P11056_1284


title: P11056_1269


title: 4W-3 mRNA

description:
4W-3
Goat kid


title: P11056_1266


title: P11056_1267


title: Uninjured-3

description: non treated control, replicate 3

value: 6 month


title: Uninjured-2

description: non treated control, replicate 2


title: P11056_1264


title: P11056_1265


title: 4W-2 mRNA

description:
4W-2
Goat kid


title: Uninjured-1

description: non treated control, replicate 1


title: P11056_1263


title: Amputation 7dpa-1


title: P11056_1262


title: 4W-1 mRNA

description:
4W-1
Goat kid


title: rab-11.1 RNAi_rep 3

city: Dallas

first: Peter

middle: M

last: Douglas

address: 6000 Harry Hines Blvd

department: Department of Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

description: rab-11.1 RNAi biological replicate 3

data_processing:
Basecalling and trimming were performed using CLC Genomics Workbench ver. 9.5
Sequences were mapped to the whole Caenorhabidits elegans genome (release: ) using CLC 9.5.
Expression values and Reads per kilobase million (RPKM) were calculated according to default CLC settings.
Genome_build: WBcel235
Supplementary_files_format_and_content: excel file contains RPKM values for each transcript

organism: Caenorhabditis elegans

source_name: All tissue

growth_protocol: 20°C on HT115 bacteria and NGM plates supplemented with IPTG and Carbenicillin

extract_protocol:
Whole worm RNA was extracted using Trizol with freeze/thawing and vortexing. RNA was later enriched for mRNA using oligo(dt) beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNAi treatment for entirety of develpoment

value: L4 larcae

value: wild type

value: rab-11.1 RNAi


title: 2W-5 mRNA

description:
2W-5
Goat kid

value: 2 weeks of age


title: P11056_1259


title: rab-11.1 RNAi_rep 2

description: rab-11.1 RNAi biological replicate 2

value: L4 larvae


title: P11056_1258


title: 2W-4 mRNA

description:
2W-4
Goat kid


title: P11056_1273


title: P11056_1257


title: P11056_1256


title: 2W-3 mRNA

description:
2W-3
Goat kid


title: P11056_1255


title: P11056_1254


title: 2W-2 mRNA

description:
2W-2
Goat kid


title: EV RNAi control_rep 3

description: empty vector RNAi biological replicate 3

value: EV RNAi


title: P11056_1253


title: P11056_1252


title: EV RNAi control_rep 2

description: empty vector RNAi biological replicate 2


title: 2W-1 mRNA

description:
2W-1
Goat kid


title: P11056_1268


title: EV RNAi control_rep 1

description: empty vector RNAi biological replicate 1


title: 1D-5 mRNA

description:
1D-5
Goat kid

value: 1 day of age


title: P11056_1251


title: P11056_1249


title: Sample 12 CD8 memory T cells skin

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

institute: Technical University of Munich

data_processing:
Alignment: The reads were mapped to the reference transcriptome built from the human genome assembly GRCh38.p12 (Gencode release 28) using STAR v2.7.6a with the following parameters: --runMode alignReads --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted.
Read counting: Transcripts were quantified with salmon v0.11.3 in the alignment-based mode using the "quant" algorithm and library type "A".
Differential expression: Transcript abundance estimates were imported using tximport R package. Differentially expressed genes were identified using the R package DESeq2, considering the effect of samples originating from the same donor by using the design "~ replicate + condition". No fold change cutoff was set for determining differentially expressed genes and only the genes with a false discovery rate (FDR) < 0.05 by the Wald Test were considered significantly dysregulated. For GSEA and genes were ranked according to the shrunken fold change values calculated by DESeq2using the adaptive t prior shrinkage estimator ("apeglm").
Genome_build: GRCh38.p12 (Gencode release 28)
Supplementary_files_format_and_content: The files with the raw counts for transcript abundance contain the output from salmon ("quant.sf" file) containing the gene id, length, effective length, calculated TPM and raw counts. The file with the normalized counts for gene abundance is the output from DESeq2 "counts" function with "normalized=T" on the output of the "DESeq" function and contains the normalized counts for all genes in each sample. The file with the differential expression is the output from DESeq2 "results" function containing all genes and their mean of normalized counts for all samples, log2 fold change between skin versus blood, standard error, Wald statistic, Wald test p-value and Benjamini & Hochberg-adjusted p-values, along with gene symbol and gene description.

source_name: skin derived

growth_protocol: CD4+CD45RA– and CD8+CD45RA– viable CD3+ T cells were sorted from matched skin and blood from three healthy human donors for mRNAseq analysis.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: ex vivo isolation according to surface markers.

tag: donor

tag: health state

value: healthy

tag: cd3 status

tag: cd45ra status

tag: cd4 status

tag: cd8 status


title: P11056_1248

tag: tissue


title: 1D-4 mRNA

description:
1D-4
Goat kid

tag: age

value: liver


title: P11056_1247


title: P11056_1246


title: 1D-3 mRNA

description:
1D-3
Goat kid


title: Sample 11 CD4 memory T cells skin


title: Sample 10 CD8 memory T cells blood

source_name: blood derived


title: P11056_1261


title: P11056_1245


title: P11056_1244


title: P11056_1260


title: 1D-2 mRNA

description:
1D-2
Goat kid


title: Sample 9 CD4 memory T cells blood


title: 1D-1 mRNA

description:
1D-1
Goat kid


title: P11056_1243


title: P11056_1242


title: Sample 8 CD8 memory T cells skin


title: P11056_1239


title: P11056_1240


title: rab-11.1 RNAi_rep 1

description: rab-11.1 RNAi biological replicate 1

tag: genotype

tag: treatment


title: P11056_1238


title: Sample 7 CD4 memory T cells skin


title: P11056_1237


title: Sample 6 CD8 memory T cells blood


title: Sample 5 CD4 memory T cells blood


title: P11056_1241


title: P11056_1236


title: P11056_1234


title: P11056_1250


title: P11056_1233


title: Sample 4 CD8 memory T cells skin


title: P11056_1232


title: P11056_1231


title: P11056_1230


title: Sample 3 CD4 memory T cells skin


title: P11056_1229


title: P11056_1227


title: P11056_1228


title: Sample 2 CD8 memory T cells blood


title: Sample 1 CD4 memory T cells blood


title: P11056_1226


title: P11056_1225


title: P11056_1223


title: P11056_1222


title: P11056_1221


title: P11056_1220


title: WGBS_GL_rep2

city: Chongqing

first: Chuan

last: Liu

address: Chongwen Road

institute: Chongqing University of Posts and Telecommunications

data_processing:
Bisulfite-seq Data Processing: Quality control of WGBS data was performed using FastQC (version 0.11.9, Babraham Bioinformatics, UK). Sequencing adapters and low-quality reads were removed using Trimmomatic (Bolger et al., 2014). The trimmed reads were then aligned and mapped to the rice reference genome of Nipponbare (MSU_v7.0) using Bismark (Krueger and Andrews, 2011). The percentage methylation level was calculated by mC/(mC + umC), where mC and umC represent the number of methylated and unmethylated reads, respectively.
RNA-seq Data Processing: Sequencing adapters and low-quality reads were removed with fastp (version 0.20.1) (Chen et al., 2018), and the quality of raw reads was evaluated with FastQC (version 0.11.9, Babraham Bioinformatics, UK). The remaining clean reads were mapped to the rice reference genome of Nipponbare (MSU_v7.0) using Hisat2 (version 2.1.0) (Kim et al., 2019). TPMCalculator was used to count the reads mapped to individual genes as well as to measure gene expression levels by calculating transcripts per million (TPM) read values (Vera Alvarez et al., 2019).
Genome_build: Nipponbare (MSU_v7.0)
Supplementary_files_format_and_content: bigWig and expression matrix

organism: Oryza sativa Indica Group

source_name: Guangluai 4

growth_protocol: Rice was planted in a growth chamber (PRX-380B, Shanghai Guning Instrument Co., Ltd) for 15 days after germination

extract_protocol:
Cetyltrimethylammonium bromide method was used for genomic DNA extraction. Total RNA from rice leaves was extracted using TRIzol Reagent (Invitrogen, CA, USA) for RNA sequencing
Genomic DNA (2-µg) spiked with 5-ng unmethylated Lambda DNA (Promega, Madison, WI, USA) was fragmented by sonication to generate fragments measuring 300–500 bp. These fragments were then ligated with 5-methylcytosine-modiﬁed adapters and subjected to bisulfide conversion using the ZYMO EZ DNA Methylation-Gold Kit (Zymo Research, Irvine, CA, USA). The bisulfide-converted DNA was purified, recycled, and then amplified by PCR with 10 cycles using KAPA HiFi HotStart Uracil + ReadyMix (Kapa Biosystems, Wilmington, MA, USA) and Illumina 8-bp index primers. RNA sequencing libraries were generated from the purified mRNA using the VAHTS Universal V6 RNA-seq Library Kit for MGI (Vazyme, Nanjing, China) following the manufacturer's recommendations with unique index codes.

treatment_protocol: The growth chamber was set at 28°C under a 14-h light/10-h dark cycle with the light period of 6:00–20:00

tag: cultivar

value: Guangluai 4

value: WT

value: leaves

value: 15 days


title: P11056_1219


title: WGBS_OE_rep1

source_name: OsPRR37 overexpression line (Guangluai 4 was used as recipient parent)

value: OsPRR37 overexpression


title: WGBS_OE_rep2


title: WGBS_GL_rep1


title: P11056_1216


title: P11056_1235


title: P11056_1215


title: P11056_1218


title: P11056_1213


title: P11056_1212


title: CTL_GFPlow_1

city: Concepción

first: Claudio

last: Carril Pardo

state: Biobío

address: Lientur 1457

country: Chile

institute: Universidad San Sebastian

data_processing:
Sequences were trimmed in order to remove adaptors and low quality bases
Reads were mapped and aligned to the zebrafish genome GRCz11 from Ensembl gene annotation version 92 using STAR
Gene expression levels were calculated with featureCounts
differential expression determined with DESeq2
Genome_build: GRCz11
Supplementary_files_format_and_content: raw counts for annotations for each Sample

source_name: Sst1.1:GFP +, low fluorescence

growth_protocol: Zebrafish (Danio rerio) were raised according to standard protocols

extract_protocol:
The main islets from 2-4 pancreata of Tg(sst1.1:eGFP); Tg(ins:NTR*-P2A-mCherry) adult fish (6–10 months old, males and females) were dissected under epifluorescence to eliminate a maximum of non-fluorescent surrounding exocrine tissue and collected and washed in HBSS without Ca2+/Mg2+. Live cell dissociation was performed in Tryple Select 1x solution (GIBCO) supplemented with 100 U/mL collagenase IV (Life Technologies 17104-019) and 40 µg/mL proteinase K (Invitrogen, 25530031) for 10 min at 28 °C, and stopped with 15% FBS. The GFP+ cells, mCherry+ cell and double GFP+ mCherry+ cells were sorted on FACS Aria III under purity mode and after exclusion of the doublets. The purity of the sorted cells was confirmed by epifluorescence microscopy (~95 %). Cells (about 1000-5000/fish depending on the cell type) were immediately lysed with 0.5% Triton X-100 containing 2U/µl RNAse inhibitor and stored at –80 °C.
cDNAs were prepared from lysed cells according to SMART-Seq2.0 (Picelli S et al 2014 ) for low input RNA sequencing and libraries were prepared with Nextera® DNA Library kit (Illumina)

treatment_protocol: Adult fish were treated in fish water with 2.5 µM NFP. Control treatments consisted of E3 containing 0.16% DMSO. The fish were treated for 18 hours in the dark and maintained up to 20 days post treatment (dpt)

value: pancreas

value: adult fish, 6-10 months old

value: CTL / DMSO


title: 4d_PE_6_tub

description: total RNA from day 4 mouse heart tissue harvested after 10mg/kg phenylephrine injections on day 0 and day 2

data_processing: The geometric means of the positive control values were used to threshold followed by data normalization using the geometric means of the three housekeeping genes (GAPDH, Rpl4, Tbp).

source_name: heart tissue

extract_protocol: total RNA was extracted from ~10mg of heart tissue using RNAzol as per the manufacturer's protocol

tag: time

value: Phenylephrine


title: 4d_PE_5_tub


title: P11056_1211


title: P11056_1210


title: CTL_GFPlow_3

tag: strain


title: 4d_PE_8_tub


title: CTL_Beta_7

source_name: ins:mCherry +


title: 4d_PE_4_tub


title: P11056_1209

source_name: EAE

tag: cell type


title: P11056_1208


title: 4d_PE_3_tub


title: CTL_Beta_6


title: P11056_1205


title: P11056_1206


title: P11056_1207


title: CTL_Beta_5


title: P11056_1224


title: 4d_PE_1_tub


title: 4d_PE_2_tub


title: CTL_Beta_4


title: P11056_1204


title: P11056_1203


title: P11056_1217


title: P11056_1202


title: 4d_Iso_8_tub

description: total RNA from day 4 mouse heart tissue harvested after 5mg/kg isoproterenol injections on day 0 and day 2

value: Isoproterenol


title: CTL_Beta_3


title: P11056_1201


title: P11056_1200


title: CTL_Beta_2


title: P11056_1198


title: P11056_1199


title: CTL_Beta_1


title: CTL_GFPlow_2


title: 4d_Iso_6_tub


title: P11056_1197


title: 4d_Iso_5_tub


title: P11056_1194


title: P11056_1193


title: P11056_1192


title: P11056_1191


title: P11056_1190


title: 20dpt_Bi_hormonal_5

source_name: sst1.1:GFP +/ins:mCherry +

value: Ablation NFP


title: 20dpt_Bi_hormonal_4


title: 20dpt_Bi_hormonal_3


title: 4d_Ctrl_8_tub

description: total RNA from day 4 mouse heart tissue harvested after ascorbic acid injections on day 0 and day 2

value: Ascorbic acid


title: P11056_1189


title: P11056_1188


title: 20dpt_Bi_hormonal_2


title: P11056_1187


title: 4d_Ctrl_7_tub


title: P11056_1186


title: 20dpt_Bi_hormonal_1


title: P11056_1185


title: 4d_Ctrl_6_tub


title: P11056_1184


title: CTL_GFPhigh_3

source_name: Sst1.1:GFP +, high fluorescence


title: P11056_1183


title: 4d_Ctrl_5_tub


title: 4d_Iso_7_tub


title: P11056_1196


title: 4d_Ctrl_4_tub


title: P11056_1182


title: 20dpt_Bi_hormonal_6


title: CTL_GFPhigh_2


title: P11056_1181


title: P11056_1195


title: CTL_GFPhigh_1


title: P11056_1180


title: P11056_1179


title: P11056_1178


title: 4d_Ctrl_2_tub


title: 4d_Iso_3_tub


title: 4d_Ctrl_1_tub


title: P11056_1177


title: Trizol-301KO-3-1

city: Guangzhou

first: Xiaodong

last: Ma

address: Rm406,Building 29, South China Normal University

institute: South China Normal University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.1.0 with default parameters. The number of reads mapped to each gene was calculated by Htseq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and counts for each Sample

source_name: mouse Hippocampal Tissue

growth_protocol: all mice were housed under standard conditions

extract_protocol:
Total RNA was harvested using Trizol reagent. Poly(A) RNAs were purified by using the Dynabeads mRNA purification kit and Poly(A) RNAs were fragmented at 94℃ for 5 min before reverse transcribed to cDNA with random primers. cDNA fragments were blunted and ligated to sequencing adaptors.
Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3µl USER Enzyme (NEB,USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X)Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: untreated

value: hippocampus


title: 4d_Iso_2_tub

city: Philadelphia

first: Benjamin

last: Prosser

institute: University of Pennsylvania


title: P11056_1176


title: 4h_PE_6_tub

description: total RNA from mouse heart tissue harvested after 4 hours of 10mg/kg phenylephrine injection


title: P11056_1175


title: P11056_1174


title: 4h_PE_5_tub


title: Trizol-301KO-1-1


title: P11056_1173


title: P11056_1172


title: P11056_1171


title: 4h_PE_4_tub


title: P11056_1170


title: Trizol-WT-2-1

value: wild type


title: P11056_1169


title: P11056_1168


title: P11056_1214


title: 4h_PE_3_tub


title: Trizol-WT-1-1


title: P11056_1167


title: P11056_1165


title: Spatial transcriptomics of MPL

first: Bing

address: No. 280, South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Library strategy: Spatial Transcriptomics
Space Ranger (version 1.1.0) analyze the raw sequencing data produced from Visium Spatial Gene Expression.
To generate spatial feature counts for a single library using automatic fiducial alignment and tissue detection, run spaceranger count with the following arguments.
spaceranger count --id=HJ --transcriptome=/opt/refdata-gex-mm10-2020-A_v2 --fastqs=fastq_path --image=V19D02-051-D1.jpg --slide=V19D02-051 --area=D1 --r2-length 90
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 file is a binary format of feature-barcode matrix. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column).
Supplementary_files_format_and_content: aligned_fiducials.jpg has the dimensions of tissue_hires_image.png. Fiducial spots found by the fiducial alignment algorithm are highlighted in red.
Supplementary_files_format_and_content: detected_tissue_image.jpg has the dimensions of the tissue_hires_image.png and shows the portion of the image where tissue is discriminated from background.
Supplementary_files_format_and_content: scalefactors_json.json contains the scaling factor that converts pixel positions in the original, full-resolution image to pixel positions in tissue_hires_image.png and tissue_lowres_image.png.
Supplementary_files_format_and_content: tissue_hires_image.png and tissue_lowres_image.png are downsampled versions of the original, full-resolution brightfield image provided by the user.
Supplementary_files_format_and_content: tissue_positions_list.csv contains a table with rows that correspond to spots. Columns correspond to the sequence of the barcode associated to the spot, and row/column coordinates of the spot.

source_name: Brain

extract_protocol:
Tissue sections placed on Capture Areas are fixed and stained, permeabilized, and cellular mRNA is captured by the primers on the gene expression spots. All the steps are performed according to Visium Spatial Gene Expression Reagent Kits User Guide (CG000239 Rev D)
RNA libraries were prepared for sequencing using standard Visium Spatial Gene Expression Library Construction protocols (CG000239 Rev D)

tag: Sex

value: male

value: brain


title: P11056_1164

data_processing:
Libraries were sequenced in Hiseq 2500 with a 50-8-8-50 read set-up and a minimum of 25000 read pairs per cell.
Reads were trimmed and aligned to mm10 reference assembly using Bowtie2. Reads were called individually for each sample using MACS2. Called peaks were merged using bedtools mergedbed. Fragment files and counts were obtained using the individual bam files as input for ChromVar R package, Resulting on 1029 cells.
ATAC signal was binarized and convert to gene activity score over 500bp promoters regions, then integrated using Seurat2 to scRNA-seq (Falcao, van Bruggen wt al. 2018) to assign cell identities “Predicted_celltypes”.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data as R object from Seurat package, includes scATAC fragments counts as “gene activity” over promoter region in the RNA assay. Integrated assay includes integration with scRNA-seq Falcao, van Bruggen et al. 2018.

extract_protocol:
Immediately after dissociation, cells were fixed in 1% formaldehyde (28906, ThermoFisher Scientific) for 10 minutes and quenched with glycine (125 mM) for 5 minutes at room temperature and then washed and stored in 0.5% BSA in PBS with 0.1% sodium azide at 4°C until further processing. The cells were counted and aliquots of 500.000 cells were centrifuged for 10 minutes at 1000xg and room temperature. Cells were resuspended in lysis buffer (containing 0.05% IGEPAL (CA-630), 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) and incubated for 5 minutes at room temperature. After a 20-minute centrifugation at 1000xg at room temperature, the cells were incubated with anti-GFP antibody (FITC, 1:100, Ab6662, Abcam) and DAPI (0.5 ug/ml) in PBS containing 5% BSA for 20 minutes at room temperature. The cells were centrifuged for 10 minutes at 1000xg and resuspended in tagmentation mix (dH2O, 2x TD buffer (Wang et al., 2013) and Tn5 enzyme (Picelli et al., 2014)) and incubated for 30 minutes at 37°C. For both lysis and tagmentation buffers the volume was scaled up to match the number of cells (50 ul per 50.000 cells). Tagmentation reaction was stopped by addition of 40 mM EDTA. Cells were then centrifuged for 10 minutes at 1000xg and room temperature and resuspended in PBS + 0.5% BSA. Sox10 GFP+/DAPI+ cells were sorted on an Influx (BD Biosciences) in reverse crosslinking buffer (Chen et al., 2018) with single cells in each well of 96 well plates. Also Sox10 GFP-/DAPI+ cells were sorted as a negative control for the OL lineage. The plates were incubated overnight at 65°C ending with 10 minutes at 80°C the next day. PCR master mixes (NEBNext High fidelity, M0541S, NEB) containing unique barcoding primers per well were dispensed on top of the reverse crosslinking buffer and DNA was amplified with the following cycling conditions: 72°C for 5 min, 98°C for 30s; 20 cycles at 98°C for 10s, 63°C for 30s and 72°C for 1 min. PCR products were purified with the MinElute purification kit (Qiagen) and then PAGE purified to remove adapter dimers. Three EAE and two CFA-control animals were used for independent replicates. Libraries were sequenced on an Illumina Hiseq 2500 with a 50-8-8-50 read set-up and a minimum of 25 000 read pairs per cell.
scATACseq (PI-ATAC Chen et al., 2018)


title: 4h_PE_1_tub

address: 700 CRB, 415 Curie Blvd


title: P11056_1163


title: 4h_Iso_6_tub

description: total RNA from mouse heart tissue harvested after 4 hours of 5mg/kg isoproterenol injection


title: 4h_Iso_5_tub


title: NaCl treatment rep2 [NaCl_2]

city: Xiamen

first: Hongrui

last: Zhu

state: Fujian

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District, Xiamen, Fujian Province, China

institute: Xiamen University

description: HDAC3 inhibitor vs NaCl.txt

data_processing:
Preparation included 75-bp paired-end reads, and the sequencing run was carried out over 5 lanes. On average, 55 million reads were obtained. Reads were aligned to the mouse GRCm38 reference genome using STAR (v.2.4.0), and an average uniquely aligned rate of 80.9 ± 1.1% (mean ± s.e.m.) was obtained. Read counts for RefSeq genes (mm10) were generated by HTSeq v.0.6.1. Low-count genes were filtered, and fragments per kilobase per million mapped reads (FPKM) values were generated. Differentially expressed genes were identified using the Limma package.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample;Matrix table with raw gene counts for every gene and every sample.

extract_protocol:
Brain tissues were removed and RNA was extracted using Trizol reagent. INEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® was used with 1 ug of total RNA. for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RGFP109 (RGFP109, Selleck Chemicals) was dissolved in DMSO and diluted in 30% (w/v) hydroxypropyl-β-cyclodextrin (#HK388-5g, Bio Basic Inc., Toronto, Canada) with100 mM sodium acetate (pH 5.4). Then, RGFP109 was administered subcutaneously once per day for 2 weeks with 60 mg/kg dose.

tag: strain background

value: amygdala

tag: days

value: PTS + RS (stroke mice with plus restraint stress)


title: NaCl treatment rep1 [Nacl_1]

description: HDAC3 inhibitor vs NaCl.txt

value: cortex


title: P11056_1161

first: Eneritz

institute: Karolinska Institutet


title: P11056_1160


title: 4h_Iso_4_tub


title: P11056_1159


title: Trizol-301KO-2-2


title: P11056_1158


title: HDAC3 inhibitor treatment rep1 [H3_1]

description: HDAC3 inhibitor vs NaCl.txt


title: 4h_Iso_3_tub


title: P11056_1156


title: P11056_1155


title: RS rep2 [B2RS]

description: PTS + RS vs RS.txt

value: RS (restraint stress)


title: Trizol-WT-2-2


title: 4h_Iso_2_tub


title: 4h_Iso_1_tub


title: P11056_1154


title: 4h_Ctrl_6_tub

description: total RNA from mouse heart tissue harvested after 4 hours of ascorbic acid injection


title: RS rep1 [B1RS]

description: PTS + RS vs RS.txt


title: P11056_1151


title: P11056_1153


title: P11056_1152


title: P11056_1150


title: PTS + RS rep2 [A2PR]

description: PTS + RS vs RS.txt


title: P11056_1166


title: P11056_1148


title: 4h_Ctrl_5_tub


title: PTS + RS rep1 [A1PR]

description: PTS + RS vs RS.txt


title: P11056_1147


title: HDAC3 inhibitor treatment rep2 [H3_2]

description: HDAC3 inhibitor vs NaCl.txt


title: P11056_1149


title: 4h_Ctrl_4_tub


title: P11056_1162


title: P11056_1143


title: P11056_1145


title: P11056_1146


title: P11056_1142


title: P11056_1157


title: P11056_1144