title: GRA415A174

description: PTB Culture Positive


title: GRA415A171

status: Public on Sep 04 2021

type: SRA

city: London

first: Anne

last: OGarra

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Insititue

description: PTB Culture Positive

library_source: transcriptomic

data_processing:
Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long.The filtered reads were aligned to the Homo sapiens genome Ensembl GRCh38 (release 95) using HISAT2 v2.1.0 with default settings and RF rna-strandedness. The mapped and aligned reads were quantified to obtain the gene-level counts using HtSeq v0.6.1 with default settings and reverse strandedness
Raw readcounts were processed using the bioconductor package DESeq2 v.1.12.4 in R v.3.5.1 and normalized using the DESeq method to remove the library-specific artefacts. Genes with 5 read counts or more in at least 12 samples were considered and normalized with variance stabilizing transformation to obtain normalized log2 gene expression values.
Genome_build: Ensembl GRCh38 (release 95)
Supplementary_files_format_and_content: VST log2 normalised expression values. Rows = genes; Columns = samples.

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Total RNA was isolated, from blood from tuberculosis progressors and Treatment reponse cohorts, and IGRA-ve healthy controls simultaneously, from 1ml whole blood using the MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit . Globin RNA was depleted from the total RNA (1.5–2 μg) using the human GLOBINclear kit.
Samples (200 ng) with an RQS > 6 were used to prepare a cDNA library using the TruSeq Stranded mRNA HT Library Preparation Kit (Illumina). The tagged libraries were sized and quantitated in duplicate (Agilent TapeStation system) using D1000 ScreenTape and reagents (Agilent), normalised, pooled and then clustered using the HiSeq® 3000/4000 PE Cluster Kit (Illumina). The libraries were imaged and sequenced on an Illumina HiSeq 4000 sequencer using the HiSeq® 3000/4000 SBS kit (Illumina) at a minimum of 25 million paired-end reads (100 bp) per sample

tag: patient id

tag: subgroup

value: PTB Culture Positive

tag: group

value: PTB

tag: gender

value: F

value: Positive

tag: igra

value: Pos

tag: resistance

tag: ethnicity

value: British

value: UK Born

tag: age


title: GRA415A168

description: PTB Culture Positive


title: GRA415A173

description: PTB Culture Positive


title: GRA415A169

description: PTB Culture Positive


title: GRA415A170

description: PTB Culture Positive


title: GRA415A165

description: PTB Culture Positive

value: M


title: GRA415A161

description: PTB Culture Positive


title: GRA415A167

description: PTB Culture Positive


title: GRA415A158

description: PTB Culture Positive


title: GRA415A160

description: PTB Culture Positive


title: GRA415A164

description: PTB Culture Positive


title: GRA415A155

description: PTB Culture Positive


title: GRA415A156

description: PTB Culture Positive


title: GRA415A157

description: PTB Culture Positive


title: GRA415A154

description: PTB Culture Positive


title: GRA415A152

description: PTB Culture Positive


title: GRA415A163

description: PTB Culture Positive


title: GRA415A162

description: PTB Culture Positive


title: GRA415A149

description: Other TB Progressor

value: Other TB Progressor

value: Negative

value: FS

value: South Asia (ISC)

value: Foreign Born


title: GRA415A153

description: PTB Culture Positive


title: GRA415A146

description: Other TB Progressor

value: Incipent TB


title: GRA415A151

description: Other TB Progressor


title: GRA415A148

description: Other TB Progressor

value: Clinical TB


title: GRA415A150

description: Other TB Progressor


title: GRA415A144

description: PTB Culture Positive

value: similar

value: East African (Somalia)


title: GRA415A138

description: PTB Culture Positive

value: PTB Culture Positive


title: GRA415A140

description: PTB Culture Positive

value: PTB


title: GRA415A145

description: Other TB Progressor

value: F


title: GRA415A139

description: PTB Culture Positive

value: Positive


title: GRA415A142

description: PTB Culture Positive

value: Pos


title: GRA415A159

description: PTB Culture Positive

value: British


title: GRA415A143

description: PTB Culture Positive


title: GRA415A141

description: PTB Culture Positive


title: GRA415A147

description: Other TB Progressor


title: GRA415A137

description: PTB Culture Positive


title: GRA415A133

description: PTB Culture Positive

value: East African (Sudan)


title: GRA415A129

description: PTB Culture Positive

value: M


title: GRA415A128

description: PTB Culture Positive


title: GRA415A132

description: PTB Culture Positive


title: GRA415A135

description: PTB Culture Positive


title: GRA415A127

description: PTB Culture Positive

value: weaker

value: South Asia (Sri Lanka)


title: GRA415A124

description: PTB Culture Positive


title: GRA415A180

description: PTB Culture Positive


title: GRA415A126

description: PTB Culture Positive


title: GRA415A122

description: PTB Culture Positive


title: GRA415A125

description: PTB Culture Positive


title: GRA415A131

description: PTB Culture Positive

value: Negative


title: GRA415A123

description: PTB Culture Positive


title: GRA415A120

description: PTB Culture Positive


title: GRA415A134

description: PTB Culture Positive


title: GRA415A113

description: PTB Culture Positive

value: South Asia (ISC)


title: GRA415A117

description: PTB Culture Positive

value: Foreign Born


title: GRA415A116

description: PTB Culture Positive


title: GRA415A115

description: PTB Culture Positive


title: GRA415A136

description: PTB Culture Positive


title: GRA415A130

description: PTB Culture Positive


title: GRA415A114

description: PTB Culture Positive


title: GRA415A111

description: PTB Culture Positive


title: GRA415A112

description: PTB Culture Positive


title: GRA415A119

description: PTB Culture Positive


title: GRA415A109

description: PTB Culture Positive


title: GRA415A107

description: TB Drug Resistance

value: TB Drug Resistance

value: H, E

value: Central Europe (Poland)


title: GRA415A110

description: PTB Culture Positive


title: GRA415A105

description: TB Drug Resistance


title: GRA415A106

description: TB Drug Resistance


title: GRA415A104

description: TB Drug Resistance


title: GRA415A100

description: TB Drug Resistance


title: GRA415A108

description: PTB Culture Positive


title: GRA415A118

description: PTB Culture Positive


title: GRA415A103

description: TB Drug Resistance


title: GRA415A121

description: PTB Culture Positive


title: GRA415A95

description: Other TB Progressor

value: Other TB Progressor


title: GRA415A181

description: PTB Culture Positive

value: PTB Culture Positive


title: GRA415A102

description: TB Drug Resistance

value: PTB


title: GRA415A89

description: Other TB Progressor


title: GRA415A101

description: TB Drug Resistance


title: GRA415A96

description: Other TB Progressor


title: GRA415A84

description: Other TB Progressor

value: Subclinical TB


title: GRA415A82

description: PTB Culture Positive

value: Positive


title: GRA415A94

description: Other TB Progressor

value: Pos


title: GRA415A79

description: PTB Culture Positive


title: GRA415A97

description: TB Drug Resistance


title: GRA415A98

description: TB Drug Resistance


title: GRA415A88

description: Other TB Progressor


title: GRA415A99

description: TB Drug Resistance


title: GRA415A86

description: Other TB Progressor


title: GRA415A93

description: Other TB Progressor


title: GRA415A85

description: Other TB Progressor


title: GRA415A92

description: Other TB Progressor


title: GRA415A81

description: PTB Culture Positive


title: GRA415A91

description: Other TB Progressor


title: GRA415A87

description: Other TB Progressor


title: GRA415A80

description: PTB Culture Positive


title: GRA415A77

description: PTB Culture Negative

value: PTB Culture Negative


title: GRA415A78

description: PTB Culture Positive

value: PTB_sampled before diagnosis

value: Clinical TB


title: GRA415A83

description: PTB Culture Positive

value: M


title: GRA415A90

description: Other TB Progressor

value: weaker


title: GRA415A76

description: PTB Culture Negative

value: Negative


title: GRA415A74

description: PTB Culture Negative

value: South Asia (ISC)


title: GRA415A73

description: PTB Culture Negative

value: Foreign Born


title: GRA415A75

description: PTB Culture Negative


title: GRA415A69

description: PTB Culture Positive


title: GRA415A68

description: PTB Culture Positive


title: GRA415A67

description: PTB Culture Positive


title: GRA415A71

description: PTB Culture Negative


title: GRA415A70

description: PTB Culture Positive


title: GRA415A72

description: PTB Culture Negative


title: GRA415A66

description: PTB Culture Positive


title: GRA415A65

description: PTB Culture Positive


title: GRA415A59

description: PTB Culture Positive

value: similar

value: East African (Zimbabwe)


title: GRA415A54

description: PTB Culture Positive

value: F


title: GRA415A58

description: PTB Culture Positive


title: GRA415A63

description: PTB Culture Positive


title: GRA415A62

description: PTB Culture Positive


title: GRA415A60

description: PTB Culture Positive


title: GRA415A53

description: PTB Culture Positive


title: GRA415A56

description: PTB Culture Positive


title: GRA415A51

description: PTB Culture Positive


title: GRA415A52

description: PTB Culture Positive


title: GRA415A64

description: PTB Culture Positive


title: GRA415A57

description: PTB Culture Positive


title: GRA415A50

description: PTB Culture Positive


title: GRA415A47

description: PTB Culture Positive


title: GRA415A61

description: PTB Culture Positive


title: GRA415A49

description: PTB Culture Positive


title: GRA415A43

description: PTB Culture Positive


title: GRA415A44

description: PTB Culture Positive


title: GRA415A46

description: PTB Culture Positive


title: GRA415A45

description: PTB Culture Positive


title: GRA415A41

description: PTB Culture Positive


title: GRA415A42

description: PTB Culture Positive


title: GRA415A40

description: PTB Culture Positive


title: GRA415A55

description: PTB Culture Positive


title: GRA415A39

description: PTB Culture Positive


title: GRA415A37

description: PTB Culture Positive


title: GRA415A38

description: PTB Culture Positive


title: GRA415A48

description: PTB Culture Positive


title: GRA415A34

description: PTB Culture Positive


title: GRA415A36

description: PTB Culture Positive


title: GRA415A35

description: PTB Culture Positive


title: GRA415A33

description: PTB Culture Positive


title: GRA415A32

description: PTB Culture Positive


title: GRA415A30

description: Other TB Progressor

value: Other TB Progressor

value: Unknown (OOA)


title: GRA415A27

description: TB Drug Resistance

value: TB Drug Resistance

value: PTB

value: H


title: GRA415A29

description: Other TB Progressor

value: Positive

value: Pos


title: GRA415A23

description: TB Drug Resistance


title: GRA415A24

description: TB Drug Resistance


title: GRA415A20

description: TB Drug Resistance


title: GRA415A21

description: TB Drug Resistance


title: GRA415A22

description: TB Drug Resistance


title: GRA415A25

description: TB Drug Resistance


title: GRA415A28

description: Other TB Progressor

value: Incipent TB


title: GRA415A26

description: TB Drug Resistance


title: GRA415A18

description: TB Drug Resistance


title: GRA415A17

description: TB Drug Resistance


title: GRA415A16

description: TB Drug Resistance


title: GRA415A15

description: TB Drug Resistance


title: GRA415A12

description: TB Drug Resistance


title: GRA415A14

description: TB Drug Resistance


title: GRA415A11

description: TB Drug Resistance


title: GRA415A10

description: TB Drug Resistance

value: Z


title: GRA415A8

description: TB Drug Resistance

value: M


title: GRA415A9

description: TB Drug Resistance


title: GRA415A13

description: TB Drug Resistance

value: weaker


title: GRA415A31

description: PTB Culture Positive

value: PTB Culture Positive

value: Negative


title: GRA415A7

description: TB Drug Resistance

value: South Asia (ISC)

value: Foreign Born


title: H_QG_2

city: Harbin

first: ziwei

last: zhang

state: Heilongjiang

address: No. 600, Changjiang Road, Xiangfang District

country: China

institute: Northeast Agricultural University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: TXT file contains counts for each sample

organism: Gallus gallus

source_name: trachea

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Anhydrous hydrogen sulfide was metered continuously into chambers H (the hydrogen sulfide group) to maintain 24-h levels of 3.5≤H2S≤4.5 mg/kg from week 0 to 3, and 19.5≤H2S≤20.5 mg/kg, from week 4 to 6. No H2S was added to chamber C (the control group).

tag: tissue

value: trachea

tag: stress

value: hydrogen sulfide


title: C_QG_2

value: control


title: GRA415A4

description: TB Drug Resistance


title: GRA415A19

description: TB Drug Resistance


title: C_QG_1


title: GRA415A2

description: TB Drug Resistance


title: GRA415A3

description: TB Drug Resistance


title: GRA415A5

description: TB Drug Resistance


title: H_QG_1


title: RT5: Blood monocyte RT rep5

city: Genève

first: Noushin

last: Hadadi

address: 1 rue Michel-Servet

department: Physiology and Cellular Metabolism

country: Switzerland

institute: University of Geneva

data_processing:
The reads were mapped with STAR aligner v.2.5.3a to the UCSC Mus musculus mm10
reference. The average mapping rate is 80 %.
The transcriptome metrics were evaluated with the Picard tools v.1.141
The table of counts with the number of reads mapping to each gene feature of the UCSC Mus
Genome_build: musculus mm10 was prepared with HTSeq v0.6p1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: blood-monocytes

extract_protocol:
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Cells were sorted into RLT buffer and their RNA extracted using Qiagen RNeasy kit. Illumina RNA Kits were used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
TruSeq stranded mRNA kit

treatment_protocol: Cold exposure at 10 °C for 2 weeks with an initial acclimatization period of 5 days at 18°C and 5 days at 14°C

tag: strain

value: male

value: blood-monocytes

value: week 11

tag: genotype

value: wild type

tag: treatment

value: RT


title: RT3: Blood monocyte RT rep3


title: GRA415A6

description: TB Drug Resistance

value: TB Drug Resistance

value: PTB

value: Positive

value: Pos


title: RT2: Blood monocyte RT rep2


title: CE4: Blood monocyte CE rep4

value: CE


title: RT1: Blood monocyte RT rep1


title: RT4: Blood monocyte RT rep4


title: CE3: Blood monocyte CE rep3


title: CE2: Blood monocyte CE rep2


title: GRA415A1

description: TB Drug Resistance

value: M

value: Z


title: CE1: Blood monocyte CE rep1


title: ER-nonrecurrence, biological rep05

type: RNA

city: Shanghai

first: Enuo

last: Liu

address: 2140 Xietu Road

institute: Shanghai Institute for Biomedical and Pharmaceutical Technologies

description: gene expression data from ER- breast cancer tissue with positive lymph nodes

hyb_protocol: Labeled cDNA samples were used to hybridize to microarrays.

scan_protocol: After washing and staining, the microarrays were scanned by the Affymetrix Scanner 3000 (Affymetrix).

data_processing: For microarray analysis, Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for gene analysis.

label: biotin

source_name: FFPE of breast tissue

label_protocol: Briefly, total RNAs were transcribed to double strand cDNAs and purification. Next, 2nd cycle cDNAs were uesd to followed fragmentation and biotin labeling.

growth_protocol: Twenty-five FFPE samples of ductual breast cancer patients with recurrent cancer and 12 FFPE samples of ductal breast cancer patients with no recurrence were selected to analyze the gene expression difference.

extract_protocol: The RecoverAll™ Total Nucleic Acid Isolation Kit (AMBION, AM1975) was used to extract total RNA from paraffin-embedded (FFPE) tissues according to the manufacturer’s protocol.

treatment_protocol: Sections of formalin-fixed paraffin embedded (FFPE) were prepared from frozen fresh breast tumors of patients and well preserved.

value: ER- tumor tissue without recurrence


title: ER-nonrecurrence, biological rep06


title: BR3: Blood monocyte EAE RE rep3

value: week 12

value: RT-EAE


title: ER-nonrecurrence, biological rep04


title: Control_3

city: China

first: Liu

last: longbin

state: Zhejiang province

address: 568 Zhongxing N Rd, Yuecheng District, Shaoxing, Zhejiang, China575 Pingjiang Rd, Yuecheng District, Shaoxing, Zhejiang, China

institute: Affiliated Hospital of Shaoxing University

description: Gene expression in healthy human serum

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G5761A) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Serum

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.25 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit (Norgen Biotek,Ontario, Canada) following the manufacturer's recommendations.RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Serum

tag: disease state


title: ER-nonrecurrence, biological rep01


title: ER-recurrence, biological rep08

value: ER- tumor tissue with recurrence


title: ER+nonrecurrence, biological rep06

description: gene expression data from ER+ breast cancer tissue with positive lymph nodes

value: ER+ tumor tissue without recurrence


title: ER-nonrecurrence, biological rep02


title: SBR-84h_B

first: Marietta

last: Zinner

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

description:
barcodes.tsv.gz
genes.tsv.gz
UMI_counts_spliced_raw.mtx.gz
UMI_counts_unspliced_raw.mtx.gz
UMI_counts_spliced_normalized_log2.mtx.gz

data_processing:
Reference and Quantification: In order to estimate levels of both spliced transcripts and introns for use in RNA velocity analysis, a reference for pseudo-alignment was constructed similar to the "alevin_sep_gtr" method described in [REF: https://doi.org/10.1371/journal.pcbi.1008585]: Genome sequence and transcript annotation was obtained from Gencode Mouse release M24 (GRCm38 primary assembly and annotation gtf file from ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M24), and the coordinates of transcripts and introns were extracted using R (https://r-project.org, version 3.6) and the getFeatureRanges function from the eisaR package (version 0.9 available from https://github.com/fmicompbio/eisaR/tree/bbd8787d7e4b87d158a276af0787226530867b88) with arguments featureType = c("spliced", "intron"), intronType = "separate", flankLength = 0, joinOverlappingIntrons = FALSE. A transcript-to-gene map was created using the getTx2Gene function from eisaR, which links transcripts to genes, and introns to distinct genes for simultaneous quantification (see below). Sequences were extracted from the genome using extractTranscriptSeqs from the GenomicFeatures package (version 1.38.2, [REF: https://doi.org/10.1371/journal.pcbi.1003118]) and indexed with Salmon (version 1.1.0, [REF: https://doi.org/10.1038/nmeth.4197]) with arguments -k 23 –gencode and using the genome as a decoy. Reads were then quantified using Salmon/Alevin (version 1.1.0, [REF: https://doi.org/10.1186/s13059-019-1670-y]) with parameters -l ISR --chromiumV3 and the transcript-to-gene map created above.
Quality control and filtering: Technical quality of single cell experiments, cell barcode identification and quantification were assessed using the Bioconductor package alevinQC (version 1.4.0, https://doi.org/doi:10.18129/B9.bioc.alevinQC). Salmon/Alevin counts from all six timepoints were imported into R (version 4.0.2) using the tximeta package (version 1.6.3, [REF: https://doi.org/10.1371/journal.pcbi.1007664]) and stored in a SingleCellExperiment container for downstream analysis (54446 genes, 41270 cells). The number of detected genes per cell and the fraction of counts in genes encoded on the mitochondrion (chrM) were calculated using the addPerCellQC function from the scater package (version 1.16.2, [REF: https://doi.org/10.1093/bioinformatics/btw777]), and cells with more than 1800 detected genes and less than 10% mitochondrial counts were retained. Furthermore, ribosomal protein genes (genes associated with the GeneOntology term "structural constituent of ribosome", GO:0003735, based on the org.Mm.eg.db package, version 3.11.4) were removed, resulting in a final analysis set of 54298 genes and 33964 cells.
Cell type annotation: Cell size factors for normalization of raw counts were calculated using the scran package (version 1.16.0, [REF: https://doi.org/10.12688/f1000research.9501.2]), by first clustering the cells using the quickCluster function with method="igraph" and then computeSumFactors with min.mean=0.5, which implements the deconvolution strategy described in [REF: https://doi.org/10.1186/s13059-016-0947-7]. Log-transformed normalized counts were then calculated using the logNormCounts function from the scater package. A similarly processed single cell transcriptomics dataset with cell type classification from [REF: https://doi.org/10.1038/s41586-019-0933-9] was obtained using the EmbryoAtlasData function from the MouseGastrulationData package (version 1.2.0, https://doi.org/doi:10.18129/B9.bioc.MouseGastrulationData). The cell type labels from the published dataset were then transferred to our data using the SingleR function from the SingleR package (version 1.2.4, [REF: https://doi.org/10.1038/s41590-018-0276-y]) with default parameters and pruning.
Genome_build: GRCm38 primary assembly
Supplementary_files_format_and_content: barcodes.tsv.gz: tab-seperated text file with two column containing cell barcodes and cell type annotation (columns of mtx files); genes.tsv.gz: tab-separated text file with two columns containing gene ENSEMBL identifier and Symbol (rows of mtx files); *.mtx.gz: sparse matrices in MatrixMarket format of dimensions 54298 rows (genes) by 33964 columns (cell barcodes). Three separate count matrices are provided: UMI_counts_spliced_raw.mtx.gz - raw UMI counts from spliced transcripts; UMI_counts_unspliced_raw.mtx.gz - raw UMI counts from introns; UMI_counts_spliced_normalized_log2.mtx.gz - normalized, log2-transformed UMI counts from spliced transcripts.

molecule: polyA RNA

source_name: Gastruloids

growth_protocol: ESCs were grown in GMEM supplemented with 10% embryonic stem cell qualified FBS, GlutaMAX, sodium pyruvate, EmbryoMAX MEM NEAA, beta-mercaptoethanol, 0.1 µg/ml LIF, 3 µM CHIR99021, and 1 µM PD0305901. Gastruloids were generated from 300 cells and grown in 96-well ulta-low-attachment U-bottom plates in N2B27 medium (DMEM/F-12, Neurobasal medium, N2, B-27, GlutaMAX, HEPES, and beta-mercaptoethanol) and pulsed with 3 µM CHIR99021 from 48 to 72 hours.

extract_protocol:
Gastruloids (24h: 240 gastruloids; 36h: 96 gastruloids; 48h: 48 gastruloids; 60h: 48 gastruloids; 72h: 24 gastruloids; 84h: 2x 24 gastruloids) were dissociated with Accutase and per sample 12,000 alive cells were sorted by FACS. Cellular supensions were loaded on a 10x Genomics Chromium Single Cell instrument.
Single cell RNAseq libraries were prepared using the 10x Genomics Single Cell 3’ Gel Bead and Library Kit according to CG000183 Single Cell 3' Reagent Kit v3 User Guide_RevA. GEMRT was performed in a Bio-Rad PTC-200 Thermal Cycler with 0.2ml PCR Tube Strips (Eppendorf P/N 0030 124.359): 53 °C for 45 minutes, 85 °C for 5 minutes; held at 4 °C. After RT, GEMs were broken and the single strand cDNA was cleaned up with DynaBeads® MyOneTM Silane Beads (Life Technologies P/N 37002D). cDNA was amplified using a Bio-Rad PTC-200 Thermal cycler with 0.2ml PCR Tube Strips (Eppendorf P/N 0030 124.359): 98 °C for 3 min; cycled 11x: 98 °C for 15 s, 63 °C for 20 s, and 72 °C for 1 min; 72 °C for 1 min; held at 4 °C. Amplified cDNA product was cleaned up with the SPRIselect Reagent Kit (0.6X SPRI). Indexed sequencing libraries were constructed using the reagents in the Chromium Single Cell 3’ library kit V3 ( 10x Genomics P/N1000078), following these steps: 1) Fragmentation, End Repair and A-Tailing; 2) Post Fragmentation, End Repair & A-Tailing Double Sided Size Selection with SPRIselect Reagent Kit (0.6X SPRI and 0.8X SPRI); 3) adaptor ligation; 4) post-ligation cleanups with SPRIselect (0.8X SPRI); 5) sample index PCR using the Chromium Multiplex kit (10x Genomics P/N-120262); 6) Post Sample Index Double Sided Size Selection- with SPRIselect Reagent Kit (0.6X SPRI and 0.8X SPRI). The barcode sequencing libraries were quantified using a Qubit 2.0 with a Qubit TM dsDNA HS Assay Kit (Invitrogen P/N Q32854) and the quality of the libraries were performed on a 2100 Bioanalyzer from Agilent using an Agilent High Sensitivity DNA kit (Agilent P/N 5067-4626). Sequencing libraries were loaded at 1.6pM on an Illumina Nextseq500 with 75cycle kits using the following read length: 28 cycles Read1, 8 cycles i7 Index and 56 cycles Read2.

treatment_protocol: Gastruloids were not treated.

tag: cell type

value: embryonic stem cells

tag: cell line

value: SBR (Sox1/Brachyury reporter)/CGR8

tag: time point


title: Control_2

description: Gene expression in healthy human serum

value: control


title: ER-recurrence, biological rep01


title: ER-recurrence, biological rep09


title: Control_1

description: Gene expression in healthy human serum


title: ER-recurrence, biological rep02


title: ISR_3

description: Gene expression in In-stent Restenosis human serum

value: In-stent Restenosis


title: ER-nonrecurrence, biological rep03


title: ISR_2


title: ER-recurrence, biological rep05


title: ER-recurrence, biological rep07


title: ER-recurrence, biological rep06


title: BR2: Blood monocyte EAE RE rep2

value: male

value: blood-monocytes

value: wild type


title: BC4: Blood monocyte EAE CE rep4

value: CE-EAE


title: ER+nonrecurrence, biological rep04


title: ER+nonrecurrence, biological rep05


title: ISR_1


title: ER+nonrecurrence, biological rep03


title: BR1: Blood monocyte EAE RE rep1


title: SBR-84h_A


title: ER-recurrence, biological rep03


title: ER-recurrence, biological rep04


title: BC2: Blood monocyte EAE CE rep2


title: D20RT7: Spinalcord d20 RT rep5

source_name: spinal cord

value: spinal cord

value: week 14


title: BC3: Blood monocyte EAE CE rep3


title: SBR-72h


title: D20RT5: Spinalcord d20 RT rep3


title: BC1: Blood monocyte EAE CE rep1


title: D20RT6: Spinalcord d20 RT rep4


title: ER+nonrecurrence, biological rep02


title: SBR-36h


title: SBR-60h


title: SBR-48h


title: D20RT4: Spinalcord d20 RT rep2


title: D20RT3: Spinalcord d20 RT rep1


title: D20CE8: Spinalcord d20 CE rep5


title: SBR-24h


title: D20CE7: Spinalcord d20 CE rep4


title: 08-20_KO_S7

city: Boston

first: Yushi

last: Hayashi

state: MA

address: 243 Charles St

department: Department of Otolaryngology

country: USA

institute: Harvard Medical School

data_processing:
base-calling/read filtering: Illumina Real-Time Analysis (RTA) version 2.4.11
demultiplexing/adapter trimming: bcl2fastq2 v2.20; --barcode-mismatches 0 --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --minimum-trimmed-read-length 1 --no-lane-splitting
Pseudoalignments with salmon,0.14.2
Differntial expresison with tximport 1.14.0 and DESeq2 1.26.0
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements

source_name: Cochlea hair cells_KO

extract_protocol:
12-20 cochlear sensory epithelia were dissected, then collected into a tube. After being trypsinized with TrypLE and mechinically dissociated, the cells were pelletized with a centrifuge. The pellet was suspended in PBS, then hair cells were sorted with a hair cell marker, Atoh1-GFP. Total RNA was extracted from the sorted hair cells using the RNeasy Plus Micro Kit.
Full-length cDNA was prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA, Inc., 640170) with 1.6-2.4 pg of total RNA and sequencing libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096).

tag: strain background

value: mixed C57BL/6 and 129

value: Ndp KO

value: Postnatal day 4-6

tag: tissue/cell type

value: Cochlea hair cells


title: 08-15_WT1_S1

source_name: Cochlea hair cells_WT

value: WT


title: 07-30_KO_S5


title: 06-19_KO_S8


title: ER+recurrence, biological rep12

value: ER+ tumor tissue with recurrence


title: 07-25_KO_S6


title: sn-RNAseq of Pangolin Liver

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

description: single-cell gene expression of Manis javanica

data_processing:
Library strategy: snRNA-Seq
To facilitate the integration of cross-species lung single cell dataset, we converted genes from other species to mouse homologs. Firstly, we downloaded homologs between eight species (cat, tiger, dog, hamster, goat, rabbit, lizard, duck) and mouse using BioMart. As for pangolin, pigeon and deer, which lack homologs records on Ensemble. single-copy orthologs were identified from two species genomes, by cluster analysis of gene families using OrthoFinder (OrthoFinder version 2.3.3) with the default parameters. The single-copy genes were extracted from the OrthoFinder output file. Then, if a 1:1 match existed between a non-mouse gene and a mouse gene, the non-mouse gene name was converted to the mouse gene name.
Sequencing data were filtered using custom script and gene expression matrix were obtained by Cell Ranger 3.0.2 (10X Genomics).
Genome_build: dog: GCF_000002285.3; duck: GCA_002743455.1; tiger: GCF_000464555.1; hamster: GCA_000349665.1; lizard: GCA_000090745.1; pangolin: GCF_001685135.1; pigeon: GCF_000337935.1; goat: GCA_001704415.1; cat: GCA_000181335.4; rabbit: GCF_000003625.3.
Supplementary_files_format_and_content: tab-delimited text files include single cell-gene expression values for each Sample

organism: Manis javanica

source_name: Pangolin Liver

extract_protocol:
Tissue samples were obtained from a total of 11 animals, which included 1) four pet animals: a cat (Felis catus), a dog (Canis lupus familiaris), a hamster (Mesocricetus auratus) and a lizard (Anolis carolinensis); 2) two livestock species: a goat (Capra aegagrus hircus) and a rabbit (Oryctolagus cuniculus domesticus); 3) two poultry species: a duck (Anas platyrhynchos domesticus) and a pigeon (Columba livia domestica); 4) three wild animals: a tiger (Panthera tigris altaica), a pangolin (Manis javanica) and a deer (Cervus nippon). The Manis javanica samples were collected from a pangolin died of naturally cause in Guangdong Provincial Wildlife Rescue Center and were immediately stored in -80°C freezer after dissection. The samples from the tiger were obtained from a naturally dead tiger from the Siberian Tiger Park in Heilongjiang Province. Deer sample and corresponding genome assembly was kindly provided by institute of special animal and plant of sciences (ISAPS) of Chinese Academy of Agricultural Sciences. Other animals were obtained from farm market with the permissions from BGI Ethics Committee. Animals were kept in a pathogen-free environment and provided sufficient living space and adequate food and water. After the euthanasia of animals in accordance with the ethics of animal experiment guidelines issued by the Ministry of Science and Technology, China. Dissection was carried out quickly to separate each tissue. The collected tissues were rinsed by 1X PBS, then quick-frozen and stored in liquid nitrogen. The single cell nuclei of each tissue were separated by mechanical extraction method.85 Briefly, the tissues were first thawed, infiltrated by 1X homogenization buffer (containing 30mM CaCl2, 18mM Mg(Ac)2, 60mM Tris-HCl (pH 7.8), 320mM sucrose, 0.1% NP-40, 0.1mM EDTA and 0.2U/µl RNase inhibitor), then cut into smaller pieces, and the single nucleus was isolated by 2ml Dounce homogenizer set. After filtration with 30µm strainer, the nuclei extraction was resuspended by 1%BSA containing 0.2U/µl RNase inhibitor and span down at the speed of 500g for 10 min at 4°C (to carefully discard the cellular impurities within the supernatant). This step was repeated twice, and finally the nuclei were recollected with 0.1% BSA containing 0.2U/µl RNase inhibitor. Subsequently, DAPI was used to stain the nuclei, and the nucleus density was calculated under a fluorescence microscope to prepare for the subsequent library construction.
The separated single nucleus of different tissues were constructed using Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (PN-1000075) following the standard user guide provided by manufacturer.

value: Liver

value: Adult


title: sn-RNAseq of Pangolin Stomach

source_name: Pangolin Stomach

value: Stomach


title: sn-RNAseq of Hamster Lung

description: single-cell gene expression of Mesocricetus auratus

organism: Mesocricetus auratus

source_name: Hamster Lung

value: Lung


title: sn-RNAseq of Pangolin Lung

source_name: Pangolin Lung


title: sn-RNAseq of Pangolin Kidney

source_name: Pangolin Kidney

value: Kidney


title: sn-RNAseq of Pangolin Spleen

source_name: Pangolin Spleen

value: Spleen


title: sn-RNAseq of Pangolin Large intestine

source_name: Pangolin Large intestine

value: Large intestine


title: ER+recurrence, biological rep11


title: ER+recurrence, biological rep14


title: ER+recurrence, biological rep06


title: ER+recurrence, biological rep15


title: 08-01_WT_S2


title: ER+recurrence, biological rep13


title: ER+recurrence, biological rep16


title: ER+recurrence, biological rep10


title: D20CE6: Spinalcord d20 CE rep3

value: male

value: wild type


title: ER+recurrence, biological rep08


title: ER+nonrecurrence, biological rep01

value: ER+ tumor tissue without recurrence


title: ER+recurrence, biological rep04


title: ER+recurrence, biological rep01


title: 05-14_WT_281_S4


title: sn-RNAseq of Cat Rectum

description: single-cell gene expression of Felis catus

organism: Felis catus

source_name: Cat Rectum

value: Rectum


title: sn-RNAseq of Pangolin Heart

source_name: Pangolin Heart

value: Heart


title: ER+recurrence, biological rep03


title: sn-RNAseq of Cat Lung

source_name: Cat Lung


title: ER+recurrence, biological rep09


title: 07-25_WT_S3

value: mixed C57BL/6 and 129


title: D20CE5: Spinalcord d20 CE rep2

value: spinal cord

value: week 14

value: CE-EAE


title: sn-RNAseq of Cat Liver

source_name: Cat Liver


title: sn-RNAseq of Pangolin Esophagus

source_name: Pangolin Esophagus

value: Esophagus


title: ER+recurrence, biological rep02

source_name: FFPE of breast tissue

value: ER+ tumor tissue with recurrence


title: sn-RNAseq of Cat Heart

source_name: Cat Heart

value: Adult


title: ER+recurrence, biological rep07


title: ER+recurrence, biological rep05


title: bovine milk extracellular vesicles-rep3

city: Beijing

first: Xiao-Hui

last: Tan

address: 8, Xishiku Street, Xicheng District

institute: Peking University First Hospital

data_processing:
The sequences were added to the name of the read as a unique molecular identifier (UMI) using UMI tools.
The FASTQ data were checked using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence using cutadapt (version 2.7)
Perl5 (version 26) was used to process reads with UMIs less than 12bp and reads without UMI, and identify UMIs.
Trimmed reads were aligned to the reference database using Bowtie (version 1.2.2)
Small RNAs were mapped to miRBase and Rfam in sequence, and counted using customized R scripts
Genome_build: miRbase (version 22.1) & Rfam (version 14.4)
Supplementary_files_format_and_content: Matrix table with raw UMI counts and CPM values for every miRNA and every sample

organism: Bos taurus

source_name: extracellular vesicles

extract_protocol:
Extracellular vesicles were separated using a novel salting-out method. RNA was harvested from extracellular vesicles using Trizol reagent (Invitrogen/Life Technologies).
RNA libraries were constructed using QIAseq miRNA Library Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. Individual libraries were constructed using 100ng of total RNA isolated from each sample.

value: milk

value: normal

value: untreated

tag: sample type

value: extracellular vesicles


title: D20CE1: Spinalcord d20 CE rep1

source_name: spinal cord

tag: gender


title: sn-RNAseq of Pangolin Duodenum

source_name: Pangolin Duodenum

value: Duodenum


title: sn-RNAseq of Cat Esophagus

source_name: Cat Esophagus


title: WT,AC4620

city: Barcelona

first: Manuel

last: Morales-Ruiz

address: 170 Villarroel

country: Spain

institute: Hospital Clinic/IDIBAPS/Ciberehd

description: Stranded RNA

data_processing:
Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 2.7.6) and followed by generation of FASTQ sequence files by CASAVA.
Genes were quantified with RSEM version 1.2.2868 using the gencode M12 version.
Differential expression analysis was performed with DESeq2 version 1.1869 with default parameters.
Differential alternative splicing was performed with rMATS70.
Significant splicing events with FDR<5%, absolute inclusion difference >5% and >70 number of reads were considered significant.
Genome_build: RNA-seq reads were mapped against the mouse reference genome (GRCm38) using STAR version 2.5.2a67 with ENCODE parameters for long RNA.
Supplementary_files_format_and_content: FASTQ

source_name: Liver sinusoid

growth_protocol: Endothelial cells were cultured in Microvascular Endothelial Cell Growth Complete Medium (Pelobiotech, Planegg, Germany) in humified atmosphere at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol (Invitrogene) following the manufacturer's recommendations. Total RNA from Mus musculus was quantified by Qubit® RNA BR Assay kit (Thermo Fisher Scientific) and the RNA integrity was estimated by using RNA 6000 Nano Bioanalyzer 2100 Assay (Agilent).
The RNASeq libraries were prepared with KAPA Stranded mRNA-Seq Illumina® Platforms Kit (Roche-Kapa Biosystems) following the manufacturer´s recommendations. Briefly, 500ng of total RNA was used as the input material, the poly-A fraction was enriched with oligo-dT magnetic beads and the mRNA was fragmented. The strand specificity was achieved during the second strand synthesis performed in the presence of dUTP instead of dTTP. The blunt-ended double stranded cDNA was 3´-adenylated and Illumina indexed adapters (Illumina) were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay.
The libraries were sequenced on HiSeq 4000 (Illumina, Inc) in paired-end mode with a read length of 2x76bp using HiSeq 4000 SBS kit in a fraction of a HiSeq 4000 PE Cluster kit sequencing flow cell lane, following the manufacturer’s protocol

treatment_protocol: The silencing of DHX15 was carried out in mouse primary hepatic endothelial cells immortalized with the SV40 virus (LEC ; abmGood, Richmond, Canada), through shRNA by lentiviral infection (Dharmacon, Lafayette, Colorado, USA). The SMARTvector incorporated the bipartite 3G Tet-On® induction system, an inducible system with minimal basal expression and potent activation after induction with doxycycline.

value: liver sinusoidal endothelial cell


title: WT,AC4621

description: Stranded RNA


title: L-histidine rep3 (C3)

city: Muang District

first: Satoshi

last: Kubota

state: Nakhon Ratchasima

address: 111 University Avenue, Suranaree Sub-District,

country: Thailand

institute: Suranaree University of Technology

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument，image analysis and base calling were conducted by the NovaSeq Control Software (NCS) + OLB + GAPipeline-1.6 (Illumina) on the NovaSeq instrument，image analysis and base calling were conducted by the Zebeacall on the MGI2000 instrument.
Low-quality and technical sequences were removed from the raw sequencing reads using Cutadapt version 1.9.1
Hisat2 version 2.0.1 was used to align the clean reads against the chicken reference genome, GRCg6a (GenBank Assembly ID: GCA_000002315.5).
Gene expression levels were estimated based on fragments per kilobase of transcript per million fragments mapped (FPKM) using HTSeq version 0.6.1. The DESeq2 Bioconductor package was used for differential expression analysis between control and supplemented groups.
Genome_build: GRCg6a (GCA_000002315.5)
Supplementary_files_format_and_content: Column 1, gene_id: gene ID; Column 2, Exonic.gene.sizes:exon length; Column 3-17, Sample:count count of each gene; Column 18-32, Sample_FPKM: FPKM of each gene; Column 33-36, Chr, Start, End, Strand: gene location, including chromosome, start position, end position and strand; Column 37, GeneSymbol: gene symbol; Column 38, Description: gene description

source_name: Breast muscle

extract_protocol:
Total RNA was extracted from the breast muscle of fifteen chickens, one chicken from each replication of the treatment group, using TRIzol Reagent (Thermo Fisher Scientific, Massachusetts, USA).
The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, and fragments of ~400 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR andP5/ P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

tag: genetic line

value: Korat chicken

value: Breast muscle

value: 10 weeks of age

value: Supplemented with L-histidine


title: C3

first: wang

address: No.23, Postal street, Nangang distric

department: Neurosurgery

institute: First Affiliated hospital of Harbin Medical Univesity

library_source: genomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Bismark software was used to perform alignments of bisulfite-treated reads to a reference genome (-X 700 --dovetail). The reference genome was firstly transformed into bisulfite-converted version (C-to-T and G-to-A converted) and then indexed using bowtie2.
Sequence reads were transformed into fully bisulfite-converted versions (C-to-T and G-to-A converted) before they are aligned to similarly converted versions of the genome.
Genome_build: lambda genome
Supplementary_files_format_and_content: tab-delimited text files include values of methylation level for each Sample.The methylation level of each site equals to mC counts/(mC counts+umC counts).

molecule: genomic DNA

source_name: TLE patients without HS

extract_protocol:
After tissue homogenization, DNA was extracted according to the instructions of TIANamp Genomic DNA Kit (Cat#DP304)
A total amount of 5.2 microgram genomic DNA spiked with 26 ng lambda DNA were fragmented by sonication to 200-300bp with Covaris S220, followed by end repair and adenylation. DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), before the resulting single-strand DNA fragments were PCR amplificated using KAPA HiFi HotStart Uracil + ReadyMix (2X). Library concentration was quantified by Qubit® 2.0 Flurometer (Life Technologies, CA, USA) and quantitative PCR, and the insert size was assayed on Agilent Bioanalyzer 2100 system.

tag: subject status

value: temporal lobe epilepsy (TLE) patient

tag: hippocampal sclerosis

value: Without hippocampal sclerosis (HS)

tag: pathological type

value: No hippocampal sclerosis

value: Brain; Hippocampus


title: L-histidine rep2 (C2)

tag: tissue

tag: age


title: L-histidine rep1 (C1)


title: β-alanine rep3 (B3)

value: Supplemented with β-alanine


title: L-histidine rep5 (C5)


title: sn-RNAseq of Cat Kidney

source_name: Cat Kidney

value: Kidney


title: β-alanine rep5 (B5)


title: KO,AC4624

description: Stranded RNA

tag: strain

value: silenced for DHX-15 gene


title: KO,AC4625

description: Stranded RNA


title: sn-RNAseq of Cat Eyelid

source_name: Cat Eyelid

value: Eyelid

value: Adult


title: WT,AC4619

description: Stranded RNA

value: untreated


title: sn-RNAseq of Deer Lung

description: single-cell gene expression of Cervus nippon taiouanus

organism: Cervus nippon taiouanus

source_name: Deer Lung

value: Lung


title: KO,AC4623

description: Stranded RNA


title: L-histidine rep4 (C4)


title: I1-2

source_name: TLE patients with HS ILAE type1

value: With hippocampal sclerosis (HS)

value: International League Against Epilepsy (ILAE) type 1


title: bovine milk extracellular vesicles-rep1

value: milk

value: normal

value: extracellular vesicles


title: C1


title: β-alanine rep4 (B4)

value: Korat chicken

value: Breast muscle

value: 10 weeks of age


title: WT,AC4622

description: Stranded RNA

value: liver sinusoidal endothelial cell


title: Control rep2 (A2)

value: Non-supplemented


title: Control rep1 (A1)


title: I1-1

value: temporal lobe epilepsy (TLE) patient

value: Brain; Hippocampus


title: β-alanine rep2 (B2)

value: Supplemented with β-alanine


title: β-alanine rep1 (B1)


title: bovine milk extracellular vesicles-rep2


title: Control rep5 (A5)


title: OBOB_9

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

data_processing:
Raw-RNA-reads have been analysed using salmon,DESEQ2 and Whippet
Genome_build: mm10
Supplementary_files_format_and_content: Excle file with found splice events and differently gene expression values

source_name: pancreas

extract_protocol:
miRNeasy Mini Kit
done by company GATC (Eurofins)

tag: Sex

value: male


title: OBOB_11


title: Control rep3 (A3)

tag: treatment


title: KO,AC4626

description: Stranded RNA

value: silenced for DHX-15 gene


title: D28 Mtb infected_T863 treated animal10 [SD21]

city: New Delhi

first: Sheetal

last: Gandotra

address: Sukhdev Vihar, Mathura Road

department: Chemical and System Biology

country: India

institute: CSIR-Institute of Genomics and Integrative Biology

data_processing:
Adaptor sequence and low quality sequence were trimmed using Trimmomatic-0.39
Mapped to mm10 whole genome using HISAT2
Read counts were generated using FeatureCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with counts for each sample

source_name: D28 Mtb infected_T863 treated_whole lung

extract_protocol:
Total lung RNA extracted using RNAzol reagent, RNA samples were purified using RNeasy mini kit from Qiagen. Purified RNA was further treated with turbo Dnase and later 1 μg of total RNA was used for the construction of sequencing libraries.
A modified NEBNext 594 RNA Ultra II directional protocol was used to prepare the libraries for total RNA sequencing. 595 The first step involved the removal of ribosomal RNA of cytoplasmic and mitochondrial origin 596 using biotinylated, target-specific oligos combined with rRNA removal beads. Following 597 purification, the RNA was fragmented using divalent cations under elevated temperature. 598 Next, the cDNA was synthesized using Reverse transcriptase and random hexamers in a 599 first strand synthesis reaction. Subsequently, the cDNA was converted to double stranded 600 cDNA where Uracil was added instead of Thymine. The strand specificity was preserved by 601 a USER enzyme based digestion of second strand thereby leaving one functional strand 602 which maps to the DNA strand which it was transcribed from. The USER digested single 603 strand molecules were enriched and indexed in a limited cycle PCR followed by AMPure 604 bead purification to create final cDNA library for sequencing.

treatment_protocol: intravenouse treatment of infected mice for 3 weeks with T863 or vehicle control

value: M. tuberculosis infected mouse lung

value: T863 treated

tag: cfu group

value: low


title: D28 Mtb infected_T863 treated animal9 [SD20]


title: OBOB_8


title: D28 Mtb infected_T863 treated animal11 [SD23]

value: high


title: I1-3

value: With hippocampal sclerosis (HS)

value: International League Against Epilepsy (ILAE) type 1


title: 17608/6 iPSC

city: Esch-sur-Alzette

first: Kamil

last: Grzyb

email: kamilgen@gmail.com, kamil.grzyb@uni.lu

address: 2, avenue de l'Université

country: Luxembourg

institute: University of Luxembourg - LCSB

data_processing:
Bcl2fastq ver 2.0 was used for the base calling
Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation (Macosko et al; 2015), the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCm38.87 using STAR genome aligner - with default parameters
Genome_build: Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text files include raw counts

source_name: Fibroblasts

growth_protocol: Fibroblasts were cultured on gelatin-coated plates (10% gelatin in PBS, coated for 10 min at room temperature) in KO DMEM +10% FBS + 1% penicillin/streptomycin (stock was 10,000 units penicillin and 10 mg streptomycin ml-1) at standard culture conditions (37°C, 5% CO2).

extract_protocol:
Single cell RNA seq using Dropseq - 3' bead based enrichment technique, using SMART synthesis (Macosko et al, 2015 doi: 10.1016/j.cell.2015.05.002)
Libraries were prepared according to Drop-seq methods (Macosko et al, 2015 doi: 10.1016/j.cell.2015.05.002). After cDNA tagmenation, PCR amplification was performed using Illumina primers (N701,N702,N707,N710, A501). The purified cDNA fragments of ~600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.

treatment_protocol: The protocol used to differentiate iPSCs into mDA neurons was modified from24,121 (Table 1). The iPSCs were grown to 95% confluence, dissociated using accutase, and 1.5 wells were combined into one well at day -1. They were allowed to recover in the presence of ROCK inhibitor for about 8 hours and then in mTeSR without ROCK inhibitor for about 16 hours. After this, day 0 media were applied (Table 1).

value: Stem cells (iPSCs)

value: iPSC


title: C2

value: Without hippocampal sclerosis (HS)

value: No hippocampal sclerosis


title: OBOB_7


title: ND40066-8 iPSC


title: 17608/6 D50

value: iPSCs derived mDA neurons

value: mDA neurons differentiation protocol

tag: differentiation day


title: Control rep4 (A4)

value: Korat chicken

value: Breast muscle

value: 10 weeks of age

value: Non-supplemented


title: D28 Mtb infected_T863 treated animal5 [SD16]


title: 17608/6 D26

tag: cell line


title: OBOB_6

value: male


title: 17608/6 D35


title: NZO_10

value: NZO/HiBomDife


title: D28 Mtb infected_T863 treated animal6 [SD17]

value: M. tuberculosis infected mouse lung

value: T863 treated


title: ND40066-8 D06


title: D28 Mtb infected_T863 treated animal2 [SD13]

value: low


title: D28 Mtb infected_T863 treated animal4 [SD15]

value: high


title: D28 Mtb infected_vehicle treated animal11 [SD11]

source_name: D28 Mtb infected_vehicle treated_whole lung

value: vehicle treated

value: control


title: ND40066-8 D15


title: NZO_2


title: NZO_1


title: D28 Mtb infected_vehicle treated animal9 [SD9]


title: 17608/6 D10


title: ND40066-8 D21


title: 17608/6 D06


title: D28 Mtb infected_T863 treated animal7 [SD18]


title: D28 Mtb infected_vehicle treated animal6 [SD6]


title: D28 Mtb infected_vehicle treated animal8 [SD8]


title: D28 Mtb infected_vehicle treated animal5 [SD5]


title: D28 Mtb infected_T863 treated animal3 [SD14]


title: D28 Mtb infected_T863 treated animal8 [SD19]


title: D28 Mtb infected_vehicle treated animal7 [SD7]


title: 17608/6 D15


title: sn-RNAseq of Tiger Spleen

description: single-cell gene expression of Panthera tigris altaica

organism: Panthera tigris altaica

source_name: Tiger Spleen

value: Spleen

value: Infant


title: D28 Mtb infected_T863 treated animal1 [SD12]


title: 17608/6 D21


title: sn-RNAseq of Tiger Lung

source_name: Tiger Lung

value: Lung


title: NZO_5


title: sn-RNAseq of Dog Lung

description: single-cell gene expression of Canis lupus familiaris

organism: Canis lupus familiaris

source_name: Dog Lung

value: Adult


title: D28 Mtb infected_vehicle treated animal10 [SD10]


title: sn-RNAseq of Tiger Liver

source_name: Tiger Liver

value: Liver


title: sn-RNAseq of Goat Lung

description: single-cell gene expression of Capra aegagrus

organism: Capra aegagrus

source_name: Goat Lung


title: D28 Mtb infected_vehicle treated animal3 [SD3]


title: sn-RNAseq of Rabbit Lung

description: single-cell gene expression of Oryctolagus cuniculus

organism: Oryctolagus cuniculus

source_name: Rabbit Lung


title: D28 Mtb infected_vehicle treated animal2 [SD2]


title: Cornea S2

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the human reference genome (hg38, gencode release 34) with RNA STAR Galaxy Version 2.7.2b (default parameters) using the Gencode annotation file (Gencode 34)
Reads mapped to the human reference genome were counted using featureCounts Galaxy Version 1.6.4 (default parameters) using the aforementioned annotation file.
The output of featureCounts was imported to RStudio (Version 1.2.1335, R Version 3.5.3). Gene symbols and gene types were determined based on ENSEMBL release 100 (Human genes, GRCh38.p12, download on 05/25/2020). Reads were normalized using the R package DESeq2 Version 1.22.2 24 with default parameters.
Genome_build: hg38

source_name: Cornea

extract_protocol:
Total RNA was isolated from ten to fifteen formalin-fixed and paraffin-embedded (FFPE) 4-µm-thick sections of all specimens using the Quick-RNA FFPE Kit (Zymo Research, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorometer (Life Technologies, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, USA). The fragment size of all RNA samples ranged between 120 and 150 bp.
RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method. The preparation of MACE libraries was carried out using 1 µg of total RNA, as previously described. The barcoded libraries were sequenced simultaneously on the NextSeq 500 (Illumina, USA) with 1× 75 bp. PCR bias was removed using an unique molecular identifier.

value: cornea

tag: disease state

value: healthy


title: Cornea S3


title: D28 Mtb infected_vehicle treated animal4 [SD4]


title: sn-RNAseq of Pigeon Lung

description: single-cell gene expression of Columba livia

organism: Columba livia

source_name: Pigeon Lung


title: sn-RNAseq of Lizard Lung

description: single-cell gene expression of Anolis carolinensis

organism: Anolis carolinensis

source_name: Lizard Lung


title: sn-RNAseq of Duck Lung

description: single-cell gene expression of Anas platyrhynchos

organism: Anas platyrhynchos

source_name: Duck Lung


title: sn-RNAseq of Tiger Kidney

source_name: Tiger Kidney

value: Kidney


title: D28 Mtb infected_vehicle treated animal1 [SD1]


title: HSMI, week 9, fish 3

status: Public on Sep 03 2021

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: Arrays were scanned with Agilent G2565BA DNA microarray scanner at a resolution of 5 microns.

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1. After removal of flagged spots lowess normalization was performed.

organism: Salmo salar

source_name: Normal heart

label_protocol: Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol.

growth_protocol: Salmon post smolts were kept in tanks with sea water.

extract_protocol: RNA was isolated using the iPrep™ TRIzol® Plus kit (Invitrogen), and purified with RNeasy mini kit (QIAGEN).

treatment_protocol: Fish were infected with ip injection (PRV) and cohabitation with shedders (SAV).

value: Heart

value: Uninfected control

source_name: Infected heart

value: PRV

tag: time point

value: Week 9


title: Cornea S1


title: HSMI, week 9, fish 4


title: HSMI, week 11, fish 1

value: Week 11


title: sn-RNAseq of Tiger Heart

source_name: Tiger Heart


title: HSMI, week 9, fish 2


title: HSMI, week 8, fish 3

value: Week 8


title: HSMI, week 11, fish 5


title: HSMI, week 11, fish 2


title: HSMI, week 9, fish 1


title: HSMI, week 9, fish 5


title: HSMI, week 11, fish 3


title: HSMI, week 7, fish 5

value: Week 7


title: HSMI, week 7, fish 4


title: HSMI, week 8, fish 1


title: HSMI, week 8, fish 5


title: HSMI, week 8, fish 2


title: HSMI, week 11, fish 4


title: HSMI, week 7, fish 3


title: HSMI, week 8, fish 4


title: HSMI, week 7, fish 2


title: HSMI, week 7, fish 1


title: HSMI, week 6, fish 5

value: Week 6


title: PD, day 35, fish 5

value: SAV

value: Day 35


title: HSMI, week 6, fish 2


title: HSMI, week 6, fish 4


title: PD, day 35, fish 6


title: PD, day 35, fish 2


title: HSMI, week 6, fish 1


title: PD, day 35, fish 4


title: PD, day 28, fish 1

value: Day 28


title: PD, day 28, fish 5


title: PD, day 28, fish 3


title: PD, day 28, fish 4


title: PD, day 28, fish 7


title: PD, day 35, fish 3


title: PD, day 28, fish 6


title: PD, day 21, fish 5

value: Day 21


title: PD, day 17, fish 1

value: Day 17


title: PD, day 17, fish 2


title: PD, day 21, fish 4


title: PD, day 35, fish 1


title: PD, day 21, fish 6


title: PD, day 28, fish 2


title: PD, day 21, fish 2


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2G1_032021.2

city: Bethesda

first: Chao-Jung

last: Wu

state: MD

address: 9000 Rockville Pike

institute: NIH

data_processing:
Paired-end data were processed as single-end for alignment and quantification. Cutadapt v3.4 was used to extract the first 75 bp of the read 1 (command line options -j 0 -l 75)
Single-end and processed paired-end data were quality filtered and adapter trimmed using trimgalore v0.6.6 using "-j 4 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC" command line options.
Reads were aligned to CP052845.1 reference genome using bwa mem v0.7.17 with default parameters.
CDS mapping reads were counted using htseq v0.11.4 with "--stranded reverse" and "--mode union" arguments (comand line options -i locus_tag -t CDS -f bam -s reverse -m union)
Genome_build: CP052845.1
Supplementary_files_format_and_content: htseq-count tab-delimited file includes CDS locus tag and counts.

organism: Bordetella hinzii

source_name: Liquid culture (LB broth)

growth_protocol: Overnight bacterial culture was adjusted to OD600 = 0.01 in 60 ml LB broth and aliquoted into four vented 50 ml falcon tubes (15 ml for each tube). After 4 hours incubation at 37 ℃ with 220 rpm shaking, the bacterial culture was mixed with 2 volumes of RNAprotect prior to RNA extraction.

extract_protocol: Total RNA was extracted using Monarch Total RNA Miniprep Kit (NEB #T2010) with in-tube Turbo DNase I treatment.

tag: isolate

tag: growth time


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2G1_031521


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2G1_032021.1


title: PD, day 21, fish 7


title: PD, day 21, fish 1


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2B3_032021


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2G1_032021.1

growth_protocol: Overnight bacterial culture was adjusted to OD600 = 0.01 in 60 ml LB broth and aliquoted into four vented 50 ml falcon tubes (15 ml for each tube). After 10 hours incubation at 37 ℃ with 220 rpm shaking, the bacterial culture was mixed with 2 volumes of RNAprotect prior to RNA extraction.


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2G1_030521


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B3_030521


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2G1_032021.2


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B3_032021


title: RNA-Seq of Bordetella hinzii isolates, sample: 4hATCC51783_020921.F

growth_protocol: Single colony was inoculated into 10 ml LB broth in a 50 ml falcon tube, and incubated overnight at 37 ℃ with 220 rpm shaking. Overnight culture was diluted to OD600 = 0.01 in 15 ml LB broth in a vented 50 ml falcon tube and grown at 37℃ with 220 rpm shaking. After 4 or 10 hours, the bacterial culture was mixed with 2 volumes of RNAprotect prior to RNA extraction.

extract_protocol:
Total RNA was extracted using MagMAX Viral/Pathogen kit with additional DNase I treatment step on a KingFisher instrument (Thermo-Fisher).
Total RNA samples underwent rRNA depletion using NEBNext rRNA Depletion kit (Bacteria) (E7850). RNA-Seq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760).


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h8B1_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 4hATCC51783_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 4hATCC51730_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h1B1b_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2B3_030521


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2B3_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h5G1a_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2G2_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h3G2_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B3_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h4G1b_020921


title: NZO_3

source_name: pancreas

value: male

value: NZO/HiBomDife


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h4G1a_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h1G1_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h4G1c_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2B2a_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h3G1_020921.2


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2B1_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h3G3_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2G1_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h3G1_020921.1


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h3B1_020921


title: PD, day 21, fish 3


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h1B1a_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 10hATCC51783_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 10hATCC51783_020921.F


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h1G1_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h1B1b_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 8h3G2_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 8h1B1b_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 8h3B1_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 8h3G2_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 6h3G2_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 8h1B1a_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B1_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 8h3B1_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 6h3G2_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h4G1c_020921


title: RNA-Seq of Bordetella hinzii isolates, sample: 6h1B1b_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 6h3B1_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 6h1B1a_030420


title: RNA-Seq of Bordetella hinzii isolates, sample: 6h1B1a_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 6h1B1b_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 6h1B1b_030420


title: RNA-Seq of Bordetella hinzii isolates, sample: 6h3B1_030420


title: RNA-Seq of Bordetella hinzii isolates, sample: 6h3B1_030620


title: LP-C3

city: Kaifeng

first: Lisa

last: Lei

address: Jinming Xi Street

institute: Henan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used KOBAS software to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: Araport11
Supplementary_files_format_and_content: fpkm.txt: Tab-delimited text file includes FPKM values for each Sample.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: After a growth period of 7 days, Wild-type (Col-0) and R9 seedlings were then transferred to either a normal (MS) or low Pi (LP) growth medium containing either 1.25 mM or 2.5 μM KH2PO4 respectively for 14 days.

extract_protocol:
500 mg of each whole seedling was harvested and snap-frozen using liquid nitrogen. RNA were extracted.
RNA-sequencing was then conducted off-site by the Novogene using an Illumina NovaSeq 6000 platform.

treatment_protocol: Wild-type (Col-0) and R9 seedlings were treated with low Pi.

tag: genotype

value: WT (Col-0)

value: seedlings

value: low Pi


title: LP-C2


title: LP-C1


title: r9-1

description: untreated

value: normal Pi


title: LP-r9-2


title: LP-r9-3


title: r9-3

description: untreated


title: C-3

description: untreated


title: LP-r9-1


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h8B1_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h7B1_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 6h1B1a_030320


title: r9-2

description: untreated


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h5G1b_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h5G1a_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h5G1a_030620


title: PP

city: Toronto

first: Yasaman

last: Aghazadeh

state: ON

address: 101, College St

country: Canada

institute: McEwen Stem Cell Institute

description: Unspliced RNA

data_processing:
Considering that any ambiguously assigned reads (e.g. for homologous genes) are removed from the data and do not contribute towards UMI counts and are not in the final read matrix, we removed the INS-IGF2 entries from the human GTF file to unmask the INS transcripts.
The UMIs were generated using cellranger (v3.1). A custom reference was used. To create a reference for multiple species, we used the mkref command with multiple FASTA and GTF files for mm10, Ratus6.0.98 and GRCh38. The single-nuclei RNA-seq assay captures unspliced pre-mRNA as well as mature mRNA. However, after alignment, cellranger count only counts reads aligned to exons. Since the pre-mRNA will generate intronic reads, it may be useful to count these reads as well. As recommended by 10xGenomics, we created three custom “pre-mRNA” GTF files, listing each gene transcript locus as an exon, in order to count intronic reads.   Considering that any ambiguously assigned reads (e.g. for homologous genes) are removed from the data and don’t go towards UMI counts and are not in the final read matrix, we removed the INS-IGF2 entries from the human GTF file to unmask the INS transcripts.
The distribution of total features detected in each reference genome per cell were analyzed to determine thresholds for assigning species identity (data not shown). Nuclei were assigned as either originating from human, mouse or rat if the feature count from the respective genome was over 1000, 300, or 200 features. 5421 human, 2862 mouse, and 334 rat cells were identified. 3333 nuclei had feature counts below the threshold for all three organisms and were omitted. One cell passed the threshold for both the human and rat genome and was omitted
Counts were normalized (method = “LogNormalize”, scale.factor = 10 000) before scaling (ScaleData) to regress the influence from variable UMIs.
Genome_build: mm10 (mus musculus), Ratus6.0.98 (rattus norvegicus) and GRCh38 (homo sapiens)
Supplementary_files_format_and_content: CSV

organism:
Homo sapiens
Mus musculus

source_name: Human embryonic stem cells differentiated to pancreatic progenitors , transplanted in mice.

growth_protocol: hESCs were cultured on mouse embrynic fibroblasts, using hES media and rock inhibitor.

extract_protocol:
Cells were embedded in hydrogels and transplanted in the mice. Hydrogels were reteieved adter 100 days and snap frozen. Nuceli was isolated as per 10X genomic published protocols. Details can be found : https://support.10xgenomics.com/isolation-of-nuclei
The Unique Molecular ID (UMI) were generated using Cellranger (v3.1). A custom reference for multiple species was made using the mkref command with FASTA and GTF files for mm10, Ratus6.0.98 and GRCh38. Single nuclei reads were mapped to this custom reference genome using Cellranger.  The sNuc-Seq assay captured unspliced pre-mRNA as well as mature mRNA. However, after alignment, Cellranger only counted reads aligned to exons. A three custom “pre-mRNA” GTF file was created listing each gene transcript locus as an exon, in order to count intronic reads.

treatment_protocol: hESC were differentiated to PP through a 4 step process, using "Nostro protocol" Derails published at: Korytnikov R, Nostro MC, Methods, 2016, DOI: 0.1016/j.ymeth.2015.10.017.

tag: cell type

value: Cells differentiated in vivo from PP (transplanted) and cells infilterated from the mouse.

value: Host mice is Scid Beige


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h7B1_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 4hATCC51784_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h8B1_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h5G1b_030420


title: C-1

description: untreated


title: RNA-Seq of Bordetella hinzii isolates, sample: 4hATCC51784_030620


city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

description:
Nnat+/-p male ARC 45% hfd Diet, Sample 53
SLX-14772_arc_raw_count.tsv

data_processing:
STAR 2.5.0a was used to map the fastq reads to the mouse GRCm38 genome and the gene-level count was also performed using the same software
Genome_build: GRCm38
Supplementary_files_format_and_content: raw count in text delimited format

organism: Mus musculus

source_name: ARC

extract_protocol:
Fresh frozen brains were collected from Nnat+/+ and Nnat+/-p male mice between 13 and 14 weeks of age. Coronal sections of 20-μm thickness were prepared on a cryostat (Bright OTF5000 cryostat) and mounted on RNase-free membrane-coated glass slides (Superfrost Plus, Thermo Fisher Scientific). Brain sections were fixed in 95% ethanol (30 seconds) and rehydrated in an ethanol series (75% ethanol, 50% ethanol) prior to staining with cresyl violet (Ambion). Sections were then dehydrated in another ethanol series of 50%, 75%, 95%, and 100% ethanol and left to air dry prior to laser capture. PVN and ARC, were then dissected using a PALM Microbeam Laser Capture Microdissection System (Zeiss) on a ×5 objective as previously described [18]. Briefly, tissues were captured on AdhesiveCap Clear PCR tubes (Zeiss) and stored in 80μl of QIAzol (QIAGEN) on dry ice prior to RNA extraction. Laser capture and subsequent cDNA library preparation were performed. RNA from laser-captured nuclei was extracted using the miRNeasy Micro RNA Extraction Kit (QIAGEN). Quality and quantity of the samples were then checked on an Agilent 2100 Bioanalyzer using Agilent RNA 600 pico and/or nano chips, with a typical sample RNA concentration in the range of 1 to 5 ng/μl.
RNA libraries were prepared for sequencing using Takara Clontech Smartseq Pico Input V2 reagents according to manufacturer's instruction

value: Nnat+/-p

value: ARC

tag: diet

value: 45% hfd

value: adult

tag: weight (g)


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h7B1_030420


description:
Nnat+/-p male ARC 45% hfd Diet, Sample 52
SLX-14772_arc_raw_count.tsv


title: RNA-Seq of Bordetella hinzii isolates, sample: 4hATCC51783_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 4hATCC51783_030420


title: RNA-Seq of Bordetella hinzii isolates, sample: 4hATCC51730_030620


title: C-2

description: untreated


title: RNA-Seq of Bordetella hinzii isolates, sample: 4hATCC51730_030420


title: RNA-Seq of Bordetella hinzii isolates, sample: 4hATCC51783_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 4hATCC51784_030420


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h4G1d_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h5G1b_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h4G1d_030320


description:
Nnat+/-p male ARC 45% hfd Diet, Sample 50
SLX-14772_arc_raw_count.tsv


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h4G1c_030420


description:
Wild-type male ARC 45% hfd Diet, Sample 49
SLX-14772_arc_raw_count.tsv

value: Wild-type


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h4G1d_030420


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h4G1b_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h4G1c_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h4G1b_030420


description:
Wild-type male ARC 45% hfd Diet, Sample 47
SLX-14772_arc_raw_count.tsv


description:
Wild-type male ARC 45% hfd Diet, Sample 48
SLX-14772_arc_raw_count.tsv


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h4G1a_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h3G2_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h3G3_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h4G1a_030420


description:
Nnat+/-p male ARC 45% hfd Diet, Sample 51
SLX-14772_arc_raw_count.tsv


description:
Wild-type male ARC 45% hfd Diet, Sample 44
SLX-14772_arc_raw_count.tsv


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h3G3_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2G2_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h3G2_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h3B1_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2G2_030320


description:
Wild-type male ARC 45% hfd Diet, Sample 45
SLX-14772_arc_raw_count.tsv


title: Nnat+/-p male ARC chow Diet, Sample 42

description:
Nnat+/-p male ARC chow Diet, Sample 42
SLX-14772_arc_raw_count.tsv

value: chow


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2G1_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h3G1_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2G1_030320


title: Nnat+/-p male ARC chow Diet, Sample 41

description:
Nnat+/-p male ARC chow Diet, Sample 41
SLX-14772_arc_raw_count.tsv


title: Nnat+/-p male ARC chow Diet, Sample 43

description:
Nnat+/-p male ARC chow Diet, Sample 43
SLX-14772_arc_raw_count.tsv


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h3B1_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2B3_030620


description:
Wild-type male ARC 45% hfd Diet, Sample 46
SLX-14772_arc_raw_count.tsv


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2B3_030420


title: Nnat+/-p male ARC chow Diet, Sample 40

description:
Nnat+/-p male ARC chow Diet, Sample 40
SLX-14772_arc_raw_count.tsv


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h4G1c_030320


title: OSCA-40_Week8-1

city: Minneapolis

first: Lauren

last: Mills

state: MN

address: 420 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

data_processing:
50bp paired-end sequencing RNAseq was performed on the Illumina HiSeq 2500.
Initial quality control analysis of RNA sequencing FASTQ data was performed using FastQC software (v0.11.5).
FASTQ data were trimmed with Trimmomatic (v0.33.0).
Kallisto (v0.43.0) was used for pseudoalignment and quantifying transcript abundance.
For alignment of sequencing reads to canine and murine genes, a kallisto index was built from a multi-sequence FASTA file containing both the canine (CanFam3.1) and murine (GRCm38.p5) genomes
Genome_build: CanFam3.1 and GRCm38.p5

source_name: At necropsy, pooled serum of mice intratibially injected with OSCA-40

extract_protocol:
Exosome enrichment was performed with ExoQuick reagent.
RNA was extracted with SeraMir ExoRNA Amp kit.
Library prep was performed with Clontech SMARTer Stranded Total RNA-seq Kit v2 - Pico Input Mammalian Kit.

treatment_protocol: Mice were injected intratibially with 10ul of either PBS (control), or a canine osteosarcoma cell line (1 x 10^5 cells of either OSCA-32 or OSCA-40)

value: NCr nu/nu

value: serum exosomes


title: Nnat+/-p male ARC chow Diet, Sample 39

description:
Nnat+/-p male ARC chow Diet, Sample 39
SLX-14772_arc_raw_count.tsv


title: Nnat+/-p male ARC chow Diet, Sample 38

description:
Nnat+/-p male ARC chow Diet, Sample 38
SLX-14772_arc_raw_count.tsv


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2B2b_030420


title: OSCA-40_Week8-2


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2B2b_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2B2a_030620


title: Nnat+/-p male ARC chow Diet, Sample 36

description:
Nnat+/-p male ARC chow Diet, Sample 36
SLX-14772_arc_raw_count.tsv


title: Nnat+/-p male ARC chow Diet, Sample 37

description:
Nnat+/-p male ARC chow Diet, Sample 37
SLX-14772_arc_raw_count.tsv


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2B2a_030320


title: Cells exposed to poly(I:C), replicate 1

scan_protocol: Arrays were scanned with GenePix® 4100A. Microarray Scanner.

data_processing: Images were processed using the standard procedures of the feature extraction. After removal of flagged spots lowess normalization was performed.

source_name: Treated cells

label_protocol: RNA was amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol.

growth_protocol: Cells were cultivated in L-15 medium supplemented with gentamicin, glutamine and fetal bovine serum.

treatment_protocol: Virus and poly(I:C) were inoculated to flasks.

value: Head kidney cells

value: 5 days

source_name: Control cells

value: Untreated


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2B2b_030620


title: Cells exposed to poly(I:C), replicate 2


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2B1_030620


title: Control_Week8-1

source_name: At necropsy, pooled serum of control mice wihtout injection of tumor cells

value: PBS


title: Week0-2

source_name: Before injection of tumor cells, pooled serum of all mice

value: Control


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h1G2_030620


title: OSCA-32_Week8-2

source_name: At necropsy, pooled serum of mice intratibially injected with OSCA-32


title: OSCA-32_Week8-1


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2B1_030420


title: Control_Week8-2


title: Wild-type male ARC chow Diet, Sample 35

description:
Wild-type male ARC chow Diet, Sample 35
SLX-14772_arc_raw_count.tsv

value: male


title: Wild-type male ARC chow Diet, Sample 34

description:
Wild-type male ARC chow Diet, Sample 34
SLX-14772_arc_raw_count.tsv


title: CD3+_T_EAU_P_N2

city: Guangzhou

first: Guanyu

last: Chen

state: Guangdong

address: Xianlienan Road NO. 54

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description: EAU model treated with nimodipine

data_processing:
The total RNA was processed by the Yale Center for Genome Analysis (YCGA) using the Ribo-Zero rRNA removal kit
libraries were constructed and subjected to standard illumina HiSeq2000 sequencing

source_name: CD3+ T cells

extract_protocol:
The total RNAs were isolated with Direct-zol RNA MicroPrep kits (Zymo Research, R2062) processed.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human IRBP1-20was emulsified with complete Freund’s adjuvant (CFA) containing 5 mg/ml heat-denatured M. tuberculosis in a 1:1 volume ratio (v/v). C57BL/6J mice were immunized via subcutaneous injection of 200 µl of emulsion at the base of the tail and two thighs; 200 ng of pertussis toxin was injected intraperitoneally to each mouse on day 0 and day 2 after immunization.Mice were injected with nimodipine daily (10 mg/kg).

value: CD3+ T cells

value: EAU + nimodipine


title: Week0-1


title: Infected cells harvested after five days, replicate 2

value: ISAV infection

value: Uninfected


title: Infected cells harvested after one day, replicate 2

value: 1 day


title: ATACseq Invivo Chd4dPax7ER sample3

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

institute: UPF

data_processing:
Raw reads were assessed for quality, adaptor content and duplication rates with FastQC 0.11.8,
Reads were trimmed by Cutadapt 1.18
Reads  were terminally aligned to the Ensemble mouse genome version mm10 (GRCm38) by HISAT2 2.1.0. for RNAseq or by Picard 2.18.15 for ATACseq
For ATACseq, regions of open chromatin were identified by MACS2 2.1.2 while HOMER was used for peak annotation. Differentially peaks near the Transcriptional Start Site (TSS ± 500 bp) were identified using DESeq2 3.6 (p < 0.01).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RNA-seq: Tab-delimited text files include normalized RPKM values. ATACseq:  Bigwig files

source_name: Satellite cells

extract_protocol:
Library preparation was done on FACS-purified satellite cells following the Omni-ATAC protocol ( http://www.nature.com/articles/nmeth.4396).
Time of incubation with transposase was set to 40 min after extensive setup with Chd4 fl/fl satellite cells. Library quality was assessed by Agilent BioAnalyzer (DNA High Sensitivity Chip). Paired-end sequencing (Illumina HiSeq 2500) was performed in the Genomic Unit of the CRG.

treatment_protocol: Cells were isolated from skeletal muscle

value: Freshly sorted satellite cells

value: young (2-4 months old)

tag: muscle state

value: 3 days after injury (Cardiotoxin)


description:
Nnat+/-p male ARC 45% hfd Diet, Sample 32
SLX-14620_pvn_raw_count.tsv

value: Nnat+/-p

tag: tissue

value: ARC

value: 45% hfd

value: adult


title: CD3+_T_EAU_P_N3

description: EAU model treated with nimodipine


description:
Nnat+/-p male PVN 45% hfd Diet, Sample 30
SLX-14620_pvn_raw_count.tsv

source_name: PVN

value: PVN

tag: age


title: Wild-type male ARC chow Diet, Sample 33

description:
Wild-type male ARC chow Diet, Sample 33
SLX-14772_arc_raw_count.tsv

tag: strain

value: Wild-type

value: chow


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h1G2_030320


title: ATACseq Invivo Chd4dPax7ER sample4


title: ATACseq Invivo Chd4dPax7ER sample1


description:
Wild-type male PVN 45% hfd Diet, Sample 28
SLX-14620_pvn_raw_count.tsv

tag: Sex


description:
Nnat+/-p male PVN 45% hfd Diet, Sample 29
SLX-14620_pvn_raw_count.tsv


title: ATACseq Invivo Chd4fl/fl sample4


description:
Nnat+/-p male PVN 45% hfd Diet, Sample 31
SLX-14620_pvn_raw_count.tsv


title: CD3+_T_EAU_P_N1

description: EAU model treated with nimodipine

tag: treatment


title: Infected cells harvested after one day, replicate 1

value: Head kidney cells


title: ATACseq Invivo Chd4fl/fl sample3


title: ATACseq Invivo Chd4dPax7ER sample2


title: ATACseq Invivo Chd4fl/fl sample2


title: CD3+_T_EAU3

description: EAU model

value: EAU


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h1B1b_030420


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h1G1_030420


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h1G1_030320


title: CD3+_T_EAU2

description: EAU model

value: CD3+ T cells


description:
Wild-type male PVN 45% hfd Diet, Sample 24
SLX-14620_pvn_raw_count.tsv

value: male


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h1B1a_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h1G2_030420


title: CD3+_T_BLANK2

description: Blank control whithout treatment

value: Control


title: CD3+_T_EAU1

description: EAU model


title: Input_CORT

first: Mar

last: Gonzalez-Ramirez

address: C/ Dr Aiguader 88

institute: Center for Genomic Regulation (CRG)

data_processing:
RNA-seq analysis: Alignment: Sequence reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
ChIP-seq analysis: Alignment: Sequence reads of the samples with spike-in were mapped to a synthetic genome containing the mouse and the fruit fly chromosomes (mm9+dm3) using BOWTIE (PubMed ID 19261174) with the option -m 1. Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIP-seq genome-wide profiles with spike-in were normalized by the total number of fly reads of each sample.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.bedgraph: Genome-wide ChIP-seq/RNA-seq.
Supplementary_files_format_and_content: *.bed: ChIP-seq peaks.
Supplementary_files_format_and_content: *.txt: Output files DESeq2 and DiffBind:
Supplementary_files_format_and_content: CORT-VEH_5W_results.txt: DESeq2 differential analysis
Supplementary_files_format_and_content: CORT-VEH_15W_results.txt: DESeq2 differential analysis
Supplementary_files_format_and_content: mouse_FPKMs.txt: FPKMs
Supplementary_files_format_and_content: H3K27ac_CORT5-VEH5_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K27ac_CORT15_2-VEH15_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K27ac_Peaks_CORT5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27ac_Peaks_VEH5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27ac_Peaks_VEH15_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27me3_CORT5-VEH5_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K27me3_CORT15-VEH15_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K27me3_Peaks_CORT5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27me3_Peaks_CORT15_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27me3_Peaks_VEH5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27me3_Peaks_VEH15_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K4me3_CORT5-VEH5_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K4me3_CORT15-VEH15_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K4me3_Peaks_CORT5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K4me3_Peaks_CORT15_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K4me3_Peaks_VEH5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K4me3_Peaks_VEH15_results.txt: DiffBind differential analysis vs. Input

extract_protocol:
For RNAseq: RNA was extracted using RNeasy Lipid Tissue Mini kit (Qiagen).
For ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013).
Libraries were prepared according to Illumina instructions.

treatment_protocol: CORT mice were treated with corticosterone as described in PMID: 31117053.

value: visceral adipose tissue

tag: status

value: CS

tag: chip antibody

tag: drosophila spike-in

value: YES


title: Infected cells harvested after five days, replicate 1

value: ISAV infection

value: 5 days

value: Uninfected


description:
Wild-type male PVN 45% hfd Diet, Sample 26
SLX-14620_pvn_raw_count.tsv


description:
Wild-type male PVN 45% hfd Diet, Sample 27
SLX-14620_pvn_raw_count.tsv


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h1G1_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h5G1b_030620


title: ATACseq Invivo Chd4fl/fl sample1

value: Freshly sorted satellite cells

value: young (2-4 months old)

value: 3 days after injury (Cardiotoxin)


title: CD3+_T_BLANK1

description: Blank control whithout treatment


title: RNAseq Invivo Chd4dPax7ER sample2

extract_protocol: none provided by the submitter


title: Nnat+/-p male PVN chow Diet, Sample 21

description:
Nnat+/-p male PVN chow Diet, Sample 21
SLX-14620_pvn_raw_count.tsv

value: Nnat+/-p

value: PVN

value: adult


title: RNAseq Invivo Chd4dPax7ER sample4


title: H3K4me3_VEH_2_15w

value: VEH (recovery)


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h1B1b_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h5G1b_030320


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h1B1a_030320


title: RNAseq Invivo Chd4fl/fl sample4


title: RNAseq Invivo Chd4dPax7ER sample3


description:
Wild-type male PVN 45% hfd Diet, Sample 23
SLX-14620_pvn_raw_count.tsv

value: Wild-type

value: 45% hfd


title: Nnat+/-p male PVN chow Diet, Sample 19

description:
Nnat+/-p male PVN chow Diet, Sample 19
SLX-14620_pvn_raw_count.tsv

value: male

value: chow


title: Nnat+/-p male PVN chow Diet, Sample 22

description:
Nnat+/-p male PVN chow Diet, Sample 22
SLX-14620_pvn_raw_count.tsv


title: H3K4me3_VEH_1_5w

value: visceral adipose tissue

value: VEH (active)


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h4G1c_030320


title: Nnat+/-p male PVN chow Diet, Sample 18

description:
Nnat+/-p male PVN chow Diet, Sample 18
SLX-14620_pvn_raw_count.tsv


description:
Wild-type male PVN 45% hfd Diet, Sample 25
SLX-14620_pvn_raw_count.tsv


title: RNAseq Invivo Chd4dPax7ER sample1


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h5G1b_030420


title: H3K4me3_VEH_1_15w

value: YES


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h4G1c_030620


title: Nnat+/-p male PVN chow Diet, Sample 20

description:
Nnat+/-p male PVN chow Diet, Sample 20
SLX-14620_pvn_raw_count.tsv


title: RNAseq Invitro AdCRE sample4

source_name: Primary myoblasts

growth_protocol: Cells were cultured on collagen-coated dishes with HAM’s F10 medium (Gibco), 20% Fetal Bovine Serum (FBS), 1:10000 Fibroblast Growth Factor (FGF) and 1% penicillin/streptomycin and kept in an incubator (37ºC, 5% CO2)

extract_protocol: Total RNA was isolated from cultured satellite cells with the RNeasy Micro kit (QIAGEN) with on-column DNA digestion

treatment_protocol: Cells were harvested from culture

value: Satellite cell-derived primary myoblasts cultured in proliferative conditions

value: resting non-injured muscle

value: Adenovirus CRE 72h


title: Input_VEH

value: VEH


title: Wild-type male PVN chow Diet, Sample 15

description:
Wild-type male PVN chow Diet, Sample 15
SLX-14620_pvn_raw_count.tsv


title: RNAseq Invitro AdCRE sample3

value: young (2-4 months old)


title: Wild-type male PVN chow Diet, Sample 14

description:
Wild-type male PVN chow Diet, Sample 14
SLX-14620_pvn_raw_count.tsv


title: RNAseq Invivo Chd4fl/fl sample3

value: Freshly sorted satellite cells

value: 3 days after injury (Cardiotoxin)


title: H3K4me3_CORT_2_15w

value: CS (recovery)


title: RNAseq Invivo Chd4fl/fl sample1


title: H3K4me3_VEH_2_5w


title: H3K4me3_CORT_2_5w

value: CS (active)


title: RNAseq Invivo Chd4fl/fl sample2


title: H3K27me3_VEH_2_15w

value: VEH (recovery)

value: H3K27me3 (Millipore #07–449)


title: Nnat+/-p male PVN chow Diet, Sample 17

description:
Nnat+/-p male PVN chow Diet, Sample 17
SLX-14620_pvn_raw_count.tsv

value: Nnat+/-p

value: PVN

value: adult


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h4G1b_030620


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h3G2_030620


title: H3K4me3_CORT_1_15w

value: visceral adipose tissue


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h4G1b_030320


title: Nnat+/-p male PVN chow Diet, Sample 16

description:
Nnat+/-p male PVN chow Diet, Sample 16
SLX-14620_pvn_raw_count.tsv

value: male

value: chow


title: H3K4me3_CORT_1_5w

value: YES


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h4G1b_030420


description:
Nnat+/-p female PVN chow Diet, Sample 12
SLX-13087_pvn_raw_count.tsv

value: female


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h3G2_030320


title: Wild-type male PVN chow Diet, Sample 13

description:
Wild-type male PVN chow Diet, Sample 13
SLX-14620_pvn_raw_count.tsv

value: Wild-type


title: H3K27me3_VEH_1_15w


title: RNAseq Invitro AdCRE sample2

value: Satellite cell-derived primary myoblasts cultured in proliferative conditions

value: resting non-injured muscle

value: Adenovirus CRE 72h


title: RNAseq Invitro Ad GFP sample4

value: young (2-4 months old)

value: Adenovirus GFP 72h


title: RNAseq Invitro AdCRE sample1


description:
Nnat+/-p female PVN chow Diet, Sample 10
SLX-13087_pvn_raw_count.tsv


title: H3K27me3_VEH_1_5w

value: VEH (active)


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h3G2_030420