title: G129_D, ATAC

city: Campinas

first: Diogo

middle: Fernando Troggian

last: Veiga

state: SP

address: Rua Vital Brasil, 80

department: Department of Translational Medicine

country: Brazil

institute: Universidade Estadual de Campinas

description:
G129_D_barcodes.tsv.gz
G129_D_features.tsv.gz
G129_D_matrix.mtx.gz

data_processing:
CellRanger-arc 2.0.2 count was used to generate barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files for each sample
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: 10x Multiome single-cell

extract_protocol:
The nuclei extraction protocol for human brain tissue was adapted from Jessa et al, 2019. Briefly, frozen tissue was dounce homogenized and incubated for 2 minutes in lysis buffer containing 0.1% NP-40. Then, suspension was filtered through a 30 m cell strainer (MACS), and washed in buffer containing 10% BSA to remove debris, followed by a centrifugation at 500g and 4oC for 5 minutes. Next, suspension was carefully layered on a double 29% and 50% iodixanol (Sigma) cushion layers, and centrifuged at 10,000g and 4oC for 30 minutes for additional removal of debris and cell aggregates. Retrieved nuclei was resuspended and counted. Nuclei were stained with Trypan blue and counted using a hemocytometer. Nuclei integrity was evaluated under microscope using 40X or 60X magnifications, and nuclei was considered viable if they were roundish and with an intact membrane.
Libraries were prepared using the Multiome ATAC + Gene Expression kit (10X Genomics) in accordance with the manufacture’s protocol CG000338 revision E.

value: cerebral cortex

tag: disease

value: focal cortical dysplasia

tag: library type

value: ATAC

tag: Sex

value: Male

tag: age at_surgery

tag: age at_onset

tag: duration

tag: lobe

value: Parietal

tag: lateralization

value: R

tag: histological assessment

tag: surgery reason

value: FCD

tag: seq batch


title: G4-TH-2-plasma intensity none

status: Public on Oct 15 2024

type: SRA

city: Stanford

first: Tony

last: Wyss-Coray

state: CA

address: 290 Jane Stanford way, RM E365 TWC-Neurology

country: USA

institute: Stanford University

description: smart-seq 2

library_source: transcriptomic

data_processing:
raw sequencing files in blc format were demultiplexed with bcl2fastq to generate fastq files and were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore!. Trimmed reads were aligned using STAR (v.2.5.3a) GeneCounts function, multi-mapped reads were filtered, and gene expression matrices were generated using SeqMonk. Seurat package was used to perform all downstream analysis.
Assembly: mm10
Supplementary files format and content: counttable (Text file)

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
cells were lysed in the lysis buffer and follow the smart-seq2 pipeline to generate cDNA
smart-seq2 in house pipeline

tag: tissue

value: Brain

tag: cell line

value: isolated cells

tag: cell type

value: microglia


title: control_BIOT.009_1

city: Brno

first: Martina

last: Zapletalová

address: Kamenice 5

department: Department of Biochemistry

country: Czech Republic

institute: Masaryk University

data_processing:
Raw sequencing reads were quality-checked using FastQC and were subsequently trimmed using Trim Galore. Following this, the reads were aligned to the human genome sequence hg38, employing the R packages Rbowtie2 and Rsamtools. Differential analysis of count data was performed using the R package DeSeq2. Transcripts exhibiting |log2 fold change| > 1 and q < 0.01 (FDR-adjusted P-values) were identified as differentially expressed genes (DEGs). Cluster analysis was conducted using the R packages pvclust and dendextend. To determine the cell type, the R package clustifyr was employed against the scRNA-seq human cortex database. Cellular deconvolution was carried out using BrainDeconvShiny with the assistance of dtangle and the NG database. Heatmaps were constructed using R package ComplexHeatmap.
Assembly: hg38
Supplementary files format and content: tab-delimited file includes raw count for each sample

organism: Homo sapiens

source_name: iPSC-derived astrocyte

growth_protocol:
NPCs were thawed in completed neural maintenance medium (NMM) (containing 50% DMEM/F12 with glutamine, 50% Neurobasal medium, 1X B27 supplement, 1X N2 supplement, 1% Penicillin/Streptomycin, 1% GlutaMax (all purchased from Gibco), non-essential amino-acids (Sigma), completed with 10 ng/mL recombinant human epidermal growth factor, and 10 ng/mL basic fibroblast growth factor) supplemented with Rhock-inhibitor at a final concentration of 10 µM and plated into poly-L-ornithine/laminin-coated dishes. On the next day, the medium was changed to completed NMM. The cell culture medium was changed every two days. Thawed NPC lines were propagated for the next passage (with a density of 100.000 cells/cm2) and seeded into Matrigel-coated dishes for astrocyte differentiation at day 10, upon reaching confluence again, (with a cell-density of 50.000/cm2).
LSFP method of Astrocyte differentiation: NPCs at day 10 were seeded into poly-L-ornithine/laminin-coated plates at a density of 50.000 cells/cm2 and maintained in GPC expansion medium (containing DMEM/F12 Glutamax, 1X B27-A supplement, 1X N2 supplement completed with 10 ng/ml recombinant human epidermal growth factor (EGF) and 10 ng/ml basic fibroblast growth factor (FGF2)) for 2 weeks. The medium was changed every two days. At day 24, cells were seeded into Matrigel-coated plates at a density of 50.000 cells/cm2 and maintained in astrocyte induction medium (containing DMEM/F12 Glutamax with 1X B27-A supplement, 1X N2 supplement completed with 10 ng/ml recombinant human epidermal growth factor (EGF), and 10 ng/ml leukemia inhibitory factor (LIF)) for 2 weeks. The medium was changed every two days. At day 36, cells were plated into Matrigel (50.000 cells/cm2) in astrocyte maturation medium, which was DMEM/F12 Glutamax medium containing 1X B27-A supplement, 1X N2 supplement, and 20 ng/ml recombinant human ciliary neurotrophic factor (CNTF, by Peprotech). Cells were kept in maturation medium for 4 more weeks with medium changes every two days and cultures were inspected by light microscopic imaging.
SSFP method of Astrocyte differentiation: NPCs at day 10 were seeded into Matrigel-coated plates at a density of 50.000 cells/cm2 and maintained in astrocyte induction medium (containing DMEM/F12 Glutamax with 1X B27-A supplement, 1X N2 supplement completed with 10 ng/ml recombinant human epidermal growth factor (EGF), and 10 ng/ml leukemia inhibitory factor (LIF)) for 2 weeks. Medium was changed every two days. When the culture reached confluence, cells were passaged using Accutase for cell-dissociation and seeded into Matrigel-coated 6-well plates with 50.000 cells/cm2. At day 24, cells were plated into Matrigel (50.000 cells/cm2) in astrocyte maturation medium, which was DMEM/F12 Glutamax medium containing 1X B27-A supplement, 1X N2 supplement and 20 ng/ml recombinant human ciliary neurotrophic factor (CNTF, by Peprotech). Cells were kept in maturation medium for 4 more weeks with medium changes every two days and cultures were inspected by light microscopic imaging.
TUSP method of Astrocyte differentiation and treatment: The NPCs at day 10 were seeded into Matrigel-coated plates at a density of 50.000 cells/cm2 and maintained in the astrocyte induction medium (ScienceCell’s astrocyte growth medium supplemented with 2% FBS) for 4 weeks. The medium was changed every two days. When the culture reached confluence, cells were passaged using Accutase for cell dissociation and seeded into Matrigel-coated 6-well plates with 50.000 cells/cm2. At day 42, cells were plated into Matrigel (50.000 cells/cm2) in astrocyte maturation medium, which was serum-free astrocyte growth medium containing 20 ng/ml recombinant human ciliary neurotrophic factor (CNTF, by Peprotech). Cells were kept in maturation medium for 4 more weeks with medium changes every two days and cultures were inspected by light microscopic imaging. On day 70 after the end of maturation phase the cells were treated in triplicates with 500 nM A42 (Biotalentum, HU) or 150 uM H2O2 for 2 hours. Cellular pellets for RNAseq and cellular media for IL-6 analysis were collected 72 hours after the treatment.

extract_protocol: The cellular pellet samples were used to isolate total RNA with TRI Reagent (Merck, USA) and RapidOutput DNA removal kit (ThermoFisher Scientific, USA). A Qubit 4 fluorometer (ThermoFisher Scientific, USA) and Fragment Analyzer (Agilent, USA) were used to analyse the isolated RNA for quantity and quality, respectively. Complementary DNA (cDNA) libraries were synthesized using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, UK). The concentration and quality of cDNA libraries were assessed using a Qubit 4 fluorometer (ThermoFisher Scientific, USA) and Fragment Analyzer (Agilent, USA). The cDNA samples were then diluted to 4 nM and sequenced on the Illumina NextSeq® platform with NextSeq® 500/550 High Output Kit v2.5 (150 cycles) (Illumina, USA), generating 75 bp pair-end reads, and on the Illumina NovaSeq® 6000 platform with NovaSeq® S4 300 kit (Illumina, USA), generating 150 bp pair-end reads.

treatment_protocol: On day 70 after the end of maturation phase the cells were treated in triplicates with 500 nM AB42 (Biotalentum, HU) or 150 uM H2O2 for 2 hours. Cellular pellets for RNAseq were collected 72 hours after the treatment.

tag: differentiation protocol

value: TUSP method

value: iPSC-derived astrocyte

tag: genotype

value: control, healthy

tag: treatment

value: non-treated

tag: donor

value: healthy, 35-years old, female


title: G2-TH-2-plasma intensity none

description: smart-seq 2


title: G129_D, GEX

molecule: polyA RNA

tag: disease

tag: library type

value: mRNA


title: G1-TH-2-plasma intensity none

description: smart-seq 2


title: F22-TH-2-plasma intensity high

description: smart-seq 2


title: G210_D, GEX

description:
G210_D_barcodes.tsv.gz
G210_D_features.tsv.gz
G210_D_matrix.mtx.gz

tag: Sex

value: Female

tag: age at_surgery

value: Temporo-Occipital

value: L


title: WT_ReD

city: Canton

first: jieyi

last: Ma

state: Guangdong province

address: No.58 Zhong Shan Er Road

department: 1Department of Otolaryngology

country: China

institute: the First affiliated hospital of Sun Yat-sen University

data_processing:
instrument model: MGI2000
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015).
Assembly: mm10
Supplementary files format and content: Homo_cleavage_score_for_TRAC-seq.txt
Supplementary files format and content: WT_cleavage_score_for_TRAC-seq.txt
Library strategy: TRAC-Seq

source_name: brain

growth_protocol: C57BL/6N WDR4 mutated knock-in (mKI) mice with NM_021322.2 c.664G>T mutation were generated using CRISPR-Cas9 system by Biocytogen Co., Ltd.  Mice were grown under SPF condition.

extract_protocol:
RNA was extracted according to TRIzol protocol. Small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Libraries were prepared according to the NEBNext® Small RNA Library Prep Set.

treatment_protocol: Two month old wild type and WDR4 homozygous mutated mice were sacrified and the brain of mice were isolated for RNA extracttion.

value: brain

value: demethylated by ALKB; NaBH4/Aniline induced reduction and cleavage

value: wild type

tag: fraction

value: small RNA


title: WT_DeM

value: demethylated by ALKB


title: F23-TH-2-plasma intensity high

description: smart-seq 2

value: Brain


title: F21-TH-2-plasma intensity high

description: smart-seq 2

value: isolated cells


title: G3-TH-2-plasma intensity none

description: smart-seq 2

value: microglia


title: hand2 FLD-/- 20 hpf CMs_rep3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description:
Mut_3
ExpB_counts.matrix.norm_anno

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 (ensemble release 104) using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 (log2 ± 0.59), a maximum Benjamini–Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed.
Assembly: danRer11
Supplementary files format and content: library size normalized counts

organism: Danio rerio

source_name: embryonic heart

extract_protocol:
miRNeasy micro Kit (Qiagen), using low input DNase protocol
Approximately 1ng of total RNA was used as starting material for SMART®-Seq HT Kit (Takara Bio).

value: embryonic heart

value: cardiomyocytes

value: hand2 mutant

value: sorted cells by FACS


title: G210_D, ATAC

library_source: genomic

molecule: genomic DNA

value: cerebral cortex

value: focal cortical dysplasia

value: ATAC

tag: age at_onset

tag: duration

tag: lobe

value: FCD


title: G159_D, ATAC

description:
G159_D_barcodes.tsv.gz
G159_D_features.tsv.gz
G159_D_matrix.mtx.gz

value: Female

value: Frontal

tag: lateralization

value: R

tag: histological assessment

tag: surgery reason


title: F20-TH-2-plasma intensity high

description: smart-seq 2

tag: tissue

tag: cell line


title: G9-TH-2-plasma intensity low

description: smart-seq 2

tag: cell type


title: G159_D, GEX

value: mRNA

tag: seq batch


title: F19-TH-2-plasma intensity high

description: smart-seq 2


title: F18-TH-2-plasma intensity high

description: smart-seq 2


title: G5-TH-2-plasma intensity none

description: smart-seq 2


title: G7-TH-2-plasma intensity none

description: smart-seq 2


title: Homo_1

data_processing:
instrument model: MGI2000
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to mouse reference genome (mm10) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as FPKM using edegR.
Assembly: mm10
Supplementary files format and content: mRNA_expression_for_ RNA-seq.txt

extract_protocol:
RNA was extracted according to TRIzol protocol.
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit

treatment_protocol: 6 weeks old wild type and WDR4 homozygous mutated mice were sacrified and the brain of mice were isolated for RNA extracttion.

value: brain

tag: genotype

value: WDR4 mKI


title: Homo_ReD

tag: treatment

value: demethylated by ALKB; NaBH4/Aniline induced reduction and cleavage

value: small RNA


title: F17-TH-2-plasma intensity high

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: G171_D, ATAC

description:
G171_D_barcodes.tsv.gz
G171_D_features.tsv.gz
G171_D_matrix.mtx.gz

tag: donor

tag: disease


title: F15-TH-2-plasma intensity low

description: smart-seq 2


title: F16-TH-2-plasma intensity low

description: smart-seq 2


title: WT_2

value: Negative control


title: G171_D, GEX

tag: library type

tag: Sex


title: F14-TH-2-plasma intensity low

description: smart-seq 2


title: WT_1


title: F13-TH-2-plasma intensity low

description: smart-seq 2


title: G150_D, ATAC

description:
G150_D_barcodes.tsv.gz
G150_D_features.tsv.gz
G150_D_matrix.mtx.gz

tag: age at_surgery


title: F12-TH-2-plasma intensity low

description: smart-seq 2


title: F11-TH-2-plasma intensity low

description: smart-seq 2


title: Homo_2


title: RNC_Homo2

data_processing:
instrument model: MGI2000
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to mouse reference genome (mm10) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as TPM (Transcripts Per Kilobase of exon model per Million mapped reads).
Assembly: mm10
Supplementary files format and content: mRNA_expression_for_ Ribosome nascent-chain complex-bound mRNAs seq
Library strategy: RNC-seq


title: F10-TH-2-plasma intensity low

description: smart-seq 2


title: RNC_Homo3

value: Ribosome nascent-chain complex-bound mRNAs


title: G150_D, GEX

value: cerebral cortex

tag: age at_onset


title: F8-TH-2-plasma intensity none

description: smart-seq 2


title: F7-TH-2-plasma intensity none

description: smart-seq 2


title: RNC_Homo1


title: F9-TH-2-plasma intensity low

description: smart-seq 2


title: F6-TH-2-plasma intensity none

description: smart-seq 2


title: RNC_WT3


title: G187_D, ATAC

description:
G187_D_barcodes.tsv.gz
G187_D_features.tsv.gz
G187_D_matrix.mtx.gz

value: focal cortical dysplasia

value: Male

tag: duration

value: Temporal

value: L


title: RNC_WT2


title: F5-TH-2-plasma intensity none

description: smart-seq 2


title: F4-TH-2-plasma intensity none

description: smart-seq 2


title: F3-TH-2-plasma intensity none

description: smart-seq 2


title: G187_D, GEX

tag: lobe

value: FCD


title: G133_D.2, ATAC

description:
G133_D_FL_barcodes.tsv.gz
G133_D_FL_features.tsv.gz
G133_D_FL_matrix.mtx.gz

value: ATAC

value: Female

value: Frontal

tag: lateralization

value: R


title: G133_D.2, GEX

value: mRNA

tag: histological assessment


title: F2-TH-2-plasma intensity none

description: smart-seq 2


title: F1-TH-2-plasma intensity none

description: smart-seq 2


title: G133_N.2, ATAC

description:
G133_N_FL_barcodes.tsv.gz
G133_N_FL_features.tsv.gz
G133_N_FL_matrix.mtx.gz

value: Normal

tag: surgery reason


title: E23-TH-2-plasma intensity high

description: smart-seq 2

tag: tissue

value: Brain


title: Input_Homo3

value: brain

value: control

value: WDR4 mKI


title: E22-TH-2-plasma intensity high

description: smart-seq 2

tag: cell line

value: isolated cells

value: microglia


title: Input_Homo2


title: G133_N.2, GEX

value: cerebral cortex

value: focal cortical dysplasia


title: E19-TH-2-plasma intensity high

description: smart-seq 2

tag: cell type


title: E21-TH-2-plasma intensity high

description: smart-seq 2


title: E20-TH-2-plasma intensity high

description: smart-seq 2


title: E18-TH-2-plasma intensity high

description: smart-seq 2


title: Input_Homo1


title: E17-TH-2-plasma intensity high

description: smart-seq 2


title: G120_D.3_ATAC

description:
G120_D_FL_barcodes.tsv.gz
G120_D_FL_features.tsv.gz
G120_D_FL_matrix.mtx.gz

tag: seq batch


title: Input_WT3

tag: genotype

value: Negative control


title: G120_D.3, GEX

value: L


title: E16-TH-2-plasma intensity low

description: smart-seq 2


title: E15-TH-2-plasma intensity low

description: smart-seq 2


title: E13-TH-2-plasma intensity low

description: smart-seq 2


title: G120_D.2, ATAC

description:
G120_D_TL_barcodes.tsv.gz
G120_D_TL_features.tsv.gz
G120_D_TL_matrix.mtx.gz

value: Temporal

value: FCD


title: Input_WT2

tag: treatment


title: E14-TH-2-plasma intensity low

description: smart-seq 2


title: E12-TH-2-plasma intensity low

description: smart-seq 2


title: Input_WT1


title: G120_D.2, GEX

tag: donor

value: Female


title: RKO cells, LOC101927668 overexpression3

city: Beijing

first: wang

last: zaozao

state: Beijing

address: No. 52 Fucheng Rd., Haidian District

department: Key Laboratory of Carcinogenesis and Translational Research

institute: Peking University Cancer Hospital & Institute

data_processing:
Seqtk was used to remove rRNA reads, adaptors and poor quality reads (length < 25 or Q20>0.01).
Clean reads were mapped to hg38 genome by Hisat2 v2.0.4 (Pertea M et al., 2016) with default parameters.
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) of gene expression was calculated by Stringtie v1.3.0 (Pertea M et al., 2016).
Assembly: hg38
Supplementary files format and content: excel files include counts of samples
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: RKO

growth_protocol: RKO  cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (Hyclone) in humidified atmosphere with 5% CO2 at 37°.

extract_protocol:
Total RNA  was extracted by using TRIZOL.
The sequencing library of each sample of RNA was prepared according to the protocol provided by the manufacture.

treatment_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: RKO

value: CRC

value: LOC101927668 overexpression


title: E11-TH-2-plasma intensity low

description: smart-seq 2


title: RKO cells, LOC101927668 overexpression2


title: E9-TH-2-plasma intensity low

description: smart-seq 2


title: 9027

city: Shanghai

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAP nuke.
Trimmed sequence reads were mapped to the reference genome (hGRC38) using HISAT 4 (v2.1.0).
Read count extraction and normalization were performed using RSEM (v1.2.8).
Assembly: hGRC38
Supplementary files format and content: csv files includes raw counts for each Sample

source_name: Lung

growth_protocol: The progenitor cells were isolated from a small amount of airway epithelium obtained through bronchoscopic brushing and were expanded to more than 100 million cells within 3-5 weeks.

extract_protocol:
Total RNA was harvested using TRIzol Reagent (Invitrogen, Life Technologies, USA) followed the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the BGI-NSG platform following manufacturer's protocols.

value: Lung

value: P63+ lung progenitor cells

value: lung progenitor cells

value: BE


title: E8-TH-2-plasma intensity none

description: smart-seq 2

value: Brain


title: E7-TH-2-plasma intensity none

description: smart-seq 2

value: isolated cells


title: RKO cells, LOC101927668 overexpression1


title: 9021


title: RKO cells, Negative control3

value: Control


title: E6-TH-2-plasma intensity none

description: smart-seq 2

value: microglia


title: RKO cells, Negative control2


title: 9018


title: E4-TH-2-plasma intensity none

description: smart-seq 2


title: E5-TH-2-plasma intensity none

description: smart-seq 2


title: 9013


title: E3-TH-2-plasma intensity none

description: smart-seq 2


title: E2-TH-2-plasma intensity none

description: smart-seq 2


title: E1-TH-2-plasma intensity none

description: smart-seq 2


title: D22-TH-2-plasma intensity high

description: smart-seq 2


title: D23-TH-2-plasma intensity high

description: smart-seq 2


title: E10-TH-2-plasma intensity low

description: smart-seq 2


title: RKO cells, Negative control1


title: 9035


title: Fibroblasts, TGF-β 72h, Cytokine-primed hMSC(AT)-CM 72h, rep5

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
Low-quality bases (Phred < 33) and adaptor sequences were removed with the Trimmomatic v.0.36 tool using the following arguments: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:TRUE HEADCROP:4 LEADING:5 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36
Trimmed reads were aligned to the human GRCh38 (hg38) reference genome using HISAT2 v2.2.1
Raw counts were quantified by counting the number of strand-specific reads aligning to gene exon features using featureCounts (Subread package v2.0.5)
Raw read count libraries were filtered to remove residual rRNA reads and to retain genes expressed above 5 counts per million reads (CPM) in at least 3 samples, for a total of 11,163 expressed genes
Assembly: hg38
Supplementary files format and content: For each sample, a tab-delimited text file with raw counts for all host genes (.txt format)
Supplementary files format and content: For all samples, a matrix with raw counts for all genes (.txt format)
Supplementary files format and content: For all samples, a matrix with CPM values for all genes expressed at or greater than 5 CPM in at least 3 samples (.txt format)

growth_protocol: Immortalized normal human diploid fibroblasts (HCA2) expressing the telomerase catalytic subunit (hTERT) were grown on a plastic surface at 37°C in a 5% CO2 atmosphere in complete fibroblast culture medium [high glucose DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin]. At 80% confluency, fibroblasts were detached with 0.25% Trypsin-EDTA (37 °C for 5 min) and re-seeded at a density of 5000 cells/cm2.

extract_protocol:
Fibroblasts (F), myofibroblasts (M), and myofibroblasts treated with resting (R) or cytokine-primed (P) hMSC(AT)-CM were collected and preserved in RNAprotect Cell Reagent (Qiagen, Germany) and stored at − 80 °C until RNA isolation. RNA was isolated with the RNeasy Micro Kit (Qiagen, Germany) according to the manufacturer’s protocol.
RNA library preparation and sequencing were done by the molecular biology platform of the Institut de recherches cliniques de Montréal (IRCM). The RNA was quantified with a Qubit (Invitrogen), and RNA quality was measured on a BioAnalyzer chip (Agilent); the RNA integrity (RIN) was 7 or greater. Ribosomal RNA was depleted for 400 ng of total RNA (Ribocop depletion kit v 3.1; Lexogen), and libraries were prepared with the KAPA RNA hyperprep kit (Roche). Briefly, depleted RNA was reverse transcribed, the resulting cDNA was fragmented (94 °C 8 min), blunt-ended, and indexed adaptors were ligated. Ligated products were then amplified by PCR (9 cycles) and purified on KAPA pure beads (1:1 ratio). The final library had an average size distribution of 344 bp, and libraries were quantified by qPCR, and sequenced in paired-end 100 bp reads on Illumina NovaSeq 6000.

treatment_protocol: For activation, fibroblasts 5x10e3/cm2 were seeded in 6-well cell culture plates in complete media. Once attached, media was replaced by DMEM with 1% penicillin/ streptomycin (serum-free DMEM) and 5ng/mL of TGF-β was added to each well. After 72h, TGF-β activation (i.e. myofibroblast phenotype), was confirmed by determining α-SMA and procollagen I protein levels, visualizing stress fibers and collagen I by immunofluorescence, evaluating acquired apoptosis resistance by flow cytometry. Human adipose tissue-derived mesenchymal multipotent stromal cell hMSC(AT) were primed with IFN-ɣ and TNF-α as per the ISCT recommendations [Krampera M et al. Cytotherapy, 2013. 15(9): p. 1054-1061]. To evaluate the capacity of hMSC(AT)-CM to modulate/revert the myofibroblast phenotype, 5x10e3 fibroblasts/cm2 were seeded in 6 well plates. Following activation with TGF-β, myofibroblasts were washed with PBS, and medium was replaced by resting or primed hMSC(AT)-CM for 72h. Serum-free DMEM was used as control. The readouts for these experiments included protein levels of α-SMA and procollagen I and transcriptomic analysis for fibroblasts (F), myofibroblasts (M), myofibroblasts treated with resting (R) or primed (P) hMSC(AT)-CM.

value: 5ng/mL TGF-β in serum-free DMEM for 72 hours; followed by 72 hours with cytokine-primed (IFN-γ and TNF-α) human adipose tissue derived multipotent mesenchymal stromal cell conditioned media [hMSC(AT)-CM]

tag: phenotype group

value: Myofibroblast with cytokine-primed hMSC(AT)-CM treatment

tag: group id

value: P


title: RNC_WT1

value: brain

value: Ribosome nascent-chain complex-bound mRNAs

value: Negative control


title: Fibroblasts, TGF-β 72h, Cytokine-primed hMSC(AT)-CM 72h, rep4

source_name: Immortalized normal human diploid fibroblasts (HCA2) expressing the telomerase catalytic subunit (hTERT)


title: D21-TH-2-plasma intensity high

description: smart-seq 2


title: D20-TH-2-plasma intensity high

description: smart-seq 2


title: Fibroblasts, TGF-β 72h, Cytokine-primed hMSC(AT)-CM 72h, rep3

value: Immortalized normal human diploid fibroblasts (HCA2) expressing the telomerase catalytic subunit (hTERT)


title: D19-TH-2-plasma intensity high

description: smart-seq 2


title: Drosophila_yakuba_testes_G_z24_130917_I1135

city: Davis

first: Ben

last: Hopkins

address: One Shields Avenue

department: Evolution & Ecology

institute: UC Davis

data_processing:
After quality filtering with trimmomatic, we obtained 10, 22, 38, and 54 million reads for each of the 4 or five libraries.
Mapped paired-end reads to the genome and annotation from each species using STAR v. 2.5.3 (Dobin et al. 2013).
Assemlbed reference-only transcripts using Stringtie v. 1.3.4 (Pertea et al. 2015) to estimate expression in Transcrpts per million (TPM).
Assembly: Flybase: Dmel_r6.12, Dsim_r2.02, Dyak_r1.05, Dana_r1.05  NCBI: Dbia_2.0, Dbip_2.0, Dele_2.0, Deug_2.0, Dfic_2.0, Dkik_2.0, Dtak_2.0
Supplementary files format and content: Tab delimmited TPM files. One column for each biological replicate

organism: Drosophila yakuba

source_name: testes

extract_protocol:
We isolated mRNA from total RNA using NEBNext Poly(A) mRNA magnetic isolation.
Constructed RNA-seq directional paired-end libraries using NEBNext Ultra Directional RNA Library prep kit. We quantified library size using NEBNext Library Quant Kit (New England BioLabs, Ipswich, MA)

value: testes

tag: sample id

tag: library name

tag: strain information


title: D17-TH-2-plasma intensity high

description: smart-seq 2


title: Drosophila_yakuba_testes_G_z24_131017_I1125


title: D18-TH-2-plasma intensity high

description: smart-seq 2


title: Fibroblasts, TGF-β 72h, Cytokine-primed hMSC(AT)-CM 72h, rep2


title: D15-TH-2-plasma intensity low

description: smart-seq 2


title: D16-TH-2-plasma intensity low

description: smart-seq 2


title: Drosophila_yakuba_ag_G_z23_130917_I1135

source_name: accessory glands

value: accessory glands


title: Fibroblasts, TGF-β 72h, Cytokine-primed hMSC(AT)-CM 72h, rep1


title: Drosophila_yakuba_ag_G_z23_131017_I1125


title: D14-TH-2-plasma intensity low

description: smart-seq 2


title: 9007

value: Lung


title: Drosophila_simulans_testes_NG_z20_131017_I1125

organism: Drosophila simulans


title: D12-TH-2-plasma intensity low

description: smart-seq 2


title: Fibroblasts, TGF-β 72h, Resting hMSC(AT)-CM 72h, rep5

value: 5ng/mL TGF-β in serum-free DMEM for 72 hours; followed by 72 hours with resting human adipose tissue derived multipotent mesenchymal stromal cell conditioned media [hMSC(AT)-CM]

value: Myofibroblast with resting hMSC(AT)-CM treatment

value: R


title: D10-TH-2-plasma intensity low

description: smart-seq 2

value: Brain


title: 9001

value: P63+ lung progenitor cells

value: lung progenitor cells

value: BE


title: D11-TH-2-plasma intensity low

description: smart-seq 2

value: isolated cells

value: microglia


title: D9-TH-2-plasma intensity low

description: smart-seq 2


title: Drosophila_simulans_testes_G_z18_131017_I1125


title: Fibroblasts, TGF-β 72h, Resting hMSC(AT)-CM 72h, rep4


title: Drosophila_simulans_testes_G_z18_130917_I1135


title: D8-TH-2-plasma intensity none

description: smart-seq 2


title: Fibroblasts, TGF-β 72h, Resting hMSC(AT)-CM 72h, rep3


title: D7-TH-2-plasma intensity none

description: smart-seq 2


title: Drosophila_simulans_ag_NG_z19_130917_I1135


title: D6-TH-2-plasma intensity none

description: smart-seq 2


title: Drosophila_simulans_ag_NG_z19_131017_I1125


title: D13-TH-2-plasma intensity low

description: smart-seq 2


title: D3-TH-2-plasma intensity none

description: smart-seq 2


title: Drosophila_simulans_ag_G_z17_131017_I1125


title: D1-TH-2-plasma intensity none

description: smart-seq 2


title: D2-TH-2-plasma intensity none

description: smart-seq 2


title: C23-TH-2-plasma intensity high

description: smart-seq 2


title: Drosophila_simulans_ag_G_z17_130917_I1135


title: Fibroblasts, TGF-β 72h, Non-treated 72h, rep4

value: 5ng/mL TGF-β in serum-free DMEM for 72 hours; followed by serum-free DMEM for 72 hours

value: Myofibroblast

value: M


title: C21-TH-2-plasma intensity high

description: smart-seq 2


title: Fibroblasts, TGF-β 72h, Non-treated 72h, rep3


title: C22-TH-2-plasma intensity high

description: smart-seq 2


title: Fibroblasts, TGF-β 72h, Non-treated 72h, rep1


title: C20-TH-2-plasma intensity high

description: smart-seq 2


title: C18-TH-2-plasma intensity high

description: smart-seq 2


title: myopba3

city: Ithaca

first: Abigail

last: Benvie

address: 526 Campus Rd

institute: Cornell University

data_processing:
Basic analysis including preprocessing, mapping to reference genome, and gene expression analysis to generate normalized counts and statistical analysis of differential gene expression
reads were trimmed for low quality and adaptor sequences with TrimGalore v0.6.0, a wrapper for cutadapt  and fastQC .
reads were mapped to the reference genome/transcriptome using STAR v2.7.0e
SARTools and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression
Assembly: reference genome: Ensembl GRCm38
Supplementary files format and content: CSV files including all samples used in analysis, indivudal normalized counts, and gene names/IDs  across groups
Supplementary files format and content: processed data was not distributed per sample and instead in bulk (matrix table) with all biological replicates per group; CONT_MYOPB_norm.count.csv and CONT_MYOPBA_norm.count.csv

source_name: skeletal muscle

extract_protocol:
RNA was extracted using the standard chloroform extraction and isopropanol precipitation method. RNA concentrations and quality were determined using a TECAN infinite F-nano+ spectrophotometer.
750 ng of Poly (A) enriched RNA was used for directional RNAseq library preparation using the NEBNext Ultra II RNA Library Prep Kit according to standard protocol.

value: skeletal muscle

tag: Sex

value: male

value: PdgfrB D489V

tag: age

value: 2 month old


title: C17-TH-2-plasma intensity high

description: smart-seq 2


title: Fibroblasts, TGF-β 72h, Resting hMSC(AT)-CM 72h, rep2

value: Immortalized normal human diploid fibroblasts (HCA2) expressing the telomerase catalytic subunit (hTERT)


title: C19-TH-2-plasma intensity high

description: smart-seq 2


title: myopba5


title: C16-TH-2-plasma intensity low

description: smart-seq 2


title: D4-TH-2-plasma intensity none

description: smart-seq 2


title: Fibroblasts, Non-treated, rep5

value: None; Cells cultured in serum-free DMEM for 144 hours

value: Fibroblast

value: F


title: D5-TH-2-plasma intensity none

description: smart-seq 2

value: Brain


title: myopba4


title: myopba2


title: Fibroblasts, TGF-β 72h, Resting hMSC(AT)-CM 72h, rep1

value: 5ng/mL TGF-β in serum-free DMEM for 72 hours; followed by 72 hours with resting human adipose tissue derived multipotent mesenchymal stromal cell conditioned media [hMSC(AT)-CM]

value: Myofibroblast with resting hMSC(AT)-CM treatment

value: R


title: Fibroblasts, TGF-β 72h, Non-treated 72h, rep5


title: Homo_DeM

value: brain

value: demethylated by ALKB

value: WDR4 mKI

tag: fraction

value: small RNA


title: C14-TH-2-plasma intensity low

description: smart-seq 2

value: isolated cells

value: microglia


title: myopba1

value: skeletal muscle

value: male


title: C13-TH-2-plasma intensity low

description: smart-seq 2


title: C12-TH-2-plasma intensity low

description: smart-seq 2


title: Fibroblasts, TGF-β 72h, Non-treated 72h, rep2

value: 5ng/mL TGF-β in serum-free DMEM for 72 hours; followed by serum-free DMEM for 72 hours

value: Myofibroblast

value: M


title: C15-TH-2-plasma intensity low

description: smart-seq 2


title: C11-TH-2-plasma intensity low

description: smart-seq 2


title: Fibroblasts, Non-treated, rep3

value: Immortalized normal human diploid fibroblasts (HCA2) expressing the telomerase catalytic subunit (hTERT)

value: None; Cells cultured in serum-free DMEM for 144 hours

value: Fibroblast


title: Fibroblasts, Non-treated, rep4

value: F


title: Myopb5

value: PdgfrB Knock Out

value: 2 month old


title: Myopb4


title: Fibroblasts, Non-treated, rep2


title: C8-TH-2-plasma intensity none

description: smart-seq 2

value: Brain


title: Fibroblasts, Non-treated, rep1


title: C10-TH-2-plasma intensity low

description: smart-seq 2


title: C7-TH-2-plasma intensity none

description: smart-seq 2


title: C9-TH-2-plasma intensity low

description: smart-seq 2


title: C6-TH-2-plasma intensity none

description: smart-seq 2


title: C5-TH-2-plasma intensity none

description: smart-seq 2


title: Myopb2


title: C3-TH-2-plasma intensity none

description: smart-seq 2


title: C4-TH-2-plasma intensity none

description: smart-seq 2


title: Myopb3


title: High miR-1, replicate 6, RNA-seq

city: Lexington

first: Benjamin

last: Burke

state: KY

address: 741 S. Limestone

institute: University of Kentucky

data_processing:
Read sequences in fastq format were aligned to the human genome (hg38).
Assembly: hg38
Supplementary files format and content: Text document read counts.

source_name: Adipose tissue

extract_protocol:
Adipose biopsies were homogenized and total RNA was isolated.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Human participants underwent a single bout of total body resistance exercise. Adipose tissue biopsies were taken approximately 70 minutes after exercise.

value: Adipose tissue

value: Resistance exercise


title: Low miR-1, replicate 6, RNA-seq


title: Low miR-1, replicate 5, RNA-seq


title: C2-TH-2-plasma intensity none

description: smart-seq 2


title: C1-TH-2-plasma intensity none

description: smart-seq 2


title: Myopb1


title: B22-TH-2-plasma intensity high

description: smart-seq 2


title: Myocont 5

value: wild type


title: B21-TH-2-plasma intensity high

description: smart-seq 2

value: isolated cells


title: B23-TH-2-plasma intensity high

description: smart-seq 2

value: microglia


title: High miR-1, replicate 5, RNA-seq


title: Myocont 4

value: skeletal muscle


title: B20-TH-2-plasma intensity high

description: smart-seq 2


title: B19-TH-2-plasma intensity high

description: smart-seq 2


title: Myocont 3

value: male


title: Low miR-1, replicate 4, RNA-seq


title: B18-TH-2-plasma intensity high

description: smart-seq 2


title: Myocont 2


title: B17-TH-2-plasma intensity high

description: smart-seq 2


title: B16-TH-2-plasma intensity low

description: smart-seq 2


title: Low miR-1, replicate 2, RNA-seq


title: Myocont 1


title: UV2 (lncRNA)

city: Kunming

first: Yi hang

last: Huang

state: Yunnan

address: No. 1168 Chunrong West Road, Yuhua Street, Chenggong District, Kunming City

institute: Kunming Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw dataswere calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead etal., 2009) without mismatch to analyze their expression and distribution on the reference
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself.
The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA. The available software miREvo (Wen et al., 2012) and mirdeep2 (Friedlander et al., 2011) were integrated to predict novel miRNA through exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the small RNA tags unannotated in the former steps. At the same time, custom scripts were used to obtain the identified miRNA counts as well as base bias on the first position with certain length and on each position of all identified miRNA respectively.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes differential lnC RNA between Control and UV
Supplementary files format and content: tab-delimited text file includes differential TF between Control and UV

source_name: back skin

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7775L) was used with 0.4 ug of total RNA for the construction of sequencing libraries.
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina®(NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, NEB 3' SR Adaptor was directly, and specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5´ SR Adaptor in the subsequent ligation step. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H–). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X) primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips

value: back skin

value: UV


title: UV3 (lncRNA)


title: High miR-1, replicate 2, RNA-seq


title: High miR-1, replicate 3, RNA-seq


title: B14-TH-2-plasma intensity low

description: smart-seq 2


title: B13-TH-2-plasma intensity low

description: smart-seq 2


title: B12-TH-2-plasma intensity low

description: smart-seq 2


title: B11-TH-2-plasma intensity low

description: smart-seq 2


title: High miR-1, replicate 4, RNA-seq


title: B6-TH-2-plasma intensity none

description: smart-seq 2


title: B9-TH-2-plasma intensity low

description: smart-seq 2


title: C3 (lncRNA)

value: control


title: B8-TH-2-plasma intensity none

description: smart-seq 2


title: High miR-1, replicate 1, RNA-seq


title: Low miR-1, replicate 3, RNA-seq


title: C2 (lncRNA)


title: B5-TH-2-plasma intensity none

description: smart-seq 2


title: B7-TH-2-plasma intensity none

description: smart-seq 2


title: C1 (lncRNA)


title: B15-TH-2-plasma intensity low

description: smart-seq 2


title: MGC-803,LV-KR-4

city: Taizhou

first: Yang

last: Yang

address: 366 Taihu Road

institute: Taizhou People’s Hospital Affiliated to Nanjing Medical University

data_processing:
To identify differentially expressed genes (DEGs) between cells of TRPV1K823R and TRPV1WT, each transcript expression level was calculated according to the fragments per kb of transcript per million mapped reads (FPKM) method. The gene abundances were quantified using the RSEM software, while EdgeR software was used for differential expression analysis and quantified transcript read counts. In addition, the differential expression analysis was carried out on an online platform (www.majorbio.com) followed by multiple check calibration (BH). A differentially expressed gene is identified as relative read counts > 2 fold change and adjusted p value (q value) < 0.05. KEGG enrichment analysis was performed using the ‘‘KOBAS 2.0’’ software followed by Fisher’s exact test. If the adjusted q value is < 0.05, we consider the GO terms or KEGG signaling pathways to be significantly enriched.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each Sample
Supplementary files format and content: tab-delimited text file include RPKM values for each Sample

extract_protocol:
The samples were delivered to the company (Majorbio Bio-pharm Technology) to prepare RNA samples and conduct high-throughput RNA-seq. Total RNA was extracted from cells using TRIzol Reagent according to the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (Takara). RNA quality was determined by 2100 Bioanalyser (Agilent Technologies) and quantified using ND-2000 (NanoDrop Technologies). Only high-quality RNA samples (OD260/280 = 1.8~2.2, OD 260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, > 1 μg) were used to construct a sequencing library. RNA integrity was also confirmed with agarose gel electrophoresis.
1 mg RNA samples were used to construct a sequencing library. Briefly, messenger RNA (mRNA) was first isolated from total RNA samples and then fragmented in a fragmentation buffer. Second, double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA, USA) with random hexamer primers (Illumina, CA, USA). Third, the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Then, 200-300 bp cDNA target fragments were isolated using 2% agarose followed by PCR amplification. The isolated cDNA fragments were selected to construct a sequencing library. Libraries were quantified by TBS380 and sequenced with the Illumina HiSeqxten/NovaSeq 6000 sequencer (2×150bp read length) (Illumina).

value: KR


title: MGC-803,LV-KR-3


title: B3-TH-2-plasma intensity none

description: smart-seq 2


title: B2-TH-2-plasma intensity none

description: smart-seq 2


title: B1-TH-2-plasma intensity none

description: smart-seq 2


title: UV3 (miRNA)

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw dataswere calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead etal., 2009) without mismatch to analyze their expression and distribution on the reference
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself.
The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA. The available software miREvo (Wen et al., 2012) and mirdeep2 (Friedlander et al., 2011) were integrated to predict novel miRNA through exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the small RNA tags unannotated in the former steps. At the same time, custom scripts were used to obtain the identified miRNA counts as well as base bias on the first position with certain length and on each position of all identified miRNA respectively.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes differential expression genes between Control and UV


title: UV2 (miRNA)


title: A23-TH-2-plasma intensity high

description: smart-seq 2


title: MGC-803,LV-KR-2


title: Low miR-1, replicate 1, RNA-seq


title: A22-TH-2-plasma intensity high

description: smart-seq 2


title: B10-TH-2-plasma intensity low

description: smart-seq 2


title: MGC-803,LV-KR-1


title: UV1 (miRNA)


title: A21-TH-2-plasma intensity high

description: smart-seq 2


title: MGC-803,LV-WT-4

value: WT


title: A20-TH-2-plasma intensity high

description: smart-seq 2


title: A18-TH-2-plasma intensity high

description: smart-seq 2


title: C3 (miRNA)


title: B4-TH-2-plasma intensity none

description: smart-seq 2


title: MGC-803,LV-WT-2


title: A16-TH-2-plasma intensity low

description: smart-seq 2


title: A15-TH-2-plasma intensity low

description: smart-seq 2


title: C2 (miRNA)


title: A13-TH-2-plasma intensity low

description: smart-seq 2


title: UV1 (lncRNA)


title: A19-TH-2-plasma intensity high

description: smart-seq 2


title: MGC-803,LV-WT-1


title: A14-TH-2-plasma intensity low

description: smart-seq 2


title: C1 (miRNA)


title: A12-TH-2-plasma intensity low

description: smart-seq 2


title: A11-TH-2-plasma intensity low

description: smart-seq 2


title: FHD,knock-in FTOrs9939609-A, Day35

first: lu

last: guang

address: 1 Beichen West Road

department: Institute of Zoology

institute: Chinese Academy of Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.featureCounts v1.5.0-p3 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.
Assembly: human NCBI genome build 38.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: To differentiate into myotubes, myoblasts were seeded at 80% confluency and differentiation medium supplemented with 2% B27 was added the next day.

extract_protocol:
Total RNA was purified with TRIzol reagents (Thermo Scientific).RNA concentration was measured by NanoDrop 8000 Spectrophotometer (Thermo Scientific) or a Qubit Fluorometer (Thermo Scientific).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: To genetically engineer FTOrs9939609-TT H1 hESCs to carry the FTOrs9939609-A allele at the endogenous FTO locus, a point mutation was introduced into the endogenous FTO locus using CRISPR-Cas9 prime editing technology.

value: FHD

value: myotube

value: myotube differentiation


title: A10-TH-2-plasma intensity low

description: smart-seq 2


title: Brain_GF_6843

city: Kiel

first: Lena

last: Best

address: Michaelis-Straße 5

department: Institute of Experimental Medicine

institute: Christian-Albrechts-University Kiel

description:
H11
21Jun109_H11-L1

data_processing:
Demultiplexing was conducted with zero mismatches allowed in the barcodes. Reads were mapped using the nextflow pipeline of nf-core/rnaseq (https://nf-co.re/rnaseq). In short, the reads were quality trimmed using trimGalore (version 0.6.7) with a minimum phred score cutoff of 20 and a minimum read length of 20 bp and potential PCR-duplicates were removed with dupRadar (version 3.14) using defaults. For quality control we employed fastQC (version 0.11.9) and multiQC (version 1.10.1). Quality processed reads were mapped against the GRCm39 mouse reference genome using STAR (version 2.6.1d) and read counts were estimated using salmon (version 1.5.2) with default parameters.
Assembly: GRCm39 (mm39)
Supplementary files format and content: Tabular delimited matrix text files of read counts per GRCm39 gene (rows) and sample (columns).

growth_protocol: As for the analysis of host responses to microbial colonization, tissues of female C57BL/6J mice (n = 24) obtained from the Experimental Biomedicine facility at the University of Gothenburg, Sweden. Throughout the experiment, the mice had ad libitum access to chow and water and were exposed to a 12:12 h light-dark cycle. The mice were divided into three treatment groups: germ-free (GF, n = 8), conventionally raised (CONVR, n = 8), and conventionalized (CONVD, n = 8). The mice within each group were not all littermates. A CONVR mouse, which was not part of the sampled CONVR group and was ~10 weeks old, served as the donor for the conventionalization process. Germ-free mice were orally gavaged with gut microbiome at 10 weeks of age on average. The gut microbiome used for conventionalization was extracted from the cecum and mixed with reduced phosphate-buffered saline (PBS) to obtain a final volume of 200 μL.

extract_protocol:
At ~12 weeks of age, all mice were sacrificed for the extraction of brain, colon, liver, gonadal white adipose tissue (gWAT), and quadriceps tissues. RNA was isolated from brain, colon, liver, and quadriceps via the “RNeasy mini kit” (Qiagen, Hilden, Germany) according to the manufacturer's protocol, while RNA from gWAT was isolated using the TRIZOL method as previously described 98. Briefly, 1 ml TRIzol was added to 50–75 mg pestle-homogenized tissue followed by vortexing, a 5-min incubation at room temperature, and addition of 200 μl chloroform. After mixing, further incubation at room temperature for 2–3 min and centrifugation (12.000 g) at 4 °C for 5 min, the clear supernatant was mixed with 500 μl isopropanol followed by incubation at room temperature for 10 min. After further centrifugation (12.000 g) at 4 °C for 10 min, the supernatant was discarded and the pellet washed with 1 ml cold 75% EtOH followed by vortexing and centrifugation (7.500 g, 4 °C, 5 min). The pellet was dried and dissolved in RNase-free water. All animal protocols were approved by the Gothenburg Animal Ethics Committee (vote #2652-19).
RNA was reverse-transcribed into Illumina shotgun sequencing libraries with TruSeq RNA stranded kit and polyA enrichment following the manufacturer’s protocol (Illumina, San Diego, CA) at the Competence Centre for Genomic Analysis (Kiel, Germany) and sequenced for 2×100 cycles in paired-end mode on an Illumina NovaSeq6000 machine.

value: GF

tag: strain

value: Female

value: 12.0 weeks

tag: library batch

value: Run 2


title: Brain_CONVR_6851

description:
H12
21Jun109_H12-L1

tag: tissue

value: Brain

value: CONVR

value: 11.1 weeks


title: A9-TH-2-plasma intensity low

description: smart-seq 2

data_processing:
raw sequencing files in blc format were demultiplexed with bcl2fastq to generate fastq files and were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore!. Trimmed reads were aligned using STAR (v.2.5.3a) GeneCounts function, multi-mapped reads were filtered, and gene expression matrices were generated using SeqMonk. Seurat package was used to perform all downstream analysis.
Assembly: mm10
Supplementary files format and content: counttable (Text file)

tag: cell line

value: isolated cells

value: microglia


title: Brain_CONVD_6835

description:
H10
21Jun109_H10-L1

value: CONVD

value: 11.7 weeks


title: GSCs, ShMDH2-63_set 2

city: Pittsburgh

first: Jeremy

last: Rich

state: PA

address: 5115 Centre Ave

department: Hillman Cancer Center

institute: University of Pittsburgh Medical Center

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence- quality sequence using CLC genomic benchmark (paraeter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38 using CLC genomic benchmark (parametes- mismatch
Read count extraction and normalization was performed using CLC genomic benchmark
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts and RPKM for each sample

source_name: 387 GSC

growth_protocol: Cells were cultured as spheres in Neurobasal medium supplemented with B27, L-glutamine, sodium pyruvate, 1% penicillin/streptomycin, 10 ng/ml basic fibroblast growth factor (bFGF), and 10 ng/ml epidermal growth factor (EGF).

extract_protocol:
TRIzol reagent (Sigma Aldrich) was used to isolate total cellular RNA from cell pellets
Library construction was performed by Novogene

value: 387 GSC

tag: cell type

value: Glioblastoma stem cells


title: Quadriceps_CONVR_6851

description:
H09
21Jun109_H09-L1

source_name: Quadriceps

value: Quadriceps


title: A7-TH-2-plasma intensity none

description: smart-seq 2


title: A8-TH-2-plasma intensity none

description: smart-seq 2


title: A6-TH-2-plasma intensity none

description: smart-seq 2


title: MGC-803,LV-WT-3

value: WT


title: A17-TH-2-plasma intensity high

description: smart-seq 2


title: Quadriceps_GF_6843

description:
H08
21Jun109_H08-L1


title: A4-TH-2-plasma intensity none

description: smart-seq 2


title: GSCs, shMDH2-03_set 2


title: A5-TH-2-plasma intensity none

description: smart-seq 2


title: A3-TH-2-plasma intensity none

description: smart-seq 2


title: A2-TH-2-plasma intensity none

description: smart-seq 2


title: Quadriceps_CONVD_6835

description:
H07
21Jun109_H07-L1


title: P23-TH-1-plasma intensity high

description: smart-seq 2


title: A1-TH-2-plasma intensity none

description: smart-seq 2


title: gWAT_CONVR_6851

description:
H06
21Jun109_H06-L1

source_name: gWAT

value: gWAT


title: GSCs, ShMDH2-63_set 1


title: GSCs, shMDH2-03_set 1


title: P22-TH-1-plasma intensity high

description: smart-seq 2


title: H1D,control, Day35

value: skeletal muscle

value: myotube

value: myotube differentiation


title: P21-TH-1-plasma intensity high

description: smart-seq 2


title: GSCs, shCONT set 1

value: shCONT


title: P19-TH-1-plasma intensity high

description: smart-seq 2


title: gWAT_CONVD_6835

description:
H04
21Jun109_H04-L1

value: Female

value: Run 2


title: P20-TH-1-plasma intensity high

description: smart-seq 2

value: Brain


title: P18-TH-1-plasma intensity high

description: smart-seq 2


title: 200029

city: Los Angeles

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

data_processing:
Adapter sequences were trimmed off from the raw reads using Cutadapt (Martin, 2011) and only reads with minimum 30bp were kept for downstream analysis.  Reads were aligned to GRCh38 reference genome using bsbolt align function and the duplicated reads were marked with samtools markdup function before calling methylation using bsbolt callmethylation function (Farrell et al, 2021).  CGmaps from all samples were aggregated into one methylation count matrix using bsbolt aggregatematrix function with parameters -min-coverage 20 -min-sample 1.0.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing methylation level per CpG site for each sample

source_name: Blood

extract_protocol:
8ml of blood was drawn into the ACD tube.  After Ficol density gradient centrifugation, PBMCs were separated isolated  and cryopreserved in FCS/DMSO.
Genomic DNA was extracted from PBMCs using phenol-chloroform method (Guha et al, 2018).  500ng genomic DNA was sheared and subject to end-repair, A-tailing and ligated with methylated adaptors.  Purified libraries were hybridized to biotinylated probes and subjected for bisulfite conversion (Zymo Cat# D5030).  Captured DNA was PCR amplified with KAPA HiFi HotStart Uracil+ (Cat# KK2801) into a final TBS-seq library.  Library quality was evaluated using TapeStation with the high-sensitivity D1000 tape (Agilent Cat# 5067- 5584).  A comprehensive TBS-seq protocol is demonstrated in (Morselli et al, 2021).

value: Blood

value: PBMC

value: F

tag: ethnicity

value: Black

tag: cmv r

value: NEG

tag: cmv d

value: POS

tag: time

value: PreTx


title: Liver_CONVR_6851

description:
H03
21Jun109_H03-L1

source_name: Liver

value: Liver

tag: treatment

value: CONVR

value: 11.1 weeks


title: P17-TH-1-plasma intensity high

description: smart-seq 2

source_name: Brain

extract_protocol:
cells were lysed in the lysis buffer and follow the smart-seq2 pipeline to generate cDNA
smart-seq2 in house pipeline

value: isolated cells

value: microglia


title: P15-TH-1-plasma intensity low

description: smart-seq 2


title: Liver_GF_6843

description:
H02
21Jun109_H02-L1

value: GF

value: 12.0 weeks


title: 190098

value: M

value: Asian


title: P16-TH-1-plasma intensity low

description: smart-seq 2

value: Brain


title: GSCs, shCONT set 2

value: 387 GSC

value: Glioblastoma stem cells

value: shCONT


title: 200006

value: Blood

value: PBMC

value: F

value: White


title: Liver_CONVD_6835

description:
H01
21Jun109_H01-L1

value: Liver

value: CONVD

value: Female

value: 11.7 weeks

value: Run 2


title: P13-TH-1-plasma intensity low

description: smart-seq 2

value: isolated cells

value: microglia


title: P11-TH-1-plasma intensity low

description: smart-seq 2


title: P12-TH-1-plasma intensity low

description: smart-seq 2


title: 190071

value: POS

value: PreTx


title: Brain_CONVR_6850

description:
G12
21Jun109_G12-L1

value: Brain

value: CONVR

value: 11.1 weeks


title: gWAT_GF_6843

description:
H05
21Jun109_H05-L1

value: gWAT

value: GF

value: 12.0 weeks


title: P9-TH-1-plasma intensity low

description: smart-seq 2


title: P10-TH-1-plasma intensity low

description: smart-seq 2


title: 190050

value: Blood

value: PBMC

value: F

value: Asian


title: Brain_GF_6842

description:
G11
21Jun109_G11-L1

value: Female


title: Brain_CONVD_6834

description:
G10
21Jun109_G10-L1

value: CONVD

value: 11.7 weeks


title: P7-TH-1-plasma intensity none

description: smart-seq 2

value: isolated cells


title: Quadriceps_CONVR_6850

description:
G09
21Jun109_G09-L1

value: Quadriceps

value: Run 2


title: 190020

value: Other

value: NEG

value: POS

value: PreTx


title: P14-TH-1-plasma intensity low

description: smart-seq 2

value: Brain

value: microglia


title: Quadriceps_GF_6842

description:
G08
21Jun109_G08-L1

value: GF

value: 12.0 weeks


title: P3-TH-1-plasma intensity none

description: smart-seq 2


title: 190014

value: Blood

value: PBMC

value: Hispanic


title: P4-TH-1-plasma intensity none

description: smart-seq 2


title: O23-TH-1-plasma intensity high

description: smart-seq 2


title: Quadriceps_CONVD_6834

description:
G07
21Jun109_G07-L1

value: Female


title: P2-TH-1-plasma intensity none

description: smart-seq 2


title: P1-TH-1-plasma intensity none

description: smart-seq 2


title: 190013

value: M

value: White


title: gWAT_CONVR_6850

description:
G06
21Jun109_G06-L1

value: gWAT

value: CONVR

value: 11.1 weeks


title: O20-TH-1-plasma intensity high

description: smart-seq 2

value: isolated cells


title: 190067

value: F

value: NEG


title: O21-TH-1-plasma intensity high

description: smart-seq 2


title: 180077

value: POS

value: PreTx


title: O19-TH-1-plasma intensity high

description: smart-seq 2

value: Brain

value: microglia


title: gWAT_CONVD_6834

description:
G04
21Jun109_G04-L1

value: CONVD

value: 11.7 weeks

value: Run 2


title: gWAT_GF_6842

description:
G05
21Jun109_G05-L1

value: GF

value: 12.0 weeks


title: O22-TH-1-plasma intensity high

description: smart-seq 2


title: P8-TH-1-plasma intensity none

description: smart-seq 2


title: 190034

value: Blood

value: PBMC

value: M


title: P6-TH-1-plasma intensity none

description: smart-seq 2


title: P5-TH-1-plasma intensity none

description: smart-seq 2


title: 190009

value: White


title: O17-TH-1-plasma intensity high

description: smart-seq 2


title: O16-TH-1-plasma intensity low

description: smart-seq 2


title: Liver_CONVR_6850

description:
G03
21Jun109_G03-L1

value: Liver

value: CONVR

value: Female

value: 11.1 weeks


title: 180071

value: F

value: Hispanic

value: POS


title: O14-TH-1-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: O18-TH-1-plasma intensity high

description: smart-seq 2


title: O13-TH-1-plasma intensity low

description: smart-seq 2


title: Liver_GF_6842

description:
G02
21Jun109_G02-L1

value: Run 2


title: O15-TH-1-plasma intensity low

description: smart-seq 2


title: Liver_CONVD_6834

description:
G01
21Jun109_G01-L1

value: CONVD

value: 11.7 weeks


title: 180067

value: Blood

value: NEG

value: UNK

value: PreTx


title: Brain_CONVR_6849

description:
F12
21Jun109_F12-L1


title: O11-TH-1-plasma intensity low

description: smart-seq 2


title: O12-TH-1-plasma intensity low

description: smart-seq 2


title: O10-TH-1-plasma intensity low

description: smart-seq 2


title: O8-TH-1-plasma intensity none

description: smart-seq 2


title: 180064

value: PBMC

value: M


title: 180073

value: White


title: O9-TH-1-plasma intensity low

description: smart-seq 2


title: Brain_GF_6841

description:
F11
21Jun109_F11-L1

value: GF

value: Female

value: 12.0 weeks


title: 180056

value: Hispanic

value: POS


title: O7-TH-1-plasma intensity none

description: smart-seq 2

value: Brain

value: isolated cells


title: O6-TH-1-plasma intensity none

description: smart-seq 2

value: microglia


title: O5-TH-1-plasma intensity none

description: smart-seq 2


title: 180037

value: F


title: 180052


title: Brain_CONVD_6833

description:
F10
21Jun109_F10-L1

value: CONVD

value: 11.7 weeks

value: Run 2


title: Quadriceps_CONVR_6849

description:
F09
21Jun109_F09-L1

value: Quadriceps

value: CONVR

value: 11.1 weeks


title: 180034

value: Blood

value: PBMC

value: PreTx


title: O4-TH-1-plasma intensity none

description: smart-seq 2


title: O3-TH-1-plasma intensity none

description: smart-seq 2


title: Quadriceps_GF_6841

description:
F08
21Jun109_F08-L1

value: GF

value: Female


title: O1-TH-1-plasma intensity none

description: smart-seq 2


title: O2-TH-1-plasma intensity none

description: smart-seq 2


title: N23-TH-1-plasma intensity high

description: smart-seq 2


title: N22-TH-1-plasma intensity high

description: smart-seq 2


title: Quadriceps_CONVD_6833

description:
F07
21Jun109_F07-L1


title: 180032

value: M

value: White

value: NEG


title: gWAT_GF_6841

description:
F05
21Jun109_F05-L1

value: gWAT

value: 12.0 weeks


title: 180030

value: F

value: Hispanic

value: POS


title: N21-TH-1-plasma intensity high

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: 180019


title: N20-TH-1-plasma intensity high

description: smart-seq 2


title: gWAT_CONVD_6833

description:
F04
21Jun109_F04-L1

value: CONVD

value: 11.7 weeks

value: Run 2


title: N17-TH-1-plasma intensity high

description: smart-seq 2


title: N16-TH-1-plasma intensity low

description: smart-seq 2


title: 180018

value: Blood

value: PBMC

value: PreTx


title: Liver_CONVR_6849

description:
F03
21Jun109_F03-L1

value: Liver

value: CONVR

value: Female

value: 11.1 weeks


title: N18-TH-1-plasma intensity high

description: smart-seq 2


title: N19-TH-1-plasma intensity high

description: smart-seq 2


title: 180019-2

value: NEG

value: PostTx


title: Liver_GF_6841

description:
F02
21Jun109_F02-L1

value: GF

value: 12.0 weeks


title: 180013

value: F

value: White

value: POS


title: 180009

value: M

value: Hispanic


title: N15-TH-1-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: N13-TH-1-plasma intensity low

description: smart-seq 2


title: N12-TH-1-plasma intensity low

description: smart-seq 2


title: N14-TH-1-plasma intensity low

description: smart-seq 2


title: Liver_CONVD_6833

description:
F01
21Jun109_F01-L1

value: CONVD

value: 11.7 weeks

value: Run 2


title: N11-TH-1-plasma intensity low

description: smart-seq 2


title: 170061

value: Blood

value: PBMC

value: PreTx


title: Brain_CONVR_6848

description:
E12
21Jun109_E12-L1

value: CONVR

value: Female

value: 11.1 weeks


title: N9-TH-1-plasma intensity low

description: smart-seq 2


title: Brain_GF_6840

description:
E11
21Jun109_E11-L1

value: GF

value: 12.0 weeks


title: Brain_CONVD_6832

description:
E10
21Jun109_E10-L1


title: 170060

value: POS


title: N8-TH-1-plasma intensity none

description: smart-seq 2


title: N6-TH-1-plasma intensity none

description: smart-seq 2


title: N10-TH-1-plasma intensity low

description: smart-seq 2


title: N5-TH-1-plasma intensity none

description: smart-seq 2


title: 170055

value: F

value: White

value: NEG


title: Quadriceps_CONVR_6848

description:
E09
21Jun109_E09-L1

value: Quadriceps


title: Quadriceps_GF_6840

description:
E08
21Jun109_E08-L1


title: N4-TH-1-plasma intensity none

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: Quadriceps_CONVD_6832

description:
E07
21Jun109_E07-L1

value: CONVD

value: 11.7 weeks

value: Run 2


title: 160080

value: Blood

value: PBMC

value: M

value: PreTx


title: N2-TH-1-plasma intensity none

description: smart-seq 2


title: N1-TH-1-plasma intensity none

description: smart-seq 2


title: 160068

value: UNK


title: gWAT_CONVR_6848

description:
E06
21Jun109_E06-L1

value: gWAT

value: CONVR

value: Female

value: 11.1 weeks


title: M23-TH-1-plasma intensity high

description: smart-seq 2


title: 160068-2

value: White

value: POS

value: PostTx


title: gWAT_GF_6840

description:
E05
21Jun109_E05-L1

value: GF

value: 12.0 weeks


title: 170058

value: Hispanic


title: M21-TH-1-plasma intensity high

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: 160058

value: Blood

value: PBMC

value: F

value: NEG


title: N7-TH-1-plasma intensity none

description: smart-seq 2


title: M19-TH-1-plasma intensity high

description: smart-seq 2


title: M18-TH-1-plasma intensity high

description: smart-seq 2


title: gWAT_CONVD_6832

description:
E04
21Jun109_E04-L1

value: gWAT

value: CONVD

value: 11.7 weeks

value: Run 2


title: 160058-2


title: Liver_CONVR_6848

description:
E03
21Jun109_E03-L1

value: Liver

value: CONVR

value: Female

value: 11.1 weeks


title: M17-TH-1-plasma intensity high

description: smart-seq 2


title: M15-TH-1-plasma intensity low

description: smart-seq 2


title: N3-TH-1-plasma intensity none

description: smart-seq 2


title: 160048

value: M

value: White

value: POS

value: PreTx


title: M14-TH-1-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: M16-TH-1-plasma intensity low

description: smart-seq 2


title: 160048-2

value: Blood

value: PBMC

value: PostTx


title: Liver_GF_6840

description:
E02
21Jun109_E02-L1

value: GF

value: 12.0 weeks


title: M12-TH-1-plasma intensity low

description: smart-seq 2


title: 160044

value: F

value: Black

value: NEG


title: M13-TH-1-plasma intensity low

description: smart-seq 2


title: M22-TH-1-plasma intensity high

description: smart-seq 2


title: M11-TH-1-plasma intensity low

description: smart-seq 2


title: Liver_CONVD_6832

description:
E01
21Jun109_E01-L1

value: Liver

value: CONVD

value: Female

value: 11.7 weeks

value: Run 2


title: M20-TH-1-plasma intensity high

description: smart-seq 2


title: M10-TH-1-plasma intensity low

description: smart-seq 2


title: Brain_CONVR_6847

description:
D12
21Jun109_D12-L1

value: CONVR


title: M9-TH-1-plasma intensity low

description: smart-seq 2

value: Brain


title: M8-TH-1-plasma intensity none

description: smart-seq 2

value: isolated cells


title: 160043

value: White

value: POS

value: PreTx


title: 160036

value: Blood

value: PBMC

value: M


title: Brain_CONVD_6831

description:
D10
21Jun109_D10-L1


title: M6-TH-1-plasma intensity none

description: smart-seq 2

value: microglia


title: 160020

value: F

value: Hispanic


title: M2-TH-1-plasma intensity none

description: smart-seq 2


title: Brain_GF_6839

description:
D11
21Jun109_D11-L1

value: GF

value: 11.9 weeks


title: Quadriceps_CONVR_6847

description:
D09
21Jun109_D09-L1

value: Quadriceps

value: Female

value: 12.0 weeks


title: 160014


title: M1-TH-1-plasma intensity none

description: smart-seq 2


title: 160013

value: NEG

value: UNK


title: Quadriceps_CONVD_6831

description:
D07
21Jun109_D07-L1

value: CONVD

value: 11.7 weeks

value: Run 2


title: L23-TH-1-plasma intensity high

description: smart-seq 2

value: Brain

value: isolated cells


title: L22-TH-1-plasma intensity high

description: smart-seq 2


title: M5-TH-1-plasma intensity none

description: smart-seq 2


title: gWAT_CONVR_6847

description:
D06
21Jun109_D06-L1

value: gWAT

value: CONVR


title: 140468

value: Blood

value: PBMC

value: POS

value: PreTx


title: L21-TH-1-plasma intensity high

description: smart-seq 2

value: microglia


title: L20-TH-1-plasma intensity high

description: smart-seq 2


title: gWAT_GF_6839

description:
D05
21Jun109_D05-L1

value: GF

value: 11.9 weeks


title: 140460

value: F

value: Hispanic


title: M7-TH-1-plasma intensity none

description: smart-seq 2


title: L19-TH-1-plasma intensity high

description: smart-seq 2


title: gWAT_CONVD_6831

description:
D04
21Jun109_D04-L1

value: Female


title: L17-TH-1-plasma intensity high

description: smart-seq 2


title: L18-TH-1-plasma intensity high

description: smart-seq 2


title: 140430

value: White


title: 160036-2

value: M

value: NEG

value: PostTx


title: Liver_CONVR_6847

description:
D03
21Jun109_D03-L1

value: Liver

value: 12.0 weeks

value: Run 2


title: M4-TH-1-plasma intensity none

description: smart-seq 2

value: Brain

value: isolated cells


title: L16-TH-1-plasma intensity low

description: smart-seq 2


title: Quadriceps_GF_6839

description:
D08
21Jun109_D08-L1

value: Quadriceps


title: L15-TH-1-plasma intensity low

description: smart-seq 2


title: M3-TH-1-plasma intensity none

description: smart-seq 2


title: 140430-2

value: Blood

value: PBMC

value: POS


title: L14-TH-1-plasma intensity low

description: smart-seq 2

value: microglia


title: L13-TH-1-plasma intensity low

description: smart-seq 2


title: 140427

value: PreTx


title: L12-TH-1-plasma intensity low

description: smart-seq 2


title: Liver_CONVD_6831

description:
D01
21Jun109_D01-L1

value: CONVD

value: 11.7 weeks


title: L11-TH-1-plasma intensity low

description: smart-seq 2


title: 140426

value: F

value: White


title: L10-TH-1-plasma intensity low

description: smart-seq 2


title: Brain_CONVR_6846

description:
C12
21Jun109_C12-L1

value: CONVR

value: Female


title: Brain_GF_6838

description:
C11
21Jun109_C11-L1

value: GF

value: 11.9 weeks


title: L7-TH-1-plasma intensity none

description: smart-seq 2


title: L9-TH-1-plasma intensity low

description: smart-seq 2


title: 140394

value: Hispanic


title: L8-TH-1-plasma intensity none

description: smart-seq 2

value: Brain


title: 140380


title: L6-TH-1-plasma intensity none

description: smart-seq 2

value: isolated cells


title: L4-TH-1-plasma intensity none

description: smart-seq 2


title: Brain_CONVD_6830

description:
C10
21Jun109_C10-L1

value: 12.6 weeks

value: Run 2


title: L3-TH-1-plasma intensity none

description: smart-seq 2


title: L1-TH-1-plasma intensity none

description: smart-seq 2


title: L5-TH-1-plasma intensity none

description: smart-seq 2


title: Quadriceps_CONVR_6846

description:
C09
21Jun109_C09-L1

value: Quadriceps

value: 12.0 weeks


title: 140375

value: Blood

value: PBMC

value: POS


title: L2-TH-1-plasma intensity none

description: smart-seq 2

value: microglia


title: Quadriceps_GF_6838

description:
C08
21Jun109_C08-L1


title: 140361

value: F

value: NEG

value: PreTx


title: Liver_GF_6839

description:
D02
21Jun109_D02-L1

value: Liver

value: Female


title: 140351

value: White


title: gWAT_CONVR_6846

description:
C06
21Jun109_C06-L1

value: gWAT

value: CONVR


title: Quadriceps_CONVD_6830

description:
C07
21Jun109_C07-L1

value: CONVD


title: K23-TH-1-plasma intensity high

description: smart-seq 2

value: Brain

value: isolated cells


title: K21-TH-1-plasma intensity high

description: smart-seq 2


title: K22-TH-1-plasma intensity high

description: smart-seq 2


title: 140335

value: Asian


title: 140387


title: K20-TH-1-plasma intensity high

description: smart-seq 2


title: K19-TH-1-plasma intensity high

description: smart-seq 2


title: gWAT_GF_6838

description:
C05
21Jun109_C05-L1

value: GF

value: 11.9 weeks

value: Run 2


title: K18-TH-1-plasma intensity high

description: smart-seq 2


title: K17-TH-1-plasma intensity high

description: smart-seq 2


title: K16-TH-1-plasma intensity low

description: smart-seq 2


title: gWAT_CONVD_6830

description:
C04
21Jun109_C04-L1

value: 12.6 weeks


title: Liver_CONVR_6846

description:
C03
21Jun109_C03-L1

value: 12.0 weeks


title: K15-TH-1-plasma intensity low

description: smart-seq 2

value: microglia


title: K14-TH-1-plasma intensity low

description: smart-seq 2


title: K13-TH-1-plasma intensity low

description: smart-seq 2


title: Liver_GF_6838

description:
C02
21Jun109_C02-L1


title: 140307

value: Blood

value: PBMC

value: F

value: POS


title: K12-TH-1-plasma intensity low

description: smart-seq 2


title: 140330

value: Black

value: UNK

value: PreTx


title: K11-TH-1-plasma intensity low

description: smart-seq 2


title: K10-TH-1-plasma intensity low

description: smart-seq 2


title: Liver_CONVD_6830

description:
C01
21Jun109_C01-L1

value: Liver

value: CONVD

value: Female


title: Brain_CONVR_6845

description:
B12
21Jun109_B12-L1

value: Brain

value: CONVR


title: K9-TH-1-plasma intensity low

description: smart-seq 2

value: isolated cells


title: Brain_GF_6837

description:
B11
21Jun109_B11-L1

value: GF

value: 12.4 weeks

value: Run 2


title: 140307-2

value: White

value: PostTx


title: K8-TH-1-plasma intensity none

description: smart-seq 2

value: microglia


title: K7-TH-1-plasma intensity none

description: smart-seq 2


title: 140333

value: Blood

value: PBMC

value: M

value: Other

value: NEG


title: K5-TH-1-plasma intensity none

description: smart-seq 2


title: K6-TH-1-plasma intensity none

description: smart-seq 2


title: Quadriceps_CONVR_6845

description:
B09
21Jun109_B09-L1

value: Quadriceps

value: 12.0 weeks


title: 140331

value: F

value: POS

value: PreTx


title: K2-TH-1-plasma intensity none

description: smart-seq 2

value: Brain

value: isolated cells


title: 140301


title: Quadriceps_GF_6837

description:
B08
21Jun109_B08-L1

value: GF

value: Female

value: 12.4 weeks


title: J23-TH-1-plasma intensity high

description: smart-seq 2


title: K1-TH-1-plasma intensity none

description: smart-seq 2


title: 140282

value: White


title: K4-TH-1-plasma intensity none

description: smart-seq 2

value: microglia


title: J21-TH-1-plasma intensity high

description: smart-seq 2


title: J20-TH-1-plasma intensity high

description: smart-seq 2


title: 140279

value: Blood


title: Quadriceps_CONVD_6829

description:
B07
21Jun109_B07-L1

value: CONVD

value: 12.6 weeks

value: Run 2


title: J22-TH-1-plasma intensity high

description: smart-seq 2


title: 140270

value: PBMC

value: M

value: Black

value: NEG


title: gWAT_CONVR_6845

description:
B06
21Jun109_B06-L1

value: gWAT

value: CONVR

value: 12.0 weeks


title: J17-TH-1-plasma intensity high

description: smart-seq 2

value: Brain

value: isolated cells


title: J18-TH-1-plasma intensity high

description: smart-seq 2


title: J19-TH-1-plasma intensity high

description: smart-seq 2


title: K3-TH-1-plasma intensity none

description: smart-seq 2


title: 140304

value: POS

value: PreTx


title: 140302

value: White

value: UNK


title: J16-TH-1-plasma intensity low

description: smart-seq 2

value: microglia


title: Brain_CONVD_6829

description:
B10
21Jun109_B10-L1

value: CONVD

value: Female


title: 140316

value: Blood

value: Hispanic


title: J15-TH-1-plasma intensity low

description: smart-seq 2


title: 130246

value: PBMC

value: F


title: 130239

value: M


title: Liver_CONVR_6845

description:
B03
21Jun109_B03-L1

value: Liver

value: Run 2


title: J14-TH-1-plasma intensity low

description: smart-seq 2


title: J12-TH-1-plasma intensity low

description: smart-seq 2


title: gWAT_CONVD_6829

description:
B04
21Jun109_B04-L1

value: gWAT

value: 12.6 weeks


title: J13-TH-1-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells


title: Liver_GF_6837

description:
B02
21Jun109_B02-L1

value: GF

value: 12.4 weeks


title: 130238

value: White

value: NEG

value: POS

value: PreTx


title: J11-TH-1-plasma intensity low

description: smart-seq 2

value: microglia


title: J10-TH-1-plasma intensity low

description: smart-seq 2


title: 130262

value: Blood

value: UNK


title: Liver_CONVD_6829

description:
B01
21Jun109_B01-L1

value: CONVD

value: Female


title: 130220

value: PBMC

value: F


title: J7-TH-1-plasma intensity none

description: smart-seq 2


title: Brain_CONVR_6844

description:
A12
21Jun109_A12-L1

value: CONVR

value: 12.0 weeks

value: Run 2


title: 130217

value: M

value: Hispanic


title: J5-TH-1-plasma intensity none

description: smart-seq 2

value: Brain

value: isolated cells


title: Brain_GF_6836

description:
A11
21Jun109_A11-L1

value: GF

value: 12.4 weeks


title: gWAT_GF_6837

description:
B05
21Jun109_B05-L1

value: gWAT


title: 130207

value: White

value: NEG

value: PreTx


title: Brain_CONVD_6828

description:
A10
21Jun109_A10-L1

value: CONVD

value: 12.6 weeks


title: J8-TH-1-plasma intensity none

description: smart-seq 2

value: microglia


title: J2-TH-1-plasma intensity none

description: smart-seq 2


title: Quadriceps_CONVR_6844

description:
A09
21Jun109_A09-L1

value: Quadriceps

value: Female


title: 130178

value: Blood

value: PBMC

value: F

value: POS

value: UNK


title: J1-TH-1-plasma intensity none

description: smart-seq 2

value: Brain

value: isolated cells


title: J4-TH-1-plasma intensity none

description: smart-seq 2


title: 130176


title: I23-TH-1-plasma intensity high

description: smart-seq 2


title: Quadriceps_GF_6836

description:
A08
21Jun109_A08-L1

value: GF

value: 12.4 weeks

value: Run 2


title: I21-TH-1-plasma intensity high

description: smart-seq 2


title: J3-TH-1-plasma intensity none

description: smart-seq 2


title: J9-TH-1-plasma intensity low

description: smart-seq 2


title: 130138

value: White


title: I22-TH-1-plasma intensity high

description: smart-seq 2


title: I20-TH-1-plasma intensity high

description: smart-seq 2


title: gWAT_CONVR_6844

description:
A06
21Jun109_A06-L1

value: gWAT

value: CONVR

value: 12.0 weeks


title: I18-TH-1-plasma intensity high

description: smart-seq 2

value: microglia


title: 130116

value: Hispanic

value: NEG

value: PreTx


title: I17-TH-1-plasma intensity high

description: smart-seq 2


title: gWAT_GF_6836

description:
A05
21Jun109_A05-L1

value: Female


title: J6-TH-1-plasma intensity none

description: smart-seq 2


title: I16-TH-1-plasma intensity low

description: smart-seq 2


title: I15-TH-1-plasma intensity low

description: smart-seq 2


title: I14-TH-1-plasma intensity low

description: smart-seq 2


title: 130103

value: Blood

value: PBMC

value: M


title: Liver_CONVR_6844

description:
A03
21Jun109_A03-L1

value: Liver


title: gWAT_CONVD_6828

description:
A04
21Jun109_A04-L1

value: CONVD

value: 12.6 weeks


title: Liver_GF_6836

description:
A02
21Jun109_A02-L1

value: GF

value: 12.4 weeks


title: I12-TH-1-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells


title: 130086

value: White


title: I13-TH-1-plasma intensity low

description: smart-seq 2


title: I10-TH-1-plasma intensity low

description: smart-seq 2


title: Quadriceps_CONVD_6828

description:
A07
21Jun109_A07-L1

value: Quadriceps

value: Run 2


title: Liver_CONVD_6828

description:
A01
21Jun109_A01-L1


title: 130078

value: F

value: POS


title: I7-TH-1-plasma intensity none

description: smart-seq 2

value: microglia


title: I11-TH-1-plasma intensity low

description: smart-seq 2


title: 130075

value: Asian

value: NEG

value: PreTx


title: 130093

value: Blood

value: PBMC


title: I8-TH-1-plasma intensity none

description: smart-seq 2


title: I19-TH-1-plasma intensity high

description: smart-seq 2


title: 130059

value: M

value: UNK


title: Colon_CONVR_6850_DC, REP23

description:
REP23
21Feb66_G03

source_name: Colon

value: Colon

value: CONVR

value: Female

value: 11.1 weeks

value: Run 1


title: 130034

value: White


title: I6-TH-1-plasma intensity none

description: smart-seq 2

value: Brain

value: isolated cells


title: Colon_CONVR_6849_DC, REP22

description:
REP22
21Feb66_F03


title: 130135

value: Hispanic

value: POS


title: 130029


title: I2-TH-1-plasma intensity none

description: smart-seq 2

value: microglia


title: I9-TH-1-plasma intensity low

description: smart-seq 2


title: Colon_CONVR_6848_DC, REP21

description:
REP21
21Feb66_E03


title: Colon_CONVR_6851_DC, REP24

description:
REP24
21Feb66_H03


title: Colon_CONVR_6847_DC, REP20

description:
REP20
21Feb66_D03

value: 12.0 weeks


title: I1-TH-1-plasma intensity none

description: smart-seq 2


title: H22-TH-1-plasma intensity high

description: smart-seq 2


title: H23-TH-1-plasma intensity high

description: smart-seq 2


title: 130021

value: NEG

value: PreTx


title: H20-TH-1-plasma intensity high

description: smart-seq 2


title: H21-TH-1-plasma intensity high

description: smart-seq 2


title: H19-TH-1-plasma intensity high

description: smart-seq 2


title: H18-TH-1-plasma intensity high

description: smart-seq 2


title: Colon_CONVR_6845_DC, REP18

description:
REP18
21Feb66_B03


title: J.gamma1 shLDB1_rep1

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

description:
Gamma_shLDB1_gene_count_matrix.txt
Gamma_shLDB1-1

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Transcripts per Kilobase of exon model per Million mapped reads (TPM) were calculated using a methodology adapted from the StringTie software. In brief, all isoforms of a gene were assembled and merged to generate a composite transcript model. The number of reads mapped to the exonic regions of this composite transcript model was tallied and subsequently normalized. Normalization was achieved by dividing the read count by the length of the composite transcript model (in kilobases) and then scaling the result by the size of the total mapped library (in millions of reads).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample.

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: T-ALL cells

tag: genotype


title: Colon_CONVR_6846_DC, REP19

description:
REP19
21Feb66_C03


title: J.gamma1 shLDB1_rep2

description:
Gamma_shLDB1_gene_count_matrix.txt
Gamma_shLDB1-2


title: I5-TH-1-plasma intensity none

first: Tony

last: Wyss-Coray

address: 290 Jane Stanford way, RM E365 TWC-Neurology

institute: Stanford University

description: smart-seq 2


title: I4-TH-1-plasma intensity none

description: smart-seq 2


title: H16-TH-1-plasma intensity low

description: smart-seq 2


title: I3-TH-1-plasma intensity none

description: smart-seq 2


title: Colon_CONVR_6844_DC, REP17

description:
REP17
21Feb66_A03


title: H15-TH-1-plasma intensity low

description: smart-seq 2


title: J.gamma1 shControl_rep2

description:
Gamma_shLDB1_gene_count_matrix.txt
Gamma_NC-2

value: shControl


title: H12-TH-1-plasma intensity low

description: smart-seq 2


title: 130010

value: Blood

value: PBMC

value: M

value: Black


title: H14-TH-1-plasma intensity low

description: smart-seq 2


title: Colon_GF_6843_DC, REP16

description:
REP16
21Feb66_H02

value: Colon

value: GF

value: Female


title: Colon_GF_6842_DC, REP15

description:
REP15
21Feb66_G02

value: Run 1


title: 6T-CEM shLDB1_rep1

description:
6T_shLDB1_gene_count_matrix.txt
6T_shLDB1-1


title: J.gamma1 shControl_rep1

description:
Gamma_shLDB1_gene_count_matrix.txt
Gamma_NC-1


title: H8-TH-1-plasma intensity none

description: smart-seq 2

value: Brain

value: isolated cells


title: H9-TH-1-plasma intensity low

description: smart-seq 2


title: H13-TH-1-plasma intensity low

description: smart-seq 2


title: Colon_GF_6841_DC, REP14

description:
REP14
21Feb66_F02


title: 6T-CEM shLDB1_rep2

description:
6T_shLDB1_gene_count_matrix.txt
6T_shLDB1-2


title: H7-TH-1-plasma intensity none

description: smart-seq 2


title: H10-TH-1-plasma intensity low

description: smart-seq 2


title: 6T-CEM shControl_rep1

description:
6T_shLDB1_gene_count_matrix.txt
6T_NC-1


title: Colon_GF_6840_DC, REP13

description:
REP13
21Feb66_E02


title: Colon_GF_6839_DC, REP12

description:
REP12
21Feb66_D02

value: 11.9 weeks


title: H6-TH-1-plasma intensity none

description: smart-seq 2

value: microglia


title: H5-TH-1-plasma intensity none

description: smart-seq 2


title: H4-TH-1-plasma intensity none

description: smart-seq 2


title: 6T-CEM shControl_rep2

description:
6T_shLDB1_gene_count_matrix.txt
6T_NC-2


title: H17-TH-1-plasma intensity high

description: smart-seq 2


title: 6T-CEM-shLDB1, H3K27ac, CUT&Tag

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output. CUT&Tag reads were trimmed using Fastp v0.23.2 with default settings, and were aligned to the UCSC hg38 genome using Bowtie2 version v2.4.4 with parameter --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700.
Peaks were identified using MACS3 (v3.0.0a6) with the significance cut-off FDR<0.01
bigWig files were generated using bedGraphToBigWig tool.
Assembly: hg38
Supplementary files format and content: bigwig files
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).

value: H3K27ac(Abcam, #ab4729)


title: H3-TH-1-plasma intensity none

description: smart-seq 2


title: Colon_GF_6838_DC, REP11

description:
REP11
21Feb66_C02


title: Colon_GF_6837_DC, REP10

description:
REP10
21Feb66_B02

value: 12.4 weeks


title: H2-TH-1-plasma intensity none

description: smart-seq 2


title: H1-TH-1-plasma intensity none

description: smart-seq 2


title: H11-TH-1-plasma intensity low

description: smart-seq 2


title: 6T-CEM-shControl, H3K27ac, CUT&Tag


title: G23-TH-1-plasma intensity high

description: smart-seq 2


title: Colon_GF_6836_DC, REP9

description:
REP9
21Feb66_A02


title: G21-TH-1-plasma intensity high

description: smart-seq 2


title: G22-TH-1-plasma intensity high

description: smart-seq 2


title: 6T-CEM, IgG, CUT&Tag, rep2

value: IgG(Abcam, #ab172730)


title: G20-TH-1-plasma intensity high

description: smart-seq 2


title: G19-TH-1-plasma intensity high

description: smart-seq 2


title: G16-TH-1-plasma intensity low

description: smart-seq 2


title: Colon_CONVD_6832_DC, REP5

description:
REP5
21Feb66_E01

value: CONVD

value: 11.7 weeks


title: Colon_CONVD_6835_DC, REP8

description:
REP8
21Feb66_H01


title: 6T-CEM, LDB1, CUT&Tag, rep1

value: T-ALL cells

value: LDB1(Abcam, #ab96799)


title: Colon_CONVD_6833_DC, REP6

description:
REP6
21Feb66_F01


title: G14-TH-1-plasma intensity low

description: smart-seq 2


title: 6T-CEM, IgG, CUT&Tag, rep1


title: Colon_CONVD_6834_DC, REP7

description:
REP7
21Feb66_G01


title: G15-TH-1-plasma intensity low

description: smart-seq 2


title: G13-TH-1-plasma intensity low

description: smart-seq 2


title: 6T-CEM, LDB1, CUT&Tag, rep2


title: 6T-CEM, IRF1, CUT&Tag, rep2

value: IRF1(Proteintech, #11335-1-AP)


title: G17-TH-1-plasma intensity high

description: smart-seq 2


title: 6T-CEM, IRF1, CUT&Tag, rep1


title: Colon_CONVD_6830_DC, REP3

description:
REP3
21Feb66_C01

value: 12.6 weeks


title: G18-TH-1-plasma intensity high

description: smart-seq 2


title: Colon_CONVD_6831_DC, REP4

description:
REP4
21Feb66_D01

value: Colon


title: Pool of 12-16 non-adapted larvae.

city: Irkutsk

first: Tuyana

last: Sidorova

address: 3, Ulan-Batorskaya

department: Siberian Branch of the Russian Academy of Sciences

country: Russia

institute: Limnological Institute

description: Coregonus baicalensis Dybowski, 1874

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v. 0.36.
The preprocessed reads were subjected to a de novo assembly procedure the Trinity v.2.13.2. software package
Read count extrraction and normalization were perfomed using the R package EdgeR v4.0.3.
Assembly: de novo assembly
Supplementary files format and content:tab-delimited text file includes normalized FPKM values ??for each sample

organism: Coregonus baicalensis

source_name: Pool of 12-16 non-adapted larvae.

extract_protocol:
Total RNA was isolated with TRIzol reagent (Ambion) from each individual sample (the whole larvae). RNA samples from the same group (12-16 individuals) have been combined into mixtures to obtain four RNA pools.
The library was examined using Qubit and real-time PCR for quantification and size distribution detection. Quantified libraries were pooled in equimolar amounts and sequenced on Illumina NovaSeq 6000 High Throughput Sequencer using a NovaSeq 6000 Reagent Kit v1.5 in 150 bp paired-end reads at Novogen company (China).

value: Pool of 12-16 non-adapted larvae.


title: Pool of 12-16 non-adapted larvae after acute stress.

description: Coregonus baicalensis Dybowski, 1874


title: G12-TH-1-plasma intensity low

city: Stanford

description: smart-seq 2


title: 6T-CEM, ETV6, CUT&Tag, rep2

value: ETV6(Abclonal, #A1637)


title: G11-TH-1-plasma intensity low

description: smart-seq 2


title: Colon_CONVD_6829_DC, REP2

description:
REP2
21Feb66_B01

value: Female

value: Run 1


title: G10-TH-1-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells


title: Colon_CONVD_6828_DC, REP1

description:
REP1
21Feb66_A01


title: Pool of 12-16 preadapted larvae after acute stress.

description: Coregonus baicalensis Dybowski, 1874


title: 6T-CEM, ERG, CUT&Tag, rep2

value: ERG(Proteintech, #14356-1-AP)


title: G9-TH-1-plasma intensity low

description: smart-seq 2

value: microglia


title: G8-TH-1-plasma intensity none

description: smart-seq 2


title: SJ donor 4 PBMC and SJ donor 4 Biopsy (SJ04_PBMC_SJ04_Biopsy) - GEX

city: Woolloongabba

first: Ranjeny

last: Thomas

address: 37 Kent St

country: Australia

institute: University of Queensland Diamantina Institute, Translational Research Institute

description:
SJ04_PBMC_Biopsy_filtered_feature_bc_matrix.tar.gz
All_donors_tissues_integrated_metadata.csv.gz
All_donors_tissues_integrated_metadata.csv.gz

data_processing:
Single cell RNA-seq data was processed using the 10x Genomics Cell Ranger Software (v3.0.2). The command “cellranger mkfastq” was used to demultiplex raw BCL files and generate FASTQ files for individual samples. The command “cellranger count” was used to align RNA-Seq reads to the pre-built human reference genome GRCh38 and to filter out low quality cell barcodes and unique molecular identiﬁers (UMI). The resulting single-cell gene count matrices were further processed using the Seurat R package (v3.0.5)
Assembly: human GRCh38
Supplementary files format and content: tsv, csv.gz

source_name: CD45+ cells

extract_protocol:
Salivary gland biopsy were collected from all donors and stored in cryostor. Biopsy was disaggregated using a protocol published by the AMP consortia and CD45+ cells from all thawed disaggregated ST samples were sorted via flow cytometric activated cell sorting. PBMC were collected from each participant and frozen. CD45+ immune cells from all thawed PBMC samples were sorted via flow cytometric activated cell sorting.
The 10x Genomics Chromium instrument was used to partition each single cell with barcoded beads. GEM generation and barcoding, cDNA amplification, cell surface protein and library construction was performed according to the 10X Genomics Chromium User Guide. Sequencing was performed using the Illumina NovaSeq 6000.

value: PBMC and salivary gland


title: G6-TH-1-plasma intensity none

description: smart-seq 2