title: SMM36142 [T lymphocytes]

city: Cosenza

first: Cirino

last: Botta

address: Via Migliori

department: Hematology Unit

country: Italy

institute: "Annunziata" Hospital of Cosenza

description:
10x Genomics
sc_BM_T_humans.RDS

data_processing:
scRNA-seq and scTCR-seq data from humans and mice were analyzed separately. Sample demultiplexing, alignment to the hg38 human reference genome (or the respective mice genome) and single-cell gene count was performed using the Cell Ranger Single-Cell Software Suite v.2.0.1 (https://www.10xgenomics.com/). Expression matrixes were analyzed with the R package seurat 4.0 (https://satijalab.org/seurat/) and cells were filtered according to < 10% mitochondrial expression and at least 200 (but less than 2500) mRNA counts per cell. Once scaled and normalized, a genelist including the most variable genes was obtained by the FindVariableFeatures function. After removing genes belonging to the immunoglobulin families (which could work as a confounding factor during clustering), the genelist was used to derive the principal component analysis (PCA) vectors for each sample. The first 100 PCA were used to align samples (batch removal) using the R package harmony. The new harmonized coordinates were used to develop UMAPs (dimensionality reduction). The shared nearest neighbor (SNN) algorithm based on 50 batch-corrected dimensions was used for clustering the cells into homogeneous groups that were manually identified according to the expression of canonical genes (see Supplemental Information) obtained from curated gene-sets. A sequential subclustering strategy (which consists basically in repeating the same steps as before on a specific subpopulation) to focus on clonotypic T cells was performed. Reconstruction of T cell trajectories was performed by ordering single cells in “pseudotime” according to their RNA expression through Monocle 2 R package. This package accurately resolves biological processes (ordering cells) by learning an explicit principal graph from the single cell genomics data through Reverse Graph Embedding algorithm.
TCR sequences defined by their CDR3 were obtained from Cell Ranger. T cells were considered as clonotypic if their frequency was >2/1000 cells and present in at least 3 cells, and this information was added to the Seurat object to analyze the transcriptome of these cells. scRepertoire R package was used to assess clonotype distribution as well as to investigate clonal “diversity”, characterized by clones frequency, repertoire richness and convergence (Borcherding, Bormann and Kraus, 2020; Chiffelle et al., 2020). To estimate clonal diversity and richness we used Chao and ACE indices which have been developed to deal with under sampling (i.e. ‘unseen species’), and could therefore mitigate the fact that for technical reasons, only a fraction of repertoires is sequenced and analyzed (Chiffelle et al., 2020).
Assembly: GRCh38  and mm10BM_T_humans.RDS
Supplementary files format and content: We allegated 2 different RDS files: which ventually include oll the parients
Supplementary files format and content: sc_BM_T_humans.RDS
Supplementary files format and content: sc_BM_T_mice.RDS

source_name: bone marrow

extract_protocol:
scRNA-seq + scTCR-seq were performed in 17 bone marrow aspirates from 3 healthy adults, 3 MGUS, 2 SMM, 9 MM patients and 8 bone marrow aspirates from 2 healthy (Ycɣ1), 3 MGUS (BIcɣ1) and 3 MM (BIcɣ1) bearing mice. Cells were FACS sorted (a mix of 0.8x105 T cells + 0.8x105 NK cells + 0.25x105 monocytes + 0.15x105 B cells) in 100 µL of PBS+0.05% BSA. Samples with at least 90% viability were processed using the 10X Genomics (CA, USA) scRNA/TCRseq kit, following the manufacturer’s instructions (Chromium Next GEM Single Cell V(D)J v1.1 protocol rev F for human samples and Chromium Next GEM Single Cell 5’ v2 Dual Index protocol rev B for mice samples). Quality control was performed with Qubit Fluorometric Quantification (ThermoFisher Scientific, MA, USA) using the double-stranded DNA high-sensitivity assay kit, and with TapeStation (Agilent, Santa Clara, CA) using high-sensitivity screentapes. Libraries were sequenced on a NextSeq 550 (Illumina, San Diego, CA).
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell V(D)J v1.1 protocol rev F for human samples and Chromium Next GEM Single Cell 5’ v2 Dual Index protocol rev B for mice samplesl, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Of note, according to TCR-seq protocol from manufacturer, we further sequenced (after specific amplification) CDR3 sequences from each CD3+ T cells.

value: bone marrow

value: T lymphocytes

value: T cells


title: genomic DNA from Zebra Blood 203203210213_R01C02

status: Public on Aug 05 2023

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

description: genomic DNA from Zebra Blood

hyb_protocol: standard protocols from Illumina regarding Infinium arrays

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

data_processing:
Following data collection, the SeSaMe normalization method was used to define beta values for each probe (W. Zhou et al 2018. PMID: 30085201). If a CpG does not map to a given species, it takes a value of 0.5. The mammalian array design is similar to the Illumina Infinium 450K array but it contains fewer up to 37492 CpGs.  Additional material on the mappability of CpGs can be found on the Github page https://github.com/shorvath/MammalianMethylationConsortium/  A vignette on using the mammal methylation array with SeSAMe is available from https://bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/mammal.html.
normalized (Sesame) Beta values

molecule: genomic DNA

organism: Equus quagga

source_name: Blood

label_protocol: Zymo EZ DNA Methylation Kit

extract_protocol: none provided

tag: age

tag: confidenceinageestimate

tag: female

tag: speciescommonname

value: Zebra

tag: maximumlifespanyears

tag: ageatsexualmaturityyears

tag: networktrainingset

value: yes

tag: panmammalianclocktrainingset


title: SMM34800 [T lymphocytes]

type: SRA

description:
10x Genomics
sc_BM_T_humans.RDS

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type


title: genomic DNA from Zebra Blood 203203210213_R06C01

description: genomic DNA from Zebra Blood


title: D35 43_E5

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

library_source: transcriptomic

data_processing:
Read quality control (QC) analyses and filtering of high-quality reads, were executed using FastQC and mulitQC
Mapping reads to GRCh38 was performed using STAR run in the 2-pass mode
Gene expression quantification was performed with featureCounts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file that includes TPM for each sample

source_name: donor-derived hiPSC

extract_protocol:
Total RNA was harvested using MN NucleoSpin RNA Kit.
Library construction, QC and sequencing was performed by Novogene Co., Ltd. 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. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: donor-derived hiPSC

value: Pancreatic beta-like cells

tag: treatment

value: CRISPR-correcterd 43

tag: genotype

value: WT

tag: time


title: D34-Day24

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Fastqs were generated using CellRanger v6 mkfastq or CellRanger-ARC v2 mkfastq
Sequencing reads were aligned using CellRanger and CellRanger-ARC count for the hg38 reference genome in the standard 10x distribution.
Reads were subsequently quantified against the HHV6 reference genome using kallisto|bustools and chromap to produce per-cell, per-equivalence count class UMIs (.txt) and viral fragments (.bed).
Assembly: hg38
Supplementary files format and content: Per gene expression counts

source_name: T lymphocytes

growth_protocol: CAR T cells were grown after initial activation (aCD3/aCD28 stimulation) in IL2 and harvested at the indicated time point.

extract_protocol:
Standard protocol
10x Genomics 5' scRNA-seq

tag: day collected post culture

tag: hhv6 source

value: Reactivation


title: D35 43_C12

value: CRISPR-correcterd 44


title: PBMC-Day15infection

source_name: Peripheral blood mononuclear cells

value: Primary infection


title: MGUS36784 [T lymphocytes]

description:
10x Genomics
sc_BM_T_humans.RDS


title: genomic DNA from Zebra Blood 203203210213_R05C01

description: genomic DNA from Zebra Blood


title: MGUS35162 [T lymphocytes]

description:
10x Genomics
sc_BM_T_humans.RDS


title: D35 43

value: Donor-derived hiPSC


title: D35 TSL_G11

value: CRISPR-corrected TSLa


title: genomic DNA from Zebra Blood 203203210213_R04C01

description: genomic DNA from Zebra Blood


title: D35 TSL_D9


title: MGUS34661 [T lymphocytes]

description:
10x Genomics
sc_BM_T_humans.RDS


title: genomic DNA from Zebra Blood 203203210213_R03C01

description: genomic DNA from Zebra Blood


title: HD4 [T lymphocytes]

description:
10x Genomics
sc_BM_T_humans.RDS


title: D35 TSL_C12


title: D35 TSLb

value: TSLb


title: genomic DNA from Zebra Blood 203203210213_R02C02

description: genomic DNA from Zebra Blood

value: no


title: D35 TSL_G12


title: AE_lung_sample1,replicate1,scRNA-seq

city: shenzhen

first: CNSA

last: CNGB

address: BGI

country: China

institute: BGI

description: DNBelab

data_processing:
Cell Ranger v3.0.2 was used for processing raw sequencing data generated using the Chromium Single Cell 3’ v2 kit, while DNBelab C Series scRNA analysis software (MGI,https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software)  was used to process the other data.
Assembly: CNGB (CNA0019297,https://db.cngb.org/search/project/CNP0001614/)
Supplementary files format and content: sparse matrix for count value
Supplementary files format and content: barcode list of count matrix cell name
Supplementary files format and content: gene list of count matrix rowname

molecule: polyA RNA

organism: Protopterus annectens

source_name: lung

extract_protocol:
The “AE_” samples were collected from terrestrialized lungfish for 33 days. Fresh collected tissues disaggregation and enzymatic dissociation were performed independently. Following dissociation, the resulting suspension was passed through a 40 μm filter (BD # 352340), and the filter was washed with 2 ml cold PBS to ensure efficient digestion and sufficient collection. The filter suspension was transferred to a 15 ml centrifuge tube and centrifuge at 4 ℃ with 300x g for 5 minutes. Then the supernatant was removed, and the centrifugation sediment was washed with 5 ml PBS+0.04%BSA and centrifuged again (4 ℃ at 300x g for 5 minutes), and the centrifugation sediment was rewashed with 5 ml PBS+0.04%BSA. After the centrifugation, the cell pellets were re-suspended in 300 μl PBS+0.04%BSA. All samples were stained, and cell viability was measured using Trypan Blue (Invitrogen) and manually counted using a hemocytometer (INCYTO). The cell suspension concentration was reconstituted to 1000 cells per µL in DPBS for DNBelab C4 system library preparation.
Except for two freshwater gill samples, all single-cell RNA-seq libraries were prepared using a DNBelab C Series Single Cell Library Prep Set (MGI, 1000021082) as previously described 122. These included 21 libraries from the lung (eleven libraries of the freshwater group and ten libraries of terrestrialized group) and 27 libraries from the gill (seventeen libraries of the freshwater group and ten libraries of terrestrialized group, libraries) were obtained. Briefly, single-cell suspensions were used for droplet generation, emulsion breakage, bead collection, reverse transcription, and cDNA amplification to generate barcoded libraries. Indexed libraries were constructed according to the manufacturer’s protocol. Libraries were constructed and the DNA nanoballs (DNBs) were loaded into the patterned nanoarrays and sequenced on a DNBSEQ-T1 sequencer at the China National GeneBank (Shenzhen, China) with the following sequencing strategy: 41-bp read length for read 1 and 100-bp read length for read 2.Two freshwater gill libraries (FW-gill9 and FW-gill10) were generated with a 10x Genomics Chromium 3′Reagent Kit instructions (v2) and sequenced on a MGISEQ 2000 sequencer. Gill cells were resuspended in PBS with 0.04% BSA and loaded into a 10x Genomics Chromium cell controller to generate a library for sequencing (28 base pairs for read 1 and 98 for read 2).

value: lung


title: genomic DNA from Zebra Blood 203203210213_R02C01

description: genomic DNA from Zebra Blood


title: HD3 [T lymphocytes]

description:
10x Genomics
sc_BM_T_humans.RDS

value: bone marrow


title: genomic DNA from Zebra Blood 203203210213_R01C01

description: genomic DNA from Zebra Blood


title: HD2 [T lymphocytes]

description:
10x Genomics
sc_BM_T_humans.RDS

value: T lymphocytes


title: D35 TSL_B3

value: CRISPR-Sham control


title: D35 TSLa

value: TSLa


title: D35 TSL_G3


title: genomic DNA from Zebra Blood 203203210185_R06C02

description: genomic DNA from Zebra Blood

value: Zebra

value: yes


title: D35 F1

source_name: SB hiPSC

value: SB hiPSC

value: Pancreatic beta-like cells

value: CRISPR-introduced p.His192His


title: D35 E6

value: Sham control

value: WT


title: D35 B1


title: T12 [T lymphocytes]

description:
10x Genomics
sc_BM_T_humans.RDS

value: T cells


title: genomic DNA from Zebra Blood 203203210185_R05C02

description: genomic DNA from Zebra Blood


title: D35 43_E4

value: donor-derived hiPSC

value: CRISPR-Sham


title: T11 [T lymphocytes]

description:
10x Genomics
sc_BM_T_humans.RDS


title: D35 F4_B2

value: CRISPR-introduced p.X186X


title: T10 [T lymphocytes]

description:
10x Genomics
sc_BM_T_humans.RDS


title: genomic DNA from Zebra Blood 203203210185_R04C02

description: genomic DNA from Zebra Blood


title: D35 F4_H5

value: CRISPR-edited PAX4-KO


title: D35 D2_F3


title: D35 B5_D3


title: genomic DNA from Zebra Blood 203203210185_R03C02

description: genomic DNA from Zebra Blood


title: D35 E6_E3


title: genomic DNA from Zebra Blood 203203210185_R02C02

description: genomic DNA from Zebra Blood


title: T8 [T lymphocytes]

description:
10x Genomics
sc_BM_T_humans.RDS


title: T9 [T lymphocytes]

description:
10x Genomics
sc_BM_T_humans.RDS


title: genomic DNA from Zebra Blood 203203210185_R01C02

description: genomic DNA from Zebra Blood


title: D35 H1_B7


title: D35 F3_H3


title: D20 43_C12

value: Endocrine progenitor cells

value: Donor-derived hiPSC


title: T7 [T lymphocytes]

description:
10x Genomics
sc_BM_T_humans.RDS

value: bone marrow

value: T lymphocytes


title: D20 43


title: T4 [T lymphocytes]

description:
10x Genomics
sc_BM_T_humans.RDS


title: genomic DNA from Zebra Blood 203203210185_R04C01

description: genomic DNA from Zebra Blood

value: no


title: genomic DNA from Zebra Blood 203203210185_R05C01

description: genomic DNA from Zebra Blood

value: Zebra


title: Ts12L-2

city: Lanzhou

first: Jinqiang

last: Huang

address: Yintanlu stress

institute: Gansu Agricultural University

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss Omyk_1.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Oncorhynchus mykiss

source_name: liver tissues

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver tissues

value: acute hypoxia

tag: phenotype

value: wild-type


title: D20 43_E4


title: Ts12L-1


title: T2 [T lymphocytes]

description:
10x Genomics
sc_BM_T_humans.RDS


title: genomic DNA from Zebra Blood 203203210185_R06C01

description: genomic DNA from Zebra Blood

tag: age

value: yes


title: T5 [T lymphocytes]

description:
10x Genomics
sc_BM_T_humans.RDS


title: Ts12L-3


title: D20 TSL_G11

value: CRISPR-corrected TSLa


title: genomic DNA from Zebra Blood 203203210185_R03C01

description: genomic DNA from Zebra Blood

tag: confidenceinageestimate


title: Tm12L-3

value: moderate hypoxia


title: D20 TSL_D9

value: WT


title: genomic DNA from Zebra Blood 203203210185_R02C01

description: genomic DNA from Zebra Blood

tag: female


title: D20 TSL_C12

value: donor-derived hiPSC


title: D20 43_E5

value: CRISPR-correcterd 43


title: Tm12L-2


title: Tm12L-1


title: genomic DNA from Zebra Blood 203203210185_R01C01

description: genomic DNA from Zebra Blood

tag: speciescommonname


title: genomic DNA from Zebra Blood 203203210171_R06C02

description: genomic DNA from Zebra Blood

tag: maximumlifespanyears


title: D20 TSL_G12


title: Trachea.V.3

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode human transcriptome using RSEM
The gene expression level was calculated by using  RSEM
Reads were aligned to the mouse reference genome hg38 with bowtie2, and RSEM was used to quantify the reads mapped to each gene. Gene expression was normalized by EDASEQ. Differentially expressed genes were obtained using DESeq2 (version 1.10.1), a cutoff of Q-value < 0.05 and log2 (fold-change) > 1 was used for identify differentially expressed genes. All differentially expressed mRNAs were selected for GO analyses clusterProfiler. Other analysis was performed using glbase
Genome_build: hg38

extract_protocol: Total RNA in the cells was extracted using Trizol (Invitrogen) according to the manufacturer’s protocol, and 1ug RNA was used to reverse transcribed into cDNA using Oligo (dT). Fragmented RNA (average length approximately 200 bp) was subjected to first strand and second strand cDNA synthesis followed by adaptor ligation and enrichment with a low-cycle according to the instructions of NEBNext" UltraTM RNA Library Prep Kit for Illumina (NEB, USA). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit"2.0(Life Technologies, USA).

treatment_protocol: Infected with SARS-CoV-2 strain EPI_ISL_402124 [https://www.nature.com/articles/s41586-020-2012-7]

value: Trachea

value: SARS-CoV-2 infection

tag: sars-cov-2 strain


title: Trachea.V.2


title: Trachea.V.1


title: CL-3

value: control


title: D20 43_H11

value: Endocrine progenitor cells

value: CRISPR-Sham


title: Trachea.M.3

value: Mock


title: D20 TSLb

value: TSLb

value: Donor-derived hiPSC


title: genomic DNA from Zebra Blood 203203210171_R04C02

description: genomic DNA from Zebra Blood

value: Zebra

tag: ageatsexualmaturityyears

tag: networktrainingset


title: D20 TSLa

tag: tissue

value: TSLa


title: Trachea.M.1


title: genomic DNA from Zebra Blood 203203210171_R03C02

description: genomic DNA from Zebra Blood

tag: panmammalianclocktrainingset


title: Trachea.M.2


title: CL-2

value: liver tissues

value: wild-type


title: D20 TSL_B3

tag: cell line

tag: cell type

value: CRISPR-Sham control


title: CL-1

tag: treatment


title: genomic DNA from Zebra Blood 203203210171_R02C02

description: genomic DNA from Zebra Blood

value: yes


title: Lung.V.3

value: Lung


title: Lung.V.2


title: D20 TSL_G3

value: donor-derived hiPSC

tag: genotype

tag: time


title: genomic DNA from Zebra Blood 203203210171_R01C02

description: genomic DNA from Zebra Blood


title: Lung.V.1


title: D20 B1

value: SB hiPSC

value: CRISPR-introduced p.His192His


title: genomic DNA from Zebra Blood 203203210171_R05C02

description: genomic DNA from Zebra Blood


title: Lung.M.3


title: genomic DNA from Zebra Blood 203203210171_R05C01

description: genomic DNA from Zebra Blood


title: genomic DNA from Zebra Blood 203203210171_R06C01

description: genomic DNA from Zebra Blood


title: Lung.M.2


title: D20 E6

value: Sham control

value: WT


title: TAT+AEA_B_BR2

type: RNA

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: The dried sample was resuspended in nuclease free water and mixed with Hybridization Mix containing blocking solution (Agilent Technologies, Part Number: 5190-0456) and Hi-RPM Hybridization Buffer (Agilent Technologies, Part Number: 5190-0456) and incubated at 100oC for 5 minutes followed by snap chill on ice for 5 minutes.  The samples were hybridized on the Human miRNA 8x60K Arrays. The hybridization was carried out at 55°C for 20 hours. After hybridization, the slides were washed using Gene Expression Wash Buffer1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 5 minutes and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37oC for 5 minutes.

scan_protocol: The microarray slide was scanned on a G2600D scanner (Agilent Technologies)

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 50th percentile shift miRNA based.

source_name: Human Brain

label_protocol: The miRNA labeling was performed using miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Part Number: 5190-0456).The total RNA sample was diluted to 100ng/ul in nuclease free water. About 200ng of total RNA was dephosphorylated using Calf Intestinal Alkaline Phosphatase (CIP) master mix (Agilent Technologies, Part Number: 5190-0456) by incubating at 37oC for 30 minutes. The dephosphorylated miRNA sample was denatured by adding Dimethyl Sulfoxide (DMSO) and heating at 100 oC for 10 minutes and transferred to ice-water bath. The Ligation master mix (Agilent Technologies, Part Number: 5190-0456) containing Cyanine 3-pCp was added to the denatured miRNA sample and incubated at 16oC for 2 hours. The Cyanine 3-pCp labeled miRNA sample was dried completely in the vacuum concentrator (Eppendorf, Concentrator Plus, Catalog Number 5305000) at 45oC for 2 hour.

growth_protocol: Normal Human Astrocyte (Cat. No: CC-2565 ) from Lonza had been cultured with Lonza AGMTM Astrocyte Growth Medium Bullet KitTM  (basal medium and Single QuotesTM Kit; Cat. No: CC-3186) for cell specific growth. Cells were seeded into a T75 culture flask and allowed to grow in CO2 incubator for a week to attain 80% confluency. Cells were split in 6 well plates for treatment.

extract_protocol: Treated astrocyte cells were harvested by using TRIzol™ Reagent (Cat. No: 15596018) InvitrogenTM. By using 200 μl of chloroform reagent, phase separation was obtained after centrifugation at 12000 rpm for 15 minutes at 4 degree C. The clear upper aqueous phase was collected and the RNA was precipitated by using 500 μl ice cold isopropanol. Isopropanol is removed then by using 70% ethanol at 12000 rpm for 10 minutes. Then the precipitate was air dried and dissolved in RNase free water.

treatment_protocol: Once the cells attained 80% confluency, they were treated with HIV-1 TAT recombinant protein, AEA and TAT+AEA for 24 hours.

value: miRNA expression with 24 hr TAT+AEA treatment


title: TAT+AEA_ C_BR3


title: D20 F4_B2

value: Endocrine progenitor cells

value: CRISPR-introduced p.X186X


title: genomic DNA from Zebra Blood 203203210171_R04C01

description: genomic DNA from Zebra Blood


title: AEA_ C_BR3

value: miRNA expression with 24 hr AEA treatment


title: TAT+AEA_ A_BR1


title: genomic DNA from Zebra Blood 203203210171_R02C01

description: genomic DNA from Zebra Blood


title: D20 D2_F3

value: CRISPR-edited PAX4-KO


title: D20 F4_H5


title: ARR2PBi-Cre;Ptenf/+;Ncoa6f/f _rep4

city: Houston

first: Yonghong

last: Liu

state: Texas

address: One Baylor Plaza

department: Molecular & Cellular Biology

institute: Baylor College of Medicne

data_processing:
The paired-end reads were mapped to the mouse genome (UCSC mm10) using STAR with NCBI RefSeq genes as the reference. STAR generated read counts for each RNA was used as the measurement of gene expression.
DESeq2 was used to analyze the gene-based read counts to detect differentially expressed genes between the groups of interest.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include DESeq2 values.

organism: Mus musculus

source_name: Prostate tumor

extract_protocol:
Total RNA samples were extracted from the mouse prostate tissues and tumors using the TRIzol reagent (15596018; Thermo Fisher) followed by purification with the RNeasy Mini Kit (74106; Qiagen) according to manufacturer's instructions. Quality of the samples were checked by using the NanoDrop spectrophotometer and Agilent Bioanalyzer 2100.
250 ng of total RNA samples (measured by picogreen) that had passed the quality check was used for creating a double-stranded DNA library. ERCC RNA Spike-In Controls were added to each sample according to the manufacturer’s protocol. The fragmented and 3’ poly (A)-selected portion of total RNA together with random primers were used to create the cDNA. In the process of second strand synthesis, dTTP was replaced with dUTP to quench the second strand during amplification amd thereby achieve strand specificity. The created cDNA fragments were blunt ended, attached with an adenosine to the 3' end, and finally ligated with unique adapters to the end. The ligated products were amplified with 15 PCR cycles. The resulting libraries were quantitated using the NanoDrop Spectrophotometer and the fragment sizes were assessed with the Agilent Bioanalyzer. To determine the concentration of adapter-ligated fragments, the libraries were further quantitated by qPCR by using the Applied Biosystems ViiA7 Real-Time PCR System and a KAPA Library Quant Kit.

treatment_protocol: The prostate tissues and tumors were collected from untreated 9-month-old mice

tag: strain

value: Prostate

value: 9 months

value: Pten heterozygous KO; Ncoa6 homozygous KO


title: genomic DNA from Zebra Blood 203203210171_R03C01

description: genomic DNA from Zebra Blood

value: Zebra


title: MIOMI_TAT_RNA_24hr

value: miRNA expression with 24 hr TAT treatment in MIOM1


title: D20 F1


title: genomic DNA from Zebra Blood 203203210171_R01C01

description: genomic DNA from Zebra Blood

value: yes


title: ARR2PBi-Cre;Ptenf/+;Ncoa6f/f _rep3


title: AEA_ B_BR2


title: ARR2PBi-Cre;Ptenf/+;Ncoa6f/f _rep2


title: AEA_A_BR1


title: TAT_C_BR3

value: miRNA expression with 24 hr TAT treatment


title: genomic DNA from Vervet CerebralCortex 203203210021_R06C02

description: genomic DNA from Vervet CerebralCortex

organism: Chlorocebus sabaeus

source_name: CerebralCortex

value: Vervet


title: D20 E6_E3

value: SB hiPSC

value: CRISPR-Sham control


title: TAT_B_BR2


title: D20 F3_H3


title: genomic DNA from Vervet CerebralCortex 203203210021_R05C02

description: genomic DNA from Vervet CerebralCortex


title: ARR2PBi-Cre;Ptenf/+;Ncoa6f/f _rep1


title: ARR2PBi-Cre;Ptenf/+;Ncoa6+/+_rep4

source_name: Prostate with PIN

value: Pten heterozygous KO; Ncoa6 wild type


title: genomic DNA from Vervet CerebralCortex 203203210021_R04C02

description: genomic DNA from Vervet CerebralCortex


title: D20 H1_B7

value: WT


title: TAT_A_BR1


title: Lung.M.1

value: Lung

value: Mock


title: ARR2PBi-Cre;Ptenf/+;Ncoa6+/+_rep3


title: D0 43_E5

value: donor-derived hiPSC

value: Undifferentiated pluripotent stem cells

value: CRISPR-correcterd 44


title: genomic DNA from Vervet CerebralCortex 203203210021_R03C02

description: genomic DNA from Vervet CerebralCortex


title: ARR2PBi-Cre;Ptenf/+;Ncoa6+/+_rep2

value: Prostate


title: genomic DNA from Vervet CerebralCortex 203203210021_R02C02

description: genomic DNA from Vervet CerebralCortex


title: D0 43_C12

value: CRISPR-correcterd 43


title: D20 B5_D3

value: Endocrine progenitor cells

value: CRISPR-edited PAX4-KO


title: PKP2

city: Nanchang

first: Yi

last: Sang

state: Jiangxi

address: No.128,Xiangshan North Road

institute: Nanchang University

data_processing:
The sequencing data was filtered with SOAPnuke(v1.5.2) by removing reads with adapter, low-quality base and unknown base.
The clean reads were mapped to the reference genome using HISAT2(v2.0.4)
Ericscript(v0.5.5) and rMATS(V3.2.5) were used to detect fusion gene and differential splicing genes, respectively.
Bowtie2 was applied to align the clean reads to the gene set built by BGI(Beijing Genomic Institute in ShenZhen), the expression level of gene was calculated by RSEM(v1.2.12).
Genome_build: Alignment was to the transcriptome (GCF_000001405.38_GRCh38.p12)
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample ...

source_name: lung cancer cell lines

growth_protocol: 10% FBS in DMEM

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions

value: lung cancer cell

tag: passages


title: genomic DNA from Vervet CerebralCortex 203203210021_R01C02

description: genomic DNA from Vervet CerebralCortex

tag: age

value: yes


title: D0 43

value: Donor-derived hiPSC


title: ARR2PBi-Cre;Ptenf/+;Ncoa6+/+_rep1

value: 9 months


title: CONTROL_B_BR2

value: miRNA expression without any treatment


title: vector

description: vector


title: D0 43_H11

value: CRISPR-Sham


title: genomic DNA from Vervet CerebralCortex 203203210021_R06C01

description: genomic DNA from Vervet CerebralCortex

tag: confidenceinageestimate

value: Vervet


title: D0 43_E4


title: genomic DNA from Vervet CerebralCortex 203203210021_R05C01

description: genomic DNA from Vervet CerebralCortex

tag: female


title: Cis9w, RLDC-1

city: Augusta

first: Zhengwei

last: Ma

state: GA

address: 1460 Laney walker Blvd.

institute: Augusta University

description: PT Features(Cis9w vs CT9w)-1sta.cvs

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 5.0.1
Assembly: mm10
Supplementary files format and content: Comma Separated Values (CSV)file and matrix files

molecule: nuclear RNA

source_name: kidney

extract_protocol:
kidney samples of cortex with outer medulla were cut into <8mm3 pieces and homogenized in 2 ml of ice-cold Nuclei EZ Lysis buffer (NUC101; Sigma) with protease inhibitor (5892791001; Roche) and RNase inhibitor (N2615, Promega; AM2696, Life Technologies) using a Dounce homogenizer (885302-0002; Kimble Chase). The homogenate was further incubated on ice for 5 min with an additional 2 ml of lysis buffer. Then the homogenate was filtered through a 40-μm cell strainer (43-50040-51; pluriSelect) followed by centrifugation at 500 × g for 5 min at 4°C. The pellet was resuspended and washed with 4 ml of the buffer and incubated on ice for another 5 min. After another centrifugation, the pellet was resuspended in Nuclei Suspension Buffer (1x PBS, 1% bovine serum albumin, 0.1% RNase inhibitor) and filtered through a 5-μm cell strainer (43-50005; pluriSelect).
Nuclei were processed using Chromium Single Cell Controller and Chromium Next GEM Single Cell 3’ Reagent kit v3.1 (10x Genomics, Pleasanton, CA) according to the manufacturer’s protocol.  Briefly, 3,000-4,000 nuclei were loaded onto the Chromium Controller to generate single cell GEMs coated with unique 10x cell barcodes, unique molecular identifiers (UMI), and poly dT oligos.  RNA molecules from single nuclei were reverse-transcribed within droplets to generate barcoded cDNAs.  After break emulsion, cDNA molecules were pre-amplified, fragmented, ligated to an adaptor, and amplified with sample indices, followed by a double-sided size selection using SPRI beads (Beckman Coulter).  The final libraries were assessed by Bioanalyzer 2100 (Agilent) and Qubit HS DNA (ThermoFisher) and pooled.

value: kidney

value: RLDC for 9 weeks


title: genomic DNA from Vervet CerebralCortex 203203210021_R04C01

description: genomic DNA from Vervet CerebralCortex

tag: speciescommonname


title: CT9w, Control-1

description: PT Features(Cis9w vs CT9w)-1sta.cvs

value: Untreated


title: Cis9w, RLDC-2

description: 17 clusters Features


title: CONTROl_A_BR1


title: CONTROL_C_BR3


title: D0 TSL_G11

value: donor-derived hiPSC

value: CRISPR-corrected TSLa

value: WT


title: CT9w, Control-2

description: 17 clusters Features


title: D0 TSL_D9

value: Undifferentiated pluripotent stem cells


title: D0 TSL_C12


title: genomic DNA from Vervet CerebralCortex 203203210021_R03C01

description: genomic DNA from Vervet CerebralCortex

tag: maximumlifespanyears


title: GF_HFD_retina_DS16

city: Chicago

first: Rohan

middle: Nishant

last: Shah

state: IL

address: CLSC 856, 920 E. 58th Street

institute: University of Chicago

data_processing:
We used STAR (version 2.4.2 a, Stanford University, Stanford, CA, USA) aligner default parameters to align the RNA-seq reads to the reference mouse genome (GRCm38) for all eight samples.
The raw gene expression count matrix was then generated by featureCounts (version subread-1.4.6-p1).
The gene annotation was obtained from the Gencode vM23.
STAR default parameter for the maximum mismatches is 10 which is optimized based on mammalian genomes and recent RNA-seq data.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Retina

growth_protocol: Mouse experiments were approved by the University of Chicago Institutional Animal Care and Use Committee and conducted according to ophthalmic and vision research guidelines set by the Association for Research in Vision and Ophthalmology (ARVO). This study used germ-free (GF) C57B1/6 adult male mice, which were housed in the Gnotobiotic Research Animal Facility at the University of Chicago.

extract_protocol:
Whole mouse retinas were isolated on ice from freshly enucleated eyes, with all equipment, surfaces, and tubes treated with RNase decontamination solution (Thermo Fisher Scientific, Waltham, MA, USA) prior to use. Dissected retinas were stored in RNAlater solution (Thermo Fisher Scientific, Waltham, MA, USA) at −80 °C until RNA extraction using the RNeasy kit from Qiagen (Qiagen, Hilden, Germany). Concentrations were quantified using a Nanodrop (Thermo Fisher Scientific, Waltham, MA, USA) before sequencing.
The quality was evaluated using a Bioanalyzer at the University of Chicago Genomics Core and was confirmed to meet appropriate RNA integrity numbers (RIN). Next, cDNA libraries were constructed using TruSeq RNA Sample Prep kits (Illumina, San Diego, CA, USA) to generate 100-bp paired-end reads, which were indexed for multiplexing and then sequenced using PE100bp on the NovaSeq 6000 System (Illumina, San Diego, CA, USA).

treatment_protocol: At 7 weeks of age, GF mice were fed ad libitum either a normal diet (ND) or high-fat diet (HFD) for 8 consecutive weeks. The HFD consisted of 23% saturated fat. Environmental conditions, including humidity and temperature, adhered to The Guide for the Care and Use of Laboratory Animals, 8th edition, and mice were subjected to a standard 12-h light cycle. At 15 weeks of age, the mice were euthanized by carbon dioxide and subsequent cervical dislocation.

value: Retina

tag: microbiome

value: GF

value: HFD


title: GF_HFD_retina_DS13


title: genomic DNA from Vervet CerebralCortex 203203210021_R02C01

description: genomic DNA from Vervet CerebralCortex

tag: ageatsexualmaturityyears


title: GF_HFD_retina_DS15


title: GF_HFD_retina_DS19


title: GF_ND_retina_DS12

value: ND


title: genomic DNA from Vervet CerebralCortex 203203210021_R01C01

description: genomic DNA from Vervet CerebralCortex

tag: networktrainingset

value: yes


title: D0 TSL_G12

tag: tissue


title: HFrD_DW , replicate 2, scRNAseq

city: Daejeon

first: BYEONGCHANG

last: SIM

state: 대전

address: Chungnam National University School of Medicine, 282 Munhwa-ro Jung-gu, Daejeon 35015, Korea

country: South Korea

institute: Research Center for Endocrine and Metabolic Diseases, Laboratory of Endocrinology and Immune System

description: 10x Genomics

data_processing:
The multiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol: Freshly collected liver tissue from the NCD, HFrD mice were chapped in collagenase solution. After enzymatic digestion, the hepatic cells were homogenized using a GentleMACS Dissociator (Miltenyi Biotec). And then, the supernatants passed through a 70 µm nylon cell strainer (BD Falcon, Millville, NJ) for totally digestion. The cells centrifuged at 500rpm for 5 min at 4℃ and centrifuged once more with the supernatant to remove hepatocyte. After that, Red blood cells removed by RBC lysis procedure and hepatic mononuclear cells were isolated by percoll (Cytivia) gradient.

value: Mononuclear cell

value: Liver

tag: diet

value: HFrD


title: genomic DNA from Vervet CerebralCortex 203203210101_R06C02

description: genomic DNA from Vervet CerebralCortex

tag: panmammalianclocktrainingset


title: NCD_DW , replicate 1, scRNAseq

description: 10x Genomics

tag: cell type

value: NCD


title: D0 TSLb

tag: cell line

value: TSLb

tag: treatment

value: Donor-derived hiPSC


title: TRPV1cre-GOF Male Biol rep 2

city: Calgary

first: Christophe

last: Altier

address: 3300 Hospital Drive NW

country: Canada

institute: University of Calgary

data_processing:
STAR software v 2.7.9
Reference genome was indexed using STAR (parameters- runTgreadN: 12, runMode: genomeGenerate, sjdbOverhang: ReadLength-1)
Sequence reads were mapped to GRCm39/mm39 using STAR
Reads were converted using Samtools software v 1.9
Read count extraction were performed using HTSeq software v 0.9.1 (parameters- t: exon, i: gene_id, r: pos, f: bam)
Assembly: mm39
Supplementary files format and content: tab-delimited text files

source_name: Dorsal Root Ganglia

extract_protocol:
After DRG collection, RNA was extracted separately from TRPV1cre-GOF and littermate controls using a RNeasy Mini kit (Qiagen)
NEBNext Ultra II Directional RNA Library Prep Kit

value: Dorsal Root Ganglia

tag: Sex

value: Male

tag: genotype

value: Naive


title: GF_ND_retina_DS10


title: TRPV1cre-GOF Male Biol rep 1


title: GF_ND_retina_DS11


title: genomic DNA from Vervet CerebralCortex 203203210101_R05C02

description: genomic DNA from Vervet CerebralCortex

value: Vervet


title: genomic DNA from Vervet CerebralCortex 203203210101_R04C02

description: genomic DNA from Vervet CerebralCortex


title: GOF Male Biol rep 2

value: WT


title: GF_ND_retina_DS09


title: D0 TSL_G3

value: donor-derived hiPSC

value: Undifferentiated pluripotent stem cells

value: CRISPR-Sham control

tag: time


title: genomic DNA from Vervet CerebralCortex 203203210101_R03C02

description: genomic DNA from Vervet CerebralCortex

tag: age


title: GOF Male Biol rep 1


title: TRPV1cre-GOF Female Biol rep 2

value: Female


title: WT neonatal epidermis

city: Kangwon

first: Geon Seong

last: Lee

address: 1447 Pyeongchang-Ro, Daewha, Pyeongchang

institute: Seoul National University

data_processing:
Gene expression levels were estimated using Fragments Per kilobase per million (FPKM) read values using Cufflinks.
The FPKM values were normalized using the quantile normalization method using EdgeR within R (R version 3.5.1).
Data mining and graphic visualization were performed using ExDEGA (Ebiogen Inc., Seoul, Korea).
Sashimi plot analysis was conducted by aligning RNA sequencing data to the mouse genome assembly GRCm39 (mm39) using Integrative Genome Viewer (IGV version 2.9.4, Broad Institute, MA, USA)
For heat map analysis, DEGs (FC: 4.0, p = 0.01) were selected and analyzed using MultiExperiment Viewer software (version 4.9.0; http://mev.tm4.org/).

source_name: Skin (epidermis)

extract_protocol:
Total RNA was extracted from the neonatal epidermal tissue using TRIzol reagent (Thermo Fisher Scientific).
After quality assessment and RNA quantification, libraries were prepared from total RNA using a NeBNext Ultra II Directional RNA-Seq Kit (New England BioLabs, Ipswich, MA, USA).
mRNA was isolated using a poly (A) RNA selection kit (Lexogen, Wien, Austria) and subjected to cDNA synthesis and shearing according to the manufacturer’s instructions.

value: Skin (epidermis)

value: C57BL/6 WT


title: genomic DNA from Vervet CerebralCortex 203203210101_R02C02

description: genomic DNA from Vervet CerebralCortex

tag: confidenceinageestimate

value: yes


title: TRPV1cre-GOF Female Biol rep 1


title: genomic DNA from Vervet CerebralCortex 203203210101_R01C02

description: genomic DNA from Vervet CerebralCortex

tag: female


title: D0 F1

value: SB hiPSC

value: CRISPR-introduced p.His192His


title: D0 B1


title: GOF Female Biol rep 2


title: genomic DNA from Vervet CerebralCortex 203203210101_R06C01

description: genomic DNA from Vervet CerebralCortex

tag: speciescommonname


title: bv_negtive_Ctrl_2

city: shanghai

first: wang

last: pengxiang

address: No.500, Dongchuan Road

institute: ECNU

data_processing:
Evaluating the quality of sequencing dataFastQC（v0.10.1）
Sequencing data filtering（version 1.9.1） Remove the adapter sequence;Remove bases with a mass value of less than 20 or containing N at the 5 'or 3' end; Sequences with reads length less than 75 bp after removing trim.
Use Hisat2 (v2.0.1) software for short reads comparison, with default parameters.
Normalization were performed using Htseq software (V0.6.1)
Assembly: GRCm39.107
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample

source_name: Embryoidbody

growth_protocol: PSCs were cultured in DMEM (Gibco) with 1 μM PD0325901(Stemgent), 3 μM CHIR99021 (Stemgent), 1,000 units/ml LIF (Gibco),15% FBS (Gibco), 0.05 mM β-mercaptoethanol, 2 mM L-Glu, 0.1 mM NEAA, 100 units/ml penicillin, 0.1mg/ml streptomycin on feeder free wells coated with 0.2% gelatin.

extract_protocol:
RNA was harvested with RNAiso plus kit(Takara).1 μg total RNA was used for following library preparation.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers.
First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends.
Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol:
The embryoid body (EB) were generated from 1.5 x10e6 PSCs in 10cm petri dishes with differentiation medium including IMDM with 15% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C
For p20 vector-based gene expression induction, 1.5 μg/ml doxycycline were added during differentiation of day 2 to 5.Cells were cultured on a shaker in the cell incubator, with the medium changed every 2 days.

value: Embryoidbody

value: BVSC

value: pluripotent stem cells

value: empty vector control

value: Induced differentiation


title: bv_negtive_Ctrl_1


title: D0 E6

value: Sham control


title: D0 F4_B2

value: CRISPR-introduced p.X186X


title: bv_positive_Ctrl_2


title: D0 TSLa

source_name: donor-derived hiPSC

value: TSLa

value: Donor-derived hiPSC


title: genomic DNA from Vervet CerebralCortex 203203210101_R05C01

description: genomic DNA from Vervet CerebralCortex

value: Vervet

tag: maximumlifespanyears


title: GOF Female Biol rep 1

value: Dorsal Root Ganglia

value: WT

value: Naive


title: bv_positive_Ctrl_1


title: CKO3

city: Toronto

first: Byron

middle: Sze Kwong

last: Chan

state: ON

address: 25 Orde Street, RM#5-1013

institute: University of Toronto

data_processing:
The quality of RNA sequencing raw data was assessed using FASTQC (v0.11.9) to ensure high quality reads (≥35)
Reads were aligned to the GRCm38 mouse reference genome using HISAT2 (v2.2.1)
Aligned reads were counted using featureCounts (v2.0.1)
Normalization and analysis of differentially expressed genes was done in R (v4.0.5) using the DESeq2 (v1.30.1) package
Assembly: GRCm38
Supplementary files format and content: Text files include the raw counts and normalized counts from DESeq2 for each sample

source_name: Knee joint articular cartilage

extract_protocol:
Samples were processed with TissueLyser II (Qiagen) and total RNA was isolated using Rneasy kit (Qiagen) according to the manufacturer's protocol
Full length cNDA library was generated using TaKaRa SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TaKaRa) according to the manufacturer's protocol

treatment_protocol: At 8 weeks of age, mice were adminstered with 1.5mg/10g bodyweight of tamoxifen daily for 5 consecutive day. Knee joint articular cartilage samples harvested at 10 weeks of age.

value: Knee joint articular cartilage

value: 10 weeks old

value: Native articular chondrocyte

value: Adseverin knockout

value: Tamoxifen 1.5mg/10g bw


title: genomic DNA from Vervet CerebralCortex 203203210101_R04C01

description: genomic DNA from Vervet CerebralCortex

value: yes


title: genomic DNA from Vervet CerebralCortex 203203210101_R03C01

description: genomic DNA from Vervet CerebralCortex


title: D0 D2_F3

value: SB hiPSC

value: Undifferentiated pluripotent stem cells

value: CRISPR-edited PAX4-KO


title: D0 TSL_B3

value: donor-derived hiPSC

value: CRISPR-Sham control


title: L19M neonatal epidermis

value: Skin (epidermis)

value: C57BL/6 Foxn1L19M/L19M


title: bv_negtive_NRF1_OE_3

value: Embryoidbody

value: BVSC

value: pluripotent stem cells

value: NRF1 overexpression

value: Induced differentiation


title: CKO2

value: Knee joint articular cartilage

value: 10 weeks old


title: CKO1

value: Native articular chondrocyte

value: Adseverin knockout


title: D0 B5_D3


title: bv_negtive_NRF1_OE_2


title: genomic DNA from Vervet CerebralCortex 203203210101_R02C01

description: genomic DNA from Vervet CerebralCortex

value: Vervet

value: yes


title: CTRL3

value: WT

value: Tamoxifen 1.5mg/10g bw


title: bv_negtive_NRF1_OE_1


title: genomic DNA from Vervet CerebralCortex 203203210101_R01C01

description: genomic DNA from Vervet CerebralCortex


title: bv_positive_NRF1_OE_2


title: CTRL2


title: genomic DNA from Vervet CerebralCortex 203203210072_R06C02

description: genomic DNA from Vervet CerebralCortex


title: bv_positive_NRF1_OE_1


title: CTRL1


title: D0 F4_H5

value: SB hiPSC

value: Undifferentiated pluripotent stem cells

value: CRISPR-edited PAX4-KO


title: D0 H1_B7

value: CRISPR-Sham control


title: genomic DNA from Vervet CerebralCortex 203203210072_R05C02

description: genomic DNA from Vervet CerebralCortex


title: BVSC_Input_2

library_source: genomic

data_processing:
Using software Bcl2Fastq (v2.20.0.422) for image base recognition (Base Calling) on the original image data of sequencing results.
The quality evaluation of sequencing data was analyzed using software FastQC (v0.11.4).Use bowtie2 (Version: 2.2.6) alignment software to compare clean data to the reference genome sequence and calculate the alignment results.
Useing MACS2 software for peak extraction, and annotate Peaks using the R package ChIPseeker.
Detecting Significant Motif Sequences in Peaks Sequences Using MEME Software
Assembly: GRCm39.107
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, ChIP was performed  using a SimpleChIP® Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology, #9005) .
Immunoprecipitated DNA were quantified using a Qubit 3.0 Fluorometer (Invitrogen) and qualified with an Agilent Bioanalyzer 2100 (Agilent Technologies). The  ChIP product was treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation and dA-tailing in one reaction, followed by ligation to adaptors with a “T” base overhang.
Each sample was then amplified by PCR using P5 and P7 primers. The PCR products were cleaned up using beads, validated using an Agilent 2100 Bioanalyzer, and quantified by Qubit 3.0 Fluorometer.

treatment_protocol:
The embryoid body (EB) were generated from 1.5 x10e6 PSCs in 10cm petri dishes with differentiation medium including IMDM with 15% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C
Cells were cultured on a shaker in the cell incubator for 5 days, with the medium changed every 2 days.

value: Embryoidbody

tag: chip antibody


title: BVSC_Input_3

value: BVSC


title: YC102_SC

city: Cosenza

first: Cirino

last: Botta

address: Via Migliori

institute: "Annunziata" Hospital of Cosenza

description:
10x Genomics
sc_BM_T_mice.RDS

data_processing:
scRNA-seq and scTCR-seq data from humans and mice were analyzed separately. Sample demultiplexing, alignment to the hg38 human reference genome (or the respective mice genome) and single-cell gene count was performed using the Cell Ranger Single-Cell Software Suite v.2.0.1 (https://www.10xgenomics.com/). Expression matrixes were analyzed with the R package seurat 4.0 (https://satijalab.org/seurat/) and cells were filtered according to < 10% mitochondrial expression and at least 200 (but less than 2500) mRNA counts per cell. Once scaled and normalized, a genelist including the most variable genes was obtained by the FindVariableFeatures function. After removing genes belonging to the immunoglobulin families (which could work as a confounding factor during clustering), the genelist was used to derive the principal component analysis (PCA) vectors for each sample. The first 100 PCA were used to align samples (batch removal) using the R package harmony. The new harmonized coordinates were used to develop UMAPs (dimensionality reduction). The shared nearest neighbor (SNN) algorithm based on 50 batch-corrected dimensions was used for clustering the cells into homogeneous groups that were manually identified according to the expression of canonical genes (see Supplemental Information) obtained from curated gene-sets. A sequential subclustering strategy (which consists basically in repeating the same steps as before on a specific subpopulation) to focus on clonotypic T cells was performed. Reconstruction of T cell trajectories was performed by ordering single cells in “pseudotime” according to their RNA expression through Monocle 2 R package. This package accurately resolves biological processes (ordering cells) by learning an explicit principal graph from the single cell genomics data through Reverse Graph Embedding algorithm.
TCR sequences defined by their CDR3 were obtained from Cell Ranger. T cells were considered as clonotypic if their frequency was >2/1000 cells and present in at least 3 cells, and this information was added to the Seurat object to analyze the transcriptome of these cells. scRepertoire R package was used to assess clonotype distribution as well as to investigate clonal “diversity”, characterized by clones frequency, repertoire richness and convergence (Borcherding, Bormann and Kraus, 2020; Chiffelle et al., 2020). To estimate clonal diversity and richness we used Chao and ACE indices which have been developed to deal with under sampling (i.e. ‘unseen species’), and could therefore mitigate the fact that for technical reasons, only a fraction of repertoires is sequenced and analyzed (Chiffelle et al., 2020).
Assembly: GRCh38  and mm10BM_T_humans.RDS
Supplementary files format and content: We allegated 2 different RDS files: which ventually include oll the parients
Supplementary files format and content: sc_BM_T_humans.RDS
Supplementary files format and content: sc_BM_T_mice.RDS

source_name: bone marrow

extract_protocol:
scRNA-seq + scTCR-seq were performed in 17 bone marrow aspirates from 3 healthy adults, 3 MGUS, 2 SMM, 9 MM patients and 8 bone marrow aspirates from 2 healthy (Ycɣ1), 3 MGUS (BIcɣ1) and 3 MM (BIcɣ1) bearing mice. Cells were FACS sorted (a mix of 0.8x105 T cells + 0.8x105 NK cells + 0.25x105 monocytes + 0.15x105 B cells) in 100 µL of PBS+0.05% BSA. Samples with at least 90% viability were processed using the 10X Genomics (CA, USA) scRNA/TCRseq kit, following the manufacturer’s instructions (Chromium Next GEM Single Cell V(D)J v1.1 protocol rev F for human samples and Chromium Next GEM Single Cell 5’ v2 Dual Index protocol rev B for mice samples). Quality control was performed with Qubit Fluorometric Quantification (ThermoFisher Scientific, MA, USA) using the double-stranded DNA high-sensitivity assay kit, and with TapeStation (Agilent, Santa Clara, CA) using high-sensitivity screentapes. Libraries were sequenced on a NextSeq 550 (Illumina, San Diego, CA).
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell V(D)J v1.1 protocol rev F for human samples and Chromium Next GEM Single Cell 5’ v2 Dual Index protocol rev B for mice samplesl, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Of note, according to TCR-seq protocol from manufacturer, we further sequenced (after specific amplification) CDR3 sequences from each CD3+ T cells.

value: bone marrow

value: bone marrow immune cells, T lymphocytes


title: Salmonella typhimurium ATCC 14028s (STM0435 knock-out), rep3

city: Jinan

first: wei

middle: wei

last: wang

address: No. 6699 Qingdao Road, Huaiyin District, Jinan City, Shandong Province

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

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 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: https://www.ncbi.nlm.nih.gov/genome/?term=Bacteria++Salmonella+typhimurium
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: ATCC 14028s

growth_protocol: Salmonella typhimurium ATCC 14028s and Salmonella typhimurium ATCC 14028s (STM0435 knock-out) were grown to mid-log phase  in LB medium at 37 °C

extract_protocol:
RNA was harvested using Trizol reagent. 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

treatment_protocol: 3 mL bacterial cells were obtained by centrifugation (3000 rpm, 5 min) and freezing treatment in liquid nitrogen.

value: ATCC 14028s

value: LB cuture to mid-log phase

value: wild type (STM0435 knock-out)


title: YC101_SC

description:
10x Genomics
sc_BM_T_mice.RDS


title: PC3_STK3_NC

city: Wuhan

first: Gang

last: Luo

state: Hubei

address: 26 Shengli Street

institute: Huazhong University of Science and Technology

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
Deduplicated Reads were mapped to the reference genome of human using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a P-value cutoff of 0.05 to judge statistically significant enrichment. Alternative splicing events were detected by using rMATS (version 3.2.5) with an FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: reads count
Supplementary_files_format_and_content: rpkm value

source_name: prostate cancer cells

extract_protocol:
Total RNAs were extracted from samples using TRIzol reagent(Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies，Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Catalog NO. MRZG12324, Illumina) and KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on NovaSeq 6000 sequencer (Illumina) with PE150 model.

value: PC3 prostate cancer cell

value: transfected with negative control plasmid


title: PC3_STK3_OE

value: transfected with circ0004592 overexpression plasmid


title: 2752_SC

description:
10x Genomics
sc_BM_T_mice.RDS


title: Salmonella typhimurium ATCC 14028s (STM0435 knock-out), rep1


title: BVSC_NRF1_3

value: pluripotent stem cells

value: Induced differentiation


title: Salmonella typhimurium ATCC 14028s (STM0435 knock-out), rep2


title: BVSC_Input_1


title: PC3_RCAN3_OE

value: transfected with circ0003553 overexpression plasmid


title: 2751_SC

description:
10x Genomics
sc_BM_T_mice.RDS


title: Salmonella typhimurium ATCC 14028s, rep3

value: wild type


title: D0 F3_H3

city: Singapore

first: Adrian

last: Teo

address: 61 Biopolis Drive, Proteos

institute: IMCB, A*STAR

data_processing:
Read quality control (QC) analyses and filtering of high-quality reads, were executed using FastQC and mulitQC
Mapping reads to GRCh38 was performed using STAR run in the 2-pass mode
Gene expression quantification was performed with featureCounts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file that includes TPM for each sample

source_name: SB hiPSC

extract_protocol:
Total RNA was harvested using MN NucleoSpin RNA Kit.
Library construction, QC and sequencing was performed by Novogene Co., Ltd. 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. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: SB hiPSC

value: Undifferentiated pluripotent stem cells

value: WT


title: 2573_SC

description:
10x Genomics
sc_BM_T_mice.RDS


title: PC3_RCAN3_NC


title: DU145_STK3_OE

value: DU145 prostate cancer cell


title: D0 E6_E3

value: CRISPR-Sham control


title: Salmonella typhimurium ATCC 14028s, rep2


title: BVSC_NRF1_2

value: Embryoidbody

value: BVSC


title: DU145_STK3_NC


title: 2264_SC

description:
10x Genomics
sc_BM_T_mice.RDS

value: bone marrow

value: bone marrow immune cells, T lymphocytes


title: DU145_RCAN3_NC


title: FW_gill_sample2,replicate1,scRNA-seq

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

description: 10X Genomics

data_processing:
Cell Ranger v3.0.2 was used for processing raw sequencing data generated using the Chromium Single Cell 3’ v2 kit, while DNBelab C Series scRNA analysis software (MGI,https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software)  was used to process the other data.
Assembly: CNGB (CNA0019297,https://db.cngb.org/search/project/CNP0001614/)
Supplementary files format and content: sparse matrix for count value
Supplementary files format and content: barcode list of count matrix cell name
Supplementary files format and content: gene list of count matrix rowname

source_name: gill

extract_protocol:
The “AE_” samples were collected from terrestrialized lungfish for 33 days. Fresh collected tissues disaggregation and enzymatic dissociation were performed independently. Following dissociation, the resulting suspension was passed through a 40 μm filter (BD # 352340), and the filter was washed with 2 ml cold PBS to ensure efficient digestion and sufficient collection. The filter suspension was transferred to a 15 ml centrifuge tube and centrifuge at 4 ℃ with 300x g for 5 minutes. Then the supernatant was removed, and the centrifugation sediment was washed with 5 ml PBS+0.04%BSA and centrifuged again (4 ℃ at 300x g for 5 minutes), and the centrifugation sediment was rewashed with 5 ml PBS+0.04%BSA. After the centrifugation, the cell pellets were re-suspended in 300 μl PBS+0.04%BSA. All samples were stained, and cell viability was measured using Trypan Blue (Invitrogen) and manually counted using a hemocytometer (INCYTO). The cell suspension concentration was reconstituted to 1000 cells per µL in DPBS for DNBelab C4 system library preparation.
Except for two freshwater gill samples, all single-cell RNA-seq libraries were prepared using a DNBelab C Series Single Cell Library Prep Set (MGI, 1000021082) as previously described 122. These included 21 libraries from the lung (eleven libraries of the freshwater group and ten libraries of terrestrialized group) and 27 libraries from the gill (seventeen libraries of the freshwater group and ten libraries of terrestrialized group, libraries) were obtained. Briefly, single-cell suspensions were used for droplet generation, emulsion breakage, bead collection, reverse transcription, and cDNA amplification to generate barcoded libraries. Indexed libraries were constructed according to the manufacturer’s protocol. Libraries were constructed and the DNA nanoballs (DNBs) were loaded into the patterned nanoarrays and sequenced on a DNBSEQ-T1 sequencer at the China National GeneBank (Shenzhen, China) with the following sequencing strategy: 41-bp read length for read 1 and 100-bp read length for read 2.Two freshwater gill libraries (FW-gill9 and FW-gill10) were generated with a 10x Genomics Chromium 3′Reagent Kit instructions (v2) and sequenced on a MGISEQ 2000 sequencer. Gill cells were resuspended in PBS with 0.04% BSA and loaded into a 10x Genomics Chromium cell controller to generate a library for sequencing (28 base pairs for read 1 and 98 for read 2).

value: gill


title: SNU719-Input-2

status: Public on Aug 04 2023

city: Philadelphia

first: Sarah

last: Alp

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

data_processing:
Adapter sequences were removed using TrimGalore
Sequence alignment to the human gammaherpesvirus 4 (HHV4) NC_007605.1 was performed by Bismark
We used MACS2[72,73] software packages to call peaks using input samples as control
Assembly: Viral Genome Human gammaherpesvirus 4 NC_007605.1
Supplementary files format and content: bw

organism: human gammaherpesvirus 4

source_name: Human Gammaherpesvirus 4-infected gastric carcinoma cell line SNU719

extract_protocol:
Briefly, 25x10^6 cells per immunoprecipitation were collected and fixed with 1% formaldehyde for 15 min and then quenched with 0.25 M glycine for 5 min on ice. After 3 washes with 1X PBS, pellets were resuspended in 10 mL each of a series of three lysis buffers before fragmentation in Covaris ME220 sonicator (peak power 75, duty factor 25, cycles/burst 1000, average power 18.8, time 720 sec) to generate chromatin fragments roughly 200–500 bp in size as determined by DNA gel electrophoresis. Chromatin was centrifuged to clear debris and a 1:20 of this cleared chromatin was kept as standard input for comparison against immunoprecipitations. Chromatin was incubated rotating at 4°C 1h with 8 µg of antibody against CTCF (Active Motif 61311). Chromatin–antibody complexes were precipitated using 50 µL of Dynabeads Protein A (ThermoFisher, product No. 10001D) incubated rotating at 4°C overnight. DNA was purified using Promega Wizard SV Gel and PCR Clean-up Kit (product No. A9285).
Libraries for sequencing were made using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, product No. E7103) and sequenced on the NextSeq 500 (Illumina).
CTCF protein was crosslinked to the DNA. DNA is sheared by sonication and antibody precipitation pulls-down CTCF-DNA complexes. Libraries are constructed from DNA sequences which bind to CTCF.

tag: host cell line

tag: host cell type

value: Gastric Cancer

value: decitabine


title: SNU719-Input-1


title: SNU719-CTCF-2

value: anti-CTCF


title: YCCEL1-Input-2

source_name: Human Gammaherpesvirus 4-infected gastric carcinoma cell line YCCEL1


title: YCCEL1-CTCF-2


title: YCCEL1-CTCF-1


title: HA-Bcl-xL cells, IgG control, replicate 3

city: New York

first: Genomics-core-facility

last: WCM

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
The libraries were sequenced on Illumina NextSeq2000 instrucment. Basecalls were performed using bcl2fastq v2.20 (Illumina)
Data were processed using Cut&RunTools with the default settings. Reads were first adapter trimmed using Trimmomatic(0.36) thenwere aligned to the hg19 genome using bowtie2(2.2.9) with the ‘dovetail’ settings enabled.
Alignments from the < 120-bp fractions were used for peak calling with MACS2(2.1.1), followed by de novo motif searching within the peak regions with MEME suite(4.12.0)
bigWig files were generated using the Deeptools package (3.5.1). Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FBS, 0.2 mM L-glutamine, 100 units/ml penicillin, 100 µg/ml streptomycin, and 0.5 μg/ml puromycin.

extract_protocol:
Skene, P.J., Henikoff, J.G. & Henikoff, S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat Protoc 13, 1006-1019 (2018) and Improved CUT&RUN chromatin profiling tools. Meers MP, Bryson TD, Henikoff JG, Henikoff S. Elife 8, e46314 (2019).
libraries were prepared using the ThruPLEX®DNA-Seq kit (R400676, Takara) following the manufacturer’s instructions, purified with AMPure XP magnetic beads (A63881, Beckman Coulter), and quantified using a Qubit fluorometer (ThermoFisher Scientific).
CUT&RUN

treatment_protocol: Skene, P.J., Henikoff, J.G. & Henikoff, S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat Protoc 13, 1006-1019 (2018).

value: human pancreatic neuroendocrine tumor cell line

tag: cun and_run_antibody

value: rabbit anti-mouse IgG (Abcam, ab46540), 1 ul antibody to 100 ul reaction


title: HA-Bcl-xL cells, H3K4me3, replicate 3

value: H3K4me3 (CST 9751), 1 ul antibody to 100 ul reaction


title: BVSC_NRF1_1

tag: tissue

value: pluripotent stem cells

value: Induced differentiation


title: 6917_SC

description:
10x Genomics
sc_BM_T_mice.RDS


title: HA-Bcl-xL cells, H3K4me3, replicate 1


title: HA-Bcl-xL cells, H3K4me3, replicate 2


title: HA-Bcl-xL cells, IgG control, replicate 1


title: control cells, H3K4me3, replicate 3


title: control cells, IgG control, replicate 2


title: DC,scRNAseq

first: Weibin

last: Qian

state: Shandong

address: 16369 Jingshi Road

institute: Affiliated Hospital of Shandong University of Traditional Chinese Medicine

description: BD Rhapsody

data_processing:
Raw sequencing reads of the cDNA library were processed through the BD Rhapsody Whole Transcriptome Assay Analysis Pipeline (v1.8), which included filtering by reads quality, annotating reads, annotating molecules, determining putative cells and generating single-cell expression matrix. Among all the output files, Matrix of UMI counts for each gene per cell were used for downstream analysis. Genome Reference Consortium mm10 was used as reference for BD pipeline.
Assembly: mm10
Supplementary files format and content: Expression matrix file for each sample

source_name: lung

extract_protocol:
Three C57BL/6 mice were selected from each of the blank and model groups，and the lung tissues were cut into about 1-2 mm3 pieces and digested using the SoloTM Tumor Dissociation Kit (Sinotech Genomics, JZ-SC-58201) at 37°C for 30-60 min. The reaction was terminated with serum-supplemented RPMI-1640 medium, and the lysates were passed through a 40μm strainer. After the enzymatic digestion of 3 mice in each group, an equal number of cells were selected from the cell suspension of each mouse separately, and then mixed to finally prepare the final samples of a single group. The single cells were stained with Calcein AM and Draq7 to determine cell count and viability using the BD Rhapsody™ Scanner (BD Biosciences). The cells were loaded in one BD Rhapsody micro-well cartridge, followed by the cell capture beads in excess to ensure that nearly every micro-well contains one bead. The excess beads were washed off so that each microwell had a bead with unique molecular identifiers (UMI) and Barcode paired with a cell. After lysing the cells with lysis buffer, the cell capture beads were retrieved and washed prior to performing reverse transcription.
Cells were firstly stained with two fluorescent dye, Calcein AM and Draq7, for precisely determination of cell concentration and viability via BD Rhapsody™ Scanner (BD Biosciences). Cells were loaded in one BD Rhapsody micro-well cartridge based on Fan et al [1]. Cell capture beads were then loaded excessively to ensure that nearly every micro-well contains one bead, and the excess beads were washed away from the cartridge. After lysing cells with lysis buffer, Cell capture beads were retrieved and washed prior to performing reverse transcription. Microbeads-captured single cell transcriptome were generated into cDNA library containing cell labels and unique molecular identifiers (UMI) information. All procedures were performed with BD Rhapsody cDNA Kit (BD Biosciences, Cat. No. 633773) and BD Rhapsody Targeted mRNA & AbSeq Amplification Kit (BD Biosciences, Cat No. 633801) strictly following the manufacturers’ protocol. All the libraries were sequenced in a PE150 mode (Pair-End for 150bp read) on the NovaSeq platform (Illumina).

value: lung

value: control


title: control cells, IgG control, replicate 3


title: Bleomycin modeling 14-day group,scRNAseq

description: BD Rhapsody

value: Bleomycin modeling 14-day group


title: HA-Bcl-xL cells, IgG control, replicate 2


title: DU145_RCAN3_OE

value: DU145 prostate cancer cell

value: transfected with circ0003553 overexpression plasmid


title: 1728_SC

description:
10x Genomics
sc_BM_T_mice.RDS


title: Bleomycin modeling 28-day group,scRNAseq

description: BD Rhapsody

value: Bleomycin modeling 28-day group


title: Salmonella typhimurium ATCC 14028s, rep1

value: ATCC 14028s

value: LB cuture to mid-log phase

value: wild type


title: FW_gill_sample2,replicate2,scRNA-seq

description: 10X Genomics

value: gill


title: YCCEL1-Input-1

value: Gastric Cancer

value: decitabine


title: SNU719-CTCF-1

value: anti-CTCF


title: control cells, IgG control, replicate 1

value: human pancreatic neuroendocrine tumor cell line

value: rabbit anti-mouse IgG (Abcam, ab46540), 1 ul antibody to 100 ul reaction


title: control cells, H3K4me3, replicate 1

value: H3K4me3 (CST 9751), 1 ul antibody to 100 ul reaction


title: oc

city: Tsukuba

first: Xiao

last: Deng

state: Ibaraki

address: 1-1 Namiki

country: Japan

institute: National Institute for Materials Science

data_processing:
Trimmomatic 0.38 program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Trimmed reads are mapped to reference genome with Bowtie 1.1.2. After the read mapping, HTseq version 0.10.0 was used for expression profiling. Expression profile was calculated for each sample and gene as read count.
Differentially expressed genes (DEG) analysis was performed for cells incubated at −0.2 V versus the open circuit condition using edgeR.
If more than one read count value was 0, it was not included in the analysis. In order to reduce systematic bias, estimates the size factors from the count data and applies Trimmed Mean of M-values (TMM) normalization with edgeR R library.
Statistical analysis was performed using Fold Change, exactTest using edgeR. The significant results are selected on conditions of |fold change (fc)| ≥ 2 and exactTest raw p-value <0.05.
Genome_build: GCF_000195755.1
Supplementary_files_format_and_content: An excel file with a list of differentially expressed genes.

organism: Nitratidesulfovibrio vulgaris

source_name: Bacterial cells incubated under an open circuit condition

growth_protocol: Desulfovibrio vulgaris Hildenborough cells were incubated in H-type reactors for seven days with a −0.2 V (versus SHE)-poised indium tin oxide (ITO) electrode and sulfate served as the sole electron donor and acceptor, respectively. As a negative control, cells were incubated in a glass vial under an open circuit (without electrode) condition.

extract_protocol:
TAKARA Nucleobond RNA kit was used to extract total RNA from cells following the manufacturer’s instructions.
rRNA was removed from total RNA using a Ribo-Zero magnetic kit (Gram-negative bacteria), and a complementary DNA (cDNA) library was prepared for sequencing using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s guidelines.

treatment_protocol: After incubation, cells attached on the electrodes were homogenized by thoroughly pipetting with Tris-EDTA (TE) buffer (pH 8) containing 2 mg/mL lysozyme on the electrode surface. Subsequently, the cells were transferred to sterile microtubes and proceeded to RNA extraction.

tag: strain

value: Hildenoborough

tag: electrode potential

value: open circuit condition (without electrode)

tag: eletrochemical reactor

value: H-type three-electrode reactor

tag: incubation time

value: 7 days


title: control cells, H3K4me3, replicate 2

tag: cell line

tag: cell type


title: RNAseq, quadriceps, sedentary-2, mTG-sed, biol rep4

city: Basel

first: Regula

last: Furrer

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

description: Run mode: RAPIDHIGHOUTPUT

data_processing:
CLC Genomics Workbench v 21.0.5 (Quiagen)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC Genomics Workbench (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10 using CLC Genomics Workbench (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC Genomics Workbench
Assembly: mm10
Supplementary files format and content: Excel file (.xlsx) with TPM values for each sample, calculated Log2 fold change and FDR
Supplementary files format and content: GEO-processed-data_Furrer-Handschin_Exercise_RNAseq.xlsx

source_name: Skeletal muscle

extract_protocol:
RNA was isolated with TRIzol reagent (Sigma-Aldrich) and purified using the Direct-zol RNA MiniPrep Kit (Zymo Research) according to the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit following manufacturer's protocols.

value: Skeletal muscle

tag: genotype

value: PGC-1alpha muscle-specific transgenic

tag: treatment

value: untrained, sedentary


title: RNAseq, quadriceps, sedentary-2, mTG-sed, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, sedentary-2, mTG-sed, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, sedentary-2, mTG-sed, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, sedentary-2, mTG-sed, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, sedentary-2, WT-sed, biol rep5

description: Run mode: RAPIDHIGHOUTPUT

value: wildtype


title: RNAseq, quadriceps, sedentary-2, WT-sed, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, sedentary-2, WT-sed, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, sedentary-1, mKO-sed, biol rep5

description: Run mode: RAPIDHIGHOUTPUT

value: PGC-1alpha muscle-specific knockout


title: RNAseq, quadriceps, sedentary-2, WT-sed, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, sedentary-2, WT-sed, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, sedentary-1, WT-sed, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, sedentary-1, mKO-sed, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, sedentary-1, WT-sed, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, sedentary-1, mKO-sed, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, sedentary-1, WT-sed, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, sedentary-1, WT-sed, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-8h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT

value: trained, acute exercise


title: 2

source_name: Bacterial cells incubated on a −0.2 V-poised ITO electrode

value: −0.2 V versus standard hydrogen electrode


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-8h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, sedentary-1, WT-sed, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-8h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-8h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-8h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-6h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-6h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-4h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-6h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-0h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-6h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-0h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-6h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, sedentary-1, mKO-sed, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-4h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, sedentary-1, mKO-sed, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-0h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-0h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ctrl, biol rep4

description: Run mode: RAPIDHIGHOUTPUT

value: trained


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ctrl, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-0h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ctrl, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-8h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT

value: untrained, acute exercise


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-8h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ctrl, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-6h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-6h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-4h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-4h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ctrl, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-8h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-8h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-8h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-4h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-4h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-4h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-0h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-6h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-0h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-trained-ex-4h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ctrl, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ctrl, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-6h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-6h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, steady-state, mKO-trained, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, steady-state, mKO-trained, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, steady-state, mKO-untrained, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-4h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-4h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-0h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, steady-state, mKO-untrained, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-8h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-8h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-8h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-0h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ctrl, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-6h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ex-0h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-4h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ctrl, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, steady-state, mKO-trained, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, mKO-untrained-ctrl, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-4h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, steady-state, mKO-trained, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, steady-state, mKO-trained, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-4h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, steady-state, mKO-untrained, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, steady-state, mKO-untrained, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-0h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: ka114-KO_SC1005_reKap114delta_GFPyTBP_TBPChIP_Salt_Exp2

city: Taipei

first: Wei-Yi

last: Chen

address: No. 155, Sec 2, Linong St.

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
ChIP-seq reads were aligned to the sacCer3 yeast genome assembly using bowtie version 1.12 with with parameters "-n 2 -m 1 -l 36 --best"
Potential PCR duplicates in ChIP-seq reads were removed using samtools rmdup command.
The bedGraph was generated by using bedtools genomcov command.
The tag density spanning promoter region was analyzed by HOMER software
Assembly: sacCer3
Supplementary files format and content: bedGraph file for ChIP-seq.

organism: Saccharomyces cerevisiae

growth_protocol: The yeast strains  were grown in minimal medium (-Ura) at 30 °C.

extract_protocol:
Chromatin lysates were prepared by sonication and protein-DNA complexes were isolated with anti-GFP (Abcam ab290) followed by purification with PCR purification kit (Qiagen). The  isolated genomic DNA were subjected to high throughput sequencing service provided by the genomic core facility of Institute of Molecular Biology, Academia Sinica, Taiwan.
Multiplexing libraries were prepared for sequencing using KAPA Hyper prep kit according to the manufacturer's protocol.

treatment_protocol: Yeast strains  carrying GFP-yTBP resuced without or with kap114 wildtype or kap114Δ(899–956) were grown in minimal medium (-Ura) with or without 1.5 M NaCl at 30°C to reach the logarithmic phase (OD600 = 0.8). For ChIP-seq, cell were fixed with 1% formaldehyde at room temp followed by quencing with 125 mM Glycine.

value: kap114 knockout

value: anti-GFP (Abcam ab290)


title: RNAseq, quadriceps, steady-state, mKO-untrained, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-8h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-8h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: ka114-KO_SC1005_reKap114delta_GFPyTBP_TBPChIP_Exp2


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-6h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-6h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-6h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-6h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-4h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: ka114-KO_SC1005_GFPyTBP_TBPChIP_Exp2

value: pRS426 vector


title: RNAseq, quadriceps, acute-exercise, WT-trained-ctrl, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: ka114-KO_SC1005_Input_DNA_Exp2


title: kap114-KO, SC1005, reKap114delta, GFPyTBP, TBPChIP, Salt, Exp1

data_processing:
ChIP-seq reads were aligned to the sacCer3 yeast genome assembly using bowtie version 1.12 with with parameters "-n 2 -m 1 -l 36 --best"
Potential PCR duplicates in ChIP-seq reads were removed using samtools rmdup command.
The tag density spanning promoter region was analyzed by HOMER software
Assembly: sacCer3
Supplementary files format and content: Bam file for ChIP-seq.

tag: molecule type

value: ChIPed DNA


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-8h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-0h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-4h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-0h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-0h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ex-0h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-8h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-8h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: ka114-KO_SC1005_reKap114WT_GFPyTBP_TBPChIP_Salt_Exp2

value: pRS426_kap114 WT, Salt-treated


title: kap114-KO, SC1005, reKap114WT, GFPyTBP, TBPChIP, Salt, Exp1


title: RNAseq, quadriceps, acute-exercise, WT-trained-ctrl, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-6h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: kap114-KO, SC1005, GFPyTBP, TBPChIP, Exp1


title: ka114-KO_SC1005_GFPyTBP_TBPChIP_Salt_Exp2

value: pRS426 vector, Salt-treated


title: ka114-KO_SC1005_reKap114WT_GFPyTBP_TBPChIP_Exp2

value: pRS426_kap114 WT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ctrl, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-trained-ctrl, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-8h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: kap114-KO, SC1005, reKap114delta, GFPyTBP, TBPChIP, Exp1


title: Sensory Neurons SARS_3

city: Cambridge

first: Anthony

last: Flamier

state: MA

address: 455 Main Street

institute: Whitehead Institute

data_processing:
Sequence quality was controlled by FastQC
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimgalore
Trimmed sequence reads were mapped to hg38 using STAR
Read count extraction and normalization were performed using featureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts for each Sample

source_name: iPSC 7095

growth_protocol: iPSC-sensory neurons were maintained in BrainPhys media supplemented with N2/B27 supplements, NT-3, GDNF, and BDNF in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPAHypermRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were infected with WA1/2020 SARS-CoV-2 at a MOI of 1 for 48 hours.

value: iPSC 7095

value: iPSC-sensory neurons

value: WT

value: WA1/2020 SARS-CoV-2 infected

tag: time

value: 48 hrs


title: kap114-KO, SC1005, reKap114WT, GFPyTBP, TBPChIP, Exp1


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-6h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT

value: Skeletal muscle

value: wildtype


title: kap114-KO, SC1005, GFPyTBP, TBPChIP, Salt, Exp1


title: RNAseq, quadriceps, acute-exercise, WT-trained-ctrl, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: Sensory Neurons SARS_2


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-4h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-8h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: Sensory Neurons MOCK_2

value: mock

value: 0 hrs


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-4h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT

value: untrained, acute exercise


title: kap114-KO, SC1005, reKap114WT, Input DNA, Exp1

value: kap114 knockout

value: Input DNA


title: kap114-KO, SC1005, Input DNA, Exp1

value: pRS426 vector


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-6h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-6h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-6h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: Sensory Neurons MOCK_3


title: Sensory Neurons MOCK_1


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-0h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-4h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT