title: GQ-T2-RT3

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

department: ICBR

institute: UNIVERSITY OF FLORIDA

description: Library name: 36

data_processing:
Illumina basespace used for basecalling.
Reads acquired from the Illumina NovaSeq 6000 platform were cleaned up with the cutadapt program to trim off sequencing adaptors and low-quality bases with a quality phred-like score <20. Reads <40 bases were excluded from RNA-seq analysis.
The artichoke genome (Cynara cardunculus var. scolymus) from the Globe Artichoke Genome Database was used as the reference sequences for RNA-seq analysis. The cleaned reads of each sample were mapped individually to the reference sequences using the read mapper of the STAR package were done to visualize differential gene expression for each treatment with in-house R scripts. In addition, we also conducted a multi-factor analysis (e.g., control, treatment, and age) for differences between the samples while estimating the effect of the treatment on an individual animal.
Assembly: Reference_V2_function_ipr.fa
Supplementary files format and content: tab-delimited text files include the gene names and the mapped read counts for each Sample

organism: Cynara cardunculus

source_name: browning progression of artichoke cultivar green queen in day 7

extract_protocol:
With three biological replications, we extracted the heart tissue of artichoke on sampling day, wrapped in aluminum foil, frozen in liquid nitrogen, and stored at -80°C.
Sequencing sampling was done at d7 and d14 for the reason of visible and physiological changes in artichoke quality. Total RNA from heart tissues was isolated using NucleoSpin RNA Plant (Machery- Nagel, PA, USA) and Fungi kit with additional DNase (PureLink™ DNase Set, Invitrogen™, CA, USA) at different time points. Quality & concentration (300 ng/mL) of RNA was checked using ND1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol: Globe artichoke (Cynara cardunculus var. scolymus) plants of Green Globe Improved (GGI), Green Queen (GQ), Imperial Star (IS), Opal (OP) cultivars were grown in the experimental fields of Gulf Coast Research and Education Center, FL, USA under GA treatment to induce early flowering. Mature artichoke heads were harvested and transported in air-conditioned van with ice packs within 2 h to post-harvest laboratory at University of Florida, Gainesville. Prior the experiment, heads were stored at 4°C for 48h for the acclimation and reducing the physiological response during shipping. Uniform samples were used for the morphological and physiological analysis at 0, 7 and 14 days of cold storage with three biological replicates.

value: heart

tag: cultivar

value: green queen

value: browning progression

tag: time

value: day 7


title: mdTN from animal_53

status: Public on Jul 01 2026

type: SRA

city: Tempe

first: Noah

last: Snyder-Mackler

state: Arizona

address: 214 Life Sciences C

department: School of Life Sciences

country: USA

institute: Arizona State University

description:
Library name: NSM1374
3 lvl sciRNAseq

library_source: transcriptomic single cell

data_processing:
Converts base calls to fastq files with bcl2fastq/ v.2.20 (RRID:SCR_015058) (Illumina), merge read 1 which contains the barcode to read 2 files.
Removes polyA tails using Trim Galore/v.0.6.7 (RRID:SCR_011847)
Aligns trimmed reads to a reference genome with STAR/v.2.7.6 (RRID:SCR_004463)
Extracts mapped reads and removes duplicates.
Generates UMI counts for exonic and intronic regions of each gene, tabulated according to the unique three-level barcode design in sci-RNA-seq3.
Assembly: rhesus macaque reference genome (Mmul_10)
Supplementary files format and content: all_regions_cell_annotate.csv
Supplementary files format and content: all_regions_count.npz
Supplementary files format and content: all_regions_gene_annotate.csv

molecule: nuclear RNA

organism: Macaca mulatta

source_name: mediodorsal thalamic nucleus

growth_protocol: free-ranging population

extract_protocol:
Briefly, tissue was manually pulverized on dry ice, transferred to pre-chilled tubes, and stored at −80°C. For lysis, pulverized tissue was suspended in hypotonic lysis buffer A (0.3 M sucrose, 0.1% Triton X-100, 3 mM MgCl₂, 0.025% IGEPAL CA-630, 1% DEPC in PBS) for 10 min, filtered (40-μm), pelleted, and resuspended in SPBSTM buffer (0.3 M sucrose, 1X PBS, 0.1% TritonX-100, 3 mM MgCl₂, and 1% DEPC). Nuclei were fixed for 10 min in 1.5 mM dithiobis(succinimidyl propionate) (DSP), diluted from a 123 mM stock in DMSO into methanol. After washing in 0.3 M SPBSTM, nuclei were layered onto a 10:1 volume of 1.4 M SPBSTM, centrifuged (3,000 x g, 20 min, 4°C), and resuspended. Nuclei were filtered (20-μm), counted, aliquoted, and cryopreserved in 90% 0.3 M SPBSTM with 10% anhydrous DMSO at -80°C. One library per region was generated using the optimized sci-RNA-seq3 protocol with the following modifications: nuclei were counted using the ImageExpress Pico System (Molecular Devices), and 15,000-20,000 nuclei were loaded per reverse transcription well. Tagmentation used N7 adaptor-loaded Tn5 transposase (Diagenode, C01070010-20), with 6-9 μL of Tn5 per 550 μL of 2X TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl₂, 20% dimethylformamide), distributed at 5uL per well.
sci-RNA-seq3

treatment_protocol: Following veterinary euthanasia, a necropsy was immediately performed during which the brain was perfused by transcardial perfusion with sterile saline. The brain was then removed from the cranium and sagittally sectioned into left and right hemispheres. The left hemisphere was fixed in 10% formalin and not used for this study. The right hemisphere was further sectioned prior to cryopreservation. First, the cerebellum was separated from the cerebrum. The cerebrum was then placed on a custom mold and sectioned coronally into 11 ~0.5 cm-thick slices. All 12 slices (including the cerebellar hemisphere) were individually stored in Whirl-pak bags and flash frozen in a dry-ice/ethanol bath immediately before storage in ultralow (-80°C) freezers. Regions of interest were dissected in sterile, RNase-free conditions on dry ice to minimize RNA degradation. Six 1-mm tissue biopsies were then collected by biopsy punch.

tag: tissue

value: mediodorsal thalamic nucleus


title: Control-2

city: Suzhou

first: Xingchen

last: Yao

state: Jiangsu

address: No 100 Chongwen Road Suzhou Industrial Park, Suzhou

country: China

institute: Suzhou Institute of Systems Medicine   Chinese Academy of Medical Sciences

description:
Library name: Semple3
RNA immunoprecipitation sequencing (RIP-seq) was performed in HeLa cells using IPO5 or IgG control antibodies. Total RNA enriched by RIP was fragmented and sequenced using small RNA library preparation. Libraries were sequenced on Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

library_source: transcriptomic

data_processing:
Raw reads were quality-checked using FastQC (v0.11.9).
Adapter trimming and low-quality read removal were performed using Cutadapt (v3.4).
Clean reads were aligned to the human genome (GRCh38/hg38) using STAR aligner (v2.7.10a) with default parameters.
Read counts were generated using featureCounts (subread v2.0.3) based on GENCODE v38 gene annotations.
Counts were normalized to Reads Per Million (RPM) for downstream analysis.
Assembly: GRCh38 / hg38
Supplementary files format and content: The processed data file contains RIP-seq peak annotation results generated using the annotatePeaks.pl script from HOMER. The file is a tab-delimited text table listing peaks enriched in IPO5 RIP-seq samples mapped to the human transcriptome (hg38 assembly). Each row represents a peak and includes genomic coordinates, peak score, annotation details, and associated gene information. Column headers include: PeakID, chromosome (Chr), start and end positions, strand, peak score, focus ratio/region size, gene annotation, detailed annotation, distance to transcription start site (TSS), nearest promoter ID, Entrez ID, RefSeq and Ensembl gene IDs, gene symbol, gene alias, gene description, and gene type.

molecule: total RNA

organism: Homo sapiens

source_name: HeLa (a human cervical cancer cell line)

growth_protocol: HeLa cells were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
HeLa cells were lysed using IP lysis buffer (150 mM NaCl, 10 mM Tris-HCl pH 7.4, 1% NP-40, protease and RNase inhibitors). The lysates was then subjected to ultrasonic fragmentation at high power, 30 seconds on/30 seconds off for 10 cycles at 4°C. Cell lysates were incubated with antibody-conjugated magnetic beads overnight at 4°C. After immunoprecipitation, RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
RNA fragments were end-repaired and ligated with 3' and 5' adapters using the Small RNA-seq Library Preparation Kit for Illumina V3 (ABclonal, RK20312) and indexed using the Small RNA Adapter Module 96 Index (ABclonal, RK20358), following the manufacturer's instructions. cDNA was synthesized and PCR-amplified to generate sequencing-ready libraries.

treatment_protocol: No treatment was applied prior to RIP. Cells were collected at 70–80% confluence for immunoprecipitation.

tag: cell line


title: miP-PSTPIP2-solvent_2

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Raw data were checked for quality, adapter content and duplication rates using FastQC.
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 109) with STAR 2.7.11a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized gene counts.

source_name: human umbilical vein endothelial cells

extract_protocol:
Cells were lysed in a lysis buffer containing Tris-HCl pH7.5 (50mM, Applichem, Germany), NaCl (150mM, Merck, Darmstadt, Germany), MgCl2,(10mM, Invitrogen, Schwerte, Germany), NP-40 (1%, Merck) dissolved in UltraPure DNase/RNase-free DW (Invitrogen) and supplemented with NaPPi (10mM, Merck), NaF (20mM, Applichem, Germany), okadaic acid (10nM, LC laboratory, USA), Na3VO4 (2mM, Sigma-Aldrich), protease inhibitor mix, (12µl/ml, Sigma-Aldrich), PMSF (4µl/ml, Carl Roth, Germany), SUPERase In RNase Inhibitor (200U/ml, Invitrogen), TURBO DNaseI (25U/ml, Invitrogen). Total RNA was purified using the miRNeasy Micro kit (QIAGEN), according to the manufacturer’s instructions.
RNA and library preparation integrity were verified with LabChip Gx Touch 24 (Perkin Elmer). 0.5-1µg of total RNA was used as input for Corall Total RNA-Seq Library Prep Kit following manufacture’s instructions (Lexogen). Sequencing was performed on the NextSeq2000 instrument (Illumina) using P3 flowcell and 1x72bp single end setup.

tag: cell type

value: human umbilical vein endothelial cells

tag: overexpression

tag: treatment

value: solvent


title: mdTN from animal_52, rep2

description:
Library name: NSM1373-b2
3 lvl sciRNAseq


title: GQ-T2-RT2

description: Library name: 35


title: IPO5-1

description:
Library name: Semple2
RNA immunoprecipitation sequencing (RIP-seq) was performed in HeLa cells using IPO5 or IgG control antibodies. Total RNA enriched by RIP was fragmented and sequenced using small RNA library preparation. Libraries were sequenced on Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

value: HeLa (a human cervical cancer cell line)


title: miP-PSTPIP2-solvent_1


title: mdTN from animal_52

description:
Library name: NSM1373
3 lvl sciRNAseq


title: GQ-T2-RT1

description: Library name: 34


title: Control-1

description:
Library name: Semple1
RNA immunoprecipitation sequencing (RIP-seq) was performed in HeLa cells using IPO5 or IgG control antibodies. Total RNA enriched by RIP was fragmented and sequenced using small RNA library preparation. Libraries were sequenced on Illumina NovaSeq 6000 platform with 150 bp paired-end reads.


title: mdTN from animal_51, rep2

description:
Library name: NSM1372-b2
3 lvl sciRNAseq


title: GGI-T2-RT3

description: Library name: 33

source_name: browning progression of artichoke cultivar green blobe improved in day 7

value: green blobe improved


title: non-infection-IL-1b_5

value: control


title: mdTN from animal_51

description:
Library name: NSM1372
3 lvl sciRNAseq


title: HCCT11H_L001

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

institute: NCSU

description: Library name: HCCT11H_L001

library_source: genomic

data_processing:
Reads were assigned back to individuals by index reads, and aligned in silico to a bisulfite-converted reference genome (i.e., hg38 version 87). Reads without unique alignments, due to either repetitive genomic sequence or loss of specificity from bisulfite conversion of cytosines, and duplicate reads, indicative of clonal amplification of original random DNA fragments, were eliminated. The quality of each paired-end sequence file was inspected using fastqc, and adapter trimming and quality control were performed using the Trim Galore wrapper script that calls the cutadapt  script internally. Paired-end reads with a trimmed adapter sequence were aligned to the human reference genome (i.e., hg38 version 87) downloaded from Ensembl using bsmap aligner. The following options were passed to the aligner: -p 8 -L 135 -w 100 -v 10 -q 10 -R -V 1. The aligned bam files were sorted and indexed using samtools, and duplicate sequence reads were removed using the Picard application.
MOABS was used to merge the BAM files for each condition and to find differentially methylated CpGs (DMC) using the default parameters. Differentially methylated regions (DMR) were identified using MOABS mcomp function with minimum credible difference of 0.1 and minimum of 4 DMCs in a DMR. Bedtools Suites intersection function was used to find overlaps between DMRs with the ICRs.
Assembly: Ensembl hg38 version 87
Supplementary files format and content: control_merge.G.bed: Methylation summaries across 51 merged control samples
Supplementary files format and content: HCCTH_merge.G.bed: Methylation summaries across 10 HCC case samples

molecule: genomic DNA

source_name: Case

extract_protocol:
DNA extraction was done using Qiagen DNeasy Blood and Tissue kit reagents, according to manufacturer's protocols.
Library construction was done using NEBNext Enyzymatic MethylSeq cytosine conversion and library construction kits, according to manufacturer's protocols, with dual indexing.

value: whole blood

value: Hepatocellular carcinoma


title: GGI-T2-RT2

description: Library name: 32


title: non-infection-IL-1b_3


title: GGI-T2-RT1

description: Library name: 31


title: HCCT10H_L001

description: Library name: HCCT10H_L001


title: non-infection-IL-1b_2


title: IS-T2-RT3

description: Library name: 30

source_name: browning progression of artichoke cultivar imperial star in day 7

value: imperial star


title: HCCT9H_L001

description: Library name: HCCT9H_L001


title: non-infection-IL-1b_1


title: mdTN from animal_49, rep2

description:
Library name: NSM1370-b2
3 lvl sciRNAseq


title: IS-T2-RT2

description: Library name: 29


title: HCCT8H_L001

description: Library name: HCCT8H_L001


title: non-infection-solvent_5


title: mdTN from animal_49

description:
Library name: NSM1370
3 lvl sciRNAseq


title: IS-T2-RT1

description: Library name: 28


title: HCCT7H_L001

description: Library name: HCCT7H_L001


title: non-infection-solvent_4


title: mdTN from animal_48, rep2

description:
Library name: NSM1369-b2
3 lvl sciRNAseq


title: OP-T2-RT3

description: Library name: 27

source_name: browning progression of artichoke cultivar Opal in day 7

value: Opal


title: HCCT6H_L001

description: Library name: HCCT6H_L001


title: non-infection-IL-1b_4


title: non-infection-solvent_3


title: OP-T2-RT2

description: Library name: 26


title: mdTN from animal_50, rep2

description:
Library name: NSM1371-b2
3 lvl sciRNAseq


title: mdTN from animal_48

description:
Library name: NSM1369
3 lvl sciRNAseq


title: HCCT4H_L001

description: Library name: HCCT4H_L001


title: non-infection-solvent_2


title: mdTN from animal_50

description:
Library name: NSM1371
3 lvl sciRNAseq


title: HepG2.batch1.ATA.rep2.D01

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description: Library name: HepG2_Batch1_ATA_2_D01

library_source: other

data_processing:
Reads were aligned using STAR alignment on QIAGEN's CLC workbench software (v25.0.1) and Kallisto alignment on ExpressAnalyst
Raw counts were logCPM normalized and filtered for low abundance (5) and variance (15) using ExpressAnalyst
Normalized counts were analyzed for differential expression using DESeq2
Assembly: CLC workbench used hg38.p14 Ensembl v113 GCA_000001405.29; ExpressAnalyst used hg38.p14 GCA_000001405
Supplementary files format and content: raw files and count files are provided as fastq.gz files and .txt files, respectively.

molecule: other

source_name: cell lysate

growth_protocol: from ms

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol

treatment_protocol: cells were exposed to various concentrations of 6ppd-quinone for 24 hours after seeding at 35,000 cells per well

value: liver

value: hepatocyte

tag: genotype

value: cell line


title: mdTN from animal_47, rep2

description:
Library name: NSM1368-b2
3 lvl sciRNAseq


title: non-infection-solvent_1


title: HCCT2H_L001

description: Library name: HCCT2H_L001


title: mdTN from animal_47

description:
Library name: NSM1368
3 lvl sciRNAseq


title: OP-T2-RT1

description: Library name: 25

value: heart


title: GQ-T3-RT3

description: Library name: 24

source_name: browning progression of artichoke cultivar green queen in day 14

value: green queen

value: day 14


title: smORF-100_3

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl Human genome version hg38 (GRCh38) using STAR 2.7.9  with the parameters "--outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 20 --alignIntronMax 200000" (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Duplicate reads were removed with Picard 2.25.5 (https://github.com/broadinstitute/picard).
The number of reads aligning to genes was counted with featureCounts 2.0.2 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
A combined raw count matrix was produced and used for differential expression analysis using DESeq2 version 1.30.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: hg38 / GRCh38
Supplementary_files_format_and_content: The tab-delimited matrix shows DESeq normalized counts.

source_name: HEK-293 cells

growth_protocol: HEK-293 cells were obtained from the American Type Culture Collection (LGC Standards, Wesel, Germany) and cultured in minimal essential medium containing 8% heat inactivated fetal bovine serum (FBS), gentamycin (25 µg/mL) non-essential amino acids (Thermo Fisher Scientific, Schwerte, Germany) and Na pyruvate (1 mmol/L, Sigma-Aldrich, Darmstadt, Germany). Cells were transfected with plasmids encoding FLAG-tagged human miP30 (smORF-100) or a control pShuttle-CMV plasmid using Lipofectamin2000 (Invitrogen, Schwerte, Germany) according to the manufacturer’s instructions. Total RNA was extracted 48 hours after transfection.

extract_protocol:
Total  RNA was purified using the miRNeasy Micro kit (QIAGEN, Hilden, Germany), according to the manufacturer’s instructions.
Total RNA (1 µg) was used as input for ribosomal depletion with RiboGone-Mammalian (Takara Bio, Gennevilliers, France) followed by library preparation using SMARTer Stranded Total RNA Sample Prep Kit (Takara Bio, Gennevilliers, France). Sequencing was performed on the NextSeq2000 instrument (Illumina, San Diago, USA) P3 flowcell with v3 chemistry with 1x72bp paired-read setup.

treatment_protocol: no treatment

value: HEK-293 cells

tag: construct


title: HCCT1H_L001

description: Library name: HCCT1H_L001


title: mdTN from animal_46, rep2

description:
Library name: NSM1367-b2
3 lvl sciRNAseq

value: mediodorsal thalamic nucleus


title: GQ-T3-RT2

description: Library name: 23

value: browning progression


title: 207_S79_L001

description: Library name: 207_S79_L001

source_name: Control

value: Healthy control


title: mdTN from animal_46

description:
Library name: NSM1367
3 lvl sciRNAseq


title: smORF-100_2


title: Control 2

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

description: Library name: Con2

data_processing:
We used HISAT2 [2] to map reads to the genome of ftp://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/dna/.
Assembly: hg38
Supplementary files format and content: Microsoft Excel file contains raw counts for each sample

molecule: polyA RNA

source_name: skin

extract_protocol:
Quagene meRnaeasy mini-kit
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.
RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification.
After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature.

value: skin

value: keratinocyte cell line 2

value: normal neonatal keratinocytes

value: Vehicle control (0.4% BSA)


title: GQ-T3-RT1

description: Library name: 22


title: miRFP670nano-IL-1b_4

value: human umbilical vein endothelial cells


title: smORF-100_1


title: miRFP670nano-IL-1b_3


title: 205_S78_L001

description: Library name: 205_S78_L001

value: whole blood


title: mdTN from animal_45, rep2

description:
Library name: NSM1366-b2
3 lvl sciRNAseq


title: GGI-T3-RT3

description: Library name: 21

source_name: browning progression of artichoke cultivar green blobe improved in day 14

value: green blobe improved


title: miRFP670nano-IL-1b_1


title: 203_S15_L001

description: Library name: 203_S15_L001


title: CTRL_3

value: control


title: mdTN from animal_45

description:
Library name: NSM1366
3 lvl sciRNAseq


title: GGI-T3-RT2

description: Library name: 20


title: 201_S2_L001

description: Library name: 201_S2_L001


title: CTRL_2


title: mdTN from animal_44, rep2

description:
Library name: NSM1365-b2
3 lvl sciRNAseq


title: GGI-T3-RT1

description: Library name: 19


title: 199_S14_L001

description: Library name: 199_S14_L001


title: CTRL_1


title: MB from animal_3

description:
Library name: NSM1379
3 lvl sciRNAseq

source_name: midbrain

value: midbrain


title: 197_S67_L001

description: Library name: 197_S67_L001


title: mdTN from animal_43, rep2

description:
Library name: NSM1364-b2
3 lvl sciRNAseq


title: IS-T3-RT3

description: Library name: 18

source_name: browning progression of artichoke cultivar imperial star in day 14

value: imperial star


title: mdTN from animal_44

description:
Library name: NSM1365
3 lvl sciRNAseq


title: IS-T3-RT2

description: Library name: 17

value: heart


title: smORF-15_3

growth_protocol: HEK-293 cells were obtained from the American Type Culture Collection (LGC Standards, Wesel, Germany) and cultured in minimal essential medium containing 8% heat inactivated fetal bovine serum (FBS), gentamycin (25 µg/mL) non-essential amino acids (Thermo Fisher Scientific, Schwerte, Germany) and Na pyruvate (1 mmol/L, Sigma-Aldrich, Darmstadt, Germany). Cells were transfected with plasmids encoding FLAG-tagged human miP2 (smORF-15) or a control pShuttle-CMV plasmid using Lipofectamin2000 (Invitrogen, Schwerte, Germany) according to the manufacturer’s instructions. Total RNA was extracted 48 hours after transfection.


title: 195_S76_L001

description: Library name: 195_S76_L001


title: miRFP670nano-solvent_1

value: solvent


title: smORF-15_2


title: T26_0103

city: Tübingen

first: Daniel

last: Merk

address: Otfried-Müller-Str. 27

institute: Hertie-Institute for Clinical Brain Research

description: Library name: 24048a009

data_processing:
The libraries were sequenced as paired-end 50bp reads on an Illumina NovaSeq6000 (Illumina) with a sequencing depth of approximately 25 million clusters per sample.
Raw data QC and processing was performed using megSAP (version 0.2-135-gd002274) combined with ngs-bits package (version 2019_11-42-gflb98e63).
Reads were aligned using STAR v2.7.3a
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw read counts for each sample

source_name: meningioma

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 200ng of total RNA was used for the construction of sequencing libraries.
mRNA libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit

value: meningioma

tag: batch

value: METHlow


title: 193_S36_L001

description: Library name: 193_S36_L001


title: IS-T3-RT1

description: Library name: 16

value: day 14


title: mdTN from animal_43

description:
Library name: NSM1364
3 lvl sciRNAseq

value: mediodorsal thalamic nucleus


title: smORF-15_1

value: HEK-293 cells


title: Ctrl_3


title: mdTN from animal_55

description:
Library name: NSM1376
3 lvl sciRNAseq


title: 191_S22_L001

description: Library name: 191_S22_L001

value: Healthy control


title: mdTN from animal_42, rep2

description:
Library name: NSM1363-b2
3 lvl sciRNAseq


title: mdTN from animal_42

description:
Library name: NSM1363
3 lvl sciRNAseq


title: OP-T3-RT3

description: Library name: 15

source_name: browning progression of artichoke cultivar Opal in day 14

value: Opal

value: browning progression


title: OP-T3-RT1

description: Library name: 14


title: 189_S73_L001

description: Library name: 189_S73_L001


title: mdTN from animal_41, rep2

description:
Library name: NSM1362-b2
3 lvl sciRNAseq

source_name: mediodorsal thalamic nucleus


title: Ctrl_2


title: OP-T3-RT2

description: Library name: 13


title: 187_S71_L001

description: Library name: 187_S71_L001


title: D1 MOR MALE, BIO REPLICATE 3

city: Philadelphia

first: Dana

last: Zeid

state: PA

address: 1701 North 13th St

institute: Temple University

description: Library name: 174

data_processing:
Adaptors were trimmed from raw sequencing reads using TrimGalore software
Trimmed reads were mapped to the GRCr8 rat genome using Kallisto
Kallisto abundance estimates were imported into R software using the tximport package and analyzed using the DESeq2 package.
Assembly: GRCr8
Supplementary files format and content: tab delimited text file ("Normalized_counts.txt") contains normalized kallisto counts

organism: Rattus norvegicus

source_name: Brain tissue (ventral tegmental area)

extract_protocol:
Brain tissue was dissected from adult (postnatal day 60+) rats: Immediately after euthanasia via decapitation, whole brains were removed and sectioned on a 1mM brain block. VTA punches were quickly micro dissected & flash frozen on dry ice. Total RNA was isolated using a Qiazol/chloroform procedure and purified using the Qiagen RNeasy Micro kit.
Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit per manufacturer instructions

value: Brain tissue (ventral tegmental area)

tag: Sex

value: Male

tag: experimental group

value: Day1 MOR ABS


title: Ctrl_1


title: T26_0097

description: Library name: 24048a004


title: mdTN from animal_41

description:
Library name: NSM1362
3 lvl sciRNAseq


title: GQ-T1-RT3

description: Library name: 12

source_name: browning progression of artichoke cultivar green queen in day 0

value: green queen

value: day 0


title: miP-PSTPIP2-IL-1b_3

source_name: human umbilical vein endothelial cells

value: human umbilical vein endothelial cells


title: 185_S69_L001

description: Library name: 185_S69_L001

value: whole blood


title: mdTN from animal_40

description:
Library name: NSM1361
3 lvl sciRNAseq


title: 179_S28_L001

description: Library name: 179_S28_L001


title: mdTN from animal_40, rep2

description:
Library name: NSM1361-b2
3 lvl sciRNAseq


title: GQ-T1-RT1

description: Library name: 10

value: heart


title: 181_S53_L001

description: Library name: 181_S53_L001


title: 53_Control_2019_02_01_2, rep2

city: Villenave d Ornon

first: mathieu

last: fouché

state: Gironde

address: 71 avenue Edouard Bourlaux

department: UMR BFP

country: France

institute: INRAE

description: Library name: 53_cold_deprivation, 53_CTACGACA-TTGGACTC-AHGKC2BBXY_L005

data_processing:
trimming: Trimmomatic 0.36 (Bolger et al., 2014) with following settings fa:2:10:5:1 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to the sweet cherry ‘Regina’ reference genome v.1 (Vimont et al., 2021) using STAR (Dobin et al., 2013)
Raw read count was performed using HTSeq count (Anders et al., 2015)
Assembly: sweet cherry ‘Regina’ reference genome v.1 (Le Dantec et al, 2022)
Supplementary files format and content: the format is .txt and include raw counts of each gene for each sample

organism: Prunus avium

source_name: flower bud

growth_protocol: adult potted trees

extract_protocol:
Total RNA was extracted from 100 mg of frozen and grinded flower buds using RNeasy Plant Mini kit (Qiagen) with minor modification: 1.5% PVP-40 was added in the extraction buffer RLT
Library preparation was performed on 1 μg of high quality RNA (RNA integrity number equivalent superior or equivalent to 8.5) using the TruSeq Stranded mRNA Library Prep Kit High Throughput (Illumina cat. no. RS-122-2103)

value: flower bud

value: plant

value: Regina


title: 53_Control_2019_02_01_2, rep1

description: Library name: 53_cold_deprivation, 53_CTACGACA-TTGGACTC-AHGKC2BBXY_L004


title: 52_Control_2019_02_01_1, rep3

description: Library name: 52_cold_deprivation, 52_TCGTAGTG-CCAAGTCT-AHGKC2BBXY_L006


title: mdTN from animal_39, rep2

description:
Library name: NSM1360-b2
3 lvl sciRNAseq


title: GGI-T1-RT3

description: Library name: 9

source_name: browning progression of artichoke cultivar green blobe improved in day 0

value: green blobe improved


title: 52_Control_2019_02_01_1, rep2

description: Library name: 52_cold_deprivation, 52_TCGTAGTG-CCAAGTCT-AHGKC2BBXY_L005


title: 177_S14_L001

description: Library name: 177_S14_L001


title: GQ-T1-RT2

description: Library name: 11


title: GGI-T1-RT2

description: Library name: 8


title: mdTN from animal_39

description:
Library name: NSM1360
3 lvl sciRNAseq

value: mediodorsal thalamic nucleus


title: GGI-T1-RT1

description: Library name: 7


title: 173_S13_L001

description: Library name: 173_S13_L001


title: mdTN from animal_37

description:
Library name: NSM1359
3 lvl sciRNAseq


title: 48_CC2NOV_2019_01_02_3, rep3

description: Library name: 48_cold_deprivation, 48_GATTCTGC-CTCTCGTC-AHGKC2BBXY_L006


title: mdTN from animal_36, rep2

description:
Library name: NSM1358-b2
3 lvl sciRNAseq


title: 48_CC2NOV_2019_01_02_3, rep2

description: Library name: 48_cold_deprivation, 48_GATTCTGC-CTCTCGTC-AHGKC2BBXY_L005


title: IS-T1-RT3

description: Library name: 6

source_name: browning progression of artichoke cultivar imperial star in day 0

value: imperial star


title: 48_CC2NOV_2019_01_02_3, rep1

description: Library name: 48_cold_deprivation, 48_GATTCTGC-CTCTCGTC-AHGKC2BBXY_L004


title: IS-T1-RT2

description: Library name: 5


title: mdTN from animal_36

description:
Library name: NSM1358
3 lvl sciRNAseq


title: 169_S42_L001

description: Library name: 169_S42_L001

value: Healthy control


title: IS-T1-RT1

description: Library name: 4


title: 47_CC2NOV_2019_01_02_2, rep3

description: Library name: 47_cold_deprivation, 47_AGCCTCAT-TCTCTACT-AHGKC2BBXY_L006


title: mdTN from animal_35, rep2

description:
Library name: NSM1357-b2
3 lvl sciRNAseq


title: 167_S27_L001

description: Library name: 167_S27_L001


title: Caco-2.batch2.SMET.rep2.D03

description: Library name: Caco2_Batch2_SMET_2_D03

source_name: cell lysate

value: colon

value: epithelial

value: cell line


title: OP-T1-RT3

description: Library name: 3

source_name: browning progression of artichoke cultivar Opal in day 0

value: Opal

value: browning progression


title: MEL Mtg16 H3K4me3 dTAGV1 30m C

city: Nashville

first: Scott

middle: W

last: Hiebert

state: TN

address: 2220 Pierce Ave.

institute: Vanderbilt University

description: Library name: CUTRUN_H3K4me3 dTAGV1 30m C

data_processing:
Adaptor trimming was performed using TrimmomaticPE, and trimmed reads were aligned to concatenated mm39+ec (CUT&RUN) or mm39+dm3 (ChIP-Seq) genomes. Resulting alignments were then processed with samtools (v. 1.16.1) to remove low quality reads, count reads aligned to mm39, ec, and dm3 genomes, and remove spike-in reads. Peak calling was performed using MACS2 (v. 2.2.9.1), q 0.01. Read quantification was performed with DiffBind (v. 3.16.0). Differential analysis was performed using DESeq2 (v. 1.46.0) with built-in normalization.
Assembly: mm39
Supplementary files format and content: bigwig
Library strategy: CUT&Run

organism: Mus musculus

source_name: MEL Mtg16-FKBP-2XHA

growth_protocol: MEL cells were grown in RPMI 1640 supplemented with 10% heat-inactivated FBS, 1% penicillin/streptomycin, and 1% L-glutamine.

extract_protocol:
CUT&RUN experiments were performed in biological triplicate. Samples were harvested by centrifugation, washed (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine, 1X Roche Complete Protease Inhibitor tablet), and adsorbed to activated Concavalin A beads for 10min at room temperature. Samples were then incubated with primary antibody diluted in digitonin buffer + 2mM EDTA (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine, 0.2% digitonin, 1X Roche Complete Protease Inhibitor tablet) overnight at 4C. The next day, samples were washed and incubated with secondary antibody diluted in digitonin buffer + 2mM EDTA for 1hr at 4C. After secondary antibody incubation, pAG-MNase was added to the samples, then activated with CaCl2 and incubated at 4C for 2hrs. After MNase incubation, the reaction stop buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/mL RNase A, 50ug/mL glycogen, supplemented with 0.5ng E. coli gDNA per sample) was added and samples incubated for 10min at 37C. Samples were then cleaned using NEB Monarch DNA Cleanup Kit according to manufacturer instructions prior to library preparation. ChIP-Seq experiments were performed in biological triplicate. All buffers were filter sterilized and supplemented with protease inhibitors immediately prior to use (2uL aprotinin and 20uL 0.1M PMSF per 1mL buffer). 10 million cells per immunoprecipitation sample were harvested by centrifugation, washed in PBS, and fixed for 10min at room temperature in 1% methanol-free formaldehyde, then quenched with 0.125M glycine. All subsequent steps were performed on ice or at 4C. Fixed cells were lysed in cell lysis buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton-X-100) that was supplemented with 0.5 million crosslinked S2 cells per sample. After lysis, cells were washed in wash buffer (10mM Tris pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) and then sonicated for 20 cycles with a Bioruptor water bath sonicator (30s on/30s off) in sonication buffer (10mM Tris pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% SDS, 0.5% sarkosyl). Successful sonication (DNA fragments between 100-500bp) were verified via agarose gel electrophoresis for every sample prior to IP. After sonication, samples were quantified using Qubit HS, supplemented with 1% Triton-X-100, and antibody was added, followed by overnight incubation at 4C with rotation. After overnight antibody incubation, samples were incubated with equilibrated Protein A/G Dynabeads (50:50 mix) for 1hr at 4C, followed by 5 successive washes: low salt (20mM Tris pH 8.0, 150mM NaCl, 2mM EDTA, 1% Triton-X-100), high salt (20mM Tris pH 8.0, 500mM NaCl, 2mM EDTA, 1% Triton-X-100), LiCl (10mM Tris pH 8.0, 25mM LiCl, 2mM EDTA, 1% Triton X-100), TE (10mM Tris pH 8.0, 1mM EDTA), and TE. After the final wash, elution buffer (1X TE pH 8.0. 0.1% SDS, 200mM NaCl, 0.8ug/uL proteinase K) was added directly to the beads and samples were de-crosslinked overnight at 65C prior to PCR clean up.
ChIP-Seq and CUT&RUN libraries were prepared using NEBNext Ultra II DNA Library Prep Kit according to manufacturer instructions with minor modifications. The end prep reaction for both library types was performed under the following conditions: 20C 30min, 50C 1hr. ChIP-Seq libraries were prepared with size selection. CUT&RUN libraries were prepared without size selection.

treatment_protocol: 250nM dTAGV1

value: MEL Mtg16-FKBP-2XHA

value: murine erythroleukemia


title: mdTN from animal_35

description:
Library name: NSM1357
3 lvl sciRNAseq


title: 165_S13_L001

description: Library name: 165_S13_L001

source_name: Control


title: OP-T1-RT2

description: Library name: 2

value: day 0


title: 163_S26_L001

description: Library name: 163_S26_L001

value: whole blood


title: 47_CC2NOV_2019_01_02_2, rep1

description: Library name: 47_cold_deprivation, 47_AGCCTCAT-TCTCTACT-AHGKC2BBXY_L004


title: 47_CC2NOV_2019_01_02_2, rep2

description: Library name: 47_cold_deprivation, 47_AGCCTCAT-TCTCTACT-AHGKC2BBXY_L005


title: mdTN from animal_34, rep2

description:
Library name: NSM1356-b2
3 lvl sciRNAseq


title: OP-T1-RT1

description: Library name: 1

value: heart


title: mdTN from animal_34

description:
Library name: NSM1356
3 lvl sciRNAseq


title: 46_CC2NOV_2019_01_02_1, rep3

description: Library name: 46_cold_deprivation, 46_CGTTAGAA-GACCTGAA-AHGKC2BBXY_L006

value: flower bud


title: 46_CC2NOV_2019_01_02_1, rep2

description: Library name: 46_cold_deprivation, 46_CGTTAGAA-GACCTGAA-AHGKC2BBXY_L005

value: plant


title: mdTN from animal_33, rep2

description:
Library name: NSM1355-b2
3 lvl sciRNAseq


title: H9C2 cardiomyocytes, HG-Res-SIRT7-Inh group, biological replicate 2

city: Changchun

first: Naixin

last: Chen

address: No. 126, Xiantai Street

institute: China-Japan Union Hospital of Jilin University

description:
Library name: HG-Res-SIRT7-Inh-2.raw_1.fastq.gz, HG-Res-SIRT7-Inh-2.raw_2.fastq.gz
High glucose + resveratrol + SIRT7 inhibitor group biological replicate 2, total RNA-seq

data_processing:
Raw sequencing data were filtered to remove low‑quality reads, adapter sequences, and contaminating sequences to obtain clean reads using Trimmomatic software.
Assembly: Rattus norvegicus (rat) reference genome Rn6 (UCSC version rn6, GCA_000001895.4)
Supplementary files format and content: 1. Raw gene count matrix: Tab‑separated values (TSV) format, containing raw read counts of each gene across all 12 samples; 2. FPKM expression matrix: TSV format, containing normalized FPKM expression values of each gene across all 12 samples; 3. Differentially expressed gene (DEG) lists: TSV format for each pairwise comparison, containing gene ID, gene name, log₂ fold change, P value, adjusted P value, and other related statistics; 4. GO and KEGG enrichment analysis results: TSV format, containing enriched term ID, term name, gene number, P value, adjusted P value, and other related statistics; 5. Visualization files: PDF format, including volcano plots, heatmaps, enrichment scatter plots, and other related figures.
Supplementary files format and content: 1. Raw gene count matrix: Tab‑separated values (TSV) format, containing raw read counts of each gene across all 12 samples; 2. FPKM expression matrix: TSV format, containing normalized FPKM expression values of each gene across all 12 samples; 3. Differentially expressed gene (DEG) lists: TSV format for each pairwise comparison, containing gene ID, gene name, log₂ fold change, P value, adjusted P value, and other related statistics; 4. GO and KEGG enrichment analysis results: TSV format, containing enriched term ID, term name, gene number, P value, adjusted P value, and other related statistics; 5. Visualization files: PDF format, including volcano plots, heatmaps, enrichment scatter plots, and other related figures.

growth_protocol: H9C2 cardiomyocytes were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). Cells were routinely cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco, Thermo Fisher Scientific, USA) supplemented with 10% fetal bovine serum (FBS, Gibco, Thermo Fisher Scientific, USA) and 1% (v/v) penicillin‑streptomycin double antibiotic solution (100 U/mL penicillin, 100 μg/mL streptomycin, HyClone, GE Healthcare, USA). The cell culture environment was maintained at 37 °C in a humidified incubator containing 5% CO₂ (Thermo Fisher Scientific, USA). When cells reached approximately 80% confluence, culture medium was replaced for subsequent experiments.

extract_protocol:
Total RNA was isolated from H9C2 cells in each experimental group using Trizol reagent (Thermo Fisher Scientific, USA) according to the manufacturer’s instructions. The purity and integrity of RNA were detected by a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA) and agarose gel electrophoresis, respectively. Only RNA samples with A260/A280 ratio between 1.8 and 2.0 and intact 28S and 18S rRNA bands were used for subsequent transcriptome sequencing.
Transcriptome sequencing library construction and high‑throughput sequencing were performed by Novogene Co., Ltd. (China) using the Illumina NovaSeq 6000 platform. Briefly, mRNA was enriched from total RNA using oligo(dT) beads, followed by fragmentation into short fragments. First‑strand cDNA was synthesized using random hexamer primers and reverse transcriptase, followed by second‑strand cDNA synthesis. The cDNA fragments were end‑repaired, A‑tailed, and ligated with sequencing adapters. After PCR amplification and purification, the final libraries were quality‑controlled and sequenced on the Illumina NovaSeq 6000 platform to generate 150 bp paired‑end reads.

treatment_protocol: H9C2 cells were divided into four experimental groups with three independent biological replicates per group: 1) Control group: Cells were cultured in normal glucose medium (5.5 mM D‑glucose, Sigma‑Aldrich, Merck, USA) without any drug treatment; 2) High glucose (HG) group: Cells were cultured in HG medium (100 mM D‑glucose) without any drug treatment; 3) HG + Resveratrol (Res) group: Cells were cultured in HG medium and treated with 5 μM resveratrol (MedChemExpress, MCE, USA); 4) HG + Res + SIRT7 inhibitor group: Cells were cultured in HG medium and treated with 5 μM resveratrol and 5 μM SIRT7‑specific inhibitor (SirReal2, Selleck Chemicals, USA). All cells were incubated in the above‑mentioned conditions for 48 h in a 37 °C, 5% CO₂ humidified incubator before subsequent experiments.

value: cardiomyocytes

value: Wild type (WT)

value: High glucose medium treated with 5 μM resveratrol and 5 μM SIRT7 inhibitor for 48 h


title: 157_S41_L001

description: Library name: 157_S41_L001


title: mdTN from animal_33

description:
Library name: NSM1355
3 lvl sciRNAseq

value: mediodorsal thalamic nucleus


title: 46_CC2NOV_2019_01_02_1, rep1

description: Library name: 46_cold_deprivation, 46_CGTTAGAA-GACCTGAA-AHGKC2BBXY_L004

value: Regina


title: mdTN from animal_32, rep2

description:
Library name: NSM1354-b2
3 lvl sciRNAseq


title: 155_S33_L001

description: Library name: 155_S33_L001

value: Healthy control


title: H9C2 cardiomyocytes, HG-Res group, biological replicate 3

description:
Library name: HG-Res-3.raw_1.fastq.gz, HG-Res-3.raw_2.fastq.gz
High glucose + resveratrol group biological replicate 3, total RNA-seq

value: High glucose medium treated with 5 μM resveratrol for 48 h


title: 153_S19_L001

description: Library name: 153_S19_L001


title: 42_CC_2019_01_02_3, rep2

description: Library name: 42_cold_deprivation, 42_TACCGAGG-AGTTCAGG-AHGKC2BBXY_L005


title: mdTN from animal_32

description:
Library name: NSM1354
3 lvl sciRNAseq


title: 151_S12_L001

description: Library name: 151_S12_L001


title: 42_CC_2019_01_02_3, rep1

description: Library name: 42_cold_deprivation, 42_TACCGAGG-AGTTCAGG-AHGKC2BBXY_L004


title: MEL Mtg16H3K4me3 dTAGV1 30m B

description: Library name: CUTRUN_dTAGV1 30m B


title: mdTN from animal_31, rep2

description:
Library name: NSM1353-b2
3 lvl sciRNAseq


title: 149_S25_L001

description: Library name: 149_S25_L001


title: mdTN from animal_31

description:
Library name: NSM1353
3 lvl sciRNAseq


title: H9C2 cardiomyocytes, HG group, biological replicate 3

description:
Library name: HG-3.raw_1.fastq.gz, HG-3.raw_2.fastq.gz
High glucose group biological replicate 3, total RNA-seq

value: High glucose medium (100 mM D-glucose), no drug treatment


title: 147_S11_L001

description: Library name: 147_S11_L001


title: mdTN from animal_30, rep2

description:
Library name: NSM1352-b2
3 lvl sciRNAseq


title: 145_S64_L001

description: Library name: 145_S64_L001


title: H9C2 cardiomyocytes, HG group, biological replicate 2

description:
Library name: HG-2.raw_1.fastq.gz, HG-2.raw_2.fastq.gz
High glucose group biological replicate 2, total RNA-seq


title: mdTN from animal_30

description:
Library name: NSM1352
3 lvl sciRNAseq


title: 41_CC_2019_01_02_2, rep1

description: Library name: 41_cold_deprivation, 41_AATGCCTC-TGGATCGA-AHGKC2BBXY_L004


title: 143_S57_L001

description: Library name: 143_S57_L001


title: 40_CC_2019_01_02_1, rep3

description: Library name: 40_cold_deprivation, 40_GGCATTCT-CAAGCTAG-AHGKC2BBXY_L006


title: mdTN from animal_29, rep2

description:
Library name: NSM1351-b2
3 lvl sciRNAseq


title: H9C2 cardiomyocytes, Ctrl group, biological replicate 3

description:
Library name: Ctrl-3.raw_1.fastq.gz, Ctrl-3.raw_2.fastq.gz
Control group (normal glucose) biological replicate 3, total RNA-seq

value: Normal glucose medium, no drug treatment


title: 40_CC_2019_01_02_1, rep2

description: Library name: 40_cold_deprivation, 40_GGCATTCT-CAAGCTAG-AHGKC2BBXY_L005


title: 139_S26_L001

description: Library name: 139_S26_L001


title: mdTN from animal_29

description:
Library name: NSM1351
3 lvl sciRNAseq


title: mdTN from animal_28, rep2

description:
Library name: NSM1350-b2
3 lvl sciRNAseq


title: Primary mouse hepatocytes, FDI replicate #3

city: New York

first: Jennifer

last: Gamarra

state: New York

address: 1150 St Nicholas Ave, Russ Berrie Building, Floor 6-613

institute: Columbia University

description: Library name: RJ027

data_processing:
We use bases2fastq version 1.1.0.593880262  for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Mouse:GRCm38.p6) using kallisto (0.44.0). We test for differentially expressed genes under various conditions using DESeq2, R packages designed to test differential expression between two experimental groups from RNA-seq counts data.
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text files containing number of raw counts for each gene.

source_name: primary hepatocytes

extract_protocol:
RNA was extracted from primary hepatocyte samples using RNeasy Mini Kit (Qiagen #73404). RNA concentration and quality was determined by Qubit Bioanalyzer. Standard RNA-seq pipeline at Columbia Genome Center: poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1µg per sample, RIN>8).
STRPOLYA libraries were constructed using Illumina TruSeq RNA Preparation Kit according to the manufacturer’s instructions.

treatment_protocol: Primary hepatocytes were extracted from a WT C57/Bl6J mouse using a two-step collagenase protocol. Primary hepatocytes were plated in Corning M199 +10%FBS + 1%PenStrep for at least 2 hours, that evening cells were switched to serum-free medium (M199 + 1% PenStrep) for 16 hours overnight with or without 6 𝜇M MnCl2. Hepatocytes were pre-treated with 1 or 100 nM of insulin (Gibco #12585014) for 1 hour prior to 10 𝜇M forskolin/1 𝜇M dexamethasone treatment in serum-free medium for 5 hours before cell lysis.

value: primary hepatocytes

value: hepatocyte

value: WT

value: Forskolin (10uM)/Dexamethasone(1uM) + 100 nM Insulin


title: 137_S11_L001

description: Library name: 137_S11_L001

value: whole blood


title: mdTN from animal_28

description:
Library name: NSM1350
3 lvl sciRNAseq


title: Gy5x7_14d, scRNAseq

city: Chengdu

first: Wenling

last: Tu

address: No. 4 North Section 4, Second Ring Road

institute: the Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (version 5.0.0).
Assembly: mRatBN7.2/rn7 rat
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Esophagus

extract_protocol:
Fresh rat esophageal tissues from the 0Gy_7d, 35Gy_7d, 5x7Gy_7d, and 5x7Gy_14d groups were stored in MACS tissue storage solution at 4°C and shipped to the processing lab within 48 hours for scRNA-seq. Esophageal tissues from five rats per group were pooled for processing. Each pooled sample was finely chopped and enzymatically digested with 5 mg/mL collagenase I, 1 mg/mL DNase I, and 0.125% trypsin-EDTA in a shaker at 37°C for 60 minutes. The resulting cell suspension was filtered through a 70 μm strainer and sorted using a Dead Cell Removal Kit to eliminate dead cells. The cells were then resuspended in D-PBS containing 0.04% BSA at a concentration of approximately 1,000 cells/μL in preparation for scRNA-seq.
scRNA-seq libraries were prepared using the Chromium Single Cell 3' Library & Gel Bead Kit v3.1 (10x Genomics) following the manufacturer's protocol. The final libraries were sequenced using an Illumina NovaSeq 6000 sequencer.

value: Esophagus

value: Esophageal cells

tag: age

value: 6-weeks old


title: 39_Control_2019_01_02_3, rep2

description: Library name: 39_cold_deprivation, 39_TTACAGGA-GCTTGTCA-AHGKC2BBXY_L005

value: flower bud

value: plant


title: 135_S24_L001

description: Library name: 135_S24_L001


title: RDY234 SLAM-seq, 25 min IAA, rep E

city: Oklahoma City

first: John

middle: B

last: Ridenour

state: OK

address: 825 NE 13th St.

department: Cell Cycle and Cancer Biology Research Program

institute: Oklahoma Medical Research Foundation

description: Library name: RDHTS391

data_processing:
Paired-end 150 bp reads were preprocessed using fastp (version 0.23.2) and bbduk (BBMap version 39.06). Forward reads were processed using SLAM-DUNK (version 0.4.3), where reads were aligned against the Saccharomyces cerevisiae genome using NextGenMap (version 0.5.5) and SNPs were called using VarScan 2 (version 2.4.5). Total read counts were defined as all reads remaining after filtering in SLAM-DUNK. A conversion per read threshold of ≥ 2 T>C conversions was used to define T>C read counts. Preprocessing and processing steps were implemented as a Snakemake workflow (https://github.com/DonczewLab/SLAM-Seq_Analysis).
Assembly: Saccharomyces cerevisiae strain S288C version R64-3-1 (RefSeq Assembly GCF_000146045.2)
Supplementary files format and content: Raw read count tables are provided in tab-separated values (.tsv) format. *_scer_twotcreadcount_tcount.tsv provides total read counts and T>C read counts with ≥ 2 T>C conversions.

organism: Saccharomyces cerevisiae

growth_protocol: Saccharomyces cerevisiae cells were grown in YPD medium (10 g/l yeast extract, 20 g/l peptone, 20 g/l glucose, 20 mg/ml adenine sulfate) at 30°C with shaking at 220 rpm.

extract_protocol:
RNA purification and DNase I treatment were performed using a Quick-RNA Fungal/Bacterial Miniprep kit and DNase I set (Zymo Research) following the manufacturer’s recommendations with minor modifications. Reagents used during RNA purification were supplemented with DTT to maintain reducing conditions. RNA was treated with 10 mM iodoacetamide for 15 min at 50°C in the dark. Samples were protected from light when possible.
Libraries were constructed as previously described in detail (https://doi.org/10.1186/s44330-024-00008-1) and sequenced on an Illumina NovaSeq 6000 at the Oklahoma Medical Research Foundation Clinical Genomics Center.

treatment_protocol: Saccharomyces cerevisiae cells were grown to an OD600 of ~0.45. Cultures were treated with 1 mM 3-indoleacetic acid (IAA) freshly prepared in DMSO or DMSO alone, vigorously mixed, and incubated for 25 min. Immediately after IAA treatment, cultures were treated with 5 mM 4-thiouracil (4tU) freshly prepared in DMSO or DMSO alone, vigorously mixed, and incubated for 4 min. Immediately after 4tU treatment, each culture was decanted into cold 100% methanol on dry ice. The final OD600 of the cultures was ~0.7. Cells were pelleted at 3,000 g then resuspended in DNA/RNA shield (Zymo Research), flash frozen on dry ice, and stored at –80°C.

value: yeast cell

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD28:TRP1

value: 25 min IAA treatment, 4 min 4tU treatment


title: Gy5x7_7d, scRNAseq

description: 10x Genomics


title: 133_S10_L001

description: Library name: 133_S10_L001

value: Healthy control


title: 39_Control_2019_01_02_3, rep1

description: Library name: 39_cold_deprivation, 39_TTACAGGA-GCTTGTCA-AHGKC2BBXY_L004

value: Regina


title: mdTN from animal_27

description:
Library name: NSM1349
3 lvl sciRNAseq

value: mediodorsal thalamic nucleus


title: Gy35_7d, scRNAseq

description: 10x Genomics


title: 131_S63_L001

description: Library name: 131_S63_L001


title: mdTN from animal_26, rep2

description:
Library name: NSM1348-b2
3 lvl sciRNAseq


title: 38_Control_2019_01_02_2, rep3

description: Library name: 38_cold_deprivation, 38_CCGTGAAG-ATCCACTG-AHGKC2BBXY_L006


title: Gy0_7d, scRNAseq

description: 10x Genomics


title: 129_S39_L001

description: Library name: 129_S39_L001


title: mdTN from animal_26

description:
Library name: NSM1348
3 lvl sciRNAseq


title: RDY234 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS407

value: 25 min DMSO treatment, 4 min 4tU treatment


title: Bl6_Taf1_humanization_dSVAhTAF1_dSVA2_converted_D17

first: Weimin

last: Zhang

state: NY

address: 435 E 30th street

department: Institute for Systems Genetics

institute: NYU Langone Health

description: Library name: BS24264A

data_processing:
Sequencing reads were demultiplexed using bcl2fastq v2.20, and subsequently trimmed using Trimmomatic v0.39. Trimmed reads were aligned to references using BWA v0.7.17 for Illumina sequencing and minimap2 for Nanopore sequencing. Duplicates were marked using samblaster v0.1.24.
Coverage depth tracks and quantification was generated using BEDOPS v2.4.35. Sequencing data were visualized using UCSC genome browser, or IGV.
The sequencing processing pipeline is available at https://github.com/mauranolab/mapping.
Assembly: mm10, custom TAF1 refernece
Supplementary files format and content: bigwig and bedgraph files mapping to genome references

source_name: mESCs

extract_protocol:
For targeted capture sequencing,1-3 million of mESCs were harvested for genomic DNA extraction by using a QIAamp DNA Mini Kit (QIAGEN, 51306). For plasmid DNA sequencing, plasmids were extracted by using a NucleoBond Xtra BAC kit (Takara, 740436.25).
For targeted capture sequencing and plasmid sequencing, approximately 100 ng DNA was used for the library construction using the NEBNext Ultra II FS DNA library prep kit (E7805). AMPure XP beads (Beckman Coulter, A63881) were used for DNA purification on a magnetic stand.

value: mESCs


title: 127_S31_L001

description: Library name: 127_S31_L001


title: 38_Control_2019_01_02_2, rep1

description: Library name: 38_cold_deprivation, 38_CCGTGAAG-ATCCACTG-AHGKC2BBXY_L004


title: mdTN from animal_25, rep2

description:
Library name: NSM1347-b2
3 lvl sciRNAseq


title: Bl6_Taf1_humanization_dSVAhTAF1_dSVA2_converted_D15

description: Library name: BS24262A


title: 125_S17_L001

description: Library name: 125_S17_L001


title: 37_Control_2019_01_02_1, rep3

description: Library name: 37_cold_deprivation, 37_TCCAACGC-AAGTCCAA-AHGKC2BBXY_L006


title: mdTN from animal_25

description:
Library name: NSM1347
3 lvl sciRNAseq


title: 123_S4_L001

description: Library name: 123_S4_L001


title: mdTN from animal_24, rep2

description:
Library name: NSM1346-b2
3 lvl sciRNAseq


title: Bl6_Taf1_humanization_WThTAF1_dSVA2_converted_A01

description: Library name: BS24257A


title: 121_S16_L001

description: Library name: 121_S16_L001


title: 37_Control_2019_01_02_1, rep1

description: Library name: 37_cold_deprivation, 37_TCCAACGC-AAGTCCAA-AHGKC2BBXY_L004


title: mdTN from animal_24

description:
Library name: NSM1346
3 lvl sciRNAseq


title: Caco-2.batch2.PER.rep1.H02

description: Library name: Caco2_Batch2_PER_1_H02

value: colon

value: epithelial

value: cell line


title: Bl6_Taf1_humanization_dSVAhTAF1_Converted_ E5

description: Library name: BS19228A


title: 119_S9_L001

description: Library name: 119_S9_L001

value: whole blood


title: 161_S12_L001

description: Library name: 161_S12_L001


title: 159_S65_L001

description: Library name: 159_S65_L001


title: mdTN from animal_23, rep2

description:
Library name: NSM1345-b2
3 lvl sciRNAseq


title: 117_S62_L001

description: Library name: 117_S62_L001


title: Bl6_Taf1_humanization_dSVAhTAF1_Converted_ B10

description: Library name: BS19224A


title: 36_CC2NOV_2018_12_03_3, rep2

description: Library name: 36_cold_deprivation, 36_CTTGGTAT-GGACTTGG-AHGKC2BBXY_L005


title: mdTN from animal_23

description:
Library name: NSM1345
3 lvl sciRNAseq


title: Bl6_Taf1_humanization_WThTAF1_A09

description: Library name: BS15076A


title: 115_S38_L001

description: Library name: 115_S38_L001


title: 36_CC2NOV_2018_12_03_3, rep1

description: Library name: 36_cold_deprivation, 36_CTTGGTAT-GGACTTGG-AHGKC2BBXY_L004


title: mdTN from animal_22, rep2

description:
Library name: NSM1344-b2
3 lvl sciRNAseq


title: 113_S24_L001

description: Library name: 113_S24_L001


title: mdTN from animal_22

description:
Library name: NSM1344
3 lvl sciRNAseq


title: Bl6_Taf1_humanization_WThTAF1_A01

description: Library name: BS15074A


title: 111_S9_L001

description: Library name: 111_S9_L001


title: 35_CC2NOV_2018_12_03_2, rep2

description: Library name: 35_cold_deprivation, 35_GTCGGAGC-TTATAACC-AHGKC2BBXY_L005


title: mdTN from animal_21, rep2

description:
Library name: NSM1343-b2
3 lvl sciRNAseq


title: cHLA047-IgG

description:
Library name: BS27170A
FCHGW32BGXW

data_processing:
Sequencing reads were demultiplexed using bcl2fastq v2.20, and subsequently trimmed using Trimmomatic v0.39. Trimmed reads were aligned to references using BWA v0.7.17. Duplicates were marked using samblaster v0.1.24.
Coverage depth tracks and quantification was generated using BEDOPS v2.4.35. Sequencing data were visualized using UCSC genome browser.
The sequencing processing pipeline is available at https://github.com/mauranolab/mapping.
Assembly: mm10, custom TAF1 reference
Supplementary files format and content: bigwig files mapping to genome reference (mm10) and custom TAF1 reference
Library strategy: CUT&Run

growth_protocol: For mESCs, the culture medium consisted of ES medium (85% (v/v) KnockOut DMEM (Fisher Scientific, 10829018), 15% (v/v) Fetal Bovine Serum (Hyclone, SH30070.03), 0.5 mg/ml Penicillin-Streptomycin-Glutamine (Gibco, 10378016), 7 μL 2-Mercaptoethanol (Sigma-Aldrich, M6250), 0.1 mM MEM Non-Essential Amino Acids (Gibco, 11140050) and 1 U/ml LIF (EMD Millipore, ESG1107), 3 µM CHIR99021 and 1 µM PD0325901). Tissue culture treated plates were coated with 0.1% gelatin solution before use. All cells were grown in a humidified tissue culture incubator at 37°C supplied with 5% CO2.

extract_protocol:
About 500,000 mESCs were used for each CUT&RUN reaction by following vendor’s instructions (EpiCypher, 14-1048).
Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (E7645L).

tag: antibody

value: IgG

value: Male


title: 37_Control_2019_01_02_1, rep2

description: Library name: 37_cold_deprivation, 37_TCCAACGC-AAGTCCAA-AHGKC2BBXY_L005


title: Bl6_Taf1_humanization_WThTAF1_dSVA2_converted_A05

description: Library name: BS24259A


title: 35_CC2NOV_2018_12_03_2, rep1

description: Library name: 35_cold_deprivation, 35_GTCGGAGC-TTATAACC-AHGKC2BBXY_L004


title: 109_S22_L001

description: Library name: 109_S22_L001


title: mdTN from animal_21

description:
Library name: NSM1343
3 lvl sciRNAseq

data_processing:
Converts base calls to fastq files with bcl2fastq/ v.2.20 (RRID:SCR_015058) (Illumina), merge read 1 which contains the barcode to read 2 files.
Removes polyA tails using Trim Galore/v.0.6.7 (RRID:SCR_011847)
Aligns trimmed reads to a reference genome with STAR/v.2.7.6 (RRID:SCR_004463)
Extracts mapped reads and removes duplicates.
Generates UMI counts for exonic and intronic regions of each gene, tabulated according to the unique three-level barcode design in sci-RNA-seq3.
Assembly: rhesus macaque reference genome (Mmul_10)
Supplementary files format and content: all_regions_cell_annotate.csv
Supplementary files format and content: all_regions_count.npz
Supplementary files format and content: all_regions_gene_annotate.csv

extract_protocol:
Briefly, tissue was manually pulverized on dry ice, transferred to pre-chilled tubes, and stored at −80°C. For lysis, pulverized tissue was suspended in hypotonic lysis buffer A (0.3 M sucrose, 0.1% Triton X-100, 3 mM MgCl₂, 0.025% IGEPAL CA-630, 1% DEPC in PBS) for 10 min, filtered (40-μm), pelleted, and resuspended in SPBSTM buffer (0.3 M sucrose, 1X PBS, 0.1% TritonX-100, 3 mM MgCl₂, and 1% DEPC). Nuclei were fixed for 10 min in 1.5 mM dithiobis(succinimidyl propionate) (DSP), diluted from a 123 mM stock in DMSO into methanol. After washing in 0.3 M SPBSTM, nuclei were layered onto a 10:1 volume of 1.4 M SPBSTM, centrifuged (3,000 x g, 20 min, 4°C), and resuspended. Nuclei were filtered (20-μm), counted, aliquoted, and cryopreserved in 90% 0.3 M SPBSTM with 10% anhydrous DMSO at -80°C. One library per region was generated using the optimized sci-RNA-seq3 protocol with the following modifications: nuclei were counted using the ImageExpress Pico System (Molecular Devices), and 15,000-20,000 nuclei were loaded per reverse transcription well. Tagmentation used N7 adaptor-loaded Tn5 transposase (Diagenode, C01070010-20), with 6-9 μL of Tn5 per 550 μL of 2X TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl₂, 20% dimethylformamide), distributed at 5uL per well.
sci-RNA-seq3


title: cHLA045-IgG

description:
Library name: BS27169A
FCHGW32BGXW


title: 34_CC2NOV_2018_12_03_1, rep3

description: Library name: 34_cold_deprivation, 34_ACTAAGAT-CCGCGGTT-AHGKC2BBXY_L006


title: 107_S15_L001

description: Library name: 107_S15_L001


title: mdTN from animal_20, rep2

description:
Library name: NSM1342-b2
3 lvl sciRNAseq


title: cHLA023-IgG

description:
Library name: BS27168A
FCHGW32BGXW


title: 105_S47_L001

description: Library name: 105_S47_L001


title: MEL Mtg16 dTAGV1+A485 1h A

description:
Library name: PROSeq_dTAGV1_A485_1h_1
Processed data file 1 is DESeq2 normalized gene counts. Processed data file 2 is DESeq2 normalized enhancer (dREG) counts.
12662-AJ_deseq_normcounts_table_fulltimecourse.txt
12662-AJ_dREG_deseq_normcounts_alltimepoints.txt

data_processing:
Adaptors were trimmed from the R1 file from paired-end PRO-Seq experiments using TrimmomaticSE. Reverse complements were generated using FASTX Toolkit (v. 0.0.13). Trimmed reverse complement reads were then aligned to a concatenated mm39+dm3 genome using Bowtie2 (v. 2.2.2). Resulting alignments were then processed with samtools (v. 1.16.1) to remove low quality reads, count reads aligned to mm39 and dm3 genomes, and remove spike-in reads. Differential expression of protein coding genes was assessed using NRSA. Regions with non-coding transcriptional activity for all samples were identified using dREG. To generate a set of enhancer regions, raw peak files from all samples were concatenated using bedtools, filtered for only intergenic or intronic regions using Homer. Only regions with a maximum RPM over 10 across all samples were carried forward. FeatureCounts (v. 2.0.1) was used to quantify reads in each of the final enhancer regions. Differential expression of enhancers was determined using DESeq2 (v. 1.46.0). Both built-in and spike-in normalization (minimum read count) was performed for all PRO-Seq experiments. Built-in DESeq2 normalization was used for all analyses presented, except for PRO-Seq experiments with A485, where spike-in normalization was used.
Assembly: mm39
Supplementary files format and content: count tables for genes and enhancers
Library strategy: PRO-Seq

extract_protocol:
Total RNA from nuclei was isolated by Trizol LS extraction, hydrolyzed in 0.2 N NaOH, and biotin-CTP containing nascent RNAs were isolated by streptavidin bead (Invtirogen) pulldown.
RNA was reverse transcribed and amplified following 3′ adaptor ligation, 5′ cap removal and triphosphate repair, 5′ hydroxyl repair, and 5′ adapter ligation. PAGE purified cDNA libraries were provided to the Vanderbilt University Medical Center VANTAGE Core for sequencing. Libraries were sequenced on a NovaSeq 6000 or NovaSeq X (50 x 106 reads per sample).

treatment_protocol: 250nM dTAGV1, 10uM A485, 5nM LBH589

value: MEL Mtg16-FKBP-2XHA

value: murine erythroleukemia

value: dTAGV1+A485 1h


title: CN from animal_30, rep2

description:
Library name: NSM1453-b2
3 lvl sciRNAseq

source_name: caudate nucleus

value: caudate nucleus


title: 34_CC2NOV_2018_12_03_1, rep2

description: Library name: 34_cold_deprivation, 34_ACTAAGAT-CCGCGGTT-AHGKC2BBXY_L005

value: flower bud

value: plant


title: mdTN from animal_20

description:
Library name: NSM1342
3 lvl sciRNAseq


title: cHLA021-IgG

description:
Library name: BS27167A
FCHGW32BGXW


title: H358_shPGAM5_3

city: Dalian

first: Jianxin

last: Wang

state: Liaoning

address: West Lushun South Road

institute: Dalian Medical University

description: Library name: Sample 6

data_processing:
hisat2 for sequence alignment
stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
samtools tools for related file processing
Assembly: hg38
Supplementary files format and content: genes_fpkm_expression.xlsx

growth_protocol: Human lung cancer cell lines H358 were purchased from the American Type Culture Collection. Cells were cultured at 37℃ in 5% CO2 with RPMI-1640 (Gibco) medium supplemented with 10% fetal bovine serum, 100 unit/mL penicillin and 100 mg/mL streptomycin

extract_protocol:
After the total RNA extraction,RNA degradation and contamination was detected by 1% agarose gels; RNA purity and concentration was checked by Nanodrop2000（Thermo Fisher Scientific，MA，USA）；RNA concentration was checked using the Qubit® 3.0 Flurometer（Thermo Fisher Scientific，MA，USA）；RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The lentiviral vectors encoding short hairpin RNAs (GIPZ shRNAs) targeting PGAM5 and scrambled shRNA were purchased from Dharmacon (America). The plasmids were transiently transfected into cells with Lipofectamine 3000 (Invitrogen, CA) according to the manufacturer’s protocol. Cells were harvested and analyzed 36 h after transfection.

value: Lung cancer

value: Knockdown PGAM5 gene


title: 34_CC2NOV_2018_12_03_1, rep1

description: Library name: 34_cold_deprivation, 34_ACTAAGAT-CCGCGGTT-AHGKC2BBXY_L004

value: Regina


title: mdTN from animal_19, rep2

description:
Library name: NSM1341-b2
3 lvl sciRNAseq

value: mediodorsal thalamic nucleus


title: 36_CC2NOV_2018_12_03_3, rep3

description: Library name: 36_cold_deprivation, 36_CTTGGTAT-GGACTTGG-AHGKC2BBXY_L006


title: cWZ205-IgG

description:
Library name: BS27166A
FCHGW32BGXW

value: mESCs


title: H358_shPGAM5_2

description: Library name: Sample 5


title: 30_CC_2018_12_03_3, rep3

description: Library name: 30_cold_deprivation, 30_ATGAGGCC-CAATTAAC-AHGKC2BBXY_L006


title: mdTN from animal_19

description:
Library name: NSM1341
3 lvl sciRNAseq


title: cWZ201-IgG

description:
Library name: BS27165A
FCHGW32BGXW


title: H358_shPGAM5_1

description: Library name: Sample 4


title: mdTN from animal_18, rep2

description:
Library name: NSM1340-b2
3 lvl sciRNAseq


title: 30_CC_2018_12_03_3, rep2

description: Library name: 30_cold_deprivation, 30_ATGAGGCC-CAATTAAC-AHGKC2BBXY_L005


title: MK6-IgG

description:
Library name: BS27162A
FCHGW32BGXW

value: Wild type


title: H358_shCON_3

description: Library name: Sample 3

value: Negative Control


title: 30_CC_2018_12_03_3, rep1

description: Library name: 30_cold_deprivation, 30_ATGAGGCC-CAATTAAC-AHGKC2BBXY_L004


title: mdTN from animal_18

description:
Library name: NSM1340
3 lvl sciRNAseq


title: cHLA047-H3K4me3

description:
Library name: BS27161A
FCHVGNNBGXW


title: H358_shCON_2

description: Library name: Sample 2


title: 29_CC_2018_12_03_2, rep3

description: Library name: 29_cold_deprivation, 29_GCAGAATT-TGGCCGGT-AHGKC2BBXY_L006


title: mdTN from animal_17, rep2

description:
Library name: NSM1339-b2
3 lvl sciRNAseq


title: cHLA045-H3K4me3

description:
Library name: BS27160A
FCHVGNNBGXW


title: H358_shCON_1

description: Library name: Sample 1


title: 35_CC2NOV_2018_12_03_2, rep3

description: Library name: 35_cold_deprivation, 35_GTCGGAGC-TTATAACC-AHGKC2BBXY_L006


title: Bl6_Taf1_humanization_WThTAF1_A02

description: Library name: BS15075A


title: 29_CC_2018_12_03_2, rep2

description: Library name: 29_cold_deprivation, 29_GCAGAATT-TGGCCGGT-AHGKC2BBXY_L005


title: cHLA023-H3K4me3

description:
Library name: BS27159A
FCHVGNNBGXW


title: mdTN from animal_17

description:
Library name: NSM1339
3 lvl sciRNAseq


title: HG00731, SMC1 HiChIP, HU

city: Warsaw

first: Dariusz

last: Plewczynski

state: mazovia

address: Banacha 2c

department: Centre of New Technologies

country: Poland

institute: University of Warsaw

description: Library name: HU_SMC1_HiChIP_GM12878_Rep1

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
HiChIP dataset were processed using the nf-HiChIP pipeline
HiChIP reads were aligned to the UCSC hg38 genome using Burrows-Wheeler Alignment Tool version v0.7.17
Peaks were called uing MACS3 v3.0.1 with the significance cut-off q-value <=0.01
Assembly: hg38
Supplementary files format and content: bedpe files include chromatin interactions (loops)
Library strategy: HiChIP

growth_protocol: Human GM12878 lymphoblastoid cell line, was grown in RPMI 1640 (Biowest) with 15% foetal bovine albumin (Biowest) and 2mM L-glutamine (Gibco). Cells were cultured at 37 °C in a humid environment containing 5% CO2.

extract_protocol:
The HiChIP experiment was performed using Arima-HiC+ Kit (HiChIP User Guide for Mammalian Cells and Tissues using Transcription Factors and Histones (A101020) with modifications. Cell fixation was carried out according to FA-EGS cross-linking (Buka et al., 2025). Chromatin immunoprecipitation step (ChIP) was performed with 10 μg of SMC1 (Bethyl Laboratories, A300-055A).
Library preparation was performed as described in the Arima-HiC+ Kit HiChIP Library Preparation using Swift Biosciences Accel-NGS 2S Plus DNA Library Kit protocol.

treatment_protocol: The cells were treated with either 0.4 μM aphidicolin (APH) or 0.2 mM hydroxyurea (HU) for 18 hours. For the controls, the cells were treated with dimethyl sulfoxide (DMSO) or water (H₂O) respectively.

value: Lymphoblastoid Cell Line

value: HU


title: mdTN from animal_16, rep2

first: Noah

last: Snyder-Mackler

address: 214 Life Sciences C

institute: Arizona State University

description:
Library name: NSM1338-b2
3 lvl sciRNAseq


title: 29_CC_2018_12_03_2, rep1

description: Library name: 29_cold_deprivation, 29_GCAGAATT-TGGCCGGT-AHGKC2BBXY_L004


title: cHLA021-H3K4me3

description:
Library name: BS27158A
FCHVGNNBGXW


title: 28_CC_2018_12_03_1, rep3

description: Library name: 28_cold_deprivation, 28_AACGTTCC-AGTACTCC-AHGKC2BBXY_L006


title: HG00731, SMC1 HiChIP, H2O

description: Library name: H2O_SMC1_HiChIP_GM12878_Rep1


title: mdTN from animal_16

description:
Library name: NSM1338
3 lvl sciRNAseq


title: cWZ205-H3K4me3

description:
Library name: BS27157A
FCHVGNNBGXW


title: HG00731, SMC1 HiChIP, APH

description: Library name: APH_SMC1_HiChIP_GM12878_Rep1

value: APH


title: 28_CC_2018_12_03_1, rep2

description: Library name: 28_cold_deprivation, 28_AACGTTCC-AGTACTCC-AHGKC2BBXY_L005


title: mdTN from animal_15, rep2

description:
Library name: NSM1337-b2
3 lvl sciRNAseq


title: cWZ201-H3K4me3

description:
Library name: BS27156A
FCHVGNNBGXW

value: Male


title: HG00731, SMC1 HiChIP, DMSO

description: Library name: DMSO_SMC1_HiChIP_GM12878_Rep1

value: DMSO


title: 28_CC_2018_12_03_1, rep1

description: Library name: 28_cold_deprivation, 28_AACGTTCC-AGTACTCC-AHGKC2BBXY_L004


title: mdTN from animal_15

description:
Library name: NSM1337
3 lvl sciRNAseq


title: 27_Control_2018_12_03_3, rep3

description: Library name: 27_cold_deprivation, 27_GGTACCTT-GACGTCTT-AHGKC2BBXY_L006


title: MK6-H3K4me3

description:
Library name: BS27153A
FCHVGNNBGXW


title: mdTN from animal_14, rep2

description:
Library name: NSM1336-b2
3 lvl sciRNAseq


title: HT1080_WT_SW138-3

city: New Orleans

first: Terry

middle: J

last: Watt

state: LA

address: 1 Drexel Dr.

department: Chemistry

institute: Xavier University of Louisiana

description:
Library name: HT1080_WT_SW138-3
HT1080_WT_SW138-3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic v0.39 with default settings
Trimmed sequence reads were mapped to GrCh38.83 using bowtie2 v2.5.4 as implemented by RSEM v1.3.3, with default settings
Mapped sequences were annotated and counted using RSEM v1.3.3 with default settings
Read count extraction was performed using tximport v1.30.0
Read count statistical analysis was performed using DESeq2 v1.42.0
Assembly: Human NCBI genome build GrCH38 build 83
Supplementary files format and content: Expected counts from RSEM output and ENSEMBL entries, cross-referenced to gene names and UNIPROT entries

source_name: Connective tissue

growth_protocol: HT1080 cells were maintained in MEM supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
3x10^6 cells were pelleted, resuspended in MEM with 5% glycerol, and frozen at -80 °C. Cells were shipped on dry ice, and total RNA extracted by Creative Genomics using a commercially available kit. Quality of RNA was verified using RNA Screen Tape (Agilent). RNA was rRNA-depleted using the Ribo-Zero plus kit (Illumina).
Libraries were prepared using the PE150 platform (Illumina) following the manufacturer's instructions.

treatment_protocol: 1 uM SW-113 or SW-138 for 48 hours added to ~50% confluent cells.

value: Connective tissue

value: fibrosarcoma

value: WT

value: SW-138 1 uM 48 hours


title: HT1080_WT_SW138-2

description:
Library name: HT1080_WT_SW138-2
HT1080_WT_SW138-2


title: OPE 2um #3

city: Yangsan-si

first: Hyerin

last: Lee

address: 49, Busandaehak-ro

country: South Korea

institute: Pusan National University

description: Library name: oxi3

data_processing:
Raw sequencing data quality and basic statistics were assessed using FastQC to ensure the integrity of the data before analysis. Reads with low quality (e.g., those with more than 10% N bases or a quality score below 20) were removed.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Danio rerio

source_name: whole body

extract_protocol:
TRIzol reagent protocol
The libraries were prepared for 150bp paired-end sequencing using TruSeq Stranded mRNA Sample Prep Kit. Namely, mRNA molecules were purified and fragmented from 0.1-1μg of total RNA using oligo (dT) magnetic beads. The fragmented mRNAs were synthesized as single-stranded cDNAs through random hexamer priming. By applying this as a template for second strand synthesis, double-stranded cDNA was prepared. After sequential process of end repair, A-tailing and adapter ligation, cDNA libraries were amplified with PCR (Polymerase Chain Reaction). Quality of these cDNA libraries was evaluated with the Agilent 2100 BioAnalyzer (Agilent, CA, USA). They were quantified with the KAPA library quantification kit (Kapa Biosystems, MA, USA) according to the manufacturer’s library quantification protocol. Following cluster amplification of denatured templates, sequencing was progressed as paired-end (2×150bp) using Illumina Novaseq 6000 (Illumina, CA, USA).

value: whole body

value: oxidized polyethylene


title: 27_Control_2018_12_03_3, rep2

description: Library name: 27_cold_deprivation, 27_GGTACCTT-GACGTCTT-AHGKC2BBXY_L005

value: flower bud

value: plant


title: OPE 2um #2

description: Library name: oxi2


title: mdTN from animal_14

city: Tempe

description:
Library name: NSM1336
3 lvl sciRNAseq

source_name: mediodorsal thalamic nucleus

value: mediodorsal thalamic nucleus


title: 41_CC_2019_01_02_2, rep3

description: Library name: 41_cold_deprivation, 41_AATGCCTC-TGGATCGA-AHGKC2BBXY_L006

value: Regina


title: OPE 2um #1

description: Library name: oxi1


title: HT1080_WT_SW138-1

description:
Library name: HT1080_WT_SW138-1
HT1080_WT_SW138-1


title: 27_Control_2018_12_03_3, rep1

description: Library name: 27_cold_deprivation, 27_GGTACCTT-GACGTCTT-AHGKC2BBXY_L004


title: mdTN from animal_13, rep2

description:
Library name: NSM1335-b2
3 lvl sciRNAseq


title: HT1080_WT_SW113-3

description:
Library name: HT1080_WT_SW113-3
HT1080_WT_SW113-3

value: SW-113 1 uM 48 hours


title: 25_Control_2018_12_03_1, rep3

description: Library name: 25_cold_deprivation, 25_GCACGGAC-TGCGAGAC-AHGKC2BBXY_L006


title: CTRL #3

description: Library name: con3

value: Vehicle


title: mdTN from animal_13

description:
Library name: NSM1335
3 lvl sciRNAseq


title: 25_Control_2018_12_03_1, rep2

description: Library name: 25_cold_deprivation, 25_GCACGGAC-TGCGAGAC-AHGKC2BBXY_L005


title: HT1080_WT_SW113-2

description:
Library name: HT1080_WT_SW113-2
HT1080_WT_SW113-2


title: mdTN from animal_12, rep2

description:
Library name: NSM1334-b2
3 lvl sciRNAseq


title: 25_Control_2018_12_03_1, rep1

description: Library name: 25_cold_deprivation, 25_GCACGGAC-TGCGAGAC-AHGKC2BBXY_L004


title: CTRL #2

description: Library name: con2


title: HT1080_WT_SW113-1

description:
Library name: HT1080_WT_SW113-1
HT1080_WT_SW113-1


title: mdTN from animal_12

description:
Library name: NSM1334
3 lvl sciRNAseq


title: CTRL #1

description: Library name: con1


title: mdTN from animal_11, rep2

description:
Library name: NSM1333-b2
3 lvl sciRNAseq


title: donor 2, bronchial epithelial brushing, time point 9, replicate 1

city: St Louis

first: Jeffery

last: Haspel

state: MO

address: 660 S Euclid Avenue

institute: Washington University, St Louis

description:
Library name: Sample46
ajdy441_tp9_1

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5
Transcript counts were produced by Sailfish version 0.6.3
Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation, and read distribution over known gene models with RSeQC version 2.3
Gene-level and transcript counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for sample differences in library size.
The TMM size factors and the matrix of counts were imported into R/Bioconductor package Limma, and weighted likelihoods based on the observed mean-variance relationship of every gene/transcript were then calculated for all samples with the Voom function
Assembly: Ensembl release 76 assembly
Supplementary files format and content: tab-delimited text files include log2 counts per million (CPM) values for each Sample.

source_name: Bronchial

growth_protocol: We performed serial bronchoscopies every 4 hours for minimum of 24 hours on organ donors awaiting for organ procurement. Bronchial brushings were taken with each bronchoscopies. Samples were preserved in RNAlater and frozen at -80 until RNA extraction.

extract_protocol:
RNA was extracted from cells using RNeasy Mini Kit
RNA from cells were converted to cDNA libraries for sequencing using the the SMARTer kit following manufacturer protocols

value: Bronchial

value: epithelial cells


title: 141_S40_L001

city: RALEIGH

first: Dereje

last: Jima

address: 850 Main Campus Drive

institute: NCSU

description: Library name: 141_S40_L001

data_processing:
Reads were assigned back to individuals by index reads, and aligned in silico to a bisulfite-converted reference genome (i.e., hg38 version 87). Reads without unique alignments, due to either repetitive genomic sequence or loss of specificity from bisulfite conversion of cytosines, and duplicate reads, indicative of clonal amplification of original random DNA fragments, were eliminated. The quality of each paired-end sequence file was inspected using fastqc, and adapter trimming and quality control were performed using the Trim Galore wrapper script that calls the cutadapt  script internally. Paired-end reads with a trimmed adapter sequence were aligned to the human reference genome (i.e., hg38 version 87) downloaded from Ensembl using bsmap aligner. The following options were passed to the aligner: -p 8 -L 135 -w 100 -v 10 -q 10 -R -V 1. The aligned bam files were sorted and indexed using samtools, and duplicate sequence reads were removed using the Picard application.
MOABS was used to merge the BAM files for each condition and to find differentially methylated CpGs (DMC) using the default parameters. Differentially methylated regions (DMR) were identified using MOABS mcomp function with minimum credible difference of 0.1 and minimum of 4 DMCs in a DMR. Bedtools Suites intersection function was used to find overlaps between DMRs with the ICRs.
Assembly: Ensembl hg38 version 87
Supplementary files format and content: control_merge.G.bed: Methylation summaries across 51 merged control samples
Supplementary files format and content: HCCTH_merge.G.bed: Methylation summaries across 10 HCC case samples

extract_protocol:
DNA extraction was done using Qiagen DNeasy Blood and Tissue kit reagents, according to manufacturer's protocols.
Library construction was done using NEBNext Enyzymatic MethylSeq cytosine conversion and library construction kits, according to manufacturer's protocols, with dual indexing.

value: whole blood

value: Healthy control


title: 21_CC_2018_10_31_3, rep3

description: Library name: 21_cold_deprivation, 21_ATGTAAGT-CATAGAGT-AHGKC2BBXY_L006


title: donor 2, bronchial epithelial brushing, time point 8, replicate 1

description:
Library name: Sample45
ajdy441_tp8_1


title: mdTN from animal_11

description:
Library name: NSM1333
3 lvl sciRNAseq


title: 21_CC_2018_10_31_3, rep2

description: Library name: 21_cold_deprivation, 21_ATGTAAGT-CATAGAGT-AHGKC2BBXY_L005


title: H9C2 cardiomyocytes, Ctrl group, biological replicate 2

description:
Library name: Ctrl-2.raw_1.fastq.gz, Ctrl-2.raw_2.fastq.gz
Control group (normal glucose) biological replicate 2, total RNA-seq

value: cardiomyocytes

value: Wild type (WT)

value: Normal glucose medium, no drug treatment


title: M2 macrophages, donor #3

type: RNA

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

institute: CNRS

description: Gene expression data from M2 macrophages

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 for 16h at 45°C and 60 rpm on hgu133plus2 Chip. GeneChips were washed and stained in the Affymetrix Fluidics

scan_protocol: Affymetrix GeneChip Scanner 7G and Affymetrix GeneChip Command Console software (AGCC)

data_processing: Data preprocessing using the Robust Multi-array Average (RMA) method (Affy bioconductor package).

label: biotin

source_name: Monocyte-derived macrophages

label_protocol: RNA were processed using Affymetrix GeneChip® Two-Cycle Target Labeling Kit

growth_protocol: Human peripheral blood mononuclear cells were isolated from healthy donors by Ficoll density gradient centrifugation. Monocytes were allowed to adhere to the culture plates for 4 hours and were then differentiated into macrophages as in Chinetti-Gbaguidi et al, Circ res 2011

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen) and reverse transcribed using the High Capacity cDNA Reverse Transcription kit (Applied Biosystems, USA). Total RNA was checked for quantity and quality using the Agilent 2100 Bioanalyzer (Agilent Biotechnologies)

treatment_protocol: Resting macrophages (RM) were left untreated. Alternatively differentiated macrophages (M2) were obtained by stimulation with recombinant human IL-4 (15 ng/mL) (Promocell, Germany) for 6 days.

value: alternatively-polarized macrophage


title: donor 2, bronchial epithelial brushing, time point 7, replicate 1

description:
Library name: Sample44
ajdy441_tp7_1


title: RM macrophages, donor #3

description: Gene expression data from RM macrophages

value: non-polarized macrophage


title: mdTN from animal_10, rep2

description:
Library name: NSM1332-b2
3 lvl sciRNAseq


title: donor 2, bronchial epithelial brushing, time point 6, replicate 1

description:
Library name: Sample43
ajdy441_tp6_1


title: 20_CC_2018_10_31_2, rep3

description: Library name: 20_cold_deprivation, 20_CGGCGTGA-ACAGGCGC-AHGKC2BBXY_L006

data_processing:
trimming: Trimmomatic 0.36 (Bolger et al., 2014) with following settings fa:2:10:5:1 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to the sweet cherry ‘Regina’ reference genome v.1 (Vimont et al., 2021) using STAR (Dobin et al., 2013)
Raw read count was performed using HTSeq count (Anders et al., 2015)
Assembly: sweet cherry ‘Regina’ reference genome v.1 (Le Dantec et al, 2022)
Supplementary files format and content: the format is .txt and include raw counts of each gene for each sample

extract_protocol:
Total RNA was extracted from 100 mg of frozen and grinded flower buds using RNeasy Plant Mini kit (Qiagen) with minor modification: 1.5% PVP-40 was added in the extraction buffer RLT
Library preparation was performed on 1 μg of high quality RNA (RNA integrity number equivalent superior or equivalent to 8.5) using the TruSeq Stranded mRNA Library Prep Kit High Throughput (Illumina cat. no. RS-122-2103)


title: mdTN from animal_10

description:
Library name: NSM1332
3 lvl sciRNAseq


title: 21_CC_2018_10_31_3, rep1

description: Library name: 21_cold_deprivation, 21_ATGTAAGT-CATAGAGT-AHGKC2BBXY_L004


title: 20_CC_2018_10_31_2, rep2

description: Library name: 20_cold_deprivation, 20_CGGCGTGA-ACAGGCGC-AHGKC2BBXY_L005


title: M2 macrophages, donor #2


title: donor 2, bronchial epithelial brushing, time point 3, replicate 1

description:
Library name: Sample42
ajdy441_tp3_1


title: mdTN from animal_9, rep2

description:
Library name: NSM1331-b2
3 lvl sciRNAseq


title: RM macrophages, donor #2


title: donor 2, bronchial epithelial brushing, time point 2, replicate 1

description:
Library name: Sample41
ajdy441_tp2_1


title: M2 macrophages, donor #1


title: mdTN from animal_9

description:
Library name: NSM1331
3 lvl sciRNAseq


title: 20_CC_2018_10_31_2, rep1

description: Library name: 20_cold_deprivation, 20_CGGCGTGA-ACAGGCGC-AHGKC2BBXY_L004


title: donor 2, bronchial epithelial brushing, time point 11, replicate 1

description:
Library name: Sample40
ajdy441_tp11_1


title: mdTN from animal_8, rep2

description:
Library name: NSM1330-b2
3 lvl sciRNAseq


title: mdTN from animal_27, rep2

description:
Library name: NSM1349-b2
3 lvl sciRNAseq


title: day7_OE_4,C2C12 cells,ChREBP overexpression,day7

city: Shanghai

first: Lu

last: Junyu

address: 800th Xiangyin Street, shanghai,China

department: Department of Cell Biology

institute: Naval Medical University

description:
Library name: day7_OE_4
Column name in C2C12_OE_expression.csv:OE_4

data_processing:
Illumina Novaseq6000.
Reads obtained from the sequencing machines were further filtered by fastp(version 0.18.0)
Short reads alignment tool Bowtie2(version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 2.1.0 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Mus_musculus.GRCm39.
Supplementary files format and content: FPKM value for each sample

growth_protocol: Mice were housed in a specific pathogen free barrier facility under controlled temperature (23–25°C) with a 12 h light:12 h darkness cycle. The mice were fed ad libitum normal chow diet.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA)
The enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).

treatment_protocol: 1.Hypoxic exposure:C57BL/6 and ChMKO mice were maintained in a hypoxic chamber designed to simulate an altitude of approximately 5500 meters, with atmospheric pressure regulated between 46 and 49 kPa and a partial. 2.High-fructose diet (HFD):20% protein, 68% fructose, and 12% fat in calories.

value: myoblast

value: ChREBP-overexpression

value: Myogenic Differentiation


title: 19_CC_2018_10_31_1, rep3

description: Library name: 19_cold_deprivation, 19_TAATACAG-GTGAATAT-AHGKC2BBXY_L006

value: flower bud

value: plant


title: donor 2, bronchial epithelial brushing, time point 10, replicate 1

description:
Library name: Sample39
ajdy441_tp10_1


title: RM macrophages, donor #1


title: 19_CC_2018_10_31_1, rep2

description: Library name: 19_cold_deprivation, 19_TAATACAG-GTGAATAT-AHGKC2BBXY_L005

value: Regina


title: mdTN from animal_8

description:
Library name: NSM1330
3 lvl sciRNAseq

value: mediodorsal thalamic nucleus


title: day7_OE_3,C2C12 cells,ChREBP overexpression,day7

description:
Library name: day7_OE_3
Column name in C2C12_OE_expression.csv:OE_3


title: donor 2, bronchial epithelial brushing, time point 1, replicate 1

description:
Library name: Sample38
ajdy441_tp1_1


title: mdTN from animal_7, rep2

description:
Library name: NSM1329-b2
3 lvl sciRNAseq


title: 19_CC_2018_10_31_1, rep1

description: Library name: 19_cold_deprivation, 19_TAATACAG-GTGAATAT-AHGKC2BBXY_L004


title: day7_OE_2,C2C12 cells,ChREBP overexpression,day7

description:
Library name: day7_OE_2
Column name in C2C12_OE_expression.csv:OE_2


title: donor 2, bronchial epithelial brushing, time point 9, replicate 2

description:
Library name: Sample37
ajdy441_9_2


title: day7_OE_1,C2C12 cells,ChREBP overexpression,day7

description:
Library name: day7_OE_1
Column name in C2C12_OE_expression.csv:OE_1


title: mdTN from animal_7

description:
Library name: NSM1329
3 lvl sciRNAseq


title: 17_Control_2018_10_31_2, rep3

description: Library name: 17_cold_deprivation, 17_AATCCGGA-AACTGTAG-AHGKC2BBXY_L006


title: donor 2, bronchial epithelial brushing, time point 8, replicate 3

description:
Library name: Sample36
ajdy441_8_4


title: mdTN from animal_6, rep2

description:
Library name: NSM1328-b2
3 lvl sciRNAseq


title: 17_Control_2018_10_31_2, rep2

description: Library name: 17_cold_deprivation, 17_AATCCGGA-AACTGTAG-AHGKC2BBXY_L005


title: day7_CON_4,C2C12 cells,vector control,day7

description:
Library name: day7_CON_4
Column name in C2C12_OE_expression.csv:CON_4

value: vector control


title: donor 2, bronchial epithelial brushing, time point 8, replicate 2

description:
Library name: Sample35
ajdy441_8_3

value: Bronchial


title: mdTN from animal_6

description:
Library name: NSM1328
3 lvl sciRNAseq


title: 17_Control_2018_10_31_2, rep1

description: Library name: 17_cold_deprivation, 17_AATCCGGA-AACTGTAG-AHGKC2BBXY_L004


title: day7_CON_3,C2C12 cells,vector control,day7

description:
Library name: day7_CON_3
Column name in C2C12_OE_expression.csv:CON_3


title: donor 2, bronchial epithelial brushing, time point 7, replicate 3

description:
Library name: Sample34
ajdy441_7_3

value: epithelial cells


title: 16_Control_2018_10_31_1, rep3

description: Library name: 16_cold_deprivation, 16_GGCTTAAG-GGTCACGA-AHGKC2BBXY_L006


title: mdTN from animal_5, rep2

description:
Library name: NSM1327-b2
3 lvl sciRNAseq


title: day7_CON_2,C2C12 cells,vector control,day7

description:
Library name: day7_CON_2
Column name in C2C12_OE_expression.csv:CON_2


title: 16_Control_2018_10_31_1, rep2

description: Library name: 16_cold_deprivation, 16_GGCTTAAG-GGTCACGA-AHGKC2BBXY_L005


title: donor 2, bronchial epithelial brushing, time point 7, replicate 2

description:
Library name: Sample33
ajdy441_7_2


title: day7_CON_1,C2C12 cells,vector control,day7

description:
Library name: day7_CON_1
Column name in C2C12_OE_expression.csv:CON_1


title: mdTN from animal_5

description:
Library name: NSM1327
3 lvl sciRNAseq


title: donor 2, bronchial epithelial brushing, time point 6, replicate 4

description:
Library name: Sample32
ajdy441_6_4


title: 16_Control_2018_10_31_1, rep1

description: Library name: 16_cold_deprivation, 16_GGCTTAAG-GGTCACGA-AHGKC2BBXY_L004


title: mdTN from animal_4, rep2

description:
Library name: NSM1326-b2
3 lvl sciRNAseq


title: GC_MLXIPL_8,C57BL6/J mice,AAV-MLXIPL

description:
Library name: GC_MLXIPL_8
Column name in AAV-ChREBP.csv:GC_MLXIPL_8

source_name: gastrocnemius muscle

value: gastrocnemius muscle

value: AAV-MLXIPL


title: donor 2, bronchial epithelial brushing, time point 6, replicate 3

description:
Library name: Sample31
ajdy441_6_3


title: 15_CC_2018_10_01_3, rep3

description: Library name: 15_cold_deprivation, 15_TTGGACTC-CTGCTTCC-AHGKC2BBXY_L006

source_name: flower bud


title: mdTN from animal_4

description:
Library name: NSM1326
3 lvl sciRNAseq


title: GC_MLXIPL_7,C57BL6/J mice,AAV-MLXIPL

description:
Library name: GC_MLXIPL_7
Column name in AAV-ChREBP.csv:GC_MLXIPL_7


title: donor 2, bronchial epithelial brushing, time point 6, replicate 2

description:
Library name: Sample30
ajdy441_6_2


title: 15_CC_2018_10_01_3, rep2

description: Library name: 15_cold_deprivation, 15_TTGGACTC-CTGCTTCC-AHGKC2BBXY_L005


title: mdTN from animal_3, rep2

description:
Library name: NSM1325-b2
3 lvl sciRNAseq


title: GC_MLXIPL_4,C57BL6/J mice,AAV-MLXIPL

description:
Library name: GC_MLXIPL_4
Column name in AAV-ChREBP.csv:GC_MLXIPL_4


title: donor 2, bronchial epithelial brushing, time point 5, replicate 2

description:
Library name: Sample29
ajdy441_5_4


title: mdTN from animal_3

description:
Library name: NSM1325
3 lvl sciRNAseq


title: 15_CC_2018_10_01_3, rep1

description: Library name: 15_cold_deprivation, 15_TTGGACTC-CTGCTTCC-AHGKC2BBXY_L004


title: GC_MLXIPL_3,C57BL6/J mice,AAV-MLXIPL

description:
Library name: GC_MLXIPL_3
Column name in AAV-ChREBP.csv:GC_MLXIPL_3


title: donor 2, bronchial epithelial brushing, time point 5, replicate 1

description:
Library name: Sample28
ajdy441_5_3


title: 14_CC_2018_10_01_2, rep3

description: Library name: 14_cold_deprivation, 14_CCAAGTCT-TCATCCTT-AHGKC2BBXY_L006


title: mdTN from animal_2, rep2

description:
Library name: NSM1324-b2
3 lvl sciRNAseq


title: GC_MLXIPL_1,C57BL6/J mice,AAV-MLXIPL

description:
Library name: GC_MLXIPL_1
Column name in AAV-ChREBP.csv:GC_MLXIPL_1


title: donor 2, bronchial epithelial brushing, time point 4, replicate 3

description:
Library name: Sample27
ajdy441_4_4


title: 14_CC_2018_10_01_2, rep2

description: Library name: 14_cold_deprivation, 14_CCAAGTCT-TCATCCTT-AHGKC2BBXY_L005


title: mdTN from animal_2

description:
Library name: NSM1324
3 lvl sciRNAseq


title: donor 2, bronchial epithelial brushing, time point 4, replicate 2

description:
Library name: Sample26
ajdy441_4_3


title: 14_CC_2018_10_01_2, rep1

description: Library name: 14_cold_deprivation, 14_CCAAGTCT-TCATCCTT-AHGKC2BBXY_L004


title: GC_CON_8,C57BL6/J mice,AAV-CON

description:
Library name: GC_CON_8
Column name in AAV-ChREBP.csv:GC_CON_8

value: AAV-CON


title: GC_CON_7,C57BL6/J mice,AAV-CON

description:
Library name: GC_CON_7
Column name in AAV-ChREBP.csv:GC_CON_7