title: mdTN from animal_1, rep2

description:
Library name: NSM1323-b2
3 lvl sciRNAseq


title: donor 2, bronchial epithelial brushing, time point 4, replicate 1

status: Public on Jul 01 2026

type: SRA

city: St Louis

first: Jeffery

last: Haspel

state: MO

address: 660 S Euclid Avenue

country: USA

institute: Washington University, St Louis

description:
Library name: Sample25
ajdy441_4_2

library_source: transcriptomic

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.

molecule: total RNA

organism: Homo sapiens

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

tag: tissue

value: Bronchial

tag: cell type

value: epithelial cells


title: 13_CC_2018_10_01_1, rep3

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: 13_cold_deprivation, 13_CTCTCGTC-AGGTTATA-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

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

tag: genotype

value: Regina

tag: treatment

tag: batch


title: mdTN from animal_1

city: Tempe

first: Noah

last: Snyder-Mackler

state: Arizona

address: 214 Life Sciences C

department: School of Life Sciences

institute: Arizona State University

description:
Library name: NSM1323
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.

value: mediodorsal thalamic nucleus


title: 13_CC_2018_10_01_1, rep2

description: Library name: 13_cold_deprivation, 13_CTCTCGTC-AGGTTATA-AHGKC2BBXY_L005


title: dlPFC from animal_55

description:
Library name: NSM1322
3 lvl sciRNAseq

source_name: dorsolateral prefrontal cortex

value: dorsolateral prefrontal cortex


title: GC_CON_4,C57BL6/J mice,AAV-CON

city: Shanghai

first: Lu

last: Junyu

address: 800th Xiangyin Street, shanghai,China

department: Department of Cell Biology

country: China

institute: Naval Medical University

description:
Library name: GC_CON_4
Column name in AAV-ChREBP.csv:GC_CON_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

organism: Mus musculus

source_name: gastrocnemius muscle

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: gastrocnemius muscle

value: AAV-CON


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

description:
Library name: Sample23
ajdy441_11_2


title: donor 2, bronchial epithelial brushing, time point 11, replicate 3

description:
Library name: Sample24
ajdy441_11_3


title: dlPFC from animal_54

description:
Library name: NSM1321
3 lvl sciRNAseq


title: GC_CON_3,C57BL6/J mice,AAV-CON

description:
Library name: GC_CON_3
Column name in AAV-ChREBP.csv:GC_CON_3


title: 13_CC_2018_10_01_1, rep1

description: Library name: 13_cold_deprivation, 13_CTCTCGTC-AGGTTATA-AHGKC2BBXY_L004


title: GC_CON_1,C57BL6/J mice,AAV-CON

description:
Library name: GC_CON_1
Column name in AAV-ChREBP.csv:GC_CON_1


title: donor 2, bronchial epithelial brushing, time point 10, replicate 3

description:
Library name: Sample22
ajdy441_10_3


title: 12_Control_2018_10_01_3, rep3

description: Library name: 12_cold_deprivation, 12_TCTCTACT-GAACCGCG-AHGKC2BBXY_L006


title: WT_C310,ChMKO mice

description:
Library name: WT_C310
Column name in ChMKO_Expression_FPKM.csv:WT_C310

value: ChREBP-flox

value: high-fructose diet


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

description:
Library name: Sample21
ajdy441_10_2


title: dlPFC from animal_53

description:
Library name: NSM1320
3 lvl sciRNAseq


title: 12_Control_2018_10_01_3, rep2

description: Library name: 12_cold_deprivation, 12_TCTCTACT-GAACCGCG-AHGKC2BBXY_L005


title: dlPFC from animal_52

description:
Library name: NSM1319
3 lvl sciRNAseq


title: WT_C301,ChMKO mice

description:
Library name: WT_C301
Column name in ChMKO_Expression_FPKM.csv:WT_C301


title: donor 1, bronchial epithelial brushing, time point 7, replicate 3

description:
Library name: Sample20
ajbv233_tp_7_3


title: WT_C294,ChMKO mice

description:
Library name: WT_C294
Column name in ChMKO_Expression_FPKM.csv:WT_C294


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

description:
Library name: Sample19
ajbv233_tp_7_1


title: dlPFC from animal_51

description:
Library name: NSM1318
3 lvl sciRNAseq


title: 12_Control_2018_10_01_3, rep1

description: Library name: 12_cold_deprivation, 12_TCTCTACT-GAACCGCG-AHGKC2BBXY_L004


title: 11_Control_2018_10_01_2, rep3

description: Library name: 11_cold_deprivation, 11_GACCTGAA-CTCACCAA-AHGKC2BBXY_L006


title: dlPFC from animal_50

description:
Library name: NSM1317
3 lvl sciRNAseq


title: WT_C292,ChMKO mice

description:
Library name: WT_C292
Column name in ChMKO_Expression_FPKM.csv:WT_C292


title: donor 1, bronchial epithelial brushing, time point 6, replicate 3

description:
Library name: Sample18
ajbv233_tp_6_3


title: 11_Control_2018_10_01_2, rep2

description: Library name: 11_cold_deprivation, 11_GACCTGAA-CTCACCAA-AHGKC2BBXY_L005


title: dlPFC from animal_49

description:
Library name: NSM1316
3 lvl sciRNAseq


title: KO_C309,ChMKO mice

description:
Library name: KO_C309
Column name in ChMKO_Expression_FPKM.csv:KO_C309

value: ChREBP-flox;Mck-cre


title: 11_Control_2018_10_01_2, rep1

description: Library name: 11_cold_deprivation, 11_GACCTGAA-CTCACCAA-AHGKC2BBXY_L004


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

description:
Library name: Sample17
ajbv233_tp_6_1


title: KO_C299,ChMKO mice

description:
Library name: KO_C299
Column name in ChMKO_Expression_FPKM.csv:KO_C299


title: donor 1, bronchial epithelial brushing, time point 5, replicate 3

description:
Library name: Sample16
ajbv233_tp_5_3


title: 10_Control_2018_10_01_1, rep3

description: Library name: 10_cold_deprivation, 10_AGTTCAGG-TCTGTTGG-AHGKC2BBXY_L006


title: dlPFC from animal_47

description:
Library name: NSM1314
3 lvl sciRNAseq


title: dlPFC from animal_48

description:
Library name: NSM1315
3 lvl sciRNAseq


title: KO_C293,ChMKO mice

description:
Library name: KO_C293
Column name in ChMKO_Expression_FPKM.csv:KO_C293


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

description:
Library name: Sample15
ajbv233_tp_5_1


title: 10_Control_2018_10_01_1, rep2

description: Library name: 10_cold_deprivation, 10_AGTTCAGG-TCTGTTGG-AHGKC2BBXY_L005


title: donor 1, bronchial epithelial brushing, time point 4, replicate 3

description:
Library name: Sample14
ajbv233_tp_4_3


title: KO_C291,ChMKO mice

description:
Library name: KO_C291
Column name in ChMKO_Expression_FPKM.csv:KO_C291


title: 10_Control_2018_10_01_1, rep1

description: Library name: 10_cold_deprivation, 10_AGTTCAGG-TCTGTTGG-AHGKC2BBXY_L004


title: dlPFC from animal_46

description:
Library name: NSM1313
3 lvl sciRNAseq


title: dlPFC from animal_45

description:
Library name: NSM1312
3 lvl sciRNAseq


title: H_WTc361,ChMKO mice

description:
Library name: H_WTc361
Column name in ChMKO_Expression_FPKM.csv:H_WTc361

value: Hypoxia


title: donor 1, bronchial epithelial brushing, time point 4, replicate 1

description:
Library name: Sample13
ajbv233_tp_4_1


title: 9_CC_2018_08_30_3, rep3

description: Library name: 9_cold_deprivation, 9_TGGATCGA-TATCGCAC-AHGKC2BBXY_L006


title: dlPFC from animal_44

description:
Library name: NSM1311
3 lvl sciRNAseq


title: H_WTc360,ChMKO mice

description:
Library name: H_WTc360
Column name in ChMKO_Expression_FPKM.csv:H_WTc360


title: 9_CC_2018_08_30_3, rep2

description: Library name: 9_cold_deprivation, 9_TGGATCGA-TATCGCAC-AHGKC2BBXY_L005


title: dlPFC from animal_43

description:
Library name: NSM1310
3 lvl sciRNAseq


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

description:
Library name: Sample12
ajbv233_tp_3_3


title: H_WTc348,ChMKO mice

description:
Library name: H_WTc348
Column name in ChMKO_Expression_FPKM.csv:H_WTc348


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

description:
Library name: Sample11
ajbv233_tp_3_1


title: H_WTc341,ChMKO mice

description:
Library name: H_WTc341
Column name in ChMKO_Expression_FPKM.csv:H_WTc341


title: dlPFC from animal_42

description:
Library name: NSM1309
3 lvl sciRNAseq


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

description:
Library name: Sample10
ajbv233_tp_2_3


title: 9_CC_2018_08_30_3, rep1

description: Library name: 9_cold_deprivation, 9_TGGATCGA-TATCGCAC-AHGKC2BBXY_L004


title: 8_CC_2018_08_30_2, rep3

description: Library name: 8_cold_deprivation, 8_CAAGCTAG-CGCTATGT-AHGKC2BBXY_L006


title: dlPFC from animal_41

description:
Library name: NSM1308
3 lvl sciRNAseq


title: H_KOc345,ChMKO mice

description:
Library name: H_KOc345
Column name in ChMKO_Expression_FPKM.csv:H_KOc345


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

description:
Library name: Sample9
ajbv233_tp_1_3


title: 8_CC_2018_08_30_2, rep2

description: Library name: 8_cold_deprivation, 8_CAAGCTAG-CGCTATGT-AHGKC2BBXY_L005


title: H_KOc340,ChMKO mice

description:
Library name: H_KOc340
Column name in ChMKO_Expression_FPKM.csv:H_KOc340


title: dlPFC from animal_40

description:
Library name: NSM1307
3 lvl sciRNAseq


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

description:
Library name: Sample8
ajbv233_tp_1_1


title: 8_CC_2018_08_30_2, rep1

description: Library name: 8_cold_deprivation, 8_CAAGCTAG-CGCTATGT-AHGKC2BBXY_L004


title: dlPFC from animal_39

description:
Library name: NSM1306
3 lvl sciRNAseq


title: H_KOc333,ChMKO mice

description:
Library name: H_KOc333
Column name in ChMKO_Expression_FPKM.csv:H_KOc333


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

description:
Library name: Sample7
ajbv233_2_tp7


title: dlPFC from animal_37

description:
Library name: NSM1305
3 lvl sciRNAseq


title: 7_CC_2018_08_30_1, rep2

description: Library name: 7_cold_deprivation, 7_GCTTGTCA-GTATGTTC-AHGKC2BBXY_L005


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

description:
Library name: Sample6
ajbv233_2_tp6


title: H_KOc332,ChMKO mice

description:
Library name: H_KOc332
Column name in ChMKO_Expression_FPKM.csv:H_KOc332


title: 7_CC_2018_08_30_1, rep3

description: Library name: 7_cold_deprivation, 7_GCTTGTCA-GTATGTTC-AHGKC2BBXY_L006


title: dlPFC from animal_36

description:
Library name: NSM1304
3 lvl sciRNAseq


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

description:
Library name: Sample5
ajbv233_2_tp5


title: N_WTc401,ChMKO mice

description:
Library name: N_WTc401
Column name in ChMKO_Expression_FPKM.csv:N_WTc401


title: 7_CC_2018_08_30_1, rep1

description: Library name: 7_cold_deprivation, 7_GCTTGTCA-GTATGTTC-AHGKC2BBXY_L004


title: dlPFC from animal_35

description:
Library name: NSM1303
3 lvl sciRNAseq


title: donor 1, bronchial epithelial brushing, time point 4, replicate 2

description:
Library name: Sample4
ajbv233_2_tp4


title: N_WTc397,ChMKO mice

description:
Library name: N_WTc397
Column name in ChMKO_Expression_FPKM.csv:N_WTc397


title: 6_Control_2018_08_30_3, rep3

description: Library name: 6_cold_deprivation, 6_ATCCACTG-ACGCACCT-AHGKC2BBXY_L006


title: dlPFC from animal_34

description:
Library name: NSM1302
3 lvl sciRNAseq


title: 6_Control_2018_08_30_3, rep2

description: Library name: 6_cold_deprivation, 6_ATCCACTG-ACGCACCT-AHGKC2BBXY_L005


title: N_WTc369,ChMKO mice

description:
Library name: N_WTc369
Column name in ChMKO_Expression_FPKM.csv:N_WTc369


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

description:
Library name: Sample3
ajbv233_2_tp3


title: dlPFC from animal_33

description:
Library name: NSM1301
3 lvl sciRNAseq


title: N_WTc368,ChMKO mice

description:
Library name: N_WTc368
Column name in ChMKO_Expression_FPKM.csv:N_WTc368


title: 6_Control_2018_08_30_3, rep1

description: Library name: 6_cold_deprivation, 6_ATCCACTG-ACGCACCT-AHGKC2BBXY_L004


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

description:
Library name: Sample2
ajbv233_2_tp2


title: dlPFC from animal_32

description:
Library name: NSM1300
3 lvl sciRNAseq


title: N_KO_380,ChMKO mice

description:
Library name: N_KO_380
Column name in ChMKO_Expression_FPKM.csv:N_KO_380


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

description:
Library name: Sample1
ajbv233_2_tp1


title: 5_Control_2018_08_30_2, rep3

description: Library name: 5_cold_deprivation, 5_AAGTCCAA-TACTCATA-AHGKC2BBXY_L006


title: dlPFC from animal_31

description:
Library name: NSM1299
3 lvl sciRNAseq


title: 5_Control_2018_08_30_2, rep2

description: Library name: 5_cold_deprivation, 5_AAGTCCAA-TACTCATA-AHGKC2BBXY_L005


title: dlPFC from animal_30

description:
Library name: NSM1298
3 lvl sciRNAseq


title: Case26_PKR-eCLIP-seq_IP

city: Tucson

first: Kevin

last: Rhine

state: AZ

address: 1703 E Mabel St

department: Pharmacology & Toxicology

institute: University of Arizona

description: Library name: eCLIP_Case26_PKR_IP

data_processing:
For RNA-seq and dsRNA-seq experiments, the fastq files were analyzed using NF-Core. For eCLIP-seq experiments, Skipper was used to analyze the sequencing files. For Riboseq, the xtail package was used to determine footprinting reads and calculate translation efficiency.
Assembly: hg38
Supplementary files format and content: For RNA-seq and dsRNA-seq experiments, the .tsv or .csv file contains the gene counts for each sample as analyzed by NF-Core. For eCLIP-seq, the .tsv file contains the reproducible enriched windows identified by Skipper.

source_name: Frontal Cortex

extract_protocol:
For RNA-seq and dsRNA-seq experiments, RNA was extracted using Trizol and purified using Rneasy or ethanol precipitation. For eCLIP-seq and Riboseq experiments, RNA was purified using lysis buffer and gel-extracted.
For RNA-seq experiments, librarires were prepared using the Illumina Stranded mRNA Prep (Ligation). For eCLIP-seq experiments, libraries were prepared using an in-house amplification procedure that closely follows the Illumina Stranded protocol.

value: Frontal Cortex

value: Apparently Healthy

value: eCLIP-seq with PKR immunoprecipitation


title: N_KO_375,ChMKO mice

description:
Library name: N_KO_375
Column name in ChMKO_Expression_FPKM.csv:N_KO_375


title: N_KO_374,ChMKO mice

description:
Library name: N_KO_374
Column name in ChMKO_Expression_FPKM.csv:N_KO_374


title: Case26_PKR-eCLIP-seq_IN

description: Library name: eCLIP_Case26_PKR_IN

value: eCLIP-seq without PKR immunoprecipitation


title: 5_Control_2018_08_30_2, rep1

description: Library name: 5_cold_deprivation, 5_AAGTCCAA-TACTCATA-AHGKC2BBXY_L004


title: dlPFC from animal_29

description:
Library name: NSM1297
3 lvl sciRNAseq


title: N_KO_370,ChMKO mice

description:
Library name: N_KO_370
Column name in ChMKO_Expression_FPKM.csv:N_KO_370


title: 4_Control_2018_08_30_1, rep3

description: Library name: 4_cold_deprivation, 4_GGACTTGG-CGTCTGCG-AHGKC2BBXY_L006


title: Case65_PKR-eCLIP-seq_IP

description: Library name: eCLIP_Case65_PKR_IP


title: dlPFC from animal_28

description:
Library name: NSM1296
3 lvl sciRNAseq


title: SOL-WT-71,ChMKO mice

description:
Library name: SOL-WT-71
Column name in fpkm.anno.csv:SOL_WT_71

source_name: soleus muscle

value: soleus muscle


title: Case65_PKR-eCLIP-seq_IN

description: Library name: eCLIP_Case65_PKR_IN


title: SOL-WT-70,ChMKO mice

description:
Library name: SOL-WT-70
Column name in fpkm.anno.csv:SOL_WT_70


title: dlPFC from animal_27

description:
Library name: NSM1295
3 lvl sciRNAseq


title: 4_Control_2018_08_30_1, rep1

description: Library name: 4_cold_deprivation, 4_GGACTTGG-CGTCTGCG-AHGKC2BBXY_L004


title: SOL-WT-59,ChMKO mice

description:
Library name: SOL-WT-59
Column name in fpkm.anno.csv:SOL_WT_69


title: Case103_PKR-eCLIP-seq_IP

description: Library name: eCLIP_Case103_PKR_IP


title: dlPFC from animal_26

description:
Library name: NSM1294
3 lvl sciRNAseq


title: 4_Control_2018_08_30_1, rep2

description: Library name: 4_cold_deprivation, 4_GGACTTGG-CGTCTGCG-AHGKC2BBXY_L005


title: Case103_PKR-eCLIP-seq_IN

description: Library name: eCLIP_Case103_PKR_IN


title: dlPFC from animal_25

description:
Library name: NSM1293
3 lvl sciRNAseq


title: 3_Control_2018_07_30_3, rep3

description: Library name: 3_cold_deprivation, 3_TTATAACC-TCGATATC-AHGKC2BBXY_L006


title: Case131_PKR-eCLIP-seq_IP

description: Library name: eCLIP_Case131_PKR_IP


title: SOL-WT-58,ChMKO mice

description:
Library name: SOL-WT-58
Column name in fpkm.anno.csv:SOL_WT_58


title: dlPFC from animal_24

description:
Library name: NSM1292
3 lvl sciRNAseq


title: Case131_PKR-eCLIP-seq_IN

description: Library name: eCLIP_Case131_PKR_IN


title: 3_Control_2018_07_30_3, rep2

description: Library name: 3_cold_deprivation, 3_TTATAACC-TCGATATC-AHGKC2BBXY_L005


title: dlPFC from animal_23

description:
Library name: NSM1291
3 lvl sciRNAseq


title: SOL-WT-57,ChMKO mice

description:
Library name: SOL-WT-57
Column name in fpkm.anno.csv:SOL_WT_57


title: SOL-KO-74,ChMKO mice

description:
Library name: SOL-KO-74
Column name in fpkm.anno.csv:SOL_KO_74


title: iPSC-diff.1_PNPT1-eCLIP-seq_IP_Replicate2

description: Library name: eCLIP_iPSC-diff.1_PNPT1_IP-2

source_name: iPSC-derived Neurons

value: iPSC-derived Neurons

value: eCLIP-seq with PNPT1 immunoprecipitation


title: dlPFC from animal_22

description:
Library name: NSM1290
3 lvl sciRNAseq


title: 1_Control_2018_07_30_1, rep3

description: Library name: 1_cold_deprivation, 1_CCGCGGTT-CTAGCGCT-AHGKC2BBXY_L006

value: flower bud

value: plant


title: 3_Control_2018_07_30_3, rep1

description: Library name: 3_cold_deprivation, 3_TTATAACC-TCGATATC-AHGKC2BBXY_L004

value: Regina


title: SOL-KO-72,ChMKO mice

description:
Library name: SOL-KO-72
Column name in fpkm.anno.csv:SOL_KO_72


title: iPSC-diff.1_PNPT1-eCLIP-seq_IP_Replicate1

description: Library name: eCLIP_iPSC-diff.1_PNPT1_IP-1


title: 1_Control_2018_07_30_1, rep2

description: Library name: 1_cold_deprivation, 1_CCGCGGTT-CTAGCGCT-AHGKC2BBXY_L005


title: iPSC-diff.1_PNPT1-eCLIP-seq_IN_Replicate2

description: Library name: eCLIP_iPSC-diff.1_PNPT1_IN-2

value: eCLIP-seq without PNPT1 immunoprecipitation


title: dlPFC from animal_20

description:
Library name: NSM1288
3 lvl sciRNAseq

value: dorsolateral prefrontal cortex


title: SOL-KO-61,ChMKO mice

description:
Library name: SOL-KO-61
Column name in fpkm.anno.csv:SOL_KO_61


title: dlPFC from animal_21

description:
Library name: NSM1289
3 lvl sciRNAseq


title: iPSC-diff.1_PNPT1-eCLIP-seq_IN_Replicate1

description: Library name: eCLIP_iPSC-diff.1_PNPT1_IN-1


title: 1_Control_2018_07_30_1, rep1

description: Library name: 1_cold_deprivation, 1_CCGCGGTT-CTAGCGCT-AHGKC2BBXY_L004


title: dlPFC from animal_19

description:
Library name: NSM1287
3 lvl sciRNAseq


title: SOL-KO-60,ChMKO mice

description:
Library name: SOL-KO-60
Column name in fpkm.anno.csv:SOL_KO_60


title: 89_16_03_2023_Control_2

description: Library name: 89_cold_exposure, 89_CTCACCAA-TTGCCTAG-AHFL5FDSXC_L004


title: SOL-KO-59,ChMKO mice

description:
Library name: SOL-KO-59
Column name in fpkm.anno.csv:SOL_KO_59


title: iPSC-diff.1_SUV3-eCLIP-seq_IP_Replicate2

description: Library name: eCLIP_iPSC-diff.1_SUV3_IP-2

value: eCLIP-seq with SUV3 immunoprecipitation


title: 88_16_03_2023_Control_1

description: Library name: 88_cold_exposure, 88_GAACCGCG-TAAGGTCA-AHC2GCDRX5_L001


title: dlPFC from animal_18

description:
Library name: NSM1286
3 lvl sciRNAseq


title: GC-WT-71,ChMKO mice

description:
Library name: GC-WT-71
Column name in fpkm.anno.csv:GC_WT_71

value: gastrocnemius muscle

value: ChREBP-flox


title: iPSC-diff.1_SUV3-eCLIP-seq_IP_Replicate1

description: Library name: eCLIP_iPSC-diff.1_SUV3_IP-1


title: GC-WT-70,ChMKO mice

description:
Library name: GC-WT-70
Column name in fpkm.anno.csv:GC_WT_70


title: dlPFC from animal_16

description:
Library name: NSM1284
3 lvl sciRNAseq


title: iPSC-diff.1_SUV3-eCLIP-seq_IN_Replicate1

description: Library name: eCLIP_iPSC-diff.1_SUV3_IN-1

value: eCLIP-seq without SUV3 immunoprecipitation


title: iPSC-diff.1_SUV3-eCLIP-seq_IN_Replicate2

description: Library name: eCLIP_iPSC-diff.1_SUV3_IN-2


title: 87_16_02_2023_Cold_August_Field_3

description: Library name: 87_cold_exposure, 87_AGGTTATA-CGGAACTG-AHFL5FDSXC_L004


title: GC-WT-69,ChMKO mice

description:
Library name: GC-WT-69
Column name in fpkm.anno.csv:GC_WT_69


title: dlPFC from animal_17

description:
Library name: NSM1285
3 lvl sciRNAseq


title: 85_16_02_2023_Cold_August_Field_1

description: Library name: 85_cold_exposure, 85_CTGCTTCC-GATCTATC-AHFL5FDSXC_L004


title: dlPFC from animal_15

description:
Library name: NSM1283
3 lvl sciRNAseq


title: 86_16_02_2023_Cold_August_Field_2

description: Library name: 86_cold_exposure, 86_TCATCCTT-AGCTCGCT-AHFL5FDSXC_L004


title: GC-WT-58,ChMKO mice

description:
Library name: GC-WT-58
Column name in fpkm.anno.csv:GC_WT_58


title: iPSC-diff.1_PKR-eCLIP-seq_IP_Replicate2

description: Library name: eCLIP_iPSC-diff.1_PKR_IP-2


title: 84_16_02_2023_Cold_July_Field_3

description: Library name: 84_cold_exposure, 84_GGTCACGA-CATAATAC-AHFL5FDSXC_L004


title: dlPFC from animal_14

description:
Library name: NSM1282
3 lvl sciRNAseq


title: HCCT12H_L001

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

institute: NCSU

description: Library name: HCCT12H_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: GC-WT-57,ChMKO mice

description:
Library name: GC-WT-57
Column name in fpkm.anno.csv:GC_WT_57


title: GC-KO-74,ChMKO mice

description:
Library name: GC-KO-74
Column name in fpkm.anno.csv:GC_KO_74

value: ChREBP-flox;Mck-cre


title: 83_16_02_2023_Cold_July_Field_2

description: Library name: 83_cold_exposure, 83_AACTGTAG-TGCGGCGT-AHFL5FDSXC_L004


title: dlPFC from animal_13

description:
Library name: NSM1281
3 lvl sciRNAseq


title: iPSC-diff.1_PKR-eCLIP-seq_IP_Replicate1

description: Library name: eCLIP_iPSC-diff.1_PKR_IP-1

value: Apparently Healthy

value: eCLIP-seq with PKR immunoprecipitation


title: iPSC-diff.1_PKR-eCLIP-seq_IN_Replicate2

description: Library name: eCLIP_iPSC-diff.1_PKR_IN-2

value: eCLIP-seq without PKR immunoprecipitation


title: dlPFC from animal_12

description:
Library name: NSM1280
3 lvl sciRNAseq


title: 82_16_02_2023_Cold_July_Field_1

description: Library name: 82_cold_exposure, 82_GTGAATAT-GAATGAGA-AHFL5FDSXC_L004


title: iPSC-diff.1_PKR-eCLIP-seq_IN_Replicate1

description: Library name: eCLIP_iPSC-diff.1_PKR_IN-1

value: iPSC-derived Neurons


title: GC-KO-72,ChMKO mice

description:
Library name: GC-KO-72
Column name in fpkm.anno.csv:GC_KO_72


title: 77_16_02_2023_Control_2

description: Library name: 77_cold_exposure, 77_GACGTCTT-GGTGAACC-AHFL5FDSXC_L004


title: dlPFC from animal_11

description:
Library name: NSM1279
3 lvl sciRNAseq


title: 76_16_02_2023_Control_1

description: Library name: 76_cold_exposure, 76_AGTACTCC-AACAGGTT-AHC2GCDRX5_L001


title: GC-KO-60,ChMKO mice

description:
Library name: GC-KO-60
Column name in fpkm.anno.csv:GC_KO_60


title: 75_26_01_2023_Cold_August_Field_3

description: Library name: 75_cold_exposure, 75_TGGCCGGT-GCGCTCTA-AHFL5FDSXC_L004


title: Tdiff.1_PNPT1-eCLIP-seq_IP_Replicate1

description: Library name: eCLIP_Tdiff.1_PNPT1_IP-1

source_name: Transdifferentiated Neurons

value: Transdifferentiated Neurons

value: eCLIP-seq with PNPT1 immunoprecipitation


title: GC-KO-59,ChMKO mice

description:
Library name: GC-KO-59
Column name in fpkm.anno.csv:GC_KO_59


title: Tdiff.1_PNPT1-eCLIP-seq_IN_Replicate2

description: Library name: eCLIP_Tdiff.1_PNPT1_IN-2


title: dlPFC from animal_10

description:
Library name: NSM1278
3 lvl sciRNAseq


title: 74_26_01_2023_Cold_August_Field_2

description: Library name: 74_cold_exposure, 74_CAATTAAC-ATATCTCG-AHFL5FDSXC_L004

value: flower bud

value: plant


title: dlPFC from animal_9

description:
Library name: NSM1277
3 lvl sciRNAseq


title: dlPFC from animal_8

description:
Library name: NSM1276
3 lvl sciRNAseq


title: Tdiff.1_PNPT1-eCLIP-seq_IP_Replicate2

description: Library name: eCLIP_Tdiff.1_PNPT1_IP-2


title: MUS_2

city: hangzhou

first: Ziwei

last: Yan

state: zhejiang

address: zhejiang university

institute: zhejiang university

description: Library name: MUS_2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Sequences were mapped to the mouse reference genome (GRCm39) using Hisat2.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm39
Supplementary files format and content: file includes FPKM values for each sample

source_name: Peritoneal cavity

extract_protocol:
Novogene uses standard extraction methods to extract RNA from cells, and then conducts strict quality control on the RNA samples. The main quality control method is through the Agilent 2100 bioanalyzer: precisely detecting RNA integrity.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Peritoneal cavity

tag: cell line

value: peritoneal macrophage

value: WT

value: LPS+ATP+MUSCONE


title: Tdiff.1_PNPT1-eCLIP-seq_IN_Replicate1

description: Library name: eCLIP_Tdiff.1_PNPT1_IN-1

value: eCLIP-seq without PNPT1 immunoprecipitation


title: MUS_1

description: Library name: MUS_1


title: Model_2

description: Library name: Model_2

value: LPS+ATP


title: dlPFC from animal_7

description:
Library name: NSM1275
3 lvl sciRNAseq

value: dorsolateral prefrontal cortex


title: Tdiff.1_SUV3-eCLIP-seq_IP_Replicate1

description: Library name: eCLIP_Tdiff.1_SUV3_IP-1

value: eCLIP-seq with SUV3 immunoprecipitation


title: 73_26_01_2023_Cold_August_Field_1

description: Library name: 73_cold_exposure, 73_GTCTACAC-ACCTTGGC-AHFL5FDSXC_L004

value: Regina


title: Tdiff.1_SUV3-eCLIP-seq_IP_Replicate2

description: Library name: eCLIP_Tdiff.1_SUV3_IP-2

value: Apparently Healthy


title: 71_26_01_2023_Cold_July_Field_2

description: Library name: 71_cold_exposure, 71_ATTGTGAA-GCAATGCA-AHFL5FDSXC_L004


title: 72_26_01_2023_Cold_July_Field_3

description: Library name: 72_cold_exposure, 72_ACTCGTGT-GTTCCAAT-AHC2GCDRX5_L001


title: dlPFC from animal_6

description:
Library name: NSM1274
3 lvl sciRNAseq


title: Model_1

description: Library name: Model_1


title: Tdiff.1_SUV3-eCLIP-seq_IN_Replicate2

description: Library name: eCLIP_Tdiff.1_SUV3_IN-2

value: eCLIP-seq without SUV3 immunoprecipitation


title: dlPFC from animal_5

description:
Library name: NSM1273
3 lvl sciRNAseq


title: 70_26_01_2023_Cold_July_Field_1

description: Library name: 70_cold_exposure, 70_GCCACAGG-ATGGCATG-AHFL5FDSXC_L004


title: Tdiff.1_SUV3-eCLIP-seq_IN_Replicate1

description: Library name: eCLIP_Tdiff.1_SUV3_IN-1


title: Con_2

description: Library name: Con_2


title: dlPFC from animal_4

description:
Library name: NSM1272
3 lvl sciRNAseq


title: 66_26_01_2023_Control_3

description: Library name: 66_cold_exposure, 66_ACACTAAG-ATATGGAT-AHFL5FDSXC_L004


title: Con_1

description: Library name: Con_1


title: Tdiff.1_PKR-eCLIP-seq_IP_Replicate2

description: Library name: eCLIP_Tdiff.1_PKR_IP-2

value: eCLIP-seq with PKR immunoprecipitation


title: 65_26_01_2023_Control_2

description: Library name: 65_cold_exposure, 65_CCATTCGA-CGGACAAC-AHFL5FDSXC_L004


title: dlPFC from animal_3

description:
Library name: NSM1271
3 lvl sciRNAseq


title: dlPFC from animal_2

description:
Library name: NSM1270
3 lvl sciRNAseq


title: MaleMASH OAL 4

city: Shreveport

first: SUMIT KUMAR

last: ANAND

state: Louisiana

institute: LSU Health, Shreveport, LA, USA

description:
Library name: 2562-YL-16_ACCGGAGT-CCTTCCTT_S44_R1_001.fastq-013
Y16

data_processing:
Gene level quantification was performed using HTSeq-counts v0.6.0 based on the GRCm38.90 genome annotations. The R package DESeq2 v1.42.1 was then used to identify significant differentially expressed genes (DEGs). Genes with adjusted p value <0.05 were considered as significant DEGs. The upregulated and downregulated DEGs were analyzed for significantly enriched KEGG pathways using the clusterProfiler v4.10.1 package. The significance of the enrichment was determined by the right-tailed Fisher’s exact test followed by Benjamini-Hochberg multiple testing adjustment.
Assembly: GRCm38.90
Supplementary files format and content: All files are infastq.gz and .csv format

source_name: Liver

growth_protocol: Mice were fed with different diets during the growth

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen)
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina using manufacturer’s instructions.

treatment_protocol: Mice were fed with OA or OA-leu

value: Liver

value: OAL


title: 64_26_01_2023_Control_1

description: Library name: 64_cold_exposure, 64_TTGCCTAG-TAAGTGGT-AHC2GCDRX5_L001


title: Tdiff.1_PKR-eCLIP-seq_IP_Replicate1

description: Library name: eCLIP_Tdiff.1_PKR_IP-1

value: Transdifferentiated Neurons


title: dlPFC from animal_1

description:
Library name: NSM1269
3 lvl sciRNAseq


title: Tdiff.1_PKR-eCLIP-seq_IN_Replicate2

description: Library name: eCLIP_Tdiff.1_PKR_IN-2

value: eCLIP-seq without PKR immunoprecipitation


title: 63_05_01_2023_Cold_August_Field_3

description: Library name: 63_cold_exposure, 63_TAAGGTCA-CTACGACA-AHFL5FDSXC_L004

value: flower bud

value: plant


title: ACC from animal_55

description:
Library name: NSM1268
3 lvl sciRNAseq

source_name: anterior cingulate cortex

value: anterior cingulate cortex


title: Tdiff.1_PKR-eCLIP-seq_IN_Replicate1

description: Library name: eCLIP_Tdiff.1_PKR_IN-1


title: Male MASH OAL 2

description:
Library name: 2562-YL-14_ATTGGACA-TCCAGCAA_S42_R1_001.fastq-015
Y14


title: 62_05_01_2023_Cold_August_Field_2

description: Library name: 62_cold_exposure, 62_CGGAACTG-TCGTAGTG-AHFL5FDSXC_L004


title: ACC from animal_54

description:
Library name: NSM1267
3 lvl sciRNAseq


title: MaleMASH OA 4

description:
Library name: 2562-YL-12_TGTGTCAG-TACAGGTG_S40_R1_001.fastq-022
Y12

value: OA


title: Male MASH OAL 1

description:
Library name: 2562-YL-13_AGAACCAG-AGAGTCGG_S41_R1_001.fastq-031
Y13


title: iPSC-diff.1_dsRNA-seq_IP_Replicate3

description:
Library name: dsRNA-seq_iPSC-diff.1_IP-3
Alias is NGN_3_IP

value: iPSC-derived Neurons

value: dsRNA-seq with J2 immunoprecipitation


title: 61_05_01_2023_Cold_August_Field_1

description: Library name: 61_cold_exposure, 61_AGCTCGCT-GATTCTGC-AHFL5FDSXC_L004


title: ACC from animal_53

description:
Library name: NSM1266
3 lvl sciRNAseq


title: Male MASH OA 3

description:
Library name: 2562-YL-11_CTAGGTTG-GCTCGAAT_S39_R1_001.fastq-004
Y11


title: 60_05_01_2023_Cold_July_Field_3

description: Library name: 60_cold_exposure, 60_GATCTATC-AGCCTCAT-AHFL5FDSXC_L004


title: iPSC-diff.1_dsRNA-seq_IP_Replicate2

description:
Library name: dsRNA-seq_iPSC-diff.1_IP-2
Alias is NGN_2_IP


title: Male MASH OA 2

description:
Library name: 2562-YL-10_AGAAGCCT-ATACTGAC_S38_R1_001.fastq-025
Y10


title: iPSC-diff.1_dsRNA-seq_IP_Replicate1

description:
Library name: dsRNA-seq_iPSC-diff.1_IP-1
Alias is NGN_1_IP


title: ACC from animal_51

description:
Library name: NSM1264
3 lvl sciRNAseq


title: 59_05_01_2023_Cold_July_Field_2

description: Library name: 59_cold_exposure, 59_CATAATAC-CGTTAGAA-AHFL5FDSXC_L004


title: Male MASH OA 1

description:
Library name: 2562-YL-9_GTTTGCTC-CTGTTGGT_S52_R1_001.fastq-011
Y9

value: Dietary


title: ACC from animal_52

description:
Library name: NSM1265
3 lvl sciRNAseq


title: ACC from animal_50

description:
Library name: NSM1263
3 lvl sciRNAseq


title: 58_05_01_2023_Cold_July_Field_1

description: Library name: 58_cold_exposure, 58_TGCGGCGT-TACCGAGG-AHFL5FDSXC_L004


title: iPSC-diff.1_dsRNA-seq_IN_Replicate3

description:
Library name: dsRNA-seq_iPSC-diff.1_IN-3
Alias is NGN_3_IN

value: dsRNA-seq without J2 immunoprecipitation


title: Male MASH 4

description:
Library name: 2562-YL-8_TTCAATAG-TCGTGGGA_S51_R1_001.fastq-008
Y8


title: iPSC-diff.1_dsRNA-seq_IN_Replicate2

description:
Library name: dsRNA-seq_iPSC-diff.1_IN-2
Alias is NGN_2_IN


title: 48_05_01_2023_Control_3

description: Library name: 48_cold_exposure, 48_ACCTTGGC-ATGAGGCC-AHFL5FDSXC_L004


title: ACC from animal_49

description:
Library name: NSM1262
3 lvl sciRNAseq


title: Male MASH 3

description:
Library name: 2562-YL-7_TTGGGTAC-GTTGGAAG_S50_R1_001.fastq-021
Y7


title: 47_05_01_2023_Control_2

description: Library name: 47_cold_exposure, 47_GTTCCAAT-GCAGAATT-AHFL5FDSXC_L004


title: ACC from animal_48

description:
Library name: NSM1261
3 lvl sciRNAseq


title: iPSC-diff.1_dsRNA-seq_IN_Replicate1

description:
Library name: dsRNA-seq_iPSC-diff.1_IN-1
Alias is NGN_1_IN


title: Male MASH 2

description:
Library name: 2562-YL-6_TATGACGT-GATTAGCG_S49_R1_001.fastq-023
Y6


title: Tdiff.5_dsRNA-seq_IP_Replicate3

description:
Library name: dsRNA-seq_Tdiff.5_IP-3
Alias is AG43_3_IP


title: 46_05_01_2023_Control_1

description: Library name: 46_cold_exposure, 46_GCAATGCA-AACGTTCC-AHFL5FDSXC_L004


title: Tdiff.5_dsRNA-seq_IP_Replicate2

description:
Library name: dsRNA-seq_Tdiff.5_IP-2
Alias is AG43_2_IP


title: ACC from animal_47

description:
Library name: NSM1260
3 lvl sciRNAseq


title: 45_15_12_2022_Cold_August_3

description: Library name: 45_cold_exposure, 45_ATGGCATG-GGTACCTT-AHFL5FDSXC_L004


title: Male CD 4

description:
Library name: 2562-YL-4_AGTCAGGT-GTGGTTAC_S47_R1_001.fastq-027
Y4


title: ACC from animal_46

description:
Library name: NSM1259
3 lvl sciRNAseq


title: Tdiff.5_dsRNA-seq_IP_Replicate1

description:
Library name: dsRNA-seq_Tdiff.5_IP-1
Alias is AG43_1_IP


title: Male CD 2

description:
Library name: 2562-YL-2_CAGGTAAG-ATTTCGAG_S45_R1_001.fastq-026
Y2


title: Tdiff.5_dsRNA-seq_IN_Replicate2

description:
Library name: dsRNA-seq_Tdiff.5_IN-2
Alias is AG43_2_IN


title: ACC from animal_45

description:
Library name: NSM1258
3 lvl sciRNAseq


title: 43_15_12_2022_Cold_August_1

description: Library name: 43_cold_exposure, 43_AAGATACT-ATGTAAGT-AHFL5FDSXC_L004


title: Male CD 1

description:
Library name: 2562_1_L000_R1_001.fastq
Y1


title: 44_15_12_2022_Cold_August_2

description: Library name: 44_cold_exposure, 44_GGAGCGTC-GCACGGAC-AHFL5FDSXC_L004


title: ACC from animal_44

description:
Library name: NSM1257
3 lvl sciRNAseq


title: Tdiff.5_dsRNA-seq_IN_Replicate1

description:
Library name: dsRNA-seq_Tdiff.5_IN-1
Alias is AG43_1_IN


title: Male CD 3

description:
Library name: 2562-YL-3_AAGGAGAC-GTTGTGAG_S46_R1_001.fastq-009
Y3


title: 42_15_12_2022_Cold_July_3

description: Library name: 42_cold_exposure, 42_GCGCAAGC-CGGCGTGA-AHFL5FDSXC_L004


title: VC4_S55.counts

city: Chicago

first: J. Julie

last: Kim

state: IL

address: 303 E. Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

description: Library name: VC4_S55

data_processing:
Raw sequencing reads were processed using an in-house pipeline, including quality control with FastQC, alignment to the hg38 reference genome using STAR, and gene-level quantification with HTSeq-count. Differential expression analysis was performed using DESeq2, with treatment conditions compared to vehicle control using the Wald test.
Assembly: hg38
Supplementary files format and content: tab delimited text file includes raw counts for each file

source_name: leiomyoma

extract_protocol:
RNA extraction was performed with the Direct-zol RNA MicroPrep (R2060, Zymo Research) according to the manufacturer’s instructions.
cDNA Libraries were generated with the Stranded mRNA-Seq Library Prep kit.

value: leiomyoma

value: leiomyoma spheroids

value: vehicle


title: ACC from animal_43

description:
Library name: NSM1256
3 lvl sciRNAseq


title: Tdiff.2_dsRNA-seq_IP_Replicate3

description:
Library name: dsRNA-seq_Tdiff.2_IP-3
Alias is C10_3_IP

value: Apparently Healthy


title: 41_15_12_2022_Cold_July_2

description: Library name: 41_cold_exposure, 41_ATATGGAT-TAATACAG-AHFL5FDSXC_L004

value: Regina


title: Tdiff.2_dsRNA-seq_IP_Replicate2

description:
Library name: dsRNA-seq_Tdiff.2_IP-2
Alias is C10_2_IP


title: ACC from animal_42

description:
Library name: NSM1255
3 lvl sciRNAseq


title: VC3_S49.counts

description: Library name: VC3_S49


title: ACC from animal_41

description:
Library name: NSM1254
3 lvl sciRNAseq


title: 40_15_12_2022_Cold_July_1

description: Library name: 40_cold_exposure, 40_CGGACAAC-AATCCGGA-AHFL5FDSXC_L004


title: VC2_S43.counts

description: Library name: VC2_S43


title: Tdiff.2_dsRNA-seq_IP_Replicate1

description:
Library name: dsRNA-seq_Tdiff.2_IP-1
Alias is C10_1_IP


title: 39_15_12_2022_Control_3

description: Library name: 39_cold_exposure, 39_TAAGTGGT-GGCTTAAG-AHFL5FDSXC_L004


title: VC1_S37.counts

description: Library name: VC1_S37


title: Tdiff.2_dsRNA-seq_IN_Replicate3

description:
Library name: dsRNA-seq_Tdiff.2_IN-3
Alias is C10_3_IN


title: 38_15_12_2022_Control_2

description: Library name: 38_cold_exposure, 38_CTACGACA-TTGGACTC-AHFL5FDSXC_L004


title: ACC from animal_40

description:
Library name: NSM1253
3 lvl sciRNAseq


title: PQEPICIZK4_S59.counts

description: Library name: PQEPICIZK4_S59

value: paraquat+estradiol+progestin+ICIZK


title: Tdiff.2_dsRNA-seq_IN_Replicate2

description:
Library name: dsRNA-seq_Tdiff.2_IN-2
Alias is C10_2_IN


title: ACC from animal_39

description:
Library name: NSM1252
3 lvl sciRNAseq


title: ACC from animal_37

description:
Library name: NSM1251
3 lvl sciRNAseq


title: 36_23_11_2022_Cold_August_3

description: Library name: 36_cold_exposure, 36_GATTCTGC-CTCTCGTC-AHFL5FDSXC_L004


title: 37_15_12_2022_Control_1

description: Library name: 37_cold_exposure, 37_TCGTAGTG-CCAAGTCT-AHFL5FDSXC_L004


title: Tdiff.2_dsRNA-seq_IN_Replicate1

description:
Library name: dsRNA-seq_Tdiff.2_IN-1
Alias is C10_1_IN


title: PQEPICIZK3_S53.counts

description: Library name: PQEPICIZK3_S53


title: PQEPICIZK2_S47.counts

description: Library name: PQEPICIZK2_S47


title: Tdiff.1_Bulk-RNA-Seq_PKRinh_Replicate3

description:
Library name: Bulk_Tdiff.1_PKRinh-3
Alias is Kplus

value: 1 μM PKR inhibitor, 24 h


title: ACC from animal_36

description:
Library name: NSM1250
3 lvl sciRNAseq


title: 35_23_11_2022_Cold_August_2

description: Library name: 35_cold_exposure, 35_AGCCTCAT-TCTCTACT-AHFL5FDSXC_L004


title: ACC from animal_35

description:
Library name: NSM1249
3 lvl sciRNAseq


title: PQEPICIZK1_S41.counts

description: Library name: PQEPICIZK1_S41


title: Tdiff.1_Bulk-RNA-Seq_PKRinh_Replicate2

description:
Library name: Bulk_Tdiff.1_PKRinh-2
Alias is Kplus

value: Transdifferentiated Neurons


title: ACC from animal_33

description:
Library name: NSM1247
3 lvl sciRNAseq


title: ACC from animal_34

description:
Library name: NSM1248
3 lvl sciRNAseq


title: 33_23_11_2022_Cold_July_3

description: Library name: 33_cold_exposure, 33_TACCGAGG-AGTTCAGG-AHFL5FDSXC_L004


title: Tdiff.1_Bulk-RNA-Seq_PKRinh_Replicate1

description:
Library name: Bulk_Tdiff.1_PKRinh-1
Alias is Kplus


title: 34_23_11_2022_Cold_August_1

description: Library name: 34_cold_exposure, 34_CGTTAGAA-GACCTGAA-AHFL5FDSXC_L004


title: PQEP4_S58.counts

description: Library name: PQEP4_S58

value: paraquat+estradiol+progestin


title: PQEP3_S52.counts

description: Library name: PQEP3_S52


title: Tdiff.1_Bulk-RNA-Seq_DMSO_Replicate3

description:
Library name: Bulk_Tdiff.1_DMSO-3
Alias is K-


title: 32_23_11_2022_Cold_July_2

description: Library name: 32_cold_exposure, 32_AATGCCTC-TGGATCGA-AHFL5FDSXC_L004

value: flower bud


title: ACC from animal_32

description:
Library name: NSM1246
3 lvl sciRNAseq


title: PQEP2_S46.counts

description: Library name: PQEP2_S46


title: Tdiff.1_Bulk-RNA-Seq_DMSO_Replicate2

description:
Library name: Bulk_Tdiff.1_DMSO-2
Alias is K-


title: PQEP1_S40.counts

description: Library name: PQEP1_S40


title: 31_23_11_2022_Cold_July_1

description: Library name: 31_cold_exposure, 31_GGCATTCT-CAAGCTAG-AHFL5FDSXC_L004

value: plant


title: PQ4_S57.counts

description: Library name: PQ4_S57

value: paraquat


title: ACC from animal_30

description:
Library name: NSM1244
3 lvl sciRNAseq

value: anterior cingulate cortex


title: ACC from animal_31

description:
Library name: NSM1245
3 lvl sciRNAseq


title: 30_23_11_2022_Control_3

description: Library name: 30_cold_exposure, 30_TTACAGGA-GCTTGTCA-AHFL5FDSXC_L004


title: Tdiff.1_Bulk-RNA-Seq_DMSO_Replicate1

description:
Library name: Bulk_Tdiff.1_DMSO-1
Alias is K-


title: 29_23_11_2022_Control_2

description: Library name: 29_cold_exposure, 29_CCGTGAAG-ATCCACTG-AHFL5FDSXC_L004


title: iPSC-diff.1_Bulk-RNA-Seq_Replicate3

description:
Library name: Bulk_iPSC-diff.1-3
Alias is NGN

value: iPSC-derived Neurons


title: ACC from animal_29

description:
Library name: NSM1243
3 lvl sciRNAseq


title: PQ3_S51.counts

description: Library name: PQ3_S51


title: iPSC-diff.1_Bulk-RNA-Seq_Replicate2

description:
Library name: Bulk_iPSC-diff.1-2
Alias is NGN


title: 28_23_11_2022_Control_1

description: Library name: 28_cold_exposure, 28_TCCAACGC-AAGTCCAA-AHFL5FDSXC_L004


title: 27_24_10_2022_Cold_August_3

description: Library name: 27_cold_exposure, 27_CTTGGTAT-GGACTTGG-AHFL5FDSXC_L004


title: PQ1_S39.counts

description: Library name: PQ1_S39


title: ACC from animal_28

description:
Library name: NSM1242
3 lvl sciRNAseq


title: iPSC-diff.1_Bulk-RNA-Seq_Replicate1

description:
Library name: Bulk_iPSC-diff.1-1
Alias is NGN


title: PQ2_S45.counts

description: Library name: PQ2_S45


title: Tdiff.5_Bulk-RNA-Seq_Replicate3

description:
Library name: Bulk_Tdiff.5-3
Alias is AG43


title: ACC from animal_27

description:
Library name: NSM1241
3 lvl sciRNAseq


title: GC-KO-61,ChMKO mice

description:
Library name: GC-KO-61
Column name in fpkm.anno.csv:GC_KO_61

value: gastrocnemius muscle

value: ChREBP-flox;Mck-cre


title: 26_24_10_2022_Cold_August_2

description: Library name: 26_cold_exposure, 26_GTCGGAGC-TTATAACC-AHFL5FDSXC_L004


title: ACC from animal_26

description:
Library name: NSM1240
3 lvl sciRNAseq


title: Tdiff.5_Bulk-RNA-Seq_Replicate2

description:
Library name: Bulk_Tdiff.5-2
Alias is AG43


title: ICIZK4_S60.counts

description: Library name: ICIZK4_S60

value: ICI+ZK


title: ACC from animal_25

description:
Library name: NSM1239
3 lvl sciRNAseq


title: 25_24_10_2022_Cold_August_1

description: Library name: 25_cold_exposure, 25_ACTAAGAT-CCGCGGTT-AHFL5FDSXC_L004


title: ICIZK3_S54.counts

description: Library name: ICIZK3_S54

value: leiomyoma


title: ACC from animal_24

description:
Library name: NSM1238
3 lvl sciRNAseq


title: ICIZK2_S48.counts

description: Library name: ICIZK2_S48

value: leiomyoma spheroids


title: Tdiff.5_Bulk-RNA-Seq_Replicate1

description:
Library name: Bulk_Tdiff.5-1
Alias is AG43


title: ACC from animal_23

description:
Library name: NSM1237
3 lvl sciRNAseq


title: 24_24_10_2022_Cold_July_3

description: Library name: 24_cold_exposure, 24_ATGAGGCC-CAATTAAC-AHFL5FDSXC_L004


title: Tdiff.4_Bulk-RNA-Seq_Replicate3

description:
Library name: Bulk_Tdiff.4-3
Alias is AG85


title: ICIZK1_S42.counts

description: Library name: ICIZK1_S42


title: 23_24_10_2022_Cold_July_2

description: Library name: 23_cold_exposure, 23_GCAGAATT-TGGCCGGT-AHFL5FDSXC_L004


title: Tdiff.4_Bulk-RNA-Seq_Replicate2

description:
Library name: Bulk_Tdiff.4-2
Alias is AG85


title: 22_24_10_2022_Cold_July_1

description: Library name: 22_cold_exposure, 22_AACGTTCC-AGTACTCC-AHFL5FDSXC_L004


title: ACC from animal_22

description:
Library name: NSM1236
3 lvl sciRNAseq


title: 175_S1_L001

description: Library name: 175_S1_L001

source_name: Control

value: whole blood

value: Healthy control


title: 52_Control_2019_02_01_1, rep1

description: Library name: 52_cold_deprivation, 52_TCGTAGTG-CCAAGTCT-AHGKC2BBXY_L004

value: Regina


title: mdTN from animal_37, rep2

description:
Library name: NSM1359-b2
3 lvl sciRNAseq

value: mediodorsal thalamic nucleus


title: 171_S66_L001

description: Library name: 171_S66_L001


title: H9C2 cardiomyocytes, HG-Res-SIRT7-Inh group, biological replicate 3

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-3.raw_1.fastq.gz, HG-Res-SIRT7-Inh-3.raw_2.fastq.gz
High glucose + resveratrol + SIRT7 inhibitor group biological replicate 3, 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.

organism: Rattus norvegicus

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: EP4_S56.counts

description: Library name: EP4_S56

value: estradiol+progestin


title: Tdiff.4_Bulk-RNA-Seq_Replicate1

description:
Library name: Bulk_Tdiff.4-1
Alias is AG85

value: Transdifferentiated Neurons

value: Apparently Healthy


title: EP3_S50.counts

description: Library name: EP3_S50


title: 20_24_10_2022_Control_2

description: Library name: 20_cold_exposure, 20_GCACGGAC-TGCGAGAC-AHFL5FDSXC_L004

value: flower bud

value: plant


title: Tdiff.2_Bulk-RNA-Seq_Replicate3

description:
Library name: Bulk_Tdiff.2-3
Alias is C10


title: 21_24_10_2022_Control_3

description: Library name: 21_cold_exposure, 21_GGTACCTT-GACGTCTT-AHFL5FDSXC_L004


title: ACC from animal_21

description:
Library name: NSM1235
3 lvl sciRNAseq

value: anterior cingulate cortex


title: ACC from animal_20

description:
Library name: NSM1234
3 lvl sciRNAseq


title: EP2_S44.counts

description: Library name: EP2_S44


title: Tdiff.2_Bulk-RNA-Seq_Replicate2

description:
Library name: Bulk_Tdiff.2-2
Alias is C10


title: ACC from animal_19

description:
Library name: NSM1233
3 lvl sciRNAseq


title: 19_24_10_2022_Control_1

description: Library name: 19_cold_exposure, 19_ATGTAAGT-CATAGAGT-AHFL5FDSXC_L004


title: EP1_S38.counts

description: Library name: EP1_S38


title: Tdiff.2_Bulk-RNA-Seq_Replicate1

description:
Library name: Bulk_Tdiff.2-1
Alias is C10


title: ACC from animal_18

description:
Library name: NSM1232
3 lvl sciRNAseq


title: 18_21_09_2022_Cold_August_3

description: Library name: 18_cold_exposure, 18_CGGCGTGA-ACAGGCGC-AHFL5FDSXC_L004


title: PTK7KO2，rep3

city: Hangzhou

first: Xueying

last: Liu

address: No. 150 Dongfang Road, Qiantang District

institute: Hangzhou lnstitute of Medicine Chinese Academy of Sciences

description:
Library name: Sample9
PTK7KO2
159ko3-8-8

data_processing:
The reference genome sequences were indexed using Hisat2 (v2.0.1), and the clean data were aligned to the reference genome using the same software.
The known gff annotation files were converted into transcripts in fasta format and indexed appropriately.
With the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

growth_protocol: Human breast cancer cell line SUM159PT (10 million cells/well) was cultured in DMEM (YESEN, 41402ES76) with 10% FBS (Sunrise, SR100180.03) and 1% penicillin/streptomycin (Biosharp) and incubated in a 5% CO2 incubator at 37 ℃.

extract_protocol:
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.
Library construction and sequencing were conducted by GENEWIZ (GENEWIZ Biotechnology Co., Ltd, Suzhou, China) on an Illumina HiSeq instrument with a 2x150 paired-end (PE) configuration, in accordance with the manufacturer's instructions.
RNA-seq

treatment_protocol: The SUM159PT cells were transfected with treatment by lentiviral of PTK7KO or NC with puromysin (1μg/ml) selection and monoclonal cell line was cultured, followed by collection for Bulk RNA-sequencing

value: sgRNA2 pretreated in the Lentivirus packaging system


title: Tdiff.1_Bulk-RNA-Seq_Replicate3

description:
Library name: Bulk_Tdiff.1-3
Alias is K17


title: 17_21_09_2022_Cold_August_2

description: Library name: 17_cold_exposure, 17_TAATACAG-GTGAATAT-AHFL5FDSXC_L004


title: ACC from animal_17

description:
Library name: NSM1231
3 lvl sciRNAseq


title: PTK7KO2，rep2

description:
Library name: Sample8
PTK7KO2
159ko3-8-2


title: Tdiff.1_Bulk-RNA-Seq_Replicate2

description:
Library name: Bulk_Tdiff.1-2
Alias is K17


title: Tdiff.1_Bulk-RNA-Seq_Replicate1

description:
Library name: Bulk_Tdiff.1-1
Alias is K17


title: 16_21_09_2022_Cold_August_1

description: Library name: 16_cold_exposure, 16_TGACGAAT-GCCTACTG-AHFL5FDSXC_L004


title: ACC from animal_16

description:
Library name: NSM1230
3 lvl sciRNAseq


title: 15_21_09_2022_Cold_July_3

description: Library name: 15_cold_exposure, 15_CAGTAGGC-ATTCGTCA-AHFL5FDSXC_L004


title: PTK7KO1，rep3

description:
Library name: Sample6
PTK7KO1
SUM159-KO-2

value: sgRNA1 pretreated in the Lentivirus packaging system


title: PTK7KO2，rep1

description:
Library name: Sample7
PTK7KO2
159ko3-8-1


title: U937 cells, KD2, RNA-seq, rep3

city: Hefei

first: Mengqing

last: Gao

state: Anhui

department: Department of Hematology

institute: The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China

description: Library name: KD2-3

data_processing:
Raw fastq reads were processed using fastp to remove low-quality reads, resulting in clean reads for subsequent data analysis.
HISAT2 was used for alignment to the reference genome hg38.
Gene expression levels were calculated in FPKM and the read counts for each gene were obtained using HTSeq-count.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

growth_protocol: Control and two BRD4 knockdown (KD1, KD2) U937 cells were maintained in RPMI-1640 supplemented with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
Total RNA from U937 cells was extracted with TRIzol reagent (Invitrogen, 15596026CN).
Transcriptome libraries were constructed using the VAHTS Universal V5 RNA-seq Library Prep Kit (Vazyme) according to the manufacturer's instructions

treatment_protocol: U937 cells were infected with lentiviral shRNAs to generante control and BRD4 KD cells.

value: acute myeloid leukemia cell lines


title: 14_21_09_2022_Cold_July_2

description: Library name: 14_cold_exposure, 14_TTGGACTC-CTGCTTCC-AHFL5FDSXC_L004


title: ACC from animal_14

description:
Library name: NSM1228
3 lvl sciRNAseq


title: ACC from animal_15

description:
Library name: NSM1229
3 lvl sciRNAseq


title: U937 cells, KD2, RNA-seq, rep2

description: Library name: KD2-2


title: PTK7KO1，rep2

description:
Library name: Sample5
PTK7KO1
SUM159-KO-1


title: ACC from animal_13

description:
Library name: NSM1227
3 lvl sciRNAseq


title: 13_21_09_2022_Cold_July_1

description: Library name: 13_cold_exposure, 13_CCAAGTCT-TCATCCTT-AHFL5FDSXC_L004


title: PTK7KO1，rep1

description:
Library name: Sample4
PTK7KO1
sum-159-ko


title: U937 cells, KD2, RNA-seq, rep1

description: Library name: KD2-1


title: 12_21_09_2022_Control_3

description: Library name: 12_cold_exposure, 12_CTCTCGTC-AGGTTATA-AHFL5FDSXC_L004


title: U937 cells, KD1, RNA-seq, rep3

description: Library name: KD1-3


title: ACC from animal_11

description:
Library name: NSM1225
3 lvl sciRNAseq


title: PTK7NC，rep3

description:
Library name: Sample3
PTK7NC
SUM159-NC-2

value: negative sgRNA pretreated in the Lentivirus packaging system


title: PTK7NC，rep2

description:
Library name: Sample2
PTK7NC
SUM159-NC-1


title: H9C2 cardiomyocytes, HG-Res-SIRT7-Inh group, biological replicate 1

description:
Library name: HG-Res-SIRT7-Inh-1.raw_1.fastq.gz, HG-Res-SIRT7-Inh-1.raw_2.fastq.gz
High glucose + resveratrol + SIRT7 inhibitor group biological replicate 1, total RNA-seq


title: ACC from animal_12

description:
Library name: NSM1226
3 lvl sciRNAseq


title: 41_CC_2019_01_02_2, rep2

description: Library name: 41_cold_deprivation, 41_AATGCCTC-TGGATCGA-AHGKC2BBXY_L005


title: H9C2 cardiomyocytes, HG-Res group, biological replicate 1

description:
Library name: HG-Res-1.raw_1.fastq.gz, HG-Res-1.raw_2.fastq.gz
High glucose + resveratrol group biological replicate 1, total RNA-seq

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


title: U937 cells, KD1, RNA-seq, rep2

description: Library name: KD1-2


title: 11_21_09_2022_Control_2

description: Library name: 11_cold_exposure, 11_TCTCTACT-GAACCGCG-AHFL5FDSXC_L004


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

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


title: ACC from animal_10

description:
Library name: NSM1224
3 lvl sciRNAseq


title: U937 cells, KD1, RNA-seq, rep1

description: Library name: KD1-1


title: 42_CC_2019_01_02_3, rep3

description: Library name: 42_cold_deprivation, 42_TACCGAGG-AGTTCAGG-AHGKC2BBXY_L006


title: PTK7NC，rep1

description:
Library name: Sample1
PTK7NC
sum-159-nc


title: 10_21_09_2022_Control_1

description: Library name: 10_cold_exposure, 10_GACCTGAA-CTCACCAA-AHFL5FDSXC_L004


title: 9_22_08_2022_Cold_July_3

description: Library name: 9_cold_exposure, 9_AGTTCAGG-TCTGTTGG-AHFL5FDSXC_L004


title: 8_22_08_2022_Cold_July_2

description: Library name: 8_cold_exposure, 8_TGGATCGA-TATCGCAC-AHFL5FDSXC_L004


title: ACC from animal_9

description:
Library name: NSM1223
3 lvl sciRNAseq


title: peaks HeLa cells, 24hrs Oligomycin + Antimycin, pS65Ub CUT&RUN, rep 3

city: South San Francisco

first: Daniel

last: Le

state: CA

address: 1 DNA Way

institute: Genentech

description: Library name: SAM24411883_OA3_pS65_bed

data_processing:
ChIP Seq: The ENCODE analysis pipeline (v2.2.1) was used, with Bowtie2 (v2.3.4.3) employed to align reads to the reference genome (hg38). Duplicated or low-quality reads were filtered out using Picard (Broad Institute - v2.20.7) and samtools (v1.9), with further filtering to remove regions where genome assembly introduces erroneous signal. The SPP data processing pipeline was used to call peaks, with the level of background signal assessed via reference to input sample. DiffBind (v3.12.0) was used to identify differential peaks as follows. RPKM-normalized ChIP Seq data was visualized using IGV (2.18.4) genome browser
CUT&RUN: Indexed libraries generated using NEBNext library prep kit 32 (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) as per manufacturers instructions. Paired-end reads were aligned to the reference genome (hg38) using Bowtie2 (-p 24 -X2000 -t -x) and sorted with Samtools (view -bS -F 4 -q 30 -u - | sort -T). PCR duplicates were marked using Picard MarkDuplicates (MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 REMOVE_DUPLICATES=true ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT). Genome-wide coverage was determined using Bedtools genomecov (-ibam -bg -scale -g), converted to a BigWig file with wigToBigWig -clip.
Assembly: hg38
Supplementary files format and content: bigwig files for each sample
Supplementary files format and content: bed files for each sample
Library strategy: CUT&Run

source_name: HeLa Cells

extract_protocol:
ChIP-Seq samples were extracted as follows: 50mM DSG (disuccinimidyl glutarate, #C1104 - ProteoChem) for 30 mins followed by 10 mins of 1% formaldehyde was used to double crosslink HeLa or iPSC-derived NGN2 neurons (5x106), followed by the addition of glycine to quench formaldehyde. Nuclei were released using ChIP Nuclear Isolation Buffer (20 mM Tris pH 8.0, 1% Triton X-100, 0.1% SDS, 150 mM NaCl and 1mM EDTA), and chromatin sheared via sonication (Covaris sonicator: Fill level – 10, Duty Cycle – 15, PIP – 350, Cycles/Burst – 200, Time – 8-mins). Solutions containing sheared chromatin were mixed with relevant antibodies and rotated at 4°C overnight before protein A magnetic beads were then added to isolate antibody-bound chromatin. The beads were washed twice in each of the following buffers: ChIP Wash Buffer #1 (20 mM Tris pH 8.0, 1% Triton X-100, 0.1% SDS, 150 mM NaCl, 1 mM EDTA, and 0.1% NaDOC), ChIP Wash Buffer #2. (20 mM Tris pH 8.0, 1% Triton X-100, 0.1% SDS, 500 mM NaCl, 1 mM EDTA, and 0.1% NaDOC) and ChIP Wash Buffer #3 (0.25 M LiCl, 0.5% NP-40, 1mM EDTA, 20 mM Tris, pH 8.0, 0.5% NaDOC), followed by single wash in TE buffer (200 mM Tris pH 8.0 and 10 mM EDTA). The mixtures were then shaken for 20 mins in Elution Buffer (100mM NaHCO3, 1% SDS), before overnight incubation at 65°C to de-crosslink DNA. The DNA fragments were purified with MinElute PCR purification kit (Qiagen), then quantified by Qubit. CUT&RUN was performed using the CUTANA ChIC/CUT&RUN Kit (Epicypher) as per manufacturers instructions with the addition of DUB inhibitor PR-619 (100μM) to Wash and Antibody buffers.
ChIP-Seq libraries were generated using Ovation Ultralow Library System V2 (Tecan) using 2ng of each sample according to the manufacturer’s instructions, then sequenced using paired-end 50bp read configuration. CUT&RUN libraries were generated using NEBNext library prep kit 32 (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) as per manufacturers instructions.

value: HeLa Cells

value: Epithelial

value: WT

value: 24hrs Oligomycin (1µM) + Antimycin (1µM)


title: peaks HeLa cells, 24hrs DMSO, pS65Ub CUT&RUN, rep 3

description: Library name: SAM24411881_V3_pS65Ub_bed

value: 24hrs DMSO


title: ACC from animal_6

description:
Library name: NSM1220
3 lvl sciRNAseq


title: peaks HeLa cells, 24hrs DMSO, pS65Ub CUT&RUN, rep 2

description: Library name: SAM24411877_V2_pS65Ub_bed


title: 6_22_08_2022_Control_3

description: Library name: 6_cold_exposure, 6_GCTTGTCA-GTATGTTC-AHFL5FDSXC_L004

value: Regina


title: U2OS, siORCA, Input, TSA Seq

city: Urbana

first: Supriya

last: Prasanth

address: 601 S Goodwin Avenue

department: Cell and Developmental Biology

institute: University of Illinois Urbana Champaign

description: Library name: U2OS_siORCA_Input

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq Conversion Software (Illumina).
Trimming of reads was performed with trimmomatic
All sequencing files were aligned to human genome (T2T-CHM13v2.0) using Bowtie2 (v) and the sam files were converted to bam files using SAMtools (v)
BAM files were further analyzed by using the method here https://github.com/lgchang27/TSA-Seq-2020v2/tree/master
Assembly: T2T-CHM13v2.0
Supplementary files format and content: bigwig files
Library strategy: TSA-seq

source_name: Bone

growth_protocol: DMEM, 5% Fetal Bowin serum, 1X Penicillin and Streptomycin. Cells were cultured at 37 C at 5% CO2

extract_protocol:
Genomic DNA was isolated using Phenol Cholorofrom method and sonicated.
Sequencing libraries were constructed using the TruSeq ChIP Sample Prep Kit (Illumina, IP-202-1012) as per manufacturer’s protocol.

treatment_protocol: Cells were transfected with control (gl3) or siORCA.

value: Bone

value: Osteosarcoma

value: siORCA


title: U937 cells, control, RNA-seq, rep1

description: Library name: Control1

value: non-targeting


title: ACC from animal_7

description:
Library name: NSM1221
3 lvl sciRNAseq


title: peaks HeLa cells, 24hrs Oligomycin + Antimycin, pS65Ub CUT&RUN, rep 1

description: Library name: SAM24411875_OA1_pS65_bed


title: 5_22_08_2022_Control_2

description: Library name: 5_cold_exposure, 5_ATCCACTG-ACGCACCT-AHFL5FDSXC_L004

value: flower bud

value: plant


title: ACC from animal_5

description:
Library name: NSM1219
3 lvl sciRNAseq

value: anterior cingulate cortex


title: peaks HeLa cells, 24hrs Oligomycin + Antimycin, pS65Ub CUT&RUN, rep 2

description: Library name: SAM24411879_OA2_pS65Ub_bed


title: 7_22_08_2022_Cold_July_1

description: Library name: 7_cold_exposure, 7_CAAGCTAG-CGCTATGT-AHFL5FDSXC_L004


title: 4_22_08_2022_Control_1

description: Library name: 4_cold_exposure, 4_AAGTCCAA-TACTCATA-AHFL5FDSXC_L004


title: peaks HeLa cells, 24hrs DMSO, pS65Ub CUT&RUN, rep 1

description: Library name: SAM24411873_V1_pS65Ub_bed


title: ACC from animal_4

description:
Library name: NSM1218
3 lvl sciRNAseq


title: 3_21_07_2022_Control_3

description: Library name: 3_cold_exposure, 3_GGACTTGG-CGTCTGCG-AHFL5FDSXC_L004


title: ACC from animal_3

description:
Library name: NSM1217
3 lvl sciRNAseq


title: U2OS, siORCA, Replicate 2, TSA Seq

description: Library name: U2OS_siORCA2


title: HeLa cells, 24hrs Oligomycin + Antimycin, pS65Ub CUT&RUN, rep 3

description: Library name: SAM24411883_OA3_pS65_bw


title: U2OS, siORCA, Replicate1, TSA Seq

description: Library name: U2OS_siORCA1


title: 1_21_07_2022_Control_1

description: Library name: 1_cold_exposure, 1_TTATAACC-TCGATATC-AHFL5FDSXC_L004


title: HeLa cells, 24hrs Oligomycin + Antimycin, IgG CUT&RUN, rep 3

description: Library name: SAM24411882_OA3_IgG_bw


title: ACC from animal_1

description:
Library name: NSM1216
3 lvl sciRNAseq


title: U2OS, Control, Replicate1, TSA Seq

description: Library name: U2OS_Control1


title: 1B_21_07_2022_Control_2

description: Library name: 1B_cold_exposure, 1B_CCGCGGTT-CTAGCGCT-AHFL5FDSXC_L004


title: HIP from animal_55

description:
Library name: NSM1215
3 lvl sciRNAseq

source_name: hippocampus

value: hippocampus


title: 147_CC_2019_05_31_3, rep3

description: Library name: 147_cold_deprivation, 147_GAACCGCG-TAAGGTCA-BHGV3GDRXY_L002

source_name: flower bud


title: HeLa cells, 24hrs DMSO, IgG CUT&RUN, rep 3

description: Library name: SAM24411880_V3_IgG_bw


title: Inflamed small intestine, Crohn's disease [10x visium spatial transcriptomics]

city: Seoul

first: Yoonho

last: Lee

address: 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea

department: Department of Biochemistry and Molecular Biology

country: South Korea

institute: University of Ulsan College of Medicine

description: Library name: CD16_Inf

data_processing:
Data were aligned to the hg38 reference genome and normalized using Space Ranger (10X Genomics, spatial 3′ v2; spaceranger-2.1.0).
Assembly: GRCh38
Supplementary files format and content: CD16_Inf_barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: CD16_Inf_features.tsv.gz: list of gene IDs
Supplementary files format and content: CD16_Inf_matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: CD16_Inf_aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: CD16_Inf_detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: CD16_Inf_scalefactors_json.json: scalefactors in json format
Supplementary files format and content: CD16_Inf_tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: CD16_Inf_tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: CD16_Inf_tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Inflamed small intestine

extract_protocol:
An inflamed OCT-embedded frozen small intestinal tissue block from a patient with CD was processed for 10x Visium analysis. Tissue blocks were sectioned at 10 μm thickness on a cryostat.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides. 10x Visium libraries were then constructed following the manufacturer’s instructions.

value: Inflamed small intestine

tag: subject status

value: a patient with CD


title: HeLa cells, 24hrs DMSO, pS65Ub CUT&RUN, rep 3

description: Library name: SAM24411881_V3_pS65Ub_bw


title: 147_CC_2019_05_31_3, rep2

description: Library name: 147_cold_deprivation, 147_GAACCGCG-TAAGGTCA-AHGV5KDRXY_L002


title: Blood, Crohn's disease, biol rep 8

description: Library name: CD15_4_Blood

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Rnager software v6.1.2.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
Small intestinal tissues were rinsed with ice cold 1× phosphate buffered saline, and the mesenteric fat and epithelial layer were mechanically removed. We meticulously isolated the lamina propria-enriched fraction (LP) and the submucosa/muscularis propria-enriched fraction (SM/MP) for uninflamed small intestinal tissues. Curved iris scissors (AC 451/10, Nopa Instruments, Tuttlingen, Germany) were used with precision to dissect within the submucosal layer, following a technique similar to that used in endoscopic submucosal dissection. The dissected LP and SM/MP fractions were minced into small pieces (<1 mm in diameter) and placed in digestion medium (0.05% collagenase IV (Sigma-Aldrich, St. Louis, MO, USA), 0.01% DNase I (Roche, Basel, Swiss) and 10% fetal bovine serum [FBS] in RPMI 1640). Tissues were digested in an incubator at 37°C for 30 min followed by 40 min with 90 rpm agitation for each LP and SM/MP. Dissociated cells were filtered through a 70 µm cell strainer (Falcon, Durham, NC, USA) and washed with RPMI 1640 containing 2% FBS following centrifugation at 400 relative centrifugal force for 10 min. Cell pellets were suspended in RPMI 1640 containing 2% FBS and filtered through a 40 µm cell strainer followed by centrifugation at 400 relative centrifugal force for 10 min. The same protocol was performed using inflamed intestinal tissues as a whole, without separating them into the LP and the SM/MP. We processed all samples by isolating CD3+ or CD45+ cells using magnetic bead sorting. Whole blood was drawn into Heparin vacutainer tube (BD, NJ, USA) and PBMCs were isolated by Ficoll-Paque® PLUS (density = 1.077 ± 0.001 g/ml; GE Healthcare, UK), according to the manufacturer’s protocol. Briefly, 5 ml of whole blood was diluted with an equal volume of 1× phosphate-buffered saline (PBS), and the diluted blood sample (10 ml) was carefully layered on 5 ml of Ficoll-Paque® PLUS and centrifuged at 400× g for 30 min at 20°C without breaks. The cell interface layer was carefully collected, followed by washing twice with 10 ml of 1× PBS (400× g for 10 min), and the cell pellet was resuspended in CELLBANKER® Cell Freezing Media (Amsbio, UK) and store at -80℃ before multiplex RNA sequencing. Frozen PBMCs were thawed and washed prior to library preparation. Cells were resuspended in 1 x PBS containing 0.04% BSA and the concentration of each sample was adjusted to 900–1,600 cells/μL. The samples were pooled into mixtures of 2–4 donors per batch (total of 3 batches).
We utilized the 10x Genomics Chromium Instrument and cDNA synthesis kit (Chromium Next GEM Single Cell 5ʹ Kit v2 & Chromium Next GEM Chip K Single Cell Kit) to generate a barcoded cDNA library for cells isolated from intestinal tissues. cDNA library quality was determined using an Agilent Bioanalyzer. Pooled PBMCs from patients with CD were loaded on Chromium platform (10x Genomics) with a target of capturing 12,000–16,000 cells. Single cell capturing and library construction were performed using Chromium Next GEM Single Cell 5’ kit v2 (10x Genomics, PN1000263) and Chromium Single Cell Human V(D)J Reagent kit (10x Genomics, PN1000252 and PN1000253). Single-cell libraries were constructed according to the manufacturer’s protocol (10x Genomics, CG000331). All libraries were sequenced on the NovaSeq 6000 platform using S2 sequencing reagent, with a target of ~600 million reads per library using dual indexing.

value: Blood

value: CD45+ T-cells


title: HIP from animal_54

description:
Library name: NSM1214
3 lvl sciRNAseq


title: HeLa cells, 24hrs Oligomycin + Antimycin, pS65Ub CUT&RUN, rep 2

description: Library name: SAM24411879_OA2_pS65Ub_bw

value: HeLa Cells

value: Epithelial


title: HIP from animal_52

description:
Library name: NSM1212
3 lvl sciRNAseq


title: 147_CC_2019_05_31_3, rep1

description: Library name: 147_cold_deprivation, 147_GAACCGCG-TAAGGTCA-AHGV5KDRXY_L001


title: HeLa cells, 24hrs Oligomycin + Antimycin, IgG CUT&RUN, rep 2

description: Library name: SAM24411878_OA2_IgG_bw

value: WT

value: 24hrs Oligomycin (1µM) + Antimycin (1µM)


title: 146_CC_2019_05_31_2, rep3

description: Library name: 146_cold_deprivation, 146_AGGTTATA-CGGAACTG-BHGV3GDRXY_L002

value: Regina


title: HIP from animal_51

description:
Library name: NSM1211
3 lvl sciRNAseq


title: HIP from animal_50

description:
Library name: NSM1210
3 lvl sciRNAseq


title: Inflamed small intestine, Crohn's disease, biol rep 6

description: Library name: CD15_1_Inf


title: Lamina propria, Uninflamed small intestine, Crohn's disease, biol rep 15

description: Library name: CD15_2_Uninf

source_name: Lamina propria of the uninflamed small intestine


title: HeLa cells, 24hrs DMSO, IgG CUT&RUN, rep 2

description: Library name: SAM24411876_V2_IgG_bw

value: 24hrs DMSO


title: 146_CC_2019_05_31_2, rep1

description: Library name: 146_cold_deprivation, 146_AGGTTATA-CGGAACTG-AHGV5KDRXY_L001


title: HeLa cells, 24hrs Oligomycin + Antimycin, pS65Ub CUT&RUN, rep 1

description: Library name: SAM24411875_OA1_pS65_bw


title: HeLa cells, 24hrs DMSO, pS65Ub CUT&RUN, rep 2

description: Library name: SAM24411877_V2_pS65Ub_bw


title: 145_CC_2019_05_31_1, rep3

description: Library name: 145_cold_deprivation, 145_TCATCCTT-AGCTCGCT-BHGV3GDRXY_L002


title: HeLa cells, 24hrs Oligomycin + Antimycin, IgG CUT&RUN, rep 1

description: Library name: SAM24411874_OA1_IgG_bw


title: Submucosa, Uninflamed small intestine, Crohn's disease, biol rep 14

description: Library name: CD14_3_Uninf

source_name: Submucosa of the uninflamed small intestine


title: HIP from animal_49

description:
Library name: NSM1209
3 lvl sciRNAseq


title: HIP from animal_47

description:
Library name: NSM1207
3 lvl sciRNAseq


title: HeLa cells, 24hrs DMSO, pS65Ub CUT&RUN, rep 1

description: Library name: SAM24411873_V1_pS65Ub_bw


title: Lamina propria, Uninflamed small intestine, Crohn's disease, biol rep 14

description: Library name: CD14_2_Uninf

value: Lamina propria of the uninflamed small intestine


title: HeLa cells, 24hrs DMSO, IgG CUT&RUN, rep 1

description: Library name: SAM24411872_V1_IgG_bw


title: HIP from animal_46

description:
Library name: NSM1206
3 lvl sciRNAseq


title: Inflamed small intestine, Crohn's disease, biol rep 5

description: Library name: CD14_1_Inf


title: HIP from animal_45

description:
Library name: NSM1205
3 lvl sciRNAseq


title: T2-low asthma_8040254034

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

country: United Kingdom

institute: University of  Oxford

description: Library name: 8040254034

data_processing:
Sequences in fastq files (in single and pair ends) were aligned using STAR aligner (version 2.7.1a)
R package (17)Rsubread was employed for quantification of reads assigned to genes
Assembly: GRCh38
Supplementary files format and content: Raw_counts_B_BR_Pl.txt
Supplementary files format and content: Normalized_counts_B_BR_Pl.txt

source_name: BRUSHING

extract_protocol:
Total RNA was extracted from subjects biopsies and brushing using RNeasy mini kits (Qiagen).
TruSeq library preparation kits were used for RNA samples. Starting with total RNA, the messenger RNA was first purified using polyA.
Single and paired-ends library were prepared.

value: BRUSHING

tag: sample group

value: T2-low asthma


title: 141_CC2MAR_2019_05_31_3, rep3

description: Library name: 141_cold_deprivation, 141_GAACCGCG-TAAGGTCA-AHGKC2BBXY_L006

value: flower bud


title: 141_CC2MAR_2019_05_31_3, rep2

description: Library name: 141_cold_deprivation, 141_GAACCGCG-TAAGGTCA-AHGKC2BBXY_L005

value: plant


title: Blood, Crohn's disease, biol rep 6

description: Library name: CD13_4_Blood


title: HIP from animal_44

description:
Library name: NSM1204
3 lvl sciRNAseq


title: T2-low asthma_8040254023

description: Library name: 8040254023


title: 145_CC_2019_05_31_1, rep2

description: Library name: 145_cold_deprivation, 145_TCATCCTT-AGCTCGCT-AHGV5KDRXY_L002


title: Submucosa, Uninflamed small intestine, Crohn's disease, biol rep 13

description: Library name: CD13_3_Uninf

value: Submucosa of the uninflamed small intestine


title: HIP from animal_43

description:
Library name: NSM1203
3 lvl sciRNAseq

value: hippocampus


title: Lamina propria, Uninflamed small intestine, Crohn's disease, biol rep 13

description: Library name: CD13_2_Uninf


title: HIP from animal_42

description:
Library name: NSM1202
3 lvl sciRNAseq


title: T2-low asthma_8040254010

description: Library name: 8040254010


title: T2-low asthma_8040254022

description: Library name: 8040254022


title: 141_CC2MAR_2019_05_31_3, rep1

description: Library name: 141_cold_deprivation, 141_GAACCGCG-TAAGGTCA-AHGKC2BBXY_L004


title: 140_CC2MAR_2019_05_31_2, rep2

description: Library name: 140_cold_deprivation, 140_AGGTTATA-CGGAACTG-AHGKC2BBXY_L005


title: Inflamed small intestine, Crohn's disease, biol rep 4

description: Library name: CD13_1_Inf

value: Inflamed small intestine


title: HIP from animal_41

description:
Library name: NSM1201
3 lvl sciRNAseq


title: T2-low asthma_8040253998

description: Library name: 8040253998


title: Blood, Crohn's disease, biol rep 5

description: Library name: CD12_3_Blood


title: 140_CC2MAR_2019_05_31_2, rep1

description: Library name: 140_cold_deprivation, 140_AGGTTATA-CGGAACTG-AHGKC2BBXY_L004


title: HIP from animal_40

description:
Library name: NSM1200
3 lvl sciRNAseq


title: Uninflamed small intestine, Crohn's disease, biol rep 12

description: Library name: CD12_2_Uninf

source_name: Uninflamed small intestine

value: Uninflamed small intestine


title: 139_CC2MAR_2019_05_31_1, rep3

description: Library name: 139_cold_deprivation, 139_TCATCCTT-AGCTCGCT-AHGKC2BBXY_L006


title: HIP from animal_39

description:
Library name: NSM1199
3 lvl sciRNAseq


title: Inflamed small intestine, Crohn's disease, biol rep 3

description: Library name: CD12_1_Inf


title: T2-low asthma_8040253953

description: Library name: 8040253953


title: 139_CC2MAR_2019_05_31_1, rep2

description: Library name: 139_cold_deprivation, 139_TCATCCTT-AGCTCGCT-AHGKC2BBXY_L005


title: HIP from animal_37

description:
Library name: NSM1198
3 lvl sciRNAseq


title: T2-intermediate asthma_8040254035

description: Library name: 8040254035

value: T2-intermediate asthma


title: Blood, Crohn's disease, biol rep 4

description: Library name: CD11_4_Blood

value: Blood

value: CD45+ T-cells


title: 139_CC2MAR_2019_05_31_1, rep1

description: Library name: 139_cold_deprivation, 139_TCATCCTT-AGCTCGCT-AHGKC2BBXY_L004


title: T2-intermediate asthma_8040254021

description: Library name: 8040254021


title: HIP from animal_36

description:
Library name: NSM1197
3 lvl sciRNAseq


title: 131_CC2MAR_2019_04_30_2, rep3

description: Library name: 131_cold_deprivation, 131_CTGCTTCC-GATCTATC-AHGKC2BBXY_L006


title: Submucosa, Uninflamed small intestine, Crohn's disease, biol rep 11

description: Library name: CD11_3_Uninf


title: T2-intermediate asthma_8040254020

description: Library name: 8040254020


title: HIP from animal_35

description:
Library name: NSM1196
3 lvl sciRNAseq


title: HIP from animal_34

description:
Library name: NSM1195
3 lvl sciRNAseq


title: T2-intermediate asthma_8040254011

description: Library name: 8040254011


title: Lamina propria, Uninflamed small intestine, Crohn's disease, biol rep 11

description: Library name: CD11_2_Uninf


title: Inflamed small intestine, Crohn's disease, biol rep 2

description: Library name: CD11_1_Inf


title: 131_CC2MAR_2019_04_30_2, rep1

description: Library name: 131_cold_deprivation, 131_CTGCTTCC-GATCTATC-AHGKC2BBXY_L004


title: HIP from animal_33

description:
Library name: NSM1194
3 lvl sciRNAseq


title: Blood, Crohn's disease, biol rep 3

description: Library name: CD10_4_Blood


title: T2-intermediate asthma_8040254000

description: Library name: 8040254000


title: 130_CC2MAR_2019_04_30_1, rep3

description: Library name: 130_cold_deprivation, 130_GGTCACGA-CATAATAC-AHGKC2BBXY_L006


title: Submucosa, Uninflamed small intestine, Crohn's disease, biol rep 10

description: Library name: CD10_3_Uninf


title: 130_CC2MAR_2019_04_30_1, rep2

description: Library name: 130_cold_deprivation, 130_GGTCACGA-CATAATAC-AHGKC2BBXY_L005


title: HIP from animal_31

description:
Library name: NSM1192
3 lvl sciRNAseq


title: HIP from animal_32

description:
Library name: NSM1193
3 lvl sciRNAseq


title: T2-intermediate asthma_8040253999

description: Library name: 8040253999


title: Lamina propria, Uninflamed small intestine, Crohn's disease, biol rep 10

description: Library name: CD10_2_Uninf


title: 130_CC2MAR_2019_04_30_1, rep1

description: Library name: 130_cold_deprivation, 130_GGTCACGA-CATAATAC-AHGKC2BBXY_L004


title: HIP from animal_30

description:
Library name: NSM1191
3 lvl sciRNAseq


title: T2-intermediate asthma_8040253997

description: Library name: 8040253997


title: T2-intermediate asthma_8040253989

description: Library name: 8040253989


title: HIP from animal_29

description:
Library name: NSM1190
3 lvl sciRNAseq


title: 126_CC2JAN_2019_04_30_3, rep3

description: Library name: 126_cold_deprivation, 126_AACTGTAG-TGCGGCGT-AHGKC2BBXY_L006


title: Blood, Crohn's disease, biol rep 2

description: Library name: CD9_3_Blood


title: Submucosa, Uninflamed small intestine, Crohn's disease, biol rep 9

description: Library name: CD9_2_Uninf


title: T2-intermediate asthma_8040253988

description: Library name: 8040253988


title: T2-intermediate asthma_8040253985

description: Library name: 8040253985


title: 126_CC2JAN_2019_04_30_3, rep1

description: Library name: 126_cold_deprivation, 126_AACTGTAG-TGCGGCGT-AHGKC2BBXY_L004


title: HIP from animal_27

description:
Library name: NSM1188
3 lvl sciRNAseq


title: 125_CC2JAN_2019_04_30_2, rep3

description: Library name: 125_cold_deprivation, 125_GTGAATAT-GAATGAGA-AHGKC2BBXY_L006


title: Lamina propria, Uninflamed small intestine, Crohn's disease, biol rep 9

description: Library name: CD9_1_Uninf


title: HIP from animal_26

description:
Library name: NSM1187
3 lvl sciRNAseq


title: T2-intermediate asthma_8040253977

description: Library name: 8040253977


title: Submucosa, Uninflamed small intestine, Crohn's disease, biol rep 8

description: Library name: CD8_2_Uninf

value: CD3+ T-cells


title: 125_CC2JAN_2019_04_30_2, rep2

description: Library name: 125_cold_deprivation, 125_GTGAATAT-GAATGAGA-AHGKC2BBXY_L005


title: T2-intermediate asthma_8040254008

description: Library name: 8040254008


title: T2-intermediate asthma_8040253975

description: Library name: 8040253975


title: HIP from animal_25

description:
Library name: NSM1186
3 lvl sciRNAseq


title: 125_CC2JAN_2019_04_30_2, rep1

description: Library name: 125_cold_deprivation, 125_GTGAATAT-GAATGAGA-AHGKC2BBXY_L004


title: Lamina propria, Uninflamed small intestine, Crohn's disease, biol rep 8

description: Library name: CD8_1_Uninf


title: HIP from animal_24

description:
Library name: NSM1185
3 lvl sciRNAseq


title: T2-intermediate asthma_8040253974

description: Library name: 8040253974


title: Blood, Crohn's disease, biol rep 1

description: Library name: CD7_3_Blood


title: Inflamed small intestine, Crohn's disease, biol rep 1

description: Library name: CD10_1_Inf


title: HIP from animal_23

description:
Library name: NSM1184
3 lvl sciRNAseq


title: Submucosa, Uninflamed small intestine, Crohn's disease, biol rep 7

description: Library name: CD7_2_Uninf


title: 124_CC2JAN_2019_04_30_1, rep2

description: Library name: 124_cold_deprivation, 124_ACAGGCGC-AGGCAGAG-AHGKC2BBXY_L005


title: 124_CC2JAN_2019_04_30_1, rep3

description: Library name: 124_cold_deprivation, 124_ACAGGCGC-AGGCAGAG-AHGKC2BBXY_L006


title: HIP from animal_22

description:
Library name: NSM1183
3 lvl sciRNAseq


title: U937 cells, control, RNA-seq, rep3

description: Library name: Control3

value: acute myeloid leukemia cell lines

value: non-targeting


title: U937 cells, control, RNA-seq, rep2

description: Library name: Control2


title: T2-intermediate asthma_8040253964

description: Library name: 8040253964


title: 126_CC2JAN_2019_04_30_3, rep2

description: Library name: 126_cold_deprivation, 126_AACTGTAG-TGCGGCGT-AHGKC2BBXY_L005

value: Regina


title: HIP from animal_28

description:
Library name: NSM1189
3 lvl sciRNAseq


title: Lamina propria, Uninflamed small intestine, Crohn's disease, biol rep 7

description: Library name: CD7_1_Uninf


title: ACC from animal_8

description:
Library name: NSM1222
3 lvl sciRNAseq

value: anterior cingulate cortex


title: 124_CC2JAN_2019_04_30_1, rep1

description: Library name: 124_cold_deprivation, 124_ACAGGCGC-AGGCAGAG-AHGKC2BBXY_L004


title: U2OS, Control, Input, TSA Seq

description: Library name: U2OS_Control_Input

value: Bone

value: Osteosarcoma


title: Submucosa, Uninflamed small intestine, Crohn's disease, biol rep 6

description: Library name: CD6_2_Uninf


title: HIP from animal_21

description:
Library name: NSM1182
3 lvl sciRNAseq


title: T2-intermediate asthma_8040253963

description: Library name: 8040253963

value: BRUSHING


title: 120_CC_2019_04_30_3, rep3

description: Library name: 120_cold_deprivation, 120_CATAGAGT-TGGTGGCA-AHGKC2BBXY_L006

value: flower bud


title: HIP from animal_20

description:
Library name: NSM1181
3 lvl sciRNAseq


title: T2-intermediate asthma_8040253962

description: Library name: 8040253962


title: Lamina propria, Uninflamed small intestine, Crohn's disease, biol rep 6

description: Library name: CD6_1_Uninf

value: Lamina propria of the uninflamed small intestine


title: 120_CC_2019_04_30_3, rep2

description: Library name: 120_cold_deprivation, 120_CATAGAGT-TGGTGGCA-AHGKC2BBXY_L005

value: plant


title: HIP from animal_19

description:
Library name: NSM1180
3 lvl sciRNAseq

value: hippocampus


title: Submucosa, Uninflamed small intestine, Crohn's disease, biol rep 5

description: Library name: CD5_2_Uninf

value: Submucosa of the uninflamed small intestine


title: T2-intermediate asthma_8040253961

description: Library name: 8040253961


title: U2OS, Control, Replicate 2, TSA Seq

description: Library name: U2OS_Control2


title: 120_CC_2019_04_30_3, rep1

description: Library name: 120_cold_deprivation, 120_CATAGAGT-TGGTGGCA-AHGKC2BBXY_L004


title: HIP from animal_18

description:
Library name: NSM1179
3 lvl sciRNAseq


title: T2-intermediate asthma_8040253951

description: Library name: 8040253951


title: Lamina propria, Uninflamed small intestine, Crohn's disease, biol rep 5

description: Library name: CD5_1_Uninf


title: 119_CC_2019_04_30_2, rep3

description: Library name: 119_cold_deprivation, 119_TGCGAGAC-CAACAATG-AHGKC2BBXY_L006


title: HIP from animal_17

description:
Library name: NSM1178
3 lvl sciRNAseq


title: HIP from animal_53

description:
Library name: NSM1213
3 lvl sciRNAseq


title: T2-intermediate asthma_8040253965

description: Library name: 8040253965


title: T2-intermediate asthma_8040253950

description: Library name: 8040253950


title: Submucosa, Uninflamed small intestine, Crohn's disease, biol rep 4

description: Library name: CD4_2_Uninf


title: 119_CC_2019_04_30_2, rep2

description: Library name: 119_cold_deprivation, 119_TGCGAGAC-CAACAATG-AHGKC2BBXY_L005


title: Submucosa, Uninflamed small intestine, Crohn's disease, biol rep 15

description: Library name: CD15_3_Uninf


title: HIP from animal_16

description:
Library name: NSM1177
3 lvl sciRNAseq


title: T2-high asthma_8040254036

description: Library name: 8040254036

value: T2-high asthma


title: 119_CC_2019_04_30_2, rep1

description: Library name: 119_cold_deprivation, 119_TGCGAGAC-CAACAATG-AHGKC2BBXY_L004


title: 146_CC_2019_05_31_2, rep2

description: Library name: 146_cold_deprivation, 146_AGGTTATA-CGGAACTG-AHGV5KDRXY_L002


title: HIP from animal_15

description:
Library name: NSM1176
3 lvl sciRNAseq


title: T2-high asthma_8040254024

description: Library name: 8040254024