title: CD45+cells-Steady-State-ID320

description:
Library name: 517259
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID322

status: Public on Nov 26 2025

type: SRA

city: Atlanta

first: Varsha

last: Bhat

state: Georgia

address: 950 Atlantic Drive, EBB1

country: USA

institute: Georgia Institute of Technology

description:
Library name: 517281
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt

library_source: transcriptomic

data_processing:
Quality control of the paired-end reads was performed using FastQC (version 0.11.9).
Read alignment was performed using STAR (version 2.7.10b) with the GRCh38 primary assembly and GENCODE annotation (release 42)
The number of reads per gene was quantified using HTSeq (version 2.0.2) with the same GENCODE annotation as reference.
Genes with zero expression in at least 10% of the samples were removed, and the raw read counts were normalized for library size with the TMM method implemented in edgeR.
Assembly: GRCh38
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 normalized counts for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: CD45+ cells

extract_protocol:
A total of 3-5 mL of whole blood was collected in EDTA tubes for each patient at steady state at a scheduled outpatient clinic visit, during hospitalization for VOE, or during a follow-up visit in clinic. The blood samples were incubated with Miltenyi Whole Blood CD45 microbeads, and CD45+ cells were extracted using an AutoMACS machine. The CD45- fraction was incubated with Miltenyi CD71 microbeads, and a similar separation was performed using the AutoMACS.
RNA sequencing (RNA-seq) libraries were prepared using the Illumina TruSeq RNA Library Prep Kit and sequenced on the Illumina NovaSeq 6000 with a paired-end 101-bp reads protocol

tag: cell type

value: CD45+ cells

tag: age

tag: Sex

value: male

tag: collection date

tag: chronic pain

value: No

tag: libprep batch

tag: subject id

tag: status

value: Steady State


title: CD45+cells-Steady-State-ID303

description:
Library name: 517374
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt

value: female


title: CD45+cells-Steady-State-ID305_2

description:
Library name: 517554
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID297_2

description:
Library name: 517188
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID401

description:
Library name: 517316
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID375

description:
Library name: 517271
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID296

description:
Library name: 517307
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID297_1

description:
Library name: 517187
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID294

description:
Library name: 517387
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID295

description:
Library name: 517361
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID273

description:
Library name: 517368
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID286

description:
Library name: 517325
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID281

description:
Library name: 517326
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID261

description:
Library name: 517448
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID266

description:
Library name: 517343
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID257

description:
Library name: 517385
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID236

description:
Library name: 517603
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID246

description:
Library name: 517416
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID330

description:
Library name: 517365
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID227

description:
Library name: 517593
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID253

description:
Library name: 517246
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID222

description:
Library name: 517358
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID225

description:
Library name: 517203
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt

value: Yes


title: CD45+cells-Steady-State-ID221

description:
Library name: 517260
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID219

description:
Library name: 517268
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID214

description:
Library name: 517598
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID212

description:
Library name: 517284
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID305_1

description:
Library name: 517205
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID210

description:
Library name: 517559
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID211

description:
Library name: 517383
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID220

description:
Library name: 517245
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID204

description:
Library name: 517201
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID199

description:
Library name: 517184
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID202

description:
Library name: 517235
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID183

description:
Library name: 517338
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID188

description:
Library name: 517362
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID177

description:
Library name: 517297
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID194

description:
Library name: 517367
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID176

description:
Library name: 517406
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID242

description:
Library name: 517400
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID170

description:
Library name: 517255
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID171

description:
Library name: 517224
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID165

description:
Library name: 517378
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID153

description:
Library name: 517283
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID151

description:
Library name: 517305
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID149

description:
Library name: 517285
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID142

description:
Library name: 517185
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID137

description:
Library name: 517299
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID141

description:
Library name: 517341
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID123

description:
Library name: 517335
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID136

description:
Library name: 517256
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID110

description:
Library name: 517216
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID113

description:
Library name: 517208
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Follow-Up-ID658

description:
Library name: 517308
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt

value: Follow-Up


title: CD45+cells-Steady-State-ID101

description:
Library name: 517434
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Follow-Up-ID59

description:
Library name: 517295
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Follow-Up-ID538

description:
Library name: 517315
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID106

description:
Library name: 517183
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID181

description:
Library name: 517196
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Follow-Up-ID474

description:
Library name: 517318
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Follow-Up-ID404

description:
Library name: 517473
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Follow-Up-ID338

description:
Library name: 517366
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Follow-Up-ID330

description:
Library name: 517329
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Follow-Up-ID495

description:
Library name: 517317
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Follow-Up-ID358

description:
Library name: 517349
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Follow-Up-ID242

description:
Library name: 517296
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Follow-Up-ID240

description:
Library name: 517421
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Follow-Up-ID199

description:
Library name: 517239
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Steady-State-ID140

description:
Library name: 517198
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Follow-Up-ID280

description:
Library name: 517413
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Follow-Up-ID194

description:
Library name: 517309
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Follow-Up-ID253

description:
Library name: 517218
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CD45+cells-Follow-Up-ID136_1

description:
Library name: 517396
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: 0h 1% oxygen_N3

city: Liverpool

first: Sonia

last: Rocha

address: Crown Street

country: United Kingdom

institute: University of Liverool

description: Library name: S5

data_processing:
Reads in fastq files were trimmed for adaptors using Cutadapt and low quality score using Sickle.
Reads were aligned to the human genome version hg38 (GRCh38, Ensembl) using STAR and the resulting binary alignment mapped (bam) files were indexed using Samtools.
Read counts for each gene(GRCh38, Ensembl) were generated using featureCounts from Subread.
Assembly: Genome_build: GRCh38
Supplementary files format and content: tab-delimited text file which contains raw counts for each sample

molecule: total RNA

source_name: SKNAS

growth_protocol: SKNAS cells were maintained in DMEM supplemented with 10% v/v FBS, 2 mM L-glutamine, 100 units/mL penicillin and 100 μg/mL streptomycin at 5% CO2 and 37 °C. Cells were cultured for no more than 30 passages and routinely tested for mycoplasma contamination using MycoAlert Mycoplasma Detection Kit.

extract_protocol:
Total RNA was extracted from cells using an RNeasy Mini Kit (Qiagen).
RNA-seq libraries (unstranded, polyA selection) were prepared using TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: Hypoxia treatments of SKNAS cells were performed by incubating cells in an InvivO2 300 hypoxia workstation (Baker Ruskinn) for 0 or 24 hours at 1% O2, 5% CO2 and 37 °C.

tag: cell line

value: SKNAS

tag: treatment

value: 0h 1% oxygen


title: 24h 1% oxygen_N2

description: Library name: S4

value: 24h 1% oxygen


title: CD45+cells-Follow-Up-ID136_3

description:
Library name: 517474
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: 0h 1% oxygen_N2

description: Library name: S3


title: 24h 1% oxygen_N1

description: Library name: S2


title: CnT_UACC257_rep263A_DOX_rep3

city: Cambridge

first: Fei

last: Ji

state: MA

address: 250 Massachusetts Ave

institute: Novartis Biomedical Research

description: Library name: CnT_UACC257_rep263A_DOX_rep3

library_source: genomic

data_processing:
The sequencing data were base called with Illumina’s Real-Time Analysis (RTA v3.4.4) software and processed into FASTQ file format, containing the sequence data, with the bcl2fastq2-v2.20.0.422 tool.
CUT&Tag reads were aligned to the hg38 genome using Bowtie2 v2.3.4.3
Peaks were called using MACS2
Assembly: hg38
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
Protocol as in "Barbosa et al., Nat Commun. 2023 Jul 3;14(1):3907": 400,000 cells were harvested, washed and mixed with concanavalin A-coated magnetic beads;
Cells were suspended in a buffer containing the primary anti-HA antibody (overnight at 4 °C), followed by secondary antibody (1 hour, room temperature). After addition of the adapter complex, washing steps and reaction termination, DNA was extracted and PCR reactions were performed with indexing primers to generate the library.

tag: genotype

value: MITF knockdown

value: doxycycline


title: 0h 1% oxygen_N1

description: Library name: S1


title: XMU_MP_1_2

city: Xinxiang

first: Zhongbo

last: li

state: Henan

country: China

institute: Xinxiang medical university

data_processing:
Using BGISEQ-500 sequencing platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38
Supplementary files format and content: xlsx files include FPKM values for each Sample

source_name: human clear cell renal carcinoma cell line 786-O

growth_protocol: 786-O cells were plated in 12-well plates at 30% fusion per well

extract_protocol:
Lysis of cells with Trizol reagent and harvesting of RNA
RNA libraries were prepared for sequencing using BGISEQ-500 protocols

treatment_protocol: 786-O cells were transfected with Vehicle or XMU_MP_1.

tag: tissue

value: kidney

value: clear cell renal carcinoma


title: Vehicle_3

value: Vehicle


title: XMU_MP_1_1


title: CnT_UACC257_rep263A_DOX_rep1

description: Library name: CnT_UACC257_rep263A_DOX_rep1


title: Vehicle_2


title: CnT_UACC257_rep217A_DOX_rep2

description: Library name: CnT_UACC257_rep217A_DOX_rep2


title: Vehicle_1


title: CnT_UACC257_rep217A_DOX_rep3

description: Library name: CnT_UACC257_rep217A_DOX_rep3


title: CnT_UACC257_Y253A_DOX_rep3

description: Library name: CnT_UACC257_Y253A_DOX_rep3


title: CD45+cells-Follow-Up-ID136_2

description:
Library name: 517464
geo_rawcounts_CD45.txt
geo_normalizedcounts_CD45.txt


title: CnT_UACC257_rep217A_DOX_rep1

description: Library name: CnT_UACC257_rep217A_DOX_rep1


title: Uninj-WT 2

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

country: Germany

institute: Klinikum rechts der Isar – Technical University Munich

description:
Library name: Sample11
RNA obtained from carotid sample

data_processing:
All FastQ files were quality checked using FastQC software (v0.12.0); then, adapter sequences were removed, and low-quality reads were filtered out using FastQC software (v0.12.0). The resulting high-quality reads were then mapped to the mouse reference genome (GRCm39).
This alignment was performed using HISAT2 2.2.1 (http://github.com/infphilo/hisat2). For the analysis of raw count data, the DESeq2 package (version 1.44.0 https://github.com/thelovelab/DESeq2) in the R programming language (version 4.4.1) was employed using the RStudio integrated development environment (RStudio version 2024.09.0 +375 "Cranberry Hibiscus").
Assembly: GRCm39
Supplementary files format and content: tab-delimited text fileincludes raw count for each sample

organism: Mus musculus

source_name: carotid artery

extract_protocol:
Mice were placed in an induction chamber with inhalation of isoflurane through a nasal tube. The artery was ligated in two loops using a 7-0 monofilament polypropylene suture proximal to the internal-external carotid bifurcation. Surgical procedures were conducted aseptically, and the surgical incision was closed with a 3-0 non-absorbable silk suture. Carotid samples were collected at 7 days (N=9 WT and N=9 c-Kit haploinsufficient male mice) after occlusion. To minimize the number of animals used, the contralateral carotid artery of each animal was used as a control.
Libraries were generated using depleted RNA obtained from 1 μg of total RNA with a TruSeq Sample Preparation RNA kit (Illumina, Inc., San Diego, CA, USA), according to the manufacturer's protocol. All libraries were sequenced on Illumina HiSeq 1000, generating paired-end reads of 100 bp.

treatment_protocol: To develop a vascular injury model, blood flow in the right common carotid artery of 8-10-week-old c-kit haploinsufficient mice and C57BL/6J WT mice was reduced.

value: carotid artery

value: wild-type mouse

value: control


title: CAL-WT 2

description:
Library name: Sample13
RNA obtained from carotid sample

value: carotid ligation


title: Uninj-WT 1

description:
Library name: Sample9
RNA obtained from carotid sample


title: 24h 1% oxygen_N3

description: Library name: S6


title: CAL-WT 1

description:
Library name: Sample8
RNA obtained from carotid sample


title: CnT_UACC257_Y253A_DOX_rep2

description: Library name: CnT_UACC257_Y253A_DOX_rep2


title: CnT_UACC257_Y253A_DOX_rep1

description: Library name: CnT_UACC257_Y253A_DOX_rep1


title: CnT_UACC257_WT_DOX_rep3

description: Library name: CnT_UACC257_WT_DOX_rep3


title: CAL-ckitw/+ 2

description:
Library name: Sample6
RNA obtained from carotid sample

value: transgenic mouse


title: XMU_MP_1_3


title: UNinj-ckitw/+ 2

description:
Library name: Sample5
RNA obtained from carotid sample


title: CAL-ckitw/+ 1

description:
Library name: Sample4
RNA obtained from carotid sample


title: CnT_UACC257_WT_DOX_rep2

description: Library name: CnT_UACC257_WT_DOX_rep2


title: CnT_UACC257_WT_DOX_rep1

description: Library name: CnT_UACC257_WT_DOX_rep1


title: CnT_UACC257_Q261A_DOX_rep3

description: Library name: CnT_UACC257_Q261A_DOX_rep3


title: CnT_UACC257_rep263A_DOX_rep2

description: Library name: CnT_UACC257_rep263A_DOX_rep2


title: CnT_UACC257_Q261A_DOX_rep2

description: Library name: CnT_UACC257_Q261A_DOX_rep2


title: UNinj-ckitw/+ 1

description:
Library name: Sample2
RNA obtained from carotid sample


title: CnT_UACC257_Q261A_DOX_rep1

description: Library name: CnT_UACC257_Q261A_DOX_rep1


title: PolysomeProf, 42C, NonDepl, Fraction with Ribosome = 4+

city: Basel

first: Attila

last: Becskei

state: Basel-Stadt

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

description: Library name: PolyProfMacro42_nonDepl_4plus_S8

data_processing:
Sequence reads were trimmed for adaptor sequences using TrimGalore (TrimGalore v0.6.7) with --illumina parameter
Trimmed sequence reads were mapped and TPM values obtained with Salmon (Salmon v1.9.0)
Salmon index was created from NCBI's reference transcriptome (mouse assembly) with Salmon index command
TPM quantification was performed with Salmon quant command
parameters: --validateMappings --seqBias --gcBias
Assembly: GRCm39
Supplementary files format and content: Microsoft excel spreadsheet with TPM values

growth_protocol: J774A.1 murine macrophage cells were grown at 37°C in DMEM high glucose with 10% FBS and L-glutamine until ∼80% confluence.

extract_protocol:
For the sampling, cells were collected by scraping in PBS supplemented with cycloheximide (CHX) at 200μg/mL. Then the mixture was spun down at 500g for 3min in a centrifuge at 4°C. The supernatant was removed and the pellet was immediately subjected to lysis. The cell lysis and gradient preparation was performed as previously described in Rahaman, et. al. Cell Reports, 2025. For the lysis, cells were dissolved in 1X mammalian Polysome Lysis Buffer [20mM Tris-HCl, 10mM MgCl2, 1mM DTT, 50mM KCl, 200μg/mL cycloheximide, 2 cOmplete EDTA free Protease Inhibitor 100mL, 16U/mL RNasIN 1% v/v Triton X-100 ]. Lysis was carried out by passing the dissolved cells through a 23G syringe 10 times, followed by 10 cycles of bead-based lysis using Zirconia/Silica beads. The lysate was then clarified by a centrifugation for 5min at 10000g. For the ultracentrifugation, the A254 of the lysate was measured by mixing sample (or blank with Polysome Lysis Buffer) with water in a 1:20 volumetric ratio. 2–4 A254 unit equivalents of the sample was loaded onto the 10–50% sucrose gradient. Ultracentrifugation was carried out with a SW41Ti rotor (swing bucket) at 40000rpm (equivalent to 275,000g) for 2h at 4°C. The polysome profile was generated with BioComp Polysome Profiling machine. 25 fractions (450μL each) corresponding to different positions in the centrifuge tube were collected. For RNA purification, the fractions were pooled according to the peaks of A254 polysome profile (free fraction, 40S, 60S, monosome, etc.), and in vitro transcribed spike-in RNAs (prepared by in vitro translation using TranscriptAid T7 High Yield Transcription Kit) were added to each pool to serve as a volumetric control. Subsequently, the pools were subjected to phenol-chloroform extraction (Phenol: chloroform: isoamyl-alcohol = 25:24:1). Precipitation was carried out with 2.5 volumes of ethanol at −80°C overnight with 2μL of GlycoBlue as co-precipitant. RNA was reconstituted with 20μL of nuclease free water containing RNasIN at 1μL/mL (40U/mL). The purified RNA was then used for qRT-PCR or RNA-Seq.
Stranded SMART-Seq (Takara)

treatment_protocol: For the standard temperature experiment, the media of the cells growing at 37°C was changed with fresh media at 37°C. For the heat shock experiment, the cells were transferred to medium at 42°C. They were grown for an additional 1h before sampling.

value: Macrophage

value: Heat-shock


title: CnT_UACC257_N278D_DOX_rep3

description: Library name: CnT_UACC257_N278D_DOX_rep3


title: PolysomeProf, 42C, NonDepl, Fraction with Ribosome = 1

description: Library name: PolyProfMacro42_nonDepl_mono_S5


title: CnT_UACC257_N278D_DOX_rep1

description: Library name: CnT_UACC257_N278D_DOX_rep1


title: PolysomeProf, 42C, NonDepl, Fraction with Ribosome = 3

description: Library name: PolyProfMacro42_nonDepl_tri_S7


title: CnT_UACC257_N278D_DOX_rep2

description: Library name: CnT_UACC257_N278D_DOX_rep2


title: PolysomeProf, 37C, NonDepl, Fraction with Ribosome = 4+

description: Library name: PolyProfMacro37_nonDepl_4plus_S4

value: Control


title: PolysomeProf, 37C, NonDepl, Fraction with Ribosome = 3

description: Library name: PolyProfMacro37_nonDepl_tri_S3


title: PolysomeProf, 37C, NonDepl, Fraction with Ribosome = 1

description: Library name: PolyProfMacro37_nonDepl_mono_S1


title: CnT_UACC257_K243A_DOX_rep1

description: Library name: CnT_UACC257_K243A_DOX_rep1


title: CnT_UACC257_K243A_DOX_rep3

description: Library name: CnT_UACC257_K243A_DOX_rep3


title: CnT_UACC257_K243A_DOX_rep2

description: Library name: CnT_UACC257_K243A_DOX_rep2


title: CnT_UACC257_G244E_DOX_rep3

description: Library name: CnT_UACC257_G244E_DOX_rep3


title: PolysomeProf, 37C, NonDepl, Fraction with Ribosome = 2

description: Library name: PolyProfMacro37_nonDepl_di_S2


title: CnT_UACC257_G244E_DOX_rep2

description: Library name: CnT_UACC257_G244E_DOX_rep2


title: CnT_UACC257_Empty_DOX_rep3

description: Library name: CnT_UACC257_Empty_DOX_rep3


title: ARC_scRNA_WT_E1205_rep2

city: shenzhen

first: Jiang

last: Yamei

address: longfei

institute: The Chinese University of Hong Kong-Shenzhen

description: Library name: ARC_scRNA_WT_E1205_rep2

library_source: transcriptomic single cell

data_processing:
Raw fastq files were aligned to the mouse mm10 reference genome using CellRanger ARC (v2.0.2). ATAC fragments were processed with Signac (v1.13.0), while RNA data were processed using Seurat (v4.4.0). Quality control filtering retained nuclei meeting the following criteria: TSS enrichment > 4, number of fragments > 1,000, 500 < nFeature_RNA < 8,000, 1,000 < nCount_RNA < 40,000, and mitochondrial gene percentage < 15%. Post-quality control nuclei underwent doublet removal using DoubletFinder (v2.0.4). Raw RNA counts were normalized and scaled with SCTransform, incorporating regression of mitochondrial read percentage and nCount_RNA. Subsequent analyses in Seurat included PCA, CCA-based batch integration (stratified by sample), nearest neighbor clustering, and UMAP embedding construction. Cell types were annotated using differential expression and knowledge of canonical gene markers. The RNA-derived annotations, normalized gene expression matrix, and UMAP embeddings were added to the Signac project onto the nuclei with the same barcodes. Following the Signac documentation, after constructing a unified peak set, we normalized the single-nucleus ATAC-seq data using the 'RunTFIDF' function. Subsequently, we employed the 'FindTopFeatures' function to calculate highly variable features and used the 'RunSVD' function for linear dimensionality reduction, selecting the 2nd to 50th dimensions for UMAP visualization. We utilized the 'GeneActivity' function in Signac to compute gene activity in the scATAC-seq dataset by counting the chromatin fragments overlapping the gene body and a 2-kilobase upstream region for each gene. To generate a joint RNA/ATAC embedding, we calculate a WNN graph, representing a weighted combination of RNA and ATAC-seq modalities. We use this graph for UMAP visualization.
Assembly: mm10
Supplementary files format and content: filtered feature barcode matrix for scRNA
Supplementary files format and content: fragment files for scATAC

source_name: lung

extract_protocol:
Timed-pregnant mice were sacrificed at the indicated time points. The uterus was removed, and embryos were harvested on ice. The embryonic lung was incubated in digestion medium [DMEM (Hyclone, SH30243.01) + 100 U/mL DNase I (NEB, M0303S) + 100 μg/mL Liberase™ (Roche, 5401119001)] for 20 min at 37°C at 300 rpm. After digestion, lung tissue was dissociated into single cells via pipetting. The cells were washed and resuspended in 1×PBS + 2% FBS (Hyclone, SH30096.03).
Single-cell multi-omics libraries were constructed using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits (10x Genomics, PN-1000283) for 2 independent biological replicates according to the manufacturer’s protocol. Briefly, after dissociation, cells (sorted epithelial cells: whole lung cells = 1:10) were collected and resuspended in a chilled Lysis Buffer to isolate nuclei. After washing, nuclei suspensions underwent incubation in a Transposition Mix containing transposase. The transposase penetrated the nuclei and selectively cleaved DNA within the open chromatin regions. Simultaneously, adapter sequences were appended to the ends of the DNA fragments. The Single Cell Multiome ATAC + GEX Gel Beads include a poly(dT) sequence that enables production of barcoded, full-length cDNA from poly-adenylated mRNA for gene expression library and a Spacer sequence that enables barcode attachment to transposed DNA fragments for ATAC library. Finally, the snATAC-seq libraries were sequenced on the Element AVITI instrument. Conversely, the snRNA-seq libraries were loaded on the NovaSeq 6000 platform using a 150 bp paired-end read configuration.

value: lung

value: whole lung cells

value: WT


title: ARC_scRNA_WT_E1205_rep1

description: Library name: ARC_scRNA_WT_E1205_rep1


title: CnT_UACC257_E260A_DOX_rep3

description: Library name: CnT_UACC257_E260A_DOX_rep3


title: CnT_UACC257_E260A_DOX_rep2

description: Library name: CnT_UACC257_E260A_DOX_rep2


title: PolysomeProf, 42C, NonDepl, Fraction with Ribosome = 2

description: Library name: PolyProfMacro42_nonDepl_di_S6


title: CnT_UACC257_E260A_DOX_rep1

description: Library name: CnT_UACC257_E260A_DOX_rep1


title: CnT_UACC257_A264C_DOX_rep3

description: Library name: CnT_UACC257_A264C_DOX_rep3


title: ACLY-Cyto, low glucose, rep2

city: Philadelphia

first: Julianna

middle: Grace

last: Supplee

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

description:
Library name: LG_CYTO_2
ACLY_Cyto_2

data_processing:
Sequencing reads were aligned to the mouse reference genome GRCm39 using Kallisto.
Data was imported to RStudio using tximport and gene names were assigned using biomaRt.
Non-detected genes were removed, and samples were TMM normalized using edgeR.
Gene expression was fitted to a linear model using limma to determine differential expression.
Assembly: GRCm39
Supplementary files format and content: log2-transformed, TMM normalized reads, and gene symbols in .csv format
Supplementary files format and content: All high glucose (HG) and low glucose (LG) samples are grouped in respective files

source_name: Acly KO mouse embryonic fibroblast

growth_protocol: Cells were cultured in DMEM + 10% CS + 1X pen/strep. 500,000 cells were seeded in 6cm plates for this experiment and allowed to attach overnight.

extract_protocol:
RNA was purified using the Qiagen RNeasy Plus Mini kit (74134) according to the manufacturer’s instructions and eluted in 50mL volume. To improve RNA purity, 125mL ethanol and 5mL 3M sodium acetate was added, and RNA was re-precipitated at -20°C for at least 1 hour. After centrifuging for 10 min at 12,000g, the RNA pellet was washed with 75% ethanol before resuspending in nucleus-free water. RNA was incubated for 5-10 min at 56°C to increase solubility and stored at -80°C.
Illumina library prep, sequencing, and QC was performed by Novogene.

treatment_protocol: Cells were washed with PBS and 10mM/1mM glucose media added. Cells were collected 24 hours later.

value: Acly KO mouse embryonic fibroblast

value: ACLY-Cyto

value: 1mM glucose

tag: batch


title: ACLY-Nuc, low glucose, rep3

description:
Library name: LG_NUC_3
ACLY_Nuc_3

value: ACLY-Nuc


title: ACLY-Nuc, low glucose, rep4

description:
Library name: LG_NUC_4
ACLY_Nuc_4


title: ACLY-Cyto, low glucose, rep4

description:
Library name: LG_CYTO_4
ACLY_Cyto_4


title: ACLY-Cyto, low glucose, rep3

description:
Library name: LG_CYTO_3
ACLY_Cyto_3


title: ACLY-Nuc, low glucose, rep2

description:
Library name: LG_NUC_2
ACLY_Nuc_2


title: ACLY-Nuc, low glucose, rep1

description:
Library name: LG_NUC_1
ACLY_Nuc_1


title: CnT_UACC257_A264C_DOX_rep1

description: Library name: CnT_UACC257_A264C_DOX_rep1

value: MITF knockdown

value: doxycycline


title: ACLY WT, low glucose, rep2

description:
Library name: LG_WT_2
ACLY_WT_2

value: ACLY WT


title: ACLY WT, low glucose, rep3

description:
Library name: LG_WT_3
ACLY_WT_3


title: ACLY-Cyto, low glucose, rep1

description:
Library name: LG_CYTO_1
ACLY_Cyto_1


title: UACC257_empty_NoDOX_rep3

description: Library name: UACC257_empty_NoDOX_rep3

data_processing:
The sequencing data were base called with Illumina’s Real-Time Analysis (RTA v3.4.4) software and processed into FASTQ file format, containing the sequence data, with the bcl2fastq2-v2.20.0.422 tool.
Gene expression TPM and raw counts were generated using SALMON v1.3.0
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts and TPM for each Sample

extract_protocol:
RNA samples were prepared using QIAshredder (Qiagen) and RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s recommendations.
MELHO cell line RNA-Seq libraries were prepared from 250 ng of total RNA using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina, 20020599), according to the manufacturer’s instructions (Illumina TruSeq Stranded mRNA Sample Preparation Guide, 15031047 Rev. E, October 2013). UACC257 cell line RNA libraries for RNA-Seq were prepared using the TruSeq Stranded mRNA Library Prep kit following manufacturer’s protocol.


title: UACC257_empty_NoDOX_rep2

description: Library name: UACC257_empty_NoDOX_rep2


title: UACC257_empty_NoDOX_rep1

description: Library name: UACC257_empty_NoDOX_rep1


title: CnT_UACC257_G244E_DOX_rep1

description: Library name: CnT_UACC257_G244E_DOX_rep1


title: ACLY WT, low glucose, rep1

description:
Library name: LG_WT_1
ACLY_WT_1


title: Acly KO, low glucose, rep4

description:
Library name: LG_KO_4
ACLY_KO_4

value: Acly KO


title: CnT_UACC257_Empty_DOX_rep2

description: Library name: CnT_UACC257_Empty_DOX_rep2


title: UACC257_empty_DOX_rep3

description: Library name: UACC257_empty_DOX_rep3


title: Acly KO, low glucose, rep3

description:
Library name: LG_KO_3
ACLY_KO_3


title: Acly KO, low glucose, rep2

description:
Library name: LG_KO_2
ACLY_KO_2


title: CnT_UACC257_Empty_DOX_rep1

description: Library name: CnT_UACC257_Empty_DOX_rep1


title: UACC257_empty_DOX_rep2

description: Library name: UACC257_empty_DOX_rep2


title: UACC257_empty_DOX_rep1

description: Library name: UACC257_empty_DOX_rep1


title: Acly KO, low glucose, rep1

description:
Library name: LG_KO_1
ACLY_KO_1


title: UACC257_WT_NoDOX_rep3

description: Library name: UACC257_WT_NoDOX_rep3


title: CnT_UACC257_A264C_DOX_rep2

description: Library name: CnT_UACC257_A264C_DOX_rep2


title: ACLY-Nuc, high glucose, rep4

description:
Library name: HG_NUC_4
ACLY_Nuc_4

value: 10mM glucose


title: ACLY WT, low glucose, rep4

description:
Library name: LG_WT_4
ACLY_WT_4


title: ACLY-Nuc, high glucose, rep2

description:
Library name: HG_NUC_2
ACLY_Nuc_2


title: ACLY-Nuc, high glucose, rep3

description:
Library name: HG_NUC_3
ACLY_Nuc_3


title: UACC257_WT_DOX_rep2

description: Library name: UACC257_WT_DOX_rep2


title: UACC257_WT_DOX_rep3

description: Library name: UACC257_WT_DOX_rep3


title: ACLY-Nuc, high glucose, rep1

description:
Library name: HG_NUC_1
ACLY_Nuc_1


title: UACC257_WT_NoDOX_rep2

description: Library name: UACC257_WT_NoDOX_rep2


title: ACLY-Cyto, high glucose, rep4

description:
Library name: HG_CYTO_4
ACLY_Cyto_4


title: UACC257_WT_NoDOX_rep1

description: Library name: UACC257_WT_NoDOX_rep1


title: UACC257_N278D_NoDOX_rep3

description: Library name: UACC257_N278D_NoDOX_rep3


title: ACLY-Cyto, high glucose, rep2

description:
Library name: HG_CYTO_2
ACLY_Cyto_2


title: UACC257_N278D_DOX_rep3

description: Library name: UACC257_N278D_DOX_rep3


title: UACC257_N278D_NoDOX_rep2

description: Library name: UACC257_N278D_NoDOX_rep2


title: UACC257_N278D_NoDOX_rep1

description: Library name: UACC257_N278D_NoDOX_rep1


title: UACC257_N278D_DOX_rep1

description: Library name: UACC257_N278D_DOX_rep1


title: ACLY WT, high glucose, rep2

description:
Library name: HG_WT_2
ACLY_WT_2


title: ACLY WT, high glucose, rep3

description:
Library name: HG_WT_3
ACLY_WT_3


title: Acly KO, high glucose, rep4

description:
Library name: HG_KO_4
ACLY_KO_4


title: ACLY WT, high glucose, rep1

description:
Library name: HG_WT_1
ACLY_WT_1


title: UACC257_K243A_NoDOX_rep3

description: Library name: UACC257_K243A_NoDOX_rep3


title: ACLY WT, high glucose, rep4

description:
Library name: HG_WT_4
ACLY_WT_4


title: UACC257_WT_DOX_rep1

description: Library name: UACC257_WT_DOX_rep1


title: UACC257_K243A_NoDOX_rep2

description: Library name: UACC257_K243A_NoDOX_rep2


title: UACC257_K243A_NoDOX_rep1

description: Library name: UACC257_K243A_NoDOX_rep1


title: Acly KO, high glucose, rep2

description:
Library name: HG_KO_2
ACLY_KO_2


title: UACC257_N278D_DOX_rep2

description: Library name: UACC257_N278D_DOX_rep2


title: UACC257_K243A_DOX_rep3

description: Library name: UACC257_K243A_DOX_rep3


title: Acly KO, high glucose, rep1

description:
Library name: HG_KO_1
ACLY_KO_1


title: ACLY-Cyto, high glucose, rep3

description:
Library name: HG_CYTO_3
ACLY_Cyto_3


title: UACC257_A264C_NoDOX_rep2

description: Library name: UACC257_A264C_NoDOX_rep2


title: UACC257_K243A_DOX_rep2

description: Library name: UACC257_K243A_DOX_rep2


title: ACLY-Cyto, high glucose, rep1

description:
Library name: HG_CYTO_1
ACLY_Cyto_1


title: UACC257_K243A_DOX_rep1

description: Library name: UACC257_K243A_DOX_rep1


title: UACC257_A264C_NoDOX_rep3

description: Library name: UACC257_A264C_NoDOX_rep3


title: UACC257_A264C_NoDOX_rep1

description: Library name: UACC257_A264C_NoDOX_rep1


title: mES-E14-WT_4

city: Oxford

first: James

last: Davies

address: John Radcliffe Hospital/Headley Way

institute: MRC Weatherall Institute of Molecular Medicine

description: Library name: Sample 4

data_processing:
The raw FASTQ file is processed to reconstruct a single read from paired-end sequencing data. These reads are then mapped to the 800bp region surrounding the capture oligonucleotide using the non-stringent aligner BLAT. This step allows the reads to be segmented into ‘slices’ based on their alignment to the sequence around the capture site, enabling the identification of ligation junctions with base-pair precision. After this, the resulting FASTQ file is aligned to the genome using Bowtie.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes contact frequency

source_name: Embryo

growth_protocol: This research was conducted under the project license PP3929317, adhering to the European Union directive 2010/63/EU and the UK Animals (Scientific Procedures) Act of 1986. All procedures were reviewed by the Animal Welfare and Ethical Review Body of the Department of Biomedical Services at the University of Oxford. Murine erythroid cells were purified using Ter119 selection (ter119-phycoerythrin antibodies (Biolegend 116208) and anti-PE MACS beads (Miltenyi, 130-048-801)) from the spleen of C57BL/6J mice following administration of phenylyhydrazine (40 mg/g body weight, 3 doses, 12 h apart). Murine HSPCs were extracted and cultured as previously described(Wilkinson et al., 2020). Murine ES cells (E14TG2a) were maintained in gelatin (Gibco 10131-035) coated flasks in Glasgow MEM x1 liquid (Gibco 21710-025) with 10% FCS (Gibco 10270-106), 1x Glutamine (Gibco 25030-024), 1 mM sodium pyruvate (Gibco 11360-039), 1x non-essential amino acids (Gibco 11140-035), mercaptoethanol (Gibco 31350-010) and LIF (Thermo Fisher PMC9484). RPE-1 cells were maintained in Dulbecco’s Modified Eagle’s Medium (Gibco, 11960044) supplemented with 10% fetal bovine serum, 1% GLUTmax (Gibco, 35050061), 1% non-essential amino acids, and 1% penicillin-streptomycin (Gibco, 15070063) in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Aliquots of 1 x 107 cells were fixed 10 ml media with Formaldehyde, 37% (vol/vol) (Sigma, 47608-250ML) at a final of concentration 2% for 10 minutes at room temperature. This reaction was quenched with 1 M glycine to a final concentration 130 mM and centrifuged (5 min, 300 g). The supernatant was removed, and the cell pellet washed with cold PBS and reconstituted in 1 ml PBS. Cells were permeabilised with Digitonin (Sigma D-141; final concentration of 0.005% wt/vol). Cells were snap frozen and stored at -80 °C. Subsequently, defrosted, permeabilised cells were centrifuged (5 min, 300 g) the supernatant discarded, and resuspended in a reduced calcium content MNase buffer (Tris-HCl pH 7.5 10 mM; CaCl2 1 mM). Cells were split into 3 separate digests to allow titration of MNase (NEB M0247) concentration, which typically ranged from 5 to 20 Kunitz units per reaction. This reaction was incubated for 1 hour at 37 °C in an Eppendorf Thermomixer at 500 rpm and was quenched by adding ethylene glycol-bis(2-aminoethylether)-N,N,N’,N’-tetraacetic acid (EGTA) (Sigma E3889) to a final concentration of 5 mM. Chromatin was decrosslinked (proteinase K, 65 °C, >2 hours) and DNA was purified using the Qiagen DNeasy blood and tissue kit (69506). Digestion and ligation efficiencies were assessed using the Agilent Tapestation (D1000 reagents).
MNase digested samples were sequenced by ligating sequencing adaptors using the NEB Ultra II reagents (NEB, 7645S) without a size-selection step. The samples were sequenced using Illumina-based sequencing with 300-bp reads (150-bp paired-end reads).

value: Embryo

value: Mouse embryonic stem cell


title: mES-E14-WT_1

description: Library name: Sample 1


title: UACC257_A264C_DOX_rep3

description: Library name: UACC257_A264C_DOX_rep3


title: mES-E14-NANOG-FKBP-dTAG-4h_HA

description: Library name: Sample 19

data_processing:
FASTQ files were quality-checked with FastQC (v0.12.1) and trimmed using trim_galore/Cutadapt (v0.6.10). Reads were aligned to the mm10 genome with Bowtie2 (v2.5.1), PCR duplicates removed with Picard MarkDuplicates (v3.0.0). Aligned files were further processed with samtools (v1.17). Peaks were called using LanceOtron (v1.0.8; score ≥0.5). BigWig tracks were generated with deepTools bamCoverage (v3.5.1; –extendReads –normalizeUsing RPKM) and visualized in the UCSC genome browser.
Assembly: mm10
Supplementary files format and content: bw files for each Sample

extract_protocol:
ES cells were fixed for 30 min with 2 mM Di (N-succinimidyl) glutarate (DSG) (Sigma-Aldrich, 80424) followed by 30 minutes with 1% formaldehyde. Fixed cells were lysed in SDS lysis buffer (1% SDS (Sigma-Aldrich, 436143-25G), 10 mM EDTA (Sigma-Aldrich, 688363), 50 mM Tris-HCl, pH 8 with protease inhibitor cocktail (Abcam, b271306)) and the lysate was syringe-passaged through a 27-gauge needle. The cell lysates were sonicated using Covaris ME220 for 10 min. The sonicated lysates were pre-cleared with a 1:1 mix of Protein A and Protein G Dynabeads (Thermo Fisher 10001D / 10003D) for 15 minutes at 4°C. After three washes of the Dynabeads in PBS containing 0.01% tween-20 (Sigma-Aldrich, P6585-10ML), the sonicated samples were incubated overnight at 4°C. 5% of the lysate was set aside as input. After incubation, the Dynabead mix was added to each immunoprecipitate and rotated at 4 ̊C for 3 h. The beads were washed three times with RIPA buffer (50 mM HEPES-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once with TE-50 mM NaCl. The chromatin was eluted from the beads with SDS lysis buffer for 30 min at 65 °C, then treated with 1µL 500 ug/ml RNase A (Invitrogen, AM2286) for 30 min at 37 °C, followed by Proteinase K (Thermo Fisher, EO0491) 1µL 14-22 mg/ml overnight at 65 °C. DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo 5201).
Library preparation for the Illumina platform was performed following the manufacturer’s instructions (NEB, 7645S).

value: Endogenous FKBP insert

value: dTAG

tag: time

tag: chip antibody

value: NANOG


title: mES-E14-NANOG-FKBP-dTAG-6h_HA

description: Library name: Sample 20


title: Acly KO, high glucose, rep3

description:
Library name: HG_KO_3
ACLY_KO_3


title: mES-E14-NANOG-FKBP-dTAG-2h_HA

description: Library name: Sample 18


title: UACC257_A264C_DOX_rep1

description: Library name: UACC257_A264C_DOX_rep1


title: mES-E14-NANOG-FKBP-DMSO-6h_HA

description: Library name: Sample 17

value: DMSO


title: MELHO_Sensitive_ctrl_rep3

description: Library name: MELHO_Sensitive_ctrl_rep3

source_name: MELHO

value: MELHO

value: Control


title: MELHO_Sensitive_MITF_KD_rep2

description: Library name: MELHO_Sensitive_MITF_KD_rep2


title: MELHO_Sensitive_ctrl_rep2

description: Library name: MELHO_Sensitive_ctrl_rep2


title: mES-E14-M14-FKBP-dTAG-6h-rep1_T7

description: Library name: Sample 13


title: mES-E14-M14-FKBP-dTAG-6h-rep4_T7

description: Library name: Sample 16


title: mES-E14-M14-FKBP-dTAG-6h-rep2_T7

description: Library name: Sample 14


title: mES-E14-M14-FKBP-dTAG-4h-rep4_T7

description: Library name: Sample 12


title: MELHO_Sensitive_ctrl_rep1

description: Library name: MELHO_Sensitive_ctrl_rep1


title: mES-E14-M14-FKBP-dTAG-6h-rep3_T7

description: Library name: Sample 15


title: MELHO_Sensitive_MITF_KD_rep1

description: Library name: MELHO_Sensitive_MITF_KD_rep1


title: MELHO_Sensitive_MITF_KD_rep3

description: Library name: MELHO_Sensitive_MITF_KD_rep3


title: MELHO_Resistant_ctrl_rep2

description: Library name: MELHO_Resistant_ctrl_rep2


title: MELHO_Resistant_ctrl_rep3

description: Library name: MELHO_Resistant_ctrl_rep3


title: mES-E14-WT_5

description: Library name: Sample 5

value: WT


title: mES-E14-M14-FKBP-dTAG-4h-rep3_T7

description: Library name: Sample 11


title: mES-E14-WT_2

description: Library name: Sample 2


title: mES-E14-M14-FKBP-dTAG-2h-rep4_T7

description: Library name: Sample 8


title: mES-E14-M14-FKBP-dTAG-2h-rep3_T7

description: Library name: Sample 7


title: mES-E14-M14-FKBP-dTAG-2h-rep2_T7

description: Library name: Sample 6


title: mES-E14-M14-FKBP-dTAG-2h-rep1_T7

description: Library name: Sample 5


title: MELHO_Resistant_ctrl_rep1

description: Library name: MELHO_Resistant_ctrl_rep1


title: mES-E14-WT_3

description: Library name: Sample 3


title: 736T3B_IDH2-WT_SRSF2-Mutant BS

city: Miami

first: Aristeidis

middle: G

last: Telonis

state: FL

address: 1550 NW 10th Ave

department: Biochemistry & Molecular Biology

institute: University of Miami

data_processing:
Adapters were trimmed from the acquired fastq files with cutadapt (v. 1.18) with parameter -m25 -U10
Reads were mapped on the GRCh37 human genome with bismark and bismark_methylation_extractor (v. 0.22.1)
Assembly: GRCh37
Supplementary files format and content: Genome-wide cytosine report file (chromosome, position, strand, count methylated, count unmethylated, C context, trinucleotide context)

source_name: Blood

extract_protocol:
AllPrep DNA/RNA kit from Qiagen (Valencia, CA)
Methyl-Seq Kit (Swift Biosciences)

value: Blood

value: F

tag: idh2 genotype

tag: srsf2 genotype

value: Mutant


title: 648T1B_IDH2-Mutant_SRSF2-WT BS

value: M


title: 633T1M_IDH2-WT_SRSF2-Mutant BS

source_name: Marrow

value: Marrow


title: mES-E14-M14-FKBP-DMSO-6h-rep3_T7

description: Library name: Sample 3

tag: cell type


title: mES-E14-M14-FKBP-DMSO-6h-rep2_T7

description: Library name: Sample 2


title: mES-E14-M14-FKBP-DMSO-6h-rep1_T7

description: Library name: Sample 1


title: mES-E14-M14-FKBP-dTAG-4h-rep2_T7

description: Library name: Sample 10


title: 614T1M_IDH2-Mutant_SRSF2-Mutant BS


title: mES-E14-MED1-FKBP-dTAG_Rep1

description: Library name: Sample 13

data_processing:
Sequencing data were processed using a standardized pipeline. First, quality control of raw paired-end FASTQ files was performed using FastQC to assess read quality. Adapter sequences and low-quality bases were trimmed using Trim Galore. Reads were then aligned to the reference genome using STAR (v2.7.1a) with the associated gene annotation GTF file. STAR was run in the --quantMode GeneCounts mode to generate gene-level read counts directly during the alignment process. The resulting BAM files were sorted and indexed using Samtools for further inspection. Gene counts from STAR were used for downstream differential expression analysis with DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: nuclear RNA

extract_protocol:
For each of the three replicates, 5x10⁷ cells were incubated with 500 μM 4-thiouridine (Enzo/Jena Bioscience, NU-1156S) for 5 minutes, followed by pelleting and lysis in Trizol (Thermofisher, 15596026).
cDNA synthesis and sequencing library preparation were done using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB E7760), following the protocol for purified mRNA.


title: MELHO_Resistant_MITF_KD_rep3

description: Library name: MELHO_Resistant_MITF_KD_rep3

value: MITF knockdown

value: doxycycline


title: mES-E14-MED1-FKBP-dTAG_Rep2

description: Library name: Sample 14


title: 587T2B_IDH2-WT_SRSF2-WT BS


title: mES-E14-MED1-FKBP-DMSO_Rep2

description: Library name: Sample 12


title: 560T3B_IDH2-WT_SRSF2-Mutant BS


title: 584T3M_IDH2-WT_SRSF2-Mutant BS


title: mES-E14-MED1-FKBP-DMSO_Rep1

description: Library name: Sample 11


title: MELHO_Resistant_MITF_KD_rep2

description: Library name: MELHO_Resistant_MITF_KD_rep2


title: H4_DKO_2M

city: Kansas City

first: Wen-Xing

last: Ding

state: Kansas

address: 3901 Rainbow Blvd.

department: Department of Pharmacology, Toxicology and Therapeutics

institute: University of Kansas Medical Center

description: Library name: H4_DKO_2M

data_processing:
We used HISAT2 v.2.1.0.13 to map the high-quality reads to the mouse reference genome (GRCm38.90). Quantification of the gene expression was generated with HTSeq-counts v0.6.0. Significant differentially expressed genes (DEGs) were generated with the R package DESeq2. Statistical significance was calculated by adjusting the P values with the Benjamini-Hochberg’s false discovery rate (FDR) (Hochberg and Benjamini 1990). The clustered heatmaps of the cGAS-STING pathway genes were plotted with ClustVis (Metsalu and Vilo 2015). Principle component analysis (PCA) and volcano plots were prepared with R. Genes with a log2 fold change >1.5 or <-1.5 with an FDR corrected q value <0.05 were used to perform the analysis.
Assembly: GRCm38.90
Supplementary files format and content: csv file include the FDR between DRP1 KO and TKO group as compared to the WT group.
Supplementary files format and content: xls file include the Ingenuity Pathway Analysis (IPA) results of enriched pathway of up-and down-regulated genes among DRP1 KO vs WT group.

source_name: Liver

extract_protocol:
Total RNA was extracted from mouse livers using TRIzol reagent.  For RNA sequencing analysis, total RNA were assessed for quality using a Qubit assay for quantification and an Agilent TapeStation gel analysis for integrity.
Sequencing libraries were constructed using 1 µg of total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). The sequencing library construction process includes mRNA purification by the polyA tails with polyT magnetic beads, fragmentation, strand-specific cDNA synthesis, end repair, 3’ end adenylation, adapter ligation, and PCR amplification. The constructed sequencing libraries were validated and quantified with Qubit and TapeStation assays. The sequencing library preps were pooled together equally by ng amount and the nM concentration of the pool was verified with an Illumina KAPA Library Quantification qPCR assay (Roche). Each library was indexed with a barcode sequence and sequenced in a multiplexed fashion. An Illumina NextSeq 550 system was used to generate single-end, 75-base sequence reads from the libraries. Base calling was carried out by the instrument’s Real-Time Analysis (RTA) software.  The base call files (bcl files) were demultiplexed and converted to compressed FASTQ files by bcl2fastq2.

value: Liver


title: MELHO_Resistant_MITF_KD_rep1

description: Library name: MELHO_Resistant_MITF_KD_rep1


title: H3_DKO_2M

description: Library name: H3_DKO_2M


title: 85T1M_IDH2-WT_SRSF2-WT BS


title: mES-E14-NANOG-FKBP-dTAG_Rep3

description: Library name: Sample 10

value: Embryo


title: mES-E14-M14-FKBP-DMSO-6h-rep4_T7

description: Library name: Sample 4

value: Mouse embryonic stem cell


title: H2_DKO_2M

description: Library name: H2_DKO_2M


title: 54T1B_IDH2-WT_SRSF2-WT BS


title: H1_DKO_2M

description: Library name: H1_DKO_2M


title: mES-E14-NANOG-FKBP-dTAG_Rep2

description: Library name: Sample 9

value: Endogenous FKBP insert


title: G4_TKO_2M

description: Library name: G4_TKO_2M


title: G3_TKO_2M

description: Library name: G3_TKO_2M


title: mES-E14-NANOG-FKBP-dTAG_Rep1

description: Library name: Sample 8


title: G1_TKO_2M

description: Library name: G1_TKO_2M


title: G2_TKO_2M

description: Library name: G2_TKO_2M


title: F4_Drp1_KO_2M

description: Library name: F4_Drp1_KO_2M


title: UACC257_A264C_DOX_rep2

description: Library name: UACC257_A264C_DOX_rep2


title: 495T1M_IDH2-Mutant_SRSF2-Mutant BS


title: mES-E14-NANOG-FKBP-DMSO_Rep3

description: Library name: Sample 7


title: 523T2B_IDH2-Mutant_SRSF2-Mutant BS


title: F3_Drp1_KO_2M

description: Library name: F3_Drp1_KO_2M


title: F1_Drp1_KO_2M

description: Library name: F1_Drp1_KO_2M


title: 556T2B_IDH2-Mutant_SRSF2-Mutant BS


title: 475T1B_IDH2-WT_SRSF2-Mutant BS


title: mES-E14-M14-FKBP-dTAG-4h-rep1_T7

description: Library name: Sample 9

value: dTAG


title: mES-E14-NANOG-FKBP-DMSO_Rep1

description: Library name: Sample 5


title: E3_Drp1_WT_2M

description: Library name: E3_Drp1_WT_2M


title: F2_Drp1_KO_2M

description: Library name: F2_Drp1_KO_2M


title: mES-E14-MED14-FKBP-dTAG

description: Library name: Sample 4


title: E4_Drp1_WT_2M

description: Library name: E4_Drp1_WT_2M


title: E2_Drp1_WT_2M

description: Library name: E2_Drp1_WT_2M


title: mES-E14-NANOG-FKBP-DMSO_Rep2

description: Library name: Sample 6


title: 543T6B_IDH2-Mutant_SRSF2-WT BS


title: D4_DKO_6M

description: Library name: D4_DKO_6M


title: 364T2M_IDH2-WT_SRSF2-WT BS


title: 316T1B_IDH2-Mutant_SRSF2-Mutant BS


title: D3_DKO_6M

description: Library name: D3_DKO_6M


title: mES-E14-MED14-FKBP-DMSO

description: Library name: Sample 3


title: 287T1M_IDH2-WT_SRSF2-Mutant BS


title: D2_DKO_6M

description: Library name: D2_DKO_6M


title: mES-E14-MED13-FKBP-dTAG

description: Library name: Sample 2


title: mES-E14-MED13-FKBP-DMSO

description: Library name: Sample 1


title: D1_DKO_6M

description: Library name: D1_DKO_6M


title: 283T9B_IDH2-Mutant_SRSF2-Mutant BS


title: C3_TKO_6M

description: Library name: C3_TKO_6M


title: mES-E14-M1-FKBP-dTAG_REP2

description: Library name: Sample 12

data_processing:
Mapping : bowtie2 -x $hg38 -1 ${read1} -2 ${read2} | samtools view -b > ${name}.unsorted.bam Sorting: samtools sort -o ${name}.srt.bam ${name}.unsorted.bam Removing duplicates: samtools rmdup Generating bigwig tracks: deeptools Genome_build: hg38 Supplementary_files_format_and_content: bigWig: bamCoverage --bam ${name}.bam -o ${name}.bw --binSize 10 --normalizeUsing RPKM --minMappingQuality 1
Assembly: mm10
Supplementary files format and content: bw files for each Sample

extract_protocol:
100,000 cells were harvested and centrifuged (500 g, 65 °C, 10 mins). The supernatant was removed, and cell pellet resuspended with 1 X lysis buffer (10 mM Tris HCL, pH 7.5, 10 nM NaCl, 3mM MgCl2, 0.1 % Igepal CA-630). Cells were centrifuged (500 g, 65 °C, 10 mins); the supernatant was removed and the nuclear pellet was incubated for 30 mins at 37 °C in 2 X tagmentation buffer (20 mM Tris-HCl pH 7.5, 10mM MgCl2, 20 % Dimethyl Formamide) with Tn5 transposase (Illumina, 20034197). Tagmented DNA was extracted with the Qiagen DNeasy blood and tissue kit.
Tagmented DNA  waas amplified for sequencing using the NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs) and further purified with the QIAquick PCR Purification Kit (QIAGEN).


title: C2_TKO_6M

description: Library name: C2_TKO_6M


title: C1_TKO_6M

description: Library name: C1_TKO_6M


title: C4_TKO_6M

description: Library name: C4_TKO_6M


title: 247T2Ba_IDH2-Mutant_SRSF2-Mutant BS


title: 603T2M_IDH2-WT_SRSF2-Mutant BS


title: mES-E14-M1-FKBP-DMSO_REP2

description: Library name: Sample 10


title: 247T2Bb_IDH2-Mutant_SRSF2-Mutant BS


title: B3_Drp1_KO_6M

description: Library name: B3_Drp1_KO_6M


title: B2_Drp1_KO_6M

description: Library name: B2_Drp1_KO_6M


title: mES-E14-M1-FKBP-dTAG_REP1

description: Library name: Sample 11


title: B1_Drp1_KO_6M

description: Library name: B1_Drp1_KO_6M


title: mES-E14-M1-FKBP-DMSO_REP1

description: Library name: Sample 9


title: 246T9B_IDH2-Mutant_SRSF2-WT BS


title: B4_Drp1_KO_6M

description: Library name: B4_Drp1_KO_6M


title: A3_Drp1_WT_6M

description: Library name: A3_Drp1_WT_6M


title: 225T15B_IDH2-WT_SRSF2-Mutant BS


title: E1_Drp1_WT_2M

description: Library name: E1_Drp1_WT_2M


title: 234T1B_IDH2-WT_SRSF2-WT BS


title: A2_Drp1_WT_6M

description: Library name: A2_Drp1_WT_6M


title: mES-E14-M14-FKBP-dTAG_REP2

description: Library name: Sample 8


title: A4_Drp1_WT_6M

description: Library name: A4_Drp1_WT_6M


title: A1_Drp1_WT_6M

description: Library name: A1_Drp1_WT_6M


title: mES-E14-M14-FKBP-dTAG_REP1

description: Library name: Sample 7


title: 201T1B_IDH2-Mutant_SRSF2-WT BS


title: Huh7pIL6_RNA-seq_rep4

city: Seoul

first: Sunyoung

last: Jang

state: Not required for this country

address: Cheongpa-ro 47-gil 100 (Cheongpa-dong 2ga), Yongsan-gu, Seoul

country: South Korea

institute: Sookmyung Women's University

data_processing:
Sequenced reads were trimmed for adaptor sequence/low-quality sequence using cutadapt 2.8
Trimmed seuquence reads were mapped to hg19 using STAR (v2.7.4a)
Aligned reads were counted using RSEM (v1.3.3)
Differential expression analysis was performed using DESeq2 R package
Assembly: hg19
Supplementary files format and content: tab-delimited text file included raw counts for each Sample

molecule: cytoplasmic RNA

growth_protocol: Hep3B cells were maintained in DMEM containing 10% FBS and 1% penicillin-streptomycin. Huh7 cells were maintained in RPMI containing 10% FBS and 1% penicillin-streptomycin. Cells were grown in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
According to the manufacturer’s instructions, RNA was extracted from cells using NucleoSpin RNA/Protein kit (Macherey-Nagel GmbH & Co., 740933)
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were treated with IL-6 (100ng/mL) for 24h. Cells treated with UltraPure distilled water served as control.

value: Hepatocellular carcinoma tumor

value: 100ng/mL IL-6


title: Group 4 Humanized Mgat2 mice fed chow. RNASeq performed at the end of the study #16

city: Hamilton

first: Joseph

last: Nickels

state: New Jersey

address: 1000 Waterview Drive

department: Institute of Metabolic Disorders

institute: Genesis Biotechnology Group

description:
Library name: Sample 64
G4-hMGAT2-chow-16_S2

data_processing:
Libraries were sequenced using the NextSeq 550 (Illumina, San Diego, CA, United States) with NextSeq 500/550 High Output Kit v2.5 (2x75 Cycles ) (Illumina, San Diego, CA, United States).  Reads were aligned to the Ensembl Mus mm39 musculus genome using STAR 2.7.  Differential gene expression analysis was performed with DEseq2 (v 1.26.0). Genes with a Benjamini and Hochberg adjusted p ≤ 0.05 (5% False Discovery Rate) were regarded as statistically significantly regulated.  Enrichment analysis of Gene Ontology pathways were performed using the cluster Profiler package for R
Read alignment software STAR2.7
Differential gene expression analysis was performed with DEseq2 (v 1.26.0).
Assembly: reads were assigned to the Ensembl Mus mm39 musculus genome using STAR 2.7
Supplementary files format and content: tab-delimited text file that includes raw counts for each sample

extract_protocol:
Total RNA was isolated from liver tissue with the RNeasy® Mini kit (Qiagen, Germantown, MD). Liver tissue was homogenized in in RLT lysis buffer using a Bullet Blender® 24 Gold (Next Advance, Raymertown, NY).  200-proof (100%) ethyl alcohol (Pharmco by Greenfield Global, Toronto, Canada) was added and homogenized samples were applied to a RNeasy column.   The column was washed with RW1 buffer and subjected to DNase digestion with a RNase-Free DNase Set (Qiagen, Germantown, MD).  RNA was washed again with RNeasy RW1 and RPE buffers. Total RNA was isolated in RNase-free water, quantified using a NanoDrop® ND-1000 spectrophotometer (ThermoFisher Scientific, Waltham, MA), and stored at -80°C.
Cell extracts from 15 mg of liver tissue was used for RNASeq analysis.  RNA quantity was measured using Qubit® (Thermo Scientific, Eugene, OR, United States).  A 4150 TapeStation System was used to determine RNA quality.  An RNA integrity (RIN) score > 7 (10 is maximal) was required for going forward with sequencing.  RNA libraries were prepared using Illumina Stranded Total RNA Prep and the Ribo-Zero™ Plus” kit (Illumina, San Diego, CA, United States).


title: Group 4 Humanized Mgat2 mice fed chow. RNASeq performed at the end of the study #14

description:
Library name: Sample 62
G4-hMGAT2-chow-16_S2


title: mES-E14-M14-FKBP-DMSO_REP2

description: Library name: Sample 6

value: DMSO


title: Huh7pIL6_RNA-seq_rep3


title: Group 4 Humanized Mgat2 mice fed chow. RNASeq performed at the end of the study #13

description:
Library name: Sample 61
G4-hMGAT2-chow-16_S2


title: Group 4 Humanized Mgat2 mice fed chow. RNASeq performed at the end of the study #12

description:
Library name: Sample 60
G4-hMGAT2-chow-15_S14


title: mES-E14-M14-FKBP-DMSO_REP1

description: Library name: Sample 5


title: Group 4 Humanized Mgat2 mice fed chow. RNASeq performed at the end of the study #11

description:
Library name: Sample 59
G4-hMGAT2-chow-15_S14


title: mES-E14-M13-FKBP-dTAG_REP2

description: Library name: Sample 4


title: Huh7pIL6_RNA-seq_rep1


title: Group 4 Humanized Mgat2 mice fed chow. RNASeq performed at the end of the study #9

description:
Library name: Sample 57
G4-hMGAT2-chow-15_S14


title: Group 4 Humanized Mgat2 mice fed chow. RNASeq performed at the end of the study #8

description:
Library name: Sample 56
G4-hMGAT2-chow-14_S5


title: mES-E14-M13-FKBP-dTAG_REP1

description: Library name: Sample 3


title: Group 4 Humanized Mgat2 mice fed chow. RNASeq performed at the end of the study #10

description:
Library name: Sample 58
G4-hMGAT2-chow-15_S14


title: mES-E14-M13-FKBP-DMSO_REP2

description: Library name: Sample 2


title: Group 4 Humanized Mgat2 mice fed chow. RNASeq performed at the end of the study #6

description:
Library name: Sample 54
G4-hMGAT2-chow-14_S5


title: Group 4 Humanized Mgat2 mice fed chow. RNASeq performed at the end of the study #5

description:
Library name: Sample 53
G4-hMGAT2-chow-14_S5


title: mES-E14-M13-FKBP-DMSO_REP1

description: Library name: Sample 1


title: Group 4 Humanized Mgat2 mice fed chow. RNASeq performed at the end of the study #7

description:
Library name: Sample 55
G4-hMGAT2-chow-14_S5


title: Group 4 Humanized Mgat2 mice fed chow. RNASeq performed at the end of the study #4

description:
Library name: Sample 52
G4-hMGAT2-chow-13_S16


title: Huh7nIL6_RNA-seq_rep2

value: UltraPure Distilled Water


title: mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait_6

description:
Library name: Sample 90
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer1_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer2_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer3_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer4_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer5_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer6_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer8_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer9_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer10_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer11_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer12_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer13_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer14_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer15_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer16_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer17_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer18_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer19_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer20_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer21_combined_chimeric.txt

data_processing:
The raw FASTQ file is processed to reconstruct a single read from paired-end sequencing data. These reads are then mapped to the 800bp region surrounding the capture oligonucleotide using the non-stringent aligner BLAT. This step allows the reads to be segmented into ‘slices’ based on their alignment to the sequence around the capture site, enabling the identification of ligation junctions with base-pair precision. After this, the resulting FASTQ file is aligned to the genome using Bowtie.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes contact frequency
Library strategy: Capture-C

extract_protocol:
3C library manufacture was undertaken as described previously(Hamley et al., 2023). In brief, aliquots of 1 x 107 cells were fixed 10 ml media with Formaldehyde, 37% (vol/vol) (Sigma, 47608-250ML) at a final of concentration 2% for 10 minutes at room temperature. This reaction was quenched with 1 M glycine to a final concentration 130 mM and centrifuged (5 min, 300 g). The supernatant was removed, and the cell pellet washed with cold PBS and reconstituted in 1 ml PBS. Cells were permeabilised with Digitonin (Sigma D-141; final concentration of 0.005% wt/vol). Cells were snap frozen and stored at -80 °C. Subsequently, defrosted, permeabilised cells were centrifuged (5 min, 300 g) the supernatant discarded, and resuspended in a reduced calcium content MNase buffer (Tris-HCl pH 7.5 10 mM; CaCl2 1 mM). Cells were split into 3 separate digests to allow titration of MNase (NEB M0247) concentration, which typically ranged from 5 to 20 Kunitz units per reaction. This reaction was incubated for 1 hour at 37 °C in an Eppendorf Thermomixer at 500 rpm and was quenched by adding ethylene glycol-bis(2-aminoethylether)-N,N,N’,N’-tetraacetic acid (EGTA) (Sigma E3889) to a final concentration of 5 mM. To evaluate digestion efficiency, 20% of the reaction was removed. The remaining reaction was centrifuged (5 min, 300 g) and the supernatant containing digestion buffer was discarded. The cell pellet was washed in 1 ml PBS and the cells were resuspended in DNA ligase buffer (Thermo Scientific; final concentrations Tris-HCl pH 7.5 40 mM, MgCl2 10 mM, DTT 10 mM, 5 mM ATP) supplemented with dNTPs (final concentration 400 µM of each of dATP, dCTP, dGTP and dTTP (Thermo Fisher R0191)) and EGTA 5 mM. The reaction mixture was then treated with T4 Polynucleotide Kinase PNK (NEB M0201L) and DNA Polymerase I Large (Klenow) Fragment (NEB M0210L) at final concentrations of 200 U/ml, and 100 U/ml respectively, T4 DNA ligase (Thermo Scientific, High Concentration Ligase (30 U/µl) EL0013) was added to a final concentration of 300 U/ml and the reaction was incubated at 20°C overnight using an Eppendorf Thermomixer at 500 rpm. Chromatin was decrosslinked (proteinase K, 65 °C, >2 hours) and DNA was purified using the Qiagen DNeasy blood and tissue kit (69506). Digestion and ligation efficiencies were assessed using the Agilent Tapestation (D1000 reagents).
Sequencing library preparation. Oligonucleotide capture was performed as previously described(Hamley et al., 2023; Hua et al., 2021a). Initially, 7-10 µg of each 3C library was sonicated to an averagefragment size of 200 bp using a Covaris S220 Focussed Ultrasonicator (3 cycles of 60 seconds, duty cycle 10%, intensity 5, 200 cycles per burst). After sonication, the size of library was evaluated using an Agilent TapeStation (DNA 1000). The sample was then cleaned using Ampure XP beads (Beckman Coulter A63881). To maximise library complexity, three separate aliquots of 2 µg each of the sonicated 3C library were processed simultaneously for the addition of sequencing adaptors (NEB Ultra II (NEB 7645S)) following the standard protocol with the following alternations: 7.5 µl adapter was used in ligation reactions; all Ampure XP bead clean ups were performed at a ratio of 1 : 1.8 and  the final PCR was carried out in triplicate using the Herculase II PCR reagents (Agilent) to enhance DNA yield.

value: WT


title: Group 4 Humanized Mgat2 mice fed chow. RNASeq performed at the end of the study #2

description:
Library name: Sample 50
G4-hMGAT2-chow-13_S16


title: Group 4 Humanized Mgat2 mice fed chow. RNASeq performed at the end of the study #3

description:
Library name: Sample 51
G4-hMGAT2-chow-13_S16


title: Group 4 Humanized Mgat2 mice fed chow. RNASeq performed at the end of the study #15

description:
Library name: Sample 63
G4-hMGAT2-chow-16_S2


title: Group 4 Humanized Mgat2 mice fed chow. RNASeq performed at the end of the study #1

description:
Library name: Sample 49
G4-hMGAT2-chow-13_S16


title: mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait_5

description:
Library name: Sample 89
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer1_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer2_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer3_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer4_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer5_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer6_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer8_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer9_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer10_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer11_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer12_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer13_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer14_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer15_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer16_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer17_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer18_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer19_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer20_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer21_combined_chimeric.txt


title: Group 3 Humanized Mgat2 mice fed a HFD. RNASeq performed at the end of the study #16

description:
Library name: Sample 48
G3-hMGAT2-HFD-12_S6


title: Huh7pIL6_RNA-seq_rep2


title: mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait_4

description:
Library name: Sample 88
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer1_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer2_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer3_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer4_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer5_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer6_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer8_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer9_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer10_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer11_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer12_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer13_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer14_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer15_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer16_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer17_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer18_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer19_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer20_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer21_combined_chimeric.txt


title: Hep3BpIL6_RNA-seq_rep4


title: Group 3 Humanized Mgat2 mice fed a HFD. RNASeq performed at the end of the study #15

description:
Library name: Sample 47
G3-hMGAT2-HFD-12_S6


title: Group 3 Humanized Mgat2 mice fed a HFD. RNASeq performed at the end of the study #14

description:
Library name: Sample 46
G3-hMGAT2-HFD-12_S6


title: mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait_3

description:
Library name: Sample 87
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer1_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer2_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer3_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer4_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer5_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer6_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer8_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer9_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer10_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer11_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer12_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer13_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer14_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer15_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer16_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer17_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer18_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer19_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer20_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer21_combined_chimeric.txt


title: Group 3 Humanized Mgat2 mice fed a HFD. RNASeq performed at the end of the study #13

description:
Library name: Sample 45
G3-hMGAT2-HFD-12_S6


title: Group 3 Humanized Mgat2 mice fed a HFD. RNASeq performed at the end of the study #11

description:
Library name: Sample 43
G3-hMGAT2-HFD-11_S10


title: Group 3 Humanized Mgat2 mice fed a HFD. RNASeq performed at the end of the study #12

description:
Library name: Sample 44
G3-hMGAT2-HFD-11_S10


title: mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait_2

description:
Library name: Sample 86
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer1_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer2_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer3_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer4_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer5_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer6_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer8_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer9_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer10_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer11_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer12_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer13_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer14_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer15_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer16_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer17_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer18_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer19_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer20_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer21_combined_chimeric.txt


title: Group 3 Humanized Mgat2 mice fed a HFD. RNASeq performed at the end of the study #10

description:
Library name: Sample 42
G3-hMGAT2-HFD-11_S10


title: Huh7nIL6_RNA-seq_rep4


title: Hep3BpIL6_RNA-seq_rep3


title: Group 3 Humanized Mgat2 mice fed a HFD. RNASeq performed at the end of the study #9

description:
Library name: Sample 41
G3-hMGAT2-HFD-11_S10


title: Hep3BpIL6_RNA-seq_rep1


title: Group 3 Humanized Mgat2 mice fed a HFD. RNASeq performed at the end of the study #8

description:
Library name: Sample 40
G3-hMGAT2-HFD-10_S1


title: Hep3BnIL6_RNA-seq_rep4


title: Group 3 Humanized Mgat2 mice fed a HFD. RNASeq performed at the end of the study #7

description:
Library name: Sample 39
G3-hMGAT2-HFD-10_S1


title: Huh7nIL6_RNA-seq_rep1


title: Group 3 Humanized Mgat2 mice fed a HFD. RNASeq performed at the end of the study #5

description:
Library name: Sample 37
G3-hMGAT2-HFD-10_S1


title: Hep3BnIL6_RNA-seq_rep3


title: mES-E14-WT-SOX2Bound-EnhancerBait_6

description:
Library name: Sample 84
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer1_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer2_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer3_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer4_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer5_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer6_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer8_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer9_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer10_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer11_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer12_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer13_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer14_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer15_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer16_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer17_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer18_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer19_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer20_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer21_combined_chimeric.txt


title: Group 3 Humanized Mgat2 mice fed a HFD. RNASeq performed at the end of the study #4

description:
Library name: Sample 36
G3-hMGAT2-HFD-9_S12


title: Hep3BnIL6_RNA-seq_rep2


title: Huh7nIL6_RNA-seq_rep3


title: Hep3BpIL6_RNA-seq_rep2


title: Group 3 Humanized Mgat2 mice fed a HFD. RNASeq performed at the end of the study #3

description:
Library name: Sample 35
G3-hMGAT2-HFD-9_S12


title: Group 3 Humanized Mgat2 mice fed a HFD. RNASeq performed at the end of the study #1

description:
Library name: Sample 33
G3-hMGAT2-HFD-9_S12


title: Group 3 Humanized Mgat2 mice fed a HFD. RNASeq performed at the end of the study #2

description:
Library name: Sample 34
G3-hMGAT2-HFD-9_S12


title: Group 2 WT mice fed chow. RNASeq performed at end of the study #16

description:
Library name: Sample 32
G2-WT-chow-8_S15


title: mES-E14-WT-SOX2Bound-EnhancerBait_4

description:
Library name: Sample 82
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer1_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer2_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer3_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer4_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer5_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer6_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer8_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer9_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer10_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer11_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer12_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer13_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer14_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer15_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer16_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer17_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer18_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer19_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer20_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer21_combined_chimeric.txt


title: mES-E14-WT-SOX2Bound-EnhancerBait_3

description:
Library name: Sample 81
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer1_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer2_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer3_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer4_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer5_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer6_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer8_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer9_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer10_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer11_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer12_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer13_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer14_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer15_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer16_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer17_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer18_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer19_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer20_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer21_combined_chimeric.txt


title: Hep3BnIL6_RNA-seq_rep1


title: 2465A-1 (SC)

city: Houston

first: Pavel

last: Sumazin

state: TX

address: 1102 Bates St

department: Pediatric

institute: Baylor College of Medicine

description:
RD_58957
10x Chromium

data_processing:
The resulting scRNA-seq data were analyzed by cellranger v6.0.2 and an anchor-based approach with the Seurat package v4.30.
Assembly: hg19
Supplementary files format and content: A Seurat object as a .RDS file format provided which includes cell count data plus sample's annotation and cluster IDs.

source_name: Bone Marrow

extract_protocol:
Single-cell samples were profiled by  10x chromium Single Cell RNA sequensing.
Single-cell gene expression libraries were prepared according to the Chromium NextGEM Single Cell Gene Expression 3v3.1 kit (10x Genomics). Briefly, single cells, reverse transcription reagents, gel beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single-cell GEMs (Gel Bead-In-Emulsion). Full-length cDNA was synthesized and barcoded within each GEM. Subsequently, GEMs were broken, and cDNA was pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA was amplified by PCR. The amplified product was fragmented prior to end-repair, A-tailing, and adaptor ligation.
PDX samples were flow-sorted, gating for CD45-dim and SSC low cells; 10K–15K cells were then labeled using the 10x Genomics (Pleasanton, CA) Chromium Next GEM Single Cell 3' Kit v3.1 and sequenced at 200 M reads per sample using an Illumina NovaSeq 6000.

value: Bone Marrow

tag: pdx id2

tag: pdx model

value: Saline


title: mES-E14-WT-SOX2Bound-EnhancerBait_5

description:
Library name: Sample 83
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer1_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer2_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer3_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer4_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer5_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer6_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer8_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer9_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer10_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer11_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer12_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer13_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer14_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer15_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer16_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer17_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer18_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer19_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer20_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer21_combined_chimeric.txt


title: 2459-5 (SC)

description:
RD_58956
10x Chromium

value: AraC


title: Group 2 WT mice fed chow. RNASeq performed at end of the study #13

description:
Library name: Sample 29
G2-WT-chow-8_S15


title: Group 2 WT mice fed chow. RNASeq performed at end of the study #14

description:
Library name: Sample 30
G2-WT-chow-8_S15


title: Group 2 WT mice fed chow. RNASeq performed at end of the study #15

description:
Library name: Sample 31
G2-WT-chow-8_S15


title: mES-E14-WT-SOX2Bound-EnhancerBait_1

description:
Library name: Sample 79
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer1_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer2_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer3_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer4_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer5_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer6_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer8_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer9_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer10_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer11_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer12_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer13_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer14_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer15_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer16_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer17_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer18_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer19_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer20_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer21_combined_chimeric.txt


title: mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait_1

description:
Library name: Sample 85
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer1_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer2_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer3_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer4_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer5_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer6_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer8_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer9_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer10_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer11_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer12_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer13_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer14_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer15_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer16_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer17_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer18_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer19_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer20_combined_chimeric.txt
mES-E14-SOX2-FKBP-SOX2Bound-EnhancerBait-Enhancer21_combined_chimeric.txt


title: Group 2 WT mice fed chow. RNASeq performed at end of the study #12

description:
Library name: Sample 28
G2-WT-chow-7_S3


title: Group 2 WT mice fed chow. RNASeq performed at end of the study #11

description:
Library name: Sample 27
G2-WT-chow-7_S3


title: 2451-3 (SC)

description:
RD_58955
10x Chromium


title: mES-E14-SOX2-FKBP-PromoterBait_6

description:
Library name: Sample 78
mES-E14-SOX2-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: Group 2 WT mice fed chow. RNASeq performed at end of the study #10

description:
Library name: Sample 26
G2-WT-chow-7_S3


title: Group 3 Humanized Mgat2 mice fed a HFD. RNASeq performed at the end of the study #6

description:
Library name: Sample 38
G3-hMGAT2-HFD-10_S1


title: 2451-2 (SC)

description:
RD_58954
10x Chromium


title: Group 2 WT mice fed chow. RNASeq performed at end of the study #9

description:
Library name: Sample 25
G2-WT-chow-7_S3


title: mES-E14-SOX2-FKBP-PromoterBait_5

description:
Library name: Sample 77
mES-E14-SOX2-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: Group 2 WT mice fed chow. RNASeq performed at end of the study #8

description:
Library name: Sample 24
G2-WT-chow-6_S9


title: Group 2 WT mice fed chow. RNASeq performed at end of the study #7

description:
Library name: Sample 23
G2-WT-chow-6_S9


title: 2443-2 (SC)

description:
RD_58953
10x Chromium


title: mES-E14-SOX2-FKBP-PromoterBait_4

description:
Library name: Sample 76
mES-E14-SOX2-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: mES-E14-WT-SOX2Bound-EnhancerBait_2

description:
Library name: Sample 80
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer1_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer2_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer3_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer4_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer5_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer6_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer8_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer9_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer10_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer11_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer12_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer13_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer14_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer15_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer16_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer17_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer18_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer19_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer20_combined_chimeric.txt
mES-E14-WT-SOX2Bound-EnhancerBait-Enhancer21_combined_chimeric.txt


title: Group 2 WT mice fed chow. RNASeq performed at end of the study #6

description:
Library name: Sample 22
G2-WT-chow-6_S9


title: 2439-4 (SC)

description:
RD_58952
10x Chromium


title: mES-E14-SOX2-FKBP-PromoterBait_3

description:
Library name: Sample 75
mES-E14-SOX2-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: Group 2 WT mice fed chow. RNASeq performed at end of the study #5

description:
Library name: Sample 21
G2-WT-chow-6_S9


title: M164 (SC)

description:
RD_59311
10x Chromium

value: PATDRZ


title: Group 2 WT mice fed chow. RNASeq performed at end of the study #2

description:
Library name: Sample 18
G2-WT-chow-5_S7


title: mES-E14-SOX2-FKBP-PromoterBait_2

description:
Library name: Sample 74
mES-E14-SOX2-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: M163 (SC)

description:
RD_59310
10x Chromium


title: mES-E14-NANOG-FKBP-PromoterBait_6

description:
Library name: Sample 72
mES-E14-NANOG-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: Group 1 WT mice fed a HFD. RNASeq performed at end of study #16

description:
Library name: Sample 16
G1-WT-HFD-4_S4


title: Group 1 WT mice fed a HFD. RNASeq performed at end of study #14

description:
Library name: Sample 14
G1-WT-HFD-4_S4


title: mES-E14-SOX2-FKBP-PromoterBait_1

description:
Library name: Sample 73
mES-E14-SOX2-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-SOX2-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: Group 2 WT mice fed chow. RNASeq performed at end of the study #3

description:
Library name: Sample 19
G2-WT-chow-5_S7


title: 2465-1 (SC)

description:
RD_59308
10x Chromium

value: PAWLTL


title: Group 1 WT mice fed a HFD. RNASeq performed at end of study #15

description:
Library name: Sample 15
G1-WT-HFD-4_S4


title: Group 1 WT mice fed a HFD. RNASeq performed at end of study #13

description:
Library name: Sample 13
G1-WT-HFD-4_S4


title: 2323-5 (SC)

description:
RD_59307
10x Chromium