title: 8025, Arpc4 KO-1, 75% MatrigelI

description: Library name: Mko1

data_processing:
Raw data was normally provided in FASTQ format. Two FASTQ files were obtained for each sample containing sequences measured from both ends.Most of its base quality scores can reach or exceed Q30.
Trim adapter contaminations and Remove nucleotides with low Quality-score to get Clean data.
RNA-seq reads was mapped by HISAT2
StringTie was applied to assemble the mapped reads
FPKM was applied to measure the expression level of a gene or transcript by StringTie using maximum flow algorithm.
Assembly: Mus_musculus.GCF_000001635.27.genome.fa.
Supplementary files format and content: .xls
Supplementary files format and content: Count matrix, FPKM matrix

extract_protocol:
Total RNA was extracted by adding TRIzol reagent (Thermo Fisher, USA) to the gel after removing the supernatant and dissolving the gel by thorough mixing. Chloroform (Thermo Fisher, USA) was then added, followed by vigorous vortexing for 15 seconds. After incubation at room temperature for 3 minutes, the mixture was centrifuged at 12,000×g for 15 minutes at 4°C. The upper aqueous phase was carefully transferred to a fresh tube, mixed with an equal volume of ≥95% ethanol, and purified using the Monarch Total RNA Miniprep Kit (New England Biolabs, Germany) according to the manufacturer’s protocol. RNA sequencing was performed by Biomarker Technologies(BMKGENE), Münster, Germany.
The concentration of extracted nucleic acid was detected with Nanodrop2000, , and the integrity was detected with Agient2100, LabChip GXPerkin Elmer LabChip GX). (manufacturer and model:Perkin Elmer LabChipGX). VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina NR605 was used to construct the mRNA library and strand-specific mRNA library in strict accordance with the protocol provided by Vazyme. The library preparations were sequenced on the Illumina Novaseq X platform (Illumina, SanDiego, CA) and reads were generated.

treatment_protocol: Transfections were carried out using Lipofectamine 3000 (Thermo Fisher, USA) according to the manufacturer’s protocol. Forty-eight hours post-transfection, green fluorescent cells were sorted via fluorescence-activated cell sorting (FACS) and selected using puromycin (InvivoGen, Toulouse, France) at concentrations of 0.7 mg/mL for 8025 cells. After 5–7 days of puromycin selection, cells were seeded into 96-well plates for clonal expansion. Arpc4 knockout (Arpc4ko) clones were validated via Western blot analysis.The ex vivo microtumor(3D) models were composed of either control or Arpc4 knockout (KO) KC 8025 cells embedded in different matrices containing three condition:25% collagen I, 25% collagen I + 75% Matrigel, and 75% Matrigel for 5 days.

value: primary tumor cell line from KC mice

tag: group


title: primary tumor cell line from KC mice, with mPSC and macrophages, Arpc4 KO-3

status: Public on Dec 21 2025

type: SRA

city: Heidelberg

first: Yina

last: Qiao

country: Germany

institute: Heidelberg University Hospital

description:
Library name: X3_8025_K
X3_8025_K

library_source: transcriptomic

data_processing:
Counts per million normalization and Log2 transformation
Assembly: mm9
Supplementary files format and content: .xlsx
Supplementary files format and content: Count matrix (2D), Log2CPM normalized (3D)

molecule: total RNA

organism: Mus musculus

source_name: pancreas

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 µg/mL streptomycin. Cells were maintained at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted using the Monarch Total RNA Miniprep Kit in accordance with the manufacturer’s protocol. RNA sequencing was performed at the Core Unit Bioinformatics, Medical Faculty, Ulm University.Ex vivo microtumor models were constructed using organoids, mouse primary pancreatic stellate cells (PSCs), and bone marrow-derived macrophages embedded in a matrix consisting of 75% Matrigel, 25% Type I collagen, 5 μg/mL fibronectin, and 2.5 μg/mL vitronectin. Total RNA was extracted by adding TRIzol reagent (Thermo Fisher, USA) to the gel after removing the supernatant and dissolving the gel by thorough mixing. Chloroform (Thermo Fisher, USA) was then added, followed by vigorous vortexing for 15 seconds. After incubation at room temperature for 3 minutes, the mixture was centrifuged at 12,000×g for 15 minutes at 4°C. The upper aqueous phase was carefully transferred to a fresh tube, mixed with an equal volume of ≥95% ethanol, and purified using the Monarch Total RNA Miniprep Kit (New England Biolabs, Germany) according to the manufacturer’s protocol.
200ng of total RNA, measured by Qubit® analysis, was used as input material for library construction using TruSeq RNA Sample Preparation Kit v2 (Illumina). Correct size distribution of the libraries was determined on a DNA1000 ScreenTape® using a Tape Station 4200 (Agilent)

treatment_protocol: Transfections were carried out using Lipofectamine 3000 (Thermo Fisher, USA) according to the manufacturer’s protocol. Forty-eight hours post-transfection, green fluorescent cells were sorted via fluorescence-activated cell sorting (FACS) and selected using puromycin (InvivoGen, Toulouse, France) at concentrations of 0.7 mg/mL for 8025 cells and 1.2 mg/mL for R254 cells. After 5–7 days of puromycin selection, cells were seeded into 96-well plates for clonal expansion. Arpc4 knockout (Arpc4ko) clones were validated via Western blot analysis.

tag: cell line

tag: cell type

value: primary tumor cell line from KP mice

tag: genotype

value: p48Cre/+; LSL-KrasG12D/+

tag: treatment

value: Arpc4 knockout

tag: batch


title: primary tumor cell line from KC mice, with mPSC and macrophages, Arpc4 KO-1

description:
Library name: X1_8025_K
X1_8025_K


title: MCF7_cycling_rep1

city: Jerusalem

first: Rami

last: Aqeilan

address: Ein Kerem

country: Israel

institute: Hebrew University of Jerusalem

description: Library name: MCF7_cycling_rep1

library_source: genomic

data_processing:
Reads are trimmed and filtered with trim_galore and quality is tested with fastqc.
Reads are mapped to the genome with hisat2.
Bam files are de-duplicated with umi_tools dedup (breakome files).
Deduplicated bam files are converted to bed and bedgraph fies with bedtools bamtobed and custom R scripts. Bedgraph files are converetd to bigwig files with UCSC bedGraphToBigWig tool.
Count tables and downstream analysis are performed wih custom R scripts.
ChIP-Seq bigwig file is create with deeptools bamCompare tool.
Assembly: hg38
Supplementary files format and content: tab-delemited text file including raw and density counts per sample, Density is raw divided by gene size multiplied by 1E5.
Supplementary files format and content: Bigwig file including ratio between ChIP-Seq and input.

molecule: genomic DNA

organism: Homo sapiens

source_name: cell line

growth_protocol: MCF7 (HTB-22) and T-47D (HTB-133) cells were grown in RPMI supplemented with 10% (vol/vol) fetal bovine serum FBS (GIBCO), glutamine, and penicillin/streptomycin. HEK-293 (CRL-1573), MDA-MB-468 (HTB-132), MDA-MB-231 (HTB-26), and HeLa cells (CCL-2) were grown in DMEM supplemented with 10% (vol/vol) FBS, glutamine, and penicillin/streptomycin. A-4098 cells (HTB-44) were grown in. EMEM supplemented with 10% FBS, glutamine, and penicillin/streptomycin. SH-SY5Y (CRL-2266) were grown in DMEM/F12 supplemented with 10% FBS, glutamine, and penicillin/streptomycin. HMLE cells were grown in Promocell mammary epithelial cell basal media (C-21010) with added supplements (c-93110) whereas MCF10A were grown on DMEM/F12 supplemented with 5% Horse serum, 20 ng/ml EGF, 0.5 mg/ml Hydrocortisone, 100 ng/ml Cholera toxin, 10 mg/ml Insulin and Pen/Strep. MCF-7 cells were synchronized in the G1 cell cycle stage by culturing in serum-free media for 72 hours followed by replacing the media with 5% FBS media for 5 hours. Cells were grown at 37°C under a humidified atmosphere with 5% CO2. Cells were routinely authenticated by STR profiling, and tested for mycoplasma, and cell aliquots from early passages were used.

extract_protocol:
sBLISS was conducted as previously described33,60. In summary, 106 cells were fixed in 2% paraformaldehyde in 10% FCS/PBS for 10 minutes at room temperature. The fixation was quenched with 125 mM glycine for 5 minutes at room temperature, followed by another 5 minutes on ice and two washes in ice-cold PBS. Cells were lysed for 60 minutes on ice, and their nuclei were permeabilized for 60 minutes at 37°C. Next, nuclei were rinsed twice with CutSmart Buffer containing 0.1% Triton X-100 (CS/TX100), and double-strand break (DSB) ends were blunted in situ using NEB’s Quick Blunting Kit for 60 minutes at room temperature. The blunted nuclei were then washed twice with 1x CS/TX100 before in situ ligation of the sBLISS adapters to the DSB ends. Adaptor ligation was carried out with T4 DNA Ligase for 20-24 hours at 16°C, with BSA and ATP added. Following ligation, the nuclei underwent two washes with 1x CS/TX100, and genomic DNA was extracted using Proteinase K at 55°C for 14-18 hours while shaking at 800 rpm. Proteinase K was then heat-inactivated for 10 minutes at 95°C, followed by extraction using Phenol:Chloroform:Isoamyl Alcohol, Chloroform, and ethanol precipitation. The purified DNA was sonicated in 100 μL of ultra-pure water using Covaris M220 for 60 seconds. Sonicated samples were concentrated with AMPure XP beads (Beckman Coulter), and fragment sizes were evaluated using a BioAnalyzer 2100 (Agilent Technologies), targeting a range of 300 bp to 800 bp with a peak around 400-600 bp. The sonicated DNA was then in vitro transcribed using the MEGAscript T7 Kit for 14 hours at 37°C. After RNA purification and ligation of the 3’-Illumina adaptors, the RNA underwent reverse transcription. The final library indexing and amplification step was performed with NEBNext® Ultra™ II Q5® Master Mix.MCF7 cells (~106) were crosslinked with 1% formaldehyde (methanol free, Thermo Scientific 28906) for 10 min at room temperature and quenched with glycine, 125 mM final concentration. Fixed cells were washed twice in PBS and incubated in sonication buffer (0.5M NaCl, 0.5%SDS RIPA buffer containing PMSF, protease and phosphatase inhibitors) for 30min on ice. Cells were sonicated using Covaris M220 for 10min to produce chromatin fragments of ~200-300 bp. The sheared chromatin was centrifuged 10min at maximum speed. From the supernatant, 50ul were saved as input DNA and the rest was diluted in RIPA buffer without NaCl and SDS. The chromatin was immunoprecipitated by incubation with 5 μg of gamma-H2AX (phospho S139; Abcam, AB2893) antibody pre mixed with 100ul Dynabeads Protein G (ThermoFisher, 10004D) and incubated over-night at 4°C with rotation. Immunoprecipitates were washed twice with RIPA buffer + 150mM NaCl, twice with RIPA buffer + 300 mM NaCl, and twice with TE buffer. The chromatin was eluted from the beads with 200ul of direct elution buffer (10mM Tris pH 8, 0.3M NaCl, 5mM EDTA, 0.5% SDS) and incubated overnight at 65°C to reverse the cross-linking. Samples were treated with RNAse for 1h at 37 °C and with proteinase K at 55 °C for 2 h. DNA was cleaned up by QIAquick PCR purification column (Qiagen), according to the manufacturer’s instructions, and eluted in 30 μl of elution buffer. The ChIPed and the Input DNA were used for real-time PCR or to prepare libraries by Truseq (Ilumina) and sequenced in Nextseq (Illumina).
sBLISS fastq files are initially de-multiplexed using sample barcodes. Quality control is performed with trim galore to eliminate residual adapters, trim reads to a base quality of at least 20, and filter out short reads smaller than 20 bp. Initial and final sample qualities are assessed with fastqc. Quality-processed fastq files are aligned to the GRCh38 assembly with hisat2, then sorted and indexed using samtools. The resulting bam files are de-duplicated with umi-tools, utilizing genomic coordinates and Unique Molecular Identifiers (UMI). Custom Python and R scripts are employed to identify read start positions and convert bam files to bigwig format for downstream analysis. An additional custom R script is used to discard a blacklist of positions, primarily within centromeres.

treatment_protocol: Cells were treated with DMSO (Sigma-Aldrich), dBET6 (Sigma-Aldrich, SML2638), or CDK9i (NVP-2) (MCE, Cat# Y-12214A) 100 nM for 4 hours. Cells were then treated with DMSO or ATMi (20 uM, KU-55933, Sigma) for 5 hours. Transient transfection of siXRCC4 (Dharmacon; SMARTpool siRNA, Catalog ID: L-004494-00-0005) and siSc (Dharmacon; D-00181010) was carried out using Lipofectamine (ThermoFisher). On the day of transfection, cells were seeded to achieve a confluency of 60-70%. The transfection solution was prepared by mixing 1.5 ml of serum and antibiotic-free RPMI with 30 µL of Lipofectamine and incubating for 5 minutes before adding a mixture of 1.5 ml RPMI and 0.6 nmoles of siRNA, followed by a 20-minute incubation at room temperature. This mixture was then added to cells in a 10 cm plate cultured in antibiotic and serum-free media. The media was replaced with fully supplemented media after 5-6 hours, and the cells were incubated in the incubator for 48 hours.

value: cell line


title: NOD mouse, progressor to hyperglycemia, 6 weeks of age, mouse 4 (biol rep 4)

city: Ann Arbor

first: Lonnie

middle: D

last: Shea

state: MI

address: 1600 Huron Parkway

department: Biomedical Engineering

country: USA

institute: University of Michigan

description:
Library name: 6872-JK-4
column name in og_gene_expected_count.annot.csv matches library name

data_processing:
Data processing methods provided by the Advanced Genomics Core at the University of Michigan.
Sequence reads were trimmed using Cutadapt  (Martin, 2011). FastQC (Andrews, 2010) was used to ensure the quality of data and Fastq Screen  (Wingett and Andrews, 2018) was used to screen for various types of contamination.
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR (Dobin et al., 2013) and assigned count estimates to genes with RSEM (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.
Multiqc compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016).
Assembly: GRCm38
Supplementary files format and content: og_gene_expected_count.annot.csv: csv file including gene expected counts for all samples run in the first batch
Supplementary files format and content: vc_gene_expected_count.annot.csv: csv file including gene expected counts for all samples run in the ssecond batch

source_name: scaffold immunological niche

extract_protocol:
Scaffolds were lysed in 800µl TRIzol reagent (Fisher Scientific)) and homogenized at 15000 RPM. The homogenized scaffold solution was centrifuged to pellet any remaining scaffold debris, and the supernatant was taken for RNA isolation. RNA isolation was performed using the Zymo Direct-zol RNA miniprep kit (Fisher Scientific).
RNA libraries were prepared by the Advanced Genomics Core at the University of Michigan using the Illumina ribo depletion assay.

tag: tissue

value: scaffold immunological niche

tag: strain

value: NOD/ShiLtJ

tag: time

value: 6 weeks of age


title: 8025, Arpc4 KO-3, 75% Matrigel

description: Library name: Mko3


title: MCF7_CDK9i_rep2

description: Library name: MCF7_CDK9i_rep2


title: 8025, control-1,75% Matrigel

description: Library name: Mnc1

value: control


title: MCF7_CDK9i_rep1

description: Library name: MCF7_CDK9i_rep1


title: MCF7_cycling_rep2

description: Library name: MCF7_cycling_rep2


title: primary tumor cell line from KC mice, with mPSC and macrophages, control-3

description:
Library name: X3_8025_Ctr
X3_8025_Ctr


title: 8025, control-3,75% Matrigel

description: Library name: Mnc3


title: 8025, Arpc4 KO-3, 25% collagen I + 75% Matrigel

description: Library name: CMko3


title: primary tumor cell line from KC mice, with mPSC and macrophages, control-2

description:
Library name: X2_8025_Ctr
X2_8025_Ctr


title: 8025, Arpc4 KO-2, 25% collagen I + 75% Matrigel

description: Library name: CMko2


title: MCF7_ATMi_ver3

description: Library name: MCF7_ATMi_ver3

value: ATMi


title: 8025, Arpc4 KO-1, 25% collagen  + 75% MatrigelI

description: Library name: CMko1


title: MCF7_ATMi_ver2

description: Library name: MCF7_ATMi_ver2


title: 8025, control-3, 25% collagen I + 75% Matrigel

description: Library name: CMnc3


title: 8025, control-2, 25% collagen I + 75% Matrigel

description: Library name: CMnc2


title: primary tumor cell line from KC mice, with mPSC and macrophages, control-1

description:
Library name: X1_8025_Ctr
X1_8025_Ctr


title: Sham - J16

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

institute: Goethe University Frankfurt

data_processing:
Sequence reads were processed using Qiagen's software CLC Genomics workbench (v21.0.5) with CLC's default settings for RNA-Seq analysis. Reads were aligned to GRCm38 genome. Expression value unit is TPM.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files of feature IDs and TPM normalized feature counts for each sample of all genes

source_name: mouse brain cortex

extract_protocol:
Lesional-perilesional brain tissue was removed (Bregma +0.64 mm to -2.86 mm) and immediately frozen on dry ice. Total RNA was isolated using RNeasy plus micro kit (Qiagen). Quantity of total RNA was assessed with Qubit 2.0 and quality was checked using a RNA 6000 Nano chip on Agilent's bioanalyzer. 200 ng of total RNA was send to Novogene (Cambridge, UK) for library preparation and sequencing.
Barcoded mRNA seq libraries were prepared from 200 ng total RNA. For library preparation at Novogene, the mRNA present in the total RNA sample was isolated with magnetic beads of oligos d(T)25. This method is known as polyA-tailed mRNA enrichment. Subsequently, mRNA was randomly fragmented and cDNA synthesis proceeded through the use of random hexamers and the reverse transcriptase enzyme. Once the synthesis of the first chain was finished, the second chain was synthesized with the addition of an Illumina buffer. With this and together with the presence of dNTPs, RNase H and polymerase I from E.coli, the second chain was obtained by Nick translation. The resulting products went through purification, end-repair, A-tailing and adapter ligation. Fragments of the appropriate size were enriched by PCR, where indexed P5 and P7 primers were introduced, and final products were purified. The library was checked with Qubit 2.0 and real-time PCR for quantification and bioanalyzer Agilent 2100 for size distribution detection. Quantified libraries have been pooled and sequenced on Illumina Novaseq 6000 platform, according to effective library concentration and data amount. Sequencing strategy was paired-end 150 cycles (PE150).

treatment_protocol: PLX3397 (290 mg/kg of food pellets, feeding at libitum, starting 90 min after CCI up to 5 days after TBI) versus anakinra (100 mg/kg s.c.  5 min, 24h, 48h, and 72h after CCI) versus PLX3397+anakinra versus vehicle. The sample size was n = 5 per treatment group. A control group of n = 4 was subjected to sham surgery.

value: sham cortex

tag: age

tag: gender

value: male

value: Sham

tag: time after tbi

value: 5 dpi


title: 8025, Arpc4 KO-2, 75% Matrigel

description: Library name: Mko2


title: 8025, control-1,25% collagen + 75% Matrigel I

description: Library name: CMnc1


title: 8025, Arpc4 KO-2, 25% collagen I

description: Library name: Cko2


title: Sham - J15


title: Sham - J08


title: 8025, Arpc4 KO-3, 25% collagen I

description: Library name: Cko3


title: MCF10A_rep1

description: Library name: MCF10A_rep1


title: 8025, control-2, 25% collagen I

description: Library name: Cnc2


title: 8025, control-2,75% Matrigel

description: Library name: Mnc2


title: Sham - J07


title: 8025, control-3, 25% collagen I

description: Library name: Cnc3


title: 8025, control-1,25% collagen I

description: Library name: Cnc1


title: HMLE_rep4

description: Library name: HMLE_rep4


title: NOD mouse, progressor to hyperglycemia, onset, mouse 10 (biol rep 10)

description:
Library name: 11067-JK-46
column name in vc_gene_expected_count.annot.csv matches library name

value: hyperglycemia onset


title: PLX3397+Anakinra - J17_TBI

value: post TBI cortex


title: NOD mouse, progressor to hyperglycemia, onset, mouse 9 (biol rep 9)

description:
Library name: 11067-JK-45
column name in vc_gene_expected_count.annot.csv matches library name


title: NOD mouse, progressor to hyperglycemia, onset, mouse 7 (biol rep 7)

description:
Library name: 11067-JK-43
column name in vc_gene_expected_count.annot.csv matches library name


title: HMLE_rep3

description: Library name: HMLE_rep3


title: MCF7_ATMi_ver1

description: Library name: MCF7_ATMi_ver1


title: PLX3397+Anakinra - J10_TBI


title: PLX3397+Anakinra - J09_TBI


title: HMLE_rep2

description: Library name: HMLE_rep2


title: HMLE_rep1

description: Library name: HMLE_rep1


title: NOD mouse, progressor to hyperglycemia, 1 weeks before onset, mouse 10 (biol rep 10)

description:
Library name: 11067-JK-41
column name in vc_gene_expected_count.annot.csv matches library name

value: 1 week before onset


title: NOD mouse, progressor to hyperglycemia, 1 weeks before onset, mouse 8 (biol rep 8)

description:
Library name: 11067-JK-39
column name in vc_gene_expected_count.annot.csv matches library name


title: 8025, Arpc4 KO-1, 25% collagen I

description: Library name: Cko1

value: primary tumor cell line from KC mice


title: NOD mouse, progressor to hyperglycemia, 1 weeks before onset, mouse 9 (biol rep 9)

description:
Library name: 11067-JK-40
column name in vc_gene_expected_count.annot.csv matches library name


title: NOD mouse, progressor to hyperglycemia, 1 weeks before onset, mouse 6 (biol rep 6)

description:
Library name: 11067-JK-37
column name in vc_gene_expected_count.annot.csv matches library name


title: NOD mouse, progressor to hyperglycemia, onset, mouse 6 (biol rep 6)

description:
Library name: 11067-JK-42
column name in vc_gene_expected_count.annot.csv matches library name


title: NOD mouse, progressor to hyperglycemia, 1 weeks before onset, mouse 7 (biol rep 7)

description:
Library name: 11067-JK-38
column name in vc_gene_expected_count.annot.csv matches library name


title: MCF10A_rep2

description: Library name: MCF10A_rep2


title: PLX3397+Anakinra - J03_TBI


title: HeLa_siSc_rep2

description: Library name: HeLa_siSc_rep2

value: scrambled siRNA


title: Anakinra - J22_TBI

value: Anakinra


title: NOD mouse, progressor to hyperglycemia, 3 weeks before onset, mouse 9 (biol rep 9)

description:
Library name: 11067-JK-35
column name in vc_gene_expected_count.annot.csv matches library name

value: 3 weeks before onset


title: NOD mouse, progressor to hyperglycemia, 3 weeks before onset, mouse 8 (biol rep 8)

description:
Library name: 11067-JK-34
column name in vc_gene_expected_count.annot.csv matches library name


title: NOD mouse, progressor to hyperglycemia, 3 weeks before onset, mouse 7 (biol rep 7)

description:
Library name: 11067-JK-33
column name in vc_gene_expected_count.annot.csv matches library name


title: PLX3397+Anakinra - J04_TBI


title: NOD mouse, progressor to hyperglycemia, onset, mouse 8 (biol rep 8)

description:
Library name: 11067-JK-44
column name in vc_gene_expected_count.annot.csv matches library name


title: Anakinra - J14_TBI


title: Anakinra - J21_TBI


title: HeLa_siXRCC4_rep1

description: Library name: HeLa_siXRCC4_rep1

value: cell line

value: siXRCC4 siRNA


title: NOD mouse, progressor to hyperglycemia, 5 weeks before onset, mouse 9 (biol rep 9)

description:
Library name: 11067-JK-30
column name in vc_gene_expected_count.annot.csv matches library name

value: scaffold immunological niche

value: NOD/ShiLtJ

value: 5 weeks before onset


title: NOD mouse, progressor to hyperglycemia, 3 weeks before onset, mouse 6 (biol rep 6)

description:
Library name: 11067-JK-32
column name in vc_gene_expected_count.annot.csv matches library name


title: HeLa_siXRCC4_rep2

description: Library name: HeLa_siXRCC4_rep2


title: NOD mouse, progressor to hyperglycemia, 5 weeks before onset, mouse 8 (biol rep 8)

description:
Library name: 11067-JK-29
column name in vc_gene_expected_count.annot.csv matches library name


title: NOD mouse, progressor to hyperglycemia, 5 weeks before onset, mouse 10 (biol rep 10)

description:
Library name: 11067-JK-31
column name in vc_gene_expected_count.annot.csv matches library name


title: HeLa_DMSO_rep3

description: Library name: HeLa_DMSO_rep3

value: DMSO


title: Anakinra - J06_TBI


title: HeLa_DMSO_rep1

description: Library name: HeLa_DMSO_rep1


title: HeLa_DMSO_rep2

description: Library name: HeLa_DMSO_rep2


title: NOD mouse, progressor to hyperglycemia, 7 weeks before onset, mouse 10 (biol rep 8)

description:
Library name: 11067-JK-26
column name in vc_gene_expected_count.annot.csv matches library name

value: 7 weeks before onset


title: NOD mouse, progressor to hyperglycemia, 5 weeks before onset, mouse 7 (biol rep 7)

description:
Library name: 11067-JK-28
column name in vc_gene_expected_count.annot.csv matches library name


title: NOD mouse, progressor to hyperglycemia, 7 weeks before onset, mouse 9 (biol rep 7)

description:
Library name: 11067-JK-25
column name in vc_gene_expected_count.annot.csv matches library name


title: Anakinra - J05_TBI

value: male


title: NOD mouse, progressor to hyperglycemia, 5 weeks before onset, mouse 6 (biol rep 6)

description:
Library name: 11067-JK-27
column name in vc_gene_expected_count.annot.csv matches library name


title: NOD mouse, progressor to hyperglycemia, 3 weeks before onset, mouse 10 (biol rep 10)

description:
Library name: 11067-JK-36
column name in vc_gene_expected_count.annot.csv matches library name


title: NOD mouse, progressor to hyperglycemia, 7 weeks before onset, mouse 7 (biol rep 6)

description:
Library name: 11067-JK-24
column name in vc_gene_expected_count.annot.csv matches library name


title: PLX3397 - J20_TBI


title: HeLa_dBET6_rep3

description: Library name: HeLa_dBET6_rep3


title: NOD mouse, progressor to hyperglycemia, 7 weeks before onset, mouse 6 (biol rep 5)

description:
Library name: 11067-JK-23
column name in vc_gene_expected_count.annot.csv matches library name


title: HeLa_dBET6_rep2

description: Library name: HeLa_dBET6_rep2


title: HeLa_siSc_rep1

description: Library name: HeLa_siSc_rep1


title: PLX3397 - J19_TBI


title: PODO/TERT256 human podocytes, fractal topography, THP-1, rep 3

city: Toronto

first: Milica

last: Radisic

state: Ontario

address: 160 College St

country: Canada

institute: University of Toronto

description: Library name: fractal_THP-1_3

data_processing:
Original image data file from the Illumina high-throughput sequencing platform was transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Raw reads were filtered by: - removing reads with adapter contamination - removing reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%) - removing reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read
Cleaned reads were aligned to the reference human genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads mapped to each gene.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was extracted using the PicoPure RNA extraction and isolation kit (Applied Biosystems).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non strand specific library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on the Illumina NovaSeq X Plus platform with a read length of 2x150 paired-end reads to a depth of 20 million reads in each direction.

value: podocyte

tag: protocol

value: fractal topography


title: NOD mouse, progressor to hyperglycemia, 6 weeks of age, mouse 8 (biol rep 8)

description:
Library name: 11067-JK-20
column name in vc_gene_expected_count.annot.csv matches library name

value: 6 weeks of age


title: PLX3397 - J12_TBI

value: post TBI cortex

value: 5 dpi


title: NOD mouse, progressor to hyperglycemia, 6 weeks of age, mouse 10 (biol rep 10)

description:
Library name: 11067-JK-22
column name in vc_gene_expected_count.annot.csv matches library name


title: NOD mouse, progressor to hyperglycemia, 6 weeks of age, mouse 7 (biol rep 7)

description:
Library name: 11067-JK-19
column name in vc_gene_expected_count.annot.csv matches library name


title: NOD mouse, progressor to hyperglycemia, 6 weeks of age, mouse 9 (biol rep 9)

description:
Library name: 11067-JK-21
column name in vc_gene_expected_count.annot.csv matches library name


title: HeLa_dBET6_rep1

description: Library name: HeLa_dBET6_rep1


title: NOD mouse, progressor to hyperglycemia, 6 weeks of age, mouse 6 (biol rep 6)

description:
Library name: 11067-JK-18
column name in vc_gene_expected_count.annot.csv matches library name


title: PLX3397 - J02_TBI


title: PODO/TERT256 human podocytes, smooth topography, THP-1, rep 3

description: Library name: smooth_THP-1_3

value: smooth topography


title: Vehicle - J19B_TBI

value: Vehicle


title: HeLa_CDK9i_rep3

description: Library name: HeLa_CDK9i_rep3


title: PODO/TERT256 human podocytes, fractal topography, THP-1, rep 2

description: Library name: fractal_THP-1_2


title: PODO/TERT256 human podocytes, smooth topography, THP-1, rep 2

description: Library name: smooth_THP-1_2


title: Vehicle - J18B_TBI


title: NOD mouse, non-progressor to hyperglycemia, 14 weeks of age, mouse 9 (biol rep 9)

description:
Library name: 11067-JK-16
column name in vc_gene_expected_count.annot.csv matches library name

value: 14 weeks of age


title: PODO/TERT256 human podocytes, smooth topography, THP-1, rep 1

description: Library name: smooth_THP-1_1


title: NOD mouse, non-progressor to hyperglycemia, 14 weeks of age, mouse 8 (biol rep 8)

description:
Library name: 11067-JK-15
column name in vc_gene_expected_count.annot.csv matches library name


title: PLX3397 - J01_TBI


title: HeLa_CDK9i_rep2

description: Library name: HeLa_CDK9i_rep2


title: PODO/TERT256 human podocytes, fractal topography, THP-1, rep 1

description: Library name: fractal_THP-1_1


title: HeLa_CDK9i_rep1

description: Library name: HeLa_CDK9i_rep1


title: PODO/TERT256 human podocytes, fractal topography, cytokines, rep 3

description: Library name: fractal_cytokines_3

value: cytokines


title: Vehicle - J20B_TBI


title: HEK_293_rep3

description: Library name: HEK_293_rep3

value: cell line


title: HEK_293_rep2

description: Library name: HEK_293_rep2


title: PODO/TERT256 human podocytes, fractal topography, cytokines, rep 1

description: Library name: fractal_cytokines_1


title: P2

city: Harbin

first: Qiye

last: Le

address: Baojian Subdistrict, Nangang District, Harbin City, Heilongjiang Province

country: China

institute: The Second Affiliated Hospital of Harbin Medical University

description: Library name: sample5

library_source: transcriptomic single cell

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17  to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted. After that, we used STAR v2.6.1a  to map reads to the reference genome GRCh38 (ensembl version 92 annotation). UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1  software, and used to generate expression matrix files for subsequent analysis.
Assembly: mm10
Supplementary files format and content: A compressed package containing all sample MTX format results

molecule: polyA RNA

source_name: Brain

extract_protocol:
Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters.
The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) . Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: Brain


title: P3

description: Library name: sample6


title: NOD mouse, non-progressor to hyperglycemia, 14 weeks of age, mouse 10 (biol rep 10)

description:
Library name: 11067-JK-17
column name in vc_gene_expected_count.annot.csv matches library name

value: scaffold immunological niche


title: NOD mouse, non-progressor to hyperglycemia, 14 weeks of age, mouse 5 (biol rep 5)

description:
Library name: 11067-JK-12
column name in vc_gene_expected_count.annot.csv matches library name

value: NOD/ShiLtJ


title: Vehicle - J17B_TBI


title: HEK_293_rep1

description: Library name: HEK_293_rep1


title: Vehicle - J01B_TBI


title: PODO/TERT256 human podocytes, smooth topography, cytokines, rep 3

description: Library name: smooth_cytokines_3


title: NOD mouse, non-progressor to hyperglycemia, 14 weeks of age, mouse 7 (biol rep 7)

description:
Library name: 11067-JK-14
column name in vc_gene_expected_count.annot.csv matches library name


title: A4098_rep3

description: Library name: A4098_rep3


title: A4098_rep1

description: Library name: A4098_rep1


title: NOD mouse, non-progressor to hyperglycemia, 6 weeks of age, mouse 11 (biol rep 11)

description:
Library name: 11067-JK-11
column name in vc_gene_expected_count.annot.csv matches library name


title: PODO/TERT256 human podocytes, fractal topography, cytokines, rep 2

description: Library name: fractal_cytokines_2


title: PODO/TERT256 human podocytes, smooth topography, cytokines, rep 2

description: Library name: smooth_cytokines_2


title: NOD mouse, non-progressor to hyperglycemia, 14 weeks of age, mouse 6 (biol rep 6)

description:
Library name: 11067-JK-13
column name in vc_gene_expected_count.annot.csv matches library name


title: NOD mouse, non-progressor to hyperglycemia, 6 weeks of age, mouse 10 (biol rep 10)

description:
Library name: 11067-JK-10
column name in vc_gene_expected_count.annot.csv matches library name


title: A4098_rep2

description: Library name: A4098_rep2


title: NK-92 shmiR155HG cells rep1

city: Beijing

first: Yongjie

last: Liu

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology

data_processing:
Raw reads were first aligned to the hg38 reference genome using HISAT2 with default parameters
StringTie (run with the ‘-e’ parameter) joint prepDE.py3 was used to calculate and merge read count information
Only genes with 2 or more samples in the dataset with CPM (Counts per million) > 1 were maintained
Differentially expressed genes were identified using the EdgeR exact-Test (lfc set to log2(1.2)) and p-value less than 0.01 is considered to be significant
Assembly: hg38
Supplementary files format and content: csv

extract_protocol:
Total RNA was isolated from NK-92-shCtrl/shmiR155HG cells stimulated with IL-2 (1000 U/mL) + IL-12 (10 ng/mL) for 12 h using AG RNAex Pro Reagent (Accurate Biotechnology), and the concentration and quantity of RNA was measured using a BioDrop μLite equipment (Biochrom Ltd).
mRNA was isolated by Oligo(dT)-attached magnetic beads and then randomly fragmented in fragmentation buffer. First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers. Adapters were added by incubating to end repair. After RNA-seq libraries were constructed, qualified libraries were uploaded on Illumina NovaSeq 6000 platform for sequencing with read length of PE150.


title: PODO/TERT256 human podocytes, fractal topography, control, rep 3

description: Library name: fractal_control_3

value: control


title: P1

description: Library name: sample4


title: L3

description: Library name: sample3


title: NK-92 shmiR155HG cells rep2


title: L1

description: Library name: sample1


title: NOD mouse, non-progressor to hyperglycemia, 6 weeks of age, mouse 9 (biol rep 9)

description:
Library name: 11067-JK-9
column name in vc_gene_expected_count.annot.csv matches library name


title: NK-92 shCtrl cells rep3

value: shCtrl


title: PODO/TERT256 human podocytes, smooth topography, cytokines, rep 1

description: Library name: smooth_cytokines_1


title: SD_3

city: ZHENGZHOU

first: SHENZHEN

last: HUANG

address: Weiwu Road No. 7

institute: Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital

description:
Library name: L01_OES211295350B
one sample from murine ELG tissue

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: murine ELG tissue

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol. scRNA-seq

value: murine ELG tissue

value: tissue


title: NOD mouse, non-progressor to hyperglycemia, 6 weeks of age, mouse 8 (biol rep 8)

description:
Library name: 11067-JK-8
column name in vc_gene_expected_count.annot.csv matches library name


title: NK-92 shmiR155HG cells rep3


title: SD_2

description:
Library name: L04_OES211294350B
one sample from murine ELG tissue


title: PODO/TERT256 human podocytes, smooth topography, control, rep 3

description: Library name: smooth_control_3

value: podocyte


title: NOD mouse, non-progressor to hyperglycemia, 6 weeks of age, mouse 7 (biol rep 7)

description:
Library name: 11067-JK-7
column name in vc_gene_expected_count.annot.csv matches library name


title: NK-92 shCtrl cells rep2


title: PODO/TERT256 human podocytes, smooth topography, control, rep 2

description: Library name: smooth_control_2


title: PODO/TERT256 human podocytes, fractal topography, control, rep 2

description: Library name: fractal_control_2

value: fractal topography


title: PODO/TERT256 human podocytes, fractal topography, control, rep 1

description: Library name: fractal_control_1


title: L2

description: Library name: sample2


title: SD_1

description:
Library name: L03_OES211293350B
one sample from murine ELG tissue


title: NK-92 shCtrl cells rep1


title: NOD mouse, non-progressor to hyperglycemia, 6 weeks of age, mouse 6 (biol rep 6)

description:
Library name: 11067-JK-6
column name in vc_gene_expected_count.annot.csv matches library name

value: 6 weeks of age


title: GABPb1l/b2 dKO rep2

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

data_processing:
FastQC version 0.11.5 was used to identify features of the raw data that may indicate quality problems
Low quality bases were removed using Trimmomatic version 0.36
Reads were mapped to the mouse reference genome (mm9) with Tophat2 version 2.1.1. and post-processed with RSEM version 1.3.0. Default parameter settings were used for alignment
The uniquely mapped reads were assigned to genes using Htseq version 0.6.1
The fold change and p-value of all the detected genes were estimated by DESeq2 version 1.32.0
Genome_build: mm9
Supplementary_files_format_and_content: txt format. Read counts for each gene, TPM and FPKM for each gene

source_name: CD3e-NK1.1+CD49b+ cells

growth_protocol: NK cells were isolated by cell sorting from Ctrl or GABPb1l/b2 double deficient mice

extract_protocol:
Total RNA was extracted from  NK cells using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
Libraries are constructed according to the standard protocol for Smart-seq2

treatment_protocol: NK cells were sorted with a BD AriaII directly into Trizol reagent

tag: issue

value: Bone marrow

value: 6~8 weeks

tag: cell sorting strategy

value: FACS-sorted


title: NOD mouse, non-progressor to hyperglycemia, 6 weeks of age, mouse 5 (biol rep 5)

description:
Library name: 11067-JK-5
column name in vc_gene_expected_count.annot.csv matches library name


title: NOD mouse, progressor to hyperglycemia, 7 weeks before onset, mouse 4 (biol rep 4)

description:
Library name: 11067-JK-4
column name in vc_gene_expected_count.annot.csv matches library name

value: 7 weeks before onset


title: Flp-In T-REx 293 cells, Flag-HA DIS3, KD cl8, biol rep 2

city: Regensburg

first: Gerhard

last: Lehmann

address: Universitaetsstrasse 31

department: Biochemistry 1

institute: University of Regensburg

data_processing:
Base calling was performed using bcl2fastq v2.20 on NovaSeq output.
Raw reads were trimmed by Trimmomatics (version 0.32, parameters: PE -threads 5 -phred33 ILLUMINACLIP:TruSeq3PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36) to remove adaptors and low quality bases.
Reads aligned to hg38 rDNA sequences (5S, 5.8S,18S, 28S) by Bowtie2 (version 2.3.5, parameters: -p 10 --score-min L,-16,0 --rfg 0,7 --rdg 0,7 --mp 7,7) were also removed.
Remaining reads were used for circRNA quantification by CIRCexplorer3.
Assembly: hg38
Supplementary files format and content: CIRCscores_FPBcirc_Foldchange.xlsx

source_name: Flp-In T-REx 293 cells

growth_protocol: Flp-In T-REx 293 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM; Sigma Aldrich) supplemented with 10% fetal bovine serum (FBS; Gibco) 100 U/mL penicillin, and 100 mg/mL streptomycin (Sigma) under standard condition at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA Kit (Macherey-Nagel)
Libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit (NEB) and NEBNext rRNA Depletion Kit v2 (NEB) according to the manufacturer’s instructions

treatment_protocol: The medium for Flp-In T-Rex 293 cells was further supplemented  with 15 µg/ml blasticidin (Gibco) and 150 µg/ml hygromycin B (Invitrogen).

value: Flp-In T-REx 293 cells

value: human embryonic kidney cells

value: Flag-HA DIS3 integrated + DIS3 KD


title: Flp-In T-REx 293 cells, Flag-HA DIS3, KD cl8, biol rep 1


title: PODO/TERT256 human podocytes, smooth topography, control, rep 1

description: Library name: smooth_control_1

value: smooth topography


title: NOD mouse, progressor to hyperglycemia, 7 weeks before onset, mouse 2 (biol rep 2)

description:
Library name: 11067-JK-2
column name in vc_gene_expected_count.annot.csv matches library name

value: scaffold immunological niche


title: Flp-In T-REx 293 cells, Flag-HA DIS3, control, biol rep 1

value: Flag-HA DIS3 integrated


title: NOD mouse, progressor to hyperglycemia, 7 weeks before onset, mouse 3 (biol rep 3)

description:
Library name: 11067-JK-3
column name in vc_gene_expected_count.annot.csv matches library name

value: NOD/ShiLtJ


title: GABPb1l/b2 dKO rep1


title: Flp-In T-REx 293 cells, Flag-HA DIS3, control, biol rep 2


title: Aerobic_Tumor_Clod

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

description: clodronate injection

data_processing:
Illumina Casava-1.8.2 performed basecalling.
TopHat 2.0.9 with bowtie 0.12.9 aligned sequences to mouse RefSeq genes on the mouse genome (NCBI37/mm9) using parameters --bowtie1 --segment-length 21 --no-coverage-search. Cufflinks-2.2.1 assembles transcripts with parameters -N --compatible-hits-norm. Cuffcompare compared transcript assemblies to annotation.
The expression levels for individual genes or transcripts were measured by RPKM (reads per kilobase per million mapped reads). Cuffdiff was used to identify differentially expressed genes and transcripts with parameters -N --compatible-hits-norm.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Aerobic tumor cells from LLC tumor-bearing mice with Clod injection

growth_protocol: EML cells were maintained in medium containing stem cell factor (SCF). EML cells were grown in IMDM containing 20% FBS and SCF (200 ng/ml, PeproTech).

extract_protocol:
TRIzol (Invitrogen, Carlsbad, CA) or RNeasy RNA isolation kit (Qiagen, Germany) extracted Total RNA.
Sequencing libraries were manually constructed. Epicentre DNA END-Repair kit (Epicentre Biotechnologies, Madison, WI) filled up either end of DNA strands. Taq DNA polymerase (New England Biolabs, Beverly, MA) added a single adenine residue at 3’ ends by under dATP conditions. Quick Ligation kit (Qiagen, Germany) connected Illumina’s adaptor oligomers at both ends of DNA strands. After purified twice, DNA libraries are amplified using Solexa primers (Illumina, San Diego, CA) and Pusion PCR master mix (Thermo Scientific, Hudson, NH).

value: wild type

value: subcutaneous LLC tumor


title: shMTHFD2_Tgfb1_2

status: Public on Dec 20 2025

first: Sangmyung

last: Rhee

state: --None--

address: 84, Heukseok-ro, Dongjak-gu, Seoul, Republic of Korea

institute: Chung-Ang University

description: Library name: MRC5_shMTHFD2_Tgfb1_2

data_processing:
mRNA-Seq reads were aligned using STAR 2.7.1a, with reference indices generated from genome assembly or representative transcript sequences. Transcript assembly, quantification, and differential expression analysis were performed using FPKM values processed in the DESeq2 package (version 1.32.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

source_name: Lung fibroblasts

extract_protocol:
Total RNA was isolated from cells using the RNAiso Plus reagent (#9109; TaKaRa, Tokyo, Japan) according to the manufacturer’s instructions.
Total RNA was extracted from A549 shMock and shDUSP23 tumor cluster cells. RNA quality was assessed using a bioanalyzer (RNA 600 Nano kit; Agilent Technologies, Santa Clara, CA, USA). Library construction was performed using an mRNA-seq Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. High-throughput sequencing was performed using the NovaSeq 6000 platform (Illumina).

treatment_protocol: TGF-b1 4 ng treatment, 24h incubation

value: Lung fibroblasts

value: Human Lung fibroblast cell line

value: MTHFD5 knockdown


title: Aerobic_Tumor_Veh

description: vehicle injection

source_name: Aerobic tumor cells from LLC tumor-bearing mice with Veh injection


title: Ctrl rep2

value: Ctrl


title: Ctrl rep1

value: Bone marrow


title: shMock_control_2

description: Library name: MRC5_shMock_control_2

value: mock

value: control


title: shMock_Tgfb1_1

description: Library name: MRC5_shMock_Tgfb1_1


title: NOD mouse, progressor to hyperglycemia, 7 weeks before onset, mouse 1 (biol rep 1)

description:
Library name: 11067-JK-1
column name in vc_gene_expected_count.annot.csv matches library name

value: 7 weeks before onset


title: shMTHFD2_control_1

description: Library name: MRC5_shMTHFD2_control_1

value: MTHFD2 knockdown


title: shMTHFD2_control_2

description: Library name: MRC5_shMTHFD2_control_2

value: MTHFD3 knockdown


title: v2a_24h_3

city: stanfofd

first: Zhainib

last: Ugokwe

state: ca

address: 318 campus dr e350

department: biology

institute: stanford university

description: Library name: Z18

data_processing:
Raw FASTQ files were quality-checked and trimmed for adapters and low-quality bases using Trim Galore v0.6.7.
Reads were aligned to the human reference genome GRCh38 (GENCODE v39) using STAR v2.7.10a.
Gene-level counts were generated with featureCounts v2.0.4, counting uniquely mapped reads.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: raw counts  excel file and fastq files have been uploaded to FTP. Tab-delimited file includes metadata.

source_name: endothelial cells

growth_protocol: hPSC-derived endothelial cells were maintained in predefined CDM2 media as described in Ang et al. 2022 Cell.

extract_protocol:
RNA was extracted using Qiagen RNAeasy kit.
libraries were prepared by Novogene using NEBNext Ultra II kit (paired-end)

treatment_protocol: the vein-to-artery EC protocol included treating vein and prevein ECs with arterial media for 24 and 48 hours.

value: endothelial cells

value: artery media


title: shMTHFD2_Tgfb1_1

description: Library name: MRC5_shMTHFD2_Tgfb1_1

value: MTHFD4 knockdown


title: v2a_24h_2

description: Library name: Z17


title: v2a_24h_1

description: Library name: Z16


title: shMock_Tgfb1_2

description: Library name: MRC5_shMock_Tgfb1_2


title: v2a_48h_3

description: Library name: Z21


title: shMock_control _1

description: Library name: MRC5_shMock_control_1


title: v2a_48h_2

description: Library name: Z20


title: vEC_1

description: Library name: Z7

value: hPSC-differentiation


title: v2a_48h_1

description: Library name: Z19


title: p2a_48h_2

description: Library name: Z14


title: p2a_48h_1

description: Library name: Z13


title: p2a_24h_3

description: Library name: Z12


title: X998_RO_T_RNA

city: Geneva

first: MELIVOIA

last: RAPTI

address: Rue du Général-Dufour

department: Medicine

country: Switzerland

institute: University of Geneva

description: Library name: X998_RO_T_RNA

data_processing:
Workflow: Nextflow: 22.04.0,  nf-core/rnaseq: 3.8.1
Read trimming: trimgalore: 0.6.7
Transcript expression quantification: salmon: 1.5.2
Summarize expression to genes: bioconductor-tximeta: 1.8.0,  r-base: 4.0.3
Assembly: GRCh38
Supplementary files format and content: tab separated value (TSV) files with gene read counts and TPM from Salmon

source_name: CRC sample

extract_protocol:
RNA was extracted from the intervening sections using the RNAeasy kit (Qiagen, Netherlands) and itsÕ quality and quantity controlled using a tape station (Agilent, Santa Clara, CA, USA).
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat reagents (Illumina, San Diego, USA). Following quality assessment on the Fragment Analyzer (Agilent, Santa Clara, USA), libraries were 100nt paired-end sequenced to a target of 50 million clusters per library on the Illumina NovaSeq 6000 (Illumina, San Diego, USA).

treatment_protocol: Cryosections of the fresh frozen blocks were cut and the first and last sections stained using standard techniques and the tumor content verified by a trained pathologist. Only samples with a tumor cell content of more than 30% were used for further analysis

value: Colon/Rectum

tag: disease state

value: colorectal cancer


title: X993_PO_T_RNA

description: Library name: X993_PO_T_RNA


title: p2a_24h_2

description: Library name: Z11


title: p2a_24h_1

description: Library name: Z10


title: pVEC_3

description: Library name: Z6


title: vEC_3

description: Library name: Z9


title: X979_TR_T_RNA

description: Library name: X979_TR_T_RNA


title: pVEC_2

description: Library name: Z5


title: pVEC_1

description: Library name: Z4


title: aEC_1

description: Library name: Z1


title: X981_TR_T_RNA

description: Library name: X981_TR_T_RNA


title: X970_CO_T_RNA

description: Library name: X970_CO_T_RNA


title: X998_PA_T_RNA

description: Library name: X998_PA_T_RNA


title: aEC_3

description: Library name: Z3


title: X994_WA_T_RNA

description: Library name: X994_WA_T_RNA


title: X962_CA_T_RNA

description: Library name: X962_CA_T_RNA


title: aEC_2

description: Library name: Z2


title: X989_SC_T_RNA

description: Library name: X989_SC_T_RNA


title: X971_CA_T_RNA

description: Library name: X971_CA_T_RNA


title: p2a_48h_3

description: Library name: Z15


title: X960_MO_T_RNA

description: Library name: X960_MO_T_RNA


title: X941_JA_T_RNA

description: Library name: X941_JA_T_RNA


title: X931_VI_T_RNA

description: Library name: X931_VI_T_RNA


title: X983_RA_T_RNA

description: Library name: X983_RA_T_RNA


title: X980_AZ_T_RNA

description: Library name: X980_AZ_T_RNA


title: X922_NE_T_RNA

description: Library name: X922_NE_T_RNA


title: X910_KU_T_RNA

description: Library name: X910_KU_T_RNA


title: X977_D_T_RNA

description: Library name: X977_D_T_RNA


title: X909_BE_T_RNA

description: Library name: X909_BE_T_RNA


title: X975_TO_T_RNA

description: Library name: X975_TO_T_RNA


title: vEC_2

description: Library name: Z8


title: X907_GU_T_RNA

description: Library name: X907_GU_T_RNA


title: X959_ON_T_RNA

description: Library name: X959_ON_T_RNA


title: X933_MO_T_RNA

description: Library name: X933_MO_T_RNA


title: X924_WA_T_RNA

description: Library name: X924_WA_T_RNA


title: X910_HA_T_RNA

description: Library name: X910_HA_T_RNA


title: X893_MO_T_RNA

description: Library name: X893_MO_T_RNA


title: X898_DU_T_RNA

description: Library name: X898_DU_T_RNA


title: X970_SI_T_RNA

description: Library name: X970_SI_T_RNA


title: X884_MO_T_RNA

description: Library name: X884_MO_T_RNA


title: X925_PI_T_RNA

description: Library name: X925_PI_T_RNA


title: X883_NE_T_RNA

description: Library name: X883_NE_T_RNA


title: X908_FA_T_RNA

description: Library name: X908_FA_T_RNA


title: X904_DI_T_RNA

description: Library name: X904_DI_T_RNA


title: X946_TR_T_RNA

description: Library name: X946_TR_T_RNA


title: X903_GI_T_RNA

description: Library name: X903_GI_T_RNA


title: X900_LE_T_RNA

description: Library name: X900_LE_T_RNA


title: X897_SA_T_RNA

description: Library name: X897_SA_T_RNA


title: X986_OT_T_RNA

description: Library name: X986_OT_T_RNA


title: X879_DE_T_RNA

description: Library name: X879_DE_T_RNA


title: X896_PE_T_RNA

description: Library name: X896_PE_T_RNA


title: X856_BR_T_RNA

description: Library name: X856_BR_T_RNA


title: X865_PR_T_RNA

description: Library name: X865_PR_T_RNA


title: X890_BU_T_RNA

description: Library name: X890_BU_T_RNA


title: X903_BE_T_RNA

description: Library name: X903_BE_T_RNA


title: X883_VA_T_RNA

description: Library name: X883_VA_T_RNA


title: X881_MO_T_RNA

description: Library name: X881_MO_T_RNA


title: X881_CH_T_RNA

description: Library name: X881_CH_T_RNA


title: X880_BL_T_RNA

description: Library name: X880_BL_T_RNA


title: X853_BE_T_RNA

description: Library name: X853_BE_T_RNA


title: X836_PU_T_RNA

description: Library name: X836_PU_T_RNA


title: X834_Z_T_RNA

description: Library name: X834_Z_T_RNA


title: X851_BO_T_RNA

description: Library name: X851_BO_T_RNA


title: X829_CA_T_RNA

description: Library name: X829_CA_T_RNA


title: X823_TA_T_RNA

description: Library name: X823_TA_T_RNA


title: X850_SI_T_RNA

description: Library name: X850_SI_T_RNA


title: X819_PA_T_RNA

description: Library name: X819_PA_T_RNA


title: X839_BA_T_RNA

description: Library name: X839_BA_T_RNA


title: X844_AT_T_RNA

description: Library name: X844_AT_T_RNA


title: X822_BA_T_RNA

description: Library name: X822_BA_T_RNA


title: X810_CA_T_RNA

description: Library name: X810_CA_T_RNA


title: X832_GO_T_RNA

description: Library name: X832_GO_T_RNA


title: X852_AL_T_RNA

description: Library name: X852_AL_T_RNA


title: X804_BA_T_RNA

description: Library name: X804_BA_T_RNA


title: X819_TA_T_RNA

description: Library name: X819_TA_T_RNA


title: X846_ME_T_RNA

description: Library name: X846_ME_T_RNA


title: X818_MA_T_RNA

description: Library name: X818_MA_T_RNA


title: X797_GO_T_RNA

description: Library name: X797_GO_T_RNA


title: X798_KI_T_RNA

description: Library name: X798_KI_T_RNA


title: X814_JA_T_RNA

description: Library name: X814_JA_T_RNA


title: X809_EI_T_RNA

description: Library name: X809_EI_T_RNA


title: X878_GL_T_RNA

description: Library name: X878_GL_T_RNA


title: X832_RY_T_RNA

description: Library name: X832_RY_T_RNA


title: X792_GO_T_RNA

description: Library name: X792_GO_T_RNA


title: X808_LE_T_RNA

description: Library name: X808_LE_T_RNA


title: X802_ZA_T_RNA

description: Library name: X802_ZA_T_RNA


title: X817_BE_T_RNA

description: Library name: X817_BE_T_RNA


title: X768_DU_T_RNA

description: Library name: X768_DU_T_RNA


title: X798_TO_T_RNA

description: Library name: X798_TO_T_RNA


title: X766_JA_T_RNA

description: Library name: X766_JA_T_RNA


title: X766_CO_T_RNA

description: Library name: X766_CO_T_RNA


title: X792_DO_T_RNA

description: Library name: X792_DO_T_RNA


title: X795_LE_3_2_0

description: Library name: X795_LE_3_2_0


title: X788_BU_T_RNA

description: Library name: X788_BU_T_RNA


title: X757_CH_T_RNA

description: Library name: X757_CH_T_RNA


title: X758_BO_T_RNA

description: Library name: X758_BO_T_RNA


title: X784_GR_T_RNA

description: Library name: X784_GR_T_RNA


title: X740_SO_T_RNA

description: Library name: X740_SO_T_RNA


title: X776_PR_T_RNA

description: Library name: X776_PR_T_RNA


title: X775_CH_T_RNA

description: Library name: X775_CH_T_RNA


title: X766_HE_T_RNA

description: Library name: X766_HE_T_RNA


title: X773_TU_T_RNA

description: Library name: X773_TU_T_RNA


title: X728_RO_T_RNA

description: Library name: X728_RO_T_RNA


title: X728_JA_T_RNA

description: Library name: X728_JA_T_RNA


title: X725_BL_T_RNA

description: Library name: X725_BL_T_RNA


title: X771_BA_T_RNA

description: Library name: X771_BA_T_RNA


title: X721_ME_T_RNA

description: Library name: X721_ME_T_RNA


title: X717_SA_T_RNA

description: Library name: X717_SA_T_RNA


title: X768_BO_T_RNA

description: Library name: X768_BO_T_RNA


title: X717_FA_T_RNA

description: Library name: X717_FA_T_RNA


title: X716_PI_T_RNA

description: Library name: X716_PI_T_RNA


title: X761_GA_T_RNA

description: Library name: X761_GA_T_RNA


title: X759_GU_T_RNA

description: Library name: X759_GU_T_RNA


title: X762_PO_T_RNA

description: Library name: X762_PO_T_RNA


title: X712_DI_T_RNA

description: Library name: X712_DI_T_RNA


title: X710_DE_T_RNA

description: Library name: X710_DE_T_RNA


title: X793_PU_T_RNA

description: Library name: X793_PU_T_RNA


title: X709_CO_T_RNA

description: Library name: X709_CO_T_RNA


title: X706_AR_T_RNA

description: Library name: X706_AR_T_RNA


title: X723_HE_T_RNA

description: Library name: X723_HE_T_RNA


title: X686_MA_T_RNA

description: Library name: X686_MA_T_RNA


title: X753_PA_T_RNA

description: Library name: X753_PA_T_RNA


title: X754_BE_T_RNA

description: Library name: X754_BE_T_RNA


title: X752_OZ_T_RNA

description: Library name: X752_OZ_T_RNA


title: X664_VI_T_RNA

description: Library name: X664_VI_T_RNA


title: X750_BO_T_RNA

description: Library name: X750_BO_T_RNA


title: X666_PU_T_RNA

description: Library name: X666_PU_T_RNA


title: X749_LE_T_RNA

description: Library name: X749_LE_T_RNA


title: X746_PI_T_RNA

description: Library name: X746_PI_T_RNA


title: X646_RA_T_RNA

description: Library name: X646_RA_T_RNA


title: X737_PU_T_RNA

description: Library name: X737_PU_T_RNA


title: X639_MI_T_RNA

description: Library name: X639_MI_T_RNA


title: X639_MA_T_RNA

description: Library name: X639_MA_T_RNA


title: X737_LA_T_RNA

description: Library name: X737_LA_T_RNA


title: X733_CE_T_RNA

description: Library name: X733_CE_T_RNA


title: X730_RO_T_RNA

description: Library name: X730_RO_T_RNA


title: X726_CA_T_RNA

description: Library name: X726_CA_T_RNA


title: X720_BU_T_RNA

description: Library name: X720_BU_T_RNA


title: X623_GE_T_RNA

description: Library name: X623_GE_T_RNA


title: X623_DA_T_RNA

description: Library name: X623_DA_T_RNA


title: X629_RO_T_RNA

description: Library name: X629_RO_T_RNA


title: X702_DO_T_RNA

description: Library name: X702_DO_T_RNA


title: X681_GO_T_RNA

description: Library name: X681_GO_T_RNA


title: X620_RO_T_RNA

description: Library name: X620_RO_T_RNA


title: X686_CO_T_RNA

description: Library name: X686_CO_T_RNA


title: X679_DE_T_RNA

description: Library name: X679_DE_T_RNA


title: X679_MU_T_RNA

description: Library name: X679_MU_T_RNA


title: X671_RE_T_RNA

description: Library name: X671_RE_T_RNA


title: X671_GR_T_RNA

description: Library name: X671_GR_T_RNA


title: X656_GA_T_RNA_2

description: Library name: X656_GA_T_RNA_2


title: X630_OE_T_RNA

description: Library name: X630_OE_T_RNA


title: X656_CH_T_RNA

description: Library name: X656_CH_T_RNA


title: X587_WE_T_RNA

description: Library name: X587_WE_T_RNA


title: X656_GA_T_RNA_1

description: Library name: X656_GA_T_RNA_1


title: X583_PE_T_RNA

description: Library name: X583_PE_T_RNA


title: X648_DE_T_RNA

description: Library name: X648_DE_T_RNA


title: X654_SC_T_RNA

description: Library name: X654_SC_T_RNA


title: X674_FA_T_RNA

description: Library name: X674_FA_T_RNA


title: X588_VO_T_RNA

description: Library name: X588_VO_T_RNA


title: X582_TO_T_RNA

description: Library name: X582_TO_T_RNA


title: X632_BU_T_RNA

description: Library name: X632_BU_T_RNA


title: X611_ZU_T_RNA

description: Library name: X611_ZU_T_RNA


title: X698_KO_T_RNA

description: Library name: X698_KO_T_RNA


title: X570_MA_T_RNA

description: Library name: X570_MA_T_RNA


title: X582_PE_T_RNA

description: Library name: X582_PE_T_RNA


title: X577_SC_T_RNA

description: Library name: X577_SC_T_RNA


title: X604_DI_T_RNA

description: Library name: X604_DI_T_RNA


title: X561_RO_T_RNA

description: Library name: X561_RO_T_RNA


title: X631_BO_T_RNA

description: Library name: X631_BO_T_RNA


title: X563_KO_T_RNA

description: Library name: X563_KO_T_RNA


title: X561_GA_T_RNA

description: Library name: X561_GA_T_RNA


title: X651_DU_T_RNA

description: Library name: X651_DU_T_RNA


title: X606_OP_T_RNA

description: Library name: X606_OP_T_RNA


title: X604_SI_T_RNA

description: Library name: X604_SI_T_RNA


title: X605_LU_T_RNA

description: Library name: X605_LU_T_RNA


title: X529_MO_T_RNA

description: Library name: X529_MO_T_RNA


title: X530_GE_T_RNA

description: Library name: X530_GE_T_RNA


title: X599_NO_T_RNA

description: Library name: X599_NO_T_RNA


title: X528_RO_T_RNA

description: Library name: X528_RO_T_RNA


title: X522_BO_T_RNA

description: Library name: X522_BO_T_RNA


title: X521_JO_T_RNA

description: Library name: X521_JO_T_RNA


title: X513_PE_T_RNA

description: Library name: X513_PE_T_RNA


title: X509_KL_T_RNA

description: Library name: X509_KL_T_RNA


title: X505_PF_T_RNA

description: Library name: X505_PF_T_RNA


title: X608_DA_T_RNA

description: Library name: X608_DA_T_RNA


title: X500_BR_T_RNA

description: Library name: X500_BR_T_RNA


title: X503_KR_T_RNA

description: Library name: X503_KR_T_RNA


title: X500_BA_T_RNA

description: Library name: X500_BA_T_RNA


title: X492_NO_T_RNA

description: Library name: X492_NO_T_RNA


title: X561_MO_T_RNA

description: Library name: X561_MO_T_RNA


title: X487_SA_T_RNA

description: Library name: X487_SA_T_RNA


title: X465_MA_T_RNA

description: Library name: X465_MA_T_RNA


title: X468_PE_T_RNA

description: Library name: X468_PE_T_RNA


title: X591_CH_T_RNA

description: Library name: X591_CH_T_RNA


title: X544_JA_T_RNA

description: Library name: X544_JA_T_RNA


title: X459_BE_T_RNA

description: Library name: X459_BE_T_RNA


title: X457_HA_T_RNA

description: Library name: X457_HA_T_RNA


title: X541_ST_T_RNA

description: Library name: X541_ST_T_RNA


title: X504_PI_T_RNA

description: Library name: X504_PI_T_RNA


title: X453_DE_1_T_RNA

description: Library name: X453_DE_1_T_RNA


title: X450_HO_T_RNA

description: Library name: X450_HO_T_RNA


title: X488_BA_T_RNA

description: Library name: X488_BA_T_RNA


title: X538_AR_T_RNA

description: Library name: X538_AR_T_RNA


title: X521_PF_T_RNA

description: Library name: X521_PF_T_RNA


title: X534_PI_T_RNA

description: Library name: X534_PI_T_RNA


title: X447_DU_T_RNA

description: Library name: X447_DU_T_RNA


title: X518_AB_T_RNA

description: Library name: X518_AB_T_RNA


title: X508_LI_T_RNA

description: Library name: X508_LI_T_RNA


title: X443_BO_T_2_RNA

description: Library name: X443_BO_T_2_RNA


title: X439_DA_T_RNA

description: Library name: X439_DA_T_RNA


title: X429_VA_T_RNA

description: Library name: X429_VA_T_RNA


title: X547_SI_T_RNA

description: Library name: X547_SI_T_RNA


title: X492_PA_T_RNA

description: Library name: X492_PA_T_RNA


title: X503_KR_T_2_RNA

description: Library name: X503_KR_T_2_RNA


title: X426_ZA_T_RNA

description: Library name: X426_ZA_T_RNA


title: X421_PF_T_RNA

description: Library name: X421_PF_T_RNA


title: X448_RO_T_RNA

description: Library name: X448_RO_T_RNA


title: X412_BA_T_RNA

description: Library name: X412_BA_T_RNA


title: X483_SC_T_RNA

description: Library name: X483_SC_T_RNA


title: X411_LU_T_RNA

description: Library name: X411_LU_T_RNA


title: X462_BO_T_RNA

description: Library name: X462_BO_T_RNA


title: X458_SE_T_RNA

description: Library name: X458_SE_T_RNA


title: X460_RO_T_RNA

description: Library name: X460_RO_T_RNA


title: X454_GI_T_RNA

description: Library name: X454_GI_T_RNA


title: X411_BO_T_RNA

description: Library name: X411_BO_T_RNA


title: X453_DE_2_T_RNA

description: Library name: X453_DE_2_T_RNA


title: X447_ST_T_RNA

description: Library name: X447_ST_T_RNA


title: X397_MA_T_RNA

description: Library name: X397_MA_T_RNA


title: X451_MI_T_RNA

description: Library name: X451_MI_T_RNA


title: X391_HA_T_RNA

description: Library name: X391_HA_T_RNA


title: X390_BE_T_RNA

description: Library name: X390_BE_T_RNA


title: X446_CR_T_RNA

description: Library name: X446_CR_T_RNA


title: X435_LA_T_RNA

description: Library name: X435_LA_T_RNA


title: X443_BO_T_RNA

description: Library name: X443_BO_T_RNA


title: X385_CH_T_RNA

description: Library name: X385_CH_T_RNA


title: X386_HE_T_RNA

description: Library name: X386_HE_T_RNA


title: X382_SC_T_RNA

description: Library name: X382_SC_T_RNA


title: X422_BO_T_RNA

description: Library name: X422_BO_T_RNA


title: X385_RU_T_RNA

description: Library name: X385_RU_T_RNA


title: X428_BA_T_RNA

description: Library name: X428_BA_T_RNA


title: X381_LE_T_RNA

description: Library name: X381_LE_T_RNA


title: X417_BE_T_RNA

description: Library name: X417_BE_T_RNA


title: X339_ME_T_RNA

description: Library name: X339_ME_T_RNA


title: X371_RO_T_RNA

description: Library name: X371_RO_T_RNA


title: 266-6-Cpa1N256K (pMMLV-mCpa1*-3xGS-Myc-IRES-Puro), replicate 3

city: Halle (Saale)

first: Ferdinand

last: Krannich

address: Ernst Grube Street 40

department: Department of Internal Medicine I

institute: Martin Luther University Halle-Wittenberg, University Medicine Halle (Saale)

description:
Library name: A266_6NK3
266-6_all_FPKM.csv

data_processing:
Adapter sequences as well as low quality read ends were clipped off using Cutadapt (v2.8). The processed sequencing reads were aligned to the mouse reference genome (UCSC mm10) using HiSat2. Samtools (v1.10) was used to extract primary alignments and to index the resulting BAM files. FeatureCounts (v2.0.0) was used for summarising gene-mapped reads. ENSEMBL GRCm38 v.100 was used as annotation basis.
Assembly: mm10
Supplementary files format and content: FPKM values for each sample (.csv)

growth_protocol: 266-6 cells (RRID:CVCL_3481), and 266-6 cells stably expressing Cpa1 or Cpa1N256 after ecotropic retroviral infection, were cultured in DMEM supplemented with 10% FCS.

extract_protocol:
Cells were collected for RNAseq analysis after culturing for 24 hours. RNA for RNAseq experiments was isolated using RNeasy Mini Kit (Qiagen, 74106)
Library construction was performed by Novogene (Cambridge, UK).

value: acinar cell line


title: X330_BA_T_RNA

description: Library name: X330_BA_T_RNA


title: X392_BI_T_RNA

description: Library name: X392_BI_T_RNA


title: X413_CO_T_RNA

description: Library name: X413_CO_T_RNA


title: X330_LE_T_RNA

description: Library name: X330_LE_T_RNA


title: X390_SC_RNA_T1

description: Library name: X390_SC_RNA_T1


title: X411_KO_T_RNA

description: Library name: X411_KO_T_RNA


title: X375_BA_T_RNA

description: Library name: X375_BA_T_RNA


title: 266-6-Cpa1N256K (pMMLV-mCpa1*-3xGS-Myc-IRES-Puro), replicate 2

description:
Library name: A266_6NK2
266-6_all_FPKM.csv


title: X390_SC_RNA_T2

description: Library name: X390_SC_RNA_T2


title: Pancreas, Cpa1, VisiumHD

description: Library name: CHPA250619_2

library_source: other

data_processing:
Reads and images were processed using Space Ranger (v3.1.3).
Assembly: mm10
Supplementary files format and content: Space Ranger output (.tar), high resolution (.tiff) and CytAssist (.tif) images.
Library strategy: Spatial Transcriptomics

molecule: other

source_name: Pancreas

extract_protocol:
Pancreata of 8-week-old male Cre and Cpa1 mice were isolated. Mice were euthanized by cervical dislocation, pancreata immediately isolated, rinsed with cold PBS buffer, and processed as described in the histology section. Paraffin blocks were stored at 4°C until further processing. Tissue blocks were incubated on ice bath 20 minutes before sectioning. For each specimen, two sections at 10 µm thickness were cut, and RNA was isolated using Deparaffinization Solution (Qiagen GmbH, 19093), and RNeasy®FFPE Kit for RNA Extraction (Qiagen GmbH, 73504) according to the manufacturer’s protocol. RNA quality was assessed by measuring the percentage of total RNA fragments greater than 200 nucleotides (DV200) with the 2100 Bioanalyzer Instrument using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Inc.; 5067-1511). Cre DV200 was 83%, Cpa1 DV200 48%; 10x Genomics recommended minimum requirement 30%. Next, tissue sections at 5 µm thickness were prepared and placed on poly-L-lysine-coated glass slides (Sigma-Aldrich Co., P0425-72EA) and dried for 30 minutes on a heating plate at 42°C, followed by subjecting to a 42°C dry-incubation in an oven for three hours. Subsequently, the sections were stored at room temperature in a desiccator for 24 hours.
Library preparation process was conducted in accordance with the manufacturer’s protocols (10x Genomics Inc.; Visium HD FFPE Tissue Preparation Handbook, CG000684 and Spatial Gene Expression Reagent Kits User Guide, CG000685), and reagents (Visium HD Spatial Gene Expression Reagent Kit – small, 1000668; and Visium HD Mouse Transcriptome Probes v2 – small, 1000667). In brief, the sections were deparaffinized and H&E stained to assess tissue morphology. For deparaffinization tissue slides were incubated for two-hours at 60°C in an oven, cooled for five minutes at room temperature and deparaffinized by immersing slides twice for 10 minutes in xylene (Sigma-Aldrich, 214736). Next, slides were rehydrated in an ethanol (Fisher Scientific GmbH, 17740239) series consisting of 2 × 100%, 2 × 96%, and 1 × 70% ethanol, with each step lasting three minutes, following incubation in distilled water for 20 seconds. Deparaffinized and rehydrated slides were stained with 1 mL of Gill II hematoxylin solution (Sigma-Aldrich, GHS232) and incubated at room temperature for 30 seconds. Excessive staining solution was removed by immersing the slides in three water beakers. 1 mL of the bluing buffer (Agilent Technologies, Inc., CS70230-2) was added, and slides were incubated for one minute prior to being immersed in a water beaker. Subsequent staining was performed using alcoholic eosin (Sigma-Aldrich, HT110116) by applying 1 ml of eosin for one minute and washing out by immersing the slides in two water beakers. Finally, slides were coverslipped using 85% glycerol (Thermo Scientific Chemicals, 327255000) mounting medium. For imaging Axio Scan Z.1 slide scanner (Carl Zeiss AG) was used, and the area of interest (AOI) was determined. Following the removal of the coverslips, tissue slides were placed in the tissue cassettes (10x Genomics Inc., Visium Tissue Slide Cassette S3, 1000684), and destained to remove residual hematoxylin and eosin. Subsequent to the initial destaining step, samples underwent decrosslinking to enhance the accessibility of probes to target RNA molecules. Then, hybridization was performed using mouse transcriptome specific probes. In the subsequent phase – probe ligation – a ligase was incorporated, resulting in the formation of a ligation product. The cassettes were then maintained at a temperature of 4°C. Visium HD slide (10x Genomics Inc., Visium HD Slide, 1000670) was thawed and prepared prior to the execution of the Visium CytAssist device. Further steps, including probe release and capture, are facilitated within the Visium CytAssist device. Subsequent to being released from the tissue, the ligation products were captured on the Visium slide and extended by the addition of the spatial barcode. The spatially-barcoded ligation products were amplified, followed by SPRIselect cleanup (SPRIselect DNA Size Selection Reagent, Beckman Coulter Inc., B23317). Next, quantitative polymerase chain reaction (qPCR) was performed to establish the sample index PCR cycle number for gene expression libraries. Following amplification, the material was subjected to indexing via sample index PCR, thereby generating library molecules. Subsequent to the cDNA amplification, the libraries were purified using SPRIselect and qualitatively assessed with the 2100 Bioanalyzer Instrument using the High Sensitivity DNA Kit (Agilent Technologies, Inc., 5067-4626). The final libraries were sequenced by Novogene (Munich, Germany) on an Illumina NovaSeq X Plus Series platform in paired-end mode (PE150). Raw data was obtained in FASTQ format.

value: Pancreas

value: Cpa1:N256K/N256K, Kras:wt/wt

tag: Sex

value: male


title: X362_RE_T_RNA

description: Library name: X362_RE_T_RNA


title: X325_LO_T_RNA

description: Library name: X325_LO_T_RNA


title: 266-6-Cpa1N256K (pMMLV-mCpa1*-3xGS-Myc-IRES-Puro), replicate 1

description:
Library name: A266_6NK1
266-6_all_FPKM.csv


title: 266-6-Cpa1 (pMMLV-mCpa1-3xGS-Myc-IRES-Puro), replicate 2

description:
Library name: A266_6wt2
266-6_all_FPKM.csv


title: 266-6-Cpa1 (pMMLV-mCpa1-3xGS-Myc-IRES-Puro), replicate 3

description:
Library name: A266_6wt3
266-6_all_FPKM.csv


title: 266-6-pMMLV-Puro, replicate 3

description:
Library name: A266_6eV3
266-6_all_FPKM.csv


title: X340_WE_T_RNA

description: Library name: X340_WE_T_RNA


title: 266-6-Cpa1 (pMMLV-mCpa1-3xGS-Myc-IRES-Puro), replicate 1

description:
Library name: A266_6wt1
266-6_all_FPKM.csv


title: X351_CA_T_RNA

description: Library name: X351_CA_T_RNA


title: X330_ME_T_RNA

description: Library name: X330_ME_T_RNA


title: 266-6-pMMLV-Puro, replicate 2

description:
Library name: A266_6eV2
266-6_all_FPKM.csv


title: X325_ME_T_RNA

description: Library name: X325_ME_T_RNA


title: X322_FA_T_RNA

description: Library name: X322_FA_T_RNA


title: X326_MA_T_RNA

description: Library name: X326_MA_T_RNA


title: Pancreas, Cre, VisiumHD

description: Library name: CHPA250619_1

value: Cre

value: Kras:wt/wt, p48-cre:ki/wt


title: X323_YE_T_RNA

description: Library name: X323_YE_T_RNA


title: 266-6, replicate 2

description:
Library name: A266_6nV2
266-6_all_FPKM.csv


title: X305_MA_T_RNA

description: Library name: X305_MA_T_RNA


title: 266-6-pMMLV-Puro, replicate 1

description:
Library name: A266_6eV1
266-6_all_FPKM.csv


title: X323_CH_1_1_9

description: Library name: X323_CH_1_1_9


title: X301_CO_T_RNA

description: Library name: X301_CO_T_RNA


title: KCCpa1_240730, 18W

description:
Library name: KIM1_sc240730_1
10X Genomics

data_processing:
FASTQ files were aligned to the reference genome using Cell Ranger (v9.0.0).
Assembly: GRCm39 (2024-A)
Supplementary files format and content: Count matrices of individual samples before quality control (QC) (.h5), integrated count matrix after QC (.csv) and metadata (.csv) are provided.

extract_protocol:
After anaesthetizing the mouse with isoflurane, cardiac perfusion using ice-cold 1X PBS was performed. The pancreas was excised and cut into small pieces in digestion medium containing 1mg/ml or 2mg/ml collagenase P depending upon the hardness of the tissue. The tissue pieces were digested for 20 – 40 minutes at 37°C on MACS rotator. For fibrotic tissue, an additional digestion step of 20 minutes with Accutase was also performed. After each digestion step, the samples were quenched with RPMI + 10% FCS and subjected to centrifugation at 350rcf for 5 minutes at 4°C to obtain a pellet. The pellet was washed with HBSS supplemented with trypsin inhibitor and DNase I. Subsequently, the samples were passed through a 70µm filter followed by 40µm filter and pelleted. The pellet was resuspended in HBSS supplemented with trypsin inhibitor, DNase I and Y-27632 dihydrochloride and kept on ice until further processing. Before loading on Chromium, trypsin inhibtor, DNase I and Y-27632 dihydrochloride was removed.
Library was prepared as per the manufacturer's instructions Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index)

value: 18.4 weeks


title: KC_2407241, 15W

description:
Library name: KIM1_sc2407241_1
10X Genomics

value: KC

value: 14.9 weeks


title: Cre_111709, 8W

description:
Library name: Cre_111709
10X Genomics

value: 8 weeks


title: X299_ME_T_RNA

description: Library name: X299_ME_T_RNA


title: X310_AG_T_RNA

description: Library name: X310_AG_T_RNA


title: X291_CU_T_RNA

description: Library name: X291_CU_T_RNA


title: X296_DE_T_RNA

description: Library name: X296_DE_T_RNA


title: X295_BL_T_RNA

description: Library name: X295_BL_T_RNA


title: 266-6, replicate 3

description:
Library name: A266_6nV3
266-6_all_FPKM.csv


title: X315_PE_T_RNA

description: Library name: X315_PE_T_RNA


title: 266-6, replicate 1

description:
Library name: A266_6nV1
266-6_all_FPKM.csv


title: KCCpa1_105331, 52W

description:
Library name: KCCpa1_105331
10X Genomics

value: 52 weeks


title: X282_WI_T_RNA

description: Library name: X282_WI_T_RNA


title: X305_AK_T_RNA

description: Library name: X305_AK_T_RNA


title: Cpa1_110466, 8W

description:
Library name: Cpa1_110466
10X Genomics


title: X274_BA_T_RNA

description: Library name: X274_BA_T_RNA


title: Wk10 H21792 RPMI 8

city: Tempe

first: Madeline

middle: Gail

last: Andrews

state: AZ

address: 550 E. Orange Street

department: School of Biological and Health Systems Engineering

institute: Arizona State University

description: Library name: Sample 36

data_processing:
Cellranger (v8.0.1) from 10x Genomics was used for data pre-processing. Barcode correction and reference genome alignment (GRCh38) were done using cellranger count with default parameters on fastq files for each organoid sample. (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: Human GRCh38 - 2024-A
Supplementary files format and content: tab-seperated values files and matrix files

extract_protocol:
Organoids were dissociated with a Papain dissociation kit for 60 minutes, spun down at 300g for 5 min, resuspended in 1XPBS + 0.1% BSA, filtered, and counted while verifying single cell dissociation and >90% viability.
Library construction was performed using 10X Genomics Chromium Single Cell 3’ v3.1 kit per manufacturer’s instructions by the Genomics Core Facility at Arizona State University.

tag: time point

value: week 10

tag: media

value: RPMI

tag: glucose

tag: oxygen

value: 8 percent


title: Wk10 H21792 Plasmax 8

description: Library name: Sample 35

tag: cell line

value: Plasmax


title: X299_PY_T_RNA

description: Library name: X299_PY_T_RNA

value: Colon/Rectum


title: X296_RI_T_RNA

description: Library name: X296_RI_T_RNA

value: colorectal cancer


title: Cre_111706, 8W

description:
Library name: Cre_111706
10X Genomics

tag: genotype


title: KCCpa1_105568, 52W

description:
Library name: KCCpa1_105568
10X Genomics

tag: tissue


title: KCCpa1_110467, 8W

description:
Library name: KCCpa1_110467
10X Genomics


title: Cpa1_110463, 8W

description:
Library name: Cpa1_110463
10X Genomics


title: X290_CO_T_RNA

description: Library name: X290_CO_T_RNA


title: Wk10 H21792 Control 8

description: Library name: Sample 33

value: Control

tag: batch


title: Cpa1_110465, 8W

description:
Library name: Cpa1_110465
10X Genomics

value: Pancreas


title: Wk10 H21792 DMEM 20

description: Library name: Sample 30

value: DMEM

value: 20 percent


title: X306_JO_T_RNA

description: Library name: X306_JO_T_RNA


title: E18.5 Emx1-Upf2cKO cortex (Replicate 3)

city: Riverside

first: Sika

last: Zheng

state: CA

address: University Ave 900

department: School of Medicine

institute: University of California, Riverside

description: Library name: KO_3

data_processing:
To process and align the raw bulk RNA-seq reads, we used the Snakemake workflow “preprocessing_RNAseq.smk” provided in SnakeNgs (version 0.2.0) (https://github.com/NaotoKubota/SnakeNgs). Initially, low-quality reads were filtered out using fastp (version 0.23.4). The filtered reads were then aligned to the mouse reference genome (mm10) using STAR (version 2.7.11a), with Ensembl transcript annotations (v102). Quality metrics were collected using Picard (version 3.1.1) (http://broadinstitute.github.io/picard/) and compiled with MultiQC (version 1.25). For PCA and differential expression analysis, Shiba (version 0.4.0) was applied to the aligned reads with default settings, leveraging DESeq2 for statistical testing. Genes with adjusted P value < 0.05 and the absolute log2 fold change greater than 1 were considered DEGs.
Assembly: mm10
Supplementary files format and content: Gene expression values in excel format

source_name: Cortex

extract_protocol:
Mouse cortex samples were collected from E18.5 Emx1-Upf2cKO cortices and proceeded to total RNA extraction. All samples passed the QC test in the bioanalyzer analysis (RIN≥9.0).
RNA-Seq libraries were constructed using Illumina TruSeq Stranded Total RNA LT Sample Prep kits (Illumina, RS-122-2101) according to the manufacturer’s protocol. Briefly, 2 ug total RNA per sample was used for library construction. mRNA was purified and fragmented for first-strand cDNA synthesis. Then, second-strand cDNA synthesis was performed, followed by adenylation of the 3’ ends of the double-stranded DNA fragments to facilitate adaptor ligation with unique index sequences. The libraries were conducted to confirm that the fragment sizes ranged from 200 to 650 bp. Indexed samples were pooled in equal amounts before sequencing. All premade RNA-seq libraries were sequenced using NovaSeq X plus platform by Novogene Corporation Inc., generating >120M reads per sample for subsequent analysis.

value: Cortex

value: Upf2 fl/fl;Emx1-Cre


title: Wk6 H21792 RPMI 8

description: Library name: Sample 28

value: week 6


title: X272_BE_T_RNA

description: Library name: X272_BE_T_RNA


title: Wk6 H21792 Plasmax 8

description: Library name: Sample 27


title: KC_110270, 8W

description:
Library name: KC_110270
10X Genomics

value: KC


title: X268_BU_T_RNA

description: Library name: X268_BU_T_RNA


title: E17.5 Emx1-Upf2cKO cortex

description: Library name: KO

data_processing:
For quantification of unique molecular identifiers (UMIs) in our snRNA-seq reads from control and Emx1-Upf2cKO cortices, we employed the Snakemake workflow "kb-nac.smk" from SnakeNgs (version 0.2.0). This workflow internally executes kb-python, a wrapper of kallisto and bustools, to obtain UMI count matrix. We ran this workflow with mouse genome (mm10) and transcript annotation files that contain the reference Gencode mouse genes. The UMI count matrix was then processed by Scanpy (version 1.9.5). We used Scrublet for cell doublets detection and Harmony for batch-effect correction. Cell types were manually assigned based on the expression level of curated marker genes. Cell clustering was performed by leiden algorithm with default parameters. Cells were embedded using UMAP and PHATE to visualize cell clusters and trajectories. Trajectory inference and pseudotime analysis were performed with STREAM. Differential gene expression analysis between control and KO cells for each cluster was performed using scanpy’s rank_genes_groups function with the “t-test_overestim_var” method.
Assembly: mm10
Supplementary files format and content: UMI count matrix in anndata format

extract_protocol:
Single nuclei were isolated from E17.5 Emx1-Upf2cKO cortex and littermate control according to the 10x Genomics protocol (CG000124). In brief, the cortex tissue was minced on ice in 3 ml chilled lysis medium containing 0.05% Nonidet P40 Substitute for 5 minutes. Then 3 ml chilled HEB medium was added to the lysed cells and mixed 20 times with the fire-polished pipette. Next, the cell debris and clumps were removed by 30 μm MACS SmartStrainer. The nuclei pellet was collected after centrifugation at 500 rcf for 5 min at 4 ºC. Then the isolated nuclei were washed twice with 3 ml Nuclei Wash and Resuspension Buffer (1x PBS with 1% BSA and 0.2 U/μl RNase inhibitor). We resuspended with Nuclei Wash and Resuspension Buffer to get a concentration of 800 nuclei per μl in wild-type and 1200 nuclei per μl in Emx1-Upf2cKO.
The single nuclei solutions were loaded into the single-cell chip with a target recovery of 10k cells in the 10x Genomic Chromium machine. After completing the 10x Genomics program, 100 µL of Gel Bead-in-Emulsions (GEMs) per sample were recovered for GEM-RT incubation. The resulting cDNA was purified, amplified over 12 PCR cycles, and subjected to QC, where samples passed if their fragment sizes fell within the 300–9,000 bp range. For library preparation, 20 µL of cDNA per sample was fragmented, followed by end repair and A-tailing. Adapters were then ligated, and samples underwent 14 additional PCR cycles using unique indices (either from the 10x index plate or custom IDT-synthesized indices). Post-amplification, PCR products were purified and size-selected (300–600 bp), with successful QC confirmation required for sequencing. Finally, libraries of equal mass were pooled for multiplexed sequencing.


title: Wk10 H21792 DMEM 8

description: Library name: Sample 34


title: KC_110266, 8W

description:
Library name: KC_110266
10X Genomics


title: E18.5 Emx1-Upf2cKO cortex (Replicate 2)

description: Library name: KO_2


title: E17.5 control cortex

description: Library name: Ctrl

value: Upf2 fl/+


title: X266_TS_T_RNA

description: Library name: X266_TS_T_RNA


title: Wk10 H21792 Plasmax 20

description: Library name: Sample 31


title: E18.5 Emx1-Upf2cKO cortex (Replicate 4)

description: Library name: KO_4


title: X265_TH_T_RNA

description: Library name: X265_TH_T_RNA


title: X241_SO_T_RNA

description: Library name: X241_SO_T_RNA


title: Wk6 H21792 Plasmax 20

description: Library name: Sample 23


title: Wk10 H21792 Control 20

description: Library name: Sample 29


title: X257_DU_T_RNA

description: Library name: X257_DU_T_RNA


title: E18.5 control cortex (Replicate 4)

description: Library name: Ctrl_4

value: Upf2 fl/fl


title: X254_SA_T_RNA

description: Library name: X254_SA_T_RNA


title: Wk6 H21792 DMEM 8

description: Library name: Sample 26


title: X248_HU_T_RNA

description: Library name: X248_HU_T_RNA


title: E18.5 Emx1-Upf2cKO cortex (Replicate 1)

description: Library name: KO_1


title: Wk10 H21792 RPMI 20

description: Library name: Sample 32


title: Wk10 13234 Plasmax 8

description: Library name: Sample 19


title: X234_WE_T_RNA

description: Library name: X234_WE_T_RNA


title: E18.5 control cortex (Replicate 3)

description: Library name: Ctrl_3


title: Wk6 H21792 DMEM 20

description: Library name: Sample 22


title: Wk10 13234 DMEM 8

description: Library name: Sample 18


title: Wk6 H21792 Control 20

description: Library name: Sample 21


title: Wk6 H21792 Control 8

description: Library name: Sample 25


title: X239_PO_T_RNA

description: Library name: X239_PO_T_RNA


title: Wk10 13234 RPMI 20

description: Library name: Sample 16


title: E18.5 control cortex (Replicate 2)

description: Library name: Ctrl_2


title: Wk10 13234 RPMI 8

description: Library name: Sample 20


title: E18.5 control cortex (Replicate 1)

description: Library name: Ctrl_1


title: Wk10 13234 Plasmax 20

description: Library name: Sample 15


title: X231_BR_T_RNA

description: Library name: X231_BR_T_RNA


title: Wk10 13234 Control 8

description: Library name: Sample 17


title: Wk6 13234 RPMI 8

description: Library name: Sample 12


title: Wk6 H21792 RPMI 20

description: Library name: Sample 24


title: Wk10 13234 DMEM 20

description: Library name: Sample 14


title: Brown adipose tissue, OGTBKO4

city: JiNan

first: luwen

last: li

state: Shandong

address: Shandong University Baotuquan Campus, Baotuquan Subdistrict, Lixia District, Jinan City, Shandong Province, China

institute: Shandong University

description:
Library name: OGTBKO4
OGTBKO

data_processing:
Raw sequencing data were filtered to remove adapter-containing reads and low-quality reads (defined as reads with ≥50% of bases having Qphred ≤ 5).
Clean reads were aligned to the reference genome using HISAT2 (2.0.5) to obtain precise mapping locations of the reads.
Quantitative analysis was performed using the featureCounts (1.5.0-p3) tool from the subread software package.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing FPKM values for each gene and sample.

source_name: Brown adipose tissue

growth_protocol: All mice were maintained at 23°C with standard chow and water. After 8 weeks, mice were induced with gomaxifen. Two months later, brown adipose tissue was collected from the mice for sequencing.

extract_protocol:
RNA is extracted from the tissue, followed by rigorous quality control of the RNA samples. The primary method for quality control is through the Agilent 2100 Bioanalyzer, which precisely assesses RNA integrity.
The library was constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®, strictly following the manufacturer's protocol.

treatment_protocol: Harvest brown adipose tissue from the mouse and carefully remove the surrounding white adipose tissue.

value: Brown adipose tissue

tag: cell type

value: adipocytes

value: OGTBKO

tag: treatment


title: X225_BL_T_RNA

description: Library name: X225_BL_T_RNA


title: Wk6 13234 DMEM 8

description: Library name: Sample 10

value: 8 percent


title: Wk10 13234 Control 20

description: Library name: Sample 13

value: week 10


title: Wk6 13234 Control 8

description: Library name: Sample 9


title: X229_VE_T_RNA

description: Library name: X229_VE_T_RNA

value: Colon/Rectum


title: Brown adipose tissue, WT4

description:
Library name: WT4
WT

value: WT

value: control


title: X214_VA_T_RNA

description: Library name: X214_VA_T_RNA

value: colorectal cancer


title: Brown adipose tissue, OGTBKO3

description:
Library name: OGTBKO3
OGTBKO


title: Wk6 13234 Plasmax 8

description: Library name: Sample 11

value: Plasmax


title: X215_NI_T_RNA

description: Library name: X215_NI_T_RNA


title: Brown adipose tissue, OGTBKO2

description:
Library name: OGTBKO2
OGTBKO


title: X220_AN_T_RNA

description: Library name: X220_AN_T_RNA


title: Brown adipose tissue, OGTBKO1

description:
Library name: OGTBKO1
OGTBKO


title: Wk6 13234 RPMI 20

description: Library name: Sample 8

value: RPMI

value: 20 percent


title: Wk6 13234 Plasmax 20

description: Library name: Sample 7


title: Wk6 H1 Control 20

description: Library name: Sample 1

value: Control


title: X215_BU_T_RNA

description: Library name: X215_BU_T_RNA


title: Brown adipose tissue, WT1

description:
Library name: WT1
WT


title: Donor 5, mNG control

city: Providence

first: Jacob

middle: Andrew

last: Myers

state: RI

address: 171 Meeting St.

institute: Brown University

description: Library name: D5-MNG_S31

data_processing:
Sequencing reads were mapped to the human reference genome (GRCh38 p13) via Hisat2 (v2.1.0).
Quality control on raw sequence data for each sample was performed with FastQC
Gene quantification was done via Feature Counts for raw read counts
Genes differentially expressed between WT and conditional KO and skeletal site were determined using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: GRCh38
Supplementary files format and content: pbNK_NKAR_rawcounts.txt and KLF2_Nkar_rawcounts.txt

source_name: Natural Killer cells

growth_protocol: See SERIES summary or associated publication

extract_protocol:
Qiagen Rneasy Plus Universal
TruSeq Stranded mRNA

value: Natural Killer cells

tag: condition

value: Post-transduction, pre-activation

value: Day 0


title: Donor 5, KLF2-mNG

description: Library name: D5-KLF2_S30

treatment_protocol: See SERIES summary or associated publication


title: Wk6 13234 Control 20

description: Library name: Sample 5

value: week 6


title: Wk10 H1 DMEM 20

description: Library name: Sample 4

value: DMEM


title: Brown adipose tissue, WT3

description:
Library name: WT3
WT

value: Brown adipose tissue

value: adipocytes


title: Wk6 13234 DMEM 20

description: Library name: Sample 6


title: Wk10 H1 Control 20

description: Library name: Sample 3


title: X212_KR_T_RNA

description: Library name: X212_KR_T_RNA


title: X206_CE_T_RNA

description: Library name: X206_CE_T_RNA


title: X211_SC_T_RNA

description: Library name: X211_SC_T_RNA


title: Brown adipose tissue, WT2

description:
Library name: WT2
WT


title: Wk6 H1 DMEM 20

description: Library name: Sample 2


title: Donor 3, mNG control, Isotype control

description: Library name: D3-MNG-ISO_S25

value: Isotype control

value: Day 4


title: E18.5 embryonic BAT, replicate 3

city: Philadelphia

first: Patrick

last: Seale

state: PA

address: 3400 Civic Center Blvd., SCTR 12th Floor

institute: University of Pennsylvania

description: Library name: E18.5_3

data_processing:
Reads were pseudoaligned to the mouse genome (GRCm39), and transcript abundances were quantified using kallisto v0.46.2 with default parameters.
RNA abundances were converted to counts using tximport with the “lengthScaledTPM” option.
Assembly: GRCm39
Supplementary files format and content: CSV file containing estimated counts for each gene, as converted from kallisto-computed abundances using tximport with the "lengthScaledTPM" option.

extract_protocol:
Tissues were lysed in TRIzol (Invitrogen #15596018) using a TissueLyser II (QIAGEN) for 4 minutes at 24 Hz in pre-chilled tube adapters. Total RNA of BAT from E15.5-E18.5 embryos and P0.5 neonates was isolated using TRIzol and purified using PureLink RNA Mini columns (Invitrogen #12183025).
Library preparation with poly(A) selection and Illumina sequencing were completed by Azenta/GENEWIZ.

tag: age

value: wild-type


title: X200_HE_T_RNA_1

description: Library name: X200_HE_T_RNA_1

value: Colon/Rectum


title: X211_BE_T_RNA

description: Library name: X211_BE_T_RNA


title: P0.5 embryonic BAT, replicate 3

description: Library name: P0.5_3


title: Donor 4, mNG control

description: Library name: D4-MNG_S29


title: Donor 2, mNG control, Isotype control

description: Library name: D2-MNG-ISO_S19


title: P0.5 embryonic BAT, replicate 2

description: Library name: P0.5_2


title: Donor 4, KLF2-mNG

description: Library name: D4-KLF2_S28


title: Donor 3, mNG control

description: Library name: D3-MNG_S27


title: E18.5 embryonic BAT, replicate 1

description: Library name: E18.5_1


title: Donor 2, KLF2-mNG, Isotype control

description: Library name: D2-KLF2-ISO_S16


title: Donor 3, mNG control, NKAR

description: Library name: D3-MNG-NKAR_S26

value: NKAR


title: Donor 3, KLF2-mNG

description: Library name: D3-KLF2_S24


title: X202_AM_T_RNA

description: Library name: X202_AM_T_RNA

value: colorectal cancer


title: Donor 3, KLF2-MNG, NKAR

description: Library name: D3-KLF2-NKAR_S23


title: P0.5 embryonic BAT, replicate 1

description: Library name: P0.5_1


title: X200_HE_T_RNA_2

description: Library name: X200_HE_T_RNA_2


title: X195_PI_T_RNA

description: Library name: X195_PI_T_RNA


title: Donor 3, KLF2-mNG, Isotype control

description: Library name: D3-KLF2-ISO_S22


title: Donor 2, mNG control

description: Library name: D2-MNG_S21


title: X191_DE_T_RNA

description: Library name: X191_DE_T_RNA


title: Donor 4, Day 4, Isotype control

description: Library name: Day_4_D4_iso_S160


title: E18.5 embryonic BAT, replicate 2

description: Library name: E18.5_2


title: Donor 2, mNG control, NKAR

description: Library name: D2-MNG-NKAR_S20


title: X200_HE_T_RNA

description: Library name: X200_HE_T_RNA


title: X205_IM_T_RNA

description: Library name: X205_IM_T_RNA


title: E17.5 embryonic BAT, replicate 2

description: Library name: E17.5_2


title: X189_RO_T_RNA

description: Library name: X189_RO_T_RNA


title: Donor 1, mNG control

description: Library name: D1-MNG_S15


title: Donor 4, Day 4, NKAR

description: Library name: Day_4_D4_X_S167


title: E17.5 embryonic BAT, replicate 1

description: Library name: E17.5_1


title: X189_GI_T_RNA

description: Library name: X189_GI_T_RNA


title: Donor 3, Day 4, Isotype control

description: Library name: Day_4_D3_iso_S159


title: Donor 1, mNG control, NKAR

description: Library name: D1-MNG-NKAR_S14


title: Donor 1, KLF2-mNG, NKAR

description: Library name: D1-KLF2-NKAR_S11


title: Donor 1, mNG control, Isotype control

description: Library name: D1-MNG-ISO_S13


title: Donor 2, KLF2-mNG

description: Library name: D2-KLF2_S18


title: Donor 1, KLF2-mNG, Isotype control

description: Library name: D1-KLF2-ISO_S10


title: X192_HU_T_RNA

description: Library name: X192_HU_T_RNA


title: E16.5 embryonic BAT, replicate 3

description: Library name: E16.5_3


title: Donor 1, KLF2-mNG

description: Library name: D1-KLF2_S12


title: Donor 2, KLF2-mNG, NKAR

description: Library name: D2-KLF2-NKAR_S17


title: X196_DE_T_RNA

description: Library name: X196_DE_T_RNA


title: E16.5 embryonic BAT, replicate 2

description: Library name: E16.5_2


title: E16.5 embryonic BAT, replicate 1

description: Library name: E16.5_1


title: Donor 13, Day 4, Isotype control

description: Library name: Day_4_D13_iso_S163


title: E15.5 embryonic BAT, replicate 3

description: Library name: E15.5_3


title: X184_DI_T_RNA

description: Library name: X184_DI_T_RNA


title: Donor 11, Day 4, NKAR

description: Library name: Day_4_D11_X_S169