title: A159V-aPD1-1, RNAseq

description: Library name: A159V-aPD1-1


title: Patient 47_mes68

status: Public on Sep 03 2025

type: RNA

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

country: Italy

institute: Azienda USL- IRCCS di Reggio Emilia

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes68

hyb_protocol: RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol. Each reporter probe provided by the manufacturer was labeled with a propierty flourescent barcode system specific for each transcript.

scan_protocol: Scaning was conducted using the NanoString Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files. The data were normalized using 5 HK genes (DHX16, ERCC3, GPATCH3, GUSB, TMUB2). Raw values are the number of copies of each molecular barcode representative of a specific transcript.
Mean count of negative controls plus two standard deviations was subtracted from each gene count to eliminate negative background. Then normalization on synthetic positive controls was conducted by multiplying the count of each gene for a correction factor. This factor was calculated for each sample as the ratio between the quadratic mean of positive controls counts and the mean of quadratic means in all samples. In order to performed CodeSet Content normalization on housekeeping genes, three reference genes were selected among the forty available in the panel based on the lowest coefficients of variation (CV= ratio between mean counts and standard deviations across all samples). Finally, CodeSet Content normalization was performed by multiplying genes counts for a further correction factor calculated on reference genes as described for positive technical controls. After completion of normalization processes, counts were log2 transformed.

label: Molecular barcode on reporter probe

molecule: total RNA

organism: Homo sapiens

source_name: Diffuse Pleural Mesothelioma

label_protocol: RNA was not labeled, but it was pre-processed following the NanoString manufacturer's protocol.

extract_protocol: Formalin-fixed, paraffin-embedded (FFPE) tumor diagnostic biopsies of Diffuse Pleural Mesothelioma were reviewed by two different pathologists. For RNA purification, five 5um FFPE slides were cut for each tumor. Total RNA was extracted by Maxwell® RSC RNA FFPE kit (Promega). RNA quantity and quality were assessed by NanoDrop2000 (Thermo Fisher Scientific). For samples that reached the quality standards (A260/A280 ≥ 1.7 and A260/A230 ≥ 1.8), we evaluated the expression profile of 770 genes by NanoString using the nCounter PanCancer Immune Profiling Panel (NanoString Technologies).

treatment_protocol: Diagnostic biopsies or surgical pleuroctomy from Diffuse Pleural Mesothelioma patients

tag: gender

value: Male

tag: age

tag: histology

value: biphasic

value: DELETED


title: A159V-IgG-2, RNAseq

type: SRA

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

country: USA

institute: Cincinnati Children's Hospital Research Foundation

description: Library name: A159V-IgG-2

library_source: transcriptomic

data_processing:
Reads were aligned to the mm10 genome to create bam files. Aligned reads were counted with the R library GenomicAlignments function summarizeOverlaps to generate a
reads per gene counts matrix for each sample.
Assembly: mm10
Supplementary files format and content: Tab-separated values, raw counts

organism: Mus musculus

extract_protocol:
Qiagen; RNeasy Micro Kit
Illumina RNA-seq Library Preparation Kit

tag: cell line

tag: cell type

value: adenocarcenoma

tag: genotype

tag: treatment

value: IgG


title: 68G

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description: Library name: RNA_S8112Nr43

data_processing:
Raw sequences were trimmed according to quality using Trimmomatic (Bolger, Lohse, and Usadel 2014) (version 0.39) using the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:20.
Trimmed sequences were mapped to the H. sapiens reference genome provided by ENSEMBL, (grch38) using Hisat2 (Kim, Langmead, and Salzberg 2015) with default parameters.
Optical duplicates were removed using MarkDuplicates tool from GATK (McKenna et al. 2010) package (version 4.2.3.0) with default parameters except OPTICAL_DUPLICATE_PIXEL_DISTANCE set to 12000.
Mapped reads were associated with transcripts from Ensembl GRCh38 genome (version 109) using HTSeq-count (Anders, Pyl, and Huber 2015) (version 0.9.1) with default parameters except –stranded set to “reverse”.
Differentially expressed genes were selected using the DESeq2 package (Love, Huber, and Anders 2014) (version 1.42).
Assembly: grch38
Supplementary files format and content: htseq-count output: tab delimited raw counts

source_name: tumour bladder

extract_protocol:
Total RNA that was isolated from fresh frozen BC tumor and BM tissues using the mirVana™ PARIS™ RNA and Native Protein Purification Kit (Thermo Fisher Scientific, Waltham, MA, USA), following the manufacturer's instructions. Isolated RNA concentration and its purity were assessed by NanoDropTM 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) determining the A260/280 and A260/230 ratios, respectively. RNA integrity number (RIN) and distribution value 200 (DV200) were assessed with an Agilent RNA 6000 Nano Kit on a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). The RNA isolates were stored at -80° C. Next, 10 ng of RNA was used to prepare the RNA libraries.
During the library preparation, rRNA was depleted using KAPA RNA HyperPrep with RiboErase and KAPA Globin Depletion Hybridization Oligos (Roche, Basel, Switzerland). SMART-Seq Stranded Kit (Takara Bio, Kusatsu, Japan) was used for low input RNA quantities. The libraries were sequenced on the NovaSeq 6000 platform (Illumina, San Diego, CA, USA). Depths of 30 million (6Gb) paired-end 100 bp reads were generated for each sample.

tag: tissue

value: tumour bladder

tag: Sex

value: male

tag: Stage

value: TA

tag: grade

value: LOW


title: A159V-IgG-5, RNAseq

description: Library name: A159V-IgG-5


title: WT-aPD1

description:
Library name: WT-aPD1
10x genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Single-cell suspensions were processed through Chromium 10X to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: WT


title: Patient 37_mes55

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes55

value: epithelioid


title: Colon Tumor from injected KPN SI tumor Organoid Rep 3

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

description:
Library name: MGR18210204_S12
Column name in MGR18210204_Raw_counts_matrix.csv

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts

source_name: Colon

growth_protocol: Organoids were grown in advanced DMEM media suplemented with L-glutamine (2mM) HEPES (10mM) Penicillin (100u/ml) Streptomycin (100ug/ml), N2 supplement (1x) B27 supplement (1x) human EGF (50ng/ml) and murine Noggin (100ng/ml). Organoids were passaged up to 3 times a week depending on growth and media was refreshed 3 times a week. Organoids were incubated at 37°C, 5% CO2, 21% O2.

extract_protocol:
For tissues, pieces of tumor or intestinal tissue were sampled from mice, placed in RNAlater and stored at -80°C before extraction. For organoids, confluent organoid samples were grown and a cell pellet was snapped frozen on dry ice. RNA was extracted from samples using the RNeasy Mini Kit (Qiagen) following manufacturer’s instructions. For tissues, homogenisation was done by using Precellys ceramic bead filled tubes in a Precellys Evolution machine (Bertin Instruments). For organoid pellets, cells were dissociated using pipetting in the 1st step of the extraction protocol.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina TruSeq RNA LT kit, then run on an Illumina NextSeq 500 (2x36 cycles, paired end, single index).

value: Colon

tag: sample type

value: Intracolonic tumor

tag: injected organoid_id

value: RKAC13.1e SIT

value: VilCreER KrasG12D/+ p53 fl/fl NotchTg/+

value: Injected SI tumor Organoids

tag: batch


title: 67G

description: Library name: RNA_S8112Nr42

value: Ta


title: Patient 38_mes56

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes56

value: Male


title: Patient 36_mes54

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes54

value: Female


title: Colon Tumor from injected KPN SI tumor Organoid Rep 2

description:
Library name: MGR18210204_S11
Column name in MGR18210204_Raw_counts_matrix.csv


title: A159V-IgG-1, RNAseq

description: Library name: A159V-IgG-1


title: 4G

description: Library name: RNA_S8112Nr4

value: HIGH


title: Colon Tumor from injected KPN SI tumor Organoid Rep 1

description:
Library name: MGR18210204_S10
Column name in MGR18210204_Raw_counts_matrix.csv


title: Patient 35_mes50

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes50


title: CLP+GDF11_3

city: Wenzhou

first: Hongwei

last: Wang

address: No. 322 Nanbaixiang Street

country: China

institute: The First Affiliated Hospital of Wenzhou Medical University

description:
Library name: Sample6
Column name in raw_counts_All_Samples.txt:CLP+GDF11_3

data_processing:
RNA sequencing was conducted on the Illumina NovaSeq 6000 platform.
Raw sequencing reads were processed with fastp (version 0.22.0) to eliminate low-quality reads and adapters.
The resulting clean reads were aligned to the Ensembl mouse reference genome (mm10) using HISAT2.
Read count extraction and normalization were performed using featurecounts
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: kidney

growth_protocol: Eight-week-old C57BL/6J WT mice were housed in a specific pathogen-free environment under controlled conditions (12-hour light or dark cycle, temperature 24±2 ℃, and humidity 40-60%.

extract_protocol:
Total RNA was extracted from fresh mouse kidney tissues using TRIzol reagent. 1.3 ug of total RNA was used for the construction of sequencing libraries.
cDNA libraries were subsequently prepared following the manufacturer’s instructions using the NEBNext UltraTM RNA-seq Library Prep Kit (NEB, USA).

treatment_protocol: The SAKI mouse model was developed using cecal ligation and puncture (CLP) surgery.rGDF11 was dissolved in phosphate-buffered saline (PBS) and administered intraperitoneally to mice post-CLP at the dose of  500 μg/kg. Mice were anesthetized with 2% isoflurane (RWD Life Science, PRC) and euthanized 24 h after the CLP procedure. kidneys were collected for further analysis.

value: kidney

tag: strain

value: cecal ligation and puncture treatment plus recombinant GDF11 (500μg/kg) treatment for 24h


title: 65G

description: Library name: RNA_S8112Nr40

value: tumour bladder


title: Patient 34_mes49

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes49


title: Colon Tumor from injected KPN Liver Met Organoid Rep 6

description:
Library name: MGR18210204_S9
Column name in MGR18210204_Raw_counts_matrix.csv

value: RKAC13.1e LMET

value: Injected Liver Met Organoids


title: Colon Tumor from injected KPN Liver Met Organoid Rep 5

description:
Library name: MGR18210204_S8
Column name in MGR18210204_Raw_counts_matrix.csv


title: Colon Tumor from injected KPN SI tumor Organoid Rep 5

description:
Library name: MGR18210204_S5
Column name in MGR18210204_Raw_counts_matrix.csv

value: RKAC3.2f SIT


title: CLP+GDF11_1

description:
Library name: Sample4
Column name in raw_counts_All_Samples.txt:CLP+GDF11_1

value: WT


title: Colon Tumor from injected KPN SI tumor Organoid Rep 4

description:
Library name: MGR18210204_S4
Column name in MGR18210204_Raw_counts_matrix.csv


title: Patient 39_mes57

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes57

value: epithelioid


title: 69G

description: Library name: RNA_S8112Nr44

value: male

value: TA

value: LOW


title: Patient 33_mes48

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes48

value: biphasic


title: Colon Tumor from injected KPN Liver Met Organoid Rep 4

description:
Library name: MGR18210204_S7
Column name in MGR18210204_Raw_counts_matrix.csv

value: Colon

value: Intracolonic tumor

value: VilCreER KrasG12D/+ p53 fl/fl NotchTg/+


title: 64G

description: Library name: RNA_S8112Nr39


title: CLP_3

description:
Library name: Sample3
Column name in raw_counts_All_Samples.txt:CLP_3

value: cecal ligation and puncture treatment for 24h


title: 62G

description: Library name: RNA_S8112Nr37

value: HIGH


title: Patient 32_mes47

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes47

value: Male


title: CLP_2

description:
Library name: Sample2
Column name in raw_counts_All_Samples.txt:CLP_2

value: kidney


title: CLP+GDF11_2

description:
Library name: Sample5
Column name in raw_counts_All_Samples.txt:CLP+GDF11_2

value: cecal ligation and puncture treatment plus recombinant GDF11 (500μg/kg) treatment for 24h


title: Colon Tumor from injected KPN Liver Met Organoid Rep 3

description:
Library name: MGR18210204_S3
Column name in MGR18210204_Raw_counts_matrix.csv

value: RKAC3.2f LMET


title: 61G

description: Library name: RNA_S8112Nr36

value: tumour bladder


title: Colon Tumor from injected KPN Liver Met Organoid Rep 2

description:
Library name: MGR18210204_S2
Column name in MGR18210204_Raw_counts_matrix.csv

value: Injected Liver Met Organoids


title: Patient 30_mes44

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes44

value: sarcomatoid

value: DELETED


title: CLP_1

description:
Library name: Sample1
Column name in raw_counts_All_Samples.txt:CLP_1

value: WT


title: Patient 29_mes43

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes43


title: 66G

description: Library name: RNA_S8112Nr41

value: male

value: TA


title: Colon Tumor from injected KPN Liver Met Organoid Rep 1

description:
Library name: MGR18210204_S1
Column name in MGR18210204_Raw_counts_matrix.csv

value: RKAC.2f LMET


title: 60MDg

description: Library name: RNA_S8112Nr35

value: Ta


title: Inguinal stromal vascular fraction cells isolated from wild-type mice

city: Los Angeles

first: LI

last: Zhang

state: CA

address: 650 Charles E Young Dr S, A2-237

department: Medicine Cardiology

institute: University of California, Los Angeles

description:
Library name: 4 week WT inguinal
10X Genomics

data_processing:
CellRanger count pipeline v6.1.1
Sequenced reads in FASTQ format were aligned and analyzed via the CellRanger count pipeline v6.1.1 (10X Genomics) using the refdata-gex-GRCm39-2024-A mouse (10X Genomics) reference database under default settings.
Assembly: Mus musculus genome
Supplementary files format and content: Tab separated value files and matrix files

source_name: Stromal vascular fraction cells

extract_protocol:
Stromal vascular fraction (SVF) cells from inguinal (subcutaneous) white adipose tissue were isolated, using a modification of a previously described methodology. Briefly, the inguinal fat was dissected, minced, and digested in 0.1% (w/v) collagenase II solution (Sigma, #C6885) at 37°C for 30 min with gentle agitation. DMEM supplemented with 20% FBS was used to stop the digestion. The digested adipose tissue was filtered through a 100 µm-cell strainer and centrifuged at 500 rpm for 5 min. The pelleted layer included the SVF cells, and blood cells, which were disrupted using Erythrocyte lysis buffer. The remaining SVF cells were washed twice with FACS buffer (5 mm ethylenediaminetetraacetic acid (EDTA) and 2% FBS in Dulbecco’s Phosphate-Buffered Saline (DPBS), pH 7.4).  After dead and imuno cells were removed by DAPI and Cd45 staining using FACS, live SVF cells were sent for scRNA-sequencing.
Library was contructed per 10X Genomics instructions

value: Stromal vascular fraction cells

value: Wild-type


title: 58g

description: Library name: RNA_S8112Nr33


title: Colon Tumor from injected AKPS SI tumor Organoid Rep 3

description:
Library name: MGR18210204_S15
Column name in MGR18210204_Raw_counts_matrix.csv

value: Colon

value: Intracolonic tumor

value: RKAN15.2a SIT

value: VilCreER Apc fl/fl KrasG12D/+ p53 fl/fl Smad4 fl/fl

value: Injected SI tumor Organoids


title: 57g

description: Library name: RNA_S8112Nr32

value: LOW


title: Inguinal stromal vascular fraction cells isolated from Pdgfra-cre mediated Mgp deletion mice

description:
Library name: 4 week Mgp-floxed,Pdcre inguinal
10X Genomics

value: Pd-KO


title: Patient 26_mes39

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes39

value: Male

value: biphasic


title: Patient 31_mes46

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes46

value: Female


title: Colon Tumor from injected AKPS SI tumor Organoid Rep 2

description:
Library name: MGR18210204_S14
Column name in MGR18210204_Raw_counts_matrix.csv


title: Patient 23_mes35

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes35

value: epithelioid

value: WT


title: Patient 27_mes40

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes40


title: Patient 22_mes34

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes34


title: Patient 25_mes38

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes38

value: DELETED


title: 54g

description: Library name: RNA_S8112Nr31

value: tumour bladder

value: male

value: HIGH


title: 46G

description: Library name: RNA_S8112Nr26

value: Ta


title: 51G

description: Library name: RNA_S8112Nr30


title: Apc Organoid from SI tumor Rep 2

description:
Library name: RJR18200309_S20
Column name in RJR18200309_Raw_counts_matrix.csv

source_name: SI

value: SI

value: Organoid from SI tumor

value: vilCreER Apcfl/+


title: AKPT Organoid from SI tumor Rep 4

description:
Library name: RJR18200309_S4
Column name in RJR18200309_Raw_counts_matrix.csv

value: VilCreER Apc fl/fl KRasG12D/+ p53 fl/fl Tgfbr1 fl/fl


title: Colon Tumor from injected AKPS SI tumor Organoid Rep 1

description:
Library name: MGR18210204_S13
Column name in MGR18210204_Raw_counts_matrix.csv

value: Colon

value: Intracolonic tumor

value: RKAN15.2a SIT

value: VilCreER Apc fl/fl KrasG12D/+ p53 fl/fl Smad4 fl/fl

value: Injected SI tumor Organoids


title: Inguinal stromal vascular fraction cells isolated from global Mgp deletion mice

description:
Library name: 4 week Mgp-KO inguinal
10X Genomics

value: Stromal vascular fraction cells

value: Mgp-KO


title: AKPT Primary SI tumor Rep 1

description:
Library name: RJR18200309_S23
Column name in RJR18200309_Raw_counts_matrix.csv

value: Female

value: SI Primary Tumor


title: 6 weeks female mouse immunized intranasally with rVSV_M4, replication 3

city: Xiamen

first: yee

last: chen

state: Fujian

address: Xiangannanlu

department: School of Public Health

institute: Xiamen University

description: Library name: rVSV_M4_12h_3

data_processing:
Sequence reads were trimmed and adaptor removed by using fastp.
Assembly: GRcm39
Supplementary files format and content: tab-delimited txt files include raw count values for each Sample

source_name: lung

extract_protocol:
1. put the tissue block directly into the mortar, add a small amount of liquid nitrogen, grind quickly, wait for the tissue to soften, add a small amount of liquid nitrogen, and then grind until the grinding is complete. Then, add the tissue sample to 1 ml of Trizol at 50-100 mg and transfer it to a centrifuge tube.2. Add chloroform, which accounts for 1/5 of the total volume. Cap the centrifuge tube tightly and shake vigorously for 15 sec and let stand at room temperature for 2-3min. Then centrifuge at 12,000 rpm at 4°C for 10-15 min. Carefully pipette the upper aqueous phase into a new centrifuge tube and add equal volumes of isopropyl alcohol. Mix upside down and leave at room temperature for 10min. Then centrifuge at 12,000 rpm at 4°C for 10 min. Carefully discard the supernatant and add 1 ml of 75% ethanol prepared with DEPC water. Wash the tube cap and wall well and flick the tube bottom, let the pellet float. Centrifuge at 12,000 rpm at 4°C for 3 min, discard supernatant. Leave at room temperature for 2-3min and let dry. Add an appropriate amount of RNase free water (DEPC water), after complete dissolution, take a small amount for testing, and store the rest at -80°C. 3. RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) . RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beverly, USA). Then 3 µL USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent 5400 system（Agilent， USA） and quantified by QPCR (1.5 nM). The qualified libraries were pooled and sequenced on Illumina platforms with PE150 strategy in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to effective library concentration and data amount required.

value: lung


title: 48g

description: Library name: RNA_S8112Nr28

value: tumour bladder

value: male

value: Ta(m)

value: LOW


title: 6 weeks female mouse immunized intranasally with PBS, replication 3

description: Library name: PBS_3


title: 6 weeks female mouse immunized intranasally with PBS, replication 2

description: Library name: PBS_2


title: 47s

description: Library name: RNA_S8112Nr27

value: HIGH


title: 6 weeks female mouse immunized intranasally with rVSV_M4, replication 2

description: Library name: rVSV_M4_12h_2


title: 49g

description: Library name: RNA_S8112Nr29

value: Ta


title: Apc Organoid from SI tumor Rep 1

description:
Library name: RJR18200309_S19
Column name in RJR18200309_Raw_counts_matrix.csv

value: SI

value: Organoid from SI tumor

value: vilCreER Apcfl/+


title: 6 weeks female mouse immunized intranasally with rVSV_M4, replication 1

description: Library name: rVSV_M4_12h_1


title: Patient 28_mes41

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes41

value: Male

value: epithelioid

value: WT


title: Patient 24_mes37

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes37


title: 6 weeks female mouse immunized intranasally with PBS, replication 1

description: Library name: PBS_1


title: AKPT Primary SI tumor Rep 2

description:
Library name: RJR18200309_S24
Column name in RJR18200309_Raw_counts_matrix.csv

value: VilCreER Apc fl/fl KRasG12D/+ p53 fl/fl Tgfbr1 fl/fl


title: 41g

description: Library name: RNA_S8112Nr25


title: Patient 20_mes31

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes31

value: biphasic

value: DELETED


title: AKPT Organoid from SI tumor Rep 2

description:
Library name: RJR18200309_S2
Column name in RJR18200309_Raw_counts_matrix.csv


title: 6 weeks female mouse immunized intranasally with rVSV_M2,replication 3

description: Library name: rVSV_M2_12h_3


title: 40g

description: Library name: RNA_S8112Nr24


title: 37g

description: Library name: RNA_S8112Nr23

value: TA


title: 6 weeks female mouse immunized intranasally with rVSV_M2, replication 1

description: Library name: rVSV_M2_12h_1

value: lung


title: Patient 17_mes28

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes28


title: 2G

description: Library name: RNA_S8112Nr2

value: tumour bladder


title: Patient 18_mes29

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes29

value: Female


title: 6 weeks female mouse immunized intranasally with rVSV_WT, replication 3

description: Library name: rVSV_WT_12h_3


title: AKPT Organoid from SI tumor Rep 1

description:
Library name: RJR18200309_S1
Column name in RJR18200309_Raw_counts_matrix.csv


title: Patient 16_mes26

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes26


title: Patient 21_mes32

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes32


title: 6 weeks female mouse immunized intranasally with rVSV_WT, replication 2

description: Library name: rVSV_WT_12h_2


title: 35g

description: Library name: RNA_S8112Nr22

value: male


title: AKPS Organoid from SI tumor Rep 1

description:
Library name: RJR18200309_S5
Column name in RJR18200309_Raw_counts_matrix.csv

value: vilCreER Apcflfl KrasG12D/+ p53fl/fl Smad4fl/fl


title: AKPS Organoid from SI tumor Rep 2

description:
Library name: RJR18200309_S6
Column name in RJR18200309_Raw_counts_matrix.csv


title: 34g

description: Library name: RNA_S8112Nr21

value: Ta(m)

value: LOW


title: 30g

description: Library name: RNA_S8112Nr20


title: AKP Organoid from Colon tumor Rep 2

description:
Library name: RJR18200309_S22
Column name in RJR18200309_Raw_counts_matrix.csv

value: Colon

value: Organoid from Colon tumor

value: vilCreER Apcfl/fl KrasG12D/+ p53fl/fl


title: Patient 14_mes22

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes22

value: Male


title: AKP Organoid from Colon tumor Rep 1

description:
Library name: RJR18200309_S21
Column name in RJR18200309_Raw_counts_matrix.csv


title: PbANKA Day5 rep3

city: Shenyang

first: Yan

last: Zhao

address: China Medical University, Shenbei New District, Shenyang City, Liaoning Province

department: Department of Immunology

institute: China Medical University

description: Library name: CPbAD5SP6

data_processing:
Hisat2 v2.0.5.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Assembly: mm10
Supplementary files format and content: gene_FPKM.txt

source_name: spleen

growth_protocol: Six to eight-week-old, female and male C57BL/6J mice (B6, WT mice) were purchased from Beijing HFK Bioscience Co., Ltd. (Beijing, China). All mice were maintained with the same feeding conditions and a specific pathogen-free environment within a treatment room (12-h light/dark cycle, 22±2°C, 60–65% relative humidity).

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: The mice were bred in the animal facility, at China Medical University, Shenyang, China. Six to eight-week-old, female mice were used for infection. To begin infections, mice were inoculated intraperitoneally with 1×106 P.berghei ANKA parasitized red blood cells (pRBCs).

value: spleen

value: splenocyte

value: PbANKA infection


title: 155S

description: Library name: RNA_S8112Nr200

source_name: normal bladder

value: normal bladder

value: female


title: AKPT Organoid from SI tumor Rep 3

description:
Library name: RJR18200309_S3
Column name in RJR18200309_Raw_counts_matrix.csv

value: SI

value: Organoid from SI tumor

value: VilCreER Apc fl/fl KRasG12D/+ p53 fl/fl Tgfbr1 fl/fl


title: AK Organoid from Colon tumor Rep 3

description:
Library name: RJR18200309_S18
Column name in RJR18200309_Raw_counts_matrix.csv

value: vilCreER Apcfl/+ KrasG12D/+


title: Patient 19_mes30

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes30

value: epithelioid

value: WT


title: Patient 13_mes19

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes19

value: biphasic

value: DELETED


title: 6 weeks female mouse immunized intranasally with rVSV_M2, replication 2

description: Library name: rVSV_M2_12h_2

value: lung


title: 154S

description: Library name: RNA_S8112Nr199

value: male

value: HIGH


title: Patient 12_mes17

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes17

value: Male

value: sarcomatoid


title: AK Organoid from Colon tumor Rep 2

description:
Library name: RJR18200309_S17
Column name in RJR18200309_Raw_counts_matrix.csv

value: Colon

value: Female

value: Organoid from Colon tumor


title: Patient 15_mes24

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes24


title: AK Organoid from Colon tumor Rep 1

description:
Library name: RJR18200309_S16
Column name in RJR18200309_Raw_counts_matrix.csv


title: normal rep3

description: Library name: CNSP3

value: spleen

value: splenocyte

value: PBS


title: Patient 11_mes16

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes16


title: PbANKA Day5 rep1

description: Library name: CPbAD5SP4

value: PbANKA infection


title: Patient 9_mes11

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes11


title: Patient 10_mes12

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes12


title: normal rep1

description: Library name: CNSP1


title: 153S

description: Library name: RNA_S8112Nr198

value: normal bladder


title: 152S

description: Library name: RNA_S8112Nr197

value: female

value: TA

value: LOW


title: HY60760 slide_2 ROI_39

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

description: Library name: G12C_s2_39

data_processing:
Raw FASTQ files were processed via Nanostring's NGS pipeline (v1.0) with default parameters.
Processed DCC files were then mapped to target genes.
Normalized counts were log2 transformed.
Assembly: mm10
Supplementary files format and content: Excel file with Q3 normalized gene counts
Supplementary files format and content: tab-delimited text file log2 normalized gene counts for each sample
Library strategy: Spatial Transcriptomics

source_name: Pancreas

extract_protocol:
GeoMx digital spatial profiler (DSP) for RNA profiling in formalin-fixed paraffin-embedded tissue sections from pancreas of  4 genetically engineered mice (2 KRAS G12C mutant and 2 KRAS G12D mutant) at ages of 16 weeks were processed for GeoMX RNA profiling. For each section, 13-20 AOIs of 200 µm in diameter were selected based on PanCK+ expression for detailed molecular profiling with RNA probe cocktail.
Library preparation was performed according to the manufacturer’s instructions and involved PCR amplification to add Illumina adapter sequences and unique sample indices. Pooled libraries were sequenced at 2x75 base pairs and with the single-index workflow on an Illumina NextSeq to generate 458 M raw reads.

value: Pancreas

value: Kras G12C


title: HY60760 slide_2 ROI_38

description: Library name: G12C_s2_38


title: 6 weeks female mouse immunized intranasally with rVSV_WT, replication 1

description: Library name: rVSV_WT_12h_1

value: lung


title: 151S

description: Library name: RNA_S8112Nr196

value: male

value: HIGH


title: 147s

description: Library name: RNA_S8112Nr194


title: Patient 8_mes10

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes10

value: Male

value: biphasic

value: DELETED


title: normal rep2

description: Library name: CNSP2

value: WT


title: HY60760 slide_2 ROI_37

description: Library name: G12C_s2_37


title: 155G

description: Library name: RNA_S8112Nr193

value: tumour bladder


title: C2C12 cells, Cr5, D4, biol rep 2

city: New York

first: Sun Young

last: Park

address: 341 East 25th Street

institute: NYU Grossman School of Medicine

description:
Library name: Sample 29
Column name in GE CPM: CR5 - D4 - S29 (GE) - CPM

data_processing:
CLC Genomics Workbench Version 21.0.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork
Trimmed sequence reads were mapped to mus musculus ensemble V80 using CLC genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mus musculus ensemble V80
Supplementary files format and content: tab-delimited text file includes counts per million (CPM) values for each sample

growth_protocol: C2C12 myoblasts were maintained in high-glucose DMEM supplemented with 20% fetal bovine serum (FBS) and 1% pen/strep in a humidifed atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol reagent (Thermo Fisher)
RNA libraries for RNA-seq were prepared using Illumina TruSeq RNA Library Prep Kit following manufacturer's protocols

treatment_protocol:
Myogenic differentiation was induced by switching to differentiation medium consisting of DMEM supplemented with 2% horse serum and 1% pen/strep for four days.
Cr(VI) treatment was done by adding 0, 2, or 5 uM of potassium chromate in differentiation medim

value: muscle progenitor cells

value: 5 µM of Cr(VI)

tag: time

value: differentiation day 4


title: C2C12 cells, Cr5, D4, biol rep 3

description:
Library name: Sample 30
Column name in GE CPM: CR5 - D4 - S30 (GE) - CPM


title: PbANKA Day5 rep2

description: Library name: CPbAD5SP5

value: spleen

value: splenocyte

value: PbANKA infection


title: C2C12 cells, Cr5, D4, biol rep 1

description:
Library name: Sample 28
Column name in GE CPM: CR5 - D4 - S28 (GE) - CPM


title: HY60760 slide_2 ROI_36

description: Library name: G12C_s2_36


title: 154G

description: Library name: RNA_S8112Nr192


title: Patient 6_mes8

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes8

value: epithelioid


title: HY60760 slide_2 ROI_40

description: Library name: G12C_s2_40

value: Pancreas


title: 29g

description: Library name: RNA_S8112Nr19

value: Ta

value: LOW


title: Patient 5_mes7

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes7


title: Patient 4_mes5

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes5


title: C2C12 cells, Cr5, D2, biol rep 2

description:
Library name: Sample 26
Column name in GE CPM: CR5 - D2 - S20 (GE) - CPM

value: differentiation day 2


title: C2C12 cells, Cr5, D2, biol rep 1

description:
Library name: Sample 25
Column name in GE CPM: CR5 - D2 - S19 (GE) - CPM


title: HY60760 slide_2 ROI_35

description: Library name: G12C_s2_35

value: Kras G12C


title: Patient 1_mes2

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes2


title: Patient 7_mes9

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes9

value: Female


title: HY60760 slide_2 ROI_32

description: Library name: G12C_s2_32


title: Patient 2_mes3

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes3

value: Male

value: biphasic


title: 145S

description: Library name: RNA_S8112Nr185

value: normal bladder

value: male

value: TA


title: 151G

description: Library name: RNA_S8112Nr189

value: tumour bladder

value: HIGH


title: HY60760 slide_2 ROI_34

description: Library name: G12C_s2_34


title: 153G

description: Library name: RNA_S8112Nr191


title: HY60760 slide_2 ROI_30

description: Library name: G12C_s2_30


title: 147g

description: Library name: RNA_S8112Nr187


title: 150G

description: Library name: RNA_S8112Nr188

value: female


title: HY60760 slide_2 ROI_33

description: Library name: G12C_s2_33


title: Fentanyl_Sample2

city: Palo Alto

first: Yu

last: Liu

address: 1215 Welch Road

department: CVI

institute: Stanford University

description: Library name: SCVI77FENT

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore
Trimmed data was mapped to hg38 whole genome using STAR
Raw read counts were counted by using FeatureCounts
Assembly: hg38
Supplementary files format and content: TPM_FentanylandControl.csv

source_name: iPSC-CM

growth_protocol: hiPSCs were routinely maintained in 6-well plates as described above. Cells were grown to reach 90% confluency and then subjected to differentiation in RPMI/B27 without insulin medium (Life Technologies) supplemented with 6 µM CHIR99021 (Selleckchem). Following 48h, the cells were subjected to the same medium supplemented with 4 µM IWR-1-endo (Selleckchem). On day 7, the medium was changed to RPMI-B27 with insulin and exchanged every other day. Beating hiPSC-CMs usually can be observed around day 7 to day 10. On day 11, the medium was switched to RPMI-B27 without D-glucose (Life Technologies) for 4 days to purify cardiomyocytes. Then, hiPSC-CM were maintenanced in RPMI/27 (change every other day) to complete maduration (around day 30) and perform study.

extract_protocol:
RNA for transcriptome sequencing was isolated using Direct-zol RNA Microprep kit (Zymo Research).
Sequencing was performed on the NovaSeq PE150 platform (Novogene).

treatment_protocol: iPSC-CMs from 2 healthy donors were exposed to three doses of 89 nM fentanyl for 5 days.

value: iPSC-CM

value: Human iPSC-derived cardiomyocytes

value: three doses of 89 nM fentanyl for 5 days (dose 1 at day 0, dose 2 day 2 and dose 3 day 4)


title: HY60760 slide_2 ROI_29

description: Library name: G12C_s2_29

value: Pancreas


title: HY60760 slide_2 ROI_31

description: Library name: G12C_s2_31


title: C2C12 cells, Cr5, D1, biol rep 3

description:
Library name: Sample 24
Column name in GE CPM: CR5 - D1 - S12 (GE) - CPM

value: muscle progenitor cells

value: 5 µM of Cr(VI)

value: differentiation day 1


title: 146S

description: Library name: RNA_S8112Nr186


title: C2C12 cells, Cr5, D1, biol rep 2

description:
Library name: Sample 23
Column name in GE CPM: CR5 - D1 - S11 (GE) - CPM


title: C2C12 cells, Cr5, D1, biol rep 1

description:
Library name: Sample 22
Column name in GE CPM: CR5 - D1 - S10 (GE) - CPM


title: Control_Sample2

description: Library name: SCVI77CTRL

value: three doses of control (methanol) for 5 days (dose 1 at day 0, dose 2 day 2 and dose 3 day 4)


title: C2C12 cells, Cr2, D4, biol rep 3

description:
Library name: Sample 21
Column name in GE CPM: CR2 - D4 - S27 (GE) - CPM

value: 2 µM of Cr(VI)

value: differentiation day 4


title: 144S

description: Library name: RNA_S8112Nr184


title: HY60760 slide_2 ROI_28

description: Library name: G12C_s2_28

value: Kras G12C


title: Fentanyl_Sample1

description: Library name: SCVI15FENT


title: Control_Sample1

description: Library name: SCVI15CTRL


title: 143s

description: Library name: RNA_S8112Nr183

value: normal bladder

value: LOW


title: HY60760 slide_2 ROI_27

description: Library name: G12C_s2_27


title: 142s

description: Library name: RNA_S8112Nr182

value: male


title: HY60760 slide_2 ROI_26

description: Library name: G12C_s2_26


title: 28MD_g

description: Library name: RNA_S8112Nr18

value: tumour bladder

value: Ta


title: HRECs, DMFu rep 6

city: Baulkham Hills

first: Fergus

middle: Campbell

last: McLellan

state: NSW

address: 13 Delaigh Avenue

department: School of Vision Science

country: Australia

institute: University of New South Wales

description:
Library name: Sample_24
Azenta GENEWIZ

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
Trimmed reads were mapped to reference genome GRCH38 using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated using feature Counts from the subread package v.1.5.2.
Assembly: HRCh38
Supplementary files format and content: Text document files including raw counts for each sample.

molecule: polyA RNA

source_name: Primary

growth_protocol: Primary Human Retinal Endothelial Cells (Cell Systems [#ACBRI 181]) grown in Endothelial Basal Media-2  BulletKit Media (Lonza #CC-3162) coated in 0.2% gelatin from porcine skin (Sigma-Aldrich, #G1890) for 30 minutes.

extract_protocol:
Total RNA was extracted using E.Z.N.A.Total RNA Kit I (Omega Bio-Tech, Norcross, GA, USA).
RNA libraries for RNA-seq were prepared using the NEBNExt Ultra RNA Library Prep Kit for Illumina using the manufacturer's instructions.

treatment_protocol: HRECs were treated for 24 hours with 10 ng/ml VEGF and/or 80 µM DMFu with 0.004% DMSO vehicle control.

value: Primary

value: Retinal Microvascular Endothelial Cells

value: Dimethyl Fumarate


title: 139s

description: Library name: RNA_S8112Nr181

value: TA


title: HRECs, DMFu rep 5

description:
Library name: Sample_23
Azenta GENEWIZ


title: C2C12 cells, Cr2, D2, biol rep 1

description:
Library name: Sample 16
Column name in GE CPM: CR2 - D2 - S16 (GE) - CPM

value: differentiation day 2


title: HRECs, DMFu rep 4

description:
Library name: Sample_22
Azenta GENEWIZ


title: HY60760 slide_2 ROI_24

description: Library name: G12C_s2_24

value: Pancreas


title: C2C12 cells, Cr2, D2, biol rep 2

description:
Library name: Sample 17
Column name in GE CPM: CR2 - D2 - S17 (GE) - CPM

value: muscle progenitor cells


title: HY60760 slide_2 ROI_25

description: Library name: G12C_s2_25


title: C2C12 cells, Cr5, D2, biol rep 3

description:
Library name: Sample 27
Column name in GE CPM: CR5 - D2 - S21 (GE) - CPM

value: 5 µM of Cr(VI)


title: HY60760 slide_2 ROI_22

description: Library name: G12C_s2_22


title: Patient 3_mes4

description:
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
mes4

value: Male

value: biphasic

value: DELETED


title: HY60760 slide_2 ROI_23

description: Library name: G12C_s2_23

value: Kras G12C


title: HRECs, DMFu rep 2

description:
Library name: Sample_20
Azenta GENEWIZ


title: C2C12 cells, Cr2, D1, biol rep 3

description:
Library name: Sample 15
Column name in GE CPM: CR2 - D1 - S9 (GE) - CPM

value: 2 µM of Cr(VI)

value: differentiation day 1


title: HRECs, DMFu rep 3

description:
Library name: Sample_21
Azenta GENEWIZ


title: C2C12 cells, Cr2, D1, biol rep 2

description:
Library name: Sample 14
Column name in GE CPM: CR2 - D1 - S8 (GE) - CPM


title: 137S

description: Library name: RNA_S8112Nr179

value: normal bladder

value: male

value: HIGH


title: 136AS

description: Library name: RNA_S8112Nr178

value: LOW


title: C2C12 cells, Cr2, D4, biol rep 2

description:
Library name: Sample 20
Column name in GE CPM: CR2 - D4 - S26 (GE) - CPM

value: differentiation day 4


title: HY60760 slide_2 ROI_21

description: Library name: G12C_s2_21


title: C2C12 cells, Cr2, D2, biol rep 3

description:
Library name: Sample 18
Column name in GE CPM: CR2 - D2 - S18 (GE) - CPM


title: 135S

description: Library name: RNA_S8112Nr177

value: female


title: C2C12 cells, Cr2, D4, biol rep 1

description:
Library name: Sample 19
Column name in GE CPM: CR2 - D4 - S25 (GE) - CPM


title: HRECs, DMFu rep 1

description:
Library name: Sample_19
Azenta GENEWIZ

value: Primary

value: Retinal Microvascular Endothelial Cells

value: Dimethyl Fumarate


title: C2C12 cells, Cr0, D4, biol rep 3

description:
Library name: Sample 12
Column name in GE CPM: CR0 - D4 - S24 (GE) - CPM

value: muscle progenitor cells

value: 0 µM of Cr(VI)


title: HRECs, VEGF + DMFu rep 6

description:
Library name: Sample_18
Azenta GENEWIZ

value: Vascular Endothelial Growth Factor A + Dimethyl Fumarate


title: HY2132 slide_2 ROI_20

description: Library name: G12D_s2_20

value: Pancreas

value: Kras G12D


title: 138S

description: Library name: RNA_S8112Nr180

value: TA


title: 134S

description: Library name: RNA_S8112Nr176


title: C2C12 cells, Cr0, D4, biol rep 2

description:
Library name: Sample 11
Column name in GE CPM: CR0 - D4 - S23 (GE) - CPM


title: HY2132 slide_2 ROI_18

description: Library name: G12D_s2_18


title: 130s

description: Library name: RNA_S8112Nr174

value: Ta


title: 131S

description: Library name: RNA_S8112Nr175


title: HRECs, VEGF + DMFu rep 5

description:
Library name: Sample_17
Azenta GENEWIZ


title: C2C12 cells, Cr0, D2, biol rep 3

description:
Library name: Sample 9
Column name in GE CPM: CR0 - D2 - S15 (GE) - CPM

value: differentiation day 2


title: HY2132 slide_2 ROI_19

description: Library name: G12D_s2_19


title: C2C12 cells, Cr0, D4, biol rep 1

description:
Library name: Sample 10
Column name in GE CPM: CR0 - D4 - S22 (GE) - CPM


title: HY2132 slide_2 ROI_17

description: Library name: G12D_s2_17


title: HRECs, VEGF + DMFu rep 4

description:
Library name: Sample_16
Azenta GENEWIZ


title: 129S

description: Library name: RNA_S8112Nr173

value: normal bladder


title: HY2132 slide_2 ROI_16

description: Library name: G12D_s2_16


title: HRECs, VEGF + DMFu rep 3

description:
Library name: Sample_15
Azenta GENEWIZ


title: HRECs, VEGF + DMFu rep 2

description:
Library name: Sample_14
Azenta GENEWIZ


title: HY2132 slide_2 ROI_15

description: Library name: G12D_s2_15


title: C2C12 cells, Cr0, D2, biol rep 2

description:
Library name: Sample 8
Column name in GE CPM: CR0 - D2 - S14 (GE) - CPM


title: C2C12 cells, Cr0, D2, biol rep 1

description:
Library name: Sample 7
Column name in GE CPM: CR0 - D2 - S13 (GE) - CPM


title: HRECs, VEGF + DMFu rep 1

description:
Library name: Sample_13
Azenta GENEWIZ


title: C2C12 cells, Cr2, D1, biol rep 1

description:
Library name: Sample 13
Column name in GE CPM: CR2 - D1 - S7 (GE) - CPM

value: 2 µM of Cr(VI)

value: differentiation day 1


title: 127S

description: Library name: RNA_S8112Nr172

value: male

value: HIGH


title: HY2132 slide_2 ROI_14

description: Library name: G12D_s2_14


title: C2C12 cells, Cr0, D1, biol rep 3

description:
Library name: Sample 6
Column name in GE CPM: CR0 - D1 - S6 (GE) - CPM


title: 126S

description: Library name: RNA_S8112Nr171


title: HY2132 slide_2 ROI_13

description: Library name: G12D_s2_13


title: HY2132 slide_2 ROI_12

description: Library name: G12D_s2_12


title: HRECs, VEGF rep 5

description:
Library name: Sample_11
Azenta GENEWIZ

value: Vascular Endothelial Growth Factor A + DMSO


title: HRECs, VEGF rep 4

description:
Library name: Sample_10
Azenta GENEWIZ

value: Primary


title: HY2132 slide_2 ROI_10

description: Library name: G12D_s2_10


title: C2C12 cells, Cr0, D0, biol rep 2

description:
Library name: Sample 2
Column name in GE CPM: CR0 - D0 - S2 (GE) - CPM

value: differentiation day 0


title: HRECs, VEGF rep 3

description:
Library name: Sample_9
Azenta GENEWIZ

value: Retinal Microvascular Endothelial Cells


title: 121s

description: Library name: RNA_S8112Nr167

value: female

value: LOW


title: HRECs, VEGF rep 2

description:
Library name: Sample_8
Azenta GENEWIZ


title: 124S

description: Library name: RNA_S8112Nr169


title: HY2132 slide_2 ROI_11

description: Library name: G12D_s2_11


title: 123S

description: Library name: RNA_S8112Nr168


title: C2C12 cells, Cr0, D0, biol rep 3

description:
Library name: Sample 3
Column name in GE CPM: CR0 - D0 - S3 (GE) - CPM

value: muscle progenitor cells

value: 0 µM of Cr(VI)


title: HRECs, VEGF rep 6

description:
Library name: Sample_12
Azenta GENEWIZ


title: C2C12 cells, Cr0, D0, biol rep 1

description:
Library name: Sample 1
Column name in GE CPM: CR0 - D0 - S1 (GE) - CPM


title: HRECs, VEGF rep 1

description:
Library name: Sample_7
Azenta GENEWIZ


title: 26G

description: Library name: RNA_S8112Nr17

value: tumour bladder


title: 120s

description: Library name: RNA_S8112Nr166


title: 116s

description: Library name: RNA_S8112Nr165


title: HY2132 slide_2 ROI_08

description: Library name: G12D_s2_08

value: Pancreas

value: Kras G12D


title: HRECs, Control rep 5

description:
Library name: Sample_5
Azenta GENEWIZ

value: No Treatment


title: C2C12 cells, Cr0, D1, biol rep 2

description:
Library name: Sample 5
Column name in GE CPM: CR0 - D1 - S5 (GE) - CPM


title: C2C12 myoblasts-Cas9M3-DM3 (input)

city: Guangzhou

first: TAN

last: YEYA

state: Guangdong

address: Jinsui Road, Tianhe District, Guangzhou City, Guangdong Province

department: Guangzhou Women and Children's Medical Center

institute: Guangzhou Medical University

description: Library name: Cas9M3-DM3-input

data_processing:
Fastp software was used to remove the reads that contained adaptor contamination, low-quality bases and undetermined bases with the default parameters. The sequence quality of the IP and input samples was subsequently verified using fastp.
We used HISAT2 to map reads to the reference genome and retained unique mapped reads via SAMtools on the basis of a mapping quality greater than 30.
Mapped reads from the IP and input libraries were loaded into the R package exomePeak.
HOMER was used for de novo motif discovery on the basis of the top 1000 most enriched peaks. Called peaks were annotated by intersecting with the gene architecture using bedtools and custom python scripts.
m6A metagene plot was plotted using the Guitar package in R
Assembly: GRCm38
Supplementary files format and content: bigwig

source_name: skeletal muscle

growth_protocol: The mouse skeletal myoblast C2C12  cells were cultured in growth medium, which consisted of high-glucose Dulbecco's modified Eagle's medium supplemented with 10% FBS and 1% penicillin/streptomycin, at 37 °C in 5% CO2. The cells were plated and cultured to 100% confluence and then transferred to differentiation medium consisting of DMEM containing 2% horse serum and 1% penicillin/streptomycin for further culture.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent following the manufacturer’s procedure. The RNA integrity was assessed with a Bioanalyzer 2100 with a RIN > 7.0 and confirmed by electrophoresis with a denaturing agarose gel.
Poly(A) RNA was purified from 50 µg of total RNA using Dynabeads Oligo (dT) 25-61005. Then, the poly(A) RNA was fragmented into small pieces via the Magnesium RNA Fragmentation Module. Then, the cleaved RNA fragments were incubated with an m6A-specific antibody. Then, the IP RNA was reverse transcribed to create cDNA, which was subsequently fled to synthesize U-labeled second-strand DNAs. After ligation with the adapter to the A-tailed fragmented DNA, the ligated products were amplified with PCR.

value: skeletal muscle

value: C2C12 myoblasts


title: HY2132 slide_2 ROI_07

description: Library name: G12D_s2_07


title: C2C12 cells, Cr0, D1, biol rep 1

description:
Library name: Sample 4
Column name in GE CPM: CR0 - D1 - S4 (GE) - CPM

value: differentiation day 1


title: C2C12 myoblasts-Cas9M3-DM3 (IP)

description: Library name: Cas9M3-DM3-IP


title: 125S

description: Library name: RNA_S8112Nr170

value: normal bladder

value: TA


title: HRECs, Control rep 6

description:
Library name: Sample_6
Azenta GENEWIZ


title: 115s

description: Library name: RNA_S8112Nr164

value: Ta


title: HY2132 slide_2 ROI_06

description: Library name: G12D_s2_06


title: C2C12 myoblasts-CTRL-DM3 (IP)

description: Library name: CTRL-DM3-IP


title: HRECs, Control rep 3

description:
Library name: Sample_3
Azenta GENEWIZ

value: Primary


title: 114S

description: Library name: RNA_S8112Nr163


title: 109S

description: Library name: RNA_S8112Nr161


title: C2C12 myoblasts-Cas9M3-GM (IP)

description: Library name: Cas9M3-GM-IP


title: HRECs, Control rep 4

description:
Library name: Sample_4
Azenta GENEWIZ


title: C2C12 myoblasts-CTRL-DM3 (input)

description: Library name: CTRL-DM3-input


title: C2C12 myoblasts-Cas9M3-GM (input)

description: Library name: Cas9M3-GM-input


title: HRECs, Control rep 1

description:
Library name: Sample_1
Azenta GENEWIZ


title: HRECs, Control rep 2

description:
Library name: Sample_2
Azenta GENEWIZ


title: 25G

description: Library name: RNA_S8112Nr16

value: male


title: HY2132 slide_2 ROI_03

description: Library name: G12D_s2_03


title: 501_TFEB-HA_Torin_HA_R2

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

institute: Ludwig Institute for Cancer Research

library_source: genomic

data_processing:
Raw fastq files (with base-calling quality score) were obtained form Wellcome Trust Genomics service
Processed fastq files were mapped using STAR 2.5.1b {Dobin, 2013} against hg38 build
Mapped SAM-files were used for peak calling using the Homer 4.8 {Heinz, 2010}
Homer was used to generatedbigWig normalised to 1e7
Assembly: hg38
Supplementary files format and content: bigwig of normalised counts for uniqely aligned reads

molecule: genomic DNA

growth_protocol: All cell lines were grown at 37°C with 10% CO2 in RPMI-1640 (Gibco BRL, Invitrogen) supplemented with penicillin and streptomycin, 10% fetal bovine serum (FBS, Biosera).

extract_protocol:
Samples were prepared as described in PMID: 37770430 and 32531202. Briefly 30x-15cm dishes of 501mel cells were fixed in 0.4% PFA then cheared with a Covaris S220 for 15 minutes (160 W peak incident power, 5% duty cycle and 200 cycles per burst). The sonicated chromatin were precleared and ChIP was performed using 120ug of the indicated antibodies. Purification of the ChIP-DNA was done using QIAGEN PCR clean-up column.
Libraries were prepared using recommended Illumina protocols
Libraries were constructed by the Oxford Genomics Centre using Takara DNA SMART ChIP-Seq Kit

treatment_protocol: 5ng/ml Doxycycline overnight followed by 6h 250nM Torin1

value: melanoma

value: 5ng Dox Overnight followed by 6h 250nM Torin1


title: HY2132 slide_2 ROI_02

description: Library name: G12D_s2_02


title: 105s

description: Library name: RNA_S8112Nr159

value: female

value: LOW


title: 99S

description: Library name: RNA_S8112Nr157

value: Ta(m)


title: HY2132 slide_2 ROI_01

description: Library name: G12D_s2_01


title: C2C12 myoblasts-CTRL-GM (input)

description: Library name: CTRL-GM-input


title: HY2132 slide_2 ROI_04

description: Library name: G12D_s2_04


title: 501_TFEB-HA_Torin_Input_R2


title: C2C12 myoblasts-CTRL-GM (IP)

description: Library name: CTRL-GM-IP


title: 104S

description: Library name: RNA_S8112Nr158

value: HIGH


title: HY2132 slide_2 ROI_09

description: Library name: G12D_s2_09

value: Pancreas


title: 501_TFEB-HA_Torin_Input_R1


title: 106S

description: Library name: RNA_S8112Nr160


title: HY60758 slide_1 ROI_33

description: Library name: G12C_s1_33

value: Kras G12C


title: HY60758 slide_1 ROI_31

description: Library name: G12C_s1_31


title: 97s

description: Library name: RNA_S8112Nr155


title: C2C12 myoblasts-M3-DM4 (input)

description: Library name: M3_DM4_input


title: HY2132 slide_2 ROI_05

description: Library name: G12D_s2_05

value: Kras G12D


title: 501_TFEB-HA_CTRL_HA_R2

value: 5ng Dox Overnight


title: HY60758 slide_1 ROI_32

description: Library name: G12C_s1_32


title: HY60758 slide_1 ROI_30

description: Library name: G12C_s1_30


title: C2C12 myoblasts-M3-GM (IP)

description: Library name: M3_GM_IP

value: skeletal muscle

value: C2C12 myoblasts


title: 93S

description: Library name: RNA_S8112Nr153

value: normal bladder


title: C2C12 myoblasts-GFP-DM4 (IP)

description: Library name: GFP_DM4_IP


title: C2C12 myoblasts-M3-GM (input)

description: Library name: M3_GM_input


title: HY60758 slide_1 ROI_28

description: Library name: G12C_s1_28


title: 95S

description: Library name: RNA_S8112Nr154


title: 501_TFEB-HA_Torin_HA_R1


title: 21g

description: Library name: RNA_S8112Nr15

value: tumour bladder


title: 501_TFEB-HA_CTRL_HA_R1


title: HY60758 slide_1 ROI_27

description: Library name: G12C_s1_27


title: Con F3e Rep 3

city: Sioux Falls

first: Michael

last: Kareta

state: SD

address: 2301 East 60th Street North

department: Genetics & Genomics

institute: Sanford Research

description: Library name: MB20

data_processing:
Sequenced reads were aligned to the rat genome (rn7) using Cell Ranger (Version 9.0.1, 10X Genomics, Pleasanton, CA). To assign the species of each cell to either human (HEK-293T) or rat, the output bam file from cellranger was parsed into individual bam files for each unique barcode using the subsetbamlinux script (Version 1.1.0, 10X Ge-nomics, Pleasanton, CA), then BedTools (Version 2.29.1) was used to convert each bam into a fastq file. Each single cell fastq file was then aligned to either the rat or human genome using STAR (version 2.7.11b). The mapping rate to each genome was then used to determine the species of that cell, and human (HEK-293T) data was excluded from anal-yses. Cells were filtered to exclude those with more than 25% mitochondrial reads and retained if they had a detected unique gene count between 500 and 8000, ensuring the inclusion of cells with a sufficient number of expressed genes. Quality control steps were applied to remove low-quality cells while retaining ability to compare differences in genes encoded by the mitochondrial genome (mtDNA). All preprocessing was performed using Seurat v5.2.1 [44]. Data normalization was conducted using SCTransform. During this step, the percentage of ribosomal gene expression was regressed out to minimize its po-tential confounding effect on downstream analyses. Cells were clustered based on shared expression profiles and visualized using UMAP embeddings.
Assembly: rn7
Supplementary files format and content: CellRanger output

organism: Rattus norvegicus

source_name: E4.5 blastocysts

growth_protocol: Rats were housed in an AAALAC approved certified facility under the guidance of a local IACUC

extract_protocol:
On E4.5 dams were sacrificed and embryos flushed from the uterine horns. Blastocysts were cultured in EmbryoLoveTM  media (EmbryoTechTM Laboratories Inc., Haverhill, MA) for 2-4 hours then washed in 1x DPBS with 0.04% BSA. They were transferred to pre-warmed Acidic Tyrode’s solution (Sigma-Aldrich, St. Louis, MO) for 1-2 minutes to remove the zona pellucida. Embryos were washed again, then transferred to pre-warmed dissociation media (GibcoTM TrypLETM Select Enzyme, Thermo Fisher Scientific, Waltham, MA) for 10 minutes at 37°C followed by careful trituration by pipetting through a pulled glass capillary tube.
Libraries were made using the 10X Genomics scRNA-seq platform. Due to the low number of cells collected from the embryos and the cell number requirements for the 10X platform, the rat cells were combined with 1000 human 293T cells. Specifically, all cells were suspended in 1x DPBS with 0.04% BSA, which was mixed into a reaction containing reverse transcription reagents and loaded onto a Chromium Next GEM Chip G (Catalog number 1000120, 10X Genomics, Pleasanton, CA). Reverse transcription, GEM generation and library preparation were performed using the Chromium Next GEM Single Cell 3' Kit v3.1 (Catalog number 1000268, 10X Genomics, Pleasanton, CA). The 10X Genomics Chromium Controller instrument was used to per-form GEM (Gel beads-in-emulsion) generation. Full-length barcoded cDNAs were pro-duced from poly-adenylated mRNA by reverse transcription within the GEMs. The tran-scripts were recovered from the GEMs, and the cDNAs were purified and amplified using 13 amplification cycles as per manufacturer recommendation. After clean-up of the amplification reaction, the concentration of cDNA solution (1µl) was determined a Bioana-lyzer with the High Sensitivity DNA kit (Agilent, Santa Clara, CA). To prepare sequencing libraries compatible with the Illumina platform, the entire cDNA reaction was fragmented, followed by end repair, A-tailing and adapter ligation. cDNA samples were am-plified using dual sample indexes in the final step of library preparation, which enabled multiplexing during sequencing, then cleaned up, quantified, and sent to an outside ven-dor (Novogene, Durham, NC) for sequencing

treatment_protocol: F0 dams were fed control diet that was 3.2kcal/g consisting of 16.6% fat, 22.9% protein and 60.5% carbohydrates or a high fat (HF) diet that was 4.3kcal/g consisting of 39.7% fat, 18.8% protein and 41.4% carbohydrates for 28 days prior to breeding. On embryonic day (E )14, HF-fed dams were administered streptozotocin to induce diabetes during the last third of pregnancy. Diabetes was treated with twice daily sliding scale insulin. F2 pups were cross-fostered to healthy dams in equal sized litters and grown to adulthood for breeding to create F2 and F3 embryos

value: E4.5 blastocysts

tag: diet

tag: generation


title: 501_TFEB-HA_CTRL_Input_R2


title: 98S

description: Library name: RNA_S8112Nr156


title: C2C12 myoblasts-GFP-DM4 (input)

description: Library name: GFP_DM4_input


title: HY60758 slide_1 ROI_29

description: Library name: G12C_s1_29


title: C2C12 myoblasts-GFP-GM (input)

description: Library name: GFP_GM_input


title: Con F3e Rep 1

description: Library name: MB18

value: 16.6% fat, 22.9% protein and 60.5% carbohydrates


title: C2C12 myoblasts-M3-DM4 (IP)

description: Library name: M3_DM4_IP


title: 92S

description: Library name: RNA_S8112Nr152


title: 501_TFEB-HA_CTRL_Input_R1


title: Con F2e Rep 3

description: Library name: MB15


title: 88s

description: Library name: RNA_S8112Nr148

value: Ta


title: HY60758 slide_1 ROI_23

description: Library name: G12C_s1_23


title: Con F2e Rep 2

description: Library name: MB14


title: HY60758 slide_1 ROI_26

description: Library name: G12C_s1_26


title: C2C12 myoblasts-GFP-GM (IP)

description: Library name: GFP_GM_IP


title: HY60758 slide_1 ROI_25

description: Library name: G12C_s1_25


title: KO_HFD_REP3

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

country: Germany

institute: University of Cologne

description: Library name: 182292

data_processing:
The RNA-seq dataset was processed on the CHEOPS HPC cluster at the University of Cologne using the nf-core. RNA-seq pipeline (v3.7) within a Singularity environment and managed by Nextflow (v21.10.6). Quality control, including adapter trimming and sequence filtering, was performed with Trim Galore (v0.6.7), ensuring high-quality reads. Read quality was assessed via MultiQC (v1.11)(95), aggregating FastQC(96), Picard(97), and Preseq(98) reports. No issues were detected.
Reads were aligned to the GRCm38 reference genome with STAR (v2.7.10a), and gene quantification was done using Salmon (v1.5.2). Differential expression analysis was performed in DESeq2 (v1.38.1)(100), with multiple testing corrections applied using the Benjamini-Hochberg method. Gene Ontology (GO) analysis, focusing on genes with an absolute log2FoldChange >1 and adjusted p-value <0.05, was carried out using gprofiler2 (v0.2.1)(101). Positively and negatively enriched pathways were identified separately using default parameters, including g_SCS correction. Pearson correlation tests were initially performed on the log2 fold changes of all genes between the Ctrl (HFD vs CD) and CD (HoipA-KO vs Ctrl) comparisons. Genes were then grouped by significance in either or both comparisons, and correlation analyses were repeated for each group. All tests showed strong to very strong correlations (0.77 to 0.94), with statistically significant results.
Cell-type deconvolution was performed using the deconvolute function from Granulator (v1.6.0) and the dtangle method(102). As input we used Salmon’s TPM values generated by the nf-core pipeline and perigonadal samples from the single-nuclei dataset GSE176171. The preprocessed Seurat object (mouse_all.rds) was sourced from https://gitlab.com/rosen-lab/white-adipose-atlas and restricted to male perigonadal tissue.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited tsv files containing raw counts for each sample
Supplementary files format and content: Tab-delimited tsv files containing raw counts for each sample Restricted to protein coding genes
Supplementary files format and content: Tab-delimited tsv files containing DESeq2 results additional annotation and CPM values

source_name: Gonadal/Visceral White adipose Tissue

growth_protocol: Hoip A-KO mice where genetated using Hoip (Rnf31) flox flox line and cross with Adiponectin Cre (AdipoQ.Cre) to generate mature adipocyte Hoip deletion

extract_protocol:
at 16 weeks of diet, gonadal/visceral  white adipose tissue (GWAT or VAT) was colected and snap freeze in liquid nitrogen, and kept at -80 until RNA extraction. 100 mg of fat tissue was in 1 ml of QIAyol Lysis buffer (RLT Plus + DX). To reach the miligrams of weight GWAT from 3 mice need it to be pooled from HoipA-KO, WT controls were treated in the same way for consistency .  5 mm bead was use to homogenised the tissue in TissueLyser II in two rounds for 2 minutes at 30 1/s. Samples were processed according to the manufacturer's instructions using the kit RNAeasy Lipid Mini Kit (74804, Qiagen). A DNase digest kit was employed, involving the addition of 350 µl of Buffer RW1 to the RNeasy Mini spin column, followed by the addition of DNase I. The resulting RNA was evaluated for purity and concentration using a Nanodrop spectrophotometer from TECAN Reader (model)
For RNA sequencing, we used 2 μg of total RNA per sample concentration range 50-200 ng/µL, at least 10µL volume, checking the quality by RIN > 7, OD260/280 = 1,8-2,1 and OD260/230 >1,5. mRNA libraries were prepared by mRNA Seq (Poly A+ selection) using ERCC RNA Spike-In controls. Libraries were prepared using the Illumina® Stranded TruSeq® RNA sample preparation kit. ERCC RNA Spike-In Mix (Thermo Fischer) was added to the samples before library preparation. Library preparation started with 1000 ng total RNA. After poly-A selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers. This was followed by second strand cDNA synthesis with DNA Polymerase I and RNase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (15 cycles) to create the final cDNA libraries. After library validation and quantification (Agilent Tape Station), equimolar amounts of library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System. The pool was sequenced on an Illumina NovaSeq6000 sequencing instrument with a PE100 protocol aiming for 40 million clusters per sample.

treatment_protocol: A 6 weeks of age mice star the diet with 14% fat (Control diet or CD) or 60% fat (High fat diet or HFD). Mice were fed for 16 weeks prior to tissue harvesting

value: Gonadal/Visceral White adipose Tissue

value: Hoip A-KO(Hoip fl/fl AdipoQ.Cre+)

value: 60% fat High Fat Diet


title: HY60758 slide_1 ROI_22

description: Library name: G12C_s1_22


title: Con F3e Rep 2

description: Library name: MB19


title: KO_CD_REP3

description: Library name: 182286

value: 14% fat Control diet


title: 91s

description: Library name: RNA_S8112Nr151

value: female


title: 89s

description: Library name: RNA_S8112Nr149

value: LOW


title: KO_HFD_REP2

description: Library name: 182290


title: Con F2e Rep 1

description: Library name: MB11


title: HY60758 slide_1 ROI_24

description: Library name: G12C_s1_24

value: Pancreas


title: KO_CD_REP1

description: Library name: 182282


title: 87s

description: Library name: RNA_S8112Nr147

value: Ta(m)


title: HY60758 slide_1 ROI_21

description: Library name: G12C_s1_21

value: Kras G12C


title: 82s

description: Library name: RNA_S8112Nr144

value: male

value: HIGH


title: KO_HFD_REP1

description: Library name: 182288


title: HY1903 slide_1 ROI_19

description: Library name: G12D_s1_19

value: Kras G12D


title: KO_CD_REP2

description: Library name: 182284


title: HY1903 slide_1 ROI_20

description: Library name: G12D_s1_20


title: HF-STZ F3e rep 4

description: Library name: MB09

value: 39.7% fat, 18.8% protein and 41.4% carbohydrates


title: 78s

description: Library name: RNA_S8112Nr142

value: normal bladder


title: 84S

description: Library name: RNA_S8112Nr146


title: WT_HFD_REP3

description: Library name: 182280

value: WT (Hoip fl/fl AdipoQ.Cre-)


title: HY1903 slide_1 ROI_18

description: Library name: G12D_s1_18


title: 81MD_p

description: Library name: RNA_S8112Nr143


title: 83s

description: Library name: RNA_S8112Nr145


title: HY1903 slide_1 ROI_17

description: Library name: G12D_s1_17


title: HF-STZ F3e rep 3

description: Library name: MB08

value: E4.5 blastocysts


title: WT_HFD_REP2

description: Library name: 182278


title: HY1903 slide_1 ROI_16

description: Library name: G12D_s1_16


title: WT_CD_REP3

description: Library name: 182274


title: HF-STZ F2e rep 3

description: Library name: MB04


title: 76S

description: Library name: RNA_S8112Nr141


title: HY1903 slide_1 ROI_15

description: Library name: G12D_s1_15


title: HF-STZ F3e rep 2

description: Library name: MB07


title: WT_HFD_REP1

description: Library name: 182276


title: HF-STZ F3e rep 1

description: Library name: MB06


title: HY1903 slide_1 ROI_14

description: Library name: G12D_s1_14


title: 73S

description: Library name: RNA_S8112Nr140

value: TA


title: 72S

description: Library name: RNA_S8112Nr139


title: HF-STZ F2e rep 1

description: Library name: MB02


title: HY1903 slide_1 ROI_13

description: Library name: G12D_s1_13


title: WT_4

city: Dresden

first: Ben

last: Wielockx

address: Fetscherstrasse 74

institute: IKL, Carl Gustav Carus Universitätklinikum Dresden

description: Library name: WT_4

data_processing:
Low quality nucleotides were removed Illumina fastq filter (http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/).
Reads were further subjected adaptor trimming using cutadapt.
Alignment of the reads to the Mouse genome was done using STAR Aligner using the parameters: “--runMode alignReads --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat”. Mouse Genome version GRCm38 (release M12 GENC
HTSeq-0.6.1p1 was used to count the reads that map to the genes in the aligned sample files. Read Quantification was performed using the parameters: 'htseq-count -f bam -s reverse -m union -a 20'. The GTF file (gencode.vM12.annotation.gtf) used for read
Assembly: GRCm38
Supplementary files format and content: Tab-Delimited Gene-Wise Raw read counts text file

source_name: Bone Marrow

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq

value: Bone Marrow

value: Haematopoietic Stem Cells

value: WT


title: MOF_Gel3 (MgPA-Gel3)

city: guangzhou

first: Lei

last: Zhou

state: guangdong

address: 63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province

institute: The Third Affiliated Hospital of Guangzhou Medical University

description: Library name: MOF_Gel3

data_processing:
Clustering and sequencing (Novogene Experimental Department): The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Quality control: Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Novel transcripts prediction The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed. (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Assembly: ensembl_97_rattus_norvegicus_rnor_6_0_toplevel
Supplementary files format and content: TXT files include FPKM values for each Sample

source_name: Femoral fracture middle end

growth_protocol: Sprague Dawley (SD) rats (female, 6 weeks old) and C57BL/6 mice (male, 3 weeks old) were conducted under the guidelines assessed and approved by the Ethics Committee for Animal Experiments of South China Agricultural University.

extract_protocol:
RNA was hanvested using Rneasy mini plus kit (Qiagen). 1.3 μg oftotal RNA was used for the construction of sequencing libranes.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Osteoporosis was induced by bilateral ovariectomy in 8-weeks-old-female SD rats. 12 weeks later, the left femur of the osteoporotic rats was transversely osteotomized at the midshaft and fixed with intramedullary nails (Φ=1.2 mm). MgPA-Gel bone adhesive and other groups were injected peripherally at the fracture site after the fracture ends were well aligned.

value: Femoral fracture middle end

value: Sprague  Dawley

tag: condition

value: bilateral ovariectomy

value: MgPA-Gel


title: 69S

description: Library name: RNA_S8112Nr137

data_processing:
Raw sequences were trimmed according to quality using Trimmomatic (Bolger, Lohse, and Usadel 2014) (version 0.39) using the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:20.
Trimmed sequences were mapped to the H. sapiens reference genome provided by ENSEMBL, (grch38) using Hisat2 (Kim, Langmead, and Salzberg 2015) with default parameters.
Optical duplicates were removed using MarkDuplicates tool from GATK (McKenna et al. 2010) package (version 4.2.3.0) with default parameters except OPTICAL_DUPLICATE_PIXEL_DISTANCE set to 12000.
Mapped reads were associated with transcripts from Ensembl GRCh38 genome (version 109) using HTSeq-count (Anders, Pyl, and Huber 2015) (version 0.9.1) with default parameters except –stranded set to “reverse”.
Differentially expressed genes were selected using the DESeq2 package (Love, Huber, and Anders 2014) (version 1.42).
Assembly: grch38
Supplementary files format and content: htseq-count output: tab delimited raw counts

extract_protocol:
Total RNA that was isolated from fresh frozen BC tumor and BM tissues using the mirVana™ PARIS™ RNA and Native Protein Purification Kit (Thermo Fisher Scientific, Waltham, MA, USA), following the manufacturer's instructions. Isolated RNA concentration and its purity were assessed by NanoDropTM 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) determining the A260/280 and A260/230 ratios, respectively. RNA integrity number (RIN) and distribution value 200 (DV200) were assessed with an Agilent RNA 6000 Nano Kit on a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). The RNA isolates were stored at -80° C. Next, 10 ng of RNA was used to prepare the RNA libraries.
During the library preparation, rRNA was depleted using KAPA RNA HyperPrep with RiboErase and KAPA Globin Depletion Hybridization Oligos (Roche, Basel, Switzerland). SMART-Seq Stranded Kit (Takara Bio, Kusatsu, Japan) was used for low input RNA quantities. The libraries were sequenced on the NovaSeq 6000 platform (Illumina, San Diego, CA, USA). Depths of 30 million (6Gb) paired-end 100 bp reads were generated for each sample.

value: LOW


title: WT_CD_REP1

description: Library name: 182269

value: Gonadal/Visceral White adipose Tissue

value: 14% fat Control diet


title: HF-STZ F2e rep 4

description: Library name: MB05


title: WT_3

description: Library name: WT_3


title: 68S

description: Library name: RNA_S8112Nr136

value: male


title: HY1903 slide_1 ROI_11

description: Library name: G12D_s1_11

value: Pancreas

value: Kras G12D


title: MOF_Gel1 (MgPA-Gel1)

description: Library name: MOF_Gel1

value: female


title: 20MDg

description: Library name: RNA_S8112Nr14

value: tumour bladder

value: HIGH


title: HY1903 slide_1 ROI_12

description: Library name: G12D_s1_12


title: 67S

description: Library name: RNA_S8112Nr135

value: normal bladder

value: Ta


title: WT_2

description: Library name: WT_2

value: Bone Marrow

value: Haematopoietic Stem Cells


title: MOF_Gel2 (MgPA-Gel2)

description: Library name: MOF_Gel2

value: Femoral fracture middle end


title: WT_CD_REP2

description: Library name: 182272

value: WT (Hoip fl/fl AdipoQ.Cre-)


title: HY1903 slide_1 ROI_10

description: Library name: G12D_s1_10


title: Con3 (Gel3)

description: Library name: Con3

value: Sprague  Dawley

value: bilateral ovariectomy

value: control


title: Con2 (Gel2)

description: Library name: Con2


title: 66S

description: Library name: RNA_S8112Nr134

value: TA

value: LOW


title: HY1903 slide_1 ROI_09

description: Library name: G12D_s1_09


title: WT_1

description: Library name: WT_1

value: WT


title: HF-STZ F2e rep 2

description: Library name: MB03

value: E4.5 blastocysts

value: 39.7% fat, 18.8% protein and 41.4% carbohydrates


title: 65S

description: Library name: RNA_S8112Nr133

value: male


title: HY1903 slide_1 ROI_08

description: Library name: G12D_s1_08

value: Pancreas

value: Kras G12D


title: KO_4

description: Library name: KO_4

value: KO


title: 64S

description: Library name: RNA_S8112Nr132

value: normal bladder

value: HIGH


title: HY1903 slide_1 ROI_07

description: Library name: G12D_s1_07


title: 19g

description: Library name: RNA_S8112Nr13

value: tumour bladder


title: KO_3

description: Library name: KO_3

value: Bone Marrow

value: Haematopoietic Stem Cells


title: KO_2

description: Library name: KO_2


title: HY1903 slide_1 ROI_06

description: Library name: G12D_s1_06


title: 63S

description: Library name: RNA_S8112Nr131


title: 62S

description: Library name: RNA_S8112Nr130


title: KO_1

description: Library name: KO_1


title: HY1903 slide_1 ROI_04

description: Library name: G12D_s1_04


title: 61S

description: Library name: RNA_S8112Nr129


title: KO_5

description: Library name: KO_5


title: Top2beta null MEF rep2

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Library name: Top2betanull_2

data_processing:
Unprocessed reads were first quality and adapter trimmed using cutadapt55 version 1.8.1 using a quality threshold of 20. Reads were then aligned to the GRCm38 genome from Ensembl using STAR56 version 2.5.2b, with settings as recommended by TEtranscripts57. Both repeats and genes were then quantified using TEtranscripts version 2.0.3
Assembly: mm10
Supplementary files format and content: counts.tsv

source_name: MEF

growth_protocol: Cells were maintained in high glucose DMEM containing 10% FBS, 2 mM L-glutamine, 0.1 mM b-mercaptoethanol, 1x non-essential amino acids, 1 mM sodium pyruvate, in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using TRI Reagent and ethanol precipitation. 10 ug of total RNA was further processed to remove the remaining DNA with TURBO DNase and column purified prior to library construction.
Total RNA libraries were prepared using Illumina Stranded Total RNA w/Ribo-Zero Plus following manufacturer's protocol.

value: MEF

value: mouse embryonic fibroblast

value: top2beta null

value: untreated


title: HY1903 slide_1 ROI_03

description: Library name: G12D_s1_03


title: Top2beta null MEF rep1

description: Library name: Top2betanull_1


title: RT112, 0.1% hypoxia_3

city: Bangor

first: Tim

last: Smith

address: Dean Street Bangor LL57 1UT

institute: Bangor University

hyb_protocol: Sample hybridisation on Clariom S arrays was carried out by Yourgene Health (Manchester, UK).

scan_protocol: Affymetrix protocol

data_processing: Batches of CEL files were GC SST (Signal Space Transformation with probe Guanine Cytosine Count Correction) RMA normalised using Affymetrix Array Power Tools. (https://www.thermofisher.com/uk/en/home/life-science/microarray-analysis/microarray-analysis-partners-programs/affymetrix-developers-network.html)

label: biotin

source_name: RT112, 0.1% hypoxia

label_protocol: 8ng/microlitre (9ul) added to deep 96 well plates frozen and sent to Clariom S for RNA determination

growth_protocol: Eagle's Minimum Essential Medium + 10% FBS

extract_protocol:
Cells lysed using lysis buffer (in hypoxia if hypoxic samples)
Samples RNA extracted using Qiagen RNA extraction kits

treatment_protocol: Incubated 24h in 5%CO2:95% air (21%O2) then kept at this or transferred to hypoxia cabinets at 1%, 0.2% or 0.1% O2for 24h.

value: 0.1%O2 (hypoxia)


title: 59s

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

institute: Uniwersytet Warszawski

description: Library name: RNA_S8112Nr127


title: RT112, 1% hypoxia_3

source_name: RT112, 1% hypoxia

value: 1%O2 (hypoxia)


title: 60MDp

description: Library name: RNA_S8112Nr128

value: Ta


title: HY1903 slide_1 ROI_01

description: Library name: G12D_s1_01


title: Con1 (Gel1)

description: Library name: Con1

value: Femoral fracture middle end

value: female

value: Sprague  Dawley

value: bilateral ovariectomy

value: control


title: RT112, 0.2% hypoxia_3

source_name: RT112, 0.2% hypoxia

value: 0.2%O2 (hypoxia)


title: HY1903 slide_1 ROI_02

description: Library name: G12D_s1_02

value: Pancreas

value: Kras G12D


title: wild-type, control MEF rep1

description: Library name: wild-type_1

value: wild-type


title: wild-type, control MEF rep2

description: Library name: wild-type_2


title: HY1903 slide_1 ROI_05

description: Library name: G12D_s1_05


title: mESC, EZH2-A733T mutant, SUZ12 (ChIP)

city: Dublin

first: Adrian

middle: P.

last: Bracken

address: The Smurfit Institute, The University of Dublin Trinity College, College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

description: Library name: A733T_SUZ12

data_processing:
Chromosome names for the human genome were modified with the prefix hg38_ and a metagenome was created by concatenating the mouse and human reference genomes (mm10 and hg38, respectively) before indexing with Bowtie 2 version 2.3.5. Reads were aligned to the metagenome using Bowtie 2 with default parameters, with the exception of –no-unal.
Non-unique read alignments were filtered out using SAMtools version 1.10 to exclude those with an alignment quality of <2, and the hg38_  prefix appended to chromosome names was used to separate reads as aligned to the reference mouse or spike-in human genomes.
Spike-in normalization factors were calculated for each ChIP using the formula for normalized reference-adjusted reads per million (RRPM); 1 per million spike-in reads.
BigWig files were generated using the bamCoverage tool from the deepTools suite version 3.5.0 with a bin size of 10 and scaled using the RRPM normalization factor derived for each sample.
Assembly: mm10
Supplementary files format and content: BigWig

source_name: Mouse embryonic stem cells

extract_protocol:
Enriched DNA fragments were Rnase (Thermo Fisher) and Proteinase K (Sigma) treated prior to purification using Qiagen MinElute PCR Purification Kit (Qiagen; 28006).
ChIP-purified DNA was quantified by fluorimetry using the Qubit dsDNA High Sensitivity Assay Kit (Thermo Fisher), and 0.5–50 ng of DNA/ChIP was used for library preparation using the NEBNext Ultra II DNA Library Kit for Illumina (NEB E7645) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and 2; NEB E7335 and E7500). Library DNA was quantified using the Qubit, and size distributions were ascertained on a TapeStation (Agilent) using the D1000 ScreenTape assay reagents (Agilent; 5067- 5583).

value: Mouse embryonic stem cells

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-A733T mutant

tag: antibody


title: SG TCR, DC, Female 2

city: Gainesville

first: Cuong

last: Nguyen

state: Florida

address: 2015 SW 16th Ave

institute: University of Florida

description: Library name: TCR-DCF2

data_processing:
Corresponded to GSE268532, scRepertoire (v2.0.4) was used to analyze TCR V(D)J data from the 10x Cell Ranger.
Assembly: GRCm38
Supplementary files format and content: Comma-separated values (CSV) files contained filtered contig annotations.
Library strategy: scTCR-seq

source_name: Salivary gland

extract_protocol:
Salivary glands of C57BL/6.NOD-Aec1/2 (51 weeks old, n=2 female, 2 male) and B6 (64 weeks old, n=2 female, 2 male) mice were explanted and digested in a buffer containing 1 mg/ml DNase (Sigma-Aldrich, St. Louis, MO) and 1 mg/ml Collagenase Type 4 (Worthington, Lakewood, NJ, USA) in RPMI (Lonza, Allendale, NJ) complete media (10% FBS, 2 mM L-glutamine, 0.05 mM β-mercaptoethanol). Tissues were placed in a MACS C tube (Miltenyi Biotec, San Diego, CA) for desiccation on GentleMACS V1.02 for a pulse of 38 seconds. After a 10-minute incubation at 37°C, the digest buffer was removed and placed into 4°C RPMI complete media. The process was repeated twice. Single-cell suspensions were centrifuged (2500 rpm, 10 min, 4°C) and resuspended in PBS for filtration through a 70-μm sterile cell strainer (Fisher, Pittsburgh, PA). After a wash with PBS, cells were resuspended again in PBS for lymphocyte isolation with Lympholyte-M cell separation media (Cedar Lane, Burlington, Canada) per the manufacturer's instructions. Single-cell suspensions were stained for DAPI, and live cells were sorted with a sorter (SH800S, Sony, San Jose, CA) into RPMI containing 10% FBS on ice for single-cell sequencing library preparation.
A total of 8 samples were loaded onto a Chromium Next GEM Chip G, analyzed by the Chromium Controller (10x Genomics, Pleasanton, CA) for Gel Beads-in-emulsion (GEMs) generation and reverse transcription. The generated cDNA was purified with SPRIselect (Beckman Coulter Inc, Indianapolis, IN) and used for 5′ gene expression with V(D)J library construction. The cDNAs and libraries were examined for quality control using D5000 ScreenTape (Agilent Technologies, Waldbronn, Germany), and Qubit (Thermo Fisher Scientific, Waltham, MA) was used for quantification. To achieve 5000 reads per cell for the V(D)J library, the libraries were sequenced using the Illumina NovaSeq6000 system (Illumina, San Diego, CA).

value: Salivary gland


title: RT112, 0.1% hypoxia_2

tag: cell line


title: mESC, EZH2-Y728 mutant, SUZ12 (ChIP), rep2

description: Library name: Y728_SUZ12_rep2

tag: cell type

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-Y728 mutant


title: 54s

description: Library name: RNA_S8112Nr124

value: normal bladder

value: male

value: HIGH


title: mESC, EZH2-A677T mutant, SUZ12 (ChIP), rep2

description: Library name: A677T_SUZ12_rep2

tag: genotype

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-A677T mutant


title: SG TCR, B6, Female 2

description: Library name: TCR-B6F2


title: SG TCR, DC, Female 1

description: Library name: TCR-DCF1


title: RT112, Control_2

source_name: RT112, Control

tag: treatment

value: 21%O2 (normoxia)


title: 51S

description: Library name: RNA_S8112Nr123

tag: tissue

value: Ta

value: LOW


title: RT112, Control_3


title: RT112, 1% hypoxia_2

value: 1%O2 (hypoxia)


title: mESC, EZH2-WT, SUZ12 (ChIP), rep2

description: Library name: WT_SUZ12_rep2

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-WT


title: SG TCR, B6, Female 1

description: Library name: TCR-B6F1

tag: Sex

value: female


title: RT112, 0.1% hypoxia_1

value: 0.1%O2 (hypoxia)


title: 58s

description: Library name: RNA_S8112Nr126

tag: Stage


title: 49s

description: Library name: RNA_S8112Nr122

tag: grade


title: mESC, EZH2-A733T mutant, CBX7 (ChIP)

description: Library name: A733T_CBX7


title: SG TCR, DC, Male 2

description: Library name: TCR-DCM2


title: 18g

description: Library name: RNA_S8112Nr12

source_name: tumour bladder

value: tumour bladder


title: mESC, EZH2-Y728 mutant, CBX7 (ChIP), rep2

description: Library name: Y728_CBX7_rep2


title: RT112, 0.2% hypoxia_1

value: 0.2%O2 (hypoxia)


title: mESC, EZH2-A677T mutant, CBX7 (ChIP), rep2

description: Library name: A677T_CBX7_rep2

value: Mouse embryonic stem cells


title: 48s

description: Library name: RNA_S8112Nr121

source_name: normal bladder

value: Ta(m)


title: SG TCR, DC, Male 1

description: Library name: TCR-DCM1

value: Salivary gland


title: 47g

description: Library name: RNA_S8112Nr120


title: mESC, EZH2-WT, CBX7 (ChIP), rep2

description: Library name: WT_CBX7_rep2


title: RT4, 0.1% hypoxia_3

source_name: RT4, 0.1% hypoxia


title: 1G

description: Library name: RNA_S8112Nr1


title: mESC, EZH2-A733T mutant, H3K27ac (ChIP)

description: Library name: A733T_H3K27ac

value: Ezh2 heterozygous knockout mESCs exogenously expressing  EZH2-A733T mutant


title: 46S

description: Library name: RNA_S8112Nr119

value: normal bladder


title: RT4, 0.2% hypoxia_3

source_name: RT4, 0.2% hypoxia