title: BrdU-ip-seq from RPE1 cells grown in 50 µM BrdU [Input]

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

country: United Kingdom

institute: Earlham Institute

data_processing:
*library strategy: BrdU-ip-seq
Pre-barcodes were demultiplexed using FASTX barcode splitter and removed with  FASTX barcode trimmer
Sequencing and barcode trimming steps were checked for quality using FASTQC
Reads were mapped to hg38 using BWA-MEM, and filtered for uniquely mapping reads and duplicate reads excluded using Samtools.
Proportion of BrdU incorporation per sample is calculated as number of uniquely mapped reads with duplicates excluded IP/INPUT, as a proportion of the total pooled sample.
Assembly: Hg38
Supplementary files format and content: bigwig with ip/input

growth_protocol: HeLa-S3 (adherent) and hTERT-RPE1 were maintained in DMEM Glutamax (HeLa-S3) or DMEM/F12 Glutamax (hTERT-RPE1, both Gibco), with the addition of 10% foetal bovine serum (Sigma) and 1% penicillin/streptomycin (Gibco). Cells were maintained at 70% confluency in 5% CO2 at 37 °C.

extract_protocol:
DNA was extracted using classical phenol:chloroform and precipitation techniques.
Immunoprecipitated DNA was purified using AMPure XP beads at 0.9x. IP and input DNA were amplified separately using Illumina compatible indexes and NEBNext Ultra II Q5 Master Mix (M0544) for an equal number of cycles, typically 15-17, depending on recovery, and purified using AMPure XP beads at 0.9x.

treatment_protocol: Cells were treated with or without BrdU at the indicated concentrations for the indicated timespans.

value: hTERT-immortalized retinal pigment epithelial cells

value: Grown in 50 µM BrdU for 27 hrs

tag: sample type

value: input


title: BrdU-ip-seq from RPE1 cells grown in 300 nM BrdU [Input]

status: Public on Apr 03 2025

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment

value: Grown in 300 nM BrdU for 27 hrs


title: Liver_Veh-4

city: La Jolla

first: R

middle: Luke

last: Wiseman

state: California

address: 10550 N Torrey Pines Rd, Mb110 Receiving Department

country: USA

institute: The Scripps Research Institute

description:
Library name: Sample 14
Column name in liver_IXA62_7days_raw counts_all samples, Veh _4_liver

library_source: transcriptomic

data_processing:
Alignment of reads was performed using DNAstar Lasergene SeqManPro
Aligned reads were imported into ArrayStar 12.2 with QSeq (DNAStar Inc.) to quantify gene expression levels.
Differential expression analysis and statistical significance calculations between different conditions were assessed using DEseq2 v. 1.42.1 in R
Assembly: HEK293 reads were aligned to the human genome GRCh38 assembly. Reads generated from mouse kidney and liver samples were aligned to the mouse genome GRCm39 assembly.
Supplementary files format and content: csv files contain raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: liver

growth_protocol: Male C57BL/6J mice, aged 8-10 weeks, were obtained from the rodent breeding colonies at Scripps Research and were housed under a 12-h light/dark cycle with ad libitum access to food and water. HEK 293 cells were cultured in high-glucose Dulbecco’s Modified Eagle’s Medium (DMEM) (Corning Cellgro) supplemented with 10% fetal bovine serum (FBS) (Omega Scientific), 2 mM L-glutamine (Gibco), 100 U/mL penicillin and 100 μg/mL streptomycin (Gibco) and under typical tissue culture conditions (37°C, 5% CO2).

extract_protocol:
For mouse tissue experiments, 4-5 biological replicates were studied for each treatment condition. Total RNA from liver or kidney was isolated using Zymo Research Direct-zol RNA Miniprep kits following the manufacturer’s instructions after homogenization in TRIzol reagent. For HEK293 cells, 3 biological replicates were studied for each treatment condition.Total RNA from HEK293 cells were isolated using QuickRNA mini kit (Zymo) according to the manufacturer′s instructions. Whole transcriptome RNA sequencing was conducted by BGI Americas on the BGI Proprietary platform.
libraries were constructed at BGI

treatment_protocol: For in vivo study, IXA62 was prepared in a formulation of 10% DMSO, 30% Kolliphor EL:ethanol (2:1 ratio), and 60% saline at a concentration of 10 mg/mL. mice were weighted and administered IXA62 (50 mpk) or vehicle by IP injection once daily in the morning for 7 days, and sacrificed 4 h after the final injection. For HEK 293 cells, DMSO, 10 uM compounds, including IXA21(Life chemicals, Cat #F2574-0132), IXA62 (Enamine, Cat #T5347952), IXA76 (ChemDiv, Cat #1486-0766), IXA502 (ChemDiv, Cat #K898-0862), IXA554 (Life chemicasl,Cat #F2506-1107), IXA624 (Life chemicals, Cat# F5772-8755) or 0.5 uM Thapsigargin (Tg) (Fisher, Cat # 50-464-295) were treated for 6 h.

tag: tissue

value: liver

value: veh


title: P3F1_pcHiC_Rep2

city: Badalona

first: Gerard

last: Martinez-Cebrian

state: Barcelona

address: Edifici Josep carreras, Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Institut Josep carreras

data_processing:
For HiC, raw sequencing reads were processed using juicer v1.4 with genome assembly hg38 and ARIMA’s restriction sites. Technical replicates for each cell line were merged after alignment within the juicer pipeline. For pCHiC, raw sequencing reads were processed using ARIMA’s pipeline for promoter capture experiments (Arima-CHiC-v1.4). Briefly, we used the HiCUP pipeline from the Babraham Institute to map with bowtie2 each pair of the ligated fragments to the human genome (hg38 assembly). Next, BAM files were converted into CHiCAGO input files and processed with CHiCAGO to obtain interaction confidence scores for each cell line.
Assembly: hg38
Supplementary files format and content: interaction bed files and hic files
Library strategy: pcHi-C

source_name: induced pluripotent stem cell muscle progenitor

growth_protocol: Human iPS cells expressing PAX7 (muscle progenitors)(Wu et al., 2016) were grown on 0.1% gelatin-coated culture plates in GlutaMAX supplemented IMDM (Gibco) with 15% stem cell qualified fetal bovine serum (Gemini), 1% penicillin/streptomycin (Corning), 50 μg/ml L-ascorbic acid (Sigma), 4.5mM 1-thioglycerol (Sigma), and 10 ng/ml recombinant human basic-FGF (Peprotech). These muscle progenitors were infected using lentiviral doxycycline-inducible or constitutive (EF1α promoter) constructs driving expression of a cDNA encoding the exact PAX7-FOXO1 or PAX3-FOXO1 fusion protein found in ARMS tumors. PAX7 transgene expression was induced by adding Dox (Sigma-Aldrich, final concentration 1 μg/ml), and then maintained throughout the protocol by replacing the medium (including dox) with 10 ng/ml human basic-FGF (Preprotech) every 2 days.

extract_protocol:
For HiC and pCHiC, we used a commercial kit from Arima Genomics (A510008). Briefly, 106 cells were cross-linked with formaldehyde and extracted following the manufacturer’s instructions. 4 mg of DNA per condition were digested and ligated, and biotin was incorporated to select successfully ligated fragments. Ligated DNA was sonicated with a Diagenode Bioruptor for 20 min, 30 seconds ON/OFF, at 4°C to obtain ~400 bp DNA fragments. Biotinylated DNA was purified using streptavidin beads.
HiC and pcHiC libraries were constructed using the library preparation protocol in ARIMA’s HiC kit. A fraction of the HiC library was used for sequencing in an Illumina NovaSeq 6000 for 300 cycles pair-end at a depth of ~200M reads per sample. Next, the remainder of the HiC library was used for promoter capture using ARIMA’s custom panel of human promoters (~84,000 probes for ~26,000 promoters). After promoter capture, the pcHiC libraries were amplified following the manufacturer’s instructions and sequenced with Illumina NovaSeq 6000 (300 bp, paired-end) at a depth of ~200M reads per sample.

treatment_protocol: For cultures without Dox, cells were harvested at day 3 following Dox removal for analysis.

tag: genotype


title: Liver_IXA62-5

description:
Library name: Sample 19
Column name in liver_IXA62_7days_raw counts_all samples, IXA62_5_liver

value: 50 mpk IXA62


title: P3F1_pcHiC_Rep1

value: induced pluripotent stem cell muscle progenitor


title: BrdU-ip-seq from RPE1 cells grown in 10 µM BrdU [Input]

value: Grown in 10 µM BrdU for 27 hrs


title: Liver_Veh-3

description:
Library name: Sample 13
Column name in liver_IXA62_7days_raw counts_all samples, Veh _3_liver


title: BrdU-ip-seq from RPE1 cells grown in 1500 nM BrdU [Input]

value: Grown in 1500 nM BrdU for 27 hrs


title: BrdU-ip-seq from HeLa-S3 cells grown in 50 µM BrdU [Input]

value: Grown in 50 µM BrdU for 20 hrs


title: Liver_Veh-2

description:
Library name: Sample 12
Column name in liver_IXA62_7days_raw counts_all samples, Veh _2_liver


title: BrdU-ip-seq from HeLa-S3 cells grown in 1500 nM BrdU [Input]

value: Grown in 1500 nM BrdU for 20 hrs


title: OVCAR5 Adipo CC rep1

city: Chicago

first: Daniela

middle: Elena

last: Matei

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

data_processing:
Fastq files were pre-analyzed using FastQC (0.11.5)
Reads were aligned to the ENSEMBL human genome GRCh38 (release 91) using STAR (2.5.2)
BAM files from STAR alignment were sorted by name using Samtools (1.6)
HTSeq-count (anaconda 3.6) was used to generate raw counts for each BAM file
Assembly: GRCh38
Supplementary files format and content: counts

molecule: polyA RNA

source_name: ascites

growth_protocol: OVCAR5 Cells were cultured in RPMI 1640 (Corning), 10% fetal bovine serum (FBS) (Corning), 1% penicillin/streptomycin (Sigma), and 1X GlutaMAX (Gibco), OVCAR8 cells were grown in DMEM (Corning), 10% fetal bovine serum (FBS) (Corning), 1% penicillin/streptomycin (Sigma), both cell lines were growth in a humidify atmosphere, 5% and 37°C.

extract_protocol:
RNA was isolated by using TRIzol (Invitrogen) according to the manufacturer’s instructions and quantified using a NanoDrop 3300 Fluorospectrometer.
The RNA-sequencing (RNA-seq) libraries were prepared from 1 μg of total RNA of OVCAR5, and OVCAR8 mono- or co-culture. Libraries were generated using the NEBNext Ultra II RNA library prep kit from Illumina (New England Biolabs, Inc.). Library preparation was performed accoding to manufacter's protocol.

treatment_protocol: OVCAR8 and OVCAR5 cells were co-cultured on with mature viseral adipocytes for 3 days and then FACS separated.

value: ascites

value: High grade serous ovarian cancer

value: transfected with GFP

value: Adipocyte Co-culture


title: BrdU-ip-seq from HeLa-S3 cells grown in 300 nM BrdU [Input]

value: Grown in 300 nM BrdU for 20 hrs


title: P7F1_pcHiC_Rep2


title: Liver_Veh-1

description:
Library name: Sample 11
Column name in liver_IXA62_7days_raw counts_all samples, Veh _1_liver


title: BrdU-ip-seq from HeLa-S3 cells grown in 10 µM BrdU [Input]

value: Grown in 10 µM BrdU for 20 hrs


title: BrdU-ip-seq from HeLa-S3 cells grown in 0 µM BrdU [Input]

value: Grown in 0 µM BrdU for 20 hrs


title: AD025

city: Southampton

first: Andres

middle: Felipe

last: Vallejo Pulido

address: University of Southampton

department: Medicine

institute: University of Southampton

data_processing:
High-quality reads filtered at 15M depth across all samples were mapped to the human genome (GRCh38) using Kallisto
Raw counts from RNA-Seq were processed in Bioconductor package EdgeR (54) and SLEUTH
Following demultiplexing, raw FASTQ files were aligned to the human genome (GRCh38), using kallisto-bustools
Doublet detection and hashing demultiplexing was done using Solo. Empty barcodes and percentage of mitochondrial genes were checked within Scanpy.
CellBender was used to remove empty technical artefacts.
Assembly: GRCh38
Supplementary files format and content: CSV table with counts and TPM as estimated by Kallisto

source_name: FACS sorted CD207+

growth_protocol: primary cells isolated by digestion from skin punch biopsies

extract_protocol:
For bulk RNA-seq RNA was isolated using Direct-zol RNA micro prep (Zymo, UK) as per the manufacturer’s protocol.
For Bulk RNA-seq cDNA libraries were generated using SMART-Seq Stranded Library Preparation for Ultra Low Input according to the SMART-Seq Stranded Kit User Manual  following the Ultra low input workflow (Takara Bio). Samples were pooled (12/batch) for library preparation. For Drop-seq High Sensitivity DNA Assay Nextera kit, Illumina, was used. For Constellation cDNA was aplified using targeted linear amplification (20 rounds) and further prepared using True-seq, Illumina.

value: FACS sorted CD207+

value: AD


title: OVCAR5 Control rep2

value: Control


title: BrdU-ip-seq from RPE1 cells grown in 50 µM BrdU [IP]

value: hTERT-immortalized retinal pigment epithelial cells

value: Grown in 50 µM BrdU for 27 hrs

value: IP


title: AD023


title: BrdU-ip-seq from RPE1 cells grown in 300 nM BrdU [IP]

value: Grown in 300 nM BrdU for 27 hrs


title: Kidney_IXA62-4

description:
Library name: Sample 9
Column name in liver_IXA62_7days_raw counts_all samples, IXA62_4_Kidney

source_name: Kidney

value: Kidney

value: 50 mpk IXA62


title: AD022


title: BrdU-ip-seq from RPE1 cells grown in 1500 nM BrdU [IP]

value: Grown in 1500 nM BrdU for 27 hrs


title: BrdU-ip-seq from RPE1 cells grown in 10 µM BrdU [IP]

value: Grown in 10 µM BrdU for 27 hrs


title: Kidney_IXA62-5

description:
Library name: Sample 10
Column name in liver_IXA62_7days_raw counts_all samples, IXA62_5_Kidney


title: Kidney_IXA62-3

description:
Library name: Sample 8
Column name in liver_IXA62_7days_raw counts_all samples, IXA62_3_Kidney


title: BrdU-ip-seq from RPE1 cells grown in 0 µM BrdU [IP]

value: Grown in 0 µM BrdU for 27 hrs


title: BrdU-ip-seq from HeLa-S3 cells grown in 300 nM BrdU [IP]


title: Kidney_IXA62-2

description:
Library name: Sample 7
Column name in liver_IXA62_7days_raw counts_all samples, IXA62_2_Kidney


title: AD020


title: AD021


title: BrdU-ip-seq from RPE1 cells grown in 0 µM BrdU [Input]

value: input


title: OVCAR5 Control rep1

value: ascites

value: High grade serous ovarian cancer

value: transfected with GFP


title: Control_pcHiC_Rep1

value: induced pluripotent stem cell muscle progenitor

value: WT


title: Control_pcHiC_Rep2


title: AD019

value: FACS sorted CD207+

value: AD


title: BrdU-ip-seq from HeLa-S3 cells grown in 10 µM BrdU [IP]

value: Grown in 10 µM BrdU for 20 hrs


title: BrdU-ip-seq from HeLa-S3 cells grown in 0 µM BrdU [IP]

value: Grown in 0 µM BrdU for 20 hrs


title: Kidney_IXA62-1

description:
Library name: Sample 6
Column name in liver_IXA62_7days_raw counts_all samples, IXA62_1_Kidney


title: Kidney_Veh-5

description:
Library name: Sample 5
Column name in liver_IXA62_7days_raw counts_all samples, Veh _5_Kidney

value: Veh


title: Kidney_Veh-4

description:
Library name: Sample 4
Column name in liver_IXA62_7days_raw counts_all samples, Veh _4_Kidney


title: P_025

value: P


title: SCNT4

city: Urumchi

first: weijian

last: li

address: 311 East Nongda Road

country: China

institute: Xinjiang Agricultural University

description: Library name: SCNT4

data_processing:
The raw data were processed using fastp (version 0.23.4) to trim sequencing adapters, remove low-quality reads (-q 20 -u 40 -3 20 -5 20 -c), and exclude reads containing N (-n 0). Retain the default values for other parameters. The cleaned reads were subsequently aligned to the reference genomes using Hisat2  (version 2.2.1). Mapping was performed using the parameters --new-summary -p 16 -x -S with quality-filtered paired-end sequencing data. Retain the default values for other parameters. The reference genomes used for alignment were as follows: ARS-UI_Ramb_v3.0 for sheep, ARS-UCD2.0 for cattle, ARS1.2 for goats, GRCm39 for mice, and Sscrofa11.1 for pigs. Finally, gene-level counts for each sample were obtained using Rsubread(version 2.14.2).
Assembly: ARS-UI_Ramb_v3.0
Supplementary files format and content: TPM

organism: Ovis aries

extract_protocol:
SCNT embryos and fertilized embryos were allowed to develop to the 8-cell stage, at which point low input transcriptomic samples were collected. Each group was subjected to at least three independent trials. Following collection, RNA was extracted using single-cell lysis buffer (Invitrogen, Carlsbad, CA, USA), and first-strand cDNA was synthesized using the Single Cell Reverse Transcription Kit (Invitrogen, Carlsbad, CA, USA). The cDNA was subsequently amplified by PCR for 20 cycles. The amplification products were purified using Ampure XP beads and their concentration was determined using the Qubit® 3.0 Fluorometer (Thermo, Waltham, Massachusetts, USA). The integrity of the cDNA was assessed with the Agilent 2100 Bioanalyzer and the Agilent 2100 High Sensitivity DNA Assay Kit (Agilent, Santa Clara, CA, USA). Finally, paired-end sequencing (PE 150, smart-seq2) was performed on the constructed libraries.
SCNT embryos and fertilized embryos were allowed to develop to the 8-cell stage, at which point low input transcriptomic samples were collected. Each group was subjected to at least three independent trials. Following collection, RNA was extracted using single-cell lysis buffer (Invitrogen, Carlsbad, CA, USA), and first-strand cDNA was synthesized using the Single Cell Reverse Transcription Kit (Invitrogen, Carlsbad, CA, USA). The cDNA was subsequently amplified by PCR for 20 cycles. The amplification products were purified using Ampure XP beads and their concentration was determined using the Qubit® 3.0 Fluorometer (Thermo, Waltham, Massachusetts, USA). The integrity of the cDNA was assessed with the Agilent 2100 Bioanalyzer and the Agilent 2100 High Sensitivity DNA Assay Kit (Agilent, Santa Clara, CA, USA). Finally, paired-end sequencing (PE 150, smart-seq2) was performed on the constructed libraries.

value: embryo

value: SCNT


title: PSN1_Tr_3

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

country: Germany

institute: Christian-Albrechts-University Kiel

data_processing:
Fastq files were generated using Illuminas base calling software GenerateFASTQ v1.1.0.64 and overall sequencing quality was analyzed using the FastQC script.
For RNA-seq, reads were aligned to the human genome (hg19) using Tophat v2.1.1 (Kim et al., 2013) and Bowtie2 v2.3.2 (Langmead et al., 2012) using the parameters  –n 1 -- and samples were normalized to the number of mapped reads in the smallest sample.
For gene expression analysis, reads per gene (Ensembl gene database) were counted with the “summarizeOverlaps” function from the R package “GenomicAlignments” using the “union”-mode and non- or weakly expressed genes were removed (mean read count over all samples <1).
Genome_build: hg19
Supplementary_files_format_and_content: table of counts per gene

source_name: pancreatic cancer cells

extract_protocol:
Total RNA was extracted using manufactors instructions (Rneasy, Qiagen)
mRNA was enriched with NEBNext Poly(A) mRNA Magnetic Isolation kit and RNA libraries were prepared using NEBNext Ultra II Directional RNA Library according to the manufacturer’s instructions

value: parental cell line


title: P_023


title: SCNT3

description: Library name: SCNT3


title: Kidney_Veh-3

description:
Library name: Sample 3
Column name in liver_IXA62_7days_raw counts_all samples, Veh _3_Kidney

value: Kidney


title: SCNT2

description: Library name: SCNT2


title: PSN1_Tr_2


title: PSN1_Tr_1


title: Kidney_Veh-2

description:
Library name: Sample 2
Column name in liver_IXA62_7days_raw counts_all samples, Veh _2_Kidney


title: BrdU-ip-seq from HeLa-S3 cells grown in 50 µM BrdU [IP]

value: Grown in 50 µM BrdU for 20 hrs

value: IP


title: SCNT1

description: Library name: SCNT1


title: PSN1KONX_Tr_3

value: NOXA knockout


title: P_020


title: Kidney_Veh-1

description:
Library name: Sample 1
Column name in liver_IXA62_7days_raw counts_all samples, Veh _1_Kidney


title: PSN1KONX_Tr_2


title: BrdU-ip-seq from HeLa-S3 cells grown in 1500 nM BrdU [IP]

value: Grown in 1500 nM BrdU for 20 hrs


title: P_019


title: IVF3

description: Library name: IVF3

value: IVF


title: B6.129S4 Strain, Urethane treated, #43

city: Houston

first: Jianjuan

last: Zhang

address: 1515 Holcombe Blvd.

institute: MD Anderson Cancer Center

description:
Library name: 129S4-Urethane-43
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were generated using the CellRanger (8.0.0) software.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Lung

extract_protocol:
Fresh lung and tumor samples were collected from mice, washed with PBS, and minced into ~1 mm³ pieces in RPMI-1640 medium (Thermo Fisher Scientific) containing 10% fetal bovine serum (FBS, Gibco). The tissues were enzymatically digested with a solution of 1 mg/ml collagenase A, 0.4 mg/ml hyaluronidase, and BSA fraction V (1:5) for 1 ~ 2 hours at 37°C on a rotor, following the manufacturer’s instructions.  The digested samples were centrifuged at 350g for 5 minutes, the supernatant was removed, and 1 ~ 5 ml of pre-warmed Trypsin-EDTA was added. The cells were resuspended and gently pipetted for 1–3 minutes, resulting in a stringy consistency due to the lysis of dead cells and released DNA. After adding 10 ml of cold RPMI-1640 without phenol red supplemented with 2% FBS, the samples were centrifuged again at 350g for 5 minutes, and the supernatant was discarded.  If cell clumps persisted, 5 ml of pre-warmed Dispase (5 U/mL) and 50 µL of DNase I solution (10 mg/ml in 0.15 M NaCl) were added, followed by 1 minute of pipetting. For persistent stringiness, an additional 50 µL of DNase I was used. The dissociated cells were diluted with 10 ml of cold RPMI-1640 without phenol red (2% FBS), filtered through a 40 µm cell strainer, and centrifuged at 450g for 5 minutes.  To remove red blood cell contamination, the cell pellet was treated with a 1:4 mixture of cold RPMI-1640 (2% FBS) and ammonium chloride solution, centrifuged, and resuspended in PBS with 1% BSA. The final cell suspension, with viability ≥70% and a density of 7 × 105 to 1.2 × 106 cells/ml, was loaded onto the Chromium Single Cell Controller (10x Genomics) for single-cell gel bead-in-emulsion generation.  scRNA-seq libraries were prepared using the Single Cell 3′ Library and Gel Bead Kit v3.1 and sequenced on the NovaSeq 6000 platform (Illumina).
5ʹ Gene Expression (GEX) Library Construction 5.1 GEX Fragmentation, End Repair & A-tailing 5.2 GEX Post Fragmentation, End Repair & A-tailing Double Sided Size Selection – SPRIselect 5.3 GEX Adaptor Ligation 5.4 GEX Post Ligation Cleanup – SPRIselect 5.5 GEX Sample Index PCR 5.6 GEX Post Sample Index Double Sided Size Selection – SPRIselect 5.7 GEX Post Library Construction QC

treatment_protocol: Urethane 1mg/g body weight within 8 days(1st; 4th; 8th)

value: Lung

tag: age

value: 48 weeks

value: Wild type

value: Urethane

tag: batch

value: C


title: IVF2

description: Library name: IVF2


title: P_018

value: FACS sorted CD207+


title: P_017


title: PSN1KONX_Tr_1


title: PSN1KONX_Control_3

value: vehicle


title: AC_pCDH150

city: Camperdown

first: Graham

middle: Gregory

last: Neely

state: NSW

address: John Hopkins Drive

country: Australia

institute: Charles Perkins Centre, The University of Sydney

description: Isolated transgenic sequence from pSFV-DE_eGFP-LUC plasmid DNA, sequenced to control for identification of transgene substitutions in VLPs.

library_source: other

data_processing:
Raw FASTQ files were aligned to transgene reference sequences (FASTA) with minimap2. Any mate-pair issues were fixed in the output .sam files with the samtools fixmate command before reads were sorted (samtools sort) and reformatted (samtools mpileup). VarScan 2.3.9 was used to call for variants with command mpileup2snp with arguments --min-coverage 10000 --min-reads2 15 --min-var-freq 0.00025 --p-value 0.01. Further annotation was performed with vcf-annotator using default commands, aligning to transgene reference sequences (GenBank format).
Assembly: ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTCAGGATCCGGAGCCACGAACTTCTCTCTGTTAAAGCAAGCAGGAGACGTGGAAGAAAACCCCGGGCCCATGGAAGATGCCAAAAACATTAAGAAGGGCCCAGCGCCATTCTACCCACTCGAAGACGGGACCGCCGGCGAGCAGCTGCACAAAGCCATGAAGCGCTACGCCCTGGTGCCCGGCACCATCGCCTTTACCGACGCACATATCGAGGTGGACATTACCTACGCCGAGTACTTCGAGATGAGCGTTCGGCTGGCAGAAGCTATGAAGCGCTATGGGCTGAATACAAACCATCGGATCGTGGTGTGCAGCGAGAATAGCTTGCAGTTCTTCATGCCCGTGTTGGGTGCCCTGTTCATCGGTGTGGCTGTGGCCCCAGCTAACGACATCTACAACGAGCGCGAGCTGCTGAACAGCATGGGCATCAGCCAGCCCACCGTCGTATTCGTGAGCAAGAAAGGGCTGCAAAAGATCCTCAACGTGCAAAAGAAGCTACCGATCATACAAAAGATCATCATCATGGATAGCAAGACCGACTACCAGGGCTTCCAAAGCATGTACACCTTCGTGACTTCCCATTTGCCACCCGGCTTCAACGAGTACGACTTCGTGCCCGAGAGCTTCGACCGGGACAAAACCATCGCCCTGATCATGAACAGTAGTGGCAGTACCGGATTGCCCAAGGGCGTAGCCCTACCGCACCGCACCGCTTGTGTCCGATTCAGTCATGCCCGCGACCCCATCTTCGGCAACCAGATCATCCCCGACACCGCTATCCTCAGCGTGGTGCCATTTCACCACGGCTTCGGCATGTTCACCACGCTGGGCTACTTGATCTGCGGCTTTCGGGTCGTGCTCATGTACCGCTTCGAGGAGGAGCTATTCTTGCGCAGCTTGCAAGACTATAAGATTCAATCTGCCCTGCTGGTGCCCACACTATTTAGCTTCTTCGCTAAGAGCACTCTCATCGACAAGTACGACCTAAGCAACTTGCACGAGATCGCCAGCGGCGGGGCGCCGCTCAGCAAGGAGGTAGGTGAGGCCGTGGCCAAACGCTTCCACCTACCAGGCATCCGCCAGGGCTACGGCCTGACAGAAACAACCAGCGCCATTCTGATCACCCCCGAAGGGGACGACAAGCCTGGCGCAGTAGGCAAGGTGGTGCCCTTCTTCGAGGCTAAGGTGGTGGACTTGGACACCGGTAAGACACTGGGTGTGAACCAGCGCGGCGAGCTGTGCGTCCGTGGCCCCATGATCATGAGCGGCTACGTTAACAACCCCGAGGCTACAAACGCTCTCATCGACAAGGACGGCTGGCTGCACAGCGGCGACATCGCCTACTGGGACGAGGACGAGCACTTCTTCATCGTGGACCGGCTGAAGAGCCTGATCAAATACAAGGGCTACCAGGTAGCCCCAGCCGAACTGGAGAGCATCCTGCTGCAACACCCCAACATCTTCGACGCCGGGGTCGCCGGCCTGCCCGACGACGATGCCGGCGAGCTGCCCGCCGCAGTCGTCGTGCTGGAACACGGTAAAACCATGACCGAGAAGGAGATCGTGGACTATGTGGCCAGCCAGGTTACAACCGCCAAGAAGCTGCGCGGTGGTGTTGTGTTCGTGGACGAGGTGCCTAAAGGACTGACCGGCAAGTTGGACGCCCGCAAGATCCGCGAGATTCTCATTAAGGCCAAGAAGGGCGGCAAGATCGCCGTGTCGACTGTTTAA
Supplementary files format and content: .vcf file (openable in Excel) containing analysis of mutation calls.
Library strategy: Amplicon sequencing

molecule: other

organism: synthetic construct

source_name: synthetic construct

extract_protocol:
Maxiprepped plasmid DNA. RT-PCR to amplify transgene sequences (amplicons used for library construction).
Samples were sequenced with Novogene using their ‘Microbial PCR Product Whole Genome Sequencing’ strategy. Amplicons underwent fragmentation prior to PCR-free library preparation and sequencing using NovaSeq PE250 technology.

value: synthetic construct


title: IVF1

description: Library name: IVF1

value: embryo


title: B6.129S4 Strain, Urethane treated, #42

description:
Library name: 129S4-Urethane-42
10x Genomics


title: PSN1KONX_Control_2


title: B6.129S4 Strain, Urethane treated, #41

description:
Library name: 129S4-Urethane-41
10x Genomics


title: P_015

value: P


title: P_016


title: PSN1KONX_Control_1


title: P_022


title: B6.129S4 Strain, Urethane treated, #33

description:
Library name: 129S4-Urethane-33
10x Genomics

value: 38 weeks

value: B


title: H2B-mice, Replicate 2,  Blood

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

description: 10X Genomics

data_processing:
Cellranger (version 6.0.1) was used to map FASTQ files to the mouse genome (refdata-gex-mm10-2020-A). Count tables were then opened in R (v. 4.2.0), and Seurat (v. 4.1.0) was used for downstream analysis. Only genes with a minimum of 10 cells expressing the gene were selected. Moreover, only cells with at least 200 genes expressed were selected and maximum 6000 genes (3000 genes for the blood), this last point in order to remove doublets. To avoid dying cells, a maximum of 20 percent (10 percent for the blood) of mitochondrial content was accepted. Data was log-normalized and scaled on the 4000 most variable features using variance-stabilizing method, and principal component analysis was performed on those variable features. The UMAP was obtained on the first 30 PCs (cutoff was obtained using the Elbow-plot method). The SNN graph was obtained using default parameters, and resolutions between 0.1 and 0.8 were tested. Finally, a resolution of 0.15 (0.25 for the skin and 0.1 for the blood) was chosen to annotate the broad clusters.
Supplementary files format and content: Filtered counts tab-separated matrix,barcodes and features
Assembly: mm10

source_name: Blood

growth_protocol: The bone marrow, spleen, blood and dysplastic ear skin of HPV mice (n=3), the cervical tumor of HPV-E2 mice (n=3), and control tissues from H2b mice (n=3) were used to generate single cell suspensions as described previously. Cells were loaded into the 10X Genomics Chromium platform.

extract_protocol:
Bone marrow single cell suspensions were generated from femurs and tibiae of mice. Cells were flushed by centrifuging the bones cut at the knee joint. The isolate was filtered through a 40 ?m cell strainer.  Single cell suspensions of spleens were generated by mashing the spleen through a 40 ?m cell strainer. Tumors were harvested and minced using a scalpel and digested for 30 minutes using collagenase A (0.33 U/mL, Roche), dispase (0.85 U/mL, Roche), and DNAse I (144 U/mL, Roche) in RPMI medium with intermittent shaking at 37°C. Afterward, tumor single cell suspensions were passed through a 70 ?m cell strainer. Blood was collected by intracardiac punction into EDTA-coated tubes. Red blood cells were lyzed with BD Pharm Lyse Lysing buffer (BD Biosciences, ref. 555899) according to the manufacturer?s instructions. Cell suspensions were further used for single cell RNA sequencing.
Single-cell gene expression libraries were prepared following the manufacturer?s protocol with the 10x Genomics Next GEM Single Cell 5? Kit v2, and then sequenced on an Illumina HiSeq4000 platform.

value: Blood


title: P_013


title: B6.129S4 Strain, Urethane treated, #31

description:
Library name: 129S4-Urethane-31
10x Genomics


title: H2B-mice, Replicate 1,  Blood

description: 10X Genomics


title: P_014


title: HPV-mice, Replicate 3,  Blood

description: 10X Genomics


title: PSN1_KOAML_Tr_2

value: RUNX1 knockout


title: PSN1_KOAML_Tr_3


title: PSN1_KOAML_Tr_1


title: B6.129S4 Strain, Urethane treated, #22

description:
Library name: 129S4-Urethane-22
10x Genomics

value: 22 weeks


title: P_012


title: P_011


title: PSN1_KOAML_Control_3


title: HPV-mice, Replicate 2,  Blood

description: 10X Genomics


title: HPV-mice, Replicate 1, Blood

description: 10X Genomics


title: P_010


title: H2B-mice, Replicate 3,  Blood

description: 10X Genomics


title: B6.129S4 Strain, Urethane treated, #32

description:
Library name: 129S4-Urethane-32
10x Genomics


title: H2B-mice, Replicate 3,  Ear

description: 10X Genomics

source_name: Ear

value: Ear


title: PSN1_KOAML_Control_2


title: PSN1_KOAML_Control_1


title: B6.129S4 Strain, Urethane treated, #13

description:
Library name: 129S4-Urethane-13
10x Genomics

value: 15 weeks


title: H2B-mice, Replicate 2,  Ear

description: 10X Genomics


title: PSN1_Control_3

value: parental cell line


title: B6.129S4 Strain, Urethane treated, #12

description:
Library name: 129S4-Urethane-12
10x Genomics

value: Lung


title: B6.129S4 Strain, Urethane treated, #11

description:
Library name: 129S4-Urethane-11
10x Genomics

value: Wild type


title: P_008


title: P_007


title: H2B-mice, Replicate 1,  Ear

description: 10X Genomics


title: PSN1_Control_2


title: HPV-mice, Replicate 3,  Ear

description: 10X Genomics


title: B6.129S4 Strain, Urethane treated, #23

description:
Library name: 129S4-Urethane-23
10x Genomics

value: Urethane


title: P_006


title: PSN1_Control_1


title: B6.129S4 Strain, Untreated

description:
Library name: 129S4-Urethane-0
10x Genomics

value: 8 weeks

value: No

value: A


title: Sham3

city: chongqing

first: Dadi

last: Peng

address: 1 Mittraphap Road Street, yuanjiagang

department: Department of Hepatobiliary Surgery

institute: the First Affiliated Hospital of Chongqing Medical University

description:
Library name: sample6
Sham group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM value for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: liver

value: Only laparotomy, no hepatic ischemia reperfusion intervention


title: Sham2

description:
Library name: sample5
Sham group, replicate biosample 2


title: Panc1_Treatment_2


title: P_005

value: FACS sorted CD207+

value: P


title: B6.129S4 Strain, Urethane treated, #21

description:
Library name: 129S4-Urethane-21
10x Genomics

value: B


title: HPV-mice, Replicate 1, Ear

description: 10X Genomics


title: P_004


title: Sham1

description:
Library name: sample4
Sham group, replicate biosample 1


title: Panc1_Treatment_1


title: P_009


title: H2B-mice, Replicate 3, Bone Marrow

description: 10X Genomics

source_name: Bone Marrow

value: Bone Marrow


title: P_003


title: Panc1_Tr_3


title: P_002


title: H2B-mice, Replicate 2, Bone Marrow

description: 10X Genomics


title: IR injury 3

description:
Library name: sample3
IR injury group, replicate biosample 3

value: Hepatic ischemia reperfusion injury was performed after laparotomy


title: IR injury 2

description:
Library name: sample2
IR injury group, replicate biosample 2


title: Panc1_KOAML_Tr_2

value: RUNX1 knockout


title: H2B-mice, Replicate 1, Bone Marrow

description: 10X Genomics


title: NP_030

value: NP


title: Panc1_KOAML_Tr_1


title: NP_026


title: HPV-mice, Replicate 3, Bone Marrow

description: 10X Genomics


title: Panc1_KOAML_Control_3


title: tdTomato+ hCD2+ DCs extraced from mLNs of 15 days old Gm38411-iCre-hCD2 R26 tdTomato mice_Hashtag

city: St. Louis

first: Marco

last: Colonna

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University School of Medicine in St. Louis

description:
Library name: Hashtag_tdTomato+ hCD2+
HTO

data_processing:
3' scRNAseq data was processed using the cellranger count pipeline (CellRanger version 8.0.1, 10X Genomics).
Assembly: mm10
Supplementary files format and content: Four files per sample: barcodes.tsv.gz,  features.tsv.gz and matrix.mtx.gz as well as assignment_confidence_table.csv

molecule: protein

source_name: mLN

extract_protocol:
We followed the Chromium Single Cell 3′ Reagent Kit v4 User Guide.
Chromium Single Cell 3′ Reagent Kit v4 User Guide was followed for library preparation.

value: mLN

value: DCs

value: Gm38411-iCre-hCD2 R26 tdTomato

value: No treatment

tag: library type

value: HTO

tag: hto

value: TotalSeq™-B0301 anti-mouse Hashtag 1 until TotalSeq™-B0312 anti-mouse Hashtag 12


title: HPV-mice, Replicate 2,  Ear

description: 10X Genomics

value: Ear


title: HPV-mice, Replicate 2, Bone Marrow

description: 10X Genomics


title: NP_025


title: tdTomato+ hCD2+ DCs extraced from mLNs of 15 days old Gm38411-iCre-hCD2 R26 tdTomato mice_RNA

description:
Library name: RNA_tdTomato+ hCD2+
polyA RNA

value: RNA


title: HPV-mice, Replicate 1, Bone Marrow

description: 10X Genomics


title: Panc1_KOAML_Control_2


title: NP_022


title: H2B-mice, Replicate 3, Spleen

description: 10X Genomics

source_name: Spleen

value: Spleen


title: Panc1_KOAML_Control_1


title: NP_021


title: tdTomato+ hCD2– DCs extraced from mLNs of 15 days old Gm38411-iCre-hCD2 R26 tdTomato mice_Hashtag

description:
Library name: Hashtag_tdTomato+ hCD2–
HTO


title: tdTomato+ hCD2– DCs extraced from mLNs of 15 days old Gm38411-iCre-hCD2 R26 tdTomato mice_RNA

description:
Library name: RNA_tdTomato+ hCD2–
polyA RNA


title: NP_020


title: H2B-mice, Replicate 2, Spleen

description: 10X Genomics


title: Panc1_Control_3

value: vehicle

value: parental cell line


title: DCs extraced from mLNs and siLP of 15 days old Gm38411-iCre-hCD2_Hashtag

description:
Library name: Hashtag
HTO

extract_protocol:
We followed the Chromium Single Cell 3′ Reagent Kit v3 User Guide.
The Chromium Single Cell 3′ Reagent Kit v3 User Guide was used for library preparation.

value: TotalSeq™-B0302 anti-mouse Hashtag 2 Antibody, TotalSeq™-B0304 anti-mouse Hashtag 4 Antibody, TotalSeq™-B0305 anti-mouse Hashtag 5 Antibody,TotalSeq™-B0306 anti-mouse Hashtag 6 Antibody, TotalSeq™-B0308 anti-mouse Hashtag 8 Antibody, TotalSeq™-B0309 anti-mouse Hashtag 9 Antibody


title: Panc1_Control_2


title: NP_018

value: FACS sorted CD207+


title: DCs extraced from mLNs and siLP of 15 days old Gm38411-iCre-hCD2_RNA

description:
Library name: RNA
polyA RNA


title: Panc1_Control_1


title: HPV-mice, Replicate 3, Spleen

description: 10X Genomics


title: MIAPaCa2_Tr_4


title: HPV-mice, Replicate 2, Spleen

description: 10X Genomics


title: H2B-mice, Replicate 1, Spleen

description: 10X Genomics


title: NP_017


title: IR injury 1

description:
Library name: sample1
IR injury group, replicate biosample 1

value: liver


title: NP_016


title: DCs and ILC3 extraced from mLNs of 15 days old Rorc+7kb enhancer KO mice_RNA

description:
Library name: Rorc+7kb enhancer KO_RNA
polyA RNA

extract_protocol:
We followed the Chromium Single Cell 3′ Reagent Kit v3 User Guide.
For sample preparation on the 10x Genomics platform, the Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 16 rxns (PN-1000075), Chromium Chip B Single Cell Kit, 48 rxns (PN-1000073) and Chromium i7 Multiplex Kit (PN-120262) were used. The single cell libraries were then sequenced on the Illumina NovaSeq 6000 S4 200 cycle flow cell generating 28x98 reads. A median sequencing depth of 50,000 reads/cell was targeted for each sample.

value: DCs and ILC3

value: Rorc +7kb enhancer KO


title: HPV-mice, Replicate 1, Spleen

description: 10X Genomics


title: NP_015

value: NP


title: H2B-mice, Replicate 3, Cervix

description: 10X Genomics

source_name: Cervix

value: Cervix


title: DCs and ILC3 extraced from mLNs of 15 days old C57BL/6 mice_Hashtag

description:
Library name: C57BL/6_Hashtag
HTO

value: mLN

value: TotalSeq™-B0302 anti-mouse Hashtag 2 Antibody, TotalSeq™-B0304 anti-mouse Hashtag 3 Antibody, TotalSeq™-B0304 anti-mouse Hashtag 4 Antibody, TotalSeq™-B0305 anti-mouse Hashtag 5 Antibody


title: NP_014


title: MIAPaCa2_Tr_2


title: MIAPaCa2_Tr_3


title: MIAPaCa2_Tr_1


title: DCs and ILC3 extraced from mLNs of 15 days old C57BL/6 mice_RNA

description:
Library name: C57BL/6_RNA
polyA RNA

value: No treatment


title: MIAPaCa2_KONX_Tr_3

value: NOXA knockout


title: H2B-mice, Replicate 1, Cervix

description: 10X Genomics


title: NP_011


title: NP_013


title: Foxg1 cKO

city: Nanjing

first: Zhao

last: Chunjie

state: Jiangsu

address: Hunan Road Street

department: School of Medicine

institute: Southeast University

description: Library name: Foxg1 cKO

data_processing:
Raw fastq reads were trimmed by Cutadapt to trim adapter and low-quality sequence, and then high-quality sequencing data (clean reads) were obtained. We utilized Bowtie2 to align clean reads with mouse genome (mm10), followed by a quality assessment of the alignment results to accomplish secondary data quality control. Model-based Analysis of ChIP-Seq (MACS2) was used for peak calling. Bigwig file, which is used for the display of dense and continuous data as a graph, was generated by the bamCoverage command in deepTools.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

source_name: ganglionic eminences

extract_protocol:
Cells were washed with 500 μl of wash buffer and centrifuged at 600 g for 5 min at RT. The cell pellets were resuspended in 100 μl of wash buffer. Concanavalin A-coated magnetic beads were washed twice with binding buffer. Next, 10 μl of activated beads were added and incubated at RT for 10 min. Bead-bound cells were resuspended in 50 μl of antibody buffer (antibody buffer, 5% digitonin). Then, 1 μg of primary antibody (rabbit polyclonal anti-FOXG1 antibody) was added and incubated at 4° overnight. The primary antibody was removed using a magnet stand. Secondary antibody (1 μg, goat anti-rabbit) was diluted in 50 μl of Dig-wash buffer [10× wash buffer (-), 50× protease inhibitor cocktail, ddH2O, 5% digitonin] and cells were incubated at RT for 1 h. Cells were washed three times with Dig-wash buffer to remove unbound antibodies. The Hyperactive pA/G-Transposon (2 µM; 2 µl) was diluted in 98 μl of Dig300 buffer [10× Dig-300 buffer (-), 5% digitonin, 50× protease inhibitor cocktail, ddH2O]. The cells were incubated with Dilute 100 μl of the pA/G-Tnp transposons at RT for 1 h. The cells were washed three times with Dig-300 buffer. Then, the cells were resuspended in 50μl of diluted TTBL (5xTrueprep Tagment Buffer L, Dig300 buffer) and incubated at 37° C for 1 h. Add 5 μl of Proteinase K, 100 μl of Buffer L/B, and 20 μl of DNA Extract Beads to each sample, fully mix by vortexing, and incubate at 55°C for 10 min. For library amplification, 15μl Fragmented DNA after purification was mixed with 25μl 2x CAM (CUT&Tag Amplification Mix), and 5 μl of uniquely barcoded i5 and i7 primers from TruePrep Index Kit V2 for Illumina. A total of 50 μl of the sample was placed in a thermocycler and subjected to the following program: 72°C for 3 min; 95°C for 3 min; 11 cycles of 98°C for 10 s, 60°C for 5s; 72°C for 1 min and hold at 4°C. To purify the PCR products, 100μl VAHTS DNA Clean Beads were added and incubated at RT for 10 min. The libraries were washed twice with 80% ethanol and eluted in 22 μl of ddH2O.
The libraries were sequenced on an Illumina NovaSeq platform, and 150-bp paired-end reads were generated.

value: ganglionic eminences


title: MIAPaCa2_KONX_Tr_2


title: HPV-mice, Replicate 3, Cervix

description: 10X Genomics


title: NP_010


title: DCs and ILC3 extraced from mLNs of 15 days old Rorc+7kb enhancer KO mice_Hashtag

description:
Library name: Rorc+7kb enhancer KO_Hashtag
HTO

value: HTO


title: C57-Proline-A048

city: Guangzhou

first: Tuliang

last: Liang

state: Guangdong

address: Office 213, Guangdong Provincial Academy of Chinese Medical Sciences

institute: The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hos

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: Lung Tumor

value: Lung Tumor

value: Proline


title: MIAPaCa2_KONX_Tr_1


title: HPV-mice, Replicate 2, Cervix

description: 10X Genomics


title: MIAPaCa2_KONX_Control_3

value: vehicle


title: NP_008


title: MIAPaCa2_KONX_Control_2


title: HPV-mice, Replicate 1, Cervix

description: 10X Genomics


title: NP_006


title: C57-Taurine-A029

value: Taurine


title: H2B-mice, Replicate 2, Cervix

description: 10X Genomics


title: C57-Taurine-A027


title: MIAPaCa2_KOAML_Tr_3

value: RUNX1 knockout


title: NP_005

value: FACS sorted CD207+


title: 3dpa blastema exercised exp bio rep 5

city: Eugene

first: Victor

last: Lewis

state: OR

address: 1229 University of Oregon 1318 Franklin Blvd.

department: Institute of Molecular Biology

institute: University of Oregon

description:
Library name: Exp_5_raw.fastq.gz
replicate 5

data_processing:
Reads were aligned with Kallisto (Pachter lab) against zebrafish reference transcriptome.
Assembly: GRCz11
Supplementary files format and content: .h5 counts abundance files

organism: Danio rerio

source_name: whole caudal fin 3 dpa blastema

growth_protocol: Zebrafish age 3-12 months were housed at approximately 28.5°C. Animals were maintained on a 14:10 day:night cycle and fed twice daily

extract_protocol:
RNA was prepared using a Direct-Zol RNA prep kit (Zymogenetics) and eluted into water. RNA was pooled from 2 male and 2 female size-matched fish for each replicate with replicates spanning two independent swimming cohorts.
Libraries were prepared with 1 ug of input RNA using a TruSeq library prep kit, indexed and pooled, and sequenced using an Illumina NovaSeq 6000 to a read depth of approximately 25 million reads per library.

treatment_protocol: Fish with caudal fin amputations were exercised twice at 48 and 72 hours post amputation and then whole regenerate fin tissue collected into Trizol reagent on ice 4 hours later.

value: whole caudal fin 3 dpa blastema

value: WT

value: Swim exercised


title: MIAPaCa2_KOAML_Tr_2


title: MIAPaCa2_KONX_Control_1


title: 3dpa blastema exercised exp bio rep 3

description:
Library name: Exp_3_raw.fastq.gz
replicate 3


title: 3dpa blastema exercised exp bio rep 4

description:
Library name: Exp_4_raw.fastq.gz
replicate 4


title: NP_002

value: NP


title: C57-Proline-A039


title: 3dpa blastema exercised exp bio rep 2

description:
Library name: Exp_2_raw.fastq.gz
replicate 2


title: C57-Model-A020

value: Model


title: C57-Model-A018


title: 3dpa blastema unexercised control bio rep 5

description:
Library name: Control_5_raw.fastq.gz
replicate 5

value: Control


title: MIAPaCa2_KOAML_Control_3


title: 3dpa blastema exercised exp bio rep 1

description:
Library name: Exp_1_raw.fastq.gz
replicate 1


title: C57-Model-A010


title: NP_023


title: MIAPaCa2_KOAML_Control_2


title: NP_027


title: NP_024


title: C57-Proline-A038


title: MIAPaCa2_KOAML_Tr_1


title: C57-Taurine-A028


title: C57-Control-A002


title: C57-Control-A001


title: MIAPaCa2_KOAML_Control_1


title: 3dpa blastema unexercised control bio rep 4

description:
Library name: Control_4_raw.fastq.gz
replicate 4


title: NP_019


title: NP_007


title: NP_009


title: C57-Control-A000


title: MIAPaCa2_Control_4

value: parental cell line


title: 3dpa blastema unexercised control bio rep 3

description:
Library name: Control_3_raw.fastq.gz
replicate 3


title: NP_004


title: MIAPaCa2_Control_3


title: 3dpa blastema unexercised control bio rep 2

description:
Library name: Control_2_raw.fastq.gz
replicate 2


title: 3dpa blastema unexercised control bio rep 1

description:
Library name: Control_1_raw.fastq.gz
replicate 1


title: MIAPaCa2_Control_2


title: murine plexiform neurofibroma, snRNAseq

city: Indianapolis

first: Steven

last: Rhodes

state: IN

address: 1044 W. Walnut St.; Bldg R4, Rm 325

institute: Indiana University

description: 10x Genomics

data_processing:
FASTQ files were processed with Cell Ranger software (v.7.0.0, 10X Genomics) with default parameters. Reads were aligned against the mouse reference assembly (mm10) with the STAR aligner. Mapped, non-PCR duplicates with valid barcodes and UMIs were filtered to generate a gene-barcode matrix for downstream analysis in scanpy.
Assembly: mm10
Supplementary files format and content: Tab-separatived values files and matrix files

molecule: nuclear RNA

source_name: murine plexiform neurofibroma from sciatic nerve

extract_protocol:
PNF bearing sciatic nerve tissues pooled from five, 11-month-old Nf1flox/flox;PostnCre+ mice were harvested, flash frozen at -80°C and shipped on dry ice to Novogene for single nucleus capture, library preparation and sequencing.  Single nuclei suspensions were loaded onto Chromium Chips (10x Genomics) for 3’ library preparation according to the manufacturer’s recommendations.
Library quality control was performed by Qubit 2.0 for preliminary determination of the library concentration, Agilent 2100 to determine the insert size, and Q-PCR to precisely quantify the library effective concentration.


title: 21-day-old N. benthamiana [miRNA-Seq]

city: Hangzhou

first: fan

last: xiaoping

state: zhejiang

address: Hangzhou, China

institute: LC-Bio Technology Co.

description:
Library name: YNB
Column name in Table5_All_Expressed_miRNA.txt:YNB

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: https://solgenomics.net/organism/Nicotiana_benthamiana/genome
Supplementary files format and content: txt,expression profiles

organism: Nicotiana benthamiana

source_name: leaf

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare one small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: 21-day-old Nicotiana benthamiana leaf

value: leaf


title: MLO-Y4 cells, Loaded 12 h, rep2

first: Yue

last: Guo

address: No. 22, Hankou Road, Nanjing, China

institute: NanJing University

data_processing:
The adaptors-trimmed and quality-filtered reads were mapped to mm10 genome using HISAT2 (version 2.1.0).
Transcript assembly was performed using StringTie (version 1.3.5).
The output files from StringTie were used to generate the count matrices for genes by executing prepDE.py.
Differential expression was analyzed using DESeq2 (version 1.32.0), with differentially expressed genes identified based on an adjusted p-value (padj) of less than 0.01.
DESeq2 (version 1.32.0) was also used to perform Principal Component Analysis (PCA) on the unloaded and loaded groups.
Assembly: mm10
Supplementary files format and content: text files include raw counts for each sample

source_name: bone

growth_protocol: MLO-Y4 cell line was maintained in DMEM medium (Gibco, 12800-017) with 5% FBS (Gibco, 10270-1106) and 5% NBCS (Gibco, 16010-159) at 37°C in a 5% (v/v) CO2 humidified incubator.

extract_protocol:
Cells were lysed using TRIzol (Invitrogen). Each sample contained more than 1.5 µg of total RNA.
The library was constructed and sequenced by Allwegene Company.

treatment_protocol: For the loaded group, MLO-Y4 cells were plated onto UniFlex™ Culture Plates coated with type I collagen (Flexcell International Corporation), which are 6-well plates with a soft silicone rubber membrane at the bottom of each well. When the cells reached 60% confluency, the plates were subjected to the Flexcell FX5000 Tension System and treated with equiaxial dynamic stretching at 0.5 Hz and 20% strain for 12 hours. For the unloaded group, , MLO-Y4 cells were plated onto 6-well cell culture plate (Corning). When the cell density reached 60% confluency, the plates were transferred to the cell incubator of the Flexcell FX5000 Tension System for 12 hours, serving as the control group.

value: bone

value: osteocyte-like cell line

value: Mechanical loading for 12 h


title: MIAPaCa2_Control_1


title: MLO-Y4 cells, Loaded 12 h, rep1


title: NP_001

source_name: FACS sorted CD207+


title: FC2_2_BLTL_31_F289

city: Chapel Hill

last: Garcia

state: North Carolina

address: 120 Mason Farm Rd CB #7042

department: Division of Infectious Diseases

institute: University of North Carolina at Chapel Hill

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC2_2_BLTL_31_F289

data_processing:
Sequence quality was assessed using FASTQC (v).
No issues were detected with the data and quality was typical for RNA extracted from fresh frozen material.
Samples were performed in two batches and batch corrected using COMBatseq.
Raw reads were mapped to the human, mouse, and SARS-CoV-2 reference genomes simultaneously (GRCh38.p13, GRCm38.p6 M25, NC_045512, respectively) using the BBsplit function in BBmap (version 38.86). This step minimized cross mapping of reads among genomes.
We then mapped and quantified on a transcript and gene model basis using STAR (version 2.7.5a) and Salmon (version 1.2.1)
Reads mapping to multiple locations were dropped from analysis.
Assembly: GRCh38.p13, GRCm38.p6 M25, NC_045512
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: lung

growth_protocol: Viruses were directly injected into the human lung tissue of BLTL and lung tissue collected either 2, 6, or 14 days post-exposure for virus titer determination and/or analysis by histology, electron microscopy, or RNA-seq

extract_protocol:
Trizol Plus RNA extraction kit (Thermo Fisher)
This was performed in two batches, with some samples overlapping in each batch. Batch 1 was performed with a single index NEBNext Ultra II library prep kit with polyA RNA selection. Due to a small amount of observed barcode hopping,44 we used dual index KAPA RNA HyperPrep for the second batch.

value: lung

tag: time point

value: day 2

value: BLT-L

value: infected


title: 21-day-old N. benthamiana [YNBdgd]

description: Library name: YNBdgd

data_processing:
Raw sequencing reads were obtained using Illumina’s software to remove adaptors and low quality reads.
The extracted sequencing reads were then used to identify potentially cleaved targets by the CleaveLand pipeline.
The degradome reads were matched to transcriptome to generate the degradome density file. In addition, the targeted mRNA sequences of the miRNAs were predicted using TargetFinder software (http://targetfinder.org/). The overlapped mRNAs of the predicted target mRNAs and the mRNAs in degradome density file were considered as the target genes of the miRNAs.
Assembly: https://solgenomics.net/organism/Nicotiana_benthamiana/genome
Supplementary files format and content: txt,expression profiles

source_name: Leaf

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Poly(A) RNA is purified from plant total RNA(20ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Because of the 3′ cleavage product of the mRNA contains a 5′-monophosphate，the 5' adapters were ligated to the 5' end of the 3′ cleavage product of the mRNA by the RNA ligase. The next step is reverse transcription to make the first strand of cDNA with a 3′-adapter random primer. and size selection was performed with AMPureXP beads.Then the cDNA were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 15cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 200-400 bp. At last, we performed the 50bp single-end sequencing on an Illumina Hiseq 2500 (LC Bio, China) following the vendor's recommended protocol.

value: Leaf


title: MLO-Y4 cells, Unloaded,  rep2

value: Unloaded


title: MLO-Y4 cells, Unloaded,  rep1


title: FC2_6_BLTL_30_F288

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC2_6_BLTL_30_F288

value: day 6


title: SUM159PT; FP-transplanted tumour

city: Utrecht

first: Stefan

last: Prekovic

address: Universiteitsweg 100

department: CMM

country: Netherlands

institute: UMC Utrecht

description:
6438_GRCh38_genecounts.txt
6438_9_SUM159_CGTACGT_S79

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyzer (using 65bp reads) and were processed by the Illumina pipeline.
For RNA sequencing data was aligned to hg38 using TopHat and Differential expression (DE) was performed using optimized DESeq2 pipeline.
Assembly: hg38
Supplementary files format and content: Count data are included as .txt

source_name: breast cancer

growth_protocol: Cells were grown in their respective medium according to description in Supplementary material in corresponding publication.

extract_protocol:
RNA was harvested using RNAeasy column purification (qiagen).
Libraries were constructed using Illumina TruSeq polyA stranded RNA prep and QC was performed on Bioanalyzer DNA 7500.

value: breast cancer

value: SUM159PT; FP-transplanted tumour

value: human breast cancer


title: T-47D; FP-transplanted tumour

description:
6438_GRCh38_genecounts.txt
6438_10_T47D_GAGTGGA_S80

value: T-47D; FP-transplanted tumour


title: FC2_2_BLTL_29_F285

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC2_2_BLTL_29_F285


title: SUM149PT; FP-transplanted tumour

description:
6438_GRCh38_genecounts.txt
6438_8_SUM149_GTTTCGG_S78

value: SUM149PT; FP-transplanted tumour


title: Input, MLO-Y4, ChIP

data_processing:
The adaptors-trimmed and quality-filtered reads were aligned to the mm10 using Bowtie2 with default parameters and uniquely mapped reads were used for peak calling with MACS2.
A pairwise comparison of NRF2 peaks in MLO-Y4 and astrocytes was performed as peak overlapping by “intersectBed” of “bedtools”.
The heatmaps of ChIP-seq results were generated by Seqplots (Bioconductor package).
De novo motifs were identified using “findMotifsGenome.pl” function in Homer with the parameter “–size given” for NRF2-binding regions.
The R package ChIPseeker (version 1.28.3) was used for annotating the distribution of enriched ChIP-seq peaks.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
MLO-Y4 cells of each group were fixed by 1% formaldehyde solution (Sigma, F8775-25ML) and quenched with 1.25M glycine (Amresco, 200-272-2). Chromatin was collected and sheared using the Bioruptor Plus with 30 seconds on and 30 seconds off for 18 cycles. Immunoprecipitation was performed using 3–5 μg of H3K27ac (Abcam, ab4729); H3K4me3 (Abcam, ab8580) or NRF2 (Proteintech, 80593-1-RR) antibodies. DNA was purified using the DNA Clean & Concentrator-5 kit (Zymo, D4014).
Libraries were then constructed from ChIP samples using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, E7370) and sequenced on a NovaSeq by Annoroad Gene Tech (Beijing) Co., Ltd. Two biological replicates were performed for each group.

tag: chip antibody

value: none (input)


title: Loaded, MLO-Y4, NRF2, ChIP

value: NRF2, Proteintech, 80593-1-RR


title: FC2_Control_BLTL_27_F283

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC2_Control_BLTL_27_F283

value: control


title: SUM52PE; FP-transplanted tumour

description:
6438_GRCh38_genecounts.txt
6438_7_SUM52_GTGGCCT_S77

value: SUM52PE; FP-transplanted tumour


title: Unloaded, MLO-Y4, NRF2,ChIP

value: bone

value: osteocyte-like cell line


title: SK-BR-7; FP-transplanted tumour

description:
6438_GRCh38_genecounts.txt
6438_6_SK-BR-7_GGCTACA_S71

value: SK-BR-7; FP-transplanted tumour


title: AC_190_191

description: RNA from HEK293T cells expressing eGFP, to identify RT-PCR-generated substitutions.

extract_protocol:
Total cellular RNA from HEK293T cells expressing eGFP extracted. RT-PCR to amplify eGFP sequences (amplicons used for library construction).
Samples were sequenced with Novogene using their ‘Microbial PCR Product Whole Genome Sequencing’ strategy. Amplicons underwent fragmentation prior to PCR-free library preparation and sequencing using NovaSeq PE250 technology.


title: SK-BR-5; FP-transplanted tumour

description:
6438_GRCh38_genecounts.txt
6438_5_SK-BR-5_TAGCTTA_S76

value: SK-BR-5; FP-transplanted tumour


title: FC2_Control_BLTL_26_F283

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC2_Control_BLTL_26_F283

value: lung

value: BLT-L


title: FC2_2_BLTL_25_F276

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC2_2_BLTL_25_F276

value: day 2

value: infected


title: Unloaded, MLO-Y4, H3K4me3, rep2, ChIP

value: H3K4me3, Abcam, ab8580


title: MDA-MB-231; FP-transplanted tumour

description:
6438_GRCh38_genecounts.txt
6438_4_MDA-MB-231_GATCAGA_S75

value: breast cancer

value: MDA-MB-231; FP-transplanted tumour


title: Loaded, MLO-Y4, H3K4me3, rep1, ChIP


title: FC2_6_BLTL_24_F168

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC2_6_BLTL_24_F168

value: day 6


title: FC2_2_BLTL_28_F285

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC2_2_BLTL_28_F285


title: N/TERT, IFN-b 1

type: RNA

city: Paris

first: Chloé

last: Grolleau

address: 1 avenue Claude Vellefaux

department: Hopital saint Louis

country: France

institute: INSERM U1342, eq 16

description:
NTERT_IFNB1_(HTA-2_0).sst-rma-combined-dabg.chp Signal
KC-B1

hyb_protocol: Each sample was hybridized onto GeneChip® Human Transcriptome Array 2.0 (ThermoFisher Scientific), washed, and stained with the Affymetrix® Fluidics Station 450

scan_protocol: Scanning was performed with the Affymetrix® GeneChip Scanner 3000 7G (ThermoFisher Scientific)

data_processing:
The data were analyzed using the Affymetrix Transcriptome Analysis Console (TAC) software v.4 (ThermoFisher Scientific)
RMA expression value derived from Affymetrix Transcriptome Analysis Console  software v.4
annotation=HTA-2_0.r3.na36.hg19.a1.transcript.csv

label: biotin

source_name: N/TERT, IFN-b 10ng/ml, 24h

label_protocol: Ten nanogram of Total RNA was amplified, labeled, and fragmented using GeneChip WT Reagent Kit (ThermoFisher Scientific)

growth_protocol: N/TERT cells were cultured in Epilifife HKGS supplemented medium (ThermoFisher).

extract_protocol: RNAs were extracted from N/TERT cell cultures using RNeasy microkit (Qiagen).

treatment_protocol: Cells at proper confluency were subsequently treated with recombinant human IFN-a2 (viraferon©, 1000U/ml), IFN-b1 (10 ng/ml, R&D Systems) or IFN-g (10 ng/ml, R&D Systems) for 24 hours before RNA extraction.

value: N/TERT

value: Immortalized primary human keratinocytes

value: IFN-b 10ng/ml


title: FC2_Control_BLTL_21_E863

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC2_Control_BLTL_21_E863

value: control


title: MCF10DCIS.com; FP-transplanted tumour

description:
6438_GRCh38_genecounts.txt
6438_3_MCF10DCIS_com_ACTTGAA_S74

value: MCF10DCIS.com; FP-transplanted tumour

value: human breast cancer


title: Unloaded, MLO-Y4, H3K4me3, rep1, CcIP

value: bone

value: osteocyte-like cell line


title: N/TERT, IFN-g 1

description:
NTERT_IFNG1_(HTA-2_0).sst-rma-combined-dabg.chp Signal
KC-G1

source_name: N/TERT, IFN-g 10ng/ml, 24h

value: IFN-g 10ng/ml


title: Evsa-T; FP-transplanted tumour

description:
6438_GRCh38_genecounts.txt
6438_1_EVSA-T_ATCACGA_S72

value: Evsa-T; FP-transplanted tumour


title: N/TERT, IFN-g 2

description:
NTERT_IFNG2_(HTA-2_0).sst-rma-combined-dabg.chp Signal
KC-G2


title: MCF-7; FP-transplanted tumour

description:
6438_GRCh38_genecounts.txt
6438_2_MCF7_TTAGGCA_S73

value: MCF-7; FP-transplanted tumour


title: Loaded, MLO-Y4, H3K27ac, rep2, ChIP

value: H3K27ac, Abcam, ab4729


title: N/TERT, IFN-b 3

description:
NTERT_IFNB3_(HTA-2_0).sst-rma-combined-dabg.chp Signal
KC-B3


title: N/TERT, IFN-b 2

description:
NTERT_IFNB2_(HTA-2_0).sst-rma-combined-dabg.chp Signal
KC-B2


title: Loaded, MLO-Y4, H3K27ac, rep1, ChIP


title: N/TERT, IFN-g 3

description:
NTERT_IFNG3_(HTA-2_0).sst-rma-combined-dabg.chp Signal
KC-G3


title: Loaded, MLO-Y4, H3K4me3, rep2, ChIP


title: N/TERT, IFN-a 3

description:
NTERT_IFNA3_(HTA-2_0).sst-rma-combined-dabg.chp Signal
KC-A3

source_name: N/TERT, IFN-a 1000U/ml, 24h

value: IFN-a 1000U/ml


title: N/TERT, IFN-a 2

description:
NTERT_IFNA2_(HTA-2_0).sst-rma-combined-dabg.chp Signal
KC-A2


title: Unloaded, MLO-Y4, H3K27ac, rep2, ChIP


title: FC2_Control_BLTL_18_E862

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC2_Control_BLTL_18_E862

value: lung

value: BLT-L


title: SUM225CWN; MIND-transplanted tumour

description:
6175_readcounts.txt
6157_20_SUM225_GGCTACA_S55

value: breast cancer

value: SUM225CWN; MIND-transplanted tumour


title: SK-BR-3; MIND-transplanted tumour

description:
6175_readcounts.txt
6157_19_SK-BR-3_TAGCTTA_S54

value: SK-BR-3; MIND-transplanted tumour


title: FC2_Control_BLTL_20_E863

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC2_Control_BLTL_20_E863


title: FC1_Control_BLTL_21_E863

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC1_Control_BLTL_21_E863


title: Unloaded, MLO-Y4, H3K27ac, rep1, ChIP


title: MDA-MB-468; MIND-transplanted tumour

description:
6175_readcounts.txt
6157_18_MDA-MB-468_GATCAGA_S53

value: MDA-MB-468; MIND-transplanted tumour


title: KO mice, exercise [KS3]

city: Boston

first: Haobo

last: Li

state: MA

address: MEDR410 / Lunder Bldg Dock, 255 Charles St

department: Department of Anesthesia, Critical Care, and Pain Medicine

institute: Massachusetts General Hospital and Harvard Medical School

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw sequeence image files from the sequencer were converted to the fastq format and checked for quality: per base sequence quality, the per base sequence content, per base N content, sequence length distribution, adapter and k-mer content and sequence duplication levels are collected for each sequencing run using fastqc.
fastqs are then aligned to the mouse reference genome (mm9) using STAR46 aligner.
Alignment statistics such as average red length, percentage of uniquely mapped reads, percentage of multi-mapped reads and number of splice junctions are collated. Only reads that are uniquely mapped will be considered for read annotation to gene features. Reads are annotated with the ENSEMBL 75 gene transfer format (gtf) file using Salmon.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: whole heart sample

growth_protocol: CITED4 flox/flox (Flox) mice were crossed with aMHC-cre mice to generated cardiomyocyte specific CITED4 knockout (KO) mice

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries. Libraries were made with the RiboZero kit followed by the NEB RNA lib kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Flox and KO mice were either received sedentary or volunatry wheel running for 8 weeks

value: whole heart sample

value: Knockout

value: Exercise

tag: time

value: 8 weeks


title: N/TERT, unprimed 3

description:
NTERTunprimed3_(HTA-2_0).sst-rma-combined-dabg.chp Signal
KC-3

source_name: N/TERT, unprimed

value: N/TERT

value: Immortalized primary human keratinocytes

value: unprimed


title: N/TERT, unprimed 2

description:
NTERTunprimed2_(HTA-2_0).sst-rma-combined-dabg.chp Signal
KC-2


title: Mus,ORM2_05

city: Berlin

first: Hanyang

last: Liu

address: Augustenburger Platz 1

department: Department of Hepatology and Gastroenterology (CCM/CVK),

institute: Charité Universitätsmedizin Berlin

data_processing:
Raw data was processed following the online protocol: Bulk RNA-seq Data Standards and Processing Pipeline – ENCODE (encodeproject.org)
Assembly: GRCm39
Supplementary files format and content: CSV file containing the normalized gene count for each sequenced gene in each sample

source_name: Liver

extract_protocol:
Mouse cell (liver macrophage) RNA samples were extracted and purified using Qiagen Rneasy kit
TruSeq Stranded mRNA.Library preparation: low input (10pg-10ng) total RNA library  (with rRNA depletion)

value: Liver

value: Primary

value: Liver cells

value: C57BL/6J wild-type


title: MDA-MB-453; MIND-transplanted tumour

description:
6175_readcounts.txt
6157_17_MDA-MB-453_ACTTGAA_S52

value: MDA-MB-453; MIND-transplanted tumour

value: human breast cancer


title: KO mice, exercise [KS2]


title: N/TERT, IFN-a 1

description:
NTERT_IFNA1_(HTA-2_0).sst-rma-combined-dabg.chp Signal
KC-A1

value: IFN-a 1000U/ml


title: FC1_Control_BLTL_20_E863

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC1_Control_BLTL_20_E863

value: lung

value: BLT-L

value: control


title: FC1_Control_BLTL_19_E862

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC1_Control_BLTL_19_E862


title: KO mice, exercise [KS1]

value: whole heart sample


title: MDA-MB-175-VII; MIND-transplanted tumour

description:
6175_readcounts.txt
6157_15_MDA-MB-175-VII_GCCAATA_S45

value: breast cancer


title: HCC1937; MIND-transplanted tumour

description:
6175_readcounts.txt
6157_14_HCC1937_ACAGTGA_S50

value: HCC1937; MIND-transplanted tumour


title: FC1_Control_BLTL_18_E862

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC1_Control_BLTL_18_E862


title: KO mice, sedentary [KE3]

value: Knockout

value: Sedentary

value: 8 weeks


title: Mus,ORM2_01


title: FC1_14_BLTL_15_E860

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC1_14_BLTL_15_E860

value: day 14

value: infected


title: KO mice, sedentary [KE2]


title: Mus,Ctrl_05

value: Liver

value: Primary

value: Untreated


title: FC1_14_BLTL_14_E858

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC1_14_BLTL_14_E858


title: CAMA-1; MIND-transplanted tumour

description:
6175_readcounts.txt
6157_13_CAMA-1_TGACCAA_S49

value: CAMA-1; MIND-transplanted tumour


title: KO mice, sedentary [KE1]


title: BT-474; MIND-transplanted tumour

description:
6175_readcounts.txt
6157_12_BT474_TTAGGCA_S48

value: BT-474; MIND-transplanted tumour

value: human breast cancer


title: Flox mice, exercise [FS3]

value: Flox/flox

value: Exercise


title: BT-20; MIND-transplanted tumour

description:
6175_readcounts.txt
6157_11_BT-20_CGATGTA_S47

value: BT-20; MIND-transplanted tumour


title: Mus,Ctrl_04

value: Liver cells

value: C57BL/6J wild-type


title: N/TERT, unprimed 1

description:
NTERTunprimed1_(HTA-2_0).sst-rma-combined-dabg.chp Signal
KC-1

value: N/TERT

value: Immortalized primary human keratinocytes

value: unprimed


title: T-47D; MIND-transplanted tumour

description:
5502_readcounts.txt
5502_10_T47D_CCGTCCC_S30

value: breast cancer

value: T-47D; MIND-transplanted tumour


title: FC1_6_BLTL_08_E855

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC1_6_BLTL_08_E855

value: lung

value: day 6

value: BLT-L

value: infected


title: Flox mice, exercise [FS2]

value: whole heart sample

value: 8 weeks


title: Mus,Ctrl_03

value: Liver

value: Primary

value: Untreated


title: Mus,ORM2_04


title: SUM159PT; MIND-transplanted tumour

description:
5502_readcounts.txt
5502_9_SUM159_ATGTCAG_S29

value: SUM159PT; MIND-transplanted tumour

value: human breast cancer


title: Flox mice, exercise [FS1]

value: Flox/flox

value: Exercise


title: Mus,ORM2_02

value: Liver cells

value: C57BL/6J wild-type


title: FC1_6_BLTL_07_E744

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC1_6_BLTL_07_E744


title: Flox mice, sedentary [FE3]

value: Sedentary


title: FC2_Control_BLTL_19_E862

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC2_Control_BLTL_19_E862

value: control


title: Mus,Ctrl_01


title: SUM149PT; MIND-transplanted tumour

description:
5502_readcounts.txt
5502_8_SUM149_AGTTCCG_S28

value: breast cancer

value: SUM149PT; MIND-transplanted tumour


title: Flox mice, sedentary [FE2]


title: SUM52PE; MIND-transplanted tumour

description:
5502_readcounts.txt
5502_7_SUM52_AGTCAAC_S27

value: SUM52PE; MIND-transplanted tumour


title: MCM, scRNAseq

city: Osaka

first: Yasunori

last: Shintani

address: 6-1, Kishibe-shinmachi, Suita

department: Molecular Pharmacology

country: Japan

institute: National Cerebral and Cardiovascular Center

description: 10X Genomics

data_processing:
Demultiplexing of cell barcodes, read mapping and alignment was performed by Cell Ranger pipeline provided by 10X Genomics.
Assembly: mm10 (mouse), GRCh38 (human)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart

extract_protocol:
Nuclei isolation from mouse heart tissues: Nuclei were isolated according to Frankenstein protocol with minor modifications. Heart tissue was homogenized by using glass douncer in EZ PREP lysis buffer. Homogenate was filtered through a 70 μm followed by 20 μm and centrifuged at 500 x g for 5 min at 4°C to remove cell debris and aggregates. Nuclei pellet was suspended in ice-cold EZ PREP lysis buffer and incubated on ice for 3 min. After centrifugation at 500 x g for 5 min at 4°C, nuclei pellet was incubated with nuclei washing and resuspension buffer consisting of 1X PBS, 1% BSA, 0.1% Tween-20 and 0.2 U/μl RNase inhibitor (TAKARA Bio) for 5 min before an additional resuspension. Nuclei were centrifuged at 500 x g for 5 min at 4°C and the nuclei pellet was resuspended with nuclei washing and resuspension buffer then sorted by FACS.  Nuclei isolation from human heart tissues: Nuclei were isolated using Singulator 100 system (S2 Genomics, Inc) according to manufacturer’s recommendations. Collected nuclei were centrifuged at 500 x g for 10 min at 4°C and pellets were resuspended with 4 ml nuclei washing and resuspension buffer containing 1X PBS, 1% BSA, and 0.2 U/μl RNase inhibitor. Additional centrifugation at 500 x g for 5 min at 4°C was performed and the nuclei pellet was resuspended with another washing and resuspension buffer.
Droplets capturing single nucleus from whole heart nuclei suspension were used for library generation in the 10X Genomics Chromium controller according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagent Kit v.3 User Guide.

value: Heart

tag: Sex

value: Female

value: Cardiac cell populations

tag: disease state

value: mitochondrial cardiomyopathy

value: young


title: Pre-infusion scTCR for CAR-T from Patient 116

city: Chicago

first: Jun

last: Huang

address: Eckhardt, 5640 S Ellis Ave

department: Institute for Molecular Engineering

institute: University of Chicago

description:
Pre_scTCR_116
scTCR
All_TCR_Aggregated_clonotypes.csv
All_TCR_Aggregated_consensus_annotations.csv
All_TCR_Aggregated_filtered_contig_annotations.csv

data_processing:
The RNA-seq and paired Total-seq reads were aligned to the GRCh38 reference genome, which was modified with the CAR transgene sequence used in axicabtagene ciloleucel, and quantified using the cellranger count (10x Genomics, version 6.0.0). The filtered gene/feature-barcode matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the quality control were used for downstream analyses. In two patients with fewer CAR-T cells where hashtag multiplexing was used, cellranger multi pipeline was used to demultiplex and quanity.
The TCR-seq reads from each sample were aligned to the 10x curated GRCh38 vdj reference genome and quantified using the cellranger vdj (10x Genomics, version 6.0.0). The results were then aggregated using the cellranger aggr function, with the source patient (donor) and timepoint (origin) of each sample supplied in the metadata to guide the clonotype assignment. The resultant clonotype and filtered contig annotation data were used for downstream analyses. Each unique clonotype is defined by the nucleotide sequence of CDR3 regions for paired productive TCRα and TCRβ chains.
Assembly: GRCh38
Supplementary files format and content: scRNA and Totalseq -- mtx: final merged raw count matrices of scRNA and Totalseq (ADT); csv: row and column names; metadata
Supplementary files format and content: scTCR -- csv: aggregated clonotype results from cellranger vdj

source_name: PBMC

extract_protocol:
scRNA-Seq and OTHER (TotalSeq, scTCR, and Hastag-Multiplex for 2 patients with fewer CAR-T)
Cryopreserved patient biospecimens were thawed in warm RPMI+10% FBS and washed with cold FACS buffer (PBS, 2% BSA, 0.05% sodium azide). Next, Fc receptors were blocked by incubation with Human TruStain FcX (BioLegend, 422301) at 1:50 dilution for 5 minutes at 4°C. Then, cells were incubated for 30 minutes at 4°C in the dark with a staining solution containing BV421-anti-CD3E (clone SK7), CITE-seq antibodies, and Alexa Fluor 647-labeled antigen-tetramers at 3 nM final concentration for CAR-detection. Subsequently, cells were incubated with LIVE/DEAD Fixable Near-IR viability dye (Invitrogen, L34975) diluted 1:1000 in PBS for 5 minutes at room temperature. Finally, cells were washed three times in cold cell media. Infusion products were partitioned and analyzed directly. Peripheral blood mononuclear cells were subject to fluorescence-activated cell sorting before single-cell partitioning and analysis.
T cells were partitioned into droplets for single-cell omics assays via Chromium Next GEM Single-Cell 5’Kit v2 (10x Genomics, 1000263). From the resulting barcoded nucleic acids, TCR-seq libraries were prepared via the Chromium Single-Cell Human TCR Amplification Kit (10x Genomics, 1000252). Sequencing libraries were quantified via the Qubit dsDNA HS Assay Kit (Invitrogen, Q32851), quality-checked for fragment sizes via a high-sensitivity D5000 screentape (Agilent, 5067-5592), pooled, and sequenced (Illumina, NovaSeq-6000).

value: PBMC

tag: disease

value: Diffuse Large B-Cell Lymphoma

value: CAR-T


title: FC1_14_BLTL_13_E856

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC1_14_BLTL_13_E856

value: lung

value: day 14

value: BLT-L

value: infected


title: Flox mice, sedentary [FE1]

value: whole heart sample

value: Flox/flox

value: Sedentary

value: 8 weeks


title: SK-BR-7; MIND-transplanted tumour

description:
5502_readcounts.txt
5502_6_SK-BR-7_CTTGTAA_S26

value: breast cancer

value: SK-BR-7; MIND-transplanted tumour

value: human breast cancer


title: cKO input cytoplasmic fraction biol rep 3

city: Minneapolis

first: Nobuaki

last: Kikyo

state: MN

address: University of Minnesota, MTRF, Room 2-216, 2001 6th St SE

institute: University of Minnesota

description:
biol rep 3
cKO3_input

data_processing:
Raw reads of fastq format were first processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter or ploy-N and low quality reads. At the same time, Q20, Q30 and GC contents in the clean data were calculated. All the downstream analyses were based on the clean data.
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.
featureCounts v1.5.0-p3 was used to count read numbers mapped to each gene and calculate FPKM based on the length of the gene and read counts mapped to the gene.
Assembly: mm10
Supplementary files format and content: A composite Excel file "gene_fpkm" contains fpkm values of all samples.

source_name: Limb buds

extract_protocol:
Total RNA wad prepared with a Quick RNA Microprep (Zymo Research, R1051).
NEB Next Ultra II RNA Library Prep by Illumina following manufacturer's protocols.

value: Limb buds

value: Limb bud cells

value: Mettl14 flox/flox

value: Mettl14 knockout


title: Pre-infusion scTCR for CAR-T from Patient 048

description:
Pre_scTCR_048
scTCR
All_TCR_Aggregated_clonotypes.csv
All_TCR_Aggregated_consensus_annotations.csv
All_TCR_Aggregated_filtered_contig_annotations.csv

value: PBMC

value: Diffuse Large B-Cell Lymphoma


title: FC1_6_BLTL_09_E861

description:
batch_corr_victor_2020_counts_tximport.csv
batch_corr_victor_2020_TPM.csv
FC1_6_BLTL_09_E861

value: lung

value: day 6


title: SK-BR-5; MIND-transplanted tumour

description:
6175_readcounts.txt
6157_5_1_SK-BR-5_re-take_ATCACGA_S46

value: SK-BR-5; MIND-transplanted tumour


title: cKO polysome fraction biol rep 2

description:
biol rep 2
cKO2_poly


title: Mus,Ctrl_02

value: Liver

value: Primary

value: Liver cells

value: C57BL/6J wild-type

value: Untreated


title: TB66SL

city: New York

first: Andrei

middle: V.

last: Tkatchenko

state: NY

department: Edward S. Harkness Eye Institute

institute: Columbia University

data_processing:
The FASTQ raw data files generated by the Illumina sequencing system were imported into Partek Flow software package (Partek), libraries were separated based on their barcodes, adapters were trimmed and remaining sequences were subjected to pre-alignment quality control using the Partek Flow pre-alignment QA/QC module
After the assessment of various quality metrics, bases with the quality score < 34 were removed (≤ 5 bases) from each end.
Sequencing reads were then mapped to the mouse reference genome Genome Reference Consortium Mouse Build 38 (GRCm38/mm10, NCBI) using the STAR aligner resulting in 98.12 ± 0.06% mapped reads per library, which covered 30.1 ± 1.7% of the genome.
Aligned reads were quantified to transcriptome using the Partek E/M annotation model and the NCBI’s RefSeq annotation file to determine read counts per gene/genomic region.
The generated read counts were normalized by the total read count and subjected to the Gene Specific Analysis (GSA) to detect differentially expressed genes
Assembly: mm10
Supplementary files format and content: Tab-delimited text file including matrix table with normalized gene counts for every gene and every sample

source_name: Left eye RPE/choroid/sclera

extract_protocol:
The retinae were washed in RNAlater (Thermo Fisher Scientific) for 5 min., frozen in liquid nitrogen, and stored at -80°C. To isolate RNA, tissue samples were homogenized at 4°C in a lysis buffer using Bead Ruptor 24 tissue homogenizer (Omni). Total RNA was extracted from each tissue sample using miRNAeasy mini kit (QIAGEN) following the manufacturer’s protocol.
Illumina sequencing libraries were constructed from 1 μg of total RNA using the TruSeq Stranded Total RNA LT kit with the Ribo-Zero Gold ribosomal RNA depletion module (Illumina).

treatment_protocol: Myopia was induced in mice by applying a plastic goggle holding a -20D lens onto one of the eyes and refractive development of the treated eye was compared to that of the contralateral eye which was not treated with a lens. On the first day of the experiment (P24), animals were anesthetized via intraperitoneal injection of ketamine and xylazine and goggles were attached to the skin surrounding the eye. Goggles were removed and the refractive state of both treated and control eyes was assessed using an automated infrared photorefractor after 10 days of treatment.

tag: strain

value: RPE/choroid/sclera

value: postnatal day 34

value: wild type


title: cKO input cytoplasmic fraction biol rep 2

description:
biol rep 2
cKO2_input

value: Limb buds


title: MDA-MB-231; MIND-transplanted tumour

description:
5502_readcounts.txt
5502_4_MDA-MB-231_GCCAATA_S24

value: breast cancer

value: MDA-MB-231; MIND-transplanted tumour

value: human breast cancer


title: TB68SL


title: cKO polysome fraction biol rep 1

description:
biol rep 1
cKO1_poly

value: Limb bud cells

value: Mettl14 flox/flox

value: Mettl14 knockout


title: cKO input cytoplasmic fraction biol rep 1

description:
biol rep 1
cKO1_input


title: Pre-infusion scRNA and TotalSeq for CAR-T from Patient 116

description:
Pre_scRNA_TotalSeq_116
scRNA and Feature Barcoding
Pre_Infusion_scRNA_Raw_Counts.mtx
Pre_Infusion_scRNA_Raw_Counts_features(rownames).csv
Pre_Infusion_ADT_Raw_Counts.mtx
Pre_Infusion_scADT_Raw_Counts_features(rownames).csv
Pre_Infusion_scADT_and_scRNA_Raw_Counts_cells(colnames).csv
Pre_Infusion_scADT_and_scRNA_Raw_Counts_metaData.csv

value: PBMC

value: Diffuse Large B-Cell Lymphoma

value: CAR-T


title: cHet polysome fraction biol rep 3

description:
biol rep 3
cHet3_poly

value: Mettl14 wt/flox

value: Mettl14 hetero as control


title: TB65SR

source_name: Right eye RPE/choroid/sclera


title: cKO polysome fraction biol rep 3

description:
biol rep 3
cKO3_poly


title: Pre-infusion scRNA and TotalSeq for CAR-T from Patient 048

description:
Pre_scRNA_TotalSeq_048
scRNA and Feature Barcoding
Pre_Infusion_scRNA_Raw_Counts.mtx
Pre_Infusion_scRNA_Raw_Counts_features(rownames).csv
Pre_Infusion_ADT_Raw_Counts.mtx
Pre_Infusion_scADT_Raw_Counts_features(rownames).csv
Pre_Infusion_scADT_and_scRNA_Raw_Counts_cells(colnames).csv
Pre_Infusion_scADT_and_scRNA_Raw_Counts_metaData.csv


title: TB65SL


title: T-47D; cell line

description:
5481_readcounts.txt
5481_10_T47D_TAGCTTA_S10

value: T-47D; cell line


title: cHet input cytoplasmic fraction biol rep 3

description:
biol rep 3
cHet3_input


title: Evsa-T; MIND-transplanted tumour

description:
5502_readcounts.txt
5502_1_EVSA-T_CGATGTA_S21

value: Evsa-T; MIND-transplanted tumour


title: TB68SR

value: RPE/choroid/sclera


title: cHet polysome fraction biol rep 2

description:
biol rep 2
cHet2_poly


title: TB64SR

value: postnatal day 34


title: Pre-infusion scRNA and TotalSeq for CAR-T from Patient 031

description:
Pre_scRNA_TotalSeq_031
scRNA and Feature Barcoding
Pre_Infusion_scRNA_Raw_Counts.mtx
Pre_Infusion_scRNA_Raw_Counts_features(rownames).csv
Pre_Infusion_ADT_Raw_Counts.mtx
Pre_Infusion_scADT_Raw_Counts_features(rownames).csv
Pre_Infusion_scADT_and_scRNA_Raw_Counts_cells(colnames).csv
Pre_Infusion_scADT_and_scRNA_Raw_Counts_metaData.csv


title: Pre-infusion scRNA and TotalSeq for CAR-T from Patient 039

description:
Pre_scRNA_TotalSeq_039
scRNA and Feature Barcoding
Pre_Infusion_scRNA_Raw_Counts.mtx
Pre_Infusion_scRNA_Raw_Counts_features(rownames).csv
Pre_Infusion_ADT_Raw_Counts.mtx
Pre_Infusion_scADT_Raw_Counts_features(rownames).csv
Pre_Infusion_scADT_and_scRNA_Raw_Counts_cells(colnames).csv
Pre_Infusion_scADT_and_scRNA_Raw_Counts_metaData.csv


title: SUM159PT; cell line

description:
5481_readcounts.txt
5481_9_SUM159_GATCAGA_S9

value: SUM159PT; cell line


title: Post-infusion scTCR for CAR-T from Patient 031 and 039 (hashtagged) on WK4

description:
Post_scTCR_031039-S2b-CART
scTCR + Hashtag Multiplex
All_TCR_Aggregated_clonotypes.csv
All_TCR_Aggregated_consensus_annotations.csv
All_TCR_Aggregated_filtered_contig_annotations.csv


title: Pre-infusion scTCR for CAR-T from Patient 031

description:
Pre_scTCR_031
scTCR
All_TCR_Aggregated_clonotypes.csv
All_TCR_Aggregated_consensus_annotations.csv
All_TCR_Aggregated_filtered_contig_annotations.csv


title: TB66SR

value: wild type


title: Pre-infusion scTCR for CAR-T from Patient 039

description:
Pre_scTCR_039
scTCR
All_TCR_Aggregated_clonotypes.csv
All_TCR_Aggregated_consensus_annotations.csv
All_TCR_Aggregated_filtered_contig_annotations.csv


title: SUM149PT; cell line

description:
5481_readcounts.txt
5481_8_SUM149_ACTTGAA_S8

value: breast cancer

value: SUM149PT; cell line


title: cHet input cytoplasmic fraction biol rep 2

description:
biol rep 2
cHet2_input

value: Limb buds


title: TB64SL


title: MCF-7; MIND-transplanted tumour

description:
5502_readcounts.txt
5502_2_MCF7_TGACCAA_S22

value: MCF-7; MIND-transplanted tumour

value: human breast cancer


title: MCF10DCIS.com; MIND-transplanted tumour

description:
5502_readcounts.txt
5502_3_MCF10DCIS_com_ACAGTGA_S23

value: MCF10DCIS.com; MIND-transplanted tumour


title: Post-infusion scTCR for CAR-T from Patient 031 and 039 (hashtagged) on WK3

description:
Post_scTCR_031039-S2a-CART
scTCR + Hashtag Multiplex
All_TCR_Aggregated_clonotypes.csv
All_TCR_Aggregated_consensus_annotations.csv
All_TCR_Aggregated_filtered_contig_annotations.csv

value: PBMC


title: Post-infusion scTCR for CAR-T from Patient 031 and 039 (hashtagged) on WK1-WK2

description:
Post_scTCR_031039-S1-CART
scTCR + Hashtag Multiplex
All_TCR_Aggregated_clonotypes.csv
All_TCR_Aggregated_consensus_annotations.csv
All_TCR_Aggregated_filtered_contig_annotations.csv

value: Diffuse Large B-Cell Lymphoma


title: SUM52PE; cell line

description:
5481_readcounts.txt
5481_7_SUM52_CAGATCA_S7

value: SUM52PE; cell line


title: cHet polysome fraction biol rep 1

description:
biol rep 1
cHet1_poly

value: Limb bud cells

value: Mettl14 wt/flox


title: TB61SR


title: TB61SL


title: cHet input cytoplasmic fraction biol rep 1

description:
biol rep 1
cHet1_input

value: Mettl14 hetero as control


title: Post-infusion scTCR for CAR-T from Patient 116 on D28

description:
Post_scTCR_116-d28-CART
scTCR
All_TCR_Aggregated_clonotypes.csv
All_TCR_Aggregated_consensus_annotations.csv
All_TCR_Aggregated_filtered_contig_annotations.csv

value: CAR-T


title: cKO IP biol rep 3

description: biol rep 3

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases, and undetermined bases with default parameter.
Sequence quality of IP and input samples were also verified using fastp.
HISAT2 (http://daehwankimlab.github.io/hisat2) was used to map reads to the reference genome of Mus musculus.
Assembly: mm10
Supplementary files format and content: A composite Excel file "genes_fpkm_expression" contains fpkm values of all six samples.
Library strategy: m6A-seq

extract_protocol:
Total RNA was prepared with TRIzol Reagent (Thermo Fisher, 15596026)
NEB Next Ultra II RNA Library Prep by Illumina following manufacturer's protocols.

value: Mettl14 flox/flox

value: Mettl14 knockout


title: SK-BR-5; cell line

description:
5481_readcounts.txt
5481_5_SK-BR-5_ACAGTGA_S5

value: SK-BR-5; cell line


title: Post-infusion scTCR for CAR-T from Patient 116 on D21

description:
Post_scTCR_116-d21-CART
scTCR
All_TCR_Aggregated_clonotypes.csv
All_TCR_Aggregated_consensus_annotations.csv
All_TCR_Aggregated_filtered_contig_annotations.csv


title: TB68RL

source_name: Left eye retina

value: Retina

value: postnatal day 34

value: wild type


title: TB68RR

source_name: Right eye retina


title: cKO input biol rep 3

description: biol rep 3

value: Limb buds


title: MDA-MB-231; cell line

description:
5481_readcounts.txt
5481_4_MDA-MB-231_TGACCAA_S4

value: breast cancer

value: MDA-MB-231; cell line


title: cKO IP biol rep 2

description: biol rep 2


title: Post-infusion scTCR for CAR-T from Patient 116 on D10

description:
Post_scTCR_116-d10-CART
scTCR
All_TCR_Aggregated_clonotypes.csv
All_TCR_Aggregated_consensus_annotations.csv
All_TCR_Aggregated_filtered_contig_annotations.csv


title: MCF10DCIS.com; cell line

description:
5481_readcounts.txt
5481_3_MCF10DCIS_com_TTAGGCA_S3

value: MCF10DCIS.com; cell line

value: human breast cancer


title: cKO input biol rep 2

description: biol rep 2


title: Post-infusion scTCR for CAR-T from Patient 048 on D21

description:
Post_scTCR_048-d21-CART
scTCR
All_TCR_Aggregated_clonotypes.csv
All_TCR_Aggregated_consensus_annotations.csv
All_TCR_Aggregated_filtered_contig_annotations.csv

value: PBMC

value: Diffuse Large B-Cell Lymphoma


title: MCF-7; cell line

description:
5481_readcounts.txt
5481_2_MCF7_CGATGTA_S2

value: MCF-7; cell line


title: TB65RR


title: TB66RL


title: cKO IP biol rep 1

description: biol rep 1

value: Limb bud cells


title: Evsa-T; cell line

description:
5481_readcounts.txt
5481_1_EVSA-T_ATCACGA_S1

value: Evsa-T; cell line


title: Post-infusion scTCR for CAR-T from Patient 048 on D14

description:
Post_scTCR_048-d14-CART
scTCR
All_TCR_Aggregated_clonotypes.csv
All_TCR_Aggregated_consensus_annotations.csv
All_TCR_Aggregated_filtered_contig_annotations.csv

value: CAR-T


title: SK-BR-7; cell line

description:
5481_readcounts.txt
5481_6_SK-BR-7_GCCAATA_S6

value: SK-BR-7; cell line


title: Post-infusion scRNA and TotalSeq for CAR-T from Patient 031 and 039 (hashtagged) on WK4

description:
Post_scRNA_TotalSeq_031039-S2b-CART
scRNA and Feature Barcoding + Hashtag Multiplex
Post_Infusion_scRNA_Raw_Counts.mtx
Post_Infusion_scRNA_Raw_Counts_features(rownames).csv
Post_Infusion_ADT_Raw_Counts.mtx
Post_Infusion_scADT_Raw_Counts_features(rownames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_cells(colnames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_metaData.csv


title: cKO input biol rep 1

description: biol rep 1

value: Mettl14 flox/flox

value: Mettl14 knockout


title: cHet IP biol rep 3

description: biol rep 3

value: Mettl14 wt/flox

value: Mettl14 hetero as control


title: TB64RR

description:
TB64RR
Raw files for this sample contain different numbers of reads due to some read corruption and removal in the R2 file.

value: Retina

value: postnatal day 34

value: wild type


title: TB65RL


title: Eye_ALAN_Female4

city: Edinburgh

first: Violeta

last: Trejo-Reveles

address: Old College, South Bridge, Edinburgh

institute: The University of Edinburgh

description: Library name: 144EA

data_processing:
Raw fastq files were processed by trimming using trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic) with the following parameters: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10; SLIDINGWINDOW:10:30; LEADING:28; TRAILING:28; MINLEN:75. After trimming the quality of the reads was checked using FASTQC
Reads were aligned using STAR aligner version 2.7.11a (https://github.com/alexdobin/STAR), with the ENSEMBL green anole (Anolis carolinensis) genome and gtf (AnoCar2.0v2, Anolis_carolinensis.AnoCar2.0v2.112.gtf) as references. BAM files were counted using featurecounts (https://subread.sourceforge.net/).
Assembly: AnoCar2.0v2
Supplementary files format and content: csv files contain ether raw counts for each sample

organism: Anolis carolinensis

source_name: Eye

growth_protocol: Twenty-four free-living adult green anole lizards (Anolis carolinensis; twelve of each sex) were captured in the breeding season, in May 2024, on the urban campus of Trinity University in San Antonio, Texas, USA, during daylight hours. Green anole lizards were collected by using a dental floss loop attached to an extendable fishing pole or by hand and were transported individually to the Trinity University vivarium in cotton bags. On the day of capture, the body mass of each anole was measured to the nearest 0.1 g using a Pesola spring scale and snout-vent length measured to the nearest mm using a clear plastic ruler (Males: range 52-69mm, average 62mm; Females: range 51-57mm, average 55mm). Each individual was given a unique identification number on the lower jaw using a non-toxic permanent marker.

extract_protocol:
RNAeasy kit
Library construction performed by BGI Genomics

treatment_protocol: Each anole was  randomly assigned to one of three treatment groups: Midday, Midnight, or ALAN. Sex was determined by the presence of hemipenes and the size of the dewlap; four anoles of each sex were assigned to each treatment group

value: Eye

value: Female

value: WT

value: ALAN


title: Post-infusion scRNA and TotalSeq for CAR-T from Patient 031 and 039 (hashtagged) on WK3

description:
Post_scRNA_TotalSeq_031039-S2a-CART
scRNA and Feature Barcoding + Hashtag Multiplex
Post_Infusion_scRNA_Raw_Counts.mtx
Post_Infusion_scRNA_Raw_Counts_features(rownames).csv
Post_Infusion_ADT_Raw_Counts.mtx
Post_Infusion_scADT_Raw_Counts_features(rownames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_cells(colnames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_metaData.csv

value: PBMC

value: Diffuse Large B-Cell Lymphoma


title: Eye_ALAN_Female3

description: Library name: 143EA


title: TB66RR


title: Eye_ALAN_Female2

description: Library name: 142EA


title: TB61RR


title: Post-infusion scRNA and TotalSeq for CAR-T from Patient 031 and 039 (hashtagged) on WK1-WK2

description:
Post_scRNA_TotalSeq_031039-S1-CART
scRNA and Feature Barcoding + Hashtag Multiplex
Post_Infusion_scRNA_Raw_Counts.mtx
Post_Infusion_scRNA_Raw_Counts_features(rownames).csv
Post_Infusion_ADT_Raw_Counts.mtx
Post_Infusion_scADT_Raw_Counts_features(rownames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_cells(colnames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_metaData.csv


title: cHet input biol rep 3

description: biol rep 3

value: Limb buds

value: Limb bud cells


title: cHet IP biol rep 2

description: biol rep 2


title: Post-infusion scRNA and TotalSeq for CAR-T from Patient 116 on D28

description:
Post_scRNA_TotalSeq_116-d28-CART
scRNA and Feature Barcoding
Post_Infusion_scRNA_Raw_Counts.mtx
Post_Infusion_scRNA_Raw_Counts_features(rownames).csv
Post_Infusion_ADT_Raw_Counts.mtx
Post_Infusion_scADT_Raw_Counts_features(rownames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_cells(colnames).csv
Post_Infusion_scADT_and_scRNA_Raw_Counts_metaData.csv

value: CAR-T