title: Lung, PBS, Csf2rb KO, rep1

description: Library name: Sample 4


title: 4508

status: Public on Oct 21 2025

type: SRA

city: Asheville

first: Melissa

middle: Marie

last: Heintz

state: NC

address: 31 College Place, Suite B118

country: USA

institute: ToxStrategies

description: Library name: Sample 41

library_source: transcriptomic

data_processing:
Sequencing reads are demultiplexed using the standard sequencing instrument software and sample-specific barcodes to give a FASTQ file for each sample
bcl2fastq2 v2.20 for demultiplexing
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
fastq files were aligned to a pseudo transcriptome using Bowtie allowing up to 2 mismatches
Assembly: templated oligo sequencing
Supplementary files format and content: comma-separated text file includes raw count values for each gene_probe

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Mounted, unstained FFPE liver samples were scraped from the slides and processed according to the TempO-Seq® protocol by BioSpyder Technologies
TempO-Seq® protocol by BioSpyder Technologies

treatment_protocol: Female B6C3F1 mice within, 9-11 weeks of age with a weight range of 15-25 g were used in these studies. Animals received a subcutaneously implanted electronic identification chip and assigned to exposure groups by a stratified randomization scheme designed to achieve similar group mean body weights. Following randomization, mice were single- housed to ensure accurate water consumption data on a per-animal basis. Nine mice per group were exposed to TBA in drinking water at concentrations of 0, 10, 20, and 40 mg/mL for 14 or 28 days of consecutive exposure. Following the last day of exposure, mice were euthanized by CO2 anesthesia and exsanguination. Livers were fixed in 10% neutral-buffered formalin, embedded in paraffin (FFPE), and sections approximately 4 – 6 µm in thickness were mounted to glass slides.

tag: tissue

value: liver

tag: Sex

value: female

tag: strain

tag: exposure route

value: drinking water

tag: exposure duration

tag: treatment

value: 20 mg/mL


title: Injured, Replicate 2, snRNAseq

city: Cincinnati

first: Steven

middle: Allen

last: Crone

state: OH

address: 3333 Burnet Ave, MLC 7007

department: Pediatric Neurosurgery

institute: Cincinnati Children's Hospital Medical Center

description:
10x Genomics
Integrated_Uninjured_Injured_Cohorts_Adults.rds

library_source: transcriptomic single cell

data_processing:
Cell Ranger (10x Genomics) version 6.0.1 version was used to demultiplex Illumina base call file, align reads to the mouse reference genome and quantify gene expression.
Ambient RNA was removed using 0.5 contaminant cut-off in SOUPX
Seurat v5.0.0 was used to perform downstream analysis including filtration, scaling, log-normalization, integration of datasets and label transfer.
cellHarmony from AltAnalyze version 2.1.4 was used to compare the gene expression changes in V2a neurons before and after injury.
Augur version 1.0.3 was used to perform cell prioritizatio to identify most perturbed cluster following injury.
Enrichr was used to perform gene enrichment analysis.
Assembly: mm10
Supplementary files format and content: Soupx output files (barcodes, genes and matrix) and Seurat processed rds files/

molecule: nuclear RNA

source_name: Spinal cord (C3-C8)

extract_protocol:
Nuclei were isolated from cervical spinal cord tissue using dounce-type homogenization method and myelin removal beads. The GFP nuclei were sorted using FACSAria and sequenced using  10x Genomics and Illumina protocols.
Library was perforemd according to the manufacturer's instruction (single cell 3' v3 prtocol, 10X genomics).

value: Spinal cord (C3-C8)

value: Female

tag: genotype

value: C2 hemisection injury


title: Splenic.CD4_HTGTS_TCR_seq_TcrJ_mix_rep1

city: Shanghai

first: Haiqiang

last: Dai

address: 320 Yue Yang Road

country: China

institute: Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell  Science

description: Library name: sample43

library_source: genomic

data_processing:
For Tcra and Tcrb gene rearrangement analysis, sequencing reads were aligned to the mm10 reference genome for mouse T cells and to the hg38 reference genome for human T cells. All duplicate junctions were retained in the analyses. To quantify the utilization level of V, D and J segments in TCR α and β gene rearrangements, we defined “on-target” sequences as the 40-bp regions flanking the recombination signal sequences (RSS) (RSS ± 40 bp). which were then used to determine the usage of V(D)J segments. To quantify TCR repertoires, we employed a pipeline called "HTGTSrep" to identify the productive and non-productive V(D)J rearrangements, as well as to analyze the motifs and length distribution of CDR3 regions.
Assembly: mm10;hg38
Supplementary files format and content: tlx

molecule: genomic DNA

source_name: Spleen

extract_protocol:
Cells were collected and lysed in cell lysis buffer using proteinase K. Genomic DNA was later precipitated and dissolved in TE before shearing.
3-20 μg DNA was fragmented via sonication on Qsonic biorupter and subjected to linear PCR amplification with a biotinylated primer as following PCR conditions: 95°C 2 min; 95°C 30s; 58°C 30 s; 72°C 90 s; 80 cycles; 72°C 2 min. Primers were removed by VAHTS DNA Clean Beads (Vazyme, N411). The resulting single-strand biotinylated PCR products were collected via Dynabeads MyONE C1 streptavidin beads (ThermoFisher, 65002) and ligated to bridge adapters overnight in the presence of 15% PRG8000. Ligation were conducted following 25°C 60 min; 22°C 120 min; 16°C 9-12 h. Subsequently, i5-indexed bait-specific inner primers and i7-index adapter primers were added to adapter-ligated products by nested PCR. Excess primers were removed by VAHTS DNA Clean Beads (Vazyme, N411), and the purified PCR products were further tagged with Illumina sequencing adapter sequences. Libraries were size-selected by resolving PCR products on a 2% agarose gel, isolating fragments between 300-700 bp for mouse or human samples, with recovery performed via gel extraction. The HTGTS-TCR-seq libraries were sequenced on NovaXplus (Illumina) using 150-bp paired-end reads.

value: Spleen

tag: cell type

value: Splenic CD4+ T cells

value: WT


title: Splenic.CD8_HTGTS_TCR_seq_TcrJ_mix_rep2

description: Library name: sample47

value: Splenic CD8+ T cells


title: NRP1-SUM159-siNRP1.3-RNA.1

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

data_processing:
Paired-end sequencing on the MGI DNBSEQ-G400 sequencer at QUT Central Analytical Research Facility (CARF), Brisbane, Queensland, Australia with a read length of 150 bp and ~40M read pairs per sample.
Quality control of the raw reads was performed using FastQC (v.0.11.9).
Raw sequencing reads were trimmed for quality control using TrimGalore (v.0.6.5).
Trimmed sequence reads were mapped to the human genome and transcriptome using the STAR (v.2.7.2b) aligner.
Read quantification was performed using RSEM (v.1.3.3).
Assembly: GRCh38 / hg38 and Ensembl.v.114 / Gencode.v.48 (May-2025).
Supplementary files format and content: Tab separated TXT files with raw COUNTS, TPM and ISOPCT (Isoform Percentage) values for human genes and transcript variants, respectively, for each sample as generated by RSEM.

organism: Homo sapiens

source_name: Breast Cancer cell line

growth_protocol: MDA-MB-231, HS578T and SUM159PT claudin-low breast cancer cell lines were maintained in Dulbecco's Modified Eagle Medium (DMEM), High Glucose, Pyruvate supplemented with 10% Fetal Bovine Serum (FBS) both from Gibco. HEK293T cells were cultured in DMEM, High Glucose, Pyruvate supplemented with 5% FBS (Gibco, Thermofisher Scientific). All cells were maintained in 37 degrees celcius, 5% CO2 incubators.

extract_protocol:
Cells were lysed with TriZol reagent (Invitrogen, Thermofisher Scientific). Total RNA isolation was performed using the Direct-zol RNA Miniprep Plus kit (Zymo Research) as per manufacturer’s instructions. The 2100 Bioanalyzer (Agilent Technologies) was used to determine the RNA integrity number (RIN), with the RNA 6000 Nano Kit (Agilent Technologies) according to manufacturer’s instructions used for sample preparation. Samples with a RIN >8 were submitted for sequencing.
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit (strand-specific, polyA enrichment), no ERCC controls. Input for each sample was 500 ng.

treatment_protocol: siRNA reverse transfection: 20 nM siRNA was reverse transfected into 0.7 x 106 SUM159PT, MDA-MB-231 and HS578T cells using 1:500 Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen, Thermofisher Scientific) and 1:10 Opti-MEM™ Reduced Serum Medium (Gibco, Thermofisher Scientific) to DMEM supplemented with 10% FBS (Gibco, Thermofisher Scientific). RNA was extracted from the cells at 72hrs post-transfection. A predesigned Silencer™ Select negative control (Negative Control siRNA No. 1, #4390844, Thermofisher Scientific) was used in addition to two custom Silencer™ Select NRP1-targeting siRNAs (Thermofisher Scientific) which are siNRP1 3 and siNRP1 5. siNRP1 3 targeted transmembrane-NRP1 only, whereas siNRP1 5 targeted total NRP1. Lentiviral transduction of shRNA: 1.5 x 10^6 HEK293T cells per shRNA were seeded and cultured in 10 mL of DMEM, High Glucose, Pyruvate supplemented with 10% heat inactivated FBS (Gibco, Thermofisher Scientific). FBS heat inactivation was done by a 30-minute incubation in a 56 degrees cecius water bath. At 50-60% confluency, the HEK293T cells were transfected with 200 µL of lentiviral transfection mix. Transfection mix was prepared as follows: serum-free DMEM (Gibco), 12 µL X-tremeGENE™ HP DNA Transfection Reagent (Sigma Aldrich), 1.8 µg pCMV Delta 8.2 R (Addgene), 0.2 µg pCMV-VSV-G (Addgene) and 2.0 µg of shRNA cloned to the pLKO.1 lentiviral vector (Addgene) was combined to a 200 µL final volume and incubated for 15 minutes at room temperature. After an overnight incubation at 37oC with 5% CO2, all transfection media was aspirated from the HEK293T cells and replaced with 7 mL of regular culture media. Viral supernatant was then harvested at 48 hrs and 72 hrs post-transfection. For transduction of the shRNA, 0.7 x 106 HS578T, MDA-MB-231 and SUM159PT cells per shRNA were cultured to 30-50% confluency. The cells were then incubated at 37 degrees celcius overnight in 4.6 mL of previously harvested lentiviral supernatant with 6 µg/mL of protamine sulfate (Sigma Aldrich). Successfully transduced cells were selected with 1 µg/mL puromycin (Gibco, Thermofisher Scientific) for a minimum of three days for before use and maintained in regular culture media. Cells were seeded at 0.7 x 10^6 and RNA was extracted at 80-90% confluency. The shRNAs used were a non-targeting shRNA (Thermofisher Scientific), and two custom NRP1-targeting shRNA sequences obtained from Thermofisher Scientific, which are shNRP1 3 and shNRP1 5. shNRP1 3 targets transmembrane-NRP1 only, whereas shNRP1 5 targets total NRP1.

value: Breast Cancer cell line

tag: cell line

value: siNRP1 3


title: 4512

description: Library name: Sample 44


title: Aged_HTGTS_TCR_seq_Traj_mix_rep1

description: Library name: sample40

source_name: Aged Thymus (16-18 month)

value: Aged Thymus (16-18 month)

value: Thymocytes


title: Lung, HCoV-OC43, Csf2rb KO, rep3

city: Beijing

first: Chen

last: Dong

address: Haidian District

institute: Tsinghua University

description: Library name: Sample 3

data_processing:
Briefly, the reads were aligned to mm10 by HISAT2 v.2.2.1 (Kim et al., 2019) with default parameters and the uniquely mapping reads were summarized by feature Counts (from Subread v.2.0.1) (Liao et al., 2014).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Lung

extract_protocol:
Total cellular RNA was extracted with the Magzol reagent (Magen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Lung

value: Csf2rb KO


title: NRP1-SUM159-shNT-RNA.3

value: shNT


title: 4511

description: Library name: Sample 43

value: liver

value: female


title: 4504

description: Library name: Sample 39

value: drinking water

value: 20 mg/mL


title: Uninjured, Replicate 2, snRNAseq

description:
10x Genomics
UninjuredCohorts_Adults.rds
Integrated_Uninjured_Injured_Cohorts_Adults.rds

source_name: Spinal cord (C1-C8)

value: Spinal cord (C1-C8)

value: Female

value: Uninjured


title: 4510

description: Library name: Sample 42


title: NRP1-SUM159-shNT-RNA.2


title: Lung, HCoV-OC43, Csf2rb KO, rep1

description: Library name: Sample 1


title: Splenic.CD4_HTGTS_TCR_seq_TcrJ_mix_rep3

description: Library name: sample45

value: Spleen

value: Splenic CD4+ T cells


title: NRP1-SUM159-shNRP1.3-RNA.3

value: shNRP1 3


title: Splenic.CD4_HTGTS_TCR_seq_TcrJ_mix_rep2

description: Library name: sample44

value: WT


title: Lung, PBS, Csf2rb KO, rep2

description: Library name: Sample 5


title: 3530

description: Library name: Sample 36

value: 10 mg/mL


title: NRP1-SUM159-shNT-RNA.1

value: Breast Cancer cell line


title: Young_HTGTS_TCR_seq_Traj_mix_rep2

description: Library name: sample37

source_name: Thymus

value: Thymus

value: Thymocytes


title: NRP1-SUM159-shNRP1.5-RNA.3

value: shNRP1 5


title: NRP1-SUM159-shNRP1.5-RNA.1


title: 4506

description: Library name: Sample 40


title: Injured, Replicate 1, snRNAseq

value: Spinal cord (C3-C8)

value: C2 hemisection injury


title: Aged_HTGTS_TCR_seq_Traj_mix_rep2

description: Library name: sample41

value: Aged Thymus (16-18 month)


title: NRP1-SUM159-shNRP1.5-RNA.2


title: NRP1-MDA.MB.231-siNT-RNA.3

value: siNT


title: Aged_HTGTS_TCR_seq_Trav_mix_rep2

description: Library name: sample33


title: 4503

description: Library name: Sample 38

value: liver

value: female

value: drinking water

value: 20 mg/mL


title: MP0016_M1004I

city: New York

first: Somnath

last: Tagore

state: NY

address: 650W, 168th Street

institute: Columbia University

data_processing:
We used Picard for demultiplexing, followed by Kallisto for abundance calculation and counts generation.
Assembly: GRCh38
Supplementary files format and content: Abundance data (*.tsv) and Counts data (*.csv)

extract_protocol:
Briefly, pHAGE constructs of PIK3CA variants and wild-type genes were expanded from the sequence-validated glycerol stocks for plasmid DNA extraction. The backbone pHAGE constructs, together with the packaging plasmids (pCMVR8.74 and pMD2.G), were co-transfected into the LentiX-293T cells. The virus-containing medium was harvested at 36h, 48h, 60h and 72h post-transfection and then filtered with 0.45 μM filter. 3 x 10^5 cells were plated in each well of a 6-well plate 24h before transduction. The cell culture medium were replaced with 3 mL viral medium and underwent spinoculation at 1000g for 3h in the presence of 8 ug/mL polybrene. Cells were washed with PBS 16h after transduction and recovered in culture medium for another 48h. The transduced cells were then selected with puromycin for 96h and recovered for at least 48h before getting used in subsequent culture and assays.
As described in Bush et al., 2017 (PMID: 28740083).
PLATE-seq

value: Epithelial cell

tag: amino acid change

value: Antibiotics selection (Puromycin)

tag: time


title: NRP1-MDA.MB.231-siNT-RNA.2


title: MP1254_V105_R108del


title: Young_HTGTS_TCR_seq_Traj_mix_rep4

description: Library name: sample39


title: Aged_HTGTS_TCR_seq_Trav_mix_rep1

description: Library name: sample32


title: 3524

description: Library name: Sample 32


title: NRP1-SUM159-shNRP1.3-RNA.2

value: shNRP1 3


title: Uninjured, Replicate 1, snRNAseq

value: Spinal cord (C1-C8)

value: Female

value: Uninjured


title: Young_HTGTS_TCR_seq_Trav_mix_rep2

description: Library name: sample29

value: Thymus

value: WT


title: MP0680_E542E


title: Young_HTGTS_TCR_seq_Traj_mix_rep3

description: Library name: sample38

value: Thymocytes


title: 4502

description: Library name: Sample 37


title: MP1257_F614I


title: MP0427_T1025T


title: 3522

description: Library name: Sample 31

value: 10 mg/mL


title: 3529

description: Library name: Sample 35


title: Young_HTGTS_TCR_seq_Traj_mix_rep1

description: Library name: sample36


title: NRP1-MDA.MB.231-siNRP1.5-RNA.2

value: Breast Cancer cell line

value: siNRP1 5


title: Young_HTGTS_TCR_seq_Trav_mix_rep1

description: Library name: sample28


title: 3520

description: Library name: Sample 30


title: NRP1-SUM159-shNRP1.3-RNA.1


title: MP0683_E109_I112delinsD


title: NRP1-MDA.MB.231-siNRP1.5-RNA.1


title: 3526

description: Library name: Sample 34


title: Aged_HTGTS_TCR_seq_Trbv_mix_rep1

description: Library name: sample24

value: Aged Thymus (16-18 month)


title: MP0681_F70F


title: 3525

description: Library name: Sample 33

value: liver


title: NRP1-MDA.MB.231-siNT-RNA.1

value: siNT


title: NRP1-MDA.MB.231-siNRP1.5-RNA.3


title: NRP1-MDA.MB.231-siNRP1.3-RNA.2

value: siNRP1 3


title: 3518

description: Library name: Sample 29

value: female

value: drinking water


title: 3514

description: Library name: Sample 27


title: Aged_HTGTS_TCR_seq_Trbv_mix_rep2

description: Library name: sample25


title: NRP1-MDA.MB.231-siNRP1.3-RNA.1


title: MP1246_E542V

value: Epithelial cell

value: Antibiotics selection (Puromycin)


title: 3513

description: Library name: Sample 26


title: MP1255_R398H


title: NRP1-MDA.MB.231-siNRP1.3-RNA.3


title: 3517

description: Library name: Sample 28


title: NRP1-MDA.MB.231-shNT-RNA.3

value: shNT


title: Young_HTGTS_TCR_seq_Trbv_mix_rep3

description: Library name: sample23


title: MP1241_E542K


title: NRP1-MDA.MB.231-shNT-RNA.2


title: MP0018_M1043L


title: Young_HTGTS_TCR_seq_Trbv_mix_rep2

description: Library name: sample22


title: 3510

description: Library name: Sample 24


title: Aged_HTGTS_TCR_seq_Trbj_mix1_rep3

description: Library name: sample20


title: Aged_HTGTS_TCR_seq_Trbj_mix1_rep2

description: Library name: sample19


title: MP1240_E545K


title: MP1250_A1020V


title: 3509

description: Library name: Sample 23


title: Young_HTGTS_TCR_seq_Trbv_mix_rep1

description: Library name: sample21


title: NRP1-MDA.MB.231-shNRP1.5-RNA.3

value: shNRP1 5


title: NRP1-MDA.MB.231-shNT-RNA.1


title: Aged_HTGTS_TCR_seq_Trbj_mix1_rep1

description: Library name: sample18


title: MP1244_C420R


title: 3508

description: Library name: Sample 22


title: NRP1-MDA.MB.231-shNRP1.5-RNA.2


title: 3504

description: Library name: Sample 21


title: MP1242_G1007R


title: Young_HTGTS_TCR_seq_Trbj_mix1_rep2

description: Library name: sample16


title: MP1249_H701R


title: MP1248_Q546R


title: 3502

description: Library name: Sample 20


title: NRP1-MDA.MB.231-shNRP1.5-RNA.1


title: Young_HTGTS_TCR_seq_Trbj_mix1_rep1

description: Library name: sample15


title: 3501

description: Library name: Sample 19


title: NRP1-MDA.MB.231-shNRP1.3-RNA.3

value: shNRP1 3


title: 1614

description: Library name: Sample 18

value: 0 mg/mL


title: PreselectionDP_HTGTS_TCR_seq_Trav_mix_rep4

description: Library name: sample14

value: Thymus

value: Preselection DP thymocytes

value: WT


title: MP0710_M1043I


title: NRP1-MDA.MB.231-shNRP1.3-RNA.2

value: Breast Cancer cell line


title: NRP1-MDA.MB.231-shNRP1.3-RNA.1


title: MP1252_M1043V


title: PreselectionDP_HTGTS_TCR_seq_Trav_mix_rep2

description: Library name: sample12


title: 1529

description: Library name: Sample 17


title: NRP1-HS578T-siNT-RNA.3


title: 1528

description: Library name: Sample 16


title: Young_HTGTS_TCR_seq_Trbj_mix1_rep3

description: Library name: sample17

value: Thymocytes


title: PreselectionDP_HTGTS_TCR_seq_Trav_mix_rep1

description: Library name: sample11


title: MP1243_L456Afs*13


title: NRP1-HS578T-siNT-RNA.2


title: 1526

description: Library name: Sample 15


title: NRP1-HS578T-siNT-RNA.1


title: MP1239_G11D


title: MP1245_E453K


title: MP0895_R38C


title: PreselectionDP_HTGTS_TCR_seq_Traj_mix_rep4

description: Library name: sample10


title: 1522

description: Library name: Sample 13


title: MP1253_H1047L


title: 1524

description: Library name: Sample 14


title: PreselectionDP_HTGTS_TCR_seq_Trav_mix_rep3

description: Library name: sample13


title: NRP1-HS578T-siNRP1.5-RNA.2

value: siNRP1 5


title: MP0011_I910V


title: PreselectionDP_HTGTS_TCR_seq_Traj_mix_rep1

description: Library name: sample7


title: MP0689_E1037K


title: NRP1-HS578T-siNRP1.5-RNA.1


title: NRP1-HS578T-siNRP1.5-RNA.3


title: DN3_HTGTS_TCR_seq_Trbj_mix2_rep3

description: Library name: sample6

value: Thymic T progenitor cells after T-lineage commitment (CD4- CD8- CD44- CD25+ DN3)


title: PreselectionDP_HTGTS_TCR_seq_Traj_mix_rep3

description: Library name: sample9


title: PreselectionDP_HTGTS_TCR_seq_Traj_mix_rep2

description: Library name: sample8


title: DN3_HTGTS_TCR_seq_Trbj_mix2_rep2

description: Library name: sample5


title: 1520

description: Library name: Sample 11

value: liver


title: NRP1-HS578T-siNRP1.3-RNA.1

value: siNRP1 3


title: NRP1-HS578T-siNRP1.3-RNA.3


title: 1515

description: Library name: Sample 8

value: female


title: MP0024_V344M


title: 1519

description: Library name: Sample 10

value: drinking water


title: MP1247_E545A

value: Epithelial cell


title: NRP1-HS578T-siNRP1.3-RNA.2


title: 3512

description: Library name: Sample 25

value: 10 mg/mL


title: NRP1-HS578T-shNT-RNA.3

value: shNT


title: MP0405_R115L

value: Antibiotics selection (Puromycin)


title: 1513

description: Library name: Sample 7


title: DN3_HTGTS_TCR_seq_Trbj_mix1_rep3

description: Library name: sample3


title: MP0010_E545D


title: DN3_HTGTS_TCR_seq_Trbj_mix1_rep1

description: Library name: sample1


title: NRP1-HS578T-shNT-RNA.1


title: 1507

description: Library name: Sample 5


title: 1521

description: Library name: Sample 12


title: MP044I_C604R


title: NRP1-HS578T-shNT-RNA.2


title: MEF P6 β-amyrin

city: Obu

first: Masataka

last: Sugimoto

state: Aichi

address: 7-430 Morioka-cho

department: Cellular Pathology

country: Japan

institute: National Center for Geriatrics and Gerontology

description: Library name: SAMPLE6

data_processing:
The quality of the raw paired-end sequence reads was assessed with FastQC (Version 0.11.7; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Low quality (< 20) bases and adapter sequences were trimmed by Trimmomatic software (Version 0.38) with following parameters: ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36.
The trimmed reads were aligned to the reference genome using RNA-seq aligner HISAT2 (Version 2.1.0).
The HISAT2-resultant .sam files were converted into .bam files with Samtools (Version 1.9).
The .bam files were used to estimate the abundance of uniquely mapped reads with featureCounts (Version 1.6.3).
The raw read counts were normalized with Fragments Per Kilobase of exon per Million mapped fragments (FPKM).
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample
Supplementary files format and content: tab-delimited text file including FPKM values for each sample

molecule: polyA RNA

source_name: Mouse embryopnic fibroblasts (MEFs)

growth_protocol: MEFs were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA were extracted using NucleoSpin RNA (Macherey Nagel), and poly A were purified form the total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module.
RNA libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit.

treatment_protocol: Cells were treated or untreated with 20 µM of α-amyrin or β-amyrin for 3 days.

value: Mouse embryopnic fibroblasts (MEFs)

value: Senescent

value: Wild-type

value: β-amyrin


title: MP1050_H1047R


title: 1509

description: Library name: Sample 6

value: 0 mg/mL


title: DN3_HTGTS_TCR_seq_Trbj_mix1_rep2

description: Library name: sample2

value: Thymus

value: WT


title: DN3_HTGTS_TCR_seq_Trbj_mix2_rep1

description: Library name: sample4


title: 1506

description: Library name: Sample 4


title: NRP1-HS578T-shNRP1.5-RNA.3

value: Breast Cancer cell line

value: shNRP1 5


title: MP0079_E39K


title: NRP1-HS578T-shNRP1.5-RNA.2


title: MP0685_E469insDK


title: 1502

description: Library name: Sample 2

value: liver


title: NRP1-HS578T-shNRP1.5-RNA.1


title: MEF P6 Vehicle

description: Library name: SAMPLE4

value: Vehicle


title: 1503

description: Library name: Sample 3

value: female


title: MEF P1 β-amyrin

description: Library name: SAMPLE3

value: Non-senescent


title: MP0406_R108H

value: Epithelial cell


title: MP0020_E542A


title: 1501

description: Library name: Sample 1

value: drinking water


title: NRP1-HS578T-shNRP1.3-RNA.2

value: shNRP1 3


title: MEF P1 α-amyrin

description: Library name: SAMPLE2

value: α-amyrin


title: NRP1-HS578T-shNRP1.3-RNA.1


title: MEF P1 Vehicle

description: Library name: SAMPLE1

value: Mouse embryopnic fibroblasts (MEFs)


title: MP0439_P471L

value: Antibiotics selection (Puromycin)


title: OPL14, lung, Sarcomatoid, None, DSP_1001660021708_E_C07

status: Public on Oct 20 2025

city: Okayama

first: Shuta

last: Tomida

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Center for Comprehensive Genomic Medicine

institute: Okayama University Hospital

description: Library name: DSP_1001660021708_E_C07

data_processing:
FASTQ files were converted into DCC files using GeoMx NGS Pipeline (v3.1.1.6), and subsequent preprocess was performed GeomxTools (v3.8.0) as per NanoString’s official workflow.
ROIs were retained if they met the following criteria: ≥1,000 total reads, ≥80% alignment rate, ≥80% stitching and trimming rates, ≥50% sequencing saturation, ≥100 nuclei, and an area of ≥5,000 μm². Probes were globally removed if their geometric mean count across all segments was <10% of the target probe set mean or if flagged as outliers in >20% of segments by Grubbs' test.
Gene counts from multiple probes were aggregated using the geometric mean. ROI segments with gene detection rates <5% were excluded, and genes detected in <10% of all segments were removed. A Limit of Quantification (LOQ) was determined per segment based on the greater of twice the negative control SD or a minimum threshold of 2.
A total of 11,327 genes and 114 ROIs were retained. Finally, Q3 (75th percentile) normalization was applied.
Assembly: hg38
Supplementary files format and content: raw_assay_counts.csv: Include raw assay count values for each ROI.
Supplementary files format and content: processed_q3norm_gene_expr.csv: Include preprocessed (QC and filtering) and 75th percentile normalized gene expression values for each ROI.
Supplementary files format and content: Hs_R_NGS_WTA_v1.0.pkc: PKC file
Library strategy: Spatial Transcriptomics

source_name: Pulmonary pleomorphic carcinoma

extract_protocol:
FFPE tissues were processed following the GeoMx DSP Automated Slide Preparation User Manual (MAN-10151-04). The GeoMx DSP scanned the slides, capturing detailed images of the selected ROIs.
Hybridization was performed using the Human Whole Transcriptome Atlas, targeting human protein-coding transcripts. UV light was used to release oligonucleotide tags from selected regions. The released tags were collected separately and uniquely indexed. PCR reactions were purified, and libraries were paired-end sequenced (2x150) on a NovaSeq X Plus.

value: Pulmonary pleomorphic carcinoma

tag: patientid

tag: age

value: male

tag: smoker

value: no

tag: pn (uicc_8th)

tag: pstage (uicc_8th)

tag: segmentation

tag: lesion

value: lung

tag: component

value: Sarcomatoid

value: surgical resection

tag: slide name

tag: nuclei


title: OPL14, lung, Sarcomatoid, None, DSP_1001660021708_E_C06

description: Library name: DSP_1001660021708_E_C06

tag: tissue

tag: Sex


title: OPL13, lung, Sarcomatoid, None, DSP_1001660021708_E_C02

description: Library name: DSP_1001660021708_E_C02

value: yes

tag: treatment


title: GEMM KPT UPS

first: Jonathan

last: Rub

address: 417 E 68th St

department: Cancer Biology and Genetics

institute: MSKCC

description:
Library name: GEMM_KPT_UPS
10x Genomics

data_processing:
Raw sequencing data from cDNA and multiplexed libraries was demultiplexed and aligned with the 10X Genomics Cell Ranger pipeline (v.7.2.0).
Assembly: For mouse experiments, data was aligned to a custom GRCm38/mm10 reference genome including the tdTomato transgene used in this study.
Assembly: For human PDX experiments, data was aligned to a combined human (GRCh38) 2020-A and GRCm38/mm10 reference genome.
Supplementary files format and content: Tab-separated values files, matrix files, and h5ad scanpy files

source_name: Undifferentiated Pleomorphic Sarcoma

growth_protocol: Autochthonous tumors were induced in KrasLSL-G12D/+; Trp53flox/flox; Rosa26tdtomato/+ (KPT) mice with 9x10^7 plaque-forming units (PFU) of AdCMV-Cre (Iowa Viral Vector Core) as previously described, in mice that were between 9-24 weeks of age. Immunocompromised NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (aka NSG mice)  (The Jackson Laboratory, catalog #005557) mice were used for transplantation of patient-derived xenografts (PDXs).

extract_protocol:
For isolation of tumor cells from KPT mice and PDXs, mice were euthanized at the indicated time points. Dissected tumors were dissociated with a mixture of Dispase II, Collagenase Type IV, and DNase I for 1 hr. The dissociated cells were filtered using a 100 µm filter and spun at 1000 rpm for 10 min at 4 °C. The supernatant was removed by aspiration and red blood cell lysis was performed using BD Pharm Lyse for 1 minute on ice. Cells were then washed with sterile media containing 2% heat inactivated FBS, passed through a 40 µm filter, and pelleted at 300 g for 5 min at 4 °C. The supernatant was removed and cells were resuspended in Fluorescence-Activated Cell Sorting (FACS) buffer media (2% heat-inactivated FBS in PBS) and counted for use in FACS.
Single cell suspensions from UPS tumors were prepared and stained as above. Live sorted cells were collected by flow cytometry, washed once with PBS containing 2% heat inactivated FBS (HI-FBS) and resuspended to a final concentration of 700–1,300 cells per μl of SMEM + 2% HI-FBS. The viability of cells in all experiments was confirmed to be above 80% by 0.2% (w/v) Trypan Blue staining (Invitrogen, Countess II) and processed by droplet based scRNA-seq using the 10X genomics Chromium Single Cell 3’ Library & Gel bead Kit >=V3 according to manufacturer’s protocol. Following reverse transcription and cell barcoding in droplets, emulsions were broken, and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification as per manufacturer’s instructions. Between 10,000 to 30,000 cells were targeted for each droplet formulation lane using Chromium. Samples were multiplexed using the TotalSeq B cell hashing protocol (Biolegend). Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).

treatment_protocol: Mice were treated with intraperitoneal Doxorubicin (0.9-1 mg/kg) twice a week for up to 4 weeks. NSG mice bearing UPS2236 PDXs were harvested at 3 weeks, approximately 1 week earlier than the preplanned endpoint of 4 weeks due to tumor growth constraints.

value: Undifferentiated Pleomorphic Sarcoma

value: Doxorubicin


title: OPL14, lung, Adenocarcinomas, None, DSP_1001660021708_E_C05

description: Library name: DSP_1001660021708_E_C05

value: Adenocarcinomas


title: MEF P6 α-amyrin

description: Library name: SAMPLE5

tag: cell type

value: Senescent

tag: genotype

value: Wild-type


title: OPL10, lung, Sarcomatoid, None, DSP_1001660021708_E_B12

description: Library name: DSP_1001660021708_E_B12


title: OPL14, lung, Adenocarcinomas, None, DSP_1001660021708_E_C04

description: Library name: DSP_1001660021708_E_C04


title: 1516

description: Library name: Sample 9

value: liver

value: female

tag: strain

tag: exposure route

value: drinking water

tag: exposure duration

value: 0 mg/mL


title: OPL13, lung, Sarcomatoid, None, DSP_1001660021708_E_C03

description: Library name: DSP_1001660021708_E_C03

tag: patientid

tag: age


title: OPL10, lung, Adenocarcinomas, None, DSP_1001660021708_E_B11

description: Library name: DSP_1001660021708_E_B11

tag: smoker

tag: pn (uicc_8th)


title: OPL9, lung, Sarcomatoid, None, DSP_1001660021708_E_B09

description: Library name: DSP_1001660021708_E_B09

tag: pstage (uicc_8th)

tag: segmentation


title: OPL9, lung, Sarcomatoid, None, DSP_1001660021708_E_B08

description: Library name: DSP_1001660021708_E_B08

tag: lesion

tag: component


title: OPL10, mediastinal lymph node, Adenocarcinomas, None, DSP_1001660021708_E_B07

description: Library name: DSP_1001660021708_E_B07

value: mediastinal lymph node

tag: slide name

tag: nuclei


title: OPL10, mediastinal lymph node, Adenocarcinomas, None, DSP_1001660021708_E_B06

description: Library name: DSP_1001660021708_E_B06

tag: tissue

value: Pulmonary pleomorphic carcinoma

tag: Sex


title: OPL9, lung, Normal, None, DSP_1001660021708_E_B05

description: Library name: DSP_1001660021708_E_B05

value: Normal

tag: treatment


title: OPL10, lung, Normal, None, DSP_1001660021708_E_A10

description: Library name: DSP_1001660021708_E_A10

value: male


title: OPL14, lung, Normal, None, DSP_1001660021708_E_B01

description: Library name: DSP_1001660021708_E_B01

value: no

value: lung


title: OPL10, lung, Normal, None, DSP_1001660021708_E_A11

description: Library name: DSP_1001660021708_E_A11

value: surgical resection


title: OPL8, lung, Sarcomatoid, None, DSP_1001660021708_E_A09

description: Library name: DSP_1001660021708_E_A09

value: Sarcomatoid


title: OPL8, lung, Adenocarcinomas, None, DSP_1001660021708_E_A07

description: Library name: DSP_1001660021708_E_A07


title: OPL8, lung, Sarcomatoid, None, DSP_1001660021708_E_A08

description: Library name: DSP_1001660021708_E_A08


title: OPL10, lung, Sarcomatoid, None, DSP_1001660021708_E_C01

description: Library name: DSP_1001660021708_E_C01

value: yes


title: OPL14, lung, Adenocarcinomas, CD45+, DSP_1001660021708_E_A05

description: Library name: DSP_1001660021708_E_A05


title: OPL14, lung, Sarcomatoid, CD45+, DSP_1001660021708_E_A06

description: Library name: DSP_1001660021708_E_A06


title: OPL14, lung, Adenocarcinomas, CD45-, DSP_1001660021708_E_A02

description: Library name: DSP_1001660021708_E_A02


title: OPL13, lung, Sarcomatoid, CD45+, DSP_1001660021707_D_H11

description: Library name: DSP_1001660021707_D_H11


title: OPL13, lung, Sarcomatoid, CD45-, DSP_1001660021707_D_H10

description: Library name: DSP_1001660021707_D_H10


title: OPL14, lung, Sarcomatoid, CD45-, DSP_1001660021708_E_A03

description: Library name: DSP_1001660021708_E_A03


title: OPL14, lung, Sarcomatoid, CD45-, DSP_1001660021708_E_A04

description: Library name: DSP_1001660021708_E_A04


title: OPL14, lung, Adenocarcinomas, CD45-, DSP_1001660021707_D_H12

description: Library name: DSP_1001660021707_D_H12


title: OPL10, lung, Adenocarcinomas, None, DSP_1001660021708_E_B10

description: Library name: DSP_1001660021708_E_B10


title: OPL13, lung, Sarcomatoid, CD45-, DSP_1001660021707_D_H09

description: Library name: DSP_1001660021707_D_H09


title: OPL10, lung, Adenocarcinomas, CD45+, DSP_1001660021707_D_H07

description: Library name: DSP_1001660021707_D_H07


title: OPL9, lung, Normal, None, DSP_1001660021708_E_B04

description: Library name: DSP_1001660021708_E_B04


title: OPL10, lung, Sarcomatoid, CD45+, DSP_1001660021707_D_H08

description: Library name: DSP_1001660021707_D_H08


title: OPL10, lung, Sarcomatoid, CD45-, DSP_1001660021707_D_H05

description: Library name: DSP_1001660021707_D_H05


title: OPL10, lung, Sarcomatoid, CD45-, DSP_1001660021707_D_H06

description: Library name: DSP_1001660021707_D_H06


title: OPL9, lung, Mixture_Squamous_Sarcomatoid, None, DSP_1001660021708_E_B03

description: Library name: DSP_1001660021708_E_B03


title: OPL14, lung, Normal, None, DSP_1001660021708_E_A12

description: Library name: DSP_1001660021708_E_A12


title: OPL10, lung, Adenocarcinomas, CD45-, DSP_1001660021707_D_H04

description: Library name: DSP_1001660021707_D_H04


title: OPL10, lung, Adenocarcinomas, CD45-, DSP_1001660021707_D_H03

description: Library name: DSP_1001660021707_D_H03


title: OPL9, lung, Mixture_Squamous_Sarcomatoid, None, DSP_1001660021708_E_B02

description: Library name: DSP_1001660021708_E_B02


title: OPL9, lung, Sarcomatoid, CD45-, DSP_1001660021707_D_G10

description: Library name: DSP_1001660021707_D_G10


title: OPL9, lung, Sarcomatoid, CD45-, DSP_1001660021707_D_G11

description: Library name: DSP_1001660021707_D_G11


title: OPL9, lung, Normal, CD45-, DSP_1001660021707_D_H01

description: Library name: DSP_1001660021707_D_H01


title: OPL9, lung, Sarcomatoid, CD45+, DSP_1001660021707_D_G12

description: Library name: DSP_1001660021707_D_G12


title: OPL9, lung, Mixture_Squamous_Sarcomatoid, CD45-, DSP_1001660021707_D_G08

description: Library name: DSP_1001660021707_D_G08


title: OPL14, lung, Normal, CD45+, DSP_1001660021707_D_G06

description: Library name: DSP_1001660021707_D_G06


title: OPL9, lung, Mixture_Squamous_Sarcomatoid, CD45-, DSP_1001660021707_D_G07

description: Library name: DSP_1001660021707_D_G07


title: OPL9, lung, Mixture_Squamous_Sarcomatoid, CD45+, DSP_1001660021707_D_G09

description: Library name: DSP_1001660021707_D_G09


title: OPL14, lung, Normal, CD45-, DSP_1001660021707_D_G05

description: Library name: DSP_1001660021707_D_G05


title: OPL8, lung, Sarcomatoid, CD45+, DSP_1001660021707_D_G02

description: Library name: DSP_1001660021707_D_G02


title: OPL8, lung, Sarcomatoid, CD45-, DSP_1001660021707_D_G01

description: Library name: DSP_1001660021707_D_G01


title: OPL8, lung, Adenocarcinomas, CD45-, DSP_1001660021707_D_F11

description: Library name: DSP_1001660021707_D_F11


title: OPL12, lung, Sarcomatoid, None, DSP_1001660021707_D_F09

description: Library name: DSP_1001660021707_D_F09


title: OPL10, lung, Normal, CD45-, DSP_1001660021707_D_G03

description: Library name: DSP_1001660021707_D_G03


title: OPL12, lung, Normal, None, DSP_1001660021707_D_F08

description: Library name: DSP_1001660021707_D_F08


title: OPL8, lung, Sarcomatoid, CD45-, DSP_1001660021707_D_F12

description: Library name: DSP_1001660021707_D_F12


title: OPL9, lung, Normal, CD45+, DSP_1001660021707_D_H02

description: Library name: DSP_1001660021707_D_H02


title: OPL12, lung, Adenocarcinomas, None, DSP_1001660021707_D_F06

description: Library name: DSP_1001660021707_D_F06


title: OPL13, lung, Adenocarcinomas, None, DSP_1001660021707_D_F03

description: Library name: DSP_1001660021707_D_F03


title: OPL13, lung, Adenocarcinomas, None, DSP_1001660021707_D_F04

description: Library name: DSP_1001660021707_D_F04


title: OPL12, lung, Adenocarcinomas, None, DSP_1001660021707_D_F05

description: Library name: DSP_1001660021707_D_F05


title: OPL8, lung, Normal, None, DSP_1001660021707_D_F01

description: Library name: DSP_1001660021707_D_F01


title: OPL13, lung, Normal, None, DSP_1001660021707_D_E11

description: Library name: DSP_1001660021707_D_E11


title: OPL12, lung, Normal, None, DSP_1001660021707_D_F07

description: Library name: DSP_1001660021707_D_F07


title: OPL8, lung, Normal, None, DSP_1001660021707_D_F02

description: Library name: DSP_1001660021707_D_F02


title: OPL13, lung, Normal, None, DSP_1001660021707_D_E12

description: Library name: DSP_1001660021707_D_E12


title: OPL12, mediastinal lymph node, Adenocarcinomas, None, DSP_1001660021707_D_E10

description: Library name: DSP_1001660021707_D_E10


title: OPL12, mediastinal lymph node, Adenocarcinomas, None, DSP_1001660021707_D_E09

description: Library name: DSP_1001660021707_D_E09


title: OPL5, lung, Sarcomatoid, None, DSP_1001660021707_D_E07

description: Library name: DSP_1001660021707_D_E07


title: OPL8, lung, Adenocarcinomas, None, DSP_1001660021707_D_E08

description: Library name: DSP_1001660021707_D_E08


title: OPL10, lung, Normal, CD45+, DSP_1001660021707_D_G04

description: Library name: DSP_1001660021707_D_G04


title: OPL5, lung, Adenocarcinomas, None, DSP_1001660021707_D_E05

description: Library name: DSP_1001660021707_D_E05


title: OPL5, lung, Adenocarcinomas, None, DSP_1001660021707_D_E04

description: Library name: DSP_1001660021707_D_E04


title: OPL5, lung, Sarcomatoid, None, DSP_1001660021707_D_E06

description: Library name: DSP_1001660021707_D_E06


title: OPL7, mediastinal lymph node, Adenocarcinomas, None, DSP_1001660021707_D_E02

description: Library name: DSP_1001660021707_D_E02


title: OPL12, lung, Sarcomatoid, None, DSP_1001660021707_D_F10

description: Library name: DSP_1001660021707_D_F10


title: OPL5, lung, Normal, None, DSP_1001660021707_D_E01

description: Library name: DSP_1001660021707_D_E01


title: OPL5, lung, Normal, None, DSP_1001660021707_D_D12

description: Library name: DSP_1001660021707_D_D12


title: OPL7, lung, Normal, None, DSP_1001660021707_D_D11

description: Library name: DSP_1001660021707_D_D11


title: OPL7, lung, Normal, None, DSP_1001660021707_D_D10

description: Library name: DSP_1001660021707_D_D10


title: OPL7, lung, Adenocarcinomas, None, DSP_1001660021707_D_D09

description: Library name: DSP_1001660021707_D_D09


title: OPL7, mediastinal lymph node, Adenocarcinomas, None, DSP_1001660021707_D_E03

description: Library name: DSP_1001660021707_D_E03


title: OPL7, lung, Sarcomatoid, None, DSP_1001660021707_D_D07

description: Library name: DSP_1001660021707_D_D07


title: OPL3, lung, Normal, None, DSP_1001660021707_D_D05

description: Library name: DSP_1001660021707_D_D05


title: OPL12, lung, Sarcomatoid, CD45+, DSP_1001660021707_D_D01

description: Library name: DSP_1001660021707_D_D01


title: OPL3, lung, Normal, None, DSP_1001660021707_D_D04

description: Library name: DSP_1001660021707_D_D04


title: OPL3, lung, Sarcomatoid, None, DSP_1001660021707_D_D02

description: Library name: DSP_1001660021707_D_D02


title: OPL3, lung, Sarcomatoid, None, DSP_1001660021707_D_D03

description: Library name: DSP_1001660021707_D_D03


title: OPL12, lung, Sarcomatoid, CD45-, DSP_1001660021707_D_C12

description: Library name: DSP_1001660021707_D_C12


title: OPL12, lung, Normal, CD45+, DSP_1001660021707_D_C10

description: Library name: DSP_1001660021707_D_C10


title: OPL12, lung, Sarcomatoid, CD45-, DSP_1001660021707_D_C11

description: Library name: DSP_1001660021707_D_C11


title: OPL12, lung, Normal, CD45-, DSP_1001660021707_D_C09

description: Library name: DSP_1001660021707_D_C09


title: OPL13, lung, Adenocarcinomas, CD45+, DSP_1001660021707_D_C08

description: Library name: DSP_1001660021707_D_C08


title: OPL13, lung, Adenocarcinomas, CD45-, DSP_1001660021707_D_C07

description: Library name: DSP_1001660021707_D_C07


title: OPL12, lung, Adenocarcinomas, CD45-, DSP_1001660021707_D_C04

description: Library name: DSP_1001660021707_D_C04


title: OPL7, lung, Adenocarcinomas, None, DSP_1001660021707_D_D08

description: Library name: DSP_1001660021707_D_D08


title: OPL8, lung, Normal, CD45-, DSP_1001660021707_D_C01

description: Library name: DSP_1001660021707_D_C01


title: OPL5, lung, Sarcomatoid, CD45+, DSP_1001660021707_D_B08

description: Library name: DSP_1001660021707_D_B08


title: OPL8, lung, Adenocarcinomas, CD45-, DSP_1001660021707_D_B09

description: Library name: DSP_1001660021707_D_B09


title: OPL7, lung, Sarcomatoid, None, DSP_1001660021707_D_D06

description: Library name: DSP_1001660021707_D_D06


title: OPL5, lung, Adenocarcinomas, CD45+, DSP_1001660021707_D_B07

description: Library name: DSP_1001660021707_D_B07


title: OPL5, lung, Sarcomatoid, CD45-, DSP_1001660021707_D_B06

description: Library name: DSP_1001660021707_D_B06


title: OPL12, lung, Adenocarcinomas, CD45-, DSP_1001660021707_D_C03

description: Library name: DSP_1001660021707_D_C03


title: OPL7, lung, Normal, CD45+, DSP_1001660021707_D_A12

description: Library name: DSP_1001660021707_D_A12


title: OPL5, lung, Normal, CD45+, DSP_1001660021707_D_B02

description: Library name: DSP_1001660021707_D_B02


title: OPL13, lung, Normal, CD45-, DSP_1001660021707_D_B11

description: Library name: DSP_1001660021707_D_B11


title: OPL8, lung, Adenocarcinomas, CD45+, DSP_1001660021707_D_B10

description: Library name: DSP_1001660021707_D_B10


title: OPL13, lung, Adenocarcinomas, CD45-, DSP_1001660021707_D_C06

description: Library name: DSP_1001660021707_D_C06


title: OPL5, lung, Sarcomatoid, CD45-, DSP_1001660021707_D_B05

description: Library name: DSP_1001660021707_D_B05


title: OPL8, lung, Normal, CD45+, DSP_1001660021707_D_C02

description: Library name: DSP_1001660021707_D_C02


title: OPL5, lung, Adenocarcinomas, CD45-, DSP_1001660021707_D_B03

description: Library name: DSP_1001660021707_D_B03


title: OPL3, lung, Normal, CD45+, DSP_1001660021707_D_A06

description: Library name: DSP_1001660021707_D_A06


title: OPL13, lung, Normal, CD45+, DSP_1001660021707_D_B12

description: Library name: DSP_1001660021707_D_B12


title: OPL7, lung, Normal, None, DSP_1001660021707_D_A10

description: Library name: DSP_1001660021707_D_A10


title: OPL7, lung, Sarcomatoid, CD45+, DSP_1001660021707_D_A09

description: Library name: DSP_1001660021707_D_A09


title: OPL7, lung, Sarcomatoid, CD45-, DSP_1001660021707_D_A08

description: Library name: DSP_1001660021707_D_A08


title: OPL7, lung, Sarcomatoid, CD45-, DSP_1001660021707_D_A07

description: Library name: DSP_1001660021707_D_A07


title: OPL3, lung, Normal, CD45-, DSP_1001660021707_D_A05

description: Library name: DSP_1001660021707_D_A05


title: OPL3, lung, Sarcomatoid, CD45+, DSP_1001660021707_D_A04

description: Library name: DSP_1001660021707_D_A04


title: OPL3, lung, Sarcomatoid, CD45-, DSP_1001660021707_D_A03

description: Library name: DSP_1001660021707_D_A03


title: OPL12, lung, Adenocarcinomas, CD45+, DSP_1001660021707_D_C05

description: Library name: DSP_1001660021707_D_C05


title: OPL5, lung, Adenocarcinomas, CD45-, DSP_1001660021707_D_B04

description: Library name: DSP_1001660021707_D_B04


title: OPL3, lung, Sarcomatoid, CD45-, DSP_1001660021707_D_A02

description: Library name: DSP_1001660021707_D_A02


title: OPL7, lung, Adenocarcinomas, CD45+, DSP_1001660021707_D_A11

description: Library name: DSP_1001660021707_D_A11


title: GeoMx ROI D03

city: Augsburg

first: Pascal

middle: David

last: Johann

address: Stenglinstrasse 2

department: Paediatric Oncology

country: Germany

institute: University Hospital Augsburg

description:
Library name: D03
GeoMx DSP

data_processing:
The melanoma.rds file (a Seurat object of the scRNA-Seq data from the primary tumour) was generated using Seurat v5 using the Read10X function on the filtered_feature_bs_matrix file from cellranger count. The resulting file was used to generate the Seurat file using CreateAssayObject and then CreateSeuratObject with min.cells = 3 and min.features = 200.
The GeoMx_qnorm.txt file: Raw FASTQ files were processed using the DSP Standalone Software, and the resulting files were imported into R (v.4.3) for analysis using the NanostringNCTools 1.10.1, GeomxTools 3.6.2 and GeomxWorkflows 1.8.0 packages. Segment QC was performed using the following parameters: minSegmentReads = 1000, percentTrimmed = 80, percentStitched = 80, percentAligned = 80, percentSaturation = 50, minNegativeCount = 4, maxNTCCount = 1000, minNuclei = 100, minArea = 5000. All 39 collected ROIs passed QC. Genes detected in less than 10% ROIs were filtered out, resulting in 11,752 genes remaining, and the data was then nomalised using Q3 normalisation.
Assembly: hg38
Supplementary files format and content: melanoma.rds - seurat object of the scRNA-Seq data
Supplementary files format and content: GeoMx_qnorm.txt - a matrix of q3 normalised expression data from the GeoMx experiment.
Supplementary files format and content: Annotation.txt - annotation of ROIs from the GeoMx experiment
Library strategy: Spatial Transcriptomics

source_name: Lymph node

extract_protocol:
GeoMx: Formalin-fixed paraffin-embedded (FFPE) blocks were sectioned using a rotating microtome at 5 µm thickness and placed on standard, positively charged microscopy slides (TOMA). Slides were prepared for DSP according to the manufacturer’s protocol. In brief, sections were deparaffinized and subjected to heat-induced protein epitope retrieval (using retrieval buffer at pH 9, Thermo Fisher Scientific, #00-4956-58) for 15 min at 100 °C using a steam cooker. Retrieval for mRNA was performed using proteinase K (Thermo Fisher Scientific, #25530049) at 1µg/ml for 15 min. Slides were then incubated with the human Whole Transcriptome Atlas (WTA) probe panel (Nanostring, #NA-GMX-RNA-NGS-HuWTA-4, Lot HWTA21003) at 37°C in a hybridization oven overnight. Sections were washed according to standard protocols and direct immunofluorescence was performed with a Melanoma morphology marker panel (Nanostring) composed of S100B, CD454 and a nuclear counterstain (SYTO-13). snRNA-Seq: Nucleus isolation with ST buffers was performed as per Slyper et al. 2020, and single nuclei were preapred using manufacturer's protocol (10X Genomics).
GeoMx: Library was constructed using the manufacturer's protocol. The resulting library was sequenced by Novogene using an Illumina sequencer with the specifications provided by Nanostring (paired-end reads at length 27, index length 8) with 5% PhiX spike-in using a NovaSeq X Plus 25B PE150. snRNA-seq: Library was constructed using the 10X Genomics 3' v3.1 dual index manual, as per manufacturer's recommendations. The library was sequenced on Illumina NovaSeq X Plus 25B PE150 by Novogene, assuming approximately 50,000 reads per cell.

value: Lymph node


title: GeoMx ROI D02

description:
Library name: D02
GeoMx DSP


title: OPL5, lung, Normal, CD45-, DSP_1001660021707_D_B01

description: Library name: DSP_1001660021707_D_B01


title: GeoMx ROI D01

description:
Library name: D01
GeoMx DSP


title: GeoMx ROI D04

description:
Library name: D04
GeoMx DSP


title: GeoMx ROI C10

description:
Library name: C10
GeoMx DSP

source_name: Recurrence

value: Recurrence


title: GeoMx ROI C11

description:
Library name: C11
GeoMx DSP


title: GeoMx ROI C06

description:
Library name: C06
GeoMx DSP


title: GeoMx ROI C12

description:
Library name: C12
GeoMx DSP


title: GeoMx ROI C03

description:
Library name: C03
GeoMx DSP


title: GeoMx ROI C07

description:
Library name: C07
GeoMx DSP


title: GeoMx ROI B09

description:
Library name: B09
GeoMx DSP

source_name: Primary tumour

value: Primary tumour


title: GeoMx ROI B12

description:
Library name: B12
GeoMx DSP


title: GeoMx ROI C08

description:
Library name: C08
GeoMx DSP


title: GeoMx ROI C05

description:
Library name: C05
GeoMx DSP


title: GeoMx ROI B06

description:
Library name: B06
GeoMx DSP


title: GeoMx ROI B10

description:
Library name: B10
GeoMx DSP


title: GeoMx ROI C01

description:
Library name: C01
GeoMx DSP


title: GeoMx ROI C04

description:
Library name: C04
GeoMx DSP


title: GeoMx ROI B11

description:
Library name: B11
GeoMx DSP


title: GeoMx ROI C02

description:
Library name: C02
GeoMx DSP


title: GeoMx ROI B08

description:
Library name: B08
GeoMx DSP

source_name: Skin

value: Skin


title: GeoMx ROI B04

description:
Library name: B04
GeoMx DSP


title: GeoMx ROI C09

description:
Library name: C09
GeoMx DSP


title: GeoMx ROI B05

description:
Library name: B05
GeoMx DSP


title: GeoMx ROI B03

description:
Library name: B03
GeoMx DSP


title: GeoMx ROI B02

description:
Library name: B02
GeoMx DSP


title: GeoMx ROI B01

description:
Library name: B01
GeoMx DSP


title: GeoMx ROI B07

description:
Library name: B07
GeoMx DSP


title: GeoMx ROI A10

description:
Library name: A10
GeoMx DSP


title: GeoMx ROI A12

description:
Library name: A12
GeoMx DSP


title: GeoMx ROI A09

description:
Library name: A09
GeoMx DSP


title: GeoMx ROI A11

description:
Library name: A11
GeoMx DSP


title: GeoMx ROI A08

description:
Library name: A08
GeoMx DSP


title: GeoMx ROI A06

description:
Library name: A06
GeoMx DSP


title: GeoMx ROI A05

description:
Library name: A05
GeoMx DSP


title: GeoMx ROI A07

description:
Library name: A07
GeoMx DSP


title: GeoMx ROI A04

description:
Library name: A04
GeoMx DSP


title: GeoMx ROI A03

description:
Library name: A03
GeoMx DSP


title: Lenalidomide_6Hr_3

city: Cambridge

first: Walter

last: Lenoir

state: MA

address: 301 Binney St

institute: Kronos Bio

data_processing:
First, reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming.
Next, preprocessed reads are aligned by STAR aligner. Aligned reads are summarized to gene-level counts by the featureCounts tool.
FastQC reports, alignment statistics, QoRTs QC, RNA-SeQC and rRNA/globin depletion rate QC information is automatically summarized by the MultiQC tool.
Assembly: hg19
Supplementary files format and content: MM1S_SOC_TPM.csv

growth_protocol: Cells were grown in RPMI 1640 media with 10% fetal bovine serum (FBS).

extract_protocol:
RNA purification kit from Zymo following their recommended protocol (R2051)
Strand-specific mRNA-Seq (NEB Cat # E7490 and E7765)

tag: cell line

tag: cell type

value: cancer cell line

tag: genotype


title: GeoMx ROI A02

description:
Library name: A02
GeoMx DSP


title: Lenalidomide_24Hr_3


title: Lenalidomide_24Hr_1


title: Lenalidomide_6Hr_1


title: GeoMx negative control well

description:
Library name: A01
GeoMx DSP

source_name: No template control

value: No template control


title: Lenalidomide_DMSO_0Hr_3

value: WT

value: DMSO


title: JQ1_24Hr_3


title: Lenalidomide_6Hr_2


title: JQ1_6Hr_3


title: JQ1_24Hr_2


title: Lenalidomide_DMSO_0Hr_1


title: scRNA-Seq, Primary tumour

description:
Library name: scRNA-Seq primary tumour
10X Genomics

data_processing:
The melanoma.rds file (a Seurat object of the scRNA-Seq data from the primary tumour) was generated using Seurat v5 using the Read10X function on the filtered_feature_bs_matrix file from cellranger count. The resulting file was used to generate the Seurat file using CreateAssayObject and then CreateSeuratObject with min.cells = 3 and min.features = 200.
The GeoMx_qnorm.txt file: Raw FASTQ files were processed using the DSP Standalone Software, and the resulting files were imported into R (v.4.3) for analysis using the NanostringNCTools 1.10.1, GeomxTools 3.6.2 and GeomxWorkflows 1.8.0 packages. Segment QC was performed using the following parameters: minSegmentReads = 1000, percentTrimmed = 80, percentStitched = 80, percentAligned = 80, percentSaturation = 50, minNegativeCount = 4, maxNTCCount = 1000, minNuclei = 100, minArea = 5000. All 39 collected ROIs passed QC. Genes detected in less than 10% ROIs were filtered out, resulting in 11,752 genes remaining, and the data was then nomalised using Q3 normalisation.
Assembly: hg38
Supplementary files format and content: melanoma.rds - seurat object of the scRNA-Seq data
Supplementary files format and content: GeoMx_qnorm.txt - a matrix of q3 normalised expression data from the GeoMx experiment.
Supplementary files format and content: Annotation.txt - annotation of ROIs from the GeoMx experiment

source_name: Melanoma primary tumour

value: Melanoma primary tumour


title: JQ1_24Hr_1


title: JQ1_6Hr_2


title: JQ1_DMSO_0Hr_3


title: JQ1_DMSO_0Hr_2


title: JQ1_6Hr_1


title: CCS1477_24Hr_3


title: CCS1477_24Hr_2


title: JQ1_DMSO_0Hr_1


title: CCS1477_6Hr_3


title: Lenalidomide_24Hr_2


title: CCS1477_24Hr_1


title: CCS1477_6Hr_2


title: CCS1477_6Hr_1


title: CCS1477_DMSO_0Hr_3


title: GNE781_24Hr_3


title: GNE781_24Hr_2


title: Lenalidomide_DMSO_0Hr_2


title: GNE781_6Hr_2


title: GNE781_6Hr_1


title: GNE781_24Hr_1


title: GNE781_6Hr_3


title: CCS1477_DMSO_0Hr_1


title: GNE781_DMSO_0Hr_3


title: KB528_24Hr_2


title: GNE781_DMSO_0Hr_2


title: GNE781_DMSO_0Hr_1


title: KB528_24Hr_3


title: KB528_6Hr_3


title: KB528_24Hr_1


title: KB528_6Hr_2


title: KB528_6Hr_1


title: KB528_DMSO_0Hr_3


title: KB528_DMSO_0Hr_2


title: KB528_DMSO_0Hr_1


title: CCS1477_DMSO_0Hr_2


title: RPMI8226_KB528_24hr_2

data_processing:
First, reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming.
Next, preprocessed reads are aligned by STAR aligner. Aligned reads are summarized to gene-level counts by the featureCounts tool.
FastQC reports, alignment statistics, QoRTs QC, RNA-SeQC and rRNA/globin depletion rate QC information is automatically summarized by the MultiQC tool.
Assembly: hg19
Supplementary files format and content: RPMI8226_KB528_timeseries_TPM.txt is a TPM file of related samples


title: RPMI8226_KB528_6hr_3


title: RPMI8226_KB528_3hr_3


title: RPMI8226_KB528_24hr_3


title: RPMI8226_KB528_6hr_1


title: RPMI8226_KB528_6hr_2


title: RPMI8226_KB528_3hr_2


title: RPMI8226_KB528_3hr_1


title: RPMI8226_KB528_1hr_1


title: RPMI8226_KB528_1hr_3


title: PBMC_KB528_24hr_3

data_processing:
First, reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming.
Next, preprocessed reads are aligned by STAR aligner. Aligned reads are summarized to gene-level counts by the featureCounts tool.
FastQC reports, alignment statistics, QoRTs QC, RNA-SeQC and rRNA/globin depletion rate QC information is automatically summarized by the MultiQC tool.
Assembly: hg19
Supplementary files format and content: PBMC_KB528_timeseries_TPM.txt is a TPM file of related samples

source_name: blood

extract_protocol:
RNA purification kit from Zymo following their recommended protocol (R2051)
Strand-specific mRNA-Seq (NEB Cat # E7490 and E7765) with Invitrogen ERCC RNA spike-in (Cat # 4456740)addition

value: blood

value: peripheral blood mononuclear cells


title: RPMI8226_DMSO_2


title: PBMC_KB528_24hr_2


title: RPMI8226_DMSO_1


title: RPMI8226_KB528_1hr_2


title: PBMC_KB528_6hr_1


title: PBMC_KB528_3hr_3


title: PBMC_KB528_6hr_2


title: PBMC_KB528_6hr_3


title: PBMC_KB528_3hr_1


title: PBMC_KB528_3hr_2


title: PBMC_KB528_1hr_3


title: RPMI8226_KB528_24hr_1


title: PBMC_KB528_1hr_2


title: PBMC_KB528_1hr_1


title: PBMC_DMSO_3


title: PBMC_DMSO_2


title: PBMC_DMSO_1


title: MM1S_KB528_24hr_3

data_processing:
First, reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming.
Next, preprocessed reads are aligned by STAR aligner. Aligned reads are summarized to gene-level counts by the featureCounts tool.
FastQC reports, alignment statistics, QoRTs QC, RNA-SeQC and rRNA/globin depletion rate QC information is automatically summarized by the MultiQC tool.
Assembly: hg19
Supplementary files format and content: MM1S_KB528_timeseries_TPM.txt is a TPM file of related samples


title: MM1S_KB528_24hr_1


title: MM1S_KB528_24hr_2


title: MM1S_KB528_6hr_3


title: RPMI8226_DMSO_3


title: MM1S_KB528_6hr_2


title: PBMC_KB528_24hr_1


title: MM1S_KB528_6hr_1


title: MM1S_KB528_3hr_2


title: MM1S_KB528_3hr_1


title: MM1S_KB528_1hr_2


title: MM1S_DMSO_3


title: MM1S_KB528_1hr_1


title: MM1S_DMSO_1


title: CBE_mRNA_CITTA_2

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St Jude Children's Research Hospital

description:
Library name: GM_VK2444
Hybrid Capture Sequencing
CBE.hybrid_capture.CIITA.pivot_tabe.add_chi_square_stats.csv

data_processing:
1. adapter trimming -a AGATCGGAAGAGC -A AGATCGGAAGAGC. 2. FLASH merge R1 and R2. Unmerged reads are treated as individual molecule. 3. UMI-deduplication for merged and unmerged reads using https://github.com/aryeelab/umi 4. bwa mapping to hg38
5. CRISPRessoWGS is used to quantify indel frequency and base editing frequency.
Assembly: hg38
Supplementary files format and content: tsv format

source_name: Human peripheral blood

extract_protocol:
Genomic DNA extracted from edited primary T - cells or unedited control cells using Agencourt DNAdvance according to manufacturer’s protocol.
Genomic DNA from edited primary T - cells or unedited control cells used to perform hybrid capture sequencing according to manfacturer's instructions. CBE and ABE libraries were pooled and loaded separately on NextSeq 2000 and NovaSeq X with paired-end sequencing 146 15 15 146 cycles according to the manufacturer’s instructions

treatment_protocol: Primary Human T-cells were nucleofected with respective editors like ABE8e, eA3A-BE3, and Cas9-3xNLS mRNA, cultured in X-VIVO media with cytokines, and harvested cells at day 5 after electroporation.

value: Human peripheral blood

value: Primary Human T-cells

value: CD4+ CD8+

tag: sample group


title: MM1S_DMSO_2


title: CBE_mRNA_CBLB_2

description:
Library name: GM_VK2442
Hybrid Capture Sequencing
CBE.hybrid_capture.CBLB.pivot_tabe.add_chi_square_stats.csv


title: CBE_mRNA_PDCD1_2

description:
Library name: GM_VK2445
Hybrid Capture Sequencing
CBE.hybrid_capture.PDCD1.pivot_tabe.add_chi_square_stats.csv


title: MM1S_KB528_1hr_3


title: CBE_Control_2

description:
Library name: GM_VK2440
Hybrid Capture Sequencing


title: CBE_mRNA_PDCD1_1

description:
Library name: GM_VK2438
Hybrid Capture Sequencing
CBE.hybrid_capture.PDCD1.pivot_tabe.add_chi_square_stats.csv


title: CBE_mRNA_CD7_2

description:
Library name: GM_VK2443
Hybrid Capture Sequencing
CBE.hybrid_capture.CD7.pivot_tabe.add_chi_square_stats.csv


title: CBE_mRNA_CITTA_1

description:
Library name: GM_VK2437
Hybrid Capture Sequencing
CBE.hybrid_capture.CIITA.pivot_tabe.add_chi_square_stats.csv


title: CBE_mRNA_CBLB_1

description:
Library name: GM_VK2435
Hybrid Capture Sequencing
CBE.hybrid_capture.CBLB.pivot_tabe.add_chi_square_stats.csv


title: CBE_mRNA_CD7_1

description:
Library name: GM_VK2436
Hybrid Capture Sequencing
CBE.hybrid_capture.CD7.pivot_tabe.add_chi_square_stats.csv


title: CBE_Control_1

description:
Library name: GM_VK2433
Hybrid Capture Sequencing


title: CBE_mRNA_B2M_1

description:
Library name: GM_VK2434
Hybrid Capture Sequencing
CBE.hybrid_capture.B2M.pivot_tabe.add_chi_square_stats.csv


title: CHANGE_seq_BE_Control_CBE_2

description:
Library name: GM212
CHANGE-seq-BE for CBE targets

data_processing:
CHANGE-seq-BE analysis. Adapter trimming was performed using cutadapt (v1.18) with parameters of "--overlap 40 -e 0.15" to remove Tn5 adapter (CTGTCTCTTATACACATCTACGTAGATGTGTATAAGAGACAG). Then paired-end reads were mapped using bwa mem with default parameters. Reads with zero mapping quality were filtered out (e.g., MAPQ=0). CHANGE-seq-BE paired-end reads should be in an outward orientation with some degree of self-overlapping bases. For ABE, assuming an editing window from position 1 to position 10, we used min_overlap=5 and max_overlap=15, because the deamination event occurred at +2 position. Similariy, for CBE, we used min_overlap=6 and max_overlap=16, because the deamination event occurred at +1 position. Reads were filtered based on the above criteria. The start positions of the valid reads were then tabulated, and genomic intervals enriched in nuclease-treated samples were identified. The interval and 30 bp of flanking reference sequence on either side were searched for potential nuclease-induced off-target sites with up to 6 mismatches, 1 insertion, or 1 deletion. CHANGE-seq-BE data analyses were performed using open-source CHANGE-seq analysis software (https://github.com/tsailabSJ/changeseq/dev).
Assembly: hg38
Supplementary files format and content: csv

source_name: Tcell

extract_protocol:
Genomic DNA extracted from primary human T-cells (unedited controls) using Gentra Puregene Kit (Qiagen) according to manufacturer’s protocol.
Purified genomic DNA was tagmented  and circularized using a custom Tn5-transposome. Genomic DNA circles modified by base editors and selectively sequenced by end-repair and adaptor ligation for sequencing. CBE libraries were pooled and loaded on NextSeq 2000 with paired-end sequencing 151 8 8 151 cycles according to the manufacturer’s instructions.

treatment_protocol: Primary Human T-cells were activated and cultured in X-VIVO media with cytokines. Cells were harvested accordingly to extract required genomic DNA for CHANGE-seq-BE.

value: Tcell

value: Human Primary T-Cells


title: MM1S_KB528_3hr_3


title: CBE_CIITA_E2

description:
Library name: GM210
CHANGE-seq-BE for CBE targets


title: CBE_CD7_E2

description:
Library name: GM209
CHANGE-seq-BE for CBE targets


title: CBE_CBLB_E2

description:
Library name: GM208
CHANGE-seq-BE for CBE targets


title: CBE_B2M_E2

description:
Library name: GM207
CHANGE-seq-BE for CBE targets


title: CBE_PDCD1_E1

description:
Library name: GM205
CHANGE-seq-BE for CBE targets


title: CBE_CBLB_E1

description:
Library name: GM202
CHANGE-seq-BE for CBE targets


title: CBE_B2M_E1

description:
Library name: GM201
CHANGE-seq-BE for CBE targets


title: CHANGE_seq_BE_Control_CBE_1

description:
Library name: GM200
CHANGE-seq-BE for CBE targets


title: CBE_mRNA_B2M_2

description:
Library name: GM_VK2441
Hybrid Capture Sequencing
CBE.hybrid_capture.B2M.pivot_tabe.add_chi_square_stats.csv


title: CHANGE-seq-BE_CD40L_Control

description:
Library name: GM254
CHANGE-seq-BE

data_processing:
CHANGE-seq-BE data analyses were performed using open-source CHANGE-seq analysis software (https://github.com/tsailabSJ/changeseq/dev). Adapter trimming was performed using cutadapt (v1.18) with parameters of "--overlap 40 -e 0.15" to remove Tn5 adapter (CTGTCTCTTATACACATCTACGTAGATGTGTATAAGAGACAG). Then paired-end reads were mapped using bwa mem with default parameters.
Assembly: hg38
Supplementary files format and content: tsv

source_name: Human Blood

extract_protocol:
Genomic DNA extracted from patient dervied cells using Gentra Puregene Kit (Qiagen) according to manufacturer’s protocol.
Purified genomic DNA was tagmented  and circularized using a custom Tn5-transposome. Genomic DNA circles modified by base editors and selectively sequenced by end-repair and adaptor ligation for sequencing. ABE libraries were pooled and loaded on NextSeq 2000 with paired-end sequencing 151 8 8 151 cycles according to the manufacturer’s instructions.

treatment_protocol: Patient dervied cells were cultured and harvested accordingly to extract required genomic DNA for CHANGE-seq-BE.

value: Human Blood

value: Peripheral Blood Mononuclear Cells


title: CHANGE-seq-BE_CD40L_E1

description:
Library name: GM255
CHANGE-seq-BE


title: CHANGE-seq-BE_CD40L_E2

description:
Library name: GM256
CHANGE-seq-BE


title: 2D_KiPS_ZNF398_(3_4)

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

description: Library name: Sample 12

data_processing:
Following quality controls, sequencing reads were trimmed according to the recommendations indicated in the Lexogen data analysis protocol. After trimming, reads were aligned to the Homo sapiens genome (GRCm38.p13) using STAR (v. 2.7.6a). Gene expression levels were quantified using featureCounts (v. 2.0.1).
Assembly: GRCh38.p13/hg38
Supplementary files format and content: counts

source_name: PSCs

growth_protocol: KiPS cell line OE an Empty vector or ZNF398 were detached as single cells using TrypLE. A well of a Chamber slide was covered with 40µl of pure ice-cold growth factor reduced Matrigel and incubated for 2 minutes (min) at 37°C to allow Matrigel to solidify. 50,000 cells (for each well of a chamber slide) were resuspended in 250μl of E8 medium with 10µM ROCKi. 10 min after plating, the medium was removed and replaced with 250µl of E8 + 10µM ROCKi containing 5% Matrigel with or without SB43. After 24 hours, the medium was changed (E8 medium containing 5% of Matrigel v/v with or without SB43). The 3D structures were grown at 37°C, 5% CO2, 21% O2 for 4 days. Note that 2 replicates of 2D KiPS Empty and 2 replicates for 2D KiPS ZNF398 OE cells were also collected at day 0 ("2D_KiPS_Empty" and "2D_KiPS_ZNF398" respectively).

extract_protocol:
Total RNA was isolated using Total RNA Purification Kit (Norgen Biotek 37500)
QuantSeq 3' Forward (FWD) mRNAseq Library Prep kit (Lexogen) was used for library construction, following the manufacturer’s protocol.

treatment_protocol: The 3D Empty or ZNF398 OE cells were treated without or with SB43 (TGF-beta inhibition)

tag: replicate

tag: condition

tag: sample code

value: FKL

tag: time

tag: cell culture

value: PSCs


title: 2D_KiPS_ZNF398_(1_2)

description: Library name: Sample 11

value: FKK


title: 2D_KiPS_Empty_(1_2)

description: Library name: Sample 9

value: FKI


title: Sir3D_mRNA_Fig6_2_doublings_after_release_replicate

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS

description:
mRNA from a Sir3 deletion mutant in a  timecourse after exit from starvation
yeast derived from S288C (MRL5.1 ( MATa  ura3-delta  leu2-delta  his3-delta  met15-delta sir3-delta:KANR))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
second doubling after release from starvation,

data_processing:
Illumina OLB-1.8.0/CASAVA_v1.7.0 were used for base calling
reads were mapped to the yeast S288C and the S.pombe genomes using BLAT
The read density distribution was determined for each species in each dataset separately. The average S.pombe genomic read density per bp (F and R reads were processed together) was determined for each dataset. For spike-in normalization, S.cerevisiae read densities per bp were then divided with the corresponding S.pombe average genomic read density.
Normalized read densities for each gene were aligned by the transcription start site and divided into sense and antisense transcripts. The median read density for each gene (from the tss to the end of the coding sequence) was then determined for each transcript. Intron regions were excluded from the calculation. Median read densities for each gene in each replicate of each time point were finally divided by the genome average mRNA S.cerevisiae/S.pombe count ratio for the whole time course of the corresponding replicate, to allow for direct comparisons between replicates and strains.
Assembly: Saccer1 and Schizosaccharomyces pombe (assembly ASM294v2)
Supplementary files format and content: tab-delimited text files of  normalized median read densities for each gene in indicated strains and time points.

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in YPD or YPGal (for Sir3 over expression  (oeSir3) cells) for 72hrs at 30°C till saturation and growth arrest.  Cells were then released into fresh media and aliquots were flash frozen in liquid N2 in a timecourse for several cell generations. S.pombe  cells  (strain FY2319, courtesy of S. Forsburg) were grown in YES.

extract_protocol:
Cells were resuspended in Trizol, cell walls were broken with bead beating and total RNA was extracted and DNAseI treated. Extracted total RNA amounts were measured with  the Qubit fluorimeter and the Nanodrop spectrophotometer and the quality was checked by a Bioanalyzer scan (Agilent). Each S.cerevisiae total RNA extract was mixed with the S.pombe total RNA extract at a mass ratio of 10:1.
total RNA was used to make stranded Illumina RNA_seq libraries with the Illumina  TruSeq Stranded mRNA kit or the Illumina Stranded mRNA Prep Ligation kit .

treatment_protocol: Cells were flash frozen in liquid N2

tag: cell cycle

value: exit from growth arrest after nutrient depletion

value: yeast


title: 3D_KiPS_ZNF398_E7+SB43_2

description: Library name: Sample 8

value: FKH


title: Sir3D_mRNA_Fig6_1_doubling_after_release_replicate

description:
mRNA from a Sir3 deletion mutant in a  timecourse after exit from starvation
yeast derived from S288C (MRL5.1 ( MATa  ura3-delta  leu2-delta  his3-delta  met15-delta sir3-delta:KANR))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
first doubling after release from starvation,


title: Sir3D_mRNA_Fig6_90min_after_release_replicate

description:
mRNA from a Sir3 deletion mutant in a  timecourse after exit from starvation
yeast derived from S288C (MRL5.1 ( MATa  ura3-delta  leu2-delta  his3-delta  met15-delta sir3-delta:KANR))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
1h30min after release from starvation,


title: 3D_KiPS_ZNF398_E7+SB43_1

description: Library name: Sample 7

value: FKG


title: 3D_KiPS_ZNF398_E8_2

description: Library name: Sample 6

value: FKF


title: CBE_PDCD1_E2

description:
Library name: GM211
CHANGE-seq-BE for CBE targets


title: 3D_KiPS_ZNF398_E8_1

description: Library name: Sample 5

value: FKE


title: Sir3D_mRNA_Fig6_5min_after_release_replicate

description:
mRNA from a Sir3 deletion mutant in a  timecourse after exit from starvation
yeast derived from S288C (MRL5.1 ( MATa  ura3-delta  leu2-delta  his3-delta  met15-delta sir3-delta:KANR))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
5min after release from starvation,


title: Sir3D_mRNA_Fig6_starvation_replicate

description:
mRNA from a Sir3 deletion mutant in a  timecourse after exit from starvation
yeast derived from S288C (MRL5.1 ( MATa  ura3-delta  leu2-delta  his3-delta  met15-delta sir3-delta:KANR))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
72h incubation, starvation after growth in glucose,


title: CBE_CIITA_E1

description:
Library name: GM204
CHANGE-seq-BE for CBE targets


title: 3D_KiPS_Empty_E7+SB43_2

description: Library name: Sample 4

value: FKD


title: CBE_CD7_E1

description:
Library name: GM203
CHANGE-seq-BE for CBE targets


title: 3D_KiPS_Empty_E7+SB43_1

description: Library name: Sample 3

value: FKC


title: Sir3D_mRNA_Fig6_midlog_replicate

description:
mRNA from a Sir3 deletion mutant in a  timecourse after exit from starvation
yeast derived from S288C (MRL5.1 ( MATa  ura3-delta  leu2-delta  his3-delta  met15-delta sir3-delta:KANR))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
log phase before arrest in starvation,


title: 3D_KiPS_Empty_E8_2

description: Library name: Sample 2

value: FKB


title: Sir2D_mRNA_Fig6_2_doublings_after_release_replicate

description:
mRNA from a Sir2 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir2-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
second doubling after release from starvation,


title: 3D_KiPS_Empty_E8_1

description: Library name: Sample 1

value: FKA


title: Sir2D_mRNA_Fig6_1_doubling_after_release_replicate

description:
mRNA from a Sir2 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir2-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
first doubling after release from starvation,


title: experiment_2_DAY6

description: Library name: Sample 6

data_processing:
Following quality controls, sequencing reads were quality and adaptor trimmed using Trim Galore! v0.5.0 (parameters: --stringency 3 –q 20). Trimmed reads were next aligned to human reference genome (GRCh38.p13) using Hisat2 [3]. Indexes for transcriptome-guided genome alignment were generated for the human GENCODE release 32 annotation (extract_exons.py and extract_splice_sites.py scripts). Gene expression levels were quantified with featureCounts v1.6.1 (options: -t exon -g gene_name) using the human GENCODE release 32 annotation (https://www.gencodegenes.org/human/release_32.html). Multi-mapped reads were excluded from quantification.
Assembly: GRCh38.p13/hg38
Supplementary files format and content: raw_counts.txt

growth_protocol: H9 hESCs were detached as single cells using TrypLE. A well of a Chamber slide was covered with 40µl of pure ice-cold growth factor reduced Matrigel and incubated for 2 minutes (min) at 37°C to allow Matrigel to solidify. 50,000 cells (for each well of a chamber slide) were resuspended in 250μl of E8 medium with 10µM ROCKi. 10 min after plating, the medium was removed and replaced with 250µl of E8 + 10µM ROCKi containing 5% Matrigel. After 24 hours, the medium was changed (E8 medium containing 5% of Matrigel v/v). The 3D structures were grown at 37°C, 5% CO2, 21% O2 respectively for 0, 2 and 5 days in E8 medium containing 5% of Matrigel v/v.

extract_protocol:
For single cell library prep, ~30 3D cysts structures for each time point were collected and dissociated using Trypsin/EDTA for 5 min at room temperature. Cells were then washed with PBS, and the resulting cell suspension was used to sort individual live cells in 96 well plate.
Full length single cell RNA-seq was performed using a modified version of the Smart-seq2 protocol. Briefly, individual cells were sorted into 96 well plates containing lysis buffer in presence of RNase inhibitor, dNTPs and OligodT. Reverse transcription of the polyadenylated RNA was performed with Maxima H Minus Reverse Transcriptase and Template Switching Oligos. The resulting cDNA was amplified with 23 cycles of PCR and libraries were prepared for sequencing with miniaturized NexteraXT Illumina protocol. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75bp reads).

treatment_protocol: None - All the samples were cultured in E8 media.

tag: batch


title: Sir2D_mRNA_Fig6_90min_after_release_replicate

description:
mRNA from a Sir2 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir2-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
1h30min after release from starvation,


title: 2D_KiPS_Empty_(3_4)

description: Library name: Sample 10

value: FKJ


title: experiment_2_DAY2

description: Library name: Sample 5


title: experiment_2_DAY0

description: Library name: Sample 4


title: Sir2D_mRNA_Fig6_30min_after_release_replicate

description:
mRNA from a Sir2 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir2-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
30min after release from starvation,


title: Sir2D_mRNA_Fig6_5min_after_release_replicate

description:
mRNA from a Sir2 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir2-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
5min after release from starvation,


title: experiment_1_DAY4

description: Library name: Sample 3


title: Sir2D_mRNA_Fig6_starvation_replicate

description:
mRNA from a Sir2 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir2-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
72h incubation, starvation after growth in glucose,


title: Sir2D_mRNA_Fig6_midlog_replicate

description:
mRNA from a Sir2 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir2-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
log phase before arrest in starvation,


title: Sir4D_mRNA_Fig6_1_doubling_after_release_replicate

description:
mRNA from a Sir4 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir4-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
first doubling after release from starvation,


title: experiment_1_DAY2

description: Library name: Sample 2


title: Sir3D_mRNA_Fig6_30min_after_release_replicate

description:
mRNA from a Sir3 deletion mutant in a  timecourse after exit from starvation
yeast derived from S288C (MRL5.1 ( MATa  ura3-delta  leu2-delta  his3-delta  met15-delta sir3-delta:KANR))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
30min after release from starvation,


title: H9_day_8_rep1

description: Library name: Sample 11

data_processing:
Following quality controls, sequencing reads were trimmed according to the recommendations indicated in the Lexogen data analysis protocol. After trimming, reads were aligned to the Homo sapiens genome (GRCm38.p13) using STAR (v. 2.7.6a). Gene expression levels were quantified using featureCounts (v. 2.0.1).
Assembly: GRCh38.p13/hg38
Supplementary files format and content: Tab-delimited text file of raw read counts per gene/samples.

growth_protocol: hPSCs were detached as single cells using TrypLE. A well of a Chamber slide was covered with 40µl of pure ice-cold growth factor reduced Matrigel and incubated for 2 minutes (min) at 37°C to allow Matrigel to solidify. 50,000 cells (for each well of a chamber slide) were resuspended in 250μl of E8 medium with 10µM ROCKi. 10 min after plating, the medium was removed and replaced with 250µl of E8 + 10µM ROCKi containing 5% Matrigel. After 24 hours, the medium was changed (E8 medium containing 5% of Matrigel v/v). The 3D structures were grown at 37°C, 5% CO2, 21% O2 respectively for 4 and 8 days.

extract_protocol:
Total RNA was extracted with a RNA purification kit (Norgen Biotek 37500).
QuantSeq 3' Forward (FWD) mRNAseq Library Prep kit (Lexogen) was used for library construction, following the manufacturer’s protocol.

tag: sample id


title: Sir4D_mRNA_Fig6_2_doublings_after_release_replicate

description:
mRNA from a Sir4 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir4-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
second doubling after release from starvation,


title: Sir4D_mRNA_Fig6_90min_after_release_replicate

description:
mRNA from a Sir4 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir4-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
1h30min after release from starvation,


title: Sir4D_mRNA_Fig6_30min_after_release_replicate

description:
mRNA from a Sir4 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir4-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
30min after release from starvation,


title: KIPS_day_8_rep1

description: Library name: Sample 9

source_name: KIPS

value: KIPS


title: H9_day_4_rep2

description: Library name: Sample 8


title: Sir4D_mRNA_Fig6_5min_after_release_replicate

description:
mRNA from a Sir4 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir4-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
5min after release from starvation,


title: H9_day_4_rep1

description: Library name: Sample 7


title: KIPS_day_8_rep2

description: Library name: Sample 10


title: Sir3_3xHA_mRNA_Fig6_2_doublings_after_release_replicate

description:
mRNA from a  Sir3_3xHA hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated before the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
second doubling after release from starvation,


title: KIPS_day_4_rep2

description: Library name: Sample 6


title: Sir4D_mRNA_Fig6_starvation_replicate

description:
mRNA from a Sir4 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir4-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
72h incubation, starvation after growth in glucose,


title: H9_day_0_rep2

description: Library name: Sample 4


title: H9_day_0_rep1

description: Library name: Sample 3


title: Sir3_3xHA_mRNA_Fig6_90min_after_release_replicate

description:
mRNA from a  Sir3_3xHA hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated before the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
1h30min after release from starvation,


title: Sir3_3xHA_mRNA_Fig6_5min_after_release_replicate

description:
mRNA from a  Sir3_3xHA hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated before the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
5min after release from starvation,


title: Sir3_3xHA_mRNA_Fig6_30min_after_release_replicate

description:
mRNA from a  Sir3_3xHA hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated before the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
30min after release from starvation,


title: KIPS_day_0_rep1

description: Library name: Sample 1


title: 3D-hE-gastruloids_gRNA_ZNF398_induced_Day4_2

description:
Library name: Sample 8
UNIPD-006-Q04

growth_protocol: ZNF398_CRISPRi was cultured in Feeder-free on pre-coated plates with 0.5% growth factor-reduced Matrigel (vol/vol in PBS with MgCl2/CaCl2, Sigma-Aldrich D8662) in E8 medium at 37°C, 5% CO2, 5% O2. For the formation of 3D-hE-Gastruloids, the ZNF398_CRISPRi cell line was initially plated in 2D and cultured in E8 medium for 2 days. The medium was then switched to E8 supplemented with DOX (0.1 µg/ml) and TMP (10 µM) for additional 2 days for ZNF398_CRISPRi. Then, it was detached as single cells using TrypLETM Select (1X). A well of a Chamber slide was covered with 40µl of pure ice-cold growth factor reduced Matrigel and incubated for 2 minutes at 37°C to allow Matrigel to solidify. 45,000 cells (for each well of a chamber slide) were resuspended in 250μl of E8 medium with 10µM ROCKi + DOX (0.1 µg/ml) and TMP (10 µM). 10 min after plating, the medium was removed and replaced with 250µl of E8 + 10µM ROCKi + DOX (0.1 µg/ml) and TMP (10 µM) containing 5% Matrigel. After 24 hours, the medium was changed (E8 medium containing 5% of Matrigel v/v + DOX (0.1 µg/ml) and TMP (10 µM)). The 3D structures were grown at 37°C, 5% CO2, 21% O2.

treatment_protocol: ZNF398_CRISPRi was treated with DOX (0.1 µg/ml) and TMP (10 µM) or without (control) for in 2D cultures and 3D cultures.

value: gRNA-ZNF398 PSCs


title: 3D-hE-gastruloids_gRNA_ZNF398_not_induced_Day4_2

description:
Library name: Sample 6
UNIPD-006-Q02


title: Sir3_3xT7_mRNA_Fig6_2_doublings_after_release_replicate

description:
mRNA from a  Sir3_3xT7 hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated after the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
second doubling after release from starvation,


title: Sir3_3xHA_mRNA_Fig6_midlog_replicate

description:
mRNA from a  Sir3_3xHA hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated before the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
log phase before arrest in starvation,


title: H9_day_8_rep2

description: Library name: Sample 12


title: 3D-hE-gastruloids_gRNA_ZNF398_induced_Day4_1

description:
Library name: Sample 7
UNIPD-006-Q03


title: 3D-hE-gastruloids_gRNA_ZNF398_not_induced_Day4_1

description:
Library name: Sample 5
UNIPD-006-Q01


title: Sir4D_mRNA_Fig6_midlog_replicate

description:
mRNA from a Sir4 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir4-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
log phase before arrest in starvation,


title: Sir3_3xT7_mRNA_Fig6_90min_after_release_replicate

description:
mRNA from a  Sir3_3xT7 hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated after the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
1h30min after release from starvation,


title: KIPS_day_4_rep1

description: Library name: Sample 5


title: Sir3_3xT7_mRNA_Fig6_30min_after_release_replicate

description:
mRNA from a  Sir3_3xT7 hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated after the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
30min after release from starvation,


title: 2D-PSCs_gRNA_ZNF398_induced_Day7_1

description:
Library name: Sample 3
UNIPD-006-P98


title: 2D-PSCs_gRNA_ZNF398_induced_Day7_2

description:
Library name: Sample 4
UNIPD-006-P99


title: Sir3_3xHA_mRNA_Fig6_1_doubling_after_release_replicate

description:
mRNA from a  Sir3_3xHA hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated before the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
first doubling after release from starvation,


title: KIPS_day_0_rep2

description: Library name: Sample 2


title: Sir3_3xT7_mRNA_Fig6_5min_after_release_replicate

description:
mRNA from a  Sir3_3xT7 hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated after the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
5min after release from starvation,


title: Sir3_3xT7_mRNA_Fig6_midlog_replicate

description:
mRNA from a  Sir3_3xT7 hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated after the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
log phase before arrest in starvation,


title: 2D-PSCs_gRNA_ZNF398_not_induced_Day7_1

description:
Library name: Sample 1
UNIPD-006-P96


title: 2D-PSCs_gRNA_ZNF398_not_induced_Day7_2

description:
Library name: Sample 2
UNIPD-006-P97


title: Sir3_3xHA_mRNA_Fig6_starvation_replicate

description:
mRNA from a  Sir3_3xHA hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated before the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
72h incubation, starvation after growth in glucose,


title: oeSir3_mRNA_Fig6_2_doublings_after_release_replicate

description:
mRNA from the over expression Sir3 strain  in a  timecourse after exit from starvation
yeast derived from W303 with the a GAL1-Sir3-3xHA cassette in a Sir3D background. (THC70 (W303: MATa HMLa HMRa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 mat∆::TRP1 hmr::rHMRa hml∆::kanMX ura3-1::GAL10P–Sir3HA::URA3 bar1∆::hisG lys2∆ sir3∆::HIS3))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
second doubling after release from starvation,

value: exit from starvation after galactose depletion and release into galactose


title: HAN-SCM-M5-EM-H08

city: Sdyney

first: Yanran

last: Zhao

address: Sydney NSW 2033

institute: UNSW

data_processing:
Illumina NextSeq500 was used
Sequenced paired-end reads were trimmed using Trimmomatic (v0.39) (using parameters:  LEADING = 3, TRAILING = 3, SLIDINGWINDOW = 4:10, MINLEN = 50), then aligned to the human reference genome (GRCh38) using STAR (v2.7.3a). Gene expression was then quantified at the counts and TPM level with RSEM (v1.3.1)
Assembly: GRCh38
Supplementary files format and content: .mtx.gz files contain matrices including raw counts, TPM and scaled TPM values for each sample and each gene.
Supplementary files format and content: .txt and and .tsv files contain tab delimited information on sample names and gene names (as per ordering in matrices), and gene annotation information.

source_name: CD8 T

extract_protocol:
Single CMV-specific CD8+ T cells were sorted using flow cytometry, with RNA isolation and sequencing library construction performed according to the Smart-seq2 protocol.
Single cell RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject

value: HAN

tag: gen1 phenotype

value: SCM

tag: gen2 phenotype

value: EM

tag: clone

tag: epitope

value: NLV

value: CD8 T


title: HAN-SCM-M5-EM-E08


title: experiment_1_DAY0

description: Library name: Sample 1

tag: cell line


title: HAN-SCM-M5-EM-G08

tag: cell type


title: HAN-SCM-M5-EM-C08


title: HAN-SCM-M5-EM-B08


title: Sir3_3xT7_mRNA_Fig6_starvation_replicate

description:
mRNA from a  Sir3_3xT7 hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated after the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
72h incubation, starvation after growth in glucose,

value: exit from growth arrest after nutrient depletion

value: yeast


title: oeSir3_mRNA_Fig6_1_doubling_after_release_replicate

description:
mRNA from the over expression Sir3 strain  in a  timecourse after exit from starvation
yeast derived from W303 with the a GAL1-Sir3-3xHA cassette in a Sir3D background. (THC70 (W303: MATa HMLa HMRa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 mat∆::TRP1 hmr::rHMRa hml∆::kanMX ura3-1::GAL10P–Sir3HA::URA3 bar1∆::hisG lys2∆ sir3∆::HIS3))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
first doubling after release from starvation,


title: Sir3_wt2_mRNA_Fig6_2_doublings_after_release_replicate

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (JOY1 (S288C(BY4741 parent): MATa  ura3D  leu2D  his3D  met15D  bar1D:HIS5)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
second doubling after release from starvation,


title: HAN-SCM-M5-EM-A08


title: Sir3_wt2_mRNA_Fig6_1_doubling_after_release_replicate

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (JOY1 (S288C(BY4741 parent): MATa  ura3D  leu2D  his3D  met15D  bar1D:HIS5)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
first doubling after release from starvation,


title: Sir3_wt2_mRNA_Fig6_90min_after_release_replicate

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (JOY1 (S288C(BY4741 parent): MATa  ura3D  leu2D  his3D  met15D  bar1D:HIS5)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
1h30min after release from starvation,


title: oeSir3_mRNA_Fig6_90min_after_release_replicate

description:
mRNA from the over expression Sir3 strain  in a  timecourse after exit from starvation
yeast derived from W303 with the a GAL1-Sir3-3xHA cassette in a Sir3D background. (THC70 (W303: MATa HMLa HMRa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 mat∆::TRP1 hmr::rHMRa hml∆::kanMX ura3-1::GAL10P–Sir3HA::URA3 bar1∆::hisG lys2∆ sir3∆::HIS3))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
1h30min after release from starvation,


title: Sir3_3xT7_mRNA_Fig6_1_doubling_after_release_replicate

description:
mRNA from a  Sir3_3xT7 hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated after the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
first doubling after release from starvation,


title: HAN-SCM-M5-EM-F08


title: HAN-SCM-M5-EM-D08


title: oeSir3_mRNA_Fig6_30min_after_release_replicate

description:
mRNA from the over expression Sir3 strain  in a  timecourse after exit from starvation
yeast derived from W303 with the a GAL1-Sir3-3xHA cassette in a Sir3D background. (THC70 (W303: MATa HMLa HMRa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 mat∆::TRP1 hmr::rHMRa hml∆::kanMX ura3-1::GAL10P–Sir3HA::URA3 bar1∆::hisG lys2∆ sir3∆::HIS3))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
30min after release from starvation,


title: oeSir3_mRNA_Fig6_5min_after_release_replicate

description:
mRNA from the over expression Sir3 strain  in a  timecourse after exit from starvation
yeast derived from W303 with the a GAL1-Sir3-3xHA cassette in a Sir3D background. (THC70 (W303: MATa HMLa HMRa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 mat∆::TRP1 hmr::rHMRa hml∆::kanMX ura3-1::GAL10P–Sir3HA::URA3 bar1∆::hisG lys2∆ sir3∆::HIS3))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
5min after release from starvation,