title: p53_PBS_M11_ROI-018_TMA5B

description: Library name: TMA5B__018


title: p53_VEGF-PARPi-OCDC_M8_ROI-015_TMA5B

status: Public on Jun 09 2026

type: SRA

city: Lausanne

first: Aspram

last: Minasyan

address: Bugnon 25A

country: Switzerland

institute: Ludwig Institute for Cancer Research / CHUV

description: Library name: TMA5B__015

library_source: transcriptomic

data_processing:
Raw sequencing data were processed with the bcl2fastq program from Illumina to generate FASTQ files.
FASTQ files were converted into Digital Count Conversion (DCC) format through Nanotring's GeoMx DnD pipeline v2.0.0.16.
QC was performed using the R package GeoMxTools v3.4.0.
Batch effect correction was done by substracting  background and then minimum value was added per batch.
Q3 normalization were performed on the merged corrected experiment.
Assembly: probe-based quantification, Mm_R_NGS_WTA_v1.0.pkc
Supplementary files format and content: DCC files are count files converted from FASTQ files
Supplementary files format and content: data_matrix.csv contains corrected and Q3-normalized read counts from all QC-passed AOIs and filtered genes.
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Mus musculus

source_name: tumor

extract_protocol:
Tissue microarrays were prepared by extracting 2 mm punches from FFPE blocks to prepare nine slides, each containing up to 30 tumor sections. 5µm FFPE tissue microarrays were baked at 60°C for 1hour, then deparaffinized and underwent antigen retrieval at 100°C for 15 minutes, followed by 1µg/mL proteinase K at 37°C for 15 min. The slides were incubated overnight with the RNA probe mix (Whole Transcriptome Atlas).Tissues were stained with visualization markers panCK-AF647, CD68-AF594 and CD3-AF488 along with the nuclear marker Syto83. Tissue slides were then loaded into the GeoMx DSP instrument for scanning. Probe barcodes from each ROI were UV-photocleaved, collected into a 96-well plate, followed by library preparation and sequencing.
GeoMx DSP Whole Transcriptomic Atlas (WTA) library construction involving probe hybridization, ligation and PCR amplification were done according to Nanostring's protocol (GeoMx DSP NGS readout User Manual Library Preparation & GeoMx NGS Pipeline, MAN-10153-01).

treatment_protocol: Treatment of mice carrying ID8 tumors started 10 days after tumor graft and continued for 3 weeks. Mice were vaccinated intradermally with 1 x 106 OCDC every week. Anti-VEGF (40 µg, together with OCDC, Absolute Antibody) and anti-PD1 (200 µg, every 3 days, BioXcell) were given intraperitoneally (i.p.). Olaparib (PARPi) was administered orally at 40 mg/kg/day. As treatment controls, tumor-bearing mice were treated with PBS or isotype controls.

tag: tissue

value: tumor

tag: mouse id

tag: slide id

tag: region of_interest

tag: model

tag: treatment

tag: ck

value: low

tag: batch

value: B


title: p53_PBS_M11_ROI-016_TMA5B

description: Library name: TMA5B__016

value: PBS

value: medium


title: p53_VEGF-PARPi-OCDC_M8_ROI-014_TMA5B

description: Library name: TMA5B__014

value: high


title: p53_VEGF-PARPi-OCDC_M8_ROI-013_TMA5B

description: Library name: TMA5B__013


title: p53_VEGF-PARPi-OCDC_M7_ROI-012_TMA5B

description: Library name: TMA5B__012


title: p53_VEGF-PARPi-OCDC_M7_ROI-011_TMA5B

description: Library name: TMA5B__011


title: p53_VEGF-PARPi-OCDC_M7_ROI-010_TMA5B

description: Library name: TMA5B__010


title: p53_VEGF-PARPi-OCDC_M6_ROI-009_TMA5B

description: Library name: TMA5B__009


title: p53_VEGF-PARPi-OCDC_M6_ROI-007_TMA5B

description: Library name: TMA5B__007


title: p53_VEGF-PARPi_M3_ROI-004_TMA5B

description: Library name: TMA5B__004


title: p53_VEGF-PARPi_M1_ROI-003_TMA5B

description: Library name: TMA5B__003


title: p53_VEGF-PARPi_M1_ROI-002_TMA5B

description: Library name: TMA5B__002


title: p53_VEGF-PARPi_M1_ROI-001_TMA5B

description: Library name: TMA5B__001


title: p53_VEGF-PARPi_M3_ROI-097_TMA4B

description: Library name: TMA4B__097


title: p53_VEGF-PARPi_M3_ROI-098_TMA4B

description: Library name: TMA4B__098


title: BRAC2_OCDC_M59_ROI-096_TMA4B

description: Library name: TMA4B__096

value: OCDC


title: BRAC2_OCDC_M59_ROI-095_TMA4B

description: Library name: TMA4B__095


title: BRAC2_OCDC_M58_ROI-093_TMA4B

description: Library name: TMA4B__093


title: BRAC2_OCDC_M58_ROI-092_TMA4B

description: Library name: TMA4B__092


title: BRAC2_OCDC_M58_ROI-090_TMA4B

description: Library name: TMA4B__090


title: BRAC2_OCDC_M58_ROI-091_TMA4B

description: Library name: TMA4B__091


title: BRAC2_OCDC_M58_ROI-089_TMA4B

description: Library name: TMA4B__089


title: BRAC2_OCDC_M57_ROI-084_TMA4B

description: Library name: TMA4B__084


title: BRAC2_OCDC_M57_ROI-082_TMA4B

description: Library name: TMA4B__082


title: BRAC2_OCDC_M57_ROI-086_TMA4B

description: Library name: TMA4B__086


title: BRAC2_OCDC_M57_ROI-085_TMA4B

description: Library name: TMA4B__085


title: BRAC2_PARPi_M56_ROI-081_TMA4B

description: Library name: TMA4B__081

value: PARPi


title: BRAC2_PARPi_M56_ROI-079_TMA4B

description: Library name: TMA4B__079


title: BRAC2_PARPi_M56_ROI-080_TMA4B

description: Library name: TMA4B__080


title: BRAC2_PARPi_M56_ROI-078_TMA4B

description: Library name: TMA4B__078


title: BRAC2_PARPi_M56_ROI-077_TMA4B

description: Library name: TMA4B__077


title: BRAC2_PARPi_M56_ROI-076_TMA4B

description: Library name: TMA4B__076


title: BRAC2_PARPi_M56_ROI-075_TMA4B

description: Library name: TMA4B__075


title: BRAC2_PARPi_M56_ROI-074_TMA4B

description: Library name: TMA4B__074


title: BRAC2_PARPi_M55_ROI-072_TMA4B

description: Library name: TMA4B__072


title: BRAC2_PARPi_M55_ROI-070_TMA4B

description: Library name: TMA4B__070


title: BRAC2_PARPi_M55_ROI-069_TMA4B

description: Library name: TMA4B__069


title: BRAC2_PARPi_M55_ROI-066_TMA4B

description: Library name: TMA4B__066


title: BRAC2_PARPi_M55_ROI-065_TMA4B

description: Library name: TMA4B__065


title: BRAC2_VEGF_M54_ROI-058_TMA4B

description: Library name: TMA4B__058

value: VEGF


title: BRAC2_VEGF_M54_ROI-057_TMA4B

description: Library name: TMA4B__057


title: BRAC2_VEGF_M54_ROI-056_TMA4B

description: Library name: TMA4B__056


title: BRAC2_VEGF_M53_ROI-055_TMA4B

description: Library name: TMA4B__055


title: BRAC2_VEGF_M53_ROI-053_TMA4B

description: Library name: TMA4B__053


title: BRAC2_VEGF_M53_ROI-052_TMA4B

description: Library name: TMA4B__052


title: BRAC2_VEGF_M53_ROI-051_TMA4B

description: Library name: TMA4B__051


title: BRAC2_VEGF_M53_ROI-049_TMA4B

description: Library name: TMA4B__049


title: BRAC2_VEGF_M53_ROI-050_TMA4B

description: Library name: TMA4B__050


title: BRAC2_VEGF_M53_ROI-048_TMA4B

description: Library name: TMA4B__048


title: BRAC2_VEGF_M53_ROI-047_TMA4B

description: Library name: TMA4B__047


title: BRAC2_VEGF_M53_ROI-045_TMA4B

description: Library name: TMA4B__045


title: BRAC2_VEGF_M53_ROI-044_TMA4B

description: Library name: TMA4B__044


title: BRAC2_PARPi_M55_ROI-064_TMA4B

description: Library name: TMA4B__064


title: BRAC2_PARPi_M55_ROI-067_TMA4B

description: Library name: TMA4B__067


title: BRAC2_VEGF_M52_ROI-042_TMA4B

description: Library name: TMA4B__042


title: BRAC2_VEGF_M52_ROI-043_TMA4B

description: Library name: TMA4B__043


title: BRAC2_VEGF_M52_ROI-040_TMA4B

description: Library name: TMA4B__040


title: E14.5 kidney control 1

city: Cincinnati

first: Cristina

last: Cebrian

state: Ohio

address: 240 Albert Sabin Way

department: Division of Developmental Biology

country: USA

institute: Cincinnati Children's Hospital Medical Center

description: Library name: c755_6

data_processing:
Raw data was processed with fastp (version 0.23.2) for initial trimming and quality control.
Pseudoalignment was performed with kallisto (version 0.46.0) against the mm10 transcriptome.
DESeq2 (version 1.40.2) was used for differential expression and visualization
Assembly: mm10
Supplementary files format and content: Raw counts and TPM in CSV format

source_name: E14.5 Kidney

extract_protocol:
Both kidneys from Etv4/5 mutant embryos and control littermates were isolated at E14.5 and snap frozen using dry ice. RNA was extracted from 4 controls and 4 experimental kidney pairs using the Nucleospin RNA prep kit (Takara Bio, 740984.50)
Library preparation and sequencing was performed by Novogene. Library was prepared by polyA enrichment of submitted RNA. Sequencing was performed using Illumina NovaSeq PE150

value: E14.5 Kidney

tag: genotype

value: Six2-GFPcre tg/+; Etv4+/-; Etv5fl/fl


title: BRAC2_VEGF_M52_ROI-039_TMA4B

description: Library name: TMA4B__039


title: BRAC2_VEGF_M52_ROI-038_TMA4B

description: Library name: TMA4B__038


title: BRAC2_VEGF_M52_ROI-036_TMA4B

description: Library name: TMA4B__036


title: BRAC2_VEGF_M52_ROI-035_TMA4B

description: Library name: TMA4B__035


title: BRAC2_VEGF_M54_ROI-042_TMA5B

description: Library name: TMA5B__042


title: BRAC2_PBS_M51_ROI-034_TMA4B

description: Library name: TMA4B__034


title: BRAC2_PBS_M50_ROI-036_TMA5B

description: Library name: TMA5B__036


title: BRAC1_OCDC_M37_ROI-031_TMA5B

description: Library name: TMA5B__031


title: BRAC2_PBS_M51_ROI-031_TMA4B

description: Library name: TMA4B__031


title: BRAC2_PBS_M51_ROI-032_TMA4B

description: Library name: TMA4B__032


title: BRAC2_PBS_M51_ROI-033_TMA4B

description: Library name: TMA4B__033


title: BRAC1_OCDC_M37_ROI-030_TMA5B

description: Library name: TMA5B__030


title: BRAC2_PBS_M51_ROI-030_TMA4B

description: Library name: TMA4B__030


title: BRAC2_PBS_M49_ROI-026_TMA4B

description: Library name: TMA4B__026


title: BRAC2_PARPi_M48_ROI-025_TMA4B

description: Library name: TMA4B__025


title: BRAC2_PARPi_M48_ROI-024_TMA4B

description: Library name: TMA4B__024


title: BRAC1_VEGF-PARPi-OCDC_M25_ROI-023_TMA5B

description: Library name: TMA5B__023


title: BRAC2_PARPi_M48_ROI-023_TMA4B

description: Library name: TMA4B__023


title: BRAC2_PARPi_M48_ROI-022_TMA4B

description: Library name: TMA4B__022


title: BRAC2_PARPi_M48_ROI-020_TMA4B

description: Library name: TMA4B__020


title: BRAC2_PARPi_M48_ROI-016_TMA4B

description: Library name: TMA4B__016


title: BRAC2_PARPi_M48_ROI-018_TMA4B

description: Library name: TMA4B__018


title: p53_PBS_M11_ROI-017_TMA5B

description: Library name: TMA5B__017


title: BRAC2_PARPi_M48_ROI-015_TMA4B

description: Library name: TMA4B__015


title: BRAC2_VEGF-PARPi-OCDC_M47_ROI-014_TMA4B

description: Library name: TMA4B__014


title: BRAC2_VEGF-PARPi-OCDC_M47_ROI-012_TMA4B

description: Library name: TMA4B__012


title: BRAC2_VEGF-PARPi-OCDC_M47_ROI-013_TMA4B

description: Library name: TMA4B__013


title: BRAC2_VEGF-PARPi-OCDC_M47_ROI-011_TMA4B

description: Library name: TMA4B__011


title: BRAC2_VEGF-PARPi-OCDC_M47_ROI-010_TMA4B

description: Library name: TMA4B__010


title: BRAC2_VEGF-PARPi-OCDC_M47_ROI-009_TMA4B

description: Library name: TMA4B__009


title: BRAC2_VEGF-PARPi-OCDC_M46_ROI-008_TMA4B

description: Library name: TMA4B__008


title: BRAC2_VEGF-PARPi-OCDC_M46_ROI-007_TMA4B

description: Library name: TMA4B__007


title: BRAC2_VEGF-PARPi-OCDC_M46_ROI-005_TMA4B

description: Library name: TMA4B__005


title: p53_VEGF-PARPi-OCDC_M6_ROI-008_TMA5B

description: Library name: TMA5B__008


title: BRAC2_VEGF-PARPi-OCDC_M46_ROI-003_TMA4B

description: Library name: TMA4B__003


title: BRAC2_VEGF-PARPi-OCDC_M46_ROI-002_TMA4B

description: Library name: TMA4B__002


title: BRAC2_VEGF-PARPi-OCDC_M46_ROI-001_TMA4B

description: Library name: TMA4B__001


title: BRAC1_OCDC_M36_ROI-023_TMA4A

description: Library name: TMA4A__023

value: A


title: BRAC2_VEGF-PARPi-OCDC_M46_ROI-004_TMA4B

description: Library name: TMA4B__004


title: p53_VEGF-PARPi-OCDC_M6_ROI-006_TMA5B

description: Library name: TMA5B__006


title: BRAC1_VEGF-PARPi_M43_ROI-021_TMA4A

description: Library name: TMA4A__021


title: BRAC1_OCDC_M36_ROI-022_TMA4A

description: Library name: TMA4A__022


title: BRAC1_VEGF_M41_ROI-018_TMA4A

description: Library name: TMA4A__018


title: BRAC1_VEGF_M41_ROI-017_TMA4A

description: Library name: TMA4A__017


title: BRAC1_VEGF-PARPi_M43_ROI-020_TMA4A

description: Library name: TMA4A__020


title: BRAC1_VEGF_M40_ROI-016_TMA4A

description: Library name: TMA4A__016


title: BRAC1_OCDC_M36_ROI-013_TMA4A

description: Library name: TMA4A__013


title: BRAC1_OCDC_M36_ROI-012_TMA4A

description: Library name: TMA4A__012


title: BRAC1_OCDC_M36_ROI-010_TMA4A

description: Library name: TMA4A__010


title: BRAC1_OCDC_M35_ROI-009_TMA4A

description: Library name: TMA4A__009


title: BRAC1_OCDC_M35_ROI-008_TMA4A

description: Library name: TMA4A__008


title: BRAC1_OCDC_M35_ROI-007_TMA4A

description: Library name: TMA4A__007


title: gcl control, biological rep3

status: Public on Jun 10 2026

type: RNA

city: Frankfurt

first: Jessica

last: Schlaudraff

address: Heinrich-Hoffmann-Straße

country: Germany

institute: Klinische Neuroanatomie

description:
gene expression data from tissue of the granule cell layer without lesion
batch remover, other scan date

hyb_protocol: The Encore Biotin Module Kit (NuGEN) was then used for fragmentation and labeling of cDNA for analysis on Affymetrix Gene Chips. Samples were hybridized on a Mouse Gene 1.0 ST array  (Affymetrix)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Applied Biosystems)

data_processing: The data were checked with Expression console (Affymetrix) and analyzed with Partek-Software 6.5 (Partek) using default analysis settings.

label: biotin

source_name: without lesion

label_protocol: Total RNA was transcribed into cDNA and amplified with Single Primer Isothermal Amplification (SPIA) technology including in Ovation® Pico WTA System (NuGEN).

growth_protocol: 12 weeks old adult male Wildtype mice (C57Bl6/J@RJ ) were purchased from Janvier.

extract_protocol: Total RNA was isolated with RNeasy Plus Micro Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Experimental animals with transaction of the perforant path (n = 2-3 each time point) were allowed to survive 1, 3, 7, 14 or 28 days.

value: granule cell layer


title: BRAC1_OCDC_M35_ROI-003_TMA4A

description: Library name: TMA4A__003


title: BRAC1_OCDC_M35_ROI-002_TMA4A

description: Library name: TMA4A__002


title: BRAC2_VEGF-PARPi-OCDC_M45_ROI-083_TMA3B

description: Library name: TMA3B__083


title: BRAC2_VEGF-PARPi-OCDC_M45_ROI-079_TMA3B

description: Library name: TMA3B__079


title: BRAC2_VEGF-PARPi-OCDC_M45_ROI-077_TMA3B

description: Library name: TMA3B__077


title: BRAC2_VEGF-PARPi-OCDC_M45_ROI-078_TMA3B

description: Library name: TMA3B__078


title: BRAC2_VEGF-PARPi-OCDC_M45_ROI-082_TMA3B

description: Library name: TMA3B__082


title: BRAC2_VEGF-PARPi_M43_ROI-074_TMA3B

description: Library name: TMA3B__074


title: BRAC2_VEGF-PARPi_M43_ROI-073_TMA3B

description: Library name: TMA3B__073


title: BRAC2_VEGF-PARPi_M43_ROI-072_TMA3B

description: Library name: TMA3B__072


title: BRAC2_VEGF-PARPi_M43_ROI-071_TMA3B

description: Library name: TMA3B__071


title: BRAC1_OCDC_M36_ROI-011_TMA4A

description: Library name: TMA4A__011


title: BRAC2_VEGF-PARPi_M43_ROI-069_TMA3B

description: Library name: TMA3B__069


title: BRAC2_VEGF-PARPi_M42_ROI-068_TMA3B

description: Library name: TMA3B__068


title: BRAC2_VEGF-PARPi_M42_ROI-067_TMA3B

description: Library name: TMA3B__067


title: BRAC2_VEGF-PARPi_M42_ROI-064_TMA3B

description: Library name: TMA3B__064


title: BRAC2_VEGF-PARPi_M41_ROI-062_TMA3B

description: Library name: TMA3B__062


title: BRAC2_VEGF-PARPi_M41_ROI-063_TMA3B

description: Library name: TMA3B__063


title: BRAC2_VEGF-PARPi_M41_ROI-061_TMA3B

description: Library name: TMA3B__061


title: BRAC2_VEGF-PARPi_M41_ROI-060_TMA3B

description: Library name: TMA3B__060


title: BRAC2_VEGF-PARPi_M41_ROI-058_TMA3B

description: Library name: TMA3B__058


title: BRAC2_VEGF-PARPi_M40_ROI-057_TMA3B

description: Library name: TMA3B__057


title: BRAC2_VEGF-PARPi_M40_ROI-056_TMA3B

description: Library name: TMA3B__056


title: BRAC2_VEGF-PARPi_M40_ROI-054_TMA3B

description: Library name: TMA3B__054


title: BRAC2_VEGF-PARPi_M40_ROI-053_TMA3B

description: Library name: TMA3B__053


title: BRAC2_VEGF-PARPi_M39_ROI-051_TMA3B

description: Library name: TMA3B__051


title: BRAC2_VEGF-PARPi_M39_ROI-050_TMA3B

description: Library name: TMA3B__050


title: BRAC2_VEGF-PARPi_M39_ROI-048_TMA3B

description: Library name: TMA3B__048


title: BRAC2_VEGF-PARPi_M39_ROI-047_TMA3B

description: Library name: TMA3B__047


title: BRAC1_OCDC_M38_ROI-045_TMA3B

description: Library name: TMA3B__045


title: BRAC2_VEGF-PARPi_M39_ROI-049_TMA3B

description: Library name: TMA3B__049


title: BRAC1_OCDC_M38_ROI-044_TMA3B

description: Library name: TMA3B__044


title: BRAC1_OCDC_M37_ROI-042_TMA3B

description: Library name: TMA3B__042


title: BRAC1_OCDC_M37_ROI-041_TMA3B

description: Library name: TMA3B__041


title: BRAC1_OCDC_M37_ROI-040_TMA3B

description: Library name: TMA3B__040


title: BRAC1_OCDC_M37_ROI-038_TMA3B

description: Library name: TMA3B__038


title: BRAC1_OCDC_M37_ROI-037_TMA3B

description: Library name: TMA3B__037


title: BRAC1_OCDC_M36_ROI-035_TMA3B

description: Library name: TMA3B__035


title: BRAC1_OCDC_M36_ROI-034_TMA3B

description: Library name: TMA3B__034


title: BRAC1_OCDC_M36_ROI-032_TMA3B

description: Library name: TMA3B__032


title: BRAC1_OCDC_M36_ROI-033_TMA3B

description: Library name: TMA3B__033


title: BRAC1_OCDC_M36_ROI-031_TMA3B

description: Library name: TMA3B__031


title: BRAC1_PARPi_M35_ROI-029_TMA3B

description: Library name: TMA3B__029


title: BRAC1_OCDC_M36_ROI-030_TMA3B

description: Library name: TMA3B__030


title: BRAC1_PARPi_M35_ROI-028_TMA3B

description: Library name: TMA3B__028


title: BRAC1_PARPi_M35_ROI-027_TMA3B

description: Library name: TMA3B__027


title: BRAC1_PARPi_M35_ROI-026_TMA3B

description: Library name: TMA3B__026


title: BRAC1_PARPi_M35_ROI-025_TMA3B

description: Library name: TMA3B__025


title: BRAC1_PARPi_M34_ROI-023_TMA3B

description: Library name: TMA3B__023


title: BRAC1_PARPi_M34_ROI-022_TMA3B

description: Library name: TMA3B__022


title: BRAC1_PARPi_M34_ROI-021_TMA3B

description: Library name: TMA3B__021


title: BRAC1_PARPi_M34_ROI-019_TMA3B

description: Library name: TMA3B__019


title: BRAC1_PARPi_M34_ROI-018_TMA3B

description: Library name: TMA3B__018


title: BRAC1_PARPi_M33_ROI-017_TMA3B

description: Library name: TMA3B__017


title: BRAC1_PARPi_M33_ROI-016_TMA3B

description: Library name: TMA3B__016


title: BRAC1_PARPi_M33_ROI-014_TMA3B

description: Library name: TMA3B__014


title: BRAC1_PARPi_M33_ROI-013_TMA3B

description: Library name: TMA3B__013


title: BRAC1_VEGF_M32_ROI-012_TMA3B

description: Library name: TMA3B__012


title: BRAC1_VEGF_M32_ROI-011_TMA3B

description: Library name: TMA3B__011


title: BRAC1_VEGF_M32_ROI-010_TMA3B

description: Library name: TMA3B__010


title: BRAC1_VEGF_M32_ROI-009_TMA3B

description: Library name: TMA3B__009


title: BRAC1_VEGF_M32_ROI-008_TMA3B

description: Library name: TMA3B__008


title: BRAC1_VEGF_M32_ROI-007_TMA3B

description: Library name: TMA3B__007


title: BRAC1_VEGF_M31_ROI-006_TMA3B

description: Library name: TMA3B__006


title: BRAC1_VEGF_M31_ROI-005_TMA3B

description: Library name: TMA3B__005


title: BRAC1_VEGF_M31_ROI-004_TMA3B

description: Library name: TMA3B__004


title: BRAC1_PARPi_M35_ROI-024_TMA3B

description: Library name: TMA3B__024


title: BRAC1_VEGF_M31_ROI-003_TMA3B

description: Library name: TMA3B__003


title: BRAC1_VEGF_M31_ROI-002_TMA3B

description: Library name: TMA3B__002


title: BRAC1_VEGF_M31_ROI-001_TMA3B

description: Library name: TMA3B__001


title: BRAC1_PBS_M34_ROI-082_TMA3A

description: Library name: TMA3A__082


title: BRAC1_OCDC_M35_ROI-081_TMA3A

description: Library name: TMA3A__081


title: BRAC1_OCDC_M35_ROI-080_TMA3A

description: Library name: TMA3A__080


title: BRAC1_PBS_M34_ROI-079_TMA3A

description: Library name: TMA3A__079


title: BRAC1_OCDC_M35_ROI-004_TMA4A

description: Library name: TMA4A__004


title: BRAC1_OCDC_M35_ROI-078_TMA3A

description: Library name: TMA3A__078


title: BRAC1_OCDC_M35_ROI-006_TMA4A

description: Library name: TMA4A__006


title: BRAC1_OCDC_M35_ROI-001_TMA4A

description: Library name: TMA4A__001


title: BRAC1_OCDC_M35_ROI-077_TMA3A

description: Library name: TMA3A__077


title: BRAC1_OCDC_M35_ROI-076_TMA3A

description: Library name: TMA3A__076


title: BRAC1_OCDC_M35_ROI-075_TMA3A

description: Library name: TMA3A__075


title: BRAC2_VEGF-PARPi-OCDC_M45_ROI-081_TMA3B

description: Library name: TMA3B__081


title: BRAC1_OCDC_M35_ROI-074_TMA3A

description: Library name: TMA3A__074


title: BRAC1_OCDC_M35_ROI-072_TMA3A

description: Library name: TMA3A__072


title: BRAC1_OCDC_M35_ROI-073_TMA3A

description: Library name: TMA3A__073


title: BRAC1_OCDC_M35_ROI-071_TMA3A

description: Library name: TMA3A__071


title: BRAC2_VEGF-PARPi_M43_ROI-070_TMA3B

description: Library name: TMA3B__070


title: BRAC1_OCDC_M35_ROI-070_TMA3A

description: Library name: TMA3A__070


title: BRAC1_OCDC_M35_ROI-067_TMA3A

description: Library name: TMA3A__067


title: BRAC2_VEGF-PARPi_M42_ROI-066_TMA3B

description: Library name: TMA3B__066


title: BRAC1_OCDC_M35_ROI-066_TMA3A

description: Library name: TMA3A__066


title: BRAC2_VEGF-PARPi_M42_ROI-065_TMA3B

description: Library name: TMA3B__065


title: BRAC1_OCDC_M35_ROI-065_TMA3A

description: Library name: TMA3A__065


title: BRAC1_OCDC_M35_ROI-064_TMA3A

description: Library name: TMA3A__064


title: BRAC1_OCDC_M35_ROI-061_TMA3A

description: Library name: TMA3A__061


title: BRAC1_OCDC_M35_ROI-063_TMA3A

description: Library name: TMA3A__063


title: BRAC1_OCDC_M35_ROI-060_TMA3A

description: Library name: TMA3A__060


title: BRAC1_OCDC_M35_ROI-058_TMA3A

description: Library name: TMA3A__058


title: BRAC1_OCDC_M35_ROI-059_TMA3A

description: Library name: TMA3A__059


title: BRAC2_VEGF-PARPi_M40_ROI-055_TMA3B

description: Library name: TMA3B__055


title: BRAC1_OCDC_M35_ROI-056_TMA3A

description: Library name: TMA3A__056


title: BRAC1_OCDC_M35_ROI-057_TMA3A

description: Library name: TMA3A__057


title: BRAC1_OCDC_M35_ROI-054_TMA3A

description: Library name: TMA3A__054


title: BRAC1_OCDC_M35_ROI-053_TMA3A

description: Library name: TMA3A__053


title: BRAC1_OCDC_M35_ROI-055_TMA3A

description: Library name: TMA3A__055


title: BRAC1_OCDC_M35_ROI-051_TMA3A

description: Library name: TMA3A__051


title: BRAC1_OCDC_M35_ROI-050_TMA3A

description: Library name: TMA3A__050


title: BRAC1_OCDC_M35_ROI-049_TMA3A

description: Library name: TMA3A__049


title: BRAC2_VEGF-PARPi_M40_ROI-052_TMA3B

description: Library name: TMA3B__052


title: BRAC1_PBS_M34_ROI-048_TMA3A

description: Library name: TMA3A__048


title: BRAC1_PBS_M34_ROI-047_TMA3A

description: Library name: TMA3A__047


title: BRAC1_PBS_M34_ROI-046_TMA3A

description: Library name: TMA3A__046


title: BRAC1_PBS_M34_ROI-043_TMA3A

description: Library name: TMA3A__043


title: BRAC1_PBS_M34_ROI-042_TMA3A

description: Library name: TMA3A__042


title: BRAC1_PBS_M34_ROI-045_TMA3A

description: Library name: TMA3A__045


title: BRAC1_PBS_M34_ROI-041_TMA3A

description: Library name: TMA3A__041


title: BRAC1_PBS_M34_ROI-044_TMA3A

description: Library name: TMA3A__044


title: BRAC1_PBS_M34_ROI-040_TMA3A

description: Library name: TMA3A__040


title: BRAC1_PBS_M34_ROI-036_TMA3A

description: Library name: TMA3A__036


title: BRAC1_PBS_M34_ROI-035_TMA3A

description: Library name: TMA3A__035


title: BRAC1_PBS_M34_ROI-038_TMA3A

description: Library name: TMA3A__038


title: BRAC1_PBS_M34_ROI-034_TMA3A

description: Library name: TMA3A__034


title: BRAC1_PBS_M34_ROI-033_TMA3A

description: Library name: TMA3A__033


title: BRAC1_PBS_M34_ROI-032_TMA3A

description: Library name: TMA3A__032


title: BRAC1_OCDC_M38_ROI-043_TMA3B

description: Library name: TMA3B__043


title: BRAC1_PBS_M34_ROI-030_TMA3A

description: Library name: TMA3A__030


title: BRAC1_PBS_M34_ROI-029_TMA3A

description: Library name: TMA3A__029


title: BRAC1_PBS_M34_ROI-028_TMA3A

description: Library name: TMA3A__028


title: BRAC1_PBS_M34_ROI-027_TMA3A

description: Library name: TMA3A__027


title: BRAC1_PBS_M34_ROI-026_TMA3A

description: Library name: TMA3A__026


title: BRAC1_PBS_M34_ROI-022_TMA3A

description: Library name: TMA3A__022


title: BRAC1_PBS_M34_ROI-023_TMA3A

description: Library name: TMA3A__023


title: BRAC1_PBS_M34_ROI-021_TMA3A

description: Library name: TMA3A__021


title: BRAC1_PBS_M34_ROI-024_TMA3A

description: Library name: TMA3A__024


title: BRAC2_VEGF_M24_ROI-017_TMA3A

description: Library name: TMA3A__017


title: BRAC2_VEGF_M24_ROI-015_TMA3A

description: Library name: TMA3A__015


title: BRAC2_VEGF_M24_ROI-014_TMA3A

description: Library name: TMA3A__014


title: BRAC2_VEGF_M24_ROI-013_TMA3A

description: Library name: TMA3A__013


title: BRAC2_VEGF_M24_ROI-012_TMA3A

description: Library name: TMA3A__012


title: BRAC2_VEGF_M24_ROI-010_TMA3A

description: Library name: TMA3A__010


title: BRAC2_VEGF_M24_ROI-011_TMA3A

description: Library name: TMA3A__011


title: BRAC2_VEGF_M24_ROI-009_TMA3A

description: Library name: TMA3A__009


title: BRAC2_PARPi_M22_ROI-007_TMA3A

description: Library name: TMA3A__007


title: BRAC2_PARPi_M22_ROI-006_TMA3A

description: Library name: TMA3A__006


title: BRAC2_PARPi_M22_ROI-005_TMA3A

description: Library name: TMA3A__005


title: BRAC2_PARPi_M22_ROI-004_TMA3A

description: Library name: TMA3A__004


title: BRAC1_VEGF_M30_ROI-088_TMA2B

description: Library name: TMA2B__088


title: BRAC1_VEGF_M30_ROI-090_TMA2B

description: Library name: TMA2B__090


title: BRAC1_VEGF_M30_ROI-089_TMA2B

description: Library name: TMA2B__089


title: BRAC1_VEGF_M30_ROI-087_TMA2B

description: Library name: TMA2B__087


title: BRAC1_VEGF_M30_ROI-086_TMA2B

description: Library name: TMA2B__086


title: BRAC1_PBS_M29_ROI-085_TMA2B

description: Library name: TMA2B__085


title: BRAC1_PBS_M29_ROI-084_TMA2B

description: Library name: TMA2B__084


title: BRAC1_PBS_M29_ROI-083_TMA2B

description: Library name: TMA2B__083


title: BRAC1_PBS_M29_ROI-081_TMA2B

description: Library name: TMA2B__081


title: BRAC1_PBS_M29_ROI-080_TMA2B

description: Library name: TMA2B__080


title: BRAC1_PBS_M29_ROI-079_TMA2B

description: Library name: TMA2B__079


title: BRAC1_PBS_M27_ROI-072_TMA2B

description: Library name: TMA2B__072


title: BRAC1_PBS_M28_ROI-077_TMA2B

description: Library name: TMA2B__077


title: BRAC1_PBS_M28_ROI-076_TMA2B

description: Library name: TMA2B__076


title: BRAC1_PBS_M28_ROI-075_TMA2B

description: Library name: TMA2B__075


title: BRAC1_PBS_M28_ROI-073_TMA2B

description: Library name: TMA2B__073


title: BRAC1_PBS_M28_ROI-074_TMA2B

description: Library name: TMA2B__074


title: BRAC1_PBS_M28_ROI-078_TMA2B

description: Library name: TMA2B__078


title: BRAC1_PBS_M27_ROI-071_TMA2B

description: Library name: TMA2B__071


title: BRAC1_PBS_M27_ROI-069_TMA2B

description: Library name: TMA2B__069


title: BRAC1_VEGF-PARPi-OCDC_M26_ROI-066_TMA2B

description: Library name: TMA2B__066


title: BRAC1_VEGF-PARPi-OCDC_M26_ROI-063_TMA2B

description: Library name: TMA2B__063


title: BRAC1_VEGF-PARPi-OCDC_M26_ROI-064_TMA2B

description: Library name: TMA2B__064


title: BRAC1_VEGF-PARPi-OCDC_M26_ROI-062_TMA2B

description: Library name: TMA2B__062


title: BRAC1_VEGF-PARPi-OCDC_M26_ROI-065_TMA2B

description: Library name: TMA2B__065


title: BRAC1_VEGF-PARPi-OCDC_M25_ROI-056_TMA2B

description: Library name: TMA2B__056


title: BRAC1_VEGF-PARPi-OCDC_M26_ROI-060_TMA2B

description: Library name: TMA2B__060


title: BRAC1_VEGF-PARPi-OCDC_M25_ROI-059_TMA2B

description: Library name: TMA2B__059


title: BRAC1_VEGF-PARPi-OCDC_M24_ROI-054_TMA2B

description: Library name: TMA2B__054


title: BRAC1_VEGF-PARPi-OCDC_M25_ROI-057_TMA2B

description: Library name: TMA2B__057


title: BRAC1_VEGF-PARPi-OCDC_M25_ROI-058_TMA2B

description: Library name: TMA2B__058


title: BRAC1_VEGF-PARPi-OCDC_M24_ROI-055_TMA2B

description: Library name: TMA2B__055


title: BRAC1_VEGF-PARPi-OCDC_M24_ROI-053_TMA2B

description: Library name: TMA2B__053


title: BRAC1_VEGF-PARPi-OCDC_M24_ROI-051_TMA2B

description: Library name: TMA2B__051


title: BRAC1_VEGF-PARPi-OCDC_M24_ROI-050_TMA2B

description: Library name: TMA2B__050


title: BRAC1_VEGF-PARPi-OCDC_M23_ROI-048_TMA2B

description: Library name: TMA2B__048


title: BRAC1_VEGF-PARPi-OCDC_M24_ROI-049_TMA2B

description: Library name: TMA2B__049


title: BRAC1_VEGF-PARPi-OCDC_M23_ROI-047_TMA2B

description: Library name: TMA2B__047


title: BRAC1_VEGF-PARPi-OCDC_M23_ROI-045_TMA2B

description: Library name: TMA2B__045


title: BRAC1_VEGF-PARPi-OCDC_M23_ROI-046_TMA2B

description: Library name: TMA2B__046


title: BRAC1_VEGF-PARPi-OCDC_M22_ROI-040_TMA2B

description: Library name: TMA2B__040


title: BRAC1_VEGF-PARPi-OCDC_M23_ROI-043_TMA2B

description: Library name: TMA2B__043


title: BRAC1_VEGF-PARPi-OCDC_M23_ROI-044_TMA2B

description: Library name: TMA2B__044


title: BRAC1_VEGF-PARPi-OCDC_M22_ROI-041_TMA2B

description: Library name: TMA2B__041


title: BRAC1_VEGF-PARPi-OCDC_M22_ROI-037_TMA2B

description: Library name: TMA2B__037


title: BRAC1_VEGF-PARPi-OCDC_M22_ROI-039_TMA2B

description: Library name: TMA2B__039


title: BRAC1_VEGF-PARPi-OCDC_M22_ROI-036_TMA2B

description: Library name: TMA2B__036


title: BRAC1_VEGF-PARPi-OCDC_M22_ROI-035_TMA2B

description: Library name: TMA2B__035


title: BRAC1_VEGF-PARPi_M21_ROI-034_TMA2B

description: Library name: TMA2B__034


title: BRAC1_VEGF-PARPi_M21_ROI-033_TMA2B

description: Library name: TMA2B__033


title: BRAC1_VEGF-PARPi_M21_ROI-032_TMA2B

description: Library name: TMA2B__032


title: BRAC1_VEGF-PARPi_M21_ROI-030_TMA2B

description: Library name: TMA2B__030


title: BRAC1_VEGF-PARPi_M21_ROI-028_TMA2B

description: Library name: TMA2B__028


title: BRAC1_VEGF-PARPi_M20_ROI-027_TMA2B

description: Library name: TMA2B__027


title: BRAC1_VEGF-PARPi_M21_ROI-029_TMA2B

description: Library name: TMA2B__029


title: BRAC1_VEGF-PARPi_M20_ROI-024_TMA2B

description: Library name: TMA2B__024


title: BRAC1_VEGF-PARPi_M20_ROI-025_TMA2B

description: Library name: TMA2B__025


title: BRAC1_VEGF-PARPi_M20_ROI-023_TMA2B

description: Library name: TMA2B__023


title: BRAC1_VEGF-PARPi_M20_ROI-026_TMA2B

description: Library name: TMA2B__026


title: BRAC1_VEGF-PARPi_M20_ROI-021_TMA2B

description: Library name: TMA2B__021


title: BRAC1_VEGF-PARPi_M20_ROI-022_TMA2B

description: Library name: TMA2B__022


title: BRAC1_VEGF-PARPi_M19_ROI-020_TMA2B

description: Library name: TMA2B__020


title: BRAC1_VEGF-PARPi_M19_ROI-019_TMA2B

description: Library name: TMA2B__019


title: BRAC1_VEGF-PARPi_M19_ROI-018_TMA2B

description: Library name: TMA2B__018


title: BRAC1_VEGF-PARPi_M19_ROI-016_TMA2B

description: Library name: TMA2B__016


title: BRAC1_VEGF-PARPi_M19_ROI-015_TMA2B

description: Library name: TMA2B__015


title: BRAC1_VEGF-PARPi_M18_ROI-012_TMA2B

description: Library name: TMA2B__012


title: BRAC1_VEGF-PARPi_M19_ROI-014_TMA2B

description: Library name: TMA2B__014


title: BRAC1_VEGF-PARPi_M18_ROI-013_TMA2B

description: Library name: TMA2B__013


title: BRAC1_VEGF-PARPi_M18_ROI-011_TMA2B

description: Library name: TMA2B__011


title: BRAC1_VEGF-PARPi_M18_ROI-008_TMA2B

description: Library name: TMA2B__008


title: Control (maintained under well-watered ) and sampling after the first drought stress , Root, rep 3

city: Beaucouze

first: Sandrine

last: Balzergue

address: 42 rue G. Morel

country: France

institute: INRAE

description: Library name: C3_S1_RO

data_processing:
Raw data quality was checked using FastQC (Andrews, 2010) and the estimation of transcript-level abundance was performed by Salmon tool (Patro et al., 2017) using default parameters. The reads were aligned against the Malus domestica GDDH13 genome v1.1 (Daccord et al., 2017).
The differential gene analysis was performed by the R package DESeq (Anders and Huber, 2010). The genes presenting a p-value lower than 0.05 were considered as differentially expressed in this study.
Assembly: Malus domestica GDDH13 genome v1.1 (Daccord et al., 2017).
Supplementary files format and content: for each comparison, txt file with at list logCPM_Ttmt_Drought, logCPM_Ctrl_Control, logFC,pval_DESeq2and BH_DESeq2

organism: Malus domestica

source_name: Root

growth_protocol: Apple seedlings were grown in the greenhouses of France's National Research Institute for Agriculture, Food and Environment (INRAe) in Angers, France (47° 28' 36.804'' N 0° 36' 41.4'' W). The seeds from ‘Golden Delicious’ double haploid 18 (GDDH18; Daccord et al., 2017) were stratified for 3 months in a 1:1 mixture of sand and vermiculite (humidity of 70%) and kept at 3 °C for 90 days. After the period of stratification, the seeds were sown in a soil mixture containing 50% peat moss, 40% perlite, 10% coco fibers, 7.5kg/ea carbonates and N-P-K mix 14-16-18. The sowing was performed in three blocks, interspersed by one week each, representing three biological replicates. The germination was carried out in a greenhouse (ambient light; 21 °C ± 5 °C; relative humidity 60 % ± 20). Four weeks after germination, the seedlings were transplanted into 0.4 L plastic pots using the same soil mixture and maintained under the same environmental conditions. At eight weeks of age, the seedlings were transferred to final 1 L pots and grown for an additional four weeks before the initiation of drought stress (DS) cycles.

extract_protocol:
For each tissue and condition, approximately 50 mg (fresh weight) were used for total RNA extraction using the NucleoSpin® RNA Plus kit (Macherey Nagel, Germany).
libraries were built using the NEB® mRNA stranded library preparation kit (New England Biolabs, USA). Sequencing was performed using Illumina NovaSeq S4 in a paired-end (PE) mode with read length 100 bp. A minimum of 25 million PE reads per sample were generated

treatment_protocol: Irrigation management was conducted by monitoring the soil water content (SWC) of all plants every two days using pot weighing. During well-watered (WW) periods, plants were maintained near field capacity (FC; 80% SWC), whereas during drought stress (DS) periods, irrigation was adjusted to maintain SWC at 45% of FC. The SWC corresponding to 100% FC was determined for the previously described soil mix by saturating pots with water and allowing free drainage for 24 hours. Two distinct irrigation regimes were established : (I) Control group (64 plants): maintained under WW conditions throughout the entire experiment. (II) Multiple-DS group (61 plants): subjected to three consecutive drought cycles, each consisting of three weeks under DS conditions followed by three weeks of recovery (as WW condition). To investigate long-term transcriptomic and epigenetic memory responses, in year n+1, roots and leaves from Control and Multiple-DS plants were also sampled prior to the application of a new stress (Before Stress – BS), after completing one winter cycle. For root samples only,  two biological replicates was performed due to the limited availability of root for this treatment.

value: Root

value: Golden Delicious double haploid 18 (GDDH18)

value: Control

value: replicate 3


title: BRAC1_VEGF-PARPi_M18_ROI-009_TMA2B

description: Library name: TMA2B__009

value: tumor


title: Control (maintained under well-watered ) and sampling after the first drought stress , Root, rep 2

description: Library name: C2_S1_RO

value: replicate 2


title: BRAC1_VEGF-PARPi_M17_ROI-007_TMA2B

description: Library name: TMA2B__007

value: B


title: BRAC1_VEGF-PARPi_M18_ROI-010_TMA2B

description: Library name: TMA2B__010

value: low


title: BRAC1_VEGF-PARPi_M17_ROI-003_TMA2B

description: Library name: TMA2B__003


title: BRAC1_VEGF-PARPi_M17_ROI-002_TMA2B

description: Library name: TMA2B__002

value: medium


title: BRAC2_OCDC_M19_ROI-073_TMA2A

description: Library name: TMA2A__073


title: BRAC2_OCDC_M19_ROI-071_TMA2A

description: Library name: TMA2A__071

value: high


title: BRAC2_OCDC_M19_ROI-070_TMA2A

description: Library name: TMA2A__070

value: OCDC


title: BRAC2_OCDC_M19_ROI-072_TMA2A

description: Library name: TMA2A__072


title: BRAC2_OCDC_M19_ROI-069_TMA2A

description: Library name: TMA2A__069


title: BRAC2_OCDC_M19_ROI-067_TMA2A

description: Library name: TMA2A__067


title: BRAC2_OCDC_M19_ROI-064_TMA2A

description: Library name: TMA2A__064


title: BRAC2_OCDC_M19_ROI-068_TMA2A

description: Library name: TMA2A__068


title: BRAC2_OCDC_M19_ROI-062_TMA2A

description: Library name: TMA2A__062


title: BRAC2_OCDC_M19_ROI-063_TMA2A

description: Library name: TMA2A__063


title: BRAC2_OCDC_M19_ROI-061_TMA2A

description: Library name: TMA2A__061


title: BRAC2_OCDC_M19_ROI-060_TMA2A

description: Library name: TMA2A__060


title: BRAC2_OCDC_M19_ROI-059_TMA2A

description: Library name: TMA2A__059


title: BRAC2_PBS_M18_ROI-058_TMA2A

description: Library name: TMA2A__058

value: PBS


title: BRAC2_PBS_M18_ROI-057_TMA2A

description: Library name: TMA2A__057


title: BRAC2_PBS_M18_ROI-053_TMA2A

description: Library name: TMA2A__053


title: BRAC2_PBS_M18_ROI-055_TMA2A

description: Library name: TMA2A__055


title: BRAC2_PBS_M18_ROI-052_TMA2A

description: Library name: TMA2A__052


title: BRAC2_PBS_M18_ROI-051_TMA2A

description: Library name: TMA2A__051


title: BRAC2_PBS_M18_ROI-049_TMA2A

description: Library name: TMA2A__049


title: BRAC2_PBS_M18_ROI-046_TMA2A

description: Library name: TMA2A__046


title: BRAC2_PBS_M18_ROI-045_TMA2A

description: Library name: TMA2A__045


title: BRAC2_PBS_M18_ROI-042_TMA2A

description: Library name: TMA2A__042


title: BRAC2_PBS_M18_ROI-044_TMA2A

description: Library name: TMA2A__044


title: BRAC2_PBS_M18_ROI-040_TMA2A

description: Library name: TMA2A__040


title: BRAC2_PBS_M18_ROI-043_TMA2A

description: Library name: TMA2A__043


title: BRAC2_PBS_M18_ROI-038_TMA2A

description: Library name: TMA2A__038


title: BRAC2_PBS_M18_ROI-037_TMA2A

description: Library name: TMA2A__037


title: BRAC2_PBS_M18_ROI-036_TMA2A

description: Library name: TMA2A__036


title: BRAC2_PBS_M18_ROI-035_TMA2A

description: Library name: TMA2A__035


title: BRAC2_PBS_M18_ROI-033_TMA2A

description: Library name: TMA2A__033


title: BRAC2_PBS_M18_ROI-031_TMA2A

description: Library name: TMA2A__031


title: BRAC2_PBS_M18_ROI-032_TMA2A

description: Library name: TMA2A__032


title: BRAC2_PBS_M18_ROI-030_TMA2A

description: Library name: TMA2A__030


title: p53_VEGF-PARPi_M12_ROI-026_TMA2A

description: Library name: TMA2A__026


title: p53_VEGF-PARPi_M11_ROI-025_TMA2A

description: Library name: TMA2A__025


title: p53_VEGF-PARPi-OCDC_M15_ROI-021_TMA2A

description: Library name: TMA2A__021


title: p53_VEGF-PARPi-OCDC_M15_ROI-020_TMA2A

description: Library name: TMA2A__020


title: p53_VEGF-PARPi-OCDC_M15_ROI-019_TMA2A

description: Library name: TMA2A__019


title: p53_VEGF-PARPi-OCDC_M15_ROI-018_TMA2A

description: Library name: TMA2A__018


title: p53_VEGF-PARPi-OCDC_M16_ROI-016_TMA2A

description: Library name: TMA2A__016


title: BRAC1_VEGF-PARPi_M17_ROI-005_TMA2B

description: Library name: TMA2B__005


title: BRAC1_VEGF-PARPi_M17_ROI-006_TMA2B

description: Library name: TMA2B__006


title: p53_VEGF-PARPi-OCDC_M16_ROI-015_TMA2A

description: Library name: TMA2A__015


title: BRAC1_VEGF-PARPi_M17_ROI-004_TMA2B

description: Library name: TMA2B__004


title: p53_VEGF-PARPi-OCDC_M16_ROI-014_TMA2A

description: Library name: TMA2A__014


title: p53_VEGF-PARPi-OCDC_M16_ROI-013_TMA2A

description: Library name: TMA2A__013


title: p53_VEGF-PARPi_M12_ROI-012_TMA2A

description: Library name: TMA2A__012


title: p53_VEGF-PARPi_M12_ROI-011_TMA2A

description: Library name: TMA2A__011


title: p53_VEGF-PARPi_M11_ROI-010_TMA2A

description: Library name: TMA2A__010


title: p53_VEGF-PARPi_M11_ROI-009_TMA2A

description: Library name: TMA2A__009


title: p53_VEGF-PARPi_M11_ROI-008_TMA2A

description: Library name: TMA2A__008


title: BRAC2_OCDC_M19_ROI-066_TMA2A

description: Library name: TMA2A__066


title: p53_VEGF-PARPi_M11_ROI-007_TMA2A

description: Library name: TMA2A__007


title: p53_VEGF-PARPi_M11_ROI-006_TMA2A

description: Library name: TMA2A__006


title: p53_VEGF-PARPi_M11_ROI-005_TMA2A

description: Library name: TMA2A__005


title: p53_VEGF-PARPi_M11_ROI-004_TMA2A

description: Library name: TMA2A__004


title: BRAC2_PBS_M18_ROI-056_TMA2A

description: Library name: TMA2A__056


title: p53_VEGF-PARPi_M11_ROI-003_TMA2A

description: Library name: TMA2A__003


title: p53_VEGF_M16_ROI-062_TMA1B

description: Library name: TMA1B__062

value: VEGF


title: p53_VEGF_M16_ROI-061_TMA1B

description: Library name: TMA1B__061


title: p53_VEGF_M16_ROI-060_TMA1B

description: Library name: TMA1B__060


title: BRAC2_PBS_M18_ROI-054_TMA2A

description: Library name: TMA2A__054


title: p53_VEGF_M16_ROI-059_TMA1B

description: Library name: TMA1B__059


title: p53_VEGF_M15_ROI-057_TMA1B

description: Library name: TMA1B__057


title: p53_VEGF_M15_ROI-053_TMA1B

description: Library name: TMA1B__053


title: p53_VEGF_M16_ROI-058_TMA1B

description: Library name: TMA1B__058


title: p53_VEGF_M15_ROI-056_TMA1B

description: Library name: TMA1B__056


title: BRAC2_PBS_M18_ROI-048_TMA2A

description: Library name: TMA2A__048


title: p53_VEGF_M15_ROI-055_TMA1B

description: Library name: TMA1B__055


title: p53_VEGF_M15_ROI-054_TMA1B

description: Library name: TMA1B__054


title: p53_VEGF_M15_ROI-052_TMA1B

description: Library name: TMA1B__052


title: p53_PBS_M14_ROI-051_TMA1B

description: Library name: TMA1B__051


title: BRAC2_PBS_M18_ROI-039_TMA2A

description: Library name: TMA2A__039


title: p53_PBS_M14_ROI-047_TMA1B

description: Library name: TMA1B__047


title: p53_PBS_M14_ROI-050_TMA1B

description: Library name: TMA1B__050


title: p53_PBS_M14_ROI-049_TMA1B

description: Library name: TMA1B__049


title: p53_PBS_M14_ROI-048_TMA1B

description: Library name: TMA1B__048


title: p53_PBS_M14_ROI-046_TMA1B

description: Library name: TMA1B__046


title: p53_PARPi_M13_ROI-041_TMA1B

description: Library name: TMA1B__041

value: PARPi


title: p53_PARPi_M13_ROI-040_TMA1B

description: Library name: TMA1B__040


title: p53_OCDC_M5_ROI-045_TMA1B

description: Library name: TMA1B__045


title: p53_OCDC_M5_ROI-044_TMA1B

description: Library name: TMA1B__044


title: p53_PARPi_M13_ROI-042_TMA1B

description: Library name: TMA1B__042


title: p53_OCDC_M5_ROI-043_TMA1B

description: Library name: TMA1B__043


title: p53_PARPi_M13_ROI-039_TMA1B

description: Library name: TMA1B__039


title: p53_VEGF-PARPi-OCDC_M16_ROI-028_TMA2A

description: Library name: TMA2A__028


title: p53_PARPi_M13_ROI-038_TMA1B

description: Library name: TMA1B__038


title: p53_PARPi_M12_ROI-035_TMA1B

description: Library name: TMA1B__035


title: p53_PARPi_M13_ROI-037_TMA1B

description: Library name: TMA1B__037


title: p53_PARPi_M12_ROI-034_TMA1B

description: Library name: TMA1B__034


title: p53_PARPi_M12_ROI-033_TMA1B

description: Library name: TMA1B__033


title: p53_PARPi_M12_ROI-030_TMA1B

description: Library name: TMA1B__030


title: p53_PARPi_M12_ROI-032_TMA1B

description: Library name: TMA1B__032


title: p53_PBS_M11_ROI-029_TMA1B

description: Library name: TMA1B__029


title: p53_PBS_M11_ROI-027_TMA1B

description: Library name: TMA1B__027


title: p53_VEGF-PARPi-OCDC_M9_ROI-024_TMA1B

description: Library name: TMA1B__024


title: p53_VEGF-PARPi-OCDC_M9_ROI-023_TMA1B

description: Library name: TMA1B__023


title: p53_PBS_M11_ROI-026_TMA1B

description: Library name: TMA1B__026


title: p53_VEGF-PARPi-OCDC_M9_ROI-022_TMA1B

description: Library name: TMA1B__022


title: p53_PBS_M11_ROI-028_TMA1B

description: Library name: TMA1B__028


title: p53_VEGF-PARPi-OCDC_M9_ROI-025_TMA1B

description: Library name: TMA1B__025


title: p53_VEGF-PARPi-OCDC_M9_ROI-020_TMA1B

description: Library name: TMA1B__020


title: p53_VEGF-PARPi-OCDC_M8_ROI-019_TMA1B

description: Library name: TMA1B__019


title: p53_VEGF-PARPi-OCDC_M7_ROI-015_TMA1B

description: Library name: TMA1B__015


title: p53_VEGF-PARPi-OCDC_M8_ROI-017_TMA1B

description: Library name: TMA1B__017


title: p53_VEGF-PARPi-OCDC_M8_ROI-018_TMA1B

description: Library name: TMA1B__018


title: p53_VEGF-PARPi-OCDC_M7_ROI-014_TMA1B

description: Library name: TMA1B__014


title: p53_VEGF-PARPi-OCDC_M7_ROI-013_TMA1B

description: Library name: TMA1B__013


title: p53_OCDC_M5_ROI-012_TMA1B

description: Library name: TMA1B__012


title: p53_OCDC_M5_ROI-011_TMA1B

description: Library name: TMA1B__011


title: p53_OCDC_M5_ROI-010_TMA1B

description: Library name: TMA1B__010


title: p53_VEGF-PARPi_M4_ROI-006_TMA1B

description: Library name: TMA1B__006


title: p53_VEGF-PARPi_M4_ROI-009_TMA1B

description: Library name: TMA1B__009


title: p53_VEGF-PARPi_M4_ROI-008_TMA1B

description: Library name: TMA1B__008


title: p53_VEGF-PARPi_M4_ROI-004_TMA1B

description: Library name: TMA1B__004


title: p53_VEGF-PARPi_M4_ROI-007_TMA1B

description: Library name: TMA1B__007


title: p53_VEGF-PARPi_M3_ROI-003_TMA1B

description: Library name: TMA1B__003


title: p53_VEGF-PARPi_M3_ROI-002_TMA1B

description: Library name: TMA1B__002


title: p53_VEGF-PARPi_M3_ROI-001_TMA1B

description: Library name: TMA1B__001


title: p53_OCDC_M4_ROI-106_TMA1A

description: Library name: TMA1A__106


title: p53_OCDC_M4_ROI-105_TMA1A

description: Library name: TMA1A__105


title: p53_OCDC_M4_ROI-103_TMA1A

description: Library name: TMA1A__103


title: p53_OCDC_M4_ROI-102_TMA1A

description: Library name: TMA1A__102


title: p53_OCDC_M4_ROI-100_TMA1A

description: Library name: TMA1A__100


title: p53_OCDC_M4_ROI-104_TMA1A

description: Library name: TMA1A__104


title: p53_OCDC_M4_ROI-099_TMA1A

description: Library name: TMA1A__099


title: p53_OCDC_M4_ROI-097_TMA1A

description: Library name: TMA1A__097


title: p53_OCDC_M4_ROI-092_TMA1A

description: Library name: TMA1A__092


title: p53_OCDC_M4_ROI-098_TMA1A

description: Library name: TMA1A__098


title: p53_OCDC_M4_ROI-091_TMA1A

description: Library name: TMA1A__091


title: p53_OCDC_M4_ROI-090_TMA1A

description: Library name: TMA1A__090


title: p53_OCDC_M4_ROI-096_TMA1A

description: Library name: TMA1A__096


title: p53_OCDC_M4_ROI-089_TMA1A

description: Library name: TMA1A__089


title: p53_OCDC_M3_ROI-086_TMA1A

description: Library name: TMA1A__086


title: p53_OCDC_M3_ROI-084_TMA1A

description: Library name: TMA1A__084


title: p53_OCDC_M3_ROI-083_TMA1A

description: Library name: TMA1A__083


title: p53_OCDC_M3_ROI-081_TMA1A

description: Library name: TMA1A__081


title: p53_OCDC_M3_ROI-082_TMA1A

description: Library name: TMA1A__082


title: p53_OCDC_M3_ROI-076_TMA1A

description: Library name: TMA1A__076


title: p53_OCDC_M3_ROI-077_TMA1A

description: Library name: TMA1A__077


title: p53_OCDC_M3_ROI-075_TMA1A

description: Library name: TMA1A__075


title: p53_OCDC_M3_ROI-074_TMA1A

description: Library name: TMA1A__074


title: p53_OCDC_M3_ROI-071_TMA1A

description: Library name: TMA1A__071


title: p53_OCDC_M3_ROI-072_TMA1A

description: Library name: TMA1A__072


title: p53_OCDC_M3_ROI-069_TMA1A

description: Library name: TMA1A__069


title: p53_OCDC_M3_ROI-070_TMA1A

description: Library name: TMA1A__070


title: p53_OCDC_M3_ROI-068_TMA1A

description: Library name: TMA1A__068


title: p53_OCDC_M3_ROI-067_TMA1A

description: Library name: TMA1A__067


title: p53_OCDC_M3_ROI-066_TMA1A

description: Library name: TMA1A__066


title: p53_OCDC_M3_ROI-062_TMA1A

description: Library name: TMA1A__062


title: p53_OCDC_M3_ROI-061_TMA1A

description: Library name: TMA1A__061


title: p53_OCDC_M3_ROI-056_TMA1A

description: Library name: TMA1A__056


title: p53_OCDC_M3_ROI-055_TMA1A

description: Library name: TMA1A__055


title: p53_PBS_M2_ROI-054_TMA1A

description: Library name: TMA1A__054


title: p53_PBS_M2_ROI-049_TMA1A

description: Library name: TMA1A__049


title: p53_OCDC_M3_ROI-057_TMA1A

description: Library name: TMA1A__057


title: p53_PBS_M2_ROI-051_TMA1A

description: Library name: TMA1A__051


title: p53_PBS_M2_ROI-040_TMA1A

description: Library name: TMA1A__040


title: p53_PBS_M2_ROI-039_TMA1A

description: Library name: TMA1A__039


title: p53_PBS_M2_ROI-038_TMA1A

description: Library name: TMA1A__038


title: p53_PBS_M2_ROI-037_TMA1A

description: Library name: TMA1A__037


title: p53_PBS_M2_ROI-036_TMA1A

description: Library name: TMA1A__036


title: p53_PBS_M2_ROI-034_TMA1A

description: Library name: TMA1A__034


title: p53_PBS_M2_ROI-035_TMA1A

description: Library name: TMA1A__035


title: p53_PBS_M2_ROI-033_TMA1A

description: Library name: TMA1A__033


title: p53_PBS_M1_ROI-032_TMA1A

description: Library name: TMA1A__032


title: p53_PBS_M1_ROI-031_TMA1A

description: Library name: TMA1A__031


title: p53_PBS_M1_ROI-030_TMA1A

description: Library name: TMA1A__030


title: p53_PBS_M1_ROI-029_TMA1A

description: Library name: TMA1A__029


title: p53_PARPi_M6_ROI-026_TMA1A

description: Library name: TMA1A__026


title: p53_PBS_M1_ROI-028_TMA1A

description: Library name: TMA1A__028


title: p53_PBS_M1_ROI-025_TMA1A

description: Library name: TMA1A__025


title: p53_PBS_M1_ROI-024_TMA1A

description: Library name: TMA1A__024


title: p53_PBS_M1_ROI-023_TMA1A

description: Library name: TMA1A__023


title: p53_PBS_M1_ROI-021_TMA1A

description: Library name: TMA1A__021


title: WGBS SetDB1 KO serum-to-2i mouse ESCs, day3

city: Nijmegen

first: Nick

last: Bovee

state: Gelderland

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: RIMLS

description:
Library name: Serum-2i_SetDB1O_d3
day3

library_source: genomic

data_processing:
All WGBS analyses were performed using the Mus musculus NCBI GRCm39 genome assembly (mm39). The WGBS data, including FASTQ and BED, have been deposited in this entry. Paired-end reads from the FASTQ files were trimmed using Trim Galore with the flags --paired --trim1. The trimmed reads were then aligned to the reference genome using the Bismark package in combination with Bowtie 2 (Krueger, F., & Andrews, S. R. (2011). Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. bioinformatics, 27(11), 1571-1572.) with the flag -n 1 --bowtie2. BAM files were deduplicated using Deduplicate Bismark with the flag -p. Cytosine methylation levels were calculated using the Bismark Methylation Extractor with the flags -p --no_overlap and applying a minimum read coverage threshold of ≥5. Methylation levels of genomic features were determined by intersecting them with genomic coordinates of the mm39 reference genome.
Assembly: NCBI GRCm39 genome assembly (mm39)
Supplementary files format and content: BED

molecule: genomic DNA

source_name: SetDB1 CKO mouse ESCs, Matsui et al. (2010)

growth_protocol: ESCs were maintained at 37 °C, 5% CO2 and routinely tested negative for mycoplasma. Serum ESCs were cultured on 0.1% gelatin-coated culture plates in DMEM-Glutamax basal medium (Gibco) supplemented with 0.1mM non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco), 0.1mM 2-mercaptoethanol, 5·105U leukemia inhibitory factor (LIF) (home-made), 10% fetal bovine serum and 25U/ml Penstrep (Gibco). 2i ESCs were maintained on 0.2% gelatin-coated culture plates in Ndiff 227 medium (Takara) supplemented with 1uM MEK inhibitor PD0325901, 3uM GSK3 inhibitor CHIR99021, together known as ‘2i’, 5·105U leukemia inhibitory factor (LIF) (home-made) and 25U/ml Penstrep (Gibco).

extract_protocol:
DNA from ESCs was isolated using either (i) a Cell Culture DNA Midi Kit (Qiagen), following the manufacturer’s instructions, or (ii) a standard protocol for phenol/chloroform extraction with ethanol precipitation. WGBS on isolated DNA was conducted as previously described: Kulis, M., Heath, S., Bibikova, M., Queirós, A. C., Navarro, A., Clot, G., ... & Martín-Subero, J. I. (2012). Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nature genetics, 44(11), 1236-1242.
Libraries were sequenced on an Illumina HiSeq 2000 platform in paired-end mode (2x100 nucleotides).

treatment_protocol: Addition of 4-OHT (4-hydroxytamoxifen) for 4 days, or DMSO (control)

tag: cell line

tag: cell type

value: Mouse pluripotency stem cells

value: SetDB1 CKO


title: p53_PBS_M1_ROI-022_TMA1A

description: Library name: TMA1A__022

value: A


title: p53_PBS_M1_ROI-019_TMA1A

description: Library name: TMA1A__019


title: p53_PARPi_M6_ROI-018_TMA1A

description: Library name: TMA1A__018


title: Ovarian cancer cell line with shRNA for RelB, spheroid growth condition, replicate 3

city: San Diego

first: Mikella

last: Robinson

address: 5500 Campanile Drive

institute: San Diego State University

description: Library name: Spheroid3_shRelB

data_processing:
Adapter trimming: Cutadapt
Alignment: STAR
Normalization: RSEM - CPM - TMM
Assembly: Genome_build: hg38 (GRCh38)
Supplementary files format and content: RSEM counts for each sample
Supplementary files format and content: Tab-delimited normalized RSEM-CPM-TMM counts matrix with all samples

organism: Homo sapiens

source_name: ovarian serous carcinoma

growth_protocol: Adherent OV90 cells were grown in RPMI 1640 medium supplemented with Tetracycline-free Fetal Calf Serum (10%) and 1% penicillin/streptomycin. Spheroids were grown in ultra-low attachment plates or flasks in DMEM-F12 media supplemented with 1% KnockOut serum replacement, 1% penicillin/streptomycin, 0.1% insulin-transferrin-selenium, and 0.4% bovine serum albumin and growth factors EGF 20 ng/mL and FGF 10 ng/mL.

extract_protocol:
Total RNA was collected from cells according to the manufacturer's instructions using the RNeasy Mini Kit (Qiagen 74104).
Libraries were prepared according to the manufacturer's instructions using TruSeq Stranded mRNA library kit (Illumina 20020594).

treatment_protocol: 6 days growth in each condition, fresh medium was supplemented after 72 hours.

value: ovarian serous carcinoma

value: ovarian cancer cell line

value: shRelB

tag: growth condition

value: Spheroid


title: p53_PBS_M2_ROI-015_TMA1A

description: Library name: TMA1A__015

value: tumor


title: p53_PBS_M1_ROI-017_TMA1A

description: Library name: TMA1A__017


title: KS44

city: New Haven

first: Jeffrey

last: Ishizuka

state: CT

address: 300 George Street

institute: Yale University

description: Library name: KS44

data_processing:
RNA-seq reads were preprocessed with fastp for adaptor trimming. The trimmed reads were first aligned to the human reference genome (GRCh38.p14) using STAR and the aligned reads were quantified with Salmon. The unmapped reads were then extracted and quantified against the KSHV reference transcriptome derived from NC_009333 using Salmon. Transcript abundance estimates in transcripts per million (TPM) and estimated read counts were generated for both human and KSHV alignments.
Assembly: GRCh38.p14, NC_009333
Supplementary files format and content: Clinical metadata annotations for each samples
Supplementary files format and content: Salmon quantification summarized in csv files for counts and/or TPM for KSHV and human genes

source_name: Tumor

extract_protocol:
RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue using the FormaPure XL RNA Kit (Beckman Coulter) according to the manufacturer’s protocol. RNA quantity and purity were assessed by micro-volume spectrophotometry (NanoDrop 2000, Thermo Scientific), and RNA integrity was evaluated using the Agilent 2100 Bioanalyzer.
RNA-seq libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (Roche/KAPA Biosystems). Briefly, ribosomal RNA was depleted by hybridization to complementary DNA oligonucleotides followed by RNase H and DNase treatment. The remaining RNA was fragmented using heat and magnesium, followed by first-strand cDNA synthesis using random priming and second-strand synthesis incorporating dUTP to enable strand-specific sequencing. Adapters were ligated, and libraries were PCR-amplified. Library quality and fragment size distribution were assessed using the Agilent Bioanalyzer or LabChip GX, and libraries were quantified by qPCR.

value: Tumor

tag: disease state

value: Kaposi sarcoma (KS)


title: KS45

description: Library name: KS45


title: KS43

description: Library name: KS43


title: gcl control, biological rep2

value: granule cell layer


title: p53_PBS_M1_ROI-013_TMA1A

description: Library name: TMA1A__013


title: p53_PBS_M1_ROI-014_TMA1A

description: Library name: TMA1A__014

value: low


title: KS41

description: Library name: KS41


title: p53_PBS_M1_ROI-012_TMA1A

description: Library name: TMA1A__012

value: high


title: KS42

description: Library name: KS42


title: KS40

description: Library name: KS40


title: p53_PBS_M1_ROI-011_TMA1A

description: Library name: TMA1A__011


title: KS38

description: Library name: KS38


title: KS39

description: Library name: KS39


title: p53_PBS_M1_ROI-009_TMA1A

description: Library name: TMA1A__009

value: medium


title: p53_PBS_M1_ROI-007_TMA1A

description: Library name: TMA1A__007

value: PBS


title: KS36

description: Library name: KS36


title: p53_PBS_M1_ROI-006_TMA1A

description: Library name: TMA1A__006


title: KS35

description: Library name: KS35


title: p53_PBS_M1_ROI-005_TMA1A

description: Library name: TMA1A__005


title: KS34

description: Library name: KS34


title: p53_PBS_M1_ROI-002_TMA1A

description: Library name: TMA1A__002


title: p53_PBS_M1_ROI-001_TMA1A

description: Library name: TMA1A__001


title: KS33

description: Library name: KS33


title: NPCs, liver, C.sinensis 16 wpi, TCR, Rep2

city: Shanghai

first: Jiashun

last: Li

address: 280 S. Chongqing Rd

department: Department of Immunology and Microbiology

country: China

institute: Shanghai Jiao Tong University School of Medicine

description:
Library name: Sample 16
10x Genomics

data_processing:
Demultiplexing, barcode processing and gene-count matrix generation were performed with Cell Ranger 6.0.1 (10x Genomics, default parameters). Demultiplexing, TCR contig assembly and annotation were performed with Cell Ranger 6.0.1 (10x Genomics, default parameters).
Assembly: mouse mm10
Assembly: vdj_GRCm38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: TCR-Seq

molecule: polyA RNA

source_name: liver

extract_protocol:
Liver dissociation was performed by Liver Dissociation Kit (Miltenyi Biotec, 130-105-807) according to the manufacturer’s instructions. Then the liver single cell suspension was subjected to density centrifugation using 30% Histodenz-HBSS (Sigma-Aldrich, D2158) gradient centrifugation as described. In brief, suspended the cells with 30% Histodenz, slowly added some HBSS on it and centrifuged at 1400 g for 20 min at 4 °C without braking. Cells at the interface were enriched liver non-parenchymal cells (NPCs).
Libraries were prepared with the 10x Genomics Chromium Single Cell 5′ Gene Expression chemistry following the manufacturer’s user guide. Cells were encapsulated in GEMs, where poly-A RNA was reverse-transcribed to barcoded cDNA. Barcoded cDNA was purified, PCR-amplified, size-selected with SPRIselect, and finalized as paired-end sequencing libraries. T cell receptor libraries were constructed with the 10x Genomics Chromium Single Cell V(D)J chemistry according to the official protocol. Barcoded full-length cDNA generated in GEMs underwent two rounds of targeted PCR to enrich TCR variable regions, followed by purification and indexing to yield paired-end sequencing libraries.

treatment_protocol: Clonorchis sinensis infection

value: liver

value: non-parenchymal cell

tag: infection

value: C.sinensis 16 wpi


title: KS31

description: Library name: KS31


title: KS32

description: Library name: KS32


title: NPCs, liver, C.sinensis 16 wpi, TCR, Rep1

description:
Library name: Sample 15
10x Genomics


title: KS30

description: Library name: KS30


title: NPCs, liver, C.sinensis 6 wpi, TCR, Rep3

description:
Library name: Sample 14
10x Genomics

value: C.sinensis 6 wpi


title: KS29

description: Library name: KS29


title: NPCs, liver, C.sinensis 6 wpi, TCR, Rep2

description:
Library name: Sample 13
10x Genomics


title: KS28

description: Library name: KS28


title: NPCs, liver, C.sinensis 6 wpi, TCR, Rep1

description:
Library name: Sample 12
10x Genomics


title: KS27

description: Library name: KS27


title: NPCs, liver, uninfected, TCR, Rep2

description:
Library name: Sample 10
10x Genomics

value: uninfected


title: KS24

description: Library name: KS24


title: NPCs, liver, C.sinensis 16 wpi, GEX, Rep2

description:
Library name: Sample 8
10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing and gene-count matrix generation were performed with Cell Ranger 6.0.1 (10x Genomics, default parameters). Demultiplexing, TCR contig assembly and annotation were performed with Cell Ranger 6.0.1 (10x Genomics, default parameters).
Assembly: mouse mm10
Assembly: vdj_GRCm38
Supplementary files format and content: Tab-separated values files and matrix files


title: KS23

description: Library name: KS23


title: KS22

description: Library name: KS22


title: NPCs, liver, uninfected, TCR, Rep1

description:
Library name: Sample 9
10x Genomics


title: NPCs, liver, C.sinensis 16 wpi, GEX, Rep1

description:
Library name: Sample 7
10x Genomics


title: NPCs, liver, C.sinensis 6 wpi, GEX, Rep3

description:
Library name: Sample 6
10x Genomics


title: KS21

description: Library name: KS21


title: NPCs, liver, C.sinensis 6 wpi, GEX, Rep1

description:
Library name: Sample 4
10x Genomics


title: KS19

description: Library name: KS19


title: NPCs, liver, uninfected, GEX, Rep3

description:
Library name: Sample 3
10x Genomics


title: KS18

description: Library name: KS18


title: NPCs, liver, uninfected, GEX, Rep2

description:
Library name: Sample 2
10x Genomics


title: KS17

description: Library name: KS17


title: KS16

description: Library name: KS16


title: KS14

description: Library name: KS14


title: mESCs, LIF HP, rep2

city: Bristol

first: Lucia

last: Marucci

state: UK

address: University Walk

department: Engineering Mathematics and School of cellular and molecular biology.

country: United Kingdom

institute: University of Bristol

description: Library name: Sample 20

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw counts

growth_protocol: Cell lines were maintained in Ndiff227 basal media supplemented with CHIR99021 3uM and PD03259011uM for 1 week and then at each passagge we adopted a regimen of alternating drug administration and withdrawal in the basal medium (NDiff) with CH, PD and LIF

extract_protocol:
RNeasy Plus Mini Kit from Qiagen
Libraries were prepared from 125 ng of total RNA using mRNA-seq research grade sequencing service (Next Generation Diagnostics srl)

value: Mouse embryionic stem cells

value: LIF HP

value: pluripotency maintainance


title: mESCs, LIF HP, rep1

description: Library name: Sample 19


title: mESCs, LIF HP, rep3

description: Library name: Sample 21


title: KS13

description: Library name: KS13


title: mESCs, CH+LIF HP, rep3

description: Library name: Sample 18

value: CH+LIF HP


title: mESCs, CH+LIF HP, rep2

description: Library name: Sample 17


title: KS10

description: Library name: KS10


title: KS09

description: Library name: KS09


title: mESCs, CH+LIF HP, rep1

description: Library name: Sample 16


title: KS08

description: Library name: KS08


title: mESCs, 2i+LIF HP, rep2

description: Library name: Sample 14

value: 2i+LIF HP


title: KS07

description: Library name: KS07

value: Tumor


title: mESCs, 2i+LIF HP, rep1

description: Library name: Sample 13


title: mESCs, LIF LP, rep3

description: Library name: Sample 12

value: LIF LP


title: KS04

description: Library name: KS04

value: Kaposi sarcoma (KS)


title: mESCs, 2i+LIF HP, rep3

description: Library name: Sample 15


title: KS03

description: Library name: KS03


title: mESCs, LIF LP, rep2

description: Library name: Sample 11


title: mESCs, LIF LP, rep1

description: Library name: Sample 10


title: mESCs, CH+LIF LP, rep3

description: Library name: Sample 9

value: CH+LIF LP


title: KS01

description: Library name: KS01


title: mESCs, CH+LIF LP, rep2

description: Library name: Sample 8


title: mESCs, CH+LIF LP, rep1

description: Library name: Sample 7


title: Whole skin, distant photoprotected, library 2

city: Woolloongabba

first: Katie

middle: June

last: Lee

state: QLD

address: 37 Kent St

department: Frazer Institute

country: Australia

institute: The University of Queensland

description:
Library name: Distant Library 2
10x Chromium Flex with Fixed RNA Profiling

data_processing:
bcl files were converted into fastq files with cellranger v7.1.0 and bcl2fastq2 v2.20
Quality control and analysis was performed with Seurat v4.4.0. Results from each pool were filtered to exclude cells with <100 and >2500 genes per cell, and mtDNA transcripts >5%. Data from each pool was then merged with merge function and transformed with SCTransform v0.4.1.
Assembly: Human hg38
Supplementary files format and content: scar.adjacent.rds: RDS file containing data for scar-adjacent biopsy pooled cells
Supplementary files format and content: proximal.rds: RDS file containg data for proximal biospy pooled cells
Supplementary files format and content: distant.photoprotected.rds: RDS file containing data for distant photoprotected biopsy pooled cells
Supplementary files format and content: Nonlesional.skin.all.sites.rds: RDS file with all biopsies, merged and SCTransformed

source_name: skin

extract_protocol:
Cryopreserved tissues were dissociated into a fixed, single cell suspension with a GEM-X Flex Sample Preparation Kit (10x Genomics, Pleasanton, CA, USA) according to the 10x Genomics Demonstrated Protocol Tissue Fixation and Dissociation for Chromium Fixed RNA Profiling (Revision A CG000553). Briefly, the sample was minced finely and fixed overnight at 4°C in 4% paraformaldehyde, then dissociated with Liberase TH (Roche, Basel, Switzerland) and a gentleMACS Octo Dissociator (Miltenyi Biotec, Bergish Gladbach, Germany) according to the manufacturer’s instructions. The manual dissociation protocol was modified to include two cycles of: 50rpm for 20 minutes at 37°C, 2000rpm clockwise for 30 seconds at 37°C, and 2000rpm anticlockwise for 30 seconds at 37°C, due to the difficulty of thoroughly dissociating skin samples. Cell suspensions were passed through a 70uM filter and stored in Enhancer (supplied in 10x Genomics kit) and glycerol at -80°C. Due to low cell recovery, samples were pooled based on biopsy site to produce  a scar-adjacent pool, a proximal pool and a distant photoprotected pool.
GEM and library generation was performed with the 10x Genomics Chromium Flex Gene Expression chemistry with a Fixed RNA Profiling Reagent Kit following the manufacturer’s Kit User Guide (Revision D CG000527). Briefly, probes were hybridised to the fixed single cells overnight at 42°C, then loaded to a Chromium Next GEM Chip Q with gel beads, partitioning oil and 50% glycerol and run on a Chromium X instrument to generate GEMs. GEMs were incubated in a thermal cycler according to the User Guide, then recovery, pre-amplification PCR and cleanup with SPRIselect beads was performed. Sample index PCR cycles were determined with qPCR, gene expression libraries were generated, and quality control performed with an Agilent Bioanalyzer High Sensitivity Chip. Sequencing was performed on the Illlumina NovaSeq platform.

value: skin

value: distant photoprotected


title: TMA2_samples

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

description: Library name: TMA2

data_processing:
Sequencing was performed on an Illumina HiSeq 4000 platform using a paired-end 2 × 150 bp configuration. Libraries were multiplexed and sequenced by a commercial sequencing provider.
Images were manually aligned using the Loupe browser (version 8.1.2) from 10X Genomics.  FASTQ files, images, and manual alignment files were processed by Space Ranger (version 3.1.2) to generate matrix files and all other files necessary for downstream analysis.
Downstream analysis was performed using Seurat (version 5.2.0).  All samples were read into Seurat and merged into a single dataset.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefacors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.parquet: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: RDS: processed Seurat object
Library strategy: Spatial Transcriptomics

source_name: smooth muscle

growth_protocol: Human myometrial cells (Myo-hTERT and primary human myometrial cells) were cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic at 37°C in a humidified incubator with 5% CO₂. Cells were passaged at ~90% confluence. Stable cell lines expressing MnSOD wild-type (K68) or acetylation-mimetic mutant (K68Q) were generated via lentiviral transduction followed by puromycin selection and clonal expansion. For in vivo studies, cells were expanded in vitro prior to implantation. Cell line xenografts: Myo-hTERT cells (5 × 10⁶ cells) were resuspended in Matrigel and injected subcutaneously into bilateral flanks of female immunodeficient NOD mice (6–8 weeks old). Primary cell xenografts: Human primary myometrial cells were embedded in type I collagen and grafted under the renal capsule of ovariectomized NOD/SCID mice supplemented with estradiol and progesterone pellets. Mice were maintained under standard conditions and monitored throughout the study.

extract_protocol:
For in vitro samples, total RNA was extracted directly from cultured cells. For in vivo samples, xenograft tissues were excised at endpoint, and regions of interest were identified. Tumor or graft tissues were either processed fresh or formalin-fixed and paraffin-embedded (FFPE), depending on downstream application. Total RNA was extracted using the Qiagen miRNeasy Mini Kit (for fresh samples) or appropriate FFPE RNA extraction kits following manufacturer protocols. RNA concentration was measured using Qubit 2.0 Fluorometer, and RNA integrity was assessed using Agilent TapeStation 4200. Samples with RNA integrity number (RIN) ≥ 9 (for fresh RNA) or acceptable DV200 metrics (for FFPE samples) were used for library preparation.
RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina. Briefly mRNA was enriched using oligo(dT) beads. RNA was fragmented at 94°C for 15 minutes. First- and second-strand cDNA synthesis was performed. cDNA fragments were end-repaired, A-tailed, and adapter-ligated. Libraries were PCR-amplified and indexed Library quality was assessed using Agilent TapeStation and quantified using Qubit and qPCR.

treatment_protocol: Oxidative stress was induced using two complementary approaches. In vitro: Cells were treated with paraquat (PQ, 100 μM) to induce oxidative stress. In vivo Mice bearing xenografts were provided PQ in drinking water (10 mg/kg/day) to induce chronic oxidative stress. Control animals received standard drinking water. Xenografts were harvested at ~40 weeks for subcutaneous cell line xenografts and ~12–16 weeks for renal capsule primary cell xenografts

value: smooth muscle


title: TMA3_samples

description: Library name: TMA3


title: Whole skin, distant photoprotected, library 1

description:
Library name: Distant Library 1
10x Chromium Flex with Fixed RNA Profiling


title: mESCs, 2i+LIF LP, rep2

description: Library name: Sample 5

value: 2i+LIF LP


title: Whole skin, proximal

description:
Library name: Proximal library 1
10x Chromium Flex with Fixed RNA Profiling

value: proximal


title: mESCs, 2i+LIF PO, rep3

description: Library name: Sample 3

value: 2i+LIF PO


title: Whole skin, scar-adjacent

description:
Library name: Scar Library 1
10x Chromium Flex with Fixed RNA Profiling

value: scar-adjacent


title: mESCs, 2i+LIF PO, rep2

description: Library name: Sample 2


title: mESCs, 2i+LIF PO, rep1

description: Library name: Sample 1


title: Seborrhoeic keratosis, batch 3

city: WOOLLOONGABBA

first: Mitchell

middle: S

last: Stark

description: Library name: Slide2_A1

data_processing:
The data was processed with Space Ranger version 2.0.1 from 10x Genomics.
Assembly: GRCh38
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials
Supplementary files format and content: barcodes.tsv.gz: spatial barcodes
Supplementary files format and content: cytassist_image.tiff: visium CytAssist image
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression matrix
Supplementary files format and content: scalefactors_json.json: scale factors
Supplementary files format and content: tissue_hires_image.png: high resolution tissue image
Supplementary files format and content: tissue_lowres_image.png: low resolution tissue image
Supplementary files format and content: tissue_positions.csv: barcodes and spatial coordinates
Library strategy: Spatial Transcriptomics

source_name: Skin

extract_protocol:
The tissue sections used for the project were obtained from skin lesions that had been surgically excised, formalin-fixed and paraffin-embedded.
Samples were processed on the 10x Genomics Visium CytAssist platform in accordance with the manufacturer’s protocols and sequencing libraries were prepared and sequenced according to the standard 10x Genomics library preparation and sequencing guidelines.

value: Skin


title: CITE-Seq, Myb KO T-cells, CSP

city: Melbourne

first: Nikita

last: Potemkin

state: Vic

address: 792 Elizabeth St

department: The Peter Doherty Institute for Infection and Immunity

institute: University of Melbourne

description: Library name: Myb_CSP

library_source: other

data_processing:
CITE-seq and multiome files were demultiplexed using Cellranger mkfastq
Demultiplexed data were processed using the Cellranger Multi pipeline
Assembly: mm10
Supplementary files format and content: Cellranger multi output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig.fastq
Library strategy: CITE-seq

molecule: protein

source_name: spleen

extract_protocol:
PD1+CD4+ T cells were sorted and hashtaged in accordance with the manusfacturers' protocol (Biolegend)
Library construction was performed in accordance with the manufacturer’s instructions (single cell 5’ v2 protocol, 10x Genomics)

value: spleen

value: CD4 T cells

value: Mybfl/fl, Mybfl/flCd4cre

value: infected with LCMV Docile


title: Seborrhoeic keratosis, batch 4

description: Library name: Slide2_B1


title: Seborrhoeic keratosis, batch 1

description: Library name: Slide1_A1


title: NSCLC, Patient 16, Spatial Transcriptomics (Visium)

first: Arjun

last: Raman

address: 900 E. 57th Street, KCBD rm. 4126

department: Department of Pathology and Duchossois Family Institute

institute: University of Chicago

description: Library name: NSCLC_P16

data_processing:
FASTQ files were processed using Space Ranger 2.0.0 with GRCh38 reference in the manual alignment mode. Filtered gene-barcode matrices from Space Ranger output were created using default settings and used for downstream analyses.
Assembly: GRCh38
Supplementary files format and content: *_filtered_feature_bc_matrix.tar.gz contains gene expression matrices produced by spaceranger : barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz
Supplementary files format and content: *_spatial.tar.gz contains mainly images : aligned_fiducials, detected_tissue_image, scalefactors_json.json, tissue_hires_image, tissue_lowres_image and tissue_positions_list
Supplementary files format and content: *_filtered_feature_bc_matrix.h5 is a compressed binary format file to access gene expression matrices produced by spaceranger.
Library strategy: Spatial Transcriptomics

source_name: NSCLC tumor

extract_protocol:
Selected formalin-fixed paraffin-embedded (FFPE) tumor samples were identified and used for cutting five-mm µm-thin FFPE sections to be mounted on standard glass slides. Extraction, whole transcriptome probe hybridization, release, and capture were performed according to 10X Genomics Visium protocols CG000520 and CG000495.
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium protocol CG000495.

value: NSCLC tumor

tag: Stage

tag: biopsy site

value: pleura

tag: treatment regimen

value: ipi/nivo

tag: treatment response

value: NR


title: CITE-Seq, Eomes KO T-cells, CSP

description: Library name: Eomes_CSP

tag: tissue

value: Cd4Cre, Eomesfl/flCd4cre


title: NSCLC, Patient 15, Spatial Transcriptomics (Visium)

description: Library name: NSCLC_P15

value: lung

value: Nivolumab


title: CITE-Seq, Eomes KO T-cells, GEX

description: Library name: Eomes_GEX


title: NSCLC, Patient 14, Spatial Transcriptomics (Visium)

description: Library name: NSCLC_P14

value: carbo/gem/pembro


title: mESCs, 2i+LIF LP, rep1

description: Library name: Sample 4

value: Mouse embryionic stem cells

value: 2i+LIF LP

value: pluripotency maintainance


title: CITE-Seq, Eomes KO T-cells, VDJ

description: Library name: Eomes_VDJ


title: NSCLC, Patient 13, Spatial Transcriptomics (Visium)

description: Library name: NSCLC_P13

value: cheek

value: carbo/pem/pembro


title: CITE-Seq, Cd4 T-cells, GEX

description: Library name: CD4_GEX

source_name: spleen and LN

value: spleen and LN

value: wildtype

value: infected with either LCMV Armstrong or LCMV Docile


title: NSCLC, Patient 12, Spatial Transcriptomics (Visium)

description: Library name: NSCLC_P12

value: R


title: CITE-Seq, Cd4 T-cells, CSP

description: Library name: CD4_CSP

value: CD4 T cells


title: Seborrhoeic keratosis, batch 2

description: Library name: Slide1_B1

value: Skin


title: CITE-Seq, Myb KO T-cells, GEX

description: Library name: Myb_GEX

value: spleen

value: Mybfl/fl, Mybfl/flCd4cre

value: infected with LCMV Docile


title: NSCLC, Patient 11, Spatial Transcriptomics (Visium)

description: Library name: NSCLC_P11

value: NSCLC tumor

value: brain

value: ipi/nivo


title: CITE-Seq, Cd4 T-cells, VDJ

description: Library name: CD4_VDJ


title: CITE-Seq, Myb KO T-cells, VDJ

description: Library name: Myb_VDJ


title: NSCLC, Patient 10, Spatial Transcriptomics (Visium)

description: Library name: NSCLC_P10

value: carbo/taxol/pembro


title: C. difficile ATCC43255 prdB mutant 24 hours post infection Mouse 8

city: Boston

first: Lynn

last: Bry

state: MA

address: 75 Francis St.

department: Pathology

institute: Brigham and Women's Hospital

data_processing:
Bowtie2 was used to align filtered and trimmed reads to a library consisting of C. diffcile and Mus musculus DNA sequences for all reactions to ensure specific alignments to C. difficile gene features.
Reads were assigned to features in alignments using HTSeq. Reads overlapping multiple features were assigned to both to account for polycistronic RNAs.
Reads were also analyzed with Kraken2 to check for contaminants. Note - mouse chow contains RNAs which are present in caecal contents.
A 10 read average cutoff was applied. C. difficile genomic features were analyzed.
DESeq2 was used to normalize read counts and for subsequent differential expression analyses.
Assembly: C. difficile ATCC 43255 https://www.bv-brc.org/view/Genome/1496.5150, M. musculus GRCm39 https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001635.27/
Supplementary files format and content: HTSeq CDS read counts per gene.

source_name: Mouse caecal contents

growth_protocol: 6-7 week-old male and female gnotobiotic (germ-free) mice were inoculated by gavage with10^3 C. difficile ATCC43255 wild-type or prdB mutant spores.

extract_protocol:
Mice were sacrificed at the indicated timepoint and dissected. Cecal contents were immediately cryogenically stored for RNA extraction.
Purified RNAs were rRNA depleted and eukaryotic (mouse) poly-A mrRNA depleted. Illumina NovaSeq S4-300 with paired-end 150 nucleotide runs were performed.

value: Mouse caecal contents

tag: agent


title: KS37

description: Library name: KS37

value: Tumor

value: Kaposi sarcoma (KS)


title: p53_PBS_M1_ROI-008_TMA1A

description: Library name: TMA1A__008

value: tumor

tag: mouse id

tag: slide id

tag: region of_interest

value: PBS

value: low

value: A


title: NSCLC, Patient 9, Spatial Transcriptomics (Visium)

description: Library name: NSCLC_P9

value: carbo/pem/pembro

value: R


title: C. difficile ATCC43255 prdB mutant 24 hours post infection Mouse 7


title: NSCLC, Patient 8, Spatial Transcriptomics (Visium)

description: Library name: NSCLC_P8

value: lung

value: pembro


title: C. difficile ATCC43255 prdB mutant 24 hours post infection Mouse 6


title: NSCLC, Patient 7, Spatial Transcriptomics (Visium)

description: Library name: NSCLC_P7


title: C. difficile ATCC43255 prdB mutant 24 hours post infection Mouse 4


title: NSCLC, Patient 5, Spatial Transcriptomics (Visium)

description: Library name: NSCLC_P5


title: C. difficile ATCC43255 prdB mutant 24 hours post infection Mouse 3


title: NSCLC, Patient 6, Spatial Transcriptomics (Visium)

description: Library name: NSCLC_P6


title: NPCs, liver, uninfected, TCR, Rep3

description:
Library name: Sample 11
10x Genomics

value: liver

value: non-parenchymal cell

value: uninfected


title: C. difficile ATCC43255 prdB mutant 24 hours post infection Mouse 2


title: KS26

description: Library name: KS26


title: NSCLC, Patient 4, Spatial Transcriptomics (Visium)

description: Library name: NSCLC_P4

value: NSCLC tumor

value: brain

value: carbo/taxol/bev/atezo


title: KS25

description: Library name: KS25


title: C. difficile ATCC43255 prdB mutant 24 hours post infection Mouse 1

value: Mouse caecal contents


title: KS20

description: Library name: KS20

value: Tumor


title: NSCLC, Patient 3, Spatial Transcriptomics (Visium)

description: Library name: NSCLC_P3

value: lymph node


title: C. difficile ATCC43255 prdB mutant 20 hours post infection Mouse 8


title: NPCs, liver, C.sinensis 6 wpi, GEX, Rep2

description:
Library name: Sample 5
10x Genomics

value: C.sinensis 6 wpi


title: C. difficile ATCC43255 prdB mutant 20 hours post infection Mouse 7


title: NSCLC, Patient 1, Spatial Transcriptomics (Visium)

description:
Library name: NSCLC_P1
Column names for 'sample_metadata.csv': (1) TumorType = Broad tumor type category, (2) Stage = Clinical stage at time of sample collection, (3) ID_Patient = Deidentified patient ID for study cohort, (4) ID_Sample = Deidentified sampled ID for study cohort, (5) Bx_Tissue = Location of sample collection, (6) Diagnosis_Subtype = Diagnosis subtype, (7) PDL1 = PDL1 tumor proportion score, (8) PDL1_Cat = PDL1 category, (9) OncoPanelVersion = Oncoplus_Oncoscreen_UCHgenomicspanel_version, (10) EGFR_nonclassical = EGFR nonclassical somatic mutation present, (11) KRAS_G12C = KRAS G12C somatic mutation present, (12) BRAF = BRAF somatic mutation present, (13) TP53 = TP53 somatic mutation present, (14) STK11 = STK11 nonclassical somatic mutation present, (15) PreSample_Treatment = Patient treated prior to sample collection, (16) PostSample_Treatment = Treatment regimen following sample collection, (17) Tx_End_Reason = Reason for treatment regimen stopping, (18) Tx_Duration_Months = Treatment regimen duration in months, (19) Tx_Response = Treatment Response at 6 months following treatment start, (20) PFS_Months = Progression free survival in months, (21) COO_Hans = DLBCL cell of origin by Hans algorithm, (22) PDL1_FISH = PDL1 FISH status, (23) PDL1_Hscore = PDL1 H-score

value: ipi/nivo


title: NSCLC, Patient 2, Spatial Transcriptomics (Visium)

description: Library name: NSCLC_P2


title: C. difficile ATCC43255 prdB mutant 20 hours post infection Mouse 4


title: C. difficile ATCC43255 prdB mutant 20 hours post infection Mouse 5


title: MDAMB231_gCTRL_90nM_48h_rep2

city: Kyoto

first: Kosuke

last: Yusa

state: Kyoto

address: 53 Shogoin Kawaharacho, Sakyo-ku

department: Institue for Life and Medical Sciences

country: Japan

institute: Kyoto University

description: Library name: MDAMB231_gCTRL_90nM_48h_rep2

data_processing:
Sequencing reads were mapped to reference human genome hg38 using HISAT2 (v2.2.1), and converted to bam format using samtools(v1.14)
reads assigned to genes were counted using featureCounts (v2.0.3)
Differentially expressed genes were analyzed using DESeq2 (v1.38.2) with filtering out genes with low expression (average read counts in all conditions are less than 1)
Assembly: hg38
Supplementary files format and content: tab-delimited text

growth_protocol: OVCAR8 cells were cultured in RMPI1640 supplemented with 10% FBS. MDA-MB-231 cells were cultured in DMEM/F12 supplemented with 10% FBS.

extract_protocol:
After PBS wash twice, cells were directly lysed on 10-cm dish with Buffer RLT. Lysate was collected and total RNA was extracted using the RNeasy Mini kit (Qiagen) according to the manufacturer’s protocol.
RNA-seq libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

treatment_protocol: 2 million cells were seeded to a 10-cm dish a day before treatment. On the following day, CTX-439 was added at the indicated concentration and incubated for the indicated duration.

value: Breast cancer cell line

value: CDK10 wildtype

tag: treatment

value: CTX-439 90nM for 48h


title: MDAMB231_gCTRL_90nM_48h_rep1

description: Library name: MDAMB231_gCTRL_90nM_48h_rep1


title: C. difficile ATCC43255 prdB mutant 20 hours post infection Mouse 3


title: KS15

description: Library name: KS15

value: Kaposi sarcoma (KS)


title: MDAMB231_gCTRL_90nM_24h_rep1

description: Library name: MDAMB231_gCTRL_90nM_24h_rep1

value: CTX-439 90nM for 24h


title: C. difficile ATCC43255 prdB mutant 20 hours post infection Mouse 1


title: NPCs, liver, uninfected, GEX, Rep1

description:
Library name: Sample 1
10x Genomics


title: MDAMB231_gCTRL_90nM_6h_rep2

description: Library name: MDAMB231_gCTRL_90nM_6h_rep2

value: CTX-439 90nM for 6h


title: C. difficile WT ATCC43255 24 hours post infection Mouse 8


title: MDAMB231_gCTRL_90nM_6h_rep1

description: Library name: MDAMB231_gCTRL_90nM_6h_rep1


title: MDAMB231_gCTRL_0nM_0h_rep2

description: Library name: MDAMB231_gCTRL_0nM_0h_rep2


title: MDAMB231_gCTRL_0nM_0h_rep1

description: Library name: MDAMB231_gCTRL_0nM_0h_rep1


title: C. difficile WT ATCC43255 24 hours post infection Mouse 4


title: C. difficile WT ATCC43255 24 hours post infection Mouse 5


title: MDAMB231_gCDK10-1_90nM_48h_rep2

description: Library name: MDAMB231_gCDK10-1_90nM_48h_rep2

value: CDK10 knockout


title: C. difficile WT ATCC43255 24 hours post infection Mouse 3


title: MDAMB231_gCDK10-1_90nM_48h_rep1

description: Library name: MDAMB231_gCDK10-1_90nM_48h_rep1


title: C. difficile WT ATCC43255 20 hours post infection Mouse 8


title: MDAMB231_gCDK10-1_90nM_24h_rep2

description: Library name: MDAMB231_gCDK10-1_90nM_24h_rep2


title: C. difficile WT ATCC43255 20 hours post infection Mouse 7


title: MDAMB231_gCDK10-1_90nM_6h_rep2

description: Library name: MDAMB231_gCDK10-1_90nM_6h_rep2


title: C. difficile WT ATCC43255 20 hours post infection Mouse 6


title: MDAMB231_gCDK10-1_90nM_24h_rep1

description: Library name: MDAMB231_gCDK10-1_90nM_24h_rep1


title: MDAMB231_gCDK10-1_90nM_6h_rep1

description: Library name: MDAMB231_gCDK10-1_90nM_6h_rep1


title: C. difficile WT ATCC43255 20 hours post infection Mouse 3


title: MDAMB231_gCDK10-1_0nM_0h_rep2

description: Library name: MDAMB231_gCDK10-1_0nM_0h_rep2


title: C. difficile WT ATCC43255 20 hours post infection Mouse 2


city: OXFORD

first: Liliana

last: Minichiello

address: Department of Pharmacology, University of Oxford, Mansfield Road, University of Oxford

institute: University of Oxford

description: Library name: Dataset_B_Quiescent Neural Stem Cell of the Subventricular Zone

data_processing:
First, raw FASTQ files generated per cell were concatenated, followed by FASTQC (v0.12.1) quality check. Then, we aligned the reads to the GENCODE mouse genome release M37 (GRCm39) using STAR (v2.7.10b). Reads were counted using the featureCounts function from the subread package (v2.1.1) using the GENCODE vM37 primary assembly annotation
Assembly: mm10
Supplementary files format and content: tab deliminited text file includes raw count for each cell from both experiments
Supplementary files format and content: Colnames are names of cells and rownames are gene names

source_name: SVZ/striatal tissue

extract_protocol:
Mice were anaesthetised with pentobarbital and perfused with artificial cerebrospinal fluid in sucrose. The striata were then microdissected, and the tissue was chopped, placed in Accutase (Stem Cell Technologies, 07920) for 30 min at 4˚C, centrifuged for 2 min at 450 g, and the pellet was resuspended in Hibernate A (Brain Bits, HA). The pellet was triturated and crudely filtered using 100 µm and 40 µm cell strainers. A Percoll (Sigma, P1644) density gradient was set up, and the cell suspension was placed on the top layer, followed by centrifugation at 430 g for 5 min at 4˚C. The top layer containing debris was aspirated, and the remaining layers were mixed and placed back into the centrifuge for 5 min at 550 g. The pellet was resuspended in Hibernate A. Cells were counted using LIVE/DEAD viability dye (Thermo Fisher, L34963). The dye was removed by centrifuging the cells for 5 min at 550 g, followed by resuspension in Hibernate A. Cells were then either sorted directly as tdTomato+ (dataset B) or incubated with CD11b_APC antibody (1:400, BioLegend, 101211) for 15 min, to eliminate a microglia signature (dataset A), followed by centrifugation for 5 min at 550 g, and resuspension in Hibernate A. The cells were then sorted as tdTomato+/CD11b- population (dataset A), or all tdTomato+ cells (Dataset B) using the FACSAria II Cell Sorter (BD Biosciences) using a 100 µm nozzle.
Single cells processed by FACS were collected into 96-well plates (Thermo Fisher, AB0800) containing 0.4% Triton + RNase inhibitor (2 µL); dNTPs (10mM; 1µL); Oligo dT30VN (10 µM; 1 µL). The plates were then spun down at 700 g, frozen on dry ice, and stored in -80 ˚C until further processing. Reverse transcription was performed using Superscript II first strand buffer (5x, 2 µL); DTT (100 mM, 0.5 µL); Betaine (5M, 2 µL); MgCl2 (1M, 0.1 µL); RNase inhibitor (40 U/µL, 0.25 µL); TSO (100 µM, 0.1 µL); Superscript II RT (200 U/µL, 0.25 µL); and water (0.8 µL). Then, the cDNA was preamplified using KAPA HiFi HS Ready mix (2x, KAPA Biosystems, KK2601); ISPCR primers (10 µM) and water as per manufacturer instructions. The cDNA was purified using Agincourt Ampure XP beads (Beckman Coulter, A63881). The cDNA-bound beads were washed with 80% ethanol, and the pellet was resuspended in elution buffer (Qiagen, 19086). The beads were then removed by placing the mixture on the magnetic stand, and the eluted cDNA was placed into fresh 96-well plates. The cDNA quality check was performed using Bioanalyzer analysis according to manufacturer instructions (Agilent Technologies). The cells were then tagmented and indexed using the Nexetra XT kit (Illumina, FC-131-1096). Briefly, Tagmentation Buffer (2.5 µL), cDNA (1.25 µL), and Amplicon Tagment Mix (1.25 µL) were added to each well, and the plates were then sealed, vortexed, and spun down, followed by tagmentation at 55 ˚C for 5 min. The tagmentation was stopped by Neutralisation buffer (1.25 µL). The indexing was performed by adding Nextera PCR master mix (3.75 µL), Index 1 primers, and Index 2 primers (1.25 µL each) per well, followed by PCR reaction. The DNA concentration was quantified using the Quant-It PicoGreen system (Thermo Fisher, P7589) as per manufacturer instructions. The samples were denatured using NaOH (0.2M, 5 µL) for 5 min and stopped using Tris-HCl (200 mM).

value: SVZ/striatal tissue

value: WT


title: MDAMB231_gCDK10-1_0nM_0h_rep1

description: Library name: MDAMB231_gCDK10-1_0nM_0h_rep1


title: Dataset_B_Neuroblast

description: Library name: Dataset_B_Neuroblast

value: Neuroblast


title: C. difficile WT ATCC43255 20 hours post infection Mouse 1


title: Dataset_A_Neuroblast

description: Library name: Dataset_A_Neuroblast


title: DSS-BXD-H-3

city: Fuzhou

first: xiuli

last: Zhang

address: No. 1 Qiuyang Road, Minhou Street, Fuzhou City, Fujian Province

institute: Fujian University of Chinese Medicine

description:
Library name: Sample 12
Mice were administered 2.5% DSS for 5 days followed by normal drinking water for 5 days, while simultaneously being given 15.2  g/kg/day of BXD, and this process was repeated for three cycles.

data_processing:
Utilize the bcl2fastq software to perform Base Calling on the original image files from Illumina high-throughput sequencing and convert them into original sequencing reads.
Use the FastQC software to analyze the base quality from 5' to 3' of the sequencing reads and assess the content of A, T, C, and G bases in the sequencing data, evaluating the base type ratio at each position from an overall level.
Utilize the fastp software to filter the raw data, removing reads that do not meet the analysis criteria, in order to obtain clean reads that can be used for subsequent alignment, statistics, and further analysis.
After quality control of the raw sequencing data, clean data is obtained. The clean data is then assessed to review the effectiveness of the quality control, and ultimately, the clean data is used for analysis.
Read count extraction and normalization were performed using RseQC software
Assembly: mm10

source_name: colon

extract_protocol:
RNA was harvested using TRIzol® Reagent (invitrogen.). 1 µgof total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Nebnext ultra-RNA library preparation kit following manufacturer's protocols.

value: Intestine

value: Mus musculus

value: 2.5% DSS+BXD15.2 gg/kg /day


title: Sufficiency MPRA, GFP, Soma Rep4

city: Aurora

last: Taliaferro

state: CO

institute: University of Colorado Anschutz Medical Campus

description: Library name: sufficiency_GFPS4

data_processing:
MPRA oligos were extracted from sequencing reads and aligned against known oligo sequences using bowtie2. UMI deduplication was performed to minimize contributions from differences in PCR amplification efficiency.
Assembly: mm10
Supplementary files format and content: For each oligo, the number of reads containing that oligo and the number of unique UMIs seen in those reads are reported.

source_name: CAD

growth_protocol: Mouse CAD cells were grown in DMEM/F12 supplemented with 10% FBS and pen/strep. Reporter transcript expression was induced by adding 1 ug/mL doxycycline for 48 hours.

extract_protocol:
RNA was extracted from soma and neurite fractions using a QuickRNA micro kit (Zymo).
Targeted sequencing libraries, with UMIs, were constructed through RT-PCR of an amplicon of the reporter transcript used in the MPRA. To minimize effects due to a particular reporter RNA, two reporters RNAs were used. One encoded GFP while the other encoded firefly luciferase.

treatment_protocol: CAD cells were mechanically fractionated into soma and neurite fractions by growing them on porous membranes to allow neurite growth through the membrane followed by scraping of the top of the membrane to separate soma and neurites.

value: CAD

value: Sufficiency MPRA, GFP, Soma


title: OVCAR8_gCTRL_90nM_48h_rep1

description: Library name: OVCAR8_gCTRL_90nM_48h_rep1

value: Ovarian cancer cell line


title: Sufficiency MPRA, GFP, Soma Rep3

description: Library name: sufficiency_GFPS3


description: Library name: Dataset_A_Quiescent Neural Stem Cell of the Subventricular Zone


title: Sufficiency MPRA, GFP, Soma Rep2

description: Library name: sufficiency_GFPS2


title: DSS-BXD-H-2

description:
Library name: Sample 11
Mice were administered 2.5% DSS for 5 days followed by normal drinking water for 5 days, while simultaneously being given 15.2  g/kg/day of BXD, and this process was repeated for three cycles.

value: 2.5% DSS+BXD 15.2 g g/kg /day


title: Sufficiency MPRA, GFP, Soma Rep1

description: Library name: sufficiency_GFPS1


title: DSS-BXD-H-1

description:
Library name: Sample 10
Mice were administered 2.5% DSS for 5 days followed by normal drinking water for 5 days, while simultaneously being given 15.2  g/kg/day of BXD, and this process was repeated for three cycles.


title: OVCAR8_gCTRL_90nM_24h_rep1

description: Library name: OVCAR8_gCTRL_90nM_24h_rep1


title: Sufficiency MPRA, GFP, Neurite Rep4

description: Library name: sufficiency_GFPN4

value: Sufficiency MPRA, GFP, Neurite


title: Sufficiency MPRA, GFP, Neurite Rep3

description: Library name: sufficiency_GFPN3


title: Sufficiency MPRA, GFP, Neurite Rep2

description: Library name: sufficiency_GFPN2


title: DSS-BXD-L-3

description:
Library name: Sample 9
Mice were administered 2.5% DSS for 5 days followed by normal drinking water for 5 days, while simultaneously being given 7.60 g/kg/day of BXD, and this process was repeated for three cycles.

value: 2.5% DSS+BXD 7.60 g/kg /day


title: OVCAR8_gCTRL_90nM_6h_rep2

description: Library name: OVCAR8_gCTRL_90nM_6h_rep2

value: CDK10 wildtype


title: DSS-BXD-L-2

description:
Library name: Sample 8
Mice were administered 2.5% DSS for 5 days followed by normal drinking water for 5 days, while simultaneously being given 7.60 g/kg/day of BXD, and this process was repeated for three cycles.


title: Sufficiency MPRA, GFP, Neurite Rep1

description: Library name: sufficiency_GFPN1


title: Sufficiency MPRA, Firefly, Soma Rep4

description: Library name: sufficiency_FFS4

value: Sufficiency MPRA, Firefly, Soma


title: OVCAR8_gCTRL_90nM_6h_rep1

description: Library name: OVCAR8_gCTRL_90nM_6h_rep1


title: Sufficiency MPRA, Firefly, Soma Rep3

description: Library name: sufficiency_FFS3


title: DSS-BXD-L-1

description:
Library name: Sample 7
Mice were administered 2.5% DSS for 5 days followed by normal drinking water for 5 days, while simultaneously being given 7.60 g/kg/day of BXD, and this process was repeated for three cycles.