title: Group 1_Isotype Control_G1_6_Tumor_12_Run1_3

description: Library name: Lib-DSP-1001660037468-C-B01


title: Group 1_Isotype Control_G1_6_Tumor_15_Run1_3

status: Public on Apr 20 2026

type: SRA

city: Cambridge

first: Julien

last: Tessier

state: MA

address: 350 Water Street

country: USA

institute: Sanofi US

description: Library name: Lib-DSP-1001660037468-C-B04

library_source: transcriptomic

data_processing:
BCL were then converted to FASTQ files which were then processed through the GeoMx NGS Pipeline v1.2 for Digital count conversion (DCC). Finally, counts from the DCC file were mapped back to tissue location on the GeoMx DSP instrument, yielding a spatially resolved digital profile of analyte abundance. In the end, 474 ROIs were successfully sequenced and mapped back to tissue location for this study.
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes)
Supplementary files format and content: DCC
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Mus musculus

growth_protocol: Female C57BL/6J mice were obtained from the Jackson Laboratory (Bar Harbor, ME). B16-F10-OVA cells were grown in Dulbecco Modified Eagle Medium (DMEM) (Life technologies, Cat No. 11995065) supplemented with 10% heat inactivated Fetal Bovine Serum (HI FBS) (Life technologies, Cat No. 10082-147), Blasticidin at 7.5 µg/ml (Gibco, Cat No. 05756), and incubated at 37°C with 5% CO2. The cells were harvested using 0.25% Trypsin-Ethylenediaminetetraacetic (EDTA) (Life technologies, Cat No. 2520056), and re-suspended in Dulbecco's phosphate-buffered saline (DPBS) (Gibco, Cat No. 14190-144). On day 0, 120 animals were subcutaneously implanted with 0.5 x 106 B16-F10-OVA tumor cells into the right flank.

extract_protocol:
On day 21, tumors were harvested. One half was fixed in 10% neutral buffered formalin for 24h, followed by transfer to 70% ethanol before paraffin embedding. Samples were then embedded in paraffin and sectioned for downstream GeoMx DSP spatial transcriptomics analysis. The freshly cut sections were then processed within two weeks of sectioning following the Nanostring GeoMx DSP Automated RNA Slide Preparation user manual (MAN-10151-04, section “Fully Automated RNA Slide Preparation protocol for FFPE”). ISH hybridization was performed using NanoString Mouse Whole Transcriptome Atlas probe mix (>20,000 genes). Acquisition runs of four slides (one slide of each study group) were performed on the Nanostring GeoMx DSP instrument. For each tumor, we defined 3 compartments (“Leading Edge”, “Tumor” and “Necrosis”) based on morphological markers and H&E staining. For each compartment, we then harvested 8 circular (250μm in diameter) ROIs, so a total of 24 per tumor (23 ROIs per tumor for the isotype control group as the first well on each collection plate was dedicated to the no-template control). ROI placement for each compartment was done within the tumor boundaries, including for the “Leading Edge” one.
Libraries were prepared from released tags according to the Nanostring GeoMx DSP NGS readout user manual (MAN-10153-02). Library quality was assessed using Agilent 4200 Tapestation system and the D1000 DNA ScreenTape (Agilent Technologies, catalog# 5067-5582). Library concentration was assessed using Qubit™ Flex Fluorometer and Qubit™ 1X dsDNA BR Assay Kit (ThermoFisher Scientific, catalog# Q33262). Libraries were sequenced on the NovaSeq 6000 platform (Illumina) using Illumina v1.5 reagent kits with a read length of 27 for both reads and i5 reverse sequence orientation.

treatment_protocol: On day 9 post implantation, the mice were pooled and randomly distributed to the control and treatment groups (10 mice per group), with tumor size ranging from 46 to 148 mm3. On day 10, mice started treatment as follow: Isotype Control (intraperitoneal; 10mg/kg; twice weekly), anti-mPD-1 (intraperitoneal; 10mg/kg; twice weekly), mIgG-mutmIL15 (intraveneous; 1 mg/kg; once weekly), anti-mPD-1-mutmIL15 (intraveneous; 1 mg/kg; once weekly).

tag: cell line

tag: treatment

value: Isotype Control

tag: batch

tag: mouse id

tag: region of_interest,_label

value: Tumor

tag: region of_interest,_id


title: Group 1_Isotype Control_G1_6_Tumor_10_Run1_3

description: Library name: Lib-DSP-1001660037468-C-A11


title: Group 1_Isotype Control_G1_6_Tumor_11_Run1_3

description: Library name: Lib-DSP-1001660037468-C-A12


title: Slide 1; ROI 007; Segment: CK

city: Oklahoma city

first: Bethany

last: Hannafon

state: OK

address: 975 NE 10th Street

department: Obstetrics and Gynecology

institute: University of Oklahoma Health Sciences Center

description:
Library name: DSP-1001660008101-A-B06
Sample/column name in raw count matrix = Slide 1 | 007 | CK ; in normalized count matrix = DCIS_Normal_CK_S1_007. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 007; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

data_processing:
Raw paired-end reads were processed with Bruker GeoMx NGS Pipeline v3.1.0.194 to assign reads to Human Whole Transcriptome Atlas targets and generate gene-level count outputs. Quality control and downstream normalization were performed in R using standR v1.10.0. ROIs were excluded if they failed preset thresholds for minimum segment reads (1000), percent trimmed (80), percent stitched (80), percent aligned (80), percent sequencing saturation (50), maximum no-template-control count (1000), minimum area (1000), and minimum nuclei (50, when available). For slide 5, nuclei-based filtering was not available. Genes with fewer than 5 counts in more than 60% of regions were removed in the discovery cohort. Normalized expression matrices were generated using trimmed mean of M-values normalization and RUV5 correction for slide-level effects; differential expression testing was performed with limma-voom v3.62.2.
Assembly: hg38
Supplementary files format and content: Raw count matrix of slide 1-4: raw_count14.csv  | Raw count matrix of slide 5: raw_count5.csv | Normalized count matrix of slide 1-4: GeoMx_tmm_ruv_normalized_count_linear_S14.csv | Normalized count matrix of slide 5: GeoMx_tmm_ruv_normalized_count_linear_S5.csv | Metadata of slide 1-4: sampleAnnoFile_S14.csv | Metadata of slide 5: sampleAnnoFile_S5.csv
Supplementary files format and content: In Metadata, "library" column  matches the library name above, "SegmentDisplayName" column matches the columns/samples in the raw count matrix, "sampleID" column matches the columns/samples in the normalized count matrix.
Library strategy: Spatial Transcriptomics

organism: Homo sapiens

source_name: breast tissue

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) breast tissues from patients diagnosed with ductal carcinoma in situ (DCIS) or invasive ductal carcinoma (IDC) were obtained from the Department of Pathology at the University of Oklahoma Health Campus (Oklahoma City, OK). A pathologist confirmed the histopathologic diagnosis using routine diagnostic criteria. Patient demographic and clinicopathologic data were abstracted from the medical record, samples were de-identified, and their use was approved under University of Oklahoma IRB 12384. FFPE sections were mounted on Apex BOND Adhesive slides with tissue positioned within the GeoMx imaging area and baked at 60°C for at least 30 minutes. Slides were prepared on the Leica BOND RX using the GeoMx NGS RNA FFPE BOND workflow for breast tissue, including: bake and dewax preparation, ER2 heat-induced epitope retrieval for 10 minutes at 100°C, and Proteinase K digestion at 0.1 μg/mL for 15 minutes. Human Whole Transcriptome Atlas RNA probes containing UV-photocleavable barcoded oligonucleotides were hybridized overnight at 37°C. After stringent washes at 37°C (two 25-minute washes in Stringent Wash solution followed by two 2-minute washes in 2X SSC), slides were blocked in Buffer W for 30 minutes and stained for 1 hour at room temperature with the four-color morphology panel alpha smooth muscle actin (SMA)-647, SYTO 13 nuclear stain, pan-cytokeratin (CK)-532, and leukocyte (CD45)-AF594. Morphology markers guided ROI selection and segmentation of CK+, SMA+, and/or CD45+ compartments. Prepared slides were loaded onto the GeoMx DSP, each ROI was illuminated with UV light, and released oligonucleotides were collected by microcapillary aspiration into separate wells of a 96-well plate.
Region-specific oligonucleotides released on the GeoMx DSP were collected into individual wells of a 96-well plate and converted into sequencing libraries according to the manufacturer’s GeoMx RNA library preparation workflow for the Human Whole Transcriptome Atlas assay. Libraries were indexed according to the GeoMx protocol and sequenced as paired-end 150-bp reads on an Illumina NovaSeq X Plus instrument at the University of Colorado Anschutz Medical Campus shared-resource facility in Aurora, Colorado.

tag: tissue

value: breast tissue

tag: cell type

value: epithelial cells

tag: slide

value: Slide 1

tag: roi

value: ROI 007

tag: segment

value: CK


title: Group 1_Isotype Control_G1_6_Tumor_13_Run1_3

description: Library name: Lib-DSP-1001660037468-C-B02


title: Slide 1; ROI 006; Segment: CD45

description:
Library name: DSP-1001660008101-A-B02
Sample/column name in raw count matrix = Slide 1 | 006 | CD45 ; in normalized count matrix = DCIS_Normal_CD45_S1_006. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 006; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: leukocytes

value: ROI 006


title: Group 1_Isotype Control_G1_6_Tumor_9_Run1_3

description: Library name: Lib-DSP-1001660037468-C-A10


title: Group 1_Isotype Control_G1_6_Leading Edge_8_Run1_3

description: Library name: Lib-DSP-1001660037468-C-A09

value: Leading Edge


title: Slide 2; ROI 003; Segment: CK

description:
Library name: DSP-1001660008101-A-C01
Sample/column name in raw count matrix = Slide 2 | 003 | CK ; in normalized count matrix = IDC_Normal_CK_S2_003. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 2; ROI 003; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: Slide 2

value: ROI 003


title: Slide 1; ROI 004; Segment: SMA

description:
Library name: DSP-1001660008101-A-A11
Sample/column name in raw count matrix = Slide 1 | 004 | SMA ; in normalized count matrix = DCIS_High_SMA_S1_004. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 004; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: fibroblasts/myoepithelial cells

value: ROI 004

value: SMA


title: Slide 1; ROI 006; Segment: CK

description:
Library name: DSP-1001660008101-A-B03
Sample/column name in raw count matrix = Slide 1 | 006 | CK ; in normalized count matrix = DCIS_Normal_CK_S1_006. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 006; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 1; ROI 006; Segment: SMA

description:
Library name: DSP-1001660008101-A-B04
Sample/column name in raw count matrix = Slide 1 | 006 | SMA ; in normalized count matrix = DCIS_Normal_SMA_S1_006. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 006; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 1; ROI 004; Segment: CK

description:
Library name: DSP-1001660008101-A-A10
Sample/column name in raw count matrix = Slide 1 | 004 | CK ; in normalized count matrix = DCIS_High_CK_S1_004. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 004; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 1; ROI 005; Segment: CK

description:
Library name: DSP-1001660008101-A-A12
Sample/column name in raw count matrix = Slide 1 | 005 | CK ; in normalized count matrix = DCIS_High_CK_S1_005. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 005; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 005


title: Slide 1; ROI 005; Segment: SMA

description:
Library name: DSP-1001660008101-A-B01
Sample/column name in raw count matrix = Slide 1 | 005 | SMA ; in normalized count matrix = DCIS_High_SMA_S1_005. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 005; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 1_Isotype Control_G1_6_Leading Edge_7_Run1_3

description: Library name: Lib-DSP-1001660037468-C-A08


title: Slide 1; ROI 004; Segment: CD45

description:
Library name: DSP-1001660008101-A-A09
Sample/column name in raw count matrix = Slide 1 | 004 | CD45 ; in normalized count matrix = DCIS_High_CD45_S1_004. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 004; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 1; ROI 003; Segment: CK

description:
Library name: DSP-1001660008101-A-A08
Sample/column name in raw count matrix = Slide 1 | 003 | CK ; in normalized count matrix = IDC_High_CK_S1_003. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 003; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 1_Isotype Control_G1_6_Leading Edge_3_Run1_3

description: Library name: Lib-DSP-1001660037468-C-A04


title: Group 1_Isotype Control_G1_6_Leading Edge_5_Run1_3

description: Library name: Lib-DSP-1001660037468-C-A06


title: Group 1_Isotype Control_G1_6_Leading Edge_4_Run1_3

description: Library name: Lib-DSP-1001660037468-C-A05


title: Group 1_Isotype Control_G1_6_Leading Edge_6_Run1_3

description: Library name: Lib-DSP-1001660037468-C-A07


title: Slide 1; ROI 003; Segment: CD45

description:
Library name: DSP-1001660008101-A-A07
Sample/column name in raw count matrix = Slide 1 | 003 | CD45 ; in normalized count matrix = IDC_High_CD45_S1_003. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 003; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Slide 1; ROI 002; Segment: CK

description:
Library name: DSP-1001660008101-A-A06
Sample/column name in raw count matrix = Slide 1 | 002 | CK ; in normalized count matrix = IDC_High_CK_S1_002. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 002; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: ROI 002


title: NTC_NTC_NTC_NTC_NTC_Run1_3

description: Library name: Lib-DSP-1001660037468-C-A01

source_name: NTC

value: NTC


title: Slide 1; ROI 002; Segment: CD45

description:
Library name: DSP-1001660008101-A-A05
Sample/column name in raw count matrix = Slide 1 | 002 | CD45 ; in normalized count matrix = IDC_High_CD45_S1_002. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 002; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Necrosis_24_Run1_2

description: Library name: Lib-DSP-1001660037467-B-H12

value: Necrosis


title: Slide 1; ROI 001; Segment: SMA

description:
Library name: DSP-1001660008101-A-A04
Sample/column name in raw count matrix = Slide 1 | 001 | SMA ; in normalized count matrix = IDC_High_SMA_S1_001. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 001; Segment: SMA
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: breast tissue

value: ROI 001


title: Group 1_Isotype Control_G1_6_Leading Edge_2_Run1_3

description: Library name: Lib-DSP-1001660037468-C-A03

value: Isotype Control


title: Slide 1; ROI 001; Segment: CK

description:
Library name: DSP-1001660008101-A-A03
Sample/column name in raw count matrix = Slide 1 | 001 | CK ; in normalized count matrix = IDC_High_CK_S1_001. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 001; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: epithelial cells

value: Slide 1


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Necrosis_23_Run1_2

description: Library name: Lib-DSP-1001660037467-B-H11


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Necrosis_22_Run1_2

description: Library name: Lib-DSP-1001660037467-B-H10


title: Group 1_Isotype Control_G1_6_Leading Edge_1_Run1_3

description: Library name: Lib-DSP-1001660037468-C-A02


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Necrosis_21_Run1_2

description: Library name: Lib-DSP-1001660037467-B-H09


title: Micro-C of RIVA ARID1A Het ARID2 KO clone 2 rep 2

city: New York City

first: Christopher

middle: Russell

last: Chin

state: NY

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

description: Library name: 11_MicroC_RIVA_ARID1AHet_ARID2KO_DQ4_rep2

library_source: genomic

data_processing:
Paired-end reads were aligned to the human genome (hg38) using BWA-MEM v0.7.18 for Novaseq output. Valid read pairs were retained using the parse module from pairtools v0.3.0. The pairtools split module was then used to generate a .bam and .pairs file, from which conact matrices (cool format) where generated using cooler cload pairix v0.9.3 and KR-normalized at 10kb resolution.
TADs were called using HiTAD v0.4.5 on 20kb cool matrices
Assembly: hg38
Supplementary files format and content: cool (raw and normalized contact matrices)
Supplementary files format and content: bed (TAD calls)

molecule: genomic DNA

source_name: RIVA

growth_protocol: 20% IMDM with P/S, GlutaMax

extract_protocol:
Two ARID1A wild-type and two heterozygous clones were used. Cells were crosslinked with 1% formaldehyde at room temperature for 10 min and quenched with 750 mM Tris-HCl (pH 7.4). Chromatin was digested with micrococcal nuclease. Digested DNA ends were repaired using biotinylated oligos and subjected to proximity ligation. For library preparation, biotynilated DNA was purified with streptavidin beads.
For library preparation, the DNA was bound to MyOne Streptavidin C1 beads from Invitrogen, washed with TBW, and processed using the NEB Ultra II DNA Library Prep Kit. Libraries were amplified using 10 PCR cycles, quantified via BioAnalyzer and Tapestation, and then sequenced on the NovoSeq X Plus platform using the PE150 SP Kit.

value: RIVA

value: B-cell lymphoma ABC-DLBCL

tag: genotype

value: ARID1A HET


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Tumor_15_Run1_2

description: Library name: Lib-DSP-1001660037467-B-H03

value: Tumor


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Necrosis_20_Run1_2

description: Library name: Lib-DSP-1001660037467-B-H08


title: Micro-C of RIVA ARID1A Het ARID2 KO clone 2 rep 3

description: Library name: 12_MicroC_RIVA_ARID1AHet_ARID2KO_DQ4_rep3

value: ARID1A WT


title: Micro-C of RIVA ARID1A Het ARID2 WT rep 2

description: Library name: 02_MicroC_RIVA_ARID1AHet_ARID2WT_TQ2_rep2


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Necrosis_19_Run1_2

description: Library name: Lib-DSP-1001660037467-B-H07


title: Micro-C of RIVA ARID1A Het ARID2 KO clone 2 rep 1

description: Library name: 10_MicroC_RIVA_ARID1AHet_ARID2KO_DQ4_rep1


title: Micro-C of RIVA ARID1A Het ARID2 WT rep 1

description: Library name: 01_MicroC_RIVA_ARID1AHet_ARID2WT_TQ2_rep1


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Tumor_12_Run1_2

description: Library name: Lib-DSP-1001660037467-B-G12


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Necrosis_18_Run1_2

description: Library name: Lib-DSP-1001660037467-B-H06


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Tumor_11_Run1_2

description: Library name: Lib-DSP-1001660037467-B-G11


title: Micro-C of RIVA ARID1A Het ARID2 KO clone 1 rep 2

description: Library name: 08_MicroC_RIVA_ARID1AHet_ARID2KO_DQ3_rep2


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Necrosis_17_Run1_2

description: Library name: Lib-DSP-1001660037467-B-H05


title: Micro-C of RIVA ARID1A Het ARID2 KO clone 1 rep 1

description: Library name: 07_MicroC_RIVA_ARID1AHet_ARID2KO_DQ3_rep1


title: Micro-C of RIVA ARID1A Het ARID2 KO clone 1 rep 3

description: Library name: 09_MicroC_RIVA_ARID1AHet_ARID2KO_DQ3_rep3


title: Micro-C of RIVA ARID1A Het ARID2 WT rep 3

description: Library name: 03_MicroC_RIVA_ARID1AHet_ARID2WT_TQ2_rep3


title: Slide 4; ROI 008; Segment: CK

description:
Library name: DSP-1001660008101-A-G09
Sample/column name in raw count matrix = Slide 4 | 008 | CK ; in normalized count matrix = DCIS_Normal_CK_S4_008. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 4; ROI 008; Segment: CK
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: Slide 4

value: ROI 008

value: CK


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Tumor_16_Run1_2

description: Library name: Lib-DSP-1001660037467-B-H04


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Tumor_14_Run1_2

description: Library name: Lib-DSP-1001660037467-B-H02


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Tumor_10_Run1_2

description: Library name: Lib-DSP-1001660037467-B-G10


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Tumor_9_Run1_2

description: Library name: Lib-DSP-1001660037467-B-G09


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Tumor_13_Run1_2

description: Library name: Lib-DSP-1001660037467-B-H01


title: Slide 1; ROI 001; Segment: CD45

description:
Library name: DSP-1001660008101-A-A02
Sample/column name in raw count matrix = Slide 1 | 001 | CD45 ; in normalized count matrix = IDC_High_CD45_S1_001. FFPE human breast tissue GeoMx DSP sample prepared on an Apex BOND Adhesive slide using the Human Whole Transcriptome Atlas RNA assay and four-color morphology panel (aSMA-647, SYTO13, CK-532, CD45-AF594); Slide 1; ROI 001; Segment: CD45
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

value: leukocytes


title: Human LC Visium, Caudal block, Lower section

city: New York

first: Fahrunisa Meryem Betul

last: Erol Gulsen

address: 1150 St Nicholas Ave

department: Pediatrics

institute: Columbia University

description:
Library name: Lower_Caudal
10x Genomics Visium CytAssist v2; slide V43L24-365 position D1; Space Ranger output

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline (spaceranger count, v2.0.0) to generate filtered feature-barcode matrices and spatial output files for each section. The human genome reference GRCh38-3.0.0 was used for alignment.
Spot-level quality control and downstream analysis were performed in R (v4.3.2) using Seurat (v5.0.1). Section-specific spatial cropping was applied based on Visium spot coordinates to remove low-quality peripheral spots.
The four Basak LC Visium sections were merged with published LC Visium data (Weber et al., eLife 2024, DOI: 10.7554/eLife.84628; 20,380 spots) into a single Seurat object (32,875 spots total). Integration was performed using SCTransform normalization followed by RPCA-based multi-sample integration.
Assembly: GRCh38-3.0.0
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 file containing the Space Ranger filtered gene-barcode count matrix (genes × spots) for each Visium section.
Supplementary files format and content: tissue_positions.csv: comma-separated file with spot barcodes and their array/pixel coordinates on the Visium slide.
Supplementary files format and content: scalefactors_json.json: JSON file with pixel-to-spot scale factors for image alignment.
Supplementary files format and content: tissue_hires_image.png: high-resolution brightfield tissue image (2000 px).
Supplementary files format and content: tissue_lowres_image.png: low-resolution tissue image (600 px).
Supplementary files format and content: aligned_fiducials.jpg: image showing fiducial alignment overlaid on the tissue.
Supplementary files format and content: meta_visium_seurat.rds: R/Seurat object containing the integrated Visium dataset (Basak + Weber LC sections, 32,875 spots) with SCT-normalized expression, RPCA embeddings, UMAP coordinates, and cell-type annotations.
Library strategy: Spatial Transcriptomics

source_name: locus coeruleus

extract_protocol:
Frozen postmortem human brainstem tissue blocks containing the locus coeruleus were embedded in O.C.T. compound (Thermo Fisher Scientific, cat. 23730571) and flash-frozen on dry ice. Five 10-µm thick cryosections were prepared using a CryoStar NX70 cryostat (Epredia) at -16°C in an RNase-free environment and mounted onto positively charged glass slides (Superfrost Plus, Fisherbrand #22-037-246). Sections were stored at -80°C until use. For each rostro-caudal level, two consecutive sections were placed on the same Visium CytAssist slide: the rostral pair (Upper Rostral, Lower Rostral) on slide V52L19-072 (positions A1 and B1), and the caudal pair (Upper Caudal, Lower Caudal) on slide V43L24-365 (positions A1 and D1).
Spatial gene expression libraries were prepared using the 10x Genomics Visium CytAssist FFPE v2 protocol (Visium V5 Slide; Visium Human Transcriptome Probe Set v2.0, targeting 18,061 human genes) following the manufacturer's instructions.

value: locus coeruleus

tag: age

tag: Sex

value: female

tag: donor id

tag: disease state

value: neurotypical

tag: lc region

value: caudal


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Leading Edge_8_Run1_2

description: Library name: Lib-DSP-1001660037467-B-G08

tag: cell line

value: Leading Edge


title: MGG152_monoculture_irradiation_rep2

city: New Haven

first: Kevin

middle: C

last: Johnson

state: CT

address: 333 Cedar Street

department: Neurosurgery

institute: Yale University

description: Library name: RV12_152-r-2

library_source: transcriptomic single cell

data_processing:
cellranger-9.0.1 using include-introns parameter set to `True`.
Assembly: GRCh38_and_mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

growth_protocol: Macrophages were isolated from the peritoneal cavity of stimulated mice (C57BL/6 - wild type). The macrophages were collected from 3 male and 3 female mice aged 10 weeks, pooled together, divided into aliquots, and frozen for downstream experiments. Frozen murine primary macrophages were later thawed quickly on Day 1 of the co-culture experiment and 250,000 cells were seeded in 6-well plates in DMEM medium (ThermoFisher, Gibco 11965092) with 10% FBS (ThermoFisher, Gibco A5670701) supplemented and 10 ng/ml of recombinant M-CSF (BioLegend 576406). After 12 hours, macrophage cells were washed with MGG152 complete medium --- Neurobasal (ThermoFisher, Gibco 21103049) with 0.5% N-2 supplement (100x) (ThermoFisher, Gibco 17502048), 2% B-27 Supplement (50X) (ThermoFisher, Gibco 17504044), 1.5% L-Glutamine (Corning 25-005-CI), 0.5% Antibiotic-antimycotic (Corning 30-004-CI), 20 ng/ml human FGF (PeproTech AF-100-26), 40 ng/ml human EGF (PeproTech AF-100-15), and 10 ng/ml recombinant M-CSF --- for 4 times to remove FBS. 450,000 dissociated MGG152 cells were seeded into the wells with macrophage cells for co-culture.

extract_protocol:
Cells were dissociated into single cells and submitted for 10x single cell RNA-sequencing.
The four different experimental conditions were performed with the same parental MGG152 line per batch. The four different experimental conditions were submitted as a single batch to 10x single-cell RNA sequencing  3' v4 (polyA) OCM.

treatment_protocol: Monoculture and co-culture cells were irradiated using Irradiator X-RAD 320 (Precision X-ray) with 2 Gy dose on each of the following 3 days. After 72-hour recovery period, the cells were harvested.

value: Brain

value: Glioma

value: IDH1 R132H

tag: treatment

value: monoculture plus irradiation

value: Replicate 2


title: Human LC Visium, Caudal block, Upper section

description:
Library name: Upper_Caudal
10x Genomics Visium CytAssist v2; slide V43L24-365 position A1; Space Ranger output


title: Human LC Visium, Rostral block, Lower section

description:
Library name: Lower_Rostral
10x Genomics Visium CytAssist v2; slide V52L19-072 position B1; Space Ranger output

value: rostral


title: MGG152_monoculture_rep2

description: Library name: RV12_152-2

value: monoculture

tag: batch


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Leading Edge_7_Run1_2

description: Library name: Lib-DSP-1001660037467-B-G07

tag: mouse id


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Leading Edge_4_Run1_2

description: Library name: Lib-DSP-1001660037467-B-G04

tag: region of_interest,_label


title: MGG152_monoculture_irradiation_rep3

description: Library name: LZ1_152-r-3

value: Replicate 3


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Leading Edge_6_Run1_2

description: Library name: Lib-DSP-1001660037467-B-G06

tag: region of_interest,_id


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Leading Edge_5_Run1_2

description: Library name: Lib-DSP-1001660037467-B-G05


title: MGG152_monoculture_rep1

description: Library name: RV11_152-1

tag: tissue

value: Replicate 1


title: Human LC Visium, Rostral block, Upper section

description:
Library name: Upper_Rostral
10x Genomics Visium CytAssist v2; slide V52L19-072 position A1; Space Ranger output


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Leading Edge_2_Run1_2

description: Library name: Lib-DSP-1001660037467-B-G02


title: MGG152_monoculture_irradiation_rep1

description: Library name: RV11_152-r-1

tag: cell type


title: Group 3_mIgG-mutmIL15_G3_24_Necrosis_24_Run1_2

description: Library name: Lib-DSP-1001660037467-B-F12

value: Necrosis


title: Group 3_mIgG-mutmIL15_G3_24_Necrosis_23_Run1_2

description: Library name: Lib-DSP-1001660037467-B-F11


title: MGG152_monoculture_rep3

description: Library name: LZ1_152-3


title: MGG152_monoculture_irradiation_rep4

description: Library name: LZ2_152-r-4

value: Replicate 4


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Leading Edge_3_Run1_2

description: Library name: Lib-DSP-1001660037467-B-G03


title: MGG152_monoculture_rep4

description: Library name: LZ2_152-4


title: CD34+ Female cells, shGFP, harvested at Day 3 of myeloid differentiation

city: Charlottesville

first: Shafaque

last: Zahra

state: VA

address: MR6, 345 Crispell Drive

department: Pathology

institute: University of Virginia

description:
Library name: F1023
10x Genomics

data_processing:
Single-cell RNA sequencing data was processed using kb_python 0.28.2.
kb ref: Used to build a kallisto index and generate a transcript-to-gene mapping (t2g) from the reference genome (FASTA) and annotation (GTF/GFF3) files.
kb count: Executed on the single-cell FASTQ files to perform alignment with kallisto and collapse UMI/cell barcode data with bustools.
kb count command was specifically run with the required flags to ensure the output count matrix is in a Cell Ranger-compatible format:
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: Tab-separated values and matrix files for both F1023 and F972 samples
Supplementary files format and content: F1023_cells_x_genes.barcodes.txt; F1023_cells_x_genes.genes.names.txt; F1023_cells_x_genes.mtx; F972_cells_x_genes.barcodes.txt; F972_cells_x_genes.genes.names.txt; F972_cells_x_genes.mtx

source_name: CD34+ cells

extract_protocol:
CD34⁺ hematopoietic stem cells derived from a female human donor were thawed and pre-stimulated for 4 days in stem cell expansion medium supplemented with SCF, FLT3L, TPO, and IL-3. After pre-stimulation, cells were transduced with lentiviral vectors encoding shUBA1–CDK16 or shGFP control. Transduced cells underwent 3 days of puromycin selection to enrich for knockdown populations. Myeloid differentiation was initiated by transferring cells to differentiation medium supplemented with human GM-CSF and CC100 myeloid differentiation supplement. Cells were differentiaited for 3 days under standard conditions. On day 3 of differentiation, 1×10⁶ viable cells were collected  and frozen in CryoStor (StemCell Technologies) freezing medium. After successful confirmation of UBA1–CDK16 knockdown, cryopreserved samples were submitted for single-cell RNA-sequencing analysis.
The library construction for the 10x Genomics GEM-X Single Cell 3' Gene Expression wasdone as per manufacturer's protocol. Viable single cells were partitioned into nanoliter-volume GEMs (Gel Bead-in-Emulsions) alongside Gel Beads and reaction reagents using the 10x Chromium instrument . Within these GEMs, a Reverse Transcription (RT) reaction took place, where poly-A mRNA transcripts were captured by poly(dT) oligos on the bead, which led to the synthesis of cDNA that was uniquely tagged with a Cell Barcode and a UMI (Unique Molecular Identifier). Following the disruption of the GEMs, the barcoded cDNA was purified and subsequently pre-amplified via PCR to ensure sufficient starting material. Finally, this amplified product underwent enzymatic fragmentation, end repair, and adapter ligation to incorporate the requisite Illumina sequencing adapters (P5/P7) and sample indices (i7/i5), yielding the finalized library structure which was then checked for quality and sequenced on Illumina platform.

value: CD34+ cells

value: hematopoietic stem cells

value: Control

value: myeloid differentiation

tag: time

value: Day 3


title: Group 3_mIgG-mutmIL15_G3_24_Necrosis_22_Run1_2

description: Library name: Lib-DSP-1001660037467-B-F10


title: Group 4_anti-mPD-1-mutmIL15_G4_32_Leading Edge_1_Run1_2

description: Library name: Lib-DSP-1001660037467-B-G01

value: Leading Edge


title: CD34+ Female cells, shUBA1-CDK16, harvested at Day 3 of myeloid differentiation

description:
Library name: F972
10x Genomics

value: UBA1-CDK16 knockdown


title: DIvA-OHT-Rep3

city: tianjin

first: zhanjie

last: xiu

address: HUANHU XI ROAD, TIYUAN BEI, HEXI DISTRICT

country: China

institute: TIANJIN MEDICAL UNIVERSITY CANCER INSTITUTE & HOSPITAL

description:
Library name: Sample6
column name in gene_count_matrix.csv and gene_FPKM_matrix.csv: OHT-pos2

data_processing:
Quality control: FASTQC and Fastp: -l 25 --detect_adapter_for_pe -p --trim_poly_g
STAR
stringtie
Assembly: hg38
Supplementary files format and content: FPKM and counts

molecule: nuclear RNA

source_name: Human Cervical Cancer

growth_protocol: cells were grown and sustained in DMEM (Gibco, USA) enriched with 10% fetal bovine serum (FBS) (Gibco, USA) and 1% penicillin streptomycin solution (Gibco, USA), incubated at a temprature of 37°C in an atmosphere containing 5% CO2. For AsiSI induced DSB generation, AiDIvA cells were treated with doxycycline (1 ng/ml) for 24 hours and 4-OHT (0.5 mM) for an additional 4 hours to stabilize ER-AsiSI and promote its nuclear translocation.

extract_protocol:
The nuclear RNA was isolated by TRIzol (Sigma, USA) and the mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads.
RNA standard Protocol

treatment_protocol: AiDIvA cells treated with doxycycline and in the absence or presence of 4-OHT were collected

value: Human Cervical Cancer

value: HELA DIvA

value: Human Cervical Cancer Cell

value: presence of 4-OHT


title: DIvA-OHT-Rep2

description:
Library name: Sample5
column name in gene_count_matrix.csv and gene_FPKM_matrix.csv: OHT-pos2


title: DIvA-WT-Rep3

description:
Library name: Sample3
column name in gene_count_matrix.csv and gene_FPKM_matrix.csv: OHT-con3

value: absence of 4-OHT


title: DIvA-OHT-Rep1

description:
Library name: Sample4
column name in gene_count_matrix.csv and gene_FPKM_matrix.csv: OHT-pos1


title: Group 3_mIgG-mutmIL15_G3_24_Necrosis_19_Run1_2

description: Library name: Lib-DSP-1001660037467-B-F07


title: Group 3_mIgG-mutmIL15_G3_24_Necrosis_21_Run1_2

description: Library name: Lib-DSP-1001660037467-B-F09


title: Group 3_mIgG-mutmIL15_G3_24_Necrosis_18_Run1_2

description: Library name: Lib-DSP-1001660037467-B-F06


title: DIvA-WT-Rep2

description:
Library name: Sample2
column name in gene_count_matrix.csv and gene_FPKM_matrix.csv: OHT-con2


title: Group 3_mIgG-mutmIL15_G3_24_Necrosis_17_Run1_2

description: Library name: Lib-DSP-1001660037467-B-F05


title: Group 3_mIgG-mutmIL15_G3_24_Tumor_15_Run1_2

description: Library name: Lib-DSP-1001660037467-B-F03

value: Tumor


title: H2ax-DIvA-WT(CUT&Tag)

description: Library name: H2ax_Normal,CUT_Tag

data_processing:
Quality control: FASTQC and Fastp: -l 20 --detect_adapter_for_pe -p --trim_poly_g
bowtie2: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
samtools
sambamba markdup
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol: CUT&Tag standard Protocol

tag: antibody


title: Group 3_mIgG-mutmIL15_G3_24_Necrosis_20_Run1_2

description: Library name: Lib-DSP-1001660037467-B-F08


title: DIvA-WT-Rep1

description:
Library name: Sample1
column name in gene_count_matrix.csv and gene_FPKM_matrix.csv: OHT-con1


title: H2ax-DIvA-OHT(CUT&Tag)

description: Library name: H2ax_OHT,CUT_Tag


title: Group 3_mIgG-mutmIL15_G3_24_Tumor_14_Run1_2

description: Library name: Lib-DSP-1001660037467-B-F02


title: CRTC2-DIvA-WT(CUT&Tag)

description: Library name: CRTC2_Normal,CUT_Tag

value: CRTC2(Proteintech, 12497-1-AP)


title: CRTC2-DIvA-OHT(CUT&Tag)

description: Library name: CRTC2_OHT,CUT_Tag


title: Group 3_mIgG-mutmIL15_G3_24_Tumor_12_Run1_2

description: Library name: Lib-DSP-1001660037467-B-E12


title: Group 3_mIgG-mutmIL15_G3_24_Tumor_11_Run1_2

description: Library name: Lib-DSP-1001660037467-B-E11


title: liver, MASLD-D5, R7

city: Barcelona

first: Maria

last: Martell

state: Barcelona

address: Pg Vall Hebron 119

department: Liver Diseases

country: Spain

institute: Institut de Recerca Hospital Vall d'Hebron

data_processing:
FASTQC v0.11.9 was used for quality control of the raw data.
MultiQC v1.8 was used to group and summarize the analysis results from FastQC.
Cutadapt v2.10 was used for adapter trimming. Trimmed sequences of less than 10 bp length were discarded.
Salmon v1.3.0 was used for quasi-mapping of raw reads to the transcriptome and summarization of counts to the transcript level
Variance Stabilizing Transformation with R DESeq2 v1.24.0 package, using varianceStabilizingTransformation()
Assembly: Rattus norvegicus; 7.2 (mRatBN7.2)
Supplementary files format and content: RawCounts.csv. In this count matrix, each row represents an Ensembl gene, each column a sequenced RNA library (sample)

organism: Rattus norvegicus

source_name: liver

growth_protocol: Sprague Dawley rats were fed for 20 weeks with control diet (CD), diet 4 (2% Cholesterol) or diet 5 (2% Cholesterol + 0.1% Cholic Acid). High-cholesterol diets were supplemented with glucose-fructose beverage (110 g/L, 45% glucose and 55% fructose).

extract_protocol:
RNeasy Mini Kit (Qiagen) was used for RNA extraction. 0,375ug of total RNA was used for the library construction
RNA libraries for RNA-seq were prepared by Novogene. Quality control is performed at each step consisting on Qubit 2.0, Agilent 2100 and Qpcr.

value: liver

value: Diet 5 (HFD+2%Chol+0,1% CA)


title: Group 3_mIgG-mutmIL15_G3_24_Tumor_13_Run1_2

description: Library name: Lib-DSP-1001660037467-B-F01


title: liver, MASLD-D5, R36


title: Group 3_mIgG-mutmIL15_G3_24_Leading Edge_8_Run1_2

description: Library name: Lib-DSP-1001660037467-B-E08


title: liver, MASLD-D5, R17


title: liver, MASLD-D5, R45


title: Group 3_mIgG-mutmIL15_G3_24_Leading Edge_7_Run1_2

description: Library name: Lib-DSP-1001660037467-B-E07


title: liver, MASLD-D4, R52

value: Diet 4 (HFD+2%Chol)


title: Group 3_mIgG-mutmIL15_G3_24_Tumor_16_Run1_2

description: Library name: Lib-DSP-1001660037467-B-F04


title: Group 3_mIgG-mutmIL15_G3_24_Leading Edge_6_Run1_2

description: Library name: Lib-DSP-1001660037467-B-E06


title: Group 3_mIgG-mutmIL15_G3_24_Tumor_9_Run1_2

description: Library name: Lib-DSP-1001660037467-B-E09


title: Group 3_mIgG-mutmIL15_G3_24_Tumor_10_Run1_2

description: Library name: Lib-DSP-1001660037467-B-E10


title: liver, MASLD-D4, R51


title: liver, MASLD-D5, R27


title: liver, MASLD-D4, R33


title: Group 3_mIgG-mutmIL15_G3_24_Leading Edge_5_Run1_2

description: Library name: Lib-DSP-1001660037467-B-E05


title: Group 3_mIgG-mutmIL15_G3_24_Leading Edge_4_Run1_2

description: Library name: Lib-DSP-1001660037467-B-E04


title: liver, MASLD-D4, R16


title: Group 3_mIgG-mutmIL15_G3_24_Leading Edge_3_Run1_2

description: Library name: Lib-DSP-1001660037467-B-E03


title: Group 2_anti-mPD-1_G2_15_Necrosis_23_Run1_2

description: Library name: Lib-DSP-1001660037467-B-D11

value: Necrosis


title: Group 3_mIgG-mutmIL15_G3_24_Leading Edge_2_Run1_2

description: Library name: Lib-DSP-1001660037467-B-E02


title: liver, control, R19

value: Chow diet


title: liver, control, R10


title: liver, MASLD-D4, R5


title: liver, control, R55


title: Group 3_mIgG-mutmIL15_G3_24_Leading Edge_1_Run1_2

description: Library name: Lib-DSP-1001660037467-B-E01


title: iPSC_organoid_injured_iMacs_d25_R2

city: Clayton

first: Nitika

last: Kandhari

state: VIC

address: Wellington Road

country: Australia

institute: Monash University

data_processing:
Raw fastq files have been analysed with nfcore/RNAseq pipeline using STAR with STAR aligner option (Dobin et al., 2013) mapping raw reads to the mus musculus GRCm38-mm10 (GCF_000001635.20, NCBI) reference genome, reads were quantified with salmon.
Raw counts were then analysed with Degust (Powell 2015) web tool to do differential expression analysis to produce list of differentially expressed genes and several quality plots including classical multidimensional scaling (MDS) and MA plots
In this analysis limma voom (Law et al. 2014) was used for differential expression analysis. Degust (Powell 2015) largely follows limma voom workflow with typical counts per million (CPM) library size normalisation and trimmed mean of M values (TMM) normalisation (Robinson and Oshlack 2010) for RNA composition normalisation.
Assembly: GRCh38.release-109
Supplementary files format and content: raw gene counts, text file, comma separated, includes all samples

source_name: iPSC_kidney organoid

extract_protocol:
RNA Extraction (ISOLATE II RNA Mini Kit 50): BIO-52072. Following manufacturer's instruction
RNA libraries for RNA-seq were prepared at Monash Health Translational Precinct (MHTP), Medical Genomics Facility using Novel RNA-Seq pipeline (Version 01/09/2021). Briefly index is added during initial pA priming and pooled samples amplified using template switching oligo.

value: iPSC_kidney organoid

value: 522.3 iPSCs - female (16 year old)

value: Kidney


title: Group 2_anti-mPD-1_G2_15_Necrosis_18_Run1_2

description: Library name: Lib-DSP-1001660037467-B-D06


title: liver, control, R37


title: Group 2_anti-mPD-1_G2_15_Necrosis_24_Run1_2

description: Library name: Lib-DSP-1001660037467-B-D12


title: iPSC_organoid_hyp_iMacs_d20_R3


title: liver, control, R38


title: Group 2_anti-mPD-1_G2_15_Necrosis_17_Run1_2

description: Library name: Lib-DSP-1001660037467-B-D05


title: Group 2_anti-mPD-1_G2_15_Necrosis_22_Run1_2

description: Library name: Lib-DSP-1001660037467-B-D10


title: iPSC_organoid_hyp_iMacs_d20_R2


title: iPSC_organoid_hyp_iMacs_d20_R1


title: Group 2_anti-mPD-1_G2_15_Necrosis_21_Run1_2

description: Library name: Lib-DSP-1001660037467-B-D09


title: iPSC_organoid_control_iMacs_d25_R3


title: iPSC_organoid_control_iMacs_d25_R2


title: Group 2_anti-mPD-1_G2_15_Tumor_16_Run1_2

description: Library name: Lib-DSP-1001660037467-B-D04


title: Group 2_anti-mPD-1_G2_15_Tumor_15_Run1_2

description: Library name: Lib-DSP-1001660037467-B-D03


title: iPSC_organoid_injured_iMacs_d25_R3


title: Group 2_anti-mPD-1_G2_15_Necrosis_20_Run1_2

description: Library name: Lib-DSP-1001660037467-B-D08


title: Group 2_anti-mPD-1_G2_15_Necrosis_19_Run1_2

description: Library name: Lib-DSP-1001660037467-B-D07


title: Group 2_anti-mPD-1_G2_15_Tumor_11_Run1_2

description: Library name: Lib-DSP-1001660037467-B-C11


title: iPSC_organoid_control_iMacs_d20_R3


title: iPSC_organoid_injured_iMacs_d25_R1


title: Group 2_anti-mPD-1_G2_15_Tumor_12_Run1_2

description: Library name: Lib-DSP-1001660037467-B-C12


title: Group 2_anti-mPD-1_G2_15_Tumor_14_Run1_2

description: Library name: Lib-DSP-1001660037467-B-D02


title: iPSC_organoid_control_iMacs_d25_R1


title: Group 2_anti-mPD-1_G2_15_Tumor_9_Run1_2

description: Library name: Lib-DSP-1001660037467-B-C09


title: Group 2_anti-mPD-1_G2_15_Leading Edge_8_Run1_2

description: Library name: Lib-DSP-1001660037467-B-C08

value: Leading Edge


title: iPSC_organoid_injured d25_R2


title: iPSC_organoid_hyp d20_R3


title: iPSC_organoid_injured d25_R1


title: Group 2_anti-mPD-1_G2_15_Tumor_13_Run1_2

description: Library name: Lib-DSP-1001660037467-B-D01


title: iPSC_organoid_control_iMacs_d20_R2


title: Group 2_anti-mPD-1_G2_15_Tumor_10_Run1_2

description: Library name: Lib-DSP-1001660037467-B-C10


title: iPSC_organoid_control_iMacs_d20_R1


title: iPSC_organoid_hyp d20_R1


title: iPSC_organoid_injured d25_R3


title: Group 2_anti-mPD-1_G2_15_Leading Edge_7_Run1_2

description: Library name: Lib-DSP-1001660037467-B-C07


title: Group 2_anti-mPD-1_G2_15_Leading Edge_6_Run1_2

description: Library name: Lib-DSP-1001660037467-B-C06


title: iPSC_organoid_hyp d20_R2


title: Group 2_anti-mPD-1_G2_15_Leading Edge_1_Run1_2

description: Library name: Lib-DSP-1001660037467-B-C01


title: Group 2_anti-mPD-1_G2_15_Leading Edge_5_Run1_2

description: Library name: Lib-DSP-1001660037467-B-C05


title: sub-tiling of mammalian CRE BC library version 2

city: Seattle

first: Tony

last: Li

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: Library name: subtiles_v2

data_processing:
Reads were preprocessed to remove adapter reads and low quality base calling using trim_galore63 (default parameters for paired-end reads). After trimming, forward and reverse CRE reads were then joined and error-corrected with PEAR64 (small amplicons: options -v 4; larger amplicons: options -v 20). Next, CRE reads were mapped to their respective reference libraries using bowtie2 65 (v2.5.3) and BC reads were merged and tallied for each mapped CRE using custom Python and R scripts. Following this, BCs were filtered based on read count to remove low-abundance barcodes from the CRE-BC association. The resulting CRE-BC association dictionaries were utilized for downstream analyses, which included processing valid barcode counts for bulk MPRA.
Assembly: GRm38/mm10
Supplementary files format and content: barcode dictionary maps

extract_protocol:
Libraries were electroporated in NEB 3020K electro-competent cells. Plasmids from cells were bottlenecked and extracted using the Zymo MidiPrep kits per manufacture's instructions.
PCR amplification was performed from the plasmid libraries to generate the CRE-BC libraries. The reaction consisted of 12.5 µl KAPA2G Robust master mix, 1.25 μl 10 μM oJBL060 (appending Nextera P7 adapter), 1.25 μl 10 μM custom-indexed P5 primers (NextP5_index1-9), 0.25 μl of SYBr green 100×, and 8.75 μl water. PCR step was amplified with tracking by qPCR with 1 min at 95 °C, and cycles up to the qPCR inflection point with 15 s at 95 °C, 15 s at 65 °C and 1 min at 72 °C. The resulting amplified libraries are purified by 1.0× Ampure XP beads (Beckman Coulter).  Sequencing libraries were pooled and paired-end sequenced on the NextSeq2000 with the following primers and cycle numbers: read1 (CRE forward): 159 cycles, primer oJBL681/oJBL684; index1 (BC read): 15 cycles, primer oJBL061; read2 (CRE reverse): 158 cycles, primer oJBL683/oJBL686; index2 (sample index): 6 cycles, primer oJBL064. For libraries with larger amplicons, cycle numbers were adjusted: read1: 401 cycles; index1: 15 cycles; read2: 212 cycles; index2: 10 cycles.

value: parietal endoderm

tag: group

value: sub-tiling of mammalian


title: Group 1_Isotype Control_G1_5_Necrosis_23_Run1_2

description: Library name: Lib-DSP-1001660037467-B-B12

value: Isotype Control


title: sub-tiling of mammalian CRE BC library version 1

description: Library name: subtiles_v1


title: Group 2_anti-mPD-1_G2_15_Leading Edge_4_Run1_2

description: Library name: Lib-DSP-1001660037467-B-C04


title: model-optimized mammalian CRE BC library

description: Library name: CRE_optimization

value: model-optimized mammalian


title: model-driven evolutionary reconstitution CRE BC library

description: Library name: evo_model


title: Group 2_anti-mPD-1_G2_15_Leading Edge_2_Run1_2

description: Library name: Lib-DSP-1001660037467-B-C02


title: Group 2_anti-mPD-1_G2_15_Leading Edge_3_Run1_2

description: Library name: Lib-DSP-1001660037467-B-C03


title: compactification mammalian CRE BC library

description: Library name: compact

value: compactification mammalian


title: random evolutionary reconstitution CRE BC library

description: Library name: evo_random

value: random evolutionary reconstitution


title: Group 1_Isotype Control_G1_5_Tumor_16_Run1_2

description: Library name: Lib-DSP-1001660037467-B-B05

value: Tumor


title: Group 1_Isotype Control_G1_5_Necrosis_21_Run1_2

description: Library name: Lib-DSP-1001660037467-B-B10


title: Group 1_Isotype Control_G1_5_Necrosis_20_Run1_2

description: Library name: Lib-DSP-1001660037467-B-B09


title: Full length mammalian controls CRE BC library

description: Library name: full_length_CRE

value: Full length mammalian controls


title: Group 1_Isotype Control_G1_5_Necrosis_17_Run1_2

description: Library name: Lib-DSP-1001660037467-B-B06


title: Group 1_Isotype Control_G1_5_Necrosis_22_Run1_2

description: Library name: Lib-DSP-1001660037467-B-B11


title: internal IGVF promoter control CRE BC library

description: Library name: IGVF_controls

value: internal IGVF promoter control


title: deep saturation mutagenesis CRE BC library

description: Library name: DMS

value: deep saturation mutagenesis


title: derivatization mammalian CRE BC library

description: Library name: pCRE_v2

value: derivatization mammalian


title: minP-only control CRE BC library

description: Library name: negative_ctrls

value: minP-only control


title: Group 1_Isotype Control_G1_5_Tumor_15_Run1_2

description: Library name: Lib-DSP-1001660037467-B-B04


title: Group 1_Isotype Control_G1_5_Tumor_14_Run1_2

description: Library name: Lib-DSP-1001660037467-B-B03


title: Group 1_Isotype Control_G1_5_Tumor_12_Run1_2

description: Library name: Lib-DSP-1001660037467-B-B01


title: Kat6a HET KO proliferating, rep 4

city: Parkville

first: Nishika

last: Ranathunga

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute of Medical Research

description: Library name: P_5063_3

data_processing:
Base calling and quality scoring was performed by Illumina Real-Time Analysis (v2) software. FASTQ file generation and de-multiplexing was performed by bcl2fastq conversion software (v2.15.0.4).
Reads were aligned to the mouse genome by Rsubread version 2.10.5
Fragment (read pair) counts were summarized by Entrez Gene ID using the Rsubread's featureCounts function and NCBI's RefSeq annotation.
Assembly: mm39
Supplementary files format and content: tab-delimited text files (tsv). Columns represent Entrez Gene Id, Gene Symbol, total gene length (total base count of all exons) and the number of fragments mapping to that gene.

source_name: Neural stem cells

growth_protocol: The dorsal telencephalon of E12.5 embryos dissected and placed in 1 mL of NSC proliferation medium in an Eppendorf tube on ice. The tissue was mechanically dissociated and centrifuged at 200 g for 5 min and resuspended in fresh neural stem cell (NSC) proliferation medium [Neurocult medium and proliferation supplement mouse or rat (Stem Cell Technologies, 05702), 4 µg/ml heparin solution (Stem Cell Technologies, 07980), 10 ng/ml bovine recombinant fibroblast growth factor 2 (FGF2), 20 ng/ml murine epidermal growth factor (EGF)]. Cells were passed through a 70 µm cell strainer and plated onto 6 cm tissue culture Petri dishes and grown at at 37oC and 5% CO2. Neural stem cells (NSCs) were cultured as non-adherent neurospheres, 3x105 cells were passaged every 5-6 days into 10 cm dishes. For passaging, cells were collected in 15 cm Falcon tubes and chemically dissociated with Accutase (Stemcell Technologies, 07920), centrifuged at 200 g for 5 min, washed and resuspended in 2 mL of NSC proliferation medium. Live cells were quantified using trypan blue (Bio-Rad, 1450021) exclusion for viability with the Luna II automated cell counter (Logos Biosystems). Cells were frozen in NSC freezing medium [Neurocult medium and proliferation supplement mouse or rat, 4 µg/ml heparin solution, 10 ng/ml FGF2, 20 ng/ml EGF, 10% DMSO] at either passage 3 or passage 4 after approximately 72 h of growth without prior dissociation.

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen, 74106) for proliferating cells or RNeasy micro kit (Qiagen, 74004) for differentiating cells according to the manufacturer’s instructions, with the addition of the DNase I supplemental protocol.  RNA concentration and quality was analysed on the Agilent 4200 Tapestation using RNA tape (Agilent, 5067-5579).
200 ng of RNA per sample was used to generate stranded sequencing libraries using the TruSeq Stranded mRNA (100 ng plus kit, Illumina) according to the manufacturer’s instructions. The Samples were barcoded, pooled and sequenced on a NextSeq2000 instrument (Illumina).

treatment_protocol: Proliferating cells were plated in 6 well plates (1.5x10^5 cells) and cultures for 3 days before RNA collection.   To differentiate NSCs, cells were passaged after 72 h of growth, 6x10^5 cells were washed and resuspended in 3 mL of NSC differentiation medium [Neurocult medium and proliferation supplement mouse or rat, 1% heat inactivated embryonic stem cell qualified fetal bovine serum (HI ES-FBS) (Gibco, 30044333)] and plated onto 6 well plates precoated with 15 µg/mL poly-L-ornithine (Sigma-Aldrich, P4957) and 4.5 µg/mL laminin (Sigma-Aldrich, L2020). Differentiated cells were grown for 3 days at 37oC and 5% CO2.

value: Neural stem cells

tag: cell population

value: Proliferating

tag: litter

tag: kat6a genotype

value: HET KO


title: Kat6a HOM KO proliferating, rep 4

description: Library name: P_5063_1

value: HOM KO


title: orthologous mammalian CRE BC library

description: Library name: oCRE_v2

value: orthologous mammalian


title: Group 1_Isotype Control_G1_5_Tumor_13_Run1_2

description: Library name: Lib-DSP-1001660037467-B-B02


title: Group 1_Isotype Control_G1_5_Necrosis_19_Run1_2

description: Library name: Lib-DSP-1001660037467-B-B08

value: Necrosis


title: Group 1_Isotype Control_G1_5_Tumor_10_Run1_2

description: Library name: Lib-DSP-1001660037467-B-A11


title: EEF1aP-only control CRE BC library

description: Library name: positive_ctrls

value: parietal endoderm

value: EEF1aP-only control


title: Kat6a HOM KO proliferating, rep 3

description: Library name: P_4746_4


title: Kat6a WT proliferating, rep 4

description: Library name: P_4746_2

value: WT


title: Group 1_Isotype Control_G1_5_Tumor_11_Run1_2

description: Library name: Lib-DSP-1001660037467-B-A12

value: Isotype Control


title: Kat6a WT proliferating, rep 3

description: Library name: P_4633_8


title: Group 1_Isotype Control_G1_5_Leading Edge_8_Run1_2

description: Library name: Lib-DSP-1001660037467-B-A09

value: Leading Edge


title: Group 1_Isotype Control_G1_5_Tumor_9_Run1_2

description: Library name: Lib-DSP-1001660037467-B-A10

value: Tumor


title: Group 1_Isotype Control_G1_5_Leading Edge_7_Run1_2

description: Library name: Lib-DSP-1001660037467-B-A08


title: Kat6a HOM KO proliferating, rep 2

description: Library name: P_4633_6


title: Kat6a HET KO proliferating, rep 3

description: Library name: P_4633_5


title: Group 1_Isotype Control_G1_5_Leading Edge_4_Run1_2

description: Library name: Lib-DSP-1001660037467-B-A05


title: Kat6a HOM KO proliferating, rep 1

description: Library name: P_4633_1


title: Group 1_Isotype Control_G1_5_Leading Edge_5_Run1_2

description: Library name: Lib-DSP-1001660037467-B-A06


title: Group 1_Isotype Control_G1_5_Necrosis_18_Run1_2

description: Library name: Lib-DSP-1001660037467-B-B07


title: Group 1_Isotype Control_G1_5_Leading Edge_3_Run1_2

description: Library name: Lib-DSP-1001660037467-B-A04


title: Group 1_Isotype Control_G1_5_Leading Edge_2_Run1_2

description: Library name: Lib-DSP-1001660037467-B-A03


title: NTC_NTC_NTC_NTC_NTC_Run1_2

description: Library name: Lib-DSP-1001660037467-B-A01

value: NTC


title: Group 1_Isotype Control_G1_5_Leading Edge_1_Run1_2

description: Library name: Lib-DSP-1001660037467-B-A02


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Necrosis_24_Run1_1

description: Library name: Lib-DSP-1001660037466-A-H12


title: Kat6a HOM KO differentiating NSC, rep 2

description: Library name: D_4633_6

value: Differentiating


title: Kat6a HOM KO differentiating NSC, rep 3

description: Library name: D_4746_4


title: Group 1_Isotype Control_G1_5_Leading Edge_6_Run1_2

description: Library name: Lib-DSP-1001660037467-B-A07


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Necrosis_22_Run1_1

description: Library name: Lib-DSP-1001660037466-A-H10


title: Kat6a HET KO proliferating, rep 2

description: Library name: P_4633_3


title: Kat6a HOM KO differentiating NSC, rep 1

description: Library name: D_4633_4


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Necrosis_23_Run1_1

description: Library name: Lib-DSP-1001660037466-A-H11


title: Kat6a WT proliferating, rep 2

description: Library name: P_4346_7


title: Kat6a HET KO differentiating NSC, rep 4

description: Library name: D_4844_4


title: Kat6a WT proliferating, rep 1

description: Library name: P_4113_7


title: Kat6a HET KO differentiating NSC, rep 2

description: Library name: D_4746_7


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Necrosis_20_Run1_1

description: Library name: Lib-DSP-1001660037466-A-H08


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Necrosis_19_Run1_1

description: Library name: Lib-DSP-1001660037466-A-H07


title: Kat6a HET KO differentiating NSC, rep 1

description: Library name: D_4633_5


title: Kat6a HET KO proliferating, rep 1

description: Library name: P_4113_6


title: Kat6a HOM KO differentiating NSC, rep 4

description: Library name: D_5063_1


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Necrosis_21_Run1_1

description: Library name: Lib-DSP-1001660037466-A-H09


title: Kat6a WT differentiating NSC, rep 3

description: Library name: D_4633_8


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Tumor_16_Run1_1

description: Library name: Lib-DSP-1001660037466-A-H04


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Necrosis_17_Run1_1

description: Library name: Lib-DSP-1001660037466-A-H05


title: Kat6a HET KO differentiating NSC, rep 3

description: Library name: D_4809_2


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Tumor_15_Run1_1

description: Library name: Lib-DSP-1001660037466-A-H03


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Necrosis_18_Run1_1

description: Library name: Lib-DSP-1001660037466-A-H06


title: Kat6a WT differentiating NSC, rep 1

description: Library name: D_4113_7


title: Kat6a WT differentiating NSC, rep 4

description: Library name: D_4746_1


title: Kat6a WT differentiating NSC, rep 2

description: Library name: D_4364_7


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Tumor_14_Run1_1

description: Library name: Lib-DSP-1001660037466-A-H02


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Tumor_11_Run1_1

description: Library name: Lib-DSP-1001660037466-A-G11


title: IgG, Kat6a+/– differentiating NSPCs, replicate 3

first: Waruni

last: Abeysekera

state: Victoria

department: Bioinformatics

description: Library name: b3_II_Diff.IgG_Kat6A_HET-3

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the Mus musculus (mm39) genome by Rsubread version 2.12.3.
Read counts were summarized by genomic regions - Promoters (TSS - 1kb to TSS + 1kb) and Gene body of protein coding genes, and H3K4me1+/H3K27ac+ enhancer enriched regions - using the Rsubread's featureCounts function and Rsubread's inbuilt mm39 NCBI annotation.
Assembly: mm39
Supplementary files format and content: Tab-delimited text files for Promoter region counts of protein coding genes; columns represent Entrez Gene ID, region length in base counts, and the number of sequence reads mapping to that region.
Supplementary files format and content: Tab-delimited text files for Gene body counts of protein coding genes; columns represent Entrez Gene ID, gene length in base counts, and the number of reads mapping to that gene.
Supplementary files format and content: Tab-delimited text files for H3K4me1+ enhancer enriched regions; columns represent region ID, region length in base counts, and the number of reads mapping to that region.
Supplementary files format and content: Tab-delimited text files for H3K27ac+ enhancer enriched regions; columns represent region ID, region length in base counts, and the number of reads mapping to that region.
Supplementary files format and content: Tab-delimited text files for overlapping H3K4me1+/H3K27ac+ enhancer enriched regions; columns represent region ID, region length in base counts, and the number of reads mapping to that region.
Supplementary files format and content: Separate supplementary files containing sequence read counts for all samples in matrix form are also provided for each genomic region.
Library strategy: CUT&Tag

source_name: Differentiating Neural stem and progenitor cells

growth_protocol: Neural stem and progenitor cell isolation and culture The dorsal telencephalon of E12.5 embryos was dissected and placed in 1 ml of neural stem cell (NSC) proliferation medium  [Neurocult medium with the addition of proliferation supplement mouse or rat (STEMCELL Technologies, 05702), 4 µg/ml heparin solution (STEMCELL Technologies, 07980), 10 ng/ml bovine recombinant fibroblast growth factor 2 (FGF2), 20 ng/ml murine epidermal growth factor (EGF)] in Eppendorf tubes on ice. The tissue was mechanically dissociated and centrifuged at 200 g for 5 min and resuspended in fresh NSC proliferation medium. Cells were passed through a 70 µm cell strainer and plated onto 6 cm tissue culture Petri dishes and grown at 37oC in 5% CO2 in air. Proliferating neural stem and progenitor cell (NSPC) colonies were cultured as non-adherent neurospheres, 3x105 cells were passaged every 5-6 days into 10 cm dishes. For passaging, cells were collected in 15 ml Falcon tubes and chemically dissociated with Accutase (STEMCELL Technologies, 07920), centrifuged at 200 g for 5 min, washed and resuspended in 2 ml of NSC proliferation medium. Live cells were quantified using trypan blue (Bio-Rad, 1450021) exclusion in an automated cell counter (Luna II, Logos Biosystems). Cells were frozen in NSC freezing medium [Neurocult medium and proliferation supplement mouse or rat, 4 µg/ml heparin solution, 10 ng/ml FGF2, 20 ng/ml EGF, 10% DMSO] at either passage 3 or passage 4 after approximately 72 h of growth without prior dissociation.  Neural stem and progenitor cell differentiation To induce differentiation, NSPCs were passaged after 72 h of growth, 6x105 cells were washed and resuspended in 3 ml of NSC differentiation medium [Neurocult medium and proliferation supplement mouse or rat, 1% heat inactivated embryonic stem cell qualified foetal bovine serum (HI ES-FBS, Gibco, 30044333)] and plated onto 6 well plates precoated with 15 µg/mL poly-L-ornithine (Sigma-Aldrich, P4957) and 4.5 µg/mL laminin (Sigma-Aldrich, L2020). Differentiated cells were grown for 3 days at 37oC and 5% CO2.

extract_protocol:
Automated CUT&Tag sequencing To assess multiple histone marks and genome protein occupancies in each NSPCs preparation from an individual embryo, we followed an automated CUT&Tag protocol developed by Henikoff and colleagues (Janssens et al., 2021), which allows parallel processing of many samples detecting many targets in a 96-well plate format. We used a liquid handling robot (Bluewasher) for removing liquids and adding wash buffers to plates. For these CUT&Tag experiment, 1x106 NSPCs were cultured in a 20 cm dish for 3 days under proliferating conditions or 2x106 NSPCs were plated onto 10 cm dishes and cultured for 3 days under differentiation conditions. Both proliferating and differentiating NSPCs underwent chemical dissociation with Accutase (STEMCELL Technologies, 07920). NSPCs were collected, counted and washed. Cells were bound to concanavalin-A beads and permeabilised using 0.05% digitonin and 0.01% NP-40A. Permeabilised cells were counted, and 50,000 cells were aliquoted for each CUT&Tag reaction in a 96 well plate well. Cells were stained with primary antibody at 1:50 dilution overnight. Cells were stained with nanobody-Tn5 at 1:50 and tagmentation reactions were performed for 1 hour at 37˚C.
Tagmented fragments were isolated using SPRI beads. Optimal indexing PCR cycle number was determined by qPCR and all reactions for the same primary antibody were indexed using dual indexing primer (Mezger et al., 2018) for 9-20 PCR cycles. Sequencing libraries concentration ranged between 0.5-15 ng/µl as determined by QuantiFluor dsDNA. Indexed sequencing libraries were pooled and sequenced on NextSeq2000 using one P3 (1.2B reads) and three P2 (400M reads) kits producing 50 bp paired end reads and 8 bp dual indexing reads and standard Illumina sequencing primer. Some samples were re-amplified using the same number of indexing PCR cycles to acquire more material for sequencing. The antibodies to the following antigens were used: H3K9ac (Cell Signaling Technology, 9649), H3K14ac (Abcam, ab52946), H3K23ac (Millipore, 07355), MLL1 (Cell Signaling Technology, 14689), H3K4me3 (Active Motif, 36090), RNA polymerase II subunit A phosphorylated on Ser2 [POLR2A; also known as Phospho-Rpb1 CTD; (Cell Signaling Technology, 13499)], IgG (Epicypher, 13-0042).

tag: genotype

value: Kat6a Heterozygous

tag: cut&tag antibody

value: IgG (Epicypher 13-0042)


title: IgG, Kat6a-/– differentiating NSPCs, replicate 1

description: Library name: b3_II_Diff.IgG_Kat6A_HOM-1

value: Kat6a Homozygous

value: Differentiating Neural stem and progenitor cells


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Leading Edge_8_Run1_1

description: Library name: Lib-DSP-1001660037466-A-G08


title: IgG, Kat6a-/– differentiating NSPCs, replicate 3

description: Library name: b3_II_Diff.IgG_Kat6A_HOM-3


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Tumor_10_Run1_1

description: Library name: Lib-DSP-1001660037466-A-G10


title: IgG, Kat6a+/+ differentiating NSPCs, replicate 1

description: Library name: b3_II_Diff.IgG_Kat6A_WT-1

value: Kat6a Wildype


title: RNAP2, Kat6a-/– differentiating NSPCs, replicate 2

description: Library name: b3_II_Diff.RNAP2_Kat6A_HOM-2

value: POLR2A (Ser1616) phosphate subunit of RNA Pol II (Cell Signaling Technology 13499)


title: RNAP2, Kat6a+/– differentiating NSPCs, replicate 4

description: Library name: b3_Diff.RNAP2_Kat6A_HET-4


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Tumor_12_Run1_1

description: Library name: Lib-DSP-1001660037466-A-G12


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Tumor_9_Run1_1

description: Library name: Lib-DSP-1001660037466-A-G09


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Leading Edge_6_Run1_1

description: Library name: Lib-DSP-1001660037466-A-G06


title: RNAP2, Kat6a-/– differentiating NSPCs, replicate 3

description: Library name: b3_II_Diff.RNAP2_Kat6A_HOM-3


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Leading Edge_2_Run1_1

description: Library name: Lib-DSP-1001660037466-A-G02


title: RNAP2, Kat6a+/+ differentiating NSPCs, replicate 3

description: Library name: b3_Diff.RNAP2_Kat6A_WT-3


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Leading Edge_7_Run1_1

description: Library name: Lib-DSP-1001660037466-A-G07


title: RNAP2, Kat6a-/– differentiating NSPCs, replicate 1

description: Library name: b3_Diff.RNAP2_Kat6A_HOM-1


title: RNAP2, Kat6a+/+ differentiating NSPCs, replicate 1

description: Library name: b3_Diff.RNAP2_Kat6A_WT-1


title: Group 3_mIgG-mutmIL15_G3_21_Necrosis_24_Run1_1

description: Library name: Lib-DSP-1001660037466-A-F12


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Leading Edge_5_Run1_1

description: Library name: Lib-DSP-1001660037466-A-G05


title: RNAP2, Kat6a+/– differentiating NSPCs, replicate 3

description: Library name: b3_Diff.RNAP2_Kat6A_HET-3


title: Group 3_mIgG-mutmIL15_G3_21_Necrosis_23_Run1_1

description: Library name: Lib-DSP-1001660037466-A-F11


title: RNAP2, Kat6a+/– differentiating NSPCs, replicate 2

description: Library name: b3_Diff.RNAP2_Kat6A_HET-2


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Leading Edge_4_Run1_1

description: Library name: Lib-DSP-1001660037466-A-G04


title: RNAP2, Kat6a+/– differentiating NSPCs, replicate 1

description: Library name: b3_Diff.RNAP2_Kat6A_HET-1


title: H3K4me3, Kat6a-/– differentiating NSPCs, replicate 3

description: Library name: b3_II_Diff.H3K4me3_Kat6A_HOM-3

value: H3K4me3 (Active Motif 36090)


title: H3K4me3, Kat6a-/– differentiating NSPCs, replicate 1

description: Library name: b3_Diff.H3K4me3_Kat6A_HOM-1


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Leading Edge_3_Run1_1

description: Library name: Lib-DSP-1001660037466-A-G03


title: H3K4me3, Kat6a-/– differentiating NSPCs, replicate 2

description: Library name: b3_II_Diff.H3K4me3_Kat6A_HOM-2


title: Group 3_mIgG-mutmIL15_G3_21_Necrosis_20_Run1_1

description: Library name: Lib-DSP-1001660037466-A-F08


title: Group 3_mIgG-mutmIL15_G3_21_Necrosis_18_Run1_1

description: Library name: Lib-DSP-1001660037466-A-F06


title: Group 3_mIgG-mutmIL15_G3_21_Necrosis_19_Run1_1

description: Library name: Lib-DSP-1001660037466-A-F07


title: RNAP2, Kat6a+/+ differentiating NSPCs, replicate 2

description: Library name: b3_Diff.RNAP2_Kat6A_WT-2


title: Group 4_anti-mPD-1-mutmIL15_G4_31_Leading Edge_1_Run1_1

description: Library name: Lib-DSP-1001660037466-A-G01


title: H3K4me3, Kat6a+/– differentiating NSPCs, replicate 4

description: Library name: b3_Diff.H3K4me3_Kat6A_HET-4


title: Group 3_mIgG-mutmIL15_G3_21_Necrosis_21_Run1_1

description: Library name: Lib-DSP-1001660037466-A-F09


title: Group 3_mIgG-mutmIL15_G3_21_Necrosis_22_Run1_1

description: Library name: Lib-DSP-1001660037466-A-F10


title: Group 3_mIgG-mutmIL15_G3_21_Tumor_16_Run1_1

description: Library name: Lib-DSP-1001660037466-A-F04


title: H3K4me3, Kat6a+/– differentiating NSPCs, replicate 1

description: Library name: b3_Diff.H3K4me3_Kat6A_HET-1


title: H3K4me3, Kat6a+/+ differentiating NSPCs, replicate 1

description: Library name: b3_Diff.H3K4me3_Kat6A_WT-1


title: H3K4me3, Kat6a+/– differentiating NSPCs, replicate 3

description: Library name: b3_Diff.H3K4me3_Kat6A_HET-3


title: H3K4me3, Kat6a+/+ differentiating NSPCs, replicate 3

description: Library name: b3_Diff.H3K4me3_Kat6A_WT-3


title: Group 3_mIgG-mutmIL15_G3_21_Tumor_13_Run1_1

description: Library name: Lib-DSP-1001660037466-A-F01


title: Group 3_mIgG-mutmIL15_G3_21_Tumor_15_Run1_1

description: Library name: Lib-DSP-1001660037466-A-F03


title: Group 3_mIgG-mutmIL15_G3_21_Necrosis_17_Run1_1

description: Library name: Lib-DSP-1001660037466-A-F05


title: H3K4me3, Kat6a+/+ differentiating NSPCs, replicate 2

description: Library name: b3_Diff.H3K4me3_Kat6A_WT-2


title: H3K4me3, Kat6a+/– differentiating NSPCs, replicate 2

description: Library name: b3_Diff.H3K4me3_Kat6A_HET-2


title: MLL1, Kat6a-/– differentiating NSPCs, replicate 2

description: Library name: b3_II_Diff.MLL1_Kat6A_HOM-2

value: MLL1 (Cell Signaling Technology 14689)


title: MLL1, Kat6a-/– differentiating NSPCs, replicate 3

description: Library name: b3_II_Diff.MLL1_Kat6A_HOM-3


title: Group 3_mIgG-mutmIL15_G3_21_Tumor_11_Run1_1

description: Library name: Lib-DSP-1001660037466-A-E11


title: Group 3_mIgG-mutmIL15_G3_21_Tumor_14_Run1_1

description: Library name: Lib-DSP-1001660037466-A-F02


title: Group 3_mIgG-mutmIL15_G3_21_Tumor_9_Run1_1

description: Library name: Lib-DSP-1001660037466-A-E09


title: MLL1, Kat6a-/– differentiating NSPCs, replicate 1

description: Library name: b3_Diff.MLL1_Kat6A_HOM-1


title: Group 3_mIgG-mutmIL15_G3_21_Tumor_10_Run1_1

description: Library name: Lib-DSP-1001660037466-A-E10


title: Group 3_mIgG-mutmIL15_G3_21_Leading Edge_8_Run1_1

description: Library name: Lib-DSP-1001660037466-A-E08


title: Group 3_mIgG-mutmIL15_G3_21_Leading Edge_7_Run1_1

description: Library name: Lib-DSP-1001660037466-A-E07


title: Group 3_mIgG-mutmIL15_G3_21_Leading Edge_6_Run1_1

description: Library name: Lib-DSP-1001660037466-A-E06


title: MLL1, Kat6a+/– differentiating NSPCs, replicate 1

description: Library name: b3_Diff.MLL1_Kat6A_HET-1


title: MLL1, Kat6a+/– differentiating NSPCs, replicate 3

description: Library name: b3_Diff.MLL1_Kat6A_HET-3


title: Group 3_mIgG-mutmIL15_G3_21_Leading Edge_5_Run1_1

description: Library name: Lib-DSP-1001660037466-A-E05


title: MLL1, Kat6a+/– differentiating NSPCs, replicate 4

description: Library name: b3_Diff.MLL1_Kat6A_HET-4


title: Group 3_mIgG-mutmIL15_G3_21_Leading Edge_4_Run1_1

description: Library name: Lib-DSP-1001660037466-A-E04


title: MLL1, Kat6a+/+ differentiating NSPCs, replicate 1

description: Library name: b3_Diff.MLL1_Kat6A_WT-1


title: H3K23ac, Kat6a-/– differentiating NSPCs, replicate 3

description: Library name: b3_II_Diff.H3K23ac_Kat6A_HOM-3

value: H3K23ac (Millipore 07355)


title: Group 3_mIgG-mutmIL15_G3_21_Leading Edge_3_Run1_1

description: Library name: Lib-DSP-1001660037466-A-E03


title: MLL1, Kat6a+/– differentiating NSPCs, replicate 2

description: Library name: b3_Diff.MLL1_Kat6A_HET-2


title: MLL1, Kat6a+/+ differentiating NSPCs, replicate 3

description: Library name: b3_Diff.MLL1_Kat6A_WT-3


title: Group 3_mIgG-mutmIL15_G3_21_Leading Edge_2_Run1_1

description: Library name: Lib-DSP-1001660037466-A-E02


title: Group 3_mIgG-mutmIL15_G3_21_Tumor_12_Run1_1

description: Library name: Lib-DSP-1001660037466-A-E12


title: H3K23ac, Kat6a-/– differentiating NSPCs, replicate 2

description: Library name: b3_II_Diff.H3K23ac_Kat6A_HOM-2


title: H3K23ac, Kat6a-/– differentiating NSPCs, replicate 1

description: Library name: b3_Diff.H3K23ac_Kat6A_HOM-1


title: Group 2_anti-mPD-1_G2_14_Necrosis_24_Run1_1

description: Library name: Lib-DSP-1001660037466-A-D12

value: Necrosis


title: MLL1, Kat6a+/+ differentiating NSPCs, replicate 2

description: Library name: b3_Diff.MLL1_Kat6A_WT-2


title: Group 3_mIgG-mutmIL15_G3_21_Leading Edge_1_Run1_1

description: Library name: Lib-DSP-1001660037466-A-E01


title: Group 2_anti-mPD-1_G2_14_Necrosis_21_Run1_1

description: Library name: Lib-DSP-1001660037466-A-D09


title: Group 2_anti-mPD-1_G2_14_Necrosis_22_Run1_1

description: Library name: Lib-DSP-1001660037466-A-D10


title: Group 2_anti-mPD-1_G2_14_Necrosis_23_Run1_1

description: Library name: Lib-DSP-1001660037466-A-D11


title: H3K23ac, Kat6a+/– differentiating NSPCs, replicate 3

description: Library name: b3_Diff.H3K23ac_Kat6A_HET-3


title: H3K23ac, Kat6a+/– differentiating NSPCs, replicate 1

description: Library name: b3_Diff.H3K23ac_Kat6A_HET-1


title: H3K23ac, Kat6a+/+ differentiating NSPCs, replicate 3

description: Library name: b3_Diff.H3K23ac_Kat6A_WT-3


title: Group 2_anti-mPD-1_G2_14_Necrosis_19_Run1_1

description: Library name: Lib-DSP-1001660037466-A-D07


title: Group 2_anti-mPD-1_G2_14_Necrosis_17_Run1_1

description: Library name: Lib-DSP-1001660037466-A-D05


title: Group 2_anti-mPD-1_G2_14_Necrosis_20_Run1_1

description: Library name: Lib-DSP-1001660037466-A-D08


title: H3K23ac, Kat6a+/+ differentiating NSPCs, replicate 2

description: Library name: b3_Diff.H3K23ac_Kat6A_WT-2


title: H3K23ac, Kat6a+/– differentiating NSPCs, replicate 4

description: Library name: b3_Diff.H3K23ac_Kat6A_HET-4


title: H3K23ac, Kat6a+/– differentiating NSPCs, replicate 2

description: Library name: b3_Diff.H3K23ac_Kat6A_HET-2


title: Group 2_anti-mPD-1_G2_14_Necrosis_18_Run1_1

description: Library name: Lib-DSP-1001660037466-A-D06


title: H3K14ac, Kat6a-/– differentiating NSPCs, replicate 2

description: Library name: b3_II_Diff.H3K14ac_Kat6A_HOM-2

value: H3K14ac (Abcam, ab52946)


title: H3K23ac, Kat6a+/+ differentiating NSPCs, replicate 1

description: Library name: b3_Diff.H3K23ac_Kat6A_WT-1


title: Group 2_anti-mPD-1_G2_14_Tumor_14_Run1_1

description: Library name: Lib-DSP-1001660037466-A-D02


title: H3K14ac, Kat6a+/– differentiating NSPCs, replicate 4

description: Library name: b3_Diff.H3K14ac_Kat6A_HET-4


title: Group 2_anti-mPD-1_G2_14_Tumor_12_Run1_1

description: Library name: Lib-DSP-1001660037466-A-C12


title: Group 2_anti-mPD-1_G2_14_Tumor_15_Run1_1

description: Library name: Lib-DSP-1001660037466-A-D03


title: H3K14ac, Kat6a+/– differentiating NSPCs, replicate 2

description: Library name: b3_Diff.H3K14ac_Kat6A_HET-2


title: Group 2_anti-mPD-1_G2_14_Tumor_13_Run1_1

description: Library name: Lib-DSP-1001660037466-A-D01


title: Group 2_anti-mPD-1_G2_14_Tumor_16_Run1_1

description: Library name: Lib-DSP-1001660037466-A-D04


title: Group 2_anti-mPD-1_G2_14_Tumor_11_Run1_1

description: Library name: Lib-DSP-1001660037466-A-C11


title: H3K14ac, Kat6a+/– differentiating NSPCs, replicate 1

description: Library name: b3_Diff.H3K14ac_Kat6A_HET-1


title: H3K14ac, Kat6a-/– differentiating NSPCs, replicate 3

description: Library name: b3_II_Diff.H3K14ac_Kat6A_HOM-3


title: H3K14ac, Kat6a+/+ differentiating NSPCs, replicate 2

description: Library name: b3_Diff.H3K14ac_Kat6A_WT-2


title: Group 2_anti-mPD-1_G2_14_Tumor_9_Run1_1

description: Library name: Lib-DSP-1001660037466-A-C09


title: H3K14ac, Kat6a+/+ differentiating NSPCs, replicate 3

description: Library name: b3_Diff.H3K14ac_Kat6A_WT-3


title: H3K14ac, Kat6a-/– differentiating NSPCs, replicate 1

description: Library name: b3_Diff.H3K14ac_Kat6A_HOM-1


title: Group 2_anti-mPD-1_G2_14_Leading Edge_8_Run1_1

description: Library name: Lib-DSP-1001660037466-A-C08


title: H3K14ac, Kat6a+/– differentiating NSPCs, replicate 3

description: Library name: b3_Diff.H3K14ac_Kat6A_HET-3


title: H3K9ac, Kat6a-/– differentiating NSPCs, replicate 3

description: Library name: b3_II_Diff.H3K9ac_Kat6A_HOM-3

value: H3K9ac (Cell Signaling Technology 9649)


title: Group 2_anti-mPD-1_G2_14_Leading Edge_7_Run1_1

description: Library name: Lib-DSP-1001660037466-A-C07


title: H3K14ac, Kat6a+/+ differentiating NSPCs, replicate 1

description: Library name: b3_Diff.H3K14ac_Kat6A_WT-1


title: Group 2_anti-mPD-1_G2_14_Leading Edge_6_Run1_1

description: Library name: Lib-DSP-1001660037466-A-C06


title: Group 2_anti-mPD-1_G2_14_Tumor_10_Run1_1

description: Library name: Lib-DSP-1001660037466-A-C10


title: H3K9ac, Kat6a+/– differentiating NSPCs, replicate 3

description: Library name: b3_Diff.H3K9ac_Kat6A_HET-3


title: Group 2_anti-mPD-1_G2_14_Leading Edge_3_Run1_1

description: Library name: Lib-DSP-1001660037466-A-C03


title: H3K9ac, Kat6a+/– differentiating NSPCs, replicate 4

description: Library name: b3_Diff.H3K9ac_Kat6A_HET-4


title: H3K9ac, Kat6a-/– differentiating NSPCs, replicate 1

description: Library name: b3_Diff.H3K9ac_Kat6A_HOM-1


title: Group 2_anti-mPD-1_G2_14_Leading Edge_4_Run1_1

description: Library name: Lib-DSP-1001660037466-A-C04


title: H3K9ac, Kat6a+/– differentiating NSPCs, replicate 1

description: Library name: b3_Diff.H3K9ac_Kat6A_HET-1


title: H3K9ac, Kat6a+/– differentiating NSPCs, replicate 2

description: Library name: b3_Diff.H3K9ac_Kat6A_HET-2


title: Group 2_anti-mPD-1_G2_14_Leading Edge_5_Run1_1

description: Library name: Lib-DSP-1001660037466-A-C05


title: Group 1_Isotype Control_G1_2_Necrosis_22_Run1_1

description: Library name: Lib-DSP-1001660037466-A-B11

value: Isotype Control


title: H3K9ac, Kat6a-/– differentiating NSPCs, replicate 2

description: Library name: b3_II_Diff.H3K9ac_Kat6A_HOM-2


title: Group 1_Isotype Control_G1_2_Necrosis_21_Run1_1

description: Library name: Lib-DSP-1001660037466-A-B10


title: Group 1_Isotype Control_G1_2_Necrosis_20_Run1_1

description: Library name: Lib-DSP-1001660037466-A-B09


title: Group 1_Isotype Control_G1_2_Necrosis_23_Run1_1

description: Library name: Lib-DSP-1001660037466-A-B12


title: IgG, Kat6a-/– proliferating NSPCs, replicate 3

description: Library name: b2_Prol.IgG_Kat6A_HOM-3

source_name: Proliferating Neural stem and progenitor cells


title: H3K9ac, Kat6a+/+ differentiating NSPCs, replicate 2

description: Library name: b3_Diff.H3K9ac_Kat6A_WT-2


title: Group 2_anti-mPD-1_G2_14_Leading Edge_2_Run1_1

description: Library name: Lib-DSP-1001660037466-A-C02

value: Leading Edge


title: Group 2_anti-mPD-1_G2_14_Leading Edge_1_Run1_1

description: Library name: Lib-DSP-1001660037466-A-C01


title: Group 1_Isotype Control_G1_2_Necrosis_17_Run1_1

description: Library name: Lib-DSP-1001660037466-A-B06


title: IgG, Kat6a-/– proliferating NSPCs, replicate 1

description: Library name: b2_Prol.IgG_Kat6A_HOM-1

value: Proliferating Neural stem and progenitor cells


title: H3K9ac, Kat6a+/+ differentiating NSPCs, replicate 1

description: Library name: b3_Diff.H3K9ac_Kat6A_WT-1


title: IgG, Kat6a+/– proliferating NSPCs, replicate 3

description: Library name: b2_Prol.IgG_Kat6A_HET-3


title: H3K9ac, Kat6a+/+ differentiating NSPCs, replicate 3

description: Library name: b3_Diff.H3K9ac_Kat6A_WT-3


title: Group 1_Isotype Control_G1_2_Necrosis_19_Run1_1

description: Library name: Lib-DSP-1001660037466-A-B08


title: IgG, Kat6a-/– proliferating NSPCs, replicate 2

description: Library name: b2_Prol.IgG_Kat6A_HOM-2


title: IgG, Kat6a+/– proliferating NSPCs, replicate 4

description: Library name: b2_Prol.IgG_Kat6A_HET-4


title: Group 1_Isotype Control_G1_2_Necrosis_18_Run1_1

description: Library name: Lib-DSP-1001660037466-A-B07


title: Group 1_Isotype Control_G1_2_Tumor_13_Run1_1

description: Library name: Lib-DSP-1001660037466-A-B02

value: Tumor


title: IgG, Kat6a+/– proliferating NSPCs, replicate 1

description: Library name: b2_Prol.IgG_Kat6A_HET-1


title: Group 1_Isotype Control_G1_2_Tumor_16_Run1_1

description: Library name: Lib-DSP-1001660037466-A-B05


title: Group 1_Isotype Control_G1_2_Tumor_11_Run1_1

description: Library name: Lib-DSP-1001660037466-A-A12


title: Group 1_Isotype Control_G1_2_Tumor_12_Run1_1

description: Library name: Lib-DSP-1001660037466-A-B01


title: IgG, Kat6a+/– proliferating NSPCs, replicate 2

description: Library name: b2_Prol.IgG_Kat6A_HET-2


title: IgG, Kat6a+/+ proliferating NSPCs, replicate 1

description: Library name: b2_Prol.IgG_Kat6A_WT-1


title: IgG, Kat6a+/+ proliferating NSPCs, replicate 2

description: Library name: b2_Prol.IgG_Kat6A_WT-2


title: IgG, Kat6a+/+ proliferating NSPCs, replicate 3

description: Library name: b2_Prol.IgG_Kat6A_WT-3


title: RNAP2, Kat6a-/– proliferating NSPCs, replicate 2

description: Library name: b2_Prol.RNAP2_Kat6A_HOM-2


title: Group 1_Isotype Control_G1_2_Tumor_10_Run1_1

description: Library name: Lib-DSP-1001660037466-A-A11


title: Group 1_Isotype Control_G1_2_Tumor_14_Run1_1

description: Library name: Lib-DSP-1001660037466-A-B03


title: Group 1_Isotype Control_G1_2_Leading Edge_7_Run1_1

description: Library name: Lib-DSP-1001660037466-A-A08


title: Group 1_Isotype Control_G1_2_Leading Edge_8_Run1_1

description: Library name: Lib-DSP-1001660037466-A-A09


title: Group 1_Isotype Control_G1_2_Tumor_15_Run1_1

description: Library name: Lib-DSP-1001660037466-A-B04


title: RNAP2, Kat6a+/– proliferating NSPCs, replicate 2

description: Library name: b2_Prol.RNAP2_Kat6A_HET-2


title: RNAP2, Kat6a-/– proliferating NSPCs, replicate 1

description: Library name: b2_Prol.RNAP2_Kat6A_HOM-1


title: RNAP2, Kat6a+/– proliferating NSPCs, replicate 3

description: Library name: b2_Prol.RNAP2_Kat6A_HET-3


title: Group 1_Isotype Control_G1_2_Leading Edge_5_Run1_1

description: Library name: Lib-DSP-1001660037466-A-A06


title: RNAP2, Kat6a-/– proliferating NSPCs, replicate 3

description: Library name: b2_Prol.RNAP2_Kat6A_HOM-3


title: Group 1_Isotype Control_G1_2_Leading Edge_4_Run1_1

description: Library name: Lib-DSP-1001660037466-A-A05


title: Group 1_Isotype Control_G1_2_Tumor_9_Run1_1

description: Library name: Lib-DSP-1001660037466-A-A10


title: Group 1_Isotype Control_G1_2_Leading Edge_6_Run1_1

description: Library name: Lib-DSP-1001660037466-A-A07


title: RNAP2, Kat6a+/– proliferating NSPCs, replicate 4

description: Library name: b2_Prol.RNAP2_Kat6A_HET-4


title: H3K4me3, Kat6a-/– proliferating NSPCs, replicate 3

description: Library name: b2_Prol.H3K4me3_Kat6A_HOM-3


title: Group 1_Isotype Control_G1_2_Leading Edge_3_Run1_1

description: Library name: Lib-DSP-1001660037466-A-A04


title: RNAP2, Kat6a+/+ proliferating NSPCs, replicate 1

description: Library name: b2_Prol.RNAP2_Kat6A_WT-1


title: RNAP2, Kat6a+/– proliferating NSPCs, replicate 1

description: Library name: b2_Prol.RNAP2_Kat6A_HET-1


title: RNAP2, Kat6a+/+ proliferating NSPCs, replicate 3

description: Library name: b2_Prol.RNAP2_Kat6A_WT-3


title: HyHS_scRNA-Seq

city: Changsha

first: Xu

last: Feng

state: Hunan

address: 87# Xiangya Road

department: Department of Endocrinology, Endocrinology Research Center

institute: Xiangya Hospital of Central South University

description:
Library name: HS
10x Genomics

data_processing:
Raw 10x Genomics data were processed with Cell Ranger (v5.0.0) using default parameters to generate a gene-by-cell UMI count matrix. Downstream analysis was performed in Seurat (v3.1.2). Low-quality cells were filtered based on detected genes (<200), UMI counts (<1000), log10GenesPerUMI (<0.7), mitochondrial reads (>10%), or hemoglobin reads (>5%). The filtered matrix was normalized and scaled, variable genes were selected, and PCA/UMAP were performed for clustering. Marker genes and differential expression were identified using Seurat (FindAllMarkers/FindMarkers; P < 0.05, |log2FC| > 0.58). Cell types were annotated using SingleR. Astrocytes were subclustered using the same workflow, and pathway activity was assessed by GSVA.
Assembly: Mouse mm10
Supplementary files format and content: 10x Genomics filtered feature-barcode matrix

source_name: hypothalamus

extract_protocol:
Hypothalamus tissues from PF, HS, and QS mice were dissected and enzymatically digested with collagenase II, followed by mechanical dissociation. After dissociation, cell suspensions were collected for downstream single-cell library preparation.
Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3′ Reagent Kit v3 (10x Genomics) according to the manufacturer’s user guide. Briefly, single cells were partitioned into nanoliter-scale droplets and barcoded, and 10x cell barcodes and unique molecular identifiers (UMIs) were incorporated during reverse transcription to associate sequencing reads with individual cells. Following cDNA amplification, sequencing libraries were constructed and sequenced using an Illumina platform. The resulting 10x barcodes were used to assign reads back to individual partitions/cells.

value: hypothalamus

value: HS


title: Group 1_Isotype Control_G1_2_Leading Edge_2_Run1_1

description: Library name: Lib-DSP-1001660037466-A-A03


title: Group 1_Isotype Control_G1_2_Leading Edge_1_Run1_1

description: Library name: Lib-DSP-1001660037466-A-A02


title: NTC_NTC_NTC_NTC_NTC_Run1_1

description: Library name: Lib-DSP-1001660037466-A-A01

value: NTC


title: RNAP2, Kat6a+/+ proliferating NSPCs, replicate 2

description: Library name: b2_Prol.RNAP2_Kat6A_WT-2


title: HyQS_scRNA-Seq

description:
Library name: QS
10x Genomics

value: QS


title: HyPF_scRNA-Seq

description:
Library name: PF
10x Genomics

value: PF


title: H3K4me3, Kat6a+/– proliferating NSPCs, replicate 3

description: Library name: b2_Prol.H3K4me3_Kat6A_HET-3

value: Kat6a Heterozygous


title: H3K4me3, Kat6a-/– proliferating NSPCs, replicate 2

description: Library name: b2_Prol.H3K4me3_Kat6A_HOM-2

value: Kat6a Homozygous


title: Multiome, spleen T cells, ATAC

first: Yulong

last: Wei

address: 295 Congress Avenue

department: Microbial Pathogenesis

description: Library name: Spleen_ATAC

library_source: genomic single cell

data_processing:
Cite-seq, TCR, and Multiome files were demultiplexed using Cellranger mkfastq.
Assembly: mm10
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, per_barcode_metrics.csv
Supplementary files format and content: CellRanger output files: atac_cut_sites.bigwig, atac_fragments.tsv, atac_fragments.tsv.gz.tbi, atac_peak_annotation.tsv, atac_peaks.bed

source_name: spleen

extract_protocol:
Cite-seq with TCR: CD4 and CD8 T cells were isolated from kidney, spleen, and renal lymph node of lupus-prone MRL/MpJ-Faslpr/J or MRL/MpJ-Faslpr/J.Nur77-eGFP (sorted on eGFP expression). Single cells were encapsulated in Gel-Beads-in-Emulsion (GEMs) using the 10x Genomics Chromium Controller and Chromium Single Cell 5′ chemistry (5P HT v2 Next-GEM). Multiome: CD44hi T cells were isolated from  kidney, spleen and renal lymph node of lupus-prone MRL/MpJ-Faslpr/J mice. Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10x Genomics Chromium Controller with the Chromium Single Cell Multiome ATAC + Gene Expression kit. Library preparation and sequencing were performed at the Yale Center for Genome Analysis (YCGA).
The 10x Single Cell 5' with Feature Barcoding and Immune Receptor Mapping protocols (CG000330 Rev F,  CG000208 Rev G) with TotalSeq™-C cell hashing (HTO) was used to generate 5′ gene expression, TCR V(D)J enrichment , and  HTO (hashtag) libraries.
The Single Cell Multiome ATAC + Gene Expression portocol described by 10X Genomics (CG000338 Rev G) was used to generate 3' gene expression library and ATAC libraries.

value: spleen

value: T cells

value: Faslpr (MRL/MpJ-Faslpr/J)

tag: library type

value: TCR


title: H3K4me3, Kat6a-/– proliferating NSPCs, replicate 1

description: Library name: b2_Prol.H3K4me3_Kat6A_HOM-1

value: H3K4me3 (Active Motif 36090)


title: H3K4me3, Kat6a+/+ proliferating NSPCs, replicate 3

description: Library name: b2_Prol.H3K4me3_Kat6A_WT-3

value: Kat6a Wildype


title: Multiome, kidney T cells, ATAC

description: Library name: Kidney_ATAC

source_name: kidney

value: kidney


title: Multiome, spleen T cells, GEX

description: Library name: Spleen_RNA

molecule: polyA RNA


title: H3K4me3, Kat6a+/– proliferating NSPCs, replicate 4

description: Library name: b2_Prol.H3K4me3_Kat6A_HET-4


title: Multiome, kidney T cells, GEX

description: Library name: Kidney_RNA


title: Cite with TCR, mouse 4, eGFP negative, CD4 T cells, TCR

description:
Library name: Mouse_4_GFPneg_CD4_TCR
TCR V(D)J enrichment

data_processing:
Cite-seq, TCR, and Multiome files were demultiplexed using Cellranger mkfastq.
Assembly: mm10
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, per_barcode_metrics.csv
Supplementary files format and content: CellRanger output files: atac_cut_sites.bigwig, atac_fragments.tsv, atac_fragments.tsv.gz.tbi, atac_peak_annotation.tsv, atac_peaks.bed
Library strategy: TCR-Seq

source_name: mixed sample (kidney, spleen, renal lymph node)

value: CD4 T cells

value: Faslpr; Nur77-eGFP reporter (MRL/MpJ-Faslpr/J.Nur77-eGFP)

tag: hto


title: MLL1, Kat6a-/– proliferating NSPCs, replicate 3

description: Library name: b2_Prol.MLL1_Kat6A_HOM-3

value: Proliferating Neural stem and progenitor cells

value: MLL1 (Cell Signaling Technology 14689)


title: Cite with TCR, mouse 4, eGFP negative, CD4 T cells, GEX

description:
Library name: Mouse_4_GFPneg_CD4_RNA
polyA RNA

data_processing:
Cite-seq, TCR, and Multiome files were demultiplexed using Cellranger mkfastq.
Assembly: mm10
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, per_barcode_metrics.csv
Supplementary files format and content: CellRanger output files: atac_cut_sites.bigwig, atac_fragments.tsv, atac_fragments.tsv.gz.tbi, atac_peak_annotation.tsv, atac_peaks.bed
Library strategy: CITE-seq

value: mixed sample (kidney, spleen, renal lymph node)


title: H3K4me3, Kat6a+/– proliferating NSPCs, replicate 2

description: Library name: b2_Prol.H3K4me3_Kat6A_HET-2


title: Cite with TCR, mouse 4, eGFP positive, CD4 T cells, HTO

description:
Library name: Mouse_4_GFPpos_CD4_HTO
Hashtag Oligonucleotide
HTO_cellranger_antibody_list_with_barcode.csv

library_source: other

molecule: protein


title: Multiome, rLN T cells, ATAC

description: Library name: rLN_ATAC

source_name: renal lymph node

value: renal lymph node


title: Cite with TCR, mouse 4, eGFP positive, CD4 T cells, TCR

description:
Library name: Mouse_4_GFPpos_CD4_TCR
TCR V(D)J enrichment


title: MLL1, Kat6a+/– proliferating NSPCs, replicate 3

description: Library name: b2_Prol.MLL1_Kat6A_HET-3


title: Cite with TCR, mouse 4, eGFP positive, CD4 T cells, GEX

description:
Library name: Mouse_4_GFPpos_CD4_RNA
polyA RNA


title: Cite with TCR, mouse 3, eGFP negative, CD4 T cells, TCR

description:
Library name: Mouse_3_GFPneg_CD4_TCR
TCR V(D)J enrichment


title: MLL1, Kat6a+/+ proliferating NSPCs, replicate 2

description: Library name: b2_Prol.MLL1_Kat6A_WT-2


title: Multiome, rLN T cells, GEX

description: Library name: rLN_RNA


title: Cite with TCR, mouse 3, eGFP positive, CD4 T cells, TCR

description:
Library name: Mouse_3_GFPpos_CD4_TCR
TCR V(D)J enrichment


title: H3K4me3, Kat6a+/+ proliferating NSPCs, replicate 2

description: Library name: b2_Prol.H3K4me3_Kat6A_WT-2


title: H3K23ac, Kat6a-/– proliferating NSPCs, replicate 3

description: Library name: b2_Prol.H3K23ac_Kat6A_HOM-3

value: H3K23ac (Millipore 07355)


title: H3K4me3, Kat6a+/– proliferating NSPCs, replicate 1

description: Library name: b2_Prol.H3K4me3_Kat6A_HET-1


title: H3K4me3, Kat6a+/+ proliferating NSPCs, replicate 1

description: Library name: b2_Prol.H3K4me3_Kat6A_WT-1


title: Cite with TCR, mouse 3, eGFP positive, CD4 T cells, GEX

description:
Library name: Mouse_3_GFPpos_CD4_RNA
polyA RNA


title: Cite with TCR, mouse 2, eGFP negative, CD4 T cells, HTO

description:
Library name: Mouse_2_GFPneg_CD4_HTO
Hashtag Oligonucleotide
HTO_cellranger_antibody_list_with_barcode.csv


title: Cite with TCR, mouse 3, eGFP negative, CD4 T cells, GEX

description:
Library name: Mouse_3_GFPneg_CD4_RNA
polyA RNA


title: Cite with TCR, mouse 4, eGFP negative, CD4 T cells, HTO

description:
Library name: Mouse_4_GFPneg_CD4_HTO
Hashtag Oligonucleotide
HTO_cellranger_antibody_list_with_barcode.csv


title: H3K23ac, Kat6a+/– proliferating NSPCs, replicate 3

description: Library name: b2_Prol.H3K23ac_Kat6A_HET-3


title: Cite with TCR, mouse 2, eGFP negative, CD4 T cells, GEX

description:
Library name: Mouse_2_GFPneg_CD4_RNA
polyA RNA


title: MLL1, Kat6a-/– proliferating NSPCs, replicate 2

description: Library name: b2_Prol.MLL1_Kat6A_HOM-2


title: MLL1, Kat6a-/– proliferating NSPCs, replicate 1

description: Library name: b2_Prol.MLL1_Kat6A_HOM-1


title: MLL1, Kat6a+/– proliferating NSPCs, replicate 4

description: Library name: b2_Prol.MLL1_Kat6A_HET-4


title: MLL1, Kat6a+/– proliferating NSPCs, replicate 2

description: Library name: b2_Prol.MLL1_Kat6A_HET-2


title: MLL1, Kat6a+/– proliferating NSPCs, replicate 1

description: Library name: b2_Prol.MLL1_Kat6A_HET-1


title: Cite with TCR, mouse 3, eGFP negative, CD4 T cells, HTO

description:
Library name: Mouse_3_GFPneg_CD4_HTO
Hashtag Oligonucleotide
HTO_cellranger_antibody_list_with_barcode.csv


title: H3K23ac, Kat6a+/– proliferating NSPCs, replicate 1

description: Library name: b2_Prol.H3K23ac_Kat6A_HET-1


title: MLL1, Kat6a+/+ proliferating NSPCs, replicate 3

description: Library name: b2_Prol.MLL1_Kat6A_WT-3


title: Cite with TCR, mouse 4, eGFP negative, CD8 T cells, GEX

description:
Library name: Mouse_4_GFPneg_CD8_RNA
polyA RNA

value: CD8 T cells


title: H3K14ac, Kat6a-/– proliferating NSPCs, replicate 3

description: Library name: b2_Prol.H3K14ac_Kat6A_HOM-3

value: H3K14ac (Abcam, ab52946)


title: Cite with TCR, mouse 3, eGFP positive, CD4 T cells, HTO

description:
Library name: Mouse_3_GFPpos_CD4_HTO
Hashtag Oligonucleotide
HTO_cellranger_antibody_list_with_barcode.csv


title: MLL1, Kat6a+/+ proliferating NSPCs, replicate 1

description: Library name: b2_Prol.MLL1_Kat6A_WT-1


title: H3K23ac, Kat6a-/– proliferating NSPCs, replicate 2

description: Library name: b2_Prol.H3K23ac_Kat6A_HOM-2

value: Kat6a Homozygous


title: H3K14ac, Kat6a-/– proliferating NSPCs, replicate 1

description: Library name: b2_Prol.H3K14ac_Kat6A_HOM-1


title: Cite with TCR, mouse 4, eGFP positive, CD8 T cells, GEX

description:
Library name: Mouse_4_GFPpos_CD8_RNA
polyA RNA


title: Cite with TCR, mouse 4, eGFP negative, CD8 T cells, TCR

description:
Library name: Mouse_4_GFPneg_CD8_TCR
TCR V(D)J enrichment