title: Monocyte after 4 days in co-culture with PDO30

city: Mannheim

first: Volker

last: Ast

address: Theodor-Kutzer-Ufer 1-3

department: NGS Core Facility

institute: University Hospital Mannheim

description:
Library name: M0_p30
10x Genomics

data_processing:
Single-cell sequencing data were processed with the 10x Genomics Cell Ranger v7.0.0 software using the human reference genome GRCh38-3.0.0
Each pooled sample was subsequently demultiplexed by means of the SNP-based demultiplexing tool Freemuxlet (popscle. https://github.com/statgen/popscle)
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated values and matrix files

source_name: PBMC

growth_protocol: For the PDO/monocyte co-cultures, freshly isolated monocytes and 5-7 days old PDOs of PDO19 (M_PDO19) or PDO30 (M_PDO30) were resuspended in co-culture medium containing 20 ng/ml M-CSF and liquid 5% BME at a ratio of 2:1 (immune cell: PDO cell). The co-culture medium was freshly prepared by mixing equal parts of monocyte medium (RPMI supplemented with 10% heat-inactivated FCS, 100 U/ml Pen/Strep, 1 mM Sodium Pyruvate, 1X NEAA, 55 µM β mercaptoethanol), and PDO medium (Betge et al., Nature Communications 2022 13:1. 2022;13:1–15. doi: 10.1038/s41467-022-30722-9) excluding the apoptosis inhibitor Y-27632 and Nicotinamide. Monocyte/PDO co-culture were culture as suspension culture in UpCell cell culture plates for 4 days at 37°C. After 4 days of culture, cells were harvested by filtering through a 40 µm strainer, followed by counting and pooling the biological replicates. In addition to monocytes in monoculture (M_d4), polarization controls were conducted for each donor and polarized for 24 h prior to harvesting using 100 ng/ml LPS + 100 ng/ml IFN-g (M_LPS/IFNg) or 20 ng/ml IL-4 (M_IL4).  Additionally, monocytes of each donor were sequenced 16 h after immune cell isolation to provide an undifferentiated control (M_d0). Live CD45+ cells were sorted and loaded onto the Chromium Single-Cell Controller.

extract_protocol:
The sorted single-cell suspensions were loaded onto the Chromium Single-Cell Controller (10X Genomics) for droplet-based single-cell capture according to the manufacturer’s protocol.
Subsequent library preparation was performed according to the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10X Genomics, 14-16 cycles). Quality and quantity of the libraries was evaluated using the Bioanalyzer (Agilent) and Qubit (ThermoFisher), respectively. Sequencing was performed on an Illumina NovaSeq 6000 platform (paired-end, 150 bp reads length).

treatment_protocol: Monocytes was either cultured in monoculture (M_d4) or in co-culture with PDO19 or PDO30 for four days (M_PDO19 and M_PDO30). Polarizated monocytes were produced by stimulating for final 24h with 100 ng/ml LPS + 100 ng/ml IFN-g (M_LPS/IFNg) or 20 ng/ml IL-4 (M_IL4).

value: PBMC

value: myeloid cell

tag: timepoint


title: #5 KTC;Trp53fl/fl  (RNA-seq)

status: Public on Feb 18 2026

type: SRA

city: Stanford

first: Sofia

last: Ferreira

state: CA

address: 269 Campus Drive

department: Radiation Oncology

country: USA

institute: Stanford University School of Medicine

description: Library name: BF675 (KPT)

library_source: transcriptomic

data_processing:
We used 10X Genomics Long Ranger pipeline to map the reads to the mm10 reference mouse genome,
Assembly: Reads were aligned to the GRCm38 mouse genome using HISAT2 (v 2.0.4; RRID:SCR_015530)
Supplementary files format and content: xlsv format, normalized reads

molecule: total RNA

organism: Mus musculus

source_name: Pancreatic Ductal Adenocarcinoma

growth_protocol: Unless indicated otherwise, mice were aged until morbidity.

extract_protocol:
RNeasy midi kit (Qiagen, Cat#75144)
Illumina TruSeq RNA Sample Preparation kit (Cat# RS-122-2001) and Illumina HiSeq4000 (RRID:SCR_016386)

treatment_protocol: At 8-10 weeks of age, mice were administered 5 mg tamoxifen dissolved in 2% ethanol/corn oil via oral gavage once per day for 3 consecutive days.

tag: tissue

value: Pancreatic Ductal Adenocarcinoma

tag: cell type

value: Acinar-derived Pancreatic Ductal Adenocarcinoma

tag: genotype

value: KTC;Trp53fl/fl (K= KrasLSL-G12D; T=Rosa26LSL-tdTomato/LSL-tdTomato; C= Ptf1aCreER)


title: Monocyte after 4 days in co-culture, polarized with LPS/IFN-g

country: Germany

description:
Library name: M1
10x Genomics

library_source: transcriptomic single cell

organism: Homo sapiens

tag: treatment


title: #1 KrasLSL-G12D;Rosa26LSL-tdTomato/LSL-tdTomato;Ptf1aCreER (RNA-seq)

description:
Library name: SM5847 (KT)
Not represented in norm_counts.csv.


title: 103_P05_E03

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

description: Expression_CountValue.tsv,Expression_FPKM.tsv,Expression_TPM.tsv,Mutations.tsv

data_processing:
We used GATK Best Practices to call mutations from scRNAseq, bWTS and bWES datasets. Depends on the data there are some modifications in the pipeline. Briefly, after trimming and quality control of reads by FastQ (v0.11.9) and Trim Galore (v0.6.5), raw reads were mapped to the mouse genome (GRCm38, mm10) using STAR (v2.7.3a) in two-pass mode which improves the mapping quality at junction sites. Then Picard (v2.22.3) was used for removing duplicated mapped reads and doing indel realignment and base re-calibration. During base quality recalibration, dbSNP variants were used as known sites. In the next step, HaplotypeCaller (v3.8) was used to call the mutations for every single cell separately in GVCF mode. After that, GenotypeGVCFs was used to call the mutations in a joint mode (as pseudo-bulk). These steps keep specificity and sensitivity of calling mutations high. Afterward, the mutations were annotated using ANNOVAR (v2019.10.24). Following that, mutations that were marked as unknown and non-exonic were filtered out. For further confidence, mouse SNPs/Indels filtration was applied to the VCF files based on normal mouse spleen SNPs in addition to a curated in-house database. Finally, somatic-mutations associated with less than 10 reads in at least 2 cells were filtered out. RSEM (v1.3.2) was used to extract expected counts, TPM and FPKM information.
Assembly: mouse mm10
Supplementary files format and content: tab-delimited text files include expression matrix where rows are samples and columns are genes
Supplementary files format and content: tab-delimited text file include all exonic mutations in the samples

source_name: Tumor #103

extract_protocol: Smart-seq2 (Nature Protocol, 2014, 9: 171)

value: Melanoma cell line-derived tumor

tag: strain

value: HGF-tg C57BL6

tag: microbiota status

tag: sorting strategy

value: CD45-, CD31-, alive, nucleated cells


title: GM12878-DMSO-RAD21-CUTTAG-Rep2

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

library_source: genomic

data_processing:
CUT&TAG data were processed using the CUT&RUN tools 2.0 (https://github.com/XiangYe-Vandy/CUTRUN_tools) by selecting CUT&TAG (default) as the experiment type.
In brief, raw reads were trimmed tro remove sequencing adapters and mapped to the reference genome using bowtie2.
bigWig files were generated using bamCoverage and normalized with CPM.
Heatmaps and metagene plots were generated using Deeptools (v3.5.2).
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&TAG

molecule: genomic DNA

source_name: blood

extract_protocol:
Cells were dissociated with trypsin and wash twice with 1x PBS at RT.
0.1 million cells were used as input and processed with CUT&Tag kit (Vazyme, TD903) according to the manufacturer’s instructions. RAD21 primary antibody (GeneTex, GTX106012) was used.

value: blood

tag: cell line

value: lymphoblastoid

value: WT

value: DMSO


title: GM12878-DMSO-RAD21-CUTTAG-Rep1


title: 103_P05_D12


title: Monocyte after 4 days in co-culture with PDO19

description:
Library name: M0_p19
10x Genomics


title: 103_P05_E01


title: Monocyte after 4 days in co-culture, polarized with IL-4

description:
Library name: M2
10x Genomics


title: GM-batch1-TPT_8h_rep2

data_processing:
library strategy: Micro-C
Bulk Micro-C datasets were processed using distiller-nf pipeline.
Assembly: hg38
Supplementary files format and content: contact matrices (hic and mcool files) for each sample

extract_protocol:
For Micro-C, cells were permeabilized with 100 μL Micro-C buffer1 (50 mM NaCl, 10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 1 mM CaCl2, 0.2% IGEPAL CA630, 1 x PIC), incubate on ice for 20 min.
Micro-C

value: Topotecan

tag: biomaterial provider


title: Monocyte after 4 days in culture

description:
Library name: M0
10x Genomics


title: #2 KTC;Trp53fl/fl  (RNA-seq)

description: Library name: BF1987 (KPT)


title: GM-batch1-ETO_8h_rep2

value: Etoposide


title: GM-batch1-TPT_8h_rep1


title: #3 KTC;Trp53fl/fl  (RNA-seq)

description: Library name: BF2117 (KPT)


title: 103_P05_D11


title: #1 KTC;Trp53fl/fl  (RNA-seq)

description: Library name: BF1905 (KPT)


title: 103_P05_D10


title: KID018C, tumor tissue

city: Yokohama

first: Taku

last: Kouro

state: Kanagawa

address: 2-3-2 Nakao, Asahi-ku

department: Division of Cancer Immunotherapy

country: Japan

institute: Kanagawa Cancer Center Research Institute

description: Library name: KID018C

data_processing:
fastp 0.23.2, STAR 2.7.10b, RSEM v1.2.28
Assembly: GRCh38.113
Supplementary files format and content: text file containing gene_id, transcript_id, length, effective length, expected_count, TPM and FPKM

source_name: Kidney

extract_protocol:
Manufacturer's instructions for Rneasy plus mini was followed.
SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (TaKaRa) was used.

value: Kidney

value: ccRCC

tag: Stage

value: I

tag: Sex

value: female

value: No


title: 103_P05_D09


title: GM-batch1-ETO_8h_rep1


title: #5 KTC;Trp53fl/fl;Arf-fl/fl  (RNA-seq)

description: Library name: BF6418 (KPAT)

value: Pancreatic Ductal Adenocarcinoma

value: KTC;Trp53fl/fl;Arf-fl/fl (K= KrasLSL-G12D; T=Rosa26LSL-tdTomato/LSL-tdTomato; C= Ptf1aCreER)


title: GM-batch1-DMSO_8h_rep2


title: #4 KTC;Trp53fl/fl;Arf-fl/fl  (RNA-seq)

description: Library name: BF6393 (KPAT)

value: Acinar-derived Pancreatic Ductal Adenocarcinoma


title: KID016C, tumor tissue

description: Library name: KID016C

value: male


title: 103_P05_D08

value: Melanoma cell line-derived tumor

value: HGF-tg C57BL6


title: 103_P05_D07

value: CD45-, CD31-, alive, nucleated cells


title: KID015C, tumor tissue

description: Library name: KID015C

value: III


title: GM-batch1-DMSO_8h_rep1

value: blood

value: lymphoblastoid

value: WT


title: #3 KTC;Trp53fl/fl;Arf-fl/fl  (RNA-seq)

description: Library name: BF6322 (KPAT)


title: KID014C, tumor tissue

description: Library name: KID014C


title: 103_P05_D06


title: GM-103

data_processing:
Sequencing reads were mapped to the human reference genome assembly GRCh38 using STAR.
Read count extraction was performed using RSEM.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA counts for each cell

molecule: polyA RNA

extract_protocol:
Isolated single cell was lysed wih gentle lysis buffer (containing 0.45% NP-40), and the supernant was collected for the construction of sequencing library.
Collected supernant was amplified with standard Smart-seq2 protocol, then perform library preparation with homemade Tn5 transposase.
Smart-seq2

value: no treatment


title: GM-104


title: #2 KTC;Trp53fl/fl;Arf-fl/fl  (RNA-seq)

description: Library name: BF6296 (KPAT)


title: #1 KTC;Trp53fl/fl;Arf-fl/fl  (RNA-seq)

description: Library name: BF6271 (KPAT)


title: KID012C, tumor tissue

description: Library name: KID012C

value: Kidney


title: KID013C, tumor tissue

description: Library name: KID013C

value: ccRCC


title: 103_P05_D05


title: #4 KTC;Arf-fl/fl  (RNA-seq)

description: Library name: BF5630 (KAT)

value: KTC;Arf-fl/fl (K= KrasLSL-G12D; T=Rosa26LSL-tdTomato/LSL-tdTomato; C= Ptf1aCreER)


title: #5KTC;Arf-fl/fl  (RNA-seq)

description: Library name: BF5642 (KAT)


title: GM-102


title: GM-101


title: 103_P05_D03


title: 103_P05_D04


title: KID010C, tumor tissue

description: Library name: KID010C


title: #3KTC;Arf-fl/fl  (RNA-seq)

description: Library name: BF5628 (KAT)


title: 103_P05_D02


title: Monocyte after PBMC isolation

description:
Library name: Mono
10x Genomics

value: PBMC

value: myeloid cell


title: GM-100


title: GM-099


title: KID011C, tumor tissue

description: Library name: KID011C

value: female

value: No


title: 103_P05_D01


title: #1 KTC;Arf-fl/fl  (RNA-seq)

description: Library name: BF4405 (KAT)

value: Pancreatic Ductal Adenocarcinoma

value: Acinar-derived Pancreatic Ductal Adenocarcinoma


title: #2 KTC;Arf-fl/fl  (RNA-seq)

description: Library name: BF4855 (KAT)


title: GM-097


title: KID007C, tumor tissue

description: Library name: KID007C

value: IV

value: male


title: KID005C, tumor tissue

description: Library name: KID005C


title: 103_P05_C11

value: Melanoma cell line-derived tumor

value: HGF-tg C57BL6

value: CD45-, CD31-, alive, nucleated cells


title: 103_P05_C12


title: GM-096

value: blood

value: lymphoblastoid


title: GM-098

value: WT

value: no treatment


title: KID009C, tumor tissue

description: Library name: KID009C

value: Kidney

value: ccRCC


title: KID002C, tumor tissue

description: Library name: KID002C

value: I


title: liver tisue, HFD control5

city: Nanjing

first: Han

last: Chen

state: Jiangsu

address: #300 Guzhou Road, Gulou District

institute: Nanjing Medical University

description:
Library name: Sample9
liver tisue, HFD control5

data_processing:
GLC genomics Workbench
Assembly: hg38
Supplementary files format and content: CSV files

source_name: liver

extract_protocol:
RNA was harvested using Rensay mini plus kit. total  TNA was used for the construction of sequenceing library
RNA library for RNA-seq was prepared using SMARTER mRNA-seq Library Prep kit following manufacturer‘s protocols.’

value: liver


title: GM-095


title: liver tisue, HFD control4

description:
Library name: Sample8
liver tisue, HFD control4


title: GM-094


title: liver tisue, HFD control3

description:
Library name: Sample7
liver tisue, HFD control3


title: 103_P05_C09


title: 103_P05_C10


title: GM-093


title: liver tisue, HFD control2

description:
Library name: Sample6
liver tisue, HFD control2


title: KID001C, tumor tissue

description: Library name: KID001C


title: KID-018_T_cell_for_TCR, stage I RCC

description: Library name: KID-018_TCR

data_processing:
fastq files were proccessed with CellRanger pipline.
Output files of CellRanger were proccessed with Seurat v5.
Generated Seurat objects wree integrated using CCAIntegration argorithm.
TCR information generated by CellRanger were put into metadata slot of the integrated seurat object.
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx files were generated from the integrated Suerat object. TCR information was exported as Seurat metadata as cell_metadata.csv file.

source_name: kidney

extract_protocol: Manufacture's protocol for Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) was followed.

treatment_protocol: cut tissues were subjected to GentleMACS Oct with heater with protocol 37C_h_TDK_2. Dissociated cells were stained with anti-CD3e mAb and CD3e+ cells were sorted on FACSAriaII instrument.

value: kidney

tag: tissue type/stage

value: stage I RCC

value: T-cell


title: 103_P05_C08


title: KID-016_T_cell_for_TCR, stage I RCC

description: Library name: KID-016_TCR


title: 103_P05_C07


title: KID-015_T_cell_for_TCR, stage III RCC

description: Library name: KID-015_TCR

value: stage III RCC


title: GM-091


description:
Library name: Sample4
liver tisue, after Faecalibacterium prausnitzii treatment4

value: Faecalibacterium prausnitzii


title: liver tisue, HFD control1

description:
Library name: Sample5
liver tisue, HFD control1


title: KID-014_T_cell_for_TCR, stage III RCC

description: Library name: KID-014_TCR


description:
Library name: Sample3
liver tisue, after Faecalibacterium prausnitzii treatment3

data_processing:
GLC genomics Workbench
Assembly: hg38
Supplementary files format and content: CSV files
Library strategy: MeRIP-Seq


title: 103_P05_C05


title: GM-092


title: GM-090


title: KID-013_T_cell_for_TCR, stage III RCC

description: Library name: KID-013_TCR


description:
Library name: Sample2
liver tisue, after Faecalibacterium prausnitzii treatment2


title: GM-088


title: KID-011_T_cell_for_TCR, stage III RCC

description: Library name: KID-011_TCR


title: 103_P05_C04


title: 103_P05_C03


title: 103_P05_C01


title: 103_P05_C06


title: KID-012_T_cell_for_TCR, stage I RCC

description: Library name: KID-012_TCR


title: KID-010_T_cell_for_TCR, stage III RCC

description: Library name: KID-010_TCR


title: 103_P05_C02


title: Control

city: Chicago

first: Pinelopi

last: Kapitsinou

state: Il

address: 303 East Superior Street

department: Medicine/Nephrology

institute: Northwestern University, Feinberg School of Medicine

description:
Library name: Cre-IR
10X Genomics

data_processing:
Raw sequencing data in base call format (.bcl) was demultiplexed using Cell Ranger from 10x Genomics, converting the raw data into FASTQ format. Cell Ranger was also used for alignment of the FASTQ files to the mouse reference genome (mm10) and to count the number of reads from each cell that align to each gene
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Single-cell suspensions were prepared using Multi Tissue Dissociation Kit 2 (Miltenyi Biotec; Catalog # 130-110-203) following the instructions provided with the kit. Cell suspension was filtered through 100 µm and then 30 µm cell strainer.  Cell suspension was centrifuged at 400 x g for 10 minutes. Cell pellet was incubated with 1mL of RBC lysis buffer on ice for 1 minute. 10 mL neutralizing buffer (PBS with 2% Ffetal bovine serum) was added, and cells were recentrifuged at 400 x g for 5 minutes. Cell pellets were suspended in 10mL neutralizing buffer and centrifuged again at 100 x g for 5 minutes. Finally. cell pellet was suspended in 1X PBS with 0.04% BSA and filtered through 30 µm. Cell number and viability were analyzed using the Nexcelom Cellometer Auto 2000 with the AOPI fluorescent staining method.
The cDNA and library were generated using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics; Catalog # PN-1000286) and single Index Kit T Set A (10X Genomics; Catalog # PN-1000213) according to the  manufacturer’s manual. For the cell hashing library, it was constructed according to Biolegend’s published protocol on HTO library preparation guidelines with single index adapters . Quality control for the constructed library was performed by the Agilent Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies; Catalog # 5067-4626) and Qubit DNA HS Assay Kit for qualitative and quantitative analysis, respectively. The multiplexed libraries were pooled and sequenced on an Illumina HiSeq 4000 sequencer with 2X50 paired-end kits using the following read lengths: 28 bp for Read1 for cell barcode and UMI, and 90 bp for Read2 for transcript.

value: Cre-

value: Kidney ischemia reperfusion injury (IRI) induced by unilateral renal artery claming, followed by 4 total tamoxifen injections and analysis at Day 14 post IRI

tag: batch


title: Endothelial PHD3 haplodeficient

description:
Library name: PHD3-IR
10X Genomics

value: Cdh5-CreERT2; Phd3f/+


title: KID-009_T_cell_for_TCR, stageIV RCC

description: Library name: KID-009_TCR

value: stageIV RCC


title: GM-089

value: blood


title: 103_P05_B12

value: Melanoma cell line-derived tumor

value: HGF-tg C57BL6

value: CD45-, CD31-, alive, nucleated cells


description:
Library name: Sample1
liver tisue, after Faecalibacterium prausnitzii treatment1

value: WT


title: GM-087

value: lymphoblastoid

value: no treatment


title: GM-085


title: C23_318

description:
C1-C24 are clonal subline derived from single cells isolated from B2905 mouse melanoma cell lines (Nature Med. 2020, 26:781 )
Expression_CountValue.tsv, Expression_FPKM.tsv, Expression_TPM.tsv, Mutations.tsv

source_name: Melanoma cell line-derived tumor

extract_protocol:
Qiagen Rneasy (https://www.qiagen.com/cn/resources/download.aspx?id=14e7cf6e-521a-4cf7-8cbc-bf9f6fa33e24&lang=en)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: host strain


title: KID-006_T_cell_for_TCR, stage III RCC

description: Library name: KID-006_TCR


title: GM-086


title: KID-007_T_cell_for_TCR, stage IV RCC

description: Library name: KID-007_TCR

value: stage IV RCC


title: GM-083


title: 103_P05_B09


title: 103_P05_B11


title: GM-084


title: 103_P05_B10


title: C23_319


title: KID-002_T_cell_for_TCR, stage I RCC

description: Library name: KID-002_TCR

value: kidney


title: C22_315


title: KID-004_T_cell_for_TCR, stage III RCC

description: Library name: KID-004_TCR


title: C23_317


title: GM-082


title: GM-080


title: GM-081


title: C22_313


title: KID-018_T_cell_for_GEX, stage I RCC

description: Library name: KID-018_GEX

value: stage I RCC


title: 103_P05_B07


title: C22_311


title: 103_P05_B06


title: GM-079


title: 103_P05_B08


title: C18_295


title: 103_P05_B05


title: C18_292


title: KID-001_T_cell_for_TCR, stage I RCC

description: Library name: KID-001_TCR

value: T-cell


title: C18_293


title: GM-077


title: 103_P05_B03


title: KID-015_T_cell_for_GEX, stage III RCC

description: Library name: KID-015_GEX

value: stage III RCC


title: KID-014_T_cell_for_GEX, stage III RCC

description: Library name: KID-014_GEX


title: C16_282


title: GM-078


title: C16_285


title: GM-076


title: C16_281


title: GM-074


title: KID-012_T_cell_for_GEX, stage I RCC

description: Library name: KID-012_GEX


title: 103_P05_B02


title: KID-016_T_cell_for_GEX, stage I RCC

description: Library name: KID-016_GEX


title: 103_P05_B01


title: C15_578


title: GM-075


title: KID-013_T_cell_for_GEX, stage III RCC

description: Library name: KID-013_GEX


title: GM-073


title: 103_P05_B04


title: KID-011_T_cell_for_GEX, stage III RCC

description: Library name: KID-011_GEX


title: 103_P05_A11


title: KID-010_T_cell_for_GEX, stage III RCC

description: Library name: KID-010_GEX


title: GM-072


title: 103_P05_A12


title: GM-071


title: KID-009_T_cell_for_GEX, stageIV RCC

description: Library name: KID-009_GEX


title: GM-070


title: 103_P05_A09


title: KID-007_T_cell_for_GEX, stage IV RCC

description: Library name: KID-007_GEX


title: C15_561


title: C14_551


title: C15_560


title: GM-069


title: C14_543


title: KID-005_T_cell_for_GEX, stage IV RCC

description: Library name: KID-005_GEX


title: 103_P05_A08


title: 103_P05_A10


title: KID-006_T_cell_for_GEX, stage III RCC

description: Library name: KID-006_GEX


title: C14_544


title: 103_P05_A07


title: 103_P05_A06


title: GM-066


title: GM-067


title: KID-004_T_cell_for_GEX, stage III RCC

description: Library name: KID-004_GEX


title: 103_P05_A05


title: KID-005_T_cell_for_TCR, stage IV RCC

description: Library name: KID-005_TCR


title: KID-002_T_cell_for_GEX, stage I RCC

description: Library name: KID-002_GEX


title: C12_263


title: GM-068


title: C12_264


title: GM-065


title: KID-001_T_cell_for_GEX, stage I RCC

description: Library name: KID-001_GEX


title: pnet_009_MT2

city: Boston

first: William

last: Hwang

state: Massachusetts

address: 185 Cambridge St

department: Center for Systems Biology

institute: Massachusetts General Hospital

description:
Library name: pnet_009_MT2
pnet9_toshare.rds

data_processing:
BCL files were converted to FASTQ using bcl2fastq2-v2.20.
CellRanger v6.0.0 was used to demultiplex the FASTQ reads, align them to the hg38 human transcriptome (pre-mRNA) reference and extract the UMI and nuclei barcodes.
For each sample, doublets were identified and removed using scDblFinder v.1.22.0 with default parameters
Nuclei were filtered for minimum number of features of 200, proportion of mitochondrial genes and maximum number of features with thresholds determined for each sample.
UMI counts were normalized by the total number of UMIs per nucleus and converted to transcripts-per-10,000 (TP10K) as the final expression unit.
Assembly: hg38
Supplementary files format and content: CellRanger outputs

molecule: nuclear RNA

source_name: liver metastasis

extract_protocol:
Resected primary tumor samples were snap frozen and stored at -80°C. Selected tissue was transferred into an NSTcPA buffer and manually minced. Nuclei from each sample were loaded into each channel of a Chromium single-cell 3’ chip according to the manufacturer’s instructions. Single nuclei were partitioned into droplets with gel beads in the Chromium Controller to form emulsions, after which nuclear lysis, barcoded reverse transcription of mRNA, cDNA amplification, enzymatic fragmentation, and 5’ adaptor and sample index attachment were performed according to manufacturer’s instructions.
The snRNA-seq sample libraries were pooled (3-4 samples per flow cell line) and sequenced on the NovaSeq 6000 with the following paired end read configuration: read 1, 28 nt; read 2, 90 nt; index read, 10 nt.

value: liver metastasis

value: untreated


title: GM-064


title: C12_265


title: 103_P05_A04


title: C11_508


title: 103_P05_A01


title: GM-063


title: pnet_009_MT1

description:
Library name: pnet_009_MT1
pnet9_toshare.rds


title: 103_P05_A02


title: C11_506


title: C11_502


title: 103_P05_A03


title: GM-062


title: C8_245


title: MGH_021

description:
Library name: MGH_021
pnet_primary_toshare.rds

source_name: primary pancreas tumor

value: primary pancreas tumor


title: GM-060


title: C8_244


title: mesc_rad21_depletion_untreated_192, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv

data_processing:
Smart-seq3 data were processed using zUMIs (https://github.com/sdparekh/zUMIs).
Bulk RNA-seq data were mapped to human reference genome using STAR and RSEM was used to calculate mRNA count for each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA counts for each cell and sample
Supplementary files format and content: tab-delimited text files include cell barcode and sample information for Smart-seq3

source_name: mouse embryonic stem cell

extract_protocol:
Isolated single cell was lysed wih gentle lysis buffer (containing 0.45% NP-40), and the supernant was collected for the construction of sequencing library.
Collected supernant was amplified with standard Smart-seq3 protocol, then perform library preparation with homemade Tn5 transposase.
Smart-seq3 & bulk RNA-seq

value: mouse embryonic stem cell

value: untreat


title: mesc_rad21_depletion_untreated_191, Smart-seq3


title: pnet_023

description:
Library name: pnet_023
pnet_primary_toshare.rds


title: pnet_022

description:
Library name: pnet_022
pnet_primary_toshare.rds


title: GM-058

value: blood


title: mesc_rad21_depletion_untreated_190, Smart-seq3


title: pnet_009_PT1

description:
Library name: pnet_009_PT1
pnet9_toshare.rds


title: C8_241

value: Melanoma cell line-derived tumor


title: mesc_rad21_depletion_untreated_189, Smart-seq3


title: pnet_021

description:
Library name: pnet_021
pnet_primary_toshare.rds


title: C4_225


title: pnet_019

description:
Library name: pnet_019
pnet_primary_toshare.rds


title: C4_222


title: GM-056


title: GM-057


title: mesc_rad21_depletion_untreated_187, Smart-seq3


title: pnet_017

description:
Library name: pnet_017
pnet_primary_toshare.rds


title: GM-055


title: mesc_rad21_depletion_untreated_186, Smart-seq3


title: pnet_016

description:
Library name: pnet_016
pnet_primary_toshare.rds


title: C1_480


title: C4_223


title: C1_481


title: GM-054


title: GM-053


title: mesc_rad21_depletion_untreated_185, Smart-seq3


title: mesc_rad21_depletion_untreated_184, Smart-seq3


title: pnet_015

description:
Library name: pnet_015
pnet_primary_toshare.rds


title: GM-052


title: GM-051


title: mLN_Light_treatment

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

description: Library name: mLN_Light_treatment

data_processing:
The raw data was quality control using fastqc and then trimmed of the Nextera adaptor. Following trimming, the Drop-seq-Tools pipeline was used to filter the data with a Phred quality score threshold of 30 for sample barcode and UMI identify and poly(A) trimming. The filtered data was mapped to the mouse genome(mm10) using STAR 2.5.1a, and the reads counted using Drop-seq-Tools.
Assembly: mm10

source_name: lymph node

extract_protocol:
RNA were extrat from the cell using the magic-beads combined with poly T
RNAs were extracted with oligo-dT magnetic beads. The isolated RNA was incubated with the 20 μL reverse transcription mix consisting of 100 unit Hiscript III Reverse Transcriptase (Vazyme, R303), 40 unit RNase Inhibitor (Vazyme, R301),1 μL 25 mM dNTP mix, 1 μL 100 mM DTT, 1 μL 1 val Betaine (Sigma, B0300-1VL), 0.5 μL 5% Digitonin, 0.5 μL TSO-LNA and 0.5 μL 5 μM Probe. The reaction was incubated at 42℃ for 90 min. Following cDNA synthesis, the sample were pooled, cleaned and concentrated with cleanup beads at a 1:0.8 of DNA to beads ration and eluted in 30 μL of ddH2O. Second-strand synthesis and pre-amplification were performed in a 50 μL reaction, consisting of 2 X KAPA HiFi Ready mix and 0.5 μM TSO-PCR primer, with the following PCR setup initial denaturation at 98 °C for 3 min, (denaturation at 98 °C for 15 s, annealing at 65 °C for 30 s, elongation at 72 °C for 6 min) repeated for 8 cycle, and a final elongation at 72 °C for 10 min. The DNA was cleanup using DNA cleanup beads at a ratio of 1:0.8 of DNA to beads and eluted with 30 μL of ddH2O. The library was prepared with the TruePrep DNA Library Prep Kit V2 for Illumina according to the manufacturer. Probe was designed by TSO, sample barcode(7-mer), UMI(8-mer) and Oligo(dT).

treatment_protocol: Mice were irradiated with a laser device (LaserMedix1500, Fotonmedix Mecal Laser, China) with an output power of 1.22 W, a wavelength of 980 nm, 80% duty, covering 4 square centimeters of spots, and each treatment was performed for five minutes every two days.

value: lymph node

value: CD4 T cell

value: 980 nm Light treatment


title: pnet_014

description:
Library name: pnet_014
pnet_primary_toshare.rds


title: mesc_rad21_depletion_untreated_183, Smart-seq3


title: mLN_Control

description: Library name: mLN_Control

value: Control


title: pnet_013

description:
Library name: pnet_013
pnet_primary_toshare.rds


title: GM-050

value: lymphoblastoid

value: WT

value: no treatment


title: pnet_010

description:
Library name: pnet_010
pnet_primary_toshare.rds


title: Colon_Light_treatment

description: Library name: Colon_Light_treatment

source_name: Colon

value: Colon


title: mesc_rad21_depletion_untreated_182, Smart-seq3


title: mesc_rad21_depletion_untreated_181, Smart-seq3


title: GM-049


title: Colon_Control

description: Library name: Colon_Control


title: GM-048


title: mesc_rad21_depletion_untreated_180, Smart-seq3


title: pnet_8

description:
Library name: pnet_8
pnet_primary_toshare.rds


title: mesc_rad21_depletion_untreated_179, Smart-seq3


title: GM-047


title: pnet_012

description:
Library name: pnet_012
pnet_primary_toshare.rds


title: Si

city: Hangzhou

first: wang

last: my

address: Cangqian Street, Cangxing Street

institute: BoYu Intelligent Health Innovation Laboratory, Hangzhou, 311100, P. R. China.

description: Library name: Sample4

data_processing:
seeksoultools Single-Cell toolkit [version 1.2.0] was applied to align reads against the mm10 mouse reference genome and generatethe preliminary unigue molecular identifier (UMI) matrix. The R package Seurat (version 4.4.0) was used to analyze the snRNA-seq data.We performed stringent quality control to filter out low-quality cells based , First, we filter out genes that appear in fewer than 3 cells and cells with fewer than 200 genes when creating the Seurat object. Then we use two metrics， including the number of detected genes, and the proportion of mitochondrial gene UMI counts. Specifically, cells with (1) less than 200 olmore than 4,000 detected genes, and (2) more than 5%  mitochondrial genecounts, were filtered out. We then adopted the Seurat-implemented NomalzeData function to perform the library-size correctionand logarithm transformation, with the obtained expression matrix used for downstream analyses.
We used the reciprocal PCA integration approach on the 2000 most variable features to combine the nuclei from each sample. We first found the integration anchors with the FindIntegrationAnchors function then used the IntegrateData function in Seurat v4 to integrate all our filtered nuclei.
We used the reciprocal PCA integration approach on the 2000 most variable features to combine the nuclei from each sample. We first found the integration anchors with the FindIntegrationAnchors function then used the IntegrateData function in Seurat v4 to integrate all our filtered nuclei.
The integrated dataset was scaled using the ScaleData function in Seurat. First, PCA dimensionality reduction analyses were done to identify 30 principal components (PCs). To further reduce the dimensionality and cluster our nuclei by their gene expression profile, we conducted UMAP analyses on the 30 PCs with highest standard deviation with RunUMAP function in Seurat. Then, we clustered our cells using FindNeighbors (reduction = "pca", dims = 1:30) and FindClusters (resolution = 0.8) function in Seurat.
Adipose-related pathway activities were quantified at single-cell resolution using AUCell(version 1.24.0). Genes within each cell were ranked by expression, and the area under the curve (AUC) for cumulative distributions of predefined gene sets was computed. Scores were stored as an assay in the Seurat object and visualized via Dotplot to compare pathway activities across cell types.
CellChat (version 1.6.0) inferred ligand-receptor-mediated communication networks by integrating expression data with a curated interaction database. Interaction weights were derived from ligand/receptor co-expression and pathway hierarchy. Network significance was assessed using permutation tests (1,000 iterations), and the Trimean-L/R model quantified signal transmission strength. Secreted signaling networks centered on adipocyte progenitors were analyzed to elucidate adipocyte-microenvironment crosstalk. By assigning a cell communication probability value to each interaction and conducting permutation tests, we inferred biologically meaningful cell-cell communication.
The GSVA R package (v1.48.0) evaluated enrichment scores for IGF- and VEGF-related pathways across cell types. This non-parametric method identified gene sets with significant expression variation by comparing their ranked expression profiles to a background model.
First we do batch correction and data integration and dimensionality reduction clustering of adipocytes in brown adipose tissue.Then, the top 2000 highly variable genes (HVGs were selected by the FindvariableFeatures function (Seurat) with the parameter selection.method = "vst". Efectsof the total UMI count and mitochondrial gene percentage were then regressed out from the HVG expression matrix with the ScaleData function (Seurat). The principal component analysis was then performed by the RunPCA function (Seurat) on the scaled HVG expression matrix, To further reduce the dimensionality and cluster our nuclei by their gene expression profile, we conducted UMAP analyses on the 30 PCs with highest standard deviation with RunUMAP function in Seurat. Then, we clustered our cells using FindNeighbors (reduction = "pca", dims = 1:30) and FindClusters (resolution = 0.3) function in Seurat.Cell differentiation trajectories were reconstructed with Monocle2 (v2.26.0). After dimensionality reduction via DDRTree, a minimum spanning tree (MST) was constructed to order cells along pseudotime. Branch points and dynamic gene expression patterns were identified to delineate AP differentiation into myofibroblasts (myoFBs) and characterize AP subpopulation trajectories.
Assembly: mm10
Supplementary files format and content: The processed data for each sample contains three files: matrix.mtx.gz, feature.tsv.gz, and barcodes.tsv.gz

source_name: Beige Adipose Tissue

extract_protocol:
After euthanasia, the target adipose tissue was rapidly isolated under sterile conditions and rinsed to remove blood vessels and connective tissues. The tissue was then minced, enzymatically digested, and filtered through a sieve. Finally, the cells were resuspended in PBS, and cell viability was assessed before adjusting the concentration for single-cell sequencing.
Library construction was performed according to the SeekGene single-cell sequencing protocol.

value: Beige Adipose Tissue

value: High-Fat Diet Surgery Group


title: pnet_7

description:
Library name: pnet_7
pnet_primary_toshare.rds


title: GM-059


title: mesc_rad21_depletion_untreated_178, Smart-seq3


title: GM-046


title: Ji

description: Library name: Sample2

value: High-Fat Diet Sham Group


title: GM-045


title: mesc_rad21_depletion_untreated_177, Smart-seq3


title: pnet_6

description:
Library name: pnet_6
pnet_primary_toshare.rds

value: untreated


title: pnet_4

description:
Library name: pnet_4
pnet_primary_toshare.rds

value: primary pancreas tumor

value: CAPTEM and lanreotide


title: Je

description: Library name: Sample1

source_name: Brown Adipose Tissue

value: Brown Adipose Tissue


title: mesc_rad21_depletion_untreated_176, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv

value: mouse embryonic stem cell

value: untreat


title: pnet_3

description:
Library name: pnet_3
pnet_treated_toshare.rds

value: CAPTEM and chemoradiation


title: Se

description: Library name: Sample3


title: mesc_rad21_depletion_untreated_175, Smart-seq3


title: pnet_2

description:
Library name: pnet_2
pnet_treated_toshare.rds


title: GM-043

value: blood


title: GM-042


title: E912_CKDL230036284-1A_HGLGMDSX7_L1, Mutation_3

city: Columbus

first: Ganesh

middle: Ram

last: Koshre

state: OH

address: 460 W 12th Ave

institute: The Ohio State University

description: Library name: Sample12

data_processing:
fastqc is used to check the sequencing quality (fastqc v0.11.8)
trimming is done while using the cutadapt for adapter removal (cutadapt v1.9.1)
geneome alignment is done with hg38 while suing star alignment tools (star_alignment v2.7.2b)
samtools is sued to convert sam to bam, sorting and index file generation
featurecounts are used to count the fpkm and Deseq2 is used for differential analysis (DESeq2.1.48.1)
Assembly: hg38
Supplementary files format and content: countdata with txt format
Supplementary files format and content: countdata with txt format

source_name: Epithelial Adenocarcinoma

growth_protocol: MDMB231 cells were maintained in DMEM sypplemented with 10% Fetal Bovine Serum (FBS) and antibiotics in humidified atomsphere with 5% CO2 at 37C

extract_protocol:
cells were seed and wait for 70% confluency in DMEM media
RNA was extracted while using the Rneasy mini kit 1.5ug of RNA is used for library preparation (cat. No. 74104), RNA library preparation is made while using NEBNexta kit protocols and screened with Tapestation HS-DNA1000 (10-1000pg/ul) (NEBNexta poly(A)mRNA E7490L)

treatment_protocol: WT_Dicer DNA and Mutatnt Dicer DNA was transfected cells while using the lipofectamine 3000 reagent in MDMB231 cells

value: Epithelial Adenocarcinoma

value: Mutation_3 plasmid transfection


title: GM-044

value: lymphoblastoid


title: SFN_ZH_Chip_Rad21_S0410_nipbl_clone17_release_no_auxin

city: Shenzhen

first: Haoyue

last: Zhang

address: Gaoke Innovation Center, Guangqiao Road, Guangming District, Shenzhen

institute: Shenzhen Bay Lab

description: Library name: sample15

data_processing:
In-situ Hi-C from all samples were processed through HiC-Pro(v3.0.0) workflow. Reads were aligned to the mouse reference genome mm9 using the bowite2(v2.3.5.1) software (global parameters: --very-sensitive -L 30 --score-min L, -0.6, -0.2 --end-to-end –reorder; local parameters: --very-sensitive -L 20 --score-min L, -0.6, -0.2 --end-to-end --reorder). The output SAM files were subsequently sorted and mapped to the bed files labeled with corresponding restriction sites to get the hic fragments. Finally, the fragments were merged into valid interaction pairs as output. We then converted the output pair files into “.hic” files using juicertools (v 1.19.02).  HiC files were also converted to “.cool” files with different resolutions using the Hicexplorer (v3.7). By default, all contact maps, saddle plots, compiled plots (such as APA plots) in the main figures are merged plots of all corresponding clones or biological replicates.
ChIP-seq and CUT&Tag data were processed in a similar pipeline as follows. Briefly, ChIP-seq paired-end reads were aligned to mouse reference genome mm9 through the Bowtie2 (v2.3.5.1) software with default parameters, while CUT&Tag adopted stricter parameters setting as ‘--very-sensitive -I 10 -X 700’. All unmapped reads and low-quality alignments with MAPQ score lower than 30 were removed using SAMtools (v1.9). PCR duplicates were removed using Picard (v2.23.3) with default parameters. The de-duplicated data was then converted into bed file format to remove the reads aligned to mitochondria, random contigs and blacklisted regions using BEDtools (v2.27.1). Finally, the bed files were reconverted into bam files and were mapped to the genome using bamcoverage from deeptools(v3.1.3), with normalization method set to CPM.
Assembly: mm9
Supplementary files format and content: cool, hic and bigwig files of each individual biological replicate are provided.

source_name: erythroid

growth_protocol: G1E-ER4 is a subline of the GATA1-null proerythroblast cell line G1E (Weiss et al, Mol. Cell. Biol. 17, 1642–51 (1997).). Cells were cultered in IMDM medium, supplemented with 15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha at 37 degrees with 5% CO2 (as described in Weiss et al., 1997).

extract_protocol:
For Hi-C, FACS purified cells (0.1 million) were lysed in 1ml cold Cell Lysis Buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40/Igepal) for 10min on ice. Nuclei were pelleted at 4℃ and washed once with cold 1.4 × NEB buffer 3.1 (NEB Cat#B7203S). Nuclei were then re-suspended in 25ul of 1.4 × NEB buffer 3.1 and treated with 0.1% SDS for 10min at 65℃. Nuclei were then treated with 1% Triton X-100 to quench SDS for 1h at 37℃. Chromatin was digested with 25U DpnII restriction enzyme (NEB, Cat#R0543M) at 37℃ overnight with shaking (950rpm on a thermal mixer). After overnight digestion, an additional stroke of 25U DpnII was added into the system to further digest the genome for 4 hours at 37℃. After the 2nd stroke of digestion, nuclei were incubated at 65℃ for 20min to inactivate DpnII. Digested chromatin fragments were then cooled down to room temperature and blunted with dCTP, dGTP, dTTP (Diamond Cat#B110049, B110050, B110051) and Biotin-14-dATP (active motif, Catalog No: 14138) using 6.6U DNA Polymerase I, Large (Klenow) fragment (NEB, Cat#M0210). Chromatin was then ligated in-situ with 2000U T4 DNA ligase (NEB, Cat#M0202M) for 4 hours at 16℃ followed by further incubation for 2 hours at room temperature. Chromatin was then reverse-crosslinked overnight at 65℃ in the presence of 1% SDS and proteinase K (G-clone Cat#EZ0970). After reverse-crosslinking, DNase-free RNase A (Vazyme Cat#DE111-01) was added to the system for 30min at 37℃ to remove RNA. DNA was then extracted by phenol-chloroform extraction, precipitated, and dissolved in 130ul of nuclease free water. For ChIP-seq, FACS purified cells were re-suspended in 1ml cold Cell Lysis Buffer (10mM Tris pH 8, 10mM NaCl and 0.2% NP-40) supplemented with 1:500 protease inhibitor and 1:100 PMSF for 20min on ice. Notably, for Rad21 ChIP-seq experiments in the WapldTag/SororinmAID and WapldTag/SMC2mAID/SororinmAID cells, roughly 30% of crosslinked 293T cells were added into the cell mixture. Nuclei were then pelleted and re-suspended in 1ml Nuclear Lysis Buffer (50mM Tris pH 8, 10mM EDTA, 1% SDS, fresh supplemented with PI and PMSF) for 20min on ice. Chromatin was then fragmented by sonication (Qsonica Q800R3, 80% amplitude, 20s ON, 40s OFF) for 17min. Cell debris were removed by centrifugation at 15000g for 10min at 4℃. The supernatant was collected and diluted with 4 volumes of IP dilution buffer (20mM Tris pH 8.0, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS) supplemented with protease inhibitor, PMSF and 50l of A/G agarose beads (Santa Cruz Cat#sc-2003). Preclear of chromatin was performed at 4℃ for 4-8h with rotation. Precleared chromatin was then incubated with 35μl A/G agarose beads (A:G = 1:1) pre-bound with antibody and incubated on a rotator at 4℃ overnight. Beads were washed once with IP wash buffer I (20mM Tris pH 8, 2mM EDTA, 50mMNaCl, 1% Triton X-100, 0.1% SDS), twice with high salt buffer (20mMTris pH 8, 2mM EDTA, 500mMNaCl, 1% Triton X-100, 0.01% SDS), once with IP wash buffer II (10mMTris pH 8, 1mM EDTA, 0.25 M LiCl, 1% NP-40/Igepal, 1% sodium deoxycholate) and twice with TE buffer (10mM Tris pH 8, 1mM EDTA pH 8). All washing steps were performed on ice. Beads were moved to room temperature and DNA was eluted in 200μl fresh Elution Buffer (100mM NaHCO3, 1%SDS). ChIP and input chromatin were reverse crosslinked at 65℃ overnight in the presence of proteinase K.  IP and input samples were supplemented with 10ul of 3M sodium acetate (pH 5.2), and DNA was purified with PCR purification kit (QIAGEN Cat#28106).  For Cleavage Under Targets and Tagmentation (CUT&Tag), G1E-ER4 cells expressing mCherry tagged murine cyclin B1 mitotic degron (mCherry-MD) were arrested to prometaphase through nocodazole treatment for 8 h. Cells were harvested at 45 min, 1h, 2h or 4h after nocodazole release. Cells were fixed with 95% pre-cooled methanol for 15 min at -20℃. After fixation, cells were pelleted and resuspended in 1 mL 1× PBS buffer (fresh supplemented with 1:500 protease inhibitors and 1:100 PMSF) containing 1 μL Hoechst 33342 (10 mg/mL). Cells were purified for G1 phase cells via FACS based on Hoechst 33342 and mCherry signals. Following sorting, CUT&Tag was then performed using an Hieff NGS® G-Type In-Situ DNA Binding Profiling Library Prep Kit for Illumina® (Yeasen, 12598). In brief, Con A magnetic beads were used to capture cells and 5% Digitonin was utilized to perforate the cell membrane. The target protein was recognized by primary antibody (Lamin A/C (Abcam, ab238303), Lamin B1 (Abcam, ab16048) or Lamin B Receptor (Abcam, ab232731)), followed by incubation with the secondary antibody (Goat Anti-Rabbit IgG H&L (Abcam, ab150079) or Goat Anti-Mouse IgG H&L (Abcam, ab150115)) and Protein A/G-Tn5. The targeted DNA sequence bound by the target protein was sheared by the transposase and PCR amplification was then performed to obtain the DNA library. CUT&Tag libraries were sequenced on the illumina Novaseq 6000 sequencing platform.
For Hi-C, DNA was sonicated to 200-300bp fragments with a QSonica Q800R3 sonicator (40% amplitude, 15s ON and 15s OFF, 13min sonication) and purified with VAHTS DNA Clean Beads (Vazyme Cat#N411). Biotin-labeled DNA fragments was enriched by incubation with 100μl Dynabeads MyOne Streptavidin C1 beads (Thermal Fisher Scientific, Cat#65002) at room temperature for 15min. Streptavidin C1 beads were then washed twice with 1 × B&W buffer (5mM Tris-HCl, pH 7.5; 0.5mM EDTA; 1M NaCl). Beads were re-suspended in 30ul of 1 × NEB Buffer2 (NEB Cat#7002S) containing 9U of T4 DNA polymerase (NEB, Cat#M0203S) and 40uM dATG/dGTP and incubated at 20℃ for 4 hours to remove unligated fragments. Beads were then washed twice with 1 × B&W buffer and subject to library construction. DNA end repair, dA-tailing and adaptor ligation were constructed on beads, using the AHTS Universal DNA Library Prep Kit for Illumina or MGI (Vazyme, Cat# ND627-01, NDM607-02) based on the manufacture’s protocol. To eluted DNA from streptavidin beads, the library mixture was treated with 0.1% SDS and incubated at 98℃ for 10min. Released DNA was collected from the supernatant and purified with VAHTS DNA Clean Beads. Finally, the library was amplified for 9 cycles on a thermal cycler, using the VAHTS® HiFi Amplification Mix. PCR products were then purified with VAHTS DNA Clean Beads and sequenced on an Illumina NextSeq500 or MGI DNBSEQ-T7 sequencing platform.  For ChIP,  libraries were constructed using the VAHTS Universal DNA Library Prep Kit for MGI (Vazyme, Cat#NDM607-02) according to the manufacture’s protocol. ChIP libraries were sequenced on the MGI DNBSEQ-T7 sequencing platform. For Cleavage Under Targets and Tagmentation (CUT&Tag), G1E-ER4 cells expressing mCherry tagged murine cyclin B1 mitotic degron (mCherry-MD) were arrested to prometaphase through nocodazole treatment for 8 h. Cells were harvested at 45 min, 1h, 2h or 4h after nocodazole release. Cells were fixed with 95% pre-cooled methanol for 15 min at -20℃. After fixation, cells were pelleted and resuspended in 1 mL 1× PBS buffer (fresh supplemented with 1:500 protease inhibitors and 1:100 PMSF) containing 1 μL Hoechst 33342 (10 mg/mL). Cells were purified for G1 phase cells via FACS based on Hoechst 33342 and mCherry signals. Following sorting, CUT&Tag was then performed using an Hieff NGS® G-Type In-Situ DNA Binding Profiling Library Prep Kit for Illumina® (Yeasen, 12598). In brief, Con A magnetic beads were used to capture cells and 5% Digitonin was utilized to perforate the cell membrane. The target protein was recognized by primary antibody (Lamin A/C (Abcam, ab238303), Lamin B1 (Abcam, ab16048) or Lamin B Receptor (Abcam, ab232731)), followed by incubation with the secondary antibody (Goat Anti-Rabbit IgG H&L (Abcam, ab150079) or Goat Anti-Mouse IgG H&L (Abcam, ab150115)) and Protein A/G-Tn5. The targeted DNA sequence bound by the target protein was sheared by the transposase and PCR amplification was then performed to obtain the DNA library. CUT&Tag libraries were sequenced on the illumina Novaseq 6000 sequencing platform.

treatment_protocol: For parent G1E-ER4 cells. Asynchronously growing cells were synchronized with prometaphase through nocodazole treatment (200ng/ml) for 8 hours at a density of 0.5million/ml. To obtain post-mitotic cells at defined time points, nocodazole synchronized cells were pelleted at 1200rpm for 3min. Cells were washed twice with PBS and then immediately re-suspended in fresh warm medium free of nocodazole. Cells were allowed to enter G1 phase for 45 minutes, 1 hour, 2 hours or 4 hours respectively.  For LmnamAID cells. The exact same procedure of nocodazole mediated arrest release was applied to this cell line. To degrade Lamin A/C during mitosis, 5-Ph-IAA (1M) was added into the culture for 4 hours before nocodazole release. Nocodazole release was performed in 5-Ph-IAA containing medium for 1 hour, 2 hours, 4 hours or 6 hours respectively. Control cells treated without 5-Ph-IAA treatment were processed in parallel.  For LmnamAID/LbrdTag cells. The exact same procedure of nocodazole mediated arrest release was applied to this cell line. To completely degrade LBR, dTag13 (1M) was added into the culture for 4 hours before nocodazole release. Cells with or without 5-Ph-IAA treatment were both collected. To assess the impact of residual LBR signals in the LmnamAID/LbrdTag cells, a similar strategy was implemented but without dTag13 treatment.  For NipblmAID/WapldTag cells. The exact same procedure of nocodazole mediated arrest release was applied to this cell line. To deplete Nipbl or Wapl, cells were treated with 5-Ph-IAA or dTag13 for 4 hours before nocodazole release. Late-G1 phase cells were then harvested at 6h after nocodazole release. Cells without any treatment were processed in parallel as control.

value: erythroid

value: G1E-ER4 cells

value: erythroblasts


title: SFN_ZH_Chip_Rad21_S0409_nipbl_clone3_release_with_auxin

description: Library name: sample14


title: mesc_rad21_depletion_untreated_172, Smart-seq3


title: SFN_ZH_Chip_Rad21_S0411_nipbl_clone17_release_with_auxin

description: Library name: sample16


title: GM-041

value: WT

value: no treatment


title: E910_CKDL230036282-1A_HGLGMDSX7_L1, Mutation_3

description: Library name: Sample10


title: GM-040


title: Ttseq_S0014_nipbl_clone3_with_auxin_4h_5ug

description: Library name: sample12


title: mesc_rad21_depletion_untreated_188, Smart-seq3


title: E76_CKDL230036278-1A_HGLGMDSX7_L1, Mutation_2

description: Library name: Sample_9

value: Mutation_2 plasmid transfection


title: GM-039


title: mesc_rad21_depletion_untreated_171, Smart-seq3


title: mesc_rad21_depletion_untreated_174, Smart-seq3


title: GM-038


title: Ttseq_S0013_nipbl_clone3_no_auxin_4h_5ug

description: Library name: sample11


title: mesc_rad21_depletion_untreated_170, Smart-seq3


title: Ttseq_S0012_nipbl_clone3_with_auxin_45min_5ug

description: Library name: sample10


title: GM-037


title: E911_CKDL230036283-1A_HGLGMDSX7_L1, Mutation_3

description: Library name: Sample11


title: mesc_rad21_depletion_untreated_169, Smart-seq3


title: E75_CKDL230036277-1A_HGLGMDSX7_L1, Mutation_2

description: Library name: Sample_8


title: SFN_ZH_Chip_Rad21_S0408_nipbl_clone3_release_no_auxin

description: Library name: sample13


title: E74_CKDL230036276-1A_HGLGMDSX7_L1, Mutation_2

description: Library name: Sample_7


title: mesc_rad21_depletion_untreated_168, Smart-seq3


title: C49_CKDL230036281-1A_HGLGMDSX7_L1, Mutation_1

description: Library name: Sample_6

value: Mutation_1 plasmid transfection


title: GM-036


title: Ttseq_S0010_nipbl_clone17_with_auxin_4h_5ug

description: Library name: sample8


title: GM-034


title: GM-035


title: Ttseq_S0009_nipbl_clone17_no_auxin_4h_5ug

description: Library name: sample7


title: C48_CKDL230036280-1A_HGLGMDSX7_L1, Mutation_1

description: Library name: Sample_5


title: mesc_rad21_depletion_untreated_167, Smart-seq3


title: mesc_rad21_depletion_untreated_166, Smart-seq3


title: Ttseq_S0011_nipbl_clone3_no_auxin_45min_5ug

description: Library name: sample9


title: C47_CKDL230036279-1A_HGLGMDSX7_L1, Mutation_1

description: Library name: Sample_4


title: mesc_rad21_depletion_untreated_173, Smart-seq3


title: C1_478

description:
C1-C24 are clonal subline derived from single cells isolated from B2905 mouse melanoma cell lines (Nature Med. 2020, 26:781 )
Expression_CountValue.tsv, Expression_FPKM.tsv, Expression_TPM.tsv, Mutations.tsv

value: Melanoma cell line-derived tumor


title: Ttseq_S0008_nipbl_clone17_with_auxin_45min_5ug

description: Library name: sample6


title: GM-033


title: mesc_rad21_depletion_untreated_165, Smart-seq3


title: Ttseq_S0007_nipbl_clone17_no_auxin_45min_5ug

description: Library name: sample5


title: wt3_CKDL230036275-1A_HGLGMDSX7_L1, wt_3

description: Library name: Sample_3

value: Wild-type plasmid transfection


title: WT2_CKDL230036274-1A_HGLGMDSX7_L1, WT_2

description: Library name: Sample_2


title: Ttseq_S0006_nipbl_clone3_with_auxin_4h_1ug

description: Library name: sample4


title: GM-032


title: mesc_rad21_depletion_untreated_163, Smart-seq3


title: mesc_rad21_depletion_untreated_164, Smart-seq3


title: mesc_rad21_depletion_untreated_162, Smart-seq3


title: WT1_CKDL230036273-1A_HGLGMDSX7_L1, WT_1

description: Library name: Sample_1


title: GM-031


title: case-3

city: Changchun

first: Simiao

last: Wang

state: other

address: Jilin university

institute: Simiao Wang

description: Library name: R22312577-R22056224LU01-1089584-6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: non-small cell lung cancer

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: non-small cell lung cancer

value: tissue


title: mesc_rad21_depletion_untreated_158, Smart-seq3

value: mouse embryonic stem cell

value: untreat


title: GM-028

value: blood


title: Ttseq_S0005_nipbl_clone3_no_auxin_4h_1ug

description: Library name: sample3


title: case-1

description: Library name: R22312575-R22056222LU01-1089746-5


title: nipbl_clone17_no_auxin_1h

description: Library name: sample4

data_processing:
Reads were mapped to mm9 reference genome using bowtie2.
Hi-C Pro (v3.0.0) was used to pair reads, remove PCR duplicates and generate interaction pair files. Pair files were converted to .hic files with the hicpro2juicebox utility. Cool files were genereated usign HiCxplorer.
Assembly: mm9
Supplementary files format and content: cool: 10kb-binned contact matrices

source_name: G1E-ER4 cells

extract_protocol:
DNA was digested with DpnII and proximity ligated. Ligated DNA was isolated using phenol-chloroform precipitation. Isolated DNA was sonicated using a Qsonica Q800R3 sonicator.
Sequencing libraries were prepared using the AHTS Univresal DNA Library Prep Kit for Illumina (Zazyme, ND627-01).


title: GM-025


title: GM-030


title: mesc_rad21_depletion_untreated_161, Smart-seq3


title: mesc_rad21_depletion_untreated_157, Smart-seq3


title: mesc_rad21_depletion_untreated_156, Smart-seq3


title: Ttseq_S0004_nipbl_clone3_with_auxin_45min_1ug

description: Library name: sample2


title: mesc_rad21_depletion_untreated_160, Smart-seq3


title: scRNAseq, B16-F10 melanoma cells, scrambled control (SCR)

first: Hao

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology (SUSTech)

description: Library name: scRNAseq-WT

data_processing:
Processed reads were aligned to the reference genome (gencode GRCm39) by the STAR (v2.7.10a)80, allowing for at most two mismatches. For Ribo-seq data, quality control and translational profiles was analyzed by RiboseQC. Transcriptome assembly and quantification were performed using StringTie (v2.1.7)81. For TCR-seq, data were analysed using ImmunoSEQ Analyzer 3.0, an Adaptive Biotechnologies online analysis platform. For scRNA-seq, Single-cell RNA sequencing (scRNA-seq) data were processed using standardized bioinformatics workflows. Raw sequencing data were aligned to the Mouse reference genome (GRCm39) and converted into unique molecular identifier (UMI) count matrices using Cell Ranger.
Assembly: GRCm39.genome.fa

source_name: B16-F10 melanoma cells

growth_protocol: The B16-F10 melanoma cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Biological Industries), 1% penicillin-streptomycin (Thermo Fisher Scientific), and 1% SaveIt mycoplasma inhibitor (Hanbio Biotechnology). Cells were maintained in a humidified incubator at 37°C with 5% CO₂ and routinely tested for bacterial and mycoplasma contamination.

extract_protocol:
For Ribo-Seq, cells were incubated with 100 μg/ml Cycloheximide (MCE) for 8 min at 37°C and were then lysed on ice for 10min in 400uL lysis buffer (20 mM Tris–HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml Cycloheximide, 1% Triton X-100). The supernatant was collected via centrifugation at 12 000 g for 10 min at 4 °C, and its' absorbance at 260nm was measured. The ribosomes with equal A260 in each group were reserved for RNA sequencing. For TCR-Seq, PBMCs were isolated from whole blood of C57BL/6N mice that had been inoculated with either control B16F10 cells or Mettl5-KO cells 12 days prior.   For scRNA-Seq,  Tumors were surgically resected and preserved in MACS Tissue Storage Solution, then transferred to the laboratory at low temperature. Following the manufacturer's instructions for the Miltenyi Biotec dissociation kit, the tumors were dissociated into a single-cell suspension. Post-dissociation, cells were resuspended in MACS Tissue Storage Solution to maintain viability. Cell counting and concentration adjustment were performed, followed by labeling with Zombie NIR viability dye to distinguish live and dead cells. Subsequently, cells were incubated with Fc blocker in FACS buffer to prevent non-specific antibody binding. Cells were then incubated with an antibody cocktail containing anti-CD45 antibodies. After incubation, cells were washed, filtered through a 70-μm Macs SmartStrainer to remove aggregates and debris, ensuring a high-quality single-cell suspension. Finally, CD45+ live immune cells were sorted using a BD FACSAria II instrument for downstream scRNA-seq analysis with the 10X Genomics 5' platform. This method ensures the isolation of viable immune cells, crucial for studying the tumor immune microenvironment.
For Ribo-Seq, added 15U RNase1 (Thermo Fisher Scientific) for each 1OD of lysate, and incubated the reactions at 22°C for 40 min with gentle mixing. Ribosome-protected fragments (RPFs) were collected by MicroSpin S-400 columns (Cytiva) and purified by Zymo Research RNA Clean & Concentrator-25 kit (Zymo). The RPFs were then separated with 15% polyacrylamide TBE–urea gel, excised the gel slices between 17 and 34 nucleotides and recovered RNA from PAGE gel by ZR small-RNA™ PAGE Recovery Kit (Zymo). Purified RNA was treated with PNK(NEB), and the RNA library was prepared by VAHTSTM Small RNA Library Prep Kit for Illumina®(Vazyme). The library concentration was analyzed using the VAHTSTM Library Quantification Kit for Illumina®, and equimolar pools of libraries were sequenced. For TCR-Seq, DNA was extracted from PBMC using a QIAamp DNA Blood Mini Kit (Qiagen), and the concentration was tested using NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific). The DNA was used as a template for PCR amplification, which was performed to generate the library of TCR and BCR. The step 1 PCR amplification protocol was as follows: 95 °C for 5 min; 95 °C for 30 s, 59 °C for 30 s; 72 °C for 1 min for 30 cycles; and 72 °C for 10 min. The step 2 PCR amplification protocol was as follows: 98 °C for 2 min; 98 °C for 30 s, 65 °C for 30 s; 72 °C for 30 s for 10 cycles; and 72 °C for 5 min. The PCR products were purified, and the barcodes were confirmed. The annealed region of these primers was the CDR3 region, as shown by Multiplex PCR Amplifies. The CDR3 regions were sequenced on Illumina NextSeq500 (MyGenostics).  For scRNA-Seq, Following cell sorting, live CD45+ immune cells were resuspended in PBS + 0.04% BSA at 1,000 cells/μL. Libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 5' v2 Kit according to manufacturer protocol, targeting 10,000 cells per sample. cDNA amplification and fragmentation were performed before Illumina adapter ligation.

value: B16-F10 melanoma cells

value: scrambled control (SCR)


title: GM-029

source_name: blood

value: lymphoblastoid


title: case-2

description: Library name: R22312576-R22056223LU01-1090647-15


title: mesc_rad21_depletion_untreated_155, Smart-seq3


title: scRNAseq, B16-F10 melanoma cells, Mettl5 KO

description: Library name: scRNAseq-KO

value: Mettl5 KO


title: Ttseq_S0003_nipbl_clone3_no_auxin_45min_1ug

description: Library name: sample1

value: erythroid

value: G1E-ER4 cells


title: mesc_rad21_depletion_untreated_159, Smart-seq3


title: 77-80 div propofol-treatment 4

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

description: Library name: Sample_19

data_processing:
Sequence reads were processed using Qiagen's software CLC Genomics workbench (v23.0.2) with CLC's default settings for RNA-Seq analysis (Reference sequence = Homo sapiens (GRCh38); Gene track = Homo sapiens (GRCh38.109); mRNA track = Homo sapiens (GRCh38.109); Use spike-in controls = no; Mismatch cost = 2; Insertion cost = 3; Deletion cost = 3; Length fraction = 0,8; Similarity fraction = 0,8; Global alignment = No; Strand specific = Both; Library type = Bulk; Maximum number of hits for a read = 10; Count paired reads as two = No; Ignore broken pairs = Yes; Expression value = TPM). Reads were aligned to GRCh38 genome. Expression value unit is TPM.
Assembly: GRCh38; GRCh38.109
Supplementary files format and content: xlsx files; include feature Ids, total gene reads as well as TPM and RPKM for each sample.

source_name: brain organoid

growth_protocol: Brain organoids were generated following the protocol (Sutcliffe and Lancaster, 2019). From 16 div, organoids were cultured in differentiation medium containing retinoic acid until the end of the experiment at either 60 or 90 div. All the incubation phases were conducted at 37 °C with 5% CO2.

extract_protocol:
total RNA was extracted using Rneasy plus micro kit (Qiagen). 200 ng of total RNA (RIN>8) was used for library preparation
Barcoded mRNA seq libraries were prepared from 200 ng total RNA. For library preparation, the mRNA present in the total RNA sample was isolated with magnetic beads of oligos d(T)25. This method is known as polyA-tailed mRNAenrichment. Subsequently, mRNA was randomly fragmented and cDNA synthesis proceeds through the use of random hexamers and the reverse transcriptase enzyme. Once the synthesis of the first chain is finished, the second chain is synthesized with the addition of an Illumina buffer. With this and together with the presence of dNTPs, RNase H and polymerase I from E.coli, the second chain is obtained by Nick translation. The resulting products go through purification, end-repair, A-tailing and adapter ligation. Fragments of the appropriate size are enriched by PCR, where indexed P5 and P7 primers are introduced, and final products are purified. The library was checked with Qubit 2.0 and real-time PCR for quantification and bioanalyzer Agilent 2100 for size distribution detection. Quantified libraries have been pooled and sequenced on Illumina Novaseq 6000 platform, according to effective library concentration and data amount. Sequencing strategy was paired-end 150 cycles (PE150).

treatment_protocol: A concentration of 50 µM propofol (diluted in DMSO) was added into the culture medium at either 47 or 77 div for a duration of 72 hours. In the control group, an equivalent volume of DMSO was added as mock treatment.

value: brain organoid

value: H1 ESC

value: embryonic stem cell

value: propofol

tag: time

value: 90 day


title: mesc_rad21_depletion_untreated_154, Smart-seq3


title: GM-022

value: WT

value: no treatment


title: GM-027


title: 77-80 div propofol-treatment 3

description: Library name: Sample_18


title: control-2

description: Library name: R22312574-FJ221128001-1082607

value: non-small cell lung cancer

value: tissue


title: control-3

description: Library name: R22312574-FJ221128001-1087171


title: control-1

description: Library name: R22312573-R22056219LU01-1082712


title: nipbl_clone17_no_auxin_45min

description: Library name: sample3


title: GM-026


title: GM-024


title: mesc_rad21_depletion_untreated_151, Smart-seq3

value: mouse embryonic stem cell

value: untreat


title: nipbl_clone3_no_auxin_45min

description: Library name: sample1


title: GM-023

value: blood


title: nipbl_clone3_no_auxin_1h

description: Library name: sample2


title: 77-80 div propofol-treatment 5

description: Library name: Sample_20


title: GM-019


title: mesc_rad21_depletion_untreated_150, Smart-seq3


title: nipbl_noc_4h_no_auxin_clone17

tag: clone

value: 4h no auxin


title: mesc_rad21_depletion_untreated_153, Smart-seq3


title: nipbl_noc_4h_with_auxin_clone3

value: 4h with auxin


title: GM-018

value: lymphoblastoid


title: GM-021


title: 77-80 div propofol-treatment 2

description: Library name: Sample_17


title: nipbl_noc_4h_with_auxin_clone17

value: erythroid


title: GM-017


title: nipbl_noc_45min_with_auxin_clone17

value: G1E-ER4 cells

value: 45min with auxin


title: GM-020


title: 90 div mock-treatment 2

description: Library name: Sample_12

value: brain organoid

value: H1 ESC

value: control


title: mesc_rad21_depletion_untreated_148, Smart-seq3


title: nipbl_noc_1h_with_auxin_clone3

value: 1h with auxin


title: mesc_rad21_depletion_untreated_152, Smart-seq3


title: nipbl_noc_45min_with_auxin_clone3


title: 77-80 div propofol-treatment 1

description: Library name: Sample_16

value: embryonic stem cell

value: propofol

value: 90 day


title: nipbl_noc_4h_no_auxin_clone3


title: mesc_rad21_depletion_untreated_147, Smart-seq3


title: 90 div mock-treatment 5

description: Library name: Sample_15


title: GM-016

value: WT

value: no treatment


title: 90 div mock-treatment 4

description: Library name: Sample_14


title: 90 div mock-treatment 3

description: Library name: Sample_13


title: GM-014


title: mesc_rad21_depletion_untreated_149, Smart-seq3

value: mouse embryonic stem cell

value: untreat


title: mesc_rad21_depletion_untreated_146, Smart-seq3


title: GM-015

value: blood


title: nipbl_noc_0h_clone3


title: nipbl_noc_1h_with_auxin_clone17


title: mesc_rad21_depletion_untreated_145, Smart-seq3


title: 60 div mock-treatment 5

description: Library name: Sample_10

value: 60 day


title: 60 div mock-treatment 4

description: Library name: Sample_9


title: 90 div mock-treatment 1

description: Library name: Sample_11


title: GM-012

value: lymphoblastoid


title: mesc_rad21_depletion_untreated_144, Smart-seq3


title: GM-013


title: 60 div mock-treatment 3

description: Library name: Sample_8


title: GM-011


title: GM-010


title: mesc_rad21_depletion_untreated_142, Smart-seq3


title: Lox uKO, Day 6 pregnant uterus, replicate-2

city: Bunkyo-ku

first: Shizu

last: Aikawa

state: Tokyo

address: 7-3-1 Hongo

institute: The University of Tokyo

data_processing:
*library strategy: Spatial transcriptomics
Raw reads were processed by Cell Ranger with default setting.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5.gz:The filtered feature count matrix generated from Cell Ranger.
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions.csv.gz: list of spatial barcodes and the coodinates specifying spots

source_name: Mouse uterus

extract_protocol:
After reaction with Proteinase K for 30 min, the sections were hybridized with spatial tags on the slides according to manufacturer's protocol.
Following the hybridization with spatial tags, reverse-transcribed in situ according to manufacturer's protocol.

value: Mouse uterus

value: Lox-flox/flox; Pgr-Cre/+


title: mesc_rad21_depletion_untreated_143, Smart-seq3


title: mesc_rad21_depletion_untreated_141, Smart-seq3


title: Lox-floxed, Day 6 pregnant uterus, replicate-2

value: Lox-flox/flox


title: 60 div mock-treatment 2

description: Library name: Sample_7

value: brain organoid


title: nipbl_noc_0h_clone17

value: G1E-ER4 cells

value: erythroid


title: 60 div mock-treatment 1

description: Library name: Sample_6

value: H1 ESC

value: control


title: Lox uKO, Day 6 pregnant uterus, replicate-1


title: mesc_rad21_depletion_untreated_140, Smart-seq3


title: 47-50 div propofol-treatment 5

description: Library name: Sample_5

value: embryonic stem cell

value: propofol


title: Lox-floxed, Day 6 pregnant uterus, replicate-1


title: 47-50 div propofol-treatment 4

description: Library name: Sample_4


title: GM-008

value: WT


title: GM-009

value: no treatment


title: Hif2a uKO, Day 6 pregnant uterus

value: Hif2s-flox/flox; Pgr-Cre/+


title: mesc_rad21_depletion_untreated_137, Smart-seq3

value: mouse embryonic stem cell

value: untreat


title: GM-005

value: blood


title: Hif2a-floxed, Day 6 pregnant uterus


title: mesc_rad21_depletion_untreated_138, Smart-seq3


title: 47-50 div propofol-treatment 1

description: Library name: Sample_1

value: 60 day


title: mesc_rad21_depletion_untreated_136, Smart-seq3


title: GM-006

value: lymphoblastoid


title: mesc_rad21_depletion_untreated_139, Smart-seq3


title: 000792A33E

city: La Jolla

first: Daniel

last: Munro

address: 9500 Gilman Drive

department: Psychiatry

institute: UC San Diego

description:
Library name: 000792A33E
Removed: no matching genotype sample

data_processing:
Expression levels were quantified using kallisto
Assembly: GRCr8
Supplementary files format and content: Log2-transformed read counts per gene per sample in BED format. Start/end coordinates indicate only the gene's TSS coordinate.

organism: Rattus norvegicus

source_name: whole brain hemisphere

growth_protocol: Naive outbred laboratory rats

extract_protocol:
RNA was extracted from frozen tissue microdissections using a TRIzol-based protocol after mechanical homogenization with a bullet blender to maximize tissue disruption and RNA yield.
RNA-seq libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina following polyA enrichment with the NEBNext Poly(A) mRNA Magnetic Isolation Module

treatment_protocol: No treatment

value: whole brain hemisphere


title: 47-50 div propofol-treatment 2

description: Library name: Sample_2


title: GM-004

data_processing:
Sequencing reads were mapped to the human reference genome assembly GRCh38 using STAR.
Read count extraction was performed using RSEM.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA counts for each cell

extract_protocol:
Isolated single cell was lysed wih gentle lysis buffer (containing 0.45% NP-40), and the supernant was collected for the construction of sequencing library.
Collected supernant was amplified with standard Smart-seq2 protocol, then perform library preparation with homemade Tn5 transposase.
Smart-seq2


title: mesc_rad21_depletion_untreated_135, Smart-seq3


title: 000792A1A2

description:
Library name: 000792A1A2
Removed: no matching genotype sample


title: iAT1_CUT2_H3K27me3

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

institute: Kyoto University

description: Library name: Sample 12

library_source: other

data_processing:
We used “DNA-mapping” in snakePipes (v2.7.3) (PMID: 31134269) to trim adapter sequences with fastp (v0.23.2) (PMID: 38868435) and to subsequently map the remaining sequences with bowtie2 (v2.4.5) (PMID: 22388286) against the reference sequence created from the human T2T-CHM13v2.0 genome assembly without Y chromosome together with the complete genome sequence of Escherichia coli strain BL21 (GenBank: CP010816.1) and the 3XFlag-pA-Tn5-Fl plasmid sequence (Addgene, #124601).
We obtained a bam file only with properly-paired alignments mapped to the human chromosomes 1 to 22 and X with the MAPQ score greater than or equal to 10 using samtools view command (v1.15.1) (PMID: 19505943) with the option “-f 2 -F 256 -x XA -q 10.
We further created bigwig tracks from the bam files using “bamCoverage” in deeptools (v3.5.1) (PMID: 27079975) with the option “--binSize 25 --effectiveGenomeSize 3054815472 --normalizeUsing CPM".
We called peaks with MACS2 callpeak (v2.2.7.1) (PMID: 18798982) with the option “-f BAM -g hs --nomodel” using the snakemake wrapper v2.1.0 in a snakemake workflow (PMID: 22908215).
Assembly: Human T2T-CHM13v2.0
Supplementary files format and content: BigWig files include signal intensity values across the genome for each sample
Library strategy: CUT&Tag

molecule: other

growth_protocol: The MACS-isolated iPSC-derived lung progenitor cells (LPs) were seeded in the 24-well micro-patterned plates for "2.5-dimensional culture" (Tosoh Co., Ltd.) with multiple round shaped cell-attachment areas in 100 μm diameter pre-coated with 0.5 ug/cm2 of iMatrix-511 silk (TaKaRa bio, 892021) at the cell densities 1x10^5 cells/well. These cells were cultured in "DCIK+3i" (CHIR99021, SB431542, and Y27632) medium for 7 days to induce AT2 cells, followed by an additional 7-day maintenance with DCIK+3i medium to induce AT2 cells, DCI+LATS medium to induce AT1 cells, or PAL medium to induce iATCs, respectively.

extract_protocol:
For the isolation of iAT2 and iAT1 cells, the cells cultured on micro-patterned plates were first stained with Hoechst-33342 for 30 minutes at 37°C, followed by incubation with Accutase at 37°C for 20 minutes and dissociation by gentle pipetting. For the isolation of iATCs, the cells were incubated with Accutase, gently dissociated by pipetting, and stained with an APC-conjugated anti-human CD54 antibody for 20 minutes at 4°C. Each positive cell population was then sorted using fluorescence-activated cell sorting.
To make the CUT&Tag libraries, the dissociated cells were washed with PBS supplemented with 1X Protease Inhibitor (Roche, # 11873580001), and subsequently washed with wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.25 mM spermidine, 1X Protease Inhibitor (Roche, # 11873580001)). Then, we resuspended 50,000 cells in 500 µl of the wash buffer supplemented with 5 mM sodium butyrate. We added 2 µl of the concanavalin A-conjugated magnetic beads to the cell suspension. Next, after magnetic separation of the beads and removal of the supernatant, we resuspended the beads in 50 µL of ice-cold wash buffer, supplemented with 5 mM sodium butyrate, 0.05% digitonin, 2 mM EDTA, and 0.1% BSA together with 0.5 µl primary antibody against H3K4me3 (MAB Institute, MABI0304) and H3K27me3 (MAB Institute, MABI0323). After rotating incubation at room temperature for 3 hours, the buffer containing the primary antibody was replaced with 100 µl of ice-cold wash buffer, supplemented with 5 mM sodium butyrate, 0.05% digitonin, together with 1 µl secondary rabbit anti-mouse IgG antibody (Abcam, #ab46540), and was incubated at 4 °C for overnight. After washing the beads with Dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, 1X Protease Inhibitor (Roche, # 11873580001), 5 mM sodium butyrate) twice, we applied 100 µl of the Dig-300 buffer containing 3.6 femtomol pA-Tn5 transposome and incubated the mixture for 1 hour at room temperature. After washing the beads with the Dig-300 buffer twice, we resuspended the beads in 50 µl of the Dig-300 buffer supplemented with 10 mM MgCl2 and incubated them at 37 °C for 1 hour. We then removed the supernatant and resuspended the beads in 20 µl of 10 mM TAPS buffer (pH 8.5) together with 0.5 µl thermolabile proteinase K (NEB, #P8111S), and incubated the mixture at 37 °C for 30 minutes, followed by incubation at 55 °C for 20 minutes to inactivate the proteinase. We directly performed PCR-amplification of the library from the tube after adding the reaction mixture (KAPA BIOSYSTEMS, #KK2602) using index primers. The amplified libraries were purified with 1.3 volumes of AMPure XP beads.

value: iPSC-derived alveolar epithelial cells


title: 47-50 div propofol-treatment 3

description: Library name: Sample_3

value: brain organoid


title: GM-003


title: 00079FD154

description:
Library name: 00079FD154
Removed: matched to genotype of another rat that already had matching RNA-seq sample


title: GM-007


title: iATCs_CUT2_H3K27me3

description: Library name: Sample 10


title: iAT2_CUT2_H3K27me3

description: Library name: Sample 11


title: mesc_rad21_depletion_untreated_134, Smart-seq3


title: mesc_rad21_depletion_untreated_133, Smart-seq3


title: 0007D60ADC

description: Library name: 0007D60ADC


title: 0007D6151C

description: Library name: 0007D6151C


title: mesc_rad21_depletion_untreated_132, Smart-seq3


title: iAT2_CUT1_H3K27me3

description: Library name: Sample 8


title: 0007D6063F

description: Library name: 0007D6063F


title: GM-002


title: iAT1_CUT1_H3K27me3

description: Library name: Sample 9


title: mesc_rad21_depletion_untreated_130, Smart-seq3


title: GM-001


title: mesc_rad21_depletion_untreated_131, Smart-seq3


title: 0007D5FD51

description: Library name: 0007D5FD51


title: iAT1_CUT2_H3K4me3

description: Library name: Sample 6


title: iATCs_CUT1_H3K27me3

description: Library name: Sample 7


title: iAT2_CUT2_H3K4me3

description: Library name: Sample 5


title: 0007D5B7D6

description: Library name: 0007D5B7D6


title: 0007D3A794

description: Library name: 0007D3A794


title: mesc_rad21_depletion_untreated_127, Smart-seq3


title: 0007D600E0

description: Library name: 0007D600E0


title: iATCs_CUT2_H3K4me3

description: Library name: Sample 4


title: Bhlhe41 dTomato-Cre/dTomato-Cre KO3

type: RNA

city: Xuzhou

first: Hui

address: 209 Tongshan Road, Kejiao A513

department: Pathogenic Biology and Immunology

institute: XuZhou Medical University

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a total volume of 25ul following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE v2 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Bhlhe41 dTomato-Cre/dTomato-Cre, biological replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using a LowInput QuickAmp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Microglia were enriched by 40% Percoll from young Bhlhe41 dTomato-Cre/+ mice (N = 3, Control) and Bhlhe41 dTomato-Cre/dTomato-Cre mice (N = 3, Bhlhe41 KO group), which were further purified by flow cytometri sorting of CD45lowCD11b+Cx3cr1+ cells.

value: Purified microglia

value: Bhlhe41 dTomato-Cre/dTomato-Cre


title: Bhlhe41 dTomato-Cre/dTomato-Cre KO2

source_name: Bhlhe41 dTomato-Cre/dTomato-Cre, biological replicate 2


title: 0007A3F68B

description: Library name: 0007A3F68B


title: mesc_rad21_depletion_untreated_126, Smart-seq3


title: 0007A3D743

description: Library name: 0007A3D743


title: mesc_rad21_depletion_untreated_128, Smart-seq3


title: Bhlhe41 dTomato-Cre/dTomato-Cre KO1

source_name: Bhlhe41 dTomato-Cre/dTomato-Cre, biological replicate 1


title: BAT WT High Fat Diet 9

city: Philadelphia

last: Kelly

state: PA

address: 3400 Civic Center Blvd

department: Penn Cardiovascular Institute

institute: University of Pennsylvania

description: Library name: BAT9

data_processing:
Reads in each known mm10 transcript were quantified using Salmon 1.10.3
Assembly: mm10
Supplementary files format and content: Salmon quantification files, tab separated

source_name: BAT

extract_protocol:
RNA isolation and qRT-PCR. Total RNA was isolated from frozen tissues or cells using the RNeasy Mini Kit (QIAGEN) and treated with RNase-Free DNase Set (QIAGEN) per manufacturer’s instructions. cDNA was synthesized using the Affinity Script cDNA Synthesis Kit (Agilent Technologies) or High-Capacity cDNA Reverse Transcription Kit (ThermoFisher Scientific #4368814) with 0.25 μg total RNA.
RNA-Seq library preparation, sequencing and analysis. GENEWIZ, LLC. (South Plainfield, NJ) performed RNA library preparations and sequencing reactions per standard operating procedure [16, 17].

treatment_protocol: standard chow (Lab Diet 5010) or a 60% fat HFD (Research Diets, D12492i)

value: BAT

value: High Fat Diet


title: Bhlhe41 dTomato-Cre/+ Ctrl 1

source_name: Bhlhe41 dTomato-Cre/+, biological replicate 1

value: Bhlhe41 dTomato-Cre/+


title: iAT1_CUT1_H3K4me3

description: Library name: Sample 3


title: mesc_rad21_depletion_untreated_125, Smart-seq3

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

source_name: mouse embryonic stem cell


title: mesc_rad21_depletion_untreated_129, Smart-seq3


title: 0007A3C18F

description: Library name: 0007A3C18F


title: mesc_rad21_depletion_untreated_124, Smart-seq3


title: iATCs_CUT1_H3K4me3

description: Library name: Sample 1


title: 0007A3D3A3

description: Library name: 0007A3D3A3


title: Bhlhe41 dTomato-Cre/+ Ctrl 3

source_name: Bhlhe41 dTomato-Cre/+, biological replicate 3


title: BAT MondoAKO Chow Diet 8

description: Library name: BAT8

value: MondoAKO

value: Chow Diet


title: 3i_2_Day7

description:
Library name: Sample 6
10x Genomics

data_processing:
The 10X Genomics Cell Ranger pipeline (version 7.1.0) was used to perform sample demultiplexing, alignment to the hg38 human reference genome (refdata-gex-GRCh38-2020-A from 10X Genomics) and the reporter sequences, barcode/UMI processing, and gene counting for each cell.
Assembly: hg38
Supplementary files format and content: A tab-delimited text file listing the unique cell barcodes detected in the dataset. A sparse matrix in Matrix Market (MTX) format, containing accessibility count values for each peak across all barcoded cells.

growth_protocol: The MACS-isolated iPSC-derived lung progenitor cells (LPs) were seeded in the 24-well micro-patterned plates for "2.5-dimensional culture" (Tosoh Co., Ltd.) with multiple round shaped cell-attachment areas in 100 μm diameter pre-coated with 0.5 ug/cm2 of iMatrix-511 silk (TaKaRa bio, 892021) at the cell densities 1x10^5 cells/well. These cells were cultured in "DCIK+3i" (CHIR99021, SB431542, and Y27632) medium for 7 days to induce AT2 cells, followed by an additional 7-day maintenance with DCIK+3i medium to induce AT2 cells, DCI+LATS medium to induce AT1 cells, and PAL medium to induce iATCs

extract_protocol:
The cell suspension after CPM MACS sorting was used as "CPM_MACS_progenitor". The micro-patterned cultured cells were dissociated by  0.5 mM EDTA/PBS and Accutase treatment and subjected to scRNA-seq.
The collected cells were loaded into a 10X Genomics Chromium system. The scRNA-seq libraries were constructed using Single Cell 3' Reagent Kits (v.3.1, 10X Genomics).


title: Bhlhe41 dTomato-Cre/+ Ctrl 2

source_name: Bhlhe41 dTomato-Cre/+, biological replicate 2


title: iAT2_CUT1_H3K4me3

description: Library name: Sample 2


title: BAT MondoAKO Chow Diet 7

description: Library name: BAT7


title: 3i_1_Day7

description:
Library name: Sample 5
10x Genomics


title: mesc_rad21_depletion_untreated_123, Smart-seq3


title: 0007A3BD9F

description: Library name: 0007A3BD9F


title: mesc_rad21_depletion_untreated_122, Smart-seq3


title: 3i_PAL_1_Day14

description:
Library name: Sample 3
10x Genomics


title: 0007A3B423

description: Library name: 0007A3B423


title: BAT MondoAKO Chow Diet 6

description: Library name: BAT6


title: BAT WT Chow Diet 3

description: Library name: BAT3

value: WT


title: BAT MondoAKO Chow Diet 5

description: Library name: BAT5


title: 3i_LATS_2_Day14

description:
Library name: Sample 2
10x Genomics


title: 3i_PAL_2_Day14

description:
Library name: Sample 4
10x Genomics


title: 0007A3B51B

description: Library name: 0007A3B51B


title: 0007A39567

description: Library name: 0007A39567


title: 0007A3AA83

description: Library name: 0007A3AA83


title: 0007A3B7B0

description: Library name: 0007A3B7B0


title: BAT WT Chow Diet 2

description: Library name: BAT2


title: mesc_rad21_depletion_untreated_112, Smart-seq3


title: BAT WT Chow Diet 4

description: Library name: BAT4


title: 3i_LATS_1_Day14

description:
Library name: Sample 1
10x Genomics


title: mesc_rad21_depletion_untreated_121, Smart-seq3


title: 0007A39048

description: Library name: 0007A39048


title: mesc_rad21_depletion_untreated_110, Smart-seq3


title: mesc_rad21_depletion_untreated_111, Smart-seq3


title: iAT2_CUT2_H3

description: Library name: Sample 11

data_processing:
We used “DNA-mapping” in snakePipes (v2.7.3) (PMID: 31134269) to trim adapter sequences with fastp (v0.23.2) (PMID: 38868435) and to subsequently map the remaining sequences with bowtie2 (v2.4.5) (PMID: 22388286) against the reference sequence created from the human T2T-CHM13v2.0 genome assembly without Y chromosome together with the complete genome sequence of Escherichia coli strain BL21 (GenBank: CP010816.1) and the 3XFlag-pA-Tn5-Fl plasmid sequence (Addgene, #124601).
We obtained a bam file only with properly-paired alignments mapped to the human chromosomes 1 to 22 and X with the MAPQ score greater than or equal to 10 using samtools view command (v1.15.1) (PMID: 19505943) with the option “-f 2 -F 256 -x XA -q 10.
We further created bigwig tracks from the bam files using “bamCoverage” in deeptools (v3.5.1) (PMID: 27079975) with the option “--binSize 25 --effectiveGenomeSize 3054815472 --normalizeUsing CPM.
We called peaks with MACS2 callpeak (v2.2.7.1) (PMID: 18798982) with the option “-f BAM -g hs --nomodel” using the snakemake wrapper v2.1.0 in a snakemake workflow (PMID: 22908215).
Assembly: Human T2T-CHM13v2.0
Supplementary files format and content: BigWig files include signal intensity values across the genome for each sample
Library strategy: CUT&Tag

extract_protocol:
For the isolation of iAT2 and iAT1 cells, the cells cultured on micro-patterned plates were first stained with Hoechst-33342 for 30 minutes at 37°C, followed by incubation with Accutase at 37°C for 20 minutes and dissociation by gentle pipetting. For the isolation of iATCs, the cells were incubated with Accutase, gently dissociated by pipetting, and stained with an APC-conjugated anti-human CD54 antibody for 20 minutes at 4°C. Each positive cell population was then sorted using fluorescence-activated cell sorting.
To make the CUT&Tag libraries, the dissociated cells were washed with PBS supplemented with 1X Protease Inhibitor (Roche, # 11873580001), and subsequently washed with wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.25 mM spermidine, 1X Protease Inhibitor (Roche, # 11873580001)). Then, we resuspended 50,000 cells in 500 µl of the wash buffer supplemented with 5 mM sodium butyrate. We added 2 µl of the concanavalin A-conjugated magnetic beads to the cell suspension. Next, after magnetic separation of the beads and removal of the supernatant, we resuspended the beads in 50 µL of ice-cold wash buffer, supplemented with 5 mM sodium butyrate, 0.05% digitonin, 2 mM EDTA, and 0.1% BSA together with 0.5 µl primary antibody against H3K27Ac (MAB Institute, #MABI0309) or H3 (MAB Institute, #MABI0301). After rotating incubation at room temperature for 3 hours, the buffer containing the primary antibody was replaced with 100 µl of ice-cold wash buffer, supplemented with 5 mM sodium butyrate, 0.05% digitonin, together with 1 µl secondary rabbit anti-mouse IgG antibody (Abcam, #ab46540), and was incubated at 4 °C for overnight. After washing the beads with Dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, 1X Protease Inhibitor (Roche, # 11873580001), 5 mM sodium butyrate) twice, we applied 100 µl of the Dig-300 buffer containing 3.6 femtomol pA-Tn5 transposome and incubated the mixture for 1 hour at room temperature. After washing the beads with the Dig-300 buffer twice, we resuspended the beads in 50 µl of the Dig-300 buffer supplemented with 10 mM MgCl2 and incubated them at 37 °C for 1 hour. We then removed the supernatant and resuspended the beads in 20 µl of 10 mM TAPS buffer (pH 8.5) together with 0.5 µl thermolabile proteinase K (NEB, #P8111S), and incubated the mixture at 37 °C for 30 minutes, followed by incubation at 55 °C for 20 minutes to inactivate the proteinase. We directly performed PCR-amplification of the library from the tube after adding the reaction mixture (KAPA BIOSYSTEMS, #KK2602) using index primers. The amplified libraries were purified with 1.3 volumes of AMPure XP beads.


title: BAT MondoAKO High Fat Diet 16

description: Library name: BAT16


title: mesc_rad21_depletion_untreated_109, Smart-seq3

data_processing:
Smart-seq3 data were processed using zUMIs (https://github.com/sdparekh/zUMIs).
Bulk RNA-seq data were mapped to human reference genome using STAR and RSEM was used to calculate mRNA count for each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA counts for each cell and sample
Supplementary files format and content: tab-delimited text files include cell barcode and sample information for Smart-seq3

extract_protocol:
Isolated single cell was lysed wih gentle lysis buffer (containing 0.45% NP-40), and the supernant was collected for the construction of sequencing library.
Collected supernant was amplified with standard Smart-seq3 protocol, then perform library preparation with homemade Tn5 transposase.
Smart-seq3 & bulk RNA-seq


title: mesc_rad21_depletion_untreated_108, Smart-seq3


title: BAT MondoAKO High Fat Diet 14

description: Library name: BAT14


title: iAT1_CUT2_H3

description: Library name: Sample 12


title: 0007A35B32

description: Library name: 0007A35B32


title: BAT MondoAKO High Fat Diet 15

description: Library name: BAT15


title: 0007A3748E

description: Library name: 0007A3748E


title: iATCs_CUT2_H3

description: Library name: Sample 10


title: 0007A06BBD

description: Library name: 0007A06BBD


title: iAT1_CUT1_H3

description: Library name: Sample 9


title: BAT MondoAKO High Fat Diet 13

description: Library name: BAT13


title: 0007A05F18

description:
Library name: 0007A05F18
Removed: insufficient reads


title: BAT WT High Fat Diet 12

description: Library name: BAT12


title: iAT2_CUT1_H3

description: Library name: Sample 8


title: mesc_rad21_depletion_untreated_105, Smart-seq3


title: BAT WT High Fat Diet 11

description: Library name: BAT11


title: mesc_rad21_depletion_untreated_107, Smart-seq3


title: 0007A037D1

description: Library name: 0007A037D1


title: iATCs_CUT1_H3

description: Library name: Sample 7


title: mesc_rad21_depletion_untreated_103, Smart-seq3


title: mesc_rad21_depletion_untreated_106, Smart-seq3


title: iAT2_CUT2_H3K27ac

description: Library name: Sample 5


title: mesc_rad21_depletion_untreated_101, Smart-seq3


title: BAT WT High Fat Diet 10

description: Library name: BAT10


title: iAT1_CUT2_H3K27ac

description: Library name: Sample 6


title: 0007A036FA

description: Library name: 0007A036FA


title: 0007A027D6.

description: Library name: 0007A027D6


title: mesc_rad21_depletion_untreated_102, Smart-seq3


title: 60day post TBI microglia Vehicle TBI  3

first: Mecca

middle: Bennta Abour Rahim

last: Islam

state: IL

address: 240 E Huron St., M410

institute: Northwestern University

description: Library name: 60D_Mic_2022_PBSlip_TBI3

data_processing:
Sample quality control, processing, and library preparation were performed by the Northwestern University Next Generation Sequencing Core.
Assembly: Trimmed fastq files were aligned to the mouse reference genome (mm10, Genome Reference Consortium GRCm38) using the STAR algorithm
Supplementary files format and content: tab-delimnted text file include raw counts for each smaple

source_name: Microglia

extract_protocol:
FACSorted microglia were lysed and RNA extracted with the Arcturus PicoPure RNA isolation kit (ThermoFisher Scientific, Waltham, MA, USA), per manufacturer instructions.
The cDNA was amplified through 11 cycles of PCR. Subsequently, cDNA libraries were prepared for Illumina sequencing using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, USA). Sample quality control, processing, and library preparation were performed by the Northwestern University Next Generation Sequencing Core.

value: Microglia

value: PBS lipsomes


title: 60day post TBI microglia Vehicle TBI  4

description: Library name: 60D_Mic_2022_PBSlip_TBI4


title: iAT1_CUT1_H3K27ac

description: Library name: Sample 3


title: iATCs_CUT2_H3K27ac

description: Library name: Sample 4


title: 60day post TBI microglia Vehicle TBI  2

description: Library name: 60D_Mic_2022_PBSlip_TBI2


title: 0007A01C94

description: Library name: 0007A01C94


title: 0007A001C5

description: Library name: 0007A001C5


title: mesc_rad21_depletion_untreated_100, Smart-seq3

first: Xiaoliang

value: mouse embryonic stem cell

value: untreat


title: mesc_rad21_depletion_untreated_098, Smart-seq3


title: 60day post TBI microglia Clodroante TBI  4

description: Library name: 60D_Mic_2022_Colip_TBI4

value: Clodorante lipsomes

value: 60 day


title: iAT2_CUT1_H3K27ac

description: Library name: Sample 2


title: mesc_rad21_depletion_untreated_099, Smart-seq3


title: 0007A01109

description: Library name: 0007A01109

value: whole brain hemisphere


title: mesc_rad21_depletion_untreated_096, Smart-seq3


title: 00079FFAEA

description: Library name: 00079FFAEA


title: 0007A01A7C

description: Library name: 0007A01A7C