title: SAECs infected with MERS-CoV

city: Rotterdam

first: Bart

last: Haagmans

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

description:
Library name: HUB-JB-g003
10x Genomics

data_processing:
Demultiplexing, barcode processing and gene counting were performed using the Cell Ranger software v3.1.0.
Assembly: Human genome GRCh38 supplemented with the sequence for MERS-CoV
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung parenchyma

growth_protocol: Organoids were kept at 37°C in a humidified CO2 incubator. Growth medium (AO medium) was replaced every 4 to 5 days. Organoids were split into ~1:5 fractional ratios using TrypLE digestion, depending on cell density.

extract_protocol:
Human SAECs from one donor were infected with MERS-CoV at a moi 1. At 1 dpi cells were harvested and re-suspended into a single cell solution using TryplE digestion. The single cells were subsequently methanol fixed according to 10x Genomics demonstrated protocol “Methanol Fixation of Cells for Single Cell RNA Sequencing” and stored at -80°C until the day of the sequencing. Prior to loading the cells on the 10x Chromium chip, cells were rehydrated according to the same demonstrated protocol. Cells were filtered and counted.
Library was performed at Single Cell Discoveries according to standard 10× Genomics 3’ V3.1 chemistry protocol. In short, the cells were loaded on a 10x Genomics chip, and the chip was run on a Chromium controller to initiate GEM formation. Library preparation was performed, following standard 10x Genomics guidelines 3’ v3.1, to generate Gene Expression (GEX) libraries. The resulting DNA libraries were paired-end sequenced on an Illumina Novaseq S4 with an Illumina 2×150 bp kit.

treatment_protocol: MERS-CoV infection

value: Lung parenchyma

value: Infected with MERS-CoV


title: HN35 Pre Gene expression data

status: Public on Feb 24 2025

type: SRA

city: Chapel Hill

first: Robert

middle: L

last: Ferris

state: NC

address: 450 West Drive

country: USA

institute: UNC Lineberger Comprehensive Cancer Center

description: Library name: HN35_Pre_GEX

library_source: transcriptomic single cell

data_processing:
Fastq files were demultiplexed using Cellranger mkfastq
Demultiplexed data (GEX,ADT and VDJ) were processed using Cellranger Multi pipeline
Assembly: GRCh38
Supplementary files format and content: Cellranger output files for GEX, ADT and VDJ libraries

molecule: polyA RNA

organism: Homo sapiens

source_name: Tumor

extract_protocol:
FACS sorting was used to extract CD45+ CD3+ or CD45+ cells from baseline and post treatment samples of HNSCC patients
10x genomics protocol for GEX, ADT and VDJ libraries was followed

tag: tissue

value: Tumor

tag: cell type

value: CD45+ CD3+ T cells

tag: library type

value: GEX


title: HN34 Pre Gene expression data

description: Library name: HN34_Pre_GEX


title: HN35 Post Gene expression data

description: Library name: HN35_Post_GEX

value: CD45+ cells


title: 20M-15022

status: Public on Feb 28 2025

type: genomic

city: Seoul

first: Hwan Young

last: Lee

address: 103, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University College of Medicine

description: Illumina Infinium MethylationEPIC BeadChip kits

hyb_protocol: Bisulfite converted DNA was amplified, fagmented and hybridised to Infinium HumanMethylation EPIC BeadChip using standard Illumina protocol

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing: Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles. Background intensity computed from a set of negative controls was subtracted from each analytical data point. The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100). The ß-value reflects the methylation level of each CpG site. A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: semen

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using Qiagen DNA Mini Kit (Qiagen, Hilden, Germany) based on the manufacturers’ instructions

value: semen

tag: age

tag: Sex

value: Male

tag: ethnicity

value: Korean-Asian


title: HN33 Post CITE-Seq expression data

description: Library name: HN33_Post_ADT

library_source: other

data_processing:
Fastq files were demultiplexed using Cellranger mkfastq
Demultiplexed data (GEX,ADT and VDJ) were processed using Cellranger Multi pipeline
Assembly: GRCh38
Supplementary files format and content: Cellranger output files for GEX, ADT and VDJ libraries
Library strategy: CITE-Seq

molecule: protein

value: ADT


title: HN34 Post CITE-Seq expression data

description: Library name: HN34_Post_ADT


title: HN34 Pre TCR-Seq data

description: Library name: HN34_Pre_VDJ

library_source: transcriptomic

data_processing:
Fastq files were demultiplexed using Cellranger mkfastq
Demultiplexed data (GEX,ADT and VDJ) were processed using Cellranger Multi pipeline
Assembly: GRCh38
Supplementary files format and content: Cellranger output files for GEX, ADT and VDJ libraries
Library strategy: TCR-Seq

value: VDJ


title: HN34 Pre CITE-Seq expression data

description: Library name: HN34_Pre_ADT


title: HN33 Post TCR-Seq data

description: Library name: HN33_Post_VDJ


title: HN35 Post TCR-Seq data

description: Library name: HN35_Post_VDJ


title: HN33 Post Gene expression data

description: Library name: HN33_Post_GEX


title: HN32 Post TCR-Seq data

description: Library name: HN32_Post_VDJ


title: HN33 Pre Gene expression data

description: Library name: HN33_Pre_GEX


title: 20M-15040


title: HN33 Pre CITE-Seq expression data

description: Library name: HN33_Pre_ADT


title: HN33 Pre TCR-Seq data

description: Library name: HN33_Pre_VDJ


title: HN32 Post CITE-Seq expression data

description: Library name: HN32_Post_ADT


title: HN32 Post Gene expression data

description: Library name: HN32_Post_GEX


title: HN32 Pre TCR-Seq data

description: Library name: HN32_Pre_VDJ


title: HCT8 cells, Input

city: Guangzhou

first: Tanxing

last: Cai

state: Guangdong

address: 26 Erheng Road, Yuancun, Tianhe District

department: Department of General Surgery

country: China

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

description: Library name: Input

library_source: genomic

data_processing:
Basecalls were performed for Illumina NovaSeq 6000 output.
ChIP-seq reads were trimmed using Trimmomatic v0.38.
ChIP-seq reads were aligned to the Homo sapiens reference genome GRCh37 using BowTie v1.1.2.
Peaks were called using MACS2 v2.1.1.20160309 and duplicate reads were processed using Picard v0.118.
Peaks annotated using ChIPseeker 1.16.1.
Assembly: GRCh37
Supplementary files format and content: bigwig

growth_protocol: HCT8 cells were mainteined in DMEM supplemented with 10 fetal bovine serum(FBS) and antibodics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Cells were fixed with 37% formaldehyde for 10 minutes. After quenching and cell lysis, chrmatin was sonicated using a SimpleChIP® Plus Sonication Chromatin IP Kit(CST,56383S)
Libraries were constructed using the Rapid Plus DNA Lib Prep Kit for Illumina V2 (RK20255, ABclonal, China). Procedures included DNA end repair, 3'-end adenylation, adapter ligation, and PCR amplification.

treatment_protocol: HCT8 cells transfected with control plasmid or KDM4A overexpression plasmid

tag: cell line

value: colorectal cancer

tag: genotype

value: KDM4A overexpression

tag: treatment

value: HCT8 cells transfected with KDM4A plasmid

tag: chip antibody


title: HN32 Pre CITE-Seq expression data

description: Library name: HN32_Pre_ADT


title: HN32 Pre Gene expression data

description: Library name: HN32_Pre_GEX


title: HN34 Post Gene expression data

description: Library name: HN34_Post_GEX


title: HN31 Pre TCR-Seq data

description: Library name: HN31_Pre_VDJ


title: HN31 Pre CITE-Seq expression data

description: Library name: HN31_Pre_ADT


title: HN30 Pre CITE-Seq expression data

description: Library name: HN30_Pre_ADT


title: HN30 Pre Gene expression data

description: Library name: HN30_Pre_GEX


title: HN31 Pre Gene expression data

description: Library name: HN31_Pre_GEX


title: HN30 Pre TCR-Seq data

description: Library name: HN30_Pre_VDJ


title: HN29 Pre Gene expression data

description: Library name: HN29_Pre_GEX


title: HN29 Pre TCR-Seq data

description: Library name: HN29_Pre_VDJ


title: HN28 Pre CITE-Seq expression data

description: Library name: HN28_Pre_ADT


title: HN28 Pre TCR-Seq data

description: Library name: HN28_Pre_VDJ


title: HN28 Post CITE-Seq expression data

description: Library name: HN28_Post_ADT


title: HN28 Pre Gene expression data

description: Library name: HN28_Pre_GEX


title: HN27 Post TCR-Seq data

description: Library name: HN27_Post_VDJ


title: HN29 Pre CITE-Seq expression data

description: Library name: HN29_Pre_ADT


title: HN27 Post CITE-Seq expression data

description: Library name: HN27_Post_ADT


title: HN27 Post Gene expression data

description: Library name: HN27_Post_GEX


title: HN28 Post Gene expression data

description: Library name: HN28_Post_GEX


title: HN28 Post TCR-Seq data

description: Library name: HN28_Post_VDJ


title: HN27 Pre CITE-Seq expression data

description: Library name: HN27_Pre_ADT


title: HN27 Pre TCR-Seq data

description: Library name: HN27_Pre_VDJ


title: HN26 Post TCR-Seq data

description: Library name: HN26_Post_VDJ


title: HN26 Post CITE-Seq expression data

description: Library name: HN26_Post_ADT


title: HN27 Pre Gene expression data

description: Library name: HN27_Pre_GEX


title: HN26 Post Gene expression data

description: Library name: HN26_Post_GEX


title: HN26 Pre TCR-Seq data

description: Library name: HN26_Pre_VDJ


title: HN26 Pre Gene expression data

description: Library name: HN26_Pre_GEX


title: HN25 Post CITE-Seq expression data

description: Library name: HN25_Post_ADT


title: HN25 Post TCR-Seq data

description: Library name: HN25_Post_VDJ


title: HN25 Post Gene expression data

description: Library name: HN25_Post_GEX


title: HN25 Pre TCR-Seq data

description: Library name: HN25_Pre_VDJ


title: HN25 Pre CITE-Seq expression data

description: Library name: HN25_Pre_ADT


title: HN24 Post Gene expression data

description: Library name: HN24_Post_GEX


title: HN24 Post TCR-Seq data

description: Library name: HN24_Post_VDJ


title: HN24 Pre TCR-Seq data

description: Library name: HN24_Pre_VDJ


title: HN24 Pre CITE-Seq expression data

description: Library name: HN24_Pre_ADT

value: CD45+  cells


title: HN23 Post CITE-Seq expression data

description: Library name: HN23_Post_ADT


title: HN23 Pre Gene expression data

description: Library name: HN23_Pre_GEX


title: HN23 Pre TCR-Seq data

description: Library name: HN23_Pre_VDJ


title: HN23 Post Gene expression data

description: Library name: HN23_Post_GEX


title: HN22 Post TCR-Seq data

description: Library name: HN22_Post_VDJ


title: HN22 Post Gene expression data

description: Library name: HN22_Post_GEX


title: HN23 Post TCR-Seq data

description: Library name: HN23_Post_VDJ


title: HN23 Pre CITE-Seq expression data

description: Library name: HN23_Pre_ADT


title: HN22 Pre CITE-Seq expression data

description: Library name: HN22_Pre_ADT


title: HN21 Post CITE-Seq expression data

description: Library name: HN21_Post_ADT


title: HN21 Post TCR-Seq data

description: Library name: HN21_Post_VDJ


title: HN22 Post CITE-Seq expression data

description: Library name: HN22_Post_ADT


title: HN26 Pre CITE-Seq expression data

description: Library name: HN26_Pre_ADT


title: HN22 Pre Gene expression data

description: Library name: HN22_Pre_GEX


title: HN22 Pre TCR-Seq data

description: Library name: HN22_Pre_VDJ


title: HN21 Post Gene expression data

description: Library name: HN21_Post_GEX


title: HN21 Pre TCR-Seq data

description: Library name: HN21_Pre_VDJ


title: HN21 Pre CITE-Seq expression data

description: Library name: HN21_Pre_ADT


title: HN21 Pre Gene expression data

description: Library name: HN21_Pre_GEX


title: HN20 Post CITE-Seq expression data

description: Library name: HN20_Post_ADT


title: HN20 Post TCR-Seq data

description: Library name: HN20_Post_VDJ


title: HN25 Pre Gene expression data

description: Library name: HN25_Pre_GEX


title: HN24 Post CITE-Seq expression data

description: Library name: HN24_Post_ADT


title: HN20 Post Gene expression data

description: Library name: HN20_Post_GEX


title: HN24 Pre Gene expression data

description: Library name: HN24_Pre_GEX


title: HN20 Pre TCR-Seq data

description: Library name: HN20_Pre_VDJ


title: HN20 Pre CITE-Seq expression data

description: Library name: HN20_Pre_ADT

value: CD45+ T cells


title: HN19 Post TCR-Seq data

description: Library name: HN19_Post_VDJ


title: HN20 Pre Gene expression data

description: Library name: HN20_Pre_GEX


title: HN19 Post CITE-Seq expression data

description: Library name: HN19_Post_ADT


title: HN19 Post Gene expression data

description: Library name: HN19_Post_GEX


title: HN19 Pre TCR-Seq data

description: Library name: HN19_Pre_VDJ


title: HN19 Pre CITE-Seq expression data

description: Library name: HN19_Pre_ADT


title: HN19 Pre Gene expression data

description: Library name: HN19_Pre_GEX


title: HN18 Post TCR-Seq data

description: Library name: HN18_Post_VDJ


title: HN17 Pre CITE-Seq expression data

description: Library name: HN17_Pre_ADT


title: HN17 Pre TCR-Seq data

description: Library name: HN17_Pre_VDJ


title: HN18 Post CITE-Seq expression data

description: Library name: HN18_Post_ADT


title: HN17 Pre Gene expression data

description: Library name: HN17_Pre_GEX


title: HN16 Post CITE-Seq expression data

description: Library name: HN16_Post_ADT


title: HN16 Pre Gene expression data

description: Library name: HN16_Pre_GEX


title: HN15 Post TCR-Seq data

description: Library name: HN15_Post_VDJ


title: HN16 Pre TCR-Seq data

description: Library name: HN16_Pre_VDJ


title: HN16 Post Gene expression data

description: Library name: HN16_Post_GEX


title: HN15 Post CITE-Seq expression data

description: Library name: HN15_Post_ADT


title: HN15 Post Gene expression data

description: Library name: HN15_Post_GEX


title: HN14 Post Gene expression data

description: Library name: HN14_Post_GEX


title: HN16 Pre CITE-Seq expression data

description: Library name: HN16_Pre_ADT


title: HN14 Pre TCR-Seq data

description: Library name: HN14_Pre_VDJ


title: HN14 Pre Gene expression data

description: Library name: HN14_Pre_GEX


title: HN14 Post CITE-Seq expression data

description: Library name: HN14_Post_ADT


title: HN13 Post CITE-Seq expression data

description: Library name: HN13_Post_ADT


title: HN12 Post CITE-Seq expression data

description: Library name: HN12_Post_ADT


title: HN12 Post TCR-Seq data

description: Library name: HN12_Post_VDJ


title: HN13 Post Gene expression data

description: Library name: HN13_Post_GEX


title: HN18 Post Gene expression data

description: Library name: HN18_Post_GEX


title: HN12 Post Gene expression data

description: Library name: HN12_Post_GEX


title: HN12 Pre CITE-Seq expression data

description: Library name: HN12_Pre_ADT


title: HN12 Pre TCR-Seq data

description: Library name: HN12_Pre_VDJ


title: HN11 Post TCR-Seq data

description: Library name: HN11_Post_VDJ


title: HN16 Post TCR-Seq data

description: Library name: HN16_Post_VDJ


title: HN11 Post Gene expression data

description: Library name: HN11_Post_GEX


title: HN11 Pre TCR-Seq data

description: Library name: HN11_Pre_VDJ


title: HN11 Pre Gene expression data

description: Library name: HN11_Pre_GEX


title: HN10 Post TCR-Seq data

description: Library name: HN10_Post_VDJ


title: HN10 Post CITE-Seq expression data

description: Library name: HN10_Post_ADT


title: HN11 Pre CITE-Seq expression data

description: Library name: HN11_Pre_ADT


title: HN10 Post Gene expression data

description: Library name: HN10_Post_GEX


title: HN10 Pre TCR-Seq data

description: Library name: HN10_Pre_VDJ


title: HN10 Pre Gene expression data

description: Library name: HN10_Pre_GEX


title: HN14 Post TCR-Seq data

description: Library name: HN14_Post_VDJ


title: HN14 Pre CITE-Seq expression data

description: Library name: HN14_Pre_ADT


title: HN10 Pre CITE-Seq expression data

description: Library name: HN10_Pre_ADT


title: HN09 Post TCR-Seq data

description: Library name: HN09_Post_VDJ


title: HN09 Post CITE-Seq expression data

description: Library name: HN09_Post_ADT


title: HN09 Post Gene expression data

description: Library name: HN09_Post_GEX


title: HN13 Post TCR-Seq data

description: Library name: HN13_Post_VDJ


title: HN09 Pre CITE-Seq expression data

description: Library name: HN09_Pre_ADT


title: HN09 Pre TCR-Seq data

description: Library name: HN09_Pre_VDJ


title: HN09 Pre Gene expression data

description: Library name: HN09_Pre_GEX


title: HN12 Pre Gene expression data

description: Library name: HN12_Pre_GEX


title: HN08 Post CITE-Seq expression data

description: Library name: HN08_Post_ADT


title: HN07 Post TCR-Seq data

description: Library name: HN07_Post_VDJ


title: HN08 Post Gene expression data

description: Library name: HN08_Post_GEX


title: HN11 Post CITE-Seq expression data

description: Library name: HN11_Post_ADT


title: HN06 Post CITE-Seq expression data

description: Library name: HN06_Post_ADT


title: HN07 Post CITE-Seq expression data

description: Library name: HN07_Post_ADT


title: HN05 Post CITE-Seq expression data

description: Library name: HN05_Post_ADT


title: HN05 Post TCR-Seq data

description: Library name: HN05_Post_VDJ


title: HN05 Pre CITE-Seq expression data

description: Library name: HN05_Pre_ADT


title: HN05 Pre Gene expression data

description: Library name: HN05_Pre_GEX


title: HN05 Post Gene expression data

description: Library name: HN05_Post_GEX


title: HN05 Pre TCR-Seq data

description: Library name: HN05_Pre_VDJ


title: HN04 Post CITE-Seq expression data

description: Library name: HN04_Post_ADT


title: HN04 Post Gene expression data

description: Library name: HN04_Post_GEX


title: HN04 Pre TCR-Seq data

description: Library name: HN04_Pre_VDJ


title: HN03 Post TCR-Seq data

description: Library name: HN03_Post_VDJ


title: HN03 Post Gene expression data

description: Library name: HN03_Post_GEX


title: HN03 Pre TCR-Seq data

description: Library name: HN03_Pre_VDJ


title: HN04 Pre CITE-Seq expression data

description: Library name: HN04_Pre_ADT


title: HN04 Pre Gene expression data

description: Library name: HN04_Pre_GEX


title: HN03 Pre CITE-Seq expression data

description: Library name: HN03_Pre_ADT


title: HN03 Pre Gene expression data

description: Library name: HN03_Pre_GEX


title: HN07 Post Gene expression data

description: Library name: HN07_Post_GEX


title: HN06 Post TCR-Seq data

description: Library name: HN06_Post_VDJ


title: HN02 Pre TCR-Seq data

description: Library name: HN02_Pre_VDJ


title: HN02 Pre CITE-Seq expression data

description: Library name: HN02_Pre_ADT


title: HN02 Post CITE-Seq expression data

description: Library name: HN02_Post_ADT


title: HN02 Pre Gene expression data

description: Library name: HN02_Pre_GEX


title: HN01 Post TCR-Seq data

description: Library name: HN01_Post_VDJ


title: HN06 Post Gene expression data

description: Library name: HN06_Post_GEX


title: HN01 Post CITE-Seq expression data

description: Library name: HN01_Post_ADT


title: HN01 Pre TCR-Seq data

description: Library name: HN01_Pre_VDJ


title: HN01 Pre Gene expression data

description: Library name: HN01_Pre_GEX


title: HN01 Post Gene expression data

description: Library name: HN01_Post_GEX


title: HN01 Pre CITE-Seq expression data

description: Library name: HN01_Pre_ADT


title: 293_KSHV_GCV_AAV-TK_rep1

status: Public on Feb 19 2025

city: Sacramento

first: Yoshihiro

last: Izumiya

state: CA

department: Dermatology

institute: UC Davis

description: Library name: Sample 15

data_processing:
Raw sequence reads (FASTQ format) were mapped using star to the reference human genome assembly (GRCh38/hg38, GENCODE release 46) combined with the complete genome sequence of KSHV, NC009333.
Gene level raw counts were generated using htseq against human GENCODE release 46 gtf and the simplified gtf for KSHV, PMC5371899.
Assembly: hg38 which included the complete genome sequence of KSHV, NC009333
Supplementary files format and content: tab-delimited text file consisting of the Ensembl ID (column 1), HGNC Symbol (column 2), and raw count (columns 3).

molecule: total RNA

source_name: embryonic kidney

growth_protocol: 293 and iSLK cells were cultured in DMEM supplemented in 10% fetal bovine serum and antibiotics with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested by quick RNA miniprep kit (Zymo research), and treated with DNaseI for following analysis.
Stranded mRNA-seq libraries were prepared from total RNA (100 ng) using the KAPA Stranded mRNA-Seq kit (Roche) according to the manufacturer’s standard protocol. Libraries were pooled and multiplex sequenced on an Illumina NovaSeq 6000 System (150-bp, paired-end, >30 × 106 reads per sample).

treatment_protocol: Cells were infeected with AAV8-TR2-Orip-TK, followed by GCV (5nM) treatment.

value: embryonic kidney

value: Epithelial carcinoma cells

value: AAV8-TR2-OriP-TK infection with GCV


title: 293_KSHV_AAV-TK_rep2

description: Library name: Sample 14

value: AAV8-TR2-OriP-TK infection


title: HN03 Post CITE-Seq expression data

description: Library name: HN03_Post_ADT

value: Tumor

value: CD45+ CD3+ T cells


title: 293_KSHV_GCV_rep2

description: Library name: Sample 12

value: GCV


title: HN08 Post TCR-Seq data

description: Library name: HN08_Post_VDJ


title: iSLK_KSHV_GCV_AAV-TK_rep2

description: Library name: Sample 8

source_name: renal epithelium

value: renal epithelium

value: iSLK


title: 293_KSHV_GCV_rep1

description: Library name: Sample 11


title: 293_KSHV_rep1

description: Library name: Sample 9

value: No treatment


title: 293_KSHV_rep2

description: Library name: Sample 10


title: 293_KSHV_AAV-TK_rep1

description: Library name: Sample 13


title: HN02 Post Gene expression data

description: Library name: HN02_Post_GEX

value: GEX


title: HN02 Post TCR-Seq data

description: Library name: HN02_Post_VDJ

value: VDJ


title: iSLK_KSHV_GCV_rep2

description: Library name: Sample 4


title: iSLK_KSHV_AAV-TK_rep1

description: Library name: Sample 5


title: iSLK_KSHV_rep2

description: Library name: Sample 2


title: iSLK_KSHV_GCV_AAV-TK_rep1

description: Library name: Sample 7


title: iSLK_KSHV_rep1

description: Library name: Sample 1


title: iSLK_KSHV_GCV_rep1

description: Library name: Sample 3


title: iSLK_KSHV_AAV-TK_rep2

description: Library name: Sample 6


title: MDA-MB-468_Radioresistant2

status: Public on Feb 13 2025

city: Worcester

first: Rui

last: Li

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

description: Library name: HRR2

data_processing:
The analysis were performed on the OneStopRNASeq platform.
Specifically, paired-end RNASeq reads were aligned to huamn T2T genome (GCA_009914755.4) with STAR
Gene expression were quantified with featureCounts
Genome annotation file used was GCA_009914755.4-2022_07
Differential analysis processed with DESeq2
Assembly: human T2T
Supplementary files format and content: excel: count and TPM

source_name: MDA-MB-468 (TNBC cell line)

extract_protocol:
RNA was harvested using the Macherey-Nagel RNA Nucleospin Kit.
400ng of total RNA was used for library preparation

value: MDA-MB-468 (TNBC cell line)

value: breast cancer cell line


title: MDA-MB-468_Parental3

description: Library name: HPar3


title: MDA-MB-468_Parental2

description: Library name: HPar2


title: MDA-MB-468_Radioresistant3

description: Library name: HRR3


title: MDA-MB-468_Radioresistant1

description: Library name: HRR1


title: HN04 Post TCR-Seq data

description: Library name: HN04_Post_VDJ


title: MDA-MB-468_Parental1

description: Library name: HPar1


title: Chtf18 mutant lineage depleted hematopoietic progenitors – Replicate 2

status: Public on Feb 12 2025

city: Philadelphia

first: David

last: Wiest

address: 333 Cottman Ave

institute: Fox Chase Cancer Center

description:
Library name: CHTF18mut-2
10x Genomics

data_processing:
Barcoding and DNA purification was performed according to the manufacturer’s protocol. Sequencing was performed using 2 x 150 pair-end configuration on an NovaSeqX Plus platform at a sequencing depth of 375G/lane. Cell-barcode and unique molecular identifiers were extracted and aligned through Cell Ranger and expression analysis was performed using Seurat V4, as described (Stuart et al., 2019). Uniform Manifold Approximation and Projection (UMAP) plots were used to visualize the data based on canonical component analysis of the top 1000 genes with highest dispersion between all sample groups. Gene ontology and Gene Set Enrichment analysis was performed using EnrichR.
Assembly: mm10
Supplementary files format and content: tsv and matrix files

organism: Mus musculus

source_name: bone marrow

extract_protocol:
Whole bone marrow cells were isolated from one mouse per replicate followed by depletion of lineage positive cells using Miltenyi direct lineage depletion kit
Library construction was performed according to Chromium v3.1 3’ Single Cell Expression kit

value: bone marrow

value: HSPCs

value: Mutant


title: 293_KSHV_GCV_AAV-TK_rep2

description: Library name: Sample 16

value: embryonic kidney


title: Wildtype lineage depleted hematopoietic progenitors – Replicate 2

description:
Library name: WT-2
10x Genomics

value: WT


title: Chtf18 mutant lineage depleted hematopoietic progenitors – Replicate 1

description:
Library name: CHTF18mut-1
10x Genomics


title: Wildtype lineage depleted hematopoietic progenitors – Replicate 1

description:
Library name: WT-1
10x Genomics


title: Pleuroperitoneal folds, GD 13.5, Rep 1

city: Edmonton

first: Robin

middle: D

last: Clugston

state: Alberta

address: 7-49 Medical Sciences Building

department: Physiology

country: Canada

institute: University of Alberta

description: 10X genomics

data_processing:
Libraries were sent to Novogene for sequencing, and the processed utilizing the CellRanger Pipeline utilizing the 10X Genomics Cloud Service. Data was analyzed utilizing R version 4.1. Cells were excluded if they had less than 200 features or more than 10% mitochondrial counts.
Assembly: Mouse (mm10) 2020-A
Supplementary files format and content: Processed Datacontains the cellranger output of the libraries.

source_name: Pleuroperitoneal Folds

extract_protocol:
Pleuroperitoneal folds from a mouse embryo were carefully dissected at GD 13.5. Following this, the tissue was incubated in 0.25% trypsin-EDTA for approximately 10 minutes at 37 degrees celsius. Trypsin was inactivated by adding 1 mL of 10% Fetal bovine Serum, and the solution was centrifuged for 5 minutes at 340xg. The supernatant was discarded and the pellet was resuspended in 1 mL of 10% fetal bovine serum.
The cells were sent to the high content analysis core at the University of Alberta and the libraries were generated using the Chromium Next GEM single cell 3' Gene expression v3.1

value: Pleuroperitoneal Folds

tag: strain

value: Balb/C

tag: developmental stage


title: TO_EVTenrich_TO82_SN

status: Public on Feb 08 2025

city: Durham

first: Madeline

last: Keenen

state: North Carolina

address: 308 Research Drive

department: Cell Biology

institute: Duke University

description: Library name: Sample 18

data_processing:
De-multiplexing, barcode assignment, gene counts, and matrix creation was done with CellRanger v6.1.2
Assembly: hg38
Supplementary files format and content: Cell ranger output files
Supplementary files format and content: RDS count matrices

source_name: placenta

extract_protocol:
Detailed extraction protocols can be found in the associated eLife manuscript. Briefly,  individual cells were isolated for SC RNA sequencing with enzymatic digestion and filtration from either 1-term placenta tissue or 2-the trophoblast organoid samples grown in different culture conditions. Individual nuclei were isolated via the 10X Genomics Chromium Nuclear Isolation Kit.
All samples were loaded into individual chip wells and run on a 10x chromium controller with the Chromium Single Cell 3’ Reagent Reagent Kit v3.1 (Dual Index). Subsequent library preparation was all done as per the manusfacturers instructions.

value: placenta

value: trophoblast organoid

value: trophoblast

tag: gestational age

value: male

tag: to passage_number


title: TO_EVTenrich_TO74_SN

description: Library name: Sample 16


title: TO_STBout_TO82_SN

description: Library name: Sample 15


title: TO_STBout_TO81_SN

description: Library name: Sample 14

value: female


title: TO_STBin_TO82_SN

description: Library name: Sample 12


title: TO_STBin_TO81_SN

description: Library name: Sample 11


title: TO_STBout_TO74_SN

description: Library name: Sample 13


title: TO_STBin_TO74_SN

description: Library name: Sample 10


title: TO_STBin_TO82_SC

description: Library name: Sample 9


title: TO_STBin_TO68_SC

description: Library name: Sample 7


title: TO_STBin_TO81_SC

description: Library name: Sample 8


title: AGPL4_SC

description: Library name: Sample 3

value: primary tissue

value: multiple


title: AGPL3_SN

description: Library name: Sample 4


title: AGPL5_SN

description: Library name: Sample 6


title: AGPL4_SN

description: Library name: Sample 5


title: Primary microglia-LysoPS rep2

status: Public on Jan 30 2025

city: Hefei

first: XiqQiong

last: Wang

state: Anhui

address: School of Life Sciences, No. 443 Huangshan Road

institute: University Of Science And Technology Of China

data_processing:
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data.
Raw reads were filtered by Trimmomatic (version 0.36) according to several steps: 1) Removing sequences with N bases; 2) Removing adaptor sequence if reads contains; 3) Removing low quality bases from reads 3’ to 5’ (Q < 20); 4) Removing low quality bases from reads 5’ to 3’ (Q < 20); 5) Using a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp); 6) Removing reads with reads length less than 35nt and its pairing reads. And the remaining clean data was used for further analysis.
RNA-seq reads were aligned to the reference genome using HISAT2, And uniquely mapped reads were used for further analysis.
Then we use stringtie to calculate Raw Counts, FPKM and TPM of genes
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts,FPKM and TPM for every gene and every sample

source_name: Primary microglia

growth_protocol: After removing the meninges, the brains of newborn mice we dissociated using 0.25% trypsin, filtered with a 40 µm cell strainer and then cultured in complete DMEM medium. After 2 weeks of cultivation (with medium changes at 24 hr and then every 3 d), microglia were collected by gently shaking the culture for 1 min.

extract_protocol:
The RNA of all cells was harvested using Trizol reagent.
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina®(12301ES96, YEASEN, China) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in 1nd Strand Synthesis Reaction Buffer First. Second strand cDNA synthesis was subsequently performed using 2nd Strand Synthesis Buffer. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, adaptor was ligated to prepare for library. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with Hieff NGS™ DNA Selection Beads DNA(12601ES56, YEASEN, China). Then PCR was performed with 2×Super CanaceTM High-Fidelity Mix，Primer mix and Adapter Ligated DNA. At last, PCR products were purified (Hieff NGS™ DNA Selection Beads) and library quality was assessed on the Qubit®2.0 Flurometer. The libraries were then quantified and pooled. Paired-end sequencing of the library was performed on the MGISEQ2000 sequencers .

treatment_protocol: One replicate was LysoPS treated for 4 hours.

value: Primary microglia

value: treated with LysoPS for 4 hours


title: Primary microglia-mock rep2

value: untreated


title: AGPL2_SC

description: Library name: Sample 1


title: Primary microglia-LysoPS rep1


title: Primary microglia-mock rep1


title: KLE DMSO control replicate 2 (batch 3)

status: Public on Jan 21 2025

city: Boston

first: Sarah

middle: J.

last: Hill

state: MA

address: 450 Brookline Ave., Dana Building, Room 1410C

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Raw fastq data were aligned and preprocessed using the VIPER pipeline
Reads were aligned to hg19 using STAR v2.7.0f
Multimapping reads (mapq=0) were filtered out using samtools v1.19 and PCR duplicates removed with picard MarkDuplicates v2.21.8
Aligned read counts were extracted and analysed; differential expression analysis was performed with DESeq2 v1.40.2
Assembly: hg19

source_name: Endometrial Cancer

growth_protocol: ARK1 and ARK2 cells were grown in Roswell Park Memorial Institute (RPMI) 1640 (Gibco Cat. #11875-093), 10% FBS (Sigma Cat. #F2442), and 1% penicillin/streptomycin (P/S) (Gibco Cat. #15140-122). HEC1B and AN3CA cells were grown in Minimum Essential Medium (MEM, Corning Cat. #10-010-CV), 10% FBS, and 1% P/S. KLE cells were grown in Dulbecco's Modified Eagle Medium (DMEM)/F12 1:1 (Gibco Cat. # 11320-033), 10% FBS, and 1% P/S. Organoids were grown in advanced DMEM/F12 (Gibco Cat. #12634-028), supplemented with 1% P/S, 1% HEPES (Gibco Cat. # 15630080), 1X Glutamax (Gibco Cat. # 35050061), 500nM A83-01 (BioGems Cat. #9094360), 10µM SB202190 (BioGems Cat. #1523072), 10mM Nicotinamide (Sigma Aldrich Cat. #N0636), 1X B-27 (Gibco Cat. #17504044), 1.25mM N-acetylcysteine (Sigma Aldrich Cat. #A9165), 1µM Prostaglandin E2 (BioGems Cat. # 3632464), 10% Noggin and 10% R-Spondin1 conditioned media, 10ng/mL FGF-10 (Peprotech Cat. #100-26), 50ng/mL EGF (Peprotech Cat. #100-15), and 10ng/mL FGF2 (Peprotech Cat. #100-18B). Cells were treated as described in the Overall Design and Treatment protocol sections.

extract_protocol:
Cell lines were trypsinized and organoids scraped. Cells were pelleted and stored at -80°C until RNA was prepared. RNA was prepared using Qiagen's RNEasy Mini kit (Qiagen Cat #74104) with on-column DNASE digest (Qiagen Cat. #79254) according to the manufacturer's protocol. RNA was snap frozen and sent to GENEWIZ (South Plainfield, NJ) for Standard RNA sequencing.
RNA libraries for RNA-seq were prepared by GENEWIZ.

treatment_protocol: For cell lines, doubling times were calculated. For HEC1B and ARK1 models, cells were treated for one doubling time (approximately 26 hours for ARK1 and 33.5 hours for HEC1B) with either 0.25µM Abemaciclib methanesulfonate (referred to as "Abemaciclib" henceforth) or media containing DMSO vehicle (used for analysis as batch 1). For organoids, a subset of the organoids were treated with media containing either 0.25µM Abemaciclib or media containing DMSO vehicle for 24 hours (used for analysis as batch 2). For additional cell lines and organoids to be used only for baseline transcriptomic comparisons, the cells were treated with media containing DMSO at 1:100,000 for 24 hours (used for analysis as batch 3). After treatments, cell lines and organoids were harvested and stored at -80°C until RNA was prepared. RNA was prepared using Qiagen's RNEasy Mini kit (Qiagen Cat #74104) with on-column DNASE digest (Qiagen Cat. #79254) according to the manufacturer's protocol. RNA was snap frozen and sent to GENEWIZ (South Plainfield, NJ) for Standard RNA sequencing. Each individual sample was sequenced in duplicate to provide technical replicates for validation.

value: Endometrial Cancer

value: DMSO

tag: batch


title: HEC1B DMSO control replicate 4 (batch 3)


title: HEC1B DMSO control replicate 3 (batch 3)


title: AN3CA DMSO control replicate 2 (batch 3)


title: AN3CA DMSO control replicate 1 (batch 3)


title: ARK1 DMSO control replicate 3 (batch 3)


title: ARK1 DMSO control replicate 4 (batch 3)


title: CS-B DMSO control replicate 2 (batch 3)


title: CS-B DMSO control replicate 1 (batch 3)


title: TO_EVTenrich_TO81_SN

description: Library name: Sample 17


title: EMCA-A DMSO control replicate 4 (batch 3)


title: CS-A DMSO control replicate 4 (batch 3)


title: UPSC-A DMSO control replicate 3 (batch 3)


title: UPSC-A DMSO control replicate 4 (batch 3)


title: AGPL3_SC

description: Library name: Sample 2


title: EMCA-A DMSO control replicate 3 (batch 3)


title: UPSC-A Abema replicate 1 (batch 2)

value: Abemaciclib


title: UPSC-A Abema replicate 2 (batch 2)


title: CS-A DMSO control replicate 3 (batch 3)


title: UPSC-A DMSO control replicate 1 (batch 2)


title: CS-A DMSO control replicate 1 (batch 2)


title: CS-A Abema replicate 2 (batch 2)


title: CS-A DMSO control replicate 2 (batch 2)


title: EMCA-A Abema replicate 2 (batch 2)


title: EMCA-A DMSO control replicate 2 (batch 2)


title: EMCA-A Abema replicate 1 (batch 2)


title: UPSC-A DMSO control replicate 2 (batch 2)


title: EMCA-A DMSO control replicate 1 (batch 2)


title: KLE DMSO control replicate 1 (batch 3)


title: HAP1,Micro-C rep5

status: Public on Jan 10 2025

city: Tianjin

first: Ke

last: Zhao

address: Qixiangtai Road, No.22

institute: Tianjin Medical University

description: Library name: MicroC-HAP1 rep 5

data_processing:
The micro-C data was analyzed according to the procedures outlined in the documentation at https://micro-c.readthedocs.io/en/latest/. Initially, raw sequencing reads underwent quality checks and filtering to eliminate low-quality sequences. The remaining reads were then aligned to the hg19 reference genome using BWA-MEM. After alignment, the data was processed to identify contact interactions by pairing aligned reads, sorting, and filtering for low-quality events, PCR duplicates, and invalid pairs using Pairtools (https://pairtools.readthedocs.io/en/latest). These filtered reads were then assigned to interaction pairs. Finally, chromatin loops were identified using the HiCCUPS loop-calling program at 10 kb and 5 kb resolutions, utilizing hic files generated from unique valid read pairs.
Assembly: hg19
Supplementary files format and content: bedpe

source_name: cell line

growth_protocol: HAP1 (Horizon Discovery) cells were cultured in IMDM (ThermoFisher) supplemented with 10% fetal bovine serum in 5% CO2 at 37°C.

extract_protocol:
The Micro-C assay was carried out in diploid HAP1 cells, using a published protocol.
Micro-C library preparation was prepared as previously described(Hsieh et al., 2020; Hsieh et al., 2016). Briefly, HAP1 cells (~1.5 × 10⁷) were fixed in 1% formaldehyde (Sigma-Aldrich, F8775) in PBS at room temperature for 10 min. Crosslinking was quenched with 1 M Tris-HCl (pH 7.5) to a final concentration of 375 mM for 5 min at room temperature. Cells were spun down and washed twice with cold PBS. Cell pellets were crosslinked again with freshly prepared 3 mM DSG (ThermoFisher, 20593) crosslinking solution for 45 min at RT. Crosslinking termination and washing is the same as in the previous step. Crosslinked cell pellets were resuspended in MB#1 (50 mM NaCl, 10 mM Tris-HCl pH = 7.5, 5 mM MgCl2, 1mM CaCl2, 0.2% NP-40, 1x Roche cOmplete EDTA-free (Roche diagnostics, 04693132001)) at a concentration of 1x106 cells/100 µL and were incubated for 20 min on ice. Then wash nuclei pellet in MB#1 at a concentration of 1x106 cells/100 μL. Centrifuge at ~2,000 x g for 5 min at 4°C. Added the appropriate amount of MNase (as determined by an MNase titration experiment on the same sample batch) to digest chromatin to an 80-90% monomer / 20-10% dimer ratio. The MNase reaction was inactivated by adding 4 mM EGTA and incubated for 10 min at 65°C. Digested chromatin was washed twice with 1 mL of cold MB2 (50 mM NaCl, 10 mM Tris-HCl pH 7.5, 10 mM MgCl2).  Next, the pellet was resuspended in the end-repair buffer (50 mM NaCl, 10 mM Tris-HCl pH 7.5, 10 mM MgCl2, 100 µg/mL BSA, 2 mM ATP, 5 mM DTT) and 25 units of T4 Polynucleotide Kinase (NEB, M0201) for 15 min at 37°C while shaking in a thermomixer at 1000 rpm. Then, we added 25 units of DNA Polymerase I, Large (Klenow) Fragment (NEB, M0210) directly to the reaction and incubated the tube for an additional 15 min at 37°C while shaking in a thermomixer at 1000 rpm. Finally, in order to repair the cut end of the enzyme to form a blunt and ligatable ends, we supplemented 66 µM of dNTPs (dTTP, dGTP (NEB, N0446), biotin-dATP (Jena Bioscience, NU-835-BIO14), biotin-dCTP (Jena Bioscience, NU-809-BIOX), 100 µg/mL BSA and 1X T4 DNA ligase reaction buffer (NEB, B0202) directly into the reaction and incubated for 45 min at 25°C while shaking in a thermomixer at 1000 rpm. The end-repair reaction was then inactivated with 30 mM EDTA for 20 min at 65°C without shaking. Next, chromatin was pelleted washed once with cold MB3 (50 mM Tris-HCl pH 7.5, 10 mM MgCl2). End-repaired nucleosomes were then subjected to proximity ligation with ~5000 U of T4 DNA ligase (NEB, M0202) in 1X T4 DNA ligase reaction buffer (NEB, B0202) for at least 2 hours at RT with slow rotation using a gentle nutator. The unligated ends of biotin-dNTPs were removed with ~500 units of Exonuclease III (NEB, M0206) in 1X NEBuffer 1 (NEB, B7001) for 15 min at 37°C while shaking in a thermomixer at 1000 rpm.  The samples were digested by protease K and DNA was extracted with phenol chloroform.250-350bp DNA was purified by 2% agarose gel. Using Dynabeads MyOne Streptavidin C1 beads (ThermoFisher, 65001) to capture biotinylated DNA fragments. The VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607-01) was used to construct the library. The Micro-seq library were sequenced on the Illumina NovaSeq 6000 platform, producing pair-end reads of 150 bp.

treatment_protocol: Diploid HAP1 cells were isolated from Hoechst (MCE)-stained HAP1 cells by flow sorting.

value: cell line

tag: enzyme

value: Mnase


title: HAP1,Micro-C rep2

description: Library name: MicroC-HAP1 rep 2


title: HAP1,Micro-C rep4

description: Library name: MicroC-HAP1 rep 4


title: HAP1,Micro-C rep1

description: Library name: MicroC-HAP1 rep 1


title: HAP1,Micro-C rep6

description: Library name: MicroC-HAP1 rep 6


title: JH331_D56-Rep2

status: Public on Jan 09 2025

first: Kai

last: Tan

state: PA

address: 3501 Civic Center Boulevard

department: Pediatrics

institute: Children's Hospital of Philadelphia

description:
Bulk RNA-seq
JH331-D56-Rep2
JH331_d56_rux

data_processing:
Reads were aligned to the human genome (GRCh38) using STAR v2.7.3a with default parameters. Expression was quantified using featureCounts v2.0.6.
Assembly: hg38
Supplementary files format and content: Gene counts quantified by featureCounts

source_name: Leukemia

extract_protocol:
RNA from leukemia cells harvested directly from PDX spleens was extracted using Qiagen RNeasy kit.
Libraries prepared by GeneWiz

value: Leukemia

value: Ph-Like ALL

tag: pdx

tag: time

tag: response

value: resistant

value: Ruxolitinib

tag: preengraftment

value: No


title: JH331_D3-Rep2

description:
Bulk RNA-seq
JH331-D3-Rep2
JH331_d3_rux

tag: tissue


title: JH331_D3-Rep1

description:
Bulk RNA-seq
JH331-D3-Rep1
JH331_d3_rux


title: JH331_D56-Rep1

description:
Bulk RNA-seq
JH331-D56-Rep1
JH331_d56_rux


title: JH331_D3_Control2

description:
Bulk RNA-seq
JH331-D3-Control2
JH331_d0_control

value: baseline

value: Control


title: ALL4988-Input

description:
Bulk RNA-seq
ALL4988-Input
ALL4988_input_control

value: Input

value: Yes


title: ALL4988-D7-Rep2

description:
Bulk RNA-seq
ALL4988-Rep2-D7
ALL4988_d7_rux

value: sensitive


title: JH331_D3_Control1

description:
Bulk RNA-seq
JH331-D3-Control1
JH331_d0_control


title: JH331_D28-Rep2

description:
Bulk RNA-seq
JH331-D28-Rep2
JH331_d28_rux


title: ALL4988-D7-Rep1

description:
Bulk RNA-seq
ALL4988-Rep1-D7
ALL4988_d7_rux


title: JH331_D28-Rep1

description:
Bulk RNA-seq
JH331-D28-Rep1
JH331_d28_rux


title: ALL4988-D56-Rep2

description:
Bulk RNA-seq
ALL4988-D56-Rep2
ALL4988_d56_rux


title: CS-A Abema replicate 1 (batch 2)


title: ALL4988-D56-Rep1

description:
Bulk RNA-seq
ALL4988-Rep1-D56
ALL4988_d56_rux


title: JH331_D7-Rep1

description:
Bulk RNA-seq
JH331-D7-Rep1
JH331_d7_rux


title: ALL4988-D3-Rep1

description:
Bulk RNA-seq
ALL4988-Rep1-D3
ALL4988_d3_rux


title: ALL4988-D3-Control2

description:
Bulk RNA-seq
ALL4988-D3-Control2
ALL4988_d0_control


title: ALL4988-D28-Rep1

description:
Bulk RNA-seq
ALL4988-Rep1-D28
ALL4988_d28_rux


title: ALL4364-Rep2-D7

description:
Bulk RNA-seq
ALL4364-Rep2-D7
ALL4364_d7_rux


title: ALL4988-D3-Rep2

description:
Bulk RNA-seq
ALL4988-Rep2-D3
ALL4988_d3_rux


title: ALL4364-Rep2-D56

description:
Bulk RNA-seq
ALL4364-Rep2-D56
ALL4364_d56_rux


title: ALL4364-Rep2-D3

description:
Bulk RNA-seq
ALL4364-Rep2-D3
ALL4364_d3_rux


title: HAP1,Micro-C rep3

description: Library name: MicroC-HAP1 rep 3


title: ALL4364-Rep1-D7

description:
Bulk RNA-seq
ALL4364-Rep1-D7
ALL4364_d7_rux


title: ALL4364-Rep2-D28

description:
Bulk RNA-seq
ALL4364-Rep2-D28
ALL4364_d28_rux


title: JH331-Input

description:
Bulk RNA-seq
JH331-Input
JH331_input_control


title: ALL4364-Rep1-D28

description:
Bulk RNA-seq
ALL4364-Rep1-D28
ALL4364_d28_rux


title: ALL4364-Rep1-D56

description:
Bulk RNA-seq
ALL4364-Rep1-D56
ALL4364_d56_rux


title: ALL4364-Control2-D3

description:
Bulk RNA-seq
ALL4364-Control2-D3
ALL4364_d0_control


title: ALL4364-Control1-D3

description:
Bulk RNA-seq
ALL4364-Control1-D3
ALL4364_d0_control


title: ALL2128-D7-R860

description:
Bulk RNA-seq
ALL2128-D7-Rep2
ALL2128_d7_rux


title: ALL2128-D7-R857

description:
Bulk RNA-seq
ALL2128-D7-Rep1
ALL2128_d7_rux


title: ALL2128-D56-R867

description:
Bulk RNA-seq
ALL2128-D56-Rep2
ALL2128_d56_rux


title: ALL2128-D56-R866

description:
Bulk RNA-seq
ALL2128-D56-Rep1
ALL2128_d56_rux


title: ALL2128-D28-R865

description:
Bulk RNA-seq
ALL2128-D28-Rep2
ALL2128_d28_rux


title: ALL2128-D28-R864

description:
Bulk RNA-seq
ALL2128-D28-Rep1
ALL2128_d28_rux


title: RMCr2C1_SNF5_TET2_053d

status: Public on Jan 06 2025

city: Houston

first: Amrit

last: Koirala

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description:
Library name: RMCr2C1_SNF5_TET2_053d
RMC2C transfected with SMARCB1 and treated with doxycycline for 3 days (expressing SMARCB1)

data_processing:
Paired-end reads were trimmed using TrimGalore
Trimmed fastq files were mapped using STAR
Features were quantified using featureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw read counts for each sample

source_name: Kidney

extract_protocol:
RNA was extracted from cell lines using the RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Total RNA was converted into a library of template molecules for sequencing on Illumina HiSeq2000, with a paired-end read length of 100 to 125 nt.

value: Kidney

tag: transfected with

value: doxycycline

tag: time of_dox_treatment

value: 3 days

tag: smarcb1 expression

value: yes

tag: muc16 expression


title: RMCr2C1_SNF5_Dox_3d

description:
Library name: RMCr2C1_SNF5_Dox_3d
RMC2C transfected with SMARCB1 and treated with doxycycline for 3 days (expressing SMARCB1)

tag: cell line

tag: treatment


title: ALL4988-D3-Control1

description:
Bulk RNA-seq
ALL4988-D3-Control1
ALL4988_d0_control

tag: genotype


title: ALL2128-D0-R852

description:
Bulk RNA-seq
ALL2128-D0-Rep1
ALL2128_d0_control


title: RMCr2C1

description:
Library name: RMCr2C1
Parental RMC2C. Does not express MUC16

value: Parental

value: no


title: RMCr219_SNF5_DOX_3D

description:
Library name: RMCr219_SNF5_DOX_3D
RMC219 transfected with SMARCB and treated with doxycycline for 3 days (expressing SMARCB1)

value: Reduced


title: RMCr2C1_SNF5_TET2

description:
Library name: RMCr2C1_SNF5_TET2
RMC2C transfected with SMARCB1 and not treated with doxycycline (not expressing SMARCB1)

value: 0 days


title: RMCr2C1_S1

description:
Library name: RMCr2C1_S1
RMC2C expressing SMARCB1 (clone S1)


title: RMCr219_EV_DOX_3D

description:
Library name: RMCr219_EV_DOX_3D
RMC219 transfected with empty vector control and treated with doxycycline for 3 days

value: Empty vector


title: RMCr100745C

description:
Library name: RMCr100745C
This is the original parental cell line where RMC2C came from. It may express MUC16

value: Unknown


title: RMCr219_EV_DOX_0

description:
Library name: RMCr219_EV_DOX_0
RMC219 transfected with empty vector control and not treated with doxycycline


title: RMCr2C1_S16

description:
Library name: RMCr2C1_S16
RMC2C expressing SMARCB1 (clone S16)


title: RMCr219

description:
Library name: RMCr219
Parental RMC219. Expresses MUC16


title: ALL4364-Rep1-D3

description:
Bulk RNA-seq
ALL4364-Rep1-D3
ALL4364_d3_rux

value: Leukemia

value: Ph-Like ALL

value: Ruxolitinib


title: ALL4364-Input

description:
Bulk RNA-seq
ALL4364-Input
ALL4364_input_control

value: baseline

value: Control


title: DarkRear_P18_M

status: Public on Dec 12 2024

city: Cambridge

first: Harris

last: Kaplan

address: 16 Divinity Ave., Room 4019

department: MCB

institute: Harvard University

description:
processed_data_file: may24_darkrear_p18_gex_inhibitory_IDd_noNA.RDS
processed_data_file: may24_darkrear_p18_gex_excitatory_IDd_noNA.RDS

data_processing:
Illumina sequencing reads were aligned to the mouse genome using the 10x Genomics CellRanger ARC pipeline with default parameters. For initial analysis, we relied on the R package Seurat and standard data analysis practices. We filtered out nuclei with under 400 or over 100,000 UMIs, with under 250 genes, and with over 20% of UMIs belonging to one gene. While rare, nuclei with over 10% mitochondrial or ribosomal UMIs, or over 1% IEG, apoptotic, or red blood cell UMIs, were also filtered out. We defined major cell classes (glia, neurons) and separated out inhibitory and excitatory neurons using Seurat clustering and known marker gene enrichment. Please see Kaplan et al., 2024 for information on how cell types were subsequently defined.
Assembly: mm10
Supplementary files format and content: RDS files from C57Bl6/j or mutant strains, separated by excitatory or inhibitory.  In our initial submission to GEO, we are uploading only GEX (i.e. snRNA-seq) data; ATAC-seq data will follow.

source_name: age: P18 sex: male strain: C57Bl6/j rep: DarkRear_P18_M_2

extract_protocol:
At each age, we dissected the anterior portion of the mouse hypothalamus containing the POA and surrounding regions, pooling tissue from three brains per sample, and performed nuclei isolation and library preparation for two biological replicates per sex per age (samples always contained only male or only female brains).Except for experiments on mutant strains affecting sensory input, C57BL/6J mice were used for all sequencing experiments. Mothers of all C57BL/6J experiments subjects were placed in a fresh cage when embryos were ~E12. For samples collected at P28 and P65, animals were separated from parents and opposite-sex siblings at P21, and group-housed, and kept separated from the opposite sex until dissection. C57BL/6J brains were collected during the first three hours of the dark cycle. Cnga2, Trpc2, and Trpm8 mutants were treated the same, whereas Piezo2 cKO and Gabrb3 cKO animals and littermate controls were raised in another facility (Harvard Medical School) and thus brains were collected over a wider time window (2-7 hours into the start of the light phase of 12h:12h light cycle).Brains were dissected (P10+) or whole heads were removed (E14 to P4) and frozen in Optimal Cutting Temperature medium and placed at -80℃. The preoptic area and surrounding regions were dissected on a cryostat at -15℃ using the Paxinos Developing and Adult Brain Atlases to determine locations for dissection based on landmarks. At all ages, tissue was collected from the anterior-most portion of MnPO to the posterior-most portion of the POA. To achieve this, after slicing away anterior material, thin (10-20µm) sections were collected and examined under a dissecting microscope to identify landmarks. At E16 to P65, the anterior commissure on each brain hemisphere is distinctly visible and moves medially as the brain is sliced from anterior to posterior. When the medial edge of the anterior commissure lined up underneath the ventral tip of the lateral ventricle, we began collecting tissue for sequencing. At E14, the anterior commissure is not clearly visible; we instead began collecting tissue when we first saw the ventral tips of lateral ventricles reach their full extents. To collect tissue, we first used a razor blade to remove large blocks of tissue lateral to the lateral ventricles, and then sliced 200µm-thick sections to collect approximately the ventral-most 1/3rd of the brain into a 2-mL tube. At E14, we collected 800µm; at E16 to P4, we collected 1.2mm; and at P10 to P65, we collected 1.4mm. Dissected tissue was placed in a 2-mL tube and kept at -80℃ until the day of library preparation.  For library preparation, 4-8 samples were prepared simultaneously, pairing mutant/control and male/female samples on the same day. Dissected tissues from 3 mice (C57BL6/J samples) or 2-3 mice (mutant/control samples) were pooled for each sample. 2 female and 2 male samples were collected at each of the 8 ages, except for E16, where only 1 female and 1 male sample were collected. Nuclei preparation was modified from 10x Genomics demonstrated protocol CG000375.
Libraries were sequenced on an Illumina NovaSeq 6000 S4 200 flowcell (8 samples per flowcell of either RNA-seq only or ATAC-seq only, targeting 200,000 reads per cell) using instructions provided by 10x Genomics Multiome protocol (GEX: read 1=26bp, i1=10bp, i2=10bp, read 2=90bp; ATAC: read 1=50bp, i1=8bp, i2=24bp, read 2=49bp), to a saturation of at least 70% for each run. Paired-end sequencing with read lengths of 100 nt was performed for all samples.  In our initial submission to GEO, we are uploading only GEX (i.e. snRNA-seq) data; ATAC-seq data will follow.

value: Preoptic area of the hypothalamus and surrounding tissue

tag: age

tag: Sex

value: male

value: Reared in total darkness

tag: rep


title: NormRear_P18_M

source_name: age: P18 sex: male strain: C57Bl6/j rep: NormRear_P18_M_2

value: Control for dark rearing - reared in the same facility but in normal light-dark conditions


title: DarkRear_P18_F

source_name: age: P18 sex: female strain: C57Bl6/j rep: DarkRear_P18_F_1

value: female


title: NormRear_P10_M

description:
processed_data_file: may24_darkrear_p10_gex_inhibitory_IDd_noNA.RDS
processed_data_file: may24_darkrear_p10_gex_excitatory_IDd_noNA.RDS

source_name: age: P10 sex: male strain: C57Bl6/j rep: NormRear_P10_M_2


title: ALL2128-D0-R855

description:
Bulk RNA-seq
ALL2128-D0-Rep2
ALL2128_d0_control

value: No


title: DarkRear_P10_M

source_name: age: P10 sex: male strain: C57Bl6/j rep: DarkRear_P10_M_2


title: DarkRear_P10_F

source_name: age: P10 sex: female strain: C57Bl6/j rep: DarkRear_P10_F_1


title: NormRear_P10_F

source_name: age: P10 sex: female strain: C57Bl6/j rep: NormRear_P10_F_1


title: Cnga2_P65_M_ctrl_2

description:
processed_data_file: june23_cnga2_p65_gex_inhibitory_IDd.rds
processed_data_file: june23_cnga2_p65_gex_excitatory_IDd.rds

source_name: age: P65 sex: male strain: Cnga2+/y rep: ctr_2

value: No treatment


title: Cnga2_P65_M_ctrl_1

source_name: age: P65 sex: male strain: Cnga2+/y rep: ctr_1


title: Cnga2_P18_M_ctrl_2

description:
processed_data_file: sep23apr24_cnga2_p18_gex_inhibitory_IDd.rds
processed_data_file: sep23apr24_cnga2_p18_gex_excitatory_IDd.RDS

source_name: age: P18 sex: male strain: Cnga2+/y rep: ctr_2


title: Cnga2_P18_M_ctrl_1

source_name: age: P18 sex: male strain: Cnga2+/y rep: ctr_1


title: Cnga2_P65_M_mut_2

source_name: age: P65 sex: male strain: Cnga2-/y rep: mut_2


title: Cnga2_P18_M_mut_1

source_name: age: P18 sex: male strain: Cnga2-/y rep: mut_1


title: Cnga2_P18_M_mut_2

source_name: age: P18 sex: male strain: Cnga2-/y rep: mut_2


title: RMCr219_SNF5_DOX_0

description:
Library name: RMCr219_SNF5_DOX_0
RMC219 transfected with SMARCB1 and not treated with doxycycline (not expressing SMARCB1)

value: Kidney

value: no

value: Yes


title: Cnga2_P65_M_mut_1

source_name: age: P65 sex: male strain: Cnga2-/y rep: mut_1


title: Cnga2_P10_M_ctrl_1

description:
processed_data_file: sep23apr24_cnga2_p10_gex_inhibitory_IDd.rds
processed_data_file: sep23apr24_cnga2_p10_gex_excitatory_IDd.rds

source_name: age: P10 sex: male strain: Cnga2+/y rep: ctr_1


title: Trpm8_P18_F_mut

description:
processed_data_file: nov23_trpm8_p18_gex_inhibitory_IDd.rds
processed_data_file: nov23_trpm8_p18_gex_excitatory_IDd.rds

source_name: age: P18 sex: female strain: Trpm8-/- rep: mut

value: mut


title: Cnga2_P10_M_mut_2

source_name: age: P10 sex: male strain: Cnga2-/y rep: mut_2


title: Trpm8_P18_M_mut

source_name: age: P18 sex: male strain: Trpm8-/- rep: mut


title: Trpm8_P10_M_mut

description:
processed_data_file: nov23_trpm8_p10_gex_inhibitory_IDd.rds
processed_data_file: nov23_trpm8_p10_gex_excitatory_IDd.rds

source_name: age: P10 sex: male strain: Trpm8-/- rep: mut


title: NormRear_P18_F

source_name: age: P18 sex: female strain: C57Bl6/j rep: NormRear_P18_F_1


title: Gabrb3_P65_M_ctrl

description:
processed_data_file: nov23_gabrb3_p65_gex_inhibitory_IDd.rds
processed_data_file: nov23_gabrb3_p65_gex_excitatory_IDd.rds

source_name: age: P65 sex: male strain: Advillin-Cre(-/+) ; Gabrb3-fl(-/+)/+ rep: ctrl

value: Advillin-Cre(-/+) ; Gabrb3-fl(-/+)/+

value: ctrl


title: Gabrb3_P65_F_ctrl

source_name: age: P65 sex: female strain: Advillin-Cre(-/+) ; Gabrb3-fl(-/+)/+ rep: ctrl


title: Cnga2_P10_M_ctrl_2

source_name: age: P10 sex: male strain: Cnga2+/y rep: ctr_2


title: Gabrb3_P65_M_mut

source_name: age: P65 sex: male strain: Advillin-Cre ; Gabrb3-fl/+ rep: mut

value: Advillin-Cre ; Gabrb3-fl/+


title: Trpm8_P10_F_mut

source_name: age: P10 sex: female strain: Trpm8-/- rep: mut


title: Gabrb3_P65_F_mut

source_name: age: P65 sex: female strain: Advillin-Cre ; Gabrb3-fl/+ rep: mut


title: Piezo2_P18_F_ctrl_2

description:
processed_data_file: nov23_piezo2_p18_fm_merged_gex_inhibitory_IDd.rds
processed_data_file: nov23_piezo2_p18_fm_merged_gex_excitatory_IDd.rds

source_name: age: P18 sex: female strain: Cdx2-Cre(-/+) ; Piezo2-fl/(-/+) rep: ctr_2


title: Piezo2_P18_F_mut_2

source_name: age: P18 sex: female strain: Cdx2-Cre ; Piezo2-fl/fl rep: mut_2

value: Cdx2-Cre ; Piezo2-fl/fl


title: Piezo2_P18_F_ctrl_3

source_name: age: P18 sex: female strain: Cdx2-Cre(-/+) ; Piezo2-fl/(-/+) rep: ctr_3


title: Piezo2_P18_M_ctrl_1

source_name: age: P18 sex: male strain: Cdx2-Cre(-/+) ; Piezo2-fl/(-/+) rep: ctr_1


title: Piezo2_P18_F_ctrl_1

source_name: age: P18 sex: female strain: Cdx2-Cre(-/+) ; Piezo2-fl/(-/+) rep: ctr_1


title: Piezo2_P18_M_mut_1

source_name: age: P18 sex: male strain: Cdx2-Cre ; Piezo2-fl/fl rep: mut_1


title: Piezo2_P18_F_mut_1

source_name: age: P18 sex: female strain: Cdx2-Cre ; Piezo2-fl/fl rep: mut_1


title: Piezo2_P10_F_ctrl

description:
processed_data_file: june23_piezo2_p10_gex_inhibitory_IDd.rds
processed_data_file: june23_piezo2_p10_gex_excitatory_IDd.rds

source_name: age: P10 sex: female strain: Cdx2-Cre(-/+) ; Piezo2-fl/(-/+) rep: ctrl


title: Piezo2_P10_M_mut

source_name: age: P10 sex: male strain: Cdx2-Cre ; Piezo2-fl/fl rep: mut


title: Piezo2_P10_M_ctrl

source_name: age: P10 sex: male strain: Cdx2-Cre(-/+) ; Piezo2-fl/(-/+) rep: ctrl


title: Piezo2_P10_F_mut

source_name: age: P10 sex: female strain: Cdx2-Cre ; Piezo2-fl/fl rep: mut


title: Trpc2_P65_F_ctrl

description:
processed_data_file: july23_trpc2_p65_gex_inhibitory_IDd.rds
processed_data_file: june23_trpc2_p18_gex_excitatory_IDd.rds

source_name: age: P65 sex: female strain: Trpc2-/+ rep: ctrl


title: Trpc2_P65_M_mut

source_name: age: P65 sex: male strain: Trpc2-/- rep: mut


title: Cnga2_P10_M_mut_1

source_name: age: P10 sex: male strain: Cnga2-/y rep: mut_1


title: Trpc2_P65_M_ctrl

source_name: age: P65 sex: male strain: Trpc2-/+ rep: ctrl


title: Trpc2_P65_F_mut

source_name: age: P65 sex: female strain: Trpc2-/- rep: mut


title: Trpc2_P18_M_ctrl

description:
processed_data_file: june23_trpc2_p18_gex_inhibitory_IDd.rds
processed_data_file: june23_trpc2_p18_gex_excitatory_IDd.rds

source_name: age: P18 sex: male strain: Trpc2-/+ rep: ctrl


title: Trpc2_P18_F_mut

source_name: age: P18 sex: female strain: Trpc2-/- rep: mut


title: Trpc2_P10_M_ctrl_2_V1

description: processed_data_file: trpc2_v1_neurons_IDd.RDS

source_name: age: P10 sex: male strain: Trpc2-/+ rep: ctr_2_V1

value: Visual cortex


title: Trpc2_P18_F_ctrl

source_name: age: P18 sex: female strain: Trpc2-/+ rep: ctrl


title: Trpc2_P18_M_mut

source_name: age: P18 sex: male strain: Trpc2-/- rep: mut


title: Trpc2_P10_F_ctrl_2_V1

source_name: age: P10 sex: female strain: Trpc2-/+ rep: ctr_2_V1


title: Trpc2_P10_M_mut_2

description:
processed_data_file: trpc2_july23oct23_p10_gex_inhibitory_noNA.RDS
processed_data_file: trpc2_july23oct23_p10_gex_excitatory_noNA.RDS

source_name: age: P10 sex: male strain: Trpc2-/- rep: mut_2


title: Trpc2_P10_M_mut_2_V1

source_name: age: P10 sex: male strain: Trpc2-/- rep: mut_2_V1


title: Trpc2_P10_M_ctrl_2

source_name: age: P10 sex: male strain: Trpc2-/+ rep: ctr_2


title: Piezo2_P18_F_mut_3

source_name: age: P18 sex: female strain: Cdx2-Cre ; Piezo2-fl/fl rep: mut_3


title: Trpc2_P10_F_ctrl_2

source_name: age: P10 sex: female strain: Trpc2-/+ rep: ctr_2


title: Trpc2_P10_F_mut_2_V1

source_name: age: P10 sex: female strain: Trpc2-/- rep: mut_2_V1


title: Trpc2_P10_M_ctrl_1

source_name: age: P10 sex: male strain: Trpc2-/+ rep: ctr_1


title: Trpc2_P10_F_mut_2

source_name: age: P10 sex: female strain: Trpc2-/- rep: mut_2


title: Trpc2_P10_M_mut_1

source_name: age: P10 sex: male strain: Trpc2-/- rep: mut_1


title: Trpc2_P10_F_mut_1

source_name: age: P10 sex: female strain: Trpc2-/- rep: mut_1


title: Trpc2_P0_M_ctrl

description:
processed_data_file: july23_trpc2_p0_gex_inhibitory_IDd.rds
processed_data_file: july23_trpc2_p0_gex_excitatory_IDd.rds

source_name: age: P0 sex: male strain: Trpc2-/+ rep: ctrl


title: Trpc2_P0_F_mut

source_name: age: P0 sex: female strain: Trpc2-/- rep: mut


title: E14_M_2

description:
processed_data_file: e14_excitatory_IDd_withNA.rds
processed_data_file: e14_inhibitory_IDd_withNA.rds

source_name: age: E14 sex: male strain: C57Bl6/j rep: 2


title: E14_F_2

source_name: age: E14 sex: female strain: C57Bl6/j rep: 2


title: E14_M_1

source_name: age: E14 sex: male strain: C57Bl6/j rep: 1


title: E14_F_1

source_name: age: E14 sex: female strain: C57Bl6/j rep: 1


title: P65_F_2

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p65f_apr23

source_name: age: P65 sex: female strain: C57Bl6/j rep: 2


title: P65_M_2

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p65m_aug

source_name: age: P65 sex: male strain: C57Bl6/j rep: 2


title: P28_M_2

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p28m_may22

source_name: age: P28 sex: male strain: C57Bl6/j rep: 2


title: P28_M_1

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p28m

source_name: age: P28 sex: male strain: C57Bl6/j rep: 1


title: P65_M_1

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p65m_april

source_name: age: P65 sex: male strain: C57Bl6/j rep: 1


title: P18_M_1

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p18m

source_name: age: P18 sex: male strain: C57Bl6/j rep: 1


title: P18_M_2

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p18m_oct

source_name: age: P18 sex: male strain: C57Bl6/j rep: 2


title: P28_F_2

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p28f_may22

source_name: age: P28 sex: female strain: C57Bl6/j rep: 2


title: P18_F_1

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p18f

source_name: age: P18 sex: female strain: C57Bl6/j rep: 1


title: Trpc2_P10_F_ctrl_1

source_name: age: P10 sex: female strain: Trpc2-/+ rep: ctr_1


title: P10_F_2

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p10f_mar23

source_name: age: P10 sex: female strain: C57Bl6/j rep: 2


title: P28_F_1

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p28f

source_name: age: P28 sex: female strain: C57Bl6/j rep: 1


title: P4_M_2

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p4m_mar23

source_name: age: P4 sex: male strain: C57Bl6/j rep: 2


title: P4_M_1

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p4m

source_name: age: P4 sex: male strain: C57Bl6/j rep: 1


title: Trpc2_P0_M_mut

source_name: age: P0 sex: male strain: Trpc2-/- rep: mut


title: Trpc2_P0_F_ctrl

source_name: age: P0 sex: female strain: Trpc2-/+ rep: ctrl


title: P18_F_2

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p18f_oct

source_name: age: P18 sex: female strain: C57Bl6/j rep: 2


title: P10_M_2

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p10m_apr23

source_name: age: P10 sex: male strain: C57Bl6/j rep: 2


title: P10_M_1

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p10m

source_name: age: P10 sex: male strain: C57Bl6/j rep: 1


title: P0_F_2

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p0f_mar23

source_name: age: P0 sex: female strain: C57Bl6/j rep: 2


title: P0_M_1

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p0m_april

source_name: age: P0 sex: male strain: C57Bl6/j rep: 1


title: P0_F_1_techrep2

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p0f2

source_name: age: P0 sex: female strain: C57Bl6/j rep: techrep2


title: P65_F_1

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p65f_april

source_name: age: P65 sex: female strain: C57Bl6/j rep: 1


title: P0_F_1_techrep1

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p0f

source_name: age: P0 sex: female strain: C57Bl6/j rep: techrep1


title: P4_F_2

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p4f_oct

source_name: age: P4 sex: female strain: C57Bl6/j rep: 2


title: E18_M_2

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is e18m_may22

source_name: age: E18 sex: male strain: C57Bl6/j rep: 2


title: P4_F_1

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p4f

source_name: age: P4 sex: female strain: C57Bl6/j rep: 1


title: E16_F

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is e16f

source_name: age: E16 sex: female strain: C57Bl6/j rep: 1


title: E18_M_1

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is e18m

source_name: age: E18 sex: male strain: C57Bl6/j rep: 1


title: E0771_VEC

status: Public on Dec 05 2024

city: New Haven

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

department: Genetics

institute: Yale University School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 with --expect-cells=5000 --nosecondary commands. Raw paired-end fastq read files were filtered and demultiplexed using Cutadapt. Raw fastq read files were then trimmed to the 23 bp sgRNA spacer sequences. The 23 bp sgRNA spacer sequences from each demulitplexed sample were mapped the sgRNA spacers to the custom library using Bowtie 1.3.1. Using the resultant mapping output, we quantitated the number of reads that had mapped to each sgRNA within the library.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: E0771 tumor

extract_protocol:
Single-cell suspensions from tumor were collected. The cells were labeled with an antimouse-CD45-Percp/Cy5.5 antibody and a live/dead dye. FACS-sorted cells were gated on CD45+ live cells. Sorted cells from 5 mice were combined and were washed with PBS, and cell numbers and viabilities were assessed by trypan blue staining. The 10,000 CD45+ cells isolated from the lung were used for scRNA-seq library prep. The MUCIG pool plasmids were extratced by the Takara Maxi-prep kit.
scRNA-seq library prep was  following the protocol from 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kits V2. The sgRNA library readout was performed using readout PCR strategy

value: E0771 tumor

tag: cell type

value: CD45+ cells


title: P10_F_1

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p10f

source_name: age: P10 sex: female strain: C57Bl6/j rep: 1

value: Preoptic area of the hypothalamus and surrounding tissue


title: E18_F_2

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is e18f_may22

source_name: age: E18 sex: female strain: C57Bl6/j rep: 2


title: E16_M

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is e16m_apr23

source_name: age: E16 sex: male strain: C57Bl6/j rep: 1

value: male


title: E18_F_1

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is e18f

source_name: age: E18 sex: female strain: C57Bl6/j rep: 1


title: COLON26_VEC

description: 10x Genomics

source_name: Colon26 tumor

value: Colon26 tumor


title: COLON26_PGGC

description: 10x Genomics


title: COLON26_PBS

description: 10x Genomics

value: PBS


title: Pacbio_E14.neuron

status: Public on Dec 04 2024

city: Chicago

first: Xiaochang

last: Zhang

state: IL

department: Department of Human Genetics

institute: University of Chicago

description:
Library name: Pacbio_LR01_E14.5_MM_Cortex.neuron
Pacbio unaligned bam file. MM E14.5 Cortex. Neuron

data_processing:
Raw reads were trimmed by fastp and aligned to mouse mm10 with STAR aligner with GENCODE m25 annotation.
PSI values were calculated by rMATS. Raw counts were quantified by Salmon.
Read counts were transformated to VSD and removed batch effect by DESeq2 and limma.
PacBio long reads were analyzed using the Iso-Seq3 pipeline (v3.8.0). The reads were categorized into neuron, IPC, and RCG cells based on barcodes annotated by scRNA-seq and subsequently quantified using FLAIR.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes PSI value of SE events of Tubb3 samples. Tab-delimited text file includes for N2a samples. The tab-delimited text file contains the read counts of expressed transcripts in neurons, IPCs, and RCGs from long-read sequencing of the E14.5 brain.

source_name: dorsal cortical tissues

extract_protocol:
Three to five IUE positive embryonic dorsal cortices of the same litter or batch were pooled together before Papain dissociation (Worthington), and cells were sorted directly into Trizol for RNA extraction with Direct-zol (Zymo). PacBio library was prepared with amplified cDNA using SMRTbell Express Template Prep Kit V2.0
Total RNA was extracted from FACS sorted primary cell and cell lines, subjected to stranded mRNA-Seq library preparation following standard protocols (Illumina Tru-Seq). Pacbio long-read sequencing was performed on the Pacbio Sequel platform.

value: dorsal cortical tissues

value: neuron


title: E0771_PBS

description: 10x Genomics


title: P0_M_2

description:
processed_data_file: excitatory_merged_noNA.RDS
processed_data_file: inhibitory_merged_noNA.RDS
Sample name within processed data RDS file is p0m_july

source_name: age: P0 sex: male strain: C57Bl6/j rep: 2

value: No treatment


title: Pacbio_E14.RGC

description:
Library name: Pacbio_LR01_E14.5_MM_Cortex.RGC
Pacbio unaligned bam file. MM E14.5 Cortex. RGC

value: RGC


title: Pacbio_E14.IPC

description:
Library name: Pacbio_LR01_E14.5_MM_Cortex.IPC
Pacbio unaligned bam file. MM E14.5 Cortex. IPC

value: IPC


title: Neuro2a_Meis2_RGC_replicate_3

description:
Library name: Neuro2a_Meis2_RGC_replicate_3
pCAG-HA-Flag-Meis2-v4-ires-EGFP (Meis2, NM_001159568.1), Neuro2a_Meis2_RGC_Isoform  REP3

source_name: Neuro2a neuroblastoma cell line

value: Neuro2a neuroblastoma cell line

value: Neuroblastoma cell line

tag: batch


title: Neuro2a_Meis2_Neuron_replicate_4

description:
Library name: Neuro2a_Meis2_Neuron_replicate_4
pCAG-HA-Flag-Meis2-v3-ires-EGFP (Meis2, NM_001159567.1 ), Neuro2a_Meis2_Neuron_Isoform REP4


title: Neuro2a_Meis2_Neuron_replicate_3

description:
Library name: Neuro2a_Meis2_Neuron_replicate_3
pCAG-HA-Flag-Meis2-v3-ires-EGFP (Meis2, NM_001159567.1 ), Neuro2a_Meis2_Neuron_Isoform REP3


title: Neuro2a_Control_replicate_4

description:
Library name: Neuro2a_Control_replicate_4
pCAG-IRES-EGFP, Neuro2a_Ctrl_REP4


title: Neuro2a_Control_replicate_3

description:
Library name: Neuro2a_Control_replicate_3
pCAG-IRES-EGFP, Neuro2a_Ctrl_REP3


title: Neuro2a_Meis2_RGC_replicate_1

description:
Library name: Neuro2a_Meis2_RGC_replicate_1
pCAG-HA-Flag-Meis2-v4-ires-EGFP (Meis2, NM_001159568.1), Neuro2a_Meis2_RGC_Isoform  REP1


title: Neuro2a_Meis2_RGC_replicate_4

description:
Library name: Neuro2a_Meis2_RGC_replicate_4
pCAG-HA-Flag-Meis2-v4-ires-EGFP (Meis2, NM_001159568.1), Neuro2a_Meis2_RGC_Isoform  REP4


title: Neuro2a_Meis2_Neuron_replicate_2

description:
Library name: Neuro2a_Meis2_Neuron_replicate_2
pCAG-HA-Flag-Meis2-v3-ires-EGFP (Meis2, NM_001159567.1 ), Neuro2a_Meis2_Neuron_Isoform REP2


title: Neuro2a_Meis2_Neuron_replicate_1

description:
Library name: Neuro2a_Meis2_Neuron_replicate_1
pCAG-HA-Flag-Meis2-v3-ires-EGFP (Meis2, NM_001159567.1 ), Neuro2a_Meis2_Neuron_Isoform REP1


title: Neuro2a_Control_replicate_2

description:
Library name: Neuro2a_Control_replicate_2
pCAG-IRES-EGFP, Neuro2a_Ctrl_REP2


title: E14_Tubb3_GFP_positive_replicate_2

description:
Library name: E14_Tubb3_GFP_positive_replicate_2
EGFP+ cells sorted from E14.5 Tubb3-EGFP trangenic mice, Tubb3:EGFP_Positive Rep2

source_name: dorsal forebrain

value: dorsal forebrain


title: Neuro2a_Control_replicate_1

description:
Library name: Neuro2a_Control_replicate_1
pCAG-IRES-EGFP, Neuro2a_Ctrl_REP1


title: E14_Tubb3_GFP_positive_replicate_1

description:
Library name: E14_Tubb3_GFP_positive_replicate_1
EGFP+ cells sorted from E14.5 Tubb3-EGFP trangenic mice, Tubb3:EGFP_Positive Rep1


title: E14_Tbr2_GFP_negative_replicate_1

description:
Library name: E14_Tbr2_GFP_negative_replicate_1
EGFP- cells sorted from E14.5 Tbr2-EGFP trangenic mice, Eomes:EGFP_Negative Rep1


title: E14_Tbr2_GFP_positive_replicate_2

description:
Library name: E14_Tbr2_GFP_positive_replicate_2
EGFP+ cells sorted from E14.5 Tbr2-EGFP trangenic mice, Eomes:EGFP_Positive Rep2


title: IUE_PCIG_E13_to_E14_replicate_2

description:
Library name: IUE_PCIG_E13_to_E14_replicate_2
pCAG-IRES-EGFP, IUE_E13-E14_Ctrl Rep2


title: IUE_Rbfox3_E13_to_E14_replicate_2

description:
Library name: IUE_Rbfox3_E13_to_E14_replicate_2
pCAG-Rbfox3-IRES-EGFP, IUE_Rbfox3_E13-E14 Rep2


title: IUE_Rbfox3_E13_to_E14_replicate_1

description:
Library name: IUE_Rbfox3_E13_to_E14_replicate_1
pCAG-Rbfox3-IRES-EGFP, IUE_Rbfox3_E13-E14 Rep1


title: E0771_PGGC

description: 10x Genomics


title: E14_Tbr2_GFP_positive_replicate_1

description:
Library name: E14_Tbr2_GFP_positive_replicate_1
EGFP+ cells sorted from E14.5 Tbr2-EGFP trangenic mice, Eomes:EGFP_Positive Rep1


title: IUE_PCIG_E13_to_E14_replicate_1

description:
Library name: IUE_PCIG_E13_to_E14_replicate_1
pCAG-IRES-EGFP, IUE_E13-E14_Ctrl Rep1


title: BMDM_SLIT2_r2

status: Public on Dec 03 2024

first: Jean-Leon

last: Thomas

address: 800 Howard Ave

institute: Yale University

data_processing:
Quality control of RNA-Seq reads was performed using FastQC v0.11.9, samtools v1.7 and Picard v2.23.8. Transcripts were quantified with Salmon v1.4.01 and reads aligned using STAR v2.7.62 to the mouse genome (mm10/GRCm38, gencode vM24).
Downstream analysis was performed in R, differential expression was analysed with DESeq2 v1.30.14 with standard models and normal shrinkage estimators. Gene set enrichment analyses were performed with fgsea v1.16.0 using log2 fold change estimates from DESeq2 and gene sets from MSigDB or internal data as indicated.
Assembly: mm10
Supplementary files format and content: rlog normalized counts

source_name: Bone marrow

growth_protocol: Bone-marrow derived macrophages (BMDMs) were isolated from C57BL/6 mice as previously described (21). Briefly, bone marrowBM was obtained by flushing the femur and tibia with PBS. The bone marrow cells were resuspended in DMEM GlutaMax (Gibco) containing 1% Pen/Strep (Gibco), 20% FBS (Gibco) and 100 ng/mL M-CSF (R&D Systems). Cells were incubated for 2 days at 37 °C and 5% CO2 in non-treated bacterial dishes for adhesion of bone-marrow resident macrophages, and then changed for treated plastic dishes and culture for 6 days with medium change every 2 days.

extract_protocol:
RNA isolation was performed on frozen cell pellets on DNA/RNA Shield (Zymo research) using Direct-zol RNA Miniprep kit (Zymo Research). RNA concentration was measured by NanoDrop 1000 (Thermo Fisher Scientific) and RNA integrity was determined using Bioanalyzer (Agilent).
Library construction of 300 ng total RNA for each sample was made using KAPA Stranded mRNA-Seq Kit (Illumina Platforms; Kapa Biosystems) using 10 cycles of PCR amplification. Libraries were purified using AxyPrep Mag PCR Clean-up kit (AxygenTM). Each library was quantified using a Qubit fluorometer (Life Technologies) and the size distribution assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA). Sequencing was performed on an Illumina® Hiseq 2500 (Illumina, San Diego, CA, USA) instrument using the TruSeq PE Cluster Kit V4-cBot-HS (Illumina®) to generate 101 bp Paired-end reads sequencing with v4 chemistry.

treatment_protocol: Isolated BMDMs were treated with 6 nM Slit2 for 16 hours and analyzed by bulk RNA sequencing.

value: Bone marrow

value: Macrophage

value: WT

tag: strain

value: 6 nM Slit2 for 16 hours


title: BMDM_CTRL_r4

value: vehicle control


title: BMDM_CTRL_r1


title: BMDM_SLIT2_r3


title: BMDM_CTRL_r3


title: RNA-seq_SUV39H2-KO-RKO_SUV39H1_KD+DNMT1i_rep3

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Avenue NE

institute: Van Andel Research Institute

description: Library name: RNA-seq_SUV39H1-KD+DNMT1i_3

data_processing:
Raw 50 bp paired-end reads were trimmed with TrimGalore! followed by quality control analysis with FastQC. Trimmed reads were aligned to GRCh38.p12 and indexed to GENCODE v29 via STAR (v2.5.3a) aligner with flags ‘-twopassMode Basic\ -quantMode GeneCounts’ for feature counting. ReadsPerGene output count files were constructed into a raw read count matrix in R. Low count genes were filtered (1 count in at least one sample) prior to edgeR (v3.36.0) count normalization. Differential expression analysis was conducted using DESeq2(1.40.1). Genes were considered differentially expressed if |Log2FC| > 1 and FDR < 0.01.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts and CPM normalzied counts for each sample
Supplementary files format and content: tsv file includes DESeq2 analyses of differential expression results between treatment groups

source_name: RKO

growth_protocol: RKO cells were cultured in RPMI 1640 medium with L-glutamine (Gibco), supplied with 1X penicillin/streptomycin (Invitrogen), 0.1 mM non-essential amino acids (GIBCO), 1 mM Sodium Pyruvate (GIBCO), and 10% Fetal Bovine Serum (Millipore Sigma) at 5% CO2 and 37°C. Cells were passaged every 2−3 days by removal of medium, wash in PBS, dissociation by 1X trypsin, resuspension in medium, and pelleting by centrifugation, followed by resuspension, and plating at a density of approximately 1 million cells/10 cm dish.

extract_protocol:
TRIzol Reagent (Invitrogen) was added directly to adhered cells, collected, and stored at -80°C. After thawing, total RNA was extracted following the manufacturer’s protocol, and RNA was resuspended in DEPC Nuclease-Free water.
Libraries were prepared by the Van Andel Institute Genomics Core (RRID:SCR_022913) from 500 ng of total RNA using the KAPA RNA HyperPrep Kit (Kapa Biosystems, Wilmington, MA USA). Ribosomal RNA material was reduced using the QIAseq FastSelect –rRNA HMR Kit (Qiagen, Germantown, MD, USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT for Illumina TruSeq UD Indexed adapters (Illumina Inc, San Diego CA, USA). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.) and QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA).  Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer to an average depth of 50M raw paired-reads per transcriptome. Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq (v1.9.0).

treatment_protocol: RNA-seq was performed in RKO cells with SUV39H2 KO and doxycycline (dox)-inducible SUV39H1 shRNA knockdown (KD). There are four treatment groups: 1. DMSO control; 2. 20 ng/mL doxycycline (SUV39H1 KD); 3. 1  M GSK3484862 (DNMT1 inhibition); 4. Doxycycline + GSK3484862 (SUV39H1 KD + DNMT1 inhibition). Cells were treated for 5 days before RNA collection.

value: RKO

value: shSUV39H1_doxycycline+DNMT1 inhibitor


title: RNA-seq_SUV39H2-KO-RKO_SUV39H1_KD+DNMT1i_rep1

description: Library name: RNA-seq_SUV39H1-KD+DNMT1i_1


title: Neuro2a_Meis2_RGC_replicate_2

description:
Library name: Neuro2a_Meis2_RGC_replicate_2
pCAG-HA-Flag-Meis2-v4-ires-EGFP (Meis2, NM_001159568.1), Neuro2a_Meis2_RGC_Isoform  REP2


title: RNA-seq_SUV39H2-KO-RKO_DNMT1i_rep3

description: Library name: RNA-seq_DNMT1i_3

value: 1uM DNMT1 inhibitor_GSK3484863


title: RNA-seq_SUV39H2-KO-RKO_DNMT1i_rep2

description: Library name: RNA-seq_DNMT1i_2

value: 1uM DNMT1 inhibitor_GSK3484862


title: RNA-seq_SUV39H2-KO-RKO_SUV39H1_KD_rep3

description: Library name: RNA-seq_SUV39H1-KD_3


title: BMDM_SLIT2_r4


title: RNA-seq_SUV39H2-KO-RKO_DNMT1i_rep1

description: Library name: RNA-seq_DNMT1i_1


title: RNA-seq_SUV39H2-KO-RKO_DMSO control_rep3

description: Library name: RNA-seq_CTL_3

value: DMSO


title: RNA-seq_SUV39H2-KO-RKO_SUV39H1_KD_rep1

description: Library name: RNA-seq_SUV39H1-KD_1


title: RNA-seq_SUV39H2-KO-RKO_DMSO control_rep2

description: Library name: RNA-seq_CTL_2


title: E14_Tbr2_GFP_negative_replicate_2

description:
Library name: E14_Tbr2_GFP_negative_replicate_2
EGFP- cells sorted from E14.5 Tbr2-EGFP trangenic mice, Eomes:EGFP_Negative Rep2


title: RNA-seq_SUV39H2-KO-RKO_SUV39H1_KD_rep2

description: Library name: RNA-seq_SUV39H1-KD_2


title: RNA-seq_SUV39H2-KO-RKO_DMSO control_rep1

description: Library name: RNA-seq_CTL_1


title: Unc5bflfl

description:
Library name: Sample 3
10X genomics

data_processing:
RNA sequencing quality assurance was performed using FastQC (version 0.11.9), by looking for the presence of adapters and sequence quality. Genome alignment was mapped to the mouse genome (mm10-3.0.0) using 10x Genomics Cell Ranger pipeline (version 5.0.0). The resulting filtered feature-barcode matrices were used for downstream analysis. The filtered count matrices were loaded on RStudio (version 4.1.1), and the Seurat (version 4.0.6) class object was used to store the data. We started with 110951 cells across all samples. The identically aged (P12) control littermate Cre-negative samples from both mutant mice were combined (Unc5Bfl/fl and Ntn1fl/fl). Control steps filtered out genes that were expressed in less than 10 cells. Lastly, only cells which had between 300 and 4250 genes and less than 15% of the unique molecular identifiers (UMIs) originating from mitochondrial genes were retained for further analysis. After quality control a total of 107140 cells were kept (cells from control samples, Ntn1iKO, Unc5biECKO, Unc5biECKO;Ctnnb1flex3/+). Normalized gene expression data, generated using the NormalizeData function, was used for differential gene expression analysis. For visualization, individual samples were normalized using the SCTransform function. Seurat v3-SCTransform multiple dataset integration was performed on merged Ntn1iKO and Unc5biECKO datasets to correct for batch effects. Dimensional reduction of the data was performed using Uniform Manifold Approximation and Projection (UMAP) (arXiv:1802.03426) as implemented in the RunUMAP function, where the number of PCA dimensions used for the dims parameter was adjusted on a per-dataset basis and all other settings were default. Louvain graph-based clustering was performed on a shared nearest neighbor graph, generated using the first two UMAP dimensions as input. Cell type annotations were assigned to clusters through visualization of canonical cell type markers and differential gene expression. Gene markers defining each cell cluster regardless of cell genotype were identified using the FindAllMarkers function implemented on Seurat (Table S1).  The endothelial cell cluster comprising 3735 endothelial cells was then selected and reclustered. The cell subset was re-analyzed, rescaled and normalized. These were then further subclustered into different endothelial cells based on known markers (Table S2). GSEA was conducted using the R package Fast Gene Set Enrichment Analysis (fgsea) with KEGG, Reactome and Hallmark reference gene lists as well as previously published gene lists. Bioinformatics analysis scRNA-seq dataset: The scRNA-seq data from P6 and P10 control retinas were extracted from our previous work that is publicly available on NCBI’s Gene Expression Omnibus (accession no. GSE175895)44. Data processing and clustering were performed as previously described44. Gene expression analysis was conducted using the Seurat R-package (version 3.2.2).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Retina

extract_protocol:
Ntn1flfl and Unc5bflfl controls and corresponding littermate Ntn1iKO and Unc5biECKO, as well as Unc5biECKO;Ctnnb1flex3/+  and corresponding littermate Unc5biECKO mice were TAM injected from P6 to P8. P12 mice were anesthetized with isoflurane and euthanized by cervical dislocation. The retinas were dissected. 4-8 retinas from each group were dissected in cold DPBS and dissociated with the Neural Tissue Dissociation kit (P) (Miltenyi Biotec, Cat#130- 092-628). The retinas were digested 5min in buffer P supplemented with DNase I (2000U/mL, Qiagen #79254). The digestion was stopped by adding FBS (10% final) and the cells were immediately filtered through a 70μm cell strainer. After centrifugation (300g for 3min), the cells were resuspended in PBS supplemented with 2mM EDTA and 0.5% BSA. The single cell suspension was enriched for ECs using CD31 MicroBeads (Miltenyi Biotec, Cat#130-097-418) according to the manufacturer’s instructions. Library preparation, sequencing and scRNA-seq bioinformatic analysis are described in SI appendix
Single cell suspensions of retinal cells were resuspended in PBS containing 0.04% ultra-pure BSA. ScRNA-seq libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3′ Library Construction Kit V3.1 (CG000204.. Generated libraries were sequenced on an Illumina HiSeq4000 for 150bp paired end reads.

value: Retina


title: Ntn1iKO

description:
Library name: Sample 2
10X genomics


title: BMDM_SLIT2_r1


title: Ntn1flfl

description:
Library name: Sample 1
10X genomics


title: BMDM_CTRL_r2


title: Unc5bIECKO

description:
Library name: Sample 4
10X genomics


title: ROBO_CD45

data_processing:
Demultiplexing, barcode processing and gene quantififcation were performed with CellRanger v2.1.1
After generation of gene expression matrices using CellRanger (10x Genomics), processing and analysis of the data were performed using the Seurat R-package (v4)
First, quality control steps filtered out genes that were expressed in less than 10 cells and cells that expressed fewer than 100 genes. Lastly, only cells which had fewer than 60000 counts, between 500 and 7500 genes and less than 20% of the unique molecular identifiers (UMIs) originating from mitochondrial genes were retained for further analysis.
For clustering and visualization, individual samples were normalized using the SCTransform function. Seurat SCTransform dataset integration was performed to merge P17 Control and Anti-Robo1/2 datasets to correct for batch effects. Dimensional reduction was performed using Uniform Manifold Approximation and Projection (UMAP) as implemented in the RunUMAP function, where 15 dimensions were used for the dims parameter and all other settings were default
Assembly: mm10
Supplementary files format and content: h5Seurat files with counts and scaled data

growth_protocol: For the induction of OIR, the mother and P7 pups were placed in 75% O2 until P12. Upon return to room air, the pups were placed for adoption with a nursing mother and treated. Eyes were collected at P17.

extract_protocol:
Briefly, 8 retinas per group were dissected and dissociated with the Neural Tissue Dissociation kit (P) (Miltenyi Biotec, Cat#130- 092-628). The digestion was stopped by adding BSA (5% final) and the cells were immediately filtered through a 70 mm cell strainer. After centrifugation (600g for 5 min), cells were resuspended in PBS supplemented with 2mM EDTA and 0.5% BSA. The single cell suspension was enriched for ECs and immune cells using CD31 and CD45 MicroBeads (Miltenyi Biotec) according to the manufacturer’s instructions.
Single cell suspensions of retinal cells were resuspended in PBS containing 0.04% ultra-pure BSA. scRNA-seq  libraries were prepared using the Chromium Single Cell 30 Reagent Kits v3.1 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s instructions. The target cell recovery for each library was 10,000. Generated libraries were sequenced on an Illumina HiSeq4000.

treatment_protocol: For antibody treatment, 10mg/kg of antibodies or isotype control IgG were diluted in 200uL of sterile 0.9% NaCl and given i.p. at P12, P14 and P16. For IPI-549 treatment, 15mg/kg of the inhibitor was diluted in 200uL of sterile vehicle (0.9% NaCl 2%DMSO) and given i.p. daily from P12 to P16; and control mice were treated i.p. with 200uL of vehicle.

value: Immune cell

value: ROBO1/2 blocking antibodies


title: ROBO_CD31

value: Edothelial


title: Normoxia_CD31


title: RNA-seq_SUV39H2-KO-RKO_SUV39H1_KD+DNMT1i_rep2

description: Library name: RNA-seq_SUV39H1-KD+DNMT1i_2


title: IgG_CTRL_CD45

value: Isotype control IgG


title: IgG_CTRL_CD31


title: PAN + Pio, rep3

status: Public on Dec 01 2024

city: Columbus

first: Julie

middle: A

last: Dougherty

state: OH

address: 700 Children's Dr, Research Building 2

department: Research

institute: Nationwide Children's Hospital, Columbus, Ohio

data_processing:
.  Sequencing adapters matching at least 6 bases were then removed from the reads, as well as low-quality bases (<10) using v1.10 of cutadapt  (https://cutadapt.readthedocs.io/en/stable/index.html)
An alignment report was also generated, using custom scripts, and manually reviewed to ensure that at least ~80% of reads aligned to the expected reference, and that at least ~50% of the reads aligned to features annotated as protein coding
Each sample was aligned to the Rnor_6.0 assembly of the Rattus norvegicus reference from the National Center for Biotechnology Information (NCBI) using version 2.5.0c of the RNA-Seq aligner STAR (http://bioinformatics.oxfordjournals.org/content/29/1/15)
Transcript features were identified from the general feature format (GFF) file that came with the assembly from the NCBI. Feature coverage counts were calculated using HTSeq (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html).
raw RNA-Seq gene expression data were normalized, and post-alignment statistical analyses and figure generation were performed using DESeq2 (http://genomebiology.com/2014/15/12/550) and custom analysis scripts written in R.
Comparisons of gene expression and associated statistical analyses were made between different conditions of interest using the normalized read counts. All fold-change values were expressed as test condition / control condition, where values <1 were denoted as the negative of its inverse (note that there will be no fold change values between –1 and 1, and that the fold changes of “1” and “-1” represent the same value)
Transcripts were considered significantly differentially expressed using a 10% false discovery rate (DESeq2 adjusted P value < 0.1). Genes were removed from comparisons if they were not expressed above a background threshold (0.5 reads per million) for most samples within each group
Assembly: Rnor_6.0 assembly
Supplementary files format and content: htseq.cov files contain waw counts of reads per gene generated by HTSeq v0.6.1p1.
Supplementary files format and content: AllData_160322_RNASeq_Smoyer_Results_iScience.xlsx contains DESeq2 normalized counts per gene for all samples.

organism: Rattus norvegicus

source_name: kidney, glomeruli

growth_protocol: ad libitum water and standard chow, 12h/12h light/dark cycle, temperature/humidty controlled environment

extract_protocol:
Total RNA from the isolated glomeruli was extracted using the RNeasy Mini Kit #74104, Qiagen
350 ng total RNA was prepared to libraries with TruSeq Standard total RNA with Ribo-Zero Globin Complete kit, Illumina
To generate directional signals in RNA seq data, libraries were constructed from first strand cDNA using TruSeq Standard total RNA with Ribo-Zero Globin Complete kit from Epicentre Biotechnologies

treatment_protocol: day 0 tail vein injection of 50 mg/kg PAN, treatment thereafter 15mg/kg MP IP injection or 10mg/kg Pio PO daily. Healthy and disease controls received vehicle PO daily.

value: kidney, glomeruli

value: PAN + Pio


title: PAN + Pio, rep2


title: PAN + Pio, rep4


title: PAN + MP, rep3

value: PAN + MP


title: PAN + Pio, rep1


title: PAN only, rep4

value: PAN only


title: PAN + MP, rep4


title: PAN only, rep3


title: PAN + MP, rep2


title: Sham Control, rep4

value: Sham Control


title: Sham Control, rep3


title: PAN only, rep2


title: Sham Control, rep2


title: Unc5biECKO;Ctnnb1flex/3

description:
Library name: Sample 5
10X genomics


title: Sham Control, rep1