title: KDM5B, Input

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

description: Library name: KDM5B_Input

data_processing:
Raw sequencing data were aligned to the human reference genome using Bowtie2 and peaks were called by MACS2 software. Enriched binding peaks were generated after ﬁltering through the control IgG.
Assembly: hg38
Supplementary files format and content: wig files were generated using MACS2.

growth_protocol: MCF-7 cells were cultured in a humidified incubator equilibrated with 5% CO2 at 37 °C. The media (Dulbecco Modified Eagle Medium (DMEM)) was supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, and 100 mg/mL streptomycin

extract_protocol:
Chromatin DNA was precipitated using either normal goat IgG (control) or polyclonal antibodies against KDM5B or CUL4B. DNA was puriﬁed with the Qiagen PCR puriﬁcation kit.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: ER+ breast cancer cell

tag: chip antibody


title: iATCs_CUT1_H3K27ac

status: Public on Feb 18 2026

type: SRA

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

description: Library name: Sample 1

library_source: other

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

molecule: other

organism: Homo sapiens

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

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

tag: cell line

tag: cell type

value: iPSC-derived alveolar epithelial cells

tag: treatment


title: CUL4B, Input

description: Library name: CUL4B_Input

library_source: genomic

molecule: genomic DNA


title: mesc_rad21_depletion_untreated_104, Smart-seq3

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

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

library_source: transcriptomic single cell

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

molecule: polyA RNA

organism: Mus musculus

source_name: mouse embryonic stem cell

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

value: mouse embryonic stem cell

tag: genotype

value: untreat


title: 60day post TBI microglia Clodroante TBI  1

city: Chicago

first: Mecca

middle: Bennta Abour Rahim

last: Islam

state: IL

address: 240 E Huron St., M410

country: USA

institute: Northwestern University

description: Library name: 60D_Mic_2022_Colip_TBI1

library_source: transcriptomic

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

molecule: total RNA

source_name: Microglia

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

value: Microglia

value: Clodorante lipsomes

tag: time

value: 60 day


title: 00079FFF4F

city: La Jolla

first: Daniel

last: Munro

state: CA

address: 9500 Gilman Drive

department: Psychiatry

institute: UC San Diego

description: Library name: 00079FFF4F

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

organism: Rattus norvegicus

source_name: whole brain hemisphere

growth_protocol: Naive outbred laboratory rats

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

treatment_protocol: No treatment

tag: tissue

value: whole brain hemisphere


title: mesc_rad21_depletion_untreated_097, Smart-seq3


title: 60day post TBI microglia Clodroante TBI  3

description: Library name: 60D_Mic_2022_Colip_TBI3


title: 60day post TBI microglia Vehicle TBI  1

description: Library name: 60D_Mic_2022_PBSlip_TBI1

value: PBS lipsomes


title: CUL4B, IP

description: Library name: CUL4B_IP

value: CUL4B (Sigma-Aldrich, #C9995)


title: mesc_rad21_depletion_untreated_094, Smart-seq3


title: BAT WT Chow Diet 1

city: Philadelphia

last: Kelly

state: PA

address: 3400 Civic Center Blvd

department: Penn Cardiovascular Institute

institute: University of Pennsylvania

description: Library name: BAT1

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

source_name: BAT

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

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

value: BAT

value: WT

value: Chow Diet


title: 60day post TBI microglia Clodroante TBI  2

description: Library name: 60D_Mic_2022_Colip_TBI2


title: 00079FF7D6

description: Library name: 00079FF7D6


title: mesc_rad21_depletion_untreated_095, Smart-seq3


title: 00079FF018

description: Library name: 00079FF018


title: KDM5B, IP

description: Library name: KDM5B_IP


title: 00079FF1CB

description: Library name: 00079FF1CB


title: 60day post TBI microglia  Sham  4

description: Library name: 60D_Mic_2022_Naiive4

value: No treatment


title: 60day post TBI microglia  Sham  5

description: Library name: 60D_Mic_2022_Naiive5


title: MCF-7cells, shKDM5B, replicate2

description: Library name: Sample 5

data_processing:
Raw sequencing reads were mapped to the reference human genome with HISAT2 software. Gene expression levels were represented as fragments per kilobase per million mapped fragments (FPKM) and analyzed by featureCounts.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: breast cancer cell

extract_protocol:
Total RNA was extracted from MCF-7 cells transfected with shSCR or shKDM5B using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells with KDM5B knockdown (shKDM5B) or control (shSCR).

value: breast cancer cell

value: KDM5B knock down


title: mesc_rad21_depletion_untreated_093, Smart-seq3


title: 00079FEE59

description: Library name: 00079FEE59


title: MCF-7cells, shKDM5B, replicate3

description: Library name: Sample 6


title: MCF-7cells, shKDM5B, replicate1

description: Library name: Sample 4


title: 00079FE6B4

description: Library name: 00079FE6B4


title: mesc_rad21_depletion_untreated_091, Smart-seq3


title: 60day post TBI microglia  Sham  3

description: Library name: 60D_Mic_2022_Naiive3


title: 60day post TBI  microglia only TBI  4

description: Library name: 60D_Mic_2022_TBI4

value: No treatment only injury


title: mesc_rad21_depletion_untreated_092, Smart-seq3


title: 00079FE238

description: Library name: 00079FE238


title: mesc_rad21_depletion_untreated_090, Smart-seq3


title: 60day post TBI  microglia only TBI  3

description: Library name: 60D_Mic_2022_TBI3


title: MCF-7 cells, shSCR, replicate3

description: Library name: Sample 3

value: ER+ breast cancer cell

value: Control


title: MCF-7 cells, shSCR, replicate2

description: Library name: Sample 2


title: mesc_rad21_depletion_untreated_089, Smart-seq3

value: mouse embryonic stem cell


title: 60day post TBI  microglia only TBI  2

description: Library name: 60D_Mic_2022_TBI2


title: MCF-7cells, shSCR, replicate1

description: Library name: Sample 1


title: mesc_rad21_depletion_untreated_088, Smart-seq3

value: untreat


title: 1day pTBI microglia Vehicle TBI  4

description: Library name: 24hr_Mic_2021_PBSlip_TBI4

value: Microglia

value: 1 day


title: PBMCs, HTO-derived cDNA

city: Milwaukee

first: Bonnie

last: Dittel

address: 8727 Watertown Plank Rd

institute: Versiti

description:
Library name: ST
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the BD Rhapsody pipeline run on Seven Bridges where ADT and HTO sequences were concatenated and aligned to the GENCODE GRCh38 genome build
Further processing was done with Seurat v4.3 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis) and Python (Bokeh data visualization, Palantir (v1.3.0) trajectory analysis)
Assembly: GENCODE GRCh38
Supplementary files format and content: BD Rhapsody output files: DBEC_MolsPerCell_Unfiltered.csv.gz ; Sample_Tag_Calls.csv

molecule: protein

source_name: peripheral blood

extract_protocol:
CD19+IgM+IgDlow/- cells and CD19+IgM+IgDhigh cells from three deidentified human donors were purified by flow cytometry. Purified cells were then stained with Antibody Derived Tag directed against CD27, CD21, CD24 and CD38 and barcoded with a unique Oligonucleotide Hash Tag. After Hash- and Cite-tagged cells were counted and checked for viability using a hematocytometer, 40e4 cells (10e3 cells for each sample: 3 IgDlow, 1 IgDhigh) were loaded into a Rhapsody single-lane cartridge (BD Biosciences).
Library was prepared using BD Rhapsody System protocol rev. 2022-11 (BD Biosciences). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the BD Rhapsody System protocol rev 2022-11 (BD Biosciences) and with specific primers amplifying the antibody-derived tags. AMPure XP bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180-200bp). For the mRNA derived cDNA library and antibody-derived tagged library preparation, we further proceeded according to the manufacturer’s instructions (BD Rhapsody mRNA Whole Transcriptome Analysis (WTA), BD AbSeq, and Sample Tag Library Preparation Protocol, rev 2022-11). The Nextera N712 i7 primer (Illumina) and Truseq D501 i5 primer (Illumina) were used to for both CITE- and HASH- seq library amplification.
Following the final bead purification, all three libraries were pooled as 91% mRNA library, 7% ADT library and 2% HTO library before sequencing.

value: peripheral blood

value: Peripheral blood mononuclear cells (PBMCs)

tag: library type

value: HTO

tag: antibodies/tags

value: BD Human SMK Universal marker:021822/Sample Tag-01 ; 012122/Sample Tag-02; 021122/Sample Tag-03 ; 021822/Sample Tag-04 (IgDhi neg. control)


title: 00079FD64F

description: Library name: 00079FD64F

value: whole brain hemisphere


title: 00079FD9EB

description: Library name: 00079FD9EB


title: 1day pTBI microglia Vehicle TBI  1

description: Library name: 24hr_Mic_2021_PBSlip_TBI1

value: PBS lipsomes


title: 00079FC3E9

description: Library name: 00079FC3E9


title: PBMCs, mRNA-derived cDNA

description:
Library name: WTA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: mRNA


title: 1day pTBI microglia Clodroante TBI  3

description: Library name: 24hr_Mic_2021_Clolip_TBI3

value: Clodorante lipsomes


title: PBMCs, ADT-derived cDNA

description:
Library name: Abseq
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)

value: ADT


title: mesc_rad21_depletion_untreated_085, Smart-seq3


title: mesc_rad21_depletion_untreated_086, Smart-seq3


title: 1day pTBI microglia Clodroante TBI  2

description: Library name: 24hr_Mic_2021_Clolip_TBI2


title: mesc_rad21_depletion_untreated_087, Smart-seq3


title: 00079FB999

description: Library name: 00079FB999


title: 00079FD6BE

description: Library name: 00079FD6BE


title: IOMM-Lee hyp_biol rep3

city: New Delhi

first: Dr. Ritu

last: Kulshreshtha

state: New Delhi

address: Room 134, Block I

department: Dept of Biochemical Engineering and Biotechnology

country: India

institute: Indian Institute of Technology

data_processing:
RNA sequencing data was preprocessed using fastp (v0.20.1).
Alignment of reads to the reference genome was performed using HISAT2 (v2.1.0) and quantified with featureCounts (v2.0.1).
Gene IDs for protein-coding genes were segregated using Ensembl Biomart.
DESeq2 (v1.37.5) was used for differential expression analysis.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

source_name: IOMM-Lee

growth_protocol: IOMM-Lee cells were cultured in DMEM media enriched with 10% Fetal Bovine Serum, 100 U/ml Penicillin, and 100 g/ml Streptomycin. The cells were incubated at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated using the RNeasy mini kit from QIAGEN. RNA samples meeting the standard RNA integrity number (RIN) criterion of ≥9.0 and a 28S/18S ratio of ≥1.9 were utilized for RNA-Seq analysis.
With the help of the NEBNext Ultra II RNA Library Prep Kit, RNA-seq libraries were created.

treatment_protocol: Cells were grown in for 48h in a hypoxia workstation maintained at 37°C with 0.2% O2 and 5% CO2

value: IOMM-Lee

value: malignant (grade 3) meningioma cells

tag: group

value: Test

value: Hypoxic (0.2% O2)


title: 1day pTBI microglia Clodroante TBI  1

description: Library name: 24hr_Mic_2021_Clolip_TBI1


title: mesc_rad21_depletion_untreated_084, Smart-seq3

value: mouse embryonic stem cell


title: 00079FB9D9

description: Library name: 00079FB9D9


title: 00079299D9

description:
Library name: 00079299D9
Original label before genotype mismatch fix: 00079FB742


title: mesc_rad21_depletion_untreated_083, Smart-seq3

value: untreat


title: mesc_rad21_depletion_untreated_081, Smart-seq3


title: IOMM-Lee hyp_biol rep2


title: 0007899712

description:
Library name: 0007899712
Original label before genotype mismatch fix: 00079FAA78


title: IOMM-Lee norm_biol rep3

value: Control

value: Normoxic


title: IOMM-Lee norm_biol rep2


title: 30day post TBI  microglia Vehicle TBI  2

description: Library name: 30D_Mic_2018_PBSlip_TBI2

value: Microglia

value: 30 day


title: 00079FA065

description: Library name: 00079FA065


title: IOMM-Lee norm_biol rep1


title: mesc_rad21_depletion_untreated_079, Smart-seq3


title: 30day post TBI  microglia Vehicle TBI  1

description: Library name: 30D_Mic_2018_PBSlip_TBI1


title: 30day post TBI  microglia Vehicle TBI  4

description: Library name: 30D_Mic_2018_PBSlip_TBI4


title: IOMM-Lee hyp_biol rep1


title: mesc_rad21_depletion_untreated_080, Smart-seq3


title: mesc_rad21_depletion_untreated_082, Smart-seq3


title: mesc_rad21_depletion_untreated_078, Smart-seq3


title: 30day post TBI  microglia Clodroante TBI  3

description: Library name: 30D_Mic_2018_Clolip_TBI3


title: 30day post TBI  microglia Clodroante TBI  2

description: Library name: 30D_Mic_2018_Clolip_TBI2


title: 00079FA868

description: Library name: 00079FA868


title: 30day post TBI  microglia Vehicle TBI  3

description: Library name: 30D_Mic_2018_PBSlip_TBI3


title: 00079F99EA

description: Library name: 00079F99EA


title: 00079FA000

description: Library name: 00079FA000


title: 30day post TBI  microglia Clodroante TBI  4

description: Library name: 30D_Mic_2018_Clolip_TBI4


title: BC_Pac_TMA_15

city: Madrid

first: Carolina

last: Rubio

state: Madrid

address: Avda Complutense, 40

country: Spain

institute: CIEMAT

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads' quality, total bases, total reads, GC (%) and basic statistics are calculated
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner.
Transcript is assembled by StringTie with aligned reads.
Expression profiles are represented as read count.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include total counts values for each sample

source_name: NMIBC

extract_protocol:
Total RNA was extracted using the miRNAeasy FFPE kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. 500 ng of total RNA was sent for RNAseq analysis by Macrogen RNA-seq services (Seoul, South Korea).
Sequencing of the samples was performed by Macrogen.

value: NMIBC

tag: cd44 expression

value: Neg

tag: cd44v6 expression

value: High


title: BC_Pac_TMA_13


title: 30day post TBI   microglia  Sham  3

description: Library name: 30D_Mic_2018_Naive4

value: No treatment


title: 00079F8DC9

description: Library name: 00079F8DC9

value: whole brain hemisphere


title: 00079F9C01

description: Library name: 00079F9C01


title: BC_Pac_TMA_14


title: mesc_rad21_depletion_untreated_077, Smart-seq3


title: BC_Pac_TMA_6

source_name: MIBC

value: MIBC


title: 30day post TBI   microglia  Sham  1

description: Library name: 30D_Mic_2018_Naive1


title: 00079F96AB

description: Library name: 00079F96AB


title: mesc_rad21_depletion_untreated_076, Smart-seq3


title: mesc_rad21_depletion_untreated_072, Smart-seq3


title: BC_Pac_TMA_12


title: 30day post TBI  microglia Clodroante TBI  1

description: Library name: 30D_Mic_2018_Clolip_TBI1

value: Clodorante lipsomes


title: 00079F939A

description: Library name: 00079F939A


title: 00079F86E9

description: Library name: 00079F86E9


title: 30day post TBI  microglia only TBI  4

description: Library name: 30D_Mic_2018_TBI4

value: No treatment only injury


title: BC_Pac_TMA_5


title: BC_Pac_TMA_10


title: mesc_rad21_depletion_untreated_075, Smart-seq3


title: 30day post TBI   microglia  Sham  4

description: Library name: 30D_Mic_2018_Naive5


title: mesc_rad21_depletion_untreated_069, Smart-seq3


title: 00079F6AE2

description: Library name: 00079F6AE2


title: 00079F8EC8

description: Library name: 00079F8EC8


title: BC_Pac_TMA_2


title: 00079F6009

description: Library name: 00079F6009


title: BC_Pac_TMA_3


title: 0007929BA5

description:
Library name: 0007929BA5
Original label before genotype mismatch fix: 00079F5F7E


title: mesc_rad21_depletion_untreated_074, Smart-seq3


title: BC_Pac_TMA_8


title: mesc_rad21_depletion_untreated_066, Smart-seq3


title: 14day post TBI  microglia Vehicle TBI  4

description: Library name: 14D_Mic_2018_PBSlip_TBI4

value: PBS lipsomes

value: 14 day


title: RT-112_CD44v6_3

source_name: cell line

extract_protocol:
Total RNA was extracted using the miRNAeasy Mini kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. 500 ng of total RNA was sent for RNAseq analysis by Macrogen RNA-seq services (Seoul, South Korea).
Sequencing of the samples was performed by Macrogen.

value: cell line

value: Bladder Cancer


title: 00079F578F

description: Library name: 00079F578F


title: mesc_rad21_depletion_untreated_073, Smart-seq3

value: mouse embryonic stem cell

value: untreat


title: 14day post TBI  microglia Vehicle TBI  3

description: Library name: 14D_Mic_2018_PBSlip_TBI3


title: 14day post TBI  microglia Vehicle TBI  2

description: Library name: 14D_Mic_2018_PBSlip_TBI2


title: mesc_rad21_depletion_untreated_064, Smart-seq3


title: 000792A80C

description: Library name: 000792A80C


title: 30day post TBI   microglia  Sham  2

description: Library name: 30D_Mic_2018_Naive2


title: BC_Pac_TMA_7


title: RT-112_CD44v6_1


title: mesc_rad21_depletion_untreated_063, Smart-seq3


title: 00079F8945

description: Library name: 00079F8945


title: mesc_rad21_depletion_untreated_071, Smart-seq3


title: 000792A7DB

description: Library name: 000792A7DB


title: 00079F73D2

description: Library name: 00079F73D2


title: mesc_rad21_depletion_untreated_070, Smart-seq3


title: 14day post TBI  microglia Clodroante TBI  5

description: Library name: 14D_Mic_2018_Clolip_TBI5


title: 30day post TBI  microglia only TBI  3

description: Library name: 30D_Mic_2018_TBI3


title: RT-112_CD44_High_1


title: mesc_rad21_depletion_untreated_060, Smart-seq3


title: 30day post TBI  microglia only TBI  2

description: Library name: 30D_Mic_2018_TBI2


title: 14day post TBI  microglia Vehicle TBI  5

description: Library name: 14D_Mic_2018_PBSlip_TBI5


title: mesc_rad21_depletion_untreated_068, Smart-seq3


title: mesc_rad21_depletion_untreated_067, Smart-seq3


title: 30day post TBI  microglia only TBI  1

description: Library name: 30D_Mic_2018_TBI1


title: BC_Pac_TMA_1


title: BC_Pac_TMA_4


title: 000792A62A

description: Library name: 000792A62A


title: mesc_rad21_depletion_untreated_059, Smart-seq3


title: mesc_rad21_depletion_untreated_058, Smart-seq3


title: 000792A597

description:
Library name: 000792A597
Removed: no matching genotype sample


title: mesc_rad21_depletion_untreated_062, Smart-seq3


title: RT-112_CD44_Low_1

value: Low


title: RT-112_CD44v6_2


title: mesc_rad21_depletion_untreated_065, Smart-seq3


title: RT-112_CD44_High_3


title: 14day post TBI  microglia Vehicle TBI  1

description: Library name: 14D_Mic_2018_PBSlip_TBI1

value: Microglia


title: 000792A7B4

description: Library name: 000792A7B4


title: 14day post TBI  microglia Clodroante TBI  4

description: Library name: 14D_Mic_2018_Clolip_TBI4


title: 14day post TBI   microglia  Sham  3

description: Library name: 14D_Mic_2017_Naiive3


title: 00079F5D6C

description: Library name: 00079F5D6C


title: mesc_rad21_depletion_untreated_061, Smart-seq3


title: 14day post TBI   microglia  Sham  2

description: Library name: 14D_Mic_2017_Naiive2


title: 000792A6D1

description: Library name: 000792A6D1


title: 000792A41F

description: Library name: 000792A41F


title: 14day post TBI   microglia  Sham  1

description: Library name: 14D_Mic_2017_Naiive1


title: 000792A420

description: Library name: 000792A420


title: RT-112_Par3

value: Control


title: RT-112_CD44_High_2


title: 000792A415

description: Library name: 000792A415


title: 14day post TBI  microglia Clodroante TBI  3

description: Library name: 14D_Mic_2018_Clolip_TBI3


title: RT-112_CD44_Low_3


title: 14day post TBI  microglia Clodroante TBI  2

description: Library name: 14D_Mic_2018_Clolip_TBI2


title: RT-112_CD44_Low_2


title: 14day post TBI  microglia only TBI  3

description: Library name: 14D_Mic_2017_TBI3


title: mesc_rad21_depletion_untreated_056, Smart-seq3


title: mesc_rad21_depletion_untreated_053, Smart-seq3


title: 000792A409

description: Library name: 000792A409


title: mesc_rad21_depletion_untreated_057, Smart-seq3


title: 14day post TBI  microglia Clodroante TBI  1

description: Library name: 14D_Mic_2018_Clolip_TBI1


title: 000792A3F9

description: Library name: 000792A3F9


title: 000792A428

description: Library name: 000792A428


title: 14day post TBI  microglia only TBI  1

description: Library name: 14D_Mic_2017_TBI1


title: J82_CD44v6_1


title: 000792A3EA

description: Library name: 000792A3EA


title: RT-112_Par2


title: mesc_rad21_depletion_untreated_055, Smart-seq3


title: J82_CD44v6_3


title: mesc_rad21_depletion_untreated_050, Smart-seq3


title: J82_CD44_High_3


title: mesc_rad21_depletion_untreated_052, Smart-seq3


title: mesc_rad21_depletion_untreated_054, Smart-seq3


title: J82_CD44_High_2


title: RT-112_Par1


title: 7day post TBI  microglia Vehicle TBI  4

description: Library name: 7D_Mic_2018_PBSlip_TBI4

value: 7 day


title: J82_CD44v6_2


title: mesc_rad21_depletion_untreated_049, Smart-seq3


title: 7day post TBI  microglia Vehicle TBI  5

description: Library name: 7D_Mic_2018_PBSlip_TBI5


title: J82_CD44_High_1


title: 14day post TBI  microglia only TBI  2

description: Library name: 14D_Mic_2017_TBI2


title: 000792A3E7.

description: Library name: 000792A3E7


title: 7day post TBI  microglia Vehicle TBI  3

description: Library name: 7D_Mic_2018_PBSlip_TBI3


title: J82_CD44_Low_3


title: mesc_rad21_depletion_untreated_048, Smart-seq3


title: 000792A3D1

description: Library name: 000792A3D1


title: 000792A3E1

description: Library name: 000792A3E1


title: 000792A3DB

description: Library name: 000792A3DB


title: J82_CD44_Low_2


title: 7day post TBI  microglia Vehicle TBI  2

description: Library name: 7D_Mic_2018_PBSlip_TBI2


title: mesc_rad21_depletion_untreated_047, Smart-seq3


title: 000792A3D0

description: Library name: 000792A3D0


title: mesc_rad21_depletion_untreated_046, Smart-seq3


title: 000792A383

description: Library name: 000792A383


title: 7day post TBI  microglia Clodroante TBI  3

description: Library name: 7D_Mic_2018_Clolip_TBI3


title: mesc_rad21_depletion_untreated_044, Smart-seq3


title: J82_CD44_Low_1


title: 000792A382

description: Library name: 000792A382


title: 000792A7A4

description: Library name: 000792A7A4


title: mesc_rad21_depletion_untreated_045, Smart-seq3


title: 7day post TBI  microglia Clodroante TBI  1

description: Library name: 7D_Mic_2018_Clolip_TBI1


title: 000792A38F

description: Library name: 000792A38F


title: 7day post TBI  microglia Clodroante TBI  5

description: Library name: 7D_Mic_2018_Clolip_TBI5


title: 7day post TBI  microglia Clodroante TBI  4

description: Library name: 7D_Mic_2018_Clolip_TBI4


title: J82_parental_1


title: 000792A371

description: Library name: 000792A371


title: 7day post TBI   microglia  Sham  4

description: Library name: 7D_Mic_2018_Naiive4


title: J82_parental_3


title: J82_parental_2


title: mesc_rad21_depletion_untreated_043, Smart-seq3


title: mesc_rad21_depletion_untreated_042, Smart-seq3


title: mesc_rad21_depletion_untreated_041, Smart-seq3


title: DLBCL_nonGC, EBV-, Study_ID_10

city: Ann Arbor

first: Elliott

middle: Daniel

last: SoRelle

state: MI

address: 1137 Catherine St.

department: Microbiology & Immunology

institute: The University of Michigan

description:
Luf_10
FFPE spatial transcriptomic sequencing

data_processing:
*library strategy: Spatial transcriptomics
Raw sequence data were processed using the 10x Genomics Spaceranger pipeline to create FASTQ files and tissue image alignments
Sequence data were aligned to the hg38 reference genome using Spaceranger default settings to generate gene expression count matrices
Gene expression quantification and analyses were conducted in RStudio using Seurat V5
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: spatial spot barcodes
Supplementary files format and content: features.tsv.gz: gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count matrix in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: alignd fiducial tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and their spatial (x,y) coordinates

source_name: EBV- non-GC DLBCL (recurrence)

extract_protocol:
FFPE tissues were sectioned to 5 micron thickness, H&E stained, and used for spatial transcriptomics
ST sequencing libraries were prepared using 10x Genomics Visium V2 with CytAssist according to manufacturer's instructions

value: EBV- non-GC DLBCL (recurrence)

tag: Sex

value: M


title: 7day post TBI   microglia  Sham  3

description: Library name: 7D_Mic_2018_Naiive3

value: No treatment


title: 000792A358

description: Library name: 000792A358

value: whole brain hemisphere


title: 7day post TBI   microglia  Sham  2

description: Library name: 7D_Mic_2018_Naiive2


title: 000792A33B

description: Library name: 000792A33B


title: mesc_rad21_depletion_untreated_039, Smart-seq3


title: 7day post TBI  microglia Clodroante TBI  2

description: Library name: 7D_Mic_2018_Clolip_TBI2


title: DLBCL_PC, EBV-, Study_ID_6

description:
Luf_6
FFPE spatial transcriptomic sequencing

source_name: EBV- DLBCL with Plasma Cell features

value: EBV- DLBCL with Plasma Cell features


title: 000792A34C

description: Library name: 000792A34C


title: mesc_rad21_depletion_untreated_040, Smart-seq3


title: 7day post TBI   microglia  Sham  1

description: Library name: 7D_Mic_2018_Naiive1


title: mesc_rad21_depletion_untreated_051, Smart-seq3


title: 000792A32B

description: Library name: 000792A32B


title: DLBCL_nonGC, EBV-, Study_ID_8

description:
Luf_8
FFPE spatial transcriptomic sequencing

source_name: EBV- non-GC DLBCL (relapse)

value: EBV- non-GC DLBCL (relapse)


title: 7day post TBI  microglia only TBI  5

description: Library name: 7D_Mic_2018_TBI5

value: No treatment only injury


title: mesc_rad21_depletion_untreated_037, Smart-seq3


title: 000792A300

description: Library name: 000792A300


title: HG_GC, EBV-, Study_ID_4

description:
Luf_4
FFPE spatial transcriptomic sequencing

source_name: EBV- High Grade GC B cell NHL

value: EBV- High Grade GC B cell NHL


title: 7day post TBI  microglia only TBI  4

description: Library name: 7D_Mic_2018_TBI4


title: 000792A2EF

description: Library name: 000792A2EF


title: mesc_rad21_depletion_untreated_036, Smart-seq3


title: DLBCL_PC, EBV+, Study_ID_7

description:
Luf_7
FFPE spatial transcriptomic sequencing

source_name: EBV+ High Grade Plasma Cell Neoplasm

value: EBV+ High Grade Plasma Cell Neoplasm


title: mesc_rad21_depletion_untreated_034, Smart-seq3


title: DLBCL_GC, EBV-, Study_ID_2

description:
Luf_2
FFPE spatial transcriptomic sequencing

source_name: EBV- GC DLBCL

value: EBV- GC DLBCL

value: F


title: 7day post TBI  microglia only TBI  3

description: Library name: 7D_Mic_2018_TBI3


title: 000792A2DF

description: Library name: 000792A2DF


title: mesc_rad21_depletion_untreated_035, Smart-seq3

value: mouse embryonic stem cell


title: mesc_rad21_depletion_untreated_038, Smart-seq3

value: untreat


title: 7day post TBI  microglia only TBI  2

description: Library name: 7D_Mic_2018_TBI2


title: 000792A2C6

description: Library name: 000792A2C6


title: 000792A2B8.

description: Library name: 000792A2B8


title: mesc_rad21_depletion_untreated_033, Smart-seq3


title: DLBCL_IB, EBV+, Study_ID_1

description:
Luf_1
FFPE spatial transcriptomic sequencing

source_name: EBV+ Immunoblastic Lymphoma

value: EBV+ Immunoblastic Lymphoma


title: 7day post TBI  microglia only TBI  1

description: Library name: 7D_Mic_2018_TBI1

value: Microglia


title: 000792A288

description: Library name: 000792A288


title: Polymorphic, EBV+, Study_ID_9

description:
Luf_9
FFPE spatial transcriptomic sequencing

source_name: EBV+ Polymorphic Lymphoma

value: EBV+ Polymorphic Lymphoma


title: BL, EBV+, Study_ID_5

description:
Luf_5
FFPE spatial transcriptomic sequencing

source_name: EBV+ Burkitt Lymphoma

value: EBV+ Burkitt Lymphoma


title: mesc_rad21_depletion_untreated_032, Smart-seq3

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

source_name: mouse embryonic stem cell


title: DLBCL_PB, EBV+, Study_ID_3

description:
Luf_3
FFPE spatial transcriptomic sequencing

source_name: EBV+ Plasmablastic Lymphoma

value: EBV+ Plasmablastic Lymphoma


title: mesc_rad21_depletion_untreated_031, Smart-seq3


title: WT_gene_10x_lane3

city: Cambridge

first: Mohamed

middle: A.

last: El-Brolosy

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

data_processing:
Following sequencing, reads were used as input to Cell Ranger v6.1.2 for alignment.
genome build/assembly: GRCh38
processed data files format and content tab separated value files, matrix files, h5 file and protocopacer calls per cells

extract_protocol:
Cells were prepared for single-cell RNA-sequencing by resuspension in 1X PBS with 0.04% BSA as detailed in the 10x Genomics Single Cell Protocols Cell Preparation Guide (10x Genomics, CG00053 Rev C). For the WT experiment, cells were then separated into droplet emulsions using the Chromium Controller (10x Genomics) with Chromium Single-Cell 3′ Gel Beads v3 (10x Genomics, PN-1000075) across 3 “lanes”/”GEM groups” following the 10x Genomics Chromium Single Cell 3ʹ Reagent Kits v3 User Guide with Feature Barcode technology for CRISPR Screening (CG000184 Rev C) with the goal of recovering ∼20,000 cells per GEM group.  For the ILF3 KO cells were cells were separated into droplet emulsions using the Chromium Controller (10x Genomics) with Chromium Single Cell 3’ HT Gel Bead Kit v3.1 (10x Genomics, PN-1000370) across 2 “lanes”/”GEM groups” following the Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 User Guide with Feature Barcode technology for CRISPR Screening (CG000421Rev D) with the goal of recovering ∼30,000 cells per GEM group before filtering.
For preparation of gene expression and sgRNA libraries, samples were processed according to 10x Genomics Chromium Single Cell 3ʹ Reagent Kits v3 or HT v3.1 User Guide with Feature Barcode technology for CRISPR Screening (CG000184 Rev C, CG000421Rev D). For sequencing, mRNA and sgRNA libraries were pooled to avoid index collisions at a 10:1 ratio.

value: myelogenous leukemia cell line

value: WT


title: 1day post TBI  microglia Clodroante TBI  4

description: Library name: 24hr_Mic_2018_Clolip_TBI4

source_name: Microglia

value: Clodorante lipsomes

value: 1 day


title: 000792A25B

description: Library name: 000792A25B

source_name: whole brain hemisphere

value: whole brain hemisphere


title: mesc_rad21_depletion_untreated_030, Smart-seq3


title: 1day post TBI  microglia Vehicle TBI  2

description: Library name: 24hr_Mic_2018_PBSlip_TBI2

value: PBS lipsomes


title: 000792A251

description: Library name: 000792A251


title: 1day post TBI  microglia Clodroante TBI  3

description: Library name: 24hr_Mic_2018_Clolip_TBI3


title: mesc_rad21_depletion_untreated_029, Smart-seq3


title: WT_gene_10x_lane1


title: 1day post TBI  microglia Clodronate TBI  1

description: Library name: 24hr_Mic_2018_Clolip_TBI1


title: mesc_rad21_depletion_untreated_028, Smart-seq3


title: 1day post TBI  microglia Vehicle TBI  1

description: Library name: 24hr_Mic_2018_PBSlip_TBI1


title: WT_gRNA_10x_lane3


title: 000792A23C

description: Library name: 000792A23C


title: 000792A223

description:
Library name: 000792A223
Removed: no matching genotype sample


title: 1day post TBI   microglia  Sham  5

description: Library name: 24hr_Mic_2018_Naiive5

value: No treatment


title: WT_gene_10x_lane2


title: WT_gRNA_10x_lane2


title: 000792A21D

description: Library name: 000792A21D


title: WT_gRNA_10x_lane1


title: 1day post TBI   microglia  Sham  4

description: Library name: 24hr_Mic_2018_Naiive4


title: 000792A21B

description: Library name: 000792A21B


title: 000792A24E

description: Library name: 000792A24E


title: mesc_rad21_depletion_untreated_025, Smart-seq3


title: 000792A20E

description: Library name: 000792A20E


title: mesc_rad21_depletion_untreated_027, Smart-seq3


title: 1day post TBI   microglia  Sham  2

description: Library name: 24hr_Mic_2018_Naiive2


title: MDA-MB-231-adapted-308Kpa-R3 (RRBS)

city: College Station

first: Ting-Ching

last: Wang

address: 101 Bizzell St

institute: Texas A&M University

data_processing:
TrimGalore package was used to filter out reads with a phred33 quality score below 30. Adapter trimming was performed and reads shorter than 20 base pairs were discarded.
The trimmed reads were aligned to the reference genome  (hg38) using the Bismark tool  (version 0.23.1). Bismark performs alignment by incorporating bisulfite conversion information to accurately align reads to the appropriate genomic positions.
Methylation information was extracted from the aligned reads using Bismark, producing a file containing the cytosine methylation calls for each genomic position. The edgeR package  (version 3.36.0) in R  (version 4.1.3) was employed for the statistical analysis of the differential methylation data.
Assembly: hg38
Supplementary files format and content: Genomic coverage for each sample which contains the number of methylated and number of unmethylated for each C in the sequenced genomic region.

growth_protocol: Cells were maintained in a humidified incubator at 37 °C and 5% CO2. Human breast carcinoma cells MDA-MB-231  (ATCC) were cultured in Dulbecco’s Modified Eagle’s Medium with 4.5 g/l glucose  (Corning), supplemented with 10% v/v donor bovine serum  (Gibco) and 1% v/v penicillin/streptomycin  (Corning).

extract_protocol:
DNA was extracted for ancestral and selected populations using the PureLink Genomic DNA Mini Kit  (ThermoFisher Scientific).
Libraries were prepared from genomic DNA using Ovation RRBS Methyl-Seq Kit  (Tecan Trading AG) at the MD Anderson Cancer Center  (MDACC) Epigenomics Profiling Core.

treatment_protocol: Selection of MDA-MB-231 were initiated by plating 20,000 cells on polyacrylamide gels of Young’s modulus E = 1 kPa  (soft) and 308 kPa  (stiff) conjugated with type I collagen. Cell populations were allowed to grow for approximately seven days, and then 20,000 cells were passaged onto fresh substrates of the same  (corresponding) stiffness. This procedure was carried out for 75 days.

value: Breast adenocarcinoma cells

value: selected on stiff


title: 1day post TBI   microglia  Sham  3

description: Library name: 24hr_Mic_2018_Naiive3


title: mesc_rad21_depletion_untreated_024, Smart-seq3


title: mesc_rad21_depletion_untreated_026, Smart-seq3


title: 1day post TBI   microglia  Sham  1

description: Library name: 24hr_Mic_2018_Naiive1


title: mesc_rad21_depletion_untreated_023, Smart-seq3


title: 000792A1F9.

description: Library name: 000792A1F9


title: MDA-MB-231-adapted-308Kpa-R2 (RRBS)


title: MDA-MB-231-adapted-308Kpa-R4 (RRBS)


title: MDA-MB-231-adapted-308Kpa-R1 (RRBS)


title: 000792A1F6

description: Library name: 000792A1F6


title: 1day post TBI  microglia only TBI  5

description: Library name: 24hr_Mic_2018_TBI5

value: No treatment only injury


title: 1day post TBI  microglia only TBI  4

description: Library name: 24hr_Mic_2018_TBI4


title: mesc_rad21_depletion_untreated_022, Smart-seq3

value: mouse embryonic stem cell


title: 000792A1F4

description: Library name: 000792A1F4


title: 1day post TBI  microglia only TBI  3

description: Library name: 24hr_Mic_2018_TBI3


title: 000792A1D1

description: Library name: 000792A1D1


title: MDA-MB-231-adapted-1kPa-R4 (RRBS)

value: selected on soft


title: mesc_rad21_depletion_untreated_021, Smart-seq3

value: untreat


title: MDA-MB-231-adapted-1kPa-R3 (RRBS)


title: mesc_rad21_depletion_untreated_020, Smart-seq3


title: MDA-MB-231-adapted-1kPa-R2 (RRBS)


title: 000792A1C7

description: Library name: 000792A1C7


title: mesc_rad21_depletion_untreated_019, Smart-seq3


title: 1day post TBI  microglia only TBI  1

description: Library name: 24hr_Mic_2018_TBI1

value: Microglia


title: 000792A1C2

description: Library name: 000792A1C2


title: mesc_rad21_depletion_untreated_018, Smart-seq3


title: MDA-MB-231-adapted-1kPa-R1 (RRBS)


title: mesc_rad21_depletion_untreated_017, Smart-seq3


title: 000792A1BD

description: Library name: 000792A1BD


title: Heart ventricle, Pooled DNA, spikein, NR4A2 (Input)

city: Houston

first: Romain

last: Harmancey

state: Texas

address: 1881 East Rd.

department: Internal Medicine - Division of Cardiology

institute: The University of Texas Health Science Center at Houston

description: Library name: Pooled DNA, INPUT

data_processing:
ChIP-seq reads were aligned to genome assembly GRCm38 (mm10) using the BWA algorithm.
Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches, and mapped uniquely to the reference genome were used as tags in the subsequent analysis.
Aligned tags were extended in silico at their 3’-ends to a length of 200 bp fragments, and the density of fragments along the genome determined across 32-nucleotide bins.
Intervals corresponding to genomic regions with local enrichment in tag numbers were determined by peak calling using MACS via comparison with input chromatin.
Spike-in normalization was carried out by adjusting the number of tags by a factor resulting in the same number of spike-in drosophila tags for each sample.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for input samples)

source_name: Heart, ventricle

growth_protocol: Mice with cardiomyocyte-specific, tamoxifen-inducible overexpression of NR4A2 (Nr4a2-icTg) were generated by crossing Nr4a2-reporter conditional knockin EGE-GJ-095 ROSA26-KI mice with B6.FVB(129)-A1cfTg(Myh6-cre/Esr1*)1Jmk/J mice (The Jackson Laboratory; Strain #005657).

extract_protocol:
ChIP was performed using 30 µg of chromatin precleared with protein A agarose beads and 5.5 ug of antibody. 200 ng of D. melanogaster chromatin and 0.4 µg of drosophila-specific H2Av antibody (Active Motif; Cat. no. 39715) were added to each reaction for normalization purposes. Complexes were washed and eluted from beads with SDS buffer. ChIP and pooled chromatin input samples were subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation at 65°C and DNA was purified.
ChIP-seq libraries were prepared using the DNA Library Prep Kit for Illumina (Active Motif).

treatment_protocol: The expression of NR4A2 was induced in 8- to 9-week-old mice through a single intraperitoneal injection of 40 mg/kg body weight tamoxifen; αMHC-MerCreMer, Cre recombinase inducible littermates were used to control for potential tamoxifen-dependent effects.

value: Heart, ventricle

value: Pooled aMHC-MerCreMer and cardiomyocyte-specific NR4A2 overexpression

value: Tamoxifen

value: Day 3


title: MDA-MB-231-ancestral-308Kpa-R4 (RRBS)

value: WT

value: ancestral on stiff


title: mesc_rad21_depletion_untreated_016, Smart-seq3


title: Heart ventricle, Nr4a2-icTg mouse 2, spikein, NR4A2 (ChIP)

description:
Library name: NR4A2 Mouse 2, ChIP
column name in Diff_Peak_Analysis-Control_vs_NR4A2-All_peaks.tsv: 05_NR4A2-Mouse-2

value: NR4A2 (9D12) + H2Av (Active Motif, #39715) for spikein normalization


title: 000792A1AA

description: Library name: 000792A1AA

value: whole brain hemisphere


title: mesc_rad21_depletion_untreated_015, Smart-seq3


title: MDA-MB-231-ancestral-308Kpa-R3 (RRBS)


title: 1day post TBI  microglia only TBI  2

description: Library name: 24hr_Mic_2018_TBI2

value: 1 day


title: Heart ventricle, Nr4a2-icTg mouse 1, spikein, NR4A2 (ChIP)

description:
Library name: NR4A2 Mouse 1, ChIP
column name in Diff_Peak_Analysis-Control_vs_NR4A2-All_peaks.tsv: 04_NR4A2-Mouse-1


title: Heart ventricle, Cre control mouse 3, spikein, NR4A2 (ChIP)

description:
Library name: Control Mouse 3, ChIP
column name in Diff_Peak_Analysis-Control_vs_NR4A2-All_peaks.tsv: 03_Control-Mouse-3

value: aMHC-MerCreMer


title: MDA-MB-231-ancestral-308Kpa-R2 (RRBS)

value: Breast adenocarcinoma cells


title: 000792A1A6

description: Library name: 000792A1A6


title: MDA-MB-231-ancestral-308Kpa-R1 (RRBS)


title: MDA-MB-231-ancestral-1kPa-R4 (RRBS)

value: ancestral on soft


title: 000792A1B5

description: Library name: 000792A1B5


title: mesc_rad21_depletion_untreated_014, Smart-seq3


title: MDA-MB-231-ancestral-1kPa-R3 (RRBS)


title: 000792A1A5

description: Library name: 000792A1A5


title: mesc_rad21_depletion_untreated_013, Smart-seq3


title: 000792A180

description: Library name: 000792A180


title: Heart ventricle, Cre control mouse 2, spikein, NR4A2 (ChIP)

description:
Library name: Control Mouse 2, ChIP
column name in Diff_Peak_Analysis-Control_vs_NR4A2-All_peaks.tsv: 02_Control-Mouse-2


title: mesc_rad21_depletion_untreated_012, Smart-seq3


title: Heart ventricle, Cre control mouse 1, spikein, NR4A2 (ChIP)

description:
Library name: Control Mouse 1, ChIP
column name in Diff_Peak_Analysis-Control_vs_NR4A2-All_peaks.tsv: 01_Control-Mouse-1


title: MDA-MB-231-ancestral-1kPa-R2 (RRBS)


title: mesc_rad21_depletion_untreated_011, Smart-seq3


title: 000792A17C

description: Library name: 000792A17C


title: MDA-MB-231-ancestral-1kPa-R1 (RRBS)


title: 000792A179

description: Library name: 000792A179


title: Heart ventricle, Nr4a2-icTg mice 7328-7342, antibody validation, NR4A2 (ChIP)

description: Library name: Mice 7328-7342, ChIP


title: 000792A177

description: Library name: 000792A177


title: MDA-MB-231, selected on stiff, rep 3 (ATAC-seq)

data_processing:
Reads were trimmed using trimmomatic (v 0.36) and QC on the original and trimmed reads was performed using FastQC (v 0.11.4) and MultiQC (v 1.1).
The reads were aligned to the human genome version GRCh38 using Bowtie (v. 2.4.5) and ATAC peak calling was performed using the MACS (v 2.2.7.1).
Assembly: GRCh38
Supplementary files format and content: Peak detection lists as csv files

growth_protocol: Cells were maintained in a humidified incubator at 37 °C and 5% CO2. Human breast carcinoma cells MDA-MB-231 (ATCC) were cultured in Dulbecco’s Modified Eagle’s Medium with 4.5 g/l glucose (Corning), supplemented with 10% v/v donor bovine serum (Gibco) and 1% v/v penicillin/streptomycin (Corning).

extract_protocol:
Nuclei were isolated from 200,000 cells.
ATAC-seq libraries were prepared on aliquots of 50,000 nuclei using an ATAC-seq library preparation kit (Active Motif).

treatment_protocol: Selection of MDA-MB-231 were initiated by plating 20,000 cells on polyacrylamide gels of Young’s modulus E = 1 kPa (soft) and 308 kPa (stiff) conjugated with type I collagen. Cell populations were allowed to grow for approximately seven days, and then 20,000 cells were passaged onto fresh substrates of the same (corresponding) stiffness. This procedure was carried out for 75 days.

value: selected on stiff


title: male-WT-Tau.773

first: Gregory

last: Donahue

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

description: Library name: Tau.WT.Male.773

data_processing:
Demultiplexing: sequencing data was demultiplexed using native applications on BaseSpace.
Alignment: FASTQs were aligned by RNA-STAR v2.5.2 to assembly mm10 (GRCm38) of the mouse genome with parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000.
Quantification: aligned reads were converted to BAM format using samtools v1.1 view -bS and mapped to genomic features using HTSeq v0.9.1 (parameters: -r pos -s rev -t exon -i gene_id) and a GTF of RefSeq genes for mm10.
Differential expression: library size adjustment, and differential gene expression analysis were performed using DESeq2. The significance of gene alterations was determined using the Wald test with multiple test correction (Benjamini-Hochberg FDR < 0.05). For study group comparisons, other samples were removed prior to DESeq2 operations (e.g., if comparing male-WT-PBS vs male-KO-Tau, we exclude all other samples and thus library size adjustment / dispersion estimation will reflect only those samples).
Assembly: GRCm38
Supplementary files format and content: A single gene-level counts table (result of HTSeq) is provided.

source_name: dorsal hippocampus

growth_protocol: To prevent genetic drift, Acss2KO and corresponding WT controls were generated through homozygous crosses of F1 progeny from heterozygote breeding cages. Mice were housed on a 12/12h light/dark cycle (7 am to 7 pm), with food and water provided ad libitum.

extract_protocol:
Animals were transcardially perfused with 1× PBS followed by 4% paraformaldehyde in PBS. Following dissection, total RNA was extracted using Trizol-chloroform from 1 mm-thick slices of dHPC (comprising the CA1, CA2, CA3, and dentate gyrus). Total RNA quality was assessed on the Bioanalyzer platform using the RNA 6000 Nano assay (Agilent).
mRNA was isolated from 300 ng total RNA using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490L), and libraries were prepared using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (E7770).

treatment_protocol: Tau protein was purified in the following way: 6–14 g of frontal cortical gray matter from AD patients was homogenized using a Dounce homogenizer in nine volumes (v/w) of high-salt buffer (10 mM Tris-HCl, pH 7.4, 0.8 M NaCl, 1 mM EDTA, and 2 mM dithiothreitol [DTT], with protease inhibitor cocktail, phosphatase inhibitor, and PMSF) with 0.1% sarkosyl and 10% sucrose added and centrifuged at 10,000 g for 10 min at 4°C. Pellets were reextracted once or twice using the same buffer conditions as the starting materials, and the supernatants from all two to three initial extractions were filtered and pooled. Additional sarkosyl was added to the pooled low-speed supernatant to reach 1%. After 1h nutation at room temperature, samples were centrifuged again at 300,000 g for 60 min at 4°C. The resulting sarkosyl-insoluble pellets, which contain pathological Tau, were washed once in PBS and then resuspended in PBS (∼100 μl/g gray matter) by passing through 27-G 0.5-in needles. The resuspended pellets were further purified by a brief sonication (20 pulses at ∼0.5 s/pulse) using a hand-held probe (QSonica) followed by centrifugation at 100,000 g for 30 min at 4°C, whereby the majority of protein contaminants were partitioned into the supernatant, with 60–70% of tau remaining in the pellet fraction. The pellets were resuspended in PBS at one fifth to one half of the precentrifugation volume, sonicated with 20–60 short pulses (∼0.5 s/pulse), and spun at 10,000 g for 30 min at 4°C to remove large debris. The final supernatants were used in the study and referred to as AD Tau.  6 months old male and female WT and ACSS2 KO mice were anaesthetized with isoflurane gas (1–5% to maintain surgical plane) and placed in a sterile field within a stereotaxic device. Artificial tears were applied to eyes to ensure sufficient lubrication. Animals received an injection of bupivacaine (2.5 mg kg−1) for local anaesthesia before the skin was disinfected with betadine solution and the skull exposed with a short incision using sterile surgical equipment. A small hole (about 0.5 mm) was drilled in the skull over the target area using a stereotax and a stereotactic drill. A micro-syringe filled with AD Tau lysate was inserted into the right dorsal hippocampus and slowly removed following injection of 1 ug Tau (AP, − 2.5 mm; DV, − 1.4 mm; ML, + 2 mm from bregma). All animals received a single dose of subcutaneous meloxicam (5 mg/kg) as analgesia at induction and one dose per day for two days postoperatively as needed. To allow sufficient time for the development of AD-like pathology, mice underwent behavioral or molecular characterization 6 months post-injection.

value: dorsal hippocampus

value: Tau

value: male


title: Heart ventricle, Nr4a2-icTg mice 7328-7342, antibody validation, NR4A2 (Input)

description: Library name: Mice 7328-7342, INPUT


title: mesc_rad21_depletion_untreated_009, Smart-seq3

value: mouse embryonic stem cell

value: untreat


title: 000792A166

description: Library name: 000792A166


title: MDA-MB-231, selected on stiff, rep 2 (ATAC-seq)


title: MDA-MB-231, selected on stiff, rep 1 (ATAC-seq)


title: mesc_rad21_depletion_untreated_007, Smart-seq3


title: mesc_rad21_depletion_untreated_010, Smart-seq3


title: male-WT-Tau.771

description: Library name: Tau.WT.Male.771


title: MDA-MB-231, selected on soft, rep 4 (ATAC-seq)

value: selected on soft


title: mesc_rad21_depletion_untreated_006, Smart-seq3


title: MDA-MB-231, selected on stiff, rep 4 (ATAC-seq)


title: 000792A14A

description: Library name: 000792A14A


title: male-WT-Tau.772

description: Library name: Tau.WT.Male.772


title: female-WT-Tau.331

description: Library name: Tau.WT.Female.331

value: female


title: 000792A14D.

description: Library name: 000792A14D


title: mesc_rad21_depletion_untreated_008, Smart-seq3


title: 000792A135

description: Library name: 000792A135


title: mesc_rad21_depletion_untreated_005, Smart-seq3


title: MDA-MB-231, selected on soft, rep 3 (ATAC-seq)


title: female-WT-Tau.341

description: Library name: Tau.WT.Female.341


title: 000792A131

description: Library name: 000792A131


title: mesc_rad21_depletion_untreated_004, Smart-seq3


title: 000792A12F

description: Library name: 000792A12F


title: male-KO-Tau.713

description: Library name: Tau.KO.Male.713


title: MDA-MB-231, selected on soft, rep 1 (ATAC-seq)


title: mesc_rad21_depletion_untreated_003, Smart-seq3


title: mesc_rad21_depletion_untreated_002, Smart-seq3


title: 000792A110

description:
Library name: 000792A110
Removed: no matching genotype sample


title: male-KO-Tau.712

description: Library name: Tau.KO.Male.712


title: male-KO-Tau.711

description: Library name: Tau.KO.Male.711


title: 000792A126

description: Library name: 000792A126


title: MDA-MB-231, ancestral on stiff, rep 4 (ATAC-seq)


title: mesc_rad21_depletion_IAA-6h_192, Smart-seq3

value: IAA (6h)


title: MDA-MB-231, ancestral on stiff, rep 3 (ATAC-seq)

value: WT


title: 000792A109

description: Library name: 000792A109


title: MDA-MB-231, ancestral on stiff, rep 2 (ATAC-seq)

value: ancestral on stiff


title: female-KO-Tau.324

description: Library name: Tau.KO.Female.324


title: MDA-MB-231, selected on soft, rep 2 (ATAC-seq)


title: female-KO-Tau.314

description: Library name: Tau.KO.Female.314


title: mesc_rad21_depletion_IAA-6h_191, Smart-seq3


title: Heart ventricle, Nr4a2-icTg mouse 3, spikein, NR4A2 (ChIP)

description:
Library name: NR4A2 Mouse 3, ChIP
column name in Diff_Peak_Analysis-Control_vs_NR4A2-All_peaks.tsv: 06_NR4A2-Mouse-3

value: Heart, ventricle

value: Tamoxifen

value: Day 3

value: NR4A2 (9D12) + H2Av (Active Motif, #39715) for spikein normalization


title: 000792A105

description: Library name: 000792A105

value: whole brain hemisphere


title: mesc_rad21_depletion_IAA-6h_190, Smart-seq3


title: male-WT-PBS.793

description: Library name: PBS.WT.Male.793

value: PBS


title: mesc_rad21_depletion_untreated_001, Smart-seq3


title: MDA-MB-231, ancestral on soft, rep 4 (ATAC-seq)

value: Breast adenocarcinoma cells

value: ancestral on soft


title: female-KO-Tau.325

description: Library name: Tau.KO.Female.325

value: dorsal hippocampus

value: Tau


title: 000792A0EC

description: Library name: 000792A0EC


title: mesc_rad21_depletion_IAA-6h_189, Smart-seq3

value: mouse embryonic stem cell


title: MDA-MB-231, ancestral on soft, rep 3 (ATAC-seq)


title: MDA-MB-231, ancestral on stiff, rep 1 (ATAC-seq)


title: 000792A0EB

description:
Library name: 000792A0EB
Removed: no matching genotype sample


title: male-WT-PBS.791

description: Library name: PBS.WT.Male.791

value: male


title: mesc_rad21_depletion_IAA-6h_188, Smart-seq3


title: 000792A0FF

description: Library name: 000792A0FF


title: MDA-MB-231, ancestral on soft, rep 2 (ATAC-seq)


title: 000792A0EA

description: Library name: 000792A0EA


title: male-WT-PBS.792

description: Library name: PBS.WT.Male.792


title: male-KO-PBS.753

description: Library name: PBS.KO.Male.753


title: mesc_rad21_depletion_IAA-6h_187, Smart-seq3


title: MDA-MB-231, ancestral on soft, rep 1 (ATAC-seq)


title: mesc_rad21_depletion_IAA-6h_186, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_185, Smart-seq3


title: 000792A0D6

description: Library name: 000792A0D6


title: US-748_3_6h

city: Basel

first: Yongzhan

last: Zhang

address: Otto-Stern-Weg 7 HPL H17.2

country: Switzerland

institute: ETH Zurich

data_processing:
Total RNA-seq reads were trimmed from the 3’ end until the final base had a quality score >30 , utilizing Trimmomatic version 0.33 and aligned to the human reference genome UCSC hg38 using STAR
Aligned reads were counted using HTSeq.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files includes raw counts for each sample

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) as per the manufacturer’s instructions.
Illumina Truseq mRNA

value: Circulating tumor cells


title: US-748_3_2h


title: male-KO-PBS.751

description: Library name: PBS.KO.Male.751


title: 000792A0E0

description: Library name: 000792A0E0


title: 000792A0D5

description: Library name: 000792A0D5


title: male-KO-PBS.752

description: Library name: PBS.KO.Male.752


title: mesc_rad21_depletion_IAA-6h_184, Smart-seq3


title: 000792A0A9

description: Library name: 000792A0A9


title: US-748_2_6h


title: mesc_rad21_depletion_IAA-6h_183, Smart-seq3


title: 000792A09C

description: Library name: 000792A09C


title: US-748_2_2h


title: 4T1-sgCPT1A-derived Xenograft scRNA-Seq B1 additional

city: Chongqing

first: Chenglong

last: LI

address: No. 30 Gaotanyan Zhengjie, Shapingba District

institute: Army Medical University

description:
Library name: YY82095
10x Genomics

data_processing:
The output CellRanger expression profile matrix was loaded into Seurat (version 4.1.0) for filtering of low quality cells from scRNA-seq data, and the filtered data was downscaled and clustered. Filtering low cell quality thresholds: number of genes expressed per cell >500, mitochondrial genes expressed in <25% of cells. Cells were projected into 2D space using t-SNE or UMAP.These steps include:
calculating gene expression values using the LogNormalize method of Seurat's "Normalization" function;
performing principal component analysis (PCA) using the normalized expression values, using the top 20 PCs for clustering, and Findcluster analysis.
analyze the marker genes of each cluster based on Findallmarker, and the marker genes were selected based on the following criteria: expressed in more than 10% of cells in each cluster, P value ≤ 0.01, gene expression ploidy logFC ≥ 0.26;
Hypergeometric testing was used to perform GO and KEGG enrichment analysis onthe differential genes of each cluster obtained from Findallmarker analysis relative to otherclusters. In human and mouse species, singleR database, scCATCH database and our self-developed LC-Marker were used to identify each cluster cell type, and some cells were re-clustered based on the identification results of SingleR database to find marker genes, cell communication analysis and Pseudotime analysis to provide ideas for further analysis.
Assembly: GRCm38
Supplementary files format and content: .barcodes.tsv, features.tsv and  matrix.mtx

source_name: Cell-line-derived Xenograft

growth_protocol: The tumor-bearing mice were housed in the laboratory animal facility for 8 days.

extract_protocol:
The single-cell RNA-seq experiment was performed by experimental personnel in the laboratory of NovelBio Co., Ltd. The tissues were removed and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing. The tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with PBS containing 0.5% BSA, Papain 20 U/mL (Worthington), DNase I 30 U / mL for 10 min at 37°C, with agitation. After digestion, samples were sieved through a 70µm cell strainer, after the supernatant was removed, the pelleted cells were re-suspended and re-filtered through a 35 μm cell strainer. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer.
The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3 Reagent Kits (10X Genomics, Pleasanton, CA). Briefly, cells were concentrated to approximately 1000 cells/µL and loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs). After the RT step, GEMs were broken and barcoded-cDNA was purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors and index PCR amplified. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) and the size distribution of the libraries were determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent). All libraries were sequenced by DNBSEQ-T7 Sequencer (MGI, Shenzhen, China) on a 150 bp paired-end run.

treatment_protocol: After one week of environmental adaptation, the tumor-bearing mice were established using a specific cell line

value: Cell-line-derived Xenograft

value: female

tag: age

value: 8-10 weeks old

value: All cellular components of the tumor tissue

value: CPT1A knowkdown

value: Digestion of tumor tissue to obtain a single-cell suspension


title: 4T1-sgCPT1A-derived Xenograft scRNA-Seq B1

description:
Library name: YY82093
10x Genomics


title: US-748_1_6h

value: WT


title: 4T1-sgVC-derived Xenograft scRNA-Seq A1

description:
Library name: YY82091
10x Genomics


title: US-748_1_2h


title: mesc_rad21_depletion_IAA-6h_181, Smart-seq3

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

value: IAA (6h)


title: 000792A095

description: Library name: 000792A095

value: whole brain hemisphere


title: US-464_3_6h


title: mesc_rad21_depletion_IAA-6h_179, Smart-seq3


title: 000792A08A

description: Library name: 000792A08A


title: 000792A08F

description: Library name: 000792A08F


title: US-464_3_2h


title: 000792A082

description:
Library name: 000792A082
Removed: no matching genotype sample


title: mesc_rad21_depletion_IAA-6h_178, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_177, Smart-seq3


title: HexBHD_13A1

city: Allschwil

first: Pijus

last: Brazauskas

address: Hegenheimermattweg 91

institute: Idorsia Pharmaceuticals

description: Library name: HexBHD_13A1_S17

data_processing:
Sequenced reads were aligned with STAR v2.5 to the Mouse Reference genome (Mus_musculus_GRCm38_98), and alignments per gene (exons) quantified with featureCounts using Ensembl gene annotations.
Assembly: Mus_musculus_GRCm38_98
Supplementary files format and content: tab-delimited text file for raw counts

source_name: Hippocampus

extract_protocol:
The mice hippocampi were collected in RNAlater (ThermoFisher Scientific). Individual tissue samples were lysed and homogenized in 850 µl of TRI Reagent (ThermoFisher Scientific) using the Tissue-Lyzer (Qiagen). Total RNA was isolated from the tissue lysate using MagMax 96 microarray kit (AM1839, Life Technologies) according to the manufacturer's instructions.
RNAseq libraries derived from poly(A)-selected RNA were isolated from total RNA using the Universal Plus mRNA-Seq kit ((NuGen Technologies/Tecan) according to the manufacturer recommendations.

treatment_protocol: Hexb‑/- mice were treated from week 4 to week 15 with sinbaglustat at either 30 mg/kg/day, for primary inhibition of GBA2, or 300 mg/kg/day, for inhibition of both GBA2 and GCS. Untreated Hexb‑/- and untreated WT mice served as comparator and control. Sinbaglustat tartrate or vehicle (mannitol) was provided as part of pelleted feed

value: Hippocampus

value: Hexb-/-

value: Sinbaglustat 300 mg/kg/d


title: HexBHD_9J1

description: Library name: HexBHD_9J1_S17


title: HexBHD_9F2

description: Library name: HexBHD_9F2_S16


title: US-464_2_6h


title: 000792A096

description: Library name: 000792A096

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


title: HexBHD_9J2

description: Library name: HexBHD_9J2_S18


title: US-464_2_2h


title: 000789990A.

description:
Library name: 000789990A
Original label before genotype mismatch fix: 000792A080


title: mesc_rad21_depletion_IAA-6h_176, Smart-seq3

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


title: HexBHD_12E2

description: Library name: HexBHD_12E2_S16


title: US-464_1_6h


title: mesc_rad21_depletion_IAA-6h_175, Smart-seq3


title: 000792A07E

description: Library name: 000792A07E


title: US-463_3_6h


title: HexBHD_11E2

description: Library name: HexBHD_11E2_S19


title: HexBHD_11E5

description: Library name: HexBHD_11E5_S8


title: 000792A049

description: Library name: 000792A049


title: 000792A063

description: Library name: 000792A063


title: US-464_1_2h


title: mesc_rad21_depletion_IAA-6h_172, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_174, Smart-seq3


title: US-463_3_2h


title: 0007929C40

description: Library name: 0007929C40


title: US-463_2_6h


title: HexBHD_11E4

description: Library name: HexBHD_11E4_S8


title: mesc_rad21_depletion_IAA-6h_171, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_173, Smart-seq3


title: 0007929C2B

description: Library name: 0007929C2B


title: 0007929C19

description: Library name: 0007929C19


title: US-463_2_2h


title: HexBHD_10B2

description: Library name: HexBHD_10B2_S18


title: mesc_rad21_depletion_IAA-6h_169, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_170, Smart-seq3


title: US-463_1_2h


title: HexBLD_9I2

description: Library name: HexBLD_9I2_S13

value: Sinbaglustat 30 mg/kg/d


title: HexBHD_10E1

description: Library name: HexBHD_10E1_S19


title: US-463_1_6h


title: HexBHD_11E1

description: Library name: HexBHD_11E1_S18


title: mesc_rad21_depletion_IAA-6h_168, Smart-seq3


title: 0007929BF4

description: Library name: 0007929BF4


title: 0007929BF5

description: Library name: 0007929BF5


title: HexBHD_10B1

description: Library name: HexBHD_10B1_S17


title: HexBLD_9I1

description: Library name: HexBLD_9I1_S12


title: mesc_rad21_depletion_IAA-6h_167, Smart-seq3


title: PLS-69_3_6h


title: PLS-69_3_2h


title: 0007929BF2

description: Library name: 0007929BF2


title: HexBLD_9A4

description: Library name: HexBLD_9A4_S12


title: HexBLD_9E2

description: Library name: HexBLD_9E2_S12


title: 0007929BEF

description: Library name: 0007929BEF


title: mesc_rad21_depletion_IAA-6h_165, Smart-seq3


title: HexBLD_9A2

description: Library name: HexBLD_9A2_S11


title: mesc_rad21_depletion_IAA-6h_166, Smart-seq3


title: 0007929BE1

description: Library name: 0007929BE1


title: PLS-69_2_2h


title: 0007929BE8

description: Library name: 0007929BE8


title: PLS-69_2_6h


title: 0007929BDB

description: Library name: 0007929BDB


title: mesc_rad21_depletion_IAA-6h_182, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_163, Smart-seq3


title: HexBLD_12A2

description: Library name: HexBLD_12A2_S15


title: PLS-69_1_6h


title: PLS-69_1_2h


title: mesc_rad21_depletion_IAA-6h_162, Smart-seq3


title: HexBLD_11C4

description: Library name: HexBLD_11C4_S15


title: 0007929BBD

description: Library name: 0007929BBD


title: IIIM-368_3_6h


title: 00079F5F7E

description:
Library name: 00079F5F7E
Original label before genotype mismatch fix: 0007929BA5


title: mesc_rad21_depletion_IAA-6h_161, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_164, Smart-seq3


title: HexBLD_11C1

description: Library name: HexBLD_11C1_S15


title: HexBLD_12C2

description: Library name: HexBLD_12C2_S16


title: IIIM-368_3_2h


title: 0007929B96

description: Library name: 0007929B96


title: mesc_rad21_depletion_IAA-6h_160, Smart-seq3


title: HexBLD_10F3

description: Library name: HexBLD_10F3_S14


title: HexBLD_10F4

description: Library name: HexBLD_10F4_S14


title: 0007929B8F

description: Library name: 0007929B8F


title: IIIM-368_2_6h


title: 0007929B91

description: Library name: 0007929B91


title: IIIM-368_2_2h


title: mesc_rad21_depletion_IAA-6h_157, Smart-seq3


title: HexBLD_10F1

description: Library name: HexBLD_10F1_S14


title: 0007929B83

description: Library name: 0007929B83


title: IIIM-368_1_6h


title: HexBLD_10C2

description: Library name: HexBLD_10C2_S13


title: mesc_rad21_depletion_IAA-6h_158, Smart-seq3


title: IIIM-368_1_2h


title: DF-06_3_6h


title: mesc_rad21_depletion_IAA-6h_159, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_156, Smart-seq3


title: HexBLD_10C1

description: Library name: HexBLD_10C1_S13


title: DF-06_3_2h


title: 0007929B78

description: Library name: 0007929B78


title: mesc_rad21_depletion_IAA-6h_180, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_155, Smart-seq3


title: HexB_9H3

description: Library name: HexB_9H3_S9

value: Vehicle


title: 0007929B70

description: Library name: 0007929B70


title: mesc_rad21_depletion_IAA-6h_154, Smart-seq3

value: mouse embryonic stem cell


title: HexB_9B5

description: Library name: HexB_9B5_S8


title: 0007929B67

description: Library name: 0007929B67


title: DF-06_2_6h


title: HexB_9B3

description: Library name: HexB_9B3_S7


title: DF-06_2_2h


title: HexB_9B1

description: Library name: HexB_9B1_S7


title: HexB_13C1

description: Library name: HexB_13C1_S11


title: DF-06_1_6h


title: 0007929B37

description: Library name: 0007929B37


title: mesc_rad21_depletion_IAA-6h_151, Smart-seq3


title: 0007929B36

description: Library name: 0007929B36


title: DF-06_1_2h


title: HexB_11F2

description: Library name: HexB_11F2_S11


title: 0007929B45

description: Library name: 0007929B45


title: 0007929B58

description: Library name: 0007929B58


title: mesc_rad21_depletion_IAA-6h_153, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_149, Smart-seq3


title: HexB_11F1

description: Library name: HexB_11F1_S10


title: mesc_rad21_depletion_IAA-6h_150, Smart-seq3


title: 0007929B17

description: Library name: 0007929B17


title: 0007929B2F

description: Library name: 0007929B2F


title: mesc_rad21_depletion_IAA-6h_152, Smart-seq3


title: Control_2_6h

value: Control


title: mesc_rad21_depletion_IAA-6h_148, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_147, Smart-seq3


title: 0007929B15

description: Library name: 0007929B15


title: Control_2_2h

value: Circulating tumor cells


title: Control_3_2h


title: HexB_11B2

description: Library name: HexB_11B2_S10


title: HexB_11B3

description: Library name: HexB_11B3_S10


title: 0007929B0A

description: Library name: 0007929B0A


title: Control_3_6h


title: mesc_rad21_depletion_IAA-6h_146, Smart-seq3


title: HexB_10D2

description: Library name: HexB_10D2_S9


title: Control_1_6h


title: mesc_rad21_depletion_IAA-6h_144, Smart-seq3


title: WT_9G4

description: Library name: WT_9G4_S2


title: 0007929AFF

description: Library name: 0007929AFF


title: Control_1_2h


title: mesc_rad21_depletion_IAA-6h_143, Smart-seq3


title: Non Selected Lymph Node VDJ

city: Boston

first: Michael

last: Tolstorukov

address: 360 Longwood Avenue

department: Informatics

institute: Dana Farber Cancer Institute

description:
Library name: NS_LN_TCR
10X Genomics

data_processing:
Gene expression and TCR fastq files were processed using CellRanger version 3.1.0 (Zheng et al) using the GRCm38 reference databases.
Assembly: GRCM38
Supplementary files format and content: CellRanger count filtered_feature_bc_matrix
Supplementary files format and content: CellRanger vdj clonotypes.csv and filtered_contig_annotations.csv

source_name: Mediastinal lymph nodes

extract_protocol:
Cell density was adjusted to analyze 10,000 cells per sample. Single-cell gene expression (scRNA-seq) was performed using Chromium Single Cell 5’ Library and Gel Bead Kit with V(D)J enrichment kit (10x Genomics).
Gel Bead-in-Emulsion reverse transcription (GEM-RT) reaction, clean-up, and PCR amplification were performed to obtain cDNA for library generation. Single cell sequencing libraries were generated using 5’GEXv1 according to manufacturer’s protocol. Libraries were uniquely indexed for multiplexed sequencing. Libraries were single i7-indexed using the Chromium i7 Multiplex kit (indices listed in table). Following isolation and clean-up of library DNA, concentration and fragment size were assessed using an Agilent Bioanalyzer and quantification by Qubit analysis (ThermoFisher).

value: Mediastinal lymph nodes

value: T Cells


title: HexB_10D1

description: Library name: HexB_10D1_S9


title: 0007929AF5

description: Library name: 0007929AF5

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


title: D4 Lymph Node VDJ

description:
Library name: D4_LN_TCR
10X Genomics


title: WT_9C2

description: Library name: WT_9C2_S1


title: 0007929AD0

description: Library name: 0007929AD0


title: WT_9C1

description: Library name: WT_9C1_S1


title: mesc_rad21_depletion_IAA-6h_142, Smart-seq3


title: 0007929B06

description: Library name: 0007929B06


title: 0007929ACD

description: Library name: 0007929ACD


title: mesc_rad21_depletion_IAA-6h_141, Smart-seq3


title: 0007929ADD

description: Library name: 0007929ADD


title: WT_13D2

description: Library name: WT_13D2_S7


title: mesc_rad21_depletion_IAA-6h_140, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_145, Smart-seq3


title: WT_9G1

description: Library name: WT_9G1_S1


title: Non Selected Lymph Node Gene Expression

description:
Library name: NS_LN_GEX
10X Genomics


title: D2 Lymph Node VDJ

description:
Library name: D2_LN_TCR
10X Genomics


title: D2 Lymph Node Gene Expression

description:
Library name: D2_LN_GEX
10X Genomics


title: mesc_rad21_depletion_IAA-6h_139, Smart-seq3


title: D4 Lymph Node Gene Expression

description:
Library name: D4_LN_GEX
10X Genomics


title: NP Lymph Node VDJ R2

description:
Library name: NP2_TCR
10X Genomics


title: WT_13B2

description: Library name: WT_13B2_S6


title: 0007929AC8

description: Library name: 0007929AC8


title: mesc_rad21_depletion_IAA-6h_138, Smart-seq3


title: WT_13D1

description: Library name: WT_13D1_S6


title: 0007929AAC

description: Library name: 0007929AAC


title: WT_13B1

description: Library name: WT_13B1_S6


title: mesc_rad21_depletion_IAA-6h_137, Smart-seq3


title: 0007929ABE

description: Library name: 0007929ABE


title: WT_12D2

description: Library name: WT_12D2_S5


title: 0007929AA4

description: Library name: 0007929AA4


title: mesc_rad21_depletion_IAA-6h_135, Smart-seq3


title: 0007929AA5

description: Library name: 0007929AA5


title: 0007929A96

description: Library name: 0007929A96


title: WT_12D1

description: Library name: WT_12D1_S5


title: NP Lymph Node VDJ R1

description:
Library name: NP1_TCR
10X Genomics


title: NP Lymph Node Gene Expression R1

description:
Library name: NP1_GEX
10X Genomics


title: mesc_rad21_depletion_IAA-6h_136, Smart-seq3


title: 0007929A8E

description: Library name: 0007929A8E


title: mesc_rad21_depletion_IAA-6h_134, Smart-seq3


title: NP Lymph Node Gene Expression R2

description:
Library name: NP2_GEX
10X Genomics


title: 0007929A8A

description: Library name: 0007929A8A


title: B2905_C23

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

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

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

source_name: Clonal subline C23

extract_protocol: Twenty-four exome libraries were prepared by Genomics Lab using Agilent SureSelectXT Mouse All Exon target enrichment kit. Samples were pooled and run on ten lanes of HiSeq3000 with Illumina Hiseq 3000/4000 chemistry

tag: strain

value: HGF-tg


title: WT_12B2

description: Library name: WT_12B2_S5


title: mesc_rad21_depletion_IAA-6h_132, Smart-seq3

last: Xie

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University


title: B2905_C24

source_name: Clonal subline C24


title: mesc_rad21_depletion_IAA-6h_133, Smart-seq3


title: 00079299F3

description:
Library name: 00079299F3
Original label before genotype mismatch fix: 0007929A87


title: WT_11F3

description: Library name: WT_11F3_S4


title: B2905_C22

source_name: Clonal subline C22


title: WT_11D3

description: Library name: WT_11D3_S3


title: B2905_C21

source_name: Clonal subline C21


title: 0007929A79

description: Library name: 0007929A79


title: WT_12B1

description: Library name: WT_12B1_S4


title: mesc_rad21_depletion_IAA-6h_130, Smart-seq3


title: WT_11D5

description: Library name: WT_11D5_S4


title: WT_11A2

description: Library name: WT_11A2_S3


title: B2905_C20

source_name: Clonal subline C20


title: 0007929A6C

description: Library name: 0007929A6C


title: WT_11A1

description: Library name: WT_11A1_S3


title: B2905_C19

source_name: Clonal subline C19


title: B2905_C18

source_name: Clonal subline C18


title: mesc_rad21_depletion_IAA-6h_131, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_129, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_128, Smart-seq3


title: 0007929A44

description: Library name: 0007929A44


title: 0007929A87

description:
Library name: 0007929A87
Original label before genotype mismatch fix: 00079299F3


title: WT_10A7

description: Library name: WT_10A7_S2


title: WT_10A6

description: Library name: WT_10A6_S2


title: mesc_rad21_depletion_IAA-6h_126, Smart-seq3

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


title: mesc_rad21_depletion_IAA-6h_127, Smart-seq3


title: WT6

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

data_processing:
RNAseq mapping pipeline (trimming, fastQC, STAR mapping, Salmon quantification, multiQC report)
DESeq2 downstream analysis (exclusion of ko4)
Assembly: GRCm39 release 107
Supplementary files format and content: Salmon.csv : raw counts matrix
Supplementary files format and content: Table_Counts.csv : DESeq2 normalized counts matrix

source_name: intestinal epithelial cells (IECs)

extract_protocol:
Total RNAs were extracted by using the E.Z.N.A.® Total RNA Kit (Omega Bio-tek) according to the manufacturer’s protocol.Total RNAs before elution were treated with TURBOTMDNase (ThermoFisher Scientific, AM2238). RNA integrity was verified on a Bioanalyser 2100 with RNA 6000 Nano chips (Agilent technologies). RNA integrity number score was above 9 for every sample.
Libraries were prepared using Truseq® stranded mRNA Sample Preparation Kits (Illumina) following manufacturer’s instructions. Libraries were validated using QIAxcel Advanced System and quantified by qPCR using the KAPA library quantification kit.

value: intestinal epithelial cells (IECs)

value: AOM DSS


title: B2905_C15

source_name: Clonal subline C15


title: 00079299EE

last: Munro

address: 9500 Gilman Drive

institute: UC San Diego

description: Library name: 00079299EE


title: 0007929A68

description: Library name: 0007929A68


title: B2905_C16

source_name: Clonal subline C16


title: WT5


title: mesc_rad21_depletion_IAA-6h_125, Smart-seq3

city: Beijing

first: Xiaoliang

source_name: mouse embryonic stem cell


title: 0007929A14

description: Library name: 0007929A14

source_name: whole brain hemisphere


title: 00079299E6

description: Library name: 00079299E6


title: mesc_rad21_depletion_IAA-6h_123, Smart-seq3


title: WT4


title: mesc_rad21_depletion_IAA-6h_124, Smart-seq3


title: B2905_C14

source_name: Clonal subline C14


title: 00079FB742

description:
Library name: 00079FB742
Original label before genotype mismatch fix: 00079299D9


title: B2905_C13

source_name: Clonal subline C13


title: WT3


title: mesc_rad21_depletion_IAA-6h_122, Smart-seq3


title: 00079299D7

description: Library name: 00079299D7


title: mesc_rad21_depletion_IAA-6h_121, Smart-seq3


title: B2905_C12

source_name: Clonal subline C12


title: WT2


title: B2905_C11

source_name: Clonal subline C11


title: mesc_rad21_depletion_IAA-6h_120, Smart-seq3


title: WT1


title: 00079299D6

description: Library name: 00079299D6


title: 00079299B5

description: Library name: 00079299B5


title: mesc_rad21_depletion_IAA-6h_119, Smart-seq3


title: B2905_C10

source_name: Clonal subline C10


title: KO6

value: STARD7 KO


title: B2905_C9

source_name: Clonal subline C9


title: mesc_rad21_depletion_IAA-6h_117, Smart-seq3


title: B2905_C7

source_name: Clonal subline C7


title: B2905_C8

source_name: Clonal subline C8


title: 0007929917

description: Library name: 0007929917


title: 0007929938

description: Library name: 0007929938


title: KO4


title: B2905_C6

source_name: Clonal subline C6


title: mesc_rad21_depletion_IAA-6h_115, Smart-seq3


title: B2905_C17

source_name: Clonal subline C17


title: KO5


title: KO2


title: B2905_C5

source_name: Clonal subline C5


title: mesc_rad21_depletion_IAA-6h_116, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_118, Smart-seq3


title: 00079298E2

description: Library name: 00079298E2


title: mesc_rad21_depletion_IAA-6h_114, Smart-seq3


title: mesc_rad21_depletion_IAA-6h_113, Smart-seq3


title: B2905_C3

source_name: Clonal subline C3


title: 00079298DD

description: Library name: 00079298DD


title: KO3

source_name: intestinal epithelial cells (IECs)


title: 0007929956

description: Library name: 0007929956


title: B2905_C4

source_name: Clonal subline C4


title: 00079298F7

description: Library name: 00079298F7


title: B2905_C2

source_name: Clonal subline C2


title: 00079298B3

description: Library name: 00079298B3


title: mesc_rad21_depletion_IAA-6h_112, Smart-seq3

source_name: mouse embryonic stem cell


title: ovarian cells, Hh,Ltop4.4, replicate 2

city: Marburg

first: Katja

last: Rust

address: Emil-Mannkopff-Str. 2

country: Germany

institute: Phillips-University Marburg

description: Library name: Hh,Ltop4.4-2

data_processing:
Demultiplexing was performed according to sample specific barcodes.
Assembly: dmel_r6.32
Supplementary files format and content: comma separated file, RNA counts
Supplementary files format and content: comma separated file, cell names, dataset, genotype, UMAP coordinates

organism: Drosophila melanogaster

source_name: adult ovary

growth_protocol: 109-30-Gal4;tub-Gal80ts females were crossed to the respective males (w1118 or UAS-Hh;UAS-RasV12 or UAS-Hh;UAS-Ltop4.4) and offspring was reared at 18°C. Adult F1 offspring was then shifted to 29°C for 5 days and fed wet yeast until dissection.

extract_protocol:
Ovaries were dissected within 30 min in ice cold Schneider’s Insect Medium with 10% FBS and 167 mg/ml insulin on an ice pack. We enriched for the younger, non-vitellogenic stages of the ovary using micro-scissors. Tissue was transferred to an eppendorf tube containing ice-cold Cell Dissociation Buffer (Thermo Fisher Scientific #13151014) and rinsed once with the buffer. Dissociation was performed at RT in Cell Dissociation Buffer with 4 mg/ml elastase (Worthington Biochemical LS002292) and 2.5 mg/ml collagenase (Invitrogen # 17018-029) with nutation and regular pipetting with a P200 to aid tissue dissociation. After 20 min the solution was passed through a 50 μm filter  and the solution incubated for additional 10 min before passage through a 30 μm filter. Enzymes were quenched by adding 500 μl of dissection solution and cells were centrifuged for 5 min at 4 °C and 3500 rcf. Cells were washed in dissection solution and centrifuged again before being resuspended in ice-cold 200 μl PBS with 0.04% ultrapure BSA (Thermo Fisher Scientific AM2616). Dissociation was verified and cells were counted using a cell counting chamber and the solution adjusted to 1000 cells per μl before subjection to single-cell RNA-sequencing.
The library was constructed using the Chromium Next GEM Single-Cell 3´LT Kit v3.1 (10× Genomics) according to manufacturer's instructions.

value: adult ovary

value: adult ovarian cells

value: temp shifted from 18 to 29°C for 5d and fed with wet yeast


title: ovarian cells, Hh,RasV12, replicate 2

description: Library name: Hh,RasV12-2


title: KO1


title: ovarian cells, Hh,Ltop4.4, replicate 1

description: Library name: Hh,Ltop4.4-1


title: 00079298A9

city: La Jolla

first: Daniel

description: Library name: 00079298A9

source_name: whole brain hemisphere

value: whole brain hemisphere


title: B2905_C1

source_name: Clonal subline C1


title: LV, RZ, patch, 4wks, rep2

city: Suita

first: Kosuke

last: Torigata

state: Osaka

address: 2-2 Yamadaoka

department: Graduate School of Medicine, Department of Cardiovascular Surgery

institute: The University of Osaka

description:
Library name: LV_RZ_patch_4wks_rep2
uninjured remote myocardium

data_processing:
Whole transcriptome sequencing was applied to the RNA samples on an Illumina HiSeq 2500 platform in a 75-base single-end mode. Illumina Casava ver.1.8.2 software was used for base calling. Obtained reads were quality filtered by FastQC ver. 0.7.2 and Trim Galore ver. 0.5.0, then aligned to in silico combined human (GRCh38)-rat (Rattus norvegicus, Rnor_6.0) by HISAT2 ver.2.1.026 with default setting as described previously. The uniquely aligned reads were annotated to genes and calculated read-count by featureCounts function of Subread ver. 1.6.248 for human and rat, respectively. For data deposition, reads were aligned to the rat reference genome (Rnor_6.0), and uniquely mapped reads (MAPQ >= 60) were retained to ensure species-specificity. Gene-level count tables used in the published analyses are provided as processed data files to ensure reproducibility of the reported results.
Assembly: rat (Rattus norvegicus, Rnor_6.0) and human (GRCh38)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: left ventricular

growth_protocol: Six to eight week old male nude rats (F344/NJcl-rnu/rnu) were anesthetized with endotracheal intubation using isoflurane (2%). A left thoracotomy was performed, and the left anterior descending artery was permanently ligated with a 5-0 nylon monofilament. Successful ligation was confirmed by the color change of the anterior left ventricular (LV) wall. After each surgery, all rats were allowed to recover in individual temperature-controlled cages. These rats were maintained in a specific pathogen-free room in our animal facility on a 12-hour light/12-dark cycle with free access to food and water. Rats were euthanized and the heart specimens were harvested at predetermined timepoints.

extract_protocol:
Each snap frozen heart tissue (timepoint; Day3, 1wk, 4wks, tissue; IZ, BZ, RZ for each group) were homogenized in Buffer RLT by disrupter MS-100R (TOMY). Total-RNA was extracted using RNeasy Mini Kit (74106, Qiagen) according to the manufacturer’s instructions. The quality of purified RNAs was assessed by Bioanalyzer 2100 (Agilent Technologies).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (RS-122-2101, Illumina) according to the manufacturer’s instructions.

treatment_protocol: After 1 week of LAD-ligation, rats underwent re-thoracotomy for the exposed pericardial space and were then randomly assigned into a control (without patch transplantation) group or a patch transplanted group. hiPSC-derived CM patches were transplanted over the epicardium of the anterior and lateral left-ventricular walls. hiPSC-derived CM patches were spread manually to cover both infarct and border areas of the heart and fixed by covering with pericardial membrane. The chest was closed with a 4-0 nylon monofilament.

value: left ventricular

tag: condition

value: myocaridal infarction

value: hiPSC-derived CM patch

value: 4 weeks


title: ovarian cells, Hh,RasV12, replicate 1

description: Library name: Hh,RasV12-1


title: mesc_rad21_depletion_IAA-6h_111, Smart-seq3

value: mouse embryonic stem cell

value: IAA (6h)


title: mesc_rad21_depletion_IAA-6h_108, Smart-seq3


title: 0007929894

description: Library name: 0007929894


title: 00079298B1

description: Library name: 00079298B1


title: LV, RZ, patch, 4wks, rep3

description:
Library name: LV_RZ_patch_4wks_rep3
uninjured remote myocardium


title: mesc_rad21_depletion_IAA-6h_110, Smart-seq3


title: ovarian cells, w1118, replicate 2

description: Library name: w1118-2


title: mesc_rad21_depletion_IAA-6h_109, Smart-seq3


title: LV, RZ, patch, 4wks, rep1

description:
Library name: LV_RZ_patch_4wks_rep1
uninjured remote myocardium


title: ovarian cells, w1118, replicate 1

description: Library name: w1118-1


title: mesc_rad21_depletion_IAA-6h_107, Smart-seq3


title: LV, RZ, control, 4wks, rep3

description:
Library name: LV_RZ_control_4wks_rep3
uninjured remote myocardium

value: untransplanted sham control


title: 00078A2648

description: Library name: 00078A2648


title: mesc_rad21_depletion_IAA-6h_106, Smart-seq3


title: 00078A25EF

description: Library name: 00078A25EF


title: 0007928310

description: Library name: 0007928310