title: S87_P16_utA

city: Boston

first: Amanda

middle: Joy

last: Kedaigle

address: 1325 Boylston St

department: Systems Biology - Molecular Innovation

institute: Decibel Therapeutics

data_processing:
Cellranger (10X Genomics) was used to demultiplex & align the data - v3.1.0
Assembly: mm10
Supplementary files format and content: h5 files containing gene expression values as UMI counts (filtered by CellRanger to remove empty droplets)

source_name: Utricle

growth_protocol: 4-10-week-old CD-1 wild type mice (#022, Charles River; #030, Envigo) were used.

extract_protocol:
Utricles from 5 mice were microdissected in ice-cold DMEM/F12 media and collected in separate tubes, on ice. The pooled tissue was then placed in a pre-warmed dissociation buffer of EBSS solution containing 33 units of papain (Worthington Biochemical), 1.67 mM L-cysteine, 0.83 mM EDTA, 15 mM HEPES, and 10 Kunitz/ml DNase I. The tissues were incubated for 45 – 60 min at 37°C, triturating with a 200 μL pipette every 10 min for tissue dissociation.  At the end of the 37°C incubation, the solution was passed through a 25G needle a few times to ensure a single cell suspension. An equal volume of DMEM/F12 media containing 20% ovomucoid protease inhibitor (Worthington Biochemical) was added, and the dissociated cells were passed through a 40 μm filter (pluriSelect) to remove debris. The cells were pelleted at 300 g for 5 min, washed twice with DMEM/F12 containing 0.04% BSA, and then pelleted and resuspended in the DMEM/F12 with BSA solution. The cells were counted with the Luna-FL automated fluorescence cell counter using an AO/PI viability assay (Logos Biosystems) and immediately loaded on the 10x Chromium controller (10x Genomics) for partitioning single cells into droplets.
For each sample, 15,000 cells were loaded in one or two channel(S) of a Chromium Chip (10x Genomics). 3’ v3 chemistry was used to profile all other samples. cDNA and gene expression libraries were generated according to the manufacturer's instructions (10x Genomics). cDNA and gene expression library fragment sizes were assessed with a DNA High Sensitivity Bioanalyzer Chip (Agilent). cDNA and gene expression libraries were quantified using the Qubit dsDNA High Sensitivity assay kit (Thermo Fisher Scientific). Gene expression libraries were multiplexed and sequenced on the Novaseq 6000 (Illumina) with the following read structure: Read 1: 28 cycles, Read 2: 72 - 100 cycles, Index Read 1: 8 cycles.

treatment_protocol: N/A for these samples.

value: Utricle

tag: strain

tag: age


title: S87_P16_utB

status: Public on Sep 24 2024

type: SRA

state: MA

country: USA

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: tissue


title: Control, differentiated enteroids, rep-1

city: Nashville

first: Izumi

last: Kaji

state: TN

address: Rm 10465H, MRB IV

department: Surgery

institute: Vanderbilt University Medical Center

description:
gene_fpkm.xls
gene_count.xls

library_source: transcriptomic

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP).
Alignments were parsed using Tophat program.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene (Mortazavi et al. 2008).
Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: Excel includes comparisons of differential expression genes by FPKM

source_name: Jejunum organoids

growth_protocol: Isolated crypts of mouse jejunum were embeded in BME-R1 and organoids were grown in Mouse IntestiCult Medium (Stem Cell Technology). Organoids were passaged twice before the tamoxifen induction.

extract_protocol:
Following the differentiation, enteroids were placed in Organoid Harvesting Solution (3700-100-01; Cultrex) for 1 hr at 4˚C. Enteroids were washed with PBS and centrifuged. Enteroid pellets were immersed in TRIzol reagent (15596026; Invitrogen) supplemented with glycogen (G1767; Sigma Aldrich)
Libraries were prepared by Novogene Corporation Inc. (Sacramento, CA). mRNA is purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA is first fragmented randomly by addition of fragmentation buffer. Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified doublestranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization(1). In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.

treatment_protocol: G519R and iKO enteorids were treated with 4-OH-tamoxifen (1 µM) to induce Cre recombinase 24 hours before switching medium to the differentiation medium. Compound-1 (100 nM) or vehicle (PBS) was added into differentiation medium for 2 days.

tag: cell type

value: Jejunum organoids

tag: genotype

value: Control

tag: treatment


title: S86_P10_utB


title: S87_P12_utB


title: 438-18_35958_MesLN_ADT

city: Beaverton

first: Benjamin

middle: N

last: Bimber

state: OR

address: 505 NW 185th Ave

data_processing:
CellRanger/Seurat
Assembly: Mmul_10
Supplementary files format and content: Count Matrix / Seurat Object

molecule: polyA RNA

organism: Macaca mulatta

source_name: MesLN

extract_protocol:
N/A
10x Genomics 5' Chemistry

tag: cdna library_id

tag: subjectid

value: MesLN

value: Primary cells

tag: plateid

tag: hto


title: 438-17_35958_Spleen_HTO

source_name: Spleen

value: Spleen


title: 438-17_35958_Spleen_GEX


title: 438-17_35958_Spleen_ADT


title: S80_E14_vestB


title: S87_P12_utA


title: S86_P10_utA


title: S80_E14_vestA


title: S80_P6_utA


title: 438-17_35958_Liver_TCR

source_name: Liver

value: Liver


title: 438-17_35958_Liver_HTO


title: S80_P6_utB


title: S80_P4_ut


title: S80_P5_utB


title: S80_P3_utB


title: 438-16_35958_PBMC_ADT

source_name: PBMC

value: PBMC


title: S80_P5_utA


title: 438-17_35958_Liver_ADT


title: 438-16_35958_PBMC_TCR


title: S80_P2_utA


title: 438-16_35958_Bone marrow_TCR

source_name: Bone marrow

value: Bone marrow


title: 438-16_35958_Bone marrow_HTO


title: S80_P1_utB


title: 438-17_35958_Spleen_TCR


title: S80_P1_utA


title: 438-17_35958_Liver_GEX


title: S80_P0_utB


title: 438-14_35317_Spleen_TCR


title: S80_P3_utA


title: 438-14_35317_Spleen_HTO


title: S80_E18_utB


title: 438-16_35958_PBMC_HTO


title: S80_E18_utA


title: 438-14_35317_Liver_TCR


title: S80_P0_utA


title: S80_E16_utB


title: 438-14_35317_Spleen_ADT


title: S80_E16_utA


title: S63_P6_ut


title: 438-14_35317_Liver_HTO


title: 438-16_35958_Bone marrow_ADT


title: 438-14_35317_Liver_GEX


title: S63_P1_Ut


title: 438-13_35317_PBMC_HTO


title: S63_E18_Ut


title: S63_P12_Ut


title: CAR-Trem2-Ms

city: Chongqing

first: Wen

last: Zeng

address: Gaotanyan street

department: Department of Cell Biology

country: China

institute: Army Medical University

description: scRNA-seq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skin

extract_protocol:
A single cell sequencing library was constructed using a 10X standard kit for sequencing. In short, three tissue samples from the same group were placed in RPMI medium on an ice dish and cut into small pieces (2-4 mm). Then, small pieces of tissue were added to the RPMI/enzyme mixture (Miltenyi Biotec), further transferred to a mild MACS C tube containing the RPMI/enzyme mixture, connected to the sleeve of the MACS Octo dissociator, and dissociated using a standard program. After the program was completed, the cells were centrifuged at 300g, resuspended in RPMI, passed through a 70 micron filter, and repeated centrifugation. Centrifuge resuspended at 100 µ l RPMI. The number of living cells was measured using Luna FL dual fluorescence cell counters (Logos Biosystems) to obtain the expected number of cells of 10000 for each channel.
The samples were loaded onto a 10x G chip and run on a Chromium controller system (10x Genomics) to construct a single cell oil-in-water structure. Further library construction was carried out using the Chromium Single Cell 3 ′ v.3.1 kit (10x Genomics, no. PN-1000121), and the constructed library was sequenced using the NovaSeq 6000 platform.

treatment_protocol: mouse skin tissues after wound at 14 days and treatment with mMN-loaded CAR-Ms and CAR-Trem2-Ms.

value: skin

value: skin cell

value: skin tissues at 14 days after treatment with mMN-loaded CAR-Trem2-Ms


title: 438-13_35317_PBMC_GEX


title: S63_E15_Ut


title: 438-13_35317_PBMC_ADT


title: 438-13_35317_Bone marrow_HTO


title: POD

description: scRNA-seq

value: skin tissues at 14 days after POD


title: 438-13_35317_Bone marrow_TCR


title: CAR-Trem2-Ms rep3

data_processing:
reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2.2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
Assembly: mm10
Supplementary files format and content: raw counts, TPM for each Sample

growth_protocol: 7 days of continuous culture in complete DMEM with 20 ng/mL M-CSF

extract_protocol:
RNA was harvested using Trizol reagent kit
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: the lentivirus infection plasmid was added to create CAR-Ms. After induction with 1 μM VD3 for 24 h, and CAR-Trem2-Ms were sorted by flow cytometry.

tag: cell line

value: macrophage


title: 438-13_35317_Bone marrow_GEX


title: 438-14_35317_Spleen_GEX


title: CAR-Trem2-Ms rep2

value: the lentivirus infection plasmid was added to create CAR-Ms. After induction with 1 μM VD3 for 24 h, and CAR-Trem2-Ms were sorted by flow cytometry.


title: 438-13_35317_PBMC_TCR


title: 438-14_35317_Liver_ADT


title: 438-13_35317_Bone marrow_ADT


title: 438-12_34268_PLN_HTO

source_name: PLN

value: PLN


title: CAR-Trem2-Ms rep1


title: 438-12_34268_PLN_TCR


title: CAR-Ms rep3

value: WT

value: the lentivirus infection plasmid was added to create CAR-Ms


title: 438-12_34268_PLN_ADT


title: CAR-Ms rep2


title: CAR-Ms rep1


title: 438-12_34268_PLN_GEX


title: CAR-Ms

description: scRNA-seq

value: skin tissues at 14 days after treatment with mMN-loaded CAR-Ms


title: BAT, CP2-KO +PRDM16, rep3

city: Taipei

first: Yi-Shuian

last: Huang

address: 128 Sec. 2, Academia Rd. Nankang

country: Taiwan

institute: Institute of Biomedical Sciences, Academia Sinica

description:
KP76
Gene_Count_3333.csv

data_processing:
The sequence was determined using Illumina's sequencing-by-synthesis (SBS) technology (Illumina, USA). Sequencing data (FASTQ reads) were generated using Welgene Biotech's pipeline based on Illumina's basecalling program bcl2fastq v2.20.
Both adaptor clipping and sequence quality trimming were performed using Trimmomatic v0.36 with a sliding-window approach.
Alignment Tool: HISAT2
Assembly: Mouse (GRCm38.p6)
Supplementary files format and content: Read count of genes

source_name: BAT (brown adipose tissue)

growth_protocol: Male mice were housed in a 12-h light-dark (lights on from 8:00 to 20:00) room with ad libitum access to food (9% chow diet) and water.

extract_protocol:
Total RNA was extracted by using TRIzol following the manufacturer's protocol (Thermo Fisher Scientific).
All RNA sample preparation procedures were carried out according to the Illumina's official protocol. SureSelect XT HS2 mRNA Library Preparation kit (Agilent, USA) was used for library construction followed by AMPure XP beads (Beckman Coulter, USA) size selection.

treatment_protocol: BATs from male CPEB2-WT and -KO mice were collected at the age of 21-25 weeks. For resuce groups, 16-week-old male mice received 2 × 10^10 vg (vector genome) recombinant AAV in 30 μl PBS which was injected triangularly into interscapular BAT (10 μl per site). After 9 weeks (age of 25 weeks), BATs were collected and trimmed for RNA isolation.

value: BAT (brown adipose tissue)

value: PRDM16 virus


title: BAT, CP2-KO +PRDM16, rep1

description:
KP59
Gene_Count_3333.csv


title: BAT, CP2-KO +GFP, rep2

description:
KG64
Gene_Count_3333.csv

value: GFP virus


title: 438-11_34268_Spleen_TCR

value: Spleen

value: Primary cells


title: BAT, CP2-KO +GFP, rep1

description:
KG57
Gene_Count_3333.csv


title: 438-11_34268_Spleen_GEX


title: 438-12_34268_MesLN_GEX

value: MesLN


title: BAT, CP2-WT +PRDM16, rep3

description:
WP80
Gene_Count_3333.csv


title: 438-12_34268_MesLN_TCR


title: BAT, CP2-WT +PRDM16, rep1

description:
WP63
Gene_Count_3333.csv


title: BAT, CP2-WT +GFP, rep2

description:
WG65
Gene_Count_3333.csv


title: 438-12_34268_MesLN_HTO


title: 438-11_34268_Liver_HTO

value: Liver


title: BAT, CP2-WT +GFP, rep1

description:
WG56
Gene_Count_3333.csv


title: BAT, CP2-KO +PRDM16, rep2

description:
KP65
Gene_Count_3333.csv


title: 438-11_34268_Spleen_ADT


title: BAT, CP2-KO +GFP, rep3

description:
KG69
Gene_Count_3333.csv


title: 438-12_34268_MesLN_ADT


title: BAT, CP2-KO, rep5

description:
KO_297
Gene_Count_Young55.csv


title: 438-10_34268_PBMC_TCR

value: PBMC


title: BAT, CP2-KO, rep3

description:
KO_205
Gene_Count_Young55.csv


title: 438-11_34268_Liver_ADT


title: 438-10_34268_PBMC_ADT


title: 438-10_34268_PBMC_GEX


title: BAT, CP2-KO, rep2

description:
KO_192
Gene_Count_Young55.csv


title: 438-11_34268_Liver_GEX


title: BAT, CP2-KO, rep4

description:
KO_295
Gene_Count_Young55.csv


title: 438-10_34268_Bone marrow_TCR

value: Bone marrow


title: BAT, CP2-WT +PRDM16, rep2

description:
WP64
Gene_Count_3333.csv


title: BAT, CP2-KO, rep1

description:
KO_191
Gene_Count_Young55.csv


title: BAT, CP2-WT, rep5

description:
WT_204
Gene_Count_Young55.csv


title: BAT, CP2-WT +GFP, rep3

description:
WG89
Gene_Count_3333.csv


title: 438-10_34268_Bone marrow_HTO


title: 438-11_34268_Liver_TCR


title: 438-10_34268_PBMC_HTO


title: 438-10_34268_Bone marrow_GEX


title: 438-10_34268_Bone marrow_ADT


title: BAT, CP2-WT, rep4

description:
WT_194
Gene_Count_Young55.csv


title: S80_P2_utB

value: Utricle


title: BAT, CP2-WT, rep2

description:
WT_125
Gene_Count_Young55.csv


title: BAT, CP2-WT, rep3

description:
WT_193
Gene_Count_Young55.csv


title: 438-1_34854_PBMC_TCR


title: BAT, CP2-WT, rep1

description:
WT_121
Gene_Count_Young55.csv


title: 438-1_34854_PBMC_GEX


title: In vivo cristae, IDPN only, 4wk, rep2

description: 10x Genomics

data_processing:
Cellranger (10X Genomics) was used to demultiplex & align the data - v3.0.2 for Explants, v3.1.0 for invivo
Assembly: mm10 plus custom transgene (WPRE sequence)
Supplementary files format and content: h5 files containing gene expression values as UMI counts (filtered by CellRanger to remove empty droplets)

source_name: Mouse utricle

extract_protocol:
Samples were processed fresh on the day of collection.  For explant studies, 7-8 utricles were used per treatment group.  For in vivo studies, cristae and utricles from 6 treated ears were microdissected in ice-cold DMEM/F12 media and collected in separate tubes, on ice. The pooled tissue was then placed in a pre-warmed dissociation buffer of EBSS solution containing 33 units of papain (Worthington Biochemical), 1.67 mM L-cysteine, 0.83 mM EDTA, 15 mM HEPES, and 10 Kunitz/ml DNase I. The tissues were incubated for 45 – 60 min at 37°C, triturating with a 200 μL pipette every 10 min for tissue dissociation.  At the end of the 37°C incubation, the solution was passed through a 25G needle a few times to ensure a single cell suspension. An equal volume of DMEM/F12 media containing 20% ovomucoid protease inhibitor (Worthington Biochemical) was added, and the dissociated cells were passed through a 40 μm filter (pluriSelect) to remove debris. The cells were pelleted at 300 g for 5 min, washed twice with DMEM/F12 containing 0.04% BSA, and then pelleted and resuspended in the DMEM/F12 with BSA solution. The cells were counted with the Luna-FL automated fluorescence cell counter using an AO/PI viability assay (Logos Biosystems) and immediately loaded on the 10x Chromium controller (10x Genomics) for partitioning single cells into droplets.
For each sample, 15,000 cells were loaded in one channel of a Chromium Chip (10x Genomics). 3’ v2 chemistry was used to profile one explant study and 3’ v3 chemistry was used to profile all other samples. cDNA and gene expression libraries were generated according to the manufacturer's instructions (10x Genomics). cDNA and gene expression library fragment sizes were assessed with a DNA High Sensitivity Bioanalyzer Chip (Agilent). cDNA and gene expression libraries were quantified using the Qubit dsDNA High Sensitivity assay kit (Thermo Fisher Scientific). Gene expression libraries were multiplexed and sequenced on the Novaseq 6000 (Illumina) with the following read structure: Read 1: 28 cycles, Read 2: 72 - 100 cycles, Index Read 1: 8 cycles.

value: Mouse utricle

tag: timepoint

value: 4 wk

value: IDPN


title: In vivo cristae, GFAP-ATOH1, 4wk, rep2

description: 10x Genomics

value: IDPN and GFAP-ATOH1


title: 438-1_34854_PBMC_ADT


title: 438-1_34854_PBMC_HTO


title: 438-16_35958_PBMC_GEX


title: 438-1_34854_Bone marrow_TCR


title: In vivo utricle,GFAP-ATOH1, 4wk

description: 10x Genomics


title: In vivo utricle, IDPN only, 4wk, rep1

description: 10x Genomics


title: In vivo utricle, IDPN only, 4wk, rep2

description: 10x Genomics


title: 438-1_34854_Bone marrow_GEX


title: In vivo cristae, Untreated, 4wk

description: 10x Genomics

value: Untreated


title: In vivo cristae, GFAP-ATOH1, 4wk, rep1

description: 10x Genomics


title: In vivo cristae, IDPN only, 4wk, rep1

description: 10x Genomics


title: 438-1_34854_Bone marrow_ADT


title: 566-7_37274_Lung-R_TCR

source_name: Lung-R

value: Lung-R


title: 566-7_37274_Lung-R_HTO


title: In vivo utricle, Untreated, 2wk

description: 10x Genomics

value: 2 wk


title: 566-7_37274_Lung-R_GEX


title: In vivo utricle, GFAP-ATOH1, 2wk

description: 10x Genomics


title: 566-6_37274_Lung-L_TCR

source_name: Lung-L

value: Lung-L


title: 566-6_37274_Lung-L_HTO


title: 566-6_37274_Lung-L_GEX


title: In vivo utricle, IDPN only, 2wk

description: 10x Genomics


title: 566-7_37274_Lung-R_ADT


title: In vivo cristae, IDPN only, 2wk

description: 10x Genomics

source_name: Mouse cristae

value: Mouse cristae


title: 566-6_37274_Lung-L_ADT


title: Explant, RLBP1-ATOH1, day 20, rep1

description: 10x Genomics

source_name: Cultured utricle

value: Cultured utricle

value: day 20

value: Gentamycin and RLBP1-ATOH1


title: In vivo cristae, Untreated, 2wk

description: 10x Genomics


title: 565-7_36740_Lung-R_TCR

value: Primary cells


title: Explant, RLBP1-ATOH1, day 12, rep2

description: 10x Genomics

value: day 12


title: In vivo cristae, GFAP-ATOH1, 2wk

description: 10x Genomics


title: 565-7_36740_Lung-R_HTO


title: 565-7_36740_Lung-R_GEX


title: Explant, GFAP-ATOH1, day 12, rep3

description: 10x Genomics

value: Gentamycin and GFAP-ATOH1


title: Perio1

city: Sendai

first: Shigeki

last: Suzuki

state: Miyagi

address: 4-1, Seiryo-machi, Aoba-ku

country: Japan

institute: Tohoku University Graduate School of Den

data_processing:
Bioinformatics analysis using Gene Ontology of Biological Processes was performed using the BGI proprietary Dr. TOM software and BGI in-house customized data-mining system
Assembly: hg38
Supplementary files format and content: Excel file includes TPM and FPKM values for each Sample

organism: Homo sapiens

source_name: gingival fibroblasts isolated from periodontitis patient

growth_protocol: PD1and GF1/2 cells were maintained in DMEM supplemented with 10%fetal bovine serum (FBS) and antibiotics in humidified atmosphere  with 5% CO2 at 37℃

extract_protocol:
Both PD1and GF1/2 cells were washed twice with PBS after confluence, and cells were collected.
The RNA integrity was measured using an Agilent 2100 bioanalyzer. RNA sequencing (RNA-seq) was performed using BGI Genomics

value: gingiva

value: gingival fibroblasts

tag: condition

value: periodontitis patient

tag: culture type

value: normal culture


title: 565-7_36740_Lung-R_ADT


title: Fibro2_3

source_name: gingival fibroblasts isolated from idiopathic gingival fibromatosis patient 2


title: 438-1_34854_Bone marrow_HTO

value: Bone marrow


title: Fibro2_2

value: idiopathic gingival fibromatosis patient 2


title: Fibro2_1


title: Explant, CMV-ATOH1, day 20, rep1

description: 10x Genomics

value: Gentamycin and CMV-ATOH1


title: 565-6_36740_Lung-L_TCR


title: Fibro1_3

source_name: gingival fibroblasts isolated from idiopathic gingival fibromatosis patient 1


title: Perio3


title: Fibro1_2

value: idiopathic gingival fibromatosis patient 1


title: Fibro1_1


title: Explant, GFAP-ATOH1, day 20, rep1

description: 10x Genomics


title: 565-6_36740_Lung-L_HTO


title: Explant, CMV-ATOH1, day 12, rep3

description: 10x Genomics


title: 565-6_36740_Lung-L_ADT


title: Explant, GFAP-ATOH1, day 12, rep2

description: 10x Genomics


title: Perio2


title: lung 456 CD44/SSEA4+ cells

city: minneappolis

first: LiBang

last: yang

state: MN

address: 420 delaware st

department: medicine

institute: University of minnesota

data_processing:
Sequencing reads were mapped to the rat reference genome (Homo_sapiens.GRCh38.100) using Hisat2.
Genes differentially expressed were determined using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: Homo_sapiens.GRCh38.100
Supplementary files format and content: RawCountHenke26.txt

source_name: lung

growth_protocol: DMEM with 10% FBS

extract_protocol:
Qiagen mRNA extraction kit and protocol
illumina kit and protocol

value: lung

value: IPF

value: primary

value: stemlike


title: lung 442 CD44/SSEA4+ cells


title: Explant, RLBP1-ATOH1, day 12, rep1

description: 10x Genomics

value: Cultured utricle


title: 565-6_36740_Lung-L_GEX

value: Lung-L


title: lung 458 CD44/SSEA4+ cells


title: 564-7_36127_Lung-R_TCR

value: Lung-R

value: Primary cells


title: Explant, CMV-ATOH1, day 12, rep2

description: 10x Genomics

value: day 12


title: lung 215 CD44/SSEA4+ cells

value: control


title: 564-7_36127_Lung-R_HTO


title: lung 210 CD44/SSEA4+ cells


title: Explant, GFAP-ATOH1, day 12, rep1

description: 10x Genomics

value: Gentamycin and GFAP-ATOH1


title: lung 205 CD44/SSEA4+ cells


title: Explant, CMV-ATOH1, day 12, rep1

description: 10x Genomics


title: lung 424 CD44/SSEA4+ cells


title: lung 445 CD44/SSEA4+ cells


title: 564-7_36127_Lung-R_GEX


title: 438-16_35958_Bone marrow_GEX


title: lung 459 CD44/SSEA4+ cells


title: lung 190 CD44/SSEA4+ cells


title: 564-7_36127_Lung-R_ADT


title: HU190_LQ101b_c.MYC_spCas9.CBE.ND4.fused.with.TX2_rp2

city: Beijing

first: Jinchun

last: Wu

address: No. 5, Yiheyuan street

institute: Peking University

description: Cells were transfected by mito-CBE targeting ND4(L1397C 12mg+12mg, fused with TX2 (nuclease dead) )  and spCas9 targeting c-MYC (15 mg) for 3 days

library_source: genomic

data_processing:
Followed the PEM-Q pipeline described in Liu et al., 2021
Assembly: hg38
Supplementary files format and content: tab file containing mtDNA integration events on c.MYC locus

molecule: genomic DNA

source_name: cultured cell

growth_protocol: HEK-293T cells (a gift from Dr. Frederick Alt Lab, Harvard Medical School) were cultured in Dulbecco′s modified Eagle′s medium (Gibco) with 10% Fetal Bovine Serum (ExCell Bio), Penicillin-Streptomycin Solution(cytiva), and L-Glutamine Solution(Sigma) at 37 °C with 5% CO2.

extract_protocol:
Followed the PEM-seq protocol that described in Yin et al., 2019.
Followed the PEM-seq protocol that described in Yin et al., 2019.

treatment_protocol: The genomic DNA DNA were extracted for PEM-seq library construction.

value: wild type

tag: clone


title: Explant, CMV-ATOH1, day 7, rep1

description: 10x Genomics

value: day 7


title: HU190_LQ101a_c.MYC_spCas9.CBE.ND4.fused.with.TX2_rp1


title: HU190_LQ101c_c.MYC_spCas9.CBE.ND4.fused.with.TX2_rp3

description: Cells were transfected by mito-CBE targeting ND4(L1397C 12mg+12mg, fused with TX2 (nuclease dead) )  and spCas9 targeting  c-MYC (15 mg) for 3 days


title: Explant, GFAP-ATOH1, day 7, rep1

description: 10x Genomics


title: 564-6_36127_Lung-L_HTO


title: HU190_LQ100d_c.MYC_spCas9.CBE.ND4.MTS.TX2_rp3

description: Cells were transfected by mito-CBE targeting ND4(L1397C 12mg+12mg, with MTS-TX2 (nuclease dead) )  and spCas9 targeting c-MYC (15 mg) for 3 days


title: 564-6_36127_Lung-L_TCR


title: HU190_LQ099c_c.MYC_spCas9.CBE.ND4.fused.with.TX2_rp2

description: Cells were transfected by mito-CBE targeting ND4(L1397C 12mg+12mg, fused with TX2)  and spCas9 targeting c-MYC (15 mg) for 3 days


title: HU190_LQ099d_c.MYC_spCas9.CBE.ND4.fused.with.TX2_rp3

description: Cells were transfected by mito-CBE targeting ND4(L1397C 12mg+12mg, fused with TX2)  and spCas9 targeting  c-MYC (15 mg) for 3 days


title: AmU90_Cerebell

city: Durham

first: Matthew

last: Tegowski

state: NC

address: 153 Research Dr.

department: Biochemistry

institute: Duke University

data_processing:
Adapter sequences were trimmed with Flexbar (3.0.3) and aligned to the mm10 genome using STAR 2.7.5. The STAR aligner was also used to mark PCR duplicates
Bullseye (https://github.com/mflamand/Bullseye) was used to generate a nucleotide representation matrix using parseBAM.pl. Marked PCR duplicates were ignored at this step.
m6A sites were called using Bullseye (Find_edit_site.pl) with 1%-95% C2U, a minimum of 25 reads of coverage at the site, %C2U at least 1.5-fold higher in APOBEC1-YTH than APOBEC1-YTHmut regions, occuring within a GAC or RAC motif, and in at least 2 biological replicates
Assembly: mm10
Supplementary files format and content: Text files consisting of called m6A methylation sites within each brain region.  (The APOBEC1-YTHmut is used as a negative control to eliminate background editing driven by APOBEC1, but that are not dependent on the YTH domain. So the list of identified sites in the processed data represent the sites in APOBEC1-YTH samples, compared to the APOBEC1-YTHmut samples.)

source_name: Whole Cerebellum

extract_protocol:
Mice were euthanized, and then tissues dissected and immediately flash frozen in liquid nitrogen. Then samples were homogenized in Trizol and total RNA was extracted according to manufacturer's protocol.
900ng of total RNA was used as input for library preparation using the UltraII Directional Library Preparation Kit (NEB) using the PolyA Selection Module

treatment_protocol: Mice were treated with 20mg/kg tamoxifen every 24 hours for 5 days via intraperitoneal injection. Samples were collected 7 days after last treatment

value: Whole Cerebellum

value: Tamoxifen


title: AmU72_Cerebell


title: 564-6_36127_Lung-L_GEX


title: HU190_LQ100b_c.MYC_spCas9.CBE.ND4.MTS.TX2_rp1

description: Cells were transfected by mito-CBE targeting ND4(L1397C 12mg+12mg, with MTS TX2 (nuclease dead) )  and spCas9 targeting c-MYC (15 mg) for 3 days


title: HU190_LQ098d_c.MYC_spCas9.CBE.ND4.MTS.TX2_rp3

description: Cells were transfected by mito-CBE targeting ND4(L1397C 12mg+12mg, with MTS-TX2)  and spCas9 targeting c-MYC (15 mg) for 3 days


title: HU190_LQ098b_c.MYC_spCas9.CBE.ND4.MTS.TX2_rp2


title: AU156_Cerebell


title: HU190_LQ099b_c.MYC_spCas9.CBE.ND4.fused.with.TX2_rp1


title: AU154_Cerebell


title: HU190_LQ100c_c.MYC_spCas9.CBE.ND4.MTS.TX2_rp2

description: Cells were transfected by mito-CBE targeting ND4(L1397C 12mg+12mg, with MTS-TX2 (nuclease dead)  )  and spCas9 targeting c-MYC (15 mg) for 3 days


title: 564-6_36127_Lung-L_ADT


title: HU190_LQ095d_c.MYC_spCas9.CBE.ND4.fused.with.TX1_rp3

description: Cells were transfected by mito-CBE targeting ND4(L1397C 12mg+12mg, fused with TX1)  and spCas9 targeting c-MYC (15 mg) for 3 days


title: 563-7_33156_Lung-R_HTO


title: HU190_LQ098a_c.MYC_spCas9.CBE.ND4.MTS.TX2_rp1


title: AmU92_Cerebell


title: HU190_LQ095b_c.MYC_spCas9.CBE.ND4.fused.with.TX1_rp2


title: AU123_Cerebell


title: 563-7_33156_Lung-R_TCR


title: HU190_LQ095a_c.MYC_spCas9.CBE.ND4.fused.with.TX1_rp1


title: 563-7_33156_Lung-R_GEX


title: HU190_LQ094b_c.MYC_spCas9.CBE.ND4.MTS.TX1_rp2

description: Cells were transfected by mito-CBE targeting ND4(L1397C 12mg+12mg, with MTS-TX1)  and spCas9 targeting c-MYC (15 mg) for 3 days


title: AU122_Cerebell


title: HU190_LQ094c_c.MYC_spCas9.CBE.ND4.MTS.TX1_rp3


title: 563-7_33156_Lung-R_ADT


title: HU190_LQ094a_c.MYC_spCas9.CBE.ND4.MTS.TX1_rp1


title: 438-11_34268_Spleen_HTO

source_name: Spleen

value: Spleen


title: HU190_LQ093c_c.MYC_spCas9.CBE.ND4_rp2

description: Cells were transfected by  mito-CBE targeting ND4(L1397C 12mg+12mg)  and spCas9 targeting c-MYC (15 mg) for 3 days


title: 563-6_33156_Lung-L_TCR


title: 563-6_33156_Lung-L_HTO


title: HU190_LQ093d_c.MYC_spCas9.CBE.ND4_rp3


title: AmU90_Hippo

source_name: Whole Hippocampus

value: Whole Hippocampus


title: AU156_Hippo


title: HU190_LQ092d_c.MYC_spCas9_rp3

description: Cells were transfected by spCas9 targeting c-MYC (15mg) for 3 days


title: HU190_LQ093b_c.MYC_spCas9.CBE.ND4_rp1


title: HU190_LQ092c_c.MYC_spCas9_rp2


title: HU190_LQ092b_c.MYC_spCas9_rp1


title: AU154_Hippo


title: 563-6_33156_Lung-L_ADT


title: HU188_HU189_LQ086d_ND4_CBE.ND4.fused.with.TX2_rp3

description: Cells were transfected by mito-CBE targeting ND4(L1397C 12mg+12mg, fused with TX2)  for 3 days

data_processing:
Followed the PEM-Q pipeline described in Liu et al., 2021
Assembly: hg38
Supplementary files format and content: tab file containing tranlocation events on ND4 locus

treatment_protocol: The nuclear DNA DNA were extracted for PEM-seq library construction.


title: AU122_Hippo


title: 488-9_38090_PBMC_TCR

source_name: PBMC

value: PBMC


title: AU123_Hippo


title: HU188_HU189_LQ085d_ND4_CBE.ND4.MTS.TX2_rp3

description: Cells were transfected by mito-CBE targeting ND4(L1397C 12mg+12mg, with MTS-TX2)  for 3 days


title: HU188_HU189_LQ086b_ND4_CBE.ND4.fused.with.TX2_rp2


title: 563-6_33156_Lung-L_GEX


title: HU188_HU189_LQ085c_ND4_CBE.ND4.MTS.TX2_rp2


title: HU188_HU189_LQ082c_ND4_CBE.ND4.fused.with.TX1_rp3

description: Cells were transfected by mito-CBE targeting ND4(L1397C 12mg+12mg, fused with TX1)  for 3 days


title: 488-9_38090_PBMC_GEX


title: AmU92_Hippo


title: HU188_HU189_LQ085b_ND4_CBE.ND4.MTS.TX2_rp1


title: 488-9_38090_PBMC_HTO


title: HU188_HU189_LQ082b_ND4_CBE.ND4.fused.with.TX1_rp2


title: AmU92_Ctx

source_name: Whole Cortex

value: Whole Cortex


title: 488-9_38090_PBMC_ADT


title: HU188_HU189_LQ081a_ND4_CBE.ND4.MTS.TX1_rp1

description: Cells were transfected by mito-CBE targeting ND4(L1397C 12mg+12mg, with MTS-TX1)  for 3 days


title: HU188_HU189_LQ086a_ND4_CBE.ND4.fused.with.TX2_rp1


title: HU188_HU189_LQ080d_ND4_CBE.ND4_rp3

description: Cells were transfected by  mito-CBE targeting ND4(L1397C 12mg+12mg)  for 3 days


title: 488-9_38089_PBMC_HTO


title: AU156_Ctx


title: HU188_HU189_LQ081b_ND4_CBE.ND4.MTS.TX1_rp2


title: 488-9_38089_PBMC_TCR


title: HU188_HU189_LQ080c_ND4_CBE.ND4_rp2


title: AU154_Ctx


title: HU188_HU189_LQ079c_ND4_unedited_rp3


title: 488-9_38089_PBMC_GEX


title: HU188_HU189_LQ080b_ND4_CBE.ND4_rp1


title: AU123_Ctx


title: HU188_HU189_LQ079b_ND4_unedited_rp2


title: HU188_HU189_LQ079a_ND4_unedited_rp1


title: AU122_Ctx


title: HU188_HU189_LQ082a_ND4_CBE.ND4.fused.with.TX1_rp1


title: AmU90_Ctx


title: ECs, S3

city: Tianjin

first: Yi

last: Lei

address: Qixiangtai street NO.22

institute: Tianjin Medical University General Hospital

data_processing:
To identify DEGs, the expression level of each transcript was calculated according to the TPM method, RSEM was used to quantify gene abundance. We use DESeq2 and functional-enrichment analysis including Wiki pathway at P-value <0.05.
Assembly: hg38
Supplementary files format and content: tab-delimited text file included raw counts for each sample

source_name: retina

extract_protocol:
Cells were harvested for RNA extraction using TRIzol reagent (SIGMA, #101254514). RNA concentration was determined by spectrophotometry using a Nanodrop ND-1000 (Thermo Fisher Scientific, USA).
RNA libraries for RNA-seq were prepared following Illumina Stranded mRNA Prep, Ligation using iug of totel RNA

value: retina

value: HRCECs

value: EC

value: siYAP/TAZ


title: 488-9_38089_PBMC_ADT


title: KO2-LSC RNA

city: wuhan

first: Haojian

last: Zhang

state: Hubei

address: Donghu Rd

department: Medical Research Institute

institute: Wuhan university

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low quality sequances, then pseudoaligned to GRCm38 whole transcriptome using hisat2(version 2.1.0) with default parameters
FeatureCounts were used to summary raw counts from bam files
differential genes' expression  were performed by  DESeq2
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow

extract_protocol:
Total RNA of TAMs were extracted with Trizol and mRNA were isolated with Oligo dT beads.
Libraries were prepared according to VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (Part# NR601). Briefly, mRNA was interrupted with metal ions in interrupted buffer , cDNA synthesis using random primers for reverse transcription of mRNA. The cDNA strands in the hybrid double strands were digested by RNaseH to synthesize cDNA complementary strands for cDNA second strand synthesis. Repair sticky ends were repaired to blunt ends   add A-tail,and connection connector.After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: bone marrow

tag: disease state

value: leukemia


title: 488-9_35547_PBMC_TCR

value: Primary cells


title: 488-9_35547_PBMC_HTO


title: ECs, S2


title: cells stimulated with eltrombopag (10000 ng/mL), scRNA-seq

city: Machida

first: Naoki

last: Onoda

state: Tokyo

address: 3-6-6, Asahi-machi

institute: Kyowa Kirin Co., Ltd.

description: 10x Genomics

data_processing:
Sequencing results (BCL files) were converted into FASTQ files and mapped to the human reference genome (GRCh38) using Cell Ranger software (v. 6.0.0; 10× Genomics).
Assembly: GRCh38
Supplementary files format and content: Hierarchical Data Format 5

source_name: cord blood-derived CD34+ cells

growth_protocol: Four batches of frozen human cord blood–derived CD34+ cells were thawed and mixed to prepare sufficient amount of cells. These cells were seeded at a density of 2×105 cells/mL in StemSpanTM Serum-Free Medium II.

extract_protocol:
For each sample, the quantity and viability of cells were confirmed, and the absence of aggregated cells or debris was microscopically observed. Single cells were encapsulated into emulsion droplets using Chromium Connect (10× Genomics).
Single-cell RNA-seq libraries were constructed using Chromium Next GEM Automated Single Cell 3′ Library and Gel Bead Kit v. 3.1 (10× Genomics), Chromium Next GEM Automated Chip G Single Cell Kit (10× Genomics), and Dual Index Kit TT Set A (10× Genomics) following the manufacturer’s instructions (CG000286_Rev_E).

treatment_protocol: TPOR agonists were added to the cells, after which the cells were incubated for 2 days at 37℃ and 5% CO2.

value: cord blood-derived CD34+ cells

value: Eltrombopag 10000 ng/mL


title: HU188_HU189_LQ081c_ND4_CBE.ND4.MTS.TX1_rp3

value: wild type


title: AmU72_Ctx


title: KO1-LSC RNA


title: cells stimulated with eltrombopag (1000 ng/mL), scRNA-seq

description: 10x Genomics

value: Eltrombopag 1000 ng/mL


title: ECs, S1


title: 488-9_35547_PBMC_GEX


title: ECs, C3

value: siCtrl


title: WT2-LSC RNA

value: WT


title: cells stimulated with romiplostim (10 ng/mL), scRNA-seq

description: 10x Genomics

value: Romiplostim


title: 488-9_35547_PBMC_ADT


title: cells stimulated with recombinant human TPO (10 ng/mL), scRNA-seq

description: 10x Genomics

value: rhTPO


title: ECs, C2


title: cells treated with vehicle, scRNA-seq

description: 10x Genomics

value: Vehicle


title: ECs, C1


title: KO2-LSC-H3K27ac

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using hisat2(version 2.1.0) default parameters
peaks were called using Macs2 with the following setting:q-value 0.01
deeptools were used to generate bigwig files
Assembly: mm10
Supplementary files format and content: bigwig files were generated using Bamcoverage; Scores represent RPKM

extract_protocol:
For histone ChIP-seq, lysates were clarified from MNase digested nuclei and histone-DNA complexes were isolated with H3K4me1,H3K4me3 or H3K27Ac antibodies.
Illumina libraries were constructed using a modified custom paired-end protocol. In brief, samples were end-repaired (1*T4 DNA ligase buffer, 0.4 mM dNTP mix, 2.25 U T4 DNA polymerase, 0.75 U Klenow DNA polymerase and 7.5 U T4 polynucleotide kinase; 30 min at 21–25 C), A-tailed (1*NEB buffer 2, 0.4 mM dNTPs and 3.75 U of Klenow (exo-); 30 min at 37 C) and ligated (1*rapid DNA ligation buffer, 1 mM Illumina PE adapters and 1,600 U DNA ligase; 1–8 h at 21–25 C). Ligated fragments were amplified using indexed primers (Illumina) for 8–12 PCR cycles. DNA was purified with 1.8 volume KAPA DNA purification beads between each step.

tag: antibody


title: KO1-LSC-H3K27ac


title: ECs, P_4

data_processing:
To identify DEGs, the expression level of each transcript was calculated acordng to the TPMmethod, RSEM was used to quantify gene abundance. We use DESeq2 and functional-enrichment analysis including Wiki pathway at P-value <0.05.
Assembly: hg38
Supplementary files format and content: tab-delimited text file included raw counts for each sample

value: PUGNAc


title: 488-8_36767_Spleen_HTO

value: Spleen


title: Patient_13-HGSC

type: genomic

city: Moscow

first: Pavel

last: Grebnev

email: grepavel@gmail.com, pgrebnev@cspfmba.ru

state: --- Select One ---

address: Pogodinskaya Street, 10, bld. 1, 119121 Moscow, Russia

country: Russia

institute: CSP

hyb_protocol: Nanostring CNV Hybridization Protocol (MAN-10093-01 (December 2020))

scan_protocol: Scanned with Nanostring nCounter FLEX

data_processing: nSolver 4.0. Background substraction with mean of Negative Controls. Normalization with Codeset Content, using mean. Fold change estimation with reference from nanostring.

source_name: ovary

extract_protocol: DNA was isolated from samples of fresh frozen tissues using the QIAamp DNA Mini Kit (Qiagen)

value: high-grade serous carcinoma

tag: Stage

value: IIIC

tag: t

tag: n

value: x

tag: m

tag: ihc ki-67

value: high

value: mut type (+++)


title: WT2-LSC-H3K27ac

tag: tissue

value: bone marrow

value: leukemia

tag: genotype


title: 488-8_36767_Spleen_ADT

tag: cdna library_id

tag: subjectid

tag: cell type

value: Primary cells


title: ECs, P_3

value: retina

tag: cell line

value: HRCECs

value: EC

tag: treatment


title: 488-8_36767_Spleen_GEX

tag: plateid

tag: hto


title: WT1-LSC-H3K27ac

value: WT


title: WT1-LSC RNA


title: ECs, P_2


title: KO2-LSC-H3K9me2


title: ECs, P_1


title: 488-8_36767_PLN_TCR

source_name: PLN

value: PLN


title: 488-8_36767_PLN_HTO


title: Patient_13-NT

value: normal tissue

tag: age


title: KO1-LSC-H3K9me2

tag: disease state


title: Patient_12-HGSC


title: ECs, C_3

value: control


title: 488-8_36767_PLN_GEX


title: ECs, C_2


title: Patient_11-HGSC

value: IIа

value: mut type (-)


title: Patient_12-NT


title: 488-8_36767_Spleen_TCR

value: Spleen


title: WT2-LSC-H3K9me2

tag: antibody


title: ECs, C_1


title: Patient_11-NT

tag: Stage


title: Patient_10-HGSC

value: high-grade serous carcinoma

value: IVB

tag: t


title: WT1-LSC-H3K9me2


title: KO2-LSC-H3K4me2


title: Patient_10-NT

tag: n

value: x

value: high


title: 488-8_36767_MesLN_HTO

source_name: MesLN

value: MesLN


title: MYC1_mitoTALEN_ND4_Rep3

description: Cells were transfected by mito-TALEN targeting ND4(L1397N 12ug+12ug) and spCas9 targeting Myc1 (15 ug) for 2 days

data_processing:
none provided
Assembly: hg38
Supplementary files format and content: bed file containing DNA sequences combined by R1 and R2 fastq files

extract_protocol: Followed the  target sequencing protocol that described in Yin et al., 2019.

treatment_protocol: The genomic DNA were extracted for target sequencing library construction.

value: wild type


title: MYC1_mitoTALEN_ND4_Rep2


title: WT2-LSC-H3K4me2

value: bone marrow

value: leukemia


title: 488-8_36767_MesLN_GEX

data_processing:
CellRanger/Seurat
Assembly: Mmul_10
Supplementary files format and content: Count Matrix / Seurat Object

value: Primary cells


title: MYC1_mitoTALEN_ND4_Rep1


title: Patient_9-HGSC

value: IIIC

tag: m


title: WT1-LSC-H3K4me2

value: WT


title: KO1-LSC-H3K4me2


title: 488-8_36767_PLN_ADT

value: PLN


title: 488-8_36767_MesLN_ADT


title: MYC1_control_mitoTALEN_Rep3

description: Cells were transfected by spCas9 targeting Myc1 (15ug) for 2 days


title: MYC1_control_mitoTALEN_Rep1


title: KO1-LSC-H4K4me1


title: 488-8_36767_Bone marrow_HTO

source_name: Bone marrow

value: Bone marrow


title: KO2-LSC-H4K4me1


title: Patient_8-HGSC

value: IIIС

tag: ihc ki-67

value: mut type (+++)


title: Patient_9-NT

tag: tissue

value: normal tissue

value: mut type (-)


title: 488-8_36767_Bone marrow_GEX


title: Patient_7-HGSC

value: high-grade serous carcinoma

value: IIIc


title: Patient_8-NT

value: x


title: WT2-LSC-H4K4me1

tag: genotype


title: 488-8_36767_Bone marrow_ADT

tag: cdna library_id


title: 488-8_36767_MesLN_TCR

tag: subjectid


title: MYC1_PQ_Rep3

description: Cells were transfected by spCas9 targeting Myc1 (15ug) for 2 days, treated with 500 uM Paraquat for 2 days after medium change


title: Patient_7-NT

value: high


title: WT1-LSC-H4K4me1


title: 488-7_36686_Spleen_TCR

value: Spleen

tag: cell type


title: Patient_6-HGSC

value: IVB


title: MYC1_PQ_Rep2

tag: cell line

value: wild type


title: 488-8_36767_Bone marrow_TCR


title: Patient_6-NT


title: MYC1_control_mitoTALEN_Rep2


title: 488-7_36686_Spleen_HTO


title: MYC1_CCCP_Rep3

description: Cells were transfected by spCas9 targeting Myc1 (15ug) for 2 days, treated with 10uM CCCP for 1 day after medium change, and replaced with fresh medium for another day


title: KO1-LSC-input

value: bone marrow

value: leukemia


title: 488-7_36686_Spleen_GEX

value: Primary cells


title: Patient_5-HGSC

value: IIIa


title: MYC1_CCCP_Rep2


title: WT2-LSC-input

value: WT


title: 488-7_36686_Spleen_ADT


title: Patient_5-NT


title: WT1-LSC-input


title: MYC1_CCCP_Rep1


title: 488-7_36686_PLN_TCR

value: PLN


title: KO2-LSC ATAC

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using bowtie2 with default parameters
Peaks were called by MACS2
Normalized ATAC signal was generated by deeptools
Assembly: mm10
Supplementary files format and content: bigwig files were generated by deeptools

extract_protocol:
DNA
leukemia stem cells were pelleted by centrifugation at 500g for 5 min at 4 °C. All supernatant was removed carefully. Fifty microliters of transposase mixture (25μl of 2× TD buffer, 1μl of Tn5, 0.5μl of 1% digitonin, and 23.5μl of nuclease-free water) were added to the cells, and the pellet was disrupted by pipetting. Transposition reactions were incubated at 37 °C for 30 min with agitation at 300 rpm. Transposed DNA was purified using a QIAGEN MinElute Reaction Cleanup kit (28204), and purified DNA was eluted in 10 μl of elution buffer (10 mM Tris-HCl, pH 8).


title: KO1-LSC ATAC


title: MYC1_control_mito_stress_Rep2


title: MYC1_control_mito_stress_Rep3


title: 488-7_36686_PLN_HTO


title: Patient_4-NT

value: IIIC


title: 488-7_36686_PLN_GEX


title: Patient_3-HGSC

value: mut type (+++)


title: KO2-LSC-input


title: MYC1_PQ_Rep1


title: WT2-LSC ATAC


title: MYC1_control_mito_stress_Rep1


title: 488-7_36686_PLN_ADT


title: WT1-LSC ATAC


title: Patient_2-HGSC

value: Ia


title: HU109_JC280c_c.MYC_spCas9.Paraquat_rp3

data_processing:
Followed the PEM-Q pipeline described in Liu et al., 2021
Assembly: hg38
Supplementary files format and content: tab file containing mtDNA integration events on c-MYC locus

extract_protocol: Followed the PEM-seq protocol that described in Yin et al., 2019.


title: 488-7_36686_MesLN_TCR

extract_protocol:
N/A
10x Genomics 5' Chemistry

value: MesLN


title: Patient_4-HGSC

value: high-grade serous carcinoma


title: LL_3

city: Harbin

first: Linyong

last: Shen

state: Heilongjiang

address: No.600, Changjiang Road, Xiangfang District

institute: Northeast Agricultural University

data_processing:
This sequencing was conducted by Frasergen (Wuhan, China), yielding an average sequencing depth of 231.99X per sample. To construct a more comprehensive Hi-C interaction matrix, we amalgamated Hi-C data from three biological replicates each line. The data was processed using the Juicer pipeline (https://github.com/aidenlab/juicer/). Contact matrices at varying resolutions (1, 5, 10, 25, 100, and 500 kb) were normalized using the KR algorithm.
Assembly: GRCg7b genome
Supplementary files format and content: .hic

organism: Gallus

source_name: Abdominal fat tissue

extract_protocol:
Cells were treated with formaldehyde to fix the conformation of DNA. After cell lysis, cross-linked DNA was digested with restriction enzymes to generate sticky ends.
Biotinylated DNA was captured using streptavidin magnetic beads. The DNA fragments were then end-repaired, adenylated, and ligated to adapters. The optimal number of PCR amplification cycles was evaluated before purifying the library, completing the library preparation.

value: Abdominal fat tissue


title: Patient_2-NT

value: normal tissue

value: mut type (-)


title: 488-7_36686_MesLN_HTO


title: HU109_JC280b_c.MYC_spCas9.Paraquat_rp2


title: LL_2


title: 488-7_36686_MesLN_GEX


title: HU109_JC280a_c.MYC_spCas9.Paraquat_rp1


title: LL_1


title: Patient_1-EC

value: endometrioid carcinoma

value: IIc

value: high


title: Patient_1-NT


title: HU109_JC279c_c.MYC_spCas9.CCCP_rp3

value: wild type


title: 488-7_36686_Bone marrow_HTO

value: Bone marrow


title: Patient_3-NT


title: 488-7_36686_Bone marrow_TCR

value: Primary cells


title: Sample_22_SH-SY5Y differentiated samples [22_GTCCGC_L008]

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

country: United Kingdom

institute: Newcastle University

data_processing:
Quality assessment with FastQC Version 0.11.2
Read trimming with FASTX-Trimmer from FASTX-Toolkit version 0.0.13
TPM abundances calculated using Salmon, with index created from GRCh37 release 75 transcripts
Genome_build: GRCh37 release 75
Supplementary_files_format_and_content: A matrix of TPM values for each transcript as a tab delimited text file. TPMs in the matrix are not normalized.

source_name: RNA from SH-SY5Y differentiated samples

growth_protocol: SH-SY5Y cells  were cultured in Dulbecco's modified Eagle's medium (DMEM)/F12:1 with GlutaMAX™ (Gibco, Paisley, UK) supplemented with foetal calf serum (10%), penicillin (100 IU. ml− 1) and streptomycin (100 IU.ml− 1)

extract_protocol:
Extraction of total RNA from samples was performed using Rneasy mini kit from Qiagen according to the manufacturers instructions.
Illumina's stranded mRNA kit

treatment_protocol: SH-SY5Y cells were differentiated by incubation with 1 micromolar 9-cis retinoic acid for 7 days.

value: differentiated

tag: treatment


title: FL_2


title: Sample_24_SH-SY5Y differentiated samples [24_TTAGGC_L008]

value: 1 micromolar 9-cis retinoic acid for 7 days.


title: 488-7_36686_Bone marrow_ADT

tag: plateid


title: HU109_JC278b_c.MYC_spCas9_control.for.MTstress_rp2


title: Sample_20_SH-SY5Y undifferentiated samples [20_CGTACG_L008]

source_name: RNA from SH-SY5Y undifferentiated samples

value: undifferentiated


title: Sample_21_SH-SY5Y differentiated samples [21_GAGTGG_L008]


title: 488-7_36686_MesLN_ADT

tag: hto


title: FL_3


title: HU109_JC278a_c.MYC_spCas9_control.for.MTstress_rp1


title: 488-6_37826_Spleen_TCR

value: Spleen


title: Sample_19_SH-SY5Y undifferentiated samples [19_GGCTAC_L008]


title: Spleen from normal fish, 5 days of recovery, rep4

city: Wuhan

first: Yong

last: Long

address: No. 7 Donghu South Rd.

institute: Institute of Hydrobiology, Chinese Academy of Sciences

data_processing:
The raw reads were preprocessed using fastp (v0.23.2) with default parameters to trim the adaptors and filter the low quality reads.
The clean read pairs were mapped to the reference transcriptome sequences of LMB (NCBI accession: GCF_014851395.1, accessed on October 3, 2023) using salmon (v1.10.0) with default settings.
Gene transcriptional abundance (transcript per million, TPM) was calculated using the R package tximport (v1.26.1).
Assembly: GCF_014851395.1
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

organism: Micropterus salmoides

growth_protocol: Largemouth bass fingerlings (body weight 11.99 ± 4.34 g, standard length 10.32 ± 3.02 cm) were obtained from a breeding farm in Daye, China. Before transportation, the fish were raised in a 5 m × 3 m × 1 m concrete pond and fed with a commercial extruded feed to satiation twice daily.

extract_protocol:
Total RNA of the tissue samples was extracted using the TRIzol™ Reagent from Thermo Fisher Scientific (Waltham, MA, USA).
For library construction, 1 mg of DNase I-treated total RNA of each sample was used for sequencing library construction. The NEBNext® rRNA Depletion Kit was used for rRNA depletion. The RNAs were purified by using the Agencourt RNAClean XP Beads from Beckman Coulter. RNA fragmentation, first strand and second strand cDNA synthesis and double-stranded cDNA end repair were performed using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of the NEBNext Multiplex Oligos for Illumina. Finally, the Q5 Hot Start HiFi PCR Master Mix (NEB) was used for PCR enrichment of the adaptor-ligated DNA. Concentration and quality of the libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies.

treatment_protocol: For transportation, 125 fish were put into a 54 cm × 38 cm × 32 cm plastic box filled with 30 L water. The boxes were put into the trunk of a car and 500 fish assigned into 4 boxes were transported each time. During transportation, the water was continuously aerated using a rechargeable inflation pump. After 4 hours of transportation, the fish in each box were transferred into an indoor plastic aquarium (diameter 100 cm, height 125 cm, filled with 600 L water) for recovery. The aquaria were supplied with recycled water and the room temperature was controlled at 28 °C using an air conditioner. The fish were checked every 12 hour and the dead ones were removed and counted. The fish were not fed during the experiment.

tag: time point

value: After 5 days of recovery


title: 488-6_37826_Spleen_HTO


title: Spleen from normal fish, 5 days of recovery, rep2


title: HU109_JC279b_c.MYC_spCas9.CCCP_rp2


title: HU109_JC279a_c.MYC_spCas9.CCCP_rp1


title: 488-6_37826_Spleen_GEX


title: Sample_18_SH-SY5Y undifferentiated samples [18_GTGGCC_L007]


title: Spleen from normal fish, 5 days of recovery, rep1


title: HU110_JC285a_c.MYC_spCas9.TALEN.ND4_rp1


title: Sample_17_SH-SY5Y undifferentiated samples [17_ACTTGA_L007]


title: HU110_JC285b_c.MYC_spCas9.TALEN.ND4_rp2


title: Liver from normal fish, 5 days of recovery, rep4

source_name: Liver

value: Liver


title: 488-6_37826_Spleen_ADT


title: FL_1


title: Liver from normal fish, 5 days of recovery, rep3


title: 488-7_36686_Bone marrow_GEX


title: HU109_JC278c_c.MYC_spCas9_control.for.MTstress_rp3

source_name: cultured cell


title: HU110_JC285c_c.MYC_spCas9.TALEN.ND4_rp3


title: Spleen from normal fish, 5 days of recovery, rep3


title: Sample_23_SH-SY5Y differentiated samples [23_ACTGAT_L008]


title: HU110_JC284c_c.MYC_spCas9_control.for.TALEN.ND4_rp3


title: 488-6_37826_PLN_TCR

value: PLN


title: CAR-T cells + melanoma PDOTS + PD-1 blockade cultured for 24h

first: Russell

last: Jenkins

address: 55 Fruit Street

institute: Masschussetts General Hospital

description: 10x Genomics NextGEM 5 prime v2

data_processing:
Read alignment and quantification was performed using CellRanger (v8.0.0) and a custom GRCh38 (Ensembl 112) human genome reference with the full CAR plasmid construct included
Samples were aggregated, filtered, and normalized using Cumulus (v1.4.3) (29), removing barcodes with genes less than 150 or greater than 5000 genes. Barcodes containing > 20% mitochondrial genes were also filtered
Counts were normalized to 10,000 per cell and then log transformed
Assembly: custom GRCh38 (Ensembl 112) human genome reference with the full CAR plasmid construct included
Supplementary files format and content: filtered h5 files output from CellRanger

source_name: patient-derived organotypic tumor spheroids (melanoma, 10214) + B7-H3.CAR-T cells

extract_protocol:
B7-H3.CAR-T cells and cryopreserved PDOTS (melanoma, 10214) were thawed and rested media to serve as baseline (0 hour) controls.  Remaining PDOTS were prepared in collagen for 3D culture.  B7-H3.CAR-T cells (E:T 1:1) were added with or without TBK1i (1 μM), 250 μg/mL pembrolizumab (Meck Sharp&Dobine, NDC 000^-3026-01), or the combination, compared to untreated control for 24 hours before PDOTS +/- CAR-T were collected for processing.
10x Chromium Next GEM single cell 5’ kit v2 (1000263)

value: CAR-T cells + PD-1 blockade


title: CAR-T cells + melanoma PDOTS + TBK1 inhibitor cultured for 24h

description: 10x Genomics NextGEM 5 prime v2

value: patient-derived organotypic tumor spheroids (melanoma, 10214) + B7-H3.CAR-T cells

value: CAR-T cells + TBK1 inhibitor


title: HU110_JC284b_c.MYC_spCas9_control.for.TALEN.ND4_rp2


title: Liver from normal fish, 5 days of recovery, rep2


title: CAR-T cells + melanoma PDOTS + TBK1 inhibitor + PD-1 blockade cultured for 24h

description: 10x Genomics NextGEM 5 prime v2

value: CAR-T cells + TBK1 inhibitor + PD-1 blockade


title: 488-6_37826_PLN_HTO


title: Liver from normal fish, 5 days of recovery, rep1


title: CAR-T cells at baseline

description: 10x Genomics NextGEM 5 prime v2

source_name: B7-H3.CAR-T cells

value: B7-H3.CAR-T cells

value: untreated


title: 488-6_37826_PLN_GEX


title: Spleen from abnormal fish, 5 days of recovery, rep4

source_name: Spleen


title: HU110_JC284a_c.MYC_spCas9_control.for.TALEN.ND4_rp1


title: JC289c_ND5.1_DdCBE_rp1

description: Cells were transfected by DdCBE targeting ND5.1 (L1397N) for 3 days.

data_processing:
Followed the PEM-Q pipeline described in Liu et al., 2021.
Assembly: hg38
Supplementary files format and content: Tab-delimited files containing translocation events on ND5.1 locus.
Library strategy: PEM-seq

growth_protocol: HEK-293T cells (a gift from Dr. Frederick Alt Lab, Harvard Medical School) were cultured in Dulbecco′s modified Eagle′s medium (Gibco) with 10% Fetal Bovine Serum (ExCell Bio), Penicillin-Streptomycin Solution(cytiva), and L-Glutamine Solution (Sigma) at 37 °C with 5% CO2.

treatment_protocol: The nuclear DNA were extracted for PEM-seq library construction.


title: CAR-T cells + melanoma PDOTS cultured for 24h

description: 10x Genomics NextGEM 5 prime v2

value: CAR-T cells


title: Spleen from abnormal fish, 5 days of recovery, rep3


title: JC289b_ND5.1_DdCBE_rp1

value: wild type


title: 488-6_37826_PLN_ADT


title: Melanoma PDOTS at baseline

description: 10x Genomics NextGEM 5 prime v2

source_name: patient-derived organotypic tumor spheroids (melanoma, 10214)


title: 488-6_37826_MesLN_HTO

value: MesLN


title: JC289a_ND5.1_DdCBE_rp1


title: 488-6_37826_MesLN_GEX

value: Primary cells


title: Liver from abnormal fish, 5 days of recovery, rep4


title: Spleen from abnormal fish, 5 days of recovery, rep1


title: Non-treated melanoma PDOTS cultured for 24h

description: 10x Genomics NextGEM 5 prime v2

value: patient-derived organotypic tumor spheroids (melanoma, 10214)


title: BJ, ChIP H3K9me3, shSETDB1, Infected with HSV-1 in1374

city: LYON

first: Armelle

last: Corpet

state: Rhône-Alpes

address: Faculté de Médecine et de Pharmacie, 8 avenue Rockefeller

country: France

institute: Institut NeuroMyoGène (INMG)

description:
Instrument model: Element Biosciences Aviti
BJ_H3K9me3_ChIP_7

data_processing:
Raw reads were filtered by trimming Illumina adapters and removing low-quality reads using Trimmomatic (v.0.39) with default parameters. Trimmed reads (containing more than 36 nucleotides) were aligned to the human (hg38) reference genome concatenated with the HSV-1 genome (GCF_000859985.2.fa) using bowtie2 (v2.5.1).
Sequence alignment map files, including uniquely mapped and multi-mapped reads, were transformed and sorted into BAM files using SAMtools (v.1.15.1).
Duplicate reads were removed using the MarkDuplicates function of Picard (v.2.23.5) (https://github.com/broadinstitute/picard) with REMOVE_DUPLICATES = true
Alignment files in the BAM format were converted to read coverage files in Bigwig format using deepTools bamCoverage (v.3.5.0) with RPGC normalization and 10 bp window size.
Peak calling was performed using macs2 (v.2.2.7.1) in a broad mode with a broad cutoff of 0.01.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: BJ

growth_protocol: DMEM, 5% fetal bovine serum, 1X penicillin/streptomycin. Cells were cultured at 37°C at 5% CO2.

extract_protocol:
Cells were crosslinked and processed for ChIP as described in Kleijwegt et al., 2023 and Becker et al., 2017.
Libraries were prepared with 10ng of DNA (input/ChIP) using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina.

treatment_protocol: BJ cells were transduced with fresh lentiviruses encoding shRNAs against the HUSH complex, MORC2 or SETDB1 (see plasmids section) for 48h to allow the depletion of the specific proteins, before being infected with HSV-1 in1374 at an MOI of 3 for 24h.

value: BJ

value: human foreskin fibroblasts

value: Infected with HSV-1 in1374

tag: chip antibody

value: H3K9me3, Abcam ab8904


title: JC288b_ND5.1_mitoTALEN_rp2

description: Cells were transfected by mitoTALEN targeting ND5.1 for 3 days.


title: BJ, ChIP H3K9me3, shMORC2, Infected with HSV-1 in1374

description:
Instrument model: Element Biosciences Aviti
BJ_H3K9me3_ChIP_6

value: H3K9me3, Abcam ab8903


title: 488-6_37826_MesLN_TCR


title: JC288a_ND5.1_mitoTALEN_rp1


title: JC288c_ND5.1_mitoTALEN_rp3


title: 488-6_37826_MesLN_ADT


title: Liver from abnormal fish, 5 days of recovery, rep3

value: Liver

value: After 5 days of recovery


title: JC287c_ND5.1_control.for.mitoTALEN_rp3


title: BJ, ChIP H3K9me3, shPPHLN1, Infected with HSV-1 in1374

description:
Instrument model: Element Biosciences Aviti
BJ_H3K9me3_ChIP_5

value: H3K9me3, Abcam ab8902


title: 488-6_37826_Bone marrow_HTO

value: Bone marrow


title: 488-6_37826_Bone marrow_TCR


title: Liver from abnormal fish, 5 days of recovery, rep2


title: Liver from abnormal fish, 5 days of recovery, rep1


title: Spleen from abnormal fish, 5 days of recovery, rep2

value: Spleen


title: BJ, ChIP H3K9me3, shMPP8, Infected with HSV-1 in1374

description:
Instrument model: Element Biosciences Aviti
BJ_H3K9me3_ChIP_4

value: H3K9me3, Abcam ab8901


title: JC287b_ND5.1_control.for.mitoTALEN_rp2


title: 488-6_37826_Bone marrow_GEX


title: Spleen from normal fish, 4 days of recovery, rep4

value: After 4 days of recovery


title: BJ, ChIP H3K9me3, shTASOR, Infected with HSV-1 in1374

description:
Instrument model: Element Biosciences Aviti
BJ_H3K9me3_ChIP_3

value: shTASOR

value: H3K9me3, Abcam ab8900


title: BJ, ChIP H3K9me3, shCtl, Infected with HSV-1 in1374

description:
Instrument model: Element Biosciences Aviti
BJ_H3K9me3_ChIP_2

value: shCtl

value: H3K9me3, Abcam ab8899


title: 488-6_37826_Bone marrow_ADT

value: Primary cells


title: JC315d_ND5.3_CBE.ND5.3_rp3

description: Cells were transfected by mito-CBE targeting ND5.3 (L1397C 20ug+20ug) for 3 days.

data_processing:
Followed the PEM-Q pipeline described in Liu et al., 2021.
Assembly: hg38
Supplementary files format and content: Tab-delimited files containing translocation events on ND5.3 locus.
Library strategy: PEM-seq

value: wild type


title: 488-5_37826_PBMC_TCR

source_name: PBMC

value: PBMC


title: Spleen from normal fish, 4 days of recovery, rep3


title: Spleen from normal fish, 4 days of recovery, rep2


title: BJ, ChIP H3K9me3, shCtl, Non infected

description:
Instrument model: Element Biosciences Aviti
BJ_H3K9me3_ChIP_1

value: BJ

value: human foreskin fibroblasts

value: Non infected

value: H3K9me3, Abcam ab8898


title: 488-5_37826_PBMC_HTO


title: 488-5_37826_PBMC_GEX


title: Liver from normal fish, 4 days of recovery, rep4

value: Liver


title: 488-5_37826_PBMC_ADT


title: BJ, Input, shPPHLN1, Infected with HSV-1 in1374

description:
Instrument model: Element Biosciences Aviti
BJ_Input_5

value: Infected with HSV-1 in1374


title: Spleen from normal fish, 4 days of recovery, rep1


title: Liver from normal fish, 4 days of recovery, rep3


title: JC315b_ND5.3_CBE.ND5.3_rp1


title: JC315c_ND5.3_CBE.ND5.3_rp2


title: JC314c_ND5.3_control.for.CBE.ND5.3_rp3


title: Liver from normal fish, 4 days of recovery, rep2


title: JC314a_ND5.3_control.for.CBE.ND5.3_rp1


title: BJ, Input, shTASOR, Infected with HSV-1 in1374

description:
Instrument model: Element Biosciences Aviti
BJ_Input_3


title: JC314b_ND5.3_control.for.CBE.ND5.3_rp2


title: 488-5_36767_PBMC_TCR


title: 488-5_36767_PBMC_HTO


title: Liver from normal fish, 4 days of recovery, rep1


title: JC287a_ND5.1_control.for.mitoTALEN_rp1


title: 488-5_36767_PBMC_GEX


title: JC342c_ND4_mitoTALEN_rp3

description: Cells were transfected by mitoTALEN targeting ND4 for 3 days.

data_processing:
Followed the PEM-Q pipeline described in Liu et al., 2021.
Assembly: hg38
Supplementary files format and content: Tab-delimited files containing translocation events on ND4 locus.
Library strategy: PEM-seq


title: Spleen from abnormal fish, 4 days of recovery, rep4


title: JC342b_ND4_mitoTALEN_rp2


title: BJ, Input, shCtl, Infected with HSV-1 in1374

description:
Instrument model: Element Biosciences Aviti
BJ_Input_2


title: 488-5_36767_PBMC_ADT


title: BJ, Input, shSETDB1, Infected with HSV-1 in1374

description:
Instrument model: Element Biosciences Aviti
BJ_Input_7


title: BJ, Input, shMORC2, Infected with HSV-1 in1374

description:
Instrument model: Element Biosciences Aviti
BJ_Input_6


title: Spleen from abnormal fish, 4 days of recovery, rep3


title: BJ, Input, shCtl, Non infected

description:
Instrument model: Element Biosciences Aviti
BJ_Input_1


title: JC342a_ND4_mitoTALEN_rp1


title: HSC_Male_NASH_4

city: New York

first: Sofie

last: Delbare

state: NY

address: 435 East 30th Street

institute: NYU Langone

data_processing:
Fastq files were aligned to the mm10 assembly of the mouse genome with STAR and gene expression was quantified with featureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: liver

extract_protocol:
After cannulation of the inferior vena cava, the portal vein was cut, followed by retrograde stepwise perfusion with solutions containing protease (14 mg/mouse, Sigma Aldrich) and collagenase D (3.7 U/mouse, Roche). Livers were then minced with forceps. The minced livers were further digested in the solution containing 1% DNase, protease (25 mg/mouse) and collagenase D (4.4 U/mouse) for 25 min on a GentleMacs instrument. Digested livers were filtered through a 70-μm cell strainer to get rid of non-digested tissue. The cell suspensions were first centrifuged at 70 x g to isolate the primary hepatocytes which were stored in Qiazol at -80°C until sample processing. The supernatant was transferred to a fresh tube and again centrifuged at 580 x g for 10 min at 4°C. Cell pellets were washed with Gey’s Balanced Salt Solution (Sigma Aldrich) twice. Cells were then subjected to gradient centrifugation on 9.7% Nycodenz (Accurate Chemical) to isolate hepatic stellate cells, which were then stored in Qiazol at -80°C until sample processing. RNA was isolated with RNeasy® Plus Micro Kit (Qiagen).
Samples with a minimum RIN of 9.0 were prepared for sequencing using the NuGEN Ovation RNA-Seq system v2 reagents for cDNA preparation and the Ovation Ultralow DR Multiplex system for the adapter ligation step.

treatment_protocol: Male and female C57BL/6J mice were fed fructose-palmitate-cholesterol (FPC-NASH) diet or standard chow (SC) for 16 weeks.

tag: Sex

value: Male

value: liver

value: NASH

tag: celltype

value: Hepatic stellate cell


title: 488-5_36686_PBMC_TCR

first: Benjamin

last: Bimber

address: 505 NW 185th Ave


title: JC341c_ND4_control.for.mitoTALEN_rp3


title: BJ, Input, shMPP8, Infected with HSV-1 in1374

description:
Instrument model: Element Biosciences Aviti
BJ_Input_4


title: Spleen from abnormal fish, 4 days of recovery, rep2

value: Spleen

value: After 4 days of recovery


title: 488-5_36686_PBMC_HTO


title: Spleen from abnormal fish, 4 days of recovery, rep1


title: JC341b_ND4_control.for.mitoTALEN_rp2


title: HSC_Male_NASH_2


title: JC341a_ND4_control.for.mitoTALEN_rp1


title: Liver from abnormal fish, 4 days of recovery, rep4


title: 488-5_36686_PBMC_GEX


title: 488-5_36686_PBMC_ADT


title: 488-4_37246_Spleen_TCR


title: Liver from abnormal fish, 4 days of recovery, rep3


title: HSC_Male_NASH_3


title: HSC_Male_NASH_1


title: JC294d_ND4_CBE.ND4_rp3

description: Cells were transfected by mito-CBE targeting ND4 (L1397C 20ug+20ug) for 3 days.


title: HSC_Male_Chow_4

value: Chow


title: Liver from abnormal fish, 4 days of recovery, rep2


title: JC294b_ND4_CBE.ND4_rp2


title: Liver from abnormal fish, 4 days of recovery, rep1


title: 488-4_37246_Spleen_HTO


title: HSC_Male_Chow_2


title: 488-4_37246_Spleen_GEX


title: JC294a_ND4_CBE.ND4_rp1


title: HSC_Male_Chow_3


title: Spleen from normal fish, 3 days of recovery, rep3

value: After 3 days of recovery


title: 488-4_37246_Spleen_ADT

value: Primary cells


title: JC293d_ND4_control.for.CBE.ND4_rp3

value: wild type


title: Spleen from normal fish, 3 days of recovery, rep2


title: HSC_Male_Chow_1


title: Spleen from normal fish, 3 days of recovery, rep1


title: HSC_Female_NASH_4

value: Female


title: 488-4_37246_PLN_TCR

value: PLN


title: JC293b_ND4_control.for.CBE.ND4_rp2


title: Liver from normal fish, 3 days of recovery, rep3


title: 488-4_37246_PLN_HTO


title: JC293a_ND4_control.for.CBE.ND4_rp1


title: HSC_Female_NASH_3


title: Liver from normal fish, 3 days of recovery, rep2


title: HSC_Female_NASH_2


title: 488-4_37246_PLN_GEX


title: Donor3, T cell, Mock

city: Hong Kong

first: Qian

last: Zhao

state: Hong Kong

address: Room Y1125, Block Y, The Hong Kong Polytechnic University Lee Shau Kee Building, Yuk Choi Rd, Hung Hom

department: ABCT

institute: The Hong Kong Polytechnic University

data_processing:
Raw reads of RNAseq were firstly clean up by fastp(v0.23.2).
5' Adapter sequence (AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT) and 3' adapter sequence  (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGATGACTATCTCGTATGCCGTCTTCTGCTTG) were used to trim retained adapter sequence.
Next, clean reads were aligned to human genome(GRCh38.p13) by hisat2(v2.2.1) with default parameter.
All possible transcripts were assembled using stringtie(v2.2.0).
Then, read count of transcripts were calculated by featureCounts(v2.0.3).
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

source_name: Blood

extract_protocol:
T cells were harvested and wash with ice-cold PBS buffer twice. Total RNA was extracted with TRIzol™ reagent (Sigma,# T9424). Quality assessment of total RNA was performed by Agilent 2100 Bioanalyzer (Agilent Technologies). RNA samples with RNA integrity number (RIN) bigger than 9 were subjected to RNA sequencing.
All the RNA samples were transferred to Novogene for library construction and sequencing. Briefly, mRNA was enriched from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Libraries passed quality control procedure were sequenced on Hiseq 4000 (Illumina). Around 100M PE150 reads were generated from each sample.

treatment_protocol: T cell activation was performed either with phorbol PMA 25 ng/mL and Iono 1 μg/mL or with anti-CD3/CD28-coated microbeads (ThermoFisher Scientific, #11161D) at a bead to cell ratio of 1: 1, at 37 °C with 5% CO2 for 24 hours.

value: Blood

value: PBMC

tag: cell subtype

value: T cell

value: WT

value: Mock


title: Liver from normal fish, 3 days of recovery, rep1

value: Liver


title: Donor3, T cell, PMA/Ionomycin

value: PMA/Ionomycin


title: 488-4_37246_MesLN_TCR

city: Beaverton

value: MesLN


title: 488-4_37246_PLN_ADT


title: Donor3, T cell, CD3/CD28


title: 488-4_37246_MesLN_HTO


title: HSC_Female_Chow_2

value: liver

value: Hepatic stellate cell


title: HSC_Female_Chow_4


title: Donor2, T cell, PMA/Ionomycin


title: Spleen from abnormal fish, 3 days of recovery, rep2

value: Spleen


title: 488-4_37246_MesLN_GEX


title: Donor2, T cell, Mock


title: Spleen from abnormal fish, 3 days of recovery, rep1


title: Donor1, T cell, PMA/Ionomycin


title: Liver from abnormal fish, 3 days of recovery, rep3


title: Donor2, T cell, CD3/CD28


title: Hepato_Male_NASH_4

value: Male

value: NASH

value: Hepatocyte


title: HSC_Female_NASH_1


title: Spleen from abnormal fish, 3 days of recovery, rep3

value: After 3 days of recovery


title: 488-4_37246_Bone marrow_TCR

value: Bone marrow

value: Primary cells


title: Liver from abnormal fish, 3 days of recovery, rep2


title: Hepato_Male_NASH_3


title: HSC_Female_Chow_1

value: Female

value: Chow


title: Hepato_Male_NASH_2


title: Donor1, T cell, CD3/CD28

value: Blood

value: PBMC

value: T cell


title: 488-4_37246_Bone marrow_GEX


title: Spleen, 1 day of recovery, rep4

value: After 1 day of recovery


title: UPN-1, GS716054 , 72hrs, r3

city: London

first: Findlay

last: Bewicke-Copley

address: John Vane Science Centre, Barts Cancer Institute

institute: Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London

data_processing:
Raw reads were aligned to the reference genome using Hisat2 (2.2.1)
Read counting was done using htseq-count (version 0.13.5)
Assembly: GRCh38
Supplementary files format and content: Counts files contain gene names (as Ensembl IDs) and raw read counts.

growth_protocol: cell lines, were cultured in a 5% CO2, 37°C humidified incubator using RPMI-1640 supplemented with 20% FBS, 1% L-glutamine and 1% Pen-Strap

extract_protocol: Qiagen mRNA Prep kit

tag: time post_treatment_(hours)

tag: biological replicate


title: 488-4_37246_Bone marrow_ADT


title: Hepato_Male_Chow_4


title: Spleen, 1 day of recovery, rep3


title: UPN-1, GS716054 , 72hrs, r2


title: 488-3_36131_Spleen_TCR


title: 488-4_37246_MesLN_ADT


title: Hepato_Male_Chow_3


title: UPN-1, GS716054 , 72hrs, r1


title: 488-3_36131_Spleen_HTO


title: Spleen, 1 day of recovery, rep2


title: Hepato_Male_Chow_2


title: 488-4_37246_Bone marrow_HTO


title: Donor1, T cell, Mock

value: WT

value: Mock


title: UPN-1, DMSO, 72hrs, r3

value: DMSO


title: Spleen, 1 day of recovery, rep1


title: Liver, 1 day of recovery, rep4

value: Liver


title: Liver from abnormal fish, 3 days of recovery, rep1


title: Liver, 1 day of recovery, rep3


title: Hepato_Female_NASH_4

value: liver


title: Hepato_Male_NASH_1

value: Male


title: 488-3_36131_Spleen_GEX

value: Spleen


title: Hepato_Male_Chow_1

value: Hepatocyte


title: 488-3_36131_Spleen_ADT


title: UPN-1, DMSO, 72hrs, r2


title: UPN-1, DMSO, 72hrs, r1


title: 488-3_36131_PLN_TCR

value: PLN


title: Liver, 1 day of recovery, rep2


title: UPN-1, GS716054 , 24hrs, r3


title: Hepato_Female_NASH_3

value: NASH


title: 488-3_36131_PLN_HTO

value: Primary cells


title: Hepato_Female_NASH_2

value: Female


title: Liver, 1 day of recovery, rep1


title: 488-3_36131_PLN_GEX


title: UPN-1, GS716054 , 24hrs, r2


title: Spleen, at the end of transportation, rep4

value: At the end of transportation


title: Spleen, at the end of transportation, rep3


title: 488-3_36131_PLN_ADT


title: Hepato_Female_Chow_4

value: Chow


title: UPN-1, DMSO, 24hrs, r3


title: Hepato_Female_Chow_3


title: 488-3_36131_MesLN_TCR

value: MesLN


title: Spleen, at the end of transportation, rep2


title: 488-3_36131_MesLN_HTO


title: UPN-1, DMSO, 24hrs, r2


title: Hepato_Female_Chow_2


title: Spleen, at the end of transportation, rep1


title: MINO, GS716054 , 72hrs, r3

source_name: MINO

value: MINO


title: Liver, at the end of transportation, rep4


title: 488-3_36131_MesLN_ADT


title: Hepato_Female_Chow_1


title: Female, NASH, rep3

extract_protocol:
RNA was isolated from the top left lobe of the liver with RNeasy® Plus Micro Kit (Qiagen)
Samples with a minimum RIN of 9.0 were prepared for sequencing using the NuGEN Ovation RNA-Seq system v2 reagents for cDNA preparation and the Ovation Ultralow DR Multiplex system for the adapter ligation step.


title: UPN-1, DMSO, 24hrs, r1


title: 488-3_36131_MesLN_GEX


title: 488-2_35112_Spleen_TCR


title: Female, NASH, rep2


title: MINO, GS716054 , 72hrs, r1


title: Liver, at the end of transportation, rep2


title: 488-2_35112_Spleen_HTO


title: MINO, GS716054 , 72hrs, r2


title: Hepato_Female_NASH_1


title: UPN-1, GS716054 , 24hrs, r1


title: Female, NASH, rep1


title: Liver, at the end of transportation, rep1


title: Spleen, before transportation, rep4

value: Before transportation


title: Female, SC, rep3

value: SC


title: 488-2_35112_Spleen_GEX


title: MINO, DMSO, 72hrs, r3


title: 488-2_35112_Spleen_ADT


title: Female, SC, rep2


title: MINO, DMSO, 72hrs, r2


title: MINO, DMSO, 72hrs, r1


title: Spleen, before transportation, rep3


title: MINO, GS716054 , 24hrs, r3


title: Male, SC, rep3


title: Female, SC, rep1


title: 488-2_35112_MesLN_HTO


title: Spleen, before transportation, rep1


title: Spleen, before transportation, rep2


title: Liver, at the end of transportation, rep3


title: Male, SC, rep2


title: MINO, GS716054 , 24hrs, r2


title: Male, SC, rep1


title: Liver, before transportation, rep3


title: 488-16_37012_Spleen_TCR


title: MINO, DMSO, 24hrs, r3


title: Male, NASH, rep3


title: 488-2_35112_MesLN_ADT


title: MINO, DMSO, 24hrs, r2


title: Male, NASH, rep2


title: Liver, before transportation, rep1


title: MINO, DMSO, 24hrs, r1


title: 488-16_37012_Spleen_GEX


title: Male, NASH, rep1


title: 488-2_35112_MesLN_GEX


title: MINO, GS716054 , 24hrs, r1


title: NeuronalNuclei1

data_processing:
Adapter sequences were trimmed with Flexbar (3.0.3) and aligned to the mm10 genome using STAR 2.7.5. The STAR aligner was also used to mark PCR duplicates
Bullseye (https://github.com/mflamand/Bullseye) was used to generate a nucleotide representation matrix using parseBAM.pl. Marked PCR duplicates were ignored at this step.
Bullseye find_edit_sites.pl was used to find editing sites corresponding to m6A methylation.
Assembly: mm10
Supplementary files format and content: A bed file with the identified m6A sites in neuronal nuclei
Library strategy: DART-seq

source_name: Cortex (Brain)

growth_protocol: Mice were 10 weeks old at the start of tamoxifen treatment and housed under normal conditions

extract_protocol:
Mice were placed under anesthesia and perfused with ACSF. The brain was removed, cortex isolated and cut into pieces and digested with Neuronal Isolation Enzyme with Papain (Thermo Fisher). Tissue was gently disrupted with 10mL pipettes to release single cells. Debris was removed by centrifuging for 25 min at 250xg in 30% percoll solution. Cells were counted and viablity measured. Nuclei were extracted using a mild detergent buffer and washed 2x in ACSF.Nuclei were fixed with 50% ethanol and washed 2x before staining with NeuN antibody conjugated to AlexaFluor488 (Abcam).
Libraries were prepared with SMARTer Stranded Total RNA-seq Kit v3 - Pico Input Mammalian (Takara).

treatment_protocol: Mice were treated with 20mg/kg tamoxifen every 24 hours for five days. 7 days after the final treatment, biological material was collected.

value: Cortex (Brain)

value: Neuron (Nuclei)

value: Tamoxifen


title: 488-16_37012_Spleen_ADT


title: 488-16_37012_PLN_TCR

source_name: PLN


title: JEKO, GS716054 , 72hrs, r3

source_name: JEKO

value: JEKO


title: 30-KO2-48h-H

city: Birmingham

first: Hongxing

state: AL

address: 1700 6TH AVE S, HSROC 2222N

department: Department of Radiation Oncology

institute: University of Alabama at Birmingham

description:
T cell differentiation
Suppl Table 1-Hypoxia WT vs HIF1a-KO.xlsx

data_processing:
For RNA-seq data analysis, paired-end transcriptome sequences were mapped to theMus musculusGRCm38 reference genome available on ENSEMBL using the STAR aligner (version 2.7.5a.
Read counts per gene were calculated using htseq-count in the HTseq package (version 0.11.2)
Then the read counts per gene were used for downstream differential gene expression analysis and pathway enrichment analysis
Assembly: mm10
Supplementary files format and content: excel files including baseMean, fold change and p values

source_name: Naive CD4 T cells

growth_protocol: All cells were cultured in a humidified 37 °C incubator with 5% CO2. For hypoxic condition, cultures were placed in a hypoxic chamber with oxygen level set at 1% to mimick the O2 tension in the TME of solid tumors.

extract_protocol:
Cells were directly lysed on the plate and total RNA was extracted immediately by RNeasy Plus Mini Kit from QIAGEN, Inc.
Briefly, total RNA was enriched with Poly A selection and sequencing was performed on Illumina platform

treatment_protocol: Naïve T cells were activated with plate-bond anti-CD3 plus anti-CD28 in presence of 100U/mL IL-2 for 48h

value: hypoxia

value: Naive CD4 T cells


title: Liver, before transportation, rep4

value: Liver


title: 488-2_35112_MesLN_TCR

source_name: MesLN


title: JEKO, GS716054 , 72hrs, r2


title: 488-16_37012_PLN_HTO

value: PLN


title: Patient 59, extension

city: Los Angeles

first: Lu

last: Sun

state: California

address: 10833 Le Conte Avenue

institute: University of California, LA

description: mRNA from fresh surgical samples

data_processing:
Paired-end, 2 × 100 base pair (bp) transcriptome reads generated using Illumina NovaSeq S4 were mapped to the Genome Reference Consortium Human Build 38 (GRCh38) reference genome using HISAT2 (version 2.0.6).
The gene level counts were generated by the HTSeq-count program (version 0.5.4p5)
We utilized the edgeR (version 3.38.1 ) R package's cpm() function to compute the normalized gene expression values from the raw gene expression counts. These normalized expression values were log2 transformed after adding a pseudo count of 1. We used the limma (version 3.52.4) R package's removeBatchEffect() to remove batch effects of the log2 transformed normalized expression data.
Assembly: GRCh38
Supplementary files format and content: Gene level raw counts of each sample as computed by htseq-count (tab delimited)

source_name: glioblastoma

extract_protocol:
RNA were extracted from resected tumor specimens preserved in AllProtect tissue reagent (Qiagen) at the time of surgery. For the initial cohort, we simultaneously isolated RNA and DNA using Qiagen AllPrep DNA/RNA kits (#80204). In the expanded cohort, we divided the tumor tissue in half and employed the Qiagen RNeasy Mini Kit (#74104) for RNA isolation.
TruSeq RNA exome kit is used to construct the RNA sequencing libraries

value: glioblastoma

value: neoadjuvant pembrolizumab


title: 29-KO1-48h-H


title: Patient 58, extension

description: mRNA from fresh surgical samples


title: JEKO, GS716054 , 72hrs, r1


title: JEKO, DMSO, 72hrs, r3

value: DMSO


title: JEKO, DMSO, 72hrs, r2


title: Patient 56, extension

description: mRNA from fresh surgical samples


title: 488-16_37012_Spleen_HTO

data_processing:
CellRanger/Seurat
Assembly: Mmul_10
Supplementary files format and content: Count Matrix / Seurat Object

value: Spleen

value: Primary cells


title: 27-WT3-48-H

value: WT


title: 488-16_37012_PLN_ADT


title: 26-WT2-48-H


title: Liver, before transportation, rep2

source_name: Liver


title: NeuronalNuclei2


title: 488-16_37012_PLN_GEX


title: 31-KO3-48h-H


title: 488-16_37012_MesLN_TCR

value: MesLN


title: 25-WT1-48-H


title: Patient 54, extension

description: mRNA from fresh surgical samples


title: 488-16_37012_MesLN_HTO


title: 23-KO3-48h-Norm

description:
T cell differentiation
Suppl Table 2-Normoxia WT vs HIF1a-KO.xlsx

value: normoxia


title: Patient 51, extension

description: mRNA from fresh surgical samples


title: JEKO, GS716054 , 24hrs, r3


title: 22-KO2-48h-Norm


title: 488-16_37012_MesLN_GEX


title: JEKO, GS716054 , 24hrs, r2


title: 488-16_37012_MesLN_ADT


title: Patient 50, extension

description: mRNA from fresh surgical samples


title: JEKO, GS716054 , 24hrs, r1


title: 19-WT3-48h-Norm


title: 21-KO1-48h-Norm


title: Patient 49, extension

description: mRNA from fresh surgical samples


title: 488-16_37012_Bone marrow_TCR

source_name: Bone marrow

value: Bone marrow


title: JEKO, DMSO, 24hrs, r2


title: 488-16_37012_Bone marrow_HTO


title: Patient 55, extension

description: mRNA from fresh surgical samples


title: Patient 48, extension

description: mRNA from fresh surgical samples


title: 488-16_37012_Bone marrow_GEX


title: Patient 47, extension

description: mRNA from fresh surgical samples


title: 17-WT1-48h-Norm


title: Patient 52, extension

description: mRNA from fresh surgical samples


title: 488-16_37012_Bone marrow_ADT


title: MKP Replicate 4

city: New Haven

first: Evrett

middle: Nathanial

last: Thompson

state: CT

address: 333 Cedar Street

department: Cell Biology

institute: Yale School of Medicine

data_processing:
STAR v2.7.7a was used to align reads to the human reference genome hg38. Set --outFilterMismatchNmax 2, kept all other parameters default.
The htseq-count v0.13.5 from the HTSeq package was used to count reads from the alignments generated using STAR. Set parameters -s reverse -m union -r pos, all other parameters kept default.
Read counts for each sample were input directly into DESeq2, which was used to carry out normalization and differential gene analysis using default parameters.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw read counts generated by HTSeq per sample.

extract_protocol:
Individual cell populations were isolated via FACS from CD34-selected G-CSF mobilized peripheral blood. Total RNA was then extracted using the RNAqueous-Micro kit (Invitrogen) per manufacturer's protocol.
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit. Sequencing was conducted using standard Illumina protocols.

value: MKP

tag: donor

value: Donor 4


title: HU145_mESC_c.Myc_Hypa_rp3

city: Beijing

first: Jinchun

last: Wu

address: No. 5, Yiheyuan street

institute: Peking University

description: The cells cultured in 6-cm dish were transfected with 2mg gRNA-Hypa-puroR plasmid targeting c-MYC locus, with 1mg/ml puromycin selection from 24h to 60h post-transfection,  then the genomic DNA were extracted for PEM-seq library construction at 84h post-transfection.

data_processing:
Followed the PEM-Q pipeline described in Liu et al., 2021
Assembly: mm10
Supplementary files format and content: tab file containing mtDNA integration events on c-Myc locus
Library strategy: PEM-seq

source_name: cultured cell

growth_protocol: mESCs were cultured in Knockout DMEM (Gibco) containing 15% Fetal Bovine Serum(Gibco), MEM Non-essential Amino Acids Solution(Sigma), Nucleotides (Millipore), Penicillin-Streptomycin Solution(cytiva), L-Glutamine Solution(Sigma),2-Mercaptoethanol(Sigma), PD0325901 (Selleck), CHIR99021 (Selleck), and LIF (Millipore) at 37 °C with 5% CO2.

value: v6.5 mESC

value: C57BL/6 X 129/sv wild type


title: Patient 46, extension

description: mRNA from fresh surgical samples

tag: tissue


title: HU145_mESC_c.Myc_Hypa_rp2

tag: genotype


title: Patient 44, extension

description: mRNA from fresh surgical samples


title: Patient 42, extension

description: mRNA from fresh surgical samples


title: MKP Replicate 2

source_name: CD34-selected G-CSF mobilized peripheral blood

value: Donor 3


title: JEKO, DMSO, 24hrs, r3

value: JEKO


title: HU145_mESC_c.Myc_Hypa_rp1


title: 18-WT2-48h-Norm

value: Naive CD4 T cells


title: 488-15_36683_Spleen_GEX

source_name: Spleen

tag: cdna library_id


title: Patient 41, extension

description: mRNA from fresh surgical samples


title: 488-15_36683_Spleen_ADT

tag: subjectid


title: HU145_mESC_c.Myc_HF1_rp2

description: The cells cultured in 6-cm dish were transfected with 2mg gRNA-HF1-puroR plasmid targeting c-MYC locus, with 1mg/ml puromycin selection from 24h to 60h post-transfection,  then the genomic DNA were extracted for PEM-seq library construction at 84h post-transfection.


title: HU145_mESC_c.Myc_HF1_rp3


title: Patient 40, extension

description: mRNA from fresh surgical samples


title: ERP Replicate 5

value: CD34-selected G-CSF mobilized peripheral blood

tag: cell type

value: ERP


title: 488-15_36683_PLN_TCR

value: PLN


title: JEKO, DMSO, 24hrs, r1

tag: cell line

value: DMSO


title: HU145_mESC_c.Myc_HF1_rp1


title: Patient 38, extension

description: mRNA from fresh surgical samples

value: glioblastoma

tag: treatment

value: neoadjuvant pembrolizumab


title: ERP Replicate 4


title: 488-15_36683_PLN_HTO

value: Primary cells

tag: plateid


title: HU145_mESC_c.Myc_FeCas9_rp3

description: The cells cultured in 6-cm dish were transfected with 2mg gRNA-FeCas9-puroR plasmid targeting c-MYC locus, with 1mg/ml puromycin selection from 24h to 60h post-transfection,  then the genomic DNA were extracted for PEM-seq library construction at 84h post-transfection.


title: ERP Replicate 3


title: 488-15_36683_PLN_GEX

tag: hto


title: Patient 37, extension

description: mRNA from fresh surgical samples


title: 488-15_36683_Spleen_TCR

value: Spleen


title: MKP Replicate 3


title: 488-15_36683_Spleen_HTO


title: JEKO, DMSO, 72hrs, r1


title: MKP Replicate 1


title: ERP Replicate 2

value: Donor 2


title: HU145_mESC_c.Myc_FeCas9_rp2


title: HU145_mESC_c.Myc_FeCas9_rp1


title: Patient 36, extension

description: mRNA from fresh surgical samples


title: ERP Replicate 6


title: 488-15_36683_MesLN_TCR

value: MesLN


title: 488-15_36683_PLN_ADT


title: 488-15_36683_MesLN_HTO


title: HU145_mESC_c.Myc_eCas9_rp2

description: The cells cultured in 6-cm dish were transfected with 2mg gRNA-eCas9-puroR plasmid targeting c-MYC locus, with 1mg/ml puromycin selection from 24h to 60h post-transfection,  then the genomic DNA were extracted for PEM-seq library construction at 84h post-transfection.


title: Patient 7, initial trial

description: mRNA from fresh surgical samples


title: 488-15_36683_MesLN_GEX


title: MEP Replicate 5

value: MEP


title: T1_10770_S32

city: Columbia

first: Rachel

middle: Ann

last: Carroll

state: MO

address: 1201 Rollins St.

department: Bond Life Science Center

institute: University of Missouri

description: 10X Genomics

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were done using Cell Ranger v7.0.1
Cell barcodes from the pseudobulk count matrix analysis output were used as input into pyDESeq2 v0.3.5
To cluster cells, we used the Scanpy platform v1.9.1 and a process based on best practices established in Luecken and Theis, 2019. Briefly, we filtered out nuclei expressing fewer than 200 or more than 2,000 genes, nuclei with total counts greater than 5,000, and nuclei with more than 3% of counts assigned to mitochondrial transcripts or 5% of counts assigned to ribosomal transcripts. We normalized and log-scaled the counts matrix, computed highly variable genes, and regressed out counts per nuclei. We performed principal component analysis (PCA) and then integrated across samples using Harmonypy v0.0.9 to create an adjusted PCA basis. We computed the 10-neighbor graph with the first 20 adjusted principal components clustering using the Leiden algorithm with resolution of 0.5, and visualized it in two dimensions with uniform manifold approximation and projection.
Assembly: GRCg7b
Supplementary files format and content: h5 files

organism: Gallus gallus

source_name: Thymus

extract_protocol:
After euthanizing the birds, thymus were aseptically removed, and flash frozen in liquid nitrogen then stored at -80. The nuclei isolation methods performed were done via the Singulator2 instrument per manufacturer’s protocols (S2 Genomics; Livermore, CA) with storage buffers containing 0.4U/ul RNase inhibitor (source), prior to microfluidic encapsulation on the 10X Chromium instrument (10x Genomics®, Pleasanton, CA) to nanoliter-scale Gel bead-in-EMulsions (GEMs). Single-nuclei libraries were generated using the GemCode Single-Cell Instrument and Single Cell 3′ Library and Gel Bead Kit v3 and Chip Kit (10x Genomics®, Pleasanton, CA) according to the manufacturer’s protocol. Before sequencing, every library was analyzed on a Bioanalyzer high sensitivity chip to ensure the expected cDNA fragment size distribution was achieved. The appropriate number of individually barcoded GEM libraries were pooled and sequenced on a NovaSeq 6000 instrument (Illumina) with 2×150bp length using these sequencing parameters: 26 bp read 1 – 8 bp index 1 (i7) – 98 bp read 2 with 200 cycles.Single nuclei capture and cDNA preparation were performed with the 10X Genomics Chromium Single Cell 3’ kit, version 2, and lipid encapsulation instrument (10X Genomics, Pleasanton, CA) according to the manufacturer’s recommendations. Pooled libraries were barcoded by sample and sequenced (2x 150 bp length) on an Illumina HiSeq 6000 instrument (Illumina, Inc., San Diego, CA) to achieve 50,000 reads per nuclei.
The individual tissue-specific sequenced Gel Bead-In Emulsion (GEM) libraries were each processed with the CellRanger v7.0.1 pipeline (10X Genomics), which performs demultiplexing, alignment, barcode processing, and sample aggregation to create a cellular barcode by genomic feature matrix. The chicken reference used for all single-nuclei read alignments was bGalGal1b or GRCg7b. First, we used the “cellranger mkgtf” command to filter out everything except protein-coding genes and long non-coding RNAs from the annotation, and then use the “cell ranger mkref” command to create the necessary indices. We aligned reads to this modified GRCg7b reference and generated count matrices for each sample individually using the command “cellranger count” with default options. Molecular barcodes that were most likely to be ambient signals and doublets were eliminated using the default settings of cellranger’s “remove-background” v.0.2.0 function, and cell counts were calculated using cellranger default parameters

value: Thymus

value: Female

value: Immune

value: 5 weeks


title: T2_10771_S33

description: 10X Genomics


title: ERP Replicate 1

value: Donor 1


title: MEP Replicate 6

value: Donor 4


title: HU145_mESC_c.Myc_eCas9_rp1

value: v6.5 mESC

value: C57BL/6 X 129/sv wild type


title: MEP Replicate 4

value: CD34-selected G-CSF mobilized peripheral blood

value: Donor 3


title: LL_3

data_processing:
Approximately 28.89 Gb of raw sequence data per sample were obtained, with base sequence quality assessed using FastQC software. Low-quality bases and artefacts were removed using Trim Galore software. High-quality 150 bp paired-end reads were aligned to the reference GRCg7b genome, using BWA mem software. PCR duplicates and mitochondrial data were removed using SAMtools software. BAM files from three biological replicates were merged using SAMtools software, forming four biological replicates for downstream analysis. Filtered BAM files were converted to bedpe format and then to tagAlign files using BEDtools software (version 2.30.0). Peaks were called using MACS3 software (version 3.0.0b1) with specified parameters.
Assembly: GRCg7b genome
Supplementary files format and content: narrowPeak files include peaks values for each sample.

source_name: Abdominal fat tissue

extract_protocol:
Samples was collected, and the cell suspension was prepared. Cell membrane were lysed to obtain the nucleus. Then, Tn5 transposase was added to cut open DNA.
The DNA fragments cut by the enzyme were amplified by PCR and then sequenced on Illumina NovaSeq 6000 platform.

value: Abdominal fat tissue

tag: group

value: LL


title: 488-15_36683_MesLN_ADT

value: Primary cells


title: 488-15_36683_Bone marrow_TCR

value: Bone marrow


title: MEP Replicate 3


title: HU145_mESC_c.Myc_SuperFi_rp3

description: The cells cultured in 6-cm dish were transfected with 2mg gRNA-SuperFi-puroR plasmid targeting c-MYC locus, with 1mg/ml puromycin selection from 24h to 60h post-transfection,  then the genomic DNA were extracted for PEM-seq library construction at 84h post-transfection.

extract_protocol: Followed the PEM-seq protocol that described in Yin et al., 2019.


title: LL_2


title: HU145_mESC_c.Myc_SuperFi_rp2


title: 488-15_36683_Bone marrow_HTO

extract_protocol:
N/A
10x Genomics 5' Chemistry


title: MEP Replicate 2

value: Donor 2


title: LL_1


title: HU145_mESC_c.Myc_eCas9_rp3


title: HU145_mESC_c.Myc_SuperFi_rp1


title: HU145_mESC_c.Myc_SpCas9_rp3

description: The cells cultured in 6-cm dish were transfected with 2mg gRNA-SpCas9-puroR plasmid targeting c-MYC locus, with 1mg/ml puromycin selection from 24h to 60h post-transfection, then the genomic DNA were extracted for PEM-seq library construction at 84h post-transfection.


title: FL_3

value: FL


title: FL_2


title: MEP Replicate 1

value: MEP


title: 488-15_36683_Bone marrow_GEX


title: CMP Replicate 6

value: CMP


title: FL_1


title: 488-15_36683_Bone marrow_ADT


title: CMP Replicate 5


title: 488-14_36562_Spleen_TCR

value: Spleen


title: BBP_4

city: Boston

first: Shannan

last: Ho Sui

address: 401 Park Drive

institute: Harvard

data_processing:
Reads were processed to counts through the bcbio RNA-seq pipeline implemented in bcbio-nextgen v1.2.9-8eb78b7
Assembly: WBcel235, Annotation Version WS272
Supplementary files format and content: normalized counts (TPM) processed by salmon then by tximport

organism: Caenorhabditis elegans

source_name: whole organism

extract_protocol:
RNA purification was performed using the Direct-zol RNA Miniprep Plus kit (Zymo Research) following manufacturer’s instructions.
The RNA was prepared for sequencing with the Kapa mRNA HyperPrep kit (Roche)

treatment_protocol: Following 24-hour exposure to either 0.1% DMSO alone or BBP dissolved in DMSO, 1,200 worms per condition were washed five times with M9, then collected in 500 μl of Trizol (Invitrogen) for RNA extraction, and frozen at -80°C.

value: whole organism

value: benzyl butyl phthalate


title: CMP Replicate 4


title: HU145_mESC_c.Myc_control_of_Cas9_rp3


title: 488-14_36562_Spleen_HTO


title: BBP_3


title: 488-14_36562_Spleen_GEX


title: HU145_mESC_c.Myc_control_of_Cas9_rp2


title: CMP Replicate 3


title: HU145_mESC_c.Myc_control_of_Cas9_rp1


title: 488-14_36562_Spleen_ADT


title: BBP_2


title: CMP Replicate 1

value: Donor 1


title: CMP Replicate 2


title: DMSO_4

value: DMSO


title: 488-14_36562_PLN_TCR

value: PLN


title: BBP_1


title: 488-14_36562_PLN_HTO


title: HA-tagged RUNX1-4D Transduced HEL Cell RNA-seq Rep 1

source_name: HEL

growth_protocol: The cells were grown in RPMI1640 Medium (Gibco) supplemented with 10% FBS, 1% Pen/Strep and 1% L-Glutamine, with 2μg/ml puromycin to select for transduced cells. The cells were incubated at 37°C, 5% CO2.

extract_protocol:
Total RNA was extracted using the RNAqueous-Micro kit (Invitrogen) per manufacturer's protocol.
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit. Sequencing was conducted using standard Illumina protocols.

value: HEL


title: HA-tagged WT RUNX1 Transduced HEL Cell RNA-seq Rep 1

value: HA-WT RUNX1


title: DMSO_2


title: 488-14_36562_PLN_GEX


title: HA-tagged RUNX1-4A Transduced HEL Cell RNA-seq Rep 1


title: HU145_mESC_c.Myc_SpCas9_rp2

value: v6.5 mESC

value: C57BL/6 X 129/sv wild type


title: HU145_mESC_c.Myc_SpCas9_rp1


title: DMSO_3


title: Empty Vector Transduced HEL Cell RNA-seq Rep 1

value: Empty Vector


title: DMSO_1


title: 488-14_36562_PLN_ADT

value: Primary cells


title: 488-14_36562_MesLN_TCR

value: MesLN