title: KOPTK1 cells, shDHX15+MYC-3

city: Hubei

first: Qilong

last: Li

address: Donghu road

institute: Wuhan university

data_processing:
RNA-seq reads were analyzed by FastQC (version 0.11.9) and mapped to the human genome reference assembly (hg38) using Hisat2 software (version 2.2.1). Differential gene expression was analyzed by DESeq2 (version 1.32.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text includes  raw counts for each Sample

source_name: KOPTK1 cells

growth_protocol: Human T-ALL KOPTK1 cells were grown in RPMI-1640 (Gibco) supplemented with 10% fetal bovine serum (FBS, Hyclone), 1% penicillin/streptomycin (Hyclone), 1% non-essential amino acids (Gibco), 2mM L-glutamine (Sigma), 1 mM sodium pyruvate (Sigma) and 55 μM β-mercaptoethanol (Sigma).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and subjected to quality control for RNA integrity by Agilent Bioanalyzer 2100 system (Agilent Technologies). Total RNA was further purified by RNAClean XP Kit (Beckman Coulter) and RNase-Free DNase Set (QIAGEN).
Poly(A)+ RNA libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme) and sequenced as 150 bp paired-end reads by Illumina NovaSeq 6000 (Annoroad Gene Technology Corporation).

treatment_protocol: KOPTK1 cells were transduced with lentiviruses expressing DHX15 shRNA or in combination with ectopic expression of MYC coding region.

value: KOPTK1 cells

value: T-ALL cell lines


title: KOPTK1 cells, shDHX15+MYC-2

status: Public on Nov 19 2023

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

value: WT


title: ChIP-seq of PGR at T30 in 2D culture

city: Parma

first: Roberto

last: Ferrari

state: Parma

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

description: 2D growth

library_source: genomic

data_processing: Analysis of sequence data was carried out as previously described (Ferrari et al., 2014) with minor modifications. Reads were aligned to the hg38 human genome reference sequence (GRCh38) using Bowtie (Langmead et al., 2009) and aligning parameters of uniqueness (-S –m1 –v2 –t –q). p values for the significance of ChIP-seq counts compared to input DNA were calculated as described (Pellegrini and Ferrari, 2012) using a threshold of 10−8 and a false discovery rate (FDR) < 1%.

molecule: genomic DNA

source_name: breast

growth_protocol:
2D growth of cells.T47D breast cancer cells were routinely grown in 10 cm dishese with RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100μg/ml streptomycin.
3D growth of cells. Prechilled p60 plates were coated with a thin layer of Matrigel (Corning Life Sciences) and then incubated for 20–30 min at 37ºC to allow polymerization without over drying. 200,00 cells trypsinized cells were resuspended and plated on-top of the Matrigel without disrupting the capsule. Culture was maintained for 10 days changing the medium every 2-3 days.  Spheroids extraction from 3D matrix: Dishes containing the spheroids grown for 10 days were rinsed twice with PBS followed by addition of 3 ml ice-cold PBS-EDTA. Matrigel including the 3D spheroids was carefully detached with a plastic scraper and left on ice for 30 min to allow complete depolymerization of the gel. The liquid solution was transferred to a conical tube, centrifuged for 5 min at 112 x g and rinsed twice with 0.5 volume of PBS-EDTA. The cell pellet was then ready for further processing.

extract_protocol:
ChIP assays were performed as described (Strutt and Paro, 1999)
Single-end (SE) ChIP-seq libraries were constructed from 0,1-1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp of the human genome for each condition.

treatment_protocol:
For the experiments with hormones, cells were plated in RPMI medium without phenol red supplemented with 10% dextran-coated charcoal treated FBS (DCC/FBS) and 48 h later medium was replaced by fresh medium without serum. After 24h in serum-free conditions, cells were incubated with 10 nM R5020 for different times at 37ºC.
For hormonal induction on the 3D spheroids, T47D cells were plated on top of phenol red-free Matrigel and after 7 days of culture medium was replaced by RPMI medium without phenol red supplemented with 10% dextran-coated charcoal treated FBS (DCC/FBS) and 48 h later medium was replaced by fresh medium without serum. After 24h in serum-free conditions, cells were incubated with 10 nM R5020 for different times at 37ºC.

tag: tissue

value: breast

value: Epithelial cancer metastatic

tag: treatment

value: 2D cluture, charcolized serum + serum starvation + R5020 for 30min


title: IS-caput, WT, rep1

city: Nagoya

first: Daiji

last: Kiyozumi

state: Aichi

address: Furocho, Chikusa-ku

department: Research Institute of Environmental Medicine

country: Japan

institute: Nagoya University

data_processing:
NovaSeq6000 (Illumina) using 101 bp single-ended mode
sequence reads were mapped onto mouse reference genome (mm10) using TopHat ver. 2.1.1
Fragments Per Kilobase of exon per Million mapped reads (FPKM) values for each gene were calculated using Cufflinks ver. 2.2.1
Assembly: mm10
Supplementary files format and content: A Microsoft Excel file including FPKM values for each Sample

organism: Mus musculus

source_name: IS-caput epididymis

extract_protocol:
RNA was harvested using RNeasy (Invitrogen).
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA sample prep kit (Illumina) following manufacturer's protocols.

value: Wild-type

value: IS-caput epididymis

tag: age

value: no treatment


title: KOPTK1 cells, shDHX15+MYC-1


title: BS-Seq CTFR-bESC-3i

city: Hohhot

first: jing

last: wang

state: Nei Mongol

address: Zhaojun Road

institute: Inner Mongolia University

data_processing:
First of all, we use FastQC (fastqc_v0.11.5) to perform basic statistics on the quality of the raw reads. Then, those reads sequences produced by the Illumina pipleline in FASTQ format were pre-processed through Trimmomatic (Trimmomatic-0.36) software use the parameter (SLIDINGWINDOW: 4:15 ; LEADING:3, TRAILING:3 ; ILLUMINACLIP: adapter.fa: 2: 30: 10 ; MINLEN:36) The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last, we use FastQC to perform basic statistics on the quality of the cleandata reads.
Bismark software (version 0.16.3; Krueger F, 2011) was used to perform alignments of bisulfite-treated reads to a reference genome (-X 700 --dovetail). The reference genome was firstly transformed into bisulfite-converted version (C-to-T and G-to-A converted) and then indexed using bowtie2 (Langmead B, 2012). Sequence reads were also transformed into fully bisulfite-converted versions (C-to-T and G-to-A converted) before they are aligned to similarly converted versions of the genome in a directional manner. Sequence reads that produce a unique best alignment from the two alignment processes (original top and bottom strand) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred. The same reads that aligned to the same regions of genome were regarded as duplicated ones. The sequencing depth and coverage were summarized using deduplicated reads.
The results of methylation extractor (bismark_methylation_extractor, --no_overlap) were transformed into bigWig format for visualization using IGV browser. The sodium bisulfite non-coversion rate was calculated as the percentage of cytosine sequenced at cytosine reference positions in the lambda genome.
Differentially methylated regions (DMRs) were identified using the DSS software (Hao Feng HaoWu, 2014；Hao Wu，2015；Yongseok Park Hao Wu,2016 ) , The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.
Assembly: ARS-UCD1.2
Supplementary files format and content: CX_report

organism: Bos taurus

source_name: bovine embryonic stem cells

growth_protocol: In short, bovine ovaries were obtained from a local abattoir, and oocytes were cultured for 22–24 h after maturation and fertilized with frozen cattle sperm. Six hours after fertilization, the eggs were transferred to the embryonic culture medium. When the embryos had developed to the 8-cell stage at 48 h, MM-102, PD0325901 and CHIR99021 (2i), or MM-102 plus PD0325901 and CHIR99021 (3i), was added to the medium. The embryos were then cultured for 7–8 days to develop into blastocysts.The bovine blastocysts obtained via in vitro fertilization were removed from the zona pellucida and plated in 4-well plates, and mTeSR-E6 (05946, STEMCELL Technologies  , Vancouver,Canada) was added with 20 ng/mL FGF-2 (100-18B, STEMCELL Technologies, Vancouver,Canada), 2.5 μM IWR-1 (I0161, Sigma-Aldrich, Shanghai, ChinaUSA) and 0.1328 g/mL low fatty acid BSA (219989925, MP Biomedicals NZ, New Zealand, USA), and were incubated at 37 °C and 5% CO2. After 48–72 h, ICMs adhered to the feeder layer, and the medium was changed daily. Outgrowths (after 8–10 days in culture) were dissociated and passaged using TrypLE (12563011, Gibco, California, USA) and were reseeded in the presence of 10 μM Rho kinase (ROCK) inhibitor Y-27632 (SCM075, Sigma, Shanghai, ChinaGermany). The established bESC lines were grown in 12-well plates and were passaged every 5 days at a 1:4–1:6 split ratio. To increase cell survival, the ROCK inhibitor Y-27632 (10 μM) was added to the wells 1 h before passaging and was also added to the newly prepared wells containing MEFs treated with mitomycin and fresh culture medium during the first 24 h of cultivation.

extract_protocol:
Genomic DNA degradation and contamination was monitored on agarose gels. DNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA).
A total amount of 5.2 microgram genomic DNA spiked with 26 ng lambda DNA were fragmented by sonication to 200-300bp with Covaris S220, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturer’s instructions. Then these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), before the resulting single-strand DNA fragments were PCR amplificated using KAPA HiFi HotStart Uracil + ReadyMix (2X). Library concentration was quantified by Qubit® 2.0 Flurometer (Life Technologies, CA, USA) and quantitative PCR, and the insert size was assayed on Agilent Bioanalyzer 2100 system.

treatment_protocol: Bovine ovaries were obtained from a local abattoir, and oocytes were cultured for 22–24 h after maturation and fertilized with frozen cattle sperm. Six hours after fertilization, the eggs were transferred to the embryonic culture medium. When the embryos had developed to the 8-cell stage at 48 h, MM-102, PD0325901 and CHIR99021 (2i), or MM-102 plus PD0325901 and CHIR99021 (3i), was added to the medium. The embryos were then cultured for 7–8 days to develop into blastocysts.The bovine blastocysts obtained via in vitro fertilization were removed from the zona pellucida and plated in 4-well plates, and mTeSR-E6 (05946, STEMCELL Technologies  , Vancouver,Canada) was added with 20 ng/mL FGF-2 (100-18B, STEMCELL Technologies, Vancouver,Canada), 2.5 μM IWR-1 (I0161, Sigma-Aldrich, Shanghai, ChinaUSA) and 0.1328 g/mL low fatty acid BSA (219989925, MP Biomedicals NZ, New Zealand, USA), and were incubated at 37 °C and 5% CO2. After 48–72 h, ICMs adhered to the feeder layer, and the medium was changed daily. Outgrowths (after 8–10 days in culture) were dissociated and passaged using TrypLE (12563011, Gibco, California, USA) and were reseeded in the presence of 10 μM Rho kinase (ROCK) inhibitor Y-27632 (SCM075, Sigma, Shanghai, ChinaGermany). The established bESC lines were grown in 12-well plates and were passaged every 5 days at a 1:4–1:6 split ratio. To increase cell survival, the ROCK inhibitor Y-27632 (10 μM) was added to the wells 1 h before passaging and was also added to the newly prepared wells containing MEFs treated with mitomycin and fresh culture medium during the first 24 h of cultivation.

value: bovine embryonic stem cells

value: MM-102 plus PD0325901 and CHIR99021were added to embryo cultures


title: IS-caput, UOD, rep3

value: unilateral orchidectomy (ipsilateral)


title: IS-caput, WT, rep3


title: ChIP-seq of PGR at T0 in 2D culture

description: 2D growth

value: 2D cluture, charcolized serum + serum starvation


title: KOPTK1 cells, shDHX15-3


title: IS-caput, UOD, rep2


title: BS-Seq CTFR-bESC-2i

value: PD0325901 and CHIR99021were added to embryo cultures


title: KOPTK1 cells, shDHX15-2


title: IS-caput, UOD, rep1


title: BS-Seq CTFR-bESC-102

value: MM-102 was added to embryo cultures


title: input in normal media in 2D culture

description: 2D growth

value: 2D culture nomal media


title: KOPTK1 cells, shDHX15-1


title: IS-caput, contra, rep3

value: unilateral orchidectomy (contralateral)


title: BS-Seq CTFR-bESC-F7

value: CTFR


title: ChIP-seq of H3K27ac in normal media in 2D culture

description: 2D growth


title: KOPTK1 cells, shcControl-3

value: KOPTK1 cells

value: T-ALL cell lines


title: BS-Seq CTFR-bESC-F7-102-5

value: WT

value: 5 uM of MM-102 to CTFR in long-term cultures


title: IS-caput, contra, rep2


title: ChIP-seq of H3K18ac in normal media in 2D culture

description: 2D growth

value: breast

value: Epithelial cancer metastatic


title: ChIP-seq of Pol2 in normal media in 2D culture replicate

description: 2D growth


title: BS-Seq CTFR-bESC-F7-102-50

value: bESCs were cultured for 7 days with the addition of 50 uM MM-102


title: IS-caput, contra, rep1

value: Wild-type

value: IS-caput epididymis


title: KOPTK1 cells, shcControl-1


title: KOPTK1 cells, shcControl-2


title: ChIP-seq of CTCF in normal media in 2D culture with Drosophila Spike-in replicate

description: 2D growth

value: 2D culture nomal media + spikein


title: BS-Seq bovine fetal fibroblasts

source_name: bovine fetal fibroblasts

value: bovine fetal fibroblasts

value: BFF


title: ChIP-seq of CTCF in normal media in 2D culture with Drosophila Spike-in

description: 2D growth


title: IS-caput, BOD, rep3

value: bilateral orchidectomy


title: KOLF-2 cells, PTCHD1_trunc, Day 24, biol rep 1

city: Nedlands

first: Kathryn

middle: Olivia

last: Farley

state: WA

address: 15 Hospital Avenue

department: Precision Health

country: Australia

institute: Telethon Kids Institute

description:
Trunc 1 = NM_173495.2(PTCHD1_i001):p.(Leu827Alafs*4)
NPC_trunc1

data_processing:
Raw sequencing reads were processed using the ENCODE/DCC pipeline (https://github.com/ENCODE-DCC/rna-seq-pipeline)
Reads were aligned to GRCh39 and quantified using kallisto.
Gene expression tables were created for downstream analysis with DESeq2 and limma using the tximport package.
Assembly: GRCh39

source_name: KOLF-2 derived NPCs

growth_protocol: KOLF-2 iPSCs were grown in TeSR-E8 medium (stemcell technologies). STEMdiff SMADi neural induction kit (StemCell Technologies) was used for neural induction

extract_protocol:
2 x 106 cells were taken for RNA extraction by RNeasy kit (QIAGEN, Australia)
RNA integrity was determined on the Agilent 4200 Tapestation System with High Sensitivity RNA ScreenTape analysis. RNA sequencing was performed according to sure select strand-specific RNA library preparation for Illumina Multiplexed Sequencing paired end, 100bp, 30M read RNA sequencing on the NOVAseq 6000 platform (Illumina, USA) at Genomics WA (Perth, Australia).

value: KOLF-2 derived NPCs

value: Neural progenitor cells

value: Truncation


title: mES ATRXKOG34R PMLInput

city: Clayton

first: Hsiao Phin

middle: Joanna

last: Voon

state: Victoria

address: Monash University, Wellington Road

department: Biochemistry and Molecular Biology

institute: Monash University

data_processing:
ChIP-seq of H3.3 and PML were aligned to the mouse genome (mm9) with Bowtie (v1.0.0) with default settings except (m -5).
Unmapped and duplicated reads were removed with SAMtools (v 1.10.0) and converted to wig files.
BigWig files were generated with Wig/BedGraph-to-bigWig converter (Galaxy Version 1.1.1) and files were visualised in the UCSC browser
assembly: mm9
processed data files format and content: BigWig and Wig files of reads mapped to mm9 mouse genome

source_name: mES

growth_protocol: Mouse ES cells and derived cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 12% heat-inactivated foetal calf serum, 10^3 units/ml leukaemia inhibitory factor (Merck), 0.1 mM β-mercaptoethanol, non-essential amino acids, L-glutamine and penicillin/streptomycin. Cells were maintained in 37 °C incubator under 5% CO2.

extract_protocol:
5 million cells were fixed in growth media with 0.4% formaldehyde for 10 min and quenched with 125 mM glycine. Chromatin was released by sequential lysis with cells lysis buffer (10 mM Tris pH 8, 10 mM NaCl, 0.2% Igepal) and nuclear lysis buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS). Chromatin was sheared to ≈300 bp with 12 rounds of sonication (30 s on, 30 s off) on a Bioruptor (Diagenode) and incubated overnight at 4 ᵒC with 5 μg H3.3 antibody (Abcam, Ab176840). Samples were immunoprecipitated with Protein A Agarose beads (Sigma-Aldrich, 05015979001) and washed sequentially with low salt (20 mM Tris pH 8, 2 mM EDTA, 50 mM NaCl, 1% Triton X-100, 0.1% SDS), high salt (20 mM Tris pH 8, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.01% SDS), and LiCl buffers (10 mM Tris pH 8, 1 mM EDTA, 0.25 M LiCl, 1% Igepal, 1% sodium deoxycholate). Chromatin was eluted with elution buffer (1% SDS, 100 mM NaHCO3), decrosslinked overnight at 65ᵒC, incubated with Proteinase K, phenol chloroform extracted and ethanol precipitated. For PML chromatin immunoprecipitation, cells were treated as above except that they were fixed with 2 mM EGS (Pierce 26103) for 45 min at room temperature in PBS. Formaldehyde was then added to 1% for 20 min and quenched with 125 mM glycine. Chromatin was sheared to under 500 bp with 20 rounds of sonication (30 s on, 30 s off) on a Bioruptor (Diagenode) and lysates were immunoprecipitated with 10 μg PML antibody (Millipore, mab3738).
For the WT H3.3 R1 and H3.3 K27M H3.3 ChIP R1 samples: Ovation Ultralow System V2 using Nugen protocols M01379 v3.1. c-bot clustering using 200pM of library pool. Illumina Protocol 15006165 v02 Jan 2016. 75bp PE sequencing using Illumina HiSeq 3000. Illumina Protocol 15066493 Rev A, February 2015. For all other samples: Ovation Ultralow System V2 using Nugen protocols M01379 v3.1. Denaturing and on-board clustering using 2pM of library pool containing 1% PhiX, Illumina protocol 15048776 v15 Apr 2020. 75 SR sequencing using Illumina NextSeq550 High output mode and v2.5 chemistry. Illumina Protocol 15069765 v06, Jul 2019.

value: mES

value: mouse embryonic stem cells

value: ATRX KO/H3.3 G34R

value: Input


title: IS-caput, BOD, rep2


title: KOLF-2 cells, PTCHD1_WT, Day 24, biol rep 2

value: WT


title: mES G34R PMLInput


title: KOLF-2 cells, PTCHD1_trunc, Day 24, biol rep 2

description:
Trunc 2 = NM_173495.2(PTCHD1_i001):p.(Leu823Glyfs*5)
NPC_trunc2


title: ChIP-seq of H3K27ac at T30 in 2D culture

description: 2D growth

value: breast

value: 2D cluture, charcolized serum + serum starvation + R5020 for 30min


title: IS-caput, BOD, rep1


title: mES K27M PMLInput


title: KOLF-2 cells, PTCHD1_WT, Day 24, biol rep 3


title: mES WT PMLInput


title: KOLF-2 cells, PTCHD1_SNV, Day 24, biol rep 3

description:
SNV = NM_173495 c.2489T>G (p.Ile830Arg)]
NPC_SNV3

value: SNV


title: IS-caput, sham, rep2

value: Wild-type

value: sham operation


title: IS-caput, sham, rep3

value: IS-caput epididymis


title: mES ATRXKOG34R PMLChIP

value: PML ChIP (Millipore, mab3738)


title: ChIP-seq of CTCF at T30 in 2D culture

description: 2D growth

value: Epithelial cancer metastatic


title: KOLF-2 cells, PTCHD1_SNV, Day 24, biol rep 2

description:
SNV = NM_173495 c.2489T>G (p.Ile830Arg)]
NPC_SNV2


title: Ovary, Hypoxia, E3.5

first: Hossam

middle: Hassan

last: Shawki

address: Mizuho Ward, Ōtachō, 3-chōme−1

department: Comparative and Experimental medicine

institute: Nagoya City University

data_processing:
Galaxy platform version 23.1.rc1 (https://usegalaxy.eu/).
Quality of RNA sequences was checked by FastQC (Galaxy version 0.73).
The FASTQ files were mapped to the mm10 mouse genome using HISAT2 (Galaxy version 2.2.1).
The mapped reads were quantified using HTSeq-count (Galaxy version 0.9.1).
Differential expression was defined between hypoxic and Normoxic using DESeq2 (Galaxy Version 2.11.40.7).
Assembly: mm10
Supplementary files format and content: DEGs_Uterus.xlsx: The Excel file comprises Differentially Expressed Genes (DEGs) between Uterus Hypoxia and Uterus Normoxia, with a Log2-fold change (FC) threshold of ≥ 2.
Supplementary files format and content: DEGs_Ovary.xlsx: The Excel file comprises Differentially Expressed Genes (DEGs) between Ovary Hypoxia and Ovary Normoxia, with a Log2-fold change (FC) threshold of ≥ 2.

source_name: Ovary

extract_protocol:
Total RNAs were extracted using ISOGEN II (Nippon gene, Japan). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA sequencing libraries were prepared with an NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, USA) and MGI Easy RNA Directional Library Prep Set (MGI Tech Co. Ltd) according to the manufacturer’s instructions.

value: Ovary

value: Hypoxic


title: IS-caput, sham, rep1


title: ChIP-seq of CTCF at T0 in 2D culture

description: 2D growth

value: 2D cluture, charcolized serum + serum starvation


title: KOLF-2 cells, PTCHD1_WT, Day 24, biol rep 1

value: KOLF-2 derived NPCs

value: Neural progenitor cells


title: Ovary, Normoxia, E3.5

value: Ctrl


title: WT4

city: Beijing

first: Gu

last: Qianchong

address: No. 3, yard 1, Beichen West Road

institute: Institute of Microbiology, Chinese Academy of Sicences

data_processing:
Run fastqc and multiqc.
Run trimmomatic.
Run hisat2.
Run samtools.
Use bamCoverage to generate bigwig file, run macs2 peak calling.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: Tregs

extract_protocol:
Lymphocytes were isolated from the spleen and lymph nodes of 6- to 8-week-old Foxp3RFP/∆2Foxp3GFP-creR26YFP female mice and enriched for CD4+ T cells using magnetic beads. Then, CD4+YFP+RFP+ (WT Tregs) and CD4+YFP+RFP- (Foxp3∆2 tTregs) cells were sorted to a typical purity of >95%. CUT&Tag libraries were generated with the Hyperactive In-Situ ChIP Library Prep Kit for Illumina Kit (Vazyme Biotech, TD901).
Briefly, 50,000 cells for each CUT&Tag library were incubated with 10 μl balanced concanavalin A-coated magnetic beads at RT for 10 min. The bead-bound cells were resuspended with 50 μl of antibody buffer. In all, 1 μg anti-Foxp3 antibody (Abcam, ab150743) was then added to the bead-bound cells. After 2-h incubation at RT, the primary antibody was discarded carefully and 0.5 μl goat anti-rabbit IgG (Vazyme, Ab206-10-AA) diluted with 50 μl Dig-wash buffer was added to the cells. The cells were then incubated at RT for 1 h. Afterward, samples were washed gently with 800 μl Dig-wash buffer, and 0.58 μl pG–Tn5 together with 100 μl Dig-300 buffer was added to the samples. After 1-h incubation at RT, samples were washed gently with 800 μl Dig-300 buffer. In all, 300 μl tagmentation buffer was then added to each sample and the samples were incubated at 37 °C for 1 h. The interactions were quenched by adding 10 μl 0.5 M EDTA, 3 μl 10% SDS, and 2.5 μl 20 mg/ml Proteinase K and incubating the samples at 50 °C for 1 h. Phenol–chloroform and ethanol precipitation, as well as PCR and size selection, were performed as described in Hi-C library construction. All CUT&Tag libraries were sequenced on Illumina Nova Seq 6000 platform at PE150 mode subsequently.

value: Tregs

value: Foxp3 WT

tag: Sex

value: Female

tag: antibody


title: Exon24

value: Foxp3 Exon2KO


title: ChIP-seq of CTCF in normal media in 2D culture rep1

description: 2D growth

value: breast

value: 2D culture nomal media


title: mES G34R PMLChIP

value: mES

value: mouse embryonic stem cells


title: mES WT PMLChIP

value: WT


title: mES K27M PMLChIP

value: PML ChIP (Millipore, mab3738)


title: ChIP-seq of H3K27ac at T0 in 2D culture

description: 2D growth

value: Epithelial cancer metastatic


title: Uterus, Normoxia, E3.5

source_name: Uterus

value: Uterus


title: KOLF-2 cells, PTCHD1_SNV, Day 24, biol rep 1

description:
SNV = NM_173495 c.2489T>G (p.Ile830Arg)]
NPC_SNV1

value: SNV


title: mES ATRXKOG34R H33Input

value: ATRX KO/H3.3 G34R

value: Input


title: Uterus, Hypoxia, E3.5

value: Hypoxic


title: mES G34R H33Input


title: Exon21


title: KOLF-2 cells, PTCHD1_WT, Day 0, biol rep 2

source_name: KOLF-2 cells, Day 0

value: KOLF-2 cells, Day 0

value: induced pluripotent stem cells


title: WT1

value: Tregs

value: Foxp3 WT


title: mES WT H33Input R1


title: Ph+_B-ALL_IL-17A_3

first: Yunxuan

address: Nanwei road

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data).
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other style.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Million Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq2 (v1.16.1) was used for differential gene expression analysis between two samples with non biological replicates.
Assembly: mm10
Supplementary files format and content: *.txt: Tab-delimited text files include FPKM values for each Sample.

source_name: primary Ph+ B-ALL cells

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: primary Ph+ B-ALL cells

tag: strain

value: BCR-ABLtTA


title: KOLF-2 cells, PTCHD1_trunc, Day 0, biol rep 2

description:
Trunc 2= NM_173495.2(PTCHD1_i001):p.(Leu823Glyfs*5)
iPSC_trunc2

value: Truncation


title: IGFBP6_Ctrl_3

city: Moscow

first: Maxim

last: Shkurnikov

address: 2 bld. 85, Ugreshkaya st.

country: Russia

institute: SRC Bioclinicum

data_processing:
The quality of FASTQ files was assessed with FastQC v0.11.9 (Babraham Bioinformatics, United Kingdom) and multiQC v1.9 (Ewels et al., 2016). The adapters were trimmed with fastp 0.21.1 (Chen, 2023). The trimmed mRNA-seq reads were mapped on the reference human genome GENCODE release 37 (GENCODE GRCh38. primary assembly) with STAR 2.7.7a (Dobin et al., 2013). GENCODE release 37 genome annotation (gencode.v37. primary assembly) was used to generate the count matrix with the featureCounts tool from Subread-2.0.1 aligner  (Liao et al., 2013).
Assembly: GENCODE GRCh38. primary assembly
Supplementary files format and content: DESeq2 rlog-normalized RNA-seq data

extract_protocol:
The RNA extraction was performed using the miRNeasy Micro Kit (Qiagen, Germany). RNA samples were treated for ribosomal RNA removal using the MGIEasy rRNA Depletion Kit (MGI, China)
RNA library was prepared for NGS using MGIEasy Library Prep Set (MGI, China).


title: Ph+_B-ALL_IL-17A_2


title: IGFBP6_Ctrl_2


title: KOLF-2 cells, PTCHD1_WT, Day 0, biol rep 3


title: Ph+_B-ALL_IL-17A_1


title: IGFBP6_Ctrl_1


title: mES ATRXKOG34R H33ChIP

value: mES

value: H3.3 ChIP (Abcam, Ab176840)


title: KOLF-2 cells, PTCHD1_SNV, Day 0, biol rep 3

description:
SNV = NM_173495 c.2489T>G (p.Ile830Arg)]
iPSC_SNV3


title: LUC_Ctrl_3

value: shLUC


title: Ph+_B-ALL_con_3

value: control


title: KOLF-2 cells, PTCHD1_trunc, Day 0, biol rep 1

description:
Trunc 1 = NM_173495.2(PTCHD1_i001):p.(Leu827Alafs*4)
iPSC_trunc1


title: mES WT H33ChIP

value: mouse embryonic stem cells

value: WT


title: KOLF-2 cells, PTCHD1_SNV, Day 0, biol rep 2

description:
SNV = NM_173495 c.2489T>G (p.Ile830Arg)]
iPSC_SNV2

value: SNV


title: LUC_Ctrl_2


title: mES G34R H33ChIP


title: Ph+_B-ALL_con_2


title: KOLF-2 cells, PTCHD1_WT, Day 0, biol rep 1


title: Exon2KO Tregs

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house  perl script
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b)  (Mihaela Pertea.et al. 2015) in a reference-based approach
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.16.1)
Assembly: mm10
Supplementary files format and content: tab-delimited Excel files include RPKM values for each Sample

source_name: colon lamina propria

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).A total amount of 1 µg RNA per sample was used as input material for the RNA  sample preparation.
Sequencing libraries were generated using NEBNext® UltraTM  RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s  recommendations and index codes were added to attribute sequences to each sample

value: female

value: colon lamina propria


title: LUC_Ctrl_1


title: KOLF-2 cells, PTCHD1_SNV, Day 0, biol rep 1

description:
SNV = NM_173495 c.2489T>G (p.Ile830Arg)]
iPSC_SNV1


title: Ph+_B-ALL_con_1


title: WT Tregs


title: Liver, BDL- treated  GPR65-KO mice, biological rep3

status: Public on Nov 18 2023

city: Tianjin

first: Kun

last: Zhang

address: Qixiangtai Road NO.22

department: Department of Histology and Embryology

institute: Tianjin medical university

data_processing:
basecalls performed using BGISEQ-500
SOAPnuke was used to get the "clean reads"
Mapping clean reads to hg19 whole genome using BWA
Bowtie2 was used to get mapping ratio
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKMs for every gene and every sample

source_name: BDL- treated  GPR65-KO mice

growth_protocol: Male 6-8 weeks old wild-type (WT) mice and Gpr65 conventional knockout mice on a C57BL/6N background were used in BDL-induced liver fibrosis model

extract_protocol:
RNA of liver tissues were  isolated useing Trizol reagent. Total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer
The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: For BDL-induced mouse liver fibrosis model, mice were treated with sham operation or BDL operation for 21 days.

value: male

value: 6-8 weeks old

value: liver

value: BDL


title: Liver, BDL- treated  GPR65-KO mice, biological rep2


title: Adipose, Degarelix+FSH, biolrep4

city: Aurora

first: Paul

last: MacLean

state: CO

department: Endocrinology, Metabolism, & Diabetes

country: USA

institute: University of Colorado Anschutz Medical Campus

data_processing:
All reads were trimmed for adapters, filtered based on quality score using FASTP and aligned to the rat genome (rn6) using the STAR aligner using default settings. Resulting read alignments for each sample were imported in Seqmonk for gene level quantification as counts mapping to annotated genes. Raw counts were imported into Integrated Differential Expression and Pathway analysis (iDEP version .95).  iDEP.95 is an online graphical user interface that provides access to a number of Bioconductor packages required for RNAseq analysis within RStudio.  Low abundance signals were filtered by using a minimum of 0.5 counts per million (CPM) in at least one library.  Counts were transformed using the EdgeR package for differential gene expression analysis throughput using a CPM of 0.5 and a pseudocount (c) of 1.  The DESeq2 package was utilized to calculate differentially-expressed genes (DEG).
Assembly: rn6
Supplementary files format and content: Processed data are provided as data matrix where rows are gene level quantitation (counts/reads) and columns include samples. A single file is included for all samples.

organism: Rattus norvegicus

source_name: Retroperitoneal White Adipose

extract_protocol:
RNA was extracted from snap-frozen retroperitoneal white adipose tissue from individual female ovariectomized wild-type Wistar rats receiving either degarelix-only (n=6) or degarelix+FSH (n=5) using the RNeasy Mini Kit per manufacturer’s instructions including on-column DNase digestion. Total RNA was quantified using a Qubit RNA BR Assay Kit and RNA integrity was assessed on an RNA ScreenTape.
mRNA-seq libraries were prepared using a TruSeq Stranded RNA HT Sample Prep Kit (Illumina, Cat. No. RS-122-2303) on a Perkin Elmer Sciclone G3 platform. An additional standard 1.0x manual bead cleanup was performed using AMPure XP Beads (Beckman Coulter, A63881) after the libraries were completed to remove primer-dimers. Qubit dsDNA BR Assay kit was used to determine the concentration of the completed library and a Fragment Analyzer Standard Sensitivity NGS Fragment Kit
Paired-end, opposing strand directional libraries

treatment_protocol: 10-week-old female Wistar rats were placed on western diet for 6 weeks and then ovariectomized. Rats were given degarelix and then implanted with osmotic pumps.  6 of the rats had vehicle-only in their pumps.  5 of the rats had FSH delivered in their pumps at 6 ug/kg/day. Rats were calorically-limited on western diet to maintain their pre-OVX body weight for 12 days for metabolic measurement.  Rats were then allowed to eat ad libitum for 7 days.  Finally, rats were fasted for 4 hours and then harvested for tissues.

value: Retroperitoneal White Adipose

value: Wistar

tag: age at harvest

value: :19 Weeks

value: Degarelix + FSH


title: Mock, ATAC, rep2

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
10x Genomics Multiome
combined_filtered.rds

library_source: genomic single cell

data_processing:
Sequence data were processed to obtain single cell feature counts by running cellranger (v6.0.1) and cellranger-arc (v2.0.0) for snRNA-seq and snATAC-seq, respectively. For snRNA-seq, the –include-introns option was used to align reads to the A. thaliana nuclear transcriptome built with the TAIR10 genome and Araport 11 transcriptome. Count data were analyzed with the R packages Seurat v4 (Hao et al. 2021) and Signac (Stuart et al. 2021).
QC matrices for snATAC-seq were generated by a modified version of loadBEDandGenomeData function in the R package Socrates. ACRs were identified with MACS2 (Zhang et al. 2008) with the following parameters: -g (genomesize)=0.8e8, shift=-50, extsize=100, and --qvalue=0.05, --nomodel, --keep-dup all. Fraction of reads mapping to within 2kb upstrem or 1kb downstream TSS was calculated. Nuclei were filtered with the following criteria: 200 < RNA UMI count < 7000, RNA gene count > 180, 200 < ATAC UMI count <20000, fraction of RNA reads mapped to mitochondrial genome < 5%. Seurat objects of individual samples were merged with the Merge_Seurat_List function of the scCustomize package.
Supplementary files format and content: combined_filtered.rds contains snRNA-seq and snATAC-seq data from all samples after cell filtering
Supplementary files format and content: Processed files except for combined_filtered.rds contains snRNA-seq and snATAC-seq data of each sample before cell filtering

organism: Arabidopsis thaliana

source_name: Leaf

extract_protocol:
Fresh Nuclei purification buffer (NPB; 15mM Tris pH 7.5, 2mM EDTA, 80mM KCl, 20mM NaCl, 0.5mM spermidine, 0.2mM spermine, 1:100 BSA, and 1:100 protease inhibitor cocktail) was prepared before the experiment and chilled on ice. All the following procedures were performed on ice or at 4ºC. Twenty leaves were chopped in 500-1,000 µL of cold NPB with 1:500 Protector RNase IN with a razor blade on ice for 5 min to release nuclei and incubated in 20 mL of NPB. The crude nuclei extract was sequentially filtered through 70 µm and 30 µm cell strainers. Triton-X and NP40 were added to the extract at the final concentration of 0.1% each, and the extract was incubated at 4ºC for 5 min with rotation. The nuclei suspension was centrifuged at 50 x g for 3 min in a swing-rotor centrifuge to pellet non-nuclei debris, and the supernatant was taken. Nuclei were pelleted by centrifugation at 500 x g for 5 min with a swing-rotor centrifuge. When the pellet was green, the pellet was resuspended in 20 mL of NPBd (NPB, 0.1% Triton-X, and 0.1% NP40) with 1:1000 Protector RNase IN by pipetting, followed by centrifugation at 700 x g for 5 min. When the pellet was translucent, this step was skipped. The pellet was then washed by resuspending it in 20 mL of NPB with 1:1000 Protector RNase IN and centrifuging at 500 x g for 5 min with a swing-rotor centrifuge. The pellet was resuspended in 950 µL of 1X Nuclei Buffer (10X Genomics; PN-2000207) with 1:20 Protector RNase IN and 1mM DTT. The nuclei suspension was centrifuged at 50 x g for 3 min in a swing-rotor centrifuge to pellet non-nuclei debris, and the supernatant was taken. This step was repeated one more time. Then, nuclei were counted manually with a hemocytometer. Nuclei were pelleted by centrifugation at 500 x g for 5 min with a swing-rotor centrifuge and removed supernatant leaving approximately 10 µL of buffer. Nuclei were counted again, and up to 16k nuclei were used for the following steps. Single-cell RNA-seq and ATAC-seq libraries were constructed according to the manufacturer’s instruction (10X Genomics, catalog: CG000338). Single-nucleus RNA-seq libraries were sequenced with Illumina NovaSeq 6000 in dual-indexmode with 10 cycles for i7 and i5 index. Single-nucleus ATAC-seq libraries were also sequenced with Illumina NovaSeq 6000 in dual-indexmode with eight and 24 cycles for i7 and i5 index, respectively.
We followed the 10X genomics multiome assay protocols

value: Leaf

tag: cultivar

value: Mock


title: Liver, BDL- treated  GPR65-KO mice, biological rep1


title: Liver, sham operation- treated GPR65-KO mice, biological rep3

source_name: sham operation- treated GPR65-KO mice

value: sham operation


title: Adipose, Degarelix+FSH, biolrep5


title: Sixth

city: Jinan

first: jianhua

last: zhang

address: gongyebei street No. 23788

institute: Shandong Academy of Agricultural Sciences

description: Sixth instar

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Assembly: GCA_012979215.2
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

organism: Spodoptera frugiperda

source_name: Spodoptera frugiperda

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol.

value: Spodoptera frugiperda

tag: developmental stage

value: Sixth instar


title: Third

description: Third instar

value: Third instar


title: Adipose, Degarelix+FSH, biolrep3


title: Second

description: Second instar

value: Second instar


title: Adipose, Degarelix-only, biolrep6

value: female

value: Degarelix-only


title: Adipose, Degarelix+FSH, biolrep1


title: Liver, sham operation- treated GPR65-KO mice, biological rep2

value: male


title: Adipose, Degarelix-only, biolrep5


title: Pupa-M-4d

description: Four days of male pupa

value: Four days of male pupa


title: Adipose, Degarelix-only, biolrep3


title: Liver, sham operation- treated GPR65-KO mice, biological rep1

value: 6-8 weeks old

value: liver


title: Adipose, Degarelix-only, biolrep2

value: Retroperitoneal White Adipose


title: Liver, BDL- treated WT mice, biological rep3

source_name: BDL- treated WT mice

value: WT

value: BDL


title: AvrRpt2, 9h, ATAC, rep2

value: AvrRpt2 9h


title: Adipose, Degarelix-only, biolrep1

value: Wistar

value: :19 Weeks


title: Pupa-M-1d

description: One day of male pupa

value: One day of male pupa


title: AvrRpt2, 9h, RNA, rep2

library_source: transcriptomic single cell

value: Leaf


title: T47D mammospheres

city: Yogyakarta

first: Adam

last: Hermawan

state: DI Yogyakarta

address: Sekip Utara II

department: Pharmacy

country: Indonesia

institute: Universitas Gadjah Mada

data_processing:
The qualities of cleaned reads were assessed using FastQC version 0.11.9 (https://github.com/s-andrews/FastQC)
the reports were compiled using MultiQC version 1.1 (https://multiqc.info).
The transcript were quantified using the pseudo-alignment method employing kallsito version 0.461
Supplementary files format and content: tab-delimited text files

source_name: Breast

growth_protocol: MCF-7 and T47D cells were culture in Poly HEMA-coated plate using DMEM supplemented with EGF, insulin, B27 in 5% CO2 incubator

extract_protocol:
RNA was harvested using Bioline - Isolate II RNA Mini Kit.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: MCF-7 cells as control

value: Breast

value: epithelial


title: Mock, RNA, rep2

value: Mock


title: MCF-7 mammospheres


title: Pupa-F-7d

description: Seven days of female pupa

value: Spodoptera frugiperda

value: Seven days of female pupa


title: Adipose, Degarelix+FSH, biolrep2

value: female

value: Degarelix + FSH


title: ATM KO B16 tumor 3

city: Durham

first: Chuan-Yuan

state: NC

address: 905 S. Lasalle St

institute: Duke University Medical Center

data_processing:
RNA-seq data was processed using the TrimGalore tool kit which employs Cutadapt to  trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads.
Only reads that were 20nt or longer after trimming were kept for further analysis.
Reads were mapped to the  GRCm38 of the mouse genome and transcriptome using the STAR RNA-seq alignment  tool.
Reads were kept for subsequent analysis if they mapped to a single genomic location  using the SAMtools.
Gene counts were compiled using the HTSeq tool. Only genes that  had at least 10 reads in any given library were used in subsequent analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: melanoma

growth_protocol: About 100,000 ATM knockout or vector control B16 cells were inoculated subcutaneously into C57BL/6J mice.

extract_protocol:
Tumor tissues were collected on day  13. Total RNA from tumor was prepared using RNeasy plus Universal Mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tumor tissue

tag: genotype/variation

value: ATM KO B16


title: Liver, BDL- treated WT mice, biological rep1

value: male

value: 6-8 weeks old

value: liver


title: ATM KO B16 tumor 2


title: Pupa-M-7d

description: Seven days of male pupa

value: Seven days of male pupa


title: Adipose, Degarelix-only, biolrep4

value: Retroperitoneal White Adipose

value: Wistar

value: Degarelix-only


title: vector control B16 tumor 3

value: vector control


title: Liver, sham operation- treated WT mice, biological rep3

source_name: sham operation- treated WT mice

value: WT

value: sham operation


title: Pupa-F-4d

description: Four days of female pupa

value: Four days of female pupa


title: vector control B16 tumor 2


title: vector control B16 tumor 1


title: Prepupa

description: Prepupa

value: Spodoptera frugiperda

value: Prepupa


title: Pupa-F-1d

description: One day of female pupa

value: One day of female pupa


title: Liver, sham operation- treated WT mice, biological rep1


title: ATM KO 4T1 cells 2

data_processing:
RNA-seq data was processed using the TrimGalore tool kit which employs Cutadapt to  trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads. Only reads  that were 20nt or longer after trimming were kept for further analysis.
Reads were mapped to the  GRCm38 of the mouse genome and transcriptome using the STAR RNA-seq alignment  tool.
Reads were kept for subsequent analysis if they mapped to a single genomic location  using the SAMtools.
Gene counts were compiled using the HTSeq tool. Only genes that  had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression were carried out using the DESeq2 Bioconductor package with the R statistical programming environment.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with normalized expression for every gene and every sample

source_name: breast cancer

extract_protocol:
Total cellular RNA from vector control and ATM KO 4T1 cells was prepared using  RNeasy Plus RNA extraction kits (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Balb/c

value: tumor cells

value: ATM KO 4T1


title: Fourth

description: Fourth instar

value: Fourth instar


title: ATM KO 4T1 cells 3


title: Liver, BDL- treated WT mice, biological rep2

value: male

value: 6-8 weeks old

value: BDL


title: Smarca4 cKO pooled DN2 and DN3 thymocytes Rep2

city: Chicago

first: Alexandra

last: Bradu

state: IL

address: 924 East 57th Street

department: Pathology

institute: University Of Chicago

data_processing:
Adaptor sequences were trimmed using SeqPurge (v2019_11)
Trimmed RNA-seq reads were mapped to the mm10 mouse genome assembly using TopHat (v2.1.1) with settings –microexon-search
Unmapped, unpaired and low quality reads (MAPQ < 5) were removed using samtools (v1.9) view with settings -q 5 -f 2
Paired reads were counted for each gene using featureCounts from Subread (v2.0.1)
‘Transcripts-per-million’ (TPM) values were calculated for each gene to quantify the relative abundance of transcripts for clustering analysis.
‘Trimmed mean of M values’ (TMM) was calculated for each gene for differential comparisons across samples using edgeR (calcNormFactors). Common dispersions were estimated using estimateCommonDisp and Benjamini-Hochberg false discovery rates (FDRs) were calculated for pairwise comparisons using exactTest. Genes exhibiting FDR < 0.05 were regarded as significant.
Assembly: mm10
Supplementary files format and content: RNA_Master_Matrix.txt

source_name: bone marrow

extract_protocol:
RNA-seq library preparation was performed by UChicago genomics core facility. Briefly: 50,000-100,000 primary thymocytes or DN cells from OP9-DL4 co-cultures were FACS-sorted directly into RULT lysis buffer from Qiagen RNeasy UCP Micro Kit and total RNA was extracted using manufacturer’s instructions.
mRNA was enriched and RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA Kit. Paired-end, dual-index sequencing was performed on the Illumina NovaSeq 6000 platform.

value: bone marrow

value: 2-4 months

value: pooled male and female

value: DN2 and DN3 thymocytes

tag: replicate

value: Smarca4f/f; Rosa26nTnG/CreERT2

value: Tamoxifen


title: vector control 4T1 cells 3

value: vector control


title: Smarca4 WT pooled DN2 and DN3 thymocytes Rep2

value: Ethanol


title: vector control 4T1 cells 2


title: ATM KO 4T1 cells 1


title: vector control 4T1 cells 1


title: First

description: First instar

value: Spodoptera frugiperda

value: First instar


title: Fifth

description: Fifth instar

value: Fifth instar


title: ATM KO B16 tumor 1

value: tumor tissue

value: ATM KO B16


title: Urethane4

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

country: Germany

institute: Helmholz Zentrum Munich

data_processing:
Base calling and quality score was performed with Illumina sequencing Q scores
Alignment was performed with STAR aligner32 (v2.7.1a)
Reads per feauture per genes were calculated using the FeatureCounts funtion from Subread29 software (v1.6.5)
Data were filtered, normalized and the differential gene expression was computed using the packages limma (https://bioconductor.org/packages/release/bioc/html/limma.html) and edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html) on R (v3.6.0)
Genome_build: GRCm38/mm9
Supplementary_files_format_and_content: Tab-delimited text files including CPM values for each sample

source_name: lung tumor

extract_protocol:
lungs were taken, total RNA was extracted using the Trizol protocol followed by purification with Qiagen RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with saline or urethane (1 g/Kg, i.p.)

value: FVB/NJ

value: urethane induced lung tumor

tag: time point of harvest

value: 6 months


title: Smarca4 cKO pooled DN2 and DN3 thymocytes Rep1


title: Urethane2


title: Liver, sham operation- treated WT mice, biological rep2

value: male

value: 6-8 weeks old

value: liver

value: WT

value: sham operation


title: Urethane1


title: Smarca4 WT pooled DN2 and DN3 thymocytes Rep1

value: bone marrow

value: 2-4 months

value: pooled male and female

value: DN2 and DN3 thymocytes

value: Smarca4f/f; Rosa26nTnG/CreERT2


title: Ctrl3

source_name: lung

value: normal mouse lung


title: Smarca4 cKO DN1 thymocytes Rep2

value: DN1 thymocytes

value: Tamoxifen


title: Ctrl1


title: Smarca4 WT DN1 thymocytes Rep2

value: Ethanol


title: Adult-M-1d

description: One day of male adult

value: Spodoptera frugiperda

value: One day of male adult


title: Ctrl2

value: FVB/NJ

value: 6 months


title: Smarca4 cKO DN1 thymocytes Rep1


title: Smarca4 WT DN1 thymocytes Rep1


title: Adult-M-4d

description: Four days of male adult

value: Four days of male adult


title: Trio6.Father.Input

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

data_processing:
The adapters and low quality bases were removed by using cutadapt
The Fastq files were aligned to reference genome hg38 by using Hisat2
The m6A peak calling method was modified from published work.The longest isoform of each gene was scanned using a 100-bp sliding window with 10-bp steps. We excluded windows with read counts less than 1/20 of the top window in both the input and m6A-IP sample to reduce bias from potentially inaccurate gene structure annotation and the arbitrary use of the longest isoform.
For each gene, the read counts in each window were normalized by the median count of all windows of that gene. The differential windows between the input and IP samples were identified with a negative binomial model by using the edgeR package.
Sequence motifs on m6A peaks were identified by HOMER
Assembly: GRCh38
Supplementary files format and content: bed
Library strategy: MeRIP-seq

molecule: polyA RNA

source_name: lymphoblastoid cell line (LCL)

growth_protocol: LCLs were cultured in RPM1640 media with 15% FBS and Penicillin-Streptomycin, Fifty million cells were harvested for each m6A-seq experiment, and three technical replicates were performed for each individual.

extract_protocol:
Total RNA was extracted by 5PRIME PerfectPure RNA Cultured Cell kit and poly(A) mRNA pacificated by The FastTrack MAG mRNA Isolation kit
The input mRNA and purfied mRNA (m6A-IP) samples were used for library construction by TrueSeq mRNA stranded kit (Illumina )

treatment_protocol: mRNA was fragmented to ~100nt, and enriched by m6A specific antibody

tag: population

value: YRI

value: lymphoblastoid cell line (LCL)

value: No treatment


title: Trio6.Father.IP

value: anti-m6A antibody (202003, Synaptic System)


title: HeLa_HPV18_4C_rep2

city: Bangalore

first: Anurag

middle: Kumar

last: Singh

address: GKVK, Bellary Road

country: India

institute: National Centre for Biological Sciences

data_processing:
4C-ker package (Raviram et al., 2016) was used to analyse the 4C-seq data.
Assembly: hg19
Supplementary files format and content: bedGraph; cis normalized counts file
Library strategy: 4C-seq

source_name: HeLa

growth_protocol: HeLa cells grown according to the ATCC protocol.

extract_protocol:
The 4C-seq experiment was done following the protocol mentioned in Farooq et al., 2021, Cell Reports. The primary digestion was performed with DpnII (NEB) and the secondary digestion was done with NlaIII enzyme (NEB). The primer used for the HPV18 viewpoint in HeLa and the number of reads in each replicate is mentioned in the Supplementary Table 3 of the manuscript.
4C-seq

value: HeLa

value: WT


title: Trio6.Mother.Input


title: Trio6.Child.IP


title: Trio6.Child.Input


title: Adult-F-4d

description: Four days of female adult

value: Four days of female adult


title: Adult-F-1d

description: One day of female adult

value: One day of female adult


title: Runx1 cKO DN3 thymocytes Rep2

value: bone marrow

value: 2-4 months

value: pooled male and female

value: DN3 thymocytes

value: Runx1f/f; Rosa26nTnG/CreERT2


title: Trio5.Father.IP


title: Egg

description: Egg

value: Spodoptera frugiperda

value: Egg


title: Trio5.Father.Input


title: Runx1 WT DN3 thymocytes Rep2

value: Ethanol


title: Runx1 cKO DN3 thymocytes Rep1

value: Tamoxifen


title: Trio5.Mother.IP

value: YRI


title: Pyruvate-2

type: RNA

city: Fukui

first: Fuga

last: Masuda

state: Fukui

address: 3-9-1 Bunkyo

department: Applied Chemistry & Biotechnology

institute: University of Fukui

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. • Transfer 130μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0002

scan_protocol: Gene ChIP Scanner 3000 7G System

data_processing:
Data were processed using R. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: RaGene-2_0-st.pgf
meta-probeset file: RaGene-2_0-st.mps

label: biotin

source_name: Rat lense, 30mM galactose, 6days, 20mM Pyruvate added, replicate2

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: The lens removed from the culture medium was ground with a biosmasher until it fell apart. Then treat the sample with TRIZOL, cDNA synthesis and amplification was performed

value: Sprague Dawley

value: lens


title: Trio5.Child.IP

value: lymphoblastoid cell line (LCL)

value: No treatment

value: anti-m6A antibody (202003, Synaptic System)


title: HeLa_HPV18_4C_rep1

value: HeLa

value: WT


title: Runx1 WT DN3 thymocytes Rep1

value: bone marrow


title: Trio5.Child.Input


title: Pyruvate-1

source_name: Rat lense, 30mM galactose, 7days, 20mM Pyruvate added, replicate1

value: 30mM galactose, 6days, 20mM Pyruvate added


title: Trio6.Mother.IP


title: Trio4.Father.IP


title: Runx1 cKO DN2 thymocytes Rep2

value: 2-4 months

value: pooled male and female

value: DN2 thymocytes


title: Trio4.Father.Input


title: Trio4.Mother.IP


title: Trio4.Child.IP


title: Runx1 cKO DN2 thymocytes Rep1

value: Runx1f/f; Rosa26nTnG/CreERT2


title: WRENJ_1

city: Seoul

first: Han-Sung

last: Jung

address: 50, Yonsei-ro, Seodaemun-gu

department: Dental School

country: South Korea

institute: Yonsei University

data_processing:
Reads qualified and pre-processed using FastQC (v0.11.9) and Trim Galore (v0.6.5) were aligned on a reference genome (GRCm38) using TopHat (v2.1.1).
Assembly: GRCm38
Supplementary files format and content: comma-delimited text files include FPKM values for each sample

source_name: Dental epithelium

growth_protocol: Dental epithelial tissue of apical mouse incisor buds was extracted from 9-week-old female C57BL/6J mouse as previously described1. Collected epithelial tissues were immersed in dissociation solution (a 1:1:1 mixture of TrypLE, 2.2 U/ml Dispase II, and 1 mg/ml collagenase IV) and placed on ice. Using a Pasteur pipette drawn into a capillary as previously described2, tissues were triturated by repeatedly aspirating and expelling the solution and incubated at 37 °C water bath for 30 min. Then equal volumes of chilled basal media (DMEM/F12 containing 2% [v/v] B27, 1% [v/v] N2, and 1% [v/v] penicillin-streptomycin) were added to the solution. The solution was passed through a 40-μm cell strainer and centrifuged at 400g for 5 min. The supernatant was discarded, and the pellet was suspended in pre-melted Matrigel. The 20 μl of Matrigel containing 5 x 103 cells was seeded per a well of pre-warmed 24 well culture plates and solidified in 37 °C incubator for 10 min before media overlay. All media were supplemented with 1 mM N-acetylcysteine, 10 μM Y27632, 50% (v/v) Wnt3a-conditioned media (CM), 5% (v/v) R-spondin1-CM, and 100 μg/ml EGF (WRE). Some media were supplemented with one or more of the following: 200 μg/ml Noggin (N), 100 μg/ml FGF10 (F), 10 μM DBZ (D), 0.5 μM A83-01 (A), and/or 10 mM nicotinamide (Ni). Subculture was performed every 14 days. For subculture, Matrigel was disrupted by pipetting with chilled basal media and organoids were pelleted at 200g for 5 min. The pellet was resuspended and triturated in pre-warmed TrypLE by pipetting through a pipette as described before. The suspended pieces of organoids were incubated in the dissociation solution  at 37 °C for 10 min. The dissociated cells were filtered and embedded into Matrigel in same manner as described above.

extract_protocol:
RNA isolation of organoids and tissues were performed with RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions. Reverse transcription was performed using Maxime RT PreMix (#25081; iNtRON, Korea).
A library was constructed using TruSeq RNA Library Prep Kit (Illumina) from total RNA and sequenced on an Illumina HiSeq 2000 sequencer.

value: Dental epithelium

value: Primary epithelial cells

value: Wild-type

value: Organoids were grown from aDESCs embedded in Matrigel using media supplemented with Wnt3a, R-spondin1, Egf, Noggin, and Jagged1 for 14 days


title: Galactose-2

source_name: Rat lense, 30mM galactose, 6days, replicate2

value: Sprague Dawley

value: 30mM galactose, 6days


title: Runx1 WT DN2 thymocytes Rep1

value: Ethanol


title: Galactose-3

source_name: Rat lense, 30mM galactose, 6days, replicate3

value: lens


title: Trio5.Mother.Input

value: YRI

value: lymphoblastoid cell line (LCL)

value: No treatment


title: Trio3.Father.Input


title: WRENFJ

value: Organoids were grown from aDESCs embedded in Matrigel using media supplemented with Wnt3a, R-spondin1, Egf, Noggin, Fgf10, and Jagged1 for 14 days


title: Trio3.Mother.IP

value: anti-m6A antibody (202003, Synaptic System)


title: Trio4.Child.Input


title: Control-Day6

source_name: Rat lense, without galactose, 6 days

value: without galactose, 6 days


title: Trio3.Father.IP


title: Control-Day4

source_name: Rat lense, without galactose, 4 days

value: without galactose, 4 days


title: Runx1 cKO DN1 thymocytes Rep2

value: bone marrow

value: 2-4 months

value: pooled male and female

value: DN1 thymocytes

value: Tamoxifen


title: Runx1 WT DN1 thymocytes Rep2

value: Runx1f/f; Rosa26nTnG/CreERT2


title: Trio3.Child.IP


title: Trio3.Mother.Input


title: Trio3.Child.Input


title: WRENF_1

value: Dental epithelium

value: Primary epithelial cells

value: Wild-type

value: Organoids were grown from aDESCs embedded in Matrigel using media supplemented with Wnt3a, R-spondin1, Egf, Noggin, and Fgf10 for 14 days


title: Trio2.Father.IP

value: YRI


title: Trio2.Father.Input

value: lymphoblastoid cell line (LCL)


title: Trio4.Mother.Input

value: No treatment


title: WRENFD_1

value: Organoids were grown from aDESCs embedded in Matrigel using media supplemented with Wnt3a, R-spondin1, Egf, Noggin, Fgf10, and dibenzazepine for 14 days


title: Runx1 cKO DN1 thymocytes Rep1


title: WREND_1

value: Organoids were grown from aDESCs embedded in Matrigel using media supplemented with Wnt3a, R-spondin1, Egf, Noggin, and dibenzazepine for 14 days


title: Trio2.Mother.IP

value: anti-m6A antibody (202003, Synaptic System)


title: Runx1 WT DN1 thymocytes Rep1

value: Ethanol


title: Runx1 WT DN2 thymocytes Rep2

value: bone marrow

value: DN2 thymocytes


title: Trio2.Mother.Input


title: Trio2.Child.IP


title: WREN_1

value: Organoids were grown from aDESCs embedded in Matrigel using media supplemented with Wnt3a, R-spondin1, Egf, and Noggin for 14 days


title: Galactose-1

source_name: Rat lense, 30mM galactose, 6days, replicate1

value: Sprague Dawley

value: lens

value: 30mM galactose, 6days


title: Trio2.Child.Input


title: NOD/LTJ, SJQYD5

first: Sun

last: Peng

address: 260 Baichuan Street

institute: Zhejiang chinese medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Submandibular gland

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Submandibular gland

value: WT

value: SJQYD


title: Trio1.Father.IP


title: NOD/LTJ, SJQYD4


title: Trio1.Mother.IP


title: T cell, Cas9 genome edited, MULTI-seq barcode

city: Berkeley

first: Marena

middle: Isabelle

last: Trinidad

address: 2151 Berkeley Way

institute: Innovative Genomics Institute

description: Data for MULTI-seq barcode PCR

data_processing:
Processing of the GEX and MultiSeq libraries into cellranger files: The command `cellranger multi` is used to create the six assignment_confidence_table.csv files (one per sample).
Concatenating the sgRNA raw fastq files across the two libraries (JDCT003 and JDCT004).
Processing of the sgRNA and GEX libraries: The command `cellranger count` is used to count the number of reads per guide per cell (protospacer_calls_per_cell.csv for each of the 6 samples) and to create the gene-expression matrix (filtered_feature_bc_matrix.h5).
Processing of GEX, MultiSeq and guide calls into a single h5ad file (fully_processed.h5ad) by 1) combining the raw h5 gene-expression data with the guide counts (across the 6 samples), 2) finding the first and second most common guide per cell and using a binomial test to determine whether the most common guide has significantly more counts the the second most common one, 3) adding sample calls, and 4) calculating QC metrics.
Constructing the gene metadata file for inferCNV (inferCNVgeneName.txt) using the gtf_to_position_file.py script provided by inferCNV.
Applying quality-control filters (singlet filter, <10K total counts filter, and <10%mito filter) to create qced.h5ad from fully_processed.h5ad.
Running inferCNV by splitting the QC-ed dataset (qced.h5ad) into 9 batches (each batch containing a subset of the cells), resulting in 9 infercnv.observations.txt files.
Concatenating the 9 inferCNV files (infercnv.observations.txt) into a single Python pkl file (concat_InferCNV.pkl).
Calculating candidate breakpoints per cell per chromosome by scanning along each chromosome for a potential breakpoint where the difference between the average inferCNV values to the left and right is greatest to produce aneuploidy_events.csv.
Assembly: GRCh38 (Cellranger's refdata-gex-GRCh38-2020-A)
Supplementary files format and content: sample{1-6}-assignment_confidence_table.csv: The cellranger multi files (CSV) across the 6 samples (1-6).
Supplementary files format and content: sample{A-F}-filtered_feature_bc_matrix.h5: The gene-expression matrix (H5) across the 6 samples (A-F).
Supplementary files format and content: sample{A-F}-protospacer_calls_per_cell.csv: Count of the number of reads per guide per cell (CSV) across the 6 samples (A-F).
Supplementary files format and content: fully_processed.h5ad: The fully processed gene-expression AnnData object with both the gene-expression matrix and guide counts (h5ad), after integrating all samples into a single dataset.
Supplementary files format and content: inferCNVgeneName.txt: The name of chromosomal location of each of the inferCNV genes (tab-separated values).
Supplementary files format and content: qced.h5ad: The full quality-controled dataset (h5ad).
Supplementary files format and content: Batch{1-9}-infercnv.observations.txt: The inferCNV output files with estimated copy number of each inferCNV gene in each cell (space-separated values), separated into 9 batches (1-9).
Supplementary files format and content: concat_InferCNV.pkl: A concatenation of all inferCNV outputs into a single file covering all cells (Python pkl format).
Supplementary files format and content: aneuploidy_events.csv: For each cell and chromosome, the number of inferCNV genes and average inferCNV values to the left and right of the most likely breakpoint (CSV).

source_name: T cell

growth_protocol: T cells were isolated from primary, frozen PBMCs using EasySep Human T Cell Isolation Kits (StemCell Technologies) and cultured in X-Vivo 15 medium (Lonza) with 5% FBS, 50 uM mercaptoethanol, and 10 mM N-acetyl L-cysteine. One day post-isolation, cells were activated and stimulated with a 1:1 ratio of anti-human CD3/CD28 magentic Dynabeads (Thermo Fisher) to cells, as well as 5 ng/mL IL-7, 5 ng/mL IL-15, and 300 U/mL IL-2 for three days. After bead removal, T cells were cultured in medium with 300 U/mL IL-2 and maintained at a density of 0.5-1E6 cells/mL.

extract_protocol:
Four days post-electroporation, T cells were labeled via MULTI-seq as previously described in McGinnis et al. Nat Methods (2019). Briefly, a lipid-modified oligonucleotide (LMO) was combined with a unique oligonucleotide barcode at a 1:1 molar ratio in PBS (−/−). 500,000 cells or fewer were washed twice with PBS (−/−) and then resuspended in PBS (−/−). The LMO/barcode solution was mixed with each cell suspension and incubated on ice for 5 minutes before addition of a co-anchor LMO and incubation on ice for an additional 5 minutes. Cold 1% BSA in PBS (−/−) was added to sequester free LMOs before washing cells twice with cold 1% BSA in PBS (−/−). Uniquely labeled cells were pooled in equal numbers in 1% BSA in PBS (−/−) to a final concentration of ~1,600 cells/mL. 10x Genomics Chromium Next GEM Single Cell 3’ Gene Expression Kits (v3.1) were utilized to extract polyA RNA according to the manufacturer’s instructions, with the following modification. Lanes of a standard Chromium chip were “super loaded” with ~50,000 cells to yield a target cell recovery of ~25,000 cells.
scRNA-seq library construction was performed according to the 10x Genomics Chromium Next GEM Single Cell 3’ Gene Expression Kit (v3.1) manufacturer’s instructions, with the following modifications. During the cDNA amplification, 1 μL of a 2.5 μM MULTI-seq primer (see McGinnis et al.) was added. Supernatant from the cDNA bead cleanup was saved because it contained the MULTI-seq barcode amplicon. Supernatants were further cleaned by addition of SPRIselect beads and isopropanol with a conventional magnetic bead cleanup protocol. 3.5 ng of each cleaned amplicon was used in a PCR reaction to add sequencing indices; the reactions included KAPA HiFi HotStart ReadyMix (Roche), a unique i5 primer, and a unique RPI i7 primer. The PCR reactions were cleaned with SPRIselect beads before final library QC. The CROP-seq sgRNA was also enriched from the resulting cDNA according to Hill et al Nat Methods (2018). Briefly, 25 ng of cDNA was added to eight separate KAPA HiFi HotStart ReadyMix PCR reactions and amplified for 10 cycles with an annealing temperature of 65° C to enrich for the gRNA. Individual PCR reactions were pooled together and cleaned with SPRIselect beads. 8 µL of cleaned PCR1 product was added to a second KAPA HiFi HotStart ReadyMix PCR reaction and amplified for 10 cycles with an annealing temperature of 65° C to add Illumina sequencing adaptors. Gene expression, MULTI-seq barcode, and CROP-seq enrichment libraries were sequenced on an Illumina NovaSeq 600. Multiple iterations of library sequencing were concatenated to achieve the desired sequencing depth.

treatment_protocol: 24 hours after activation/stimulation, lentivirus was added to the cells at a multiplicity of infection (MOI) of ~0.3. After three days of activation/stimulation, dynabeads were removed from T cells. Multiple batches of 250,000 activated and stimulated primary human T cells were resuspended in P3 buffer (Lonza) and mixed with 50 pmol spCas9 (IDT) and 100 pmol crRNA:tracrRNA (IDT) prior to electroporation on a Lonza 4D-Nucleofector (pulse code EH-115). Cells were kept in X-Vivo 15 medium with 300 U/mL IL-2 for four days. GFP+ cells were enriched via fluorescence-activated cell sorting.

value: T cell

value: Cas9 genome edited


title: NOD/LTJ, SJQYD3


title: T cell, Cas9 genome edited, CROP-seq gRNA

description: Data for CROP-seq sgRNA PCR enrichment


title: Trio1.Mother.Input

value: YRI

value: lymphoblastoid cell line (LCL)


title: NOD/LTJ, SJQYD2


title: Trio1.Child.IP

value: No treatment


title: Trio1.Child.Input


title: P8_20pos

city: New York

first: Liora

middle: s

last: Katz

state: NY

address: One Gustave L. Levy Place, Box 1152, Atran building 5-17

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw count data was pre-filtered to keep genes with CPM>1.0 for at least 60% of the samples.
Count data was normalized via the weighted-trimmed mean of M-Values, normalized counts were transformed into normally distributed expression values via the voom transformation using covariates model.
Statistical analysis was carried out using R language version 3.0.3
Assembly: GRCh38/hg38

source_name: Islets of Langerhans

extract_protocol:
Total RNA from ~100 human islets isolated using the RNAeasy micro kit (Qiagen) according to the manufacturer’s protocol.
Samples were submitted to the New York Genome Center and RNA was amplified via the NuGEN Ovation RNA-Seq System V2 prior to RNA sequencing. 35-40 million 2x50 bp paired-end reads were sequenced per sample on the HiSeq2500 instrument (Illumina)

value: Islets of Langerhans

tag: donor

value: 20mM glucose, 10nM T3


title: p8_20neg

value: 20mM glucose, 0nM T3


title: T cell, Cas9 genome edited, MULTI-seq barcodes

description: Data for MULTI-seq barcode PCR

data_processing:
The command cellranger count was peformed on the three pools. The number of cells called was set using the parameter --force-cells=15000
For each pool, cell demultiplexing was performed as the MULTI-seq barcodes were used. To perform demultiplexing, the python tool MULTI-seq barcode alignment was used - https://github.com/mtvector/py-multi-seq
The downstream processing of the cellranger outputs for each pool was performed. The input used was the filtered_feature_bc_matrix folder. The scanpy tool in python was used to perform the processing. The demultiplexing results were also combined. The final product was a h5ad file.
Constructing the gene metadata file for inferCNV (inferCNVgeneName.txt) using the gtf_to_position_file.py script provided by inferCNV.
To perform inferCNV, the h5ad was converted to h5seurat to be compatible with R. inferCNV performed on converted h5seurat object.
Assembly: GRCh38 (Cellranger's refdata-gex-GRCh38-2020-A)
Supplementary files format and content: rawSingletForR15Kcells.h5ad: Unfiltered gene-expression AnnData object with both the gene-expression matrix (h5ad).
Supplementary files format and content: cas9ProcessedAneuploidyStatus.h5ad: The fully processed gene-expression AnnData object with both the gene-expression matrix (h5ad).
Supplementary files format and content: inferCNVgeneName.txt: The name of chromosomal location of each of the inferCNV genes (tab-separated values).
Supplementary files format and content: GUIDEvsNT_CHR14_RESULTS.txt: The inferCNV output file with estimated copy number of each inferCNV gene in each cell (space-separated values).
Supplementary files format and content: TRAC_aneuploidy_breakpoints_ALLChromo.csv: For each cell and chromosome, the number of inferCNV genes and average inferCNV values to the left and right of the most likely breakpoint (CSV).

extract_protocol:
Four days post-electroporation, T cells were labeled via MULTI-seq as previously described in McGinnis et al. Nat Methods (2019). Briefly, a lipid-modified oligonucleotide (LMO) was combined with a unique oligonucleotide barcode at a 1:1 molar ratio in PBS (−/−). 500,000 cells or fewer were washed twice with PBS (−/−) and then resuspended in PBS (−/−). The LMO/barcode solution was mixed with each cell suspension and incubated on ice for 5 minutes before addition of a co-anchor LMO and incubation on ice for an additional 5 minutes. Cold 1% BSA in PBS (−/−) was added to sequester free LMOs before washing cells twice with cold 1% BSA in PBS (−/−). Uniquely labeled cells were pooled in equal numbers in 1% BSA in PBS (−/−) to a final concentration of ~1,600 cells/mL. 10x Genomics Chromium Next GEM Single Cell 3’ Gene Expression Kits (v3.1) were utilized to extract polyA RNA according to the manufacturer’s instructions, with the following modification. Lanes of a standard Chromium chip were “super loaded” with ~50,000 cells to yield a target cell recovery of ~25,000 cells.
scRNA-seq library construction was performed according to the 10x Genomics Chromium Next GEM Single Cell 3’ Gene Expression Kit (v3.1) manufacturer’s instructions, with the following modifications. During the cDNA amplification, 1 μL of a 2.5 μM MULTI-seq primer (see McGinnis et al.) was added. Supernatant from the cDNA bead cleanup was saved because it contained the MULTI-seq barcode amplicon. Supernatants were further cleaned by addition of SPRIselect beads and isopropanol with a conventional magnetic bead cleanup protocol. 3.5 ng of each cleaned amplicon was used in a PCR reaction to add sequencing indices; the reactions included KAPA HiFi HotStart ReadyMix (Roche), a unique i5 primer, and a unique RPI i7 primer. The PCR reactions were cleaned with SPRIselect beads before final library QC. Gene expression and MULTI-seq barcode libraries were pooled 6:1 (molar ratio) prior to sequencing.

treatment_protocol: Approximately 250,000 activated and stimulated primary human T cells were resuspended in P3 buffer (Lonza) and mixed with 50 pmol spCas9 (IDT) and 100 pmol crRNA:tracrRNA (IDT) prior to electroporation on a Lonza 4D-Nucleofector (pulse code EH-115). Cells were kept in X-Vivo 15 medium with 300 U/mL IL-2 for four days until 10x Genomics 3' scRNA-seq.


title: NOD/LTJ, SJQYD1


title: T cell, Cas9 genome edited, Gene expression

description: 10X GEX data


title: T cell, Cas9 genome edited, GEX scrnaseq

description: 10X GEX data


title: Sal-delropB-LE-rep-3_S15

city: Houston

first: Muthiah

last: Kumaraswami

state: Texas

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

description: Exponential growth of SAL nrpr mutant in THY at OD600 of 2.0

data_processing:
CLC-Genomics WorkBench, version 5 (CLC Bio
For RNA-seq analysis, the total number of reads per gene between the replicates was normalized by TPKM [(transcripts/kilobase of gene)/(million reads aligning to the genome)].
Using the TPKM values, pair-wise comparisons were carried out between the two samples to identify the differentially expressed genes. Genes with 2-fold difference and P < 0.05 after applying Bonferroni’s correction considered to be statistically significant.
Assembly: SsalK12v1
Supplementary files format and content: Excel file compared nip* in marker background
Supplementary files format and content: Excel file compared ▲nrpR in marker background

organism: Streptococcus salivarius K12

source_name: bacteria

growth_protocol: SAL strains were grown in THY medium to mid-exponential phase of growth (A600 ~ 2.0) and a total of 3 biological replicates per strain were used

extract_protocol:
Total RNA was purified using a RNeasy (Qiagen) mini kit according to the manufacturer’s protocol. RNA was analyzed for quality and concentration with an Agilent 2100 Bioanalyzer.
The ribosomally RNA depleted sample was used to synthesize adaptor tagged cDNA libraries using the ScriptSeq V2 RNA-seq library preparation kit (Epicenter).

tag: growth phase

value: Exponential growth

value: bacteria

tag: genetic modification

value: nrpr knockout


title: P8_6pos

value: 6mM glucose, 10nM T3


title: Hashtag T cell Cas9 genome edited

description: Data for hashtag oligos

data_processing:
The cellranger multi command was used to process the four pools of GEX and MULTI fastqs. The output results were aggregated using cellranger aggr.
The outputs from cellranger aggr were processed in python using the scanpy tool. The result is an h5ad file for day 4 and day 7 timepoints.
Using the day 4 and day 7 h5ad files, the required input files for inferCNV were created for each timepoint and donor (donor 6 and donor 7).
inferCNV was performed by using the input created previously and by converting the h5ad to h5seurat so that it is compatible with R.
The inferCNV results were added merged with the combined h5ad (both day 4 and day 7).
Calculating candidate breakpoints per cell per chromosome by scanning along each chromosome for a potential breakpoint where the difference between the average inferCNV values to the left and right is greatest to produce aneuploidy_events.csv.
Assembly: GRCh38 (Cellranger's refdata-gex-GRCh38-2020-A)
Supplementary files format and content: CAR-T_ALL-CELLS.h5ad: The fully processed gene-expression AnnData object with both the gene-expression matrix and guide counts (h5ad).
Supplementary files format and content: inferCNV_results_CAR-T_Donor{6-7}_Day{4-7}.txt: The inferCNV output files with estimated copy number of each inferCNV gene in each cell (space-separated values), separated for 2 separate donors (6 and 7) over two timepoints each (day 4 and 7).
Supplementary files format and content: inferCNVgeneName.txt: The name of chromosomal location of each of the inferCNV genes (tab-separated values).
Supplementary files format and content: CART_UCSF_aneuploidy_breakpoints.csv: For each cell and chromosome, the number of inferCNV genes and average inferCNV values to the left and right of the most likely breakpoint (CSV).

growth_protocol: T cells were isolated from primary, frozen PBMCs using EasySep Human T Cell Isolation Kits (StemCell Technologies) and cultured in X-Vivo 15 medium (Lonza) with 5% FBS, 5 ng/mL IL-7, and 5 ng/mL IL-15. Cells were activated and stimulated with a 1:1 ratio of anti-human CD3/CD28 magentic Dynabeads (Thermo Fisher) to cells, as well as 5 ng/mL IL-7, 5 ng/mL IL-15, and 300 U/mL IL-2 for three days. After bead removal, T cells were cultured in medium with 300 U/mL IL-2 and maintained at a density of 0.5-1E6 cells/mL.

extract_protocol:
CAR T cells were harvested at two time points after independent nucleofections (day four and day seven post-nucleofection). TotalSeq-A0251-1 anti-human Hashtag reagents (BioLegend) were used to label different cell conditions. For the experiment, 500,000 cells from each condition were labeled with the hash antibodies in Cell Staining Buffer at 4° C for 30 min. After labeling, cells were washed three times with Cell Staining Buffer at 4° C and then resuspended in PBS (-/-) containing 0.04% BSA. Labeled cells were pooled and 50,000 cells were “super loaded” into four lanes (two lanes for day four samples and the other two lanes for day seven samples) of a 10X Chromium Single-Cell G Chip. A 10x Genomics Chromium Next GEM Single Cell 3’ Gene 778 Expression Kit (v3.1) was utilized according to the manufacturer’s instructions, and the subsequent library was sequenced on an Illumina NovaSeq 600 S4 Flow Cell.
scRNA-seq library construction was performed according to the 10x Genomics Chromium Next GEM Single Cell 3’ Gene Expression Kit (v3.1) manufacturer’s instructions.

treatment_protocol: Approximately 2,000,000 activated and stimulated primary human T cells were resuspended in P3 buffer (Lonza) and mixed with 60 pmol spCas9 (IDT) and 120 pmol crRNA:tracrRNA (IDT) prior to electroporation on a Lonza 4D-Nucleofector (pulse code EH-115). 30-60 min after electoporation, recombinant AAV6 encoding a CAR HDR template was added to cells at an MOI of 10E5. Cells were kept in X-Vivo 15 medium with 300 U/mL IL-2 for four or seven days until 10x Genomics 3' scRNA-seq.

tag: cell type


title: Sal-delropB-LE-rep-2_S14


title: NOD/LTJ, Model3

tag: tissue

tag: genotype


title: NOD/LTJ, Model4

tag: treatment


title: NOD/LTJ, Model5


title: p7_20neg


title: Sal-delropB-LE-rep-1_S13


title: P7_20pos


title: Trio1.Father.Input

tag: cell line


title: Donor Young-2, HSC or CD34+CD45RA-CD90+ enriched cells from BMMC, mitochondrial DNA, sample 9

city: Boston

first: Chen

last: Weng

state: OH

address: 415 Main St, Cambridge

department: Genetics

institute: Broad Institute and Whitehead Institute

description: mtDNA library (Cell barcodes are matchable with mRNA and ATAC lib in sample 9): read1 file contains one end of mitochondrial genomic region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of mitochondrial genomic region.

data_processing:
The data preprocessing for the joint single-cell RNA and ATAC data was performed using 10X Genomics data preprocessing software Cell-ranger-arc.  The basic quality control analysis was as follows: RNA UMI: 1,000~25,000 transcripts per cell, unique ATAC fragment: 1,000 ~ 70,000, Fragment on peak minimum percentage: 10%, minimum mtDNA copies per position per cell: 10X. Finally, the possible doublets are removed by Amulet (using default parameter). Unsupervised community detection-based clustering was performed on weighted nearest neighbour (WNN) using Seurat. Cell types are firstly annotated by gene expression using the latest signature (van Galen under review) which was further validated by sorted bulk RNA-seq data (https://sankaranlab.shinyapps.io/geneExpression/). The ATAC unique fragments for each clustered cell type were further aggregated to generate pseudo-bulk ATAC tracks. The single cell motif analysis was performed using ChromVar using the JASPAR human transcription factor (TF) database. The deviation of the TF frequency was computed for each cell for the downstream analysis.
The mutation calling pipeline is in following steps using package redeemV: 1, Data Preprocessing and eUMI grouping. 2, Consensus filtering. 3, Strand bias removal. 4, Lineage informative variants identification
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: mtDNA mutation count matries (Cell-to-mito variants, MatrixMarket file)
Library strategy: mtDNA-seq

source_name: Bone Marrow

extract_protocol:
Bone marrow was collected from healthy young or aged donors. Bone marrow aspirate was diluted with an equal volume of Wash Buffer (PBS, 2% FBS, 1mM EDTA). Ficoll medium was added to SepMateTM (Catalog #85460) tubes and then the diluted bone marrow sample was layered on top followed by centrifuging at 1200 g for 20 minutes at room temperature. The top layer, containing the mononuclear cells, was transferred to a new tube, which was then filled up by Wash Buffer. The mononuclear cells were centrifuged at 300 g for 8 minutes. The supernatant was discarded, and the cells were washed twice and resuspended in Wash Buffer for further enrichment or in Freezing buffer (10% DMSO in FBS). Starting with the BMMCs isolated from the previous step, we enriched CD34+ cells following EasySep™ Human Cord Blood CD34 Positive Selection Kit II (Catalog #17896). Briefly, EasySep™ Human CD34 Positive Selection Cocktail (Catalog #18096C) was added to BMMCs suspension to 100 ul/ml and incubated at room temperature for 10 minutes. EasySep™ Dextran RapidSpheres™ (Catalog #50100) was vortexed and added to each sample to 50 µl/ml.  The mix was incubated for 3 minutes at room temperature. Next, Wash Buffer (7 ml) was added to the tube, The cells were then washed 4 times in "The Big Easy" EasySep™ Magnet (Catalog #18001). Finally, cells were resuspended in Wash Buffer and were centrifuged at 300g for 10 min. The CD34+ positive cell pellet was then resuspended in a freezing buffer (10% DMSO in FBS).  To further enrich the hematopoietic stem cells (HSCs), an aliquot of the enriched CD34+ cells were stained by one of the following two antibody panels. 1) CD34 PerCP-Cy5.5 (Catalog #347222); CD45RA Alexa Fluor 488 (Catalog #304114); CD90 PE-Cy7 (Catalog #561558); and  DAPI (Catalog #D1306) as viability dye. Or 2) CD34 BV421 (Catalog #562577); CD45RA-APC-H7 (Catalog #560674); CD90 PE-Cy7 (Catalog #561558), and 7-AAD as viability dye(Catalog #559925). The cells were further sorted using BD FACSAriaTM for CD34+CD45RA-CD90+ to enrich HSCs. BMMCs, as well as enriched CD34+ and CD34+CD45RA-CD90+ cells were cryopreserved. After thawing, cells were immediately processed for experiment as soon as possible without any culturing.
RNA lib and ATAC lib prep:  After tagmentation, cells were immediately processed for GEM generation & barcoding following 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Manual  (version CG000338 Rev A, 10x Genomics) with Step 2. Next, the Post GEM Incubation Cleanup and Pre-Amplification PCR were performed following the same User Manual with Step 3 and Step 4. The pre-amplified library was eluted in 100ul EB buffer instead of 160ul. For RNA library prep, we took an aliquot of 35 ul pre-amplified library and followed the same User Manual (version CG000338 Rev A, 10x Genomics) from Step 6 and Step 7. We developed an in-house protocol to generate the massive ATAC library with enough material for both direct sequencing and mtDNA hybridization. For each sample, 8 reactions of the following were performed (each in 50 ul). 5 μl pre-amplified product, 25 μl NEBnext mix (Catalog M0541L), 2.4 μl 10 μM Nextera N70X primer (Supplementary Data 2), 2.4 μl 10X SI PCR primer B (Catalog #PN2000128), 0.5 μl 100X SYBR Green (Catalog #S7563), and 14.7 μl water. The thermocycler program started with 98°C 45 s., followed by the 6-12 cycles of: 98°C for 10 s., 63°C for 30 s., and 72°C for 20 s.; The actual cycle numbers are determined using the amplification curve and the qPCR was stopped when the curve started to reach plateau. The qPCR products (50ul * 8 wells) were combined and purified using SPRI beads (Catalog #B23318) with size selection 0.4X~1.55X. The expected yield is 2,000 ng to 4,000 ng.
mtDNA lib prep: We designed 4 sets of DNA probes, with each probe set covering the whole mitochondrial genome and containing 138 biotinylated oligos that are 120 bp long. The 4 sets of probes ((v1, v2, v3, and v4) are staggered by 30 bp with each other and ensure good coverage on junction areas (Supplementary Data 2). The hybridization started with 500 ng ATAC library products for each probe set. In total, 4 independent reactions were performed in parallel and combined at the end (2,000ng input in total). The detailed incubation and wash methods largely followed the Tube Protocol in IDT xGen Hybridization Capture of DNA Libraries protocol.  Briefly, 500 ng input was combined with Cot DNA and purified by SPRI beads, which was eluted by hybridization mix that contains hybridization buffer, hybridization buffer enhancer, one of the probe set, as well as xGen™ Universal Blockers NXT (Catalog #1079584). The hybridization reaction was performed as below: 95C 30 seconds followed by 65C overnight.  The biotin-streptavidin Dynabeads purification was carried out on Day 2 using xGen Hybridization and Wash Kit. The Dynabeads after capturing and washing were used for final quick qPCR amplification (3-5 cycles). The reaction mix is as below: 20ul beads, 25ul KAPA HiFi HotStart ReadyMix (Catalog #KK2601), Primer 2.4ul P5 (Supplementary Data 2), Primer P7 (Supplementary Data 2), 0.5ul 100X SYBR Green (Catalog #S7563). The PCR program started with 98°C 45 s, followed by the 3-5 cycles of: 98°C for 10 s., 63°C for 30 s., and 72°C for 20 s. The final enriched mtDNA was purified by SPRI beads (1.6X)

value: Bone Marrow

value: Hematopoietic Stem cells (HSC or CD34+CD45RA-CD90+ enriched cells from BMMCs)


title: P7_6pos


title: NOD/LTJ, Model1

value: Submandibular gland


title: NOD/LTJ, Model2

value: WT


title: Sal-sip-LE-rep-3_S11

description: Exponential growth of SAL nip mutant in THY at OD600 of 2.0

value: nip knockout


title: Donor Young-2, HSC or CD34+CD45RA-CD90+ enriched cells from BMMC, mRNA-derived cDNA, sample 9

description: 3' mRNA library (Cell barcodes are matchable with ATAC and mtDNA lib in sample 9): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains transcript.

data_processing:
The data preprocessing for the joint single-cell RNA and ATAC data was performed using 10X Genomics data preprocessing software Cell-ranger-arc.  The basic quality control analysis was as follows: RNA UMI: 1,000~25,000 transcripts per cell, unique ATAC fragment: 1,000 ~ 70,000, Fragment on peak minimum percentage: 10%, minimum mtDNA copies per position per cell: 10X. Finally, the possible doublets are removed by Amulet (using default parameter). Unsupervised community detection-based clustering was performed on weighted nearest neighbour (WNN) using Seurat. Cell types are firstly annotated by gene expression using the latest signature (van Galen under review) which was further validated by sorted bulk RNA-seq data (https://sankaranlab.shinyapps.io/geneExpression/). The ATAC unique fragments for each clustered cell type were further aggregated to generate pseudo-bulk ATAC tracks. The single cell motif analysis was performed using ChromVar using the JASPAR human transcription factor (TF) database. The deviation of the TF frequency was computed for each cell for the downstream analysis.
The mutation calling pipeline is in following steps using package redeemV: 1, Data Preprocessing and eUMI grouping. 2, Consensus filtering. 3, Strand bias removal. 4, Lineage informative variants identification
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: mtDNA mutation count matries (Cell-to-mito variants, MatrixMarket file)


title: p7_6neg

value: 6mM glucose, 0nM T3


title: P520_pos


title: Donor Young-2, HSPC or CD34 enriched cells from BMMC, mitochondrial DNA, sample 8

description: mtDNA library (Cell barcodes are matchable with mRNA and ATAC lib in sample 8): read1 file contains one end of mitochondrial genomic region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of mitochondrial genomic region.

value: Hematopoietic Stem and progenitors (HSPC or CD34 enriched cells from BMMCs)


title: Sal-sip-LE-rep-2_S10


title: ICR mice, Control4


title: Sal-sip-LE-rep-1_S9


title: ICR mice, Control5


title: Donor Young-2, HSPC or CD34 enriched cells from BMMC, mRNA-derived cDNA, sample 8

description: 3' mRNA library (Cell barcodes are matchable with ATAC and mtDNA lib in sample 8): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains transcript.


title: Donor Young-2, BMMCs, mitochondrial DNA , sample 7

description: mtDNA library (Cell barcodes are matchable with mRNA and ATAC lib in sample 7): read1 file contains one end of mitochondrial genomic region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of mitochondrial genomic region.

value: Bone Marrow Mononuclear Cells (BMMCs)


title: p5_20neg


title: P5_6pos


title: Sal-marker2-LE-rep-2_S6

description: Exponential growth of SAL wild type in THY at OD600 of 2.0


title: Sal-marker2-LE-rep-4_S8


title: ICR mice, Control3


title: p8_6neg


title: GEX T cell Cas9 genome edited

description: 10X GEX data

value: T cell

value: Cas9 genome edited


title: Donor Young-2, HSC or CD34+CD45RA-CD90+ enriched cells from BMMC, ATAC, sample 9

description: ATAC library (Cell barcodes are matchable with mRNA and mtDNA lib in sample 9): read1 file contains one end of accessible region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of accessible region.


title: Donor Young-2, BMMCs, ATAC, sample 7

description: ATAC library (Cell barcodes are matchable with mRNA and mtDNA lib in sample 7): read1 file contains one end of accessible region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of accessible region.


title: ICR mice, Control2


title: Sal-marker2-LE-rep-3_S7