title: liver, BPA treated, male, biol rep2

city: Columbia

first: Ramji

last: Bhandari

state: MO

address: 1200 University Ave

department: Division of Biological Sciences

institute: University of Missouri

description:
B3F2li
liverMaleF2_treatmentM_vs_controlM_rnaseq_normExp_diffExp.tsv

data_processing:
The reads were first preprocessed with fastp (v 0.23.2), an ultra-fast all-in-one FASTQ preprocessor, which does quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data
The fastp-processed reads were then mapped on medaka genome (Oryzias_latipes.ASM223467v1) using STAR (2.7.7a)
Finally, DESeq2 (v1.34.0) was used to do the differential expression analysis
Assembly: Oryzias_latipes.ASM223467v1
Supplementary files format and content: liverFemaleF2_treatmentF_vs_controlF_rnaseq_normExp_diffExp.tsv: Normalized log2 expression values and differential expression for female samples in tab-delimited text-file
Supplementary files format and content: liverMaleF2_treatmentM_vs_controlM_rnaseq_normExp_diffExp.tsv: Normalized log2 expression values and differential expression for male samples in tab-delimited text-file

organism: Oryzias latipes

source_name: liver

extract_protocol:
The liver of control and BPA lineage were used for total RNA extraction by using Quick RNA/DNA Miniprep Plus Kit (#D-7003, Zymo Research, CA, USA) according to the manufacturer's protocol
The RNA of the liver from three fishes were pooled as one biological replicate. Transcriptome libraries were prepared using NEBNext Ultra II RNA Kit following manufacturer’s protocol.

value: liver

tag: Sex

value: male

value: BPA


title: SF3B3 overexpression, repeat1

status: Public on Jun 12 2024

type: SRA

city: Shanghai

first: Zhan

last: Ding

address: 300 Feng Lin Road

country: China

institute: CAS Center for Excellence in Molecular Plant Sciences

description: SF3B3-oe rep1

library_source: transcriptomic

data_processing:
The adapter sequences were removed from raw reads by cutadapt (version 1.15).
Clean reads from RNA-seq were quality filtered, and then mapped to the human genome (hg38) and Drosophila melanogaster genome (dm6) by STAR.
Assembly: dm6, hg38
Supplementary files format and content: tab-delimited text files include TPM values for mRNA samples.

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
Total RNAs from the human and Drosophila cells and tissues were isolated by TRIzol (Sigma) and treated with RNase-free DNase I (Invitrogen). For RT-PCR, reverse transcription was performed using PrimeScript RT reagent Kit with gDNA Eraser (TaKaRa) and the obtained cDNA was amplified by 2×Hieff PCR Master Mix (Yeasen). the construction of cDNA libraries and sequencing were performed using Illumina HiseqXten-PE150 by Novogene.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell type

value: Human embryonic kidney

tag: genotype

value: SF3B3 overexpression


title: Targeted Bisulfite-Seq PBMC_day28_s395

city: Los Angeles

first: Matteo

last: Pellegrini

state: California

address: 610 Charles E. Young Drive South TLSB room 5146, Pellegrini Lab

department: Molecular, Cell, and Developmental Biology

country: USA

institute: University of California, Los Angeles

library_source: genomic

data_processing:
BSBolt (v1.3.0) was used to align the reads to the reference GRCh38 genome
Samtools was used to remove PCR duplicates using the markdup function
methylation calling was performed using the BSBolt CallMethylaiton function
Assembly: grch38 genome
Supplementary files format and content: csv, day 0 (pre-vaccination) methylation calling matrix
Supplementary files format and content: csv, day 28 (post-vaccination) methylation calling matrix

molecule: genomic DNA

source_name: blood

extract_protocol:
the standard phenol-chloroform extraction method for blood samples
For the TBS-seq library preparation, adapter ligation and dA-tailing were performed using the NEBNext Ultra II Library prep kit and custom pre-methylated adapters (IDT). Purified libraries were then hybridized to the biotinylated probes. Under the following conditions: 2 min at 98°C; 14 cycles of (98°C for 20 sec; 60°C for 30 sec; 72°C for 30 sec); 72°C for 5 minutes; hold at 4°C, PCR amplification was performed after bisulfite treatment on captured DNA using KAPA HiFi Uracil+. Library quality control was conducted on the high-sensitivity D1000 assay on a 2200 Agilent TapeStation.
Targeted Bisulfite Sequencing
Adapter sequences were removed using cutadapt (v2.10) for the demultiplexed FastQ files

tag: tissue

value: blood

value: PBMC

tag: treatment

value: post-vaccination


title: PBMC, Type 2 diabetes, scBCR, batch8

city: Seoul

first: Do-eon

last: GU

state: Korea

address: 81 Irwon-Ro, Gangnam-gu

country: South Korea

institute: Sungkyunkwan University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Barcoded processing, gene coungting were made using the Cell Ranger software v5.0.0.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

source_name: PBMC

extract_protocol:
Whole blood samples were collected using BD Vacutainer CPTTM Tubes containing sodium heparin (Cat. No. 362753). PBMCs were isolated from blood samples collected in CPT tubes (maintained at room temperature) within 2¬–24 hours after blood collection for optimal results. PBMC isolation utilized Ficoll-Paque density gradient centrifugation.
For each batch, samples from four controls were pooled. The library preparation utilized a Chromium Next GEM Single Cell 5’Kit v2 (10x Genomics), with a cell recovery target of 4,000 per patient, following the manufacturer’s instructions. Libraries were processed according to the manufacturer’s recommendations (10x Genomics) and sequenced on a HiSeq 2500 system with 100-bp paired-end sequencing. Raw sequencing reads underwent processing using CellRanger (version 5.0.1) (10x Genomics) with default parameter values. The human reference sequence (version GRCh38) and annotation (version GENCODE v32) were employed, utilizing pre-built reference packages provided by 10x Genomics (version 2020-A).


title: SF3B4 overexpression, repeat3

description: SF3B4-oe rep3

value: SF3B4 overexpression


title: Targeted Bisulfite-Seq PBMC_day0_s395

value: pre-vaccination


title: liver, BPA treated, male, biol rep1

description:
B2F2li
liverMaleF2_treatmentM_vs_controlM_rnaseq_normExp_diffExp.tsv


title: PBMC, Type 2 diabetes, scTCR, batch8

description: 10X Genomics


title: liver, control, male, biol rep2

description:
C2F2li
liverMaleF2_treatmentM_vs_controlM_rnaseq_normExp_diffExp.tsv

value: control


title: SF3B4 overexpression, repeat2

description: SF3B4-oe rep2


title: Targeted Bisulfite-Seq PBMC_day28_s260


title: PBMC, Type 2 diabetes, scTCR, batch9

description: 10X Genomics


title: SF3B4 overexpression, repeat1

description: SF3B4-oe rep1


title: PBMC, Type 2 diabetes, scRNA-seq, batch8

description: 10X Genomics


title: SF3B3 overexpression, repeat2

description: SF3B3-oe rep2


title: Targeted Bisulfite-Seq PBMC_day0_s260


title: liver, BPA treated, female, biol rep3

description:
B3F2Fli
liverFemaleF2_treatmentF_vs_controlF_rnaseq_normExp_diffExp.tsv

value: female


title: Targeted Bisulfite-Seq PBMC_day28_s249


title: PBMC, Type 2 diabetes, scBCR, batch7

description: 10X Genomics


title: blank vector, repeat2

description: vector rep2

value: blank vector


title: PBMC, Type 2 diabetes, scTCR, batch7

description: 10X Genomics


title: blank vector, repeat3

description: vector rep3


title: liver, control, male, biol rep1

description:
C1F2li
liverMaleF2_treatmentM_vs_controlM_rnaseq_normExp_diffExp.tsv


title: liver, BPA treated, female, biol rep2

description:
B2F2Fli
liverFemaleF2_treatmentF_vs_controlF_rnaseq_normExp_diffExp.tsv


title: PBMC, Type 2 diabetes, scRNA-seq, batch7

description: 10X Genomics


title: Targeted Bisulfite-Seq PBMC_day0_s249


title: liver, BPA treated, female, biol rep1

description:
B1F2Fli
liverFemaleF2_treatmentF_vs_controlF_rnaseq_normExp_diffExp.tsv


title: blank vector, repeat1

description: vector rep1


title: Targeted Bisulfite-Seq PBMC_day28_s244


title: PBMC, Type 2 diabetes, scBCR, batch6

description: 10X Genomics


title: PBMC, Type 2 diabetes, scTCR, batch6

description: 10X Genomics


title: Targeted Bisulfite-Seq PBMC_day0_s244


title: liver, control, female, biol rep3

description:
C3F2Fli
liverFemaleF2_treatmentF_vs_controlF_rnaseq_normExp_diffExp.tsv


title: KO_T0_brg1i_DSB2_3

city: Heidelberg

first: Christoph

last: Plass

address: Im Neueneimer Feld 280

department: Division of Cancer Epigenomics

country: Germany

institute: DKFZ (German Cancer Research Center)

data_processing:
The data was processed using the pipe4C pipeline.
Assembly: GRCh37
Supplementary files format and content: bigwig tracks
Library strategy: 4C-seq

source_name: AID-DivA

extract_protocol:
Cells were harvested and cross-linked with 2% formaldehyde for 10 min at room temperature, lysed and digested with MboI (New England Biolabs, Cat# R0147L) for three rounds of 4h each. Then first ligation step was performed by T4 DNA ligase (New England Biolabs, Cat# M0202L), and ligated DNA was decrosslinked and purified. A second digestion step was performed with NlaIII overnight (New England Biolabs, Cat# R0125L). Afterwards, a second ligation step was performed. DNA was purified and measured by Qubit.
5ng of DNA were amplified in PCR using the viewpoint primers. Three viewpoints were used: one close to HR-prone DSB (DSB2), one close to NHEJ-prone DSB (DSB3), and one with no adjacent DSB (ctrl). The PCR products were purified by AMPure XP beads and measured by Qubit. For 4C–seq library preparation, a final qPCR using 2ng DNA was performed with the inverse primers including the Illumina adaptor sequences and a unique index for each condition. DNA libraries were purified by AMPure XP beads and measured by Qubit. Fragment size was checked by Tape station. Libraries were pooled and subjected to 75-bp paired-end sequencing on a Nextseq550 platform at DKFZ Next Generation Sequencing Core Facility.

treatment_protocol: We used both WT AID-DivA cells and AID-DivA cells with an ARID1A knock-out. Cells were either untreated (UT) or treated with 300 nM 4-hydroxytamoxifen (4OHT) and incubated for 4h. Then treated with Auxin to stop the enzymatic generation of the double-strand breaks. Cells were collected immediately after auxin treatment (T0) or 4h after addition of auxin (T4). In addition, cells were either treated with BRG1 inhibitors (brg1i) or not (nobrg1i).

value: AID-DivA

value: osteosarcoma

value: ARID1A KO

value: 0h after auxin treatment

tag: viewpoint

tag: replicate


title: liver, control, female, biol rep2

description:
C2F2Fli
liverFemaleF2_treatmentF_vs_controlF_rnaseq_normExp_diffExp.tsv

value: liver


title: KO_T0_brg1i_DSB2_1


title: Targeted Bisulfite-Seq PBMC_day28_s238


title: KO_UT_nobrg1i_ctrl_6

value: untreated

value: ctrl


title: liver, control, female, biol rep1

description:
C1F2Fli
liverFemaleF2_treatmentF_vs_controlF_rnaseq_normExp_diffExp.tsv


title: PBMC, Type 2 diabetes, scBCR, batch5

description: 10X Genomics


title: KO_UT_nobrg1i_ctrl_5


title: PBMC, Type 2 diabetes, scTCR, batch5

description: 10X Genomics


title: Targeted Bisulfite-Seq PBMC_day0_s238


title: KO_UT_nobrg1i_ctrl_4


title: Targeted Bisulfite-Seq PBMC_day28_s227


title: Targeted Bisulfite-Seq PBMC_day0_s227


title: Targeted Bisulfite-Seq PBMC_day28_s224


title: KO_UT_nobrg1i_ctrl_2


title: KO_UT_nobrg1i_ctrl_3


title: C3H dual-lineage receiver, Day 3, mCherry ligand rows, rep 1

first: Song

last: Li

address: 404 Westwood Plaza, Eng VI

institute: UCLA

data_processing:
FASTQ files were processed with 10x Genomics’ Cell Ranger analysis pipelines. The read count matrix generated by CellRanger was then analyzed using Seurat v5.0.2. 32288 genes were detected across no ligand (7877 and 7745 cells tested for replicates), GFP pattern (10539 and 11923 cells tested for replicates), mCherry pattern (10671 and 10068 cells tested for replicates), and Dual Pattern (8710 and 16266 cells tested for replicates). Cells that had unique feature counts with at least 700 genes but no more than 7000 genes and cells that had <55% mitochondrial counts were filtered and normalized based on the feature expression and total expression of each cell. The normalized expression data were then used for subsequent analysis.
Principal component analysis was performed after merging replicates and integrating all the conditions. Highly variable genes in each sample after linear transformation and the first 30 PC scores were used for tSNE analysis to cluster the cells into 12 groups (FindNeighbors and FindClusters functions implemented in the Seurat package, dims = 30, resolution = 0.4). The marker genes of each cluster were identified using FindAllMarkers or FindMarkers function with default parameters. Clusters were annotated using signature genes and DAVID pathway analysis to identify fibroblast-, muscle-, or endothelial- like cell types across the different conditions. tSNE clusters that were enriched in proliferation, extracellular matrix, or EGF pathways were identified as fibroblasts. Clusters that were enriched in lineage-specific markers, muscle or angiogenesis pathways, were used to identify muscle- and endothelial- like clusters, respectively.
A pseudobulk method was applied to investigate gene expression among different conditions at the population level. Specifically, the raw gene counts of each sample were extracted after filtering. The counts were then aggregated to the sample level and the expression of genes of interest including transgenes were examined across conditions.
Assembly: mm10
Supplementary files format and content: tar.gz file contains matrix, barcodes, and features

organism: Mus musculus

growth_protocol: Cells were maintained in high glucose DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
cells were trypsinized and cells were lysed in IGEPAL CA630-containing lysis buffer for 7 minutes to isolate individual nuclei.
Library construction was performed according to the manufacturer’s protocol (10x Genomics single cell 3’ v3.1 protocol). Briefly, after resuspension and counting, 16,000 GCs per experiment were resuspended in master mix and loaded (together with partitioning oil and gel beads), onto each lane of an 8 lane chip G to generate the gel bead-in-emulsion (GEMs). Reverse transcription was primed with an oligonucleotide carrying an Illumina TruSeq R1 read-sequencing primer, a 16 nucleotide 10x cell barcode, a 12 nucleotide UMI, and a 30 nucleotide anchored poly dT sequence. Full length cDNA was amplified from heteroduplex RNA:cDNA using 12 cycles of PCR. The full-length cDNA was cleaned up on SPRIselect beads, and QCed on Qubit and BioAnalyzer. One fourth of the resulting ds cDNA was fragmented and prepared for sample index PCR, with 11 cycles of amplification. After QC, the libraries were pooled and submitted for sequencing on 2 lanes of a 10B 100 flowcell on the Illumina NovaSeqX sequencer, targeting a minimum read depth per cell of 25,000. Sequencing was performed at the UCSF CAT

treatment_protocol: All cells were droplet seeded onto Ibidi wells patterned using capillary fluidic device with No ligand, GFP rows, mcherry rows, or both GFP and mCherry interdigiting rows and cultured for 3 days before single nuclei RNA extraction and sequencing. Droplet seeding was done as follows: 3.3x10^4 dual-lineage cells were seeded in a 30uL droplet on top of the patterns, allowed to attach for 30 minutes, prior to adding additional media.

value: SFFV_myc- LaG17_synNotch_TetRVP64 , TRE_MyoD-P2A-miRFP, EF1a_flag-LaM4_synNotch_Gal4-VP64 , UAS_ETV2-P2A-tBFP_PGK_HygromycinR

value: mCherry ligand rows


title: C3H dual-lineage receiver, Day 3, mCherry ligand rows, rep 2


title: C3H dual-lineage receiver, Day 3, GFP and mCherry ligand interdigiting rows, rep 2


title: C3H dual-lineage receiver, Day 3, GFP and mCherry ligand interdigiting rows, rep 1


title: Targeted Bisulfite-Seq PBMC_day0_s224

value: blood


title: PBMC, Type 2 diabetes, scTCR, batch4

description: 10X Genomics

value: PBMC


title: C3H dual-lineage receiver, Day 3, GFP ligand rows, rep 2

value: GFP ligand rows


title: KO_UT_nobrg1i_ctrl_1


title: C3H dual-lineage receiver, Day 3, GFP ligand rows, rep 1


title: Targeted Bisulfite-Seq PBMC_day28_s221

value: post-vaccination


title: PBMC, Type 2 diabetes, scBCR, batch3

description: 10X Genomics


title: PBMC, Type 2 diabetes, scRNA-seq, batch6

description: 10X Genomics


title: Targeted Bisulfite-Seq PBMC_day0_s221

value: pre-vaccination


title: PBMC, Type 2 diabetes, scRNA-seq, batch4

description: 10X Genomics


title: KO_T4_nobrg1i_ctrl_5

value: 4h after auxin treatment


title: PBMC, Type 2 diabetes, scRNA-seq, batch5

description: 10X Genomics


title: KO_T4_nobrg1i_ctrl_2


title: C3H dual-lineage receiver, Day 3, No ligand, rep 2

value: No ligand


title: Targeted Bisulfite-Seq PBMC_day28_s220


title: PBMC, Type 2 diabetes, scTCR, batch3

description: 10X Genomics


title: C3H dual-lineage receiver, Day 3, No ligand, rep 1


title: PBMC, Type 2 diabetes, scBCR, batch4

description: 10X Genomics


title: Targeted Bisulfite-Seq PBMC_day0_s220


title: PBMC, Type 2 diabetes, scRNA-seq, batch3

description: 10X Genomics


title: KO_T0_nobrg1i_ctrl_6


title: Targeted Bisulfite-Seq PBMC_day28_s219


title: PBMC, Type 2 diabetes, scTCR, batch2

description: 10X Genomics


title: PBMC, Type 2 diabetes, scBCR, batch2

description: 10X Genomics


title: Targeted Bisulfite-Seq PBMC_day0_s219


title: bEnd.3, Day 2, No ligand rep 2

data_processing:
Fastqc files were trimmed with trimmomatic v0.39 using default settings. Trimmed fastQ files were aligned to GRCm38 reference genome supplemented with custom transgenic sequences using STAR v2.7.10b with default parameters. Transcriptome alignments were quantified using featureCount using the custom gene annotation file combining GENCODE annotation file and transgenes.
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample

growth_protocol: All cell types were maintained in high glucose DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA extraction using miRNeasy kit (Qiagen), RNA cleanup and concentrator (Zymo), before being sequenced by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads by Novogene.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: All cells were droplet seeded onto Fibronectin treated PDMS coverslips microcontact printed either with or without its activating ligand (GFP or mCherry). Cells were allowed to culture for 2 days before total RNA extraction. Droplet seeding was performed as follows: 6x10^4 cells were seeded in a 50uL droplet on top of the patterns, allowed to attach for 30 minutes, prior to adding additional media.

value: WT


title: Targeted Bisulfite-Seq PBMC_day28_s215


title: C2C12, Day 2, No ligand, rep 4


title: C2C12, Day 2, No ligand, rep 2


title: WT_UT_nobrg1i_ctrl_5

value: AID-DivA


title: KO_T0_nobrg1i_ctrl_4

value: osteosarcoma


title: C2C12, Day 2, No ligand, rep 1


title: WT_UT_nobrg1i_ctrl_6


title: PBMC, Type 2 diabetes, scRNA-seq, batch2

description: 10X Genomics


title: C2C12, Day 2, No ligand, rep 3


title: PBMC, Type 2 diabetes, scBCR, batch1

description: 10X Genomics


title: KO_T0_nobrg1i_ctrl_1

value: ARID1A KO


title: PBMC, Type 2 diabetes, scTCR, batch1

description: 10X Genomics


title: KO_T0_nobrg1i_ctrl_3

value: 0h after auxin treatment


title: Targeted Bisulfite-Seq PBMC_day0_s214


title: C3H anti-mCherry ETV2 and BFP receiver, Day 2, mCherry +, rep 2

value: mCherry ligand


title: Targeted Bisulfite-Seq PBMC_day28_s214


title: bEnd.3, Day 2, No ligand rep 1


title: PBMC, Type 2 diabetes, scRNA-seq, batch1

description: 10X Genomics


title: WT_T4_nobrg1i_ctrl_6


title: Targeted Bisulfite-Seq PBMC_day0_s213


title: C3H anti-mCherry ETV2 and BFP receiver, Day 2, mCherry +, rep 1


title: WT_T4_nobrg1i_ctrl_5


title: CRC adjnormal N160 [DREAM]

city: Camden

first: Jean-Pierre

middle: J

last: Issa

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

data_processing:
library strategy: Digital Restriction Enzyme Analysis of Methylation (DREAM)
Illumina HiSeq 2500 or NovaSeq 6000 paired ends sequencing
Raw sequencing data were converted to fastq.gz files.
bowtie2 --sensitive alignment of the reads in fastq files to mm10 and generating SAM files
generating sorted bam files from the sam files with samtools
counting methylated CCGGG signatures and unmethylated GGG at the reads aligned to CCCGGG sites
Adjusting methylation values based on the spiked in standards. At each SmaI/XmaI site, let Xma be the number of reads corresponding to methylated CpG (i.e., reads starting with CCGGG) and Sma be the number of reads corresponding to unmethylated CpG (i.e., reads starting with GGG), the methylation value was calculated as 100%*(c*(Xma+0.5)/(c*(Xma+0.5)+Sma+0.5)), where c was the correction factor calculated based on observed and expected methylation of spiked-in standards.
Assembly: mm9
Supplementary files format and content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_mm9 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), meth_reads (observed number of reads corresponding to methylated CpG, Xma),  unmeth_reads (observed number of reads corresponding to unmethylated CpG, Sma), total_reads, raw_methylation (unadjusted methylation value), adjusted_methylation (methylation value adjusted based on the spiked in standards).

source_name: colon

extract_protocol:
tissues were lysed in 2% SDS and 25 mM EDTA overnight. Ammonium acetate (10M) was added to make the precipitate of SDS with proteins and was removed by centrifugation at 12,000 rpm. Next, DNA was precipitated using isopropanol, washed with 70% ethanol, and dissolved in dissolved in LTET (Tris 10 mM, EDTA, 0.1 mM + Tween 20,0.1% )
Two micrograms of genomic DNA spiked with 20 ng of methylation standards with defined methylation levels of 0, 25, 50, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'→5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments. Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

value: colon

tag: tissue type

value: CRC adjnormal


title: Targeted Bisulfite-Seq PBMC_day28_s213


title: Targeted Bisulfite-Seq PBMC_day0_s215


title: WT_T0_nobrg1i_ctrl_4

value: ctrl


title: CRC adjnormal N159 [DREAM]


title: CRC adjnormal N146 [DREAM]


title: WT_T0_nobrg1i_ctrl_5


title: Targeted Bisulfite-Seq PBMC_day28_s203


title: Targeted Bisulfite-Seq PBMC_day0_s207


title: C3H anti-mCherry ETV2 and BFP receiver, Day 2, No ligand, rep 2


title: C3H anti-mCherry ETV2 and BFP receiver, Day 2, No ligand, rep 1


title: Targeted Bisulfite-Seq PBMC_day0_s203


title: CRC adjnormal N127 [DREAM]


title: Targeted Bisulfite-Seq PBMC_day28_s207


title: C3H anti-GFP myoD and mCherry receiver, Day 2, GFP +, rep 3

value: SFFV_myc- LaG17_synNotch_TetRVP64 , TRE_MyoD-P2A-mCherry

value: GFP ligand


title: C3H anti-GFP myoD and mCherry receiver, Day 2, GFP +, rep 4


title: CRC adjnormal N121 [DREAM]


title: WT_UT_nobrg1i_ctrl_2

value: untreated


title: CRC adjnormal N135 [DREAM]


title: WT_UT_nobrg1i_ctrl_4


title: WT_UT_nobrg1i_ctrl_3


title: C3H anti-GFP myoD and mCherry receiver, Day 2, GFP +, rep 2


title: Targeted Bisulfite-Seq PBMC_day28_s196

value: blood

value: PBMC


title: CRC adjnormal N118 [DREAM]


title: WT_UT_nobrg1i_ctrl_1


title: C3H anti-GFP myoD and mCherry receiver, Day 2, GFP +, rep 1


title: WT_T4_nobrg1i_ctrl_3


title: Targeted Bisulfite-Seq PBMC_day0_s196

value: pre-vaccination


title: CRC adjnormal N110 [DREAM]


title: C3H anti-GFP myoD and mCherry receiver, Day 2, No ligand, rep 2


title: WT_T4_nobrg1i_ctrl_2

value: 4h after auxin treatment


title: WT_T0_nobrg1i_ctrl_2


title: C3H anti-GFP myoD and mCherry receiver, Day 2, No ligand, rep 1

value: No ligand


title: Targeted Bisulfite-Seq PBMC_day0_s194


title: CRC adjnormal N092 [DREAM]


title: WT_T0_nobrg1i_ctrl_1

value: WT


title: CRC adjnormal N093 [DREAM]


title: C3H anti-GFP mCherry reporter, Day 2, GFP + , rep 2

value: SFFV_myc- LaG17_synNotch_TetRVP64 , TRE_mCherry


title: CRC adjnormal N065 [DREAM]


title: Targeted Bisulfite-Seq PBMC_day0_s190


title: C3H anti-GFP mCherry reporter, Day 2, No ligand, rep 2


title: C3H anti-GFP mCherry reporter, Day 2, GFP + , rep 1


title: WT_UT_brg1i_ctrl_5

value: AID-DivA

value: osteosarcoma


title: CRC adjnormal N100 [DREAM]


title: WT_UT_brg1i_ctrl_6


title: Targeted Bisulfite-Seq PBMC_day28_s190

value: post-vaccination


title: C3H anti-GFP mCherry reporter, Day 2, No ligand, rep 1


title: Targeted Bisulfite-Seq PBMC_day28_s188


title: Targeted Bisulfite-Seq PBMC_day0_s188


title: WT_UT_brg1i_ctrl_4


title: Targeted Bisulfite-Seq PBMC_day28_s194


title: CRC adjnormal N011 [DREAM]


title: CRC adjnormal N007 [DREAM]


title: WT_UT_brg1i_ctrl_3


title: C3H parental, Day 2, No ligand, rep 2


title: C3H parental, Day 2, No ligand, rep 1


title: WT_UT_brg1i_ctrl_2


title: Targeted Bisulfite-Seq PBMC_day0_s185


title: Targeted Bisulfite-Seq PBMC_day28_s185


title: CRC tumor T157 [DREAM]

value: CRC tumor


title: WT_UT_brg1i_ctrl_1


title: CRC adjnormal N035 [DREAM]

value: colon


title: Targeted Bisulfite-Seq PBMC_day0_s184


title: CKI_HTO_S1,S2,S3,S4,S5

city: NEW YORK

first: LEVI

last: MANGARIN

state: NY

address: 413 E 69TH STREET

department: MEYER CANCER CENTER

institute: WEILL CORNELL MEDICINE

data_processing:
Filtered gene expression matrices were generated using 10X CellRanger (version 6.1.1).
Assembly: mm10 (GENCODE vM23/Ensembl 98)
Supplementary files format and content: count_matrix.txt
Supplementary files format and content: count_matrix_adt.txt
Supplementary files format and content: bacode.csv

source_name: tumor draining lymph nodes

extract_protocol:
Hash-tagged and Total-seq-C cocktail labelled cells wee sorted for live CD45+ and equal cell numbers of 5 samples from each treatment group were pooled into one sample per treatment group. Total RNA was extracted and quantified prior to sequencing.
GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 6,700-11,400 cells proceeded using the Chromium Next GEM Single Cell 5’ Kit v2 (10X Genomics PN 1000263) according to the manufacturer’s protocol. cDNA amplification included 13 cycles and 9.4-43 ng of the material was used to prepare sequencing libraries with 14-16 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/88 run using the NovaSeq 6000 S1 or S2 Reagent Kit (100 cycles) (Illumina).  An average of 44 thousand reads was generated per cell. Amplification products generated using the methods described above included both cDNA and feature barcodes tagged with cell barcodes and unique molecular identifiers. Smaller feature barcode fragments were separated from longer amplified cDNA using a 0.6X cleanup using aMPure XP beads (Beckman Coulter catalog # A63882). Libraries were constructed using the 5’ Feature Barcode Kit (10X Genomics PN 1000256) according to the manufacturer’s protocol with 8 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/88 run using the NovaSeq 6000 S1 Reagent Kit (100 cycles) (Illumina). An average of 58 million reads was generated per sample.

value: tumor draining lymph nodes

tag: model

value: LLC flank tumor

tag: strain

value: female

tag: library type

value: HTO


title: GITRCTLA4_HTO_S1,S2,S3,S4,S5


title: Targeted Bisulfite-Seq PBMC_day28_s179


title: WT_T4_brg1i_ctrl_6

value: ctrl


title: CRC tumor T154 [DREAM]


title: CRC tumor T153 [DREAM]


title: CKIGITRCTLA4_RNA_S1,S2,S3,S4,S5

value: mRNA


title: CRC tumor T151 [DREAM]


title: Targeted Bisulfite-Seq PBMC_day28_s184

value: blood

value: PBMC


title: WT_T4_brg1i_ctrl_3

value: 4h after auxin treatment


title: Targeted Bisulfite-Seq PBMC_day28_s177


title: Targeted Bisulfite-Seq PBMC_day0_s179

value: pre-vaccination


title: GITRCTLA4_RNA_S1,S2,S3,S4,S5


title: CRC tumor T158 [DREAM]


title: Targeted Bisulfite-Seq PBMC_day0_s177


title: CRC tumor T150 [DREAM]


title: CKIGITRCTLA4_HTO_S1,S2,S3,S4,S5


title: CRC tumor T146 [DREAM]


title: CKI_RNA_S1,S2,S3,S4,S5


title: WT_T4_brg1i_ctrl_1

value: WT


title: CRC tumor T156 [DREAM]


title: WT_T4_brg1i_ctrl_4


title: Veh_HTO_S1,S2,S3,S4,S5

value: Vehicle


title: Veh_RNA_S1,S2,S3,S4,S5


title: WT_T0_brg1i_ctrl_6

value: AID-DivA

value: 0h after auxin treatment


title: Targeted Bisulfite-Seq PBMC_day0_s171


title: CRC tumor T143 [DREAM]


title: WT_T0_brg1i_ctrl_5

value: osteosarcoma


title: CRC tumor T142 [DREAM]

value: CRC tumor


title: BM, Mature B, WT, rep2

city: Farmington

first: Tingting

last: Geng

state: CT

address: 263 Farmington Avenue

department: Department of Immunology

institute: Uconn Health

data_processing:
High-quality sequencing reads were aligned to the mouse reference genome (GRCm39)using Hisat2 (version 2.2.1).
Aligned reads were quantified at the gene level using the featureCounts function from the Subread package (version 2.0.3). The annotation gtf file (gencode.vM34.basic.annotation.gtf.gz) corresponding to the GRCm39 genome release was utilized to guide the quantification process.
Differential gene expression analysis was conducted using the DESeq2 package (version 1.38.3) in R(4.2.3).
Assembly: GRCm39/mm39
Supplementary files format and content: Raw count for each sample.
Supplementary files format and content: Differential gene expression data

source_name: Bone marrow

extract_protocol:
Mature B subset total RNA was harvested using RNAeasy mini plus kit (Qiagen). 400ng of total RNA was used for the construction of sequencing libraries
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Cre+ Ubxn3bf/f mice were treated with tamoxifen (TMX) (Ubxn3b-/-) or corn oil (Ubxn3b+/+) every two days for 8 days. 5 days after the last dose of tamoxifen treatment,we collected bone marrow from mice treated with either tamoxifen or a control oil and isolated various B cell subsets by sorting.

value: Bone marrow

value: B cell

value: Mature B cell

value: Oil


title: Targeted Bisulfite-Seq PBMC_day28_s170

value: post-vaccination


title: BM, Mature B, WT, rep1


title: Targeted Bisulfite-Seq PBMC_day28_s169


title: WT_T0_brg1i_ctrl_2

value: ctrl


title: CRC tumor T136 [DREAM]

value: colon


title: Targeted Bisulfite-Seq PBMC_day0_s170

value: blood


title: BM, Mature B, Ubxn3b KO, rep3

value: Ubxn3b KO

value: Tamoxifen


title: WT_T4_brg1i_ctrl_5

value: 4h after auxin treatment


title: WT_T0_brg1i_ctrl_3

value: WT


title: Targeted Bisulfite-Seq PBMC_day28_s171

value: PBMC


title: WT_T4_brg1i_ctrl_2

value: AID-DivA


title: CRC tumor T135 [DREAM]


title: KO_UT_brg1i_ctrl_6

value: ARID1A KO

value: untreated


title: BM, Mature B, Ubxn3b KO, rep2


title: BM, Mature B, Ubxn3b KO, rep1


title: KO_UT_brg1i_ctrl_5

value: osteosarcoma


title: Targeted Bisulfite-Seq PBMC_day28_s166


title: CRC tumor T131 [DREAM]

value: CRC tumor


title: Targeted Bisulfite-Seq PBMC_day0_s169

value: pre-vaccination


title: CRC tumor T128 [DREAM]


title: 90wk_OVAposLPSposPGPC_IFA_Mouse_5

city: Cambridge

first: Ramnik

last: Xavier

state: MA

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

description:
instrument model: Illumina NovaSeq X
90 weeks old, OVA+LPS+PGPC treated

data_processing:
Bclconvert (v3.10.5) was used to convert bcl files to fastq.gz. Demultiplexing, barcode processing, gene counting, and aggregating were done with CellRanger Multi (v7.1.0)
Counts were log normalized
PCA
UMAP
Assembly: mm10-2020A
Supplementary files format and content: h5ad

source_name: Spleen

extract_protocol:
8 weeks old or 90 weeks old C57BL/6J mice were injected on the right back with PBS or were immunized with 200μg/mouse endotoxin-free OVA, in combination with 10μg/mouse LPS plus 65μg/mouse PGPC all emulsified in incomplete Freund’s adjuvant. Immunized mice received two boost injections with the same dose of OVA+LPS+PGPC on the left back. 7 days post the last boost injection, skin draining lymph nodes from immunized mice were collected and dissociated into a single cell suspension. T cells were enriched using anti-CD3e beads (Miltenyi) following the manufacturer’s protocol. Enriched T cells were filtered onto a 70um then 40um filters (Miltenyi). T cell purity was assessed by flow cytometry and was above 90% for all samples. T cells were filtered onto 30um filters before counting and were resuspended in the NOVAseq 10x master mix at a concentration 12,000 cells in 43.1 ul per sample volume.
Library was performed according to the manufacturer's instructions (single cell 5' v2, 10x Genomics). Approximately 20,000 single cells per sample were loaded into each channel of a Chromium single-cell 5′ chip (v2, 10x Genomics) at the Genomics Platform of the Broad Institute. Single cells were partitioned into droplets with gel beads in the Chromium Controller. After emulsions were formed, barcoded reverse transcription of RNA took place. This was followed by cDNA amplification, amplification of full-length V(D)J segments. Fragmentation, adaptor ligation, and sample index attachment were performed on full-length cDNA and V(D)J segments to create 5’ gene expression and TCR libraries, respectively. Libraries from 30 10x channels were pooled together, with the TCR libraries being pooled at 25% molarity. The libraries were sequenced across 6 lanes of an Illumina NovaSeqX flow cell (10B reads, up to 300 cycles), with paired end reads as follows: read 1, 26 cycles; read 2, 90 cycles; index 1, 10 cycles; index 2, 10 cycles.

value: Spleen

tag: age

value: 90 weeks

value: CD3e T cell

value: OVA+LPS+PGPC


title: KO_UT_brg1i_ctrl_4

value: ctrl


title: KO_UT_brg1i_ctrl_3


title: Targeted Bisulfite-Seq PBMC_day28_s161

value: blood

value: post-vaccination


title: 90wk_OVAposLPSposPGPC_IFA_Mouse_4


title: 90wk_OVAposLPSposPGPC_IFA_Mouse_3


title: Targeted Bisulfite-Seq PBMC_day0_s166


title: CRC tumor T126 [DREAM]

value: colon


title: KO_UT_brg1i_ctrl_2


title: Targeted Bisulfite-Seq PBMC_day0_s161


title: 90wk_OVAposLPSposPGPC_IFA_Mouse_2


title: CRC tumor T123 [DREAM]


title: 90wk_OVAposLPSposPGPC_IFA_Mouse_1


title: Targeted Bisulfite-Seq PBMC_day28_s155


title: CRC tumor T121 [DREAM]


title: Targeted Bisulfite-Seq PBMC_day0_s155


title: KO_T4_brg1i_ctrl_6

value: 4h after auxin treatment


title: 90wk_OVAposPBS_IFA_Mouse_5

description:
instrument model: Illumina NovaSeq X
90 weeks old, OVA+PBS treated

value: OVA+PBS


title: CRC tumor T118 [DREAM]


title: KO_T4_brg1i_ctrl_5


title: KO_T4_brg1i_ctrl_4


title: Targeted Bisulfite-Seq PBMC_day28_s151

value: PBMC


title: 90wk_OVAposPBS_IFA_Mouse_3


title: 90wk_OVAposPBS_IFA_Mouse_4


title: CRC tumor T113 [DREAM]


title: CRC tumor T127 [DREAM]


title: KO_T4_brg1i_ctrl_3

value: AID-DivA


title: CRC tumor T112 [DREAM]


title: CRC tumor T116 [DREAM]


title: Targeted Bisulfite-Seq PBMC_day0_s151


title: Targeted Bisulfite-Seq PBMC_day28_s149


title: 90wk_OVAposPBS_IFA_Mouse_2


title: CRC tumor T111 [DREAM]


title: Targeted Bisulfite-Seq PBMC_day0_s149


title: 90wk_OVAposPBS_IFA_Mouse_1


title: Targeted Bisulfite-Seq PBMC_day28_s65


title: CRC tumor T110 [DREAM]


title: KO_T0_brg1i_ctrl_6

value: ARID1A KO

value: 0h after auxin treatment


title: CRC tumor T109 [DREAM]


title: KO_UT_brg1i_ctrl_1

value: osteosarcoma

value: untreated


title: Targeted Bisulfite-Seq PBMC_day28_s64


title: KO_T0_brg1i_ctrl_4


title: CRC tumor T108 [DREAM]

value: CRC tumor


title: 90wk_PBS_Only_Mouse_3

description:
instrument model: Illumina NovaSeq X
90 weeks old, PBS treated

value: Spleen

value: PBS


title: KO_T0_brg1i_ctrl_1


title: CRC tumor T105 [DREAM]


title: CRC tumor T104 [DREAM]


title: 90wk_PBS_Only_Mouse_2

value: 90 weeks

value: CD3e T cell


title: WT_T12_BRG1i_3

data_processing:
Sequencing reads were processed using the CWL-based ATAC-Seq workflow available at https://github.com/CompEpigen/ATACseq_workflows
Assembly: GRCh37
Supplementary files format and content: bigwig tracks

extract_protocol:
50,000 viable cells were pelleted and washed in PBS. Subsequently, nuclei were isolated and resuspended in 2x transposition buffer (20mM Tris-HCl pH 7.6, 3mM MgCl2, 20% Dimethyl Formamide) and the tagmentation reaction was performed by adding 2.5µl of Tagment DNA Enzyme 1 (Illumina). The mixture was incubated for 30 minutes at 37°C with mixing at 1000 rpm. Reaction was stopped by 5M Guanidinium thiocyanate (Sigma-Aldrich) and DNA was further purified using AMPure XP beads.
Libraries were amplified in PCR reactions by adding 25 µl of NEBNext High Fidelity 2x Master Mix (NEB), 0.8 µl of 10 µM Custom Nextera PCR Primer 1, and 0.8 µl of 10 µM Custom Nextera PCR Barcode to 25 µl of the transposed DNA. The libraries were purified with AMPure XP beads. The concentration of the library was determined using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).

treatment_protocol: We used both WT AID-DivA cells and AID-DivA cells with an ARID1A knock-out. Cells were either untreated (UT) or treated with 300 nM 4-hydroxytamoxifen (4OHT) and incubated for 4h. Then treated with Auxin to stop the enzymatic generation of the double-strand breaks. Cells were collected immediately after auxin treatment (T0) or 2h after addition of auxin (T2), or 4h (T4), or 12h (T12). Some cells were untreated with 4OHT but collected 12h after auxin treatment (UT12). Cells were either treated with a BRG1 inhibitor (BRM014) or not.

value: WT

value: 12h after auxin treatment

value: BRG1 inhibitor


title: Targeted Bisulfite-Seq PBMC_day28_s58

value: blood

value: post-vaccination


title: KO_T4_brg1i_ctrl_2

value: 4h after auxin treatment

value: ctrl


title: Targeted Bisulfite-Seq PBMC_day0_s58

value: PBMC

value: pre-vaccination


title: CRC tumor T102 [DREAM]

value: colon


title: 8wk_OVAposLPSposPGPC_IFA_Mouse_5

description:
instrument model: Illumina NovaSeq X
8 weeks old, OVA+LPS+PGPC treated

value: 8 weeks

value: OVA+LPS+PGPC


title: WT_T12_BRG1i_2

value: AID-DivA

value: osteosarcoma


title: KO_T4_brg1i_ctrl_1

value: ARID1A KO


title: CRC tumor T100 [DREAM]

value: CRC tumor


title: 8wk_OVAposLPSposPGPC_IFA_Mouse_4

value: Spleen

value: CD3e T cell


title: 90wk_PBS_Only_Mouse_4

value: 90 weeks

value: PBS


title: WT_T12_BRG1i_1

value: WT

value: 12h after auxin treatment

value: BRG1 inhibitor


title: Targeted Bisulfite-Seq PBMC_day0_s65

value: blood


title: 90wk_PBS_Only_Mouse_5


title: CRC tumor T098 [DREAM]


title: 8wk_OVAposLPSposPGPC_IFA_Mouse_3


title: Targeted Bisulfite-Seq PBMC_day28_s34

value: PBMC

value: post-vaccination


title: Targeted Bisulfite-Seq PBMC_day0_s64

value: pre-vaccination


title: CRC tumor T093 [DREAM]

value: colon


title: 8wk_OVAposLPSposPGPC_IFA_Mouse_2

value: 8 weeks

value: OVA+LPS+PGPC


title: WT_T4_BRG1i_2

value: AID-DivA

value: osteosarcoma

value: 4h after auxin treatment


title: WT_T4_BRG1i_3


title: KO_T0_brg1i_ctrl_3

value: ARID1A KO

value: 0h after auxin treatment

value: ctrl


title: 90wk_PBS_Only_Mouse_1

value: Spleen

value: 90 weeks

value: CD3e T cell

value: PBS


title: 8wk_OVAposLPSposPGPC_IFA_Mouse_1


title: WT_T4_BRG1i_1

value: WT

value: BRG1 inhibitor


title: Targeted Bisulfite-Seq PBMC_day28_s22

value: blood

value: PBMC

value: post-vaccination


title: Targeted Bisulfite-Seq PBMC_day28_s47


title: CRC tumor T091 [DREAM]

value: colon

value: CRC tumor


title: 8wk_OVAposPBS_IFA_Mouse_5

description:
instrument model: Illumina NovaSeq X
8 weeks old, OVA+PBS treated

value: 8 weeks

value: OVA+PBS


title: CRC tumor T092 [DREAM]


title: Targeted Bisulfite-Seq PBMC_day28_s17


title: 8wk_OVAposPBS_IFA_Mouse_4


title: Targeted Bisulfite-Seq PBMC_day0_s47

value: pre-vaccination


title: CRC tumor T087 [DREAM]


title: 8wk_OVAposPBS_IFA_Mouse_3


title: Targeted Bisulfite-Seq PBMC_day0_s34


title: Targeted Bisulfite-Seq PBMC_day0_s17


title: CRC tumor T089 [DREAM]


title: WT_T0_BRG1i_2

value: AID-DivA

value: osteosarcoma


title: CRC tumor T085 [DREAM]


title: WT_T0_BRG1i_1

value: 0h after auxin treatment


title: WT_UT_BRG1i_3

value: untreated


title: Targeted Bisulfite-Seq PBMC_day28_s16


title: 8wk_OVAposPBS_IFA_Mouse_1

value: Spleen


title: CRC tumor T083 [DREAM]


title: 8wk_PBS_Only_Mouse_5

description:
instrument model: Illumina NovaSeq X
8 weeks old, PBS treated

value: CD3e T cell


title: Targeted Bisulfite-Seq PBMC_day0_s16


title: CRC tumor T081R [DREAM]


title: WT_UT_BRG1i_1


title: WT_UT_BRG1i_2


title: Targeted Bisulfite-Seq PBMC_day0_s22


title: Targeted Bisulfite-Seq PBMC_day28_s14


title: Targeted Bisulfite-Seq PBMC_day0_s14


title: WT_UT12_3

value: untreated with 4OHT; 12h after auxin treatment

value: no BRG1 inhibitor


title: WT_T0_BRG1i_3

value: WT

value: BRG1 inhibitor


title: CRC tumor T079 [DREAM]


title: 8wk_PBS_Only_Mouse_3

value: PBS


title: WT_UT12_2


title: Targeted Bisulfite-Seq PBMC_day28_s1

value: blood

value: PBMC

value: post-vaccination


title: CRC tumor T075 [DREAM]

value: colon

value: CRC tumor


title: 8wk_OVAposPBS_IFA_Mouse_2

value: 8 weeks

value: OVA+PBS


title: Targeted Bisulfite-Seq PBMC_day0_s1

value: pre-vaccination


title: 8wk_PBS_Only_Mouse_2


title: WT_UT12_1

value: AID-DivA

value: osteosarcoma


title: 8wk-PBS-Only-Mouse-1

value: Spleen


title: KO_UT12_3

value: ARID1A KO


title: KO_UT12_2

value: untreated with 4OHT; 12h after auxin treatment


title: RGC, experiment5, CMO-multiplex, scRNA-seq

city: Houston

first: Justin

last: Ma

state: Texas

address: 1 Baylor Plaza, Baylor College of Medicine

department: ophthalmology

institute: Baylor College of Medicine

description:
10x Genomics
Ma_Atlas_filtered.csv

data_processing:
Demultiplexing was done using the Cell Ranger Multi Pipeline (in Cell Ranger v6.1.2) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/using/multi)
Assembly: GRCm38/mm10-2020A
Supplementary files format and content: We provide a universal comma-separated values file (.csv) for the filtered expression data. We also provide unprocessed barcode/feature/matrix data per experiment and the assignment confidence table based on a cell ranger's calculation using a confidence level of 0.9.

source_name: Retina

extract_protocol:
Fresh mouse retinas were dissected out from Vglut2-Tdtomato-Ai9 mice in oxygenated Ames media. Retinas are digested in papain and dissociated into single cells by manual trituration in low-ovomucoid solution. RGCs were enriched by negative-rod immunopanning using an anti-CD73 antibody. RGCs were labeled with a Thy1-APC antibody. RGCs were incubated with cholesteral-modified oligos using the 10x Genomics 3' CellPlex Kit (PN-1000261). RGCs from up to 6 retinas are pooled and resuspended in oxygenated Ames media, then enriched using FACS to isolate APC and Tdtomato positive cells. Unless specified, all steps were performed in oxygenated Ames, in the presence of Actinomycin D. All steps were also performed on individual retinas up until FACS.
Library construction was performed according to the manufacturer's instructions for the Chromium Next GEM 3' Kit v3.1

value: Retina

value: Retinal ganglion cells


title: CRC tumor T073 [DREAM]


title: Human, CC, Normal,1

city: Zhuhai

first: Liangyu

last: Zhao

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

data_processing:
Primer spots were stained by hybridization of fluorescently labeled probes and imaged on the Metafer Slide Scanning platform. The resulting spot image was loaded into the BSTMatrix and BSTViewer along with the previously obtained BF tissue image of the same area. The two images were aligned and the built-in tissue recognition tool was used to extract spots covered by tissue.
Assembly: GRCh38_release95
Supplementary files format and content: spots-genes martrix and the HE staining of the CC slide
Library strategy: Spatial Transcriptomics

source_name: corpus cavernosum

extract_protocol:
The surgically obtained ex vivo CC tissue from human and rat were trimmed to form a regular cylindrical shape. And tissue surfaces were quickly rinsed with a pre-cooled solution of 1X PBS (RNase free) or normal saline to remove residual blood, and sterile gauze was used to blot the surface fluid. Small fragments of each tissue were snap-frozen in isopentane pre-chilled with liquid nitrogen and optimum cutting temperature (OCT) compound (SAKURA,Cat#: 4583). Then, the frozen tissue was cut in a pre-cooled cryostat at 10µm thickness and systematically placed on chilled BMKMANU S1000 Tissue Optimization Slides and BMKMANU S1000 Gene Expression Slides, and stored at −80℃ until use.
Reverse transcription (RT), second-strand cDNA synthesis, adaptor ligation and a second RT was generated and libraries were constructed according to the performer’s protocol. Sequencing handles and indexes were added in an indexing PCR and the finished libraries were purified and quantified. Sequencing was performed on the Illumina NovaSeq 6000 with a sequencing depth of at least 50,000 reads per spot (100μm) and 150bp (PE150) paired-end reads (performed by Biomarker Technologies Corporation, Beijing, China).

value: corpus cavernosum

value: primary cells

value: all corpus cavernosum cells in tissue


title: CC DMED-3

data_processing:
The raw sequencing reads were processed by Cell Ranger (v.3.1.0) with the default parameters.
Assembly: The reference genome was GRh38-1.2.0
Supplementary files format and content: Cell Ranger files (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

extract_protocol:
Fresh CC tissue samples of about 1×1-cm size were first immersed in 15 ml PBS with vigorous shaking to remove residual blood cells. Then, tissues were cut into pieces of 1×1-mm size and enzymatically digested with 2.5 mg/ml collagenase type I (17104-019, gibco), 4 mg/ml collagenase type IV (17018029, gibco), 0.1 mg/ml neutral protease, and 2 mg/ml DNase I (#AMPD1, Sigma-Aldrich) at 37°C for 40 min. Subsequently, the cell suspension was filtered through a 40-mm nylon mesh, and the cells were sorted by MACS with a Dead Cell Removal Kit (130-090-101, Miltenyi Biotec) to remove dead cells. The cells were resuspended in 0.05% BSA/PBS buffer before cDNA library preparation.
Standard protocol of 10X Genomics

value: all CC cells

tag: condition

value: DMED


title: KO_UT12_1

value: no BRG1 inhibitor


title: CRC tumor T063 [DREAM]

value: colon

value: CRC tumor


title: RGC, experiment4, CMO-multiplex, scRNA-seq

description:
10x Genomics
Ma_Atlas_filtered.csv


title: 8wk_PBS_Only_Mouse_4

value: 8 weeks

value: CD3e T cell

value: PBS


title: CRC tumor T081 [DREAM]


title: WT_T12_3

value: AID-DivA

value: osteosarcoma

value: WT

value: 12h after auxin treatment


title: DMSO treated

data_processing:
The adapter sequences were removed from raw reads by cutadapt (version 1.15).Clean reads from RNA-seq were quality filtered, and then mapped to the human genome (hg38) by STAR.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for mRNA samples.

growth_protocol: 293Tcell lines were cultured in DMEM (Gibco) supplemented with 10% FBS and 1% Penicillin and Streptomycin at 37°C.

extract_protocol:
RNA was isolated with Trizol.
RNA librarys for RNA-seq were  prepared using Superscript II  reverse transcriptase  and special prime.

treatment_protocol: 293T cell was transfected with SF3B3-MMS1 plasmid or empty vector. 293T cell was treated with NAI-N3 or DMSO at 37°C for 10min.

value: epithelial-like cell from the kidney

value: DMSO treated


title: NAI-N3 treated

value: NAI-N3 treated


title: CRC tumor T057 [DREAM]


title: CRC tumor T061 [DREAM]


title: WT_T12_2


title: CRC tumor T053 [DREAM]


title: RGC, experiment3, CMO-multiplex, scRNA-seq

description:
10x Genomics
Ma_Atlas_filtered.csv

value: Retina

value: Retinal ganglion cells


title: SF3B3-MMS1-OE 3

value: no


title: WT_T12_1


title: CRC tumor T049 [DREAM]


title: KO_T12_3

value: ARID1A KO


title: SF3B3-MMS1-OE 1


title: RGC, experiment2, CMO-multiplex, scRNA-seq

description:
10x Genomics
Ma_Atlas_filtered.csv


title: KO_T12_2

value: no BRG1 inhibitor


title: WT3


title: CRC tumor T065 [DREAM]

value: colon


title: CRC tumor T045 [DREAM]

value: CRC tumor


title: WT2


title: KO_T12_1


title: CRC tumor T041 [DREAM]


title: CRC tumor T043 [DREAM]


title: RGC, experiment1, CMO-multiplex, scRNA-seq

description:
10x Genomics
Ma_Atlas_filtered.csv


title: WT1


title: CRC tumor T039 [DREAM]


title: WT_T4_3

value: 4h after auxin treatment


title: KO_UT_5

data_processing:
The data was processed using the DKFZ RNAseq workflow: https://github.com/DKFZ-ODCF/RNAseqWorkflow
Assembly: GRCh37
Supplementary files format and content: tsv files containing for each gene, the number of reads, and the normalized FPKM and TPM values.

extract_protocol:
RNA was extracted from cells using the TRIzol RNA Isolation Reagents (Thermofisher). RNA was then purified using the RNeasy Mini spin columns kit (Qiagen) according to manufacturer’s instructions. The integrity of the extracted RNA was analyzed by Agilent 2100 Bioanalyzer using Agilent RNA 600 Nano Kit according to the manufacturer’s protocol.
Sequencing libraries were prepared by the Genomics and Proteomics Core Facility (DKFZ, Heidelberg) from total RNA using the Illumina TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions. Multiplexes were sequenced in a paired-end setting (100 bp) on an Illumina NovaSeq 6000 machine for sequencing.

value: untreated


title: WT_T4_1


title: WT_T4_2


title: KO_UT_4


title: CRC tumor T037 [DREAM]


title: CRC tumor T035R [DREAM]


title: KO_T4_3


title: CRC tumor T035 [DREAM]


title: SF3B3-MMS1-OE 2


title: KO_UT_3


title: PBS-treated and α4β7-treated cells, load 2, GEX

city: New York

first: Darwin

last: D'Souza

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

description:
total RNA
PabloCELLPLEX3_raw_matrix.h5ad

data_processing:
Libraries have been processed with Cell Ranger v6.1.2 and aligned to referencemm10-2020-A
Assembly: mm10-2020-A
Supplementary files format and content: Unfiltered raw matrix from cellranger and gene expression and hashtag counts
Library strategy: CITE-Seq

source_name: Peyer's patch

extract_protocol:
Peyer's patches (PP) were individually collected and weighed. Each PP was incubated in collagenase D (Sigma-Aldrich, 400IU/ml) for 30 min and mechanically homogenized to obtain a single-cell suspension
Libraries were prepared according to manufacturer's instructions using the Single Cell 3' v3 CellPlex Kit (10x Genomics).
CITESeq with HTO only (no ADT)

value: Peyer's patch

value: mixed sample (PBS and anti-alpha4β7 antibody

value: mRNA


title: PBS-treated and α4β7-treated cells, load 2, HTO

description:
Hashtag-derived Oligonucleotide (HTO
PabloCELLPLEX3_raw_matrix.h5ad

value: HTO

tag: hto


title: KO_T4_2

value: AID-DivA

value: osteosarcoma


title: CRC tumor T025 [DREAM]


title: WT_UT_5

value: WT


title: PBS-treated and α4β7-treated cells, load 1,  HTO

description:
Hashtag-derived Oligonucleotide (HTO
PabloCELLPLEX2_raw_matrix.h5ad


title: KO_T4_1


title: WT_UT_4


title: CRC tumor T013 [DREAM]


title: WT_UT_3


title: PBS-treated and α4β7-treated cells, load 1, GEX

description:
total RNA
PabloCELLPLEX2_raw_matrix.h5ad


title: WT_T2_3

value: 2h after auxin treatment


title: WT_Thymus_HTO [GA41207]

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: processed data linked to sample: WT_Thymus_GEX [GA41203]

library_source: other

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 50+91 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (cellranger-6.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence) - cell (barcode) combination and T cell receptor repertoire profiling.
Assembly: refdata-cellranger-vdj-GRCm38-alts-ensembl-4.0.0 and refdata-gex-mm10-2020-A
Supplementary files format and content: mouse_Thymus_genematrix.csv : comma-delimited text files including UMI counts for each feature (gene or HTO) and cell (barcode) conbination
Supplementary files format and content: airr_rearrangement.tsv : tab-delimited text file including detected clonotypes for each cell (barcode)
Supplementary files format and content: clonotypes.csv : comma-delimited text file including the TCR clonotype information

molecule: protein

source_name: thymus

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller. Hashtag oligonucleotides or cDNAs with UMIs and a cell barcode were generated at single-cell level in each droplet.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide.

treatment_protocol: Thymocyte were homoginized and enriched MR1-5-OP-RU tetramer positive T cells by MACS sorting.

value: thymus

value: thymocyte

value: wild type

value: Hashtag oligonucleotide (HTO)


title: 6-MCTCpositive

city: Tianjin

first: Junya

last: Ning

state: -- None --

address: Huanhuxi Road, Hexi District, Tianjin

institute: Tianjin Medical University Cancer Institute & Hospital

description: 10× Genomics

data_processing:
the demultiplexing, barcoded processing,gene counting and aggregation were made using the Cell Ranger software.
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Hepatocellular carcinoma

extract_protocol:
The frozen tissues were homogenized on ice in lysis buffer containing: 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.01% NP-40 (ThermoFisher), 1 mM β-mercaptoethanol, and 0.2 U/ μL RNase inhibitor (Promega) by a glass homogenizer. Tissues were dounced until there were no visible clumps. Homogenates were incubated on ice for 5 min, and an equal volume of HEB medium (Hibernate E/B27/ GlutaMAX, Gibco) was added to stop lysis. Cell debris and large clumps were removed using 40-μm filters (pluriSelect), and the supernatant was centrifuged at 500× g and 4 °C for 5 min. To further remove debris, Debris Removal Solution was applied according to the manufacturer’s instructions. Nuclei were washed 1–2 times and resuspended in wash and resuspension buffer containing 1× PBS, 1% bovine serum albumin (BSA, Sigma), and 0.2U/μL RNase inhibitor, then collected by centrifugation at 500× g and 4 °C for 5 min. DAPI DNA dye (ThermoFisher) was added and nuclei were counted manually under a fluorescence microscope (BX53, Olympus). The nuclear suspension was diluted to a concentration of 500–1000 nuclei/μL for loading onto the 10× Chromium instrument.
Nuclear suspension loading onto the Chromium Next GEM Chip, nuclear barcoding, cDNA amplification, and library construction were carried out according to the 10× Genomics protocols (CG000204 Rev D). Libraries were sequenced on the Illumina NovaSeq 6000 System at LC- Bio Technology Co., Ltd. in Hangzhou, China.

value: Hepatocellular carcinoma


title: CRC tumor T009 [DREAM]

value: colon


title: WT_T2_2

value: no BRG1 inhibitor


title: WT_Thymus_TCR [GA41205]

value: TCR V(D)J segments


title: WT_T2_1


title: 5-MCTCnegative

description: 10× Genomics


title: CRC tumor T007 [DREAM]

value: CRC tumor


title: WT_Thymus_GEX [GA41203]

value: poly A RNA


title: 4-MCTCnegative

description: 10× Genomics


title: CRC tumor T005 [DREAM]


title: KO_T2_3

value: ARID1A KO


title: 3-MCTCpositive

description: 10× Genomics


title: KO_T2_2


title: R3_vehicle&RT_survival

city: Memphis

first: Jared

last: Andrews

state: Tennessee

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description: OE0290_allografts_treatment_R3_vehiclert-surv-0

data_processing:
Data was processed, normalized and analyzed via the R2: Genomics Analysis and Visualization Platform (http://r2.amc.nl)
Assembly: mm10
Supplementary files format and content: TAB-delimited text file includes TPM counts for each sample

source_name: Tumor

extract_protocol:
AllPrep DNA/RNA/Protein Mini Kit (Qiagen)
TruSeq (Standard)

value: Tumor


title: KO_T2_1


title: CRC tumor T003 [DREAM]


title: 2-MCTCnegative

description: 10× Genomics


title: Rat, CC, Normal,1

data_processing:
Primer spots were stained by hybridization of fluorescently labeled probes and imaged on the Metafer Slide Scanning platform. The resulting spot image was loaded into the BSTMatrix and BSTViewer along with the previously obtained BF tissue image of the same area. The two images were aligned and the built-in tissue recognition tool was used to extract spots covered by tissue.
Assembly: mRatBN7.2
Supplementary files format and content: spots-genes martrix and the HE staining of the CC slide
Library strategy: Spatial transcriptomics

organism: Rattus norvegicus

extract_protocol:
The surgically obtained ex vivo CC tissue from rat were trimmed to form a regular cylindrical shape. And tissue surfaces were quickly rinsed with a pre-cooled solution of 1X PBS (RNase free) or normal saline to remove residual blood, and sterile gauze was used to blot the surface fluid. Small fragments of each tissue were snap-frozen in isopentane pre-chilled with liquid nitrogen and optimum cutting temperature (OCT) compound (SAKURA,Cat#: 4583). Then, the frozen tissue was cut in a pre-cooled cryostat at 10µm thickness and systematically placed on chilled BMKMANU S1000 Tissue Optimization Slides and BMKMANU S1000 Gene Expression Slides, and stored at −80℃ until use.
Reverse transcription (RT), second-strand cDNA synthesis, adaptor ligation and a second RT was generated and libraries were constructed according to the performer’s protocol. Sequencing handles and indexes were added in an indexing PCR and the finished libraries were purified and quantified. Sequencing was performed on the Illumina NovaSeq 6000 with a sequencing depth of at least 50,000 reads per spot (100μm) and 150bp (PE150) paired-end reads (performed by Biomarker Technologies Corporation, Beijing, China).

value: corpus cavernosum

value: primary cells

value: all corpus cavernosum cells in tissue


title: R3_vehicle_pd

description: OE0290_allografts_treatment_R3_vehicle-pd-0


title: hy5-215-3

city: Anseong-si

first: Dasom

last: Choi

state: Gyeonggi-do

address: 4726, Seodong-daero

institute: Chung-Ang University

description: replicate 3

data_processing:
Quality of raw reads were pre-checked using the FastQC software.
Trimmed reads of each sample were aligned to the Arabidopsis TAIR10 genome using STAR aligner with default parameters.
Mapped reads were converted to digital counts using FeatureCounts and were analyzed using edgeR.
DEGs were identified based on an adjusted p-value <0.05 and an absolute log2 fold change ≥ 1.
Assembly: Arabidopsis thaliana reference genome (TAIR10) was downloaded via the TAIR database (https://www.arabidopsis.org/)
Supplementary files format and content: bw files for individual samples

organism: Arabidopsis thaliana

source_name: Whole plants

extract_protocol:
Total RNAs were isolated using the RNeasy Plant Mini Kit (QIAGEN, Valencia, CA) and treated with DNase I (NEB, USA).
RNA-seq libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., USA).

value: Whole plants

tag: ecotype

value: mutants hy5-215


title: WT_T0_3

value: AID-DivA

value: osteosarcoma

value: WT

value: 0h after auxin treatment


title: R3_vehicle_survival

description: OE0290_allografts_treatment_R3_vehicle-surv-0


title: CRC tumor T011 [DREAM]


title: T24, siACAT1-2, biol rep 3

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster, resulting in 65,536 clusters. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-cluster. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated. Duplicate consensus sequences were removed and used for standard RNA-seq analysis. They were mapped to the human genome (assembly GRCh38) using STAR software (Version 2.5.3) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor), and then RPKMs were calculated.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts or RPKM values for each Sample

source_name: Bladder cancer

extract_protocol:
Total RNAs were extracted from samples using TRIzol (Invitrogen). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with Nanodrop OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with Qubit RNA Broad Range Assay kit (Life Technologies).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-Digital Stranded mRNA Library Prep Kit for Illumina (Catalog NO. DR08502, Seqhealth Technology Co., Ltd. Wuhan, China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules.

value: Bladder cancer

value: T24 cell line

value: Human bladder transitional cell cancer cells

value: ACAT1 knockdown

value: Use siACAT1-2


title: R3_cri&RT_survival

description: OE0290_allografts_treatment_R3_crirt-surv-0


title: hy5-215-2

description: replicate 2


title: 1-MCTCpositive

description: 10× Genomics

value: Hepatocellular carcinoma


title: WT_T0_2

value: no BRG1 inhibitor


title: WT_T0_1


title: T24, siACAT1-2, biol rep 2


title: hy5-215-1

description: replicate 1


title: T24, siACAT1-2, biol rep 1


title: R3_vehicle&RT_pd

description: OE0290_allografts_treatment_R3_vehiclert-pd-0

value: Tumor


title: KO_T0_3

value: ARID1A KO


title: R3_cri_survival

description: OE0290_allografts_treatment_R3_cri-surv-0


title: R3_cri&RT_pd

description: OE0290_allografts_treatment_R3_crirt-pd-0


title: Col-0-2

description: replicate 2

value: wildtype


title: T24, siACAT1-1, biol rep 3

value: Use siACAT1-1


title: R3_cri_pd


title: KO_T0_2


title: T24, siACAT1-1, biol rep 2


title: Col-0-1

description: replicate 1

value: Whole plants


title: KO_T0_1


title: R3_cap&RT_survival

description: OE0290_allografts_treatment_R3_caprt-surv-0


title: T24, siACAT1-1, biol rep 1


title: WT_UT_3

value: untreated


title: PKCAwt_3

city: DERIO

first: VERONIQUE

middle: FRANÇOISE

last: CALLEJA

state: Vizcaya

address: ASTONDO BIDEA 612

country: Spain

institute: Hawk Biosystems

data_processing:
The sequencing was done using HiSeq4000 with a SR75 sequencing configuration.
Sequencing was performed on an machine. The "Trim Galore!" utility version 0.4.2 was used to remove sequencing adaptors and to quality trim individual reads with the q-parameter set to 20. Then sequencing reads were aligned to the mouse genome and transcriptome (Ensembl release-95) using RSEM version 1.3.0  in conjunction with the STAR aligner version 2.5.2. Sequencing quality of individual samples was assessed using FASTQC version 0.11.5
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file contains the raw counts for each sample (columns) for each gene (rows)

growth_protocol: U87MG cells were plated in a 6-well plate at 300,000 cells per well and transfected 24h later with pBABE puro-Myc-PKC WT or mutants. The cells were then selected with puromycin until the control non-transfected cells were all dead (approx. one week). RNA extraction was done on the cells expressing constitutively Myc-PKCa and mutants but also parental non-transfected cells.

extract_protocol:
RNeasy kit from Qiagen
The library was made usingKapa mRNA hyper prep kitwith polyA capture. After samples were prepared 1ug was used as input for the libraries.

value: Myc-PKCa-WT

value: Untreated


title: WT_UT_2

value: AID-DivA

value: osteosarcoma

value: WT


title: T24, siNC, biol rep 3

value: Bladder cancer

value: T24 cell line

value: Use siNC


title: PKCAwt_2


title: PKCAD463N_3


title: R3_cap_pd


title: R3_cap_survival

description: OE0290_allografts_treatment_R3_cap-surv-0


title: WT_UT_1


title: T24, siNC, biol rep 2

value: Human bladder transitional cell cancer cells


title: Col-0-3

description: replicate 3


title: PKCAD463N_2


title: T24, siNC, biol rep 1


title: R2_vehicle&RT_survival

description: OE0290_allografts_treatment_R2_vehiclert-surv-0


title: KO_UT_2


title: KO_UT_3


title: UM-UC-3, siACAT1-2, biol rep 3

value: UM-UC-3 cell line

value: ACAT1 knockdown

value: Use siACAT1-2


title: R2_vehicle&RT_pd

description: OE0290_allografts_treatment_R2_vehiclert-pd-0

value: Tumor


title: PKCAD463N_1


title: UM-UC-3, siACAT1-2, biol rep 2


title: KO_UT_1

value: ARID1A KO

value: no BRG1 inhibitor


title: PKCAD463H_3


title: R2_vehicle_survival

description: OE0290_allografts_treatment_R2_vehicle-surv-0


title: R2_vehicle_pd

description: OE0290_allografts_treatment_R2_vehicle-pd-0


title: UM-UC-3, siACAT1-2, biol rep 1


title: PKCAD463H_2


title: R3_cap&RT_pd

description: OE0290_allografts_treatment_R3_caprt-pd-0


title: SGBS cells, replicate v5, d8

city: Leipzig

first: Jana

last: Schor

state: Saxony

address: Permoserstr. 15

department: Molecular Systems Biology

institute: Helmholtz Centre for Environmental Research

data_processing:
Transcriptomic data analysis was performed in analogue to Schubert et al. (2021). Very briefly, obtained sequencing reads were transformed into a quantitative presence/absence table using uap (Kampf et al., 2019).
Files were merged, quality controlled and quality filtered using FastQC (f. Babraham Bioinformatics, 2023) and FASTXToolkit (Hannon Lab, 2023).
Adapter trimming was facilitated using Trim Galore (T. G. Babraham Bioinformatics, 2023.
HISAT2 (Kim et al., 2019) mapped the reads to the human genome (GRCh38).
Alignments were filtered for correct pairing and sorting with the samtools suite (Li et al., 2009) and further processed with HTseq (Anders et al., 2015) to generate read counts overlapping annotated genes.
Assembly: read mapping to human genome GRCh38, GENCODE gene annotation (Release 34) (gencodegenes.org/human) served as reference.
Supplementary files format and content: Tab-delimited text files including read counts for each sample

source_name: SGBS

growth_protocol: Human SGBS cells were provided by the laboratory of Prof. Dr. Wabitsch at the University Clinic Ulm. Cells were differentiated according to the standard protocol described previously (Wabitsch et al., 2001). Briefly, SGBS preadipocytes were grown to reach full confluence in basal culture medium, consisting of Dulbecco’s modified Eagle’s F12 (DMEM/F12; Gibco, USA) supplemented with 33 µM biotin (Sigma Aldrich, USA), 17 µM panthothenate (Sigma Aldrich, USA) and 100 U/l penicillin/streptomycin (Sigma Aldrich, USA) and complemented with 10 % fetal calf serum (FCS; Gibco, USA). Differentiation was initiated (day 0 to day 4) and maintained (day 4 to day 12) by an exchange to serum-free basal medium supplemented with 0.1 µM cortisol, 0.01 mg/ml apo-transferin, 0.2 nM triiodothyronine and 20 nM insulin and specifically for the first four days additionally containing 2 µM rosiglitazone, 25 nM dexamethasone and 200 µM 3isobutyl1methylxanthine (all supplements purchased from Sigma Aldrich, USA). New media was provided every four days.

extract_protocol:
SGBS cells were differentiated as described above and harvested at day 0, after 6 h and days 1, 2, 4, 8 and 12 post adipogenic induction. RNA transcripts were prepared as reported previously (Schubert et al., 2021). Briefly, cell lysis was performed in 700 µl TRIzol (Thermo Fisher Scientific, USA), RNA was extracted applying the miRNeasy Mini Kit (Thermo Fisher Scientific, USA) in combination with Maxtract High Density tubes (Qiagen, Germany). DNA remains were removed using the Ambion TURBO DNA-free Kit (Thermo Fisher Scientific, USA), RNA was precipitated for cleaning with ethanol and concentrations were determined using the Quant-iT RNA kit (Thermo Fisher Scientific, USA) on a Qubit 2.0 instrument (Thermo Fisher Scientific, USA). RNA integrity was determined applying the RNA 6000 Nano Assay at an Agilent 2100 Bioanalyzer (Agilent, USA) and only samples with an RNA integrity number (RIN) > 8 were used for rRNA depletion of 100 ng total RNA sample using the Ribo-Zero Gold Human/Mouse/Rat Magnetic Kit (Illumina, USA).
A sequencing library was generated utilizing the ScripSeqv2 Kit (Illumina, USA), quality controlled with the High Sensitivity DNA Kit (Agilent, USA) at the Agilent 2100 Bioanalyzer system and the library concentration was determined using the Quant-iT dsDNA High Sensitivity kit (Thermo Fisher Scientific, USA) and a Qubit 2.0.
Two pools (one per sequencing FlowCell) were generated with 8 ng of each library and selected for fragments of 150700 bp on a preparative agarose gel in conjunction with the MinElute Gel Extraction Kit (Qiagen, Germany). Pairedend sequencing at a length of 100 bases with a sequencing depth of 160 million read pairs per sample was carried out on a HiSeq2000 device (Illumina, USA).

value: SGBS

value: preadipocyte cells

value: adipogenic differentiation


title: SGBS cells, replicate v5, d12


title: R2_cri&RT_survival

description: OE0290_allografts_treatment_R2_crirt-surv-0


title: UM-UC-3, siACAT1-1, biol rep 3

value: Use siACAT1-1


title: PKCAD463H_1

value: Untreated


title: SGBS cells, replicate v5, d4


title: UM-UC-3, siACAT1-1, biol rep 2


title: R2_cri&RT_pd

description: OE0290_allografts_treatment_R2_crirt-pd-0


title: UM-UC-3, siACAT1-1, biol rep 1


title: Parental_2

value: Parental


title: R2_cri_survival

description: OE0290_allografts_treatment_R2_cri-surv-0


title: SGBS cells, replicate v5, d2


title: SGBS cells, replicate v5, d1


title: UM-UC-3, siNC, biol rep 3

value: WT


title: Parental_1


title: R2_cri_pd


title: SGBS cells, replicate v5, 6h


title: UM-UC-3, siNC, biol rep 2

value: Bladder cancer


title: R2_cap&RT_survival

description: OE0290_allografts_treatment_R2_caprt-surv-0


title: Rhytidome 94

city: 17003 Girona

first: Mercè

last: Figueras

state: Girona

address: C/ Mª Aurèlia Campmany, 41 (campus Montilivi)

institute: Universitat de Girona

data_processing:
RNA-seq data were first analysed for quality control with FastQC (Andrews, 2010)
First low-quality 12 bp removal was performed with Trimmomatic v. 0.40 (Bolger et al., 2014)
Reads were mapped with GSNAP (Wu et al., 2016) against Q. suber genome (GCF_002906115.1_CorkOak1.0_genomic.fna)
Reads from each library were assembled with Cufflinks 2.2.1 (Trapnell et al., 2010)
The consensus transcriptome for all the samples was generated assembling each library with the Cuffmerge script from Cufflinks
different isoforms were collapsed and total counts were estimated by HTSeq-count 0.11.1 (Anders et al., 2015)
The count matrix generated was used to identify differentially expressed genes (DEGs) using the DESeq2 package v.1.38.3
Read counts per locus were corrected by rlog transformation and DEGs were obtained by pairwise comparisons
Assembly: GCF_002906115.1_CorkOak1.0
Supplementary files format and content: One unique file with a matrix table with regularized and log transformed read counts for each cork oak gene (locus identifier) and sample

organism: Quercus ilex

source_name: outer bark of tree trunk

extract_protocol:
Total RNA was extracted from outer barks by some modifications of the method described previously (Chang et al., 1993; Chaves et al., 2014).
cDNA libraries were obtained using the MGIEasy RNA Library Prep Kit V3.1 and 3 µg of each sample

value: outer bark of tree trunk


title: SGBS cells, replicate v5, d0


title: UM-UC-3, siNC, biol rep 1

value: Use siNC


title: R2_cap&RT_pd

description: OE0290_allografts_treatment_R2_caprt-pd-0


title: Rhytidome 68


title: SGBS cells, replicate v4, d12


title: R2_cap_survival

description: OE0290_allografts_treatment_R2_cap-surv-0


title: U937_wildtype_FURIN_rep3

city: Singapore

first: Sujoy

last: Ghosh

address: 8 College Rd

country: Singapore

institute: National University of Singapore

description:
nonribo.U937_3_Aligned.sortedByCoord.out.bam
output_counts_gene_name_all_info.txt

data_processing:
The quality of RNA-seq reads was ascertained via FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc)
Adapter trimming was performed via BBDuk (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/)
Sequencing reads were mapped to the human reference genome (GRCh38) via STAR (2.5.1b)
Raw count matrices of RNA sequencing data were obtained via the featureCountspackage in R and further processed for gene quantification and identification of differentially expressed genes using the limma package
Gene counts were log2 transformed and normalized for sequencing depth via the trimmed means of M values (TMM) method
Assembly: GRCh38
Supplementary files format and content: Each file contains unfiltered raw data (not normalized, not log transformed) for all genes

growth_protocol: Cells were cultured in DMEM media (11885-084) with 10% FBS and 1% pen-strep at 37 degree with 5% CO2 incubator

extract_protocol:
Total RNAs were extracted from WT, HZ and NZ FURIN clones of U937 cells via TRIzol (Life Technologies)
Ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. Following is the workflow of library construction:

treatment_protocol: Hemizygous (1 copy) and nullizygous (0 copy) clones of FURIN gene were generated via CRISPR technology on U937 cells and compared to wild-type cells

value: pro-monocytic


title: SGBS cells, replicate v4, d8


title: Rhytidome 67


title: Rhytidome 33


title: U937_wildtype_FURIN_rep2

description:
nonribo.U937_2_Aligned.sortedByCoord.out.bam
output_counts_gene_name_all_info.txt


title: Parental_3


title: U937_wildtype_FURIN_rep1

description:
nonribo.U937_1_Aligned.sortedByCoord.out.bam
output_counts_gene_name_all_info.txt


title: R2_cap_pd


title: SGBS cells, replicate v4, d4


title: U937_nullizygous_FURIN_rep3

description:
nonribo.Homo_3_Aligned.sortedByCoord.out.bam
output_counts_gene_name_all_info.txt


title: U937_nullizygous_FURIN_rep2

description:
nonribo.Homo_2_Aligned.sortedByCoord.out.bam
output_counts_gene_name_all_info.txt


title: SGBS cells, replicate v4, d1


title: R1_vehicle&RT_pd

description: OE0290_allografts_treatment_R1_vehiclert-pd-0


title: CD8+ HD4 PVR

type: RNA

city: Barcelona

first: Ester

last: Lozano

address: Diagonal Av. 643

department: Cell Biology, Physiology and Immunology

institute: University of Barcelona

description: RNA was extracted using RNeasy kit (Qiagen)  as per manufacturer's specifications

hyb_protocol: A minimum of 300 ng of total RNA per sample was loaded and run on the nCounter MAX/FLEX system for analysis of the nCounter Immune Exhaustion Panel

scan_protocol: The sample cartridge was scanned by an nCounter Digital Analyse (NanoString Technologies) at 555 fields of view.

data_processing: The raw data were re-scaled to account for the differences in raw code counts. This was performed using nSolver Analysis Software (NanoString Technologies), incorporating positive, negative and 'normalisation' gene target counts.

label: NanoString

source_name: RNA - CD8 from PBMC from healthy donors

label_protocol: Capture probes and reporter probes (NanoString Technologies) were added to the extracted 300ng of mRNA according to manufacturer guidelines.

growth_protocol: EasySep™ Human CD8+ T Cell Isolation Kit (STEMCELL Technologies) was used for negative selection of CD8+ T cells from PBMC from healthy donors.

extract_protocol: After 24h, total RNA was isolated with RNeasy kit (Qiagen).

treatment_protocol: CD8+ T cells were cultured for onto 2 microg/mL of human PVR-Fc, Nectin-2-Fc or IgG control (RnDSystems). After 1h pre-incubation, human IL-2 (10 U/mL) and MACSiBead particles with CD2, CD3, and CD28 antibodies (Treg Suppression Inspector, Miltenyi Biotec) were added to each well.

tag: agent

value: PVR


title: SGBS cells, replicate v4, 6h


title: R1_vehicle_pd

description: OE0290_allografts_treatment_R1_vehicle-pd-0


title: CD8+ HD4 Ctrol

value: Control


title: SGBS cells, replicate v4, d0


title: U937_nullizygous_FURIN_rep1

description:
nonribo.Homo_1_Aligned.sortedByCoord.out.bam
output_counts_gene_name_all_info.txt


title: SGBS cells, replicate v2, d12


title: U937_hemizygous_FURIN_rep2

description:
nonribo.Hetero_2_Aligned.sortedByCoord.out.bam
output_counts_gene_name_all_info.txt


title: CD8+ HD3 PVR


title: U937_hemizygous_FURIN_rep3

description:
nonribo.Hetero_3_Aligned.sortedByCoord.out.bam
output_counts_gene_name_all_info.txt


title: CD8+ HD3 nectin-2


title: U937_hemizygous_FURIN_rep1

description:
nonribo.Hetero_1_Aligned.sortedByCoord.out.bam
output_counts_gene_name_all_info.txt


title: SGBS cells, replicate v2, d8


title: R1_cri&RT_pd

description: OE0290_allografts_treatment_R1_crirt-pd-0


title: R1_vehicle&RT_survival

description: OE0290_allografts_treatment_R1_vehiclert-surv-0


title: SGBS cells, replicate v4, d2


title: U251 cell lines, si-HNRNPC, 48h, rep2

city: Nanchang

first: Junjun

last: Chen

address: No.461, Bayi Avenue, Nanchang City, Jiangxi Province

institute: Nanchang University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genomeHomo sapiens (Version: v101).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak)
Assembly: Homo sapiens, Ensembl v96
Supplementary files format and content: tab-delimited text flie includes FPKM values for each sample

source_name: cell line

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min.
Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was 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 is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are 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 are 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 library was 300±50 bp.

value: cell line

value: glioblastoma cells


title: R1_cri_survival

description: OE0290_allografts_treatment_R1_cri-surv-0

value: Tumor


title: CD8+ HD3 Ctrol


title: SGBS cells, replicate v2, d4


title: R1_vehicle_survival

description: OE0290_allografts_treatment_R1_vehicle-surv-0


title: SGBS cells, replicate v2, d2


title: U251 cell lines, si-HNRNPC, 48h, rep1


title: R1_cri_pd

description: OE0290_allografts_treatment_R1_caprt-surv-0


title: R1_cap&RT_survival


title: CD8+ HD4 nectin-2


title: SGBS cells, replicate v2, d1


title: R1_cap&RT_pd

description: OE0290_allografts_treatment_R1_caprt-pd-0


title: CD8+ HD2 Ctrol


title: U251 cell lines, si-NC, 48h, rep1


title: CD8+ HD2 nectin-2


title: SGBS cells, replicate v2, 6h


title: U251 cell lines, si-NC, 48h, rep2


title: R1_cri&RT_survival

description: OE0290_allografts_treatment_R1_crirt-surv-0


title: R1_cap_survival

description: OE0290_allografts_treatment_R1_cap-surv-0


title: CD8+ HD1 PVR


title: U251 cell lines, si-HNRNPC, input, rep2


title: SGBS cells, replicate v2, d0


title: TFG-MET_Allograft_3

type: genomic

description: Methylation data from murine allograft tumors with human TFG-MET fusion gene.

hyb_protocol: Illumina protocol

scan_protocol: Illumina HiScan System according to the manufacturer's protocol

data_processing:
Raw IDAT files from the mouse model MM285k arrays were pre-processed with the sesame package (v1.14.2) with the default "TQCDPB" preprocessing steps. Noob normalization was applied to all samples to derive beta values.
Noob normalized beta values

label: bioton/DNP

label_protocol: Illumina protocol

extract_protocol: Illumina protocol


title: R1_cap_pd


title: SGBS cells, replicate v1, d12


title: CD8+ HD2 PVR


title: CD8+ HD1 Ctrol


title: CD8+ HD1 nectin-2


title: SGBS cells, replicate v1, d8


title: U251 cell lines, si-HNRNPC, input, rep1


title: WT P6, scRNAseq

city: West Haven

first: Francesc

last: Lopez

department: Department of Genetics

institute: Yale University

description:
WTP6
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: tab-separated value files and matrix files produced with CellRanger

extract_protocol:
Standard cell disscoiaiton  followed by FACS sorting
Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SRPIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, pair-end construct with P5 and P7 sequences and a sample index were added.

value: Retina

value: Tamoxifen at P1 harvest at P6


title: TFG-MET_Allograft_2


title: U251 cell lines, si-NC, input, rep2


title: SGBS cells, replicate v1, d4

value: SGBS

value: preadipocyte cells


title: TFG-MET_Allograft_1


title: WT P10, scRNAseq

description:
WT-Mfsd
10x Genomics

value: Tamoxifen at P1 harvest at P10


title: RNA-Seq_MCF7_E2_siCARM1

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

data_processing:
Reads were aligned to the hg38 using STAR version 2.7.10, with Ensembl v36 as the genome annotation.
bedGraphToBigWig was used to generate bigWig file from the bedGraph files generated by STAR
Assembly: hg38
Supplementary files format and content: bigWig, a binary file format used for efficiently storing and displaying large-scale genome-wide data

growth_protocol: MCF7 cells were cultured in DMEM medium supplemented with 10% FBS

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L).

treatment_protocol: MCF7 cells were transfected with control siRNA (siCTL) or siRNA specifically against CARM1 (siCARM1) in stripping medium for three days, and then treated with or without iCARM1 (5 mM) in the presence or absence of estrogen (E2, 10−7M, 6 h), followed by RNA-seq analysis.

value: Human breast cancer cell


title: U251 cell lines, si-NC, input, rep1


title: RNA-Seq_MCF7_CTL_siCARM1

value: CTL


title: SGBS cells, replicate v1, d2

value: adipogenic differentiation


title: Wild Type male fly, repeat3

city: Shanghai

first: Zhan

address: 300 Feng Lin Road

institute: CAS Center for Excellence in Molecular Plant Sciences

description: Male_WT- rep3

data_processing:
The adapter sequences were removed from raw reads by cutadapt (version 1.15).
Clean reads from RNA-seq were quality filtered, and then mapped to the human genome (hg38) and Drosophila melanogaster genome (dm6) by STAR.
Assembly: dm6, hg38
Supplementary files format and content: tab-delimited text files include TPM values for mRNA samples.

organism: Drosophila melanogaster

source_name: whole body

extract_protocol:
Total RNAs from the human and Drosophila cells and tissues were isolated by TRIzol (Sigma) and treated with RNase-free DNase I (Invitrogen). For RT-PCR, reverse transcription was performed using PrimeScript RT reagent Kit with gDNA Eraser (TaKaRa) and the obtained cDNA was amplified by 2×Hieff PCR Master Mix (Yeasen). the construction of cDNA libraries and sequencing were performed using Illumina HiseqXten-PE150 by Novogene.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole body


title: SGBS cells, replicate v1, d1


title: Ccm3 KORapa, scRNAseq

description:
KO-RapaP9
10x Genomics

value: Tamoxifen+Rapamycin


title: RNA-Seq_MCF7_E2_iCARM1

value: siCTL


title: Wild Type male fly, repeat2

description: Male_WT- rep2


title: SGBS cells, replicate v1, 6h


title: SGBS cells, replicate v1, d0


title: Ccm3 KOP10, scRNAseq

description:
KO-Mfsd
10x Genomics


title: Ccm3 KOVehicle, scRNAseq

description:
Ccm3KOP9
10x Genomics

value: Tamoxifen+Vehicle


title: RNA-Seq_MCF7_CTL_iCARM1


title: Wild Type male fly, repeat1

description: Male_WT- rep1


title: Posion exon exclusion in male fly, repeat3

description: Male_PE- rep3


title: K3

first: xiuxian

last: guo

state: Shanghai

address: 393 Middle Huaxia Road, Pudong

institute: ShanghaiTech University

data_processing:
For RNA-seq data analysis, raw reads were filtered using Seqtk (v.1.4) to remove adapters and low-quality regions, and mapped to the GRCm38 genome using Hista258 (v.2.0.4). Reads on each gene were counted by Stringtie59 (v.1.3.0). Differential expressed genes (DEGs) were identified using edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts  for each sample

source_name: Dentate Gyrus

extract_protocol:
The DG was microdissected and dissociated with papain-based enzymatic digestion. 2,000 EYFP+ cells were sorted using the BD FACS Aria III instrument into a 200-μl PCR tube containing lysis buffer and RNase inhibitor. After sorting, the tubes were immediately snap-frozen.
Total RNA was reverse transcribed using the SMART-Seq HT Kit (Clontech, 634437), and cDNAs were used to produce the sequencing library. The libraries were purified and sequenced using the Illumina HiSeq 2500 system.

value: Dentate Gyrus

value: Kdm4a shRNA


title: K2


title: Vpr_25

city: Bethesda

first: Teruhiko

last: Yoshida

state: Maryland

address: 10 Center Drive, 9N208

department: NIDDK - KDB

institute: National Institutes of Health

data_processing:
Illumina RTA v3.4.4 software was used fro base calling, Cellranger 6.1.2 (Bcl2fastq v2.20) was used for sample demultiplexing
The analysis was performed with the Cell Ranger v6.1.2 software using the default parameters with premRNA analysis turned on. The reference was built from mm10 reference genome and HIV-1 virus sequence added.
Assembly: mm10 and HIV-1: NC_001802.1
Supplementary files format and content: tar.gz files contain filtered_features_bc_matrix folder output from CellRanger Count

source_name: Mouse Kidney Cortex

extract_protocol:
Nuclei from frozen mouse kidney outer cortex tissue samples were prepared following the published protocol. Briefly, ~ 8 mm3 tissue fragments were cut by razor blade in EZlysis buffer (#NUC101-1KT, Sigma, Darmstadt, Germany) and homogenized 30 times using a loose Dounce homogenizer and 5 times by tight pestle. After 5 mins of incubation, the homogenate was passed through a 40 µm filter (PluriSelect, El Cajon, CA) and centrifuged at 500g at 4°C and for 5 min. The pellet was washed with EZlysis buffer (Sigma Aldrich, St Louis, MO) and again centrifuged at 500g at 4°C for 5 min. The pellet was resuspended with DPBS with 1% FBS and passed through a 5 µm filter (PluriSelect, El Cajon, CA) to make final nuclei prep for loading on to a 10xChromium Chip G (10X Genetics, San Francisco, CA) for formation of gel beads in emulsion (GEM).
10x Genomics Chromium 3’ V3.1 mRNA-seq library protocol

treatment_protocol: Mice were maintained on a diet containing doxycycline (TD 98186, Envigo, Madison, WI) to inhibit the expression of Vpr. Mice were switched from doxycycline diet to 65% protein food (TD 190088, Envigo) for two weeks to induce transgene promoter activity. Then, the mice were fed with freshly prepared semi-solid sodium-deficient food [TD 90228 (3 g), containing casein (33.3%), agar (0.5%), sodium (0.045%), and 2.67 mL of water] for four days.

value: Kidney Cortex

value: Pepck-Vpr

value: Salt Depletion


title: RNA-Seq_MCF7_E2_siCTL


title: Ccm3 KOP6, scRNAseq

description:
KOP6
10x Genomics

value: Retina


title: Posion exon exclusion in male fly, repeat1

description: Male_PE- rep1


title: PC9 IP, treatment,  H3K9me2, rep1

city: Shenyang

first: cheng

last: yang

address: wenhua street  number 103

institute: Shenyang Pharmaceutical University

data_processing:
Raw sequencing data was first filtered by fastp (version 0.23.4), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of GRCh38 using STAR software (version 2.5.3a) with default parameters.
The MACS2 software（Version 2.1.1）was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis.
The differentially binding peaks were identified by csaw(version 1.30.1).
The Homer（version 4.10）was used for motifs analysis.
Assembly: GRCh38
Supplementary files format and content: Bigwig

source_name: lung

extract_protocol:
The cell was fixed in 1% formaldehyde for 10 min at room temperature. After quenching cell was treated with cell lysis buffer and nucleus was collected by centrifuging at 2000g for 5min. Then, nucleus was treated with nucleus lysis buffer and sonicated to fragment chromatin DNA.
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bp were enriched and quantified.

value: lung

value: lung cell line

value: post-SCLC transformation

tag: chip antibody


title: RNA-Seq_MCF7_CTL_siCTL

tag: cell line


title: Posion exon exclusion in male fly, repeat2

description: Male_PE- rep2


title: Tregs, Aluminum, rep 1

city: Chicago

first: Booki

last: Min

state: IL

address: 300 E. Superior Street

department: Microbiology-Immunology

institute: Northwestern University

data_processing:
The 10X results were subjected to processing through the Cell Ranger pipeline version 3.1.0 to generate Fastq files.
Fastq files were subsequently aligned using the Cell Ranger Count v7.1.0 pipeline within the 10X Genomics cloud analysis platform (https://www.10xgenomics.com/products/cloud-analysis), employing the Single Cell 3' Gene Expression library type.
Matrices, barcodes and genes were outputed from cloud platform for downstream processing and analysis.
Assembly: Mouse GRCm39 (mm39)
Supplementary files format and content: Tab separated value files and matrix files.

source_name: Lung

extract_protocol:
Lung tissue were minced and digested with collagenase and DNase, and a single cell suspension was obtained. Mononuclear cells were isolated using a Percoll gradient centrifugation. RBCs were then lysed using a ACK lysis buffer. Tregs from FACS sorted using a FACS Melody cell sorter, and then captured for library generation and sequencing using 10X Chromium single cell capture chip according to the manufacturers protocol.
The single-cell RNAseq libraries were prepared according to manufacturer’s Chromium Single Cell 3ʹ protocol (10X Genomics, document # CG000204). 10,000 FACS sorted Tregs were targeted using the 10x Genomics Chromium Controller for cDNA synthesis and barcoding. cDNA quality and quantity of each sample were assessed using a Bioanalyzer High Sensitivity DNA assay. cDNA was used to begin fragmentation, followed by end-repair, adapter ligation, and sample indexing. Sample libraries were then assessed for proper construction using the same Bioanalyzer assay. Constructed libraries were pooled and quantified using a Quantabio Q cycler, and then denatured and sequenced on an Illumina Novaseq 6000 high-throughput sequencing platform with 28 cycles for the forward read and 91 cycles for the reverse read.  Each cell was sequenced to a minimum of 20,000 reads per cell per manufacturer’s recommendations.

value: Lung

tag: cell type

value: regulatory T cells

value: aluminum hydroxide


title: Tregs, CFA, rep 1

value: CFA


title: C3

value: control shRNA


title: Wild Type female fly, repeat3

description: Female_WT rep3

value: whole body

tag: genotype


title: PC9 IP, control,  H3K9me2, rep1

tag: tissue

value: pre-LUAD