title: Beta-hydroxybutyrate 3

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10
The processed reads were aligned to the mouse transcriptome and genome version GRCh39 with annotations from Ensembl release 106 using TopHat v2.1.1
Counts per gene quantification was done using htseq-count v2.01
Genes with counts below 10 over all samples were filtered out. Normalization and differential expression analysis were done with the DESeq2 package v 1.36.0
Assembly: mouse transcriptome and genome version GRCh39
Supplementary files format and content: Each row in the file contains a certain ensembl Gene ID, Symbol, gene name  raw counts and DESEq2 normalized counts per sample. Missing values are denoted by  are for genes with a too low expression that were filtered out prior to normalization (sum of counts in all samples lower than 10).
Supplementary files format and content: RNA_seq_raw_norm_counts.xlsx

source_name: Embryonic kidney

growth_protocol: All animal experiments were approved by the Institutional Animal Care and Use Committee of the Hadassah Hebrew University. All mice were housed in the Hebrew University Specific Pathogen–Free Animal Facility Unit. The study utilized CD1 outbred mice, including transgenic mice. Specifically, we used the transgenic mice line Tg(Six2-EGFP/cre) Amc (herein Six2 Cre+/tg). Heterozygous Six2 Cre+/tg embryos were generated by mating male Six2 Cre+/tg  mice (8 to 10 weeks old) with wild-type (WT) CD1 females (8 to 10 weeks old). The day of vaginal plug detection was considered embryonic day 0.5 of pregnancy. Pregnant females were randomly assigned to the different experimental groups. 70% of the average daily intake was provided once daily to the calorie restricted diet (CRD) treated pregnant females. Unrestricted diet (URD)–treated mice were not subjected to any food restriction during pregnancy. On E17.5, pregnant females were euthanized using ketamine/xylazine, followed by cervical dislocation. Kidneys were dissected from all embryos, and no gender-specific analysis was performed.

extract_protocol:
The E17.5 embryonic kidneys were carefully dissected and excised in ice-cold HBSS buffer. Using a surgical scalpel, the kidneys were sliced and chopped into approximately 0.5- to 1-mm pieces on ice. The chopped kidney fragments were then transferred into an HBSS solution supplemented with 1 mg/ml collagenase (11213865001; Sigma-Aldrich) and dispase (D4693-1G; Sigma-Aldrich) and incubated at 37°C for 30 minutes. The cell suspension was filtered through a 40-mm nylon cell strainer (Corning) and washed twice with cold HBSS. Six2 Cre+/tg GFP+ NPCs were isolated by cell flow cytometry-based cell sorting at the Hebrew University Faculty of Medicine Core Facility. For RNA extraction, 50,000-100,000 cells were washed in cold HBSS, and total RNA was extracted using the Qiagen RNeasy Micro Kit (74004; Qiagen).
Libraries were prepared from RNA samples using a SMARTer® Stranded Total RNA-Seq Kit v3 (634485; Takara Bio). The libraries were barcoded and pooled for multiplex sequencing. The pooled DNA library was loaded on a NovaSeq 6000 SP Reagent Kit v1.5 (100 cycles) cartridge (Illumina) and sequenced on an Illumina Novaseq 6000 System using a single-read sequencing condition of 100 cycles.

treatment_protocol: . The pregnant mice were randomly assigned to one of three regimens from conception until embryonic day E17.5: control diet, control diet with supplementation of the ketone body β-hydroxybutyrate, and the ketogenic diet. on E17.5, the embryos were extracted, and the nephron progenitor cells were sorted

value: Embryonic kidney

value: nephron progenitor cells

value: Heterozygous CD-1 WT/ Six2 Cre+/tg embryos

value: ketogenic diet


title: DEX-25167, APOE2, no_LDLR, batch_C, tech_replicate_2

status: Public on Nov 10 2024

type: SRA

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

country: USA

institute: Denali Therapeutics

library_source: transcriptomic

data_processing:
Sequencing data was processed using nf-core/rnaseq (v3.11.2) of the nf-core collection of workflows, using STAR (v2.7.9a) and salmon (v1.10.1) for alignment of reads to the GRCh38 human reference genome and quantification of Gencode (v42) gene models, respectively.
One library (HSA-000031753) failed QC (fewer than 1 million total counts) and was excluded from downstream analysis.
Differential expression analysis was performed for protein-coding genes with the edgeR (v3.42.4) and limma (v 3.56.2) Bioconductor packages using R v4.3.1. In brief, count matrices were subset to protein-coding genes, and library size factors were calculated with the TMM method. Gene-wise linear models with experimental group and collection batch as covariates were fit with the voomLmFit function, setting the sample weights argument to TRUE. The relationships of technical and biological replicates were specified via the block argument. Fold changes and p-values for the contrasts of interest were obtained with the eBayes function.
Assembly: GRCh38
Supplementary files format and content: Microsoft excel file with three worksheets: 1) sample metadata, 2) raw counts for all protein-coding genes, 3) normalized counts-per-million for all protein-coding genes

molecule: polyA RNA

organism: Homo sapiens

source_name: Human Episomal iPSC Line A18965

growth_protocol: Hematopoietic progenitor cells (HPCs) were generated based on a protocol published by Guttikonda et al, 2021 with modifications. To differentiate HPCs into microglia (iMG), frozen vials of HPCs were thawed in 37°C water bath. Cryoprotectant was washed away by titrating cells into DMEM-F12 and centrifuging at 500 g for 5 min. Cells were resuspended in Microglia Differentiation Medium (STEMCELL Technologies, Catalog No. 100-0019) and differentiated according to the manufacturer’s protocol with suggested medium changes and splitting. After 24 days of differentiation, cells were switched into Microglia Maturation Medium (STEMCELL Technologies, Catalog No. 100-0020). More than 90% of the iMG were double positive for CD45 and CD11b, and were plated for experiments between 31 days and 39 days.

extract_protocol:
Cells were lysed with Qiagen RLT-plus buffer containing β -mercaptoethanol. Samples were stored at -80°C until cell lysates from all individual experiments were collected. ERRC control RNA that was pre-diluted at 1:10,000 and spiked into each sample at a volume  proportional to the cell count determined by microscopy. RNA extraction was performed using the RNeasy Plus Micro Kit (Qiagen, 74034).
For each of the 12 independent biological samples, two replicate sequencing libraries were prepared from 10-60 ng of total RNA each using the QuantSeq 3' mRNA-seq Library Prep Kit FWD for Illumina (Lexogen A01173). The UMI second strand synthesis module was used to introduce unique molecular identifiers. Library quantity and quality were assessed with the High Sensitivity D1000 ScreenTape (Agilent 5067-5584). Libraries were pooled in equimolar ratios and the sequencing pool was purified with magnetic beads to remove residual adaptor dimers.

treatment_protocol: LPS-stimulated APOE KO iMG were treated with ApoE isoforms (ApoE2/E3/E4) pre-complexed with BODIPY-CE and HDL -/+ recombinant LDLR ECD for 1 day prior to RNA harvest.

tag: experiment id

tag: group

tag: cell line

value: Human Episomal iPSC Line A18965

tag: cell type

value: iPSC-derived microglia

tag: genotype

tag: technical replicate

tag: qc pass

value: TRUE

tag: batch

value: C

tag: ldlr ecd_treated

value: FALSE


title: PC3_rep1, PCHI-C

city: Brisbane

first: Jonathan

last: Beesley

state: QLD

address: 300 Herston Rd Herston

country: Australia

institute: QIMR Berghofer

library_source: genomic

data_processing:
PCHiC reads were analysed with HiCUP (version 0.5.9).
Raw sequencing reads were aligned to the hg38 human reference genome with Bowtie2 version 2.2.9
Chromatin interactions were identified using CHiCAGO following generation of genome indices, HindIII restriction fragment digest files, and the bait map.
The CHiCAGO pipeline was run independently for each library for quality control, followed by merging of replicates for subsequent analyses. Interactions with CHiCAGO score ≥ 5 were treated as high confidence for target gene analysis and visualisation.
Assembly: hg38
Supplementary files format and content: ChiCAGO peak matrix file for merged biological replicates, listing chromatin interactions obseverd in at least 1 sample
Library strategy: Promoter capture Hi-C

molecule: genomic DNA

source_name: PC3 cell line

extract_protocol:
PCHiC libraries were prepared from 4-5 x 1e7 cells per library (two biological replicates per cell line using in-nucleus ligation).
The HiC libraries were amplified using the SureSelectXT ILM Indexing pre-capture primers (Agilent Technologies) with 8 PCR amplification cycles. Each HiC library (750 ng) was hybridized and captured individually using the SureSelectXT Target Enrichment System reagents and protocol (Agilent Technologies). After library enrichment, a post-capture PCR amplification step was carried out using SureSelectXT ILM Indexing post-capture primers (Agilent Technologies) with 14–16 PCR amplification cycles.

value: PC3 cell line

value: Prostate cancer cell line


title: DEX-25165, APOE4, no_LDLR, batch_B, tech_replicate_2

source_name: Human Episomal iPSC Line A18963

value: Human Episomal iPSC Line A18963

value: B


title: Beta-hydroxybutyrate 1

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: treatment


title: Beta-hydroxybutyrate 2


title: KO1

city: Nantong

first: Yinchuan

last: Li

state: Jiangsu

address: 16 wenfeng road, Chongchuan

department: Medical School

country: China

institute: Nantong University

data_processing:
Raw reads were cleaned with fastp (v0.18.0).  Bowtie2 (v2.2.8) was used for mapping for reads to ribosome RNA (rRNA) database.  Paired-end clean reads were further mapped to reference genome by HISAT2 2.1.0 and  assembled by StringTie v1.3.1. Gene expression abundance and variations were performed by calculating FPKM value through software RSEM.
Assembly: Ensembl-release106
Supplementary files format and content: Excel file containing both KO and WT samples

source_name: testis

extract_protocol:
Total RNA  from adult mouse testes were extracted with Trizol reagent. mRNA was further extracted by mRNA Capture Beads.
Full-length cDNAs were reverse-transcribed from poly-adenylated mRNA. dA-tailed first-strand cDNAs were then ligated with adaptors and amplified by PCR to generate sufficient mass for library construction.

value: testis

value: Fam170a Knockout


title: WT1

value: WT


title: WT2


title: KO2

value: Fam171a Knockout


title: Keogenic diet 3

value: Embryonic kidney

value: normal diet + Beta-hydroxy butyrate


title: Keogenic diet 4

value: nephron progenitor cells

value: Heterozygous CD-1 WT/ Six2 Cre+/tg embryos


title: DEX-25157, APOE4, no_LDLR, batch_A, tech_replicate_2

source_name: Human Episomal iPSC Line A18959

value: Human Episomal iPSC Line A18959

value: A


title: DEX-25158, APOE4, LDLR, batch_A, tech_replicate_2

source_name: Human Episomal iPSC Line A18960

value: Human Episomal iPSC Line A18960

value: iPSC-derived microglia

value: TRUE


title: Keogenic diet 1


title: DEX-25156, APOE3, no_LDLR, batch_A, tech_replicate_2

source_name: Human Episomal iPSC Line A18958

value: Human Episomal iPSC Line A18958

value: FALSE


title: Keogenic diet 2


title: DEX-25155, APOE2, no_LDLR, batch_A, tech_replicate_2

source_name: Human Episomal iPSC Line A18957

value: Human Episomal iPSC Line A18957


title: Normal diet 4

value: normal diet


title: DEX-25154, APOE4, LDLR, batch_C, tech_replicate_1

source_name: Human Episomal iPSC Line A18956

value: Human Episomal iPSC Line A18956

value: C


title: Normal diet 3


title: Beta-hydroxybutyrate 4

value: ketogenic diet


title: DEX-25152, APOE3, no_LDLR, batch_C, tech_replicate_1

source_name: Human Episomal iPSC Line A18954

value: Human Episomal iPSC Line A18954


title: Normal diet 2

value: Embryonic kidney


title: DEX-25164, APOE3, no_LDLR, batch_B, tech_replicate_2

source_name: Human Episomal iPSC Line A18962

value: Human Episomal iPSC Line A18962

value: B


title: DEX-25153, APOE4, no_LDLR, batch_C, tech_replicate_1

source_name: Human Episomal iPSC Line A18955

value: Human Episomal iPSC Line A18955


title: DEX-25151, APOE2, no_LDLR, batch_C, tech_replicate_1

source_name: Human Episomal iPSC Line A18953

value: Human Episomal iPSC Line A18953


title: Normal diet 1

value: nephron progenitor cells

value: Heterozygous CD-1 WT/ Six2 Cre+/tg embryos


title: DEX-25150, APOE4, LDLR, batch_B, tech_replicate_1

source_name: Human Episomal iPSC Line A18952

value: Human Episomal iPSC Line A18952

value: iPSC-derived microglia


title: Lung, LPS2, 24hours

city: 合肥市

first: 林贵

last: 顾

state: 安徽省

address: 安徽省合肥市蜀山区梅山路安徽医科大学基础医学院

institute: 安徽医科大学

data_processing:
The quality of fastq data was controlled by Fastqc and analyzed using the RNA-seq pipeline described as "Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature Protocols 2016, 11(9):1650-1667."
Assembly: mm10
Supplementary files format and content: text file includes raw counts for each sample

source_name: Lung

extract_protocol:
RNA was harvested using TRIzol (Ambion, #400008) .5μg of total RNA was used for the construction of sequencing libraries
mRNA were enriched using VAHTS® mRNA Capture Beads (Vazyme #N401), and fragmentation was made using Tn5 (Transgen, Cat# KP101-11).

treatment_protocol: The mice were first anesthetized with pentobarbital sodium through intraperitoneal injection at a dose of 30 mg/kg, then LPS (Sigma, #L2880) or LCWE (Prepared in the study) in PBS were administered into the mouse lungs from the trachea at 1, 3, and 6 mg/kg. After 24 hours, the mice were sacrificed and lung tissues were collected for RNA and protein samples.

value: Lung

value: WT

value: LPS induce 24hours


title: DEX-25163, APOE2, no_LDLR, batch_B, tech_replicate_2

source_name: Human Episomal iPSC Line A18961

value: Human Episomal iPSC Line A18961

value: TRUE

value: FALSE


title: Lung, LPS1, 24hours

address: 安徽省合肥市蜀山区梅山路安徽医科大学基础医学院


title: DEX-25148, APOE3, no_LDLR, batch_B, tech_replicate_1

source_name: Human Episomal iPSC Line A18950

value: Human Episomal iPSC Line A18950


title: Lung, LCWE1, 24hours

address: 安徽省合肥市蜀山区梅山路安徽医科大学基础医学院

value: LCWE induce 24hours


title: Lung, LCWE2, 24hours

address: 安徽省合肥市蜀山区梅山路安徽医科大学基础医学院


title: DEX-25147, APOE2, no_LDLR, batch_B, tech_replicate_1

source_name: Human Episomal iPSC Line A18949

value: Human Episomal iPSC Line A18949


title: DEX-25142, APOE4, LDLR, batch_A, tech_replicate_1

source_name: Human Episomal iPSC Line A18948

value: Human Episomal iPSC Line A18948

value: A


title: Lung, PBS2, 24hours

address: 安徽省合肥市蜀山区梅山路安徽医科大学基础医学院

value: PBS induce 24hours


title: Lung, PBS1, 24hours

address: 安徽省合肥市蜀山区梅山路安徽医科大学基础医学院


title: DEX-25140, APOE3, no_LDLR, batch_A, tech_replicate_1

source_name: Human Episomal iPSC Line A18946

value: Human Episomal iPSC Line A18946


title: WT ileum crypt tom+ cells, scRNA-seq rep2

city: Boston

first: Ramesh

middle: A

last: Shivdasani

state: MA

address: 450Brookline Ave.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The barcoded processing and gene counting were done using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include STAR raw counts for each Sample

source_name: Ileum

growth_protocol: To activate CreER-T2 in Atoh1CreER-T2;R26RTom  or Atoh1Cre;Apcfl/fl;R26RTom mice, we administered 2 doses of 1 mg/mL tamoxifen (Sigma-Aldrich, T5648; stocks prepared in cornflower oil) by intraperitoneal (IP) injection 24 h apart; and 12 h later we harvested intestinal TOM+  crypt cells for scRNA-seq.

extract_protocol:
Pieces of small intestine were rinsed in PBS, then rotated in 5 mM EDTA (pH 8) in PBS for 45 min at 4°C with manual shaking every 10 min and a change of solution after 30 min. Released epithelium was passed through a 70-µm strainer to separate villi from crypts and was dissociated into single cells by rotating in 4% TrypLE solution (ThermoFisher, A1217702) for 30-45 min at 37°C. Single cells were diluted in Dulbecco’s modified Eagle medium (DMEM, Corning. 17-205-CV) containing 2% FBS. Tom+ cells were isolated on a FACSAria II SORP flow cytometer, with elimination of dead (DAPI+) cells, pelleted by centrifugation, and trypan blue-excluding cells were counted manually.
Library preparation was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

value: Ileum

value: Intestine Epithelium

value: Tamoxifen (1mg/ml)


title: DEX-25149, APOE4, no_LDLR, batch_B, tech_replicate_1

source_name: Human Episomal iPSC Line A18951

value: Human Episomal iPSC Line A18951

value: iPSC-derived microglia

value: B


title: WT ileum crypt tom+ cells, scRNA-seq rep1

description: 10x Genomics

treatment_protocol: To activate CreER-T2 in Atoh1CreER-T2;R26RTom  or Atoh1Cre;Apcfl/fl;R26RTom mice, we administered 2 doses of 1 mg/mL tamoxifen (Sigma-Aldrich, T5648; stocks prepared in cornflower oil) by intraperitoneal (IP) injection 24 h apart; and 12 h later we harvested intestinal TOM+  crypt cells for scRNA-seq.


title: DEX-25141, APOE4, no_LDLR, batch_A, tech_replicate_1

source_name: Human Episomal iPSC Line A18947

value: Human Episomal iPSC Line A18947


title: BZH4

city: Guang Dong

first: Ting

last: Xie

state: Guang Dong

address: No.66,Gongchang Road,Guangming District,Shenzhen,Guangdong 518107,P.R.China

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Illumina NovaseqTM 6000 platform by LC-Bio Technologies
Assembly: GRCm39
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: brain

extract_protocol:
mRNA was purified from total RNA (1μg) using Dynabeads Oligo (dT) 25-61005 (Thermo Fisher, CA, USA) with two rounds of purification.
The RNA was reverse-transcribed into cDNA using SuperScript™ II Reverse Transcriptase (Invitrogen, USA).

value: brain

tag: Sex

value: Female

value: c-Flip+/-

value: ZIKV


title: DEX-25139, APOE2, no_LDLR, batch_A, tech_replicate_1

source_name: Human Episomal iPSC Line A18945

value: Human Episomal iPSC Line A18945

value: TRUE

value: FALSE


title: BZH3


title: SON, Pladienolide-B, input, rep 4

city: Zurich

first: A

last: McIntyre

address: Winterthurerstrasse 190

department: Molecular Life Sciences

country: Switzerland

institute: University of Zurich

data_processing:
Trimmomatic v0.39 (Bolger et al., 2014) was used to trim adapter sequences from raw reads with the following settings: ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to the human reference genome (hg38, GRCh38.p14 primary genome assembly) using GENCODE v40 gene annotations with STAR v2.7.3a (Dobin et al., 2013)
Count tables were generated using the featureCounts (Y. Liao et al., 2014) function of the R package Rsubread v2.10.5 (Y. Liao et al., 2019). Transcript quantification was performed using Salmon v0.12.0 (Patro et al., 2017) with the --numGibbsSamples option set to 30 to generate Gibbs samples.
Differential Gene Expression (DGE) analysis was performed with DESeq2 v1.36.0 (Love et al., 2014). Differential transcript expression analysis was performed using Fishpond v2.2.0 (Zhu et al., 2019).
Assembly: hg38
Supplementary files format and content: csv file includes read counts for each gene in each sample
Supplementary files format and content: csv file includes TPM for each transcript, quantified by salmon

source_name: hiPSC

extract_protocol:
hiPSCs were lysed by adding RNA lysis buffer (Zymo Research, R1060-1-50). Total RNA was purified using Zymo Quick-RNA Miniprep kit (Zymo Research, R1054)
Libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara, 634411), including ribosomal cDNA depletion step

value: hiPSC

value: human induced pluripotent stem cells

value: APEX2-GFP-SON endogenous tag

value: Pladienolide-B

tag: time


title: SON, Pladienolide-B, input, rep 5


title: BZH2


title: FR-3

city: NanNing

first: Jianping

last: Jiang

state: Guangxi

address: No. 189, Changgang Road, Xingning District, Nanning, Guangxi

institute: Guangxi Botanical Garden of Medicinal Plants, Naning, China

data_processing:
Quality control, Trimmomatic (v0.39), default parameters
Mapping reference genome, TopHat (v2.21), default parameters
Transcripts assembly, Cufflinks (v2.2.1), default parameters
Quantification of gene expression, RSEM (v1.3.3), default parameters
Identification of differential expression genes, limma (v3.54.2) , default parameters
Assembly: http://identifiers.org/ncbi/insdc:JBGBDH000000000
Supplementary files format and content: The Excel (.xls) file contains the raw read counts for protein-coding genes in each sample.
Supplementary files format and content: The Excel (.xls) file contains the normalized Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values for protein-coding genes in each sample.

organism: Zanthoxylum nitidum

source_name: fruit

extract_protocol:
mRNA was isolated using Oligo(dT)-attached magnetic beads and then randomly fragmented in a fragmentation buffer. First-strand cDNA synthesis was performed using the fragmented mRNA as a template and random hexamers as primers, followed by second-strand synthesis with the addition of PCR buffer, dNTPs, RNase H, and DNA polymerase I.
The cDNA was purified using AMPure XP beads and subjected to end repair, adenosine addition, and adapter ligation. AMPure XP beads were again used to select fragments within a specific size range. Finally, a cDNA library was generated through several rounds of PCR amplification on the cDNA fragments obtained from the previous step.In order to ensure the quality of library, Qubit 2.0 and Agilent 2100 were used to examine the concentration of cDNA and insert size. Q-PCR was processed to obtain a more accurate library concentration and assure adequate library concentration.

value: fruit


title: SON, Pladienolide-B, input, rep 2


title: FR-2


title: LE-3

source_name: leave

value: leave


title: BZH1


title: SON, Pladienolide-B, biotinylated, rep 5


title: LE-2


title: LE-1


title: BZWT2

value: wild type


title: BZWT4


title: TS-2

source_name: stem

value: stem


title: TS-3


title: SON, Pladienolide-B, biotinylated, rep 2


title: SON, Pladienolide-B, biotinylated, rep 4


title: SON, Pladienolide-B, biotinylated, rep 3


title: FR-1


title: BZWT1


title: TS-1


title: OS-2


title: OS-3


title: BPH3

value: PBS


title: SON, Pladienolide-B, biotinylated, rep 1


title: BPH4


title: SON, GSK626616, input. rep 5


title: SON, GSK626616, input, rep 4


title: SR-2

source_name: root

value: root


title: BPH2

value: brain


title: SR-1


title: MR-3


title: BZWT3

value: Female


title: SON, GSK626616, input, rep 2


title: MR-2


title: BPH1

value: c-Flip+/-


title: MR-1


title: BPWT4


title: OS-1


title: SON, GSK626616, biotinylated, rep 4


title: BR-3


title: 18°C_3mg/L_3

city: Qingdao

first: Dongxue

last: Xu

address: Changcheng road No.700

institute: Qingdao Agricultural University

data_processing:
Sequence reads were trimmed for adaptor sequence and low-quality sequence in order to acquire the clean reads.
Clean reads were mapped to genome of Apostichopus japonicus.
Gene expression profiling was based on the number of reads.
FPKM (fragments per kb of exon model per million mapped reads) values were used to estimate the expressed values and transcript levels.
Assembly: https://doi.org/10.6084/m9.figshare.22140020
Supplementary files format and content: tab-delimited text file includes FPKM values for all samples

organism: Apostichopus japonicus

source_name: intestine tissue

growth_protocol: sea cucumber (around 100g)

extract_protocol:
Total RNA of each individua was extracted using Trizol RNA isolation reagent (Invitrogen) following the manufacturer’s instructions.
The mRNA was purified from the total RNA and cut into fragments using the TruSeq RNA Sample Prep Kit (Illumina). Qualified RNA samples were prepared to build cDNA libraries. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. After purification with AMPureXP beads, the ligated products with about 250-300 bp were amplified to generate high quality cDNA libraries, which were then sequenced by an Illumina Hiseq platform at Novogene Bioinformatics Technology (Beijing, China).

treatment_protocol: heat stress at 26°C and hypoxia stress at 3mg/L

value: intestine tissue


title: BR-2


title: 18°C_3mg/L_2


title: BR-1


title: BPWT2


title: 26°C_7mg/L_3


title: SR-3


title: 18°C_3mg/L_1


title: SON, GSK626616, biotinylated, rep 2


title: BPWT1


title: 26°C_7mg/L_1


title: SON, GSK626616, biotinylated, rep 1


title: 26°C_3mg/L_3


title: Memory, Tumor, Exp2, TR1 [ATAC-seq]

city: Aurora

first: Terry

last: Fry

state: CO

institute: University of of Colorado Denver and Children's Hospital Col

description:
6-17-22_Vax_ATAC_1_S16_L001_R1_001
Memory-derived CD8+/CAR+ T cells infused into leukemia-bearing hosts at 1e6 CAR+ cells per mouse, then sorted out of pooled bone marrow from 10x mice for sequencing.

data_processing:
Raw sequencing reads were de-multiplexed using bcl2fastq.
Fastq files were used to map to the mm10 genome using the ENCODE ATAC-seq pipeline, with default parameters, except bam files used for peak calling were randomly downsampled to a maximum of 50 million mapped reads.
Peaks with a MACS2 computed q value of less than 0.0001 in at least one replicate were merged with bedtools function intersect and processed to uniform peaks with the functions getPeaks and resize from R package ChromVAR.
Reads overlapping peaks were enumerated with getCounts function from ChromVAR and normalized and log2-transformed with voom from R package limma.
Peaks with 6or more normalized counts per million mapped reads in at least one replicate were included to define a global peak set of 99,317 peaks.
Assembly: mm10
Supplementary files format and content: bigWig files

source_name: Spleen-derived T cells, harvested from bone marrow

growth_protocol: CD8+ T cells were maintained in RPMI1640 media supplemented with L-Glutamine, non-essential amino acids, sodium pyruvate, HEPES, antibiotics and 10% FBS.

extract_protocol:
For ATACseq, cells were processed using the Omni-ATAC protocol. Sorted cells were washed once in 1X PBS, lysed, washed once in Wash Buffer and then the transposition reaction was carried out at 32°C for 30 minutes on a thermomixer set to 1000 rpm. Transposed chromatin was then purified using the Zymo Clean and Concentrator 5 Kit using manufacturer protocols.
DNA was then run on PCR for 12 total cycles with dual-index barcoding primers. PCR reactions were then size-selected using AMPure XP beads and checked for quality and size distribution using TapeStation 4200 with D5000 reagents. Libraries were pooled at equimolar ratios for sequencing.

treatment_protocol: Vaccination was carried out with whole ovalbumin protein, anti-mouse CD40 and PolyI:C, with concurrent adoptive transfer of 5000 OT-I CD8+ T cells. OT-I T cells were isolated from vaccinated mice on day 28 post-vaccination from pooled vaccinated hosts (memory), or age-matched naïve mice (naïve). CD8+ T cells were activated using anti-CD3/anti-CD28 Dynabeads in the presence of IL-2 and IL-7, and transduced with a murine anti-mouse CD19 CAR containing CD28 costimulatory domain and CD3zeta domain. CAR T cells were infused into leukemia-bearing C57BL/6-background Rag1-/- mice at 1e6 CAR+ cells/mouse.

value: CD8+ T cell

value: Rag2-/- OT-I TCR transgenic

value: CAR+Vaccine


title: 26°C_3mg/L_2


title: SON, DRB, input, rep 5

value: hiPSC

value: DRB


title: Control3


title: Naïve, Tumor, Exp2, TR3 [ATAC-seq]

description:
6-17-22_Naive_ATAC_3_S15_L001_R1_001
Naïve-derived CD8+/CAR+ T cells infused into leukemia-bearing hosts at 1e6 CAR+ cells per mouse, then sorted out of pooled bone marrow from 10x mice for sequencing.

value: Spleen-derived T cells, harvested from bone marrow

value: CAR


title: SON, GSK626616, biotinylated, rep 5

value: human induced pluripotent stem cells

value: APEX2-GFP-SON endogenous tag


title: Control2


title: Control1


title: SON, DRB, input, rep 4


title: SON, DRB, biotinylated, rep 5


title: THP-1 cells, p4HA-LegC4, LegC4 IP, biol rep 4

city: Clayton

first: Kathleen

last: McCaffrey

state: VIC

address: 25-31 Wright Street

institute: Hudson Institute of Medical Research

data_processing:
Image analysis was performed in real time by the NextSeq Control Software (NCS) and Real Time Analysis (RTA) running on the instrument computer. Then the Illumina Protocol 1000000109376( v3 Nov2020) was used to generate the sequence data.
Trimmed reads were mapped to hg38 using HISAT2 v2.2.1
RNA binding sites (RBS) were assigned uisng PureCLIP v1.0.4
Assembly: Homo sapiens genome (hg38)
Supplementary files format and content: BED file of RBS assigned using PureCLIP.

growth_protocol: THP-1 monocytes [Homo sapiens, male] (ATCC Cat#TIB-202) were cultured in RPMI 1640 supplemented with Glutamax (Gibco Cat#61870036) and 10 % foetal bovine serum (FBS) (Bovagen Cat#SFBS-AU) at 37C and 5 % CO2. THP-1 monocytes were seeded at 2.5x105 cells/cm2 in tissue-culture dishes and differentiated for 48 h prior to infection using 50 ng/mL phorbol 12-myristate 13-acetate (PMA) (Sigma Aldrich Cat#P8139).

extract_protocol:
Cell monolayers were then transferred into ice-cold PBS and subject to ultraviolet (UV) cross-linking (254 nm) at 150 mJ/cm2 using a Stratalinker Ultraviolet Crosslinker (Stratagene). After cell lysis and limiting RNase I digestion, 4HA-LegC4 was immunoprecipitated from four independent infection experiments using Anti-HA-tag mAb-Magnetic Beads (MBL Biosciences Cat#M180-9).
cDNA libraries were prepared according to the iCLIP2 protocol (Buchbender et al, 2020).

treatment_protocol: THP-1 monolayers in 150 mm dishes were infected at an MOI of 10 with the L. pneumophila deltalegC4-mutant strains carrying the p4HA-LegC4 plasmid or the vector control plasmid (p4HA). At 2 h post-infection, cell monolayers were treated with gentamicin at 100 g/mL (Gibco Cat#15750060) to kill all remaining extracellular bacteria, prior to washing and replacement with fresh media for an additional 3-4 h.

value: Monocyte

tag: clip antibody

value: PMA differentiated, 48 h


title: THP-1 cells, p4HA-LegC4, LegC4 IP, biol rep 3

value: Anti-HA-tag mAb-Magnetic Beads (MBL Biosciences Cat#M180-9)


title: Naïve, Tumor, Exp2, TR1 [ATAC-seq]

description:
6-17-22_Naive_ATAC_1_S13_L001_R1_001
Naïve-derived CD8+/CAR+ T cells infused into leukemia-bearing hosts at 1e6 CAR+ cells per mouse, then sorted out of pooled bone marrow from 10x mice for sequencing.


title: THP-1 cells, p4HA, Control IP, biol rep 4


title: 26°C_7mg/L_2


title: BPWT3

value: wild type

value: PBS


title: SON, DRB, biotinylated, rep 4


title: 26°C_3mg/L_1


title: SON, GSK626616, biotinylated, rep 3


title: Naïve, Tumor, Exp2, TR2 [ATAC-seq]

description:
6-17-22_Naive_ATAC_2_S14_L001_R1_001
Naïve-derived CD8+/CAR+ T cells infused into leukemia-bearing hosts at 1e6 CAR+ cells per mouse, then sorted out of pooled bone marrow from 10x mice for sequencing.


title: SON, DRB, input, rep 2


title: THP-1 cells, p4HA-LegC4, LegC4 IP, biol rep 2


title: THP-1 cells, p4HA-LegC4, LegC4 IP,  biol rep 1


title: THP-1 cells, p4HA, Control IP, biol rep 2


title: THP-1 cells, p4HA, Control IP, biol rep 1


title: SON, DRB, biotinylated, rep 2


title: Memory, PostCAR, Exp2, TR2 [ATAC-seq]

description:
6-13-22_Vax_ATAC_2_S11_L001_R1_001
Memory-derived CD8+/CAR+ T cells were collected in vitro after 5 day CAR-transduction protocol.

source_name: Splenic T cells

value: Splenic T cells


title: SON, DRB, biotinylated, rep 3


title: Naïve, PostCAR, Exp2, TR3 [ATAC-seq]

description:
6-13-22_Naive_ATAC_3_S9_L001_R1_001
Naïve-derived CD8+/CAR+ T cells were collected in vitro after 5 day CAR-transduction protocol.


title: Synovium, Immunotype 3, Sample 95, scRNA-seq

city: Charlotte

first: Sarah

last: Romereim

state: NC

address: 1000 Blythe Blvd, CRC 305

department: Musculoskeletal Institute

institute: Atrium Health

description: 10X Genomics

data_processing:
Mapping and analysis were performed by the Wake Forest University School of Medicine Bioinformatics Shared Resource Group with Cell Ranger and Loupe software (10X Genomics). Cells were filtered by nFeature_RNA > 200 & nFeature_RNA < 2500 & percent.mt < 5 and genes were filtered by min_cells=3. Unfiltered processed data is provided in this submission.
Assembly: hg38
Supplementary files format and content: hierarchical data format (.h5) archives of molecule info and feature matrices with an aggregation comma-separated value (.csv) file

source_name: synovium

extract_protocol:
At the time of ACL reconstruction, an arthroscopic synovial biopsy (200-300 mg) from the prefemoral synovium was obtained. Synovial tissue was enzymatically digested with an RPMI 1640 (Cytiva SH30027.02) media solution containing 4 mg/mL collagenase type 4 (Worthington Biochemical LS004189), 0.8 mg/mL dispase II (Millipore Sigma 04942078001), plus 0.1 mg/mL DNase I (Millipore Sigma 11284932001). Digest was passed through a 70 µm filter to obtain a single cell suspension. For cell suspensions containing >20% erythrocytes, lysis was performed with RBC lysis buffer (BD 555899) according to the manufacturer’s instructions. 60,000 cells were set aside for scRNA-seq library preparation.
Single cell partitioning and RNA library preparation were performed by the the Atrium Health Molecular Biology Core Facility  on the same day as cell isolation (separate days for each of the six samples). Nanoliter-scale Gel Beads-in-emulsion (GEMs) were generated consisting of barcoded single cell 3ʹ v3.1 gel beads, a master mix containing cells, and partitioning oil onto Chromium next GEM chip G (10x Genomics). Thereafter, the gel bead was dissolved resulting in the release of the primers. cDNA was produced using the poly(dT) primer included on the gel beads. Each cell’s transcriptome was indexed using a pool of individual 10x barcodes whereas all generated cDNA shared a common 10x barcode. Barcoded, full-length cDNA was then PCR amplified, enzymatically fragmented, and size selected to the optimum amplicon length. Following end repair, A-tailing, adaptor ligation, and PCR, the final libraries contained Illumina adaptors (P5, P7), primers (Read1, Read2), and index sequences which were sequenced with 26 cycles for read1, and 98 cycles for read2. Sequencing was performed in two batches on separate days. Batch 1 included Sample 78, Sample 80, and Sample 84. Batch 2 included Sample 85, Sample 93, and Sample 95.

value: synovium

value: tissue

tag: age

value: M

tag: immunotype group


title: SON, DRB, biotinylated, rep 1


title: Memory, PostCAR, Exp2, TR1 [ATAC-seq]

description:
6-13-22_Vax_ATAC_1_S10_L001_R1_001
Memory-derived CD8+/CAR+ T cells were collected in vitro after 5 day CAR-transduction protocol.

value: CD8+ T cell

value: Rag2-/- OT-I TCR transgenic


title: THP-1 cells, p4HA, Control IP, biol rep 3


title: Synovium, Immunotype 3, Sample 84, scRNA-seq

description: 10X Genomics


title: Synovium, Immunotype 2, Sample 93, scRNA-seq

description: 10X Genomics

value: F


title: Synovium, Immunotype 2, Sample 80, scRNA-seq

description: 10X Genomics


title: Synovium, Immunotype 1, Sample 85, scRNA-seq

description: 10X Genomics


title: Synovium, Immunotype 1, Sample 78, scRNA-seq

description: 10X Genomics


title: Jurkat

city: Singapore

first: Rui

last: Yokomori

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore, National University of Singapore

description: MYB-enriched total RNA

library_source: other

data_processing:
Full-length (FL) reads were generated from HiFi reads using PacBio SMRT Link version 11.1 lima with the options “--isoseq --peek-guess --biosample-csv <BioSample.csv>”.
FL reads were refined by trimming poly(A) tails and removing concatemers using isoseq3 refine with a primer sequence file and the option “--required-polya”.
Refined FL reads were clustered using isoseq3 cluster with the option “--use-qvs”.
Clustered reads were aligned to the hg19 genome (no alt analysis set) using pbmm2 align with the options “--unmapped --preset ISOSEQ --sort” to detect isoforms.
A genome index file for the alignment was created using pbmm2 index with the options “-k 15 -w 5 -u”.
Detected isoforms were collapsed using isoseq3 collapse with the option “--do-not-collapse-extra-5exons” to generate non-redundant isoforms.
Quality control was performed on non-redundant isoforms using SQANTI3 QC (version 5.2) with GENCODE v35 (comprehensive gene annotation) and the options “-c <SJ_out.tab> --SR_bam <RNAseq_aligned_BAM.fofn> --CAGE_peak <TSS_peak.bed>”.
The SJ_out.tab file and RNA-seq aligned read file (BAM file) were obtained by aligning Jurkat short-read RNA-seq reads using STAR (version 2.7.7a) with the options “--twopassMode Basic --sjdbGTFfile <GENCODEv35_comprehensive.gtf> --outSAMstrandField intronMotif --outSJfilterOverhangMin 1 1 1 1 --outSJfilterCountUniqueMin 0 0 0 0 --outSJfilterCountTotalMin 1 1 1 1 --outSJfilterDistToOtherSJmin 0 0 0 0 --outSJfilterIntronMaxVsReadN 589824 --alignSoftClipAtReferenceEnds No”.
The TSS_peak BED file (refTSS v3.1) for hg38 was obtained from the data directory of the SQANTI3 tool, and coordinates were converted to those for hg19 using the UCSC liftOver tool.
Non-redundant isoforms were filtered using SQANTI3 Filter (version 5.2) with the default rule including the following additional rules: “ratio_TSS:1.5” and “within_CAGE_peak:TRUE”.
Assembly: hg19
Supplementary files format and content: GFF, MYB-associated isoforms
Library strategy: ISO-seq

molecule: other

source_name: Jurkat

growth_protocol: Jurkat and MOLT-4 cells were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.

extract_protocol:
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen). MYB transcripts were enriched with NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module (NEB) and an xGen Hybridization and Wash Kit (Integrated DNA Technologies).
SMRTBell library construction and Sequel II long-read sequencing were performed at PacBio.

treatment_protocol: Cells were not treated.

value: Jurkat

value: T lymphoblast

value: Wild type


title: Memory, PreCAR, Exp2, TR3 [ATAC-seq]

description:
6-8-22_Vax_ATAC_3_S6_L001_R1_001
We adoptively transferred 5000 C57BL/6-background Rag2-/- OT-I TCR transgenic CD8+ T cells (CD45.2+) into C57BL/6-background CD45.1+ hosts, followed by vaccination (ovalbumin, anti-mouse CD40, PolyI:C), and then harvested CD45.2+/CD8+ T cells from pooled spleens at 28 days post-vaccination.

value: Vaccine


title: SON, DMSO, input, rep 4

value: hiPSC

value: human induced pluripotent stem cells

value: APEX2-GFP-SON endogenous tag

value: DMSO


title: SON, DMSO, input, rep 2


title: SON, DMSO, input, rep 5


title: DFCI15_PDX

description: MYB-enriched total RNA

source_name: Patient-derived xenograft

value: Patient-derived xenograft


title: Memory, PostCAR, Exp2, TR3 [ATAC-seq]

description:
6-13-22_Vax_ATAC_3_S12_L001_R1_001
Memory-derived CD8+/CAR+ T cells were collected in vitro after 5 day CAR-transduction protocol.

value: CAR+Vaccine


title: Naïve, PostCAR, Exp2, TR1 [ATAC-seq]

description:
6-13-22_Naive_ATAC_1_S7_L001_R1_001
Naïve-derived CD8+/CAR+ T cells were collected in vitro after 5 day CAR-transduction protocol.

value: Splenic T cells

value: CAR


title: MOLT-4

description: MYB-enriched total RNA


title: Naïve, PostCAR, Exp2, TR2 [ATAC-seq]

description:
6-13-22_Naive_ATAC_2_S8_L001_R1_001
Naïve-derived CD8+/CAR+ T cells were collected in vitro after 5 day CAR-transduction protocol.


title: SON, DMSO, biotinylated, rep 5


title: Memory, PreCAR, Exp2, TR1 [ATAC-seq]

description:
6-8-22_Vax_ATAC_1_S4_L001_R1_001
We adoptively transferred 5000 C57BL/6-background Rag2-/- OT-I TCR transgenic CD8+ T cells (CD45.2+) into C57BL/6-background CD45.1+ hosts, followed by vaccination (ovalbumin, anti-mouse CD40, PolyI:C), and then harvested CD45.2+/CD8+ T cells from pooled spleens at 28 days post-vaccination.


title: SON, DMSO, biotinylated, rep 4


title: Naïve, PreCAR, Exp2, TR3 [ATAC-seq]

description:
6-8-22_Naive_ATAC_3_S3_L001_R1_001
Splenic CD8+ T cells were harvested from naïve mice.


title: Control_replicate3

city: Houston

first: Akdes

last: Serin Harmanci

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v8 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: glioma

extract_protocol:
Mouse gliomas were dissociated into single cells. RNA was extracted using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3. RNA libraries were prepared for sequencing using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.
Library was performed according to the manufacter’s instructions (Single Cell 3' v3 or Single Cell 3' v4, 10X Genomics).

value: glioma


title: Control_replicate2

description: 10X Genomics


title: SON, DMSO, biotinylated, rep 3


title: Naïve, PreCAR, Exp2, TR2 [ATAC-seq]

description:
6-8-22_Naive_ATAC_2_S2_L001_R1_001
Splenic CD8+ T cells were harvested from naïve mice.


title: SON, DMSO, biotinylated, rep 2


title: melanocytes, H3K27me3 ChIPseq, rep1

city: Orem

first: Eric

last: Domyan

state: UT

address: 800 W University Parkway

department: Department of Biology

institute: Utah Valley University

description: H3K27me3 ChIPseq

data_processing:
Basecalls and demultiplexing was performed using bcl2fastq2 (v2.20) for Novaseq output.
Adapter sequences were trimmed from reads using homerTools (v4.11) trim function with the following parameters: -mis 1 -minMatchLength 4 -min 15
Sequences were mapped to the pigeon genome (Cliv2.1) using bowtie2 (v2.2.9).
Sequences were converted to bam format filtered for MAPQ > 10 using samtools (v1.16).
Peaks were called using macs3 (v.3.0.0) using the following parameters: --keep-dup auto -g 1e+9. For the H3K27ac and H3K27me3 analyses, parameter: --broad was added.
Assembly: Cliv2.1
Supplementary files format and content: BED file.

organism: Columba livia

source_name: primary melanocytes

growth_protocol: Ham's F10 supplmented with 10% FBS, 5% Nu-serum, 1x penicillin/streptomycin, 1x fungizone, 85 nM TPA, 40 ng/mL cholera toxin, and 10 ng/mL endothelin-3

extract_protocol:
Melanocytes were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp with Active Motif’s EpiShear probe sonicator (cat# 53051). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantitation by Clariostar (BMG Labtech). Extrapolation to the original chromatin volume allowed determination of the total chromatin yield.
Illumina sequencing libraries (a custom type, using the same paired read adapter oligonucleotides described by Bentley et al., (2008)) were prepared from the ChIP and Input DNAs on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s  NovaSeq 6000 (75 nt reads, single end). Illumina library: Bentley D.R. et al., Nature. 2008 November 6; 456(7218): 53–59. doi:10.1038/nature07517, PMCID: PMC2581791

value: primary melanocytes

value: wild-type

tag: chip antibody

value: H3K27me3 (Active Motif, 39155)


title: Memory, PreCAR, Exp2, TR2 [ATAC-seq]

description:
6-8-22_Vax_ATAC_2_S5_L001_R1_001
We adoptively transferred 5000 C57BL/6-background Rag2-/- OT-I TCR transgenic CD8+ T cells (CD45.2+) into C57BL/6-background CD45.1+ hosts, followed by vaccination (ovalbumin, anti-mouse CD40, PolyI:C), and then harvested CD45.2+/CD8+ T cells from pooled spleens at 28 days post-vaccination.

value: CD8+ T cell

value: Rag2-/- OT-I TCR transgenic


title: Naïve, PreCAR, Exp2, TR1 [ATAC-seq]

description:
6-8-22_Naive_ATAC_1_S1_L001_R1_001
Splenic CD8+ T cells were harvested from naïve mice.


title: SON, DMSO, biotinylated, rep 1


title: DFCI09_PDX

description: MYB-enriched total RNA

value: T lymphoblast


title: melanocyes, H3K27ac ChIPseq, rep1

description: H3K27ac ChIPseq

value: H3K27ac (Active Motif, 39133)


title: Memory, Tumor, Exp1, TR3 [ATAC-seq]

description:
5_6_22_Vax_ATAC_3_S42_L003_R1_001
Memory-derived CD8+/CAR+ T cells infused into leukemia-bearing hosts at 1e6 CAR+ cells per mouse, then sorted out of pooled bone marrow from 10x mice for sequencing.

value: Spleen-derived T cells, harvested from bone marrow


title: Memory, Tumor, Exp1, TR1 [ATAC-seq]

description:
5_6_22_Vax_ATAC_1_S40_L003_R1_001
Memory-derived CD8+/CAR+ T cells infused into leukemia-bearing hosts at 1e6 CAR+ cells per mouse, then sorted out of pooled bone marrow from 10x mice for sequencing.


title: Memory, Tumor, Exp1, TR2 [ATAC-seq]

description:
5_6_22_Vax_ATAC_2_S41_L003_R1_001
Memory-derived CD8+/CAR+ T cells infused into leukemia-bearing hosts at 1e6 CAR+ cells per mouse, then sorted out of pooled bone marrow from 10x mice for sequencing.


title: NLS, Pladienolide-B, input, rep 5

value: hiPSC

value: APEX2-GFP-NLS insert

value: Pladienolide-B


title: GSC1228_S5_1

city: Nagoya

first: Keiko

last: Shinjo

state: Aichi

address: 65 Tsurumai, Showa-ku

department: Cancer Biology

country: Japan

institute: Nagoya Univ. Graduate School of Medicine

data_processing:
RNA-seq was aligned using HISAT2 under default setting to Homo Sapience hg38
TPM were generated using StringTie and differential expression analysis were performed using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts each sample

growth_protocol: GSC cells were cultured in Neurobasal Medium (Life Technologies, Carlsbad, CA, USA) containing N2 and B27 supplements (Life Technologies) along with human recombinant basic fibroblast growth factor and epidermal growth factor (20 ng/ml each; R&D Systems, Minneapolis, MN, USA). Cells were cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA from the cell lines was extracted using TRIzol (Thermo Fisher Scientific)
Illumina TruSeq RNA sample preparation was conducted

treatment_protocol: Cells per were treatment with DMSO or LSD1 inhibitors for 96 h.

value: glioma stem cell


title: melanocytes, input, rep1

description: Input


title: GSC1228_DMSO_5

value: DMSO


title: melanocytes, Sox10 ChIPseq, rep1

description: SOX10 ChIPseq


title: GSC1228_S5_5


title: GSC1228_S5_3


title: GSC1228_S5_2


title: NLS, Pladienolide-B, input, rep 4

value: human induced pluripotent stem cells


title: Control_replicate1

description: 10X Genomics


title: NLS, Pladienolide-B, input, rep 2


title: GSC1228_DMSO_2


title: Naïve, Tumor, Exp1, TR3 [ATAC-seq]

description:
5_6_22_Naive_ATAC_3_S39_L003_R1_001
Naïve-derived CD8+/CAR+ T cells infused into leukemia-bearing hosts at 1e6 CAR+ cells per mouse, then sorted out of pooled bone marrow from 10x mice for sequencing.


title: GSC1228_DMSO_1


title: NLS, Pladienolide-B, biotinylated, rep 5


title: Naïve, Tumor, Exp1, TR2 [ATAC-seq]

description:
5_6_22_Naive_ATAC_2_S38_L003_R1_001
Naïve-derived CD8+/CAR+ T cells infused into leukemia-bearing hosts at 1e6 CAR+ cells per mouse, then sorted out of pooled bone marrow from 10x mice for sequencing.


title: GSC1228_S_K9m2

data_processing:
ChIP-seq clean reads were obtained from raw reads by the removal of adaptors and low-quality reads.
The clean reads were aligned to the human genome (hg38) using Bowtie2 (version 2.4.2)
The levels of histone modification at gene promoters were estimated by counting the numbers of reads mapped within a 2 kb region around the transcriptional start site using HOMER
Assembly: hg38
Supplementary files format and content: bigWig (except for input)

extract_protocol:
Cells (1 × 106) were treated with 1% formaldehyde for 8 min to crosslink histones to DNA. After washing with cold PBS, cell pellets were lysed with lysis buffer (10 mM Tris-HCl, 0.25% Triton X-100, 10 mM EDTA, and 0.1 M NaCl). Cell nuclei were collected after centrifugation and re-suspended in SDS lysis buffer (1% SDS, 150 mM NaCl, 50 mM HEPES-KOH, 2 mM EDTA, 1% Triton X-100, and 0.1% sodium deoxycholate). Chromatin was sonicated using Covaris S220. Lysates were incubated overnight with 50 μl of Dynabeads Protein G which were pre-coated with antibodies. The beads were washed and protein-DNA complexes were eluted with elution buffer (1% SDS, 10 mM EDTA, and 50mM Tris-HCl) and then treated with RNase for 2 h at 37°C followed by proteinase K treatment overnight. DNA was extracted by the phenol/chloroform method, ethanol-precipitated and resuspended in 0.1 × TE buffer. 10% of the lysate was treated with RNase and proteinase K and de-crosslinked as input samples.
NEBNext Ultra II DNA library Prep kit

value: H3K9me2(abcam ab1220)


title: NLS, Pladienolide-B, biotinylated, rep 4


title: Control_replicate1

description: 10X Genomics

library_source: genomic single cell

extract_protocol:
Mouse gliomas were dissociated into single cells and nuclei were extracted. DNA was extracted and processed using the 10X Genomics Chromium Next GEM Single Cell ATAC Kit v2
Library was performed according to the manufacter’s instructions (10X Genomics Chromium Next GEM Single Cell ATAC Kit v2).


title: PDGFB-NLS-overexpression-replicate1

description: 10X Genomics


title: Naïve, Tumor, Exp1, TR1 [ATAC-seq]

description:
5_6_22_Naive_ATAC_1_S37_L003_R1_001
Naïve-derived CD8+/CAR+ T cells infused into leukemia-bearing hosts at 1e6 CAR+ cells per mouse, then sorted out of pooled bone marrow from 10x mice for sequencing.

value: CAR


title: GSC1228_S_K4m3

value: H3K4me3(Active Motif 39159)


title: GSC1228_S_K4m1

value: H3K4me1(abcam ab8895)


title: NLS, Pladienolide-B, biotinylated, rep 3


title: Memory, PostCAR, Exp1, TR3 [ATAC-seq]

description:
5_2_22_Vax_ATAC_3_S36_L003_R1_001
Memory-derived CD8+/CAR+ T cells were collected in vitro after 5 day CAR-transduction protocol.

value: Splenic T cells

value: CAR+Vaccine


title: NLS, Pladienolide-B, biotinylated, rep 2


title: Memory, PostCAR, Exp1, TR2 [ATAC-seq]

description:
5_2_22_Vax_ATAC_2_S35_L003_R1_001
Memory-derived CD8+/CAR+ T cells were collected in vitro after 5 day CAR-transduction protocol.

value: CD8+ T cell


title: GSC1228_S_K4m2

value: H3K4me2(Active Motif 39141)


title: GSC1228_S_input


title: Memory, PostCAR, Exp1, TR1 [ATAC-seq]

description:
5_2_22_Vax_ATAC_1_S34_L003_R1_001
Memory-derived CD8+/CAR+ T cells were collected in vitro after 5 day CAR-transduction protocol.

value: Rag2-/- OT-I TCR transgenic


title: GSC1228_D_K4m1


title: NLS, GSK626616, input. rep 5


title: GSC1228_D_K4m3


title: GSC1228_DMSO_3


title: Naïve, PostCAR, Exp1, TR3 [ATAC-seq]

description:
5_2_22_Naive_ATAC_3_S33_L003_R1_001
Naïve-derived CD8+/CAR+ T cells were collected in vitro after 5 day CAR-transduction protocol.


title: GSC1228_D_K4m2


title: NLS, GSK626616, input, rep 4


title: GSC1228_D_K9m2


title: shATF4_5FU48h_2

city: Hangzhou

first: Yifan

last: Zhao

address: Banshan

institute: Zhejiang Cancer Hospital

data_processing:
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: tab-separated values files and matrix files

growth_protocol: SW620 was obtained from the Chinese Academy of Sciences (Shanghai, China) and cultured in DMEM, supplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was extracted from cells using the RNeasy Mini Kit (QIAGEN)
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-Toligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: shScramble SW620 cells(vehicle control) and shATF4 SW620 cells(ATF4 knockdown) were treated with 5μM 5-FU for 24h or 48h

value: Human colorectal cancer cells

value: ATF4 knockdown

value: 5uM 5-FU for 24 hours


title: NLS, Pladienolide-B, biotinylated, rep 1

value: hiPSC

value: APEX2-GFP-NLS insert


title: Naïve, PostCAR, Exp1, TR2 [ATAC-seq]

description:
5_2_22_Naive_ATAC_2_S32_L003_R1_001
Naïve-derived CD8+/CAR+ T cells were collected in vitro after 5 day CAR-transduction protocol.


title: shATF4_5FU48h_1


title: NLS, GSK626616, input, rep 2


title: Naïve, PostCAR, Exp1, TR1 [ATAC-seq]

description:
5_2_22_Naive_ATAC_1_S31_L003_R1_001
Naïve-derived CD8+/CAR+ T cells were collected in vitro after 5 day CAR-transduction protocol.


title: NLS, GSK626616, biotinylated, rep 5


title: shATF4_5FU24h_3


title: shATF4_5FU24h_2


title: NLS, GSK626616, biotinylated, rep 4


title: Memory, PreCAR, Exp1, TR3 [ATAC-seq]

description:
4_27_22_Vax_ATAC_3_S30_L003_R1_001
We adoptively transferred 5000 C57BL/6-background Rag2-/- OT-I TCR transgenic CD8+ T cells (CD45.2+) into C57BL/6-background CD45.1+ hosts, followed by vaccination (ovalbumin, anti-mouse CD40, PolyI:C), and then harvested CD45.2+/CD8+ T cells from pooled spleens at 28 days post-vaccination.

value: Vaccine


title: tg_okn_155_14

city: Oklahoma City

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to hg38 with STAR software then raw counts were computed with featureCounts for each gene in each sample.
Read-count normalization and differentially expressed analyses were performed using the edgeR package from Bioconductor.
Ingenuity Pathway Analysis (IPA, QIAGEN, Redwood City CA) was used to identify and interactively explore significantly altered pathways, functional sets and gene networks, enriched among the set of DE genes.
Assembly: GRCm39 (mm39)
Supplementary files format and content: rawCounts.txt: tab delimited text file with raw counts per gene per sample

extract_protocol:
RNA was isolated from the spinal cord of two groups of mice: one group treated and the other untreated, consisting of both wild type and G93A mice. Each sample weighed 25 mg, and the TRIzol reagent from Invitrogen, CA, USA was used according to the manufacturer's instructions for the extraction process.
Libraries were constructed using the TruSeq Stranded mRNA Library Kit from Illumina

tag: strain

value: 155 days


title: tg_okn_155_13


title: Memory, PreCAR, Exp1, TR2 [ATAC-seq]

description:
4_27_22_Vax_ATAC_2_S29_L003_R1_001
We adoptively transferred 5000 C57BL/6-background Rag2-/- OT-I TCR transgenic CD8+ T cells (CD45.2+) into C57BL/6-background CD45.1+ hosts, followed by vaccination (ovalbumin, anti-mouse CD40, PolyI:C), and then harvested CD45.2+/CD8+ T cells from pooled spleens at 28 days post-vaccination.


title: shATF4_5FU24h_1


title: tg_unt_155_12

value: untreated


title: NLS, GSK626616, biotinylated, rep 3

value: human induced pluripotent stem cells


title: GSC1228_D_input

value: glioma stem cell

value: DMSO


title: shATF4_3

value: Control


title: NLS, GSK626616, biotinylated, rep 2


title: tg_unt_155_11


title: Naïve, PreCAR, Exp1, TR3 [ATAC-seq]

description:
4_27_22_Naive_ATAC_3_S27_L003_R1_001
Splenic CD8+ T cells were harvested from naïve mice.

value: Splenic T cells


title: tg_okn_155_16


title: shATF4_2


title: Naïve, PreCAR, Exp1, TR2 [ATAC-seq]

description:
4_27_22_Naive_ATAC_2_S26_L003_R1_001
Splenic CD8+ T cells were harvested from naïve mice.


title: tg_unt_155_10


title: NLS, GSK626616, biotinylated, rep 1


title: tg_okn_155_15


title: shATF4_1


title: shSc_5FU48h_2

value: Scramble knockdown(negative control)


title: tg_unt_155_9


title: Naïve, PreCAR, Exp1, TR1 [ATAC-seq]

description:
4_27_22_Naive_ATAC_1_S25_L003_R1_001
Splenic CD8+ T cells were harvested from naïve mice.

value: CD8+ T cell


title: Memory, PreCAR, Exp1, TR1 [ATAC-seq]

description:
4_27_22_Vax_ATAC_1_S28_L003_R1_001
We adoptively transferred 5000 C57BL/6-background Rag2-/- OT-I TCR transgenic CD8+ T cells (CD45.2+) into C57BL/6-background CD45.1+ hosts, followed by vaccination (ovalbumin, anti-mouse CD40, PolyI:C), and then harvested CD45.2+/CD8+ T cells from pooled spleens at 28 days post-vaccination.


title: NLS, DRB, input, rep 2

value: DRB


title: Memory, Tumor, Exp2, TR1 [RNA-seq]

description: Memory-derived CD8+/CAR+ T cells infused into leukemia-bearing hosts at 1e6 CAR+ cells per mouse, then sorted out of pooled bone marrow from 10x mice for sequencing.

data_processing:
Raw sequencing reads were de-multiplexed using bcl2fastq.
Quality of fastq files was accessed using FastQC (v.0.11.8) , FastQ Screen (v.0.13.0) and MultiQC (v.1.8).
Illumina adapters and low-quality reads were filtered out using BBDuk (v. 38.87).
Trimmed fastqc files were aligned to the mm10 murine reference genome and aligned counts per gene were quantified using STAR (v.2.7.9a).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts.

extract_protocol:
For RNAseq, cells were homogenized in QIAzol Lysis Reagent and processed using the miRNeasy Micro Kit with on-column DNase treatment, both according to manufacturer protocols. RNA purity, quantity and integrity was determined with NanoDrop and TapeStation 4200 analysis.
The Universal Plus mRNA-Seq library preparation kit with NuQuant was used with an input of 200ng of total RNA to generate RNA-Seq libraries.

value: Spleen-derived T cells, harvested from bone marrow

value: Rag2-/- OT-I TCR transgenic

value: CAR+Vaccine


title: wt_okn_155_7

source_name: wildtype

value: wildtype


title: NLS, DRB, input, rep 4

value: hiPSC


title: NLS, DRB, biotinylated, rep 5

value: APEX2-GFP-NLS insert


title: wt_okn_155_8


title: shSc_5FU48h_1

value: Human colorectal cancer cells

value: 5uM 5-FU for 24 hours


title: shSc_5FU24h_2


title: wt_okn_155_6

value: 155 days


title: Naïve, Tumor, Exp2, TR2 [RNA-seq]

description: Naïve-derived CD8+/CAR+ T cells infused into leukemia-bearing hosts at 1e6 CAR+ cells per mouse, then sorted out of pooled bone marrow from 10x mice for sequencing.

value: CAR


title: wt_okn_155_5


title: NLS, DRB, biotinylated, rep 4

value: human induced pluripotent stem cells


title: NLS, DRB, input, rep 5


title: shSc_5FU24h_1


title: NLS, DRB, biotinylated, rep 3


title: Memory, PostCAR, Exp2, TR2 [RNA-seq]

description: Memory-derived CD8+/CAR+ T cells were collected in vitro after 5 day CAR-transduction protocol.


title: wt_unt_155_4

value: untreated


title: Naïve, Tumor, Exp2, TR1 [RNA-seq]


title: Memory, PostCAR, Exp2, TR1 [RNA-seq]


title: wt_unt_155_3


title: shSc_2

value: Control


title: NLS, DRB, biotinylated, rep 1


title: Memory, Tumor, Exp2, TR2 [RNA-seq]


title: wt_unt_155_2


title: NLS, DMSO, input, rep 5

value: DMSO


title: Naïve, PostCAR, Exp2, TR1 [RNA-seq]

description: Naïve-derived CD8+/CAR+ T cells were collected in vitro after 5 day CAR-transduction protocol.

value: Splenic T cells


title: shSc_5FU24h_3

value: Scramble knockdown(negative control)


title: shSc_1


title: wt_unt_155_1


title: meRIP-seq-TTCKO_IP-Caco2

city: Xiamen

first: you

middle: a

last: bin

state: Fujian

address: 55 Zhenhai Road, Siming District, Xiamen

institute: the First Affiliated Hospital of Xiamen University

data_processing:
Library strategy: meRIP-seq
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg38 genome assembly using Tophat version 2.1.1.
Genome_build: hg38

growth_protocol: The Caco2 cell line was grown in minimal essential medium（MEM）medium containing 10%FBS，1% non-essential amino acids and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was isolated using TRIzol (Thermo Fisher Scientific, Waltham, MA, USA) reagents according to the manufacturer’s instructions. mRNA was isolated from the total RNA using Dynabeads mRNA DIRECT purification kit (61011, Thermo Fisher, USA).
Purified mRNA fragments were used for meRIP-sequencing library generation and sequenced with Illumina HiSeq 4000.

treatment_protocol: Caco2 cells were transfected with the CRISPR/Cas9 and guide RNA or siRNA specifically targeting TTC22 and maintained in  MEM medium supplemented with 10%FBS，1% non-essential amino acids and 1% penicillin/streptomycin.

value: Human colorectal cancer cell line


title: Memory, PreCAR, Exp2, TR2 [RNA-seq]

description: We adoptively transferred 5000 C57BL/6-background Rag2-/- OT-I TCR transgenic CD8+ T cells (CD45.2+) into C57BL/6-background CD45.1+ hosts, followed by vaccination (ovalbumin, anti-mouse CD40, PolyI:C), and then harvested CD45.2+/CD8+ T cells from pooled spleens at 28 days post-vaccination.

value: CD8+ T cell

value: Vaccine


title: tg_okn_90_16

first: Jonathan

value: 90 days


title: NLS, DMSO, input, rep 4


title: meRIP-seq-TTCKO_In-Caco2


title: tg_okn_90_15


title: shSc_3


title: NLS, DMSO, biotinylated, rep 5


title: NLS, DMSO, biotinylated, rep 4


title: meRIP-seq-Ctrl_IP-Caco2


title: meRIP-seq-Ctrl_In-Caco2


title: NLS, DRB, biotinylated, rep 2

value: DRB


title: tg_okn_90_13


title: tg_okn_90_14


title: Memory, Tumor, Exp1, TR3 [RNA-seq]

value: Spleen-derived T cells, harvested from bone marrow

value: Rag2-/- OT-I TCR transgenic

value: CAR+Vaccine


title: Naïve, PreCAR, Exp2, TR1 [RNA-seq]

description: Splenic CD8+ T cells were harvested from naïve mice.


title: Naïve, PreCAR, Exp2, TR2 [RNA-seq]


title: Naïve, PostCAR, Exp2, TR2 [RNA-seq]


title: meRIP-seq-SiTTC_IP-Caco2


title: NLS, DMSO, biotinylated, rep 3

value: hiPSC

value: APEX2-GFP-NLS insert


title: NLS, DMSO, input, rep 2


title: NLS, DMSO, biotinylated, rep 2


title: Memory, Tumor, Exp1, TR2 [RNA-seq]


title: tg_unt_90_11


title: Memory, PreCAR, Exp2, TR1 [RNA-seq]


title: meRIP-seq-SiNC_IP-Caco2


title: tg_unt_90_10


title: meRIP-seq-SiNC_In-Caco2


title: Memory, Tumor, Exp1, TR1 [RNA-seq]


title: tg_unt_90_9


title: nucleus, rep 5

data_processing:
Trimmomatic v0.39 (Bolger et al., 2014) was used to trim adapter sequences from raw reads with the following settings: ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to the human reference genome (hg38, GRCh38.p14 primary genome assembly) using GENCODE v40 gene annotations with STAR v2.7.3a (Dobin et al., 2013)
Count tables were generated using the featureCounts (Y. Liao et al., 2014) function of the R package Rsubread v2.10.5 (Y. Liao et al., 2019)
Differential Gene Expression (DGE) analysis was performed with DESeq2 v1.36.0 (Love et al., 2014)
Assembly: hg38
Supplementary files format and content: csv file includes read counts for each gene in each sample

extract_protocol:
Cells were fractionated into chromatin, nuclei and cytoplasm fractions using a protocol adapted from Mayer & Churchman, 2017. To isolate RNA, 3.5 sample volumes of RLT buffer (Qiagen, 79216) was added to each fraction. After mixing, 2.5 volumes of ice-cold 75% ethanol was added. RNA was then cleaned up using the RNeasy Mini kit (Qiagen, 74104).
libraries were prepared using Truseq Stranded mRNA kit (Illumina, 20020594)

tag: fraction

value: nucleus

value: SON-mEGFP endogenous tag


title: orange adductor muscles of QN Orange scallops 3

first: JunLin

last: Song

address: Changcheng Road

institute: JunLin Song

data_processing: none provided

organism: Argopecten irradians irradians

source_name: adductor muscle

extract_protocol: none provided

value: adductor muscle

value: orange


title: Naïve, Tumor, Exp1, TR2 [RNA-seq]

value: CAR


title: tg_unt_90_12

value: untreated


title: Naïve, Tumor, Exp1, TR3 [RNA-seq]


title: orange adductor muscles of QN Orange scallops 2


title: nucleus, rep 4

tag: cell line

value: human induced pluripotent stem cells


title: wt_okn_90_8

value: wildtype


title: meRIP-seq-SiTTC_In-Caco2

value: Human colorectal cancer cell line


title: orange adductor muscles of QN Orange scallops 1


title: nucleus, rep 3

tag: cell type


title: wt_okn_90_6


title: wt_okn_90_7


title: Memory, PostCAR, Exp1, TR3 [RNA-seq]

value: Splenic T cells

value: CD8+ T cell

tag: genotype


title: nucleus, rep 2


title: white adductor muscles of Bohai Red scallops 3

value: white


title: NLS, DMSO, biotinylated, rep 1

data_processing:
Trimmomatic v0.39 (Bolger et al., 2014) was used to trim adapter sequences from raw reads with the following settings: ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to the human reference genome (hg38, GRCh38.p14 primary genome assembly) using GENCODE v40 gene annotations with STAR v2.7.3a (Dobin et al., 2013)
Count tables were generated using the featureCounts (Y. Liao et al., 2014) function of the R package Rsubread v2.10.5 (Y. Liao et al., 2019). Transcript quantification was performed using Salmon v0.12.0 (Patro et al., 2017) with the --numGibbsSamples option set to 30 to generate Gibbs samples.
Differential Gene Expression (DGE) analysis was performed with DESeq2 v1.36.0 (Love et al., 2014). Differential transcript expression analysis was performed using Fishpond v2.2.0 (Zhu et al., 2019).
Assembly: hg38
Supplementary files format and content: csv file includes read counts for each gene in each sample
Supplementary files format and content: csv file includes TPM for each transcript, quantified by salmon

extract_protocol:
hiPSCs were lysed by adding RNA lysis buffer (Zymo Research, R1060-1-50). Total RNA was purified using Zymo Quick-RNA Miniprep kit (Zymo Research, R1054)
Libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara, 634411), including ribosomal cDNA depletion step

value: DMSO


title: wt_okn_90_5

value: 90 days


title: Memory, PostCAR, Exp1, TR2 [RNA-seq]

value: Rag2-/- OT-I TCR transgenic

value: CAR+Vaccine


title: white adductor muscles of Bohai Red scallops 2


title: wt_unt_90_4


title: Memory, PostCAR, Exp1, TR1 [RNA-seq]


title: white adductor muscles of Bohai Red scallops 1


title: cytoplasm, rep 5

value: cytoplasm

value: hiPSC


title: cytoplasm, rep 4

value: SON-mEGFP endogenous tag


title: cytoplasm, rep 3


title: Naïve, Tumor, Exp1, TR1 [RNA-seq]

value: Spleen-derived T cells, harvested from bone marrow


title: Naïve, PostCAR, Exp1, TR2 [RNA-seq]


title: IB27

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W. Walnut St. R2 202

department: Medicine

institute: Indiana University

data_processing:
The basecalling was done using Guppy basecaller: guppy_basecaller --compress_fastq --fast5_out -i ./fast5_pass/ -s ./fastq/ --device 'auto' --num_callers 1 --flowcell "FLO-MIN106" --kit "SQK-DCS109"
Mapping was carried out using Minimap2: minimap2 -a -L -t 12 -x splice --junc-bed Human_ensembl_release_100/Homo_sapiens.GRCh38.100.bed --MD Human_ensembl_release_100/hg38-ont.mmi ./fastq/*.fastq.gz 2> ./minimap2.err > ./SAM/$sample.sam
Counts were generated using featureCounts with -L option and -t exon.
Assembly: hg38
Supplementary files format and content: counts table in text format

source_name: kidney

extract_protocol:
Snap-frozen mouse kidney tissue (<100 mg) was homogenized in 800 µl of Tri Reagent using a Minilys tissue homogenizer at the highest speed for 45 seconds and then incubated for 5 minutes. Total RNA was extracted from 600 µl of the supernatant using the Direct-zol RNA miniprep Plus (Zymo Research), including on-column DNase I digestion. The RNA was eluted in 100 µl of water and subjected to mRNA polyA enrichment using the Dynabeads mRNA DIRECT Micro kit (Thermo Fisher 61021). After two rounds of washing and enrichment of mRNA following the manufacture’s protocol, polyA+ mRNA was eluted in 10 µl of water.
We proceeded with ~50 ng of polyA+ mRNA as the starting material. Reverse transcription and strand-switching was done using Maxima H Minus Reverse Transcriptase following the Nanopore protocol (SQK-DCS109). After end-prep, adapter ligation, and AMPure XP bead binding, sequencing was conducted on R9.4.1 flow cells using the GridIon platform.

value: kidney


title: cytoplasm, rep 2


title: wt_unt_90_2


title: IB26


title: wt_unt_90_1


title: IB25


title: nucleus, rep 1

value: nucleus


title: cytoplasm, rep 1


title: chromatin, rep 5

value: chromatin


title: TFEB43

city: Shenzhen

first: cong

last: liu

address: 628 Zhenyuan Road, Guangming District, Shenzhen City

institute: Seventh Affiliated Hospital, Sun Yat-sen University

data_processing:
data filtering The raw data obtained by sequencing was filtered using SOAPnuke (v1.5.6) to filter out reads(joint contamination) containing 1). 2) reads with unknown base N content greater than 5%; 3) clean data were obtained from low-quality reads (those with a mass value of less than 15 bases accounting for more than 20% of the total base number of the reads). Subsequent use Dr. Tom multiple omics data mining system (https://biosys.bgi.comopen in new window) for data analysis, mapping and mining. Differential gene analysis uses HISAT2 (v2.1.0) software to match clean data to a reference genome. The clena data was compared to the reference gene set using Bowtie2(v2.3.4.3). The reference gene set is provided by the Dr. Tom multi-omics data Mining System. RSEM (v1.3.1) software was used to quantify gene expression, and pheatmap (v1.0.8) was used to draw the clustering heatmap of gene expression in different samples. Differential gene testing is performed using DESeq2 (v1.4.5) (or DEGseq or PoissonDis) if Q value≤0.05 or FDR≤0.001. KEGG and GO enrichment analyses further explored gene functions associated with phenotypic change. Based on hypergeometric tests, Use Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distributionopen in new window) GO on genetic variations (http://www.geneontology.org/open in new window) and KEGG (https://www.kegg.jp/open in new window) enrichment analysis, threshold for Qvalue 0.05 or less, Meeting this condition is defined as significant enrichment in candidate genes.
Assembly: mm10
Supplementary files format and content: teb-delimited texed file include raw counts for each sample
Supplementary files format and content: teb-delimited texed file include RPKM values for each sample

source_name: heart

extract_protocol:
Appropriate amount of tissue sample was taken into the corresponding number of grinding and crushing pipe. Add 1.5mL TRIzol lysate, put it into a tissue grinder, grind it for 30s, take it out and leave it for 5min to fully lysate the tissue cells. The liquid nitrogen was ground and crushed, and 1.5mL TRIzol lysate was divided into 2mL EP tubes. An appropriate amount of tissue sample was taken and ground into powder under the protection of liquid nitrogen, and then transferred into the lysate. Lay flat for 5min to fully lyse the tissue cells. Appropriate amount of TRIzol lysate was added into the cell sample tube (the reference dosage was 1 mL of TRIzol for every 1×106 cells), and the cells were placed at room temperature for 5min after swirling and mixing, so as to fully lysate the cells. The ground and broken tissue samples were centrifuged (cell samples did not need to be centrifuged) at 4℃ for 5min at 12000 ×g. The supernatant was transferred into an EP tube filled with 300µL chloroform/isoamyl alcohol (24:1), reversed and violently shook and mixed; Centrifuge at 4℃ at 12000×g for 8min. If the middle layer is thick and the water is turbidity, the same supernatant volume of chloroform/isoamyl alcohol (24:1) can be extracted again. Absorb the supernatant into a new 1.5mL centrifuge tube, add isopropyl alcohol (isopropyl alcohol) containing 2/3 of the supernatant liquid (2µL 5mg/mL glycogen can be added during precipitation), invert and mix gently, and place in the refrigerator at -20℃ for more than 2h. Centrifuge at 4℃ at 17500×g for 25min, discard the supernatant, wash with 0.9mL 75% ethanol, suspend precipitation upside down, centrifuge at 4℃ at 17500×g for 3min(depending on the precipitation, it can be washed again with 75% ethanol, centrifuge at 4℃ at 17500×g for 3min). Discard the supernatant, remove the residual liquid after a short centrifugation, and let dry for 3-5min. Dissolve precipitation with 20-200μL DEPC water or RNase-free water.
Sample testing According to the sample and product requirements to select the appropriate test method for quality inspection. A certain amount of RNA samples were isolated, the secondary structure was opened by thermal denaturation, and the mRNA was enriched by oligo(dT) magnetic beads. mRNA interruption The mRNA obtained in the previous step is fragmented by adding an interruption reagent to the mRNA obtained in the previous step and reacting at a certain temperature for a certain time. A chain synthesis reaction system was prepared for cDNA synthesis, and the reaction program was set to synthesize a chain cDNA. The two-strand synthesis reaction system was prepared and the reaction program was set up to synthesize two-strand cDNA. The reaction system was prepared by terminal repair, adding "A" and joint connection, and the reaction program was set to repair the end of double-stranded cDNA and add A base to the 3 'end. The joint joint reaction system was prepared, and the reaction program was set to connect the joint with cDNA. PCR The PCR reaction system was prepared, and the reaction program was set to amplify the product. Library testing According to the product requirements to select the corresponding detection method to the library quality inspection. After the PCR product was denaturated to single strand, the cyclization reaction system was prepared, and the reaction program was set to obtain the single strand ring product, and the linear DNA molecules that were not cycled were digested. Single-stranded circular DNA molecules are replicated by rolling rings to form a DNA nanosphere (DNB) containing multiple copies. The DNBs obtained were added to the mesh holes on the chip using high-density DNA nanochip technology, and sequenced by combined probe anchoring polymerization (cPAS).

value: heart

value: mouse primary fibroblasts

value: fibrocyte

value: TFEB overexpression

value: ligate the anterior descending branch of the mice’s left coronary artery


title: Memory, PreCAR, Exp1, TR3 [RNA-seq]

value: Splenic T cells

value: CD8+ T cell

value: Vaccine


title: Naïve, PostCAR, Exp1, TR1 [RNA-seq]

value: Rag2-/- OT-I TCR transgenic

value: CAR


title: PDGFB-NLS-overexpression-replicate1

description: 10X Genomics

value: glioma


title: chromatin, rep 4

source_name: hiPSC

value: hiPSC

value: human induced pluripotent stem cells


title: TFEB41


title: Memory, PreCAR, Exp1, TR2 [RNA-seq]


title: TFEB34


title: PDGFB-NLS-overexpression-replicate2

description: 10X Genomics


title: Memory, PreCAR, Exp1, TR1 [RNA-seq]


title: Naïve, PreCAR, Exp1, TR3 [RNA-seq]


title: Naïve, PostCAR, Exp1, TR3 [RNA-seq]


title: PDGFB-WT-overexpression-replicate2

description: 10X Genomics


title: wt_unt_90_3

value: wildtype

value: untreated

value: 90 days


title: Naïve, PreCAR, Exp1, TR2 [RNA-seq]


title: chromatin, rep 2

value: chromatin

value: SON-mEGFP endogenous tag


title: contral36

value: heart

value: mouse primary fibroblasts

value: WT


title: PDGFB-WT-overexpression-replicate1

description: 10X Genomics


title: PDGFB-WT-overexpression-replicate1

description: 10X Genomics


title: chromatin, rep 1


title: contral35

value: fibrocyte

value: ligate the anterior descending branch of the mice’s left coronary artery


title: Patient_22_Week4_PBMC_TIL_GEX

status: Public on Nov 09 2024

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

data_processing:
Sequencing runs were demultiplexed using bcl2fastq (v2.20.0)
FASTQ files were aligned to GRCh38 using Cellranger count (v6.0.1).
For TCR reconstruction, FASTQ files from TCR specific libraries were used as input into CellRanger vdj.
For CITEseq, TotalSeq specific libaries were aligned using CITEseqCount (v1.4.3).
Feature barcodes matrices were read into Seurat (v4.0.5) to create an aggregrated object for downstream analysis. CD8+ T cell were identified and subset from this overall object for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: *_GEX files are tar archives containing a directory with barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz (i.e. the output from CellRanger count).
Supplementary files format and content: *_CITEseq files are tar archives containing a directory with umi counts for each TotalSeq barcode in the format of barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz (i.e. the output from CITEseqCount).

source_name: Tumor

extract_protocol:
Whole blood was collected by venipuncture into EDTA tubes. Peripheral blood mononuclear cells were isolated by Ficoll-Hypaque density gradient centrifugation. Tumor biopsies were collected into RPMI supplemented with 10% fetal bovine serum. Tumor tissue was mechanically disrupted and passed over a 100 micron filter. Live CD45+ cells were sorted from both blood and tumor specimens. Samples were collected at baseline, following four weeks of therapy, and at 12-16 weeks or upon evidence of disease progression.
Libraries were created using 10X Genomics 5' GEX and VDJ kits as per the manufacturer's instructions.

treatment_protocol: Patients with advanced melanoma received intravenous infusions of monotherapy with relatlimab (anti-LAG3; 160 mg), montherapy with nivolumab (anti-PD1; 480 mg) or the combination of relatlimab+nivolumab (480 mg + 160 mg, respectively) for a lead-in period of 4 weeks.

value: Tumor

tag: timepoint

value: Week 4

value: Live CD45+ immune cells

tag: library type

value: Gene expression

tag: disease stage

value: IIIC

tag: biological sex

value: male

value: relalimab+nivolumab


title: Patient_1_Week4_PBMC_TIL_GEX

tag: tissue

value: IV


title: Patient_1_Week4_PBMC_TIL_CITEseq

value: CITEseq

tag: treatment


title: Patient_21_Week16_TIL_GEX

value: Week 16

value: IIIB


title: Patient_23_Week16_PBMC_GEX

source_name: Blood

value: Blood


title: PDGFB-WT-overexpression-replicate3

description: 10X Genomics

value: glioma


title: VAESBJ_R_noDOX_Input

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

data_processing:
Sequencing was performed on a NovaSeq 6000 Paired-End 50bp SP chip by the DKFZ NSG Core facility. Using the DKFZ galaxy platform, the sequencing reads were mapped with BWA for medium and long reads (>150 bp) against the hg19 reference genome and post-processed using NGS: SAMtools, Filter SAM or BAM for any read with mapping quality less than 20. Correlation among different targets was assessed using NGS: DeepTools, multiBamSummary. Processed reads were visualized in IGV using bamCoverage. Peaks were called using MACS2 on the BAM datasets.
Assembly: hg19
Supplementary files format and content: bed, narrowPeak (except for Input sample)

source_name: VAESBJ

growth_protocol: All cell lines were cultured in RPMI 1640 with stable glutamine (Gibco) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin (Sigma-Aldrich) at 37°C in a fully humidified 5% CO2 atmosphere. Cell lines were routinely tested for Mycoplasma contamination using a custom nested PCR protocol.

extract_protocol: Refer to ChIP-Seq protocols from diagenode

treatment_protocol: 96h Dox or control

value: VAESBJ

value: Epithelioid Sarcoma

value: Control


title: chromatin, rep 3

city: Zurich

first: A

last: McIntyre

address: Winterthurerstrasse 190

institute: University of Zurich

value: chromatin

value: hiPSC

value: human induced pluripotent stem cells

value: SON-mEGFP endogenous tag


title: Patient_22_Week4_PBMC_TIL_CITEseq

value: Tumor

value: Week 4

value: Live CD45+ immune cells


title: Patient_21_Week16_PBMC_GEX

value: Gene expression

value: male

value: relalimab+nivolumab


title: contral37

value: heart

value: mouse primary fibroblasts

value: fibrocyte

value: WT

value: ligate the anterior descending branch of the mice’s left coronary artery


title: Patient_24_Week16_PBMC_GEX

value: Blood

value: Week 16

value: IIID


title: VAESBJ_R_nDOX_H3K27ac

value: VAESBJ

value: Epithelioid Sarcoma

value: H3K27ac, ab4729, abcam

value: Control


title: VAESBJ_R_nDX_H3K27me3

value: H3K27me3, C15410069, Diagenode


title: VAESBJ_R_noDOX_BAF47

value: BAF47, #91735, Cell Signaling


title: VAESBJ_R_nDOX_H3K4me3

value: H3K4me3, C15410003, Diagenode


title: Patient_13_Week16_PBMC_GEX

value: Live CD45+ immune cells

value: Gene expression

value: IV

value: female


title: VAESBJ_R_DOX_Input

value: doxycycline


title: VAESBJ_R_noDOX_BRG1

value: BRG1, ab110641, Abcam


title: VAESBJ_R_DOX_BRG1


title: VAESBJ_R_D_H3K27me3


title: VAESBJ_R_DOX_H3K4me3


title: VAESBJ_R_DOX_BAF47


title: VAESBJ_DOX_BAF47


title: VAESBJ_DOX_H3K27me3


title: VAESBJ_DOX_Input


title: VAESBJ_R_DOX_H3K27ac


title: VAESBJ_noDOX_Input


title: VAESBJ_noDOX_BRG1


title: VAESBJ_DOX_H3K4me3


title: VAESBJ_DOX_BRG1


title: VAESBJ_DOX_H3K27ac


title: VAESBJ_nDOX_H3K27me3


title: HS-ES-2M_BRM_R2

data_processing:
Sequencing was performed on a NovaSeq 6000 Paired-End 100bp S4 chip by the DKFZ NSG Core facility. Using the DKFZ galaxy platform, the sequencing reads were pre-processed with TrimGalore! to filter out adapter sequences, then mapped with bowtie2 against the hg19 reference genome and post-processed using Filter BAM to filter out improperly paired reads, mapping quality less than 30 and/or mapping to the mitochondrial chromosome. Duplicate reads were removed using MarkDuplicates. Processed reads were visualized in IGV using bamCoverage. Peaks were called using MACS2 on the BAM datasets.
Assembly: hg19
Supplementary files format and content: bed, narrowPeak

extract_protocol: Refer to ATAC-Seq protocols from diagenode

treatment_protocol: 96h Dox, BRM014 (1µM) or control


title: HS-ES-2M_DOX_R2


title: VAESBJ_noDOX_H3K4me3


title: VAESBJ_noDOX_BAF47


title: FU-EPS-1_BRM_R2


title: HS-ES-2M_DOX_R1


title: FU-EPS-1_DOX_R2


title: VAESBJ_noDOX_H3K27ac


title: HS-ES-2M_CTRL_R2


title: FU-EPS-1_CTRL_R2


title: HS-ES-2M_CTRL_R1


title: FU-EPS-1_BRM_R1


title: NEPS_BRM_R2

source_name: NEPS

value: NEPS


title: HS-ES-2M_BRM_R1


title: FU-EPS-1_CTRL_R1


title: NEPS_BRM_R1


title: NEPS_CTRl_R2


title: NEPS_DOX_R1


title: VAESBJ_BRM_R2


title: VAESBJ_CTRL_R2


title: VAESBJ_DOX_R2


title: VAESBJ_DOX_R1


title: NEPS_CTRl_R1


title: VAESBJ_CTRL_R1


title: VAESBJ_BRM_R1

value: BRM


title: APLN-PC3-2

city: Taichung

first: Chih-Hsin

last: Tang

address: 91 Xueshi

country: Taiwan

institute: China Medical University

data_processing:
Quality Control: In order to remove technical sequences, pass filter data of fastq format were processed by Trimmomatic (v0.30) to be high quality clean data. Data processing includes the following steps: (1) remove the adapter sequences (2) remove the 5 'or 3' end bases that contains N's or of quality values below 20 (3) remove bases with average quality score below 20 using the sliding window of 4bp (4) remove reads that are less than 18 bp long after trimming
MicroRNA Identify: According to miRDeep2[2], a software that discovering know and novel miRNAs from deep sequencing, we can get all the identified microRNA and their expression data.
Differential Expression Analysis: Differential expression analysis was conducted using the DESeq2 package from Bioconductor. Genes or microRNAs with a fold change ≥ 2 were considered differentially expressed.
GO and KEGG enrichment analysis: GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of microRNA target genes with a significant padj less than 0.05. And topGO was used to plot DAG.
Assembly: miRbase (V22)
Supplementary files format and content: excel file include raw reads for each sample
Supplementary files format and content: excel file include TPM value for each sample

source_name: Prostate

growth_protocol: The PC-3 cells were cultured in a Dulbecco’s Modified Eagle Medium (DMEM) medium, 10% fetal bovine serum (FBS) and antibiotics then maintained in a humidified incubator at 37 °C in 5% CO2

extract_protocol:
RNA was haversted using TRIzol reagent
1μg total RNA or 10ng small RNA was used for library preparation. 3 ´SR Adaptor for Illumina was ligated to the small RNA using 3´ Ligation Enzyme. To prevent adaptor-dimer, the excess of 3 ´SR Adaptor were hybrid with SR RT Primer for Illumina. 5 ´SR Adaptor for Illumina was ligated to the small RNA using 5´ Ligation Enzyme and first strand cDNA was synthesized using ProtoScript II Reverse Transcriptase. Each sample was then amplified by PCR using P5 and P7 primers, the PCR product were purified by DNA clean beads. The purified products of 140- 160bp were recovered and cleaned up using PAGE, validated using an Agilent 2100 Bioanalyzer.

treatment_protocol: PC-3 was treated with Apelin (10 μg/mL) for 24 h in the culture medium.

value: Prostate

value: cancer cell

value: Apelin


title: control-PC3-2


title: control-PC3-1


title: FU-EPS-1_DOX_R1

value: Epithelioid Sarcoma


title: NEPS_DOX_R2


title: L-E14-13, Cerebellum, Ctrl

city: Edinburgh

first: Anna

last: Williams

state: Edinburgh

address: 5 Little France Drive, Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

data_processing:
FASTQ files were aligned with the human reference genome GRCh38 using 10X Genomics CellRanger v3.0.2. Velocyto (v.0.17.16) [32] was used to reintroduce unspliced mRNAs to the feature count matrix.
For .rds file: Quality control was carried out using Scater. Doublets were removed using scDblFinder. Data were normalised using Scran. Downstream analysis was carried out in Seurat: CCA was used to adjust for batch effects, PCA and UMAP were used for dimensional reduction. Clustering was performed as follows: A K-Nearest Neighbour (KNN) graph was built as basis for community detection using a Louvain algorithm.
Assembly: GRCh38
Supplementary files format and content: .fastq files: Index, R1 and R2 from L001 and L002 for each sample. .h5 files: Filtered and raw feature barcode matrix for each sample. .rds file: Seurat object containing all samples and annotations, .csv file: metadata corresponding to the Seurat object

molecule: nuclear RNA

source_name: CB

extract_protocol:
Extraction of nuclei was performed with the Nuclei PURE Prep Isolation Kit (Sigma-Aldrich, NUC201-1KT) as described in https://www.protocols.io/view/nuclei-isolation-from-human-cnssamples-using-nuc2-261genq1og47/v1
10X Genomics 3’ gene expression V3

value: CB


title: EBBSD031_14, Cerebellum, Ctrl


title: L-HD231, Cerebellum, HD


title: NBB13-076,  Caudate nucleus, HD

source_name: CN

value: CN


title: NBB17-124, Caudate nucleus, Ctrl


title: APLN-PC3-1


title: NBB16-056, Cerebellum, Ctrl


title: NBB17-124,Cerebellum, Ctrl


title: L-HD240, Hippocampus, HD

source_name: HC

value: HC


title: NBB95-310, Caudate nucleus, Ctrl


title: EBBSD031_14, Caudate nucleus, Ctrl


title: NBB17-124, Hippocampus, Ctrl


title: NBB17-005, Cerebellum, Ctrl


title: L-HD240, Frontal cortex, HD

source_name: FrCx

value: FrCx


title: NBB13-076,  Cerebellum, HD


title: L-HD241, Hippocampus,  HD


title: L-HD241, Frontal cortex,  HD


title: EBBSD031_14, Hippocampus, Ctrl


title: NBB17-060, Caudate nucleus, HD


title: NBB17-081, Hippocampus, HD


title: NBB17-060, Cerebellum, HD


title: L-HD241, Caudate nucleus,  HD


title: NBB17-081, Inferior frontal gyrus, HD

source_name: IFG

value: IFG


title: G-MDSCs, sham, POD4, rep3

city: Ramat Gan

first: Niv

last: Pencovich

address: 2 Derech Sheba

department: Surgery and transplantation

institute: Sheba medical center

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome using STAR  v2.4.2a
Counting proceeded over genes annotated in Ensembl gene annotations, using htseq-count
Assembly: GRCm38
Supplementary files format and content: Excel file includes the raw counts

source_name: Liver

extract_protocol:
G-MDSC from BALB/C mice livers were extracted at different time points (one, two, three and four days) after hepatectomy or sham operation, using magnetic-activated cell sorting (MACS). Briefly, livers were minced and incubated with digestion buffer [5% fetal bovine serum (FBS), 0.5mg/ml Collagenase VIII (Sigma Aldrich, St. Louis, Missouri; C2139) and 0.1mg/ml DNase I in PBS] for 45 min at 37°C. The cell suspension was passed through a 100µm strainer and centrifuged 3 times at 400 rpm for 5 min with the pellet discarded each time. The supernatant was then centrifuged at 1400 rpm for 5 min to obtain non-parenchymal cells. Pellets were treated with red blood cell lysis buffer and resuspended in MACS buffer (0.5% FBS, 2mM EDTA in PBS). CD11b+Ly6G+ cells were then separated sequentially using the MACS kit for G-MDSC isolation on LS and MS columns (Miltenyi Biotec) according to manufacturer's instructions. RNA was extracted using the QIAGEN RNAeasy mini-kit.
Inhouse poly A based RNA seq

treatment_protocol: 8 weeks old BALB/C male mice were subject to either 70% hepatectomy or a sham operation, in which only midline laparotomy was performed.

value: Liver

value: BALB/C

tag: Sex

value: Male

value: G-MDSCs

value: WT

value: Sham


title: NBB17-124, Inferior frontal gyrus, Ctrl


title: NBB17-060, Inferior frontal gyrus, HD


title: G-MDSCs, sham, POD3, rep3


title: NBB13-076,  Hippocampus, HD


title: Control

first: Ashiq

last: Masood

address: Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine

department: Hematology & Oncology

institute: IU School Of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggreagation was made using the Cell Ranger v6.1 with default setups.
Assembly: mm10
Supplementary files format and content: Tab seperated value files and matrix files

source_name: PDAC

extract_protocol:
Portions of the tumor tissues (~1g of tumor obtained in total from three animals of each group) were collected in a labeled C-tube with 5 ml of digesting media to isolate single cells from the tumor tissues. Digestion media is DMEM with 1% FBS, 1.5mg/ml collagenase D, 2000 U DNase I, and 25μg/ml of liberase. Tumors were manually excised into small pieces with sterile scissors into a C-tube containing digestion media. Tumors were dissociated twice on each tube using a gentle MACS dissociator followed by incubation at 370C for 15 mins while constantly shaking. The cell suspension (Miltenyi Biotec) was passed through a 100µm cell strainer into a 50 ml conical tube. The cell suspension was washed with DPBS and spun at 1700rpm (575g) for 5 mins. After several washes with DPBS, the cells were resuspended in an appropriate media for downstream analysis.
Viable tumor single cells were employed to produce scRNA-Seq libraries using a standard 10X genomics approach. After the filter, single-cell transcriptome results of mice were obtained.

value: PDAC

value: PBS and served as a control


title: GPH

description: 10x Genomics

value: group received GnP-H (G, 60mg/kg (I.P.);


title: G1

description: 10x Genomics

value: gemcitabine


title: H-P1

description: 10x Genomics

value: paricalcitol (P) and hydroxychloroquine (H)


title: G-MDSCs, sham, POD4, rep1


title: EBBSD025_13, Hippocampus, Ctrl


title: NBB95-310, Cerebellum, Ctrl


title: L-HD231, Hippocampus, HD


title: NBB95-310, Hippocampus, Ctrl


title: G-MDSCs, sham, POD3, rep1


title: L-HD240, Cerebellum, HD


title: G-MDSCs, sham, POD2, rep3


title: NBB16-056, Hippocampus, Ctrl


title: G-MDSCs, sham, POD2, rep2


title: NBB17-060, Hippocampus, HD


title: NBB16-056, Inferior frontal gyrus, Ctrl


title: G-MDSCs, sham, POD4, rep2


title: NBB17-005, Hippocampus, Ctrl


title: G-MDSCs, sham, POD1, rep3


title: NBB16-056, Caudate nucleus, Ctrl


title: G-MDSCs, sham, POD1, rep1


title: G-MDSCs, sham, POD1, rep2


title: G-MDSCs, hepatectomy, POD4, rep3

value: 70% Hepatectomy


title: EBBSD025_13, Inferior frontal gyrus, Ctrl


title: G-MDSCs, hepatectomy, POD3, rep3


title: G-MDSCs, hepatectomy, POD3, rep2


title: NBB13-076,  Inferior frontal gyrus, HD


title: NBB17-005, Caudate nucleus, Ctrl


title: NBB95-310, Inferior frontal gyrus, Ctrl


title: NBB17-005, Inferior frontal gyrus, Ctrl


title: G-MDSCs, sham, POD3, rep2


title: NBB17-081, Cerebellum, HD

value: CB


title: G-MDSCs, hepatectomy, POD4, rep1


title: G-MDSCs, hepatectomy, POD4, rep2


title: G-MDSCs, sham, POD2, rep1


title: L-HD241, Cerebellum,  HD


title: L-HD240, Caudate nucleus, HD

value: CN


title: G-MDSCs, hepatectomy, POD3, rep1


title: G-MDSCs, hepatectomy, POD2, rep3


title: G-MDSCs, hepatectomy, POD2, rep1


title: G-MDSCs, hepatectomy, POD2, rep2


title: EBBSD025_13, Caudate nucleus, Ctrl


title: H146 cells, PAX5 knocked down, rep3

city: Tianjin

first: Yujie

last: Hao

address: 22 Qixiangtai Road

institute: Tianjin Medical University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: SCLC cells

value: PAX5 knocked down

value: untreated


title: H146 cells, PAX5 knocked down, rep2


title: G-MDSCs, hepatectomy, POD1, rep3

value: Liver


title: H146 cells, PAX5 knocked down, rep1


title: G-MDSCs, hepatectomy, POD1, rep2

value: BALB/C


title: H146 cells, control, rep2


title: G-MDSCs, hepatectomy, POD1, rep1

value: Male


title: H146 cells, control, rep3


title: H146 cells, control, rep1