title: Untreated NCI-Meso63 tumor, rep 1

first: Mingming

last: Zhao

address: 9000 Rockville Pike

institute: national institutes of health

description:
Library name: Untreated_tumor1
10X Genomics

data_processing:
Base calling was performed using RTA 3.4.4, demultiplexing was performed using cellranger v8.0.0 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v8.0.0 (STAR 2.7.2a). Sequenced reads were aligned to a custom human GRCh38 and mouse GRCm39 reference sequence made by adding hYP218-scFv sequence to the refdata-gex-GRCh38_and_GRCm39-2024-A reference. UMI-adjusted aligned reads were used to generate a single cell barcode and gene expression matrix for downstream analysis.
Assembly: Custom human GRCh38 and mouse GRCm39 reference sequence made by adding hYP218-scFv sequence to the refdata-gex-GRCh38_and_GRCm39-2024-A reference.
Supplementary files format and content: Filtered matrix files (.h5).

source_name: intraperitoneal xenograft human tumor

growth_protocol: Pre-infusion product CAR-IL-15 iNK were in vitro expanded in the presence of LCL feeder cells, IL-2 and IL-21 for 7 days.

extract_protocol:
The pre-infusion product CAR-IL-15 iNK were harvested from in vitro expanded culture. The mouse peritoneal tumors were harvested in cold serum-free RPMI-1640 medium and total cells were isolated using tumor dissociation kit (Miltenyi Biotec) according to manufacturer’s instructions. Briefly, tumor tissues were digested in serum-free RPMI-1640 medium supplemented with human tumor dissociation kit enzymes (Miltenyi Biotec) at 37°C under continuous rotation for 90 min. Dissociated single cell suspensions were then filtered through a 70 μm mesh filter and pelleted at 300 × g for 5 minutes. The harvested pre-infusion CAR-IL-15 iNK products and the single cells isolated from the tumors were washed with PBS+0.04% BSA. Dead cells and debris were removed using Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101) following the manufacturer’s instructions.
Single cell suspensions were washed once with ice-cold PBS with 0.04% BSA by centrifugation at 350g and gently resuspended in fresh buffer. The cellular samples were loaded in the lane according to the 10X Genomics Chromium Next GEM Single Cell 5’ v2 (Dual Index) User Guide with a single capture lane per sample. The recovery was 6,000 cells per lane. Cell partitioning completed with a uniform emulsion consistency, and the reverse transcription PCR was run. All subsequent steps of library preparation and quality control were performed as described in the 10x Genomics user guide. Then the sequencing was performed on the NovaSeq 6000 system with the NovaSeq S2 Reagent kit v1.5 (100 cycles) following the cycling parameters: 26bp (read1), 10bp (index 1), 10bp (index2), 90bp (read2).

treatment_protocol: 8 single cell samples were prepared for scRNA-seq, including 2 samples of pre-infusion product, 3 samples of total cells isolated from the untreated tumors (individual mouse as one sample) and 3 samples of total cells isolated from the MSLN.CAR-IL-15 iNK-treated tumors (4 mice pooled as one sample).

value: intraperitoneal xenograft human tumor

tag: cell type

value: total cells isolated from tumor (human and mouse cells mixed)

value: Untreated


title: CAR-IL15 iNK treated NCI-Meso63 tumor, rep3

status: Public on Apr 09 2025

type: SRA

city: Bethesda

country: USA

description:
Library name: CARIL15iNK_treated_tumor3
10X Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: treatment

value: CAR-IL15 iNK treated


title: Untreated NCI-Meso63 tumor, rep 3

description:
Library name: Untreated_tumor3
10X Genomics


title: CAR-IL15 iNK treated NCI-Meso63 tumor, rep1

description:
Library name: CARIL15iNK_treated_tumor1
10X Genomics


title: CAR-IL15 iNK product, rep2

description:
Library name: CARIL15iNK_product2
10X Genomics

source_name: CAR-IL15 iNK pre-infusion product

value: CAR-IL15 iNK pre-infusion product

value: iPSC-NK cells, feeder cells

value: in vitro expanded with LCL feeder cells


title: CAR-IL15 iNK product, rep1

description:
Library name: CARIL15iNK_product1
10X Genomics


title: SEPSIS_patient_P8 (mRNA)

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

library_source: transcriptomic

data_processing:
Sequencing was performed on MGISeq-2000 or NovaSeq 6000 platform in a 100+100-base paired-end mode.
On NovaSeq 6000 platform, Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Mapped read counts for each gene-sample combination were quantified with featureCounts ( -M -O --fraction option) of subread-2.0.0 package.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read counts for each sample

source_name: blood

extract_protocol:
Toal RNA was harvested using PAXgene Blood RNA System (BD Biosciences, San Jose, CA).
Each cDNA was generated using a Clontech SMART-Seq HT Kit (Takara Clontech, Mountain View, CA, USA), and each library was prepared using a Nextera XT DNA Library Prep Kit (Illumina, San Diego, USA).

value: blood

tag: disease state


title: Healthy Bone Marrow Sample 2

city: Atlanta

first: Hope

last: Mumme

address: 1760 Haygood Dr NE

institute: Emory University

description:
Library name: HB2
10x Genomics

data_processing:
Raw scRNA-seq data was demultiplexed, aligned to human reference genome, and processed for single cell gene counting using the Cell Ranger Software from 10x Genomics (v7.0.0).
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab separated value files and matrix files

source_name: Bone marrow

extract_protocol:
Frozen BM were thawed viably using standardized protocol. Briefly the cells were thawed quickly (37C for ~2 minutes till a small ice crystal remains), and warm complete medium (RPMI1640, 10% heat inactivated FBS, 1x Penicillin. Streptomycin) was added gradually. The cells were pelleted (380g, RT, 5min), and washed one more time with complete medium, which was followed by one more wash with PBS containing BSA (0.04 to 1.0%). For cell multiplexing, cells were labelled with specific anti-human TotalSeq-B Hashtag antibodies (Biolegend) according to manufacturer’s protocol. The cells were resuspended in cell staining buffer (Biolegend) or PBS with1% BSA to get an optimal cell concentration of 700-1200 cells/µl.
The single cell RNA-seq libraries were prepared using the Chromium single cell 3’v2 reagent kits (10x Genomics), with CMO tagging. Libraries were assessed by Qubit Fluorometric Quantification (Thermo Fisher Scientific) and capillary electrophoresis on a TapeStation 4200 (Agilent), normalized and pooled at the molar ratio corresponding to the required reads for each library. The libraries were sequenced at 20,000 reads/per cell with a PE100 configuration over two lanes of an S4 flow cell on an Illumina NovaSeq 6000.

value: Bone marrow

tag: disease group

value: healthy

value: Bone marrow cells

tag: age

value: pediatric


title: WT-p13_rep2

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome mm10 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). Rsubread (Liao et al., Nucleic Acids Research, 2013) was was applied to calculate raw read counts.
Assembly: mm10
Supplementary files format and content: raw read counts from RNA-seq samples

organism: Mus musculus

source_name: Mammary gland

growth_protocol: RNA-seq was done for the mammary tissues at day 13 and 18 of pregnant (p13, p18) at 2-month-old age for wild-type and mutant mice carrying a point mutation in Stat5b-Y665.

extract_protocol:
Total RNA was extracted from frozen mammary tissue from mice and purified with RNeasy Plus Mini Kit (Invitrogen, 12183018A). Ribosomal RNA was removed from 1ug of total RNAs and cDNA was synthesized using SuperScript III (Invitrogen). Libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301) and paired-end sequencing was done with a HiSeq 3000 or Novaseq 6000 instrument (Illumina).
Libraries for sequencing were prepared using standard Illumina protocols.

value: Mammary gland

tag: strain

tag: Stage

value: day 13 of pregnancy (p13)

tag: genotype

value: WT


title: MDA-MB-231-DR cells,rep2

city: Lexington

first: Xiang

last: Song

state: Kentucky

address: Virginia Ave

institute: University of Kentucky

description: Library name: MDA-MB-231-DR cells,rep2

data_processing:
fastqc version 0.12.1
Assembly: hg38
Supplementary files format and content: gene_expression; FPKM, counts

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen).
RNA libraries for RNA-seq were prepared by Novagene.


title: Healthy Bone Marrow Sample 1

description:
Library name: HB1
10x Genomics


description: Library name: MDA-MB-231-DR cells treated with CYT,rep2

value: Cyperotundone (CYT)


description: Library name: MDA-MB-231-DR cells treated with CYT,rep3


description: Library name: MDA-MB-231-DR cells treated with CYT,rep1


title: L1-Input-rep2

description: Library name: Sample 4

library_source: genomic

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9). Quality filtering and alignment of the raw reads was done using Trimmomatic (version 0.36) and Bowtie (version 1.2.2) and Samtools (version 1.8), with the parameter ‘-m 1’ to keep only uniquely mapped reads, using the reference genome mm10. Homer30 (version 4.9.1) software was applied to generate bedGraph files, seperately. Integrative Genomics Viewer (version 2.3.98) was used for visualization with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools to remove duplicates. Homer software was applied  for the generation of bedGraph files.
Assembly: mm10
Supplementary files format and content: bedgraph of ChIP-seq

molecule: genomic DNA

growth_protocol: Mouse mammary gland tissues were harvested at day 13 and 18 of pregnant (p13, p18) of 2-month-old age for wild-type and mutant mice carrying a point mutation in Stat5b-Y665 and at day 10 of lactation (L10) after second pregnancy of Y665H mutant.

extract_protocol:
Chromatin was fixed with formaldehyde (1% final concentration) for 10min at room temperature, and then quenched with glycine (0.125 M final concentration). Samples were processed as previously described. The following antibodies were used for ChIP-seq: STAT5A (Santa Cruz Biotechnology, sc-271542), STAT5B (ThermoFisher scientific, 13-5300), NFIB (Sigma-Aldrich, HPA003956), H3K27ac (Abcam, ab4729) and RNA polymerase II (Abcam, ab5408). Libraries for next-generation sequencing were prepared and sequenced with a HiSeq 3000 or Novaseq 6000 instrument (Illumina). Libraries for sequencing were prepared using standard Illumina protocols.
Libraries for sequencing were prepared using standard Illumina protocols.

value: day 1 of lactation (L1)

tag: chip-seq antibody

value: IgG


title: TNBC_C3

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description: Library name: S3HCCC

data_processing:
Using STAR software [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/], FASTQ files were aligned to Genome data base (hG38) and read counts obtained for each gene
For the detection of diﬀerentially expressed genes, the following method has been applied: DESeq2 [https://www.ncbi.nlm.nih.gov/pubmed/25516281]: a shrinkage estimation has been applied for dispersions and calculation of expression fold changes, to improve stability and interpretability of estimates
Assembly: hG38
Supplementary files format and content: A matrix is generated as a plain text file (*.txt), in which each column is a sample, each row is a gene (ensembl_ID), and in each cell indicates the number of raw counts obtained by STAR per sample and gene.

molecule: polyA RNA

growth_protocol: Cell lines were cultured with RPMI-1640 medium supplemented with 10% Fetal Bovine Serum and Penicillin-Streptomycin-Amphotericin B solution (Gibco, Waltham, MA USA) at 37 °C and 5% CO2 in a humidified atmosphere

extract_protocol:
Total RNA of adhered cells was isolated with the Total RNA purification kit (Norgen, Thorold, ON, Canada) and the quantity and integrity of the RNA was evaluated using the QubitTM RNA HS Assay Kit (Invitrogen, Waltham, MA, USA) and Agilent RNA 600 NanoChips (Agilent Technologies, Santa Clara, CA, USA)
mRNA stranded libraries were prepared following “TruSeq Stranded mRNA Sample Preparation Guide (Part # 15031058 Rev. E)” using the “TruSeq® Stranded mRNA Library Prep” kit  (Illumina Inc. Cat. # 20020594) and TruSeq RNA CD Index Plate (96 Indexes, 96 Samples) (Illumina Inc. Cat. # 20019792)

treatment_protocol: Cells were treated with Ocoxin dilutedin RPMI-1640 medium supplemented  with 1% Fetal Bovine Serum  (Gibco, Waltham, MA USA) for 48 hours.

value: Triple Negative Breast Cancer

value: Ocoxin 1:700


title: TNBC_O1

description: Library name: S1HCCO


title: COAD_O2

description: Library name: S2SWO

source_name: Colon

value: Colon

value: Colorectal adenocarcinoma


title: COAD_O3

description: Library name: S3SWO


title: TNBC_C1

description: Library name: S1HCCC


title: TNBC_C2

description: Library name: S2HCCC


title: COAD_O1

description: Library name: S1SWO


title: CAR-IL15 iNK treated NCI-Meso63 tumor, rep2

description:
Library name: CARIL15iNK_treated_tumor2
10X Genomics

value: intraperitoneal xenograft human tumor

value: total cells isolated from tumor (human and mouse cells mixed)

value: CAR-IL15 iNK treated


title: MDA-MB-231-DR cells,rep1

description: Library name: MDA-MB-231-DR cells,rep1


title: MDA-MB-231-DR cells,rep3

description: Library name: MDA-MB-231-DR cells,rep3


title: TNBC_O3

description: Library name: S3HCCO


title: PAAD_O3

description: Library name: S3BxO

source_name: Pancreas

value: Pancreas

value: Pancreatic adenocarcinoma

value: Ocoxin 1:500


title: PRAD_O1

description: Library name: S_04

source_name: Prostate

value: Prostate

value: LNCaP

value: Prostate adenocarcinoma

value: Ocoxin 1:50


title: CTL019 CAR T cells, Cas9 SpyFi mRNA 4KO, End of CAE, ND602, RNA-seq

city: Philadelphia

first: Regina

middle: M.

last: Young

state: Pennsylvania

address: 3400 Civic Center BLVD

department: CCI

institute: University of Pennsylvania

description: Library name: ND602 CTL019 Cas9 SpyFi mRNA 4KO End of CAE RNA

data_processing:
Sequence reads were trimmed using Trimmomatic v0.36
Reads were aligned to the Homo sapiens GRCh38 reference genome with the STAR aligner v2.5.2b
Unique gene hit counts were obtained using featureCounts from the Subread package v1.5.2, counting only unique reads within exon regions
Assembly: GRCh38
Supplementary files format and content: counts.txt generated by DEseq2

source_name: primary human T cells

growth_protocol: Primary human T cells were maintained in CTS Optimizer media in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Live, CD45+, GFP- cells were isolated via FACS and preserved in RNAprotect Cell Reagent with storage at -80C until processing. Total RNA was extracted from fresh frozen cell pellets using the Qiagen RNeasy Plus Universal Mini Kit.
cDNA synthesis was conducted using the SMART-Seq HT kit (Takara). Indexed libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: CD19 CAR T cells were stimulated every 3 to 4 days with CD19⁺ NALM6 leukemia cells for at least 2 weeks. The effector-to-target (E:T) was re-adjusted to 1:4 at every re-stimulation point.

value: primary human T cells

value: lentivirally transduced with the anti-CD19-4-1BB-zeta CAR (CTL019) construct; KO of TRAC, B2M, CIITA and PVR

value: Chronic antigen exposure assay (D19)


title: CTL019 CAR T cells, Cas9 SpyFi Protein 4KO, D0, ND602, RNA-seq

description: Library name: ND602 CTL019 Cas9 SpyFi Protein 4KO D0 RNA

value: End of CAR T expansion (D0)


title: CTL019 CAR T cells, Cas9 SpyFi mRNA 4KO, D0, ND602, RNA-seq

description: Library name: ND602 CTL019 Cas9 SpyFi mRNA 4KO D0 RNA


title: CTL019 CAR T cells, Cas9 SpyFi Protein 4KO, End of CAE, ND602, RNA-seq

description: Library name: ND602 CTL019 Cas9 SpyFi Protein 4KO End of CAE RNA


title: CTL019 CAR T cells, Cas9 WT mRNA 4KO, D0, ND602, RNA-seq

description: Library name: ND602 CTL019 Cas9 WT mRNA 4KO D0 RNA


title: CTL019 CAR T cells, ABE mRNA 4KO, End of CAE, ND602, RNA-seq

description: Library name: ND602 CTL019 ABE8e mRNA 4KO End of CAE RNA

value: lentivirally transduced with the anti-CD19-4-1BB-zeta CAR (CTL019) construct; KO of CD3E, B2M, CIITA and PVR


title: CTL019 CAR T cells, No EP, En of CAE, ND602, RNA-seq

description: Library name: ND602 CTL019 No EP End of CAE RNA

value: lentivirally transduced with the anti-CD19-4-1BB-zeta CAR (CTL019) construct


title: CTL019 CAR T cells, Cas9 WT mRNA 4KO, End of CAE, ND602, RNA-seq

description: Library name: ND602 CTL019 Cas9 WT mRNA 4KO End of CAE RNA


title: CTL019 CAR T cells, Cas9 SpyFi Protein 4KO, End of CAE, ND541, RNA-seq

description: Library name: ND541 CTL019 Cas9 SpyFi Protein 4KO End of CAE RNA

value: Chronic antigen exposure assay (D16)


title: UTD T cells, No EP, D0, donor ND602, RNA-seq

description: Library name: ND602 UTD No EP D0 RNA


title: CTL019 CAR T cells, ABE mRNA 4KO, D0, ND602, RNA-seq

description: Library name: ND602 CTL019 ABE8e mRNA 4KO D0 RNA


title: CTL019 CAR T cells, Cas9 SpyFi Protein 4KO, D0, ND541, RNA-seq

description: Library name: ND541 CTL019 Cas9 SpyFi Protein 4KO D0 RNA


title: CTL019 CAR T cells, No EP, D0, ND602, RNA-seq

description: Library name: ND602 CTL019 No EP D0 RNA


title: CTL019 CAR T cells, Cas9 SpyFi mRNA 4KO, End of CAE, ND541, RNA-seq

description: Library name: ND541 CTL019 Cas9 SpyFi mRNA 4KO End of CAE RNA


title: CTL019 CAR T cells, Cas9 SpyFi mRNA 4KO, D0, ND541, RNA-seq

description: Library name: ND541 CTL019 Cas9 SpyFi mRNA 4KO D0 RNA


title: CTL019 CAR T cells, Cas9 WT mRNA 4KO, End of CAE, ND541, RNA-seq

description: Library name: ND541 CTL019 Cas9 WT mRNA 4KO End of CAE RNA


title: CTL019 CAR T cells, Cas9 WT mRNA 4KO, D0, ND541, RNA-seq

description: Library name: ND541 CTL019 Cas9 WT mRNA 4KO D0 RNA


title: CTL019 CAR T cells, ABE mRNA 4KO, D0, ND541, RNA-seq

description: Library name: ND541 CTL019 ABE8e mRNA 4KO D0 RNA


title: CTL019 CAR T cells, ABE mRNA 4KO, End of CAE, ND541, RNA-seq

description: Library name: ND541 CTL019 ABE8e mRNA 4KO End of CAE RNA


title: PRAD_O3

description: Library name: S_06


title: CTL019 CAR T cells, No EP, D0, ND541, RNA-seq

description: Library name: ND541 CTL019 No EP D0 RNA


title: CTL019 CAR T cells, No EP, En of CAE, ND541, RNA-seq

description: Library name: ND541 CTL019 No EP End of CAE RNA


title: CTL019 CAR T cells, Cas9 SpyFi Protein 4KO, End of CAE, ND502, RNA-seq

description: Library name: ND502 CTL019 Cas9 SpyFi Protein 4KO End of CAE RNA


title: CTL019 CAR T cells, Cas9 SpyFi Protein 4KO, D0, ND502, RNA-seq

description: Library name: ND502 CTL019 Cas9 SpyFi Protein 4KO D0 RNA


title: UTD T cells, No EP, D0, donor ND541, RNA-seq

description: Library name: ND541 UTD No EP D0 RNA


title: CTL019 CAR T cells, Cas9 SpyFi mRNA 4KO, D0, ND502, RNA-seq

description: Library name: ND502 CTL019 Cas9 SpyFi mRNA 4KO D0 RNA


title: CTL019 CAR T cells, Cas9 SpyFi mRNA 4KO, End of CAE, ND502, RNA-seq

description: Library name: ND502 CTL019 Cas9 SpyFi mRNA 4KO End of CAE RNA


title: CTL019 CAR T cells, Cas9 WT mRNA 4KO, D0, ND502, RNA-seq

description: Library name: ND502 CTL019 Cas9 WT mRNA 4KO D0 RNA


title: CTL019 CAR T cells, ABE mRNA 4KO, End of CAE, ND502, RNA-seq

description: Library name: ND502 CTL019 ABE8e mRNA 4KO End of CAE RNA


title: CTL019 CAR T cells, Cas9 WT mRNA 4KO, End of CAE, ND502, RNA-seq

description: Library name: ND502 CTL019 Cas9 WT mRNA 4KO End of CAE RNA


title: COAD_C3

description: Library name: S3SWC

value: Colon

value: Colorectal adenocarcinoma

value: Ocoxin 1:700


title: CTL019 CAR T cells, ABE mRNA 4KO, D0, ND502, RNA-seq

description: Library name: ND502 CTL019 ABE8e mRNA 4KO D0 RNA


title: CTL019 CAR T cells, No EP, End of CAE, ND502, RNA-seq

description: Library name: ND502 CTL019 No EP End of CAE RNA


title: UTD T cells, No EP, D0, donor ND502, RNA-seq

description: Library name: ND502 UTD No EP D0 RNA


title: CTL019 CAR T cells, No EP, D0, ND502, RNA-seq

description: Library name: ND502 CTL019 No EP D0 RNA


title: CTL019 CAR T cells, Cas9 SpyFi Protein 4KO, D0, TMP511, ATAC-seq

description: Library name: TMP511 CTL019 Cas9 SpyFi Protein 4KO D0 ATAC

data_processing:
Sequence reads were trimmed using Trim Galore in the NextFlow ATAC-seq pipeline v2.1.2
Reads were aligned to the Homo sapiens GRCh38 reference genome using the Bowtie2 aligner in the NextFlow ATAC-seq pipeline v2.1.2
Read duplicates were marked usiing picard in the NextFlow ATAC-seq pipeline v2.1.2
Reads were filtered using SAMtools, BEDTools, BAMTools and Pysam in the NextFlow ATAC-seq pipeline v2.1.2
Normalised bigWig files scaled to 1 million mapped reads were generated using BEDTools and bedGraphToBigWig in the NextFlow ATAC-seq pipeline v2.1.2
Assembly: GRCh38
Supplementary files format and content: peaks files generated by peak calling software

extract_protocol:
Cryopreserved vials of cells were thawed, washed, and treated with DNase I (Life Technologies) to eliminate genomic DNA contamination. Following cell lysis and cytosol removal, nuclei were treated with Tn5 transposase (Illumina, Cat. #20034197) for 30 minutes at 37 °C and purified using the MinElute PCR Purification Kit (Qiagen, Cat. #28004) to generate tagmented DNA.
Tagmented DNA was barcoded with the Nextera Index Kit v2 (Illumina, Cat. #FC-131-2001) and amplified via PCR, followed by SPRI bead cleanup to obtain purified DNA libraries.


title: CTL019 CAR T cells, Cas9 SpyFi mRNA 4KO, D0, TMP511, ATAC-seq

description: Library name: TMP511 CTL019 Cas9 SpyFi mRNA 4KO D0 ATAC


title: CTL019 CAR T cells, Cas9 WT mRNA 4KO, D0, TMP511, ATAC-seq

description: Library name: TMP511 CTL019 Cas9 WT mRNA 4KO D0 ATAC


title: PAAD_C2

description: Library name: S2BxC

value: Pancreas


title: CTL019 CAR T cells, ABE mRNA 4KO, D0, TMP511, ATAC-seq

description: Library name: TMP511 CTL019 ABE8e mRNA 4KO D0 ATAC


title: CTL019 CAR T cells, No EP, D0, TMP511, ATAC-seq

description: Library name: TMP511 CTL019 No EP D0 ATAC


title: CTL019 CAR T cells, Cas9 SpyFi Protein 4KO, D0, ND632, ATAC-seq

description: Library name: ND632 CTL019 Cas9 SpyFi Protein 4KO D0 ATAC


title: CTL019 CAR T cells, Cas9 SpyFi mRNA 4KO, D0, ND632, ATAC-seq

description: Library name: ND632 CTL019 Cas9 SpyFi mRNA 4KO D0 ATAC


title: CTL019 CAR T cells, Cas9 WT mRNA 4KO, D0, ND632, ATAC-seq

description: Library name: ND632 CTL019 Cas9 WT mRNA 4KO D0 ATAC


title: CTL019 CAR T cells, ABE mRNA 4KO, D0, ND632, ATAC-seq

description: Library name: ND632 CTL019 ABE8e mRNA 4KO D0 ATAC


title: CTL019 CAR T cells, No EP, D0, ND632, ATAC-seq

description: Library name: ND632 CTL019 No EP D0 ATAC


title: CTL019 CAR T cells, Cas9 SpyFi mRNA 4KO, D0, ND602, ATAC-seq

description: Library name: ND602 CTL019 Cas9 SpyFi mRNA 4KO D0 ATAC


title: CTL019 CAR T cells, Cas9 WT mRNA 4KO, D0, ND602, ATAC-seq

description: Library name: ND602 CTL019 Cas9 WT mRNA 4KO D0 ATAC


title: CTL019 CAR T cells, ABE mRNA 4KO, D0, ND602, ATAC-seq

description: Library name: ND602 CTL019 ABE8e mRNA 4KO D0 ATAC


title: CTL019 CAR T cells, No EP, D0, ND602, ATAC-seq

description: Library name: ND602 CTL019 No EP D0 ATAC


title: CTL019 CAR T cells, Cas9 SpyFi Protein 4KO, D0, ND589, ATAC-seq

description: Library name: ND589 CTL019 Cas9 SpyFi Protein 4KO D0 ATAC


title: PAAD_C1

description: Library name: S1BxC

value: Pancreatic adenocarcinoma


title: CTL019 CAR T cells, Cas9 WT mRNA 4KO, D0, ND589, ATAC-seq

description: Library name: ND589 CTL019 Cas9 WT mRNA 4KO D0 ATAC


title: CTL019 CAR T cells, No EP, D0, ND589, ATAC-seq

description: Library name: ND589 CTL019 No EP D0 ATAC


title: CTL019 CAR T cells, Cas9 SpyFi mRNA 4KO, D0, ND589, ATAC-seq

description: Library name: ND589 CTL019 Cas9 SpyFi mRNA 4KO D0 ATAC


title: CTL019 CAR T cells, ABE mRNA 4KO, D0, ND589, ATAC-seq

description: Library name: ND589 CTL019 ABE8e mRNA 4KO D0 ATAC


title: CTL019 CAR T cells, Cas9 SpyFi Protein 4KO, D0, ND502, ATAC-seq

description: Library name: ND502 CTL019 Cas9 SpyFi Protein 4KO D0 ATAC


title: CTL019 CAR T cells, Cas9 SpyFi mRNA 4KO, D0, ND502, ATAC-seq

description: Library name: ND502 CTL019 Cas9 SpyFi mRNA 4KO D0 ATAC


title: CTL019 CAR T cells, ABE mRNA 4KO, D0, ND502, ATAC-seq

description: Library name: ND502 CTL019 ABE8e mRNA 4KO D0 ATAC


title: CTL019 CAR T cells, Cas9 WT mRNA 4KO, D0, ND502, ATAC-seq

description: Library name: ND502 CTL019 Cas9 WT mRNA 4KO D0 ATAC


title: CTL019 CAR T cells, No EP, D0, ND502, ATAC-seq

description: Library name: ND502 CTL019 No EP D0 ATAC


title: TNBC_O2

description: Library name: S2HCCO

value: Mammary gland

value: Triple Negative Breast Cancer


title: PAAD_O2

description: Library name: S2BxO

value: Ocoxin 1:500


title: Untreated NCI-Meso63 tumor, rep 2

description:
Library name: Untreated_tumor2
10X Genomics

value: intraperitoneal xenograft human tumor

value: total cells isolated from tumor (human and mouse cells mixed)

value: Untreated


title: GBM28 cells, OncoD-3

city: Augusta

first: Balveen

last: Kaur

state: GA

address: CN-3205, 1410 Laney-Walker Blvd

department: Pathology

institute: Augusta University

description: Library name: Sample 15

data_processing:
Dual-indexed i5 and i7 paired-end libraries were sequenced on the NovaSeq 6000 system (Illumina, Inc.) with an average of 40-50 million reads per sample.
The RNA-seq data analysis started with QC using FastQC (version: v0.12.1) to assess the raw reads, followed by Cutadapt (version: 2.8) to trim Illumina Universal Adapter sequences.
The cleaned reads were aligned to the Homo sapiens (human) genome assembly GRCh38 (hg38) reference genome using STAR aligner (version: 2.7.3a), generating BAM files. Using R (version: 4.4.1), read count data from the BAM files were merged, and genes with zero counts were excluded.
Functional enrichment analysis was carried out using clusterProfiler. Visualization was done using ggplot2 and heatmaps were generated using the heatmap package to illustrate gene expression patterns.
hg38
Assembly: Homo sapiens, GRCh38 (hg38)
Supplementary files format and content: CSV files with raw gene expression values.

growth_protocol: GBM12 and GBM28 cells were maintained as adherent cells in DMEM supplemented with 2% FBS and Pen/Strep at 37C and 5% CO2

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using RiboGone and SMART (Switching Mechanism At 5' end of RNA Template) technologies to generate Illumina-compatible libraries without the need for adapter ligations.

treatment_protocol: GBM cells were seeded in 12-well plates and infected after 18h with OncoD (0.01 MOI) or PBS. Media containing virus was removed after 1h of infection and replaced with fresh media. Cells were harvested after 24h.

value: Glioblastoma

value: OncoD-treated


title: CTL019 CAR T cells, Cas9 SpyFi Protein 4KO, D0, ND602, ATAC-seq

description: Library name: ND602 CTL019 Cas9 SpyFi Protein 4KO D0 ATAC

value: primary human T cells

value: lentivirally transduced with the anti-CD19-4-1BB-zeta CAR (CTL019) construct; KO of TRAC, B2M, CIITA and PVR

value: End of CAR T expansion (D0)


title: GBM28 cells, PBS-3

description: Library name: Sample 11

value: PBS-treated


title: PAAD_O1

description: Library name: S1BxO


title: GBM28 cells, OncoD-4

description: Library name: Sample 16


title: GBM28 cells, OncoD-2

description: Library name: Sample 14


title: GBM28 cells, OncoD-1

description: Library name: Sample 13


title: GBM28 cells, PBS-4

description: Library name: Sample 12


title: GBM28 cells, PBS-2

description: Library name: Sample 10


title: GBM28 cells, PBS-1

description: Library name: Sample 9


title: PAAD_C3

description: Library name: S3BxC


title: GBM12 cells, OncoD-3

description: Library name: Sample 7


title: GBM12 cells, OncoD-4

description: Library name: Sample 8


title: GBM12 cells, OncoD-1

description: Library name: Sample 5


title: GBM12 cells, PBS-4

description: Library name: Sample 4


title: COAD_C2

description: Library name: S2SWC

value: Colon


title: GBM12 cells, PBS-1

description: Library name: Sample 1


title: GBM12 cells, PBS-2

description: Library name: Sample 2


title: GBM12 cells, PBS-3

description: Library name: Sample 3


title: hCMEC/D3 cells, 0 μM rutin, 24 h, bio rep 2

city: Beijing

first: Zhao-Wei

last: Sun

address: 27# Taiping Road

country: China

institute: Beijing Institute of Basic Medical Sciences

description:
Library name: C2
Column name in gene_count.txt and gene_fpkm.txt: C2

data_processing:
Rawdata(raw reads) of fastq format were firstly processed through fastp software. 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. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built 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. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis for two conditions/groups was performed using the DESeq2 R package (1.20.0).
Assembly: hg38
Supplementary files format and content: gene_count.txt: raw counts for each sample
Supplementary files format and content: gene_fpkm.txt: FPKM value for each sample

growth_protocol: The human brain microvascular endothelial cell line hCMEC/D3 were maintained in hCMEC/D3-specific medium (Procell, China) in a humidified incubator at 37 °C containing 5% CO2.

extract_protocol:
Total RNA was extracted via TRIzol reagent, and RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Rutin was dissolved in DMSO and diluted with sterile phosphate-buffered saline (PBS) to the indicated concentrations (0 and 25 μM). The cells were collected for further analysis following 24 h of treatment.

value: human brain capillary  endothelial cells

value: 0 μM rutin for 24 h


title: hCMEC/D3 cells, 25 μM rutin, 24 h, bio rep 2

description:
Library name: R2
Column name in gene_count.txt and gene_fpkm.txt: R2

value: 25 μM rutin for 24 h


title: SUDHL5 cells, 1 nM TCIP3 treatment, 4 hours, bio rep 3

city: Stanford

first: Sai

last: Gourisankar

state: CA

address: 240 Pasteur Dr, Rm 4700

department: Chemical Systems Biology

institute: Stanford

description: Library name: _T3_RNA_15

data_processing:
Raw reads were checked for quality using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were trimmed from adapters using cutadapt using parameters cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -b AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --nextseq-trim=20 --minimum-length 1.
Transcripts were quantified using kallisto against the human Gencode v33 indexed transcriptome and annotations.
Assembly: human Gencode v33
Supplementary files format and content: tab-delimited files include TPM values for each Sample

extract_protocol:
Cells were plated at 1M/mL and harvested in TRIsure (Bioline 38033). RNA was extracted using Direct-zol RNA MicroPrep columns (Zymo R2062) treated with DNAseI.
For sequencing library preparation, rRNA was depleted (NEB E7400) and total RNA prepared into paired-end libraries (NEB E7765) and indexed (NEB E7335). Library size distributions were confirmed using an Agilent Bioanalyzer and High Sensitivity DNA reagents (Agilent 5067) and concentrations determined by qPCR

treatment_protocol: Treated at 1million cells/mL density at indicated timepoints and doses with final DMSO concentration of 0.1%

value: DLBCL

value: WT

value: 1 nM TCIP3

tag: time

value: 4 hours


title: hCMEC/D3 cells, 0 μM rutin, 24 h, bio rep 3

description:
Library name: C3
Column name in gene_count.txt and gene_fpkm.txt: C3


title: hCMEC/D3 cells, 25 μM rutin, 24 h, bio rep 1

description:
Library name: R1
Column name in gene_count.txt and gene_fpkm.txt: R1


title: SUDHL5 cells, 1 nM TCIP3 treatment, 4 hours, bio rep 1

description: Library name: _T3_RNA_13


title: SUDHL5 cells, 1 nM TCIP3 treatment, 4 hours, bio rep 2

description: Library name: _T3_RNA_14


title: SUDHL5 cells, 1 nM TCIP3 treatment, 2 hours, bio rep 3

description: Library name: _T3_RNA_12

value: 2 hours


title: hCMEC/D3 cells, 0 μM rutin, 24 h, bio rep 1

description:
Library name: C1
Column name in gene_count.txt and gene_fpkm.txt: C1


title: SUDHL5 cells, 1 nM TCIP3 treatment, 1 hour, bio rep 3

description: Library name: _T3_RNA_9

value: 1 hour


title: SUDHL5 cells, 1 nM TCIP3 treatment, 2 hours, bio rep 2

description: Library name: _T3_RNA_11


title: SUDHL5 cells, 1 nM TCIP3 treatment, 2 hours, bio rep 1

description: Library name: _T3_RNA_10


title: SUDHL5 cells, 1 nM TCIP3 treatment, 1 hour, bio rep 2

description: Library name: _T3_RNA_8


title: SUDHL5 cells, 1 nM TCIP3 treatment, 0.5 hours, bio rep 2

description: Library name: _T3_RNA_5

value: 0.5 hours


title: SUDHL5 cells, 1 nM TCIP3 treatment, 0.5 hours, bio rep 3

description: Library name: _T3_RNA_6


title: SUDHL5 cells, DMSO treatment, 4 hours, bio rep 3

description: Library name: _T3_RNA_3


title: SUDHL5 cells, 1 nM TCIP3 treatment, 0.5 hours, bio rep 1

description: Library name: _T3_RNA_4


title: hCMEC/D3 cells, 25 μM rutin, 24 h, bio rep 3

description:
Library name: R3
Column name in gene_count.txt and gene_fpkm.txt: R3


title: SUDHL5 cells, DMSO treatment, 4 hours, bio rep 2

description: Library name: _T3_RNA_2


title: SUDHL5 cells, DMSO treatment, 4 hours, bio rep 1

description: Library name: _T3_RNA_1


title: SUDHL5 cells, Input, 1 nM TCIP3 treatment, 1 hour, bio rep 1

description: Library name: DHL5_5b

data_processing:
The data quality was checked using fastq (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The raw reads were trimmed from adapters with cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT).
Raw reads were aligned to hg38 human genome assembly using bowtie2 (parameters: --local --maxins 1000).
Low quality reads, duplicated reads and reads with multiple alignments were removed using samtools and Picard (https://broadinstitute.github.io/picard/).
macs2 was used to map position of peaks with FDR cutoff of 0.05.
Bedtools was used to find a consensus set of peaks by merging peaks across multiple conditions (bedtools merge), count number of reads in peaks (bedtools intersect -c) and generate genome coverage (bedtools genomecov -bga).
deepTools was used to generate coverage densities across multiple experimental conditions (deeptools computeMatrix and deeptools plotProfile) and to generate bigwig files (deeptools bamCoverage), where reads mapping to ENCODE blacklist regions were excluded.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Cells were washed in PBS containing TCIP3 or DMSO and crosslinked for 11 min in CiA Fix Buffer (50 mM HEPES pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl) with addition of formaldehyde to a final concentration of 1%. The crosslinking reaction was quenched by glycine added at 0.125 M final concentration. Crosslinked cells were centrifuged at 1,000 x g for 5 min. Nuclei were prepared by 10 min incubation of resuspended pellet in CiA NP-Rinse 1 buffer (50 mM HEPES pH 8.0, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IPEGAL CA-630, 0.25% Triton X100) followed by wash in CiA NP-Rinse 2 buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl). The pellet was resuspended in CiA Covaris Shearing Buffer (0.1% SDS,1 mM EDTA pH 8.0, 10 mM Tris HCl pH 8.0) with protease inhibitors and sonicated for 20 min with a Covaris E220 sonicator (Peak Power 140, Duty Factor 5.0, Cycles/Burst 200). The distribution of fragments was confirmed with D1000 Tapestation or by agarose gel electrophoresis. 20 µg of chromatin per ChIP was used with anti-H3K27ac antibodies (abcam ab4729) and anti-H2Bk20ac antibodies (Cell Signaling D709W), with 40 ng Drosophila chromatin (53083, ActiveMotif) spiked in. After overnight incubation at 4 C in IP buffer (50 mM HEPES pH 7.5, 300mM NaCl, 1mM EDTA, 1% Triton X100, 0.1% sodium deoxycholic acid salt (DOC), 0.1% SDS), IPs were washed twice with IP buffer, once with DOC buffer (10 mM Tris pH 8, 0.25 M LiCl, 0.5% IPEGAL CA-630, 0.5% sodium deoxycholic acid salt (DOC), 1mM EDTA), and once with 10 mM Tris/1 mM EDTA buffer (TE) pH 8. IPs and inputs were reverse-crosslinked in TE/0.5% SDS/0.5 µg/µL proteinase K for 55 C /3 h then 65 C /18 h, then DNA was purified using a PCR cleanup spin column (Takara #74609).
Paired-end sequencing libraries were constructed using an NEBNext Ultra II DNA kit (E7645S) and indexed (NEB E7335). Library size distributions were confirmed using an Agilent Bioanalyzer and High Sensitivity DNA reagents (Agilent 5067) and concentrations determined by qPCR.


title: SUDHL5 cells, H2BK20ac ChIP, 1 nM TCIP3 treatment, 2 hours, bio rep 2

description: Library name: DHL5_16

tag: chip antibody

value: H2BK20ac (Cell Signaling D709W)


title: SUDHL5 cells, H2BK20ac ChIP, 1 nM TCIP3 treatment, 1 hour, bio rep 2

description: Library name: DHL5_14


title: SUDHL5 cells, H2BK20ac ChIP, 1 nM TCIP3 treatment, 2 hours, bio rep 1

description: Library name: DHL5_15


title: COAD_C1

description: Library name: S1SWC

value: Colorectal adenocarcinoma

value: Ocoxin 1:700


title: SUDHL5 cells, H2BK20ac ChIP, 1 nM TCIP3 treatment, 1 hour, bio rep 1

description: Library name: DHL5_13


title: SUDHL5 cells, H2BK20ac ChIP, 1 nM TCIP3 treatment, 0.25 hours, bio rep 2

description: Library name: DHL5_12


title: SUDHL5 cells, H2BK20ac ChIP, 1 nM TCIP3 treatment, 0.25 hours, bio rep 1

description: Library name: DHL5_11


title: SUDHL5 cells, H2BK20ac ChIP, DMSO treatment, 2 hours, bio rep 1

description: Library name: DHL5_9


title: GBM12 cells, OncoD-2

description: Library name: Sample 6

value: Glioblastoma

value: OncoD-treated


title: PRAD_O2

description: Library name: S_05

value: Prostate

value: LNCaP

value: Prostate adenocarcinoma

value: Ocoxin 1:50


title: SUDHL5 cells, H3K27ac ChIP, 1 nM TCIP3 treatment, 2 hours, bio rep 2

description: Library name: DHL5_8

value: H3K27ac (abcam ab4729)


title: SUDHL5 cells, H3K27ac ChIP, 1 nM TCIP3 treatment, 2 hours, bio rep 1

description: Library name: DHL5_7

value: DLBCL


title: SUDHL5 cells, H3K27ac ChIP, 1 nM TCIP3 treatment, 1 hour, bio rep 1

description: Library name: DHL5_5


title: SUDHL5 cells, H3K27ac ChIP, 1 nM TCIP3 treatment, 1 hour, bio rep 2

description: Library name: DHL5_6


title: SUDHL5 cells, 1 nM TCIP3 treatment, 1 hour, bio rep 1

description: Library name: _T3_RNA_7

value: WT


title: SUDHL5 cells, H3K27ac ChIP, 1 nM TCIP3 treatment, 0.25 hours, bio rep 2

description: Library name: DHL5_4


title: SUDHL5 cells, H3K27ac ChIP, DMSO treatment, 2 hours, bio rep 2

description: Library name: DHL5_2


title: SUDHL5 cells, H2BK20ac ChIP, DMSO treatment, 2 hours, bio rep 2

description: Library name: DHL5_10


title: PRAD_C3

description: Library name: S_03


title: SUDHL5 cells, H3K27ac ChIP, DMSO treatment, 2 hours, bio rep 1

description: Library name: DHL5_1


title: Pt19 Relapse L

city: Aarhus

first: Hakim

last: Ben Abdallah

state: Denmark

address: Palle Juul-Jensens Boulevard 45

department: Dermatology and Venerology

country: Denmark

institute: Aarhus University Hospital

description: Library name: 30

data_processing:
R package Subread (version 2.10.3)
Raw reads were aligned to the human reference genome (GRCh38.p14 primary assembly)
Gene counts were obtained by uniquely aligned unambiguous reads
Assembly: GRCh38.14 primary assembly
Supplementary files format and content: Rawcounts.xlsx

source_name: Skin

extract_protocol:
Total RNA was isolated using the SV 96 Total RNA Isolation System (Promega) according to the manufacturer’s instructions
RNA sequencing library was prepared with 100 ng of total RNA using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
2x150 Sequence mode to obtain at approx. 20 million read pairs

value: Skin


title: PRAD_C2

description: Library name: S_02


title: Pt19 End-of-treatment L

description: Library name: 29


title: PRAD_C1

description: Library name: S_01


title: Pt19 Baseline L

description: Library name: 28


title: Pt19 Baseline NL

description: Library name: 27


title: Pt14 End-of-treatment L

description: Library name: 26


title: SUDHL5 cells, Input, DMSO treatment, 2 hours, bio rep 1

description: Library name: DHL5_1b


title: Pt14 Baseline L

description: Library name: 25


title: Pt13 End-of-treatment L

description: Library name: 22


title: Pt14 Baseline NL

description: Library name: 24


title: Pt13 Baseline L

description: Library name: 21


title: Pt13 Baseline NL

description: Library name: 20


title: Pt9 L Relapse

description: Library name: 19


title: Pt9 End-of-treatment L

description: Library name: 18


title: Pt9 Baseline L

description: Library name: 17


title: SUDHL5 cells, H3K27ac ChIP, 1 nM TCIP3 treatment, 0.25 hours, bio rep 1

description: Library name: DHL5_3


title: Pt9 Baseline NL

description: Library name: 16


title: Pt8 Baseline NL

description: Library name: 12


title: Pt8 Baseline L

description: Library name: 13


title: Pt4 Baseline L

description: Library name: 10


title: Pt4 End-of-treatment L

description: Library name: 11


title: Pt8 L Relapse

description: Library name: 15


title: Pt3 L End-of-treatment

description: Library name: 7


title: Pt4 Baseline NL

description: Library name: 9


title: Pt1 End-of-treatment L

description: Library name: 3


title: Pt3 NL Baseline

description: Library name: 5


title: Pt1 Baseline L

description: Library name: 2


title: Pt1 Baseline NL

description: Library name: 1


title: P3-com

city: Wuhan

first: wang

last: boyu

address: No. 1095 Jiefang Dadao, Hubei Province, Jiaokou District, Wuhan City

department: Tongji Hospital

institute: Huazhong University of Science and Technology

data_processing:
Based-calling software, version, parameters
Data filtering steps
Read alignment software, version, parameters
Assembly: mm10
Supplementary files format and content: NGS (Next Generation Sequencing) technology uses high-throughput sequencers (e.g. Illumina NovaSeq6000) to sequence cDNA. The original image file is first obtained, and then through base identification and error filtering, the original sequencing fragment, which can be used for analysis, is finally obtained, which is called Reads. The results are stored in fastq format, which includes the base composition information of the sequence and the corresponding sequence quality information. _1, _2.

source_name: CD4+T cells

extract_protocol:
total RNA was extracted using MJzol Animal RNA Isolation Kit (Majorivd) and according to the standard operating procedures provided by the manufacturer. Purification was performed using the RNAClean XP Kit (Beckman Coulter) and RNase-Free DNase Set (QIAGEN). RNA integrity was detected by Agilent 2100 Bioanalyzer/Agilent 4200 TapeStation (Agilent technologies). The total amount and purity of RNA were determined by Qubit 2.0 fluorescence quantifier (Thermo Fisher Scientific) and NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific).
The mRNA sequencing library was constructed by mRNA separation, fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, end repair, 3 'end A addition, splicing, enrichment and other steps of the purified Total RNA. Qubit 2.0 fluorescence quantifier (Thermo Fisher Scientific) was used to detect the library concentration, and Agilent 4200 TapeStation (Agilent technologies) was used to detect the library fragment distribution.

value: CD4+T cells


title: Pt3 L Baseline

description: Library name: 6


title: Pt1 Relapse

description: Library name: 4


title: P2-com


title: Pt13 L Relapse

description: Library name: 23


title: P4-com


title: P3-b

value: anti-CD3/28 plus IL-15


title: P1-b


title: P2-b


title: P1-com


title: lung tissue L8

city: Shanghai

first: Zilu

last: Wen

address: No. 2901, Caolang Road, Jinshan District, Shanghai

institute: SHANGHAI PUBLIC HEALTH CLINICAL CENTER

data_processing:
Illumina Casava1.7
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: lung tissue with background or low 18F-FDG avidity

extract_protocol:
Total RNA of each lung sample was extracted by using TRIzol Reagent (Invitrogen, US) and further purified using the RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, USA), NanoDrop (Thermo Fisher Scientific Inc., USA) and 1% agarose gel. Total RNA (1 μg) with the value of RNA integrity number (RIN) > 7 was used for library preparation of the following next generation sequencing, with the NEBNext Ultra II Directional RNA Library Prep. Kit for Illumina. The rRNA was depleted from total RNA using Ribo-Zero™ rRNA removal Kit (Illumina, USA), and cDNA libraries were generated following manufacture’s protocols.
Libraries with different indices were multiplexed and loaded on Illumina HiSeq instrument (Illumina, USA) for 2 × 150 paired-end sequencing according to manufacturer’s instructions.

value: human lung cells

value: Extracting Total RNA from Digestive Lung Tissue


title: lung tissue L9

value: lung tissue with background or low 18F-FDG avidity


title: lung tissue L7


title: Pt8 End-of-treatment L

description: Library name: 14


title: lung tissue H9

source_name: lung tissue with 18F-FDG avidity

value: lung tissue with 18F-FDG avidity


title: lung tissue L6


title: lung tissue H8


title: Pt3 L Relapse

description: Library name: 8


title: lung tissue H6


title: lung tissue H7


title: PANC-1_siB_5

first: Aditi

last: Jain

state: PA

address: 1015 Walnut Street

department: Surgery

institute: Thomas Jefferson University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. 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 1 reads were aligned to the reference genome using Hisat2 v2.0. featureCounts [3] 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.
Assembly: Homo Sapiens(GRCh37/hg19)
Supplementary files format and content: tab-delimited text files include raw counts for each samples
Supplementary files format and content: tab-delimited text files include FPKM counts for each samples

growth_protocol: Cells were grown in humidified atmosphere with 5%CO2 and at 37 degree celsius

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library

treatment_protocol: Cells were transfected with siRNAs for 48 hours and then harvested for RNA

value: Pancreatic cancer cell

value: BARD1 knockdown

value: BARD1 siRNA


title: PANC-1_siB_3


title: PANC-1_siSCR_5

value: SCR siRNA


title: PANC-1_siB_1


title: P4-b


title: siMiaPaCa-2_siBARD_4


title: PANC-1_siSCR_1


title: siMiaPaCa-2_siBARD_2


title: siMiaPaCa-2_siBARD_1


title: PANC-1_siSCR_3


title: siMiaPaCa-2_siBARD_3


title: lung tissue L9

data_processing:
Illumina Casava1.7
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: human lung cells


title: lung tissue L8


title: siMiaPaCa-2_siSCR_2


title: siMiaPaCa-2_siSCR_3


title: siMiaPaCa-2_siSCR_1


title: lung tissue L5


title: PANC-1_siSCR_4


title: lung tissue L7


title: siMiaPaCa-2_siSCR_4


title: lung tissue L4


title: lung tissue L6


title: PANC-1_siB_4


title: lung tissue L2


title: lung tissue L1


title: lung tissue L3


title: lung tissue H8


title: lung tissue H9


title: lung tissue H6


title: PLM_136_R2_Day 7

type: protein

city: COLUMBUS

first: Joseph

middle: S

last: Bednash

state: OH

address: 473 W 12th Avenue, DHLRI 509

department: Medicine

institute: Ohio State University

description: SS-2338065_v4.1_CitratePlasma.hybNorm.medNormInt.plateScale.calibration.anmlQC.qcCheck.anmlSMP.adat

hyb_protocol: Per SomaLogic protocols. Full details available at PMID: 23023596 and PMID: 23139410

scan_protocol: SomaLogic uses an Agilent custom microarray and the Agilent SureScan Microarray Scanner. Full details available at PMID: 23023596 and PMID: 23139410

data_processing: Raw data undergoes several normalization and calibration steps, including hybridization normalization where each microarray is scaled according to the signal of 12 control aptamers to account for technical variability in individual microarrays, interpolate median signal normalization and plate scaling, calibration of each aptamer to the median value observed in Calibrator Control samples, and adaptive normalization to a reference using Adaptive Normalization by Maximum Likelihood (ANML) to adjust for inter-sample variability in total signal within and between runs.

label: SOMAmer reagent

molecule: protein

source_name: Plasma, COVID-19 ARDS

extract_protocol: Whole blood was collected in sodium citrate vacutainer tubes, followed by immediate centrifugation to separate blood components. Plasma was stored as 500 microliter aliquots and stored at -80 degrees celsius prior to shipping for analysis by SomaLogic.

tag: subject

tag: run

value: Day 7

tag: sofa

tag: Sex

value: Female

tag: bmi

tag: hospital mortality

value: No


title: lung tissue H7

tag: tissue

tag: cell type


title: lung tissue H4

tag: treatment


title: lung tissue H5


title: PLM_133_R2_Day 7

label_protocol: Per SomaLogic protocols. Full details available at PMID: 23023596 and PMID: 23139410

value: Male

value: Yes


title: PLM_136_R1_Day 1

description: SS-2214759_v4.1_EDTA_Plasma.hybNorm.medNormInt.plateScale.calibration.anmlQC.qcCheck.anmlSMP.adat

value: Day 1


title: PLM_133_R1_Day 1


title: PLM_128_R1_Day 1


title: lung tissue H3

value: WT


title: PLM_128_R2_Day 7


title: lung tissue H2


title: Library 4 - 12 Samples ADT

city: Bronx

first: Deepa

last: Rastogi

address: 3415 Bainbridge Ave

institute: Albert Einstein College of Medicine

description: A04,B04,C04,D04,A05,B05,C05,D05,A06,B06,C06,D06 ADT

data_processing:
cellRanger for quality control, alignment, and count quantification
Seurat package in R used for demultiplexing and analysis
Assembly: hg38
Supplementary files format and content: barcodes and features tsv files, matrix mtx files, and csv feature reference files

source_name: Primary CD4+ T Cells

extract_protocol:
N/A - Single Cell
10X Genomics - CITESeq

value: Primary CD4+ T Cells


title: PLM_127_R1_Day 1


title: PLM_127_R2_Day 7


title: Library 4 - 12 Samples GEX

description: A04,B04,C04,D04,A05,B05,C05,D05,A06,B06,C06,D06 GEX


title: lung tissue H1


title: PLM_119_R2_Day 7


title: Library 3 - 4 Samples ADT

description: A03,B03,C03,D03 ADT


title: Library 4 - 12 Samples HTO

description: A04,B04,C04,D04,A05,B05,C05,D05,A06,B06,C06,D06 HTO


title: PLM_118_R2_Day 7


title: Library 3 - 4 Samples HTO

description: A03,B03,C03,D03 HTO


title: PLM_108_R1_Day 1


title: Library 3 - 4 Samples GEX

description: A03,B03,C03,D03 GEX


title: PLM_101_R2_Day 7


title: Library 2 - 4 Samples HTO

description: A02,B02,C02,D02 HTO


title: Library 2 - 4 Samples ADT

description: A02,B02,C02,D02 ADT


title: PLM_097_R2_Day 7


title: PLM_101_R1_Day 1


title: Library 1 - 4 Samples ADT

description: A01,B01,C01,D01 ADT


title: PLM_118_R1_Day 1


title: Library 2 - 4 Samples GEX

description: A02,B02,C02,D02 GEX


title: Library 1 - 4 Samples HTO

description: A01,B01,C01,D01 HTO


title: Library 1 - 4 Samples GEX

description: A01,B01,C01,D01 GEX


title: PLM_097_R1_Day 1


title: VC1mM_6

city: Kizugawa

first: Akari

last: Kuwano

state: Kyoto

address: 6-5-4 Kunimidai

institute: Rohto Pharmaceutical Co., Ltd.

data_processing:
To analyse the bisulfite sequencing results, the quality of the raw paired-end sequence reads was assessed with FastQC (version 0.11.7). Low-quality (< 20 bases) or 5'-end 10-base sequences and adapter sequences were trimmed by Trim Galore (version 0.5.0) with the options "-q 20 --phred33 --clip_R1 10 --clip_R2 10 --paired". The trimmed reads were aligned to the reference genome using methylpy (version 1.4.6) with the options "--remove-clonal True --trim-reads FALSE". Annotation was performed with in-house software. The number of methylated cytosines in the 1,000 bases of nonoverlapping windows across the whole genome was estimated by the tileMethylCounts function from the methylKit (version 1.10.0) package. Normalization was performed using the normalizeCoverage function in methylKit. Bases with less than 10× read coverage and bases with more than 99.9th percentile coverage in each sample (likely PCR artifacts with abnormally high coverage) were removed by the filterByCoverage function of methylKit. All the samples were then merged by using the unite function in methylKit with the destrand = FALSE option. To identify DMRs, differential methylation was calculated using the calculate DiffMeth function of methylKit. Regions with a q value less than 0.01 and a methylation change greater than 25% between the groups were considered significant DMRs. A cluster analysis heatmap of the DMRs and DEGs was generated with ComplexHeatmap (version 2.12.1). To perform an integrated analysis of the gene expression and DNA methylation profiles, normalization of the gene expression levels was performed using the robust multiarray average (RMA) method with oligo software, and the expression levels were corrected among the samples. The program limma was used for comparisons between the groups.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: human epidermal equivalent

growth_protocol: Normal human epidermal keratinocytes (#420811D) were purchased from Japan Tissue Engineering Co., Ltd. (Aichi, Japan). Cryopreserved keratinocytes were thawed and suspended in cAssayulture  mMedium containing fetal bovine serum (#402250, Japan Tissue Engineering Co., Ltd.). Cell aliquots were seeded into 24-well culture inserts (Corning Co., Ltd., NY, USA) placed in multiwell culture plates in which each well had been filled with 1.5 mL of culture medium and incubated in a humidified atmosphere of 5% CO2 at 37°C. Keratinocytes seeded in the culture inserts were submerged when the medium was present in the inserts. After 24 h of incubation, the keratinocytes were exposed to the air‒liquid interface to construct an epidermal equivalent by removing the both medium in the 24-well culture inserts and multiwell culture plates

extract_protocol:
Genomic DNA was extracted from a half portion of human epidermal equivalents using the Monarch Genomic DNA Purification Kit (New England Biolabs, Ipswich, MA, US). The integrity and quality of the DNA were evaluated using a NanoDrop One and TapeStation (Agilent Technologies) prior to analysis.
Bisulfite treatment was performed by using a Swift Biosciences Accel-NGS® Methyl-Seq DNA Library Kit (Swift Biosciences, Ann Arbor, Michigan, US) to generate WGBS libraries. The amplified libraries were sequenced using an Illumina Nova Seq 6000 with 150 bp paired-end reads following standard Illumina sequencing protocols.

treatment_protocol: Human epidermal equivalents treated with or without 1.0 mM VC for 14 days

value: human epidermal equivalent

tag: cell line

value: keratinocyte

value: with 1mM VC


title: PLM_090_R2_Day 7

tag: age


title: VC1mM_5


title: VC1mM_4


title: PLM_078_R2_Day 7


title: PLM_119_R1_Day 1


title: PLM_078_R1_Day 1


title: VC1mM_1


title: VC1mM_2


title: VC1mM_3


title: PLM_075_R2_Day 7


title: PLM_076_R1_Day 1


title: VC0mM_6

value: without VC


title: PLM_075_R1_Day 1


title: VC0mM_3


title: VC0mM_4


title: PLM_066_R2_Day 7


title: PLM_059_R2_Day 7


title: PLM_097_R2_Day 1


title: VC0mM_1


title: siH1-0_2, replicate 4

city: Düsseldorf

first: Vera

middle: Helena

last: Jepsen

address: Moorenstraße 5

country: Germany

institute: University Hospital Düsseldorf

description:
AS-865986-LR-66165
processed_data_REH_RNAseq_cpm.txt

data_processing:
Analysis of fastq files was performed by using the Partek Flow software (Partek Incorporated, St. Louis, MO, USA). After assessing the read quality, a trimming step was performed (both ends: 13 bases at the 5’ end and 1 base at the 3’ end). After trimming, reads were aligned to the hg38 genome using the STAR v2.4.1d aligner. Unaligned reads were further processed using Bowtie 2 v2.2.5 aligner. Aligned reads were combined and expression was quantified against the Ensembl database (release 84) by the Partek Expectation-Maximization algorithm. Partek flow default settings were used in all analyses.
One technical replicate of siH1-0_1 was excluded from the analysis since it did not pass quality control.
Assembly: hg38
Supplementary files format and content: text files include CPM values for each sample

source_name: REH (DSMZ, #ACC 22)

growth_protocol:
hiPSCs were cultured at 37 °C and 5% CO2 on Geltrex-coated (Thermo Fisher Scientific) culture plates in mTeSR Plus (Stemcell Technologies) and were passaged in aggregates every 3-5 days using Versene solution (Thermo Fisher Scientific) according to the manufacturer’s instructions. hiPSC lines were cultured for a maximum of 40 passages.
Reh cells were maintained at 37 °C and 5% CO2 in RPMI GlutaMAX (Thermo Fisher Scientific) with 20% fetal bovine serum (Biowest).

extract_protocol:
HW8 and ChiPSC12 hiPSCs of similar passage number (±2 passages) were lysed on ice using RLT buffer (Qiagen) and detached by scraping. RNA was isolated using the RNeasy Mini kit (Qiagen) with on-column DNA digestion (Qiagen).
REH cells were transfected with siRNA and RNA was extracted after 48 hours. Cells were washed with PBS and dissolved in RLT buffer (Qiagen). RNA was isolated using the RNeasy Mini kit (Qiagen) with on-column DNA digestion (Qiagen).
Barcoded libraries were prepared from 0.5 µg of total RNA using the TruSeq RNA Sample Preparation v2 kit (low-throughput protocol, Illumina) and quantified with the Bioanalyzer system (Agilent). 7.5 pM denatured libraries were used as input for cBot (Illumina) and subjected to deep sequencing using the HiSeq 4000 (Illumina) for 101 cycles, with an additional 7 cycles for index reading.

treatment_protocol: 1 x 10^6 REH cells were transfected with 200 pmol of each siRNA pool (siCtrl, siH1-0_1, siH1-0_2) in a 100 µl nucleocuvette using the 4D Nucleofector system (Lonza, SF solution, program DS-150).

value: REH (DSMZ, #ACC 22)

value: B cell precursor leukemia

value: human pseudodiploid karyotype, ETV6::RUNX1 fusion gene

value: female


title: PLM_090_R1_Day 1


title: siH1-0_2, replicate 3

description:
AS-865985-LR-66165
processed_data_REH_RNAseq_cpm.txt


title: siH1-0_2, replicate 2

description:
AS-865984-LR-66165
processed_data_REH_RNAseq_cpm.txt


title: PLM_058_R1_Day 1


title: PLM_058_R2_Day 1


title: siH1-0_2, replicate 1

description:
AS-865983-LR-66165
processed_data_REH_RNAseq_cpm.txt


title: PLM_076_R2_Day 7


title: PLM_057_R2_Day 7


title: siH1-0_1, replicate 4

description:
AS-865982-LR-66165
processed_data_REH_RNAseq_cpm.txt


title: siH1-0_1, replicate 3

description:
AS-865981-LR-66165
processed_data_REH_RNAseq_cpm.txt


title: PLM_057_R1_Day 1


title: siH1-0_1, replicate 2

description:
AS-865980-LR-66165
processed_data_REH_RNAseq_cpm.txt


title: PLM_053_R1_Day 1


title: siCtrl, replicate 4

description:
AS-865978-LR-66165
processed_data_REH_RNAseq_cpm.txt


title: PLM_053_R2_Day 7


title: VC0mM_5


title: PLM_075_R2_Day 1


title: siCtrl, replicate 3

description:
AS-865977-LR-66165
processed_data_REH_RNAseq_cpm.txt


title: PLM_051_R2_Day 7


title: siCtrl, replicate 2

description:
AS-865976-LR-66165
processed_data_REH_RNAseq_cpm.txt


title: PLM_051_R1_Day 1


title: PLM_048_R2_Day 7


title: VC0mM_2


title: PLM_066_R1_Day 1


title: PLM_059_R1_Day 1


title: siCtrl, replicate 1

description:
AS-865966-LR-66165
processed_data_REH_RNAseq_cpm.txt


title: ChiPSC12, ETV6::RUNX1, clone 1, replicate 2

description:
AS-595586-LR-56201
processed_data_iPSC_RNAseq_cpm.txt

source_name: Cellartis Human iPS Cell Line 12 (ChiPSC12, Takara, #Y00280)

value: human induced pluripotent stem cells (hiPSC)

value: male


title: PLM_048_R2_Day 1


title: ChiPSC12, ETV6::RUNX1, clone 1, replicate 3

description:
AS-595587-LR-56202
processed_data_iPSC_RNAseq_cpm.txt

value: Cellartis Human iPS Cell Line 12 (ChiPSC12, Takara, #Y00280)


title: PLM_058_R2_Day 7

description: SS-2338065_v4.1_CitratePlasma.hybNorm.medNormInt.plateScale.calibration.anmlQC.qcCheck.anmlSMP.adat

value: Day 7

value: Female

value: No


title: ChiPSC12, ETV6::RUNX1, clone 1, replicate 1

description:
AS-595585-LR-56201
processed_data_iPSC_RNAseq_cpm.txt


title: PLM_048_R1_Day 1

description: SS-2214759_v4.1_EDTA_Plasma.hybNorm.medNormInt.plateScale.calibration.anmlQC.qcCheck.anmlSMP.adat

value: Day 1

value: Male

value: Yes


title: PLM_045_R1_Day 1


title: PLM_045_R2_Day 7


title: PLM_044_R2_Day 7


title: ChiPSC12, WT, replicate 3

description:
AS-589029-LR-56201
processed_data_iPSC_RNAseq_cpm.txt


title: ChiPSC12, WT, replicate 1

description:
AS-589027-LR-56200
processed_data_iPSC_RNAseq_cpm.txt


title: PLM_043_R1_Day 1


title: PLM_044_R1_Day 1


title: HW8, ETV6::RUNX1, clone 2, replicate 2

description:
AS-589025-LR-56200
processed_data_iPSC_RNAseq_cpm.txt

source_name: HW8 (National Cancer Institute, NIH)

value: HW8 (National Cancer Institute, NIH)


title: PLM_036_R2_Day 7


title: HW8, ETV6::RUNX1, clone 2, replicate 3

description:
AS-589026-LR-56200
processed_data_iPSC_RNAseq_cpm.txt


title: HW8, ETV6::RUNX1, clone 2, replicate 1

description:
AS-589024-LR-56200
processed_data_iPSC_RNAseq_cpm.txt


title: PLM_036_R1_Day 1


title: HW8, ETV6::RUNX1, clone 1, replicate 3

description:
AS-589023-LR-56199
processed_data_iPSC_RNAseq_cpm.txt


title: PLM_035_R1_Day 1


title: PLM_035_R2_Day 7


title: PLM_019_R1_Day 1


title: HW8, ETV6::RUNX1, clone 1, replicate 1

description:
AS-589021-LR-56199
processed_data_iPSC_RNAseq_cpm.txt


title: HW8, ETV6::RUNX1, clone 1, replicate 2

description:
AS-589022-LR-56199
processed_data_iPSC_RNAseq_cpm.txt


title: HW8, WT, replicate 3

description:
AS-589020-LR-56199
processed_data_iPSC_RNAseq_cpm.txt


title: HW8, WT, replicate 2

description:
AS-589019-LR-56198
processed_data_iPSC_RNAseq_cpm.txt


title: PLM_014_R2_Day 7


title: PLM_014_R1_Day 1


title: PLM_011_R2_Day 7


title: NCI-H1299 cells, KO-IGF2BP3, #2

city: Linhai, Zhejiang

first: Jiapei

last: Ding

state: Zhejiang

address: Xi Men Street No.150

department: Department of Radiation Oncology

institute: Taizhou Hospital of Wenzhou Medical University

data_processing:
After using Cutadapt to filter out unqualified sequences (sequencing joints, low quality sequences, etc.) from the original Data to obtain Clean Data, the reference genome is compared using Hisat2. According to the comparison results of Hisat2, The transcript was reconstructed using StringTie and the expression levels of all genes in each sample were calculated.
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: GRCh38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: NCI-H1299 cells

extract_protocol:
NCI-H1299 was obtained from the Cell Bank of the Chinese Academy of Sciences (Shanghai, China). The cells were grown and maintained at 37°C in a humid atmosphere with and 5% CO2 and were cultured in Gibco’s RPMI 1640 Medium (Thermo Fisher, Schwerte, Germany) supplemented with 10% FBS and 1% PAA. CHOPCHOP (https://chopchop.rc.fas.harvard.edu/) and CRISPR design (http://crispr.mit.edu/) were used to design two single guide RNAs (sgRNA, Supplementary Table 3) targeted to the BsmBI of IGF2BP3 (NCBI GeneID 10643).  Annealed oligonucleotides were ligated into LentiCrisprv2 (GENECARE, GC010100605). The plasmids were sequenced to confirm successful ligation. For transfection, 4*105 293T cells were plated overnight in antibiotic-free medium and then transfected with 4µg of LentiCrisprv2 using Lipofectamine 3000. After high speed centrifugation, supernatant was collected and frozen at -80 ° C. NCI-H1299 cells were then infected with the supernatant, and selected under puromycin (2.0 µg/ml) for 48 hours and subsequently plated onto 96 well plates (10 cells/ml). Single cell colonies were expanded for RNA extraction, protein extraction and cryopreservation. The knockout efficiency was validated by western blot analysis, demonstrating successful knockout of IGF2BP3 at the protein levels in NCI-H1299 . Total RNA was isolated from IGF2BP3 knockout and control NCI-H1299 cells using TRIzol Reagent. RNA sequencing (RNA-seq) analysis was performed at Lian Chuan Biotech Inc. (Hangzhou, China).
After using Cutadapt to filter out unqualified sequences (sequencing joints, low quality sequences, etc.) from the original Data to obtain Clean Data, the reference genome is compared using Hisat2. According to the comparison results of Hisat2, The transcript was reconstructed using StringTie and the expression levels of all genes in each sample were calculated.

value: NCI-H1299 cells

value: LUAD cells

value: IGF2BP3 knockout


title: PLM_011_R1_Day 1


title: NCI-H1299 cells, KO-IGF2BP3, #3

growth_protocol: The cells were grown and maintained at 37°C in a humid atmosphere with and 5% CO2 and were cultured in Gibco’s RPMI 1640 Medium (Thermo Fisher, Schwerte, Germany) supplemented with 10% FBS and 1% PAA.


title: PLM_010_R2_Day 7


title: ChiPSC12, WT, replicate 2

description:
AS-589028-LR-56201
processed_data_iPSC_RNAseq_cpm.txt


title: PLM_010_R1_Day 1


title: NCI-H1299 cells, KO-IGF2BP3, #1


title: NCI-H1299 cells, KO-NC, #2

value: control


title: PLM_009_R2_Day 7


title: PLM_009_R1_Day 1


title: NCI-H1299 cells, KO-NC, #1


title: PLM_003_R2_Day 7


title: Eosinophils, D07_EVEN_076

city: San Diego

first: Gregory

last: Seumois

address: 9420 Athena Cir, La Jolla

institute: La Jolla Institute for immunology

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.1.2 (-S --fr)
Filtered reads were mapped against the human GRCh38 reference using STAR(v 2.6.1c )
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ-lite v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using featureCounts program (v1.6.5)  and features with 0 counts across all samples were removed
Assembly: GRCh38
Supplementary files format and content: count matrix with rows as genes and columns as samples

source_name: Eosinophils, E-cig vapor extract with PEG and Glycerin, no nicotine (EVEneg)

growth_protocol: We used primary cell eosinophils isolated directly from blood - No growth procedure was applied

extract_protocol:
At the end of incubation, cells were washed once with 10 ml of PBS (Phosphate Buffer Saline (pH 7.4) and centrifuged at 400 x g for 5 minutes at 4 ˚C. Supernatant was discarded and cell pellet immediately resuspended in 1 ml of Quiazol cell lysis solution (Quiagen). Cell were lysed following the steps described in Rosales et al ,2018 and stroed at - 80 ˚ C till completion of the study and sample collection. RNA extraction was performed unsing miRNAeasy Kit as recommended by manufacterer including DNAse I treatment. Quality of RNA was assess by capillary electrophoresis (Fragment Analyzer), and quantified by qPCR for B2M gene, a stable house keeping gene (Rosales et al. 2018). Tot RNA was stored in -80 ˚C.
Roughly 10 nanograms of purified RNA was amplified according to the Smart-seq2 protocol (Picelli et al. 2023, Rosales et al. 2018). Using poly-dT oligos, mRNA was captured and reverse transcribed into full-length cDNA. The cDNA was then amplified by PCR for 13 cycles. It was then purified using AMPure XP magnetic beads with a 0.8:1 ratio (Beckman Coulter) by an automated platform (Epimotion5075, Eppendorf). Next, 500 picograms of cDNA was used to prepare NextEra XT sequencing libraries with dual indexing(NextEra XT DNA Library Prep Kit # FC-131-1096 and IDT 8bp UDI Index Kits for illumina ).  Whole-transcriptome and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Quality control steps were included to determine cDNA quality and quantity as well as to optimize the number of PCR cycles needed, and fragment size. The libraries which passed quality control were pooled and sequenced on the Illumina Sequencing Novaseq6000 platform. Libraries were sequenced to a depth of roughly > 8 million 100 x 100 bp Pair-ended reads per sample (Novaseq XP 4-lane kit v1.5; Illumina).
RNA-seq 100 x 100 Paired-end sequencing reads

treatment_protocol: Eosinophils were isolated from blood using magnetic negative selection following the protocol outlined in Akuthota et al. (2012) and cultured at a concentration of 1 million cells/ml in conditioned culture medium for 48 hours at 37°C with 5% CO2.  Four different conditioned culture media were employed, including a negative control (NT) composed of RPMI1640 supplemented with 10% fetal bovine serum, human recombinant Interleukin-5 (IL-5) at 1 ng/ml, penicillin (500 ng/ml), and streptomycin (500 ng/ml). The remaining three conditioned culture media were "vaped" according to the procedure by Corriden et al. (2020) and supplemented with 10% fetal bovine serum, human recombinant Interleukin-5 (IL-5) at 1 ng/ml, penicillin (500 ng/ml), and streptomycin (500 ng/ml) right before to use. Three E-cigarette vapor extract conditioned media were prepared: EB medium composed solely of RPMI 1640, EVE+ containing "vaped" propylene glycol (PEG) and glycerin (Gly) in a 70:30 vol:vol ratio with nicotine at 59 mg/ml, and EVE– lacking nicotine. Preparation involved the vaping of e-Cigarette loading liquid containing PEG/Gly with or without nicotine, collecting the vapor into RPMI 1640 culture medium, and filtering the conditioned media for sterility using a 0.22 µm Millex-MP disposable polyethersulfone syringe filter (Millipore) before storage at -80°C.

value: Blood

value: primary cell

value: Eosinophil

tag: donor

value: EVEneg


title: A10

city: hefei

first: Xiaoke

last: Yang

address: Sanlian street

department: Department of Rheumatology and Immunology

institute: First Affiliated Hospital of Anhui Medical University

description:
Library name: sample5
FPKM.A10

data_processing:
Raw data;Clean Data (fastq format) Remove low quality reads and adapter [software:Cutadapt,FASTQC];Map the reads of each sample to the reference gename [software: tophat] Transcripts Assembly [gtf format) Assemble each sample independently [software: StringTiel]  Merged all assemblies to create a single merged gtf [software: StringTle]  Merged all assemblies to create a single merged gtf [software: gffcompara]  Transcripts exprossion profilos (mRNAs, IncRNAs,.l [software: StringTie]
Candidate IncRNAs ;Remove unqualified transcripts Length s 200 and covernees3; Ditferent expression known mRNAs, known IncRNAs and novel nshoas [Taofkware: Ballgown]
Assembly: GRCh38.p12
Supplementary files format and content: FPKM values for each Sample

source_name: blood

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen,CA,USA) following the manufacturer's procedure. The total RNA quantity and punity were analysis of Bioanalyzer 2100(Agilent, CA,USA) with RIN number >7.0. Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(illumina. San Diego, USA). And then we performed the single end sequencing (36bp or 50bp ) on an Illumina Hiseq2500 at the LC-B10 /Hangzhou, China) following the vendar's recommended protocol
Whole transcriptome sequencing requires the construction of two sequencing libraries, a small RNA library and a strand-specific library with ribosomal RNA depletion, and then sequencing on the machine. The length of the small RNA is short, generally less than 50 nt, and the sequencing strategy is 50 SE. The other three types of RNA sequences are generally larger than 200, usually more than 1000, and up to tens of thousands, and 150PE sequencing libraries are constructed by fragmentation. Finally, miRNA sequence information can be obtained from small RNA libraries, and mRNA, lncRNA, and circRNA sequence information can be obtained from strand-specific libraries of deribosomes.

value: blood

value: PBMC

tag: sample group

value: HCs


title: Eosinophils, D07_EVEP_076

description: 70_by_30_and_6mg_per_mlnicotine_number_076_28

source_name: Eosinophils, E-cig vapor extract with PEG and Glycerin, with nicotine (EVEpos)

value: Female

value: EVEPos


title: PLM_003_R1_Day 1

value: Day 1


title: A6

description:
Library name: sample4
FPKM.A6


title: PLM_019_R2_Day 7

value: Day 7

value: Male

value: No


title: Eosinophils, D07_EB_076

source_name: Eosinophils, Extract Buffer (EB)

value: ExtractBuffer


title: XR5

description:
Library name: sample2
FPKM.XR5

value: rheumatoid arthritis (RA)


title: Eosinophils, D07_NT_076

source_name: Eosinophils, No Treatment (NT)

value: NoTreatment


title: U937-282-A

first: Jia

middle: bing

last: Li

address: 197, Ruijin Er Street

institute: Shanghaijiaotong university

description: U937 cell line expressed p53-R282W mutation treated with ATO

data_processing:
The raw reads were initially processed using FastQC (v0.10.1) for quality control;
adapter sequences and poor-quality reads were removed using Cutadapt (v1.9.1)
Quality-filtered reads were then aligned to the Mus musculus genome (GRCm38) using HISAT2 (v2.0.1)
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS
Total RNA was isolated using TRIzol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: condition

tag: genotype

value: R282W Mutation

value: ATO


title: PLM_002_R1_Day 1

tag: time


title: XR4

description:
Library name: sample1
FPKM.XR4


title: U937-282-C

description: U937 cell line expressed p53-R282W mutation treated with PBS

value: PBS


title: PLM_002_R2_Day 7

description: SS-2338065_v4.1_CitratePlasma.hybNorm.medNormInt.plateScale.calibration.anmlQC.qcCheck.anmlSMP.adat


title: NCI-H1299 cells, KO-NC, #3

value: NCI-H1299 cells

value: LUAD cells

value: control


title: Eosinophils, D06_EVEP_075

description: 70_by_30_and_6mg_per_mlnicotine_number_075_24

value: Blood

value: primary cell

value: Eosinophil


title: scRNA_Nfib_OE_replicate4

city: Martinsried

first: Christian

last: Mayer

address: Am Klopferspitz 18

institute: Max Planck Institute for Biological Intelligence

description: Library name: Sample 48

data_processing:
Mapping and demultiplexing were performed for all experiments using Cellranger (v8.0.1) with the custom reference genome.
Dataset filtering and preliminary analysis were conducted using Seurat.
Assembly: mm10
Supplementary files format and content: Expression matrix

source_name: ganglionic eminence, cortex, striatum

extract_protocol:
Mouse embryo brains were dissected and dissociated into single cells using the Wortington/GentleMACS protocol; electroported cells were subsequently FACS-sorted based on the preferred fluorescence marker.
Gene expression and sgRNA libraries according to the manufacturer’s manual using the Chromium Library v.3.1 kit (PN-1000121), Feature Barcode Library Kit (PN-1000079) and Single Index Kit (PN-1000213) from 10X Genomics.

treatment_protocol: Nfib/Nfix KO samples were generated using tCROP-seq with CRISPR/Cas9-mediated perturbation targeting Nfib and Nfix, while Nfib OE samples were created via overexpression using the pCAGG-NFIB2 plasmid.

value: ganglionic eminence, cortex, striatum

value: wild type C57BL/6

value: Control OE


title: Eosinophils, D06_EVEN_075

value: Female

value: EVEneg


title: A11

description:
Library name: sample6
FPKM.A11

value: blood

value: PBMC

value: HCs


title: Eosinophils, D06_EB_075

value: ExtractBuffer


title: scRNA_Nfib_OE_replicate3

description: Library name: Sample 47

value: Nfib OE


title: bESC_1-XscF

city: Xianyang

first: Young

last: Tang

state: Shaanxi

address: #22 Xinong Road, Yangling District

department: College of Veterinary Medicine

institute: Northwest A&F University

description: Library name: Sample4

data_processing:
1.Clean reads were obtained by removing adapter-containing, poly-N, and low-quality reads from raw data. The reference genome index was built using Hisat2 v2.0.5, and paired-end clean reads were aligned to the reference genome.
2.The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
3.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.
4.Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
5.Used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: ncbi_bos_taurus_gcf_002263795_3_ars_ucd2_0 and ensembl_107_mus_musculus_c57bl6nj_c57bl_6nj_v1_toplevel
Supplementary files format and content: Normalized Counts.csv

organism: Bos taurus

source_name: Blastocyst

extract_protocol:
Total RNA was extracted from bESCs and mESCs using the RNeasy Mini Kit (Qiagen, #74104) following the manufacturer’s protocol.
Total RNA was purified to obtain mRNA using poly-T beads. mRNA was fragmented and reverse transcribed into first-strand cDNA with random hexamers and M-MuLV Reverse Transcriptase. Second-strand synthesis was done with DNA Polymerase I and RNase H. DNA ends were blunted and adenylated, followed by ligation of hairpin loop adaptors. cDNA fragments (370–420 bp) were selected using AMPure XP system. PCR amplification was performed with Phusion polymerase, universal primers, and index primers. Final PCR products were purified and library quality assessed on Agilent Bioanalyzer 2100.

value: Blastocyst

value: embryonic stem cells

value: WT

tag: batch


title: b_1_G_M_D5

description: Library name: Sample7


title: b_1_G_N_D5

description: Library name: Sample8


title: b_1_M_D5

description: Library name: Sample5


title: scRNA_Nfib_OE_replicate1

description: Library name: Sample 45


title: Eosinophils, D06_NT_075

value: NoTreatment


title: bESC3-1_WwjF

description: Library name: Sample3


title: b_1_N_D5

description: Library name: Sample6


title: Eosinophils, D05_EVEP_066

description: 70_by_30_and_6mg_per_mlnicotine_number_066_20

value: Blood

value: Male

value: EVEPos


title: Eosinophils, D05_EVEN_066

value: primary cell

value: Eosinophil


title: Eosinophils, D05_EB_066


title: scRNA_Nfib_Nfix_KO_replicate3

description: Library name: Sample 43

value: ganglionic eminence, cortex, striatum

value: wild type C57BL/6

value: gNfib, gNfix, gLacZ


title: scRNA_Nfib_Nfix_KO_replicate4

description: Library name: Sample 44


title: HW8, WT, replicate 1

description:
AS-589018-LR-56198
processed_data_iPSC_RNAseq_cpm.txt

value: HW8 (National Cancer Institute, NIH)

value: human induced pluripotent stem cells (hiPSC)

value: male


title: scRNA_Nfib_Nfix_KO_replicate2

description: Library name: Sample 42


title: scRNA_Nfib_OE_replicate2

description: Library name: Sample 46

value: Control OE


title: bESC1-2_WwjF

description: Library name: Sample2


title: T_A_3

city: Fenyang

first: Songhao

last: Tian

address: No. 16 College Road

institute: Fenyang College of Shanxi Medical University

data_processing:
Spliced Transcripts Alignments to a Reference v2.5.2b
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: thoracic aorta

extract_protocol:
The cultured cells were examined under a microscope to ensure cell integrity and prevent RNA degradation by RNases released from damaged cells. Cells were then washed twice with pre-chilled 1×PBS to remove impurities. Appropriate amounts of Ambion TRIzol were added to isolate total RNA from each cell sample.
For each sample, 1.5 µg of RNA was used as input material, and the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was employed for library preparation, with index codes added to differentiate samples. mRNA was purified using poly-T oligonucleotide-conjugated magnetic beads, and fragmentation was carried out at high temperatures using the NEBNext First Strand Synthesis Reaction Buffer. First-strand cDNA was synthesized using random hexamer primers and M-MuLV reverse transcriptase, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. Overhang ends were converted to blunt ends using exonuclease/polymerase activity, followed by adenylation of the 3' ends.NEBNext adapters with hairpin loop structures were then ligated for subsequent hybridization. Selected cDNA fragments of 200-250 bp were purified using the AMPure XP system, followed by treatment with USER enzyme and PCR amplification. The final PCR products were purified again and quality assessed using the Agilent Bioanalyzer 2100 system. Sequencing was performed on the Illumina NovaSeq 6000 platform at Allwegene Technology in Beijing, generating 150 bp paired-end reads. Sequencing data were aligned with the reference genome, and FPKM values were calculated to quantify gene/transcript expression.

value: thoracic aorta

value: VSMCs

value: Vascular smooth muscle cells

value: CTSD transfection + AGE treatment


title: Eosinophils, D05_EVEN_035

value: EVEneg


title: T_A_1


title: Eosinophils, D05_NT_066

value: Blood

value: NoTreatment


title: NC_A_3

value: Empty vector transfection + AGE treatment


title: scRNA_Nfib_Nfix_KO_replicate1

description: Library name: Sample 41


title: HepG2_oeHELLS 1

type: RNA

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: liver cancer cell line

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

growth_protocol: All cells were cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using TRIzol reagent, digested with DNase I and reverse transcribed using a High Capacity cDNA Reverse Transcription Kit

treatment_protocol: shRNA were selected in the presence of 1.25 μg/mL puromycin.

tag: shRNA

value: oeHELLS


title: Eosinophils, D05_EB_035

value: primary cell

value: Eosinophil

value: Male

value: ExtractBuffer


title: HepG2_oeHELLS 2


title: bESC1-1_WwjF

description: Library name: Sample1

value: Blastocyst

value: embryonic stem cells

value: WT


title: HepG2_shHELLS 2

value: shHELLS


title: Spinal cord injury site, 3, 7, 14 days after Vehicle administration (10, 14, 21 d after injury) and uninjured control 1

city: Columbus

first: Heithem

last: El-Hodiri

address: 333 W 10th Ave

institute: Ohio State University College of Medicine

description:
Library name: CONTROL
10X Genomics FLEX mouse WTA BC001 - BC004

data_processing:
FASTQ sequence files were de-multiplexed, aligned and annotated to a custom mm10 genome and probe set file using 10X Genomics Cell Ranger Multi v8.0.1 software (10X Genomics Cloud analysis).  The custom genome included the eGFP FASTA file and transcript information as outlined by 10X Genomics (URL: https://www.10xgenomics.com/support/software/cell-ranger/latest/tutorials/cr-tutorial-mr).  The custom probe set file included the eGFP probes used in library preparation and was prepared as outlined by 10X Genomics (URL: https://kb.10xgenomics.com/hc/en-us/articles/17824038751885-How-to-Add-Custom-Probes-to-Cell-Ranger-and-Space-Ranger).
Assembly: mm10
Supplementary files format and content: CellRanger outjput feature, barcode, and matrix files

source_name: spinal cord

extract_protocol:
Tissues were chopped on a glass petri dish maintained on ice and transferred to a 2 ml sterile tube with 1 ml of fixation buffer and stored at 4°C for 20 hours. Samples were then processed for long-term storage at -80°C according to 10X Genomics instructions. After completing sample collection, the samples were thawed at RT and incubated at 37°C in a dissociation solution (2 ml/sample containing 0.4 mg/ml liberase) for 1 hour in agitation. Tissues were then dissociated using a glass pipette (~30 strokes/sample). Dissociated tissues were passed through a 30 μm cell strainer to remove debris. Samples were further dissociated (~10 strokes/sample) by adding 1 ml of PBS to the remaining tissue pellet. After passing all cell suspension on the 30 μm cell strainer, cells were centrifuged at 850 rcf for 5 minutes at RT. After removing the supernatant, cells were resuspended in 1 ml chilled quenching buffer.
Cell suspensions were mixed with propidium iodide dye and counted (Countess 3 FL; Invitrogen). Single cell libraries were prepared using Chromium next GEM Fixed RNA Profiling Kits for Multiplexed Samples (10X Genomics). Barcoded probe hybridization was carried out with up to 2,000,000 cells per sample. Customized probes for eGFP spike-in were included during the hybridization step based on the technical note provided by 10X Genomics (Technical Note # CG000621). Each single cell cDNA library was prepared for a target of 10,000 post-probe hybridization cells per sample. Cells and 10X Genomics Chromium 3' Flex Next-GEM reagents were loaded onto chips to capture cells using a 10X Genomics Chromium iX Controller. Library preparation was according to manufacturer's protocols.

value: spinal cord

value: SCI/Vehicle or naïve


title: HepG2_shcon 2

value: shControl


title: HepG2_Mock 2

value: Mock


title: HepG2_shHELLS 1


title: NC_B_2

value: thoracic aorta

value: VSMCs

value: Vascular smooth muscle cells

value: Empty vector transfection


title: NC_B_1


title: Eosinophils, D05_EVEP_035

description: 70_by_30_and_6mg_per_mlnicotine_number_035_16

value: Blood

value: EVEPos


title: HepG2_Mock 1


title: HepG2_shcon 1


title: Elp1_WT_Ptch1_tumor_S6

city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description: Library name: 3222494_Patch_ELP1_WT_3_S11

data_processing:
barcoded processing, gene counting and aggregation were made using the STARsolo (v2.7.3a)
Assembly: mm10
Supplementary files format and content: Tab-separated files

molecule: nuclear RNA

source_name: tumor

extract_protocol:
Single cells from developing mouse cerebellar tissue were processed using the microfluidics-based 10x Chromium protocol, according to manufacturer instructions
mouse cerebellar tissue  were isolated and processed using the 10x Chromium technology

value: tumor


title: Spinal cord injury site, 3, 7, 14 days after PDGF-BB administration (10, 14, 21 d after injury) and uninjured control 2

description:
Library name: PDGF
10X Genomics FLEX mouse WTA BC001 - BC004

value: SCI/PDGF-BB or naïve


title: Elp1_WT_Ptch1_tumor_S5

description: Library name: 3222493_Patch_ELP1_WT_2_S10


title: NC_A_1

value: Empty vector transfection + AGE treatment


title: Eosinophils, D04_EVEP_029

description: 70_by_30_and_6mg_per_mlnicotine_number_029_12

value: primary cell

value: Eosinophil

value: Female


title: val2-1 mutant, rep2, RNA-seq

city: Cerdanyola del Vallès

first: Julia

middle: I.

last: Qüesta

state: Barcelona

address: Carrer de la Vall Moronta

institute: Centre for Research in Agricultural Genomics

description:
mRNA
YJ-VAL2-8

data_processing:
The raw sequencing data was trimmed using cutadapt and mapped to the TAIR10 genome version with STAR.
Gene counts computed with stringtie and the Araport11 gene annotations. The gene counts were collected using the prepDE.py3 script from stringtie.
Differential expression analysis and calculation of transcript per million values were performed using the DEseq2 R package.
Assembly: TAIR10
Supplementary files format and content: Gene-level tab-separated quantification tables containing the gene ID and read counts for each RNA-seq sample.
Supplementary files format and content: Gene-level tab-separated quantification tables containing the gene ID and normalized transcripts per million values for each RNA-seq sample.

organism: Arabidopsis thaliana

source_name: shoot apic meristem

growth_protocol: Seeds were surface sterilized during 10 minutes using 75% (v/v) ethanol containing 0.01% Triton X-100, and then washed three times with ddH2O. Seeds were sown in plates containing 0.5xMS media with agar (without sucrose, with added vitamins), incubated 48h at 4 degrees for stratification, and then moved to 22 degrees at short-day conditions (SD, 8 hours in the light/ 16 hours in the dark). 7-day-old seedlings were transferred from plates to soil.

extract_protocol:
Total RNA was isolated from dissected shoot apices (0.5 g) from 6-week-old plants grown under SD, using a RNeasy Plant Mini Kit (QIAGEN) and purified using an RNase-free DNase kit (QIAGEN).
RNA sequencing libraries were prepared using a polyA-enrichment strategy with the Illumina TruSeq stranded mRNA kit.

value: shoot apic meristem

value: val2-1 mutant


title: val1-2 mutant, rep2, RNA-seq

description:
mRNA
YJ-VAL1-6

value: val1-2 mutant


title: val2-1 mutant, rep1, RNA-seq

description:
mRNA
YJ-VAL2-7


title: T_A_2

value: CTSD transfection + AGE treatment


title: Col-0, rep2, RNA-seq

description:
mRNA
YJ-COL-0-3


title: Elp1_WT_Ptch1_tumor_S4

description: Library name: 3222492_Patch_ELP1_WT_1_S9


title: val1-2 mutant, rep1, RNA-seq

description:
mRNA
YJ-VAL1-5


title: Col-0, rep1, RNA-seq

description:
mRNA
YJ-COL-0-1


title: Elp1_MUT_Ptch1_tumor_S5

description: Library name: 3222490_Patch_ELP1_mut_2_S7


title: NC_B_3


title: Eosinophils, D01_EVEP_007

description: 70_by_30_and_6mg_per_mlnicotine_number_007_8

value: Male


title: Eosinophils, D03_NT_029

value: NoTreatment


title: Col_input_ChIP_rep2

city: Cambridge

last: Harris

address: Downing Street

department: Department of Plant Sciences

country: United Kingdom

institute: University of Cambridge

data_processing:
The reads were aligned to the TAIR10 reference genome using Bowtie2 (version 2.5.3), the duplicated reads were removed by Samtools (version 1.19.2). Deeptools (version 3.5.5) was used to generate the tracks using RPGC for normalization. As there were few differences between the biological replicates in all ChIPs, we merged the biological replicates for downstream analysis. The IGV genome browser was used to visualize the data. MACS2 (version 2.2.9.1) was used for peak calling and differential peaks were identified by DiffBind in R. Peaks were annotated by ChIPseeker in R. Deeptools was used to generate the metaplots and heatmaps.
Assembly: TAIR10
Supplementary files format and content: bigWig

source_name: seedling

growth_protocol: The arabidopsis seeds were either grew on 1/2 MS plates for 15 days or directly on soil under LD conditions (16 h light and 8 h dark at 22 °C)

extract_protocol:
ChIPs were performed as previously described(Harris et al., 2024) https://doi.org/10.7554/eLife.89353.2. Cells were fixed in vitro with 1% formaldehyde for 10 min. After quenching and cell lysis, chromatin wea sonicated by a Diagenode Bioruptor Plus Sonicator.
Libraries were generated with NuGen Ovation Ultra Low System V2 kits following the manufacturer’s instructions.

value: seedling

tag: chip antibody


title: Col_H3_ChIP_rep2

value: anti-H3 (ab1791, Abcam)


title: Col_H3_ChIP_rep1


title: Col_input_ChIP_rep1


title: Eosinophils, D01_EVEN_007

value: EVEneg


title: Eosinophils, D03_EB_029

value: Blood

value: ExtractBuffer


title: Elp1_WT_Ptch1_tumor_S3

description: Library name: 3181761_Patch_ELP1_WT_3

value: tumor


title: Eosinophils, D01_EB_007


title: Col_H3K4me3_ChIP_rep1

value: anti-H3K4me3 (ab8580, Abcam)


title: Col_H3K4me3_ChIP_rep2


title: Elp1_WT_Ptch1_tumor_S2

description: Library name: 3181760_Patch_ELP1_WT_2


title: Col_H2AZ_ChIP_rep2

value: anti-H2A.Z (AS10718, Agrisera)


title: Eosinophils, D05_NT_035

value: primary cell


title: NC_A_2

value: thoracic aorta

value: VSMCs

value: Vascular smooth muscle cells

value: Empty vector transfection + AGE treatment


title: Elp1_MUT_Ptch1_tumor_S6

description: Library name: 3222491_Patch_ELP1_mut_3_S8


title: Eosinophils, D01_NT_007

value: Eosinophil


title: Col_H2AZ_ChIP_rep1


title: Elp1_WT_Ptch1_tumor_S1

description: Library name: 3181759_Patch_ELP1_WT_1


title: Eosinophils, D02_EVEP_008

description: 70_by_30_and_6mg_per_mlnicotine_number_008_4

value: EVEPos


title: Elp1_MUT_Ptch1_tumor_S3

description: Library name: 3181758_Patch_ELP1_mut_3


title: al7m_input_ChIP_rep2


title: Eosinophils, D02_EVEN_008

value: Male


title: Elp1_MUT_Ptch1_tumor_S4

description: Library name: 3222489_Patch_ELP1_mut_1_S6


title: al7m_input_ChIP_rep1


title: Eosinophils, D02_EB_008


title: Elp1_MUT_Ptch1_tumor_S2

description: Library name: 3181757_Patch_ELP1_mut_2