title: RNA-seq of Mus musculus (ICR): 9-month-old male testis, blueberry extract (100 mg/kg/d) treatment, replicate 2

description:
Library name: Treat2_2
replicate 2 of Treat2 group


title: Final-090A-Aug-OED-08-16-2024-EPI-002

status: Public on Jun 30 2026

type: SRA

city: Kansas City

first: Harsh

last: Pathak

state: KS

address: 3901 Rainbow Blvd

country: USA

institute: KUMC

description: Library name: DSP-1001660019855-D-E04

library_source: transcriptomic

data_processing:
FASTQ files downloaded from the NextSeq are converted into the DCC file format using the GeoMxNGSPipeline (version-2.3.3.10).
Assembly: GRCh38.p13
Supplementary files format and content: .dcc: probe count data
Supplementary files format and content: .xlsx: annotation file containing segment annotation info
Supplementary files format and content: .pkc: probe metadata linking probe barcodes with target genes IDs
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: OED

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) slides were prepared following the “RNA Slide Preparation Protocol” in MAN-10150 in the Manual Slide Preparation User Manual, available from NanoString. The RNA probe hybridization solution was prepared using the GeoMx® Cancer Transcriptome Atlas (CTA) RNA probe mix (NanoString), following the recommended dilution (10% probe mix + 10% DEPC water + 80% Buffer R).
Library prep was performed according to instructions provided in NanoString’s NGS Readout Library Prep User Manual (MAN-10117-05), followed by paired-end (27 x 27 cycles) sequencing on the Illumina NextSeq 550 sequencer using a high-output flow cell.

tag: cell type

value: Epi

tag: tissue

value: OED

tag: transformed status

value: Yes


title: diagnostic sample, 371

city: Roma

first: Serena

last: Travaglini

address: Via Montpellier 1

country: Italy

institute: Università di Roma Tor Vergata

data_processing:
Paired reads were aligned to the human reference genome (GRCh38/hg38) using the splice-aware aligner STAR v 2.5.0c
Per-gene read counts were generated using the STAR quantMode geneCounts option.
Raw per-gene read counts were then processed using the Bioconductor package DESeq2 package v. 1.30 in order to perform the differential expression analysis.
Assembly: hg38
Supplementary files format and content: excel with normalised counts

source_name: primary Acute myeloid leukemia cells

extract_protocol:
Trizol extraction
poly A enrichment / rRNA depletion

value: primary Acute myeloid leukemia cells

tag: genotype

value: inv(16) AML

tag: group

value: primary inv(16) AML cells at diagnosis


title: MT-173

city: seoul

first: Dakyung

last: Lee

address: 101 Daehakro

country: South Korea

institute: University

description: Library name: MT-173

data_processing:
RNA sequencing data were processed using RSEM, which employs the STAR aligner to map reads to the GRCh38 human reference genome.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: primary tumor

extract_protocol:
To isolate RNA from tumor tissues of patients and PDX models, approximately 5 mm³ of tumor tissue was snap-frozen in liquid nitrogen and homogenized in 1 ml of Tri-RNA Reagent (Favorgen, Cat# FATRR001, Taiwan) using a Biomasher (Takara, Cat# 9791A, Japan). Subsequently, 200 µl of chloroform was added for phase separation, followed by isopropanol precipitation to extract total RNA from the homogenized tissue.
TruSeq RNA

value: primary tumor


title: Final-090A-Aug-OED-08-16-2024-Immune-001

description: Library name: DSP-1001660019855-D-E03

value: Immune


title: Preterm infant blood miRNA - D03 (Control)

type: RNA

city: Almaty

first: Iskander

last: Isgandarov

address: Timiryazev 45

country: Kazakhstan

institute: Institute of plant biology and biotechnology

hyb_protocol: Labeled samples hybridized to Affymetrix GeneChip miRNA 4.1 Array using GeneTitan Multi-Channel (MC) instrument, 96-well plate format, per Affymetrix miRNA Assay protocol.

scan_protocol: Arrays scanned using Affymetrix GeneTitan MC instrument.

data_processing: Raw CEL files imported in R using oligo package (v1.62). RMA normalization applied (background=FALSE). All 36,353 probe set intensity values (RMA log2 scale) provided in Matrix table. Probe set names correspond to Affymetrix miRNA-4_1-st-v1 annotation (20160922). For differential expression: human miRNA probes (n=2,578) with mean log2 intensity >5 were retained (n=233); limma (v3.54) with empirical Bayes, adjusted for gestational age and birth weight.

label: biotin

source_name: Peripheral blood

label_protocol: RNA (100 ng) labeled with Affymetrix FlashTag Biotin HSR RNA Labeling Kit per manufacturer protocol.

growth_protocol: N/A - clinical study; preterm newborns managed per standard NICU protocols.

extract_protocol: Peripheral blood (1 ml) collected from each infant on days 10-14 of life. Total RNA including miRNA extracted using miRNeasy Mini Kit (Qiagen) per manufacturer instructions. Quality assessed by Agilent Bioanalyzer (RIN >7) and NanoDrop.

treatment_protocol: N/A - no experimental treatment applied.

tag: disease status

value: Control

tag: gestational age (weeks)

tag: birth weight (g)

tag: age at sampling (days of life)

tag: rds

value: grade 1

tag: surfactant administration

value: yes

tag: mechanical ventilation from birth

value: no

tag: ivh


title: Final-090A-Aug-OED-08-16-2024-EPI-001

description: Library name: DSP-1001660019855-D-E02


title: U22-pop5, Blasts

extract_protocol:
Trizol extraction
SMARTer Stranded Total RNA-Seq Kit v2- Pico Input Mammalian protocol.

tag: sorted cells

value: Blasts

tag: pair id


title: RNA-seq of Mus musculus (ICR): 9-month-old male testis, blueberry extract (100 mg/kg/d) treatment, replicate 1

city: Nanjing

first: Lu

last: Guo

email: 3230204169@qq.com, luguo280@gmail.com

state: Jiangsu

address: Xuanwu District of Nanjing City, Jiangsu Province.

department: College of Animal Science and Technology

country: China

institute: Nanjing Agricultural University

description:
Library name: Treat2_1
replicate 1 of Treat2 group

data_processing:
Raw data (fastq) were processed using Trimmomatic to remove adapters and low-quality bases.
Clean reads were aligned to the mouse reference genome (mm10) using STAR software.
Gene expression counts were quantified using featureCounts.
Differential expression analysis was performed using the DESeq2 R package.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-delimited Excel file containing raw read counts for each gene.

molecule: polyA RNA

organism: Mus musculus

source_name: testis

growth_protocol: ICR mice were housed in a specific pathogen-free (SPF) facility under a standard 12-hour light/dark cycle with controlled temperature (22±2°C) and humidity. Food and water were provided ad libitum.

extract_protocol:
Total RNA was extracted from fresh frozen testis tissue using Trizol reagent (Invitrogen) following the manufacturer's instructions. RNA integrity and concentration were assessed using the Agilent 2100 Bioanalyzer and NanoDrop spectrophotometer.
Sequencing libraries were generated using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer's recommendations. Poly-A mRNA was purified from total RNA using oligo-dT magnetic beads and then fragmented. cDNA was synthesized, adapter-ligated, and amplified.

treatment_protocol: Mice were randomly divided into control and treatment groups. The treatment group was administered blueberry extract via intragastric gavage daily for the experimental period. The control group received an equal volume of saline (or vehicle) via gavage.

value: testis

value: wild type

tag: treatment

value: Blueberry extract 100mg/kg

tag: batch


title: B-LCLs,gene expression profiles among the control B-LCLs,low

city: guangzhou

first: mengye

last: he

state: guangdong

address: guangzhou

institute: guangzhoucunzhongkeji

description: Library name: B-C2

data_processing:
Raw sequencing reads in FASTQ format were first assessed for quality using FastQC (v0.11.9). Adapter sequences and low-quality bases (Q < 20) were trimmed with Trimmomatic (v0.39) or fastp (v0.23.2) with the following parameters: leading:3, trailing:3, sliding_window:4:20, minlen:50. Cleaned reads were then aligned to the reference genome (Homo sapiens GRCh38.p13 or Mus musculus GRCm39) using STAR (Spliced Transcripts Alignment to a Reference, v2.7.10b) with two-pass alignment for improved splice junction detection.  Gene-level read counts were quantified from aligned BAM files using featureCounts (part of Subread package, v2.0.3), based on annotations from Ensembl Release 104 (or GENCODE v44). Only primary alignments were included, and reads overlapping exons of protein-coding genes were counted under a union model.  To enable cross-sample comparison, raw read counts were normalized into Transcripts Per Million (TPM) values as follows:  For each gene, fragments per kilobase (FPK) was calculated by dividing the number of mapped fragments by the gene length in kilobases. The sum of FPK values across all genes in each sample was computed and divided by 1,000,000 to obtain a scaling factor. TPM for each gene = FPK / scaling factor. TPM values were used for downstream analyses including gene expression profiling, clustering (hierarchical clustering and PCA), differential expression analysis (using edgeR or DESeq2), and pathway enrichment (e.g., GO, KEGG via clusterProfiler)
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: B-LCLs

extract_protocol:
RNA was harvested using  Trizol Kit (BeyoPure). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was extracted from [tissue/cell line] samples using the BeyoPure™ Total RNA Extraction and Purification Kit (Beyotime Biotechnology, China, Cat# RN0516) according to the manufacturer’s instructions. RNA quality was assessed using a NanoDrop spectrophotometer (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies), with all samples exhibiting RNA Integrity Number (RIN) > 8.0. Poly(A)+ mRNA was enriched from total RNA using oligo(dT) magnetic beads. The RNA was then fragmented into short fragments (approximately 200–300 bp) under elevated temperature in fragmentation buffer. First-strand cDNA was synthesized using reverse transcriptase and random hexamer primers, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. The double-stranded cDNA libraries were constructed by end repair, 3'-end adenylation, adapter ligation, and size selection using AMPure XP beads (Beckman Coulter). Libraries were amplified by PCR and purified again. Finally, library quality was validated on the Bioanalyzer, and quantification was performed using qPCR. Libraries were sequenced on an Illumina NovaSeq 6000 platform with paired-end 150 bp (PE150) reads

tag: cell line

value: B-LCLs

tag: cell type

value: mesenchymal stem cells


title: Final-190-Aug-Benign-08-16-2024-Immune-005

description: Library name: DSP-1001660019855-D-E01

source_name: Benign

tag: tissue

value: Benign

tag: transformed status


title: Final-190-Aug-Benign-08-16-2024-EPI-004

description: Library name: DSP-1001660019855-D-D12

value: Epi


title: U15-pop5, Blasts

value: primary Acute myeloid leukemia cells

tag: genotype


title: RNA-seq of Mus musculus (ICR): 9-month-old male testis, blueberry extract (50 mg/kg/d) treatment, replicate 3

description:
Library name: Treat1_3
replicate 2 of Treat1 group

value: Blueberry extract 50mg/kg


title: Final-190-Aug-Benign-08-16-2024-Immune-003

description: Library name: DSP-1001660019855-D-D11


title: Final-190-Aug-Benign-08-16-2024-EPI-003

description: Library name: DSP-1001660019855-D-D10


title: 2070-pop3, Blasts


title: Final-149-Aug-OSCC-08-16-2024-EPI-006

description: Library name: DSP-1001660019855-D-H07

source_name: OSCC

value: OSCC


title: Final-190-Aug-Benign-08-16-2024-Immune-002

description: Library name: DSP-1001660019855-D-D09


title: RNA-seq of Mus musculus (ICR): 9-month-old male testis, blueberry extract (50 mg/kg/d) treatment, replicate 2

description:
Library name: Treat1_2
replicate 2 of Treat1 group


title: RNA-seq of Mus musculus (ICR): 9-month-old male testis, blueberry extract (50 mg/kg/d) treatment, replicate 1

description:
Library name: Treat1_1
replicate 1 of Treat1 group


title: 1962-pop7, Blasts


title: Final-190-Aug-Benign-08-16-2024-EPI-002

description: Library name: DSP-1001660019855-D-D08


title: Final-190-Aug-Benign-08-16-2024-Immune-001

description: Library name: DSP-1001660019855-D-D07


title: RNA-seq of Mus musculus (ICR): 9-month-old male testis, saline control, replicate 3

description:
Library name: Con3
replicate 3 of control group


title: 1653-pop 7, Blasts


title: Final-190-Aug-Benign-08-16-2024-EPI-001

description: Library name: DSP-1001660019855-D-D06


title: stomach, day35, Arid1a mutant, ChIP, Mist1, rep2

city: Mississauga

first: Ho Sung

last: Rhee

state: ON

address: 3359 Mississauga Rd

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

description:
Library name: 8ChIPseq_Mist1_day35_KO_rep2
Tamoxifen - 35 days after treatment

library_source: genomic

data_processing:
To remove adapter sequences from the sequencing data, raw sequencing reads were trimmed using TrimGalore (www.bioinformatics.babraham.ac.uk/).
The raw trimmed reads were aligned to the mm10 mouse genome using the bowtie2 aligner (http://bowtie-bio.sourceforge.net/).
bigWig files were generated using Galaxy (usegalaxy.org)
Assembly: mm10
Supplementary files format and content: BIGWIG (wiggle type files using the program wigToBigWig)

molecule: genomic DNA

source_name: Stomach

growth_protocol: Arid1a mice were grwon and stomachs glands were isolated after 0, 7 or 35 days after the treatment.

extract_protocol:
Tissue and cells were lysed and chromatin pellets were isolated, and then solubilized and fragmented by sonication. Fragmented chromatin was then subject to immunoprecipitation using antibodies against the protein of interest.
ChIP-seq libraries were prepared according to the standard Illumina protocols. Briefly, DNA was end-repaired and ligated to sequencing adaptors, then PCR amplified and gel purified. The purified DNA libraries were sequenced following the manufacturer's protocols.

treatment_protocol: Arid1a mice were treated with 5mg/20g tamoxifen for 3 consecutive days.

value: Stomach

value: Mist1 (D7N4B) (Cell Signaling, 14896)


title: Final-184-Aug-Benign-08-15-2024-Immune-004

description: Library name: DSP-1001660019855-D-D05

value: Immune


title: RNA-seq of Mus musculus (ICR): 9-month-old male testis, saline control, replicate 2

description:
Library name: Con2
replicate 2 of control group

value: Control


title: Final-184-Aug-Benign-08-15-2024-EPI-004

description: Library name: DSP-1001660019855-D-D04


title: Final-184-Aug-Benign-08-15-2024-Immune-003

description: Library name: DSP-1001660019855-D-D03


title: 1604-pop5, Blasts


title: Final-184-Aug-Benign-08-15-2024-Immune-002

description: Library name: DSP-1001660019855-D-D01


title: Final-184-Aug-Benign-08-15-2024-Immune-001

description: Library name: DSP-1001660019855-D-C11


title: U22-pop4, LPCs

value: LPCs


title: Final-184-Aug-Benign-08-15-2024-EPI-002

description: Library name: DSP-1001660019855-D-C12


title: Final-155-Aug-OSCC-08-14-2024-Immune-004

description: Library name: DSP-1001660019855-D-C09


title: B16.F10 cells, Hif-1α knockdown + Doxorubicin biol rep 1

city: Cluj-Napoca

first: Bogdan

last: Dume

address: Mihail Kogălniceanu, no. 1

country: Romania

institute: Babes-Bolyai University

description: Library name: Sample 13

data_processing:
Raw data quality was assessed using FastQC v0.11.7.
Adapter sequences and low-quality bases were removed using Trimmomatic v0.38.
Trimmed reads were aligned to Mus musculus reference genome (mm10, NCBI_108 annotation) using HISAT2 v2.1.0 and Bowtie2 v2.3.4.1.
Aligned reads were assembled into transcripts with StringTie v2.1.3b and transcript abundance was determined, quantified as read counts, and normalized to FPKM and TPM values.
Assembly: mm10, NCBI_108 annotation
Supplementary files format and content: csv files include raw counts for each sample

growth_protocol: B16.F10 murine melanoma cells were cultured as monolayer in DMEM (37°C, 80% humidity, 5% CO2, and 1% O2) supplemented with 10% (v/v) FBS, 1mM sodium pyruvate, 4 mM L-glutamine, and antibiotics (100 μg/ml streptomycin and 100 IU/ml penicillin).

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen).
RNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Reference guide #1000000040498 v00, Illumina).

treatment_protocol: B16.F10 cells were seeded at the density of 2.5×104 cells/cm2 and revers-transfected with lipoplexes containing siRNA at a final concentration of 25 nM and incubated for 24 h. After, doxorubicin hydrochloride was added to the culture media at a final concentration of 0.25 μM and cells were further incubated for another 24 h in 1% hypoxia.

value: Melanoma cell

value: Hif-1a knockdown

value: Anti Hif-1α siRNA + Doxorubicin


title: Final-155-Aug-OSCC-08-14-2024-EPI-004

description: Library name: DSP-1001660019855-D-C08


title: 2070-pop4, LPCs


title: Final-155-Aug-OSCC-08-14-2024-Immune-003

description: Library name: DSP-1001660019855-D-C07


title: Final-155-Aug-OSCC-08-14-2024-EPI-003

description: Library name: DSP-1001660019855-D-C06


title: B16.F10 cells, Doxorubicin biol rep 3

description: Library name: Sample 12

value: WT

value: Doxorubicin


title: Final-155-Aug-OSCC-08-14-2024-EPI-002

description: Library name: DSP-1001660019855-D-C04


title: 1653-pop 5, LPCs


title: 1962-pop1, LPCs


title: Final-155-Aug-OSCC-08-14-2024-Immune-001

description: Library name: DSP-1001660019855-D-C03


title: B16.F10 cells, Doxorubicin biol rep 1

description: Library name: Sample 10


title: Final-156-1-Aug-OSCC-08-14-2024-Immune-003

description: Library name: DSP-1001660019855-D-B11


title: B16.F10 cells, Hif-1α knockdown biol rep 2

description: Library name: Sample 8

value: Anti Hif-1α siRNA


title: Final-156-1-Aug-OSCC-08-14-2024-EPI-003

description: Library name: DSP-1001660019855-D-B10


title: B16.F10 cells, Hif-1α knockdown biol rep 1

description: Library name: Sample 7


title: siYB13

first: Huilong

last: Li

address: China Pharmaceutical University

institute: China Pharmaceutical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for acaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmedsequence reads weremappedtoGrCM38/mm10usingCLCgenomic benchwork (parameters-mismath cost: 2 insertion cost:3 deletion cost: 3 length faction: 0.8 similarity faction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: MDA-MB-231 cells with siRNA interference of YB3

growth_protocol: Cells were cultured in DMEM medium (Gibco, Grand Island, NY, USA) at 37 °C under a humidified atmosphere with 5% CO2, and supplemented with 10% FBS (Gibco), 80 U/ml penicillin, and 0.08 mg/ml streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MDA-MB-231 cells were transfected with YB1 or NC siRNA. Subjected to  deep sequencing, in triplicate, using  Illumina NovaSeq 6000.

value: breast cancer cell line

value: siRNA interference of YB1


title: Final-156-1-Aug-OSCC-08-14-2024-EPI-002

description: Library name: DSP-1001660019855-D-B08

value: Epi


title: siYB12

source_name: MDA-MB-231 cells with siRNA interference of YB2


title: Final-156-1-Aug-OSCC-08-14-2024-Immune-001

description: Library name: DSP-1001660019855-D-B07


title: Final-156-1-Aug-OSCC-08-14-2024-EPI-001

description: Library name: DSP-1001660019855-D-B06


title: siYB11

source_name: MDA-MB-231 cells with siRNA interference of YB1


title: B16.F10 cells, Negative control siRNA biol rep 2

description: Library name: Sample 5

value: Negative control siRNA


title: Final-152-Aug-OSCC-08-14-2024-EPI-004

description: Library name: DSP-1001660019855-D-B04


title: NC3

source_name: MDA-MB-233 cells with siRNA interference of NC

value: siRNA interference of NC


title: Final-152-Aug-OSCC-08-14-2024-Immune-003

description: Library name: DSP-1001660019855-D-B03

value: OSCC


title: 1021-pop6, Blasts

value: primary Acute myeloid leukemia cells

value: Blasts


title: B16.F10 cells, Hif-1α knockdown + Doxorubicin biol rep 3

description: Library name: Sample 15


title: U15-pop4, LPCs


title: Final-155-Aug-OSCC-08-14-2024-Immune-002

description: Library name: DSP-1001660019855-D-C05

value: Immune


title: Final-152-Aug-OSCC-08-14-2024-EPI-003

description: Library name: DSP-1001660019855-D-B02


title: NC2

source_name: MDA-MB-232 cells with siRNA interference of NC


title: Final-152-Aug-OSCC-08-14-2024-Immune-002

description: Library name: DSP-1001660019855-D-B01


title: B16.F10 cells, Control biol rep 3

description: Library name: Sample 3


title: Final-152-Aug-OSCC-08-14-2024-EPI-002

description: Library name: DSP-1001660019855-D-A12


title: 1604-pop4, LPCs


title: Final-152-Aug-OSCC-08-14-2024-Immune-001

description: Library name: DSP-1001660019855-D-A11


title: NC1

source_name: MDA-MB-231 cells with siRNA interference of NC


title: B16.F10 cells, Control biol rep 2

description: Library name: Sample 2


title: oeRNPC13

description: MCF-7 cells with RNPC1 overexpression

data_processing:
Illumina casav2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell
Assembly: mm9
Supplementary files format and content: tab-delimited text files include readcount values for each sample

treatment_protocol: MCF-7 cells were transfected with RNPC1 overexpression plasmid and the vector plasmid. Subjected to  deep sequencing, in triplicate, using  Illumina NovaSeq 6000.


title: Final-152-Aug-OSCC-08-14-2024-EPI-001

description: Library name: DSP-1001660019855-D-A10


title: B16.F10 cells, Control biol rep 1

description: Library name: Sample 1


title: oeRNPC12

description: MCF-7 cells with RNPC1 overexpression


title: Final-147-Aug-OSCC-08-14-2024-Immune-004

description: Library name: DSP-1001660019855-D-A08


title: Final-147-Aug-OSCC-08-14-2024-EPI-004

description: Library name: DSP-1001660019855-D-A07


title: ALD4

city: Hefei

first: Yue

last: Wang

address: 218 Jixi Road

institute: First Affiliated Hospital of Anhui Medical University

description:
Library name: E4
FPKM

data_processing:
RNA-seq
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequencellow-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm 10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8sim
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files Include FPKM values for each Sample

source_name: Liver

extract_protocol:
RNAwas havested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries.
RNA Iibraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Liver

value: Hepatocyte

value: Alcohol


title: Final-147-Aug-OSCC-08-14-2024-EPI-003

description: Library name: DSP-1001660019855-D-A06


title: oeRNPC11

description: MCF-7 cells with RNPC1 overexpression


title: ALD3

description:
Library name: E3
FPKM


title: Final-152-Aug-OSCC-08-14-2024-Immune-004

description: Library name: DSP-1001660019855-D-B05


title: Final-147-Aug-OSCC-08-14-2024-EPI-002

description: Library name: DSP-1001660019855-D-A04


title: Final-147-Aug-OSCC-08-14-2024-Immune-001

description: Library name: DSP-1001660019855-D-A03


title: ALD2

description:
Library name: E2
FPKM


title: Ph+ B-ALL12

city: Dalian

first: Xuehong

last: Zhang

state: Liaoning

address: No. 9 West Section Lvshun South Road, Dalian 116044, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

description: Library name: Sample36

data_processing:
For the gene expression, we mapped the sequencing data to reference genome (hg38) using STAR, and defined transcript coordinates according to the gene annotation format file (GTF file) from GENCODE (Release 27, GRCh38).
The Gene abundances are given as Reads Per Kilobase per Million mapped reads (RPKM) with “cuffnorm” command using the Cufflinks package.
Assembly: human GRCh38
Supplementary files format and content: Excel file includes FPKM values for all Samples

source_name: Bone Marrow

extract_protocol:
Total RNA of cryopreserved mononucleated cells (MNCs) of bone marrow aspirate samples were extracted using the QIAamp AllPrep RNA Mini Kit (Cat# 80204, QIAGEN), according to the manufacturer's specifications.
Libraries were constructed using the TruSeq RNA Sample Preparation Kits (Illumina), and the quality of the library was assessed using Bioanalyzer 2100 (Agilent Technologies).

value: Bone Marrow

tag: disease stage

value: Ph+ B-ALL


title: Final-147-Aug-OSCC-08-14-2024-EPI-001

description: Library name: DSP-1001660019855-D-A02


title: DSP-1001660019855-D-A01-NTC

description: Library name: DSP-1001660019855-D-A01

value: Non-template-control


title: ALD1

description:
Library name: E1
FPKM

value: WT


title: Final-Slide-125-OSCC-01-24-2024-Immune-010

description: Library name: DSP-1001660020045-D-H12


title: Ph+ B-ALL11

description: Library name: Sample35


title: Control4

description:
Library name: N4
FPKM

value: saline


title: Final-Slide-125-OSCC-01-24-2024-Immune-008

description: Library name: DSP-1001660020045-D-H10


title: Ph+ B-ALL10

description: Library name: Sample34


title: Final-Slide-125-OSCC-01-24-2024-Immune-007

description: Library name: DSP-1001660020045-D-H09


title: Final-147-Aug-OSCC-08-14-2024-Immune-005

description: Library name: DSP-1001660019855-D-A09


title: Control3

description:
Library name: N3
FPKM


title: Final-Slide-125-OSCC-01-24-2024-Epi-006

description: Library name: DSP-1001660020045-D-H08


title: Ph+ B-ALL9

description: Library name: Sample33


title: Final-Slide-125-OSCC-01-24-2024-Epi-005

description: Library name: DSP-1001660020045-D-H07


title: Final-Slide-125-OSCC-01-24-2024-Epi-004

description: Library name: DSP-1001660020045-D-H06


title: Control2

description:
Library name: N2
FPKM


title: Ph+ B-ALL8

description: Library name: Sample32


title: Final-Slide-125-OSCC-01-24-2024-Epi-003

description: Library name: DSP-1001660020045-D-H05


title: Control1

description:
Library name: N1
FPKM


title: Ph+ B-ALL13

description: Library name: Sample37


title: Ph+ B-ALL7

description: Library name: Sample31


title: Final-Slide-125-OSCC-01-24-2024-Immune-002

description: Library name: DSP-1001660020045-D-H04


title: Final-147-Aug-OSCC-08-14-2024-Immune-002

description: Library name: DSP-1001660019855-D-A05


title: Wildtype395

city: Shanghai

first: Xingming

address: No. 270, Dong'an Road, Xuhui District, Shanghai

institute: Fudan University Shanghai Cancer Center

description: Library name: WT395

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: prostate

extract_protocol:
TRIzol® reagent (Thermo Fisher Scientific) was utilized for total RNA extraction from PCa cells according to the manufacturer’s instructions.
Total RNA was purified using the RNA Clean XP Kit (A63987, Beckman Coulter, Kraemer Boulevard Brea, CA, USA) and DNase set (79254, QIAGEN, Germany). Complementary DNA was synthesized with 1 μg of total RNA using VAHTS® mRNA-seq V2 Library Prep Kit for Illumina (NR603, Vazyme, Nanjing, China), followed by amplification and subjected to paired-end150 (PE150) Hiseq. Each sample contained pooled RNA from 3 biological replicates and was mixed with equal mass to minimize variation across samples.

value: prostate


title: Final-Slide-125-OSCC-01-24-2024-Epi-002

description: Library name: DSP-1001660020045-D-H03


title: RNA-seq of Mus musculus (ICR): 9-month-old male testis, saline control, replicate 1

description:
Library name: Con1
replicate 1 of control group

value: testis

value: wild type

value: Control


title: Final-184-Aug-Benign-08-15-2024-EPI-003

description: Library name: DSP-1001660019855-D-D02

value: Epi

value: Benign


title: Ph+ B-ALL6

description: Library name: Sample30


title: Final-Slide-125-OSCC-01-24-2024-Immune-001

description: Library name: DSP-1001660020045-D-H02

value: OSCC


title: Final-Slide-125-OSCC-01-24-2024-Epi-001

description: Library name: DSP-1001660020045-D-H01


title: Wildtype371

description: Library name: WT371


title: Final-184-Aug-Benign-08-15-2024-EPI-001

description: Library name: DSP-1001660019855-D-C10


title: Final-Slide-134-OSCC-01-24-2024-Immune-006

description: Library name: DSP-1001660020045-D-G12


title: Ph+ B-ALL5

description: Library name: Sample29


title: B16.F10 cells, Hif-1α knockdown + Doxorubicin biol rep 2

description: Library name: Sample 14

value: Melanoma cell

value: Hif-1a knockdown

value: Anti Hif-1α siRNA + Doxorubicin


title: Final-Slide-134-OSCC-01-24-2024-Epi-006

description: Library name: DSP-1001660020045-D-G11


title: Final-Slide-125-OSCC-01-24-2024-Immune-009

description: Library name: DSP-1001660020045-D-H11

value: Immune


title: Ph+ B-ALL4

description: Library name: Sample28


title: Wildtype353

description: Library name: WT353


title: Final-Slide-134-OSCC-01-24-2024-Epi-005

description: Library name: DSP-1001660020045-D-G09


title: Final-Slide-134-OSCC-01-24-2024-Immune-005

description: Library name: DSP-1001660020045-D-G10


title: B16.F10 cells, Doxorubicin biol rep 2

description: Library name: Sample 11

value: Doxorubicin


title: T663

description: Library name: T663

value: PB-Cre; Pten knockout


title: Final-Slide-134-OSCC-01-24-2024-Immune-004

description: Library name: DSP-1001660020045-D-G08


title: Final-Slide-134-OSCC-01-24-2024-Epi-004

description: Library name: DSP-1001660020045-D-G07


title: T664

description: Library name: T664


title: Ph+ B-ALL3

description: Library name: Sample27

value: Bone Marrow

value: Ph+ B-ALL


title: Final-Slide-134-OSCC-01-24-2024-Immune-003

description: Library name: DSP-1001660020045-D-G06


title: Vector3

description: MCF-7 cells with Vector expression

value: breast cancer cell line

value: Vector


title: Final-156-1-Aug-OSCC-08-14-2024-Immune-004

description: Library name: DSP-1001660019855-D-C01


title: B16.F10 cells, Hif-1α knockdown biol rep 3

description: Library name: Sample 9

value: Anti Hif-1α siRNA


title: Final-155-Aug-OSCC-08-14-2024-EPI-001

description: Library name: DSP-1001660019855-D-C02


title: Final-156-1-Aug-OSCC-08-14-2024-EPI-004

description: Library name: DSP-1001660019855-D-B12


title: Final-Slide-134-OSCC-01-24-2024-Epi-003

description: Library name: DSP-1001660020045-D-G05


title: Final-Slide-134-OSCC-01-24-2024-Immune-002

description: Library name: DSP-1001660020045-D-G04


title: T684

description: Library name: T684

value: prostate


title: Final-Slide-134-OSCC-01-24-2024-Epi-002

description: Library name: DSP-1001660020045-D-G03


title: Final-Slide-134-OSCC-01-24-2024-Immune-001

description: Library name: DSP-1001660020045-D-G02


title: Vector1

description: MCF-7 cells with Vector expression


title: E14.5-cKO rep3

city: Guangzhou

first: Zhenyi

last: Huang

state: GuangDong

address: ShaTaiNan Street 1023-1063,Baiyun

department: Development

institute: Southern Medical University

description:
Library name: E14.5-cKO-rep3
10x Genomcis

library_source: transcriptomic single cell

data_processing:
Sequencing reads were aligned to the mouse reference genome (mm10) and digital gene expression matrix was built using STAR algorithm in SeekSoulTools.
Assembly: mm10
Supplementary files format and content: matrix files

source_name: Female fetal ovaries

growth_protocol: Mice were housed under specific pathogen-free (SPF) conditions on a standard 12 h light/12 h dark cycle with free access to food and water. The ambient temperature was maintained at 20–25°C with 40%–70% relative humidity.

extract_protocol:
An appropriate number of cells were mixed with the reverse transcription (RT) reagent to capture cellular RNA,
Sample were loaded into the sample well of the SeekOne® DD Chip S3 (Chip S3). Barcoded Hydrogel Beads (BHBs) and partitioning oil were subsequently dispensed into their designated wells in the same chip. Following emulsion droplet generation, reverse transcription was carried out at 42 °C for 90 min and terminated at 85 °C for 5 min. cDNA was then recovered from the disrupted droplets, purified, and amplified by PCR. The amplified cDNA was cleaned, fragmented, end-repaired, A-tailed, and ligated to sequencing adapters. Indexed PCR was performed to amplify DNA fragments corresponding to the 3′ poly(A) termini of expressed genes, each containing a Cell Barcode and Unique Molecular Index. Final libraries were purified using SPRI beads, quantified by quantitative PCR (KAPA Biosystems, KK4824), and sequenced on  the Illumina NovaSeq 6000 platform (PE150).

treatment_protocol: Gata2flox/+ Prdm1-Cre males were crossed with Gata2flox/flox females. Female embryos were collected at E14.5 from pregnant mice and genotyped.Ovaries from Gata2WT and Gata2cKO embryos were dissociated using 0.05% Trypsin at 37 °C, and the reaction was quenched with DMEM containing 10% FBS and 1% SP. The cell suspension was filtered through 40 μm strainers

value: Female fetal ovaries

value: C57BL/6J mice

value: Ovarian cells

value: Trypsin digestion

tag: Sex

value: female

tag: time

value: Replicate 3


title: Vector2

description: MCF-7 cells with Vector expression


title: Final-Slide-134-OSCC-01-24-2024-Epi-001

description: Library name: DSP-1001660020045-D-G01

value: Epi

value: OSCC


title: Final-Slide-068-OED-01-24-2024-Immune-007

description: Library name: DSP-1001660020045-D-F12

source_name: OED

value: Immune

value: OED

value: No


title: E14.5-cKO rep2

description:
Library name: E14.5-cKO-rep2
10x Genomcis

value: Replicate 2


title: Final-Slide-068-OED-01-24-2024-Epi-006

description: Library name: DSP-1001660020045-D-F11


title: Pt-12_PBMC sort CD3, T  NK cell subset bmref

city: Cambridge

first: Mirco

middle: Julian

last: Friedrich

state: MA

address: 72 Ames St

institute: Broad Institute

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Reference mapping to identify and filter impurities and map all samples to a reference of annotated T-cells in the multiple myeloma bone marrow
CDR3 sequences were retrieved from the cellranger output and matched using the R-package scRepertoire. CDR3 sequences can be found in the cell_metadata
Annotation of tumor-reactive CDR3 sequences can be found in the cell_metadata
Assembly: GRCh38
Supplementary files format and content: Single cell expression objects in h5seurat format created by the package SeuratDisk
Supplementary files format and content: Filtered single cell matrix containing data from CD3+ T & NK cells. Cell type annotation and CDR3 amino-acid sequence are included in the seurat file

source_name: human peripheral blood mononuclear cells

extract_protocol:
Bone marrow mononuclear fractions were isolated through Ficoll density gradients coupled with magnetic sorting of CD3+ T cells.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
5' scRNA/TCR-seq

tag: individual

tag: cell subset

value: T and NK cells

tag: disease state

value: newly diagnosed multiple myeloma


title: Final-Slide-068-OED-01-24-2024-Immune-005

description: Library name: DSP-1001660020045-D-F10


title: Pt-12_BMNC sort CD3, T  NK cell subset bmref

source_name: human bone marrow mononuclear cells

value: human bone marrow mononuclear cells


title: E14.5-WT rep3

description:
Library name: E14.5-WT-rep3
10x Genomcis


title: Final-Slide-068-OED-01-24-2024-Immune-004

description: Library name: DSP-1001660020045-D-F08


title: Final-Slide-068-OED-01-24-2024-Epi-004

description: Library name: DSP-1001660020045-D-F07


title: Pt-11_BMNC sort CD3, T  NK cell subset bmref


title: E14.5-cKO rep1

description:
Library name: E14.5-cKO-rep1
10x Genomcis

value: Replicate 1


title: Final-Slide-068-OED-01-24-2024-Immune-003

description: Library name: DSP-1001660020045-D-F06


title: Final-Slide-068-OED-01-24-2024-Epi-003

description: Library name: DSP-1001660020045-D-F05


title: Pt-10_PBMC sort CD3, T  NK cell subset bmref

value: human peripheral blood mononuclear cells


title: Final-Slide-068-OED-01-24-2024-Immune-002

description: Library name: DSP-1001660020045-D-F04


title: Final-Slide-068-OED-01-24-2024-Immune-001

description: Library name: DSP-1001660020045-D-F02


title: Pt-10_BMNC sort CD3, T  NK cell subset bmref


title: Retina, ONC 7d

first: Caiwen

last: Xiao

state: -- Select State/Province --

address: Zhizaoju Road

institute: Shanghai Ninth People's Hospital

description:
Library name: S7d
one sample from murine retina tissue

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Retina

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: Retina

value: optic nerve crush

value: ONC 7d


title: Final-Slide-068-OED-01-24-2024-Epi-001

description: Library name: DSP-1001660020045-D-F01


title: Retina, ONC 3d

description:
Library name: S3d
one sample from murine retina tissue

value: ONC 3d


title: Final-Slide-068-OED-01-24-2024-Epi-002

description: Library name: DSP-1001660020045-D-F03


title: Retina, ONC 1d

description:
Library name: S1d
one sample from murine retina tissue

value: ONC 1d


title: Pt-09_PBMC sort CD3, T  NK cell subset bmref


title: Final-Slide-083-OED-01-24-2024-Immune-008

description: Library name: DSP-1001660020045-D-E10

value: Yes


title: Final-Slide-083-OED-01-24-2024-Immune-009

description: Library name: DSP-1001660020045-D-E12


title: Final-Slide-083-OED-01-24-2024-Epi-008

description: Library name: DSP-1001660020045-D-E09

value: Epi


title: Pt-08_PBMC sort CD3, T  NK cell subset bmref


title: Retina, ONC 8h

description:
Library name: S8h
one sample from murine retina tissue

value: ONC 8h


title: Final-Slide-083-OED-01-24-2024-Immune-004

description: Library name: DSP-1001660020045-D-E07

value: Immune


title: Retina, ONC 2h

description:
Library name: S2h
one sample from murine retina tissue

value: ONC 2h


title: Final-Slide-083-OED-01-24-2024-Epi-004

description: Library name: DSP-1001660020045-D-E06

value: OED


title: Final-Slide-083-OED-01-24-2024-Immune-003

description: Library name: DSP-1001660020045-D-E05


title: Pt-08_BMNC sort CD3, T  NK cell subset bmref


title: Retina, Control

description:
Library name: Control
one sample from murine retina tissue

value: Control


title: Final-Slide-083-OED-01-24-2024-Epi-002

description: Library name: DSP-1001660020045-D-E03


title: Heparin2

city: qingdao

first: tianyu

last: wang

address: yushanlu 5#

institute: Ocean University of China

description: Library name: Sample 5

data_processing:
Raw FASTQ files were processed using fastp to ensure high-quality data. We performed adapter auto-detection and trimmed the first 20 bp from the 5' end of both forward and reverse reads (--trim_front1 20 --trim_front2 20). Reads with low-quality bases (Phred score < 20) and those shorter than 15 bp were filtered out
The cleaned paired-end reads were aligned to the Mouse reference genome (GRCm39) using HISAT2. The alignment results were processed using Samtools to generate sorted BAM files and their corresponding indices.
Gene expression levels were quantified using featureCounts (Subread). Reads were assigned to genomic features at the exon level (-t exon) and summarized by Gene ID (-g gene_id) based on the Mus_musculus.GRCm39.103.chr.gtf annotation file. The -p flag was applied to count fragments for paired-end data.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files in a matrix format

extract_protocol:
Total RNA was extracted according to the instruction manual of the TRlzol Reagent. A total amount of 1 μg RNA per sample was used. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina. The libraries were sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads, accordingto the manufacturer’s instructions.
For library construction, 1 μg of total RNA per sample was used. mRNA libraries were prepared according to the manufacturer’s protocol using the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen, Shanghai, China). Briefly, mRNA was enriched using oligo(dT) magnetic beads, followed by first- and second-strand cDNA synthesis. cDNA ends were blunted, 3′-adenylated, and ligated to hairpin-structured adaptors. Libraries were purified with AMPure XP beads, treated with USER enzyme, and amplified by PCR using indexed primers. Final libraries were purified and quality-controlled using an Agilent Bioanalyzer 2100.

value: Mouse hepatocytes


title: Final-Slide-083-OED-01-24-2024-Immune-001

description: Library name: DSP-1001660020045-D-E02

data_processing:
FASTQ files downloaded from the NextSeq are converted into the DCC file format using the GeoMxNGSPipeline (version-2.3.3.10).
Assembly: GRCh38.p13
Supplementary files format and content: .dcc: probe count data
Supplementary files format and content: .xlsx: annotation file containing segment annotation info
Supplementary files format and content: .pkc: probe metadata linking probe barcodes with target genes IDs
Library strategy: Spatial Transcriptomics

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) slides were prepared following the “RNA Slide Preparation Protocol” in MAN-10150 in the Manual Slide Preparation User Manual, available from NanoString. The RNA probe hybridization solution was prepared using the GeoMx® Cancer Transcriptome Atlas (CTA) RNA probe mix (NanoString), following the recommended dilution (10% probe mix + 10% DEPC water + 80% Buffer R).
Library prep was performed according to instructions provided in NanoString’s NGS Readout Library Prep User Manual (MAN-10117-05), followed by paired-end (27 x 27 cycles) sequencing on the Illumina NextSeq 550 sequencer using a high-output flow cell.


title: Final-Slide-083-OED-01-24-2024-Epi-001

description: Library name: DSP-1001660020045-D-E01


title: Pt-07_BMNC sort CD3, T  NK cell subset bmref

value: T and NK cells

value: newly diagnosed multiple myeloma


title: RRBS_dHIP_18mo_male_sample11

city: Irvine

first: Jiachun

state: CA

address: Samueli School of Engineering University of California, Irvine

institute: University of California Irvine

description: Library name: 18mo_sample11

data_processing:
Paired-end sequenced data was aligned to reference genome mm10 using Bismark following the kit manufacturer’s instructions.
Assembly: mm10
Supplementary files format and content: bed

source_name: dorsal hippocampus

extract_protocol:
DNA was extracted using the Qiagen DNEasy Blood and Tissue kit (Qiagen, 69504). Extracted DNA for each sample was measured on the Nanodrop 2000 for a 260/280 ratio over 1.9, ensuring purity. Extracted DNA was then enzymatically digested (MSP 1, NEB, R0106S) in a water bath for 3 hours, followed by purification and size selection (Chinn et al., 2021). Size selected fragments were then bisulfite converted (EZ DNA Methylation-Gold, Zymo Research, D5006) before initiating library construction.
Libraries were constructed by using the xGen Methyl-seq DNA Library Prep Kit (IDT, 10009824) and UDI primers added following manufacturer's instructions. Paired-end sequenced data was aligned to reference genome mm10 using Bismark following the kit manufacturer’s instructions.

value: dorsal hippocampus

tag: age

value: 18 months

value: male


title: Pt-06_BMNC sort CD3, T  NK cell subset bmref

value: human bone marrow mononuclear cells


title: Final-Slide-017-OED-01-24-2024-Immune-006

first: Harsh

address: 3901 Rainbow Blvd

institute: KUMC

description: Library name: DSP-1001660020045-D-D12

value: No


title: Final-Slide-017-OED-01-24-2024-Epi-006

description: Library name: DSP-1001660020045-D-D11


title: Final-Slide-017-OED-01-24-2024-Immune-005

description: Library name: DSP-1001660020045-D-D10


title: Pt-05_BMNC sort CD3, T  NK cell subset bmref


title: Final-Slide-017-OED-01-24-2024-Immune-004

description: Library name: DSP-1001660020045-D-D08


title: Final-Slide-017-OED-01-24-2024-Epi-004

description: Library name: DSP-1001660020045-D-D07


title: RRBS_dHIP_18mo_male_sample8

description: Library name: 18mo_sample8


title: Final-Slide-017-OED-01-24-2024-Immune-003

description: Library name: DSP-1001660020045-D-D06


title: RRBS_dHIP_18mo_male_sample7

description: Library name: 18mo_sample7


title: Final-Slide-017-OED-01-24-2024-Immune-002

description: Library name: DSP-1001660020045-D-D04


title: Pt-03_BMNC sort CD3, T  NK cell subset bmref


title: Final-Slide-017-OED-01-24-2024-Epi-002

description: Library name: DSP-1001660020045-D-D03


title: RRBS_dHIP_18mo_male_sample6

description: Library name: 18mo_sample6


title: Final-Slide-017-OED-01-24-2024-Immune-001

description: Library name: DSP-1001660020045-D-D02


title: Pt-02_BMNC sort CD3, T  NK cell subset bmref


title: Final-Slide-017-OED-01-24-2024-Epi-001

description: Library name: DSP-1001660020045-D-D01


title: Final-Slide-068-OED-01-24-2024-Epi-005

description: Library name: DSP-1001660020045-D-F09


title: RRBS_dHIP_18mo_male_sample5

description: Library name: 18mo_sample5


title: Pt-11_PBMC sort CD3, T  NK cell subset bmref

value: human peripheral blood mononuclear cells


title: E14.5-WT rep2

description:
Library name: E14.5-WT-rep2
10x Genomcis

value: Female fetal ovaries

value: C57BL/6J mice

value: Ovarian cells

value: Trypsin digestion

value: female

value: Replicate 2


title: DSP-1001660020045-D-A01-NTC

description: Library name: DSP-1001660020045-D-A01

value: Non-template-control


title: E14.5-WT rep1

description:
Library name: E14.5-WT-rep1
10x Genomcis

value: Replicate 1


title: Pt-01_BMNC sort CD3, T  NK cell subset bmref

description: Filtered single cell matrix containing data from CD3+ T & NK cells. Cell type annotation and CDR3 amino-acid sequence are included in the seurat file


title: Rep-Final-slide-167-Benign-02-23-2024-Immune-004

description: Library name: DSP-1001660037559-D-H12

source_name: Benign

value: Immune

value: Benign


title: Final-Slide-083-OED-01-24-2024-Epi-009

description: Library name: DSP-1001660020045-D-E11

value: Epi

value: OED

value: Yes


title: RRBS_dHIP_18mo_male_sample4

description: Library name: 18mo_sample4

value: dorsal hippocampus

value: 18 months

value: male


title: Rep-Final-slide-167-Benign-02-23-2024-Epi-004

description: Library name: DSP-1001660037559-D-H11


title: BT-549 cells

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

institute: Istituto Italiano di Tecnologia

description:
BT-549
10X Genomics

data_processing:
Read alignment, UMI counting, cell-containing barcode (CB) calling were performed using cellranger count from CellRanger (v2.1)
Assembly: hg38
Supplementary files format and content: barcodes.tsv: tab separated value files
Supplementary files format and content: genes.tsv: tab separated value files
Supplementary files format and content: matrix.mtx: matrix files

growth_protocol: HMLE were grown in mamamry epithelial cell growth medium (Lonza) according to the manufacturer’s protocol. BT-549 were grown in DMEM+10%FBS+2mM L-Glutamine+1%P/S

extract_protocol:
Single-cell suspensions (500-1000 cells/μL) were mixed with reverse transcription mix using the 10x Genomics Chromium Single-cell 3’ reagent kit protocol V2 (BT-549 and HMLE)
Libraries were generated as by manufacturers’ instructions V2.

treatment_protocol: To FACS sort CD44highCD24low and CD44lowCD24high populations from HMLE, cells were blocked with PBS-BSA 10% for 1 h at 4°C and then stained with CD44-APC (clone C26; BD Pharmigen) and CD24-PE (clone ML5; BD Pharmigen) antibodies for 45 min at 4°C. Cells were sorted on a BD InFlux V7 flow cytometer.

value: BREAST CANCER


title: Pt-09_BMNC sort CD3, T  NK cell subset bmref

value: human bone marrow mononuclear cells

value: T and NK cells

value: newly diagnosed multiple myeloma


title: Rep-Final-slide-167-Benign-02-23-2024-Immune-003

description: Library name: DSP-1001660037559-D-H10


title: Final-Slide-083-OED-01-24-2024-Immune-007

description: Library name: DSP-1001660020045-D-E08


title: RRBS_dHIP_18mo_male_sample3

description: Library name: 18mo_sample3


title: Rep-Final-slide-167-Benign-02-23-2024-Epi-002

description: Library name: DSP-1001660037559-D-H09


title: FAC-sorted HMLE cells, CD44highCD24low Population, Experiment 2

description:
HMLE_CD44_2
10X Genomics

source_name: HMLE

value: HMLE

value: BREAST NORMAL

tag: cell population

value: CD44highCD24low Population


title: Rep-Final-slide-167-Benign-02-23-2024-Immune-001

description: Library name: DSP-1001660037559-D-H08


title: RRBS_dHIP_18mo_male_sample2

description: Library name: 18mo_sample2


title: Final-Slide-083-OED-01-24-2024-Epi-003

description: Library name: DSP-1001660020045-D-E04


title: Rep-Final-slide-167-Benign-02-23-2024-Epi-001

description: Library name: DSP-1001660037559-D-H07


title: FAC-sorted HMLE cells, CD44highCD24low Population, Experiment 1

description:
HMLE_CD44_1
10X Genomics


title: RRBS_dHIP_18mo_male_sample12

description: Library name: 18mo_sample12


title: RRBS_dHIP_18mo_male_sample1

description: Library name: 18mo_sample1


title: Rep-Final-slide-199-Benign-02-23-2024-Epi-009

description: Library name: DSP-1001660037559-D-H05


title: Rep-Final-slide-199-Benign-02-23-2024-Immune-008

description: Library name: DSP-1001660037559-D-H04


title: FAC-sorted HMLE cells, CD44lowCD24high Population, Experiment 1

description:
HMLE_CD24_1
10X Genomics

value: CD44lowCD24high Population


title: RRBS_dHIP_16mo_male_sample12

description: Library name: 16mo_sample12

value: 16 months


title: FAC-sorted HMLE cells, Bulk Population

description:
HMLE_bulk
10X Genomics

value: Bulk Population


title: Rep-Final-slide-199-Benign-02-23-2024-Immune-007

description: Library name: DSP-1001660037559-D-H02

value: Immune

value: Benign


title: Rep-Final-slide-199-Benign-02-23-2024-Immune-009

description: Library name: DSP-1001660037559-D-H06


title: RRBS_dHIP_16mo_male_sample11

description: Library name: 16mo_sample11


title: RRBS_dHIP_18mo_male_sample10

description: Library name: 18mo_sample10


title: Rep-Final-slide-199-Benign-02-23-2024-Epi-007

description: Library name: DSP-1001660037559-D-H01

value: Epi


title: SUM159PT_CRISPRi_NREP_KD_sgRNA_4

data_processing:
Reads were trimmed, filtered and aligned using STAR (2.7.3).
Read count extraction and TPM normalization were performed using FeatureCounts.
Assembly: hg38
Supplementary files format and content: TPM_counts_SERPINE_MDE_KO.xlsx: excel file that includes normalized reads (transcript per million reads, TPM) for all genes; SERPINE MRE KO clones
Supplementary files format and content: TPM_counts_NREP_KD.xlsx: excel file that includes normalized reads (transcript per million reads, TPM) for all genes; NREP knock down experiment

growth_protocol: SUM159PT were cultured in Ham’s F12 medium, supplemented with 5% FBS (South American origin), 2mM Glutamine, 5 μg/mL insulin, 1 μg/mL hydrocortisone, 10mM HEPES

extract_protocol:
Total RNA was isolated through the miRNeasy mini kit (Qiagen).
Libraries for RNA-seq were prepared from 1 ug of total RNA using Truseq Total RNA Library Prep Kit (Illumina) following manufacturer's protocols.

tag: miRNA substrate


title: Rep-Final-slide-199-Benign-02-23-2024-Epi-006

description: Library name: DSP-1001660037559-D-G12


title: Rep-Final-slide-199-Benign-02-23-2024-Immune-005

description: Library name: DSP-1001660037559-D-G11


title: RRBS_dHIP_16mo_male_sample10

description: Library name: 16mo_sample10


title: SUM159PT_CRISPRi_NREP_KD_sgRNA_3


title: RRBS_dHIP_18mo_male_sample9

description: Library name: 18mo_sample9


title: Pt-04_BMNC sort CD3, T  NK cell subset bmref


title: Final-Slide-017-OED-01-24-2024-Epi-005

description: Library name: DSP-1001660020045-D-D09

value: OED

value: No


title: Rep-Final-slide-199-Benign-02-23-2024-Epi-005

description: Library name: DSP-1001660037559-D-G10


title: RRBS_dHIP_16mo_male_sample9

description: Library name: 16mo_sample9

value: dorsal hippocampus


title: Rep-Final-slide-199-Benign-02-23-2024-Immune-004

description: Library name: DSP-1001660037559-D-G09


title: SUM159PT_CRISPRi_NREP_KD_sgRNA_2


title: RRBS_dHIP_16mo_male_sample8

description: Library name: 16mo_sample8

value: male


title: Rep-Final-slide-199-Benign-02-23-2024-Epi-004

description: Library name: DSP-1001660037559-D-G08


title: SUM159PT_CRISPRi_NREP_KD_sgRNA_1

value: BREAST CANCER


title: Rep-Final-slide-199-Benign-02-23-2024-Epi-008

description: Library name: DSP-1001660037559-D-H03


title: Rep-Final-slide-199-Benign-02-23-2024-Immune-002

description: Library name: DSP-1001660037559-D-G05


title: RRBS_dHIP_16mo_male_sample7

description: Library name: 16mo_sample7


title: Pt-03_PBMC sort CD3, T  NK cell subset bmref

value: human peripheral blood mononuclear cells


title: RRBS_dHIP_16mo_male_sample6

description: Library name: 16mo_sample6


title: Rep-Final-slide-199-Benign-02-23-2024-Epi-001

description: Library name: DSP-1001660037559-D-G04


title: Rep-Final-slide-165-Benign-02-23-2024-R-Epi-004

description: Library name: DSP-1001660037559-D-G03


title: Rep-Final-slide-165-Benign-02-23-2024-R-Immune-003

description: Library name: DSP-1001660037559-D-G02


title: SUM159PT_CRISPRi_CTRL_sgRNA_2


title: RRBS_dHIP_16mo_male_sample5

description: Library name: 16mo_sample5


title: Rep-Final-slide-165-Benign-02-23-2024-R-Epi-003

description: Library name: DSP-1001660037559-D-G01


title: Rep-Final-slide-165-Benign-02-23-2024-R-Immune-002

description: Library name: DSP-1001660037559-D-F12


title: Rep-Final-slide-199-Benign-02-23-2024-Epi-003

description: Library name: DSP-1001660037559-D-G06


title: RRBS_dHIP_16mo_male_sample4

description: Library name: 16mo_sample4


title: SUM159PT_SERPINE1_MRE_KO_clone_5


title: Rep-Final-slide-165-Benign-02-23-2024-R-Epi-002

description: Library name: DSP-1001660037559-D-F11


title: RRBS_dHIP_16mo_male_sample3

description: Library name: 16mo_sample3


title: Rep-Final-slide-165-Benign-02-23-2024-R-Immune-001

description: Library name: DSP-1001660037559-D-F10


title: Rep-Final-slide-165-Benign-02-23-2024-R-Epi-001

description: Library name: DSP-1001660037559-D-F09


title: SUM159PT_SERPINE1_MRE_KO_clone_4


title: Rep-Final-slide-169-Benign-02-23-2024-R-Immune-002

description: Library name: DSP-1001660037559-D-F08


title: Rep-Final-slide-169-Benign-02-23-2024-R-Epi-002

description: Library name: DSP-1001660037559-D-F07


title: RRBS_dHIP_16mo_male_sample2

description: Library name: 16mo_sample2


title: SUM159PT_SERPINE1_MRE_KO_clone_3


title: Rep-Final-slide-169-Benign-02-23-2024-R-Immune-001

description: Library name: DSP-1001660037559-D-F06


title: Rep-Final-slide-06-OED-02-22-2024-Immune-007

description: Library name: DSP-1001660037559-D-F05

value: Yes


title: RRBS_dHIP_16mo_male_sample1

description: Library name: 16mo_sample1


title: SUM159PT_SERPINE1_MRE_KO_clone_2


title: Rep-Final-slide-06-OED-02-22-2024-Epi-007

description: Library name: DSP-1001660037559-D-F04


title: SUM159PT_SERPINE1_MRE_KO_clone_1


title: Rep-Final-slide-06-OED-02-22-2024-Immune-006

description: Library name: DSP-1001660037559-D-F03


title: RRBS_dHIP_12mo_male_sample11

description: Library name: 12mo_sample11

value: 12 months


title: SUM159PT_wild_type_unedited_clone_4


title: Rep-Final-slide-06-OED-02-22-2024-Epi-005

description: Library name: DSP-1001660037559-D-E12


title: Rep-Final-slide-06-OED-02-22-2024-Immune-005

description: Library name: DSP-1001660037559-D-F01


title: SUM159PT_wild_type_unedited_clone_3


title: Rep-Final-slide-06-OED-02-22-2024-Immune-004

description: Library name: DSP-1001660037559-D-E11


title: CUS2-12

city: Nantong

first: tong

last: peng

address: No. 19 Qixiu Road, Chongchuan District, Nantong City, Jiangsu Province, China**

institute: Nantong University

description: Library name: SAMPLES3

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mouse mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Testis tissue from Cus-1-treated busulfan-induced oligozoospermia mouse.

extract_protocol: Take 100 mg of testicular tissue from each group, chop it up, and extract total RNA.

treatment_protocol: After creating the animal bus model, treat it with CUS

value: testis


title: BPA9

description: Library name: SAMPLES2

source_name: Testis tissue from busulfan-induced oligozoospermia mouse model


title: BPA8

description: Library name: SAMPLES1


title: Rep-Final-slide-06-OED-02-22-2024-Immune-003

city: Kansas City

last: Pathak

description: Library name: DSP-1001660037559-D-E09


title: Rep-Final-slide-06-OED-02-22-2024-Epi-004

description: Library name: DSP-1001660037559-D-E10


title: Rep-Final-slide-06-OED-02-22-2024-Epi-003

description: Library name: DSP-1001660037559-D-E08


title: Rep-Final-slide-06-OED-02-22-2024-Immune-002

description: Library name: DSP-1001660037559-D-E07


title: SUM159PT_wild_type_no_Cas9_clone_1


title: RRBS_dHIP_12mo_male_sample8

description: Library name: 12mo_sample8


title: RRBS_dHIP_12mo_male_sample7

description: Library name: 12mo_sample7


title: Rep-Final-slide-06-OED-02-22-2024-Epi-001

description: Library name: DSP-1001660037559-D-E06


title: SUM159PT_CTRL_2_cells expressing the Scrambled_Control_rep4

data_processing:
FASTQ data were trimmed using cutadapt-1.9.1; then trimmed data was aligned to custom sequence libraries listing all isoforms of small RNA molecules by using Bowtie with --best and -v 0 switches and saved in .map output format.
Isomirage software was used to count the number of occurrences in the .map file of each isoform listed in the .genome file
Raw counts were converted into TPM and all templated forms for each miRNA were summed together
Assembly: custom genome, containing all human microRNAs (canonical and Isoforms)
Supplementary files format and content: TPM_counts.xlsx: excel file that includes normalized reads (transcript per million reads, TPM, normalized  to the size of each library) for all miRNAs in all samples. Reported values are the total reads for all templated forms (canonical miRNA and 3'  templated variants)

extract_protocol:
Total RNA, including microRNAs, was isolated through the miRNeasy mini kit (Qiagen).
1000 nanograms of total RNA were used to prepare Small RNA libraries following the Illumina TruSeqTM Small RNA kit instructions

treatment_protocol: Cells were infected with each individual lentiviral construct and then collected after 7 days.


title: Rep-Final-slide-126-OSCC-02-22-2024-Immune-009

description: Library name: DSP-1001660037559-D-E05

source_name: OSCC

value: OSCC


title: Rep-Final-slide-126-OSCC-02-22-2024-Epi-009

description: Library name: DSP-1001660037559-D-E04


title: RRBS_dHIP_12mo_male_sample6

description: Library name: 12mo_sample6


title: Rep-Final-slide-126-OSCC-02-22-2024-Epi-008

description: Library name: DSP-1001660037559-D-E03


title: SUM159PT_CTRL_1_cells expressing the Scrambled_Control_rep3


title: Rep-Final-slide-126-OSCC-02-22-2024-Immune-007

description: Library name: DSP-1001660037559-D-E02


title: RRBS_dHIP_12mo_male_sample5

description: Library name: 12mo_sample5


title: Rep-Final-slide-126-OSCC-02-22-2024-Immune-006

description: Library name: DSP-1001660037559-D-E01


title: Rep-Final-slide-126-OSCC-02-22-2024-Immune-004

description: Library name: DSP-1001660037559-D-D11


title: RRBS_dHIP_12mo_male_sample4

description: Library name: 12mo_sample4


title: SUM159PT_CRISPRi_CTRL_sgRNA_3


title: SUM159PT_HADHB_2_cells expressing ABCA1 3'UTR_rep2


title: SUM159PT_HADHB_1_cells expressing ABCA1 3'UTR_rep1


title: Rep-Final-slide-126-OSCC-02-22-2024-Epi-005

description: Library name: DSP-1001660037559-D-D12


title: Rep-Final-slide-126-OSCC-02-22-2024-Epi-004

description: Library name: DSP-1001660037559-D-D10


title: Final-080-Aug-OED-08-08-2024-Immune-001

description: Library name: DSP-1001660020046-C-D11


title: Final-080-Aug-OED-08-08-2024-EPI-002

description: Library name: DSP-1001660020046-C-D12


title: RRBS_dHIP_12mo_male_sample3

description: Library name: 12mo_sample3


title: Rep-Final-slide-126-OSCC-02-22-2024-Immune-003

description: Library name: DSP-1001660037559-D-D09


title: Rep-Final-slide-199-Benign-02-23-2024-Immune-003

description: Library name: DSP-1001660037559-D-G07


title: SUM159PT_CRISPRi_CTRL_sgRNA_1


title: Rep-Final-slide-126-OSCC-02-22-2024-Epi-003

description: Library name: DSP-1001660037559-D-D08


title: RRBS_dHIP_12mo_male_sample2

description: Library name: 12mo_sample2


title: SUM159PT_ABCA_2_cells expressing ABCA1 3'UTR_rep2


title: Rep-Final-slide-126-OSCC-02-22-2024-Immune-002

description: Library name: DSP-1001660037559-D-D07


title: SUM159PT_ABCA_1_cells expressing ABCA1 3'UTR_rep1


title: Rep-Final-slide-126-OSCC-02-22-2024-Epi-002

description: Library name: DSP-1001660037559-D-D06


title: Rep-Final-slide-126-OSCC-02-22-2024-Immune-001

description: Library name: DSP-1001660037559-D-D05


title: SUM159PT_CTRL_2_cells expressing the Scrambled_Control_rep2


title: RRBS_dHIP_12mo_male_sample1

description: Library name: 12mo_sample1


title: Rep-Final-slide-126-OSCC-02-22-2024-Epi-001

description: Library name: DSP-1001660037559-D-D04


title: Rep-Final-slide-05-OED-02-22-2024-R-Immune-004

description: Library name: DSP-1001660037559-D-D03


title: SUM159PT_CTRL_1_cells expressing the Scrambled_Control_rep1


title: RRBS_dHIP_6mo_male_sample12

description: Library name: 6mo_sample12

value: 6 months


title: Rep-Final-slide-05-OED-02-22-2024-R-Epi-004

description: Library name: DSP-1001660037559-D-D02


title: RRBS_dHIP_6mo_male_sample11

description: Library name: 6mo_sample11


title: Rep-Final-slide-05-OED-02-22-2024-R-Immune-003

description: Library name: DSP-1001660037559-D-D01


title: RRBS_dHIP_6mo_male_sample10

description: Library name: 6mo_sample10


title: Rep-Final-slide-05-OED-02-22-2024-R-Epi-003

description: Library name: DSP-1001660037559-D-C12


title: SUM159PT_TRAF6_2_cells expressing TRAF6 3'UTR_rep2


title: Rep-Final-slide-05-OED-02-22-2024-R-Immune-002

description: Library name: DSP-1001660037559-D-C11


title: RRBS_dHIP_6mo_male_sample9

description: Library name: 6mo_sample9


title: SUM159PT_TRAF6_1_cells expressing TRAF6 3'UTR_rep1


title: Rep-Final-slide-05-OED-02-22-2024-R-Epi-002

description: Library name: DSP-1001660037559-D-C10


title: MDA-MB-361_ZSWIM8_KD_3_cells expressing the ZSWIM targeting sgRNA_3

data_processing:
FASTQ data were trimmed using cutadapt-1.9.1; then trimmed data was aligned to custom sequence libraries listing all isoforms of small RNA molecules by using Bowtie with --best and -v 0 switches and saved in .map output format.
Isomirage software was used to count the number of occurrences in the .map file of each isoform listed in the .genome file
Raw counts were converted into TPM and all templated forms for each miRNA were summed together
Assembly: custom genome, containing all human microRNAs (canonical and Isoforms)
Supplementary files format and content: TPM_counts.xlsx: excel file that includes normalized reads (transcript per million reads, TPM, normalized  to the size of each library) for all miRNAs in all samples

treatment_protocol: Cells were treated infected with lentivirus expressing the sgRNAs and then treated with 1 ug/mL doxycycline, to activate the dCas9-KRAB transgene, for 7 passages

value: ZSWIM8 knock down


title: Rep-Final-slide-05-OED-02-22-2024-R-Immune-001

description: Library name: DSP-1001660037559-D-C09


title: RRBS_dHIP_12mo_male_sample12

description: Library name: 12mo_sample12

value: 16 months


title: Rep-Final-slide-05-OED-02-22-2024-R-Epi-001

description: Library name: DSP-1001660037559-D-C08


title: Rep-Final-slide-06-OED-02-22-2024-Epi-006

description: Library name: DSP-1001660037559-D-F02


title: RRBS_dHIP_6mo_male_sample8

description: Library name: 6mo_sample8


title: Rep-Final-slide-205-Benign-02-22-2024-Epi-006

description: Library name: DSP-1001660037559-D-C07


title: MDA-MB-361_ZSWIM8_KD_2_cells expressing the ZSWIM targeting sgRNA_2


title: Rep-Final-slide-205-Benign-02-22-2024-Immune-005

description: Library name: DSP-1001660037559-D-C06


title: RRBS_dHIP_6mo_male_sample7

description: Library name: 6mo_sample7


title: Rep-Final-slide-205-Benign-02-22-2024-Epi-004

description: Library name: DSP-1001660037559-D-C04


title: Rep-Final-slide-205-Benign-02-22-2024-Immune-004

description: Library name: DSP-1001660037559-D-C05


title: MDA-MB-361_ZSWIM8_KD_1_cells expressing the ZSWIM targeting sgRNA_1


title: RRBS_dHIP_12mo_male_sample10

description: Library name: 12mo_sample10


title: RRBS_dHIP_6mo_male_sample6

description: Library name: 6mo_sample6


title: Rep-Final-slide-205-Benign-02-22-2024-Immune-003

description: Library name: DSP-1001660037559-D-C03


title: MDA-MB-361_CTRL_3_cells expressing the negative control sgRNA_3

value: untreated


title: Rep-Final-slide-205-Benign-02-22-2024-Epi-003

description: Library name: DSP-1001660037559-D-C02


title: RRBS_dHIP_6mo_male_sample5

description: Library name: 6mo_sample5


title: SUM159PT_wild_type_unedited_clone_2


title: RRBS_dHIP_12mo_male_sample9

description: Library name: 12mo_sample9


title: MDA-MB-361_CTRL_2_cells expressing the negative control sgRNA_2


title: Rep-Final-slide-205-Benign-02-22-2024-Epi-002

description: Library name: DSP-1001660037559-D-B12


title: RRBS_dHIP_6mo_male_sample4

description: Library name: 6mo_sample4


title: Rep-Final-slide-205-Benign-02-22-2024-Immune-002

description: Library name: DSP-1001660037559-D-C01

value: Immune


title: Rep-Final-slide-205-Benign-02-22-2024-Immune-001

description: Library name: DSP-1001660037559-D-B11

value: Benign


title: MDA-MB-361_CTRL_1_cells expressing the negative control sgRNA_1


title: RRBS_dHIP_6mo_male_sample3

description: Library name: 6mo_sample3


title: Rep-Final-slide-205-Benign-02-22-2024-Epi-001

description: Library name: DSP-1001660037559-D-B10

value: Epi


title: Rep-Final-slide-143-OSCC-02-21-2024-Immune-005

description: Library name: DSP-1001660037559-D-B09


title: Rep-Final-slide-143-OSCC-02-21-2024-Epi-005

description: Library name: DSP-1001660037559-D-B08


title: RRBS_dHIP_6mo_male_sample2

description: Library name: 6mo_sample2


title: SK-BR-3_ZSWIM8_KD_3_cells expressing the ZSWIM targeting sgRNA_3


title: SK-BR-3_ZSWIM8_KD_2_cells expressing the ZSWIM targeting sgRNA_2


title: Rep-Final-slide-143-OSCC-02-21-2024-Immune-004

description: Library name: DSP-1001660037559-D-B07


title: Rep-Final-slide-143-OSCC-02-21-2024-Epi-004

description: Library name: DSP-1001660037559-D-B06


title: RRBS_dHIP_6mo_male_sample1

description: Library name: 6mo_sample1


title: SK-BR-3_ZSWIM8_KD_1_cells expressing the ZSWIM targeting sgRNA_1


title: Rep-Final-slide-143-OSCC-02-21-2024-Epi-003

description: Library name: DSP-1001660037559-D-B04


title: Rep-Final-slide-143-OSCC-02-21-2024-Immune-003

description: Library name: DSP-1001660037559-D-B05


title: Rep-Final-slide-143-OSCC-02-21-2024-Immune-002

description: Library name: DSP-1001660037559-D-B03


title: RRBS_dHIP_2mo_male_sample11

description: Library name: 2mo_sample11

value: 2 months


title: SK-BR-3_CTRL_3_cells expressing the negative control sgRNA_3


title: Rep-Final-slide-143-OSCC-02-21-2024-Immune-001

description: Library name: DSP-1001660037559-D-B01


title: RRBS_dHIP_2mo_male_sample12

description: Library name: 2mo_sample12


title: SK-BR-3_CTRL_2_cells expressing the negative control sgRNA_2


title: Rep-Final-slide-143-OSCC-02-21-2024-Epi-002

description: Library name: DSP-1001660037559-D-B02


title: Rep-Final-slide-143-OSCC-02-21-2024-Epi-001

description: Library name: DSP-1001660037559-D-A12


title: Rep-Final-slide-148-OSCC-02-21-2024-Immune-006

description: Library name: DSP-1001660037559-D-A11


title: RRBS_dHIP_2mo_male_sample10

description: Library name: 2mo_sample10


title: SK-BR-3_CTRL_1_cells expressing the negative control sgRNA_1


title: Rep-Final-slide-148-OSCC-02-21-2024-Epi-005

description: Library name: DSP-1001660037559-D-A10


title: Rep-Final-slide-148-OSCC-02-21-2024-Immune-004

description: Library name: DSP-1001660037559-D-A09


title: RRBS_dHIP_2mo_male_sample8

description: Library name: 2mo_sample8


title: Rep-Final-slide-148-OSCC-02-21-2024-Epi-004

description: Library name: DSP-1001660037559-D-A08


title: T47D_ZSWIM8_KD_3_cells expressing the ZSWIM targeting sgRNA_3


title: RRBS_dHIP_2mo_male_sample9

description: Library name: 2mo_sample9


title: Rep-Final-slide-148-OSCC-02-21-2024-Immune-003

description: Library name: DSP-1001660037559-D-A07


title: Rep-Final-slide-148-OSCC-02-21-2024-Epi-003

description: Library name: DSP-1001660037559-D-A06


title: Rep-Final-slide-148-OSCC-02-21-2024-Epi-002

description: Library name: DSP-1001660037559-D-A04


title: RRBS_dHIP_2mo_male_sample6

description: Library name: 2mo_sample6


title: T47D_ZSWIM8_KD_2_cells expressing the ZSWIM targeting sgRNA_2


title: T47D_ZSWIM8_KD_1_cells expressing the ZSWIM targeting sgRNA_1


title: Rep-Final-slide-148-OSCC-02-21-2024-Immune-001

description: Library name: DSP-1001660037559-D-A03


title: Rep-Final-slide-148-OSCC-02-21-2024-Epi-001

description: Library name: DSP-1001660037559-D-A02


title: RRBS_dHIP_2mo_male_sample7

description: Library name: 2mo_sample7


title: DSP-1001660037559-D-A01-NTC

description: Library name: DSP-1001660037559-D-A01

value: Non-template-control


title: Rep-Final-slide-148-OSCC-02-21-2024-Immune-002

description: Library name: DSP-1001660037559-D-A05


title: RRBS_dHIP_2mo_male_sample5

description: Library name: 2mo_sample5

value: dorsal hippocampus


title: T47D_CTRL_3_cells expressing the negative control sgRNA_3


title: Pt-07_PBMC sort CD3, T  NK cell subset bmref

value: T and NK cells

value: newly diagnosed multiple myeloma


title: T47D_CTRL_2_cells expressing the negative control sgRNA_2

value: BREAST CANCER


title: 011-Pre-Malignanat-07-11-23-EPI-003

description: Library name: DSP-1001660015531-A-C06

value: OED

value: No


title: 011-Pre-Malignanat-07-11-23-Immune-003

description: Library name: DSP-1001660015531-A-C07


title: RRBS_dHIP_2mo_male_sample4

description: Library name: 2mo_sample4

value: male


title: 011-Pre-Malignanat-07-11-23-Immune-002

description: Library name: DSP-1001660015531-A-C05


title: T47D_CTRL_1_cells expressing the negative control sgRNA_1


title: 011-Pre-Malignanat-07-11-23-EPI-002

description: Library name: DSP-1001660015531-A-C04


title: RRBS_dHIP_2mo_male_sample3

description: Library name: 2mo_sample3


title: MCF-7_ZSWIM8_KD_3_cells expressing the ZSWIM targeting sgRNA_3


title: 011-Pre-Malignanat-07-11-23-Immune-001

description: Library name: DSP-1001660015531-A-C03


title: RRBS_dHIP_2mo_male_sample1

description: Library name: 2mo_sample1


title: MCF-7_ZSWIM8_KD_2_cells expressing the ZSWIM targeting sgRNA_2


title: RRBS_dHIP_2mo_male_sample2

description: Library name: 2mo_sample2


title: 011-Pre-Malignanat-07-11-23-EPI-001

description: Library name: DSP-1001660015531-A-C02


title: Slide-063-PreMalignant-07-10-2023-Immune-004

description: Library name: DSP-1001660015531-A-C01

value: Yes


title: Slide-063-PreMalignant-07-10-2023-Immune-001

description: Library name: DSP-1001660015531-A-B09


title: Slide-063-PreMalignant-07-10-2023-Immune-002

description: Library name: DSP-1001660015531-A-B11


title: RNA-seq sequencing data 2 of mice liver tissues with DEHP exposure

city: wuhan

first: neng

middle: bin

last: xie

address: 115 donghu road

institute: wuhan university

description: Library name: Simple 5

data_processing:
After removing adaptor sequences, ambiguous ‘N’ nucleotides (with a ratio of ‘N’ exceeding 10%) and low-quality sequences (with a quality score below 5), the remaining clean reads were assembled using Trinity software for de novo transcriptome assembly.
Assembly: GRCm38.p6
Supplementary files format and content: excel file of raw gene counts for all samples

source_name: liver tissues

extract_protocol:
Total RNA was isolated from mouse liver tissues using TRIzol (Beyotime); mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Briefly, total RNA was isolated from mouse liver tissues using TRIzol (Beyotime). RNA concentration and integrity were assessed using a Nanodrop photometer and an Agilent 5400 bioanalyzer. Sequencing libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina in accordance with the manufacturer’s recommendations. First, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and subsequently fragmented in NEBNext First Strand Synthesis Reaction Buffer with divalent cations. The first cDNA strand was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). The synthesis of the second cDNA strand was performed with DNA polymerase I, where all dTTPs in the reaction buffer were replaced by dUTPs. The remaining overhangs were converted into blunt ends through exonuclease and polymerase activities. Following the adenylation of the 3' end of the DNA fragments, NEBNext Adaptors with a hairpin loop structure were ligated. Next, 3 μl of USER Enzyme (NEB, USA) was incubated with the size-selected, adaptor-ligated cDNA at 37 °C for 15 min, followed by a 5-min incubation at 95 °C. PCR amplification was then performed using Phusion High-Fidelity DNA polymerase, universal PCR primers, and index primers. The PCR products were purified using KAPA Pure Beads. Library quality was assessed with the Agilent 5400 system (Agilent, USA). Paired-end sequencing of the samples was performed on the Illumina platform (Illumina, USA)

value: liver tissues


title: Slide-063-PreMalignant-07-10-2023-EPI-001

description: Library name: DSP-1001660015531-A-B08


title: MCF-7_CTRL_3_cells expressing the negative control sgRNA_3


title: MCF-7_CTRL_2_cells expressing the negative control sgRNA_2


title: Slide-094-PreMalignant-07-10-2023-EPI-004

description: Library name: DSP-1001660015531-A-B06


title: MCF-7_CTRL_1_cells expressing the negative control sgRNA_1


title: Slide-094-PreMalignant-07-10-2023-EPI-003

description: Library name: DSP-1001660015531-A-B05


title: MCF-7_ZSWIM8_KD_1_cells expressing the ZSWIM targeting sgRNA_1

value: ZSWIM8 knock down


title: Slide-094-PreMalignant-07-10-2023-Immune-002

description: Library name: DSP-1001660015531-A-B04


title: RNA-seq sequencing data 2 of mice liver tissue without DEHP exposuree

description: Library name: Simple 2


title: MDA-MB-436_ZSWIM8_KD_3_cells expressing the ZSWIM targeting sgRNA_3


title: Slide-094-PreMalignant-07-10-2023-EPI-002

description: Library name: DSP-1001660015531-A-B03


title: Slide-051-PreMalignant-07-10-2023-Immune-004

description: Library name: DSP-1001660015531-A-B01


title: Slide-051-PreMalignant-07-10-2023-EPI-004

description: Library name: DSP-1001660015531-A-A12


title: RNA-seq sequencing data 1 of mice liver tissue without DEHP exposuree

description: Library name: Simple 1


title: OP9 cells, Empty vector, RNAseq,batch1, rep2

first: Xin

state: Guangdong

address: 132 Daxuecheng Outer Ring E Rd

department: School of Medicine

institute: Sun Yat-sen University

description:
Library name: EV_batch1_rep2
dicer-EV-2_kallisto

data_processing:
Transcript abundances were quantified using the kallisto (version 0.48.0) under default settings. The transcript-level abundance estimates results were then imported into the R package tximport to summarize the gene-level abundance estimates for downstream analysis.
Assembly: GENCODE.vM29
Supplementary files format and content: xlsx file include TPM values for each Sample

growth_protocol: OP9 mesenchymal stem cells were maintained in MEMα supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Ultrapure RNA Kit (Omega, R6834-02), 1 ug of total RNA was used for the construction of sequencing libraries
The extracted mRNA is enriched using mRNA Capture Beads. After purification with beads, the mRNA is fragmented using high temperatures. The fragmented mRNA is then used as a template   to synthesize the first strand of cDNA in a reverse transcription enzyme mixture system. While synthesizing the second strand of cDNA, end repair and A-tailing are completed. Next, adapters are ligated, and Hieff NGS® DNA Selection Beads are used for purification to select target fragments. PCR library amplification is then performed, and finally, detection is carried out using the MGI DNBSEQ-T7 or Illumina Novaseq X Plus.The total RNA of OP9 cells was extracted using Ultrapure RNA Kit (CW BIO, CW0581M) and sent to BGI for library preparation and sequencing by MGISEQ2000.

treatment_protocol: OP9 cells were plated, and rosiglitazone was added to the medium at a concentration of 1 μM when the cells reached 100% confluence. This treatment was continued for 10 days.

value: mesenchymal stem cell

value: WT

value: adipogenic differentiation


title: PNC079_B1

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Prime View Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Prime View Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000 7G. GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000 7G.

data_processing:
The data were analyzed using the “limma”package and R studio version 4.2.2.
The data were analyzed using the “limma”package and R studio version 4.2.2.

source_name: pancreas transplant biopsy

label_protocol:
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA

extract_protocol:
Trizol-chloroform extraction of total RNA was performed according to the manufacturer's instructions.
Trizol-chloroform extraction of total RNA was performed according to the manufacturer's instructions.

tag: age at biopsy

tag: histology cathegory

value: Marginal


title: MDA-MB-436_CTRL_3_cells expressing the negative control sgRNA_3

tag: treatment

value: untreated


title: Slide-051-PreMalignant-07-10-2023-Immune-002

description: Library name: DSP-1001660015531-A-A10

value: Immune


title: OP9 cells, Empty vector, RNAseq,batch1, rep1

description:
Library name: EV_batch1_rep1
dicer-EV-1_kallisto

tag: cell line

tag: batch


title: Slide-051-PreMalignant-07-10-2023-EPI-002

description: Library name: DSP-1001660015531-A-A09

tag: cell type

value: Epi

tag: tissue


title: Slide-051-PreMalignant-07-10-2023-EPI-001

description: Library name: DSP-1001660015531-A-A08

tag: transformed status


title: MDA-MB-436_CTRL_2_cells expressing the negative control sgRNA_2

tag: genotype


title: Slide-041-PreMalignant-07-10-2023-Immune-005

description: Library name: DSP-1001660015531-A-A07


title: OP9 cells, Dicer1 KO, RNAseq,batch1, rep2

description:
Library name: Dicer1_KO_batch1_rep2
dicer-KO-2_kallisto

value: Dicer1 KO


title: MDA-MB-436_CTRL_1_cells expressing the negative control sgRNA_1


title: OP9 cells, Dicer1 KO, RNAseq,batch1, rep1

description:
Library name: Dicer1_KO_batch1_rep1
dicer-KO-1_kallisto


title: Slide-041-PreMalignant-07-10-2023-Immune-004

description: Library name: DSP-1001660015531-A-A06


title: Slide-041-PreMalignant-07-10-2023-Immune-002

description: Library name: DSP-1001660015531-A-A04


title: MDA-MB-231_ZSWIM8_KD_3_cells expressing the ZSWIM targeting sgRNA_3


title: Slide-041-PreMalignant-07-10-2023-EPI-002

description: Library name: DSP-1001660015531-A-A03


title: Slide-041-PreMalignant-07-10-2023-EPI-001

description: Library name: DSP-1001660015531-A-A02


title: MRR, 2007132

city: Budapest

first: <Up loaded by Bioinformatics core  facility>

last: <PI shown in the article>

address: Szigony st 43.

country: Hungary

institute: HUN-REN Institute of Experimental Medicine

description:
Library name: 2007132
MRR

data_processing:
Read quality was checked with fastqc
Trimmed adapter seq and low phredscore 3’ ends; if a read became shorter than 50 bp it and it’s pair was removed; read pairs where one at least on of the reads consisted of only 3 type of nucleotides were removed
STAR aligner (2.7.10a) was used to align reads to the reference and to count reads mapped to genes; reads mapped to introns were not considered valid
Assembly: Mouse genome mm39 with ensEMBL annotation v110 was supplemented with Addgene_pAAV-EF1a-DIO-mCherry (Plasmid #50459); Cre (NCBI/Nucleotide:NC_005856.1); and sYFP (NCBI/Nucleotide:GQ221700.1).
Supplementary files format and content: A tab separated count matrix on a gene level consisting of genes as rows and samples as columns

source_name: MRR

growth_protocol: We used vGluT2-iRES-Cre adult (at least 6 weeks-old) mice that had access to food and water ad libitum and were housed in a vivarium (3-5 mice/cage) until used in experiments. Mice were injected with AAVretro-EF1a-DIO-mCherry into bilateral LHb (60 nl per site) then were placed into separate cages. After 2-5 weeks of incubation time mice were sacrificed during the light phase and 200-250 μm thick horizontal slices were made from the pontine region of the brainstem of vGLuT2-Cre mice.

extract_protocol:
Mice were decapitated under deep anesthesia and slices were prepared in ice-cold cutting solution (85 mM NaCl, 75 mM sucrose, 2.5 mM KCl, 25 mM glucose, 1.25 mM NaH2PO4, 4 mM MgCl2, 0.5 mM CaCl2, and 24 mM NaHCO3) using a VT1200S vibratome (Leica). Slices were incubated at 35 °C for ~30 min and then kept at room temperature until use. During recordings the slices are kept at 35 °C in continuously perfused with artificial cerebrospinal fluid (126 mM NaCl, 2.5 mM KCl, 26 mM NaHCO3, 2 mM CaCl2, 2 mM MgCl2, 1.25 mM NaH2PO4, and 10 mM glucose, saturated with carbogen,) Fluorescently labeled MRR neurons were visualized in an upright microscope (Eclipse FN-1; Nikon) with epifluorescent illumination (Lambda FLED @ 530 nm; Sutter Instrument) combined with a CMOS camera (DaVinci 1k, RedShirtImaging). The neurons were patched with thin-wall borosilicate pipettes (pipette resistance: 3.69±0.09 MΩ, BF150-117-10, Sutter Instrument) filled with small amount (~1 µl) of intracellular solution containing 133.5 mM K-gluconate, 1.8 mM NaCl, 1.7 mM MgCl2, 0.05 mM EGTA, 10 mM HEPES, 2 mM Mg-ATP, 0.4 mM Na2-GTP, 10 mM phosphocreatine, and 8 mM biocytin (pH 7.25;  290-300 mOsm). Pipette capacitance and the bridge balance were carefully compensated in all current clamp recordings. For the RNA harvesting, the recordings were made using a HEKA EPC800 amplifier (HEKA Elektronik) digitized with a Digidata1440A A/D converter (Molecular Devices). The data acquisition was controlled by the pClamp10 software package. After patching the identified neurons, we measured the basic electrophysiological parameters of the cells including the resting membrane potential, the spontaneous synaptic activity, and the firing pattern. The length of the recording session was limited to 5 min from the break-in. The cytosol together with the nucleus was extracted from the neuron by the application of small negative pressure to the pipette. The tip of the quickly removed pipette was gently pushed into a microtube containing ice cold reaction buffer (lysis buffer with RNase inhibitor, Takara SMART-Seq HT PLUS Kit). The sample containing tubes was spun briefly and snap-frozen on dry ice. To suppress RNase contamination, the workplace including parts of the experimental setup was cleaned each day before the start of the sample collection with RNase AWAY (Thermo Fisher).
Sample collection: After electrophysiological recordings, the cells’ cytosol was aspirated via the same recording glass pipette that used for recording, and using a positive pressure, expelled into microtubes containing 1 µl of 1x lysis buffer with RNase inhibitor (SMART-Seq HT PLUS Kit, Takara). The samples were immediately frozen on dry ice and stored at -80°C until further processing. cDNA and library preparation for next-generation sequencing: Single-cell mRNA processing was performed using the SMART-Seq HT PLUS Kit (Takara) and according to manufacturer’s protocol. In brief, samples were reverse transcribed to cDNA, amplified, and purified with AMPure XP beads (Beckman Coulter). The quantity and the quality of the purified cDNA was assessed using Fragment Analyzer (Advanced Analytical). Subsequently, the cDNA was fragmented and adapters including indices for cell identification were added to the fragments. The quality and quantity were again assessed using Fragment Analyzer. For library preparation, the single cell samples with unique index adapters were pooled in equal amounts. The sequencing was performed on a NovaSeq 6000 (Illumina) instrument using 150 bp paired end configuration and a full SP-flowcell. Processing of sequencing data: After sequencing, raw reads were de-multiplexed with Illumina’s bcl2fastq2 (v2.20).

treatment_protocol: All vGluT2-Cre mice were injected with AAVretro-EF1a-DIO-mCherry into bilateral LHb (60 nl per site) to label MRR vGluT2 neurons.

value: MRR


title: DSP-1001660015531-A-A01-NTC

description: Library name: DSP-1001660015531-A-A01

value: Non-template-control


title: Tumor_FFPE_P16_Pre

city: Philadelphia

first: Nelson

last: Freeburg

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

description:
Library name: Tumor_FFPE_P16_Pre
Column = P16_Pre_1

data_processing:
FASTQ files aligned and preprocessed using 10x Genomics CellRanger Multi v8.0.1 pipeline
For Single-cell, single-nucleus gene expression: Ambient RNA contamination removed using CellBender Remove-Background (CellBender v0.3.0).
For single-cell, single-nucleus gene expression, cellbender-adjusted counts imported intor seurat. Genes and cells were filtered for quality and expression thresholds, and data were lognormalized. Cells were annotated manually based on marker gene expression.
For bulk RNA sequencing, Fastq files were trimmed with umi_tools (v1.1.6) to extract UMIs. Cutadapt (v5.2) was used to trim nonbiological sequences from reads. Reads were aligned using the STAR aligner (v2.7.9a). Reads were deduplicated based on UMI identity using umi_tools (v1.1.6) and counted using FeatureCounts (v2.1.1). Normalized counts are in transcripts per milliion (TPM). Raw counts are also provided.
Assembly: GRCh38
Supplementary files format and content: Processed gene expression data is in .h5 format and contains CellBender-processed gene expression counts.
Supplementary files format and content: Processed V(D)J data is the output of CellRanger and in .csv format. It contains cell barcode and TCR A a B chain sequence as DNA and protein.
Supplementary files format and content: Supplementary .rds files contain Seurat objects for single-cell CSF, single-cell Infusion product, and single-nucleus tumor samples

source_name: Glioblastoma tumor

extract_protocol:
Tumors (single-nucleus): Single cell supsensions produced by tumor sample dissociation with gentleMACS Octo Dissociator and filtered through 75 uM strainer before single nucleus prep with CHAPS; Cerebrospinal and infusion product: Cells or nucei input directly into 10x genomics single cell library preparation protocol. Tumors (Bulk RNAseq from FFPE). Malignant cell-enriched regions were extracted from slides using laser-capture microdissection. RNA was extracted using a Qiagen RNA FFPE kit.
Chromium GEM-X Single Cell 5' Kit v3 with Chromium Single Cell Human TCR Amplification kit (single-cell, single-nucleus). SMART-Seq® Total RNA Pico Input with UMIs (ZapR™ Mammalian) (Bulk RNA sequencing)

treatment_protocol: 5e6, 1e7 or 2.5e7 bivalent CAR T cells targeting EGFR and IL13RA2 administered intracerebroventricularly

value: Glioblastoma tumor

value: Primary cells

value: GBM tumor cells

value: EGFR amplified

value: Pre-treatment


title: MRR, 2006131

description:
Library name: 2006131
MRR


title: Tumor_FFPE_P14_Post

description:
Library name: Tumor_FFPE_P14_Post
Column = P14_Post_1

value: Copy number gain, EGFRvIII

value: 5e6 bivalent CAR T cells (EGFR, IL13RA2)


title: MDA-MB-231_CTRL_3_cells expressing the negative control sgRNA_3

value: BREAST CANCER


title: Tumor_FFPE_P14_Pre

description:
Library name: Tumor_FFPE_P14_Pre
Column = P14_Pre_1


title: MRR, 2005126

description:
Library name: 2005126
MRR


title: Tumor_FFPE_P13_Post

description:
Library name: Tumor_FFPE_P13_Post
Column = P13_Post_1


title: MDA-MB-231_CTRL_2_cells expressing the negative control sgRNA_2


title: Tumor_FFPE_P13_Pre

description:
Library name: Tumor_FFPE_P13_Pre
Column = P13_Pre_1


title: MRR, 2004124

description:
Library name: 2004124
MRR


title: Tumor_FFPE_P7_Post

description:
Library name: Tumor_FFPE_P7_Post
Column = P07_Post_1

value: EGFR Potential copy number gain

value: 2.5e7 bivalent CAR T cells (EGFR, IL13RA2)


title: MDA-MB-231_CTRL_1_cells expressing the negative control sgRNA_1


title: Tumor_FFPE_P7_Pre

description:
Library name: Tumor_FFPE_P7_Pre
Column = P07_Pre_1


title: Tumor_FFPE_P4_Post

description:
Library name: Tumor_FFPE_P4_Post
Column = P04_Post_1

value: EGFR Copy number gain


title: BT-549_ZSWIM8_KD_3_cells expressing the ZSWIM targeting sgRNA_3

value: ZSWIM8 knock down


title: RNA-seq sequencing data 3 of mice liver tissues with DEHP exposure

description: Library name: Simple 6

value: liver tissues


title: Tumor_FFPE_P4_Pre

description:
Library name: Tumor_FFPE_P4_Pre
Column = P04_Pre_1


title: Tumor_FFPE_P1_Post

description:
Library name: Tumor_FFPE_P1_Post
Column = P01_Post_1

value: Copy number gain, p.R108K

value: 1e7 bivalent CAR T cells (EGFR, IL13RA2)


title: BT-549_ZSWIM8_KD_2_cells expressing the ZSWIM targeting sgRNA_2


title: Slide-094-PreMalignant-07-10-2023-Immune-005

description: Library name: DSP-1001660015531-A-B07

value: Immune

value: OED

value: Yes


title: Tumor_FFPE_P1_Pre_R2

description:
Library name: Tumor_FFPE_P1_Pre_R2
Column = P01_Pre_2

value: Glioblastoma tumor

value: Primary cells


title: Tumor_FFPE_P1_Pre_R1

description:
Library name: Tumor_FFPE_P1_Pre_R1
Column = P01_Pre_1

value: GBM tumor cells


title: MRR, 2004117

description:
Library name: 2004117
MRR

value: MRR


title: BT-549_ZSWIM8_KD_1_cells expressing the ZSWIM targeting sgRNA_1


title: H27907_PolII

city: Toronto

first: Shraddha

last: Pai

address: 160 College Street, Room 602

institute: University of Toronto

description: Library name: 5_08YD_017CSCRI_27907-102M_TotalPol2_hs_i93

data_processing:
Sequence Analysis: The 75-nt single-end (SE75) sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm(Li and Durbin 2009) (“bwa aln/samse” with default settings). Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome were used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) were  removed. Determination of Fragment Density: Since the 5´-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags were extended in silico (using Active Motif software) at their 3´- ends to a length of 200 bp, which corresponds to the average fragment length in the size-selected library. To identify the density of fragments (extended tags) along the genome, the genome was divided into 32-nt bins and the number of fragments in each bin was determined. Peak calling: Processing statistics are in Supplementary Table 10. Peaks were called using either MACS 2.1.019 or SICER20 algorithms. MACS default cutoff was pvalue 1e-7 for narrow peaks and 1e-1 for broad peaks. SICER default cutoff was FDR 1e-10 with gap parameter of 600 bp. Peak filtering was performed by removing false ChIP-Seq peaks as defined within the ENCODE blacklist. Proximal H3K27ac peaks within 2 kbp upstream or downstream of transcription start sites that did not overlap with H3K4me3 peaks or distal H3K27ac peaks residing outside the +-2k bp window were annotated as enhancer-like elements. H3K4me3 peaks overlapping transcription start site +- 200 bp windows were annotated as canonical promoter-like elements22. The elements were annotated for each sample and then combined for downstream analyses. Superenhancers were called by the ActiveMotif pipeline. The identification of Super Enhancers uses a proprietary algorithm that gives a very similar result as the ROSE software. In a first step, MACS or SICER peaks generated by the standard ChIP-Seq analysis are merged (or “stitched together”) if their inner distance is equal or less than 12,500 bp. In the second step, the stitched peak regions with the strongest signals (top 5%) are identified as Super Enhancers. Super Enhancer intervals are ranked by their signal strength (= tag numbers in stitched peak regions). For each sample, the top-ranked Super Enhancer is thus at the top of the list.
Assembly: hg38
Supplementary files format and content: BED file containing histone peak calls. BED files containing "_SE" in the filename are super-enhancer calls

source_name: Cerebellum

extract_protocol:
A standard laboratory protocol for DNA extraction was used by ActiveMotif
ActiveMotif used a standard library extraction protocol.

treatment_protocol: Fresh frozen cerebellum (130-180 mg) was sent to Active Motif for ChIP-seq using the following antibodies: H3K4me3 (Active Motif, cat#39159), H3K27Ac (Active Motif, cat #39133) and RNA Pol II (Active Motif, cat # 91151).

value: Cerebellum

tag: sample

tag: post conception_weeks

tag: antibody

value: PolII

tag: Sex

value: male


title: BT-549_CTRL_3_cells expressing the negative control sgRNA_3

value: BREAST CANCER

value: untreated


title: MRR, 2004116

description:
Library name: 2004116
MRR


title: H27907_H3K4me3

description: Library name: 3_08YB_017CSCRI_27907-102M_H3K4me3_hs_i91


title: H27556_H3K27Ac

description: Library name: 2_08YA_017CSCRI_27556-132M_H3K27Ac_hs_i90


title: MRR, 2003113

description:
Library name: 2003113
MRR


title: BT-549_CTRL_2_cells expressing the negative control sgRNA_2


title: H27907_H3K27Ac

description: Library name: 1_08Y9_017CSCRI_27907-102M_H3K27Ac_hs_i89


title: Slide-041-PreMalignant-07-10-2023-EPI-003

description: Library name: DSP-1001660015531-A-A05

value: Epi

value: No


title: MRR, 199897

description:
Library name: 199897
MRR