title: Preterm infant blood miRNA - A08 (BPD)

tag: birth weight (g)

tag: age at sampling (days of life)


title: HMLE, TWIST1-V5, ChIP, no doxy

status: Public on Jun 30 2026

type: SRA

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

country: Italy

institute: Istituto Italiano di Tecnologia

library_source: genomic

data_processing:
ChIP‐seq NGS reads were aligned to the human reference genome hg19 through the BWA aligner using default settings.
Peaks were called using the MACS2 software (v2.0.10) with the option “– mfold=7,30 ‐p 0.00001”, thus outputting only enriched regions withP‐value<10−5.
Assembly: hg19
Supplementary files format and content: excel file containing all the MACS2 peaks (p<0.00001)
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

source_name: breast

extract_protocol:
The preparation and processing of ChIP‐seq samples were performed as previously described (Sabò et al, 2014; PMID:25043028).
The ChIP protocol  was performed as previously described (Sabò et al, 2014; PMID:25043028), with an anti V5 antibody (Abcam, ab9116 ChIP grade, 10ug). DNA libraries were prepared with 2–10 ng of DNA using an in-house protocol (Blecher-Gonen et al., 2013 PMID:23429716) and sequenced on an Illumina HiSeq 2000.

tag: tissue

value: breast

tag: cell line

value: HMLE

tag: cell type

value: female

tag: chip antibody

value: V5 (Abcam, ab9116)

tag: treatment

value: untreated

tag: genotype


title: CRC777ORG

city: Tampere

first: Toni

middle: T

last: Seppälä

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

description:
Library name: CRC777ORG
Column name in raw_counts_pdtos.txt: CRC777ORG

library_source: transcriptomic

data_processing:
kallisto v.0.50.1 was used to extract transcript-level counts from fastq files. The human transcriptome index constructed from the Ensembl reference transcriptome version 108 was downloaded (https://github.com/pachterlab/kallisto-transcriptome-indices/releases) and the tximport R package v.1.32.0 was used to summarize transcript-level counts to gene-level and create a count matrix.
Assembly: Ensembl human reference transcriptome version 108
Supplementary files format and content: Tab-delimited text file contains estimated raw counts for each sample

molecule: total RNA

source_name: rectum

growth_protocol: Patient-derived tumor organoids were maintained in Organoid Culture Medium supplemented with growth factors in a humidified atmosphere with 5% CO2 at 37 C

extract_protocol:
Total RNA was extracted by using NucleoSpin RNA Plus Isolation Kit
Total RNA (100 ng) was ribo-depleted using Illumina's Stranded Total RNA Prep with Ribo-Zero Plus (20040529) and library preparation was completed using standard Illumina protocols.

treatment_protocol: Patient-derived tumor organoids were not treated prior to RNA isolation

value: rectum

value: Patient-derived tumor organoids

tag: passage

tag: sequencing batch


title: CRC986ORG

description:
Library name: CRC986ORG
Column name in raw_counts_pdtos.txt: CRC986ORG


title: HMLE, TWIST1-V5, input


title: Preterm infant blood miRNA - A07 (BPD)

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: BPD

tag: gestational age (weeks)

tag: rds

value: grade 1

tag: surfactant administration

value: yes

tag: mechanical ventilation from birth

value: no

tag: ivh

value: grade 2


title: CRISPRi lncRNA screen ML-2 replicate 1 Day 0

city: Frankfurt

first: Robert

last: Winkler

state: Hesse

address: Theodor-Stern-Kai 7

department: Department of Pediatrics

country: Germany

institute: Goethe University Frankfurt

description:
Library name: ML-2.R1.T0
Column name in counttable_screen_filtered.txt: ML-2.R1.T0

data_processing:
50 bp single-end reads were quantified using MAGeCK count 0.5.9.5 with the CRISPRi lncRNA library reference.
Screen hits were identified using the MAGeCK MLE algorithm 0.5.9.5 with copy number variation correction (--cnv-norm) and --norm-method none (counts were pre-normalized by total read count).
Assembly: GRCh38
Supplementary files format and content: counttable_screen_filtered.txt: Tab-delimited text file containing library-size normalized sgRNA counts. Columns: sgRNA (sgRNA identifier), Gene (target gene name), and one column per sample with normalized count values.
Library strategy: CRISPR Screen

growth_protocol: Human myeloid leukemia cell lines K562, THP-1, ML-2, M-07e, SKNO-1 and NOMO-1 were procured from DSMZ (Braunschweig, Germany). All cell lines were maintained as per the supplier's recommendations and were subjected to routine testing for Mycoplasma contamination.

extract_protocol:
Genomic DNA was extracted from samples at the beginning and end of the screen using the JetFlex Genomic DNA Purification Kit (Thermo Fisher Scientific).
The integrated sgRNA cassettes were amplified by PCR (NEBNext High-Fidelity 2x PCR Master Mix, New England Biolabs), gel-purified (GeneJET Gel Extraction Kit, Thermo Fisher Scientific), and sequenced on an Illumina HiSeq 2000 instrument (50 bp single-end).

treatment_protocol: Stable cell lines expressing the CRISPRi effector were generated with pLKO5d.SFFV.dCas9-KRAB.MeCP2.P2A.BSD. A custom CRISPRi library targeting a comprehensive list of lncRNAs assembled from GENCODE v25, LNCipedia 4.0 and NONCODE v4 was cloned into the SGL40C.EFS.dTomato vector (Addgene #89395) via BsmBI restriction sites. The library comprises three to nine sgRNAs per target, tiling the 250 bp window immediately downstream of the annotated transcription start site, and incorporates non-targeting controls against luciferase and positive depletion controls targeting essential genes such as MYC, MYB, and RPL9. Cells were transduced with the lentiviral library at 30% efficacy and then cultured for 18 population doublings, ensuring a library representation of at least 1000-fold was maintained throughout.

value: acute myeloid leukemia

tag: replicate

tag: timepoint

value: Day 0


title: CRC297ORG

description:
Library name: CRC297ORG
Column name in raw_counts_pdtos.txt: CRC297ORG


title: Preterm infant blood miRNA - B08 (Control)

value: Control

tag: birth weight (g)

tag: age at sampling (days of life)


title: In vivo Tcf7 sort CRISPR screen 2 sample-barcode pool

city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 415 Main Street, Room 6032

department: Cell Circuits Program / Center for Cell Circuits

country: USA

institute: Broad Institute

description:
Library name: pooled_crispr_in_vivo_tcf7_2_in_vivo_tcf7_2
Sample-barcode-demultiplexed sgRNA amplicon sequencing library from the second B16-OVA in vivo Tcf7 sort screen. Cas9-expressing OT-I CD8 T cells were transduced with a follow-up sgRNA library targeting candidate Tcf7 regulators and control guides, enriched for Thy1.1+ cells, and transferred into B16-OVA tumor-bearing recipient mice. Recovered tumor and draining-lymph-node samples included input or lymph-node sgRNA-representation controls and tumor-infiltrating Tcf7-high and Tcf7-low fractions sequenced to quantify in vivo sgRNA enrichment. Processed guide-count matrix columns are Male_input, Female_input, tcf7_negative, tcf7_positive, dLN, CP3_plasmid_1 in file in_vivo_2.txt.
in_vivo_2.txt

data_processing:
Guide sequencing reads were processed with PoolQ using sample-barcode or condition tables and the corresponding guide sequence sets.
Supplementary files format and content: Tab-delimited guide-by-sample count matrices. Rows are sgRNAs with guide sequence, guide identifier, and target-gene fields where available; columns contain complete sgRNA counts for the submitted samples or conditions.
Library strategy: CRISPR Screen

organism: Mus musculus

source_name: B16-OVA tumor and draining lymph node

growth_protocol: Primary Cas9-expressing mouse CD8 T cells were isolated from spleen and lymph node and transduced with pooled sgRNA lentiviral libraries on RetroNectin-coated plates in complete T cell medium containing IL-7, IL-15, and LentiBOOST. Cells were maintained without TCR activation through day 5 post-transduction before Thy1.1 enrichment or screen-specific culture. For in vivo Tcf7 sort screens, transduced Cas9 x OT-I CD8 T cells were transferred into congenic recipient mice, and recipients were implanted bilaterally with B16-OVA tumors 1 day after T cell transfer.

extract_protocol:
Genomic DNA was isolated from sorted cell populations, input cell populations, tumor-infiltrating T cell samples, draining-lymph-node samples, or plasmid-library controls for guide-count sequencing. Standard cell pellets were processed using QIAamp DNA Mini Kit or QIAamp Mini spin-column workflows. Fixed or low-input sorted material was recovered using SPRI-based DNA cleanup where appropriate. Tumor-infiltrating T cell guide-count samples were prepared from tumor digests enriched over Lympholyte-M and/or with CD8 TIL MicroBeads before pelleting or freezing for genomic DNA isolation. The extracted genomic DNA or plasmid DNA was used as input for integrated sgRNA cassette amplification.
Integrated sgRNA cassettes were amplified from genomic DNA using indexed Illumina-compatible primers following Broad/GPP pooled-screen PCR workflows. Standard pXPR guide-count PCR used up to 10 ug genomic DNA per 100 uL reaction with Titanium Taq DNA polymerase, DMSO, a staggered P5 primer mix, and a unique indexed P7 primer. Primer sets were selected for the vector backbone, including pXPR_045-compatible and pXPR_206 or pRDA_206-derived vectors. For lower-input or nested tissue workflows, PCR cycle number was selected by qPCR using Q5 Hot Start high-fidelity polymerase, and available genomic DNA was split across multiple reactions to limit PCR jackpotting. No-template controls and test gels were used to check contamination and expected amplicon size. PCR products were pooled by sample and purified by AMPure XP cleanup, double-sided AMPure XP size selection at 0.6x/1.2x, or gel extraction depending on amplicon workflow and input complexity. Purified amplicons were quantified by Qubit and Bioanalyzer or TapeStation, pooled, and sequenced on Illumina MiSeq or NextSeq instruments using custom sequencing primers where required.

treatment_protocol: In vitro screen samples included unsorted input and plasmid-library controls and sorted Tcf7-, Prdm1-, Eomes-, or Tox-high and -low populations. Acute stimulation used overnight culture on plates coated with anti-CD3 clone 145-2C11 and anti-CD28 clone 37.51 at 5 ug/mL each, followed by culture off stimulation plates in cytokine-containing T cell medium. Chronic stimulation kept cells on anti-CD3/CD28-coated plates throughout the experiment, and hypoxia screens were cultured under 1% oxygen. Tcf7, Prdm1, Eomes, and Tox screens used intracellular transcription-factor staining to identify high- and low-expressing cells except where Tcf7-GFP reporter sorting was used; some Tcf7 sorts were divided into four bins to separate highest and lower-high populations from lowest and higher-low populations. In vivo Tcf7 sort screens recovered input cells, draining-lymph-node samples, tumor-infiltrating Tcf7-high and Tcf7-low fractions, and plasmid-library controls, typically 14 days after tumor implantation; male and female samples were processed separately where indicated.

tag: tissue

value: B16-OVA tumor and draining lymph node

value: CD8 T cells

value: in vivo B16-OVA tumor challenge; Tcf7 sort screen 2 recovered tumor and draining-lymph-node sample-barcode pool


title: In vivo Tcf7 sort CRISPR screen 1 sample-barcode pool

description:
Library name: pooled_crispr_in_vivo_1_in_vivo_1
Sample-barcode-demultiplexed sgRNA amplicon sequencing library from the first B16-OVA in vivo Tcf7 sort screen. Cas9-expressing OT-I CD8 T cells were transduced with a follow-up sgRNA library targeting candidate Tcf7 regulators and control guides, enriched for Thy1.1+ cells, and transferred into B16-OVA tumor-bearing recipient mice. Recovered tumor and draining-lymph-node samples included input or lymph-node sgRNA-representation controls and tumor-infiltrating Tcf7-high and Tcf7-low fractions sequenced to quantify in vivo sgRNA enrichment. Processed guide-count matrix columns are Male_input, Female_input, Male_dLN, Female_dLN, TIL_GFP_Positive, TIL_GFP_Negative, CP1_plasmid in file in_vivo_1.txt.
in_vivo_1.txt

tag: cell type

value: in vivo B16-OVA tumor challenge; Tcf7 sort screen 1 recovered tumor and draining-lymph-node sample-barcode pool


title: CRC899ORG

description:
Library name: CRC899ORG
Column name in raw_counts_pdtos.txt: CRC899ORG

tag: cell line


title: Preterm infant blood miRNA - A06 (BPD)


title: Focused Tcf7-GFP reporter D-high bin

description:
Library name: Tcf7_GFP_bin_D_high
sgRNA amplicon sequencing library from the focused in vitro Tcf7-GFP reporter CRISPR screen. Cas9-expressing CD8 T cells were transduced with a focused Tcf7-regulator sgRNA library, stimulated with anti-CD3/CD28, sorted as live cells by Tcf7-GFP reporter expression into the D-high bin, the highest Tcf7-expression bin. The library was sequenced to quantify sgRNA abundance in that sorted Tcf7-expression bin. Processed guide-count matrix column is Tcf7_GFP_bin_D_high in file in_vitro_tcf7_gfp.txt.
in_vitro_tcf7_gfp.txt

source_name: spleen and lymph node

value: spleen and lymph node

tag: treatment

value: focused Tcf7-regulator sgRNA library; anti-CD3/CD28 stimulation; live Tcf7-GFP D-high sort


title: Preterm infant blood miRNA - A05 (BPD)


title: Focused Tcf7-GFP reporter B-low bin

description:
Library name: Tcf7_GFP_bin_B_low
sgRNA amplicon sequencing library from the focused in vitro Tcf7-GFP reporter CRISPR screen. Cas9-expressing CD8 T cells were transduced with a focused Tcf7-regulator sgRNA library, stimulated with anti-CD3/CD28, sorted as live cells by Tcf7-GFP reporter expression into the B-low bin, the second-lowest Tcf7-expression bin. The library was sequenced to quantify sgRNA abundance in that sorted Tcf7-expression bin. Processed guide-count matrix column is Tcf7_GFP_bin_B_low in file in_vitro_tcf7_gfp.txt.
in_vitro_tcf7_gfp.txt

value: focused Tcf7-regulator sgRNA library; anti-CD3/CD28 stimulation; live Tcf7-GFP B-low sort


title: Focused Tcf7-GFP reporter C-high bin

description:
Library name: Tcf7_GFP_bin_C_high
sgRNA amplicon sequencing library from the focused in vitro Tcf7-GFP reporter CRISPR screen. Cas9-expressing CD8 T cells were transduced with a focused Tcf7-regulator sgRNA library, stimulated with anti-CD3/CD28, sorted as live cells by Tcf7-GFP reporter expression into the C-high bin, the second-highest Tcf7-expression bin. The library was sequenced to quantify sgRNA abundance in that sorted Tcf7-expression bin. Processed guide-count matrix column is Tcf7_GFP_bin_C_high in file in_vitro_tcf7_gfp.txt.
in_vitro_tcf7_gfp.txt

value: focused Tcf7-regulator sgRNA library; anti-CD3/CD28 stimulation; live Tcf7-GFP C-high sort


title: CRC879ORG

description:
Library name: CRC879ORG
Column name in raw_counts_pdtos.txt: CRC879ORG

value: rectum

value: Patient-derived tumor organoids


title: Focused Tcf7-GFP reporter A-low bin

description:
Library name: Tcf7_GFP_bin_A_low
sgRNA amplicon sequencing library from the focused in vitro Tcf7-GFP reporter CRISPR screen. Cas9-expressing CD8 T cells were transduced with a focused Tcf7-regulator sgRNA library, stimulated with anti-CD3/CD28, sorted as live cells by Tcf7-GFP reporter expression into the A-low bin, the lowest Tcf7-expression bin. The library was sequenced to quantify sgRNA abundance in that sorted Tcf7-expression bin. Processed guide-count matrix column is Tcf7_GFP_bin_A_low in file in_vitro_tcf7_gfp.txt.
in_vitro_tcf7_gfp.txt

value: focused Tcf7-regulator sgRNA library; anti-CD3/CD28 stimulation; live Tcf7-GFP A-low sort


title: Preterm infant blood miRNA - A04 (BPD)

value: BPD

value: grade 1

value: yes


title: CRC882ORG

description:
Library name: CRC882ORG
Column name in raw_counts_pdtos.txt: CRC882ORG


title: Focused intracellular Tcf7 antibody D-high bin

description:
Library name: Tcf7_Ab_bin_D_high
sgRNA amplicon sequencing library from the focused in vitro intracellular Tcf7 antibody CRISPR screen. Cas9-expressing CD8 T cells were transduced with a focused Tcf7-regulator sgRNA library, stimulated with anti-CD3/CD28, fixed, stained intracellularly for Tcf7, and sorted into the D-high bin, the highest Tcf7-expression bin. The library was sequenced to quantify sgRNA abundance in that sorted Tcf7-expression bin. Processed guide-count matrix column is Tcf7_Ab_bin_D_high in file in_vitro_tcf7_antibody.txt.
in_vitro_tcf7_antibody.txt

value: focused Tcf7-regulator sgRNA library; anti-CD3/CD28 stimulation; intracellular Tcf7 antibody D-high sort


title: Preterm infant blood miRNA - A03 (BPD)

value: grade 2


title: Focused intracellular Tcf7 antibody C-high bin

description:
Library name: Tcf7_Ab_bin_C_high
sgRNA amplicon sequencing library from the focused in vitro intracellular Tcf7 antibody CRISPR screen. Cas9-expressing CD8 T cells were transduced with a focused Tcf7-regulator sgRNA library, stimulated with anti-CD3/CD28, fixed, stained intracellularly for Tcf7, and sorted into the C-high bin, the second-highest Tcf7-expression bin. The library was sequenced to quantify sgRNA abundance in that sorted Tcf7-expression bin. Processed guide-count matrix column is Tcf7_Ab_bin_C_high in file in_vitro_tcf7_antibody.txt.
in_vitro_tcf7_antibody.txt

value: focused Tcf7-regulator sgRNA library; anti-CD3/CD28 stimulation; intracellular Tcf7 antibody C-high sort


title: CRC622ORG

description:
Library name: CRC622ORG
Column name in raw_counts_pdtos.txt: CRC622ORG


title: Focused intracellular Tcf7 antibody B-low bin

description:
Library name: Tcf7_Ab_bin_B_low
sgRNA amplicon sequencing library from the focused in vitro intracellular Tcf7 antibody CRISPR screen. Cas9-expressing CD8 T cells were transduced with a focused Tcf7-regulator sgRNA library, stimulated with anti-CD3/CD28, fixed, stained intracellularly for Tcf7, and sorted into the B-low bin, the second-lowest Tcf7-expression bin. The library was sequenced to quantify sgRNA abundance in that sorted Tcf7-expression bin. Processed guide-count matrix column is Tcf7_Ab_bin_B_low in file in_vitro_tcf7_antibody.txt.
in_vitro_tcf7_antibody.txt

value: focused Tcf7-regulator sgRNA library; anti-CD3/CD28 stimulation; intracellular Tcf7 antibody B-low sort


title: Focused intracellular Tcf7 antibody A-low bin

description:
Library name: Tcf7_Ab_bin_A_low
sgRNA amplicon sequencing library from the focused in vitro intracellular Tcf7 antibody CRISPR screen. Cas9-expressing CD8 T cells were transduced with a focused Tcf7-regulator sgRNA library, stimulated with anti-CD3/CD28, fixed, stained intracellularly for Tcf7, and sorted into the A-low bin, the lowest Tcf7-expression bin. The library was sequenced to quantify sgRNA abundance in that sorted Tcf7-expression bin. Processed guide-count matrix column is Tcf7_Ab_bin_A_low in file in_vitro_tcf7_antibody.txt.
in_vitro_tcf7_antibody.txt

value: CD8 T cells

value: focused Tcf7-regulator sgRNA library; anti-CD3/CD28 stimulation; intracellular Tcf7 antibody A-low sort


title: CRC165ORG

description:
Library name: CRC165ORG
Column name in raw_counts_pdtos.txt: CRC165ORG


title: Focused Tcf7-regulator pilot OT-I stimulated input

description:
Library name: OT1stim_Lib
Unsorted sgRNA amplicon sequencing library from the focused in vitro Tcf7-regulator pilot CRISPR screen. OT-I CD8 T cells were transduced with the focused sgRNA library and stimulated with anti-CD3/CD28. The library was sequenced to quantify sgRNA representation for the OT-I intracellular Tcf7 antibody arm. Processed guide-count matrix column is OT1stim_Lib in file in_vitro_tcf7_pilot_controls.txt.
in_vitro_tcf7_pilot_controls.txt

value: focused Tcf7-regulator sgRNA library; anti-CD3/CD28 stimulation; OT-I unsorted input


title: Focused Tcf7-regulator pilot OT-I unstimulated input

description:
Library name: OT1unstim_lib
Unsorted sgRNA amplicon sequencing library from the focused in vitro Tcf7-regulator pilot CRISPR screen. OT-I CD8 T cells were transduced with the focused sgRNA library and maintained without CD3/CD28 stimulation. The library was sequenced to quantify sgRNA representation for the OT-I unstimulated arm. Processed guide-count matrix column is OT1unstim_lib in file in_vitro_tcf7_pilot_controls.txt.
in_vitro_tcf7_pilot_controls.txt

value: spleen and lymph node

value: focused Tcf7-regulator sgRNA library; no CD3/CD28 stimulation; unsorted input


title: Focused Tcf7-regulator pilot Tcf7-GFP stimulated input

description:
Library name: Tcf7stim_Lib
Unsorted sgRNA amplicon sequencing library from the focused in vitro Tcf7-regulator pilot CRISPR screen. Tcf7-GFP reporter CD8 T cells were transduced with the focused sgRNA library and stimulated with anti-CD3/CD28. The library was sequenced to quantify sgRNA representation for the Tcf7-GFP reporter arm. Processed guide-count matrix column is Tcf7stim_Lib in file in_vitro_tcf7_pilot_controls.txt.
in_vitro_tcf7_pilot_controls.txt

value: focused Tcf7-regulator sgRNA library; anti-CD3/CD28 stimulation; Tcf7-GFP reporter unsorted input


title: Focused Tcf7-regulator pilot OT-I Tcf7 antibody D-high bin

description:
Library name: OT1_D
sgRNA amplicon sequencing library from the focused in vitro Tcf7-regulator pilot CRISPR screen. OT-I CD8 T cells were transduced with the focused sgRNA library, stimulated with anti-CD3/CD28, stained intracellularly for Tcf7, and sorted into the D-high bin, the highest Tcf7-expression bin. The library was sequenced to quantify sgRNA abundance in that Tcf7-expression bin. Processed guide-count matrix column is OT1_D in file in_vitro_tcf7_pilot_controls.txt.
in_vitro_tcf7_pilot_controls.txt


title: CRC356ORG_1

description:
Library name: CRC356ORG_1
Column name in raw_counts_pdtos.txt: CRC356ORG_1


title: Preterm infant blood miRNA - A01 (BPD)


title: Preterm infant blood miRNA - A02 (BPD)


title: Focused Tcf7-regulator pilot OT-I Tcf7 antibody C-high bin

description:
Library name: OT1_C
sgRNA amplicon sequencing library from the focused in vitro Tcf7-regulator pilot CRISPR screen. OT-I CD8 T cells were transduced with the focused sgRNA library, stimulated with anti-CD3/CD28, stained intracellularly for Tcf7, and sorted into the C-high bin, the second-highest Tcf7-expression bin. The library was sequenced to quantify sgRNA abundance in that Tcf7-expression bin. Processed guide-count matrix column is OT1_C in file in_vitro_tcf7_pilot_controls.txt.
in_vitro_tcf7_pilot_controls.txt


title: CRC839ORG

description:
Library name: CRC839ORG
Column name in raw_counts_pdtos.txt: CRC839ORG


title: Focused Tcf7-regulator pilot OT-I Tcf7 antibody A-low bin

description:
Library name: OT1_A
sgRNA amplicon sequencing library from the focused in vitro Tcf7-regulator pilot CRISPR screen. OT-I CD8 T cells were transduced with the focused sgRNA library, stimulated with anti-CD3/CD28, stained intracellularly for Tcf7, and sorted into the A-low bin, the lowest Tcf7-expression bin. The library was sequenced to quantify sgRNA abundance in that Tcf7-expression bin. Processed guide-count matrix column is OT1_A in file in_vitro_tcf7_pilot_controls.txt.
in_vitro_tcf7_pilot_controls.txt


title: Focused Tcf7-regulator pilot OT-I Tcf7 antibody B-low bin

description:
Library name: OT1_B
sgRNA amplicon sequencing library from the focused in vitro Tcf7-regulator pilot CRISPR screen. OT-I CD8 T cells were transduced with the focused sgRNA library, stimulated with anti-CD3/CD28, stained intracellularly for Tcf7, and sorted into the B-low bin, the second-lowest Tcf7-expression bin. The library was sequenced to quantify sgRNA abundance in that Tcf7-expression bin. Processed guide-count matrix column is OT1_B in file in_vitro_tcf7_pilot_controls.txt.
in_vitro_tcf7_pilot_controls.txt


title: Focused Tcf7-regulator pilot unstimulated A-low bin

description:
Library name: UnstimA
sgRNA amplicon sequencing library from the focused in vitro Tcf7-regulator pilot CRISPR screen. Cas9-expressing CD8 T cells were transduced with the focused sgRNA library and maintained without CD3/CD28 stimulation, then sorted into the A-low bin, the lowest Tcf7-expression bin. The library was sequenced to quantify sgRNA abundance in that Tcf7-expression bin. Processed guide-count matrix column is UnstimA in file in_vitro_tcf7_pilot_controls.txt.
in_vitro_tcf7_pilot_controls.txt

value: focused Tcf7-regulator sgRNA library; no CD3/CD28 stimulation; Tcf7 A-low sort


title: CRC303ORG

description:
Library name: CRC303ORG
Column name in raw_counts_pdtos.txt: CRC303ORG

value: rectum


title: Focused Tcf7-regulator pilot unstimulated D-high bin

description:
Library name: UnstimD
sgRNA amplicon sequencing library from the focused in vitro Tcf7-regulator pilot CRISPR screen. Cas9-expressing CD8 T cells were transduced with the focused sgRNA library and maintained without CD3/CD28 stimulation, then sorted into the D-high bin, the highest Tcf7-expression bin. The library was sequenced to quantify sgRNA abundance in that Tcf7-expression bin. Processed guide-count matrix column is UnstimD in file in_vitro_tcf7_pilot_controls.txt.
in_vitro_tcf7_pilot_controls.txt

value: focused Tcf7-regulator sgRNA library; no CD3/CD28 stimulation; Tcf7 D-high sort


title: Human glomerular endothelial cell, Donor 3, 24hr hypoxia, miRNA

city: Singapore

first: Chong Yun

last: Pang

address: 60 Nanyang Dr, School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description:
Library name: Sample12
Column in rawount file: 30667-012 - Total counts

data_processing:
miRNA sequencing was processed using Qiagen CLC Genomics Server V21.0.4 using standard parameters  to map to miRBase V22.
Assembly: miRBase V22 for miRNA
Supplementary files format and content: csv files include rawcounts for miRNA.

source_name: Primary glomerular endothelial cells

growth_protocol: Primary glomerular endothelial cells were cultured with complete endothelial media (Cell Biologics) in a humidified incubator at 37C.

extract_protocol:
RNA were extracted using miRNeasy mini kit (Qiagen). 1ug of Total RNA was sent to Qiagen for miRNA  library preparation.
miRNA library was prepared using Qiaseq miRNA library kit (Qiagen).

treatment_protocol: Cells were cultured under 1% oxygen condition in a hypoxic incubator to mimic ischemia for the stipulated duration.

value: Primary glomerular endothelial cells

value: Hypoxia


title: Human glomerular endothelial cell, Donor 3, 12hr hypoxia, miRNA

description:
Library name: Sample11
Column in rawount file: 30667-011 - Total counts


title: CRC128ORG

description:
Library name: CRC128ORG
Column name in raw_counts_pdtos.txt: CRC128ORG

value: Patient-derived tumor organoids


title: Human glomerular endothelial cell, Donor 3, Untreated, miRNA

description:
Library name: Sample9
Column in rawount file: 30667-009 - Total counts

value: Untreated


title: CRC049ORG

description:
Library name: CRC049ORG
Column name in raw_counts_pdtos.txt: CRC049ORG


title: Human glomerular endothelial cell, Donor 3, 4hr hypoxia, miRNA

description:
Library name: Sample10
Column in rawount file: 30667-010 - Total counts


title: Human glomerular endothelial cell, Donor 2, 24hr hypoxia, miRNA

description:
Library name: Sample8
Column in rawount file: 30667-008 - Total counts


title: CRC634ORG

description:
Library name: CRC634ORG
Column name in raw_counts_pdtos.txt: CRC634ORG


title: Human glomerular endothelial cell, Donor 2, 4hr hypoxia, miRNA

description:
Library name: Sample6
Column in rawount file: 30667-006 - Total counts


title: Human glomerular endothelial cell, Donor 2, 12hr hypoxia, miRNA

description:
Library name: Sample7
Column in rawount file: 30667-007 - Total counts


title: Human glomerular endothelial cell, Donor 2, Untreated, miRNA

description:
Library name: Sample5
Column in rawount file: 30667-005 - Total counts


title: CRC146ORG

description:
Library name: CRC146ORG
Column name in raw_counts_pdtos.txt: CRC146ORG

source_name: colon

value: colon


title: Human glomerular endothelial cell, Donor 1, 24hr hypoxia, miRNA

description:
Library name: Sample4
Column in rawount file: 30667-004 - Total counts


title: Human glomerular endothelial cell, Donor 1, 12hr hypoxia, miRNA

description:
Library name: Sample3
Column in rawount file: 30667-003 - Total counts


title: CRC228ORG

description:
Library name: CRC228ORG
Column name in raw_counts_pdtos.txt: CRC228ORG


title: Human glomerular endothelial cell, Donor 1, 4hr hypoxia, miRNA

description:
Library name: Sample2
Column in rawount file: 30667-002 - Total counts


title: CRC074ORG

description:
Library name: CRC074ORG
Column name in raw_counts_pdtos.txt: CRC074ORG


title: Human glomerular endothelial cell, Donor 1, Untreated, miRNA

description:
Library name: Sample1
Column in rawount file: 30667-001 - Total counts


title: CRC024ORG

description:
Library name: CRC024ORG
Column name in raw_counts_pdtos.txt: CRC024ORG


title: CRC153ORG

description:
Library name: CRC153ORG
Column name in raw_counts_pdtos.txt: CRC153ORG


title: Final-186-Aug-Benign-08-13-2024-Segment 2-005

city: Kansas City

first: Harsh

last: Pathak

state: KS

address: 3901 Rainbow Blvd

institute: KUMC

description: Library name: DSP-1001660020046-C-H11

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

source_name: Benign

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.

value: Immune

value: Benign

tag: transformed status


title: Final-186-Aug-Benign-08-13-2024-EPI-005

description: Library name: DSP-1001660020046-C-H10

value: Epi


title: Final-186-Aug-Benign-08-13-2024-EPI-004

description: Library name: DSP-1001660020046-C-H08


title: CRC321ORG

description:
Library name: CRC321ORG
Column name in raw_counts_pdtos.txt: CRC321ORG

tag: passage


title: Final-186-Aug-Benign-08-13-2024-EPI-003

description: Library name: DSP-1001660020046-C-H07


title: Final-186-Aug-Benign-08-13-2024-Segment 2-004

description: Library name: DSP-1001660020046-C-H09


title: CRC997ORG

description:
Library name: CRC997ORG
Column name in raw_counts_pdtos.txt: CRC997ORG

tag: sequencing batch


title: Final-186-Aug-Benign-08-13-2024-Segment 2-002

description: Library name: DSP-1001660020046-C-H06


title: Final-186-Aug-Benign-08-13-2024-EPI-002

description: Library name: DSP-1001660020046-C-H05


title: Final-186-Aug-Benign-08-13-2024-Segment 2-001

description: Library name: DSP-1001660020046-C-H04


title: Final-054-Aug-OED-08-13-2024-Immune-005

description: Library name: DSP-1001660020046-C-H02

source_name: OED

value: OED

value: No


title: Final-186-Aug-Benign-08-13-2024-EPI-001

description: Library name: DSP-1001660020046-C-H03


title: Male patient 3 recurrent tumor

city: Iowa City

first: Zhijie

last: Li

state: IA

address: 285 Newton Road

institute: University of Iowa

description:
Library name: Samples 16
Male_Patients_Recurrent_vs_Nonrecurrent_RNAseq_Differential_test.xlsx

data_processing:
All the raw sequencing data were assessed by FastQC for quality control, and reads were mapped with STAR to human reference genome hg38 with default parameters. FeatureCounts were used to calculate read counts for each gene from STAR output bam files. Differential gene expression analysis was performed using DEseq2. P-value < 0.05 was used as the threshold for statistically significant difference.
Assembly: hg38
Supplementary files format and content: Counts for each sample
Supplementary files format and content: Differentially expressed features for each sample

source_name: Papillary thyroid cancer

extract_protocol:
RNA-seq experiments were performed on formalin-fixed, paraffin-embedded (FFPE) tissue specimens of thyroid cancer patient. RNA was isolated using the PureLink FFPE RNA isolation Kit (457015, Qiagen) according to the manufacturer’s instructions.
RNA was submitted to CD Genomics (Shirley, NY) for library construction and RNA sequencing with 75 bp paired-end reads on Novaseq6000 platform.

tag: Sex

value: Male

value: Papillary thyroid cancer

tag: biopsy proven_recurrence

value: Yes


title: CRC561ORG

description:
Library name: CRC561ORG
Column name in raw_counts_pdtos.txt: CRC561ORG


title: Final-054-Aug-OED-08-13-2024-EPI-005

description: Library name: DSP-1001660020046-C-H01


title: Male patient 2 recurrent tumor

description:
Library name: Samples 15
Male_Patients_Recurrent_vs_Nonrecurrent_RNAseq_Differential_test.xlsx


title: Final-054-Aug-OED-08-13-2024-EPI-004

description: Library name: DSP-1001660020046-C-G12


title: Male patient 1 recurrent tumor

description:
Library name: Samples 14
Male_Patients_Recurrent_vs_Nonrecurrent_RNAseq_Differential_test.xlsx


title: Final-054-Aug-OED-08-13-2024-Immune-002

description: Library name: DSP-1001660020046-C-G09


title: Final-054-Aug-OED-08-13-2024-Immune-003

description: Library name: DSP-1001660020046-C-G11


title: Final-054-Aug-OED-08-13-2024-EPI-003

description: Library name: DSP-1001660020046-C-G10


title: M1 cells-shIGF2BP1, rep2

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Neuroscience and Experimental Therapeutics

institute: Penn State University

description: Library name: M4_2

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.20.0.422) allowing no mismatches in the index read. BBDuk was used to trim/filter low quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the mouse reference genome (GRCm38) was done using HISAT2 (version 2.1.0) applying --no-mixed and --no-discordant options. Read counts were calculated using HTSeq by supplementing Ensembl gene annotation (GRCm38.78).
Assembly: GRCm38.78
Supplementary files format and content: raw read counts are provided in a csv file

growth_protocol: Both cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% v/v FBS and 100 units/ml penicillin and streptomycin, in humidified atmosphere with 5% CO2 at 37 degree.

extract_protocol:
Total RNA was extracted using Direct-zol™ RNA Miniprep Kit (Zymo Research), and 600 ng of total RNA was used for mRNA purification.
The cDNA libraries were prepared using the Illumina® Stranded mRNA Prep, Ligation kit (Illumina) as per the manufacturer’s instructions. Briefly, polyA RNA was purified from 200 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique dual index sequences (IDT® for Illumina® RNA UD Indexes Set A, Ligation, Illumina) were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). The libraries were pooled and diluted to 3 nM using 10 mM Tris-HCl, pH 8.5 and then denatured using the Illumina protocol. The denatured libraries were loaded onto an S1 flow cell on an Illumina NovaSeq 6000 (Illumina) and run for 2X53 cycles according to the manufacturer's instructions.

treatment_protocol: shRNA expression was induced by 4-6 ug/ml of doxycycline (6 days treatment).

value: neuroblastoma cell line

tag: genotype

value: IGF2BP1 knockdown

value: doxycycline, for shRNA induction


title: M1 cells-shIGF2BP1, rep3

description: Library name: M4_3


title: Final-054-Aug-OED-08-13-2024-EPI-002

description: Library name: DSP-1001660020046-C-G08


title: Female patient 5 recurrent tumor

description:
Library name: Samples 13
Female_Patients_Recurrent_vs_Nonrecurrent_RNAseq_Differential_test.xlsx

value: Female


title: Final-054-Aug-OED-08-13-2024-Immune-001

description: Library name: DSP-1001660020046-C-G07


title: Final-038-Aug-OED-08-09-2024-Immune-004

description: Library name: DSP-1001660020046-C-G06


title: Female patient 4 recurrent tumor

description:
Library name: Samples 12
Female_Patients_Recurrent_vs_Nonrecurrent_RNAseq_Differential_test.xlsx


title: Final-038-Aug-OED-08-09-2024-EPI-004

description: Library name: DSP-1001660020046-C-G05


title: M1 cells-shIGF2BP1, rep1

description: Library name: M4_1


title: Final-038-Aug-OED-08-09-2024-Immune-003

description: Library name: DSP-1001660020046-C-G04


title: M1 cells-shNT control, rep3

description: Library name: SC_3

value: WT


title: Female patient 3 recurrent tumor

description:
Library name: Samples 11
Female_Patients_Recurrent_vs_Nonrecurrent_RNAseq_Differential_test.xlsx


title: Final-038-Aug-OED-08-09-2024-EPI-003

description: Library name: DSP-1001660020046-C-G03


title: M1 cells-shNT control, rep2

description: Library name: SC_2


title: Female patient 2 recurrent tumor

description:
Library name: Samples 10
Female_Patients_Recurrent_vs_Nonrecurrent_RNAseq_Differential_test.xlsx


title: Final-038-Aug-OED-08-09-2024-EPI-002

description: Library name: DSP-1001660020046-C-G01


title: M1 cells-shNT control, rep1

description: Library name: SC_1


title: Final-038-Aug-OED-08-09-2024-Immune-002

description: Library name: DSP-1001660020046-C-G02


title: Female patient 1 recurrent tumor

description:
Library name: Samples 9
Female_Patients_Recurrent_vs_Nonrecurrent_RNAseq_Differential_test.xlsx


title: Final-038-Aug-OED-08-09-2024-EPI-001

description: Library name: DSP-1001660020046-C-F11


title: Final-038-Aug-OED-08-09-2024-Immune-001

description: Library name: DSP-1001660020046-C-F12


title: Final-203-Aug-Benign-08-09-2024-Immune-004

description: Library name: DSP-1001660020046-C-F10


title: Male patient 3 non-recurrent tumor

description:
Library name: Samples 8
Male_Patients_Recurrent_vs_Nonrecurrent_RNAseq_Differential_test.xlsx


title: BEMF spheroid, doxorubicin-treated, biological replicate 1

city: Cluj Napoca

first: Ovidiu

middle: Ilie

last: Pavel

state: Cluj

address: Clinicilor 5-7

department: Doctoral School of Integrative Biology

country: Romania

institute: Babes-Bolyai University

description:
Library name: BEMF_D1
BEMF Doxorubicin 1

data_processing:
Raw paired-end reads were quality controlled using fastp (v0.23.4) with default parameters; QC metrics aggregated and inspected using MultiQC (v1.28).
Transcript abundances were quantified using Salmon (v1.10.3) in mapping-based mode with a decoy-aware index (k=31) built from GENCODE vM36 transcript annotations and the GRCm39 primary genome assembly.
Transcript-level estimates were imported into R (v4.5.1) using tximport (v1.36.1) and summarized to gene-level counts using GENCODE vM36 transcript-gene annotations.
Gene-level counts were normalized and modelled using DESeq2 (v1.48.2) with a design formula of ~cell_composition + treatment + cell_composition:treatment; genes were filtered to require a normalized count >=10 in at least 2 samples.
Log2 fold changes were shrunken using the apeglm method (v1.30.0); multiple-testing correction was applied using the Benjamini-Hochberg procedure.
Assembly: GRCm39 (GENCODE vM36)
Supplementary files format and content: Tab-delimited transcript counts as exported by Salmon

source_name: N/A (in vitro 3D spheroid culture)

growth_protocol: Spheroids were formed by the liquid overlay technique in ultra-low attachment plates. B16.F10 melanoma cells, 2H11 endothelial cells, and bone marrow-derived macrophages were embedded in 1.5% extracellular matrix (Sigma-Aldrich) at a ratio of 1:1:4 (BEM); BEMF spheroids additionally incorporated primary murine dermal fibroblasts at a ratio of 1:1:4:1. Plates were centrifuged (350 x g, 15 min) and incubated at 37C, 5% CO2 for 4 days to allow spheroid formation.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, 74104) according to the manufacturer's instructions. Spheroids were lysed in RLT buffer and loaded onto RNeasy spin columns; RNA was eluted in 40 microL RNase-free water. RNA concentration and purity were assessed using a NanoDrop 1000 spectrophotometer (Thermo Scientific).
Strand-specific cDNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina), with quality control performed by Macrogen Europe (Netherlands).

treatment_protocol: 4-day-old spheroids were treated with doxorubicin (Sigma-Aldrich) at the model-specific IC30 concentration (0.56 microM for BEM; 0.79 microM for BEMF) for 48 h; untreated spheroids served as controls.

value: N/A (in vitro 3D spheroid culture)

value: Melanoma cells, endothelial cells, bone marrow-derived macrophages, and primary dermal fibroblasts (1:1:4:1)

value: Wild-type (C57BL/6 background)

value: Doxorubicin, 0.79 microM (IC30), 48 h


title: Final-203-Aug-Benign-08-09-2024-Immune-003

description: Library name: DSP-1001660020046-C-F08

value: Immune


title: BEMF spheroid, doxorubicin-treated, biological replicate 2

description:
Library name: BEMF_D2
BEMF Doxorubicin 2


title: Final-203-Aug-Benign-08-09-2024-EPI-004

description: Library name: DSP-1001660020046-C-F09

value: Benign


title: Male patient 2 non-recurrent tumor

description:
Library name: Samples 7
Male_Patients_Recurrent_vs_Nonrecurrent_RNAseq_Differential_test.xlsx


title: BEMF spheroid, untreated control, biological replicate 1

description:
Library name: BEMF_C1
BEMF Control 1

value: Untreated control, 48 h


title: Final-203-Aug-Benign-08-09-2024-EPI-002

description: Library name: DSP-1001660020046-C-F06

value: Epi


title: Female patient 5 non-recurrent tumor

description:
Library name: Samples 5
Female_Patients_Recurrent_vs_Nonrecurrent_RNAseq_Differential_test.xlsx

value: No


title: Final-145B-Aug-OSCC-08-09-2024-Immune-004

description: Library name: DSP-1001660020046-C-F03

source_name: OSCC

value: OSCC


title: Final-203-Aug-Benign-08-09-2024-EPI-001

description: Library name: DSP-1001660020046-C-F04


title: BEM spheroid, doxorubicin-treated, biological replicate 2

description:
Library name: BEM_D2
BEM Doxorubicin  2

value: Melanoma cells, endothelial cells, and bone marrow-derived macrophages (1:1:4)

value: Doxorubicin, 0.56 microM (IC30), 48 h


title: Final-145B-Aug-OSCC-08-09-2024-EPI-004

description: Library name: DSP-1001660020046-C-F02


title: BEM spheroid, doxorubicin-treated, biological replicate 1

description:
Library name: BEM_D1
BEM Doxorubicin 1


title: Female patient 4 non-recurrent tumor

description:
Library name: Samples 4
Female_Patients_Recurrent_vs_Nonrecurrent_RNAseq_Differential_test.xlsx

value: Papillary thyroid cancer


title: Female patient 3 non-recurrent tumor

description:
Library name: Samples 3
Female_Patients_Recurrent_vs_Nonrecurrent_RNAseq_Differential_test.xlsx


title: Final-145B-Aug-OSCC-08-09-2024-Immune-002

description: Library name: DSP-1001660020046-C-E11


title: BEM spheroid, untreated control, biological replicate 2

description:
Library name: BEM_C2
BEM Control 2


title: Final-145B-Aug-OSCC-08-09-2024-Immune-001

description: Library name: DSP-1001660020046-C-E09


title: Final-145B-Aug-OSCC-08-09-2024-EPI-001

description: Library name: DSP-1001660020046-C-E08


title: BEM spheroid, untreated control, biological replicate 1

description:
Library name: BEM_C1
BEM Control 1


title: Female patient 1 non-recurrent tumor

description:
Library name: Samples 1
Female_Patients_Recurrent_vs_Nonrecurrent_RNAseq_Differential_test.xlsx


title: Final-080-Aug-OED-08-08-2024-EPI-005

description: Library name: DSP-1001660020046-C-E06

value: OED

value: Yes


title: Final-080-Aug-OED-08-08-2024-Immune-004

description: Library name: DSP-1001660020046-C-E05


title: Final-080-Aug-OED-08-08-2024-EPI-004

description: Library name: DSP-1001660020046-C-E04


title: JAG2

city: Zhuhai

first: Biao

last: Liu

address: meihuadong road

country: China

institute: The Fifth Affiliated Hospital, Sun Yat-sen University

data_processing:
CLC Genomics Workbeach v 11.0.1
Supplementary files format and content: tab delimited text files include FPKM values for each Sample

source_name: fibroblast

growth_protocol: CC fibroblasts were maintained in DMEM supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
RNA was harvested using Rneasy mini plus kit. 1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq library prep Kit following manufacturer's protocols

value: fibroblast

value: Notch agonist


title: Final-080-Aug-OED-08-08-2024-Immune-003

description: Library name: DSP-1001660020046-C-E03


title: MX_227

city: seoul

first: Dakyung

last: Lee

address: 101 Daehakro

country: South Korea

institute: University

description: Library name: MX_227

data_processing:
WES reads were aligned to the GRCh38 human reference genome using the Burrows–Wheeler Aligner. Subsequently, we used GATK best practices, followed by Markduplicates and BaseRecalibrator analyses. Quality metrics were examined employing GATK DepthofCoverage and Flagstat. Somatic mutation calling was conducted using Mutect2 according to GATK best practices.  For xenograft samples, reads were aligned separately to the GRCh38 human reference genome and the mm10 mouse reference genome. To remove murine contamination, we applied XenofilteR, which takes the bam files aligned to both references as input and filter out mouse-derived reads from the human aligned bam file. Subsequent preprocessing and variant calling were performed using the same GATK-based pipeline as described above. The blood samples were matched controls.
Assembly: GRCh38
Supplementary files format and content: WES reads were aligned to the GRCh38 human reference genome using the Burrows–Wheeler Aligner. Subsequently, we used GATK best practices, followed by Markduplicates and BaseRecalibrator analyses. Quality metrics were examined employing GATK DepthofCoverage and Flagstat.

source_name: xenograft tumor

extract_protocol:
For genomic DNA extraction, we used the Dneasy Blood & Tissue Kit (Qiagen, Cat# 69504, Germany) and followed the manufacturer’s protocol.
SureSelect SureSelect All Exon V5

value: xenograft tumor


title: Final-080-Aug-OED-08-08-2024-EPI-003

description: Library name: DSP-1001660020046-C-E02


title: JAG1


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

description: Library name: DSP-1001660020046-C-E01


title: H15kpa_3


title: MT1_434

description: Library name: MT1_434

source_name: primary tumor

value: primary tumor


title: KO4

city: Gunagzhou

first: Min

last: Xiao

state: Guangdong

address: changgang dong Road

department: Department of Hematology

institute: The Second Afﬁliated Hospital of Guangzhou Medical University

description:
Library name: T4
Osteoblasts were isolated from the skulls of mice in the knockout groups and then sent for sequencing.

data_processing:
Raw sequencing reads were aligned to the mouse reference genome mm10 (GRCm38) using STAR v2.7.11b with parameters: --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --twopassMode Basic. The resulting alignments (BAM) were processed for gene-level quantification using featureCounts v2.x.x against the mm10 reference gene annotation (refGene GTF), using parameters: -p -T 8 -g gene_id -t exon. Strandedness was set to unstranded (parameter -s 0) as indicated by the library type.
Assembly: mm10
Supplementary files format and content: csv files include Counts values for each sample

molecule: polyA RNA

source_name: calvaria

extract_protocol:
RNA was harvested using TIANGEN Polysaccharide and Polyphenol Plant Total RNA Extraction Kit. 2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit following manufacturer’s protocols.

value: calvaria

value: Primary cells

value: Osteoblasts


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

description: Library name: DSP-1001660020046-C-D10


title: CML-CP7

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: Sample7

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: CML-CP


title: CML-CP11

description: Library name: Sample11


title: H15kpa_2


title: Final-144-Aug-OSCC-08-08-2024-Immune-007

description: Library name: DSP-1001660020046-C-D09

value: Immune


title: H15kpa_1


title: Final-144-Aug-OSCC-08-08-2024-Immune-006

description: Library name: DSP-1001660020046-C-D08


title: Final-144-Aug-OSCC-08-08-2024-Immune-005

description: Library name: DSP-1001660020046-C-D07


title: Final-144-Aug-OSCC-08-08-2024-EPI-005

description: Library name: DSP-1001660020046-C-D06

value: Epi


title: DAPT3

value: Notch inhibitor


title: Final-144-Aug-OSCC-08-08-2024-Immune-004

description: Library name: DSP-1001660020046-C-D05

value: OSCC


title: CML-CP8

description: Library name: Sample8


title: KO1

description:
Library name: T1
Osteoblasts were isolated from the skulls of mice in the knockout groups and then sent for sequencing.


title: DAPT2


title: Final-144-Aug-OSCC-08-08-2024-EPI-003

description: Library name: DSP-1001660020046-C-D03


title: control4

description:
Library name: T4R
Osteoblasts were isolated from the skulls of mice in the control groups and then sent for sequencing.

value: WT


title: CML-CP2

description: Library name: Sample2


title: Final-144-Aug-OSCC-08-08-2024-Immune-002

description: Library name: DSP-1001660020046-C-D02


title: KO3

description:
Library name: T3
Osteoblasts were isolated from the skulls of mice in the knockout groups and then sent for sequencing.


title: DAPT1


title: Final-144-Aug-OSCC-08-08-2024-EPI-002

description: Library name: DSP-1001660020046-C-D01


title: control3

description:
Library name: T3R
Osteoblasts were isolated from the skulls of mice in the control groups and then sent for sequencing.


title: KO2

description:
Library name: T2
Osteoblasts were isolated from the skulls of mice in the knockout groups and then sent for sequencing.


title: Final-144-Aug-OSCC-08-08-2024-EPI-001

description: Library name: DSP-1001660020046-C-C12


title: Sample_STE_057_Tcell

city: Rochester

first: Gowrishankar

last: Muthukrishnan

state: New York

address: 665-G, 601 Elmwood Ave

department: Orthopaedics, Center for Musculoskeletal Research

institute: University of Rochester Medical Center

library_source: transcriptomic single cell

data_processing:
demultiplexing: cellranger 7.0.1 mkfastq ran using default parameters
cell and gene counting: cellranger multi 7.0.1 multi ran using default parameters OR cellranger counts 6.0.1 /  cellranger vdj 4.0.0
Assembly: 10X provided GRCh38-2020-A reference, vdj-GRCh38-alts-ensembl-7.0 OR  vdj_GRCh38_alts_ensembl-4.0.0
Supplementary files format and content: compressed folders containing barcode, feature, and matrix files for each GEX  sample
Supplementary files format and content: contig and clontoype files for each B or T cell sample

source_name: Bone Marrow Cells

extract_protocol:
Extraction is included within the 10X genomics scRNA protocol
Cellular suspensions were loaded on a Chromium controller (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead-in-Emulsions (GEMs). Single-cell RNA-Seq libraries were prepared using Chromium Single-Cell 5′ v2 Library & Gel Bead Kit (PN-1000265, PN-1000264, 10x Genomics). The beads were dissolved and cells were lysed per manufacturer’s recommendations. Briefly, the beads were dissolved, cells were lysed, and GEM reverse transcription (GEM-RT) was performed to produce barcoded, full-length cDNA. After incubation, GEMs were broken, the pooled post-GEM-RT reaction mixtures were recovered, and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, PN-37002D ThermoFisher Scientific, Waltham, MA). cDNA was amplified by PCR, generating sufficient material to construct B cell-enriched, T cell-enriched, and 5’ gene expression libraries. The barcoded, full-length V(D)J segments were enriched by PCR with primers specific to the BCR and TCR constant regions using the Chromium Single Cell Human BCR Amplification kit (PN-1000253, 10x Genomics) and Chromium Single Cell Human TCR Amplification kit (PN-1000252, 10x Genomics), respectively. cDNA library amplicon size was optimized by enzymatic fragmentation and size selection. 5’ gene expression, BCR, and TCR indexed sequencing libraries were constructed by End Repair, A-tailing, Adaptor Ligation, and PCR. Final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification. The 5’ gene expression, BCR, and TCR libraries were sequenced following 10X Genomics read length and sequencing depth guidelines on the NovaSeq6000 sequencer (Illumina).

value: Bone Marrow Cells

value: Sterile sham Control

tag: library type

value: TCR


title: Final-178-Aug-Benign-08-08-2024-Immune-003

description: Library name: DSP-1001660020046-C-C11

value: Benign


title: control2

description:
Library name: T2R
Osteoblasts were isolated from the skulls of mice in the control groups and then sent for sequencing.


title: Male patient 1 non-recurrent tumor

description:
Library name: Samples 6
Male_Patients_Recurrent_vs_Nonrecurrent_RNAseq_Differential_test.xlsx

value: Male

value: Papillary thyroid cancer

value: No


title: Final-203-Aug-Benign-08-09-2024-EPI-003

description: Library name: DSP-1001660020046-C-F07


title: Final-203-Aug-Benign-08-09-2024-Immune-001

description: Library name: DSP-1001660020046-C-F05


title: CML-CP13

description: Library name: Sample13


title: Final-178-Aug-Benign-08-08-2024-EPI-003

description: Library name: DSP-1001660020046-C-C10


title: Sample_STE_057_GEX

value: GEX


title: Final-178-Aug-Benign-08-08-2024-Immune-002

description: Library name: DSP-1001660020046-C-C09


title: control1

description:
Library name: T1R
Osteoblasts were isolated from the skulls of mice in the control groups and then sent for sequencing.

value: calvaria

value: Primary cells


title: Final-145B-Aug-OSCC-08-09-2024-Immune-003

description: Library name: DSP-1001660020046-C-F01


title: Final-178-Aug-Benign-08-08-2024-EPI-002

description: Library name: DSP-1001660020046-C-C08


title: Final-178-Aug-Benign-08-08-2024-Immune-001

description: Library name: DSP-1001660020046-C-C07


title: Sample_STE_075_Bcell

value: BCR


title: Final-145B-Aug-OSCC-08-09-2024-EPI-003

description: Library name: DSP-1001660020046-C-E12


title: 5785-KT-8_Nfatcre-Tie2flfl

city: Nashville

first: Qi

state: Tennessee

address: 2525 WEST END AVE

institute: Vanderbilt University Medical Center

description: Library name: 5785-KT-8

data_processing:
FASTQ files were aligned using CellRanger to generate 10X format count directories
Assembly: mm10
Supplementary files format and content: Processed data includes standard outputs of CellRanger

source_name: Heart

extract_protocol:
The entire cardiogenic region was dissected at E10.5. Isolated hearts were dissociated as described (de Soysa et al., 2019)
Sequencing was done using 10X Genomics Chromium Controller. ~10,000 cells each genotype were encapsulated and libraries were prepared using P/N 1000006, 1000080, and 1000020 following the manufacturer's protocol. The libraries were sequenced using the NovaSeq 6000 with 150 bp paired end reads.  All libraries were sequenced to a mean read depth of at least 50,000 total aligned reads per cell.

value: Heart


title: Sample_INF_057_Tcell

value: MRSA


title: Final-019-Aug-OED-08-07-2024-Immune-007

description: Library name: DSP-1001660020046-C-C05

value: Immune

value: OED


title: Final-145B-Aug-OSCC-08-09-2024-EPI-002

description: Library name: DSP-1001660020046-C-E10

value: Epi

value: OSCC


title: Final-144-Aug-OSCC-08-08-2024-EPI-004

description: Library name: DSP-1001660020046-C-D04


title: Female patient 2 non-recurrent tumor

description:
Library name: Samples 2
Female_Patients_Recurrent_vs_Nonrecurrent_RNAseq_Differential_test.xlsx

value: Female


title: 5785-KT-7_Tie2flfl

description: Library name: 5785-KT-7


title: Final-178-Aug-Benign-08-08-2024-EPI-001

description: Library name: DSP-1001660020046-C-C06


title: Final-019-Aug-OED-08-07-2024-EPI-007

description: Library name: DSP-1001660020046-C-C04


title: Sample_INF_057_GEX

value: Bone Marrow Cells


title: Final-080-Aug-OED-08-08-2024-Immune-005

description: Library name: DSP-1001660020046-C-E07

value: Yes


title: Final-019-Aug-OED-08-07-2024-Immune-006

description: Library name: DSP-1001660020046-C-C03


title: 5785-KT-6_Nfatcre-Tie2flfl

description: Library name: 5785-KT-6


title: Final-019-Aug-OED-08-07-2024-EPI-006

description: Library name: DSP-1001660020046-C-C02


title: Sample_INF_057_Bcell


title: Final-019-Aug-OED-08-07-2024-Immune-005

description: Library name: DSP-1001660020046-C-C01


title: BEMF spheroid, untreated control, biological replicate 2

description:
Library name: BEMF_C2
BEMF Control 2

value: N/A (in vitro 3D spheroid culture)

value: Melanoma cells, endothelial cells, bone marrow-derived macrophages, and primary dermal fibroblasts (1:1:4:1)

value: Wild-type (C57BL/6 background)

value: Untreated control, 48 h


title: CUS2-13

city: Nantong

first: tong

last: peng

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

institute: Nantong University

description: Library name: SAMPLES4

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: Final-019-Aug-OED-08-07-2024-EPI-005

description: Library name: DSP-1001660020046-C-B12

value: No


title: Sample_STE_059_BT_Tcell

value: Sterile sham Control

value: TCR


title: Final-019-Aug-OED-08-07-2024-Immune-004

description: Library name: DSP-1001660020046-C-B11


title: 5785-KT-5_Tie2flfl

description: Library name: 5785-KT-5

value: Heart


title: JAG3

value: fibroblast

value: Notch agonist


title: JZ25073064-P250429-G2-HF0008946-B2_combined

city: Suzhou

first: Xiaoyu

last: Lin

address: No. 100, Chongwen Road, Suzhou Industrial Park

institute: Suzhou Institute of Systems Medicine

description: Library name: B2

data_processing:
Data filtering: The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification: Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis: Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: GRCm39.106

source_name: infrapatellar fat pad

extract_protocol:
1. Experimental Procedures
1.1 Sample Lysis
1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107).
1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min.
1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column.
1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification.
1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification.
1.2 DNA Purification
1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate.
1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate.
1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube.
1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min.
1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA.
1.3 RNA Purification
1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting.
1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow.
1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.
1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.
1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.
1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube.
1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min.
1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
1) the target RNA was interrupted by adding ion-interrupting reagent and random primer, and the random primer was combined with the target RNA; 2) the target RNA was reversely transcribed into cDNA by adding 1-strand reverse transcription reagent, and the hybrid chain of RNA and cDNA was formed; 3) the RNA in cDNA and RNA hybrid chain was cleaved by adding 2-strand synthetic reagent, and the double-stranded cDNA was synthesized by using the remaining RNA as the primer; 4) the double-stranded cDNA synthesis product was subjected to end-padding and a-addition; the“Y”-shaped linker was ligated; 5) the linker self-connecting fragment was removed by magnetic bead screening; 6) the library template was enriched by PCR amplification; 7) the library was recovered by magnetic beads. Reagent: VAHTS Universal V 8rna-seq Prep Library Kit for Illumina

value: infrapatellar fat pad

value: Achilles tendon

tag: batch


title: Sample_STE_059_BT_GEX

value: GEX


title: Final-019-Aug-OED-08-07-2024-EPI-003

description: Library name: DSP-1001660020046-C-B09

value: Epi

value: OED


title: Final-019-Aug-OED-08-07-2024-Immune-002

description: Library name: DSP-1001660020046-C-B08

value: Immune


title: Sample_STE_059_BT_Bcell

value: Bone Marrow Cells

value: BCR


title: Final-019-Aug-OED-08-07-2024-EPI-002

description: Library name: DSP-1001660020046-C-B07


title: JZ25069777-P250425-3-HF0008575-A2

description: Library name: A2

value: Rectus femoris


title: Final-019-Aug-OED-08-07-2024-Immune-001

description: Library name: DSP-1001660020046-C-B06


title: Sample_STE_058_BT_Tcell


title: Sample_STE_058_BT_GEX


title: Final-181-Aug-Benign-08-07-2024-Immune-004

description: Library name: DSP-1001660020046-C-B03

value: Benign


title: JZ24212791-P241110-GY4-HE0023548-F2_Letrozol_combined

description: Library name: F_L2

value: Fat Pad


title: Final-181-Aug-Benign-08-07-2024-EPI-004

description: Library name: DSP-1001660020046-C-B02


title: Final-181-Aug-Benign-08-07-2024-EPI-003

description: Library name: DSP-1001660020046-C-B01


title: Sample_STE_058_BT_Bcell


title: Final-019-Aug-OED-08-07-2024-EPI-004

description: Library name: DSP-1001660020046-C-B10

value: No


title: JZ24212790-P241110-GY3-HE0023547-F1_Letrozol_combined

description: Library name: F_L1


title: Final-181-Aug-Benign-08-07-2024-Immune-002

description: Library name: DSP-1001660020046-C-A12


title: Sample_INF_56_059_BT_Tcell

value: MRSA


title: Final-181-Aug-Benign-08-07-2024-EPI-002

description: Library name: DSP-1001660020046-C-A11


title: Final-181-Aug-Benign-08-07-2024-Immune-001

description: Library name: DSP-1001660020046-C-A10


title: Sample_INF_56_059_BT_GEX


title: B-LCLs,LPS-treated B-LCLs plus STAT inhibitor,high

city: guangzhou

first: mengye

last: he

state: guangdong

address: guangzhou

institute: guangzhoucunzhongkeji

description: Library name: B-L-I3

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

value: B-LCLs

value: mesenchymal stem cells


title: B-LCLs,LPS-treated B-LCLs plus STAT inhibitor,low

description: Library name: B-L-I2


title: Sample_INF_56_059_BT_Bcell


title: Final-141-Aug-OSCC-08-07-2024-Immune-004

description: Library name: DSP-1001660020046-C-A09

value: OSCC


title: Final-141-Aug-OSCC-08-07-2024-Immune-003

description: Library name: DSP-1001660020046-C-A07


title: Sample_INF_34_058_BT_Tcell

value: TCR


title: B-LCLs,LPS-treated B-LCLs plus STAT inhibitor,0

description: Library name: B-L-I1


title: Final-141-Aug-OSCC-08-07-2024-Immune-002

description: Library name: DSP-1001660020046-C-A05


title: B-LCLs, LPS-treated B-LCLs,high

description: Library name: B-L3


title: Sample_INF_34_058_BT_GEX


title: Final-141-Aug-OSCC-08-07-2024-Immune-001

description: Library name: DSP-1001660020046-C-A03


title: B-LCLs, LPS-treated B-LCLs,low

description: Library name: B-L2


title: Final-141-Aug-OSCC-08-07-2024-EPI-001

description: Library name: DSP-1001660020046-C-A02


title: DSP-1001660020046-C-A01-NTC

description: Library name: DSP-1001660020046-C-A01

value: Non-template-control


title: B-LCLs, LPS-treated B-LCLs,0

description: Library name: B-L1


title: MGO_hRECs_rep3

city: Naples

first: Valerio

last: Costa

state: Italy

address: Via P. Castellino, 111

department: Institute of Genetics and Biophysics

institute: National Research Council

data_processing:
Reads quality was assessed by FastQC and mapping was executed by TopHat (version 2.0.10). Human genome (hg19 release) and transcriptome (GENCODE v19).
RNASeqGUI was used for data normalization. The Counts per Million (CPM) function was used and low count genes (0.1) were filtered out. The samples labeled "control_hRECs_rep1" and "MGO_hRECs_rep1" were removed from further analyses after quality check. Feature Counts was used to count gene expression. Differential expression analysis was performed using EdgeR (threshold FDR<0.05).
Assembly: hg19
Supplementary files format and content: tab-delimited text file containing normalized counts per sample

source_name: retina

growth_protocol: Human Retinal Endothelial Cells were cultured in Endothelial cell medium supplemented with fetal Bovine Serum (FBS), Endothelial Cell Growth Supplement (ECGS) and penicillin/streptomycin (P/S) solution.

extract_protocol:
Total RNA samples were extracted by cell pellets using TRIzol Reagent (Life Technologies) according to the manufacturer’s instructions. NanoDrop spectrophotometer was used for RNA quantification for samples to be processed by RNA-Seq
Illumina TruSeq mRNA Stranded

treatment_protocol: Before treatments, cells were serum starved for 16h. Cells were treated with 500 μM MGO for 72h (non-toxic and chronic exposure) before transcriptome and miRNome analysis.

value: retina

value: hREC

value: Retinal Endothelial

value: WT

value: methylglyoxal (500 μM)


title: Final-149-Aug-OSCC-08-16-2024-Immune-008

description: Library name: DSP-1001660019855-D-H12

value: Immune


title: Final-141-Aug-OSCC-08-07-2024-EPI-002

description: Library name: DSP-1001660020046-C-A04

value: Epi


title: Final-149-Aug-OSCC-08-16-2024-EPI-008

description: Library name: DSP-1001660019855-D-H11


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

description: Library name: B-C3


title: Final-149-Aug-OSCC-08-16-2024-Immune-007

description: Library name: DSP-1001660019855-D-H10


title: MGO_hRECs_rep2


title: Final-149-Aug-OSCC-08-16-2024-EPI-007

description: Library name: DSP-1001660019855-D-H09


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

description: Library name: DSP-1001660019855-D-H08


title: MGO_hRECs_rep1


title: B-LCLs,gene expression profiles among the control B-LCLs,0

description: Library name: B-C1


title: Final-149-Aug-OSCC-08-16-2024-Immune-005

description: Library name: DSP-1001660019855-D-H06


title: control_hRECs_rep3

value: untreated


title: Final-149-Aug-OSCC-08-16-2024-EPI-005

description: Library name: DSP-1001660019855-D-H05


title: Final-149-Aug-OSCC-08-16-2024-Immune-004

description: Library name: DSP-1001660019855-D-H04


title: control_hRECs_rep2


title: Final-149-Aug-OSCC-08-16-2024-EPI-004

description: Library name: DSP-1001660019855-D-H03


title: 10X Fixed RNA-seq: 13 Lung samples (2 cell lines): CD45 negative (HDM, 2xNRG1, PBS)  CD45positive (3xHDM, 3xNRG1, 3xPBS)

city: Columbus

first: Mitchell

middle: H.

last: Grayson

state: OH

address: 700 Children's Dr

institute: Nationwide Children's Hospital

description:
Library name: FixedRNA-11020
Multiplexed 10x Flex scRNA-seq library containing 13 biological samples from atopic model. Samples demultiplexed by probe barcodes (see FixedRNA-11020.csv). Treatment groups: CD45 negative: HDM(n=1), NRG1(n=2), PBS(n=1); CD45 positive: HDM(n=3), NRG1(n=3), PBS(n=3).

data_processing:
Raw FASTQ files were processed using Cell Ranger multi ( v7.1) with the 10x Genomics Fixed RNA Profiling pipeline for probe-based demultiplexing. Reads were aligned to the mouse reference genome (mm10, version 2020A) using the Chromium Mouse Transcriptome Probe Set v1.0.1. Downstream analysis including quality control, normalization, dimensionality reduction (PCA, UMAP), clustering, and cell type annotation was performed using Seurat (v4.3.0).
Assembly: mm10
Supplementary files format and content: all_samples_filtered_bc_matrix.tar: feature-barcode matrices for all 16 samples. Each file within the archive is prefixed with its corresponding sample name (SampleName_barcodes.tsv.gz， SampleName_features.tsv.gz， SampleName_matrix.mtx.gz)  FixedRNA-11020.csv: Cell Ranger multi configuration files specifying probe barcode-to-sample mapping for 10x Flex demultiplexing

source_name: lung

extract_protocol:
Whole lungs were removed from selected mice and incubated in digest media for 45 min followed by the addition of EDTA (2 mM final concentration) for 15 min. Digest medium consisted of Dulbecco’s modified Eagle’s media supplemented with 5% fetal calf serum, sodium bicarbonate, penicillin/streptokinase, 10 mM HEPES, 5 U/ml Hyaluronidase, 50 u/ml DNAse and 40 U/mL Liberase . To make cell suspension lung tissue was disrupted using Gentle MACS dissociator (Milteney Biotec). The samples were filtered and the single cell suspension was treated with Red Blood Cell Lysing Buffer (Sigma-Aldrich). Cells were then stained with Alexa Fluor® 488 anti-mouse CD45.2 antibody clone 104  (cat# 109816, Biolegend) using standard techniques, and FACS was performed sorting for both CD45+ and CD45- populations. Samples were prepared for single-cell RNA sequencing  using Next GEM Single Cell Fixed RNA sample preparation kit (cat# 1000414) following the manufacturer’s protocol (CG000782 Rev C, 10X Genomics). For long term storage fixed cells were spun down at 850 rcf, 5 min and 0.1 volume (10%) of the pre-warmed enhancer (10Xgenomics, #1000414) was added to fixed samples in quenching buffer and 50% glycerol (Millipore Sigma, #G5516-100ml). Pipette mixed and stored at (-80°C) for use within 3 months. By quantification of the total cell number of each sample 13  samples were qualified to proceed to do the preparation of scRNA-seq libraries using Chromium fixed RNA profiling reagent kits No. 1000497 and Dual Index kit TS set A, 96 rxn No. 1000251 according to the manufacturer’s protocol (CG000527 Rev D, 10X Genomics) followed by sequencing using Novaseq6000 platform and Flow cell-type is SP100-cycle.
Samples were prepared for single-cell RNA sequencing following the manufacturer’s protocol (CG000782 Rev C, 10X Genomics). The fixed cell suspensions were then prepared for sequencing library generation using Chromium fixed RNA profiling reagent kits No. 1000497 and Dual Index kit TS set A, 96 rxn No. 1000251 according to the manufacturer’s protocol (CG000527 Rev D, 10X Genomics) and Chromium Next GEM Chip Q Single Cell Kit, 16 rxns (PN-1000422).  The pooled barcode cDNA which contained the 10x Barcode was amplified for subsequent library construct. Library preparation type was 10x fixed RNA profiling for mouse specie. Illumina Sequencing platform was NovaSeq-SP full cell. During the library construction paired-end constructs, with index (i7) sequence [CAAGCGTTAG] and the index (i5) sequence [CGCATTCGCG]  for reverse complimentary strand, were added.

value: lung

value: CD45 positive, CD45 negative

value: LEC, AEC, VEC, gCAP, aCAP, AF1, AF2, Pericyte, ASMC, Mesothelial, AT1, AT2, Club, Ciliated, Mature_DC, pDC, DC1, DC2, Alveolar_Mph, M2_like_Mph, Nonclassical_Mon, S100a8_9_pos_Mon, Naive_CD4_T, CD4_TRM, Treg, Naive_CD8_T, gamma_delta_T, B, ILC, NK, Neutrophil, Mast, B_T_mix

value: wild-type

value: HDM, NRG1, PBS


title: Final-149-Aug-OSCC-08-16-2024-Immune-003

description: Library name: DSP-1001660019855-D-H02


title: control_hRECs_rep1


title: Final-149-Aug-OSCC-08-16-2024-EPI-003

description: Library name: DSP-1001660019855-D-H01


title: Final-149-Aug-OSCC-08-16-2024-Immune-002

description: Library name: DSP-1001660019855-D-G12


title: Heparin3

city: qingdao

first: tianyu

last: wang

address: yushanlu 5#

institute: Ocean University of China

description: Library name: Sample 6

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: K group replicate 2

city: Beijing

first: hebing

last: chen

address: taiping road 27

institute: Institute of Health Service  and Transfusion Medicine

description:
K2
K_50000_iced.matrix

data_processing:
HiC-Pro was used to obtain .allValidPairs files and merge technical replicates. Merged .allValPairs files are down-sampled for consistent sequencing depth. Juicer tools (v1.22.01 and hic2cool (v0.8.3) are used to convert .allValidPairs files to .hic and .mcool files. dcHiC was deployed to identified Hi-C compartments at 100-kb resolution. OnTAD  is used to define hierarchy TAD in 50-kb resolution.
Assembly: hg19
Supplementary files format and content: 50000_iced.matrix

extract_protocol:
5×105 cells was collected in the 1.5 ml tube with 1mL culture medium(Gibco,11965092),and formaldehyde solution was added to achieve a final concertration of 1%. Then, the tube was placed in a Rotator for 15minuters at RT. After cross-linking, the remaining formaldehyde was sequestered by adding 27.9 μL of 2 M glycine (Sigma, G7126) and continued to rotate for 10 minutes at RT.
Then, the restriction enzyme HaeIII was used for digestion. Biotin-labeled bridge linkers was used to ligate DNA fragments. Purify labled DNA fragments with Dynabeads(Invitrogen, 11047 ).Quantify the recovered DNA.The purified DNA is used directly for cluster generation and sequencing analysis using the Illumina novaseq6000 following the manufacturer’s protocols.
BL-HiC

value: Human bladder cancer cell line

value: hMSH2 deficiency


title: Final-149-Aug-OSCC-08-16-2024-EPI-002

city: Kansas City

first: Harsh

address: 3901 Rainbow Blvd

institute: KUMC

description: Library name: DSP-1001660019855-D-G11

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.

value: OSCC


title: Final-149-Aug-OSCC-08-16-2024-EPI-001

description: Library name: DSP-1001660019855-D-G09


title: K group replicate 1

description:
K1
K_50000_iced.matrix


title: E group replicate 2

description:
E2
E_50000_iced.matrix

value: control


title: Final-185-Aug-Benign-08-16-2024-Immune-004

description: Library name: DSP-1001660019855-D-G06

source_name: Benign

value: Benign


title: Control3

description: Library name: Sample 3


title: E group replicate 1

description:
E1
E_50000_iced.matrix


title: Heparin1

description: Library name: Sample 4


title: Final-185-Aug-Benign-08-16-2024-EPI-004

description: Library name: DSP-1001660019855-D-G05


title: B141

description: Library name: B141

source_name: blood

value: blood


title: Control2

description: Library name: Sample 2


title: Final-185-Aug-Benign-08-16-2024-EPI-003

description: Library name: DSP-1001660019855-D-G03


title: Final-185-Aug-Benign-08-16-2024-Immune-002

description: Library name: DSP-1001660019855-D-G02


title: relapsing sample, BM1914/15

city: Roma

first: Serena

last: Travaglini

address: Via Montpellier 1

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

value: inv(16) AML

tag: group

value: primary inv(16) AML cells at relapse


title: Final-185-Aug-Benign-08-16-2024-EPI-002

last: Pathak

description: Library name: DSP-1001660019855-D-G01

value: Epi


title: Final-185-Aug-Benign-08-16-2024-Immune-001

description: Library name: DSP-1001660019855-D-F12

value: Immune


title: Heparin_3

city: Qingdao

first: Shaoyun

last: Zhou

address: No. 5, Yushan Road, Shinan District

description: Library name: Sample 6

source_name: liver

extract_protocol:
Liver 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: liver


title: Final-185-Aug-Benign-08-16-2024-Immune-005

description: Library name: DSP-1001660019855-D-G08


title: relapsing sample, BM2664/19


title: Heparin_2

description: Library name: Sample 5


title: FInal-195-Aug-Benign-08-16-2024-EPI-003

description: Library name: DSP-1001660019855-D-F10


title: Final-185-Aug-Benign-08-16-2024-Immune-003

description: Library name: DSP-1001660019855-D-G04


title: relapsing sample, BM889/17


title: relapsing sample, BM739/21


title: Control1

description: Library name: Sample 1


title: FInal-195-Aug-Benign-08-16-2024-EPI-002

description: Library name: DSP-1001660019855-D-F09


title: Heparin_1

description: Library name: Sample 4


title: FInal-195-Aug-Benign-08-16-2024-EPI-001

description: Library name: DSP-1001660019855-D-F08


title: relapsing sample, BM2114/21


title: JZ25073063-P250429-G1-HF0008945-B1_combined

description: Library name: B1

value: infrapatellar fat pad

value: Achilles tendon


title: Final-146-Aug-OSCC-08-16-2024-Immune-004

description: Library name: DSP-1001660019855-D-F07

source_name: OSCC


title: Final-181-Aug-Benign-08-07-2024-EPI-005

description: Library name: DSP-1001660020046-C-B04


title: Final-181-Aug-Benign-08-07-2024-Immune-005

description: Library name: DSP-1001660020046-C-B05


title: Control_3

description: Library name: Sample 3


title: JZ25069776-P250425-2-HF0008574-A1

description: Library name: A1

value: Rectus femoris


title: Final-146-Aug-OSCC-08-16-2024-EPI-004

description: Library name: DSP-1001660019855-D-F06


title: CRC109ORG

city: Tampere

first: Toni

last: Seppälä

address: Arvo Ylpön katu 34

institute: Tampere University

description:
Library name: CRC109ORG
Column name in raw_counts_pdtos.txt: CRC109ORG

data_processing:
kallisto v.0.50.1 was used to extract transcript-level counts from fastq files. The human transcriptome index constructed from the Ensembl reference transcriptome version 108 was downloaded (https://github.com/pachterlab/kallisto-transcriptome-indices/releases) and the tximport R package v.1.32.0 was used to summarize transcript-level counts to gene-level and create a count matrix.
Assembly: Ensembl human reference transcriptome version 108
Supplementary files format and content: Tab-delimited text file contains estimated raw counts for each sample

source_name: rectum

extract_protocol:
Total RNA was extracted by using NucleoSpin RNA Plus Isolation Kit
Total RNA (100 ng) was ribo-depleted using Illumina's Stranded Total RNA Prep with Ribo-Zero Plus (20040529) and library preparation was completed using standard Illumina protocols.

value: rectum

value: Patient-derived tumor organoids


title: MX_130

description: Library name: MX_130

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: xenograft 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: xenograft tumor


title: AML12 cells, SMF2

city: Xi'an

first: Xuan

last: Han

state: ShaanXi

address: Medical department of Xi'an JiaoTong University

institute: Xi'an Jiaotong University

description: Library name: Sample5

data_processing:
Filter In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data). The steps are: 1) Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both of the reads must be removed ); 2) Remove the contaminated reads for adapters The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove both ends of the reads); 3) Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15% . If either one of the PE Reads defined as low quality, we will remove both ends of the reads); 4) Remove the reads whose N base more than 5% for total bases (If either one of the PE Reads had high Ns bases, we will remove both ends of the reads); Alignment The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Assembly: GRCm39
Supplementary files format and content: txt files include FPKM values for each Sample

extract_protocol:
Invitrogen TRIZOL Reagent were used for RNA extraction; VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina were used for library construction (1) The Nanodrop2000 microspectrophotometer detects sample purity and concentration; (2) The Labchip GX touch microfluidic capillary system detects the integrity of RNA samples.
(1) The library was constructed starting with Total RNA and mRNA with ployA tails was enriched by Oligo(dT) magnetic beads; (2) Add Fragmentation Buffer for mRNA fragmentation; (3) One strand of cDNA was synthesised using a six-base random primer using mRNA as a template, followed by the synthesis of the second strand of cDNA using buffer, dNTPs, DNA polymerase I and RNase H, and cDNA purification; (4) Purified double-stranded cDNA was subjected to end repair, base A was added, sequencing junctions were added, and fragments were screened to recover cDNA around 350 bp; (5) PCR enrichment was performed to obtain cDNA libraries; (6) Double-stranded cDNA is denatured at high temperature into single-stranded DNA, and cyclisation primers are added to form a single stranded Circular DNA library (single stranded Circular DNA).

value: SMF


title: Final-146-Aug-OSCC-08-16-2024-Immune-003

description: Library name: DSP-1001660019855-D-F05

value: OSCC


title: relapsing sample, BM518/18


title: Control_2

description: Library name: Sample 2


title: diagnostic sample, 588

value: primary inv(16) AML cells at diagnosis


title: Control_1

description: Library name: Sample 1


title: Final-146-Aug-OSCC-08-16-2024-Immune-002

description: Library name: DSP-1001660019855-D-F03


title: Final-146-Aug-OSCC-08-16-2024-EPI-003

description: Library name: DSP-1001660019855-D-F04


title: Final-141-Aug-OSCC-08-07-2024-EPI-003

description: Library name: DSP-1001660020046-C-A06


title: Final-146-Aug-OSCC-08-16-2024-Immune-001

description: Library name: DSP-1001660019855-D-F01


title: RNA-seq of Mus musculus (ICR): 9-month-old male testis, blueberry extract (200 mg/kg/d) treatment, replicate 3

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

institute: Nanjing Agricultural University

description:
Library name: Treat3_3
replicate 2 of Treat3 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.

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

value: Blueberry extract 200mg/kg


title: Final-146-Aug-OSCC-08-16-2024-EPI-002

description: Library name: DSP-1001660019855-D-F02


title: diagnostic sample, 337

value: primary Acute myeloid leukemia cells

value: inv(16) AML


title: Final-141-Aug-OSCC-08-07-2024-EPI-004

description: Library name: DSP-1001660020046-C-A08

value: Epi


title: Final-146-Aug-OSCC-08-16-2024-EPI-001

description: Library name: DSP-1001660019855-D-E12


title: diagnostic sample, 336


title: Final-090A-Aug-OED-08-16-2024-Immune-005

description: Library name: DSP-1001660019855-D-E11

source_name: OED

value: Immune

value: OED

value: Yes


title: RNA-seq of Mus musculus (ICR): 9-month-old male testis, blueberry extract (200 mg/kg/d) treatment, replicate 2

description:
Library name: Treat3_2
replicate 2 of Treat3 group


title: Final-185-Aug-Benign-08-16-2024-EPI-001

description: Library name: DSP-1001660019855-D-F11

value: Benign


title: diagnostic sample, 91


title: Final-090A-Aug-OED-08-16-2024-EPI-005

description: Library name: DSP-1001660019855-D-E10


title: Final-090A-Aug-OED-08-16-2024-Immune-004

description: Library name: DSP-1001660019855-D-E09


title: RNA-seq of Mus musculus (ICR): 9-month-old male testis, blueberry extract (200 mg/kg/d) treatment, replicate 1

description:
Library name: Treat3_1
replicate 1 of Treat3 group


title: Sample_INF_34_058_BT_Bcell

value: Bone Marrow Cells

value: MRSA

value: BCR


title: RNA-seq of Mus musculus (ICR): 9-month-old male testis, blueberry extract (100 mg/kg/d) treatment, replicate 3

description:
Library name: Treat2_3
replicate 2 of Treat2 group

value: Blueberry extract 100mg/kg


title: diagnostic sample, 487


title: Final-090A-Aug-OED-08-16-2024-EPI-004

description: Library name: DSP-1001660019855-D-E08


title: Final-090A-Aug-OED-08-16-2024-EPI-003

description: Library name: DSP-1001660019855-D-E06


title: diagnostic sample, 454


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

description: Library name: DSP-1001660019855-D-E05


title: Final-090A-Aug-OED-08-16-2024-Immune-003

description: Library name: DSP-1001660019855-D-E07