title: 1013_BX7-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-52-10


title: Expression of eGFP-BLG, delayed sampling, replicate 1

status: Public on Aug 21 2025

type: SRA

city: Kgs. Lyngby

first: Christoffer

last: Rode

address: Søltofts Plads, Building 220

country: Denmark

institute: Technical University of Denmark

description:
Library name: ecoli_CR_00036
Column name in log_tpm.csv: ecoli_CR_00036

library_source: transcriptomic

data_processing:
Mapping and logtpm determined using the iModulonMiner workflow, https://doi.org/10.1371/journal.pcbi.1012546
Assembly: Genome assembly ASM584v2
Supplementary files format and content: logtpm.csv contains log-TPM values for each sample

molecule: total RNA

organism: Escherichia coli

source_name: bacterial cell

growth_protocol: Cells were grown in minimal M9 growth medium with 0.2% glycerol in 250 mL shake flasks at 40 mL working volume, shaking at 37C and at 225 RPM.

extract_protocol:
Total RNA was extracted from cultures following the protocol in the RNAprotect Bacteria Reagent Handbook (Qiagen). Once main cultures reached OD600 = 2, 2.5 mL culture was added to 5 mL RNAprotect Bacteria Reagent (Qiagen), vortexed, and incubated at room temperature for 5 minutes. Sample pellets were resuspended in 400 L elution buffer and split into two aliquots which were stored at -80C. Total RNA was then extracted and purified from thawed pellets on a QIAcube Connect Instrument (Qiagen) using the RNeasy Protect Bacteria Mini Kit (Qiagen). Lysozyme was used for enzymatic lysis of cells together with Proteinase K for degrading protein and SUPERaseIn RNAse inhibitor (Thermo Fisher) for protecting RNA. A DNase treatment step was added to the protocol to remove DNA contamination. Total RNA was eluted in 30 L RNase-free water, then stored at -80 C. The extracted RNA was shipped to sequencing at Azenta Life Sciences.
Enrichment, cDNA synthesis, and adapter ligation

tag: strain

tag: cell type

value: bacterial cell

tag: genotype

value: SDT507 (gly2 rhaBADM KO) pSD178

tag: treatment

value: M9 glycerol ampicillin

tag: batch

value: Replicate 1


title: Affymetrix Exon array from patient 1016

type: RNA

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

country: USA

institute: National Cancer Institute

description: Affymetrix Human Exon array of prostate biopsy from patient 1016

hyb_protocol: Samples were hybridized using Affymetrix kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was processed using the Affymetrix Transcriptome Analysis Console
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: biotin

organism: Homo sapiens

source_name: prostate tissues prior to treatment with neoadjuvant ADT plus enzalutamide

label_protocol: RNA was amplified, fragmented, and biotinylated using the WT-Ovation FFPE system (NuGEN) according the manufacturer's recommendations with minor modifications.

extract_protocol: After pathologic review, tissue was harvested from formalin-fixed, paraffin-embedded slides by macrodissection under RNase-free conditions. Total RNA was extracted and purified using the RNease FFPE kit (Qiagen)

tag: gender

value: male

tag: case

tag: tissue

value: prostate


title: 1010_BX15A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-184-12

data_processing:
Base-calling was performed with CASAVA 1.9
FASTQ files were pre-processed to remove sequencing adaptors with Trimmomatic v0.36.
Paired-end trimmed FASTQ files were aligned to hg19 using STAR.
RSEM was used to estimate read counts for each genomic feature.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values, gene symbol, description, transcripts-per-million (TPM)

source_name: prostate

extract_protocol:
Total RNA was extracted from cells adhered to caps using the Qiagen RNeasy FFPE kit.
rRNA-depleted RNA was converted into cDNA and assembled into strand-specific libraries using the NEBNext Ultra II Directional RNA-Seq kit.

treatment_protocol: FFPE human prostate tissues were sectioned onto metal frame membrane slides, and regions of interest were excised onto caps using laser capture microdissection.

tag: regionofinterest


title: Affymetrix Exon array from patient 1012

description: Affymetrix Human Exon array of prostate biopsy from patient 1012


title: 1010_BX14A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-184-11


title: Control, delayed sampling, replicate 1

description:
Library name: ecoli_CR_00035
Column name in log_tpm.csv: ecoli_CR_00035

value: SDT507 (gly2 rhaBADM KO) pSD122


title: #975_LTI3_d5_r1

city: Los Angeles

first: Yago

last: Jannini-Sa

state: California

address: 8700 Beverly Blvd. AHSP Room A9401

department: Medicine / Lung Institute

institute: Cedars-Sinai Medical Center

description: Library name: 975955_counts

data_processing:
align with STAR 2.6.0b-1
raw count generated by featrueCounts 1.6.0.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes counts for each sample

source_name: Lung

extract_protocol:
Bulk RNA sequencing was performed on tissue from 4 separate PCLS. Briefly, PCLS were minced manually in 2 mm pieces in Trizol (ThermoFisherScientific) before bead homogenization for 95 seconds (40+20+15+10+10 seconds) at 50 Hz. RNA was purifiedusing a column-based workflow (Machery Nagel, 740984.250). RNA quantity and quality was assessed by RNA integrity number (RIN) via 4200 TapeStation system (Agilent).
RNAseq libraries were prepared using Truseq stranded mRNA kit (Illumina; 20020594). Sequencing libraries were pooled and submitted for next-generation sequencing of 100bp single-end reads (Illumina NovaSeq sequencer, AGCT Core; Los Angeles, CA).

treatment_protocol: LTI-03 (Sequence: FTTFTVT; Lot# AJF73B//474-33-TI344 Lonza), the inactive control peptide CP (Sequence: FAAFAVA; Lot# PD200120-1, Ambiopharm) were suspended in PCLS culture media at 0.3, 5.0, or 10 μM for treatments. Nintedanib (Boehringer Ingelheim Pharmaceuticals, Inc #S1010) was prepared in a 1mM stock solution with sterile filtered DMSO and used at 0.1 μM or 1 μM. PCLS were treated every 12hrs and supernatant was harvested 12 hours following the last of either three (day 2), seven (day 4) or nine treatments (day 5). Tissue was harvested after 9 treatments (day 5).

tag: condition

value: idiopathic pulmonary fibrosis (IPF)

value: Lung

tag: tissue format

value: Precision cut lung slices

tag: sample

tag: time


title: Affymetrix Exon array from patient 1011

description: Affymetrix Human Exon array of prostate biopsy from patient 1011


title: Expression of eGFP-ALA, replicate 1

description:
Library name: ecoli_CR_00034
Column name in log_tpm.csv: ecoli_CR_00034

value: SDT507 (gly2 rhaBADM KO) pSD180


title: #975_LTI05_d5_r1

description: Library name: 975952_counts


title: 1010_BX14A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-184-10


title: Affymetrix Exon array from patient 1010

description: Affymetrix Human Exon array of prostate biopsy from patient 1010


title: Expression of eGFP-BLG, replicate 1

description:
Library name: ecoli_CR_00033
Column name in log_tpm.csv: ecoli_CR_00033


title: #975_UT_d2_r2

description: Library name: 975951_counts

value: UT


title: 1010_BX4A-3

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-108-14


title: #975_LTI10_d5_r1

description: Library name: 975958_counts


title: 1010_BX4A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-108-13


title: #975_UT_d2_r1

description: Library name: 975950_counts


title: Affymetrix Exon array from patient 1009

description: Affymetrix Human Exon array of prostate biopsy from patient 1009


title: Control, replicate 7

description:
Library name: ecoli_CR_00031
Column name in log_tpm.csv: ecoli_CR_00031

value: Replicate 7


title: Expression of eGFP, replicate 1

description:
Library name: ecoli_CR_00032
Column name in log_tpm.csv: ecoli_CR_00032

value: SDT507 (gly2 rhaBADM KO) pSD174


title: Affymetrix Exon array from patient 1013

description: Affymetrix Human Exon array of prostate biopsy from patient 1013


title: #975_LTI3_d5_r3

description: Library name: 975957_counts


title: Affymetrix Exon array from patient 1008

description: Affymetrix Human Exon array of prostate biopsy from patient 1008


title: Affymetrix Exon array from patient 1007

description: Affymetrix Human Exon array of prostate biopsy from patient 1007


title: #975_LTI10_d2_r2

description: Library name: 975949_counts


title: 1010_BX3A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-108-11


title: #975_N_d2_r2

description: Library name: 975947_counts

value: N


title: Expression of MFP5, intact rhaBADM, replicate 2

description:
Library name: ecoli_CR_00030
Column name in log_tpm.csv: ecoli_CR_00030

value: SDT492 (gly2) pSD114

value: Replicate 2


title: #975_LTI3_d5_r2

description: Library name: 975956_counts


title: Expression of eGFP-BLG, intact rhaBADM, replicate 2

description:
Library name: ecoli_CR_00028
Column name in log_tpm.csv: ecoli_CR_00028

value: bacterial cell

value: SDT492 (gly2) pSD178


title: #975_N_d2_r3

description: Library name: 975948_counts


title: 1009_BX5A6A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-81-6


title: Affymetrix Exon array from patient 1005

description: Affymetrix Human Exon array of prostate biopsy from patient 1005


title: Expression of BLG, intact rhaBADM, replicate 2

description:
Library name: ecoli_CR_00029
Column name in log_tpm.csv: ecoli_CR_00029

value: SDT492 (gly2) pSD108

value: M9 glycerol ampicillin


title: Control, intact rhaBADM, replicate 2

description:
Library name: ecoli_CR_00027
Column name in log_tpm.csv: ecoli_CR_00027

value: SDT492 (gly2) pSD122


title: 1009_BX5A6A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-81-5

value: male


title: Expression of MFP5, intact rhaBADM, replicate 1

description:
Library name: ecoli_CR_00026
Column name in log_tpm.csv: ecoli_CR_00026

value: Replicate 1


title: Affymetrix Exon array from patient 1003

description: Affymetrix Human Exon array of prostate biopsy from patient 1003

value: prostate


title: Affymetrix Exon array from patient 1002

description: Affymetrix Human Exon array of prostate biopsy from patient 1002


title: 1008_BX56A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-77-18


title: #975_CP_d2_r1

description: Library name: 975945_counts

value: idiopathic pulmonary fibrosis (IPF)

value: Lung

value: CP


title: #975_LTI10_d2_r1

description: Library name: 975941_counts

value: Precision cut lung slices


title: Expression of BLG, intact rhaBADM, replicate 1

description:
Library name: ecoli_CR_00025
Column name in log_tpm.csv: ecoli_CR_00025


title: Day 5 pregnant uterus, implantation site

city: Bunkyo-ku

first: Shizu

last: Aikawa

state: Tokyo

address: 7-3-1 Hongo

country: Japan

institute: The University of Tokyo

description: Library name: sample1

data_processing:
Raw reads were processed by Cell Ranger with default setting.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5.gz:The filtered feature count matrix generated from Cell Ranger.
Supplementary files format and content: barcodes.tsv.gz: list of list of spatial barcodes (10x Visium)
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coodinates specifying spots
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: Mouse uterus

extract_protocol:
After reaction with Proteinase K for 40 min, the sections were hybridized with spatial tags on the slides according to manufacturer's protocol.
Following the hybridization with spatial tags, reverse-transcribed in situ according to manufacturer's protocol.

value: Mouse uterus

value: wildtype


title: Affymetrix Exon array from patient 1004

description: Affymetrix Human Exon array of prostate biopsy from patient 1004


title: 1008_BX56A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-77-19


title: Affymetrix Exon array from patient 1001

description: Affymetrix Human Exon array of prostate biopsy from patient 1001


title: 1008_BX2A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-77-17


title: Yjlab_chip_S016_male_rep2_k27ac

city: Shenzhen

first: Haoyue

last: Zhang

address: Gaoke Innovation Center, Guangqiao Road, Guangming District, Shenzhen

country: China

institute: Shenzhen Bay Lab

description: Library name: sample16

library_source: genomic

data_processing:
Reads were aligned to mouse genome assembly mm9. Alignments were then filtered for low-quality reads (MAPC <30), PCR duplicates and reads that aligned to mitochondria random contigs and ENCODE blacklisted regions were removed.  Valid reads that aligned to mouse genome was then normalized using the above counts per million through Deeptools (v3.1.3).
Assembly: mm9
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: primary cells

growth_protocol: The hepatic stellate cells were directly isolated from male or female LratCre;Ai32(RCL-ChR2(H134R)/EYFP)+/- mice with liver fibrosis. Hepatic stellate cells were sorted through fluorescence activated cell sorting based on EYFP+/CD45- and collected with 2ml DMEM containing 10% bovine serum albumin, 100 U/ml penicillin,100 μg/ml streptomycin, and 10μM 17β-estradiol.

extract_protocol:
Cells were then fixed with 1% formadelhyde for 10min at room temperature and then quenched with glycine for 5min. Crosslinked cells were resuspended in 1ml of pre-chilled cell lysis buffer supplemented with 1:500 protease inhibitor and 1:100 PMSF. Cells were incubated on ice for 20min. After cell lysis, nuclei were pelleted at 7200rpm for 2min at 4℃. Nuclei were then resuspended in 1ml nuclear lysis buffer supplemented with 1:500 protease inhibitor and 1:100 PMSF for 20min on ice. Nuclei lysate (chromatin) was then subject to sonication on a Qsonica Q800R3 sonicator (80% amplitude, 20s ON/40s OFF for 17min). Sonicated samples were centrifuged at 15000g for 10min at 4℃ to remove cell debris. Chromatin in the supernatant was collected and diluted with 4 volumes of IP dilution buffer (20mM Tris-HCl pH=8.0, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS) containing 1:500 protease inhibitor and 1:100 PMSF. 50ul of A/G agarose beads (Santa Cruz, sc-2003) was then added into the system to for preclear. Preclear of chromatin was performed at 4℃ for 8h with rotation. Precleared chromatin was then incubated with 35ml A/G agarose beads (A:G = 1:1) pre-bound with ChIP grade antibody mentioned in article at 4℃ overnight. Beads were washed once with IP wash buffer I (20mM Tris-HCl pH=8.0, 2mM EDTA, 50mM NaCl, 1% Triton X-100, 0.1% SDS), twice with high salt buffer (20mM Tris-HCl pH=8.0, 2mM EDTA, 500mM NaCl, 1% Triton X-100, 0.01% SDS), once with IP wash buffer II (10mM Tris-HCl pH=8.0, 1mM EDTA, 0.25M LiCl, 1% NP-40/Igepal, 1% sodium deoxycholate) and twice with TE buffer (10mM Tris-HCl pH=8.0, 1mM EDTA pH=8). All washing steps were performed on ice. Beads were moved to room temperature and DNA was eluted in 200µl fresh Elution Buffer (100mM NaHCO3, 1%SDS). ChIP chromatin was reverse crosslinked at 65℃ overnight in the presence of proteinase K. Samples were supplemented with 10ml of 3M sodium acetate (pH=5.2), and DNA was purified with QIAquick PCR purification kit (QIAGEN, 28106).
ChIP-seq libraries were constructed using the AHTS Universal DNA Library Prep Kit for MGI (Vazyme, NDM607-02) according to the manufacture’s protocol.

tag: cell line

value: hepatic stellate cells


title: Expression of eGFP-BLG, intact rhaBADM, replicate 1

description:
Library name: ecoli_CR_00024
Column name in log_tpm.csv: ecoli_CR_00024


title: 1010_BX4A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-108-12


title: Yjlab_chip_S017_female_rep2_k27ac

description: Library name: sample17


title: 1010_BX2A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-108-10


title: Yjlab_chip_S014_male_rep1_k27ac

description: Library name: sample14


title: Control, replicate 6

description:
Library name: ecoli_CR_00022
Column name in log_tpm.csv: ecoli_CR_00022

value: SDT507 (gly2 rhaBADM KO) pSD122

value: Replicate 6


title: 1007_BX17A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-108-8


title: 1007_BX16A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-108-7


title: Control, replicate 4

description:
Library name: ecoli_CR_00020
Column name in log_tpm.csv: ecoli_CR_00020

value: bacterial cell

value: Replicate 4


title: Yjlab_chip_S013_female_rep2_k9me3

description: Library name: sample13


title: Control, intact rhaBADM, replicate 1

description:
Library name: ecoli_CR_00023
Column name in log_tpm.csv: ecoli_CR_00023


title: 1007_BX17A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-108-9


title: Yjlab_chip_S015_female_rep1_k27ac

description: Library name: sample15


title: #975_N_d2_r1

description: Library name: 975946_counts

value: N


title: Yjlab_chip_S012_male_rep2_k9me3

description: Library name: sample12


title: Control, replicate 3

description:
Library name: ecoli_CR_00019
Column name in log_tpm.csv: ecoli_CR_00019

value: M9 glycerol ampicillin

value: Replicate 3


title: Control, replicate 5

description:
Library name: ecoli_CR_00021
Column name in log_tpm.csv: ecoli_CR_00021

value: Replicate 5


title: 1007_BX16A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-108-6

value: male


title: 1007_BX14A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-108-4


title: Yjlab_chip_S009_female_rep2_k4me1

description: Library name: sample9


title: Yjlab_chip_S008_male_rep2_k4me1

description: Library name: sample8


title: Expression of MFP5, replicate 2

description:
Library name: ecoli_CR_00016
Column name in log_tpm.csv: ecoli_CR_00016

value: SDT507 (gly2 rhaBADM KO) pSD114

value: Replicate 2


title: 1007_BX14A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-108-5


title: Yjlab_chip_S010_male_rep1_k9me3

description: Library name: sample10


title: 1005_BX3A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-108-2


title: 1004_BX5-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-47-5


title: Expression of MFP5, replicate 1

description:
Library name: ecoli_CR_00015
Column name in log_tpm.csv: ecoli_CR_00015

value: Replicate 1


title: Expression of Ovalbumin, replicate 2

description:
Library name: ecoli_CR_00014
Column name in log_tpm.csv: ecoli_CR_00014

value: SDT507 (gly2 rhaBADM KO) pSD112


title: Expression of BLG, replicate 1

description:
Library name: ecoli_CR_00011
Column name in log_tpm.csv: ecoli_CR_00011

value: SDT507 (gly2 rhaBADM KO) pSD108


title: 1005_BX2A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-108-1


title: Expression of ALA, replicate 2

description:
Library name: ecoli_CR_00010
Column name in log_tpm.csv: ecoli_CR_00010

value: SDT507 (gly2 rhaBADM KO) pSD107


title: Yjlab_chip_S007_female_rep1_k4me1

description: Library name: sample7


title: Expression of BLG, replicate 2

description:
Library name: ecoli_CR_00012
Column name in log_tpm.csv: ecoli_CR_00012


title: 1004_BX11-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-47-1


title: Yjlab_chip_S006_male_rep1_k4me1

description: Library name: sample6


title: Expression of Brazzein, replicate 2

description:
Library name: ecoli_CR_00008
Column name in log_tpm.csv: ecoli_CR_00008

value: SDT507 (gly2 rhaBADM KO) pSD103


title: Estradiol_1

description: tissue derived primary cells

data_processing:
The sequencing data was filtered with SOAPnuke(v1.5.6)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.
Bowtie2(2.3.4.3)(parameter: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200) was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM, TPM and read counts of gene expression for each Sample.
Supplementary files format and content: tab-delimited text files include FPKM, TPM and read counts of RNA expression for each Sample.

source_name: liver

growth_protocol: For mAHSC group, the hepatic stellate cells were directly isolated from LratCre;Ai32(RCL-ChR2(H134R)/EYFP)+/- mice with CCl4 i.p. (10% dissolved in corn oil, 5μl per gram of body weight, twice a week for three weeks)induced liver fibrosis. Hepatic stellate cells were sorted through fluorescence activated cell sorting based on EYFP+/CD45- signals. For the estrodial group, Hepatic stellate cells from healthy wild type female C57/B6J mice(8 to 10 weeks old) were cultured in Dulbecco's modified Eagle's medium (DMEM, Gibco, C11995500BT) containing 10% bovine serum albumin (New Zerum, FBS-UE500), 100 U/ml penicillin, and 100 mg/ml streptomycin before treatment.

extract_protocol:
Total RNAs of 1 million hepatic stellate cells were extracted by the RNeasy Mini Kit (Qiagen).
All the RNA samples were then subjected to single-end RNA-seq by the BGI Genomics.

value: liver

value: hepatic stellate cells

value: WT

value: 10μm 17β-estradiol


title: Yjlab_chip_S005_female_input_rep1

description: Library name: sample5


title: 1003_BX6A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-146-3


title: 1005_BX5A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-108-3


title: 1004_BX7-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-47-3


title: Yjlab_chip_S004_male_input_rep1

description: Library name: sample4


title: Expression of ALA, replicate 1

description:
Library name: ecoli_CR_00009
Column name in log_tpm.csv: ecoli_CR_00009

value: bacterial cell


title: Yjlab_chip_S011_female_rep1_k9me3

description: Library name: sample11


title: 1004_BX7-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-47-2


title: Control, replicate 2

description:
Library name: ecoli_CR_00004
Column name in log_tpm.csv: ecoli_CR_00004

value: SDT507 (gly2 rhaBADM KO) pSD138


title: YJlab_chip_S001_hepatic

source_name: hepatic stellate cells

growth_protocol: The hepatic stellate cells were directly isolated from LratCre;Ai32(RCL-ChR2(H134R)/EYFP)+/- mice with CCl4 induced liver fibrosis. 5 million mouse hepatic stellate cells were sorted through fluorescence activated cell sorting based on EYFP+/CD45- and collected with 2ml DMEM containing 10% bovine serum albumin, 100 U/ml penicillin,100 μg/ml streptomycin, and 10μM 17β-estradiol.

extract_protocol:
Cells were then fixed with 1% formadelhyde for 10min at room temperature and then quenched with glycine for 5min. Crosslinked cells were resuspended in 1ml of pre-chilled cell lysis buffer supplemented with 1:500 protease inhibitor and 1:100 PMSF. Cells were incubated on ice for 20min. After cell lysis, nuclei were pelleted at 7200rpm for 2min at 4℃. Nuclei were then resuspended in 1ml nuclear lysis buffer supplemented with 1:500 protease inhibitor and 1:100 PMSF for 20min on ice. Nuclei lysate (chromatin) was then subject to sonication on a Qsonica Q800R3 sonicator (80% amplitude, 20s ON/40s OFF for 17min). Sonicated samples were centrifuged at 15000g for 10min at 4℃ to remove cell debris. Chromatin in the supernatant was collected and diluted with 4 volumes of IP dilution buffer (20mM Tris-HCl pH=8.0, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS) containing 1:500 protease inhibitor and 1:100 PMSF. 50ul of A/G agarose beads (Santa Cruz, sc-2003) was then added into the system to for preclear. Preclear of chromatin was performed at 4℃ for 8h with rotation. Precleared chromatin was then incubated with 35ml A/G agarose beads (A:G = 1:1) pre-bound with ChIP grade anti ESR1antibody (Abcam, ab32063, 10ml) at 4℃ overnight. Beads were washed once with IP wash buffer I (20mM Tris-HCl pH=8.0, 2mM EDTA, 50mM NaCl, 1% Triton X-100, 0.1% SDS), twice with high salt buffer (20mM Tris-HCl pH=8.0, 2mM EDTA, 500mM NaCl, 1% Triton X-100, 0.01% SDS), once with IP wash buffer II (10mM Tris-HCl pH=8.0, 1mM EDTA, 0.25M LiCl, 1% NP-40/Igepal, 1% sodium deoxycholate) and twice with TE buffer (10mM Tris-HCl pH=8.0, 1mM EDTA pH=8). All washing steps were performed on ice. Beads were moved to room temperature and DNA was eluted in 200µl fresh Elution Buffer (100mM NaHCO3, 1%SDS). ChIP chromatin was reverse crosslinked at 65℃ overnight in the presence of proteinase K. Samples were supplemented with 10ml of 3M sodium acetate (pH=5.2), and DNA was purified with QIAquick PCR purification kit (QIAGEN, 28106).
ChIP-seq libraries were constructed using the AHTS Universal DNA Library Prep Kit for MGI (Vazyme, NDM607-02) according to the manufacture’s protocol.

value: primary cells


title: 1002_BX5A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-52-3


title: Estradiol_2

description: tissue derived primary cells


title: 1003_BX2A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-146-1


title: Control_2

description: tissue derived primary cells

value: Control


title: Expression of Brazzein, replicate 1

description:
Library name: ecoli_CR_00007
Column name in log_tpm.csv: ecoli_CR_00007

value: M9 glycerol ampicillin


title: 1004_BX5-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-47-4

value: male


title: Expression of Ovalbumin, replicate 1

description:
Library name: ecoli_CR_00013
Column name in log_tpm.csv: ecoli_CR_00013


title: mAHSC_female2

description: tissue derived primary cells

value: CCl4 i.p. for 3 weeks


title: Expression of MNEI, replicate 2

description:
Library name: ecoli_CR_00006
Column name in log_tpm.csv: ecoli_CR_00006

value: SDT507 (gly2 rhaBADM KO) pSD98

value: Replicate 2


title: 1003_BX3A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-146-2


title: 1002_BX4A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-52-2


title: Expression of MNEI, replicate 1

description:
Library name: ecoli_CR_00005
Column name in log_tpm.csv: ecoli_CR_00005

value: Replicate 1


title: 1002_BX2A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-52-1


title: Control_1

description: tissue derived primary cells


title: Expression of MBP, replicate 1

description:
Library name: ecoli_CR_00001
Column name in log_tpm.csv: ecoli_CR_00001

value: SDT507 (gly2 rhaBADM KO) pSD51


title: FUS-5

status: Public on Aug 20 2025

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

data_processing:
Reads were aligned to the mouse mm10 genome using STAR
Counts were obtained using featureCounts
Differential expression analysis was carried out using edgeR
Assembly: mm10
Supplementary files format and content: text file containing featureCount counts

source_name: myoblasts

growth_protocol: C2C12 myoblast cells were purchased from ATCC (ATCC® CRL-1772™). Cells were cultured in Dulbecco’s modified Eagle’s medium containing 10% Foetal Bovine Serum (Fisher scientific, 11531831) and 1% Penicilin-Streptomycin (Sigma, P4333) at 37 °C in an incubator with 5% CO2. Between 60 and 80% of confluency, myoblasts were differentiated in myotubes with differentiation medium (identical medium, with 0.1% Fetal Bovine Serum). Culture medium was changed every day and transfections were performed between 5-15 passages.

extract_protocol:
RNA quality was measured using the Agilent Bioanalyzer system according to the manufacturer’s recommendations.
Library was described previously (Parkhomchuk et al., 2009). 8 pM of amplified libraries was used for sequencing on the Illumina GA2 for 72 cycle. Bioinformatic analysis was performed with Distant Regulatory Elements of co regulated genes (Gotea and Ovcharenko, 2008)

treatment_protocol: C2C12 were cultured in 6-well plates until 60% of confluency. Cells were transfected with siRNA in differentiation medium using Lipofectamine RNA iMAX (Fischer scientific sas, 13778150) according to the manufacturer’s instructions. siRNA against FUS, Mef2a, ETV1, ETV, ETV5 and negative control siRNA were provided by Dharmacon. Cells were harvested 48h after transfection.

value: myoblasts

value: siFUS


title: Control, replicate 1

description:
Library name: ecoli_CR_00003
Column name in log_tpm.csv: ecoli_CR_00003


title: mAHSC_male1

description: tissue derived primary cells

value: liver


title: mAHSC_male2

description: tissue derived primary cells

value: hepatic stellate cells


title: Expression of MBP, replicate 2

description:
Library name: ecoli_CR_00002
Column name in log_tpm.csv: ecoli_CR_00002


title: FUS-4


title: FUS-3


title: CT-6

value: siCT


title: mAHSC_female1

description: tissue derived primary cells


title: CT-5


title: Extracellular RNA derived from senescent MG-63 cells (RNA pulled from 5 biol rep each of 3 technical rep)

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

description: Library name: P-27_S2

data_processing:
trimming and filtering was performed using Cutadapt software
Cleaned, good quality reads were mapped to the Human GRCh38.p14 assembly with Hisat2 aligner
Htseq-count was used for reads counting
Assembly: Human GRCh38.p14
Supplementary files format and content: raw counts from Htseq-count

molecule: polyA RNA

extract_protocol:
To collect RNA released from dying cells (RNA D), U-2 OS, SaOS-2, MG-63, and 143B cells were treated with 15, 10, 20, and 10 µM etoposide for 72 h, respectively. To collect RNA released from senescent cells (RNA S), U-2 OS, SaOS-2, MG-63, and 143B cells were treated with 1, 1, 5 and 2 µM etoposide for 24 h, respectively, and left in the culture for additional 7 days. Cell culture medium was then collected, cellular debris were removed from cell culture medium by centrifugation (300xg, 5 min, RT) and RNA D and RNA S were extracted from supernatants using acid phenol: chloroform: isoamyl alcohol (125:24:1, pH 4.5) solution according to the manufacturer’s instructions (AM9722, Thermo Fisher Scientific, Waltham, MA, USA). The purity and concentration of isolated RNA were analyzed using NanoDropTM 2000 UV-Vis spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Analyzed RNA was pulled from 5 biol rep samples each of 3 technical rep. RNA samples were kept at -86 °C until further use (stimulation analysis).
Library was prepared from 50 ng of total RNA with the NEBNext®UltraTM II Directional RNA Library Prep Kit for Illumina® (NEB) libraries

value: Osteosarcoma (OS)

value: Etoposide


title: CT-1


title: Extracellular RNA derived from dying  MG-63 cells (RNA pulled from 5 biol rep and  3 technical rep)

description: Library name: P-12_S1


title: HeLaS3 Cells, Ctrl_2, RNA

city: Cheongju-si

first: Junho

last: Noh

state: Chungcheongbuk-do

address: 1, Chungdae-ro, Seowon-gu

department: Biological science and biotechnology

country: South Korea

institute: Chungbuk National University

description: Library name: Sample 2

data_processing:
Sequenced reads were mapped to the reference human genome (hg38 assembly) using STAR aligner (v 2.7.1a) with default parameters
The expression levels of genes in each sample were normalized by means of fragments per kilobase of transcript per million mapped reads (FPKM).
Differentially expressed genes (DEGs) were identified using DEseq2 with raw read counts.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample.

source_name: Uterus; Cervix

growth_protocol: Human cervical cancer cell line HeLaS3 was cultured in RPMI 1640 (No. 11875-119; Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS; No. 16000-044; Gibco) and 1% penicillin– streptomycin (No. 15070-063; Gibco). The cell line was routinely cultured at 37°C in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA was extracted with Ribospin II (GeneAll Biotechnology, Seoul, Republic of Korea), and 0.5 µg total RNA was reverse transcribed with a RevertAid First Strand cDNA Synthesis kit (Thermo Fisher Scientific).
RNA libraries for sequencing were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: HeLaS3 cells were treated with OSM (No. 30010T, PeproTech, Rocky Hill, NJ, USA) and SD-36 (No. HY129602, MedCheExpress, Monmouth Junction, NJ, USA) for 24 h.

value: Uterus; Cervix

value: Human cervical adenocarcinoma

value: WT

value: DMSO


title: HeLaS3 Cells, Ctrl_1, RNA

description: Library name: Sample 1


title: HeLaS3 Cells, SD36_2, RNA

description: Library name: Sample 6


title: HeLaS3 Cells, OSM_SD36_1, RNA

description: Library name: Sample 7


title: HeLaS3 Cells, SD36_1, RNA

description: Library name: Sample 5


title: HeLaS3 Cells, OSM_SD36_2, RNA

description: Library name: Sample 8


title: HeLaS3 Cells, OSM_2, RNA

description: Library name: Sample 4

value: OSM


title: HeLaS3 Cells, OSM_1, RNA

description: Library name: Sample 3


title: RIP-Seq, anti-ORFP1p antibody, 300mM salt concentration, replicate 2

city: Toronto

first: Sajid

middle: A

last: Marhon

state: ON

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

description:
Library name: sample_17
column name in supplementary files: JL220826.017

data_processing:
mapping to hg38 with STAR
computing read counts for genes using featureCounts program from subread package
computing read counts for sens and antisense transcripts of repeat elements using SquIRE
Assembly: hg38
Supplementary files format and content: tab delimited files with raw read count for genes and repeat elements (sense and antisense separately)

growth_protocol: N2102Ep Clone 2/A6 cells (Merk, #06011803) were cultured in DMEM (high glucose, no sodium pyruvate; Thermo Fisher, #11965092), supplemented with 10% (v/v) fetal bovine serum, 1x penicillin/streptavidin and 2 mM Glutamine (Thermo Fisher, #25030024).

extract_protocol:
RNA was eluted from the affinity media using TRIzol Reagent, followed by chloroform phase separation in Phasemaker tubes to isolate the aqueous phase.
RNA-seq cDNA libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v3


title: untreated POP92 cell line, replicate 2

city: New York

first: John

last: LaCava

address: 1230 York ave

institute: The Rockefeller University

description:
Library name: J2-S3
column name in supplementary files: J2.S3

data_processing:
mapping with STAR
computing read counts for genes using featureCounts program from subread package
computing read counts for sens and antisense transcripts of repeat elements using SquIRE
Assembly: GRCh38
Supplementary files format and content: tab delimited files with raw read count for genes and repeat elements (sense and antisense separately)

growth_protocol: The patient-derived colon cancer stem cell (CSC)-enriched spheroid line POP92 was used for J2 immunoprecipitation.

extract_protocol:
Protein G Dynabeads were washed twice and resuspended in antibody conjugation buffer (1x PBS, 2mM EDTA, 0.1% BSA (w/v). 5 µg of anti-dsRNA mAb (J2) (SCICONS, cat# 10010500) were bound to 30 µl of washed beads overnight at 4° C on a rotating wheel. 107 POP92 cells per IP were fixed with 0.1% paraformaldehyde at room temperature (RT) for 10 min. Immediately, cells were quenched by adding glycine and washed twice with cold PBS. Crosslinked cells were lysed in lysis buffer (20mM Tris [pH 7.5], 150mM NaCl, 10mM EDTA, 10% Glycerol, 0.1% NP-40, 0.5% Triton X-100, supplemented with protease inhibitor tablet) for 15 minutes on ice. Following a spin at 12,000g at 4° C for 15 minutes, supernatant was transferred to a new eppendorf. The lysate was then immunoprecipitated using 30 µL antibody-conjugated Dynabeads per IP reaction overnight at 4° C in a rotator. Following magnetic separation, beads were washed three times with high salt wash buffer (20 mM Tris pH 7.5, 500 mM NaCl, 10 mM EDTA, 10% glycerol) and resuspended in 1X TBS. Per IP, 2 µL of Promega RNasinPlus RNase inhibitor (Fisher Scientific, PRN2611) and 0.5 µL of proteinase K (NEB, P8107S) was added. Decrosslinking was performed for all the IP samples at 65° C for 15 minutes. The Direct-zol RNA MiniPrep kit (Zymo Research, R2051) was used to extract RNA from IP supernatant. Samples were treated with Turbo DNase to remove any DNA contamination in the extracted RNA.
Library prep was performed using Illumina Stranded total RNA ligation with Ribo Zero plus according to the manufacturers protocol.


title: total RNA control, 500mM salt concentration, replicate 2

description:
Library name: sample_20
column name in supplementary files: JL220826.020


title: total RNA control, 300mM salt concentration, replicate 1

description:
Library name: sample_15
column name in supplementary files: JL220826.015


title: FUS-1


title: RIP-Seq, anti-ORFP1p antibody, 500mM salt concentration, replicate 1

description:
Library name: sample_14
column name in supplementary files: JL220826.014


title: total RNA control, 300mM salt concentration, replicate 2

description:
Library name: sample_19
column name in supplementary files: JL220826.019


title: RIP-Seq, anti-ORFP1p antibody, 500mM salt concentration, replicate 2

description:
Library name: sample_18
column name in supplementary files: JL220826.018


title: RIP-Seq, anti-ZCCHC3 antibody, 300mM salt concentration, replicate 2

description:
Library name: sample_05
column name in supplementary files: JL220826.005


title: RIP-Seq, mock antibody, 300mM salt concentration, replicate 2

description:
Library name: sample_07
column name in supplementary files: JL220826.007


title: RIP-Seq, mock antibody, 500mM salt concentration, replicate 2

description:
Library name: sample_08
column name in supplementary files: JL220826.008


title: RIP-Seq, anti-ORFP1p antibody, 300mM salt concentration, replicate 1

description:
Library name: sample_13
column name in supplementary files: JL220826.013


title: RIP-Seq, anti-ZCCHC3 antibody, 500mM salt concentration, replicate 1

description:
Library name: sample_02
column name in supplementary files: JL220826.002


title: RIP-Seq, mock antibody, 500mM salt concentration, replicate 1

description:
Library name: sample_04
column name in supplementary files: JL220826.004


title: untreated POP92 cell line, replicate 1

description:
Library name: J2-S1
column name in supplementary files: J2.S1


title: RIP-Seq, mock antibody, 300mM salt concentration, replicate 1

description:
Library name: sample_03
column name in supplementary files: JL220826.003


title: MDA-MB-468, E2F3 KO, clone 3, rep3

city: Torino

first: Aurora

last: Savino

state: Piemonte

address: via Nizza, 52

country: Italy

institute: Università di Torino

description: Library name: Poli_EL3-3

data_processing:
Reads were aligned to the Hg38 human genome and the reads aligned to each gene computed with featureCounts
Assembly: Hg38
Supplementary files format and content: gene_count.xlsx worksheet with  raw counts for each sample (batch 1)
Supplementary files format and content: GEP.count tab delimited file with raw counts for each sample (batch 2)

source_name: Breast cancer

growth_protocol: Hs578T, MDA-MB-231 and MDA-MB-468 cells were purchased by ATCC, cultured under standard conditions (37 °C, 5% CO₂, humidified atmosphere) and routinely tested for Mycoplasma contamination. MDA-MB-231 and MDA-MB-468 were grown in DMEM, Hs578T in RPMI, all supplemented with GLUTAMAX, 10% (v/v) heat-inactivated FBS, 100 U/ml penicillin, and 100 μg/ml streptomycin (Gibco).

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Thermo Fisher Scientific)
RNA Integrity was quantified with the TapeStation automated electrophoresis system, standard mRNA stranded Illumina protocols were employed for library preparation and 40 Million Paired-end 150bp reads per sample were sequenced. Libraries were prepared and sequenced in two batches: Hs578T, MDA-MB-231 and MDA-MB-468 TFDP1 KO and corresponding controls, were processed and sequenced by Novogene. MDA-MB-468 E2F3 KO and corresponding controls were processed and sequenced by the IIGM Genomics Facility at the University of Turin.

treatment_protocol: Arrays with 3 sgRNAs against either E2F3 or TFDP1 genes were cloned in pCI-152-pLenti-SiT-Cas12a (Addgene, cat. 258283). Lentiviral particles were produced and supernatants used for transduction of Hs578T, MDA-MB-231 and MDA-MB-468 basal-like breast cancer cell lines, followed by puromycin selection (2ug/ml) for 3 days.  Single cells were cloned by limiting dilution, and clones analysed by Western blot analysis to identify E2F3/TFDP1 null clones. Two independent clones were analysed for each cell line/gene. Cells transduced with the empty vector were used as control (EV).

value: Breast cancer

value: E2F3 KO

tag: clone id

tag: replicate


title: MDA-MB-468, E2F3 KO, clone 3, rep2

description: Library name: Poli_EL3-2


title: total RNA control, 500mM salt concentration, replicate 1

description:
Library name: sample_16
column name in supplementary files: JL220826.016


title: MDA-MB-468, E2F3 KO, clone 3, rep1

description: Library name: Poli_EL3-1


title: MDA-MB-468, E2F3 KO, clone 1, rep3

description: Library name: Poli_EL1-3


title: MDA-MB-468, EV, rep2, batch2

description: Library name: Poli_C2

value: EV


title: MDA-MB-231, TFDP1 KO, clone 21, rep3

description: Library name: S231_T21_3

value: TFDP1 KO


title: MDA-MB-468, EV, rep1, batch2

description: Library name: Poli_C1


title: MDA-MB-468, E2F3 KO, clone 1, rep2

description: Library name: Poli_EL1-2


title: MDA-MB-231, TFDP1 KO, clone 21, rep2

description: Library name: S231_T21_2


title: MDA-MB-231, TFDP1 KO, clone 6, rep2

description: Library name: S231_T6_2


title: MDA-MB-231, TFDP1 KO, clone 21, rep1

description: Library name: S231_T21_1


title: MDA-MB-231, TFDP1 KO, clone 6, rep3

description: Library name: S231_T6_3


title: MDA-MB-231, E2F3 KO, clone 20, rep1

description: Library name: S231_E20_1


title: MDA-MB-468, E2F3 KO, clone 1, rep1

description: Library name: Poli_EL1-1


title: MDA-MB-231, E2F3 KO, clone 18, rep3

description: Library name: S231_E18_3


title: RIP-Seq, anti-ZCCHC3 antibody, 300mM salt concentration, replicate 1

description:
Library name: sample_01
column name in supplementary files: JL220826.001


title: MDA-MB-231, E2F3 KO, clone 18, rep1

description: Library name: S231_E18_1


title: MDA-MB-231, E2F3 KO, clone 20, rep3

description: Library name: S231_E20_3


title: MDA-MB-231, EV, rep2

description: Library name: S231_CTR_2


title: Hs578T, TFDP1 KO, clone 18, rep3

description: Library name: HS_T18_3


title: MDA-MB-231, TFDP1 KO, clone 6, rep1

description: Library name: S231_T6_1


title: Hs578T, TFDP1 KO, clone 18, rep2

description: Library name: HS_T18_2


title: RIP-Seq, anti-ZCCHC3 antibody, 500mM salt concentration, replicate 2

description:
Library name: sample_06
column name in supplementary files: JL220826.006


title: Hs578T, TFDP1 KO, clone 14, rep3

description: Library name: HS_T14_3


title: Hs578T, TFDP1 KO, clone 14, rep2

description: Library name: HS_T14_2


title: MDA-MB-231, EV, rep3

description: Library name: S231_CTR_3


title: MDA-MB-468, EV, rep3, batch2

description: Library name: Poli_C3


title: Hs578T, EV, rep2

description: Library name: HS_CTR_2


title: Hs578T, TFDP1 KO, clone 14, rep1

description: Library name: HS_T14_1


title: MDA-MB-468, TFDP1 KO, clone 9, rep2

description: Library name: S468_T9_2


title: Hs578T, EV, rep1

description: Library name: HS_CTR_1


title: MDA-MB-468, TFDP1 KO, clone 9, rep1

description: Library name: S468_T9_1


title: MDA-MB-231, E2F3 KO, clone 20, rep2

description: Library name: S231_E20_2


title: MDA-MB-468, TFDP1 KO, clone 4, rep2

description: Library name: S468_T4_2


title: MDA-MB-468, TFDP1 KO, clone 9, rep3

description: Library name: S468_T9_3


title: MDA-MB-468, EV, rep3

description: Library name: S468_CTR_3


title: MDA-MB-468, EV, rep1

description: Library name: S468_CTR_1


title: MDA-MB-468, EV, rep2

description: Library name: S468_CTR_2


title: A549,shUXS1,rep1

city: South San Francisco

first: Melat

middle: T.

last: Gebru

address: 1170 Veterans Blvd

department: Oncology

institute: Calico Life Sciences LLC.

description:
Library name: Sample10
Column name in A549_RNAseq_6d_count.xlsx: A549_shUXS1_1

data_processing:
Sequencing reads were aligned to the human genome using STAR aligner20 (RRID:SCR_005622) and transcript counts for aligned reads were generated using Feature Count21.
Assembly: GRCh38
Supplementary files format and content: xlsx files include count files for each sample

growth_protocol: H2122 and A549 cells were grown in RPMI media supplemented with 10% FBS and 1% GlutMax in humidified atmosphere with 5% CO2 at 37oC

extract_protocol:
RNA was extracted using Qiagen's Rneasy kit (Cat#74106).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit with polyA enrichment (New England Bio Labs Cat. No. E7760L) according to the manufacturer's instructions. Samples were sequenced on the NovaSeq 6000 (illunima).

treatment_protocol: NTC or shUXS1 expressing H2122 and A549 cells were treated with 0.5uM doxycycline (Dox) to induce shRNA expression. RNA was extracted after 5 or 5 days of dox treatment from H2122 and A549 cells respecitvely.

value: NSCLC

value: Doxycycline


title: A549,shNTC,rep3

description:
Library name: Sample9
Column name in A549_RNAseq_6d_count.xlsx: A549_shNTC_3


title: A549,shUXS1,rep2

description:
Library name: Sample11
Column name in A549_RNAseq_6d_count.xlsx: A549_shUXS1_2


title: H2122,shNTC,rep2

description:
Library name: Sample2
Column name in H2122_RNAseq_5d_count.xlsx: H2122_NTC_2


title: H2122,shNTC,rep3

description:
Library name: Sample3
Column name in H2122_RNAseq_5d_count.xlsx: H2122_NTC_3


title: A549,shNTC,rep1

description:
Library name: Sample7
Column name in A549_RNAseq_6d_count.xlsx: A549_shNTC_1


title: H2122,shUXS1,rep2

description:
Library name: Sample5
Column name in H2122_RNAseq_5d_count.xlsx: H2122_shUXS1_2


title: A549,shNTC,rep2

description:
Library name: Sample8
Column name in A549_RNAseq_6d_count.xlsx: A549_shNTC_2


title: Hs578T, TFDP1 KO, clone 18, rep1

description: Library name: HS_T18_1


title: MDA-MB-468, TFDP1 KO, clone 4, rep3

description: Library name: S468_T4_3


title: MDA-MB-231, EV, rep1

description: Library name: S231_CTR_1


title: MDA-MB-231, E2F3 KO, clone 18, rep2

description: Library name: S231_E18_2


title: Hs578T, EV, rep3

description: Library name: HS_CTR_3


title: H2122,shNTC,rep1

description:
Library name: Sample1
Column name in H2122_RNAseq_5d_count.xlsx: H2122_NTC_1


title: H2122,shUXS1,Day0

description:
Library name: Sample7
Column name in H460_Count_T0.xlsx: H2122_shUXS1_count_T0

data_processing:
SgRNA count data was used to determine relative guide abundance in shUXS1 vs shNTC cells using method outlined in Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK).
Assembly: GRCh38
Supplementary files format and content: xlsx files include count files for each sample
Library strategy: CRISPR Screen

growth_protocol: H460 and H2122 cells were grown in RPMI media supplemented with 10% FBS and 1% GlutMax in humidified atmosphere with 5% CO2 at 37oC

extract_protocol:
Genomic DNA was extracted from cells using Macherey Nagel Nucleospin Blood XL kit (Item number- 740950.50)
sgRNA regions of library cassette were amplified using Phusion HiFi Polymerase Master Mix in two PCR steps. In PCR 1, to increase sequence diversity, libraries are amplified in two primer orientations named SET A and SET B. In SET A orientation, the protospacer is sequenced during read 1. In SET B orientation, the protospacer is sequenced during read 2. The orientation of the amplicon is determined during round 1 PCR. In PCR 2 unique primers are used to tag each sample for the purpose of disambiguating each sample as they are pooled together

treatment_protocol: Cell were transduced with CRISPR library followed by puromycine selection for 5 days after which cells were treated with 0.5uM doxycycline to induce shRNA expression for 11 days before DNA extraction.


title: H2122,shNTC,Day0

description:
Library name: Sample5
Column name in H460_Count_T0.xlsx: H2122_NTC_count_T0


title: H2122,shNTC,Day11

description:
Library name: Sample6
Column name in H460_Count_T0.xlsx: H2122_NTC_count_11d


title: H460,shNTC,Day11

description:
Library name: Sample2
Column name in H460_Count_T0.xlsx: H460_NTC_count_11d


title: H460,shUXS1,Day0

description:
Library name: Sample3
Column name in H460_Count_T0.xlsx: H460_shUXS1_count_T0


title: A549,shUXS1,rep3

description:
Library name: Sample12
Column name in A549_RNAseq_6d_count.xlsx: A549_shUXS1_3


title: H2122,shUXS1,Day11

description:
Library name: Sample8
Column name in H460_Count_T0.xlsx: H2122_shUXS1_count_11d


title: H460,shUXS1,Day11

description:
Library name: Sample4
Column name in H460_Count_T0.xlsx: H460_shUXS1_count_11d


title: H460,shNTC,Day0

description:
Library name: Sample1
Column name in H460_Count_T0.xlsx: H460_NTC_count_T0


title: H2122,shUXS1,rep1

description:
Library name: Sample4
Column name in H2122_RNAseq_5d_count.xlsx: H2122_shUXS1_1


title: H2122,shUXS1,rep3

description:
Library name: Sample6
Column name in H2122_RNAseq_5d_count.xlsx: H2122_shUXS1_3


title: 293T_WT_NSD1

city: WASHINGTON

first: Jia-Ray

last: Yu

state: DC

address: 7144 13th PL NW

institute: Virginia Tech

description: Library name: CH120_293T_WT_NSD1

data_processing:
Data was processed with the nf-core/chip-seq v2.1.0 pipeline, with default settings for 150bp reads.
Spike-in was performed by re-running the pipeline with dm6 genome, and dividing uniquely mapped paired hg38 reads by dm6 reads. The wild type sample’s ratio was set to 1, and mutant samples were calculated relative to the wild type. Coverage tracks were then generated using the bam_coverage function of deepTools, with the scaling factor manually set as calculated for each sample
Assembly: mm10, hg38
Supplementary files format and content: Supplementary_files_format_and_content:

source_name: Kidney

growth_protocol: 37 degree and 5% CO2 in humidified incubators.

extract_protocol:
crosslinked and sheared chromatin
NEBNext Ultra II

treatment_protocol: Spiked with equal amounts Drosophila chromatin for normalization

value: Kidney

value: fibroblast

tag: chip antibody


title: 293T_NONO-KO_NSD1

description: Library name: CH122_293T_NONO-KO_NSD1

value: NONO-KO


title: 293T_WT_NONO

description: Library name: CH128_293T_WT_NONO

value: NONO


title: 293T_CRISPRi-NEAT1_H3K36me2

description: Library name: CH41_293T_CRISPRi-NEAT1_H3K36me2

value: infected with dCas9-KRAB and NEAT1 sgRNA


title: 293T_WT_H3K36me2

description: Library name: CH50_293T_WT_H3K36me2


title: 293T_WT_H3K36me2_CRISPRi control

description: Library name: CH40_293T_WT_H3K36me2


title: A431 cell line, DSG2 KO #1

city: Clinton

first: Austin

middle: Young

last: Shull

state: SC

address: 503 South Broad Street, Box 130

department: Biology

institute: Presbyterian College

description:
Library name: A431_DSG2KO1
column name in raw_counts_DSG2KO

data_processing:
CLC Genomics Workbench Version 23.0.4
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file contains total counts for each sample

growth_protocol: A431 cells are grown in 5% CO2 at 37°C. The recommended growth medium is Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 4.5 g/L Glucose, 1.0 mM Sodium pyruvate, 1.5 g/L NaHCO3, and 4 mM L-Glutamine.

extract_protocol:
RNA was harvested using  Direct-zol RNA Miniprep kit (Zymo)
RNAeq libraries were prepared using NEBNext Ultra RNA Library Prep Kit

value: human epidermoid carcinoma cell line

value: DSG2 KO


title: A431 cell line, control #2

description:
Library name: A431_CTRL2
column name in raw_counts_DSG2KO


title: A431 cell line, DSG2 KO #3

description:
Library name: A431_DSG2KO3
column name in raw_counts_DSG2KO


title: A431 cell line, DSG2 KO #2

description:
Library name: A431_DSG2KO2
column name in raw_counts_DSG2KO


title: A431 cell line, control #3

description:
Library name: A431_CTRL3
column name in raw_counts_DSG2KO


title: A431 cell line, control #1

description:
Library name: A431_CTRL1
column name in raw_counts_DSG2KO


title: MDA-MB-468, TFDP1 KO, clone 4, rep1

description: Library name: S468_T4_1


title: H441_TET1_KO_2

city: Minneapolis

first: Abdur

last: Rahim

state: Minnesota

address: 2231 6th street SE

department: Department of Medicinal Chemistry

institute: University of Minnesota

description: Library name: RNA-seq_sample9

data_processing:
Sequencing reads were mapped to the human reference genome (GRCh38 p13) via Hisat2 (v2.1.0).
Quality control on raw sequence data for each sample was performed with FastQC
Gene quantification was done via Feature Counts for raw read counts
Genes differentially expressed =were determined using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: human (GRCh38 p13)
Supplementary files format and content: rawcountsTret.txt
Supplementary files format and content: rawcountsTret.txt

source_name: lung

growth_protocol: H441 cells were grown in RPMI media supplemented with 10% fetal bovine serum (FBS) and 1% penstrep antibiotics in humidified atmosphere with 5% CO2 at 37 C.

extract_protocol:
RNA was isolated using AllPrep DNA/RNA mini kit (Qiagen). 1.0 ug of total RNA was used for the construction of the library sequencing.
Total RNA samples were converted to Illumina sequencing libraries using SMARTer Stranded Total RNA-Seq Kit – Pico Mammalian Input (Takara Bio USA, Mountain View CA).

treatment_protocol: For TET1 overexpression, H441 cells were transfected with human full length TET1 plasmid. And for TET1 knock out (KO), TET1 gene was knocked out from H441-WT cells via CRISPR-Cas9

value: lung

value: epithelial cell

value: TET1 knock out


title: H441_WT_1

description: Library name: RNA-seq_sample5

value: wild type (no treatment)


title: H441_Lipo_2

description: Library name: RNA-seq_sample1


title: H441_WT_2

description: Library name: RNA-seq_sample6


title: H441_OE_2

description: Library name: RNA-seq_sample4

value: Transient TET1 overexpression


title: H441_Lipo_3

description: Library name: RNA-seq_sample2


title: H441_OE_1

description: Library name: RNA-seq_sample3


title: 293T_NSD1-KO_NONO

description: Library name: CH129_293T_NSD1-KO_NONO


title: H441_TET1_KO_1

description: Library name: RNA-seq_sample8


title: H441_TET1_KO_3

description: Library name: RNA-seq_sample10


title: placenta, normal_3

city: Shenyang

first: Yan

last: Zhao

address: No.36 Sanhao Street

institute: Shengjing Hospital of China Medical University

description: Library name: Sample 7

data_processing:
The original fluorescence image files obtained from Illumina platform were transformed to short reads (Raw data) by base calling and these short reads were recorded into FASTQ format, which contains sequence information and correspondingg sequenceing quiality information. Quality control of the raw reads were performed using Fastp as follows: a, discard a paired reads if either one read contained adapter contamination; b, discard a paired reads if more than 10% of bases were uncertain in either one reads; c, discard a paired reads if the proportion of low quality (phred quality < 5) bases was over 50% in either one read.
Assembly: CRCh38
Supplementary files format and content: xlsx file containing read counts of each sample
Supplementary files format and content: xlsx file containing gene information

source_name: placenta

growth_protocol: No.

extract_protocol:
Total RNA was harvested using TRIpure RNA Extraction Kit (BioTeke Corporation Co., Ltd., Beijing, China).
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit Illumina (NEB, USA, Catalog #: E7530L) following manufacturer's recommendations and index codes were added attribute sequences to each sample.

treatment_protocol: The placentas were collected from PE patients or control healthy pregnant women after delivery. The placenta sample were taken from a prepresentative block of the central portion of tissue below one third of the placenta, near maternal side.

value: placenta

value: healthy pregnant women

value: trophoblast

value: No


title: placenta, normal_1

description: Library name: Sample 5


title: placenta, PE_2

description: Library name: Sample 2

value: preeclampsia (PE) patient


title: placenta, PE_4

description: Library name: Sample 4


title: placenta, PE_3

description: Library name: Sample 3


title: VASAseq_Lane_5

city: Leiden

first: Valeria

last: Orlova

address: Einthovenweg 20

country: Netherlands

institute: Leiden University Medical Center

description:
Library name: VASAseq_Lane_5
All 18 samples were multiplexed and sequenced across 5 different lanes. This is the raw data for lane #5. Barcodes for demultiplexing of individual samples are listed in processed data "samplesheet.csv". Mapped read counts data for all samples after demultiplexing are listed in processed data "RPKM_normalized_VASAseq.csv".

data_processing:
Bulk RNAseq of day 6 and 8 of CMEC and PMEC differentiation were performed at BGI (Shenzhen, China) using the Illumina Hiseq4000 (100bp paired end reads). Raw data was processed using the LUMC BIOPET Gentrap pipeline (https://github.com/biopet/biopet), which comprises FASTQ preprocessing, alignment and read quantification. Sickle (v1.2) was used to trim low-quality read ends (https://github.com/najoshi/sickle). Cutadapt (v1.1) was used for adapter clipping (Martin, 2011), reads were aligned to the human reference genome GRCh38 using GSNAP (gmap-2014-12-23) (Wu and Nacu, 2010; Wu and Watanabe, 2005) and gene read quantification with htseq-count (v0.6.1p1) against the Ensembl v87 annotation (Yates et al., 2015). Gene length and GC content bias were normalized using the R package cqn (v1.28.1) (Hansen et al., 2012).  For VASA-seq: The first 8 bases of read 2 contain the unique molecular identifier, and the next 8 bases contain the sample barcode (specific to each well), while read 1 contains the transcript information. Reads 1 with a valid sample barcode were selected and trimmed using TrimGalore (v.0.6.6) with default parameters. In addition, homopolymers at the end of the read were also trimmed out. Next, in silico ribosomal depletion was performed as described in [2]. Resulting reads were mapped using STAR (v2.7.7a) with default parameters using the human GRCh38 genome (Ensembl 102). Deduplicated reads were removed using fumi-tools (v0.17.0). Count tables were generated using featureCounts (from subread-2.0.1) with the following options: -M -O --fraction -s 1 -t exon -g gene_name. We used the human custom made gtf file from (Hita et al., 2022) that integrates different biotypes.
Assembly: GRch38
Supplementary files format and content: fq.gz: compressed raw fastq file from illumina sequencing; count_matrix: matrix of UMI counts where cells are columns and genes rows; barcode_list: list of 12bp barcodes corresponding to the columns of matrix; gene_list: HUGO and ensembl identifiers corresponding to the rows of matrix; RPKM_normalized_CMEC_PMEC_bulk.csv: RPKM normalized based on gene length and GC content; fastq.gz: compressed raw fastq file from illumina sequencing; RPKM_normalized_VASAseq.csv: RPKM of VASAseq data normalized based on gene length and GC content; samplesheet_VASAseq.csv: sample information of VASAseq with barcode for demultiplexing.

source_name: human iPSCs

growth_protocol: CMEC differentiation was performed as follow: Briefly, 25 × 103 cells per cm2 were seeded on plates coated with 75 µg/ml matrigel growth factor reduced (Corning) the day before differentiation (day -1). At day 0, cardiac mesoderm was induced by changing E8 to BPEL medium (Bovine Serum Albumin [BSA] Polyvinyl alcohol Essential Lipids; 5, supplemented with a mixture of cytokines (20 ng/ml BMP4, R&D Systems; 20 ng/ml ACTIVIN A, Miltenyi Biotec; 1.5 μM GSK3 inhibitor CHIR99021, Axon Medchem). After 3 days, cytokines were removed and a Wnt inhibitor (5 μM XAV939, Tocris) and VEGF (50 ng/ml, R&D Systems) was added for 3 days. BPEL medium was refreshed every 3 days. PMEC differentiation was performed as follow: hiPSCs were split with a 1:12 ratio and seeded on 6-well plates coated with 75 µg/mL (growth factor reduced) Matrigel (Corning) on day -1. At day 0, paraxial mesoderm was induced by changing TeSR-E8 to BPEL medium, supplemented with 8 µM CHIR99021 (Axon Medchem). At day 2, cells were refreshed with BPEL supplemented 5 µM XAV939 (Tocris Bioscience). At day 3, cells were refreshed with BPEL supplemented 8 µM CHIR99021. From day 5 onwards, cells were refreshed every 3 days with BPEL medium supplemented with 50 ng/ml VEGF.

extract_protocol:
MTs were incubated in 290 U/mg of pre-warmed collagenase type II (Worthington) in HBSS solution (Sigma Aldrich). Single cells were used for single-cell RNAseq. Total RNA for bulk samples was purified using the NucleoSpin RNA Kit  (Bioke’) according to the manufacturer’s protocol.
10X library: Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Reagent Kit, Version 2 Chemistry (10x Genomics) according to the manufacturer's protocol. For bulk RNA-seq: RNA libraries were prepared for sequencing using standard Illumina protocols. For VASA-seq samples: Bulk RNAseq of ECs sorted on day 6 and 27 of CMEC differentiation, and day 27 MT_cmec were performed using VASA-seq. A 96-well plate (Greiner Bio-One, 652250) was filled with 50 μL mineral oil (Merck, M5904) and 1 μL CEL-seq2 primer (Hashimshony et al., 2016) per well with a concentration of 7.5 ng/µl. RNA samples were diluted to 20ng/µl in nuclease free water. Of the dilution, 1µl from each sample was added to different wells of the barcoded 96-well plate. The plates were sealed (Greiner Bio-One, 676090) and spun down at 500 x g for 2 min at 4˚C. Next, library preparation for bulk samples was done as previously described (Salmen et al., 2022) . In short, RNA fragmentation was performed by adding 2 µl of fragmentation mixture per sample consisting of 0.68x First-strand buffer (Invitrogen, Y02321) and the rest, ddH2O. Fragmentation was carried out using a Thermal Cycler (Bio-Rad, T100) set at 85˚C for 3 min with the lid at 105˚C. Next, 2 µl of end repair and poly(A)-tailing mix consisting of 0.12x First-strand buffer (Invitrogen, Y02321), 20 mM DTT(Invitrogen, y00147), 7.5 µM ATP (NEB, P0756S), 0.15 U of E. coli Poly(A) Polymerase (NEB, M0267L), 2 U of T4 PNK (NEB, M0201L) and 8 U of RNaseOUT (Invitrogen, 10777019) was added to each well. Repair and tailing were done at 37˚C in a Thermal Cycler for 1 hour with the lid at 70˚C. For reverse transcription, 2 µl of a mix consisting of 2 mM (each) dNTP (Solis Biodyne, 02-21-00400) and 32 U of SuperScript III (Invitrogen, 18080085) was added to each sample. Reverse transcription was done using a Thermal Cycler set at 50˚C for 1 hour with the lid at 70˚C. The plates were snap-chilled on ice. Next, 11 µl of second strand mix containing 0.23x Second-Strand Buffer (Invitrogen, 10812014), 0.23 mM (each) dNTP, 3.5 U of E. coli DNA Polymerase I (Invitrogen, 18010025) and 0.2 U of RNaseH (Invitrogen, 18021071). Second strand synthesis was done at 16˚C for 2 hours, followed by 85˚C for 20 min with the lid of the Thermo Cycler set to 105˚C. After each aforementioned step, plates were spun down at 500xg for 2 min at 4˚C. The samples were pooled together and the mineral oil was removed. Bead clean-up was performed by adding 1x volumetric ratio of diluted RNAClean XP beads (Beckman Coulter, A63987). The beads were diluted 1:2 in bead binding buffer (20% PEG8000 (Promega, V3011) and 2.5M NaCl). RNA was eluted in 6.4 µl of nuclease-free water. Next, 9.6 µl of IVT mix containing 12mM MegaScript T7 buffer, T7 enzyme, ATP, CTP, GTP and UTP (Invitrogen, AM1334) was added to the pooled sample. IVT was done at 37˚C for 14 hours with the lid set to 70˚C. Following IVT, 6 µl of ExoSAP-IT (Invitrogen, 75001.1.ML) was added and the sample was incubated at 37˚C for 15 min with the lid set to 70˚C. Concentration of aRNA was measured using a Qubit (Invitrogen, Q32853) and adjusted to 100 ng/µl. The rRNA depletion, adaptor ligation, cDNA synthesis, RNA degradation, PCR amplification and final clean-up was used as previously described (Salmen et al., 2022), with a few modifications. The primers used are shown in detail in Table S15. Paired-end sequencing with a read length of 150 bp was performed on the Illumina NovaSeq sequencing platform.

treatment_protocol: Prior to microtissue (MT) formation, hiPSC-ECs and hiPSC-CFs were prepared as follow: briefly, 2-3 days before MT formation, a vial of cryopreserved hiPSC-ECs and a vial of cryopreserved hiPSC-CFs were thawed and cultured either in BPEL medium supplemented with VEGF on plates coated with fibronectin (hiPSC-ECs), or in FGM3 medium on uncoated plates (hiPSC-CFs). The day of MT formation (day 0), hiPSC-ECs, hiPSC-CFs, SFs, ACFs, Cx43-sh-RNA CFs, SFs Empty LV and SFs CX43 LV were detached using TrypLE 1X for 5 min at 37 oC, 5% CO2, centrifuged for 3 min at 1100 rpm, resuspended in BPEL medium and counted. hiPSC-CMs at day 14-21 that showed > 80% purity, measured as the percentage of troponin positive cells by FACS analysis, were dissociated using the Multi Tissue Dissociation Kit 3 (Miltenyi Biotec) following the manufacturer’s instructions, resuspended in BPEL medium and counted. For MT, cell suspensions were combined together to 5000 cells (70% cardiomyocytes, 15% endothelial cells and 15% cardiac fibroblasts) per 50μl BPEL medium supplemented with VEGF (50 ng/ml) and FGF2 (5 ng/ml).  For all microtissues, cell suspensions were seeded on V-bottom 96 well microplates (Greiner bio-one) and centrifuged for 10 min at 1100 rpm. MTs were incubated at 37 oC, 5% CO2 for 21 days with media refreshed every 3-4 days. Dibutyryl cAMP (dbcAMP) treatment was performed on CMECFs in BPEL medium supplemented with 0.5 mM dbcAMP for 7 days (from day 14 to day 21). scRNAseq analysis of all MTs was performed after 21 days.

value: human iPSCs

value: Endothelial cells


title: VASAseq_Lane_4

description:
Library name: VASAseq_Lane_4
All 18 samples were multiplexed and sequenced across 5 different lanes. This is the raw data for lane #4. Barcodes for demultiplexing of individual samples are listed in processed data "samplesheet.csv". Mapped read counts data for all samples after demultiplexing are listed in processed data "RPKM_normalized_VASAseq.csv".


title: 293T_NONO-KO_H3K36me2

description: Library name: CH51_293T_NONO-KO_H3K36me2

value: Kidney

value: fibroblast

value: NONO-KO


title: placenta, normal_4

description: Library name: Sample 8


title: H441_WT_3

description: Library name: RNA-seq_sample7


title: VASAseq_Lane_2

description:
Library name: VASAseq_Lane_2
All 18 samples were multiplexed and sequenced across 5 different lanes. This is the raw data for lane #2. Barcodes for demultiplexing of individual samples are listed in processed data "samplesheet.csv". Mapped read counts data for all samples after demultiplexing are listed in processed data "RPKM_normalized_VASAseq.csv".


title: VASAseq_Lane_3

description:
Library name: VASAseq_Lane_3
All 18 samples were multiplexed and sequenced across 5 different lanes. This is the raw data for lane #3. Barcodes for demultiplexing of individual samples are listed in processed data "samplesheet.csv". Mapped read counts data for all samples after demultiplexing are listed in processed data "RPKM_normalized_VASAseq.csv".


title: VASAseq_Lane_1

description:
Library name: VASAseq_Lane_1
All 18 samples were multiplexed and sequenced across 5 different lanes. This is the raw data for lane #1. Barcodes for demultiplexing of individual samples are listed in processed data "samplesheet.csv". Mapped read counts data for all samples after demultiplexing are listed in processed data "RPKM_normalized_VASAseq.csv".


title: Late in vivo, BCMA CAR T cells, CRISPR sgRNA (13)

city: Cambridge

first: Kevin

last: Bi

state: MA

address: 300 Binney Street

institute: Broad Institute

description: Library name: crispr_day21_106_13_S12

library_source: other

data_processing:
Alignment and count aggregation were performed using CellRanger (v.7.1.0). Gene expression and sgRNA reads were aligned using cellranger count with default settings. Gene expression reads were aligned to the “refdata-gex-GRCh38-2020-A” human transcriptome. sgRNA reads were aligned to the library using the pattern TTCCAGCATAGCTCTTAAAC(BC).
QC, batch correction, clustering, and annotation were performed as described in manuscript methods.
Assembly: GRCh38
Supplementary files format and content: h5ad file containing fully processed and annotated AnnData object

molecule: other

source_name: T cell

extract_protocol:
Modified CAR+ T cells were enriched using a NGFR-PE antibody and PE-positive selection kit.
We performed droplet based scRNA seq using the 10x Chromium Next GEM Single Cell 5' Reagent Kit v2 (Dual Index) with Feature Barcode technology for CRISPR Screening. Sequencing was performed on an Illumina NovaSeq 6000 instrument.

value: T cell


title: Late in vivo, BCMA CAR T cells, CRISPR sgRNA (12)

description: Library name: crispr_day21_106_12_S11


title: Late in vivo, BCMA CAR T cells, CRISPR sgRNA (11_2

description: Library name: crispr_day21_106_11_2_S10


title: Late in vivo, BCMA CAR T cells, Gene expression (13)

description: Library name: gex_day21_106_13_S12

library_source: transcriptomic single cell


title: Late in vivo, BCMA CAR T cells, Gene expression (12)

description: Library name: gex_day21_106_12_S11


title: Late in vivo, BCMA CAR T cells, Gene expression (11_2)

description: Library name: gex_day21_106_11_2_S10


title: Late in vivo, BCMA CAR T cells, Gene expression (11_1)

description: Library name: gex_day21_106_11_1_S9


title: placenta, normal_2

description: Library name: Sample 6


title: 19870X9 SkBr3 Obese secretome Rep1

city: Salt Lake City

first: Keren

last: Hilgendorf

state: Utah

address: 15 N Medical Drive East Rm 4100

department: Biochemistry

institute: University of Utah

description:
Library name: Sample 9
19870R_raw_counts.txt

data_processing:
Mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 108
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR 2.7.9a in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Assembly: GRCm39
Supplementary files format and content: Feature count output files combined into a tab-delimited count matrix

growth_protocol: E0771, NMuMG, and SkBr3 cells were plated at subconfluency and allowed to grow for 36 hours, before treatment addition. E0771 and SkBr3 cells were grown in DMEM with 10% FBS. NMuMG cells were grown in DMEM with 10% FBS, 4.5 g/L glucose and 10 mcg/ml insulin.

extract_protocol:
The cells (E0771, NMuMG, and SkBr3) were washed once post treatment with PBS then collected in RLT-bME buffer. The RNA was isolated using Qiagen RNeasy kit.
RNA was sequenced using Illumina Sequencing with Agilent RNA ScreenTape Assay for QC and NovaSeq S4 Reagent Kit v1.5_150x150 bp Sequencing (2500 M read-pairs/lane). The library was prepped using NEBNext Ultra II Directional RNA Library Prep with poly(A) mRNA Isolation with adapter read 1 (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) and adapter read 2 (AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT).

treatment_protocol: The treatments,  standard growth media, lean inguinal adipocyte secretome, or obese inguinal adipocyte secretome (50% secretome, 50% standard growth media) was added to the cells for 16 hours.

value: Breast Cancer

value: Obese Inguial Adipocyte Secretome


title: 19870X8 SkBr3 Lean secretome Rep4

description:
Library name: Sample 8
19870R_raw_counts.txt

value: Lean Inguinal Adipocyte Secretome


title: 19870X10 SkBr3 Obese secretome Rep2

description:
Library name: Sample 10
19870R_raw_counts.txt


title: 19870X12 SkBr3 Obese secretome Rep4

description:
Library name: Sample 12
19870R_raw_counts.txt


title: 19870X7 SkBr3 Lean secretome Rep3

description:
Library name: Sample 7
19870R_raw_counts.txt


title: 19870X5 SkBr3 Lean secretome Rep1

description:
Library name: Sample 5
19870R_raw_counts.txt


title: 19870X11 SkBr3 Obese secretome Rep3

description:
Library name: Sample 11
19870R_raw_counts.txt


title: 19870X4 SkBr3 Control Rep4

description:
Library name: Sample 4
19870R_raw_counts.txt

value: Control


title: 19870X3 SkBr3 Control Rep3

description:
Library name: Sample 3
19870R_raw_counts.txt


title: 19870X1 SkBr3 Control Rep1

description:
Library name: Sample 1
19870R_raw_counts.txt


title: 19870X2 SkBr3 Control Rep2

description:
Library name: Sample 2
19870R_raw_counts.txt


title: 19870X6 SkBr3 Lean secretome Rep2

description:
Library name: Sample 6
19870R_raw_counts.txt


title: EV4

city: Geneva

first: Natacha

last: Civic

address: Rue Michel-Servet 1

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

description: Library name: CSFEVUCRXT01

data_processing:
Libraries were sequenced on a NovaSeq 6000 Illumina sequencer for 30 Million of SR100 reads.
After adapters trimming with Trimmomatic v.0.38, the reads were aligned with STAR v.2.7.4 to the human Ensembl genome assembly GRCh38.p13.Gene expression and biotypes were quantified with Subread v. 2.0.3 featureCounts and normalized
Genes with at least 10 counts were kept for the analysis
The functional analysis was done using the R/Bioconductor package enrichplot.
Assembly: GRCh38.p13
Supplementary files format and content: raw counts in text format for each sample

source_name: extracellular vesicles from CSF

growth_protocol: CSF was collected by lumbar puncture at the Geneva University Hospital with 22-gauge needles. Non-hemorrhagic CSF samples were selected and centrifuged at 2000 x g, 4°C for 20 minutes to pellet cells and cellular debris. Four aliquots of 7.5 mL supernatant were used to enrich EVs using 4 different protocols: UF-SEC70 (sample EV1), UF-SEC35 (sample EV2), UC-SEC35 (sample EV3) and UC (sample EV4).

extract_protocol:
Total RNA was extracted using the qEV RNA Extraction Kit (RXT01, IZON Science LTD) according to manufacturer’s instructions. RNA separation, detection and quantitation was performed on a 2100 Bioanalyzer (Agilent Technologies).
The SMART-Seq mRNA kit from Takara was used for reverse transcription and cDNA amplification according to manufacturer’s specifications, starting with 5 ng in average of RNA as input. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies)

value: extracellular vesicles from CSF


title: EV2

description: Library name: CSFEVSEC35RXT01


title: EV3

description: Library name: CSFEVSEC35UCRXT01


title: EV1

description: Library name: CSFEVSEC70RXT01


title: placenta, PE_1

description: Library name: Sample 1


title: Extracellular RNA derived from senescent U-2 OS cells (RNA pulled from 5 biol rep each of 3 technical rep)

description: Library name: S-6_S51

source_name: U-2 OS

value: U-2 OS

value: Osteosarcoma (OS)

value: Etoposide


title: Late in vivo, BCMA CAR T cells, CRISPR sgRNA (11_1)

description: Library name: crispr_day21_106_11_1_S9


title: Extracellular RNA derived from senescent SaOS-2 cells (RNA pulled from 5 biol rep each of 3 technical rep)

description: Library name: S-4_S49


title: Extracellular RNA derived from dying  U-2 OS cells (RNA pulled from 5 biol rep each of 3 technical rep)

description: Library name: M-5_S50


title: Extracellular RNA derived from senescent 143B cells (RNA pulled from 5 biol rep each of 3 technical rep)

description: Library name: S-2_S47


title: Extracellular RNA derived from dying  143B cells  (RNA pulled from 5 biol rep each of 3 technical rep)

description: Library name: M-1_S46


title: Extracellular RNA derived from dying SaOS-2 cells  (RNA pulled from 5 biol rep each of 3 technical rep)

description: Library name: M-3_S48