title: 3D culture, timepoint 3, replicate 3 [s3DT3r3]

city: San Francisco

first: Valerie

middle: M

last: Weaver

address: 513 Parnassus Avenue, HSE 560

department: Surgery

institute: UCSF

description:
3D_T3_3_20190223_S53_L004_R1_001-012
processed data file:
raw_gene_counts_allsamples.txt
log2cpm.txt
DE_t3.txt

data_processing:
Alignment performed using STAR (v2.7.1a)
Quantified reads in features (genes) using HOMER analyzeRepeats.pl (v4.9.1) with parameters -count exons -condenseGenes -gid -noadj
Features were filtered out that did not have more than one CPM in at least three samples
Counts were normalized using edgeR calcNormFactors; method="TMM" (weighted trimmed mean of M-values)
Clustering was performed using limma plotMDS on the log2(CPM) of normalized counts
Differential expression analysis using Limma-Voom
Gene ontology analysis performed using GAGE on log2(CPM) values using attributes ‘ensembl_gene_id_version’ and ‘name_1006’ from the ‘ensembl’ mart on biomaRt and ‘paired’ comparison
Genome_build: Gencode V31 hg38 primary assembly
Supplementary_files_format_and_content:
Matrix table with raw gene counts for every gene and every sample
log2(CPM) values for all samples except s2DT3r1
DE_t*.txt: Differential expression analysis using Limma-Voom at timepoint 1, timepoint2 and timepoint 3 (EXCLUDING sample s2DT3r1).

source_name: MCF10A_3D culture_timepoint 3

growth_protocol: Polyacrylamide hydrogels were prepared as described in (PMID: 26342256). Briefly, compliant PA gels were polymerized on silanized coverslips and were functionalized with Matrigel (50 µg/ml) overnight. PA gels were washed three times and equilibrated overnight at 37C prior to cell seeding. MCF10A cells were cultured in DMEM/F12 Ham’s mixture (Invitrogen) supplemented with 5% horse serum (Invitrogen), 20ng/ml EGF (PeproTech), 10ug/ml insulin (Sigma), 100ng/ml cholera toxin (Sigma), and 0.5mg/ml hydrocortisone (Sigma).

extract_protocol:
RNA was isolated using TRIzolTM (Life Technologies) followed by chloroform extraction. RNA pellets were washed three times in 75% isopropanol and resuspended in RNAse-free water. The integrity of total RNA was examined by formaldehyde-agarose gel electrophoresis.
RNA-seq libraries were constructed using a combination of KAPA mRNA HyperPrep Kit (Illumina) and NEBNext RNA Library Prep Kit (New England Biolabs) protocols. The poly-A-containing mRNA (500 ng) were purified using oligo(dT) beads and fragmented into 200-300bp fragments using heat and magnesium. The cleaved RNA fragments were reversed transcribed into first strand cDNA using random primers. Second strand synthesis and A-tailing step were performed following Kapa kit instructions. NEBNextAdaptor was ligated to dA-tailed DNA and the end products were gel purified to remove excess unligated adaptors. USER enzyme was used to cleave at the uracil incorporation sites followed by library amplification using NEBNext index primers for multiplexing. At the final stage, the cDNA library was again purified using gel electrophoresis method. The libraries were sent for sequencing with HiSeq4000 (Illumina) at Vincent J. Coates Genomics Sequencing Laboratory at University of California, Berkeley. cDNA library quality was assessed by Bioanalyzer and quantity was determined using Qubit (Invitrogen). A 50bp single-end sequencing was performed on all samples.

treatment_protocol: Cells were trypsinized and plated on compliant PA gel sparsely to reduce cell-cell interaction. After 1hr cell plating, unattached cells were removed by replacing the supernatant with regular growth media. In 2D condition, cells were replaced with fresh media. In 3D condition, the supernatant was replaced with growth media supplemented with 2% Matrigel, which polymerizes around the cell to generate a 3D scaffold. Samples were harvested at 3hr, 12hr, and 21 hr post plating.

value: Non-malignant breast epithelial cells

tag: dimensionality

tag: timepoint

tag: replicate


title: human_methylation_TLE+HS_rep1

status: Public on Jun 08 2022

type: genomic

city: ChangSha

first: ZhaoQian

last: Liu

state: China

address: xiangya road 110

country: China

institute: Xiangya Hospital, Central South University

description: DNA Methylation of human brain tissue in TLE+HS and NTP

hyb_protocol: The labeled product is purified by the Nucleospin® Extract II kit in an elution volume of about 30 µL. 100µL of hybridization solution was added to the hybridization cover fence. The hybridization box is installed on the rotor of the hybridization furnace, Meanwhile, after adding appropriate amount of ultrapure water in the tray, hybridize at 45°C overnight.

scan_protocol: Agilent G2565CA Microarray Scanner was used to scan the slides.

data_processing: Agilent Feature Extraction Software v10.7 was used to analyze the scanned pictures of the microarray.

molecule: genomic DNA

organism: Homo sapiens

source_name: Brain tissue, TLE+HS

label_protocol: The volume of cDNA product obtained after reverse transcription and purification was concentrated to 14µL, mixed with 4µL Random Primer, briefly centrifuged and placed on a PCR instrument, denatured at 95°C for 3 minutes and ice bath for 5 minutes. Add the reagents (5 µL 5×Klenow Buffer; 1 µL Cy3-dCTP; 1.2 µL Klenow Fragmen) in sequence and mix well by blowing 2-3 times with a pipette. After a short centrifugation, place on a PCR instrument and react for 1.5 h at 37°C and 5 min at 70°C. Hold at 4°C. After the fluorescent dye labeling reaction, cDNA was purified using the Nucleospin® Extract II (MN, Cat. No. 740609.250) kit, and the purified fluorescently labeled products were quantified for fluorescence admixture and nucleic acid using a UV spectrophotometer.

extract_protocol: MirVana miRNA Isolation Kit was used to purify total microRNA. The DNA sample was bisulfite converted using the Zymo EZ DNA Methylation Kit (Zymo Research) as directed. The Illumina 450k BeadChip was used to measure methylation.

treatment_protocol: All of the tissue was taken from Hippocampus or cerebral cortex (temporal or parietal cortices). Tissues were obtained and kept at –80°C until microarray analysis.

tag: tissue

value: Hippocampus

tag: gender

value: Female

tag: age


title: scRNA-seq: G12-EA02

type: SRA

city: Stanford

first: Seung

last: Kim

state: CA

address: 279 Campus Dr B303

department: Developmental Biology

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Raw reads passed quality control using FastQC
Reads were aligned to a custom reference genome consisting of Fasta files for mm10, ERCC knock in, and three transgenes: eGFP, tdTomato, and cre. STAR was used to create the custom genome and read alignment
BAM/SAM files created a counts table using ht-seq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes a matrix of normalized tag counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Pancreas

extract_protocol: Smart-Seq2 (Picelli et al 2014) was used to extract total RNA from single cells.

tag: embryonic stage

tag: plate code

value: endocrine

tag: genotype

value: Pancreas


title: scRNA-seq: G3-EA02


title: Liver Fig3-GO1_D6_3mkg_rep4

city: Cambridge

first: Joseph

last: Barry

state: MA

address: 675 West Kendall St

institute: Alnylam Pharmaceuticals

data_processing:
Raw RNAseq reads were filtered with minimal mean quality scores of 25 and minimal remaining length of 36, using the ea-utils software fastq-mcf.
Filtered reads were aligned to the Rattus norvegicus genome (Rnor_6.0) [rat liver and primary hepatocyte samples], or combined Human (hgl9/GRCh37) and HBV (GenBank nucleotide ID U95551; NCBI GeneID: 7276) genomes using STAR (ultrafast universal RNAseq aligner) [HepG2.2.15 samples].
Differential gene expression analysis was performed by the R package DESeq2 v1.16.1 with the betaPrior parameter set to TRUE to shrink log2 fold-change estimates for noisy, low-count genes.
Assembly: Rnor_6.0, GRCh37

organism: Rattus norvegicus

source_name: Liver

growth_protocol: HepG2.2.15 cells, a HepG2 derived cell line stably transfected with full genome HBV, were diluted with culture media to a final concentration of 187,500 cells/mL, and 80 µL was pipetted into 96-well collagen coated plates (BD Biocoat, Cat#356407) to give a final concentration of 15,000 cells/well.  RNAiMAX (ThermoFisher, Cat#13778150) was diluted with Opti-MEM (ThermoFisher Cat#31985062) at a concentration of 0.3 µL RNAiMAX/10 µL Opti-MEM and incubated for 5 minutes at room temperature.  After incubation, 10 µL/well was added to each well of 96-well collagen coated plates (BD Biocoat, Cat#356407), along with 10 µL/well of the appropriate dsRNA agent dilution (as appropriate in 1x PBS), mixed gently and incubated for 20 minutes at room temperature.  80 µL of prepared cell suspension was added to each well to give final cell density of 15,000 cells/well and final dsRNA agent concentrations of 10 nM.  Cells were incubated in a 37 °C incubator with 5% CO2 for 16-22 hours. Primary Rat Hepatocyte cells followed a similar protocol, but were incubated for 48 hours.

extract_protocol:
Rat livers collected at the end of the toxicity studies were snap-frozen, powdered, and RNA was extracted with the miRNeasy kit (Qiagen). HepG2.2.15 RNA was isolated using the ThermoFisher RNAqueous-96 Total RNA Isolation Kit, as per the protocol.
cDNA libraries were prepared with the TruSeq Stranded Total RNA Library Prep Kit (Illumina) and sequenced on a NextSeq500 sequencer (Illumina), all according to manufacturers’ instructions.

tag: strain

value: Sprague Dawley

value: 6-8 weeks

tag: Sex

value: male

tag: cell line


title: Liver Fig3-GO1_D6_60mkg_rep2


title: scRNA-seq: F9-EA02


title: scRNA-seq: G11-EA02


title: human_methylation_TLE+HS_rep2

value: Male


title: Liver Fig3-GO1_D6_3mkg_rep3


title: human_methylation_TLE+HS_rep3


title: human_methylation_TLE+HS_rep5


title: scRNA-seq: F7-EA02


title: 3D culture, timepoint 3, replicate 2 [s3DT3r2]

description:
3D_T3_2_20190221_S47_L004_R1_001
processed data file:
raw_gene_counts_allsamples.txt
log2cpm.txt
DE_t3.txt

tag: cell type


title: scRNA-seq: F6-EA02


title: scRNA-seq: F8-EA02


title: 3D culture, timepoint 3, replicate 1 [s3DT3r1]

description:
3D_T3_1_20190218_S59_L004_R1_001
processed data file:
raw_gene_counts_allsamples.txt
log2cpm.txt
DE_t3.txt


title: 3D culture, timepoint 2, replicate 2 [s3DT2r2]

description:
3D_T2_2_20190221_S45_L004_R1_001
processed data file:
raw_gene_counts_allsamples.txt
log2cpm.txt
DE_t2.txt

source_name: MCF10A_3D culture_timepoint 2


title: Liver Fig3-GO1_D6_3mkg_rep1


title: scRNA-seq: F5-EA02


title: Liver Fig3-GO1_D6_30mkg_rep3


title: scRNA-seq: F2-EA02


title: 3D culture, timepoint 1, replicate 2 [s3DT1r2]

description:
3D_T1_2_20190221_S43_L004_R1_001
processed data file:
raw_gene_counts_allsamples.txt
log2cpm.txt
DE_t1.txt

source_name: MCF10A_3D culture_timepoint 1


title: 3D culture, timepoint 2, replicate 1 [s3DT2r1]

description:
3D_T2_1_20190218_S57_L004_R1_001
processed data file:
raw_gene_counts_allsamples.txt
log2cpm.txt
DE_t2.txt


title: scRNA-seq: F4-EA02


title: 3D culture, timepoint 2, replicate 3 [s3DT2r3]

description:
3D_T2_3_20190223_S51_L004_R1_001-006
processed data file:
raw_gene_counts_allsamples.txt
log2cpm.txt
DE_t2.txt


title: 3D culture, timepoint 1, replicate 3 [s3DT1r3]

description:
3D_T1_3_20190223_S49_L004_R1_001-011
processed data file:
raw_gene_counts_allsamples.txt
log2cpm.txt
DE_t1.txt


title: scRNA-seq: F3-EA02


title: Liver Fig3-GO1_D6_30mkg_rep1


title: scRNA-seq: F10-EA02


title: Liver Fig3-GO1_D6_120mkg_rep3


title: 3D culture, timepoint 1, replicate 1 [s3DT1r1]

description:
3D_T1_1_20190218_S55_L004_R1_001
processed data file:
raw_gene_counts_allsamples.txt
log2cpm.txt
DE_t1.txt


title: Liver Fig3-GO1_D6_120mkg_rep4


title: 2D culture, timepoint 3, replicate 3 [s2DT3r3]

description:
2D_T3_3_20190223_S52_L004_R1_001-001
processed data file:
raw_gene_counts_allsamples.txt
log2cpm.txt
DE_t3.txt

source_name: MCF10A_2D culture_timepoint 3


title: scRNA-seq: F1-EA02


title: scRNA-seq: E9-EA02


title: Liver Fig3-GO1_D6_30mkg_rep4


title: Liver Fig3-GO1_D6_10mkg_rep4


title: Liver Fig3-GO1_D6_3mkg_rep2


title: scRNA-seq: F11-EA02


title: Liver Fig3-GO1_D6_30mkg_rep2


title: 2D culture, timepoint 2, replicate 2 [s2DT2r2]

description:
2D_T2_2_20190221_S44_L004_R1_001
processed data file:
raw_gene_counts_allsamples.txt
log2cpm.txt
DE_t2.txt

source_name: MCF10A_2D culture_timepoint 2


title: Liver Fig3-GO1_D6_120mkg_rep2


title: Liver Fig3-GO1_D6_120mkg_rep1


title: 2D culture, timepoint 3, replicate 1 [s2DT3r1]

description:
2D_T3_1_20190218_S58_L004_R1_001
processed data file:
raw_gene_counts_allsamples.txt


title: Liver Fig3-GO1_D6_10mkg_rep3


title: scRNA-seq: E6-EA02


title: 2D culture, timepoint 2, replicate 1 [s2DT2r1]

description:
2D_T2_1_20190218_S56_L004_R1_001-018
processed data file:
raw_gene_counts_allsamples.txt
log2cpm.txt
DE_t2.txt


title: 2D culture, timepoint 1, replicate 3 [s2DT1r3]

description:
2D_T1_3_20190223_S48_L004_R1_001
processed data file:
raw_gene_counts_allsamples.txt
log2cpm.txt
DE_t1.txt

source_name: MCF10A_2D culture_timepoint 1


title: 2D culture, timepoint 3, replicate 2 [s2DT3r2]

description:
2D_T3_2_20190221_S46_L004_R1_001
processed data file:
raw_gene_counts_allsamples.txt
log2cpm.txt
DE_t3.txt


title: BE2C-HDAC2-dTAG cells, dTAG13 (500 nM), 24 h, biol rep 3

city: La Jolla

first: Yuxiang

last: Zhang

address: 10550 N. Torrey Pines Rd.

department: Chemistry

institute: The Scripps Research Institute

description:
mRNA-seq_ERCC-normalized_CPM_all_treatments_all_replicates_all_genes.txt
24h_dtag13_3

data_processing:
Raw basecall (or BCL) files from the NextSeq2000 sequencer were converted to sample fastqs using an in-house custom built wrapper around Illumina’s bcl2fastq conversion software v2.19.0.
SLAM-dunk was used for read alignment, CPM calculation, and conversion rate calculation.
For ERCC normalization, normalize.loess function of the affy v1.50.0 R package76 was used. Locally estimated scatterplot smoothing (LOESS) normalization was applied to all CPM values of transcripts with the model specified by the distribution of the SIRV-Set-3 spike-ins.
Unexpressed genes were filtered out with the cutoff of CPM < 3 in all 8-h and 24-h DMSO and 500 nM dTAG-13 treated samples.
Assembly: hg19
Supplementary files format and content: T-to-C conversion rates of all genes in each sample for SLAM-seq, ERCC-normalized CPMs of all genes in each sample for 3' end mRNA-seq

source_name: Neuroblastoma

growth_protocol: BE(2)-C cells were cultured in DMEM supplemented with 10% FBS and Gibco Antibiotic-Antimycotic.

extract_protocol:
RNA was extracted with RNeasy miniprep kit (Qiagen). For SLAM-seq, 5 µg RNA of 4sU laballed RNA for each sample was subjected to alkylation by 100 mM iodoacetamide.
1 µg of RNA of each sample was used for libarary synthesis with QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, #015) following manufacturer's protocols.
3' end mRNA-seq.

treatment_protocol: For SLAM-seq cells were treated with 100 µM 4-thiouracil (4sU) for 1 hour for newly synthesized mRNA labeling. For 3' end mRNA-seq 2.1 ng/mL of ERCC RNA Spike-In Control SIRV Set 3 (Lexogen, #051.0) per sample was added for ERCC normalization.

value: Neuroblastoma

value: endogenous HDAC2-dTAG

tag: treatment

tag: time point

value: 24 hours


title: Liver Fig3-GO1_D6_10mkg_rep2


title: Liver Fig3-GO1_D6_10mkg_rep1


title: 2D culture, timepoint 1, replicate 2 [s2DT1r2]

description:
2D_T1_2_20190221_S42_L004_R1_001
processed data file:
raw_gene_counts_allsamples.txt
log2cpm.txt
DE_t1.txt


title: scRNA-seq: E5-EA02


title: 2D culture, timepoint 2, replicate 3 [s2DT2r3]

description:
2D_T2_3_20190223_S50_L004_R1_001
processed data file:
raw_gene_counts_allsamples.txt
log2cpm.txt
DE_t2.txt


title: 2D culture, timepoint 1, replicate 1 [s2DT1r1]

description:
2D_T1_1_20190218_S54_L004_R1_001-014
processed data file:
raw_gene_counts_allsamples.txt
log2cpm.txt
DE_t1.txt


title: Sample 20 GEXSCOPETM

city: Nanjing

first: Hongyi

state: Jiangsu

address: 264 Guangzhou Road

department: Neurosurgery

institute: Nanjing Brain Hospital Affiliated to Nanjing Medical University

data_processing:
Raw reads were processed to generate gene expression profiles using an internal pipeline. Briefly, after filtering read one without polyT tails, cell barcode and UMI was extracted.
Adapters and polyA tails were trimmed before read two was mapped to GRCh38 with ensemble version 92 gene annotation.
Reads with the same cell barcode, UMI and gene were grouped together to calculate the number of UMIs per gene per cell.
Cell number was then determined based on the ‘knee’ method.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each Cell.

source_name: high-grade primary glioma

extract_protocol:
Single cell RNA was captured by microfluidic technology using millions of unique Barcode-labeles.
The genomic DNA is subjected to steps of interruption, damage repair and end repair to generate a complete double-stranded DNA after interruption, and a hairpin-like linker with a sequencing primer is ligated to both ends of the double-stranded DNA by a linker, and then subjected to digestion. Screening and other steps to generate circular DNA containing no unligated and redundant linkers, and then repaired and purified to obtain a complete DNA library.

tag: race

value: Asian

value: brain


title: scRNA-seq: E3-EA02


title: CLP Heart NMNb rep3 [B18-Heart]

city: Nyon

first: Nicolas

last: Hulo

address: Avenue Reverdil 4

country: Switzerland

institute: Nuvamid SA

data_processing:
Sequenced reads were mapped to mm10 genome using STAR (v2.7.3a) with default parameter. The bam output files were then passed to featureCounts (v2.0.0) with the mm10 gencode gtf file to generate the count table
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (csv format)

source_name: Organs from thioglycollate-induced peritonitis

extract_protocol:
Experimental peritonitis was induced in 7- to 12-week-old male mice by either  cecal ligation and punction (CLP model)  or injecting i.p. with 1 mL of Brewer thioglycollate medium (TGC, 4% in distillated water) (TGC model). Administration of β-NMN (185 mg/kg/day) and vehicle (saline, 0.9% NaCl) were performed immediately after peritonitis induction, followed by daily injections for up to 4 days before euthanasia and the last treatment was 24 hours before sacrifices. For heart and lungs, 10 mg of tissues were treated with RNAlater solution. In TGC model, cells from peritoneal lavage were plated at 0.5x10 6 cells/well in HBSS+/+ and stimulated during 6 hours at 37°C, 5% CO 2 , with E.coli (7.5x10 6 bacteria; MOI of 1:15). Supernatants were discarded and cells were treated with 100 µL of RNAlater solution.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: beta-NMN (185mg/kg)

value: Heart CLP model


title: CLP Lung NMNb rep3 [B18-Lung]

value: Lung CLP model


title: scRNA-seq: F12-EA02


title: scRNA-seq: E4-EA02


title: scRNA-seq: E7-EA02


title: BE2C-HDAC2-dTAG cells, DMSO (0.1%), 24 h, biol rep 3

description:
mRNA-seq_ERCC-normalized_CPM_all_treatments_all_replicates_all_genes.txt
24h_dmso_3

value: DMSO, 0.1percent


title: CLP Lung NMNb rep2 [B17-Lung]


title: BE2C-HDAC2-dTAG cells, DMSO (0.1%), 24 h, biol rep 2

description:
mRNA-seq_ERCC-normalized_CPM_all_treatments_all_replicates_all_genes.txt
24h_dmso_2


title: scRNA-seq: E8-EA02


title: Sample 16 GEXSCOPETM

source_name: brain


title: scRNA-seq: E2-EA02


title: CLP Heart NMNb rep3 [B17-Heart]


title: Sample 12 GEXSCOPETM


title: Sample 7 GEXSCOPETM


title: scRNA-seq: E12-EA02


title: CLP Lung NMNb rep1 [B16-Lung]


title: scRNA-seq: E11-EA02


title: CLP Heart NMNb rep1 [B16-Heart]


title: Sample 3 GEXSCOPETM


title: BE2C-HDAC2-dTAG cells, dTAG13 (500 nM), 24 h, biol rep 2

description:
mRNA-seq_ERCC-normalized_CPM_all_treatments_all_replicates_all_genes.txt
24h_dtag13_2


title: BE2C-HDAC2-dTAG cells, dTAG13 (500 nM), 8 h, biol rep 3

description:
mRNA-seq_ERCC-normalized_CPM_all_treatments_all_replicates_all_genes.txt
8h_dtag13_3

value: 8 hours


title: BE2C-HDAC2-dTAG cells, DMSO (0.1%), 24 h, biol rep 1

description:
mRNA-seq_ERCC-normalized_CPM_all_treatments_all_replicates_all_genes.txt
24h_dmso_1


title: scRNA-seq: E1-EA02


title: Sample 2 GEXSCOPETM


title: BE2C-HDAC2-dTAG cells, dTAG13 (500 nM), 24 h, biol rep 1

description:
mRNA-seq_ERCC-normalized_CPM_all_treatments_all_replicates_all_genes.txt
24h_dtag13_1


title: BE2C-HDAC2-dTAG cells, dTAG13 (500 nM), 8 h, biol rep 2

description:
mRNA-seq_ERCC-normalized_CPM_all_treatments_all_replicates_all_genes.txt
8h_dtag13_2


title: CLP Lung Vehicle rep3 [A18-Lung]

value: Vehicle


title: CLP Heart Vehicle rep3 [A18-Heart]


title: BE2C-HDAC2-dTAG cells, dTAG13 (500 nM), 8 h, biol rep 1

description:
mRNA-seq_ERCC-normalized_CPM_all_treatments_all_replicates_all_genes.txt
8h_dtag13_1


title: CLP Lung Vehicle rep2 [A17-Lung]


title: Sample 1 GEXSCOPETM

value: female


title: scRNA-seq: D3-EA02

value: endocrine

value: Pancreas


title: CLP Heart Vehicle rep2 [A17-Heart]


title: scRNA-seq: C9-EA02


title: scRNA-seq: D2-EA02


title: BE2C-HDAC2-dTAG cells, DMSO (0.1%), 8 h, biol rep 3

description:
mRNA-seq_ERCC-normalized_CPM_all_treatments_all_replicates_all_genes.txt
8h_dmso_3


title: BE2C-HDAC2-dTAG cells, DMSO (0.1%), 8 h, biol rep 2

description:
mRNA-seq_ERCC-normalized_CPM_all_treatments_all_replicates_all_genes.txt
8h_dmso_2


title: Sample_9_HT 3

city: ATLANTA

first: Dong

last: Li

state: GEORGIA

address: 2015 UPPERGATE DR

department: Pediatrics

institute: Emory University

description: Sample_9_HT 3

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5).
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
Supplementary files format and content: tab delimited text file containing raw or normalized read counts for each sample (in columns) and each annotated transcript (in rows).

molecule: polyA RNA

source_name: Cardiomyocytes

extract_protocol:
IMR90 iPSCs were induced for cardiac differentiation using a growth factor-guided protocol. Cardiac spheres were generated from cells at differentiation day 5 and subjected to NRF2 activator CDDO-Me or DMSO treatment from day 14 to day 24. RNA samples from cells at differentiation day 24 or LV samples were prepared using Bio-Rad RNA extraction kit and 1 µg of total RNA/sample was used for the construction of sequencing libraries using Illumina TruSeq RNA Sample Prep Kit.
Libraries were generated using the Illumina standard TruSeq protocol and next-generation sequencing was done through an Illumina HiSeq 2500, 75bp paired end sequencing.

value: pediatric heart samples

tag: developmental stage

value: tissue samples of left ventricle

tag: condition

value: tissue

value: No treatment


title: Sample_8_HT 2

description: Sample_8_HT 2


title: BE2C-HDAC2-dTAG cells, DMSO (0.1%), 8 h, biol rep 1

description:
mRNA-seq_ERCC-normalized_CPM_all_treatments_all_replicates_all_genes.txt
8h_dmso_1

value: Neuroblastoma

value: endogenous HDAC2-dTAG


title: Sample_7_HT 1

description: Sample_7_HT 1


title: CLP Lung Vehicle rep1 [A16-Lung]


title: BE2C-HDAC2-dTAG cells, dTAG13 (500 nM), 2 h, biol rep 3

description:
SLAM-seq_conversion_rate_2h_treatment_all_replicates_all_genes.txt
2h_acy957_3

value: 2 hours


title: Sample_6_NRF2_CDDO-Me 3

description: Sample_4_NRF2_CDDO-Me 3

value: IMR90 iPSC derived cardiomyocytes

value: Day 24 differentiated cells

value: 3D cardiac spherese

value: maturation culture+CDDO-Me


title: scRNA-seq: C8-EA02


title: scRNA-seq: C7-EA02


title: scRNA-seq: D4-EA02


title: CLP Heart Vehicle rep1 [A16-Heart]

value: Heart CLP model


title: Sample_5_NRF2_CDDO-Me 2

description: Sample_4_NRF2_CDDO-Me 2


title: TGC peritoneal cells NMNb rep5 [M11C6]

source_name: Peritoneal exudates from sterile peritonitis induced by injecting i.p. with 1 mL of Brewer thioglycollate medium after stimulation with E. coli

value: beta-NMN (185mg/kg)

value: Peritoneal cells TGC model


title: BE2C-HDAC2-dTAG cells, dTAG13 (500 nM), 2 h, biol rep 2

description:
SLAM-seq_conversion_rate_2h_treatment_all_replicates_all_genes.txt
2h_acy957_2


title: scRNA-seq: C6-EA02


title: scRNA-seq: C5-EA02


title: TGC peritoneal cells NMNb rep4 [M10C5]


title: BE2C-HDAC2-dTAG cells, ACY957 (5 µM), 2 h, biol rep 3

description:
SLAM-seq_conversion_rate_2h_treatment_all_replicates_all_genes.txt
2h_dtag13_3

value: ACY-957, 5 microM


title: scRNA-seq: C4-EA02

value: endocrine


title: BE2C-HDAC2-dTAG cells, ACY957 (5 µM), 2 h, biol rep 2

description:
SLAM-seq_conversion_rate_2h_treatment_all_replicates_all_genes.txt
2h_dtag13_2


title: TGC peritoneal cells NMNb rep3 [M9C4]


title: Sample_2_NRF2_DMSO 2

description: Sample_1_NRF2_DMSO 2

value: 3D cardiac spheres

value: maturation culture+DMSO


title: BE2C-HDAC2-dTAG cells, dTAG13 (500 nM), 2 h, biol rep 1

description:
SLAM-seq_conversion_rate_2h_treatment_all_replicates_all_genes.txt
2h_acy957_1


title: scRNA-seq: C3-EA02

value: Pancreas


title: TGC peritoneal cells NMNb rep2 [M8C3]


title: BE2C-HDAC2-dTAG cells, ACY957 (5 µM), 2 h, biol rep 1

description:
SLAM-seq_conversion_rate_2h_treatment_all_replicates_all_genes.txt
2h_dtag13_1


title: scRNA-seq: C12-EA02


title: D150-MGC-P5-3

city: Guangzhou

first: Xiufeng

last: Zhong

address: 54 xianlie Rd

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description: Müller glial cells derived from BC1-GFP hiPSCs: 5th day of passage 5

data_processing:
Raw reads were filtered and the clean reads were obtained. Afterwards, an index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 (Kim et al., 2015). The mapped reads of each sample were assembled by using StringTie (Pertea et al., 2016).
For each transcription region, a fragment per kilobase of transcript per million mapped reads (FPKM) value was calculated to quantify its expression abundance and variations, using RSEM software (Li and Dewey, 2011).
Correlation analysis was performed by R. Correlation and principal component analysis (PCA) was performed with R package gmodels (http://www.r-project.org/).
Differential expression analysis was performed by DESeq2 software (Love et al., 2014) between two different groups. The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥2 were considered differentially expressed genes/transcripts (DEGs).
Assembly: Homo_sapiens_Ensemble_94
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

growth_protocol: BC1-GFP hiPSCs were cultured on Matrigel-coated (Corning, USA) plates in mTeSR1 medium (Stem Cell Technologies, Canada) and passaged at ~80% confluence every 5–7 days. RO induction was performed as previously described (Zhong et al., 2014; Li et al., 2018; Guan et al., 2021). Briefly, on differentiation day (D) 0, hiPSCs were dissociated and cultured in low adherent dishes to form embryoid bodies (EBs). EBs were plated on Matrigel-coated dishes during D5–D7 with neural induction medium (NIM), which was composed of DMEM/F12 (1:1), 1% N2 supplement (Invitrogen), 1% non-essential amino acids (NEAA) (Gibco) and 2μg/ml heparin (Sigma-Aldrich). From D16, the culture medium was changed to retinal differentiation medium (RDM), containing DMEM/F12 (12:5), 2% B27 (without vitamin A, Invitrogen), 1% NEAA, and 1% antibiotic-antimycotic (Gibco). By week (W) 4–6, optic vesicles with neural retina (NR) domains turned up and were lifted up with tungsten needles, then cultured in suspension to spontaneously form ROs. Retinal culture medium (RCM), which comprised RDM, 10% fetal bovine serum (FBS) (Gibco), 100 μM Taurine (Sigma-Aldrich), and 2 mM GlutaMAX (Invitrogen) were used after 1 week of detachment. From D90, B27 supplemented in RCM was replaced by N2 for long-term RO culture. Medium was changed twice a week.

extract_protocol:
MGCs were isolated from ROs at D150 after initiation of RO induction. NR layers were isolated from ROs at different timepoints (D60, D90, D120 and D150) after differentiation, dissected into small pieces with a pair of tungsten needles, and then dissociated into single cells by incubation of accutase (Gibco) for 15–25 minutes at 37°C. Afterwards, cell suspension was plated at a density of 1×104 cells per cm2 on Matrigel-coated plates with MGC culture medium consisting of DMEM, 10% FBS, 2 mM GlutaMAX, 1% NEAA and 1% antibiotic-antimycotic. These cells were noted as passage 0 (P0). After cells were expanded, they were passaged at approximately 90% confluence every 6–10 days. Medium was changed every 3–4 days. Samples from BC1-GFP hiPSCs and their derivatives were used to perform RNA-seq and data analysis. HiPSCs (approximate 2×106 cells per experiment, 3 independent experiments), NR layers isolated from D70-ROs and D150-ROs (5 ROs per experiment, 3 independent experiments), P1 and P5 iMGCs from NR layers of D150-ROs (approximate1×106 cells per experiment, 3 independent experiments) were collected in Trizol reagent (Invitrogen) and stored in a -80℃ freezer. Total RNA was extracted using Trizol reagent kit (Invitrogen) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies).Oligo (dT) beads were used to isolate the poly mRNA from the total RNA.
The enriched mRNA was fragmented and reverse transcribed into cDNA using random primers. After synthesis of the second strand, the cDNA was purified, end-repaired and ligated to Illumina sequencing adapters. The ligation products were size selected, amplified, and sequenced.

value: Muller glial cells derived from BC1-GFP hiPSCs

value: WT

value: total RNA

tag: time

value: 5th day of passage 5


title: Sample_4_NRF2_CDDO-Me 1

description: Sample_4_NRF2_CDDO-Me 1


title: scRNA-seq: C11-EA02


title: scRNA-seq: C10-EA02


title: D150-MGC-P5-2


title: TGC peritoneal cells Vehicle rep5 [M5B6]

value: Vehicle


title: scRNA-seq: B9-EA02


title: BE2C-HDAC2-dTAG cells, DMSO (0.1%), 2 h, biol rep 1

description:
SLAM-seq_conversion_rate_2h_treatment_all_replicates_all_genes.txt
2h_dmso_1

value: Neuroblastoma

value: endogenous HDAC2-dTAG

value: DMSO, 0.1percent

value: 2 hours


title: TGC peritoneal cells Vehicle rep6 [M6B7]


title: D150-MGC-P5-1


title: Sample_3_NRF2_DMSO 3

description: Sample_1_NRF2_DMSO 3

value: IMR90 iPSC derived cardiomyocytes

value: Day 24 differentiated cells


title: Sample_1_NRF2_DMSO 1

description: Sample_1_NRF2_DMSO 1


title: set63.Y336F-KI.Ribo-seq.rep3

city: Baltimore

first: Weidong

last: Wang

state: MD

address: 251 Bayview Blvd

department: National Institute on Aging

institute: Shuaikun Su

description: sample 37,40,43,46 are in one group

data_processing:
For Ribo-seq, low-quality reads and the linker sequence (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were removed by FASTX-Toolkit from FastQ files. Then reads less than 25 nt were also removed by FASTX-Toolkit. Align the remaining reads to an rRNA reference using the Bowtie short-read alignment program, discard the rRNA alignments and collect unaligned reads. For PRO-seq, adaptor sequences (ADAPT1=GATCGTCGGACTGTAGAACTCTGAA, ADAPT2=TGGAATTCTCGGGTGCCAAGG) were removed by cutadpt. For eCLIP-seq, adaptor sequences were also removed before mapping to the genome.
RNA-seq, Ribo-seq and eCLIP-seq reads were mapped to the hg38 human genome with HISAT2 or TopHat. PRO-seq reads were mapped to the genome using Bowtie2 allowing maximum of 2 mismatches.
For RNA-seq and Ribo-seq, the raw counts were generated using HTSeq-Counts. Then DESeq2 was used to identify the differentially expressed genes (DEGs) and generate the normalized counts. The genes with total counts (untreated and treated groups) less than 10 were filtered. The genes (Fold change > 1.5 and adjust P-value < 0.1) were identified as DEGs. The bedGraph files were generated by deepTools and normalized using RPKM. The bedGraph files were visualized using the Integrative Genomics Viewer (IGV). For PRO-seq, normalized reads at specific sub-regions were used to calculate the DEGs (fold change > 1.2-fold). eCLIP-seq reads were mapped to the genome using TopHat. Other steps were similar to the RNA-seq analysis pipeline. Genes with criterion (WT-IP_fpkm/WT-Input_fpkm > 1.5 and WT-IP_fpkm/TOP3B-KO-IP_fpkm > 1.5) in both biological replicates were selected as TOP3B eCLIP targets. RSeQC was used to analyze the read distribution of Ribo-seq, RNA-seq and eCLIP-seq on CDS, 5’UTR and 3’UTR.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph file

source_name: human colorectal carcinoma cell line

growth_protocol: HCT116 cells were cultured in  DMEM with 10% fetal bovine serum (HyClone) and 1% antibiotics (Penicillin-Streptomycin, Sigma).

extract_protocol:
Different sequencing types have different protocols, please follow the protocols in the "Materials and Methods" part in the article. Briefly, for RNA-seq, total RNAs were extracted with TRizol. For Ribo-seq, ribosome protected fragments were collected through sucrose cushion and extracted with TRizol, then the 24 to 34 nt RNA fragments were collected through 15% TBE-Urea gel. For eCLIP-seq, protein-RNA complexes were isolated with antibody. For PRO-seq, nascent RNA fragments were extractd and made library.
For RNA-seq, library construction protocol can be found here (Y. Joo et al., Topoisomerase 3beta knockout mice show transcriptional and behavioural impairments associated with neurogenesis and synaptic plasticity. Nat Commun 11, 3143 (2020).). For Ribo-seq, library was constructed using NEBNext® Multiplex Small RNA Library Prep Set for Illumina (E7300S, New England BioLabs). For eCLIP-seq, library construction protocol can be found here (E. L. Van Nostrand et al., Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP). Methods Mol Biol 1648, 177-200 (2017).). For PRO-seq, library construction protocol can be found here (D. B. Mahat et al., Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nature Protocols 11, 1455-1476 (2016).).
RNA-seq; Ribo-seq; eCLIP-seq; PRO-seq

treatment_protocol: For the Ribo-seq samples and the RNA-seq samples, cells were treated with 100µg/mL cycloheximide for 10min

value: Cells were treated with 100µg/mL cycloheximide for 10min and then lysed in polysome lysis buffer. After centrifugation, 100 µL cell lysates were used to extract RNA with TRIzol. Then 5~10 µg RNA was used to purify mRNAs with oligo dT beads. The purified mRNAs were used for RNA-seq library preparation.

tag: molecule

value: Ribosome protected RNA fragments


title: TGC peritoneal cells Vehicle rep4 [M4B5]

tag: tissue

value: Peritoneal cells TGC model


title: TGC peritoneal cells NMNb rep6 [M12C7]

value: beta-NMN (185mg/kg)


title: BE2C-HDAC2-dTAG cells, DMSO (0.1%), 2 h, biol rep 2

description:
SLAM-seq_conversion_rate_2h_treatment_all_replicates_all_genes.txt
2h_dmso_2


title: TGC peritoneal cells NMNb rep1 [M7C2]


title: D150-MGC-P1-3

description: Müller glial cells derived from BC1-GFP hiPSCs: 5th day of passage 1

value: 5th day of passage 1


title: BE2C-HDAC2-dTAG cells, DMSO (0.1%), 2 h, biol rep 3

description:
SLAM-seq_conversion_rate_2h_treatment_all_replicates_all_genes.txt
2h_dmso_3


title: TGC peritoneal cells Vehicle rep3 [M3B4]


title: D150-MGC-P1-2


title: set63.Y336F-KI.Ribo-seq.rep2

description: sample 36,39,42,45 are in one group


title: scRNA-seq: B7-EA02

value: endocrine

value: Pancreas


title: set63.Y336F-KI.Ribo-seq.rep1

description: sample 35,38,41,44 are in one group


title: TGC peritoneal cells Vehicle rep2 [M2B3]


title: TGC peritoneal cells Vehicle rep1 [M1B2]


title: D150-MGC-P1-1

value: Muller glial cells derived from BC1-GFP hiPSCs

value: WT


title: D150-RO-3

description: 150 days post induction of retinal organoids derived from BC1-GFP hiPSCs

value: Neural retinas isolated from retinal organoids derived from BC1-GFP hiPSCs

value: total RNA

value: 150 days post induction


title: scRNA-seq: B6-EA02


title: scRNA-seq: B5-EA02


title: AP-20

city: Hangzhou

first: Ying

last: Xiao

address: Qingchun East Road

institute: Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University

data_processing:
Clean Data were mapped to the mouse genome (mm10) by using STAR
Read Count for each gene in each sample is counted by HTSeq, and FPKM (Fragments Per Kilobase Millon Mapped Reads) were then calculated to Represent the expression level of genes in each sample
read count normalization and differential gene expression (DGE) were analyzed by using DESeq2
Genome_build: mm10

source_name: Skin

extract_protocol:
Skin samples without interfollicular epidermis were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wildtype

value: Alpinetin


title: set63.WT.3.Ribo-seq.rep2

description: sample 36,39,42,45 are in one group

value: Wild type


title: scRNA-seq: B4-EA02


title: D70-RO-3

description: 70 days post induction of retinal organoids derived from BC1-GFP hiPSCs

value: 70 days post induction


title: set63.Y336F-KI.RNA-seq.rep3

description: sample 37,40,43,46 are in one group

value: polyA RNA


title: D150-RO-1


title: scRNA-seq: B3-EA02


title: AP-16


title: AP-17


title: scRNA-seq: B2-EA02


title: scRNA-seq: B12-EA02


title: set63.Y336F-KI.RNA-seq.rep1

description: sample 35,38,41,44 are in one group

value: Cells were treated with 100µg/mL cycloheximide for 10min and then lysed in polysome lysis buffer. After centrifugation, 100 µL cell lysates were used to extract RNA with TRIzol. Then 5~10 µg RNA was used to purify mRNAs with oligo dT beads. The purified mRNAs were used for RNA-seq library preparation.


title: set63.WT.3.Ribo-seq.rep1

description: sample 35,38,41,44 are in one group

value: Ribosome protected RNA fragments


title: scRNA-seq: B11-EA02


title: set63.WT.3.RNA-seq.rep3

description: sample 37,40,43,46 are in one group


title: D70-RO-1


title: hiPSC-3

description: BC1-GFP hiPSCs

value: BC1-GFP hiPSCs


title: VC-O3

value: 65% ethanol


title: scRNA-seq: B10-EA02


title: set63.Y336F-KI.RNA-seq.rep2

description: sample 36,39,42,45 are in one group


title: VC-O2


title: scRNA-seq: B1-EA02


title: AP-19


title: D150-RO-2


title: set63.WT.3.RNA-seq.rep2

description: sample 36,39,42,45 are in one group


title: hiPSC-2

description: BC1-GFP hiPSCs


title: VC-O1


title: D70-RO-2


title: hiPSC-1

description: BC1-GFP hiPSCs


title: set63.WT.3.RNA-seq.rep1

description: sample 35,38,41,44 are in one group


title: EC_4

city: Yayoi, Bunkyo-ku

first: Tomoatsu

last: Hayashi

state: Tokyo

country: Japan

institute: The University of Tokyo

data_processing:
Libraries were sequenced for 65 cycles on an Illumina HiSeq 2500 according to the manufacturer’s instructions.
BAM-formatted map files were generated using STAR version 2.6.1d with default parameters.
The gene-level expression values (counts and TPM) were estimated by RSEM version 1.3.1 with default paramters.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw read counts per gene.
Supplementary_files_format_and_content: tab-delimited text files include transcripts per kilobase million (TPM).

source_name: Ovarian cancer tissue

extract_protocol:
Total RNA was extracted from fresh frozen ovarian cancer tissue using TRIsure reagent (Bioline) according to the manufacturer’s protocol and then treated with DNase I (TAKARA) for 1h. DNase I-treated RNA was cleaned using NucleoSpin RNA Clean‑up, Mini kit (MACHEREY-NAGEL). RNA concentration and quality were evaluated using a NanoDrop 3000 spectrophotometer (Thermo Fisher Scientific) and a TAPESTATION (Agilent), respectively.
All cDNA libraries were prepared using the Illumina TruSeq Stranded Total RNA and the Ribo- Zero Gold LT Sample Prep Kit according to manufacturer's  instructions.

tag: cell subtype

value: Endometrioid

value: ovary

value: primary


title: set57.FMR1-KO.Ribo-seq.rep1

description: sample 17,20,23,26,29,32 are in one group

value: Cells were treated with 100µg/mL cycloheximide for 10min and then were used for Ribo-seq.


title: scRNA-seq: A9-EA02

value: endocrine

value: Pancreas


title: scRNA-seq: A8-EA02


title: 5_1264_WT

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Fastq files were aligned to the GRCm39 reference genome using STAR and default parameters
Ensmebl v04 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method
Genome_build: mm9
Supplementary_files_format_and_content: Voom transformed abundance measurements

growth_protocol: Lungs were homogenized by a combination of physical and enzymatic digestion before lineage traced AT2 cells were isolated by fluorescence activated cell sorting.

extract_protocol: RNA-seq standard protocol

tag: age

value: Adult

value: SftpcCreERT2+/-; eYFP+/-

value: C57BL/6 CD1 mixed

value: male

value: Hyperoxia


title: EC_3


title: set57.TDRD3-KO.Ribo-seq.rep1


title: 5_1250_KO

value: SftpcCreERT2+/-;Klf5 fl/fl; eYFP-/-


title: set63.WT.3.Ribo-seq.rep3

description: sample 37,40,43,46 are in one group

value: Wild type


title: scRNA-seq: A7-EA02

tag: embryonic stage


title: scRNA-seq: A6-EA02

tag: plate code


title: set57.WT.2.Ribo-seq.rep1

tag: genotype


title: set57.FMR1-KO.RNA-seq.rep1

value: Cells were treated with 100µg/mL cycloheximide for 10min and then lysed in polysome lysis buffer. After centrifugation, 100 µL cell lysates were used to extract RNA with TRIzol. Then 5~10 µg RNA was used to purify mRNAs with oligo dT beads. The purified mRNAs were used for RNA-seq library preparation.

value: polyA RNA


title: 4_1248_KO

tag: strain


title: scRNA-seq: A5-EA02


title: EC_2


title: 3_1244_KO

tag: Sex

value: female


title: HGSC_8

value: High grade serous


title: EC_1

value: Endometrioid


title: scRNA-seq: A4-EA02


title: HGSC_7

value: ovary


title: 4_1262_KO


title: set57.TDRD3-KO.RNA-seq.rep1

tag: cell line


title: set57.WT.2.RNA-seq.rep1


title: 2_1259_KO


title: HGSC_6

tag: cell type

value: primary


title: scRNA-seq: A3-EA02


title: UC3_siYAP1_4R

city: Yuseong-gu

first: Seung Woo

last: Baek

state: Daejeon

address: Gwahak-ro 125

country: South Korea

institute: Korea Research Institute Biology & Biotechnology

description: replicate 4

data_processing:
Reference genome indexing and read mapping of samples were performed using STAR software (ver. 2.6.1a).
FeatureCounsts (ver. 1.6.2) was used to calculate genereated binary alignment map (BAM) files.
The read counts per million fragments mapped (CPM) of each samples were used to estimate the expression level of each gene.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

growth_protocol: UC3 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS, 10%) and 1% penicillin/streptomycin (Capricorn Scientific). All of the cell lines were incubated at 37℃ in a humidified atmosphere of 5% CO2.

extract_protocol:
RNA samples for sequencing were isolated using the Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Total RNA isolation was performed in a reverse transcription reaction with poly(dT) primers using PrimeScriptTM reverse transcriptase (TAKARA, Shiga, Japan) according to the manufacturer’s protocol. The library’s quality and quantity were measured by a Nanodrop spectrophotometer (ND-1000; Thermo Scientific, Waltham, MA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Knockdowns of siCON or siYAP1 UC3 bladder cancer cells were performed using jetPRIME transfection reagent.

tag: transfection

value: Bladder cancer


title: 2_1255_WT

value: SftpcCreERT2+/-; eYFP-/-

tag: treatment


title: scRNA-seq: A12-EA02

value: endocrine

value: Pancreas


title: UC3_siYAP1_3R

description: replicate 3


title: 1_1258_WT

value: Adult


title: UC3_siYAP1_2R

description: replicate 2


title: HGSC_5


title: scRNA-seq: A11-EA02


title: 1_1254_KO

value: C57BL/6 CD1 mixed


title: HGSC_4


title: UC3_siYAP1_1R

description: replicate 1


title: HGSC_3


title: VC-O5

value: wildtype

value: 65% ethanol


title: HGSC_1


title: UC3_siCON_4R

description: replicate 4

value: siCON


title: HGSC_2


title: UC3_siCON_3R

description: replicate 3


title: scRNA-seq: H2-EA01


title: scRNA-seq: H4-EA01


title: scRNA-seq: H3-EA01


title: CCC_10

value: Cear cell


title: CCC_9


title: scRNA-seq: H1-EA01


title: scRNA-seq: A10-EA02


title: 18385X1

city: Salt Lake City

first: Eric

last: Snyder

state: UT

address: 2000 Circle of Hope Drive

department: Pathology

institute: University of Utah, Huntsman Cancer Institute

description: single cell RNA sequencing

data_processing:
Fastq files were demultiplexed with cellranger mkfastq version 2.2.0 to create I1 sample index, R1 cell barcode and UMI, R2 RNA sequence
Reads were aligned to the refdata-cellranger-mm10-1.2.0 reference from 10X Genomics with modifications detailed in manuscript.
Barcodes and UMIs were counted using cellranger count with expected-cells=3000
Genome_build: mm10
Supplementary_files_format_and_content: Filtered feature-barcode matricies in TSV and MEX format from cellranger count

source_name: KPF1F2 pre-depletion

growth_protocol: Tumors initiated with Ad5-mSPC-FlpO and collected 12 weeks post initiation

extract_protocol:
Briefly, tumors were macrodissected from lungs, diced, and digested with Collagen Type I, Dispase, and DNase I.  Cells were then filtered and treated with erythrocyte lysis buffer.  Depleted samples were depleted of CD45-positive and CD31-positive cells using MACS
10X Genomics Next GEM Single Cell  3' Gene Expression Library prep v3.1  with UDI
Single cell 3` RNAseq

treatment_protocol: 4 daily injections of Tamoxifen (120mg/kg) 10 weeks post tumor initiation

value: Mixed 129/B6

value: Lung adenocarcinoma

value: KrasFSF-G12D, p53frt, Rosa-FSF-CreERT2, Foxa1flox, and Foxa2flox

tag: timepoint

value: 12 weeks post tumor initiation


title: 19063X8

description:
Bulk RNA sequencing
19063R_counts.txt

data_processing:
The human GRCm38 FASTA and GTF files were downloaded from Ensembl release 102.
The reference database was created using STAR version 2.7.6a with splice junctions optimized for 125 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.5.1
Non-coding features, histones, and ribosomal RNAs were removed and differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: FeatureCounts output files combined into a single tab-delimited matrix

growth_protocol: Organoids were established by digesting individual murine LUAD tumors. Cells are suspended in Matrigel and are cultured in L-WRN conditioned media

extract_protocol:
PureLink RNA Mini Kit
NEBNext Ultra II Directional RNA Library Prep

treatment_protocol: Organoids were treated with vehicle or 2 um 4-OHT for 72 hours. Cells were crosslinked 21 days post-tamoxifen treatment.

tag: disease state

value: 4-hydroxytamoxifen (2 um)


title: 18836X4

description: single cell RNA sequencing

source_name: KP post-depletion

value: KrasFSF-G12D, p53frt, Rosa-FSF-CreERT2, Foxa1flox/+, and Foxa2flox/+

value: 4 daily injections of Tamoxifen (120mg/kg) 10 weeks post tumor initiation


title: 18836X3

description: single cell RNA sequencing

source_name: KP pre-depletion


title: 19063X7

description:
Bulk RNA sequencing
19063R_counts.txt

value: Vehicle (Ethanol)


title: scRNA-seq: G9-EA01

source_name: Pancreas


title: CCC_8

value: ovary

value: primary


title: 19063X6

description:
Bulk RNA sequencing
19063R_counts.txt

source_name: 1027B shScramble


title: 18836X5

description: single cell RNA sequencing

source_name: KPF1F2 post-depletion


title: TCR-seq HC58

city: Xian

first: chengsheng

last: zhang

state: Shaanxi

address: 277 West Yanta Road, Xi'an, Shaanxi, P.R.China

department: precision medicine center

institute: First Affiliated Hospital of Xi 'an Jiaotong University

data_processing:
Library strategy: TCR-seq
Illumina bcl2fastq software used for for basecalling.
Barcoded, full-length TCR V(D)J segments could be enriched from amplified cDNA from 5′ libraries via PCR amplification with primers specific to the TCR prior to library construction using a Chromium Single-Cell V(D)J Enrichment kit according to the manufacturer’s protocol (10X Genomics). If both T cells are expected to be present in the partitioned cell population, TCR transcripts can be enriched in separate reactions from the same amplified cDNA material. Cell Ranger for V(D)J (https://support.10xgenomics.com/single-cell-vdj) is a set of analysis pipelines that process Chromium single cell 5′ RNA-seq output to assemble, quantify, and annotate paired V(D)J transcript sequences. Cell Ranger workflow starts by demultiplexing the Illumina sequencer's base call files (BCLs) for each flowcell directory into FASTQ files. Cell calling is performed independently of V(D)J read filtering and assembly. A clonotype is a set of cells that share the same paired receptor sequences (presumably derived from the same progenitor cell) Cell barcodes are grouped together into clonotypes if they share the same set of productive CDR3 nucleotide sequences by exact match. Repertoire informations of all samples are exhibited using a set of basic features: CDR3 abundance, CDR3 bases length, Variable (V) and Joining (J) segment usage(the frequency of associated reads for each of V/J gene present in samples), the length of V/J gene in CDR3 region, and V-J gene paired frequency in CDR3 junctions. We use hierarchical cluster (https://stat.ethz.ch/R-manual/Rdevel/library/stats/html/hclust.html) and Kruskal’s Non-metric Multidimensional Scaling (isoMDS, https://cran.r-project.org/web/ packages/MASS/MASS.pdf) to estimate Immune Repertoires similarity.
Genome_build: GRCh38_v96

source_name: Peripheral blood

extract_protocol:
Retrieving the PBMC-containing cryo-tubes from the -196℃ liquid nitrogen storage tank and placing them in a 37℃ water bath for rapid thawing. PBMCs were mixed with 10 mL washing medium (90% DMEM+10% FBS) in a 15-mL polypropylene tube and centrifuged at 500g for 20 min. The supernatant was then aspirated (repeat twice). The cell pellets were resuspended with 500 μl× PBS (0.04% BSA) in the sterile RNase-free vacutainer tubes and added with 5 ml 1× red blood cell lysis buffer (MACS 130-094-183, 10×) and incubated at room temperature for 10 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 500g for 20 min at room temperature. The suspension was resuspended in 100 μl Dead Cell Removal MicroBeads (MACS 130-090-101) and remove dead cells using Miltenyi ® Dead Cell Removal Kit (MACS 130-090-101). Then the suspension was resuspended in 1× PBS (0.04% BSA) and centrifuged at 300 g for 3 min at 4 °C (repeat twice). The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion, which needed to be above 85%, single cell suspensions were counted using a Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
manufacturer's protocols for 5'barcoded GEX and V(D)J TCR

tag: peripheral blood

value: peripheral blood mono-nuclear cells

tag: gender

value: male

tag: disease symptom

value: Health control

tag: thymalfasin treatment

value: No


title: scRNA-seq: A1-EA02

value: endocrine

tag: tissue

value: Pancreas


title: CCC_7

tag: cell subtype

value: Cear cell


title: TCR-seq HC60

tag: age

value: female


title: CCC_11


title: 19063X5

description:
Bulk RNA sequencing
19063R_counts.txt

value: Mixed 129/B6

value: Lung adenocarcinoma


title: scRNA-seq: G7-EA01

tag: embryonic stage

tag: plate code


title: TCR-seq HC39


title: scRNA-seq: G8-EA01

tag: genotype


title: UC3_siCON_1R

description: replicate 1

value: siCON

value: Bladder cancer


title: CCC_6


title: UC3_siCON_2R

description: replicate 2


title: scRNA-seq: G6-EA01


title: TCR-seq HC36


title: TCR-seq HC31


title: 19063X3

description:
Bulk RNA sequencing
19063R_counts.txt

tag: strain

value: KrasFSF-G12D, p53frt, Rosa-FSF-CreERT2, Foxa1flox, and Foxa2flox


title: CCC_5


title: scRNA-seq: G5-EA01


title: TCR-seq HC23

value: Yes


title: CCC_4


title: 19063X2

description:
Bulk RNA sequencing
19063R_counts.txt

value: 4-hydroxytamoxifen (2 um)


title: TCR-seq HC21


title: scRNA-seq: G3-EA01


title: scRNA-seq: G4-EA01


title: CCC_2

value: ovary


title: scRNA-seq: G11-EA01


title: 17992X3

description:
Bulk RNA sequencing
17699R_17992R_counts.txt

value: Vehicle (Ethanol)


title: CCC_1

value: primary


title: TCR-seq HC07

value: peripheral blood mono-nuclear cells


title: 19063X4

description:
Bulk RNA sequencing
19063R_counts.txt


title: scRNA-seq: G10-EA01


title: TCR-seq HC05

value: Health control


title: 17992X2


title: scRNA-seq: G1-EA01


title: TCR-seq HC01


title: JHOC5_D0_rep1

description: sgRNA fragment library

library_source: genomic

data_processing:
FASTQ files were trimmed by "cutadapt -g TTGTGGAAAGGACGAAACACCG -O 24 -m 20 --trimmed-only -e 0.1 (Version 2.1)"
Reads for each sgRNA were counted by "mageck count --list-seq tkov3_guide_sequence.csv (Version 0.5.6)"
Genome_build: Human CRISPR Knockout Pooled Library (Toronto KnockOut (TKO) CRISPR Library -Version 3, TKOv3). A list of TKOv3 sgRNA sequences is deposited in Addgene #90294.
Supplementary_files_format_and_content: tab-delimited text file includes read counts per sgRNA for each target across all samples, together with the targeted gene name and sgRNA ID.

growth_protocol: Human ovarian cancer OVISE and JHOC5 cells were cultured in DMEM and RPMI1640 medium supplemented with 10% fetal bovine serum (FBS), respectively. TOV21G cells were cultured in a 1:1 mixture of MCDB 105 medium and Medium 109 supplemented with 15% FBS. ES2 cells were grown in McCoy 5A supplemented with 10% FBS. All cell lines were cultured at 37°C under a 5% CO2 atmosphere.

extract_protocol:
Genomic DNA was extracted using a QIAGEN Blood and Cell Culture DNA Midi Kit (#13343) according to the manufacturer’s protocol.
125 μg of genomic DNA from each sample was split into 2.5 μg fractions and sgRNA sequences were amplified using Herculase II enzyme following published protocols and instructions supplied by authors on Addgene #90294 (Hart T et al., G3 (Bethesda) 2017. 7(8): 2719-2727). Reactions were measured for fragment size using the Agilent 2200 Tapestation, and quantified using the KAPA SYBR Fast qPCR Kit (KAPA Biosystems, #7959362001).

treatment_protocol: Pooled lentiviral libraries were transduced at the multiplicity of infection (MOI) 0.3 followed by selection with puromycin for 2 days. After selection, a sample of 2 x 10^7 cells was pelleted and frozen under liquid nitrogen as a Day 0 sample (file names are labeled with 'D0'). Cells were then passaged until they had undergone 8 doublings. To maintain sufficient sgRNA coverage, the total number of cells was maintained above 2 x 10^7 for the duration of the culture period. Cells cultured for 8 cell doublings from Day 0  were taken as a final time point sample (file names are labeled with 'Final').

tag: cell line

tag: sgrna library

value: TKOv3 library

tag: time

value: ovarian cancer cell


title: JHOC5_Final_rep1

description: sgRNA fragment library

value: Final

tag: cell type


title: 17992X1

tag: treatment


title: scRNA-seq: F9-EA01

value: Pancreas


title: CCC_3

value: Cear cell


title: TCR-seq HC20

value: male

tag: disease state


title: 19063X1

description:
Bulk RNA sequencing
19063R_counts.txt

value: Mixed 129/B6

value: Lung adenocarcinoma


title: 17699X8


title: scRNA-seq: F8-EA01


title: TCR-seq COV165

tag: peripheral blood

value: female

value: symptomatic

value: Severe Recovery

value: No

tag: disease duration

value: long term

tag: patient comorbidity


title: ES2_D0_rep2

description: sgRNA fragment library


title: 17699X7

value: Vehicle (Ethanol)

value: KrasFSF-G12D, p53frt, Rosa-FSF-CreERT2, Foxa1flox, and Foxa2flox


title: TCR-seq COV166

value: peripheral blood mono-nuclear cells

tag: gender

tag: disease symptom

tag: thymalfasin treatment

value: Yes


title: scRNA-seq: B8-EA02

value: endocrine

tag: tissue


title: 17992X4

value: 4-hydroxytamoxifen (2 um)


title: ES2_Final_rep1

description: sgRNA fragment library

value: TKOv3 library

value: Final

value: ovarian cancer cell


title: scRNA-seq: F7-EA01

tag: embryonic stage

value: Pancreas


title: 17699X6

value: Mixed 129/B6


title: TCR-seq COV164

tag: age


title: scRNA-seq: F6-EA01

tag: plate code

tag: genotype


title: ES2_D0_rep1

description: sgRNA fragment library

tag: cell line


title: 17699X5

tag: strain

value: Lung adenocarcinoma


title: scRNA-seq: F5-EA01


title: TOV21G_Final_rep2

description: sgRNA fragment library

tag: sgrna library

tag: time


title: TCR-seq COV161

value: male


title: 17699X4

tag: treatment


title: scRNA-seq: F4-EA01


title: TCR-seq COV163

value: female

value: symptomatic

tag: disease state


title: TCR-seq COV159

tag: peripheral blood

value: Severe Recovery

value: No


title: 17699X3

value: Vehicle (Ethanol)


title: scRNA-seq: F3-EA01


title: ES2_Final_rep2

description: sgRNA fragment library

tag: cell type


title: TCR-seq COV158

tag: disease duration

value: long term

tag: patient comorbidity


title: TOV21G_D0_rep2

description: sgRNA fragment library


title: TOV21G_Final_rep1

description: sgRNA fragment library


title: 6-21_Tam_Input

description: ChIPseq

data_processing:
Fastq reads were aligned to the standard mouse chromosomes (build mm10) with Novocraft novoalign (v4.03.01) using their default Novaseq tuned settings. Standard Illumina adapter sequences were provided to novoalign for masking. Alignments were run through samtools fixmate (v1.12).
Alignments were put through the MultiRepMacsChIPSeq pipeline (v17, https://github.com/HuntsmanCancerInstitute/MultiRepMacsChIPSeq). Exclusion intervals were generated  de novo by calling peaks on combined, unfiltered Input sample alignments. Alignments on the mitochondrial chromosome and overlapping these exclusion intervals were subsequently discarded from analysis. Only properly paired alignments were used. Optical duplicates with a threshold of 2500 pixels were discarded. Coordinate duplicate alignments were randomly subsampled to a uniform 5% rate. Peaks were independently called for each sample using Macs2 on filtered alignments using a q-value threshold of 0.01, minimum peak length of 200 bp, and minimum peak gap of 100 bp.
Fragment coverage tracks were generated using MultiRepMacsChIPSeq pipeline based on properly-paired, filtered alignments. Multi-mapping alignments were scored as a fraction based on the reported number of hits in the genome (alignment tag NH). Tracks were depth-normalized to 1 million fragments.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: BigWig files representing depth-normalized, fragment coverage of ChIP samples

source_name: 1027B Organoids

extract_protocol:
Lysates were sonicated and NKX2-1:chromatin complexes were immunoprecipitated using Chromatrap ChIPseq kits. IP and input DNA purified with Zymo ChIP DNA Clean and Concentrator columns
NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: Organoids were treated with vehicle or 2 um 4-OHT for 72 hours. Cells were crosslinked 14-20 days post-tamoxifen treatment.

value: KrasFSF-G12D, p53frt, Rosa-FSF-CreERT2, Foxa1flox, and Foxa2flox

tag: chip antibody

value: no antibody


title: scRNA-seq: F2-EA01

data_processing:
Raw reads passed quality control using FastQC
Reads were aligned to a custom reference genome consisting of Fasta files for mm10, ERCC knock in, and three transgenes: eGFP, tdTomato, and cre. STAR was used to create the custom genome and read alignment
BAM/SAM files created a counts table using ht-seq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes a matrix of normalized tag counts for each sample

extract_protocol: Smart-Seq2 (Picelli et al 2014) was used to extract total RNA from single cells.


title: TOV21G_D0_rep1

description: sgRNA fragment library


title: 6-21_Tam_NKX_IP_7-11

description: ChIPseq

value: TTF1 Abcam ab133737


title: TCR-seq COV055

value: peripheral blood mono-nuclear cells

tag: gender

tag: disease symptom

tag: thymalfasin treatment

value: Yes


title: TCR-seq COV119

tag: age

value: short term


title: OVISE_Final_rep2

description: sgRNA fragment library

value: OVISE

value: TKOv3 library

value: Final

value: ovarian cancer cell


title: scRNA-seq: F12-EA01

tag: embryonic stage

tag: plate code

tag: tissue

value: Pancreas


title: 6-26_Tam_NKX_IP_7-11

description: ChIPseq

tag: strain

value: Mixed 129/B6

value: Lung adenocarcinoma

tag: genotype


title: 6-26_Tam_Input

description: ChIPseq


title: scRNA-seq: F11-EA01


title: scRNA-seq: F10-EA01


title: scRNA-seq: F1-EA01


title: 6-26_EtOH_Input

description: ChIPseq

value: 4-hydroxytamoxifen (2 um)


title: TCR-seq COV057

value: male

value: symptomatic

value: Severe


title: scRNA-seq: E8-EA01


title: OVISE_Final_rep1

description: sgRNA fragment library

tag: cell line

tag: sgrna library

tag: time


title: OVISE_D0_rep1

description: sgRNA fragment library


title: TCR-seq COV045

tag: peripheral blood

value: female

tag: disease state

value: Severe Recovery

value: No


title: TCR-seq COV037

value: peripheral blood mono-nuclear cells

tag: disease duration


title: TCR-seq COV047

tag: patient comorbidity

value: Yes


title: 6-21_EtOH_Input

description: ChIPseq

tag: treatment

value: Vehicle (Ethanol)

value: KrasFSF-G12D, p53frt, Rosa-FSF-CreERT2, Foxa1flox, and Foxa2flox

tag: chip antibody

value: no antibody


title: 6-21_EtOH_NKX_IP_7-7

description: ChIPseq

value: TTF1 Abcam ab133737


title: scRNA-seq: E7-EA01


title: scRNA-seq: E9-EA01


title: TCR-seq COV029

tag: gender

tag: disease symptom

value: short term


title: SCC25 Control Cells Rep2 mRNA

city: Buffalo

first: Rose-Anne

last: Romano

state: NY

address: 3435 Main Street

department: Oral Biology

institute: State University of New York at Buffalo

data_processing:
Base calling was done using cassava 1.5
Alignment of RNA-Seq fastq file was done using tophat v2.1.1
RNA-seq alignment reads were counted using featureCounts v 1.5.3 with the following arguments -t exon -g gene_id -T 16 -p -a
Alignment of ChIP-Seq fastq file was done using bowtie v1.1.1 with the following parameters: -0 -m 1 -p 8 -S
Peak calling of CHIP-seq data was done using macs v 2.2.7.1 with default parametes (qvalue =0.05)
DESeq2 (v1.12.4) was used to normalize the read counts and derive TPM values were calculated according to the method of Wagner et al., Theory in Bioscience, 2012
Genome_build: ncbi-hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: SCC25 Control Cells Rep2

growth_protocol: All cells were grown in recommended media (DMEM/F12 for SCC25, DMEM for CAL27, and McCoy's 5A Iwakata and Grace Modified media) supplemented with 10% FBS and 1% Pen/Strep.

extract_protocol:
All cells were harvested in Trizol and total RNA was extracted using  Direct-Zol RNA mini-prep kit (zymo research) according to manufacturer's protocol.
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Total RNA was enriched for mRNA before library construction.

treatment_protocol: EHF overexpressing A253 and SCC25 cells were treated with 1ug doxycycline to induce EHF expression

tag: cell type

value: HNSCC

tag: media

value: Grown in regular media

tag: genotype/variation

value: Control


title: SCC25 EHF Expressed Rep1 mRNA

source_name: SCC25 EHF Expressed Rep1

value: Grown in media with doxycycline

value: EHF Overexpressing


title: TCR-seq COV126

tag: age

value: male

value: symptomatic

tag: thymalfasin treatment


title: OVISE_D0_rep2

description: sgRNA fragment library

value: OVISE

value: TKOv3 library

value: ovarian cancer cell


title: 6-26_EtOH_NKX_IP_7-11

description: ChIPseq

tag: strain

value: Mixed 129/B6

value: Lung adenocarcinoma

value: 4-hydroxytamoxifen (2 um)

tag: genotype


title: 1-9_EtOH_Input

description: ChIPseq

value: Vehicle (Ethanol)

value: KrasFSF-G12D, p53frt, Rosa-FSF-CreERT2, Foxa1flox, and Foxa2flox


title: scRNA-seq: E6-EA01

tag: embryonic stage

tag: plate code

tag: tissue

value: Pancreas


title: scRNA-seq: E4-EA01


title: scRNA-seq: E5-EA01


title: SCC25 Control Cells Rep1 mRNA

source_name: SCC25 Control Cells Rep1

tag: cell line


title: 1-9_Tam_IP

description: ChIPseq

tag: disease state

value: TTF1 Abcam ab133737


title: 1-9_Tam_Input

description: ChIPseq

value: no antibody


title: SCC25 EHF Expressed Rep2 mRNA

source_name: SCC25 EHF Expressed Rep2

value: HNSCC


title: TCR-seq COV021

tag: peripheral blood

value: peripheral blood mono-nuclear cells

value: female

value: Severe

value: Yes

tag: disease duration

value: short term

tag: patient comorbidity

value: No


title: TCR-seq COV013

tag: gender

value: male

value: symptomatic


title: A253 EHF Expressing Rep2 mRNA

source_name: A253 EHF Expressing Rep2

value: Grown in media with doxycycline

value: EHF Overexpressing


title: 1-9_EtOH_IP

description: ChIPseq

value: Mixed 129/B6

value: Lung adenocarcinoma

tag: treatment

tag: chip antibody


title: 1-3_Tam_Input

description: ChIPseq

value: 4-hydroxytamoxifen (2 um)

value: KrasFSF-G12D, p53frt, Rosa-FSF-CreERT2, Foxa1flox, and Foxa2flox


title: A253 EHF Control Rep3 mRNA

source_name: A253 EHF Control Rep3

tag: cell type

tag: media

value: Grown in regular media

value: Control


title: 1-3_Tam_IP

description: ChIPseq

value: TTF1 Abcam ab133737


title: scRNA-seq: E2-EA01

value: Pancreas


title: 1-3_EtOH_Input

description: ChIPseq

value: Vehicle (Ethanol)

value: no antibody


title: A253 EHF Expressing Rep3 mRNA

source_name: A253 EHF Expressing Rep3

value: HNSCC

tag: genotype/variation


title: scRNA-seq: E3-EA01


title: TCR-seq COV016

value: peripheral blood mono-nuclear cells

tag: age

tag: disease symptom

value: Severe

tag: thymalfasin treatment

value: Yes

value: short term


title: TCR-seq COV012

value: male

value: symptomatic

value: No


title: A253 EHF Control Rep2 mRNA

source_name: A253 EHF Control Rep2


title: A253 EHF Expressing Rep1 mRNA

source_name: A253 EHF Expressing Rep1

value: Grown in media with doxycycline

value: EHF Overexpressing


title: scRNA-seq: E12-EA01

tag: embryonic stage

tag: genotype


title: TCR-seq COV007


title: 1-3_EtOH_IP

description: ChIPseq

tag: strain

value: Mixed 129/B6

value: Lung adenocarcinoma

value: KrasFSF-G12D, p53frt, Rosa-FSF-CreERT2, Foxa1flox, and Foxa2flox


title: TCR-seq COV077


title: TCR-seq COV009


title: scRNA-seq: E10-EA01

tag: plate code

tag: tissue


title: Untreated_RNASeq_Rep3

city: Bethesda

first: David

last: Sturgill

state: MARYLAND

address: Building 41, Rm B622

department: NCI

institute: NIH

data_processing:
Raw reads were pre-processed to remove low quality bases and adapter sequences using cutadapt
For Ribo-Seq: After trimming, reads were stringently filtered for the presence of ribosomal RNA using a two-step process.  First, we performed local alignments to the ribosomal repeating subunit (gb|U13369.1) in very sensitive mode using bowtie2 (v.2.3.5.1)). Second, we mapped remaining reads using Hisat2 (v2.2.1.0), explicitly allowing for mismatches at the first nucleotide position. Trimmed and filtered reads were then aligned to a reference composed of canonical transcript sequence from the UCSC genome browser in the hg19 assembly, using bowtie2 (v.2.3.5.1)
RedaC:T-seq reads were aligned to the human genome (hg19) and the human transcriptome (longest isoform from UCSC) using STAR (v 2.5.4.a) in local alignment mode, keeping uniquely aligned reads and allowing five mismatches per read. Separate alignments to 18S rRNA, 28S rRNA and tRNA sequences were performed to specifically analyze reads originating from these features. Variant calls were performed in pooled biological replicates using Samtools mpileup including a minimum base quality -Q 20, the BAQ (Base Alignment Quality) and -C50 parameters activated and supplying a -f indexed reference fasta file. mpileup results were then tabulated using the mpileup2readcounts script.
For Polysome sequencing: reads were aligned to the human genome (hg19 assembly) containing the Luciferase Spike-in sequence using Hisat2 (v2.2.1.0). Gene counts within each fraction were obtained using StringTie2, normalized to the spike-in probe and converted to Transcripts per million (TPM)
Genome_build: hg19
Supplementary_files_format_and_content: HR_riboseq.txt contains P-sites called from Harringtonine-treated Ribo-seq
Supplementary_files_format_and_content: RedaCTseq_ac4C_sites.txt contains data for ac4C sites called from RedaCT-Seq
Supplementary_files_format_and_content: Counts text files contain raw gene abundance values from Stringtie2

source_name: HeLa cells

growth_protocol: Parental HeLa (Human cervix carcinoma, female, ATCC, Cat. #: CCL-2) and NAT10-/- cells were cultured in Dulbeccos’ Modified Eagle Medium (DMEM, ThermoFisher Scientific, Cat. #: 10313021) containing 25 mM glucose, 1 mM sodium pyruvate and supplemented with 2 mM L-glutamine (ThermoFisher Scientific, Cat. #: 25030149) and 10% bovine calf serum (BCS, HyClone, Cat. #: SH30073.03), in the absence of antibiotics.

extract_protocol:
RNA was precipitated from each fraction using 2 volumes of 100% ethanol followed by extraction using TRIzol Reagent.
Sequencing libraries were constructed with the Illumina TruSeq Stranded Total RNA Library Prep Kit (RS-122-2201).

treatment_protocol: Wildtype HeLa cells (2 x 106 cells) were seeded in 10 cm tissue culture dishes in 10 mL of complete DMEM medium and grown for 48 hrs at 37°C, 5% CO2.

value: WT


title: A253 EHF Control Rep1 mRNA

source_name: A253 EHF Control Rep1

tag: cell line

value: Grown in regular media

value: Control


title: scRNA-seq: D4-EA01

value: Pancreas


title: scRNA-seq: E1-EA01


title: scRNA-seq: D2-EA01


title: Slc-HKO, Chow, mouse 1

city: Pittsburgh

first: Andrew

middle: W.

last: Duncan

address: 450 Technology Drive, Suite 300

institute: University of Pittsburgh

description: Slc-HKO model, chow-fed

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Fastp (version 0.20.1).
Reads were aligned to mouse reference genome mm10 by Spliced Transcripts Alignment to a Reference (STAR) software (version 2.6.1d).
Gene counts were quantified by FeatureCounts (version 1.5.0-p3).
Genome_build: mm10
Supplementary_files_format_and_content: Readcount with gene names for all samples (xlsx format). Columns show gene ID (gene_id); the readcount of genes in each sample (sample name); gene name (gene_name); chromosome/scaffold ID (gene_chr); start coordinate (gene_start); end coordinate (gene_end); strand specificity (gene_strand); novel gene length (gene_length); the type of novel gene (gene_biotype); description from PFAM annotation (gene_description); the TF family of novel gene (tf_family)

source_name: Liver

growth_protocol: LoxP sites were inserted into the promoter and intron 1 of Slc25a34 genomic DNA to generate a floxed allele. To specifically delete Slc25a34 in hepatocytes from 2-month-old floxed mice, Cre recombinase was delivered by adeno-associated virus driven by the thyroxine binding globulin (TBG) promoter, AAV8-TBG-Cre, which targets >95% of hepatocytes, generating a hepatocyte-specific Slc25a34 knockout (Slc-HKO). As a control, Slc25a34 floxed mice were injected with AAV8-TBG-GFP, which does not affect Slc25a34 expression (WT control).

extract_protocol:
Livers were homogenized and total RNA isolated by Trizol according to the manufacturer's instructions.
RNA was sent to Novogene where libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were maintained on chow diet for 1 month after AAV8 injection and then maintained on either chow diet for 2 additional months or FFD for 2 months (Slc-HKO, n = 3 males / diet; WT control, n = 3 males / diet). Mice were fasted for 16 hours prior to liver harvest.

value: liver

tag: diet

value: chow

value: Slc-HKO


title: NaBH4_NAT10_Rep_2

data_processing:
Library strategy: RedaCTseq
Raw reads were pre-processed to remove low quality bases and adapter sequences using cutadapt
For Ribo-Seq: After trimming, reads were stringently filtered for the presence of ribosomal RNA using a two-step process.  First, we performed local alignments to the ribosomal repeating subunit (gb|U13369.1) in very sensitive mode using bowtie2 (v.2.3.5.1)). Second, we mapped remaining reads using Hisat2 (v2.2.1.0), explicitly allowing for mismatches at the first nucleotide position. Trimmed and filtered reads were then aligned to a reference composed of canonical transcript sequence from the UCSC genome browser in the hg19 assembly, using bowtie2 (v.2.3.5.1)
RedaC:T-seq reads were aligned to the human genome (hg19) and the human transcriptome (longest isoform from UCSC) using STAR (v 2.5.4.a) in local alignment mode, keeping uniquely aligned reads and allowing five mismatches per read. Separate alignments to 18S rRNA, 28S rRNA and tRNA sequences were performed to specifically analyze reads originating from these features. Variant calls were performed in pooled biological replicates using Samtools mpileup including a minimum base quality -Q 20, the BAQ (Base Alignment Quality) and -C50 parameters activated and supplying a -f indexed reference fasta file. mpileup results were then tabulated using the mpileup2readcounts script.
For Polysome sequencing: reads were aligned to the human genome (hg19 assembly) containing the Luciferase Spike-in sequence using Hisat2 (v2.2.1.0). Gene counts within each fraction were obtained using StringTie2, normalized to the spike-in probe and converted to Transcripts per million (TPM)
Genome_build: hg19
Supplementary_files_format_and_content: HR_riboseq.txt contains P-sites called from Harringtonine-treated Ribo-seq
Supplementary_files_format_and_content: RedaCTseq_ac4C_sites.txt contains data for ac4C sites called from RedaCT-Seq
Supplementary_files_format_and_content: Counts text files contain raw gene abundance values from Stringtie2

extract_protocol:
Total RNA was purified from wildtype and NAT10-/- HeLa cells using TRIzol Reagent followed by treatment with TurboTM DNase I
Illumina libraries were constructed from two biological replicates using the NEBNext® UltraII™ Directional RNA Library Prep Kit for Illumina® (NEB, Cat. #: E7760) following manufacturer’s suggestions with the reverse transcription step performed at 48 °C. Libraries were multiplexed on an Illumina HiSeq2500 instrument using TruSeq V4.0 chemistry and sequenced for 126 cycles in paired-end mode

treatment_protocol: DNase-treated Total RNA (1 µg) was ribo-depleted using the NEBNext® rRNA Ribodepletion step (NEB, Cat. #: E7850) and following the manufacturer’s instructions. Ribodepleted RNA was treated with 100 mM NaBH4 in a 20 µl volume at 55 °C in the dark for 1 hr. This step reduces ac4C to tetrahydrocytidine and fragments RNA to ~100-200 bp. During the incubation time, tube lids were opened every 10 min to release pressure from NaBH4-induced bubbling. NaBH4-treated RNA was precipitated using 0.3M sodium acetate [pH 5.5], 15 µg/mL linear acrylamide (carrier) and 2.5X ethanol.


title: scRNA-seq: C9-EA01

city: Stanford

first: Seung

institute: Stanford University

source_name: Pancreas


title: TCR-seq COV157

tag: peripheral blood

value: peripheral blood mono-nuclear cells

tag: disease state

value: Moderate

tag: disease duration

value: long term

tag: patient comorbidity


title: TCR-seq COV011

tag: gender

value: male

value: symptomatic

value: Severe

value: short term

value: Yes


title: WT Control, Chow, mouse 1

description: WT model, chow-fed

value: WT Control


title: NaBH4_NAT10_Rep_1


title: scRNA-seq: E11-EA01


title: Untreated_RNASeq_Rep2


title: NaBH4_WT_Rep_2


title: scRNA-seq: C7-EA01


title: TCR-seq COV101

value: female


title: Slc-HKO, Chow, mouse 2

description: Slc-HKO model, chow-fed


title: Untreated_RNASeq_Rep1

value: WT


title: NaBH4_WT_Rep_1


title: Slc-HKO, Chow, mouse 3

description: Slc-HKO model, chow-fed


title: TCR-seq COV091


title: TCR-seq COV156

value: No


title: WT Control, Chow, mouse 3

description: WT model, chow-fed


title: TCR-seq COV102


title: TCR-seq COV078


title: human_miRNA_NTP_rep9

type: RNA

city: ChangSha

first: ZhaoQian

last: Liu

address: xiangya road 110

institute: Xiangya Hospital, Central South University

description: miRNA expression of human brain tissue in TLE+HS and NTP

data_processing: Agilent Feature Extraction Software v10.7 was used to analyze the scanned pictures of the microarray.

source_name: Brain tissue, normal temporal or parietal cortices

extract_protocol: Total RNA was extracted with Invitrogen’s TRIzol Reagent, purified with NucleoSpin RNA clean-up, and quantified with a NanoDrop. Gel electrophoresis was used to check the RNA’s purity and integrity.

value: Parietal lobe

value: Male


title: scRNA-seq: C6-EA01

last: Kim

address: 279 Campus Dr B303

value: Pancreas


title: WT Control, Chow, mouse 2

description: WT model, chow-fed

value: liver

value: chow


title: scRNA-seq: C8-EA01


title: TCR-seq COV098

value: peripheral blood mono-nuclear cells


title: Slc-HKO, FFD, mouse 3

description: Slc-HKO model, FFD-fed

value: FFD

value: Slc-HKO


title: Slc-HKO, FFD, mouse 1

description: Slc-HKO model, FFD-fed


title: Slc-HKO, FFD, mouse 2

description: Slc-HKO model, FFD-fed


title: human_miRNA_NTP_rep8

value: Temporal lobe


title: scRNA-seq: C4-EA01


title: TCR-seq COV089

value: symptomatic

value: Moderate

value: long term


title: scRNA-seq: C3-EA01


title: WT Control, FFD, mouse 3

description: WT model, FFD-fed


title: scRNA-seq: C12-EA01


title: TCR-seq COV087

value: male

value: Yes

value: short term


title: human_miRNA_NTP_rep6


title: scRNA-seq: C5-EA01


title: TCR-seq COV076

value: female


title: human_miRNA_NTP_rep7


title: TCR-seq COV086

value: No


title: human_miRNA_NTP_rep5


title: TCR-seq COV074


title: AP_rep3

city: shanghai

first: Qianwen

last: Hu

address: 重庆南路280号

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Using HISAT2 RNA-sequencing alignment software, the raw reads were aligned to the mouse reference genome (version mm10). The mapping rate was 96%, on average, across all the samples in the dataset.
The alignment files (bam files) were processed to generate read counts for every gene using HISAT and HTSeq.
The read counts were normalized using the R package DESeq2 and then were centered and scaled for each gene, generating z-scores. P values obtained from multiple tests were adjusted using the Benjamini-Hochberg correction.
Genome_build: mm10
Supplementary_files_format_and_content: excel file containing read count for each gene

source_name: active precursor B cell

extract_protocol:
Transferred CD19+IgD+ NP-specific naive B cells were FACS-sorted from the host on day0, NP+IgD-CD19-CD138+ plasma cell,  NP+CD19+IgD-GL7-CD38+ memory B cell, NP+CD19+IgD-GL7+CD38- germianl center B cell, and NP+CD19+IgD-GL7+CD38+ active precursor B cell were FACS-sorted from the host on day5,   RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: wild type spleen naive B cells were isolated and adoptively transferred together with OT-II CD4+ T cells into the wild-type hosts . One day later, the recipients were sacrificed directly or immunized with NP-OVA and sacrificed for analysis at day5.

value: spleen

tag: cell type

value: active precursor B cell

tag: treatment

value: post NP-OVA immunization day5


title: scRNA-seq: C10-EA01

value: Pancreas


title: scRNA-seq: C11-EA01


title: TCR-seq COV072

source_name: Peripheral blood

tag: age


title: human_miRNA_NTP_rep3

value: Female


title: human_miRNA_NTP_rep4

value: Male


title: AP_rep1


title: TCR-seq COV155

value: peripheral blood mono-nuclear cells

tag: disease symptom

value: asymptomatic


title: WT Control, FFD, mouse 1

description: WT model, FFD-fed

value: liver

value: FFD

value: WT Control


title: TCR-seq COV048

value: symptomatic

value: Moderate

tag: thymalfasin treatment


title: scRNA-seq: B9-EA01

tag: embryonic stage


title: scRNA-seq: C1-EA01

tag: genotype


title: AP_rep2

tag: strain


title: MBC_rep3

source_name: memory B cell

value: memory B cell


title: scRNA-seq: B8-EA01

tag: plate code


title: MBC_rep2

tag: tissue


title: scRNA-seq: B7-EA01


title: TCR-seq COV146

value: male

value: short term


title: human_miRNA_NTP_rep2

value: Temporal lobe


title: WT Control, FFD, mouse 2

description: WT model, FFD-fed


title: TCR-seq COV147

value: No


title: MBC_rep1

value: spleen


title: human_miRNA_TLE+HS_rep6

source_name: Brain tissue, TLE+HS

value: Hippocampus


title: TCR-seq COV154

value: Yes


title: scRNA-seq: B5-EA01

value: Pancreas


title: scRNA-seq: B6-EA01


title: GCB_rep2

source_name: germinal center B cell

value: germinal center B cell

value: post NP-OVA immunization day5


title: TCR-seq COV144

value: peripheral blood mono-nuclear cells

value: female

value: asymptomatic


title: GCB_rep3


title: human_miRNA_TLE+HS_rep4

value: Female


title: scRNA-seq: B4-EA01


title: human_miRNA_NTP_rep1


title: scRNA-seq: B3-EA01


title: CAL27 Control Cells Rep2 mRNA

source_name: CAL27 Control Cells Rep2

tag: cell line

value: HNSCC

tag: media

value: Grown in regular media

tag: genotype/variation

value: Control


title: GCB_rep1


title: PC_rep3

source_name: plasma cell

value: plasma cell


title: human_miRNA_TLE+HS_rep5


title: human_miRNA_TLE+HS_rep1


title: CAL27 EHF Knockdown Cells 2 Rep2 mRNA

source_name: CAL27 EHF Knockdown Cells 2 Rep2

value: EHF Knockdown 2


title: PC_rep2


title: scRNA-seq: B11-EA01


title: scRNA-seq: B12-EA01


title: CAL27 Control Cells Rep1 mRNA

source_name: CAL27 Control Cells Rep1


title: CAL27 EHF Knockdown Cells 2 Rep1 mRNA

source_name: CAL27 EHF Knockdown Cells 2 Rep1


title: CAL27 EHF Knockdown Cells 1 Rep2 mRNA

source_name: CAL27 EHF Knockdown Cells 1 Rep2

value: EHF Knockdown 1


title: scRNA-seq: B1-EA01


title: CAL27 EHF Knockdown Cells 1 Rep1 mRNA

source_name: CAL27 EHF Knockdown Cells 1 Rep1


title: human_miRNA_TLE+HS_rep3

value: Male


title: PC_rep1

value: spleen


title: human_miRNA_TLE+HS_rep2

value: Hippocampus


title: scRNA-seq: B10-EA01


title: CAL27 Input DNA

source_name: CAL27 Control Cells


title: human_RNA_NTP_rep9

description: RNA expression and of human brain tissue in TLE+HS and NTP

value: Parietal lobe


title: scRNA-seq: A9-EA01

value: Pancreas


title: NB_rep1

source_name: naive B cell

value: naive B cell

value: untreated


title: scRNA-seq: A8-EA01


title: CAL27 EHF ChIP


title: scRNA-seq: A7-EA01


title: SOXC_Prx1Cre_E17.5

first: Véronique

last: Lefebvre

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC 912

department: Division of Orthopaedic Surgery

institute: The Children's Hospital of Philadelphia Research Institute

data_processing:
Alignment, demultiplexing, barcode assignment and UMI quantification: Cell Ranger (10X Genomics)
Clustering and gene expression analysis: Seurat v3
Pseudotime analysis: Monocle 3
RNA velocity: velocyto.py and velocyto.R
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files as Matrix (.mtx) format and gene expression analysis from Seurat as Excel Spreadsheet (.xlsx)
Table 1.xlsx: Table containing markers for clusters after integration of the control samples
Table 2.xlsx: Table containing markers for mesenchymal control clusters
Table 3.xlsx: Table containing differentially expressed genes between control and SOXC-mutant mesenchymal clusters

source_name: Calvarium

extract_protocol:
Cranial tissues were digested in LiberaseTM to obtain single cell suspensions
Chromium Single Cell 3’ v2 Reagent Kit (10X Genomics) for E15.5 samples, and Chromium Single Cell 3’ v3 Reagent Kit (10X Genomics) for all the other samples. Libraries were sequenced using a NovaSeq sequencer.

value: Sox4fl/fl Sox11fl/fl Sox12fl/fl Prx1Cre

value: Cranial bones


title: human_RNA_NTP_rep8

value: Temporal lobe


title: human_RNA_NTP_rep6


title: human_RNA_NTP_rep7


title: NB_rep2


title: PKM2_KD_Ecto_3

city: Xiamen

first: Peipei

last: Hou

state: Fujian

address: Xiangan South Road, Xiangan District

department: School of Life Sciences

institute: Xiamen University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Ctrl_vs_Scramble_Ecto_vs_PKM2_KD_Ecto_count.txt was generated by integrating raw count value of genes from each sample.

extract_protocol:
RNA was extracted by Trizol. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) and sequenced on an Illumina Hiseq platform.

tag: shRNA

tag: agent

value: ectosomes


title: PKM2_KD_Ecto_1


title: PKM2_KD_Ecto_2


title: scRNA-seq: A6-EA01

source_name: Pancreas


title: human_RNA_NTP_rep5

source_name: Brain tissue, normal temporal or parietal cortices


title: scRNA-seq: A5-EA01


title: human_RNA_NTP_rep4


title: SOXC_WT_E13.5

value: Sox4fl/fl Sox11fl/fl Sox12fl/fl

value: Cranial mesenchyme


title: scRNA-seq: A4-EA01


title: scRNA-seq: A3-EA01


title: scRNA-seq: A12-EA01


title: Scramble_Ecto_2

value: Scramble


title: Scramble_Ecto_1


title: Scramble_Ecto_3


title: human_RNA_NTP_rep2


title: 50 days cortical organoid_HRP2+NRG1_26 hours_n=3

city: Atlanta

first: Adriana

last: Harbuzariu

state: Georgia

address: 615 Michael Street, Room 425, Department of Cell Biology

institute: Atlanta

description: Organoids containing neurons, astrocytes, microglia were used

hyb_protocol: Hybridization was performed by creating first a Master Mix (by adding Hybridization buffer to the Reporter CodeSet tube). Then, each sample was added to the Master Mix, followed by Capture ProbeSet. The tubes were then placed immediately in the thermal cycler for at least 16 hours. After that, the samples were taken to nCounter Prep Station and scanend.

scan_protocol: After hybridization, the excess probes were removed, and the target-probe complexes were aligned on the imaging surface. The samples were then scanned with an automated fluorescent microscope and labeled barcodes were counted. Housekeeping genes were included in this format.

data_processing: The raw data was supplied by NanoString and showed here in a separate sheet that includes the control and housekeeping genes genes. To process the data, we used nCounter software.

label: biotin

source_name: brain cortical organoids 50 days culture

label_protocol: RNA was directly tagged with a capture probe and a reporter probe that are specific for Immunology gene pannel with more than 500 target genes, creating a unique target-probe complex.

growth_protocol: After iPSC dissociation using Accutase, cells were seeded in low attachment plates using ROCK inhibitor to form embryoid bodies (EB). After 6 days, EB were grow in induction medium and then expanded in Matrigel droplets at day 13. On day 17, the Matrigel matrix was mechanically removed and organoids were cultured in maturation medium until harvest at 50 days. All the materials used were purchased from Stem Cell Technologies.

extract_protocol: Cortical organoids grown for 50 days in culture and treated with HRP2+/- NRG1 were collected and RNA was extracted using PARIS kit (Thermo Fisher Scientific) as per manufacturer’s recommendations. The RNA concentration was determined by reading the absorption at 260/280 nm using a NanoDrop Spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: Organoids were treated with 4.2 μg/ml HRP2 for 26 hours. In some experiments, after 8 hours of HRP2 treatment, NRG1 was added at 100ng/m for 18 hours.

value: brain cortical organoids


title: human_RNA_NTP_rep3

value: Female


title: 50 days cortical organoid_HRP2_26 hours_n=3


title: scRNA-seq: A10-EA01


title: Ctrl_3

value: Ctrl


title: human_RNA_TLE+HS_rep6

value: Male


title: 50 days cortical organoid_Basal untreated_26 hours_n=3


title: human_RNA_NTP_rep1


title: Ctrl_2


title: Poly_CHX_Inp_WT_Rep_1

source_name: HeLa cells

extract_protocol:
RNA was precipitated from each fraction using 2 volumes of 100% ethanol followed by extraction using TRIzol Reagent. Fractions were spiked in with a luciferase RNA probe and combined to generate light and heavy polysomes pools.
Sequencing libraries for monosome, light polysome, and heavy polysome samples were constructed with the Illumina TruSeq Stranded Total RNA Library Prep Kit (RS-122-2201), including RiboZero treatment. Libraries were multiplexed on two lanes of an Illumina HiSeq3000 instrument in paired-end mode.

treatment_protocol: Wildtype and NAT10-/- HeLa cells (2 x 106 cells) were seeded in 10 cm tissue culture dishes in 10 mL of complete DMEM medium and grown for 48 hrs at 37°C, 5% CO2. Cycloheximide (CHX, Sigma, Cat. # C7698, dissolved at 50 mg/mL in DMSO) was added to the medium at a final concentration of 100 µg/mL and immediately aspirated. Plates were placed on top of liquid nitrogen and transferred to dry ice. Cells were scraped into lysis buffer (500 μL, 10 mM Tris-HCl [pH 7.4], 5 mM MgCl2, 100 mM KCl, 1% Triton X-100, 2 mM DTT, 100 μg/mL CHX),  passed through a 26-G needle 10 times, and clarified by spinning at 20,000 x g for 10 min at 4 °C. OD260 was measured in the Nanodrop-1000 and ~250 µL of lysates were loaded on a 10%–45% sucrose gradient, previously prepared in gradient buffer (100 mM Tris-HCl [pH 7.5], 75 mM KCl, 1.5 mM MgCl2) using a BioComp Gradient Master (Short Run, Sucr 10-45% SW41, wt15t). Fractions were collected using a Brandel Density Gradient Fractionation system.

value: WT


title: Ctrl_1


title: scRNA-seq: A1-EA01


title: scRNA-seq: A11-EA01


title: Poly_CHX_Inp_WT_Rep_2


title: human_RNA_TLE+HS_rep4

value: Hippocampus


title: RNAP_1.0X_2 [rich media]

status: Public on Jun 07 2022

city: Tampere

first: Andre

middle: Sanches

last: Ribeiro

state: Pirkanmaa

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

data_processing:
RNA sequencing reads were trimmed to remove possible adapter sequences and nucleotides with poor quality with Trimmomatic v.0.36
Trimmed reads were then mapped to the reference genome, E. coli MG1655 (NC_000913.3), using the Bowtie2 v.2.3.5.1 aligner, which outputs BAM files
featureCounts from the Rsubread R package (v.1.34.7) was used to calculate unique gene hit counts
Gene hit counts was then used for the subsequent differential expression analysis. For this, we used the DESeq2 R package (v.1.24.0) to compare gene expression between groups of samples and calculate p-values and log2 of fold changes (LFC) using Wald tests (function nbinomWaldTest). Genes with less than 5 counts in more than 3 samples, and genes whose mean counts are less than 10 were removed from further analysis.
P-values were adjusted for multiple hypotheses testing (Benjamini–Hochberg, BH procedure)
Genome_build: Escherichia coli str. K-12 substr. MG1655 (NC_000913.3)
Supplementary_files_format_and_content: tab-delimited .csv file containing raw counts
Supplementary_files_format_and_content: tab-delimited .csv file containing normalized raw counts
Supplementary_files_format_and_content: tab-delimited .csv file containing results from differential expression analysis

growth_protocol: From glycerol stocks (at - 80 ºC), cells were streaked on lysogeny broth (LB) agar plates with appropriate antibiotics and kept at 37 ºC overnight. Next, a single colony was picked and inoculated into fresh LB medium and kept at 30 ºC overnight, with appropriate antibiotics and aeration at 250 rpm. From overnight cultures (ONC), cells were diluted to 1:1000 in tailored LB media (see below), with antibiotics, and incubated at 37 ºC with aeration and allowed to grow until reaching the mid-log phase (with optical density at 600 nm (OD600) ≈ 0.4).   Using this protocol, to attain cells with different intracellular RNAP concentration, starting from LB, we used tailored various media differing in richness, denoted as ‘LB1.0x', ‘LB1.5x’, ‘LB2.0x’ and ‘LB2.5x’ specifically. Their composition for 100 ml (pH of 7.0) are, respectively: (LB1.0x) 1 g tryptone, 0.5 g yeast extract and 1 g NaCl;  (LB1.5x) 1.5 g tryptone, 0.75 g yeast extract and 1 g NaCl; (LB2.0x) 2 g tryptone, 1 g yeast extract and 1 g NaCl; (LB2.5x) 2.5 g tryptone, 1.25 g yeast extract and 1 g NaCl.

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen).
RNA-seq libraries were constructed according to the Illumina's protocol.

treatment_protocol: Cells from 3 independent biological replicates of MG1655 in each modified LB medium richness were treated with RNA protect bacteria reagent (Qiagen, Germany), to prevent degradation of RNA.

tag: intracellular rnap concentration


title: RNAP_2.5X_3

organism: Escherichia coli str. K-12 substr. MG1655


title: RNAP_1.0X_3 [rich media]


title: human_RNA_TLE+HS_rep3

state: China

tag: gender


title: RNAP_1.0X_1 [rich media]


title: human_RNA_TLE+HS_rep2


title: RNAP_2.5X_2


title: RNAP_1.5X_3


title: RNAP_2.5X_1


title: RNAP_2.0X_3


title: RNAP_1.5X_2


title: RNAP_2.0X_2


title: RNAP_2.0X_1


title: human_RNA_TLE+HS_rep5


title: RNAP_1.5X_1


title: Trigeminal Ganglia,SARSCOV2,31dpi,4

city: New York

first: Justin

middle: J

last: Frere

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

institute: NYU Langone Health

data_processing:
Base calling and sample deconvolution performed via Illumina BaseSpace
Reads aligned to MesAur1.0 genome assembly using Ensembl GTF file and quantified using Salmon as made available in Illumina BaseSpace "RNA-Seq Alignment" application
Assembly: Mesocricetus Auratus MesAur1.0
Supplementary files format and content: .quant.genes.sf Salmon files (show raw and normalized read counts by gene)

organism: Mesocricetus auratus

source_name: Trigeminal Ganglia

extract_protocol:
Trizol Phenol Chloroform
Poly A tail enrichment and preparation using True Strand RNA-seq Prep

value: Trigeminal Ganglia

tag: infection

value: SARS-CoV-2 (1000 PFU)

tag: time

value: 31 dpi


title: Trigeminal Ganglia,SARSCOV2,3dpi,2

value: 3 dpi


title: Trigeminal Ganglia,SARSCOV2,3dpi,3


title: Trigeminal Ganglia,SARSCOV2,3dpi,1


title: Trigeminal Ganglia,SARSCOV2,31dpi,3


title: Trigeminal Ganglia,SARSCOV2,31dpi,2


title: Trigeminal Ganglia,MOCK,3dpi,3

value: Mock (PBS-treated)


title: human_RNA_TLE+HS_rep1

source_name: Brain tissue, TLE+HS

tag: age


title: Trigeminal Ganglia,MOCK,31dpi,4


title: Trigeminal Ganglia,MOCK,3dpi,2


title: Trigeminal Ganglia,MOCK,31dpi,5


title: Trigeminal Ganglia,MOCK,31dpi,3


title: Trigeminal Ganglia,MOCK,31dpi,2


title: Trigeminal Ganglia,MOCK,3dpi,1


title: Trigeminal Ganglia,SARSCOV2,31dpi,1


title: Trigeminal Ganglia,MOCK,31dpi,1


title: Trigeminal Ganglia,IAV,3dpi,2

value: Influenza (100,000 PFU)


title: Trigeminal Ganglia,IAV,3dpi,3


title: Trigeminal Ganglia,SARSCOV2,31dpi,5


title: Trigeminal Ganglia,IAV,31dpi,1


title: Trigeminal Ganglia,IAV,31dpi,5


title: Thalamus,SARSCOV2,3dpi,3

source_name: Thalamus

value: Thalamus


title: Trigeminal Ganglia,IAV,3dpi,1


title: Trigeminal Ganglia,IAV,31dpi,3


title: Trigeminal Ganglia,IAV,31dpi,4


title: Trigeminal Ganglia,IAV,31dpi,2


title: Thalamus,SARSCOV2,31dpi,3


title: Thalamus,SARSCOV2,3dpi,2


title: Thalamus,SARSCOV2,31dpi,2


title: Thalamus,MOCK,3dpi,2


title: Thalamus,MOCK,3dpi,1


title: Thalamus,MOCK,31dpi,5


title: Thalamus,MOCK,31dpi,3


title: Thalamus,MOCK,31dpi,1


title: Thalamus,IAV,3dpi,3


title: Thalamus,SARSCOV2,3dpi,1


title: Thalamus,IAV,3dpi,1


title: Thalamus,IAV,31dpi,1


title: Thalamus,IAV,31dpi,2


title: Thalamus,SARSCOV2,31dpi,1


title: Thalamus,IAV,3dpi,2


title: Thalamus,MOCK,3dpi,3


title: Striatum,SARSCOV2,3dpi,3

source_name: Striatum

value: Striatum