title: D5_red_rep3

city: Reykjavik

first: Agnes

middle: Katharina

last: Ulfig

address: Sturlugata 8

department: Translational Medicine

country: Iceland

institute: University of Iceland

data_processing:
Reads that contained adaptor contamination, low quality bases and undetermined bases were removed using Cutadapt and in-house perl scripts (LC Sciences), and sequence quality was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were mapped to the Mus musculus genome using HISAT2. Mapped reads of each sample were assembled into transcripts using StringTie. Transcriptomes were merged using perl scripts and gffcompare. StringTie and ballgown (Bioconductor) were used to determine the expression levels of all transcripts by calculating FPKM. mRNAs differential expression analysis was performed using the R package DESeq2between two different groups (and by R package edgeR between two samples). The mRNAs with the parameter of false discovery rate (FDR) < 0.05 and absolute fold change ≥ 1.5 were considered as differentially expressed.
Assembly: mm10
Supplementary files format and content: text files include FPKM values for each sample

growth_protocol: E14Tg2a cells expressing nuclear Grx1-roGFP2 redox sensor were cultured in gelatin-coated (0.1% gelatin type B from bovine skin dissolved in ddH2O)  tissue culture-treated dishes in KnockOut DMEM, containing 15% ESC-grade fetal bovine serum, supplemented with penicillin/streptomycin, 2 mM glutamine, 55 µM beta-mercaptoethanol, 100 mM MEM non-essential amino acids, 103 U/mL LIF and 1X 2i supplement (ESGRO) in a 37°C humidified cell culture incubator with 5% CO2.

extract_protocol:
Total RNA was isolated using the GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich) according to the manufacturer's instructions. DNA contamination was eliminated from eluted RNA samples using the RNase-Free DNase I treatment Kit from Thermo Fisher Scientific.
Poly(A) RNA seq libraries were prepared following the TruSeq-stranded-mRNA sample preparation protocol (Illumina, Inc, San Diego CA). Oligo-(dT) magnetic beads were used to isolate poly(A) tail-containing mRNAs, with two rounds of purification. Poly(A) RNA was then fragmented using divalent cation buffer in elevated temperature. Paired-end sequencing was performed on Illumina's NovaSeq 6000 sequencing system

treatment_protocol:
Embryoid bodies (EBs) were formed using the hanging drop method. Briefly, pluripotent, nuclear Grx1-roGFP2 expressing E14Tg2a cells were dissociated with ESGRO Complete Accutase, counted using a hemocytometer and added to EB differentiation medium (i.e., complete 2iLIF/serum medium without 2i/LIF) at a concentration of 20,000 cells/mL. 30 µL drops each containing approximately 600 cells were then placed in the lids of square 100-mm bacteriological petri dishes using a multichannel pipette. After 48 hrs of incubation, the obtained EBs were individually transferred into wells of round-bottom 96-well plates, pre-coated with Anti-Adherence Rinsing Solution (Stemcell Technologies) and containing 100 µL complete EB differentiation medium, using Axygen 200 µL wide-bore pipette tips (Fisher Scientific). After 48 hrs, 100 µL of fresh complete EB medium were added. EBs were then incubated until differentiation day 5  and medium was replenished every other day by removing and replacing 100 µL of spent medium with 100 µL fresh medium.
At differentiation day 5, EBs were dissociated with ESGRO Complete Accutase. For the exclusion of nonviable cells, cells were stained with Propidium Iodide (PI) Ready Flow Reagent (Invitrogen) per manufacturer's protocol immediately before analysis. Cells were analyzed on the CytoFLEX SRT Benchtop cell sorter. PI signal was detected using the yellow laser (561 nm) and the 675/30-nm bandpass filter (channel Y675). Cell debris and cells positive for PI staining were gated out and only the remaining live cells were further analyzed with respect to their redox status. Oxidized and reduced roGFP were excited with the violet (405 nm) and blue (488 nm) laser, respectively, and detected using the 525/40-nm bandpass filter (i.e., channels V525 and B525). For direct measurement and visualization of the ratio of oxidized to reduced roGFP, channel V525 was divided by channel B525 and multiplied with the factor 100. The resulting ratio was then plotted against the number of events to generate univariate histograms. Individual differentiated cells in EBs were sorted based on the oxidized to reduced roGFP ratio (405/488 nm ratio) into the two subpopulations EB_ox and EB_red by drawing two gates, "ox" and "red", in the histogram that encompass the 10% most oxidized (i.e., highest 405/488 nm ratio) and 10% most reduced (i.e., lowest 405/488 nm ratio) cells, respectively. At least 1,000,000 cells per gate were sorted into FACS tubes pre-filled with 200 µL of the cell lysis buffer RLT from the RNeasy Mini Kit (Qiagen) for subsequent RNA isolation. A, B, and C indicate biological replicates.

value: embryonic stem cells

value: WT

value: differentiation to embryoid bodies

tag: time

value: day 5

tag: comparison

value: D5_ox vs D5_red


title: D5_red_rep2

status: Public on Jul 07 2024

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: shCerS4 IgG

city: Charleston

first: Wyatt

last: Wofford

state: SC

address: 86 Jonathan Lucas St

country: USA

institute: MUSC

data_processing:
Partek
Sequence reads were aligned using STAR - 2.7.8a tool in Partek.
Sequence reads were quantified to Ensembl Transcripts annotation model with strict paired-end compatibility and a minimum 100% read overlap with feature using Partek.
Read count extraction and and normalization were performed using Partek.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for each sample

molecule: polyA RNA

growth_protocol: 4T1 cells were maintained in DMEM plus 10% FBS, 1x antibiotics,  plasmocin prophylactic, and 4ug/mL puromycin in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Qiazol (Qiagen). 500ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNAseq were constructed using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocol.

value: cancer cell

value: stably expressing CerS4 shRNA


title: D5_ox_rep2


title: D5_ox_rep1


title: D5_red_rep1


title: Pluripotent E14Tg2a cells, untreated, timepoint 24 h, rep1

growth_protocol: E14Tg2a cells were cultured in gelatin-coated (0.1% gelatin type B from bovine skin dissolved in ddH2O)  tissue culture-treated dishes in KnockOut DMEM, containing 15% ESC-grade fetal bovine serum, supplemented with penicillin/streptomycin, 2 mM glutamine, 55 µM beta-mercaptoethanol, 100 mM MEM non-essential amino acids, 103 U/mL LIF and 1X 2i supplement (ESGRO) in a 37°C humidified cell culture incubator with 5% CO2.

treatment_protocol: E14Tg2a cells were treated with 500 µM hydrogen peroxide for 30 mins. Medium was then removed and replaced with spent medium from untreated cells.

value: untreated


title: Pluripotent E14Tg2a cells, untreated, timepoint 24 h, rep3


title: resistant2

status: Public on Jul 08 2024

city: Guang Zhou

first: Yiwen

last: Lu

state: China

address: 107 Yanjiang West Road Guangzhou 510120, P.R.China

country: China

institute: Sun Yat-Sen University 2nd Affiliated Hospital: Sun Yat-Sen Memorial Hospital

data_processing:
Sequencing was carried out using the Illumina novaseq-6000 instrument
Read quality was checked for each sample using FastQC v0.11.2(http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/).
StringTie software was used to calculate the FPKM value for each sample, and the values were log2 transformed.
Alignment was initially to the transcriptome (hg38)
Mapping of RNA-Seq reads were performed using STAR aligner.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Homo sapiens

source_name: breast cacer

extract_protocol:
For RNA extraction, total RNA from each biopsies obtained as described above were isolated using the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA). RNA quality was examined by gel electrophoresis and with a Nanodrop spectrophotometer (Thermo, Waltham, MA, USA). Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), and sequencing was carried out based on the Illumina novaseq-6000 instrument. The raw data was handled by Perl and data quality was checked by FastQC v0.11.2
TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA)

tag: tissue

value: breast cacer

value: therapeutic resistant


title: Pluripotent E14Tg2a cells, untreated, timepoint 24 h, rep2


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 24 h, rep2

description: H2O2_24hVSUT_24h_Gene_differential_expression.txt

value: hydrogen peroxide


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 10 h, rep3

description: H2O2_10hVSUT_0h_Gene_differential_expression.txt

value: H2O2_10h vs UT_0h


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 24 h, rep3


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 10 h, rep2


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 24 h, rep1


title: Combo 4

data_processing:
Raw sequence reads were aligned using Gencode vM23 mouse genome annotation and Gencode Grcm38.p6 mouse reference genome using TopHat with default parameters.
Cufflinks were used to assemble and quantify transcripts from the mapped sequences.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for each sample

source_name: Breast tumor

growth_protocol: Breast tumors were collected from 12 week old  transgenic MMTV-PyMT mice and reimplanted into  the  4th mammary fat pad of FVB mice

extract_protocol:
RNA was harvested using Qiazol (Qiagen).
Ribosomal (r)RNA-depleted stranded libraries

treatment_protocol: FVB mice harboring PyMT tumors were treated with vehicle, twice weekly 5 mg/kg anti-PD-L1, daily 20 mg/kg sonidegib, or combination for 28 days

value: Breast tumor

value: MMTV-PyMT

value: anti-PD-L1 + Sonidegib


title: Combo 3


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 8 h, rep3

description: H2O2_8hVSUT_0h_Gene_differential_expression.txt

value: 8 h

value: H2O2_8h vs UT_0h


title: Combo 2


title: CN at day3, after noise rep1

type: RNA

city: Seoul

first: Sohyeon

last: Park

state: Seoul

address: 71, Daehak-ro

department: Interdisciplinary Program in Neuroscience

country: South Korea

institute: Seoul National University College of Natural Sciences

description: microRNA list from CN after noise at day3

hyb_protocol: The labeled RNA was fractionated and hybridized for 16 hr at 48C on Affymetrix 450 Fluidics Station (Affymetrix, Santa Clara, California, United States).

scan_protocol: GeneChops were scanned with an Affymetrix GCS 3000 scanner (Affymetrix, Santa Clara, California, United States).

data_processing:
The data were analyzed with 'rma' function in R library 'oligo' (version 1.58.0)
normalized Affy microarray intensity

label: biotin

organism: Rattus norvegicus

source_name: Cochler Nucleus, after noise, day3

label_protocol: RNA samples were labeled with the FlashTag Biotin RNA Labeling Kit (Genisphere, Hatfield, PA, USA).

growth_protocol: SD rats were maintained under a 12-hour light-dark cycle, with free access to food and water.

extract_protocol: Whole brain tissue was separated from the craninal bone and each CN, SOC, IC, AC and peripheral blood were harvested and total RNA was extracted in Trizol solution.

treatment_protocol: SD rats were exposed to white noise(2-20kHz) at 115 dB SPL for 2 hours in a sound-attenuating booth under anesthesia.

tag: strain

value: Sprague-Dawley

value: Cochlear Nucleus

tag: age

value: 5 weeks

tag: gender

value: male

value: after noise, day3


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 8 h, rep2

value: embryonic stem cells

value: WT


title: D5_ox_rep3

value: differentiation to embryoid bodies

value: day 5

value: D5_ox vs D5_red


title: Combo 1


title: Sonidegib 4

value: Sonidegib


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 8 h, rep1

value: hydrogen peroxide


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 6 h, rep3

description: H2O2_6hVSUT_0h_Gene_differential_expression.txt

value: 6 h

value: H2O2_6h vs UT_0h


title: Sonidegib 2

value: Breast tumor

value: MMTV-PyMT


title: Sonidegib 1


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 6 h, rep1


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 4 h, rep3

description: H2O2_4hVSUT_0h_Gene_differential_expression.txt

value: 4 h

value: H2O2_4h vs UT_0h


title: Sonidegib 3


title: PD-L1 3


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 4 h, rep1


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 6 h, rep2


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 4 h, rep2


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 10 h, rep1

value: H2O2_10h vs UT_0h


title: PD-L1 1


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 2 h, rep2

description: H2O2_2hVSUT_0h_Gene_differential_expression.txt

value: 2 h

value: H2O2_2h vs UT_0h


title: Replication 2 of Se treatment for 48h (Se48)

city: Tianjin

first: Jinyang

last: Li

address: No. 32, Xiqi Road, Tianjin Airport Economic Park

institute: Chinese Academy of Sciences

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke (v1.4.0) (parameter– l 15 -q 0.2 -n 0.1).
Clear reads were mapped to Aspergillus oryzae RIB40 genome using HISAT2 (v2.1.0) with parameters --dta --phred64 unstranded --new-summary -x index -1 read_r1 -2 read_r2 (PE).
The counts of reads uniquely mapped to only one gene for each gene were calculated by RSEM (v1.2.8) with default parameters.
The normalized expression values for each gene were calculated by the number of uniquely mapped fragments per kilobase of transcript per million mapped reads (FPKM) and differential gene expression was determined by DESeq2 package.
Assembly: GCF_000184455.2
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

organism: Aspergillus oryzae

source_name: Mycelium

growth_protocol: Conidia from 10-day-old agar culture were collected and counted by haemocytometer, then inoculated into 100 mL liquid MMC medium and grown at 28˚C and 200 rpm 4 d. The mycelial biomass was washed with sterilized water at least two times and then transferred to 100 mL MMC medium with or without 15 mM CuCl2 for 6 h before RNA extraction.

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

value: Mycelium

tag: treatment time

value: Se treatment


title: Vehicle 4

value: Vehicle


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 2 h, rep3

value: embryonic stem cells

value: WT


title: Replication 3 of Se treatment for 48h (Se48)


title: PD-L1 2


title: Replication 1 of Se treatment for 48h (Se48)


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 2 h, rep1


title: Replication 3 of Se treatment for 24h (Se24)


title: Vehicle 3


title: Replication 2 of Se treatment for 24h (Se24)


title: Vehicle 2


title: PD-L1 4


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 0.5 h, rep3

description: H2O2_0_5hVSUT_0h_Gene_differential_expression.txt

value: H2O2_0_5h vs UT_0h


title: Replication 1 of Se treatment for 24h (Se24)


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 0.5 h, rep2


title: Pluripotent E14Tg2a cells, hydrogen peroxide treated, timepoint 0.5 h, rep1


title: Replication 3 of Control for 48h (Con48)

value: No treatment


title: Vehicle 1


title: Replication 2 of Se treatment for 12h (Se12)


title: Replication 2 of Control for 48h (Con48)


title: BHK-21 cells, expressing nsP4 in trans, harboring repRNA-v4 RNA,

city: Beijing

first: Yihan

last: Lin

address: No.5 Yiheyuan Road, Haidian

institute: Peking University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cleaned reads were demultiplexed, barcode processed, gene counted using the Cell Ranger software v4.0.0. against the Mesocricetus auratus genome (GCF_017639785.1_BCM_Maur_2.0_genomic.fna) and the genome of alphaviral RNA replication system. The genome annotation file (GCF_017639785.1_BCM_Maur_2.0_genomic.gff) was downloaded from NCBI and modified to include annotation about the genome of the alphaviral RNA replication system. Subsequent analyses were performed using the Seurat package with default or recommended parameters.
Assembly: Mesocricetus auratus genome  (GCF_017639785.1_BCM_Maur_2.0_genomic.fna) and the genome of the alphaviral RNA replication system
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: fa and gtf files for the alphaviral RNA replication system

organism: Mesocricetus auratus

source_name: kidney

growth_protocol: BHK-21 cells were cultivated in Minimum Essential Medium with Earle's Balanced Salts (MEM/EBSS) supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, 100 μg/ml streptomycin, 1% MEM Non-Essential Amino Acids Solution (Gibco, #11140050)  and 10 μg/ml puromycin in a humidified 37℃ incubator with 5% CO2.

extract_protocol:
After removing the culture medium, the cells were washed once with DPBS and then digested with trypsin for 3 minutes. The digestion was terminated by adding culture medium containing 10% serum, and the cells were then dispersed by pipetting. Subsequently, the cells were centrifuged at 1000 rpm for 3 minutes, and the pellet was washed twice with cold DPBS containing 0.05% BSA. Finally, the cells were resuspended in DPBS containing 0.05% BSA.
The library was constructed following the manufacturer's instructions for the Chromium Next GEM Single Cell 5' Kit v2 from 10x Genomics.

treatment_protocol: No treatment

value: kidney

value: fibroblast cells

value: harboring repRNA-v4 RNA and expressing nsP4 in trans

value: No


title: MEK1_day14_Cobimetinib_mca825

description: No

data_processing:
The PE250 sequencing data were initially processed using Trimmomatic 0.39 to remove the 5’ end 25-bp primer sequences used for PCR amplification, and to remove the 3’ end 125 bp low-quality sequences, and to discard sequences with an average sequencing quality score below the Q36 threshold. The filtered sequences were then aligned to the coding region of MEK1 using BWA 0.7.17-r1188 software. In order to analyze mismatch variations across different samples, reads containing base deletions or insertions were excluded. Subsequently, an in-house Python script was employed to tally the types of variants and the frequency of mutations per sequencing reads from the resulting BAM files.
Assembly: human MEK1 coding sequence
Supplementary files format and content: *mutants.number.remove.dis.xlsx: number of mutants for each samples
Supplementary files format and content: MEK1_mutation_number_200bp_all_samples.xlsx: frequency of mutation numbers per sequencing reads for each samples

growth_protocol: BHK-21 cells were cultivated in Minimum Essential Medium with Earle's Balanced Salts (MEM/EBSS) supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, 100 μg/ml streptomycin, and 1% MEM Non-Essential Amino Acids Solution (Gibco, #11140050) in a humidified 37℃ incubator with 5% CO2.

extract_protocol:
Each sample collected ~ 50,000 cells for RNA isolation using TRIzol™ Reagent (Thermo Fisher Scientific, #15596018). 1 μg genomic RNA was used for reverse transcription.
The MEK1 cDNA mutant libraries were subjected to 28 cycles of PCR amplification using MEK1 gene specific primers containing Illumina sequencing indexes (resulting in 595 bp amplicons). The PCR products were purified and used for sequencing on the Illumina platform.

treatment_protocol: Medium was replaced with fresh medium containing 5 μg/ml puromycin 24 h post-electroporation (i.e., Day 1). After 4 d of selection (i.e., Day 5), 2 μM of molnupiravir was added to the medium. On Day 7, cobimetinib was added to the medium. The cells were continued to be cultured and selected in medium with molnupiravir and cobimetinib (2-5 μM) for 7 days.

value: expressing replicative RNA repRNA-v4-MEK1

value: Cobimetinib


title: Replication 3 of Control for 24h (Con24)


title: Replication 1 of Control for 48h (Con48)


title: Pluripotent E14Tg2a cells, untreated, timepoint 0 h, rep2

value: untreated

value: 0 h


title: Replication 2 of Control for 24h (Con24)


title: Pluripotent E14Tg2a cells, untreated, timepoint 0 h, rep1


title: MEK1_day1_mca784

description: No


title: Replication 3 of Control for 12h (Con12)


title: Replication 1 of Control for 24h (Con24)


title: KRAS_Day9_without_Mo_mcb190

description: No

data_processing:
The paired-end sequencing data were initially processed using Trimmomatic 0.39 to remove the 25-bp primer sequences used for PCR amplification and to discard sequences with an average sequencing quality score below the Q36 threshold. The filtered sequences were then aligned to the coding region of KRAS (S17N) using BWA 0.7.17-r1188 software. In order to analyze mismatch variations across different samples, reads containing base deletions or insertions were excluded. Subsequently, an in-house Python script was employed to tally the types of variants and the frequency of mutations per sequencing reads from the resulting BAM files.
Assembly: human KRAS (S17N) coding sequence
Supplementary files format and content: *mutants.number.remove.dis.xlsx: number of mutants for each samples
Supplementary files format and content: KRAS_mutation_number_250bp_all_samples.xlsx: frequency of mutation numbers of sequencing reads for each samples

extract_protocol:
Each sample collected ~ 1 million cells for RNA isolation using TRIzol™ Reagent (Thermo Fisher Scientific, #15596018). 3μg genomic RNA or 500 ng in vitro transcribed RNA was used for reverse transcription.
The KRAS (S17N) DNA or  KRAS (S17N) cDNA mutant libraries were subjected to 28 cycles of PCR amplification using KRAS gene specific primers containing Illumina sequencing indexes (resulting in 330 bp amplicons). The PCR products were purified and used for sequencing on the Illumina platform.

treatment_protocol: Medium was replaced with fresh medium containing 5 μg/ml puromycin 24 h post-electroporation (i.e., Day 1). After 4 d of selection (i.e., Day 5), 2 μM of molnupiravir was added to the medium. The cells were continued to be cultured and selected in medium with molnupiravir and puromycin for 10 days.

value: expressing replicative RNA repRNA-v4-KRAS (S17N)


title: Replication 2 of Control for 12h (Con12)


title: Control2, WES

city: Nashville

first: Mirazul

last: Islam

state: TN

address: 2213 Garland Ave

department: Cell and Developmental Biology

institute: Vanderbilt University

description: WES

library_source: genomic

data_processing:
Data was aligned using BWA and mutation was caled using GATK (mutect2) standard pipeline.
Assembly: mm10
Supplementary files format and content: Tab-sepatated value files
Library strategy: WES

molecule: genomic DNA

source_name: Normal intestinal epithelium

extract_protocol:
DNA  was extracted using QIAGEN kit.
Library was constructed using Twist Bioscience mouse whole exome panel protocol.

value: Normal intestinal epithelium

value: Mix background


title: KRAS_Day14_Mo_mca821

description: No

value: molnupiravir


title: BHK-21 cells, repRNA-v4, bio_rep 2, 12h

description: no

data_processing:
Cleaned paired-end reads were aligned to the Mesocricetus auratus genome (GCF_017639785.1_BCM_Maur_2.0_genomic.fna) and the genome of the alphaviral RNA replication system using STAR 2.7.8a. Genome annotation file (GCF_017639785.1_BCM_Maur_2.0_genomic.gtf) was downloaded from NCBI and edited to add the annotation information of the alphaviral RNA replication system. Transcript abundances were estimated using featureCounts, then normalized to RPKM using in-house R scripts.
Assembly: Mesocricetus auratus genome  (GCF_017639785.1_BCM_Maur_2.0_genomic.fna) and the genome of the alphaviral RNA replication system
Supplementary files format and content: tab-delimited text files include raw transcript abundances estimated using featureCounts.

growth_protocol: BHK-21 cells were cultivated in Minimum Essential Medium with Earle's Balanced Salts (MEM/EBSS) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 μg/ml streptomycin, and 1% MEM Non-Essential Amino Acids Solution (Gibco, #11140050) in a humidified 37℃ incubator with 5% CO2.

extract_protocol:
Each sample collected about 500,000 cells for RNA isolation using TRIzol™ Reagent (Thermo Fisher Scientific, #15596018). 1 μg RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using a VAHTS Universal V6 RNA-seq Library Prep Kit for MGI (Vazyme, #NRM604-2) following manufacturer's user guide.

treatment_protocol: 10 µg of repRNA-v4 RNA was transfected into 4 million wildtype BHK-21 cells via electroporation. Samples were collected at 1-hour, 3-hour, and 12-hour time points for subsequent RNA-seq analysis.

value: BHK-21 WT, transfected with repRNA-v4


title: Replication 3 of Se treatment for 12h (Se12)

value: Mycelium

value: Se treatment


title: Replication 1 of Control for 12h (Con12)

value: WT


title: BHK-21 cells, repRNA-v4, bio_rep 2, 3h

description: no


title: BHK-21 cells, repRNA-v4, bio_rep 2, 1h

description: no


title: Control1, WES

description: WES


title: KRAS_Day12_Mo_mca810

description: No


title: Replication 1 of Se treatment for 12h (Se12)


title: TC2, WES

description: WES

source_name: Mouse intestinal tumor

value: Mouse intestinal tumor


title: Pluripotent E14Tg2a cells, untreated, timepoint 0 h, rep3

value: embryonic stem cells


title: TC1, WES

description: WES


title: KRAS_Day9_Mo_mca799

description: No

value: kidney

value: fibroblast cells


title: BHK-21 cells, repRNA-v4, bio_rep 1, 3h

description: no

value: No


title: BHK-21 cells, repRNA-v4, bio_rep 1, 1h

description: no


title: BHK-21 cells, expressing nsP4 in trans, repRNA-v4,biol rep 2

data_processing:
Cleaned paired-end 150 bp reads were aligned to the Mesocricetus auratus genome (GCF_017639785.1_BCM_Maur_2.0_genomic.fna) and the alphaviral RNA replication system genome using STAR 2.7.8a.
Genome annotation (GCF_017639785.1_BCM_Maur_2.0_genomic.gtf) was downloaded from NCBI and edited to add the information of the alphaviral RNA replication system. Transcript abundances were estimated using featureCounts, and then normalized and statistically compared using DESeq2.
Assembly: BCM_Maur_2.0
Supplementary files format and content: tab-delimited text files include raw transcript abundances estimated using featureCounts.

extract_protocol:
Each sample collected 300,000 cells for RNA isolation using TRIzol™ Reagent (Thermo Fisher Scientific, #15596018). All the RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using a VAHTS Universal V6 RNA-seq Library Prep Kit for MGI (Vazyme, #NRM604-2) following manufacturer's user guide.

value: expressing repRNA-v4 and expressing nsP4 in trans


title: BHK-21 cells, repRNA-v3, biol rep 2

value: expressing repRNA-v3


title: TI4, WES

description: WES


title: BHK-21 cells, expressing nsP4 in trans, repRNA-v4, biol rep 1


title: KRAS_Day5_mca787

description: No


title: BHK-21 cells, repRNA-v3, biol rep 1


title: TI3, WES

description: WES


title: KRAS_Day1_mca780

description: No


title: BHK-21 cells, expressing nsP4 in trans, biol rep 2

value: expressing nsP4 in trans


title: KRAS_invitroRNA

description: No


title: BHK-21 cells, expressing nsP4 in trans, biol rep 1


title: TI2, WES

description: WES


title: 1759

city: Valencia

first: Jose Santiago

last: Ibanez-Cabellos

state: VALENCIA

address: Av. de Blasco Ibanez, 15

country: Spain

institute: Universitat de Valencia

data_processing:
Sequenced reads were trimmed for adaptor sequence and filtered by size and quality using Cutadapt
The remaining sequences were aligned to the human genome reference (Hg38)
The expression of every miRNA per sample was measured using the annotation file with mature miRNAs from miRBase (v22) and the R package Rsubread.
Assembly: GRCh38/Ensembl
Supplementary files format and content: tab-delimited text file includes raw counts of sequencing reads of every miRNA per sample

source_name: Plasma

extract_protocol:
Blood samples were collected in EDTA tubes and centrifuged at 2500 rpm for 10 minutes. Once plasma was obtained, each sample was stored at −80°C until RNA extraction. 400 µL of plasma were used to isolate cell-free total RNA (including miRNAs) using the miRNeasy Serum/Plasma kit (Qiagen, Valencia, CA, USA) following the manufacturer’s protocol.
The libraries were generated and indexed using a modified Illumina TruSeq small RNA protocol. In this modified protocol the libraries were size selected (range 90-170pb) using the Blue Pippin instrument (Sage Science, Beverly,MA, USA). A positive RNA control was included (Thermo Fisher Scientific Human Brain Total RNA catalogue #AM7962). SmallRNA-sequencing (smallRNAseq) was performed by single-end sequencing on Illumina NextSeq550 platform on High Output 1x50pb RUN (NextSeq 500/ 550 High Output v2 75 cycles kit, FC-404-2005).

value: Plasma

tag: Sex

value: Female

tag: genotype 1

value: Cushing's syndrome

tag: genotype 2

value: No Sarcopenia


title: 1760

value: Healthy subjects


title: TJ3, WES

description: WES

value: Mix background


title: TI1, WES

description: WES


title: 1757

value: Sarcopenia


title: BHK-21 cells, repRNA-v4, bio_rep 1, 12h

description: no

value: BHK-21 WT, transfected with repRNA-v4


title: 1758


title: 1756


title: 1750


title: TJ2, WES

description: WES


title: 1751


title: HIKHOM1 Fibroblasts, Gen6

city: Aurora

first: Kevin

last: Ess

state: Co

address: 12700 East 19th Avenue

department: Pediatrics

institute: University Colorado Denver

data_processing:
paired-end reads were obtained from Illumina NovaSeq6000 PE150 Sequencing
pyrpipe v0.0.5
sequence adapters were trimmed with Trimgalore v0.6.6
sequences were aligned with STAR v2.7.7a to the Genome Reference Consortium Human Build 38 patch release 14 (GRCh38.p14)
alignments were assembled with StringTie v2.14 and the GRCh38.p14 NCBI RefSeq annotation assembly (GCF_000001405.40)
gene reads were extracted with prepDE.py provided by Johns Hopkins University Center for Computational Biology
Assembly: GRCh38.p14
Supplementary files format and content: CSV files of gene IDs and raw reads

source_name: Fibroblasts

growth_protocol: Skin biopsies were plated in DMEM high glutamine with 10% FBS and Pen/Strep. Biopsies were incubated at 37C and 5% CO2

extract_protocol:
RNA was extracted from fibroblasts using the Qiagen RNAeasy Kit (Qiagen 74104) and Qiagen RNA-free DNase kit (Qiagen 79254)
Stranded mRNA (polyA-selected) library preparation kit

treatment_protocol: Biopsy was passaged 6 to 16 times, extracted fibroblasts were plated or frozen

value: Fibroblasts

value: HIKHOM

value: 6th Generation, 190 days from biopsy


title: HIKHet2 Fibroblasts, Gen6

value: HIKHet

value: 6th Generation, 159 days from biopsy


title: 1748


title: 1746


title: TD4, WES

description: WES

value: Mouse intestinal tumor


title: 1745


title: 1747


title: 1749


title: TD3, WES

description: WES


title: 1743


title: KRAS_DNA

description: No

value: kidney

value: fibroblast cells

value: expressing replicative RNA repRNA-v4-KRAS (S17N)

value: No


title: HIKHet2 Fibroblasts, Gen1

value: 1st Generation, 9 days from biopsy


title: 1744

value: Plasma

value: Female


title: HIKHOM1 Fibroblasts, Gen16

value: 16th Generation, 473 days from biopsy


title: TD2, WES

description: WES

value: Mix background


title: TD1, WES

description: WES


title: 1742

value: Healthy subjects

value: No Sarcopenia


title: DOHH2,TSN 50nM 2

city: Chengdu

first: Qian

last: Hu

address: No.37 Guoxue Alley, Wuhou District

department: Hematology

institute: West China Hospital

data_processing:
Perform quality control by processing raw reads with fastp to obtain clean, high-quality data for all downstream analyses.
Download the reference genome and annotation files. Use Hisat2 v2.0.5 to build the genome index and align paired-end clean reads, leveraging its ability to generate splice junction databases for better mapping results.
Use featureCounts v1.5.0-p3 to quantify gene expression levels by counting the number of reads mapped to each gene.
Evaluate differential gene expression between TSN-treated groups and the solvent control using the 'DESeq' package. Identify significantly differentially expressed genes with an adjusted p-value < 0.05 and |Log2-fold change| > 1.
Assembly: Download the reference genome and annotation files from the genome website. Build the genome index and align paired-end clean reads using Hisat2 v2.0.5.
Supplementary files format and content: The submitted document is a text file containing counts matrices of gene expression for each sample.

extract_protocol:
RNA was extracted using Magzol reagent (Magen, China) according to the manufacturer's instructions. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.
The RNA libraries for RNA-seq were prepared  using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) following the manufacturer’s instructions.

value: diffuse large B-cell lymphoma

value: 50nM toosendanin


title: DOHH2,TSN 50nM 3


title: 1740


title: DOHH2,TSN 50nM 1


title: 1741


title: HIKHOM1 Fibroblasts, Gen1

value: Fibroblasts

value: HIKHOM

value: 1st  Generation, 71 days from biopsy


title: PBMC, scRNAseq

description: Custom inDrop

data_processing:
The demultiplexing, barcode processing, gene count matrix and aggregation were made by dropEst method (https://github.com/kharchenkolab/dropEst).
Assembly: mm10, hg38
Supplementary files format and content: Tab sepatated value files and matrix files

source_name: Peripheral blood from mouse

extract_protocol:
Freshly collected tissues or cel lines were dissociated using TrypLE at 37 C and neutralized using serum containing buffer, followed by cold PBS wash (3x). Re-suspended single cells were encapsulated using custom inDrop platform, as mentioned in supplemental method section of the paper.
Library was performed according to modified inDrop protocol using TruSeq methods (inDrop V2, PMID: 32616006). Please check the supplemental method section for further details.

value: Peripheral blood from mouse


title: TJ1, WES

description: WES

value: Mouse intestinal tumor


title: DOHH2,TSN 25nM 2

value: 25nM toosendanin


title: 1739

value: Cushing's syndrome

value: Sarcopenia


title: 1738


title: 1737


title: ApcMin_Tumor, scRNAseq

description: Custom inDrop

source_name: Small intestine

value: Small intestine


title: DOHH2,TSN 25nM 1


title: 1735

value: Plasma


title: Duo_MC3, scRNAseq

description: Custom inDrop

source_name: Duodenum

value: Duodenum


title: DOHH2,Ctrl 3

value: solvent control


title: 1733

value: Female


title: Duo_MC2, scRNAseq

description: Custom inDrop

value: Mix background


title: 1732

value: No Sarcopenia


title: DOHH2,Ctrl 2

value: diffuse large B-cell lymphoma


title: DOHH2,Ctrl 1


title: Duo_MC1, scRNAseq

description: Custom inDrop


title: 1729


title: Embryo1_E14.5, scRNAseq

description: Custom inDrop

source_name: Fetal gut

value: Fetal gut


title: 1727


title: Embryo2_E9.5, scRNAseq

description: Custom inDrop

source_name: Whole embryo

value: Whole embryo


title: PBMC_rep4_BCR

city: Cambridge

first: Darrell

middle: J.

last: Irvine

state: MA

address: 77 Massachusetts Ave

institute: Massachusetts Institute of Technology

data_processing:
The demultiplexing, barcoded processing, and gene counting were done using the 10x Genomics Clound Analysis with the Cell Ranger Count v7.1.0.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values and matrix files

source_name: PBMC

extract_protocol:
A commercially purchased vial of human PBMC was thawed, washed, and split in half. Half of the vial were split into 4 replicates for subsequent analysis by single cell RNA sequencing. The other half of PBMC were enriched for B cells using immunomagnetic selection and then split into 4 replicates for subsequent analysis by single cell RNA sequencing.
Library was performed according to the manufacter's instruction (single cell 3` v3 protocol, 10x Genomics).

value: PBMC


title: 1725

value: Healthy subjects


title: Embryo1_E9.5, scRNAseq

description: Custom inDrop


title: 1723


title: 1736


title: PBMC_rep2_BCR


title: 1721


title: 1719


title: PBMC_rep3_BCR


title: 1722


title: 1734


title: 1720


title: Embryo2_E8.5, scRNAseq

description: Custom inDrop


title: PBMC_rep1_BCR


title: Embryo1_E7.75, scRNAseq

description: Custom inDrop


title: 1730


title: PBMC_Bcell_rep4_BCR

value: B cell


title: NCI-H2052, NF1 mutant, VT107, R2

city: Melbourne

first: Kieran

last: Harvey

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description:
H2052_sgNF1 TEADi RNAseq.tsv
Column name in processed data file: AK-NF1-TEADi-R2_sorted.bam

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for Nextseq
Reads were aligned to human genome (hg19)
Assembly: Hg19
Supplementary files format and content: counts matrix generated from Galaxy, in tsv and txt formats

growth_protocol: Grown in RPMI+10% FBS at 37⁰C and 5% CO2

extract_protocol:
Trizol-based extraction of RNA
PCR-based library preparation with indexing

treatment_protocol: 1uM VT107 or the equivalent %(v/v) DMSO for 24 hours

value: Pleural mesothelioma

value: NF1 mutant

value: 1µM VT107 for 24 hours


title: NCI-H2052, NF1 mutant, VT107, R3

description:
H2052_sgNF1 TEADi RNAseq.tsv
Column name in processed data file: AK-NF1-TEADi-R3_sorted.bam


title: PBMC_Bcell_rep3_BCR


title: 1718

value: Cushing's syndrome


title: 40672 Fetal Aorta, Control

city: PORTLAND

first: Hillary

last: Le

state: OR

address: 3303 S Bond Ave

institute: Oregon Health & Science University

data_processing:
Raw data were checked for quality using FastQC,
trimmed using Trimmomatic,
aligned using STAR,
analyzed for differential gene expression using DESeq2 in R.
Pathway analysis was performed with STRING .
Assembly: Mmul_10
Supplementary files format and content: .csv files are the normalized counts following DESeq2 differential gene expression analysis
Supplementary files format and content: NA

organism: Macaca mulatta

source_name: Fetal Aorta

extract_protocol:
RNA was isolated using RNeasy Micro kit (Qiagen) and quality was assessed using Agilent 2100 Bioanalyzer with RNA 6000 Pico chip by Oregon Health & Science University (OHSU) Gene Profiling Shared Resource.
All samples had a RIN score above 5.0. NovaSeq short read sequencing assays (1 x 100 bp) were performed by the OHSU Massively Parallel Sequencing Shared Resource.

value: Fetal Aorta

tag: sample

value: Endothelial cells

value: Control


title: 40671 Fetal Aorta, Control


title: 1728

value: Plasma

value: Sarcopenia


title: NCI-H2052, NF1 mutant, VT107, R1

description:
H2052_sgNF1 TEADi RNAseq.tsv
Column name in processed data file: AK-NF1-TEADi-R1_sorted.bam


title: NCI-H226, VT107, R2

description:
H226_TEADivDMSO.txt
Column name in processed data file: AK-H226-TEADR2_sorted.bam


title: 40335 Fetal Aorta, THC

value: THC


title: PBMC_Bcell_rep2_BCR


title: NCI-H226, VT107, R1

description:
H226_TEADivDMSO.txt
Column name in processed data file: AK-H226-TEADR1_sorted.bam


title: PBMC_Bcell_rep1_BCR


title: NCI-H2052, VT107, R3

description:
H2052_sgNF1 TEADi RNAseq.tsv
Column name in processed data file: 17092020-H2052-TEADi-R3_sorted.bam


title: NCI-H2052, VT107, R2

description:
H2052_sgNF1 TEADi RNAseq.tsv
Column name in processed data file: 17092020-H2052-TEADi-R2_sorted.bam


title: 40229 Fetal Aorta, THC


title: NCI-H2052, NF1 mutant, control, R3

description:
H2052_sgNF1 TEADi RNAseq.tsv
Column name in processed data file: AK-NF1-DMSO-R3_sorted.bam

value: DMSO %(v/v) equivalent to 1µM VT107 for 24 hours


title: 40161 Fetal Aorta, THC


title: NCI-H2052, VT107, R1

description:
H2052_sgNF1 TEADi RNAseq.tsv
Column name in processed data file: 17092020-H2052-TEADi-R1_sorted.bam


title: PBMC_rep4


title: PBMC_rep3


title: PDX3_PC106_Vehicle_HTO

city: New York

first: Anupriya

last: Singhal

state: New York

address: 1275 York Avenue

institute: Memorial Sloan Kettering

library_source: other

data_processing:
Raw sequencing data from cDNA and hash libraries was demultiplexed and aligned with the 10X Genomics Cell Ranger pipeline (v.7.2.0).  For mouse experiments, data was aligned to a custom GRCm38/mm10 reference genome including the tdTomato transgene used in this study. For human PDX experiments, data was aligned to a combined human (GRCh38) 2020-A and GRCm38/mm10 reference genome. Processing and quality control of single cell data. All downstream analysis was performed in Python using the scanpy analysis package and custom scripts. scRNA-seq data from treated and control replicates were dehashed and compiled into a combined count matrix. Cells with less than 500 Unique molecular identifiers (UMIs), more than 15% mitochondrial UMIs, and low complexity (based on number of detected genes vs. number of UMIs) were removed. For PDX analyses, cells with primarily mouse RNA expression were removed. The human gene MALAT1 was also removed due to its high ubiquitous expression in all single cell RNA-seq datasets.  Biological replicates were identified using a custom algorithm for assigning hashes. This algorithm uses gaussian mixture model (GMM) to define background counts from true counts.  Cells were assigned to biological replicates based on this model, and doublets were removed. Each dataset was normalized with scanpy function normalize_total with target_sum=1e4, and then logp1 transformed. Cancer cells were identified by removal of cell populations expressing immune markers (PTPRC) and fibroblasts (DCN). For studies using mouse models, identification of relevant cell clusters was further refined by detecting the expression of cancer cell-line specific transgenes (tdTomato)
Assembly: human (GRCh38) 2020-A and GRCm38/mm10
Supplementary files format and content: MousePDAC.h5ad, PC69_PDX1.h5ad, GA60_PDX2.h5ad, PC106_PDX3.h5ad

molecule: protein

source_name: Pancreas

growth_protocol: Orthotopic transplantation of cells into NSG mice

extract_protocol:
Tumor dissociation to single cells followed by FACS sorting of live, non-immune cells
Sorted cell suspensions were prepared for scRNA-seq using the 3′ v3 10X Genomics Chromium platform

treatment_protocol: MRTX1133 vs. vehicle

value: Pancreas

value: Pancreatic Cancer

value: Vehicle


title: NCI-H2052, NF1 mutant, control, R2

description:
H2052_sgNF1 TEADi RNAseq.tsv
Column name in processed data file: AK-NF1-DMSO-R2_sorted.bam


title: PBMC_rep2

value: PBMC


title: 40125 Fetal Aorta, Control


title: NCI-H2052, NF1 mutant, control, R1

description:
H2052_sgNF1 TEADi RNAseq.tsv
Column name in processed data file: AK-NF1-DMSO-R1_sorted.bam


title: NCI-H226, VT107, R3

description:
H226_TEADivDMSO.txt
Column name in processed data file: AK-H226-TEADR3_sorted.bam


title: PDX3_PC106_Vehicle_RNA


title: NCI-H226, control, R3

description:
H226_TEADivDMSO.txt
Column name in processed data file: AK-H226-DMSOR3_sorted.bam


title: PDX3_PC106_MRTX_HTO


title: PBMC_rep1


title: 39627 Fetal Aorta, Control


title: 39626 Fetal Aorta, Control


title: PDX3_PC106_MRTX_RNA


title: NCI-H226, control,R2

description:
H226_TEADivDMSO.txt
Column name in processed data file: AK-H226-DMSOR2_sorted.bam


title: 39625 Fetal Aorta, THC


title: NCI-H226, control,R1

description:
H226_TEADivDMSO.txt
Column name in processed data file: AK-H226-DMSOR1_sorted.bam


title: PDX2_GA60_Vehicle_RNA


title: PDX2_GA60_Vehicle_HTO


title: PBMC_Bcell_rep2


title: 40672 Umbilical Vein, Control

source_name: Umbilical Vein

value: Umbilical Vein


title: 40160 Fetal Aorta, THC


title: NCI-H2052, control,R3

description:
H2052_sgNF1 TEADi RNAseq.tsv
Column name in processed data file: 17092020-H2052-DMSO-R3_sorted.bam


title: 40672 Umbilical Artery, Control

source_name: Umbilical Artery

value: Umbilical Artery


title: PDX2_GA60_MRTX_HTO


title: Dox EXOSC10

data_processing:
Partek
Sequence reads were aligned using STAR - 2.7.8a tool in Partek.
Sequence reads were quantified to Ensembl Transcripts annotation model with strict paired-end compatibility and a minimum 100% read overlap with feature using Partek.
Read count extraction and and normalization were performed using Partek.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw count for each sample

growth_protocol: LM2-4175 cells were maintained in DMEM plus 10% FBS, 1x antibiotics,  plasmocin prophylactic,  6 ug/mL puromycin, and 1000 ug/mL hygromycin in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Qiazol (Qiagen). 500ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNAseq were constructed using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocol.

treatment_protocol: Dox-treated cells were incubated with 5 ug/mL doxycycline for 48 hrs prior to anaylsis.

value: Cancer cell

value: a dox-inducible CerS4 construct

value: 5 ug/mL doxycycline for 48 hrs


title: PBMC_Bcell_rep1

value: B cell


title: PDX2_GA60_MRTX_RNA


title: 40671 Umbilical Vein, Control


title: PBMC_Bcell_rep4


title: Dox IgG


title: NCI-H2052, control,R1

description:
H2052_sgNF1 TEADi RNAseq.tsv
Column name in processed data file: 17092020-H2052-DMSO-R1_sorted.bam

value: Pleural mesothelioma


title: PDX1_PC69_Vehicle_HTO


title: 40671 Umbilical Artery, Control

value: Endothelial cells


title: 40335 Umbilical Vein, THC


title: No Dox IgG

value: no dox


title: No Dox EXOSC10


title: CO-LPS-2_5,scRNAseq

city: Cheongju-si

first: Dayeon

last: Gil

state: Chungcheongbuk-do

address: 202 Osongsaengmyung 2-ro, Heungdeok-gu

department: Division of intractable disease research

institute: Korea national institute of health

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/5.0/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung organoid co-cultured with macrophage,LPS-treated

extract_protocol:
The matrigel was gently removed by pipetting and spinning down liver organoids, and the organoids were then washed with co-culture media. Organoids were chopped into pieces and collected. Organoid fragments were repeatedly incubated and pipetted following TrypLE addition, and washed with co-culture media to make single cells. Following LUNA-fl cell counting, libraries for scRNA-seq were created in a 10x Chromium platform.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, single cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.


title: CO-LPS-1_6,scRNAseq

description: 10x Genomics

value: Lung organoid co-cultured with macrophage,LPS-treated


title: PDX1_PC69_MRTX_HTO


title: 40335 Umbilical Artery, THC


title: CO-NT_4,scRNAseq

description: 10x Genomics

source_name: Lung organoid co-cultured with macrophage


title: NCI-H2052, control,R2

description:
H2052_sgNF1 TEADi RNAseq.tsv
Column name in processed data file: 17092020-H2052-DMSO-R2_sorted.bam


title: 40229 Umbilical Vein, THC


title: PDX1_PC69_MRTX_RNA


title: BEAS2B_veh-2

city: Denver

first: Sarah

last: Sasse

state: CO

address: 1400 Jackson St., K720

department: Medicine

institute: National Jewish Health

data_processing:
Paired-end Micro-C data were analyzed using the HiC-Pro(v. 2.11.4) pipeline (PMCID: PMC4665391), which independently aligns R1 vs R2 reads to the hg38 reference genome using bowtie2 (v. 2.2.9) in end-to-end mode. Prior to inputting raw fastq data into HiC-Pro we merged R1 and R2 reads from each replicate, respectively.
HiC-Pro then filters for valid interactions within specified bins of the genome using samtools (v. 1.1), python (v. 2.7), and the python packages bx-python (v. 0.8.9), scipy (v. 1.2.3), pysam (v. 0.16.0.1) and pandas (v. 0.24.2) to generate raw contact counts between corresponding pairs of loci, output as a single, non-normalized bedGraph coverage file. HiC-Pro was configured to remove all singleton, multimapped, and duplicate reads, and binned reads at 1 kb intervals, in accordance with the highest suggested resolution for Micro-C.
To account for systematic biases inherent in chromatin conformation assays, contact counts were normalized using the iced normalization package (v. 0.5.7).
Assembly: hg38
Supplementary files format and content: A single non-normalized bedGraph coverage file output by HiC-Pro, containing the filtered contact counts between indicated interacting genomic loci, representing combined data from both replicates and read pairs (R1 and R2).
Library strategy: Micro-C

source_name: BEAS-2B airway epithelial cells

growth_protocol: BEAS-2B cells obtained from ATCC were cultured in Dulbecco’s Modified Eagle Medium (DMEM) containing L-glutamine and 4.5 g/L glucose and supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
Micro-C was performed as described by Hsieh et al (PMCID: PMC7703524). The cell pellet was resuspended in Micro-C Buffer #1 (MB #1: 50 mM NaCl, 10 mM Tris-HCl-pH 7.5, 5 mM MgCl2, 1 mM CaCl2, 0.2% NP-40, 1X Protease Inhibitor Cocktail) and immediately divided equally into 2 replicate samples containing ~10 million cells each prior to incubation on ice for 20 min to release intact nuclei. Chromatin was fragmented using Micrococcal Nuclease (New England Biolabs) at a final concentration of 2000 gel units/ml (1:1000 dilution) in MB #1 and incubating at 37°C for 20 min with shaking at 850 rpm. Fragmented chromatin ends were repaired, blunted and biotinylated using biotin-ATP and -CTP (obtained from Axxora) and crosslinked nucleosomes were ligated by T4 DNA Ligase (New England Biolabs) for 2.5 hr at room temperature. Fragment ends were cleaned with Exonuclease III (New England Biolabs) and crosslinks were reversed by overnight incubation in 2 mg/ml Proteinase K (Sigma) in 1% SDS at 65C. Chromatin was then phenol:chloroform:isoamyl alcohol extracted, ethanol precipitated, treated with RNase A (Invitrogen), and purified with a DNA Clean and Concentrator-5 Kit (Zymo) prior to separation on a 3.5% NuSieve Agarose Gel (Lonza). The band containing the ligated di-nucleosomal DNA (~250-400 bp) was excised from the gel and DNA purified for library preparation using a ZymoGel Purification Kit (Zymo).
Biotinylated di-nucleosomal DNA was captured using DYNAL MyOne Dynabeads Streptavidin C1 (Invitrogen) and used as input for the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs), which includes standard procedures for end-repair, A-tailing, and adaptor ligation. Five cycles of initial library amplification employing KAPA HiFi HotStart ReadyMix (KAPA Biosystems) and Multiplex Oligos for Illumina, Index Primers Set 1 (New England Biolabs; for i7 barcoding) were followed by quantitative PCR assessment of 10% of the pre-amplified product to determine the lowest number of additional PCR cycles for sufficient final library amplification with minimal PCR duplication. Pre-amplified libraries underwent 8 additional cycles of amplification and were then size-selected and purified using Ampure XP Beads (Agencourt) at 0.9X volumes. Libraries were pooled and sequenced on an Illumina NovaSeq 6000 instrument using paired-end 2x150 bp reads by the Genomics Shared Resource at the University of Colorado Anschutz Medical Campus.

treatment_protocol: BEAS-2B cells were grown to confluence on 2 x 15 cm tissue culture plates and treated with a 1:1000 dilution of ethanol (vehicle) in fresh complete medium for 1 hr. Dual-crosslinking was sequentially performed in situ using freshly prepared 1% methanol-free formaldehyde for 10 min and disuccinimidyl glutarate (reconstituted in DMSO) at a final concentration of 3 mM for 45 min at room temperature. Cells were scraped in PBS into a conical tube and pelleted by centrifugation, then snap frozen in a dry ice/ethanol bath for storage at -80C.

value: BEAS-2B airway epithelial cells

value: vehicle (ethanol)


title: BEAS2B_veh-1


title: 40229 Umbilical Artery, THC

value: THC


title: Mouse_Vehicle_HTO

value: Pancreas

value: mTmG


title: LO_2,scRNAseq

description: 10x Genomics

source_name: Lung Organoid

value: Lung Organoid


title: iMAC-2W-CO3

description: macrophages isolated from the macrophage-contained alveolar organoid- 2 weeks post coculture

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
FPKM were calculated by using StringTie version 1.3.4d, with parameter --rf -l -o -G -A -e
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol: A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA). The libraries were quantified using KAPA Library Quantificatoin kits for Illumina Sequecing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS) and qualified using the TapeStation D1000 ScreenTape  (Agilent Technologies, Böblingen, Germany).

value: human embryonic stem cell derived macrophages co-cultured with alveolar organoids

tag: timepoint

value: 2 weeks post coculture


title: Mouse_Vehicle_RNA

value: Pancreatic Cancer

value: Vehicle


title: 40161 Umbilical Vein, THC

value: Umbilical Vein


title: PDX1_PC69_Vehicle_RNA


title: LO-1_1,scRNAseq

description: 10x Genomics


title: 40161 Umbilical Artery, THC

value: Umbilical Artery


title: Mouse_MRTX1133_HTO


title: scKPC1242_PBS_s3

city: Cold Spring Harbor

first: Jiayun

state: NY

address: 1 Bungtown Rd

department: Cancer Center

institute: Cold Spring Harbor Laboratory

data_processing:
FastQC, STAR, featurecounts and RSEM were used for data analysis with the standard setting.
Assembly: M31
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: tumor

growth_protocol: 2.5 x 10^5 KPC1242 cells were s.c. injected to C57BL/6J mice for tumor formation.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen). RNA with a RIN > 8 determined by using 2100 Bioanalyzer System with RNA 6000 Nano Kit (Agilent Technologies) was used for library preparation. 4 μg of RNA was used for the preparation.
Sequencing library was prepared using TruSeq Stranded Total RNA kit (Illumina) according to the manufacturer’s instructions, except 12 PCR cycles were used.

treatment_protocol: Mice were treated daily with 2 mg FA or PBS through oral gavage from day 8 to day 12 after tumor inoculation. Tumors were then harvested on day 14.

value: tumor

value: PDAC

value: PBS


title: Mouse_MRTX1133_RNA


title: 40160 Umbilical Vein, THC

value: Endothelial cells


title: resistant3

data_processing:
Sequencing was carried out using the Illumina novaseq-6000 instrument
Read quality was checked for each sample using FastQC v0.11.2(http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/).
StringTie software was used to calculate the FPKM value for each sample, and the values were log2 transformed.
Alignment was initially to the transcriptome (hg38)
Mapping of RNA-Seq reads were performed using STAR aligner.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: breast cacer

extract_protocol:
For RNA extraction, total RNA from each biopsies obtained as described above were isolated using the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA). RNA quality was examined by gel electrophoresis and with a Nanodrop spectrophotometer (Thermo, Waltham, MA, USA). Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), and sequencing was carried out based on the Illumina novaseq-6000 instrument. The raw data was handled by Perl and data quality was checked by FastQC v0.11.2
TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA)

value: breast cacer

value: therapeutic resistant


title: iMAC-2W-CO1

source_name: macrophages isolated from the macrophage-contained alveolar organoid- 2 weeks post coculture


title: hMDM-CD14-DR-D7-2

description: CD14 positive monocyte derived macrophage cells -Day7 differentiation into macrophage

value: human monocyte derived macrophage

value: Day7 differentiation into macrophage


title: UC_3

city: Guangzhou

first: Ruifang

last: Zhang

state: Guangdong

address: Haizhu District

institute: Guangzhou Laboratory

data_processing:
RNA-seq reads were aligned to the hg38 using RSEM, bowtie2.
Assembly: hg38
Supplementary files format and content: TPM value

source_name: hUC

growth_protocol: Pre-somatic mesoderm cells (UiPSM) were induced on day 0 to about day 10, using mixed media. Then, UiPSMs were induced to Endodermal progenitor cells (UiEPC) from day 11 to about day 20. They were induced to Hindgut endoderm (U-iHE) from day 21 to day 24, to Intestinal progenitor cells (U-iIP) from day 25 to day 31, and Intestinal organoid (U-iIO) differentiated from U-iIP from day 38.

extract_protocol: Total RNA was isolated from cells using RNA-easy Isolation Reagent (Vazyme) and 1000 ng RNA were prepared for RNA libraries construction. 1000 ng RNA were prepared for RNA libraries construction. RNA libraries were established using VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme) according to the manufacturer’s protocol.

value: hUC


title: scKPC1242_PBS_s2


title: 40160 Umbilical Artery, THC

value: THC


title: CO-NT_3,scRNAseq

description: 10x Genomics

value: Lung organoid co-cultured with macrophage


title: hMDM-CD14-DR-D7-1

source_name: CD14 positive monocyte derived macrophage cells -Day7 differentiation into macrophage


title: UC_2


title: 40125 Umbilical Vein, Control

value: Control


title: scKPC1242_FA_s3

value: Folinic acid


title: UC_1


title: scKPC1242_FA_s2


title: 40125 Umbilical Artery, Control


title: hMDM-CD14-DR-D0

description: CD14 positive monocyte derived macrophage cells -Day0 differentiation into macrophage

value: Day0 differentiation into macrophage


title: iMAC-2W-CO2

value: human embryonic stem cell derived macrophages co-cultured with alveolar organoids

value: 2 weeks post coculture


title: H9-MAC-D60-2

description: macrophages from human embryonic stem cells- 60 day maturation

value: human embyronic stem cell derived macrophage

value: 60 day maturation


title: scKPC1242_FA_s1

value: tumor

value: PDAC


title: H9-MAC-D60-1

source_name: macrophages from human embryonic stem cells- 60 day maturation


title: 39627 Umbilical Artery, Control

value: Umbilical Artery

value: Endothelial cells


title: U-iIO-1_P7

source_name: 3D hUC-derived intestinal organoid

value: 3D hUC-derived intestinal organoid


title: Ag+ CD8 T cells, aCD45-Cyt, rep5

data_processing:
RNAseq reads were aligned to the mouse genome with STAR (v2.7.9a) using ensembl GRCm39 primary assembly as the reference.
Aligned reads were quantified using RSEM (v1.3.1) with ensembl GRCm39 (release 110) transcript annotations
The resulting counts were analyzed in R using DESeq2 for differential expression analysis, fgsea for gene set enrichment analysis (GSEA), and msigDB for the gene set database
Sample A4 was removed from downstream analysis due to low input RNA quality.
Assembly: GRCm39
Supplementary files format and content: Comma-separated values file includes raw counts for each sample

source_name: Ag+ CD8 T cells, aCD45-Cyt

growth_protocol: Female C57BL/6J mice at 6-8 weeks age were purchased from The Jackson Laboratory (000664) and maintained in the animal facility at MIT.

extract_protocol:
2-40k live CD3+CD8+ CD44+p15E+ cells processed from tumor draining lymph nodes were sorted using a Sony MA900.
RNA libraries were prepared using the Clontech SMARTer Stranded Total RNA-Seq Kit - Pico Input for Mammalian cells

treatment_protocol:
Mice were injected subcutaneously in the shaved right flank with 1M B16F10 tumor cells in a volume of 50 μL PBS.
1μg IL-12 immunocytokines and 10μg IL-15 immunocytokines are both dosed intratumorally in 20 μL PBS.

value: WT

value: Live CD3+CD8+CD44+p15E+

value: Female


title: U-iIO-1_P20


title: H9-MAC-D20-2

description: macrophages from human embryonic stem cells- 20 day maturation

value: 20 day maturation


title: scKPC1242_PBS_s1

value: PBS


title: Ag+ CD8 T cells, aCD45-Cyt, rep4


title: U-iIO-1_P15


title: 39626 Umbilical Vein, Control

value: Umbilical Vein

value: Control


title: U-iIO-1_P10


title: 39626 Umbilical Artery, Control


title: MT13

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read. BBDuk was used to trim/filter low quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the human reference genome (GRCh38) was done using HISAT2 (version 2.1.0) applying --no-mixed and --no-discordant options. Read counts were calculated using HTSeq by supplementing Ensembl gene annotation (GRCh38.78).
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file containing raw read counts for each sample

growth_protocol: Human lung adenocarcinoma cell line,  NCI-H1299 was otained from American Type Culture Collection (ATCC, Manassas, VA) and grown in DMEM (GE Healthcare Life Sciences, Logan, UT), supplemented with 5% Fetal Bovine Serum (Atlanta biological, Lawrenceville, GA) and 1% GlutaMAXTM (Life Technologies, Carlsbad, CA) at 37ºC humidified 5% CO2 atmosphere incubator.

extract_protocol:
Total RNA was isolated from cell lines using RNeasy Mini kit (Qiagen, Germantown, MD) according to the manufacturer’s protocol. Optical density values of extracted RNA were measured using NanoDrop (Thermo Scientific) to confirm an A260:A280 ratio above 1.9. RNA integration number (RIN) was measured using BioAnalyzer (Agilent Technologies) RNA 6000 Nano Kit.
The cDNA libraries were prepared using the NEXTflex™ Illumina Rapid Directional RNA-Seq Library Prep Kit (BioO Scientific) as per the manufacturer’s instructions. Briefly, polyA RNA was purified from 200 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique index sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).
Pooled libraries were diluted to 2 nM in EB buffer (Qiagen) and then denatured using the Illumina protocol. The denatured libraries were diluted to 10 pM by pre-chilled hybridization buffer and loaded onto a TruSeq v2 Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.

treatment_protocol: NCI-H1299 cells were overexpressed with MTSS1 mCherry tagged plasmid (GeneCopoeia, Rockville, MD) using HEK293T stable transfection. The cells were put under hygromycin selection pressure and then sorted using BD FACS Diva8.0.1.

value: lung adenocarcinoma

tag: reporter gene expression

value: H1299 MTSS1 overexpressed


title: 39625 Umbilical Vein, THC

value: THC


title: U-iIO-1_FBS_r2


title: Ag+ CD8 T cells, aCD45-Cyt, rep2


title: MT12

value: H1299 wild type


title: 39625 Umbilical Artery, THC


title: Ag+ CD8 T cells, aCD45-Cyt, rep1


title: MT10


title: U-iIO-1_FBS_r1


title: 39627 Umbilical Vein, Control


title: Ag+ CD8 T cells, IgG-Cyt, rep5

source_name: Ag+ CD8 T cells, IgG-Cyt

value: IgG-Cyt


title: DCV injected dmostm1_KO flies

city: Kumamoto

first: Shingo

last: Usuki

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics (IMEG)

country: Japan

institute: Kumamoto University

data_processing:
Adaptor trimming and QC were done using Trim galore (v0.6.6)
21 nt reads were extracted using seqkit (v2.4.0)
Mapping of the trimmed reads on the reference genome was done using Bowtie (v1.3.1)
RNA counts were performed using featureCounts (v2.0.1)
Assembly: Ensembl Drosophila melanogaster BDGP6.32
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

organism: Drosophila melanogaster

source_name: adult females

growth_protocol: Samples 11-14 were maintained in a standard cornflour-yeast-glucose Drosophila food at 25°C.  Sample 5-10 were maintained in Scheider's Drosophila medium supplimented with 10% FBS at 25°C.

extract_protocol:
Cell lysates were prepared and immunoaffinity-purified with anti-Ago2 antibody as described in Kawamura et al. Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. Nature 453, 793–797 (2008). doi:0.1038/nature06938
Sequencing libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina

treatment_protocol: Samples 11-14:  70 nL of control saline or viral suspension (10e6 TCID50/mL) was injected into fly using Nanoject II. Flies were cultured for 24 hours and stored at -80°C until lysate preparation. Samples 5-10: dsRNA administration was carried out as described in Li & Zamore RNAi in Drosophila S2 Cells by dsRNA Soaking. Cold Spring Harb Protoc (2019). doi:10.1101/pdb.prot097477

value: adult females

value: DCV-injected


title: U-iIO-1_EGF


title: MT09


title: Ag+ CD8 T cells, IgG-Cyt, rep4


title: U-iIO-1


title: DCV injected clc-b_KO flies


title: H9-MAC-D20-1

source_name: macrophages from human embryonic stem cells- 20 day maturation

value: human embyronic stem cell derived macrophage


title: DCV injected w flies


title: Ag+ CD8 T cells, IgG-Cyt, rep3


title: Ag+ CD8 T cells, aCD45-Cyt, rep3


title: MT03


title: control saline injected w flies

value: saline injected


title: MT02


title: Gastric adenocarcinoma cells - AGS NAT10 KO-2 Input

city: GUANGZHOU

first: Min

last: Deng

state: GUANGDONG

address: Affiliated Cancer Hospital & Institute of Guangzhou Medical University, NO.78, Hengzhigang Road.

data_processing:
Cutadapt (v2.5 ) was used to trim adapters and filter for sequences
Hisat2 aligner (v2.1.0) was used to align the reads to the reference genome under parameters: “--rna-strandness RF”.
ExomePeak R package (v2.13.2) was used to identify ac4C peaks under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”.
Identified ac4C peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 12 -rna”.
Genome_build: GRCh38
Supplementary_files_format_and_content: The peak files are the results of ac4C peaks.

source_name: AGS

extract_protocol:
Total RNA was extracted from NAT10 knockout or control AGS cells using Trizol reagent, then digested with DNase I and fragmented into 100~200 nt nucleotides by RNA fragmentation reagent (Ambion). After saving 50ng fragmented RNA as input, the rest (150 μg) was used for RNA immunoprecipitation with ac4C antibody (Abcam). ac4C RNAs were immunoprecipitated with Dynabeads Protein G (Invitrogen), and purified with HiPure cell miRNA (Magen). Ribosomal RNA was removed from input RNA and ac4C-enriched RNA samples. RNA sequencing libraries for input RNA (RNA-seq) and ac4C-enriched RNA (acRIP-seq) were simultaneously constructed with the EpiTM mini longRNA-seq kit (Epibiotek), and then sequenced on the Illumina NovaSeq 6000 with two independent biological replicates.
RNA libraries were prepared for sequencing using standard Illumina6000 protocols
acRIP-seq

value: Gastric adenocarcinoma cells

value: AGS

value: NAT10 knockout

tag: rip antibody


title: Gastric adenocarcinoma cells - AGS NAT10 KO-2 IP

institute: Affiliated Cancer Hospital & Institute of Guangzhou Medical University

value: ac4C antibody (Abcam)


title: Ag+ CD8 T cells, IgG-Cyt, rep2

value: WT

value: Live CD3+CD8+CD44+p15E+

value: Female


title: Odz4-ICD Tet (+)

city: Hiroshima

first: Anqi

last: Dong

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Department of Physiology and Biophysics

institute: Hiroshima University

description: 10× Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v7.1.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: were cultured on feeder cells in ES medium (DMEM supplemented with 20% fetal bovine serum, 1× non-essential amino acids solution (Gibco), 1 mM sodium pyruvate solution (Sigma-Aldrich), 10-4 M 2-mercaptoethanol (Sigma-Aldrich), 100 units/ml penicillin-streptomycin (Gibco), and Leukemia Inhibitory Factor (1,000 U ml -1) (Wako) to maintain their undifferentiated state.

extract_protocol:
EBs cultured for 2, 2+3, 2+5, and 2+7 days were washed using HBSS by 2 times then dissociated with collagenase B for 1 hour. Then differentiation medium (DMEM supplemented with 20% fetal bovine serum, 1× non-essential amino acids solution (Gibco), 1 mM sodium pyruvate solution (Sigma-Aldrich), 10-4 M 2-mercaptoethanol (Sigma-Aldrich), 100 units/ml penicillin-streptomycin (Gibco)) was added and pipetting gentally. Dissociated cells were filted with 40um cell strainer and washed and resuspend in PBS with 0.04% BSA.
The cDNA library was prepared using the Chromium Next GEM Single Cell 5' Kit v2 for Dual Index (10× Genomics) following the protocol outlined in the 10× Genomics Single Cell Protocols and Cell Preparation Guide.

treatment_protocol: ES cells were dissociated with 0.05% trypsin-EDTA on day 0 and cultured in hanging drops (400–800 cells per 20 μl) to form embryoid bodies (EBs) for 2 days. On day 2, round EBs were selected and transferred to 24-well plates or 10-cm dishes (Falcon) for tissue culture. In the Odz4-ICD Tet (–) group, Tet (1.1 μg/ml) was removed on day 0, while in the Odz4-ICD Tet (+) group, Tet was continuously added until sample harvest to prevent gene expression.

value: ES cell


title: Ag+ CD8 T cells, IgG-Cyt, rep1


title: Gastric adenocarcinoma cells - AGS NAT10 KO-1 IP


title: Ag+ CD8 T cells, PBS, rep5

source_name: Ag+ CD8 T cells, PBS

value: PBS


title: Sample 9_dmostem-KO S2 cells without dsRNA in the medium

growth_protocol: Samples 1-4 were maintained in a standard cornflour-yeast-glucose Drosophila food at 25°C.  Sample 5-10 were maintained in Scheider's Drosophila medium supplimented with 10% FBS at 25°C.

treatment_protocol: Samples 1-4:  70 nL of control saline or viral suspension (10e6 TCID50/mL) was injected into fly using Nanoject II. Flies were cultured for 24 hours and stored at -80°C until lysate preparation. Samples 5-10: dsRNA administration was carried out as described in Li & Zamore RNAi in Drosophila S2 Cells by dsRNA Soaking. Cold Spring Harb Protoc (2019). doi:10.1101/pdb.prot097477

value: hemocyte-like


title: Gastric adenocarcinoma cells - AGS NAT10 KO-1 Input


title: T4_mcb152

city: Beijing

first: Yihan

address: No.5 Yiheyuan Road, Haidian

institute: Peking University

description: no

data_processing:
The resulting sequencing data were demultiplexed based on samples and barcodes, and the EGFP region was extracted for alignment using pbmm2 1.10.0. Mutation (mismatch) information for each sequencing read was obtained from the bam file. A custom Python script was used to quantify the mutation information at Y66 and T203 within the EGFP region.
Assembly: EGFP_PuroR.fa
Supplementary files format and content: *EGFP_aa_66_203_information.xlsx: mutation information for aa 66 and 203 of EGFP of each barcodes for each samples
Supplementary files format and content: GFP_region_mismatch_number_using_barcode_data_sorted.xlsx: frequency of mutations per sequencing reads for each samples

source_name: kidney

extract_protocol:
Each sample collected ~ 1 million cells for RNA isolation using TRIzol™ Reagent (Thermo Fisher Scientific, #15596018). 3μg genomic RNA was used for reverse transcription.
The extracted RNA was subjected to reverse transcription, followed by amplification using primers specific to genomic RNA targeting the EGFP-PuroR-barcode region. The purified PCR products underwent adapter ligation, fragment selection, primer and polymerase binding, and were then sequenced using a PacBio Sequel IIe instrument to obtain Circular Consensus Sequencing (CCS) reads.

treatment_protocol: Twenty-four hours post-electroporation (referred to as T1), the medium was replaced with fresh medium containing 5 μg/ml puromycin. After four days of selection (referred to as T5), 10 μM of molnupiravir was added to the medium for a 2-day treatment. Subsequently, the cells were allowed to grow for four days (referred to as T3) and then subjected to flow cytometry sorting. The sorted cells were cultured for approximately one week (referred to as T4) and subsequently treated with molnupiravir for another 2 days (referred to as T5).

value: kidney

value: fibroblast cells

value: harboring barcoded repRNA-v4 library

value: No


title: Gastric adenocarcinoma cells - AGS CTR-2 IP

value: control


title: Sample 7_clc-b_KO S2 cells without dsRNA in the medium


title: T5_mcb160

description: no

value: molnupiravir


title: Ag+ CD8 T cells, PBS, rep4

description: Sample A4 was removed from downstream analysis due to low input RNA quality.


title: Sample 8_clc-b_KO S2 cells with dsRNA in the medium

value: dsRNA in the medium


title: Gastric adenocarcinoma cells - AGS CTR-2 Input

value: Gastric adenocarcinoma cells


title: Sample 6_S2 cells with dsRNA in the medium

value: wild-type


title: Ag+ CD8 T cells, PBS, rep2


title: Sample 5_S2 cells withour dsRNA in the medium


title: Sample 10_dmostem-KO S2 cells with dsRNA in the medium


title: Gastric adenocarcinoma cells - AGS CTR-1 IP

value: AGS


title: Ag+ CD8 T cells, PBS, rep1


title: Ag+ CD8 T cells, PBS, rep3


title: T1_mcb94

description: no


title: T2_mcb104

description: no


title: Gastric adenocarcinoma cells - AGS CTR-1 Input


title: Odz4-ICD Tet (–)

description: 10× Genomics


title: Lgals3bp KO-IFNa2

status: Public on Jul 06 2024

city: Hwasun-gun

first: Dae-Hwan

last: Kim

state: Jeollanam-do

address: 264, Seoyang-ro, Hwasun-eup

department: Hematology and Oncology

institute: Chonnam National University Medical School and Hwasun Hospital

description: Sample 11

data_processing:
The synthesized DNA-nanoball library was quantified using a QuantiFluor DNA System
Sequencing was conducted using the MGIseq-2000 system (MGI Tech) with paired-end 150-base pair reads.
Adapter sequences and low-quality bases in the raw reads were trimmed using Skewer (0.2.2).
The remaining high-quality reads were mapped to the reference genome using STAR (2.5).
Differentially expressed genes were defined as those showing a >2-fold change between vehicle-treated and recombinant interferon alpha treated wild type or Lgals3bp KO mouse primary hepatocytes.
Assembly: mm10
Supplementary files format and content: The csv files include results for each sample

source_name: mouse liver

growth_protocol: Isolated mouse primary hepatocytes were cultured in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using a Ribospin II Kit
Total RNA (1 µg) was used to prepare an mRNA sequencing library using the MGIEasy RNA Directional Library Prep Kit

treatment_protocol: Primary hepatocytes were treated with vehicle or recombinant interferon alpha for 6h

value: mouse liver

value: mouse primary hepatocytes

value: recombinant interferon alpha


title: Lgals3bp KO-Veh3

description: Sample 09

value: veh


title: Lgals3bp KO-IFNa1

description: Sample 10


title: Lgals3bp KO-IFNa3

description: Sample 12


title: dLN-Vehicle3 mouse

first: Yuanchen

last: Ma

state: State

address: No74,Zhongshan Road2, Yuexiu District,Guangzhou,Guangdong China

institute: SYSU

data_processing:
Sequencing reads were trimmed for adaptor sequence/low quality sequence using trim_galore version 0.6.2(parameter -q 20 --length 25 -e 0.1)
Trimmed sequence reads were mapped to mm19 using hisat2 version 2.1.0
Read count extraction were performed using HTSeq version 0.11.2 (parameter -a 10 -t exon)
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: Lymph node

extract_protocol:
lymph node samples from 4 different mouse were used for the genome-wide RNA-seq analysis. TRI Reagent (TR118, Molecular Research Center, Inc.) was used to extract total RNA according to the manufacturer’s protocol.
RNA samples with an RNA integrity number > 8 were used to prepare libraries, and paired-end sequencing was performed by CapitalBio Technology (China) following a standard protocol.

value: Lymph node


title: dLN-Vehicle1 mouse


title: dLN-BrQ3 mouse


title: Wild type-Veh3

description: Sample 03


title: Wild type-IFNa1

description: Sample 04


title: Wild type-Veh2

description: Sample 02


title: Wild type-IFNa3

description: Sample 06


title: Wild type-IFNa2

description: Sample 05


title: Lgals3bp KO-Veh1

description: Sample 07


title: T3_mcb115

last: Lin

description: no


title: Wild type-Veh1

description: Sample 01


title: Hepa-1c1c7-rLgals3bp3-RNA

data_processing:
The synthesized DNA-nanoball library was quantified using a QuantiFluor DNA System
Sequencing was conducted using the MGIseq-2000 system (MGI Tech) with paired-end 150-base pair reads.
Adapter sequences and low-quality bases in the raw reads were trimmed using Skewer (0.2.2).
The remaining high-quality reads were mapped to the reference genome using STAR (2.5).
Differentially expressed genes were defined as those showing a >1.5-fold change between vehicle-treated and rLgals3bp-treated Hepa-1c1c7 cells.
Assembly: mm10
Supplementary files format and content: The csv files of results for each sample

growth_protocol: Hepa-1c1c7 cells were cultured in alpha minimum essential medium with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from Hepa-1c1c7 cells treated with vehicle or 5 µg rLgals3bp using a Ribospin II Kit
Total RNA (1 µg) was used to prepare an mRNA sequencing library using the MGIEasy RNA Directional Library Prep Kit

treatment_protocol: The 16h serum-starved Hepa-1c1c7 cells were treated with vehicle or 5ug/mL of recombinant Lgals3bp for 6h

value: Mouse Hepatoma

value: recombinant Lgals3bp


title: Hepa-1c1c7-rLgals3bp2-RNA


title: Hepa-1c1c7-rLgals3bp1-RNA


title: Hepa-1c1c7-Veh2-RNA


title: Hepa-1c1c7-Veh1-RNA


title: dLN-BrQ1 mouse


title: Liver,DMSO,Day1

city: Wuhan

first: RUI

last: Zhou

address: Donghu Road 185

institute: Wuhan University

data_processing:
Base calling of sequencing data was performed using bcl2fastq software (the software is officially delivered by illumina) to obtain fastq software.
Use fastp (v 0.19.7) fastq data for filtering to get cleandata. The main parameters are (-W 5-M 20-3-l 20-w 10).
Use the HiSat2 software (2.1.0) to compare cleandata to the reference genome with default parameters.
Use StringTie software (v1.3.4d) and annotate the result to calculate the data expression FPKM (Gene.FPKM.xls); Calculate ReadsCount (i.e. Gene.Count.xls) according to the script given by the official StringTie.
Assembly: GRCm39
Supplementary files format and content: bw

source_name: liver

growth_protocol: Male C57BL/6 mice aged 8 weeks were housed in conditions with standard temperature and humidity control and a 12 h light/dark cycle.

extract_protocol:
RNA was harvested using Trizol（Takara）. 0.5ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kit following manufacturer's protocols

treatment_protocol: Intraperitoneal injection of 0.75mg/kg Pladienolide B was given to the experimental group, while an equal volume of DMSO was given to the control group. Liver tissues were collected for histological examination 1 day after the injection.

value: liver

value: male

value: DMSO


title: Liver,PB,Day1

value: Pladienolide B


title: Hepa-1c1c7-Veh3-RNA


title: NRVMs_ad5-Adssl1_4

city: Shanghai

first: Xiaxi

address: No.197, Ruijin 2nd Road (Yongjia Intersection)

department: Department of Cardiovascular Medicine, Ruijin Hospital

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
SOAPnuke was used to remove reads containing sequencing adapters, and clean reads were saved in FASTQ format. FASTQ les were aligned against rat reference data (mRatBN7.2) using HISAT2 and STAR aligner. Read quantification was performed with featureCounts available within the Subread package. Differential expression analysis of all mapped genes was performed using DESeq2.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

source_name: Neonatal Rat Cardiomyocyte

growth_protocol: Within 1-3 d of birth, the hearts of neonatal Sprague Dawley rats were removed and cut into 1 mm3 sections. Myocardial granules were incubated in 0.04% trypsin overnight at 4℃. A cardiomyocyte-rich fraction was digested using cell digestion mixture (0.01% trypsin and 0.01% collagenase, type 2) at 37℃ for 8 min, and the supernatant suspension was stopped with DMEM with 10% fetal bovine serum (complete medium). The process was repeated 4-5 times until the myocardial tissue was completely digested. The cell suspension was cultured in complete medium for 1 h to remove cardiac fibroblasts, and cardiomyocytes were cultured in complete medium.

extract_protocol:
Total RNA was extracted from NRVMs using Trizol Reagent.
RNA sequencing libraries were prepared using the BGISEQ-500 platform (BGI, Wuhan, China).

treatment_protocol: NRVMs were isolated and cultured for 48h and adenovirus (ad5-Adssl1 and ad5-CTR; Moi = 20) was added to infect cells overnight. Fresh culture medium was added and NRVMs were cultured for 48 h.

value: Neonatal Rat Cardiomyocyte

value: Adssl1 adenovirus overexpression or adenovirus empty(Moi = 20)


title: Patient derived TANs

city: San Francisco

first: Manish

last: Aghi

state: CA

address: 505 Parnassus Avenue, #M774A

institute: UCSF

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were performed using the Cell Ranger software v6.1.2.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
Cells were purified via FACS as detailed above into Protector RNase Inhibitor, then validated for viability on a Countess automated cell counter.
Library preparation was performed as per manufacturer recommendations (single cell 3' v3 10x Genomics) for processing granulocytes.

value: Brain

value: Neutrophils


title: NRVMs_ad5-Adssl1_3


title: shKSRP-2.mRNA

description:
shKSRP HL7702 cells
RNA-20190613-RNA-20190613-shKSRP2_L1

data_processing:
bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

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

tag: genotype/variation

value: shKSRP

tag: tissue source


title: Patient derived PBNs

source_name: Blood

value: Blood

tag: cell type


title: Lgals3bp KO-Veh2

description: Sample 08

value: mouse liver


title: PBMC_Bcell_rep3

city: Cambridge

first: Darrell

address: 77 Massachusetts Ave

institute: Massachusetts Institute of Technology

data_processing:
The demultiplexing, barcoded processing, and gene counting were done using the 10x Genomics Clound Analysis with the Cell Ranger Count v7.1.0.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values and matrix files

source_name: PBMC

extract_protocol:
A commercially purchased vial of human PBMC was thawed, washed, and split in half. Half of the vial were split into 4 replicates for subsequent analysis by single cell RNA sequencing. The other half of PBMC were enriched for B cells using immunomagnetic selection and then split into 4 replicates for subsequent analysis by single cell RNA sequencing.
Library was performed according to the manufacter's instruction (single cell 3` v3 protocol, 10x Genomics).

value: PBMC

value: B cell


title: D8 NK monocultured spheroid

city: Suwon-si

first: Seokgyu

last: Han

state: Gyeonggi-do

address: 2066, Seobu-ro

department: Mechanical Engineering

institute: Sungkyunkwan univerisity

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Read count and normalized values were calculated by using StringTie version 2.1.3b, with parameter --rf -l -o -G -A -e
Assembly: GRCh38
Supplementary files format and content: tab-delimitedtextfilesincluderawreadcountandnormalizedvaluesforeachsample.

source_name: NK

growth_protocol: Patient-derived GBM spheroids were cultured in Dulbecco’s modified Eagle’s high glucose medium (SH30243.01, Hyclone) supplemented with 10% fetal bovine serum (FBS) (SH30919.03, Cytiva) and 1% penicillin straptomycin  (15140-122, Gibco).

extract_protocol:
Total RNA extraction was performed using the using QIAzol lysis reagent (Qiagen,79306 ) according to the manufacturer’s instructions
Libraries for bulk RNA-seq were prepared using the TruSeq Stranded mRNA Library Prep Kit.

value: NK


title: shKSRP-1.mRNA

description:
shKSRP HL7702 cells
RNA-20190613-RNA-20190613-shKSRP1_L1

tag: cell line


title: shNC-2.mRNA

description:
shNC HL7702 cells
RNA-20190613-RNA-20190613-NC2_L1

value: shNC


title: NRVMs_ad5_NC_3

tag: treatment


title: shNC-1.mRNA

description:
shNC HL7702 cells
RNA-20190613-RNA-20190613-NC1_L1


title: NRVMs_ad5-Adssl1_2


title: D8 MG monocultured spheroid

source_name: MG

value: MG


title: NRVMs_ad5-Adssl1_1


title: Hepa-1c1c7-rLgals3bp2-ATAC

data_processing:
The ATAC-seq libraries were quantified using a Qubit 2.0 Fluorometer.
Sequencing was conducted using an Illumina NextSeq 500 with paired-end 75-base pair reads.
Potential sequence adapters and low-quality reads were trimmed using the Skewer software. The cleaned quality reads were mapped to the reference genome using bowtie2 (2.3.2). Strand cross-correlation analysis was performed to check the suitability of ATAC-seq data for further analysis.
MACS2 (2.1) with ‘default’ or ‘broad’ parameters was used to identify the significantly enriched regions.
Motif enrichment in peaks was performed using findMotifGenome.pl in Homer (4.9)
Assembly: mm10
Supplementary files format and content: The csv files include accesible chromatin sequences of each sample

extract_protocol:
The cells were lysed and DNA was transposed simultaneously in a transposition mix. After tagmentation, the transposed DNA fragments were purified and amplified using PCR.
ATAC-seq libraries are prepared using ATAC-seq kit. The final libraries were purified using AmPure XP Magnetic Beads

value: Mouse Hepatoma

value: recombinant Lgals3bp


title: D8 GBM-MG-NK tri-cultured spheroid

source_name: GBM-MG-NK

value: GBM-MG-NK


title: Hepa-1c1c7-rLgals3bp1-ATAC


title: NRVMs_ad5_NC_1


title: D8 GBM-NK-MG tri-cultured spheroid

source_name: GBM-NK-MG

value: GBM-NK-MG


title: Hepa-1c1c7-Veh3-ATAC

value: veh


title: D5 NK monocultured spheroid


title: Hepa-1c1c7-Veh2-ATAC


title: Hepa-1c1c7-Veh1-ATAC


title: D8 GBM monocultured spheroid

source_name: GBM

value: GBM


title: Light-seq E14 mGFP midgut 4

city: Boston

first: Hasreet

last: Gill

address: 77 Avenue Louis Pasteur, NRB 360

department: Genetics

institute: Harvard Medical School

description: Columns 12, 24, 36 in processed data file

data_processing:
Light-seq barcode and UMI sequences were extracted from raw Read 1 data using the UMI-tools package
Reads were mapped to the Gallus gallus genome using STAR
QC was performed on count data using qualimap and multiqc, which showed that Hindgut replicate 1 (Sample 1 above) had an unusual featureCounts profile. This replicate was excluded from further differential expression analyses
DESeq2 was used to perform read count normalization and differential gene expression analyses
In the processed data file, each of 12 samples includes the 3 tissue types listed above, resulting in 36 columns. Only "InnerMes" was used for Figure S7 of the associated manuscript.
Assembly: GRCg6a
Supplementary files format and content: .csv Excel file includes raw counts for each sample at e14, where columns indicate tissue origin inferred from read barcodes

organism: Gallus gallus

source_name: Intestinal mesoderm

growth_protocol: Chicken embryos were incubated at 38 degrees Celsius

extract_protocol:
in situ reverse transcription was used to generate cDNA from tissue sections on slides, which was displaced from RNA via incubation for 45min in a solution containing RNaseH (NEB) and 10X Thermopol buffer
RNA-seq libraries were constructed using the Nextera XT Library Preparation Kit, following the manufacturer's protocol

treatment_protocol: in ovo electroporation of retroviral constructs--RCAS-mGFP and RCAS-Hoxd13--into midgut-level splanchnic lateral plate mesoderm at HH17

tag: tissue

value: Intestinal mesoderm

value: subepithelial mesenchyme (InnerMes in processed data file), inner longitudinal muscle (MuscMuco in processed data file), inner superficial circumferential muscle (InnerCirc in processed data file)

tag: genotype

value: RCAS-mGFP

value: RCAS-mGFP electroporation into splanchnic LPM at HH17


title: old_thc_d_4

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

data_processing:
Adaptor trimming with cutadapt
Quantification using Salmon 0.8.1v
DESeq2 normalization
Assembly: Gencode vM17 mouse assembly
Supplementary files format and content: Transcript length count and count per million (TPM)

source_name: hippocampus

extract_protocol:
phenol-chloroform extraction
TruSeq RNA library v2

treatment_protocol: intraperitoneal injection of either THC:ethanol:cremophor:saline vehicle (THC dose of 0.002 mg/kg; THC donated by Prof. Mechoulam, the Hebrew University, Jerusalem) or a THC-free vehicle solution in a single administration, in a total volume of 0.1 mL/10 g bodyweight.

value: hippocampus

tag: type

value: fastq


title: old_thc_d_3


title: CCl4 24 h 3

data_processing:
bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: CCl4 injected mouse livers

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

value: CCl4 injected

value: liver


title: Hepa-1c1c7-rLgals3bp3-ATAC


title: Light-seq E14 mGFP midgut 2

description: Columns 6, 18, 30 in processed data file


title: D5 MG monocultured spheroid


title: NRVMs_ad5_NC_2

value: Neonatal Rat Cardiomyocyte

value: Adssl1 adenovirus overexpression or adenovirus empty(Moi = 20)


title: D5 GBM-NK co-cultured spheroid

source_name: GBM-NK

value: GBM-NK


title: Light-seq E14 mGFP midgut 1

description: Columns 3, 15, 27 in processed data file


title: old_thc_d_2


title: CCl4 24 h 1


title: U-iIO-2

data_processing:
RNA-seq reads were aligned to the hg38 using RSEM, bowtie2.
Assembly: hg38
Supplementary files format and content: TPM value

source_name: 3D hUC-derived intestinal organoid

extract_protocol: Total RNA was isolated from cells using RNA-easy Isolation Reagent (Vazyme) and 1000 ng RNA were prepared for RNA libraries construction. 1000 ng RNA were prepared for RNA libraries construction. RNA libraries were established using VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme) according to the manufacturer’s protocol.

value: 3D hUC-derived intestinal organoid


title: Light-seq E14 Hox midgut 4

description: Columns 11, 23, 35 in processed data file

value: RCAS-Hoxd13 electroporation into splanchnic LPM at HH17


title: old_thc_4


title: old_thc_d_1


title: Normal 3

source_name: mouse livers


title: D5 GBM-MG co-cultured spheroid

source_name: GBM-MG

value: GBM-MG


title: Light-seq E14 Hox midgut 3

description: Columns 8, 20, 32 in processed data file


title: D5 GBM monocultured spheroid


title: Light-seq E14 mGFP midgut 3

description: Columns 9, 21, 33 in processed data file


title: old_thc_3


title: D2 NK monocultured spheroid

value: NK


title: old_thc_2


title: D2 MG monocultured spheroid

value: MG


title: Light-seq E14 Hox midgut 2

description: Columns 5, 17, 29 in processed data file


title: Normal 2


title: Light-seq E14 Hox midgut 1

description: Columns 2, 14, 26 in processed data file


title: D2 GBM monocultured spheroid

value: GBM


title: old_thc_1


title: shKSRP-GFP+2

description:
shKSRP-GFP+2 mouse primary hepatocytes
RNA-210222-RNA-210222-shksrp-GFP+2_L4

data_processing:
bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

value: mouse primary hepatocytes

value: shKSRP-GFP+


title: Light-seq E14 mGFP hindgut 4

description: Columns 10, 22, 34 in processed data file

value: Intestinal mesoderm

value: subepithelial mesenchyme (InnerMes in processed data file), inner longitudinal muscle (MuscMuco in processed data file), inner superficial circumferential muscle (InnerCirc in processed data file)

value: RCAS-mGFP


title: old_control_4

value: hippocampus

value: vehicle

value: fastq


title: CCl4 24 h 2

value: CCl4 injected

value: liver