title: TSC_RNAseq_rep1

description:
ESC_and_TSC_tpm_gene_counts_matrix.tsv
Biological replicate 1 of 2.

data_processing:
Adaptor sequences and low-quality reads were excluded using Trimmomatic (version 0.36) (Bolger et al., 2014). RNA-seq reads were aligned to mouse genome (mm10) using HISAT2 command (version 2.1.0) with default parameters (Kim et al., 2015). The read counts for all RefSeq genes were calculated using featureCounts command (version 1.6.2) with default parameters, whereas expression levels were quantified to transcripts per million (TPM) using StringTie command (version 2.1.1) (Liao et al., 2014; Pertea et al., 2015) .
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

extract_protocol: RNeasy Mini Kit (Qiagen #74134) was used for RNA extraction according to manufactures instruction. RNA-seq library preparation and sequencing were performed at Macrogen Japan Corporation. Briefly, libraries were prepared using TruSeq stranded mRNA Library (Illumina #20020594), then sequenced by NovaSeq6000 for paired-end 100 bp.

tag: strain

value: hybrid C57BL/6 / DBA2

value: TSC


title: gastric cancer cells AGS_cell_rep2

status: Public on Mar 14 2022

type: SRA

city: Fuzhou

first: Sheng

last: Zhang

state: Fujian

address: 20 Cha Zhong Lu

department: Department of Pathology

country: China

institute: The First Affiliated Hospital of Fujian Medical University

description: non-coding RNA

library_source: transcriptomic

data_processing:
remove adapter, poly Ns, reads samller than 17 nts with fastqc
using miRDeep2, we align clean reads against sequences in miRBase22 library to predict known miRNA expression.
The expression levels were normalized to RPM (Reads per Million), that is number of reads mapping to miRNA/ number of reads in Clean data)×1000000
Differential expressed miRNAs were calculated using edgeR, and filtered using |log2(Fold Change)| >= 1 and p-value < 0.05
Assembly: miRBase22(reads were blasted directly against library)
Supplementary files format and content: comma seprated values; expressions of human miRNAs in RPM
Supplementary files format and content: comma seprated values; expressions of EBV miRNAs in RPM

molecule: total RNA

organism: Homo sapiens

source_name: gastric epithelial cells

growth_protocol: SNU-719 (EBV positive gastric cancer cell line) and AGS (EBV negative gastric cancer cell line) were cultured in RPMI-1640 and F12, respectively. 5% fetal bovine serum without exosomes and penicillin and streptomycin (100U/ mL) were added into the culture medium before use. When the cells grow vigorously (with a degree of fusion up to about 70%), the supernatant is collected.

extract_protocol:
Total RNA was extracted from cells and exosomes using the high pure RNA extraction kit (TRIzol) in accordance with the manufaxturer’s protocol. The OD260 and OD280 values and ratios of 1μL extracted samples were determined by ultraviolet spectrophotometer to determine the concentration and purity of extracted samples.
Approximately 1 μg of total RNA from each sample was used to prepare the miRNA sequencing library. The strips between 17 and 32 nt were cut by polyacrylamide gel electmphoresis（PAGE) and the products were recycled. T4 RNA ligase (Epicenter, San Diego, CA, USA) was used to connect the isolated small RNA to the 3' end and then the isolated small RNA to the 5 'end using the same method. The sRNA connected by the connector was used as the template for RT-PCR, and the single-stranded cDNA template was amplified into double-stranded cDNA, and then PCR amplification was conducted. Then the gel was cut and the target fragment library was recycled. The constructed library was used to detect quality and yield using Agilent 2100 Bioanalyzer and ABI StepOnePlus Real Time PCR System. The library with qualified quality test was sequenced.

treatment_protocol: No special treatment other than growth protocol described above was conducted.

tag: ebv status

value: negative

tag: tissue

value: Stomach

tag: treatment

value: untreated

tag: cell line

value: AGS

tag: rna population

value: whole cell


title: hESC_lung_M1

city: Chicago

first: Joyce

middle: huanhuan

last: Chen

state: IL

address: 5801 S Ellis Ave, Chicago

department: Pritzker School of Molecular Engineering

country: USA

institute: Uchicago

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v3.0.2)
Cellranger mkfastq was used for sample demultiplexing and fastq generation.
Cellranger count was used to align reads to either the 10X pre-built human reference genome (GRCh38 v3.0.0) for hESC_lung_ctrl, M1 and M2
Genome_build: 10X pre-built human reference genome (GRCh38 v3.0.0) for hESC_lung_ctrl, M1 and M2
Supplementary_files_format_and_content: matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

source_name: Lung cells and M1 macrophages co-culture

growth_protocol: The hESC line-RUES2 or H1 was cultured on irradiated mouse embryonic fibroblasts (Global Stem) at a density of 20,000- 25,000 cells/cm2 in a medium of DMEM/F12, 20% knockout serum replacement (Life Technologies), 0.1 mM β-mercaptoethanol (Sigma Aldrich) and 20 ng/ml bFGF (R&D Systems), and medium was changed daily. hESC cultures were maintained in an undifferentiated state at 37 °C in a 5% CO2/air environment until stem cells reached about 90% confluence.

extract_protocol:
Single-cell suspensions were generated by dissociating the cultured RUES2 cells with 0.05% Trypsin/0.02% EDTA for 10-15 min, followed with passing through 40µM strainer.
Single-cell capture, reverse transcription, cell lysis, and library preparation was performed using the Single Cell 3' version 2 kit and chip according to the manufacturer’s protocol (10x Genomics)

treatment_protocol: hESC differentiation into endoderm was performed in serum-free differentiation (SFD) medium of IMDM/F12 (3:1) (Life Technologies) supplemented with N2 (Life Technologies), B27 (Life Technologies), 50 μg/ml  ascorbic acid, 2 mM Glutamax, 0.4 μM monothioglycerol, 0.05% BSA at 37 °C in a 5% CO2/5% O2/95% N2 environment. hESCs were treated with Accutase (Stemcell Technologies)  and plated onto low attachment 6-well plates (Corning Incorporated), resuspended in endoderm induction medium containing 10 μM Y-27632, 0.5 ng/ml human BMP-4, 2.5 ng/ml human bFGF, 100 ng/ml human Activin A, for 72-76 hours dependent on the formation rates of endoderm cells. On day 3, the endoderm bodies were dissociated into single cells using 0.05% Trypsin/0.02% EDTA and plated onto fibronectin-coated, 24-well tissue culture plates (~100,000–150,000 cells/well). For induction of anterior foregut endoderm (AFE), the endoderm cells were cultured in SFD medium supplemented with 1.5 μM Dorsomorphin dihydrochloride (R&D Systems) and 10 μM SB431542 (R&D Systems) for 48 h, and then switched to 24 h of 10 μM SB431542 and 1 μM IWP2 (R&D Systems) treatment. For induction of early stage lung progenitor cells (day 6–15), the resulting anterior foregut endoderm was treated with 3 μM CHIR99021, 10 ng/ml human FGF10, 10 ng/ml human FGF-7, 10 ng/ml human BMP-4 and 50-60nM all-trans retinoic acid (ATRA), in SFD medium for 8–10 d. The day 10-15 cultures were maintained in a 5% CO2/air environment. On days 15 and 16, the lung progenitor cells were replated after one minute trypsinization onto fibronectin-coated plates, in the presence of SFD containing 3 μM CHIR99021, 10 ng/ml human FGF10, 10 ng/ml human FGF7, in a 5% CO2/air environment. For differentiation of mature lung cells (day 25 to 55), cultures were re-plated after brief trypsinization onto 3.3% Matrigel-coated 24-well plates in SFD media containing maturation components containing 3 μM CHIR99021, 10 ng/ml human FGF-10; 10 ng/ml human FGF-7, and DCI (50 nM Dexamethasone, 0.1 mM 8-bromo-cAMP (Sigma Aldrich) and 0.1 mM IBMX (3,7-dihydro-1-methyl-3-(2-methylpropyl)-1H-purine-2,6-dione) (Sigma Aldrich)). For macrophages polarization, 100ng/mL LPS and 10ng/mL IFNγ were added for M1 macrophage induction, or 20 ng/m IL-4 was added for M2 macrophage supplemented with 50 ng/mL M-CSF, respectively.

value: RUES2 and H1 human embryonic stem cell

tag: cell types

value: hESC-derived lung cells and M1 macrophages

tag: protocol

value: co-culture


title: TSC_RNAseq_rep2

city: Tsukuba

first: Masashi

last: Hada

state: Ibaraki

address: Koyadai 3-1-1

department: Bioresource Research Center

country: Japan

institute: RIKEN

description:
ESC_and_TSC_tpm_gene_counts_matrix.tsv
Biological replicate 2 of 2.

molecule: polyA RNA

organism: Mus musculus

source_name: Trophoblast stem cell

growth_protocol: ESC and TSC lines were established from blastocysts generated by IVF. IVF was undertaken using oocytes from C57BL/6NCrSlc female mice and spermatozoa from DBA/2 male mice or JF1/Ms male mice. For establishment of ESCs, developing blastocysts were dropped onto Acidic Tyrode (Millipore #MR-004-D) to remove zona pellucida, then transferred to ESC medium containing KnockOut DMEM (Gibco # 10829018), 15% KnockOut serum replacement (KSR, Thermo #10828028), MEM Non-Essential Amino Acids Solution (Gibco #1140050), GlutaMAX supplement (Gibco #35050061), 100 µM 2-mercaptoethanol (2-ME, Sigma-Aldrich #M-7522), ESGRO Recombinant Mouse LIF Protein (Millipore #ESG1107), 1 µM PD0325901 (Stem gent #04-0006), and 1 µM CHIR99021 (Stem gent #04-0004). These blastocysts were putted onto layers of primary mouse embryonic fibroblasts treated with mitomycin-C (MMC-MEFs). After several passages, cell lines with typical ESC colonies were picked up and used for further analysis. In the case of TSCs, developing blastocysts were directory transferred to TSC medium containing the same amount of neurobasal medium (Gibco #21103049) and Dulbecco’s modified Eagle’s medium/F12 (Ham’s) (1:1) (Gibco #11320033), N2 supplement (Gibco #17502048), B27 supplement (Gibco #17504044), GlutaMAX supplement, 150 µM 2-ME, 1 µg/ml heparin (Sigma #H3149), 0.05% bovine serum albumin (Millipore #12657), 1% KSR, 50 ng/ml recombinant mouse basic FGF (Wako #062-05181), 20 ng/ml recombinant human activin A (R&D systems #338-AC), 10 µM XAV939 (Calbiochem #575545), and 5 µM Y27632 (Wako #036-24023) onto MMC-MEFs (Hirose et al., 2018; Ohinata and Tsukiyama, 2014). After several passages, cell lines with typical TSC colonies were used for further experiment.  Established ESC and TSC lines were adapted for feeder-free conditions. Briefly, ESCs were placed onto gelatin coated dish with ESC medium in which PD0325901 and CHIR99021 were removed and 1 µM GSK-3 Inhibitor IX (Millipore #361550) was added. TSCs were placed onto the dishes coated with 15 mg/ml human plasma fibronectin (Millipore #FC010) with TSC medium (Hirose et al., 2018; Ohinata and Tsukiyama, 2014). Medium was replaced every day and cells were passaged every 2 days

tag: cell type


title: hESC_lung_ctrl

source_name: Lung cells

value: RUES2 human embryonic stem cell

value: hESC-derived lung cells

value: control


title: gastric cancer cells AGS_cell_rep1

description: non-coding RNA


title: ESC_RNAseq_rep2

value: ESC


title: shCont_TSC_H3K9me3_rep1

description:
Biological replicate 1 of 2.
shControl_H3K9me3.bw

library_source: genomic

data_processing:
Adaptor sequences and low-quality reads were excluded using Trimmomatic (version 0.36) (Bolger et al., 2014). ChIP-seq reads were aligned to the mouse genome (mm10) or human genome (hg38) using bowtie command (version 1.2.2) with “-n 2 -M 1 --best --strata” option (Langmead et al., 2009). PCR duplicates were removed by samtools rmdup command. Signal tracks for each sample were generated using deeptools (version 3.4.3) bamCompare or bamCoveraeg command with default parameters and were normalized to 1 million reads (RPKM). Signals were visualized by the Integrative Genomics Viewer (version 2.5.3) (Robinson et al., 2011b).
To identify broad domain, we first divided the genome into 100-kb consecutive bins and calculated normalized signal to 10 million reads using parse2wig command (version 3.7.0) with “-n GR -f BAM -of 3 -np 10000000 -showzero” options [ref: nakato]. Sex chromosomes were removed for further analysis. Bines with no value in input sample and less than 300 in ChIP sample were removed, then the ChIP signals were divided by the input signals using corresponding bines. Regions in which ChIP/input ration is over 2.0 (H3K9me3) or 1.5 (H3.1/H3.2) was classified as a domain.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

extract_protocol:
ChIP were performed as described previously (Harada et al., 2012). Briefly, 1x107 ESCs or TSCs were collected by trypsinization, and fixed using truChIP Chromatin Shearing Kits (Covaris #520154). Totally 2x107 cells were suspended with 2 ml of ChIP buffer (10 mM Tris-HCL pH8.0, 200 mM KCL, 1 mM CaCL2, 0.5%NP40, protease inhibitor cocktail) and incubated on ice for 5 min. Cells were sonicated using Handy Sonic (Tomy Seiko #UR-20P) with 5 sec sonication (intensity 7) and 15 sec interval for three times, then incubated with micrococcal nuclease (NEB #M0247) for 25 min at 37℃. Reaction was stopped by EDTA, then lysates were centrifuged by 15,000 rpm for 15 min at 4°C. Aliquot of supernatants were kept for input. Antibodies were pre-bounded to Dynabeads Protein G or Protein A (Invitrogen #10001D and #10004D) for at least 2 hours at 4°C with rotation. Supernatants were incubated with beads complexes at 4°C with rotation, then the immunocomplexes were washed by using ChIP buffer for 2 times, wash buffer (10 mM Tris-HCL pH8.0, 500 mM KCL, 1 mM CaCL2, 0.5%NP40, protease inhibitor cocktail) for 2 times, and TE buffer for one time. These complexes were eluted by elution buffer (10 mM Tris-HCl, 1% SDS, 5 mM EDTA and 300 mM NaCl) at 65°C for 30 min. Crosslinking was reversed by incubation at 65°C for 6 h, after which RNAs and proteins were degraded by adding RNase (Ambion #AM2286) at 37°C for 30 min and Proteinase K (Zymo Research #D3001-2) at 55°C for 2 hours, respectively. ChIPed-DNAs were purified using QIAquick PCR purification kits (Qiagen #28106).
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645) according to manufactures instructions. Single-end 65 bp sequencing was performed on a Hiseq 2500.

treatment_protocol: To establish stable TSC lines which express shRNA for LacZ and P150 by DOX dependent manner, 10 µg/ml blasticidin S (Fujifilm #026-18711) was added at next day after lentiviral infection, then cells were cultured for at least 1 week. To start knockdown, 2 µg/ml DOX was added in culture medium for two days.

value: hybrid C57BL/6 / JF1

tag: antibody


title: 48M2V_B

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
After trimming the adaptors with cutadapt (version1.18),RNA reads were aligned and mapped to the GRCh38 human reference genome plus SARS-CoV-2 genome(NC_045512.2) by STAR (Version2.5.2) , and transcriptome reconstruction was performed by Cufflinks (Version 2.1.1)
The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM)
Genome_build: GRCh38
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

source_name: H1 ESC-derived M2 macrophages

growth_protocol: H1 human ES cells were maintained in a medium of DMEM/F12, 20% knockout serum replacement, 0.1 mM β-mercaptoethanol and 20 ng/ml bFGF. Human ES cells were differentiated to mesoderm, hematopoietic progenitor cells, monocytes and macrophages using growth factor and small molecule cocktails inclduing inclduing BMP, CHIR, FGF2,VEGF,SB431542,IL3,M-CSF,etc.

extract_protocol:
Total RNA was isolated using Direct-zol RNA Miniprep kit. Following RNA isolation, total RNA integrity was checked using a 2100 Bioanalyzer. RNA concentrations were measured using the NanoDrop system.
Preparation of RNA sample library and RNA-seq were performed by the Genomics Core Laboratory at Weill Cornell Medicine. Messenger RNA was prepared using TruSeq Stranded mRNA Sample Library Preparation kit (Illumina), according to the manufacturer’s instructions.

treatment_protocol: For macrophage polarization, monocytes from differentiating day13-15 were treated with 10ng/ml IFNγ+100ng/ml LPS to genarate M1 macrophages, 20ng/ml IL4 to generate M2 macrophages,respectively. To assay SARS-CoV-2 infection on macrophages, live SARS-CoV-2 was added at MOI=0.1 for 24hrs or 48hrs.

value: H1 ESC-derived M2 macrophages

tag: genotype

value: WT

value: SARS-CoV-2 infection

tag: treatment time


title: ∆HDAC8 synthetic viability screen

city: Amsterdam

first: Angela

last: Sedeno Cacciatore

state: Noord-Holland

address: Plesmanlaan 121

department: Gene regulation

country: Netherlands

institute: Netherlands Cancer Institute

description: ∆HDAC8 synthetic viability screen

data_processing:
Insertion mapping and data analysis was performed as described in detail in (Haarhuis et al., 2017). In brief, the dataset was normalized to aggregated insertion counts of 4 HAP1 wildtype datasets (see Blomen et al., 2015 for details). A binomial test was performed for the distribution of sense and antisense orientation insertions. Genes of interest reported here were examined for the percentage of sense orientation insertions in both the ∆HDAC8 cell line generated in this study, and four previously reported wild type HAP1 datasets (Blomen et al., 2015; NCBI SRA accession no. SRP058962).
Genome_build: hg19
Supplementary_files_format_and_content: Excel sheet containing the screen results. These include the genes, amount of sense integrations, and the amount of antisense integrations in each genotype.

growth_protocol: One day prior to infection, 20 million ∆HDAC8 cells were seeded in a single T175 flask.

extract_protocol:
Cells were harvested and fixed with BD fix buffer I (BD Biosciences) for 10 min at 37°C. Cells were stained with DAPI (1 ug/ml) for 1 h at RT to visualize G1 cells. 24 million G1 haploid cells were sorted using a BD FACSAria Fusion, followed by gDNA extraction.
Library preparation as described in (Blomen et al., 2015).

treatment_protocol: To map fitness genes in ∆HDAC8 HAP1 cells, mutagenized cells were passaged for an additional 14 days after genetrap virus infection.


title: ESC_RNAseq_rep1

value: hybrid C57BL/6 / DBA2


title: shCont_TSC_input_rep2

description:
Biological replicate 2 of 2.
none

value: input


title: Zebrafish Flow Block RNA-Seq Rep2

city: PHILADELPHIA

first: Arndt

last: Siekmann

state: Pennsylvania

address: 421 Curie Boulevard, 1114 Biomedical Research Building II/III

department: Perelman School of Medicine

institute: UNIVERSITY OF PENNSYLVANIA

data_processing:
Sequencing reads were aligned to hg19 (human) or danRer10 (zebrafish) genomes
RNA-Seq. Data was mapped using TopHat2 v2.1.1. and differential gene expression analysis between flow-treated samples and static controls was performed using DESeq2. Read counts were obtained with HTSeq
ChIP-Seq. Sequencing reads from ChIP and input samples were mapped with Bowtie 2 v2.3.5. and Samtools v1.9.was used to edit the alignments. Reads were downsampled to equivalent read depth. Peak calling was performed with Genrich (https://github.com/jsh58/Genrich) applying the following parameters: genrich -v -e Y,MT -E blacklist.bed -t Sample1ChIP.bam, Sample2ChIP.bam -c Sample1Input.bam, Sample2Input.bam -o Sample.narrowPeak -k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50and peaks with FDR < 0.05 were used for further analysis.
ATAC-Seq. Sequencing reads were mapped with Bowtie2, downsampled to equivalent read depth and peak calling was performed with Genrich in ATAC-Seq mode using the following parameters: genrich -j -v -y -r -e Y,MT -E blacklist.bed -t Sample1.bam, Sample2.bam -o Sample.narrowPeak -k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50 and peaks with FDR < 0.05 were used for further analysis.
ChIP-Seq and ATAC-Seq tracks were produced with deepTools bamCoverage and normalized to sequencing depth
Assembly: hg19
Assembly: danRer10

organism: Danio rerio

source_name: Endothelial cells

growth_protocol:
HUVEC were seeded on 6-cm BTF glass plates coated with cross-linked gelatin and cultured to confluence (approximately 105 cells/cm2) in EC growth medium.
Zebrafish were grown and crossed under standard conditions

extract_protocol:
RNA for RNA-Seq was extracted with RNeasy Micro Kit (Qiagen). Cells were cross-linked with formaldehyde (final concentration 1 %) for 5 min, sonicated and the cromatin was used for H3K27ac ChIP. For ATAC HUVEC were first frozen in the medium containing 10 % DMSO and used for OMNI-ATAC after thawing. For zebrafish RNA-Seq 300 embryos per condition were collected in ice cold 10 % DMSO and kept at -80°C for 2 min. Afterwards, embryos were washed twice with 1x Hanks’Balanced Salt Solution (HBSS, Gibco, # 14185-052)and deyolked with calcium-free Ringer’s solution. Embryos were then dissociated with trypsin-EDTA (0.5 %) and collagenase type IV (50 mg/ml). The reaction was stopped by addition of FCS (5 %) andcells were collected by centrifugation at 350 g for 5 min at 4°C and washed twice with 1x HBSS followed by centrifugation. After a final wash, cells were resuspended in 1x HBSS, passed through a 40 m nylon filter to obtain a single cell suspension, which was subjected to fluorescence-activated cell sorting (FACS). EGFP positive ECs were collected in RLT buffer (RNeasy Micro kit, Qiagen).
RNA Seq libraries were prepared using TruSeq Stranded Total RNA Sample Prep with RiboZero depletion. ChIP-Seq libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina). ATAC-Seq libraries were prepared using the protocol by Buenorosto et al (Buenorosto, Nat Met, 2013)

treatment_protocol:
The maximum flow of 18 dyn/cm2 was achieved by computer-controlled cone rotation in culture medium containing 3% polyvinylpyrrolidone (PVP) within ten minutes (ramp function) and then kept constant for the required time. The experiments were perfomed in in a BioTechFlow system (BTF system; MOS Technologies) at 37°C and under constant CO2 perfusion. Static controls were incubated in a cell culture incubator.
48 hpf Tg(kdrl:H2B-EGFP)mu122 zebrafish embryos were dechorionated at 48 hours post fertilization (hpf) using pronase and treated for 4 h with nifedipine (12.5 nM, Biomol, # Cay11106) and tricaine (1.3 mM, Sigma-Aldrich, # A5040) to stop the heart beat or with a corresponding amount of DMSO as a control.

value: Flow Block for 4 h

tag: transgene


title: shCont_TSC_input_rep1

description:
Biological replicate 1 of 2.
none


title: 48M2V_A


title: Zebrafish Flow Block RNA-Seq Rep1


title: 48M1V_B

source_name: H1 ESC-derived M1 macrophages

value: H1 ESC-derived M1 macrophages


title: TSC_H3p3_rep2

description:
Biological replicate 2 of 2.
TSC_H3p3.bw


title: Zebrafish Control RNA-Seq Rep2

value: DMSO


title: 48M1V_A


title: shP150_TSC_RNAseq_rep1

description: Biological replicate 1 of 2.

data_processing:
Adaptor sequences and low-quality reads were excluded using Trimmomatic (version 0.36) (Bolger et al., 2014). RNA-seq reads were aligned to mouse genome (mm10) using HISAT2 command (version 2.1.0) with default parameters (Kim et al., 2015). The read counts for all RefSeq genes were calculated using featureCounts command (version 1.6.2) with default parameters, whereas expression levels were quantified to transcripts per million (TPM) using StringTie command (version 2.1.1) (Liao et al., 2014; Pertea et al., 2015) .
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

tag: transfection


title: shCont_TSC_RNAseq_rep2

description: Biological replicate 2 of 2.

value: shCont


title: TSC_H3p3_rep1

description:
Biological replicate 1 of 2.
TSC_H3p3.bw


title: Zebrafish Control RNA-Seq Rep1


title: 48M0V_B

source_name: H1 ESC-derived M0 macrophages

value: H1 ESC-derived M0 macrophages


title: TSC_H3p12_rep2

description:
Biological replicate 2 of 2.
TSC_H3p12.bw


title: shCont_TSC_RNAseq_rep1

description: Biological replicate 1 of 2.


title: TSC_H3p12_rep1

description:
Biological replicate 1 of 2.
TSC_H3p12.bw


title: 10_DPI

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 270 S. Russell Street

institute: Purdue University

data_processing:
all data was processed using the default parameters for 10X genomics CellRanger software to align the reads to the mouse genome and create count matrices of genes for each cell
Data was subsequently pooled and analyzed using Seurat's SCTransform() function in R
Cells with more than 15% mitochondrial reads and less than 200 UMIs were excluded from downstream analysis
Data was normalized using Seurat's SCTransform function and clusters were formed based on the top 10 PCAs
Cells were then visualized using UMAP. Current datafile is embedded in 2-dimensions. 3D embedding available upon request
Genome_build: mm10, Grc38m
Supplementary_files_format_and_content: in expression_mat.txt (contains genes as rownames and cell barcodes as colnames); cell information in cell_info.txt (contains cellBC (barcodes), corresponding timepoint (timepoint) and metacluster identity)

source_name: tibialis anterior 10 days post CTX injury SCs

extract_protocol:
GF+ SCs cells were isolated from muscle at the indicated timepoints following a published protocol (Liu et al., 2015). Cells were sorted using a live/dead stain to exclude debris or dead cells and GFP+ cells were subsequently selected and sorted for scRNA-seq
libraries were prepared following 10X Genomics protocol for v3 3' single-cell sequencing and samples were prepared for high throughput sequencing following Illumina's specifications. Prior to sequencing all samples were evaluated using an Agilent Bioanalyzer high sensitivity chip
single-cell RNA sequencing

value: tibialis anterior

value: muscle stem cells

tag: strain/genotype

value: C5BL/6; Pax7GakaCreER;sfGFP

tag: age

value: 3 months

tag: gender

value: male


title: 48M0V_A


title: shCont_TSC_H3p12_rep1

description:
Biological replicate 1 of 2.
shControl_H3p12.bw

tag: strain


title: TSC_H3K9me3_rep2

description:
Biological replicate 2 of 2.
TSC_H3K9me3.bw


title: 24M2V_A


title: TSC_H3K9me3_rep1

description:
Biological replicate 1 of 2.
TSC_H3K9me3.bw


title: Non-injured

source_name: tibialis anterior non-injured SCs


title: M2MOCK_B


title: shZRF1-2.3

type: RNA

city: Barcelona

first: Carlos

last: Jimenez

state: Barcelona

address: Pg. Vall dHebron 119-129, Edificio Collserola, lab 207

department: Pediatric Oncology

country: Spain

institute: Vall d'Hebron Institut de Recerca

hyb_protocol: Three hundred nanograms of total RNA were hybridized to Human ClariomTM S assay (Affymetrix, Santa Clara, CA, USA) arrays with the GeneChip WT Terminal Labeling Hybridization Kit (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Transcription analysis console (Applied Biosystem, version 4.0.0.25)
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: SK-N-BE(2)_pLKO-shZRF1 #3

growth_protocol: SK-N-BE(2) cells were grown in Iscove’s modified Dulbecco’s medium (Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 20% heat-inactivated fetal bovine serum (South America Premium, Biowest, Nuaillé, France) and 1% of insulin–transferrin–selenium Supplement (Life Technologies).

extract_protocol: RNA was then isolated using the miRNeasy mini kit (Qiagen, #509217004). RNA quality was evaluated using Agilent Bioanalyzer 2100 Eukaryote Total RNA Pico assay (Agilent Technologies, Santa Clara, CA).

treatment_protocol: SK-N-BE(2) cells (250000 cells per well) were seeded in 6-well plates with 1.5 ml of lentiviral supernatant produced in HEK-293T contianing pLKO-NSC or shZRF1 lentiviral particles.

value: neuroblastoma cell line

tag: genotype/variation

value: pLKO-shZRF1 #3


title: M2MOCK_A

value: H1 ESC-derived M2 macrophages


title: TSC_input_rep2

description:
Biological replicate 2 of 2.
none


title: TSC_input_rep1

description:
Biological replicate 1 of 2.
none


title: shP150_TSC_RNAseq_rep2

description: Biological replicate 2 of 2.

value: hybrid C57BL/6 / JF1


title: M1MOCK_B

value: WT


title: shZRF1-2.1

label_protocol: GeneChip WT Terminal Labeling Hybridization Kit


title: 24M1V_B

value: SARS-CoV-2 infection


title: ESC_H3p3_rep2

description:
Biological replicate 2 of 2.
ESC_H3p3.bw

source_name: Embryonic stem cell


title: 24M1V_A


title: NSC.2

value: pLKO-NSC (Non Silencing Control)


title: 24M0V_B


title: ESC_H3p3_rep1

description:
Biological replicate 1 of 2.
ESC_H3p3.bw


title: shZRF1-1.3

source_name: SK-N-BE(2)_pLKO-shZRF1 #1

value: pLKO-shZRF1 #1


title: ESC_H3K9me3_rep2

description:
Biological replicate 2 of 2.
ESC_H3K9me3.bw


title: shZRF1-1.1


title: 5_DPI

source_name: tibialis anterior 5 days post CTX injury SCs

tag: tissue


title: CMSurface_3

city: palmerston north

first: Carl

last: Mesarich

state: Manawatu-Wanganui

address: Tennent Drive

country: New Zealand

institute: Massey University

description:
conidial suspension (1 x 105 ml) incoulated on top of cellophane mebrane overalying PDA.
SS4b

data_processing:
Sequence reads (raw data) was filtered to remove reads containg adapters, reads containin N>10% and reads containing low quality (Qscore<-5) base which is over 50% of the total base.
Reads were mapped to masked V. inaequalis MNH120 genome using Hisat2 v2.2.1.
Reads mapping to fungal genome were filtered using SAMtools v.1.12 (samtools view -b -F 4)
Reads were counted using featureCounts (featureCounts -a ../ViAnnotation/ViAnnotation.gff -o ./ViCounts2 -p -B -C -T 4 -t exon -g gene_id ../HISAT2/*.mapped.bam)
Counts were normalized using DESeq2 package v1.32.0
Assembly: V. inaequalis MNH120 genome  (https://mycocosm.jgi.doe.gov/Venin1/Venin1.info.html),  masked using mappability mask (http://lh3lh3.users.sourceforge.net/download/seqbility-20091110.tar.bz2). Gene annotation used in this RNA-seq analysis can be found in the DOI:10.5281/zenodo.6233646.
Supplementary files format and content: Raw gene counts of RNA-seq reads .csv format
Supplementary files format and content: DESeq2 normalized count reads .csv format

organism: Venturia inaequalis

source_name: V. inaequalis grown on cellophane membrane surface

growth_protocol: V. inaequalis in culture grown at 20°C for 7 days (16 hour light period/day) under white fluorescent lights.

extract_protocol:
Total RNA was extracted using a Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO, USA), and DNA removed following treatment with DNase I (InvitrogenTM, Thermo Fisher Scientific, MA, USA) according to the manufacturers’ instructions. RNA concentration and purity was quantified using a Nanodrop, ND-1000 Spectrophotometer (NanoDrop Technologies, Rockland, DE). RNA integrity was assessed on the Agilent 2100 Bioanalyser (Agilent Technologies, Waldbronn, Germany) using an Agilent RNA 6000 Nano Kit in conjunction with the Agilent 2100 Bioanalyzer software according to the manufacturer’s instructions. RNA samples with an RNA Integrity Number (RIN) value of 3.5 or more, were used for sequencing.
Library preparation based on Illumina standards:After quality control, mRNA from eukaryotic organisms was enriched using oligo(dT) beads. mRNA was fragmented randomly by addings fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom and secon-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA was completed through size selection and PCR enrichment.

tag: v.inaequalis strain

value: Fungal mycelia


title: M1MOCK_A

value: H1 ESC-derived M1 macrophages

tag: treatment


title: ESC_H3p12_rep2

description:
Biological replicate 2 of 2.
ESC_H3p12.bw


title: ESC_H3p12_rep1

description:
Biological replicate 1 of 2.
ESC_H3p12.bw


title: NSC.1

tag: cell line


title: 24M2V_B


title: ESC_H3K9me3_rep1

description:
Biological replicate 1 of 2.
ESC_H3K9me3.bw


title: CMSurface_4

description:
conidial suspension (1 x 105 ml) incoulated on top of cellophane mebrane overalying PDA.
S8b


title: 24M0V_A


title: ESC_input_rep2

description:
Biological replicate 2 of 2.
none

value: input


title: CMSurface_1

description:
conidial suspension (1 x 105 ml) incoulated on top of cellophane mebrane overalying PDA.
SS1


title: CMSurface_2

description:
conidial suspension (1 x 105 ml) incoulated on top of cellophane mebrane overalying PDA.
SS3b


title: ESC_input_rep1

description:
Biological replicate 1 of 2.
none


title: M0MOCK_A

value: H1 ESC-derived M0 macrophages


title: M0MOCK_B


title: LGE Isl1 cKO replicate 4

status: Public on Mar 13 2022

city: Cincinnati

first: Jacqueline

middle: Marie

last: Ehrman

state: Ohio

address: 3332 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hopsital and Medical Center

data_processing:
RNA-seq reads were aligned to mouse genome, mm10, using STAR aligner. Raw reads counts aligned to each genes were measured using FeatureCounts.
Differential gene expression analysis was performed using EdgeR (Robinson et al., 2010) where RUVseq (RUVs, k = 1) (Risso et al., 2014) was applied to account for unwanted variables.
BigWig files were generated in read-per-million scale in a strand-specific manner, i.e. plus- and minus-bigwig file per sample.
Assembly: mm10
Supplementary files format and content: RPM-normalized bigWig files (a pair of files for plus and minus stranded per sample); an excel file containing differential analysis results and RPKM-normalized gene expression level for individual replicates

source_name: Mouse E18.5 LGE

extract_protocol:
1 ug of total RNA was used to isolate polyA RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). Samples were further enriched using Apollo NGS library prep system (Takara Bio USA).
The library was prepared using the NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs) and quantified with the NEBNext Library Quant kit (New England BioLabs). Following proportional pooling of individually indexed libraries, sequencing (single read 1x85 bp) was performed using a NextSeq 550 sequencer (Illumina)

treatment_protocol: E18.5 embryos were collected from Dlx1-cre; Isl1flx/+ x Isl1 flx/flx crosses in ice cold PBS and the LGE and a section of embryonic tail were dissected from each embryo. LGEs were stored in RNAlater (Invitrogen) and tails were used for genotyping.

value: Lateral ganglionic eminence (LGE)

tag: developmental stage

value: Dlx1-Cre; Isl1 flx/flx


title: LGE Isl1 cKO replicate 2


title: LGE Isl1 cKO replicate 1


title: LGE control replicate 3

value: Isl1 flx/flx


title: LGE control replicate 4


title: LGE control replicate 2


title: shZRF1-1.2


title: Frugivorous bats_110min

city: Kunming

first: yanni

last: zeng

state: China,Yunnan

address: No.32 Jiaochang Donglu Kunming, Yunnan,China

department: State Key Laboratory of Genetic Resources and Evolution

institute: Kunming Institute of Zoology Chinese Academy of Sciences

data_processing:
Illumina OLB_1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low-quality reads were filtered
de novo assembly was conducted using Trintiy and SOAPdenovo-Trans assemblers
Gene expression levels were measured by RSEM. In detail, for each sample, reads were mapped to the de novo transcripts (using bowtie). Based on the annotating information and mapping result, posterior mean reads counts could be reported in gene level and transcript level. RPKM (Reads Per Kilobase of exon model per Million mapped reads) value was calculated for quantifying gene expression at gene level in each sample.
The non-redundant assembled contigs were annotated to well-known ENSEMBL genes by a series of blast processes allowing RPKM values to be calculated both at transcript level and gene level. ENSEMBL ids were used to obtain gene names (or symbols) in Biomart server. Well-annotated protein sequences of the two species of bats in ENSEMBL database were the main source for annotation, but sequences from other two bat genomes published in Science in 2012 were also utilized in the analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
Genome_build: de novo contigs
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Rousettus leschenaultii

source_name: Frugivorous bats_110min

extract_protocol:
Total RNA of their whole brains was extracted using TRIzol reagent. RNA purification was performed using the Qiangen RNeasy Mini Kit.
10µg total RNA was processed via polyA selection and fragmentation, RNA libraries were prepared for sequencing using Illumina Genome Analyzer II (GA II) sequencing protocols

value: liver


title: Sxl RNAi female rep 3

city: Balitmore

first: Mark

last: Van Doren

state: Maryland

address: 3400 N Charles street, Mudd Hall

department: Biology

institute: Johns Hopkins University

data_processing:
Quality of raw reads was assessed using the fastQC kit (Babraham Institute).
RNA-Seq reads were mapped to the Drosophila genome using Ensembl BDGP6 release 85, and Bowtie 2.2.9, TopHat 2.1.1, and HTSeq 0.9.1
Differential gene expression analysis was done using DESeq using ensemble annotation BDGP6
Differential exon analysis was done using DEXSeq
Assembly: dmel 6
Supplementary files format and content: htseq output files of gene counts

organism: Drosophila melanogaster

source_name: ovary

extract_protocol:
Gonads were dissected from 1–3 day old flies raised at 25°C. Ovaries were dissected from virgin females. 3 biological replicates were dissected for each genotype. Total RNA was isolated from all genotypes using RNA-bee (Tel-Test). Contaminating DNA was removed from the RNA using Turbo-DNA-free (Ambion).
200ng of RNA was used to prepare each library using the illumina TruSeq RNA Library Prep kit v2

value: Bam mutant

value: ovary

tag: Sex

value: female

value: Sxl RNAi


title: Frugivorous bats_control

source_name: Frugivorous bats_control


title: Sxl RNAi female rep 2


title: NSC.3

tag: cell type

value: neuroblastoma cell line


title: shZRF1-2.2

value: pLKO-shZRF1 #3


title: Sxl RNAi female rep 1


title: mcherry RNAi female rep 3

value: mcherry RNAi


title: echolocator2

description: Sample 2

data_processing:
Illumina OLB_1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low-quality reads were filtered
de novo assemly was conducted using Trintiy and SOAPdenovo-Trans assemblers
reads were mapped to de novo contigs
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
Genome_build: de novo contigs
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample (abundance measurements)

organism: Hipposideros armiger

extract_protocol:
Total RNA of their whole brains was extracted using TRIzol reagent. RNA purification was performed using the Qiangen RNeasy Mini Kit.
10µg total RNA was processed via polyA selection and fragmentation,RNA libraries were prepared for sequencing using Illumina Genome Analyzer II (GA II) sequencing protocols

value: brain


title: mcherry RNAi female rep 2


title: non-echolocator2

description: Sample 7


title: mcherry RNAi female rep 1


title: Bam mutant male rep 2

source_name: testis

value: testis

value: male


title: Bam mutant male rep 3


title: Bam mutant male rep 1


title: Bam mutant female rep 3


title: Bam mutant female rep 1


title: HS-2545_L1_806D84

city: Shanghai

first: Sibo

last: Zhu

state: China

address: songhulu 2005

institute: Fudan University

data_processing:
HiSeq 2500 instrument (Illumina) and single-end 50-bp read flow cells were used in this study
Sequenced reads were trimmed for adaptor sequence by trimmomatic(v0.36), then mapped to human genome(hg19) by Hisat2(V2.0.5), and counted by featureCounts(v1.5.2)
data was filterd under the standization that a gene expressed at least in 3 cells and a cells must express at leat 200 features
Assembly: hg19
Supplementary files format and content: csv file include raw count values for each cell

growth_protocol: tissues collected were transferred into pre-warmed DMEM medium containing 2 mg/ml collagenase P (Roche) and 10 U/µl DNase I (Roche).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We gently pipetted the mixture and then digested for 60 min at 37 °C to fully release single cells. The cell suspension solution was filtered and centrifuged. The pellet was resuspended and 2 mM ethylene diamine tetraacetic acid in phosphate-buffered saline. We employed fluorescence activated cell sorting (FACS) to ensure the living cell selections.

value: TT


title: HS-2546_L1_807D84


title: HS-2547_L1_808D84


title: LGE Isl1 cKO replicate 3


title: HS-2542_L1_803D84


title: Frugivorous bats_70min

source_name: Frugivorous bats_90min


title: HS-2544_L1_805D84


title: HS-2541_L1_802D84


title: LGE control replicate 1


title: HS-2538_L1_807D83


title: HS-2539_L1_808D83


title: HS-2540_L1_801D84


title: HS-2537_L1_806D83


title: HS-2536_L1_805D83


title: HS-2535_L1_804D83


title: HS-2534_L1_803D83


title: HS-2533_L1_802D83


title: HS-2532_L1_801D83


title: HS-2530_L1_807D87


title: HS-2529_L1_806D87


title: HS-2531_L1_808D87


title: HS-2528_L1_805D87


title: HS-2527_L1_804D87


title: Bam mutant female rep 2


title: HS-2526_L1_803D87


title: HS-2523_L1_808D82


title: HS-2522_L1_807D82


title: HS-2525_L1_802D87


title: HS-2524_L1_801D87


title: HS-2543_L1_804D84


title: HS-2519_L1_804D82


title: HS-2520_L1_805D82


title: HS-2514_L1_807D81


title: HS-2517_L1_802D82


title: HS-2518_L1_803D82


title: HS-2515_L1_808D81


title: HS-2516_L1_801D82


title: HS-2513_L1_806D81


title: HS-2511_L1_804D81


title: HS-2510_L1_803D81


title: HS-2509_L1_802D81


title: HS-2507_L1_808D80


title: HS-2506_L1_807D80


title: HS-2501_L1_802D80


title: HS-2500_L1_801D80


title: HS-2504_L1_805D80


title: HS-2502_L1_803D80


title: HS-2505_L1_806D80


title: HS-2521_L1_806D82


title: HS-2458_L1_819D86

value: TP


title: HS-2459_L1_820D86


title: HS-2457_L1_818D86


title: HS-2456_L1_816D86


title: HS-2454_L1_811D86


title: HS-2455_L1_812D86


title: HS-2453_L1_810D86


title: HS-2452_L1_809D86


title: HS-2283_L1_829D80


title: HS-2279_L1_824D80


title: HS-2276_L1_821D80


title: HS-2282_L1_828D80


title: HS-2280_L1_826D80


title: HS-2275_L1_829D79


title: HS-2277_L1_822D80


title: HS-2273_L1_827D79


title: HS-2274_L1_828D79


title: HS-2508_L1_801D81


title: HS-2512_L1_805D81


title: HS-2270_L1_823D79


title: HS-2268_L1_821D79


title: HS-2269_L1_822D79


title: HS-2494_L1_803D79


title: HS-2271_L1_824D79


title: HS-2503_L1_804D80


title: HS-2499_L1_808D79


title: HS-2493_L1_802D79


title: HS-2495_L1_804D79


title: HS-2496_L1_805D79


title: HS-2498_L1_807D79


title: HS-2489_L1_806D78


title: HS-2488_L1_805D78


title: HS-2491_L1_808D78


title: HS-2487_L1_804D78


title: HS-2272_L1_826D79


title: HS-2490_L1_807D78


title: HS-2484_L1_801D78


title: HS-2492_L1_801D79


title: HS-2481_L1_806D77


title: HS-2486_L1_803D78


title: HS-2480_L1_805D77


title: HS-2278_L1_823D80


title: HS-2483_L1_808D77


title: HS-2281_L1_827D80


title: HS-2478_L1_803D77


title: HS-2497_L1_806D79


title: HS-2473_L1_806D76


title: HS-2482_L1_807D77


title: HS-2479_L1_804D77


title: HS-2472_L1_805D76


title: HS-2476_L1_801D77


title: HS-2485_L1_802D78


title: HS-2470_L1_803D76


title: HS-2471_L1_804D76


title: HS-2266_L1_828D78


title: HS-2267_L1_829D78


title: HS-2468_L1_801D76


title: HS-2263_L1_824D78


title: HS-2469_L1_802D76


title: HS-2475_L1_808D76


title: HS-2262_L1_823D78


title: HS-2264_L1_826D78


title: HS-2258_L1_828D77


title: HS-2255_L1_824D77


title: HS-2256_L1_826D77


title: HS-2253_L1_822D77


title: HS-2477_L1_802D77


title: HS-2250_L1_828D76


title: HS-2251_L1_829D76


title: HS-2249_L1_827D76


title: HS-2247_L1_824D76


title: HS-2246_L1_823D76


title: HS-2259_L1_829D77


title: HS-2242_L1_828D75


title: HS-2236_L1_821D75


title: HS-2265_L1_827D78


title: HS-2261_L1_822D78


title: HS-2252_L1_821D77


title: HS-2232_L1_826D74


title: HS-2233_L1_827D74


title: HS-2245_L1_822D76


title: HS-2239_L1_824D75


title: HS-2243_L1_829D75


title: HS-2237_L1_822D75


title: HS-2241_L1_827D75


title: HS-2240_L1_826D75


title: HS-2257_L1_827D77


title: HS-2230_L1_823D74


title: HS-2226_L1_828D73


title: HS-2474_L1_807D76


title: HS-2231_L1_824D74


title: HS-2254_L1_823D77


title: HS-2238_L1_823D75


title: HS-2234_L1_828D74


title: HS-2235_L1_829D74


title: HS-2260_L1_821D78


title: HS-2248_L1_826D76


title: HS-2223_L1_824D73


title: HS-2244_L1_821D76


title: HS-2228_L1_821D74


title: HS-2220_L1_821D73


title: HS-2451_L1_820D85


title: HS-2229_L1_822D74


title: HS-2227_L1_829D73


title: HS-2224_L1_826D73


title: HS-2225_L1_827D73


title: HS-2449_L1_818D85


title: HS-2221_L1_822D73


title: HS-2418_L1_819D82


title: HS-2444_L1_809D85


title: HS-2222_L1_823D73


title: HS-2448_L1_816D85


title: HS-2447_L1_812D85


title: HS-2416_L1_816D82


title: HS-2445_L1_810D85


title: HS-2413_L1_810D82


title: HS-2450_L1_819D85


title: HS-2414_L1_811D82


title: HS-2409_L1_818D81


title: HS-2415_L1_812D82


title: HS-2446_L1_811D85


title: HS-2412_L1_809D82


title: HS-2410_L1_819D81


title: HS-2406_L1_811D81


title: HS-2417_L1_818D82


title: HS-2419_L1_820D82


title: HS-2407_L1_812D81


title: HS-2408_L1_816D81


title: HS-2405_L1_810D81


title: HS-2402_L1_819D80


title: HS-2403_L1_820D80


title: HS-2404_L1_809D81


title: HS-2401_L1_818D80


title: HS-2395_L1_820D79


title: HS-2396_L1_809D80


title: HS-2398_L1_811D80


title: HS-2392_L1_816D79


title: HS-2394_L1_819D79


title: HS-2389_L1_810D79


title: HS-2397_L1_810D80


title: HS-2388_L1_809D79


title: HS-2393_L1_818D79


title: HS-2384_L1_816D78


title: HS-2390_L1_811D79


title: HS-2391_L1_812D79


title: HS-2386_L1_819D78


title: HS-2387_L1_820D78


title: HS-2379_L1_820D77


title: HS-2378_L1_819D77


title: HS-2385_L1_818D78


title: HS-2377_L1_818D77


title: HS-2381_L1_810D78


title: HS-2411_L1_820D81


title: HS-2380_L1_809D78


title: HS-2382_L1_811D78


title: HS-2376_L1_816D77


title: HS-2373_L1_810D77


title: HS-2374_L1_811D77


title: HS-2375_L1_812D77


title: HS-2372_L1_809D77


title: HS-2371_L1_820D76


title: HS-2400_L1_816D80


title: HS-2369_L1_818D76


title: HS-2370_L1_819D76


title: HS-2363_L1_820D75


title: HS-2365_L1_810D76


title: HS-2399_L1_812D80


title: HS-2368_L1_816D76


title: HS-2361_L1_818D75


title: HS-2362_L1_819D75


title: HS-2357_L1_810D75


title: HS-2366_L1_811D76


title: HS-2356_L1_809D75


title: HS-2352_L1_816D74


title: HS-2350_L1_811D74


title: HS-2360_L1_816D75


title: HS-2354_L1_819D74


title: HS-2355_L1_820D74


title: HS-2348_L1_809D74


title: HS-2345_L1_818D73


title: HS-2353_L1_818D74


title: HS-2359_L1_812D75


title: HS-2351_L1_812D74


title: HS-2358_L1_811D75


title: HS-2347_L1_820D73


title: HS-2349_L1_810D74


title: HS-2383_L1_812D78


title: HS-2346_L1_819D73


title: HS-2344_L1_816D73


title: HS-2343_L1_812D73


title: HS-2339_L1_829D86


title: HS-2342_L1_811D73


title: HS-2336_L1_826D86


title: HS-2364_L1_809D76


title: HS-2341_L1_810D73


title: HS-2338_L1_828D86


title: HS-2332_L1_821D86


title: HS-2335_L1_824D86


title: HS-2337_L1_827D86


title: HS-2333_L1_822D86


title: HS-2367_L1_812D76


title: HS-2443_L1_820D84


title: HS-2440_L1_816D84


title: HS-2334_L1_823D86


title: HS-2441_L1_818D84


title: HS-2439_L1_812D84


title: HS-2438_L1_811D84


title: HS-2436_L1_809D84


title: HS-2331_L1_829D85


title: HS-2330_L1_828D85


title: HS-2329_L1_827D85


title: HS-2437_L1_810D84


title: HS-2328_L1_826D85


title: HS-2326_L1_823D85


title: HS-2327_L1_824D85


title: HS-2324_L1_821D85


title: HS-2325_L1_822D85


title: HS-2321_L1_827D84


title: HS-2323_L1_829D84


title: HS-1154_L1_126

value: LTT


title: HS-2317_L1_822D84


title: HS-2322_L1_828D84


title: HS-1155_L1_127


title: HS-1150_L1_122


title: HS-1149_L1_121


title: HS-1153_L1_125


title: HS-2318_L1_823D84


title: HS-2319_L1_824D84


title: HS-2316_L1_821D84


title: HS-1147_L1_119


title: HS-1146_L1_118


title: HS-2442_L1_819D84


title: HS-1152_L1_124


title: HS-1151_L1_123


title: HS-1148_L1_120


title: HS-1142_L1_114


title: HS-1145_L1_117


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title: HS-1133_L1_105


title: HS-1132_L1_104


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title: HS-2320_L1_826D84


title: HS-1129_L1_101


title: HS-1128_L1_100


title: HS-1135_L1_107


title: HS-1127_L1_99


title: HS-1121_L1_93


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title: HS-1123_L1_95


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title: HS-1122_L1_94


title: HS-1120_L1_92


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title: HS-1119_L1_91


title: HS-1117_L1_89


title: HS-1114_L1_86


title: HS-1115_L1_87


title: HS-1126_L1_98


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title: HS-1112_L1_84


title: HS-1111_L1_83


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title: HS-1108_L1_80


title: HS-1137_L1_109


title: HS-1109_L1_81


title: HS-1107_L1_79


title: HS-1105_L1_77


title: HS-1103_L1_75


title: HS-1106_L1_78


title: HS-1104_L1_76


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title: HS-1134_L1_106


title: HS-1100_L1_72


title: HS-1101_L1_73


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title: HS-1099_L1_71


title: HS-1094_L1_66


title: HS-1093_L1_65


title: HS-1097_L1_69


title: HS-1092_L1_64


title: HS-1090_L1_62


title: HS-1118_L1_90


title: HS-1096_L1_68


title: HS-1084_L1_56


title: HS-1091_L1_63


title: HS-1081_L1_53


title: HS-1083_L1_55


title: HS-1079_L1_51


title: HS-1095_L1_67


title: HS-1102_L1_74


title: HS-1089_L1_61


title: HS-1075_L1_47


title: HS-1071_L1_43


title: HS-1070_L1_42


title: HS-1086_L1_58


title: HS-1077_L1_49


title: HS-1074_L1_46


title: HS-1078_L1_50


title: HS-1076_L1_48


title: HS-1082_L1_54


title: HS-1073_L1_45


title: HS-1088_L1_60


title: HS-1087_L1_59


title: HS-1062_L1_34


title: HS-1060_L1_32


title: HS-1058_L1_30


title: HS-1067_L1_39


title: HS-1098_L1_70


title: HS-1056_L1_28


title: HS-1085_L1_57


title: HS-1065_L1_37


title: HS-1066_L1_38


title: HS-1072_L1_44


title: HS-1059_L1_31


title: HS-1064_L1_36


title: HS-1053_L1_25


title: HS-1055_L1_27


title: HS-1080_L1_52


title: HS-1061_L1_33


title: HS-1057_L1_29


title: HS-1068_L1_40


title: HS-1049_L1_21


title: HS-1054_L1_26


title: HS-1050_L1_22


title: HS-1051_L1_23


title: HS-1052_L1_24


title: HS-1043_L1_15


title: HS-1046_L1_18


title: HS-1040_L1_12


title: HS-1038_L1_10


title: HS-1048_L1_20


title: HS-1044_L1_16


title: HS-1047_L1_19


title: HS-1069_L1_41


title: HS-1031_L1_3


title: HS-1063_L1_35


title: HS-2435_L1_820D83


title: HS-2433_L1_818D83


title: HS-2434_L1_819D83


title: HS-2432_L1_816D83


title: HS-1034_L1_6


title: HS-1035_L1_7


title: HS-1039_L1_11


title: HS-2431_L1_812D83


title: HS-1030_L1_2


title: HS-1029_L1_1


title: HS-1036_L1_8


title: HS-2427_L1_820D87


title: HS-2426_L1_819D87


title: HS-1037_L1_9


title: HS-2428_L1_809D83


title: HS-1033_L1_5


title: HS-2423_L1_812D87


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title: HS-2314_L1_828D83


title: HS-2425_L1_818D87


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title: HS-2421_L1_810D87


title: HS-2311_L1_824D83


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title: HS-2309_L1_822D83


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title: HS-2300_L1_821D87


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title: HS-2288_L1_826D81


title: HS-2294_L1_823D82


title: HS-2315_L1_829D83


title: HS-2290_L1_828D81


title: XK1292_L2_Q806608


title: HS-2286_L1_823D81


title: XK1293_L2_Q807608


title: HS-2285_L1_822D81


title: XK1288_L2_Q802608


title: XK1287_L2_Q801608


title: XK1286_L2_Q808607


title: HS-2306_L1_828D87


title: HS-2284_L1_821D81


title: XK1294_L2_Q808608


title: XK1281_L2_Q803607


title: XK1289_L2_Q803608


title: XK1291_L2_Q805608


title: XK1285_L2_Q807607


title: XK1282_L2_Q804607


title: XK1284_L2_Q806607


title: XK1283_L2_Q805607


title: XK1280_L2_Q802607


title: XK1279_L2_Q801607


title: XK1278_L2_Q808606


title: XK1276_L2_Q806606


title: HS-2289_L1_827D81


title: XK1275_L2_Q805606


title: XK1274_L2_Q804606


title: XK1277_L2_Q807606


title: XK1272_L2_Q802606


title: XK1271_L2_Q801606


title: XK1269_L2_Q807605


title: XK1268_L2_Q806605


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title: XK1270_L2_Q808605


title: XK1263_L2_Q801605


title: XK1266_L2_Q804605


title: XK1267_L2_Q805605


title: XK1261_L2_Q807604


title: XK1258_L2_Q804604


title: XK1265_L2_Q803605


title: XK1256_L2_Q802604


title: XK1257_L2_Q803604


title: XK1264_L2_Q802605


title: XK1260_L2_Q806604


title: XK1259_L2_Q805604


title: XK1255_L2_Q801604


title: XK1252_L2_Q806603


title: XK1253_L2_Q807603


title: XK1251_L2_Q805603


title: XK1250_L2_Q804603


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title: CH1361_L2_Q811605


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title: X146_L2_7146


title: X144_L2_7144


title: X147_L2_7147


title: X143_L2_7143


title: X142_L2_7142


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title: X31_L2_7031


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title: X4_L2_7004


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title: HEK293T_totalRNA_input1000ng_shortRT_minusDM_rep2

first: Christopher

middle: D

last: Katanski

state: Illinois

department: Biochemistry

institute: The University of Chicago

data_processing:
Libraries were sequenced on Illumina Hi-Seq or Nova-seq platform. First, paired end reads were split by barcode sequence using Je demultiplex with options BPOS=BOTH BM=READ_1 LEN=4:6 FORCE=true C=false 6. BM and LEN options were adjusted for samples with a 3 nt barcode instead of 4, and for samples where the barcode is located in read 2
Next read 2 files were used to map with bowtie2 with the following parameters: -q -p 10 --local —no-unal. Reads were mapped to curated list of non-redundant tRNA genes with tRNAScane score >40; mRNA was mapped to hg38 transcriptome
Bowtie2 output sam files were converted to bam files, then sorted using samtools. Next IGV was used to collapse reads into 1 nt window. IGV output .wig files were reformatted using custom python scripts (available on GitHub at https://github.com/ckatanski/MSRR-seq).
The bowtie2 output Sam files were also used as input for a custom python script using PySam, a python wrapper for SAMTools ( https://github.com/pysam-developers/pysam) to sum all reads that mapped to each gene
Data was visualized with custom R scripts (available on GitHub at https://github.com/ckatanski/MSR-seq)
Assembly: Hg19; hg38

source_name: RNA extracted from HEK293T cell culture, without AlkB demethylase treatment

growth_protocol: HEK293T cells were cultured with complete DMEM medium under standard conditions according to ATCC. Briefly, HEK293T cells were grown in Hyclone DMEM medium (GE Healthcare Life Sciences, SH30022.01) with 10% FBS and 1% Pen-Strep (Penicillin-Streptomycin) to 80% confluency and passaged. Cells were collected and total RNA was extracted using TRIzol (ThermoFisher, 15596026) by following the manufacturer’s protocol when cells reached 80-90% confluency. MCF7 cells were cultured in EMEM medium (ATCC, 30-2003) with 10% FBS (ThermoFisher, 10082147), 0.01 mg/ml bovine insulin (Sigma-Aldrich, I0516), and 10 nM β-estradiol (Sigma- Aldrich, E2758) to 80% confluency and passaged at ratios of 1:3. Total RNA were extracted using TRIzol.

extract_protocol:
Cells were collected and total RNA was extracted using TRIzol (ThermoFisher, 15596026) by following the manufacturer’s protocol when cells reached 80-90% confluency. Poly(A)-selection was done with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490S) according to manufacturer’s instructions: 1 µg of input polyA+ RNA samples and 100 ng polysome polyA+ RNA samples were used to build sequencing libraries. The RNA fragmentation and end repair steps are the same as the CMC sequencing libraries construction. Briefly, polyA+ RNA in 18 µl were added to PCR tubes and 2 µl Magnesium RNA fragmentation buffer (NEB, E6150S) was added to each tube. The tubes were incubated at 94°C in a thermocycler for 5 mins to fragment the RNA to ~200 nt. The tubes were transferred to ice and 2 µl RNA fragmentation stop solution was then added to each tube to stop the fragmentation. Samples were spun down and diluted to 50 µl using sterile H2O. The fragmented RNA was purified using Zymo RNA clean and concentrator columns and eluted in 16 µl sterile H2O. 2 µl T4 PNK buffer and 2 µl T4 PNK were added to the tubes and the tubes were incubated at 37 °C for 30 mins to repair the ends of the fragmented RNA. MSR-seq method was then used to build sequencing libraries with the fragmented RNA. Slight modifications were made to the MSR-Seq protocol. After the first ligation step, ligation reaction was quenched by adding 50 mM EDTA. Samples were combined and ligation products over 200nt long was purified using Zymo RNA clean and concentrator columns twice. Target cDNA products were purified using AMPure
Total RNA was prepared for library construction by first deacylating in a solution of 100 mM Tris-HCl, pH 9.0 at 37 °C for 30 minutes, then neutralized by addition of sodium acetate, pH 4.8 to a final concentration of 180 mM. Deacylated RNA was then ethanol precipitated and resuspended in water, or desalted using a Zymo Research Oligo Clean-and-Concentrator spin column. First bar-code ligation: Depending on the nature of the experiment described in the main text, input RNA or total nucleic acid samples were either deacylated or had undergone one-pot deacylation and β-elimination as described above. Up to 1 µg of total RNA input was used in a ligation reaction of 50 µL with the following components: 1 U/µL T4 RNA ligase I (NEB), 1x NEB T4 RNA ligase I buffer, 15% PEG 8000, 50 µM ATP, 1 mM hexaamine cobalt chloride, and 5% DMSO. After adding the ligation mix to the sample, the capture hairpin oligo (CHO, Table S5) was added to a final concentration of 1 µM and the samples were incubated at 16 °C overnight (12+ hours). Binding to Dynabeads: The ligation mixture was diluted by adding an equal volume of water to reduce the viscosity of the solution. Next, streptavidin-coated MyOne C1 Dynabeads (ThermoFisher) were added to each sample in a 1.2:1 excess over CHO (for example, a 50 µL reaction had 50 pmol capture hairpin oligo; beads were supplied at 10 mg/ml and had binding capacity of 500 pmol biotinylated oligo per mg, so use 12 µL beads). The bead-sample mixture was incubated at room temperature for 15 minutes. After binding, supernatants were removed, and the beads washed once with high salt wash buffer (1 M NaCl, 20 mM Tris-HCl, pH 7.4) and once with low salt wash buffer (100 mM NaCl, 20 mM Tris-HCl, pH 7.4). After washing, multiple individually barcoded samples can be combined for downstream steps. At this stage, enzymatic or chemical treatments can be incorporated to the library preparation protocol such as AlkB demethylase reaction or CMC treatments (see below).Dephosphorylation: A 50 µL dephosphorylation mix containing the following was added to the multiplexed sample on bead: 0.04 U/µL calf intestine phosphatase (Roche), 10 mM MgCl2, 0.5 mM ZnCl2, 20 mM HEPES, pH 7.3. The sample was incubated at 37 °C for 30 minutes. The sample was then washed once with high salt wash buffer and once with low salt wash buffer, then resuspended in 20 µL water. Reverse transcription: 5 µL of SuperScript IV VILO 5x master mix (ThermoFisher) was added to the dephosphorylated sample (final volume of 25 µL) and then incubated at 55 °C for 10 minutes. The sample was then washed once with high salt wash buffer and once with low salt wash buffer. Identical results were obtained upon extending the reaction time to 60 minutes. For overnight reverse transcription, after the initial 10 min incubation at 55 °C, the samples are further incubated at 35 °C overnight. RNase H digestion: Beads were then resuspended into 50 µL of RNase H master mix containing 0.4 U/uL RNase H (NEB) and 1x NEB RNase H buffer and incubated at 37 °C for 15 minutes. The sample was then washed once with high salt wash buffer and once with low salt wash buffer. The sample was then resuspended in 40 µL water. Periodate oxidation: 10 µL of 250 mM freshly prepared sodium periodate, 0.5 M sodium acetate, pH 5 were added to the RNase H digested sample and incubated at room temperature for 30 minutes. Afterwards, ribose was added to a final concentration of 167 mM to quench excess periodate at room temperature for 5 minutes. The sample was then washed once with high salt wash buffer and once with low salt wash buffer. Second ligation: Beads were resuspended into 50 µL of a ligation master mix with the following components: 2U/µL T4 RNA ligase I (NEB), 1x NEB T4 RNA ligase I buffer, 2 µM second ligation oligo (Table S5), 25% PEG 8000, 50 µM ATP, 7.5% DMSO, and 1 mM hexaamine cobalt chloride. After incubation at room temperature overnight (12+ hours), the reaction was diluted with 50 µL water to reduce viscosity, washed once with high salt wash buffer and once with low salt wash buffer, and then resuspended in water. The amount of water was 6 µL per sample in the first ligation reaction, before pooling the barcoded samples. For example, if the second ligation mixture contains a pool of 6 samples, the amount of water used for resuspension would be 36 µL. Samples can be stored at 4 °C or frozen at -20 °C; both can be used for the next PCR step. PCR: A 50 µL PCR reaction was run using 5-10% of the bead slurry products from the second ligation reaction using Q5 DNA polymerase (NEB) and following the manufacturer’s instructions: 0.02 U/µL Q5 DNA polymerase, 1x Q5 reaction buffer, 0.2 mM dNTPs, 0.5 µM Illumina index primer (Table S5), and 0.5 µM Illumina multiplex primer (Table S5). Typical PCR cycles were 9-15 cycles at 10 seconds at 98 °C, 15 seconds at 55 °C, and 72 °C for 20 seconds. PCR reactions were then processed through the DNA Clean and Concentrate kit (Zymo Research). TBE-PAGE gel extraction: Following desalting, PCR products were run on 10% non-denaturing TBE gel with dsDNA size markers; lanes were cut according to the desired product size, mashed by pipette tip, and then resuspended in crush-and-soak buffer (500 mM sodium acetate, pH 5.0). The gel fragments were extracted overnight and then ethanol precipitated.
MSR-seq, mRNA-seq, DM-tRNA-seq

treatment_protocol: HEK293T cells were cultured in DMEM medium (GE Healthcare Life Sciences, SH30022.01) with 10% FBS and 1% Pen–Strep (Penicillin–Streptomycin). Twenty-four 15-cm plates of HEK293T cells (5 × 106 cells each) were seeded three days before collection. On the day of polysome profiling, 6 plates of cells (2 plates for 1 sample) were treated with different stress conditions: (1) unstressed control; (2) 42 C heat shock, 1h; (3) 0.6 mM H2O2, 2h; (4) 300 µM NaAsO2, 2h. Polysome profiling was immediately performed after stress treatment. Demethylase buffer conditions were modified from Li et al 2. Three stock solutions are made fresh immediately before reaction: L-ascorbic acid 200 mM, 2-ketogluterate 3 mM, and ammonium iron sulfate 5 mM. The final reaction mixture contained 2 mM L-ascorbic acid, 1 mM 2-ketogluterate, 0.3 mM ammonium iron sulfate, 100 mM KCl, 50 mM MES pH 6, 50 ng/µL BSA, 4 µM wild-type AlkB, and 4 µM AlkB-D135S. 50 µL of the reaction mixture was added to 5-20 µL of decanted streptavidin bead slurry after ligation, immobilization, and washing. Reaction continued for 30 min at 37 C. Following the reaction, beads were washed once with high salt wash buffer (1 M NaCl, 20 mM Tris-HCl pH 7.4) and once with low salt wash buffer (100 mM NaCl, 20 mM Tris-HCl pH 7.4). MCF7 total RNA sequencing libraries were constructed as follows. Small RNA (<200nt) was first removed from 1 μg MCF7 total RNA using spin columns (Zymo Research RNA Clean & Concentrator-5, R1016) and the large RNA (>200 nt) was eluted with 18 μl sterile H2O in a microcentrifuge tube. The RNA was transferred to PCR tubes and 2 μl Magnesium RNA fragmentation buffer (NEB, E6150S) was added to each tube and the tubes were incubated at 94 C in a thermocycler for 5 minutes to fragment the RNA to ~200 nt. 2 μl RNA fragmentation stop solution was then added to each tube. The samples were diluted to 50 μl with H2O and Zymo Research spin columns were used to purify the fragmented RNA; the RNA were eluted in 16 μl sterile H2O in a microcentrifuge tube. For 3’ end repair of the RNA fragments, 2 μl 10x T4 PNK buffer and 2 μl T4 PNK at 10U/μl (ThermoFisher, EK0032) were added and the mixture incubated at 37C for 30 minutes. The fragmented, end-repaired RNA was used to build sequencing libraries using the msRNA-seq protocol described above with the following modifications. The fragmented RNA was ligated to bar-coded capture hairpin oligonucleotides and bound to streptavidin beads. The samples were then pooled, mixed and split into two parts for ±CMC (N-cyclohexyl-N′-(2-morpholinoethyl)carbodiimide) treatment (+CMC:-CMC=1.5 : 1 ratio). 12 μl sterile H2O and 24 µl TEU buffer (50 mM Tris-HCl (pH 8.3), 4 mM EDTA, 7 M urea) were first added to each tube, then 4 µl freshly prepared 1M CMC in TEU buffer was added to +CMC samples and 4 µl sterile H2O was added -CMC samples. The samples were incubated at 30 C for 16 hours at 1400 rpm on an Eppendorf ThermoMixer. The samples were washed twice with high salt buffer and once with low salt buffer. The samples were then resuspended with 40 µl of 50 mM sodium carbonate and 2 mM EDTA (pH 10.4) buffer and incubated at 37 C for 6 hours at 1400 rpm. The beads were washed twice with high salt buffer and once with low salt buffer and then proceeded to the msRNA-seq steps such as phosphatase treatment and reverse transcription. Polysome profiling procedures were adapted from reference 3. Briefly, cells were treated with 100 µg/ml cycloheximide (CHX) in DMEM for 7 mins right after stress treatments. DMEM medium was removed. Cells were then collected using 10 ml ice-cold PBS with 100 µg/ml CHX and cell lifter. Cells were pelleted by centrifugation at 3000 RPM for 5 minutes. Cell pellet was washed twice with 5 ml ice-cold PBS with 100 µg/ml CHX. Cells from two plates were combined for one sample. Cells were resuspended in 1 ml ice-cold PBS and transferred to microcentrifuge tubes. 200 µl cell suspension from each sample was saved as input. Cells were pelleted by centrifugation at 3000 RPM for 5 mins. For input cells samples, 500 µl TRIzol reagent was added to extract the total RNA. For polysome cells samples, cell pellet was resuspended by 4 volumes of lysis buffer (20 mM HEPES, pH 7.6, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100, 100 µg/ml CHX, freshly added 1 × protease inhibitor (11873580001, Roche), 40 U/µl RNase inhibitor (AM2696, Thermo)). Cells were rotated and lysed at 4 C cold room for 30 mins. Lysed samples were centrifuged at 16000g for 15 mins to collect the clear lysate (~600-700 µl). 4 ul Turbo DNase was added to each lysate and the samples were incubated at room temperature for 15 mins. The samples were centrifuged again at 16000g for 15 mins to get clear lysate. Absorbance at 260 nm of each sample was measured. Samples were adjusted to the same absorbance using lysis buffer. 5%-50% sucrose gradient (20 mM HEPES, pH 7.6, 100 mM KCl, 5 mM MgCl2, 100 µg/ml CHX, freshly added 1 × protease inhibitor, 40 U/µl RNase inhibitor) was perpared using a Biocomp gradient station. 600 µl gradient buffer was removed from the top of the balanced sucrose gradient. 600 µl lysate was loaded onto the top of the gradient slowly while gently rotating the tube. The samples were centrifuged at 28000 RPM for 3 hours at 4 C using a Beckman SW28.1 rotor. After centrifugation, fractions were collected and measured using Biocomp gradient station (30 fractions total). Fractions were flash frozen and stored at –80 C before RNA extraction and library construction. For polysome RNA extraction, fractions from disome and higher were combined and 2 volumes of TRIzol reagent was added to extract the RNA. PolyA+ RNA was extracted from the input and polysome RNA using polyA+ RNA extraction kit from Promega (Z5310) or NEB (E7490S), respectively.

tag: fraction

value: Total RNA - 1000ng input

tag: enzyme/chemical treatment

value: AlkB demethylase treated

tag: rt condition

value: Short RT


title: X8_L2_7008


title: X3_L2_7003


title: X9_L2_7009


title: X7_L2_7007


title: Rat_Cardiac_Model3

city: Guangzhou

first: Yangbo

last: Xi

address: Huangpu avenue

institute: Jinan University

data_processing:
none provided by the submitter
Supplementary_files_format_and_content: FPKM

organism: Rattus norvegicus

source_name: left ventricular tissue of rat

extract_protocol:
Total RNA from heart samples was extracted using the mirVana™ miRNA Isolation Kit (Ambion, AM1561) following the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

treatment_protocol: After overnight fasting, model group ratswere injection with a single dose of streptozocin (STZ) solution (1% in citrate saline, freshly prepared, 50 mg/kg, i.p.). Control group rats  intraperitoneal injection of equal doses of citrate saline (STZ solvent), and feeding under the same conditions.

value: STZ injection

tag: disease state

value: Type 1 Diabetes Mellitus

value: post natal week 22


title: Rat_Cardiac_Control2

value: injection of equal doses of citrate saline (STZ solvent)

value: normal


title: Rat_Cardiac_Control4


title: Rat_Cardiac_Control3


title: Rat_Cardiac_Model2


title: Gonadal_chow_HET_8

city: Cambridge

first: Vanessa

last: Pellegrinelli

address: Metabolic Research Labs (BX289) Addenbrookes Site, Keith Day Road, Institute of Metabolic Science

country: United Kingdom

institute: Wellcome Trust Research Laboratories

data_processing:
Read mapping to GRCm38.p5  using STAR v.2.5.1b
Generation of count tables via FeatureCounts v.1.5
Assembly: GRCm38.p5
Supplementary files format and content: "liver_raw_counts.txt" contains raw counts per mice of the liver data, "gonadal_raw_counts.txt" contains raw counts per mice of the gonadal data

source_name: Gonadal adipose tissue

growth_protocol: Mice were housed 3–4 per cage in a temperature-controlled room (21°C) with a 12 hr light/dark cycle, with ‘lights on’ corresponding to six am. Animals had ad-libitum access to food and water.

extract_protocol:
Total RNA of GnW and liver was extracted using the miRNeasy mini kit (Qiagen)
Total RNA was quality checked (RIN >7) via the Agilent Bioanalyser 2100 system, using the Agilent RNA 6000 Nano Kit.  1ug of RNA was used to construct barcoded sequencing libraries with the TruSeq Stranded mRNA HT Sample Prep Kit (Illumina) following the supplier’s instruction. All the libraries were validated using the Agilent Bioanalyser DNA 12000 and then multiplexed and sequenced on two lanes of Illumina HiSeq 4000 at SE50 at CR-UK Cambridge Institute Genomics Core Facility.

treatment_protocol: Standard chow (10% calories from lipid), Control Diet, Alios Diet or HFD 45% was provided ad libitum to animals from 8weeks old during 18weeks.

tag: genotype

value: HET

tag: diet

value: Chow


title: Rat_Cardiac_Control5

tag: age


title: Rat_Cardiac_Model1


title: Rat_Cardiac_Model4


title: Gonadal_chow_HET_7


title: X16_L2_7016


title: Gonadal_chow_KO_5

value: KO


title: Rat_Cardiac_Control1


title: MCF7_totalRNA_minusCMC_shortRT_minusDM_rep2

source_name: RNA extracted from MCF7 cell culture, without CMC treatment

value: Total RNA


title: MCF7_totalRNA_minusCMC_shortRT_minusDM_rep1


title: MCF7_totalRNA_plusCMC_shortRT_minusDM_rep2

source_name: RNA extracted from MCF7 cell culture, with CMC treatment


title: HEK293T_totalRNA_input10ng_shortRT_minusDM_rep1

value: Total RNA - 10ng input


title: HEK293T_totalRNA_input100ng_shortRT_minusDM_rep1

value: Total RNA - 100 ng input


title: HEK293T_totalRNA_input1000ng_shortRT_minusDM_rep1


title: Gonadal_HFD_HET_11

value: HFD 45 percent


title: Gonadal_HFD_WT_8

value: WT


title: Rat_Cardiac_Model5


title: Gonadal_HFD_WT_6


title: MCF7_totalRNA_plusCMC_shortRT_minusDM_rep1


title: X2_L2_7002


title: HEK293T_totalRNA_input10ng_shortRT_minusDM_rep2


title: Gonadal_HFD_HET_8


title: Gonadal_chow_KO_4


title: Gonadal_chow_WT_5


title: HEK293T_totalRNA_input100ng_shortRT_minusDM_rep2


title: Gonadal_HFD_KO_6


title: Gonadal_HFD_KO_5


title: Gonadal_chow_WT_3


title: Gonadal_HFD_HET_10


title: Gonadal_HFD_WT_5


title: Gonadal_HFD_HET_9


title: Gonadal_HFD_HET_6


title: Gonadal_chow_WT_2


title: Gonadal_chow_WT_4


title: Gonadal_HFD_HET_5


title: Gonadal_HFD_KO_3


title: Gonadal_HFD_KO_9


title: Gonadal_chow_KO_3


title: Gonadal_HFD_HET_7


title: Gonadal_HFD_KO_8


title: Gonadal_HFD_KO_7


title: Gonadal_chow_HET_5


title: Gonadal_chow_HET_4


title: Gonadal_chow_HET_3


title: Gonadal_HFD_WT_7


title: Gonadal_HFD_KO_2


title: Gonadal_chow_HET_6


title: Gonadal_HFD_HET_2


title: Gonadal_HFD_WT_2


title: Gonadal_HFD_WT_1


title: Gonadal_HFD_HET_1


title: Gonadal_chow_KO_1


title: Liver_Alios_WT_6

source_name: Liver

value: Alios


title: Gonadal_chow_HET_1


title: Gonadal_HFD_KO_4


title: Liver_Control_WT_5

value: Control


title: Gonadal_HFD_WT_4


title: Liver_Alios_KO_8


title: Liver_Alios_HET_5


title: Liver_Control_KO_1


title: Liver_Alios_WT_5


title: Gonadal_chow_KO_2


title: Liver_Alios_KO_6


title: Gonadal_chow_HET_2


title: Gonadal_chow_WT_1


title: Gonadal_HFD_HET_4


title: Liver_Alios_KO_5


title: Gonadal_HFD_WT_3


title: Liver_Alios_WT_3


title: Gonadal_HFD_KO_1


title: Liver_Alios_KO_2


title: Gonadal_HFD_HET_3


title: Liver_Control_HET_3


title: Liver_Alios_KO_3


title: Liver_Alios_KO_1


title: Liver_Control_HET_4


title: Liver_Control_HET_1


title: Liver_Alios_WT_2


title: Liver_Control_WT_3


title: Liver_Control_WT_4


title: Liver_Alios_KO_7


title: Liver_Chow_HET_8


title: Liver_Alios_WT_1


title: Liver_Alios_HET_4


title: Liver_Control_HET_2


title: Liver_Control_WT_2


title: Liver_Chow_HET_7


title: Liver_Alios_HET_3


title: Liver_Chow_HET_6


title: Liver_Alios_WT_4


title: Liver_Alios_HET_2


title: Liver_Alios_KO_4


title: Liver_Alios_HET_1


title: Liver_HFD_HET_11


title: Liver_HFD_WT_8


title: Liver_Chow_HET_3


title: Liver_HFD_KO_8


title: Liver_HFD_WT_7


title: Liver_HFD_KO_9


title: Liver_Chow_HET_5


title: Liver_Control_WT_1


title: Liver_HFD_HET_10


title: Liver_HFD_WT_6


title: Liver_Chow_HET_4


title: Liver_HFD_WT_5


title: Liver_HFD_HET_8


title: Liver_HFD_HET_9


title: Parthenote PA2 (WGBS)

city: Columbus

first: Jinsoo

last: Ahn

state: OH

address: 2029 Fyffe Rd

institute: The Ohio State University

data_processing:
Sequenced reads were trimmed for adaptor sequence and low quality reads were eliminated.
The cleaned reads were aligned to the reference genome (Sscrofa11.1) using Bismark (v0.22.3) with default parameters.
After deduplication using the deduplicate_bismark command, the Bismark methylation extractor was used to calculate methylation percentage of every cytosine in CpG context.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Tab-delimited files in bedGraph format containing methylation rates

organism: Sus scrofa

source_name: embryo

growth_protocol: After electric stimulation of oocytes followed by 2 h of stabilization period, parthenogenetic embryos were placed into oviducts of each of the two LYD surrogate gilts aged 12 months at onset of estrus to produce developed parthenogenetic embryos.

extract_protocol:
From the whole collected embryos of CN and PA (n = 3 for each), genomic DNA was isolated and fragmented.
For optimization of bisulfite conversion of genomic DNA, Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, Inc. Ann Arbor, MI, USA) was used according to the manufacturer`s instructions.
Whole genome bisulfite sequencing (WGBS)

treatment_protocol: In a fusion chamber with 250 µm diameter wire electrodes, selected oocytes were placed and fusion was achieved by two DC pulses (1 sec interval) of 1.2 kV/cm for 30 µs using an LF101 Electro Cell Fusion Generator.

value: Landrace x Yorkshire x Duroc (LYD)

value: whole embryo

value: embryonic day 21

value: parthenogenesis


title: Liver_HFD_HET_6


title: Liver_Chow_KO_4


title: Parthenote PA3 (WGBS)


title: Liver_HFD_HET_7


title: Parthenote PA1 (WGBS)


title: Liver_chow_WT_5


title: Liver_Chow_KO_5


title: Liver_HFD_KO_6


title: Liver_HFD_HET_5


title: Control CN3 (WGBS)

value: untreated


title: Control CN1 (WGBS)


title: Liver_chow_WT_4


title: Liver_chow_WT_3


title: Control CN2 (WGBS)


title: TET2 knockout

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

department: Bioinformatics

institute: Coriell Institute

description: JAK2V617F;Tet2-/- Lin-cKit+ murine bone marrow cells

data_processing:
Illumina Casava1.7 software used for basecalling.
STAR with Encode parramenter for mapping
cuffdiff with -u flag for differental gene expression
Genome_build: mm10
Supplementary_files_format_and_content: gene_exp.diff.tsv - diff gene expression from cuffdiff software

source_name: murine bone marrow cells

growth_protocol: extracted cell from murine bone marrow

extract_protocol:
RNA was extracted from 5 × 106 cells using a Qiagen RNeasy Plus Mini Kit according to the manufacturer’s protocol. Total RNA was depleted of the ribosomal RNA component using RiboZero (Epicentre).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: murine bone marrow cells

value: JAK2V617F;Tet2-/- Lin-cKit+

value: control


title: TET2 wild type + ruxolitinib

description: JAK2V617F;Tet2+/+ Lin-cKit+ murine bone marrow cells treated with ruxolitinib

value: JAK2V617F;Tet2+/+ Lin-cKit+

value: ruxolitinib


title: TET2 knockout  + ruxolitinib

description: JAK2V617F;Tet2-/- Lin-cKit+ murine bone marrow cells treated with ruxolitinib


title: TET2 wild type

description: JAK2V617F;Tet2+/+ Lin-cKit+ murine bone marrow cells


title: Liver_HFD_KO_5

value: KO


title: MapR-seq CUTLL1 cell shSF3B1-Rep3 sample treat with mut-RNase H

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

description: MapR

data_processing:
Library strategy: MapR-seq
All the reads were mapped to the reference using STAR guided
BAM to bedgraph performed using bedtools. bedgraph to bigwig performed using bedGraphToBigWig v4.
Assembly: hg19
Supplementary files format and content: BigWig

growth_protocol: Cells in suspension, growing in RPMI.

extract_protocol:
Samples were collected and prepared by following MapR protocol (Q. Yan, K. Sarma. Curr. Protoc. Mol. Biol.130, e113 (2020)).
MapR were prepared by following Q. Yan's protocol (Q. Yan, K. Sarma, Curr. Protoc. Mol. Biol.130, e113 (2020) and library were prepared by using NEBNext Ultra II DNA Library Prep Kit, and following the manufacturer’s instructions.)

treatment_protocol: Cells treated with short hairpin against SF3B or scramble ctrl. Cells treated with DMSO or 3nM E7107 for 24h.

value: CUTLL1 Human T-cell Lymphoblastic Lymphoma Cell Line

tag: cell treatment

tag: sample treatment

value: mut-RNase H


title: Liver_Chow_KO_3

tag: strain

value: Chow


title: Liver_HFD_KO_7

value: HFD 45 percent


title: Liver_HFD_KO_3


title: MapR-seq CUTLL1 cell shControl-Rep2 sample treat with mut-RNase H

description: MapR

value: shControl


title: MapR-seq CUTLL1 cell shSF3B1-Rep2 sample treat with mut-RNase H

description: MapR


title: Liver_Chow_KO_2


title: Liver_HFD_HET_4

value: HET


title: MapR-seq CUTLL1 cell shSF3B1-Rep4 sample treat with WT-RNase H

description: MapR

value: WT-RNase H


title: Liver_chow_WT_1

value: WT


title: MapR-seq CUTTL1 cell 3nM E7107-Rep3 sample treat with mut-RNase H

description: MapR

value: 3nM E7107 for 24h


title: MapR-seq CUTTL1 cell 3nM E7107-Rep4 sample treat with WT-RNase H

description: MapR


title: MapR-seq CUTLL1 cell shControl-Rep1 sample treat with mut-RNase H

description: MapR


title: MapR-seq CUTLL1 cell shControl-Rep4 sample treat with WT-RNase H

description: MapR


title: MapR-seq CUTTL1 cell 3nM E7107-Rep2 sample treat with mut-RNase H

description: MapR


title: Liver_HFD_HET_3


title: Liver_HFD_KO_1


title: MapR-seq CUTTL1 cell 3nM E7107-Rep1 sample treat with mut-RNase H

description: MapR


title: Liver_HFD_HET_2


title: Liver_HFD_WT_2


title: Liver_HFD_WT_4


title: MapR-seq CUTTL1 cell DMSO-Rep3 sample treat with mut-RNase H

description: MapR

value: DMSO


title: Liver_HFD_KO_4


title: MapR-seq CUTTL1 cell DMSO-Rep4 sample treat with WT-RNase H

description: MapR


title: non-echolocator3

description: Sample 8

organism: Eonycteris spelaea

tag: tissue

value: brain


title: Liver_HFD_WT_1


title: Liver_HFD_WT_3


title: MapR-seq CUTTL1 cell DMSO-Rep1 sample treat with mut-RNase H

description: MapR


title: Liver_HFD_HET_1


title: echolocator1

description: Sample 1

organism: Rhinolophus affinis


title: Liver_chow_WT_2


title: Liver_Chow_HET_1


title: Liver_Chow_HET_2


title: Liver_HFD_KO_2


title: HEK293T_polysomepolyARNA_AsO2_longRT_minusDM_rep2

description: poly(A)-selected polysome-associated RNA

source_name: polyA selected RNA from the polysome fraction HEK293T cell culture, after AsO2 stress

value: Short RT


title: Liver_Chow_KO_1


title: HEK293T_polysomepolyARNA_AsO2_longRT_minusDM_rep3


title: HEK293T_polysomepolyARNA_AsO2_longRT_minusDM_rep1


title: HEK293T_polysomepolyARNA_H2O2_longRT_minusDM_rep3

source_name: polyA selected RNA from the polysome fraction HEK293T cell culture, after H2O2 stress


title: U266cloneF8_DabTreat_Day62

city: Boston

first: Birgit

last: Knoechel

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

data_processing:
Output for bulk RNA-seq was generated in FASTQ format (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) mapped to the human genome GRCh37 (hg19). Gene expression at transcript-level resolution was calculated using RSEM (v1.2.31) and Picard (https://broadinstitute.github.io/picard/). Annotations were derived from the Ensembl database (October 2018).Differential gene expression analysis and enrichment were performed using DESeq2 (v1.22.2) and GSEA (v4.0.3).
Genome_build: hg19
Supplementary_files_format_and_content: bulkRNA-Seq:bigwig files generated using the nf-core ATAC pipeline

growth_protocol: Single-cell clones were cultured with dabrafenib-containing media (10uM for U266 clones, 10nM for DP6 clones) which was replaced twice per week.

extract_protocol:
Timepoints were as indicated: before treatment, day 7, day 14, day 42 at time of resistance
Libraries were prepared with the TruSeq RNA Access Library Prep Kit (Illumina).
Paired-end sequencing, using 75 bp reads was performed on a NextSeq 500 (Illumina).

treatment_protocol: Aliquots of 5 x 10e5 cells were retrieved at defined time points throughout drug exposure for bulk RNA-seq.

value: MM cell line U266

value: dabrafenib

tag: treatment protocol

tag: extract protocol

value: Timepoints were as indicated:before treatment, day 7, day 14, day 42 at time of resistance

tag: library strategy


title: HEK293T_polysomepolyARNA_H2O2_longRT_minusDM_rep2

city: Chicago


title: U266cloneF8_DabTreat_Day42

tag: treatment

value: Aliquots of 5 x 10e5 cells were retrieved at defined time points throughout drug exposure for bulk RNA-seq.

value: Libraries were prepared with the TruSeq RNA Access Library Prep Kit (Illumina).

value: Paired-end sequencing, using 75 bp reads was performed on a NextSeq 500 (Illumina).


title: HEK293T_polysomepolyARNA_H2O2_longRT_minusDM_rep1


title: LPS S76

city: Düsseldorf

first: Rianne

last: Nederlof

address: Universitätsstraße 1

department: Institut für Herz-und Kreislaufphysiologie

country: Germany

institute: Heinrich-Heine University

data_processing:
The bcl2fastq tool v2.17.1.4 was used to convert the bcl files to fastq files as well for adapter trimming and demultiplexing.
The reads of all probes were adapter trimmed (Illumina TruSeq) and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2)
Mapping was done against the Mus musculus (mm10; GRCm38.86) (March 24, 2017) genome sequence using CLC Genomics Workbench (version 12.03.3).
Reads Per Kilobase and per Megabase (RPKM) were calculated using CLC Genomics Workbench v12.03.3 with standard parameters
Assembly: mm10
Supplementary files format and content: xlsx RPKM values for each sample

source_name: Neutrophils

growth_protocol: Isolated neutrophils dissolved in medium (VLE Dulbecco DMEM with 3% FCS, 1mM HEPES and 1% PenStrep) and plated in a 6-well plate 5-6 x 10*6 cells per well.

extract_protocol:
RNA isolation was performed using TRIzol reagent according to the manufacturer’s instructions. DNA digestion was perfomed using the RNEasy mini kit from Qiagen according to manufacturers' instruction
The library preparation was performed according to the manufacturer’s protocol using the ‘VAHTS™ Stranded mRNA-Seq Library Prep Kit for Illumina®’. Briefly, 300 ng total RNA were used for mRNA capturing, fragmentation, the synthesis of cDNA, adapter ligation and library amplification.

treatment_protocol: 4 hours, untreated, 20 ng/mL IL4, 10 ng/mL IGF1, 10 ng/mL insulin, 100 ng/mL insulin or 10ng/mL LPS and 2 ng/mL IFNgamma

value: bone marrow derived neutrophils

value: LPS/IFNgamma


title: MapR-seq CUTTL1 cell DMSO-Rep2 sample treat with mut-RNase H

description: MapR

value: CUTLL1 Human T-cell Lymphoblastic Lymphoma Cell Line

value: mut-RNase H


title: LPS S82


title: HEK293T_polysomepolyARNA_heatstress_longRT_minusDM_rep3

source_name: polyA selected RNA from the polysome fraction HEK293T cell culture, after heat stress


title: HEK293T_polysomepolyARNA_heatstress_longRT_minusDM_rep2


title: U266cloneF6_naive

value: before treatment


title: LPS S94


title: U266cloneF8_DabTreat_Day14


title: HEK293T_polysomepolyARNA_nostress_longRT_minusDM_rep3

source_name: polyA selected RNA from the polysome fraction HEK293T cell culture, with no stress treatment


title: U266cloneF6_DabTreat_Day7


title: HEK293T_polysomepolyARNA_nostress_longRT_minusDM_rep1


title: HEK293T_polysomepolyARNA_heatstress_longRT_minusDM_rep1


title: Ins100 S85

value: Insulin 100 ng/ml


title: U266cloneF8_naive


title: HEK293T_polyARNA_AsO2_longRT_minusDM_rep3

description: poly(A)-selected total RNA

source_name: polyA selected RNA from total RNA extracted from HEK293T cell culture, after AsO2 stress

value: poly(A)-selected total RNA


title: HEK293T_polyARNA_AsO2_longRT_minusDM_rep2

description: poly(A)-selected total RNA


title: U266cloneF6_DabTreat_Day62


title: HEK293T_polyARNA_H2O2_longRT_minusDM_rep3

description: poly(A)-selected total RNA

source_name: polyA selected RNA from total RNA extracted from HEK293T cell culture, after H2O2 stress


title: U266cloneF6_DabTreat_Day42


title: HEK293T_polyARNA_H2O2_longRT_minusDM_rep2

description: poly(A)-selected total RNA


title: HEK293T_polyARNA_AsO2_longRT_minusDM_rep1

description: poly(A)-selected total RNA


title: Ins100 S97


title: U266cloneF8_DabTreat_Day7


title: U266cloneF6_DabTreat_Day14


title: Ins100 S91


title: HEK293T_polyARNA_heatstress_longRT_minusDM_rep2

description: poly(A)-selected total RNA

source_name: polyA selected RNA from total RNA extracted from HEK293T cell culture, after heat stress


title: U266cloneD3_naive


title: HEK293T_polyARNA_heatstress_longRT_minusDM_rep3

description: poly(A)-selected total RNA


title: HEK293T_polyARNA_heatstress_longRT_minusDM_rep1

description: poly(A)-selected total RNA


title: U266cloneD3_DabTreat_Day7


title: HEK293T_polyARNA_nostress_longRT_minusDM_rep3

description: poly(A)-selected total RNA

source_name: polyA selected RNA from total RNA extracted from HEK293T cell culture, with no stress treatment


title: Ins10 S84

value: Insulin 10 ng/ml


title: HEK293T_polysomepolyARNA_nostress_longRT_minusDM_rep2


title: LPS S88


title: HEK293T_polyARNA_nostress_longRT_minusDM_rep2

description: poly(A)-selected total RNA


title: Ins10 S78


title: Ins10 S96


title: HEK293T_polyARNA_nostress_longRT_minusDM_rep1

description: poly(A)-selected total RNA


title: Ins10 S90


title: U266cloneD3_DabTreat_Day62


title: HEK293T_polysomeRNA_AsO2_longRT_minusDM_rep1

description: Polysome associated RNA

source_name: RNA extracted from the polysome fraction of HEK293T cell culture, after AsO2 stress

value: Polysome associated RNA

value: Overnight RT


title: HEK293T_polysomeRNA_AsO2_longRT_minusDM_rep2

description: Polysome associated RNA


title: Ins100 S79


title: HEK293T_polyARNA_H2O2_longRT_minusDM_rep1

description: poly(A)-selected total RNA

value: Short RT


title: HEK293T_polysomeRNA_H2O2_longRT_minusDM_rep2

description: Polysome associated RNA

source_name: RNA extracted from the polysome fraction of HEK293T cell culture, after H2O2 stress


title: U266cloneD3_DabTreat_Day42

value: MM cell line U266


title: DP6clone9_Naive

value: MM cell line DP6


title: HEK293T_polysomeRNA_H2O2_longRT_minusDM_rep3

description: Polysome associated RNA


title: HEK293T_polysomeRNA_heatstress_longRT_minusDM_rep2

description: Polysome associated RNA

source_name: RNA extracted from the polysome fraction of HEK293T cell culture, after heat stress


title: DP6clone9_DabTreat_Day7

value: dabrafenib

value: Timepoints were as indicated:before treatment, day 7, day 14, day 42 at time of resistance


title: U266cloneD3_DabTreat_Day14

value: Aliquots of 5 x 10e5 cells were retrieved at defined time points throughout drug exposure for bulk RNA-seq.

value: Libraries were prepared with the TruSeq RNA Access Library Prep Kit (Illumina).


title: IGF1 S83

value: bone marrow derived neutrophils


title: HEK293T_polysomeRNA_heatstress_longRT_minusDM_rep1

description: Polysome associated RNA


title: HEK293T_polysomeRNA_nostress_longRT_minusDM_rep1

description: Polysome associated RNA

source_name: RNA extracted from the polysome fraction of HEK293T cell culture, with no stress treatment


title: IGF1 S89


title: HEK293T_polysomeRNA_nostress_longRT_minusDM_rep3

description: Polysome associated RNA


title: IGF1 S77


title: HEK293T_polysomeRNA_H2O2_longRT_minusDM_rep1

description: Polysome associated RNA


title: HEK293T_totalRNA_AsO2_longRT_minusDM_rep2

source_name: RNA extracted from HEK293T cell culture, after AsO2 stress

value: Total RNA


title: DP6clone5_Naive

value: Paired-end sequencing, using 75 bp reads was performed on a NextSeq 500 (Illumina).


title: HEK293T_polysomeRNA_nostress_longRT_minusDM_rep2

description: Polysome associated RNA


title: HEK293T_totalRNA_AsO2_longRT_minusDM_rep1


title: HEK293T_totalRNA_AsO2_longRT_minusDM_rep3


title: DP6clone5_DabTreat_Day7


title: IL4 S81


title: HEK293T_polysomeRNA_AsO2_longRT_minusDM_rep3

description: Polysome associated RNA


title: G007-LK 30 mpk 2

city: Seoul

first: Dong Young

last: Kim

address: 75 Nowon-ro

country: South Korea

institute: KIRAMS

description: Total RNA was isolated in ileum tissue.

hyb_protocol: Reporter and capture probes were hybridized to target genes for 16 h at 65 °C

scan_protocol: The target-probe complexes were aligned onto the nCounter cartridge, and the transcripts were counted via detection of the fluorescent barcodes within the reporter probe.

data_processing: Raw expression data were analyzed using the NanoSTRING software nSolver v4.0.70 with the Advanced Analysis Module v2.0 (RRID:SCR_003382).

source_name: mouse ileum tissue

label_protocol: RNA was analyzed using the nCounter Mouse Tumor Signaling 360 Panel (#XT-CSPS-M-T360-12; NanoSTRING Technologies), which includes 760 tumor-related genes and 20 housekeeping genes.

growth_protocol: Each mouse was randomly assigned to study groups.

extract_protocol: Total RNA was extracted from ileum tissue using a MasterPureTM RNA kit (#MC85200; Lucigen) according to the manufacturer's instructions. Samples with RIN values > 7.0, were included for gene expression analysis.

treatment_protocol: DMSO and STP1002: oral administration, once daily, for 28 days / G007-LK: IP injection, twice a day, for 28 days

value: ileum

value: G007-LK, IP/BID, 30 mpk


title: DP6clone4_DabTreat_Day7


title: G007-LK 30 mpk 3

description: Total RNA was isolated in ileum tissue.


title: IL4 S75


title: DP6clone4_DabTreat_Day14


title: DP6clone4_Naive

value: before treatment


title: IL4 S87


title: HEK293T_totalRNA_H2O2_longRT_minusDM_rep2

source_name: RNA extracted from HEK293T cell culture, after H2O2 stress


title: G007-LK 30 mpk 1

description: Total RNA was isolated in ileum tissue.


title: IL4 S93


title: untreated S92

value: untreated


title: HEK293T_totalRNA_H2O2_longRT_minusDM_rep1