title: primary rat microglia + HERV-W ENV 3

value: HERV-W ENV (1µg/ml)


title: Ovary, miRNA, month 6, individual 3

status: Public on Mar 30 2024

type: SRA

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

country: China

institute: 6/5000 Shandong Agricultural University

library_source: transcriptomic

data_processing:
The raw reads were filtered using Cutadapt 1.16.
Using the Bowtie 1.0.1 filter out repeated sequences and ncRNAs based on RepeatMasker and Rfam. Next, clean reads were aligned to the reference genome (Capra hircus, ARS1.2) using BLAST 2.7.1.
MiRNAs were identified using miREvo 1.1 and miRDeep2 2.0.0.7.
MiRNA expression levels were normalized with RSEM 1.3.0
Assembly: Capra hircus, ARS1.2
Supplementary files format and content: Txt files includes read counts of all samples.

molecule: total RNA

organism: Capra hircus

source_name: Ovary

extract_protocol:
Total RNA was isolated from 20 uterine tissue and 20 ovarian tissues samples with TRIzol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. The RNA concentration, purity and integrity were calculated and checked by a NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and an Agilent 5400 Bioanalyzer (Agilent, Santa Clara, CA).
miRNA sequencing libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: Ovary

tag: timepoint

value: month 6


title: PltBS35A typhoid toxin treated-1

city: Taipei

first: Po-Yo

last: Liu

address: No.1 Jen Ai road section 1 Taipei 100 Taiwan R.O.C.

department: Department and Graduate Institute of Medical Microbiology

country: Taiwan

institute: National Taiwan University College of Medicine

description: PltB mutant TT treated-1

data_processing:
Sequencing reads in fastq format were further analyzed with CLC Genomics Workbench 21 (version 21.0.1).
Reads were first trimmed for both adapter contamination and low-quality score trimming (Q<20)
Clean reads were mapped to the Homo sapiens (GRCh38) reference sequence with default parameters of the RNA Sequencing workflow for reads counting
The counting matrix were generated and used for differential expression analysis
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: THP-1-derived macrophages

growth_protocol: THP-1 cells were cultured in Roswell Park Memorial Institute (RPMI)-1640 supplemented with 10% heat-inactivated fetal bovine serum (FBS), 4.5 g/L glucose, 10 mM HEPES and 10 mM sodium pyruvate. THP-1 cells were differentiated into macrophages by treating cells with 40 nM of phorbol 12-myristate 13- acetate (PMA) for 48 h, followed by overnight incubation in fresh medium before experiments.

extract_protocol:
Total RNAs from the cells were isolated using RNeasy purification kits (QIAGEN) following the manufacturer’s instructions. The concentration of RNA was measured by using Qubit RNA BR assay kit with Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, United States). RNA integrity Number (RIN) of RNA was assessed by using an RNA Nano 6000 assay kit and Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, United States). 100 ng of RNA with RIN ≧ 8 was used for library preparation with illumina stranded mRNA library prep Kit (Illumina, San Diego, CA , United States).
Briefly, messenger RNA (mRNA) with polyA tails was isolated by using oligo(dT) magnetic beads. Purified mRNA was fragmented into short segments and complementary DNA (cDNA) was synthesized with random hexamer primers. To achieve strand specificity, the deoxyuridine triphosphate (dUTP) was used for the replace of deoxythymidine triphosphate (dTTP) while performing second-strand cDNA synthesis. cDNA was clean up with AMPure XP beads (Beckman Coulter, Indianapolis, Indiana, United States) and followed by end repair, polyadenylation, and Illumina sequencing adapter ligation. After proper PCR amplification, final library was purified and paired-end 150 bp sequencing was performed with Illumina Novaseq to achieve 20 M reads per sample.

treatment_protocol: THP-1-derived macrophages were exposed to 160 rM of typhoid toxin at 37°C for 60 minutes and then changed to regular growth medium for 16 hours.

tag: cell line

value: THP-1-derived macrophages

tag: cell type

value: Human Monocytic Cell Line


title: Plasma, Diabetic kidney disease, rep7

city: Belfast

first: David

middle: Arthur

last: Simpson

state: N. Ireland

address: The Wellcome – Wolfson Institute for Experimental Medicine, 97 Lisburn Road

department: Wellcome-Wolfson Institite for Experimental Medicine

country: United Kingdom

institute: Queen's University Belfast

data_processing:
Raw read quality control was performed with FastQC
Adapters were trimmed with Trim Galore
Reads were collapsed with seqcluster and aligned with Bowtie1 against miRBase mature miRNA and miRBase hairpin (miRbase Ver 22, available athttp://mirbase.org)
Post-alignment processing of miRBase hairpin was performed using SAMtools and EdgeR (3.36.0) for miRBase analysis
Assembly: miRbase Ver 22
Supplementary files format and content: csv delimited text file containing raw counts of mature miRNAs

source_name: plasma

extract_protocol:
Whole blood was collected using a vacuette needle into an ethylenediaminetetraacetic acid (EDTA) collection tube for plasma isolation. Following centrifugation at 3,000 g for 10 minutes at 4°C, the supernatant was pipetted into 3 x 1 ml aliquots in RNase/DNase-free tubes and frozen at -80°C. RNA was extracted from 600 μl of plasma using the NextPrep™ MagnaZol™ cfRNA Isolation Kit (Bioo Scientific Corp, Texas, USA), following the manufacturer’s instructions, with purified RNA eluted in 16μl of nuclease-free water. RNA was quantified using the Qubit miRNA Assay kit (ThermoFisher Scientific, San Jose, USA).
miRNA libraries were prepared using QIAseq miRNA Library Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. Library concentrations were quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and quality control of library was performed using a High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies, Santa Clara, CA, USA).

value: plasma

tag: treatment

value: Diabetic kidney disease


title: Plasma, Diabetic kidney disease, rep5


title: Ovary, miRNA, month 6, individual 1


title: primary rat microglia + HERV-W ENV 2

city: Düsseldorf

first: Joel

last: Gruchot

address: Moorenstraße 5

department: Neurology

country: Germany

institute: Heinrich-Heine-University

data_processing:
raw data in FASTQ format were adapter- and quality trimmed.
Mapping was performed against the Rattus norvegicus (mRatBN7.2.1110; January 05, 2024) genome sequence using Hisat2 alignment method.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach
Assembly: mRatBN7.2.1110
Supplementary files format and content: raw counts as .txt

organism: Rattus norvegicus

source_name: cortical

growth_protocol: Briefly, dissociated P1 Wister rat cortices were cultured on T-75 cell culture flasks in Dulbecco′s Modified Eagle′s Medium (DMEM) substituted with 10% fetal calf serum (FCS) and 4 mM L-glutamine, 50 U/ml penicillin/streptomycin. After 10 days, flasks were shaken at 180 rpm/min at 37 °C and microglia-containing supernatants were collected after 2 and 24 h. To further purify the primary rat microglia, cells were sorted using MACS against CD11b/c microbeads.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen) and 150 ng of total RNA was used for the library construction
RNA libraries for RNA-Seq were prepared according to the manifacturers protocol using the VAHTS™ Universal RNA-Seq Library Prep Kit for Illumina® V6 with mRNA capture module

treatment_protocol: One day after microglial isolation or 3 days after astroglial isolation, cells were stimulated with with 1 µg/ml recombinant HERV-W ENV protein or with 100 ng/ml LPS in glial media (10% FCS, 2 mM L-glutamine, 50 U/ml penicillin/streptomycin in DMEM).

value: cortical

tag: age

value: Postnatal day 1

value: microglia

tag: strain

value: Wistar


title: Plasma, Diabetic kidney disease, rep6


title: primary rat microglia + buffer 2

value: buffer


title: BMSC-shMETTL3-2-3

city: Nanjing

first: Lan

last: Ma

address: Hanzhong street

institute: Nanjing medical university

data_processing:
Illumina NovaSeq 6000 for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human reference genome (hg38)
For each sample, the results from Reads alignment to the reference genome were assembled using StringTie software based on a location information file on the genome of known transcripts as a guide for the transcripts in the sample, the transcripts with 0 expression were filtered and the StringTie-assembled transcripts from all samples were reassembled.
Assembly: human reference genome (hg38)
Supplementary files format and content: tab-delimited text files include FPKM value for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: bone marrow mesenchymal stem cells

extract_protocol:
Total RNA was isolated from BMSC cells using an RNA Extraction Kit following the manufacturer's instructions (RX112, Vazyme, Nanjing, China).
Experimental steps: 1. MRNA isolation and fragmentation -take 500ng totalrna, adjust the volume to 50ul with water, add 50ul mrnacapturebeads and mix well -place it on the PCR instrument at 65 ℃ for 5min, and then place it at room temperature for 5min -put it on the magnetic rack for 5min and remove the supernatant -remove it from the magnetic frame, add 200ul wash buffer and mix well -put it on the magnetic rack for 5min and remove the supernatant -remove it from the magnetic frame, add 50ul trisbuffer and mix well -place it on the PCR instrument at 80 degrees for 2min and 25 degrees hold -add 50ul beadbinding buffer, mix well, and place at room temperature for 5min -put it on the magnetic rack for 5min and remove the supernatant -remove it from the magnetic frame, add 200ul wash buffer and mix well -put it on the magnetic rack for 5min and remove the supernatant -add 19ul frame / prime buffer and mix well -put it on the PCR instrument at 94 degrees for 3min and 4 degrees for hold -put it on the magnetic rack for 5min, take out 16ul to a new EP tube, and prepare 0.12mg/ml actinomysin D solution 2.Double stranded cDNA --add 26ul of 1st strand buffer, 22ul of 1st strand enzyme mix and 1ul of actinomycin D (0.12 mg / ml) into 16ul supernatant and mix well -put it on the PCR instrument, 25 degrees for 10min, 42 degrees for 15min and 70 degrees for 15min -add 25ul of 2nd strand buffer 2 (with dUTP) and 15ul of 2nd strand enzyme super mix into the reaction product of the previous step, and mix well -put it on the PCR instrument, 16 degrees for 30min and 65 degrees for 15min 2. Add a connector -add 25ul rapid ligation buffer3, 5ul rapid DNA ligase2, 2 UL connector, 3ul water, mix well, place it on the PCR instrument for 20 degrees and 15min; -add 45ul DNA clean beans, mix well, and place at room temperature for 10min; -place the magnetic rack at room temperature for 5min, remove the supernatant and do not move the beads; -add 200 UL of 80% ethanol for 30 s at room temperature, remove the supernatant and repeat once; -dry at room temperature for 10min; -add 53ul water, remove it from the magnetic frame, fully mix it, and place it at room temperature for 5min; -place it on the magnetic frame and take the supernatant 50ul into a new pipe. -add 35ul DNA clean beans, mix well, and place at room temperature for 10min; -place the magnetic rack at room temperature for 5min, remove the supernatant and do not move the beads; -add 200 UL of 80% ethanol for 30 s at room temperature, remove the supernatant and repeat once; Dry at room temperature for 10min; -add 22ul water, remove it from the magnetic frame, fully mix it, and place it at room temperature for 5min; -place it on the magnetic frame and take the supernatant 19ul into a new pipe. 3. PCR enrichment -add 19uldna, 2.5ul i7 primer+2.5ul i5 primer, 25ulhifi amplification mix and 1ulheat labile UDG successively; -37 ° 10min, 98 ° 30s, 15 cycles (98 ° 10s, 60 ° 30s, 72 ° 30s), 72 ° 5min, 4 ° hold; -add 45ul amurebeads, mix well, and place at room temperature for 15min; -place the magnetic rack at room temperature for 10min, remove the supernatant and do not move the beads; -add 200 UL of 80% ethanol for 30 s at room temperature, remove the supernatant and repeat once, -dry at room temperature for 10min; -add 33ul water, remove it from the magnetic frame, fully mix it, and place it at room temperature for 5min; -place it on the magnetic frame and take the supernatant 30ul into a new pipe. 4. Quantification: qubit quantitative RNA library.

value: bone marrow mesenchymal stem cells

tag: transduced


title: primary rat microglia + H2O 1


title: BMSC-shMETTL3-2-2


title: Plasma, Diabetic kidney disease, rep4


title: Plasma, Diabetic kidney disease, rep3


title: Ovary, miRNA, month 4, individual 4

value: month 4


title: BMSC-shMETTL3-2-1


title: Ovary, miRNA, month 4, individual 5


title: primary rat microglia + HERV-W ENV 1


title: primary rat microglia + buffer 1


title: BMSC-shMETTL3-1-2


title: Plasma, Diabetic kidney disease, rep2


title: Ovary, miRNA, month 6, individual 2


title: BMSC-shMETTL3-1-3


title: BMSC-shMETTL3-1-1


title: KO3

city: Wenzhou

first: Guang

last: Liang

address: Chashan Street

institute: Wenzhou Medical University

data_processing:
Illumina novaseq 6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus

source_name: Mouse primary peritoneal macrophages

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mouse primary peritoneal macrophages

value: mice

tag: genotype

value: KO


title: Ovary, miRNA, month 4, individual 3


title: BMSC-nc-3

value: empty vector


title: WT3

value: WT


title: BMSC-nc-2


title: Ovary, miRNA, month 4, individual 2

value: Ovary


title: Ovary, miRNA, month 2, individual 5

value: month 2


title: Plasma, Diabetic kidney disease, rep1


title: KO2


title: KO1


title: Ovary, miRNA, month 4, individual 1


title: Plasma, Non-diabetic normal renal function, rep11

value: Non-diabetic normal renal function


title: Ovary, miRNA, month 2, individual 4


title: PKO_D5_ALL_2

city: 天津市西青区

first: Shuo

last: Zhang

address: 西青区梅苑路12号

institute: 血液病医院

data_processing:
FASTQ files were evaluated for quality control using FastQC (v0.11.9) and the adapters were removed from reads from the Illumina sequencer using CutAdapt (v1.18) and trimmed for low quality reads (less than 30).
The trimmed RNA-seq reads were mapped to the GRCh38 reference genome using STAR (v2.7.9) alignment tool to acquire the Binary Alignment Map (BAM) files.
The total number of tags that overlap with the genes (exonic region only) were obtained using HTSeq (v0.10.0).
Differential genes expression analysis were performed using R-package DESeq2 (v1.30.1)
Genes with an FDR cutoff of 0.05 as well as |Log2FoldChange| >1 was considered significantly differentially expressed.
Assembly: GRCh38
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 FPKM values for each Sample

source_name: hematopoietic stem and progenitor cells

growth_protocol: 1.PEAR1+ population and PEAR1- population sorted on Day 5 in early differentiation were collected for bulk RNA sequencing (RNA-seq). 2.BC1-Day5 cells and BC1-PKO-Day5 cells were collected on Day 5 in early differentiation for bulk RNA sequencing (RNA-seq).

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Non-treatment

value: hPSC-derived hematopoietic stem and progenitor cells

tag: genotype/time point


title: Plasma, Non-diabetic normal renal function, rep7

value: plasma


title: PKO_D5_ALL_1


title: Plasma, Non-diabetic normal renal function, rep9


title: WT2


title: BMSC-nc-1


title: Plasma, Non-diabetic normal renal function, rep10


title: Plasma, Non-diabetic normal renal function, rep6


title: Ovary, miRNA, month 2, individual 3


title: Plasma, Non-diabetic normal renal function, rep8


title: KO_LDL2

value: oxLDL


title: Plasma, Non-diabetic normal renal function, rep5


title: BC1_D5_ALL_2


title: WT1


title: KO_LDL1


title: Ovary, miRNA, month 2, individual 2


title: WT_LDL3


title: PEAR1-_D5_1

description: PEAR1+ PEAR1-_rawcount


title: KO_LDL3


title: WT_LDL2


title: Ovary, miRNA, day1, individual 3


title: Ovary, miRNA, month 2, individual 1


title: Ovary, miRNA, day1, individual 2


title: Plasma, Non-diabetic normal renal function, rep2


title: Ovary, miRNA, day1, individual 5


title: BC1_D5_ALL_1


title: WT_LDL1


title: Plasma, Non-diabetic normal renal function, rep1


title: PEAR1+_D5_1

description: PEAR1+ PEAR1-_rawcount


title: Plasma, Non-diabetic normal renal function, rep3


title: A. thaliana, control, 0 h, rep1

status: Public on Mar 29 2024

city: Irapuato

first: Luis

middle: F.

last: Garcia-Ortega

state: Guanajuato

address: Km 9.6 Libramiento Norte

department: Department of Genetic Engineering

country: Mexico

institute: Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav)

data_processing:
Raw reads were quality assessed using cutadapt v1.9.1 and Trimmomatic v0.36 to remove adapter sequences and low-quality reads, respectively.
To identify sRNA source, the sRNA sequences were mapped to the T. atroviride and A. thaliana genomes using standalone BLAST version 2.11.0+  with word length 7 and e-value cut-off of 0.1.
The BLAST hits were then filtered based on their occurrence at only one location and maximum number of mismatches of 1.
Assembly: TAIR10 for A. thaliana, and JGI v2 for T. atroviride
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Arabidopsis seeds underwent surface sterilization with 75% ethanol for 3 minutes, followed by a 7-minute treatment with a 20% (v/v) chlorine solution. After three rinses with sterile distilled water (3 minutes each), the seeds were either placed on plates with 1× Murashige and Skoog (MS) medium (PhytoTech Labs, Lenexa, KS, US; Murashige and Skoog, 1962) or sown in flowerpots with a mixture of sterilized peat moss (LAMBERT™), perlite (Hortipel), and vermiculite (Verlite) in a 3:1:1 ratio. The seeds were stratified by 48 h at 4°C in the dark and were subsequently germinated on MS medium with 0.7% agar or in pots under a 12-hour light (150 µmol m-2 sec-1 light) and 12-hour dark photoperiod. In vitro-grown seedlings were collected for further analyses.

extract_protocol: Total RNA was extracted and sRNA-seq libraries were generated according to the sRNA cloning protocol provided by Solexa.

treatment_protocol: Trichoderma-Arabidopsis assays involved the sterilization and sowing of seeds as described earlier. Pots containing the seeds were placed at 21 ± 2°C, under a 12 h light (150 µmol m-2 sec-1 light) and 12 h dark photoperiod. Four-day-old seedlings were then transferred to individual inserts with the specified substrate and grown for 0, 24, 48, 72 and 96 h at 21 ± 1°C under a 12/12 h light/dark regime.

value: root

tag: ecotype

value: control

tag: time

value: 0 h


title: MO_Pax3_replicate1

city: Paris

first: Anne-Hélène

last: Monsoro-Burq

state: Ile-de-France

address: 26 rue d'Ulm

country: France

institute: Curie Institute

data_processing:
alignment with STAR
quantification with String Tie
Assembly: X.laevis 9.2
Supplementary files format and content: processed_data/expression_matrix.csv is raw counts

organism: Xenopus laevis

source_name: Neural border

growth_protocol: Xenopus laevis embryos were handled using standardized protocols (http://www.xenbase.org). Embryos were staged according to Nieuwkoop and Faber’s table (P. D. Nieuwkoop, J. Faber, Normal table of Xenopus laevis (Daudin): edited by P. D. Nieuwkoop and J. Faber Garland Publishing. Trends Genet. 11, 418 (1994)).

extract_protocol: Microdissected explants were transferred into TRIzol (Invitrogen), and total RNA was extracted according to the published protocols.

treatment_protocol: 20 ng of gene MO were injected into one blastomere of two-cell stage X. laevis embryos, according to the assay. At the desired stage, one anterior NB (stage 14) or one NC (stage 17) was dissected from the injected side and used for RNA extraction and cDNA library preparation.

tag: developmental stages

value: Neural border


title: WT_14_replicate2


title: WT_14_replicate1


title: WT_17_replicate1


title: Plasma, Non-diabetic normal renal function, rep4


title: Mo_Zic1_replicate1


title: Donor 15-3-6 MDM, AT genotype, Infected by strain 7826 (Non-G2G)

city: Boston

first: Xin

last: Wang

address: 677 Huntington Ave

country: USA

institute: Harvard University School of Public Health

data_processing:
1.8.0 - RTA, STAR, RSEM
The single-end raw reads were filtered by Trimmomatic version 0.39 to remove the adaptors and low-quality bases.
We used STAR version 2.6.0c and RSEM version 1.2.29 to quantify gene expression using human genome primary assembly (GRCh38) and its basic gene annotation from gencode human release 43 (GRCh38.p13).
The pipeline generates expected counts and transcripts per million (TPM) for each gene.
Assembly: human genome primary assembly (GRCh38)
Supplementary files format and content: Comma-separated values (csv) file format of TPM values of each sample

source_name: hMDM

growth_protocol: Mammalian cells were cultured in RPMI 1640 with 10% fetal bovine serum (FBS), 10 mM HEPES, and 2mM L-glutamine

extract_protocol:
RNA was extracted using the Zymo Direct-Zol kit.
The library was prepared using the KAPA mRNA HyperPrep kit (Roche)

treatment_protocol: hMDMs were infected by Mtb strains

value: hMDM

value: human monocyte-derived macrophage

value: FLOT1 AT

value: Infected


title: M972_Input

library_source: genomic

data_processing:
Bowtie2 alignment
MACS2 peaks calling
Target genes search with bedtools
Assembly: X.tropicalis  v.10 , X.laevis v. 9.2
Supplementary files format and content: Three tables for pax3, tfap2a, and tfap2e targets in a csv format. Target genes was searched with 10kb window around the peaks called with MACS2.

molecule: genomic DNA

source_name: Whole embryo

extract_protocol: DNA was extracted from Xenopus embryos by sonication, using a 3.2 mm tapered microtip for 13 mm horn (Branson 450 sonicator)

treatment_protocol: Embryos were injected in both blastomeres at two-cell stage with trace amounts of mRNA encoding Pax3-FLAG-HA (75 pg), Tfap2a-FLAG or Tfap2e-FLAG. Injected embryos were collected at mid-neurula stage 14 (Pax3 and Tfap2a, 100 embryos/condition) or at NC migratory stage 19 (Tfap2e, 100 embryos/condition)

value: Whole embryo


title: M963_Input


title: PEAR1+_D5_2

description: PEAR1+ PEAR1-_rawcount


title: Ovary, miRNA, day1, individual 1


title: M962_Input


title: A. thaliana, control, 0 h, rep2


title: WT_14_replicate4


title: M953_Input


title: Ovary, miRNA, day1, individual 4


title: PEAR1-_D5_2

description: PEAR1+ PEAR1-_rawcount


title: WT_14_replicate3


title: MO_Tfap2e_replicate1


title: M952_Input


title: MO_Tfap2e_replicate2


title: Trim28_Light_rep20

type: genomic

city: Grand Rapids

first: Luca

last: Fagnocchi

state: MI

address: 333 Bostwick AVE NE

institute: VAI

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridized to Illumina Infinium Mouse Methylation Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged on the iScan using standard recommended Illumina scanner setting

data_processing:
GenomeStudio software v.2011.1 and SeSAMe
single_signal_supp.txt = Unmethylated and methylated signal intensities
processed_matrix.txt = Average Beta

label: Cy5 and Cy3

organism: Mus musculus

source_name: genomic DNA from intestine

label_protocol: Standard Illumina Infinium HD Assay Methylation Protocol document #15019519 v01

growth_protocol: Curls from FFPE healthy tissues

extract_protocol: We used the Quick-DNA/RNA™ FFPE Kit (Zymo) for DNA extraction

treatment_protocol: Deparaffinization according to Quick-DNA/RNA™ FFPE Kit (Zymo)

tag: Sex

value: male

value: intestine

tag: batch


title: Trim28_Heavy_rep26


title: Mo_Zic1_replicate2


title: Trim28_Light_rep18


title: M972_Chip_Pax3


title: M971_UC_Pax3_m972_and_tfap2a_m973


title: M973_Input


title: M963_Chip_Tfap2a


title: M971_Input


title: M954_Input


title: M961_Input


title: M951_Input


title: Trim28_Heavy_rep25


title: Trim28_Light_rep19


title: M961_UC_pax3_m962_and_tfap2a_m963


title: M973_Chip_Tfap2a


title: Trim28_Light_rep15

source_name: genomic DNA from stomach

value: stomach


title: Trim28_Light_rep16


title: mdxTG, replicate 4

city: Los Angeles

first: Hafsa

last: Mamsa

state: CA

address: 610 Charles E. Young Drive East

department: Integrative Biology & Physiology

institute: University of California Los Angeles

data_processing:
Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
RNA-Seq reads were mapped to the mouse reference genome (mm10) using STAR
Expression levels were quantified for annotated genes (Ensembl v.92), and raw gene counts were normalized to CPM values (counts per million).
Differential expression analysis was performed using edgeR-QLF
Differentially expressed genes (DEGs) were identified at 1% FDR and fold-change > 2
Assembly: mm10
Supplementary files format and content: Spreadsheet with CPM values for each sample with DEG.

source_name: Tibialis Anterior

extract_protocol:
RNA was extracted using TRIzol phase separation followed by purificataion and on column DNA digestion with the RNeasy Kit (Qiagen).
RNA-Seq libraries were prepared from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: Tibialis Anterior

value: mdxTG


title: Trim28_Heavy_rep24


title: mdxTG, replicate 3


title: Trim28_Light_rep14


title: Trim28_Light_rep17


title: mdxTG, replicate 1


title: M962_Chip_Pax3


title: Trim28_Heavy_rep22


title: M954_Chip_Tfap2a


title: Trim28_Heavy_rep20


title: Trim28_Heavy_rep21


title: M953_UC_Tfap2a_m954


title: mdxTG, replicate 2


title: Trim28_Heavy_rep23


title: M951_UC_Pax3_m952


title: M952_Chip_Pax3


title: Trim28_Heavy_rep17


title: homo_PFG_H3K27ac_input

city: New York

first: Samuel

middle: Joseph

last: Kaplan

state: New York

address: 430 E 67th St

department: Developmental Biology Program

institute: Sloan Kettering Institute

data_processing:
bowtie 2 (2.5.1) alignment
MACS2 (2.2.9.1) peak calling to generate signal tracks
Assembly: hg38
Supplementary files format and content: Coverage track in bigWig format

growth_protocol: All differentiation experiments were performed on hESCs grown on vitronectin. hESCs were maintained in E8 medium for 2 days to reach ~80% confluence. hESCs were rinsed with 1X DPBS (without Mg2+ and Ca2+) and first differentiated into DE using S1/2 media, supplemented with 100 ng/ml Activin A (Bon Opus Biosciences) for three days and CHIR99021 (Stemgent, 04-0004-10) for two days (1st day, 5 µM; 2nd day, 0.5 µM).  DE cells were rinsed with 1X DPBS (without Mg2+ and Ca2+) and then exposed to S1/2 media supplemented with 50 ng/ml of KGF (FGF7) (PeproTech, 100-19) and 0.25mM vitamin C (Sigma-Aldrich, A4544) for 2 days to reach GT stage. Cells were switched to S3/4 media supplemented with 50 ng/ml of FGF7, 0.25 mM vitamin C, and 1µM retinoic acid (RA) (Sigma-Aldrich, R2625) for 2 days to reach PFG stage.

extract_protocol:
Cells were crosslinked by formaldehyde and lysed by SDS lysis buffer. Sonicated nuclei were incubated with antibody overnight and then pulled down by dynabeads. After washing, decrosslinking was performed to isolate DNA.
aMPure XP size selection followed by KAPA HTP Library Preparation Kit

tag: Stage

value: PFG stage


title: homo_PFG_H3K27ac_rep2


title: Trim28_Light_rep12


title: wild-type, replicate 3

value: WT


title: Trim28_Heavy_rep19


title: mdx, replicate 3

value: mdx


title: Trim28_Heavy_rep16


title: mdx, replicate 2


title: homo_PFG_H3K27ac_rep3


title: Trim28_Light_rep13


title: wild-type, replicate 5


title: Het2_PFG_H3K27ac_input


title: Het2_PFG_H3K27ac_rep3


title: wild-type, replicate 4


title: mdx, replicate 1


title: Het2_PFG_H3K27ac_rep2


title: Trim28_Heavy_rep14


title: Trim28_Heavy_rep18


title: homo_PFG_H3K27ac_rep1


title: Sun1_KO_CT26_purified_tumor_cells_2

city: Calgary

first: Edwin

state: Alberta

address: 2500 University Drive N.W.

country: Canada

institute: University of Calgary

description: DESeq2_CT26_Purified_Tumor_Cells_Control_vs_KO.csv

data_processing:
The raw data were first checked for quality using FastQC. The raw sequences were then trimmed and filtered to obtain clean reads, which were mapped to the reference genome (mm10) using STAR. Raw counts generated from RSEM were then used for DESeq2 analysis to obtain the differentially expressed genes.
Assembly: mm10
Supplementary files format and content: RESULTS file includes expected_count, TPM and FPKM
Supplementary files format and content: CSV file include fold change expression (WT vs. KO) and p values

source_name: purified tumor cells from tumors grown subcutaneously in BALB/c mice

growth_protocol: CT26 KO and control cells were cultured in RMPI supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted using the TRIZOL extraction method according to the manufacturer's instruction.
mRNA was enriched from total RNA, fragmented to ~300 bp in size, and reversed transribed into cDNA. After second strand cDNA synthesis, end-repair and A-tailing, adaptor ligation, size selection and purification, PCR amplification and quality control and quantification, the final products were used for sequencing on the Illumina platform (HiSeq 4000, 2x150 bp).

treatment_protocol: 1 x 10^6 CT26 cells were subcutaneously injected into the right flank, and tumors were collected at day 14.

value: mouse syngeneic cell line (colon cancer)

value: Sun1 knockout


title: mdx, replicate 4


title: Sun1_Control1_CT26_tumors_8

source_name: tumors grown subcutaneously in BALB/c mice

value: Wildtype


title: wild-type, replicate 2


title: wild-type, replicate 1


title: Sun1_Control2_CT26_purified_tumor_cells_1

value: purified tumor cells from tumors grown subcutaneously in BALB/c mice


title: wildtype mTECs, Ribo, replicate nextseq C, ALID03

city: San Francisco

first: Semil

last: Choksi

email: semilc@gmail.com, semil.choksi@ucsf.edu

address: 555 Mission Bay Blvd. South

institute: UCSF

description:
10x Genomics
RiboC_barcodes.tsv.gz
RiboC_features.tsv.gz
RiboC_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: counts and metadata for integrated dataset

source_name: mouse tracheal epithelial cells cultured at air-liquid interface

growth_protocol: Mouse tracheal epithelial cells (mTECs) were purified and cultured as previously described (You and Brody, 2013).

extract_protocol:
To generate single-cell suspensions for mTEC scRNA-seq, mTECs derived from wild-type Bl6  mice  Cells were cultured for six days submerged before initiating air/liquid interface. Ribociclib, resuspended in DMSO, was added to a final concentration of 10 uM in mTEC NS media at 1 day post air/liquid interface. Cells were collected at 3 days post air/liquid interface for scRNA-seq analysis.. Collection involved washing mTECs with PBS three times both apically and basally, incubating in 0.05% Trypsin-EDTA in Cell Dissociation Buffer (Gibco, Cat #13151014) added both apically and basally at 37°C for 15 min, gentle trituration, and inactivating trypsin in mTEC Basic with 2% Nu-Serum (Corning, Cat #355100). Additional 0.05% Trypsin-EDTA in Cell Dissociation Buffer was added to the apical surface and incubated at 37°C for 5 min. Cells were washed and resuspended in 0.04% BSA in PBS at 1000 cells/uL.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, 16,000 mTECs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: wild-type

value: 10 uM Ribo


title: Trim28_Light_rep11

source_name: genomic DNA from lungs

value: lungs


title: Sun1_Control1_CT26_purified_tumor_cells_2


title: Sun1_Control1_CT26_tumors_6

value: tumors grown subcutaneously in BALB/c mice


title: Trim28_Light_rep10


title: Sun1_KO_CT26_purified_tumor_cells_1


title: Sun1_Control1_CT26_tumors_5


title: Trim28_Heavy_rep13


title: Trim28_Heavy_rep15


title: WT_PFG_H3K27ac_input


title: WT_PFG_H3K27ac_rep1


title: Trim28_Heavy_rep11


title: wildtype mTECs, DMSO, replicate nextseq C, ALID03

description:
10x Genomics
DMSOC_barcodes.tsv.gz
DMSOC_features.tsv.gz
DMSOC_matrix.mtx.gz

value: mouse tracheal epithelial cells cultured at air-liquid interface

value: DMSO


title: Sun1_Control2_CT26_purified_tumor_cells_2


title: Trim28_Heavy_rep10

value: male


title: Trim28_Light_rep9


title: Sun1_Control1_CT26_purified_tumor_cells_1


title: Trim28_Light_rep7


title: WT_PFG_H3K27ac_rep3


title: Sun1_Control1_CT26_tumors_1


title: Trim28_Light_rep8


title: wildtype mTECs, Ribo, replicate nextseq A, ALID03

description:
10x Genomics
RiboA_barcodes.tsv.gz
RiboA_features.tsv.gz
RiboA_matrix.mtx.gz


title: WT_PFG_H3K27ac_rep2


title: Sun1_Control1_CT26_tumors_7


title: Sun1_Control1_CT26_tumors_4


title: Het2_PFG_H3K27ac_rep1


title: whole_blood_donor3_liverun

city: Canberra

first: Alexandra

last: Sneddon

state: ACT

address: 131 Garran Rd Acton

country: Australia

institute: The Australian National University

data_processing:
[globin_model_dev_datasets.tsv] Fast5 files were basecalled with Guppy (v4.0.14) using options {--flowcell FLO-MIN106 --kit SQK-RNA002} and mapped to the GENCODE reference transcriptome (release 34, assembly GRCh38.p13) with minimap2 (v2.17) using options {-ax map-ont --secondary=no -t 15}. To retain only high-confidence mappings, alignments to the reverse strand, secondary or supplementary mappings and unmapped reads were removed using samtools with option {-F 2324}. To only retain reads with a high confidence biotype label, reads were discarded if their primary mapping biotype did not match the most frequent secondary mapping biotype.
[blood_liverun_summary.tsv] For the sequencing run used for real-time testing of RISER, the sequenced reads were basecalled with Guppy (v4.0.14) using options {--flowcell FLO-MIN106 --kit SQK-RNA002} and mapped to the GENCODE reference transcriptome (release 34, assembly GRCh38.p13) with minimap2 (v2.17) using options {-ax map-ont --secondary=no -t 15}. To retain only high-confidence mappings, alignments to the reverse strand, secondary or supplementary mappings and unmapped reads were removed using samtools with option {-F 2324}. To only retain reads with a high confidence biotype label, reads were discarded if their primary mapping biotype did not match the most frequent secondary mapping biotype. For each read, the basecalling summary file and mapping summary were joined with the data from the csv file produced by RISER during live sequencing.
Assembly: GENCODE reference transcriptome (release 34, assembly GRCh38.p13)
Supplementary files format and content: [globin_model_dev_datasets.tsv] column 1: blood donor dataset; column 2: read ID; column 3: transcript ID; column 4: gene ID; column 5: gene name; column 6: transcript length (nt); column 7: transcript biotype; column 8: true if the read mapped to the reverse strand; column 9: true if the mapping was not the primary alignment; column 10: true if the mapping was a supplementary alignment; column 11: mapping quality; column 12: gene name of most common secondary mapping gene (NA if there were no secondary mappings); column 13: number of secondary mappings to the most common secondary mapping gene (NA if there were no secondary mappings).
Supplementary files format and content: [blood_liverun_summary.tsv] column 1: time that RISER retrieved the read from the ReadUntil API; column 2: read ID; column 3: MinION sequencing channel recorded by RISER; column 4: signal length (current samples); column 5: RISER model(s) used (semi-colon separated list); column 6: target probability predicted by each RISER model (one probability per model listed in column 5); column 7: probability threshold for RISER classifier; column 8: RISER mode (enrich or deplete); column 9: RISER decision (accept, reject, try_again or no_decision) (NA means RISER did not make a prediction for this molecule); column 10: row number of this read in the RISER output CSV file; column 11: filename of the fast5 file containing this read; column 12: MinION run ID; column 13: basecalling batch ID; column 14: MinION sequencing channel recorded by basecaller (should be same as column 3); column 15: the mux in the channel that the read came from; column 16: start time of the read (seconds (s) since the beginning of the run); column 17: duration of the read (s); column 18: number of events detected by MinKNOW; column 19: whether or not the read passed the default qscore filter; column 20: start time of the read portion basecalled following adapter trimming (s since the run start); column 21: legacy field from Guppy basecaller (use column 22 instead); column 22: duration of the read portion basecalled after adapter trimming (s); column 23: number of bases in the output sequence; column 24: qscore corresponding to the mean error rate of the sequence; column 25: legacy field from Guppy basecaller (ignore); column 26: median current of the read (pA); column 27: median absolute deviation (MAD) of the read; column 28: median value used by Guppy basecaller for scaling; column 29: MAD value used by Guppy basecaller for scaling; column 30: gene ID that the read mapped to; column 31: transcript ID that the read mapped to; column 32: transcript biotype.

source_name: Whole blood

extract_protocol:
Blood samples were obtained from three human donors with approval from the ethics committee from the Australian National University (ANU) under ethics protocol no. ETH.1.16.01/ETH.01.15.015. Whole blood was collected at the Centre for Personalised Immunology (ANU) in 8.5ml BD Vacutainer Acid Citrate Dextrose (ACD-A) Blood Collection Tubes. For each blood sample, total RNA was extracted using the PureLink RNA Mini kit (Thermo Fisher Scientific). The manufacturer’s instructions were followed and 4ml sample of blood per donor was used. On-column DNase treatment was additionally performed by adding 2 units of DNase I in its recommended buffer to the column-bound sample (New England BioLabs) and incubating at 37oC for 15 minutes. The resultant RNA eluate was additionally purified using AMPure XP SPRI beads (Beckman Coulter Life Sciences) according to the manufacturer’s recommendations. Briefly, the eluate RNA was supplemented with 1.2× volumes of the SPRI bead suspension and the resultant mixture incubated at room temperature for 5 minutes with periodic mixing. The SPRI beads were brought down by a brief 2,000×g spin and separated from the solution on a magnetic rack. The supernatant was removed, and the beads were resuspended in 1ml of 80% v/v ethanol, 20% v/v deionized water mixture and further washed by tube flipping. The bead and solution separation procedure and the ethanol washing process were repeated one more time. Any remaining liquid was brought down by a brief spin and removed using a pipette, and the beads were allowed to air-dry while in the magnetic rack for 2 minutes prior to elution. The purified RNA was then eluted in 20ml of deionized water and the RNA content was assessed using absorbance readout via Nanodrop.
For each of the whole blood samples, 200-600ng of total RNA was used for each 2× library preparation for each sample (all recommended volumes doubled-up). Libraries were made using the direct RNA sequencing kit SQK-RNA002 (Oxford Nanopore Technologies) following manufacturer’s recommendations. The final adaptor-ligated sample was eluted in 20μl (single preparation volume). The flow cell priming was performed as follows. The flow cells were left at 25 °C for 30 minutes to reach ambient temperature. The flow cells were then inserted into the MinION Mk1B and a quality check was performed to ensure that the pore count was above manufacturer warranty level (800 pores). Prior to the sample loading, the priming solution (Flush Buffer mixed with Flush Tether) was degassed in a vacuum chamber for 5 minutes. A similar approach was repeated when loading the RNA library. Nanopore sequencing was performed using an ONT MinION Mk1B equipped with R9.4.1 flow cells; samples were run for 24 hours. Additionally, for the third sample (whole_blood_donor3_liverun) RISER was run at the same time as the MinKNOW sequencing run. In the RISER code, the flow cell channels were split into two groups to remove the effect of inter-flow cell variability by simultaneously testing two conditions: (1) RISER depleting globin mRNA, and (2) no RISER (control). To split the flow cell channels, the channel numbers divisible by 2 were used for the RISER deplete condition (1) while the remaining channels were used for the control condition (2). RISER was started after the first pore scan finished and was run for the same duration as the sequencing run; 24 hours. The live run was performed on a computer running Ubuntu 20.04 with one NVIDIA GeForce GTX 1650 Ti GPU and python v3.8.10.
Nanopore direct RNA sequencing

value: Whole blood


title: wildtype mTECs, DMSO, replicate nextseq A, ALID03

description:
10x Genomics
DMSOA_barcodes.tsv.gz
DMSOA_features.tsv.gz
DMSOA_matrix.mtx.gz


title: Homo_PFG_RNAseq_rep3

description: Sample_homo_PFG_6_IGO_13401_B_19_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt

data_processing:
STAR alignment
Featurecounts quantification
*.bw data was generated using samtools to split aligned reads by strand, followed by generating *.bw using scale factors calculated on unsplit .bam files.
Assembly: hg38
Supplementary files format and content: Raw count table
Supplementary files format and content: bigwig

extract_protocol:
Cells were frozen and total RNA extracted with the Zymo Quick-RNA MiniPrep kit.
Illumina TruSeq Stranded Total RNA LT Kit (RS-122-1202)


title: Homo_PFG_RNAseq_rep2

description: Sample_homo_PFG_5_IGO_13401_B_13_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt


title: Sun1_Control1_CT26_tumors_2


title: Sun1_KO_CT26_tumors_7


title: wildtype mTECs, DMSO, replicate nextseq B, ALID03

description:
10x Genomics
DMSOB_barcodes.tsv.gz
DMSOB_features.tsv.gz
DMSOB_matrix.mtx.gz


title: Sun1_KO_CT26_tumors_6


title: whole_blood_donor1


title: Homo_GT_RNAseq_rep2

description: Sample_homo_GT_5_IGO_13401_B_10_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt

value: GT stage


title: Trim28_Light_rep6


title: Homo_PFG_RNAseq_rep1

description: Sample_homo_PFG_2_IGO_13401_B_7_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt


title: Sun1_KO_CT26_tumors_5


title: whole_blood_donor2


title: Homo_GT_RNAseq_rep3

description: Sample_homo_GT_6_IGO_13401_B_16_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt


title: Sun1_KO_CT26_tumors_4


title: Trim28_Heavy_rep9


title: Homo_GT_RNAseq_rep1

description: Sample_homo_GT_2_IGO_13401_B_4_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt


title: Het2_PFG_RNAseq_rep3

description: Sample_het2_PFG_6_IGO_13401_B_18_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt


title: hek293_liverun

data_processing:
[mRNA_model_dev_datasets.tsv] Fast5 files were basecalled with Guppy (v4.0.14) using options {--flowcell FLO-MIN106 --kit SQK-RNA002} and mapped to the GENCODE reference transcriptome (release 34, assembly GRCh38.p13) with minimap2 (v2.17) using options {-ax map-ont --secondary=no -t 15}. To retain only high-confidence mappings, alignments to the reverse strand, secondary or supplementary mappings and unmapped reads were removed using samtools with option {-F 2324}. To only retain reads with a high confidence biotype label, reads were discarded if their primary mapping biotype did not match the most frequent secondary mapping biotype.
[mtRNA_model_dev_datasets.tsv] Fast5 files were basecalled with Guppy (v4.0.14) using options {--flowcell FLO-MIN106 --kit SQK-RNA002} and mapped to the GENCODE reference transcriptome (release 34, assembly GRCh38.p13) with minimap2 (v2.17) using options {-ax map-ont --secondary=no -t 15}. To retain only high-confidence mappings, alignments to the reverse strand, secondary or supplementary mappings and unmapped reads were removed using samtools with option {-F 2324}. To only retain reads with a high confidence biotype label, reads were discarded if their primary mapping biotype did not match the most frequent secondary mapping biotype.
[HEK293_liverun_summary.tsv] For the sequencing run used for real-time testing of RISER, the sequenced reads were basecalled with Guppy (v4.0.14) using options {--flowcell FLO-MIN106 --kit SQK-RNA002} and mapped to the GENCODE reference transcriptome (release 34, assembly GRCh38.p13) with minimap2 (v2.17) using options {-ax map-ont --secondary=no -t 15}. To retain only high-confidence mappings, alignments to the reverse strand, secondary or supplementary mappings and unmapped reads were removed using samtools with option {-F 2324}. To only retain reads with a high confidence biotype label, reads were discarded if their primary mapping biotype did not match the most frequent secondary mapping biotype. For each read, the basecalling summary file and mapping summary were joined with the data from the csv file produced by RISER during live sequencing.
Assembly: GENCODE reference transcriptome (release 34, assembly GRCh38.p13)
Supplementary files format and content: [mRNA_model_dev_datasets.tsv] column 1: dataset; column 2: read ID; column 3: transcript ID; column 4: gene ID; column 5: gene name; column 6: transcript length (nt); column 7: transcript biotype; column 8: true if the read mapped to the reverse strand; column 9: true if the mapping was not the primary alignment; column 10: true if the mapping was a supplementary alignment; column 11: mapping quality; column 12: most common secondary mapping biotype (NA if there were no secondary mappings); column 13: number of secondary mappings to the most common secondary mapping biotype (NA if there were no secondary mappings).
Supplementary files format and content: [mtRNA_model_dev_datasets.tsv] column 1: dataset; column 2: read ID; column 3: transcript ID; column 4: gene ID; column 5: gene name; column 6: transcript length (nt); column 7: transcript biotype; column 8: true if the read mapped to the reverse strand; column 9: true if the mapping was not the primary alignment; column 10: true if the mapping was a supplementary alignment; column 11: mapping quality; column 12: most common secondary mapping biotype (NA if there were no secondary mappings); column 13: number of secondary mappings to the most common secondary mapping biotype (NA if there were no secondary mappings).
Supplementary files format and content: [HEK293_liverun_summary.tsv] column 1: time that RISER retrieved the read from the ReadUntil API; column 2: read ID; column 3: MinION sequencing channel recorded by RISER; column 4: signal length (current samples); column 5: RISER model(s) used (semi-colon separated list); column 6: target probability predicted by each RISER model (one probability per model listed in column 5); column 7: probability threshold for RISER classifier; column 8: RISER mode (enrich or deplete); column 9: RISER decision (accept, reject, try_again or no_decision) (NA means RISER did not make a prediction for this molecule); column 10: row number of this read in the RISER output CSV file; column 11: filename of the fast5 file containing this read; column 12: MinION run ID; column 13: basecalling batch ID; column 14: MinION sequencing channel recorded by basecaller (should be same as column 3); column 15: the mux in the channel that the read came from; column 16: start time of the read (seconds (s) since the beginning of the run); column 17: duration of the read (s); column 18: number of events detected by MinKNOW; column 19: whether or not the read passed the default qscore filter; column 20: start time of the read portion basecalled following adapter trimming (s since the run start); column 21: legacy field from Guppy basecaller (use column 22 instead); column 22: duration of the read portion basecalled after adapter trimming (s); column 23: number of bases in the output sequence; column 24: qscore corresponding to the mean error rate of the sequence; column 25: legacy field from Guppy basecaller (ignore); column 26: median current of the read (pA); column 27: median absolute deviation (MAD) of the read; column 28: median value used by Guppy basecaller for scaling; column 29: MAD value used by Guppy basecaller for scaling; column 30: gene ID that the read mapped to; column 31: transcript ID that the read mapped to; column 32: transcript biotype.

extract_protocol:
HEK293 and HeLa cells (human cervical cancer) were purchased from the American Type Culture Collection (ATCC) and confirmed via short tandem repeat (STR) profiling with CellBank Australia. The cells were grown in DMEM medium (Gibco) supplemented with 10% fetal bovine serum (FBS) and 1× antibiotic-antimycotic solution (Sigma). Cells were cultured following the protocol previously described (Sneddon et al. 2022). Namely, cell cultures were propagated in a 1:3 split, with replenishment of media every 4 days. Cell culture, cell pellet collection, cell lysis, polyadenylated RNA extraction and RNA cleanup with SPRI beads were performed as previously described (Sneddon et al. 2022).   The immortalized human peripheral vein-derived B-cells GM12878 and B-cell acute lymphocytic leukemia (B-ALL)-derived REH and KOPN8 cell lines were obtained from the Coriell Institute and cultured with 10% FBS-supplemented RPMI1640 media (Gibco) in T25 flasks (Corning) under 5% CO2 and 37°C. Cells were harvested by a 5 minute centrifugation at 300rcf at 4°C. The resultant cell pellet was washed with ice-cold PBS and separated by another centrifugation at 300rcf for 5 minutes and aspirated. The protocols for subculturing, cell lysis and total RNA extraction were performed as described for HEK293 and HeLa cell lines.   The lymphoblastoid cell line (LCL) GM24385 (Corielle Institute) was grown in RPMI1640 media (Gibco) supplemented with 15% Hi-FCS and 2 mM L-Glutamine in 6-well plates (Coning) under 5% CO2. Cells were harvested at a density of 106 cells/ml. Cell pellet collection was performed by transferring GM24385 cell suspension into 15 ml conical centrifuge tubes (Falcon) and centrifuging at 500×g for 10 minutes at room temperature.   To isolate RNA from the cytoplasmic and nuclei fractions, 107 cells were lysed in 200 µl of the non-denaturing lysis buffer containing 25 mM HEPES-KOH (pH 7.6 at 25°C), 50 mM KCl, 5.1 mM MgCl2, 2 mM DTT, 0.1 mM EDTA, 5% v/v glycerol, 2× Complete EDTA-free protease inhibitor and 0.5% v/v Igepal CA-630B. Cells were resuspended in the lysis buffer through pipetting and RNasin Plus (Promega) was immediately added to the final concentration of 1 U/µl. Cell lysis was completed by passing the lysate 4× through a 20-gauge needle followed by passing it 4× through a 27-gauge needle. The cell lysate was then centrifuged at 1,000× g for 5 minutes at 4°C. The supernatant was transferred into a new 1.5ml tube and mixed with 350µl of the RA1 lysis buffer, followed by RNA isolation using silica columns (Macherey Nagel) to obtain the cytoplasmic RNA fraction. The process included on-column Dnase treatment with TURBO Dnase (Thermo Fisher Scientific). The pelleted nuclei were resuspended in 1 ml of ice-cold sterile PBS and 50 µl counted using cell counter (Beckman-Coulter). The nuclei suspension was spun again at 1,000× g for 5 minutes at 4°C, the supernatant aspirated and 6.6×106 nuclei were lysed in 700 µl of the RA1 RNA lysis buffer and isolated using the silica columns as described above. RNA isolated from the cytoplasmic fraction was eluted from the columns in 80µl, and from nuclei in 120µl of Rnase-free water, and stored at -80°C.   For in vitro polyadenylation, ~9µg of the RNA in 94 µl of deionized water or 25mM HEPES-KOH (pH 7.6 at 25°C), 0.1 mM EDTA (HE) buffer were first denatured by incubating at 65°C for 3 minutes and immediately chilling in ice. The solution was then supplemented with 12µl of 10× E. coli Poly(A) Polymerase buffer (New England Biolabs), 8µl of 1mM ATP and mixed. To the resultant solution, 3µl of 40U/µl Rnasin Plus (Promega) and 3µl of 5U/µl E. coli Poly(A) Polymerase (New England Biolabs) were added and mixed, and the resultant mixture incubated at 37°C for 30 minutes. The eluate from in vitro polyadenylated RNA was further purified following the protocol previously described (Sneddon et al. 2022) for RNA cleanup with SPRI beads.
For all samples, the flow cell priming and library sequencing protocol were performed as previously described (Sneddon et al. 2022). Nanopore sequencing was performed using an ONT MinION Mk1B with R9.4.1 flow cell for 24 hours. The default settings for the MinKNOW software (standalone GUI v5.7.10, core v5.7.2) were used and the SQK-RNA002 kit was selected.   Additionally, for the sample hek293_liverun RISER was run at the same time as the MinKNOW sequencing run. In the RISER code, the flow cell channels were split into two groups to remove the effect of inter-flow cell variability by simultaneously testing two conditions: (1) RISER depleting mRNA and mtRNA, and (2) no RISER (control). To split the flow cell channels, the channel numbers divisible by 2 were used for the RISER deplete condition (1) while the remaining channels were used for the control condition (2). RISER was started after the first pore scan finished and was run for the same duration as the sequencing run; 24 hours. The live run was performed on a computer running Ubuntu 20.04 with one NVIDIA GeForce GTX 1650 Ti GPU and python v3.8.10.
Nanopore direct RNA sequencing


title: Trim28_Heavy_rep8


title: Het2_PFG_RNAseq_rep2

description: Sample_het2_PFG_5_IGO_13401_B_12_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt


title: Sun1_KO_CT26_tumors_3


title: Sun1_Control1_CT26_tumors_3


title: reh_rep3

source_name: REH

value: REH


title: Trim28_Light_rep5

source_name: genomic DNA from pancreas

value: pancreas


title: Trim28_Heavy_rep6


title: Het2_PFG_RNAseq_rep1

description: Sample_het2_PFG_2_IGO_13401_B_6_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt

value: PFG stage


title: Sun1_KO_CT26_tumors_1


title: reh_rep4


title: reh_rep1


title: Trim28_Light_rep3


title: Het2_GT_RNAseq_rep2

description: Sample_het2_GT_5_IGO_13401_B_9_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt


title: Sun1_Control2_CT26_cultured_cells

description: DESeq2_CT26_cultured_cells_Control_vs_KO.csv


title: Het2_GT_RNAseq_rep3

description: Sample_het2_GT_6_IGO_13401_B_15_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt


title: Sun1_KO_CT26_tumors_2


title: reh_rep2


title: kopn8_rep4


title: Sun1_Control1_CT26_cultured_cells


title: Het2_GT_RNAseq_rep1

description: Sample_het2_GT_2_IGO_13401_B_3_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt


title: kopn8_rep3


title: Trim28_Heavy_rep4


title: kopn8_rep2


title: WT_PFG_RNAseq_rep3

description: Sample_WT_PFG_6_IGO_13401_B_17_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt

value: WT


title: Trim28_Heavy_rep7


title: WT_PFG_RNAseq_rep2

description: Sample_WT_PFG_5_IGO_13401_B_11_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt


title: kopn8_rep1


title: Trim28_Light_rep2


title: Mouse cardiac ventricle, MAdV-3-infected, rep2

city: Roanoke

first: James

middle: W

last: Smyth

state: VA

address: 2 Riverside Circle

institute: Fralin Biomedical Research Institute

data_processing:
Sequence reads were trimmed with Trimmomatic v.0.36 to remove adapter sequences and poor quality nucleotides
Mapping of trimmed reads to Mus musculus GRCm38 was conducted with STAR aligner v.2.5.2b
featureCounts (from Subread package v.1.5.2) was used to determine unique gene hit counts, with only unique reads within exon regions counted
Assembly: Mus musculus GRCm38
Supplementary files format and content: Comma separated values file with the raw counts for each sample
Supplementary files format and content: Tab delimited txt file with unique hit counts for each sample

source_name: Cardiac ventricle

extract_protocol:
RNA was extracted from snap-frozen tissue by GeneWiz
Library construction was conducted by GeneWiz

treatment_protocol: 8-12-week-old C57BL/6 mice were anesthetized and inoculated via retro-orbital injection  with 0.9% sterile saline (mock-infected) or 5x10^5  infectious units of MAdV-3 diluted in 0.9% sterile saline. Cardiac ventricles were isolated 7 days post-infection

value: Cardiac ventricle

tag: infection


title: Trim28_Light_rep4

tag: tissue


title: Mouse cardiac ventricle, MAdV-3-infected, rep3


title: WT_PFG_RNAseq_rep1

description: Sample_WT_PFG_2_IGO_13401_B_5_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt


title: Trim28_Heavy_rep1


title: Trim28_Heavy_rep2


title: hek293-c_rep2


title: WT_GT_RNAseq_rep3

description: Sample_WT_GT_6_IGO_13401_B_14_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt


title: WT_GT_RNAseq_rep2

description: Sample_WT_GT_5_IGO_13401_B_8_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt


title: Mouse cardiac ventricle, mock-infected, rep3

value: Mock-infected


title: hek293-c_rep1


title: WT_GT_RNAseq_rep1

description: Sample_WT_GT_2_IGO_13401_B_1_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt


title: Trim28_Heavy_rep3


title: secondCohort_WT_rep8

source_name: genomic DNA from 10 days old mouse ear clips

growth_protocol: Ear punch biopsies were collected at 10 days and placed in 20 µl reaction mix composed of genomic DNA lysis buffer (100 mM Tris-HCl pH 8.5, 5 mM EDTA, 0.2% SDS, 100 mM NaCl) supplemented with 20 mg proteinase K (Thermo Scientific, EO0491).

extract_protocol: We used the DNeasy Blood & Tissue Kit (QIAGEN, 69504) for DNA extraction

treatment_protocol: Digestion was carried out overnight in a Thermocycler under the following conditions: 55C for 16 hours, 95C for 10 minutes, 4C hold (lid at 105C). After lysis, the lysate was diluted by adding 160 µl of nuclease-free water (Invitrogen, AM9938) to the same tube (180 µl final volume).

value: ear

tag: developmental stage

value: 10 days


title: Mouse cardiac ventricle, mock-infected, rep1


title: hek293-a

tag: cell line


title: Trim28_Heavy_rep5


title: Sun1_KO_CT26_cultured_cells

tag: cell type

value: mouse syngeneic cell line (colon cancer)

value: Sun1 knockout


title: BT474 Evexomostat (SDX-7320) 12 mpk 007

city: Cambridge

first: Peter

last: Cornelius

state: MA

address: One Broadway, 14th Floor

department: Translational Research

institute: SynDevRx, Inc.

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
One mismatch was allowed for index  sequence identification.
Subsequent analysis was carried out in the Watershed® Omics Bench.
Raw RNA-sequence reads were aligned to the human reference genome (GRCh37/hg19) with NCBI RefSeq annotations using STAR v2.7.5c with non-default parameters: —outFilterIntronMotifs RemoveNoncanonical, —outSAMtype BAM SortedByCoordinate.
Read counts were extracted with featurecounts (subread) v2.0.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw and RPM values for each Sample
Supplementary files format and content: tab-delimited text file of edgeR differentially expressed genes between vehicle and SDX12 samples

growth_protocol:
Female Athymic Nude mice were obtained from Charles River (Wilmington, MA) and implanted with sub-cutaneous, slow-release estrogen (90-day, 0.72 mg β-estradiol; Innovative Research of America; Sarasota, FL).
Three days after receiving the estrogen pellets, mice were injected in the fourth mammary fat pad with 2x107 BT-474 cells (suspended in 50% Matrigel / 50% RPMI-1640).
When tumors exceeded 95 mm3, they were eligible for study enrollment.

extract_protocol:
Tumors were dissected and a portion was placed into RNALater and frozen at -70.
Total RNA was extracted using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
The RNA samples received were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto, CA, USA).
Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). The RNA sequencing library was prepared using the NEBNext Ultra RNA Library
The sequencing library was validated on Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA),
and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA)  and quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
The sequencing library was clustered on one lane of a flowcell.
The flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions.
The sample was sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS).

treatment_protocol: Evexomostat (SDX-7320) was prepared fresh for each dose (administered s.c./Q4D) in 5% mannitol water while vehicle animals received 5% mannitol/water (s.c./Q4D).

value: breast cancer

tag: treatment

value: Evexomostat (SDX-7230)

value: Day 33


title: gm24385


title: hela

source_name: HeLa

value: HeLa


title: Caki-1_HA-TFE3_ChIP_2

city: Wuhan

first: suli

last: LV

address: Wuhan, Hubei, China

institute: Huazhong University of Science and Technology

description: HA-TFE3 narrow peak.bed

data_processing:
Raw reads were first filtered with Trim-Galore
Reads were aligned by Bowtie2 to human hg38 assembly
Alignments with MAPQ > 10 were kept
Bam file were then further filtered with 'RmDup' to remove PCR duplicate
Genomic coverage was generated with bamCoverage. Peak calling was done with MACS2.
Assembly: hg38
Supplementary files format and content: Genomic coverage file generated by bamCoverage tool in bigwig format
Supplementary files format and content: narrow peak generated by MACS2 in .bed format

growth_protocol: Caki-1 cells were cultured in McCoy's 5A Medium (Procell #PM150710) supplemented with 10% fetal bovine serum (FBS)(PAN, Germany. #ST30-3302). Cells were maintained in 37 °C incubator with 5% CO2.

extract_protocol:
Cells were then resuspended in buffer A (10mM HEPES PH7.9, 1.5mM MgCl2, 10mM KCl, 0.5% NP40, 0.5mM DTT) and incubated on ice for 10 minutes. Afterward, cells were resuspended in ChIP Lysis buffer (50mM Tris-Cl PH8.0, 5mM EDTA, 0.2% SDS) and sonicated with BioRuptor (Diagenode). Cell lysate was then cleared by centrifugation at 15000 g for 10 minutes at 4_C. Supernatant was taken and mixed 1:1 with ChIP dilution buffer (300mM NaCl, 2% Triton X-100) and then HA-tag antibody (Cell Signaling Technology #3724). Immunocomplex was then pulled-down with ChIP-Grade Magnetic Protein-G beads (CST 9006). Immunoprecipitate was washed extensively and immunocomplex was eluted by ChIP elution buffer (0.1M NaHCO3 and 1%SDS) with shaking at 65_C for 15 minutes. De-crosslinking was then done at 65_C overnight. DNA was purified for Next generation sequencing.
A-tailing and index adapters were added. The DNA fragments were purified by Ampure XP Beads and then amplified by PCR. PCR product was purified with Ampure XP Beads again and then analyzed on the Agilent Technologies 2100 bioanalyzer for quality control. Pair-end 150 bases reads were generated on Illumina NovaSeq 6000 platform (Illumina).

treatment_protocol: Cells were transduced with lentivirus carrying HA-TFE3 and then selected with Blasticidin.

value: Renal cell Carcinoma

value: HA-TFE3 expressing

tag: chip antibody


title: secondCohort_WT_rep7

value: male


title: gm12878-b_rep3


title: secondCohort_WT_rep6


title: Caki-1_HA-TFE3_ChIP_1

description: HA-TFE3 narrow peak.bed

value: HA-tag antibody (Cell Signaling Technology #3724)


title: Mouse cardiac ventricle, MAdV-3-infected, rep1

tag: strain


title: BT474 Evexomostat (SDX-7320) 12 mpk 005


title: Caki-1_Input_2

description: HA-TFE3 narrow peak.bed


title: secondCohort_WT_rep5


title: gm12878-b_rep2


title: Mouse cardiac ventricle, mock-infected, rep2


title: secondCohort_Trim28_rep14


title: Caki-1_Input_1

description: HA-TFE3 narrow peak.bed


title: gm12878-b_rep1


title: BT474 Evexomostat (SDX-7320) 12 mpk 003


title: HFT CAT 3

city: Napoli

first: Paolo

middle: Antonio

last: Netti

address: Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53

department: IIT - Center for Advanced Biomaterials for Healthcare

country: Italy

institute: IIT

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw counts

source_name: 3D full-thickness in vitro model of the airway

growth_protocol: The full-thickness model was cultured in the Pneumacult medium (Voden), samples were cultured at the Air Liquid Interface (ALI) into transwell or Snapwell inserts (Corning, porosity 0.4 μm) for 10 days

extract_protocol:
Samples were stored at -80°C and then processed using the RNeasy Mini Kit (Qiagen). The connective tissues were cut in small pieces and digested by vortex in 2ml eppendorf with lysis buffer and a stainless steel bead. All the samples were homogenized into QIAshredder (Qiagen) by centrifugation. Total RNA was extracted according to the manufacturer protocol.
mRNA 3'DGE research grade sequencing service (Next Generation Diagnostic srl)

treatment_protocol: Samples were washed in PBS1X and incubated with 0.1% (wt/vol) type XIV protease in PBS1X (Sigma Aldrich) for 20 hours at 4°C. Epithelial cells were detached by flushing a medium containing 20% FBS (vol/vol) and by slowly scraping the surface of the sample. Collected cells were pelleted by centrifugation and resuspended in 1ml of Trypsin (Microtech). The cell suspension was kept at 37 ° C for 5 min and then pipetted to dissociate the cells. After a second centrifugation, the dry cell pellet was stored at -80 °C. The remaining connective tissue was dry and stored at -80 °C.

value: N-HLF - Normal human lung fibroblasts -  code CC-2512, lot 0000669504 (29 Y) - Lonza

value: normal human lung fibroblasts

value: wt

value: Culture in MEM supplemented with supplemented with 20%FBS, 2% of Non-Essential Aminoacids, 1% of L-Glutamine, and 1% of penicillin/streptomycin. In the 3D culture, 0.5mM Ascorbic acid was added in the culture medium. After the seeding of the epithelial cells the culture medium was LHC/RPMI and then Pneumacult.


title: secondCohort_Trim28_rep13


title: A. thalina/T. atroviride, 96 h, rep2

organism:
Arabidopsis thaliana
Trichoderma atroviride

source_name: root

extract_protocol: Total RNA was extracted and sRNA-seq libraries were generated according to the sRNA cloning protocol provided by Solexa.

value: root

value: inoculation with T. atroviride


title: BT474 Evexomostat (SDX-7320) 12 mpk 002


title: A. thalina/T. atroviride, 96 h, rep1


title: HFT CAT 2

value: 3D full-thickness in vitro model of the airway


title: secondCohort_Trim28_rep12

value: ear

value: 10 days


title: BT474 Vehicle 007

value: breast cancer

value: Vehicle


title: Trim28_Light_rep1

value: pancreas


title: HFT CAT 1


title: A. thalina/T. atroviride, 72 h, rep2


title: BT474 Vehicle 006

value: Day 33


title: secondCohort_Trim28_rep11


title: FT CF CAT 5

value: D-HLF-CF- Disease human lung fibroblasts (cystic fibrosis) code CC-194843, lot 9F3124 (45 Y) - Lonza

value: disease human lung fibroblasts (cystic fibrosis)


title: BT474 Evexomostat (SDX-7320) 12 mpk 004

value: Evexomostat (SDX-7230)


title: A. thalina/T. atroviride, 72 h, rep1


title: A. thalina/T. atroviride, 48 h, rep2


title: FT CF CAT 2


title: A. thalina/T. atroviride, 48 h, rep1


title: secondCohort_Trim28_rep10

value: male


title: secondCohort_Trim28_rep9


title: BT474 Vehicle 004


title: BT474 Vehicle 005


title: BT474 Vehicle 001


title: secondCohort_WT_rep4


title: secondCohort_WT_rep2


title: BT474 Vehicle 003


title: H1_hESC_Adaptive_Sampling

data_processing:
*library strategy: Nanopore Sequencing
minimap2 (2.26) alignment
WhatsHap (2.2) variant phasing and haplotype block calling
Assembly: hg38
Supplementary files format and content: .vcf file with all variants called in phased ONECUT1 haplotype block
Supplementary files format and content: .bed file with regions selected for adaptive sampling

growth_protocol: All differentiation experiments were performed on hESCs grown on vitronectin. hESCs were maintained in E8 medium for 2 days to reach ~80% confluence and flash frozen.

extract_protocol:
DNA was extracted using Monarch® HMW DNA Extraction Kit for Cells & Blood (NEB, T3050), according to the manufacturer’s instructions.
Prior to ONT library preparations, DNA was sheared to ~15-20 kb fragment size using Covaris g-TUBE. Sequencing libraries were prepared from ~1–2ug of DNA, using native library preparation kit, SQK-LSK114, according to the manufacturer’s instructions.


title: FT CF CAT 1


title: NovaSeq runs Lane 1

description: Barcodes for Indrops demultiplexing are in pool1_barcodes.yaml

data_processing:
Demulteplexing with Indrops
Alignment with STAR (outFilterMatchNminOverLread 0.44 --outFilterScoreMinOverLread 0.44)
Quantification with dropEst
Data filtration and analysis with Scanpy
Assembly: X.tropicalis  v.10 genome assembly, gene models v. 10.7
Supplementary files format and content: matrix.pkl is raw counts data matrix in a pickle format (can be opened with pickle/pandas packages in python or reticulate package in R)

organism: Xenopus tropicalis

growth_protocol: Xenopus were maintained as it described in Briggs et al., 2018  (staging and collection of the embryos)

extract_protocol:
Development of a dissociation media for Xenopus embryos according to the Briggs et al., 2018 Methods
Libraries were prepared as it described in Klein et al., 2015

value: Whole embryo


title: HBE 3

value: HBE 115-Primary human bronchial epithelial cells (provided by the Primary Cell Culture Facility of the FFC (Istituto G. Gaslini, Genova)

value: cystic fibrosis bronchial epitelial cells

value: Culture in LHC/RPMI and Pneumacult


title: secondCohort_WT_rep1


title: HBE 5


title: FT CF CAT 4

value: wt

value: Culture in MEM supplemented with supplemented with 20%FBS, 2% of Non-Essential Aminoacids, 1% of L-Glutamine, and 1% of penicillin/streptomycin. In the 3D culture, 0.5mM Ascorbic acid was added in the culture medium. After the seeding of the epithelial cells the culture medium was LHC/RPMI and then Pneumacult.


title: NS- esophageal tumor 36

type: RNA

city: Hyderabad

first: Murali

middle: Dharan

last: Bashyam

address: Inner ring road, Uppal

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

description: NS- esophageal squamous cell carcinoma 36

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version v10.7)

data_processing: Agilent Feature Extraction Software (v10.7) was used for background subtraction and LOWESS normalization

source_name: Surgically resected esophagus

label_protocol: 2μg each of total RNA from tumors along with equal quantity of universal reference RNA (pooled RNA from 11 cell lines (Bashyam et al., 2005) were differentially labeled with Cy5 and Cy3 dyes using Quickamp labeling kit (Agilent Technologies, CA, USA) following manufacturer's instructions

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: M

tag: age

value: Esophageal Squamous Cell Carcinoma

tag: grade

value: I

tag: p53 status

value: unstable p53 (NS-)

source_name: pooled 11 cell line

tag: sample type

value: Universal reference RNA


title: HBE 2

value: 3D full-thickness in vitro model of the airway

tag: genotype


title: HBE 1


title: secondCohort_Trim28_rep6

value: ear

value: 10 days


title: Caki-1 shTFE3_2

data_processing:
Raw reads were first filtered with Trim-Galore
Reads were aligned by STAR to human hg38 assembly with the Gencode V39 genome annotation.
Alignments with MAPQ > 10 were kept
Bam files were then further filtered with 'RmDup' to remove PCR duplicate
Gene-level counts were generated with featureCounts and further analyzed for gene differential expression with DeSeq2 with default parameters
Assembly: hg38
Supplementary files format and content: gene_level Counts by "featureCounts" in a text file
Supplementary files format and content: Differentially regulated genes in a text file

extract_protocol:
Cells were then collected into Trizol reagent (Invitrogen #15596026) in RNAase-free microcentrifuge tubes for subsequent RNA extraction. Total RNA was extracted as recommended by the manufacturer.
Sample processing and sequencing were performed by BIG.inc (Shenzhen China). Briefly, messenger RNA was purified with magnetic beads conjugated with Oligo-dT and then fragmented with fragmentation buffer. Then first-strand cDNA was synthesized with random primer. After second-strand cDNA synthesis, A-tailing and RNA index adapters were added. The cDNA fragments were amplified by PCR and products were purified by Ampure XP Beads. The product was analyzed on the Agilent Technologies 2100 bioanalyzer for quality control. The PCR product was heat-denatured and circularized by the splint oligo sequence to get the final library. The final library was amplified with Phi29 DNA Polymerase to make DNA nanoball (DNB) which had more than 300 copies of one molecular. Pair-end 150 bases reads were generated on MGISEQ-2000RS platform (BGI, Shenzhen, China).

treatment_protocol: Caki-1 cells were transduced with lentivirus carrying TFE3-shRNA and Control sequence respectively. 24 hours after lentivirus infection, cells were divided into 6cm dishes. Puromycin (InvivoGen #ANT-PR-1) was added at a final concentration of 1 μg/ml 12 hours later. Cells were selected with puromycin for 3 days and then collected for RNA extraction.

value: Renal cell Carcinoma


title: secondCohort_WT_rep3


title: A. thalina/T. atroviride, 24 h, rep2

data_processing:
Raw reads were quality assessed using cutadapt v1.9.1 and Trimmomatic v0.36 to remove adapter sequences and low-quality reads, respectively.
To identify sRNA source, the sRNA sequences were mapped to the T. atroviride and A. thaliana genomes using standalone BLAST version 2.11.0+  with word length 7 and e-value cut-off of 0.1.
The BLAST hits were then filtered based on their occurrence at only one location and maximum number of mismatches of 1.
Assembly: TAIR10 for A. thaliana, and JGI v2 for T. atroviride
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

value: root

tag: ecotype

value: inoculation with T. atroviride

tag: time


title: HFT EPI 3


title: A. thalina/T. atroviride, 24 h, rep1


title: Caki-1 shTFE3_1


title: HFT EPI 6


title: Caki-1 shControl_2

value: WT


title: secondCohort_Trim28_rep5

data_processing:
GenomeStudio software v.2011.1 and SeSAMe
single_signal_supp.txt = Unmethylated and methylated signal intensities
processed_matrix.txt = Average Beta

tag: Sex

value: male

tag: batch


title: HFT EPI 2

value: HBE 115-Primary human bronchial epithelial cells (provided by the Primary Cell Culture Facility of the FFC (Istituto G. Gaslini, Genova)

value: cystic fibrosis bronchial epitelial cells


title: NovaSeq runs Lane 2

description: Barcodes for Indrops demultiplexing are in pool2_barcodes.yaml

source_name: Whole embryo

tag: developmental stages

value: Whole embryo


title: secondCohort_Trim28_rep8

tag: tissue


title: secondCohort_Trim28_rep4

tag: developmental stage


title: secondCohort_Trim28_rep7


title: Caki-1 shControl_1

tag: cell line


title: NS+ esophageal tumor 34

description: NS+ esophageal squamous cell carcinoma 34

tag: Stage

value: II

value: nuclear-stabilized p53 (NS+)


title: NS+ esophageal tumor 33

description: NS+ esophageal squamous cell carcinoma 33

value: M

value: Esophageal Squamous Cell Carcinoma


title: NS+ esophageal tumor 35

description: NS+ esophageal squamous cell carcinoma 35

value: I


title: NS+ esophageal tumor 32

description: NS+ esophageal squamous cell carcinoma 32

value: Universal reference RNA


title: NS+ esophageal tumor 31

description: NS+ esophageal squamous cell carcinoma 31


title: HFT EPI 1

value: 3D full-thickness in vitro model of the airway

tag: cell type

tag: treatment

value: Culture in LHC/RPMI and Pneumacult


title: wildtype mTECs, Ribo, replicate nextseq B, ALID03

description:
10x Genomics
RiboB_barcodes.tsv.gz
RiboB_features.tsv.gz
RiboB_matrix.mtx.gz

value: mouse tracheal epithelial cells cultured at air-liquid interface

value: wild-type

value: 10 uM Ribo


title: FT CF EPI 5


title: secondCohort_Trim28_rep2

value: ear

value: 10 days


title: FT CF EPI 4


title: UC_TFAP2E

data_processing:
Bowtie2 alignment
MACS2 peaks calling
Target genes search with bedtools
Assembly: X.tropicalis  v.10 , X.laevis v. 9.2
Supplementary files format and content: Three tables for pax3, tfap2a, and tfap2e targets in a csv format. Target genes was searched with 10kb window around the peaks called with MACS2.

extract_protocol: DNA was extracted from Xenopus embryos by sonication, using a 3.2 mm tapered microtip for 13 mm horn (Branson 450 sonicator)


title: FT CF EPI 2


title: NS- esophageal tumor 30

description: NS- esophageal squamous cell carcinoma 30

value: F

value: unstable p53 (NS-)


title: CCA100, YF-17D vaccination, day 7, rep 2

city: Marcy L'Etoile

first: Emilie

last: Chautard

address: 1541 Avenue Marcel Mérieux

institute: Sanofi

data_processing:
A read quality check was performed on raw data in FASTQ format using FastQC (v0.11.2).
Reads were imported and then processed in OmicSoft Array Studio software (v9.0.6.38-v9.0.8.28).
The raw data QC wizard of Array Studio was executed on the reads to assess the read quality.
The reads were aligned with OmicsSoft Aligner (OSA4; (53)) in Array Studio against the Cyno.WashU2013 reference genome using WashUGene20140620 gene annotations, including a first step of read trim per quality score (minimum of 2).
Samples (CCB102J-21, CCA100J1, CCB102J1, CCA100J14, CCA100J-21, CA100J7, CCA100J3, CCB102J3, CCA100J28) that did not meet quality criteria based on the minimal number of reads sequenced underwent a second run, and files were merged after read alignment, i.e. at the BAM file level.
Naïve read count quantification was performed with the Array Studio software using WashUGene20140620 gene annotations (In Array Studio, “Naïve” means that no EM algorithm was used to handle ambiguous reads). Multiple mapping reads and first-read-forward-strand reads were discarded from the analysis (i.e. “Exclude multi-reads” option selected, “Count First-Read-Forward-Strand reads” option unselected).
Assembly: Cyno.WashU2013
Supplementary files format and content: raw_counts.txt raw counts per sample and gene (WashUGene20140620 gene annotations)
Supplementary files format and content: Count_Annotation.txt (annotation file from OmicSoft, https://qiagen.my.salesforce-sites.com/KnowledgeBase/KnowledgeNavigatorPage?id=kA46N0000008OqZSAU&categoryName=OmicSoft_Suite)

organism: Macaca fascicularis

extract_protocol:
Whole blood from cynomolgus macaques was collected in PAXgene tubes (BD762165 –Ozyme), and stored according to the manufacturer's protocol. RNA was extracted with the PAXgene 96 Blood RNA kit (Qiagen-762331) according to manufacturer’s instructions on Tecan Evo150 workstation. The RNA quantity, purity and quality were checked on the Labchip (Caliper) and the Nanodrop Spectrophotometer (Thermo Scientific).
Extracted RNA samples with an A260/A280 ratio ~2, a RIN>8 and a minimal concentration of 70ng/µL of RNA were processed using the GLOBINclear™-Human kit (ThermoFisher - AM1980) for the depletion of the alpha and beta globin mRNA according to manufacturer’s instructions. The quantity, purity and quality of the RNA depleted of globin mRNA was reassessed as already described before library preparation for sequencing. Sequencing libraries were prepared with the TruSeq mRNA stranded kit (Illumina - 20162122/20146602) using 300ng of RNA according to manufacturer’s instructions. The quality, length distribution and quantity of the resulting libraries were analyzed with the Qubit 3.0 Fluorometer (Life Technologies) and the Labchip (Caliper). Libraries were pooled at equimolar amounts and sequenced by single reads of 75bp on high-output flowcell (Illumina – FC-404-2005) using the Nextseq500 sequencer (Illumina) in a batch of 10 samples per flowcell with the specification to achieve 30 million reads per sample. On run completion, libraries were demultiplexed, adapters trimmed and FASTQ files generated.

treatment_protocol: Live, attenuated YF-17D-204 vaccine (monodose Stamaril®, Sanofi)

value: Whole blood

tag: animal id

value: YF-17D Vaccination

value: day 7

value: male


title: CCA100, YF-17D vaccination, day 3, rep 2

value: day 3


title: CCB102, YF-17D vaccination, day 1, rep 2

value: day 1


title: secondCohort_Trim28_rep1


title: FT CF EPI 1

value: HBE 115-Primary human bronchial epithelial cells (provided by the Primary Cell Culture Facility of the FFC (Istituto G. Gaslini, Genova)

value: cystic fibrosis bronchial epitelial cells


title: CCB102, YF-17D vaccination, day 3, rep 2


title: CHP134_WT_dTAG47_4

city: Nashville

first: Jing

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

data_processing:
RNA-seq reads were aligned to the genome using STAR after adapter trimming, and quantified by featureCounts. Differential analysis were performed by DESeq2.
Assembly: hg19
Supplementary files format and content: tab-delimited text file include raw counts for each sample

growth_protocol: Engineered CHP-134 cells were maintained in RPMI with l-glut supplemented with 10% tetracycline approved fetal bovine serum and 1% Penicillin/Streptomycin. Parental CHP-134 cells were maintained similarly, except with normal FBS.

extract_protocol:
Following treatment, total RNA was extracted from approximately 2 million cells using Trizol. RNA was purified using the Zymo Direct-zol RNA mini prep kit.
RNA was submitted to the VANTAGE core at Vanderbilt University Medical Center, who handled all subsequent ribosomal RNA depletion and library generation.

treatment_protocol: For inhibition of N-MYC, engineered CHP-134 cells were plated with 1 μg/ml doxycycline for three days. For parental CHP-134 cells, they were treated with 500 nM dTAG47 or matched DMSO control diluted in there maintenance media for 18 hr

value: neuroblastoma cell line

value: 500 nM dTAG47


title: secondCohort_Trim28_rep3


title: Chip_TFAP2E

value: Whole embryo


title: NS- esophageal tumor 29

description: NS- esophageal squamous cell carcinoma 29

tag: age

value: Esophageal Squamous Cell Carcinoma

value: I

value: Universal reference RNA


title: Input_TFAP2E


title: CCA100, YF-17D vaccination, day 28, rep 2

value: day 28


title: CHP134_WT_dTAG47_3


title: NS+ esophageal tumor 27

description: NS+ esophageal squamous cell carcinoma 27

value: M

tag: grade

value: nuclear-stabilized p53 (NS+)


title: CCB102, YF-17D vaccination, day -21, rep 2

value: Whole blood

value: day -21


title: CHP134_WT_dTAG47_2


title: CCA100, YF-17D vaccination, day -21, rep 2

value: YF-17D Vaccination


title: NS+ esophageal tumor 26

description: NS+ esophageal squamous cell carcinoma 26

tag: p53 status


title: NS+ esophageal tumor 28

description: NS+ esophageal squamous cell carcinoma 28

value: F

tag: sample type


title: CCA100, YF-17D vaccination, day 14, rep 2

value: day 14

value: male


title: NS- esophageal tumor 25

description: NS- esophageal squamous cell carcinoma 25

value: unstable p53 (NS-)


title: MMTV-neu cells

first: Justin

last: Balko

address: 658 Preston Research Building

description: 10X Genomics

data_processing:
Each sample (targeting 15,000 cells per sample) was processed for single-cell 5′ RNA sequencing utilizing the 10x Chromium system. The raw data were demultiplexed and processed using the 10X Cell Ranger software.
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: MMTV-neu parental

extract_protocol:
MMTV-neu cells were harvested directly from cell culture and prepared for single cell RNA sequencing.
Sequencing was performed on the Illumina NovaSeq 6000 targeting 50,000 reads per cell for the 5’ scRNA libraries. Libraries were prepared following the manufacturer’s protocol. The libraries were sequenced using NovaSeq 6000 with 150 bp paired-end reads. RTA (v.2.4.11; Illumina) was used for base calling.

value: MMTV-neu parental

value: Cancer cells


title: CCA100, YF-17D vaccination, day 1, rep 2

value: day 1


title: Sun1_WT_CT26_snATAC

data_processing:
The raw data were first checked for quality using FastQC. The raw sequences were then trimmed and filtered to obtain clean reads, which were mapped to the reference genome (mm10) using Cell Ranger Count. Cell Ranger Arc or Seurat was then used to normalize the raw counts and output the differential expressed genes. For ATAC peaks analysis, Signac was used to identify the differential peaks. ATAC and gene expression data were further integrated to establish the gene regulatory network.
Assembly: mm10
Supplementary files format and content: tsv.gz files include count matrix data
Supplementary files format and content: csv files include the fold change and p values of differential expressed genes from sequencing data of snRNA libraries

growth_protocol: 1 x 10^6 CT26 cells were subcutaneously injected into the right flank of BALB/c mice, and tumors were collected at day 14.

extract_protocol:
Collected tumor tissues were digested with collagenase IV and Dnase I in RPMI into single cells. Single nuclei were prepared and quality controlled, and ATAC and gene expression libraries were prepared, quality controlled and sequenced according to the instruction of the 10x Chromium Single Cell Multiome ATAC + Gene Expression Kit.
Following the 10x Chromium Single Cell Multiome ATAC + Gene Expression Kit User Guide RevF to prepare separated snRNA library and snATAC library.

value: tumors grown subcutaneously in BALB/c mice

value: mouse syngeneic cell line (colon cancer)

tag: genotype

value: Wildtype


title: Sun1_KO_CT26_snATAC


title: CHP134_WT_dTAG47_1

value: neuroblastoma cell line

value: 500 nM dTAG47


title: CHP134_WT_DMSO_4

value: DMSO


title: CHP134_WT_DMSO_3


title: Sun1_KO_CT26_snRNA

description:
10xGenomics
E1_E3_Deseq2_Wald_30.csv


title: CCB102, YF-17D vaccination, day -21, rep 1


title: CCB102, YF-17D vaccination, day 3, rep 1

value: day 3


title: CHP134_WT_DMSO_2


title: CCB102, YF-17D vaccination, day 1, rep 1

value: Whole blood


title: NS+ esophageal tumor 22

description: NS+ esophageal squamous cell carcinoma 22

value: M

value: Esophageal Squamous Cell Carcinoma

value: II

value: nuclear-stabilized p53 (NS+)

value: Universal reference RNA


title: CHP134_WT_DMSO_1


title: NS+ esophageal tumor 23

description: NS+ esophageal squamous cell carcinoma 23

value: F

value: I


title: CCA100, YF-17D vaccination, day 7, rep 1

value: YF-17D Vaccination

value: day 7

value: male


title: NS+ esophageal tumor 21

description: NS+ esophageal squamous cell carcinoma 21


title: VFDM_COMBO_4

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: SclCre;FF1;Dnmt3Δ/Δ;GFP (VF;Dm)

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
Reads were mapped to the mouse genome mm10 with STAR (version 2.7.10a) with default parameters, except filtering out multimapping reads with more than 10 alignment locations (outFilterMultimapNmax=10), filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”) and reducing the minimum of read mapping length to 0.4 (outFilterScoreMinOverLread=0.4 and outFilterMatchNminOverLread=0.4) . The mm10 genome reference was supplemented with CreERT2, induceable Homo_sapiens_JAK2_V617F construct and pEGFP sequences.
All subsequent analyses were performed using the R software (version 4.3.0) and Bioconductor 3.18 packages. The featureCounts function from the Bioconductor Rsubread package (version 2.0.6) was used to count the number of reads overlapping with the exons of each gene (Ensembl release 102) assuming an exon union model
Assembly: mm10
Supplementary files format and content: gene_counts.tsv.gz: gzipped text file with tab-separated RNA-seq raw read counts for each gene; each row contains the annotation and raw counts per gene; columns correspond to: column 1. = gene Ensembl ID, column 2.-32.= read counts per gene and sample. Counts on the CreERT2, pEGFP and Homo_sapiens_JAK2_V617F construct (exons 3 to 12 and exons 13 to 25 separately) are listed at the end of the file

source_name: Bone marrow

growth_protocol: Mice were kept in the animal facility of the University of Basel according to the swiss animal welfare regulations. Bone marrow cells were isolated and sorted immediately after sacrifice.

extract_protocol:
PicoPure RNA isolation kit (ThermoFisher) was used to extract RNA. Cells were directly sorted into the extraction buffer provided with the kit, and the isolation was performed according to the manual.
Stranded RNA-seq libraries were prepared using the kit Takara SMART-Seq Stranded

treatment_protocol: Mice were treated for 8 weeks with pegylated-interferon-alpha (25 ug/kg SC weekly), 5-Azacytidine (2 mg/kg, IP QD) or the combination of both drugs (same dose as treatments alone).

value: Bone marrow

value: HSCs (Lin-Sca1+cKit+CD48-CD150+)

value: pegylated-interferon-alpha + 5-Azacytidine (IFN+Aza)


title: OMOMYC-CHP134-3

value: neuroblastoma cell line

value: 1 μg/ml doxycycline, 3 days


title: NS- esophageal tumor 24

description: NS- esophageal squamous cell carcinoma 24

value: unstable p53 (NS-)


title: OMOMYC-CHP134-2


title: CCA100, YF-17D vaccination, day 3, rep 1

value: Whole blood

value: day 3


title: CCA100, YF-17D vaccination, day 28, rep 1

value: day 28


title: Sun1_WT_CT26_snRNA

description:
10xGenomics
E1_E3_Deseq2_Wald_30.csv

value: tumors grown subcutaneously in BALB/c mice

value: mouse syngeneic cell line (colon cancer)

value: Wildtype


title: VFDM_AZA_4

description: SclCre;FF1;Dnmt3Δ/Δ;GFP (VF;Dm)

value: 5-Azacytidine (Aza)


title: VFDM_AZA_3

description: SclCre;FF1;Dnmt3Δ/Δ;GFP (VF;Dm)


title: CCA100, YF-17D vaccination, day -21, rep 1

value: day -21


title: EGFP-CHP134-3


title: OMOMYC-CHP134-1


title: NS- esophageal tumor 19

description: NS- esophageal squamous cell carcinoma 19

value: M

value: Esophageal Squamous Cell Carcinoma

value: I

value: Universal reference RNA


title: NS+ esophageal tumor 18

description: NS+ esophageal squamous cell carcinoma 18

value: nuclear-stabilized p53 (NS+)


title: VFDM_COMBO_2

description: SclCre;FF1;Dnmt3Δ/Δ;GFP (VF;Dm)

value: Bone marrow

value: HSCs (Lin-Sca1+cKit+CD48-CD150+)

value: pegylated-interferon-alpha + 5-Azacytidine (IFN+Aza)


title: EGFP-CHP134-2

value: neuroblastoma cell line

value: 1 μg/ml doxycycline, 3 days


title: VFDM_AZA_2

description: SclCre;FF1;Dnmt3Δ/Δ;GFP (VF;Dm)


title: CCA100, YF-17D vaccination, day 14, rep 1

value: Whole blood

value: YF-17D Vaccination

value: day 14

value: male


title: VFDM_COMBO_3

description: SclCre;FF1;Dnmt3Δ/Δ;GFP (VF;Dm)


title: VFDM_AZA_1

description: SclCre;FF1;Dnmt3Δ/Δ;GFP (VF;Dm)


title: EGFP-CHP134-1


title: NS- esophageal tumor 17

description: NS- esophageal squamous cell carcinoma 17

value: F

value: II

value: unstable p53 (NS-)


title: VFDM_IFN_4

description: SclCre;FF1;Dnmt3Δ/Δ;GFP (VF;Dm)

value: pegylated-interferon-alpha (IFN)


title: CCB112, YF-17D vaccination, day 7, rep 1

value: day 7


title: RNA-seq D47 rep 2

city: Murfreesboro

first: Rafet

last: Al-Tobasei

address: 358 KOM

department: Computer Science Department

institute: Middle Tennessee State University

data_processing:
RNA-seq analysis: RNA-seq reads were aligned to the genome using STAR after adapter trimming, and quantified by featureCounts. Differential analysis were performed by DESeq2.
Assembly: hg19
Supplementary files format and content: RNA-seq: tab-delimited text file include raw counts for each sample

growth_protocol: Engineered CHP-134 cells were maintained in RPMI with l-glut supplemented with 10% fetal bovine serum and 1%Penicillin/Streptomycin.

treatment_protocol: Engineered CHP-134 cells were treated with 500 nM dTAG47 or matched DMSO control diluted in this maintenance media for 24 hr

value: Cell Line


title: VFDM_IFN_3

description: SclCre;FF1;Dnmt3Δ/Δ;GFP (VF;Dm)


title: NS+ esophageal tumor 20

description: NS+ esophageal squamous cell carcinoma 20

value: M

value: Esophageal Squamous Cell Carcinoma

value: I

value: Universal reference RNA


title: CCB112, YF-17D vaccination, day 28, rep 1

value: day 28


title: RNA-seq D47 rep 1


title: RNA-seq DMSO rep 2


title: CCB112, YF-17D vaccination, day 14, rep 1


title: VFDM_IFN_2

description: SclCre;FF1;Dnmt3Δ/Δ;GFP (VF;Dm)

value: Bone marrow

value: HSCs (Lin-Sca1+cKit+CD48-CD150+)


title: VFDM_IFN_1

description: SclCre;FF1;Dnmt3Δ/Δ;GFP (VF;Dm)


title: VFDM_V_4

description: SclCre;FF1;Dnmt3Δ/Δ;GFP (VF;Dm)

value: Vehicle (V)


title: RNA-seq DMSO rep 1


title: CCA147, YF-17D vaccination, day 3, rep 1

value: Whole blood

value: YF-17D Vaccination

value: day 3


title: CCA100, YF-17D vaccination, day 1, rep 1

value: day 1

value: male


title: NS- esophageal tumor 15

description: NS- esophageal squamous cell carcinoma 15

value: F

value: II

value: unstable p53 (NS-)


title: NS- esophageal tumor 11

description: NS- esophageal squamous cell carcinoma 11