title: MHC-P-701_Well_C01

tag: strain

value: 48hr infection with LCMV Cl 13 + 6 hr stimulation with poly (I:C)


title: Muscle-invasive bladder cancer 53403

status: Public on Dec 31 2023

type: RNA

city: Bangor

first: Tim

last: Smith

address: Dean Street

department: School of Computer Science and Engineering

country: United Kingdom

institute: University of Bangor

description: Muscle-invasive bladder cancer

hyb_protocol: Sample hybridisation on Clariom S arrays was carried out by Yourgene Health (Manchester, UK). Batches of CEL files were GC SST (Signal Space Transformation with probe Guanine Cytosine Count Correction) RNA normalised using Affymetrix Array Power Tools. (https://www.thermofisher.com/uk/en/home/life-science/microarray-analysis/microarray-analysis-partners-programs/affymetrix-developers-network.html)

scan_protocol: standard Affymetrix protocol

data_processing: The log2-summarised gene level expression values generated were batch-corrected using the ComBat function from the Bioconductor package sva.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Anonymised

label_protocol: RNA extracted from both sample cohorts were subject to Clariom S analysis. RNA (8 ng/µl in a 9 µl volume) was prepared for gene expression arrays with the Clariom S pico HT human assay (Thermo Fisher Scientific).

extract_protocol: Two 10µm sections from FFPE bladder cancer embodied blocks. RNA was extracted from the two 10 µm sections using the Roche High Pure FFPET RNA isolation kit. RNA yield was determined on Qubit fluorometer (Invitrogen, Paisley, UK).

tag: condition

value: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 53404

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 52502

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 53505

description: Muscle-invasive bladder cancer


title: MHC-P-701_Well_B12

type: SRA

city: Ede

first: Alphonsus

middle: Chinedu

last: Ugwu

state: osun state

address: redeemers' university ede osun state

department: Biological Sciences

country: Nigeria

institute: Africa Centre of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s 6 University, Ede, Osun State, Nigeria

library_source: transcriptomic

data_processing:
Sequence data were analysed using the Seven Bridges Genomics bioinformatics platform (BD: Precise Whole Transcriptome Assay Analysis Pipeline v2.0). This pipeline performs all required steps to demultiplex, align, and quantitate sequencing reads from BD™ Precise Whole Transcriptome Assay. After performing a quality control assessment using FastQC, the pipeline filters and demultiplexes sequencing reads based on the sequence of the 8 base sample barcode. It aligns reads from each sample to the transcriptome using STAR, with feature counting by the union rules of HTSeq-count. The initial quantification is performed by counting the unique molecular indices (MI) mapped to each feature. Lastly, the pipeline uses two error correction algorithms to remove MI errors. In brief, MI errors that are derived from sequencing base calls and PCR substitution errors are identified and adjusted to a single MI barcode using Recursive Substitution Error Correction™ (RSEC). Subsequently, MI errors that are derived from library preparation steps or sequencing base deletion errors are adjusted using Distribution-Based Error Correction™ (DBEC).
A cell was considered to be infected if there was at least one GFP sequence read count. This information was then used to define the groups to compare in EdgeR. Differential gene expression was measured between infected and uninfected cells in each subset (Adjusted p-value less than 0.05).
Precise WTA Sample Demultiplexing:Paired-end reads are demultiplexed per well based on the sequence of the sample index. This sample index is found in the first 8 bases of Read 01. The Molecular Index is found in Read 01, in positions 8 to 16. The demultiplexing process also includes a structure filtering step. After filtering, the final step in this process stores the Molecular Index in the demultiplexed FASTQ files by appending the index to the sequence headers of Read 02 FASTQ files. The Read 02s from each well are trimmed by Flexbar to remove any Illumina adapter contaminants and mapped to the reference genome using STAR.
Precise WTA Alignment Quantification: After Read 02s are aligned using STAR, the alignments are assigned to gene counts using a custom implementation of HTSeq-count. The number of reads mapping to each gene is generated in the DBEC Read Mapping Report. The unique counts for molecular indices are calculated in the DBEC Molecular Index Mapping Report
Genome_build: mm9
Supplementary_files_format_and_content: text document (after removal of Molecular indices error using Recursive Substitution Error Correction™ (RSEC) and Distribution-Based Error Correction™ (DBEC))

organism: Mus musculus

source_name: Bone marrow derived APC

growth_protocol: BM derived cells were generated by incubating bone marrow stem cells with growth factor (GM-CSF/ IL-4) for 6 days in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10 % foetal calf serum (FCS), 100 U penicillin/ml, 0.1 mg streptomycin/ml and 50 M 2-mercaptoethanol. Differentiated cells were harvested and sorted into the three BM geoups by flow cytometry before infection with LCMV or stimulation with poly (I:C).

extract_protocol:
The cells are collected in WTA single cell encoding plate, RNA secondary structure is done at 65C for 3 minutes (hold at 4C), mastermix containing BD customised RT enzymes is added (PN 650000041) and run at 42C for 30 minutes, heat inactivated at 80C for 5 minutes before holding at 4C. The samples is pooled and purify before library prep.
Libraries of the cellular RNA were made using the BD WTA single cell kit and sequenced using MiSeq V2 from Illumina (BM-DC, BM-M, DN).

treatment_protocol: Sorted CD11c+MHC class II+ bone marrow derived cell populations (dendritic cells [BMDC], macrophages [BM-M], double negative cells [DN]) were infected with LCMV clone 13 expressing GFP, as previously described for 12 and 48hr for single cell (from the 12 h culture) sorting into customised BD WTA single cell encoding plates for RNA extraction and reverse transcription (primary infection) according to manufacturer’s instructions (PN 910000014 Rev. 03). Furthermore, a subset of infected cells (from the 48 h culture) were stimulated with 100 µg poly (I:C)/ml and incubated for another 6hr before single cell sorting as above.

tag: cell type

value: Bone marrow derived APC

tag: treatment


title: Muscle-invasive bladder cancer 53101

description: Muscle-invasive bladder cancer


title: mediastinal lymph node rep1

city: Shanghai

first: Liwen

last: Fan

address: No.241 West Huaihai Street

country: China

institute: Shanghai Chest Hospital

description: mediastinal lymph node sample from patient 1

data_processing:
Raw gene expression matrix was generated for each sample using the 10X genomics Cell Ranger toolkit (version 4.0.0) and mapped to the GRCh38 human reference genome.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.

molecule: polyA RNA

extract_protocol:
Samples were collected, washed, miced, and digested into single-cell suspensions. Cells were then lysed, and the released RNA was barcoded via reverse transcription in individual GEMs.
RNA libraries were prepared with Chromium Single cell 3' v3.1 Kits according to the manufacturer's protocol.

tag: tumor stage

tag: patient number

value: patient 1


title: Muscle-invasive bladder cancer 51204

description: Muscle-invasive bladder cancer


title: AMH-EGFP+ hiGC, D11, biol rep 2, sequenced at the same time with CD55+, CD55+AMH-EGFP- cells

city: Beijing

first: Kehkooi

last: Kee

address: Shuangqing Road, Haidian District

department: Department of Basic Medical Sciences

institute: Tsinghua University

description:
AMH-EGFP-2
Fpkms_CD55+_CD55+AMH-_AMH+

data_processing:
Trim Galor (version 0.5.0)  was used to remove adaptors and index. FastQC (version 0.11.8) was used to check the quality of raw sequencing reads.
Hisat2  (version 2.1.0)  was used for mapping.
Read count extraction and normalization were performed using Cuffnorm (version 2.2.1).
Assembly: h19
Supplementary files format and content: csv files include FPKM values for each sample

source_name: in vtiro induced human granulosa cells

extract_protocol:
RNA was extracted from cells lysed in TRIZOL. 10ng of total RNA was used for the construction of sequencing libraries.
cDNA libraries were prepared according to smart-Seq2 protocol. Final DNA libraries used for RNA-Seq were prepared using TruePrepTM DNA Library Prep Kit V2 for Illumina following manufactures' protocol.

value: in vtiro induced human granulosa cells

tag: genotype

value: WT

value: FOXL2 & NR5A1 overexpression


title: seed, Bolstar, Ina_TW2, rep2; Chrisbis44

city: Wageningen

first: Marie

last: Duhamel

address: Droevendaalsesteeg 1

department: Plant Science Group

country: Netherlands

institute: Wageningen University & Research

library_source: genomic

data_processing:
To analyse the raw sequences obtained and estimate methylation levels per chromosome and compare them across treatment between controls and seeds from plants primed by Ina, BaBa and MeJa, we used the pipeline MethPipe (Song et al.,2013)
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for adapter trimming as well as quality control, with some added functionality to remove biased methylation positions.
Abismal (de Sena Brandine et al., 2021) was used to construct the methylome and map bisulfite treated short reads on the tomato plant genome.
Supplementary files format and content: The file mw.bed is in a bed format and contains information of the hypomethylated regions from the genome of control Moneyberg tomato seeds (from untreated plants).
Supplementary files format and content: The file mb2.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Moneyberg tomato seeds from plants treated with Baba in time window 2.
Supplementary files format and content: The file mi2.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Moneyberg tomato seeds from plants treated with Ina in time window 2.
Supplementary files format and content: The file mm3.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Moneyberg tomato seeds from plants treated with MeJA in time window 3.
Supplementary files format and content: The file mb3.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Moneyberg tomato seeds from plants treated with MeJA in time window 3.
Supplementary files format and content: The file bb2.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Bolstar tomato seeds from plants treated with Baba in time window 2.
Supplementary files format and content: The file bw.bed is in a bed format and contains information of the hypomethylated regions from the genome of the control Bolstar tomato seeds (from untreated plants).
Supplementary files format and content: The file bi2.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Bolstar tomato seeds from plants treated with Ina in time window 2.

molecule: genomic DNA

organism: Solanum lycopersicum

source_name: seed

extract_protocol:
The DNA extraction was performed following the manufacturer instructions using the Quick-DNA Plant/Seed Miniprep Kit from Zymoresearch. For each sample the DNA concentration and quality was measured using a Qubit fluorometer.
Ultralow Methyl-Seq System (Tecan/NuGEN, Redwood City, CA) has been used for library preparation following the manufacturer’s instructions. DNA samples were quantified with Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA). Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay (Agilent technologies, Santa Clara, CA).
Libraries were then prepared for sequencing and sequenced on paired-end 150 bp mode on NovaSeq6000 (Illumina, San Diego, CA).

tag: tissue

value: seed

value: Bolstar


title: seed, Bolstar, Ina_TW2, rep3; Chrisbis45


title: adjacent normal lung rep2

description: adjacent normal lung sample from patient 2

value: patient 2


title: Muscle-invasive bladder cancer 17404

description: Muscle-invasive bladder cancer


title: MHC-P-701_Well_B11


title: MHC-P-701_Well_B08


title: MHC-P-701_Well_B09


title: seed, Bolstar, Control, rep6; Chrisbis42

description: bw.bed

value: Control


title: Muscle-invasive bladder cancer 17402

description: Muscle-invasive bladder cancer


title: non-small cell lung cancer rep2

description: tumor sample from patient 2


title: seed, Bolstar, Ina_TW2, rep1; Chrisbis43


title: MHC-P-701_Well_B10


title: non-small cell lung cancer rep1

description: tumor sample from patient 1


title: adjacent normal lung rep1

description: adjacent normal lung sample from patient 1


title: Muscle-invasive bladder cancer 17104

description: Muscle-invasive bladder cancer


title: MHC-P-701_Well_B07


title: WC_13

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

country: USA

institute: Penn State University

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read. R2 reads were generated as UMI sequences that were later used to extract PCR duplicates. R1 and R3 reads were used as paired sequencing reads. To assess the read quality, FastQC was run, and low quality reads were removed using sickle with default setting. BBDuk version 36_49  was used to trim/filter low quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the human reference genome GRCh38 was done using HISAT2 version 2.1.0 applying --no-mixed and --no-discordant options. UMI specific workflow that was developed and distributed by Tecan Genomics was used to extract reads that are free from PCR artifacts i.e., deduplication. The resulting deduplicated reads were summarized to each gene using HTseq-count version 0.11.2 by supplementing Ensembl gene annotation GRCh38.78 and ERCC spike-in genes.
Genome_build: GRCh38
Genome_build: mm9
Supplementary_files_format_and_content: Raw read counts are provided in TS_LC_WC_NC.txt and MouseAB_Rawcount.txt files, respectively.
paired-end (R1 and R3, R2 is UMI)

growth_protocol:
Coverslips Fisher Scientific, 12-545-80 were coated with Poly-L-Lysine PLL by incubation in PLL solution 0.01% for 30 minutes at 37°C. TOV-21G ATCC, CRL-11730 cells were grown for 48 hours on cover slips in the Complete Growth Medium [a 1:1 mixture of MCDB 105 1.5 g/L sodium bicarbonate and MCDB 199 2.2 g/L sodium bicarbonate added with fetal bovine serum at a final concentration of 15%] for RNA collection.
Mice were deeply anesthetized with isoflurane Halocarbon. A block of brain containing motor cortex MCx was removed and coronal slices 300 μm thick were cut on a vibrating microtome Leica in ice-cold physiological solution ACSF. The solution contained the following in mM: 130 NaCl, 3 KCl, 1.25 KH2PO4, 20 NaHCO3, 10 glucose, 1.3 MgSO4, 2.5 CaCl2 pH 7.35-7.4, in 95% O2-5% CO2. All solutions were made with nuclease-free, de-ionized, not DEPC-treated water Ambion AM 9938. Slices were incubated for 1 hour at 30°C, then kept at room temperature. For electrophysiological extraction of RNA, slices were held in a chamber on a motorized stage microscope Olympus BX61WI, Gibraltar Burleigh and superfused with ACSF. The location of motor cortex MCx was identified by 1.5-2.0 mm rostral to the start of the hippocampus.

extract_protocol:
For RNA extraction, cultures and slices were held separately in a chamber on a motorized stage on a motorized microscope Olympus BX61WI, Gibraltar Burleigh Thorlabs. Cultures were superfused 2-4 ml/min in a bath solution of in mM: 145 N-methylglucamine NMG, 2 CaCl2, 1 MgCl2, 10 HEPES, 60 glucose pH 7.3, osmolality 300, in 95% O2-5% CO2 . All procedures were performed with a Multiclamp 700B patch-clamp amplifier Molecular Devices, LLC and using borosilicate glass pipettes with filament, OD 1.5 mm, ID 1.10 mm, Sutter and the input resistance was in the range of 3-9 MΩ. RNA was extracted with a 1440A Digidata AD board Molecular Devices, LLC under pClamp v10. Electrodes pipettes were filled with in mM: 100 KCl, 35 N-methylglucamine NMG, 10 EGTA, 1 CaCl2, 4 MgCl2, and 10 HEPES pH 7.3, 290 mOsm for the RNA extraction from the TOV-21G cells. Electrodes were filled with in mM: 130 K-gluconate, 10 KCl, 10 HEPES, 10 EGTA, 2 MgCl2, 2 Na-ATP, 0.2 Na-GTP, and 5 glutathione pH 7.3, 280-290 mOsm for the RNA extraction from the Thy1-YFP L5 neurons. For the RNA extraction from the Thy1-GCaMP6f L2/3 neurons, electrodes were filled with in mM: 110 K-gluconate, 4 KCl, 4 NaCl, 0.2 CaCl2, 10 HEPES, 1.1 EGTA, 2 Mg-ATP, 1 MgCl2, and 5 glutathione pH 7.2-7.3, 300 mOsm. Membrane voltages were corrected for an estimated liquid junction potential of about 10 mV. Perforation was performed using -escin antibiotics 50 M from a stock solution 25 mM respective for each cellular population. All solutions were made with nuclease-free, de-ionized, not DEPC-treated water Ambion AM 9938. Lucifer yellow 50 mM was added to the electrode intracellular working solution for all cellular populations. The intercellular working solution including the antibiotics and dye was prepared fresh daily and used at room temperature and were backfilled into the electrodes for the patch-clamp experiments. Holding potentials for TOV-21G cells and cortical neurons were -80 mV and -70 mV, respectively. Electrodes were made by a PP-830 Narishige puller and positive pressure was applied as the pipettes were advanced to the cell of interest. The leak current Ilk was then used for the holding current in the current-clamp protocol and it was noted before and after the current was injected in all cellular populations. Seven current injection steps of 5 pA each was applied for a duration of 500 ms per step for the RNA extraction. Following RNA extraction, electrodes were slowly retracted while leaving the cell intact in its native environment, and the pipette solution was collected for sequencing. Each sample tube was prefilled with 2 µL of IGEPAL working mixture per tube, and positive pressure was applied to eject the internal contents of the electrode into a sample tube. The IGEPAL working mixture contained 65 µL nuclease-free de-ionized water Ambion, AM9938, 25 µL RNaseOUT™ Recombinant Ribonuclease Inhibitor ThermoFisher, 10 µL IGEPAL CA-630 Alfa Aesar, J61055 and was stored in 4°C for up two weeks. RNA was collected in 0.5 mL tubes Protein LoBind Tube 0.5 mL, Eppendorf, 022431064. After RNA extraction, samples were transferred on dry ice and stored at -80°C. After each RNA extraction, the electrode holder and silver-chloride recording electrode were cleaned with 70% ethanol. Cytosolic extraction for all cellular populations was performed by first doing whole-cell patch-clamp, then applying negative pressure light suction to harvest cellular content into IGEPAL working mixture.
The cDNA libraries were prepared using Ovation SoLo RNA-Seq System Tecan Genomics.  UMIs are used to eliminate possible PCR duplicates in sequencing datasets and facilitate unbiased gene expression profiling. For some experiments, ERCC RNA Spike-In Mix Thermo Fisher Scientific was included in the library preparation. The processed libraries were assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent Technologies. The libraries were pooled and loaded onto a TruSeq SBS v3 flow cells on an Illumina HiSeq 2500 Illumina or an S1 flow cell on an Illumina NovaSeq 6000 Illumina , and run for 2X50 cycles according to the manufacturer's instructions. De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq version 2.18.0.12 allowing no mismatches in the index read.

treatment_protocol: For some experiments, TOV-21G cells were cultured in the Complete Growth Medium added with a IκB kinase IKK inhibitor, IKK-16 IKK Inhibitor VII Sigma-Aldrich at 1 µM for 72 hours before RNA collection.

value: TOV-21G, derived from human ovarian cancer

tag: collection

value: WC-seq


title: seed, Bolstar, Control, rep4; Chrisbis40

description: bw.bed


title: seed, Bolstar, Control, rep3; Chrisbis39

description: bw.bed


title: Muscle-invasive bladder cancer 16403

description: Muscle-invasive bladder cancer


title: WC_12


title: MHC-P-701_Well_B06


title: seed, Bolstar, Control, rep5; Chrisbis41

description: bw.bed


title: WC_11


title: MHC-P-701_Well_B05


title: MHC-P-701_Well_B04


title: seed, Bolstar, Control, rep2; Chrisbis38

description: bw.bed


title: WC_10


title: WC_9


title: seed, Bolstar, Control, rep1; Chrisbis37

description: bw.bed


title: MHC-P-701_Well_B02


title: WC_8


title: seed, Bolstar, BABA_TW2, rep6; Chrisbis36


title: MHC-P-701_Well_B01


title: WC_7


title: MHC-P-701_Well_A12

value: 48hr treatment with Phosphate buffer saline (PBS)


title: WC_6


title: seed, Bolstar, BABA_TW2, rep3; Chrisbis33


title: seed, Bolstar, BABA_TW2, rep5; Chrisbis35


title: Muscle-invasive bladder cancer 15402

description: Muscle-invasive bladder cancer


title: seed, Bolstar, BABA_TW2, rep4; Chrisbis34


title: seed, Bolstar, BABA_TW2, rep2; Chrisbis32


title: Muscle-invasive bladder cancer 15401

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 15303

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 15602

description: Muscle-invasive bladder cancer


title: WC_4


title: MHC-P-701_Well_A10


title: MHC-P-701_Well_B03


title: Muscle-invasive bladder cancer 15107

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 15601

description: Muscle-invasive bladder cancer


title: seed, Bolstar, BABA_TW2, rep1; Chrisbis31


title: WC_3


title: seed, Moneyberg, BABA_TW3, rep6; Chrisbis30

value: Moneyberg


title: WC_2


title: MHC-P-701_Well_A08


title: Muscle-invasive bladder cancer 15104

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 10101

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 15302

description: Muscle-invasive bladder cancer


title: WC_5


title: MHC-P-701_Well_A11


title: Muscle-invasive bladder cancer 14406

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 15106

description: Muscle-invasive bladder cancer


title: seed, Moneyberg, BABA_TW3, rep5; Chrisbis29


title: MHC-P-701_Well_A06


title: seed, Moneyberg, BABA_TW3, rep4; Chrisbis28


title: MHC-P-701_Well_A07


title: WC_1


title: MHC-P-701_Well_A05


title: MHC-P-701_Well_A09


title: LC_24

value: LC-seq


title: LC_25


title: seed, Moneyberg, BABA_TW3, rep3; Chrisbis27


title: LC_22


title: MHC-P-701_Well_A04


title: seed, Moneyberg, BABA_TW3, rep2; Chrisbis26


title: Muscle-invasive bladder cancer 17103

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 8401

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 7602

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 7601

description: Muscle-invasive bladder cancer


title: MHC-P-701_Well_A03


title: seed, Moneyberg, BABA_TW3, rep1; Chrisbis25


title: seed, Moneyberg, MeJA_TW3, rep6; Chrisbis24


title: LC_21


title: LC_20


title: seed, Moneyberg, MeJA_TW3, rep5; Chrisbis23


title: Muscle-invasive bladder cancer 7403

description: Muscle-invasive bladder cancer


title: MHC-P-701_Well_A01


title: Muscle-invasive bladder cancer 7401

description: Muscle-invasive bladder cancer


title: LC_19


title: seed, Moneyberg, MeJA_TW3, rep4; Chrisbis22


title: MHC-P-701_Well_A02


title: seed, Moneyberg, MeJA_TW3, rep3; Chrisbis21


title: LC_17


title: seed, Moneyberg, MeJA_TW3, rep2; Chrisbis20


title: LC_16


title: Muscle-invasive bladder cancer 7202

description: Muscle-invasive bladder cancer


title: LC_15


title: N22 Drought  REP3

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

description: Transcriptome

data_processing:
Low-quality reads with Phred score >30 were filtered
The raw sequence reads were filtered using NGSQC V2.3.3.
Reads were mapped against the rice genome using Tophat V2.1.1.
Reference-based assembly was performed using cufflinks V2.2.1.
Pairwise differential expression analysis was performed using EdgeR.
Genome_build: RGAP V7.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene in the drought sensitive and tolerant cultivars under control and drought conditions

organism: Oryza sativa

source_name: Seedling

growth_protocol: Oryza sativa IR64, N22 seedling were grown in a culture room.

extract_protocol:
Total RNA was extracted using TRI Reagent. RNA quantification was performed and quality was assessed using Agilent Bioanalyzer. cDNA libraries were prepared and sequencing was performed on Illumina HiSeq platform.
RNA-seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Seedlings were given 6h treatment where RO water was used as control and 20% PEG 6000 as drought stress condition.

value: Drought

tag: age

value: 21 Days


title: seed, Moneyberg, Ina_TW2, rep6; Chrisbis18


title: Muscle-invasive bladder cancer 6601

description: Muscle-invasive bladder cancer

value: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 9501

description: Muscle-invasive bladder cancer


title: seed, Moneyberg, Ina_TW2, rep5; Chrisbis17


title: Muscle-invasive bladder cancer 7502

description: Muscle-invasive bladder cancer


title: LC_11


title: N22 Control REP3

description: Transcriptome


title: seed, Moneyberg, Ina_TW2, rep4; Chrisbis16


title: T47D/TR-2 Res2

city: Seoul

first: Mi-Ock

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

department: College of Pharmarcy

country: South Korea

institute: Seoul National University

description: Gene expression data from human breast carcinoma cell line (T47D)

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hydbridized to the Affymetrix GeneChip Array at 45°C for 16 h

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix)

data_processing: Array data export processing and analysis was performed using Affymetrix GeneChip Command Console Softward (AGCC)

source_name: Human breast carcinoma cell line, tamoxifen-resistant

label_protocol: The sense cDNA was then fragmented and bio-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: T47D/S2 and T47D/TR-2 cells were maintained in RPMI 1640 (pheno red-free) medium containing 2% FBS, glutamax, and insulin. Tamoxifen-resistant T47D/TR-2 cells were maintained with 1 μM tamoxifen contained in the base medium

extract_protocol: Trizol extractions of total RNA was performed using manufacturere's instructions

treatment_protocol: T47D/S2 and T47D/TR-2 cells were analyzed at basal state (no treatment)

tag: gender

value: female


title: Muscle-invasive bladder cancer 6432

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 6419

description: Muscle-invasive bladder cancer


title: LC_10


title: seed, Moneyberg, MeJA_TW3, rep1; Chrisbis19


title: T47D/S2 Control1

source_name: Human breast carcinoma cell line


title: LC_9


title: T47D/TR-2 Res1


title: seed, Moneyberg, Ina_TW2, rep3; Chrisbis15


title: T47D/S2 Control2


title: IR64 Control REP3

description: Transcriptome


title: LC_8


title: Muscle-invasive bladder cancer 1203

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 1206

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 1202

description: Muscle-invasive bladder cancer


title: N22 Drought  REP2

description: Transcriptome


title: LC_7


title: IR64 Drought  REP3

description: Transcriptome


title: seed, Moneyberg, Ina_TW2, rep1; Chrisbis13


title: N22 Control REP2

description: Transcriptome


title: seed, Moneyberg, BABA_TW2, rep6; Chrisbis12


title: LC_6


title: IR64 Drought  REP2

description: Transcriptome


title: Muscle-invasive bladder cancer 1105

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 1109

description: Muscle-invasive bladder cancer


title: LC_5


title: IR64 Control REP2

description: Transcriptome


title: N22 Drought  REP1

description: Transcriptome


title: Muscle-invasive bladder cancer 1101

description: Muscle-invasive bladder cancer


title: LC_4


title: seed, Moneyberg, BABA_TW2, rep4; Chrisbis10


title: seed, Moneyberg, Ina_TW2, rep2; Chrisbis14


title: N22 Control REP1

description: Transcriptome


title: seed, Moneyberg, BABA_TW2, rep5; Chrisbis11


title: Muscle-invasive bladder cancer 55506

description: Muscle-invasive bladder cancer


title: LC_3


title: LC_2


title: seed, Moneyberg, BABA_TW2, rep2; Chrisbis8


title: Muscle-invasive bladder cancer 5602 A

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 5604 A

description: Muscle-invasive bladder cancer


title: LC_1


title: seed, Moneyberg, BABA_TW2, rep1; Chrisbis7


title: Muscle-invasive bladder cancer 5506 A

description: Muscle-invasive bladder cancer


title: ALL_2_3 RNA

city: Chengdu

first: Hongli

last: Lai

state: Sichuan

address: No. 37, Guoxue Alley

institute: West China Hospital, Sichuan University

data_processing:
Clean reads were aligned by Hisat2.
StringTie were used to reads quantification.
Stringtie and Cuffmerge were used to process transcripts.
Differentially expressed sRNAs were defined as those with |log2-fold change|>1 and p<0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

source_name: leukemia cells

extract_protocol:
Long RNA was extracted by a QIAamp RNA Blood Mini Kit (QIAGEN, Germany), and ribosomal RNA was removed.
For mRNA, NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used to construct a sequencing library.

value: bone marrow

tag: state


title: seed, Moneyberg, Control, rep6; Chrisbis6

description: mw.bed


title: seed, Moneyberg, BABA_TW2, rep3; Chrisbis9


title: seed, Moneyberg, Control, rep5; Chrisbis5

description: mw.bed


title: ALL_2_1 RNA


title: seed, Moneyberg, Control, rep4; Chrisbis4

description: mw.bed


title: IR64 Drought  REP1

description: Transcriptome


title: seed, Moneyberg, Control, rep3; Chrisbis3

description: mw.bed


title: ALL_1_4 RNA


title: IR64 Control REP1

description: Transcriptome


title: ALL_2_4 RNA


title: ALL_1_3 RNA


title: seed, Moneyberg, Control, rep2; Chrisbis2

description: mw.bed


title: Muscle-invasive bladder cancer 5504 A

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 5505 A

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 5501 A0

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 5410 1A

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 5503 C

description: Muscle-invasive bladder cancer


title: ALL_2_2 RNA


title: seed, Moneyberg, Control, rep1; Chrisbis1

description: mw.bed


title: seed, Bolstar, Ina_TW2, rep6; Chris48


title: ALL_1_1 RNA


title: Muscle-invasive bladder cancer 5409 A

description: Muscle-invasive bladder cancer


title: LC_18


title: seed, Bolstar, Ina_TW2, rep5; Chris47


title: Muscle-invasive bladder cancer 5406 A

description: Muscle-invasive bladder cancer


title: ALL_1_2 RNA


title: Combi-3

city: zhengzhou

first: yichao

last: Xu

state: Henan

address: No.100 Science Avenue

department: School of Pharmaceutical Sciences

institute: Zhengzhou university

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.4.1 and paired-end clean reads were aligned to the reference genome using hisat2 v2.1.0.
The count data are anaylized by DESeq2 and generates the transformed versions of the count data.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene of every sample
Supplementary_files_format_and_content: tab-delimited text files include transformed gene values for every gene of every sample

source_name: Hela

growth_protocol: Hela cells are cultrued in RPMI 1640 with 10% FBS.

extract_protocol:
Total RNAs were extracted with TRIzol. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
mRNAs were fragmented and amplified with specific enzymes. cDNA fragments of preferentially 250~300 bp in length were selected and amplified with Phusion High-Fidelity DNA polymerase. At last, PCR products were purified and library quality was assessed by TBS380.

tag: cell line

value: Hela

value: human cervical carcinoma cell

value: oridonin, Imidazole ketone erastin


title: seed, Bolstar, Ina_TW2, rep4; Chris46

value: seed


title: tacrine_neomycin_rep1

city: Tsu

first: Yuhei

last: Nishimura

state: Mie

address: 2-174 Edobashi

department: Integrative Pharmacology

country: Japan

institute: Mie University Graduate School of Medicine

description: Gene expression in zebrafish exposed to tacrine and neomycin

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 uL containing fragmentation buffer and blocking agent according to the manufacture's protocol. After the fragmentation, 55 uL of hybridization buffer was added to the fragmentation mixture. For each reaction 100 uL was hybridized to an Agilent Zebrafish DNA Oligo Microarray (GPL14688) for 17 hours at 65°C in a rotating hybridization chamber. After the hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1, 1 minute with 37°C GE Wash buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 8.0 (Agilent). The data was normalized using Agi4x44PreProcess in Bioconductor. Features flagged in gIsSaturated, gIsFeatNonUnifOL, gIsPosAndSignif and gIsWellAboveBG were excluded from further analysis.

organism: Danio rerio

label_protocol: Cy3 labeled cRNA was prepared from 0.2 ug RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Zebrafish was maintained in fish medium (0.07 mM KCl, 2 mM CaCl2, 0.5 mM MgSO4, 0.7 mM NaHCO3, pH 7.4).

extract_protocol: Total RNA was extracted from zebrafish whole body using RNAqueous-Micro Kit (Life Technologies, Carlsbad, CA), qualified by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), and quantified using using Nano Drop ND-100 (Wilmington, DE, USA).

treatment_protocol: Zebrafish was pretreated with tacrine (50 uM) or DMSO (1%) for 1 hour and treated with neomycin (200 uM) or the vehicle for 1 hour.

value: whole body

value: 5 dpf

value: tacrine and neomycin


title: neomycin_rep2

description: Gene expression in zebrafish exposed to neomycin

value: neomycin


title: Combi-1


title: Combi-2


title: CAPAN1, siJUNB, Rep3

city: Göttingen

first: Shiv

middle: K.

last: Singh

address: Robert-Koch-Straße 40

department: Gastroenterology, GI-Oncology and Endocrinology

country: Germany

institute: University Medical Center Göttingen

data_processing:
Quality control using FastQC.
For siRNA samples: Alignment to hg38 using STAR v2.7.3a. For in vivo TNF treatment samples: Alignment to hg38 and mm38 using STAR v2.7.3a.
For in vivo TNF treatment samples: Removal of opposite species reads using XenofilteR package v1.6.
Counting of reads using htseq-count v0.11.3.
Assembly: For siRNA samples: hg38. For in vivo TNF treatment samples: hg38 and mm38.
Supplementary files format and content: Tab-delimited text file includes raw counts. Both human (hs) and murine (mm) reads are provided for in vivo TNF treatment samples.

extract_protocol:
For siRNA samples: TRIzol (Invitrogen). For in vivo TNF treatment samples: Direct-ZOL RNA Mini-prep (Zymo Research)
For siRNA samples: the library was made using 500 ng of total RNA and the Illumina TruSeq RNA Library Prep kit. For in vivo TNF treatment samples: libraries were made by Novogene.

value: siJUNB


title: Muscle-invasive bladder cancer 5404 A

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 5405 A

description: Muscle-invasive bladder cancer


title: tacrine_neomycin_rep2


title: seed, Bolstar, Ina_TW2, rep3; Chris45

value: Bolstar


title: neomycin_rep3


title: tacrine_neomycin_rep3


title: neomycin_rep1


title: seed, Bolstar, Ina_TW2, rep2; Chris44


title: CAPAN1, siJUNB, Rep2


title: IKE-3

value: Imidazole ketone erastin


title: control_rep3

description: Gene expression in zebrafish without treatment of tacrine and neomycin


title: seed, Bolstar, Ina_TW2, rep1; Chris43


title: Muscle-invasive bladder cancer 5403 A

description: Muscle-invasive bladder cancer


title: CAPAN1, siJUNB, Rep1


title: IKE-2


title: seed, Bolstar, Control, rep6; Chris42

description: bw.bed

value: Control


title: IKE-1


title: CAPAN1, siCtrl, Rep2

value: siCtrl


title: seed, Bolstar, Control, rep5; Chris41

description: bw.bed


title: Oridonin-3

value: oridonin


title: seed, Bolstar, Control, rep4; Chris40

description: bw.bed


title: Oridonin-2


title: seed, Bolstar, Control, rep3; Chris39

description: bw.bed


title: CAPAN1, siCtrl, Rep3


title: hESC derived neurons, trans-RSV, Biol Rep 3 [TR_03]

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

data_processing:
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5
Reads were mapped to the hg38 reference genome using STAR | version 2.7.2 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10
Assembly: GRCh38.98
Supplementary files format and content: tab-delimited text files include gene counts for each sample

growth_protocol: Human embryonic stem cell (hESCs) line H9 was used to differentiate human cortical neurons.

extract_protocol:
RNA extract by Zymo Quick-RNA MicroPrep Kit and cleaned by Zymo RNA Clean and Concentrator Kit. 0.5ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext dA tailling and Ultra II Directional RNA Library prep Kit(E#7600) following the manufacturer's protocols.

treatment_protocol: On day 49, the neurons were treated with cis-RSV and trans-RSV (50 mM each) for a period of 24 hours, followed by collection of cell pellet in ice-cold PBS, using cell scrapers, to obtain cell pellet for RNA extraction.

value: embryonic stem cells

value: trans-RSV 50μM


title: hESC derived neurons, trans-RSV, Biol Rep 2 [TR_02]


title: Oridonin-1


title: seed, Bolstar, Control, rep2; Chris38

description: bw.bed


title: control_rep2


title: Control-3

value: DMSO


title: Muscle-invasive bladder cancer 5402 A

description: Muscle-invasive bladder cancer

value: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 6415

description: Muscle-invasive bladder cancer


title: hESC derived neurons, trans-RSV, Biol Rep 1 [TR_01]


title: control_rep1


title: Muscle-invasive bladder cancer 5101 A

description: Muscle-invasive bladder cancer


title: Control-2

value: Hela

value: human cervical carcinoma cell


title: Muscle-invasive bladder cancer 5401 1A

description: Muscle-invasive bladder cancer


title: seed, Bolstar, BABA_TW2, rep6; Chris36

value: seed


title: hESC derived neurons, cis-RSV, Biol Rep 3 [CR_03]

value: cis-RSV 50μM


title: CAPAN1, siCtrl, Rep1


title: Muscle-invasive bladder cancer 4504 2

description: Muscle-invasive bladder cancer


title: Control-1


title: seed, Bolstar, BABA_TW2, rep5; Chris35


title: seed, Bolstar, BABA_TW2, rep4; Chris34


title: Muscle-invasive bladder cancer 3406 1

description: Muscle-invasive bladder cancer


title: hESC derived neurons, cis-RSV, Biol Rep 2 [CR_02]


title: Muscle-invasive bladder cancer 4501 1

description: Muscle-invasive bladder cancer


title: hESC derived neurons, cis-RSV, Biol Rep 1 [CR_01]


title: HT_CD45pos_h7

city: Los Angeles

first: Melissa

middle: G

last: Lechner

state: CA

address: 10833 Le Conte Ave, CHS 57-154

department: Div of Endocrinology, Diabetes, and Metabolism

institute: UCLA Geffen School of Medicine

description: scRNAseq data from immune cells from thyroid fine needle aspirates from human; patient with Hashimoto's thyroiditis

data_processing:
The reads are first mapped to GRCh38 (human) reference using cellranger software from 10x Genomics
Filtered output matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the threshold for cell detection were used for downstream analysis with Seurat
Cells with a mitochondiral gene percentage greater than or equal to 30 were removed
The raw counts and metadata from the Seurat object after IntegrateData and ScaleData step across samples are provided as processed data file
Subsequent clustering are descibed in the full manuscript
Genome_build: GRCh38
Supplementary_files_format_and_content: irae_ht_integrated_counts.csv

source_name: Human thyroid FNAB, HT

extract_protocol: Chromium Single Cell GEM, Library & Gel Bead Kit

treatment_protocol: Thyroid fine needle aspiration specimens from patients with immune checkpoint inhibitor thyroiditis or Hashimoto's thyroditis, as defined in the manuscript

tag: disease state

value: Hashimoto's thyroiditis

value: CD45+ primary human immune cells from thyroid tissue

value: Levothyroxine

value: 5' sequencing

tag: cell number


title: Muscle-invasive bladder cancer 2403 B

description: Muscle-invasive bladder cancer


title: seed, Bolstar, Control, rep1; Chris37

description: bw.bed

value: Bolstar


title: Muscle-invasive bladder cancer 2605 4D

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 4502 3

description: Muscle-invasive bladder cancer


title: hESC derived neurons, Control, Biol Rep 3 [C_03]

value: No treatment


title: Muscle-invasive bladder cancer 1608A2

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 1610A1

description: Muscle-invasive bladder cancer


title: HT_CD45pos_h6


title: Muscle-invasive bladder cancer 1607A1

description: Muscle-invasive bladder cancer


title: hESC derived neurons, Control, Biol Rep 2 [C_02]


title: HT_CD45pos_h5


title: Muscle-invasive bladder cancer 1605A

description: Muscle-invasive bladder cancer


title: seed, Bolstar, BABA_TW2, rep1; Chris31


title: hESC derived neurons, Control, Biol Rep 1 [C_01]


title: ICI_CD45pos_h4

description: scRNAseq data from immune cells from thyroid fine needle aspirates from human; patient treated with ICI who developed ICI-thyroiditis

source_name: Human thyroid FNAB, IrAE

value: ICI-thyroiditis

value: Levothyroxine; Immune checkpoint inhibitor (ICI)


title: seed, Moneyberg, BABA_TW3, rep6; Chris30

value: Moneyberg


title: human cumulus granulosa cells, biol rep 2

description:
Cumulus_2
Fpkms_AMH-EGFP_cumulus_CTRL.CSV

source_name: Ovary

value: Ovary

value: cumulus granulosa cells

value: WT


title: seed, Bolstar, BABA_TW2, rep3; Chris33


title: human cumulus granulosa cells, biol rep 1

description:
Cumulus_1
Fpkms_AMH-EGFP_cumulus_CTRL.CSV


title: Muscle-invasive bladder cancer 1603A1

description: Muscle-invasive bladder cancer

value: Muscle-invasive bladder cancer


title: seed, Moneyberg, BABA_TW3, rep5; Chris29


title: seed, Moneyberg, BABA_TW3, rep4; Chris28


title: H3K27me3 Nop16 overexpression celline 4 rep2

city: Palo Alto

first: Eric

middle: Lieberman

last: Greer

address: Alway M314 300 Pasteur Drive

department: Genetics

institute: Stanford University

data_processing:
Reads were aligned to the hg38 genome using Bowtie2
Duplicate reads and multimapper were filtered out with sambamba, keepingonly uniquely mapping reads for peak calling
Peaks were called using MACS2 broad peak calling algorithm
Genome_build: hg38
Supplementary_files_format_and_content: broadPeak files contain regions idenitifed as significantly enriched in each sample

source_name: MDA-MB231 cells

extract_protocol:
1.5x105 nuclei extracted from each cell lines were captured to Concanavalin A beads (Bangs Laboratories) and then incubated with anti-H3K27me3 antibody (1/100, 07-449, EMD Millipore). After washing, beads were incubated with 700 ng/ml pA-MNase and the MNase reaction was carried out by incubating with CaCl2 on 0 °C cold metal block. After stopping this reaction, DNA-protein complex was released by incubation at 37°C and treated with Proteinase K. DNA were extracted with Phenol-Chloroform and purified by ethanol precipitation.
For library preparation, end repair was conducted for 15 min at 12°C and 15 min at 37°C, followed by dA-tailing for 20 min at 72°C. After adaptor ligation using TruSeq DNA single indexes (Illumina) for 15 min at 20°C, adapter-ligated DNA was cleaned up by Ampure XP beads (Beckman Coulter). Libraries were PCR amplified for 14 cycle using KAPA HS HIFI polymerase. After cleaning up of PCR product by Ampure XP beads, DNA amount of library was measured by Qubit and size distribution of DNA was determined by Agilent TapeStation.
CUT&RUN-seq

tag: ChIP

tag: nop16 manipulation

value: Nop16 overexpression


title: H3K27me3 Nop16 overexpression celline 4 rep3


title: CTRL, fibroblast cells, D11, biol rep 2

description:
CTRL_D11_2
Fpkms_AMH-EGFP_cumulus_CTRL.CSV

source_name: human fibroblast cells differentiated from H9 ESC cells

value: P2K7 mock virus transduction


title: H3K27me3 Nop16 overexpression celline 4 rep1


title: seed, Moneyberg, BABA_TW3, rep3; Chris27

value: seed


title: CTRL, fibroblast cells, D11, biol rep 1

description:
CTRL_D11_1
Fpkms_AMH-EGFP_cumulus_CTRL.CSV

value: human fibroblast cells differentiated from H9 ESC cells


title: seed, Bolstar, BABA_TW2, rep2; Chris32


title: Muscle-invasive bladder cancer 1602A

description: Muscle-invasive bladder cancer


title: seed, Moneyberg, BABA_TW3, rep2; Chris26


title: ICI_h9_cd45

description: scRNAseq data from immune cells from thyroid fine needle aspirates from human; pooled specimen from 2 patients treated with ICI who developed ICI-thyroiditis


title: CTRL, fibroblast cells, D7, biol rep 2

description:
CTRL_D7_2
Fpkms_AMH-EGFP_cumulus_CTRL.CSV


title: Muscle-invasive bladder cancer 1510(1)

description: Muscle-invasive bladder cancer


title: IgG Nop16 overexpression celline 4


title: Muscle-invasive bladder cancer 1504A1

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 1503(1)

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 1512A1

description: Muscle-invasive bladder cancer


title: CTRL, fibroblast cells, D7, biol rep 1

description:
CTRL_D7_1
Fpkms_AMH-EGFP_cumulus_CTRL.CSV


title: ICI_CD45pos_h3


title: seed, Moneyberg, BABA_TW3, rep1; Chris25


title: Muscle-invasive bladder cancer 1502(1)

description: Muscle-invasive bladder cancer


title: AMH-EGFP+ hiGC, D11, biol rep 2

description:
AMH-EGFP_D11_2
Fpkms_AMH-EGFP_cumulus_CTRL.CSV

value: in vtiro induced human granulosa cells

value: FOXL2 & NR5A1 overexpression


title: H3K27me3 Nop16 overexpression celline 1 rep2


title: H3K27me3 Nop16 overexpression celline 1 rep1


title: AMH-EGFP+ hiGC, D11, biol rep 1

description:
AMH-EGFP_D11_1
Fpkms_AMH-EGFP_cumulus_CTRL.CSV


title: seed, Moneyberg, MeJA_TW3, rep5; Chris23


title: seed, Moneyberg, MeJA_TW3, rep4; Chris22


title: seed, Moneyberg, MeJA_TW3, rep3; Chris21


title: IgG Nop16 overexpression celline 1


title: H3K27me3 empty vector control rep 3


title: H3K27me3 empty vector control rep 2


title: Muscle-invasive bladder cancer 1409A1

description: Muscle-invasive bladder cancer


title: AMH-EGFP+ hiGC, D7, biol rep 2

description:
AMH-EGFP_D7_2
Fpkms_AMH-EGFP_cumulus_CTRL.CSV


title: AMH-EGFP+ hiGC, D7, biol rep 1

description:
AMH-EGFP_D7_1
Fpkms_AMH-EGFP_cumulus_CTRL.CSV


title: Muscle-invasive bladder cancer 1301A

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 1411(2)

description: Muscle-invasive bladder cancer


title: H3K27me3 empty vector control rep 1


title: seed, Moneyberg, MeJA_TW3, rep2; Chris20


title: IRE1a_Riboseq

city: DALLAS

first: Zhao

middle: V.

last: Wang

state: TX

address: 6000 Harry Hines Blvd

institute: UT southwestern medical center

description: Ribo-seq for all samples

data_processing:
Library strategy: Ribo-Seq
For ribosome profiling data, linker sequences were removed from sequencing reads
Samples were de-multiplexed using FASTX-clipper and FASTX-barcode splitter (FASTX-Toolkit).
Unique molecular identifiers and sample barcodes were then removed from reads using Python.
Bowtie v1.1.2 was used to filter out reads aligning to rRNAs and contaminants, and all surviving reads were aligned to the transcriptome
Assembly: hg19/GRCh37
Supplementary files format and content: The data format is EXCEL, we combine the RNA-seq and Ribo-seq to get the Translation effiency for each gene

extract_protocol:
For Ribo-seq, refer to DOI: 10.1126/science.aay0262
regular RNA-seq and Ribo-seq

treatment_protocol: firstly strarvation, then FBS treatment

tag: sirna

value: siCon and siIRE1a (multiplexed)


title: seed, Moneyberg, MeJA_TW3, rep1; Chris19


title: IgG empty vector control


title: siIRE-2

description: Ribo-seq for IRE1a knockdown

data_processing:
For ribosome profiling data, linker sequences were removed from sequencing reads
Samples were de-multiplexed using FASTX-clipper and FASTX-barcode splitter (FASTX-Toolkit).
Unique molecular identifiers and sample barcodes were then removed from reads using Python.
Bowtie v1.1.2 was used to filter out reads aligning to rRNAs and contaminants, and all surviving reads were aligned to the transcriptome
Assembly: hg19/GRCh37
Supplementary files format and content: The data format is EXCEL, we combine the RNA-seq and Ribo-seq to get the Translation effiency for each gene


title: seed, Moneyberg, MeJA_TW3, rep6; Chris24


title: seed, Moneyberg, Ina_TW2, rep6; Chris18


title: Muscle-invasive bladder cancer 1209B

description: Muscle-invasive bladder cancer

data_processing: The log2-summarised gene level expression values generated were batch-corrected using the ComBat function from the Bioconductor package sva.

tag: condition


title: siIRE-1

description: Ribo-seq for IRE1a knockdown


title: seed, Moneyberg, Ina_TW2, rep5; Chris17


title: IgG ng control


title: siCon_2

description: RNA-seq for control

value: siCon


title: Nop16 overexpression rep6

data_processing:
Raw sequences of RNA-seq were mapped to the hg38 human genome using  Salmon mapper (v.1.4.0).
The count of mapped reads was normalized as transcripts per million (TPM) using an R package of tximport.
Differentially expressed genes were identified using DEseq (v1.28.1) package. Significant genes were identified using a padj < 0.05
Genome_build: hg38
Supplementary_files_format_and_content: normalized count matrix -OE and empty vector controls
Supplementary_files_format_and_content: raw count matrix - OE and empty vector controls
Supplementary_files_format_and_content: normalized count matrix - KO and ng controls
Supplementary_files_format_and_content: raw count matrix - KO and ng controls

source_name: Breast adenocarcinoma cell line MDA-MB247

growth_protocol: We established two lines of NOP16-stably overexpressed MDA-MB231 cells. p3xFLAG-CMV10-NOP16 or empty (E.V.: as control) vectors were transfected into MDA-MB231 cells and selected with 1mg/ml G-418 for 3 weeks. We selected two independent NOP16-overexpressed lines (OE1, OE4). We also established two lines of NOP16 bulk knockout MDA-MB231 cells which were established by infection of lentivirus derived from LentiCRISPRv2 vector encoding each sgRNAs targeting NOP16 (sgRNA1 or sgRNA4, for control cell line, lentivirus encoding non-target sgRNA: n.g. was used) and selected with 1mg/ml puromycin for 3 days. Total RNA was extracted from 5.0x105 each cells, and RNA-seq was performed.

extract_protocol:
The total RNA was extracted from each samples using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: overexpression

tag: cell ine


title: siCon_1

description: RNA-seq for control


title: Muscle-invasive bladder cancer 1213A

description: Muscle-invasive bladder cancer

extract_protocol: Two 10µm sections from FFPE bladder cancer embodied blocks. RNA was extracted from the two 10 µm sections using the Roche High Pure FFPET RNA isolation kit. RNA yield was determined on Qubit fluorometer (Invitrogen, Paisley, UK).


title: Nop16 overexpression rep5

source_name: Breast adenocarcinoma cell line MDA-MB246


title: seed, Moneyberg, Ina_TW2, rep4; Chris16

tag: treatment


title: Muscle-invasive bladder cancer 6411

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 6410

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 1402(1)

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 6409

description: Muscle-invasive bladder cancer


title: NOZ Mock 3

first: Weijian

last: Li

state: Shanghai

address: NO. 160, Pujian Road, Pudong New District, Shanghai, China

institute: Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression
Gene Set Enrichment Analysis: Gene Set Enrichment Analysis (GSEA) is a computational approach to determine if a pre-defined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes. We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp
Supplementary_files_format_and_content: gene_fpkm.txt (FPKM values for each Sample)
Supplementary_files_format_and_content: gene_count.txt (raw gene counts for every gene and every sample)

source_name: Gallbladder cancer cell line NOZ

growth_protocol: For the NOZ cells cultures, there were two different conditions performed in biological triplicates: (I) mock (DMSO), (II) 150 μM LCA for 24 h.

extract_protocol:
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Gallbladder cancer

value: NOZ

tag: cell type

value: Gallbladder cancer cells

value: DMSO


title: seed, Moneyberg, Ina_TW2, rep3; Chris15

value: Moneyberg


title: Nop16 overexpression rep4

source_name: Breast adenocarcinoma cell line MDA-MB245


title: Nop16 overexpression rep3

source_name: Breast adenocarcinoma cell line MDA-MB244


title: NOZ Mock 2

treatment_protocol: (I) mock (DMSO), (II) 150 μM LCA for 24 h


title: seed, Moneyberg, Ina_TW2, rep1; Chris13


title: Nop16 overexpression rep2

source_name: Breast adenocarcinoma cell line MDA-MB243


title: seed, Moneyberg, Ina_TW2, rep2; Chris14

source_name: seed


title: seed, Moneyberg, BABA_TW2, rep6; Chris12


title: NOZ Mock 1


title: Nop16 overexpression rep1

source_name: Breast adenocarcinoma cell line MDA-MB242


title: NOZ LCA 3

value: LCA


title: seed, Moneyberg, BABA_TW2, rep5; Chris11


title: Muscle-invasive bladder cancer 6408

first: Tim

last: Smith

address: Dean Street

institute: University of Bangor

description: Muscle-invasive bladder cancer

source_name: Anonymised


title: Muscle-invasive bladder cancer 6407

description: Muscle-invasive bladder cancer


title: NOZ LCA 2


title: Muscle-invasive bladder cancer 6406

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 6405

description: Muscle-invasive bladder cancer


title: no guideRNA control rep3

source_name: Breast adenocarcinoma cell line MDA-MB241

value: control

value: ngcontrol


title: NOZ LCA 1


title: seed, Moneyberg, BABA_TW2, rep4; Chris10


title: seed, Moneyberg, BABA_TW2, rep3; Chris9


title: no guideRNA control rep2

source_name: Breast adenocarcinoma cell line MDA-MB240


title: no guideRNA control rep1

source_name: Breast adenocarcinoma cell line MDA-MB239


title: P7E09_5637_T_min_10 [P7E09_5637GC_T.10_R3_S30_L004_R1_001]

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

description:
Amplicon DNA
P7E09_5637GC_T.10_R3_S30_L004_R1_001

data_processing:
Library strategy: CRISPR Screen
sgRNA counts were extracted directly from R1 raw sequence reads using a custom perl script that uses regular expression string matching to exactly match sgRNA sequence flanked by 10 bases of vector sequence. The vector sequence was allowed to have one error before and after the sgRNA sequence.
The sgRNA IDs of the Brunello library were updated to current HGNC gene names using the Total Approved Symbols download from HGNC, accessed on 9/1/2020 (https://www.genenames.org/download/statistics-and-files/). Transcript IDs were matched when possible and when matches were not found, past symbols and aliases were updated to current names. Finally, 5 sgRNAs with missing updated gene names were manually curated using literature searches.
The DESeq2 R package (Love et al., 2014) was used to calculate differential abundance of genes. Gene counts were generated using the sum of counts for sgRNAs of the same gene.
Synthetic Lethality compared GemCis day 19 and GemCis day 25 vs. Saline day 19 and Saline day 25 with the day as a covariate. In the comparison integrating all cell lines, cell line was additionally modeled as a covariate. Gene essentiality was calculated by comparing Saline day 25 to Saline day 0 and in the integrated all cell lines comparison, cell line was modeled as a covariate.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text file containing sgRNA counts

growth_protocol: Gemcitabine and cisplatin resistant cell lines were grown for 10 days in IMDM + 10% FBS and passaged every 2 days in drug free media to deplete essential genes.  On day 10, cells were treated with either gemcitabine and cisplatin (GC) combination treatment or saline (control) and passaged for an additional 15 days. During treatment, cells were passaged every 3 days and maintained at subconfluent densities. All GC-resistant cell lines  in the GC treatment arm were grown in the presence of both gemcitabine and cisplatin continuously from day 10 through 25 of each screen.

extract_protocol:
Cell pellets of 2.0 x 107 were snap frozen in liquid nitrogen in 1.5mL tubes and stored at -80 prior to extraction. When possible at least 8.0 x 107 cell were used for 4 separate genomic DNA isolation which were pooled to account for any variation with pellet size. DNA isolation was performed using the Puregene cell and tissue kit (Qiagen, Cat. Number: 158388) with the addition of RNase A Solution (Qiagen, Cat Number: 158924) according to manufacturer’s instructions. DNA concentration was measured in quadruplicate using either a nanodrop spectrophotometer (Thermo), Qubit® dsDNA assay (Life Technologies) and the average DNA content per cell was determined.
Library preparation was performed using primers sequences designed by the Broad Institute’s Genetic Perturbation Platform to amplify sgRNA sequences in the LentiCRISPRv2 backbone. Each unique sample utilized a pool of eight P5 primers with to introduce a stagger in reads associated with each library and sample specific P7 primer that contained a unique sample index sequence for each timepoint, replicate, or treatment condition to be sequenced in the same pool.

treatment_protocol: Beginning at day 10 of each screen, cells in the GC treatment arm received 20ng/mL gemcitabine and 1000ng/mL cisplatin, with the exception of the KU1919-GC cells which were treated with 2000ng/mL cisplatin.

tag: time point


title: seed, Moneyberg, BABA_TW2, rep2; Chris8

data_processing:
To analyse the raw sequences obtained and estimate methylation levels per chromosome and compare them across treatment between controls and seeds from plants primed by Ina, BaBa and MeJa, we used the pipeline MethPipe (Song et al.,2013)
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for adapter trimming as well as quality control, with some added functionality to remove biased methylation positions.
Abismal (de Sena Brandine et al., 2021) was used to construct the methylome and map bisulfite treated short reads on the tomato plant genome.
Supplementary files format and content: The file mw.bed is in a bed format and contains information of the hypomethylated regions from the genome of control Moneyberg tomato seeds (from untreated plants).
Supplementary files format and content: The file mb2.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Moneyberg tomato seeds from plants treated with Baba in time window 2.
Supplementary files format and content: The file mi2.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Moneyberg tomato seeds from plants treated with Ina in time window 2.
Supplementary files format and content: The file mm3.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Moneyberg tomato seeds from plants treated with MeJA in time window 3.
Supplementary files format and content: The file mb3.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Moneyberg tomato seeds from plants treated with MeJA in time window 3.
Supplementary files format and content: The file bb2.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Bolstar tomato seeds from plants treated with Baba in time window 2.
Supplementary files format and content: The file bw.bed is in a bed format and contains information of the hypomethylated regions from the genome of the control Bolstar tomato seeds (from untreated plants).
Supplementary files format and content: The file bi2.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Bolstar tomato seeds from plants treated with Ina in time window 2.

tag: genotype


title: P7E08_5637_T_min_10 [P7E08_5637GC_T.10_R2_S29_L004_R1_001]

description:
Amplicon DNA
P7E08_5637GC_T.10_R2_S29_L004_R1_001


title: P7E07_5637_T_min_10 [P7E07_5637GC_T.10_R1_S28_L004_R1_001]

description:
Amplicon DNA
P7E07_5637GC_T.10_R1_S28_L004_R1_001


title: Muscle-invasive bladder cancer 6403

city: Bangor

description: Muscle-invasive bladder cancer

value: Muscle-invasive bladder cancer


title: Nop16 knockdown rep6

source_name: Breast adenocarcinoma cell line MDA-MB238

value: knockdown


title: seed, Moneyberg, BABA_TW2, rep1; Chris7

tag: tissue

value: seed


title: Muscle-invasive bladder cancer 4601 1

description: Muscle-invasive bladder cancer


title: P7E06_5637_T0 [P7E06_5637GC_T0_R3_S27_L004_R1_001]

description:
Amplicon DNA
P7E06_5637GC_T0_R3_S27_L004_R1_001


title: Nop16 knockdown rep5

source_name: Breast adenocarcinoma cell line MDA-MB237


title: Muscle-invasive bladder cancer 6404

description: Muscle-invasive bladder cancer


title: Nop16 knockdown rep4

source_name: Breast adenocarcinoma cell line MDA-MB236


title: Muscle-invasive bladder cancer 6102

description: Muscle-invasive bladder cancer


title: seed, Moneyberg, Control, rep5; Chris5

description: mw.bed

value: Control


title: Nop16 knockdown rep3

source_name: Breast adenocarcinoma cell line MDA-MB235


title: Muscle-invasive bladder cancer 6101

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 5601

description: Muscle-invasive bladder cancer


title: P7E05_5637_T0 [P7E05_5637GC_T0_R2_S26_L004_R1_001]

description:
Amplicon DNA
P7E05_5637GC_T0_R2_S26_L004_R1_001


title: P7E04_5637_T0 [P7E04_5637GC_T0_R1_S25_L004_R1_001]

description:
Amplicon DNA
P7E04_5637GC_T0_R1_S25_L004_R1_001


title: Nop16 knockdown rep2

source_name: Breast adenocarcinoma cell line MDA-MB234


title: seed, Moneyberg, Control, rep3; Chris3

description: mw.bed


title: Nop16 knockdown rep1

source_name: Breast adenocarcinoma cell line MDA-MB233


title: Muscle-invasive bladder cancer 5502

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 6402

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 6401

description: Muscle-invasive bladder cancer


title: Empty vector control rep2

source_name: Breast adenocarcinoma cell line MDA-MB232

value: evcontrol


title: P7E02_5637_GC_d9 [P7E02_5637GC_T9_GC_R2_S23_L004_R1_001]

description:
Amplicon DNA
P7E02_5637GC_T9_GC_R2_S23_L004_R1_001

value: GC


title: seed, Moneyberg, Control, rep1; Chris1

description: mw.bed


title: seed, Moneyberg, Control, rep2; Chris2

description: mw.bed


title: seed, Moneyberg, Control, rep6; Chris6

description: mw.bed


title: P7E01_5637_GC_d9 [P7E01_5637GC_T9_GC_R1_S22_L004_R1_001]

description:
Amplicon DNA
P7E01_5637GC_T9_GC_R1_S22_L004_R1_001


title: Muscle-invasive bladder cancer 5103

description: Muscle-invasive bladder cancer


title: P7D12_5637_Saline_d9 [P7D12_5637GC_T9_Saline_R3_S21_L004_R1_001]

description:
Amplicon DNA
P7D12_5637GC_T9_Saline_R3_S21_L004_R1_001

value: Saline


title: KU1919_Parental_B

description:
9B
Group: KU1919_Parental
RNAseq_ensembl_raw_counts.txt

data_processing:
Illumina adapters were removed, along with the first 12 base pairs using BBDuk and reads <50bp after trimming were discarded.
Reads were aligned and quantified using STAR (2.6.0a) to the Ensembl human transcriptome (hg38.p12, release 96).
Lowly abundant genes were removed as those <1 mean raw count or <1 mean count per million (CPM) across the dataset.
Differential gene expression was calculated using the voom function in limma.
Genome_build: GRCh38
Supplementary_files_format_and_content: RNAseq_ensembl_raw_counts.txt: Text file containing STAR gene count values.

growth_protocol: All cell lines were grown for several passages in the absence of antibiotics, gemcitabine or cisplatin in complete media (IMDM + 10% FBS).

extract_protocol:
RNA was extracted using the RNeasy Plus Kit (Qiagen). Cells were lysed and passed through QIAShredder column (Qiagen) according to the manufacturer’s protocol. gDNA elimination columns (Qiagen) were used to remove any residual gDNA from the purified RNA.
RNA library preparation was performed using the Universal Plus mRNA –Seq +UDI kit (Nugen Technologies).

treatment_protocol: Untreated

tag: resistance

value: Parental


title: KU1919_Parental_C

description:
9C
Group: KU1919_Parental
RNAseq_ensembl_raw_counts.txt


title: seed, Moneyberg, Control, rep4; Chris4

description: mw.bed

extract_protocol:
The DNA extraction was performed following the manufacturer instructions using the Quick-DNA Plant/Seed Miniprep Kit from Zymoresearch. For each sample the DNA concentration and quality was measured using a Qubit fluorometer.
Ultralow Methyl-Seq System (Tecan/NuGEN, Redwood City, CA) has been used for library preparation following the manufacturer’s instructions. DNA samples were quantified with Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA). Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay (Agilent technologies, Santa Clara, CA).
Libraries were then prepared for sequencing and sequenced on paired-end 150 bp mode on NovaSeq6000 (Illumina, San Diego, CA).


title: P7D11_5637_Saline_d9 [P7D11_5637GC_T9_Saline_R2_S20_L004_R1_001]

description:
Amplicon DNA
P7D11_5637GC_T9_Saline_R2_S20_L004_R1_001


title: Patient 5 SOD16 Tumor

city: Baltimore

first: Rania

middle: Hassan

last: Younis

state: MD

address: 650 W Batimore St

department: Oncology and Diagnostic Sciences

institute: University of Maryland School of Dentistry

hyb_protocol: Hybridization was carried in a regular thermal cycler. The hybridized mix was purified using magnetic beads in the nCounter machine in the institute of genome sciences (IGS) University of Maryland, Baltimore.

scan_protocol: nCounter digital analyser scan with 555FOVs was used and image acquisition was on the ncounter SPRINT system

data_processing: Data analysis was carried using IO-360 platform 770 genes code sets using the nSolver 4.0 software basic and advanced costumed analysis.

label: Biotin

source_name: Head and neck cancer

label_protocol: Biotinylated capture probes and color coded reporter probes were used for the hybridization complex, according to the manufacturer's protocol

extract_protocol:
Three to five slides of 5 um thick FFPE tissue sections of prospectively or retrospectively collected OSCC tumor tissue were used for RNA extraction using Rneasy FFPE kit (Qiagen, catalog no 73504). The tumor rich areas and 3-4mm of peritumoral stromal were identified and manually micro-dissected by a surgical oral pathologist (RY) guided by H&E stained section.
RNA quality control (QC) analysis was run on nanochip, to ensure required 200nt in 50-300ng with no prior amplification or enzymatic reaction.

value: Invasive oral squamous cell carcinoma

tag: individual

value: Patient 5

tag: age

value: Male

tag: race

value: White

tag: location

value: Oral cavity and mobile tongue

tag: Stage

value: I


title: Muscle-invasive bladder cancer 5301

description: Muscle-invasive bladder cancer


title: Patient 5 SOD16 Tumor margin

value: Morphologically normal oral epithelium transitioning to dysplasia at tumor margin

tag: gender


title: Muscle-invasive bladder cancer 5102

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 5408

description: Muscle-invasive bladder cancer


title: KU1919_Parental_A

description:
9A
Group: KU1919_Parental
RNAseq_ensembl_raw_counts.txt

tag: cell line


title: Muscle-invasive bladder cancer 4404

description: Muscle-invasive bladder cancer


title: Empty vector control rep1

source_name: Breast adenocarcinoma cell line MDA-MB231

tag: nop16 manipulation

value: control


title: 5637_Gem_and_Cis_C

description:
8C
Group: 5637_Gem_and_Cis
RNAseq_ensembl_raw_counts.txt


title: P7D09_5637_GC_d15 [P7D09_5637GC_T15_GC_R3_S18_L004_R1_001]

description:
Amplicon DNA
P7D09_5637GC_T15_GC_R3_S18_L004_R1_001


title: 5637_Gem_and_Cis_B

description:
8B
Group: 5637_Gem_and_Cis
RNAseq_ensembl_raw_counts.txt


title: P7D07_5637_GC_d15 [P7D07_5637GC_T15_GC_R1_S16_L004_R1_001]

description:
Amplicon DNA
P7D07_5637GC_T15_GC_R1_S16_L004_R1_001


title: P7D08_5637_GC_d15 [P7D08_5637GC_T15_GC_R2_S17_L004_R1_001]

description:
Amplicon DNA
P7D08_5637GC_T15_GC_R2_S17_L004_R1_001


title: Patient 4 SCC09 Tumor margin

value: Morphologically normal oral epithelium at tumor margin

value: Patient 4

value: Female

value: IV


title: Muscle-invasive bladder cancer 4402

description: Muscle-invasive bladder cancer

value: Muscle-invasive bladder cancer


title: Patient 3 SOD9 Tumor

value: Patient 3

value: African American


title: 5637_Gem_and_Cis_A

description:
8A
Group: 5637_Gem_and_Cis
RNAseq_ensembl_raw_counts.txt


title: 5637_Gem_C

description:
7C
Group: 5637_Gem
RNAseq_ensembl_raw_counts.txt

value: Gem


title: Patient 4 SCC09 Tumor


title: P7D06_5637_Saline_d15 [P7D06_5637GC_T15_Saline_R3_S15_L004_R1_001]

description:
Amplicon DNA
P7D06_5637GC_T15_Saline_R3_S15_L004_R1_001

value: Saline


title: Muscle-invasive bladder cancer 4401

description: Muscle-invasive bladder cancer


title: P7D10_5637_Saline_d9 [P7D10_5637GC_T9_Saline_R1_S19_L004_R1_001]

description:
Amplicon DNA
P7D10_5637GC_T9_Saline_R1_S19_L004_R1_001


title: Patient 3 SOD9 Tumor margin

value: Morphologicaly normal oral epithelium with lichenoid inflammatory reaction at tumor margin.


title: Muscle-invasive bladder cancer 2604

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 4503

description: Muscle-invasive bladder cancer


title: 5637_Gem_B

description:
7B
Group: 5637_Gem
RNAseq_ensembl_raw_counts.txt


title: P7D05_5637_Saline_d15 [P7D05_5637GC_T15_Saline_R2_S14_L004_R1_001]

description:
Amplicon DNA
P7D05_5637GC_T15_Saline_R2_S14_L004_R1_001


title: Patient 2 SOD4 Tumor

value: Invasive oral squamous cell carcinoma

value: Patient 2


title: P7D04_5637_Saline_d15 [P7D04_5637GC_T15_Saline_R1_S13_L004_R1_001]

description:
Amplicon DNA
P7D04_5637GC_T15_Saline_R1_S13_L004_R1_001


title: Muscle-invasive bladder cancer 2601

description: Muscle-invasive bladder cancer


title: 5637_Gem_A

description:
7A
Group: 5637_Gem
RNAseq_ensembl_raw_counts.txt


title: Patient 1 SOD3 Tumor

value: Patient 1

value: White


title: P7D03_KU1919_T_min_10 [P7D03_KU1919GC_T.10_R3_S50_L002_R1_001]

description:
Amplicon DNA
P7D03_KU1919GC_T.10_R3_S50_L002_R1_001


title: 5637_Cis_C

description:
6C
Group: 5637_Cis
RNAseq_ensembl_raw_counts.txt

value: Cis


title: F_RabbitIGG_MR-11

city: Providence

first: Erica

last: Larschan

state: RI

address: Sidney Frank Hall 367, 185 Meeting Street

department: MCB

institute: Brown University

data_processing:
FastQC was used for quality control.
Merged the fastq files and trimmed adaptor sequences (trimmomatic).
Aligned sequence reads to the dm6 genome using bowtie2. This step would remove any duplicate or unmapped reads.
Sorted the output BAM files from bowtie2 to make sorted.bam files.
MACS2 was used for peak calling. This produced narrowPeak/BED files that were used in analysis.
Assembly: dm6
Supplementary files format and content: narrowPeak files from MACS2
Library strategy: CUT&RUN

organism: Drosophila melanogaster

source_name: Kc

growth_protocol: Kc and S2 cells were maintained at 25C in Schneider's media supplemented with 10% Fetal Bovine Serum and 1.4X Antibiotic-Antimycotic. Cells were passaged every 3 days to maintain an appropriate cell density.

extract_protocol:
Cells were allowed to grow to confluency and harvested. Equal number of cells for each category suspended in wash buffer and subjected to CutnRun assay according to Skene and Heinkoff 2018.
1ng CutnRun DNA was used to generate libraries using Kapa Hyper prep kit and SeqCapAdapter Kit A. 14 PCR cycles used to amplify the libraries. Ampure Xp beads used for library purification and fragment analysis done to check quality of the libraries made.
Paired end 2X25 bp illumina Hi-seq sequencing performed.

treatment_protocol: Not Applicable

value: Kc

value: Embryonic

value: female

tag: antibody

value: RabbitIGG


title: Patient 1 SOD3 Tumor margin

value: Morphologically normal oral epithelium transitioning to dysplasia at tumor margin

value: Female

value: Oral cavity and mobile tongue

value: I


title: P7D02_KU1919_T_min_10 [P7D02_KU1919GC_T.10_R2_S49_L002_R1_001]

description:
Amplicon DNA
P7D02_KU1919GC_T.10_R2_S49_L002_R1_001


title: Muscle-invasive bladder cancer 2504

description: Muscle-invasive bladder cancer

tag: condition

value: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 2603

description: Muscle-invasive bladder cancer


title: M_RabbitIGG_MR-10

value: male


title: P7D01_KU1919_T_min_10 [P7D01_KU1919GC_T.10_R1_S48_L002_R1_001]

description:
Amplicon DNA
P7D01_KU1919GC_T.10_R1_S48_L002_R1_001


title: KC_MR-7_CLAMP_Rep2

value: CLAMP


title: Muscle-invasive bladder cancer 2503

description: Muscle-invasive bladder cancer


title: Patient 2 SOD4 Tumor margin

value: Morphologically normal oral epithelium at tumor margin


title: 5637_Parental_C

description:
5C
Group: 5637_Parental
RNAseq_ensembl_raw_counts.txt

value: Parental


title: KC_MR-3_CLAMP_Rep1


title: P7C11_KU1919_T0 [P7C11_KU1919GC_T0_R2_S46_L002_R1_001]

description:
Amplicon DNA
P7C11_KU1919GC_T0_R2_S46_L002_R1_001


title: 5637_Cis_A

description:
6A
Group: 5637_Cis
RNAseq_ensembl_raw_counts.txt


title: P7C12_KU1919_T0 [P7C12_KU1919GC_T0_R3_S47_L002_R1_001]

description:
Amplicon DNA
P7C12_KU1919GC_T0_R3_S47_L002_R1_001


title: P7C10_KU1919_T0 [P7C10_KU1919GC_T0_R1_S45_L002_R1_001]

description:
Amplicon DNA
P7C10_KU1919GC_T0_R1_S45_L002_R1_001


title: 5637_Cis_B

description:
6B
Group: 5637_Cis
RNAseq_ensembl_raw_counts.txt


title: Muscle-invasive bladder cancer 2402

description: Muscle-invasive bladder cancer


title: S2_MR-5_CLAMP_Rep3


title: Muscle-invasive bladder cancer 2502

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 2505

description: Muscle-invasive bladder cancer


title: 5637_Parental_A

description:
5A
Group: 5637_Parental
RNAseq_ensembl_raw_counts.txt


title: 253J_Gem_and_Cis_C

description:
4C
Group: 253J_Gem_and_Cis
RNAseq_ensembl_raw_counts.txt


title: P7C09_KU1919_GC_d9 [P7C09_KU1919GC_T9_GC_R3_S44_L002_R1_001]

description:
Amplicon DNA
P7C09_KU1919GC_T9_GC_R3_S44_L002_R1_001

value: GC


title: Muscle-invasive bladder cancer 2501

description: Muscle-invasive bladder cancer


title: S2_MR-1_CLAMP_Rep1


title: S2_MR-2_CLAMP_Rep2


title: P7C08_KU1919_GC_d9 [P7C08_KU1919GC_T9_GC_R2_S43_L002_R1_001]

description:
Amplicon DNA
P7C08_KU1919GC_T9_GC_R2_S43_L002_R1_001


title: 253J_Gem_and_Cis_B

description:
4B
Group: 253J_Gem_and_Cis
RNAseq_ensembl_raw_counts.txt


title: 5637_Parental_B

description:
5B
Group: 5637_Parental
RNAseq_ensembl_raw_counts.txt


title: Muscle-invasive bladder cancer 2103

description: Muscle-invasive bladder cancer


title: P7C06_KU1919_Saline_d9 [P7C06_KU1919GC_T9_Saline_R3_S41_L002_R1_001]

description:
Amplicon DNA
P7C06_KU1919GC_T9_Saline_R3_S41_L002_R1_001

value: Saline


title: Input_H3K27ac_D50_r2

city: Singapore

first: Ching Thong

last: Choo

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

data_processing:
Read quality check was performed using FASTQC and adaptors were trimmed using Trim Galore
Reads were mapped to Drosophila reference genome (BDGP6.22.98) using STAR (v2.5.3a) with following parameters: --alignEndsType EndToEnd --alignIntronMax 1
Downstream analysis was performed using Galaxy platform. Peak calling was performed using MACS2 (v2.1.1), using an effective genome size of 120000000 --no model --extsize 147 --bdg
Assembly: Drosophila melanogaster reference genome (BDGP6.22.98)
Supplementary files format and content: Alignment files (bam format) were transformed into read coverage files (bigwig format) using DeepTools: bamCompare (v3.3.2), normalized by BPM
Supplementary files format and content: peak files generated from MACS2 callpeak

source_name: Head

growth_protocol: Male Drosophila melanogaster, strain  w[1118], were cultured in standard fly media (6% cornmeal, 5% dextrose, 2.4% brewer’s yeast, 0.8% agarose and 0.3% nipagin) at 25◦C with 12-hour light/dark cycle.

extract_protocol:
Isolate D10 to D50 fly heads (50mg) for each biological replicate. Fly heads were dounced 30 times with pestle A (Sigma) in 5 ml of A1 buffer (60 mM KCl, 15 mM NaCl, 4 mM MgCl2, 15 mM HEPES pH 7.6, 0.5% NP-40, 0.5 mM DTT, 0.5 mM PMSF and protease inhibitors cocktail). Samples were filtered through MIRA cloth, and the lysate was incubated on ice for 15min. Samples was then centrifuged at 4000g for 5min at 4°C. After three additional rounds of A1 buffer wash and centrifugation, nuclear pellet was resuspended and dounced with pestle B (Sigma) in 3.3 ml of RIPA buffer (10 mM Tris pH 8.0, 1 mM EDTA, 140 mM NaCl, 1% Triton, 0.1% SDS, 0.1% sodium deoxycholate, 0.5 mM DTT, 0.5 mM PMSF, protease inhibitors cocktail). 3.3 µl of 3M CaCl2 was added to 3.3 ml of nuclear lysate and incubated at 37°C for 3min. 5µl of MNase (i-DNA Biotech, Cat# LS004798) was then added to samples and incubated at 37°C for 15 min. MNase reaction was terminated by adding STOP buffer (5µM EDTA/EGTA). Samples were briefly sonicated (10sec ON, 50sec OFF, 5 times), followed by 10 min max speed centrifugation at 4°C. The supernatant was collected as the chromatin extract and 80 µl was kept as input. 5ul of H3K4me1 (Abcam, ab8895) or H3K27ac (Abcam, ab4729) antibody was added to remaining chromatin extract and incubate in 4°C overnight. On the following day, 20 μl of pre-blocked (0.5% BSA in PBS) Protein-G Dynabeads™ (Lifetech, Cat# 10003D) was added to the chromatin extract. Following 4 hours of incubation at 4°C, DNA-antibody-beads complex was isolated using magnetic stand. The beads complex was washed with RIPA buffer for 5 times, LiCl buffer (10 mM Tris pH 8, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate) once and Tris-EDTA buffer (10 mM Tris pH 8, 1 mM EDTA) once. The DNA fragments were eluted from the beads with 500 μl elution buffer (1 M NaHCO3, 0.5% SDS), while input was topped up to 420 µl with elution buffer and samples were incubated at 37°C overnight. On the next day, samples were treated with RNase A (20 μg/ml, 1 hr at 37°C) and proteinase K (40 μg/ml, 2 hr at 37°C). DNA was extracted by phenol/chloroform and ethanol precipitation.
ChIP-sequencing was carried at BGI (Hong Kong) according to company’s protocol. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified using KAPA library amplification kit (KK2702) with Illumina primers for 11 cycles and library fragments of ~200-500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 4000.

treatment_protocol: Twenty flies were housed in one vial (diameter of 2.5 cm, height of 9.5 cm) and the food was changed every two days until the desired age of day 50.

value: Head

value: WT

value: D50 adult

tag: Sex

value: Male

tag: strain

value: H3K27ac Input


title: Input_H3K27ac_D50_r1


title: 253J_Gem_and_Cis_A

description:
4A
Group: 253J_Gem_and_Cis
RNAseq_ensembl_raw_counts.txt


title: 253J_Gem_C

description:
3C
Group: 253J_Gem
RNAseq_ensembl_raw_counts.txt

value: Gem


title: P7C05_KU1919_Saline_d9 [P7C05_KU1919GC_T9_Saline_R2_S40_L002_R1_001]

description:
Amplicon DNA
P7C05_KU1919GC_T9_Saline_R2_S40_L002_R1_001

tag: treatment


title: Muscle-invasive bladder cancer 2202

description: Muscle-invasive bladder cancer


title: Input_H3K27ac_D10_r2

value: D10 adult


title: 253J_Gem_B

description:
3B
Group: 253J_Gem
RNAseq_ensembl_raw_counts.txt


title: P7C04_KU1919_Saline_d9 [P7C04_KU1919GC_T9_Saline_R1_S39_L002_R1_001]

description:
Amplicon DNA
P7C04_KU1919GC_T9_Saline_R1_S39_L002_R1_001

tag: time point


title: Muscle-invasive bladder cancer 2102

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 2101

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 1609

description: Muscle-invasive bladder cancer


title: 253J_Cis_C

description:
2C
Group: 253J_Cis
RNAseq_ensembl_raw_counts.txt

value: Cis


title: ChIP_H3K27ac_D50_r2

tag: genotype

value: H3K27ac ChIP


title: 253J_Gem_A

description:
3A
Group: 253J_Gem
RNAseq_ensembl_raw_counts.txt


title: ChIP_H3K27ac_D50_r1

tag: tissue


title: 253J_Cis_B

description:
2B
Group: 253J_Cis
RNAseq_ensembl_raw_counts.txt

tag: resistance


title: P7C02_KU1919_GC_d15 [P7C02_KU1919GC_T15_GC_R2_S37_L002_R1_001]

description:
Amplicon DNA
P7C02_KU1919GC_T15_GC_R2_S37_L002_R1_001


title: P7C07_KU1919_GC_d9 [P7C07_KU1919GC_T9_GC_R1_S42_L002_R1_001]

description:
Amplicon DNA
P7C07_KU1919GC_T9_GC_R1_S42_L002_R1_001


title: P7C01_KU1919_GC_d15 [P7C01_KU1919GC_T15_GC_R1_S36_L002_R1_001]

description:
Amplicon DNA
P7C01_KU1919GC_T15_GC_R1_S36_L002_R1_001


title: 253J_Cis_A

description:
2A
Group: 253J_Cis
RNAseq_ensembl_raw_counts.txt


title: ChIP_H3K27ac_D10_r1


title: ChIP_H3K27ac_D10_r2


title: P7B6_TCCSUP_GC_d11 [P7B6_TCCSUP_combined.txt]

description:
Amplicon DNA
P7B6_TCCSUP_combined.txt

source_name: TCCSUP


title: TCCSUP_Gem_and_Cis_C

description:
24C
Group: TCCSUP_Gem_and_Cis
RNAseq_ensembl_raw_counts.txt

value: TCCSUP


title: Muscle-invasive bladder cancer 1506

description: Muscle-invasive bladder cancer

value: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 1601

description: Muscle-invasive bladder cancer


title: Input_H3K27ac_D10_r1


title: Muscle-invasive bladder cancer 1606

description: Muscle-invasive bladder cancer


title: Input_H3K4me1_D50_r2

value: H3K4me1 Input


title: P7C03_KU1919_GC_d15 [P7C03_KU1919GC_T15_GC_R3_S38_L002_R1_001]

description:
Amplicon DNA
P7C03_KU1919GC_T15_GC_R3_S38_L002_R1_001


title: P7B6_T24_T_min_10 [P7B6_ct_combinedruns.txt]

description:
Amplicon DNA
P7B6_ct_combinedruns.txt


title: Muscle-invasive bladder cancer 2401

description: Muscle-invasive bladder cancer


title: TCCSUP_Gem_and_Cis_B

description:
24B
Group: TCCSUP_Gem_and_Cis
RNAseq_ensembl_raw_counts.txt


title: P7B5_TCCSUP_GC_d11 [P7B5_TCCSUP_combined.txt]

description:
Amplicon DNA
P7B5_TCCSUP_combined.txt


title: Muscle-invasive bladder cancer 1505

description: Muscle-invasive bladder cancer


title: TCCSUP_Gem_and_Cis_A

description:
24A
Group: TCCSUP_Gem_and_Cis
RNAseq_ensembl_raw_counts.txt


title: Muscle-invasive bladder cancer 1410

description: Muscle-invasive bladder cancer


title: TCCSUP_Gem_C

description:
23C
Group: TCCSUP_Gem
RNAseq_ensembl_raw_counts.txt


title: P7B5_T24_T_min_10 [P7B5_ct_combinedruns.txt]

description:
Amplicon DNA
P7B5_ct_combinedruns.txt


title: Muscle-invasive bladder cancer 1604

description: Muscle-invasive bladder cancer


title: P7B4_TCCSUP_GC_d11 [P7B4_TCCSUP_combined.txt]

description:
Amplicon DNA
P7B4_TCCSUP_combined.txt


title: TCCSUP_Gem_B

description:
23B
Group: TCCSUP_Gem
RNAseq_ensembl_raw_counts.txt


title: Muscle-invasive bladder cancer 1408

description: Muscle-invasive bladder cancer


title: Input_H3K4me1_D10_r1


title: TCCSUP_Gem_A

description:
23A
Group: TCCSUP_Gem
RNAseq_ensembl_raw_counts.txt


title: P7B4_T24_T_min_10 [P7B4_ct_combinedruns.txt]

description:
Amplicon DNA
P7B4_ct_combinedruns.txt


title: P7E03_5637_GC_d9 [P7E03_5637GC_T9_GC_R3_S24_L004_R1_001]

description:
Amplicon DNA
P7E03_5637GC_T9_GC_R3_S24_L004_R1_001


title: TCCSUP_Cis_C

description:
22C
Group: TCCSUP_Cis
RNAseq_ensembl_raw_counts.txt


title: ChIP_H3K4me1_D10_r2

value: H3K4me1 ChIP


title: Input_H3K4me1_D50_r1


title: ChIP_H3K4me1_D50_r1


title: Input_H3K4me1_D10_r2


title: TCCSUP_Cis_B

description:
22B
Group: TCCSUP_Cis
RNAseq_ensembl_raw_counts.txt


title: P7B3_T24_T0 [P7B3_ct_combinedruns.txt]

description:
Amplicon DNA
P7B3_ct_combinedruns.txt


title: P7B2_TCCSUP_Saline_d11 [P7B2_TCCSUP_combined.txt]

description:
Amplicon DNA
P7B2_TCCSUP_combined.txt


title: ChIP_H3K4me1_D10_r1


title: Muscle-invasive bladder cancer 1405

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 1404

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 1407

description: Muscle-invasive bladder cancer


title: RNAi-GLAD 3

city: Shanghai

first: Yanshan

last: Fang

address: 100 Haike Rd, Building 13

institute: Interdisciplinary Research Center on Biology and Chemistry

data_processing:
The RNA-seq reads were mapped using Tophat.
Gene expression levels were measured using the reads per kb per million mapped reads criteria.
Genome_build: BDGP Release 6 + ISO1 MT/dm6
Supplementary_files_format_and_content: FPKM

source_name: Fly head

growth_protocol: All flies were raised on a standard cornmeal media and maintained at 25°C and 60% relative humidity

extract_protocol:
Total RNA from 100 fly brains of each genotype per duplicate was extracted using TRIzol (Invitrogen, 15596018) according to the manufacturer’s instruction.
Sequencing libraries were generated using NEBNext® UltraTM RNA library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Paired-end RNA-seq libraries were prepared following Illumina’s protocols and sequenced 150 bp paired-end on the Illumina HiSeq 4000 platform.

treatment_protocol: RU486 is added to the fly food to induct RNAi expression

value: TubGS>RNAi-GLAD

value: Fly head


title: P7B2_T24_T0 [P7B2_ct_combinedruns.txt]

description:
Amplicon DNA
P7B2_ct_combinedruns.txt


title: TCCSUP_Parental_C

description:
21C
Group: TCCSUP_Parental
RNAseq_ensembl_raw_counts.txt

value: Parental


title: P7B2_253J_GC_d15 [P7B2_BV_S14_L004_R1_001]

description:
Amplicon DNA
P7B2_BV_S14_L004_R1_001

value: GC


title: RNAi-GLAD 2


title: TCCSUP_Parental_B

description:
21B
Group: TCCSUP_Parental
RNAseq_ensembl_raw_counts.txt


title: Muscle-invasive bladder cancer 1401

description: Muscle-invasive bladder cancer

source_name: Anonymised


title: Muscle-invasive bladder cancer 1305

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 1403

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 1406

description: Muscle-invasive bladder cancer


title: TCCSUP_Parental_A

description:
21A
Group: TCCSUP_Parental
RNAseq_ensembl_raw_counts.txt


title: P7B12_KU1919_Saline_d15 [P7B12_KU1919GC_T15_Saline_R3_S35_L002_R1_001]

description:
Amplicon DNA
P7B12_KU1919GC_T15_Saline_R3_S35_L002_R1_001

value: Saline


title: RNAi-Ctrl 3

value: TubGS>RNAi-GFP


title: T24_Gem_and_Cis_C

description:
20C
Group: T24_Gem_and_Cis
RNAseq_ensembl_raw_counts.txt


title: virgin 6

data_processing:
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5
Reads were mapped to the Peromyscus californicus reference genome using STAR | version 2.7.2 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10
Assembly: GCF_007827085.1_ASM782708v3_genomic
Supplementary files format and content: tab-delimited text files include gene counts for each sample

organism: Peromyscus californicus

source_name: lung

extract_protocol:
Pair bonding :The bonded mice were paired for a period of four months. Afterwards, mice were scarified and lung tissues were collected for RNA extraction.
bond-disrupting: The bond-disrupted mice were paired for four months, then the male was removed from the mating cage, and lung tissue was collected one week later after bond-disruption for RNA isolation.
Virgin: For virgin mice, tissues were collected from mice of similar age housed in groups of three in each cage.
RNA was harvested using Rneasy mini plus kit (Qiagen). 1  ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext dA tailling and Ultra II Directional RNA Library prep Kit(E#7600) following the manufacturer's protocols.

value: lung

value: virgin


title: P7B10_KU1919_Saline_d15 [P7B10_KU1919GC_T15_Saline_R1_S33_L002_R1_001]

description:
Amplicon DNA
P7B10_KU1919GC_T15_Saline_R1_S33_L002_R1_001


title: RNAi-Ctrl 2


title: TCCSUP_Cis_A

description:
22A
Group: TCCSUP_Cis
RNAseq_ensembl_raw_counts.txt


title: T24_Gem_and_Cis_B

description:
20B
Group: T24_Gem_and_Cis
RNAseq_ensembl_raw_counts.txt


title: Muscle-invasive bladder cancer 2201

description: Muscle-invasive bladder cancer


title: Muscle-invasive bladder cancer 1212

description: Muscle-invasive bladder cancer


title: P7B1_TCCSUP_Saline_d11 [P7B1_TCCSUP_combined.txt]

description:
Amplicon DNA
P7B1_TCCSUP_combined.txt


title: RNAi-GLAD 1


title: RNAi-Ctrl 1


title: Muscle-invasive bladder cancer 1207

description: Muscle-invasive bladder cancer


title: T24_Gem_and_Cis_A

description:
20A
Group: T24_Gem_and_Cis
RNAseq_ensembl_raw_counts.txt


title: Muscle-invasive bladder cancer 1102

description: Muscle-invasive bladder cancer


title: virgin 5

value: Male


title: DIPG-XIII_Control_C

city: Dallas

first: Lei

last: Guo

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

description:
counts_raw_onc201_2.tsv
DIPG13_control_C_S24_L008

data_processing: Adaptors were trimmed using Trim Galore (v0.6.4). The trimmed reads were then aligned to human genome using STAR (2.7.3a). The subsequent mapped reads were quantified by featureCounts of the Subread (v1.6.3) package. Low-expressed genes were removed before any subsequent analysis. Gene expression was normalized using the Voom method from the R package limma (v 3.50.3). Differentially expressed genes were then identified using the same package. Functional enrichment analysis for the DEGs was performed using R package clusterProfiler (v4.2.2)

source_name: parental cell line

growth_protocol: Cell lines were cultured at 37°C, in 5% CO2, in TSM media with growth factors as described previously (Grasso CS et al, Nat Med. 2015 Jul;21(7):827. PMID: 26151328).

extract_protocol:
RNA was isolated using a Quick-RNA Miniprep kit (Zymo Research, Irvine, CA, USA). RNA quality/quantity of each samples was checked using RNA Nano assay using Bioanalyzer 2100 (Agilent Technologies - RNA RIN should be >8) and the RNA sample quantity was measured  using Qubit 2.0 Fluorometer (Thermo Fisher Scientific). Using 1000 ng of RNA from each sample to start library prep using TruSeq Stranded Total RNA Gold (Illumina RS-122-2303).
Sequencing library preparations were performed by Truseq Stranded Total RNA Sample Reference Guide (Illumina). RNA-seq  library quality/quantity checking was done using  Tape Station 2200 D1000 assay (Agilent Technologies) and QuantStudio 6 Flex Real time PCR System (Applied Biosystem). RNA-seq libraries were sequenced in Hiseq 3000 (Illumina) and the sequence type used was Paired End with 75 cycles.

treatment_protocol: Cells were treated with DMSO control and 5 uM, 3.0 uM, and 3.5 uM, rough IC50 values of ONC201 for 72 hours, respectively.

value: DIPG

tag: cell type

value: brain tumor cell line

tag: disease state

value: Diffuse intrinsic pontine glioma (DIPG)


title: P7B11_KU1919_Saline_d15 [P7B11_KU1919GC_T15_Saline_R2_S34_L002_R1_001]

description:
Amplicon DNA
P7B11_KU1919GC_T15_Saline_R2_S34_L002_R1_001


title: P7B1_T24_T0 [P7B1_ct_combinedruns.txt]

description:
Amplicon DNA
P7B1_ct_combinedruns.txt


title: 253J_Parental_C

description:
1C
Group: 253J_Parental
RNAseq_ensembl_raw_counts.txt


title: 253J_Parental_B

description:
1B
Group: 253J_Parental
RNAseq_ensembl_raw_counts.txt


title: virgin 2


title: P7B1_253J_GC_d15 [P7B1_BV_S13_L004_R1_001]

description:
Amplicon DNA
P7B1_BV_S13_L004_R1_001


title: virgin 3


title: P7A9_TCCSUP_Saline_d9 [P7A9_TCCSUP_combined.txt]

description:
Amplicon DNA
P7A9_TCCSUP_combined.txt


title: DIPG-XIII_Control_A

description:
counts_raw_onc201_2.tsv
DIPG13_control_A_S22_L008


title: 253J_Parental_A

description:
1A
Group: 253J_Parental
RNAseq_ensembl_raw_counts.txt