title: U266_CloneF8_Naive2_WCE

data_processing:
H3K27ac ChIP data was analyzed using the nf-core/chipseq pipeline. Quality filtering was done by FastQC and TrimGalore. Reads were aligned to UCSC_hg19 using BWA and SAMtools. IP efficiency was calculated by normalizing peak counts to their WCE using deepTools. Narrow consensus peaks were called using MACS, HOMER, BEDTools and featureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: Chip-seq: bigwig files generated using the nf-core ATAC pipeline;

extract_protocol:
Immunoprecipitation (IP) was performed with anti-H3K27ac antibody (Active Motif) and parts of the lysate were saved as whole cell extract (WCE).
Drosophila chromatin and antibody spike-ins were done for normalization. IP pulldown was performed using Protein A/G dynabeads (Invitrogen), followed by washing and elution off the beads.
Cross-linking was next reversed by proteinase K. Libraries were constructed with individual barcodes (IP and WCE).

treatment_protocol: For ChIP-seq, 2 x 10e7 cells were cross-linked using formaldehyde and sonicated on a Covaris E220 focused ultrasonicator (~200?500 bp fragment size).

value: DMSO


title: STP1002 10 mpk 3

status: Public on Mar 13 2022

type: RNA

city: Seoul

first: Dong Young

last: Kim

address: 75 Nowon-ro

country: South Korea

institute: KIRAMS

description: Total RNA was isolated in ileum tissue.

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

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

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

molecule: total RNA

organism: Mus musculus

source_name: mouse ileum tissue

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

growth_protocol: Each mouse was randomly assigned to study groups.

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

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

tag: tissue

value: ileum

tag: treatment

value: STP1002, PO/QD, 10 mg/kg


title: IGF1 S95

type: SRA

city: Düsseldorf

first: Rianne

last: Nederlof

address: Universitätsstraße 1

department: Institut für Herz-und Kreislaufphysiologie

country: Germany

institute: Heinrich-Heine University

library_source: transcriptomic

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

source_name: Neutrophils

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

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

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

tag: cell type

value: bone marrow derived neutrophils

tag: strain


title: untreated S86

value: untreated


title: STP1002 10 mpk 2

description: Total RNA was isolated in ileum tissue.


title: HEK293T_totalRNA_heatstress_longRT_minusDM_rep3

city: Chicago

first: Christopher

middle: D

last: Katanski

state: Illinois

department: Biochemistry

country: USA

institute: The University of Chicago

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

organism: Homo sapiens

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

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

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

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

tag: fraction

value: Total RNA

tag: enzyme/chemical treatment

tag: rt condition

value: Overnight RT


title: U266_CloneF8_Naive2_H3K27ac

city: Boston

first: Birgit

last: Knoechel

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

library_source: genomic

molecule: genomic DNA

value: MM cell line U266


title: DP6clone5_DabTreat_Day14

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

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

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

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

value: MM cell line DP6

value: dabrafenib

tag: treatment protocol

tag: extract protocol

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

tag: library strategy


title: HEK293T_polysomeRNA_heatstress_longRT_minusDM_rep3

description: Polysome associated RNA

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

value: Polysome associated RNA


title: untreated S80


title: STP1002 10 mpk 1

description: Total RNA was isolated in ileum tissue.


title: HEK293T_totalRNA_heatstress_longRT_minusDM_rep2


title: untreated S74


title: U266_CloneF8_Day10_Dab_WCE


title: HEK293T_totalRNA_H2O2_longRT_minusDM_rep3

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


title: U266_CloneF8_Day10_Dab_H3K27ac


title: STP1002 5 mpk 3

description: Total RNA was isolated in ileum tissue.

value: STP1002, PO/QD, 5 mg/kg


title: U266_CloneF6_Naive2_WCE


title: D.shibae ∆72kb Replicate C

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

data_processing:
The demultiplexed raw fastq-files were quality-controlled using the FASTQ-mcf suite (https://github.com/ExpressionAnalysis/ea-utils). Low quality bases and identified Illumina adaptors were clipped from the sequences. Reads were mapped to reference genomes using bowtie2 with default parameters.
The resulting sam-files were converted to binary format and indexed using samtools. A table with reads per protein coding sequence was generated from each indexed bam-file using featureCounts.
The R-package EdgeR was used for statistical analysis of differential gene expression.
Assembly: GCA_000018145.1
Supplementary files format and content: textfile, counts per gene

organism: Dinoroseobacter shibae

source_name: culture

growth_protocol: Cultivation for transcriptome analysis was performed in three biological replicates. Precultures of all D. shibae strains were cultivated overnight at 28°C in MB medium. 100 ml MB medium without antibiotics was inoculated with 2 ml of the preculture and grown in 250 ml Erlenmeyer flasks under agitation for about nine hours up to an OD600 of 0.6.

extract_protocol:
Bacterial cells were centrifuged and the pellets without remaining medium were frozen in liquid nitrogen, pestled, and stored in aliquots of about 150 mg at -80°C. The pestled bacterial cell powder was covered with 1 ml TRIzol reagent (ThermoFisher Scientific, Waltham, MA, USA) and incubated for 5 min at room temperature. The total RNA isolation starting with the centrifugation at 12,000 g for 10 min at 4°C were performed with the RNeasy mini kit (Qiagen, Hilden, Germany).
Depletion of ribosomal RNA was performed with the mRNA Ribo-Zero Magnetic Kit (Epicentre, Madison, WI, USA). The library was prepared from ribosomally depleted total RNA using Scriptseq v2 RNA-Seq Library Preparation Kit (Epicentre, Madison, WI, USA).


title: HEK293T_totalRNA_heatstress_longRT_minusDM_rep1


title: HEK293T_totalRNA_nostress_longRT_minusDM_rep3

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


title: D.shibae ∆72kb Replicate B


title: STP1002 5 mpk 2

description: Total RNA was isolated in ileum tissue.


title: HEK293T_totalRNA_nostress_longRT_minusDM_rep2


title: U266_CloneF6_Naive2_H3K27ac


title: D.shibae ∆72kb Replicate A


title: HEK293T_totalRNA_nostress_longRT_minusDM_rep1


title: Control 3

description: Total RNA was isolated in ileum tissue.


title: FeS2 rep D

city: Bozeman

first: Rachel

middle: L.

last: Spietz

state: MT

institute: Montana State University

data_processing:
Paired-end reads were processed using default settings in TrimGalore!, a wrapper that implements CutAdapt and FastQC to remove adapter sequences and filter reads, respectively.
Reads were aligned to the reference M. barkeri MS genome (ASM97002v1) using Bowtie2.
Reads were counted for each locus using HTSeq.
Normalization and statistical analyses were conducted in DESeq2 implemented in R v3.6.0.
Genome_build: ASM97002v1
Supplementary_files_format_and_content: All processed data files contain raw count data output from HTSeq. These data have not been normalized.

organism: Methanosarcina barkeri

source_name: whole cells

growth_protocol: M. barkeri strain MS was obtained from the American Type Culture Collection (ATCC 43569). Growth medium was prepared without added Fe and S in MilliQ water and using acid (10% HNO3) washed glassware. M. barkeri MS was grown in low-salinity medium (in g L-1: NaCl, 1.00; MgCl2 · 6H2O, 0.40; NH4Cl, 0.54; KCl, 0.50; CaCl2 · 2H2O, 0.10). The base salts solution was boiled for 10 minutes then purged with N2 gas passed over a heated (200 °C) and H2-reduced column containing reduced copper shavings for 1 hr L-1. After sparging, base salts medium was moved to an anaerobic chamber and allowed to cool to room temperature (~20 °C). Once cooled, NaHCO3 (2.00 g L-1) was added and the pH was adjusted to 7.0 with anoxic 2N HCl. Next, 75 mL of the base salts medium were dispensed into 165 mL serum bottles, sealed with black butyl stoppers, and capped with aluminum crimp caps. Sealed serum bottles were removed from the anaerobic chamber, the headspace was exchanged for 15 minutes with N2:CO2 (80%:20%) gas passed over a heated copper column, and then autoclaved. After autoclaving, a 100X sterile and anoxic phosphate solution containing 0.35 g L-1 K2HPO4 and 0.23 g L-1 KH2PO4 was added to each bottle of base salts medium. Prior to inoculation, the base salts medium used to cultivate both methanogen strains was amended with 1% (v/v) Wolfe’s vitamins and 1% SL-10 trace metals (no added Fe containing components). Cultures of both M. barkeri strains were provided with 0.5% (v/v) methanol and 40 mM acetate as a methanogenesis substrate and carbon source, respectively, and grown anaerobically with a N2:CO2 (80%:20%) headspace pressurized to 1.72 bar.

extract_protocol:
To harvest biomass, M. barkeri MS cells were subjected to vacuum filtration at low pressure (5 psi) onto a 47 mm 0.2-µm Supor 200 PES filter (Pall, Port Washington, NY) within an anaerobic chamber. Using flame-sterilized scissors, each filter was cut in half and each half transferred to a 1.5 mL cryotube before being removed from the anaerobic chamber and immediately flash frozen in liquid nitrogen. Frozen cells were then stored at -80 °C until processing. Total RNA from M. barkeri was extracted using TRIzol reagent (Invitrogen) following the manufacturer’s protocol with slight modification. Individual frozen half filters containing M. barkeri cells were transferred to a Lysis E tube (MP Biomedicals) on ice and 1 mL of TRIzol was immediately added to the frozen filter. TRIzol-treated M. barkeri cells were subjected to three cycles of 40 seconds of bead beating followed by resting for five minutes at room temperature (~20 °C). Two hundred µL of molecular grade chloroform was added to each tube and each tube was inverted to mix, incubated at room temperature for three minutes, and centrifuged for 15 minutes at 12,000 x g at 4 °C. The upper aqueous phase containing RNA was carefully transferred to a clean 2 mL tube. To precipitate RNA, 0.5 mL of pre-chilled (4 °C) 100% molecular grade isopropanol was added to each tube and tubes and their contents were incubated on ice for 10 minutes followed by centrifugation for 10 minutes at 12,000 x g at 4 °C. The supernatant was discarded, and 1 mL of 75% molecular grade ethanol was added to wash the RNA. After centrifugation for 5 minutes at 7,500 x g at 4 °C, the supernatant was removed, and the RNA pellet was air dried for 5-10 minutes. Total RNA was dissolved in 50 µL RNA-grade water (Fisher Scientific, Waltham, MA) by incubating in a 55 °C heat block for 10 minutes. RNA was treated with Turbo DNase (Invitrogen) to remove residual DNA per manufacturer’s instructions. After DNase treatment, the remaining total RNA was subjected to a second round of isopropanol precipitation, ethanol wash, and resuspension as described above.
Quality control was performed with a Bioanalyzer (Agilent, CA, USA), and rRNA reduction was performed with a RiboZero-Bacteria rRNA removal kit (Illumina, CA, USA) with the addition of custom M. barkeri MS-specific oligos designed using the sequences for M. barkeri MS’s large and small ribosomal subunits. Stranded cDNA libraries were prepared from rRNA-depleted mRNA using the TruSeq Stranded Total and mRNA kit (Illumina, CA, USA).

treatment_protocol: Cultures of M. barkeri MS were grown in quadruplicate on three different sources of Fe and S for RNA-Seq analysis: 2 mM FeS2, 20 µM FeCl2 and 2 mM L-cysteine, and 20 µM FeCl2 and 2 mM Na2S. Cells were harvested at mid-log growth phase, as determined by CH4 production, and final biomass was estimated by DNA quantification.

value: MS

tag: fe source

value: pyrite (FeS2)


title: D.shibae ∆86kb Replicate C


title: U266_CloneF6_Day10_Dab_WCE


title: U266_CloneF6_Day10_Dab_H3K27ac


title: Control 1

description: Total RNA was isolated in ileum tissue.


title: Control 2

description: Total RNA was isolated in ileum tissue.


title: FeS2 rep C


title: Notreated2A

city: Shen Zhen

first: Shaohua

last: Ma

state: Guangdong Sheng

address: nanshan street

country: China

institute: Tsinghua University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) .
Bowtie2 (v2.2.5)  was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Assembly: GRCm38.p6
Supplementary files format and content: xlsx file include raw counts, TPM, and FPKM values for each sample

source_name: gluteus maximus tissue

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular

value: Defect only

value: balb/c


title: U266_CloneD3_Naive2_WCE

value: DMSO


title: U266_CloneD3_Naive2_H3K27ac


title: D.shibae ∆86kb Replicate A


title: Normal1A

value: Untreated


title: D.shibae ∆191kb Replicate C


title: U266_CloneD3_Day10_Dab_WCE


title: U266_CloneD3_Day10_Dab_H3K27ac


title: D.shibae ∆191kb Replicate A


title: Fe/Cysteine rep C

value: cysteine


title: FeS2 rep A


title: D.shibae ∆191kb Replicate B


title: Lowbeads3A

value: Treated with Matrigel LDB-MSCs for one month


title: Fe/Cysteine rep D


title: CD138+/CD38+ myeloma and normal plasma scRNA-seq

description: *** Raw data not submitted to GEO due to patient privacy concerns ***

data_processing:
Processing and quality filtering of scRNA-seq data was carried out using trimmomatic, STAR, HTSeq and RSEM. Four different parameters were used to filter out low quality cells: i) library size, ii) number of genes detected, iii) percentage of reads mapping to mitochondrial genes, and iv) percentage of reads mapping to house-keeping genes. Cells that fell below three median absolute deviations were excluded from downstream analyses.As an additional approach to remove bad-quality cells without any predefined cut-offs we used the R package mvoutlier.
Genome_build: hg19
Supplementary_files_format_and_content: scRNA-Seq: htseq count matrix with raw counts for all individual cells

source_name: 1508 CD138+/CD38+ myeloma and normal plasma cells from three patients and a normal donor before and while undergoing dabrafenib/ treatment

extract_protocol:
Full-length single-cell RNA-seq libraries were prepared using Smart-seq2.
Pooled sequencing of Nextera libraries was carried out using a NextSeq 500 (Illumina, C>A).
All sequenced reads were paired-end and 36-base pair (bp) read length. A sequencing depth of 1 x 10e6 reads was aimed for in each cell.

treatment_protocol: Myeloma cells were isolated from the bone marrow or peripheral blood before dabrafenib/ trametinib, at day 7 of treatment and at end of treatment.


title: STP1002 5 mpk 1

description: Total RNA was isolated in ileum tissue.

value: ileum


title: D.shibae DSM16493 Replicate C


title: Parthenote PA3 (RNA-seq)

city: Columbus

first: Jinsoo

last: Ahn

state: OH

address: 2029 Fyffe Rd

institute: The Ohio State University

data_processing:
Sequenced reads were trimmed for adaptor sequence and low quality reads were eliminated.
Then, the cleaned reads were aligned to the reference genome (Sscrofa11.1) using STAR (v2.7.5) with default parameters.
Duplicated reads were removed using Picard MarkDuplicates and reads were filtered using SAMtools (-q 30).
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Tab-delimited text files containing normalized read counts from Salmon (v1.3.0)

organism: Sus scrofa

source_name: embryo

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

extract_protocol:
Total RNA from whole CN embryos (n = 3) and whole PA embryos (n = 3) samples was isolated with TRIzol reagent. DNase I was treated to the RNA samples to avoid genomic DNA contamination. One ug of total RNA was used to construct cDNA libraries with the TruSeq RNA Sample Prep Kit v.2.
RNA libraries were prepared for sequencing according to Illumina's instructions accompanying the TruSeq RNA Sample Prep Kit v.2.

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

value: Landrace x Yorkshire x Duroc (LYD)

value: whole embryo

tag: age

value: embryonic day 21

value: parthenogenesis


title: insectivorous bats_96min

city: Kunming

first: yanni

last: zeng

state: China,Yunnan

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

department: State Key Laboratory of Genetic Resources and Evolution

institute: Kunming Institute of Zoology Chinese Academy of Sciences

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

organism: Miniopterus schreibersii

source_name: insectivorous bats_96min

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

value: liver


title: Fe/Cysteine rep A


title: D.shibae DSM16493 Replicate A


title: D.shibae DSM16493 Replicate B


title: insectivorous bats_control

source_name: insectivorous bats_control


title: Parthenote PA1 (RNA-seq)


title: non-echolocator1

description: Sample 6

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

organism: Cynopterus sphinx

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

value: brain


title: D.shibae ∆86kb Replicate B


title: D.shibae DSM112351 Replicate C


title: Fe/Sulfide rep C

value: sulfide


title: Fe/Sulfide rep D


title: Control CN3 (RNA-seq)

value: untreated


title: Control CN2 (RNA-seq)


title: D.shibae DSM112351 Replicate A


title: echolocator4

description: Sample 4

organism: Miniopterus fuliginosus


title: Bulkgel3A

value: Treated with Matrigel HDG-MSCs for one month


title: Highbeads2A

value: Treated with Matrigel HDB-MSCs for one month


title: FeS2 rep B

value: MS

value: pyrite (FeS2)


title: echolocator5

description: Sample 5

organism: Taphozous melanopogon


title: Fe/Cysteine rep B


title: C57BL/6 day56-ATACseq-rep3

status: Public on Mar 12 2022

city: Iowa City

first: Dakota

middle: L

last: Jones

state: IA

address: 51 Newton Road

department: Department of Anatomy and Cell Biology

institute: University of Iowa

description:
day14_vs_day56_FCcut_FDRcut_anno.txt
sham_vs_day56_FCcut_FDRcut_anno.txt

data_processing:
Raw fastq files were aligned to the mm10 genome using Hisat2(Kim et al., 2019). Sam files were converted to Bam files using Picard SortSam. Count matrices were generated using featureCounts from the Subread package (Liao, Smyth and Shi, 2013). Count matrices were then used for differential gene expression using Deseq2 (Kim et al., 2019). The threshold for significant differential expression was an FDR ≤ 0.05 and a log2 fold-change of ≥ 1 or ≤ -1. Normalized read counts were obtained from Deseq2.
Paired-end reads were mapped to the mm10 genome using bowtie2 (Langmead and Salzberg, 2012) using the “--very sensitive” option. Sam files were converted to BAM and sorted by chromosomal coordinates using Picard SortSam. Reads not aligning to Chr1-20, X, or Y were removed using SAMtools (Langmead and Salzberg, 2012). PCR duplicates were removed from Bam files using Picard MarkDuplicates. Peaks were called using MACS2 with the following options “-q 0.01 --shift -37 --extsize 73 --keep-dup all” . Peaks which were observed in the blacklisted regions of the genome (Zhang et al., 2008)were removed using Bedtools (Quinlan and Hall, 2010). DiffBind was used for examination of differential chromatin accessibility(Stark and Brown, 2011). The threshold for significantly differential accessibility was an FDR ≤ 0.05 and a log2 fold-change of ≥ 1 or ≤ -1. Differential accessibility sites were then annotated to their nearest transcriptional start site (TSS) using Homer(Heinz et al., 2010).
Assembly: mm10
Supplementary files format and content: differential expression analysis (.txt), bigwig coverage files (.bigwig), and differential accessiblity analysis files (.txt)

source_name: FACS isolated Col1a2-lineage trace lung mesenchyme

growth_protocol: Col1a1-GFP+ lung mesenchyme were cultured on commercially-available 0.2kPa and 32kPa collagen1 coated PDMS substrates (Advanced Biomatrix) for 5 days. Cells were cultured in DMEM supplemented with 10% FBS and anti-anti.

extract_protocol: At the indicated timepoints, mice ketamine/xylazine solution (100 mg/kg and 10 mg/kg, respectively) injected intraperitoneally. The left ventricle of the heart was perfused with ice-cold PBS (Thermo Fisher Scientific) to remove blood content from the lung. Lungs were then immediately harvested and minced in 10-cm Petri dishes and then incubated in digestive solution (DMEM, 0.2 mg/ml Liberase DL, and 100 U/ml DNase I). Samples were digested at 37°C for 45 minutes. Digestive solution was inactivated with 1x DMEM (Thermo Fisher Scientific) containing 10% FBS (Thermo Fisher Scientific). Cell and tissue suspension was put through a 40-µm filter and centrifuged. Cell pellet was resuspended in red blood cell lysis buffer (BioLegend) for 90 seconds and then diluted in 3x volume of PBS. Cells were centrifuged and resuspended in 200 µl FACS buffer (1% BSA and 0.5 mM EDTA, pH 7.4 in PBS). The single-cell suspension was then incubated with anti-mouse CD45:PerCpCy5.5 (BioLegend; 1:200), anti-mouse CD326-APC (BioLegend; 1:200), and DAPI (Sigma-Aldrich; 1:1,000) antibodies for 30 minutes on ice. Samples were then FACS sorted using a BD FACS Aria II (BD Biosciences, San Jose, CA, USA). Samples were then FACS sorted using a BD FACS Aria II (BD Biosciences, San Jose, CA, USA). To isolate GFP+ lung mesenchyme, the following selection strategy was used: debris exclusion (FSC-A by SSC-A), doublet exclusion (SSC-W by SSC-H and FSC-W by FSC-H), dead cell exclusion (DAPI by tdTomato), CD45+ cell exclusion (PerCP-Cy5.5 by tdTomato), EpCAM+ cell exclusion and isolation of GFP+ cells (APC by GFP). For the Col1a1-GFP cell isolation and analysis, an additional antibody for anti-mouse CD31:PE (BioLegend; 1:200) was used to exclude endothelial cells. For RNA analysis, GFP+ cells were sorted directly into RLT lysis buffer (Qiagen, Valencia, CA, USA). For the in vitro vs in vivo RNAseq experiment, RNA quality was determined using the BioAnalyzer (Agilent, Santa Clara, California, USA). RNA samples that had RQN values > 6 were approved for library prep and sequencing. RNA libraries were prepared using approximately 100 ng of total RNA according to the manufacturer’s instructions for the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA), employing poly-A mRNA enrichment using oligo dT magnetic beads. The final adapter-modified cDNA fragments were enriched by 15 cycles of PCR using Illumina TruSeq PCR primers.  The concentration and size distribution of the completed libraries were determined using a Fragment Analyzer (Agilent, Santa Clara, CA, USA) and Qubit fluorometry (Invitrogen, Carlsbad, CA, USA). Libraries were sequenced at up to five samples per lane, following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cells were sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 using the HiSeq Control Software HD 3.4.0.38 collection software. Base-calling was performed using Illumina’s RTA version 2.7.7. Raw fastq files were aligned to the mm10 genome using Hisat2(Kim et al., 2019). Sam files were converted to Bam files using Picard SortSam. Count matrices were generated using featureCounts from the Subread package (Liao, Smyth and Shi, 2013). Count matrices were then used for differential gene expression using Deseq2 (Kim et al., 2019). The threshold for significant differential expression was an FDR ≤ 0.05 and a log2 fold-change of ≥ 1 or ≤ -1. Normalized read counts were obtained from Deseq2.

value: bleo

tag: time point

value: day56 post bleo


title: D.shibae DSM112351 Replicate B


title: C57BL/6 day56-ATACseq-rep4


title: C57BL/6 sham-ATACseq-rep2

description:
sham_vs_day14_diffbind_FCcut_FDRcut_anno.txt
sham_vs_day56_FCcut_FDRcut_anno.txt

value: sham


title: C57BL/6 sham-ATACseq-rep1


title: echolocator3

description: Sample 3

organism: Myotis laniger


title: Fe/Sulfide rep A


title: Parthenote PA2 (RNA-seq)


title: C57BL/6 day56-ATACseq-rep2


title: Control CN1 (RNA-seq)


title: C57BL/6 day14-ATACseq-rep4

description:
sham_vs_day14_diffbind_FCcut_FDRcut_anno.txt
day14_vs_day56_FCcut_FDRcut_anno.txt

value: day14 post bleo


title: CD1 0.2kPa-ATACseq-rep3

description:
0_2kpa_vs_32kpa_diffbind_FDRcut_FCcut_anno.txt
0_2kpa_vs_sham_diffbind_FDRcut_FCcut.txt

source_name: FACS isolated Col1a1-GFP lung mesenchyme


title: C57BL/6 day14-ATACseq-rep3


title: C57BL/6 day14-ATACseq-rep2


title: CD1 0.2kPa-ATACseq-rep1


title: C57BL/6 sham-ATACseq-rep3


title: CD1 32kPa-ATACseq-rep2

description:
0_2kpa_vs_32kpa_diffbind_FDRcut_FCcut_anno.txt
32kpa_vs_sham_diffbind_FDRcut_FCcut.txt


title: CD1 32kPa-ATACseq-rep1


title: Fe/Sulfide rep B


title: C57BL/6 day56-ATACseq-rep1


title: CD1 0.2kPa-ATACseq-rep2


title: C57BL/6 sham-ATACseq-rep4


title: CD1 sham-ATACseq-rep3

description:
0_2kpa_vs_sham_diffbind_FDRcut_FCcut.txt
32kpa_vs_sham_diffbind_FDRcut_FCcut.txt


title: CD1 32kPa-RNAseq-rep2


title: CD1 32kPa-RNAseq-rep3


title: CD1 sham-ATACseq-rep2


title: C57BL/6 day14-ATACseq-rep1


title: CD1 32kPa-RNAseq-rep1


title: CD1 sham-ATACseq-rep1


title: CD1 32kPa-ATACseq-rep3


title: CM-sM2_rep2

city: Shijiazhuang

first: Cong

last: Zhang

address: Jian Kang Road 12th

institute: The fourth hospital of Hebei medical university

description: gene expression in M2

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: GCC culture medium induced M2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: THP-1 cells were cultured with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. M0 cells were induced by THP-1 with PMA (50ng/ml) for 48h. M1 cells were induced by M0 with LPS (100ng/ml) and IFN-γ  (20ng/ml) for 48h. M2 cells were induced by M0 with IL-4 (20ng/ml) for 48h. CM-sM2 were induced by 30% GCC culture medium. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

value: GCC culture medium induced M2


title: CM-sM2_rep3

description: gene expression in M2


title: CD1 0.2kPa-RNAseq-rep3


title: macrophage M2_rep3

description: gene expression in M2

source_name: THP-1 induced M2

value: THP-1 induced M2


title: macrophage M2_rep1

description: gene expression in M2


title: macrophage M1_rep3

description: gene expression in M1

source_name: THP-1 induced M1

value: THP-1 induced M1


title: CD1 0.2kPa-RNAseq-rep2


title: 4861_Unstr

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: Taf8 Deleted Rep 4

data_processing:
Sequencing was conducted using an Illumina HiSeq 2000 to produce 100bp paired-end reads.
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.58 and Real Time Analysis (RTA) v1.18.64 to perform real-time base calling. The Illumina bcl2fastq 1.8.4 pipeline was used to generate the sequence data.
Reads were aligned to the mm10 mouse genome by the subjunc function of the Subread software suite version 1.5.0 (http://subread.sourceforge.net).
Read counts were summarized by Entrez Gene ID using the Rsubread package version 1.18.0, by the featureCounts function with minMQS=10 and Rsubread's inbuilt RefSeq annotation (https://doi.org/doi:10.18129/B9.bioc.Rsubread).
Assembly: mm10
Supplementary files format and content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

molecule: polyA RNA

source_name: Embryonic cerebral cortex

extract_protocol:
RNA was isolated with RNeasy Kit (Qiagen).
Unstranded RNA-seq libraries were prepared using a TruSeq RNA Sample Preparation kit version 2 (Illumina).

tag: animal number

tag: taf8 status

value: Taf8 -/lox

value: Embryonic cerebral cortex


title: macrophage M1_rep2

description: gene expression in M1


title: CD1 0.2kPa-RNAseq-rep1


title: 4771_Unstr

description: Taf8 Deleted Rep 3


title: CM-sM2_rep1

description: gene expression in M2


title: CD1 sham-RNAseq-rep3


title: macrophage M1_rep1

description: gene expression in M1


title: RCC4-siMESH1-2-repl3

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

hyb_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip® ____________ arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450

scan_protocol: scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

data_processing: The data were analyzed with Agilent 2100 Bioanalyzer G2939A

label: biotin

source_name: RCC4 transfected with MESH1 siRNA#2, biological rep3

growth_protocol: RCC4 cells grew in the control full DMEM media supplement with 10% FBS and Penicillin/Streptomycin

extract_protocol: RNA was extracted by RNAeasy kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: RCC4 cells were transfected with indicated siRNAs for 48 hours

tag: cell line


title: RCC4-siMESH1-2-repl1

source_name: RCC4 transfected with MESH1 siRNA#2, biological rep1

label_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip® ____________ arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450


title: RCC4-siMESH1-2-repl2

source_name: RCC4 transfected with MESH1 siRNA#2, biological rep2


title: 4721_Unstr

description: Taf8 Deleted Rep 2


title: macrophage M0_rep3

description: gene expression in M0

source_name: THP-1 induced M0

value: THP-1 induced M0


title: RCC4-siMESH1-1-repl3

source_name: RCC4 transfected with MESH1 siRNA#3, biological rep3


title: macrophage M0_rep2

description: gene expression in M0


title: RCC4-siMESH1-1-repl1

source_name: RCC4 transfected with MESH1 siRNA#1, biological rep1


title: 4561_Unstr

description: Taf8 Deleted Rep 1


title: RCC4-siMESH1-1-repl2


title: CD1 sham-RNAseq-rep2


title: macrophage M2_rep2

description: gene expression in M2


title: CD1 sham-RNAseq-rep1


title: RCC4-Control-rep2

source_name: RCC4 transfected with control siRNA, biological rep2


title: 4771_Str

description: Taf8 Knock-out Rep 3

data_processing:
Libraries were sequenced on an Illumina NextSeq 500 to produce 81bp paired-end reads.
Reads were aligned to the mm10 mouse genome by the subjunc function of the Subread software suite version 1.5.0 (http://subread.sourceforge.net).
Read counts were summarized by Entrez Gene ID using the Rsubread package version 1.18.0, by the featureCounts function with minMQS=10 and strandSpecific=2 and Rsubread's inbuilt RefSeq annotation. The reversely stranded read counts (strandSpecific=2) were used for the stranded RNA-seq analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

extract_protocol:
RNA was isolated with RNeasy Kit (Qiagen).
RNA-seq libraries were prepared using a TruSeq Stranded mRNA Library Preparation kit (Illumina).


title: RCC4-Control-rep3

source_name: RCC4 transfected with control siRNA, biological rep3


title: macrophage M0_rep1

description: gene expression in M0


title: 4721_Str

description: Taf8 Knock-out Rep 2


title: 4861_Str

description: Taf8 Knock-out Rep 4


title: C57BL/6 day56-RNAseq-rep4


title: 4092_Unstr

description: Taf8 Intact Rep 4


title: RCC4-Control-rep1

source_name: RCC4 transfected with control siRNA, biological rep1


title: 4561_Str

description: Taf8 Knock-out Rep 1


title: 4086_Unstr

description: Taf8 Intact Rep 3


title: 4086_Str

description: Taf8 Wild-type Rep 3


title: 4085_Str

description: Taf8 Wild-type Rep 2


title: 4092_Str

description: Taf8 Wild-type Rep 4


title: C57BL/6 day56-RNAseq-rep3


title: C57BL/6 day56-RNAseq-rep2


title: 4084_Str

description: Taf8 Wild-type Rep 1


title: 4085_Unstr

description: Taf8 Intact Rep 2


title: C57BL/6 day56-RNAseq-rep1


title: Leaf, hormesis, F3

city: Mlochow

first: Dorota

last: Sołtys-Kalina

address: Platanowa 19

department: Mlochow Research Centre

country: Poland

institute: IHAR-PIB

data_processing:
Zebracall process Version 0.5.0.13875 used for basecalling.
The index of the reference genome (https://www.ncbi.nlm.nih.gov/assembly/GCF_000226075.1) was built using Bowtie v2.1.0.
Poor quality and to short reads (<30 nt) were removed from analysis.
Paired-end clean reads obtained for bulks A and B were aligned to the reference genome using TopHat v2.0.9.
Assembly: GCF_000226075.1
Supplementary files format and content: csv files were generated using DESeq2 package.
Supplementary files format and content: all_samples_raw_count.xlsx: Excel file includes abundance measurements.

organism: Solanum tuberosum

source_name: Leaf

growth_protocol: Potato plants were planted in plastic pots filled with soil. Plants grew in greenhouse from May to October.

extract_protocol:
Total RNA was isolated using TRIZol method as described Chomczyński and Sacchi (1987).
The mRNA was isolated using Dynabeads® mRNA Purification Kit for mRNA enrichment (Ambion, 61006), and cDNA libraries were prepared using MGIEasy RNA Directional Library Prep Set (MGI, 1000006386). The established cDNA libraries were sequenced on the BGISEQ-500 sequencing platform (BGI Genomics, China) to generate 100-bp paired-end reads (PE100).

treatment_protocol: At stage of full anthesis, leaves were collected, ground in liquid nitrogen and freezed in -80°C until use.

value: Leaf

tag: population

value: Diploid hybrid 15-1

tag: developmental stage

value: Full anthesis

tag: phenotype

value: High glycoalkaloids, hormesis


title: Leaf, hormesis, F2

tag: tissue

tag: treatment

value: untreated


title: Leaf, hormesis, F1


title: C57BL/6 day14-RNAseq-rep4

tag: strain


title: PTD7_RS, replicate #3

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

data_processing:
FastQC v0.11.4 is used to check the quality of the samples
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.35 with parameters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:35
Sequenced reads were then mapped to mm10 transcriptome using Tophat2 v2.1.0 with parameters --library-type fr-unstranded --min-intron-length 50 --no-coverage-search
The mapping files were then filtered using samtools v0.1.18 (samtools view with parameters -bq 20) and sorted using samtools sort
Reads were counted using HTSeqCount v0.6.1p1 with parameters -f bam -m intersection-strict -s no -a 10 -t exon -i gene_id
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw counts (output HTSeqCount) for each sample

source_name: PTD7 cell line, rescued by transduction with recombinant lentivirus pLenti6(bla)-mPcdh10short-HA, and enriched for expression of short isoform 1 of Pcdh10 by FACS

growth_protocol: The PTD25 cell line was derived by a 1-h dissociation from a pinnal tumor in a male mouse with GFAP-Cretg/+;Pcdh10-/-;p53-/-;Rb-/- genotype, killed at 17 weeks after birth. The PTD7 cell line was derived by overnight dissociation from a pinnal tumor in a female mouse with GFAP-Cretg/+;Pcdh10-/-;p53-/-;Rb-/- genotype, killed at 21.5 weeks after birth. Tumors were washed and cut into small pieces in PBS with gentamycin (250 mg/ml). Uniform cell suspensions were obtained by treatment at room temperature with dissociation buffer (DMEM, 10% FCS, 250 mg/ml gentamycin, 0,5 % glucose, 0.125 U/ml Dispase II [Sigma-Aldrich], 220 U/ml crude Collagenase [Sigma-Aldrich]), followed by gentle centrifugation, filtration through cell strainers of 70 mm and 40 mm, and seeding on tissue-culture plastic substrates. To obtain the PTD25 and PTD7 cell lines, the original tumor-derived cell populations were subcloned by limiting dilution and colony picking. To obtain derivative cell lines of PTD25 and PTD7, rescued for the ablation of Pcdh10 by the introduction and expression of cDNA encoding either long isoform 4 of mouse Pcdh10 (designated _RL) or short isoform 1 of mouse Pcdh10 (designated _RS), the parental cell lines were transduced with either lentivirus pLenti6(bla)-mPcdh10long-HA or lentivirus pLenti6(bla)-mPcdh10short-HA (for construction details, see Kleinberger et al., 2021, Innovative mouse models for the tumor suppressor activity of Protocadherin-10 isoforms. Submitted for publication). The transduced cell cultures were enriched for viable Pcdh10 expressing cells by FACS. For this experiment, single-cell suspension were obtained by non-enzymatic cell dissociation solution (Sigma-Aldrich), containing 1 % BSA and 20 % fetal calf serum (FCS). The primary antibody used was a rabbit polyclonal antibody recognizing epitope AA 1-290 of human and mouse Pcdh10, which is exposed extracellularly (Invitrogen Cat. No. PA5-31043, Fisher Scientific, Merelbeke, Belgium). The second antibody was polyclonal Alexa Fluor 488 goat anti-rabbit antibody (Sigma-Aldrich). Dead cells were excluded on the basis of DAPI staining. Expression of Pcdh10 cDNA in the rescued cell lines was confirmed by immunofluorescent microscopy. All cell lines to be analyzed by RNASeq were grown to confluence in 75-cm2 tissue culture flasks containing Dulbecco’s modified MEM medium with 10 % FCS and 2 mM L-glutamate, before RNA extraction.

extract_protocol:
Total RNA was extracted with TRIZOL reagent (Life Technologies, Cat. No. 15596), followed by on column extraction with the Aurum Total RNA mini kit (Life Science Research – Bio-Rad Cat, No. 732-6820). Concentrations were measured by the NanoDrop technology (Thermo Fisher Scientific) and adjusted to 300 ng/ml. RNA quality was assessed by the Bioanalyzer RNA 6000 Nano assay (Agilent, Cat. No. 5067-1511) and found to be highly intact for all samples (RNA Integrity Number of 9.9 to 10).
Library preparation was by the VIB Nucleomics Core facility (Leuven, Belgium), using the Illumina TruSeq stranded mRNA prep kit (Illumina Inc., San Diego, CA, USA). Samples were analyzed by the Illumina NextSeq 500 High 75 Sequencing System, yielding single-end 75-bp reads.

treatment_protocol: Cell line cultures were untreated before RNA extraction.

tag: genotype

tag: malignancy

value: Low


title: PTD7_RS, replicate #4


title: bph 4 hr replicate 2

city: Minneapolis

first: Julia

last: Willett

state: Minnesota

address: 689 23rd Avenue SE, 4-149 Micro Research Facility

institute: University of Minnesota

data_processing:
Sequencing quality was evaluated using FastQC.
Reads were trimmed with Trimmomatic and imported into Rockhopper for analysis using standard settings.
Reads were aligned to the OG1RF reference genome (NC_017316.1).
Genome_build: NC_017316.1
Supplementary_files_format_and_content: text file including raw counts, normalized read counts, RPKM values, Rockhopper expression values, p values, and q values

organism: Enterococcus faecalis

source_name: bacterial culture

growth_protocol: Static liquid cultures were grown at 37 oC for 2 and 4 hr.

extract_protocol:
At indicated time points, a volume equivalent to OD600 = 1.0 was mixed with an equal volume of RNAprotect.  Cells were collected by centrifugation and stored at -80 oC.  Pellets were resuspended in TE buffer + 30 mg/mL lysozyme for 30 min, after which total RNA was extracted using a Qiagen RNeasy kit.  RNA samples were treated with Turbo DNase using the manufacturer's rigorous method to remove contaminating genomic DNA.
RNA was submitted to the University of Minnesota Genomics Center for ribosomal RNA depletion (RiboZero) and TruSeq stranded library preparation.  Samples were pooled and sequenced (2x75 bp paired ends) on an Illumina NextSeq in mid-output mode.

tag: genotype/variation

value: bph


title: bph 4 hr replicate 1


title: PTD7_RS, replicate #2


title: bph 2 hr replicate 1


title: bph 2 hr replicate 2


title: OG1RF 4 hr replicate 2


title: OG1RF 2 hr replicate 1


title: PTD7_RL, replicate #4

source_name: PTD7 cell line, rescued by transduction with recombinant lentivirus pLenti6(bla)-mPcdh10long-HA, and enriched for expression of long isoform 4 of Pcdh10 by FACS


title: OG1RF 2 hr replicate 2


title: C57BL/6 day14-RNAseq-rep2

source_name: FACS isolated Col1a2-lineage trace lung mesenchyme

value: bleo


title: OG1RF 4 hr replicate 1


title: PTD7_RS, replicate #1


title: C57BL/6 day14-RNAseq-rep1


title: C57BL/6 sham-RNAseq-rep4


title: VDJ annotations sample tags scRNAseq lymphocytes X231 X229 X431

city: Seattle

first: Joshua

last: Veatch

state: Washington

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

description: VDJ annotations

data_processing:
Each pool was sequenced on an Illumina NovaSeq SP flowcell, with basecalling and demultiplexing performed by bcl2fastq 2.20.
After manufacturer recommended preprocessing, Fastq files were uploaded to SevenBridges for analysis with BD Rhapsody Targeted Analysis Pipeline v1.9.1 (8 Oct 2020), with refined cell calling disabled.
Internally, the Targeted Analysis Pipeline aligns read 2 to the supplied panel of targeted genes using Bowtie2 v2.3.5.
Assembly: GRCh38
Supplementary files format and content: Expression matrices (raw counts) in .csv format.
Supplementary files format and content: DBEC_MolsPerCell files summarize counts of molecules per gene in each cell, generated by the Targeted Analysis Pipeline using distribution-based UMI error correction (DBEC).
Supplementary files format and content: Sample_Tag_Calls files associate cells with sample tags assigned by the Targeted Analysis Pipeline.
Supplementary files format and content: VDJ_perCell files associate cell barcode with TCR and BCR sequences reconstructed by the BD Rhapsody Targeted Analysis Pipeline.

source_name: Tumor single cell suspensions

growth_protocol: Single cell suspensions were made from fresh primary melanomas surgical resections using enzymatic digestion, the Miltenyi gentleMACS dissociator and the human tumor dissociation kit (Miltenyi) and cryopreserved.

extract_protocol:
CD45+ cells were sorted into CD45+ fractions that were either CD3- CD19- or positive for either CD3 or CD19 and CD45+ CD3- CD19- populations were sequenced separately from CD3+ and CD19+ populations. Single cells were partitioned using the BD Rhapsody system per the manufacturer's instructions.
Libraries were created following the BD Rhapsody™ System VDJ CDR3, Sample Tag, and BD AbSeq Library Preparation Protocol. In more detail: Single-cell libraries were prepared using the BD Rhapsody Express system (BD Biosciences, #633707) and Targeted mRNA and AbSeq Reagent Kit-4 pack (BD Biosciences, #633771) according to the manufacturer’s protocol (BD Biosciences). Briefly, tumor samples from each donor were thawed and labelled with sample tags using BD Single-Cell Multiplexing Kit (BD Biosciences, #633781). Cells from each donor were labelled with a unique sample tag. Cells were then washed in BD Stain buffer (BD Biosciences, #554656), pooled together and incubated in Fc block followed by labelling cells with BD AbSeq Ab-Oligos master mix (3uL per Ab-Oligo). For flow sorting various lymphoid and myeloid cell populations, cells were stained with a mixture of fluorescently labelled antibodies (BD Biosciences or BioLegend): anti-human CD3 (#OKT3), CD4 (#RPA-T4), CD8 (#RPA-T8), CD19 (#HIB19), CD45 (#2D1), for 30 mins at 4ºC. After sorting, cells were counted and pooled such that there were 20,000 cells resuspended in 620 uL of BD Sample buffer. The BD Rhapsody cartridges were primed, and the pooled cells were loaded onto the cartridges and incubated at room temperature. Next, Cell Capture beads were washed & loaded onto the cartridge. After incubation, cartridges were washed twice with BD Sample Buffer. This was followed by lysis of cells and retrieval of beads. After washing the retrieved Cell Capture beads, we proceeded immediately with reverse transcription. For the subsequent steps, we switched to BD Rhapsody system VDJ CDR3, Sample Tag, and BD AbSeq library protocol (BD Biosciences) to generate TCR and BCR libraries in addition to mRNA, AbSeq, Sample Tag libraries. Poly-T Template Switching Oligo (TSO) was added during reverse transcription reaction to allow identification of VDJ recombination events in B and T cells. This was followed by denaturation, hybridization, Klenow extension (New England Biolabs, #M0212L) and treatment with Exonuclease-I. cDNA Libraries were prepared in a two-step nested PCR reaction followed by Index PCR using BD Rhapsody Targeted mRNA and AbSeq Amplification Kit (BD Biosciences, #633774) and BD Rhapsody™ Immune Response Panel Hs (BD Biosciences, #633750). We included BD Rhapsody Supplemental Panel (BD Biosciences, #633742) to look at additional genes GATA3, MAF, CCR6, CD40L, TOX, IL6R, IL9R and IL10. After the first PCR, longer PCR products (mRNA, TCR, BCR) were separated from shorter products (AbSeq & Sample Tag) based on double-sided size selection using Agencourt AMPure XP beads (Beckman Coulter, #A63880). The concentration of libraries was estimated using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, #Q32851). The products from second PCR were diluted as per protocol’s recommendations for Index PCR. The quality check and quantification of Index libraries was performed using Agilent 2200 TapeStation with High Sensitivity D5000 ScreenTape (Agilent).

treatment_protocol: Thawed single cell suspensions were stained with fluorescent antibodies to CD45, CD8, CD4, CD3 and CD19 as well as oligonucleotide labelled abseq antibodies (BD) and sample tags (BD).

value: Melanoma

tag: cell type

value: CD45+ Cells


title: 4084_Unstr

description: Taf8 Intact Rep 1


title: VDJ annotations sample tags scRNAseq lymphocytes X215 X226 X368 X330

description: VDJ annotations


title: VDJ annotations X372 X257 X353 X275 X392

description: VDJ annotations


title: C57BL/6 sham-RNAseq-rep3

value: sham


title: C57BL/6 sham-RNAseq-rep2


title: PTD7_RL, replicate #3


title: VDJ annotations sample tags scRNAseq lymphocytes X176 X374 X222 X266

description: VDJ annotations


title: PTD7_RL, replicate #1


title: PTD7_RL, replicate #2


title: sample tags scRNAseq CD45+ cells from X431 X330 X374 X176

description: sample tags


title: C57BL/6 day14-RNAseq-rep3

value: day14 post bleo


title: PTD7, replicate #2

source_name: Pinnal tumor derived cell line #7, subcloned

value: High


title: scRNAseq CD45+ cells from X431 X330 X374 X176


title: VDJ annotations X197

description: VDJ annotations


title: VDJ annotations X198

description: sample tags


title: scRNAseq CD45+ cells from X222 X231 X226 X266


title: MOLM13 Control input

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

data_processing:
cut adapter by trim_galore (0.6.5)
aligment by bowtie2 (2.3.4.2)
remove duplicates by PICARD (2.9.0)
peak calling by MACS2 (2.1.2)
differential open region by diffReps.pl (5.28.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: macs2 called peaks

source_name: Cultured AML Cell Line

growth_protocol: Human AML MOLM13 cells were cultured in 20% FBS containing RPMI-1640 media.

extract_protocol:
Chromatin immunoprecipitation followed by Tn5 mediated tagmentation of de-crosslinked fragments.
Libraries were constructed following standard Illumina protocols for paired end indexing. DNA fragments were PCR amplified for 12 cycles. SPRI beads were used to double-size select fragments in the range of 250 bp.

treatment_protocol: 1 x 10^7 Human AML MOLM13 cells were treated for 16 hours with DMSO or 500 nM of SNDX-50469. Cells were crosslinked with 1% formaldehyde for 10 minutes, then quenched with 2.5 M Glycine for 5 minutes. Cells were washed with 1X PBS, harvested by centrifugation at 2000 rpm for 5 minutes and snap frozen with liquid nitrogen. Ultra-sonication was used to shear the chromatin for chromatin immunoprecipitation analysis.

tag: chip antibody

value: input


title: PTD7, replicate #3


title: scRNAseq Non lymphocyte CD45+ X372 X257 X353 X275 X392 X368 X229


title: MOLM13 SNDX-50469 H3K27Ac

value: H3K27Ac Active Motif (Cat# 39685) RRID:AB_2793305


title: C57BL/6 sham-RNAseq-rep1


title: PTD7, replicate #1


title: VDJ annotations

description: VDJ annotations


title: scRNAseq Non lymphocyte CD45+ X197 X198 X205 X422 X215


title: MOLM13 Control H3K27Ac


title: PTD25_RS, replicate #4

source_name: PTD25 cell line, rescued by transduction with lentiviral vector pLenti6(bla)-mPcdh10short-HA, and enriched for expression of short isoform 1 of Pcdh10 by FACS Pcdh10 expression by FACS


title: MOLM13 SNDX-50469 input


title: VDJ annotations X422

description: VDJ annotations


title: PTD25_RS, replicate #3


title: scRNAseq lymphocytes X231 X229 X431

description: scRNAseq lymphocytes X231 X229 X431


title: scRNAseq lymphocytes X197 X198 X205 X422


title: NAT4

city: Guangzhou

first: Changhao

last: Chen

state: Guangdong

address: 107 Yanjiangxi Road, Yuexiu District, Guangzhou, Guangdong Province, P. R. China

department: Urology

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome (version:hg38) using HISAT2 (version:2.0.4).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: Excel file includes FPKM values for each Sample

source_name: normal adjacent tissue

growth_protocol: The formalin-fixed, paraffin-embedded bladder cancer specimens were collected from patients who underwent surgery at Sun Yat-sen Memorial Hospital of Sun Yat-sen University. All samples were immediately snap-frozen in liquid nitrogen and stored at −80 ˚C until required. All samples were pathologically confirmed by two pathologists with hematoxylin-eosin (H&E) staining. Ethical consent was approved by Committees for Ethical Review of Research involving Human Subjects of Sun Yat-sen University. The written informed consent was obtained from all patients before sample collection.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. Total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA). Then, 3μg of total RNA was treated with DNase I which degraded double-stranded and single-stranded DNA presenting in RNA samples. And the ribosomal RNA was removed using the Ribo-off rRNA Depletion Kit (Vazyme, Inc.). Linear RNA was removed using RNase R (Epicentre, lnc). Purification was performed using Agencourt RNAClean XP magnetic beads. All other steps were performed according to the manufacturer's protocols. The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using BMG (OMEGA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: bladder cancer

value: normal adjacent tissue

tag: gender

value: Female


title: scRNAseq lymphocytes X372 X257 X353 X275 X392


title: scRNAseq lymphocytes X215 X226 X368 X330


title: scRNAseq lymphocytes X176 X374 X222 X266


title: scRNAseq CD4 and CD8 T cells from patient X422


title: PTD25_RS, replicate #2


title: PTD25_RS, replicate #1


title: scRNAseq CD8 and CD4 T cells from patient X199


title: PTD25_RL, replicate #3

source_name: PTD25 cell line, rescued by transduction with recombinant lentivirus pLenti6(bla)-mPcdh10long-HA, and enriched for expression of long isoform 4 of Pcdh10 by FACS


title: scRNAseq CD4 T cells from patient X205

description: scrnaseq CD4 T cells from patient X205


title: ns_BAV8

city: Portland

first: Cheryl

last: Maslen

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Division of Cardiovascular Medicine

institute: Oregon Health & Science University

data_processing:
Data was aligned using ENCODE WGBS standard. Raw sequencing reads were assessed for quality with FastQC v0.11.9, adapter trimmed with TrimGalore v0.6.6, aligned to the hg38 assembly using Bismark v0.23.0 and deduplicated.
Bismark coverage reports were generated using BismarkMethylationExtractor command and processed in R v3.6.2 using MethylKit v1.12.0
CpG data was filtered for 10X coverage for each sample, CpGs with majority coverage within each study group was used for differential methylation analysis
Assembly: hg38

source_name: Whole Blood

extract_protocol:
Qiagen Gentra Puregene Blood Kit
Targeted Bisulfite-seq (Illumina TruSeq-Methyl Capture EPIC)

tag: clinical group

value: NS BAV

tag: disease status

value: non-syndromic (NS)

tag: defect

value: bicuspid aortic valve (BAV)

value: Whole Blood


title: NAT2

treatment_protocol: All samples were pathologically confirmed by two pathologists with hematoxylin-eosin (H&E) staining. Ethical consent was approved by Committees for Ethical Review of Research involving Human Subjects of Sun Yat-sen University.

value: Male

tag: age


title: ns_BAV4


title: BCa3

source_name: bladder cancer tissue

value: bladder cancer tissue


title: PTD25_RL, replicate #2

value: Low


title: ns_BAV6


title: scRNAseq CD8 and CD4 T cells from patient X197

value: Melanoma


title: BCa4


title: NAT1


title: ns_BAV3


title: PTD25, replicate #3

source_name: Pinnal tumor derived cell line #25, subcloned

value: Very high


title: PTD25, replicate #2


title: ts_BAV13

value: TS BAV

value: Turner Syndrome (TS)


title: ts_BAV12


title: ts_BAV10


title: PTD25_RL, replicate #1


title: ts_BAV6


title: ts_BAV4


title: PTD25, replicate #1


title: BCa1


title: NAT3


title: circNCOR1 UM-UC-3 rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome (version:hg38) using HISAT2 (version:2.0.4).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: UM-UC-3 cells

growth_protocol: The human bladder cancer cell lines UM-UC-3 were purchased from American Type Culture Collection and cultured in an incubator with 5% CO2 at 37℃. UM-UC-3 cells were cultured in Dulbecco's modified eagle's medium contained 10% fetal bovine serum.

extract_protocol:
The indicated UM-UC-3 cells were harvested and subjected into extracting the total RNA by TRIZOL (Invitrogen, Carlsbad, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The pcDNA3.1 expression vector with circNCOR1 gene were purchased from Genepharma company (Shanghai, China) and used to overexpress the circNCOR1 gene in UM-UC-3 cells. The transfections were conducted with assistance of lipofectamine 3000 (Invitrogen, Carlsbad, CA, USA) under manufacturer’s protocols.

value: human bladder cancer UM-UC-3 cells

value: transfected with circNCOR1 overexpressing plasmids


title: Ctrl6_RNA

city: Segrate

first: Ettore

last: Mosca

address: Via F.lli Cervi 93

country: Italy

institute: National Research Council - Institute of Biomedical Technologies

description:
CSV_S7
norm_smallRNA_counts.txt

data_processing:
smallRNA reads were checked for quality control using FastQC 0.11.4
smallRNA reads were filtered and trimmed with cutadapt 1.12
smallRNA reads were mapped against Arena-Idb 10/2020 with Bowtie 1.2.3 and RSEM 1.2.15
smallRNA reads were clustered with SEED 02/2018
Normalization size factors were computed with TMM on cluster cardinalities
smallRNA expressions were normalized using normalization size factors
edgeR 3.10 was applied to compute differential expression analyses
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including normalized smallRNA read counts (smallRNA id, normalized expressions)
Supplementary files format and content: tab-delimited text file including edgeR results for comparisons of one patient vs. all the healthy controls (smallRNA id, logFC, FDR, normalized expressions)

source_name: Stool

extract_protocol: RNA, including smallRNA, was extracted from stool samples (about 200mg) using RNeasy Power Microbiome kit (Qiagen) according to manufacturer's istruction. SmallRNA libraries were prepared for sequencing using the TruSeq Small RNA Library Illumina protocol.

tag: sample source

value: stool

value: Neurotypical development

tag: age range


title: circNCOR1 UM-UC-3 rep2


title: Ctrl5_RNA

description:
CSV_S6
norm_smallRNA_counts.txt


title: ts_BAV15


title: circNCOR1 UM-UC-3 rep1


title: ts_TAV19

value: TS TAV

value: tricuspid aortic valve (TAV)


title: female_BM_neutrophil

city: Shanghai

first: Le-Xing

last: Yu

state: Shanghai

address: 225 Changhai Road

institute: Eastern Hepatobiliary Surgery Hospital

data_processing:
Primary data analysis was carried out with the standard Illumina pipeline following the manufacturer's protocol.
Sequencing depth was normalized by using CellRanger (version v3.1.0).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: bone marrow neutrophil

extract_protocol:
All murine tissues in this study were prepared from mice sacrificed by cervical dislocation at the same time. For the isolation of bone marrow cells, leg bones from murine femur were flushed using a 21-gauge needle in RPMI1640 medium containing 1% FBS. single-cell suspension of bone marrow were stained with fluorophore-conjugated antibodies (APC-conjugated-anti-CD45 and FITC-conjugated-anti-Gr1) for 30 min on ice. Fluorescence-activated cell sorting (FACS) was performed on a Moflo-XDP system (Beckman-Coulter).
FACS-sorted viable cells were loaded into a well in a microfluidic chip to generate a cDNA library using a droplet-based sequencing platform (10× Genomics). Libraries were constructed using the Single Cell 3’ Library Kit V2 (10× Genomics).

treatment_protocol: Male mice were peformed orchiectomy to remove the testes or sham-operation under Ketamine/Xylazine anesthesia. 3 weeks later, the bone marrow cells from the operated male mice or an age-matched female mouse were isolated for single-cell RNA transcriptome sequencing.

tag: Sex

value: female

value: bone marrow

value: sham-operation


title: BCa2

value: bladder cancer

tag: tissue


title: ts_TAV18

value: Whole Blood


title: Vector UM-UC-3 rep2

tag: treatment

value: transfected with Vector plasmids


title: Ctrl2_RNA

description:
CSV_S2
norm_smallRNA_counts.txt


title: ts_TAV17


title: ts_TAV9


title: ts_BAV11

value: bicuspid aortic valve (BAV)


title: Vector UM-UC-3 rep1


title: ts_TAV8


title: ASD6_RNA

description:
ASV_S13
norm_smallRNA_counts.txt
edgeR_ASV_S13_vs_Healthy.txt

value: Autism Spectrum Disorders


title: Ctrl1_RNA

description:
CSV_S1
norm_smallRNA_counts.txt


title: ts_BAV3


title: T24 cells, LINC00665 T24 rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome (version:hg38) using HISAT2 (version:2.0.4).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files includes count and FPKM values for each Sample

source_name: T24 cells, LINC00665 T24

growth_protocol: The human bladder cancer cell lines T24 were purchased from American Type Culture Collection and cultured in an incubator with 5% CO2 at 37℃. T24 cells were cultured in RPMI 1640 contained 10% fetal bovine serum.

extract_protocol:
The indicated T24 cells were harvested and subjected into extracting the total RNA by TRIZOL (Invitrogen, Carlsbad, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The pcDNA3.1 expression vector with LINC00665 gene were purchased from Genepharma company (Shanghai, China) and used to overexpress the LINC00665 gene in T24 cells. The transfections were conducted with assistance of lipofectamine 3000 (Invitrogen, Carlsbad, CA, USA) under manufacturer’s protocols.

tag: cell line

value: human bladder cancer cells

value: transfected with LINC00665 overexpressing plasmids

value: LINC00665 overexpression


title: GLU_12

city: Johnson City

first: David

last: Williams

state: TN

address: PO Box 70575

department: Surgery

institute: East Tennessee State University

data_processing:
Basecalls performed using CASAVA
Aligment performed using STAR V2.5
Reads containing adaptor contamination, uncertain nucleotides > 10%, and low quality nucleotides constituting > 50% of total read were removed.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene
Differential expression analysis between two conditions/groups was performed using the DESeq2 R package (2_1.6.3)
KEGG and GO analysis was performed using clusterProfiler
Genome_build: mm10
Supplementary_files_format_and_content: "TrainedvsControl.DEG.all.xls" is differential expression analysis generated using DESeq2
Supplementary_files_format_and_content: "TrainedvsControl.all.KEGGenrich.xls" is KEGG pathway enrichment analysis performed using clusterProfiler
Supplementary_files_format_and_content: "TrainedvsControl.all.GOenrich.xls" is gene ontology analysis performed using clusterProfiler

source_name: Bone marrow-derived macophages

growth_protocol: BMDMs generated by culturing BM cells in in RPMI 1640 with 25mM HEPES (ThermoFisher 22400071), 10% FBS, 1% Gibco antibiotic-antimycotic (ThermoFisher 15240062), and 10 ng/mL M-CSF (R&D systems 416-ML-050) for seven days.

extract_protocol:
RNA was isolated from BMDMs using the RNeasy Mini Kit (Qiagen# 74104) using manufacturer instructions
Library was contructed by Novogene using their standard protocol

treatment_protocol: After BMDMs were generated, BMDMs were treated with 10 μg/mL C. albicans-derived β-glucan or PBS for 24 hours. BMDMs were allowed to rest for 7 days with media being changed every other day.

value: Bone marrow-derived macophages

tag: strain

value: C. albicans-derived B-glucan


title: T24 cells, LINC00665 T24 rep3

tag: genotype


title: GLU_10


title: GLU_9


title: ts_TAV7

value: Turner Syndrome (TS)


title: ASD5_RNA

description:
ASV_S12
norm_smallRNA_counts.txt
edgeR_ASV_S12_vs_Healthy.txt

value: stool


title: T24 cells, LINC00665 T24 rep1


title: ORX_BM_neutrophil

value: male

value: orchiectomy


title: Ctrl4_RNA

description:
CSV_S5
norm_smallRNA_counts.txt

value: Neurotypical development


title: ts_TAV5

value: TS TAV

value: tricuspid aortic valve (TAV)


title: GLU_8


title: ts_TAV4


title: male_BM_neutrophil

value: bone marrow

value: sham-operation


title: T24 cells, Vector T24 rep3

source_name: T24 cells, Vector T24

value: transfected with Vector plasmids

value: control


title: ts_TAV3

value: Whole Blood


title: ASD2_RNA

description:
ASV_S9
norm_smallRNA_counts.txt
edgeR_ASV_S09_vs_Healthy.txt

value: Autism Spectrum Disorders


title: GLU_6


title: ASD3_RNA

description:
ASV_S10
norm_smallRNA_counts.txt
edgeR_ASV_S10_vs_Healthy.txt


title: ns_BAV2

value: NS BAV

value: non-syndromic (NS)

value: bicuspid aortic valve (BAV)


title: T24 cells, Vector T24 rep2

value: human bladder cancer cells


title: ASD1_RNA

description:
ASV_S8
norm_smallRNA_counts.txt
edgeR_ASV_S08_vs_Healthy.txt


title: T24 cells, Vector T24 rep1


title: GLU_5

value: Bone marrow-derived macophages

value: C. albicans-derived B-glucan


title: ns_BAV1


title: ts_BAV14

value: TS BAV

value: Turner Syndrome (TS)


title: CTRL_12

value: Control


title: ts_BAV5


title: ASD4_RNA

description:
ASV_S11
norm_smallRNA_counts.txt
edgeR_ASV_S11_vs_Healthy.txt

value: stool


title: CTRL_10


title: ts_BAV2


title: shVHL61-3 activated Macrophage

city: Taichung

first: Tien

last: Hsu

address: No.91, Hsueh-Shih Road

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: China Medical University

data_processing:
The bases with low quality and sequences from adapters in raw data were removed using program Trimmomatic (version 0.39)
The filtered reads were aligned to the reference genomes using Bowtie2 (version 2.3.4.1)
A user-friendly software RSEM (version 1.2.28) was applied for the quantification of the transcript abundance
Differentially expressed genes (DEGs) were identified by EBSeq (version 1.16.0)
The functional enrichment analysis of Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways among gene clusters was implemented in an R package called clusterProfiler (version 3.6.0)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with normalized count of mapped reads (FPKM) for every gene and every sample

source_name: Macrophage precursor THP-1

extract_protocol:
Using miRNeasy Mini Kit (QIAGEN, #217004)
The purified RNA was used for the preparation of the sequencing library by TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations. Briefly, mRNA was purified from total RNA (1 µg) by oligo(dT)-coupled magnetic beads and fragmented into small pieces under elevated temperature. The first-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of double-strand cDNA and adenylation on 3’ ends of DNA fragments, the adaptors were ligated and purified with AMPure XP system (Beckman Coulter, Beverly, USA). The quality of the libraries was assessed on the Agilent Bioanalyzer 2100 system and a Real-Time PCR system. The qualified libraries were then sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads with 20M clean reads per sample generated by Genomics, BioSci & Tech Co., New Taipei City, Taiwan

treatment_protocol: Macrophage was induced from THP-1 by treatment with 50 ng/ml phorbol 12-myristate-13-acetate (PMA; Sigma Aldrich #P8139) for 24 hrs, and subsequently cultured in RPMI-1640 containing 10% FBS for 24 hrs. The macrophages were seeded in the lower chamber of a Boyden chamber at 80% confluency; then human kidney tubukle cells HK-2 expressing either short-hairpin (sh) RNA specific for Luciferase (as control) or VHL (shVHL61, as VHL knockdown) were seeded in the upper chamber. Macrophages were collected for RNA purification 48 hr later.

value: Peripheral blood

value: 1 year

value: male


title: GLU_7


title: CTRL_9


title: shVHL61-2 activated Macrophage


title: ts_BAV1


title: CTRL_7


title: ts_TAV16

value: TS TAV

value: tricuspid aortic valve (TAV)


title: CTRL_5


title: shLuc-3 activated Macrophage


title: CTRL_13


title: ts_TAV14

value: Whole Blood


title: SVI-030-18

city: Fitzroy

first: Balasubramanian

last: Krishnamurthy

state: VIC

address: 41 Victoria Parade

department: Department of Endocrinology and Diabetes

institute: St. Vincent’s Hospital Melbourne

data_processing:
The raw sequencing files (.BCL) were first converted into fastq files using “cellranger mkfastq” (v3.02)
The fastq files were then processed using “cellranger count” (3.0.2) pipeline to align sequencing reads in fastq files reference genome GRCh38 and generates the raw gene count matrices for single cells in each sample
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene UMI counts for every gene and every cell for patient sample
Supplementary_files_format_and_content: Matrix table with raw gene UMI counts for every gene and every cell for control sample

source_name: single-cell RNA-seq of islets

extract_protocol:
Pancreas following partial pancreatectomy was obtained, with informed consent following research approval from the Human Research Ethics Committee at St. Vincent’s Hospital Melbourne. Human islets were isolated by intraductal perfusion and digestion of the pancreas with collagenase followed by purification using ficoll density gradients. Islets were dispersed with accutase then rested in Connaught Medical Research Laboratories (CMRL) 1066 medium (Invitrogen) supplemented with 4% human serum albumin, 100 U/ml penicillin, 100 mg/ml streptomycin and 2 mM L-glutamine (complete CMRL), in a 37°C, 5% CO2 humidified incubator for 2 hours.
Cells were then processed for single cell RNAseq using the Chromium 10x genomics platform and sequenced using the Illumina NextSeq platform at the Australian Genome Research Facility (Melbourne, Australia)

tag: disease

value: Islets from healthy control


title: CTRL_3

tag: cell type


title: shLuc-2 activated Macrophage


title: SVI-029-18

value: Islets from patient with hypoglycemia


title: ts_TAV2


title: CTRL_2


title: shLuc-1 activated Macrophage


title: SAMPLE 9_AC16-R3-D14

city: Yerevan

first: Arsen

last: Arakelyan

state: Yerevan

address: 7 Hasratyan St.

country: Armenia

institute: Institute of Molecular Biology NAS RA

description: Gene expression data from  AC16 cells treated with exosomes isolated from blood of astronaut D14 3 days after return.

hyb_protocol: Human Clariom S chips were hybridized with 2.5 µg of fragmented biotin-labeled cDNA in 100 µl hybridization cocktail.

scan_protocol: Chips were scanned on an Affymetrix GeneChip Scanner 3000 using Command Console Software (Thermo Fisher Scientific, Waltham, MA).

data_processing: Arrays were processed and RMA normalized using oligo, pd.clariom.s.human, annotate and clariomsmousetranscriptcluster.db BioConductor packages. Probe IDs were converted to ENSEMBL gene IDs.

source_name: AC16 cell line treated with exosomes of D14 austronaut at R+3

label_protocol: 100 ng of RNA was used from each sample to prepare fragmented biotin-labeled cDNA by GeneChip WT PLUS reagent kit

growth_protocol: Exosomes were isolated from blood plasma samples of 3 astronauts (D12, D13, and D14) at L-10 and R+3 using the ExoQuick Plasma prep and exosome precipitation kit (Cat # EXOQ5TM, System Biosciences, CA, USA).

extract_protocol: Total RNA was extracted from AC16 cells treated with astronaut-derived exosomes (ExoL-10 and ExoR+3) for 24 hrs using the RNeasy Mini Kit (Qiagen), according to the manufacturer's protocol. High-quality RNA was isolated using RNeasy Mini spin columns and eluted using molecular-grade water (RNAse/DNAse free).

treatment_protocol: AC16 cells, were cultured in DMEM/F12 containing 2 mM L‐Glutamine, 10% exosomes-free FBS, and 1% Penicillin/Streptomycin Solution.

value: treated

tag: time point


title: SAMPLE 6_AC16-L10-D14

description: Gene expression data from  AC16 cells treated with exosomes isolated from blood of astronaut D14 10 days before flight.

source_name: AC16 cell line treated with exosomes of D14 austronaut at L-10


title: SAMPLE 5_AC16-L10-D13

description: Gene expression data from  AC16 cells treated with exosomes isolated from blood of astronaut D13 10 days before flight.

source_name: AC16 cell line treated with exosomes of D13 austronaut at L-10


title: SAMPLE 7_AC16-R3-D12

description: Gene expression data from  AC16 cells treated with exosomes isolated from blood of astronaut D12 3 days after return.

source_name: AC16 cell line treated with exosomes of D12 austronaut at R+3


title: ts_TAV1


title: SAMPLE 3_AC16-NT

description: Gene expression data from untreated AC16 cells.

source_name: AC16 cell line untreated

value: untreated