title: Serum-D

type: RNA

city: Guiyang City

first: Youfu

last: He

state: Guizhou Province

address: No.83 Zhongshan East Road, Nanming District, Guiyang City, Guizhou Province, China

institute: Guizhou Provincial People's Hospital

description: Serum exosomes in patients with acute myocardial infarction

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) was used in Hybridization protocol.  Procedure:  1. Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing.  2. Equilibrate water bath to 60°C.  3. For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube:  4. Mix well but gently on a vortex mixer.  5. Incubate at 60°C for exactly 30 minutes to fragment RNA.   6. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction.  7. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles.  8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction.  9. Place sample on ice and load onto the array as soon as possible.   10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar.  11. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner.  12. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.   13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.  14. Hand-tighten the clamp onto the chamber.  15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles.  16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm.  17. Hybridize at 65°C for 17 hours.   Microarray Wash:  1. Prewarm enough volume of Gene Expression Wash Buffer 2 to 37°C.  2. Add the slide rack and stir bar to the staining dish.  3. Transfer the staining dish with the slide rack and stir bar to a magnetic stir plate.  4. Fill the staining dish with 100% acetonitrile.  5. Turn on the magnetic stir plate and adjust the speed to a setting of 4 (medium speed).  6. Wash for 5 minutes.  7. Discard the acetonitrile as is appropriate for your site.  8. Repeat step 2 to step 7.  9. Air dry the staining dish in the vented fume hood.  10. Wash all dishes, racks, and stir bars with Milli-Q water.   11. Completely fill slide-staining dish #1 with Gene Expression Wash Buffer 1 at room temperature.  12. Place a slide rack into slide-staining dish #2. Add a magnetic stir bar. Fill slide-staining dish #2 with enough Gene Expression Wash Buffer 1 at room temperature to cover the slide rack. Place this dish on a magnetic stir plate.  13. Place the empty dish #3 on the stir plate and add a magnetic stir bar. Do not add the prewarmed (37°C) Gene Expression Wash Buffer 2 until the first wash step has begun.  14. Remove one hybridization chamber from incubator and record time. Record whether bubbles formed during hybridization and if all bubbles are rotating freely.   15. Prepare the hybridization chamber disassembly.  a) Place the hybridization chamber assembly on a flat surface and loosen the thumbscrew, turning counterclockwise.  b) Slide off the clamp assembly and remove the chamber cover.  c) With gloved fingers, remove the array-gasket sandwich from the chamber base by grabbing the slides from their ends. Keep the microarray slide numeric barcode facing up as you quickly transfer the sandwich to slide-staining dish #1.  d) Without letting go of the slides, submerge the array-gasket sandwich into slide-staining dish #1 containing Gene Expression Wash Buffer 1.  16. With the sandwich completely submerged in Gene Expression Wash Buffer 1, pry the sandwich open from the barcode end only:  a) Slip one of the blunt ends of the forceps between the slides.  b) Gently turn the forceps upwards or downwards to separate the slides.  c) Let the gasket slide drop to the bottom of the staining dish.  d) Remove the microarray slide and place into slide rack in the slide-staining dish #2 containing Gene Expression Wash Buffer 1 at room temperature.   17. When all slides in the group are placed into the slide rack in slide-staining dish #2, stir using setting 4 for 1 minute.  18. During this wash step, remove Gene Expression Wash Buffer 2 from the 37°C water bath and pour into the slide-staining dish #3.  19. Transfer slide rack to slide-staining dish #3 containing Gene Expression Wash Buffer 2 at elevated temperature. Stir using setting 4 for 1 minute.   20. Slowly remove the slide rack minimizing droplets on the slides. It should take 5 to 10 seconds to remove the slide rack.  21. Scan slides immediately to minimize the impact of environmental oxidants on signal intensities.

scan_protocol: Instrument:  Agilent Microarray Scanner (Agilent p/n G2565BA)    Procedure:  1. Assemble the slides into an slide holder.   2. Place assembled slide holders into scanner carousel.  3. Verify scan settings for one-color scans.   Parameters  Scan region Scan Area (61 x 21.6 mm)  Scan resolution (μm) 5  5μm scanning mode Single Pass  eXtended Dynamic range (selected)  Dye channel Green  Green PMT   XDR Hi 100%   XDR Lo 10%  4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Software:  Agilent Feature Extraction    Procedure:  1. Open the Agilent Feature Extraction (FE) software.  2. Add the images (.tif) to be extracted to the FE Project.  3. Set FE Project Properties.  4. Check the Extraction Set Configuration.  5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location.  6. Select Project > Start Extracting and export data to txt.

label_protocol: Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) was used to labeling reaction. 1. Add 1ug of total RNA to a 1.5-mL microcentrifuge tube.   2. Add 1.2 μL of T7 Promoter Primer.   3. Use nuclease-free water to bring the total reaction volume to 11.5 μL.  4. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes.  5. Place the reactions on ice and incubate for 5 minutes.  6. Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice.  7. Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice.  8. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down.  9. Incubate samples at 40°C in a circulating water bath for 2 hours.  10. Move samples to a 65°C circulating water bath and incubate for 15 minutes.  11. Move samples to ice. Incubate for 5 minutes.  12. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid.  13. Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature.  14. Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting.  15. Incubate samples in a circulating water bath at 40°C for 2 hours.

growth_protocol: none.

extract_protocol: Coronary thrombus is an intracoronary thrombus in patients with T1MI diagnosed by coronary angiography in our hospital's Department of Cardiovascular Medicine (Guizhou Provincial People's Hospital). The thrombi were removed by catheter aspiration and then placed in centrifuge tubes containing 5 ml of PBS and stored at 4°C for no more than 3 days.Type II collagenase (50 U/mL) and trypsin (20 μg/mL) were added to the coronary thrombus described above. According to the instructions for type II collagenase, 5 mM calcium chloride was also added as an activator of the enzyme. The mixture was then placed on a constant temperature shaker at 37°C for 1 hour. At this time complete dissolution of the thrombus is seen. The mixture obtained above was centrifuged in a high-speed centrifuge at 4°C and 300g for 5 minutes to remove incompletely dissolved thrombus and adherent endothelial tissue. Dead cells and cell debris were then removed by centrifugation at 4°C and 2,000g for 10 minutes. After centrifugation at 4°C and 100,000g for 70 minutes, the precipitate is the exosome. Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization.Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C. Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C.At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C.

treatment_protocol: none.

tag: gender

value: male

tag: sample type

value: thrombus


title: Thrombus-C

status: Public on Feb 14 2025

country: China

description: Thrombus-derived exosomes in patients with acute myocardial infarction

molecule: total RNA

organism: Homo sapiens


title: B non-inoculated replicate 3

type: SRA

city: Valencia

first: Javier

last: Forment

address: Ingeniero Fausto Elio, s/n

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (Universitat Politècnica de València-CSIC)

description:
B.h.prior.3
Bergera koenigii

library_source: transcriptomic

data_processing:
Adapter removal and quality trimming of raw reads was done with cutadapt.
Clean reads were analysed using FastQC.
Clean read pairs longer than 20 nt were mapped to the reference genomes (for Citrus and Bergera) or de novo transcriptome (for Bergera) using STAR.
Differential expression analysis was performed with DESeq2.
Assembly: Citrus sinensis SWO.v3.0 genome + Liberibacter_asiaticus NZ_CP019958 genome, Murraya paniculata genome + Liberibacter_asiaticus NZ_CP019958 genome (Murraya_paniculata_final.chr.fasta), and Bergera transcriptome + Liberibacter_asiaticus NZ_CP019958 genome (Bergera_ST_Streptophyta.fasta) combined genomes.
Supplementary files format and content: Tab-delimited text files including count of reads for each gene in each sample.

organism: Murraya koenigii

source_name: young flush

growth_protocol: C. × sinensis ‘Valencia’ plants, and M. paniculata and B. koenigii seedlings were pruned at 15-25 cm to promote new flushes. A V2 flush was selected, and the remaining ones were eliminated.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).
Two µg of total RNA per sample were used for library generation using the TruSeq stranded total RNA Library Kit plus Ribo-Zero and NEBNext kits for ribosomal RNA depletion.
The Illumina NovaSeq6000 was used on a paired-end sequencing of 150pb. All procedures were performed according to Illumina’s protocols.

treatment_protocol: Five 15-20 days-old CLas-positive or negative adult psyllids were confined to a single flush per plant for 48 h.

tag: tissue

value: young flush

tag: treatment

value: no treatment

tag: time point

value: before exposure


title: Serum-C

source_name: Serum exosomes in patients with acute myocardial infarction

value: blood serum


title: Thrombus-D

source_name: Thrombus-derived exosomes in patients with acute myocardial infarction


title: Thrombus-A


title: Thrombus-B


title: Serum-B


title: M non-inoculated replicate 3

organism: Murraya paniculata


title: ATAC-B_rep3

city: ChangChun

first: Mingming

last: Liang

address: xi an Road 5333

institute: Jilin university

library_source: genomic

data_processing:
The paired-end raw reads were trimed for adaptor seqence and low-quality seqences (-q 30) using Trim Galore 0.4.1. The filtered ChIP-seq reads were aligned to the hg19 genome using bowtie2 (Version 2.4.1) with   default parameters. PCR duplicates in bam files were moved by using Picard tool.
MACS2 (Version 2.2.7.1 43) was used to call narrow peaks for H3K4me3 and H3K27ac with the parameters (-q 0.001) or broad peaks for H3K27me3 with the parameters (-q 0.1 --broad). The input sequencing data was set as a control.
The ChIP signal was normalized by using bamCoverage function in deeptools 3.5.0 with the parameters ( --normalizeUsing CPM,  --ignoreDuplicates,  --minMappingQuality 30,  --minFragmentLength 50)
Assembly: GRCm38（mm10）
Supplementary files format and content: bigWig files of the ChIP signal for each sample
Supplementary files format and content: Peak bed files of each sample include the significant enriched regions of the detected hitone modifications

molecule: genomic DNA

organism: Mus musculus

source_name: Tail

growth_protocol: mouse primary MEF cells were cultured in  high-glucose DMEM (Invitrogen) supplemented with 10% FBS (Invitrogen) and 1% penicillin-streptomycin (Invitrogen) at 37 °C, 5% CO2.

extract_protocol:
106 cells were crosslinked in 1% formaldehyde for 10 minutes and quenched using 125mM of Glycine for 5 minutes. The chromosome was fragmented to the fragment range of 200-400 bp in the Bioruptor® Pico via sonicating 5 cycles. The fragmented histone-DNA complexes were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose.
The VAHTS Universal DNA Library Prep Kit for Illumina V3 (ND607)  was used with 5 ng of ChIP DNA of each sample for the construction of sequencing libraries.

value: Tail

tag: cell line

value: primary MEF cell line


title: B non-inoculated replicate 2

description:
B.h.prior.2
Bergera koenigii


title: M non-inoculated replicate 2


title: Serum-A


title: B non-inoculated replicate 1

description:
B.h.prior.1
Bergera koenigii


title: ATAC-B_rep1


title: M non-inoculated replicate 1


title: LNCaP cells, siAR, H3K27ac, ChIP

status: Public on Feb 13 2025

city: Bethesda

first: David

last: Takeda

state: MD

address: 37 Convent Drive

department: National Cancer Institute

country: USA

institute: National Institutes of Health

description: Library name: ChIPseq_sample75

data_processing:
Reads were aligned to hg19 after filtering for ENCODE blacklist regions using bwa (0.7.17) and converted to BAM format using Samtools (1.17).
Duplicate reads removed using Picard (2.27.3) and peaks identified with MACS2 (2.2.7.1) with q value cutoff of 0.01.
Input subtracted bigWig files were generated using Deeptools (3.5.1).
Assembly: hg19
Supplementary files format and content: input normalized bigWig (except for input samples)

source_name: LNCaP

growth_protocol: LNCaP: RPMI with 10% fetal bovine serum in humidified atmosphere with 5% CO2 at 37C, PDX: Propagated in NOD scid gamma (NSG) mice.

extract_protocol:
Cells or tissues were fixed with 2 mM DSG for 10 min and 1% paraformaldehyde for 10 min followed by quenching with glycine. Chromatin was isolated and sonicated using Diagenode Pico sonicator.
ChIP-seq libraries were prepared using NEB Next Ultra II DNA Library Prep Kit for Illumina and amplified libraries purified using NEB purification beads. Libraries were validated using Agilent Tapestation.

treatment_protocol: For siRNA experiments, cells were transfected with siRNA 24 hours after plating and harvested 48 hours post transfection

value: LNCaP

tag: chip antibody


title: LNCaP cells, siNT, FOXA1, rep2, H3K27ac, rep4, input

description: Library name: ChIPseq_sample76


title: LNCaP cells, siAR, FOXA1, H3K27ac, input

description: Library name: ChIPseq_sample78


title: LNCaP cells, siAR, FOXA1, ChIP

description: Library name: ChIPseq_sample74

value: FOXA1 (Abcam, #ab23738)


title: LNCaP cells, siHOXB13, FOXA1, rep2, H3K27ac, rep3, input

description: Library name: ChIPseq_sample77


title: LNCaP cells, siHOXB13, FOXA1, ChIP, rep2

description: Library name: ChIPseq_sample72


title: LNCaP cells, siNT, H3K27ac, ChIP, rep4

description: Library name: ChIPseq_sample71


title: LNCaP cells, siHOXB13, H3K27ac, ChIP, rep3

description: Library name: ChIPseq_sample73


title: ATAC-B_rep2


title: LNCaP cells, siNT, FOXA1, ChIP, rep2

description: Library name: ChIPseq_sample70


title: VCaP16 cells, siHOXB13, input

description: Library name: ChIPseq_sample68


title: VCaP16 cells, siTFAP2C, input

description: Library name: ChIPseq_sample69


title: VCaP16 cells, siGATA2, input

description: Library name: ChIPseq_sample67


title: Normal-3

description: Healthy human serum exosomes

source_name: Healthy human serum exosomes


title: VCaP16 cells, siTFAP2C, H3K27ac, ChIP

description: Library name: ChIPseq_sample65


title: VCaP16 cells, siGATA2, H3K27ac, ChIP

description: Library name: ChIPseq_sample63


title: VCaP16 cells, siNT, H3K27ac, ChIP

description: Library name: ChIPseq_sample62


title: VCaP16 cells, siNT, input

description: Library name: ChIPseq_sample66


title: Normal-1

description: Healthy human serum exosomes


title: VCaP16 cells, TFAP2C, ChIP

description: Library name: ChIPseq_sample60

value: TFAP2C (Proteintech, #14572-1-AP)


title: VCaP16 cells, GATA2, ChIP

description: Library name: ChIPseq_sample58

value: GATA2 (Abcam, #ab109241)


title: VCaP16 cells, input

description: Library name: ChIPseq_sample61


title: LNCaP cells, siNT, FOXA1, input

value: siNT


title: VCaP16 cells, HOXB13, ChIP

description: Library name: ChIPseq_sample59


title: Normal-2

description: Healthy human serum exosomes


title: LNCaP cells siHOXB13, FOXA1, ChIP


title: LNCaP cells, siGATA2 siHOXB13 siTFAP2C, H3K27ac, input, rep2

value: siGATA2 siHOXB13 siTFAP2C


title: LNCaP cells, siNT, H3K27ac, input, rep3


title: LNCaP cells, siGATA2 siHOXb13, H3K27ac, input, rep2

value: siGATA2 siHOXB13


title: OVshHLpolIIIP-1

city: Chongqing

first: Qinlv

last: Wei

state: Chongqing

address: Chongqing

institute: Children’s Hospital of Chongqing Medical University

description:
Library name: IP1 of shhnRNPL cell
The raw data are being open accessed in SRA with accession number PRJNA1071467

data_processing:
Raw reads were trimmed using cutadapt version 1.18. Clean reads were aligned to the UCSC hg38 genome using Bowtie version 2.4.5. only uniquely mapping reads were used.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Ovarian cancer

growth_protocol: OVCAR3 cells were cultured in RPMI1640 medium (GIBCO) containing 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
ChIP experiments were performed using the Magna ChIP A/G Chromatin Immunoprecipitation kit, following the manufacturer’s protocol. Briefly, we performed protein-DNA cross-linking by incubating 106 cells in 1% formaldehyde for 10 min at 37°C. Micrococcal nuclease was used to digest the isolated nuclei, which was then sonicated to generate DNA/protein fragments of 150-900 bases (sample was vortex mixed every 3 min) and sonication was performed to nuclear lysate. For immunoprecipitation, 2 μg of antibody (hnRNPL antibody (Abcam, ab6106), RNA Pol II antibody (ab238146, Abcam) or mouse IgG antibody (12-371, Millipore)) was added to each sample, followed by incubation for 4 h at 4°C.
After immunoprecipitation, chromatin-protein complexes were eluted from protein G magnetic beads and reverse cross-linked. DNA was purified for PCR or sequencing.

value: Ovarian cancer

tag: cell type

value: Human Ovarian fibroblasts

tag: genotype

value: shhnRNPL

value: ab238146, Abcam


title: LNCaP cells, siNT, FOXA1, ChIP


title: OVshHLinput2

description:
Library name: Input2 of shhnRNPL cell
The raw data are being open accessed in SRA with accession number PRJNA1071467


title: OVshHLinput1

description:
Library name: Input1 of shhnRNPL cell
The raw data are being open accessed in SRA with accession number PRJNA1071467


title: OVshHLpolIIIP-2

description:
Library name: IP2 of shhnRNPL cell
The raw data are being open accessed in SRA with accession number PRJNA1071467


title: OVNCpolIIIP-2

description:
Library name: IP2 of shNC cell
The raw data are being open accessed in SRA with accession number PRJNA1071467

value: shNC


title: VCaP16 cells, siHOXB13, H3K27ac, ChIP

description: Library name: ChIPseq_sample64


title: LNCaP cells, siTFAP2C, H3K27ac, input, rep2


title: LNCaP cells, siNT, H3K27ac, ChIP, rep3


title: OVNCinput2

description:
Library name: Input2 of shNC cell
The raw data are being open accessed in SRA with accession number PRJNA1071467


title: OVNCpolIIIP-1

description:
Library name: IP1 of shNC cell
The raw data are being open accessed in SRA with accession number PRJNA1071467


title: OVNCinput1

description:
Library name: Input1 of shNC cell
The raw data are being open accessed in SRA with accession number PRJNA1071467


title: LNCaP cells, siHOXB13, H3K27ac, input, rep2


title: LNCaP cells siHOXB13, FOXA1, input


title: LNCaP cells, siNT, H3K27ac, input, rep2


title: OVCAR3, hnRNPL IP_2

description:
Library name: IP_rep2
The raw data are being open accessed in SRA with accession number PRJNA988255

extract_protocol:
Briefly, OVCAR3 cells were dissociated with 0.25% trypsin for 3 min at 37°C and washed twice with 0.1% BSA DEPC-PBS, then fixed in 4% paraformaldehyde on ice for 5 min, followed by quenching with Tris-HCl. Fixed cells were washed by cold PBS three times and the liquid was removed after centrifugation at 600 g for 5 min at 4°C. Cell pellets were added 1 mL 30% methanol and could be stored at 80°C. Frozen pellets were resuspended by 0.1% BSA DEPC-PBS and washed twice with Wash Buffer (20 mM HEPES, 150 mM NaCl, 0.5 mM Spermidine, 1× protease inhibitor cocktail (Beyotime, P1006), 1 mM PMSF and 10 mM sodium butyrate). Then, the Con-A beads were washed with 1 mL Binding Buffer (1 M HEPES, 1 M KCl, 1 M CaCl2, 1 M MnCl2) and were then resuspended with adequate Binding Buffer and applied to the cell mixture. The cell-bead mixture was incubated for 10 min and collected by the magnet stand. Next, cells were resuspended with adequate antibody buffer (0.5 M EDTA, 0.01% Digitonin-Wash Buffer) supplemented with 1× protease inhibitor cocktail, PMSF, 10 mM sodium butyrate and 0.1% Triton X-100 containing hnRNPL antibody (1:50, Abcam, ab6106) by gently flicking. The cell-antibody mixture was incubated at 4°C for 2 h. Cells were washed twice with Dig-Wash Buffer (with 0.1% Triton X-100) and finally suspended with Dig-Wash Buffer (with 0.1% Triton X-100, 1× protease inhibitor cocktail, PMSF and 10 mM sodium butyrate) containing individual combinatorial barcoded 3 μg/mL PAT-T5 and 3 μg/mL PAT-T7 (PAT-MEAB, from Aibin He lab, Peking University). The cells were incubated at 4°C for 1 h and washed with Dig-Wash Buffer with 0.1% Triton X-100 three times to get rid of free PAT-MEA/B. The reaction next was activated by suspending the cells with Reaction Buffer (10 mM TAPS-NaOH, 5 mM MgCl2, 10% DMF supplemented with 1× protease inhibitor cocktail, PMSF 10 mM sodium butyrate), followed by gently flicking and incubated at 25°C for 1 h. The reaction was terminated with 40 mM EDTA, further incubated at RT for 15 min, and added cold Sort Buffer (PBS/2% BSA/2 mM EDTA) to each well. Cells were passed through a 30 mm cell strainer to remove cell clumps, and were incubated at 55°C for 3 h for reverse crosslinking and incubated at 85°C for 15 min to deactivate proteinase K with 1.8% Triton X-100.
PCR amplification was performed by addition of 25 mM i5 index primer, 25 mM i7 index primer (He Lab, Peking University), 2× KAPA master mix and ddH2O to the adequate CoBATCH cell lysis, and the reaction was set up by incubation at 98°C for 2 min, 10-15 cycles of amplification (98°C for 20 s, 65°C for 30 s, 72°C for 1 min), and final 72°C extension for 5 min. After PCR amplification, the library was purified with XP beads once.

value: WT


title: LNCaP cells, siGATA2, H3K27ac, input, rep2


title: OVCAR3, IgG

description:
Library name: IgG Input
The raw data are being open accessed in SRA with accession number PRJNA988255

value: 12-371, Millipore


title: OVCAR3, hnRNPL IP_1

description:
Library name: IP_rep1
The raw data are being open accessed in SRA with accession number PRJNA988255


title: LNCaP cells, siHOXB13, H3K27ac, ChIP, rep2


title: LNCaP cells, siTFAP2C, H3K27ac, ChIP, rep2


title: W303 strains, grr1-deficient, Tunicamycin 0 h, replicate 2

city: Tokyo

first: Nichika

last: Sato

address: 4-6-1, Shirokanedai, Minato-ku

department: The Institute of Medical Science

country: Japan

institute: The University of Tokyo

description:
Data was used for the following comparision(s) in RNAseq.2_FC_grr1_0_RNAvs_grr1_4_RNA.csv: grr1-1-4 vs grr1-1-0, grr1-2-4 vs grr1-2-0
RNAseq.2_FC_grr1_0_RNAvs_grr1_4_RNA.csv

data_processing:
Linker sequences were trimmed with Cutadapt v2.6.
The filtered reads longer than 20 nt were mapped against rRNA and noncoding RNA genes using Bowtie2 (Langmead and Salzberg, 2012) v2.3.5 with ‘–very-sensitive’.
The unmapped reads were then mapped to the R64 reference genome using STAR (Dobin et al., 2013) v2.7.3a with parameters ‘–outFilterMultimapNmax 1 –outFilterIntronMotifs RemoveNoncanonicalUnannotated –outSAMtype BAM Unsorted –quantMode TranscriptomeSAM GeneCounts’. Alignments to transcriptome were used for subsequent analysis.
The read counts per gene outputs were proceeded to differentially expression analysis with the R package DEseq2 (Love et al., 2014).
Assembly: R64
Supplementary files format and content: Tab-delimited text file including raw counts for each nucleotide across all transcripts within each sample

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Yeast cells were cultured with synthetic complete (SC) medium with 2 % glucose at 30 ºC.

extract_protocol:
After 4 hr of tunicamycin treatment, yeast cells were harvested by filtration and frozen by liquid nitrogen. They were lysed by lysis buffer for Ribo-seq (20 mM Tris-HCl [pH 7.5], 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 0.1 mg/mL cycloheximide, 25 U/mL Turbo DNase (Invitrogen, AM2238)). Clear lysates were obtained by centrifugation at 20,000 xg for 10 min at 4 °C.
Total RNA was extracted from clear lysate using Direct-zol RNA Microprep w/ Zymo-Spin IC Columns (#R2062, funakoshi). The libraries were sequenced on a DNBSEQ-G400RS High-throughput Sequencing Kit (MGI Tech Co., Ltd.) at Bioengineering Lab, Japan.

treatment_protocol: Yeast cells were grown at 30 ºC  until OD600 = 0.2, then treated with 1 µg/ml of tunicamycin (Tm, #208-08243, Wako) for 4 hr.

value: Saccharomyces cerevisiae

tag: strain

value: Tunicamycin

tag: time

value: 0 hr


title: W303 strains, grr1-deficient, Tunicamycin 4 h, replicate 2

value: 4 hr


title: Mut1_cl2_patient_wk2

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Basecalls were generated using CASAVA v1.8
Data quality was assessed using FastQC v0.11.8
Sequenced reads were aligned to the mm10 genome assembly using STAR v2.5.3a
Reads were annotated to genes using Homer v4.10
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes the raw counts for each sample.

source_name: Neurons derived from induced pluripotent cells

growth_protocol: IPSC colonies were plated onto Matrigel-coated plates (BD Biosciences) and maintained in mTeSR1 media (Stem Cell Technologies). Early neurons were treated with TrypLE express and plated at desired concentrations in neuron maturation medium with added ROCK inhibitor (10 μM) onto plates coated with poly-ornithine (100 μg ml–1, Sigma Aldrich) and laminin (100 μg ml–1, Invitrogen). On day 7, medium was changed to neuron maturation medium without ROCK inhibitor. Following day 7, iNs underwent half medium changes with neuronal maturation medium for 3 weeks to obtain mature neurons.

extract_protocol:
RNA was isolated according to the manufacturer’s instructions and subsequently digested with TURBO DNase to remove trace quantities of DNA (ambion, Life Technologies). Before RNA-seq library preparation, assessment of RNA integrity numbers was performed using Agilent TapeStation.
Libraries were pooled and sequenced using an Illumina HiSeq 2500 with 75-bp paired-read chemistry

treatment_protocol: no treatment

tag: week

value: patient

tag: clone


title: LNCaP cells, siGATA2, H3K27ac, ChIP, rep2

value: LNCaP


title: LNCaP cells, siGATA2 siHOXb13, H3K27ac, ChIP, rep2


title: LNCaP cells, siGATA2 siHOXB13 siTFAP2C, H3K27ac, ChIP, rep2


title: W303 strains, grr1-deficient, Tunicamycin 4 h, replicate 1


title: Mut2_cl1_patient_wk2


title: W303 strains, grr1-deficient, Tunicamycin 0 h, replicate 1


title: LNCaP cells, siNT, H3K27ac, ChIP, rep2


title: Mut3_cl1_patient_wk2


title: W303 strains, wild-type, Tunicamycin 0 h, replicate 2

description:
Data was used for the following comparision(s) in RNAseq.2_FC_WT_0_RNAvs_WT_4_RNA.csv: WT-1-4 vs WT-1-0, WT-2-4 vs WT-2-0
RNAseq.2_FC_WT_0_RNAvs_WT_4_RNA.csv

value: wild-tipe


title: W303 strains, wild-type, Tunicamycin 4 h, replicate 2


title: LNCaP cells, siGATA2 siHOXB13 siTFAP2C, H3K27ac, input, rep1


title: W303 strains, wild-type, Tunicamycin 4 h, replicate 1


title: WT2_cl1_control_wk2

value: control


title: WT3_cl1_control_wk2


title: LNCaP cells, siGATA2 siHOXb13, H3K27ac, input, rep1


title: W303 strains, wild-type, Tunicamycin 0 h, replicate 1


title: LNCaP cells, siTFAP2C, H3K27ac, input, rep1


title: ApcMin 7d after 2 Gy IR biol rep 1, scRNAseq

city: Helsinki

first: Pauliina

last: Kallio

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
Library name: Sample 14
10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell ranger (version 6.1.2, 7.0.0, or 7.0.1) was used to align the reads, quantify gene expression, generate custom references, and call the cells.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Tumor tissue isolated from small intestinal tumors of ApcMin mice

extract_protocol:
Macroscopic ApcMin/+ adenomas from all different anatomical regions of the small intestine were dissected and stored in high-glucose DMEM (Gibco, #11960-044) medium on ice. After isolation of all adenomas, the medium was replaced with a cell dissociation buffer containing 4 mg/ml dispase II (Sigma, #04942078001), 1 mg/ml collagenase I (Worthington, #LS004196), 1 mg/ml collagenase H (Roche, #11074032001), and 1000 U/ml benzonase (ChemCruz, #sc-202391) in HBSS (Gibco, #14175-053). After 30 min of incubation at 37°C, trypsin-EDTA (Thermo Fisher Scientific, #25200056) was added, and incubation was continued for 10 min at 37°C. The samples were vortexed regularly during incubation. Trypsin was inactivated in high-glucose DMEM. Samples were filtered through a 40 mm filter, followed by centrifugation for 10 min at 150 RCF. 10 000 cells in 0.04% BSA in HBSS with good viability (> 70%) per sample were targeted for analysis with Chromium X. Small intestines from wild type (WT) mice were incubated in 10 mM EDTA pH 8.0 for 10 min on ice. Cells were detached by scraping with a coverslip. After washing with PBS and centrifugation for 5 min at 150 RCF, cells were incubated in 4 mg/ml dispase II (Sigma, #04942078001), 1 mg/ml collagenase I (Worthington, #LS004196), 1 mg/ml collagenase H (Roche, #11074032001), and 1000 U/ml benzonase (ChemCruz, #sc-202391) in HBSS (Gibco, #14175-053) for 30 min at 32°C. This was followed by washing with cold DMEM, filtering once with a 100 nm filter and twice with a 40 nm filter, and centrifugation for 10 min at 150 RCF. 10 000 cells in 0.04% BSA in HBSS, with good viability per sample, were targeted for 10X chromium. The ScRNA-seq experiment was repeated 3 times, and the data were pooled from four mice.
Library was performed according to the manufacturer`s instructions (single cell 3' protocol, 10x Genomics)

value: Tumor cells

value: ApcMin/+

value: 2 Gy IR

tag: age

value: 16-20 weeks old


title: ApcMin 7d after 2 Gy IR biol rep 2, scRNAseq

description:
Library name: Sample 15
10x Genomics

value: Tumor tissue isolated from small intestinal tumors of ApcMin mice


title: ApcMin 2d after 2 Gy IR biol rep 2, scRNAseq

description:
Library name: Sample 13
10x Genomics


title: WT1_cl1_control_wk2


title: LNCaP cells, siHOXB13, H3K27ac, input, rep1


title: Mut2_cl2_patient_wk2


title: ApcMin 2d after 2 Gy IR biol rep 1, scRNAseq

description:
Library name: Sample 12
10x Genomics


title: ApcMin 1d after 2 Gy IR biol rep 3, scRNAseq

description:
Library name: Sample 11
10x Genomics


title: LNCaP cells, siGATA2, H3K27ac, input, rep1


title: ApcMin 1d after 2 Gy IR biol rep 2, scRNAseq

description:
Library name: Sample 10
10x Genomics


title: Mut1_cl1_patient_wk2


title: WT3_cl1_control_wk4


title: ApcMin 1d after 2 Gy IR biol rep 1, scRNAseq

description:
Library name: Sample 9
10x Genomics


title: ApcMin ctrl biol rep 3, scRNAseq

description:
Library name: Sample 3
10x Genomics

value: Ctrl


title: ApcMin ctrl biol rep 5, scRNAseq

description:
Library name: Sample 5
10x Genomics


title: LNCaP cells, siNT, H3K27ac, input, rep1

value: siNT


title: ApcMin ctrl biol rep 2, scRNAseq

description: 10x Genomics

extract_protocol:
Macroscopic ApcMin/+ adenomas from all different anatomical regions of the small intestine were dissected and stored in high-glucose DMEM (Gibco, #11960-044) medium on ice. After isolation of all adenomas, the medium was replaced with a cell dissociation buffer containing 4 mg/ml dispase II (Sigma, #04942078001), 1 mg/ml collagenase I (Worthington, #LS004196), 1 mg/ml collagenase H (Roche, #11074032001), and 1000 U/ml benzonase (ChemCruz, #sc-202391) in HBSS (Gibco, #14175-053). After 30 min of incubation at 37°C, trypsin-EDTA (Thermo Fisher Scientific, #25200056) was added, and incubation was continued for 10 min at 37°C. The samples were vortexed regularly during incubation. Trypsin was inactivated in high-glucose DMEM. Samples were filtered through a 40 mm filter, followed by centrifugation for 10 min at 150 RCF. 10 000 cells in 0.04% BSA in HBSS with good viability (> 70%) per sample were targeted for analysis with Chromium X.
Library was performed according to the manufacturer`s instructions (single cell 3' protocol, 10x Genomics)


title: WT2_cl1_control_wk4


title: WT1_cl1_control_wk4


title: control, scRNA-seq

city: Salt Lake City

first: Monica

middle: L.

last: Vetter

state: UT

department: Neurobiology & Anatomy

institute: University of Utah

description:
10X Genomics
Pou4f2_integration_metadata.txt

data_processing:
Fastq files were aligned to the mouse transcriptome index for mm10 and GFP using cellranger-7.0.1 with expected cells set to 5000. The filtered matrix output from cellranger was imported to Seurat v4.3.0.1 and further filtered for cells with less than 4% mitochondrial transcripts, more than 1,200 genes, and fewer than 25,000 transcripts. The control and Pou4f2OE (OE- overexpression) datasets were merged, and SCTransform v0.3.5 pipeline run with all default settings. Clusters were annotated with known markers for retinal cells and combined as appropriate based on those markers. Cluster markers and differentially expressed genes between the experimental conditions were defined using the FindAllMarkers and FindMarkers functions respectively, using default settings. Integration with developmental data was achieved using Clark et al. Specifically, the developmental dataset was subset for only those cells used for pseudotime analysis, as defined in the cell metadata, and merged with the Pou4f2 single cell dataset. These were combined with the Seurat v5.1.0 IntegrateLayers function using CCA integration.
Assembly: mm10
Supplementary files format and content: CellRanger filtered matrix
Supplementary files format and content: barcodes, cluster assignments and umap position for all cells represented in the study

source_name: retina

extract_protocol:
Ten days later, retinas were collected for dissociation. Electroporated retinas were dissociated using papain as described before in Justin Brodie-Kommit et al. (2021). Briefly, papain solution (100 µL papain – 10mg/ml – containing 110 µL of L-cysteine 50mM, 110 µL of 10mM EDTA, 10 µL of 60mM 2-Mercaptoethanol) was pre-incubated at 37oC for 30 minutes before the dissociation. After that, two retinas were added to the papain solution and incubated for 10 minutes at 37oC. 50 µL of DNAse (1mg/ml) was added after 5 minutes of dissociation. To block the reaction, 2.5ml of neurobasal supplemented with 10% FBS and 500 µL of ovomucoid (10mg/ml) were added. Tubes were spun down for 5min, 300RCF at 4oC and resuspended on 500 µL of neurobasal+10% FBS. Single, viable, GFP+ cells were isolated by cell sorting with BD FACSAria 4 laser instrument using 70µm nozzle size and collected into 20 µL DMEM + 5% FBS. Multiple retinas were combined as necessary to obtain 30k GFP+ cells.
Library generation and sequencing were performed by the Huntsman Cancer Institute High-Throughput Genomics and Bioinformatics Analysis Shared Resource. Sorted cells were prepared with the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. The library was chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq 150x150 bp XP workflow (20043131). Following transfer of the flow cell to an Illumina NovaSeq 6000 instrument, a 150 x 150 cycle paired end sequence run was performed using a NovaSeq 6000 S4 reagent Kit v1.5 (20028312). Sequencing was performed to a depth of at least 200M paired reads/sample.

treatment_protocol: P0 mice were anesthetized by hypothermia and the plasmid solution was injected into the subretinal space with a Hamilton syringe with 33G blunt end needle (0.5 µL of a 5.0 µg/µL solution containing 0.1% Fast Green Dye (cat# 14335, Cayman Chemical)). Five 99V pulses were applied for 50 ms with 950 ms intervals using a forceps-type electrode (Nepagene, CUY650P7) with Neurgel (Spes Medica).

value: retina

value: GFP


title: ApcMin ctrl biol rep 1, scRNAseq

description: 10x Genomics


title: Wild type biol rep 1, scRNAseq

description:
Library name: Sample 26
10x Genomics

source_name: Mucosa of the small intestine of wild type C57 mouse

value: Mucosa

value: Wild type

value: No treatment

value: 17 weeks old


title: Pou4f2 OE, scRNA-seq

value: Pou4f2 + GFP


title: LNCaP cells, siTFAP2C, H3K27ac, ChIP, rep1

value: LNCaP


title: Cells isolated from the dorsal skin at 6-day post depilation

city: Parkville

first: Yunshun

last: Chen

state: VIC

address: 1G Royal Parade

department: ACRF Cancer Biology and Stem Cells

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: 10x Genomics

data_processing:
Libraries were sequenced on a NovaSeq 6000 PE150 lane sequencing
Read alignment and count summarization were performed using cellranger v6.1.2 using the Illumina BCL files as input.
Assembly: mm10
Supplementary files format and content: The barcode.tsv files contain the 10X barcodes used to identify cells.
Supplementary files format and content: The features.tsv files contain the corresponding Ensembl IDs and gene symbols as tab-delimited text.
Supplementary files format and content: The matrix.mtx files contain genewise read counts for all cells in the space-efficient matrix market format.

source_name: Dorsal skin

growth_protocol: Adult males (p55-57) of FVB background were used for all scRNA-seq experiments

extract_protocol:
After indicated timepoints, dorsal skins were harvested and digested by enzyme to obtain single cell suspensions. Skin from each of the two mice per timepoint were processed independently, then mixed at equal cell numbers before subjected to scRNA-seq.
sgRNA libraries were prepared using the 10X genomice Chromium Single Cell 3’ kit

treatment_protocol: The dorsal skin of two mice per timepoint were shaved and waxed to induce hair regeneration

value: Dorsal skin

value: wildtype

tag: Sex

value: male

value: FVB


title: Mut3_cl1_patient_wk4

value: patient


title: Cells isolated from the dorsal skin at 4-day post depilation

description: 10x Genomics


title: LNCaP cells, siHOXB13, H3K27ac, ChIP, rep1


title: Mut1_cl2_patient_wk4


title: LNCaP cells, siGATA2, H3K27ac, ChIP, rep1


title: Cells isolated from the dorsal skin at 16-hour post depilation

description: 10x Genomics


title: LNCaP cells, siNT, H3K27ac, ChIP, rep1


title: Cells isolated from the dorsal skin at 2-day post depilation

description: 10x Genomics


title: Cells isolated from the dorsal skin at 4-hour post depilation

description: 10x Genomics


title: Cells isolated from the dorsal skin at 0-hour

description: 10x Genomics


title: LNCaP cells, siGATA2 siHOXB13 siTFAP2C, H3K27ac, ChIP, rep1

value: siGATA2 siHOXB13 siTFAP2C


title: ApcMin ctrl biol rep 4, scRNAseq

description:
Library name: Sample 4
10x Genomics

value: Tumor tissue isolated from small intestinal tumors of ApcMin mice

value: Tumor cells

value: ApcMin/+

value: 16-20 weeks old


title: Day48_3

city: La Jolla

first: Michael

last: Croft

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the mouse GRCm38 reference using STAR v2.6.1
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using FeatureCount v1.6.5 (“union” option) and features with 0 counts across all samples were removed
Assembly: GRCm38
Supplementary files format and content: count matrix with rows as genes and columns as samples

source_name: Tissue-resident memory T cells

extract_protocol:
Quiagen miRNeasy micro kit
Illumina Nextera XT DNA Library Prep Kit

value: Tissue-resident memory T cells

tag: cd69 status

tag: disease state

value: naive


title: LuCaP 189_4, input

source_name: LuCaP 189_4

value: LuCaP 189_4


title: LNCaP cells, siGATA2 siHOXB13, H3K27ac, ChIP, rep1

value: siGATA2 siHOXB13


title: Day48_4


title: Day48_1


title: Mut2_cl2_patient_wk4


title: LuCaP 189_4, TFAP2C, ChIP

value: TFAP2C (Proteintech, #14572-1-AP)


title: Day48_2


title: Yeast W303 REP4

city: Saarbrüecken

first: Julia

last: Schulze-Hentrich

address: Campus A2.4

department: Genetics/Epigenetics

country: Germany

institute: Saarland University

description: Library name: Yeast W303 6988

data_processing:
Raw sequencing data were processed with the nf-core/rnaseq pipeline v3.12.0 using STAR-Salmon
Assembly: S288C yeast genome assembly and gene annotations based on Ensembl v109
Supplementary files format and content: CSV file with raw read counts per Ensembl gene ID

growth_protocol: Yeast strains (BY4741, W303-1A, D273-10B, RM11-1A, CEN.PK2-1c) were pre-cultured overnight (3 mL in 13 mL tubes) in synthetic complete glucose to stationary. Main cultures were innoculated at OD = 0.1 in synthetic complete glucose media and cultured at 30*C to early exponential growth phase (OD = 0.8 - 1.1). Culture volume was 50 mL in a 250-300 mL Erlenmeyerflask and flasks were shaken at 220 rpm. A volume corresponding to 20 OD was harvested, washed with MQ water, and flash frozen in liquid nitrogen.

extract_protocol:
RNA was isolated from cell pellets using Direct-zol™ RNA Miniprep kit (Zymo research #R2051) according to manufacturer instructions. In brief, cells were lysed using Trizol® and DNA was digested using provided DNAse I. After three washing steps, the RNA was eluted. RNA concentration was measured with a NanoDrop™ (ThermoFisher) and stored at -80 °C or used immediately for library preparation.
Sequencing libraries were created using the Smart-seq2 protocol (Picelli et al. 2014). In brief, 100 ng of RNA were used for reverse transcription and subsequent preamplification PCR. PCR product was purified using Ampure XP beads at 1:0.8 ratio. Concentration of purified cDNA was measured using Qubit (Thermofisher), and quality was checked using Qsep Bio-Fragment Analyzer (NIPPON Genetics).  4 ng of cDNA was tagmented using Tn5 (Nextera) barcoded and PCR amplified. PCR product was purified with Ampure XP beads at a ratio of 1:0,9. Library concentration was measured using Qubit and quality was checked using Qsep Bio-Fragment Analyzer. Libraries were sequenced on an Illumina Nextseq 500 at 75bp single-end reads.

treatment_protocol: No treatment.


title: Day48_9

value: HDM


title: LuCaP 189_4, HOXB13, ChIP


title: Day48_7


title: Yeast W303 REP3

description: Library name: Yeast W303 6987


title: LuCaP 189_4, GATA2, ChIP

value: GATA2 (Abcam, #ab109241)


title: Mut2_cl1_patient_wk4


title: Day48_10


title: Day48_5


title: Yeast W303 REP2

description: Library name: Yeast W303 6670


title: Day48_8


title: Yeast W303 REP1

description: Library name: Yeast W303 6669


title: Day48_6


title: Day47_3


title: LuCaP 170_2, input

source_name: LuCaP 170_2

value: LuCaP 170_2


title: Day47_1


title: Day47_4


title: Yeast RM11 REP4

description: Library name: Yeast RM11 7452

value: MATa leu2Delta0 ura3Delta0 HO::kanMX


title: LuCaP 170_2, TFAP2C, ChIP


title: Day47_9


title: Yeast RM11 REP3

description: Library name: Yeast RM11 7451


title: Mut1_cl1_patient_wk4


title: LuCaP 170_2, HOXB13, ChIP


title: Day47_2


title: Day47_7


title: Yeast RM11 REP2

description: Library name: Yeast RM11 6666


title: LuCaP 170_2, GATA2, ChIP


title: Yeast RM11 REP1

description: Library name: Yeast RM11 6665


title: Day47_5


title: Day47_8


title: LuCaP 170_2, H3K27ac, ChIP


title: Day47_10


title: Day47_6


title: Yeast D273 REP4

description: Library name: Yeast D273 6950

value: MATAlpha mal


title: LuCaP 77, input

source_name: LuCaP 77

value: LuCaP 77


title: Day45_3_GuSe06


title: LuCaP 189_4, H3K27ac, ChIP


title: Yeast D273 REP3

description: Library name: Yeast D273 6949


title: Day45_4_GuSe06


title: Day45_2_GuSe06


title: Day45_9_GuSe06


title: Day45_7_GuSe06


title: LuCaP 77, HOXB13, ChIP


title: LuCaP 77, GATA2, ChIP


title: LuCaP 77, TFAP2C, ChIP


title: Day45_5_GuSe06


title: Yeast D273 REP1

description: Library name: Yeast D273 6673


title: Day45_10_GuSe06


title: Yeast CENPK REP4

description: Library name: Yeast CENPK 7453

value: MATa his3Delta1 leu2-3_112 ura3-52 trp1-289 MAL2-8c SUC2


title: Day45_8_GuSe06


title: LuCaP 77, H3K27ac, ChIP


title: Day45_6_GuSe06


title: Yeast D273 REP2

description: Library name: Yeast D273 6948


title: LNCaP cells, TFAP2C, input

value: LNCaP


title: Day45_3_GuSe05


title: Yeast CENPK REP3

description: Library name: Yeast CENPK 6945


title: Yeast CENPK REP2

description: Library name: Yeast CENPK 6986


title: Day45_1_GuSe05


title: Day45_1_GuSe06


title: Yeast CENPK REP1

description: Library name: Yeast CENPK 6667


title: Day45_9_GuSe05


title: Day45_4_GuSe05


title: Day45_7_GuSe05


title: LNCaP cells, H3K27ac, HOXB13, input


title: Yeast BY4741 REP4

description: Library name: Yeast BY4741 6672

value: MATa his3Delta1 leu2Delta0 met15Delta0 ura3Delta0


title: LNCaP cells, TFAP2C, ChIP


title: Day45_5_GuSe05


title: Day45_10_GuSe05


title: Day45_8_GuSe05


title: LNCaP cells, HOXB13, ChIP


title: Day45_6_GuSe05


title: Yeast BY4741 REP2

description: Library name: Yeast BY4741 6943


title: LNCaP cells, H3K27ac, ChIP


title: Yeast BY4741 REP1

description: Library name: Yeast BY4741 6942


title: Day24_2


title: Day24_4


title: Day24_1


title: Day45_2_GuSe05


title: X8_129X1+Mtb

city: New York

first: Ziwei

last: Yang

state: NY

address: 413 East 69th Street

institute: Weill Cornell Medical College

description: Library name: X8

data_processing:
The samples were sequenced using Illumina HiSeq4000 sequencer with single 50 bps reads.
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the mm9 mouse reference genome by TopHat2 (Version2.0.11).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Assembly: mm9
Supplementary files format and content: txt files with FPKM values of each sample

source_name: Bone marrow

growth_protocol: To prepare BMDMs, mouse femurs were flushed with DMEM and the cell-containing supernatant was collected after allowing debris to settle at 1 g. The cells were centrifuged at 193 g for 8 min at room temperature (hereafter, all centrifugations were performed at room temperature unless otherwise speci- fied), and the pellet was resuspended and cultured in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 10 mM Hepes, pH 7.5, 1 mM sodium pyruvate, and 20% LCM at 37°C in a 5% CO2 incubator for 6–7 d. On the day of harvest, adherent cells were washed once with ice-cold PBS and incubated in cold PBS + 1 mM EDTA at 4°C for 10 min. Cells were dislodged by gentle pipetting, collected by centrifugation as above, resuspended in cold PBS, washed again the same way, and then cultured in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 10 mM Hepes, pH 7.5, 1 mM sodium pyruvate, and 10% LCM.

extract_protocol:
RNA was extracted using Qiagen RNA-easy kit columns. After passing quality control check, at least 3 μg RNA was submitted for library contruction.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA Library Preparation protocol.

treatment_protocol: BMDMs were infected with Mtb at an MOI of 10 for 4 h. 4 h after the addition of Mtb, macrophage monolayers were washed twice with PBS prewarmed to 37°C, and then fresh medium was replaced. Another 24 h later, cells were washed once with PBS and harvested in Trizol for RNA extraction.

value: Bone marrow

value: BMDM

value: primary macrophages

value: Mtb infection for 24 h.


title: LNCaP cells, siHOXB13, rep2

data_processing:
Reads were aligned to hg19 after filtering for ENCODE blacklist regions using bwa (0.7.17) and converted to BAM format using Samtools (1.17).
Duplicate reads removed using Picard (2.27.3) and peaks identified with MACS2 (2.2.7.1) with q value cutoff of 0.01.
bigWig files were generated using Deeptools (3.5.1).
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: RPMI with 10% fetal bovine serum in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Nuclei were isolated from 50,000 cells by incubating with digitonin followed by tagmentation at 37 C for 30 minutes.
ATAC-seq libraries were prepared using Diagenode ATAC-seq kit. Libraries were validated using Agilent Tapestation.

treatment_protocol: Cells were transfected with siRNA 24 hours after plating and harvested 48 hours post transfection


title: X7_129X1

description: Library name: X7

value: mock treatment


title: Day24_10

value: Tissue-resident memory T cells


title: LNCaP cells, siTFAP2C, rep2


title: X4_129X1+Mtb

description: Library name: X4


title: Day24_7


title: LNCaP cells, siGATA2, rep2


title: Day24_6


title: Yeast BY4741 REP3

description: Library name: Yeast BY4741 6671


title: X3_129X1

description: Library name: X3


title: LNCaP cells, siNT, rep2

value: siNT


title: Day23_1

value: naive


title: Day23_3


title: LNCaP cells, GATA2, input


title: Day23_4


title: Day24_3


title: LNCaP cells, siTFAP2C, rep1


title: LNCaP cells, GATA2, ChIP


title: Day23_2


title: Day24_9

value: HDM


title: X1_129X1

description: Library name: X1


title: S8_129S2+Mtb

description: Library name: S8


title: Day24_5


title: Day23_7


title: Day24_8


title: Day23_5


title: LNCaP cells, siGATA2, rep1


title: LNCaP cells, siHOXB13, rep1


title: Day23_10


title: S7_129S2

description: Library name: S7


title: Day23_8


title: LNCaP cells, siNT, rep1


title: S4_129S2+Mtb

description: Library name: S4


title: Day23_6


title: Day22_3


title: LNCaP cells, Promoter VP, siTFAP2C, rep2

data_processing:
Reads were aligned to h19 and processed using pipe4C pipeline workflow (Krijger PHL, Geeven G, Bianchi V, Hilvering CRE, de Laat W. Methods. 2019 Jul 26. pii: S1046-2023(18)30474-2. doi: 10.1016/j.ymeth.2019.07.014. https://doi.org/10.1016/j.ymeth.2019.07.014)
Bigwig files were generated using average mapped reads with running window of 21 fragment ends.
Assembly: hg19
Supplementary files format and content: normalized bigWig
Library strategy: 4C-seq

extract_protocol:
Cells were crosslinked with 10% paraformaldehyde for 10 min and quenched with glycine. Chromatin was serially digested and ligated with DpnII followed by NlaIII.
Libraries were produced using a two-step PCR stragegy. The first PCR is an inverse PCR using enhancer viewpoint specific primers. The second PCR incorporates the indexed Illumina sequencing adaptors. Library quality was assessed by Agilent TapeStation.


title: Day22_1


title: S3_129S2

description: Library name: S3


title: S2_129S2+Mtb

description: Library name: S2


title: Day22_4


title: LNCaP cells, Promoter VP, siGATA2, rep2


title: S1_129S2

description: Library name: S1


title: X2_129X1+Mtb

description: Library name: X2


title: LNCaP cells, Promoter VP, siNT, rep2


title: LNCaP cells, Enhancer VP, siTFAP2C, rep2


title: B8_B6+Mtb

description: Library name: B8


title: B7_B6

description: Library name: B7


title: LNCaP cells, Enhancer VP, siHOXB13, rep2


title: Day22_9


title: B4_B6+Mtb

description: Library name: B4


title: Day22_2


title: Day22_7


title: LNCaP cells, Enhancer VP, siGATA2, rep2


title: Day22_5


title: H69+GNF5-3

city: Durham

first: Ann Marie

last: Pendergast

state: North Carolina

address: 308 Research Dr

department: Pharmacology and Cancer Biology

institute: Duke University

description: Library name: Counts_FeatureCounts_Output (3G.txt)

data_processing:
Using 50-bp single-end reads generated by the Duke University Genome Sequencing facility. RNA-seq data were processed using the TrimGalore toolkit and reads that were 20nt or longer after trimming were used for further analysis
Assembly: Reads were mapped to the GRCh37 version of the human genome and transcriptome using the STAR RNA-seq alignment tool. Reads were used for subsequent analysis if they mapped to a single genomic location, and gene counts were compiled using the HTSeq tool. Only genes that had at least 10 reads in any given library were used in subsequent analysis. Normalization and differential expression were carried out using the DESeq2 Bioconductor package in the R statistical programming environment.
Supplementary files format and content: tab-delimited text file including raw counts for each sample

growth_protocol: H69 were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNA easy mini kit (Qiagen).1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NovaSeq 6000 libraries Prep Kit following manufacturer's protocols.

treatment_protocol: ABL kinase inhibitor GNF5 was used in H69 cells (20 mM for 48h). Control was treated with DMSO.

value: small cell lung cancer

value: WT

value: GNF5 (20 uM)

value: 48 hours


title: Day22_10


title: Day23_9


title: Day22_8


title: LNCaP cells, Enhancer VP, siNT, rep2


title: LNCaP cells, Promoter VP, siTFAP2C, rep1


title: LNCaP cells, Promoter VP, siHOXB13, rep2


title: B3_B6

description: Library name: B3


title: B1_B6

description: Library name: B1


title: H69+GNF5-1

description: Library name: Counts_FeatureCounts_Output (1G.txt)


title: LNCaP cells, Promoter VP, siHOXB13, rep1


title: Day22_6


title: Day21_3


title: H69 control-2

description: Library name: Counts_FeatureCounts_Output (2C.txt)

value: DMSO


title: Day21_1


title: H69 control-1

description: Library name: Counts_FeatureCounts_Output (1C.txt)


title: LNCaP cells, Promoter VP, siNT, rep1


title: C7_Ifnar1-/-+IFNg priming

description: Library name: C7

value: 10 ng/ml IFNg priming overnight.


title: Day21_4


title: LNCaP cells, Enhancer VP, siTFAP2C, rep1

value: LNCaP


title: C6_Ifnar1-/-+Mtb

description: Library name: C6


title: C5_Ifnar1-/-

description: Library name: C5


title: Myoblast CM3 Treated WGBS (replicate 2)

city: Ipswich

first: Sriharsa

last: Pradhan

state: MA

address: 240 County Road

institute: New England Biolabs

description: Library name: Myoblast(CM3)WGBS_R2

data_processing:
Adaptor and low-quality sequences were trimmed from paired-end sequencing reads using Trim Galore v 0.5.0
Trimmed read pairs were mapped to the reference genome (human: hg19) using Bwa-meth. PCR duplicates and mitochondrial reads were removed using samblaster and samtools.
The UCSC liftOver tool was employed to convert coordinates from HG38 to HG19. Subsequently, the two replicates for each myoblast culture (CM1, CM3, and CM6 for EM-seq and CM3 for WGBS) were pooled and strands were merged to obtain overall coverage and percent methylation values for each of the four samples using custom scripts in R. All CpGs with coverage in at least one of the four methylation profiles were retained.
Assembly: hg19
Supplementary files format and content: AggregateMyoblastMethylomes.txt (overall coverage and percent methylation values)

source_name: skeletal muscle

growth_protocol: DNA was purified from non-transformed myoblast cultures derived from quadriceps biopsies of control individuals {Tsumagari, 2013 #2549}, namely, Myoblast CM1 (42-year-old female), Myoblast CM3 (46-year-old male), and Myoblast CM6 (45-year-old male). Each batch of myoblasts was checked for >90% purity by immunostaining because fibroblast-like contaminating cells can easily outgrow myoblasts and give misleading methylome results {Chandra, 2015 #3328}

extract_protocol:
WGBS was performed on Myoblast CM3 using standard protocols {Chen, 2016 #4481}. Additionally, methylation profiling of CM3, CM1, and CM6 was conducted using enzymatic methyl-seq (EM-seq) {Vaisvila, 2021 #4473}. This process involved enzymatic oxidation of 5mC and 5hmC (by TET2), providing protection from further deamination by APOBEC3A while unmethylated cytosine are deaminated to uracil. Briefly, 0.2 µg of DNA was used to prepare EM-seq libraries in duplicate. The libraries were then cleaned using NEBNext® sample selection beads, pooled, and diluted to 1.5 nM for sequencing on a NovaSeq (Illumina)
Six EM-seq libraries are made for three myoblast strains i.e., CM1, CM3 and CM6, two replicates each. Similarly, myoblast stain CM3 were used to make two libraries.
EM-seq, WGBS

value: skeletal muscle

value: myoblast cells

value: Myoblast CM3 Treated


title: LNCaP cells, Enhancer VP, siHOXB13, rep1


title: B2_B6+Mtb

description: Library name: B2

value: Bone marrow

value: BMDM

value: primary macrophages


title: C4_WT+IFNg priming+Mtb

description: Library name: C4

value: 10 ng/ml IFNg priming overnight. Then infected with Mtb for 24 h


title: Day21_2

value: Tissue-resident memory T cells


title: Myoblast CM3 Treated WGBS (replicate 1)

description: Library name: Myoblast(CM3)WGBS_R1


title: LNCaP cells, Enhancer VP, siGATA2, rep1


title: C3_WT+IFNg priming

description: Library name: C3


title: Day21_9


title: LNCaP cells, Enhancer VP, siNT, rep1

value: siNT


title: Day21_7

value: HDM


title: Myoblast CM6 Treated (replicate 1)

description: Library name: Myoblast(CM6)_R1

data_processing:
Adaptor and low-quality sequences were trimmed from paired-end sequencing reads using Trim Galore v 0.5.0
Trimmed read pairs were mapped to the reference genome (human: hg19) using Bwa-meth. PCR duplicates and mitochondrial reads were removed using samblaster and samtools.
The UCSC liftOver tool was employed to convert coordinates from HG38 to HG19. Subsequently, the two replicates for each myoblast culture (CM1, CM3, and CM6 for EM-seq and CM3 for WGBS) were pooled and strands were merged to obtain overall coverage and percent methylation values for each of the four samples using custom scripts in R. All CpGs with coverage in at least one of the four methylation profiles were retained.
Assembly: hg19
Supplementary files format and content: AggregateMyoblastMethylomes.txt (overall coverage and percent methylation values)
Library strategy: EM-Seq

value: Myoblast CM6 Treated


title: C8_Ifnar1-/-+IFNg priming+Mtb

description: Library name: C8


title: H69 control-3

description: Library name: Counts_FeatureCounts_Output (3C.txt)

value: small cell lung cancer

value: WT


title: Myoblast CM6 Treated (replicate 2)

description: Library name: Myoblast(CM6)_R2


title: H69+GNF5-2

description: Library name: Counts_FeatureCounts_Output (2G.txt)

value: GNF5 (20 uM)

value: 48 hours


title: LNCaP cells, siTFAP2C, rep4

data_processing:
Data was analyzed using the VIPER RNAseq pipeline
Reads are aligned using STAR and Cufflinks used to generate normalized read counts
Assembly: hg19
Supplementary files format and content: csv file includes FPKM values for each sample

molecule: polyA RNA

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen)
RNA libraries were prepared by Novogene for Illumina sequencing

value: TFAP2C knockdown


title: C2_WT+Mtb

description: Library name: C2

value: Mtb infection for 24 h.


title: Day21_5


title: Myoblast CM3 Treated (replicate 2)

description: Library name: Myoblast(CM3)_R2

value: skeletal muscle


title: C1_WT

description: Library name: C1

value: mock treatment


title: LNCaP cells, Promoter VP, siGATA2, rep1

value: LNCaP


title: Day21_10


title: Myoblast CM3 Treated (replicate 1)

description: Library name: Myoblast(CM3)_R1

value: myoblast cells

value: Myoblast CM3 Treated


title: LNCaP cells, siHOXB13, rep4

value: HOXB13 knockdown


title: A8_Ifnar1-/-+IFNg priming+Mtb

description: Library name: A8

value: Bone marrow

value: BMDM

value: primary macrophages

value: 10 ng/ml IFNg priming overnight. Then infected with Mtb for 24 h


title: Day21_8

value: Tissue-resident memory T cells

value: HDM


title: LNCaP cells, siGATA2, rep4

value: GATA2 knockdown


title: Myoblast CM1 Treated (replicate 2)

description: Library name: Myoblast(CM1)_R2

value: Myoblast CM1 Treated


title: A7_Ifnar1-/-+IFNg priming

description: Library name: A7

value: 10 ng/ml IFNg priming overnight.


title: Day21_6


title: A6_Ifnar1-/-+Mtb

description: Library name: A6


title: GuSe03_Mo__CITE

description:
Hashtag/barcode expression matrix
Hashtag/barcode expression matrix for each cell. Each hashtag/barcode corresponds to one sample.

data_processing:
Data processing was done using Cell Ranger software v5.0.0.
The demultiplexing was performed using mkfastq
Alignment with reference mm10 and gene counting were done using Multi program
R package Seurat(v4.1.1) was used for downstream clustering and UMAP analysis
Seurat's function HTOdemux was used for hashtag demultiplexing and singlet assignment
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol: Chromium Next GEM Single Cell 5' v2 (Dual Index)

value: lung


title: LNCaP cells, siTFAP2C, rep3

value: TFAP2C knockdown


title: AT2 cells, 6 hours, 8 ug/cm2 Diesel exhaust PM, replicate 4

city: Southampton

first: James

middle: G. H.

last: Parkin

address: Level F, University Hospital Southampton

country: United Kingdom

institute: University of Southampton

description:
Library name: Diesel_4
Column name in NormalisedCounts_cpm.csv: Diesel_4

data_processing:
Kallisto v0.46.1
Reads were pseudoaligned using Kallisto running in paired-end mode.
Raw counts were read into and processed in R using the tximport package
Assembly: hg38
Supplementary files format and content: csv file containing counts per million (cpm) values for all samples

source_name: ATII (ER:KRASV12)

extract_protocol:
Following PM exposure, cells were washed with 1 ml sterile phosphate-buffered saline (PBS) and lysed with 300 µl RNA lysis buffer (Monarch® Total RNA Miniprep Kit, New England BioLabs, Massachusetts, USA) for 10 min to completely lyse cells. Lysates were stored at − 80 °C until further use.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification

value: ATII (ER:KRASV12)

value: Alveolar type-II epithelial cell

value: 8 ug/cm2 Diesel exhaust PM

value: 6 hour


title: A5_Ifnar1-/-

description: Library name: A5

value: mock treatment


title: Myoblast CM1 Treated (replicate 1)

description: Library name: Myoblast(CM1)_R1

value: skeletal muscle

value: myoblast cells


title: LNCaP cells, siHOXB13, rep3

source_name: LNCaP

value: LNCaP

value: HOXB13 knockdown


title: Bone marrow, Health-3

city: chongqing

first: Debao

last: Li

address: No. 13, Tianchi Avenue, Mudong Town, Banan District, Chongqing

institute: Chongqing International Institute for Immunology

description: Library name: Sample 9

data_processing:
Quality control evaluation of the original FASTQ documents using FastQC and MultiQC software.
Trim reads using TrimGalore software to remove sequencing adapters and low-quality bases.
Use hisat2 software to perform sequence alignment, and the download link of the reference sequence file is https://cloud.biohpc.swmed.edu/index.php/s/grcm38_tran/download.
Use featuresCounts software to quantify the number of reads mapped to each transcript or gene to obtain an expression matrix.
Convert the raw count matrix to the TPM matrix.
Assembly: GRCm38
Supplementary files format and content: csv files include count and TPM values for each Sample

growth_protocol: Sequencing was divided into three groups: bone marrow transplant group, novel transplant group with CDSCs involvement, and healthy mice of the same week age. Among them, the new transplant group of mice with bone marrow transplantation and CDSCs was first subjected to a lethal dose of whole-body irradiation at an irradiation dose of 9.5 Gy

extract_protocol:
Samples were ground under liquid nitrogen in a mortar and pestle, and the resulting powder dissolved in TRIzol™ Reagent (Invitrogen, Carlsbad, CA, USA), then extracted total RNA.
0.1-1 μg of total RNA per sample was prepared for library preparation. The ABclonal Poly(A)mRNA Capture Module and ABclonal Fast RNA-seq Lib Prep Kit V2 were used for mRNA isolation and library construction following the manufacturers’ protocols.

treatment_protocol: On the second day after irradiation, 500,000 BM and dissociated CDSCs were reinfused through the subframe vein, respectively. Two weeks after transplantation, all cells from the bone marrow of the three groups of mice were obtained separately for RNA-Seq.

value: Bone marrow

value: Bone marrow fresh primary cells

tag: group

value: Healthy


title: AT2 cells, 6 hours, 8 ug/cm2 Diesel exhaust PM, replicate 3

description:
Library name: Diesel_3
Column name in NormalisedCounts_cpm.csv: Diesel_3


title: A3_WT+IFNg priming

description: Library name: A3

value: BMDM

value: primary macrophages

value: WT


title: LNCaP cells, siNT, rep4

value: Control knockdown


title: A4_WT+IFNg priming+Mtb

description: Library name: A4

value: 10 ng/ml IFNg priming overnight. Then infected with Mtb for 24 h


title: LNCaP cells, siGATA2, rep3

value: GATA2 knockdown


title: Bone marrow, Health-2

description: Library name: Sample 8


title: AT2 cells, 6 hours, 8 ug/cm2 Diesel exhaust PM, replicate 2

description:
Library name: Diesel_2
Column name in NormalisedCounts_cpm.csv: Diesel_2

value: ATII (ER:KRASV12)

value: Alveolar type-II epithelial cell


title: AT2 cells, 6 hours, 8 ug/cm2 Diesel exhaust PM, replicate 1

description:
Library name: Diesel_1
Column name in NormalisedCounts_cpm.csv: Diesel_1

value: 8 ug/cm2 Diesel exhaust PM

value: 6 hour


title: GuSe03_Mo__Gex

description:
Gene expression matrix
Gen expression matrix for each cell

value: lung


title: LNCaP cells, siNT, rep3


title: A2_WT+Mtb

description: Library name: A2

value: Mtb infection for 24 h.


title: Bone marrow, Health-1

description: Library name: Sample 7


title: LNCaP cells, siTFAP2C, rep2

value: LNCaP

value: TFAP2C knockdown


title: AT2 cells, 6 hours, 8 ug/cm2 Ceramic brake-wear PM, replicate 4

description:
Library name: Ceramic_4
Column name in NormalisedCounts_cpm.csv: Ceramic_4

value: 8 ug/cm2 Ceramic brake-wear PM


title: A1_WT

description: Library name: A1

value: Bone marrow

value: mock treatment


title: Bone marrow, CDSCs-3

description: Library name: Sample 6

value: Bone marrow fresh primary cells

value: CDSCs


title: LNCaP cells, siHOXB13, rep2

value: HOXB13 knockdown


title: AT2 cells, 6 hours, 8 ug/cm2 Ceramic brake-wear PM, replicate 3

description:
Library name: Ceramic_3
Column name in NormalisedCounts_cpm.csv: Ceramic_3


title: cachectic_Male_20

first: Ezequiel

middle: Carlos

last: Dantas

state: Y

address: 550E First Street

institute: NYU Langone

description:
Library name: S20_R1_001.fastq.gz
Weight_Loss:-29%

data_processing:
Raw sequenced reads were aligned to the mouse reference GRCm38 using STAR (v2.4.1d, 2-pass mode) aligner and Raw counts were obtained using HTSeq (v0.6.1) (Engstr√∂m et al., 2013; Teng et al., 2016). The principal component analysis (PCA) was performed using R Studio Version 3.6.3 and DEBrowser shinny application (Kucukural et al., 2019). Genes with <10 CPM were filtered out and batch effect correction was achieved using the Combat method (Johnson et al., 2007). The differentially expressed genes (DEG) were obtained using DESeq2 and were considered statistically significant when FDR < 0.05 and Log2(FC) > 1.5. The list of DEG was then used for KEGG pathway enrichment analysis using the R package clusterProfiler (Yu et al., 2012). The probability of browning in the WAT was assessed using the online webtool BATLAS (Perdikari et al., 2018).
Assembly: Genome_build: GRCm38
Supplementary files format and content: "raw_counts.csv" are comma-delimited file containing per-gene counts for each sample.

source_name: Liver

extract_protocol:
Total RNA was extracted from liver using TRIzol (Thermo Fisher), followed up by a clean-up step using RNeasy kit (Qiagen). One microgram of total RNA of each sample was submitted to the WCM Genomics Resources Core Facility.
Following isolation, RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer and used if RNA Integrity Number (RIN) value was greater than 8. The library construction was done following the protocol from Illumina TruSeq Stranded mRNA Sample Preparation kit. DNA fragments were sequenced using HiSeq4000 on SR100 format

value: Liver

value: cachectic


title: LNCaP cells, siGATA2, rep2

value: GATA2 knockdown


title: Bone marrow, CDSCs-2

description: Library name: Sample 5


title: AT2 cells, 6 hours, 8 ug/cm2 Ceramic brake-wear PM, replicate 2

description:
Library name: Ceramic_2
Column name in NormalisedCounts_cpm.csv: Ceramic_2

value: ATII (ER:KRASV12)


title: cachectic_Male_19

description:
Library name: S19_R1_001.fastq.gz
Weight_Loss:-30%


title: AT2 cells, 6 hours, 8 ug/cm2 Ceramic brake-wear PM, replicate 1

description:
Library name: Ceramic_1
Column name in NormalisedCounts_cpm.csv: Ceramic_1

value: Alveolar type-II epithelial cell


title: Bone marrow, CDSCs-1

description: Library name: Sample 4


title: cachectic_Male_18

description:
Library name: S18_R1_001.fastq.gz
Weight_Loss:-33%


title: Bone marrow, BMT-3

description: Library name: Sample 3

value: BMT


title: LNCaP cells, siTFAP2C, rep1


title: AT2 cells, 6 hours, 8 ug/cm2 NAO brake-wear PM, replicate 4

description:
Library name: NAO_4
Column name in NormalisedCounts_cpm.csv: NAO_4

value: 8 ug/cm2 NAO brake-wear PM

value: 6 hour


title: cachectic_Male_17

description:
Library name: S17_R1_001.fastq.gz
Weight_Loss:-29%


title: Bone marrow, BMT-2

description: Library name: Sample 2


title: AT2 cells, 6 hours, 8 ug/cm2 NAO brake-wear PM, replicate 3

description:
Library name: NAO_3
Column name in NormalisedCounts_cpm.csv: NAO_3


title: LNCaP cells, siHOXB13, rep1


title: Bone marrow, BMT-1

description: Library name: Sample 1


title: cachectic_Male_16

description:
Library name: S16_R1_001.fastq.gz
Weight_Loss:-32%


title: non-cachectic_Male_15

description:
Library name: S15_R1_001.fastq.gz
Weight_Loss:-14%

value: non-cachectic


title: AT2 cells, 6 hours, 8 ug/cm2 NAO brake-wear PM, replicate 2

description:
Library name: NAO_2
Column name in NormalisedCounts_cpm.csv: NAO_2


title: LNCaP cells, siNT, rep1

value: LNCaP

value: Control knockdown


title: AT2 cells, 6 hours, 8 ug/cm2 NAO brake-wear PM, replicate 1

description:
Library name: NAO_1
Column name in NormalisedCounts_cpm.csv: NAO_1


title: non-cachectic_Male_14

description:
Library name: S14_R1_001.fastq.gz
Weight_Loss:-3%


title: Mutu Induced,  3

city: New Orleans

first: Erik

middle: K

last: Flemington

state: LA

address: 1430 Tulane Avenue

department: Pathology

institute: Tulane University

description:
MI.counts.tsv
MI-3

data_processing:
Read alignment and processing
All fastq files obtained from barcoded samples corresponding to a single replicate for each condition were concatenated to produce one consolidated fastq.gz file. To process these reads, Pychopper was employed with the following basic command: pychopper -r report.pdf -u unclassified.fq -w rescued.fq input.fq full_length_output.fq.
Subsequently, all full_length_output.fq files generated by Pychopper were aligned to the human genome plus the EBV genome using minimap2 with the following parameters: minimap2 -ax splice -t 8 hg38_plus_EBV.fa full_length_output.fq > Aligned_fullLength.sam
SAMtools (version 1.19.2) was then utilized to convert the resulting SAM files into BAM files and to perform statistical analysis on the alignment process.
After verifying the quality of the alignment results, SAMtools was again used to merge all BAM files from replicates into a single BAM file for each condition. BEDtools (v2.30.0)67 was employed to convert the BAM files into BED12 format, followed by steps of sorting, compressing, and indexing the resulting files. To investigate the potential generation of multiple EBV copies during the reactivation experiment, this entire mapping process was repeated using a reference containing five copies of the EBV genome instead of a single copy.
Finally, we used Flair software to generate the count files with the following settings: flair quantify -r reads_count.tsv -i isoforms.fa
Assembly: hg38_plus_EBV
Supplementary files format and content: Tab-delimited text file included Raw counts for each sample

organism:
Homo sapiens
human gammaherpesvirus 4

source_name: EBV+Burkitt's Lymphoma line Mutu

growth_protocol: EBV+Burkitt's Lymphoma lines, Mutu (gift from Samuel H Speck) and Akata (gift from Kenzo Takada) were cultured in RPMI (Fisher Scientific, cat no. SH30027) supplemented with 10% FBS (ThermoFisher Scientific, cat no. 10437) at 37°C with 5% CO2. Akata cells harboring the pCEP4-BMRF1p-GFP reporter plasmid were cultured in the presence of 250 ug/ml hygromycin to retain the episomal reporter.

extract_protocol:
RNA extraction Cells were resuspended in 1ml of TRIzol Reagent (Invitrogen, cat no. 15596026) and processed according to the manufacturer's protocol. RNA pellets were resuspended in 42 μl of ddH2O. 5 μl of 10× DNase buffer and 3 μl of DNase I (New England Biotechnology, cat no. M0303L) were added, and tubes were incubated at 37°C for 15 min. DNase I was removed using the Monarch RNA Cleanup Kit (New England Biotechnology, cat no. T2030L). 1μg of RNA was reverse transcribed using LunaScript (New England Biotechnology, cat no. M3010), according to the manufacturer's protocol. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent, Serial No. DE54107860) with the Agilent RNA 6000 Nano Kit (Agilent, Cat. No. 5067-1511) to ensure RNA integrity numbers of greater than 9.5.
Oxford nanopore long read sequencing ONT (Oxford Nanopore Technologies) sequencing was performed using the PromethION platform (Oxford Nanopore Technologies plc.) at the Biotechnology Center, University of Wisconsin-Madison. The sequencing run was conducted on a FLO-PRO002 flow cell with the SQK-PCB109 barcoding kit according to the manufacturer’s instructions. The experiment was run for a total duration of 72 hours.

treatment_protocol: Nucleofection Three million Mutu cells were co-transfected with CMVp-GFP (0.3 μg) plus either a control (SV40p-cntl) or Zta (SV40p-Zta) expression vector (2.7 ug) using an Amaxa Nucleofector II machine (Lonza). Plasmids were added to 100 μl of Amaxa Cell Line Nucleofector Kit R (Lonza, cat no. VCA-1001) and loaded into a cuvette and cells were electroporated using the G016 setting. Cells were then immediately transferred to flasks with growth media and placed in the incubator.  BCR crosslinking Affinipure goat α-Human IgG (Jackson ImmunoResearch, cat no. 109-005-003) was added to cell culture media of Akata cells harboring the pCEP4-BMRF1p-GFP reporter plasmid to a final concentration of 10 μg/ml. Cells were incubated for 24 h prior to harvesting for FACS isolation.

value: Mutu

value: B-cells

value: Zta


title: S. pombe_cpn1_rep3

city: Edinburgh

first: Elizabeth

middle: H

last: Bayne

address: Alexander Crum Brown Road

department: School of Biological Sciences

institute: University of Edinburgh

description: Library name: cpn1.r3

data_processing:
The adapter removal process was performed using Cutadapt v4.8
Trimmed reads were aligned to the S. pombe reference genome (ASM294v2.27) and a customised GTF file using STAR (v2.7.10b)
The raw count matrix was generated using featureCounts from the Rsubread (v2.16.0) R package
The differential expression analysis was conducted using the edgeR (v3.42.4) R package
Assembly: S. pombe reference genome ASM294v2.27 version
Supplementary files format and content: Excel workbook file includes raw counts for each sample

organism: Schizosaccharomyces pombe

growth_protocol: S. pombe cultures were grown to log phase at 32oC in rich medium (YES)

extract_protocol:
Total RNA was extracted  using the Masterpure Yeast RNA Purification Kit (Epicentre) according to the manufacturer's instructions
polyA-selected libraries were prepared by Azenta Life Sciences

value: h+ cpn1::HygMX6 ade6-210 leu1-32 ura4-D18 otr1R:ade6+


title: AT2 cells, 6 hours, 8 ug/cm2 SemiMxCu brake-wear PM, replicate 4

description:
Library name: SemiMxCu_4
Column name in NormalisedCounts_cpm.csv: SemiMxCu_4

value: 8 ug/cm2 SemiMxCu brake-wear PM


title: non-cachectic_Male_13

description:
Library name: S13_R1_001.fastq.gz
Weight_Loss:-11%


title: S. pombe_cpn1_rep2

description: Library name: cpn1.r2


title: non-cachectic_Male_12

description:
Library name: S12_R1_001.fastq.gz
Weight_Loss:-8%


title: Mutu Induced,  1

description:
MI.counts.tsv
MI-1


title: LNCaP cells, siNT, rep2

first: David

last: Takeda

institute: National Institutes of Health


title: S. pombe_cpn1_rep1

description: Library name: cpn1.r1


title: non-cachectic_Male_11

description:
Library name: S11_R1_001.fastq.gz
Weight_Loss:-4%


title: AT2 cells, 6 hours, 8 ug/cm2 SemiMxCu brake-wear PM, replicate 1

description:
Library name: SemiMxCu_1
Column name in NormalisedCounts_cpm.csv: SemiMxCu_1


title: Akata Induced, 4

description:
AI.counts.tsv
AI-4

source_name: EBV+Burkitt's Lymphoma line Akata

value: Akata

value: IgG


title: Akata Induced, 3

description:
AI.counts.tsv
AI-3


title: S. pombe_WT_rep2

description: Library name: wt.r2

value: h+ ade6-210 leu1-32 ura4-D18 otr1R:ade6+


title: LNCaP cells, siGATA2, rep1

value: GATA2 knockdown


title: 20 dyne/cm²-3

city: Guiyang

first: Haitao

address: Affiliated Hospital of Guizhou Medical University,

institute: Guizhou Medical University

description:
Library name: sample6
SFC_F3

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a pvalue cutoff of 0.05 to judge statistically significant enrichment.
Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Assembly: Rattus norvegicus  Rnor_6
Supplementary files format and content: counts values for each sample

organism: Rattus norvegicus

source_name: The Primary articular cartilage superficial layer cells

extract_protocol:
Trizol reagent (TaKaRa Bio, Tokyo, Japan)
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction


title: Mutu Induced,  4

description:
MI.counts.tsv
MI-4


title: 20 dyne/cm²-2

description:
Library name: sample5
SFC_F2

value: The Primary articular cartilage superficial layer cells


title: Akata Induced, 2

description:
AI.counts.tsv
AI-2


title: S. pombe_WT_rep1

description: Library name: wt.r1


title: AT2 cells, 6 hours, 8 ug/cm2 LowM brake-wear PM, replicate 4

description:
Library name: LowM_4
Column name in NormalisedCounts_cpm.csv: LowM_4

value: ATII (ER:KRASV12)

value: Alveolar type-II epithelial cell

value: 8 ug/cm2 LowM brake-wear PM


title: Akata Induced, 1

description:
AI.counts.tsv
AI-1


title: AT2 cells, 6 hours, 8 ug/cm2 LowM brake-wear PM, replicate 3

description:
Library name: LowM_3
Column name in NormalisedCounts_cpm.csv: LowM_3

value: 6 hour


title: 20 dyne/cm²-1

description:
Library name: sample4
SFC_F1


title: AT2 cells, 6 hours, 8 ug/cm2 LowM brake-wear PM, replicate 2

description:
Library name: LowM_2
Column name in NormalisedCounts_cpm.csv: LowM_2


title: Mutu Induced,  2

description:
MI.counts.tsv
MI-2


title: 0 dyne/cm²-3

description:
Library name: sample3
SFC_D3


title: AT2 cells, 6 hours, 8 ug/cm2 LowM brake-wear PM, replicate 1

description:
Library name: LowM_1
Column name in NormalisedCounts_cpm.csv: LowM_1


title: R588 replica 2

city: Geneve

first: George

last: Allen

state: Geneve

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

description: Library name: R588_2_1

data_processing:
Reads were mapped using Bowtie2 to Pseudomonas aeruginosa PAO1 genome assembly ASM676v1 and counts were aggregated using summarize Overlaps in the package GenomicAlignments in R using the ASM676v1 gtf version 2.2 (NCBI accession: GCF_000006765.1).
Assembly: NC_002516.2
Supplementary files format and content: Excel file of CDS read counts across all samples
Supplementary files format and content: Excel file of CDS RPKMs across all samples

organism: Pseudomonas aeruginosa

source_name: bacteria

growth_protocol: P. aeruginosa strains were cultured at 16°C on LA supplemented with 0.2% arabinose and incubated for 96 hours until colonies became visible.

extract_protocol:
The RNA extraction was performed using two tubes of pellets for each strain and replicate, with the Monarch Total RNA Miniprep kit. For lysis of the bacterial cells, the two pellets were resuspended in 250 μL of 1X Tris-EDTA (TE) buffer supplemented with 1 mg/mL of lysozyme and regrouped into one tube for each strain, incubated for 5 minutes at RT, and RNA was subsequently extracted following the manufacturer’s instructions. After RNA purification, an additional DNA removal treatment was done using TURBO DNase (Thermo Fisher) according to the manufacturer’s instructions.
Ribosomal RNA was depleted with Ribo-Zero rRNA Removal Kit (Illumina).  Subsequently, sequencing libraries were generated using the rRNA-depleted RNA and performing procedures as follow. Briefly, after fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized and dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. Samples were sequenced using the Illumina HiSeq 2000, 150 bp double end read at Novogene.

treatment_protocol: 500 μL of each culture were immediately added into four separate 1.5 mL tubes, each containing 1 mL of RNAlater (Sigma-Aldrich, cat). After harvesting of all three strains, the tubes were centrifuged for 30 minutes at 9600 x g. Supernatant was discarded and pellets were stored at -80°C until RNA extraction.

value: bacteria


title: R588 replica 3

description: Library name: R588_3_1


title: AT2 cells, 6 hours, 8 ug/cm2 SemiMxCu brake-wear PM, replicate 3

description:
Library name: SemiMxCu_3
Column name in NormalisedCounts_cpm.csv: SemiMxCu_3


title: 0 dyne/cm²-2

description:
Library name: sample2
SFC_D2


title: Top position, R1 growth stage, biological replicate 5

city: Urbana

first: Lauriebeth

last: Leonelli

state: Illinois

address: 1206 W Gregory Dr.

department: Department of Agricultural and Biological Engineering

institute: University of Illinois Urbana-Champaign

description:
VuCanopy_029
T-R1-Rep5

data_processing:
Sequence reads were trimmed using the JGI BBDuk shellscript.
Trimmed reads were mapped to the cowpea reference genome using HISAT2.
Reads mapping to exons were counted using the featureCounts program.
Assembly: Vigna unguiculata v1.2, Phytozome genome ID: 540, NCBI taxonomy ID: 3917.
Supplementary files format and content: raw read counts for each sample.
Supplementary files format and content: DESeq2 normalized read counts for each sample.

organism: Vigna unguiculata

source_name: Leaf

growth_protocol: Cowpea were planted in-ground in a Plant Care Facility greenhouse at the University of Illinois Urbana-Champaign. Seeds were planted with 3 inches between plants and 30 inches between rows. Plant maintenance involved irrigation, weekly fertilizer application, and supplemental lighting (14h/10h photoperiod, 1000 umol/m^2*s).

extract_protocol:
RNA was purified using the MagMAX kit for RNA extraction (Thermo Fisher Scientific, cat# AM1830).
Libraries were constructed using the Kapa HyperPrep mRNA kit (Roche, cat# KK8581).

value: Leaf

tag: canopy position

value: Top position

tag: developmental stage

value: R1 growth stage


title: R588

description: Library name: R588_1_1


title: Top position, R3 growth stage, biological replicate 5

description:
VuCanopy_030
T-R3-Rep5

tag: tissue

value: R3 growth stage


title: AT2 cells, 6 hours, 8 ug/cm2 SemiMxCu brake-wear PM, replicate 2

description:
Library name: SemiMxCu_2
Column name in NormalisedCounts_cpm.csv: SemiMxCu_2

tag: treatment


title: 0 dyne/cm²-1

description:
Library name: sample1
SFC_D1


title: S. pombe_WT_rep3

description: Library name: wt.r3

tag: cell line


title: AT2 cells, 6 hours, no PM control, replicate 4

description:
Library name: Ctrl_4
Column name in NormalisedCounts_cpm.csv: Ctrl_4

value: No PM control


title: Middle position, R3 growth stage, biological replicate 5

description:
VuCanopy_028
M-R3-Rep5

value: Middle position


title: R529 replica 3

description: Library name: R529_3_1


title: R529 replica 2

description: Library name: R529_2_1


title: Middle position, R1 growth stage, biological replicate 5

description:
VuCanopy_027
M-R1-Rep5


title: FNV, PNAscr, 16h, rep C

city: Würzburg

first: Jakob

middle: Jeremias

last: Jung

state: Bayern

address: Josef-Schneider-Str. 2/Bau D15

department: Institute of Molecular Infection Biology (IMIB)

institute: University of Würzburg

description: Library name: Fnv_PNAscr_16h_C

data_processing:
RNA-seq raw reads were trimmed, filtered and mapped using the F. nucleatum ssp. nucleatum ATCC 23726 (NZ_CP028109.1) annotation file with costume annotation or the F. nucleatum ssp. vincentii 3_1_36A2 (NZ_ CP003700.1) file.
To remove adapter sequences and trim nucleobases BBduk was used before mapping the reads with BBMap (v38.84).
Differential gene expression was investigated using the featureCounts methods of the Subread (2.0.1) package. For further downstream analysis R/Bioconductor packages were used.
Assembly: NZ_CP028109.1, NZ_ CP003700.1
Supplementary files format and content: raw_counts_FNN.csv is csv table with genes as rownames and samples as colnames for FNN samples
Supplementary files format and content: raw_counts_FNV.csv is csv table with genes as rownames and samples as colnames for FNV samples

organism: Fusobacterium nucleatum

source_name: subspecies vincentii 3_1_36A2

growth_protocol: Three biological replicates for each sample were grown overnight in ColB, diluted the following morning 1:50 in fresh ColB, and after the culture reached OD600 0.5, it was diluted 1:250 to 1x106 cfu ml-1 in MHB.

extract_protocol:
To isolate fusobacterial RNA, samples were incubated 1:1 (v:v) with RNAprotect Bacteria (Qiagen) for five minutes at RT, snap frozen in liquid nitrogen and stored at -80°C until further processing. To purify RNA the miRNeasy Micro kit (Qiagen) was used. Briefly, cell dilutions were thawed on ice, centrifuged at 4°C with 13,000 g for 20 minutes, the pellets resuspended in 100 μl 0.5 mg ml-1 lysozyme (Roth) in TE buffer pH 8.0 and incubated for two minutes at RT. The samples were then incubated with 700 μl Qiazol (Qiagen) for five minutes at RT and after addition of 160 μl chloroform shaken vigorously for 15 seconds to obtain phase separation. The upper aqueous phase was mixed 1:1.5 with 100% ethanol and loaded onto the Qiagen columns. Columns washes, DNase I digest and elution were performed according to the manual instructions. RNA concentrations were determined via NanoDrop measurements and samples were stored at -80°C until sequencing.
RNA quality was investigated using the 2100 Bioanalyzer together with the RNA 6000 Pico kit (Agilent Technologies). Risbosomal RNA (rRNA) depletion was performing using the RiboCop META rRNA depletion kit (Lexogen) according to the manufacturer’s instructions. Depleted RNA was further fragmented via ultrasound for 30 s at 4°C. After adapter ligation to the 3’ end, the first-strand cDNA was synthetized using the M-MLV reverse transcriptase. Following purification, 5’ Illumina TruSeq adapters were ligated to the cDNA, the cDNA amplified by PCR and the resulting product purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics). After performing library quality control using the 2100 Bioanalyzer with the DNA High Sensitivity kit (Agilent Technologies), the cDNA was pooled, purified and sequenced using an Illlumina NextSeq 500 system with 10 million reads/sample in single end mode with 75 nt read length.

treatment_protocol: 5 ml of the solution were transferred into 5 ml low-binding tubes (LABsolute) and incubated with 10 μM PNA or the respective volume of water for 30 minutes and 16 hours at 37°C in the anaerobic chamber. The reaction was stopped at the mentioned time points by adding RNAprotect Bacteria (Qiagen).

value: 16 hours

value: subspecies vincentii 3_1_36A2

value: PNA scrambled

tag: replicate

value: C


title: AT2 cells, 6 hours, no PM control, replicate 2

description:
Library name: Ctrl_2
Column name in NormalisedCounts_cpm.csv: Ctrl_2

tag: cell type


title: R529

description: Library name: R529_1_1

tag: genotype


title: Bottom position, R3 growth stage, biological replicate 5

description:
VuCanopy_026
B-R3-Rep5

value: Bottom position


title: FNV, PNAscr, 16h, rep B

description: Library name: Fnv_PNAscr_16h_B

tag: strain

value: B


title: AT2 cells, 6 hours, no PM control, replicate 1

description:
Library name: Ctrl_1
Column name in NormalisedCounts_cpm.csv: Ctrl_1

value: ATII (ER:KRASV12)

tag: time


title: FNV, PNAscr, 16h, rep A

description: Library name: Fnv_PNAscr_16h_A

value: A


title: Bottom position, R1 growth stage, biological replicate 5

description:
VuCanopy_025
B-R1-Rep5


title: PCI-13-I (miRNA-seq)

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0
Assembly: GRCh38 version 110
Supplementary files format and content: Tab-delimited miRNA counts

source_name: human OSCC cell line PCI-13

extract_protocol:
RNA isolation was performed using Trizol reagent (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer's instructions. RNA quality was assessed by measuring the RNA integri-ty number (RIN) using a Fragment Analyzer HS Total RNA Kit (Advanced Analytical Technologies, Inc.)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human OSCC cell line PCI-13


title: WT replica 3.

description: Library name: WT_3_1

value: WT


title: Top position, R3 growth stage, biological replicate 4

description:
VuCanopy_024
T-R3-Rep4


title: FNV, PNA79, 16h, rep C

description: Library name: Fnv_PNA79_16h_C


title: WT replica 2.

description: Library name: WT_2_1

value: bacteria


title: WT.

description: Library name: WT_1_1


title: Top position, R1 growth stage, biological replicate 4

description:
VuCanopy_023
T-R1-Rep4

value: Leaf


title: Middle position, R3 growth stage, biological replicate 4

description:
VuCanopy_022
M-R3-Rep4


title: FNV, PNA79, 16h, rep A

description: Library name: Fnv_PNA79_16h_A


title: cgsh2089, replicate3

city: St Petersburg

first: Rui

last: Zhou

state: FL

address: REB 4130, 501 6th Ave S

institute: Johns Hopkins University

data_processing:
Adaptor sequences and low-quality reads (those with an average quality score < 20) were removed from the paired-end raw data using Trim-galore (version 0.4.4).
The resulting cleaned reads were aligned to the Drosophila melanogaster (dm6) reference genome using the STAR splice-aware aligner (version 2.6.0c) with default parameters.
Ambiguous reads mapping to multiple regions in the genome and reads with a MAPQ score less than 10 were discarded.
Subread featureCounts (version 2.0.1) was then utilized for gene quantification, employing the FlyBase r6.40 gene annotation.
Genes without read counts in all samples were excluded from subsequent analysis.
Assembly: dm6
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: tab-delimited text file include RPKM values for every gene and every sample

organism: Drosophila melanogaster

source_name: fat body

growth_protocol: Flies were maintained at room temperature with standard fly food (molasses formula).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen).
Total RNA samples were subjected to cDNA library construction using illumine kit.

treatment_protocol: Fat bodies of wandering 3rd instar larvae of appropriate genotypes were dissected in PBS prior to RNA extraction.

value: fat body

value: wandering 3rd instar larvae


title: PCI-13-I-II (miRNA-seq)


title: Luva-I (miRNA-seq)

source_name: human mast cell line LUVA

value: human mast cell line LUVA

value: Mono-Luva


title: Middle position, R1 growth stage, biological replicate 4

description:
VuCanopy_021
M-R1-Rep4

value: Middle position

value: R1 growth stage


title: cgsh2089, replicate2


title: FNV, H20, 16h, rep C

description: Library name: Fnv_H2O_16h_C

value: 16 hours

value: subspecies vincentii 3_1_36A2

value: Control


title: AT2 cells, 6 hours, no PM control, replicate 3

description:
Library name: Ctrl_3
Column name in NormalisedCounts_cpm.csv: Ctrl_3

value: Alveolar type-II epithelial cell

value: No PM control

value: 6 hour


title: Luva-II (miRNA-seq)


title: cgsh2089, replicate1


title: Bottom position, R3 growth stage, biological replicate 4

description:
VuCanopy_020
B-R3-Rep4

value: Bottom position

value: R3 growth stage


title: Luva-I-II (miRNA-seq)


title: FNV, H20, 16h, rep A

description: Library name: Fnv_H2O_16h_A

value: A


title: FNV, PNAscr, 30min, rep C

description: Library name: Fnv_PNAscr_30m_C

value: 30 minutes

value: PNA scrambled

value: C


title: shGFP control, replicate3

value: fat body

value: wandering 3rd instar larvae

value: cg>shGFP


title: Bottom position, R1 growth stage, biological replicate 4

description:
VuCanopy_019
B-R1-Rep4

value: Leaf


title: shGFP control, replicate2


title: CoCult-PCI-13-I (miRNA-seq)

value: human OSCC cell line PCI-13


title: CoCult-PCI-13-II (miRNA-seq)


title: PCI-13-II (miRNA-seq)


title: FNV, PNAscr, 30min, rep B

description: Library name: Fnv_PNAscr_30m_B

value: B


title: FNV, PNA79, 16h, rep B

description: Library name: Fnv_PNA79_16h_B

value: 16 hours

value: subspecies vincentii 3_1_36A2


title: Top position, R1 growth stage, biological replicate 3

description:
VuCanopy_017
T-R1-Rep3

value: Top position

value: R1 growth stage


title: CoCult-PCI-13-I-II (miRNA-seq)


title: Middle position, R3 growth stage, biological replicate 3

description:
VuCanopy_016
M-R3-Rep3

value: Middle position