title: PANC1  - chronic hypoxia

city: Amman

first: Hamzeh

middle: J.

last: Al-Ameer

address: Madaba

department: Biology and Biotechnology

country: Jordan

institute: American University of Madaba

description: The effect of hypoxia on gene expression of PANC1 was studied using a 96 well glucose metabolism RT profiler PCR array, PAHS 006Z, Qiagen, USA. In this array, 96 well plates containing different primers PAHS 006Z, human metabolic array, Qiagen, USA for 84 genes known to respond to hypoxia in addition to 12 genes for quality control purposes.  Primers were supplied by the manufacturer RT profiler PCR array PAHS 006Z Qiagen, USA.

data_processing:
Quantitative PCR reactions were performed using the CFX thermo cycler, Bio-Rad, USA with the following temperature setting that depends on heat activation followed by cycling and repeating,  95 C for 10 min, 40 cycles of 95 C for 15 s, 60 C for 1 min. Data analysis was performed using the ΔΔCt method available from the Biosciences company, Qiagen, USA, web portal. Data were normalized across all plates to the actin beta ACTB housekeeping gene. The threshold cycle values of the control wells were all within the ranges recommended by the PCR array user manual.
Fold change is the normalized gene expression in the test sample divided by the normalized gene expression in the control sample. Fold regulation represents fold change values in a biologically meaningful way. Fold change values greater than 1 indicate an upregulation, and fold regulation is equal to the fold change.

label: syber green

source_name: PANC1 cells were exposed to 72-hours cycles of hypoxia once a week for a period of 5 weeks

label_protocol: A diluted complementary DNA aliquot was mixed with the RT SYBR green master mix glucose metabolism RT profiler PCR array PAHS 006Z, Qiagen, USA and loaded into the 96 well array plate.

growth_protocol: PANC1 cells were cultured in DMEM high glucose medium EuroClone, Figino, Italy, supplemented with 10% heat inactivated fetal bovine serum FBS HyClone, USA, 2 mM L glutamine HyClone, USA, and antibiotics penicillin and streptomycin HyClone, USA. PANC1 cells were grown in attached-type, filter cap culture flasks Membrane Solutions, USA. Cells were kept at 37 C in a humidified atmosphere containing 5% Carbon dioxide. All cell culture procedures were performed in sterile conditions under a class II biological safety cabinet, Heal-Force, China. All used materials and disposables were disinfected with ethanol 76% before use, and subculturing was performed twice a week at 80 to 90% confluence.

extract_protocol: RNA was isolated using RNeasy Mini kit, Qiagen, Germany. In brief, cells were disrupted in RLT buffer RNeasy lysis buffer, guanidine thiocyanate containing buffer, and homogenized by vortexing. One ml of ethanol 70% was then added to the lysate, creating conditions that promote selective binding of RNA to the RNeasy membrane. The sample was then applied to the RNeasy Mini spin column where total RNA binds to the membrane while contaminants are efficiently washed away, and high quality RNA is eluted in RNase free water. Binding, washing, and elution steps were performed by centrifugation in a micro centrifuge, Qiagen, USA. Purity of isolated RNA was determined by measuring ratio of the optical density of the samples at 260 and 280 nm. The optical density ratio OD260/OD280 was ranging from 1.9 to 2.2 for all samples. All RNA samples were stored at minus 80 C until use for complementary DNA, cDNA synthesis.

treatment_protocol:
Hypoxic atmosphere was generated using a hypoxia chamber apparatus Stem Cell Technologies, Vancouver, Canada. The chamber was connected to a gas cylinder that provides a hypoxic gas mixture 94% Nitrogen gas, 5% Carbon dioxide gas, and 1% Oxygen gas. To expose the cells to hypoxic atmosphere, PANC1 cells were placed into the chamber and purged with the gas mixture for 5 min to secure hypoxic condition. Hypoxic chamber was then placed into carbon dioxide gas incubator, NuAire, Shanghai, China.
For cycling acute hypoxia, PANC1 cells were exposed to 7 hours cycles of hypoxia, every other day for a total of 20 hypoxic cycles. For cycling chronic hypoxia, PANC1 cells were exposed to 72 hours cycles of hypoxia once a week for a period of 5 weeks. Each chronic hypoxic cycle was separated from the other by 96 hours incubation in normoxic atmosphere. For comparison, a subset of PANC1 cells were incubated alongside under normoxic 95% Oxygen gas, 5% Carbon dioxide gas conditions, control PANC1 cells.

value: pancreatic cancer

tag: treatment


title: A673_HOXD13

status: Public on Jun 28 2022

type: SRA

city: Boston

first: April

last: Apfelbaum

state: MA

address: 450 Brookline Ave

department: Pediatric Oncology

country: USA

institute: Dana-farber Cancer Institute

library_source: genomic

data_processing:
library strategy: CUT&RUN
Paired-end reads were aligned to hg38 using Bowtie2.3.5 with the following command: bowtie2 --end-to-end --very-sensitive --no-overlap --no-dovetail --no-unal --no-mixed --no-discordant -q -I 10 -X 700 -x path/to/Bowtie2/indices -1 read1.fastq.gz -2 read2.fastq.gz
Peaks were called using MACS2.2.7 with both treatment-only and IgG-controlled modes with the following parameters: --format BAMPE --gsize hs --keep-dup all -q 0.05. For H3K27me3, broad peak calling was turned on using --broad --broad-cutoff 0.1.
IgG-controlled narrow peaks were kept if they overlapped with treatment-only peaks from the same sample, q-value is less than 0.01 and fold enrichment is over 2; treatment-only broad peaks were kept if they overlap with IgG-controlled peaks from the same sample, peak width is at least 2 Kbp, q-value is less than 0.01 and fold enrichment is over 2.
For HOXD13, in addition to MACS2 narrow peak calling and peak filtering described above, SEACR 1.2 was also run with stringent mode and IgG control. Filtered MACS2 peaks that overlap with SEACR peaks were passed on to the downstream analyses.
genome coverage profiles were generated using BEDTools with the following command: bedtools genomecov -scale <scale factor to count per million> -bg -pc -ibam path/to/bam
Genome_build: Hg38
Supplementary_files_format_and_content: peak files in MACS2 narrow/broad peak format
Supplementary_files_format_and_content: genome coverage files (.bw) normalized to count per million

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: A673 was maintained in RPMI 1640 media (Gibco) supplemented with 10% FBS (Atlas Biologicals) and 2mmol/L-glutamine (Life Technologies). CHLA10 was maintained in IMDM media (Fisher scientific) supplemented with 20% FBS, 2mmol/L-glutamine, and 1X Insulin-Transferrin-Selenium (Gibco). Cells were cultured at 37°C with 5% CO2 and were split according to ATCC and COG recommendations.

extract_protocol:
Cells were bound to concanavalin A-coated magnetic beads , permeabilized with digitonin, and bound with primary antibodies. Samples are then arrayed in a 96-well plate and processed on a Beckman Biomek FX liquid handling robot equipped with a 96S Super Magnet Plate. The MNase digestion reaction is performed at 0–4 °C after the addition of 2 mM CaCl2.  Chromatin fragments released into the supernatant arae collected for the next steps.
Methods from (Janssens et al. 2018 Methodology: "Chromtin fragments are used as the substrate for end-repair and ligation with barcoded Y-adapters. Prior to ligation, the A-tailing step is performed at 58 °C to preserve sub-nucleosomal fragments in the library. End-repair and adapter ligation reactions were performed on a separate thermocycler. Chromatin proteins are then digested with Proteinase K, and adapter ligated DNA fragments are purified on the Biomek FX using two rounds of pre-PCR Ampure bead cleanups with size selection. PCR enrichment reactions are performed on a thermocycler using the KAPA PCR kit (KAPA Cat#KK2502). Two rounds post-PCR Ampure bead cleanups with size selection are performed on the Biomek FX to remove unwanted proteins and self-ligateed adapters. The size distributions of AutoCUT&RUN libraries were analyzed on an Agilent 4200 TapeStation, and library yield was quantified by Qubit Fluorometer (Thermo Fisher). Up to 24 barcoded AutoCUT&RUN libraries were pooled per lane at equimolar concentration for paired-end 25 × 25 bp sequencing on a 2-lane flow cell on the Illumina HiSeq 2500 platform at the Fred Hutchinson Cancer Research Center Genomics Shared Resource."

tag: cell line

tag: cell type

value: Ewing sarcoma

tag: antibody

value: rabbit anti-HOXD13 (1:20)


title: tumour (neuroendocrine liver metastasis) from Pt#077, tumour slice, post-recovery

type: RNA

city: London

first: Elena

last: Palma

state: -- US/Canada Only --

address: 111 Coldharbour Lane

country: United Kingdom

institute: The Roger Williams Institute of Hepatology

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their template for analysis (Instructions for Analyzing RT2 Profiler PCR Array Results with this Template).
For the normalization it uses the average of five housekeeping genes: ACTB, B2M, GAPDH, HPRT1 , RPLP0.

label: SYBR Green

molecule: total RNA

source_name: tumour, LM-NEN

label_protocol: cDNA was synthesized with RT2 First Strand Kit (Qiagen).

growth_protocol: After slicing the original tissue, each slice was cultured into a 12-well plate for 2 hours (recovery step) in 1.5 mL supplemented Williams Medium E: William’s E Medium (ThermoFisher Scientific), 5% Human AB serum (Pan-Biotech), Penicillin/Streptomycin (ThermoFisher Scientific), 2 mM Glutamine (ThermoFisher Scientific), ITS (10 mg/L Insulin + 5.5 mg/L Transferrin + 6.7 µg/L Sodium selenite, ThermoFisher Scientific), 1nM epidermal growth factor (ThermoFisher Scientific), 100nM Glucagon (Merck), 1µM Corticosterone (Merck). After the recovery slices were collected, preserved in AllProtect Tissue Reagent (Qiagen) and stored at -80C until RNA extraction.

extract_protocol: Total RNA was isolated with Allprep Mini Kit (Qiagen) according to manifacturer's instructions.

tag: sample type

value: test

tag: primary tumour type

value: LM-NEN

tag: gender

value: M

tag: age

tag: ethnicity

value: caucasian

tag: primary tumour site

value: small bowel

tag: tumour grade

tag: fibrosis score


title: A673_shNS_H3K4me1_1


title: tumour (neuroendocrine liver metastasis) from Pt#045, tumour slice, post-recovery

value: pancreatic


title: A673_shNS_H3K4me1_2


title: A673_shNS_H3K27ac_2

value: H3K27ac:Millipore MABE647 (1:50)


title: Etv2cKO_E10_25_rep2

city: Minneapolis

first: Daniel

last: Garry

state: MN

address: 2231 6th Street SE, 4th Floor

department: Lillehei Heart Institute

institute: University of Minnesota

data_processing:
Illumina used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 v2.2.4 with default parameters.
The ATAC-seq peaks were called by MACS2
Genome_build: mm10
Supplementary_files_format_and_content: peak files; bigwig files

organism: Mus musculus

extract_protocol:
Limb bud tissues were digested in 200 ml of TripLE (ThermoFisher 12605010) at 37°C in two cycles of 5 min incubation followed by trituration. Cells were cooled on ice for 5 min between incubations. Digestion was stopped with 1ml of medium with 10% fetal calf serum that was filtered through a 50 mm mesh filter (Partec). Cells were collected by centrifugation and stained with staining medium containing 0.2 mg each of CD31-APC, Tie2-APC, CD45-APC and 0.5 mg anti CD16/CD32, and EYFP positive, APC negative live cells were sorted on FACSAria (BD). Cells from EYFP negative embryos were used as a negative control for FACS sorting.
ATAC-seq libraries were prepared for sequencing using standard Illumina protocols

tag: time

tag: genotype/variation


title: PANC1  - control

source_name: not exposed  to hypoxia

value: not exposed  to hypoxia


title: PANC1  - acute hypoxia

source_name: PANC1 cells were exposed to 7 hours cycles of hypoxia, every other day for a total of 20 hypoxic cycles


title: FL_GFP_pos_rep1


title: Etv2cKO_E10_25_rep1


title: PDL1_2 RNA-seq

status: Public on Jun 27 2022

city: Atlanta

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

institute: Emory University

library_source: transcriptomic

data_processing:
Aligned with Hisat2
Reads counted with subread/featurecounts
normalization and differential expression with DEseq2
Assembly: mm10
Supplementary files format and content: csv file with raw counts for all genes and samples

source_name: Spleen

extract_protocol: RNA extracted using qiagen column

tag: tissue

value: Spleen

value: DbGP33+ CD8+ T cells


title: IL2_1 RNA-seq


title: dog1_4_03

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

description: no treatment

data_processing:
In our oligo(dT) primers two parts of UMI are split by barcode sequence, that is why we transformed read R1 fastq files using awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Read R2 of single seed libraries was trimmed to remove potential contamination with poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 54 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the count matrix for each seed from libraries and each gene was obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes and a list of used barcodes as input. Count matrixes from different libraries were combined and used for further analysis using Seurat R package.
For seed pool analysis information about UMI was put to read R2 name using umi_tools (v 1.1.0) extract with parameter --bc-pattern=NNNNNNNNNNNNNNCCCCCC. Then fastq file for read R2 was divided into separate fastq files for each replica using BRBseqTools (v 1.6) Demultiplex with parameters -p UB -UMI 14. Each file was then trimmed and mapped as for single seed libraries. Finally, mapped reads were deduplicated using umi_tools (v 1.1.0) dedup with parameter --spliced-is-unique. Counts quantified for genes using htseq-count (v 0.11.3) were used for differential gene expression analysis using DESeq2 R package.
Genome_build: TAIR10
Supplementary_files_format_and_content: count text files

organism: Arabidopsis thaliana

source_name: seeds

growth_protocol: Dry after-ripened seeds stored at least 6 months before experiment.

extract_protocol:
For single seed analysis, up to 16 seeds were sparsely placed on a cooled glass microscopic slide and crashed using another glass microscopic slide. 2 ul of cold water was fast dropped on each seed debris on both slides. Matching two parts of each seed debris were mixed with water by pipetting and combined. 3 ul of seed extract was transferred to the PCR tube on ice. For pool and split control all seeds extracts were combined into a single tube, mixed and then split into 3 ul aliquots. After all seeds were processed 2 ul of digestion buffer (10 mM Tris-HCl pH 8.0, 1% Triton X-100, 1% Tween 20, 0.5 mM EDTA, 1.3 mg/ml proteinase K) and 1 ul of 10 mM barcoded oligo(dT) primer were added and mixed. Samples were incubated for 10 min at 65°C and 1 min at 85°C and placed on ice. For isolation of RNA from seed pools, frozen seeds were ground and mixed with 1 ml of homogenization buffer (100 mM Tris pH 9.5, 5 mM EDTA, 150 mM NaCl, 1 % sarkosyl, 0.5% b-mercaptoethanol). Seeds debris was centrifuged for 5 min 11,000g, the supernatant was transferred to fresh probe with 500 ul of chloroform and vortexed for 2 min. Then 500 ul of acid phenol was added and again vortexed for 2 min followed by centrifugation for 15 min 11,000g at 4°C. 900 ul of upper phase was transferred to a new tube and mixed with 90 ul of 3M sodium acetate and 600 ul of isopropanol. After 10 min incubation, RNA was pelleted by centrifugation for 15 min 11,000g at 4°C, the pellet was washed with 80% ethanol, dried and resuspended in 1ml of TRIzol. From that point, the procedure follows the standard protocol for RNA isolation with TRIzol.
For single seed libraries, digested extracts were mixed with 4 ul of reverse transcription mix (2 mM dNTPs, 2x SuperScriptIII reaction buffer, 10 mM DTT, 50 U of SuperScriptIII, 10 U of RiboLock), incubated for 30 min 42°C, 15 min 70°C and placed on ice. 32 cDNAs obtained using different barcoded oligo(dT) primers were pooled together, purified with Ampure beads (1.2x beads to sample volumes) and eluted in 17 ul of water. 15 ul of recovered cDNA pool was mixed by pipetting with 15 ul of second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 uM dNTPs) and incubated overnight at 16°C. Reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 ul of water. 3 ul of recovered dsDNA sample was used for tagmentation using 3 ul 5x diluted B-loaded Tn5 enzyme (homemade) and 6 ul freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). Reactions were mixed by pipetting and incubated for 7 min at 55°C followed by 5 min at 80°C. Water was added up to 30 ul, samples were purified with Ampure beads (1.2x beads to sample volumes) and eluted with 11 ul of water. Illumina indexing PCR was performed using 10 ul tagmented DNA in 50 ul reactions with Q5 2× PCR Master Mix (NEB) and 0.5 uM final concentration of primers. Libraries were Illumina Next-seq sequenced to obtain 21 nt R1 (contain barcode and UMI) and 55 nt R2 (contain mRNA sequence). For transcriptomic analysis of seed pools, isolated RNA was treated with Turbo DNase (ThermoFisher) and 500 ng of it was used in reverse transcription using 50 mM different barcoded oligo(dT) primers and SuperScript III. 0.25 of each reaction was pooled and the library was prepared and sequenced exactly as above.

treatment_protocol: Secondary dormancy induction was performed by storing seeds on plates with water-soaked blue paper in 30°C in the dark for the indicated time. Seed recovery was performed by transferring these plates to long-day conditions for 24h.

tag: experiment type

value: seed pool analysis

tag: genotype

value: dry seeds


title: Double_1 RNA-seq

tag: treatment

value: PD1 and IL-2


title: IL2_2 RNA-seq


title: Untx_1 RNA-seq

value: Untreated


title: Double_2 RNA-seq


title: PDL1_1 RNA-seq


title: dog1_4_02

description: no treatment


title: Col0_01

description: no treatment


title: tumour (neuroendocrine liver metastasis) from Pt#051, tumour slice, post-recovery

value: F


title: dog1_4_01

description: no treatment


title: FL_GFP_pos_rep3


title: Untx_2 RNA-seq


title: tumour (neuroendocrine liver metastasis) from Pt#106, tumour slice, post-recovery


title: FL_GFP_pos_rep2


title: Col0_03

description: no treatment


title: sd_dog1_7d24h_1

description: 7 day of secondary dormancy induction followed by 24h of recovery

value: single seed analysis

value: 7d SD induction + 24h recovery


title: sd_Col0_7d24h_3


title: sd_dog1_7d24h_2


title: sd_dog1_7d24h_3


title: sd_Col0_7d24h_1


title: sd_Col0_7d24h_2


title: sd_dog1_3d_2

description: 3 day of secondary dormancy induction

value: 3d SD induction


title: sd_Col0_3d_2

description: 3 day of secondary dormancy induction


title: sd_dog1_3d_3

description: 3 day of secondary dormancy induction


title: sd_Col0_3d_3

description: 3 day of secondary dormancy induction


title: Col0_02

description: no treatment


title: sd7d_2

description: 7 day of secondary dormancy induction

value: 7d SD induction


title: sd7d_3

description: 7 day of secondary dormancy induction


title: sd7dPS_2

description: 7 day of secondary dormancy induction

value: single seed analysis (pool-split control)


title: sd7d24h_3


title: sd_Col0_3d_1

description: 3 day of secondary dormancy induction


title: sd5d_2

description: 5 day of secondary dormancy induction

value: 5d SD induction


title: sd3d_3

description: 3 day of secondary dormancy induction


title: sd5d_3

description: 5 day of secondary dormancy induction


title: sd7d24h_1


title: sd7dPS_1

description: 7 day of secondary dormancy induction


title: sd5d_1

description: 5 day of secondary dormancy induction


title: sd7d_1

description: 7 day of secondary dormancy induction


title: sd1d_3

description: 1 day of secondary dormancy induction

value: 1d SD induction


title: sd7d24h_2


title: CM_ReO2_3_EVs

first: Guoping

last: Li

address: Cardiovascular Research Center, 185 Cambridge St, Simches 3.5000

department: CVRC

institute: Massachusetts General Hospital

description: small RNAs

data_processing:
Library strategy: ARM-seq
Adapters were removed and reads were merged with SeqPrep [John st. John unpub] using a minimum read length of 15 and adapters AGATCGGAAGAGCACACGTC and GATCGTCGGACTGTAGAACTC.  Reads that could not be merged were discarded before mapping.
Data were analyzed with tRAX (http://trna.ucsc.edu/tRAX/), tRAX maps reads using bowtie2 v2.3.5.1 with parameters --very-sensitive --ignore-quals --np 5 -k 100,  to a custom database containing mature tRNA transcripts and the genome sequence.
ENSEMBL (release 96) small ncRNA annotations were used to count the number of small RNA transcripts using only primary alignments to prevent double counting. Transcripts with 0 reads across all samples were removed.
tDRnamer (http://trna.ucsc.edu/tDRnamer/) was used to generate unique identifiers for each of the reads which mapped to a tRNA transcript based on the isodecoder(s) they mapped to and positions of any misincorporations.
DESeq2 v1.30.1 was used to generate normalized read counts for each of the transcripts across each sample.
Genome_build: Homo Sapiens GRCh38/hg38 and Rattus Norvegicus rn6
Supplementary_files_format_and_content: Processed data files are comma-separated files containing DESeq2 normalized read counts.

organism: Rattus norvegicus

source_name: Cardiomyocytes

growth_protocol: HEK293 cells and cardiac fibroblasts (CFs) were grown in DMEM medium containing 10% FBS and 1% Pen/Strep; Bewo cells were maintained in F12K medium containing 10% FBS and 1% Pen/Strep; cardiomyocytes (CMs) were cultured in DMEM meidum containing 10% horse serum, 5% FBS and 1% Pen/Strep.

extract_protocol:
Cellular total RNAs were isolated by using TRIzol™ and then small RNAs were extracted by using mirVana™ miRNA Isolation Kit; extracellular RNAs were extracted by using exoRNeasy Midi kit.
Small RNAs were sequentially treated with DNase I, T4 PNK, and His-AlkB and then subjected to NEBNext® Multiplex Small RNA Library Prep Set for Illumina®.

treatment_protocol: For glucose and serum deprivation (GSD) treatment, HEK and Bewo cells were cultured in glucose free DMEM basal medium for 24 hours; CF and CM cells were exposed to glucose free DEME basal medium for 5 hours. For hypoxia treatment, HEK and Bewo cells were fed with complete medium and maintained in hypoxia chamber with 0.2% oxygen for 24 hours; CF and CM cells were fed with glucose free DMEM basal medium and maintained in hypoxia chamber with 0.2% oxygen for 5 hours. For oxidative stress, HEK and Bewo cells were treated with 0.7mM H2O2 and 1.7 mM H2O2 in complete medium for 24 hours; CF and CM cells were exposed to hypoxia treatment for 5 hours and then fed with complete medium in normal incubator for additional 24 hours. FBS and horse serum used here were extracellular vesicle-depleted by 24 hours of ultracentrifugation.

value: Neonatal Rat Primary Ventricular Cardiomyocytes

tag: strain

value: Sprague Dawley

value: Hypoxia for 5 hours and then reoxygenation for another 24 hours

value: Extracellular Vesicles


title: sd1d_1

description: 1 day of secondary dormancy induction


title: sd1h_2

description: 1h of imbibition in 22°C on water-soaked blue paper

value: 1h imbibition


title: sd1h_1


title: sd3d_2

description: 3 day of secondary dormancy induction


title: sd1h_3


title: sd1d_2

description: 1 day of secondary dormancy induction


title: CM_ReO2_1_EVs

description: small RNAs

tag: cell type


title: sd7dPS_3

description: 7 day of secondary dormancy induction


title: sd3d_1

description: 3 day of secondary dormancy induction


title: sd_dog1_3d_1

description: 3 day of secondary dormancy induction


title: CM_Hypoxia_2_EVs

description: small RNAs

value: Hypoxia with glucose and serum free medium for 5 hours


title: CM_GSD_3_EVs

description: small RNAs

value: Glucose and serum deprivation for 5 hours


title: CM_Hypoxia_1_EVs

description: small RNAs


title: CM_CTRL_1_EVs

description: small RNAs


title: CM_CTRL_2_EVs

description: small RNAs


title: CM_CTRL_3_EVs

description: small RNAs


title: CF_Hypoxia_3_EVs

description: small RNAs

source_name: Cardiac Fibroblasts

value: Neonatal Rat Primary Cardiac Fibroblasts


title: CF_ReO2_1_EVs

description: small RNAs


title: CM_ReO2_2_EVs

description: small RNAs


title: CF_ReO2_3_EVs

description: small RNAs


title: CF_ReO2_2_EVs

description: small RNAs


title: CF_GSD_3_EVs

description: small RNAs


title: CF_Hypoxia_2_EVs

description: small RNAs


title: CF_Hypoxia_1_EVs

description: small RNAs


title: CM_Hypoxia_3_EVs

description: small RNAs


title: CF_GSD_1_EVs

description: small RNAs


title: CM_Re-O2_2

description: small RNAs

value: Cells


title: CF_CTRL_1_EVs

description: small RNAs

value: Untreated


title: CF_GSD_2_EVs

description: small RNAs


title: CM_Hypoxia_1

description: small RNAs


title: CF_CTRL_3_EVs

description: small RNAs


title: CM_Re-O2_3

description: small RNAs


title: CM_Re-O2_1

description: small RNAs


title: CM_GSD_2_EVs

description: small RNAs


title: CM_GSD_1

description: small RNAs


title: CM_GSD_3

description: small RNAs


title: CM_Hypoxia_3

description: small RNAs


title: CM_GSD_1_EVs

description: small RNAs


title: CM_Ctrl_3

description: small RNAs


title: CM_GSD_2

description: small RNAs


title: CM_Ctrl_1

description: small RNAs


title: CF_Re-O2_3

description: small RNAs


title: CF_Re-O2_2

description: small RNAs


title: CF_Re-O2_1

description: small RNAs


title: CF_Hypoxia_3

description: small RNAs


title: CF_GSD_3

description: small RNAs


title: CF_Hypoxia_1

description: small RNAs


title: CM_Hypoxia_2

description: small RNAs


title: CF_Hypoxia_2

description: small RNAs


title: CF_CTRL_2_EVs

description: small RNAs


title: CF_Ctrl_3

description: small RNAs


title: CF_Ctrl_1

description: small RNAs


title: CF_Ctrl_2

description: small RNAs


title: CF_GSD_2

description: small RNAs


title: CF_GSD_1

description: small RNAs


title: PC6.3_Day5_replicate3

city: Helsinki

first: Maria

last: Sokolova

address: Viikinkaari 5

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

data_processing:
RNA-seq data sets were aligned using TopHat2 to version Rnor_6.0 of the Rattus norvegicus genome
Counting aligned reads per genes were performed with HTSeq
Differential expression analysis and Principal components analysis (PCA) were performed with DESeq
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text files include raw counts of sequencing reads for the features of interest for each Sample.

molecule: polyA RNA

growth_protocol: PC6.3 cells were plated to 6 well cell culture plates. PC6.3 cells  were cultured in RPMI-1640 medium (Lonza) supplemented with 10% horse serum (HS; Gibco), 5 % fetal bovine serum (FBS; Gibco), penicillin-streptomycin (Thermo Fisher Scientific) and GlutaMAX (Thermo Fisher Scientific) in 5% CO2 incubator at + 37 °C.

extract_protocol:
Total RNA was extracted with a Nucleospin RNA kit from Macherey-Nagel
NEBNext Ultra Directional RNA Library Prep Kit for Illumina.

treatment_protocol: For differentiation, cells were plated on poly-L-lysine (Merck) and laminin (Merck) coated cell culture plates in full RPMI medium. Next day, medium was replaced to low serum RPMI (RPMI-1640 supplemented with 1% HS and 1% FBS) with 50 ng/ml NGF 2.5S Native Mouse Protein (Gibco) to differentiate cells for desired time.

tag: cell line

value: pheochromocytoma cells

value: 50 ng/ml NGF


title: PC6.3_Day4_replicate4


title: CM_Ctrl_2

description: small RNAs

tag: sample type


title: PC6.3_Day5_replicate1


title: PC6.3_Day4_replicate3


title: PC6.3_Day4_replicate1


title: PC6.3_Day4_replicate2


title: PC6.3_Day3_replicate3


title: PC6.3_Day3_replicate4


title: PC6.3_Day5_replicate2


title: PC6.3_Day2_replicate3


title: PC6.3_Day3_replicate1


title: PC6.3_Day2_replicate4


title: PC6.3_Day3_replicate2


title: PC6.3_Day2_replicate1


title: PC6.3_Day2_replicate2


title: PC6.3_Day1_replicate4


title: PC6.3_Day1_replicate3


title: PC6.3_Day5_replicate4


title: PC6.3_Day1_replicate1


title: PC6.3_Day1_replicate2


title: PC6.3_Day0_replicate4

value: Non-Treated


title: DNA methylation profile for 202093120076_R05C01

type: genomic

city: Exeter

first: Eilis

last: Hannon

address: RILD building

institute: University of Exeter

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
Dasen normalized betas (BDR_processed_signals.csv.gz)
Unmethylated and methylated signal intensities (BDR_raw_Signal.csv.gz)

label: Cy3, Cy5

label_protocol:
500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit (Zymo Research) according to the manufacturer’s standard protocol.
hapten-labeled dideoxynucleotides

extract_protocol: DNA was extracted using a phenol/chloroform method

tag: developmental stage

value: adult

value: brain

tag: brain region

value: Occipital

value: female

tag: cell proportion double negative

tag: cell proportion neun+

tag: cell proportion sox10+


title: PC6.3_Day0_replicate3


title: PC6.3_Day0_replicate2


title: PC6.3_Day0_replicate1


title: DNA methylation profile for 202093120076_R07C01

tag: gender


title: DNA methylation profile for 202093120025_R06C01

value: Prefrontal


title: DNA methylation profile for 202093120076_R06C01

value: male


title: DNA methylation profile for 202073200105_R03C01


title: DNA methylation profile for 202073200105_R04C01


title: DNA methylation profile for 202093120025_R05C01


title: DNA methylation profile for 202093120066_R07C01


title: DNA methylation profile for 202093120063_R05C01


title: DNA methylation profile for 202093120058_R07C01


title: DNA methylation profile for 202093120063_R06C01


title: DNA methylation profile for 202093120058_R08C01


title: DNA methylation profile for 202093120066_R08C01


title: DNA methylation profile for 202093120024_R01C01


title: DNA methylation profile for 202093120057_R07C01


title: DNA methylation profile for 202093120024_R02C01


title: DNA methylation profile for 202093120066_R05C01


title: DNA methylation profile for 202093120076_R08C01


title: DNA methylation profile for 202093120066_R06C01


title: DNA methylation profile for 202093120076_R03C01


title: DNA methylation profile for 202093120045_R04C01


title: DNA methylation profile for 202093120026_R01C01


title: DNA methylation profile for 202093120021_R07C01


title: DNA methylation profile for 202093120026_R02C01


title: DNA methylation profile for 202093120063_R07C01


title: DNA methylation profile for 202093120063_R08C01


title: DNA methylation profile for 202093120066_R03C01


title: DNA methylation profile for 202093120066_R04C01


title: DNA methylation profile for 202093120026_R05C01


title: DNA methylation profile for 202093120057_R03C01


title: DNA methylation profile for 202093120026_R06C01


title: DNA methylation profile for 202093120026_R08C01


title: DNA methylation profile for 202093120057_R04C01


title: DNA methylation profile for 202093120026_R07C01


title: DNA methylation profile for 202093120053_R06C01


title: DNA methylation profile for 202073200090_R05C01


title: DNA methylation profile for 202093120066_R01C01


title: DNA methylation profile for 202093120076_R02C01


title: DNA methylation profile for 202093120076_R01C01


title: DNA methylation profile for 202093120053_R05C01


title: DNA methylation profile for 202093120057_R08C01


title: DNA methylation profile for 202093120066_R02C01


title: DNA methylation profile for 202093120021_R08C01


title: DNA methylation profile for 202073200090_R06C01


title: DNA methylation profile for 202093120057_R01C01


title: DNA methylation profile for 202093120026_R03C01


title: DNA methylation profile for 202093120057_R02C01


title: DNA methylation profile for 202093120024_R04C01


title: DNA methylation profile for 202093120024_R03C01


title: DNA methylation profile for 202093120057_R05C01


title: DNA methylation profile for 202093120026_R04C01


title: DNA methylation profile for 202093120057_R06C01


title: DNA methylation profile for 202093120025_R02C01


title: DNA methylation profile for 202093120065_R04C01


title: DNA methylation profile for 202093120025_R07C01


title: DNA methylation profile for 202093120065_R03C01


title: DNA methylation profile for 202093120025_R08C01


title: DNA methylation profile for 202093120079_R08C01


title: DNA methylation profile for 202093120053_R04C01


title: DNA methylation profile for 202093120065_R01C01


title: DNA methylation profile for 202093120065_R02C01


title: DNA methylation profile for 202093120021_R02C01


title: DNA methylation profile for 202093120021_R01C01


title: DNA methylation profile for 202073200090_R08C01


title: DNA methylation profile for 202073200090_R07C01


title: DNA methylation profile for 202093120024_R07C01


title: DNA methylation profile for 202093120065_R07C01


title: DNA methylation profile for 202093120024_R08C01


title: DNA methylation profile for 202093120065_R08C01


title: DNA methylation profile for 202093120063_R03C01


title: DNA methylation profile for 202093120079_R07C01


title: DNA methylation profile for 202093120063_R04C01


title: DNA methylation profile for 202093120025_R03C01


title: DNA methylation profile for 202093120058_R04C01


title: DNA methylation profile for 202093120063_R01C01


title: DNA methylation profile for 202093120063_R02C01


title: DNA methylation profile for 202093120058_R03C01


title: DNA methylation profile for 202093120053_R03C01


title: DNA methylation profile for 202093120021_R06C01


title: DNA methylation profile for 202093120058_R06C01


title: DNA methylation profile for 202073200105_R07C01


title: DNA methylation profile for 202093120058_R05C01


title: DNA methylation profile for 202093120058_R01C01


title: DNA methylation profile for 202093120058_R02C01


title: DNA methylation profile for 202073200105_R08C01


title: DNA methylation profile for 202093120079_R06C01


title: DNA methylation profile for 202073200090_R03C01


title: DNA methylation profile for 202073200090_R04C01


title: DNA methylation profile for 202093120024_R05C01


title: DNA methylation profile for 202073200105_R06C01


title: DNA methylation profile for 202093120065_R05C01


title: DNA methylation profile for 202093120065_R06C01


title: DNA methylation profile for 202073200105_R01C01


title: DNA methylation profile for 202093120025_R04C01


title: DNA methylation profile for 202073200088_R07C01


title: DNA methylation profile for 202093120053_R08C01


title: DNA methylation profile for 202093120021_R04C01


title: DNA methylation profile for 202093120021_R03C01


title: DNA methylation profile for 202073200081_R02C01


title: DNA methylation profile for 202073200088_R08C01


title: DNA methylation profile for 202073180031_R02C01


title: DNA methylation profile for 202093120024_R06C01


title: DNA methylation profile for 202073200081_R01C01


title: DNA methylation profile for 202093120021_R05C01


title: DNA methylation profile for 202073200105_R02C01


title: DNA methylation profile for 202093120068_R08C01


title: DNA methylation profile for 202073200089_R03C01


title: DNA methylation profile for 202073200089_R07C01


title: DNA methylation profile for 202073200081_R05C01


title: DNA methylation profile for 202073200105_R05C01


title: DNA methylation profile for 202073180031_R01C01


title: DNA methylation profile for 202093120053_R07C01


title: DNA methylation profile for 202073200081_R07C01


title: DNA methylation profile for 202073200081_R08C01


title: DNA methylation profile for 202093120068_R07C01


title: DNA methylation profile for 202073200081_R06C01


title: DNA methylation profile for 202093120068_R03C01


title: DNA methylation profile for 202073200079_R06C01


title: DNA methylation profile for 202073200079_R05C01


title: DNA methylation profile for 202073200089_R08C01


title: DNA methylation profile for 202073200088_R03C01


title: DNA methylation profile for 202093120068_R04C01


title: DNA methylation profile for 202073200079_R04C01


title: DNA methylation profile for 202073200088_R04C01


title: DNA methylation profile for 202073200079_R03C01


title: DNA methylation profile for 202073200077_R03C01


title: DNA methylation profile for 202073200090_R02C01


title: DNA methylation profile for 202073200077_R06C01


title: DNA methylation profile for 202073200090_R01C01


title: DNA methylation profile for 202073200077_R05C01


title: DNA methylation profile for 202073180048_R02C01


title: DNA methylation profile for 202073180018_R05C01


title: DNA methylation profile for 202073200089_R04C01


title: DNA methylation profile for 202073180050_R06C01


title: DNA methylation profile for 202073180018_R06C01


title: DNA methylation profile for 202073200077_R04C01


title: DNA methylation profile for 202073180031_R08C01


title: DNA methylation profile for 202073180048_R01C01


title: DNA methylation profile for 202073200077_R07C01


title: DNA methylation profile for 202073200077_R08C01


title: DNA methylation profile for 202093120045_R08C01


title: DNA methylation profile for 202073180048_R04C01


title: DNA methylation profile for 202073200089_R01C01


title: DNA methylation profile for 202073180050_R07C01


title: DNA methylation profile for 202073200081_R03C01


title: DNA methylation profile for 202073180018_R03C01


title: DNA methylation profile for 202073200079_R02C01


title: DNA methylation profile for 202073180050_R05C01


title: DNA methylation profile for 202073200089_R02C01


title: DNA methylation profile for 202073180018_R07C01


title: DNA methylation profile for 202073180050_R08C01


title: DNA methylation profile for 202073200079_R07C01


title: DNA methylation profile for 202073200079_R08C01


title: DNA methylation profile for 202093120068_R05C01


title: DNA methylation profile for 202093120045_R07C01


title: DNA methylation profile for 202073180031_R07C01


title: DNA methylation profile for 202073180018_R08C01


title: DNA methylation profile for 202073200077_R01C01


title: DNA methylation profile for 202073200078_R01C01


title: DNA methylation profile for 202073180048_R03C01


title: DNA methylation profile for 202073200078_R02C01


title: DNA methylation profile for 202073200081_R04C01


title: DNA methylation profile for 202073200079_R01C01


title: DNA methylation profile for 202073200077_R02C01


title: DNA methylation profile for 202073180018_R04C01


title: DNA methylation profile for 202073180031_R06C01


title: DNA methylation profile for 202073200088_R02C01


title: DNA methylation profile for 202073180048_R05C01


title: DNA methylation profile for 202073180048_R06C01


title: DNA methylation profile for 202073200088_R01C01


title: DNA methylation profile for 202073180031_R04C01


title: DNA methylation profile for 202073180050_R04C01


title: DNA methylation profile for 202073180050_R03C01


title: DNA methylation profile for 202073180031_R05C01


title: DNA methylation profile for 202093120045_R05C01


title: DNA methylation profile for 202093120045_R06C01


title: DNA methylation profile for 202073200089_R05C01


title: DNA methylation profile for 202073200089_R06C01


title: DNA methylation profile for 202073200078_R03C01


title: DNA methylation profile for 202073180050_R02C01


title: DNA methylation profile for 202093120079_R04C01


title: DNA methylation profile for 202073200060_R07C01


title: DNA methylation profile for 202093120045_R03C01


title: DNA methylation profile for 202073210040_R05C01


title: DNA methylation profile for 202073180050_R01C01


title: DNA methylation profile for 202093120079_R02C01


title: DNA methylation profile for 202073200078_R04C01


title: DNA methylation profile for 202073180031_R03C01


title: DNA methylation profile for 202073210040_R06C01


title: DNA methylation profile for 202073200078_R06C01


title: DNA methylation profile for 202093120068_R06C01


title: DNA methylation profile for 202073200078_R05C01


title: DNA methylation profile for 202073200088_R06C01


title: DNA methylation profile for 202073200088_R05C01


title: DNA methylation profile for 202073200060_R01C01


title: DNA methylation profile for 202073200078_R08C01


title: DNA methylation profile for 202073200078_R07C01


title: DNA methylation profile for 202073180018_R01C01


title: DNA methylation profile for 202073210040_R04C01


title: DNA methylation profile for 202093120028_R03C01


title: DNA methylation profile for 202073180018_R02C01


title: DNA methylation profile for 202093120076_R04C01


title: DNA methylation profile for 202073200060_R08C01


title: DNA methylation profile for 202093120079_R03C01


title: DNA methylation profile for 202073210009_R07C01


title: DNA methylation profile for 202073210009_R08C01


title: DNA methylation profile for 202073210045_R01C01


title: DNA methylation profile for 202073210018_R05C01


title: DNA methylation profile for 202073200058_R04C01


title: DNA methylation profile for 202073210009_R02C01


title: DNA methylation profile for 202073200058_R03C01


title: DNA methylation profile for 202073210027_R05C01


title: DNA methylation profile for 202093120027_R02C01


title: DNA methylation profile for 202073200060_R02C01


title: DNA methylation profile for 202073210013_R07C01


title: DNA methylation profile for 202073210008_R01C01


title: DNA methylation profile for 202073210040_R02C01


title: DNA methylation profile for 202093120028_R04C01


title: DNA methylation profile for 202073210008_R02C01


title: DNA methylation profile for 202073210040_R03C01


title: DNA methylation profile for 202073210017_R01C01


title: DNA methylation profile for 202073210017_R05C01


title: DNA methylation profile for 202093120027_R07C01


title: DNA methylation profile for 202073210017_R02C01


title: DNA methylation profile for 202073210017_R03C01


title: DNA methylation profile for 202073210045_R02C01


title: DNA methylation profile for 202073210009_R01C01


title: DNA methylation profile for 202073210017_R06C01


title: DNA methylation profile for 202093120027_R08C01


title: DNA methylation profile for 202073210013_R08C01


title: DNA methylation profile for 202093120027_R01C01


title: DNA methylation profile for 202073210017_R04C01


title: DNA methylation profile for 202073210045_R03C01


title: DNA methylation profile for 202073210040_R01C01


title: DNA methylation profile for 202093120027_R06C01


title: DNA methylation profile for 202093120079_R01C01


title: DNA methylation profile for 202093120027_R03C01


title: DNA methylation profile for 202073200033_R06C01


title: DNA methylation profile for 202073200060_R06C01


title: DNA methylation profile for 202073200060_R05C01


title: DNA methylation profile for 202093120045_R02C01


title: DNA methylation profile for 202093120027_R04C01


title: DNA methylation profile for 202093120028_R01C01


title: DNA methylation profile for 202073210027_R03C01


title: DNA methylation profile for 202093120027_R05C01


title: DNA methylation profile for 202073210027_R04C01


title: DNA methylation profile for 202073210008_R03C01


title: DNA methylation profile for 202073210013_R02C01


title: DNA methylation profile for 202073210008_R04C01


title: DNA methylation profile for 202093120045_R01C01


title: DNA methylation profile for 202073210013_R06C01


title: DNA methylation profile for 202073200033_R05C01


title: DNA methylation profile for 202073210009_R04C01


title: DNA methylation profile for 202073210009_R03C01


title: DNA methylation profile for 202073210027_R07C01


title: DNA methylation profile for 202073210013_R01C01


title: DNA methylation profile for 202093120028_R07C01


title: DNA methylation profile for 202073210018_R04C01


title: DNA methylation profile for 202073210008_R05C01


title: DNA methylation profile for 202073210045_R06C01


title: DNA methylation profile for 202093120028_R08C01


title: DNA methylation profile for 202073200060_R04C01


title: DNA methylation profile for 202073210045_R05C01


title: DNA methylation profile for 202073210013_R05C01


title: DNA methylation profile for 202073210008_R06C01


title: DNA methylation profile for 202073200060_R03C01


title: DNA methylation profile for 202073200058_R08C01


title: DNA methylation profile for 202073210018_R03C01


title: DNA methylation profile for 202093120028_R06C01


title: DNA methylation profile for 202093120028_R05C01


title: DNA methylation profile for 202073210013_R03C01


title: DNA methylation profile for 202073210013_R04C01


title: DNA methylation profile for 202073210040_R08C01


title: DNA methylation profile for 202073210008_R07C01


title: DNA methylation profile for 202073210008_R08C01


title: DNA methylation profile for 202073210027_R08C01


title: DNA methylation profile for 202073210017_R07C01


title: DNA methylation profile for 202073200058_R07C01


title: DNA methylation profile for 202073210017_R08C01


title: DNA methylation profile for 202073210018_R01C01


title: DNA methylation profile for 202073210040_R07C01


title: DNA methylation profile for 202073210018_R02C01


title: DNA methylation profile for 202073210018_R08C01


title: DNA methylation profile for 202093120028_R02C01


title: DNA methylation profile for 202073210018_R07C01


title: DNA methylation profile for 202073210027_R02C01


title: DNA methylation profile for 202073210045_R04C01


title: DNA methylation profile for 202073200043_R01C01


title: DNA methylation profile for 202073210009_R06C01


title: DNA methylation profile for 202073200043_R02C01


title: DNA methylation profile for 202073210009_R05C01


title: DNA methylation profile for 202073180006_R08C01


title: DNA methylation profile for 202073180041_R05C01


title: DNA methylation profile for 202073210027_R01C01


title: DNA methylation profile for 202073180041_R06C01


title: DNA methylation profile for 202073200045_R01C01


title: DNA methylation profile for 202073180041_R08C01


title: DNA methylation profile for 202073180012_R06C01


title: DNA methylation profile for 202073180041_R07C01


title: DNA methylation profile for 202073200043_R03C01


title: DNA methylation profile for 202073200058_R02C01


title: DNA methylation profile for 202073180010_R02C01


title: DNA methylation profile for 202073210045_R08C01


title: DNA methylation profile for 202073200045_R02C01


title: DNA methylation profile for 202073210045_R07C01


title: DNA methylation profile for 202073180012_R05C01


title: DNA methylation profile for 202073200043_R04C01


title: DNA methylation profile for 202073180010_R01C01


title: DNA methylation profile for 202073180041_R01C01


title: DNA methylation profile for 202073180006_R07C01


title: DNA methylation profile for 202073200045_R08C01


title: DNA methylation profile for 202073200044_R03C01


title: DNA methylation profile for 203734300117_R03C01


title: DNA methylation profile for 202073180041_R02C01


title: DNA methylation profile for 202073200044_R04C01


title: DNA methylation profile for 202073200045_R07C01


title: DNA methylation profile for 203734300117_R04C01


title: DNA methylation profile for 202073180048_R08C01


title: DNA methylation profile for 202073200043_R05C01


title: DNA methylation profile for 202073200007_R01C01


title: DNA methylation profile for 202073180010_R08C01


title: DNA methylation profile for 202073200003_R05C01


title: DNA methylation profile for 202073180010_R07C01


title: DNA methylation profile for 202073200007_R02C01


title: DNA methylation profile for 202073210027_R06C01


title: DNA methylation profile for 202073200058_R01C01


title: DNA methylation profile for 202073200007_R05C01


title: DNA methylation profile for 202073200003_R06C01


title: DNA methylation profile for 202073180012_R03C01


title: DNA methylation profile for 202073180010_R06C01


title: DNA methylation profile for 202073180010_R05C01


title: DNA methylation profile for 203734300115_R05C01


title: DNA methylation profile for 202073180012_R04C01


title: DNA methylation profile for 202073200007_R07C01


title: DNA methylation profile for 203734300117_R07C01


title: DNA methylation profile for 203734300115_R06C01


title: DNA methylation profile for 202073200045_R03C01


title: DNA methylation profile for 202073200007_R04C01


title: DNA methylation profile for 202073200043_R06C01


title: DNA methylation profile for 202073200007_R08C01


title: DNA methylation profile for 203734300117_R08C01


title: DNA methylation profile for 202073180012_R08C01


title: DNA methylation profile for 202073200033_R08C01


title: DNA methylation profile for 202073200007_R03C01


title: DNA methylation profile for 202073200003_R01C01


title: DNA methylation profile for 202073200003_R02C01


title: DNA methylation profile for 202073200033_R01C01


title: DNA methylation profile for 202073200033_R02C01


title: DNA methylation profile for 202073200033_R07C01


title: DNA methylation profile for 202073180012_R07C01


title: DNA methylation profile for 202073180006_R02C01


title: DNA methylation profile for 202073200044_R07C01


title: DNA methylation profile for 202073180006_R04C01


title: DNA methylation profile for 202073200044_R02C01


title: DNA methylation profile for 202073200044_R08C01


title: DNA methylation profile for 203734300115_R03C01


title: DNA methylation profile for 202073200033_R03C01


title: DNA methylation profile for 202073200007_R06C01


title: DNA methylation profile for 202073200043_R08C01


title: DNA methylation profile for 202073180006_R03C01


title: DNA methylation profile for 202073200045_R04C01


title: DNA methylation profile for 202073180010_R04C01


title: DNA methylation profile for 202073180006_R01C01


title: DNA methylation profile for 202073200044_R01C01


title: DNA methylation profile for 203734300115_R04C01


title: DNA methylation profile for 202073180012_R02C01


title: DNA methylation profile for 202073200044_R05C01


title: DNA methylation profile for 202073180041_R03C01


title: DNA methylation profile for 203205080107_R01C01


title: DNA methylation profile for 202073200043_R07C01


title: DNA methylation profile for 202073200044_R06C01


title: DNA methylation profile for 203205080107_R02C01


title: DNA methylation profile for 203205080127_R07C01


title: DNA methylation profile for 202073180041_R04C01


title: DNA methylation profile for 202410160152_R01C01


title: DNA methylation profile for 202410160152_R02C01


title: DNA methylation profile for 202073200033_R04C01


title: DNA methylation profile for 202073180010_R03C01


title: DNA methylation profile for 202073180012_R01C01


title: DNA methylation profile for 203734300115_R07C01


title: DNA methylation profile for 203205080172_R01C01


title: DNA methylation profile for 203734300115_R08C01


title: DNA methylation profile for 203205080154_R03C01


title: DNA methylation profile for 203205080127_R08C01


title: DNA methylation profile for 203205080154_R04C01


title: DNA methylation profile for 203205080127_R03C01


title: DNA methylation profile for 203205080092_R04C01


title: DNA methylation profile for 203205080092_R01C01


title: DNA methylation profile for 203205080127_R04C01


title: DNA methylation profile for 203205080092_R02C01


title: DNA methylation profile for 203205080092_R06C01


title: DNA methylation profile for 203205080092_R03C01


title: DNA methylation profile for 203205080152_R04C01


title: DNA methylation profile for 203205080092_R07C01


title: DNA methylation profile for 202410160215_R01C01


title: DNA methylation profile for 203203030022_R07C01


title: DNA methylation profile for 203205080172_R02C01


title: DNA methylation profile for 202410160100_R05C01


title: DNA methylation profile for 203203030022_R08C01


title: DNA methylation profile for 202410160100_R06C01


title: DNA methylation profile for 203205080152_R03C01


title: DNA methylation profile for 202410160215_R02C01


title: DNA methylation profile for 202410000162_R07C01


title: DNA methylation profile for 202410160215_R05C01


title: DNA methylation profile for 203203140194_R07C01


title: DNA methylation profile for 203205080092_R05C01


title: DNA methylation profile for 203203140194_R08C01


title: DNA methylation profile for 202410160113_R06C01


title: DNA methylation profile for 202410000162_R08C01


title: DNA methylation profile for 203212860046_R02C01


title: DNA methylation profile for 202410160113_R05C01


title: DNA methylation profile for 202410160215_R06C01


title: DNA methylation profile for 202410160152_R08C01


title: DNA methylation profile for 202410160152_R07C01


title: DNA methylation profile for 202410160156_R02C01


title: DNA methylation profile for 203203140137_R04C01


title: DNA methylation profile for 203212860046_R08C01


title: DNA methylation profile for 203212860046_R07C01


title: DNA methylation profile for 202410160285_R07C01


title: DNA methylation profile for 202410160100_R03C01


title: DNA methylation profile for 202410160285_R08C01


title: DNA methylation profile for 202410160100_R04C01


title: DNA methylation profile for 203203030024_R03C01


title: DNA methylation profile for 203203030024_R04C01


title: DNA methylation profile for 202410160245_R02C01


title: DNA methylation profile for 202410160245_R01C01


title: DNA methylation profile for 202410160284_R03C01


title: DNA methylation profile for 203212860023_R01C01


title: DNA methylation profile for 203212860023_R02C01


title: DNA methylation profile for 202410160284_R04C01


title: DNA methylation profile for 203212860046_R06C01


title: DNA methylation profile for 203203030022_R03C01


title: DNA methylation profile for 203203030024_R07C01


title: DNA methylation profile for 203203030022_R04C01


title: DNA methylation profile for 202410160285_R05C01


title: DNA methylation profile for 203212860048_R07C01


title: DNA methylation profile for 203203030024_R05C01


title: DNA methylation profile for 203203030024_R06C01


title: DNA methylation profile for 203203030024_R08C01


title: DNA methylation profile for 203203030024_R01C01


title: DNA methylation profile for 203203030023_R08C01


title: DNA methylation profile for 203203030024_R02C01


title: DNA methylation profile for 203203140137_R03C01


title: DNA methylation profile for 202410160113_R01C01


title: DNA methylation profile for 202410160113_R02C01


title: DNA methylation profile for 203212860023_R08C01


title: DNA methylation profile for 203212860023_R07C01


title: DNA methylation profile for 202410160113_R07C01


title: DNA methylation profile for 202410160113_R08C01


title: DNA methylation profile for 203203030023_R05C01


title: DNA methylation profile for 203212860046_R05C01


title: DNA methylation profile for 203203030023_R06C01


title: DNA methylation profile for 203203140115_R05C01


title: DNA methylation profile for 202410160136_R06C01


title: DNA methylation profile for 202410160136_R05C01


title: DNA methylation profile for 202410160285_R06C01


title: DNA methylation profile for 203203140115_R06C01


title: DNA methylation profile for 202410160284_R01C01


title: DNA methylation profile for 203203030023_R01C01


title: DNA methylation profile for 203212860048_R08C01


title: DNA methylation profile for 203203140165_R04C01


title: DNA methylation profile for 203203030023_R07C01


title: DNA methylation profile for 202410160284_R02C01


title: DNA methylation profile for 203203030023_R02C01


title: DNA methylation profile for 202410000162_R05C01


title: DNA methylation profile for 202410000162_R06C01


title: DNA methylation profile for 202410160100_R07C01


title: DNA methylation profile for 203203140194_R02C01


title: DNA methylation profile for 202410160100_R08C01


title: DNA methylation profile for 202410160245_R08C01


title: DNA methylation profile for 203203140137_R01C01


title: DNA methylation profile for 202410160245_R07C01


title: DNA methylation profile for 203203140165_R03C01


title: DNA methylation profile for 202410160156_R05C01


title: DNA methylation profile for 203203140115_R01C01


title: DNA methylation profile for 203203140137_R02C01


title: DNA methylation profile for 202410160285_R04C01


title: DNA methylation profile for 202410160285_R02C01


title: DNA methylation profile for 203203140189_R05C01


title: DNA methylation profile for 203203140137_R07C01


title: DNA methylation profile for 203203140115_R02C01


title: DNA methylation profile for 202410160245_R04C01


title: DNA methylation profile for 202410160285_R01C01


title: DNA methylation profile for 202410160284_R08C01


title: DNA methylation profile for 202410160245_R03C01


title: DNA methylation profile for 203203140165_R01C01


title: DNA methylation profile for 203212860048_R03C01


title: DNA methylation profile for 203212860046_R03C01


title: DNA methylation profile for 203203140194_R01C01


title: DNA methylation profile for 202410160284_R07C01


title: DNA methylation profile for 203212860046_R04C01


title: DNA methylation profile for 203212860066_R08C01


title: DNA methylation profile for 203203140165_R02C01


title: DNA methylation profile for 203212860066_R04C01


title: DNA methylation profile for 203212860048_R06C01


title: DNA methylation profile for 203203140194_R04C01


title: DNA methylation profile for 203212860048_R05C01


title: DNA methylation profile for 202410160285_R03C01


title: DNA methylation profile for 203212860066_R03C01


title: DNA methylation profile for 203212860066_R01C01


title: DNA methylation profile for 203212860066_R02C01


title: DNA methylation profile for 202410160284_R05C01


title: DNA methylation profile for 203212860048_R04C01


title: DNA methylation profile for 202410160185_R03C01


title: DNA methylation profile for 202410160284_R06C01


title: DNA methylation profile for 202410160185_R04C01


title: DNA methylation profile for 202410160226_R06C01


title: DNA methylation profile for 202410160185_R06C01


title: DNA methylation profile for 202410160226_R05C01


title: DNA methylation profile for 202410160185_R05C01


title: DNA methylation profile for 202410160136_R07C01


title: DNA methylation profile for 203203140115_R03C01


title: DNA methylation profile for 203205080012_R03C01


title: DNA methylation profile for 202410160113_R03C01


title: DNA methylation profile for 203203140115_R04C01


title: DNA methylation profile for 202410160152_R06C01


title: DNA methylation profile for 202410160113_R04C01


title: DNA methylation profile for 202410160152_R05C01


title: DNA methylation profile for 203203140115_R07C01


title: DNA methylation profile for 203203140194_R03C01


title: DNA methylation profile for 202410160156_R07C01


title: DNA methylation profile for 202410160156_R08C01


title: DNA methylation profile for 203203140194_R05C01


title: DNA methylation profile for 203203140189_R01C01


title: DNA methylation profile for 203203140194_R06C01


title: DNA methylation profile for 203203140189_R07C01


title: DNA methylation profile for 202410160136_R03C01


title: DNA methylation profile for 203203140165_R05C01


title: DNA methylation profile for 203212860066_R07C01


title: DNA methylation profile for 203203030022_R01C01


title: DNA methylation profile for 203203030022_R02C01


title: DNA methylation profile for 203212860023_R04C01


title: DNA methylation profile for 202410160136_R01C01


title: DNA methylation profile for 202410160136_R02C01


title: DNA methylation profile for 202410160136_R04C01


title: DNA methylation profile for 202410160185_R07C01


title: DNA methylation profile for 202410160185_R08C01


title: DNA methylation profile for 202410160152_R04C01


title: Chicken fibroblasts, ARV_24

city: Beijing

first: Linyi

last: Zhou

address: No. 2, Yuanmingyuan West Road, Haidian District, Beijing, China

country: China

institute: China Agricultural University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: mm22
Supplementary_files_format_and_content: Excel,expression profiles;txt, significant KEGG

organism: Gallus gallus

source_name: Chicken fibroblasts

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: Chicken fibroblasts

tag: infection


title: Chicken fibroblasts, NC_24

value: avian reovirus


title: DNA methylation profile for 202410000162_R03C01


title: DNA methylation profile for 202410000162_R04C01


title: DNA methylation profile for 203203140165_R06C01


title: DNA methylation profile for 203203140165_R07C01


title: DNA methylation profile for 202410160029_R07C01


title: AZD4785

city: Liverpool

first: Ian

last: Prior

address: Crown Street

department: Molecular Physiology and Cell Signalling

institute: University of Liverpool

data_processing:
Processing and analysis performed by BGI Genomics that included using some BGI informatics software.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BGI SOAPnuke software (parameter- remove reads in which unknown bases are more than 5%)
Trimmed sequence reads were mapped to GRCh38/hg38 using HISAT2 v2.0.4
StringTie v1.0.4 was used to reconstruct transcripts (parameters: -f 0.3 -j 3 -c 5 -g 100 -s 10000 -p 8). Cuffcompare cufflinks tool v2.2.1 to identify novel transcripts (parameters: -p 12). CPC v0.9-r2 to predict coding potential of novel transcripts (parameters: default)
Clean reads were mapped using Bowtie2 v1.2.12 (parameters: default) and gene expression levels calculated with RSEM v1.2.12 (parameters: default).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: H358 cells maintained in RPMI, 10% fetal bovine serum + IC90 concentrations of each inhibitor for 90 days were analysed. Media changes were carried out every 2-3 days for small molecule inhibitors and every 4-5 days for AZD4785 until the cells reached 80% confluency.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries. A Nanodrop 1000 spectrophotometer was used to assess RNA purity and concentration. RNA integrity was measured using the RNA 6000 Nano Kit (Agilent) according to the manufacturer’s instructions and samples run on the Agilent 2100 Bioanalyzer
RNA libraries for RNA-seq were prepared as follows. The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo- attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe- Anchor Synthesis Sequencing Method.

treatment_protocol: Long term incubation over 90 days. 2.63 microM ARS1323 (KRASG12C inhibitor), 87 nM selumetinib (MEK inhibitor), 2.34 microM AZD4785 (antisense KRAS). 1 replicate of each. Vehicle controls - DMSO for all inhibitors except AZD4785 where an equivalent volume of PBS was dosed.

value: lung cancer cell line

value: WT

value: non-gene edited but harbour KRAS G12C

value: 2.34 microM AZD4785, 90 days


title: DNA methylation profile for 202410160245_R05C01


title: ARS1323

value: 2.63 microM ARS1323, 90 days


title: DNA methylation profile for 202410160245_R06C01


title: DNA methylation profile for 203203030022_R06C01


title: PBS control

value: vehicle control with PBS


title: DNA methylation profile for 202410160215_R07C01


title: DNA methylation profile for 203212860023_R03C01


title: DMSO control

value: vehicle control with DMSO


title: C57BL, V1 cortex, shCSB/shNDN, replicate 1

city: Guangzhou

first: Yuming

last: Wang

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

institute: Guangzhou medical university

data_processing:
FastQC was conducted for Quality control (QC) of RNA-seq reads
Trimming was performed by seqtk for known Illumina TruSeq adapter sequences, poor reads, and ribosomal RNA reads
Trimmed reads were mapped to the Mus musculus reference genome by the Hisat 2(version:2.0.4)
String Tie(version:1.3.0) was performed for each gene count from trimmed reads
Gene counts were normalized by trimmed mean of M-values, and fragments per kilobase of transcript per million mapped reads (FPKM) in Perl script
Assembly: GRCm39
Supplementary files format and content: excel file includes FPKM values for all samples

source_name: cortex V1 region

extract_protocol:
RNA was harvested using Rneasy Lipid Tissue Mini Kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA sample Preparation Kits (Illumina) following manufacturer's protocols.

value: cortex V1 region

tag: Sex

tag: age

value: 9 weeks

value: injected with AAV-shCSB/shNDN in the V1 cortex


title: DNA methylation profile for 202410160215_R03C01

value: adult

tag: tissue

value: brain


title: DNA methylation profile for 202410160215_R08C01

value: female


title: C57BL, V1 cortex, shCSB/shNDN, replicate 2


title: DNA methylation profile for 202410160215_R04C01

value: Prefrontal


title: Selumetinib

value: 87 nM selumetinib, 90 days


title: DNA methylation profile for 202410160152_R03C01

value: Occipital


title: DNA methylation profile for 201508110045_R03C01

value: male


title: DNA methylation profile for 201438350114_R08C01


title: C57BL, V1 cortex, shCSB, replicate 2

value: injected with AAV-shCSB in the V1 cortex


title: C57BL, V1 cortex, shControl, replicate 1

value: injected with AAV-shControl in the V1 cortex


title: C57BL, V1 cortex, shControl, replicate 2


title: C57BL, V1 cortex, shCSB, replicate 1


title: DNA methylation profile for 201414140087_R07C01


title: DNA methylation profile for 203203030022_R05C01


title: May2021_mAECs_PTBP1_CRISPRKO_TNF

city: Farmington

first: Patrick

middle: A

last: Murphy

state: CT

address: 263 Farmington Ave

department: Center for Vascular Biology

institute: University of Connecticut Health Center

data_processing:
Paired end FASTQ reads were aligned to mouse transcriptome using Whippet, generating an assessment of expression level (TpM) and splicing.
Assembly: M23 (Gencode)
Supplementary files format and content: processed data file  (Whippet TpM)
Supplementary files format and content: processed data file  (Whippet Psi)
Supplementary files format and content: processed data file  (RSEM)

growth_protocol: Mouse aortic cell line (Fn AB+/- from PMID: 33207933), immortalized with TetOn-SV40 was grown in 10%FBS or Fbessence in low glucose DMEM with 2ug/mL doxycycline during expansion.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Cells were removed from doxy, and plated in 10% FBS/DMEM
Some cells were treated with 30ng/mL TNFalpha

value: aortic endothelial

value: PTBP1 KO

value: TNF stimulation


title: DNA methylation profile for 201414140087_R08C01


title: May2021_mAECs_PTBP1_CRISPRKO_hPTBP1_cDNA_Rescue_TNF

value: PTBP1 Rescue


title: May2021_mAECs_TNF

value: WT


title: DNA methylation profile for 201438350093_R06C01


title: DNA methylation profile for 201438350093_R05C01


title: May2021_mAECs_PTBP1_CRISPRKO


title: DNA methylation profile for 201508110045_R06C01


title: DNA methylation profile for 201508110045_R05C01


title: DNA methylation profile for 201438350036_R04C01


title: May2021_mAECs


title: March2022_primary_mAEC_control_male_TNFtreated

data_processing:
Paired end FASTQ reads were aligned to mouse transcriptome using Whippet, generating an assessment of expression level (TpM) and splicing.
Paired end FASTQ reads were also aligned to mouse transcriptome (mm9) using STAR, generating bam files for analysis as well as transcript analysis by RSEM (gene and isoform expression)
Assembly: M23 (Gencode)
Supplementary files format and content: processed data file  (Whippet TpM)
Supplementary files format and content: processed data file  (Whippet Psi)
Supplementary files format and content: processed data file  (RSEM)

source_name: primary

growth_protocol: Primary mouse aortic endothelial cells were derived by collagenase digestion of aorta lumen, and plated onto collagen I coated plates and cultured with ATCC +VEGF endothelial media kit and primocin in 5% oxygen and 5% carbon dioxide.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
After 4 days in culture, cells were treated (or not) with 30ng/mL TNFalpha in 10% mouse serum in DMEM for 24hrs.
Aortic endothelial cells were trypsinzed briefly and sorted based on CD45negative and Icam2+ and Cd31+

value: primary


title: DNA methylation profile for 201438350036_R03C01


title: March2022_primary_mAEC_control_male


title: DNA methylation profile for 201508110054_R01C01


title: March2022_primary_mAEC_PTBP1_ECKO_male_TNFtreated

value: PTBP ECKO


title: March2022_primary_mAEC_PTBP1_ECKO_male


title: March2022_primary_mAEC_control_female_TNFtreated


title: DNA methylation profile for 201508110054_R02C01


title: DNA methylation profile for 201438350109_R06C01


title: DNA methylation profile for 201438350109_R05C01


title: DNA methylation profile for 201438350109_R08C01


title: DNA methylation profile for 201508110010_R08C01


title: May2021_mAECs_PTBP1_CRISPRKO_hPTBP1_cDNA_Rescue


title: March2022_primary_mAEC_PTBP1_ECKO_female


title: DNA methylation profile for 201438350109_R07C01


title: March2022_primary_mAEC_PTBP1_ECKO_female_TNFtreated


title: DNA methylation profile for 201414140176_R04C01


title: DNA methylation profile for 201414140176_R03C01


title: DNA methylation profile for 201525200030_R04C01


title: DNA methylation profile for 201525200030_R03C01


title: IL2v_PDL1_2 Bulk RNA-seq

extract_protocol:
RNA extracted using qiagen column
Nugen Ovation V2

value: Spleen

value: DbGP33+ CD8+ T cells


title: DNT cells, Control-3

first: sun

middle: xiao

last: jing

address: NO.95 yongan road

institute: Beijing friendship hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text file includes Count values for each Sample

source_name: Control double negative T cells

growth_protocol: Preparing DNT cells by in vitro conversion of wild type mouse-derived CD4+ cells, then these converted DNT cells (CD3+NK1.1-CD4-CD8-) were sorted using FACS Aria II, and then stimulated with or without IL-33 (50ng/ml) for 2 days.

extract_protocol:
Double negative cells treated with or without IL-33 for 48h, then RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Converted DNT cells were stimulated with or without IL-33 (50ng/ml) for 48h

value: spleen

value: double negative T cells

value: adult

value: anti-CD3/CD28 beads 48h in vitro

tag: time


title: DNT cells, IL-33-2

source_name: IL-33 cocultured double negative Tcells

value: anti-CD3/CD28 beads and IL-33 (50ng/ml) 48h in vitro


title: DNT cells, Control-2


title: DNT cells, IL-33-1


title: DNA methylation profile for 201414140176_R05C01

value: brain

value: Prefrontal

value: male


title: DNA methylation profile for 201508110010_R07C01


title: DNT cells, IL-33-3


title: DNA methylation profile for 201414140176_R06C01

value: Occipital


title: IL2wt_PDL1_2 Bulk RNA-seq


title: aPDL1_1 Bulk RNA-seq


title: DNA methylation profile for 201438350049_R03C01

value: female


title: DNA methylation profile for 201525200076_R02C01


title: DNA methylation profile for 201438350049_R04C01


title: IL2wt_PDL1_1 Bulk RNA-seq


title: DNT cells, Control-1


title: untx_2 Bulk RNA-seq

value: Untreated


title: DNA methylation profile for 201525200079_R04C01


title: untx_1 Bulk RNA-seq


title: DNA methylation profile for 201525200079_R03C01


title: naive_2 Bulk RNA-seq

value: CD44lo CD8+ T cells

value: Uninfected


title: naive_1 Bulk RNA-seq


title: DNA methylation profile for 201525200102_R04C01


title: March2022_primary_mAEC_control_female

value: primary

value: aortic endothelial

tag: genotype

value: WT


title: epithelial ciliated cells, Cal09-sfGFP infected mice, 3 dpi, infected

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

library_source: transcriptomic single cell

data_processing:
Basecalls: CellRanger mkfastq (version 3.1.0)
Alignment: CellRanger count (version 3.1.0)
Resulting raw count maxtrix was filtered for contaminating mRNA using the R pipeline SoupX (version 1.5.2)
The filtered count matrix was then imported into Seurat (version 4.0.4)
Assembly: custom concatenated mm10 and Cal09-sfGFP
Supplementary files format and content: Normalized counts for cells includded in analyses

source_name: respiratory epithelium

extract_protocol:
Mice were anesthetized with ketamine-xylazine prior to cervical dislocation. The lungs were perfused with PBS then inflated with 1.5 mL of 1:1 mixture of dispase and 1% low-melt agarose. Lungs were removed then incubated in dispase for 45 minutes at room temp. Lungs were finely minced with a razor blade then pipetted vigorously using a 5 mL serological pipette before being filtered (70 um filter). Red blood cells were lysed with 1x RBC lysis buffer and then remaining cells were washed with 2%BSA in PBS. Single cell suspensions from 2 mice (of the same infection status and timepoint) were pooled prior to sorting on a BD DiVA.
Sorted cells were prepared for library generation (10x Genomics) according to manufacturers protocols.

treatment_protocol: Mice were treated with 40 uL PBS or Cal09-sfGFP intranasally 1-3 days prior to tissue collection.

value: respiratory epithelium

tag: fluorescent marker

value: tdTomato+GFP+

value: ciliated cell

tag: treatment

value: 28,000 PFU Cal09-sfGFP


title: IL2v_PDL1_1 Bulk RNA-seq

value: Spleen

tag: cell type

value: DbGP33+ CD8+ T cells


title: epithelial ciliated cells, Cal09-sfGFP infected mice, 3 dpi, bystander

value: tdTomato+GFP-


title: DNA methylation profile for 201525200076_R01C01

value: adult

value: brain

value: Prefrontal


title: DNA methylation profile for 201525200102_R03C01

value: female


title: DNA methylation profile for 201525200125_R02C01

value: Occipital

value: male


title: DNA methylation profile for 201525200066_R08C01


title: DNA methylation profile for 201438350116_R01C01


title: DNA methylation profile for 201525200125_R01C01


title: epithelial ciliated cells, Cal09-sfGFP infected mice, 1 dpi, bystander


title: epithelial ciliated cells, Cal09-sfGFP infected mice, 2 dpi, infected


title: aPDL1_2 Bulk RNA-seq


title: DNA methylation profile for 201438350116_R02C01


title: epithelial ciliated cells, Cal09-sfGFP infected mice, 2 dpi, bystander


title: epithelial ciliated cells, Cal09-sfGFP infected mice, 1 dpi, infected


title: DNA methylation profile for 201525200102_R06C01


title: DNA methylation profile for 201525200036_R02C01


title: DNA methylation profile for 201438350154_R04C01


title: DNA methylation profile for 201438350154_R03C01


title: DNA methylation profile for 201525200066_R07C01


title: DNA methylation profile for 201525200066_R03C01


title: LM21

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

data_processing:
Fastq files were aligned to the mm39 genome using STAR 2.7.9a using --outSAMtype BAM --outSAMunmapped Within --outSAMattributes Standard
Quantification was carried out using featureCounts 1.6.2 using -p -B -C -Q 10 --primary -s 0 as parameters
Differential analysis was carried out using DESeq2 1.32.0 using design~=condition and standard subsequent commands
Normalisation was performed using variance stabilisation transformation (vst)
Assembly: mm39
Supplementary files format and content: Tab-delimited text file containing variance stabilized transformed expression values

source_name: Organoid-derived CRC liver metastasis

growth_protocol: APTAK organoids are tumor organoids that are devoid of Apc, Tp53, Tgfbr2 and express constitutively active Kras (KrasG12D) and an activated/myristoilated isoform of Akt1. The organoids are a gift from F. Greten, Frankfurt. APTAK tumor organoids were maintained in basal medium (Advanced DMEM-F12 supplemented with penicillin/streptomycin, HEPES 10mmol/l (Invitrogen), Glutamax 1x (Invitrogen), N2 1x (Gibco), B27 1x (Gibco), and N343 Acetylcysteine 1mmol/l (Sigma)) supplemented with Hygromycin (200 ╡g/ml) and puromycin (2 ╡g/ml). The organoids were subcultured in Matrigel every 5-7 days. The APTAK organoids were isolated from a colon of p53flox/flox::Tgfbr2flox/flox mouse. The established organoids harbor loxP sites flanking exon4 of the TGFBR2 gene and Intron 1 and 10 of the TP53 gene. The APC knock out was introduced using CRISPR/Cas9 transgenesis and confirmed by Western Blotting. The organoids were transfected with Cre-IRES-puroR plasmid (Addgene #30205) that encode Cre recombinase to ablate Tgfbr2 and p53. Kras gain of function was obtained by overexpressing the constitutive active version of the murine KRAS gene KRASG12D (cloned in Addgene plasmid #111164) by retroviral transduction. Myrisilated Akt1 was obtained by overexpression the active form of Akt1 (cloned in Addgene plasmid #) by retroviral transduction. Human tumor organoids were cultured in Wnt3a, R-spondin and Noggin conditioned basal medium (Advanced DMEM-F12 supplemented with penicillin/streptomycin, HEPES 10mmol/l (Invitrogen), Glutamax 1x (Invitrogen), N2 1x (Gibco), B27 1x (Gibco), and N-Acetylcysteine 1mmol/l (Sigma)) supplemented with EGF.

extract_protocol:
RNA isolation from tumor tissue was performed with Trizol according to the manufacturer protocol.
Libraries were generated using the Illumina TruSeq protocol according to manufacturer?s instructions.

treatment_protocol: In matrigel grown APTAK organoids were dissociated into a single-cell suspension by mechanical disruption followed by enzymatic digestion for 20 minutes at 37░C using TrypLE (Gibco) and were washed once in ice-cold PBS. Single cells were then resuspended in an ice- cold Type I collagen/5x Collagen neutralization Buffer (4:1 (vol/vol) ratio) with a concentration of 150.000 cells/10 ╡l. The 5x Collagen neutralization buffer is composed of 2.5 g alpha MEM powder (5x) and 2 % (wt/vol) NAHCO3 in 45 ml Aqua dest. and 5 ml of 1M HEPES and set to pH 7.5. 10 ╡l domes of collagen were plated in 6 well plates. The domes polymerize for 45 minutes at 37 ░C. Afterwards basal medium (Advanced DMEM-F12 supplemented with penicillin/streptomycin, HEPES 10mmol/l (Invitrogen), Glutamax 1x (Invitrogen), N2 1x (Gibco), B27 1x (Gibco), and N-Acetylcysteine 1mmol/l (Sigma)) supplemented with Hygromycin and puromycin were added. The collagen domes were cultured overnight till transplantation. At the day of transplantation the mice were shaved and anesthetized with 2.5% (vol/vol) isoflurane. Analgesia was guaranteed by intraperitoneal injections with buprenorphine. The mouse is placed on its back on a heating pad and legs were fixed with leukoplast. Isoflurane was lowered to 1.8 % (vol/vol). A 10 ? 15 mm incision was made along the linea alba to open the abdomen. The cecum was placed on a wet sterile gauze. A 3 ? 4 mm incision through the cecal serosa is made at the end of the cecum in an area without vessels. The serosa was seperated from the submucosal layer and a deep pocket of about 1 cm length was performed. The pocket was enlarged to the size that the collagen dome could be deeply embedded in it. The collagen dome was placed under the serosa in the pocket and the serosa was tightly closed above the collagen dome securing the collagen dome to be tightly embedded in its pocket. The incision in the serosa was covered with a 20 x 5 mm piece of Seprafilm (Baxter). The cecum was carefully placed back in the abdomen. The peritoneum and abdominal wall are seperately closed by a continuous suture. The mice were placed on drinking water supplemented with metamizole (5 mg/ml) for 3 days.

tag: disease state

value: colorectal cancer (CRC)

value: Organoid-derived CRC liver metastasis


title: LM18


title: DNA methylation profile for 201438350124_R06C01


title: DNA methylation profile for 201525200066_R04C01


title: LM4


title: DNA methylation profile for 201438350114_R05C01


title: LM8


title: epithelial ciliated cells, mock infected mice

description: mock

value: tdTomato+

value: PBS


title: DNA methylation profile for 201525200125_R08C01


title: DNA methylation profile for 201438350107_R08C01


title: AB14156

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: MARS

data_processing:
bcl2fastq/2.20.0.422
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
paired-end (read2 used to read cell and molecule barcodes only)
Assembly: mm10
Supplementary files format and content: Tab-separated UMI matrix files

source_name: Whole brain

extract_protocol:
Mice were euthanized using an overdose of ketamine-xylazine, followed by transcardial perfusion with cold PBS, and whole brains were excised. Tissues were chopped into small pieces and subjected to 30 minutes of enzymatic digestion using papain (Worthington, LS003127) in 37oC, followed by manual trituration using a 5ml pipette and filtering through a 70μm cell strainer. Cells were pelleted at 800g for 5 min in 4oC and then suspended in ovomucoid protease inhibitor (Worthington, LS003086) solution to stop papain activity. Cells were pelleted again in 600g, 5 min, 4oC, washed, and myelin debris was removed by 30% Percoll gradient (GE healthcare, 17-0891-01). Then, cells were pelleted and washed again and subjected to 20 min Fc block (1:200), following 30 min cell surface staining. Immediately before FACS, cells were washed, filtered through a 70μm cell strainer, suspended in sorting buffer (PBS supplemented with 0.2mM EDTA pH8 and 0.5% BSA), and DAPI was added. Samples were kept on ice at all times except for enzymatic digestion. Cell populations were sorted using FACS-AriaIII or FACSymphony-S6 and FACS DIVA software (BD Biosciences, San Jose, CA). For the sorting of all the non-immune populations, samples were gated for CD45- (APC, clone 30F-11, 17-0451-82, eBioscience or 103115, BioLegend, 1:200), while excluding debris (FSC-A vs. SSC-A), dead cells (DAPI+), and doublets (FSC-A vs. FSC-H). In order to enrich for different cell populations, the following markers were used: GalC (oligodendrocytes, FITC, clone mGalC, FCMAB312F, Milli-Mark, 1:10), Ly6A/E (endothelial, BV605, clone D7, 108133, BioLegend, 1:150). Isolated cells were single-cell sorted into 384-well cell capture plates containing 2μl of lysis solution and barcoded poly(T) reverse-transcription (RT) primers for single-cell RNA-seq15. Four empty wells were kept in each 384-well plate as a no-cell control. Immediately after sorting, each plate was spun down to ensure cell immersion into the lysis solution, snap-frozen on dry ice, and stored at –80oC until processing. To record the marker level of each single cell, the FACS Diva ‘index sorting’ function was activated during single-cell sorting. Following the sequencing and analysis of the single cells, each surface marker was linked to the genome-wide expression profile. This methodology was used to optimize the gating strategy and to eliminate autofluorescent cells.
mRNA from the cells sorted into cell capture plates were barcoded, converted into cDNA, and pooled. The pooled sample was linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality as described in MARS-seq 2.0 protocol
MARS-seq2.0 protocol

value: GalC+ cells

value: Whole brain

tag: strain

value: 24 months


title: PC7


title: AB14158

description: MARS


title: PC20


title: AB14154

description: MARS


title: DNA methylation profile for 201525200036_R01C01

tag: developmental stage


title: DNA methylation profile for 201438350114_R04C01

tag: brain region


title: DNA methylation profile for 201438350114_R06C01

tag: cell proportion double negative


title: PT5

source_name: Organoid-derived primary CRC

value: Organoid-derived primary CRC


title: PT19


title: DNA methylation profile for 201525200102_R05C01

tag: cell proportion neun+


title: AB14065

description: MARS


title: DNA methylation profile for 201438350114_R03C01

tag: cell proportion sox10+


title: PC3


title: DNA methylation profile for 201524770103_R03C01

tag: gender


title: AB14064

description: MARS


title: DNA methylation profile for 201525200125_R07C01


title: AB14159

description: MARS


title: AB14157

description: MARS


title: AB14155

description: MARS


title: PT1


title: DNA methylation profile for 201438350095_R03C01


title: DNA methylation profile for 201438350107_R07C01


title: DNA methylation profile for 201438350095_R01C01


title: AB14061

description: MARS


title: AB14062

description: MARS


title: DNA methylation profile for 201438350124_R05C01


title: AB14055

description: MARS

value: 15 months


title: DNA methylation profile for 201414140087_R01C01


title: DNA methylation profile for 201438350049_R02C01


title: DNA methylation profile for 201438350095_R02C01


title: DNA methylation profile for 201438350049_R01C01


title: DNA methylation profile for 201438350095_R04C01


title: AB14063

description: MARS


title: AB14060

description: MARS


title: DNA methylation profile for 201524770103_R04C01


title: DNA methylation profile for 201438350103_R08C01


title: AB14053

description: MARS


title: DNA methylation profile for 201524770070_R08C01


title: DNA methylation profile for 201524770070_R07C01


title: DNA methylation profile for 201438350109_R02C01


title: AB14051

description: MARS


title: AB14059

description: MARS

value: 10 months


title: AB14052

description: MARS


title: DNA methylation profile for 201506830044_R08C01


title: DNA methylation profile for 201414140087_R02C01


title: AB14047

description: MARS


title: AB14046

description: MARS


title: AB14056

description: MARS


title: AB14057

description: MARS


title: AB14054

description: MARS


title: AB14048

description: MARS


title: AB9160

description: MARS


title: AB14050

description: MARS


title: DNA methylation profile for 201438350103_R07C01


title: DNA methylation profile for 201438350124_R03C01


title: DNA methylation profile for 201508130008_R01C01


title: AB9161

description: MARS


title: DNA methylation profile for 201525200125_R05C01


title: DNA methylation profile for 201506830044_R07C01


title: AB9159

description: MARS


title: DNA methylation profile for 201438350124_R04C01


title: AB9157

description: MARS


title: DNA methylation profile for 201525200125_R06C01


title: AB9158

description: MARS


title: DNA methylation profile for 201438350166_R02C01


title: DNA methylation profile for 201506830044_R03C01


title: AB9156

description: MARS


title: AB14045

description: MARS


title: DNA methylation profile for 201508130008_R02C01


title: AB14049

description: MARS


title: AB9155

description: MARS


title: DNA methylation profile for 201438350166_R01C01


title: AB10183

description: MARS


title: DNA methylation profile for 201438350178_R04C01


title: DNA methylation profile for 201525200140_R01C01


title: AB10181

description: MARS


title: AB10182

description: MARS


title: AB10184

description: MARS


title: DNA methylation profile for 201506830044_R04C01


title: DNA methylation profile for 201438350178_R03C01


title: DNA methylation profile for 201525200140_R02C01


title: DNA methylation profile for 201438350031_R06C01


title: AB10179

description: MARS


title: DNA methylation profile for 201438350031_R05C01


title: DNA methylation profile for 201508110012_R08C01


title: AB10180

description: MARS


title: AB8792

description: MARS


title: DNA methylation profile for 201508110012_R07C01


title: AB8793

description: MARS


title: DNA methylation profile for 201438350154_R06C01


title: DNA methylation profile for 201438350125_R08C01


title: AB8790

description: MARS


title: AB8789

description: MARS


title: AB8791

description: MARS


title: DNA methylation profile for 201438350154_R05C01


title: DNA methylation profile for 201524770116_R05C01


title: DNA methylation profile for 201524770116_R06C01


title: AB8788

description: MARS


title: AB8786

description: MARS


title: DNA methylation profile for 201524770062_R04C01


title: AB8787

description: MARS


title: DNA methylation profile for 201414140087_R04C01


title: AB7316

description: MARS

value: CD45- cells

value: 11 months


title: DNA methylation profile for 201414140087_R03C01

value: adult

value: brain


title: DNA methylation profile for 201508110045_R08C01


title: AB8794

description: MARS


title: AB7313

description: MARS


title: AB7314

description: MARS


title: DNA methylation profile for 201508110045_R07C01

value: Prefrontal


title: DNA methylation profile for 201438350091_R06C01

value: Occipital

value: female


title: DNA methylation profile for 201438350091_R05C01


title: AB7310

description: MARS


title: AB7311

description: MARS


title: AB6879

description: MARS

value: 6 months


title: AB7312

description: MARS


title: DNA methylation profile for 201438350103_R02C01

value: male


title: DNA methylation profile for 201438350036_R08C01


title: AB7317

description: MARS


title: DNA methylation profile for 201438350103_R01C01


title: DNA methylation profile for 201524770062_R03C01


title: DNA methylation profile for 201508110017_R08C01


title: AB6877

description: MARS


title: AB6874

description: MARS


title: AB6873

description: MARS


title: DNA methylation profile for 201438350036_R07C01


title: AB7315

description: MARS


title: AB6872

description: MARS


title: DNA methylation profile for 201525200076_R06C01


title: DNA methylation profile for 201508110017_R07C01


title: AB6871

description: MARS


title: DNA methylation profile for 201525200076_R04C01


title: DNA methylation profile for 201525200076_R05C01


title: AB6724

description: MARS


title: DNA methylation profile for 201438350116_R06C01


title: AB6870

description: MARS


title: DNA methylation profile for 201438350116_R05C01


title: AB6723

description: MARS


title: AB6722

description: MARS


title: AB6878

description: MARS


title: DNA methylation profile for 201414140087_R06C01


title: DNA methylation profile for 201438350131_R03C01


title: AB6719

description: MARS


title: AB6721

description: MARS


title: DNA methylation profile for 201414140130_R07C01


title: DNA methylation profile for 201508130008_R04C01


title: AB6720

description: MARS


title: DNA methylation profile for 201438350131_R04C01


title: DNA methylation profile for 201525200110_R07C01


title: AB6716

description: MARS


title: AB6718

description: MARS


title: DNA methylation profile for 201525200110_R08C01


title: AB6713

description: MARS


title: DNA methylation profile for 201414140130_R08C01


title: DNA methylation profile for 201525200028_R04C01


title: AB6715

description: MARS


title: AB6717

description: MARS


title: DNA methylation profile for 201525200028_R03C01


title: AB6712

description: MARS


title: AB6614

description: MARS


title: AB6613

description: MARS


title: DNA methylation profile for 201525200076_R03C01


title: DNA methylation profile for 201438350178_R05C01


title: DNA methylation profile for 201508110010_R05C01


title: DNA methylation profile for 201438350178_R06C01


title: DNA methylation profile for 201508110010_R06C01


title: DNA methylation profile for 201508130008_R03C01


title: AB6611

description: MARS


title: AB6714

description: MARS


title: DNA methylation profile for 201438350162_R04C01


title: AB6615

description: MARS


title: AB6612

description: MARS


title: AB6609

description: MARS


title: AB6608

description: MARS


title: DNA methylation profile for 201438350162_R03C01


title: AB6610

description: MARS


title: DNA methylation profile for 201438350031_R04C01


title: DNA methylation profile for 201438350031_R03C01


title: DNA methylation profile for 201508110012_R04C01


title: AB6448

description: MARS

value: 8 months


title: DNA methylation profile for 201508110012_R03C01


title: AB6605

description: MARS


title: DNA methylation profile for 201508110016_R04C01


title: AB6446

description: MARS


title: DNA methylation profile for 201508110016_R03C01


title: DNA methylation profile for 201438350091_R08C01


title: DNA methylation profile for 201414140202_R04C01


title: AB6604

description: MARS


title: AB6441

description: MARS


title: DNA methylation profile for 201438350103_R05C01


title: AB6447

description: MARS


title: AB6602

description: MARS


title: DNA methylation profile for 201414140202_R03C01


title: DNA methylation profile for 201438350091_R07C01