title: BIOPSY_4061


title: WNT Dawn 3.5h Rep 3

status: Public on Aug 15 2019

type: SRA

city: Raleigh

first: Jigar

last: Desai

state: NC

address: 128 Polk Hall

department: Biochemistry

country: USA

institute: NCSU

description:
2-3.5h_WNT.2
processed data file: Pannicle_timecourse_WNT.csv

library_source: transcriptomic

data_processing:
Trimmed files were aligned using Hisat v2. MH63 (rigw.com). The resulting bam files were then piped to htseq count version 0.6.0. Using the options -f bam, -s reverse, and -m union counts per gene were generated for the annotated genes in MH63. Counts were than normalized to counts per million.
Genome_build: MH63RS1
Supplementary_files_format_and_content: Pannicle_timecourse_WNT.csv: Comma-separated text file includes raw counts.
Supplementary_files_format_and_content: Pannicle_gradient_24_26_28_30C.csv: Comma-separated text file includes raw counts.

molecule: total RNA

organism: Oryza sativa Indica Group

source_name: Rice Panicle

growth_protocol: An IR64 land variety was grown on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.

extract_protocol:
Tissue samples were stored at -80C until needed. The panicle samples were first grinded in liquid nitrogen with a metal pestle. The tissue then lyophilized at -60C overnight before RNA extractions. Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen) with the recommended RLT lysis buffer. The RNA extraction provided protocol was followed the inclusion of DNase step. RNA concentration was then measured with NANOdrop 2000. 2ug of RNA was used with NEBNext Poly(A) Magnetic mRNA isolation kit (NEB). Oligo(dT) attached to magnetic beads isolate mRNA by attaching to ploy(A) modified mRNA.
RNA libraries were prepared for sequencing using NEB ultra directional library prep kit.

treatment_protocol: Plants were grown in a field setting. WNT were treated with IR heater at night. 24C, 26C, 28C, and 30C rice were treated with field tents for increased night temperatures.

tag: variety

tag: developmental stage

value: 50% flowering

tag: tissue

value: Panicle

tag: treatment

value: WNT

tag: time point

value: Dawn 3.5h


title: BIOPSY_4030

type: RNA

city: Leuven

first: Maarten

last: Naesens

address: Herestraat 49

department: Department of Microbiology, Immunology and Transplantation

country: Belgium

institute: KU Leuven

hyb_protocol: Fragmented cRNA was hybridized to the Human GeneChip U133 Plus 2.0 Array (Affymetrix).

scan_protocol: The arrays were washed and stained with streptavidin-phycoerytrin on an automated Fluidics Station (Affymetrix) and scanned on the GeneChip® Scanner 3000 7G System (Affymetrix).

data_processing:
The resulting image files were generated using the GeneChip® Command Console® Software (AGCC).
Log 2 RMA-normalized signal intensity (using Bioconductor tools in R version 3.5.3)

label: biotin

organism: Homo sapiens

label_protocol: Total RNA extracted from the samples was first amplified and biotinylated to complementary RNA (cRNA) using the GeneChip® 3' IVT PLUS Reagent Kit (Affymetrix Inc., High Wycombe HP10 0HH, UK). Biotinylated cRNA was purified and fragmented.

extract_protocol: * BLOOD: Total RNA from peripheral blood samples was extracted using the PAXgene Blood miRNA Kit® (PreAnalytiX GmbH, a Qiagen/ BD Company, Switzerland). The yield and purity of RNA was measured using a NanoDrop® ND-1000 spectrophotometer (Thermo Scientific™, Life Technologies Europe BV, Ghent, Belgium). RNA integrity was assessed using the RNA 6000 Nano LabChip® kit (Agilent Technologies Belgium NV, Diegem, Belgium) on the Bioanalyzer 2100 instrument™ (Agilent Technologies Belgium NV, Diegem, Belgium), and globin mRNA was depleted using the GLOBINclear™ Kit (Invitrogen™, Life Technologies Europe BV, Ghent, Belgium). After globin mRNA depletion, the quantity (absorbance at 260nm) and purity (ratio of the absorbance at 230, 260 and 280nm) of the isolated RNA were measured using the NanoDrop ND-1000™ spectrophotometer (NanoDrop Technologies, Inc., Rockland, DE, USA). The extracted RNA samples were stored at -80°C.   ** BIOPSY: Total RNA from renal allograft biopsies was extracted using the Allprep DNA/RNA/miRNA Universal Kit® (Qiagen Benelux BV, Venlo, The Netherlands) on a QIAcube instrument (Qiagen Benelux BV, Venlo, The Netherlands). The quantity (absorbance at 260nm) and purity (ratio of the absorbance at 230, 260 and 280nm) of the RNA isolated from the biopsies were measured using the NanoDrop ND-1000™ spectrophotometer (Thermo Scientific™, Life Technologies Europe BV, Ghent, Belgium). RNA integrity was evaluated using the Eukaryote nano/pico RNA Kit® (Agilent Technologies Belgium NV, Diegem, Belgium) on the Bioanalyzer 2100 instrument™ (Agilent Technologies Belgium NV, Diegem, Belgium). Samples were stored at -80°C until further analysis.

treatment_protocol: * BLOOD: Peripheral blood samples were collected at time of the renal allograft biopsies, directly in PAXgene Blood RNA tubes® (PreAnalytiX GmbH, a Qiagen/ BD Company, Switzerland). The Paxgene tubes were stored at ambient temperature for at least 24 hours, and then stored at -80°C until extraction.   ** BIOPSY: Two needle cores were taken at each kidney allograft biopsy. One was used for histology, at least half of the other one was immediately stored in Allprotect Tissue Reagent® (Qiagen Benelux BV, Venlo, The Netherlands). The Allprotect tubes were stored at 4°C (minimum 24 hours and maximum 72 hours), and then stored at -20°C until extraction.

value: kidney allograft biopsy

tag: tcmr (no

tag: abmr (no

tag: date of sample


title: granulosa cells_sownr1808_follicle1_largefollicle_LowVAR_LowCOChealth

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent Gene Expression Hybridization Kit. Samples were applied to 8*60K microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations and finally covered with an ozone-barrier slide.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (10.7.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. QC checks were done on raw data and all arrays passed. Spots with a mean signal higher than twice the background value over all arrays and both channels were considered to be expressed. Data was normalized according to Pellis et al. (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

organism: Sus scrofa

source_name: granulosa cells

label_protocol: Approximately 40 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously by van Schothorst et al. (Anal Biochem 2007;363:315-7). 32 Cy3-labeled samples with the highest cRNA yield were used for the reference pool.

extract_protocol: Total RNA was isolated from granulosa cells isolated using laser capture micro-dissection (Arcturus) and the Picopure RNA Isolation kit (Arcturus), quantified using Nanodrop (IsoGen Life Science) and qualified using TapeStation (Agilent).

treatment_protocol: A total of 29 multiparous Dutch Landrace sows (parity 3 to 5; Topigs Norsvin, Vught, the Netherlands) were used. The sows were fed a standard lactation diet (ca. 12.5MJ NE/kg, 154 g/kg CP, 9.3 g/kg lysine; Lacto Excellent, Agrifirm, Apeldoorn, The Netherlands). Within 24 hours after parturition, piglets were cross-fostered to ensure 13 suckling piglets per sow. The sows had a lactation period of 26.1±0.2 (25 to 27) days and weaned 13.0±0.9 piglets. The sows were slaughtered at the slaughterhouse by stunning and exsanguination within 2 hours after weaning.

tag: origin

value: TopigsNorsvin N-line, multiparous sows

tag: follicle size

value: large

tag: var

value: low

tag: coc health

tag: sample type

value: reference


title: granulosa cells_sownr2434_follicle1_largefollicle_LowVAR_LowCOChealth


title: WNT Dawn 3.5h Rep 2

description:
2-3.5h_WNT.1
processed data file: Pannicle_timecourse_WNT.csv


title: WNT Dawn 7h Rep 1

description:
3-7h_WNT
processed data file: Pannicle_timecourse_WNT.csv

value: Dawn 7h


title: WNT Dawn Rep 4

description:
1-Dawn_WNT.3
processed data file: Pannicle_timecourse_WNT.csv

value: Dawn


title: DKO-control_treament (DKO-anti-miR-148b)

city: Frederick

first: Shuo

last: Gu

state: MD

address: 1050 Boyles Str. Building 560 Room 11-6B

institute: National Cancer Institute

data_processing:
3ʹ adaptor sequences were removed by customized scripts. Reads without the 3′ adaptor sequences or shorter than 18 nt were discarded
For miRNA isoform analyses based on small-RNA-seq, QuagmiR (on Seven Bridges Cancer Genomics Cloud) was used with default or custermized motif files
For gene expression analyses based on RNA-seq, Raw reads were aligned to the human genome (GRCh37.75) using STAR 2.5.1.
Genome_build: GRCh37.75
Supplementary_files_format_and_content: 1) isomiR profile (tsv files) (small-RNA-seq) 2) gene expression counts (tab files) (RNA-seq)

molecule: polyA RNA

source_name: human embryonic kidney Cells

growth_protocol: HEK293T cells were maintained in DMEM (high glucose) (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Hyclone), 1X MEM Non-Essential Amino Acids (Gibco), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco). HEK293T-TUT4/TUT7 DKO cells were generated by using CRISPR/Cas9.

extract_protocol:
RNAs were extracted by using Trizol.
Sequencing libraries were constructed by either Illumina® TruSeq® RNA sample preparation kit or NEBNext® Multiplex Small RNA Library Prep Set according to the manufacturer's’ protocol with minor modifications.

treatment_protocol: HEK293T and DKO cells were transfected with Lipofectamine 3000 (Life Technologies) according to the manufacturer's’ instructions

tag: cell type

tag: genotype

value: TUT4 and TUT7 Double Knockout

tag: ip antibody


title: DKO-control_treament_replicate2

tag: cell line

value: human embryonic kidney Cells

tag: genotype/variation


title: DKO-O/E-miR-27a_replicate2

value: TUT4 and TUT7 Double Knockout with ectopic expression of miR-27a


title: DKO-O/E-miR-27a_replicate1


title: WNT Dawn 3.5h Rep 1

description:
2-3.5h_WNT
processed data file: Pannicle_timecourse_WNT.csv

tag: variety

tag: developmental stage


title: iciHHV6 patient smRNA-seq

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

description:
smallRNA
smallRNA_counts.matrix.txt

data_processing:
Basecalls performed using CASAVA version 2.17
RNA-seq reads were aligned to the hg38 and HHV-6A (NC_001664.2) genome assemblies using TopHat2 (version 2.1.1) and transcripts were quantified with HTSeq (version 0.10.0).
Differential expression of RNA-seq was performed using DESeq2 (version 3.7) using raw HTSeq count files.
SmallRNA-seq data was processed using Oasis 2.
Genome_build: hg38 or HHV6A genome (NC_001664.2)
Supplementary_files_format_and_content: Raw HTSeq count matrix for RNA-seq datasets. Raw count matrix for smallRNA-seq datasets.

organism:
Homo sapiens
Human betaherpesvirus 6A

source_name: iciHHV6 patient cells

growth_protocol: Epstein-Barr-Virus (EBV)-transformed patient derived inherited chromosomally integrated HHV-6A (iciHHV-6A) human smooth muscle cells were kindly provided by Dr. Louis Flamand (Laval University, Québec), and cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 20% fetal bovine serum (FBS), 1% penicillin-streptomycin (Pen/Strep), and 1% L-Glutamine. Human epithelial kidney cells 293T (293T, ATCC CRL-11268) cells were cultured in the same medium but supplemented with 10% FBS. All cells were maintained in 10 cm2 flasks as a monolayer culture in a humidified 5% CO2 air incubator at 37°C.

extract_protocol:
RNA was extracted from cells using Trizol Reagent (Life Technologies) and purified using Direct-zol RNA MicroPrep Kit (Zymo Research #R2060) following the manufacturer´s instructions.
1 µg of total RNA was depleted of ribosomal RNA (rRNA) using the KAPA RiboErase Kit (#KR1142) and libraries were prepared using the KAPA Stranded RNA-seq Library Preparation Kit (#KR0934). SmallRNA-seq libraries were prepared using the NEBNext Multiplex Small RNA Sample Prep for Illumina (#E7300) following the manufacturer´s protocol.

treatment_protocol: HHV6-GFP cells treated with either DMSO or 10ng/ml phorbol 12-myristate 13 acetate (TPA, Sigma) for 24 h at 37 °C. iciHHV6 cells were not treated.

tag: infection

value: iciHHV6 infected

value: smooth muscle cells


title: BIOPSY_3888

tag: tissue


title: granulosa cells_sownr2124_follicle1_largefollicle_HighVAR_HighCOChealth

value: high


title: WNT Dawn Rep 3

description:
1-Dawn_WNT.2
processed data file: Pannicle_timecourse_WNT.csv

value: 50% flowering

tag: treatment

tag: time point


title: HHV6-GFP smRNA-seq PMA replicate2

description:
smallRNA
smallRNA_counts.matrix.txt

source_name: HHV6-GFP cells

value: HHV6 infected

value: HEK293 cells


title: BIOPSY_3905

tag: tcmr (no

tag: abmr (no

tag: date of sample


title: BIOPSY_3990


title: BIOPSY_6576


title: BIOPSY_3755


title: BIOPSY_3965


title: BIOPSY_3796


title: BIOPSY_3753


title: HHV6-GFP smRNA-seq PMA replicate1

description:
smallRNA
smallRNA_counts.matrix.txt


title: BIOPSY_3479


title: WT-O/E-miR-27a_replicate2

value: WT with ectopic expression of miR-27a


title: WNT Dawn Rep 2

description:
1-Dawn_WNT.1
processed data file: Pannicle_timecourse_WNT.csv

value: Panicle

value: WNT


title: HHV6-GFP smRNA-seq DMSO replicate2

description:
smallRNA
smallRNA_counts.matrix.txt


title: WT-O/E-miR-27a_replicate1


title: HHV6-GFP RNA-seq PMA replicate1

description:
RNA
HHV6_counts.matrix.txt


title: Control Dawn 23h Rep 3

description:
8-23h_C.2
processed data file: Pannicle_timecourse_WNT.csv

value: Control

value: Dawn 23h


title: WT-control_treament_replicate1

value: WT


title: Control Dawn 23h Rep 4

description:
8-23h_C.3
processed data file: Pannicle_timecourse_WNT.csv


title: DKO-control_treament_replicate1


title: HHV6-GFP smRNA-seq DMSO replicate1

description:
smallRNA
smallRNA_counts.matrix.txt


title: HHV6-GFP RNA-seq PMA replicate2

description:
RNA
HHV6_counts.matrix.txt


title: HHV6-GFP RNA-seq DMSO replicate2

description:
RNA
HHV6_counts.matrix.txt


title: Control Dawn 23h Rep 2

description:
8-23h_C.1
processed data file: Pannicle_timecourse_WNT.csv


title: Control Dawn 17.5h Rep 4

description:
7-17.5h_C.3
processed data file: Pannicle_timecourse_WNT.csv

value: Dawn 17.5h


title: HHV6-GFP RNA-seq DMSO replicate1

description:
RNA
HHV6_counts.matrix.txt


title: PB3_CD3_S14

city: Los Angeles

first: David

last: Habiel

state: CA

address: 8700 Beverly Blvd

department: Medicine

institute: Cedars-Sinai Medical Center

description: Normal - PB3_CD3_S14_L004_R1_001 (paired) (GE) - RPKM

data_processing:
Samples were inported into CLC workbench genomics
Raw data were trimmed and QC analysis was performed. Only good quality sequences were selected for downstream analysis.
Transcripts were aligned to the human reference genome hg38.
RPKM values were generated and fold change and statistical significance were calculated using the Empirical  analysis of DGE (EDGE)
Genome_build: hg38
Supplementary_files_format_and_content: IPF vs Normal T cells EDGE analysis.txt reports RPKMs

source_name: Donor Peripheral Blood

extract_protocol:
IPF Lungs were mechanically dissociated. Resulting cell suspensions were biobanked. Biobanked samples were quickly thawed and stained with anti-CD3 antibodies and T-cells were sorted using a FACS Aria III sorter. Donor peripheral blood CD4+ cells were magnetically sorted. RNA was subsequently extracted and subject to RNA sequencing analysis.
minimum of 200 ng of total RNA was used, samples were sequenced using HiSeq 2000 SBS Sequencing v3. Raw reads in FASTQ format were aligned to the UCSC human reference genome (hg38) using CLC genomics workbench V8.5.1, RPKM values were generated and fold change and statistical significance were calculated using the Empirical  analysis of DGE (EDGE).

value: Peripheral Blood

value: T cells


title: iciHHV6 patient RNA-seq

description:
RNA
HHV6_counts.matrix.txt


title: Control Dawn 23h Rep 1

description:
8-23h_C
processed data file: Pannicle_timecourse_WNT.csv


title: IPF3_14_CD3

description: IPF - IPF3_14_CD3_S11_L004_R1_001 (paired) (GE) - RPKM

source_name: IPF Lung Explants

value: Lung


title: HHV6-GFP MNase 0.3U

description: genomic DNA

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 2.17
MNase-seq reads were aligned to the hg38 and HHV6A genome assemblies using Bowtie2 version 2.3.2. Profiles were generated for individual titration points. Data was processed using DANPOS (version 2.2.2). Essentially, clonal reads were  removed, the fragment sizes were corrected, read length was adjusted and quantile normalization was performed to produce average occupancy scores across either the HHV6A or hg38 genome.  These average occupancy scores relative all Refseq genes (hg38) or  to the ORF start sites (HHV6A).
Genome_build: hg38 or HHV6A genome (NC_001664.2)
Supplementary_files_format_and_content: text files with signal across hg38 or HHV6A

molecule: genomic DNA

extract_protocol:
MNase-seq extractions were performed using the EZ Nucleosomal DNA Prep Kit (Zymo Research #D5220) following the manufacturer´s protocol. Briefly, nuclei isolated from 1 x 106 iciHHV-6A and 293-HHV-6A cells were treated with varying concentrations of MNase (final concentrations of 0.07, 0.1, 0.2, 0.3U/100µL reaction) and incubated at room temperature for 5 min. The reaction was terminated with MNase stop buffer, and following nucleosomal DNA purification.
MNase-seq libraries were prepared with the NEB Ultra II Library Prep Kit following the manufacturer´s protocol.

tag: mnase units


title: BIOPSY_2945

value: kidney allograft biopsy


title: IPF2_14_CD3

description: IPF - IPF2_14_CD3_S10_L004_R1_001 (paired) (GE) - RPKM


title: BIOPSY_3188


title: PB2_CD3_S13

description: Normal - PB2_CD3_S13_L004_R1_001 (paired) (GE) - RPKM


title: PB1_CD3_S12

description: Normal - PB1_CD3_S12_L004_R1_001 (paired) (GE) - RPKM


title: Control Dawn 17.5h Rep 2

description:
7-17.5h_C.1
processed data file: Pannicle_timecourse_WNT.csv


title: iciHHV6 patient MNase 0.3U

description: genomic DNA

value: iciHHV6 infected


title: BIOPSY_3042


title: IPF1_14_CD3

description: IPF - IPF1_14_CD3_S9_L004_R1_001 (paired) (GE) - RPKM


title: BIOPSY_2763


title: WT-control_treament_replicate2

value: human embryonic kidney Cells


title: WNT Dawn Rep 1

description:
1-Dawn_WNT
processed data file: Pannicle_timecourse_WNT.csv

value: Dawn


title: Control Dawn 17.5h Rep 3

description:
7-17.5h_C.2
processed data file: Pannicle_timecourse_WNT.csv

value: 50% flowering


title: BIOPSY_2776


title: HHV6-GFP MNase 0.2U

description: genomic DNA

value: HHV6 infected


title: HHV6-GFP MNase 0.1U

description: genomic DNA

value: HEK293 cells


title: iciHHV6 patient MNase 0.2U

description: genomic DNA

value: smooth muscle cells


title: HOCl_30min_repA

city: Birmingham

first: Alexander

last: Rosenberg

state: AL

address: 1720 2nd Avenue South, Suite 276/11

institute: University of Alabama at Birmingham

data_processing:
FASTQC for quality assessment
Trimmomatic to trim reads to 50bp with settings: CROP:50 LEADING:3 TRILING:3 SLIDINGWINDOW:40:15 MINLENGTH:40
EDGE_Pro for read mapping and transcript abundance (EDGE_Pro uses Bowtie2 internally for read mapping): L. reuteri JCM1112, https://ncbi.nlm.nih.gov/genome/438?genome_assembly_id=300130
DESeq2 for rlog transformation clustered heat maps and PCA plots), differential expression testing with Benjamini-Hochberg multiple testing correction
Downstream visualizations performed by custom code in Matlab

organism: Limosilactobacillus reuteri

source_name: mid-log phase Lactobacillus reuteri culture

growth_protocol: L. reuteri was grown at 37°C in MEI broth without added cysteine (MEI-C) in Hungate tubes prepared, inoculated, and sealed in an anaerobic chamber (Coy Laboratory Products) in an atmosphere of 90% nitrogen, 5% CO2, and 5% H2

extract_protocol:
Cells (7 ml) were harvested at 0 min (no addition of stress; the tube which did not receive any oxidant), 5 min, 15 min and 30 min after addition of oxidants by mixing with 7 ml ice-cold isopropanol anaerobically to stop transcription, and then removing the samples from the anaerobic chamber and centrifuging at 1500 x g for 15 minutes at 4°C. The supernatant was discarded and the pellet was resuspended in the remaining isopropanol and transferred to 1.5 ml microfuge tubes. The cells were then centrifuged at 4000 x g for 10 minutes at 4°C. The supernatant was removed completely and the samples were stored at -80°C for further processing. Total RNA was extracted using the RiboPure™ RNA Purification Kit for bacteria (Ambion) following the manufacturer’s protocol. All RNA samples were DNAse treated with the optional DNAse treatment kit provided with the Ambion RiboPure Bacteria kit to remove any contaminating genomic DNA.
RNA-sequencing was performed on the Illumina HiSeq2500 using the Rapid Run v2 sequencing chemistry and flow cells as described by the manufacturer (Illumina Inc., San Diego, CA).  Briefly, the quality of the total RNA was assessed using the Agilent 2100 Bioanalyzer.  RNA with a RNA Integrity Number (RIN) of 7.0 or above was used for sequencing library preparation. We used the Agilent SureSelect Strand Specific mRNA library kit as per the manufacturer’s instructions (Agilent, Santa Clara, CA).  Cluster generation was performed according to the manufacturers recommendations for onboard clustering (Illumina).  Paired end 50 bp sequencing runs were used to allow for better alignment of the sequences to the reference genome.

treatment_protocol: Wild-type L. reuteri were grown anaerobically in 5 ml of MEI-C broth overnight at 37°C. 300 µl of the overnight culture was used to inoculate four tubes containing 15 ml of anaerobic MEI-C broth, and the cultures were grown anaerobically at 37°C to mid log phase (A600 = 0.35). HOCl (1.25 mM) or H2O2 (0.12 mM) were added anaerobically to 3 of the 4 tubes and incubation was continued at 37°C.

tag: stressor

value: HOCl

tag: minutes

tag: replicate


title: BIOPSY_2939


title: BIOPSY_2627


title: Cdiphtheriae1737deltazur_5zinc_rep3

city: Silver Spring

first: Michael

last: Schmitt

address: 10903 New Hampshire Ave

institute: US Food and Drug Administration

description: Gene expression following growth in high iron conditions

hyb_protocol: 0.6 µg of Cy3-labelled cRNA (specific activity > 30 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 m in a reaction volume of 25 µl. An equal volume (25 µl) of 2x Hi-RPM Hybridization Buffer was added to stop the fragmentation reaction. 40 µl of each sample was hybridized to Agilent Custom Microarrays designed using the Corynebacterium diphtheriae strain NCTC 13129 for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 m at room temperature with Gene Expression Wash Buffer 1 and 1 m at 37°C using Gene Expression Wash Buffer 2. Slides were scanned immediately.

scan_protocol: Slides were scanned on the Agilent G2505C Microarray Scanner using settings recommended by the manufacturer (Dye channel: G (green), Scan region: Scan Area 61 x 21.6 mm, Scan Resolution: 3 µm, and 100% Green PMT gain).

data_processing: The scanned images were analyzed with Feature Extraction Software version 12.0.3.1 (Agilent) using default parameters to obtain gProcessedSignal values. Median gProcessedSignal values were divided by the entire sample set mean and log2 transformed.

organism: Corynebacterium diphtheriae

source_name: delta zur

label_protocol: Cyanine-3 labeled cRNA was prepared from 0.1 µg RNA using the Low Input Quick Amp WT Labeling Kit (Agilent) following the manufacturer’s instructions. cRNA was purified using the RNAeasy kit (QIAGEN). Dye incorporation and cRNA yield were assessed with the GE NanoVue Plus.

growth_protocol: Wild-type C. diphtheriae or the zur mutant were grown overnight in the semi-defined medium mPGT supplemented with 1 µM FeCl3. Overnight cultures were diluted 1:1 with fresh media and allowed to grow for 2-3 h. The optical density of cultures was measured (A600) and the cells diluted to an optical density of 0.1 into mPGT supplemented with 0.5 µM FeCl3 (required for growth) and without or with 5 µM ZnCl2. For the zur mutant, cultures were only diluted into mPGT supplemented with 0.5 µM FeCl3 with 5 µM ZnCl2. Cells were harvested by centrifugation at mid-logarithmic growth.

extract_protocol: Cells were lysed in phosphate buffered saline supplemented with 10% ethanol, 0.2% phenol, and 14.3 mM beta-mercaptoethanol in Lysing Matrix B (MP Biomedicals). Appropriate volumes of TriZOL LS reagent (Thermo Fisher Scientific) were added to lysates and samples were briefly vortexed. RNA was purified following the Zymo Direct-zol RNA MiniPrep Plus protocol (Zymo Research Corporation). RNA was treated with Ambion Turbo DNAse I (Invitrogen). The RNA concentration and integrity were assessed by the Agilent Bioanalyzer 2100 following the RNA 6000 Nano protocol.

tag: strain


title: Cdiphtheriae1737_5zinc_rep3

source_name: wild type zinc


title: HOCl_30min_repC

value: mid-log phase Lactobacillus reuteri culture


title: iciHHV6 patient MNase 0.1U

description: genomic DNA

tag: cell type


title: HOCl_15min_repC


title: HOCl_30min_repB


title: Cdiphtheriae1737_nozinc_rep3

description: Gene expression following growth in low iron conditions

source_name: wild type no zinc


title: BIOPSY_2595


title: Cdiphtheriae1737deltazur_5zinc_rep2


title: HOCl_15min_repB


title: BIOPSY_2307


title: BIOPSY_242


title: Cdiphtheriae1737_5zinc_rep2


title: HHV6-GFP input

data_processing:
Basecalls performed using CASAVA version 2.17
ChIP-seq reads were aligned to the hg38 and HHV6A genome assemblies using Bowtie2 version 2.3.2.
ChIP-seq peak calling: MACS2, version 2.1.1.
Genome_build: hg38 or HHV6A genome (NC_001664.2)
Supplementary_files_format_and_content: bigwig files for fold-enrichment signal across hg38 or HHV6A

extract_protocol:
ChIP-seq: Cells were fixed with 1% formaldehyde for 10 minutes at room temperature and then quenched with 0.125M glycine for 5 minutes, prior to several washes with ice-cold PBS. Cells were lysed and IPs were performed with the indicated antibody at a ratio of 4ug antibody to 20ug chromatin (for histone modifications) and 10ug antibody to 150ug chromatin (for TRF1/2).
ChIP-seq libraries were prepared with the NEB Ultra II Library Prep Kit following the manufacturer´s protocol.

tag: chip antibody

value: control input


title: HHV6-GFP MNase 0.07U

description: genomic DNA


title: BIOPSY_2294


title: BIOPSY_2934


title: iciHHV6 patient MNase 0.07U

description: genomic DNA


title: BIOPSY_1986


title: HOCl_5min_repC


title: iciHHV6 patient input


title: Cdiphtheriae1737deltazur_5zinc_rep1


title: Cdiphtheriae1737_nozinc_rep2


title: BIOPSY_2030


title: HHV6-GFP_TRF2_ChIPSeq

value: TRF2 (GeneTex, cat#13579)


title: HOCl_5min_repB


title: HOCl_15min_repA


title: iciHHV6_TRF2_ChIPSeq


title: Cdiphtheriae1737_5zinc_rep1


title: HOCl_0min_repC


title: laeA_rep3

city: Kagoshima

first: Taiki

last: Futagami

address: Korimoto 1-21-24

department: Department of Agriculture

country: Japan

institute: Kagoshima University

description:
laeA.3
Cap analysis gene expression (CAGE)
processed data file: CTSS_ctrl_laeA_samples.txt

data_processing:
Quality check by fastqc.
The sequences were mapped to Aspergillus kawachii IFO 4308 genomes using BWA software.
CTSS (CAGE detected transcriptional start site) was counted by BEDTools.
CAGE-tag 5' coordinates were input for RECLU clustering.
Genome_build: Aspergillus kawachii IFO 4308 Akaw_assembly01
Supplementary_files_format_and_content: CTSS_ctrl_laeA_samples.txt: Tab-delimited text file includes raw count values for each sample. CAGE detected TSS information of all samples.

organism: Aspergillus luchuensis

source_name: whole cell

extract_protocol:
Total RNA was extracted from the mycelia of Aspergillus luchuensis mut. kawachii strains. Briefly, conidia (2 × 10e7 cells) of A. kawachii strains were inoculated into 100 ml of M medium, precultivated with shaking (180 rpm) at 30°C for 36 h, and then transferred to 50 ml of CAP medium and further cultivated with shaking (163 rpm) at 30°C for 12 h. The mycelia were ground to a powder using a mortar and pestle in the presence of liquid nitrogen. Then, RNA was extracted using RNAiso Plus reagent (Takara Bio, Shiga, Japan). The RNA samples were treated by the SV total RNA isolation system (Promega, Madison, WI) according to the manufacturer’s protocol.
Library was performed according to a previous paper (Kodzius, R., Kojima, M., Nishiyori, H., Nakamura, M., Fukuda, S., Tagami, M., Sasaki, D., Imamura, K., Kai, C., Harbers, M., Hayashizaki, Y., Carninci, P.: CAGE: cap analysis of gene expression, Nat. Methods, 3, 211–222. 2006).

value: sirD

tag: genotype/variation

value: <delta>laeA

value: mycelia


title: BIOPSY_1587


title: HHV6-GFP_TRF1_ChIPSeq

value: TRF1 (GeneTex, cat#32935)


title: laeA_rep2

description:
laeA.2
Cap analysis gene expression (CAGE)
processed data file: CTSS_ctrl_laeA_samples.txt


title: laeA_rep1

description:
laeA.1
Cap analysis gene expression (CAGE)
processed data file: CTSS_ctrl_laeA_samples.txt


title: BIOPSY_1694


title: BIOPSY_1386


title: iciHHV6_TRF1_ChIPSeq


title: Ctrl_rep3

description:
ctrl345.3
Cap analysis gene expression (CAGE)
processed data file: CTSS_ctrl_laeA_samples.txt

value: control


title: Cdiphtheriae1737_nozinc_rep1


title: iciHHV6_H3K9me3_ChIPSeq

value: H3K9me3 (Abcam, cat#8898)


title: iciHHV6_H3K27ac_ChIPSeq

value: iciHHV6 infected


title: HOCl_5min_repA


title: HOCl_0min_repB


title: Ctrl_rep2

description:
ctrl345.2
Cap analysis gene expression (CAGE)
processed data file: CTSS_ctrl_laeA_samples.txt


title: H202_30min_repC


title: HOCl_0min_repA


title: H202_30min_repB


title: BIOPSY_1314

value: kidney allograft biopsy


title: BIOPSY_1511


title: BIOPSY_1139


title: Ctrl_rep1

description:
ctrl345.1
Cap analysis gene expression (CAGE)
processed data file: CTSS_ctrl_laeA_samples.txt


title: iciHHV6_H3K27me3_ChIPSeq

value: H3K27me3 (Abcam, cat#6002)


title: H202_30min_repA


title: BIOPSY_1130


title: iciHHV6_H3K4me3_ChIPSeq


title: HCC4: plasma from HBV-related HCC patient, case 4

city: Shanghai

first: Wei-ping

last: Zhou

state: Shanghai

address: 225 Changhai Road, Shanghai

country: China

institute: Eastern Hepatobiliary Surgery Hospital

description: Circular RNA expression in the plasma from HBV-related HCC patient, case 4

hyb_protocol: In detail, double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 5 g digested RNA using the CbcScript reverse transcriptase with cDNA synthesis system according to the manufacturer’s protocol (Capitalbio) with T7 Oligo (dN).   After completion of double-stranded cDNA (dsDNA) synthesis using DNA polymerase and RNase H, the dsDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and eluted with 30 L elution buffer. The eluted double-stranded cDNA products were vacuum evaporated to 16 L and subjected to 40 L in vitro transcription reactions at 37℃ for 14 hr using a T7 Enzyme Mix. The amplified cRNA was purified using the RNA Clean-up Kit (MN).

scan_protocol: Klenow enzyme labeling strategy was adopted after reverse transcription using CbcScript Ⅱ reverse transcriptase. Briefly, 2 g amplified RNA was mixed with 4 g random nanomer, denatured at 65℃ for 5min, and cooled on ice. Then, 5 L of 4×first-strand buffer, 2 L of 0.1M DTT, and 1.5 L CbcScript Ⅱ reverse transcriptase were added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 L. The cDNA was mixed with 4 g random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 5 L Klenow buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (GE Healthcare) were added to final concentrations of 240 M dATP, 240 M dGTP, 240 M dTTP, 120 M dCTP, and 40 M Cy-dCTP. 1.2 L Klenow enzyme was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples labeled with Cy3-dCTP were dissolved in 80 L hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

data_processing: The circRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13.0 (Agilent). To select the differentially expressed genes, we used threshold values of ≥2 and ≤−2-fold change and a Benjamini-Hochberg corrected p vlaue of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software then further analyzed with hierarchical clustering with average linkage (Eisen et al., 1998). Finally, we performed tree visualization by using Java Treeview (Stanford University School of Medicine, Stanford, CA, USA).

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. The procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: Total RNA was extracted from plasma by using  the Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA) according to manufacter’s protocol. The purity and concentration of RNA were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000). RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

tag: gender

value: male

tag: age

value: plasma

tag: disease state

value: hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC)


title: miRNA_Patient B primary tumor

city: Tainan

first: Chia-Hao

last: Tung

address: 138 Shengli Road

department: Institute of Basic Medical Sciences

country: Taiwan

institute: National Cheng Kung University

hyb_protocol: Labeled miRNA targets enriched by NanoSep 100K (Pall Corporation, USA) were hybridized to the Human miRNA OneArray® with Phalanx hybridization buffer using OneArray® Hybridization Chamber. After 16 hrs hybridization, non-speciﬁc binding targets were washed away.

scan_protocol: The slides scanned using a DNA Microarray Scanner (Model 4000B, Molecular Devices, Sunnyvale, CA, USA). The Cy5 ﬂuorescent intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices).

data_processing: Each single sample was at least performed twice in terms of technical or biological replicates for reducing the variances. The signal intensity of each sample was analyzed by using R language. Meanwhile, we merged three repeats probe with median value and did global normalization with invariant set method (Cheng Li et al., Genome Biology 2001). Statistical p-value was calculated by student t-test and fold change was outputted for evaluating differentially expressed genes. The criteria with fold change ≥ 1.74 or ≤ -1.74 and p-value < 0.05 are strongly recommended for further analysis.

source_name: primary ovarian tumor

label_protocol: Fluorescent targets were prepared from 2 μg total RNA samples using miRNA ULSTM Labeling Kit (Kreatech Diagnostics, The Netherlands).

extract_protocol: The total RNA was extracted by TRIzol reagent (invitrogen) according to the manufacture's instructions. Only RNA purity (260/280>1.8, 260/230>1.8, RIN>7) was used for further experiments. Optical density was measured by NanoDrop ND-1000 and RIN score was determined by Agilent RNA 6000 Nano Assay.

tag: subject id

value: patient B

tag: tissue

value: ovarian tumor

tag: primary vs recurrent tumor

value: primary


title: H202_15min_repC

value: mid-log phase Lactobacillus reuteri culture


title: BIOPSY_1205

tag: tcmr (no


title: HCC3: plasma from HBV-related HCC patient, case 3

description: Circular RNA expression in the plasma from HBV-related HCC patient, case 3


title: H202_15min_repB


title: H202_15min_repA


title: miRNA_Patient B recurrent tumor 1

source_name: recurrent ovarian tumor

value: recurrent


title: HCC2: plasma from HBV-related HCC patient, case 2

description: Circular RNA expression in the plasma from HBV-related HCC patient, case 2


title: RNA of A.fumigatus infected into macrophage for 2hrs

city: Sungbuk-gu

first: HYEWON

last: SEO

state: Seoul

address: Anam-dong

country: South Korea

institute: Korea university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to Aspergillus fumigatus Af293 whole genome using Tophat
FPKM calculation using cufflinks.
Genome_build: Aspergillus fumigatus A1160 (NCBI)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Aspergillus fumigatus

source_name: conidia

growth_protocol: A. fumigatus was cultured at 37°C in AMM (glucose, salt mix, MgSO4, Hunter’s trace element (TE) solution) HL-60 cells were cultured in RPMI 1640 medium containing 10% fetal bovine serum (FBS) and 1% Gibco™ Antibiotic-Antimycotic at 37°C with 5% CO2. To induce the differentiation of HL-60 cells into macrophage-like cells, HL-60 cells were stimulated with 50 nM 12-o-tetradecanoylphorbol-13-acetate (PMA) for 2 days.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

treatment_protocol: A total of 10^3 A.fumigatus conidia were transferred to 5 × 10^4 differentiated HL-60 cells in RPMI 1640 medium supplemented with 5% FBS. These cells were incubated for 0, 1, and 2 hrs at 37°C with 5% CO2.

tag: infected host

value: HL-60 derived macrophage-like cells

tag: time point

value: 2 hrs at 37°C with 5% CO2


title: RNA of A.fumigatus infected into macrophage for 1hr

value: 1 hr at 37°C with 5% CO2


title: HCC1: plasma from HBV-related HCC patient, case 1

description: Circular RNA expression in the plasma from HBV-related HCC patient, case 1


title: H202_5min_repC


title: HCC5: plasma from HBV-related HCC patient, case 5

description: Circular RNA expression in the plasma from HBV-related HCC patient, case 5


title: miRNA_Patient A recurrent tumor 1

value: patient A


title: H202_5min_repB


title: RNA of A.fumigatus infected into macrophage for 0hr

value: 0 hr at 37°C with 5% CO2


title: CHB5: plasma from chronic hepatitis B patient, case 5

description: Circular RNA expression in the plasma from chronic hepatitis B patient, case 5

value: chronic hepatitis B


title: BIOPSY_1113

tag: abmr (no

tag: date of sample


title: CHB4: plasma from chronic hepatitis B patient, case 4

description: Circular RNA expression in the plasma from chronic hepatitis B patient, case 4


title: H202_5min_repA

tag: stressor

tag: minutes


title: TA_10months_H3K27ac

city: Guangzhou

first: Jiajian

state: Guangdong

address: No. 2 Lujing Road, Yuexiu District,

department: Dermatology Hospital

institute: Southern Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
For ChIP-seq data, sequenced reads were mapped to mm9 genome using bowtie2 with default parameters.
Peaks were called using MACS2 (v2.1.0), a q-value of 10^-2 was used as the cutoff.
Annotations of the peaks were perfomed using in-house programs against the RefSeq gene annotation.
Genome_build: mm9
Supplementary_files_format_and_content: Peak files were generated by MACS2.

organism: Mus musculus

source_name: muscle

growth_protocol: C57/BL6 mice were housed in groups of five and maintained under controlled temperature (20 ± 1 °C), humidity (55 ± 10%), and illumination (12/12 h light cycle with lights on at 07:30 am). Food and water were provided ad libitum. All mice were held in quarantine for 2 weeks before the experiments. Tubes for tunneling and nesting materials (paper towels) were routinely placed in all cages as environmental enrichment. All procedures involving animal care or treatments were approved by the Animal Ethics Committee at Chinese University of Hong Kong (CUHK) on the protection of animals used for scientific purposes. Briefly, all mice were housed in the above condition for 2, 10, and 20 months; and then H3K27ac ChIP-seq was performed on TA muscle tissues from 2 , 10, and 20 months (old) mice.

extract_protocol:
Chromatins from activated SCs were isolated and sonicated to 100-300nt for immunoprecipitation with antibodies. Purified RNAs were fragmented and the cDNA were synthesized by reverse transcription. The resulting double-stranded DNA fragments were end-repaired and A-nucleotide overhangs were added.
ChIP-seq libraries were constructed according to the standard illumina pair-end sequencing procedure.

tag: strain

value: TA muscle

tag: antibody

value: H3K27ac (Abcam ab4729)


title: miRNA_Patient A recurrent tumor 2


title: YCCZ4

city: Zhenjiang

first: Juan

last: YIN

address: Sibaidu Street, Runzhou District, Zhenjiang City, Jiangsu Province

department: School of Biotechnology

institute: Jiangsu University of Science and Technology

description: cultured in the dark for 72 hours

data_processing:
The raw data was obtained by Illumina Hiseq TM 2500 and the quality was assessed using the FastQC and Fast X-Tool kit to detect the base composition, base quality, sequencing saturation and randomness.
Clean reads were obtained by removing adaptor sequences, unknown sequences, low quality reads (Q≤5) and sequences with a length of less than 50 bp.
The clean reads were assembled by Cuffmerge software, then directly mapped to the ribosome RNAdatabase and genome of C. militaris [30] respectively using Bowtie aligner and TopHat2 aligner.
The filtered mapping data were used to reconstruct the transcripts by reference annotation based transcripts (RABT) method with Cufflinks software.
Gene identification and structure optimization
Alternative Splicing (AS) assay, Single-nucleotide polymorphism (SNP)/InDel and SNP mediated RNA editing assay
The expression levels of genes were calculated using FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and the quality was assessed by FPKM distribution assay of different samples.
The gene expression levels were compared based on the DEGSeq and P values were used to adjust the significance of multiple comparisons using the Benjamini and Hochbergmethod. Differentialexpression genes (DEGs)were filtered and identified with the edgeR (http://www.Bioconductor.org/packages/release/bioc/html/edgeR.html) criteria as False Discovery Rate (FDR) and the thresholds was FDR≤0.001 and |log2 Fold Change (Log2FC)|≥1.Cluster analysis of all genes expression patterns from different samples was accomplished too. We also performed the correlation heat ma pand sample cluster analysis based on the DEGs.
gene ontology terms (GO) and Kyoto Encyclopedia of Genes andGenomes (KEGG) enrichment analyses
Genome_build: Cordyceps militaris CM01 Genome sequencing and assembly (https://www.ncbi.nlm.nih.gov/bioproject/41129)
Supplementary_files_format_and_content: All files are named with sample name followed by content name using files format of excel. The processed data include the Gene structure optimization, Genes expression, Pearson correlation coefficient, RNA editing events based on SNP and SNP-InDel of all six samples; the differentially expressed genes of YCCZ1-vs-YCCZ2, YCCZ1-vs-YCCZ3, YCCZ1-vs-YCCZ4, YCCZ1-vs-YCCZ5 and YCCZ1-vs-YCCZ6; alternative splicing of of YCCZ1-vs-YCCZ2, YCCZ1-vs-YCCZ3, YCCZ1-vs-YCCZ4, YCCZ1-vs-YCCZ5 and YCCZ1-vs-YCCZ6.

organism: Cordyceps militaris

source_name: mycelium

growth_protocol: A clump of C. militarisYCC strain hyphae with strong vitality were picked up from slant culture-medium and added into 100 ml improved potato dextrose agar medium (Glucose 2.0 g，KH2PO40.3 g，MgSO40.15 g，Vitamin B2 1 mg，Peptone0.3 g，Yeast extract 0.5 g，Distilled water 100 ml) and cultured in the dark environment at 25±1℃, 130-140 rpm for 72 hours.

extract_protocol:
Total RNA of mycelium was extracted using RNeasy Plant Mini kit and the residual genomic DNA was digested using RNase-free DNase I according to the manufacturer’s protocol.
Poly(A) mRNA was enriched by beads with oligo (dT) and interrupted by fragmentation buffer into suitableshort fragment.100 ng purified and enriched mRNA per sample were used to construct the respective cDNA libraries using NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB,USA). cDNA fragments of 200 bps (±25 bps) were selected and purified by gel-electrophoresis as the templatesfor amplification with PCRfor end reparation andadding poly (A). Six cDNA library would be accomplished after been connectedwith sequencing adaptors

treatment_protocol: Then 5 ml mixture were inoculated into rice-medium to culture the fruiting body. The rest mixture was vacuum filtrated for 1 hour to collect the mycelium and pulverized in liquid nitrogen immediately

value: YCC

tag: passage number

value: 4th passage

value: mycelium


title: YCCZ5

description: cultured in the dark for 72 hours

value: 5th passage


title: H202_0min_repC

tag: replicate


title: CHB3: plasma from chronic hepatitis B patient, case 3

description: Circular RNA expression in the plasma from chronic hepatitis B patient, case 3

tag: gender

value: male

value: plasma


title: YCCZ3

description: cultured in the dark for 72 hours

value: 3rd passage


title: CHB2: plasma from chronic hepatitis B patient, case 2

description: Circular RNA expression in the plasma from chronic hepatitis B patient, case 2

tag: age


title: H202_0min_repB

value: mid-log phase Lactobacillus reuteri culture


title: H202_0min_repA


title: YCCZ1

description: cultured in the dark for 72 hours

value: 1st passage


title: CHB1: plasma from chronic hepatitis B patient, case 1

description: Circular RNA expression in the plasma from chronic hepatitis B patient, case 1

tag: disease state


title: YCCZ2

description: cultured in the dark for 72 hours

value: 2nd passage


title: TA_20months_H3K27ac


title: hsPool: PUS7L_+CMC

status: Public on Aug 14 2019

city: Cambridge

first: Thomas

middle: M

last: Carlile

state: Massachusetts

address: 77 Massachusetts Ave

department: Biology

institute: MIT

data_processing:
Library strategy: Pseduo-seq
Reverse reads were trimmed of 5′ amplicon sequence using cutadapt (-G)
Trimmed paired end reads collapsed using PEAR (default settings)
PCR duplicates collapsed using fastx_collapser
PCR duplicates collapsed using fastx_collapser
Sequences were trimmed of 3′ adapter (both pools) and 10 random Ns (yeast pools only) using cutadapt
Reads were mapped to bowtie indices of the pools with tophat2
Pseudouridylation was assessed using cutom python scripts (see text)
Genome_build: Bowtie indices made from fasta files of pool sequences
Supplementary_files_format_and_content: Tab delimited text files of peak values for pseudouridylation (see text)

source_name: Human Pool

extract_protocol:
Oligo pools (human, Twist Biosciences) were PCR amplified, and in vitro transcribed into RNA, which was then gel purified, folded, and pseudouridylated with a pseudouridine synthase activity source.
RNA was phenol:chloroform extracted from pseuoduridylation reactions, treated with 0.4 M CMC, followed by reversal of CMC modification in bicarbonate buffer. RT was performed, and truncated cDNAs were size selected, followed by circularization & PCR amplification.

tag: pus activity source

value: Recombinant Full Length hPUS7L

tag: cmc use

value: 0.4M CMC

tag: bowtie fasta


title: hsPool: PUS7L_-CMC


title: hsPool: PUS7_+CMC

value: Recombinant Full Length hPUS7


title: hsPool: PUS7_-CMC


title: TA_2months_H3K27ac

tag: tissue


title: hsPool: TRUB1_+CMC

value: Recombinant Full Length hTRUB1


title: hsPool: noPUS_C_+CMC


title: hsPool: PUS1_+CMC


title: hsPool: TRUB1_-CMC


title: WT and crpA deletion strain of A. fumigatus grown at 500 uM zinc conc.

hyb_protocol: After checking labeling efficiency, cyanine 3-labeled and cyanine 5-labeled cRNA target were combined and fragmented by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60 oC for 30min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Aspergillus fumigatus AF293_30K microarray (MYcroarray.com, USA). The arrays hybridized at 57oC for 17 h using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were visualized with Axon GenePix 4000B Scanner (Axon Instrument, CA)

data_processing: The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GenoWiz 4.0 (Ocimumbiosolutions, India). Gene Pix Pro 6.0 (Axon Instruments, CA) was used for background subtraction and GenoWiz 4.0 (Ocimumbiosolutions, India) was used Loess normalization.

organism: Aspergillus fumigatus Af293

label_protocol: The synthesis of target cRNA probes and hybridization were performed using Agilent’s Low Input Quick Amp WT Labeling kit, two color (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 0.2 ug total RNA was mixed with WT primer mix and incubated at 65 oC for 10min. cDNA master mix (5X First strand buffer, 0.1M DTT, 10mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to the reaction mixer. The samples were incubated at 40 oC for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 70 oC for 15min.   The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP). Transcription of dsDNA was performed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40 oC for 2 hours.

growth_protocol: Two strains of A. fumigatus were cultured at 37°C in AMM (glucose, salt mix, MgSO4, Hunter’s trace element (TE) solution) or complete medium (CM/glucose, yeast extract, casamino acid, vitamin solution, salt mix, MgSO4, TE solution) for 24 hours. If necessary, ZnSO4 solution was added.

extract_protocol: After 24 hours, each cells were harvested and total RNA was extracted using TRIzol® (Invitrogen) following the manufacturer’s instructions.

tag: genotype/variation

value: wild type

tag: cell type

value: conidia

tag: treatment

value: high (500uM) zinc concentration

source_name: ΔcrpA 500

value: {delta}crpA


title: hsPool: noPUS_C_-CMC


title: hsPool: PUS1_-CMC


title: WT and crpA deletion strain of A. fumigatus grown at 1 uM zinc conc.

source_name: WT 1

value: low (1uM) zinc concentration

source_name: ΔcrpA 1


title: WT and crpA deletion strain of A. fumigatus grown at 77 uM zinc conc.

value: minimum media (77uM Zinc conc.)

source_name: ΔcrpA 77


title: Rfx6 fl/+ #18

city: Illkirch-Graffenstaden

first: Gérard

last: Gradwohl

address: 1 rue Laurent Fries

country: France

institute: IGBMC

description: Gene expression in control

hyb_protocol: Following fragmentation, labeled cRNA were hybridized on Agilent “Mouse Gene Expression 8x60K Microarray” (Design ID: 028005), for 17 hrs, at 65°C under 10 rpm.

scan_protocol: Following washing, the slides were scanned using an Agilent G2565CA microarray Scanner System, at a 3 µm resolution in a 20-bit scan mode, according to the “AgilentG3_GX_1Color” protocol (scan resolution : 5 µm, Tiff : 20 bit).

data_processing: Raw .tif images were then extracted using Agilent “Feature Extraction, version 10.10.1.1” following “GE1_1010_Sep10” protocol.

source_name: Control, replicate 3

label_protocol: Complementary RNA (cRNA) samples were linearly amplified and labeled with cyanine 3 starting from 100 ng of total RNA (One-Color Microarray-Based Gene Expression Analysis- Low Input Quick Amp Labeling” version 6.5, May 2010, Part Number G4140-90040 protocol)

extract_protocol: Total RNA was extracted using TRI-reagent (Invitrogen)

tag: condition

value: Control


title: Rfx6 fl/+ #21

description: Gene expression in control

source_name: Control, replicate 4


title: Rfx6 fl/fl Ngn3-cre #1

description: Gene expression after an endocrine-specific deletion of Rfx6

source_name: Rfx6 fl/fl Ngn3-cre, replicate 1

value: Mutant


title: Rfx6 fl/fl Ngn3-cre #2

description: Gene expression after an endocrine-specific deletion of Rfx7

source_name: Rfx6 fl/fl Ngn3-cre, replicate 2


title: YCCZ6

description: cultured in the dark for 72 hours

value: YCC

value: 6th passage

value: mycelium


title: Rfx6+/+ #18

description: Gene expression in control


title: Rfx6-/-#11

description: Gene expression after the deletion of Rfx6

source_name: Rfx6 KO, replicate 1


title: Rfx6 fl/+ #8

description: Gene expression in control

source_name: Control, replicate 1


title: Rfx6+/+ #13

description: Gene expression in control


title: Rfx6 fl/fl #13

description: Gene expression in control

source_name: Control, replicate 2


title: Rfx6 fl/fl Ngn3-cre #19

description: Gene expression after an endocrine-specific deletion of Rfx9

source_name: Rfx6 fl/fl Ngn3-cre, replicate 4


title: Rfx6-/- #7

source_name: Rfx6 KO, replicate 4


title: Rfx6+/+ #6

description: Gene expression in control


title: Rfx6+/+ #4

description: Gene expression in control


title: Rfx6 fl/fl Ngn3-cre #4

description: Gene expression after an endocrine-specific deletion of Rfx8

source_name: Rfx6 fl/fl Ngn3-cre, replicate 3


title: Rfx6-/- #16

source_name: Rfx6 KO, replicate 2


title: Rb/Dicer1/p53-deleted PB 1

city: TORONTO

first: Eldad

last: Zacksenhaus

state: ON

address: 67 College St.

country: Canada

institute: University of Toronto

description: RMA expression value derived from Expression Console software

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 2.0 ST Arrays (Affymetrix) and scanned at the Sickkids TCAG Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data were process using Expression Console

source_name: Mouse

label_protocol: stamdard Affymetrix protocol

extract_protocol: mRNA was extracted from mouse pineoblastoma and normal cerebellum using Trizol

value: Brain Tumour


title: Rb/Dicer1/p53-deleted PB 2


title: Rb/p53-deleted PB 12


title: ENDO_MI_5

city: Würzburg

first: Gustavo

middle: Campos

last: Ramos

address: AM Schwarzenberg, 15

department: DZHI

country: Germany

institute: Universitätsklinikum Würzburg

hyb_protocol: Arrays were hybridized overnight at 45°C, including B2 control Oligo and 20 Hybridization mix (affymetrix). On the next day the arrays were washed and stained on the 450 Fluidics Station

scan_protocol: Stained arrays were scanned with the Affymetrix 7G Microchip Scanner

data_processing: The data were analysed with Expression Console (affymetrix) and Transcriptome Analysis Console (affymetrix) with treshold of <-2 or >2 fold expression and p-value (p-Anova) <0,05 and subgrouped.

label: biotin-streptavidin

source_name: CD4+ T-cells,ENDO, Sham-operation

label_protocol: after RNA-preamplification cRNA were prepared according to the standard Affymetrix protocol from 15 µg total RNA (GeneChip® WT Pico Reagent, Affymetrix).

growth_protocol: Mice were kept in individually ventilated cages under specific pathogen-free (SPF) conditions with a 12-hour light-dark cycle, at standard diet ad libitum.

extract_protocol: mice were sacrificed by cervical dislocation, whole-body perfusion with PBS was conducted, and organs were extracted for ex vivo analyses. Lymph nodes cells were obtained after grinding the tissue against a 30um filter mesh in Hank's balanced salt solution.  CD4+ TCRbeta+ single cells were FACSed (FACS Aria-II, purity > 98%) into RLT lysis buffer (Qiagen,  Hilden, Germany) and stored at -80oC. RNA purification was performed using the Qiagen microKit plus.

treatment_protocol: Myocardial infarction group: ligation of left-anterior descending coronary artery. Sham-operation group: thoracotomy without artery ligation. Pain management for 72 h post-surgery (buprenorphine s.c. 0.1 mg/kg body weight)

value: Balb/c background

value: Mediastinal Lymph node

value: CD4+ T-cells


title: ENDO_SHAM_2

source_name: CD4+ T-cells, ENDO, Sham-operation


title: ENDO_SHAM_3


title: Rb/Dicer1/p53-deleted PB 3


title: Dicer1/p53-deleted PB 2


title: Rfx6-/- #20

source_name: Rfx6 KO, replicate 3


title: ENDO_SHAM_1


title: Dicer1/p53-deleted PB 3


title: Dicer1/p53-deleted PB 1


title: ENDO_MI_2

source_name: CD4+ T-cells, ENDO, Myocardial infarction


title: ESCs, PmlKO_RNA-seq_rep3

city: Okazaki

first: Misuzu

last: Kurihara

state: Aichi

address: 5-1 Higashiyama, Myodaiji

institute: National Institute for Basic Biology

data_processing:
Sequence reads were processed with Cutadapt and aligned to mm10 using Tophat.
Differential expression analysis was performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: TDF file was generated by using IGV. XLSX file includes FC and false discovery rate (FDR) from edgeR

source_name: embryonic stem cell

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 20% FBS, GlutaMAX (Gibco), MEM Non-Essential Amino Acids (Gibco), Leukemia inhibitory factor, 1 mM sodium pyruvate, penicillin/streptomycin, 0.1 mM 2-mercaptoethanol, 3 mM CHIR99021 and 1 mM PD0325901. Cells were cultured at 37 °C under 5% CO2 in air.

extract_protocol: Libraries were prepared with TruSeq RNA prep kit (Illumina RS-122-2101).

tag: cell line

tag: genotype

value: Pml-/-


title: ESCs, WT_RNA-seq_rep3


title: ESCs, PmlKO_RNA-seq_rep1


title: ESCs, PmlKO_RNA-seq_rep2


title: ESCs, WT_RNA-seq_rep2


title: TCRM_SHAM_1

source_name: CD4+ T-cells, TCRM, Sham-operation

tag: strain


title: TCRM_MI_5


title: ENDO_MI_4


title: ENDO_MI_3


title: ENDO_MI_1


title: TCRM_SHAM_2

source_name: CD4+ T-cells, TCRM,, Sham-operation


title: TCRM_MI_2

source_name: CD4+ T-cells, TCRM, Myocardial infarction


title: TCRM_MI_3


title: miRNA_Patient A primary tumor

source_name: primary ovarian tumor

tag: subject id

value: patient A

value: ovarian tumor

tag: primary vs recurrent tumor

value: primary


title: RFVCT132

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads mapping to rRNA and ERCC spikes were identified using Bowtie version 1.0.0 and removed from the analysis.
Remaining reads were mapped onto the mm9 assembly of mouse genome using Tophat version 2.0.10 and the Bowtie2 version 2.1.0 aligner.
Quantification of gene expression was performed using HTSeq version 0.6.1 (parameter “--intersection_nonempty”) and gene annotations from Ensembl release 67
Genome_build: mm9
Supplementary_files_format_and_content: The two tab-delimited text file include raw read counts for the two experiments (at 8 days and 3 months)

source_name: RNA in water

growth_protocol: Mutant (Rfx6f/f; Vilin-CreERT2) and control mice  (Rfx6f/+, or Rfx6f/f) were generated starting from Rfx6f/+ (Piccand et al, 2014) and Vilin-CreERT2 mice (El Marjou et al 2004)

extract_protocol:
Ileon was harvested at 8 days and 3 months after tamoxifen gavage. Total RNA was extracred using TRI-reagent or RNeasy® Midi Kit (Qiagen).
Library prep for total RNA-seq Ribozero/standard quantity

treatment_protocol: Adult mice were given tamoxifen (10mg) (Sigma) by gavage twice per day, every second day during 5 days.

value: Rfx6f/f Vilin-CreERT2

tag: time


title: RFVCT129


title: RF130


title: RF124


title: TCRM_MI_1


title: ESCs, WT_RNA-seq_rep1

value: wild type


title: RF117


title: RF113


title: TCRM_SHAM_3


title: TCRM_MI_4


title: Y8_TA_Hi_95 [scRNA-seq]

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description:
mRNA
processed data file: Table_raw_counts_RNA_QSC.txt

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
Genome_build: GRCm38
Supplementary_files_format_and_content: Table_raw_counts_RNA_QSC.txt file contains the raw counts per gene quantified over the exons using the RNA-seq quantitation pipeline in Seqmonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) in the format: <gene name> <chromosome> <start> <counts cell1> <counts cell 2> .... < counts celln>

source_name: Tibialis anterior muscles

extract_protocol:
We prepared scM&T-seq libraries by isolating mRNA on magnetic beads and separating from the single-cell lysate prior to reverse transcription and amplification using Smartseq2 but with 25 PCR cycles.
scM&T-seq (C. Angermueller et al., 2016)

treatment_protocol: Muscles were chopped and put into a 15 ml Falcon tube containing 10 ml of DMEM, 0.08% collagenase D (Sigma, 11 088 882 001), 0.1% trypsin (ThermoFisher, 15090), 10 µg/ml DNaseI (Sigma, 11284932) at 37°C under gentle agitation for 25 min. The digestion was repeated 3 times until complete digestion of the muscle. The supernatants were filtered through a 70-µm cell strainer (Miltenyi, 130-098-462). Cells were spun for 15 min at 515g at 4°C and the pellets were resuspended in 1 ml freezing medium (10% DMSO (Sigma, D2438) in foetal calf serum (FCS, Invitrogen)) for long term storage in liquid nitrogen. Before FACS isolation, samples were thawed in 50 ml of cold DMEM, spun for 15 min at 515g at 4°C. Pellets were resuspended in 300 µl of DMEM 2% FCS 1 µg/mL propidium iodide (Calbiochem, 537060) and filtered through a 40-µm cell strainer (BD Falcon, 352235). Viable cells were isolated based on size, granulosity and GFP expression level (top 10% nGFPHi cells) using a MoFlo Astrios cell sorter (Beckmann Coulter). Single cells were collected in 2.5 µL cold RLT Plus buffer (Qiagen, 1053393) containing 1U/µL RNase inhibitor (Ambion, AM2694) in 96 well-plates (LoBind Eppendorf, 0030129504), flash-frozen on dry ice and stored at -80°C.

value: Muscle stem cells

value: 2 months

tag: mouse id


title: Y8_TA_Hi_96 [scRNA-seq]

tag: age


title: Y8_TA_Hi_9 [scRNA-seq]


title: RFVCT133


title: Y8_TA_Hi_94 [scRNA-seq]


title: Y8_TA_Hi_93 [scRNA-seq]


title: Y8_TA_Hi_92 [scRNA-seq]


title: RFVCT116


title: Y8_TA_Hi_90 [scRNA-seq]


title: Y8_TA_Hi_89 [scRNA-seq]


title: Y8_TA_Hi_8 [scRNA-seq]


title: Y8_TA_Hi_85 [scRNA-seq]


title: Y8_TA_Hi_88 [scRNA-seq]


title: Y8_TA_Hi_87 [scRNA-seq]


title: Y8_TA_Hi_83 [scRNA-seq]


title: Y8_TA_Hi_84 [scRNA-seq]


title: Y8_TA_Hi_80 [scRNA-seq]


title: Y8_TA_Hi_79 [scRNA-seq]


title: Y8_TA_Hi_81 [scRNA-seq]


title: Y8_TA_Hi_77 [scRNA-seq]


title: Y8_TA_Hi_78 [scRNA-seq]


title: Y8_TA_Hi_82 [scRNA-seq]


title: Y8_TA_Hi_75 [scRNA-seq]


title: Y8_TA_Hi_76 [scRNA-seq]


title: Y8_TA_Hi_74 [scRNA-seq]


title: Y8_TA_Hi_73 [scRNA-seq]


title: Y8_TA_Hi_72 [scRNA-seq]


title: Y8_TA_Hi_91 [scRNA-seq]


title: Y8_TA_Hi_70 [scRNA-seq]


title: Y8_TA_Hi_71 [scRNA-seq]


title: Y8_TA_Hi_6 [scRNA-seq]


title: Y8_TA_Hi_86 [scRNA-seq]


title: Y8_TA_Hi_69 [scRNA-seq]


title: Y8_TA_Hi_68 [scRNA-seq]


title: Y8_TA_Hi_7 [scRNA-seq]


title: Y8_TA_Hi_67 [scRNA-seq]


title: Y8_TA_Hi_65 [scRNA-seq]


title: Y8_TA_Hi_66 [scRNA-seq]


title: Y8_TA_Hi_61 [scRNA-seq]


title: Y8_TA_Hi_62 [scRNA-seq]


title: Y8_TA_Hi_63 [scRNA-seq]


title: Y8_TA_Hi_59 [scRNA-seq]


title: Y8_TA_Hi_64 [scRNA-seq]


title: Y8_TA_Hi_54 [scRNA-seq]


title: Y8_TA_Hi_52 [scRNA-seq]


title: Y8_TA_Hi_5 [scRNA-seq]


title: Y8_TA_Hi_55 [scRNA-seq]


title: Y8_TA_Hi_53 [scRNA-seq]


title: Y8_TA_Hi_58 [scRNA-seq]


title: Y8_TA_Hi_4 [scRNA-seq]


title: Y8_TA_Hi_51 [scRNA-seq]


title: Y8_TA_Hi_50 [scRNA-seq]


title: Y8_TA_Hi_49 [scRNA-seq]


title: Y8_TA_Hi_57 [scRNA-seq]


title: Y8_TA_Hi_47 [scRNA-seq]


title: Y8_TA_Hi_48 [scRNA-seq]


title: Y8_TA_Hi_46 [scRNA-seq]


title: Y8_TA_Hi_60 [scRNA-seq]


title: Y8_TA_Hi_30 [scRNA-seq]


title: Y8_TA_Hi_27 [scRNA-seq]


title: Y8_TA_Hi_2 [scRNA-seq]


title: Y8_TA_Hi_28 [scRNA-seq]


title: Y8_TA_Hi_31 [scRNA-seq]


title: Y8_TA_Hi_33 [scRNA-seq]


title: Y8_TA_Hi_39 [scRNA-seq]


title: Y8_TA_Hi_34 [scRNA-seq]


title: Y8_TA_Hi_40 [scRNA-seq]


title: Y8_TA_Hi_43 [scRNA-seq]


title: Y8_TA_Hi_38 [scRNA-seq]


title: Y8_TA_Hi_41 [scRNA-seq]


title: Y8_TA_Hi_3 [scRNA-seq]


title: Y8_TA_Hi_42 [scRNA-seq]


title: Y8_TA_Hi_26 [scRNA-seq]


title: Y8_TA_Hi_32 [scRNA-seq]


title: Y8_TA_Hi_56 [scRNA-seq]


title: Y8_TA_Hi_45 [scRNA-seq]


title: Y8_TA_Hi_44 [scRNA-seq]


title: Y8_TA_Hi_23 [scRNA-seq]


title: Y8_TA_Hi_25 [scRNA-seq]


title: Y8_TA_Hi_22 [scRNA-seq]


title: Y8_TA_Hi_29 [scRNA-seq]


title: Y8_TA_Hi_24 [scRNA-seq]


title: Y8_TA_Hi_36 [scRNA-seq]


title: Y8_TA_Hi_1 [scRNA-seq]


title: Y8_TA_Hi_20 [scRNA-seq]


title: Y8_TA_Hi_21 [scRNA-seq]


title: Y8_TA_Hi_37 [scRNA-seq]


title: Y8_TA_Hi_18 [scRNA-seq]


title: Y8_TA_Hi_16 [scRNA-seq]


title: Y8_TA_Hi_19 [scRNA-seq]


title: Y8_TA_Hi_10 [scRNA-seq]


title: Y8_TA_Hi_13 [scRNA-seq]


title: Y7_TA_Hi_8 [scRNA-seq]


title: Y8_TA_Hi_12 [scRNA-seq]


title: Y7_TA_Hi_93 [scRNA-seq]


title: Y7_TA_Hi_94 [scRNA-seq]


title: Y7_TA_Hi_90 [scRNA-seq]


title: Y8_TA_Hi_14 [scRNA-seq]


title: Y7_TA_Hi_88 [scRNA-seq]


title: Y7_TA_Hi_96 [scRNA-seq]


title: Y8_TA_Hi_11 [scRNA-seq]


title: Y7_TA_Hi_91 [scRNA-seq]


title: Y8_TA_Hi_15 [scRNA-seq]


title: Y7_TA_Hi_87 [scRNA-seq]


title: Y7_TA_Hi_95 [scRNA-seq]


title: Y7_TA_Hi_9 [scRNA-seq]


title: Y7_TA_Hi_89 [scRNA-seq]


title: Y7_TA_Hi_86 [scRNA-seq]


title: Y7_TA_Hi_85 [scRNA-seq]


title: Y7_TA_Hi_92 [scRNA-seq]


title: Y7_TA_Hi_84 [scRNA-seq]


title: Y7_TA_Hi_81 [scRNA-seq]


title: Y7_TA_Hi_83 [scRNA-seq]


title: Y7_TA_Hi_80 [scRNA-seq]


title: Y7_TA_Hi_82 [scRNA-seq]


title: Y8_TA_Hi_17 [scRNA-seq]


title: Y7_TA_Hi_7 [scRNA-seq]


title: Y7_TA_Hi_79 [scRNA-seq]


title: Y7_TA_Hi_78 [scRNA-seq]


title: Y8_TA_Hi_35 [scRNA-seq]


title: Y7_TA_Hi_76 [scRNA-seq]


title: Y7_TA_Hi_77 [scRNA-seq]


title: Y7_TA_Hi_75 [scRNA-seq]


title: Y7_TA_Hi_73 [scRNA-seq]


title: Y7_TA_Hi_72 [scRNA-seq]


title: Y7_TA_Hi_56 [scRNA-seq]


title: Y7_TA_Hi_61 [scRNA-seq]


title: Y7_TA_Hi_5 [scRNA-seq]


title: Y7_TA_Hi_59 [scRNA-seq]


title: Y7_TA_Hi_67 [scRNA-seq]


title: Y7_TA_Hi_58 [scRNA-seq]


title: Y7_TA_Hi_55 [scRNA-seq]


title: Y7_TA_Hi_68 [scRNA-seq]


title: Y7_TA_Hi_54 [scRNA-seq]


title: Y7_TA_Hi_66 [scRNA-seq]


title: Y7_TA_Hi_6 [scRNA-seq]


title: Y7_TA_Hi_62 [scRNA-seq]


title: Y7_TA_Hi_57 [scRNA-seq]


title: Y7_TA_Hi_71 [scRNA-seq]


title: Y7_TA_Hi_65 [scRNA-seq]


title: Y7_TA_Hi_64 [scRNA-seq]


title: Y7_TA_Hi_53 [scRNA-seq]


title: Y7_TA_Hi_69 [scRNA-seq]


title: Y7_TA_Hi_74 [scRNA-seq]


title: Y7_TA_Hi_63 [scRNA-seq]


title: Y7_TA_Hi_70 [scRNA-seq]


title: Y7_TA_Hi_60 [scRNA-seq]


title: Y7_TA_Hi_50 [scRNA-seq]


title: Y7_TA_Hi_49 [scRNA-seq]


title: Y7_TA_Hi_4 [scRNA-seq]


title: Y7_TA_Hi_48 [scRNA-seq]


title: Y7_TA_Hi_46 [scRNA-seq]


title: Y7_TA_Hi_52 [scRNA-seq]


title: Y7_TA_Hi_51 [scRNA-seq]


title: Y7_TA_Hi_45 [scRNA-seq]


title: Y7_TA_Hi_44 [scRNA-seq]


title: Y7_TA_Hi_41 [scRNA-seq]


title: Y7_TA_Hi_43 [scRNA-seq]


title: Y7_TA_Hi_36 [scRNA-seq]


title: Y7_TA_Hi_37 [scRNA-seq]


title: Y7_TA_Hi_31 [scRNA-seq]


title: Y7_TA_Hi_34 [scRNA-seq]


title: Y7_TA_Hi_40 [scRNA-seq]


title: Y7_TA_Hi_39 [scRNA-seq]


title: Y7_TA_Hi_33 [scRNA-seq]


title: Y7_TA_Hi_42 [scRNA-seq]


title: Y7_TA_Hi_2 [scRNA-seq]


title: Y7_TA_Hi_29 [scRNA-seq]


title: Y7_TA_Hi_28 [scRNA-seq]


title: Y7_TA_Hi_32 [scRNA-seq]


title: Y7_TA_Hi_27 [scRNA-seq]


title: Y7_TA_Hi_38 [scRNA-seq]


title: Y7_TA_Hi_30 [scRNA-seq]


title: Y7_TA_Hi_26 [scRNA-seq]


title: Y7_TA_Hi_47 [scRNA-seq]


title: Y7_TA_Hi_23 [scRNA-seq]


title: Y7_TA_Hi_22 [scRNA-seq]


title: Y7_TA_Hi_24 [scRNA-seq]


title: Y7_TA_Hi_21 [scRNA-seq]


title: Y7_TA_Hi_1 [scRNA-seq]


title: Y7_TA_Hi_35 [scRNA-seq]


title: Y7_TA_Hi_3 [scRNA-seq]


title: Y7_TA_Hi_20 [scRNA-seq]


title: Y7_TA_Hi_19 [scRNA-seq]


title: Y7_TA_Hi_16 [scRNA-seq]


title: Y7_TA_Hi_17 [scRNA-seq]


title: Y7_TA_Hi_18 [scRNA-seq]


title: Y7_TA_Hi_25 [scRNA-seq]


title: Y7_TA_Hi_15 [scRNA-seq]


title: Y7_TA_Hi_14 [scRNA-seq]


title: Y7_TA_Hi_13 [scRNA-seq]


title: Y7_TA_Hi_12 [scRNA-seq]


title: Y7_TA_Hi_10 [scRNA-seq]


title: Y5_TA_Hi_96 [scRNA-seq]


title: Y5_TA_Hi_95 [scRNA-seq]


title: Y5_TA_Hi_93 [scRNA-seq]


title: Y5_TA_Hi_9 [scRNA-seq]


title: Y5_TA_Hi_89 [scRNA-seq]


title: Y5_TA_Hi_8 [scRNA-seq]


title: Y5_TA_Hi_92 [scRNA-seq]


title: Y5_TA_Hi_91 [scRNA-seq]


title: Y5_TA_Hi_94 [scRNA-seq]


title: Y5_TA_Hi_90 [scRNA-seq]


title: Y7_TA_Hi_11 [scRNA-seq]


title: Y5_TA_Hi_87 [scRNA-seq]


title: Y5_TA_Hi_85 [scRNA-seq]


title: Y5_TA_Hi_88 [scRNA-seq]


title: Y5_TA_Hi_81 [scRNA-seq]


title: Y5_TA_Hi_84 [scRNA-seq]


title: Y5_TA_Hi_83 [scRNA-seq]


title: Y5_TA_Hi_80 [scRNA-seq]


title: Y5_TA_Hi_82 [scRNA-seq]


title: Y5_TA_Hi_7 [scRNA-seq]


title: Y5_TA_Hi_86 [scRNA-seq]


title: Y5_TA_Hi_78 [scRNA-seq]


title: Y5_TA_Hi_75 [scRNA-seq]


title: Y5_TA_Hi_74 [scRNA-seq]


title: Y5_TA_Hi_72 [scRNA-seq]


title: Y5_TA_Hi_76 [scRNA-seq]


title: Y5_TA_Hi_6 [scRNA-seq]


title: Y5_TA_Hi_64 [scRNA-seq]


title: Y5_TA_Hi_61 [scRNA-seq]


title: Y5_TA_Hi_65 [scRNA-seq]


title: Y5_TA_Hi_60 [scRNA-seq]


title: Y5_TA_Hi_66 [scRNA-seq]


title: Y5_TA_Hi_71 [scRNA-seq]


title: Y5_TA_Hi_69 [scRNA-seq]


title: Y5_TA_Hi_5 [scRNA-seq]


title: Y5_TA_Hi_59 [scRNA-seq]


title: Y5_TA_Hi_62 [scRNA-seq]


title: Y5_TA_Hi_68 [scRNA-seq]


title: Y5_TA_Hi_70 [scRNA-seq]


title: Y5_TA_Hi_67 [scRNA-seq]


title: Y5_TA_Hi_63 [scRNA-seq]


title: Y5_TA_Hi_58 [scRNA-seq]


title: Y5_TA_Hi_56 [scRNA-seq]


title: Y5_TA_Hi_55 [scRNA-seq]


title: Y5_TA_Hi_53 [scRNA-seq]


title: Y5_TA_Hi_57 [scRNA-seq]


title: Y5_TA_Hi_79 [scRNA-seq]


title: Y5_TA_Hi_54 [scRNA-seq]


title: Y5_TA_Hi_77 [scRNA-seq]


title: Y5_TA_Hi_73 [scRNA-seq]


title: Y5_TA_Hi_52 [scRNA-seq]


title: Y5_TA_Hi_51 [scRNA-seq]


title: Y5_TA_Hi_49 [scRNA-seq]


title: Y5_TA_Hi_48 [scRNA-seq]


title: Y5_TA_Hi_47 [scRNA-seq]


title: Y5_TA_Hi_46 [scRNA-seq]


title: Y5_TA_Hi_45 [scRNA-seq]


title: Y5_TA_Hi_43 [scRNA-seq]


title: Y5_TA_Hi_44 [scRNA-seq]


title: Y5_TA_Hi_3 [scRNA-seq]


title: Y5_TA_Hi_40 [scRNA-seq]


title: Y5_TA_Hi_39 [scRNA-seq]


title: Y5_TA_Hi_41 [scRNA-seq]


title: Y5_TA_Hi_35 [scRNA-seq]


title: Y5_TA_Hi_34 [scRNA-seq]


title: Y5_TA_Hi_38 [scRNA-seq]


title: Y5_TA_Hi_36 [scRNA-seq]


title: Y5_TA_Hi_37 [scRNA-seq]


title: Y5_TA_Hi_2 [scRNA-seq]


title: Y5_TA_Hi_29 [scRNA-seq]


title: Y5_TA_Hi_30 [scRNA-seq]


title: Y5_TA_Hi_32 [scRNA-seq]


title: Y5_TA_Hi_31 [scRNA-seq]


title: Y5_TA_Hi_33 [scRNA-seq]


title: Y5_TA_Hi_28 [scRNA-seq]


title: Y5_TA_Hi_26 [scRNA-seq]


title: Y5_TA_Hi_50 [scRNA-seq]


title: Y5_TA_Hi_25 [scRNA-seq]


title: Y5_TA_Hi_27 [scRNA-seq]


title: Y5_TA_Hi_4 [scRNA-seq]


title: Y5_TA_Hi_24 [scRNA-seq]


title: Y5_TA_Hi_42 [scRNA-seq]


title: Y5_TA_Hi_23 [scRNA-seq]


title: Y5_TA_Hi_20 [scRNA-seq]


title: Y5_TA_Hi_21 [scRNA-seq]


title: Y5_TA_Hi_19 [scRNA-seq]


title: Y5_TA_Hi_1 [scRNA-seq]


title: Y5_TA_Hi_22 [scRNA-seq]


title: Y5_TA_Hi_14 [scRNA-seq]


title: Y5_TA_Hi_15 [scRNA-seq]


title: Y5_TA_Hi_18 [scRNA-seq]


title: Y5_TA_Hi_17 [scRNA-seq]


title: Y5_TA_Hi_12 [scRNA-seq]


title: Y5_TA_Hi_16 [scRNA-seq]


title: Y4_TA_Hi_94 [scRNA-seq]


title: Y4_TA_Hi_96 [scRNA-seq]


title: Y4_TA_Hi_95 [scRNA-seq]


title: Y5_TA_Hi_13 [scRNA-seq]


title: Y4_TA_Hi_90 [scRNA-seq]


title: Y4_TA_Hi_89 [scRNA-seq]


title: Y4_TA_Hi_91 [scRNA-seq]


title: Y4_TA_Hi_93 [scRNA-seq]


title: Y4_TA_Hi_88 [scRNA-seq]


title: Y4_TA_Hi_87 [scRNA-seq]


title: Y4_TA_Hi_92 [scRNA-seq]


title: Y5_TA_Hi_11 [scRNA-seq]


title: Y4_TA_Hi_8 [scRNA-seq]


title: Y5_TA_Hi_10 [scRNA-seq]


title: Y4_TA_Hi_86 [scRNA-seq]


title: Y4_TA_Hi_9 [scRNA-seq]


title: Y4_TA_Hi_84 [scRNA-seq]


title: Y4_TA_Hi_85 [scRNA-seq]


title: Y4_TA_Hi_83 [scRNA-seq]


title: Y4_TA_Hi_82 [scRNA-seq]


title: Y4_TA_Hi_81 [scRNA-seq]


title: Y4_TA_Hi_79 [scRNA-seq]


title: Y4_TA_Hi_78 [scRNA-seq]


title: Y4_TA_Hi_77 [scRNA-seq]


title: Y4_TA_Hi_76 [scRNA-seq]


title: Y4_TA_Hi_75 [scRNA-seq]


title: Y4_TA_Hi_74 [scRNA-seq]


title: Y4_TA_Hi_72 [scRNA-seq]


title: Y4_TA_Hi_73 [scRNA-seq]


title: Y4_TA_Hi_70 [scRNA-seq]


title: Y4_TA_Hi_69 [scRNA-seq]


title: Y4_TA_Hi_68 [scRNA-seq]


title: Y4_TA_Hi_67 [scRNA-seq]


title: Y4_TA_Hi_64 [scRNA-seq]


title: Y4_TA_Hi_63 [scRNA-seq]


title: Y4_TA_Hi_66 [scRNA-seq]


title: Y4_TA_Hi_6 [scRNA-seq]


title: Y4_TA_Hi_60 [scRNA-seq]


title: Y4_TA_Hi_59 [scRNA-seq]


title: Y4_TA_Hi_62 [scRNA-seq]


title: Y4_TA_Hi_5 [scRNA-seq]


title: Y4_TA_Hi_58 [scRNA-seq]


title: Y4_TA_Hi_61 [scRNA-seq]


title: Y4_TA_Hi_65 [scRNA-seq]


title: Y4_TA_Hi_56 [scRNA-seq]


title: Y4_TA_Hi_55 [scRNA-seq]


title: Y4_TA_Hi_57 [scRNA-seq]


title: Y4_TA_Hi_54 [scRNA-seq]


title: Y4_TA_Hi_80 [scRNA-seq]


title: Y4_TA_Hi_7 [scRNA-seq]


title: Y4_TA_Hi_53 [scRNA-seq]


title: Y4_TA_Hi_51 [scRNA-seq]


title: Y4_TA_Hi_71 [scRNA-seq]


title: Y4_TA_Hi_52 [scRNA-seq]


title: Y4_TA_Hi_49 [scRNA-seq]


title: Y4_TA_Hi_48 [scRNA-seq]


title: Y4_TA_Hi_47 [scRNA-seq]


title: Y4_TA_Hi_46 [scRNA-seq]


title: Y4_TA_Hi_44 [scRNA-seq]


title: Y4_TA_Hi_45 [scRNA-seq]


title: Y4_TA_Hi_3 [scRNA-seq]


title: Y4_TA_Hi_37 [scRNA-seq]


title: Y4_TA_Hi_41 [scRNA-seq]


title: Y4_TA_Hi_39 [scRNA-seq]


title: Y4_TA_Hi_38 [scRNA-seq]


title: Y4_TA_Hi_36 [scRNA-seq]


title: Y4_TA_Hi_34 [scRNA-seq]


title: Y4_TA_Hi_33 [scRNA-seq]


title: Y4_TA_Hi_31 [scRNA-seq]


title: Y4_TA_Hi_35 [scRNA-seq]


title: Y4_TA_Hi_30 [scRNA-seq]


title: Y4_TA_Hi_2 [scRNA-seq]


title: Y4_TA_Hi_40 [scRNA-seq]


title: Y4_TA_Hi_29 [scRNA-seq]


title: Y4_TA_Hi_28 [scRNA-seq]


title: Y4_TA_Hi_50 [scRNA-seq]


title: Y4_TA_Hi_4 [scRNA-seq]


title: Y4_TA_Hi_26 [scRNA-seq]


title: Y4_TA_Hi_25 [scRNA-seq]


title: Y4_TA_Hi_23 [scRNA-seq]


title: Y4_TA_Hi_21 [scRNA-seq]


title: Y4_TA_Hi_20 [scRNA-seq]


title: Y4_TA_Hi_42 [scRNA-seq]


title: Y4_TA_Hi_18 [scRNA-seq]


title: Y4_TA_Hi_43 [scRNA-seq]


title: Y4_TA_Hi_1 [scRNA-seq]


title: Y4_TA_Hi_32 [scRNA-seq]


title: Y4_TA_Hi_17 [scRNA-seq]


title: Y4_TA_Hi_19 [scRNA-seq]


title: Y4_TA_Hi_16 [scRNA-seq]


title: Y4_TA_Hi_15 [scRNA-seq]


title: Y4_TA_Hi_14 [scRNA-seq]


title: Y4_TA_Hi_13 [scRNA-seq]


title: Y4_TA_Hi_12 [scRNA-seq]


title: Y4_TA_Hi_10 [scRNA-seq]


title: Y4_TA_Hi_11 [scRNA-seq]


title: Y2_TA_Hi_9 [scRNA-seq]


title: Y2_TA_Hi_94 [scRNA-seq]


title: Y2_TA_Hi_95 [scRNA-seq]


title: Y4_TA_Hi_24 [scRNA-seq]


title: Y2_TA_Hi_91 [scRNA-seq]


title: Y2_TA_Hi_90 [scRNA-seq]


title: Y2_TA_Hi_93 [scRNA-seq]


title: Y2_TA_Hi_92 [scRNA-seq]


title: Y4_TA_Hi_22 [scRNA-seq]


title: Y2_TA_Hi_8 [scRNA-seq]


title: Y2_TA_Hi_88 [scRNA-seq]


title: Y2_TA_Hi_89 [scRNA-seq]


title: Y2_TA_Hi_87 [scRNA-seq]


title: Y2_TA_Hi_85 [scRNA-seq]


title: Y2_TA_Hi_86 [scRNA-seq]


title: Y4_TA_Hi_27 [scRNA-seq]


title: Y2_TA_Hi_84 [scRNA-seq]


title: Y2_TA_Hi_83 [scRNA-seq]


title: Y2_TA_Hi_7 [scRNA-seq]


title: Y2_TA_Hi_82 [scRNA-seq]


title: Y2_TA_Hi_79 [scRNA-seq]


title: Y2_TA_Hi_81 [scRNA-seq]


title: Y2_TA_Hi_80 [scRNA-seq]


title: Y2_TA_Hi_96 [scRNA-seq]


title: Y2_TA_Hi_76 [scRNA-seq]


title: Y2_TA_Hi_75 [scRNA-seq]


title: Y2_TA_Hi_74 [scRNA-seq]


title: Y2_TA_Hi_73 [scRNA-seq]


title: Y2_TA_Hi_70 [scRNA-seq]


title: Y2_TA_Hi_6 [scRNA-seq]


title: Y2_TA_Hi_71 [scRNA-seq]


title: Y2_TA_Hi_68 [scRNA-seq]


title: Y2_TA_Hi_69 [scRNA-seq]


title: Y2_TA_Hi_67 [scRNA-seq]


title: Y2_TA_Hi_72 [scRNA-seq]


title: Y2_TA_Hi_65 [scRNA-seq]


title: Y2_TA_Hi_66 [scRNA-seq]


title: Y2_TA_Hi_64 [scRNA-seq]


title: Y2_TA_Hi_63 [scRNA-seq]


title: Y2_TA_Hi_62 [scRNA-seq]


title: Y2_TA_Hi_77 [scRNA-seq]


title: Y2_TA_Hi_5 [scRNA-seq]


title: Y2_TA_Hi_61 [scRNA-seq]


title: Y2_TA_Hi_60 [scRNA-seq]


title: Y2_TA_Hi_57 [scRNA-seq]


title: Y2_TA_Hi_58 [scRNA-seq]


title: Y2_TA_Hi_55 [scRNA-seq]


title: Y2_TA_Hi_59 [scRNA-seq]


title: Y2_TA_Hi_54 [scRNA-seq]


title: Y2_TA_Hi_78 [scRNA-seq]


title: Y2_TA_Hi_51 [scRNA-seq]


title: Y2_TA_Hi_56 [scRNA-seq]


title: Y2_TA_Hi_50 [scRNA-seq]


title: Y2_TA_Hi_4 [scRNA-seq]


title: Y2_TA_Hi_53 [scRNA-seq]


title: Y2_TA_Hi_48 [scRNA-seq]


title: Y2_TA_Hi_43 [scRNA-seq]


title: Y2_TA_Hi_46 [scRNA-seq]


title: Y2_TA_Hi_45 [scRNA-seq]


title: Y2_TA_Hi_42 [scRNA-seq]


title: Y2_TA_Hi_41 [scRNA-seq]


title: Y2_TA_Hi_44 [scRNA-seq]


title: Y2_TA_Hi_40 [scRNA-seq]


title: Y2_TA_Hi_3 [scRNA-seq]


title: Y2_TA_Hi_39 [scRNA-seq]


title: Y2_TA_Hi_37 [scRNA-seq]


title: Y2_TA_Hi_36 [scRNA-seq]


title: Y2_TA_Hi_52 [scRNA-seq]


title: Y2_TA_Hi_33 [scRNA-seq]


title: Y2_TA_Hi_32 [scRNA-seq]


title: Y2_TA_Hi_2 [scRNA-seq]


title: Y2_TA_Hi_27 [scRNA-seq]


title: Y2_TA_Hi_30 [scRNA-seq]


title: Y2_TA_Hi_35 [scRNA-seq]


title: Y2_TA_Hi_49 [scRNA-seq]


title: Y2_TA_Hi_28 [scRNA-seq]


title: Y2_TA_Hi_47 [scRNA-seq]


title: Y2_TA_Hi_24 [scRNA-seq]


title: Y2_TA_Hi_26 [scRNA-seq]


title: Y2_TA_Hi_25 [scRNA-seq]


title: Y2_TA_Hi_22 [scRNA-seq]


title: Y2_TA_Hi_38 [scRNA-seq]


title: Y2_TA_Hi_17 [scRNA-seq]


title: Y2_TA_Hi_18 [scRNA-seq]


title: Y2_TA_Hi_21 [scRNA-seq]


title: Y2_TA_Hi_23 [scRNA-seq]


title: Y2_TA_Hi_20 [scRNA-seq]


title: Y2_TA_Hi_16 [scRNA-seq]


title: Y2_TA_Hi_19 [scRNA-seq]


title: Y2_TA_Hi_34 [scRNA-seq]


title: Y2_TA_Hi_12 [scRNA-seq]


title: Y2_TA_Hi_15 [scRNA-seq]


title: Y2_TA_Hi_13 [scRNA-seq]


title: Y2_TA_Hi_31 [scRNA-seq]


title: Y2_TA_Hi_29 [scRNA-seq]


title: Y2_TA_Hi_11 [scRNA-seq]


title: O8_TA_Hi_9 [scRNA-seq]

value: 24 months


title: Y2_TA_Hi_10 [scRNA-seq]


title: O8_TA_Hi_96 [scRNA-seq]


title: O8_TA_Hi_95 [scRNA-seq]


title: O8_TA_Hi_94 [scRNA-seq]


title: O8_TA_Hi_93 [scRNA-seq]


title: O8_TA_Hi_92 [scRNA-seq]


title: Y2_TA_Hi_1 [scRNA-seq]


title: O8_TA_Hi_8 [scRNA-seq]


title: O8_TA_Hi_90 [scRNA-seq]


title: O8_TA_Hi_91 [scRNA-seq]


title: O8_TA_Hi_88 [scRNA-seq]


title: O8_TA_Hi_86 [scRNA-seq]


title: O8_TA_Hi_87 [scRNA-seq]


title: Y2_TA_Hi_14 [scRNA-seq]


title: O8_TA_Hi_81 [scRNA-seq]


title: O8_TA_Hi_82 [scRNA-seq]


title: O8_TA_Hi_83 [scRNA-seq]


title: O8_TA_Hi_84 [scRNA-seq]


title: O8_TA_Hi_7 [scRNA-seq]


title: O8_TA_Hi_80 [scRNA-seq]


title: O8_TA_Hi_85 [scRNA-seq]


title: O8_TA_Hi_79 [scRNA-seq]


title: O8_TA_Hi_78 [scRNA-seq]


title: O8_TA_Hi_76 [scRNA-seq]


title: O8_TA_Hi_77 [scRNA-seq]


title: O8_TA_Hi_75 [scRNA-seq]


title: O8_TA_Hi_69 [scRNA-seq]


title: O8_TA_Hi_67 [scRNA-seq]


title: O8_TA_Hi_73 [scRNA-seq]


title: O8_TA_Hi_74 [scRNA-seq]


title: O8_TA_Hi_71 [scRNA-seq]


title: O8_TA_Hi_70 [scRNA-seq]


title: O8_TA_Hi_68 [scRNA-seq]


title: O8_TA_Hi_6 [scRNA-seq]


title: O8_TA_Hi_64 [scRNA-seq]


title: O8_TA_Hi_61 [scRNA-seq]


title: O8_TA_Hi_62 [scRNA-seq]


title: O8_TA_Hi_5 [scRNA-seq]


title: O8_TA_Hi_66 [scRNA-seq]


title: O8_TA_Hi_89 [scRNA-seq]


title: O8_TA_Hi_63 [scRNA-seq]


title: O8_TA_Hi_58 [scRNA-seq]


title: O8_TA_Hi_56 [scRNA-seq]


title: O8_TA_Hi_55 [scRNA-seq]


title: O8_TA_Hi_53 [scRNA-seq]


title: O8_TA_Hi_52 [scRNA-seq]


title: O8_TA_Hi_54 [scRNA-seq]


title: O8_TA_Hi_57 [scRNA-seq]


title: O8_TA_Hi_59 [scRNA-seq]


title: O8_TA_Hi_72 [scRNA-seq]


title: O8_TA_Hi_51 [scRNA-seq]


title: O8_TA_Hi_50 [scRNA-seq]


title: O8_TA_Hi_60 [scRNA-seq]


title: O8_TA_Hi_49 [scRNA-seq]


title: O8_TA_Hi_4 [scRNA-seq]


title: O8_TA_Hi_48 [scRNA-seq]


title: O8_TA_Hi_47 [scRNA-seq]


title: O8_TA_Hi_44 [scRNA-seq]


title: O8_TA_Hi_45 [scRNA-seq]


title: O8_TA_Hi_38 [scRNA-seq]


title: O8_TA_Hi_35 [scRNA-seq]


title: O8_TA_Hi_39 [scRNA-seq]


title: O8_TA_Hi_37 [scRNA-seq]


title: O8_TA_Hi_40 [scRNA-seq]


title: O8_TA_Hi_46 [scRNA-seq]


title: O8_TA_Hi_3 [scRNA-seq]


title: O8_TA_Hi_41 [scRNA-seq]


title: O8_TA_Hi_34 [scRNA-seq]


title: O8_TA_Hi_36 [scRNA-seq]


title: O8_TA_Hi_32 [scRNA-seq]


title: O8_TA_Hi_2 [scRNA-seq]


title: O8_TA_Hi_30 [scRNA-seq]


title: O8_TA_Hi_29 [scRNA-seq]


title: O8_TA_Hi_31 [scRNA-seq]


title: O8_TA_Hi_28 [scRNA-seq]


title: O8_TA_Hi_33 [scRNA-seq]


title: O8_TA_Hi_26 [scRNA-seq]


title: O8_TA_Hi_27 [scRNA-seq]


title: O8_TA_Hi_42 [scRNA-seq]


title: O8_TA_Hi_43 [scRNA-seq]


title: O8_TA_Hi_25 [scRNA-seq]


title: O8_TA_Hi_24 [scRNA-seq]


title: O8_TA_Hi_23 [scRNA-seq]


title: O8_TA_Hi_22 [scRNA-seq]


title: O8_TA_Hi_20 [scRNA-seq]


title: O8_TA_Hi_19 [scRNA-seq]


title: O8_TA_Hi_18 [scRNA-seq]


title: O8_TA_Hi_15 [scRNA-seq]


title: O8_TA_Hi_12 [scRNA-seq]


title: O5_TA_Hi_9 [scRNA-seq]


title: O8_TA_Hi_14 [scRNA-seq]


title: O8_TA_Hi_13 [scRNA-seq]


title: O8_TA_Hi_10 [scRNA-seq]


title: O8_TA_Hi_11 [scRNA-seq]


title: O5_TA_Hi_96 [scRNA-seq]


title: O5_TA_Hi_95 [scRNA-seq]


title: O5_TA_Hi_94 [scRNA-seq]


title: O5_TA_Hi_91 [scRNA-seq]


title: O5_TA_Hi_92 [scRNA-seq]


title: O5_TA_Hi_93 [scRNA-seq]


title: O5_TA_Hi_89 [scRNA-seq]


title: O8_TA_Hi_21 [scRNA-seq]


title: O5_TA_Hi_88 [scRNA-seq]


title: O5_TA_Hi_86 [scRNA-seq]


title: O5_TA_Hi_8 [scRNA-seq]


title: O5_TA_Hi_85 [scRNA-seq]


title: O5_TA_Hi_87 [scRNA-seq]


title: O5_TA_Hi_84 [scRNA-seq]


title: O5_TA_Hi_82 [scRNA-seq]


title: O5_TA_Hi_83 [scRNA-seq]


title: O8_TA_Hi_16 [scRNA-seq]


title: O5_TA_Hi_81 [scRNA-seq]


title: O5_TA_Hi_78 [scRNA-seq]


title: O5_TA_Hi_79 [scRNA-seq]


title: O5_TA_Hi_76 [scRNA-seq]


title: O5_TA_Hi_77 [scRNA-seq]


title: O5_TA_Hi_75 [scRNA-seq]


title: O5_TA_Hi_73 [scRNA-seq]


title: O5_TA_Hi_72 [scRNA-seq]


title: O8_TA_Hi_1 [scRNA-seq]


title: O5_TA_Hi_90 [scRNA-seq]


title: O5_TA_Hi_80 [scRNA-seq]


title: O5_TA_Hi_71 [scRNA-seq]


title: O5_TA_Hi_70 [scRNA-seq]


title: O5_TA_Hi_74 [scRNA-seq]


title: O5_TA_Hi_6 [scRNA-seq]


title: O5_TA_Hi_69 [scRNA-seq]


title: O5_TA_Hi_7 [scRNA-seq]


title: O5_TA_Hi_68 [scRNA-seq]


title: O5_TA_Hi_67 [scRNA-seq]


title: O5_TA_Hi_65 [scRNA-seq]


title: O5_TA_Hi_66 [scRNA-seq]


title: O5_TA_Hi_64 [scRNA-seq]


title: O5_TA_Hi_62 [scRNA-seq]


title: O5_TA_Hi_63 [scRNA-seq]


title: O5_TA_Hi_5 [scRNA-seq]


title: O5_TA_Hi_59 [scRNA-seq]


title: O5_TA_Hi_60 [scRNA-seq]


title: O5_TA_Hi_61 [scRNA-seq]


title: O5_TA_Hi_55 [scRNA-seq]


title: O5_TA_Hi_51 [scRNA-seq]


title: O5_TA_Hi_56 [scRNA-seq]


title: O5_TA_Hi_57 [scRNA-seq]


title: O5_TA_Hi_53 [scRNA-seq]


title: O8_TA_Hi_17 [scRNA-seq]


title: O5_TA_Hi_47 [scRNA-seq]


title: O5_TA_Hi_54 [scRNA-seq]


title: O5_TA_Hi_49 [scRNA-seq]


title: O5_TA_Hi_50 [scRNA-seq]


title: O5_TA_Hi_48 [scRNA-seq]


title: O5_TA_Hi_45 [scRNA-seq]


title: O5_TA_Hi_58 [scRNA-seq]


title: O5_TA_Hi_46 [scRNA-seq]


title: O5_TA_Hi_4 [scRNA-seq]


title: O5_TA_Hi_3 [scRNA-seq]


title: O5_TA_Hi_41 [scRNA-seq]


title: O5_TA_Hi_43 [scRNA-seq]


title: O5_TA_Hi_42 [scRNA-seq]


title: O5_TA_Hi_39 [scRNA-seq]


title: O5_TA_Hi_37 [scRNA-seq]


title: O5_TA_Hi_44 [scRNA-seq]


title: O5_TA_Hi_38 [scRNA-seq]


title: O5_TA_Hi_52 [scRNA-seq]


title: O5_TA_Hi_31 [scRNA-seq]


title: O5_TA_Hi_35 [scRNA-seq]


title: O5_TA_Hi_33 [scRNA-seq]


title: O5_TA_Hi_30 [scRNA-seq]


title: O5_TA_Hi_32 [scRNA-seq]


title: O5_TA_Hi_2 [scRNA-seq]


title: O5_TA_Hi_29 [scRNA-seq]


title: O5_TA_Hi_34 [scRNA-seq]


title: O5_TA_Hi_28 [scRNA-seq]


title: O5_TA_Hi_25 [scRNA-seq]


title: O5_TA_Hi_26 [scRNA-seq]


title: O5_TA_Hi_24 [scRNA-seq]


title: O5_TA_Hi_23 [scRNA-seq]


title: O5_TA_Hi_21 [scRNA-seq]


title: O5_TA_Hi_40 [scRNA-seq]


title: O5_TA_Hi_27 [scRNA-seq]


title: O5_TA_Hi_20 [scRNA-seq]


title: O5_TA_Hi_1 [scRNA-seq]


title: O5_TA_Hi_36 [scRNA-seq]


title: O5_TA_Hi_18 [scRNA-seq]


title: O5_TA_Hi_17 [scRNA-seq]


title: O5_TA_Hi_19 [scRNA-seq]


title: O5_TA_Hi_16 [scRNA-seq]


title: O8_TA_Hi_65 [scRNA-seq]


title: O5_TA_Hi_14 [scRNA-seq]


title: O5_TA_Hi_12 [scRNA-seq]


title: O5_TA_Hi_15 [scRNA-seq]


title: O5_TA_Hi_22 [scRNA-seq]


title: O1_TA_Hi_96 [scRNA-seq]


title: O5_TA_Hi_11 [scRNA-seq]


title: O1_TA_Hi_9 [scRNA-seq]


title: O1_TA_Hi_94 [scRNA-seq]


title: O1_TA_Hi_95 [scRNA-seq]


title: O1_TA_Hi_93 [scRNA-seq]


title: O1_TA_Hi_90 [scRNA-seq]


title: O1_TA_Hi_91 [scRNA-seq]


title: O1_TA_Hi_89 [scRNA-seq]


title: O1_TA_Hi_8 [scRNA-seq]


title: O1_TA_Hi_88 [scRNA-seq]


title: O5_TA_Hi_13 [scRNA-seq]


title: O1_TA_Hi_81 [scRNA-seq]


title: O1_TA_Hi_86 [scRNA-seq]


title: O1_TA_Hi_7 [scRNA-seq]


title: O1_TA_Hi_87 [scRNA-seq]


title: O1_TA_Hi_78 [scRNA-seq]


title: O1_TA_Hi_85 [scRNA-seq]


title: O1_TA_Hi_80 [scRNA-seq]


title: O1_TA_Hi_82 [scRNA-seq]


title: O1_TA_Hi_83 [scRNA-seq]


title: O1_TA_Hi_79 [scRNA-seq]


title: O1_TA_Hi_92 [scRNA-seq]


title: O5_TA_Hi_10 [scRNA-seq]


title: O1_TA_Hi_84 [scRNA-seq]


title: ESCs, WT_input

data_processing:
Sequence reads were trimmed by using Trimmomatic, then mapped to mm10 using bowtie2 with parameters --maxins 2000 --very-sensitive.
Non-uniquely mapping reads were filtered out using XS tag.
PCR duplicates and ENCODE blacklisted regions were removed using Picard Tools and bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig file was generated by using bamCoverage with option --normalizeUsing RPKM and --ignoreForNormalization chrX chrY

extract_protocol:
For ChIP-seq, cells were fixed in 1% formaldehyde for 10 min at RT, and followed by glycine for 5 mins. Chromatin was sonicated to 200-500 bp, and immunoprecipitated with antibodies. Anti-mouse, rabbit IgG Dynabeads (Invitrogen) or StAv beads (Invitrogen) were added and incubated at 4°C.  After washing the beads, beads-bound chromatin was tagemented by ChIPmentation strategy. Chromatin was eluted by reverse crosslink buffer at 65 ℃ for 12 hrs and purified with Monarch DNA Cleanup Columns.
The libraries were prepared by using the Illumina Nextera DNA Library Prep Kit, and size-selected to 200-500 bp using SPRIselect beads.

tag: chip antibody


title: ESCs, PmlKO_ChIP_H3K9me3_rep2

value: H3K9me3 (C15500003, Diagenode)


title: O1_TA_Hi_77 [scRNA-seq]


title: O1_TA_Hi_75 [scRNA-seq]


title: O1_TA_Hi_69 [scRNA-seq]


title: O1_TA_Hi_70 [scRNA-seq]


title: O1_TA_Hi_74 [scRNA-seq]


title: O1_TA_Hi_73 [scRNA-seq]


title: O1_TA_Hi_68 [scRNA-seq]


title: O1_TA_Hi_72 [scRNA-seq]


title: O1_TA_Hi_76 [scRNA-seq]


title: O1_TA_Hi_6 [scRNA-seq]


title: O1_TA_Hi_66 [scRNA-seq]


title: ESCs, PmlKO_input


title: O1_TA_Hi_67 [scRNA-seq]


title: O1_TA_Hi_71 [scRNA-seq]


title: ESCs, PmlKO_ChIP_H3K9me3_rep1


title: O1_TA_Hi_64 [scRNA-seq]


title: ESCs, PmlKO_ChIP_H3K27me3_rep1

value: H3K27me3 (C36B11, Cell signaling Technology)


title: ESCs, WT_ChIP_H3K9me3_rep1


title: ESCs, WT_ChIP_H3K9me3_rep2


title: O1_TA_Hi_63 [scRNA-seq]


title: ESCs, PmlKO_ChIP_H3K27me3_rep2


title: O1_TA_Hi_65 [scRNA-seq]


title: O1_TA_Hi_62 [scRNA-seq]


title: ESCs, WT_ChIP_H3K27me3_rep1


title: ESCs, WT_ChIP_H3K27me3_rep2


title: O1_TA_Hi_60 [scRNA-seq]


title: ESCs, PmlKO_ChIP_H3K4me3_rep2

value: H3K4me3 (MABI0304, Cosmo Bio)


title: O1_TA_Hi_5 [scRNA-seq]


title: ESCs, WT_ChIP_H3K4me3_rep2


title: O1_TA_Hi_56 [scRNA-seq]


title: ESCs, WT_ChIP_H3K27ac_rep1

value: H3K27ac (MABI0309, Cosmo Bio)


title: O1_TA_Hi_54 [scRNA-seq]


title: O1_TA_Hi_52 [scRNA-seq]


title: ESCs, PmlKO_ChIP_H3K4me3_rep1


title: O1_TA_Hi_55 [scRNA-seq]


title: O1_TA_Hi_58 [scRNA-seq]


title: ESCs, PmlKO_ChIP_H3K27ac_rep1


title: O1_TA_Hi_59 [scRNA-seq]


title: O1_TA_Hi_57 [scRNA-seq]


title: O1_TA_Hi_61 [scRNA-seq]


title: O1_TA_Hi_53 [scRNA-seq]


title: ESCs, WT_ChIP_H3K27ac_rep2


title: ESCs, PmlKO_ChIP_H3K27ac_rep2


title: ESCs, WT_ATAC_rep1

data_processing:
Sequence reads were trimmed by using Trimmomatic, then mapped to mm10 using bowtie2 with parameters --maxins 2000 --very-sensitive.
Non-uniquely mapping reads were filtered out using a MAPQ threshold of 30.
PCR duplicates and ENCODE blacklisted regions were removed using Picard Tools and bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig file was generated by using bamCoverage with option --normalizeUsing RPKM and --ignoreForNormalization chrX chrY

extract_protocol:
1 x 10e5 cells were used for each transposition reaction
The libraries were prepared by using the Illumina Nextera DNA Library Prep Kit, and size-selected to 200-500 bp using SPRIselect beads.


title: ESCs, WT_ATAC_rep2


title: ESCs, PmlKO_ATAC_rep2


title: ESCs, ALaP_H2O2+_rep1

data_processing:
Sequence reads were trimmed by using Trimmomatic, then mapped to repeat masked mm10 using bowtie2 version 2.3.5.1 with parameter -N1
ENCODE blacklisted regions and grey list prepared by chipseq-greylist were removed using bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig file was generated by using bamCompare with option --scaleFactorsMethod SES --operation subtract.

extract_protocol: The libraries were prepared by using the Illumina Nextera DNA Library Prep Kit, and size-selected to 150-500 bp using SPRIselect beads.

tag: alap-seq target

value: PML

value: APEX-PML knockin


title: ESCs, PmlKO_ATAC_rep1


title: ESCs, ALaP_H2O2+_rep2


title: O1_TA_Hi_51 [scRNA-seq]


title: O1_TA_Hi_49 [scRNA-seq]


title: O1_TA_Hi_50 [scRNA-seq]


title: O1_TA_Hi_4 [scRNA-seq]


title: O1_TA_Hi_47 [scRNA-seq]


title: O1_TA_Hi_46 [scRNA-seq]


title: O1_TA_Hi_48 [scRNA-seq]


title: ESCs, WT_ChIP_H3K4me3_rep1


title: O1_TA_Hi_45 [scRNA-seq]


title: O1_TA_Hi_43 [scRNA-seq]


title: O1_TA_Hi_42 [scRNA-seq]


title: ESCs, ALaP_H2O2-_rep2


title: O1_TA_Hi_41 [scRNA-seq]


title: O1_TA_Hi_38 [scRNA-seq]


title: O1_TA_Hi_40 [scRNA-seq]


title: O1_TA_Hi_39 [scRNA-seq]


title: O1_TA_Hi_3 [scRNA-seq]


title: O1_TA_Hi_37 [scRNA-seq]


title: O1_TA_Hi_33 [scRNA-seq]


title: O1_TA_Hi_34 [scRNA-seq]


title: O1_TA_Hi_36 [scRNA-seq]


title: O1_TA_Hi_32 [scRNA-seq]


title: O1_TA_Hi_44 [scRNA-seq]


title: ESCs, ALaP_H2O2-_rep1


title: O1_TA_Hi_31 [scRNA-seq]


title: O1_TA_Hi_35 [scRNA-seq]


title: O1_TA_Hi_29 [scRNA-seq]


title: O1_TA_Hi_28 [scRNA-seq]


title: O1_TA_Hi_2 [scRNA-seq]


title: O1_TA_Hi_30 [scRNA-seq]


title: O1_TA_Hi_25 [scRNA-seq]


title: O1_TA_Hi_26 [scRNA-seq]


title: O1_TA_Hi_27 [scRNA-seq]


title: O1_TA_Hi_22 [scRNA-seq]


title: O1_TA_Hi_23 [scRNA-seq]


title: O1_TA_Hi_24 [scRNA-seq]


title: UHRF1 SUVH5 finger rescue

type: genomic

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Ave NE

department: Center for Epigenetics

institute: Van Andel Research Institute

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol.

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

data_processing: openSesame from SeSAMe R package.

label: Cy3, Cy5

label_protocol: Standard Illumina Protocol.

growth_protocol: 37ºC, 5% CO2, McCoy's 5A media with 10% FBS and 1% penicillin-streptomycin.

extract_protocol: 3x extraction: phenol, phenol/chloroform/isoamyl alcohol (25:24:1), chloroform/isoamyl alcohol (24:1); precipitation; RNase treatment; precipitation.

value: Colorectal cancer cells

tag: shRNA

tag: rescue

value: SUVH5 finger


title: O1_TA_Hi_21 [scRNA-seq]


title: O1_TA_Hi_1 [scRNA-seq]


title: NDI1 rescue


title: O1_TA_Hi_20 [scRNA-seq]


title: UHRF1 WT rescue

value: WT UHRF1


title: UHRF1 N489A rescue


title: BAR-TK22_t2wks

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

description: Genome-wide DNA methylation dynamic in obese persons

hyb_protocol: Illumina protocol

scan_protocol: iscan

data_processing: Champ package

label: Cy3 and Cy5

source_name: vastus lateralis

label_protocol: Illumina protocol

extract_protocol: using Invisorb® Genomic DNA Kit II according to the manufacturer’s protocol. An amount of 500 ng of genomic DNA from each participant was bisulfite-converted using Zymo EZ DNA Methylation-Gold kit (Zymo Research Corporation, Irvine, CA, USA)

treatment_protocol: genomic DNA was extracted from frozen muscle biopsies.

tag: tissu

value: Skeletal muscle

tag: group

value: Obese

tag: time point

value: 2 weeks after metabolic surgery


title: MM21_t2wks


title: BAR-KT41_t2wks


title: BAR-MG48_T2wks

description: this sample was included for 2 weeks comparison but not processed at 52 weeks because of bad quality


title: TR38_T2weeks


title: O1_TA_Hi_17 [scRNA-seq]

tag: cell type


title: SS52_T2wks


title: BAR-IG47_T2wks


title: MV42_T2wks


title: NA51_T2wks


title: O1_TA_Hi_19 [scRNA-seq]


title: O1_TA_Hi_18 [scRNA-seq]


title: BAR-RR44_T2wks


title: SH64_T2wks


title: O1_TA_Hi_16 [scRNA-seq]


title: nw59_t2wks


title: IK36T_2wks


title: BAR-MD35_T2wks


title: ES18_t2wks


title: O1_TA_Hi_15 [scRNA-seq]


title: O1_TA_Hi_14 [scRNA-seq]


title: O1_TA_Hi_13 [scRNA-seq]


title: BAR-DN39_T2wks


title: O1_TA_Hi_12 [scRNA-seq]


title: BAR-NS20_t2wks


title: SH64_T12months

value: 52 weeks after metabolic surgery


title: SS52_T12months


title: NA51_T12months


title: O1_TA_Hi_10 [scRNA-seq]


title: YA-12-ankH-3_S12_0

city: Louisville

first: Yousef

last: Abu Kwaik

state: KY

address: 505 S Hancock St

department: Microbiology and Immunology

institute: University of Louisville

data_processing:
Illumina BaseSpace FastQ v1.0.0 was used for basecalling
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the Homo sapiens reference genome assembly (hg38) using Tophat2 (version 2.0.13) generating alignments in bam format.
Raw read counts were obtained and normalized using Cuffnorm with Ensembl annotations (Homo sapiens GRCh38.82.gtf).
Normalized read counts for each sample were concatenated into a single tab-delimited gene matrix file.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM_TABLE file

source_name: Macrophage

extract_protocol:
Macrophages were infected with bacterial strains for 6 hours. Cell supernatants were collected and libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit- Set A (Cat# RS-122-2101) or Set B (Cat# RS-122-2102) with poly-A enrichment.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human monocyte derived macrophages

tag: treatment

value: infected with L. pneumophila isogenic mutant AnkH, for 6h


title: YA-11-ankH-2_S11_0


title: TR38_T12months


title: YA-10-ankH-1_S10_0


title: YA-06-Wildtype-3_S6_0

value: infected with wild type L. pneumophila for 6h


title: YA-05-Wildtype-2_S5_0


title: YA-04-Wildtype-1_S4_0


title: YA-01-Control-1_S1_0

value: none (control)


title: nw59_t12months


title: YA-03-Control-3_S3_0


title: SC284

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

description:
poly-adenylated RNA, surface protein expression with TotalSeq-A antibodies
SSC 11/12
This sample was sequenced twice-- once on the NextSeq 500 and once on the NovaSeq 6000. The output .h5 file contains the combined data from both of these instruments following alignment to the GRCh38 reference genome.

data_processing:
10X Genomics' Cell Ranger 3.0.2 software's mkfastq command was used for basecalling.  It is a wrapper for Illumina's bcl2fastq
Sequenced reads were then mapped to GRCh38 transcriptome using 10X Genomics' Cell Ranger 3.0.2 software's cellranger count function
Cell Ranger output of raw_feature_bc_matrix.h5 files were utilized for further downstream analysis in R with the package Seurat 2.3.4, only cells expressing at least 200 genes were kept for downstream analysis.  Cell Ranger 3.0.2's Feature Barcoding
Genome_build: GRCh38
Supplementary_files_format_and_content: The .h5 files contain gene expression and antibody capture counts for each donor or patient

source_name: mix of hashtagged upper  lobe + hashtagged lower lobe lung_scleroderma patient

extract_protocol:
Explanted lungs were finely diced and digested for 45 minutes in a mix of Liberase DL/DNAse I.  A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 2%FBS.  Cells were labeled with TotalSeq-A Cell Hashing HTO and CITE-Seq ADT antibodies according to the New York Genome Center's CITE-Seq and Cell Hashing protocol.  Follwing antibody-hashtag labeling, cells were resuspended in PBS containing 0.04% BSA and loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed according to 10X Genomics' Single Cell 3’ Reagent Kits v3 User Guide; Cell Hashing HTO and CITE-Seq ADT libraries measuring surface protein expression were generated according to the New York Genome Center's CITE-seq & Cell Hashing Protocol

tag: subject status

value: scleroderma patient

tag: tissue

value: lung

tag: lung section/portion

tag: 10x genomics chemistry

value: 10X Genomics 3 Prime V3 chemistry + Cell Hashing HTO + CITE-Seq Feature Barcoding with BioLegend Total-Seq A antibodies


title: O1_TA_Hi_11 [scRNA-seq]

tag: strain

value: Muscle stem cells

value: 24 months


title: YA-02-Control-2_S2_0


title: IK36_T12months


title: MV42_t12months


title: MM21_t12months


title: ES18_t12months