title: PBMCs from sample B8-8_Naive_CD4

description: PBMCs from sample B8-8_Naive_CD4


title: PBMCs from sample B8-8_Memory_CD8

status: Public on Feb 23 2024

type: SRA

city: Stanford

first: Aaron

middle: James

last: Wilk

state: California

address: 300 Pasteur Dr Bldg S131, Grant

country: USA

institute: Stanford University

description: PBMCs from sample B8-8_Memory_CD8

library_source: transcriptomic

data_processing:
Sequencing reads were aligned against V-, D-, J-, and C- human gene segment library database by MiXCR
Clonotypes were assembled from aligned reads by MiXCR
Assembly: Sequencing reads were aligned against V-, D-, J-, and C- human gene segment library database by MiXCR
Supplementary files format and content: .txt files containing counts of clonotypes in tabular form

molecule: total RNA

organism: Homo sapiens

source_name: PBMCs

growth_protocol: No growth or treatment performed

extract_protocol:
RNA was purified from each sorted sample using the RNAeasy Plus Micro kit (Qiagen)
Libraries were prepared for TCR sequencing as described by Rubelt, et al.. This was performed at the University of Cape Town. Briefly, purified RNA was reverse transcribed in a Rapid amplification of cDNA ends (RACE) reaction using SMARTScribe Reverse Transcriptase using previously designed oligos (isoC-5′-GTCAGATGTGTATAAGAGACAGnnnnnnnnnnCGATAGrGrGrG -3′-C3_Spacer and for the Poly A tail 5′-GTGTCACGTACAGAGTCATCtttttttttttttttttttttttttttttt -3′ VN) that captures polyadenylated transcripts and introduces a 10bp unique molecular identifier (UMI) at the 5’ end of the product. cDNA was purified with AmpureXP beads (Beckman Coulter) before whole transcriptome amplification using Advantage 2 Polymerase (Clontech) using oligos that introduce Illumina Nextera Multiplex Identifier (MID) P5 Adapter sequences. The libraries were then sent to Stanford University (Department of Microbiology and Immunology, Stanford University) in a blinded fashion, where TCRβ-specific amplification was achieved with Q5 Hot Start Master Mix (NEB) using constant region-specific oligos, simultaneously introducing P7 MID sequences. Final sequencing libraries were purified using SPRISelect beads (Beckman Coulter), quantified using the Agilent TapeStation and pooled for sequencing. Paired-end sequencing was performed on an Illumina NovaSeq SP with 2x250 cycles, performed by the Chan-Zuckerberg Biohub Initiative.

treatment_protocol: No growth or treatment performed

tag: cell type

value: PBMCs


title: PBMCs from sample B8-8_Memory_CD4

description: PBMCs from sample B8-8_Memory_CD4


title: ChIP,4do,Col0,ChIP,Rep2

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

country: Mexico

institute: School of Chemistry, UNAM

library_source: genomic

data_processing:
Reads were adapter trimmed using Trim-galore v0.4.1
Mapping was performed using Bowtie2 v2.2.8.9 with normal paired reads and no errors were allowed
Read counts on defined genomic regions were determined using bedtools v.2.25.0
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: Genome coverage per nucleotide is included for all the datasets in txt format

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Seeds were stratified in darkness at 4ºC for 48 hours, and for fourteen days-old plants, they grown on soil at 22ºC under white LED light (100 umol m-2 s-1) in 16h/8h day/night Cycle. For four days-old plants they were grown on 0.5X MS plates under continuous light (100 umol m-2 s-1).

extract_protocol:
Fifty 4-5 days-old seedlings were harvested, crosslinked with 4 % formaldehyde for 4 hours, and homogenized in chloroplast enrichment buffer (0.33 M Sorbitol, 30 mM HEPES-KOH (pH 7.5), 0.001% beta-mercaptoethanol) using a pestle. The homogenate was filtered through two layers of miracloth, and centrifuged at 1500 g for 5 minutes at 4ºC. The pelleted chloroplasts were resuspended in 1 ml of chloroplast enrichment buffer.
Sequencing libraries were prepared as reported (Bowman, et al. 2013, BMC Genomics, 14:466).

tag: tissue

value: Seedling

tag: cell line

value: Chloroplast

tag: genotype

value: wild type

tag: treatment


title: ChIP,4do,chl27,ChIP,Rep3


title: ChIP,4do,chl27,ChIP,Rep2


title: ChIP,4do,chl27,input,Rep3


title: PBMCs from sample B8-9_Naive_CD8

description: PBMCs from sample B8-9_Naive_CD8


title: PBMCs from sample B8-7_Naive_CD8

description: PBMCs from sample B8-7_Naive_CD8


title: ChIP,4do,chl27,input,Rep2


title: PBMCs from sample B8-7_Memory_CD8

description: PBMCs from sample B8-7_Memory_CD8


title: ChIP,4do,chl27,input,Rep1


title: PBMCs from sample B8-7_Naive_CD4

description: PBMCs from sample B8-7_Naive_CD4


title: PBMCs from sample B8-9_Naive_CD4

description: PBMCs from sample B8-9_Naive_CD4


title: ChIP,4do,chl27,ChIP,Rep1


title: RNA_hda15_rep2

city: Gatersleben, Stadt Seeland, Germany

first: Hua

last: Jiang

address: Corrensstraße 3

country: Germany

institute: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben

data_processing:
For RNA-seq analysis, reads were mapped to TAIR10 Col-0 and the Ler‐0 genomes with HISAT2 (Kim et al., 2019) in paired-end mode.
DEGs were analyzed via the Subread (Liao et al., 2019) and DESeq2 R packages (Love et al., 2014) with a 0.05 false discovery rate (FDR).
For MAR-seq analysis, quality control and adapter trimming of MAR-seq reads were performed with Fastp (61). Reads were aligned to the TAIR10 reference genome using Bowtie2. Mapped reads were deduplicated using MarkDuplicates (https://broadinstitute.github.io/picard). Coverage was estimated and normalized to 10 million reads. MAR-seq peaks in wild-type and mutants were called by SCIER2 (62).
Assembly: tair10
Supplementary files format and content: bedGraph, counts

source_name: 5-day-old  seedlings

growth_protocol: Seeds were sown in soil and stratified for 2 days at 4°C. The plants were then grown in a growth chamber with a photoperiod of 16 h of light and 8 h of darkness at 22°C.

extract_protocol:
Total RNA from 5-day seedling was extracted with a RNeasy Plant Mini kit (Qiagen). For RNA-seq analysis, the total RNA was treated with a Poly(A) mRNA Magnetic Isolation Module Kit (NEB #E7490). DNA of 6th, 7th and 8th leaves was purified using a DNeasy® Plant Mini Kit (Qiagen) and eluted in 150 µL of elution buffer. Experiments were performed for two biological replicates.  The nuclear matrix was isolated as previously described in (53). Briefly, Arabidopsis 5-day-old whole plants grown under LD condition (16h at 23 °C under 22 μmol·m−2·s−1 continuous white light, 8h at 23 °C dark with 70% humidity) were collected and chopped in 1 ml LB01 buffer (2 mM Na2EDTA, 20 mM NaCl, 2 mM EDTA, 80 mM KCl, 0.5 mM spermine, 15 mM β-mercaptoethanol, 0.1% Triton X-100, pH 7.5). Another 9 ml LB01 buffer was used to wash the nuclei into 1-layer miracloth filter followed by a one-time filter through 30 μm CellTrics (Sysmex, Germany, 04-0042-2316). The nuclei mixture was centrifuged at 1500g for 10 min at 4 °C. The nuclei pellet was further wash with DNase I buffer (20 mM Tris pH 7.4, 20 mM KCl, 70 mM NaCl, 10 mM MgCl2, 0.125 mM spermidine 1 mM PMSF, 0.5% Triton-X 100) until white. After centrifuge, the nuclei were resuspended in 200 μl DNase I buffer, and an aliquot of nuclei was stored for isolation and estimation of total genomic DNA as control. DNase I (Thermo Scientific, EN0525) was added and incubated at 4°C for 1 hr. Nuclei were collected by centrifugation at 3000g for 10 min at 4 °C. Digestion was followed by extraction with 0.4 M NaCl for 5 min twice on ice in Extraction Buffer (10 mM Hepes pH 7.5, 4 mM EDTA, 0.25 mM spermidine, 0.1 mM PMSF, 0.5% (v/v) Triton X-100). Another two times extraction with 2 M NaCl for 5 min on ice in Extraction Buffer. The final nuclear matrix pellet was washed twice with Wash Buffer (5 mM Tris pH 7.4, 20 mM KCl, 1 mM EDTA, 0.25 mM spermidine, 0.1 mM PMSF).
RNA-seq Libraries were prepared from the resulting mRNA with a NEBNext Ultra Kit (NEB #E7530). The libraries were constructed according to a standard protocol (Illumina). The RNA-seq libraries were sequenced at Novogene via a Novaseq instrument in 150-bp paired-end mode.  MAR-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645) according to the manufacturer’s instructions. The libraries were sequenced at Novogene (UK) via a Novaseq instrument in 150-bp paired-end mode. Two biological replicates were performed.

value: 5-day-old seedlings


title: PBMCs from sample B8-6_Naive_CD4

description: PBMCs from sample B8-6_Naive_CD4


title: PBMCs from sample B8-6_Memory_CD8

description: PBMCs from sample B8-6_Memory_CD8


title: RNA_hda15_rep1


title: PBMCs from sample B8-6_Naive_CD8

description: PBMCs from sample B8-6_Naive_CD8


title: PBMCs from sample B8-5_Naive_CD8

description: PBMCs from sample B8-5_Naive_CD8


title: RNA_ahl22 frs7 frs12_rep1

value: ahl22 frs7 frs12


title: PBMCs from sample B8-6_Memory_CD4

description: PBMCs from sample B8-6_Memory_CD4


title: RNA_frs7 frs12_rep2

value: frs7 frs12


title: RNA_frs7 frs12_rep1


title: PBMCs from sample B8-5_Memory_CD8

description: PBMCs from sample B8-5_Memory_CD8


title: RNA_ahl22_rep2


title: PBMCs from sample B8-5_Memory_CD4

description: PBMCs from sample B8-5_Memory_CD4


title: RNA_ahl22_rep1


title: PBMCs from sample B8-4_Naive_CD8

description: PBMCs from sample B8-4_Naive_CD8


title: RNA_Col_rep2

value: Col


title: RNA_Col_rep1


title: ahl22 frs7 frs12_input_rep2

data_processing:
library strategy: MAR-seq
For RNA-seq analysis, reads were mapped to TAIR10 Col-0 and the Ler‐0 genomes with HISAT2 (Kim et al., 2019) in paired-end mode.
DEGs were analyzed via the Subread (Liao et al., 2019) and DESeq2 R packages (Love et al., 2014) with a 0.05 false discovery rate (FDR).
For MAR-seq analysis, quality control and adapter trimming of MAR-seq reads were performed with Fastp (61). Reads were aligned to the TAIR10 reference genome using Bowtie2. Mapped reads were deduplicated using MarkDuplicates (https://broadinstitute.github.io/picard). Coverage was estimated and normalized to 10 million reads. MAR-seq peaks in wild-type and mutants were called by SCIER2 (62).
Assembly: tair10
Supplementary files format and content: bedGraph, counts


title: PBMCs from sample B8-4_Memory_CD8

description: PBMCs from sample B8-4_Memory_CD8


title: PBMCs from sample B8-4_Memory_CD4

description: PBMCs from sample B8-4_Memory_CD4


title: PBMCs from sample B8-3_Naive_CD8

description: PBMCs from sample B8-3_Naive_CD8


title: PBMCs from sample B8-7_Memory_CD4

description: PBMCs from sample B8-7_Memory_CD4


title: ahl22 frs7 frs12_input_rep1


title: sob3-6_input_rep2


title: PBMCs from sample B8-3_Naive_CD4

description: PBMCs from sample B8-3_Naive_CD4


title: RNA_ahl22 frs7 frs12_rep2


title: sob3-6_input_rep1


title: Col_input_rep2


title: PBMCs from sample B8-3_Memory_CD8

description: PBMCs from sample B8-3_Memory_CD8


title: PBMCs from sample B8-3_Memory_CD4

description: PBMCs from sample B8-3_Memory_CD4


title: Col_input_rep1


title: PBMCs from sample B8-2_Naive_CD8

description: PBMCs from sample B8-2_Naive_CD8


title: PBMCs from sample B8-2_Memory_CD8

description: PBMCs from sample B8-2_Memory_CD8


title: PBMCs from sample B8-5_Naive_CD4

description: PBMCs from sample B8-5_Naive_CD4


title: PBMCs from sample B8-2_Naive_CD4

description: PBMCs from sample B8-2_Naive_CD4


title: ahl22 frs7 frs12_MAR_rep2


title: sob3-6_MAR_rep2


title: PBMCs from sample B8-2_Memory_CD4

description: PBMCs from sample B8-2_Memory_CD4


title: sob3-6_MAR_rep1


title: PBMCs from sample B8-4_Naive_CD4

description: PBMCs from sample B8-4_Naive_CD4


title: Col_MAR_rep1


title: PBMCs from sample B8-1_Memory_CD8

description: PBMCs from sample B8-1_Memory_CD8


title: PBMCs from sample B8-1_Naive_CD4

description: PBMCs from sample B8-1_Naive_CD4


title: PBMCs from sample B8-1_Naive_CD8

description: PBMCs from sample B8-1_Naive_CD8


title: Col_MAR_rep2


title: PBMCs from sample B8-1_Memory_CD4

description: PBMCs from sample B8-1_Memory_CD4


title: SRF bound chromatin of OPC_R3

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

institute: Saarland University

data_processing:
ChIP-seq data analysis was performed using the nextflow-core ChIP-seq v1.2.1 pipeline (https://doi.org/10.5281/ZENODO.3966161) with default parameters, unless otherwise stated. In short, the pipeline first performs adapter trimming to the raw single-end reads using Trim Galore (option --nextseq=20) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Assembly: reads were mapped to the Rnor 6.0 rat genome obtained from Illumina iGenomes (Ensembl) using BWA 43. MACS2 44 was configured to call narrow peaks with a Benjamini-Hochberg FDR of 0.05 and an effective genome size of 2×10^9. HOMER 45 was then used to annotate peaks with information from the closest known genomic feature based on the Ensembl database. Consensus peaks for OPC and oligodendrocytes were aggregated by considering peaks present in at least one replicate of the respective cell type. We performed known and de novo motif detection in the -250 to +250 nt regions around detected peaks using MEME-ChIP 46. Next, FIMO 46 was used to get individual motif matches for MEME-ChIP results. The matrix of peak intensity around transcription start sites (TSS) was calculated using deepTools.

organism: Rattus norvegicus

source_name: brain

growth_protocol: primary Rat OPC culture by immunnopanning following protocol by Dugas & Emery, Cold Spring Harbor Protocols, 2013.

extract_protocol:
Rat OPCs were allowed to proliferate for 6 days to reach 40 million cells in multiple 15cm plates. Half of the plates were fixed at the OPC stage while the rest were switched to differentiation medium and fixed on day 3 of differentiation. Replicates in this experiment were independent OPC preps. Chromatin immunoprecipitation was performed following iDeal ChIP-seq kit for Transcription Factors (Diagenode, Cat. No. C01010055) using 7 cycles for chromatin shearing on a Bioruptor Pico sonicator (Diagenode, Cat. No. B01060001). Prior to sonication, each sample was split to 300ul reactions (containing each roughly 4 million cells) in 1.5 ml Bioruptor Microtubes (Cat. No. C30010016), sonicated, spun 16,000g for 10 min and 270ul of supernatant was collected to a new tube and stored in -80 deg. One aliquot of each sample was used for immunoprecipitation with 5ul of Rabbit-anti-SRF antibody that was validated for ChIP (SRF (D71A9) XP® Rabbit mAb, #5147) and an additional OPC and oligodendrocyte sample from each group for immunoprecipitation with an IgG control antibody (provided in the kit).
Libraries for next-generation sequencing were prepared using MicroPlex Library Preparation Kit v3 x48 rxns (C05010001, Diagenode) using 12 PCR cycles on a 96-plate thermal cycler (Biorad) and purified without size selection.
Library quantity and quality was assessed using a Bioanalyzer (Agilent) and Qubit. Libraries were pooled and sequenced on a Nextseq550 sequencer (Illumina) using single end 75bp for Read 1 and 8bp for index 1 and 8bp for Index 2 with a high output 75bp kit (20024906, Illumina).
In pilot studies, Chromatin Shearing Optimization kit - Low SDS (iDeal Kit for TFs) (Cat. No.C01020013) was used to determine optimal number of sonication shearing cycles to yield 200-300 bp fragments.

treatment_protocol: OPCs were frozen at the proliferation stage (grown with proliferation media) and OLs 3 days after switching to differentiation media.

value: brain

value: primary rat OPC culture

value: WT

value: prolifferation stage


title: SRF bound chromatin of OPC_R4


title: SRF bound chromatin of OPC_R2


title: PBMCs from sample B8-11_Naive_CD4

description: PBMCs from sample B8-11_Naive_CD4


title: PBMCs from sample B8-11_Memory_CD8

description: PBMCs from sample B8-11_Memory_CD8


title: SRF bound chromatin of OPC_R1


title: PBMCs from sample B8-11_Memory_CD4

description: PBMCs from sample B8-11_Memory_CD4


title: SRF bound chromatin of OLG_R4

value: day 3 differentiation


title: ahl22 frs7 frs12_MAR_rep1


title: PBMCs from sample B8-10_Naive_CD4

description: PBMCs from sample B8-10_Naive_CD4


title: Input chromatin of OPC_R4


title: SRF bound chromatin of OLG_R2


title: Input chromatin of OPC_R3


title: PBMCs from sample B8-10_Naive_CD8

description: PBMCs from sample B8-10_Naive_CD8


title: SRF bound chromatin of OLG_R1


title: PBMCs from sample B8-10_Memory_CD4

description: PBMCs from sample B8-10_Memory_CD4


title: Input chromatin of OPC_R2


title: PBMCs from sample B7-9_Naive_CD8

description: PBMCs from sample B7-9_Naive_CD8


title: Input chromatin of OLG_R4


title: Input chromatin of OPC_R1


title: PBMCs from sample B7-9_Memory_CD8

description: PBMCs from sample B7-9_Memory_CD8


title: Input chromatin of OLG_R2


title: Input chromatin of OLG_R1


title: PBMCs from sample B7-9_Memory_CD4

description: PBMCs from sample B7-9_Memory_CD4


title: OPC IgG control


title: PBMCs from sample B7-8_Naive_CD8

description: PBMCs from sample B7-8_Naive_CD8


title: oligodendrocyte IgG control


title: PBMCs from sample B7-8_Naive_CD4

description: PBMCs from sample B7-8_Naive_CD4


title: PBMCs from sample B7-8_Memory_CD8

description: PBMCs from sample B7-8_Memory_CD8


title: PBMCs from sample B8-11_Naive_CD8

description: PBMCs from sample B8-11_Naive_CD8


title: PBMCs from sample B7-8_Memory_CD4

description: PBMCs from sample B7-8_Memory_CD4


title: PBMCs from sample B7-7_Naive_CD4

description: PBMCs from sample B7-7_Naive_CD4


title: DGay10-30973

city: La Jolla

first: Theresa

last: Guo

address: 3855 Health Sciences Dr, MC 0987

institute: University of California, San Diego

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay10-30973

data_processing:
Sequences were trimmed for adaptor sequence using Trim Galore
Trimmed reads were mapped to GRCH37/hg19 using Salmon aligner
Transcript abundance was caputured using tximport pipeline and data was compared to previously published cohort of HPV-positive oropharyngeal cancers
Batch correction was performed using DESeq2
Assembly: GRCH37/hg19
Supplementary files format and content: tab-delimited text file shows normalized transcript abundance estimates from DESeq2

source_name: Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, Fresh Frozen Tissue

extract_protocol:
RNA was extracted from formalin fixed tissue using Qiagen AllPrep Kit
Library prep was performed using Takara SMARTer Stranded Total RNA-Seq Kit v2 using manufacturer protocols

tag: age

tag: Sex

value: F

tag: smoking history

value: Never smoker

tag: tumor stage_(ajcc_8)

tag: group

value: Normal


title: DGay11-30944

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay11-30944

value: Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, Fresh Frozen Tissue

value: M


title: DGay3-37091

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay3-37091


title: PBMCs from sample B7-7_Naive_CD8

description: PBMCs from sample B7-7_Naive_CD8

value: PBMCs


title: PBMCs from sample B8-10_Memory_CD8

description: PBMCs from sample B8-10_Memory_CD8


title: PBMCs from sample B7-6_Naive_CD4

description: PBMCs from sample B7-6_Naive_CD4


title: DGay9-30972

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay9-30972


title: DGay5-30951

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay5-30951


title: PBMCs from sample B7-7_Memory_CD4

description: PBMCs from sample B7-7_Memory_CD4


title: PBMCs from sample B7-6_Memory_CD8

description: PBMCs from sample B7-6_Memory_CD8


title: PBMCs from sample B7-6_Naive_CD8

description: PBMCs from sample B7-6_Naive_CD8


title: DGay7-30911

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay7-30911

value: Former smoker


title: PBMCs from sample B7-9_Naive_CD4

description: PBMCs from sample B7-9_Naive_CD4


title: DGay11-30975

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay11-30975


title: DGay6-30961

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay6-30961


title: DGay2-30942

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay2-30942


title: DGay8-30977

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay8-30977


title: PBMCs from sample B7-5_Memory_CD8

description: PBMCs from sample B7-5_Memory_CD8


title: DGay10-30987

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay10-30987

value: Current smoker


title: PBMCs from sample B7-6_Memory_CD4

description: PBMCs from sample B7-6_Memory_CD4


title: DGay14-31844

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay14-31844


title: PBMCs from sample B7-5_Memory_CD4

description: PBMCs from sample B7-5_Memory_CD4


title: DGay4-28668

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay4-28668


title: PBMCs from sample B7-7_Memory_CD8

description: PBMCs from sample B7-7_Memory_CD8


title: PBMCs from sample B7-4_Naive_CD4

description: PBMCs from sample B7-4_Naive_CD4


title: DGay12-27911

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay12-27911


title: PBMCs from sample B7-4_Naive_CD8

description: PBMCs from sample B7-4_Naive_CD8


title: DGay9-28661

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay9-28661


title: DGay1-28639

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay1-28639


title: DGay7-30948

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay7-30948


title: PBMCs from sample B7-4_Memory_CD8

description: PBMCs from sample B7-4_Memory_CD8


title: DGay16-25081

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay16-25081


title: PBMCs from sample B7-3_Naive_CD8

description: PBMCs from sample B7-3_Naive_CD8


title: PBMCs from sample B7-5_Naive_CD8

description: PBMCs from sample B7-5_Naive_CD8


title: PBMCs from sample B7-3_Naive_CD4

description: PBMCs from sample B7-3_Naive_CD4


title: PBMCs from sample B7-4_Memory_CD4

description: PBMCs from sample B7-4_Memory_CD4


title: DGay18-25305

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay18-25305


title: DGay13-27929

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay13-27929


title: DGay15-28675

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay15-28675


title: PBMCs from sample B7-3_Memory_CD8

description: PBMCs from sample B7-3_Memory_CD8


title: DGay20-25475

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay20-25475


title: DGay17-25343

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay17-25343


title: PBMCs from sample B7-3_Memory_CD4

description: PBMCs from sample B7-3_Memory_CD4


title: DGay20-40663

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay20-40663

source_name: HPV-positive oropharyngeal squamous cell carcinoma tumor, Fresh Frozen tissue

value: NED, 25.1 months

value: Tumor


title: PBMCs from sample B7-2_Memory_CD4

description: PBMCs from sample B7-2_Memory_CD4


title: DGay19-25341

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay19-25341


title: PBMCs from sample B7-2_Naive_CD4

description: PBMCs from sample B7-2_Naive_CD4


title: DGay21-22906

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay21-22906

value: HPV-positive oropharyngeal squamous cell carcinoma tumor, Fresh Frozen tissue

value: Died of other cause, 106.6 months


title: DGay19-25350

description:
Normal oropharyngeal tissue from uvulopalatopharyngoplasty in non cancer affected control, prevoiusly published cohort
DGay19-25350


title: DGay4-39113

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay4-39113

value: Died of other cause, 74.7 months


title: PBMCs from sample B7-5_Naive_CD4

description: PBMCs from sample B7-5_Naive_CD4


title: PBMCs from sample B7-1_Naive_CD8

description: PBMCs from sample B7-1_Naive_CD8


title: PBMCs from sample B7-1_Naive_CD4

description: PBMCs from sample B7-1_Naive_CD4


title: PBMCs from sample B7-1_Memory_CD4

description: PBMCs from sample B7-1_Memory_CD4


title: PBMCs from sample B7-1_Memory_CD8

description: PBMCs from sample B7-1_Memory_CD8


title: DGay21-40932

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay21-40932

value: Second primary (lung cancer) at 38 months, Died at 49 months


title: DGay20-40655

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay20-40655

value: Died during treatment


title: PBMCs from sample B7-2_Naive_CD8

description: PBMCs from sample B7-2_Naive_CD8


title: PBMCs from sample B7-12_Naive_CD4

description: PBMCs from sample B7-12_Naive_CD4


title: DGay12-25770

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay12-25770

value: NED, 43.8 months


title: DGay17-39152

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay17-39152

value: Recurrence at 11.7 months, died at 20.9 months


title: PBMCs from sample B7-12_Memory_CD4

description: PBMCs from sample B7-12_Memory_CD4


title: DGay13-39141

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay13-39141

value: NED, 5.4 months


title: DGay11-25769

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay11-25769

value: NED, 23.2 months


title: PBMCs from sample B7-12_Memory_CD8

description: PBMCs from sample B7-12_Memory_CD8


title: DGay23-41777

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay23-41777

value: NED, 27 months


title: PBMCs from sample B7-11_Memory_CD8

description: PBMCs from sample B7-11_Memory_CD8


title: DGay2-30686

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay2-30686

value: NED, 84 months


title: DGay9-39200

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay9-39200

value: M

value: Recurrence (lung) at 49 months, Died at 53 months


title: PBMCs from sample B7-11_Naive_CD8

description: PBMCs from sample B7-11_Naive_CD8

value: PBMCs


title: PBMCs from sample B7-2_Memory_CD8

description: PBMCs from sample B7-2_Memory_CD8


title: DGay3-37792

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay3-37792

value: F

value: Former smoker

value: NED, 63.7 months


title: PBMCs from sample B7-11_Naive_CD4

description: PBMCs from sample B7-11_Naive_CD4


title: PBMCs from sample B7-10_Naive_CD4

description: PBMCs from sample B7-10_Naive_CD4


title: DGay14-39174

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay14-39174

value: HPV-positive oropharyngeal squamous cell carcinoma tumor, Fresh Frozen tissue

value: Current smoker

value: Died of other cause, 126.6 months (skull base esthesioblastoma)

value: Tumor


title: DGay13-39133

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay13-39133

value: Died of other cause, 6.1 months


title: PBMCs from sample B7-10_Naive_CD8

description: PBMCs from sample B7-10_Naive_CD8


title: PBMCs from sample B7-11_Memory_CD4

description: PBMCs from sample B7-11_Memory_CD4


title: DGay16-39136

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay16-39136

value: NED, 81.8 months


title: DGay18-39128

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay18-39128

value: NED, 31.2 months


title: PBMCs from sample B7-10_Memory_CD8

description: PBMCs from sample B7-10_Memory_CD8


title: PBMCs from sample B7-12_Naive_CD8

description: PBMCs from sample B7-12_Naive_CD8


title: PBMCs from sample B6-9_Naive_CD8

description: PBMCs from sample B6-9_Naive_CD8


title: PBMCs from sample B6-9_Memory_CD8

description: PBMCs from sample B6-9_Memory_CD8


title: PBMCs from sample B6-8_Naive_CD8

description: PBMCs from sample B6-8_Naive_CD8


title: PBMCs from sample B7-10_Memory_CD4

description: PBMCs from sample B7-10_Memory_CD4


title: DGay14-28000

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay14-28000

value: Never smoker

value: Lost to follow up


title: DGay16-25742

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay16-25742

value: NED, 170.1 months


title: DGay19-40965

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay19-40965

value: Recurrence at 2.5 months, NED at 51.6 months


title: DGay25-27432

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay25-27432

value: M

value: NED, 9.4 months


title: PBMCs from sample B6-9_Naive_CD4

description: PBMCs from sample B6-9_Naive_CD4

value: PBMCs


title: PBMCs from sample B6-8_Memory_CD8

description: PBMCs from sample B6-8_Memory_CD8


title: PBMCs from sample B6-9_Memory_CD4

description: PBMCs from sample B6-9_Memory_CD4


title: DGay26-41780

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay26-41780

value: NED, 16.9 months


title: DGay24-27879

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay24-27879

value: NED, 44.8 months


title: DGay1-39149

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay1-39149

value: Former smoker

value: NED, 19 months


title: DGay5-39184

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay5-39184

value: HPV-positive oropharyngeal squamous cell carcinoma tumor, Fresh Frozen tissue

value: NED, 28.9 months


title: PBMCs from sample B6-8_Memory_CD4

description: PBMCs from sample B6-8_Memory_CD4


title: PBMCs from sample B6-8_Naive_CD4

description: PBMCs from sample B6-8_Naive_CD4


title: DGay2-39164

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay2-39164

value: NED, 82.2 months

value: Tumor


title: DGay6-35696

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay6-35696

value: NED, 12 months


title: DGay24-41672

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay24-41672

value: Current smoker

value: Died at 4 months


title: DGay8-30811

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay8-30811

value: NED, 86.8 months


title: DGay22-41517

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay22-41517

value: NED, 27.3 months


title: PBMCs from sample B6-6_Naive_CD4

description: PBMCs from sample B6-6_Naive_CD4


title: DGay17-40991

description:
HPV-positive oropharyngeal cancer with recurrence, prevoiusly published cohort
DGay17-40991

value: Recurrence at 7.4 months, Died of disease at 21.9 months


title: PBMCs from sample B6-7_Memory_CD8

description: PBMCs from sample B6-7_Memory_CD8


title: PBMCs from sample B6-7_Memory_CD4

description: PBMCs from sample B6-7_Memory_CD4


title: PBMCs from sample B6-7_Naive_CD8

description: PBMCs from sample B6-7_Naive_CD8


title: PBMCs from sample B6-6_Memory_CD8

description: PBMCs from sample B6-6_Memory_CD8


title: PBMCs from sample B6-6_Memory_CD4

description: PBMCs from sample B6-6_Memory_CD4


title: PBMCs from sample B6-6_Naive_CD8

description: PBMCs from sample B6-6_Naive_CD8


title: DGay8-22934

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay8-22934

value: M

value: NED, 74.8 months


title: DGay7-39182

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay7-39182

value: NED, 35.3 months


title: PBMCs from sample B6-5_Naive_CD4

description: PBMCs from sample B6-5_Naive_CD4

value: PBMCs


title: DGay23-41797

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay23-41797

value: Never smoker

value: NED, 104.6 months


title: PBMCs from sample B6-5_Naive_CD8

description: PBMCs from sample B6-5_Naive_CD8


title: DGay6-24648

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay6-24648

value: Alive at 133.3 months, second primary in oral tongue at 94 months


title: PBMCs from sample B6-5_Memory_CD8

description: PBMCs from sample B6-5_Memory_CD8


title: DGay10-26144

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay10-26144

value: HPV-positive oropharyngeal squamous cell carcinoma tumor, Fresh Frozen tissue

value: Former smoker

value: NED, 186.8 months


title: PBMCs from sample B6-7_Naive_CD4

description: PBMCs from sample B6-7_Naive_CD4


title: PBMCs from sample B6-5_Memory_CD4

description: PBMCs from sample B6-5_Memory_CD4


title: DGay26-41507

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay26-41507

value: NED, 91.3 months

value: Tumor


title: DGay5-35671

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay5-35671

value: F

value: NED, 8.2 months


title: PBMCs from sample B6-4_Naive_CD4

description: PBMCs from sample B6-4_Naive_CD4


title: DGay24-41800

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay24-41800

value: NED, 44.9 months


title: DGay23-32806

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay23-32806

value: Current smoker

value: NED, 128.4 months


title: PBMCs from sample B6-4_Memory_CD4

description: PBMCs from sample B6-4_Memory_CD4


title: DGay22-25031

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay22-25031

value: NED, 71.4 months


title: DGay1-35691

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay1-35691

value: NED, 22.7 months


title: PBMCs from sample B6-3_Naive_CD8

description: PBMCs from sample B6-3_Naive_CD8


title: PBMCs from sample B6-4_Memory_CD8

description: PBMCs from sample B6-4_Memory_CD8


title: DGay15-39125

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay15-39125

value: M

value: NED, 29.6 months


title: PBMCs from sample B6-2_Naive_CD8

description: PBMCs from sample B6-2_Naive_CD8

value: PBMCs


title: DGay15-37916

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay15-37916

value: NED, 57.6 months


title: PBMCs from sample B6-3_Memory_CD8

description: PBMCs from sample B6-3_Memory_CD8


title: DGay25-41792

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay25-41792

value: Never smoker

value: NED, 11.4 months


title: PBMCs from sample B6-3_Naive_CD4

description: PBMCs from sample B6-3_Naive_CD4


title: PBMCs from sample B6-2_Naive_CD4

description: PBMCs from sample B6-2_Naive_CD4


title: DGay3-37963

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay3-37963

value: HPV-positive oropharyngeal squamous cell carcinoma tumor, Fresh Frozen tissue

value: NED, 22.4 months


title: DGay4-37924

description:
HPV-positive oropharyngeal cancer without recurrence, prevoiusly published cohort
DGay4-37924

value: NED, 52.1 months


title: PBMCs from sample B6-2_Memory_CD4

description: PBMCs from sample B6-2_Memory_CD4


title: Antrum_380

city: Marburg

first: Laura

last: Koebbe

address: Baldingerstraße

institute: University of Marburg

data_processing:
Quality control of sequencing data was performed with FastQC v0.11.7.
For adaptor trimming bbduk from the BBMap v37.44 was used.
The read alignment against GRCh38 was performed with STAR Aligner 2.5.2b.
FeatureCounts v1.5.1 was used for quantification of gene expression using the Ensembl annotation GRCh38.89 as reference.
Further QC was performed using RSeQC.
Assembly: GRCh38
Supplementary files format and content: gastric_expression_unique_counts.csv: comma-separated file with number of unique counts per gene and sample (columns = samples, rows = genes (Ensembl Ids))

molecule: polyA RNA

source_name: Antrum

extract_protocol:
Tissue samples were mechanically homogenized with ceramic beads and a Precellys tissue homogenizer. Total RNA (and genomic DNA) was extracted using the Allprep DNA/RNA Mini Kit from Qiagen.
RNA libraries for RNA-Seq were prepared using Lexogen's QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina following manufacturer's protocol.

value: Antrum


title: PBMCs from sample B6-1_Naive_CD8

description: PBMCs from sample B6-1_Naive_CD8


title: PBMCs from sample B6-1_Naive_CD4

description: PBMCs from sample B6-1_Naive_CD4


title: Antrum_379


title: Corpus_410

source_name: Corpus

value: Corpus


title: PBMCs from sample B6-1_Memory_CD8

description: PBMCs from sample B6-1_Memory_CD8


title: PBMCs from sample B6-4_Naive_CD8

description: PBMCs from sample B6-4_Naive_CD8


title: Corpus_409


title: PBMCs from sample B6-2_Memory_CD8

description: PBMCs from sample B6-2_Memory_CD8


title: Corpus_408


title: Antrum_378


title: PBMCs from sample B6-12_Naive_CD8

description: PBMCs from sample B6-12_Naive_CD8


title: Antrum_377


title: Corpus_407


title: PBMCs from sample B6-12_Memory_CD4

description: PBMCs from sample B6-12_Memory_CD4


title: PBMCs from sample B6-3_Memory_CD4

description: PBMCs from sample B6-3_Memory_CD4


title: PBMCs from sample B6-11_Naive_CD8

description: PBMCs from sample B6-11_Naive_CD8


title: Antrum_376


title: Antrum_375


title: Corpus_405


title: PBMCs from sample B6-11_Naive_CD4

description: PBMCs from sample B6-11_Naive_CD4


title: PBMCs from sample B6-12_Memory_CD8

description: PBMCs from sample B6-12_Memory_CD8


title: PBMCs from sample B6-11_Memory_CD8

description: PBMCs from sample B6-11_Memory_CD8


title: PBMCs from sample B6-11_Memory_CD4

description: PBMCs from sample B6-11_Memory_CD4


title: Antrum_381


title: Corpus_404


title: PBMCs from sample B6-10_Naive_CD8

description: PBMCs from sample B6-10_Naive_CD8


title: Antrum_374


title: Antrum_373


title: PBMCs from sample B6-10_Naive_CD4

description: PBMCs from sample B6-10_Naive_CD4


title: PBMCs from sample B6-12_Naive_CD4

description: PBMCs from sample B6-12_Naive_CD4


title: Corpus_402


title: PBMCs from sample B6-10_Memory_CD8

description: PBMCs from sample B6-10_Memory_CD8


title: PBMCs from sample B5-9_Naive_CD8

description: PBMCs from sample B5-9_Naive_CD8


title: PBMCs from sample B5-9_Naive_CD4

description: PBMCs from sample B5-9_Naive_CD4


title: PBMCs from sample B6-1_Memory_CD4

description: PBMCs from sample B6-1_Memory_CD4


title: Antrum_372


title: Corpus_401


title: Corpus_406


title: Antrum_371


title: PBMCs from sample B5-9_Memory_CD8

description: PBMCs from sample B5-9_Memory_CD8


title: Corpus_400


title: PBMCs from sample B5-9_Memory_CD4

description: PBMCs from sample B5-9_Memory_CD4


title: PBMCs from sample B5-8_Naive_CD8

description: PBMCs from sample B5-8_Naive_CD8


title: Antrum_370


title: Antrum_369


title: Corpus_399


title: PBMCs from sample B5-8_Naive_CD4

description: PBMCs from sample B5-8_Naive_CD4


title: PBMCs from sample B5-8_Memory_CD4

description: PBMCs from sample B5-8_Memory_CD4


title: PBMCs from sample B5-8_Memory_CD8

description: PBMCs from sample B5-8_Memory_CD8


title: PBMCs from sample B5-7_Naive_CD8

description: PBMCs from sample B5-7_Naive_CD8


title: Antrum_368


title: Corpus_403


title: Corpus_397


title: PBMCs from sample B5-7_Memory_CD8

description: PBMCs from sample B5-7_Memory_CD8


title: Antrum_367


title: PBMCs from sample B6-10_Memory_CD4

description: PBMCs from sample B6-10_Memory_CD4


title: PBMCs from sample B5-7_Memory_CD4

description: PBMCs from sample B5-7_Memory_CD4


title: PBMCs from sample B5-6_Naive_CD8

description: PBMCs from sample B5-6_Naive_CD8


title: Corpus_396


title: Antrum_365


title: PBMCs from sample B5-6_Memory_CD8

description: PBMCs from sample B5-6_Memory_CD8


title: PBMCs from sample B5-6_Naive_CD4

description: PBMCs from sample B5-6_Naive_CD4


title: Corpus_394


title: PBMCs from sample B5-6_Memory_CD4

description: PBMCs from sample B5-6_Memory_CD4


title: Corpus_395


title: Antrum_364


title: PBMCs from sample B5-5_Naive_CD4

description: PBMCs from sample B5-5_Naive_CD4


title: Corpus_393


title: Corpus_398


title: Antrum_363


title: PBMCs from sample B5-5_Naive_CD8

description: PBMCs from sample B5-5_Naive_CD8


title: Corpus_392


title: PBMCs from sample B5-5_Memory_CD4

description: PBMCs from sample B5-5_Memory_CD4


title: Corpus_391


title: PBMCs from sample B5-4_Naive_CD8

description: PBMCs from sample B5-4_Naive_CD8


title: PBMCs from sample B5-5_Memory_CD8

description: PBMCs from sample B5-5_Memory_CD8


title: Antrum_362


title: PBMCs from sample B5-4_Naive_CD4

description: PBMCs from sample B5-4_Naive_CD4


title: PBMCs from sample B5-4_Memory_CD8

description: PBMCs from sample B5-4_Memory_CD8


title: Corpus_390


title: PBMCs from sample B5-7_Naive_CD4

description: PBMCs from sample B5-7_Naive_CD4


title: PBMCs from sample B5-4_Memory_CD4

description: PBMCs from sample B5-4_Memory_CD4


title: Antrum_366


title: Corpus_389


title: Antrum_360


title: PBMCs from sample B5-3_Naive_CD4

description: PBMCs from sample B5-3_Naive_CD4


title: PBMCs from sample B5-3_Memory_CD8

description: PBMCs from sample B5-3_Memory_CD8


title: Corpus_388


title: PBMCs from sample B5-3_Memory_CD4

description: PBMCs from sample B5-3_Memory_CD4


title: Antrum_359


title: Corpus_387


title: Antrum_358


title: PBMCs from sample B5-2_Naive_CD4

description: PBMCs from sample B5-2_Naive_CD4


title: PBMCs from sample B5-2_Memory_CD8

description: PBMCs from sample B5-2_Memory_CD8


title: PBMCs from sample B5-2_Naive_CD8

description: PBMCs from sample B5-2_Naive_CD8


title: PBMCs from sample B5-2_Memory_CD4

description: PBMCs from sample B5-2_Memory_CD4


title: Corpus_386


title: PBMCs from sample B5-1_Naive_CD8

description: PBMCs from sample B5-1_Naive_CD8


title: Antrum_357


title: Corpus_384


title: Antrum_356


title: PBMCs from sample B5-1_Memory_CD4

description: PBMCs from sample B5-1_Memory_CD4


title: Antrum_355


title: Antrum_361


title: PBMCs from sample B5-3_Naive_CD8

description: PBMCs from sample B5-3_Naive_CD8


title: Corpus_383


title: PBMCs from sample B5-13_Naive_CD8

description: PBMCs from sample B5-13_Naive_CD8


title: PBMCs from sample B5-13_Naive_CD4

description: PBMCs from sample B5-13_Naive_CD4


title: Corpus_385


title: PBMCs from sample B5-13_Memory_CD8

description: PBMCs from sample B5-13_Memory_CD8


title: Corpus_382


title: Antrum_353


title: PBMCs from sample B5-13_Memory_CD4

description: PBMCs from sample B5-13_Memory_CD4


title: Corpus_381


title: Antrum_352


title: Corpus_380


title: PBMCs from sample B5-1_Naive_CD4

description: PBMCs from sample B5-1_Naive_CD4


title: PBMCs from sample B5-12_Naive_CD8

description: PBMCs from sample B5-12_Naive_CD8


title: PBMCs from sample B5-1_Memory_CD8

description: PBMCs from sample B5-1_Memory_CD8


title: Corpus_379


title: PBMCs from sample B5-12_Memory_CD4

description: PBMCs from sample B5-12_Memory_CD4


title: Antrum_349


title: PBMCs from sample B5-11_Naive_CD8

description: PBMCs from sample B5-11_Naive_CD8


title: PBMCs from sample B5-11_Memory_CD8

description: PBMCs from sample B5-11_Memory_CD8


title: PBMCs from sample B5-12_Naive_CD4

description: PBMCs from sample B5-12_Naive_CD4


title: PBMCs from sample B5-11_Naive_CD4

description: PBMCs from sample B5-11_Naive_CD4


title: Antrum_348


title: Antrum_350


title: Antrum_354


title: PBMCs from sample B5-10_Naive_CD8

description: PBMCs from sample B5-10_Naive_CD8


title: PBMCs from sample B5-11_Memory_CD4

description: PBMCs from sample B5-11_Memory_CD4


title: Corpus_377


title: Antrum_347


title: PBMCs from sample B5-10_Memory_CD4

description: PBMCs from sample B5-10_Memory_CD4


title: Antrum_346


title: Corpus_378


title: PBMCs from sample B3-9_Naive_CD8

description: PBMCs from sample B3-9_Naive_CD8


title: PBMCs from sample B5-10_Memory_CD8

description: PBMCs from sample B5-10_Memory_CD8


title: PBMCs from sample B5-10_Naive_CD4

description: PBMCs from sample B5-10_Naive_CD4


title: PBMCs from sample B3-9_Naive_CD4

description: PBMCs from sample B3-9_Naive_CD4


title: Antrum_351


title: PBMCs from sample B3-9_Memory_CD8

description: PBMCs from sample B3-9_Memory_CD8


title: Corpus_376


title: Antrum_345


title: PBMCs from sample B5-12_Memory_CD8

description: PBMCs from sample B5-12_Memory_CD8


title: Corpus_374


title: PBMCs from sample B3-9_Memory_CD4

description: PBMCs from sample B3-9_Memory_CD4


title: PBMCs from sample B3-8_Naive_CD4

description: PBMCs from sample B3-8_Naive_CD4


title: PBMCs from sample B3-8_Naive_CD8

description: PBMCs from sample B3-8_Naive_CD8


title: Antrum_344


title: Corpus_373


title: Antrum_343


title: Corpus_372


title: PBMCs from sample B3-8_Memory_CD8

description: PBMCs from sample B3-8_Memory_CD8


title: Antrum_342


title: PBMCs from sample B3-8_Memory_CD4

description: PBMCs from sample B3-8_Memory_CD4


title: PBMCs from sample B3-7_Naive_CD4

description: PBMCs from sample B3-7_Naive_CD4


title: PBMCs from sample B3-7_Naive_CD8

description: PBMCs from sample B3-7_Naive_CD8


title: PBMCs from sample B3-7_Memory_CD4

description: PBMCs from sample B3-7_Memory_CD4


title: Corpus_371


title: PBMCs from sample B3-7_Memory_CD8

description: PBMCs from sample B3-7_Memory_CD8


title: Corpus_375


title: Antrum_341


title: PBMCs from sample B3-6_Naive_CD8

description: PBMCs from sample B3-6_Naive_CD8


title: Antrum_339


title: Antrum_340


title: Corpus_370


title: PBMCs from sample B3-6_Memory_CD8

description: PBMCs from sample B3-6_Memory_CD8


title: Corpus_369


title: Antrum_338


title: PBMCs from sample B3-6_Naive_CD4

description: PBMCs from sample B3-6_Naive_CD4


title: PBMCs from sample B3-5_Naive_CD4

description: PBMCs from sample B3-5_Naive_CD4


title: PBMCs from sample B3-6_Memory_CD4

description: PBMCs from sample B3-6_Memory_CD4


title: Corpus_368


title: Antrum_337


title: Corpus_367


title: Antrum_336


title: PBMCs from sample B3-5_Memory_CD8

description: PBMCs from sample B3-5_Memory_CD8


title: Antrum_335


title: PBMCs from sample B3-5_Memory_CD4

description: PBMCs from sample B3-5_Memory_CD4


title: Corpus_366


title: PBMCs from sample B3-4_Naive_CD8

description: PBMCs from sample B3-4_Naive_CD8


title: Antrum_334


title: PBMCs from sample B3-4_Memory_CD8

description: PBMCs from sample B3-4_Memory_CD8


title: Corpus_365


title: PBMCs from sample B3-3_Naive_CD8

description: PBMCs from sample B3-3_Naive_CD8


title: PBMCs from sample B3-4_Memory_CD4

description: PBMCs from sample B3-4_Memory_CD4


title: Corpus_363


title: Antrum_333


title: PBMCs from sample B3-3_Memory_CD8

description: PBMCs from sample B3-3_Memory_CD8


title: PBMCs from sample B3-3_Memory_CD4

description: PBMCs from sample B3-3_Memory_CD4


title: Antrum_332


title: PBMCs from sample B3-2_Naive_CD8

description: PBMCs from sample B3-2_Naive_CD8


title: PBMCs from sample B3-5_Naive_CD8

description: PBMCs from sample B3-5_Naive_CD8


title: PBMCs from sample B3-2_Naive_CD4

description: PBMCs from sample B3-2_Naive_CD4


title: Corpus_361


title: PBMCs from sample B3-2_Memory_CD8

description: PBMCs from sample B3-2_Memory_CD8


title: Antrum_331


title: Corpus_360


title: PBMCs from sample B3-2_Memory_CD4

description: PBMCs from sample B3-2_Memory_CD4


title: PBMCs from sample B3-1_Naive_CD8

description: PBMCs from sample B3-1_Naive_CD8


title: Corpus_359


title: Antrum_330


title: PBMCs from sample B3-4_Naive_CD4

description: PBMCs from sample B3-4_Naive_CD4


title: PBMCs from sample B3-1_Naive_CD4

description: PBMCs from sample B3-1_Naive_CD4


title: Corpus_358


title: PBMCs from sample B3-1_Memory_CD8

description: PBMCs from sample B3-1_Memory_CD8


title: PBMCs from sample B3-1_Memory_CD4

description: PBMCs from sample B3-1_Memory_CD4


title: Corpus_357


title: Corpus_364


title: PBMCs from sample B3-13_Naive_CD8

description: PBMCs from sample B3-13_Naive_CD8


title: Antrum_327


title: PBMCs from sample B3-13_Memory_CD4

description: PBMCs from sample B3-13_Memory_CD4


title: Antrum_328


title: Corpus_362


title: PBMCs from sample B3-13_Memory_CD8

description: PBMCs from sample B3-13_Memory_CD8


title: Corpus_356


title: Corpus_355


title: Antrum_326


title: PBMCs from sample B3-13_Naive_CD4

description: PBMCs from sample B3-13_Naive_CD4


title: PBMCs from sample B3-12_Naive_CD4

description: PBMCs from sample B3-12_Naive_CD4


title: Corpus_354


title: Antrum_324


title: PBMCs from sample B3-12_Memory_CD4

description: PBMCs from sample B3-12_Memory_CD4


title: Antrum_325


title: PBMCs from sample B3-12_Memory_CD8

description: PBMCs from sample B3-12_Memory_CD8


title: Corpus_353


title: PBMCs from sample B3-11_Naive_CD4

description: PBMCs from sample B3-11_Naive_CD4


title: PBMCs from sample B3-11_Memory_CD8

description: PBMCs from sample B3-11_Memory_CD8


title: Antrum_322


title: PBMCs from sample B3-11_Naive_CD8

description: PBMCs from sample B3-11_Naive_CD8


title: Antrum_323


title: Corpus_352


title: Antrum_329


title: Antrum_321


title: PBMCs from sample B3-10_Naive_CD4

description: PBMCs from sample B3-10_Naive_CD4


title: PBMCs from sample B3-10_Memory_CD8

description: PBMCs from sample B3-10_Memory_CD8


title: PBMCs from sample B3-12_Naive_CD8

description: PBMCs from sample B3-12_Naive_CD8


title: Antrum_319


title: Antrum_320


title: Corpus_351


title: PBMCs from sample B3-10_Memory_CD4

description: PBMCs from sample B3-10_Memory_CD4


title: Antrum_318


title: PBMCs from sample B2-9_Naive_CD8

description: PBMCs from sample B2-9_Naive_CD8


title: Corpus_350


title: PBMCs from sample B2-9_Naive_CD4

description: PBMCs from sample B2-9_Naive_CD4


title: PBMCs from sample B2-9_Memory_CD8

description: PBMCs from sample B2-9_Memory_CD8


title: PBMCs from sample B2-9_Memory_CD4

description: PBMCs from sample B2-9_Memory_CD4


title: Antrum_317


title: Antrum_316


title: Corpus_349


title: PBMCs from sample B3-11_Memory_CD4

description: PBMCs from sample B3-11_Memory_CD4


title: Corpus_348


title: PBMCs from sample B2-8_Memory_CD8

description: PBMCs from sample B2-8_Memory_CD8


title: PBMCs from sample B2-8_Naive_CD8

description: PBMCs from sample B2-8_Naive_CD8


title: PBMCs from sample B2-8_Memory_CD4

description: PBMCs from sample B2-8_Memory_CD4


title: PBMCs from sample B2-8_Naive_CD4

description: PBMCs from sample B2-8_Naive_CD4


title: PBMCs from sample B3-10_Naive_CD8

description: PBMCs from sample B3-10_Naive_CD8


title: Antrum_315


title: PBMCs from sample B2-7_Naive_CD8

description: PBMCs from sample B2-7_Naive_CD8


title: Corpus_347


title: Antrum_314


title: PBMCs from sample B2-7_Naive_CD4

description: PBMCs from sample B2-7_Naive_CD4


title: PBMCs from sample B2-7_Memory_CD8

description: PBMCs from sample B2-7_Memory_CD8


title: Corpus_346


title: PBMCs from sample B2-7_Memory_CD4

description: PBMCs from sample B2-7_Memory_CD4


title: Antrum_313


title: Corpus_345


title: PBMCs from sample B2-6_Naive_CD8

description: PBMCs from sample B2-6_Naive_CD8


title: PBMCs from sample B2-6_Naive_CD4

description: PBMCs from sample B2-6_Naive_CD4


title: Corpus_344


title: PBMCs from sample B2-6_Memory_CD4

description: PBMCs from sample B2-6_Memory_CD4


title: Antrum_312


title: PBMCs from sample B2-6_Memory_CD8

description: PBMCs from sample B2-6_Memory_CD8


title: Antrum_311


title: PBMCs from sample B2-5_Naive_CD4

description: PBMCs from sample B2-5_Naive_CD4


title: Corpus_343


title: Corpus_342


title: Antrum_309


title: PBMCs from sample B2-5_Memory_CD8

description: PBMCs from sample B2-5_Memory_CD8


title: PBMCs from sample B2-4_Naive_CD8

description: PBMCs from sample B2-4_Naive_CD8


title: Corpus_340


title: PBMCs from sample B2-4_Naive_CD4

description: PBMCs from sample B2-4_Naive_CD4


title: Corpus_341


title: Antrum_308


title: Corpus_339


title: PBMCs from sample B2-4_Memory_CD4

description: PBMCs from sample B2-4_Memory_CD4


title: Antrum_307


title: PBMCs from sample B2-3_Naive_CD4

description: PBMCs from sample B2-3_Naive_CD4


title: PBMCs from sample B2-4_Memory_CD8

description: PBMCs from sample B2-4_Memory_CD8


title: PBMCs from sample B2-3_Naive_CD8

description: PBMCs from sample B2-3_Naive_CD8


title: Corpus_338


title: PBMCs from sample B2-3_Memory_CD8

description: PBMCs from sample B2-3_Memory_CD8


title: Antrum_310


title: PBMCs from sample B2-3_Memory_CD4

description: PBMCs from sample B2-3_Memory_CD4


title: Antrum_306


title: Antrum_305


title: Corpus_337


title: PBMCs from sample B2-5_Memory_CD4

description: PBMCs from sample B2-5_Memory_CD4


title: Corpus_336


title: PBMCs from sample B2-2_Naive_CD4

description: PBMCs from sample B2-2_Naive_CD4


title: PBMCs from sample B2-2_Memory_CD8

description: PBMCs from sample B2-2_Memory_CD8


title: PBMCs from sample B2-2_Memory_CD4

description: PBMCs from sample B2-2_Memory_CD4


title: PBMCs from sample B2-2_Naive_CD8

description: PBMCs from sample B2-2_Naive_CD8


title: Corpus_335


title: Antrum_303


title: PBMCs from sample B2-1_Naive_CD8

description: PBMCs from sample B2-1_Naive_CD8


title: PBMCs from sample B2-1_Naive_CD4

description: PBMCs from sample B2-1_Naive_CD4


title: Corpus_334


title: Antrum_302


title: PBMCs from sample B2-1_Memory_CD4

description: PBMCs from sample B2-1_Memory_CD4


title: Antrum_301


title: PBMCs from sample B2-1_Memory_CD8

description: PBMCs from sample B2-1_Memory_CD8


title: Corpus_333


title: PBMCs from sample B2-12_Memory_CD8

description: PBMCs from sample B2-12_Memory_CD8


title: Corpus_332


title: Antrum_300


title: PBMCs from sample B2-12_Naive_CD8

description: PBMCs from sample B2-12_Naive_CD8


title: PBMCs from sample B2-12_Memory_CD4

description: PBMCs from sample B2-12_Memory_CD4


title: Antrum_299


title: Corpus_331


title: Antrum_304


title: Corpus_330


title: Antrum_298


title: PBMCs from sample B2-11_Naive_CD4

description: PBMCs from sample B2-11_Naive_CD4


title: PBMCs from sample B2-10_Naive_CD4

description: PBMCs from sample B2-10_Naive_CD4


title: PBMCs from sample B2-11_Memory_CD4

description: PBMCs from sample B2-11_Memory_CD4


title: Corpus_329


title: PBMCs from sample B2-11_Memory_CD8

description: PBMCs from sample B2-11_Memory_CD8


title: Antrum_297


title: Corpus_328


title: PBMCs from sample B2-10_Memory_CD4

description: PBMCs from sample B2-10_Memory_CD4


title: PBMCs from sample B2-5_Naive_CD8

description: PBMCs from sample B2-5_Naive_CD8


title: Antrum_295


title: Antrum_296


title: PBMCs from sample B2-10_Memory_CD8

description: PBMCs from sample B2-10_Memory_CD8


title: Corpus_327


title: PBMCs from sample B2-11_Naive_CD8

description: PBMCs from sample B2-11_Naive_CD8


title: PBMCs from sample B2-12_Naive_CD4

description: PBMCs from sample B2-12_Naive_CD4


title: Corpus_326


title: Antrum_294


title: Corpus_325


title: PBMCs from sample B1-9_Naive_CD4

description: PBMCs from sample B1-9_Naive_CD4


title: PBMCs from sample B2-10_Naive_CD8

description: PBMCs from sample B2-10_Naive_CD8


title: PBMCs from sample B1-8_Naive_CD8

description: PBMCs from sample B1-8_Naive_CD8


title: Corpus_324


title: Antrum_292


title: PBMCs from sample B1-8_Naive_CD4

description: PBMCs from sample B1-8_Naive_CD4


title: PBMCs from sample B1-8_Memory_CD8

description: PBMCs from sample B1-8_Memory_CD8


title: PBMCs from sample B1-9_Naive_CD8

description: PBMCs from sample B1-9_Naive_CD8


title: shRNAseq in TIL11 pollen Rep2B

city: Cold Spring Harbor

first: Jonathan

last: Cahn

state: NY

address: 1 Bungtown Rd

institute: CSHL

description:
TIL11_pollen_shRNA_Rep2_results.txt
TIL11_pollen_shRNAseq_Rep2B

data_processing:
Adapter trimming with cutadapt
For RNAseq and RAMPAGE: mapping to TIL11 v1.1 genome with STAR (parameters: --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 20 --quantMode GeneCounts).
For RAMPAGE only, TSS were identified by calling peak with macs2 using the corresponding RNAseq control.
For shRNA, trimmed fastq files were depleted of snoRNAs, rRNAs and tRNAs by mapping to these structural RNAs from zea mays with bowtie2, and the leftover reads were mapped to TIL11 v1.1 with ShortStack (--mmap u --dicermin 20 --dicermax 24 --bowtie_m all --mismatches 1 --foldsize 1000 --pad 250)
Assembly: TIL11 v1.1
Supplementary files format and content: For RNAseq: count table on all TIL11 v1.1 genes for each sample (combined ReadsPerGene.out.tab files from STAR)
Supplementary files format and content: For RAMPAGeE: list of identified TSS (macs2 narrowPeak format)
Supplementary files format and content: For shRNA: table of identified clusters (ShortStack Results file)

organism: Zea mays subsp. parviglumis

source_name: pollen

growth_protocol: For collecting immature ears, TIL11 plants were grown in the CSHL Uplands Farm field from September to early October to promoter floral transition by natural short day conditions. Immature TIL11 ears at an equivalent development stage (with inflorescence meristems, spikelet pair meristems, spikelet meristems and floral meristems) were collected under a dissecting microscope, frozen in LN2 stored at -80°C. For pollen samples, plants were grown in a short day (8h light/16h dark) walk-in chamber to promote floral transition. Fresh pollen was harvested, frozen in LN2 and stored at -80°C. For root tips samples, seeds were germinated on wet paper towels in a Pyrex dish kept in the incubator at 26°C in continuous darkness. After 5 days, 1-3 mm root tips were cut off with a razor blade on ice, frozen in LN2 and stored at -80°C. For coleoptilar nodes samples, seeds were germinated in flats in a long day (8h dark/16h light) growth chamber, 27°C day and 24°C night, and light at 130 μmoles at the top flat. After 5 days, seedlings were unearthed and 5 mm sections around coleoptilar nodes were dissected on ice, frozen in LN2 and stored at -80°C.

extract_protocol:
RNA was extracted with Direct-zol RNA Miniprep Kit (Zymo Reserach).
RNAseq libraries were constructed from 1ug of total RNA with TruSeq Stranded Total RNA LT Kit, including RiboZero Plant depletion and oligo(dT) and random probes for cDNA synthesis. RAMPAGE libraries were constructed from 5ug total RNA following published protocol (Batut and Gingeras 2013) using RiboMinus Plant depletion. shRNAseq libraries were constructed from 5ug of total RNA using TruSeq Small RNA protocol after RiboMinus Plant depletion and size selection of 100 to 205nt with BluePippin (Sage Science).

value: pollen

tag: inbred line

value: WT

tag: developmental stage

value: mature pollen


title: Antrum_291


title: PBMCs from sample B1-8_Memory_CD4

description: PBMCs from sample B1-8_Memory_CD4


title: Corpus_323


title: Corpus_322


title: PBMCs from sample B1-9_Memory_CD8

description: PBMCs from sample B1-9_Memory_CD8


title: shRNAseq in TIL11 pollen Rep1B

description:
TIL11_pollen_shRNA_Rep1_results.txt
TIL11_pollen_shRNAseq_Rep1B


title: Antrum_290


title: shRNAseq in TIL11 ears Rep2B

description:
TIL11_ears_shRNA_Rep2_results.txt
TIL11_ears_shRNAseq_Rep2B

source_name: immature ears

value: immature ears


title: PBMCs from sample B1-9_Memory_CD4

description: PBMCs from sample B1-9_Memory_CD4


title: Corpus_321


title: Corpus_320


title: shRNAseq in TIL11 ears Rep1B

description:
TIL11_ears_shRNA_Rep1_results.txt
TIL11_ears_shRNAseq_Rep1B


title: PBMCs from sample B1-7_Naive_CD4

description: PBMCs from sample B1-7_Naive_CD4


title: Antrum_289


title: PBMCs from sample B1-7_Memory_CD8

description: PBMCs from sample B1-7_Memory_CD8


title: Corpus_319


title: Antrum_293


title: shRNAseq in TIL11 coleoptilar node Rep2B

description:
TIL11_cn_shRNA_Rep2_results.txt
TIL11_cn_shRNAseq_Rep2B

source_name: coleoptilar nodes

value: coleoptilar nodes

value: 5 DAG


title: PBMCs from sample B1-7_Memory_CD4

description: PBMCs from sample B1-7_Memory_CD4


title: Antrum_288


title: Corpus_317


title: Antrum_287


title: PBMCs from sample B1-7_Naive_CD8

description: PBMCs from sample B1-7_Naive_CD8


title: Antrum_286


title: shRNAseq in TIL11 pollen Rep2A


title: Antrum_285


title: PBMCs from sample B1-6_Memory_CD8

description: PBMCs from sample B1-6_Memory_CD8


title: Corpus_315


title: PBMCs from sample B1-6_Naive_CD8

description: PBMCs from sample B1-6_Naive_CD8


title: Corpus_314


title: PBMCs from sample B1-6_Memory_CD4

description: PBMCs from sample B1-6_Memory_CD4


title: Corpus_316


title: Corpus_312


title: shRNAseq in TIL11 ears Rep1A


title: Corpus_313


title: Corpus_311


title: shRNAseq in TIL11 coleoptilar node Rep2A


title: shRNAseq in TIL11 ears Rep2A


title: Corpus_318


title: Corpus_309


title: PBMCs from sample B1-5_Naive_CD8

description: PBMCs from sample B1-5_Naive_CD8


title: Antrum_284


title: Corpus_308


title: PBMCs from sample B1-5_Naive_CD4

description: PBMCs from sample B1-5_Naive_CD4


title: RAMPAGE in TIL11 pollen Rep2

library_source: other

data_processing:
library strategy: RAMPAGE
Adapter trimming with cutadapt
For RNAseq and RAMPAGE: mapping to TIL11 v1.1 genome with STAR (parameters: --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 20 --quantMode GeneCounts).
For RAMPAGE only, TSS were identified by calling peak with macs2 using the corresponding RNAseq control.
For shRNA, trimmed fastq files were depleted of snoRNAs, rRNAs and tRNAs by mapping to these structural RNAs from zea mays with bowtie2, and the leftover reads were mapped to TIL11 v1.1 with ShortStack (--mmap u --dicermin 20 --dicermax 24 --bowtie_m all --mismatches 1 --foldsize 1000 --pad 250)
Assembly: TIL11 v1.1
Supplementary files format and content: For RNAseq: count table on all TIL11 v1.1 genes for each sample (combined ReadsPerGene.out.tab files from STAR)
Supplementary files format and content: For RAMPAGeE: list of identified TSS (macs2 narrowPeak format)
Supplementary files format and content: For shRNA: table of identified clusters (ShortStack Results file)

molecule: other


title: Corpus_310


title: shRNAseq in TIL11 coleoptilar node Rep1A


title: Antrum_281


title: shRNAseq in TIL11 coleoptilar node Rep1B

description:
TIL11_cn_shRNA_Rep1_results.txt
TIL11_cn_shRNAseq_Rep1B


title: Antrum_282


title: PBMCs from sample B1-5_Memory_CD8

description: PBMCs from sample B1-5_Memory_CD8


title: PBMCs from sample B1-4_Naive_CD8

description: PBMCs from sample B1-4_Naive_CD8


title: shRNAseq in TIL11 pollen Rep1A


title: Antrum_280


title: Antrum_283


title: Corpus_306


title: PBMCs from sample B1-4_Naive_CD4

description: PBMCs from sample B1-4_Naive_CD4


title: PBMCs from sample B3-3_Naive_CD4

description: PBMCs from sample B3-3_Naive_CD4


title: PBMCs from sample B1-5_Memory_CD4

description: PBMCs from sample B1-5_Memory_CD4


title: RAMPAGE in TIL11 pollen Rep1


title: RAMPAGE in TIL11 coleoptilar node Rep2


title: Corpus_305


title: PBMCs from sample B1-6_Naive_CD4

description: PBMCs from sample B1-6_Naive_CD4


title: RAMPAGE in TIL11 coleoptilar node Rep1


title: RAMPAGE in TIL11 ears Rep2


title: RAMPAGE in TIL11 ears Rep1


title: Antrum_279


title: PBMCs from sample B1-3_Naive_CD4

description: PBMCs from sample B1-3_Naive_CD4


title: Corpus_307


title: Antrum_278


title: PBMCs from sample B1-4_Memory_CD8

description: PBMCs from sample B1-4_Memory_CD8


title: Corpus_303


title: RNAseq in TIL11 pollen Rep2

description:
RNAseq_counts_TIL11_v1.1.txt
TIL11_pollen_RNAseq_Rep2


title: PBMCs from sample B1-3_Naive_CD8

description: PBMCs from sample B1-3_Naive_CD8


title: RNAseq in TIL11 roots Rep2

description:
RNAseq_counts_TIL11_v1.1.txt
TIL11_roots_RNAseq_Rep2

source_name: root tips

value: root tips


title: RNAseq in TIL11 pollen Rep1

description:
RNAseq_counts_TIL11_v1.1.txt
TIL11_pollen_RNAseq_Rep1


title: Corpus_304


title: Antrum_276


title: Corpus_302


title: Corpus_298


title: PBMCs from sample B1-3_Memory_CD8

description: PBMCs from sample B1-3_Memory_CD8


title: Corpus_300


title: RNAseq in TIL11 ears Rep2

description:
RNAseq_counts_TIL11_v1.1.txt
TIL11_ears_RNAseq_Rep2


title: Corpus_299


title: Corpus_301


title: PBMCs from sample B1-2_Naive_CD8

description: PBMCs from sample B1-2_Naive_CD8


title: Corpus_295


title: Corpus_297


title: Antrum_277


title: PBMCs from sample B1-2_Memory_CD8

description: PBMCs from sample B1-2_Memory_CD8


title: PBMCs from sample B1-2_Naive_CD4

description: PBMCs from sample B1-2_Naive_CD4


title: RNAseq in TIL11 ears Rep1

description:
RNAseq_counts_TIL11_v1.1.txt
TIL11_ears_RNAseq_Rep1


title: Antrum_274


title: Corpus_294


title: Corpus_293


title: Corpus_296


title: RNAseq in TIL11 coleoptilar node Rep2

description:
RNAseq_counts_TIL11_v1.1.txt
TIL11_cn_RNAseq_Rep2


title: RNAseq in TIL11 roots Rep1

description:
RNAseq_counts_TIL11_v1.1.txt
TIL11_roots_RNAseq_Rep1


title: PBMCs from sample B1-2_Memory_CD4

description: PBMCs from sample B1-2_Memory_CD4


title: Corpus_292


title: Antrum_273


title: RNAseq in TIL11 coleoptilar node Rep1

description:
RNAseq_counts_TIL11_v1.1.txt
TIL11_cn_RNAseq_Rep1


title: PBMCs from sample B1-3_Memory_CD4

description: PBMCs from sample B1-3_Memory_CD4


title: PBMCs from sample B1-1_Naive_CD8

description: PBMCs from sample B1-1_Naive_CD8


title: Antrum_272


title: PBMCs from sample B1-1_Naive_CD4

description: PBMCs from sample B1-1_Naive_CD4


title: Corpus_291


title: Corpus_290


title: Antrum_275


title: PBMCs from sample B1-1_Memory_CD8

description: PBMCs from sample B1-1_Memory_CD8


title: Corpus_289


title: Antrum_271


title: Heart left ventricle, excised under isoflurane anesthesia, kidney disease, 225 days, replicate 7

city: St. Louis

first: Keith

middle: A

last: Hruska

state: MO

address: 660 South Euclid Ave, Box 8208

department: Pediatrics

institute: Washington University in St. Louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.7.9a
Gene counts quantitated with Subread:featureCount 2.0.3 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

organism: Mus musculus

source_name: Heart left ventricle

growth_protocol: Col4a5 knockdown mice were housed with wildtype littermates and fed normal chow for 225 days. At this timepoint the mutant mice have progressed to human equivalent of chronic kidney disease stage 4-5.

extract_protocol:
Total RNA from tissue was isolated and purified using TRIzol (15596018, ThermoFisher Scientific) with tissue disruption by the TissueLyser II (Qiagen), Phasemaker tubes (A33248, ThermoFisher Scientific), and PureLink RNA Mini Kit (12183018a, ThermoFisher Scientific) with PureLink DNase (12185010, ThermoFisher Scientific) according to manufacturers’ instructions.
RNA quality was verified using the Bioanalyzer 2100 Expert (Agilent). All samples met minimum RNA Integrity Number of 8.0
KAPA RiboErase

treatment_protocol: At 225 days, mice were administered ketamine/xylazine, and the heart was removed en bloc. A section of midline, free wall left ventricle was used for RNA processing.

value: Heart left ventricle

value: Col4a5 Knockdown

tag: disease state

value: Chronic kidney disease

value: M

tag: time

value: 225 days


title: Heart left ventricle, excised under isoflurane anesthesia, wild type, 225 days, replicate 8

value: Wild type


title: Corpus_288


title: Heart left ventricle, excised under isoflurane anesthesia, kidney disease, 225 days, replicate 6


title: PBMCs from sample B1-1_Memory_CD4

description: PBMCs from sample B1-1_Memory_CD4

value: PBMCs


title: Antrum_270


title: Heart left ventricle, excised under isoflurane anesthesia, kidney disease, 225 days, replicate 5


title: Heart left ventricle, excised under isoflurane anesthesia, wild type, 225 days, replicate 7


title: PBMCs from sample B1-12_Naive_CD8

description: PBMCs from sample B1-12_Naive_CD8


title: Heart left ventricle, excised under isoflurane anesthesia, wild type, 225 days, replicate 6


title: Corpus_287


title: Antrum_269


title: Corpus_285


title: PBMCs from sample B1-12_Naive_CD4

description: PBMCs from sample B1-12_Naive_CD4


title: PBMCs from sample B1-12_Memory_CD4

description: PBMCs from sample B1-12_Memory_CD4


title: Heart left ventricle, excised under isoflurane anesthesia, wild type, 225 days, replicate 5


title: PBMCs from sample B1-12_Memory_CD8

description: PBMCs from sample B1-12_Memory_CD8


title: Antrum_268


title: Antrum_267


title: Corpus_284


title: Antrum_266


title: PBMCs from sample B1-10_Naive_CD8

description: PBMCs from sample B1-10_Naive_CD8


title: Antrum_264


title: Corpus_283


title: Heart left ventricle, excised under isoflurane anesthesia, wild type, 225 days, replicate 3


title: Heart left ventricle, excised under isoflurane anesthesia, kidney disease, 225 days, replicate 4


title: Corpus_286


title: Antrum_265


title: Antrum_263


title: Heart left ventricle, excised under isoflurane anesthesia, wild type, 225 days, replicate 4


title: PBMCs from sample B1-4_Memory_CD4

description: PBMCs from sample B1-4_Memory_CD4


title: PBMCs from sample B1-10_Memory_CD8

description: PBMCs from sample B1-10_Memory_CD8


title: Corpus_281


title: Corpus_282


title: Heart left ventricle, excised under isoflurane anesthesia, kidney disease, 225 days, replicate 3


title: Corpus_280


title: PBMCs from sample B1-10_Memory_CD4

description: PBMCs from sample B1-10_Memory_CD4


title: Antrum_261


title: Corpus_279


title: PBMCs from sample B1-10_Naive_CD4

description: PBMCs from sample B1-10_Naive_CD4


title: PBMCs from sample A9-9_Naive_CD8

description: PBMCs from sample A9-9_Naive_CD8


title: Heart left ventricle, excised under isoflurane anesthesia, wild type, 225 days, replicate 2


title: Antrum_260


title: PBMCs from sample A9-9_Naive_CD4

description: PBMCs from sample A9-9_Naive_CD4


title: Antrum_259


title: Antrum_258


title: Heart left ventricle, excised under isoflurane anesthesia, wild type, 225 days, replicate 1


title: Corpus_278


title: PBMCs from sample A9-9_Memory_CD4

description: PBMCs from sample A9-9_Memory_CD4


title: Heart left ventricle, excised under isoflurane anesthesia, kidney disease, 225 days, replicate 2


title: PBMCs from sample A9-9_Memory_CD8

description: PBMCs from sample A9-9_Memory_CD8


title: Corpus_277


title: Corpus_276


title: PBMCs from sample A9-8_Naive_CD8

description: PBMCs from sample A9-8_Naive_CD8


title: Antrum_256


title: Antrum_257


title: IMQ_un_m5

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

data_processing:
fastp -q 15 -n 10 -l 20 –detect_adapter_for_pe  -i target_R1.fastq -I target_R2.fastq (fastp v0.19.10)
STAR --readFilesIn target_R1.fastq target_R2.fastq --outSAMtype BAM Unsorted --outFilterMultimapNmax 4 --outFilterType BySJout --outSAMmultNmax 1 --outFilterMismatchNoverReadLmax 0.1 --outSAMstrandField intronMotif --sjdbGTFfile gencode_v33.gtf --outReadsUnmapped Fastx (STAR v2.7.3a)
samtools sort -n target_STAR.Aligned.out.bam | samtools fixmate -rm - - | samtools sort - | samtools markdup -l 800 -rs – target_STAR.Aligned.sortedByCoord.out.bam (samtools v1.9)
featureCounts -p -a gencode_v33.gtf -s 2 -o reverse_stranded.txt target_STAR.Aligned.sortedByCoord.out.bam (featureCounts v2.0.1)
Assembly: mm10
Supplementary files format and content: Excel File containing gene level counts per sample, and

source_name: ear punch biopsy

extract_protocol:
12-14 week old IMQ mice were used for RNA sequencing. RNA was extracted from ear skin using an RNEasy Kit (Qiagen, Germantown, MD) and quality confirmed on a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA).
Libraries were prepared with non-stranded and poly-A selection TruSeq RNA Sample Preparation kits.

treatment_protocol: For the IMQ-induced lupus mouse model, mice were painted on the dorsal and ventral sides of the right ear with 5% imiquimod cream (42 mg/ear/mouse) 3x/week for 4-6 weeks  prior to, and continued through experiments.

value: ear punch biopsy

value: 8-12 weeks

value: female

tag: batch


title: IMQ_un_m8


title: Corpus_275

value: Corpus


title: PBMCs from sample A9-8_Naive_CD4

description: PBMCs from sample A9-8_Naive_CD4


title: IMQ_un_m1


title: Antrum_254

value: Antrum


title: Antrum_262


title: PBMCs from sample A9-8_Memory_CD8

description: PBMCs from sample A9-8_Memory_CD8


title: IMQ_un_m14


title: Heart left ventricle, excised under isoflurane anesthesia, kidney disease, 225 days, replicate 1


title: Antrum_253


title: IMQ_un_m12


title: PBMCs from sample A9-8_Memory_CD4

description: PBMCs from sample A9-8_Memory_CD4


title: Corpus_273


title: IMQ_treat_m7


title: Antrum_249


title: Corpus_272


title: PBMCs from sample A9-7_Naive_CD8

description: PBMCs from sample A9-7_Naive_CD8


title: Antrum_250


title: IMQ_treat_m4


title: IMQ_un_m10


title: Antrum_251


title: Corpus_270


title: Antrum_252


title: Corpus_271


title: Antrum_248


title: PBMCs from sample A9-7_Memory_CD8

description: PBMCs from sample A9-7_Memory_CD8


title: PBMCs from sample A9-7_Memory_CD4

description: PBMCs from sample A9-7_Memory_CD4


title: Antrum_255


title: Corpus_269


title: IMQ_treat_m15


title: Antrum_247


title: Corpus_274


title: Corpus_268


title: PBMCs from sample A9-6_Naive_CD4

description: PBMCs from sample A9-6_Naive_CD4


title: IMQ_treat_m13


title: Corpus_267


title: Corpus_266


title: Antrum_246


title: PBMCs from sample A9-7_Naive_CD4

description: PBMCs from sample A9-7_Naive_CD4


title: PBMCs from sample A9-6_Memory_CD8

description: PBMCs from sample A9-6_Memory_CD8


title: IMQ_treat_m9


title: Corpus_264


title: IMQ_treat_m11


title: Corpus_265


title: PBMCs from sample A9-5_Naive_CD8

description: PBMCs from sample A9-5_Naive_CD8


title: CTRL_m6


title: IMQ_treat_m2


title: Antrum_245


title: PBMCs from sample A9-6_Memory_CD4

description: PBMCs from sample A9-6_Memory_CD4


title: Corpus_262


title: PBMCs from sample A9-5_Naive_CD4

description: PBMCs from sample A9-5_Naive_CD4


title: Corpus_261


title: Antrum_244


title: CTRL_m3


title: PBMCs from sample A9-6_Naive_CD8

description: PBMCs from sample A9-6_Naive_CD8


title: Antrum_243


title: Corpus_260


title: PBMCs from sample A9-5_Memory_CD4

description: PBMCs from sample A9-5_Memory_CD4


title: CTRL_m20


title: PBMCs from sample A9-5_Memory_CD8

description: PBMCs from sample A9-5_Memory_CD8


title: CTRL_m19


title: Antrum_242


title: Corpus_259


title: PBMCs from sample A9-4_Naive_CD8

description: PBMCs from sample A9-4_Naive_CD8


title: Antrum_241


title: CTRL_m18


title: Corpus_258


title: Corpus_263


title: Antrum_240


title: PBMCs from sample A9-4_Naive_CD4

description: PBMCs from sample A9-4_Naive_CD4


title: Antrum_239


title: PBMCs from sample A9-4_Memory_CD8

description: PBMCs from sample A9-4_Memory_CD8


title: CTRL_m17


title: Antrum_238


title: Corpus_257


title: Antrum_237


title: HTO_2

city: Solna

first: Bastien

last: Hervé

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

description:
10X genomics
snRNAseq.rds

data_processing:
For the scRNAseq, The count table from the output of the Cellranger 2.1.1 software was obtained as part of the standard pipeline of the 10X genomics platform. Cells expressing more than 200 genes but less than 3000 were retained. Additionally, cells with more than 15% of RNA counts being associated mitochondrial origin were removed. Counts were normalized using the sctransform function in Seurat v3.
For the snRNAseq, Cellranger software (10X genomics standard pipeline) was run twice on the single-nucleus dataset, first to unravel pre-mRNA expression of genes supported by mm10 genome and second to associate barcoded antibodies to cells, given as a list of features. Intersection of cell barcodes from both modalities wasretained. Cells expressing more than 600 genes, with UMIs higher than 1000 and lower than 30000 were selected. Moreover, cells with more than 1% of RNA counts being associated to mitochondrial environment were removed. After a centered log ratio transformation,sample of origin assignation was performed for each cell by HTODemux function from Seurat V4.0, with a positive quantile value to consider a cell positive set at 0.99. Among the 35820 valid cells processed by cellranger, 14294 were targeted by more than one unique antibody barcode, 10474 cells were classified as negative, not reaching the positive quantile threshold and 11052 cells considered as barcoded by a unique antibody were saved for downstream analysis. A total of 5198 cells were retained for the ablated condition (2 antibodies labeling the ablated samples, 2218 cells and 2980 cells) and 5854 cells were selected for the control condition (2 antibodieslabeling the controlsamples, 2639 cells and 3215 cells).
Assembly: mm10
Supplementary files format and content: Emat10x.csv : count matrix of the scRNAseq
Supplementary files format and content: Anno10xpreQC.csv : metadata matrix of the scRNAseq before QC filtering
Supplementary files format and content: Anno10xpostQC.csv : metadata matrix of the scRNAseq after QC filtering
Supplementary files format and content: snRNAseq.rds : seurat object with count and metadata matrices of the snRNAseq

source_name: Mouse brain

extract_protocol:
For the scRNAseq, Neocortices of P90 Emx/tdTom (control, n=4) and Emx/Tom/DTA (ablated, n=2) were microdissected and the tissue dissociated into single-cell suspensions, as previously described. Briefly, mice were transcardially perfused with ice-cold oxygenated artificial cerebrospinal fluid (22 mM NaCl, 0.63 mM KCl, 0.4 mM NaH2PO4 * 2H2O, 6.5 mM NaHCO3, 25 mM Saccharose, 5 mM Glucose, 0.5 mM CaCl2, 4 mM MgSO4. pH 7.3) and the brains collected. The tissue was sectioned at the vibratome in ice-cold artificial cerebrospinal fluid and the motor cortex and cingulate cortex were microdissected. Tissue dissociation was performed with the Adult Brain Dissociation Kit (Miltenyi Biotec) following manufacturer’sinstructions(red blood cells removal step was not included). After debris removal, the cells were resuspended in ice-cold 1% BSA in artificial cerebrospinal fluid, filtered with 30 μm filter (Sysmex Partec) and FACS sorted with the BD Influx System (USB. BD FACS™) to separate GFP+ and TdTom+OL lineage cells. A scRNA-Seq experiment set with a cohort of control and experimental mice was discarded due to strong batch effects, most likely due to stress during the FACS procedure
For the snRNAseq, to assess the impact of dOPC ablation immediately when ablation occurs, cortical tissue was analysed unsing single-nucleus RNA sequencing (snRNA-seq) of antibody-hashed samples. Neonatal mice were sacrificed on the day of birth by decapitation, then the motor cortex region was dissected in icecold oxygenated cutting solution containing 87mM NaCl, 2.5mM KCl, 1.25mM NaH2PO4, 26mM NaHCO3, 0.5mM CaCl2, 4mM MgSO4, 75mM sucrose, and 20mM glucose, before samples were snapfrozen on dry ice in a sterile microtube. The samples were stored at -80°C until further processed. To isolate nuclei, tissue fragments from two animals with identical genotype were combined in nuclei isolation buffer (250mM sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris buffer pH 8.0, 0.1% NP40, 0.1mM DTT and 0.4U/μl RNAse inhibitors), and gently homogenized with a plastic pestle on ice. Subsequently, the homogenate was filtered using a 40μm strainer, and the nuclear pellet was collected upon centrifugation. The pellet was then washed twice with Nuclei Wash and Resuspension buffer (NWR) containing 2% BSA in PBS and 0.4U/μl RNAse inhibitors. Finally, the nuclei were resuspended in ST Staining Buffer (ST-SB: 2% BSA, 0.02% Tween-20, 10mM Tris pH 7.5, 146mM NaCl, 1mM CaCl2, and 21mM MgCl2), filtered again with 40μm strainer and collected for inspection and counting. Hashtag antibody tagging was done as described previously with minor adjustments. Two sets of ablated and two sets of control nuclear samples (1M nuclei per 100μl of ST-SB) were first blocked with TruStain FcX™ (anti-mouse CD16/32, Biolegend #101319) before the addition of 1μg/100μl Mab414 nuclei hashing antibodies (TotalSeq™ A0451-54, Biolegend #682205, #682207, #682209, #682211). To remove the unbound antibodies, samples were washed twice with ST Wash Buffer (10mM Tris, 146mM NaCl, 1mM CaCl2, 21mM MgCl2, 2% BSA, 0.4U/μL of RNAse inhibitor) and again with NWR buffer to avoid the detergent and magnesium carry-over prior to sequencing
For the scRNAseq, the sorted cells were processed with the Chromium Single Cell A Chip kit v2 and library prep with the Chromium Single Cell 3´Library & Gel Beads kit v2 (10X Genomics) according to the manufacturer’s instructions. A total of 3,000 cells for each sample were loaded on the Chromium Single Cell A Chip, although a lower number of cells was recovered in singlet and passed the quality control.
For the snRNAseq, the nuclei were resuspended in NWR, strained with a 20μm and 10μm strainer before counting, sample pooling and downstream processing with 10X platform for single-nuclei sequencing
For the snRNAseq, 4 hastag antibodies were used to label our samples, from Biolegend TotalSeq™ A0451-54. A0451 (DTA) TTCCTGCCATTACTA, A0452 (DTA) CCGTACCTCATTGTT, A0453 (Ctrl) GGTAGATGTCCTCAG, A0454 (Ctrl) TGGTGTCATTCTTGA

treatment_protocol: All mice are on a C57BL/6-B6CBA mixed background. Breeding colonies were maintained by mating transgenic mice with wildtype B6CBA-F1 mice. Mice were fed a standard diet and were kept on a 12 hr dark/light cycle in individually ventilated cages. Experiments were performed on either neonatal (P0) or adult animals (11-14 weeks). Animals from both sexes have been used. All animal experiments conformed to the UK Animals(Scientific Procedures) Act 1986 and were approved by the Cambridge University local ethical committees before licensing by the UK Home Office.

tag: sequencing id

value: Mouse brain

tag: brain region

value: Motor cortex

value: All

value: Mixed (Emx/Tom and Emx/Tom/DTA)

tag: background strain

tag: lane

tag: abbreviation


title: Antrum_236

tag: tissue


title: RNA_2

description:
10X genomics
snRNAseq.rds

library_source: transcriptomic single cell

molecule: nuclear RNA

tag: cell type

tag: genotype

tag: treatment


title: PBMCs from sample A9-3_Naive_CD8

description: PBMCs from sample A9-3_Naive_CD8


title: Corpus_254


title: HTO_1

description:
10X genomics
snRNAseq.rds

tag: age


title: Corpus_255


title: PBMCs from sample A9-4_Memory_CD4

description: PBMCs from sample A9-4_Memory_CD4


title: Corpus_256


title: RNA_1

description:
10X genomics
snRNAseq.rds


title: ectopic_vOLCs

description:
10X genomics
Emat10x.csv
Anno10xpreQC.csv
Anno10xpostQC.csv

value: Motor cortex and cingulate cortex

value: Oligodendrocyte lineage cells

value: Emx1-Cre:Sox10-GFP-tdTom:Sox10-GFP-DTA animals, GFP+ cells (ectopic vOLCs)


title: PBMCs from sample A9-3_Naive_CD4

description: PBMCs from sample A9-3_Naive_CD4


title: Antrum_234


title: Corpus_253


title: PBMCs from sample A9-3_Memory_CD8

description: PBMCs from sample A9-3_Memory_CD8


title: PBMCs from sample A9-3_Memory_CD4

description: PBMCs from sample A9-3_Memory_CD4


title: ctrl_vOLCs

value: Emx1-Cre:Sox10-GFP-TdTom animals, GFP+ cells (vOLCs)


title: Antrum_233


title: Corpus_252


title: PBMCs from sample A9-12_Naive_CD8

description: PBMCs from sample A9-12_Naive_CD8


title: Corpus_251


title: Antrum_232


title: ctrl_dOLCs

value: Emx1-Cre:Sox10-GFP-TdTom animals,  TdTom+ cells (dOLCs)


title: Corpus_250


title: PKP2_m1e14_5825_RV

city: South San Francisco

first: Farshad

last: Farshidfar

state: CA

address: 171 Oyster Point Blvd Ste 500

institute: Tenaya Therapeutics Inc.

data_processing:
Adapter trimming by FASTP (ver. 0.23.3)
Read alignment by Salmon (ver. 1.8.0)
tximport to generate gene expression matrix in Transcript Per Million (TPM)
Protein-coding genes identification by Ensembl mouse reference genome release 107
Exclusion of mitochondrial genes and renormalization to TPM.
Assembly: GRCm39, July 2022
Supplementary files format and content: TXT

source_name: Right ventricle

extract_protocol:
Total RNA was extracted from cardiac RV and LV tissue using the RNeasy Mini or Universal Mini Kit (Qiagen Sciences, 74106 and 73404), cDNA synthesized (Invitrogen SuperScript III First-Strand Synthesis SuperMix for RT) and analyzed by qPCR using Taqman probes to mouse Pkp2 gene, heart failure genes (Nppa, Nppb), and fibrosis genes (Col1a1, Col3a1, and Timp1).  Mouse Gapdh served as an internal housekeeping gene control.  Absolute transgene mRNA copy number was determined by RT-qPCR using a WPRE-specific RNA standard (GenScript) across six orders of magnitude.  DSP protein level in both supernatant and pellet was analyzed to ensure a complete evaluation.
From each replicate, 100 ng total RNA was extracted via the polyA-tail-specific protocol according to Illumina Inc.. RNA quality control was performed before library prep using Agilent TapeStation instrument.  The RNA libraries were prepared using a Stranded Total RNA Library Prep with Ribo-Zero Plus kit (Illumina), which also removes ribosomal RNA.  The libraries were sequenced as 2x50 base pair paired-end reads using Illumina NovaSeq 6000 using V1.5 reagent kit on S1 flow cell with an average of 25.66 million reads per each read file (51.32M reads per sample).

treatment_protocol: TN-401 or AAV9:mPkp2 was given as a single dose via retro-orbital injection 1 week before (for PKP2-m3e13 and PKP2-m1e14 groups) or after (PKP2-m1e14-2.5wk group) animals were induced with tamoxifen.  HBSS, as vehicle control, was injected to WT or non-AAV treated Pkp2-cKO animals.  Tamoxifen injection activates Cre recombinase in Cre-positive animals and induces homozygous deletion of Pkp2 gene.  Pkp2fl/fl Cre-negative littermates were used as controls.

value: Right ventricle

tag: strain


title: PBMCs from sample A9-12_Memory_CD8

description: PBMCs from sample A9-12_Memory_CD8


title: Antrum_229


title: PKP2_m1e14_5825_LV

source_name: Left ventricle

value: Left ventricle


title: Antrum_231


title: PBMCs from sample A9-12_Memory_CD4

description: PBMCs from sample A9-12_Memory_CD4

source_name: PBMCs

value: PBMCs


title: Antrum_235


title: Corpus_249


title: Antrum_230


title: PBMCs from sample A9-11_Naive_CD8

description: PBMCs from sample A9-11_Naive_CD8


title: Corpus_248


title: WT_HBSS_5823_RV

value: WT

value: HBSS


title: PBMCs from sample A9-11_Naive_CD4

description: PBMCs from sample A9-11_Naive_CD4


title: PKP2_m1e14_5822_RV


title: WT_HBSS_5823_LV


title: Corpus_246


title: Corpus_247


title: Antrum_227


title: PBMCs from sample A9-11_Memory_CD8

description: PBMCs from sample A9-11_Memory_CD8


title: PKP2_m1e14_5822_LV


title: Corpus_245


title: Antrum_225


title: PBMCs from sample A9-12_Naive_CD4

description: PBMCs from sample A9-12_Naive_CD4


title: Antrum_226


title: WT_HBSS_5819_RV


title: Corpus_244


title: PBMCs from sample A9-11_Memory_CD4

description: PBMCs from sample A9-11_Memory_CD4


title: PBMCs from sample A9-10_Naive_CD8

description: PBMCs from sample A9-10_Naive_CD8


title: Corpus_243


title: Antrum_224


title: Antrum_228


title: Corpus_242


title: PKP2_m1e14_2.5wk_5814_RV


title: PBMCs from sample A9-10_Naive_CD4

description: PBMCs from sample A9-10_Naive_CD4


title: Antrum_223


title: PBMCs from sample A9-10_Memory_CD8

description: PBMCs from sample A9-10_Memory_CD8


title: PBMCs from sample A9-10_Memory_CD4

description: PBMCs from sample A9-10_Memory_CD4


title: PKP2_m1e14_2.5wk_5814_LV


title: WT_HBSS_5813_RV


title: Corpus_238


title: Antrum_222


title: Corpus_239


title: WT_HBSS_5813_LV


title: Corpus_237


title: Corpus_236


title: WT_HBSS_5819_LV


title: Corpus_241


title: Corpus_233


title: PBMCs from sample A9-2_Memory_CD8

description: PBMCs from sample A9-2_Memory_CD8


title: Corpus_235


title: Corpus_234


title: PKP2_m1e14_2.5wk_5810_RV


title: Antrum_221


title: PKP2_m1e14_2.5wk_5810_LV


title: PBMCs from sample A9-2_Naive_CD8

description: PBMCs from sample A9-2_Naive_CD8


title: PBMCs from sample A9-2_Memory_CD4

description: PBMCs from sample A9-2_Memory_CD4


title: Corpus_240


title: PBMCs from sample A9-1_Naive_CD8

description: PBMCs from sample A9-1_Naive_CD8


title: PBMCs from sample A9-1_Naive_CD4

description: PBMCs from sample A9-1_Naive_CD4


title: PBMCs from sample A9-2_Naive_CD4

description: PBMCs from sample A9-2_Naive_CD4


title: Antrum_219


title: Antrum_218


title: PKP2_m3e13_5809_RV


title: Antrum_220


title: PKP2_m1e14_2.5wk_5807_LV


title: Antrum_217


title: Corpus_230


title: PBMCs from sample A9-1_Memory_CD4

description: PBMCs from sample A9-1_Memory_CD4


title: Corpus_231


title: Antrum_216


title: Antrum_215


title: PBMCs from sample A9-1_Memory_CD8

description: PBMCs from sample A9-1_Memory_CD8


title: PKP2_m3e13_5809_LV


title: PKP2_m1e14_2.5wk_5807_RV


title: PKP2_m1e14_2.5wk_5806_LV


title: Corpus_229


title: Corpus_232


title: PBMCs from sample A8-9_Naive_CD8

description: PBMCs from sample A8-9_Naive_CD8


title: WT_HBSS_5803_RV


title: Antrum_214


title: WT_HBSS_5803_LV


title: Corpus_227


title: Antrum_213


title: PBMCs from sample A8-9_Memory_CD8

description: PBMCs from sample A8-9_Memory_CD8


title: Antrum_212


title: Corpus_226


title: Antrum_211


title: PKP2_m1e14_2.5wk_5801_RV


title: PBMCs from sample A8-9_Memory_CD4

description: PBMCs from sample A8-9_Memory_CD4


title: Corpus_225


title: PKP2_m1e14_2.5wk_5806_RV


title: Antrum_210


title: PKP2_m1e14_2.5wk_5801_LV


title: Antrum_209


title: PBMCs from sample A8-8_Naive_CD4

description: PBMCs from sample A8-8_Naive_CD4


title: PKP2_m3e13_5768_RV


title: PBMCs from sample A8-9_Naive_CD4

description: PBMCs from sample A8-9_Naive_CD4


title: Antrum_206


title: PKP2_m3e13_5759_RV


title: PBMCs from sample A8-8_Memory_CD8

description: PBMCs from sample A8-8_Memory_CD8


title: PBMCs from sample A8-8_Memory_CD4

description: PBMCs from sample A8-8_Memory_CD4


title: Corpus_223


title: PKP2_m3e13_5768_LV


title: Corpus_224


title: Antrum_207


title: PBMCs from sample A8-7_Naive_CD8

description: PBMCs from sample A8-7_Naive_CD8


title: PKP2_m3e13_5759_LV


title: Corpus_222


title: PBMCs from sample A8-8_Naive_CD8

description: PBMCs from sample A8-8_Naive_CD8


title: PBMCs from sample A8-7_Naive_CD4

description: PBMCs from sample A8-7_Naive_CD4


title: PKP2_m1e14_2.5wk_5755_RV


title: Antrum_205


title: PBMCs from sample A8-7_Memory_CD8

description: PBMCs from sample A8-7_Memory_CD8


title: Corpus_220


title: PKP2_m1e14_2.5wk_5755_LV


title: Antrum_204


title: Corpus_228


title: Antrum_203


title: Antrum_208


title: PBMCs from sample A8-7_Memory_CD4

description: PBMCs from sample A8-7_Memory_CD4


title: PKP2_m1e14_5726_RV


title: Corpus_219


title: Corpus_218


title: PKP2_m1e14_5726_LV


title: PBMCs from sample A8-6_Naive_CD8

description: PBMCs from sample A8-6_Naive_CD8


title: PBMCs from sample A8-6_Naive_CD4

description: PBMCs from sample A8-6_Naive_CD4


title: Antrum_201


title: PKP2_HBSS_3217_RV


title: Antrum_202


title: Corpus_216


title: Antrum_200


title: Corpus_221


title: PBMCs from sample A8-6_Memory_CD8

description: PBMCs from sample A8-6_Memory_CD8


title: PBMCs from sample A8-6_Memory_CD4

description: PBMCs from sample A8-6_Memory_CD4


title: Corpus_215


title: PKP2_HBSS_3213_RV


title: Corpus_214


title: Antrum_197


title: Antrum_198


title: Corpus_213


title: PBMCs from sample A8-5_Naive_CD8

description: PBMCs from sample A8-5_Naive_CD8


title: Antrum_196


title: Corpus_217


title: Corpus_212


title: PBMCs from sample A8-5_Memory_CD8

description: PBMCs from sample A8-5_Memory_CD8


title: PKP2_HBSS_2052_LV


title: PKP2_HBSS_2052_RV


title: PBMCs from sample A8-5_Memory_CD4

description: PBMCs from sample A8-5_Memory_CD4


title: Antrum_194


title: PKP2_m3e13_2048_RV


title: Antrum_199


title: Antrum_195


title: Antrum_193


title: Corpus_211


title: Antrum_192


title: Corpus_210


title: PKP2_HBSS_3217_LV


title: PBMCs from sample A8-4_Naive_CD8

description: PBMCs from sample A8-4_Naive_CD8


title: PKP2_m3e13_2048_LV


title: PBMCs from sample A8-4_Naive_CD4

description: PBMCs from sample A8-4_Naive_CD4


title: PKP2_m3e13_2047_RV


title: Antrum_191


title: PKP2_HBSS_3213_LV


title: PBMCs from sample A8-4_Memory_CD8

description: PBMCs from sample A8-4_Memory_CD8


title: PBMCs from sample A8-5_Naive_CD4

description: PBMCs from sample A8-5_Naive_CD4


title: PKP2_m3e13_2047_LV


title: Corpus_209


title: Antrum_190


title: PBMCs from sample A8-4_Memory_CD4

description: PBMCs from sample A8-4_Memory_CD4


title: PKP2_m3e13_2045_RV


title: Corpus_207


title: PBMCs from sample A8-3_Naive_CD4

description: PBMCs from sample A8-3_Naive_CD4


title: Antrum_187


title: Corpus_206


title: PKP2_m3e13_2045_LV


title: Antrum_188


title: WT_HBSS_2040_RV


title: Corpus_204


title: PBMCs from sample A8-3_Memory_CD4

description: PBMCs from sample A8-3_Memory_CD4


title: PBMCs from sample A8-3_Memory_CD8

description: PBMCs from sample A8-3_Memory_CD8


title: Corpus_201


title: PKP2_m1e14_2043_RV


title: Antrum_185


title: PBMCs from sample A8-2_Memory_CD8

description: PBMCs from sample A8-2_Memory_CD8


title: PBMCs from sample A8-2_Naive_CD4

description: PBMCs from sample A8-2_Naive_CD4


title: Corpus_205


title: Corpus_202


title: Corpus_203


title: Antrum_189


title: PKP2_m1e14_2034_RV


title: PBMCs from sample A8-2_Memory_CD4

description: PBMCs from sample A8-2_Memory_CD4


title: WT_HBSS_2040_LV


title: PKP2_m1e14_2034_LV


title: Antrum_186


title: PKP2_m1e14_2043_LV


title: PBMCs from sample A8-2_Naive_CD8

description: PBMCs from sample A8-2_Naive_CD8


title: Corpus_208


title: Corpus_200


title: Corpus_199


title: Corpus_198


title: PBMCs from sample A8-1_Naive_CD8

description: PBMCs from sample A8-1_Naive_CD8


title: Antrum_184


title: Corpus_197


title: PKP2_m3e13_2033_RV


title: Antrum_183


title: Corpus_195


title: PBMCs from sample A8-1_Naive_CD4

description: PBMCs from sample A8-1_Naive_CD4


title: Corpus_196


title: Antrum_182


title: PKP2_m3e13_2029_RV


title: PKP2_m3e13_2033_LV


title: PBMCs from sample A8-1_Memory_CD4

description: PBMCs from sample A8-1_Memory_CD4


title: Antrum_180


title: WT_HBSS_2031_LV


title: Corpus_194


title: PKP2_m3e13_2029_LV


title: PBMCs from sample A8-12_Naive_CD4

description: PBMCs from sample A8-12_Naive_CD4


title: PBMCs from sample A8-1_Memory_CD8

description: PBMCs from sample A8-1_Memory_CD8


title: Corpus_191


title: PBMCs from sample A8-12_Memory_CD8

description: PBMCs from sample A8-12_Memory_CD8


title: Corpus_193


title: Corpus_192


title: WT_HBSS_2031_RV


title: Antrum_181


title: PBMCs from sample A8-12_Naive_CD8

description: PBMCs from sample A8-12_Naive_CD8


title: WT_HBSS_2027_RV


title: Antrum_177


title: PBMCs from sample A8-12_Memory_CD4

description: PBMCs from sample A8-12_Memory_CD4


title: WT_HBSS_2027_LV


title: Antrum_179


title: Corpus_190


title: PBMCs from sample A8-11_Naive_CD8

description: PBMCs from sample A8-11_Naive_CD8


title: Antrum_178


title: PKP2_HBSS_2006_RV


title: Antrum_174


title: PBMCs from sample A8-11_Memory_CD8

description: PBMCs from sample A8-11_Memory_CD8


title: PBMCs from sample A8-11_Naive_CD4

description: PBMCs from sample A8-11_Naive_CD4


title: Antrum_175


title: WT_HBSS_2004_RV


title: Antrum_173


title: PKP2_HBSS_2006_LV


title: WT_HBSS_2004_LV


title: PBMCs from sample A8-11_Memory_CD4

description: PBMCs from sample A8-11_Memory_CD4


title: Corpus_187


title: PBMCs from sample A8-10_Naive_CD8

description: PBMCs from sample A8-10_Naive_CD8


title: Antrum_172


title: Corpus_186


title: Corpus_188


title: Corpus_185


title: WT_HBSS_13_RV


title: PBMCs from sample A8-10_Naive_CD4

description: PBMCs from sample A8-10_Naive_CD4


title: Corpus_183