title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_017]

value: whole blood

value: Male


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_016rr]

status: Public on Jan 03 2024

type: RNA

city: Leuven

first: Deniz

last: Oner

address: Gaston Geenslaan

country: Belgium

institute: KU Leuven

description: Gene expression data of infants from RESCEU case-control cohort

hyb_protocol: After fragmentation, denaturation and end-labeling the targets are hybridized on the single GO Screen plate, according to manufacturer’s instructions (Thermo Fisher; GeneChip Pico Reagent Kit).

scan_protocol: Single sample cartridge arrays were stained on a GeneChip Fluidics Station 450 and scanned on a GeneChip scanner 3000 7G while array plates were stained and imaged on the GeneTitan Multi-Channel Instrument.

data_processing:
Microarray data were preprocessed using R, Bioconductor package 40,41. Robust Multi-Array Average (RMA) function was used to normalize the raw data 42. Outliers were removed from the downstream data analysis based on visual guidance on principal component (PC) spectral map and sample clustering (Pearson correlation with complete linkage).
The clinical data necessary for batch correction (site of sample collection) is accessible by request only from the submitting party.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

label_protocol: First strand cDNA was synthesized with a combination of a Poly-dT and random primers containing a 5′-adaptor sequence. A 3’-adaptor was added to the single stranded cDNA followed by low-cycle PCR amplification. The cDNA was used as a template for in vitro transcription (IVT) that produces amplified amounts of antisense mRNA, (cRNA). The cRNA was then used as input for a second round of cDNA synthesis, producing double stranded cDNA.

extract_protocol: The whole blood samples were collected in Paxgene tubes (PAXgene® Blood RNA Tube, BD) and stored at –80 °C until the processing. The RNA was extracted using QIAsymphony PAXgene Blood RNA Kit (QIAGEN) according to the manufacturer’s instructions. After the quality control, the RNA was further processed for Clariom™ GOScreen microarray (Thermo Fisher).

tag: tissue

tag: gender / sex

tag: age in days

tag: age group

tag: visit

value: RSV visit

tag: disease classification at rsv visit based on resvinet score

value: 3 - Moderate


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_447]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_183]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_191]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_186]


title: Prime editing of CXCR4 after activation of CXCR4 in WTC11 (Rep1)

type: SRA

city: Seattle

first: Xiaoyi

last: Li

state: WA

address: 3720 15th Ave NE

department: Department of Genome Sciences

country: USA

institute: University of Washington

description: Amplicon sequencing of engogenous genes

library_source: genomic

data_processing:
T7-assisted reporter mapping: Sequencing reads were first demultiplexed using the bcl2fastq software. Under the current library design and sequencing scheme, Read1 started from genomic sequence and extended into the integrated synHEK3 construct, while Read2 contained reporter barcode information. Therefore, 1) for each sequencing read pair, the 16-bp reporter barcode was extracted from Read 2 and attached to the read name of Read 1. 2) Read1 was trimmed using cutadapt (v4.1) with following parameters: --cores=4 --discard-untrimmed -e 0.2 -m 10 -O 8 -a CCCTAGAAAGATAGTCTGCGTAAAATTGACGCATG. The adapter corresponded to the 3’ITR of piggyBac transposon. Since parameter “--discard-untrimmed” was used, only reads spanning insertion junctions were kept and trimmed. 3) Trimmed sequences were aligned to the GRCh38 reference genome using bwa mem (v0.7.17). The “-Y” option was used to enable soft clipping for supplementary alignments. 4) Reads uniquely (without XA:Z tag) and contiguously mapped near putative piggyBac landing pads (TTAA motifs) were kept using samtools (v1.9) and a custom script. 5) Aligned reads were converted to BED format using the sam2bed function in bedops (v2.4.35). Reads aligned to standard chromosomes were kept. 6) Insertion points were calculated for all reads based on strand of alignment. And reads were sorted by the insertion coordinates. 7) The first 8-bp of reads were used as UMIs. A custom script was used to collapse reads at a per-location, per-barcode, per UMI basis. A barcode-location-UMI count table was generated. 8) synHEK3 barcodes <3 Levenshtein Distance at each location were collapsed and barcodes with > 3 UMIs were kept. 9) The count table was converted to a GenomicRanges object in R. Coordinates of the last 4 base pairs of aligned reads were designated as genomic locations of the inserted synHEK3 reporters. 10) “Landing pads” of the mapped synHEK3 reporters were retrieved using the getSeq() function in the BSgenome package. Reporters that didn’t have a TTAA sequence (which could be due to PCR error, mapping error, or the use of non-canonical landing pads) were removed. 11) SynHEK3 barcodes mapped to more than one location were removed.
SynHEK3 amplicon sequencing library: Sequencing reads from the Illumina NextSeq platforms were first demultiplexed using the bcl2fastq software. The 16-bp reporter barcodes were extracted from read and attached to its read name. Sequences around the CRISPR cut site were extracted for all reads. A barcode-editing outcome table was generated. For prime editing experiments, a custom script was used to align sequences to a reference sequence and count mutation frequency for every barcode. For Cas9 mutagenesis analysis, all sequences were aggregated and editing outcomes (alleles) with the highest number of counts were selected. These most frequent alleles were then aligned to reference sequences using needleall with the following parameters: -gapopen 20 -gapextend 0.5 -endopen 20. A custom script was used to annotate the mutational events.
Amplicon sequencing of endogenous genes: Sequencing reads were demultiplexed using the bcl2fastq software (Illumina). A custom script was used to determine frequencies of the introduced substitutions.
Assembly: GRCh38
Supplementary files format and content: CRISPRa_K562_new.csv contains editing efficiencies in the CRISPRa experiments in K562 cells
Supplementary files format and content: CRISPRa_WTC11_new.csv contains editing efficiencies in the CRISPRa experiments in WTC11 cells
Supplementary files format and content: PE2max_endogenous_121_K562.csv contains editing efficiencies of the 121 epegRNAs in K562 cells
Supplementary files format and content: PE_IL2RB_libraries.csv contains corrected editing efficiencies of epegRNA pools targeting IL2RB (with and without CRISPR activation of IL2RB)
Supplementary files format and content: T7-WT-Pool1.csv contains mapped locations, editing outcomes, and chromatin scores of synHEK3 reporters in wild-type K562 cells
Supplementary files format and content: T7-WT-Pool2.csv contains mapped locations, editing outcomes, and chromatin scores of synHEK3 reporters in wild-type K562 cells

molecule: genomic DNA

growth_protocol: K562 cells (CCL-243) were purchased from ATCC and maintained in RPMI 1640 medium (Gibco) supplied with 10% FBS (Hyclone) and penicillin/streptomycin (Gibco, 100 U/ mL). The DHFR-dCas9-VPH (VP48-P65-HSF1) WTC11 (human iPSCs) line was generated by the Martin Kampmann lab (Tian et al. 2021). Cells were maintained on Geltrex (Gibco) coated plates in the mTeSR Plus medium (STEMCELL Technologies) supplied with 10 uM Y-27632 (Stemgent). 20 uM trimethoprim was added to culture for stabilization of dCas9-VPH. All cells were kept in a humidified incubator at 37 oC, 5% CO2.

extract_protocol:
K562 and WTC11 cells were lysed in a lysis buffer [100 mM Tris-HCl pH8.0, 0.05% SDS and 0.04 mg/mL proteinase K(Thermo Scientific)], and incubated at 50 oC 60 min and 80 oC 30 min.
T7-assisted reporter mapping: gDNA of K562 cells was purified using the DNeasy Blood & Tissue Kit (QIAGEN) and in vitro transcribed with the HiScribe T7 High Yield RNA Synthesis Kit (New England Biolabs). Briefly, each reaction (20 uL) contained 0.3~1 ug gDNA, NTPs (10 mM each) and 2 ul T7 RNA Polymerase Mix. The reaction mixture was incubated at 37 oC for 16 hours. Then, gDNA was digested with 2.5 uL DNase (Qiagen) in a 100 uL reaction at room temperature for 30 min. RNA was extracted with TRIzol LS Reagent (Invitrogen), and aqueous phase was precipitated with 1 volume of isopropanol and 5 ug Glycogen (Invitrogen) at -80 oC for 1 hour. RNA pellet was collected by centrifugation at 21,000 x g at 4 oC for 1 hour. The pellet was washed with 80% ice-cold ethanol and resuspended in 11.5 uL nuclease-free water. For reverse transcription, RNA was incubated with 0.5 uL 100 uM RT primer p6 (5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGNNNNNNNN-3’) and 1 uL 10 mM dNTP at 65 oC for 5 min and cooled on ice. Then, 4 uL 5X RT buffer, 1 uL 100 mM DTT, 1 uL RNaseOUT (40 U/uL) and 1 uL SuperScript IV RT (200 U/uL, Invitrogen) were added and the reaction mixture was incubated at 23 oC for 10 min, 50  oC for 15 min and 80 oC for 10 min. cDNA library was amplified with KAPA2G Robust HotStart polymerase, using primers p7 (5’- GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGAAAGGAAGCCCTGCTTCCTCCAGAGGG-3’, 0.5 uM) and p8 (5’- TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3’, 0.5 uM). PCR reaction was performed as follows: 95 oC 3 min; 95 oC 15 s, 65 oC 15 s, 72 oC 30 s, 16~18 cycles; and 72 oC 1 min. The PCR product was subjected to double-sided size selection (0.5X, 0.9X) and cleaned up with AMPure XP beads. The resulting product ranged from 200 to 1000 bp. To prepare Illumina sequencing libraries, 5-10 ng PCR product was re-amplified with the Nextera P5 and TruSeq P7 library index primers for 5 cycles. The final PCR product underwent another round of double-sided size selection (0.5X, 0.9X) and cleaned up with AMPure XP beads. The library was sequenced on an Illumina MiSeq in paired-end mode (Read 1: 254 bp; Read2: 55bp). Amplicon sequencing of synHEK3 reporters: 100~250 ng gDNA or cell lysates were amplified using KAPA2G Robust HotStart ReadyMix with primers p9 (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCTACCCCGACCACATGAAGCAGC-3’, 0.5 uM) and p10 (5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNGACCATGTCATCGCGCTTCTCGT-3’, 0.5 uM). PCR reaction was performed as follows: 95 oC 3 min; 95 oC 15 s, 68-N oC 15 s, 72 oC 30 s, for 9 cycles (N was cycle number); 95 oC 15 s, 65 oC 15 s, 72 oC 30 s, for 11 cycles; and 72 oC 1 min. To ensure enough coverage and accurate measurement of editing efficiencies, for the K562 synHEK3 pool, we pooled products from at least 16 PCR reactions. The PCR product was purified with AMPure XP beads. 5 ng PCR product was re-amplified with the Nextera P5 and TruSeq P7 library index primers for 5 cycles.  Other amplicon sequencing: Cell lysates or plasmids were directly used for PCR with the KAPA2G Robust HotStart ReadyMix with primers (0.5 uM each) designed for the endogenous targets. PCR reaction was performed as follows: 95 oC 3 min; 95 oC 15 s, 66-N oC 15 s, 72 oC 40 s, for 8 cycles (N was cycle number); 95 oC 15 s, 60 oC 15 s, 72 oC 40 s, for 11 cycles; and 72 oC 1 min. The PCR product was purified with AMPure XP beads. 5 ng PCR product was re-amplified with the Nextera P5 and TruSeq P7 library index primers for 5 cycles.
Amplicon sequencing

treatment_protocol: Transfections of K562 cells were performed using a Lonza Bioscience 4D-Nucleofector system and the SF Cell Line 4D-Nucleofector X kits (Lonza). For single nucleocuvettes (100 uL), 1-2 x 106 cells were transfected with up to 4 ug DNA. For 96-well Nucleocuvette plates (20 uL), 2 x 105 ~ 5 x 105 cells were transfected with up to 2 ug DNA. Program code was FF-120. CRISPRa experiments (K562): On Day 0, 4 x 105 K562 dCas9-VP64 cells were transfected with PB-CMV-MCP-XTEN80-p65-Rta-3xNLS-P2A-T2A-mPlum (600 ng) and paired pU6-Sp-gRNA-2XMS2 (200 ng each) plasmids targeting the same promoter. On Day 2, 4 x 105 cells from the previous transfection were transfected with pCMV-PEmax (Addgene: 174820) or PB-UCOE-EF1a-PE2max-P2A-mCherry-PGK-Blast (800 ng) and the pU6-Sp-pegRNA plasmids (400 ng). All transfections were performed using the SF Cell Line 96-well Nucleofector Kit (Lonza) with program FF-120. Cells transfected with PB-UCOE-EF1a-PE2max-P2A-mCherry-PGK-Blast were selected with 2 ug/mL Puromycin 24 hours after transfection for 2 days. Cells were lysed at Day 5 or 6 for gDNA collection. CRISPRa experiments (WTC11): On Day 0, 2 x 105 the DHFR-dCas9-VPH WTC11 cells were transfected with PB-CMV-MCP-XTEN80-p65-Rta-3xNLS-P2A-T2A-mPlum (2100 ng) and paired pU6-Sp-gRNA-2XMS2 (700 ng each) plasmids targeting the same promoter. 20 uM Trimethoprim was added to induce dCas9-VPH. On Day 3, 2 x 105 cells from the previous transfection were transfected with PB-UCOE-EF1a-PE2max-P2A-mCherry-PGK-Blast (2000 ng) and the pU6-Sp-pegRNA plasmids (1000 ng). All transfections were performed using the P3 Prime Cell 96-well Nucleofector Kit (Lonza) with program CB-150. Cells were continued to be treated with 20 uM Trimethoprim and were selected with 2 ug/mL Puromycin 24 hours after transfection for 1 day. Cells were lysed at Day 5 or 6 for gDNA collection.

tag: cell line

tag: cell type

value: hiPSC

tag: genotype

value: NGN2; DHFR-dCas9-VPH

tag: treatment

value: WTC11 CRISPRa CXCR4


title: Prime editing of EGFR after activation of CREB3L3 in WTC11 (Rep2)

description: Amplicon sequencing of engogenous genes

value: WTC11 CRISPRa CREB3L3


title: Prime editing of EGFR after activation of EGFR in WTC11 (Rep2)

description: Amplicon sequencing of engogenous genes

value: WTC11 CRISPRa EGFR


title: Prime editing of WNT3A in wild-type K562 cells  (Rep2)

description: Amplicon sequencing of engogenous genes

value: lymphoblast

value: wild-type


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_517]

value: 2 - Mild


title: Prime editing of NR2F1 in wild-type K562 cells  (Rep1)

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB in wild-type K562 cells  (Rep2)

description: Amplicon sequencing of engogenous genes


title: Prime editing of NR2F1 in wild-type K562 cells  (Rep2)

description: Amplicon sequencing of engogenous genes


title: Prime editing of EGFR in wild-type K562 cells  (Rep2)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_441]


title: Prime editing of IL2RB in wild-type K562 cells  (Rep1)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_514]


title: Prime editing of CXCR4 in wild-type K562 cells  (Rep1)

description: Amplicon sequencing of engogenous genes


title: Prime editing of EGFR in wild-type K562 cells  (Rep1)

description: Amplicon sequencing of engogenous genes


title: Prime editing of CREB3L3 in wild-type K562 cells  (Rep2)

description: Amplicon sequencing of engogenous genes


title: Prime editing of CXCR4 in wild-type K562 cells  (Rep2)

description: Amplicon sequencing of engogenous genes


title: Prime editing of WNT3A after activation of IL2RB in K562 (Rep1)

description: Amplicon sequencing of engogenous genes

value: CRISPRa IL2RB


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_426]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_408]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_413]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_409]


title: Prime editing of CREB3L3 in wild-type K562 cells  (Rep1)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_405]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_407]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_412]


title: Prime editing of WNT3A after activation of WNT3A in K562 (Rep2)

description: Amplicon sequencing of engogenous genes

value: CRISPRa WNT3A


title: Prime editing of WNT3A after activation of IL2RB in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_262]


title: Prime editing of NR2F1 after activation of WNT3A in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_173rr]


title: Prime editing of WNT3A after activation of WNT3A in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: Prime editing of NR2F1 after activation of NR2F1 in K562 (Rep1)

description: Amplicon sequencing of engogenous genes

value: CRISPRa NR2F1


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_124]


title: Prime editing of NR2F1 after activation of NR2F1 in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_121]


title: Prime editing of NR2F1 after activation of WNT3A in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB after activation of IL2RB in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB after activation of IL2RB in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB after activation of EGFR in K562 (Rep1)

description: Amplicon sequencing of engogenous genes

value: CRISPRa EGFR


title: Prime editing of IL2RB after activation of EGFR in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: Prime editing of EGFR after activation of EGFR in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_122]


title: Prime editing of EGFR after activation of CREB3L3 in K562 (Rep2)

description: Amplicon sequencing of engogenous genes

value: CRISPRa CREB3L3


title: Prime editing of EGFR after activation of CREB3L3 in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: Prime editing of EGFR after activation of EGFR in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_102]

value: whole blood


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_350]

value: Male


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_094]

value: RSV visit


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_101]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_098]


title: Prime editing of CREB3L3 after activation of NR2F1 in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_039rr]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_092]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_069]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_097]


title: Prime editing of CREB3L3 after activation of CREB3L3 in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_172]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_060]


title: Prime editing of CREB3L3 after activation of NR2F1 in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_036rr]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_032rr]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_030]


title: HEK293T, RBFOX2, Input4

city: San Diego

first: Stephanie

last: Bruns

state: California

address: 5770 Oberlin Dr

institute: Eclipsebio

library_source: transcriptomic

data_processing:
Sequencing was performed as SE72 on the NextSeq 2000 platform.
UMIs were pruned from read sequences using umi_tools (v1.1.1) and 3' adapters were trimmed from reads using cutadapt (v3.2).
Reads were mapped to a custom database of repetitive elements and rRNA sequences. Non-repeat mapped reads were then mapped to the genome UCSC version GRCh38/hg38 using STAR (v2.7.7a).
PCR duplicates were removed using umi_tools (v1.1.1).
RBP-eCLIP peaks were identified within eCLIP samples using the peak caller CLIPper (v2.0.1).
For each peak, IP versus input fold enrichments and p-values were calculated using a Chi squared test or Fisher exact test if read counts were < 5.
Annotation of peaks was performed using transcript information from GENCODE release 41 (GRCh38.p13) with a defined priority hierarchy.
Assembly: hg38
Supplementary files format and content: bw (Normalized bigwig file), bed (Input normalized file of RBP-eCLIP clusters).

growth_protocol: 10 million cells

extract_protocol:
Lysis was carried out using 1 mL of eCLIP lysis mix including 5 uL of Protease Inhibitor Cocktail and 10 uL of Murine RNase Inhibitor. One round of sonication was performed for 4 minutes with 30 seconds ON/OFF at 75% amplitude were performed using a Q800R2 Sonicator.
Pre-validated antibodies were pre-coupled to Anti-Rabbit IgG Dynabeads and added to the lysate, followed by overnight incubation at 4°C. Immunoprecipitation was performed, and 2% of the sample was taken as the paired input sample. RNA adapter ligation, IP-western, reverse transcription, DNA adapter ligation, and PCR amplification were performed.
eCLIP

treatment_protocol: UV crosslinking was performed at 400 mJoules/cm2 with 254 nm radiation.

value: Human embryonic kidney

tag: target


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_015rr]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_135]


title: HEK293T, RBFOX2, Input3


title: HEK293T, RBFOX2, Input2


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_559]

value: RSV convalescence visit

value: 4 - Severe


title: HEK293T, RBFOX2, Input1


title: HEK293T, RBFOX2, IP4


title: Prime editing of CREB3L3 after activation of CREB3L3 in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: HEK293T, RBFOX2, IP1


title: HEK293T, RBFOX2, IP2


title: Biol Rep 719_2

city: London

first: Seda

last: Eminaga

address: Westminster Bridge Road, St Thomas's Hospital

department: Cardiovascular Division

country: United Kingdom

institute: King's College London

description:
719_BC5 (norm)
719_BC4_719_BC5_719_BC6_Processed_SEminaga.xlsx

data_processing:
Data was processed according to a detailed protocol published in Eminaga et al CPMB 2013. Briefly, BioPerl module for SAGE comparison (http://search.cpan.org/∼scottzed/Bio-SAGE-Comparison-1.00/) and custom analysis package was used.  After the  removal of 3' adapter and barcode sequences, the sequences with <17 nucleotides were eliminated and the remaining sequencing reads were matched to reference mature miRNA sequences downloaded from miRBase.  Next, the read counts were normalised to counts per million by dividing the total read counts of a single miRNA by the total read counts of the sample and multiplying by 10^6.
Assembly: https://www.mirbase.org/ftp/15/
Supplementary files format and content: .xlsx files contain normalised read counts per million

organism: Mus musculus

source_name: left ventricle-heart

extract_protocol:
Total RNA was isolated using miRVana miRNA isolation kit (Ambion, cat no AM1560) according to manufacturer's instructions.
The multiplexed miRNA libraries were prepared as described in detail in Eminaga et al, 2013 (Curr Protoc Mol Biol. 2013 Jul;Chapter 4:Unit 4.17) and Vigneault et al 2012 (Curr Protoc Hum Genet. 2012 Apr;Chapter 11:11.12.1-11.12.10).

treatment_protocol: Cyclosporin treatment

value: left ventricle-heart

value: mutant (aMHC719/+)

value: Cyclosporin for 3 weeks


title: Biol Rep 719_3

description:
719_BC6 (norm)
719_BC4_719_BC5_719_BC6_Processed_SEminaga.xlsx


title: HEK293T, RBFOX2, IP3


title: Biol Rep WT_3

description:
WT_BC3 (norm)
WT1_BC1_WT2_BC2_WT3_BC3_Processed_SEminaga.xlsx

value: WT


title: Biol Rep WT_2

description:
WT_BC2 (norm)
WT1_BC1_WT2_BC2_WT3_BC3_Processed_SEminaga.xlsx


title: Biol Rep WT_1

description:
WT_BC1 (norm)
WT1_BC1_WT2_BC2_WT3_BC3_Processed_SEminaga.xlsx


title: Biol Rep 719_1

description:
719_BC4 (norm)
719_BC4_719_BC5_719_BC6_Processed_SEminaga.xlsx


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_119]


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_541]


title: Wb23619194 Memory CD4+

city: Gainesville

first: Jeremy

middle: Robert Barker

last: Newman

state: FL

address: 2033 Mowry Road

department: Genetics Institute

institute: University of Florida

data_processing:
Quality of sequencing data was assessed using GC content, and the percentage of adapter content, duplication rate, and homopolymer content in each sample using FASTQC
Samples with low coverage (<1M reads) were removed from analysis
Principal components analysis was used to assess cellular identity. Samples that did not cluster with their corresponding cell type were excluded from further analysis
Duplicated sequence reads were removed using custom Python scripts. Distinct read pairs were aligned to transcript sequences with Bowtie (xx) and quantified using RSEM
Transcript counts expressed as TPM were upper-quartile normalized
Assembly: hg19
Supplementary files format and content: tab-delimited text files include transcript counts as TPM for each sample

source_name: Memory CD4+

extract_protocol:
Cell selections were performed using Miltenyi magnetic beads and RNA was isolated using Rnease mini plus kit (Qiagen)
RNA-seq libraries were prepared according to Illumina protocols and sequenced as 2 × 101 nt reads

value: Memory CD4+

tag: Sex

value: M

tag: disease status

value: CTL

tag: age

tag: ethnicity

value: Caucasian

tag: subject id


title: Wb842518068 CD19+/CD27- B cells

source_name: CD19+/CD27- B cells

value: CD19+/CD27- B cells


title: Wb37099476 Memory CD4+

value: F


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_080]


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_246]


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_319]


title: Wb05255539 Memory CD4+


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_048rr]


title: Wb255607012 CD19+/CD27- B cells Rep 2


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_571]


title: Wb88536080 Memory CD4+/CD25- T cells

source_name: Memory CD4+/CD25- T cells

value: Memory CD4+/CD25- T cells


title: Wb16654397 CD19+/CD27- B cells


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_070]

value: whole blood


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_561rr]

value: Male


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_045]


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_043]


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_182]


title: Wb255607012 Memory CD4+/CD25- T cells Rep 2


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_217]


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_564]

value: 3 - Moderate


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_560]


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_570]


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_317]


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_082]


title: Wb113332655 CD19+/CD27- B cells


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_556]


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_494]


title: Wb489023434 Memory CD4+


title: Wb500063258 Memory CD4+


title: Wb92179688 Memory CD4+/CD25- T cells Rep 2


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_331]


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_083]


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_524]


title: Wb255279458 CD19+/CD27- B cells


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_079]


title: Wb285470206 CD19+/CD27- B cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_509]


title: Wb79484064 Memory CD4+


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_565]


title: Wb95508280 Memory CD4+


title: Wb35307192 Memory CD4+


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_379]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_493]


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_050]

value: 2 - Mild


title: Wb50316324 Memory CD4+


title: Wb57185180 Memory CD4+


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_551]

value: RSV convalescence visit


title: Wb11699868 CD19+/CD27- B cells


title: Wb86185064 Memory CD4+


title: Wb757056691 Memory CD4+/CD25- T cells Rep 2


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4397_1086]


title: Wb77694072 Memory CD4+


title: Wb598690385 CD19+/CD27- B cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_557]


title: Wb977212218 CD19+/CD27- B cells Rep 2


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_297]

value: 4 - Severe


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_513]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_553]


title: Wb72636504 Memory CD4+


title: Wb32229610 CD19+/CD27- B cells


title: Wb70658984 CD19+/CD27- B cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_547]


title: Wb88536080 Memory CD4+/CD25+ regulatory T cells

source_name: Memory CD4+/CD25+ regulatory T cells

value: Memory CD4+/CD25+ regulatory T cells


title: Wb63928904 Memory CD4+


title: Wb89130144 Memory CD4+


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_512]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_503]


title: Wb11699868 Memory CD4+/CD25+ regulatory T cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_506]


title: Wb27902628 Memory CD4+


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_478]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_488]


title: Wb45750752 Memory CD4+


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_289]


title: Wb90726008 Memory CD4+/CD25- T cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_323]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_347]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_268]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_495]


title: Wb64368444 Memory CD4+


title: Wb37099476 CD19+/CD27- B cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_269]


title: Wb29941410 CD19+/CD27- B cells


title: Wb17615230 Memory CD4+


title: Wb489023434 Memory CD4+/CD25+ regulatory T cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_256]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_280]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_242]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_232]


title: Wb78636088 Memory CD4+


title: Wb209525269 Memory CD4+/CD25+ regulatory T cells Rep 2


title: Wb64359992 CD19+/CD27- B cells Rep 1


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_052]


title: Wb11083395 Memory CD4+


title: Wb22121198 Memory CD4+


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_230]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_021rr]


title: Wb29894358 Memory CD4+


title: Wb70009472 Memory CD4+/CD25+ regulatory T cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_219]


title: Wb598690385 Memory CD4+


title: Wb67530352 Memory CD4+


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_020]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_177]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4397_1110]


title: Wb86451000 CD19+/CD27- B cells Rep 2


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4397_1093]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_498]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_303]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_341]


title: Wb24509086 Memory CD4+/CD25+ regulatory T cells


title: Wb31241246 Memory CD4+


title: Wb53681832 CD19+/CD27- B cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_391]


title: Wb34096724 Memory CD4+


title: Wb654869981 Memory CD4+/CD25+ regulatory T cells


title: Wb285470206 Memory CD4+


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_373]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_273]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_081]


title: Wb854132275 Memory CD4+/CD25+ regulatory T cells


title: Wb113332655 Memory CD4+


title: Wb61784836 Memory CD4+


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_042]


title: Wb32193536 Memory CD4+


title: Wb78636088 Memory CD4+/CD25- T cells Rep 2


title: Wb62579204 Memory CD4+/CD25- T cells Rep 2


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_026]


title: Wb83970808 Memory CD4+/CD25- T cells Rep 2


title: Wb53681832 Memory CD4+/CD25+ regulatory T cells


title: Wb41409024 Memory CD4+/CD25+ regulatory T cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_267]


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_543]


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_549]


title: Wb977212218 Memory CD4+


title: Wb476013251 Memory CD4+

value: yes


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_534]


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_536rr]


title: Wb28992844 Memory CD4+


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_531]


title: Wb18977208 Memory CD4+


title: Wb98626208 Memory CD4+


title: Wb29941410 Memory CD4+


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_533]


title: Wb89130144 Memory CD4+/CD25- T cells


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_527]


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_463]


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_479]


title: Wb88927480 Memory CD4+/CD25- T cells


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_555]


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_530]


title: Wb63150180 Memory CD4+/CD25+ regulatory T cells


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_500]


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_263]


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_142]


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_351]


title: Wb499255267 Memory CD4+


title: Wb84593528 Memory CD4+/CD25- T cells Rep 1


title: Wb65680024 Memory CD4+


title: Wb285470206 Memory CD4+/CD25+ regulatory T cells Rep 1


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_138]


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_077]


title: Wb62765928 Memory CD4+


title: Wb87313152 Memory CD4+/CD25+ regulatory T cells Rep 2


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_127]


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_075]


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_139]


title: Wb16970712 Memory CD4+


title: RSV visit, Comorbidity [A4398_187]

value: RSV visit


title: Wb84593528 CD19+/CD27- B cells


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_128]


title: Wb957775938 CD19+/CD27- B cells


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_049]


title: Wb76022648 Memory CD4+


title: Wb04251087 Memory CD4+/CD25- T cells Rep 2


title: Wb63928904 Memory CD4+/CD25+ regulatory T cells


title: Wb79550624 Memory CD4+/CD25+ regulatory T cells


title: RSV visit, Comorbidity [A4398_086]


title: RSV visit, Comorbidity [A4398_519]


title: RSV visit, Comorbidity [A4398_511]

value: Female


title: Wb75147632 Memory CD4+

value: Memory CD4+


title: Wb290146432 Memory CD4+

value: M


title: Wb814177218 Memory CD4+

value: CTL


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_505]


title: RSV visit, Comorbidity [A4398_442]


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_051]


title: Wb81333944 Memory CD4+


title: Wb12286449 Memory CD4+/CD25+ regulatory T cells

value: Caucasian


title: Wb218547683 CD19+/CD27- B cells

value: CD19+/CD27- B cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_305]


title: RSV visit, Comorbidity [A4398_369]


title: Wb76432632 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_356]


title: RSV visit, Comorbidity [A4398_360]


title: Wb476013251 CD19+/CD27- B cells

value: F


title: RSV visit, Comorbidity [A4398_449]


title: RSV visit, Comorbidity [A4398_368]


title: Wb62579204 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_282]


title: Wb702524065 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_277]


title: RSV visit, Comorbidity [A4398_258]


title: Wb654869981 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_170]


title: Wb82865160 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_169]


title: Wb368934288 CD19+/CD27- B cells


title: Wb86451000 CD19+/CD27- B cells Rep 1


title: RSV visit, Comorbidity [A4398_294]


title: Wb33161134 CD19+/CD27- B cells


title: Wb500063258 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_300]


title: RSV visit, Comorbidity [A4398_372]


title: Wb489023434 CD19+/CD27- B cells Rep 2


title: Wb22378588 CD19+/CD27- B cells Rep 2


title: Wb977212218 CD19+/CD27- B cells Rep 3


title: Wb21239448 CD19+/CD27- B cells


title: Wb89130144 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_464]


title: Wb338817210 CD19+/CD27- B cells Rep 2


title: RSV visit, Comorbidity [A4398_162rr]


title: Wb609359337 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_147rr]


title: Wb45311624 CD19+/CD27- B cells Rep 2


title: Wb77109992 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_392]


title: RSV visit, Comorbidity [A4398_433]


title: RSV visit, Comorbidity [A4398_367]


title: RSV visit, Comorbidity [A4398_363]


title: RSV visit, Comorbidity [A4398_334]


title: RSV visit, Comorbidity [A4398_352]


title: Wb35307192 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_332]


title: RSV visit, Comorbidity [A4398_306]


title: RSV visit, Comorbidity [A4398_146rr]


title: RSV visit, Comorbidity [A4398_290]


title: RSV visit, Comorbidity [A4398_292]


title: Wb90726008 CD19+/CD27- B cells


title: Wb434959941 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_286]


title: RSV visit, Comorbidity [A4398_338]


title: Wb37260428 CD19+/CD27- B cells Rep 2


title: Wb290146432 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_270]


title: RSV visit, Comorbidity [A4398_249rr]


title: RSV visit, Comorbidity [A4398_239]


title: Wb65680024 CD19+/CD27- B cells


title: Wb88927480 CD19+/CD27- B cells


title: Wb28992844 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_225]


title: Wb209525269 CD19+/CD27- B cells


title: Wb814177218 CD19+/CD27- B cells


title: Wb27902628 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_223]


title: RSV visit, Comorbidity [A4398_221]


title: RSV visit, Comorbidity [A4398_212rr]


title: Wb48429960 Memory CD4+/CD25- T cells

value: Memory CD4+/CD25- T cells


title: Wb499255267 CD19+/CD27- B cells


title: Wb29894358 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_200]

value: whole blood


title: Wb489023434 CD19+/CD27- B cells Rep 1


title: Wb87886168 CD19+/CD27- B cells


title: Wb57113768 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_175]


title: RSV visit, Comorbidity [A4398_161]


title: RSV visit, Comorbidity [A4397_1101]

value: Male


title: Wb40585324 CD19+/CD27- B cells


title: Wb04385156 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_480]


title: RSV visit, Comorbidity [A4398_152]

value: 3 - Moderate


title: Wb77571832 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_472]

value: 2 - Mild


title: Wb45311624 CD19+/CD27- B cells Rep 1


title: Wb17615230 CD19+/CD27- B cells Rep 2


title: RSV visit, Comorbidity [A4398_468]


title: Wb37683356 CD19+/CD27- B cells


title: Wb92302600 CD19+/CD27- B cells Rep 2


title: Wb32193536 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_377]


title: Wb04700691 CD19+/CD27- B cells


title: RSV visit, Comorbidity [A4398_328]


title: RSV visit, Comorbidity [A4398_298]


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_047]

value: RSV convalescence visit


title: Wb01641203 CD19+/CD27- B cells


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_025]


title: Wb42742188 CD19+/CD27- B cells


title: Wb218547683 Memory CD4+/CD25+ regulatory T cells Rep 1


title: Wb41724028 CD19+/CD27- B cells


title: Wb69075576 CD19+/CD27- B cells


title: RSV convalescence visit, RSV-infected non-hospitalised (mild disease) [A4398_044]


title: Wb43155540 CD19+/CD27- B cells


title: Wb04251087 CD19+/CD27- B cells


title: Healthy [A4398_563]

value: Healthy

value: 1 - Healthy controls


title: Healthy [A4398_522]


title: Healthy [A4398_523]


title: Healthy [A4398_567]


title: Wb64359992 CD19+/CD27- B cells Rep 2


title: RSV visit, Comorbidity [A4398_192]


title: RSV visit, Comorbidity [A4397_1095]


title: Healthy [A4398_521rr]


title: Healthy [A4398_443]


title: Wb17615230 CD19+/CD27- B cells Rep 1


title: Wb61784836 CD19+/CD27- B cells


title: Wb92302600 CD19+/CD27- B cells Rep 1


title: Healthy [A4398_440]


title: Wb02326960 CD19+/CD27- B cells


title: Healthy [A4398_568]


title: Healthy [A4398_435]


title: Wb31241246 CD19+/CD27- B cells Rep 2


title: Healthy [A4398_432]


title: Wb727301937 Memory CD4+/CD25+ regulatory T cells Rep 2

value: Memory CD4+/CD25+ regulatory T cells


title: Wb23619194 CD19+/CD27- B cells Rep 2


title: Wb24886716 CD19+/CD27- B cells


title: Healthy [A4398_428]


title: Healthy [A4398_425]


title: Wb26395716 CD19+/CD27- B cells


title: Healthy [A4398_422]


title: Wb34096724 CD19+/CD27- B cells


title: Wb60525860 CD19+/CD27- B cells


title: Wb07419492 CD19+/CD27- B cells


title: Healthy [A4398_419]


title: Healthy [A4398_421]


title: Healthy [A4398_389]


title: Wb207731668 CD19+/CD27- B cells


title: Healthy [A4398_436]


title: Wb91359464 CD19+/CD27- B cells


title: Wb31241246 CD19+/CD27- B cells Rep 1


title: Healthy [A4398_385]


title: Wb489661859 CD19+/CD27- B cells


title: Healthy [A4398_387]


title: Healthy [A4398_386]


title: Healthy [A4398_384]


title: Wb62765928 Memory CD4+/CD25+ regulatory T cells


title: Healthy [A4398_364]


title: Wb01018268 CD19+/CD27- B cells


title: Healthy [A4398_388]


title: Wb81900784 CD19+/CD27- B cells


title: Wb75147632 CD19+/CD27- B cells


title: Wb26871270 CD19+/CD27- B cells


title: Wb76104792 CD19+/CD27- B cells


title: Wb81816136 CD19+/CD27- B cells


title: Healthy [A4398_359]


title: Healthy [A4398_115]


title: Wb12290282 CD19+/CD27- B cells


title: Wb17573972 CD19+/CD27- B cells


title: Healthy [A4398_114]


title: Healthy [A4398_112]


title: Healthy [A4398_111]


title: Healthy [A4398_358]


title: Healthy [A4398_110]


title: Wb92702632 CD19+/CD27- B cells


title: Healthy [A4398_113]


title: Wb76022648 CD19+/CD27- B cells


title: Wb22121198 CD19+/CD27- B cells


title: Wb338817210 Memory CD4+/CD25+ regulatory T cells


title: Wb50316324 CD19+/CD27- B cells


title: Healthy [A4398_109]


title: Healthy [A4398_108]


title: Healthy [A4398_105]


title: Healthy [A4398_107]


title: Healthy [A4398_148]


title: Wb255607012 CD19+/CD27- B cells Rep 1


title: Wb977212218 CD19+/CD27- B cells Rep 1


title: Wb99706552 CD19+/CD27- B cells


title: Healthy [A4398_088]


title: Wb37260428 CD19+/CD27- B cells Rep 1


title: Wb73605872 CD19+/CD27- B cells


title: Healthy [A4398_103]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_380]

value: RSV visit

value: 4 - Severe


title: Wb43138648 CD19+/CD27- B cells


title: Wb63150180 CD19+/CD27- B cells


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_395]

value: Female


title: Wb67530352 CD19+/CD27- B cells


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_370]


title: Wb78111848 CD19+/CD27- B cells


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_378]


title: Wb05255539 CD19+/CD27- B cells

value: M


title: Wb69075576 Memory CD4+/CD25+ regulatory T cells


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_320]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_057]


title: Wb76979416 Memory CD4+/CD25+ regulatory T cells

value: CTL


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_061]


title: Wb04251087 Memory CD4+/CD25+ regulatory T cells

value: Caucasian


title: Wb97955272 Memory CD4+/CD25- T cells


title: Wb53681832 Memory CD4+/CD25- T cells


title: Wb10788525 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_361]


title: Wb64359992 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_326]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_375]


title: Wb05255539 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_546]


title: Wb96401360 Memory CD4+/CD25+ regulatory T cells


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_195]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_310]


title: Wb17451436 Memory CD4+/CD25+ regulatory T cells


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_065]


title: Wb48429960 Memory CD4+/CD25+ regulatory T cells Rep 2


title: Wb70009472 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_466]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_041rr]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4397_1075]


title: Wb37099476 Memory CD4+/CD25+ regulatory T cells


title: Wb16359426 Memory CD4+/CD25+ regulatory T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_417]


title: SAMPLE 25 control murine(C57BL6)

type: protein

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

description: SAMPLE 25

hyb_protocol: SomaLogic

scan_protocol: SomaLogic

data_processing: data were received in the form of Relative Fluorescent Units (RFU) for each of the 1,310 proteins in the SomaScan assay after normalizing for intraplate and interplate variation using the supplied SomaLogic software. These RFU scores for each protein were log2 and z-score transformed. Mean control expression values were compared to each individual radiation treated sample for the murine and clinical samples. Matched sample pre- and postirradiation were used for the NHP and minipig animals. The ratios of respective upregulation or downregulation of each protein was filtered using a (p < 0.05) and 1.3-fold change threshold.

molecule: protein

source_name: Plasma

label_protocol: SomaScan assay protocol

extract_protocol: Plasma samples were collected at 24 h postirradiation using venipuncture collection.

treatment_protocol: 2 male and 1 female Rhesus monkeys (Macaca mulatta) between 5–8 years of age received a single dose of TBI between 3.85 and 4.22 Gy.

tag: dose

tag: time point

value: control

tag: strain


title: Wb44884700 Memory CD4+/CD25+ regulatory T cells


title: SAMPLE 26 control murine(C57BL6)

description: SAMPLE 26


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_399]

tag: tissue

tag: gender / sex

tag: age in days


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_096]

tag: age group

tag: visit

tag: disease classification at rsv visit based on resvinet score


title: Wb92702632 Memory CD4+/CD25- T cells

tag: cell type

value: F


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_002]


title: SAMPLE 24 control murine(C57BL6)

description: SAMPLE 24


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_118]


title: SAMPLE 23 Day1 postIR murine(C57BL6)

description: SAMPLE 23

value: Day1 postIR


title: Wb96988600 Memory CD4+/CD25- T cells

value: Memory CD4+/CD25- T cells


title: Wb25634188 Memory CD4+/CD25- T cells


title: SAMPLE 22 Day1 postIR murine(C57BL6)

description: SAMPLE 22


title: Wb63150180 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_241]

value: whole blood


title: Wb285470206 Memory CD4+/CD25+ regulatory T cells Rep 2


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_056]


title: Wb30502154 Memory CD4+/CD25+ regulatory T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_470]

value: 3 - Moderate


title: Wb72894504 Memory CD4+/CD25+ regulatory T cells


title: SAMPLE 21 control murine(C57BL6)

description: SAMPLE 21


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_457]


title: Wb16654397 Memory CD4+/CD25+ regulatory T cells


title: Wb79550624 Memory CD4+/CD25- T cells


title: SAMPLE 20 control murine(C57BL6)

description: SAMPLE 20


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_439]


title: SAMPLE 19 Day1 postIR minipig(Sinclair)

description: SAMPLE 19

organism: Sus scrofa

value: minipig(Sinclair)


title: Wb78636088 Memory CD4+/CD25- T cells Rep 1


title: SAMPLE 18 Day1 postIR minipig(Sinclair)

description: SAMPLE 18


title: Wb37099476 Memory CD4+/CD25- T cells Rep 2


title: Wb24886716 Memory CD4+/CD25- T cells


title: Wb56485724 Memory CD4+/CD25- T cells


title: Wb73605872 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_434]


title: SAMPLE 17 control minipig(Sinclair)

description: SAMPLE 17


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_362]


title: SAMPLE 16 control minipig(Sinclair)

description: SAMPLE 16


title: Wb80342064 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_342]


title: SAMPLE 15 6hr postIR human

description: SAMPLE 15

value: 6hr postIR


title: Wb09648849 Memory CD4+/CD25+ regulatory T cells


title: Wb87313152 Memory CD4+/CD25+ regulatory T cells Rep 1


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_344]


title: Wb02326960 Memory CD4+/CD25+ regulatory T cells


title: SAMPLE 14 control human

description: SAMPLE 14


title: Wb84189160 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_312]


title: Wb87886168 Memory CD4+/CD25+ regulatory T cells


title: SAMPLE 13 6hr postIR human

description: SAMPLE 13


title: Wb01641203 Memory CD4+/CD25+ regulatory T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_324]


title: Wb60525860 Memory CD4+/CD25+ regulatory T cells


title: Wb17451436 Memory CD4+/CD25- T cells


title: SAMPLE 12 6hr postIR human

description: SAMPLE 12


title: Wb69075576 Memory CD4+/CD25- T cells


title: Wb11661954 Memory CD4+/CD25- T cells


title: SAMPLE 11 6hr postIR human

description: SAMPLE 11


title: Wb51558008 Memory CD4+/CD25+ regulatory T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_275]


title: SAMPLE 10 control human

description: SAMPLE 10


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_274]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_250rr]


title: SAMPLE 9 control human

description: SAMPLE 9


title: Wb75147632 Memory CD4+/CD25+ regulatory T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_308]


title: Wb51768836 Memory CD4+/CD25+ regulatory T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_245]


title: Wb12286449 Memory CD4+/CD25- T cells


title: Wb78111848 Memory CD4+/CD25- T cells


title: Wb93515984 Memory CD4+/CD25+ regulatory T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_247]


title: SAMPLE 7 control NHP

description: SAMPLE 7

organism: Macaca mulatta


title: Wb92179688 Memory CD4+/CD25+ regulatory T cells


title: Wb39397564 Memory CD4+/CD25+ regulatory T cells


title: SAMPLE 6 Day1postIR NHP

description: SAMPLE 6


title: Wb72636504 Memory CD4+/CD25- T cells Rep 2


title: Wb51558008 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_226]


title: Wb41581460 Memory CD4+/CD25+ regulatory T cells


title: Wb76022648 Memory CD4+/CD25- T cells


title: SAMPLE 5 control NHP

description: SAMPLE 5


title: Wb26395716 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_205]


title: Wb81333944 Memory CD4+/CD25- T cells

value: yes


title: Wb97288112 Memory CD4+/CD25- T cells


title: SAMPLE 8 Day1postIR NHP

description: SAMPLE 8


title: SAMPLE 4 Day1postIR NHP

description: SAMPLE 4


title: Wb727301937 Memory CD4+/CD25+ regulatory T cells Rep 1


title: SAMPLE 3 control NHP

description: SAMPLE 3


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_198]


title: Wb74450320 Memory CD4+/CD25+ regulatory T cells


title: SAMPLE 2 Day1postIR NHP

description: SAMPLE 2


title: Wb99706552 Memory CD4+/CD25- T cells


title: Wb10109318 Memory CD4+/CD25+ regulatory T cells


title: Wb57963872 Memory CD4+/CD25+ regulatory T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_193]


title: Wb92302600 Memory CD4+/CD25+ regulatory T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_210]


title: Wb87313152 Memory CD4+/CD25- T cells


title: Wb04017544 Memory CD4+/CD25- T cells


title: SAMPLE 1 control NHP

description: SAMPLE 1


title: CDC-endo-48h-rep3

city: Bundoora

first: Mathew

middle: G

last: Lewsey

state: VIC

address: AgriBio, 5 Ring Rd

department: Animal, Plant and Soil Sciences

country: Australia

institute: La Trobe University

description: raw count and normalized data were provided as processed data file

data_processing:
Sequence data quality were assessed using FastQC and Trim Galore were used to trim adaptor sequence and low-quality data.
The trimmed reads were align to SortMeRNA rRNA database using bowtie2 and unaligned reads were extracted and quantified using Salmon with the OT3098 Version 2 reference transcripts database.
Quantified reads counts were used for differential gene expression analysis using Deseq2.
Assembly: OT3098 Version2
Supplementary files format and content: tab-delimited text files include normalized values using variance stabilizing transformation (VST) for each Sample

organism: Avena sativa

source_name: endosperm

growth_protocol: Avena sativa cv. Morgan (AC) and Morrison (CDC) grains were germinated for 3, 6, 24 and 48 h in controlled growth chambers under long day conditions (23˚C 14h day/19˚C 10h night) on 3 layers of sterilised Whatman paper damp with sterile water.

extract_protocol:
The RNA was extracted using Spectrum™ Plant Total RNA Kit from Sigma-Aldrich (ref. STRN250-1KT) with some additional optimisation steps. Samples were pre-treated with 0.03% (v/v) α-amylase (Sigma-Aldrich, ref. A4551-100MG) in the lysis buffer. Ground frozen samples were vortexed for 1 min with the mixture and incubated at RT for 6 min. 0.01 % (v/v) β-mercaptoethanol was added to the samples and vortexed again for 30 sec. Samples were centrifuged at RT for 5 min at max r.p.m. Supernatant was transferred to the filtering columns and Spectrum™ Plant Total RNA protocol was used following manufacturer’s instructions including the on-column DNase treatment. Protocol A was used for the binding buffer solution. Samples were further cleaned up using RNA Clean & Concentrator-5 kit (Zymo Research, ref. R1016) to ensure purity and concentration.
Libraries were generated using TruSeq® Stranded mRNA Library Prep Kit (Illumina) according to manufacturer’s instructions and sequenced on a Nextseq 500 platform (Illumina) as single-end reads.

value: endosperm

value: germinating grain

tag: genotype

value: CDC Morrison

tag: time

value: Hour 48


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_165rr]

value: Female

value: RSV visit


title: Wb75147632 Memory CD4+/CD25- T cells

tag: Sex

value: M


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_158]


title: Wb01641203 Memory CD4+/CD25- T cells

tag: disease status

value: Caucasian


title: CDC-endo-48h-rep1


title: Wb16020031 Memory CD4+/CD25- T cells

tag: age


title: Wb24886716 Memory CD4+/CD25+ regulatory T cells

value: Memory CD4+/CD25+ regulatory T cells

value: CTL

tag: ethnicity


title: Wb46780368 Memory CD4+/CD25+ regulatory T cells

value: F

tag: subject id


title: CDC-endo-24h-rep3

value: Hour 24


title: Wb12528403 Memory CD4+/CD25- T cells

value: Memory CD4+/CD25- T cells


title: Wb72894504 Memory CD4+/CD25- T cells


title: CDC-endo-24h-rep2


title: Wb57185180 Memory CD4+/CD25- T cells


title: Wb44849832 Memory CD4+/CD25+ regulatory T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_145rr]

value: whole blood

value: 3 - Moderate


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_089]


title: Wb16654397 Memory CD4+/CD25- T cells


title: CDC-endo-24h-rep1


title: CDC-endo-48h-rep2


title: Wb22121198 Memory CD4+/CD25- T cells


title: CDC-endo-06h-rep3

value: Hour 6


title: Wb18894388 Memory CD4+/CD25+ regulatory T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_150]


title: Wb81816136 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_009]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_456]

value: 2 - Mild


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_010]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_134]


title: Wb12290282 Memory CD4+/CD25- T cells


title: Wb70658984 Memory CD4+/CD25- T cells


title: CDC-endo-06h-rep2

value: endosperm


title: Wb41409024 Memory CD4+/CD25- T cells Rep 1


title: CDC-endo-06h-rep1

value: germinating grain


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_430]


title: CDC-endo-03h-rep3

value: CDC Morrison

value: Hour 3


title: Wb80342064 Memory CD4+/CD25+ regulatory T cells


title: Wb56485724 Memory CD4+/CD25+ regulatory T cells


title: Wb34096724 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_336]

value: Female


title: Wb32639702 Memory CD4+/CD25+ regulatory T cells

value: yes


title: CDC-endo-03h-rep2


title: Wb23429854 Memory CD4+/CD25+ regulatory T cells

value: M


title: CDC-endo-03h-rep1


title: Wb01694149 Memory CD4+/CD25- T cells

value: Caucasian


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_014]

value: RSV visit


title: Wb48429960 Memory CD4+/CD25+ regulatory T cells Rep 1

value: Memory CD4+/CD25+ regulatory T cells

value: CTL


title: Wb50316324 Memory CD4+/CD25- T cells

value: F


title: Wb63145304 Memory CD4+/CD25- T cells

value: Memory CD4+/CD25- T cells


title: Wb74450320 Memory CD4+/CD25- T cells


title: Wb47020128 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_452]

value: whole blood


title: CDC-endo-00h-rep2

value: Hour 0


title: Wb31588806 Memory CD4+/CD25+ regulatory T cells


title: CDC-endo-00h-rep1


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_376]


title: Wb30502154 Memory CD4+/CD25- T cells


title: CDC-embryo-48h-rep3

source_name: embryo

value: embryo

value: Hour 48


title: Wb16020031 Memory CD4+/CD25+ regulatory T cells


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_486rr]

value: 2 - Mild


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_189]


title: Wb43138648 Memory CD4+/CD25- T cells


title: Wb66496456 Memory CD4+/CD25+ regulatory T cells


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_453]


title: Wb77109992 Memory CD4+/CD25- T cells


title: Wb37099476 Memory CD4+/CD25- T cells Rep 1


title: CDC-endo-00h-rep3

value: endosperm

value: germinating grain


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_451]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_454]


title: Wb11083395 Memory CD4+/CD25- T cells Rep 2


title: CDC-embryo-48h-rep1

value: CDC Morrison


title: Wb272686500 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_424]

value: Female


title: Wb76104792 Memory CD4+/CD25- T cells


title: CDC-embryo-24h-rep3

value: Hour 24


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_204]

value: 3 - Moderate


title: Wb82865160 Memory CD4+/CD25- T cells

value: M

value: Caucasian


title: Wb727301937 Memory CD4+/CD25- T cells


title: CDC-embryo-24h-rep2


title: Wb84593528 Memory CD4+/CD25- T cells Rep 2


title: CDC-embryo-24h-rep1


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_411]

value: RSV visit


title: Wb499255267 Memory CD4+/CD25- T cells

value: CTL


title: Wb32639702 Memory CD4+/CD25- T cells

value: yes


title: CDC-embryo-48h-rep2


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_410]


title: Wb23429854 Memory CD4+/CD25- T cells

value: Memory CD4+/CD25- T cells


title: CDC-embryo-06h-rep3

value: Hour 6


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_406]

value: whole blood


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_403]


title: Wb45311624 Memory CD4+/CD25- T cells

value: F


title: Wb17615230 Memory CD4+/CD25- T cells


title: Wb07419492 Memory CD4+/CD25- T cells


title: CDC-embryo-06h-rep2

value: embryo


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_383]

value: 2 - Mild


title: CDC-embryo-06h-rep1


title: Wb42742188 Memory CD4+/CD25- T cells


title: Wb86451000 Memory CD4+/CD25- T cells


title: CDC-embryo-03h-rep3

value: Hour 3


title: Wb28992844 Memory CD4+/CD25- T cells


title: Wb854132275 Memory CD4+/CD25- T cells


title: Wb18894388 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_366]


title: Wb113332655 Memory CD4+/CD25- T cells


title: CDC-embryo-03h-rep1

value: germinating grain


title: Wb43594080 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_354]


title: Wb70067512 Memory CD4+/CD25- T cells


title: CDC-embryo-03h-rep2

value: CDC Morrison


title: CDC-embryo-00h-rep3

value: Hour 0


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_314]

value: Female


title: Wb25755668 Memory CD4+/CD25- T cells


title: Wb32193536 Memory CD4+/CD25- T cells Rep 2


title: CDC-embryo-00h-rep2


title: Wb476013251 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_253]


title: Wb98838184 Memory CD4+/CD25- T cells


title: Wb57113768 Memory CD4+/CD25- T cells


title: CDC-embryo-00h-rep1


title: Wb41724028 Memory CD4+/CD25- T cells


title: AC-48h-endo-rep3

value: endosperm

value: AC Morgan

value: Hour 48


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_206]

value: RSV visit


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_197rr]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_125]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_126]


title: Wb04251087 Memory CD4+/CD25- T cells Rep 1

value: M

value: Caucasian


title: AC-48h-endo-rep2


title: Wb489023434 Memory CD4+/CD25- T cells

value: Memory CD4+/CD25- T cells

value: CTL


title: Wb209525269 Memory CD4+/CD25- T cells


title: Wb41409024 Memory CD4+/CD25- T cells Rep 2


title: AC-48h-embryo-rep3


title: AC-48h-endo-rep1


title: Wb702524065 Memory CD4+/CD25- T cells


title: Wb11699868 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_120]

value: whole blood


title: Wb32193536 Memory CD4+/CD25- T cells Rep 1

value: F


title: AC-48h-embryo-rep1

value: embryo


title: AC-48h-embryo-rep2


title: Wb814177218 Memory CD4+/CD25- T cells


title: Wb16970712 Memory CD4+/CD25- T cells


title: Wb64368444 Memory CD4+/CD25- T cells


title: Wb260892376 Memory CD4+/CD25- T cells


title: Wb218547683 Memory CD4+/CD25- T cells Rep 2


title: Wb842518068 Memory CD4+/CD25- T cells


title: AC-24h-endo-rep3

value: Hour 24


title: Wb207731668 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_091]

value: 2 - Mild


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_068]


title: Wb63435788 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_099]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_067]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_066]


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_059]


title: AC-24h-endo-rep2

value: germinating grain


title: Wb62579204 Memory CD4+/CD25- T cells Rep 1


title: Wb583527806 Memory CD4+/CD25- T cells


title: Wb87886168 Memory CD4+/CD25- T cells


title: Wb16359426 Memory CD4+/CD25- T cells


title: AC-24h-embryo-rep3


title: Wb72636504 Memory CD4+/CD25- T cells Rep 1


title: Wb977212218 Memory CD4+/CD25- T cells


title: Wb31384296 Memory CD4+/CD25- T cells


title: AC-24h-embryo-rep1


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_365]


title: Wb39396256 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_035]


title: Wb338817210 Memory CD4+/CD25- T cells


title: AC-06h-endo-rep3

value: Hour 6


title: AC-06h-endo-rep2


title: Wb26349718 Memory CD4+/CD25- T cells


title: Wb255279458 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_019]


title: AC-24h-endo-rep1


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_455]

value: 3 - Moderate


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_007]

value: Female


title: Wb35307192 Memory CD4+/CD25- T cells


title: AC-24h-embryo-rep2


title: AC-06h-endo-rep1

value: endosperm


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_004]


title: Wb37602472 Memory CD4+/CD25- T cells Rep 2


title: Wb28588254 Memory CD4+/CD25- T cells


title: AC-06h-embryo-rep3

value: AC Morgan


title: Wb40585324 Memory CD4+/CD25- T cells


title: AC-06h-embryo-rep2


title: Wb434959941 Memory CD4+/CD25- T cells


title: Wb93515984 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_202]


title: Wb29941410 Memory CD4+/CD25- T cells


title: Wb23619194 Memory CD4+/CD25- T cells


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_201]


title: Wb01018268 Memory CD4+/CD25- T cells


title: AC-06h-embryo-rep1


title: Wb95508280 Memory CD4+/CD25- T cells


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_526rr]

value: RSV convalescence visit

value: 4 - Severe


title: Wb21239448 Memory CD4+/CD25- T cells

value: M


title: AC-03h-endo-rep3

value: Hour 3


title: Wb83970808 Memory CD4+/CD25- T cells Rep 1

value: Memory CD4+/CD25- T cells

value: Caucasian


title: Wb44884700 Memory CD4+/CD25- T cells


title: Wb77694072 Memory CD4+/CD25- T cells


title: AC-03h-endo-rep2


title: Wb609359337 Memory CD4+/CD25- T cells

value: CTL


title: AC-03h-endo-rep1


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_381]

value: whole blood


title: Wb17573972 Memory CD4+/CD25- T cells

value: F


title: RSV visit, RSV-infected, non-hospitalized (mild disease) [A4398_123]

value: RSV visit


title: AC-03h-embryo-rep2

value: embryo


title: AC-03h-embryo-rep3

value: germinating grain


title: Wb500063258 Memory CD4+/CD25- T cells


title: Wb12735421 Memory CD4+/CD25- T cells


title: Wb63928904 Memory CD4+/CD25- T cells


title: Wb04700691 Memory CD4+/CD25- T cells


title: AC-03h-embryo-rep1


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_321]


title: Wb86185064 Memory CD4+/CD25- T cells


title: AC-00h-endo-rep3

value: Hour 0


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_078]


title: Wb76432632 Memory CD4+/CD25- T cells


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_184]


title: Wb37602472 Memory CD4+/CD25- T cells Rep 1


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_071]


title: Wb598690385 Memory CD4+/CD25- T cells


title: Wb60525860 Memory CD4+/CD25- T cells


title: JSB077-Pero-8Week-F

city: Boston

first: Jeffrey

last: Bourgeois

address: 136 Harrison Ave

institute: Tufts University

data_processing:
Genome built using RSEM and Bowtie, Genome GCF_004664715.2
Mapping completed using RSEM and STAR
Transcripts per Million for each gene saved as part of file pero_tpm_values_082923.csv
Assembly: GCF_004664715.2
Supplementary files format and content: data table containing the gene_id, transcript id(s), transcript length, effective length, expected_count (aka raw count), TPM (transcripts per million), and FPKM (fragments per kilobase of transcript per million mapped reads)

molecule: polyA RNA

organism: Peromyscus leucopus

source_name: Ear Punch

extract_protocol:
Skin placed in RNA-later, Frozen, Beadbeat in QIAzol, extracted with miRNeasy mini kit w/ additional RWT wash, digested with Turbo Dnase, repurified with Rneasy MinElute
Ear punches were placed directly in RNA-later reagent overnight. Samples were frozen at -80C before beadbeating in QIAzol and RNA isolation with the miRNeasy kit by Qiagen with an additional RWT wash. TURBO Dnase was used to degrade DNA following isolation and samples were cleaned with RNeasy MinElute Cleanup Kit by Qiagen. Purified RNA was sent to Azenta/Genewiz for library preparation and sequencing (Illumina HiSeq 2x150bp)

value: Ear Punch

tag: agent

value: B. burgdorferi strain B31

value: 8 Week post Infection


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_072]

value: Female


title: Wb39397564 Memory CD4+/CD25- T cells


title: JSB077-Pero-8Week-M

value: Male

tag: time point


title: Wb11083395 Memory CD4+/CD25- T cells Rep 1


title: Wb218547683 Memory CD4+/CD25- T cells Rep 1


title: Wb290146432 Memory CD4+/CD25- T cells


title: JSB077-Pero-4Week-M

value: 4 Week Post Infection


title: JSB077-Pero-4Week-F


title: Wb19116444 Memory CD4+/CD25- T cells

value: M


title: Wb255607012 Memory CD4+/CD25- T cells Rep 1


title: Wb757056691 Memory CD4+/CD25- T cells Rep 1


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_569]

value: RSV convalescence visit

value: 3 - Moderate


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_371]

value: 4 - Severe


title: Wb27959974 Memory CD4+/CD25- T cells

value: Memory CD4+/CD25- T cells

value: CTL

value: Caucasian


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_566]

value: whole blood


title: JSB077-Pero-2Week-F

value: 2 Week Post Infection


title: Wb27902628 Memory CD4+/CD25- T cells

value: F


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_311]


title: Wb62765928 Memory CD4+/CD25- T cells


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_196]


title: JSB077-Pero-1Week-M

value: 1 Week Post Infection


title: Wb77571832 Memory CD4+/CD25- T cells


title: Wb92302600 Memory CD4+/CD25- T cells Rep 1


title: Wb957775938 Memory CD4+/CD25- T cells


title: Wb84738880 Memory CD4+/CD25- T cells


title: JSB077-Pero-1Week-F

value: Ear Punch


title: Wb92302600 Memory CD4+/CD25- T cells Rep 2


title: JSB077-Pero-UI1Week-M

value: Uninfected


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_046]


title: Wb92179688 Memory CD4+/CD25- T cells Rep 1


title: Wb77571832 Memory CD4+/CD25+ regulatory T cells

value: Memory CD4+/CD25+ regulatory T cells


title: JSB077-Pero-UI1Week-F

value: Female


title: JSB077-Pero-2Week-M

value: B. burgdorferi strain B31

value: Male


title: Wb84738880 Memory CD4+/CD25+ regulatory T cells


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_084]


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_327]


title: Wb86185064 Memory CD4+/CD25+ regulatory T cells


title: JSB075-Pero-8Week-M

value: 8 Week post Infection


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_490]

value: RSV convalescence visit


title: Wb285470206 Memory CD4+/CD25- T cells

value: M


title: JSB075-Pero-8Week-F


title: Wb35307192 Memory CD4+/CD25+ regulatory T cells


title: Wb113332655 Memory CD4+/CD25+ regulatory T cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_552]

value: 4 - Severe


title: Wb12735421 Memory CD4+/CD25+ regulatory T cells Rep 1


title: RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4397_1068]

value: 3 - Moderate


title: Wb260892376 Memory CD4+/CD25+ regulatory T cells

value: CTL


title: Wb72636504 Memory CD4+/CD25+ regulatory T cells

value: Caucasian


title: Wb28992844 Memory CD4+/CD25+ regulatory T cells


title: JSB075-Pero-2Week-M


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_240]

value: whole blood


title: Wb98838184 Memory CD4+/CD25+ regulatory T cells


title: JSB075-Pero-4Week-M

value: 4 Week Post Infection


title: Wb89130144 Memory CD4+/CD25+ regulatory T cells

value: F


title: JSB075-Pero-2Week-F

value: 2 Week Post Infection


title: Wb842518068 Memory CD4+/CD25+ regulatory T cells


title: Wb209525269 Memory CD4+/CD25+ regulatory T cells Rep 1


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_548]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_508]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_497]


title: Wb957775938 Memory CD4+/CD25+ regulatory T cells


title: JSB075-Pero-1Week-M

value: Ear Punch

value: 1 Week Post Infection


title: Wb609359337 Memory CD4+/CD25+ regulatory T cells

value: Memory CD4+/CD25+ regulatory T cells


title: JSB075-Pero-1Week-F

value: Female


title: Wb31241246 Memory CD4+/CD25+ regulatory T cells


title: Wb67530352 Memory CD4+/CD25+ regulatory T cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_550]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_502]


title: Wb21239448 Memory CD4+/CD25+ regulatory T cells


title: Wb207731668 Memory CD4+/CD25+ regulatory T cells


title: JSB075-Pero-4Week-F

value: B. burgdorferi strain B31


title: JSB075-Pero-UI1Week-M

value: Male

value: Uninfected


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_474]

value: RSV convalescence visit


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_374]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_345]


title: Wb12735421 Memory CD4+/CD25+ regulatory T cells Rep 2


title: Wb598690385 Memory CD4+/CD25+ regulatory T cells

value: M


title: Wb11083395 Memory CD4+/CD25+ regulatory T cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_343]


title: Wb01018268 Memory CD4+/CD25+ regulatory T cells


title: AC-00h-endo-rep2

value: endosperm

value: germinating grain

value: AC Morgan

value: Hour 0


title: Wb27959974 Memory CD4+/CD25+ regulatory T cells

value: Caucasian


title: Wb255279458 Memory CD4+/CD25+ regulatory T cells

value: CTL


title: AC-00h-endo-rep1


title: Wb434959941 Memory CD4+/CD25+ regulatory T cells


title: Wb290146432 Memory CD4+/CD25+ regulatory T cells


title: AC-00h-embryo-rep3

value: embryo


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_313]

value: whole blood

value: 3 - Moderate


title: Wb17615230 Memory CD4+/CD25+ regulatory T cells

value: F


title: AC-00h-embryo-rep2


title: AC-00h-embryo-rep1


title: Wb77694072 Memory CD4+/CD25+ regulatory T cells

value: Memory CD4+/CD25+ regulatory T cells


title: Wb16970712 Memory CD4+/CD25+ regulatory T cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_309]

value: Female


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_285]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_325]


title: CDC-40d-rep3

source_name: whole grain

value: whole grain

value: developing grain

value: CDC Morrison

value: Day 40


title: Wb775170478 Memory CD4+/CD25+ regulatory T cells


title: Wb77109992 Memory CD4+/CD25+ regulatory T cells


title: Wb32193536 Memory CD4+/CD25+ regulatory T cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_276]

value: RSV convalescence visit


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_283]


title: Wb23619194 Memory CD4+/CD25+ regulatory T cells

value: M


title: Wb86451000 Memory CD4+/CD25+ regulatory T cells


title: Wb27902628 Memory CD4+/CD25+ regulatory T cells


title: CDC-40d-rep1


title: CDC-35d-rep3

value: Day 35


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_248]


title: Wb500063258 Memory CD4+/CD25+ regulatory T cells


title: Wb255607012 Memory CD4+/CD25+ regulatory T cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_244]


title: JSB075-Pero-UI1Week-F

value: Ear Punch

value: Uninfected


title: CDC-35d-rep1


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_227]


title: Wb33161134 Memory CD4+/CD25+ regulatory T cells

value: Caucasian


title: Wb84593528 Memory CD4+/CD25+ regulatory T cells


title: Wb95508280 Memory CD4+/CD25+ regulatory T cells


title: CDC-35d-rep2


title: Wb29941410 Memory CD4+/CD25+ regulatory T cells

value: CTL


title: CDC-40d-rep2


title: Wb218547683 Memory CD4+/CD25+ regulatory T cells Rep 2


title: Wb977212218 Memory CD4+/CD25+ regulatory T cells


title: Wb63928904 CD19+/CD27- B cells

value: CD19+/CD27- B cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_218]

value: whole blood


title: CDC-30d-rep2

value: Day 30


title: Wb17451436 CD19+/CD27- B cells


title: CDC-30d-rep3


title: Wb11083395 CD19+/CD27- B cells

value: F


title: Wb702524065 Memory CD4+/CD25+ regulatory T cells

value: Memory CD4+/CD25+ regulatory T cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_214]

value: Female

value: 3 - Moderate


title: Wb84738880 CD19+/CD27- B cells


title: CDC-30d-rep1

value: whole grain

value: developing grain


title: Wb499255267 Memory CD4+/CD25+ regulatory T cells


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_194]


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_168]


title: Wb74450320 CD19+/CD27- B cells


title: CDC-25d-rep3

value: CDC Morrison

value: Day 25


title: RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_180]

value: RSV convalescence visit


title: Wb16359426 CD19+/CD27- B cells


title: Wb46780368 CD19+/CD27- B cells


title: CDC-25d-rep2


title: Wb22378588 CD19+/CD27- B cells Rep 1

value: M


title: Wb338817210 CD19+/CD27- B cells Rep 1


title: CDC-25d-rep1


title: RSV convalescence, comorbidity [A4398_484]

value: 4 - Severe


title: Wb31384296 CD19+/CD27- B cells


title: Wb80342064 CD19+/CD27- B cells


title: RSV convalescence, comorbidity [A4398_477]


title: CDC-20d-rep3

value: Day 20


title: Wb48429960 CD19+/CD27- B cells

value: Caucasian


title: CDC-20d-rep2


title: Wb97288112 CD19+/CD27- B cells


title: Wb16970712 CD19+/CD27- B cells

value: CTL


title: Wb78685096 CD19+/CD27- B cells

value: CD19+/CD27- B cells


title: RSV convalescence, comorbidity [A4398_295]

value: whole blood


title: CDC-15d-rep3

value: Day 15


title: Wb31588806 CD19+/CD27- B cells

value: F


title: RSV convalescence, comorbidity [A4398_278]


title: Wb57963872 CD19+/CD27- B cells


title: CAGE-seq in Human testes

first: Elena

last: Pugacheva

department: NIAID

data_processing:
ChIP-seq, ATAC-seq, CAGE-seq data: single-end or paired-end reads were aligned either to the UCSC hg19 (human samples) or UCSC mm9 (mouse samples) genome using Bowtie version 2 under default parameters.
RNA-seq data: FASTQ files were either mapped to the UCSC mouse (build mm9) or human ((build hg19) reference genomes using STAR with default settings. Normalized gene counts and differentially expressed genes (DEG) were obtained with the R package DESeq2.
For ChIP-seq and ATAC-seq data, output BAM files were converted into bdg track files using MACS2
For CAGE-seq, ChIP-seq, ATAC-seq data, output BAM files were converted into bigwig files using bamCoverage option in deepTools 3.5.0 in order to display normilized coverage throughout the genome (in RPKM).
ChIP-seq and ATAC-seq peaks were called using Model-based Analysis for ChIP-seq (MACS2) using default parameters.
CAGE-seq clusters were called using MACS2  with parameters (--nomodel --shift -1)
bdg files were generated using  MACS2  with default settings.
Assembly: hg19 (for human) amd mm9 (for mouse)
Supplementary files format and content: bdg, xlsx (differentially expressed genes (DEG) were obtained with the R package DESeq2), bigwig (BAM files normilized using bamCoverage option in deepTools 3.5.0 (in RPKM))

source_name: Human male germ cells

growth_protocol: DMEM (NIH3T3, 293T, MDA-MB-435, MCF7 cells), RPMI (K562, CH12cells), 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2. Stable NIH3T3, MDA-MB-435 and MCF7 clones were maintained under 150 mkg/ml of Hygromycin B.

extract_protocol:
ChIP-seq protocol: 2x106 asynchronously growing cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 10 min, washed twice with 1×phosphate buffered saline (PBS), and resuspended in chromatin immunoprecipitation (ChIP) lysis buffer (150 mM NaCl, 1 % Triton X-100, 0.1 % SDS, 20 mM Tris–HCl pH8.0, 2 mM EDTA). Chromatin was sheared to 200–600 bp and immunoprecipitated with 5 μg of antibody. Immunoprecipitated DNA was purified with QIAquick columns (ZymaResearch).
ATAC-seq protocol:NIH3T3 cells (5 × 104) were pelleted by centrifugation and resuspended in 50 µL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), gently pipetting up and down 10 times. Nuclei were pelleted by centrifugation at 2500g for 10 min at 4°C and resuspended in 25 µL of 2x TD Buffer (Illumina Cat #FC-121-1030), containing 8 µL of Tn5 Transposes (Illumina Cat #FC-121-1030) and 17 µL of nuclease free water. The rection was incubated for 30 min at 37°C. Tagmented DNA was purified by using a Zymo Research DNA Clean & Concentrator™-5 - Capped Columns.
RNA-seq protocol:The RNA sequencing library preparation and sequencing procedures were carried out according to Illumina protocols. Briefly, poly(A)-mRNA was purified from 5 μg of RNA with streptavidin-coated magnetic beads. After chemical fragmentation, mRNA fragments were reverse-transcribed and converted into double-stranded cDNA. Following end repair and A-tailing, paired-end adaptors were ligated to the ends of the DNA fragments. The ligated products were amplified with 18 cycles of PCR followed by purification using AMPure beads (Beckman Coulter). The enriched libraries were diluted to a final concentration of 5 nM.
ChIP-seq libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA) or NEBNext UltraII DNA Library Prep Kit for Illumina (BioLabs, catalog # E7645S).  Libraries were amplified using 15 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
RNA-seq library were prepared using TruSeq RNA Library Prep Kit (Illumina, Inc., USA)
ATAC-seq libraries were amplified using NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs). The libraries were size-selected  by adding 1.8X volume Agencourt AMPure XP beads (Beckman, 63881).
CAGE-seq libraries were prepared by DNAFORM (Yokohama, Kanagawa, Japan).

value: Human male germ cells

tag: chip antibody

tag: treatment

value: Three males from 29-32 years old (purchased from OriGene)


title: RSV convalescence, comorbidity [A4398_171]

tag: tissue

tag: gender / sex

value: Female


title: RSV convalescence, comorbidity [A4398_281]

value: Male

tag: age in days

tag: age group


title: RNA-seq in K562 cells with depleted BORIS

description: RNA_Seq_K562_WTvs_Clone7_BORISdepleted.xlsx

tag: cell line

value: Human immortalised myelogenous leukemia cell line

value: Zinc Finger Nuclease treatment to downregulate BORIS expression

value: K562 mutant, BORIS downregulation


title: RSV convalescence, comorbidity [A4398_259]

tag: visit

value: RSV convalescence visit

tag: disease classification at rsv visit based on resvinet score


title: RNA-seq in K562 cells

tag: cell type

tag: genotype

value: wild type


title: CDC-15d-rep1

value: whole grain

value: developing grain

value: CDC Morrison

tag: time


title: Wb23619194 CD19+/CD27- B cells Rep 1

tag: Sex

value: M

tag: disease status

value: CTL

tag: age

value: Caucasian


title: CDC-10d-rep3

value: Day 10


title: RNA-seq in MDA-MB-435+BORIS cells

value: Human melanoma cancer cell line

value: Ectopic expression of BORIS from CpG-free plasmid (InvivoGen)

value: MDA-MB-435 stably expressing BORIS


title: RSV convalescence, comorbidity [A4398_301]

value: whole blood

value: 4 - Severe


title: RNA-seq in MDA-MB-435+EV cells

value: Ectopic expression of a control plasmid (empty vector, EV), expressing beta-galactosidase (CpG-free plasmid (InvivoGen))

value: MDA-MB-435 stably expressing EV (Empty Vector)


title: RSV convalescence, comorbidity [A4398_163rr]

value: Male


title: RNA-seq in 293T+BORIS cells

value: Human embryonic kidney 293 cells

value: Transient ectopic expression of BORIS from CpG-free plasmid (InvivoGen)

value: 293T transiently expressing BORIS


title: RSV convalescence, comorbidity [A4398_166]

value: Female

value: RSV convalescence visit


title: CDC-10d-rep2

value: whole grain

value: developing grain

value: CDC Morrison


title: CDC-20d-rep1

value: Day 20


title: RNA-seq in 293T+EV cells

value: Transient ectopic expression of a control plasmid (empty vector, EV), expressing beta-galactosidase (CpG-free plasmid (InvivoGen))

value: 293T transiently expressing EV (Empty Vector)


title: Wb47020128 CD19+/CD27- B cells

value: CD19+/CD27- B cells

value: F

tag: ethnicity

value: Caucasian

tag: subject id


title: CDC-10d-rep1

value: Day 10


title: RSV convalescence, comorbidity [A4398_496]

value: whole blood

value: 3 - Moderate


title: CDC-15d-rep2

value: Day 15


title: Input for MDA-MB-435+EV cells

value: Human melanoma cancer cell line

tag: chip antibody

value: Ectopic expression of a control plasmid (empty vector, EV), expressing beta-galactosidase (CpG-free plasmid (InvivoGen))

value: MDA-MB-435 stably expressing EV (Empty Vector)


title: CDC-5d-rep3

value: Day 5


title: Input for K562_WT cells

value: Human immortalised myelogenous leukemia cell line

tag: treatment

value: wild type


title: ChIP-seq with BORIS Abs in K562 cells

value: BORIS custom-made mouse monoclonal (characterized in  PMID:21659515)


title: Input for 293T cells

value: Human embryonic kidney 293 cells


title: ChIP-seq with BORIS Abs in K562 cells with depleted BORIS

value: Zinc Finger Nuclease treatment to downregulate BORIS expression


title: CDC-5d-rep2

tag: tissue

value: whole grain

value: developing grain

value: CDC Morrison


title: RSV convalescence, comorbidity [A4398_353rr]

tag: gender / sex

value: Male

value: RSV convalescence visit


title: CDC-5d-rep1


title: ChIP-seq with BORIS Abs in MDA-MB-435+EV cells


title: ChIP-seq with CTCF Abs in K562 cells with depleted BORIS

value: CTCF custom-made mouse monoclonal (characterized in PMID:15731119)

value: K562 mutant, BORIS downregulation


title: ChIP-seq with BORIS Abs in MDA-MB-435+BORIS cells

value: Ectopic expression of BORIS from CpG-free plasmid (InvivoGen)

value: MDA-MB-435 stably expressing BORIS


title: ChIP-seq with CTCF Abs in K562 cells


title: ChIP-seq with CTCF Abs in MDA-MB-435+EV cells

value: Human melanoma cancer cell line

value: Ectopic expression of a control plasmid (empty vector, EV), expressing beta-galactosidase (CpG-free plasmid (InvivoGen))


title: ChIP-seq with CTCF Abs in MDA-MB-435+BORIS cells


title: AC-40d-rep1

value: AC Morgan

value: Day 40


title: RSV convalescence, comorbidity [A4398_489]

value: whole blood

tag: age in days

value: 3 - Moderate


title: RSV convalescence, comorbidity [A4398_339]

tag: age group


title: ChIP-seq with CTCF Abs in 293T+BORIS cells

tag: cell line

value: Human embryonic kidney 293 cells

value: Transient ectopic expression of of BORIS from CpG-free plasmid (InvivoGen)

value: 293T transiently expressing BORIS


title: RSV convalescence, comorbidity [A4398_393]

tag: visit


title: ChIP-seq with CTCF Abs in 293T+EV cells

value: Transient ectopic expression of a control plasmid (empty vector, EV), expressing beta-galactosidase (CpG-free plasmid (InvivoGen))

value: 293T transiently expressing EV (Empty Vector)


title: RSV convalescence, comorbidity [A4398_333]

value: Female

tag: disease classification at rsv visit based on resvinet score


title: RSV convalescence, comorbidity [A4398_335]

value: Male

value: RSV convalescence visit


title: AC-40d-rep2

value: whole grain

tag: cell type

value: developing grain


title: RSV convalescence, comorbidity [A4398_307]


title: AC-35d-rep3

tag: genotype

value: Day 35


title: AC-35d-rep2

tag: time


title: RSV convalescence, comorbidity [A4398_291]