title: muscle, PH187, week 16, rest

description:
PH187w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: HITT


title: muscle, PH189, week 0, 24hr

status: Public on Jul 22 2025

type: SRA

city: Dayton

first: Madhavi

last: Kadakia

state: OH

address: 3640 Colonel Glenn Hwy

department: Biochemistry and Molecular Biology

country: USA

institute: Wright State University

description:
PH189w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

library_source: other

data_processing:
Data processing performed in Partek Flow v10.0.21.0706
Reads were trimmed to a fixed length based on an average PHRED quality score greater than 20.
Trimmed reads were alighed to miRbase v21/hg38 using Bowtie aligner (seed mismatch =1, seed length = 10) and quantitated using miRBase v21.
Reads were normalized using the Trimmed Mean of M values (TMM) normalization method with an offset of 1.0.
Assembly: miRBase v21 of the hg38 (GRCh38) assembly.
Supplementary files format and content: tab-delimited text files listing raw read counts for each sample
Supplementary files format and content: tab-delimited text files listing TMM-normalized read counts for each sample

molecule: other

organism: Homo sapiens

source_name: vastus lateralis muscle

extract_protocol:
Muscle: Total RNA isolated using mirVana Paris Kit (Fisher); Serum exosomes: Exosomes isolated using Total Exosome Isolation from Serum Kit (Life Tech) and exosomal RNA purified using the Total Exosome RNA and Protein Isolation Kit (Life Tech).  XX RNA was used for construction of sequencing libraries.
cDNA was barcoded with IonExpress RNA-Seq Barcode 1-16 kit (Life Tech). 7.5picomoles each of 8-10 barcoded libraries were pooled and clonally amplified onto IonSphere Particles and enriched using the OneTouch2 (Life Tech).

treatment_protocol: All participants completed 12 weeks of either TRAD or HITT exercise followed by a 4 week detraining period.

tag: tissue

value: vastus lateralis muscle

tag: participant id

tag: treatment

value: TRAD

tag: week

value: week 0

tag: time

tag: Sex

value: Female


title: ExT13_Tumor_DP_day14_cont_21

city: Noda-shi

first: Mikiya

last: Tsunoda

state: Chiba

department: Molecular Preventive Medicine

country: Japan

institute: The University of Tokyo

description: Library name: Sample 36

library_source: transcriptomic

data_processing:
Adapter trimming and quality filtering of sequencing data were performed by using Cutadapt-3.2 and PRINSEQ-0.20.4. Sequencing data were processed by MiXCR-3.0.5.
In MiXCR, Filtered reads were aligned to reference mouse TCR V/D/J sequences registered in the international ImMunoGeneTics information system: -starting-material=rna, -5-end=no-v-primers-, -3-end=c-primers, -adapters=no-adapters, vParameters.geneFeatureToAlign=VTranscript, -vjAlignmentOrder=JThenV, then identical sequences were assembled and grouped in clones with PCR and sequencing error correlation with the following parameters: -badQualityThreshold=15, –separateByV=true, –separateByJ=true, -only-productive=true, –region-of-interest=CDR3.
The Variable (V) and Joining (J) segment of TCRs were represented in IMGT gene nomenclature. List of final clones were analyzed by VDJtools-1.2.1. Then, the sequencing reads of sample was normalized to the six times of cell count in each sample by “DownSample” command of VDJtools. T-cell clones were determined as TCR reads with the same TCR V segment, J segment and CDR3 nucleotide sequence.
Assembly: IMGT reference sequences of mouse TRB
Supplementary files format and content: text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones

molecule: polyA RNA

organism: Mus musculus

source_name: Tumor

growth_protocol: Lewis lung carcinoma (LLC) cells (5 × 10^5 cells /mouse) were inoculated subcutaneously (s.c.) into the left flank, right flank and the left hip of C57BL/6 mice.

extract_protocol:
Tumors were cut into small fragments and digested for 45 minutes at 37°C with 0.2% collagenase (FUJIFILM Wako) and DNase I (Sigma-Aldrich), except for experiments for single-cell analysis, in which tumors were digested with 0.2% collagenase NB8 (Nordmark Pharma GmbH). The cells were then subjected to two-phase density separation with upper 35% Percoll PLUS (GE Healthcare) (1000g, 10 minutes at room temperature). Leukocytes were recovered, washed and resuspended in preparation medium (PM) [5%FBS, 10mM HEPES (Nacalai), Penicillin-Streptomycin (Nacalai) in RPMI-1640 (Nacalai)]. After RBC lysis with ACK buffer [155mM of NH4Cl (Nacalai), 10mM of KHCO3 (Nacalai), and 0.5mM EDTA pH8.0 (NIPPON GENE)] for 1 minute at room temperature, cells were washed and resuspended in PM, and the cell concentrations were measured using Flow-Count fluorospheres (Beckman Coulter) and a CytoFLEX S flow cytometer (Beckman Coulter).Cells were stained with a mix of Fc Block (anti-mouse CD16/CD32 mAb; clone 2.4G2, BioLegend) and fluorophore-conjugated anti-mouse monoclonal antibodies (Supplementary Table 5). Antibody mixtures were prepared using BD Horizon Brilliant Stain Buffer Plus (BD) diluted 5x with FACS buffer (D-PBS(-) supplemented with 2% FBS, and 0.05% Sodium Azide). Staining was performed for 20 minutes at 4°C. Before sorting, T cells were enriched from tumor suspensions by further staining with BD IMag APC Magnetic Particles-DM (BD Biosciences), then placed on magnetic plate. After washing by MACS buffer (D-PBS(-) supplemented with 10% BSA, and 2 mM EDTA pH8.0), APC and APC-Cy7(CD8, mouse TCRb)-positive cells were collected as positive fraction. Cell sorting was performed using a FACS Aria II or Aria III (BD Biosciences). Cells were stained with 5µg/mL of propidium iodide (PI, Sigma-Aldrich) immediately before sorting. Nonviable cells were excluded from the analysis based on forward and side scatter profiles and PI staining. For bulk TCR repertoire analysis and bulk RNA-seq analysis, cells were sorted into Lysis buffer [1% w/v LiDS, 100 mM Tris-HCl pH7.5, 500 mM LiCl, 5 mM dithiothreitol, and 10 mM EDTA pH8.0] and stored at −80°C. Cells were sorted from the CD8+, CD8+PD-1+Ly108+TIM-3-, CD8+PD-1+Ly108+TIM-3+, CD8+PD-1+Ly108-TIM-3+ and CD8+PD-1- fractions to produce five datasets per mouse.
TCR libraries were prepared on purified T cells lysed in lysis buffer [1% LiDS, 100 mM Tris-HCl (pH 7.5), 500 mM LiCl, and 10 mM EDTA]. PolyA RNAs were isolated according to a previous report with some modifications (GSE110711).To perform reverse transcription and template-swiching, beads were then suspended in 10 µL of RT mix [1× First Strand buffer (Thermo Fisher Scientific), 1 mM dNTP, 2.5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma-Aldrich), 9 mM MgCl2, 1 U/µL RNaseIn Plus Rnase Inhibitor (Promega), 10 U/µL Superscript II (Thermo Fisher Scientific), and 1µM of i5-TSO], and incubated for 60 min at 42ºC and immediately cooled on ice. Beads were washed once with with B&W-T buffer [5 mM Tris-HCl (pH 7.5), 1 M NaCl, 0.5 mM EDTA, and 0.1% Tween-20], and once with Tris-HCl (pH 8.0). To amplify the TCR cDNA containing complementarity determining region 3 (CDR3), nested PCR of the TCR locus was performed as follows. Beads with containing cDNA was resuspended with the 25 µL of first PCR mixture [0.4 µM of primers (i5, Trac_ex, and Trbc_ex), and 1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems, Wilmington, MA, #KK2602)], and the thermal cycling was performed as following condition: denaturation at 95°C for 3 min, 10 cycles of denaturation for 20 sec at 98°C, annealing for 15 sec at 65°C and extension for 30 sec at 72°C, followed by a final extension at 72°C for 2 min. Then, 2.5 µL of first PCR product was mixed with the 22.5 µl of second PCR mixture [0.35 µM of primers (i5_2nd, i7-BC_mTrac, and i7-BC_mTrbc), and 1x KAPA Hifi Hotstart ReadyMix], , and the thermal cycling was performed as following condition: denaturation at 95°C for 3 min, 18 cycles of denaturation for 20 sec at 98°C, annealing for 15 sec at 65°C and extension for 30 sec at 72°C, followed by a final extension at 72°C for 2 min.. The second-PCR products were purified by an Agencort AM Pure XP kit (Bexkman-Coulter, CA, #A63881) at a 0.7:1 ratio of beads to sample, and eluted with 20 µL of Tris-HCl (pH 8.0).To amplify TCR library and add adaptor sequence for next generation sequencer, the third PCR was performed as follows. 5µL of purified second PCR product was mixed with the 20 µl of third PCR mixture [0.4 µM of primers (i5-BC and i7-BC), and 1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems, Wilmington, MA, USA, #KK2602)], and the thermal cycling was performed under the same condition as first PCR, excepted for the number of cycles (23 cycles). The third-PCR products were purified as second PCR. The products were pooled and then purified and subjected to dual size selection using ProNex size-selective purification system (Promega) and eluted with 25 μL of Tris-HCl (pH 8.5). Final TCR libraries, whose lengths were about 600 base pairs were sequenced using an Illumina Novaseq 6000 S4 flowcell (67 bp read 1 and 140 bp read 2) (Illumina, USA). Only read2 contained the sequence regarding the definition of T cell clones.

value: Tumor

tag: cell line

value: Lewis lung carcinoma

tag: cell type

value: lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRb+,  CD4-, CD8+, PD-1+, Ly108+ and Tim3+ T cells

tag: genotype

value: WT


title: muscle, PH187, week 12, 3hr

description:
PH187w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 12


title: muscle, PH187, week 12, pre

description:
PH187w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: pre


title: ExT13_Tumor_CD8_day28_LAG3_29

description: Library name: Sample 33

value: lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRb+,  CD4-, CD8+ and T cells


title: muscle, PH187, week 0, pre

description:
PH187w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH187, week 0, 3hr

description:
PH187w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_CD8_day28_LAG3_14

description: Library name: Sample 30


title: muscle, PH186, week 12, pre

description:
PH186w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: Male


title: ExT13_Tumor_CD8_day28_LAG3_4

description: Library name: Sample 29


title: muscle, PH186, week 16, rest

description:
PH186w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 16

value: rest


title: ExT13_Tumor_CD8_day28_LAG3_2

description: Library name: Sample 28


title: ExT13_Tumor_CD8_day28_cont_30

description: Library name: Sample 27


title: muscle, PH186, week 12, 3hr

description:
PH186w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH186, week 12, 24hr

description:
PH186w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH187, week 0, 24hr

description:
PH187w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH186, week 0, pre

description:
PH186w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_CD8_day28_cont_19

description: Library name: Sample 24


title: ExT13_Tumor_DP_day14_cont_30

description: Library name: Sample 38


title: ExT13_Tumor_CD8_day28_cont_3

description: Library name: Sample 23


title: ExT13_Tumor_CD8_day28_cont_21

description: Library name: Sample 25


title: ExT13_Tumor_DP_day14_cont_19

description: Library name: Sample 35


title: muscle, PH186, week 0, 24hr

description:
PH186w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_CD8_day28_cont_28

description: Library name: Sample 26


title: ExT13_Tumor_CD8_day21_LAG3_25

description: Library name: Sample 21


title: ExT13_Tumor_DP_day14_cont_3

description: Library name: Sample 34


title: ExT13_Tumor_CD8_day28_LAG3_25

description: Library name: Sample 32


title: ExT13_Tumor_CD8_day21_LAG3_29

description: Library name: Sample 22


title: ExT13_Tumor_CD8_day21_LAG3_16

description: Library name: Sample 20


title: muscle, PH187, week 12, 24hr

description:
PH187w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH171, week 12, 3hr

description:
PH171w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH171, week 12, pre

description:
PH171w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_CD8_day28_LAG3_16

description: Library name: Sample 31


title: ExT13_Tumor_CD8_day21_LAG3_4

description: Library name: Sample 18


title: muscle, PH171, week 12, 24hr

description:
PH171w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_CD8_day21_cont_30

description: Library name: Sample 16


title: muscle, PH186, week 0, 3hr

description:
PH186w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_CD8_day21_LAG3_2

description: Library name: Sample 17


title: muscle, PH171, week 0, 3hr

description:
PH171w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH171, week 0, 24hr

description:
PH171w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH171, week 16, rest

description:
PH171w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_CD8_day21_cont_28

description: Library name: Sample 15


title: muscle, PH169, week 12, pre

description:
PH169w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH169, week 16, rest

description:
PH169w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_CD8_day21_cont_21

description: Library name: Sample 14


title: ExT13_Tumor_CD8_day21_cont_3

description: Library name: Sample 12


title: ExT13_Tumor_CD8_day14_LAG3_29

description: Library name: Sample 11


title: ExT13_Tumor_CD8_day21_cont_19

description: Library name: Sample 13


title: muscle, PH169, week 12, 3hr

description:
PH169w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH168, week 16, rest

description:
PH168w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_CD8_day14_LAG3_14

description: Library name: Sample 8


title: muscle, PH169, week 0, 24hr

description:
PH169w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_CD8_day14_LAG3_25

description: Library name: Sample 10


title: ExT13_Tumor_CD8_day14_LAG3_16

description: Library name: Sample 9


title: ExT13_Tumor_CD8_day14_LAG3_4

description: Library name: Sample 7


title: muscle, PH169, week 0, pre

description:
PH169w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH168, week 12, pre

description:
PH168w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH168, week 12, 3hr

description:
PH168w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH169, week 12, 24hr

description:
PH169w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_CD8_day21_LAG3_14

description: Library name: Sample 19


title: muscle, PH169, week 0, 3hr

description:
PH169w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH168, week 12, 24hr

description:
PH168w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_CD8_day14_cont_30

description: Library name: Sample 5


title: muscle, PH171, week 0, pre

description:
PH171w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_CD8_day14_cont_21

description: Library name: Sample 3


title: muscle, PH168, week 0, pre

description:
PH168w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_CD8_day14_cont_19

description: Library name: Sample 2


title: ExT13_Tumor_CD8_day14_cont_3

description: Library name: Sample 1


title: muscle, PH168, week 0, 24hr

description:
PH168w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH164, week 12, pre

description:
PH164w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH164, week 16, rest

description:
PH164w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH164, week 12, 3hr

description:
PH164w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: ExT13_Tumor_CD8_day14_LAG3_2

description: Library name: Sample 6


title: muscle, PH164, week 12, 24hr

description:
PH164w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: WT Organoid 2 replicate 2

city: Burlington

first: Michael

middle: J

last: Toth

state: VT

address: 149 Beaumont Avenue, HSRF 103

department: Medicine

institute: University of Vermont College of Medicine

description: Library name: C2_2

data_processing:
Reads aligned to GRCm39 reference genome using STAR (v.2.7.3.a)
BAM file filtering and indexing was carried out using SAMtools v1.9
RNA-seq library quality control was implemented using RseQC v4.0.0 and QualiMap v2.2.2-dev
Duplicate reads were marked using Picard tools v2.23.9
Assembly: GRCm39

molecule: total RNA

source_name: Organoid isolated from lung

growth_protocol: For organoids: Tumor or lung tissue from G12D or WT mice, respectively, were excised 6 weeks post-tamoxifen injection, and organoid cultures were developed, as described 83. Briefly, lung tumors or tissue were excised and minced in high glucose GlutaMAX DMEM containing 0.1% BSA and 1% penicillin-streptomycin (D-BSA). Minced tissue was incubated with 500 μL collagenase type II (20 mg/mL) and 10 μL of Rho-associated protein kinase inhibitor (10 μM) on an orbital shaker at 140 rpm for 1-2 hours at 37°C. Fetal bovine serum (FBS) was added to halt collagenase digestion and tissues were further homogenized by vigorous pipetting. The tissue suspension was strained through a 100 µM filter, centrifuged at 8°C, the supernatant aspirated leaving ~0.5 mL, and the pellets resuspended. Tissue pellets were washed twice in D-BSA and centrifuged at 8° C, and tissue pellets were resuspended in Matrigel (200 μL for a 50 μL pellet). The tissue suspension (50 μL) was seeded into each well of a 6-well plate in ~10 μL drops.

extract_protocol:
For white adipose tissues: RNA extraction was conducted after tissues were mechanically homogenized (Polytron PT2100, Kinematica, Bohemia, NY, USA) in 1 mL of TRI reagent. Thereafter, 200 μL of chloroform was added, the sample was vortexed, and centrifuged at 4°C. RNA extraction was completed using the RNeasy Lipid Tissue Mini Kit (Qiagen, Venlo, Netherlands), according to the manufacturer’s protocols, with the addition of the elective DNAse digestion steps. For organoids: media was collected from cultured organoids and the adherent organoids were rinsed with phosphate-buffered saline (PBS). Over ice, Cell Recovery Solution (Corning, Corning, NY, USA) was added to the cells, cultures were agitated by repeated pipetting and incubated at 4°C. Samples were transferred to microcentrifuge tubes and centrifuged at 4°C. Supernatant was removed and organoid pellet was washed in PBS and centrifugation step was repeated. RNA isolation was conducted using the Direct-zol™ RNA MiniPrep kit (Zymo Research Corp., Irvine, CA, USA), according to manufacturer’s instructions, with Trizol (Zymo Research Corp, Irvine, CA, USA) and column-based spin steps to remove the hydrogel matrix. Following RNA isolation, RNA Clean & Concentrator™ kit (Zymo Research Corp., Irvine, CA, USA) was used, according to the manufacturer’s instructions to concentrate RNA for library preparation. RNA quality and quantity was confirmed by Qubit (ThermoFisher Scientific, Waltham, MA, USA).
For white adipose tissue: RNA libraries were prepared from 500ng RNA using NEBNext Ultra II RNA Library Prep Kit for Illumina, following the manufacturer’s protocol.  Libraries were sequenced on an Illumina NovaSeq platform at a depth of 30 million reads per sample (150 bp, paired-end).  For organoids: RNA libraries from isolated organoids were prepared from 500 ng of total RNA using the Zymo-Seq RiboFree Total RNA Library Kit according to the manufacturer’s instructions.

value: Organoid isolated from lung

value: Wild-type

value: isolated at 6 weeks

tag: batch


title: WT organoid 2 replicate 3

description: Library name: C2_3


title: WT organoid 2 replicate 1

description: Library name: C2_1


title: WT organoid 1 replicate 3

description: Library name: C1_3


title: WT Organoid 1 Replicate 1

description: Library name: C1_1


title: Kras Organoid 2 Replicate 4

description: Library name: T20_4

value: Club cell-specific, tamoxifen-inducible KrasG12D


title: muscle, PH164, week 0, 24hr

description:
PH164w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: vastus lateralis muscle

value: HITT


title: Kras Organoid 2 Replicate 2

description: Library name: T20_2


title: muscle, PH164, week 0, pre

description:
PH164w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 0


title: muscle, PH162, week 16, rest

description:
PH162w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: TRAD


title: Kras Organoid 2 Replicate 3

description: Library name: T20_3


title: muscle, PH162, week 12, 3hr

description:
PH162w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: Kras Organoid 1 Replicate 2

description: Library name: T31_2


title: muscle, PH168, week 0, 3hr

description:
PH168w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: Female


title: muscle, PH162, week 12, pre

description:
PH162w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: Kras Organoid 1 Replicate 3

description: Library name: T31_3


title: ExT13_Tumor_CD8_day14_cont_28

description: Library name: Sample 4

value: Tumor

value: Lewis lung carcinoma


title: muscle, PH164, week 0, 3hr

description:
PH164w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH162, week 12, 24hr

description:
PH162w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 12


title: muscle, PH162, week 0, 3hr

description:
PH162w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6wk_gWAT_KRAS_3

description: Library name: S24

source_name: perigonadal white adipose tissue

value: perigonadal white adipose tissue

value: tamoxifen

value: 6 weeks


title: Kras Organoid 1 Replicate 4

description: Library name: T31_4


title: muscle, PH162, week 0, 24hr

description:
PH162w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: Male


title: 6wk_gWAT_KRAS_1

description: Library name: S22


title: 6wk_gWAT_KRAS_2

description: Library name: S23


title: muscle, PH156, week 16, rest

description:
PH156w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 16

value: rest


title: 6wk_gWAT_WT_3

description: Library name: S21

value: Wild-type


title: muscle, PH156, week 12, pre

description:
PH156w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: pre


title: 6wk_gWAT_WT_2

description: Library name: S20


title: muscle, PH156, week 0, pre

description:
PH156w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH156, week 12, 3hr

description:
PH156w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6wk_gWAT_WT_1

description: Library name: S19


title: 3wk_gWAT_KRAS_3

description: Library name: S12

value: Club cell-specific, tamoxifen-inducible KrasG12D

value: 3 weeks


title: muscle, PH156, week 0, 3hr

description:
PH156w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: vastus lateralis muscle

value: HITT


title: muscle, PH156, week 12, 24hr

description:
PH156w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH156, week 0, 24hr

description:
PH156w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 0


title: 3wk_gWAT_KRAS_2

description: Library name: S11


title: muscle, PH154, week 16, rest

description:
PH154w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 3wk_gWAT_KRAS_1

description: Library name: S10


title: 3wk_gWAT_WT_3

description: Library name: S09


title: 3wk_gWAT_WT_1

description: Library name: S07


title: muscle, PH162, week 0, pre

description:
PH162w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: TRAD


title: muscle, PH154, week 12, 3hr

description:
PH154w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 3wk_gWAT_WT_2

description: Library name: S08


title: muscle, PH154, week 12, 24hr

description:
PH154w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH154, week 12, pre

description:
PH154w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: Primary tumor, TGM2 KO mouse, rep3

city: Ottawa

first: Barbara

last: Vanderhyden

state: Ontario

address: 501 Smyth Rd

country: Canada

institute: Ottawa Hospital Research Institute

description: Library name: TGM2_KO_3

data_processing:
Transcript quantification for each sample was performed using Kallisto (v0.46.2) with the GRCm38 transcriptome reference and the -b 50 bootstrap option. Transcript-to-gene annotation was performed using the Ensembl GRCm38 database.
Assembly: GRCm38
Supplementary files format and content: The processed data file (.txt) contains transcript-per-million (TPM) values for each sample.

source_name: Primary tumor

extract_protocol:
RNA was extracted from primary tumors formed from intrabursal-injected ID8 Trp53-/- Brca1-/- cells using the RNeasy Mini Kit (Qiagen; 74106)
polyA Enriched RNA Library Preparation

value: Primary tumor

value: Cancer cells

value: Tgm2 knockout


title: Primary tumor, TGM2 KO mouse, rep2

description: Library name: TGM2_KO_2


title: muscle, PH154, week 0, 3hr

description:
PH154w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH154, week 0, 24hr

description:
PH154w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: Primary tumor, WT mouse, rep3

description: Library name: WT_3

value: WT


title: muscle, PH153, week 16, rest

description:
PH153w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: Primary tumor, WT mouse, rep1

description: Library name: WT_1


title: muscle, PH153, week 12, pre

description:
PH153w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 12


title: muscle, PH153, week 12, 3hr

description:
PH153w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH153, week 12, 24hr

description:
PH153w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: YGLN4SP

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

description:
Library name: Sample 14
YGLN4SP

data_processing:
cutadapt
BWA-mem alignment
macs2 peak-calling
Assembly: mm10
Supplementary files format and content: text file

source_name: Blood

extract_protocol:
The engineered hyperactive Tn5 transposase that is preloaded with DNA adapters thus removing the need for a separate annealing step.
ATAC-seq libraries were prepared for sequencing using standard Illumina protocols

value: Blood

value: T cells

value: CD8 T cells

value: CD79,CD39 DP


title: YGLN1SP

description:
Library name: Sample 12
YGLN1SP


title: muscle, PH153, week 0, pre

description:
PH153w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: Male


title: muscle, PH153, week 0, 24hr

description:
PH153w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: OLN4DP

description:
Library name: Sample 11
OLN4DP


title: YGLN3SP

description:
Library name: Sample 13
YGLN3SP


title: OLN1DP

description:
Library name: Sample 9
OLN1DP


title: muscle, PH151, week 12, pre

description:
PH151w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: pre


title: muscle, PH154, week 0, pre

description:
PH154w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH151, week 16, rest

description:
PH151w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 16

value: rest


title: muscle, PH151, week 12, 3hr

description:
PH151w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: vastus lateralis muscle


title: Primary tumor, TGM2 KO mouse, rep1

description: Library name: TGM2_KO_1


title: B16T2

description:
Library name: Sample 8
B16T2

value: CD39 SP


title: B16T1

description:
Library name: Sample 7
B16T1


title: muscle, PH151, week 12, 24hr

description:
PH151w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: Primary tumor, WT mouse, rep2

description: Library name: WT_2


title: AT3T2

description:
Library name: Sample 5
AT3T2


title: AT3T4

description:
Library name: Sample 6
AT3T4


title: muscle, PH151, week 0, 3hr

description:
PH151w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 0


title: AT3T1

description:
Library name: Sample 4
AT3T1


title: AT3LN3DP

description:
Library name: Sample 3
AT3LN3DP


title: muscle, PH151, week 0, 24hr

description:
PH151w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: TRAD


title: AT3LN2DP

description:
Library name: Sample 2
AT3LN2DP


title: muscle, PH151, week 0, pre

description:
PH151w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH153, week 0, 3hr

description:
PH153w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: HITT


title: B16-6

data_processing:
BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program
FASTQ files were aligned to human genome hg38, CellRanger software
Seurat v4.0 used to generate normalized matrix
Assembly: mm10
Supplementary files format and content: text files containing counts

source_name: blood

extract_protocol:
RNA was extracted with TriPure™ Isolation Reagent (Sigma-Aldrich) following the manufacturer’s instructions with phenol-chloroform extraction.
Libraries were constructing using the TruSeq Stranded mRNA protocol (Illumina) according to manufacturer's instructions.

value: blood

value: Aged


title: B16-4


title: muscle, PH148, week 12, 24hr

description:
PH148w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH148, week 12, 3hr

description:
PH148w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH148, week 12, pre

description:
PH148w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH148, week 0, pre

description:
PH148w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: B16-3

value: Young


title: muscle, PH148, week 0, 3hr

description:
PH148w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: AT3LN1DP

description:
Library name: Sample 1
AT3LN1DP


title: B16-5


title: OLN3DP

description:
Library name: Sample 10
OLN3DP

value: WT


title: muscle, PH148, week 0, 24hr

description:
PH148w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: B16-2


title: muscle, PH147, week 16, rest

description:
PH147w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: Female


title: muscle, PH147, week 12, 3hr

description:
PH147w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 12


title: muscle, PH147, week 12, pre

description:
PH147w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: AT3-6


title: muscle, PH148, week 16, rest

description:
PH148w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH147, week 12, 24hr

description:
PH147w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: AT3-5


title: AT3-4


title: AT3-1


title: B16-1


title: muscle, PH147, week 0, pre

description:
PH147w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH147, week 0, 24hr

description:
PH147w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH147, week 0, 3hr

description:
PH147w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: AT3-3


title: SVF, CTL_Hmgcs2KO_1,3BD_Adult, scRNAseq [multiplexed]

city: Taipei

first: Chung-Lin

last: Jiang

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads were normalized by the ‘NormalizeData’ function, and the top 2000 highly variable genes were identified by the ‘FindVariableFeatures’ function. Next, the ‘SelectIntegrationFeatures’ function and the ‘FindIntegrationAnchors’ function were used to find the suitable anchor for further integration among the top 2000 highly variable genes. After integrating 4 datasets into a single Seurat object by the ‘IntegrateData’ function, linear dimensional reduction was performed using PCA. The top 15 principal components (PCs) were taken for further analysis based on PCElbowplot. Cell clusters were identified by the ‘FindNeighbors’ function and ‘FindClusters’ function using the top 15 PCs and a resolution of 0.2. Following clustering, UMAP non-linear dimensional reduction was performed using the ‘RunUMAP’ function to visualize the dataset. Cluster specific genes were identified using ‘FindAllMarkers’ function of Seurat R package (Wilcoxon rank sum test, log2 fold change, p-value < 0.05, expression in ≥ 25% of cells) for comprehensively annotating clusters with cell type. To determine the identity of each cell cluster, the LinNeg_SVC_scRNAseq dataset from GEO dataset GSE180589 was analyzed as previously described. In addition, the cell clusters from the GEO dataset were automatically identified using the SingleR package (v 2.4.1) with MouseRNAseqData as the reference from the celldex package (v 1.12.0). Cluster specific genes identified from our dataset were compared to those from the GEO dataset (GSE180589), and the cell identity defined by SingleR was combined to determine cell identity of each cluster. Unintegrated and integrated UMAP plots were generated using the ‘DimPlot’ function. Individual UMAP plots for the given genes, violin plots and heatmaps were generated using the ‘FeaturePlot’ function, ‘VlnPlot’ function and ‘DoHeatmap’ function respectively. In parallel, to further elucidate the biological significance of the identified DEGs, enrichment analysis of these genes was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The analysis was conducted using the DAVID tool, and the results were visualized through histograms and scatter plots.
Assembly: mm10
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx

source_name: inguinal white adipose tissue

extract_protocol:
Each group of 100,000 cells was labeled separately with the Sample-Tags from the BD Mouse Immune Single-Cell Multiplexing Kit (BD Biosciences, San Jose, CA), as described in the "Single Cell Labeling with the BD Single-Cell Multiplexing Kits" protocol.
The whole transcriptome was prepared using the BD Rhapsody System following the BD "mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol". The quality and quantity of the final library were assessed using the Agilent 4200 TapeStation system with the Agilent High Sensitivity D1000 ScreenTape (Agilent Technologies, Santa Clara, CA) and a Qubit Fluorometer with the Qubit dsDNA HS Assay (Invitrogen, MA, USA), respectively. The sequencing of the final library was performed using a NovaSeq PE150 sequencer (Illumina, San Diego, CA).

value: inguinal white adipose tissue

value: stromal vascular fraction

value: mixed sample (non-demultiplexed)

tag: age


title: muscle, PH146, week 16, rest

description:
PH146w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: SVF, 1,3BD, BulkRNAseq_2

description:
p21iWAT_SVF_1,3BD_2_BulkRNAseq
B2

data_processing:
Data processing step was carried out by BIOTOOLS Co., Ltd.
To normalize gene expression, we performed two types of normalization depending on the presence of biological replicates. For experiments without biological replicates, we used the "Trimmed Mean of M-values" (TMM) normalization, which was performed using edgeR. For experiments with biological replicates, we used the "Relative Log Expression" (RLE) normalization, which was performed using DESeq2. To detect differentially expressed genes (DEGs) under two conditions, we used DEGseq (for experiments without biological replicates) and DESeq2 (for experiments with biological replicates), which are R packages based on the negative binomial distribution and Poisson distribution model, respectively.
Various enrichment analyses and network analyses were performed to gain insights into the differentially expressed genes (DEGs). Initially, the p-values obtained from DEG detection were adjusted using the Benjamini and Hochberg's approach to control the false discovery rate (FDR). Subsequently, Gene Ontology (GO) and KEGG pathway enrichment analyses of DEGs were conducted using clusterProfiler. Disease Ontology (DO) enrichment analysis was performed using the DOSE package against DO, DisGeNET, and NCG databases. Additionally, Gene Set Enrichment Analysis (GSEA) was utilized to identify enriched biological functions and activated pathways from the Molecular Signatures Database (MSigDB) with 1,000 permutations. MSigDB provides annotated gene sets for use with GSEA software, including hallmark gene sets, positional gene sets, curated gene sets, motif gene sets, computational gene sets, GO gene sets, oncogenic gene sets, and immunologic gene sets.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw counts for each sample.

extract_protocol:
RNA was harvested using TRIzol Reagent (Thermo Fisher, #15596018). 1 μg of total RNA was used for the construction of sequencing libraries.
A standardized input of 1 μg RNA per sample was used for RNAseq library preparation using the KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland).

value: wild type


title: SVF, 1,3BD, BulkRNAseq_1

description:
p21iWAT_SVF_1,3BD_1_BulkRNAseq
B1


title: muscle, PH146, week 12, 24hr

description:
PH146w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH146, week 12, pre

description:
PH146w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: pre


title: muscle, PH146, week 12, 3hr

description:
PH146w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH146, week 0, pre

description:
PH146w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH146, week 0, 24hr

description:
PH146w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: AT3-2


title: iWAT, KO, Cold, BulkRNAseq_2

description:
iWAT_Hmgcs2KO_Cold_2_BulkRNAseq
CK2

value: Hmgcs2 -/-

value: Cold


title: SVF, Water, BulkRNAseq_1

description:
p21iWAT_SVF_Water_1_BulkRNAseq
W1

value: Water


title: iWAT, CTL, Cold, BulkRNAseq_2

description:
iWAT_Hmgcs2CTL_Cold_2_BulkRNAseq
CC2

value: Hmgcs2 +/+


title: iWAT, KO, Cold, BulkRNAseq_1

description:
iWAT_Hmgcs2KO_Cold_1_BulkRNAseq
CK1


title: muscle, PH145, week 12, pre

description:
PH145w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: vastus lateralis muscle


title: muscle, PH145, week 16, rest

description:
PH145w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: HITT

value: week 16

value: rest


title: muscle, PH145, week 12, 3hr

description:
PH145w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: iWAT, CTL, Cold, BulkRNAseq_1

description:
iWAT_Hmgcs2CTL_Cold_1_BulkRNAseq
CC1


title: SVF, Water, BulkRNAseq_2

description:
p21iWAT_SVF_Water_2_BulkRNAseq
W2


title: iWAT, KO, RT, BulkRNAseq_1

description:
iWAT_Hmgcs2KO_RT_1_BulkRNAseq
RK1

value: RT


title: muscle, PH145, week 0, 24hr

description:
PH145w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 0


title: muscle, PH145, week 12, 24hr

description:
PH145w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: Female


title: muscle, PH145, week 0, pre

description:
PH145w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH145, week 0, 3hr

description:
PH145w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH144, week 16, rest

description:
PH144w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: Male


title: SVF, ObF1, 1,3BD, BulkRNAseq

address: Department of Biochemical Science and Technology, National Taiwan University, No.1, Sec.4, Roosevelt Rd., Taipei, 10617, Taiwan

description: The iWAT-SVC samples consisted of a pool of three mice at P21.

value: inguinal white adipose tissue


title: SVF, 1,3BD, BulkRNAseq_3

description:
p21iWAT_SVF_1,3BD_3_BulkRNAseq
B3

value: stromal vascular fraction


title: iWAT, CTL, RT, BulkRNAseq_2

description:
iWAT_Hmgcs2CTL_RT_2_BulkRNAseq
RC2


title: muscle, PH146, week 0, 3hr

description:
PH146w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: iWAT, KO, RT, BulkRNAseq_2

description:
iWAT_Hmgcs2KO_RT_2_BulkRNAseq
RK2


title: iWAT, CTL, RT, BulkRNAseq_1

description:
iWAT_Hmgcs2CTL_RT_1_BulkRNAseq
RC1


title: muscle, PH144, week 12, pre

description:
PH144w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 12


title: muscle, PH144, week 12, 3hr

description:
PH144w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: SVF, ObF1, Water, BulkRNAseq

institute: Department of Biochemical Science and Technology, National Taiwan University

value: wild type


title: muscle, PH144, week 12, 24hr

description:
PH144w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: SVF, LnF1, Water, BulkRNAseq


title: SVF, LnF1, 1,3BD, BulkRNAseq


title: muscle, PH144, week 0, pre

description:
PH144w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: pre


title: muscle, PH144, week 0, 3hr

description:
PH144w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH144, week 0, 24hr

description:
PH144w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH142, week 12, 3hr

description:
PH142w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: TRAD


title: muscle, PH142, week 12, pre

description:
PH142w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH142, week 16, rest

description:
PH142w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH142, week 12, 24hr

description:
PH142w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH142, week 0, 3hr

description:
PH142w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH142, week 0, pre

description:
PH142w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH142, week 0, 24hr

description:
PH142w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: SVF, Water, BulkRNAseq_3

description:
p21iWAT_SVF_Water_3_BulkRNAseq
W3


title: muscle, PH140, week 16, rest

description:
PH140w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH140, week 12, 3hr

description:
PH140w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH140, week 12, 24hr

description:
PH140w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH140, week 0, pre

description:
PH140w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH140, week 0, 3hr

description:
PH140w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH140, week 0, 24hr

description:
PH140w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: E11.5 WT  embryonic caudal region biol rep 1

city: wenzhou

first: yu

last: chen

address: 270 West Xueyuan Road

country: China

institute: Wenzhou Medical University

description: Library name: SAMPLES 9

data_processing:
Data quality control: Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: embryonic caudal region

extract_protocol:
RNAs were extracted using TRIzol reagent (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryonic caudal region

value: not cell line

value: embryonic cells

value: WT


title: E11.5 Ednrb-/-  embryonic trunk region biol rep 4

description: Library name: SAMPLES 8

source_name: embryonic trunk region

value: embryonic trunk region

value: Ednrb-/-


title: E11.5 Ednrb-/-  embryonic caudal region biol rep 4

description: Library name: SAMPLES 4


title: E11.5 Ednrb-/-  embryonic trunk region biol rep 2

description: Library name: SAMPLES 6


title: E11.5 Ednrb-/-  embryonic caudal region biol rep 1

description: Library name: SAMPLES 1


title: E11.5 Ednrb-/-  embryonic caudal region biol rep 2

description: Library name: SAMPLES 2


title: E11.5 WT  embryonic caudal region biol rep 2

description: Library name: SAMPLES 10


title: E11.5 Ednrb-/-  embryonic caudal region biol rep 3

description: Library name: SAMPLES 3


title: E11.5 Ednrb-/-  embryonic trunk region biol rep 1

description: Library name: SAMPLES 5


title: E11.5 Ednrb-/-  embryonic trunk region biol rep 3

description: Library name: SAMPLES 7


title: muscle, PH140, week 12, pre

description:
PH140w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: vastus lateralis muscle

value: HITT


title: muscle, PH139, week 12, 24hr

description:
PH139w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH139, week 0, pre

description:
PH139w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 0


title: muscle, PH139, week 12, 3hr

description:
PH139w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: Female


title: muscle, PH139, week 0, 3hr

description:
PH139w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH139, week 16, rest

description:
PH139w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 16

value: rest


title: Conceptus at GD 6.5 sample 2 second run

city: Edmonton

first: Meghan

last: Riddell

state: AB

institute: University of Alberta

description: Library name: D10Y_E65 run 2

data_processing:
Demultiplexing, barcode assignment, and gene counts were performed using CellRanger Cloud analysis.
Assembly: Mousme mm10
Supplementary files format and content: Tab separated values, and matrix files

source_name: Conceptus

extract_protocol:
The gestational sacs were mechanically dissociated using surgical scissors while on ice-cold PBS. Afterwards, the tissue was enzimatically dissociated utilizing 1mg/mL of Collagenase type II. Four serial 30 minutes digestions were performed on the tissue. For the first digestion, we used twice the volume as the tissue. For the further dissections, the same volume as the tissue was used.
Libraries were constructed using the Illumina Stranded mRNA prep kit following manufacturers instructions

value: Conceptus

tag: strain


title: Conceptus at GD 10.5, sample 1 run 1

description: Library name: D9Y_E105_1 run 1


title: Conceptus at GD 6.5 sample 2 first run

description: Library name: D10Y_E65 run 1


title: Conceptus at GD 10.5, sample 1 run 2

description: Library name: D9Y_E105_1 run 2


title: Conceptus at GD 10.5, sample 2 run 1

description: Library name: D9Y_E105_2 run 1


title: Conceptus at GD 10.5, sample 2 run 2

description: Library name: D9Y_E105_2 run 2


title: muscle, PH139, week 12, pre

description:
PH139w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 12


title: E11.5 WT  embryonic trunk region biol rep 4

description: Library name: SAMPLES 16


title: E11.5 WT  embryonic caudal region biol rep 4

description: Library name: SAMPLES 12


title: E11.5 WT  embryonic trunk region biol rep 1

description: Library name: SAMPLES 13


title: E11.5 WT  embryonic caudal region biol rep 3

description: Library name: SAMPLES 11


title: E11.5 WT  embryonic trunk region biol rep 3

description: Library name: SAMPLES 15


title: E11.5 WT  embryonic trunk region biol rep 2

description: Library name: SAMPLES 14


title: muscle, PH138, week 16, rest

description:
PH138w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: Male


title: muscle, PH138, week 12, 3hr

description:
PH138w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: LTbR agonist, Cd45 positive cells, scRNAseq

first: Fumiaki

last: Kanamori

state: FL

address: 600 5th Street S

department: Department of Orthopaedic Surgery

institute: Johns Hopkins All Children’s Hospital.

description:
10X genomics
C_Cd45_positive

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger Count v.7.1.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
KPC tumors were surgically resected. Tumors were excised and mechanically dissociated into smaller fragments. These fragments underwent enzymatic digestion with LiberaseTM (300 μg/mL) and mechanical dissociation using the GentleMACS Octo dissociator (protocol: hard tumor dissociation, TDK-3, 1 hour at 37°C). Following dissociation, the cell suspension was filtered using a 70 μm strainer and then washed twice with RPMI medium at 400 rcf for 5 minutes. After dead/live cell staining and blocking non-specific binding using anti-FcRII/III (Biolegends) for 10 minutes, cells were stained with anti-CD45 antibody for 1 hour at 4C. Live CD45+ leukocytes were sorted by CytoFLEX SRT (Beckman).
Library generation was performed according to the manufacturer’s instruction (Chromium GEM-X Single Cell 5’ Reagent Kits v3, 10X Genomics). Briefly, Cd45 positive cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).   Poly-adenylated mRNA contained in each single GEM was reverse transcripted to cDNA that includes an Ilumina R1 primer, Unique Molecular Identifier (UMI), and 10X barcode.  The barcoded cDNA was cleaned up with Dynabeads MyOne SILANE, amplified by PCR, and appropriate size fragments were selected with SPRI select.  For gene expression library construction, Ilumina R2 primer, paired-end constructs with P5 and P7, and sample index were added.

value: tumor

value: KPC

value: Cd45 positive cells

value: LTbR agonist


title: muscle, PH139, week 0, 24hr

description:
PH139w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: TRAD


title: Conceptus at GD 6.5 sample 1 second run

description: Library name: D8Y_E65 run 2


title: STING agonist, Cd45 positive cells, scRNAseq

description:
10X genomics
B_Cd45_positive

value: STING agonist


title: STING and LTbR agonist, Cd45 positive cells, scRNAseq

description:
10X genomics
D_Cd45_positive

value: STING and LTbR agonist


title: muscle, PH138, week 0, pre

description:
PH138w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: pre


title: Untreated, Cd45 positive cells, scRNAseq

description:
10X genomics
A_Cd45_positive

value: Untreated


title: Conceptus at GD 6.5 sample 1 first run

description: Library name: D8Y_E65 run 1


title: muscle, PH138, week 12, pre

description:
PH138w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: vastus lateralis muscle

value: HITT


title: muscle, PH138, week 0, 3hr

description:
PH138w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 0


title: muscle, PH138, week 0, 24hr

description:
PH138w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH137, week 16, rest

description:
PH137w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 16


title: muscle, PH137, week 12, pre

description:
PH137w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH137, week 12, 3hr

description:
PH137w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH137, week 0, 3hr

description:
PH137w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH137, week 0, 24hr

description:
PH137w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH137, week 12, 24hr

description:
PH137w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH138, week 12, 24hr

description:
PH138w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH137, week 0, pre

description:
PH137w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH136, week 16, rest

description:
PH136w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: rest

value: Female


title: muscle, PH136, week 12, pre

description:
PH136w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 12


title: SUM149-treated with negative control gapmer, replicate 3

type: RNA

city: Halifax

first: Paola

last: Marcato

address: 5850 College street

department: Pathology

institute: Dalhousie university

description: Cultured cancer cells

hyb_protocol: 16h at 48oC, Affymetrix miRNA 4.0

scan_protocol: Affymetrix GeneChip Scanner 3000(Scanner#4)

data_processing: RMA expression value derived from Expression Console software

label: biotin

source_name: Breast cancer cells

label_protocol: FlashTag Biotin HSR RNA Labeling Kit

growth_protocol: The cell lines were obtained from the American Type Culture Collection (ATCC) and were cultured as per ATCC guidelines

extract_protocol: cells were collected and RNA purified using the mirVana™ miRNA Isolation Kit following the manufacturer’s instructions.

treatment_protocol: cultured cells treated for 48hours with GapmeRs


title: muscle, PH136, week 0, 3hr

description:
PH136w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: SUM149-treated with negative control gapmer, replicate 2

description: Cultured cancer cells


title: MDA-MB-468-treated with negative control gapmer, replicate 3

description: Cultured cancer cells


title: SUM149-treated with Gapmer 3, replicate 1

description: Cultured cancer cells


title: SUM149-treated with negative control gapmer, replicate 1

description: Cultured cancer cells


title: muscle, PH136, week 0, pre

description:
PH136w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH133, week 16, rest

description:
PH133w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: Male


title: MDA-MB-468-treated with Gapmer 3, replicate 2

description: Cultured cancer cells


title: SUM149-treated with Gapmer 4, replicate 3

description: Cultured cancer cells


title: SUM149-treated with Gapmer 3, replicate 2

description: Cultured cancer cells


title: MDA-MB-468-treated with Gapmer 3, replicate 3

description: Cultured cancer cells


title: SUM149-treated with Gapmer 3, replicate 3

description: Cultured cancer cells


title: SUM149-treated with Gapmer 4, replicate 2

description: Cultured cancer cells


title: SUM149-treated with Gapmer 4, replicate 1

description: Cultured cancer cells


title: muscle, PH133, week 12, pre

description:
PH133w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH133, week 12, 3hr

description:
PH133w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: MDA-MB-468-treated with negative control gapmer, replicate 2

description: Cultured cancer cells


title: MDA-MB-468-treated with Gapmer 4, replicate 3

description: Cultured cancer cells


title: p1d2s2-4

city: Daejeon

first: Seung-Jae

middle: V

last: Lee

address: 291, Daehak-ro, Yuseong-gu, Daejeon, Republic of Korea

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description: Library name: Sample 15

data_processing:
Sequencing pairs were aligned to the C. elegans genome WBcel235 (ce11) and Ensembl transcriptome (release 95) by using STAR (v.2.7.0e). Aligned pairs on genes or transcripts were quantified by using RSEM (v.1.3.1). Detailed parameters of alignment and quantification were calculated by following guidelines of ENCODE long RNA-Seq processing pipeline.
Assembly: WBcel235 (ce11)
Supplementary files format and content: txt files with read counts were generated by using RSEM (v.1.3.1)

organism: Caenorhabditis elegans

source_name: Whole body

growth_protocol: All strains were maintained at 20°C, unless stated otherwise. They were grown on NGM plates as previously described in 'Maintenance of C. elegans (Stiernagle T, WormBook, 2006)'.

extract_protocol:
RNA extraction was performed as previously described (Jeong et al., 2020) with minor modifications. Synchronized animals at day 1 were harvested with S-basal buffer with 0.01% polyethylene glycol. Total RNA was extracted using RNAiso Plus and cDNA was obtained using ImProm-II Reverse Transcriptase (A3802, Promega, Madison, WI, USA) with hexamer random primers.
Libraries were constructed with TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, CA, USA) by Macrogen Inc. (Seoul, South Korea) following the manufacture’s instruction.

treatment_protocol: Synchronized wild-type(N2), daf-2(e1370), pelo-1(cc2849); skih-2(cc2854) and daf-2(e1370) pelo-1(cc2849); skih-2(cc2854) animals were placed on NGM plates seeded with 1 ml cultured OP50 bacteria and grown until reaching a pre-fertile young adult stage. Synchronized worms were harvested and washed twice with M9 buffer. Three or four biological repeats of the samples were used for all conditions.

value: Whole body

tag: development

value: Day 1 adult


title: muscle, PH136, week 12, 3hr

description:
PH136w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: MDA-MB-468-treated with negative control gapmer, replicate 1

description: Cultured cancer cells


title: p1d2s2-3

description: Library name: Sample 14


title: MDA-MB-468-treated with Gapmer 3, replicate 1

description: Cultured cancer cells


title: muscle, PH133, week 0, pre

description:
PH133w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH133, week 12, 24hr

description:
PH133w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH133, week 0, 3hr

description:
PH133w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: p1d2s2-1

description: Library name: Sample 12


title: muscle, PH136, week 0, 24hr

description:
PH136w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: p1d2s2-2

description: Library name: Sample 13


title: p1s2-3

description: Library name: Sample 10


title: MDA-MB-468-treated with Gapmer 4, replicate 2

description: Cultured cancer cells


title: muscle, PH130, week 16, rest

description:
PH130w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH133, week 0, 24hr

description:
PH133w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH130, week 12, 3hr

description:
PH130w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: p1s2-1

description: Library name: Sample 8


title: muscle, PH130, week 12, pre

description:
PH130w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH130, week 12, 24hr

description:
PH130w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: MDA-MB-468-treated with Gapmer 4, replicate 1

description: Cultured cancer cells


title: muscle, PH130, week 0, pre

description:
PH130w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: d2-2

description: Library name: Sample 5


title: muscle, PH130, week 0, 3hr

description:
PH130w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: d2-3

description: Library name: Sample 6


title: N2-4

description: Library name: Sample 4

value: wild type


title: muscle, PH129, week 16, rest

description:
PH129w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: N2-3

description: Library name: Sample 3


title: muscle, PH130, week 0, 24hr

description:
PH130w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH129, week 12, pre

description:
PH129w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: N2-2

description: Library name: Sample 2


title: N2-1

description: Library name: Sample 1


title: p1s2-4

description: Library name: Sample 11


title: muscle, PH129, week 12, 3hr

description:
PH129w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH129, week 12, 24hr

description:
PH129w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH129, week 0, pre

description:
PH129w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH129, week 0, 3hr

description:
PH129w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246173_R03C02 CD4+

type: genomic

city: Boston

first: Benjamin

middle: A

last: Raby

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: Sample collected in BD Vacutainer CPT tube with sodium heparin (Fisher Scientific, Hampton, HG)

hyb_protocol: Using standard Illumina Infinium Human Methylation 450K BeadChip array hyb protocol.

scan_protocol: Using standard Illumina Infinium Human Methylation 450K BeadChip array scan protocol.

data_processing: Normalization was performed using the within-array combination of Noob (Triche et al. 2013) in R package “minfi” and BMIQ (Teschendorff et al. 2013) in R package “wateRmelon”. The minfi package was used to identify and remove 25,165 probes with SNPs. Sex was imputed by DNA methylation and 23 samples were removed due to mismatch between reported and genetic imputed sex. ComBat (Johnson, 2017) from the sva R package (Leek, 2023) was used for batch effect correction, transforming to m-values, then back transforming to beta-values.

label: Cy3, Cy5

molecule: genomic DNA

source_name: CD4 + T-Cells from CPT Tubes

label_protocol: Cy3, Cy5

extract_protocol: PureGene Blood Kit (Qiagen, Germantown, Maryland), AllPrep DNA Mini Kit (Qiagen)

tag: sample id

tag: subject id

value: CD4 + T-Cells from CPT Tubes

value: M

tag: asthma

value: N


title: muscle, PH129, week 0, 24hr

description:
PH129w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: TRAD


title: 7800246173_R06C01 CD4+

value: Y


title: 7800246173_R05C01 CD4+


title: p1s2-2

description: Library name: Sample 9


title: d2-4

description: Library name: Sample 7


title: muscle, PH119, week 12, pre

description:
PH119w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: pre


title: 7800246173_R04C01 CD4+

value: F


title: muscle, PH119, week 16, rest

description:
PH119w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: vastus lateralis muscle


title: muscle, PH119, week 12, 3hr

description:
PH119w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246173_R01C01 CD4+


title: 7800246173_R03C01 CD4+


title: muscle, PH119, week 12, 24hr

description:
PH119w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH119, week 0, pre

description:
PH119w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 0


title: 7800246172_R06C02 CD4+


title: muscle, PH119, week 0, 24hr

description:
PH119w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH119, week 0, 3hr

description:
PH119w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246172_R04C02 CD4+


title: 7800246172_R05C02 CD4+


title: 7800246173_R02C02 CD4+


title: muscle, PH117, week 12, pre

description:
PH117w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246173_R01C02 CD4+


title: 7800246172_R01C02 CD4+


title: 7800246172_R06C01 CD4+


title: 7800246172_R05C01 CD4+


title: 7800246172_R04C01 CD4+


title: muscle, PH117, week 12, 24hr

description:
PH117w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH117, week 0, pre

description:
PH117w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH117, week 0, 3hr

description:
PH117w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246172_R03C01 CD4+


title: muscle, PH117, week 0, 24hr

description:
PH117w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246172_R02C01 CD4+


title: muscle, PH102, week 16, rest

description:
PH102w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 16


title: 7800246172_R01C01 CD4+


title: 7800246173_R02C01 CD4+


title: muscle, PH102, week 12, pre

description:
PH102w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH102, week 12, 3hr

description:
PH102w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246171_R06C02 CD4+

description: Sample collected in BD Vacutainer CPT tube with sodium heparin (Fisher Scientific, Hampton, HG)


title: 7800246172_R03C02 CD4+


title: 7800246171_R03C02 CD4+


title: 7800246171_R05C02 CD4+


title: 7800246171_R04C02 CD4+


title: muscle, PH117, week 16, rest

description:
PH117w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: rest


title: 7800246171_R02C02 CD4+


title: muscle, PH117, week 12, 3hr

description:
PH117w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246171_R04C01 CD4+


title: muscle, PH102, week 0, pre

description:
PH102w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH102, week 0, 24hr

description:
PH102w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246171_R03C01 CD4+


title: 7800246171_R01C01 CD4+


title: 7800246171_R02C01 CD4+


title: muscle, PH095, week 12, 24hr

description:
PH095w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH095, week 12, 3hr

description:
PH095w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH095, week 16, rest

description:
PH095w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH095, week 12, pre

description:
PH095w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246161_R05C02 CD4+


title: muscle, PH102, week 12, 24hr

description:
PH102w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246161_R02C02 CD4+


title: muscle, PH095, week 0, pre

description:
PH095w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246161_R03C02 CD4+


title: muscle, PH095, week 0, 3hr

description:
PH095w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246161_R01C02 CD4+


title: muscle, PH095, week 0, 24hr

description:
PH095w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH102, week 0, 3hr

description:
PH102w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246161_R06C01 CD4+


title: muscle, PH091, week 12, pre

description:
PH091w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: HITT

value: Female


title: muscle, PH091, week 16, rest

description:
PH091w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH091, week 12, 3hr

description:
PH091w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: week 12


title: 7800246161_R03C01 CD4+

description: Sample collected in BD Vacutainer CPT tube with sodium heparin (Fisher Scientific, Hampton, HG)


title: muscle, PH091, week 0, 3hr

description:
PH091w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246161_R05C01 CD4+


title: 7800246161_R02C01 CD4+


title: muscle, PH091, week 0, pre

description:
PH091w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246161_R01C01 CD4+


title: muscle, PH091, week 0, 24hr

description:
PH091w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246160_R06C02 CD4+


title: muscle, PH087, week 16, rest

description:
PH087w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt

value: Male


title: muscle, PH087, week 12, pre

description:
PH087w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH087, week 12, 3hr

description:
PH087w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246160_R01C02 CD4+


title: 7800246160_R04C02 CD4+


title: muscle, PH087, week 12, 24hr

description:
PH087w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246160_R03C02 CD4+


title: muscle, PH087, week 0, pre

description:
PH087w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246160_R06C01 CD4+


title: 7800246161_R04C01 CD4+


title: 7800246160_R04C01 CD4+


title: muscle, PH087, week 0, 24hr

description:
PH087w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH084, week 12, pre

description:
PH084w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH087, week 0, 3hr

description:
PH087w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246160_R03C01 CD4+


title: muscle, PH084, week 16, rest

description:
PH084w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH084, week 12, 24hr

description:
PH084w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246156_R05C02 CD4+


title: 7800246160_R02C01 CD4+


title: muscle, PH084, week 12, 3hr

description:
PH084w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH084, week 0, pre

description:
PH084w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246156_R03C02 CD4+


title: muscle, PH084, week 0, 3hr

description:
PH084w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246156_R04C02 CD4+

description: Sample collected in BD Vacutainer CPT tube with sodium heparin (Fisher Scientific, Hampton, HG)


title: 7800246156_R01C02 CD4+


title: 7800246156_R02C02 CD4+


title: muscle, PH083, week 16, rest

description:
PH083w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246160_R05C02 CD4+


title: muscle, PH136, week 12, 24hr

description:
PH136w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH083, week 12, pre

description:
PH083w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246160_R05C01 CD4+


title: muscle, PH083, week 12, 3hr

description:
PH083w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246156_R04C01 CD4+


title: muscle, PH083, week 12, 24hr

description:
PH083w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH083, week 0, pre

description:
PH083w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246156_R03C01 CD4+


title: 7800246156_R05C01 CD4+


title: muscle, PH083, week 0, 3hr

description:
PH083w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246156_R02C01 CD4+


title: 7800246141_R06C02 CD4+


title: muscle, PH080, week 16, rest

description:
PH080w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246156_R01C01 CD4+


title: muscle, PH083, week 0, 24hr

description:
PH083w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH084, week 0, 24hr

description:
PH084w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246141_R05C02 CD4+


title: muscle, PH080, week 12, 3hr

description:
PH080w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH080, week 12, pre

description:
PH080w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246141_R04C02 CD4+


title: muscle, PH080, week 12, 24hr

description:
PH080w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246141_R02C02 CD4+


title: 7800246141_R03C02 CD4+


title: muscle, PH080, week 0, 3hr

description:
PH080w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246141_R01C02 CD4+


title: muscle, PH080, week 0, 24hr

description:
PH080w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246156_R06C01 CD4+


title: 7800246141_R06C01 CD4+


title: muscle, PH079, week 16, rest

description:
PH079w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246141_R05C01 CD4+

description: Sample collected in BD Vacutainer CPT tube with sodium heparin (Fisher Scientific, Hampton, HG)


title: muscle, PH079, week 12, pre

description:
PH079w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246141_R04C01 CD4+


title: 7800246141_R03C01 CD4+


title: muscle, PH079, week 12, 3hr

description:
PH079w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH079, week 0, pre

description:
PH079w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 7800246141_R01C01 CD4+


title: 7800246141_R02C01 CD4+


title: muscle, PH079, week 12, 24hr

description:
PH079w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH080, week 0, pre

description:
PH080w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609108_R04C01 CD4+


title: 6285609108_R02C01 CD4+


title: 6285609108_R05C01 CD4+


title: 6285609108_R03C01 CD4+


title: 6285609108_R01C01 CD4+


title: muscle, PH078, week 12, 3hr

description:
PH078w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH078, week 12, pre

description:
PH078w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH079, week 0, 3hr

description:
PH079w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH079, week 0, 24hr

description:
PH079w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH078, week 16, rest

description:
PH078w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH078, week 12, 24hr

description:
PH078w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH078, week 0, 3hr

description:
PH078w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609107_R06C02 CD4+


title: muscle, PH078, week 0, pre

description:
PH078w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609107_R06C01 CD4+


title: muscle, PH078, week 0, 24hr

description:
PH078w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609107_R05C02 CD4+


title: 6285609107_R05C01 CD4+


title: 6285609107_R04C02 CD4+


title: muscle, PH075, week 12, pre

description:
PH075w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH075, week 12, 3hr

description:
PH075w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609108_R06C01 CD4+

description: Sample collected in BD Vacutainer CPT tube with sodium heparin (Fisher Scientific, Hampton, HG)


title: 6285609107_R04C01 CD4+


title: muscle, PH075, week 12, 24hr

description:
PH075w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609107_R03C02 CD4+


title: muscle, PH075, week 0, pre

description:
PH075w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609107_R02C02 CD4+


title: 6285609107_R02C01 CD4+


title: 6285609107_R01C02 CD4+


title: muscle, PH075, week 0, 3hr

description:
PH075w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609102_R05C02 CD4+


title: 6285609102_R06C02 CD4+


title: muscle, PH075, week 0, 24hr

description:
PH075w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH075, week 16, rest

description:
PH075w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH072, week 0, pre

description:
PH072w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH072, week 12, 3hr

description:
PH072w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH072, week 0, 3hr

description:
PH072w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609102_R06C01 CD4+


title: muscle, PH072, week 12, 24hr

description:
PH072w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH072, week 0, 24hr

description:
PH072w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609102_R04C02 CD4+


title: 6285609102_R04C01 CD4+


title: muscle, PH067, week 16, rest

description:
PH067w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609102_R03C02 CD4+


title: muscle, PH072, week 12, pre

description:
PH072w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609107_R03C01 CD4+


title: 6285609102_R02C02 CD4+


title: 6285609107_R01C01 CD4+


title: 6285609102_R03C01 CD4+


title: 6285609102_R02C01 CD4+


title: 6285609102_R01C02 CD4+


title: muscle, PH067, week 12, 24hr

description:
PH067w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH067, week 12, 3hr

description:
PH067w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH072, week 16, rest

description:
PH072w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH067, week 0, pre

description:
PH067w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609102_R01C01 CD4+

description: Sample collected in BD Vacutainer CPT tube with sodium heparin (Fisher Scientific, Hampton, HG)


title: muscle, PH067, week 0, 24hr

description:
PH067w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH067, week 0, 3hr

description:
PH067w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609101_R06C01 CD4+


title: 6285609101_R05C02 CD4+


title: muscle, PH065, week 16, rest

description:
PH065w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH065, week 12, pre

description:
PH065w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609101_R04C02 CD4+


title: 6285609101_R03C02 CD4+


title: muscle, PH065, week 12, 3hr

description:
PH065w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609101_R05C01 CD4+


title: muscle, PH067, week 12, pre

description:
PH067w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH065, week 0, 3hr

description:
PH065w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609101_R01C02 CD4+


title: 6285609101_R03C01 CD4+


title: muscle, PH065, week 0, 24hr

description:
PH065w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH065, week 0, pre

description:
PH065w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609077_R06C02 CD4+


title: muscle, PH063, week 12, pre

description:
PH063w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609101_R01C01 CD4+


title: muscle, PH063, week 16, rest

description:
PH063w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609077_R05C01 CD4+


title: muscle, PH063, week 12, 24hr

description:
PH063w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609077_R05C02 CD4+


title: muscle, PH063, week 12, 3hr

description:
PH063w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609077_R04C02 CD4+


title: 6285609077_R04C01 CD4+


title: muscle, PH063, week 0, 3hr

description:
PH063w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609077_R03C01 CD4+


title: muscle, PH063, week 0, 24hr

description:
PH063w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH065, week 12, 24hr

description:
PH065w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH063, week 0, pre

description:
PH063w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH062, week 12, pre

description:
PH062w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH062, week 16, rest

description:
PH062w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609077_R02C01 CD4+

description: Sample collected in BD Vacutainer CPT tube with sodium heparin (Fisher Scientific, Hampton, HG)


title: 6285609077_R03C02 CD4+


title: 6285609077_R02C02 CD4+


title: 6285609077_R01C02 CD4+


title: muscle, PH062, week 12, 24hr

description:
PH062w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609077_R01C01 CD4+


title: 6285609003_R06C01 CD4+


title: 6285609003_R06C02 CD4+


title: muscle, PH062, week 0, 3hr

description:
PH062w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH062, week 0, pre

description:
PH062w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH058, week 12, pre

description:
PH058w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609003_R05C01 CD4+


title: muscle, PH062, week 0, 24hr

description:
PH062w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH058, week 16, rest

description:
PH058w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH058, week 12, 3hr

description:
PH058w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609003_R04C01 CD4+


title: muscle, PH058, week 12, 24hr

description:
PH058w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609003_R03C02 CD4+


title: muscle, PH058, week 0, pre

description:
PH058w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609003_R03C01 CD4+


title: muscle, PH058, week 0, 3hr

description:
PH058w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609003_R02C02 CD4+


title: 6285609003_R02C01 CD4+


title: 6285609003_R01C02 CD4+


title: muscle, PH056, week 12, pre

description:
PH056w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609003_R01C01 CD4+


title: muscle, PH056, week 16, rest

description:
PH056w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009092_R06C02 CD4+


title: 6229009092_R05C02 CD4+


title: muscle, PH056, week 12, 3hr

description:
PH056w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH056, week 0, pre

description:
PH056w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6285609003_R04C02 CD4+


title: muscle, PH056, week 12, 24hr

description:
PH056w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009092_R04C02 CD4+


title: muscle, PH056, week 0, 3hr

description:
PH056w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH056, week 0, 24hr

description:
PH056w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009092_R03C02 CD4+

description: Sample collected in BD Vacutainer CPT tube with sodium heparin (Fisher Scientific, Hampton, HG)


title: 6229009092_R01C02 CD4+


title: 6285609003_R05C02 CD4+


title: muscle, PH054, week 16, rest

description:
PH054w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009092_R02C02 CD4+


title: 6229009092_R06C01 CD4+


title: muscle, PH058, week 0, 24hr

description:
PH058w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH054, week 12, pre

description:
PH054w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH054, week 12, 24hr

description:
PH054w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009092_R03C01 CD4+


title: 6229009092_R02C01 CD4+


title: muscle, PH054, week 0, pre

description:
PH054w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009092_R05C01 CD4+


title: muscle, PH054, week 0, 24hr

description:
PH054w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH054, week 0, 3hr

description:
PH054w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH051, week 16, rest

description:
PH051w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH051, week 12, pre

description:
PH051w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH051, week 12, 3hr

description:
PH051w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009092_R01C01 CD4+


title: 6229009114_R06C02 CD4+


title: muscle, PH062, week 12, 3hr

description:
PH062w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009114_R03C02 CD4+


title: muscle, PH051, week 12, 24hr

description:
PH051w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009114_R02C02 CD4+


title: muscle, PH051, week 0, pre

description:
PH051w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009114_R04C02 CD4+


title: muscle, PH051, week 0, 3hr

description:
PH051w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009092_R04C01 CD4+


title: 6229009114_R06C01 CD4+


title: muscle, PH054, week 12, 3hr

description:
PH054w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009114_R04C01 CD4+


title: muscle, PH051, week 0, 24hr

description:
PH051w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH050, week 16, rest

description:
PH050w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009114_R03C01 CD4+

description: Sample collected in BD Vacutainer CPT tube with sodium heparin (Fisher Scientific, Hampton, HG)


title: muscle, PH050, week 12, pre

description:
PH050w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009114_R02C01 CD4+


title: muscle, PH050, week 12, 3hr

description:
PH050w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009114_R01C01 CD4+


title: 6229009082_R06C02 CD4+


title: 6229009114_R05C02 CD4+


title: 6229009082_R05C02 CD4+


title: 6229009082_R04C02 CD4+


title: muscle, PH050, week 0, pre

description:
PH050w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH050, week 0, 3hr

description:
PH050w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009114_R01C02 CD4+


title: muscle, PH049, week 16, rest

description:
PH049w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009082_R02C02 CD4+


title: 6229009082_R03C02 CD4+


title: muscle, PH049, week 12, pre

description:
PH049w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH049, week 12, 3hr

description:
PH049w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH049, week 0, pre

description:
PH049w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH049, week 12, 24hr

description:
PH049w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009082_R03C01 CD4+


title: 6229009082_R05C01 CD4+


title: 6229009129_R06C02 CD4+


title: muscle, PH049, week 0, 3hr

description:
PH049w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009129_R05C02 CD4+


title: 6229009082_R02C01 CD4+


title: muscle, PH048, week 12, pre

description:
PH048w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH049, week 0, 24hr

description:
PH049w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH050, week 12, 24hr

description:
PH050w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH048, week 12, 3hr

description:
PH048w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009129_R03C02 CD4+


title: 6229009129_R04C02 CD4+


title: muscle, PH048, week 12, 24hr

description:
PH048w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009129_R06C01 CD4+


title: muscle, PH048, week 0, pre

description:
PH048w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH050, week 0, 24hr

description:
PH050w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH048, week 0, 3hr

description:
PH048w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009129_R05C01 CD4+

description: Sample collected in BD Vacutainer CPT tube with sodium heparin (Fisher Scientific, Hampton, HG)


title: 6229009082_R04C01 CD4+


title: 6229009129_R04C01 CD4+


title: muscle, PH048, week 0, 24hr

description:
PH048w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009061_R05C02 CD4+


title: 6229009129_R03C01 CD4+


title: 6229009061_R04C02 CD4+


title: muscle, PH047, week 12, 24hr

description:
PH047w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009061_R02C02 CD4+


title: 6229009061_R03C02 CD4+


title: 6229009061_R01C02 CD4+


title: muscle, PH047, week 0, 24hr

description:
PH047w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009061_R06C01 CD4+


title: muscle, PH045, week 16, rest

description:
PH045w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009061_R05C01 CD4+


title: 6229009061_R04C01 CD4+


title: 6229009061_R03C01 CD4+


title: muscle, PH045, week 12, 3hr

description:
PH045w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH047, week 0, 3hr

description:
PH047w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009061_R01C01 CD4+


title: muscle, PH045, week 12, pre

description:
PH045w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009104_R06C02 CD4+


title: 6229009104_R05C02 CD4+


title: muscle, PH047, week 12, pre

description:
PH047w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH045, week 0, 3hr

description:
PH045w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH045, week 0, 24hr

description:
PH045w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009104_R04C02 CD4+


title: muscle, PH047, week 12, 3hr

description:
PH047w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH047, week 16, rest

description:
PH047w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009104_R03C02 CD4+


title: muscle, PH047, week 0, pre

description:
PH047w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH044, week 16, rest

description:
PH044w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009104_R01C02 CD4+


title: muscle, PH044, week 12, 3hr

description:
PH044w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH044, week 12, pre

description:
PH044w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH044, week 12, 24hr

description:
PH044w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009104_R06C01 CD4+

description: Sample collected in BD Vacutainer CPT tube with sodium heparin (Fisher Scientific, Hampton, HG)


title: muscle, PH044, week 0, 3hr

description:
PH044w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009061_R02C01 CD4+


title: muscle, PH044, week 0, pre

description:
PH044w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH045, week 12, 24hr

description:
PH045w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH044, week 0, 24hr

description:
PH044w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009104_R04C01 CD4+


title: muscle, PH045, week 0, pre

description:
PH045w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009104_R05C01 CD4+


title: muscle, PH043, week 16, rest

description:
PH043w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009104_R03C01 CD4+


title: muscle, PH043, week 12, 3hr

description:
PH043w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009104_R01C01 CD4+


title: 6229009108_R05C02 CD4+


title: 6229009108_R04C02 CD4+


title: muscle, PH043, week 12, pre

description:
PH043w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009108_R03C02 CD4+


title: muscle, PH043, week 0, pre

description:
PH043w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH043, week 12, 24hr

description:
PH043w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH043, week 0, 24hr

description:
PH043w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009108_R06C02 CD4+


title: 6229009104_R02C02 CD4+


title: 6229009108_R02C02 CD4+


title: 6229009108_R01C02 CD4+


title: 6229009108_R06C01 CD4+


title: muscle, PH042, week 16, rest

description:
PH042w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009108_R05C01 CD4+


title: muscle, PH042, week 12, pre

description:
PH042w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH042, week 12, 3hr

description:
PH042w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH042, week 12, 24hr

description:
PH042w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009108_R04C01 CD4+


title: muscle, PH042, week 0, pre

description:
PH042w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009108_R01C01 CD4+

description: Sample collected in BD Vacutainer CPT tube with sodium heparin (Fisher Scientific, Hampton, HG)


title: muscle, PH042, week 0, 24hr

description:
PH042w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH042, week 0, 3hr

description:
PH042w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH041, week 16, rest

description:
PH041w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009108_R02C01 CD4+


title: 6229009113_R06C02 CD4+


title: muscle, PH041, week 12, pre

description:
PH041w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH043, week 0, 3hr

description:
PH043w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009113_R05C02 CD4+


title: 6229009113_R03C02 CD4+


title: 6229009113_R02C02 CD4+


title: muscle, PH041, week 12, 24hr

description:
PH041w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009113_R04C02 CD4+


title: muscle, PH041, week 12, 3hr

description:
PH041w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH041, week 0, 3hr

description:
PH041w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009113_R01C02 CD4+


title: muscle, PH041, week 0, 24hr

description:
PH041w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009113_R05C01 CD4+


title: 6229009113_R04C01 CD4+


title: 6229009108_R03C01 CD4+


title: muscle, PH039, week 16, rest

description:
PH039w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009113_R03C01 CD4+


title: muscle, PH039, week 12, 24hr

description:
PH039w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH039, week 12, 3hr

description:
PH039w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009113_R01C01 CD4+


title: muscle, PH039, week 0, 3hr

description:
PH039w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009051_R06C02 CD4+


title: 6229009113_R02C01 CD4+


title: muscle, PH039, week 0, 24hr

description:
PH039w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009051_R06C01 CD4+


title: muscle, PH039, week 0, pre

description:
PH039w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009051_R05C02 CD4+


title: muscle, PH038, week 12, pre

description:
PH038w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009051_R05C01 CD4+

description: Sample collected in BD Vacutainer CPT tube with sodium heparin (Fisher Scientific, Hampton, HG)


title: muscle, PH038, week 12, 24hr

description:
PH038w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009051_R04C02 CD4+


title: muscle, PH038, week 12, 3hr

description:
PH038w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009051_R03C02 CD4+


title: muscle, PH038, week 0, pre

description:
PH038w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009051_R03C01 CD4+


title: muscle, PH038, week 0, 3hr

description:
PH038w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH039, week 12, pre

description:
PH039w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH038, week 0, 24hr

description:
PH038w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009051_R02C02 CD4+


title: 6229009051_R02C01 CD4+


title: muscle, PH034, week 12, pre

description:
PH034w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009035_R06C01 CD4+


title: muscle, PH034, week 12, 3hr

description:
PH034w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009051_R01C01 CD4+


title: muscle, PH034, week 16, rest

description:
PH034w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH038, week 16, rest

description:
PH038w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009035_R05C02 CD4+


title: muscle, PH034, week 12, 24hr

description:
PH034w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009035_R05C01 CD4+


title: muscle, PH034, week 0, 3hr

description:
PH034w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH034, week 0, pre

description:
PH034w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009035_R04C01 CD4+


title: 6229009035_R04C02 CD4+


title: 6229009035_R03C02 CD4+


title: 6229009051_R04C01 CD4+


title: 6229009035_R03C01 CD4+


title: 6229009035_R02C02 CD4+


title: muscle, PH031, week 12, pre

description:
PH031w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH031, week 16, rest

description:
PH031w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH031, week 12, 3hr

description:
PH031w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009035_R02C01 CD4+

description: Sample collected in BD Vacutainer CPT tube with sodium heparin (Fisher Scientific, Hampton, HG)


title: 6229009035_R01C02 CD4+


title: muscle, PH031, week 0, 3hr

description:
PH031w0h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH031, week 12, 24hr

description:
PH031w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH031, week 0, pre

description:
PH031w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009033_R06C02 CD4+


title: muscle, PH031, week 0, 24hr

description:
PH031w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009035_R01C01 CD4+


title: muscle, PH025, week 16, rest

description:
PH025w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009033_R05C02 CD4+


title: muscle, PH034, week 0, 24hr

description:
PH034w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009033_R05C01 CD4+


title: muscle, PH025, week 12, 3hr

description:
PH025w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009033_R04C02 CD4+


title: 6229009033_R04C01 CD4+


title: 6229009033_R03C02 CD4+


title: 6229009033_R02C02 CD4+


title: 6229009033_R03C01 CD4+


title: muscle, PH025, week 12, 24hr

description:
PH025w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH025, week 0, pre

description:
PH025w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009033_R02C01 CD4+


title: 6229009033_R01C02 CD4+


title: 6229009033_R06C01 CD4+


title: muscle, PH025, week 12, pre

description:
PH025w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009032_R06C02 CD4+


title: muscle, PH023, week 16, rest

description:
PH023w16rst_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH023, week 0, pre

description:
PH023w0pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH025, week 0, 24hr

description:
PH025w0h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH023, week 12, 24hr

description:
PH023w12h24_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: 6229009032_R05C02 CD4+


title: muscle, PH023, week 12, pre

description:
PH023w12pre_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt


title: muscle, PH023, week 12, 3hr

description:
PH023w12h3_sn
muscle_raw_counts.txt
muscle_TMM_counts.txt