title: NFATc3_smcko_1

first: Xiu

last: Liu

state: Guangdong

address: 1838 North Guangzhou Avenue

institute: Southern Medical University

data_processing:
TruSeq PE Cluster Kit v3 cBot HS
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Assembly: mm10
Supplementary files format and content: counts and fpkms

source_name: aorta

growth_protocol: All mice were kept under a 12-hour light/dark cycle at 23°C.

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
RNA libraries for RNA-seq were preparded using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: Tamoxifen was dissolved in corn oil at a concentration of 20 mg/ml and was injected intraperitoneally into 3-week-old mice at a dose of 75 mg/kg/day for 5 consecutive days. Two weeks after tamoxifen administration, β-Aminopropionitrile models were induced in mice.

value: aorta

value: VSMC-specific NFATc3 knockout

tag: treatment

value: β-Aminopropionitrile


title: Methyl Capture, EA1, Cancer Associated Fibroblast, Post-5AzaC Treatment (10 Day)

status: Public on Jul 30 2025

type: SRA

city: Irvine

first: Farah

last: Rahmatpanah

state: CA

address: Med  scie 1 RM C220

department: Pathology

country: USA

institute: UCI

description: EA_CAF_Cutoff_1_GEO_Consensus_Peakset_2024.tsv

library_source: genomic

data_processing:
Sequencing reads were aligned to reference genome using hg38 using Bowtie2 and deduplicated to remove PCR artifacts with Strand NGS 3.1
Peaks were identified with MACS2 version callpeak function using a band width of 300 bp and a false discovery rate of q < 0.05. No control sample was used for input. A consensus peakset was derived from the aligned reads of AA and EA prostate cancer stroma samples and AA and EA CAF samples that were sequenced. For stroma samples, a minimum threshold of five of thirty-two methylated samples were used for considering a region as methylated. For AA and EA CAFs before treatment, a minimum of one of seven samples were used. For all AA CAFs and EA CAFs before, during, and after treatment, a minimum of one of nine AA CAFs and one of twelve EA CAFs were used.
Assembly: GRCh38/hg38
Supplementary files format and content: Methyl capture consesus peaksets of each AA and EA TAS sample with individual information (Chr start/end, distance to TSS, summit, fold enrichment, etc.) in TSV text file
Supplementary files format and content: Methyl capture consensus peaksets of AA CAF samples treated with 5AzaC at all time points with individual information (Chr start/end, distance to TSS, summit, fold enrichment, etc.) in TSV text file
Supplementary files format and content: Methyl capture consensus peaksets of AA&EA CAF samples before treatment with 5AzaC with individual information (Chr start/end, distance to TSS, summit, fold enrichment, etc.) in TSV text file
Supplementary files format and content: Methyl capture consensus peaksets of EA CAFs treated with 5AzaC at all time points with individual information (Chr start/end, distance to TSS, summit, fold enrichment, etc.) in TSV text file
Library strategy: methyl- captured DNA-Seq

molecule: genomic DNA

organism: Homo sapiens

source_name: Prostate

growth_protocol: Fresh prostatectomy tissue was examined to confirm the location of tumor and a 2-5 mm cube of tumor-adjacent stroma was removed. The tissues were placed in transport medium consisting of tissue culture medium without growth factors, placed on ice. Tissue specimens were cut into 2 mm pieces for digestion in a Sterilgard hood using sterile techniques. To ensure that tissue strips have been selected as tumor-adjacent stroma, largely free of other components, one face of the strip was removed with a scalpel and used for frozen section preparation. If further trimming was necessary, the tumor-stroma boundary was marked on the back of the frozen section slide under a microscope using a Pilot Ultrafine permanent fine point pen. The top of the slide was sterilized with an alcohol swab, dried, and the tissue strip was overlaid on the corresponding frozen section for manual trimming in the hood. Trimmed tissue was digested by collagenase Type I and Hyaluronidase Type II at 37ºC in the cell culture incubator. Cell suspensions were cultured in stroma cell selection media consisting of RPMI medium supplemented with 5% FCS, 1 nM testosterone and 10 ng/mL fibroblast growth factor, which selected for fibroblasts over succeeding passages. Frozen stocks of passages 1 to 5 primary cultures were prepared.

extract_protocol:
Tissue blocks were evaluated by a pathologist to identify the tumor adjacent stroma area from which gDNA could be extracted. The FFPE RNA/DNA Purification Plus Kit (Cat # 54300, Norgen Biotek Corp) was used to isolate total gDNA from patient specimens.
Genomic DNA is fragmented, quantified and assessed for quantity and quality using an Agilent 2100 Bioanalyzer and a Qubit fluorimeter, respectively. Fragmented gDNA is used to capture methylated DNAs (MethylCollectorTM Ultra, Active Motif, Cat # 55005). Methylated fractions are used to construct standard fragment libraries with Bio Scientific’s NEXTFLEX Rapid DNA-Seq Kit 2.0. For NGS, all methyl- captured DNA is sequenced at the University of California, Irvine genomic Core facility.
Bio Scientific’s NEXTFLEX Rapid DNA-Seq

treatment_protocol: At passage 5, a portion of the cells were placed in serum-free medium and incubating for 24 h. CAFs (n=7), all after passage 5, were cultured in the presence of PBS or low-dose (0.3µM). CAFs were treated with 5AzaC for 24 hours, followed by culture for 10 days in drug-free medium.

tag: tissue

value: Prostate

tag: race

value: EA

tag: tumor stage

tag: primary gleason

tag: secondary gleason

tag: treatment (pca_patients)

tag: treatment (caf)

value: Post-5AzaC (10 day)

tag: age

tag: time to_relapse_since_last_f/u_(months)

tag: total #_of_reads

tag: aligned reads/%

tag: duplicated reads

tag: cell type

value: Cancer Associated Fibroblast


title: IR64, leaf, control (moderate drought), Day 12, rep 3

city: Tsukuba

first: Taiji

last: Kawakatsu

state: Ibaraki

address: 3-1-3 Kan-nondai

country: Japan

institute: National Agriculture and Food Research Organization

description:
Library name: IRLM12C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM12C3

library_source: transcriptomic

data_processing:
The sequence reads were mapped onto the reference genome of the rice cultivar Nipponbare (IRGSP-1.0) using STAR aligner with options ‘--outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4’ (Dobin et al., 2013). The read count matrix was obtained using featureCounts (v2.0.0) with option ‘-p’ (Liao et al., 2014).
Assembly: IRGSP-1.0
Supplementary files format and content: Tab-delimited text file including raw counts for each samples

molecule: polyA RNA

organism: Oryza sativa

source_name: leaf

growth_protocol: Rice seeds were surface sterilized with 375 ppm of pefurazoate at 15°C for 24 h. Then the seeds were soaked in water to germinate in a dark place at 30°C for two days. The calcined clay (Profile Greens Grade, PROFILE Products LLC, http://www.profileevs.com) was used as the soil. The soil was washed with water before use, then dried, filled in the pots (24.5 cm upper outer diameter, 20 cm lower outer diameter, 30 cm height; SP2530P, Tecs Inc., http://www.tecs.ne.jp) up to a depth of 25cm, and irrigated with modified Kimura B (Yoshida et al., 1976) culture solution (273.2 µM K2SO4, 546.9 µM MgSO4.7H2O, 182.0 µM NaH2PO4.2H2O, 182.3 µM CaCl2.2H2O, 182.4 µM CaSO4.2H2O, 1.2 mM KNO3, 411.2 µM NH4Cl, and 4 mg L-1 FeC6H5O7.nH2O [pH 5.5]). The germinated seeds were individually planted in separate pots, and they were cultivated in a growth chamber (Nippon Medical & Chemical Instruments Co., http://www.nihonika.co.jp) under a 14 h light/ 10 h dark photoperiod, with 50% relative humidity (R.H.) at daytime and 60% R.H. at nighttime. The temperature in the growth chamber was maintained at 25°C at nighttime and varied from 25°C to 30°C at daytime.  We used iPOTs (Numajiri et al. 2021), which is a pot that incorporates auto-irrigation system to mimic soil condition similar to the drought stress in the field. The water level in the supply pot, connected in parallel with the pots through a hose, was maintained at a height of 10 cm to ensure that the upper layers of the pots were moistened during the irrigation period.

extract_protocol:
The leaf samples were frozen in liquid nitrogen immediately after sampling, ground to a fine powder with a multi-beads shocker and used for RNA extraction. Total RNA was extracted using guanidine isothiocyanate based buffer and magnetic beads as described previously (Yoshino et al., 2020).
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760L) according to the manufacture’s protocol.

treatment_protocol: In the moderate drought treatment, water supply from the supply pot was stopped on the 14 days after sowing, allowing water to drain from the inside of the pots through the hose. In the severe drought treatment, the height of the pots was elevated above the hose to promote faster drainage. In the control treatment, irrigation was maintained.

value: leaf

tag: cultivar

value: control (moderate drought)

tag: days after_treatment

tag: replicate


title: Methyl Capture, EA2, Cancer Associated Fibroblast, no 5AzaC treatment

description:
EA_CAF_Cutoff_1_GEO_Consensus_Peakset_2024.tsv
CAF_-5AzaC_Cutoff_1_Consensus_Peakset_2024.tsv


title: NFATc3_flox_3

city: Guangzhou

country: China

molecule: total RNA

organism: Mus musculus

tag: genotype

value: NFATc3 flox

tag: treatment


title: Media control for Wnt3a_MC4

type: RNA

city: Portland

first: Xiao

last: Shi

state: Oregon

address: 3181 SW Sam Jackson PK Rd

department: dept. of psychiatry

institute: Oregon Health and Science University

description: Media Control

data_processing:
The data analysis were performed according to the manufacturers instructions using Expression Suit software:
For the normalization it uses the mean expression value of all expressed and qualified miRNAs (Calculated on the mean expression value sheet). The ΔCq value for a miRNA was calculated as: ΔCq = Cq value of the miRNA – mean normalizer Cq value in the same group.
Target miRNA signals normalized to vehicle control;ΔΔCq = ΔCq for treated samples – ΔCq for vehicle control samples.The fold change (relative quantification value) for each miRNA was calculated as: 2^ - ΔΔCq.
DeltadeltaCt based fold-change calculations from the raw threshold cycle data by using Excel
Matrix normalized worksheet reports normalized signal (against mean expression value). Media control was used to exclude miRNAs from serum sources and not used for normalization.
In fold Change worksheet, relative quantification value for each miRNA was calculated as: 2 ^- ΔΔCq.  ΔΔCq = ΔCq for treated samples – ΔCq for vehicle control samples.For statistics, we used unbiased robust procedures including matched-pairs estimators of the effect sizes and rank-based testing of associations in the interest of minimizing confounding of associations by technical causes, and then to further interrogate those results with extensive sensitivity analyses designed to probe the volatility of the conclusions depending on our choice of analytical methods.

label: FAM

source_name: Extracellular vesicle for culture media

label_protocol: PCR assays were performed using the TaqMan Low Density Arrays (4444913, ThermoFisher Scientific) following the Manufacturer’s instructions. RNA (with 8-10ng of miRNA measured by Qubit miRNA assay kit) was reverse transcribed using Megaplex RT primer human pool set V3.0 (4444750, ThermoFisher Scientific) and MultiScribe Reverse Transcriptase (4311235, ThermoFisher Scientific) according to the user guide. To increase the sensitivity of qPCR analysis for miRNA targets, cDNA was pre-amplified (14 cycles) with Megaplex PreAmp primers human pool set V3.0(4444748, ThermoFisher Scientific) before qPCR.

extract_protocol: Total RNA was extracted with MagMax mirVana total RNA isolation kit.

value: U2OS cell

tag: activation agent

value: media only

tag: time

value: 0 hour


title: IR64, leaf, control (moderate drought), Day 12, rep 2

description:
Library name: IRLM12C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM12C2

tag: tissue


title: NFATc3_smcko_3


title: NFATc3_flox_2


title: PEA2

description: Test

value: selective HRH1 agonist PEA (200uM)

value: 24 hours


title: Media control for Wnt3a_MC3

description: Media Control


title: IR64, leaf, moderate drought, Day 1, rep 1

description:
Library name: IRLM1D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM1D1

value: moderate drought


title: IR64, leaf, control (moderate drought), Day 12, rep 1

description:
Library name: IRLM12C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM12C1


title: Methyl Capture, EA1, Cancer Associated Fibroblast, no 5AzaC treatment

tag: race

tag: tumor stage

tag: primary gleason

tag: secondary gleason


title: NFATc3_flox_1


title: IR64, leaf, moderate drought, Day 0, rep 2

description:
Library name: IRLM0D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM0D2


title: IR64, leaf, control (moderate drought), Day 11, rep 3

description:
Library name: IRLM11C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM11C3


title: Media control for Wnt3a_MC2

description: Media Control


title: NFATc3_smcko_2


title: IR64, leaf, control (moderate drought), Day 11, rep 2

description:
Library name: IRLM11C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM11C2


title: Media control for Wnt3a_MC1

description: Media Control


title: LNP-mRNA vaccine, panHigh_9

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

institute: Yale University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Single cell gene expression data were pre-processed with a standard Cell Ranger v6.0.1 (10x Genomics) pipeline, aligning reads to the mm10 mouse reference transcriptome.
Assembly: mm10 mouse reference transcriptome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
Blood was retro-orbitally collected from mice. The PBMCs and plasma were isolated from blood via SepMate-15 (StemCell Technologies). 200 µl blood was immediately diluted with 800 ul PBS with 2% FBS. The diluted blood was then added to SepMate-15 tubes with 5ml Lymphoprep (StemCell Technologies). 1200 x g centrifugation for 20 minutes was applied to isolate RBCs, PBMCs and plasma. 200ul diluted plasma was collected from the surface layer. Then the solution at the top layer containing PBMCs was poured to a new tube. PBMCs were washed once with PBS + 2% FBS before being used in downstream analysis. The separated plasma was used in ELISA and neutralization assay. PBMCs were collected for single cell profiling using a 10xGenomics platform.
Cell suspension were normalized to 1000 cells/ml and loaded to achieve targeted cell recovery to 10000 cells. The samples were subjected to 14 cycles of cDNA amplification. Following this, gene expression (GEX), TCR-enriched and BCR-enriched libraries were prepared according to the manufacturer’s protocol (10x Genomics). All libraries were sequenced using a NovaSeq 6000 (Illumina) with 2*150 read length.

value: Spleen

tag: cell line

value: Heterogeneous splenocyte


title: Vehicle control for Wnt3a_VC6

description: Vehicle Control

value: 0.0001% human serum albumin


title: IR64, leaf, control (moderate drought), Day 11, rep 1

description:
Library name: IRLM11C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM11C1


title: Methyl Captue, AA3, Cancer Associated Fibroblast, 5AzaC Treatment after 24 hours

description: AA_CAF_Cutoff_1_GEO_Consensus_Peakset_2024.tsv

value: AA

tag: treatment (pca_patients)

tag: treatment (caf)

tag: age

tag: time to_relapse_since_last_f/u_(months)

tag: total #_of_reads


title: Methyl Capture, AA3, Cancer Associated Fibroblast, no 5AzaC treatment

description:
AA_CAF_Cutoff_1_GEO_Consensus_Peakset_2024.tsv
CAF_-5AzaC_Cutoff_1_Consensus_Peakset_2024.tsv

value: Prostate

tag: aligned reads/%

tag: duplicated reads

tag: cell type


title: IR64, leaf, control (moderate drought), Day 10, rep 3

description:
Library name: IRLM10C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM10C3

tag: cultivar

tag: treatment

tag: days after_treatment

tag: replicate


title: Methyl Captue, EA1, Cancer Associated Fibroblast, 5AzaC Treatment after 24 hours

tag: tissue

tag: race

value: EA


title: Methyl Capture, AA2, Cancer Associated Fibroblast, Post-5AzaC Treatment (10 Day)

tag: tumor stage

tag: primary gleason

value: Post-5AzaC (10 day)


title: LNP-mRNA vaccine, panHigh_8

description: 10x Genomics

tag: cell line


title: Vehicle control for Wnt3a_VC4

description: Vehicle Control

tag: activation agent

tag: time


title: LNP-mRNA vaccine, panHigh_7

description: 10x Genomics


title: Methyl Captue, AA2, Cancer Associated Fibroblast, 5AzaC Treatment after 24 hours

tag: secondary gleason

tag: treatment (pca_patients)

tag: treatment (caf)

tag: age

value: Cancer Associated Fibroblast


title: LNP-mRNA vaccine, panHigh_6

description: 10x Genomics


title: IR64, leaf, control (moderate drought), Day 10, rep 2

description:
Library name: IRLM10C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM10C2

value: leaf


title: IR64, leaf, control (moderate drought), Day 10, rep 1

description:
Library name: IRLM10C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM10C1

value: control (moderate drought)


title: Methyl Capture, AA2, Cancer Associated Fibroblast, no 5AzaC treatment

tag: time to_relapse_since_last_f/u_(months)

tag: total #_of_reads

tag: aligned reads/%

tag: duplicated reads


title: LNP-mRNA vaccine, panLow_8

description: 10x Genomics

tag: cell type

tag: treatment


title: LNP-mRNA vaccine, panLow_9

description: 10x Genomics

tag: tissue


title: IR64, leaf, control (moderate drought), Day 9, rep 3

description:
Library name: IRLM9C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM9C3

tag: cultivar

tag: days after_treatment

tag: replicate


title: Vehicle control for Wnt3a_VC2

description: Vehicle Control


title: Vehicle control for Wnt3a_VC1

description: Vehicle Control


title: Methyl Capture, AA3, Cancer Associated Fibroblast, Post-5AzaC Treatment (10 Day)

tag: race

tag: tumor stage

tag: primary gleason


title: Methyl Capture, AA1, Cancer Associated Fibroblast, Post-5AzaC Treatment (10 Day)

tag: secondary gleason


title: IR64, leaf, control (moderate drought), Day 9, rep 2

description:
Library name: IRLM9C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM9C2


title: LNP-mRNA vaccine, panLow_7

description: 10x Genomics

tag: cell line


title: Methyl Captue, AA1, Cancer Associated Fibroblast, 5AzaC Treatment after 24 hours

tag: treatment (pca_patients)

tag: treatment (caf)


title: Wnt6

description: Test

tag: activation agent

value: selective FZD4 agonist Wnt3a (100ng/ml)

tag: time


title: Methyl Capture, AA1, Cancer Associated Fibroblast, no 5AzaC treatment

tag: age

tag: time to_relapse_since_last_f/u_(months)

tag: total #_of_reads

tag: aligned reads/%


title: IR64, leaf, control (moderate drought), Day 8, rep 3

description:
Library name: IRLM8C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM8C3

tag: tissue

tag: treatment


title: IR64, leaf, control (moderate drought), Day 9, rep 1

description:
Library name: IRLM9C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM9C1

tag: cultivar

tag: days after_treatment


title: LNP-mRNA vaccine, delta_8

description: 10x Genomics

tag: cell type


title: Wnt5

description: Test

value: U2OS cell


title: LNP-mRNA vaccine, panLow_6

description: 10x Genomics


title: Methyl Capture, EA15, Tumor Adjacent Stroma

description: all_Selected_32_TAS_Samples_Consensus_Peakset.tsv

tag: race

tag: tumor stage

value: surgery only

tag: duplicated reads

value: Tumor Adjacent Stroma


title: Wnt4

description: Test


title: Vehicle control for Wnt3a_VC5

description: Vehicle Control


title: LNP-mRNA vaccine, delta_7

description: 10x Genomics

tag: cell line


title: Wnt3

description: Test


title: LNP-mRNA vaccine, delta_6

description: 10x Genomics


title: IR64, leaf, control (moderate drought), Day 8, rep 2

description:
Library name: IRLM8C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM8C2

tag: replicate


title: Methyl Capture, EA14, Tumor Adjacent Stroma

tag: primary gleason

tag: secondary gleason

tag: treatment (pca_patients)

tag: treatment (caf)


title: LNP-mRNA vaccine, pbs_8

description: 10x Genomics

value: PBS


title: Wnt2

description: Test

tag: activation agent

tag: time

value: 24 hours


title: IR64, leaf, control (moderate drought), Day 8, rep 1

description:
Library name: IRLM8C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM8C1


title: Methyl Capture, EA12, Tumor Adjacent Stroma

value: surgery, radiation

tag: age

tag: time to_relapse_since_last_f/u_(months)

tag: total #_of_reads

tag: aligned reads/%


title: Wnt1

description: Test


title: Methyl Capture, EA13, Tumor Adjacent Stroma

tag: tissue

value: surgery, radiation, ADT


title: IR64, leaf, control (moderate drought), Day 7, rep 3

description:
Library name: IRLM7C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM7C3

tag: cultivar

tag: treatment

tag: days after_treatment


title: IR64, leaf, control (moderate drought), Day 7, rep 2

description:
Library name: IRLM7C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM7C2


title: LNP-mRNA vaccine, pbs_7

description: 10x Genomics

value: Spleen

tag: cell type

value: Heterogeneous splenocyte


title: Media control for CCPA_MC8

description: Medium contro

value: Media only

value: 0 hour


title: Methyl Capture, EA11, Tumor Adjacent Stroma

value: Prostate

tag: race

value: EA

tag: tumor stage

tag: duplicated reads


title: Vehicle control for Wnt3a_VC3

description: Vehicle Control

value: 0.0001% human serum albumin


title: Methyl Capture, EA10, Tumor Adjacent Stroma

tag: primary gleason

tag: secondary gleason


title: IR64, leaf, control (moderate drought), Day 7, rep 1

description:
Library name: IRLM7C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM7C1

value: leaf

tag: replicate


title: G5: 100 µg MD39.3 protein at week 32 HTO

city: La Jolla

first: Shane

last: Crotty

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description:
Library name: MD39_3_PBMC_Wk32_Gr5_HTO
feature_reference_Wk32.csv

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v6.1.2 or higher (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
Env-binding memory B cells at weeks 8, 10, 24, 26 and 32 in the 100 µg membrane-bound MD39.3 mRNA and 100 µg MD39.3 protein plus SMNP groups were stained with tetramerized BG505 MD39.3 probes using fluorescent-SA and TotalSeq-C oligo-tagged fluorescent-SA, surface antibodies and six different TotalSeq-C oligo-tagged anti-b2M & CD298 antibodies to multiplex animal samples. Samples were sorted on a FACSymphony S6 (BD Biosciences) into 1.5 mL tubes with FBS supplemented RPMI media.
Libraries were constructed according to the manufacturer's protocol using the Chromium Next GEM Single Cell 5’ Reagent Kit v2.

value: PBMC

value: B cell


title: LNP-mRNA vaccine, pbs_6

description: 10x Genomics

tag: cell line


title: IR64, leaf, control (moderate drought), Day 6, rep 3

description:
Library name: IRLM6C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM6C3

value: control (moderate drought)


title: Media control for CCPA_MC6

description: Medium contro

value: U2OS cell

tag: activation agent

tag: time


title: G2: 100 µg MD39.3 gp151 mRNA at week 32 HTO

description:
Library name: MD39_3_PBMC_Wk32_Gr2_HTO
feature_reference_Wk32.csv


title: Methyl Capture, EA9, Tumor Adjacent Stroma

tag: treatment (pca_patients)

tag: treatment (caf)

tag: age

tag: time to_relapse_since_last_f/u_(months)

value: Tumor Adjacent Stroma


title: IR64, leaf, control (moderate drought), Day 6, rep 2

description:
Library name: IRLM6C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM6C2

tag: tissue

tag: cultivar


title: G5: 100 µg MD39.3 protein at week 26 HTO

description:
Library name: MD39_3_PBMC_Wk26_Gr5_HTO
feature_reference_Wk26.csv


title: Media control for CCPA_MC5

description: Medium contro


title: Methyl Capture, EA8, Tumor Adjacent Stroma

tag: total #_of_reads

tag: aligned reads/%


title: IR64, leaf, control (moderate drought), Day 6, rep 1

description:
Library name: IRLM6C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM6C1

tag: treatment

tag: days after_treatment


title: Media control for CCPA_MC4

description: Medium contro

tag: cell type


title: Methyl Capture, EA7, Tumor Adjacent Stroma

tag: race

tag: tumor stage

tag: primary gleason

value: surgery only

tag: duplicated reads


title: G2: 100 µg MD39.3 gp151 mRNA at week 26 HTO

description:
Library name: MD39_3_PBMC_Wk26_Gr2_HTO
feature_reference_Wk26.csv


title: Methyl Capture, EA6, Tumor Adjacent Stroma

tag: secondary gleason


title: Media control for CCPA_MC3

description: Medium contro

tag: activation agent

tag: time


title: IR64, leaf, control (moderate drought), Day 5, rep 2

description:
Library name: IRLM5C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM5C2

tag: replicate


title: Methyl Capture, EA5, Tumor Adjacent Stroma

tag: treatment (pca_patients)

tag: treatment (caf)

tag: age


title: Media control for CCPA_MC7

description: Medium contro


title: G2 & G5: 100 µg MD39.3 gp151 mRNA & 100 µg MD39.3 protein at week 24 2/2 HTO

description:
Library name: MD39_3_PBMC_Wk24_2_Gr2_5_HTO
feature_reference_Wk24_2.csv

tag: tissue


title: G2 & G5: 100 µg MD39.3 gp151 mRNA & 100 µg MD39.3 protein at week 24 1/2 HTO

description:
Library name: MD39_3_PBMC_Wk24_1_Gr2_5_HTO
feature_reference_Wk24_1.csv


title: IR64, leaf, control (moderate drought), Day 5, rep 1

description:
Library name: IRLM5C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM5C1

tag: cultivar


title: Media control for CCPA_MC2

description: Medium contro


title: Methyl Capture, EA4, Tumor Adjacent Stroma

description: all_Selected_32_TAS_Samples_Consensus_Peakset.tsv

tag: time to_relapse_since_last_f/u_(months)

tag: total #_of_reads

tag: aligned reads/%


title: IR64, leaf, control (moderate drought), Day 4, rep 3

description:
Library name: IRLM4C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM4C3

tag: treatment

tag: days after_treatment


title: Media control for CCPA_MC1

description: Medium contro

tag: cell type


title: G5: 100 µg MD39.3 protein at week 10 HTO

description:
Library name: MD39_3_PBMC_Wk10_Gr5_HTO
feature_reference_Wk10.csv


title: G2: 100 µg MD39.3 gp151 mRNA at week 10 HTO

description:
Library name: MD39_3_PBMC_Wk10_Gr2_HTO
feature_reference_Wk10.csv


title: Methyl Capture, EA3, Tumor Adjacent Stroma

tag: race

tag: tumor stage

tag: primary gleason


title: Methyl Capture, EA2, Tumor Adjacent Stroma

tag: secondary gleason

tag: duplicated reads


title: Vehicle control for CCPA_VC5

description: Vehicle control

tag: activation agent

tag: time

value: 24 hours


title: Vehicle control for CCPA_VC6

description: Vehicle control


title: IR64, leaf, control (moderate drought), Day 4, rep 2

description:
Library name: IRLM4C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM4C2

tag: replicate


title: IR64, leaf, control (moderate drought), Day 4, rep 1

description:
Library name: IRLM4C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM4C1


title: IR64, leaf, control (moderate drought), Day 5, rep 3

description:
Library name: IRLM5C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM5C3


title: Vehicle control for CCPA_VC4

description: Vehicle control


title: Methyl Capture, EA1, Tumor Adjacent Stroma

tag: treatment (pca_patients)

value: surgery, radiation

tag: treatment (caf)

tag: age


title: IR64, leaf, control (moderate drought), Day 3, rep 3

description:
Library name: IRLM3C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM3C3

tag: tissue

tag: cultivar


title: G2: 100 µg MD39.3 gp151 mRNA at week 8 HTO

description:
Library name: MD39_3_PBMC_Wk8_Gr2_HTO
feature_reference_Wk8.csv


title: G2 & G5: 100 µg MD39.3 gp151 mRNA & 100 µg MD39.3 protein at week 8 2/2 HTO

description:
Library name: MD39_3_PBMC_Wk8_2_Gr2_5_HTO
feature_reference_Wk8_2.csv


title: Methyl Capture, AA20, Tumor Adjacent Stroma

value: AA

tag: time to_relapse_since_last_f/u_(months)

tag: total #_of_reads

tag: aligned reads/%


title: Vehicle control for CCPA_VC3

description: Vehicle control

tag: cell type


title: IR64, leaf, control (moderate drought), Day 3, rep 2

description:
Library name: IRLM3C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM3C2

tag: treatment

tag: days after_treatment


title: Vehicle control for CCPA_VC2

description: Vehicle control


title: G2 & G5: 100 µg MD39.3 gp151 mRNA & 100 µg MD39.3 protein at week 8 1/2 HTO

description:
Library name: MD39_3_PBMC_Wk8_1_Gr2_5_HTO
feature_reference_Wk8_1.csv


title: Methyl Capture, AA19, Tumor Adjacent Stroma

tag: race

tag: tumor stage

tag: primary gleason


title: Methyl Capture, AA18, Tumor Adjacent Stroma

tag: secondary gleason

value: surgery, ADT

tag: duplicated reads


title: G5: 100 µg MD39.3 protein at week 32 VDJ

description: Library name: MD39_3_PBMC_Wk32_Gr5_VDJ


title: G5: 100 µg MD39.3 protein at week 8 HTO

description:
Library name: MD39_3_PBMC_Wk8_Gr5_HTO
feature_reference_Wk8.csv


title: Vehicle control for CCPA_VC1

description: Vehicle control

tag: activation agent

tag: time


title: G2: 100 µg MD39.3 gp151 mRNA at week 32 VDJ

description: Library name: MD39_3_PBMC_Wk32_Gr2_VDJ


title: IR64, leaf, control (moderate drought), Day 2, rep 2

description:
Library name: IRLM2C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM2C2

tag: replicate


title: CCPA6

description: Test

value: selective ADORA1 agonist CCPA(10uM)


title: CCPA5

description: Test


title: IR64, leaf, control (moderate drought), Day 2, rep 1

description:
Library name: IRLM2C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM2C1


title: Methyl Capture, AA16, Tumor Adjacent Stroma

tag: treatment (pca_patients)

tag: treatment (caf)

tag: age


title: G5: 100 µg MD39.3 protein at week 26 VDJ

description: Library name: MD39_3_PBMC_Wk26_Gr5_VDJ

tag: tissue


title: IR64, leaf, control (moderate drought), Day 1, rep 3

description:
Library name: IRLM1C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM1C3

tag: cultivar


title: CCPA4

description: Test


title: G2: 100 µg MD39.3 gp151 mRNA at week 26 VDJ

description: Library name: MD39_3_PBMC_Wk26_Gr2_VDJ


title: Methyl Capture, AA14, Tumor Adjacent Stroma

tag: time to_relapse_since_last_f/u_(months)

tag: total #_of_reads

tag: aligned reads/%


title: IR64, leaf, control (moderate drought), Day 1, rep 2

description:
Library name: IRLM1C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM1C2

tag: treatment

tag: days after_treatment


title: Methyl Capture, AA17, Tumor Adjacent Stroma

description: all_Selected_32_TAS_Samples_Consensus_Peakset.tsv

tag: race

tag: tumor stage

tag: cell type


title: CCPA3

description: Test


title: IR64, leaf, control (moderate drought), Day 3, rep 1

description:
Library name: IRLM3C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM3C1


title: G2 & G5: 100 µg MD39.3 gp151 mRNA & 100 µg MD39.3 protein at week 24 2/2 VDJ

description: Library name: MD39_3_PBMC_Wk24_2_Gr2_5_VDJ


title: CCPA2

description: Test


title: IR64, leaf, control (moderate drought), Day 2, rep 3

description:
Library name: IRLM2C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM2C3


title: G2 & G5: 100 µg MD39.3 gp151 mRNA & 100 µg MD39.3 protein at week 24 1/2 VDJ

description: Library name: MD39_3_PBMC_Wk24_1_Gr2_5_VDJ


title: IR64, leaf, control (moderate drought), Day 1, rep 1

description:
Library name: IRLM1C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM1C1


title: Methyl Capture, AA12, Tumor Adjacent Stroma

tag: primary gleason

tag: secondary gleason

value: ADT, surgery

tag: duplicated reads


title: IR64, leaf, control (moderate drought), Day 0, rep 3

description:
Library name: IRLM0C3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM0C3

tag: replicate


title: G5: 100 µg MD39.3 protein at week 10 VDJ

description: Library name: MD39_3_PBMC_Wk10_Gr5_VDJ


title: Methyl Capture, AA15, Tumor Adjacent Stroma

tag: treatment (pca_patients)


title: Methyl Capture, AA9, Tumor Adjacent Stroma

tag: treatment (caf)


title: G2: 100 µg MD39.3 gp151 mRNA at week 10 VDJ

description: Library name: MD39_3_PBMC_Wk10_Gr2_VDJ


title: Media control for SDF-1_MC6

description: Media Control

tag: activation agent

value: media only

tag: time

value: 0 hours


title: Methyl Capture, AA8, Tumor Adjacent Stroma

tag: tissue

value: Prostate

tag: age


title: G5: 100 µg MD39.3 protein at week 8 VDJ

description: Library name: MD39_3_PBMC_Wk8_Gr5_VDJ


title: Media control for SDF-1_MC5

description: Media Control


title: Methyl Capture, AA7, Tumor Adjacent Stroma

tag: time to_relapse_since_last_f/u_(months)

tag: total #_of_reads


title: IR64, leaf, control (moderate drought), Day 0, rep 1

description:
Library name: IRLM0C1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM0C1

tag: cultivar

tag: treatment


title: IR64, leaf, control (moderate drought), Day 0, rep 2

description:
Library name: IRLM0C2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLM0C2

tag: days after_treatment


title: Fibroblasts, adipocytes sample 6

city: Davis

first: Robert

last: Rice

state: California

address: 4139 Meyer Hall, One Shields Avenue

department: Environmental Toxicology

institute: UC Davis

description:
Library name: FAF
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 6_FAF_bc1020
Green_Species_Consensus_Transcripts.fasta

data_processing:
Raw sequencing data were analyzed according to the IsoSeq3 pipeline (v3.4.0, https://isoseq.how/) and aligned to the Sterlet genome (ASM1064508v1).
Resulting transcripts were classified and filtered using the default criteria within Sqanti3 (v4.1) with the exception of the splice junction coverage filter, which was replaced by a minimum supporting reads filter (>= 3).
The command line implementation of blastp (v2.14.1+) was used to align the translated transcripts to the protein sequences of the Sterlet genome for functional annotation.
Alignments with an e-value less than 0.01 and at least 80% sequence identity were considered significant.
Assembly: ASM1064508v1
Supplementary files format and content: Fasta
Supplementary files format and content: counts table in .txt format

organism: Acipenser medirostris

source_name: Fibroblasts, adipocytes

growth_protocol: Tissue explants were permitted to expand to confluence in DMEM/F12 with 5% FBS plus Y27632, EGF, hydrocortisone, insuliin, transferrin, adenine, amphotericin B, ciprofloxicin.

extract_protocol:
RNA was harvested in RLT Plus lysis buffer (Qiagen) and extracted with the RNeasy Plus Mini kits (Qiagen) using gDNA eliminator columns. RNA was extracted from tissue in the same way after disruption with an Omni Bead Ruptor 24. RNA integrity was verified by Nanodrop 1000 befor library contsruction.
cDNA and SMRTbell libraries were constructed using 300 ng of total RNA for cDNA construction with the NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification Module (New England Biolabs, Ipswich, MA; Cat. #E6421L). After 15 cycles of PCR amplification, cDNA was purified using 0.86X SMRTbell cleanup beads. cDNA libraries were pooled for SMRTbell library construction using the SMRTbell prep kit 2.0 or 3.0 (Pacific Biosciences, Menlo Park, CA) with repair and A-tailing, overhang adapter ligation, and nuclease treatment. The Iso-Seq SMRTbell library was sequenced at UC Davis DNA Technologies Core (Davis, CA) using one 8M SMRT cell (Pacific Biosciences, Menlo Park, CA; Cat #101-389-001), Sequel II sequencing chemistry 2.0, and 24-hour movies on a PacBio Sequel II sequencer. cDNA preparation, amplification, and library prep were performed with the Iso-Seq Express Oligo Kit (PacBio) and SMRTbell Prep Kit 3.0 (PacBio).

value: Fibroblasts, adipocytes

tag: genotype

value: Octoploid

tag: Sex

value: Female

tag: batch


title: Media control for SDF-1_MC4

description: Media Control

tag: cell type


title: G2: 100 µg MD39.3 gp151 mRNA at week 8 VDJ

description: Library name: MD39_3_PBMC_Wk8_Gr2_VDJ

value: PBMC

value: B cell


title: CCPA1

description: Test

value: U2OS cell


title: Ampullae of Lorenini, Epithelial sample 5

description:
Library name: AF
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 5_AF_bc1019
Green_Species_Consensus_Transcripts.fasta

source_name: Ampullae of Lorenini

value: Ampullae of Lorenini

value: Epithelial


title: Methyl Capture, AA5, Tumor Adjacent Stroma

tag: race

tag: tumor stage

tag: primary gleason

tag: secondary gleason

value: surgery only

tag: aligned reads/%

tag: duplicated reads

value: Tumor Adjacent Stroma


title: G2 & G5: 100 µg MD39.3 gp151 mRNA & 100 µg MD39.3 protein at week 8 2/2 VDJ

description: Library name: MD39_3_PBMC_Wk8_2_Gr2_5_VDJ

tag: tissue


title: Media control for SDF-1_MC2

description: Media Control

tag: activation agent

tag: time


title: G2 & G5: 100 µg MD39.3 gp151 mRNA & 100 µg MD39.3 protein at week 8 1/2 VDJ

description: Library name: MD39_3_PBMC_Wk8_1_Gr2_5_VDJ


title: Methyl Capture, AA13, Tumor Adjacent Stroma

value: AA

tag: treatment (pca_patients)

tag: treatment (caf)

tag: age

tag: time to_relapse_since_last_f/u_(months)

tag: total #_of_reads


title: Oral (inside mouth, upper palate)-female, Epithelial sample 4

description:
Library name: IF
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 4_IF_bc1018
Green_Species_Consensus_Transcripts.fasta

source_name: Oral (upper palate)

value: Oral (upper palate)

tag: genotype

tag: Sex


title: Media control for SDF-1_MC1

description: Media Control

tag: cell type


title: G5: 100 µg MD39.3 protein at week 32 GEX

description: Library name: MD39_3_PBMC_Wk32_Gr5_GEX


title: Methyl Capture, AA4, Tumor Adjacent Stroma

tag: race


title: Esophagus-Green, Epithelial sample 3

description:
Library name: EM
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 3_EM_bc1012
Green_Species_Consensus_Transcripts.fasta

source_name: Esophagus

value: Esophagus

value: Male

tag: batch


title: Vehicle control for SDF-1_VC6

description: Vehicle control

value: 0.0001%human serum albumin

value: 24 hours


title: Methyl Capture, AA2, Tumor Adjacent Stroma

value: Prostate

tag: tumor stage

tag: primary gleason

value: surgery, radiation


title: Methyl Capture, AA6, Tumor Adjacent Stroma

tag: secondary gleason

tag: aligned reads/%


title: Mouth (rim of protrusible mouth), Epithelial sample 2

description:
Library name: MM
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 2_MM_bc1008
Green_Species_Consensus_Transcripts.fasta

source_name: Mouth

tag: tissue

value: Mouth

value: Octoploid


title: G5: 100 µg MD39.3 protein at week 26 GEX

description: Library name: MD39_3_PBMC_Wk26_Gr5_GEX

value: PBMC


title: Vehicle control for SDF-1_VC5

description: Vehicle control

tag: activation agent


title: Methyl Capture, AA1, Tumor Adjacent Stroma

tag: duplicated reads


title: Oral (inside mouth, upper palate)-male, Epithelial sample 1

description:
Library name: IM
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 1_IM_bc1006
Green_Species_Consensus_Transcripts.fasta


title: Media control for SDF-1_MC3

description: Media Control

value: media only

tag: time

value: 0 hours


title: Vehicle control for SDF-1_VC4

description: Vehicle control

value: U2OS cell


title: G2: 100 µg MD39.3 gp151 mRNA at week 26 GEX

description: Library name: MD39_3_PBMC_Wk26_Gr2_GEX

value: B cell


title: Differentiated LUHMES with 4sU and HSV-1 24hpi Rep2

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

description: Library name: diff_24h_4sU_2

data_processing:
Quality of the sequencing data was checked using FastQC (version 0.11.9). RNA-seq reads were mapped against the (i) the human genome (GRCh38/hg38), (ii) human rRNA sequences and (iii) the HSV-1 genome (HSV-1 strain 17, GenBank accession code: JN555585), using ContextMap 2 (version 2.7.9) using BWA as short read aligner and with default parameters. SAM output files of ContextMap2 were converted to BAM files using samtools. Number of read fragments per gene were determined from BAM files in a strand-specific manner using featureCounts and gene annotations from Ensembl (version 100). All these steps were implemented and run using the Watchdog workflow management system.
Assembly: GRCh38/hg38, JN555585
Supplementary files format and content: read counts per gene, tab separated file

organism:
Homo sapiens
Human alphaherpesvirus 1

source_name: LUHMES

extract_protocol:
Cells were lysed in TRIzol and RNA col-lected with the Direct-zol RNA Miniprep kit (Zymo Research #R2050).
Total RNA was treated with DNase I and then Ribo-Zero before fragmentation to 130-160nt.  cDNA synthesis was combined with End Repair Mix, then add A-Tailing Mix,  then the Adenylate 3'Ends DNA, RNA Index Adapter and Ligation Mix before  Ampure XP Beads purification. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. The library was amplified with phi29 to make DNA nanoball (DNB) which have more than 300 copies of one molecular. The DNBs were load into the patterned nanoarray and paired-end 100 base reads were generated in the way of combinatorial Probe-Anchor Synthesis (cPAS).

tag: cell line

value: LUHMES

tag: treatment

value: RNA in 90 microliters of 1xPBS was combined with 90 microliters of 20mM iodoacetamide for 20min at 50 degrees C.  Reactions were quenched with 20 microliters of 1M DTT, and incubated on ice for 30min before purification with Qiagen mRNeasy kit.


title: Ampullae of Lorenini, Epithelial sample 6

description:
Library name: GA1
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 6_13GA1_bc1023
Green_Species_Consensus_Transcripts.fasta

value: Ampullae of Lorenini

value: Epithelial


title: Vehicle control for SDF-1_VC3

description: Vehicle control


title: G2 & G5: 100 µg MD39.3 gp151 mRNA & 100 µg MD39.3 protein at week 24 2/2 GEX

description: Library name: MD39_3_PBMC_Wk24_2_Gr2_5_GEX


title: 48FLeuR

city: MADISON

first: REJI

middle: P

last: BABYGIRIJA

state: WI

address: 726 BEAR CLAW WAY, APT 211

institute: UW Madison

description:
Library name: Sample 48
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide

data_processing:
Analysis of significantly differentially expressed genes (DEGs) was completed in R version 3.4.3 (Team, 2017) using edgeR (Robinson et al., 2010) and limma (Ritchie et al., 2015). Gene names were converted to gene symbol and Entrez ID formats using the mygene package. Genes with too many missing values were removed, if genes were present in less than one diet/strain/sex group they were removed. To reduce the impact of external factors not of biological interest that may affect expression, data was normalized to ensure the expression distributions of each sample are within a similar range. We normalized using the trimmed mean of M-values (TMM), which scales to library size. Heteroscedasticity was accounted for using the voom function, DEGs were identified using an empirical Bayes moderated linear model, and log coefficients and Benjamini-Hochberg (BH) adjusted p-values were generated for each comparison of interest (Benjamini and Hochberg, 2018).
Assembly: #!genome-build GRCm38 #!genome-build-accession NCBI:GCA_000001635.7
Supplementary files format and content: Differentially Expressed Genes Table Males (1).csv
Supplementary files format and content: Differentially Expressed Genes Table Females (2).csv

source_name: Brain

extract_protocol:
RNA was extracted from liver using TRIzol Reagent according to the manufacturer’s protocol (Thermo Fisher Scientific). The concentration and purity of RNA were determined by absorbance at 260/280 nm using Nanodrop (Thermo Fisher Scientific) and samples were diluted to roughly 1000 ng/µl. RNA was submitted to the University of Wisconsin-Madison Biotechnology Center Gene Expression Center (RRID:SCR_017757) & DNA Sequencing Facility (RRID:SCR_017759). Each RNA sample was assayed on an Agilent RNA NanoChip to assess its integrity.  RNA samples that met Illumina’s TruSeq Stranded Total RNA Reference Guide (#1000000040499 v00) (Illumina, San Diego, CA) quality criteria were prepared for sequencing following the protocol as recommended using a 250ng total RNA input.  Libraries were multiplexed and sequenced on the NovaSeq6000 sequencer.  Reads were aligned to the mouse (Mus musculus) with genome-build GRCm38.p5 of accession NCBI:GCA_000001635.7 and expected counts were generated with ensembl gene IDs (Zerbino et al., 2018).
Illumina’s TruSeq Stranded Total RNA Reference Guide (#1000000040499 v00)

treatment_protocol: 3xTg amle and female mice were placed on individual BCAA restricted diet for 9 months and brains were collected for sequencing to see diet induced changes in brain transcriptome

value: Brain

tag: diet

value: Leucine restricted

value: Female


title: 47FLeuR

description:
Library name: Sample 47
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: G2: 100 µg MD39.3 gp151 mRNA at week 32 GEX

description: Library name: MD39_3_PBMC_Wk32_Gr2_GEX


title: 46FLeuR

description:
Library name: Sample 46
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: Vehicle control for SDF-1_VC2

description: Vehicle control

value: 0.0001%human serum albumin

value: 24 hours


title: G2 & G5: 100 µg MD39.3 gp151 mRNA & 100 µg MD39.3 protein at week 24 1/2 GEX

description: Library name: MD39_3_PBMC_Wk24_1_Gr2_5_GEX


title: G5: 100 µg MD39.3 protein at week 10 GEX

description: Library name: MD39_3_PBMC_Wk10_Gr5_GEX


title: Differentiated LUHMES with 4sU and HSV-1 12hpi Rep2

description: Library name: diff_12h_4sU_2


title: SDF6

description: Test

value: selective ACKR3 agonist SDF-1 (100ng/ml)


title: Vehicle control for SDF-1_VC1

description: Vehicle control


title: Differentiated LUHMES with 4sU and HSV-1 8hpi Rep2

description: Library name: diff_8h_4sU_2


title: 43FLeuR

description:
Library name: Sample 43
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: G2: 100 µg MD39.3 gp151 mRNA at week 10 GEX

description: Library name: MD39_3_PBMC_Wk10_Gr2_GEX


title: 44FLeuR

description:
Library name: Sample 44
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: Differentiated LUHMES with 4sU and HSV-1 24hpi Rep1

description: Library name: diff_24h_4sU_1


title: SDF5

description: Test


title: Differentiated LUHMES with 4sU and HSV-1 12hpi Rep1

description: Library name: diff_12h_4sU_1


title: 42FIleuR

description:
Library name: Sample 42
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide

value: Isoleucine restricted


title: 41FIleuR

description:
Library name: Sample 41
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: SDF4

description: Test


title: G2 & G5: 100 µg MD39.3 gp151 mRNA & 100 µg MD39.3 protein at week 8 2/2 GEX

description: Library name: MD39_3_PBMC_Wk8_2_Gr2_5_GEX


title: 40FIleuR

description:
Library name: Sample 40
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: 45FLeuR

description:
Library name: Sample 45
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: SDF3

description: Test


title: SDF2

description: Test


title: G2 & G5: 100 µg MD39.3 gp151 mRNA & 100 µg MD39.3 protein at week 8 1/2 GEX

description: Library name: MD39_3_PBMC_Wk8_1_Gr2_5_GEX


title: 39FIleuR

description:
Library name: Sample 39
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: Differentiated LUHMES with 4sU and HSV-1 4hpi Rep2

description: Library name: diff_4h_4sU_2


title: Differentiated LUHMES with 4sU and HSV-1 4hpi Rep1

description: Library name: diff_4h_4sU_1


title: SDF1

description: Test


title: RiboSeq of Pseudomonas aeruginosa UCBPP-PA14 WT 3

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

institute: Helmholtz Centre for Infection Research

description: Library name: RiboSeq_PA14_WT_PL_3

library_source: other

data_processing:
cutadapt , min read length 22
bowtie 2 - mapping to P. aeruginosa PA14 (NC_008463.1) reference genome, option “--very-sensitive-local”.
featureCounts
RiboSeq_PA14_dtrhPO_PL_1 was removed as a strong outlier in plotMDS (R package edgeR) - Methodological errors cannot be ruled out for this replication.
Assembly: NC_008463.1
Supplementary files format and content: bed files - reads per gene (featureCounts)
Library strategy: Ribo-Seq

molecule: other

organism: Pseudomonas aeruginosa UCBPP-PA14

source_name: bacteria

growth_protocol: planctonic growth in LB medium at 37°C, OD600 of 0.6

extract_protocol:
RNA footprints were isolated from monosome fractions with Tri-Reagent (Zymo clean and concentrator). Total bacterial RNA from the same culture was extracted using the RNeasy Mini Kit from Qiagen.
NEBNext Multiplex small RNA library prep for Illumina (E7300) using custom multiplex primers.

value: bacteria


title: G5: 100 µg MD39.3 protein at week 8 GEX

description: Library name: MD39_3_PBMC_Wk8_Gr5_GEX

value: PBMC


title: 38FIleuR

description:
Library name: Sample 38
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: RiboSeq of Pseudomonas aeruginosa UCBPP-PA14 WT 2

description: Library name: RiboSeq_PA14_WT_PL_2


title: 36FValR

description:
Library name: Sample 36
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide

value: Valine restricted


title: Differentiated LUHMES with 4sU and HSV-1 8hpi Rep1

description: Library name: diff_8h_4sU_1


title: RiboSeq of Pseudomonas aeruginosa UCBPP-PA14 dPA14_71820 and dPA14_53180 3

description: Library name: RiboSeq_PA14_dtrhPO_PL_3


title: Positively supercoiled pBR322 DNA cleaved by Mt gyrase with cip replicate 3

city: Bethesda

first: Ian

middle: L

last: Morgan

state: MD

address: 50 Center Dr.

institute: National Heart Lung and Blood Institute

description: Library name: pos_sc_Mt_gyrase_cip_rep3

data_processing:
Trimmomatic to trim adapters from reads
BWA-MEM to align the reads to the reference sequence
SAMtools to index the reads
Pysam to extract reads, count enzyme-cleaved DNA ends, and normalize counts by spikein reads
Assembly: pBR322_plus_spikes.fa
Supplementary files format and content: TXT file with number and location of enzyme-cleaved DNA ends from forward and reverse reads

organism: Synthetic plasmid

source_name: Synthetic plasmid

growth_protocol: Supercoiled pBR322 DNA was treated with no enzyme, B. anthracis gyrase, B. anthracis topo IV, or M. tuberculosis gyrase.

extract_protocol:
Qiagen PCR Clean-up Kit
SHAN-seq

value: Synthetic plasmid

value: 100 uM ciprofloxacin


title: Positively supercoiled pBR322 DNA cleaved by Mt gyrase with cip replicate 1

description: Library name: pos_sc_Mt_gyrase_cip_rep1


title: RiboSeq of Pseudomonas aeruginosa UCBPP-PA14 WT 1

description: Library name: RiboSeq_PA14_WT_PL_1


title: Positively supercoiled pBR322 DNA cleaved by Mt gyrase with cip replicate 2

description: Library name: pos_sc_Mt_gyrase_cip_rep2


title: G2: 100 µg MD39.3 gp151 mRNA at week 8 GEX

description: Library name: MD39_3_PBMC_Wk8_Gr2_GEX

value: B cell


title: OS myobudles, ground control, Day 2 Rep1

city: Orlando

first: Siobhan

last: Malany

state: FL

address: 6550 Sanger Rd

department: Department of Cellular and Systems Pharmacology

institute: UF Research and Academic Center at Lake Nona

description: Library name: GE6461_19_human_muscle_OS_d2_MP22 Chip 10

data_processing:
Bases called with Illumina sequencing machine (Novaseq X); files contain raw reads
Assembly: GRch38
Supplementary files format and content: tab-delimited matrix file, containing non-normalized FPKM values for all genes in all samples

source_name: muscle

growth_protocol: Injectable hydrogel mixtures (3.3 mg/mL rat tail collagen I, and 22% (v/v) Matrigel) were combined with YA- and OS-derived CD56+ enriched myoblasts. The cell-laden hydrogels were injected into the PDMS chips to a final cell density of 15 and 20 million cells/mL for YA- and OS-derived cells, respectively. Cells were allowed to polymerize at 37°C for 60 min and seeding ports were sealed using polylactic acid (PLA, Makerbot, Brooklyn, NY) plugs. Chips were perfused with degassed Skeletal Muscle Growth media supplemented with 0.1 mg/ml Primocin (InvivoGen, San Diego, CA) at a constant flow rate of 1 mL/h at 37°C and 5% CO2.

extract_protocol:
RNA was harvested using Quiagen kit. Illumina TruSeq RNA Sample Prep Kit was used with 0.5 ug of total RNA for the construction of sequencing libraries.
Sample quality was assessed using the Agilent TapeStation 4200 (Agilent Technologies, Inc). 250 ng of total RNA was used for library construction using NEB Ultra II Directional RNA-seq library preparation kit for Illumina according to manufacturer's protocol. First, 100 ng of total RNA was used for mRNA isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, catalog # E7490). Then followed by RNA library construction with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Briefly, RNA was fragmented in NEBNext First Strand Synthesis Buffer via incubation at 94 °C for the desired time. This step was followed by first-strand cDNA synthesis using reverse transcriptase and random hexamer primer.  Synthesis of ds-cDNA was performed using the 2nd strand master mix provided in the kit, followed by end-repair and adaptor ligation.  At this point, Illumina adaptors were ligated to the sample.  Finally, each library (uniquely barcoded) was enriched by 12 cycles of amplification, and purified with Agencourt AMPure beads (Beckman Coulter, catalog # A63881). 15 barcoded libraries were sized on the TapeStation 4200 and quantified with the Qubit® 2.0 Fluorometer. Finally, Barcoded libraries were pooled equimolarly for sequencing simultaneously for NovaSeq

treatment_protocol: Young- and old-derived skeletal muscle myobundles were exposed to microgravity for 12 days and matching ground control group in presence and absence of electrical stimulation.

value: muscle

value: Enriched CD56+ myoblasts

value: Wild type ( cell line)

value: OS ground control - undifferentiated


title: 34FValR

description:
Library name: Sample 34
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide

value: Brain


title: OS myobudles, ground control, Day 2 Rep2

description: Library name: GE6461_20_human_muscle_OS_d2_MP22 Chip 11


title: 35FValR

description:
Library name: Sample 35
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: RiboSeq of Pseudomonas aeruginosa UCBPP-PA14 dPA14_71820 and dPA14_53180 2

description: Library name: RiboSeq_PA14_dtrhPO_PL_2


title: 33FValR

description:
Library name: Sample 33
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: Negatively supercoiled pBR322 DNA cleaved by Mt gyrase with cip replicate 1

description: Library name: neg_sc_Mt_gyrase_cip_rep1


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 WT 3

description: Library name: RNAseq_PA14_WT_PL_3

data_processing:
cutadapt , min read length 22
bowtie 2 - mapping to P. aeruginosa PA14 (NC_008463.1) reference genome, option “--very-sensitive-local”.
featureCounts
RiboSeq_PA14_dtrhPO_PL_1 was removed as a strong outlier in plotMDS (R package edgeR) - Methodological errors cannot be ruled out for this replication.
Assembly: NC_008463.1
Supplementary files format and content: bed files - reads per gene (featureCounts)


title: YA myobudles, ground control, Day 2 Rep3

description: Library name: GE6461_15_human_muscle_YA_d2_MP22 Chip 4

value: YA ground control - undifferentiated


title: YA myobudles, ground control, Day 2 Rep2

description: Library name: GE6461_14_human_muscle_YA_d2_MP22 Chip 2


title: 32FValR

description:
Library name: Sample 32
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide

value: Female


title: OS myobudles, ground control, Day 2 Rep3

description: Library name: GE6461_21_human_muscle_OS_d2_MP22 Chip 12


title: YA myobudles, ground control, Day 2 Rep1

description: Library name: GE6461_13_human_muscle_YA_d2_MP22 Chip 1


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 WT 2

description: Library name: RNAseq_PA14_WT_PL_2


title: Negatively supercoiled pBR322 DNA cleaved by Mt gyrase with cip replicate 3

description: Library name: neg_sc_Mt_gyrase_cip_rep3


title: Positively supercoiled pBR322 DNA cleaved by Mt gyrase replicate 3

description: Library name: pos_sc_Mt_gyrase_rep3

value: Calcium


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 WT 1

description: Library name: RNAseq_PA14_WT_PL_1


title: 30FCon

description:
Library name: Sample 30
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide

value: Control


title: No E-stim OS myobudles, microgravity, Day 21 Rep3

description: Library name: GE6867_24_human_muscle_OS_NoEstim_SpX25_Chip_15_7-368_5-320_L001

value: OS microgravity ( No EStim)-differentiated


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 dPA14_71820 and dPA14_53180 3

description: Library name: RNAseq_PA14_dtrhPO_PL_3


title: Positively supercoiled pBR322 DNA cleaved by Mt gyrase replicate 2

description: Library name: pos_sc_Mt_gyrase_rep2

value: Calcum


title: Positively supercoiled pBR322 DNA cleaved by Mt gyrase replicate 1

description: Library name: pos_sc_Mt_gyrase_rep1


title: Negatively supercoiled pBR322 DNA cleaved by Mt gyrase with cip replicate 2

description: Library name: neg_sc_Mt_gyrase_cip_rep2


title: No E-stim OS myobudles, microgravity, Day 21 Rep2

description: Library name: GE6867_23_human_muscle_OS_NoEstim_SpX25_Chip_14_7-367_5-319_L001

value: OS microgravity ( No EStim) -differentiated


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 dPA14_71820 and dPA14_53180 1

description: Library name: RNAseq_PA14_dtrhPO_PL_1

value: bacteria


title: Negatively supercoiled pBR322 DNA cleaved by Mt gyrase replicate 3

description: Library name: neg_sc_Mt_gyrase_rep3


title: 29FCon

description:
Library name: Sample 29
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: Negatively supercoiled pBR322 DNA cleaved by Mt gyrase replicate 2

description: Library name: neg_sc_Mt_gyrase_rep2


title: 27FCon

description:
Library name: Sample 27
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: 28FCon

description:
Library name: Sample 28
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 dPA14_71820 and dPA14_53180 2

description: Library name: RNAseq_PA14_dtrhPO_PL_2


title: No E-stim OS myobudles, microgravity, Day 21 Rep1

description: Library name: GE6867_22_human_muscle_OS_NoEstim_SpX25_Chip_13_7-366_5-318_L001


title: E-stim OS myobudles, microgravity, Day 21 Rep3

description: Library name: GE6867_21_human_muscle_OS_Estim_SpX25_Chip_7_7-365_5-317_L001

value: OS microgravity ( EStim) -differentiated


title: Negatively supercoiled pBR322 DNA cleaved by Mt gyrase replicate 1

description: Library name: neg_sc_Mt_gyrase_rep1

value: Synthetic plasmid


title: 31FValR

description:
Library name: Sample 31
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide

value: Valine restricted


title: 25FCon

description:
Library name: Sample 25
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: Positively supercoiled pBR322 DNA cleaved by Ba topo IV with cip replicate 2

description: Library name: pos_sc_Ba_topoIV_cip_rep2

value: 100 uM ciprofloxacin


title: E-stim OS myobudles, microgravity, Day 21 Rep2

description: Library name: GE6867_20_human_muscle_OS_Estim_SpX25_Chip_6_7-364_5-316_L001

value: muscle


title: Positively supercoiled pBR322 DNA cleaved by Ba topo IV with cip replicate 3

description: Library name: pos_sc_Ba_topoIV_cip_rep3


title: E-stim OS myobudles, microgravity, Day 21 Rep1

description: Library name: GE6867_19_human_muscle_OS_Estim_SpX25_Chip_5_7-363_5-315_L001

value: Enriched CD56+ myoblasts


title: No E-stim YA myobudles, microgravity, Day 21 Rep3

description: Library name: GE6867_18_human_muscle_YA_NoEstim_SpX25_Chip_11_7-362_5-314_L001

value: Wild type ( cell line)

value: YA microgravity ( No EStim) -differentiated


title: 24MLeuR

description:
Library name: Sample 24
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide

value: Brain

value: Leucine restricted

value: Male


title: No E-stim YA myobudles, microgravity, Day 21 Rep2

description: Library name: GE6867_17_human_muscle_YA_NoEstim_SpX25_Chip_10_7-361_5-313_L001


title: Negatively supercoiled pBR322 DNA cleaved by Ba topo IV with cip replicate 3

description: Library name: neg_sc_Ba_topoIV_cip_rep3


title: Positively supercoiled pBR322 DNA cleaved by Ba topo IV with cip replicate 1

description: Library name: pos_sc_Ba_topoIV_cip_rep1


title: 23MLeuR

description:
Library name: Sample 23
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: No E-stim YA myobudles, microgravity, Day 21 Rep1

description: Library name: GE6867_16_human_muscle_YA_NoEstim_SpX25_Chip_9_7-360_5-312_L001

value: YA microgravity ( No EStim)-differentiated


title: 22MLeuR

description:
Library name: Sample 22
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: E-stim YA myobudles, microgravity, Day 21 Rep3

description: Library name: GE6867_15_human_muscle_YA_Estim_SpX25_Chip_3_7-359_5-311_L001

value: YA microgravity ( EStim) -differentiated


title: 21MLeuR

description:
Library name: Sample 21
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: E-stim YA myobudles, microgravity, Day 21 Rep2

description: Library name: GE6867_14_human_muscle_YA_Estim_SpX25_Chip_2_7-358_5-310_L001


title: Negatively supercoiled pBR322 DNA cleaved by Ba topo IV with cip replicate 1

description: Library name: neg_sc_Ba_topoIV_cip_rep1


title: 26FCon

description:
Library name: Sample 26
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide

value: Control

value: Female


title: Negatively supercoiled pBR322 DNA cleaved by Ba topo IV with cip replicate 2

description: Library name: neg_sc_Ba_topoIV_cip_rep2


title: E-stim YA myobudles, microgravity, Day 21 Rep1

description: Library name: GE6867_13_human_muscle_YA_Estim_SpX25_Chip_1_7-357_5-309_L001


title: No E-stim OS myobudles, ground control, Day 21 Rep3

description: Library name: GE6867_12_human_muscle_OS_NoEstim_TOCO2GC__Chip_16_7-356_5-308_L001

value: OS ground control (No  EStim) -differentiated


title: 18MIleuR

description:
Library name: Sample 18
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide

value: Isoleucine restricted


title: 20MLeuR

description:
Library name: Sample 20
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: Positively supercoiled pBR322 DNA cleaved by Ba topo IV replicate 3

description: Library name: pos_sc_Ba_topoIV_rep3

value: Calcium


title: 17MIleuR

description:
Library name: Sample 17
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: Positively supercoiled pBR322 DNA cleaved by Ba topo IV replicate 2

description: Library name: pos_sc_Ba_topoIV_rep2

value: Synthetic plasmid

value: Calcum


title: 19MLeuR

description:
Library name: Sample 19
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: No E-stim OS myobudles, ground control, Day 21 Rep2

description: Library name: GE6867_11_human_muscle_OS_NoEstim_TOCO2GC__Chip_15_7-355_5-307_L001


title: No E-stim OS myobudles, ground control, Day 21 Rep1

description: Library name: GE6867_10_human_muscle_OS_NoEstim_TOCO2GC__Chip_13_7-354_5-306_L001


title: Negatively supercoiled pBR322 DNA cleaved by Ba topo IV replicate 1

description: Library name: neg_sc_Ba_topoIV_rep1


title: Negatively supercoiled pBR322 DNA cleaved by Ba topo IV replicate 3

description: Library name: neg_sc_Ba_topoIV_rep3


title: No E-stim YA myobudles, ground control, Day 21 Rep3

description: Library name: GE6867_9_human_muscle_YA_NoEstim_TOCO2GC__Chip_12_7-353_5-305_L001

value: YA ground control (No  EStim) -  differentiated


title: 16MIleuR

description:
Library name: Sample 16
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: 15MIleuR

description:
Library name: Sample 15
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: Negatively supercoiled pBR322 DNA cleaved by Ba topo IV replicate 2

description: Library name: neg_sc_Ba_topoIV_rep2


title: 14MIleuR

description:
Library name: Sample 14
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: Positively supercoiled pBR322 DNA cleaved by Ba gyrase with cip replicate 3

description: Library name: pos_sc_Ba_gyrase_cip_rep3

value: 100 uM ciprofloxacin


title: Positively supercoiled pBR322 DNA cleaved by Ba gyrase with cip replicate 2

description: Library name: pos_sc_Ba_gyrase_cip_rep2


title: No E-stim YA myobudles, ground control, Day 21 Rep1

description: Library name: GE6867_7_human_muscle_YA_NoEstim_TOCO2GC__Chip_9_7-351_5-303_L001

value: muscle

value: Enriched CD56+ myoblasts


title: 13MIleuR

description:
Library name: Sample 13
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: Positively supercoiled pBR322 DNA cleaved by Ba topo IV replicate 1

description: Library name: pos_sc_Ba_topoIV_rep1


title: E-stim OS myobudles, ground control, Day 21 Rep3

description: Library name: GE6867_6_human_muscle_OS_Estim_TOCO2GC__Chip_8_7-350_5-302_L001

value: Wild type ( cell line)

value: OS ground control ( EStim) - differentiated


title: 12MValR

description:
Library name: Sample 12
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide

value: Brain

value: Valine restricted


title: E-stim OS myobudles, ground control, Day 21 Rep2

description: Library name: GE6867_5_human_muscle_OS_Estim_TOCO2GC__Chip_7_7-349_5-301_L001


title: Positively supercoiled pBR322 DNA cleaved by Ba gyrase with cip replicate 1

description: Library name: pos_sc_Ba_gyrase_cip_rep1


title: 11MValR

description:
Library name: Sample 11
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide

value: Male


title: 9MValR

description:
Library name: Sample 9
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: E-stim YA myobudles, ground control, Day 21 Rep3

description: Library name: GE6867_3_human_muscle_YA_Estim_TOCO2GC__Chip_4_7-347_5-299_L001

value: YA ground control ( EStim) -differentiated


title: 10MValR

description:
Library name: Sample 10
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: E-stim OS myobudles, ground control, Day 21 Rep1

description: Library name: GE6867_4_human_muscle_OS_Estim_TOCO2GC__Chip_6_7-348_5-300_L001


title: E-stim YA myobudles, ground control, Day 21 Rep2

description: Library name: GE6867_2_human_muscle_YA_Estim_TOCO2GC__Chip_3_7-346_5-298_L001


title: Negatively supercoiled pBR322 DNA cleaved by Ba gyrase with cip replicate 3

description: Library name: neg_sc_Ba_gyrase_cip_rep3


title: E-stim YA myobudles, ground control, Day 21 Rep1

description: Library name: GE6867_1_human_muscle_YA_Estim_TOCO2GC__Chip_2_7-345_5-297_L001


title: Negatively supercoiled pBR322 DNA cleaved by Ba gyrase with cip replicate 2

description: Library name: neg_sc_Ba_gyrase_cip_rep2


title: Negatively supercoiled pBR322 DNA cleaved by Ba gyrase with cip replicate 1

description: Library name: neg_sc_Ba_gyrase_cip_rep1


title: 8MValR

description:
Library name: Sample 8
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: 7MValR

description:
Library name: Sample 7
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: IVT mRNA, treated, rep#2

city: Chicago

first: Cheng-Wei

last: Ju

state: Illinois

address: 929 East 57th Street, GCIS, Room E313

institute: The University of Chicago

data_processing:
The sequencing data were all trimmed with cutadapt tool (v4.8) to remove adapters and low-quality reads. PCR duplicates were removed with BBMap tool (v.38.73), 5-mer random barcodes at reads ends were trimmed and low-quality or short reads (less than 20 nt) were removed using cutadapt tool.
For tRNAs, remaining reads were aligned to tRNA sequence obtained from GtRNAdb (https://gtrnadb.ucsc.edu/) using hisat-3n (v.2.2.1-3n-0.0.3). Mitochondria and chloroplast tRNA sequences are obtained from published papers.
Meanwhile, we have also aligned remaining reads to hg38, mm10, or TAIR10 genome using hisat3n to investigate D sites in other RNA species.
The generated table from hisat-3n were parsed and analyzed by inhouse scripts. Internal mutation ratio at each D candidate site suggested by hisat-3n, was further confirmed by direct IGV visualization (v.2.8.0).
Assembly: mm10 (GRCm38.102), hg38 (GRCh38.107), TAIR10
Supplementary files format and content: For samples with cellular RNA, the mutation ratio at D sites in treated, input samples are shown. For samples with RNA probes, mutations at D sites are shown.
Library strategy: Chemical Reduction Assisted Cytosine Incorporation sequencing (CRACI)

source_name: IVT mRNA

growth_protocol: Human HepG2 cell lines and mouse embryonic stem cells (mESC) used in this study were all purchased from ATCC (the American Type Culture Collection). HepG2 cell lines were maintained in DMEM (GIBCO, 11995), supplemented with 10% FBS and 1% 100X Pen/Strep (GIBCO). mESC cells were grown under a typical feeder-free culture condition: cells were cultured in DMEM (GIBCO, 11995), supplemented with 15% FBS, 1% Pen/Strep (GIBCO), 1X Glutamax (GIBCO), 1X non-essential amino acids (GIBCO), 1X 2-Mercaptoethanol (GIBCO), and 1000 U/ml leukemia inhibitory factor (Millipore, ESG1107), together with two inhibitors: 3 mM CHIR99021 (STEMCELL Technologies, dissolved in DMSO) and 1 mM PD0325901 (STEMCELL Technologies, dissolved in DMSO). mESC cells were distinctively cultured on gelatinized culture plates (0.2% Gelatin). The culture of mESC cells were passaged every 2 days. All cells were cultured at 37 Co under 5.0% CO2.

extract_protocol:
Generally, with harvesting cells as the first step, the media was aspirated, and the cells were washed once with proper volume of ice cold DPBS buffer for each plate. Then total RNA was isolated from cells with TRIzol reagent (Invitrogen) and then extracted following manufacturer’s protocol by isopropanol precipitation. Small RNA fraction was purified from total RNA with RNA Clean & Concentrator kit (Zymo Research) following manufacturer’s protocol. mRNA was extracted by two rounds of polyA+ purification with Dynabeads mRNA DIRECT kit (Ambion).
CRACI for D site detection Wild-type HepG2, mESC, and arabidopsis thaliana seedling cells (two replicates for each sample, one 10-cm plate per replicate); HepG2 siControl or DUS knockdown cells were prepared as described (two replicates for each sample, one 10-cm plate per replicate). After extracting the polyA+ RNA or small RNA from mammalian cells or plant cells, around 100 ng RNA was fragmented using RNA Fragmentation Reagents (catalog no. AM8740, Invitrogen) and heated at 70 °C for 14 min, followed by purification with Oligomer Clean and Concentrator (Zymo Research). 3′-End repair and 5′-phosphorylation were conducted with T4 polynucleotide kinase (PNK) (catalog no. EK0032, Thermo Fisher Scientific). RNA was mixed with 3 µL 10× T4 PNK reaction buffer (catalog no. B0201S, NEB) and 3 µl T4 PNK, diluted to a final volume of 30 µl, and incubated at 37 °C for 45 min; then 1.5 µl T4 PNK and 1.5 µl 10 mM ATP were added for another incubation at 37 °C for 45 min, followed by Oligomer Clean and Concentrator (Zymo Research) purification eluting with 10 µl RNase-free water.  To perform 3′-adapter ligation, 10 µl 3′-repaired and 5′-phosphorylated RNA fragments were incubated with 1.0 µl 20 µM RNA 3′ SR Adapter (5′App-NNNNNATCACG AGATCGGAAGAGCACACGTCT-3SpC3, with ATCACG as the inline barcode) at 70 °C for 2 mins and placed immediately on ice. Then, 2.5 µl 10× T4 RNA Ligase Reaction Buffer (catalog no. M0373L, NEB), 7.5 µl PEG8000 (50%), 1 µl SUPERase•In RNase Inhibitor and 2 µl T4 RNA Ligase 2 truncated KQ (catalog no. M0373L, NEB) were added to the RNA–adapter mixture48,49. The reaction was incubated at 25 °C for 2 h followed by 16 °C for 10 h. The reaction was further diluted to 47 µl with nuclease-free water, and the excessive adapters were removed with 2 µl 5′-deadenylase (catalog no. M0331S, NEB) at 30 °C for 45 min followed by adding 1 µl RecJf (catalog no. M0264L, NEB) for ssDNA digestion at 37 °C for 45 min. The 3′-end-ligated RNA was extracted by RNA Clean and Concentrator (Zymo Research) and eluted with 10 µl RNase-free water. The purified RNA was incubated with 1.2 µl 10 µM 5′ SR Adapter (5′-GUUCAGAGUUCUACAGUCCGACGAUC -3′) at 70 °C for 2 mins and placed immediately on ice. Then 2.5 µl 10× T4 RNA ligase reaction buffer, 1.0 µl 25 mM ATP, 10 µl PEG8000 (50%) and 1 µl T4 RNA Ligase 1 (high concentration, catalog no. M0437M, NEB) were added to the RNA–adapter mixture. The reaction was mixed well and incubated at 25 °C for 8 h, followed by RNA Clean and Concentrator (Zymo Research) purification, eluting with 12 µl RNase-free water.  A 2 µl aliquot of the purified RNA was saved for ‘Input1’ library construction, 2 µl aliquot of the purified RNA was saved for ‘Input2’ library construction, and the rest 6 µl was subjected to CRACI optimized reduction treatment, as the ‘Treated’ sample. The 6 µl RNA was mixed with 40 µl freshly prepared KBH4 (1 M KBH4, prepared by dissolving 54 mg KBH4 in 1000 µl RNase-free water) and Incubated the reaction mixture at 25 °C for 3 h, followed by purification with RNA Clean and Concentrator (Zymo Research) and elute with 10 µl H2O. ‘Input1’, ‘Input2’ and purified ‘Treated’ samples were diluted to 10 µl and mixed with 1.0 µl 2.0 µM SR RT primer (5′-AGACGTGTGCTCTTCCGATCT -3′) at 65 °C for 2 min and moved immediately onto ice. Then for ‘Input2’ and ‘Treated’ samples, a stock with 2 µl 10x AMV RT Buffer (New England BioLabs, cat. no. B0277AVIAL), 2 µl 1 mM dNTP Solution Mix (dilute from 10 mM dNTP Solution Mix, New England BioLabs, catalog no. N0447L), 2 µl 10mM dGTP (dilute from 100 mM dNTP Solution Mix, New England BioLabs, catalog no. N0442S), 1 µl RNaseOUT Recombinant Ribonuclease Inhibitor (catalog no. 10777019, Thermo Scientific) and 2 µl HIV RT (Worthington Biochemical, catalog no. LS05003) was added. For ‘Input1’ sample, a stock with 2 µl RNase-free water, 2 µl 10x AMV RT Buffer, 2 µl 10 mM dNTP Solution Mix (New England BioLabs, catalog no. N0447L), 1 µl RNaseOUT Recombinant Ribonuclease Inhibitor and 2 µl HIV RT was added.  The reaction mixture was heated at 70 °C for 5 min and then cDNA was purified using DNA Clean and Concentrator (Zymo Research). The eluted cDNAs (20 µl) were stored at –80 °C; 4 µl was used for each 15-cycle PCR amplification reaction, which was performed with the SR Primer for Illumina (NEB) and indexed primers (from NEBNext Multiplex Oligos for Illumina). All libraries were purified on a 3.5% low melting point agarose gel and sequenced on Illumina NovaSeqX with single-end 100 bp read length.

value: WT (IVT)

value: IVT mRNA

tag: fraction

value: mRNA


title: Positively supercoiled pBR322 DNA cleaved by Ba gyrase replicate 2

description: Library name: pos_sc_Ba_gyrase_rep2


title: No E-stim YA myobudles, ground control, Day 21 Rep2

description: Library name: GE6867_8_human_muscle_YA_NoEstim_TOCO2GC__Chip_11_7-352_5-304_L001


title: IVT mRNA, treated, rep#1

tag: genotype


title: IVT mRNA, input2, rep#2


title: IVT mRNA, input2, rep#1


title: Negatively supercoiled pBR322 DNA cleaved by Ba gyrase replicate 3

description: Library name: neg_sc_Ba_gyrase_rep3


title: 3MCon

description:
Library name: Sample 3
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide

value: Control

tag: Sex


title: Negatively supercoiled pBR322 DNA cleaved by Ba gyrase replicate 2

description: Library name: neg_sc_Ba_gyrase_rep2

tag: cell type


title: Positively supercoiled pBR322 DNA cleaved by Ba gyrase replicate 3

description: Library name: pos_sc_Ba_gyrase_rep3

value: Calcium


title: Negatively supercoiled pBR322 DNA cleaved by Ba gyrase replicate 1

description: Library name: neg_sc_Ba_gyrase_rep1

value: Synthetic plasmid


title: Gallus_2

city: Sherbrooke

first: Michelle

middle: S

last: Scott

state: QC

address: 3201 Jean-Mignault

country: Canada

institute: Université de Sherbrooke

description:
Library name: Sample 2
small RNAs (<300 nt)

data_processing:
Base callings were converted to fastq using bcl2fastq v2.20.0 with the following parameters for S. pombe, S. cerevisiae and M. musculus: --minimum-trimmed-read-length 13 --mask-short-adapter-reads 13 --no-lane-splitting -p 32. Base callings were converted to fastq using bases2fastq v1.2.0 with the following parameters for G. gallus and M. mulatta: -p 36 –detect-adapters --filter-mask R1:N*-R2:N*.
Trimming of paired-end reads was performed using Trimmomatic v0.36 (parameters: ILLUMINACLIP:<fastaWithAdaptersEtc>:2:12:10:8, TRAILING:30, LEADING:30, MINLEN:20) in order to remove adapters and low-quality reads.
FastQC v0.11.5 was used before and after trimming to assess the quality of the reads.
Alignment of reads to the reference genome was performed using STAR v2.6.1a (parameters: --runMode alignReads, --outSAMunmapped None, --outSAMtype BAM SortedByCoordinates, outFilterScoreMinOverLread 0.3, --outFilterMatchNminOverLread 0.3, --outFilterMultimapNmax 100, --winAnchorMultimapNmax 100, --alignEndsProtrude 5 ConcordantPair). The index needed to align reads was generated using STAR v2.6.1a (parameters: --runMode genomeGenerate, --sjdbOverhang 74)
Gene expression normalized in transcript per million (TPM) was obtained using CoCo v0.2.1p4 (parameters: cc, --countType both, --strand 1 --paired)
Assembly: GRCg7b (G. gallus), Mmul_10 (M. mulatta), GRCm39 (M. musculus), R64-1-1 (S. cerevisiae), ASM294v2 (S. pombe)
Supplementary files format and content: A tab-separated (.tsv) file showing the gene id, gene name and abundance (in TPM) of all annotated genes for each sample in the given species.

organism: Gallus gallus

source_name: Universal Chicken RNA

growth_protocol: Wild type 10H3 S. cerevisiae cultures were grown in Yeast Extract Peptone Dextrose (YEPD) rich media at 26°C. Wild type yAS99 S. pombe cultures were grown to mid-log phase in 25 mL of YES media at 32°C.

extract_protocol:
Phenol-chloroform RNA extraction was performed for M. musculus, S. cerevisiae and S. pombe, whereas no RNA extraction was needed for the Biochain-purchased RNA for G. gallus and M. mulatta.
TGIRT-Seq libraries were constructed as described previously (Boivin et al., RNA, 2018) using ribodepleted total RNA (S. cerevisiae and M. musculus) or gel-purified and size-selected small RNAs (S. pombe, M. mulatta and G. gallus).

value: Universal Chicken RNA


title: IVT mRNA, input1, rep#2


title: 2MCon

description:
Library name: Sample 2
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: IVT mRNA, input1, rep#1


title: HepG2, WT, mRNA, treated, rep#3

value: WT


title: HepG2, WT, mRNA, treated, rep#2


title: 5MCon

description:
Library name: Sample 5
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: 1MCon

description:
Library name: Sample 1
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide


title: Positively supercoiled pBR322 DNA cleaved by Ba gyrase replicate 1

description: Library name: pos_sc_Ba_gyrase_rep1


title: ILT3+ sample 2

city: Mainz

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v7.0.3 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Spleen and lymph nodes

extract_protocol:
-
RNA quality was assessed on a Bioanalyzer 2100 using a RNA 6000 Pico chip (both from Agilent, Santa Clara, CA). 1 ng of total RNA (integrity > 8) was used to generate full-length cDNA amplified  using SmartSeq V2 (Takarabio). Barcoded libraries have been generated using Nextera XT kit (Illumina). Library was quantified using the Qubit HS assay kit (Thermo Fisher) and the library size distribution was determined using the Bioanalyzer HS DNA assay (Agilent).

treatment_protocol: untreated

value: Spleen and lymph nodes

value: ILT3+CD4+CD25+ T cells

value: untreated


title: ILT3+ sample 1


title: ILT3+ sample 3


title: HepG2, WT, mRNA, input2, rep#3


title: Gallus_1

description:
Library name: Sample 1
small RNAs (<300 nt)


title: HepG2, WT, mRNA, treated, rep#1


title: Covid19 Severe- Replicate 2

city: Bengaluru

first: Sudarson

last: Sundarrajan

address: Sri Shankara Research Centre 1st Cross, RM hospital, Shankara Matt Premises, Shankarapuram, Basavanagudi

department: Molecular Biology

country: India

institute: Cancyte Technologies Private Limited

hyb_protocol: Total RNA was processed using the Nanostring nCounter Human Immunology V2 panel (XT-CSO-HIM2-12)

scan_protocol: Hybridized molecules are loaded to Nanostring sprint catridge and loaded onto nCounter SPRINT machine for scanning the barcodes. Raw counts data (.RCC) was retrieved from the machine after the scanning completes.

data_processing: Raw data were normalized using nSolver 4.0 software. Normalization of the raw data was performed using the positive control probes and Codeset probes as per the instructions in the manual (nSolverTM 4.0 Analysis Software User Manual (MAN-C0019-08)).

source_name: Covid19 Severe

label_protocol: NanoString uses combination of oligonucleotide based barcodes. Each probe hybridising the mRNAs will be unique with combination of color dye combination which are barcoded barcodes.

extract_protocol: Total RNA was extracted using Qiagen/Pre Analytix PAXgene Blood miRNA kit (Cat No. 763134) from all the samples.

tag: disease

value: Covid19 Severe

tag: age

tag: test

value: Positive for Covid by RT-PCR


title: 4MCon

description:
Library name: Sample 4
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide

value: Brain


title: ILT3- sample 3

value: ILT3-CD4+CD25+ T cells


title: Covid19 Severe- Replicate 1

value: Female


title: HepG2, WT, mRNA, input2, rep#2


title: ILT3- sample 2


title: Negative Control- Replicate 1

source_name: Negative Control

value: Negative Control

value: Male

value: Negative for Covid/RT-PCR


title: ILT3- sample 1


title: HepG2, WT, mRNA, input1, rep#3

value: mRNA


title: HepG2, WT, mRNA, input2, rep#1


title: mmYS-24pe, Young Sed, 24h Post-Ex, Male5

city: Ann Arbor

first: Andrew

last: Ludlow

state: Education

address: 830 N University Ave

institute: University of Michigan

data_processing:
MinKNOW v22.03.4 (parameter: q-score > 8)
Sequence reads were mapped to GRCm39/mm39 using minimap2 v2.14 (parameters: default) and subsequently converted to SAM files using SAMtools v1.13.
Read count extraction was performed using TALON (parameters: coverage=0.75, identity=0.8)
Assembly: GENCODE Release M29 (GRCm39/mm39)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Skeletal Muscle (gastrocnemius)

extract_protocol:
Total RNA from powdered tissues were isolated using the RNeasy Plus Universal Mini Kit (Qiagen, Cat# 73404). 1.2 μg of total RNA was used to isolate poly(A)-containing RNA with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Cat# E7490S).
1 ng of poly(A)-mRNA isolates was used synthesize barcoded PCR-cDNA libraries (Oxford Nanopore Technologies®, Cat# SQK-PCB109).

value: Skeletal Muscle (gastrocnemius)

value: 24 hours post-exercise

value: hTERT

value: male


title: Healthy Control- Replicate 3

source_name: Healthy Control

value: Healthy Control


title: Healthy Control- Replicate 2


title: HepG2, WT, mRNA, input1, rep#2

value: WT


title: HepG2, WT, mRNA, input1, rep#1


title: HepG2, siDUS4, SR, treated, rep#2

value: siDUS4 Knockdown

value: small RNA (<200 nt)


title: mmYS-24pe, Young Sed, 24h Post-Ex, Female3

value: female


title: 6MCon

description:
Library name: Sample 6
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide

value: Control


title: Healthy Control -Replicate 1


title: mmYS-24pe, Young Sed, 24h Post-Ex, Male1


title: mmYS-1pe, Young Sed, 1h Post-Ex, Male5

value: 1 hour post-exercise


title: Covid19 (0th day)- Replicate 2

source_name: Covid19 (0th day)

value: Covid19 (0th day)

value: Positive for Covid by RT-PCR


title: Negative Control- Replicate 2

value: Negative Control

value: Female

value: Negative by RT-PCR


title: HepG2, siDUS4, SR, input2, rep#1


title: mmYS-1pe, Young Sed, 1h Post-Ex, Female4


title: Pig S100a1_4, heart, 14 weeks post MI

city: Heidelberg

first: Patrick

last: Most

address: INF 410

institute: University Hospital Heidelberg

description: Library name: Sample 21B

data_processing:
Analysis of fastq files was performed in R (version 4.1.2)
Quality control: fastqcr (version 0.1.2) and FastQC (version 0.11.8)
Mapping against pig genome: Rsubread (version 2.7.1, annotation release 106)
For pathway analyses, pig annotations were mapped to corresponding human annotations using org.Ss.eg.db (version 3.13.0) and org.Hs.eg.db (version 3.13.0). Genome wide annotation for Human. R package version 3.8.2. 2019. Annotations that could not be mapped with these packages (14.9 %) were blasted with blastn from ncbi-blast+ (version 2.9.0-2) with rBLAST (version 0.99.2) and the best hit for mapping was identified as subject hit with sequence identity above 80 % and the lowest mean e-value below 0.01 and assigned to the queried annotation.
Gene expression: DESeq2 (version 1.33.1)
Weighted gene correlation network analysis: (WGCNA, version 1.70-3)
Additional analyses: pcaExplorer (version 2.19.0), PCAtools (version 2.5.0), clusterProfiler (version 4.1.0) and ReactomePA (version 1.37.0) based on variance stabilizing transformation (VST)-normalized feature counts
Assembly: Sscrofa11.1_GCF_000003025.6, PMID: 30783653
Supplementary files format and content: csv file contains VST normalized feature counts

organism: Sus scrofa

source_name: myocardium

extract_protocol:
Total RNA was harvested using AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany).
Sequencing libraries were prepared with TruSeq RiboZero Kits (Illumena, Santa Clara, CA)

value: myocardium


title: Pig S100a1_3, heart, 14 weeks post MI

description: Library name: Sample 15B


title: Covid19 (0th day)- Replicate 1


title: HepG2, siDUS4, SR, input2, rep#2


title: Covid19 (14th day)-Replicate 2

source_name: Covid19 (14th day)

value: Covid19 (14th day)

value: Test not conducted


title: Covid19 (14th day)- Replicate 1

value: Male


title: mmYS-1pe, Young Sed, 1h Post-Ex, Female3

value: Skeletal Muscle (gastrocnemius)

value: hTERT


title: Pig S100a1_2, heart, 14 weeks post MI

description: Library name: Sample 9B


title: mmYS-24pe, Young Sed, 24h Post-Ex, Female4

value: 24 hours post-exercise


title: mmYS-1pe, Young Sed, 1h Post-Ex, Female2


title: HepG2, siDUS4, SR, input1, rep#1

value: siDUS4 Knockdown


title: mmYS-24pe, Young Sed, 24h Post-Ex, Male2

value: male


title: Pig S100a1_1, heart, 14 weeks post MI

description: Library name: Sample 57B


title: mmYS-1pe, Young Sed, 1h Post-Ex, Male1


title: HepG2, siDUS3, SR, treated, rep#2

value: siDUS3 Knockdown

value: small RNA (<200 nt)


title: HepG2, siDUS4, SR, treated, rep#1


title: mmYS-ipe, Young Sed, Imd Post-Ex, Male5

value: immediately post-exercise


title: HepG2, siDUS3, SR, treated, rep#1


title: Pig hrLuc_3, heart, 14 weeks post MI

description: Library name: Sample 45B

value: hrLuc


title: HepG2, siDUS3, SR, input2, rep#2


title: Pig hrLuc_1, heart, 14 weeks post MI

description: Library name: Sample 33B


title: mmYS-ipe, Young Sed, Imd Post-Ex, Female4

value: female


title: mmYS-ipe, Young Sed, Imd Post-Ex, Female3


title: HepG2, siDUS4, SR, input1, rep#2


title: HepG2, siDUS3, SR, input2, rep#1


title: mmYS-ipe, Young Sed, Imd Post-Ex, Male1


title: HepG2, siDUS3, SR, input1, rep#2