title: WingDisc_H3K27M_AsxRNAi_Rep_1

description:
Library name: mRNAseq_22
H3K27M_Asx.bw


title: srcTongueXY_end1

status: Public on Sep 11 2025

type: SRA

city: Vancouver

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

country: Canada

institute: University of British Columbia

description: Single cell RNA-seq sarcoma cells

library_source: transcriptomic single cell

data_processing:
Samples were demultiplexed using cellranger mkfastq with bclfastq2.
Samples were aligned and output matrices generated using cellranger count for alignment.
cellranger aggregate for alignment, matrix etc
Assembly: mm10 with appended tdTomato and EGFP sequences
Supplementary files format and content: gene matrices, cell barcode and gene list are included as .mtx, .tsv and .tsv files, respectively

molecule: polyA RNA

organism: Mus musculus

source_name: Hic1CreERT2/CreERT2;Rosa26SSM2/SSM2 sarcoma cells 16 weeks endpoint tongue XY 1

growth_protocol: Mice were bred and raised to 8 weeks of age using standard approved animal care committee methodology.

extract_protocol:
FACS purified cells were counted and inspected by hemocytometer before input to the 10X chromium library preparation pipeline and subsequent NGS.
10X Chromium Single Cell 3' v2

treatment_protocol: Adult animals 8 weeks of age were injected with 2.5mg tamoxifen in 100uL sunflower oil daily for 5 consecutive days and allowed a ten day washout period before experments were performed.

tag: cell type

value: Mesenchymal Progenitors

tag: strain

tag: tissue

value: Tongue

tag: genotype


title: cKK-E10_MNR_45_Day_2_Rep4

city: Waltham

first: Sudha

last: Chivukula

state: MA

address: 200 West

department: mRNA Center of Excellence

country: USA

institute: Sanofi

description:
Library name: N14_s062_S68_001
Column name in count_nhp.txt: N14_s062_S68_001

library_source: transcriptomic

data_processing:
The bcl files were demultiplexed using Illumina’s bcl2fastq software.
The fastq files were processed using Array Studio software (Qiagen) and aligned to the cynomolgus Macaque CynoWashU2013 reference genome with the WashUGene2017512 gene model.
Differential gene expression analysis was performed using the Limma-Voom method, which transforms the raw read counts into log-counts per million (log-CPM) and models the mean-variance relationship of the data.
Assembly: cynomolgus Macaque CynoWashU2013 reference genome with the WashUGene2017512 gene model.
Supplementary files format and content: Tab-delimited text file including raw counts for each sample.
Supplementary files format and content: Tab-delimited text file including log-CPM for each sample.

molecule: total RNA

organism: Macaca fascicularis

source_name: Blood

growth_protocol: Primary human skeletal muscle myoblasts were obtained from Lonza (Cat. No. CC-2580) and thawed and expanded following vendor recommendations. Briefly, cryopreserved cell stocks were thawed into SkGM-2 complete media (Lonza, Cat. No. CC-3245). Media was replaced 24 h after thawing and every 48 h thereafter. Cells were expanded/passaged to P6, at which point they were seeded on 24-well culture plates pre-coated with Collagen 1 at a density of 24,000 cells/cm2 in 1 mL of culture media. The next day, media in each well was replaced with 0.5 mL of fresh media before transfection mixes were prepared. Naive male and female Mauritius origin cynomolgus macaques (Macaca fascicularis) were selected from the Sanofi NHP colony at the NIRC. Animals weighed > 2 kg and were > 2 years of age at the start of the studies. Per NIRC SOPs, all animals underwent a pre-study health assessment performed by a licensed veterinarian, which included a complete blood count and clinical chemistry analysis before being cleared for entry into the study.

extract_protocol:
Muscle cells at each collection time-point, media was aspirated, and cultures were lysed on-plate using 350 µL of RLT buffer (Qiagen Cat. No. 79216) and immediately transferred to 1.5 mL tubes and stored at -80 °C. Total RNA was extracted from whole blood NHP samples collected in PAXgene Blood RNA Tubes (Qiagen, BD Diagnostics) pre- and 2 days post-immunization using the MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit (Invitrogen) on an automated KingFisher Flex System (Thermo Scientific). The quality and yield of RNA were assessed on the 4200 TapeStation System (Agilent) and NanoDrop™ Eight Spectrophotometer (Thermo Scientific). Sequencing libraries were then prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit and sequenced on the NovaSeq 6000 Sequencing System (Illumina) using the S4 Reagent Kit v1.5 (200 cycles).
Sequencing libraries were then prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit and sequenced on the NovaSeq 6000 Sequencing System (Illumina) using the S4 Reagent Kit v1.5 (200 cycles).

treatment_protocol: Muscle cells were transfected at 2 µg of formulated RNA/million cells. For each treatment, 50 µL of transfection mix was added to the culture before an additional 0.5mL of media was added to thoroughly distribute the transfection mixture before plates were returned to the incubator for 1, 4, or 24 h. NHPs were randomized, (stratified randomization approach based on age, body weight, and sex by biostatistician) into groups of 4-6 per treatment group, were generally housed in pairs whenever possible and acclimated for at least 6 days prior to the start of the study. All NHPs were immunized with a dose of 0.5 mL of vaccine via the intramuscular (IM) route in the right forelimb on Day 0 and the left forelimb on D28 while under 10 mg/kg ketamine HCl /1 mg/kg acepromazine sedation.

value: Blood

value: PBMC

tag: treatment

tag: timepoint

tag: dose

tag: biological replicate


title: WingDisc_H3K27R_AsxRNAi_Rep_3

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

description:
Library name: mRNAseq_21
H3K27R_Asx.bw

data_processing:
Alignment of reads to the Drosophila melanogaster dm6 reference genome was done with HISAT2 v2.1.0 with a mapping quality threshold of ≥ 30. Reads below this threshold were rejected as were reads that mapped to the mitochondrial or scaffold DNA.
Assembly: dm6
Supplementary files format and content: bigwig files were formed from merged replicates and z-score normalized,

organism: Drosophila melanogaster

source_name: 3rd instar wing disc

growth_protocol: Animals were reared at 25ºC, a temperature at which GAL80 represses GAL4. Plates with molasses and yeast paste were exchanged at three-hour intervals to stage discs at time of dissection.  Embryos were aged on plates for 24 hours and picked into vials as first-instar larvae. Larvae were reared until 44 hours after egg laying (AEL), then shifted to 32ºC to inactivate GAL80 and express transgenes for 72 hours.

extract_protocol:
Imaginal wing and eye-antennal discs were harvested from crawling third-instar larvae. Larvae were staged to within 116 and 119 hours after egg laying. For each replicate, ten discs were dissected into ice cold 1X PBS solution. Three biological replicates were dissected for each genotype. After dissection, discs were incubated in Trizol for 5 minutes to dissolve tissue, then frozen at -20ºC. RNA was isolated using standard Trizol RNA isolation procedure.
Libraries were prepared using the Illumina TrueSeq RNA prep kit V2.

value: 3rd instar wing disc

value: Act5C-GAL4, alphaTub84B-GAL80ts/UAS-tH3 K27R; AsxRNAi


title: MG_C_30_JJ

city: Amsterdam

first: Han

last: Jiao

address: 9 Meibergdreef, Endocrine Laboratory, Clin. Chemistry

country: Netherlands

institute: University of Amsterdam, Amsterdam, The Netherlands.

description:
Library name: Sample 11
column name in Raw_Counts_All_Samples.csv: MG_C_30_JJ

data_processing:
Sequencing data was filtered using SOAPnuke 68 by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Assembly: Rattus_norvegicus, GCF_000001895.5_Rnor_6.0
Supplementary files format and content: csv file includes raw counts for each Sample
Supplementary files format and content: csv file includes FPKM values for each Sample

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
To study differences in microglial gene expression, bulk RNA sequencing was performed. RNA from microglial cells was isolated using the RNeasy Micro Kit (Qiagen, 74104), according to the manufacturer’s guidelines. mRNA was enriched from total RNA with the Dynabeads® mRNA Purification Kit (Invitrogen, 61006).
A strand-specific transcriptome library was constructed using the MGIEasy RNA Directional Library Prep Set (16 RXN) (MGI, 1000006385). Briefly, after cDNA synthesis, adaptor ligation was performed to ligate adaptors with the cDNAs. Subsequently, a PCR reaction was conducted to amplify the cDNAs, after which the library quality was checked using the Agilent 2100 Bioanalyzer (Agilent, G2939AA). Finally, single-stranded cyclized products were produced from single-stranded PCR products. To perform sequencing, single-stranded circle DNA molecules were replicated via rolling cycle amplification and a DNA nanoball (DNB) was generated. Sequencing was performed through combinatorial Probe-Anchor Synthesis (cPAS) on the DNBSEQ-G400 (MGI, G400).

value: Brain

value: Wistar

tag: Sex

value: Male

value: Microglia cells

value: WT

value: chow light-feeding

tag: time


title: MG_C_28_JJ

description:
Library name: Sample 10
column name in Raw_Counts_All_Samples.csv: MG_C_28_JJ


title: wtMuscleXY

description: Single cell RNA-seq tdTomato MPs quiescent

source_name: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MSC Quiescent Muscle XY

value: Hindlimb muscle


title: WingDisc_H3K27R_AsxRNAi_Rep_2

description:
Library name: mRNAseq_20
H3K27R_Asx.bw


title: WingDisc_H3K27R_AsxRNAi_Rep_1

description:
Library name: mRNAseq_19
H3K27R_Asx.bw


title: cKK-E10_MNR_45_Day_2_Rep3

description:
Library name: N14_s061_S56_001
Column name in count_nhp.txt: N14_s061_S56_001

value: Naive male and female Mauritius origin cynomolgus macaques


title: MG_C_25_JJ

description:
Library name: Sample 9
column name in Raw_Counts_All_Samples.csv: MG_C_25_JJ

value: chow ad libitum


title: MG_C_24_JJ

description:
Library name: Sample 8
column name in Raw_Counts_All_Samples.csv: MG_C_24_JJ


title: wtTongueXY1

source_name: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MSC Quiescent Tongue XY 1


title: wtTongueXX2

source_name: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MSC Quiescent Tongue XX 2


title: WingDisc_H3K27M_TrxRNAi_Rep_3

description:
Library name: mRNAseq_18
H3K27M_Trx.bw

value: Act5C-GAL4, alphaTub84B-GAL80ts/UAS-tH3 K27M; trxRNAi


title: MG_C_21_JJ

description:
Library name: Sample 7
column name in Raw_Counts_All_Samples.csv: MG_C_21_JJ


title: cKK-E10_MNR_45_Day_0_Rep2

description:
Library name: N14_s007_S73_001
Column name in count_nhp.txt: N14_s007_S73_001


title: MG_C_20_JJ

description:
Library name: Sample 6
column name in Raw_Counts_All_Samples.csv: MG_C_20_JJ


title: cKK-E10_MNR_45_Day_0_Rep3

description:
Library name: N14_s027_S28_001
Column name in count_nhp.txt: N14_s027_S28_001


title: wtTongueXX1

source_name: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MSC Quiescent Tongue XX 1


title: WingDisc_H3K27M_TrxRNAi_Rep_1

description:
Library name: mRNAseq_16
H3K27M_Trx.bw


title: MG_C_18_JJ

description:
Library name: Sample 5
column name in Raw_Counts_All_Samples.csv: MG_C_18_JJ


title: srcStifleXY_end_atac

description:
Single cell ATAC-seq sarcoma cells
transposase accessible chromatin

library_source: genomic single cell

data_processing:
Samples were demultiplexed using cellranger-atac 1.1.0 mkfastq with bcl2fastq.
Samples were aligned and output matrices generated using cellranger-atac 1.1.0 count for alignment and peak calling to cell clustering.
Assembly: mm10
Supplementary files format and content: peak matrices, cell barcode and peak list are included as .mtx, .tsv and .bed files, respectively

molecule: genomic DNA

source_name: Hic1CreERT2/CreERT2;Rosa26SSM2/SSM2 sarcoma cells 16 weeks endpoint stifle

extract_protocol:
FACS purified cells were counted and inspected by hemocytometer before input to the 10X chromium nuclei preperation pipeline.
nuclear lysis protocol: nuclei were lysed for five minutes according to 10x standard protocol and subjected to the transposition reaction followed by library preparation pipeline and subsequent NGS.
Chromium Single Cell ATAC Reagent Kits User Guide (10x Genomics; CG000168 Rev B); 2 x 75PE kit to produce 2 X 50 reads

value: Stife (hindlimb-knee)


title: WingDisc_H3K27R_TrxRNAi_Rep_3

description:
Library name: mRNAseq_15
H3K27R_Trx.bw

value: Act5C-GAL4, alphaTub84B-GAL80ts/UAS-tH3 K27R; trxRNAi


title: MG_C_17_JJ

description:
Library name: Sample 4
column name in Raw_Counts_All_Samples.csv: MG_C_17_JJ


title: srcTongueXY_end2_atac

source_name: Hic1CreERT2/CreERT2;Rosa26SSM2/SSM2 sarcoma cells 16 weeks endpoint tongue 2

value: Mesenchymal Progenitors

value: Tongue


title: cKK-E10_MNR_45_Day_2_Rep2

description:
Library name: N14_s056_S91_001
Column name in count_nhp.txt: N14_s056_S91_001

value: Blood

value: PBMC


title: srcTongueXY_end3_atac

source_name: Hic1CreERT2/CreERT2;Rosa26SSM2/SSM2 sarcoma cells 16 weeks endpoint tongue 3


title: cKK-E10_MNR_15_Day_2_Rep4

description:
Library name: N14_s312_S186_001
Column name in count_nhp.txt: N14_s312_S186_001


title: wtTongueXY2

source_name: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MSC Quiescent Tongue XY 2


title: MG_C_16_JJ

description:
Library name: Sample 3
column name in Raw_Counts_All_Samples.csv: MG_C_16_JJ


title: WingDisc_H3K27R_TrxRNAi_Rep_1

description:
Library name: mRNAseq_13
H3K27R_Trx.bw

value: 3rd instar wing disc


title: cKK-E10_MNR_15_Day_2_Rep3

description:
Library name: N14_s311_S174_001
Column name in count_nhp.txt: N14_s311_S174_001


title: srcTongueXY_end1_atac

source_name: Hic1CreERT2/CreERT2;Rosa26SSM2/SSM2 sarcoma cells 16 weeks endpoint tongue 1


title: MG_C_14_JJ

description:
Library name: Sample 1
column name in Raw_Counts_All_Samples.csv: MG_C_14_JJ

value: Brain


title: cKK-E10_MNR_15_Day_2_Rep2

description:
Library name: N14_s065_S9_001
Column name in count_nhp.txt: N14_s065_S9_001


title: cKK-E10_MNR_45_Day_2_Rep1

description:
Library name: N14_s055_S79_001
Column name in count_nhp.txt: N14_s055_S79_001


title: wingDisc_H3K27M_Rep_3

description:
Library name: mRNAseq_12
H3K27M.bw


title: WingDisc_H3K27R_TrxRNAi_Rep_2

description:
Library name: mRNAseq_14
H3K27R_Trx.bw


title: wtTongueXY2_atac

description:
Single cell ATAC-seq tdTomato MPs quiescent
transposase accessible chromatin

source_name: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MSC Quiescent Muscle


title: wtTongueXY1_atac

source_name: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MSC Quiescent Tongue 2


title: Ts12HK-3

city: Lanzhou

first: QI

last: Wang

state: Gansu

address: Yintan Road Street

department: College of Animal Science and Technology

country: China

institute: Gansu Agricultural University

description: Library name: Sample 9

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads  without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss USDA_OmykA_1.1
Supplementary files format and content: tab-delimited text file includes raw counts, FPKM for each Sample

organism: Oncorhynchus mykiss

source_name: head kidney tissues

growth_protocol: Fish weighing (130 ± 5.0) g were selected and temporarily reared for two weeks in a flow-through aquaculture system with DO of 8.5 ± 0.1 mg/L, water temperature of 12 ± 0.1℃.

extract_protocol:
The total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two weeks after rainbow trout were suspended, healthy rainbow trout were randomly divided into three groups, including normoxia, moderate hypoxia, and severe hypoxia groups, the oxygen levels were maintained at 8.5 ± 0.1, 4.5 ± 0.1, and 3.0 ± 0.1 mg/L, respectively, and the low oxygen environment was created by mixing oxygen and nitrogen.

value: head kidney tissues

value: severe hypoxia stress

tag: batch


title: cKK-E10_MNR_15_Day_2_Rep1

description:
Library name: N14_s050_S19_001
Column name in count_nhp.txt: N14_s050_S19_001


title: MG_C_15_JJ

description:
Library name: Sample 2
column name in Raw_Counts_All_Samples.csv: MG_C_15_JJ

value: Wistar

value: Male

value: Microglia cells


title: WingDisc_H3K27M_TrxRNAi_Rep_2

description:
Library name: mRNAseq_17
H3K27M_Trx.bw


title: cKK-E10_MNR_15_Day_0_Rep4

description:
Library name: N14_s032_S88_001
Column name in count_nhp.txt: N14_s032_S88_001


title: wingDisc_H3K27M_Rep_2

description:
Library name: mRNAseq_11
H3K27M.bw


title: cKK-E10_MNR_45_Day_0_Rep1

description:
Library name: N14_s002_S13_001
Column name in count_nhp.txt: N14_s002_S13_001


title: wingDisc_H3K27R_Rep_3

description:
Library name: mRNAseq_9
H3K27R.bw


title: Ts12HK-2

description: Library name: Sample 8


title: cKK-E10_MNR_15_Day_0_Rep3

description:
Library name: N14_s028_S40_001
Column name in count_nhp.txt: N14_s028_S40_001


title: Ts12HK-1

description: Library name: Sample 7


title: Tm12HK-3

description: Library name: Sample 6

value: moderate hypoxia stress


title: cKK-E10_MNR_15_Day_0_Rep1

description:
Library name: N14_s010_S14_001
Column name in count_nhp.txt: N14_s010_S14_001

value: Naive male and female Mauritius origin cynomolgus macaques


title: wingDisc_H3K27R_Rep_2

description:
Library name: mRNAseq_8
H3K27R.bw


title: cKK-E10_MNR_5_Day_2_Rep4

description:
Library name: N14_s088_S95_001
Column name in count_nhp.txt: N14_s088_S95_001


title: Tm12HK-2

description: Library name: Sample 5


title: EyeDisc_H3K27M_Rep_3

description:
Library name: mRNAseq_6
H3K27M_eye.bw

source_name: 3rd instar eye disc

value: 3rd instar eye disc


title: EyeDisc_H3K27M_Rep_2

description:
Library name: mRNAseq_5
H3K27M_eye.bw


title: cKK-E10_MNR_5_Day_2_Rep3

description:
Library name: N14_s074_S22_001
Column name in count_nhp.txt: N14_s074_S22_001


title: Tm12HK-1

description: Library name: Sample 4


title: wtMuscleXY_atac

source_name: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MSC Quiescent Tongue 1


title: cKK-E10_MNR_5_Day_2_Rep2

description:
Library name: N14_s073_S10_001
Column name in count_nhp.txt: N14_s073_S10_001

source_name: Blood


title: cKK-E10_MNR_5_Day_2_Rep1

description:
Library name: N14_s067_S33_001
Column name in count_nhp.txt: N14_s067_S33_001


title: CHK-2

description: Library name: Sample 2

value: control

value: 0 h


title: wingDisc_H3K27M_Rep_1

description:
Library name: mRNAseq_10
H3K27M.bw

source_name: 3rd instar wing disc


title: CHK-3

description: Library name: Sample 3


title: EyeDisc_H3K27M_Rep_1

description:
Library name: mRNAseq_4
H3K27M_eye.bw


title: EyeDisc_H3K27R_Rep_3

description:
Library name: mRNAseq_3
H3K27R_eye.bw


title: cKK-E10_MNR_5_Day_0_Rep4

description:
Library name: N14_s017_S3_001
Column name in count_nhp.txt: N14_s017_S3_001


title: Keratinocyte on ColI_rep2

type: RNA

city: Nedlands

first: Chee Wai

last: Wong

state: WA

address: Northern Entrance, Perth Children's Hospital, 15 Hospital Ave

country: Australia

institute: Telethon Kids Institute

description:
Collagen I (2)
Gene Expression of Keratinocyte grown on Collagen I

hyb_protocol: The arrays were washed using a GeneChip® Fluidics Station 450, using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix). This was performed in at the Biopolis Shared Facilities, Agency of Science and Technology Research, Singapore

scan_protocol: The chip arrays were scaneed on the Affymetrix GeneChip Scanner located at the Biopolis Shared Facilities, Agency of Science and Technology Research, Singapore

data_processing:
The arrays result were processed using the Affymetrix Expression Console Software
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: Biotin

organism: Homo sapiens

source_name: Keratinocyte grown on rat tail collagen I coating, technical replicate 2

label_protocol: cDNA probes were prepared as indicated by Affymetrix protocol

growth_protocol: Keratinocytes were seeded (1 × 10^4 cells/well) into wells of a 48-well tissue culture plate (NUNC) containing either collagen I, adult dermal fibroblast-derived ECM or foetal dermal fibroblast-derived ECM grown for three days in defined keratinocyte serum-free media

extract_protocol: Total RNA was extracted using TRIzol® (ThermoFisher Scientific). Contaminating DNA was removed by DNase I (Qiagen) treatment, and RNA was further purified using Qiagen’s RNeasy Mini Kit according to the manufacturer’s instructions.

tag: cell line

value: Primary


title: CHK-1

description: Library name: Sample 1


title: EyeDisc_H3K27R_Rep_2

description:
Library name: mRNAseq_2
H3K27R_eye.bw


title: Keratinocyte on ColI_rep1

description:
Collagen I (1)
Gene Expression of Keratinocyte grown on Collagen I

source_name: Keratinocyte grown on rat tail collagen I coating, technical replicate 1


title: cKK-E10_MNR_15_Day_0_Rep2

description:
Library name: N14_s024_S87_001
Column name in count_nhp.txt: N14_s024_S87_001


title: wingDisc_H3K27R_Rep_1

description:
Library name: mRNAseq_7
H3K27R.bw


title: CRC_mPAP2_B

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA43166

data_processing:
Sequencing was performed on DNBSEQ-G400 platform in 28+50-base paired-end mode.
Raw sequencing data were converted to matrices of expression using Space Ranger (version spaceranger-1.3.0, 10X Genomics).
Assembly: GRCh38-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 format file including counts data for each gene and spot-position (barcode) combination
Supplementary files format and content: filtered_feature_bc_matrix.tar.gz:  tar.gz compressed file of Space Ranger output folder "filtered_feature_bc_matrix"
Supplementary files format and content: raw_feature_bc_matrix.tar.gz:  tar.gz compressed file of Space Ranger output folder "raw_feature_bc_matrix"
Supplementary files format and content: spatial.tar.gz:  tar.gz compressed file of Space Ranger output folder "spatial"
Library strategy: Spatial Transcriptomics

source_name: lung adenocarcinoma

extract_protocol:
Visium Human Transcriptome Probe Set and Visium Spatial 3' v1 chemistry were used to extract total RNA and hybridize transcriptomic probes to the Visium slide.
Sequencing library preparation were performed according to standard protocol of the Visium Spatial Gene Expression Reagent Kits for FFPE.

value: lung adenocarcinoma


title: cKK-E10_MNR_5_Day_0_Rep3

description:
Library name: N14_s011_S26_001
Column name in count_nhp.txt: N14_s011_S26_001


title: EyeDisc_H3K27R_Rep_1

description:
Library name: mRNAseq_1
H3K27R_eye.bw


title: Keratinocyte on AdultECM(2)_rep2

description:
Adult-2(2)
Gene Expression of Keratinocyte grown on adult dermal ECM

source_name: Keratinocyte grown on adult dermal fibroblast-derived ECM, technical replicate 2 (Adult- 2)


title: Keratinocyte on FoetalECM(2)_rep2

description:
Foetal-2(2)
Gene Expression of Keratinocyte grown on foetal dermal ECM

source_name: Keratinocyte grown on foetal dermal fibroblast-derived ECM, technical replicate 2 (Foetal-2)


title: cKK-E10_MNR_5_Day_0_Rep2

description:
Library name: N14_s006_S61_001
Column name in count_nhp.txt: N14_s006_S61_001


title: Keratinocyte on FoetalECM(1)_rep1

description:
Foetal-1(1)
Gene Expression of Keratinocyte grown on foetal dermal ECM

source_name: Keratinocyte grown on foetal dermal fibroblast-derived ECM, technical replicate 1 (Fpetal-1)


title: 54_RCo20_LN_CD4

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were aligned using STAR v2.7.3a.(Dobin et al.)
Transcript abundance was estimated in STAR during alignment using the algorithm of htseq-count (Anders et al., 2015)
Assembly: macaca mulatta Reference Mmul10 (Macaca_mulatta.Mmul_10.dna.toplevel.fa), Ensemble annotation version 100 (Macaca_mulatta.Mmul_10.100.gtf)
Supplementary files format and content: comma delimited text file containing ensembl ID or gene symbol when available,  and raw read counts for each sample (in columns) for each annotated transcript (in rows).

organism: Macaca mulatta

source_name: LN

extract_protocol:
Sorted CD4+ T cells were lysed in 350 L of Buffer RLT and then extracted using the RNeasy Micro kit (Qiagen) with on-column DNase digestion. RNA quality was assessed using a TapeStation 4200 (Agilent)
Ten nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed barcodes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with SE100 reads on an Illumina NovaSeq 6000, yielding ~25 million reads per sample on average.

value: LN

tag: subject

value: Neg

tag: art start

value: Early

tag: rebound kinetics


title: Keratinocyte on FoetalECM(1)_rep2

description:
Foetal-1(2)
Gene Expression of Keratinocyte grown on foetal dermal ECM

source_name: Keratinocyte grown on foetal dermal fibroblast-derived ECM, technical replicate 2 (Foetal-1)


title: CRC_mPAP1_B

description: Library name: GA43164


title: CRC_mPAP1_A

description: Library name: GA43163


title: Wild type, rep3

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

institute: The Kids Research Institute Australia

description: Library name: 55287_WT

data_processing:
Paired end deep sequencing of the mitochondrial RNAs was performed on an Illumina MiSeq according to the manufacturers instructions.
The alignment to the Mus musculus reference genome (GRCm38) was performed using HISAT2 version 2.0.5 (--dta) (Kim et al., 2019). Alignment files were sorted and indexed with SAMtools version 1.3.1 (Li et al., 2009).
The transcript abundances were estimated with StringTie version 1.2.4 (-e -B) (Pertea et al., 2016) and raw reads count matrices at gene-level were extracted with the included prepDE.py script on Python version 2.7.6.
Differential gene expression was performed with DESeq version 1.14.1 (Love et al., 2014) after filtering of low abundance genes. Genes with an adjusted p-value < 0.05 were considered statistically significant.
Assembly: GRCm38
Supplementary files format and content: txt files containing transcript abundances
Supplementary files format and content: csv files containing differential gene expression results
Supplementary files format and content: csv file containing gene counts

source_name: heart

growth_protocol: Animals were housed in individually ventilated cages under specific-pathogen-free conditions with constant temperature (21°C) and humidity (50 - 60%) and a 12 h light/dark cycle. All mice were fed commercial rodent chow and provided with acidified water ad libitum. Mice were sacrificed by cervical dislocation.

extract_protocol:
RNA was isolated from crude heart mitochondria using the miRNeasy mini kit (QIAGEN) and the concentration, purity, and integrity was confirmed using a BioAnalyser.
RNA sequencing libraries were constructed using the Illumina TruSeq Sample Prep Kit.

value: heart

value: Lrpprc +/+ / Polrmt +/+


title: cKK-E10_MNR_5_Day_0_Rep1

description:
Library name: N14_s001_S1_001
Column name in count_nhp.txt: N14_s001_S1_001

value: Blood

value: PBMC


title: Keratinocyte on AdultECM(2)_rep1

description:
Adult-2(1)
Gene Expression of Keratinocyte grown on adult dermal ECM

source_name: Keratinocyte grown on adult dermal fibroblast-derived ECM, technical replicate 1 (Adult- 2)


title: Wild type, rep2

description: Library name: 55283_WT


title: Keratinocyte on FoetalECM(2)_rep1

description:
Foetal-2(1)
Gene Expression of Keratinocyte grown on foetal dermal ECM

source_name: Keratinocyte grown on foetal dermal fibroblast-derived ECM, technical replicate 1 (Foteal-2)


title: 45_RFo20_LN_CD4


title: Wild type, rep1

description: Library name: 55279_WT


title: 42_RUn20_LN_CD4

value: Female


title: Keratinocyte on AdultECM(1)_rep2

description:
Adult-1(2)
Gene Expression of Keratinocyte grown on adult dermal ECM

source_name: Keratinocyte grown on adult dermal fibroblast-derived ECM, technical replicate 2 (Adult-1)


title: Keratinocyte on AdultECM(1)_rep1

description:
Adult-1(1)
Gene Expression of Keratinocyte grown on adult dermal ECM

source_name: Keratinocyte grown on adult dermal fibroblast-derived ECM, technical replicate 1 (Adult-1)


title: CRC_mPAP4_A

description: Library name: GA43169


title: 39_RNn20_LN_CD4

value: PTC


title: Polrmt OE, rep3

description: Library name: 55277_Polrmt_OE

value: Polrmt +/T


title: CRC_mPAP2_A

description: Library name: GA43165


title: Polrmt OE, rep2

description: Library name: 55275_Polrmt_OE


title: CRC_mPAP3_B

description: Library name: GA43168


title: 36_RAn20_LN_CD4

value: Male


title: 51_RLq20_LN_CD4


title: 48_RZp20_LN_CD4


title: KPCic cells, untreated, anti-CIC (Input)

city: Madrid

first: Tirso

last: Pons

state: Madrid

address: C/ Darwin 3

department: Inmunology and Oncology

country: Spain

institute: Centro Nacional de Biotecnologia

description: Library name: ChIP_MVW1_CIC_Ab_In

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mouse reference genome GRCm38/mm10 using Burrows-Wheeler aligner BWA-MEM version 0.7.15 (github.com/lh3/bwa.git) with standard settings.
The aligned reads were then converted to BAM files using Picard tools 2.9.0 (http:// broadinstitute.github.io/picard). Duplicate reads were removed using Picard tools.
BAM files were processed with MACS (github.com/taoliu/MACS/) version 3.0.0b3 for peak calling with the significance cut-off q-value <= 0.05. BED files were imported into RStudio and annotated with the R/Bioconductor package ChIPseeker (github.com/YuLab-SMU/ChIPseeker). The promoter region was defined as −1 kb to +200 bp from the transcription start site (TSS).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file includes peaks annotation with ChIPseeker for each Sample

growth_protocol: Cells were grown in DMEM supplemeted with 10% FBS

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Plus Diagenode.
Library construction and sequencing was carried out by HaploX Gene Tech Limited (Hong Kong)

value: lung tumor cells


title: clh1;Amsh clh1 Rescue-rep3

city: miami

first: Laura

last: Bianchi

state: FL

address: 1600 nw 10th ave

department: Physiology and Biophysics

institute: university of miami

description: Library name: clh1;clh1R-3

data_processing:
The control software conducted image analysis and base calling. Raw sequence data (.bcl files) generated by the sequencer were converted into FASTQ files and de-multiplexed using Illumina's bcl2fastq 2.20 software, allowing for one mismatch in index sequence identification.
Assembly: The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA) and quantified using the Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
Supplementary files format and content: Raw sequence data (.bcl files) generated by the sequencer were converted into FASTQ files and de-multiplexed using Illumina's bcl2fastq 2.20 software, allowing for one mismatch in index sequence identification.

organism: Caenorhabditis elegans

source_name: all

extract_protocol: The sequencing libraries were clustered on a flow cell. After clustering, the flow cell was loaded onto the Illumina NovaSeq X Plus instrument according to the manufacturer’s instructions. The samples were sequenced using a 2x150 bp Paired-End (PE) configuration, targeting approximately 30 million reads per sample.

value: all


title: CRC_mPAP4_B

description: Library name: GA43170


title: KPCic cells, untreated, anti-CIC (ChIP)

description: Library name: ChIP_MVW1_CIC_Ab_M


title: Lrpprc/Polrmt OE, rep3

description: Library name: 55285_Double_OE

value: Lrpprc +/T / Polrmt +/T


title: Islet_1_m3

city: Cambridge

first: Byung Soo

last: Kong

address: 655 Huntington Avenue, Building 1, Room 512

department: Molecular Metabolism

institute: Harvard University

hyb_protocol: Finally, 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA.40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Mouse GE 8X60K, V2 Microarrays (Agilent®). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.). Microarray results were extracted using Agilent Feature Extraction software v11.0 (Agilent Technologies).

data_processing: Array probes that have Flag A in samples were filtered out. Selected gProcessedSignal value was transformed by logarithm and normalized by quantile method. Statistical significance of the expression data was determined using independent t-test and fold change in which the null hypothesis was that no difference exists among groups. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.

source_name: Mouse pancreatic islets

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP.

extract_protocol: Mice were euthanized, and freshly prepared collagenase P (Roche, Indianapolis, IN) solution (0.5 mg/mL) was injected into the pancreas via the common bile duct. The perfused pancreas was digested at 37C for 13 min with a short vortex every 3 min, and islets were processed with gradient centrifugation with Pancoll human solution (PAN-Biotech, Germany) and then, handpicked under a stereoscopic microscope. Then, cells were dispersed into a single cell suspension in DMEM media supplemented with 20% FBS. After MOTS-c or scrambed peptide treatment, cells were processed for the RNA extraction. RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (NanoDrop), Agilent 2100 Bioanalyzer (Agilent Technologies). RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

treatment_protocol: MOTS-c or scrambled ex vivo treatment (10 μM, 24h) was applied to pancreatic islet cells isolated from four littermates of 60-week-old C57BL/6 mice (n=2/group) to analyze transcriptional changes

tag: age

value: 60 week-old

value: Pancreatic islet cells

value: MOTS-c treated


title: Islet_1_c2

value: Scrambled peptide


title: clh1;Amsh clh1 Rescue-rep2

description: Library name: clh1;clh1R-2


title: Islet_1_m2

value: MOTS-c-treated


title: 33_RZm20_LN_CD4

value: LN

value: Neg

value: Intermediate


title: Islet_1_c1


title: CRC_mPAP3_A

description: Library name: GA43167

value: lung adenocarcinoma


title: KP cells, Trametinib, 100 nM 24h, anti-CIC (Input)

description: Library name: ChIP_MSL1_T_CIC_Ab_In

value: Trametinib 100 nM 24h


title: KP cells, Trametinib 100 nM 24h, anti-CIC (ChIP)

description: Library name: ChIP_MSL1_T_CIC_Ab_M


title: KP cells, untreated, anti-CIC (Input)

description: Library name: ChIP_MSL1_CIC_Ab_In


title: Lrpprc/Polrmt OE, rep2

description: Library name: 55281_Double_OE

value: heart


title: 24_ROz19_LN_CD4

value: PTC


title: KP cells, untreated, anti-CIC (ChIP)

description: Library name: ChIP_MSL1_CIC_Ab_M


title: 27_RCa20_LN_CD4


title: daf-rep16;clh-rep1-rep3

description: Library name: daf-16;clh-1-3


title: 21_RFz19_LN_CD4


title: daf-rep16;clh-rep1-rep2

description: Library name: daf-16;clh-1-2


title: Lrpprc OE, rep3

description: Library name: 55289_Lrp_OE

value: Lrpprc +/T


title: daf-rep16;clh-rep1-rep1

description: Library name: daf-16;clh-1-1


title: Lrpprc OE, rep2

description: Library name: 55273_Lrp_OE


title: 18_RYy19_LN_CD4

value: Male


title: JA Log 3

city: Richardson

first: Joseph

last: Boll

state: TX

address: 800 W Campbell

department: Biological Sciences

institute: University of Texas at Dallas

description: Library name: JA_3_log_S20

data_processing:
CLC genomic workbench software (Qiagen) was used to process reads
Reads were aligned  to the A. baumannii ATCC 17978 genome annotation.
The RPKM expression values and the weighted proportions fold change of expression values between meropenem treated and treated samples at the same timepoint were calcualted.
Baggerley’s test on proportions was used to generate a false discovery rate adjusted P-value.
Assembly: GCA_000015425.1
Supplementary files format and content: Each processed file is in MS Excel format and show the gene expresion levels.

organism: Acinetobacter baumannii

source_name: Acinetobacter baumannii

growth_protocol: An overnight culture of A. baumannii strain ATCC 17978 wild type or mutnats was backdiluted 1:10 in fresh, in LB and grown to OD600 of ~0.5 in triplicate.

extract_protocol:
RNA was extracted with the Direct-Zol RNA miniprep kit (Zymo Research).
Done at SeqCenter - Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI). Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.2.4)1.

value: JA

value: Acinetobacter baumannii


title: Polrmt OE, rep1

description: Library name: 55271_Polrmt_OE

value: Polrmt +/T


title: Cortical neuron, Kabuki Syndrome 1, rep3

city: Manchester

first: Siddharth

last: Banka

address: Oxford Road

country: United Kingdom

institute: University of Manchester

description:
Library name: Neur KS1 rep3 DS1
SC6_Neur_KMT2D-MUT3

data_processing:
Removed adapter or poor-quality reads with Trimmomatic v0.36 using options: "ILLUMINACLIP:Truseq3-PE-2_Nextera-PE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35”
Reads mapped to hg19 using Gencode v19 comprehensive annotation using START v2.5.3a under default parameters.
Reads were counted using FeatureCounts tool in Subread v2.0.0 keeping duplicates and counting primary alignment only.
Assembly: hg19/GRCh37
Supplementary files format and content: Unnormalised gene counts

extract_protocol:
RNeasy Mini kit (QIAGEN) according to the manufacturer's protocol.
Library preparation was performed by the Genomic Technologies Core facility at the University of Manchester.

value: Cortical Neuron

tag: time point

value: Day 18

value: Female


title: 30_RGg20_LN_CD4


title: 12_RTp19_LN_CD4

value: Late


title: daf16-rep3

description: Library name: daf16-3

value: all


title: Cortical neuron, Kabuki Syndrome 1, rep2

description:
Library name: Neur KS1 rep2 DS1
SC24_Neur_KMT2D-MUT2

tag: cell type


title: daf16-rep2

description: Library name: daf16-2


title: JA Log 1

description: Library name: JA_1_log_S18


title: ldtJ Log 3

description: Library name: ldtJ_3_log_S17

value: ldtJ


title: JA Log 2

description: Library name: JA_2_log_S19


title: Lrpprc/Polrmt OE, rep1

description: Library name: 55269_Double_OE

value: Lrpprc +/T / Polrmt +/T


title: daf16-rep1

description: Library name: daf16-1


title: clh1-rep3

description: Library name: clh1-3


title: Cortical neuron, Kabuki Syndrome 1, rep1

description:
Library name: Neur KS1 rep1 DS1
SC23_Neur_KMT2D-MUT1


title: 6_RLg19_LN_CD4

value: LN

value: Neg


title: ldtJ Log 2

description: Library name: ldtJ_2_log_S16


title: Cortical neuron, Control, rep2

description:
Library name: Neur CTRL2 DS1
SC18_Neur_CTRL2


title: clh1-rep2

description: Library name: clh1-2


title: clh1;Amsh clh1 Rescue-rep1

description: Library name: clh1;clh1R-1


title: Cortical neuron, Control, rep1

description:
Library name: Neur CTRL1 DS1
SC17_Neur_CTRL1

value: Day 17


title: 3_RKg19_LN_CD4


title: clh1-rep1

description: Library name: clh1-1


title: WT Log 3

description: Library name: WT_log_3_S14

value: WT


title: Lrpprc OE, rep1

description: Library name: 55267_Lrp_OE

value: heart


title: 53_RCo20_p_CD4

source_name: PBMC

value: PBMC

value: Early


title: 15_RVr19_LN_CD4

value: Male

value: PTC


title: Neuronal progenitor, Kabuki Syndrome 1, rep3, validation dataset DS2

description:
Library name: Prog KS1 rep3 DS2
SC15_S31

value: Neuronal Progenitor


title: N2-rep3

description: Library name: N2-3


title: WT Log 2

description: Library name: WT_log_2_S13

value: Acinetobacter baumannii


title: 9_RQc19_LN_CD4


title: 50_RLq20_p_CD4


title: WT Log 1

description: Library name: WT_log_1_S12


title: 47_RZp20_p_CD4


title: VX88, Male Soma, Biol Rep3

city: Toronto

first: Athmaja

last: Viswanath

state: Ontario

address: 25 Willcocks Street, Room 3055

department: Department of Ecology & Evolutionary Biology

institute: University of Toronto

description:
Library name: 8MS3
RNA was extracted from the soma of wild-type male Caenorhabditis latens (strain VX0088). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq

data_processing:
We used updated genome annotations for C. remanei PX506 (Teterina et al. 2020) and C. latens PX534 v2 (Adams et al. 2023) reference genomes by incorporating existing annotations along with the RNAseq data generated in this study. These updated annotations were generated by the Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada, with the repeat sequences in the genomes were analyzed with RepeatModeler2 using the default parameters (Flynn et al. 2020).
Sequence reads were quality trimmed with Trimmomatic (Bolger et al. 2014) (parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36), and duplicate reads were removed with Nubeam-dedup (Dai & Guan 2020) .
We mapped the mRNA reads against the reference genomes for each sample using STAR with default parameters (Dobin et al. 2013).
We quantified gene expression of all the genes using FeatureCounts (Liao et al. 2014) and identified 13,785 1:1 orthologous genes or to species-specific singleton genes using Orthofinder (Emms & Kelly 2015).
Assembly: For C. remanei, we used the reference genome PX506 (Teterina et al. 2020) and for C. latens we used PX534 v2 (Adams et al. 2023).
Supplementary files format and content: tab-delimited text files include raw rounts per sample

organism: Caenorhabditis latens

source_name: Soma

extract_protocol:
We cultured populations of young adult C. remanei (VX0003) and C. latens (VX0088) on NGM-agar plates with Escherichia coli OP50 at 25°C. To collect gonad and somatic tissues, ~400 young adult worms were dissected per sample using a 0.3mm x 30mm needle (BD # 305109). To isolate the tissues, the worms were initially cut behind the pharynx while in sterile water. This process led to the release of the gonads outside the body of the worm. Subsequently, the gonadal arms were separated from the carcass by making a second cut. We pooled together ~400 separated gonads to form one “gonad” tissue sample and the rest of the ~400 carcasses to form one “somatic” tissue sample. Gonad and somatic tissue samples were collected in triplicate separately for males and females of each species. All the samples were stored in Tri-reagent at -80°C for ~48-72 hours after which RNA was isolated using Zymo RNA Isolation kit (#R2051). The isolated RNA was then treated with Turbo DNase (#AM2238) and RiboLock RNase Inhibitor (#EO0381) to degrade any DNA in the samples. To get high quality and high yield of RNA, the samples were further purified using Zymo RNA Clean and Concentrator kit (#R1015) according to manufacturer protocols.
Each sample yielded an average >75 million paired-end reads (read length 150bp) generated using NovaSeq S4 flowcell. The Stranded poly(A) mRNA library preparation (NEBNext) and next generation sequencing was performed by The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada.

value: Soma

value: Somatic


title: N2-rep1

description: Library name: N2-1


title: 44_RFo20_p_CD4


title: Neuronal progenitor, Control, rep3, validation dataset DS2

description:
Library name: Prog CTRL rep3 DS2
SC12_S28

value: Day 18


title: VX88, Male Soma, Biol Rep2

description:
Library name: 8MS2
RNA was extracted from the soma of wild-type male Caenorhabditis latens (strain VX0088). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq


title: 41_RUn20_p_CD4

value: Female


title: VX88, Male Soma, Biol Rep1

description:
Library name: 8MS1
RNA was extracted from the soma of wild-type male Caenorhabditis latens (strain VX0088). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq


title: GPCR Library

city: Lafayette

first: Austin

last: Tedman

state: IN

address: 716 Brown St Apt 4

department: Chemistry

institute: Purdue University

description: Library name: GPCR Library

data_processing:
Sequencing data were processed by first removing reads derived ribosomal RNA and tRNA reads using custom scripts then mapped to the GPCR-encoding transcripts within the library. Ribosome-protected fragments ranging in size from 28-38 nt were designated as monosomes while 50-70 nt reads were designated as disomes. A meta-analysis of the ribosome pileups across different receptor sub-types was carried out using a custom software package
Assembly: GPCR-encoding scripts within the Library
Supplementary files format and content: csv files with mock-normalized RPKM values
Library strategy: Ribo-Seq

source_name: Human embryonic kidney

growth_protocol: HEK 293T cells were maintained in DMEM supplemented with 10% Fetal Bovine Serum and 90 units/mL of Penicillin-Streptomycin incubated at 37 C with 5% CO2

extract_protocol:
Total RNA was extracted using Aurum Total RNA Mini Kit (Centrifugation Protocol) with about 3.2 ug of RNA used for sequncing libraries
Library Construction using LaceSeq

treatment_protocol: Cells were treated with 10 ug/mL Cyclohexamide to arrest translation

value: Human embryonic kidney

value: HEK 293T


title: ldtJ Log 1

description: Library name: ldtJ_1_log_S15

value: ldtJ


title: Neuronal progenitor, Control, rep2, validation dataset DS2

description:
Library name: Prog CTRL rep2 DS2
SC11_S27


title: 38_RNn20_p_CD4

value: Neg


title: Mock Transfected

description: Library name: Mock Transfected


title: 35_RAn20_p_CD4


title: Neuronal progenitor, Kabuki Syndrome 1, rep2, validation dataset DS2

description:
Library name: Prog KS1 rep2 DS2
SC14_S30


title: VX88, Male Gonad, Biol Rep2

description:
Library name: 8MG2
RNA was extracted from the gonad of wild-type male Caenorhabditis latens (strain VX0088). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq

source_name: Gonad

value: Gonad

value: Germline


title: Neuronal progenitor, Kabuki Syndrome 1, rep3

description:
Library name: Prog KS1 rep3 DS1
SC5_Prog_KMT2D-MUT3


title: Neuronal progenitor, Control, rep1, validation dataset DS2

description:
Library name: Prog CTRL rep1 DS2
SC10_S26


title: 32_RZm20_p_CD4

value: Intermediate


title: VX3, Male Soma, Biol Rep3

description:
Library name: 3MS3
RNA was extracted from the soma of wild-type male Caenorhabditis remanei (strain VX0003). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq

organism: Caenorhabditis remanei

value: WT


title: VX3, Male Soma, Biol Rep2

description:
Library name: 3MS2
RNA was extracted from the soma of wild-type male Caenorhabditis remanei (strain VX0003). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq


title: VX3, Male Soma, Biol Rep1

description:
Library name: 3MS1
RNA was extracted from the soma of wild-type male Caenorhabditis remanei (strain VX0003). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq


title: Neuronal progenitor, Kabuki Syndrome 1, rep1, validation dataset DS2

description:
Library name: Prog KS1 rep1 DS2
SC13_S29


title: Neuronal progenitor, Kabuki Syndrome 1, rep2

description:
Library name: Prog KS1 rep2 DS1
SC22_Prog_KMT2D-MUT2


title: 29_RGg20_p_CD4

value: PBMC


title: VX88, Male Gonad, Biol Rep1

description:
Library name: 8MG1
RNA was extracted from the gonad of wild-type male Caenorhabditis latens (strain VX0088). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq


title: N2-rep2

description: Library name: N2-2

value: all


title: VX88, Female Soma, Biol Rep3

description:
Library name: 8FS3
RNA was extracted from the soma of wild-type female Caenorhabditis latens (strain VX0088). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq


title: Neuronal progenitor, Kabuki Syndrome 1, rep1

description:
Library name: Prog KS1 rep1 DS1
SC21_Prog_KMT2D-MUT1


title: VX88, Female Soma, Biol Rep2

description:
Library name: 8FS2
RNA was extracted from the soma of wild-type female Caenorhabditis latens (strain VX0088). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq


title: VX3, Male Gonad, Biol Rep3

description:
Library name: 3MG3
RNA was extracted from the gonad of wild-type male Caenorhabditis remanei (strain VX0003). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq


title: 26_RCa20_p_CD4

value: Male

value: PTC


title: Neuronal progenitor, Control, rep3

description:
Library name: Prog CTRL3 DS1
SC2_Prog_CTRL3

value: Neuronal Progenitor


title: VX3, Male Gonad, Biol Rep1

description:
Library name: 3MG1
RNA was extracted from the gonad of wild-type male Caenorhabditis remanei (strain VX0003). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq


title: 23_ROz19_p_CD4


title: VX88, Female Gonad, Biol Rep3

description:
Library name: 8FG3
RNA was extracted from the gonad of wild-type female Caenorhabditis latens (strain VX0088). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq


title: Neuronal progenitor, Control, rep2

description:
Library name: Prog CTRL2 DS1
SC16_Prog_CTRL2


title: 20_RFz19_p_CD4


title: VX88, Female Soma, Biol Rep1

description:
Library name: 8FS1
RNA was extracted from the soma of wild-type female Caenorhabditis latens (strain VX0088). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq

value: Soma


title: VX3, Male Gonad, Biol Rep2

description:
Library name: 3MG2
RNA was extracted from the gonad of wild-type male Caenorhabditis remanei (strain VX0003). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq


title: VX88, Male Gonad, Biol Rep3

description:
Library name: 8MG3
RNA was extracted from the gonad of wild-type male Caenorhabditis latens (strain VX0088). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq


title: 17_RYy19_p_CD4


title: VX3, Female Soma, Biol Rep3

description:
Library name: 3FS3
RNA was extracted from the soma of wild-type female Caenorhabditis remanei (strain VX0003). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq

value: Somatic


title: VX88, Female Gonad, Biol Rep2

description:
Library name: 8FG2
RNA was extracted from the gonad of wild-type female Caenorhabditis latens (strain VX0088). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq


title: iPSC, Kabuki Syndrome 1, rep3

description:
Library name: hiPSC KS1 rep3 DS1
SC4_hiPSC_KMT2D-MUT3

value: iPSC

value: Day 0


title: iPSC, Kabuki Syndrome 1, rep2

description:
Library name: hiPSC KS1 rep2 DS1
SC20_hiPSC_KMT2D-MUT2

value: Female


title: VX3, Female Soma, Biol Rep2

description:
Library name: 3FS2
RNA was extracted from the soma of wild-type female Caenorhabditis remanei (strain VX0003). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq


title: Neuronal progenitor, Control, rep1

description:
Library name: Prog CTRL1 DS1
SC15_Prog_CTRL1

value: Day 18


title: VX3, Female Soma, Biol Rep1

description:
Library name: 3FS1
RNA was extracted from the soma of wild-type female Caenorhabditis remanei (strain VX0003). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq


title: iPSC, Kabuki Syndrome 1, rep1

description:
Library name: hiPSC KS1 rep1 DS1
SC19_hiPSC_KMT2D-MUT1


title: iPSC, Control, rep3

description:
Library name: hiPSC CTRL3 DS1
SC1_hiPSC_CTRL3


title: Low-temperature, L. redmanii

city: Cairo

first: Hosam

last: Elsaied

address: 101 Kasr ELAiny St.

department: Aquaculture

country: Egypt

institute: National Institute of Oceanography and Fisheries

description: Library name: LowTemp_Lred

data_processing:
Raw FASTQ reads were assessed with FastQC v0.11.9. Adapter contamination, polyG and polyX stretches, and low-quality bases (Q < 15; length < 60 bp) were trimmed using fastp v0.23.2 with Ion Torrent–specific parameters.
High-quality reads were assembled de novo using Trinity v2.15.1 in single-end mode. Assemblies were tested with and without in silico normalization; final assembly used normalization for improved quality and efficiency.
Assembly: Transcriptome assembly statistics (transcript count, N50, mean length, GC content) were generated with TrinityStats.pl. Completeness was evaluated using BUSCO v5.8.3 against the metazoa_odb10 dataset.
Transcript redundancy was reduced using CD-HIT v4.8.1 (95% sequence identity threshold) to generate a non-redundant unigene reference.
Protein-coding sequences were predicted with TransDecoder v5.5.0. Homology searches were performed with BLASTP v2.1.8 against UniProt/SwissProt (E < 1e-5). Functional annotation was carried out with eggNOG-mapper v2.1.11 (protein mode, DIAMOND backend) to assign KO, GO, EC, gene names, and COG classifications.
Transcript abundance was quantified using Salmon v1.10.2 in quasi-mapping mode with GC bias and sequence-specific correction enabled. Abundance was reported as raw counts and TPM.
Supplementary files format and content: datafile/raw_counts
Supplementary files format and content: datafile/normalized_counts_gene_level
Supplementary files format and content: datafile/DEGs_lowsal_vs_control
Supplementary files format and content: datafile/DEGs_lowtemp_vs_control
Supplementary files format and content: datafile/DEGs_lowsal_vs_lowtemp

organism: Livoneca redmanii

source_name: whole organism

growth_protocol: Livoneca redmanii specimens were collected from Tilapia zilli hosts in Lake Qarun, Egypt. Parasites were maintained under experimental aquaculture conditions until processing.

extract_protocol:
Total RNA was extracted from whole parasite specimens using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions. RNA integrity was confirmed with agarose gel electrophoresis and quantified using Qubit fluorometer.
Libraries were prepared using the Ion Total RNA-Seq Kit v2 (Thermo Fisher). RNA was fragmented with RNase III, purified with magnetic beads, ligated to Ion adaptors, and size-selected using magnetic beads. PCR amplification was performed (18 cycles, 58°C annealing for 15 sec). Libraries were quantified using Qubit and loaded onto Ion 530 chips for sequencing on the Ion Torrent S5 platform.

treatment_protocol: Experimental treatments included: (1) Control (normal salinity 35 PSU, 26°C), (2) Low salinity stress (gradual reduction from 35 PSU to 8 PSU), and (3) Low temperature stress (temperature reduced from 26°C to 10°C).

value: whole organism


title: 8_RQc19_p_CD4

value: Neg

value: Late


title: 11_RTp19_p_CD4


title: VX88, Female Gonad, Biol Rep1

description:
Library name: 8FG1
RNA was extracted from the gonad of wild-type female Caenorhabditis latens (strain VX0088). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq

value: Gonad

value: Germline


title: 5_RLg19_p_CD4


title: VX3, Female Gonad, Biol Rep3

description:
Library name: 3FG3
RNA was extracted from the gonad of wild-type female Caenorhabditis remanei (strain VX0003). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq

value: WT


title: VX3, Female Gonad, Biol Rep2

description:
Library name: 3FG2
RNA was extracted from the gonad of wild-type female Caenorhabditis remanei (strain VX0003). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq


title: iPSC, Control, rep2

description:
Library name: hiPSC CTRL2 DS1
SC14_hiPSC_CTRL2


title: Low-salinity, L. redmanii

description: Library name: LowSalinity_Lred


title: VX3, Female Gonad, Biol Rep1

description:
Library name: 3FG1
RNA was extracted from the gonad of wild-type female Caenorhabditis remanei (strain VX0003). Dissections were performed manually to isolate gonad and soma tissues. Each sample represents a single biological replicate used for RNA-Seq


title: Control, L. redmanii

description: Library name: Control_Lred


title: 2_RKg19_p_CD4

value: PBMC


title: 14_RVr19_p_CD4


title: Vestibular epithelium, M01757EN_IDPN

status: Public on Sep 10 2025

city: Hospitalet de Llobregat

first: Jordi

last: Llorens

state: Catalunya

address: Feixa Llarga s/n

department: Ciències Fisiològiques

institute: Universitat de Barcelona

description: Library name: AD5205

data_processing:
Reads were mapped against the Mus musculus (GRCm38) reference genome with STAR 2.5.3a and ENCODE parameters
Genes were quantified with RSEM 2.3.0 with default parameters using the gencodeM15 annotation
Assembly: GRCm38
Supplementary files format and content: text file includes raw counts for each sample

source_name: Vestibular epithelium

extract_protocol:
Vestibular epithelia were quickly dissected in ice-cold PBS. Two utricles and six crista from each animal were pooled and stored at -80C. Total RNA was extracted using the Qiagen RNeasy mini kit and protocol.
RNA sequencing libraries were prepared following the SMARTseq2 protocol (Picelli et al., 2014) with some modifications. Briefly, reverse transcription of the total RNA input material of 1.8 µl (6-11 ng, in function of the sample availability) was performed using SuperScript II (Invitrogen) in the presence of oligo-dT30VN (1µM; 5′-AAG CAG TGG TAT CAA CGC AGA GTA CT30VN-3′), template-switching oligonucleotides (1 µM) and betaine (1M). The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (2x) (Roche) and 100 nM IS PCR primer (5′-AAG CAG TGG TAT CAA CGC AGA GT-3′) with 8 cycles of PCR amplification. Following purification with Agencourt Ampure XP beads (1:1 ratio; Beckmann Coulter), the product size distribution and the quantity were assessed with a Bioanalyzer High Sensitivity DNA Kit (Agilent). The amplified cDNA (200 ng) was fragmented for 10 min at 55 ºC using Nextera XT (Illumina) and amplified for 12 cycles with indexed Nextera PCR primers. The library was purified twice with Agencourt Ampure XP beads (0.8:1 ratio) and quantified on a Bioanalyzer using a High Sensitivity DNA Kit.

treatment_protocol: Subchronic ototoxicity mice were given 30 mM of 3,3'-iminodipropionitrile (CAS# 111-94-4; >98%) in the drinking water for 8 weeks; control mice received plain drinking water.

value: Vestibular epithelium

value: male

tag: strain

value: Subchronic ototoxicity


title: Vestibular epithelium, M01741EN_IDPN

description: Library name: AD5203

tag: tissue


title: Vestibular epithelium, M01743ND_Control

description: Library name: AD5201

value: Control


title: Vestibular epithelium, M01757NN_IDPN

description: Library name: AD5204


title: Transgenic mice, DOX_On_replicate 4

city: Boston

first: Steven

last: Balk

address: 3 Blackfan circle

institute: BIDMC

description: Library name: 1-105-4

data_processing:
Assembly: mm10_genome
Illumina Casava1.7 software used for basecalling, RNA-Seq raw data was mapped by Tophat2.
A transcripts per million (TPM), gene expression was calculated using the voom normalization approach. The differential expression of genes was determined from normalized sequencing data using linear model microarray analysis software package (LIMMA).
Visualization Pipeline for RNA-seq (VIPER) was used to analyze RNA-seq reads. Fastq files were aligned to hg19 reference genome using STAR aligner (2.7.0f) with default parameters
Supplementary files format and content: comma-separated values file includes differential gene expressions (log2(Fold Change) and statistical values)

source_name: Prostate

extract_protocol:
The ventral prostate epithelium was laser capture micro-dissected and snap-frozen for RNA extraction using the RNeasy Plus Kit (Qiagen) following the manufacturer’s instructions.
mRNA libraries were generated using the Illumina TruSeq stranded mRNA sample kit.
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.
mRNA libraries were generated using the Illumina TruSeq stranded mRNA sample kit.

value: Prostate

tag: genotype

value: Probasin-rtTA;tetO-ERG;Pten+/-mice

value: Long termERG induction, DOX


title: Transgenic mice, DOX_On_replicate 3

description: Library name: 1-105-3

tag: treatment


title: Vestibular epithelium, M01743EN_Control

description: Library name: AD5202


title: Vestibular epithelium, M01743NN_Control

description: Library name: AD5200


title: Transgenic mice, DOX_On_replicate 2

description: Library name: 1-105-2


title: Transgenic mice, DOX_Off_replicate 3

description: Library name: 1-105-7

value: Long termERG induction plus short term DOX withdrawal


title: Transgenic mice, DOX_On_replicate 1

description: Library name: 1-105-1


title: Transgenic mice, DOX_Off_replicate 4

description: Library name: 1-105-8


title: Transgenic mice, DOX_Off_replicate 1

description: Library name: 1-105-5


title: Transgenic mice, DOX_Off_replicate 2

description: Library name: 1-105-6


title: Replcative senescence_biol rep 2

city: Okinawa

first: Yatzu

last: Chiu

address: Tancha 1919-1

institute: Okinawa Institute of Science and Technology

description:
Library name: Sample 36
Column name in raw_counts_All.txt: RS_2

data_processing:
exceRpt small RNA-sequencing Pipeline (version 4.6.2)
Trimming was performed following the manufacturer’s instruction (NEXTFLEX ® Small RNA-Seq Kit v3)
The clean reads were mapped to the human genome GRCh38 and aligned against miRbase to create miRNA counts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

extract_protocol:
Total RNA was extracted from cells using TRIzol (Invitrogen) and the RNA Clean & Concentrator kits (Zymo)
The sequencing libraries were generated using NEXTFLEX Small RNA-Seq Kit v3 (PerkinElmer) following the manufacturer’s protocol from 100 ng of total RNA

value: normal human fibroblast

value: Replicative senescence


title: DXR-treated_D16_biol rep2

description:
Library name: Sample 34
Column name in raw_counts_All.txt: DXR_D16_2


title: DXR-treated_D16_biol rep1

description:
Library name: Sample 33
Column name in raw_counts_All.txt: DXR_D16_1


title: DXR-treated_D8_biol rep2

description:
Library name: Sample 32
Column name in raw_counts_All.txt: DXR_D8_2


title: iPSC, Control, rep1

description:
Library name: hiPSC CTRL1 DS1
SC13_hiPSC_CTRL1

value: iPSC

value: Day 0

value: Male


title: Mouse 6 das post DOX induction, replicate 1

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: RMA

label: biotin

source_name: Ventral prostate epithelium, mouse 6 das post DOX induction

label_protocol: Affymetrix protocol

extract_protocol: Ventral prostate epithelium was laser capture microdissected. For RNA isolation tissues were homogenized using a tissue ruptor. Total RNA was isolated with the RNeasy Mini Plus Kit (Qiagen)

treatment_protocol: Probasin-rtTA;tetO-ERG;Pten+/-mice wee treated  with doxycycline fo ~ 4 weeks and then sacrificed

value: Ventral prostate epithelium

value: Pten deficient mice on a C57BI/6J background


title: Mouse prior to DOX induction, replicate 2

source_name: Ventral prostate epithelium, mouse prior to DOX induction


title: DXR-treated_D6_biol rep1

description:
Library name: Sample 29
Column name in raw_counts_All.txt: DXR_D6_1


title: DXR-treated_D8_biol rep1

description:
Library name: Sample 31
Column name in raw_counts_All.txt: DXR_D8_1


title: Mouse prior to DOX induction, replicate 1


title: Mouse 3 days post DOX induction, replicate 1

source_name: Ventral prostate epithelium, mouse 3 days post DOX induction


title: Mouse 3 days post DOX induction, replicate 2


title: DXR-treated_D4_biol rep2

description:
Library name: Sample 28
Column name in raw_counts_All.txt: DXR_D4_2


title: DXR-treated_D3_biol rep2

description:
Library name: Sample 26
Column name in raw_counts_All.txt: DXR_D3_2


title: DXR-treated_D6_biol rep2

description:
Library name: Sample 30
Column name in raw_counts_All.txt: DXR_D6_2


title: Mouse 6 das post DOX induction, replicate 2


title: DXR-treated_D1_biol rep2

description:
Library name: Sample 22
Column name in raw_counts_All.txt: DXR_D1_2


title: DXR-treated_D2_biol rep1

description:
Library name: Sample 23
Column name in raw_counts_All.txt: DXR_D2_1


title: DXR-treated_D1_biol rep1

description:
Library name: Sample 21
Column name in raw_counts_All.txt: DXR_D1_1


title: DXR-treated_D4_biol rep1

description:
Library name: Sample 27
Column name in raw_counts_All.txt: DXR_D4_1


title: SDS-treated_D16_biol rep2

description:
Library name: Sample 18
Column name in raw_counts_All.txt: SDS_D16_2


title: SDS-treated_D8_biol rep1

description:
Library name: Sample 15
Column name in raw_counts_All.txt: SDS_D8_1


title: SDS-treated_D8_biol rep2

description:
Library name: Sample 16
Column name in raw_counts_All.txt: SDS_D8_2


title: DXR-treated_D3_biol rep1

description:
Library name: Sample 25
Column name in raw_counts_All.txt: DXR_D3_1


title: DXR-treated_D2_biol rep2

description:
Library name: Sample 24
Column name in raw_counts_All.txt: DXR_D2_2


title: SDS-treated_D16_biol rep1

description:
Library name: Sample 17
Column name in raw_counts_All.txt: SDS_D16_1


title: SDS-treated_D6_biol rep2

description:
Library name: Sample 14
Column name in raw_counts_All.txt: SDS_D6_2


title: Replcative senescence_biol rep 1

description:
Library name: Sample 35
Column name in raw_counts_All.txt: RS_1


title: DXR-treated_D0_biol rep1

description:
Library name: Sample 19
Column name in raw_counts_All.txt: DXR_D0_1


title: SDS-treated_D6_biol rep1

description:
Library name: Sample 13
Column name in raw_counts_All.txt: SDS_D6_1


title: SDS-treated_D3_biol rep2

description:
Library name: Sample 10
Column name in raw_counts_All.txt: SDS_D3_2


title: SDS-treated_D4_biol rep1

description:
Library name: Sample 11
Column name in raw_counts_All.txt: SDS_D4_1


title: SDS-treated_D3_biol rep1

description:
Library name: Sample 9
Column name in raw_counts_All.txt: SDS_D3_1


title: SDS-treated_D4_biol rep2

description:
Library name: Sample 12
Column name in raw_counts_All.txt: SDS_D4_2


title: SDS-treated_D2_biol rep2

description:
Library name: Sample 8
Column name in raw_counts_All.txt: SDS_D2_2


title: SDS-treated_D2_biol rep1

description:
Library name: Sample 7
Column name in raw_counts_All.txt: SDS_D2_1


title: SDS-treated_D1_biol rep2

description:
Library name: Sample 6
Column name in raw_counts_All.txt: SDS_D1_2


title: SDS-treated_D1_biol rep1

description:
Library name: Sample 5
Column name in raw_counts_All.txt: SDS_D1_1


title: Young proliferating_control_biol rep2

description:
Library name: Sample 2
Column name in raw_counts_All.txt: Ctrl_2


title: SDS-treated_D0_biol rep1

description:
Library name: Sample 3
Column name in raw_counts_All.txt: SDS_D0_1


title: Young proliferating_control_biol rep1

description:
Library name: Sample 1
Column name in raw_counts_All.txt: Ctrl_1


title: SDS-treated_D0_biol rep2

description:
Library name: Sample 4
Column name in raw_counts_All.txt: SDS_D0_2


title: DXR-treated_D0_biol rep2

description:
Library name: Sample 20
Column name in raw_counts_All.txt: DXR_D0_2


title: Immunoprecipitated OMA-1 RNP replicate 2 (sperm positive)

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description: Library name: OMA-1_DG2581_IP2_40ng

data_processing:
After trimming adapters with Trimmomatic (0.32), reads were mapped to the WBcel235/ce11 genome with STAR (v 2.5.3a) guided by gene annotations defined in Ensembl (release 91) and sorted and indexed with Samtools (v1.21). PCR duplicates were removed with Picard MarkDuplicates (v2.17.10). Gene-level abundance was estimated for Ensembl defined annotations using the featureCounts function in the Bioconductor package Rsubread (v1.28.1). Principal component analysis and inspection of 5’ vs 3’ read coverage indicated that one IP sample from DG4400 (IP2) contained degraded RNA and was excluded from further analysis. An average of 10 million high-quality (MAPQ > 55) reads mapped to non-ribosomal genes within each sample. In prior work, we found that the sets of proteins and mRNAs associated with OMA-1 were not substantially different in the presence and absence of sperm (Spike et al., 2014b). This dataset also included LIN-41 and transcripts that associated with both OMA-1 and LIN-41. We also observed that SPN-4 expression in the most proximal oocytes was independent of the presence of sperm in the gonad (Tsukamoto et al., 2017), and that the same set of proteins copurify with SPN-4 in the presence and absence of sperm (unpublished results). Thus, we combined the data from the fog-1(q252ts) and spe-9(hc88ts) backgrounds to enhance the analytical power of the data (Table S1). A comparison of LIN-41- and OMA-1-associated mRNAs with our prior datasets (Tsukamoto et al., 2017) indicated replicability (Fig. S1). Differential gene expression of Ensembl-annotated genes was determined using DESeq2 (v1.26.0). A Wald corrected t-test was used identify transcripts overrepresented in the IP samples relative to the lysates (altHypothesis=”greater”).  P values were adjusted for multiple test correction using the Benjamini–Hochberg procedure. Transcripts enriched greater than 4-fold with adjusted p values less than 0.05 were considered statistically significant.
Assembly: WBcel235/ce11
Supplementary files format and content: Raw Counts and normalized FPKM values in csv format.

source_name: sperm +

growth_protocol: Four L4-stage larvae were cultured at 15°C on each of sixteen 60 mm x 15 mm Petri dishes with NGM seeded with the E. coli strain OP50-1 as food source. After culturing for 10 days, starved larvae were collected and transferred to forty large 100 mm x 15 mm Petri dishes with peptone-enriched (40 g peptone/liter) NGM seeded with E. coli strain NA22. After culturing at 15 ºC for 5 days, embryos were collected by alkaline hypochlorite treatment (20% bleach and 0.5N NaOH), washed in M9 buffer and allowed to hatch in ten 100 mm x 15 mm Petri dishes containing 25 ml of M9 solution. After incubating at 25 ºC for 1 day, L1-stage larvae were cultured at 25°C at a density of 30,000 L1-stage larvae on each of approximately sixty 150 mm x 15 mm Petri dishes with peptone-enriched (20 g peptone/liter) NGM seeded with NA22. The cultures were never permitted to exhaust the food supply and were refed in the L4 stage with concentrated NA22 bacteria the day before harvesting (approximately the E.coli produced by a 200 ml LB liquid culture per Petri dish). After growing at 25 ºC for approximately 48 hours, 1-day adult-stage hermaphrodites were washed free of E. coli using M9 and harvested in freezing buffer (50 mM HEPES, pH 7.5, 1 mM MgCl2, 100 mM KCl, 10% glycerol). The worm slurry was frozen dropwise in liquid nitrogen and stored in –80 ºC until use.

extract_protocol:
Twenty tubes containing 800 μl of the TEV eluate/TRIzol LS mixture were thawed at room temperature and 160 μl of chloroform was added to each tube and mixed vigorously for 15 seconds. After incubation at room temperature for 10 minutes, the mixture was centrifuged at 12,000 x g for 15 minutes at 4 ºC. Supernatants were collected and applied onto two RNeasy MinElute spin columns using the RNeasy Micro Kit (Qiagen, cat #74004). Finally, about 40 μl of RNA solution was collected from each immunopurification. RNA was quantified using Qubit fluoremetric quantification (Thermo Fisher Scientific, Inc).
Total RNA was also extracted from 200 μl of the high-speed supernatant of the lysates using RNeasy Micro Kit (Qiagen, 74004) as a control. A Ribo-Zero rRNA Removal Kit (Illumina, MRZH116) was used to remove ribosomal RNA (rRNA) from the total RNA. Duplicate sequencing libraries were prepared from rRNA-depleted total RNA from the high-speed supernatant of the lysates using the same method so that enrichment over input could be calculated. The number of amplification cycles utilized was determined empirically using 1 μl of the sequencing library in a 10 μl test reaction containing a 1:10,000 dilution of SYBR Green I (Invitrogen), 2x KAPA HiFi HotStart ReadyMix (Roche) and custom barcoding primers. The empirically determined number of amplification cycles was used in a subsequent 50 μl reaction with the remaining eluate in the absence of SYBR Green using Kapa HiFi HotStart Readymix (Roche). Libraries were size-selected on a 2% E-Gel EX agarose gel (Invitrogen)  with visualization using UV-free Dark Reader transilluminator (Claire Chemical Research) and fragments between 250 bp and 400 bp were extracted using a MiniElute Gel Extraction Kit (Qiagen). Libraries were submitted to the University of Minnesota Genomics Center for 2x 36-bp sequencing using the Illumina NextSeq 500 to depth of 37-55 million reads per sample.

treatment_protocol: Approximately 10 ml of high-speed supernatant (containing 160 mg of protein) was applied to a batch binding with antibody-conjugated Dynabeads for 1 hour at 4 ºC. Basic IP buffer was 50 mM HEPES (pH7.5), 1 mM MgCl2, 100 mM KCl. After binding, unbound proteins were removed in the supernatant. The Dynabeads were washed 3 times with 10 ml of IP wash buffer [basic IP buffer with 300 mM KCl (final concentration), 0.05% NP-40, 5 mM 2-mercaptoethanol, 5 mM sodium citrate, 10 μM ZnCl2, cOmplete mini EDTA-free protease inhibitors (Roche, 1 tablet/ 10 ml) and RNasin (Promega, 20 units/ml)], and bound proteins were cleaved from the Dynabeads by adding and mixing with 4 ml of cleavage solution containing 225 units/ml of AcTEV protease (Life Technologies) for 18 hours at 4 ºC. The TEV eluate was collected in the supernatant by placing tubes on DynaMag magnet (Thermo Fisher Scientific, Inc.). 200 μl aliquots of the TEV eluate were dispensed into 20 individual 1.5 ml microcentrifuge tubes and mixed with 600 μl of TRIzol LS (Life Technologies) and flash-frozen on powered dry ice and stored at –80 ºC.

value: sperm +

tag: strain id

tag: ip antibody

value: Anti-GFP monoclonal antibodies 12A6 and 4C9 (Developmental Studies Hybridoma Bank)

value: spe-9(hc88ts) I; oma-1(zu405te33) IV; tnIs17 [pCS410(Poma-1::OMA-1::S-TEV-GFP LAP tag), pDPmm0016B(unc-119(+))] V

tag: fraction

value: IP


title: Immunoprecipitated OMA-1 RNP replicate 3 (sperm positive)

description: Library name: OMA-1_DG2581_IP3_40ng


title: OMA-1 Cell Lysate replicate 2 (sperm positive)

description: Library name: OMA-1_DG2581_Lysate2_40ng

value: LYSATE


title: OMA-1 Cell Lysate replicate 1 (sperm positive)

description: Library name: OMA-1_DG2581_Lysate1_40ng

value: spe-9(hc88ts) I; oma-1(zu405te33) IV; tnIs17 [pCS410(Poma-1::OMA-1::S-TEV-GFP LAP tag), pDPmm0016B(unc-119(+))]  V


title: Immunoprecipitated OMA-1 RNP replicate 1 (sperm positive)

description: Library name: OMA-1_DG2581_IP1_40ng


title: Immunoprecipitated OMA-1 RNP replicate 3 (sperm negative)

description: Library name: OMA-1_DG2566_IP3_40ng

source_name: sperm negative (fog-1(q253))

value: sperm negative (fog-1(q253))

value: fog-1(q253ts) I; oma-1(zu405te33) IV; tnIs17 [pCS410(Poma-1::OMA-1::S-TEV-GFP LAP tag), pDPmm0016B(unc-119(+))] V


title: Immunoprecipitated OMA-1 RNP replicate 2 (sperm negative)

description: Library name: OMA-1_DG2566_IP2_40ng


title: OMA-1 Cell Lysate replicate 2 (sperm negative)

description: Library name: OMA-1_DG2566_Lysate2_40ng


title: Immunoprecipitated LIN-41 RNP replicate 1 (sperm positive)

description: Library name: LIN-41_DG4485_IP1_10ng


title: Immunoprecipitated LIN-41 RNP replicate 3 (sperm positive)

description: Library name: LIN-41_DG4485_IP3_10ng


title: Immunoprecipitated LIN-41 RNP replicate 2 (sperm positive)

description: Library name: LIN-41_DG4485_IP2_10ng


title: OMA-1 Cell Lysate replicate 1 (sperm negative)

description: Library name: OMA-1_DG2566_Lysate1_40ng

value: fog-1(q253ts) I; oma-1(zu405te33) IV; tnIs17 [pCS410(Poma-1::OMA-1::S-TEV-GFP LAP tag), pDPmm0016B(unc-119(+))]  V


title: Immunoprecipitated LIN-41 RNP replicate 3 (sperm negative)

description: Library name: LIN-41_DG3923_IP3_10ng


title: LIN-41 Cell Lysate replicate 2 (sperm positive)

description: Library name: LIN-41_DG4485_Lysate2_10ng


title: LIN-41 Cell Lysate replicate 1 (sperm positive)

description: Library name: LIN-41_DG4485_Lysate1_10ng


title: Immunoprecipitated LIN-41 RNP replicate 1 (sperm negative)

description: Library name: LIN-41_DG3923_IP1_10ng


title: Immunoprecipitated LIN-41 RNP replicate 2 (sperm negative)

description: Library name: LIN-41_DG3923_IP2_10ng


title: LIN-41 Cell Lysate replicate 1 (sperm negative)

description: Library name: LIN-41_DG3923_Lysate1_10ng


title: LIN-41 Cell Lysate replicate 2 (sperm negative)

description: Library name: LIN-41_DG3923_Lysate2_10ng


title: Immunoprecipitated SNP4-RNP replicate 2 (sperm positive)

description: Library name: SPN-4_DG4400_IP2

value: M2 (Millipore Sigma, cat# F1804)

value: spe-9(hc88ts) I; spn-4(tn1699[spn-4::gfp::3xflag]) V


title: Immunoprecipitated SNP4-RNP replicate 3 (sperm positive)

description: Library name: SPN-4_DG4400_IP3


title: SPN-4 Cell Lysate replicate 2 (sperm positive)

description: Library name: SPN-4_DG4400_Lysate2_2ng


title: Immunoprecipitated SNP4 RNP replicate 3 (sperm negative)

description: Library name: SPN-4_DG4398_IP3


title: Immunoprecipitated SNP-4 RNP replicate 1 (sperm negative)

description: Library name: SPN-4_DG4398_IP1


title: ALCL_G

type: genomic

city: Ulm

first: Selina

last: Glaser

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University and Ulm University Medical Center

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

scan_protocol: The arrays were scanned using a iScan device.

data_processing: Raw idat files were read into the statistical program R (version 4.3.0) using the minfi package (version 1.46.0). Normalization was performed with the preprocessIllumina() function against the intrinsic controls and without background correction.

source_name: ALK-positive anaplastic large lymphoma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified according to commercially available kits from Qiagen according to standard instructions

value: ALK-positive anaplastic large lymphoma


title: Immunoprecipitated SNP-4 RNP replicate 2 (sperm negative)

description: Library name: SPN-4_DG4398_IP2


title: ALCL_E


title: ALCL_F


title: ALCL_C


title: ALCL_B


title: SPN-4 Cell Lysate replicate 2 (sperm negative)

description: Library name: SPN-4_DG4398_Lysate2_2ng


title: Immunoprecipitated OMA-1 RNP replicate 1 (sperm negative)

description: Library name: OMA-1_DG2566_IP1_40ng


title: Immunoprecipitated SNP4-RNP replicate 1 (sperm positive)

description: Library name: SPN-4_DG4400_IP1


title: ALKpos LBCL case 7

source_name: ALK-positive large B-cell lymphoma, after treatment with Crizotinib


title: ALCL_A


first: Dan

last: Barouch

address: 3 Blackfan Cir

department: CVVR

institute: Beth Israel Deaconess Medical Center

description: Library name: p23200_s018_DHHN_Male_20_21_Group_1_D12_Post_ATI_BatchC

data_processing:
The quality of the raw reads was assessed using multiQC39. Raw demultiplexed fastq paired-end read files were trimmed of adapters and filtered using the program skewer to discard those with an average phred quality score of less than 30 or a length of less than 36.
Data were aligned to the Mmul10-100 assembly and annotations of the Indian rhesus macaque genome using STAR version 2.7.3a.
Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count.
Assembly: Mmul10-100
Supplementary files format and content: siv-reservoir-biomarkers-rawCounts.csv (raw RNA sequencing counts)
Supplementary files format and content: siv-reservoir-biomarkers-normalizedCounts.csv (normalized RNA sequencing counts)

source_name: Whole blood

extract_protocol:
Total RNA was extracted from whole blood samples using the PAXgene Blood RNA Kit IVD (PreAnalytix).
RNA quality was assessed with the Fragment Analyzer (Agilent) and its Standard Sensitivity RNA kit. Total RNA was normalized to 100 ng before random hexamer priming and libraries were generated by the TruSeq Stranded Total RNA—Globin kit (Illumina). The resulting libraries were assessed on the Fragment Analyzer (Agilent) with the High Sense Large Fragment kit and quantified using a Qubit 3.0 fluorometer (Life Technologies). Medium-depth sequencing, with at least 30 million reads per sample, was performed on a NextSeq 500 (Illumina) with a PE100 configuration, paired-end run yielding ~40 million reads per sample.

value: Whole blood

tag: animal id

value: DHHN

tag: Sex

value: BatchC

tag: viral loads_(cp/ml)


description: Library name: p23200_s014_DHHN_Male_20_21_Group_1_D8_Post_ATI_BatchC

value: Male

tag: batch


description: Library name: p23200_s015_DHHN_Male_20_21_Group_1_D9_Post_ATI_BatchC


description: Library name: p23200_s016_DHHN_Male_20_21_Group_1_D10_Post_ATI_BatchC


description: Library name: p23200_s017_DHHN_Male_20_21_Group_1_D11_Post_ATI_BatchC


description: Library name: p23200_s011_L970_Male_20_21_Group_3_D10_Post_ATI_BatchC


title: SPN-4 Cell Lysate replicate 1 (sperm positive)

description: Library name: SPN-4_DG4400_Lysate1_2ng


description: Library name: p23200_s009_L997_Male_20_21_Group_3_D8_Post_ATI_BatchC


description: Library name: p23200_s013_L970_Male_20_21_Group_3_D12_Post_ATI_BatchC


description: Library name: p23200_s012_L970_Male_20_21_Group_3_D11_Post_ATI_BatchC


description: Library name: p23200_s010_L997_Male_20_21_Group_3_D9_Post_ATI_BatchC


description: Library name: p23200_s008_DHGI_Male_20_21_Group_1_D12_Post_ATI_BatchC

value: DHGI


title: SPN-4 Cell Lysate replicate 1 (sperm negative)

description: Library name: SPN-4_DG4398_Lysate1_2ng


title: ALCL_D


description: Library name: p23200_s005_DHGI_Male_20_21_Group_1_D9_Post_ATI_BatchC


description: Library name: p23200_s002_L677_Male_20_21_Group_2_D9_Post_ATI_BatchC


description: Library name: p23200_s004_L608_Male_20_21_Group_2_D9_Post_ATI_BatchC


description: Library name: p22286_s099_L997_Male_20_21_Group_3_D6_Post_ATI

value: BatchB


description: Library name: p22286_s096_L997_Male_20_21_Group_3_D2_Post_ATI


description: Library name: p23200_s003_L608_Male_20_21_Group_2_D8_Post_ATI_BatchC


title: ALKpos LBCL case 7 PDX

source_name: PDX model of a ALK-positive large B-cell lymphoma, after treatment with Crizotinib


description: Library name: p22286_s097_L997_Male_20_21_Group_3_D4_Post_ATI


description: Library name: p22286_s095_L997_Male_20_21_Group_3_D0_Post_ATI_BatchC


description: Library name: p22286_s098_L997_Male_20_21_Group_3_D5_Post_ATI


description: Library name: p22286_s100_L997_Male_20_21_Group_3_D7_Post_ATI


description: Library name: p23200_s001_L677_Male_20_21_Group_2_D8_Post_ATI_BatchC


description: Library name: p22286_s094_L990_Male_20_21_Group_3_D9_Post_ATI


description: Library name: p22286_s090_L990_Male_20_21_Group_3_D5_Post_ATI


description: Library name: p22286_s095_L997_Male_20_21_Group_3_D0_Post_ATI


description: Library name: p23200_s007_DHGI_Male_20_21_Group_1_D11_Post_ATI_BatchC


description: Library name: p22286_s089_L990_Male_20_21_Group_3_D4_Post_ATI


description: Library name: p22286_s085_L956_Male_20_21_Group_3_D6_Post_ATI


description: Library name: p22286_s095_L997_Male_20_21_Group_3_D0_Post_ATI_BatchA

value: BatchA


description: Library name: p22286_s093_L990_Male_20_21_Group_3_D8_Post_ATI


description: Library name: p22286_s092_L990_Male_20_21_Group_3_D7_Post_ATI


description: Library name: p22286_s081_L956_Male_20_21_Group_3_D0_Post_ATI_BatchA


description: Library name: p22286_s082_L956_Male_20_21_Group_3_D2_Post_ATI


description: Library name: p23200_s006_DHGI_Male_20_21_Group_1_D10_Post_ATI_BatchC


description: Library name: p22286_s081_L956_Male_20_21_Group_3_D0_Post_ATI


description: Library name: p22286_s080_L608_Male_20_21_Group_2_D7_Post_ATI


description: Library name: p22286_s088_L990_Male_20_21_Group_3_D0_Post_ATI_BatchA


description: Library name: p22286_s091_L990_Male_20_21_Group_3_D6_Post_ATI


description: Library name: p22286_s087_L956_Male_20_21_Group_3_D8_Post_ATI


description: Library name: p22286_s086_L956_Male_20_21_Group_3_D7_Post_ATI


description: Library name: p22286_s079_L608_Male_20_21_Group_2_D6_Post_ATI


description: Library name: p22286_s088_L990_Male_20_21_Group_3_D0_Post_ATI


description: Library name: p22286_s076_L608_Male_20_21_Group_2_D2_Post_ATI


description: Library name: p22286_s083_L956_Male_20_21_Group_3_D4_Post_ATI


description: Library name: p22286_s075_L608_Male_20_21_Group_2_D0_Post_ATI


description: Library name: p22286_s073_L677_Male_20_21_Group_2_D6_Post_ATI


description: Library name: p22286_s072_L677_Male_20_21_Group_2_D5_Post_ATI


description: Library name: p22286_s078_L608_Male_20_21_Group_2_D5_Post_ATI


description: Library name: p22286_s075_L608_Male_20_21_Group_2_D0_Post_ATI_BatchA


description: Library name: p22286_s074_L677_Male_20_21_Group_2_D7_Post_ATI


description: Library name: p22286_s069_L677_Male_20_21_Group_2_D0_Post_ATI_BatchC


description: Library name: p22286_s069_L677_Male_20_21_Group_2_D0_Post_ATI


description: Library name: p22286_s069_L677_Male_20_21_Group_2_D0_Post_ATI_BatchA


description: Library name: p22286_s084_L956_Male_20_21_Group_3_D5_Post_ATI


description: Library name: p22286_s064_DHJG_Male_20_21_Group_1_D4_Post_ATI

value: DHJG


description: Library name: p22286_s066_DHJG_Male_20_21_Group_1_D6_Post_ATI


description: Library name: p22286_s060_DHHN_Male_20_21_Group_1_D6_Post_ATI


description: Library name: p22286_s062_DHJG_Male_20_21_Group_1_D0_Post_ATI_BatchA


description: Library name: p22286_s068_DHJG_Male_20_21_Group_1_D8_Post_ATI


description: Library name: p22286_s065_DHJG_Male_20_21_Group_1_D5_Post_ATI


description: Library name: p22286_s067_DHJG_Male_20_21_Group_1_D7_Post_ATI


description: Library name: p22286_s063_DHJG_Male_20_21_Group_1_D2_Post_ATI


description: Library name: p22286_s075_L608_Male_20_21_Group_2_D0_Post_ATI_BatchC


description: Library name: p22286_s061_DHHN_Male_20_21_Group_1_D7_Post_ATI


description: Library name: p22286_s062_DHJG_Male_20_21_Group_1_D0_Post_ATI


description: Library name: p22286_s056_DHHN_Male_20_21_Group_1_D0_Post_ATI_BatchC


description: Library name: p22286_s057_DHHN_Male_20_21_Group_1_D2_Post_ATI


description: Library name: p22286_s059_DHHN_Male_20_21_Group_1_D5_Post_ATI


description: Library name: p22286_s052_DHEZ_Male_20_21_Group_1_D2_Post_ATI

value: DHEZ


description: Library name: p22286_s077_L608_Male_20_21_Group_2_D4_Post_ATI


description: Library name: p22286_s056_DHHN_Male_20_21_Group_1_D0_Post_ATI


description: Library name: p22286_s056_DHHN_Male_20_21_Group_1_D0_Post_ATI_BatchA


description: Library name: p22286_s055_DHEZ_Male_20_21_Group_1_D6_Post_ATI


description: Library name: p22286_s048_L991_Male_20_21_Group_3_D10_Post_ATI


description: Library name: p22286_s070_L677_Male_20_21_Group_2_D2_Post_ATI


description: Library name: p22286_s071_L677_Male_20_21_Group_2_D4_Post_ATI


description: Library name: p22286_s058_DHHN_Male_20_21_Group_1_D4_Post_ATI


description: Library name: p22286_s046_L991_Male_20_21_Group_3_D8_Post_ATI


description: Library name: p22286_s050_L991_Male_20_21_Group_3_D12_Post_ATI


description: Library name: p22286_s049_L991_Male_20_21_Group_3_D11_Post_ATI


description: Library name: p22286_s051_DHEZ_Male_20_21_Group_1_D0_Post_ATI_BatchA


description: Library name: p22286_s053_DHEZ_Male_20_21_Group_1_D4_Post_ATI


description: Library name: p22286_s045_L991_Male_20_21_Group_3_D0_Post_ATI_BatchB


description: Library name: p22286_s047_L991_Male_20_21_Group_3_D9_Post_ATI


description: Library name: p22286_s045_L991_Male_20_21_Group_3_D0_Post_ATI


description: Library name: p22286_s044_L970_Male_20_21_Group_3_D9_Post_ATI


description: Library name: p22286_s043_L970_Male_20_21_Group_3_D8_Post_ATI


description: Library name: p22286_s038_L970_Male_20_21_Group_3_D0_Post_ATI


description: Library name: p22286_s054_DHEZ_Male_20_21_Group_1_D5_Post_ATI


description: Library name: p22286_s039_L970_Male_20_21_Group_3_D4_Post_ATI


title: WT5_CTRL

city: Novato

last: Winer

state: CA

address: 8001 Redwood Blvd, Novato, CA 94945

institute: Buck Institute for Research on Aging

description: Library name: WT5_CTRL

library_source: other

data_processing:
Raw sequencing data were first processed into a count table of amplicon sequence variants (ASVs) using standard pipelines. This table was then imported into phyloseq in R for downstream analysis. Within phyloseq, relative abundance was calculated on a per-sample basis by dividing the raw counts for each ASV (or higher-level taxonomic grouping, when agglomerated) by the total sequencing depth of that sample. For example, if a sample contained 20,000 total reads and 2,000 of those were assigned to a given ASV, the relative abundance of that ASV would be 2,000   20,000 = 0.10 (10%).
This procedure was applied across all samples to generate a relative abundance matrix, where the values for each sample sum to 1. These relative abundances were then used for downstream statistical analyses and visualization of microbial community.
Assembly: RDP training set (v18)
Supplementary files format and content: csv file of the relative abundance of biota for each sample
Library strategy: 16S rRNA-seq

molecule: other

organism: mouse gut metagenome

source_name: Stool

extract_protocol:
Fecal pellets from 15-month-old mice were subject to the Quick-DNA Fecal/Soil Microbe Microprep kit (Zymo Research. Cat.# D6012).
Sequencing libraries were generated and indexes were added to attribute sequences to each sample. Briefly, PCR amplification of targeted regions was performed by using specific primers connecting with barcodes. The PCR products with proper size were selected by 2% agarose gel electrophoresis. Same amount of PCR products from each sample was pooled, end-repaired, A-tailed and further ligated with Illumina adapters. Libraries were sequenced on a paired-end Illumina platform to generate 250bp paired-end raw reads. Subsequently, library quality was assessed and quantified by QPCR. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

value: Stool


title: WT4_CTRL

description: Library name: WT4_CTRL


description: Library name: p22286_s038_L970_Male_20_21_Group_3_D0_Post_ATI_BatchB


description: Library name: p22286_s038_L970_Male_20_21_Group_3_D0_Post_ATI_BatchC


description: Library name: p22286_s051_DHEZ_Male_20_21_Group_1_D0_Post_ATI


description: Library name: p22286_s035_L681_Male_20_21_Group_3_D6_Post_ATI


description: Library name: p22286_s033_L681_Male_20_21_Group_3_D4_Post_ATI


title: WT3_INULIN

description: Library name: WT3_INULIN


title: WT3_CTRL

description: Library name: WT3_CTRL


description: Library name: p22286_s036_L681_Male_20_21_Group_3_D7_Post_ATI


description: Library name: p22286_s034_L681_Male_20_21_Group_3_D5_Post_ATI


description: Library name: p22286_s041_L970_Male_20_21_Group_3_D6_Post_ATI


description: Library name: p22286_s037_L681_Male_20_21_Group_3_D8_Post_ATI


description: Library name: p22286_s042_L970_Male_20_21_Group_3_D7_Post_ATI


description: Library name: p22286_s040_L970_Male_20_21_Group_3_D5_Post_ATI


description: Library name: p22286_s031_L681_Male_20_21_Group_3_D0_Post_ATI


description: Library name: p22286_s031_L681_Male_20_21_Group_3_D0_Post_ATI_BatchB


title: WT4_INULIN

description: Library name: WT4_INULIN


title: WT3_CELL

description: Library name: WT3_CELL


description: Library name: p22286_s032_L681_Male_20_21_Group_3_D2_Post_ATI


title: WT2_CTRL

description: Library name: WT2_CTRL


description: Library name: p22286_s029_J639_Male_20_21_Group_2_D11_Post_ATI


title: WT1_INULIN

description: Library name: WT1_INULIN


title: WT2_INULIN

description: Library name: WT2_INULIN


title: WT2_CELL

description: Library name: WT2_CELL


title: WT1_CTRL

description: Library name: WT1_CTRL


title: WT1_CELL

description: Library name: WT1_CELL


title: WT4_CELL

description: Library name: WT4_CELL


title: WT5_INULIN

description: Library name: WT5_INULIN


title: AD5_INULIN

description: Library name: AD5_INULIN


description: Library name: p22286_s027_J639_Male_20_21_Group_2_D9_Post_ATI


title: AD5_CELL

description: Library name: AD5_CELL


description: Library name: p22286_s025_J639_Male_20_21_Group_2_D7_Post_ATI


title: AD4_CTRL

description: Library name: AD4_CTRL


description: Library name: p22286_s023_TP5_Female_Group_2_D12_Post_ATI

value: Female


title: AD5_CTRL

description: Library name: AD5_CTRL


description: Library name: p22286_s024_J639_Male_20_21_Group_2_D0_Post_ATI


description: Library name: p22286_s028_J639_Male_20_21_Group_2_D10_Post_ATI


description: Library name: p22286_s021_TP5_Female_Group_2_D10_Post_ATI


title: AD4_INULIN

description: Library name: AD4_INULIN


description: Library name: p22286_s022_TP5_Female_Group_2_D11_Post_ATI


title: AD3_INULIN

description: Library name: AD3_INULIN


title: AD4_CELL

description: Library name: AD4_CELL


description: Library name: p22286_s030_J639_Male_20_21_Group_2_D12_Post_ATI


description: Library name: p22286_s019_L604_Male_20_21_Group_2_D6_Post_ATI


title: AD2_INULIN

description: Library name: AD2_INULIN


description: Library name: p22286_s020_TP5_Female_Group_2_D0_Post_ATI_BatchB


description: Library name: p22286_s017_L604_Male_20_21_Group_2_D4_Post_ATI


title: AD2_CELL

description: Library name: AD2_CELL


title: AD1_INULIN

description: Library name: AD1_INULIN


title: AD3_CTRL

description: Library name: AD3_CTRL


description: Library name: p22286_s020_TP5_Female_Group_2_D0_Post_ATI


title: AD3_CELL

description: Library name: AD3_CELL


description: Library name: p22286_s015_L604_Male_20_21_Group_2_D0_Post_ATI_BatchB


description: Library name: p22286_s018_L604_Male_20_21_Group_2_D5_Post_ATI


description: Library name: p22286_s012_DHIX_Male_20_21_Group_1_D6_Post_ATI

value: DHIX


description: Library name: p22286_s015_L604_Male_20_21_Group_2_D0_Post_ATI