title: ID8 sc 3

city: Pune

first: SHARMILA

last: BAPAT

state: Maharashtra

address: Ganeshkhind Road Pune

department: Lab 04 old building

country: India

institute: National Centre for Cell Science, Pune

description: Library name: Sample.SCT3

data_processing:
Quality check for raw data. We will check the data for bad quality reads, bases and adapter sequences. We will also remove any adapter sequences found in the reads, by appropriately trimming / removing the reads. The analysis will provide an illustrated summary of quality of the data generated.
Preprocessing of raw data includes adapter sequence removal andcontamination sequence removal (tRNA, rRNA): We will map the data to the MOUSE genome, identify reads generated from structural RNA molecules (rRNA / tRNA), and filter them. This is the contamination removal step.
Alignment of preprocessed data to MOUSE reference genome(hg19) using HiSAT2: The quality filtered / contamination / adapter removed data will be mapped to the MOUSE genome reference sequence (HG19) using HiSAT. We will provide statistics for data loss at each of the three steps (quality filtering, contamination filtering, and mapping).
Genes expression estimation (raw) using FeatureCounts: FeatureCounts will be used to derive raw read counts mapping to known genes. These read counts will normalized in DESeq2, to assess gene expression levels.
Differential expression analysis was performed using DESeq2
Assembly: mm39
Supplementary files format and content: Delimited text file with read counts of all samples

source_name: primary tumor

growth_protocol: ID8 cells were grown in Dulbecco’s Modified Essential Medium supplemented with 10% FBS.  All cell lines were maintained in a humidified incubator at 37°C under 5% CO2 atmosphere.

extract_protocol:
Trizol extraction
A modified NEBNext RNA Ultra II directional protocol is used to prepare the libraries for total RNA sequencing

treatment_protocol: Primary tumors were developed subcutaneously on right and left flank or orthotopic ID8 cells intra-bursal on right ovary. ID8-ortho further progressed to metastasis. Temporal harvesting of peritoneal tumor ascites was performed 3 times under aseptic conditions (ID8-asc tap1, ID8-asc tap2, ID8-asc tap3) using a syringe and needle.

value: primary tumor tissue

value: tumor tissue on scruff

value: ID8 cells injected to form tumors


title: Npy1R-1

status: Public on Jul 02 2025

type: SRA

city: Boston

first: KLaus

last: Schmitz-Abe

state: MA

address: 300 Longwood Avenue

department: Asthma, Allergy and Immunology

country: USA

institute: Children's Hospital Boston

description: Library name: Samples C1

library_source: transcriptomic

data_processing:
fastq file to bam file to count file Rsubread (Counts.xlsx) Default parameters
Count file to Gene differential expression file edgeR (version 3.28) Default parameters
Count file to Gene differential expression file DESeq2 (version 1.26.0) Default parameters
Count file to Gene differential expression file Lima (version 3.42.2) Default parameters
Join results VExP Pipeline
Assembly: GRCm38/mm10 (UCSC reference) Mus musculus
Supplementary files format and content: vcf files and excel file

molecule: total RNA

organism: Mus musculus

growth_protocol: Treg cell and microglia were cell sorted from CNS were cell sorted using Sony MA900 and Snap Freezed before RNA extraction

extract_protocol:
CNS cell were stain with CD4 CD45, Notch3, Npy1R and CD11b and cell sorted (Sony MA900)
RNA to cDNA was performed using the SMART-Seq v4 Ultra Low Input RNA kit using the manufacturer's protocol

treatment_protocol: 8 weeks old Foxp3YFPCRE and Foxp3YFPCre Notch3Fl/FL mice were immunized with MOG35-55 using Hooke laboratory Kit

tag: tissue

tag: cell line

value: treg Cells

tag: cell type

tag: genotype

value: WT


title: ID8 sc 2

description: Library name: Sample.SCT2

tag: treatment


title: Leaf, well-watered, ambient temp, segment 6, rep 1

city: Winnipeg

first: Olivia

last: Wilkins

state: Manitoba

address: 66 Chancellors Cir

department: Biological Sciences

country: Canada

institute: University of Manitoba

description: Library name: W30.s6.r1

data_processing:
Reads were aligned with HISAT2 (Kim et al., 2019), v2.2.1, paired-end mode
Gene counts were quantified using featureCounts (Liao et al., 2014), v2.0.6, paired-end mode, reverse stranded
Raw gene counts were batch corrected with ComBat-seq (Zhang et al., 2020), correcting for both water status (well-watered vs growth-limiting drought) and temperature (30°C vs 40°C)
For FPKMs, mean fragment size was calculated with Picard, v3.1.0, and FPKM values were then calculated with countToFPKM R package (Alhendi, 2019), v1.0
Assembly: MSU release 7.0 Oryza sativa Nipponbare reference genome (Ouyang et al., 2007; Kawahara et al., 2013)
Supplementary files format and content: 2025.Robertson_Wilkins.RawGeneCounts.csv: csv file containing raw gene counts of all genes for each sample (counted with featureCounts)
Supplementary files format and content: 2025.Robertson_Wilkins.BatchCorrectedGeneCounts.csv: csv file containing batch corrected raw counts of all genes for each sample (adjusted with ComBat-seq R package)
Supplementary files format and content: 2025.Robertson_Wilkins.BatchCorrectedFPKM.csv: csv file containing batch corrected FPKM counts of all genes for each sample (fragment size calculated with Picard, FPKMs calculated with countToFPKM R package (Alhendi, 2019))

molecule: polyA RNA

organism: Oryza sativa

source_name: Mature 3rd leaf

growth_protocol: Pregerminated rice seeds were planted into potting mix with gravimetric soil water contents (SWC; g water / g dry soil) of 3 g/g (well-watered) or 1.5 g/g (growth-limiting drought). The seedlings were grown in a Conviron growth chamber with a 12-hour daylength with 500 µmol light intensity, 30°C/25°C day/night temperature, and 80% humidity. Pots were weighed and rewatered daily to maintain SWCs until the third leaves of the rice seedlings were fully elongated (10 days for 3 g/g, 12 days for 1.5 g/g). Prior to collection, half of the pots were heat shocked at 40°C for 30 minutes, resulting in 4 total conditions: well-watered, drought, heat shock, and drought + heat shock. Third, fully elongated leaves from each condition were collected at midday (6 ZT). Leaf blades were removed by a razorblade at the sheath collar and dissected into seven equal-length segments.. We kept the center 5 segments (segments 2-6) and discarded the tip-most and base-most segments (segments 1 and 7). We collected 4 replicates per condition, each containing matched segments from 3 leaves.

extract_protocol:
Leaf segments from the above conditions were flash frozen in liquid nitrogen and stored at -80°C. Tissue was ground to a powder in a bead mill (30s, 6m/s), and total RNA was extracted with a Qiagen RNeasy Plant Mini Kit.
Total RNA was sent to Génome Québec (Montreal, Quebec) for library construction and sequencing, using Nextera XT library preparation and sequencing of 100bp paired-end reads on a NovaSeq 6000.

value: Mature 3rd leaf

tag: soil water_content_(g_water_/_g_soil)

value: 3 g/g

tag: temperature at_collection_(°c)

tag: leaf segment_(base_=_s2)

tag: replicate

tag: batch


title: C57BL6 INTESTINE

description: Library name: Sample.SM10

source_name: WT

value: Intestine

value: healthy tissue


title: back subcutaneous adipose tissue, buffalo-2 [miRNA-seq]

city: Nanning

first: Huang

last: JiePing

address: Xixiangtang District

country: China

institute: Guangxi University

description:
Library name: 1745-beizhiB
Column name in miRNA_count_all_samples.txt:beizhiB_1745

data_processing:
Raw data were filtered with Fastp (v0.20.1) to remove reads with low quality or adapter.
After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Botie2
In the annotation information of different RNAs, to ensure that each small RNA was mapped to a unique category, we set the following rules: MiRbase(v22) > pirnabank(v1.0) > snoRNA(v1.2 human/plant ) > Rfam (v12.1)> other sRNA.
The small RNA expression level is calculated by counting absolute numbers of molecules using unique molecular identifiers. The expression formula is:C is the number of UMIs of reads that were mapped to the small RNA, T is the UMI number of total clean reads of the sample.
DESeq2 version 1.24.0 was used to normalize gene readcounts and compute differential expression
Assembly: MiRbase v22（BAT）Due to the lack of a curated buffalo miRNA database, miRNA annotation was inferred from Bos taurus (cattle) entries in miRBase release 22.
Supplementary files format and content: Matrix table with normalized gene counts for every miRNA and every sample

organism: Bubalus bubalis

source_name: adipose tissue

growth_protocol: Buffaloes were weaned at 3 months of age, started to fatten at 15 months of age, and slaughtered at 20 months of age.

extract_protocol:
Total RNA was isolated using RNeasy Lipid Tissue Mini Kit (QIAGEN, GER) according to the manual instruction.
Approximately 2 μg of total RNA per sample was used for library construction according to the protocol of the TruSeq® RNA LT Sample Prep Kit v2 (Illumina, USA).

value: adipose tissue

tag: tissue type

value: back subcutaneous adipose tissue


title: Leaf, well-watered, ambient temp, segment 5, rep 1

description: Library name: W30.s5.r1


title: C57BL6 OVARY

description: Library name: Sample.SM9

value: ovary tissue


title: ID8 Met Int 3

description: Library name: Sample.SM8

source_name: metastatic tumor

value: Metastatic solid tumor on intestine

value: tumor tissue on Intestine

value: primary tumor metastasize to intestine


title: AHHO, day 05, scRNAseq

city: Seattle

first: Kelly

last: Stevens

state: WA

address: 850 Republican St

department: Bioengineering

institute: University of Washington

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

organism: Homo sapiens

source_name: Liver

growth_protocol: Adult human hepatocytes suspended in matrigel hanging drops in organoid media. Media changed every 2-3 days

extract_protocol:
Organoids in matrigel were collected from wells, pooled, and spun down at 1500 RPM. Supernatant and top layer of matrigel were aspirated. Remaining matrigel and organoid pellet were suspended in TrypLE (Thermo) and incubated for ~30 minutes at 37C with frequent agitation until digested to single cells. Single cells were pelleted and resuspended in media + 1% BSA to prevent clumping. Cells in suspension were then filtered through a Flowmi cell strainer (Millipore) and kept on ice until 10x processing.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

value: Hepatocytes

value: Liver

tag: age

value: 19 years old


title: AHHO, day 15, scRNAseq

description: 10x Genomics


title: Leaf, well-watered, ambient temp, segment 4, rep 1

description: Library name: W30.s4.r1


title: ID8 Met Int 1

description: Library name: Sample.S12


title: ID8 Met Int 2

description: Library name: Sample.SM7


title: Leaf, well-watered, ambient temp, segment 3, rep 1

description: Library name: W30.s3.r1


title: ID8 asc T2.3

description: Library name: Sample.SM2

value: Metastatic peritoneal fluid

value: Liquid tumor with cells

value: ID8 cells metastasize to form ascites harvested second


title: ID8 asc T2.1

description: Library name: Sample.SM4


title: Npy1R-2

description: Library name: Samples C2

value: treg Cells

value: WT


title: Leaf, well-watered, ambient temp, segment 2, rep 1

description: Library name: W30.s2.r1

value: Mature 3rd leaf

value: 3 g/g


title: ID8 asc T1.3

description: Library name: Sample.SM1

value: ID8 cells metastasize to form ascites harvested first


title: scRNA_seq-A8Rev_DHA1_6h-2

city: Shanghai

first: Jincan

last: He

address: siping road 1239

institute: Tongji university

description:
Library name: A8Rev_DHA1_6h-2
10X Genommics

data_processing:
Raw sequencing reads were assessed using quality metrics and analyzed using the Cell Ranger software. The “count” command was utilized to create a filtered count matrix with the default parameters.
Cells with low quality, characterized by unique detected genes less than 50, unique detected genes exceeding 400, or mitochondrial content surpassing 0.1%, were filtered out. For the remaining cells, additional outliers were removed. Cells that exhibited a median absolute deviation from the median for the total number of UMIs or unique detected genes twice the median were excluded. the R package DoubletFinder was employed to remove potential duplicates.
After filtering, the data were processed using the standard workflow implemented in Monocle3 package
Assembly: Pf 3D7 v68
Supplementary files format and content: Tab-separated values files and matrix files

organism: Plasmodium falciparum

growth_protocol: P. falciparum parasites were cultured under conditions of 5% O2, 5% CO2, and 37◦C, as previously described (Ghorbal et al., 2014). Synchronization of parasites in the ring stage was achieved using a 5% sorbitol solution, while purification of schizont-stage parasites was carried out through a 40/70% Percoll discontinuous gradient.

extract_protocol:
Highly synchronized parasites were subjected to Hoechst 33342 staining for 10 minutes at 37℃, followed by sorting of positive stained cells into 0.05% BSA/PBS solution using a FACSAria II sorter (BD Biosciences). The sorted cells underwent two washes with 0.05% BSA/PBS， were re-suspended in 100 μL 0.05% BSA/PBS, and counted using a cell counting chamber.
libraries were prepared using the Chromium Single Cell 3ʹReagent Kits v3 (10x genomics) following the instructions provided in the user guide.

value: wild type

tag: development stage

value: Ring

tag: time

tag: host

value: Homo sapiens


title: ID8 asc T1.1

description: Library name: Sample.S9


title: Culture medium myocytes_G93A/G93A_3

type: RNA

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: Primary culture of myocytes derived from the leg of mouse pup.

hyb_protocol: Labeled RNA was hybridized onto microarray slides using a rotational oven at 55°C for 22 h. At least three biological replicates were used for each condition (excluding the WTWT co-culture that was screened with two biological replicates). After hybridization, miRNA microarray slides were washed using the Wash Buffer Kit (Agilent Technologies) and dried at room temperature.

scan_protocol: Microarray slides were scanned using a G2505C scanner (Agilent Technologies) at 3 μm resolution. Probes features were extracted using the Feature Extraction Software v. 10.7.3.1 with GE 1 Sep09 protocol (Agilent Technologies).

data_processing: Raw microarray data were first filtered for the number of miRNAs presenting an expression value above the background (0% of undetected values per sample type were allowed for each miRNA) and then normalized according to the loess cyclic algorithm.

source_name: Culture medium of co-culture of primary myocytes. Co-culture was performed with hSOD1(G93A) primary myocytes.

label_protocol: 150 ng of miRNAs (according to the concentration established by the 2100 Agilent bioanalyzer runs) were labeled using miRNA Complete Labeling and Hyb Kit (Agilent Technologies), according to the manufacturer’s protocol.

growth_protocol: Primary myoblasts from newborn (1-3 days) hSOD1(WT) or hSOD1(G93A) mice were prepared as previously described 81. Briefly, the posterior limb muscles were removed, and cells isolated by three successive treatments with 0.1% trypsin in phosphate-buffered saline (PBS; 140 mM NaCl, 2 mM KCl, 1.5 mM KH2PO4, 8 mM Na2HPO4, pH 7.4) for 30 min at 37 °C, seeded at a density of 2.5 × 105 cells onto 13 mm-coverslips coated with collagen (0.1% w/v in PBS) for immunocytochemistry, or at a density of 1 × 106 cells onto 35 mm-collagen-coated plates for biochemical assays, and cultured in proliferation medium (Ham's F12 with 10% foetal bovine serum, 2 mM glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin) for 2 days (2 Days In Vitro: 2 DIV). At this time point, proliferation medium was replaced by differentiation medium (Dulbecco’s Modified Eagle Medium containing 2% horse serum, 2 mM glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin) for myoblast differentiation into myotubes. All reagents for cell culture were from Euroclone. Co-culturing experiments were carried out in 24 well-transwell plates (tw) (Sarstedt) using four different cell combinations: i) hSOD1(WT) myocytes cultured on the bottom chamber (“target cells”) and on the insert (“donor cells”) (WTWT); ii) hSOD1(G93A) and hSOD1(WT) myocytes cultured on the bottom chamber and the insert, respectively (G93AWT); iii) hSOD1(G93A) myocytes cultured on the bottom chamber and on the insert (G93AG93A); iv) hSOD1(WT) and hSOD1(G93A) myocytes cultured on the bottom chamber and on the insert respectively (WTG93A). Myoblasts were seeded in both the collagen-treated upper insert (0.4 μm pore size) and the lower collagen-treated chamber, at concentrations of 1.5 and 2.5 × 105 cells, respectively, and cultured under the same conditions as described above. The supernatant of well-tw chambers from the combinations i, ii, and iii of co-cultured cells was collected at 2 DIV, centrifuged at 16,000 × g (4° C, 5 min) to remove cell debris, and stored at -80°C for miRNA analyses.

extract_protocol: Secreted miRNAs in the MCM were extracted using the TRIzol LS solution (ThermoFisher Scientific) following the manufacturer’s protocol. Briefly, 600 µl of TRIzol LS (ThermoFischer Scientific) were added to 200 µl of culture medium; after 5 min of incubation at RT 160 µl of chloroform were added. After mixing the solution was incubated on ice for 15 min and then centrifugated at 12,000 x g at 4°C for 20 min. Aqueous phase was transferred in a new tube and precipitated at -20 °C overnight adding an isovolume of isopropanol. The RNA was washed two times with 80% of ethanol and resuspended in 10 µl of DNAse/RNAse free water (ThermoFisher Scientific). For each condition, we extracted miRNAs three times from 200 µl of medium totally using about 600 µl of medium. RNA extracted from the same sample was pooled and the concentration of miRNAs was inferred according to the run in the 2100 Agilent bioanalyzer using the smallRNA chip (Agilent Technologies) and integrating the area under desired nucleotide dimension (18-26 nt).

treatment_protocol: No treatment performed.

tag: tag

value: Male

value: Primary myocytes


title: ID8 asc T1.2

description: Library name: Sample.SM3


title: Culture medium myocytes_G93A/G93A_2


title: ID8 ortho3

description: Library name: Sample.SM6

value: primary tumor tissue

value: tumor tissue on ovary

value: ID8 cells injected to form tumors


title: ID8 ortho2

description: Library name: Sample.SM5


title: Culture medium myocytes_G93A/WT_3

source_name: Culture medium of co-culture of primary myocytes. Co-culture was performed with hSOD1(WT) and hSOD1(G93A) primary myocytes.


title: scRNA_seq-A8Rev_DHA1_6h-1

description:
Library name: A8Rev_DHA1_6h-1
10X Genommics


title: Culture medium myocytes_G93A/G93A_1


title: ID8 ortho1

description: Library name: Sample.S8


title: scRNA_seq-A8Rev_DHA0_6h-2

description:
Library name: A8Rev_DHA0_6h-2
10X Genommics


title: Culture medium myocytes_G93A/WT_2


title: ID8 cell line

description: Library name: Sample.S1

value: Epithelial cell line

value: Mouse Ovarian Surface


title: scRNA_seq-A8Rev_DHA0_6h-1

description:
Library name: A8Rev_DHA0_6h-1
10X Genommics


title: WT3

data_processing:
fastq file to bam file to count file Rsubread (Counts.xlsx) Default parameters
Count file to Gene differential expression file edgeR (version 3.28)  Default parameters
Count file to Gene differential expression file DESeq2 (version 1.26.0)  Default parameters
Count file to Gene differential expression file Lima (version 3.42.2)  Default parameters
Join results VExP Pipeline
Assembly: GRCm38/mm10 (UCSC reference) Mus musculus
Supplementary files format and content: vcf files and excel file

source_name: brain

extract_protocol:
CNS cell were stain with CD4 CD45 and CD11b and cell sorted (Sony MA900)
RNA to cDNA was performed using the SMART-Seq v4 Ultra Low Input RNA kit using the manufacturer's protocol

value: brain

value: Microglia Cells


title: WT4


title: scRNA_seq-A8_DHA1_6h-1

description:
Library name: A8_DHA1_6h-1
10X Genommics


title: Culture medium myocytes_WT/WT_2

source_name: Culture medium of co-culture of primary myocytes. Co-culture was performed with hSOD1(WT) primary myocytes.


title: ID8 asc T2.2

description: Library name: Sample.S10

value: Metastatic peritoneal fluid

value: Liquid tumor with cells

value: ID8 cells metastasize to form ascites harvested second


title: scRNA_seq-A8_DHA0_6h-1

description:
Library name: A8_DHA0_6h-1
10X Genommics


title: WT1

value: WT


title: WT2


title: Culture medium myocytes_G93A/WT_1


title: N4

value: Het


title: N3


title: N2


title: 134_post

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

description: Library name: 134_post

data_processing:
Trimming reads using fastp 0.23.4
alignment to mirbase 22.1 reference data using bowtie 1.3.0
Batch correction using ComBat-seq
Normalization and differential expression analysis using DESeq2 v1.40.2
Assembly: mirbase 22.1 human and hg38
Supplementary files format and content: Raw count data for mature miRNAs (not batch corrected)
Supplementary files format and content: Raw count data for hairpin miRNAs (not batch corrected)

source_name: PBMC

extract_protocol:
Blood samples were collected into EDTA tubes to prevent coagulation and processed within three hours to isolate peripheral blood mononuclear cells (PBMCs) using Ficoll-Paque (Cytiva) in accordance with the manufacturer’s guidelines. The PBMCs were stored in Trizol Reagent (Invitrogen) at -80°C until all samples were collected. RNA was extracted from the PBMCs following the manufacturer’s instructions, and eluted in DEPC-treated water.
RNA libraries for RNA-seq were prepared using the SMARTer smRNA-Seq Kit for Illumina (Takara) according to the manufacturer’s protocol.

value: PBMC

tag: trial

value: A

tag: participant

tag: sport

value: Cyclist

tag: bmi

tag: Sex

value: Female

tag: timing

value: post


title: WGS-A8REV_F6

description: Library name: A8REV_F6

library_source: genomic

data_processing:
Raw sequencing reads were quality-controlled using TrimGalore (v0.6.4) to remove adapter sequences and low-quality reads with default parameters. The high-quality reads were then aligned to the reference Plasmodium falciparum 3D7 genome (PlasmoDB v68) using the Burrows-Wheeler Aligner (BWA-mem v0.7.17) with default settings. The resulting alignments in SAM format were converted to position-sorted BAM files using SAMtools (v1.9).
Variant calling was performed using bcftools mpileup followed by bcftools call to generate raw BCF files. These variants were subsequently filtered using bcftools view with stringent quality thresholds (read depth between 100-300 and QUAL score >25).  Functional annotation of the identified variants was performed using ANNOVAR to determine their potential impact on protein-coding genes.
Assembly: Pf 3D7 v45
Supplementary files format and content: vcf files contain mutation information for different samples

molecule: genomic DNA

growth_protocol: Parasites were cultured in medium containing 0.5% Albumax II with O type fresh red blood cells, and a gas phase with 5% O2, 5 % CO2 at 37 °C.

extract_protocol:
Genomic DNA was extracted according to the DNeasy  Blood and Tissue Kit (QIAGEN) manufacturer's requirements.
Genomic DNA samples were randomly broken into fragments of 350 bp length by Covaris ultrasonic disruptor. TruSeq Library Construction Kit was used for library construction. The entire library preparation was completed by end repair, addition of ployA tails, addition of adaptors, purification, and PCR amplification. The libraries were sequenced by illumina.

treatment_protocol: The medium was changed every other day until parasitaemia rose to 5%.

tag: cell line

tag: genotype

value: wild type


title: N1

tag: tissue

tag: cell type


title: 148_post

description: Library name: 148_post

value: Untrained

tag: batch


title: WT-5

value: treg Cells


title: 250_pre

description: Library name: 250_pre

value: B

value: Male

value: pre


title: WT-3


title: WT-4


title: 249_post

description: Library name: 249_post


title: WGS-A8REV_A2

description: Library name: A8REV_A2


title: WT-2


title: WT-1


title: WGS-A8_E7

description: Library name: A8_E7


title: N-5


title: WGS-A8_C8

description: Library name: A8_C8


title: N-3


title: 156_post

description: Library name: 156_post


title: 257_post

description: Library name: 257_post


title: WGS-A8_B3

description: Library name: A8_B3


title: 258_pre

description: Library name: 258_pre


title: 145_post

description: Library name: 145_post


title: Culture medium myocytes_WT/WT_1

value: Primary myocytes


title: 156_pre

description: Library name: 156_pre


title: WGS-A5REV_A4

description: Library name: A5REV_A4


title: WGS-A5REV_2

description: Library name: A5REV_2


title: WGS-A8REV_B6

description: Library name: A8REV_B6


title: WGS-A5REV_A1

description: Library name: A5REV_A1


title: 159_post

description: Library name: 159_post


title: wildtype control 14

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

description: Library name: Sample_25

data_processing:
Data was analysed using in-house built pipeline
Raw reads were processed and demultiplexed using bcl2fastq (v2.20.2).
Quality control of raw sequencing data was done using FastQC (v0.11.5).
Reads were aligned to the mouse (mm10) genome with the STAR aligner (v2.5.2b)
feature Counts (v1.5.1) was used to generate read counts
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Hippocampus, CA1 Region

extract_protocol:
RNA was isolated using the RNA Clean and Concentrator Kit from Zymo following its instrucitons. 300 ng of RNA was used for library preparation.
RNA libraries were prepared using Illumina TruSeq following manufacturer's protocol

value: Hippocampus, CA1 Region

value: 6 months


title: N-4


title: 151_pre

description: Library name: 151_pre


title: wildtype control 15

description: Library name: Sample_26


title: WGS-A5_E3

description: Library name: A5_E3


title: wildtype control 12

description: Library name: Sample_23


title: 150_pre

description: Library name: 150_pre


title: N-2


title: N-1


title: wildtype control 11

description: Library name: Sample_22


title: WGS-A5_A3

description: Library name: A5_A3


title: wildtype control 10

description: Library name: Sample_21


title: ratBMMSCs_GK_rep3

city: Xi’an

first: Dian

last: Gan

state: Shaanxi

address: No. 145, Changle West Road

institute: School of Stomatology, The Fourth Military Medical University

description: Gene expression after 7-day osteogenic induciton in BMMSCs

hyb_protocol: Kit and Instruments: Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242): 10X Blocking Agent; 25X Fragmentation Buffer; 2x GEx Hybridization Buffer HI-RPM; Hybridization Chamber, stainless (Agilent p/n G2534A); Hybridization Chamber gasket slides (Agilent p/n G2534-60003); Hybridization oven (Agilent p/n G2545A); Hybridization oven rotator for Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029). Procedure: 1. Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing. 2. Equilibrate water bath to 60°C. 3. For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube: 1.65ug cyanine 3-labeled, linearly amplified cRNA; 11ul 10X Blocking Agent; ×ul Nuclease-free water; 2.2ul 25X Fragmentation Buffer ; 55ul total volume. 4. Mix well but gently on a vortex mixer. 5. Incubate at 60°C for exactly 30 minutes to fragment RNA.  6. Add 55ul 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction. 7. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles. 8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction. 9. Place sample on ice and load onto the array as soon as possible.  10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar. 11. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner (100ul).12. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.  13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces. 14. Hand-tighten the clamp onto the chamber. 15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. 16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm. 17. Hybridize at 65°C for 17 hours.

scan_protocol: Instrument: Agilent Microarray Scanner (Agilent p/n G2565BA); Procedure: 1.Assemble the slides into an slide holder. 2.Place assembled slide holders into scanner carousel. 3.Verify scan settings for one-color scans.Scan region: Scan Area (61 x 21.6 mm); Scan resolution: 5 μm; 5μm scanning mode: Single Pass; eXtended Dynamic range: (selected); Dye channel: Green; Green PMT:XDR Hi 100%, XDR Lo 10%.4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Extract data using Agilent Feature Extraction Software. Procedure:1. Open the Agilent Feature Extraction (FE) software.2. Add the images (.tif) to be extracted to the FE Project.3. Set FE Project Properties.4. Check the Extraction Set Configuration.5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location. 6. Select Project > Start Extracting and export data to txt.

organism: Rattus norvegicus

source_name: BMMSCs, GK rats , replicate 3

label_protocol: Kit and instrument: RNeasy Mini Kit (Qiagen p/n 74104); NanoDrop ND-1000. Procedure: 1. Add 20 μL of nuclease-free water to your cRNA sample, for a total volume of 100 μL. 2. Add 350 μL of Buffer RLT and mix well by pipetting. 3. Add 250 μL of ethanol (100% purity) and mix thoroughly by pipetting. Do not centrifuge. 4. Transfer the 700 μL of the cRNA sample to an RNeasy mini column in a 2 mL collection tube. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through and collection tube. 5. Transfer the RNeasy column to a new collection tube and add 500 μL of buffer RPE (containing ethanol) to the column. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through. Re-use the collection tube. 6. Add another 500 μL of buffer RPE to the column. Centrifuge the sample at 4°C for 60 seconds at 13,000 rpm. Discard the flow-through and the collection tube. 7. Elute the cleaned cRNA sample by transferring the RNeasy column to a new 1.5 mL collection tube. Add appropriate RNase-free water (Passed-please see report ”Labeling Efficiency-QC”) directly onto the RNeasy filter membrane. Wait 60 seconds, then centrifuge at 4°C for 30 seconds at 13,000 rpm. 8. Maintain the cRNA sample-containing flow-through on ice. Discard the RNeasy column. 9. Take 1.5 μl of each sample to determine the yield and specific activity by using the NanoDrop

extract_protocol: 1. Homogenization: Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. The amount of TRIzol Reagent added is based on the area of the culture dish (1 ml per 10 cm2) and not on the number of cells present. 2. Phase Separation: Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization. 3. RNA Precipitation: Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C.  4. RNA Wash: Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C. 5. Redissolving the RNA: At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passi

treatment_protocol: BMMSCs were isolated and purified from femurs of the normal and T2DM rats, and then cultured in osteogenic induction medium for 7 days. BMMSCs from normal rats were used as  the control group.

value: BMMSCs


title: ratBMMSCs_GK_rep2

source_name: BMMSCs, GK rats , replicate 2


title: wildtype control 9

description: Library name: Sample_20

value: WT


title: ratBMMSCs_GK_rep1

source_name: BMMSCs, GK rats , replicate 1


title: ratBMMSCs_Wistar_rep1

source_name: BMMSCs, Wistar rats , replicate 1


title: 153_pre

description: Library name: 153_pre


title: scRNA_seq-Y493H_DHA1_6h

description: 10X Genommics

data_processing:
Raw sequencing reads were assessed using quality metrics and analyzed using the Cell Ranger software (v3.1.0). The “count” command was utilized to create a filtered count matrix with the default parameters.
Cells with low quality, characterized by unique detected genes less than 50, unique detected genes exceeding 400, or mitochondrial content surpassing 0.1%, were filtered out. For the remaining cells, additional outliers were removed. Cells that exhibited a median absolute deviation from the median for the total number of UMIs or unique detected genes twice the median were excluded. the R package DoubletFinder (version 2.0.2) was employed to remove potential duplicates.
After filtering, the data were processed using the standard workflow implemented in Monocle3 (v0.2.2) package
Assembly: Pf 3D7 v45
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pf 3D7

tag: treatment

value: DHA

value: Ring

tag: strain

value: Pf 3D7

value: Homo sapiens


title: ratBMMSCs_Wistar_rep2

source_name: BMMSCs, Wistar rats , replicate 2


title: wildtype control 8

description: Library name: Sample_19

tag: age


title: ratBMMSCs_Wistar_rep3

source_name: BMMSCs, Wistar rats , replicate 3


title: 246_post

description: Library name: 246_post

value: PBMC

value: Female


title: wildtype control 7

description: Library name: Sample_18


title: scRNA_seq-WT_G1_DHA1_6h

description: 10X Genommics

value: wild type

value: GlcN and DHA

tag: development stage

tag: time


title: WGS-A5_B3

description: Library name: A5_B3


title: wildtype control 5

description: Library name: Sample_16


title: 259_post

description: Library name: 259_post

value: Cyclist

value: post


title: wildtype control 13

description: Library name: Sample_24


title: wildtype control 6

description: Library name: Sample_17


title: wildtype control 3

description: Library name: Sample_14


title: scRNA_seq-WT_G0_DHA1_6h

description: 10X Genommics

tag: host


title: 247_post

description: Library name: 247_post

tag: trial

value: B

value: Untrained


title: scRNA_seq-Myst_G1_DHA1_6h

description: 10X Genommics


title: scRNA_seq-Myst_G1_DHA1_9h

description: 10X Genommics


title: wildtype control 1

description: Library name: Sample_12


title: wildtype control 4

description: Library name: Sample_15


title: CaMKIIδC transgenic 11

description: Library name: Sample_11

value: TG


title: wildtype control 2

description: Library name: Sample_13

value: Hippocampus, CA1 Region


title: CaMKIIδC transgenic 10

description: Library name: Sample_10

value: 6 months


title: 136_post

description: Library name: 136_post

value: A

tag: participant


title: CaMKIIδC transgenic 9

description: Library name: Sample_9


title: scRNA_seq-Myst_G1_DHA0_6h

description: 10X Genommics

value: GlcN


title: 157_pre

description: Library name: 157_pre

tag: sport

value: Male

value: pre


title: CaMKIIδC transgenic 7

description: Library name: Sample_7


title: CaMKIIδC transgenic 8

description: Library name: Sample_8


title: scRNA_seq-Myst_G1_DHA0_9h

description: 10X Genommics

value: Ring

value: Pf 3D7


title: 251_pre

description: Library name: 251_pre

value: PBMC

tag: bmi


title: CaMKIIδC transgenic 6

description: Library name: Sample_6


title: scRNA_seq-Myst_G1_DHA0_0h

description: 10X Genommics

value: Homo sapiens


title: 135_post

description: Library name: 135_post

tag: Sex

value: Female


title: scRNA_seq-Myst_G0_DHA1_9h

description: 10X Genommics

value: DHA


title: 256_post

description: Library name: 256_post

tag: timing


title: 254_post

description: Library name: 254_post


title: CaMKIIδC transgenic 5

description: Library name: Sample_5


title: CaMKIIδC transgenic 4

description: Library name: Sample_4


title: CaMKIIδC transgenic 3

description: Library name: Sample_3


title: scRNA_seq-Myst_G0_DHA1_6h

description: 10X Genommics


title: CaMKIIδC transgenic 2

description: Library name: Sample_2


title: 247_pre

description: Library name: 247_pre


title: CaMKIIδC transgenic 1

description: Library name: Sample_1


title: 3 months, wildtype control 5

description: Library name: Sample_40

data_processing:
Data was analysed using in-house built pipeline
Raw reads were processed and demultiplexed using bcl2fastq (v2.20.2).
Quality control of raw sequencing data was done using FastQC (v0.11.5).
Quality control of raw sequencing data was done using mirtrace (v.1.0.1).
Read adapters were removed with cutadapt (v.2.8)
Assembly: Reads aligned and quantified using miRDeep (v.2.0.1.2)
Supplementary files format and content: Tab- and comma-delimited text files include raw and normalised counts for each sample

extract_protocol:
RNA was isolated using the RNA Clean and Concentrator Kit from Zymo following its instrucitons. 300 ng of RNA was used for library preparation.
RNA libraries were prepared using NEBNext Small RNA library Prep set from Illumina following manufacturer's protocol

value: WT

value: 3 months


title: scRNA_seq-Myst_G0_DHA0_9h

description: 10X Genommics


title: 3 months, wildtype control 4

description: Library name: Sample_39


title: scRNA_seq-Myst_G0_DHA0_6h

description: 10X Genommics


title: 159_pre

description: Library name: 159_pre

value: Cyclist


title: 3 months, wildtype control 2

description: Library name: Sample_37


title: 3 months, wildtype control 3

description: Library name: Sample_38


title: scRNA_seq-G538V_DHA1_6h

description: 10X Genommics


title: 3 months, CaMKIIδC transgenic 8

description: Library name: Sample_34


title: 150_post

description: Library name: 150_post

value: Untrained

value: post


title: scRNA_seq-Myst_G0_DHA0_0h

description: 10X Genommics


title: 3 months, wildtype control 1

description: Library name: Sample_36

value: Hippocampus, CA1 Region

value: TG


title: 3 months, CaMKIIδC transgenic 9

description: Library name: Sample_35


title: 253_pre

description: Library name: 253_pre

value: B


title: 3 months, CaMKIIδC transgenic 7

description: Library name: Sample_33


title: 3 months, CaMKIIδC transgenic 6

description: Library name: Sample_32


title: scRNA_seq-G538V_DHA0_6h

description: 10X Genommics


title: 3 months, CaMKIIδC transgenic 5

description: Library name: Sample_31


title: scRNA_seq-G538V_DHA0_0h

description: 10X Genommics


title: 139_post

description: Library name: 139_post

value: A

value: Runner


title: 3 months, CaMKIIδC transgenic 2

description: Library name: Sample_28


title: 160_post

description: Library name: 160_post

value: Male


title: scRNA_seq-C580Y_DHA1_6h

description: 10X Genommics

value: Ring


title: 135_pre

description: Library name: 135_pre

value: pre


title: 3 months, CaMKIIδC transgenic 1

description: Library name: Sample_27


title: 6 months, wildtype control 15

description: Library name: Sample_26

value: 6 months


title: 6 months, wildtype control 13

description: Library name: Sample_24


title: ChIP_Seq-WT_MYST-R-2

data_processing:
Initially, all the ChIP-seq reads underwent processing using TrimGalore (v0.6.4) to trim adaptor sequencers and eliminate low-quality reads.
Subsequently, the adaptor-trimmed reads were mapped to the P.falciparum 3D7 genome (PlasmoDB v45) using Bowtie2 (v2.3.5.1) with the following parameters: -t -N 0 -q --no-mixed --no-discordant.
The mapping results in SAM format were then converted to position-sorted BAM format using Samtools (v1.9). To further refine the dataset, unmapped reads and those with mapping quality scores below 20 were removed using sambamba (v0.7.0).
Additionally, multiple mapped reads and PCR duplicates were eliminated utilizing a javascript tool (MarkDuplicates.jar) from Picard (v2.20.7).
Subsequently, the BAM files were converted into bigwig files using bamCoverage from the deeptools suite (v3.3.0) with parameters: --normalizeUsing RPKM.
Assembly: Pf 3D7 v45
Supplementary files format and content: bigWig

growth_protocol: P. falciparum parasites were cultured under conditions of 5% O2, 5% CO2, and 37◦C.

extract_protocol:
To initiate cross-linking, 1% paraformaldehyde was immediately mixed with parasites and gently rotated for 10 min at 37 ℃. The cross-link reaction was quenched with 0.125 M glycine for 5 min on ice. RBCs were lysised with 0.15% saponin for 10- 15 min on ice and then subjected to three washes. Next, the parasites were incubated with 2 ml of Lysis Buffer (10 mM HEPES pH 7.9, 10 mM KCl, 0.1 mM EDTA pH8.0, 0.1mM EGTA pH8.0, 1mM DTT, 0.25% NP40, 1X protease inhibitors cocktail) for 30 min on ice, followed by dounce homogenization for 100 strokes. Following centrifugation, the precipitated nuclei were resuspended in 200 μl of SDS Lysis Buffer (containing 1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH8.0). The chromatin was sonicated using the Covaris M220 Sonicator with the following setting: 5% duty factor, 200 cycles per burst, and 75 W of peak incident power for 20 min to yield chromatin fragments at 200–500 bp in size. The chromatin fragments were diluted tenfold in a dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH8.0, 150 mM NaCl, 1X protease inhibitors cocktail) and co-incubated with Protein A/G magnetic beads (Pierce) for two hours. The supernatant was then co-incubated with Protein A/G magnetic beads and the corresponding antibody at 4 ℃ overnight. The antibodies used included 1 μg rabbit anti-GFP (Abcam, ab290), 1 μg rabbit IgG (Abcam), 3 μg anti-H3K9ac (Millipore, 07-352), anti-H3K9me3(Abcam, ab8898), and anti-H4K8ac(Abcam). The beads were subjected to several washes: once at 4℃ for 5 min with Low Salt Immune Complex Wash Buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), High Salt Immune Complex Wash Buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl) and LiCl Immune Complex Wash Buffer (0.25 M LiCl, 1% NP-40, 1% Deoxycholate, 1mM EDTA, 10 mM Tris-HCl pH 8.0), followed by two washes at room temperature for 5 min each with TE Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0). The target protein-DNA complexes were eluted with 200 μL fresh Elution Buffer (1% SDS, 0.1 M NaHCO3). These complexes were then incubated at 45°C overnight, followed by incubation at 37°C for 30 min with RNase A and at 45°C for two hours with Proteinase K. ChIP-DNA was extracted using MinElute PCR purification kit (Qiagen, 28006).
ChIP-DNA was end-repaired  (Epicentre No.ER81050), followed by the addition of 3’ A base (NEB No.M0212L). Subsequently, adapter ligation was performed (NEB No.M2200L), and the libraries were size-selected and amplified using KAPA Biosystems KB2500. The amplification was carried out with a PCR program: including 1 min at 98 ℃, 12 cycles of 10 s at 98 ℃, and 1 min at 65 ℃, followed by a final extension of 5 min at 65 ℃.

treatment_protocol: Parasites were synchronized and harvested at different stages.

tag: developmental stage

value: R

value: Pf 3D7

value: Homo sapiens

tag: chip antibody

value: GFP


title: ChIP_Seq-WT_MYST-R-1

tag: genotype


title: 250_post

description: Library name: 250_post

tag: tissue

value: PBMC


title: 149_post

description: Library name: 149_post

tag: batch


title: 6 months, wildtype control 11

description: Library name: Sample_22

value: WT


title: 6 months, wildtype control 12

description: Library name: Sample_23


title: 6 months, wildtype control 10

description: Library name: Sample_21


title: ChIP_Seq-WT_input-R-1

tag: treatment


title: 6 months, wildtype control 9

description: Library name: Sample_20


title: 6 months, wildtype control 7

description: Library name: Sample_18


title: 6 months, wildtype control 8

description: Library name: Sample_19


title: 3 months, CaMKIIδC transgenic 4

description: Library name: Sample_30

value: 3 months


title: ChIP_Seq-MYSTon_input-S-1

value: S

tag: strain


title: 148_pre

description: Library name: 148_pre

value: Untrained

value: Female


title: ChIP_Seq-MYSTon_input-R-1


title: 6 months, wildtype control 6

description: Library name: Sample_17

value: Hippocampus, CA1 Region

tag: age


title: 6 months, wildtype control 4

description: Library name: Sample_15


title: 6 months, wildtype control 5

description: Library name: Sample_16


title: 254_pre

description: Library name: 254_pre

value: B


title: 3 months, CaMKIIδC transgenic 3

description: Library name: Sample_29

value: TG


title: 154_post

description: Library name: 154_post

value: A

value: Male

value: post


title: 6 months, wildtype control 2

description: Library name: Sample_13

value: 6 months


title: 6 months, wildtype control 3

description: Library name: Sample_14


title: 251_post

description: Library name: 251_post


title: 6 months, wildtype control 1

description: Library name: Sample_12


title: 6 months, wildtype control 14

description: Library name: Sample_25


title: ChIP_Seq-MYSTon_H4K8ac-S-2


title: 6 months, CaMKIIδC transgenic 10

description: Library name: Sample_10


title: ChIP_Seq-MYSTon_H4K8ac-S-1


title: ChIP_Seq-MYSTon_H4K8ac-R-1

value: R


title: 6 months, CaMKIIδC transgenic 8

description: Library name: Sample_8


title: 147_pre

description: Library name: 147_pre

value: pre


title: 158_post

description: Library name: 158_post

value: Cyclist


title: 252_post

description: Library name: 252_post


title: ChIP_Seq-MYSTon_H4K8ac-R-2

value: Pf 3D7

value: Homo sapiens


title: ChIP_Seq-MYSTon_H4K5ac-S-2


title: 6 months, CaMKIIδC transgenic 9

description: Library name: Sample_9


title: 6 months, CaMKIIδC transgenic 11

description: Library name: Sample_11


title: 246_pre

description: Library name: 246_pre

value: PBMC


title: 258_post

description: Library name: 258_post


title: 89_ES_4

city: HOUSTON

first: Jesus

last: Eraso

state: TX

address: 6670 Bertner

department: Pathology and Genomic Medicine

institute: Methodist Hospital

description:
Library name: Sample 139
Library obtained after growth in THY, in vitro, of SDSE MGCS36089, collected at early stationary phase (ES) (replicate 4)

data_processing:
Multiplexed single-end (SE) libraries corresponding to the in vitro and the in vivo samples were sequenced on Illumina NextSeq 500/550 and Novaseq 6000 instruments, respectively. Basecalling and demultiplexing were done on the instruments, and the RNA-Seq data was output as fastq files.
RNA-seq reads generated from the in vitro-grown samples were mapped to strains MGCS36044 (GenBank accession number CP117287.1) and MGCS36089 (GenBank accession number CP117284.1), using Edge-pro v1.3.1 (Estimated Degree of Gene Expression for Prokaryotes) which generated RPKM values by normalizing the read counts for both gene length and sequencing depth. RNA-seq reads generated from the in vivo-grown samples were first mapped to the Macaca fascicularis 6.0 assembly (GenBank accession number GCA_011100615.1) using STAR. The reads mapping to M. fascicularis were excluded, and the left-over reads were mapped to strains MGCS36044 and MGCS36089 using Edge-pro v1.3.1.
Sequencing read quality was evaluated with FASTQC software.
Adapter contamination and read quality filtering was performed with Trimmomatic.
Assembly: strains MGCS36044 (GenBank accession number CP117287.1) and MGCS36089 (GenBank accession number CP117284.1) were used for read alignment.
Supplementary files format and content: Raw reads were normalized by EDGEPro. A matrix named RPKMs_all_samples has been generated.

organism: Streptococcus dysgalactiae

source_name: THY in vitro

growth_protocol: For in vitro growth, cells were grown in Todd-Hewitt broth supplemented with yeast extract (THY media) at 37° C in atmosphere supplemented with 5% CO2. Cells were collected at mid-exponential (ME) at OD=1, and at early stationary phase (ES), at OD=2.

extract_protocol:
In vitro grown pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using Turbo DNA-free (Ambion), and rRNA was depleted using NEBNext rRNA depletion kit (bacteria) (NEB). The tissue (80-100 mg) corresponding to the in vivo samples was washed in PBS, homogenized, and mechanically disrupted using ZR bashing beads, 0.1 mm and 0.5 mm, (Zymo Research). RNA was extracted (MasterPure Complete DNA and RNA purification kit, Lucigen), subjected to three consecutive DNase treatments with Turbo DNA-free (Ambion), and depletion of ribosomal RNA was performed with the NEBNext rRNA depletion kit (bacteria) supplemented with human/mouse /rat depletion mix (NEB).
cDNA libraries from in vitro and in vivo samples were generated from rRNA depleted RNA using a NEBNext Ultra II Directional RNA Library Preparation kit for Illumina (NEB).

treatment_protocol: For in vitro growth, at the desired growth stage, mid-exponential (OD 600nm 1) or early-stationary (OD 600nm 2), the culture was treated with RNAprotect Bacteria Reagent and cells were harvested by centrifugation. For the in vivo growth the excised tissue sections were submerged in RNAShield and frozen at -80°C until processed.

value: THY in vitro


title: 6 months, CaMKIIδC transgenic 7

description: Library name: Sample_7


title: ChIP_Seq-MYSTon_H4K5ac-S-1

value: S


title: 155_pre

description: Library name: 155_pre

value: Untrained


title: 6 months, CaMKIIδC transgenic 6

description: Library name: Sample_6


title: ChIP_Seq-MYSTon_H4K5ac-R-2


title: 89_ES_3

description:
Library name: Sample 138
Library obtained after growth in THY, in vitro, of SDSE MGCS36089, collected at early stationary phase (ES) (replicate 13)

value: RNA extracted from cell pellet


title: 89_ES_2

description:
Library name: Sample 137
Library obtained after growth in THY, in vitro, of SDSE MGCS36089, collected at early stationary phase (ES) (replicate 2)


title: 6 months, CaMKIIδC transgenic 5

description: Library name: Sample_5

value: Hippocampus, CA1 Region


title: 252_pre

description: Library name: 252_pre

value: B

value: Female


title: 158_pre

description: Library name: 158_pre

value: A


title: ChIP_Seq-MYSTon_H4K5ac-R-1


title: 89_ES_1

description:
Library name: Sample 136
Library obtained after growth in THY, in vitro, of SDSE MGCS36089, collected at early stationary phase (ES) (replicate 1)


title: 6 months, CaMKIIδC transgenic 4

description: Library name: Sample_4

value: TG


title: 89_ME_4

description:
Library name: Sample 135
Library obtained after growth in THY, in vitro, of SDSE MGCS36089, collected at mid-exponential phase (ME) (replicate 4)


title: 249_pre

description: Library name: 249_pre

value: Male


title: ChIP_Seq-MYSTon_H4K16ac-S-2


title: 6 months, CaMKIIδC transgenic 3

description: Library name: Sample_3

value: 6 months


title: ChIP_Seq-MYSTon_H4K16ac-S-1


title: 89_ME_3

description:
Library name: Sample 134
Library obtained after growth in THY, in vitro, of SDSE MGCS36089, collected at mid-exponential phase (ME) (replicate 3)


title: 152_post

description: Library name: 152_post

value: post


title: ChIP_Seq-MYSTon_H4K16ac-R-2

value: R


title: 6 months, CaMKIIδC transgenic 2

description: Library name: Sample_2


title: 89_ME_2

description:
Library name: Sample 133
Library obtained after growth in THY, in vitro, of SDSE MGCS36089, collected at mid-exponential phase (ME) (replicate 2)


title: 154_pre

description: Library name: 154_pre

value: pre


title: 89_ME_1

description:
Library name: Sample 132
Library obtained after growth in THY, in vitro, of SDSE MGCS36089, collected at mid-exponential phase (ME) (replicate 1)


title: 138_pre

description: Library name: 138_pre

value: Cyclist


title: m.8344 A>G High heteroplasmy cybrids, Rep3

type: genomic

city: Mendoza

first: Sergio

middle: Roberto

last: Laurito

state: Mendoza

address: Libertador Avenue 80

department: IHEM

country: Argentina

institute: CONICET

hyb_protocol: DNA samples for Infinium MethylationEPIC beadchip assay were prepared following manufacturer's instructions

data_processing:
Illumina GenomeStudio v2.0.5
tsv file including beta values for each sample

label: cy3, cy5

source_name: bone/connective

extract_protocol: CTAB/chloroform-isoamylic based protocol. Cells were collected and tissues were homogeneized in PBS using an Ultra turrax homogenizer, following centrifugation, the pellet (cells or tissue) was suspended and washed 1 time with Tris–EDTA (T10E10), suspended in cetyltrimethylammonium bromide (CTAB) solution (2 g/l CTAB Sigma-Aldrich®, 100 mM Tris/HCl, 20 mM EDTA and 2% 2-mercaptoethanol) and incubated at 60 °C for 1 h for cells or overnight for tissue. Then, chloroform-isoamyl alcohol solution (24:1) was added and the sample was centrifuged. The aqueous phase was collected into a new tube and mixed with 3 volumes of ice-cold 100% ethanol. Precipitated DNA was dissolved in T10E0.1.

value: bone/connective

tag: cell line

value: 143b/human fibroblasts

tag: cell type

value: osteosarcoma/stromal


title: 146_post

description: Library name: 146_post

value: PBMC


title: 44_ES_4

description:
Library name: Sample 131
Library obtained after growth in THY, in vitro, of SDSE MGCS36044, collected at early stationary phase (ES) (replicate 4)

value: THY in vitro


title: ChIP_Seq-MYSTon_H4K12ac-S-2

value: S

value: Pf 3D7

tag: host

value: Homo sapiens


title: 260_post

description: Library name: 260_post

tag: trial

value: B


title: ChIP_Seq-MYSTon_H4K12ac-R-2


title: 44_ES_2

description:
Library name: Sample 129
Library obtained after growth in THY, in vitro, of SDSE MGCS36044, collected at early stationary phase (ES) (replicate 2)

value: RNA extracted from cell pellet


title: 134_pre

description: Library name: 134_pre

value: A

tag: participant

value: Female


title: 44_ES_3

description:
Library name: Sample 130
Library obtained after growth in THY, in vitro, of SDSE MGCS36044, collected at early stationary phase (ES) (replicate 3)


title: m.8344 A>G High heteroplasmy cybrids, Rep1

scan_protocol: DNA samples for Infinium MethylationEPIC beadchip assay were prepared following manufacturer's instructions


title: 44_ES_1

description:
Library name: Sample 128
Library obtained after growth in THY, in vitro, of SDSE MGCS36044, collected at early stationary phase (ES) (replicate 1)


title: ChIP_Seq-MYSTon_H4K12ac-R-1


title: m.8344 A>G Low heteroplasmy cybrids, Rep2

label_protocol: DNA samples for Infinium MethylationEPIC beadchip assay were prepared following manufacturer's instructions


title: 137_pre

description: Library name: 137_pre

tag: sport


title: 44_ME_4

description:
Library name: Sample 127
Library obtained after growth in THY, in vitro, of SDSE MGCS36044, collected at mid-exponential phase (ME)(replicate 4)


title: ChIP_Seq-MYSToff_input-S-1

value: Glcn


title: 6 months, CaMKIIδC transgenic 1

description: Library name: Sample_1

value: Hippocampus, CA1 Region

value: TG

value: 6 months


title: m.8344 A>G Low heteroplasmy cybrids, Rep1


title: 245_post

description: Library name: 245_post

value: Untrained

tag: bmi

value: Male

value: post


title: ChIP_Seq-MYSTon_H4K16ac-R-1

value: R


title: 260_pre

description: Library name: 260_pre

value: PBMC

value: Cyclist

tag: Sex

value: pre


title: 44_ME_3

description:
Library name: Sample 126
Library obtained after growth in THY, in vitro, of SDSE MGCS36044, collected at mid-exponential phase (ME) (replicate 3)

value: THY in vitro


title: ChIP_Seq-MYSToff_input-R-1

value: Pf 3D7

value: Homo sapiens


title: 44_ME_2

description:
Library name: Sample 125
Library obtained after growth in THY, in vitro, of SDSE MGCS36044, collected at mid-exponential (ME) phase (replicate 2)

value: RNA extracted from cell pellet


title: ChIP_Seq-MYSToff_H4K8ac-S-2

value: S


title: m.8344 A>G High heteroplasmy cybrids, Rep2

value: bone/connective

value: 143b/human fibroblasts

value: osteosarcoma/stromal


title: ChIP_Seq-MYSTon_H4K12ac-S-1


title: m.13513G>A, High heteroplasmy cybrids,Rep2


title: m.13513G>A, High heteroplasmy cybrids,Rep1


title: ChIP_Seq-MYSToff_H4K8ac-R-2

value: Glcn


title: 89_M15_L1_run3

description:
Library name: Sample 123
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36089 (re-sequence-3)

source_name: NHP skeletal muscle

value: NHP skeletal muscle

value: RNA extracted from HNP biopsy


title: m.8344 A>G Low heteroplasmy cybrids, Rep3


title: 44_ME_1

description:
Library name: Sample 124
Library obtained after growth in THY, in vitro, of SDSE MGCS36044, collected at mid-exponential (ME) phase (replicate 1)


title: 151_post

description: Library name: 151_post

value: A

value: Untrained

value: Male

tag: timing


title: m.13513G>A, Low heteroplasmy cybrids,Rep3


title: ChIP_Seq-MYSToff_H4K8ac-S-1

tag: developmental stage


title: m.13513G>A, Low heteroplasmy cybrids,Rep2


title: 138_post

description: Library name: 138_post

value: PBMC

value: Female

value: post


title: m.13513G>A, Low heteroplasmy cybrids,Rep1


title: 89_M15_L1_run1

description:
Library name: Sample 121
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36089 (re-sequence-1)


title: m.13513G>A, High heteroplasmy cybrids,Rep3


title: ChIP_Seq-MYSToff_H4K5ac-S-2

tag: chip antibody


title: 149_pre

description: Library name: 149_pre

value: pre


title: 89_M14_L4_run3

description:
Library name: Sample 120
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36089 (re-sequence-3)

tag: genotype


title: ChIP_Seq-MYSToff_H4K5ac-S-1

value: Pf 3D7


title: wild-type cybrids, Rep2

tag: tissue

value: WT


title: ChIP_Seq-MYSToff_H4K5ac-R-2

value: R

value: Homo sapiens


title: 89_M14_L4_run2

description:
Library name: Sample 119
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36089 (re-sequence-2)


title: 257_pre

description: Library name: 257_pre

value: B

value: Cyclist

tag: batch


title: 153_post

description: Library name: 153_post


title: wild-type cybrids, Rep1

value: bone/connective

value: 143b/human fibroblasts

value: osteosarcoma/stromal


title: 245_pre

description: Library name: 245_pre


title: 147_post

description: Library name: 147_post


title: 89_M14_L4_run1

description:
Library name: Sample 118
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36089 (re-sequence-1)

value: NHP skeletal muscle

tag: treatment

value: RNA extracted from HNP biopsy


title: ChIP_Seq-MYSToff_H4K5ac-R-1

value: Glcn

tag: strain


title: Hemispheric cerebellar tissue from subject 4, array type v1

type: other

city: Los Angeles

first: Jennifer

middle: A

last: Cotter

state: CA

address: 4650 Sunset Blvd., M/S 43

department: Pathology and Laboratory Medicine

institute: Children's Hospital Los Angeles

description: EPIC

hyb_protocol: Samples were hybridized to Infinium MethylationEPIC BeadChips and single-base extension was performed followed by staining

scan_protocol: Arrays were imaged using the iScan instrument to generate IDAT files for downstream analysis.

data_processing:
minfi R package v1.44
processed data value definition: Average Beta

label: Cy3 and Cy5

molecule: other

source_name: Cerebellum (non-tumor)

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from FFPE using the QIAamp DNA FFPE Tissue Kit.

value: Cerebellum (non-tumor)

tag: age

value: 5 years


title: ChIP_Seq-MYSToff_H4K8ac-R-1


title: 89_M14_L1_run3

description:
Library name: Sample 117
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36089 (re-sequence-3)


title: 146_pre

description: Library name: 146_pre

value: PBMC

value: A

value: Untrained

value: Female


title: Hemispheric cerebellar tissue from subject 3, array type v1

description: EPIC

value: 4 months


title: ChIP_Seq-MYSToff_H4K16ac-S-2

value: S

value: Pf 3D7


title: 89_M15_L1_run2

description:
Library name: Sample 122
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36089 (re-sequence-2)


title: ChIP_Seq-MYSToff_H4K16ac-S-1

value: Homo sapiens


title: 89_M14_L1_run2

description:
Library name: Sample 116
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36089 (re-sequence-2)


title: Hemispheric cerebellar tissue from subject 2, array type v1

description: EPIC

value: 0 months


title: ChIP_Seq-MYSToff_H4K16ac-R-2

value: R


title: Hemispheric cerebellar tissue from subject 1, array type v1

description: EPIC


title: 89_M14_L1_run1

description:
Library name: Sample 115
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36089 (re-sequence-1)


title: 136_pre

description: Library name: 136_pre

value: Cyclist

value: pre


title: ChIP_Seq-MYSToff_H4K16ac-R-1


title: 89_M13_L2_run3

description:
Library name: Sample 114
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36089 (re-sequence-3)

value: NHP skeletal muscle


title: 255_pre

description: Library name: 255_pre

value: B


title: 139_pre

description: Library name: 139_pre

value: Runner


title: ChIP_Seq-MYSToff_H4K12ac-S-2

value: Glcn


title: A2780, treated with TH-588,  6 𝜇M for 48h, rep C

city: Rochester

first: Cristina

last: Correia

state: Minnesota

address: Kellen Bld 3 th Floor, 200 1st street SW

institute: Mayo Clinic

description: Library name: A2780_MTH1_C

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with TopHat to the reference genome UCSC GRCh38 with default parameters.
Reads that aligned to the human genome.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Assembly: GRCh38
Supplementary files format and content: raw counts in tab-delimited text file

source_name: Ovarian

growth_protocol: A2780 was grown RPMI 1640 medium with 10% heat-inactivated Fetal Bovine Serum (FBS), 10 𝜇g/mL insulin, 100 units/mL penicillin G, 100 𝜇g/mL streptomycin, and 2 mM glutamine

extract_protocol:
RNA was column-extracted using Rneasy Mini kit (qiagen)
RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: A2780 was treated with 6 𝜇M TH-588 for 48h before RNA collection

value: Ovarian

tag: cell line

value: TH-588,  6 𝜇M  for 48h


title: 157_post

description: Library name: 157_post

value: PBMC

value: A

value: Male

value: post


title: 89_M13_L2_run2

description:
Library name: Sample 113
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36089 (re-sequence-2)

value: RNA extracted from HNP biopsy


title: 155_post

description: Library name: 155_post

value: Untrained

value: Female


title: A2780, treated with TH-588,  6 𝜇M for 48h, rep B

description: Library name: A2780_MTH1_B


title: ChIP_Seq-MYSToff_H4K12ac-S-1

value: S

value: Pf 3D7

value: Homo sapiens


title: 137_post

description: Library name: 137_post

value: Cyclist


title: 89_M13_L2_run1

description:
Library name: Sample 112
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36089 (re-sequence-1)

value: NHP skeletal muscle


title: A2780, treated with TH-588,  6 𝜇M  for 48h, rep A

description: Library name: A2780_MTH1_A


title: ChIP_Seq-MYSToff_H4K12ac-R-2

value: R


title: 89_M13_L1_run3

description:
Library name: Sample 111
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36089 (re-sequence-3)


title: 89_M13_L1_run2

description:
Library name: Sample 110
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36089 (re-sequence-2)


title: A2780, DMSO vehicle, rep C

description: Library name: A2780_DMS0_C

value: DMSO


title: 160_pre

description: Library name: 160_pre

value: pre


title: A2780, DMSO vehicle, rep B

description: Library name: A2780_DMS0_B

value: Ovarian


title: 152_pre

description: Library name: 152_pre


title: ChIP_Seq-MYSToff_H4K12ac-R-1

value: Glcn


title: Term Placenta Bulk RNAseq rep 2

city: Durham

first: Cole

last: McCutcheon

state: North Carolina

address: 3 Genome Court

department: Department of Integrative Immunobiology

institute: Duke University

description: Library name: Placenta_term_2

data_processing:
Qiagen CLC Genomics (v20)
Assembly: Sus scrofa genome v11.1
Supplementary files format and content: Mapped Reads in .csv format (TPM, RPKM, etc.)

organism: Sus scrofa

source_name: swine placenta

extract_protocol:
Total RNA was isolated with the Sigma GenElute total mammalian RNA miniprep kit (Cat # RTN350-1KT) or Qiagen RNAeasy Mini Kit (Cat #74104)
Illumina

value: swine placenta


title: A2780, DMSO vehicle, rep A

description: Library name: A2780_DMS0_A


title: 89_M13_L1_run1

description:
Library name: Sample 109
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36089 (re-sequence-1)


title: 89_M12_L1_run3

description:
Library name: Sample 108
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 12, 24h. after infection with SDSE MGCS36089 (re-sequence-3)


title: Term Placenta Bulk RNAseq rep 1

description: Library name: Placenta_term_1


title: 145_pre

description: Library name: 145_pre

value: PBMC

value: A


title: 89_M12_L1_run2

description:
Library name: Sample 107
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 12, 24h. after infection with SDSE MGCS36089 (re-sequence-2)


title: Skin, E138A rep 2

city: Beijing

first: Chenliang

last: Wang

state: Beijing

address: Medical Science Building, Room D307, Tsinghua University

institute: Tsinghua University

description:
Library name: ES
10x Genomics

data_processing:
Following the acquisition of raw sequencing data, the 10x Genomics CellRanger 2.1.1 software was used to process the data and generate the gene expression matrix for all captured cells. For stringent quality control, cells with fewer than 500 detected genes or those with more than 10% mitochondrial gene expression were excluded from further analysis, as these cells were considered low-quality or potentially stressed, which could introduce bias into the results. This rigorous filtering ensured that only high-quality single-cell data was included for downstream analysis using the Seurat package (version 4.0).
Assembly: mm10

source_name: Ear

extract_protocol:
Animals were euthanized and ears were collected and digested with 3 mg/mL Collagenase D (Roche) and 10mM DNase I (Roche) in serum-free medium RPMI for 60 min at 37℃. Enzyme activity was inhibited by adding 10 mL of PBS supplemented with 1% of FBS. The tissues were then mechanically disrupted and filtered through a 100 mm cell strainer to obtain a single cell suspension. For surface staining, cells were stained with antibodies against surface antigens in FACS buffer (PBS supplemented with 1% FBS) on ice for 30 minutes using appropriate antibodies.
We employed the 10x Genomics Chromium Single-Cell 5’ v2 kit for library preparation, strictly adhering to the manufacturer’s guidelines. Breifly, CD45+ cell suspensions were loaded onto the 10x Genomics Chromium Controller, where individual cells were partitioned into gel dead-in emulsions (GEMs) along with barcoded beads. Within each GEM, cells were lysed and reverse transcription occurred, tagging each cDNA molecule with a cell-specific and molecular barcode (UMI). After GEMs were broken, the pooled cDNA was purified and amplified via PCR. Amplified cDNA was used to construct 5′ gene expression libraries. The resulting libraries were then quantified, quality-checked, and prepared for sequencing on an Illumina platform.

value: Ear

tag: cell type

value: CD45+ cells


title: 256_pre

description: Library name: 256_pre

value: B

value: Untrained


title: Skin, E138A rep 1

description:
Library name: EF
10x Genomics


title: 253_post

description: Library name: 253_post

value: Male

value: post


title: 89_M12_L1_run1

description:
Library name: Sample 106
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 12, 24h. after infection with SDSE MGCS36089 (re-sequence-1)

value: RNA extracted from HNP biopsy


title: Skin, WT rep2

description:
Library name: WS
10x Genomics

value: Wild type


title: HeLa, Control, H3K27me3 (ChIP), Rep2

city: New York

first: Yang

last: Luo

state: NY

address: 408 E 69th St

department: Cancer Biology and Genetics

institute: Sloan Kettering Institute

description: Library name: Control_H3K27me3_ChIP_rep2

data_processing:
ChIP-seq reads were trimmed and filtered for quality using TrimGalore (v0.4.5), with a quality setting of 15 and running cutadapt (v1.15) and FastQC (v0.11.5).
Reads were aligned to human assembly hg38 with bowtie2 (v2.3.4.1) and deduplicated using MarkDuplicates in Picard Tools(v2.16.0).
Peaks were called using MACS (v2.16.0) with a p-value setting of 0.001 and run against a matched control for each condition.
A peak atlas was created by combining the superset of all peaks using the ‘merge’ function in the BEDTools suite (v2.29.2). Read density profiles were created using deepTools 'bamCoverage’ (v3.3.0), normalized to 10 million uniquely mapped reads and with read pileups extended to 200 bp. For  histone modification data, ChIP signal was scaled to the inverse of the normalized counts to reads aligning to H3K27me3-modified synthetic nucleosome spike in barcodes. H3K27me3 ernichment was classified as two-fold enrichment of spike in signal in comparison with control.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM high glucose media supplemented with 10% fetal bovine serum (FBS) and 1% Pen/Strep in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Cells were fixed with 1% paraformaldehyde for 10 minutes. After quenching and FACS-enrichment of transfected cells, chromatin was sonicated using a Covaris E220 Focused-ultrasonicator.
ChIP-seq libraries were prepared using ThruPLEX®DNA-Seq kit (Takara), purified with SPRIselect magnetic beads (Beckman Coulter), quantified using a Qubit Flex fluorometer (ThermoFisher Scientific) and profiled with a TapeStation (Agilent).

treatment_protocol: HeLa cells were transfected with the indicated cDNA expression constructs of HA-KDM6B and GFP at 10:1 ratio (to allow FACS sorting of GFP+ cells).

value: HeLa

value: Cervical adenocarcinoma cell line

value: GFP


title: HeLa, Control, H3K27me3 (ChIP), Rep1

description: Library name: Control_H3K27me3_ChIP_rep1


title: 89_M10_L2_run3

description:
Library name: Sample 105
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 10, 24h. after infection with SDSE MGCS36089 (re-sequence-3)

value: NHP skeletal muscle


title: 255_post

description: Library name: 255_post

source_name: PBMC

value: Female


title: Skin, WT rep1

description:
Library name: WF
10x Genomics


title: HeLa, Control, HA (ChIP), Rep2

description: Library name: Control_HA_ChIP_rep2


title: 89_M10_L2_run2

description:
Library name: Sample 104
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 10, 24h. after infection with SDSE MGCS36089 (re-sequence-2)


title: HeLa, Control, HA (ChIP), Rep1

description: Library name: Control_HA_ChIP_rep1


title: 203_pre

description: Library name: 203_pre

value: Runner

value: pre


title: 89_M10_L2_run1

description:
Library name: Sample 103
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 10, 24h. after infection with SDSE MGCS36089 (re-sequence-1)


title: Hela, HA-KDM6B-IDRdel-NU, H3K27me3 (ChIP), Rep2

description: Library name: HA-KDM6B-IDRdel-NU_H3K27me3_ChIP_rep2


title: C2C12, Daxx KO, rep3

city: Creteil

first: Joana

last: Esteves de Lima

address: 8 rue du general sarrail

department: IMRB INSERM U955

country: France

institute: INSERM

data_processing:
fastq.gz groomer tool  (https://usegalaxy.org)
BOWTIE2 v2.3.4.2  (https://usegalaxy.org)
featureCounts v1.6.3+galaxy2 (https://usegalaxy.org)
Assembly: mm10
Supplementary files format and content: DESeq2 v2.11.40.6+galaxy1 (https://usegalaxy.org)

source_name: skeletal muscle cell line

growth_protocol: C2C12 control, C2C12 Hira KO and C2C12 Daxx KO cell lines were collected when grown in high serum medium at low density (proliferating conditions). C2C12 and Hira KO samples were previously deposited on: GSE161056. Here we deposit Daxx KO dataset and the dKO dataset with equivalent C2C12 control dataset.

extract_protocol:
C2C12 cells were collected for RNA extraction using Machery Nagel NucleoSpin RNA purification kit
Libraries were prepared with TruSeq Stranded Total RNA Sample preparation kit according to supplier recommendations. Briefly, the key stages of this protocol are successively, the removal of ribosomal RNA fraction from 1µg of total RNA using the Ribo-Zero Gold Kit; fragmentation using divalent cations under elevated temperature to obtain approximately 300bp pieces; double strand cDNA synthesis using reverse transcriptase and random primers, and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing

value: skeletal muscle cell line

value: myoblasts

value: Daxx -/-


title: 221_pre

description: Library name: 221_pre

value: PBMC


title: 89_M10_L1_run3

description:
Library name: Sample 102
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 10, 24h. after infection with SDSE MGCS36089 (re-sequence-3)


title: C2C12, Daxx KO, rep2


title: HeLa, Control, Input

description: Library name: Control_Input


title: Hela, HA-KDM6B-IDRdel-NU, H3K27me3 (ChIP), Rep1

description: Library name: HA-KDM6B-IDRdel-NU_H3K27me3_ChIP_rep1


title: 103_post

description: Library name: 103_post

value: A


title: Hela, HA-KDM6B-IDRdel-NU, HA (ChIP), Rep2

description: Library name: HA-KDM6B-IDRdel-NU_HA_ChIP_rep2


title: C2C12, Daxx KO, rep1


title: 89_M10_L1_run2

description:
Library name: Sample 101
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 10, 24h. after infection with SDSE MGCS36089 (re-sequence-2)


title: 130_pre

description: Library name: 130_pre

value: Cyclist


title: C2C12, input

data_processing:
fastq.gz groomer tool  (https://usegalaxy.org)
BOWTIE2 v2.3.4.2  (https://usegalaxy.org)
MACS2 v2.1.1.2 using paired-end BAM files with the cutoff q-value 5-e2 and the broad region calling off, the input was used as control (https://usegalaxy.org)
ChIPseeker v1.18.0 (https://usegalaxy.org)
Assembly: mm10
Supplementary files format and content: MACS2 resulting bedgraph file was converted to bigwig format using the wig/bedgraph-to-bigwig converter v1.1.1 (https://usegalaxy.org)

growth_protocol: C2C12 control, C2C12 Hira KO and C2C12 Daxx KO cell lines were collected when grown in high serum medium at low density (proliferating conditions). C2C12 and Hira KO samples were previously deposited on: GSE161056

extract_protocol:
Cells were subjected to nuclei isolation, chromatin fragmentation using Micrococcal Nuclease and nucleosome purification by Hydroxyapatite. Immunoprecipitation was performed overnight at 4°C with 6μg of chromatin and 5μg of antibody previously incubated with Protein-A- (for H3K27ac, H3K4me3, H3K27me3 antibodies) or Protein-G-coated (for H3.3 antibody) magnetic beads.
Library was prepared using KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series (Roche, 07962363001) with IDT for Illumina TruSeq DNA-RNA UD 96 Indexes (UDI) (Illumina, 2023784) and quantified by RT-qPCR using NEBNext Library Quant Kit for Illumina (NEB, E7640AA). Sequencing was carried out on paired-end 50bp of Illumina HiSeq4000.


title: 125_post

description: Library name: 125_post


title: 89_M10_L1_run1

description:
Library name: Sample 100
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 10, 24h. after infection with SDSE MGCS36089 (re-sequence-1)


title: 259_pre

description: Library name: 259_pre

value: B

value: Male


title: 128_post

description: Library name: 128_post

value: post


title: C2C12, H3K9me3, ChIP

value: H3K9me3 (Active Motif, 39062)


title: Hela, HA-KDM6B-U, H3K27me3 (ChIP), Rep2

description: Library name: HA-KDM6B-U_H3K27me3_ChIP_rep2

value: HeLa


title: 89_M09_L1_run2

description:
Library name: Sample 98
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36089 (re-sequence-2)

value: RNA extracted from HNP biopsy


title: C2C12, H3K27me3, ChIP

value: H3K27me3 (Cell Signalling, 9733)


title: Hela, HA-KDM6B-U, H3K27me3 (ChIP), Rep1

description: Library name: HA-KDM6B-U_H3K27me3_ChIP_rep1

value: Cervical adenocarcinoma cell line


title: Hela, HA-KDM6B-IDRdel-NU, HA (ChIP), Rep1

description: Library name: HA-KDM6B-IDRdel-NU_HA_ChIP_rep1


title: C2C12, H3K4me3, ChIP

value: H3K4me3 (Merck Millipore, 07-473)


title: 89_M09_L1_run3

description:
Library name: Sample 99
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36089 (re-sequence-3)

value: NHP skeletal muscle


title: 89_M09_L1_run1

description:
Library name: Sample 97
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 9, 24h. after infection with SDSE MGCS36089 (re-sequence-1)


title: Hela, HA-KDM6B-U, HA (ChIP), Rep2

description: Library name: HA-KDM6B-U_HA_ChIP_rep2


title: 89_M15_L5

description:
Library name: Sample 96
Library obtained after processing Layer 5 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36089


title: C2C12, H3K27ac, ChIP

value: H3K27ac (Abcam, ab4729)


title: 89_M15_L4

description:
Library name: Sample 95
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36089


title: C2C12, H3.3, ChIP

value: skeletal muscle cell line

value: H3.3 (CosmoBio, CE-040B)


title: 223_post

description: Library name: 223_post

value: Runner


title: 126_post

description: Library name: 126_post

value: PBMC


title: 89_M15_L3

description:
Library name: Sample 94
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36089


title: 209_pre

description: Library name: 209_pre

value: pre


title: 111_pre

description: Library name: 111_pre

value: A


title: Hela, HA-KDM6B-NU, H3K27me3 (ChIP), Rep2

description: Library name: HA-KDM6B-NU_H3K27me3_ChIP_rep2


title: 231_pre

description: Library name: 231_pre

value: B

value: Cyclist


title: Control_Day_12, scRNA-seq

city: Cleveland

first: Peng

last: Jiang

address: 2399 Euclid Avenue, FH468

institute: Cleveland State University

description: 10x Genomics

data_processing:
Cell Ranger was used for converting basecall to fastq files, aligning reads to mouse genes and calculating the UMI counts.
Assembly: mm10
Supplementary files format and content: tab-delimited

source_name: Bone marrow

extract_protocol:
Bone marrow-derived macrophages (BMDM) were isolated from the femurs of control and KO mice (both male and female in 1:1 ratio)
10x library prep protocol

value: Bone marrow

value: Bone marrow-derived macrophages (BMDM)


title: Hela, HA-KDM6B-NU, H3K27me3 (ChIP), Rep1

description: Library name: HA-KDM6B-NU_H3K27me3_ChIP_rep1

value: HeLa


title: Hela, HA-KDM6B-NU, HA (ChIP), Rep2

description: Library name: HA-KDM6B-NU_HA_ChIP_rep2


title: KO_Day_12, scRNA-seq

description: 10x Genomics


title: 107_post

description: Library name: 107_post

data_processing:
Trimming reads using fastp 0.23.4
alignment to mirbase 22.1 reference data using bowtie 1.3.0
Batch correction using ComBat-seq
Normalization and differential expression analysis using DESeq2 v1.40.2
Assembly: mirbase 22.1 human and hg38
Supplementary files format and content: Raw count data for mature miRNAs (not batch corrected)
Supplementary files format and content: Raw count data for hairpin miRNAs (not batch corrected)

value: Male

value: post


title: KO_Day_4, scRNA-seq

description: 10x Genomics


title: 203_post

description: Library name: 203_post


title: 89_M15_L1

description:
Library name: Sample 92
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36089

value: RNA extracted from HNP biopsy


title: Hela, HA-KDM6B-NU, HA (ChIP), Rep1

description: Library name: HA-KDM6B-NU_HA_ChIP_rep1

value: Cervical adenocarcinoma cell line


title: Control_Day_4, scRNA-seq

description: 10x Genomics


title: 89_M14_L5

description:
Library name: Sample 91
Library obtained after processing Layer 5 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36089

value: NHP skeletal muscle


title: Hela, HA-KDM6B-U, HA (ChIP), Rep1

description: Library name: HA-KDM6B-U_HA_ChIP_rep1


title: 132_post

description: Library name: 132_post


title: TB03076914-V

city: Mahasset

first: Andrew

last: Shih

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

description: Library name: Sample 8

data_processing:
Fastq files were demultiplexed, aligned to the human reference genome GRCh38 using 10× cellranger 7.0.0
Assembly: 10x GRCh38 2020A
Supplementary files format and content: h5 files

source_name: vehicle stimulated P3/4 endometrial stromal cells

growth_protocol: Control-eSCs (p1, from 4 participants) were plated in maintenance media at 7 × 105 cells/well in 6-well plates.

extract_protocol:
After 4 h, cells were harvested and processed for single cell RNA sequencing (scRNAseq)
10x Chromium Single cell 3’ v3 assay

treatment_protocol: Media was replaced with assay media and the following day eSCs were treated with either vehicle or quercetin (25 μM) (2 wells/condition).

value: endometrial stromal cells

value: vehicle


title: TB03076914-Q

description: Library name: Sample 7

source_name: quercetin stimulated P3/4 endometrial stromal cells

value: quercetin


title: LiLT17_S65

city: Riverside

first: Xiuchun

last: Li

address: 900 University Avenue

institute: UCR

description:
RNAs were sequenced with standard protocols.
LiLT17_S65

data_processing:
Sequence reads that fit any of the following parameters were removed with following standard quality control criteria: 1) the reads containing “N”; 2) the reads containing more than four bases with quality score <10; 3) the reads containing more than six bases with quality score is <13; 4) the reads with 5’ primer contaminants or without 3’ primer; 5) The reads without the insert tag; 6) the reads with ploy A.; and 7) the reads shorter than 15 nt and longer than 45 nt. The sequencing data analyses were performed upon the clean reads after data filtration.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include sequences, length of sequences and sequence counts.

source_name: Liver

growth_protocol: 8 week old C57BL/6 male mice were fed a low cholesterol or high cholesterol diet for 9 weeks

extract_protocol:
Total RNAs were extracted by Trizol (Sigma). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

treatment_protocol:
small RNA-seq processed with PANDORA-seq were treated wih AlkB and PNK4
15-50 nt RNA

value: Liver

value: high cholesterol diet

tag: time

value: 8 weeks


title: 89_M14_L3

description:
Library name: Sample 89
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36089


title: 225_post

description: Library name: 225_post

extract_protocol:
Blood samples were collected into EDTA tubes to prevent coagulation and processed within three hours to isolate peripheral blood mononuclear cells (PBMCs) using Ficoll-Paque (Cytiva) in accordance with the manufacturer’s guidelines. The PBMCs were stored in Trizol Reagent (Invitrogen) at -80°C until all samples were collected. RNA was extracted from the PBMCs following the manufacturer’s instructions, and eluted in DEPC-treated water.
RNA libraries for RNA-seq were prepared using the SMARTer smRNA-Seq Kit for Illumina (Takara) according to the manufacturer’s protocol.

value: PBMC

tag: trial

value: Female


title: 89_M14_L2

description:
Library name: Sample 88
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36089


title: 89_M15_L2

description:
Library name: Sample 93
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 15, 24h. after infection with SDSE MGCS36089


title: LiLT16_S64

description:
RNAs were sequenced with standard protocols.
LiLT16_S64


title: 131_pre

description: Library name: 131_pre

value: A

tag: participant

value: Cyclist

value: pre


title: TB03074781-Q

description: Library name: Sample 5

value: B


title: LiLT15_S63

description:
RNAs were sequenced with standard protocols.
LiLT15_S63


title: 89_M14_L1

description:
Library name: Sample 87
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36089


title: TB03074781-V

description: Library name: Sample 6


title: 216_post

description: Library name: 216_post

tag: sport

value: Runner

value: Male


title: LiLT5_S53

description:
RNAs were sequenced with standard protocols.
LiLT5_S53

value: low cholesterol diet


title: 89_M13_L5

description:
Library name: Sample 86
Library obtained after processing Layer 5 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36089

value: RNA extracted from HNP biopsy


title: TB03075025-Q

description: Library name: Sample 3


title: LiLT18_S66

description:
RNAs were sequenced with standard protocols.
LiLT18_S66


title: 89_M14_L4

description:
Library name: Sample 90
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 14, 24h. after infection with SDSE MGCS36089

value: NHP skeletal muscle


title: 89_M13_L4

description:
Library name: Sample 85
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36089


title: 219_pre

description: Library name: 219_pre

value: Untrained

tag: bmi


title: 214_post

description: Library name: 214_post

tag: Sex

value: post


title: LiLT4_S52

description:
RNAs were sequenced with standard protocols.
LiLT4_S52


title: LiLT3_S51

description:
RNAs were sequenced with standard protocols.
LiLT3_S51


title: 123_post

description: Library name: 123_post

tag: timing


title: 89_M13_L3

description:
Library name: Sample 84
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36089


title: TB03074816-Q

description: Library name: Sample 1

value: endometrial stromal cells

value: quercetin


title: LiLT2_S50

description:
RNAs were sequenced with standard protocols.
LiLT2_S50

value: Liver


title: 89_M13_L2

description:
Library name: Sample 83
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36089


title: 208_pre

description: Library name: 208_pre


title: 89_M13_L1

description:
Library name: Sample 82
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 13, 24h. after infection with SDSE MGCS36089


title: 120_post

description: Library name: 120_post


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 034 [KBRZUSPRA_0119_S19_L002]

city: Ribeirão Preto

first: Junier

middle: Marrero

last: Gutiérrez

state: São Paulo

address: Av Bandeirantes, 3900

department: Pediatric

country: Brazil

institute: Ribeirão Preto Medical School-University of São Paulo

description:
Library name: KBRZUSPRA_0119_S19_L002
ACP_034

data_processing:
FASTQ’s were merged and aligned to GRCh387 using STAR (v2.5.3a)
All sequencing reads were converted to industry standard FASTQ files using BCL2FASTQ v1.8.4, and provided by the facility. The FASTQ files were merged and aligned to the human genome version GRCh38 using STAR v2.5.3a (40). Picard Mark Duplicates (v1.128) identified duplicate reads in the aligned BAM files and with featureCounts (v1.6.0) (41) obtained counting reads for the genomic feature of interest. We applied variance-stabilizing transformation (VST) to the read counts for downstream analysis
Assembly: GRCh38
Supplementary files format and content: raw count for each sample

source_name: microdissected tumor tissue

extract_protocol:
RNA were extracted from microdissected, fresh frozen ACP samples using Rneasy kit (QIAGEN, Hilden, Germany)
NEBNext® Ultra™ II Directional RNA Library Prep Kit (E7765)

value: microdissected tumor tissue

tag: gender

tag: age at_diagnosis(years)

tag: tumor size_(cm)

value: not available

tag: volume (cm3)

tag: hypothalamic invasion

value: type 2


title: TB03075025-V

description: Library name: Sample 4

tag: treatment

value: vehicle

tag: batch

value: A


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 034 [KBRZUSPRA_0119_S19_L001]

description:
Library name: KBRZUSPRA_0119_S19_L001
ACP_034

tag: tissue


title: 89_M12_L5

description:
Library name: Sample 81
Library obtained after processing Layer 5 from a skeletal muscle biopsy extracted from NHP 12, 24h. after infection with SDSE MGCS36089

tag: genotype


title: 228_post

description: Library name: 228_post

value: PBMC

value: Cyclist


title: LiLT1_S49

description:
RNAs were sequenced with standard protocols.
LiLT1_S49

tag: strain

value: 8 weeks


title: 232_pre

description: Library name: 232_pre

value: B

value: Male

value: pre


title: LiLP18_S48

description:
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
LiLP18_S48

value: high cholesterol diet

tag: time


title: LiLP17_S47

description:
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
LiLP17_S47


title: 201_pre

description: Library name: 201_pre

tag: trial

value: Runner


title: 89_M12_L4

description:
Library name: Sample 80
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 12, 24h. after infection with SDSE MGCS36089

value: NHP skeletal muscle

value: RNA extracted from HNP biopsy


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 033 [KBRZUSPRA_0118_S18_L001]

description:
Library name: KBRZUSPRA_0118_S18_L001
ACP_033

value: Female


title: LiLP16_S46

description:
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
LiLP16_S46

value: Liver


title: 89_M12_L3

description:
Library name: Sample 79
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 12, 24h. after infection with SDSE MGCS36089


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 031 [KBRZUSPRA_0117_S11_L002]

description:
Library name: KBRZUSPRA_0117_S11_L002
ACP_031

value: microdissected tumor tissue


title: 129_pre

description: Library name: 129_pre

tag: participant

value: not applicable


title: LiLP15_S45

description:
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
LiLP15_S45


title: 89_M12_L2

description:
Library name: Sample 78
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 12, 24h. after infection with SDSE MGCS36089


title: 128_pre

description: Library name: 128_pre

tag: sport


title: 119_post

description: Library name: 119_post

value: Untrained

tag: bmi

value: post


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 028 [KBRZUSPRA_0115_S10_L002]

description:
Library name: KBRZUSPRA_0115_S10_L002
ACP_028

value: not available

value: type 2


title: LiLP5_S35

description:
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
LiLP5_S35

value: low cholesterol diet


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 033 [KBRZUSPRA_0118_S18_L002]

description:
Library name: KBRZUSPRA_0118_S18_L002
ACP_033


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 031 [KBRZUSPRA_0117_S11_L001]

description:
Library name: KBRZUSPRA_0117_S11_L001
ACP_031


title: LiLP4_S34

description:
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
LiLP4_S34

value: 8 weeks


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 028 [KBRZUSPRA_0115_S10_L001]

description:
Library name: KBRZUSPRA_0115_S10_L001
ACP_028


title: 214_pre

description: Library name: 214_pre

value: PBMC

value: B

tag: Sex


title: 89_M10_L4

description:
Library name: Sample 75
Library obtained after processing Layer 4 from a skeletal muscle biopsy extracted from NHP 10, 24h. after infection with SDSE MGCS36089


title: LiLP3_S33

description:
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
LiLP3_S33


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 027 [KBRZUSPRA_0114_S16_L002]

description:
Library name: KBRZUSPRA_0114_S16_L002
ACP_027


title: 105_pre

description: Library name: 105_pre

value: A

value: Male

tag: timing

value: pre


title: 89_M12_L1

description:
Library name: Sample 77
Library obtained after processing Layer 1 from a skeletal muscle biopsy extracted from NHP 12, 24h. after infection with SDSE MGCS36089

value: NHP skeletal muscle


title: 102_pre

description: Library name: 102_pre

value: Runner


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 024 [KBRZUSPRA_0113_S15_L002]

description:
Library name: KBRZUSPRA_0113_S15_L002
ACP_024

tag: gender

value: Female


title: Tumor RNA from adamantinomatous craniopharyngioma Tumor 027 [KBRZUSPRA_0114_S16_L001]

description:
Library name: KBRZUSPRA_0114_S16_L001
ACP_027

tag: age at_diagnosis(years)


title: 89_M10_L5

description:
Library name: Sample 76
Library obtained after processing Layer 5 from a skeletal muscle biopsy extracted from NHP 10, 24h. after infection with SDSE MGCS36089

value: RNA extracted from HNP biopsy


title: LiLP2_S32

description:
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
LiLP2_S32

value: Liver


title: 89_M10_L3

description:
Library name: Sample 74
Library obtained after processing Layer 3 from a skeletal muscle biopsy extracted from NHP 10, 24h. after infection with SDSE MGCS36089


title: LiLP1_S31

description:
RNAs were treated with T4PNK, then AlkB before cDNA library construction.
LiLP1_S31


title: 113_pre

description: Library name: 113_pre


title: 89_M10_L2

description:
Library name: Sample 73
Library obtained after processing Layer 2 from a skeletal muscle biopsy extracted from NHP 10, 24h. after infection with SDSE MGCS36089