title: lung_tumor_kras_rep5

description: Date: 2009

value: on doxycycline (KRAS activated)


title: lung_tumor_myckras_rep2

status: Public on Oct 18 2022

type: RNA

city: Stanford

first: Dean

last: Felsher

state: CA

address: 269 Campus Drive

department: Medicine

country: USA

institute: Stanford University

description: Date: 2009

hyb_protocol: A total of 1500 ng of cRNA was hybridized for each array using standard Illumina protocols with streptavidin-Cy3 being used for detection.

scan_protocol: Slides were scanned on an Illumina BeadArray reader and analyzed using BeadStudio (Illumina, Inc).

data_processing: The R package, lumi, computed normalized (log2-transformed, quantile-normalized) signal intensity valuees.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: lung adenocarcinoma

label_protocol: Each RNA sample was amplified using the Ambion Illumina RNA amplification kit with biotin UTP labeling. The Ambion Illumina RNA amplification kit uses T7 oligo(dT) primer to generate single stranded cDNA followed by a second strand synthesis to generate double-stranded cDNA, which is then column purified. In vitro transcription was done to synthesize biotin-labeled cRNA using T7 RNA polymerase. The cRNA was then column purified and measured.

extract_protocol: Total RNA was extracted using TRIzol reagent after tissue homogenization.

treatment_protocol: Doxycycline was added to mice's drinking water at a concentration of 100 µg/mL.

tag: strain

tag: treatment

value: on doxycycline (MYC and KRAS activated)


title: Breast cancer epithelial cells, 72h Control

type: SRA

city: PORTLAND

first: Hongmei

last: Zhang

state: OR

address: 2730 SW Moody Ave

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

library_source: transcriptomic

data_processing:
Raw base call files were demultiplexed with 'cellranger mkfastq' into fastq files (cellranger 2.0).
We applied 'cellranger count' to performs genome alignment, filtering, barcode counting, and UMI counting for fastq files with default parameters. The feature-barcode matrices were generated by sample.
Genome_build: human genome GRCh38
Supplementary_files_format_and_content: tab-delimited text files include UMI count for each gene in cell populations.

molecule: polyA RNA

organism: Homo sapiens

source_name: Breast cancer epithelial cells

growth_protocol: HCC1143 cells were maintained in RPMI1640 growth medium (Life Technologies Inc.) supplemented with 10% fetal bovine serum (Hyclone) incubating at 37°C with 5%.

extract_protocol:
Cell were incubated with Gel Bead-In-Emulsions(GEM) using Chromium Controller of 10x Genomics for 6.5 min. Barcoded and full length cDNA from poly A mRNA by reverse transcription were produced after incubation. The GEMs were broken and full length cDNA were pooled together.
Full-length, barcoded cDNA was then amplified by PCR to generate sufficient mass, QC(200-9000bp) with Agilent Bioanalyzer chip for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size (peaks 400-600bp) with Agilent D1000 ScreenTape prior to library construction.  P5, P7, a sample index and R2 were added during library construction via End repair, A-tailing, Adaptor ligation and PCR. The final libraries contain the P5 and P7 primers were used in Illumina bridge amplification.

treatment_protocol: Cells were seeded into 6-well plate allowed to attach for 24 hours prior to treatment with DMSO or Paclitaxel (P-9600, LC Labs) 1nM for 24 or 72 hours then collected for single cell sequence.

value: DMSO control

tag: time point

tag: cell line


title: sample49_HCC_tissue

city: Nanning

first: Meiying

last: Long

state: Guangxi

address: Guangxi nanning of China

country: China

institute: Guangxi Medical University

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L49_sample_T

data_processing:
The raw sequencing reads were preprocessed by fastp v0.23.0
HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) was used to align the transcriptome sequencing Reads to the reference genome
HTSeq was used for Reads Count calculation
Transcripts Per Million of library size (TPM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: tab-delimited text files include Count values for each Sample

source_name: tissue: liver

extract_protocol:
(1) NanoDrop™ One/OneC for RNA purity (OD260/280, OD260/230 ratios); (2) Life Invitrogen Qubit® 3.0 fluorescence quantification instrument with Qubit™ RNA HS Assay Kit for precise quantification; (3) Agilent 4200 (3) Agilent 4200 TapeStation System for accurate detection of RNA integrity (RIN value).
(1) Capture mRNA with polyA structure using magnetic beads with Oligo (DT); (2) Synthesize cDNA using fragmented mRNA as template; (3) Purify cDNA with end repair, A-tailing and sequencing connectors; (4) Screen cDNA of 200bp with AMPure XP beads, perform PCR amplification and sequencing library. (4) Screen the 200bp cDNA with AMPure XP beads, amplify the PCR and purify the PCR

tag: tissue

value: hepatocellular carcinoma


title: Breast cancer epithelial cells, 24h Treated

value: Treated with Paclitaxel


title: lung_tumor_kras_rep4

description: Date: 2009


title: Breast cancer epithelial cells, 24h Control


title: sample48_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L48_sample_T


title: V0045

type: genomic

city: Madrid

first: Lara

last: Fernández

state: Madrid

address: Carretera Cantoblanco 8

country: Spain

institute: IMDEA Food

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 121

data_processing: Results were analyzed using TaqMan Genotyper software.

label: VIC

molecule: genomic DNA

source_name: Peripheral blood

label_protocol: Genotyping was performed with QuantStudio 12 K Flex Real-Time PCR System (Life Technologies Inc., Carlsbad, CA, USA) using TaqMan OpenArray plates following manufacturer’s instructions.

extract_protocol: Genomic DNA from peripheral blood was extracted using the QIAamp DNA Blood Mini Kit (Qiagen Sciences, Inc, Germantown, MD, USA)

tag: Sex

value: Male

tag: age

tag: bmi

tag: fat mass

tag: muscle mass

label: FAM


title: sample52_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L52_sample_T


title: lung_tumor_kras_rep3

description: Date: 2009


title: sample46_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L46_sample_T


title: sample45_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L45_sample_T


title: DBL000227

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 118


title: sample47_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L47_sample_T


title: lung_tumor_kras_rep2

description: Date: 2009


title: 3F1

city: HOUSTON

first: Bin

last: Guo

state: TX

address: 4849 Calhoun Rd

institute: University of Houston

data_processing:
The RNA-seq raw fastq data were processed with RNA-Seq Alignment app within the Illumina BaseSpace app suite (www.basespace.illumina.com)
The adaptors were trimmed and reads were mapped to hg19 human reference genome using the STAR aligner to generate the BAM files, and FPKM estimation of reference genes and transcripts were performed using Cufflinks 2
Based on this gene count matrix, we used “DESeq2” package to identify differentially expressed genes between control cells vs. 3FM-dC treated cells.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files for each sample were generated

source_name: K562 cells

growth_protocol: The cell lines K-562 was purchased from American Type Culture Collection. Cells were cultured in Iscove's Modified Dulbecco's Medium containing 10% FBS.

extract_protocol:
Total RNA from the cells were extracted (Qiagen) and underwent quality control assessment using the RNA Nano 6000 chip on Bioanalyzer 2100 (Agilent) and were quantified with Qubit Fluorometer (Thermo Fisher).
RNA libraries were prepared and sequenced at University of Houston Seq-N-Edit Core per standard protocols. mRNA libraries were prepared with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (New England BioLabs) using 1000 ng input RNA.

treatment_protocol: In treatment group, K562 cells were treated with 20 µM 3FM-dC plus 2mM THU. The same amount of DMSO, dissolvant of the 3FM-dC and THU, was also added to K562 cells in control group. Cells were incubated for 24h at 37°C.

value: bone marrow

tag: passages

tag: disease

value: chronic myelogenous leukemia (CML)

tag: agent


title: 3F3


title: sample44_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L44_sample_T


title: DBL000228

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 119

value: Female


title: 3F2


title: DBL000225

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 116


title: lung_tumor_myc_rep4

description: Date: 2009

value: CCSP-rtTA/TetO-MYC

value: on doxycycline (MYC activated)


title: sample42_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L42_sample_T


title: sample43_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L43_sample_T


title: V0005

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 120


title: DBL000218

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 115


title: lung_tumor_myc_rep5

description: Date: 2009


title: lung_tumor_myc_rep3

description: Date: 2009


title: lung_tumor_kras_rep1

description: Date: 2009


title: DBL000217

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 114


title: C2

value: DMSO


title: lung_tumor_myc_rep2

description: Date: 2009


title: DBL000216

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 113


title: DBL000226

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 117


title: C3


title: sample41_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L41_sample_T


title: sample40_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L40_sample_T


title: DBL000215

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 112


title: sample39_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L39_sample_T


title: Brain, RNA, dorsal hippocampus, sedentary, biol rep2

city: Irvine

first: Autumn

middle: Skye

last: Ivy

address: 825 Health Sciences, Medical Sciences D330

institute: Universtity of California, Irvine

description: countswildtype.csv

data_processing:
Base calling, and demultiplexing was handled by the University of California, Irvine Genomics High Throughput Facility using Novaseq control software ver 1.7.5 and Real time analysis ver 3.4.4.
RNA-seq libraries were quality control checked by FastQC (0.11.9), reads were aligned using STAR Aligner 2.7.3a, Duplicates removed by Picard tools 1.87.
Processed RNA seq files were analyzed with R 4.1.0 using Genomic Alignments 1.28.0 (summarizeOverlaps mode=“IntersectionNotEmpty”, singleEnd=FALSE, ignore.strand=FALSE, fragments=TRUE), Genomic features 1.44.0 (exons by gene), R SAM Tools 2.8.0 (yeildSize=100000), Differential Gene Expression was done by DEseq2 1.32.0,  BiomaRt 2.48.1 labeled gene symbols.
Assembly: GRCmm38v6
Supplementary files format and content: A table of read counts for the RNA seq sets, one file is included for the Emx1-NuTRAP samples, and one for the C57BL/6J samples

source_name: hippocampus

extract_protocol:
SIT isolation described by "Early life exercise primes the neural epigenome to facilitate gene expression and hippocampal memory consolidation" in Raus et al. 2022 (In Review) Preprint on Biorxiv, separate isolation described by Roh et al. 2017 Cell Rep.  "Simultaneous Transcriptional and Epigenomic Profiling from Specific Cell Types within Heterogeneous Tissues In Vivo", RNA from C57Bl6J was extracted using Qiagen RNeasy kit.
Perkin-Elmer Nextflex Rapid Directional RNA-seq Kit 2.0

value: hippocampus

tag: cell type

value: bulk

tag: genotype

tag: tissue region

value: left dorsal hippocampus

tag: isolation

value: Post Natal Day 21-41 sedentary

tag: object location_memory_training_time


title: C1


title: Brain, RNA, dorsal hippocampus, sedentary, biol rep3

description: countswildtype.csv

tag: treatment


title: sample38_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L38_sample_T


title: DBL000214

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 111


title: DBL000211

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 109


title: sample36_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L36_sample_T


title: DBL000210

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 108


title: DBL000212

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 110


title: sample37_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L37_sample_T


title: Brain, RNA, dorsal hippocampus, sedentary, biol rep4

description: countswildtype.csv


title: Dd2G353Vcrt_repA

city: University Park

first: Manuel

last: Llinas

state: Pennsylvania

address: Millennium Science Complex, Pollock Rd

department: Biochemistry and Molecular Biology

institute: Penn State University

description: Biological replicate 1 of 3. PPQ-resistant PfCRT-edited G353V Dd2 line, untreated trophozoites.

hyb_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

scan_protocol: Agilent G2600D Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1).

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction.

organism: Plasmodium falciparum

source_name: Dd2-Dd2 CRT_G353V

label_protocol: 4ug of cDNA was labelled with Cy5 as described in Bozdech, Z., Mok, S., & Gupta, A. P. DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods Mol. Biol. 923, 189-211 (2013). Samples were hybridized against a common Cy3-labelled pool consisting of RNA from mixed 3D7 asexual stages.

growth_protocol: Parasite lines were cultured in vitro in 0.5% Albumax-supplemented RPMI 1640-based P. falciparum culture medium. Two consecutive 5% D-sorbitol treatments were used to tightly synchronize the cultures and magnetic column purifications were performed to obtain highly-enriched trophozoites when needed.

extract_protocol: Extraction of total RNA, cDNA synthesis and amplification of target DNA was carried out as described in Bozdech, Z., Mok, S., & Gupta, A. P. DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods Mol. Biol. 923, 189-211 (2013).

treatment_protocol: No drug treatment was performed.

tag: culture

value: in vitro

tag: Stage

value: Trophozoite asexual blood stage

tag: strain

tag: genetic modification

value: ZFN-edited

tag: pfcrt allele

tag: ppq sensitivity

value: Resistant

tag: experimental replicate

source_name: Plasmodium falciparum reference RNA pool

value: Asexual blood stage

tag: composition

value: Mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle.


title: sample35_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L35_sample_T

tag: tissue

value: hepatocellular carcinoma


title: DBL000209

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 107

tag: Sex

tag: age

tag: bmi

tag: fat mass

tag: muscle mass


title: Dd2M343Lcrt_repC

description: Biological replicate 3 of 3. PPQ-resistant PfCRT-edited M343L Dd2 line, untreated trophozoites.

source_name: Dd2-Dd2 CRT_M343L


title: Dd2G353Vcrt_repB

description: Biological replicate 2 of 3. PPQ-resistant PfCRT-edited G353V Dd2 line, untreated trophozoites.


title: Dd2M343Lcrt_repA

description: Biological replicate 1 of 3. PPQ-resistant PfCRT-edited M343L Dd2 line, untreated trophozoites.


title: Dd2M343Lcrt_repB

description: Biological replicate 2 of 3. PPQ-resistant PfCRT-edited M343L Dd2 line, untreated trophozoites.


title: Brain, RNA, dorsal hippocampus, sedentary, 10 minute, biol rep1

description: countswildtype.csv

tag: cell type

tag: genotype

tag: tissue region

tag: isolation

value: 10 minutes


title: Brain, RNA, dorsal hippocampus, sedentary, 10 minute, biol rep2

description: countswildtype.csv

tag: treatment

tag: object location_memory_training_time


title: Brain, RNA, dorsal hippocampus, sedentary, biol rep1

description: countswildtype.csv


title: lung_tumor_myc_rep1

description: Date: 2009

tag: strain


title: Dd2G353Vcrt_repC

description: Biological replicate 3 of 3. PPQ-resistant PfCRT-edited G353V Dd2 line, untreated trophozoites.

tag: culture

tag: Stage

tag: genetic modification

tag: pfcrt allele


title: sample34_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L34_sample_T

tag: tissue


title: sample33_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L33_sample_T


title: Dd2F145Icrt_repC

description: Biological replicate 3 of 3. PPQ-resistant PfCRT-edited F145I Dd2 line, untreated trophozoites.

source_name: Dd2-Dd2 CRT_F145I

tag: ppq sensitivity

tag: experimental replicate

tag: composition


title: DBL000207

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 105

tag: Sex

tag: age

tag: bmi

tag: fat mass


title: Dd2F145Icrt_repB

description: Biological replicate 2 of 3. PPQ-resistant PfCRT-edited F145I Dd2 line, untreated trophozoites.


title: sample32_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L32_sample_T


title: DBL000208

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 106

tag: muscle mass


title: Brain, RNA, dorsal hippocampus, sedentary, 3 minute, biol rep2

description: countswildtype.csv

tag: cell type

tag: genotype

tag: tissue region

tag: isolation

value: 3 minutes


title: Brain, RNA, dorsal hippocampus, sedentary, 3 minute, biol rep3

description: countswildtype.csv

tag: treatment

tag: object location_memory_training_time


title: Brain, RNA, dorsal hippocampus, sedentary, 10 minute, biol rep3

description: countswildtype.csv


title: Dd2F145Icrt_repA

description: Biological replicate 1 of 3. PPQ-resistant PfCRT-edited F145I Dd2 line, untreated trophozoites.

tag: culture

tag: Stage

tag: strain

tag: genetic modification


title: DBL000205

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 103

value: Female


title: sample31_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L31_sample_T

tag: tissue


title: Brain, RNA, dorsal hippocampus, adolescent exercised, biol rep4

description: countswildtype.csv

value: Post Natal Day 35-41 exercised


title: sample30_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L30_sample_T


title: Brain, RNA, dorsal hippocampus, sedentary, 3 minute, biol rep1

description: countswildtype.csv


title: DBL000204

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 102


title: Brain, RNA, dorsal hippocampus, adolescent exercised, biol rep2

description: countswildtype.csv


title: sample29_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L29_sample_T


title: DBL000203

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 101


title: sample28_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L28_sample_T


title: Dd2Dd2crt_repA

description: Biological replicate 1 of 2. PPQ-sensitive PfCRT-edited Dd2 line, untreated trophozoites.

source_name: Dd2-Dd2 CRT

tag: pfcrt allele

tag: ppq sensitivity

value: Sensitive

tag: experimental replicate

tag: composition


title: DBL000202

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 100

tag: Sex

tag: age

tag: bmi

tag: fat mass


title: Dd2Dd2crt_repB

description: Biological replicate 2 of 2. PPQ-sensitive PfCRT-edited Dd2 line, untreated trophozoites.


title: Brain, RNA, dorsal hippocampus, adolescent exercised, biol rep3

description: countswildtype.csv

tag: cell type

tag: genotype

tag: tissue region


title: Brain, RNA, dorsal hippocampus, adolescent exercised, biol rep1

description: countswildtype.csv

tag: isolation

tag: treatment

tag: object location_memory_training_time


title: DBL000201

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 99

tag: muscle mass


title: DBL000206

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 104


title: Brain, RNA, dorsal hippocampus, juvenile exercised, biol rep5

description: countswildtype.csv

value: Post Natal Day 21-27 exercised


title: sample25_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L25_sample_T


title: Dd2_repA

description: Biological replicate 1 of 2. PPQ-sensitive Dd2 line, untreated trophozoites.

tag: culture

tag: Stage

tag: strain

tag: genetic modification


title: Brain, RNA, dorsal hippocampus, juvenile exercised, biol rep4

description: countswildtype.csv

tag: tissue

value: hippocampus


title: sample24_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L24_sample_T


title: Mnase-Seq, shScr1_60minus

city: Houston

first: Dongyu

last: Zhao

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling. RNA-Seq raw reads were mapped to the human genome version hg19 using TopHat version 2.1.1 with default parameter values. Expression value (number of raw reads) for each gene was determined by the software HTSeq version 0.9.1 with default parameter values. Normalized (the TMM method) expression values and differentially expressed genes were determined by edgeR version 3.10.5 ran with an R version 3.2.1. The MeV version 4.8.1 was used to draw the heatmaps. We used the function genomeCoverageBed in BEDTools Version 2.16.2, along with the nor2total function in DANPOS version 2.2.2, and the tool bedGraphToBigWig (https://www.encodeproject.org/software/bedgraphtobigwig/) to generate a BigWig file that contains RNA-Seq signal (read density) at each base pair across the genome. The BigWig file was then submitted to the UCSC Genome Browser to visualize RNA-Seq signal at individual genes.
ChIP-Seq raw reads were mapped to the human genome version hg19 using Bowtie version 1.2.2 with default parameter values. We then submitted the mapped reads to the Dregion function in DANPOS version 2.2.2 (https://sites.google.com/site/danposdoc/) to calculate ChIP-Seq signal (read density) at each base pair of the genome, subtract background (input) signal, normalize read number, and define individual enrichment peaks. The Dregion stored the signal value at each base pair in a Wiggle format file, which we next converted to bigWig format using the tool WigToBigWig (https://www.encodeproject.org/software/wigtobigwig/). The bigWig files were submitted to the UCSC Genome Browser (https://genome.ucsc.edu) to visualize ChIP-Seq signal at each base pair. The Dregion also stored individual feature values for each enrichment peak of ChIP-Seq signal. These feature values include peak width, height and total signal. To calculate signal value at each base pair across each gene, we used the Profile function in DANPOS version 2.2.2. The Profile function in DANPOS 2.2.2 was also used to calculate average ChIP-Seq signal at each gene group.
MNase-Seq raw reads were mapped to the human genome version hg19 using Bowtie version 1.2.2 with default parameter values. We then submitted the mapped reads to the Dpos function (parameter: --smooth_width 0 -c 50000000 -u 1 --pheight 1e-200) in DANPOS version 2.2.2 (https://sites.google.com/site/danposdoc/) to calculate MNase-Seq signal (read density) at each base pair of the genome. The pipeline to observe MNase-Seq read density is the same as that described above for ChIP-Seq. The Profile function in DANPOS 2.2.2 was also used to calculate average MNase-Seq signal at each gene group.
Assembly: hg19
Supplementary files format and content: For RNA-Seq data, tab-delimited text files contian normalized count values for each gene of each sample. For ChIP-Seq data, bigwig files showing the average signal density accross genome are generated using DANPOS2 v2.2.3. For Mnase-Seq data, bigwig files.

source_name: Castration-resistant prostate cancer

extract_protocol:
RNA-Seq: Total RNA was isolated from cells using the RNA MiniPrep kit (ZYMO Research). ChIP-Seq: Chromatin DNA in ChIP-Seq samples was purified by using columns provided in Magna ChIP A/G Kit (Millipore Cat.17-10085). MNase-Seq: Nucleosome DNA was extracted using phenol:chloroform:isoamyl for high-throughput sequencing.
RNA-Seq: 1. Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; 2. mRNA molecules were fragmented into small pieces; 3. The fragmented mRNA was synthesized into first strand cDNA using random primers; 4. The second strand cDNA was synthesized with dUTP instead of dTTP; 5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 6. Digest the U-labeled second-strand template with Uracil-DNA-Glycosylase (UDG) and perform PCR amplification; 7. Library quality control; 8. Library circularization; 9. The library was amplified to make DNA nanoball (DNB); 10. Sequencing on DNBSEQ (DNBSEQ Technology) platform. ChIP-Seq and MNase-Seq: (1) Take IPed-DNA and Input DNA for sample qualification; (2) DNA-end repair, 3'-dA overhang and adaptor ligation; (3) PCR amplification and size selection; (4) Library quality control; (5) Library circularization;(6) The library was amplified to make DNA nanoball (DNB); (7) Sequencing on DNBSEQ (DNBSEQ Technology) platform.

tag: cell line

value: Prostate

value: Control

value: Nuclei were incubated for 60 min at 37 ºC


title: Mnase-Seq, CHD6_sh1-3_60minus

value: CHD6 knockdown


title: sample27_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L27_sample_T


title: Mnase-Seq, shScr3_60minus


title: Brain, RNA, dorsal hippocampus, juvenile exercised, biol rep6

description: countswildtype.csv

value: bulk

value: left dorsal hippocampus


title: sample26_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L26_sample_T


title: Mnase-Seq, shScr2_60minus


title: Dd2_repB

description: Biological replicate 2 of 2. PPQ-sensitive Dd2 line, untreated trophozoites.

value: in vitro

value: Trophozoite asexual blood stage

tag: pfcrt allele

tag: ppq sensitivity

tag: experimental replicate

tag: composition


title: DBL000200

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 98

tag: Sex

tag: age

tag: bmi

tag: fat mass


title: DBL000199

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 97


title: sample21_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L21_sample_T


title: DBL000198

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 96


title: DBL000197

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 95


title: Brain, RNA, dorsal hippocampus, juvenile exercised, biol rep3

description: countswildtype.csv

tag: cell type

tag: genotype

tag: tissue region

tag: isolation

tag: treatment


title: Brain, RNA, dorsal hippocampus, juvenile exercised, biol rep2

description: countswildtype.csv

tag: object location_memory_training_time


title: sample23_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L23_sample_T


title: Mnase-Seq, CHD6_sh1-2_60minus


title: Mnase-Seq, CHD6_sh1-1_60minus


title: Brain, RNA, dorsal hippocampus, 3wk exercised, biol rep2

description: countswildtype.csv

value: Post Natal Day 21-41 exercised


title: sample20_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L20_sample_T

value: hepatocellular carcinoma


title: Brain, RNA, dorsal hippocampus, 3wk exercised, biol rep1

description: countswildtype.csv


title: DBL000192

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 90

tag: muscle mass


title: sample22_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L22_sample_T

tag: tissue


title: DBL000196

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 94


title: Brain, RNA, dorsal hippocampus, juvenile exercised, biol rep1

description: countswildtype.csv


title: Mnase-Seq, shScr3_15minus

tag: cell line

value: Nuclei were incubated for 15 min at 37 ºC


title: DBL000194

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 92


title: DBL000195

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 93


title: Mnase-Seq, shScr1_15minus


title: lung_tumor_myckras_rep1

description: Date: 2009

tag: strain

value: on doxycycline (MYC and KRAS activated)


title: Brain, RNA, dorsal hippocampus, 3wk exercised, biol rep4

description: countswildtype.csv

value: 3 minutes


title: Brain, RNA, dorsal hippocampus, 3wk exercised, biol rep3

description: countswildtype.csv


title: sample19_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L19_sample_T


title: Mnase-Seq, CHD6_sh1-1_15minus


title: Mnase-Seq, shScr2_15minus


title: DBL000193

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 91

value: Female


title: Mnase-Seq, CHD6_sh1-3_15minus


title: ChIP-Seq, Input_3

tag: chip antibody


title: Mnase-Seq, CHD6_sh1-2_15minus


title: sample16_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L16_sample_T


title: Brain, RNA, right, sedentary, separate, biol rep2

description: countsNuTRAP.csv

value: neuron

value: right whole hippocampus

value: separate isolation

value: Post Natal Day 21-41 sedentary


title: Brain, RNA, left, sedentary, separate, biol rep3

description: countsNuTRAP.csv

value: hippocampus

value: left whole hippocampus


title: sample18_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L18_sample_T


title: DBL000188

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 86


title: Brain, RNA, left, sedentary, separate, biol rep2

description: countsNuTRAP.csv


title: ChIP-Seq, Input_1

value: Prostate


title: sample17_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L17_sample_T


title: Brain, RNA, right, sedentary, separate, biol rep3

description: countsNuTRAP.csv


title: DBL000191

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 89


title: DBL000190

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 88


title: sample15_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L15_sample_T


title: DBL000187

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 85

value: Male


title: Brain, RNA, left, exercised, separate, biol rep3

description: countsNuTRAP.csv


title: sample12_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L12_sample_T


title: ChIP-Seq, Input_2


title: sample13_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L13_sample_T


title: sample14_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L14_sample_T


title: DBL000189

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 87


title: ChIP-Seq, CHD6_2

value: CHD6 antibody


title: DBL000186

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 84


title: DBL000185

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 83


title: sample9_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L09_sample_T


title: Brain, RNA, exercised, SIT, biol rep4

description: countsNuTRAP.csv

value: whole bilateral hippocampus

value: SIT isolation


title: sample10_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L10_sample_T


title: Brain, RNA, right, exercised, separate, biol rep3

description: countsNuTRAP.csv

value: Post Natal Day 21-41 exercised


title: Brain, RNA, sedentary, SIT, biol rep4

description: countsNuTRAP.csv


title: RNAseq, E2F1_sh2-2

value: E2F1 knockdown


title: RNAseq, E2F1_sh2-3


title: DBL000184

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 82


title: ChIP-Seq, CHD6_3


title: RNAseq, E2F1_sh2-1


title: DBL000182

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 80


title: sample7_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L07_sample_T

value: hepatocellular carcinoma


title: Brain, RNA, left, sedentary, separate, biol rep1

description: countsNuTRAP.csv


title: ChIP-Seq, CHD6_1


title: DBL000181

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 79


title: sample11_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L11_sample_T


title: sample6_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L06_sample_T


title: Brain, RNA, right, sedentary, separate, biol rep1

description: countsNuTRAP.csv


title: Brain, RNA, right, exercised, separate, biol rep2

description: countsNuTRAP.csv


title: sample5_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L05_sample_T


title: RNAseq, E2F1_sh1-2


title: DBL000128

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 77


title: RNAseq, E2F1_sh1-3


title: Brain, RNA, sedentary, SIT, biol rep3

description: countsNuTRAP.csv


title: sample8_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L08_sample_T


title: sample4_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L04_sample_T


title: RNAseq, E2F1_sh1-1


title: RNAseq, E2F1_Control_shScr3

value: E2F1 Control


title: DBL000127

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 76


title: Brain, RNA, left, exercised, separate, biol rep2

description: countsNuTRAP.csv


title: Brain, RNA, exercised, SIT, biol rep3

description: countsNuTRAP.csv


title: DBL000183

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 81


title: RNAseq, E2F1_Control_shScr2


title: DBL000125

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 75


title: sample3_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L03_sample_T


title: sample2_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L02_sample_T


title: Brain, RNA, left, exercised, separate, biol rep1

description: countsNuTRAP.csv


title: Brain, RNA, right, exercised, separate, biol rep1

description: countsNuTRAP.csv


title: RNAseq, E2F1_Control_shScr1


title: DBL000129

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 78


title: DBL000124

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 74


title: sample1_HCC_tissue

description:
the para-cancerous tissues come from the same patients as the tumor samples.
L01_sample_T


title: DBL000123

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 73


title: Brain, RNA, sedentary, SIT, biol rep2

description: countsNuTRAP.csv


title: RNAseq, CHD6_sh2-3

value: CHD6 knockdown


title: RNA-seq-UiKOs_Gentamicin

city: guangzhou

first: huan

last: chen

address: Huangpu District

institute: Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)

data_processing:
RNA-seq reads were aligned to the hg38 using RSEM, bowtie2.
Assembly: hg38
Supplementary files format and content: TPM value

source_name: hUC

growth_protocol: hUCs were treated with cocktail medium to induce U-iIMPCs(urine cell derived intermediate mesoderm progenitor cells) from day0 to day7. Then U-iIMPCs were treated with differentiation medium to induce U-iNPCs(urine cell derived nephron progenitor cells) from day7 to day14. U-iRO(urine cell derived renal organoids) were differentiated from U-iNPCs from day14 to day 24.

extract_protocol:
Total RNA was isolated from cells using RNA-easy Isolation Reagent (Vazyme) and 1000 ng RNA were prepared for RNA libraries construction.
1000 ng RNA were prepared for RNA libraries construction. RNA libraries were established using VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme) according to the manufacturer’s protocol.

treatment_protocol: We collected samples during a three-stage process at four timepoints from different volunteers.

value: 3D hUC-derived kidney organoid Gentamicin treatment


title: Brain, RNA, sedentary, SIT, biol rep1

description: countsNuTRAP.csv

value: neuron


title: RNAseq, CHD6_sh2-2


title: RNA-seq-UiKOs_Cisplatin

value: 3D hUC-derived kidney organoid Cisplatin treatment


title: DBL000122

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 72

value: Female


title: Brain, RNA, exercised, SIT, biol rep2

description: countsNuTRAP.csv


title: RNA-seq-UiKOs_FSK

value: 3D hUC-derived kidney organoid FSK treatment


title: DBL000120

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 71


title: Brain, RNA, exercised, SIT, biol rep1

description: countsNuTRAP.csv

value: hippocampus


title: RNAseq, CHD6_sh1-3


title: DBL000119

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 70


title: RNA-seq-UiIMPLCs_P21

value: hUC-derived intermediate mesoderm progenitor like cells passage21


title: DBL000118

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 69


title: RNAseq, CHD6_sh1-2

value: Prostate


title: DBL000116

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 68


title: RNAseq, CHD6_sh1-1


title: Brain, IgG, left, sedentary, separate, biol rep1

description:
allH3k27me3sedleft.csv
allH4K8acsedleft.csv

data_processing:
Base calling, and demultiplexing was handled by the University of California, Irvine Genomics High Throughput Facility using Novaseq control software ver 1.7.5 and Real time analysis ver 3.4.4.
CUT&RUN-seq libraries were quality control checked by FastQC (0.11.9), aligned using Bowtie2 2.4.1.
CUT&RUN-seq aligned files were processed using SEACR to call peaks (FDR higher than 0.1 was considered too high for called peaks. This threshold excluded 4 samples (3 ELE H4K8ac separate isolation samples and 1 ELE H4K8ac SIT sample). Peaks were called using the stringent and 0.01 settings.), significant peaks were called using ChIPseeker 1.8.6 using TxDb.Mmusculus.UCSC.mm10.knownGene (tssRegion = c(-3000, 3000), TxDb = TxDb.Mmusculus.UCSC.mm10.knownGene, level = "transcript", assignGenomicAnnotation = TRUE, genomicAnnotationPriority = c("Promoter", "5UTR", "3UTR", "Exon", "Intron", "Downstream", "Intergenic"), annoDb = NULL, addFlankGeneInfo = FALSE, flankDistance = 5000, sameStrand = FALSE, ignoreOverlap = FALSE, ignoreUpstream = FALSE, ignoreDownstream = FALSE, overlap = "TSS", verbose = TRUE).
Assembly: GRCmm38v6
Supplementary files format and content: A table of peak calls for the CUT&RUN data sets, one file is included for each condition; bw files
Library strategy: CUT&RUN-seq

extract_protocol:
SIT isolation described by "Early life exercise primes the neural epigenome to facilitate gene expression and hippocampal memory consolidation" in Raus et al. 2022 (In Review) Preprint on Biorxiv, separate isolation described by Roh et al. 2017 Cell Rep.  "Simultaneous Transcriptional and Epigenomic Profiling from Specific Cell Types within Heterogeneous Tissues In Vivo", RNA from C57Bl6J was extracted using Qiagen RNeasy kit.
Perkin-Elmer Nextflex Rapid DNA-seq kit 2.0

value: left whole hippocampus

value: separate isolation

value: Post Natal Day 21-41 sedentary

tag: cut&run antibody

value: IgG


title: DBL000115

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 67


title: RNA-seq-UiIMPLCs_P17

value: hUC-derived intermediate mesoderm progenitor like cells passage17


title: RNAseq, CHD6_Control_shScr3

value: CHD6 Control


title: Brain, IgG, right, exercised, separate, biol rep2

description:
allH4K8acexright.csv
allH3k27me3exright.csv

value: right whole hippocampus

value: Post Natal Day 21-41 exercised


title: Brain, IgG, left, sedentary, separate, biol rep2


title: Brain, IgG, right, exercised, separate, biol rep1


title: RNAseq, CHD6_Control_shScr2


title: RNA-seq-UiIMPLCs_P5

value: hUC-derived intermediate mesoderm progenitor like cells passage5


title: RNA-seq-UiIMPLCs_P9

value: hUC-derived intermediate mesoderm progenitor like cells passage9


title: RNAseq, CHD6_Control_shScr1


title: Brain, IgG, left, exercised, separate, biol rep3

description:
allH3k27me3exleft.csv
allH4K8acexleft.csv

value: neuron


title: Brain, IgG, sedentary, SIT, biol rep3

description:
allH3k27me3sedsim.csv
allH4K8acsedsim.csv

value: whole bilateral hippocampus

value: SIT isolation


title: RNA-seq-UiIMPLCs_P1

value: hUC-derived intermediate mesoderm progenitor like cells passage1


title: DBL000113

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 65

value: Male


title: DBL000112

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 64

value: Female


title: DBL000111

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 63


title: Brain, IgG, exercised, SIT, biol rep3

description:
allH3k27me3exsim.csv
allH4K8acexsim.csv

value: hippocampus


title: d22, repair, CHX, 1

city: Ithaca

first: Joel

last: Baines

state: NY

address: Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

data_processing:
adapter trimming, genome alignment and conversion to strand-specific BigWigs using pipeline available here: https://github.com/Danko-Lab/utils/tree/master/proseq.md
normalized bedgraphs files generated by extracting read counts from the BigWig file on the HSV-1 genome using multiBigWigSummary from deepTools. Reads for each sample were scaled based on total library reads to normalize for sequencing depth.  The resulting txt file was then converted to bedgraph.
Assembly: Hg38 human genome build and HSV-1 in-house genome builds with external repeats deleted (available here: https://github.com/Baines-Lab/Public/tree/main/HSV-1)
Supplementary files format and content: library size normalized HSV-1 aligned strand-specific bedgraph files
Library strategy: PRO-Seq

growth_protocol: HEp-2 cells were maintained in DMEM supplemented with 10% NBS and pen/strep

extract_protocol:
Nuclei were extracted and nuclear run-on performed as described in: Birkenheuer and Baines 2020, Journal of Virology.
Constructed as detailed in Mahat et al. 2016. "Base-pair-resolution genome-wide mapping of active RNA Polymerases using precision nuclear run-on (PRO-seq). Nature Protocols. Aug 11(8):1455-76 doi:10.1038/nprot.2016.086

treatment_protocol: Cells were infected with HSV-1 mutant/repair at a MOI of 5 and infection allowed to proceed for 1.5 h. Timepoint indicates the time after addition of viral inoculum. For cycloheximide (CHX) treatment, 10µm of CHX was added to media for 1h prior to infection. CHX was maintained in the media during infection.

value: lung epithelial carcinoma cells

tag: time

tag: viral infection

value: HSV-1 ΔICP22 repair

tag: virus strain

value: HSV-1 F

value: Cycloheximide


title: d22, repair, CHX, 2


title: RNA-seq-UiIMPLCs_P13

value: hUC-derived intermediate mesoderm progenitor like cells passage13


title: Brain, H4K8ac, left, sedentary, separate, biol rep1

value: left whole hippocampus

value: separate isolation

value: Post Natal Day 21-41 sedentary


title: d22, repair, noCHX, 2

value: no treatment


title: Cultured human XY Testicular cells

city: TORRANCE

first: Yanhe

last: Lue

address: 1124 W. Carson St

institute: The Lundquist Institute

description: 10x Genomics

data_processing:
Mapping, cell identification, and clustering analysis were performed using 10x Cell Ranger software "software_version": "Cell Ranger 4", "format_version": 2 at the UCLA-TCGB.
Assembly: GRch38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: cloupe

source_name: testis

growth_protocol: Cryopreserved cultured testicular cells were obtained from WFIRM and revived at UCLA. Revived cells were cultured in a 25 cm2 flask with 4 ml of enriched StemPro-34 medium/flask for five days.  Cells were harvested, washed, resuspended in 0.04% BSA in PBS, and delivered to UCLA Technology Center for Genomics & Bioinformatics (TCGB).

extract_protocol:
Per manufacturer recommendations, a single cell suspension (1000 cells/µL) from each sample was loaded onto the 10x Chromium chip and controller. Ten thousand cells were targeted for capture per sample.
Cell capture and 10X single cell 3' gene expression sequence library preparation were performed. The resultant library was sequenced using a NovaSeq 6000 SP (100 Cycles).

value: testis

value: cultured testis cells

value: testis cells

value: XY


title: DBL000110

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 62

tag: Sex

tag: age

tag: bmi


title: Cultured human XXY Testicular cells

description: 10x Genomics

tag: cell type

tag: genotype

value: XXY


title: d22, repair, noCHX, 1


title: 2_HepG2

city: Bethesda

first: Ashish

last: Lal

state: Maryland

address: 37 Convent Drive, Room 6134

department: NCI

institute: NIH

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt.
Trimmed reads were aligned to the human genome (hg19) using the STAR aligner
Gene expression quantification analysis was performed for all samples using the RSEM tool
Sample specific scaling factors were calculated using DESeq2.
Normalized bigwig files were generated using BAMscale with the calculated size factors
Assembly: hg19
Supplementary files format and content: bw: normalized bigwig file
Supplementary files format and content: rsem.genes.results: raw counts quantified by RSEM

growth_protocol: HepG2 and SKHEP1 liver cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% PenStrep in a 5% CO2 atmosphere at 37°C.

extract_protocol:
RNA was harvested using RNeasy Plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Prep following manufacturer's protocols.

value: hepatocellular carcinoma

value: WT


title: DBL000114

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 66

value: Female

tag: fat mass


title: DBL000108

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 61


title: 1_SKHEP1

value: endothelial cells


title: d22, CHX, 2

value: lung epithelial carcinoma cells

value: HSV-1 ΔICP22 mutant

tag: treatment


title: Brain, H4K8ac, left, sedentary, separate, biol rep2

value: hippocampus

value: neuron

tag: tissue region

tag: isolation

tag: object location_memory_training_time


title: RNAseq, CHD6_sh2-1

tag: cell line

tag: tissue

value: Prostate

value: CHD6 knockdown


title: DBL000106

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 59

value: Male

tag: muscle mass


title: d22, CHX, 1

value: HSV-1 F

value: Cycloheximide


title: Brain, H4K8ac, right, exercised, separate, biol rep1

value: right whole hippocampus

value: separate isolation

value: Post Natal Day 21-41 exercised

tag: cut&run antibody


title: Brain, H4K8ac, right, exercised, separate, biol rep2


title: d22, noCHX, 2

tag: time

value: no treatment


title: d22, noCHX, 1

tag: viral infection


title: Brain, H4K8ac, left, exercised, separate, biol rep3

value: left whole hippocampus


title: DBL000105

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 58


title: 22_SKHEP1_PURPL_sgRNA_4_Nutlin_3

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt.
Trimmed reads were aligned to the human genome (hg38) using the STAR aligner
Gene expression quantification analysis was performed for all samples using the RSEM tool
Differentlial expression analysis was performed using DESeq2, including calculating the size factor for each sample.
Normalized bigwig files were generated with BAMscale, using the scaling factors obtained from DESeq2.
Assembly: hg38
Supplementary files format and content: bw: bigwig files  for each sample
Supplementary files format and content: Supplementary file: combined raw read counts ("RawCountFile_rsemgenes.txt")

growth_protocol: SKHEP1 CRISPRi established cell lines were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% PenStrep in a 5% CO2 atmosphere at 37°C.

treatment_protocol:
p53 induction was achieved in SKHEP1 cells with 10 μM Nutlin-3a treatment for 6 hr. DMSO was used as vehicle control.
SKEHP1 CRISPRi cells were established using two different Non-Targeting sgRNAs (NTC) or 4 sgRNAs targeting PURPL. Two biological replicates were harvested for each RNA sample.

value: CRISPRi PURPL sgRNA-4

value: 6 hr


title: 24_SKHEP1_PURPL_sgRNA_6_Nutlin_3

value: endothelial cells

value: CRISPRi PURPL sgRNA-6


title: DBL000104

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 57

value: Female


title: 21_SKHEP1_PURPL_sgRNA_2_Nutlin_3

value: CRISPRi PURPL sgRNA-2


title: Brain, H4K8ac, sedentary, SIT, biol rep3

value: hippocampus

value: neuron

value: whole bilateral hippocampus

value: SIT isolation

value: Post Natal Day 21-41 sedentary


title: DBL000103

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 56


title: DBL000102

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 55


title: Brain, H4K8ac, exercised, SIT, biol rep3


title: WT_F_3

data_processing:
adapter trimming, genome alignment and conversion to strand-specific BigWigs using pipeline available here: https://github.com/Danko-Lab/utils/tree/master/proseq.md
normalised bedgraphs files generated by extracting read counts from the BigWig file on the HSV-1 genome using multiBigWigSummary from deepTools. Reads for each sample were scaled based on drosophila spike-in reads to normalise for sequencing depth for each sequencing experiment.  The resulting txt file was then converted to bedgraph.
Assembly: Hg38 human genome build, Dm3 drosophila genome build, HSV-1 in-house genome builds with external repeats deleted (available here: https://github.com/Baines-Lab/Public/tree/main/HSV-1)
Supplementary files format and content: drosophila normalised strand-specific bedgraph files
Library strategy: PRO-Seq

growth_protocol: HEp-2 cells were maintained in DMEM supplemented with 10% NBS and pen/strep. HFF cells were maintained in  DMEM supplemented with 15% FBS and pen/strep. HEp-2 and HFF cells were maintained at 37⁰C with 5% CO2

treatment_protocol: Cells were infected with HSV-1 mutants/repairs at a MOI of 5 and infection allowed to proceed for 1.5, 3 or 6 h. Timepoints indicate the time after addition of viral inoculum. For cycloheximide (CHX) treatment, 10µm of CHX was added to media for 1h prior to infection. CHX was maintained in the media during infection.

value: lung epithelial carcinoma cells

tag: time point

tag: agent

value: infected with HSV-1 WT (F)

tag: virus strain

value: HSV-1 F


title: Brain, H3K27me3, left, sedentary, separate, biol rep1

value: separate isolation


title: WT_F_2


title: DBL000107

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 60

tag: Sex

tag: age

tag: bmi


title: WT_F_1

tag: cell type


title: DBL000101

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 54

tag: fat mass


title: 19_SKHEP1_NTC1_Nutlin_3

tag: genotype

value: CRISPRi Non-Targeting sgRNA-1

tag: treatment


title: Brain, H3K27me3, right, exercised, separate, biol rep2

tag: tissue region

value: right whole hippocampus

tag: isolation

value: Post Natal Day 21-41 exercised

tag: object location_memory_training_time


title: DBL000100

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 53

tag: muscle mass


title: d22_repair_3

tag: cell line

value: infected with HSV-1 mutant ΔICP22 repair


title: 18_SKHEP1_PURPL_sgRNA_6_Nutlin_1

value: endothelial cells

tag: time

value: 6 hr


title: Brain, H3K27me3, left, sedentary, separate, biol rep2

tag: tissue

value: left whole hippocampus

tag: cut&run antibody


title: 23_SKHEP1_PURPL_sgRNA_5_Nutlin_3

value: CRISPRi PURPL sgRNA-5


title: Brain, H3K27me3, right, exercised, separate, biol rep1

value: hippocampus


title: d22_repair_2

tag: time point

tag: agent


title: 17_SKHEP1_PURPL_sgRNA_5_Nutlin_1


title: 16_SKHEP1_PURPL_sgRNA_4_Nutlin_1

value: CRISPRi PURPL sgRNA-4


title: d22_repair_1

tag: virus strain


title: 15_SKHEP1_PURPL_sgRNA_2_Nutlin_1

value: CRISPRi PURPL sgRNA-2


title: DBL000098

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 51

tag: Sex

value: Male

tag: age


title: d22_3

tag: cell type

value: infected with HSV-1 mutant ΔICP22


title: 20_SKHEP1_NTC2_Nutlin_3

value: CRISPRi Non-Targeting sgRNA-2


title: DBL000096

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 50

value: Female

tag: bmi

tag: fat mass


title: Brain, H3K27me3, sedentary, SIT, biol rep3

value: neuron

tag: genotype

value: whole bilateral hippocampus

value: SIT isolation

tag: treatment

value: Post Natal Day 21-41 sedentary


title: 14_SKHEP1_NTC2_Nutlin_1


title: DBL000095

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 49


title: d22_2

value: lung epithelial carcinoma cells

value: HSV-1 F


title: 13_SKHEP1_NTC1_Nutlin_1

value: endothelial cells

value: CRISPRi Non-Targeting sgRNA-1


title: Brain, H3K27me3, exercised, SIT, biol rep3

tag: tissue region

tag: isolation

value: Post Natal Day 21-41 exercised


title: DBL000094

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 48

tag: muscle mass


title: d22_1

tag: cell line


title: Brain, IgG, right, sedentary, separate, biol rep3

description:
allH4K8acsedright.csv
allH3k27me3sedright.csv

value: right whole hippocampus

value: separate isolation

tag: object location_memory_training_time

value: IgG


title: 12_SKHEP1_PURPL_sgRNA_6_DMSO_3

value: CRISPRi PURPL sgRNA-6

value: DMSO

tag: time

value: 6 hr


title: n212_repair_6h_2

value: 6 h

value: infected with HSV-1 ICP0 null mutant repair

value: HSV-1 KOS


title: DBL000092

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 46

value: Male


title: n212_repair_6h_1


title: 11_SKHEP1_PURPL_sgRNA_5_DMSO_3

value: CRISPRi PURPL sgRNA-5


title: DBL000099

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 52

value: Female


title: Brain, H3K27me3, left, exercised, separate, biol rep3

tag: tissue

value: hippocampus

value: neuron

value: left whole hippocampus

tag: cut&run antibody


title: 10_SKHEP1_PURPL_sgRNA_4_DMSO_3

value: endothelial cells

value: CRISPRi PURPL sgRNA-4


title: n212_6h_2

value: lung epithelial carcinoma cells

tag: time point

tag: agent

value: infected with HSV-1 ICP0 null mutant n212


title: Brain, IgG, left, exercised, separate, biol rep2

description:
allH3k27me3exleft.csv
allH4K8acexleft.csv

value: separate isolation

value: Post Natal Day 21-41 exercised

value: IgG


title: Brain, IgG, left, exercised, separate, biol rep1


title: DBL000091

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 45

tag: Sex


title: 9_SKHEP1_PURPL_sgRNA_2_DMSO_3

value: CRISPRi PURPL sgRNA-2

value: DMSO

value: 6 hr


title: n212_6h_1

value: 6 h

tag: virus strain

value: HSV-1 KOS


title: 8_SKHEP1_NTC2_DMSO_3

tag: cell type

value: CRISPRi Non-Targeting sgRNA-2


title: DBL000089

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 43

value: Female

tag: age

tag: bmi


title: DBL000090

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 44

tag: fat mass


title: n212_repair_3h_2

value: 3 h

value: infected with HSV-1 ICP0 null mutant repair


title: Brain, IgG, exercised, SIT, biol rep4

description:
allH3k27me3exsim.csv
allH4K8acexsim.csv

value: hippocampus

value: neuron

tag: genotype

value: whole bilateral hippocampus

value: SIT isolation

tag: treatment


title: 7_SKHEP1_NTC1_DMSO_3

value: endothelial cells

value: CRISPRi Non-Targeting sgRNA-1


title: Brain, IgG, right, sedentary, separate, biol rep1

tag: tissue region

value: right whole hippocampus

tag: isolation

value: separate isolation

value: Post Natal Day 21-41 sedentary


title: DBL000088

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 42

value: Male

tag: muscle mass


title: DBL000093

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 47


title: DBL000087

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 41


title: Brain, IgG, exercised, SIT, biol rep2

description:
allH3k27me3exsim.csv
allH4K8acexsim.csv

value: Post Natal Day 21-41 exercised

tag: object location_memory_training_time

value: IgG


title: 6_SKHEP1_PURPL_sgRNA_6_DMSO_1

tag: cell line

value: CRISPRi PURPL sgRNA-6

value: DMSO

tag: time

value: 6 hr


title: n212_3h_2

value: lung epithelial carcinoma cells

value: 3 h

value: infected with HSV-1 ICP0 null mutant n212

value: HSV-1 KOS


title: n212_3h_1


title: Brain, H4K8ac, right, sedentary, separate, biol rep3

tag: tissue

value: hippocampus

value: neuron

tag: cut&run antibody


title: 4_SKHEP1_PURPL_sgRNA_4_DMSO_1

value: endothelial cells

value: CRISPRi PURPL sgRNA-4


title: DBL000085

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 39

value: Female


title: n212_repair_3h_1

tag: time point

tag: agent

value: infected with HSV-1 ICP0 null mutant repair


title: 3_SKHEP1_PURPL_sgRNA_2_DMSO_1

value: CRISPRi PURPL sgRNA-2


title: n212_repair_1.5h_2

tag: virus strain


title: Brain, IgG, exercised, SIT, biol rep1

description:
allH3k27me3exsim.csv
allH4K8acexsim.csv

tag: cell type

value: whole bilateral hippocampus

value: SIT isolation


title: DBL000084

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 38

tag: Sex

tag: age


title: 5_SKHEP1_PURPL_sgRNA_5_DMSO_1

value: CRISPRi PURPL sgRNA-5


title: Brain, H4K8ac, right, sedentary, separate, biol rep1

value: right whole hippocampus

value: separate isolation

value: Post Natal Day 21-41 sedentary


title: n212_repair_1.5h_1

value: lung epithelial carcinoma cells


title: 2_SKHEP1_NTC2_DMSO_1

value: CRISPRi Non-Targeting sgRNA-2

value: DMSO

value: 6 hr


title: n212_1.5h_2

value: infected with HSV-1 ICP0 null mutant n212

value: HSV-1 KOS


title: DBL000083

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 37

tag: bmi

tag: fat mass


title: Brain, H4K8ac, left, exercised, separate, biol rep1

value: hippocampus

value: neuron

tag: genotype

value: left whole hippocampus

tag: treatment

value: Post Natal Day 21-41 exercised


title: n212_1.5h_1


title: DBL000082

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 36

value: Female


title: DBL000081

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 35


title: DBL000086

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 40


title: n12_repair_CHX_2

value: infected with HSV-1 ICP4 null mutant repair

tag: drug treatment

value: Cycloheximide treated


title: Tubuloids FAF+Na, scRNAseq

city: Utrecht

first: Carla

last: Pou Casellas

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Read alignment software: Cell Ranger (v.6.1.2)
Data filtering steps: R Seurat package (v.4.1.0)
Assembly: GRCh38
Supplementary files format and content: comma-separated files, tab-separated files, and matrix files

source_name: Kidney Tubuloids

extract_protocol:
BME was removed by treatment with 1 mg/mL dispase II for 30 min. at 37 °C. Tubuloids were washed and dissociated using accutase at 37 °C and mechanical shearing using a flamepolished pipette. When single cells, tubuloids were washed, counted and resuspended in PBS without calcium and magnesium. -20 °C methanol was added dropwise to the samples to achieve a 80% methanol solution and then the samples were stored at -80 °C. Library preparation and sequencing were done by Single Cell Discoveries (https://www.scdiscoveries.com/).
Library preparation was performed by SingleCellDiscoveries (10x Genomics). Briefly, a pool of Gel Beads coated with barcoded primers, cells and enzymes were loaded on the 10x Genomics microfluidics chip and placed in the chromium controller. Within the chromium controller, Gel Bead-in-emulsion (GEMs) formed. Gel beads were dissolved and molecules from a single cell were captured and barcoded. Barcoded fragments were pooled, and sequencing libraries were made. After sequencing, reads were mapped back to the corresponding single cell using STAR (v. 2.6.1)

value: Kidney Tubuloids

value: WT

value: FAF+Na


title: Brain, H4K8ac, exercised, SIT, biol rep2

tag: tissue region

value: whole bilateral hippocampus

tag: isolation

value: SIT isolation


title: Tubuloids FAF+Li, scRNAseq

description: 10x Genomics

value: FAF+Li


title: DBL000080

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 34

value: Male

tag: muscle mass


title: n12_repair_CHX_1

tag: cell line

value: lung epithelial carcinoma cells


title: Brain, H4K8ac, exercised, SIT, biol rep4

tag: tissue

tag: object location_memory_training_time


title: Brain, H4K8ac, left, exercised, separate, biol rep2

value: separate isolation

tag: cut&run antibody


title: Brain, H4K8ac, exercised, SIT, biol rep1


title: Tubuloids EM, scRNAseq

description: 10x Genomics

value: EM


title: Tubuloids FAF, scRNAseq

description: 10x Genomics

value: FAF


title: DBL000077

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 32


title: DBL000079

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 33


title: n12_repair_noCHX_2

tag: time point

tag: agent

value: HSV-1 KOS

value: no treatment


title: n12_CHX_2

tag: cell type

value: infected with HSV-1 ICP4 null mutant n12

tag: virus strain


title: n12_repair_noCHX_1


title: DBL000076

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 31

tag: Sex

value: Female

tag: age


title: GCA29

city: Atlanta

first: Suresh

last: Venkateswaran

state: Georgia

address: 1760 Haygood Drive, HSRB, Room No: E-250

department: Pediatrics

institute: Emory University

description:
Single cell 5' chemistry
10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v6 (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/6.0/)
Assembly: Human reference GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Terminal ileal biopsies

extract_protocol:
Terminal ieal biopsies collected  were first minced with micro-scissors on ice in HBSS buffer containing 2mM EDTA without Ca2+/Mg2+.  The minced pieces were vortexed gently and allowed to settle for 2 min on ice.  The supernatant containing some of the loosely associated immune cells and other single cells released by the mincing process (primarily lamina propria) were removed and the sedimented minced tissue pieces were digested on ice with B. licheniformis protease for 30 minutes.  Samples were periodically vortexed gently and placed back on ice during enzymatic digestion. For each patient sample, the supernatant fraction was mixed with the enzyme digested fraction 1 : 1 for non-inflamed mucosa, and 1 : 4 for inflamed mucosa (minimizing overloading with immune cells) before being passed through a 40- and then 20-µm filter, washed and finally resuspended at the appropriate cell density for loading onto the 10X Chromium Controller (~1000-1200 cells/µL).
Tissue derived single cells were loaded onto the 10X Chromium Controller targeting 10,000 cells. Single cell capture, barcoding, GEM-RT, clean-up, cDNA amplification and library construction were performed according to the manufacturers’ instructions using Chromium Single Cell A Chip Kit (cat no: PN-1000152) and Chromium 5' Library & Gel Bead Kit (v1 chemistry; cat no: PN-1000006). Final library pools were sequenced in four batches on Illumina’s Novaseq6000 instrument at Georgia Tech Genomics Core or Yerkes Genomic Core with a targeted sequencing depth of 50,000 reads/cell.

tag: gender

tag: race

value: Asian

tag: disease status

value: Treatment-Naïve CD

value: Screening/Baseline

value: Ileal biopsies


title: DBL000075

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 30

tag: bmi

tag: fat mass


title: Brain, H3K27me3, right, sedentary, separate, biol rep1

value: hippocampus

value: neuron

tag: genotype

tag: tissue region

value: right whole hippocampus

tag: isolation

tag: treatment

value: Post Natal Day 21-41 sedentary


title: GCA27

description:
Single cell 5' chemistry
10x Genomics

value: African American

value: Established CD

tag: tissue


title: 1_SKHEP1_NTC1_DMSO_1

tag: cell line

value: endothelial cells

value: CRISPRi Non-Targeting sgRNA-1

value: DMSO

tag: time

value: 6 hr


title: GCA28

description:
Single cell 5' chemistry
10x Genomics

tag: time point


title: Brain, H4K8ac, sedentary, SIT, biol rep4

tag: cell type

value: whole bilateral hippocampus

value: SIT isolation

tag: object location_memory_training_time

tag: cut&run antibody


title: Brain, H3K27me3, sedentary, SIT, biol rep4


title: Brain, H3K27me3, left, exercised, separate, biol rep2

value: left whole hippocampus

value: separate isolation

value: Post Natal Day 21-41 exercised


title: Brain, H3K27me3, left, exercised, separate, biol rep1


title: n12_repair_HFF_2

source_name: HFF

value: HFF

value: foreskin fibroblasts

tag: agent

value: infected with HSV-1 ICP4 null mutant repair

tag: virus strain

value: HSV-1 KOS


title: DBL000074

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 29

tag: Sex

value: Male

tag: age

tag: muscle mass


title: GCA25

description:
Single cell 5' chemistry
10x Genomics

tag: gender

tag: race

value: Caucasian

tag: disease status

value: Treatment-Naïve CD

value: Screening/Baseline

value: Ileal biopsies


title: n12_noCHX_1

value: lung epithelial carcinoma cells

value: infected with HSV-1 ICP4 null mutant n12

tag: drug treatment

value: no treatment


title: DBL000073

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 28

value: Female

tag: bmi

tag: fat mass


title: Brain, H3K27me3, exercised, SIT, biol rep2

tag: tissue

value: hippocampus

value: neuron

tag: genotype

tag: tissue region

value: whole bilateral hippocampus

tag: isolation

value: SIT isolation

tag: treatment


title: n12_repair_HFF_1

tag: cell line

value: HFF

tag: cell type

tag: time point


title: Brain, H3K27me3, exercised, SIT, biol rep4

value: Post Natal Day 21-41 exercised

tag: object location_memory_training_time

tag: cut&run antibody


title: Brain, H3K27me3, right, sedentary, separate, biol rep3

value: right whole hippocampus

value: separate isolation

value: Post Natal Day 21-41 sedentary


title: GCA24

description:
Single cell 5' chemistry
10x Genomics

value: African American

tag: age

value: Established CD


title: n12_HFF_2

value: foreskin fibroblasts

tag: agent

tag: virus strain

value: HSV-1 KOS


title: Brain, H3K27me3, exercised, SIT, biol rep1


title: DBL000071

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 26

tag: Sex

value: Male

tag: muscle mass


title: Brain, IgG, sedentary, SIT, biol rep4

description:
allH3k27me3sedsim.csv
allH4K8acsedsim.csv

value: IgG


title: n12_CHX_1

value: lung epithelial carcinoma cells

value: infected with HSV-1 ICP4 null mutant n12

tag: drug treatment

value: Cycloheximide treated


title: n12_HFF_1


title: GCA26

description:
Single cell 5' chemistry
10x Genomics

tag: gender

tag: race

value: Caucasian

tag: disease status

value: Screening/Baseline

value: Ileal biopsies


title: GCA22

description:
Single cell 5' chemistry
10x Genomics

tag: tissue


title: Brain, IgG, right, sedentary, separate, biol rep2

description:
allH4K8acsedright.csv
allH3k27me3sedright.csv

value: hippocampus

value: neuron

tag: genotype

tag: tissue region

tag: isolation


title: n12_noCHX_2

tag: cell line

tag: cell type

value: no treatment


title: DBL000069

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 24

tag: bmi

tag: fat mass


title: DBL000070

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 25

value: Female

tag: age


title: DBL000068

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 23


title: n12_repair_6h_2

tag: time point

value: 6 h

tag: agent

value: infected with HSV-1 ICP4 null mutant repair


title: GCA23

description:
Single cell 5' chemistry
10x Genomics

value: Treatment-Naïve CD


title: GCA20

description:
Single cell 5' chemistry
10x Genomics

value: African American

value: Established CD


title: n12_repair_6h_1

tag: virus strain

value: HSV-1 KOS


title: DBL000066

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 21

tag: Sex

tag: muscle mass


title: Brain, IgG, left, sedentary, separate, biol rep3

description:
allH3k27me3sedleft.csv
allH4K8acsedleft.csv

value: left whole hippocampus

value: separate isolation

tag: treatment

value: Post Natal Day 21-41 sedentary

tag: object location_memory_training_time

tag: cut&run antibody

value: IgG


title: Brain, IgG, right, exercised, separate, biol rep3

description:
allH4K8acexright.csv
allH3k27me3exright.csv

tag: tissue

value: right whole hippocampus

value: Post Natal Day 21-41 exercised


title: n12_6h_2

value: lung epithelial carcinoma cells

value: infected with HSV-1 ICP4 null mutant n12


title: DBL000065

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 20


title: GCA18

description:
Single cell 5' chemistry
10x Genomics

tag: gender

value: Male

tag: race

value: Asian

tag: disease status

value: Screening/Baseline

value: Ileal biopsies


title: GCA17

description:
Single cell 5' chemistry
10x Genomics


title: GCA21

description:
Single cell 5' chemistry
10x Genomics

value: Female

value: Caucasian


title: n12_6h_1

tag: cell line

value: 6 h


title: Brain, IgG, sedentary, SIT, biol rep2

value: hippocampus

tag: cell type

value: neuron

tag: genotype

tag: tissue region

value: whole bilateral hippocampus

tag: isolation

value: SIT isolation


title: Brain, H4K8ac, right, sedentary, separate, biol rep2

value: separate isolation

value: Post Natal Day 21-41 sedentary


title: GCA19

description:
Single cell 5' chemistry
10x Genomics

tag: age

value: Treatment-Naïve CD

tag: time point


title: n12_repair_3h_2

value: 3 h

tag: agent

value: infected with HSV-1 ICP4 null mutant repair

tag: virus strain

value: HSV-1 KOS


title: Brain, IgG, sedentary, SIT, biol rep1

value: IgG


title: DBL000064

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 19

tag: Sex

tag: bmi

tag: fat mass

tag: muscle mass


title: GCA16

description:
Single cell 5' chemistry
10x Genomics

value: Male

value: Established CD

tag: tissue


title: Brain, H4K8ac, right, exercised, separate, biol rep3

value: right whole hippocampus

tag: treatment

value: Post Natal Day 21-41 exercised

tag: object location_memory_training_time

tag: cut&run antibody


title: n12_repair_3h_1

tag: cell line

value: lung epithelial carcinoma cells


title: Brain, H4K8ac, left, sedentary, separate, biol rep3

tag: cell type

value: left whole hippocampus


title: DBL000067

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 22

value: Female


title: n12_3h_2

value: infected with HSV-1 ICP4 null mutant n12


title: GCA15

description:
Single cell 5' chemistry
10x Genomics

tag: gender

tag: race

value: African American

tag: disease status

value: Not IBD

value: Screening/Baseline

value: Ileal biopsies


title: DBL000072

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 27

tag: age


title: GCA14

description:
Single cell 5' chemistry
10x Genomics

value: Asian

tag: time point


title: Brain, H4K8ac, sedentary, SIT, biol rep1

value: hippocampus

value: neuron

tag: genotype

tag: tissue region

value: whole bilateral hippocampus

tag: isolation

value: SIT isolation

value: Post Natal Day 21-41 sedentary


title: DBL000060

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 15

tag: Sex

value: Male

tag: bmi


title: GCA13

description:
Single cell 5' chemistry
10x Genomics

value: Established CD


title: DBL000062

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 17

tag: fat mass

tag: muscle mass


title: GCA12

description:
Single cell 5' chemistry
10x Genomics

tag: tissue


title: Brain, H4K8ac, sedentary, SIT, biol rep2

tag: treatment

tag: object location_memory_training_time


title: n12_repair_1.5h_2

tag: cell line

tag: agent

value: infected with HSV-1 ICP4 null mutant repair

tag: virus strain

value: HSV-1 KOS


title: GCA11

description:
Single cell 5' chemistry
10x Genomics

tag: gender

tag: race

value: Treatment-Naïve CD


title: DBL000058

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 13

value: Female

tag: age


title: DBL000063

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 18


title: DBL000059

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 14


title: n12_1.5h_2

tag: cell type

value: lung epithelial carcinoma cells

tag: time point

value: infected with HSV-1 ICP4 null mutant n12


title: Brain, H3K27me3, left, sedentary, separate, biol rep3

tag: genotype

tag: tissue region

value: left whole hippocampus

value: separate isolation

tag: cut&run antibody


title: n12_repair_1.5h_1


title: Brain, H3K27me3, right, exercised, separate, biol rep3

value: right whole hippocampus

tag: isolation

value: Post Natal Day 21-41 exercised


title: GCA10

description:
Single cell 5' chemistry
10x Genomics

value: Caucasian

tag: disease status

value: Not IBD

value: Screening/Baseline

value: Ileal biopsies


title: DBL000057

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 12

tag: Sex

tag: bmi

tag: fat mass

tag: muscle mass


title: HeLa-cas9 cells 'Unsorted' ataxin-2 with Actin control 2

first: Garam

last: Kim

address: 279 Campus Dr

department: Genetics

description:
DNA - integrated sgRNA sequence
Unsorted population of cells (ataxin-2 expressors relative to Actin)
combo_Unsorted_Actin_rep1_vs_Top_Actin_rep1_VS_Unsorted_Actin_rep2_vs_Top_Actin_rep2.csv
combo_Unsorted_Actin_rep1_vs_Bottom_Actin_rep1_VS_Unsorted_Actin_rep2_vs_Bottom_Actin_rep2.csv

data_processing:
CRISPR screen analysis
illumina basecalling
casTLE normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_CRISPR.sh
comma separated value text files with normalized abundance measurements and differential representation (output from casTLE)

source_name: HeLa (ATCC)

growth_protocol: HeLa-cas9 cells were infected with a genome-wide knockout sgRNA sublibrary were grown in 150mm plates. Cells were maintained for 7 days at 1000× coverage (~1000 cells containing each sgRNA).

extract_protocol:
Genomic DNA was extracted for all screen populations separately according to the protocol included with QIAGEN Blood Maxi Kit.
sgRNA sequences were amplified and prepared for deep-sequencing by two sequential PCR reactions as described previously (Morgens et al., 2016).

treatment_protocol: ~400 million HeLa-cas9 cells were trypsinized and pooled together, after which the screen was conducted.

tag: treatment

value: Control


title: GCA9

description:
Single cell 5' chemistry
10x Genomics

value: Male

value: African American

tag: tissue


title: Brain, H3K27me3, sedentary, SIT, biol rep2

value: hippocampus

value: neuron

value: whole bilateral hippocampus

value: SIT isolation

value: Post Natal Day 21-41 sedentary

tag: object location_memory_training_time


title: Brain, H3K27me3, right, sedentary, separate, biol rep2


title: n12_3h_1

tag: cell line

value: lung epithelial carcinoma cells

value: 3 h

tag: agent

value: infected with HSV-1 ICP4 null mutant n12

tag: virus strain

value: HSV-1 KOS


title: Brain, H3K27me3, sedentary, SIT, biol rep1

tag: cell type


title: GCA8

description:
Single cell 5' chemistry
10x Genomics

tag: gender

tag: race

tag: age

tag: time point


title: HeLa-cas9 cells 'Unsorted' ataxin-2 with Actin control 1


title: GCA7

description:
Single cell 5' chemistry
10x Genomics

value: Female


title: DBL000056

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 11


title: DBL000055

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 10


title: n12_1.5h_1


title: DBL000054

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 9


title: GCA5

description:
Single cell 5' chemistry
10x Genomics

value: Established CD


title: DBL000053

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 8


title: HeLa-cas9 cells 'Bottom 20%' ataxin-2 with Actin control 1

description:
DNA - integrated sgRNA sequence
FACS sorted for bottom 20% of ataxin-2 expressors relative to Actin
combo_Unsorted_Actin_rep1_vs_Bottom_Actin_rep1_VS_Unsorted_Actin_rep2_vs_Bottom_Actin_rep2.csv

value: Bottom 20% of ataxin-2 expressors


title: GCA3

description:
Single cell 5' chemistry
10x Genomics

value: Caucasian

value: Screening/Baseline


title: HeLa-cas9 cells 'Bottom 20%' ataxin-2 with Actin control 2


title: GCA2

description:
Single cell 5' chemistry
10x Genomics

value: Treatment-Naïve CD

value: Ileal biopsies


title: 18in_biorep3

city: Aurora

first: Victor

middle: A

last: Ruthig

state: CO

department: Pediatrics, Section of Developmental Biology

institute: University of Colorado Anschutz Medical Campus

description:
Supp_ScriptFull.txt
DND1seq__Supp_DND1seqFilters.RData
DND1seq_Supp_Dnd1Terseq_Unique.csv
DND1seq_Supp_GCList_Junique.csv
DND1seq_Supp_GCList_Lunique.csv
DND1seq_Supp_GCList_T_Iunique.csv
DND1seq_Supp_GCList_T_T1unique.csv
DND1seq_Supp_GO-0000077(DNAdamage).csv
DND1seq_Supp_GO-0003723(RNAbinding).csv
DND1seq_Supp_GO-0006119(OxidativePhosphorylation).csv
DND1seq_Supp_GO-0006412(Translation).csv
DND1seq_Supp_GO-0007010(CytoOrg).csv
DND1seq_Supp_GO-0007049(CellCycle).csv
DND1seq_Supp_GO-0016570(HistoneModification).csv
DND1seq_Supp_GO-0030198(ECMorg).csv
DND1seq_Supp_GO-0033182(HistUbi).csv
DND1seq_Supp_GO-0044391(RibosomalSubunit).csv
DND1seq_Supp_GO-0045786(NegCellCycle).csv
DND1seq_Supp_GO-0045787(PosCellCycle).csv
DND1seq_Supp_GO-0048193(Golgi).csv
DND1seq_Supp_GO-0051276(ChroOrg).csv
DND1seq_Supp_GO-0061621(CanonicalGlycolysis).csv
DND1seq_Supp_GO-0071103(DNAconCha).csv
DND1seq_Supp_GO-1902275(RchrOrg).csv
DND1seq_Supp_lohiGeneList.csv
DND1seq_Supp_RIPgeneList.csv
DND1seq_Supp_SomaList_Junique.csv
DND1seq_Supp_SomaList_Sunique.csv
DND1seq_Supp_SomaList_Tunique.csv
Proc_DND1seq_Filtering.xlsx
RIPseq_Supp_DND1-GFP_RIP-seq.RData
RIPseq_Supp_MGIBatchReport_RIP.csv
Proc_RIPseq_ripRNAseqMaster.xlsx

data_processing:
Basecalling performed on Illumina NovaSeq 6000 as 50bp paired-end reads
Reads mapped to the mm10 (GRCm38) mouse genome using Salmon (v1.3.0)
Mapped reads annotated using the Ensemble Mus musculus reference (version 79)
Differential gene expression analysis performed using DeSeq2 (v1.32.0)
Further annnotation and filtering was performed in RSQLite (v2.2.8)
Genome_build: GRCm38
Supplementary_files_format_and_content: intermediate and supporting files, including full pipeline script and Rdata environment, final output as excel file with TPM and differential expression values for each sample

source_name: Male Germ Cells

extract_protocol:
RIP-seq was performed as described in (Nicholson et al., 2017). Testes were collected from DND1(EGFP/EGFP) fetuses at E14.5, E16.5, and E18.5, testes were disassociated, cells were lysed in PLB (poly lysis buffer), DND1-GFP bound to transcript was immunoprecipitated using GFP-Trap magnetic agarose beads (ChromoTek, catalog #gtma-20), total RNA from input and immunoprecipitate was extracted using Qiagen RNeasy Micro Kit (Qiagen #74004)
Sample libraries were prepared with SMART-SeqRTM v4 UltraRTM Low Input RNA Kit (Takara Clontech Kit Cat# 63488).

tag: strain background

value: CD1 hybrid

tag: allele

tag: developmental stage


title: 18IP_biorep3

tag: molecule subtype

value: immunoprecipiated RNA


title: 18IP_biorep2


title: DBL000052

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 7

tag: Sex

value: Male

tag: bmi

tag: fat mass


title: DBL000051

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 6

tag: muscle mass


title: DBL000061

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 16


title: GCA1

description:
Single cell 5' chemistry
10x Genomics

value: African American

tag: disease status

value: Not IBD

tag: tissue


title: HeLa-cas9 cells 'Top 20%' ataxin-2 with Actin control 2

description:
DNA - integrated sgRNA sequence
FACS sorted for top 20% of ataxin-2  expressors relative to Actin
combo_Unsorted_Actin_rep1_vs_Top_Actin_rep1_VS_Unsorted_Actin_rep2_vs_Top_Actin_rep2.csv

tag: treatment

value: Top 20% of ataxin-2 expressors


title: DBL000050

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 5


title: HeLa-cas9 cells 'Unsorted' ataxin-2 with GAPDH control 2

description:
DNA - integrated sgRNA sequence
Unsorted population of cells (ataxin-2 expressors relative to GAPDH)
combo_Unsorted_GAPDH_rep1_vs_Top_GAPDH_rep1_VS_Unsorted_GAPDH_rep2_vs_Top_GAPDH_rep2.csv
combo_Unsorted_GAPDH_rep1_vs_Bottom_GAPDH_rep1_VS_Unsorted_GAPDH_rep2_vs_Bottom_GAPDH_rep2.csv

value: Control


title: DBL000049

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 4


title: 10XscRNA-seq-UiRO_3D

data_processing:
scRNA-seq reads were aligned to the hg38 using STAR, then preprocessed with scanpy and Seurat
Assembly: hg38
Supplementary files format and content: barcode, genes and matrix files

growth_protocol: hUCs were treated with cocktail medium to induce U-iIMPCs(urine cell derived intermediate mesoderm progenitor cells) from day0 to day7. Then U-iIMPCs were treated with differentiation medium to induce U-iNPCs(urine cell derived nephron progenitor cells) from day7 to day14. To generate 3D kidney organoids, the colonies were picked and re-aggregated into bigger cell clusters with 5-10 colonies per organoid using round bottom ultra-low attachment 96-well plates (Corning) at day 14. After aggregation for 24 hours, 3D kidney organoids were transferred onto the upper chamber of Transwell (Corning) for liquid-air interface culture, with daily media change was performed at the bottom chamber until day 24.

extract_protocol:
A minimum of 10000 dissociated cells were loaded per well using the Fluidigm C1 Single Cell Auto Pre System for single cell capture.
single-cell RNA-seq library was prepared with Single Cell 3’ Reagent Kits v3(10x Genomics).

treatment_protocol: Day 24 kidney organoids were dissociated into single cells with Accutase, followed by passing through a 40 mm filter thrice to remove cell clumps. Dissociated cells were subsequently stained with trypan blue and confirmed to have at least 80% viability.

value: hUC-derived 3D renal organoids


title: HeLa-cas9 cells 'Bottom 20%' ataxin-2 with GAPDH control 2

description:
DNA - integrated sgRNA sequence
FACS sorted for bottom 20% of ataxin-2 expressors relative to GAPDH
combo_Unsorted_GAPDH_rep1_vs_Bottom_GAPDH_rep1_VS_Unsorted_GAPDH_rep2_vs_Bottom_GAPDH_rep2.csv


title: DBL000047

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 3

data_processing: Results were analyzed using TaqMan Genotyper software.


title: 18in_biorep1


title: RNA-seq-UiRO_2

value: hUC-derived 2D renal organoids


title: 10XscRNA-seq-UiRO_2D


title: 16IP_biorep3


title: HeLa-cas9 cells 'Bottom 20%' ataxin-2 with GAPDH control 1


title: HeLa-cas9 cells 'Top 20%' ataxin-2 with GAPDH control 2

description:
DNA - integrated sgRNA sequence
FACS sorted for top 20% of ataxin-2 expressors relative to GAPDH
combo_Unsorted_GAPDH_rep1_vs_Top_GAPDH_rep1_VS_Unsorted_GAPDH_rep2_vs_Top_GAPDH_rep2.csv


title: 16in_biorep3


title: HeLa-cas9 cells 'Top 20%' ataxin-2 with Actin control 1


title: 18in_biorep2


title: 16IP_biorep2


title: HeLa-cas9 cells 'Unsorted' ataxin-2 with GAPDH control 1


title: RNA-seq-UiIMPC

value: hUC-derived intermediate mesoderm progenitor cells


title: RNA-seq-UiNPC

value: hUC-derived nephron progenitor cells


title: DBL000045

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 1

value: Female


title: HeLa-cas9 cells 'Top 20%' ataxin-2 with GAPDH control 1


title: 18IP_biorep1


title: gat201, LIT, rep3 [GAT201-LIT-3]

city: Seoul

first: Yong-Sun

last: Bahn

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

department: Department of Biotechnology

country: South Korea

institute: Yonsei university

data_processing:
The adapter sequences were trimmed from the sequencing reads by using Cutadpat v3.4 with Python 3.7.4. The reference genome sequence of C. neoformans H99 and annotation data were downloaded from the NCBI FTP server, derived from Broad Insitute.
The reads were aligned to the C. neoformans H99 genome sequence using Hisat2 v2.2.1 with the HISAT and Bowtie2 algorithm and processed as previously reported. Hisat2 was performed with “-p 30” and “– dta -1” options and other parameters set as default. Aligned reads were converted and then sorted by Samtools v1.9 with the “-Sb -@ 8” option for converting, and “-@ 20 –m 2000000000” option for sorting, and the other parameters were set as default.
Transcript assembly and abundance estimation were performed using Stringtie v2.1.1 by using the “-p 12” option, and also the “-B” option to run the Ballgown analysis. Assembled transcripts were merged to a single GTF ﬁle, and the relative transcript abundances were calculated via Fragments Per Kilobase of exon per Million fragments mapped (FPKM). The FPKM and read count matrix were generated by the R package “isoformswitchanalyzerR” and analyzed by DESeq2. Differentially expressed genes (DEG) analysis was performed using DESeq2 v1.24.0 with default sets with the Ballgown
The volcano plot was illustrated by using R v4.1.0 and R package "EnhancedVolcano", with the cutoff (more than two-fold changes with p< 0.05). PCA plot was generated by R package "DeBrowser" and heatmap was also generated by following R package
KEGG pathway analysis was performed using the R package "Cluster profiler", after changing H99S gene locus ID to JEC21 orthologue locus ID.
Assembly: Cryptococcus neoformans var. grubii H99 GCA_000149245.3 CNA3
Supplementary files format and content: tab-delimited excel files include gene counts for each Sample
Supplementary files format and content: tab-delimited excel files include DEG analysis value for each Sample

organism: Cryptococcus neoformans

growth_protocol: Cryptococcus neoformans strains were grown at 30°C for 16hr in a YPD medium and transferred to 50 mL of fresh YPD medium and incubated at 30°C until the OD600 reached 0.8.

extract_protocol:
Then the cells were harvested by centrifugation and lyophilized. Total RNAs were prepared as described above and purified with RNeasy Mini Kit (QIAGEN). The concentration was measured by Quant-IT RiboGreen (Invitrogen).
The quality of the RNA was verified by the TapeStation RNA screentape (Agilent). Cultured samples were prepared independently three times, and the cDNA library was constructed with the 1 µg of total RNAs for each sample by Illumina TruSeq mRNA library kit (Illumina) and sequenced by the Illumina platform.

treatment_protocol: Half of the cells were further incubated in an LIT liquid medium for 2hr

tag: cell line

value: Fungi

tag: genotype

value: gat201 knockout

value: capsule-inducing condition


title: RNA-seq-hUC

tag: cell type

value: hUC


title: 16in_biorep1


title: Chow diet 3

city: Créteil

first: Fred

last: Relaix

address: 8 rue du Général Sarrail

country: France

institute: INSERM U955 Université Paris-Est Créteil

data_processing:
usegalaxy.org
Sequence reads were trimmed for adaptor sequences using FASTQ GROOMER
Trimmed sequence reads were mapped to GrCM38/mm10 using Bowtie2
Read count extraction and normalization were performed using featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Muscle

growth_protocol: A minimum of 50 x 10^3 MuSCs per replicate were isolated by FACS.

extract_protocol:
Cells were washed with cold PBS and RNA was extracted using the Machery Nagel Nucleospin RNA Mini kit for RNA purification (Ref: 740955.50) following manufacturer’s instructions. RNA yield was measured using the Qubit Hs RNA assays (Invitrogen. Ref: Q32852) on a QubitTM 3.0 fluorometer (Thermo Fischer Scientific). RNA quality was assessed using the Tapestation 4200 with High Sensitivity RNA screentape (all from Agilent) by the RNA integrity number (RIN) algorithm. Samples with a RIN between 8.5 and 9.4 were used for library preparation.
Libraries were prepared using the Ovation® solo RNA-Seq system mouse (Tecan. Ref: 0501), with ribosomal RNA depletion and double indexing following the manufacturer’s instructions. Next generation sequencing was performed using the NextSeq 500/550 High Output Kit v2.5 (Illumina. Ref: 20024906) on the NextSeq500 system (Illumina). Runs were carried out over 75 cycles, to obtain 75-bp single reads. Illumina Pipeline software, Casava version 1.9 was used to process the sequencing data.

value: Muscle

value: satellite

value: WT

value: Chow diet


title: 16IP_biorep1

value: CD1 hybrid

value: immunoprecipiated RNA


title: 16in_biorep2


title: DBL000046

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 2

source_name: Peripheral blood

extract_protocol: Genomic DNA from peripheral blood was extracted using the QIAamp DNA Blood Mini Kit (Qiagen Sciences, Inc, Germantown, MD, USA)


title: Chow diet 1


title: ATAC-seq-UiNPC_L

data_processing:
ATAC-seq reads were aligned to the hg38 using bowtie2, then get bigwig file with bamCoverage
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: hUCs were treated with cocktail medium to induce U-iIMPCs(urine cell derived intermediate mesoderm progenitor cells) from day0 to day7. Then U-iIMPCs were treated with differentiation medium to induce U-iNPCs(urine cell derived nephron progenitor cells) from day7 to day14. 2D U-iRO(urine cell derived renal organoid) were differentiated from U-iNPCs from day14 to day 24.

extract_protocol:
A total of 50,000-80,000 cell pellets were re-suspended in 50 μL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) IGEPAL CA-630).
Then the suspension was subjected to transposition reaction and purification with MinElute Kit (QIAGEN). After PCR amplification of transposed DNA fragments, the amplified libraries were purified using a Qiaquick PCR (QIAGEN) column. Then, purified libraries were assessed by gel electrophoresis and Qsep100 (Bioptic).

treatment_protocol: We collected samples during a three-stage process at four timepoints(hUCs at day0, U-iIMPCs at day9, early U-iNPCs at d16 and late U-iNPCs at d19) from UC-001#

value: hUC-derived nephron progenitor cells-D19


title: RNA-seq-UiRO


title: gat201, basal, rep3 [GAT201-Basal-3]

value: basal


title: Chow diet 2


title: ATAC-seq-UiNPC_E

value: hUC-derived nephron progenitor cells-D16


title: 14in_biorep3


title: gat201, basal, rep2 [GAT201-Basal-2]


title: ATAC-seq-UiIMPC


title: High fat diet 2

value: High fat diet


title: High fat diet 3


title: 14IP_biorep2


title: ATAC-seq-hUC


title: gat201, basal, rep1 [GAT201-Basal-1]


title: High fat diet 1


title: bzp4, LIT, rep3 [bzp4_LIT_2hr_3]

value: bzp4 knockout


title: 14in_biorep2


title: HeLa ATP6V1A siRNA rep3

city: Stanford

institute: Stanford University

description:
ATP6V1A siRNA SMARTPool (Horizon Discovery) for 72h
NT-Control_vs_ATP6V1A-Experiment-ExpDiff.csv

data_processing:
illumina basecalling
STAR alignment
RSEM counts
DESeq2 normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_RNAseq.sh
Genome_build: hg38 for human samples, mm10 for mouse samples
Supplementary_files_format_and_content: comma separated value text files with normalized abundance measurements (output from DESeq2)

extract_protocol:
RNA extracted using a PureLink RNA Mini Kit (Ambion)
polyA enriched mRNA libraries (SureSelect Automated Strand-Specific RNA Library Prep, mRNA Library Prep for Illumina Paired-End Multiplexed Sequencing)

treatment_protocol: HeLa cells were reverse transfected with non-targeting or ATP6V1A-targeting siRNAs in 12-well plates. Cells were lysed after 72 hours.

value: ATP6V1A siRNA


title: H3K4ME3 Normoxia Sample 2

city: Cologne

first: Peter

last: Tessarz

state: Nordrhein-Westfalen

address: Joseph-Stelzman-Str 9b

country: Germany

institute: Max Planck Institute

description:
H3K4ME3_N2
H3K4me3-Normoxia_peaks.bed

data_processing:
fastq reads were mapped to mm10 genome using bowtie2 and duplicates were then removed using MarkDuplicates program of Picard Tools.
The peaks were then called using chromstaR in differential mode.
Assembly: mm10
Supplementary files format and content: Tab-separated text file of peaks called by chromstaR.

source_name: cell culture

growth_protocol: Bone-marrow MSCs were cultured in T25 flasks under humidified conditions in hypoxia (2% O2, 5% CO2, 37°C) or normoxia (21% O2, 5% CO2, 37°C). Cells were cultured in control α-MEM medium. On day 3 of cell culture the medium was changed,  on day 5 cells  were passaged, using Trypsin-EDTA. On day 12, FACS was used to isolated purified MSCs.

extract_protocol:
ChIP-seq was performed as described previously (Tessarz et al., 2014), using 105 MSCs per IP.
Following DNA purification libraries were prepared using Nextera PCR primers and the NEBNext High-Fidelity PCR Master Mix. Libraries were PCR amplified. DNA concentration of the libraries was measured with Qubit and library quality was assessed by running samples on the TapeStation.

value: 3-5 months

tag: oxygen level

value: Bone-marrow MSCs


title: bzp4, LIT, rep2 [bzp4_LIT_2hr_2]

value: Fungi


title: Input Normoxia Sample 2

description:
Input_N2
none

tag: age


title: 14IP_biorep1


title: gat201, LIT, rep1 [GAT201-LIT-1]

value: gat201 knockout

value: capsule-inducing condition


title: 14in_biorep1


title: HeLa ATP6V1A siRNA rep2


title: bzp4, LIT, rep1 [bzp4_LIT_2hr_1]


title: HeLa ATP6V1A siRNA rep1


title: 14IP_biorep3


title: H3K27AC Normoxia Sample 2

description:
H3K27AC_N2
H3K27ac-Normoxia_peaks.bed


title: bzp4, basal, rep3 [bzp4_basal_3]


title: HeLa non-targeting siRNA rep3

description:
non-targeting siRNA SMARTPool (Horizon Discovery) for 72h
NT-Control_vs_ATP6V1A-Experiment-ExpDiff.csv

value: Control


title: bzp4, basal, rep2 [bzp4_basal_2]


title: 18lo_biorep4

description:
Supp_ScriptFull.txt
DND1seq__Supp_DND1seqFilters.RData
DND1seq_Supp_Dnd1Terseq_Unique.csv
DND1seq_Supp_GCList_Junique.csv
DND1seq_Supp_GCList_Lunique.csv
DND1seq_Supp_GCList_T_Iunique.csv
DND1seq_Supp_GCList_T_T1unique.csv
DND1seq_Supp_GO-0000077(DNAdamage).csv
DND1seq_Supp_GO-0003723(RNAbinding).csv
DND1seq_Supp_GO-0006119(OxidativePhosphorylation).csv
DND1seq_Supp_GO-0006412(Translation).csv
DND1seq_Supp_GO-0007010(CytoOrg).csv
DND1seq_Supp_GO-0007049(CellCycle).csv
DND1seq_Supp_GO-0016570(HistoneModification).csv
DND1seq_Supp_GO-0030198(ECMorg).csv
DND1seq_Supp_GO-0033182(HistUbi).csv
DND1seq_Supp_GO-0044391(RibosomalSubunit).csv
DND1seq_Supp_GO-0045786(NegCellCycle).csv
DND1seq_Supp_GO-0045787(PosCellCycle).csv
DND1seq_Supp_GO-0048193(Golgi).csv
DND1seq_Supp_GO-0051276(ChroOrg).csv
DND1seq_Supp_GO-0061621(CanonicalGlycolysis).csv
DND1seq_Supp_GO-0071103(DNAconCha).csv
DND1seq_Supp_GO-1902275(RchrOrg).csv
DND1seq_Supp_lohiGeneList.csv
DND1seq_Supp_RIPgeneList.csv
DND1seq_Supp_SomaList_Junique.csv
DND1seq_Supp_SomaList_Sunique.csv
DND1seq_Supp_SomaList_Tunique.csv
Proc_DND1seq_Filtering.xlsx
hiloRNAseq_Supp_DND1-GFP_hiloRNA-seq.RData
hiloRNAseq_Supp_MGIBatchReport_hilo.csv
Proc_hiloRNAseq_hiloRNAseqMaster.xlsx

extract_protocol:
Testes were collected from DND1(EGFP/EGFP) fetuses at E16.5 and E18.5, testes were disassociated, male germ cells were sorted as DND1-lo and DND1-hi using FACS for GFP, total RNA was extracted using Qiagen RNeasy Micro Kit (Qiagen #74004)
Sample libraries were prepared with SMART-SeqRTM v4 UltraRTM Low Input RNA Kit (Takara Clontech Kit Cat# 63488).


title: H3K4ME3 Normoxia Sample 1

description:
H3K4ME3_N1
H3K4me3-Normoxia_peaks.bed


title: 18hi_biorep4


title: Input Normoxia Sample 1

description:
Input_N1
none


title: HeLa non-targeting siRNA rep2


title: H3K27AC Normoxia Sample 1

description:
H3K27AC_N1
H3K27ac-Normoxia_peaks.bed


title: bzp4, basal, rep1 [bzp4_basal_1]


title: HeLa non-targeting siRNA rep1


title: ada2, LIT, rep3 [ADA2-LIT-3]

value: ada2 knockout


title: 18hi_biorep3