title: Topo1cc_KCl_30min

city: La Jolla

first: Yuliang

last: Tan

state: California

address: Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648

department: School of Medicine

institute: University of California, San Diego

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Basecalls performed using CASAVA version 1.4
Reads were aligned to the mm10 genome assembly using Bowtie version 2.0.1.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph, bed

source_name: E15.5 C57BL/6 embryonic mouse cortices

growth_protocol: Neurons were grown in neuronal medium consisting of Neurobasal medium containing B27 supplement (2%; Thermo Fisher), penicillin-streptomycin (50 g/mL) and Glutamax (1x; Thermo Fisher). Neurons were subsequently plated and placed in a cell culture incubator that maintained a temperature of 37 °C and a CO2 concentration of 5%. Ten minutes after plating neurons, the medium was completely aspirated from cells and replaced with fresh warm neuronal medium. Neurons were grown in vitro until Day7.

extract_protocol:
CUT&RUN was performed using CUTANA™ CUT&RUN Protocol [www.epicypher.com] which is an optimized version of that previously described. For each sample, 5x105 cells were immobilized onto Concanavalin-A beads (EpiCypher #21-1401) and incubated overnight (4ºC with gentle rocking) with 0.5 µg of antibody.
CUT&RUN enriched DNA was purified, and 10 ng used to prepare sequencing libraries with the KAPA HTP/LTP Library Preparation Kits

treatment_protocol: For CUT&RUN experiments, mouse cortical neurons were plated at an approximate density of 2 × 10^6 on 35-mm dishes. Neurons were plated in 2 mL neuronal medium. One ml of the medium was replaced with 1 ml fresh warm medium on Day3 and Day6. Prior to KCl depolarization, neurons were silenced with 1 μM tetrodotoxin on Day6 (TTX; Fisher). Neurons were subsequently stimulated on Day7 by adding warmed KCl depolarization buffer (170 mM KCl, 2 mM CaCl2, 1 mM MgCl2 and 10 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES)) directly to the neuronal culture to a final concentration of 31% in the neuronal culture medium within the culture plate or well for the indicated time.

tag: age

tag: cell type

value: primary corticol neurons

tag: antibody used for cut&run

value: TopoGEN TG2017-2 (Lot# 17AG15)


title: Topo1cc_KCl_30min_exp2

status: Public on Aug 04 2022

type: SRA

country: USA

molecule: genomic DNA

organism: Mus musculus

tag: strain


title: Methylation_EPIC_sample279

type: genomic

city: Ann Arbor

first: Lulu

last: Shang

state: Michigan

address: 1415 Washington Heights

department: Biostatistics

institute: University of Michigan

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to IIllumina Infinium HumanMethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: For each chip, the Minfi R package was used to perform background correction and normalization. The regression on correlated probes (RCP) method was then used to adjust probe-type bias.

label: Cy5 and Cy3

organism: Homo sapiens

source_name: peripheral blood leukocytes

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from stored peripheral blood leukocytes using AutoGen FlexStar (AutoGen, Holliston, MA) and DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA)

tag: race

value: African American (AA)

tag: gender

value: F

tag: age(yrs)

tag: plate

tag: column

tag: row

tag: pedigreeid

tag: subjectid

tag: phase


title: Methylation_EPIC_sample278

value: M

value: E


title: Topo1cc_KCl_0min


title: Methylation_EPIC_sample277

value: H


title: Topo1cc_KCl_0min_exp2


title: Methylation_EPIC_sample292


title: Topo1cc_KCl_15min


title: PolII_KCl_60min

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to the mm10 genome assembly using Bowtie2.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

extract_protocol:
Cells were cross-linked with 1% formaldehyde at room temperature for 10 min. And then the cross-linking was quenched with 0.125M glycine for 5 min. Chromatin was fragmented using a Bioruptor® Pico (Diagenode) for 10 min at high power, with an interval of 30 s between pulses to get around 200bp fragments and precleared using 20 μl Protein G Dynabeads (Life Technologies, Cat# 10009D). Subsequently, the soluble chromatin was incubated with 2-5 μg antibodies at 4°C overnight. Immunoprecipitated complexes were collected using 30 μl Protein G Dynabeads, which have been saturated with PBS/1% BSA over night at 4°C, per reaction. For all ChIPs, after de-crosslinking overnight at 65°C, final ChIP DNA was extracted and purified using QIAquick spin columns (QIAGEN).
The libraries were constructed following Illumina’s Chip-Seq Sample prep kit.

treatment_protocol: For ChIP-seq experiments, mouse cortical neurons were plated at an approximate density of 2 × 10^6 on 35-mm dishes. Neurons were plated in 2 mL neuronal medium. One ml of the medium was replaced with 1 ml fresh warm medium on Day3 and Day6. Prior to KCl depolarization, neurons were silenced with 1 μM tetrodotoxin on Day6 (TTX; Fisher). Neurons were subsequently stimulated on Day7 by adding warmed KCl depolarization buffer (170 mM KCl, 2 mM CaCl2, 1 mM MgCl2 and 10 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES)) directly to the neuronal culture to a final concentration of 31% in the neuronal culture medium within the culture plate or well for the indicated time.

tag: chip antibody used for chip


title: Methylation_EPIC_sample276

value: G


title: Methylation_EPIC_sample275


title: PolII_KCl_180min_exp2


title: PolII_KCl_30min


title: Methylation_EPIC_sample273


title: Methylation_EPIC_sample274

value: C


title: PolII_KCl_15min


title: Methylation_EPIC_sample272


title: PolII_KCl_0min


title: Methylation_EPIC_sample271

value: D


title: Methylation_EPIC_sample284


title: PolII_KCl_0min_exp2


title: Methylation_EPIC_sample270

value: A


title: Ku70_KCl_30min


title: Ku70_KCl_15min


title: Ku70_KCl_30min_exp2


title: Methylation_EPIC_sample269


title: Methylation_EPIC_sample268


title: Methylation_EPIC_sample267


title: Ku70_KCl_0min_exp2


title: Ku70_KCl_0min


title: Methylation_EPIC_sample265


title: Methylation_EPIC_sample264


title: HP1g_KCl_30min_exp2


title: Methylation_EPIC_sample266


title: Methylation_EPIC_sample263

value: B


title: Methylation_EPIC_sample262


title: HP1g_KCl_15min


title: Methylation_EPIC_sample261


title: Methylation_EPIC_sample260


title: H3K27ac_KCl_60min


title: HP1g_KCl_0min_exp2


title: HP1g_KCl_0min


title: Methylation_EPIC_sample258


title: H3K27ac_KCl_30min


title: H3K27ac_KCl_0min


title: Methylation_EPIC_sample257


title: Methylation_EPIC_sample256


title: H3K27ac_KCl_15min


title: Methylation_EPIC_sample259


title: Sample_RNA-Lib_Act-Aac11-IR

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

description: Illumina Hiseq 2000

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
Cluster generation was performed with Illumina TruSeq cluster kit v2-cBot-HS
Single-read 50 bp sequencing was completed with Illumina TruSeq SBS kit v3-HS.
Reads were aligned using Tophat2 v2.0.12
RPKM expression values from different conditions were extracted and compared by cuffdiff v2.2.1 using Refseq gene models [2].
Assembly: dm6 Drosophila
Supplementary files format and content: FPKM for each gene and each sample, first row indicate sample name and first column indicate gene symbol

molecule: total RNA

organism: Drosophila melanogaster

source_name: Larval wing disc cells

growth_protocol: Drosophila of the relevant genotypes were cultured under standard conditions at 25 degrees Celsius in humidity-controlled incubators with 12hr light:dark cycles

extract_protocol:
Wandering stage (L3 instar) larvae were sorted for GFP expression under a dissecting microscope equipped with a Zeiss HBO lamp and a GFP filter. Larvae were rinsed in 1x PBS and then  immediately ground and  dissolved in Trizol (TM) kept on ice. Tissue+Trizol mixtures were frozen at -80 degrees Celsius. This was repeated until 10-20 larvae per genotype (Act>Aac11-RNAi or Act>control) had been collected. Samples were then pooled within genotypes as needed, and total RNA was extracted according the manufacturer's instructions and depleted for rRNA prior to analysis.
4 µg of total RNA was rRNA depleted and utilized for library construction with the Illumina TruSeq RNA Sample Preparation Kit v2 following the manufacturer's instructions. Libraries were sequenced with an Illumina HiScan platform.

value: Larval wing disc cells


title: Methylation_EPIC_sample255


title: Methylation_EPIC_sample254


title: HP1g_KCl_30min


title: Sample_RNA-Lib_Act

description: Illumina Hiseq 2000


title: Methylation_EPIC_sample253


title: Methylation_EPIC_sample252


title: Methylation_450k_sample415

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to IIllumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol


title: Methylation_450k_sample417


title: Methylation_450k_sample414


title: Methylation_EPIC_sample250


title: Methylation_450k_sample413


title: low fat diet fed - SVF-SW3 single

first: Olivia

last: Osborn

state: CA

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

description:
low fat diet fed - SVF-SW3
SVF  SW-3

data_processing:
Reads generated by the sequencer (PE 100) were first mapped to the mouse transcriptome using Bowtie2  algorithm.
Reads counted as reads per gene using RSEM and then analyzed using the statistical algorithm limma
Genes were then sorted by their posterior error probability (also called local false discovery rate, (lfdr)) in a three-way comparisons between conditions LFD, HFD and SWD. In order to detect genes significantly changed by HFD diet that do not revert to their LFD levels after switch (irreversible genes), we look for genes for which the expression (HFD-LFD) - (SWD-HFD) is significantly different from zero.  In technical language, we chose contrasts of the test to be [2,-1,-1].
Assembly: mm9
Supplementary files format and content: processed adip + SVF data.xlsx=differentially expressed genes analyzed by limma: contains normalized gene counts for each sample as well as average expression and fold change and local false discovery rate between groups
Supplementary files format and content: vWAT-adip-HF-LF-SW_gene_counts.txt/vWAT-SVF_HF-LF-SW_gene_counts.txt  contains gene counts for each sample

molecule: polyA RNA

source_name: adipose (visceral)

extract_protocol:
Adipocytes and stromal vascular cells (SVCs) were prepared from adipose tissue. Briefly, epididymal fat pads were weighed, rinsed three times in PBS, and then minced in FACS buffer (PBS + 1% low endotoxin BSA). Tissue suspensions were treated with collagenase (1 mg/ml, Sigma-Aldrich) for 30 min, and then were filtered through a 100 μm filter (BD Biosciences). After centrifugation at 500 g for 5 min, the supernatant containing adipocytes was removed and the pallet containing SVCs fraction was incubated with RBC lysis buffer (eBioscience) for 5 min followed by another centrifugation (300 g, 5 min) and resuspension in FACS buffer. Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions. The quality of the RNA was assessed using the Tapestation 2200 (Agilent) and all samples passed an RNA Integrity score (RIN) above 7.5 denoting good quality RNA.
Libraries were prepared using TruSeq Library prep kits (Illumina) and run on the Hiseq 2500 (Illumina) to obtain approximate coverage of 10 million reads per sample

treatment_protocol: Male wild type C57BL/6J mice (Jackson Laboratories) were group housed in standard cages and fed either a 10% (LFD, D12450, Research Diets, New Brunswick, NJ) or 60% fat diet (HFD, D12492) from 9-10 weeks of age. After 9 weeks of HFD feeding, half of the HFD-fed mice where switched to the LFD (SWD) for 3 weeks to induce ~10% weight loss which is sufficient to normalize glucose tolerance and insulin sensitivity to equivalent levels in observed in lean, normal chow fed mice

tag: tissue

value: adipose (visceral)

value: stromal vascular cells

tag: genotype

value: C57BL6, male

tag: treatment

value: HFD for 9 weeks, followed by LFD for 3 weeks


title: low fat diet fed - SVF-SW1 paired-end

description:
low fat diet fed - SVF-SW1
SVF  SW-1


title: low fat diet fed - SVF- SW2 single

description:
low fat diet fed - SVF- SW2
SVF  SW-2


title: low fat diet fed - SVF-SW3 paired-end

description:
low fat diet fed - SVF-SW3
SVF  SW-3


title: low fat diet fed - SVF-SW1 single

description:
low fat diet fed - SVF-SW1
SVF  SW-1


title: Methylation_EPIC_sample249


title: low fat diet fed - SVF- SW2 paired-end

description:
low fat diet fed - SVF- SW2
SVF  SW-2


title: Methylation_EPIC_sample248


title: low fat diet fed- SVF-LF2 single

description:
low fat diet fed- SVF-LF2
SVF  LF-2

value: Low fat diet fed for 12 weeks


title: low fat diet fed- SVF-LF2 paired-end

description:
low fat diet fed- SVF-LF2
SVF  LF-2


title: Methylation_450k_sample416


title: high fat diet fed -SVF-HFD 3 single

description:
high fat diet fed -SVF-HFD 3
SVF  HF-3

value: High fat diet fed for 12 weeks


title: Methylation_450k_sample412

value: African American (AA)


title: Methylation_EPIC_sample246

value: F


title: Methylation_450k_sample409

value: M


title: Methylation_450k_sample410


title: Methylation_EPIC_sample245


title: Methylation_450k_sample418


title: low fat diet fed - adipocyte - SW3 paired-end

description:
low fat diet fed - adipocyte - SW3
adip SW-3

value: adipocyte


title: high fat diet fed - SVF-HFD-2 paired-end

description:
high fat diet fed - SVF-HFD-2
SVF  HF-2


title: low fat diet fed- SVF-LF1 single

description:
low fat diet fed- SVF-LF1
SVF  LF-1


title: low fat diet fed- SVF-LF3 paired-end

description:
low fat diet fed- SVF-LF3
SVF  LF-3


title: high fat diet fed - SVF- HFD-1 single

description:
high fat diet fed - SVF- HFD-1
SVF HF-1


title: Methylation_EPIC_sample244

value: E


title: Methylation_EPIC_sample247


title: Methylation_450k_sample411

value: G


title: low fat diet fed - adipocyte - SW2 paired-end

description:
low fat diet fed - adipocyte - SW2
adip SW-2


title: Methylation_450k_sample407


title: Methylation_EPIC_sample242

value: H


title: Methylation_450k_sample408

value: C


title: high fat diet fed - SVF-HFD-2 single

description:
high fat diet fed - SVF-HFD-2
SVF  HF-2


title: Methylation_EPIC_sample241


title: Methylation_450k_sample406

value: D


title: low fat diet fed - adipocyte - LF3 paired-end

description:
low fat diet fed - adipocyte - LF3
adip LF-3


title: low fat diet fed - adipocyte - LF1 paired-end

description:
low fat diet fed - adipocyte - LF1
adip LF-1


title: Methylation_450k_sample404


title: low fat diet fed - adipocyte - LF2 single

description:
low fat diet fed - adipocyte - LF2
adip LF-2


title: Methylation_EPIC_sample240


title: low fat diet fed - adipocyte - SW1 paired-end

description:
low fat diet fed - adipocyte - SW1
adip SW-1


title: high fat diet fed - adipocyte- HFD 3 paired-end

description:
high fat diet fed - adipocyte- HFD 3
adip HF-3


title: high fat diet fed - adipocyte- HFD 3 single


title: Methylation_EPIC_sample239


title: high fat diet fed - adipocyte- HFD-1 paired-end

description:
high fat diet fed - adipocyte- HFD-1
adip HF-1


title: Methylation_EPIC_sample238


title: Methylation_EPIC_sample237


title: Ube3aOE hippocampus P7 mouse #10 [Sample 20]

city: Rotterdam

first: Mattijs

last: Punt

state: Zuid-Holland

address: Dr. Molewaterplein 40

department: Clinical Genetics

country: Netherlands

institute: Erasmus MC

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to GrCM38/mm10 using HiSat2 (version 2.1.0)
We called gene expression values using htseq-count(version 0.11.2)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: hippocampus

growth_protocol: Cortices and hippocampi were disected from 5 wildtype and 5 Ube3aOE P7 pups

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

tag: developmental stage

tag: Sex

value: female

value: hippocampus


title: Methylation_450k_sample405


title: Methylation_450k_sample400

value: A


title: Ube3aOE hippocampus P7 mouse #7 [Sample 17]


title: Methylation_450k_sample402

value: B


title: Methylation_450k_sample401


title: low fat diet fed - adipocyte - LF3 single

value: adipose (visceral)

tag: cell type

value: C57BL6, male


title: low fat diet fed - adipocyte - LF2 paired-end

value: Low fat diet fed for 12 weeks


title: Ube3aOE hippocampus P7 mouse #9 [Sample 19]

tag: strain

value: male


title: Ube3aOE hippocampus P7 mouse #6 [Sample 16]


title: Methylation_EPIC_sample243

tag: race

value: African American (AA)


title: Ube3aOE hippocampus P7 mouse #8 [Sample 18]


title: Wildtype hippocampus P7 mouse #5 [Sample 15]

value: WT


title: Methylation_450k_sample399

tag: gender

value: F


title: Methylation_450k_sample403

value: M

tag: age(yrs)


title: Wildtype hippocampus P7 mouse #4 [Sample 14]


title: Methylation_EPIC_sample236

tag: plate


title: Wildtype hippocampus P7 mouse #3 [Sample 13]


title: Methylation_EPIC_sample235

tag: column


title: high fat diet fed - adipocyte- HFD-2 paired-end

description:
high fat diet fed - adipocyte- HFD-2
adip HF-2

value: adipocyte

value: High fat diet fed for 12 weeks


title: Wildtype hippocampus P7 mouse #2 [Sample 12]


title: Wildtype hippocampus P7 mouse #1 [Sample 11]


title: Methylation_450k_sample398

tag: row

value: H


title: Methylation_450k_sample396

value: G

tag: pedigreeid


title: Ube3aOE cortex P7 mouse #9 [Sample 9]

source_name: cortex

value: cortex


title: Methylation_EPIC_sample233

value: E

tag: subjectid


title: Methylation_EPIC_sample231

value: C

tag: phase


title: Ube3aOE cortex P7 mouse#10 [Sample 10]

value: female


title: Ube3aOE cortex P7 mouse #8 [Sample 8]


title: Wildtype cortex P7 mouse #4 [Sample 4]


title: Wildtype cortex P7 mouse #2 [Sample 2]


title: Methylation_450k_sample395

value: A


title: Ube3aOE cortex P7 mouse #6 [Sample 6]


title: Methylation_450k_sample397

value: B


title: Methylation_EPIC_sample232

value: D


title: Methylation_EPIC_sample234


title: Wildtype cortex P7 mouse #5 [Sample 5]


title: Ube3aOE cortex P7 mouse #7 [Sample 7]


title: Methylation_EPIC_sample230


title: Methylation_EPIC_sample228


title: Wildtype cortex P7 mouse #3 [Sample 3]


title: Methylation_450k_sample394


title: DMSO1_plus

city: Frankfurt am Main

first: Martin

last: Wegner

state: Hessen

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry II

country: Germany

institute: University Hospital Frankfurt am Main, Germany

data_processing:
NextSeq Control Software 2.2.0.4
Demultiplexing: Illumina bcl2fastq v2.17
Adapter trimming: cutadapt v1.15 - 0.1 -g GACGAAACACCG --minimum-length 20 --discard-untrimmed --max-n 0 --nextseq-trim 20
gRNA alignment: bowtie2 2.3.0 --local -L12 -N 1 -i S,1.0,0.75 -q
Supplementary files format and content: csv table containing gRNA identifiers and their read counts

source_name: Uterus; Cervix

growth_protocol: HeLa FlpIn Trex mt-mKEIMA Parkin cells were cultured at 37°C and 5% CO2 in a humidified incubator in RPMI1640 medium (GIBCO 21875034) with 10% heat inactivated and sterile fetal bovine serum (FBS) (GIBCO 10270-106), supplemented with 4 μg/ml Blasticidine (Invitrogen) and 50 μg/ml Hygromycin B Gold (Invitrogen).

extract_protocol:
Genomic DNA was extracted from the cell pellets either from sorting or pooled cells using the GeneJET Genomic DNA Purification Kit (Thermo Scientific™, Cat. No K0721). PCR was performed with NEBNext® High-Fidelity 2X PCR Master Mix (M0541). Thermal cycler parameters were set to: initial denaturation for 5 min at 98°C, 20 cycles of denaturation at 98°C for 30 s, annealing for 30 s at 58°C, extension for 40 s at 72°C, and final extension for 5 min at 72°C. PCR products were purified via 1% agarose gel electrophoresis and QIAquick Gel Extraction Kit (Qiagen, 28706). All samples were denatured and diluted according to the Illumina NextSeq system denature and dilute libraries guide (document # 15048776 v09, illumina.com) and sequenced on an Illumina NextSeq 500.
Doench et al Nat Biotechnol. 2016 Jan 18. doi: 10.1038/nbt.3437

treatment_protocol: HeLa FlpIn Trex mt-mKEIMA Parkin cells were selected for 8 days with 2 µg/ml puromycin and placebo-treated for 16 h with 0.1 % DMSO.

value: Uterus; Cervix

tag: cell line

value: HeLa FlpIn Trex

value: epithelial

tag: cell population

value: sorted as mitophagy-positive cells

value: DMSO


title: DMSO1_complete

tag: tissue

value: without sorting


title: PL_F_72439

city: West Hollywood

first: AGCT

last: Core

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

description:
Placenta.72439
Placenta_72439_S95

data_processing:
Demultiplexed raw reads were uploaded to GeneGlobe Data Analysis Center for quality control, alignment, and expression quantification [https://www.qiagen.com/us/resources/geneglobe/]. Briefly, 3’ adapter and low quality bases were trimmed off from reads first using cutadapt v1.13 with default settings, then reads with less than 16bp insert sequences or with less than 10bp UMI sequences were discarded.
After cleanup, remaining reads were collapsed to UMI counts and aligned sequentially to miRBase release 21 mature and hairpin microRNA databases, and to piRNABank release 1 for piwi-interacting RNAs, using Bowtie v1.2.
The UMI counts of each small RNA category were quantified, and then normalized by a size factor-based method in the R package DESeq2 v1.22.2 (Bioconductor).
Differential expression analysis was performed on miRNAs to compare first vs third trimester (with fetal sex as a covariate) with all 160 samples, first vs third trimester subanalysis in females only or males only, sex differences analysis at first trimester, and sex differences analysis at third trimester.
Mature miRNA IDs were cross-referenced to precursor miRNA accession IDs using miRBase release 21 files, then precursor miRNA accession IDs were input into biomaRt R package with Ensembl release 91 (which corresponds to miRBase release 21) to extract chromosome locations.
Genome_build: miRBase release 21 for microRNAs, piRNABank release 1 for piRNAs
Supplementary_files_format_and_content: Comma-separated text file includes UMI counts of miRNAs and piRNAs for each sample, differential expression analysis, and annotated analysis files

source_name: Placenta (at delivery)

growth_protocol: Singleton pregnancies conceived without fertility treatment

extract_protocol:
Tissue was submerged in RNAlater RNA stabilization reagent (QIAGEN) and stored at -80C until further processing. Tissue was thawed on ice and homogenized using sonication and/or needles, then total RNA was isolated using the AllPrep DNA/RNA/miRNA Universal kit (QIAGEN).
The total RNA elution was used to prepare a miRNA sequencing library using the QIASeq miRNA Library Kit. A pre-adenylated DNA adapter was ligated to the 3’ ends of miRNAs, followed by ligation of an RNA adapter to the 5’ end. A reverse-transcription primer containing an integrated Unique Molecular Index (UMI) was used to convert the 3’/5’ ligated miRNAs into cDNA. After cDNA cleanup, indexed sequencing libraries were generated via sample indexing during library amplification, followed by library cleanup. Libraries were sequenced on a NextSeq 500 (Illumina, San Diego, CA) with a 1×75 bp read length and an average sequencing depth of 10.64 million reads per sample.

treatment_protocol: Placenta tissue collected after chorionic villus sampling or at delivery

value: Placenta (at delivery)

tag: sample type

value: Placenta

tag: trimester

value: Third

tag: sample gestational age in days

tag: fetal sex

value: F

tag: mode of conception

value: Spontaneous

tag: fetal race

value: Caucasian

tag: fetal ethnicity

value: Hispanic

tag: maternal age in years

tag: paternal age in years

tag: maternal bmi pre-pregnancy

tag: rna integrity number


title: Methylation_EPIC_sample227

tag: race

value: African American (AA)

tag: gender

tag: age(yrs)

tag: plate

tag: column

tag: row

value: E

tag: pedigreeid


title: Methylation_450k_sample393

value: M

value: B

tag: subjectid

tag: phase


title: Wildtype cortex P7 mouse #1 [Sample 1]

tag: strain

tag: genotype

value: WT

tag: developmental stage

tag: Sex

value: female

tag: tissue

value: cortex


title: PL_F_72424

description:
Placenta.72424
Placenta_72424_S13

tag: sample type

tag: trimester

tag: sample gestational age in days

tag: fetal sex

tag: mode of conception

tag: fetal race

tag: fetal ethnicity

value: NonHispanic

tag: maternal age in years

tag: paternal age in years


title: Methylation_EPIC_sample229

tag: race

tag: gender

tag: age(yrs)

tag: plate

tag: column

tag: row

value: A

tag: pedigreeid


title: PL_M_72420

description:
Placenta.72420
Placenta_72420_S37

tag: tissue

value: CaucasianAsian

tag: maternal bmi pre-pregnancy

tag: rna integrity number


title: Methylation_EPIC_sample251

value: C

tag: subjectid

tag: phase


title: Methylation_450k_sample392

value: G


title: PL_M_72415

description:
Placenta.72415
Placenta_72415_S109

value: Placenta (at delivery)

tag: sample type

value: Placenta

tag: trimester

value: Third

tag: sample gestational age in days

tag: fetal sex

tag: mode of conception


title: Methylation_450k_sample388

tag: race

value: F


title: Methylation_EPIC_sample225

tag: gender


title: PL_M_72408

description:
Placenta.72408
Placenta_72408_S70

value: Spontaneous

tag: fetal race

value: Caucasian

tag: fetal ethnicity

tag: maternal age in years

tag: paternal age in years


title: PL_F_72391

description:
Placenta.72391
Placenta_72391_S126

value: Hispanic


title: PL_M_72388

description:
Placenta.72388
Placenta_72388_S107

value: M


title: Methylation_450k_sample389

value: African American (AA)

tag: age(yrs)

tag: plate

tag: column

tag: row

value: H

tag: pedigreeid


title: PL_F_72475

description:
Placenta.72475
Placenta_72475_S125

tag: tissue

tag: maternal bmi pre-pregnancy

tag: rna integrity number


title: Methylation_450k_sample386

value: D

tag: subjectid

tag: phase


title: Methylation_450k_sample391


title: PL_F_72378

description:
Placenta.72378
Placenta_72378_S27

tag: sample type

tag: trimester

tag: sample gestational age in days

tag: fetal sex

tag: mode of conception


title: Methylation_EPIC_sample224

tag: race

tag: gender

value: E


title: Methylation_EPIC_sample222

tag: age(yrs)


title: Methylation_EPIC_sample226

tag: plate

value: B


title: PL_F_72375

description:
Placenta.72375
Placenta_72375_S124

tag: fetal race

tag: fetal ethnicity

value: NonHispanic

tag: maternal age in years

tag: paternal age in years


title: Methylation_450k_sample385

tag: column

tag: row

tag: pedigreeid


title: Methylation_EPIC_sample221

tag: subjectid

tag: phase


title: Methylation_450k_sample387


title: PL_F_72402

description:
Placenta.72402
Placenta_72402_S141

tag: tissue

tag: sample type

tag: trimester

value: Multiracial

tag: maternal bmi pre-pregnancy

tag: rna integrity number


title: PL_F_72387

description:
Placenta.72387
Placenta_72387_S177

tag: sample gestational age in days

tag: fetal sex

tag: mode of conception


title: Methylation_EPIC_sample223

tag: race

tag: gender

tag: age(yrs)

tag: plate


title: Methylation_EPIC_sample220

tag: column


title: Methylation_450k_sample390

tag: row


title: PL_M_72373

description:
Placenta.72373
Placenta_72373_S119

tag: fetal race

tag: fetal ethnicity

tag: maternal age in years

tag: paternal age in years


title: PL_F_72367

description:
Placenta.72367
Placenta_72367_S122

tag: tissue

tag: sample type


title: Methylation_450k_sample384

value: C

tag: pedigreeid

tag: subjectid

tag: phase


title: PL_M_72361

description:
Placenta.72361
Placenta_72361_S108

tag: trimester

tag: sample gestational age in days

tag: fetal sex

tag: maternal bmi pre-pregnancy

tag: rna integrity number


title: Methylation_EPIC_sample218

tag: race

tag: gender

tag: age(yrs)

tag: plate


title: Methylation_450k_sample381

tag: column

tag: row


title: PL_F_72359

description:
Placenta.72359
Placenta_72359_S143

tag: mode of conception

tag: fetal race

value: CaucasianAsian

tag: fetal ethnicity

tag: maternal age in years

tag: paternal age in years


title: Methylation_450k_sample383

tag: pedigreeid

tag: subjectid

tag: phase


title: Methylation_EPIC_sample216


title: PL_M_72355

description:
Placenta.72355
Placenta_72355_S32

tag: tissue

value: Placenta (at delivery)

tag: sample type

tag: trimester

tag: sample gestational age in days

tag: fetal sex


title: Methylation_450k_sample380

tag: race

tag: gender

tag: age(yrs)


title: Methylation_450k_sample382

tag: plate

tag: column

tag: row


title: PL_M_72376

description:
Placenta.72376
Placenta_72376_S85

value: Placenta

tag: mode of conception

tag: fetal race

tag: fetal ethnicity

tag: maternal bmi pre-pregnancy

tag: rna integrity number


title: PL_F_72340

description:
Placenta.72340
Placenta_72340_S1

value: Third

tag: maternal age in years

tag: paternal age in years


title: PL_M_72343

description:
Placenta.72343
Placenta_72343_S84

tag: tissue

tag: sample type


title: Methylation_EPIC_sample215

value: F

tag: pedigreeid

tag: subjectid

tag: phase


title: PL_M_72334

description:
Placenta.72334
Placenta_72334_S106

tag: trimester

tag: sample gestational age in days

tag: fetal sex

value: Spontaneous

value: BiracialOther


title: PL_M_72358

description:
Placenta.72358
Placenta_72358_S58

value: Caucasian


title: Methylation_450k_sample379

tag: race

tag: gender

tag: age(yrs)

tag: plate

tag: column


title: PL_M_72330

description:
Placenta.72330
Placenta_72330_S36

value: M

tag: mode of conception

tag: fetal race

tag: fetal ethnicity

value: Hispanic

tag: maternal bmi pre-pregnancy


title: PL_M_72341

description:
Placenta.72341
Placenta_72341_S128

tag: tissue

tag: maternal age in years

tag: paternal age in years

tag: rna integrity number


title: PL_M_72350

description:
Placenta.72350
Placenta_72350_S30

tag: sample type


title: Methylation_450k_sample378

value: African American (AA)

tag: row

tag: pedigreeid

tag: subjectid

tag: phase


title: Methylation_EPIC_sample213

tag: race

tag: gender


title: PL_M_72316

description:
Placenta.72316
Placenta_72316_S38

tag: trimester

tag: sample gestational age in days

tag: fetal sex


title: Methylation_EPIC_sample214

tag: age(yrs)

tag: plate

tag: column

value: D


title: PL_M_72319

description:
Placenta.72319
Placenta_72319_S27

tag: tissue

tag: mode of conception

tag: fetal race

tag: fetal ethnicity

tag: maternal bmi pre-pregnancy


title: Methylation_450k_sample376

tag: row

value: A


title: Methylation_EPIC_sample219

value: E

tag: pedigreeid


title: Methylation_450k_sample377

tag: subjectid


title: Methylation_EPIC_sample217

value: B

tag: phase


title: PL_M_72351

description:
Placenta.72351
Placenta_72351_S123

tag: sample type

value: NonHispanic

tag: maternal age in years

tag: paternal age in years

tag: rna integrity number


title: PL_F_72298

description:
Placenta.72298
Placenta_72298_S130

tag: trimester

tag: sample gestational age in days

tag: fetal sex


title: PL_F_72290

description:
Placenta.72290
Placenta_72290_S140


title: PL_M_72306

description:
Placenta.72306
Placenta_72306_S20


title: PL_M_72287

description:
Placenta.72287
Placenta_72287_S134


title: PL_M_72311

description:
Placenta.72311
Placenta_72311_S120


title: Methylation_EPIC_sample212

tag: race

tag: gender

tag: age(yrs)

tag: plate

tag: column


title: PL_M_72344

description:
Placenta.72344
Placenta_72344_S2

tag: tissue

tag: mode of conception

tag: fetal race

value: AfricanAmerican

tag: fetal ethnicity

tag: maternal bmi pre-pregnancy


title: Methylation_450k_sample375

tag: row

value: C

tag: pedigreeid

tag: subjectid

tag: phase


title: PL_M_72275

description:
Placenta.72275
Placenta_72275_S101

value: Placenta (at delivery)

tag: sample type

tag: trimester

tag: maternal age in years

tag: paternal age in years

tag: rna integrity number


title: Methylation_EPIC_sample210

tag: race

tag: gender

tag: age(yrs)

value: H


title: Methylation_EPIC_sample211

tag: plate

tag: column


title: PL_M_72268

description:
Placenta.72268
Placenta_72268_S102

tag: tissue

value: Placenta

value: Third

tag: sample gestational age in days

tag: fetal sex

tag: mode of conception

tag: fetal race


title: Methylation_450k_sample373

tag: row

tag: pedigreeid

tag: subjectid


title: Methylation_450k_sample374

value: F

tag: phase


title: PL_M_72273

description:
Placenta.72273
Placenta_72273_S99

tag: sample type

tag: trimester

value: Spontaneous

tag: fetal ethnicity

tag: maternal age in years

tag: maternal bmi pre-pregnancy


title: Methylation_EPIC_sample209

tag: race

tag: gender

tag: age(yrs)

value: G


title: PL_F_72314

description:
Placenta.72314
Placenta_72314_S15

tag: tissue

value: CaucasianAsian

tag: paternal age in years

tag: rna integrity number


title: PL_F_72115

description:
Placenta.72115
Placenta_72115_S139

tag: sample gestational age in days

tag: fetal sex

tag: mode of conception


title: Methylation_450k_sample371

tag: plate

tag: column

tag: row

tag: pedigreeid


title: PL_M_72145

description:
Placenta.72145
Placenta_72145_S14

tag: sample type

tag: trimester

value: M

tag: fetal race

value: Caucasian


title: PL_F_72155

description:
Placenta.72155
Placenta_72155_S35

tag: fetal ethnicity

tag: maternal age in years

tag: maternal bmi pre-pregnancy


title: Methylation_EPIC_sample208

tag: race

value: African American (AA)

tag: gender

tag: age(yrs)

tag: subjectid

tag: phase


title: Methylation_450k_sample372


title: Methylation_EPIC_sample207


title: PL_M_72111

description:
Placenta.72111
Placenta_72111_S132

tag: tissue

tag: sample gestational age in days

tag: fetal sex

value: Hispanic

tag: paternal age in years

tag: rna integrity number


title: PL_F_72109

description:
Placenta.72109
Placenta_72109_S137

tag: mode of conception


title: Methylation_450k_sample369

tag: plate

tag: column

tag: row

tag: pedigreeid


title: Methylation_EPIC_sample205


title: Methylation_450k_sample370


title: PL_F_71987

description:
Placenta.71987
Placenta_71987_S44

tag: sample type

tag: trimester

tag: fetal race

tag: fetal ethnicity

tag: maternal age in years


title: PL_M_72039

description:
Placenta.72039
Placenta_72039_S117

tag: maternal bmi pre-pregnancy


title: PL_M_71997

description:
Placenta.71997
Placenta_71997_S138


title: Methylation_EPIC_sample206

tag: race

tag: gender

tag: age(yrs)

value: D

tag: subjectid

tag: phase


title: Methylation_450k_sample367

value: A


title: CVS_M_72380

description:
CVS.72380
CVS_72380_S47

source_name: Placenta (chorionic villi)

tag: tissue

value: Placenta (chorionic villi)

value: CVS

value: First

tag: sample gestational age in days

tag: fetal sex

value: NonHispanic

tag: paternal age in years

tag: rna integrity number


title: Methylation_450k_sample368

tag: plate

tag: column

tag: row

tag: pedigreeid


title: CVS_M_72308

description:
CVS.72308
CVS_72308

tag: sample type

tag: trimester

tag: mode of conception

tag: fetal race

tag: fetal ethnicity


title: Methylation_EPIC_sample203

tag: race

tag: gender

tag: age(yrs)


title: CVS_M_72324

description:
CVS.72324
CVS_72324

tag: tissue

tag: maternal age in years

tag: maternal bmi pre-pregnancy


title: Methylation_EPIC_sample204

value: B

tag: subjectid

tag: phase


title: CVS_M_72287

description:
CVS.72287
CVS_72287_S100

tag: sample gestational age in days

tag: fetal sex

tag: paternal age in years

tag: rna integrity number


title: Methylation_450k_sample366

tag: plate

tag: column

tag: row

tag: pedigreeid


title: Methylation_450k_sample365

value: H


title: CVS_F_72109

description:
CVS.72109
CVS_72109_S112

tag: sample type

tag: trimester

tag: mode of conception

tag: fetal race

value: AfricanAmerican

tag: fetal ethnicity


title: Methylation_EPIC_sample201

tag: race

tag: gender

value: F

tag: age(yrs)


title: Methylation_450k_sample364

value: E

tag: subjectid

tag: phase


title: Methylation_EPIC_sample202


title: PL_F_72114

description:
Placenta.72114
Placenta_72114_S129

tag: tissue

value: Placenta (at delivery)

value: Placenta

value: Third

tag: sample gestational age in days

tag: fetal sex

value: Spontaneous

tag: maternal age in years

tag: maternal bmi pre-pregnancy


title: CVS_F_72098

description:
CVS.72098
CVS_72098_S79

value: Caucasian

tag: paternal age in years

tag: rna integrity number


title: Methylation_450k_sample363

value: African American (AA)

value: M

tag: plate

tag: column

tag: row

value: G

tag: pedigreeid


title: Methylation_EPIC_sample199


title: CVS_M_72054

description:
CVS.72054
CVS_72054_S6

value: Placenta (chorionic villi)

tag: sample type

tag: trimester

tag: mode of conception

tag: fetal race

tag: fetal ethnicity


title: CVS_M_72041

description:
CVS.72041
CVS_72041_S61

value: CVS

value: CaucasianAsian


title: CVS_F_72069

description:
CVS.72069
CVS_72069_S5

value: First

value: NonHispanic


title: Methylation_450k_sample362

tag: race

tag: gender

tag: age(yrs)

value: D

tag: subjectid

tag: phase


title: CVS_M_72026

description:
CVS.72026
CVS_72026_S33

tag: tissue

tag: sample gestational age in days

tag: fetal sex

tag: maternal age in years

tag: maternal bmi pre-pregnancy


title: Methylation_450k_sample361

tag: plate

tag: column

tag: row


title: CVS_F_72011

description:
CVS.72011
CVS_72011_S110

tag: sample type

tag: trimester

value: AfricanAmerican

tag: paternal age in years

tag: rna integrity number


title: Methylation_EPIC_sample198

tag: race

value: F

tag: pedigreeid


title: CVS_F_72034

description:
CVS.72034
CVS_72034_S86

tag: mode of conception

tag: fetal race

tag: fetal ethnicity


title: CVS_F_72009

description:
CVS.72009
CVS_72009_S57

tag: tissue


title: Methylation_EPIC_sample197

tag: gender

tag: age(yrs)

value: C

tag: subjectid

tag: phase


title: CVS_M_72003

description:
CVS.72003
CVS_72003_S69

tag: sample gestational age in days

tag: fetal sex

tag: maternal age in years

tag: maternal bmi pre-pregnancy


title: CVS_F_72002

description:
CVS.72002
CVS_72002_S142

tag: sample type

tag: trimester

value: Asian


title: Methylation_450k_sample360

tag: plate

tag: column

tag: row


title: Methylation_450k_sample359

tag: race

value: E

tag: pedigreeid


title: CVS_F_71949

description:
CVS.71949
CVS_71949_S22

tag: mode of conception

tag: fetal race

tag: fetal ethnicity

tag: paternal age in years

tag: rna integrity number


title: Methylation_EPIC_sample200

tag: gender

tag: age(yrs)

tag: subjectid

tag: phase


title: Methylation_EPIC_sample196

value: B


title: Methylation_EPIC_sample195

value: A


title: CVS_M_71955

description:
CVS.71955
CVS_71955_S83

tag: tissue

tag: sample gestational age in days

tag: fetal sex

value: Spontaneous

value: Caucasian

tag: maternal age in years

tag: maternal bmi pre-pregnancy


title: CVS_M_71905

description:
CVS.71905
CVS_71905_S24

tag: sample type

tag: trimester

value: M


title: CVS_F_72091

description:
CVS.72091
CVS_72091_S6


title: Methylation_EPIC_sample194

tag: race

value: African American (AA)

tag: plate

tag: column

tag: row

value: H

tag: pedigreeid


title: Methylation_450k_sample358


title: CVS_M_71895

description:
CVS.71895
CVS_71895_S9

value: Placenta (chorionic villi)

value: CVS

tag: mode of conception

tag: fetal race

tag: fetal ethnicity

tag: paternal age in years

tag: rna integrity number


title: CVS_M_72039

description:
CVS.72039
CVS_72039_S93

tag: tissue

value: First


title: Methylation_450k_sample356

tag: gender

tag: age(yrs)

tag: subjectid

tag: phase


title: CVS_F_71882

description:
CVS.71882
CVS_71882_S59

tag: sample type

tag: sample gestational age in days

tag: fetal sex

value: NonHispanic

tag: maternal age in years

tag: maternal bmi pre-pregnancy


title: Methylation_EPIC_sample192

tag: race

tag: plate

tag: column

tag: row


title: Methylation_EPIC_sample193

value: G

tag: pedigreeid


title: CVS_F_71869

description:
CVS.71869
CVS_71869_S19

tag: trimester

tag: mode of conception

tag: fetal race

tag: fetal ethnicity

tag: paternal age in years


title: CVS_M_71861

description:
CVS.71861
CVS_71861_S72

tag: tissue

tag: rna integrity number


title: CVS_F_71849

description:
CVS.71849
CVS_71849_S23

tag: sample type


title: CVS_F_71822

description:
CVS.71822
CVS_71822_S15

tag: sample gestational age in days


title: Methylation_450k_sample355

tag: gender

tag: age(yrs)

tag: subjectid

tag: phase


title: Methylation_EPIC_sample191

tag: race

tag: plate


title: Methylation_450k_sample354

tag: column

tag: row


title: Methylation_EPIC_sample190

value: D

tag: pedigreeid


title: CVS_F_71759

description:
CVS.71759
CVS_71759_S54

tag: trimester

tag: fetal sex

value: F

tag: mode of conception

tag: maternal age in years

tag: maternal bmi pre-pregnancy


title: CVS_F_71793

description:
CVS.71793
CVS_71793_S65

tag: tissue

tag: fetal race

tag: fetal ethnicity

tag: paternal age in years

tag: rna integrity number


title: Methylation_450k_sample353

tag: gender

tag: age(yrs)

tag: subjectid


title: CVS_M_71806

description:
CVS.71806
CVS_71806_S80

tag: sample type

tag: sample gestational age in days


title: Methylation_EPIC_sample189

tag: race

tag: plate

tag: column

tag: row

value: C

tag: phase


title: Methylation_450k_sample352

tag: pedigreeid


title: Methylation_450k_sample357


title: CVS_F_71757

description:
CVS.71757
CVS_71757_S4

tag: trimester

tag: fetal sex

tag: mode of conception

tag: maternal age in years

tag: maternal bmi pre-pregnancy


title: CVS_M_71756

description:
CVS.71756
CVS_71756_S53

tag: tissue

tag: fetal race

tag: fetal ethnicity

tag: paternal age in years

tag: rna integrity number


title: Methylation_450k_sample351

tag: gender

tag: age(yrs)

tag: subjectid


title: Methylation_EPIC_sample188

tag: race

tag: plate

tag: column


title: CVS_F_71743

description:
CVS.71743
CVS_71743

tag: sample type

tag: sample gestational age in days


title: Methylation_EPIC_sample187

tag: row

tag: pedigreeid

tag: phase


title: CVS_F_71702

description:
CVS.71702
CVS_71702

tag: trimester

tag: fetal sex

tag: mode of conception

tag: maternal age in years

tag: maternal bmi pre-pregnancy


title: CVS_M_71731

description:
CVS.71731
CVS_71731_S90

tag: tissue

tag: fetal race

tag: fetal ethnicity

tag: paternal age in years

tag: rna integrity number


title: Methylation_450k_sample350

tag: race

tag: gender

tag: age(yrs)

tag: plate

tag: subjectid


title: Methylation_EPIC_sample186

tag: column

tag: row

tag: pedigreeid


title: CVS_F_71707

description:
CVS.71707
CVS_71707_S92

tag: sample type

tag: trimester

tag: sample gestational age in days

tag: fetal sex


title: CVS_M_71673

description:
CVS.71673
CVS_71673_S82

tag: tissue

tag: mode of conception

tag: maternal age in years

tag: maternal bmi pre-pregnancy


title: Methylation_450k_sample348

tag: phase


title: Methylation_EPIC_sample185

tag: race


title: CVS_M_71624

description:
CVS.71624
CVS_71624_S10

tag: fetal race

tag: fetal ethnicity

tag: paternal age in years

tag: rna integrity number


title: CVS_M_71637

description:
CVS.71637
CVS_71637_S18


title: CVS_F_71652

description:
CVS.71652
CVS_71652_S2


title: CVS_F_71620

description:
CVS.71620
CVS_71620


title: CVS_M_71758

description:
CVS.71758
CVS_71758_S23


title: Methylation_EPIC_sample184

tag: gender

tag: age(yrs)

tag: plate

tag: column

tag: subjectid


title: Methylation_450k_sample347

tag: row

tag: pedigreeid


title: Methylation_EPIC_sample183


title: Methylation_450k_sample346


title: CVS_F_71607

description:
CVS.71607
CVS_71607_S50

tag: tissue

tag: sample type

tag: trimester

tag: sample gestational age in days

tag: fetal sex


title: Methylation_EPIC_sample182

tag: race

tag: phase


title: CVS_M_71503

description:
CVS.71503
CVS_71503_S8

tag: mode of conception

tag: fetal race

tag: fetal ethnicity

tag: maternal age in years

tag: maternal bmi pre-pregnancy


title: CVS_F_71527

description:
CVS.71527
CVS_71527_S81

tag: paternal age in years

tag: rna integrity number


title: Methylation_450k_sample345

tag: gender

tag: age(yrs)

tag: plate

tag: column

tag: subjectid


title: Methylation_EPIC_sample181

tag: row

tag: pedigreeid


title: CVS_F_71485

description:
CVS.71485
CVS_71485_S2

tag: tissue

tag: sample type

tag: trimester

tag: sample gestational age in days

tag: fetal sex


title: CVS_M_71491

description:
CVS.71491
CVS_71491_S28

tag: mode of conception

tag: fetal race

tag: fetal ethnicity


title: Methylation_450k_sample344

tag: race

tag: phase


title: Methylation_EPIC_sample180

tag: gender


title: Methylation_450k_sample349

tag: age(yrs)


title: CVS_M_71451

description:
CVS.71451
CVS_71451_S26

tag: maternal age in years

tag: paternal age in years

tag: maternal bmi pre-pregnancy

tag: rna integrity number


title: CVS_M_71445

description:
CVS.71445
CVS_71445_S38


title: CVS_F_71440

description:
CVS.71440
CVS_71440_S28


title: Methylation_450k_sample343

tag: plate

tag: column

tag: row

tag: pedigreeid

tag: subjectid


title: Methylation_EPIC_sample179


title: Methylation_450k_sample342


title: CVS_F_71424

description:
CVS.71424
CVS_71424_S56

tag: tissue

tag: sample type

tag: trimester

tag: sample gestational age in days

tag: fetal sex


title: CVS_F_71418

description:
CVS.71418
CVS_71418_S25

tag: mode of conception

tag: fetal race

tag: fetal ethnicity


title: CVS_F_71419

description:
CVS.71419
CVS_71419_S29

tag: maternal age in years


title: Methylation_EPIC_sample178

tag: race

tag: gender

tag: age(yrs)

tag: phase


title: Methylation_450k_sample341

tag: plate

tag: column


title: CVS_F_71579

description:
CVS.71579
CVS_71579_S1

value: Asian

tag: paternal age in years

tag: maternal bmi pre-pregnancy

tag: rna integrity number


title: CVS_M_71412

description:
CVS.71412
CVS_71412_S43

tag: tissue

tag: sample type


title: Methylation_EPIC_sample177

tag: row

tag: pedigreeid

tag: subjectid


title: CVS_F_71598

description:
CVS.71598
CVS_71598_S3

tag: trimester

tag: sample gestational age in days

tag: fetal sex

tag: mode of conception

tag: fetal race


title: CVS_M_71394

description:
CVS.71394
CVS_71394_S46

tag: fetal ethnicity

tag: maternal age in years


title: Methylation_450k_sample340

tag: race

tag: gender

tag: age(yrs)

tag: plate

tag: phase


title: Methylation_450k_sample338

tag: column


title: Methylation_EPIC_sample176


title: Methylation_450k_sample339


title: CVS_F_71369

description:
CVS.71369
CVS_71369_S35

tag: tissue

tag: sample type

tag: paternal age in years

tag: maternal bmi pre-pregnancy

tag: rna integrity number


title: CVS_F_71318

description:
CVS.71318
CVS_71318_S88

tag: trimester

tag: sample gestational age in days


title: Methylation_EPIC_sample174

tag: row

tag: pedigreeid

tag: subjectid


title: CVS_M_71290

description:
CVS.71290
CVS_71290_S21

tag: fetal sex

tag: mode of conception

tag: fetal race

tag: fetal ethnicity

tag: maternal age in years


title: Methylation_450k_sample337

tag: race

tag: gender

tag: age(yrs)

tag: plate

value: E

tag: phase


title: Methylation_EPIC_sample175

tag: column


title: Methylation_EPIC_sample173


title: CVS_M_71314

description:
CVS.71314
CVS_71314

tag: tissue

tag: sample type

tag: paternal age in years

tag: maternal bmi pre-pregnancy

tag: rna integrity number


title: Methylation_450k_sample336

tag: row

tag: pedigreeid

tag: subjectid


title: Methylation_EPIC_sample172

value: B


title: CVS_M_71286

description:
CVS.71286
CVS_71286

tag: trimester

tag: sample gestational age in days

tag: fetal sex

tag: mode of conception

tag: fetal race


title: CVS_F_71289

description:
CVS.71289
CVS_71289_S34

tag: fetal ethnicity

tag: maternal age in years


title: CVS_M_71282

description:
CVS.71282
CVS_71282_S7


title: CVS_F_71250

description:
CVS.71250
CVS_71250_S55


title: Methylation_450k_sample335

tag: race

tag: gender

tag: age(yrs)

tag: plate

tag: phase


title: CVS_F_71218

description:
CVS.71218
CVS_71218_S131

tag: tissue

tag: sample type

tag: paternal age in years

tag: maternal bmi pre-pregnancy


title: Methylation_450k_sample334

tag: column

tag: row

tag: pedigreeid

tag: subjectid


title: Methylation_EPIC_sample171

value: A


title: CVS_F_71203

description:
CVS.71203
CVS_71203_S16

tag: trimester

tag: sample gestational age in days

tag: fetal sex

tag: mode of conception

value: Spontaneous

tag: rna integrity number


title: Methylation_EPIC_sample170

tag: race

tag: gender


title: Methylation_450k_sample333

tag: age(yrs)

tag: plate


title: CVS_F_71179

description:
CVS.71179
CVS_71179_S16

tag: tissue

tag: fetal race

value: Caucasian

tag: fetal ethnicity

tag: maternal age in years


title: CVS_M_71171

description:
CVS.71171
CVS_71171

tag: sample type

value: M

tag: paternal age in years

tag: maternal bmi pre-pregnancy


title: CVS_F_71335

description:
CVS.71335
CVS_71335_S41


title: CVS_F_71146

description:
CVS.71146
CVS_71146_S66


title: CVS_M_71186

description:
CVS.71186
CVS_71186_S104


title: Methylation_EPIC_sample169

value: African American (AA)

tag: column

tag: row

tag: pedigreeid

tag: subjectid

tag: phase


title: CVS_F_71129

description:
CVS.71129
CVS_71129_S17

tag: trimester

tag: sample gestational age in days

tag: fetal sex

tag: mode of conception

value: BiracialOther

tag: rna integrity number


title: CVS_M_71128

description:
CVS.71128
CVS_71128_S12

tag: tissue

value: Placenta (chorionic villi)


title: Methylation_450k_sample331

tag: race

tag: gender

tag: age(yrs)

tag: plate


title: CVS_M_71127

description:
CVS.71127
CVS_71127_S78

tag: sample type

value: CVS

tag: fetal race

tag: fetal ethnicity

tag: maternal age in years

tag: paternal age in years


title: Methylation_EPIC_sample168

tag: column

tag: row

tag: pedigreeid

tag: subjectid


title: Methylation_EPIC_sample166

tag: phase


title: Methylation_450k_sample330


title: Methylation_450k_sample329


title: CVS_F_71104

description:
CVS.71104
CVS_71104_S67

tag: trimester

value: First

tag: sample gestational age in days

tag: fetal sex

tag: mode of conception

tag: maternal bmi pre-pregnancy


title: Methylation_EPIC_sample165

tag: race

tag: gender

tag: age(yrs)


title: CVS_F_71095

description:
CVS.71095
CVS_71095

tag: tissue

tag: sample type

tag: fetal race

value: NonHispanic

tag: rna integrity number


title: CVS_F_71035

description:
CVS.71035
CVS_71035_S63

tag: fetal ethnicity

tag: maternal age in years

tag: paternal age in years


title: CVS_M_71038

description:
CVS.71038
CVS_71038_S144


title: CVS_M_70986

description:
CVS.70986
CVS_70986_S115

value: Hispanic


title: Methylation_450k_sample328

tag: plate

tag: column

tag: row

value: H

tag: pedigreeid

tag: subjectid


title: Methylation_450k_sample327

value: F

tag: phase


title: CVS_F_70959

description:
CVS.70959
CVS_70959_S77

tag: trimester

tag: sample gestational age in days

tag: fetal sex

tag: mode of conception

tag: maternal bmi pre-pregnancy


title: Methylation_450k_sample326

tag: race

tag: gender

tag: age(yrs)

value: G


title: Methylation_EPIC_sample162


title: Methylation_450k_sample325


title: CVS_M_70973

description:
CVS.70973
CVS_70973_S31

tag: tissue

tag: sample type

tag: fetal race

tag: fetal ethnicity

tag: rna integrity number


title: Methylation_EPIC_sample163

tag: plate

tag: column

tag: row


title: CVS_F_70964

description:
CVS.70964
CVS_70964_S42

tag: maternal age in years

tag: paternal age in years


title: CVS_F_70965

description:
CVS.70965
CVS_70965_S37

tag: trimester

tag: sample gestational age in days


title: Methylation_EPIC_sample164

tag: pedigreeid

tag: subjectid

tag: phase


title: CVS_M_70956

description:
CVS.70956
CVS_70956_S68

tag: fetal sex

tag: mode of conception

value: CaucasianAsian

tag: maternal bmi pre-pregnancy


title: Methylation_450k_sample332

tag: race

tag: gender

tag: age(yrs)


title: Methylation_EPIC_sample167

value: E


title: CVS_F_71099

description:
CVS.71099
CVS_71099_S39

tag: tissue

tag: sample type

tag: fetal race

tag: fetal ethnicity

tag: rna integrity number


title: CVS_M_70949

description:
CVS.70949
CVS_70949_S51

tag: maternal age in years

tag: paternal age in years


title: Methylation_450k_sample324

tag: plate

tag: column

tag: row


title: CVS_M_71086

description:
CVS.71086
CVS_71086_S13

tag: trimester

tag: sample gestational age in days


title: CVS_F_71016

description:
CVS.71016
CVS_71016_S73

tag: fetal sex

tag: mode of conception


title: Methylation_EPIC_sample160

tag: race

value: D

tag: pedigreeid

tag: subjectid

tag: phase


title: Methylation_450k_sample323

tag: gender

tag: age(yrs)

value: B


title: CVS_F_70922

description:
CVS.70922
CVS_70922_S14

tag: tissue

tag: sample type

value: Spontaneous

tag: fetal race

tag: fetal ethnicity

tag: maternal bmi pre-pregnancy


title: CVS_M_70913

description:
CVS.70913
CVS_70913_S30

value: Caucasian

tag: maternal age in years

tag: paternal age in years

tag: rna integrity number


title: Methylation_450k_sample322

value: M

tag: plate

tag: column

tag: row


title: CVS_M_70932

description:
CVS.70932
CVS_70932_S74

tag: trimester

tag: sample gestational age in days

tag: fetal sex

tag: mode of conception


title: CVS_M_70911

description:
CVS.70911
CVS_70911_S29


title: Methylation_EPIC_sample157

tag: race

value: African American (AA)

tag: gender

tag: pedigreeid

tag: subjectid

tag: phase


title: CVS_M_70903

description:
CVS.70903
CVS_70903_S62

tag: tissue

tag: sample type

tag: fetal race

value: BiracialOther

tag: fetal ethnicity


title: Methylation_EPIC_sample156

tag: age(yrs)


title: Methylation_450k_sample319

tag: plate


title: Methylation_EPIC_sample159

tag: column

value: C


title: CVS_F_70866

description:
CVS.70866
CVS_70866_S60

value: Placenta (chorionic villi)

value: CVS

tag: maternal age in years

tag: paternal age in years

tag: maternal bmi pre-pregnancy

tag: rna integrity number


title: Methylation_EPIC_sample155

tag: row


title: CVS_M_70910

description:
CVS.70910
CVS_70910_S17

tag: trimester

value: First

tag: sample gestational age in days

tag: fetal sex

tag: mode of conception

value: NonHispanic


title: CVS_M_70893

description:
CVS.70893
CVS_70893_S20


title: CVS_F_70879

description:
CVS.70879
CVS_70879_S11


title: CVS_M_70830

description:
CVS.70830
CVS_70830_S11


title: Methylation_EPIC_sample154

tag: race

tag: gender

value: H

tag: pedigreeid

tag: subjectid

tag: phase


title: Methylation_EPIC_sample161

value: F

tag: age(yrs)


title: Methylation_450k_sample317

tag: plate

value: G


title: CVS_F_70807

description:
CVS.70807
CVS_70807

tag: tissue

tag: sample type

tag: fetal race

tag: fetal ethnicity


title: CVS_F_70847

description:
CVS.70847
CVS_70847_S64

tag: maternal age in years

tag: paternal age in years

tag: maternal bmi pre-pregnancy

tag: rna integrity number


title: CVS_M_70838

description:
CVS.70838
CVS_70838_S52

tag: trimester

tag: sample gestational age in days

tag: fetal sex


title: CVS_F_70805

description:
CVS.70805
CVS_70805_S71

tag: mode of conception

value: Hispanic


title: Methylation_450k_sample318

tag: race

tag: gender

tag: column

tag: row

value: E

tag: pedigreeid


title: CVS_M_70801

description:
CVS.70801
CVS_70801_S75

tag: tissue


title: CVS_M_70784

description:
CVS.70784
CVS_70784_S48

tag: sample type


title: Methylation_EPIC_sample158

tag: age(yrs)

tag: plate

tag: subjectid

tag: phase


title: Methylation_450k_sample315


title: CVS_M_70906

description:
CVS.70906
CVS_70906_S76

tag: fetal race

tag: fetal ethnicity

tag: maternal age in years

tag: paternal age in years

tag: maternal bmi pre-pregnancy


title: Methylation_EPIC_sample153


title: Methylation_450k_sample321

value: A


title: Methylation_EPIC_sample152

value: D


title: Methylation_450k_sample316


title: CVS_F_70738

description:
CVS.70738
CVS_70738_S89

tag: trimester

tag: sample gestational age in days

tag: fetal sex

tag: mode of conception

value: Spontaneous

tag: rna integrity number


title: CVS_M_70747

description:
CVS.70747
CVS_70747_S5

value: Caucasian


title: Methylation_450k_sample314

tag: race

tag: gender

tag: column

tag: row

tag: pedigreeid


title: CVS_F_70713

description:
CVS.70713
CVS_70713_S40

tag: tissue

tag: sample type


title: CVS_F_70710

description:
CVS.70710
CVS_70710_S87

tag: fetal race


title: Methylation_EPIC_sample150

tag: age(yrs)

tag: plate

tag: subjectid

tag: phase


title: Methylation_EPIC_sample151


title: Methylation_450k_sample320

value: M


title: Methylation_450k_sample313

value: African American (AA)


title: CVS_M_70707

description:
CVS.70707
CVS_70707_S121

tag: trimester

tag: fetal ethnicity

tag: maternal age in years

tag: paternal age in years

tag: maternal bmi pre-pregnancy


title: Methylation_450k_sample312

tag: race


title: CVS_M_70705

description:
CVS.70705
CVS_70705

tag: sample gestational age in days

tag: fetal sex

tag: mode of conception

tag: rna integrity number


title: Methylation_EPIC_sample149

tag: gender

tag: column

tag: row

tag: pedigreeid


title: Methylation_EPIC_sample147

tag: age(yrs)

tag: plate


title: Methylation_450k_sample310

tag: subjectid

tag: phase


title: Methylation_EPIC_sample148

value: B


title: Methylation_450k_sample311

value: C


title: CVS_M_70774

description:
CVS.70774
CVS_70774_S34

tag: tissue

value: Placenta (chorionic villi)

tag: sample type

tag: trimester

tag: fetal race

tag: fetal ethnicity


title: CVS_F_70696

description:
CVS.70696
CVS_70696_S49

value: CVS

tag: sample gestational age in days

tag: maternal age in years

tag: paternal age in years

tag: maternal bmi pre-pregnancy


title: -AA_polysome_rep.2

city: Würzburg

first: Florian

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

institute: Julius-Maximilians-Universität Würzburg

data_processing:
Briefly, after adapter trimming, reads were first mapped against an rRNA database using Bowtie (Version 1.0)
All remaining reads were mapped against the human genome and transcriptome (Ensembl v90). Read mappings were merged (keeping all mapping with minimal amount of mismatches). Price (Version 1.0.2) was used to map reads to P site codons.
Genome_build: HG38
Supplementary_files_format_and_content: Price (Erhard et al., Nature Methods 2018) output (identified and quantified ORFs)

source_name: ribosome profiling

growth_protocol: HEK293 cells were cultured in DMEM supplemented with 10% FBS and P/S.

extract_protocol:
Cells were washed and detached with 10 ml ice cold PBS and collected at 1000 rpm for 5 minutes at 4°C. Cells were lysed in 250 µl lysis buffer (100mM KCl, 20mM Tris pH 7.5, 5mM MgCl2, 1mM DTT, 1mM Leupeptin, 1mM Pepstatin, 1mM Aprotinin, 0,1 mM PMSF, 0,1 mM AEBSF, 0,5% NP40, 100 µg/ml cycloheximide, 40 U/ml RNAsin (Promega)) for 10 minutes on ice. Cell debris were pelleted at 10k rpm for 10 minutes in an Eppendorf tabletop centrifuge.
Ribosome protected fragments (between 17-34 nts) were purified on a 15% PAA 8M Urea page. First, the ends were repaired using T4 polynucleotide kinase (NEB) with and without ATP to create a phosphorylated 5’- and a dephosphorylated 3’-end for 1 h at 37 °C each. Afterwards, libraries were prepared using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB) following the manufacturer’s protocol with only minor modifications. All adapters and primers were diluted 1:3 and 14 cycles of PCR were performed. No further size selection was performed. Libraries were quantified using a Qubit 3.0 (Thermo Scientific) and a 2100 Bioanalyzer (Agilent) and pooled equimolar. The pool of 12 ribosome profiling libraries was sequenced on a High-Output NextSeq 500 (Illumina) sequencing run with a read length of 75 nt.

treatment_protocol: 60% confluent cells were subjected to 2h of serum serum starvation (-FBS) or 1h of amino acid starvation EBSS +MEM Vitamins +10%FBS +P/S.

tag: cell line

value: HEK293 cells


title: -serum_polysome_rep.1


title: -AA_polysome_rep.1


title: -AA_monosome_rep.1


title: -AA_monosome_rep.2


title: Methylation_EPIC_sample145

tag: race

tag: gender

tag: column


title: -serum_monosome_rep.2


title: Methylation_450k_sample307

tag: age(yrs)

tag: row

tag: pedigreeid


title: Methylation_EPIC_sample143

tag: plate

tag: subjectid

tag: phase


title: Methylation_EPIC_sample146


title: LogPhase_monosome_rep.1


title: Methylation_450k_sample309


title: Methylation_450k_sample305


title: Methylation_EPIC_sample141


title: -serum_polysome_rep.2


title: -serum Lysate

data_processing:
Raw data were processed using kallisto (version 0.44.0) with parameters “--single -l 150 -s 15 --rf-stranded -b 100”. A custom index was prepared using the CCDS subset of Ensembl (version 90) transcripts, the ERCC92 spike-in sequences and the luciferase spike-in sequence.
The obtained transcript per million transcripts (TPM) values (including bootstraps) were then further processed using sleuth (version 0.29.0).
Whole lysates and gradient fractions were processed separately. For gradient fractions, the standard normalization factor of sleuth was substituted by the median luciferase spike-in expression.
To obtain gene-level values, spike-in normalized TPMs from transcripts were summarized.
The likelihood ratio test was computed from a generalized linear model based on natural cubic splines over the gradient fractions with 4 degrees of freedom (R package splines, ns function) and the three conditions, either with or without interaction term.
Then, all genes with total, spike-in normalized TPM of at least 100 summed over all gradient fractions for any of the three conditions were used for further analyzes. The polysomal peak was defined as the TPM weighted average of the polysomal fractions (14-22).
Genome_build: HG38
Supplementary_files_format_and_content: Tsv file containing the gene-wise transcripts per million (TPM) values inferred by kallisto

source_name: Poly(A)+ sequencing

extract_protocol:
Cells were washed and detached with 10 ml ice cold PBS supplemented with 100 µg/ml cycloheximide / 15cm culture dish and collected at 1000 rpm for 5 minutes at 4°C. Cells were lysed in 250 µl lysis buffer (100mM KCl, 20mM Tris pH 7.5, 5mM MgCl2, 1mM DTT, 1mM Leupeptin, 1mM Pepstatin, 1mM Aprotinin, 0,1 mM PMSF, 0,1 mM AEBSF, 0,5% NP40, 100 µg/ml cycloheximide, 40 U/ml RNAsin (Promega)) for 10 minutes on ice. Cell debris were pelleted at 10k rpm for 10 minutes in an Eppendorf tabletop centrifuge.
Library preparation was performed according to the Illumina TruSeq stranded mRNA Sample Preparation Guide with 300 - 500 ng of input RNA and 15 PCR cycles. All libraries were dual-indexed during PCR. Libraries were pooled equimolar and sequenced on an Illumina NextSeq 500 with a read length of 75 nt.

treatment_protocol: 60% confluent cells were subjected to 2h of serum serum starvation (-FBS) or 1h of amino acid starvation EBSS +MEM Vitamins +10%FBS +P/S. Cells were treated for 10 minutes with cyclohexamide in their respective medium.

tag: time post infection

value: Input Lysate


title: -serum_monosome_rep.1


title: Methylation_EPIC_sample144


title: LogPhase_polysome_rep.2


title: LogPhase_polysome_rep.1


title: Methylation_EPIC_sample140


title: -AA Fraction 22

value: Fraction 22


title: LogPhase_monosome_rep.2


title: Methylation_450k_sample306

value: F


title: -AA Fraction 20

value: Fraction 20


title: -AA Fraction 19

value: Fraction 19


title: Methylation_EPIC_sample138

value: G


title: -AA Fraction 18

value: Fraction 18


title: -AA Lysate


title: Methylation_EPIC_sample142

value: D


title: LogPhase Lysate


title: Methylation_EPIC_sample137


title: Methylation_450k_sample308


title: -AA Fraction 21

value: Fraction 21


title: Methylation_450k_sample304


title: Methylation_EPIC_sample139

value: A


title: -AA Fraction 16

value: Fraction 16


title: Methylation_450k_sample303

value: African American (AA)


title: Methylation_450k_sample299

value: M


title: Methylation_450k_sample302


title: Methylation_450k_sample301

value: H


title: -AA Fraction 15

value: Fraction 15


title: Methylation_450k_sample300

value: B


title: -AA Fraction 14

value: Fraction 14


title: -AA Fraction 17

value: Fraction 17


title: Methylation_450k_sample296


title: Methylation_EPIC_sample135


title: Methylation_EPIC_sample133


title: -AA Fraction 7

value: Fraction 7


title: -AA Fraction 12

value: Fraction 12


title: -AA Fraction 11

value: Fraction 11


title: -AA Fraction 13

value: Fraction 13


title: Methylation_EPIC_sample132

value: F


title: Methylation_450k_sample298


title: -AA Fraction 9

value: Fraction 9


title: Methylation_450k_sample297


title: Methylation_EPIC_sample136

value: D


title: Methylation_EPIC_sample130


title: Methylation_450k_sample294

value: G


title: Methylation_450k_sample295

value: E


title: -AA Fraction 3

value: Fraction 3


title: Sm5_e5

city: Vienna

first: Sylvia

last: Knapp

address: Währinger Gürtel 18-20

country: Austria

institute: Medical University of Vienna

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm38 (UCSC Genome Browser mm10) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.1a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.12 package DESeq2 1.30.0, running under R 4.0.0.
Assembly: UCSC mm10 based on GRCm38
Supplementary files format and content: rnaseq_deseq_global_counts_raw.tsv.gz: Per gene and sample raw (integer) counts in tab-separated value (TSV) format
Supplementary files format and content: rnaseq_deseq_global_fpkms.tsv.gz: Per gene and sample DESeq2-calculated FPKMs in tab-separated value (TSV) format

source_name: Spleen

extract_protocol: Full-length cDNA was prepared with the Smart-seq2 protocol (Picelli, S. et al, Nat Protoc. 2014 Jan;9(1):171-81. doi:10.1038/nprot.2014.006). The subsequent library preparation from the amplified cDNA was performed using the Nextera XT DNA library prep kit (Illumina). The libraries were sequenced on a Illumina HiSeq 4000 instrument with 50-bp single-read configuration.

tag: tissue

value: Spleen

tag: strain

tag: cell type

value: Ly6G+ Neutrophils

tag: treatment

value: LPS/Nacl treatment

tag: age

value: 10 weeks

tag: Sex

value: female


title: Methylation_450k_sample293

value: African American (AA)


title: Sm8_e8


title: Methylation_EPIC_sample129

value: C


title: -AA Fraction 5

tag: cell line

value: Fraction 5


title: Methylation_EPIC_sample131

tag: race

value: M


title: -AA Fraction 8

value: Fraction 8


title: Methylation_EPIC_sample134

tag: gender

value: H


title: -AA Fraction 4

value: Fraction 4


title: Sm3_e3


title: -serum Fraction 22

value: Fraction 22


title: Methylation_EPIC_sample128

tag: column

value: B


title: -AA Fraction 6

value: Fraction 6


title: -AA Fraction 10

value: Fraction 10


title: Sm4_e4


title: Methylation_450k_sample292

value: F

tag: age(yrs)


title: Sm9_e9

value: Spleen


title: Methylation_EPIC_sample127

tag: row

value: A


title: Methylation_450k_sample291

tag: pedigreeid


title: Methylation_450k_sample290

tag: plate

value: E


title: -serum Fraction 21

value: Fraction 21


title: Sm27_f10

value: Ly6G+ Neutrophils

value: Nacl/Infection

value: 10 weeks

value: female


title: Methylation_EPIC_sample126

value: African American (AA)

tag: subjectid


title: Methylation_450k_sample289

value: D

tag: phase


title: -serum Fraction 20

tag: time post infection

value: Fraction 20


title: Methylation_EPIC_sample125

value: M

value: C


title: -serum Fraction 19

value: Fraction 19


title: Methylation_450k_sample288


title: -serum Fraction 18

value: Fraction 18


title: Sm24_f7

tag: tissue


title: Sm23_f6

tag: strain


title: Methylation_EPIC_sample124

value: B


title: Methylation_450k_sample287

value: F


title: -serum Fraction 17

value: Fraction 17


title: Methylation_EPIC_sample123

value: A


title: Methylation_450k_sample286


title: -serum Fraction 16

value: Fraction 16


title: Sm15_f5

value: Spleen

tag: cell type

value: LPS/Infection


title: Methylation_450k_sample285


title: Methylation_450k_sample284


title: -serum Fraction 14

value: Fraction 14


title: Methylation_EPIC_sample121


title: Sm13_f3

value: Ly6G+ Neutrophils

tag: treatment

value: 10 weeks


title: Methylation_450k_sample283

value: African American (AA)


title: Sm26_f9

value: Nacl/Infection

tag: age

value: female


title: Sm10_e10

value: LPS/Nacl treatment

tag: Sex


title: Methylation_EPIC_sample119


title: -serum Fraction 15

tag: cell line

value: Fraction 15


title: BMm9_c9

source_name: Bone Marrow

value: Bone Marrow


title: -serum Fraction 13

value: Fraction 13


title: Methylation_450k_sample282

tag: race

value: H


title: -serum Fraction 12

value: Fraction 12


title: Methylation_EPIC_sample118

tag: gender

value: F


title: Methylation_450k_sample281

value: M

tag: column

value: B


title: Methylation_EPIC_sample117

tag: age(yrs)

value: D


title: BMm8_c8


title: -serum Fraction 11

value: Fraction 11


title: BMm7_c7


title: Methylation_EPIC_sample122

tag: row


title: -serum Fraction 10

value: Fraction 10


title: Sm14_f4

value: Spleen

value: Ly6G+ Neutrophils

value: LPS/Infection


title: BMm5_c5

value: 10 weeks


title: Methylation_EPIC_sample120

value: African American (AA)

tag: pedigreeid


title: Methylation_EPIC_sample116

tag: plate


title: Methylation_450k_sample279

value: A

tag: subjectid


title: Methylation_EPIC_sample115

tag: phase


title: Methylation_450k_sample278


title: BMm4_c4

value: LPS/Nacl treatment

value: female


title: Methylation_EPIC_sample114


title: Methylation_450k_sample280

value: G


title: -serum Fraction 9

tag: time post infection

value: Fraction 9


title: -serum Fraction 8

value: Fraction 8


title: Methylation_EPIC_sample113

value: F


title: Methylation_EPIC_sample112


title: Methylation_450k_sample276

value: M


title: BMm3_c3

tag: tissue

value: Bone Marrow


title: Methylation_450k_sample277

value: B


title: Methylation_450k_sample275


title: -serum Fraction 7

value: Fraction 7


title: BMm26_d9

tag: strain

value: Nacl/Infection


title: -serum Fraction 6

value: Fraction 6


title: BMm27_d10

tag: cell type

value: Ly6G+ Neutrophils


title: -serum Fraction 5

value: Fraction 5


title: BMm25_d8

tag: treatment

value: 10 weeks


title: Methylation_EPIC_sample111

value: African American (AA)


title: Methylation_450k_sample274

value: H


title: -serum Fraction 4

value: Fraction 4


title: Methylation_450k_sample273

value: E


title: Methylation_450k_sample270

value: C


title: Methylation_450k_sample272

value: D


title: Methylation_EPIC_sample110


title: Methylation_450k_sample271


title: Methylation_EPIC_sample107


title: BMm23_d6

tag: age

value: female


title: BMm14_d4

value: LPS/Infection

tag: Sex


title: -serum Fraction 3

tag: cell line

value: Fraction 3


title: LogPhase Fraction 20

value: Fraction 20


title: Methylation_450k_sample269

tag: race

value: F


title: BMm1_c1

value: Bone Marrow

value: LPS/Nacl treatment


title: LogPhase Fraction 21

value: Fraction 21


title: Methylation_EPIC_sample109

tag: gender

value: G


title: LogPhase Fraction 22

value: Fraction 22


title: Methylation_EPIC_sample108

tag: column


title: BMm24_d7

value: Ly6G+ Neutrophils

value: Nacl/Infection

value: 10 weeks


title: BMm13_d3


title: Methylation_EPIC_sample105

value: African American (AA)

tag: age(yrs)


title: BMm11_d1


title: Methylation_EPIC_sample104

tag: row

value: B


title: LogPhase Fraction 18

value: Fraction 18


title: BMm10_c10


title: LogPhase Fraction 17

value: Fraction 17


title: Methylation_450k_sample268

value: D

tag: pedigreeid


title: Methylation_450k_sample267

tag: plate


title: LogPhase Fraction 19

value: Fraction 19


title: BMm15_d5

value: LPS/Infection

value: female


title: Methylation_EPIC_sample106

value: F

tag: subjectid


title: Methylation_EPIC_sample102

value: H

tag: phase


title: Methylation_450k_sample266

value: C


title: Methylation_EPIC_sample101


title: Bm9_a9

source_name: Blood

value: Blood

value: LPS/Nacl treatment


title: LogPhase Fraction 16

tag: time post infection

value: Fraction 16


title: LogPhase Fraction 15

value: Fraction 15


title: Methylation_450k_sample264


title: LogPhase Fraction 12

value: Fraction 12


title: Methylation_450k_sample262

value: M

value: A


title: Bm7_a7

tag: tissue

value: Ly6G+ Neutrophils

value: 10 weeks


title: Methylation_450k_sample263

value: African American (AA)


title: Methylation_EPIC_sample100


title: Bm6_a6

tag: strain


title: LogPhase Fraction 14

value: Fraction 14


title: Bm8_a8

tag: cell type


title: Methylation_450k_sample261


title: Bm5_a5

tag: treatment


title: Methylation_EPIC_sample103


title: LogPhase Fraction 13

value: Fraction 13


title: Methylation_EPIC_sample99

value: E


title: Methylation_EPIC_sample97

value: B


title: Methylation_EPIC_sample98

value: F


title: Methylation_450k_sample260

value: H


title: Bm4_a4

tag: age

value: female


title: LogPhase Fraction 11

value: Fraction 11


title: Methylation_EPIC_sample96


title: Methylation_450k_sample265


title: Bm3_a3

value: Blood

value: LPS/Nacl treatment

tag: Sex


title: Bm2_a2


title: Methylation_EPIC_sample95


title: Methylation_450k_sample259


title: Methylation_450k_sample258

value: G


title: Bm26_b10

value: Nacl/Infection


title: Methylation_EPIC_sample93


title: Methylation_EPIC_sample92

value: M


title: Methylation_450k_sample257

value: A


title: LogPhase Fraction 7

tag: cell line

value: Fraction 7


title: LogPhase Fraction 8

value: Fraction 8


title: Bm25_b9

value: Ly6G+ Neutrophils

value: 10 weeks


title: LogPhase Fraction 9

value: Fraction 9


title: LogPhase Fraction 6

value: Fraction 6


title: LogPhase Fraction 5

value: Fraction 5


title: Bm24_b8


title: Methylation_450k_sample254

tag: race

value: African American (AA)


title: Methylation_EPIC_sample90

tag: gender

value: F

value: B


title: LogPhase Fraction 4

value: Fraction 4


title: Methylation_450k_sample256

tag: column

value: H


title: Methylation_450k_sample253

tag: age(yrs)


title: Methylation_450k_sample255

tag: row


title: Methylation_EPIC_sample91

value: C

tag: pedigreeid


title: LogPhase Fraction 3

value: Fraction 3


title: Bm1_a1

value: Blood

value: LPS/Nacl treatment

value: female


title: LogPhase Fraction 10

value: Fraction 10


title: Methylation_EPIC_sample89

tag: plate

value: A


title: Bm15_b5

value: Ly6G+ Neutrophils

value: LPS/Infection


title: Bm23_b7

value: Nacl/Infection

value: 10 weeks


title: Methylation_EPIC_sample94

value: M

value: G

tag: subjectid


title: Methylation_450k_sample252

value: African American (AA)

value: F

tag: phase


title: Methylation_450k_sample251

value: E


title: Bm14_b4


title: Methylation_EPIC_sample87


title: Methylation_EPIC_sample86


title: Bm13_b3


title: Methylation_450k_sample250


title: Methylation_450k_sample249

value: D


title: Bm12_b2


title: Methylation_450k_sample248


title: Methylation_450k_sample247

value: C


title: Bm11_b1


title: Methylation_EPIC_sample83


title: Methylation_EPIC_sample85

value: H


title: w11_Mutant4

type: RNA

city: Dresden

first: Anne

last: Grapin-Botton

state: Saxony

address: Pfotenhauerstrasse 108

institute: Max Planck Institute of Molecular Cell Biology and Genetics, Dresde

description: 843M mutant Pdx1CreER Tg+; Wnt4fl/fl

hyb_protocol: 600ng of Cy3-labelled cRNA was used for hybridization step using the Gene Expression Hybridization kit (AgilentTechnologies, #5188-5242) following the manufacturers instructions. Cy3-labelled cRNA was hybridized to Agilent Whole Mouse Genome Oligo Microarrays 4x44k (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried and scanned.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for GE 8x60k microarrays array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng of RNA with the low input Quick Amp Labeling Kit (Agilent Technologies, #5190-2305) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop 2000 Spectrophotometer.

growth_protocol: Mice were crossed to C57BL/6J and raised under SPF condition

extract_protocol: RNA was prepared using RNeasy Plus Micro Kit (Qiagen, # 74034) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop 2000 spectrophotometer and with the Agilent 2100 Bioanalyzer.

treatment_protocol: 4-5 week-old control and Wnt4βKO mice were injected with 200 mL Tamoxifen solution (50mg/mL) twice every other day by gavage. These mice were euthanized at 7 weeks islet collection

tag: genotype

value: Wnt4 betaKO


title: w11_Mutant3

description: 835M mutant Pdx1CreER Tg+; Wnt4fl/fl


title: Methylation_450k_sample246


title: Methylation_EPIC_sample82


title: w11_Mutant2

description: 811M mutant Pdx1CreER Tg+; Wnt4fl/fl


title: w11_Mutant1

description: 809M mutant Pdx1CreER Tg+; Wnt4fl/fl


title: H3K27me3_KCl_0min_exp1

value: primary corticol neurons

tag: antibody used for cut&run


title: H3K27me3_KCl_0min_exp2

tag: strain


title: w11_Control3

description: 833C control Pdx1CreER Tg-; Wnt4fl/fl

value: WT


title: w11_Control4

description: 855C control Pdx1CreER Tg-; Wnt4fl/fl


title: exp2_r2_hrs16-20_b1_L004

city: Seattle

first: Diego

last: Calderon

address: 3720 15th Ave NE

institute: University of Washington

data_processing:
The sci-ATAC-seq3 raw reads were processed using the pipeline described in (Domcke et al. 2020). Reads were mapped to the dm6 reference genome. The non-duplicate fragments are used for peak calling with MACS2 (Zhang et al. 2008) in each sample, and then merged together with bedtools (Quinlan and Hall 2010). We generate sparse matrices counting reads falling into the merged peak set for cells passing a sample-specific threshold for each sample.
Genome_build: dm6
Supplementary_files_format_and_content: MM sparse matrix containing the sci-ATAC-seq read count for peaks (rows) by nuclei (cols).

source_name: whole embryo

extract_protocol:
Drosophila melanogaster embryos were collected as previously described (Sandmann, Jakobsen, and Furlong 2006; Cusanovich et al. 2018).
To create the sci-ATAC-seq3 libraries, we followed the protocol from (Domcke et al. 2020).

tag: developmental stage

value: Drosophila embryo (0-20 hrs)


title: Methylation_EPIC_sample88


title: Methylation_EPIC_sample81


title: w11_Control2

description: 827C control Pdx1CreER Tg-; Wnt4fl/fl


title: Methylation_450k_sample244


title: Methylation_450k_sample243


title: Methylation_EPIC_sample80


title: Bm10_a10

tag: tissue

value: Blood

tag: cell type

tag: treatment

value: female


title: Methylation_EPIC_sample79

value: B


title: Methylation_EPIC_sample84


title: exp2_r2_hrs16-20_b1_L002


title: exp2_r2_hrs16-20_b1_L003


title: Methylation_450k_sample245


title: Methylation_EPIC_sample78

value: A


title: exp2_r2_hrs14-18_b1_L004


title: Methylation_450k_sample241


title: exp2_r2_hrs16-20_b1_L001


title: Methylation_EPIC_sample77


title: VC88.6H.MA

city: Bronx

first: Joan

middle: W

last: Berman

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: Methamphetamine treated sample 1

data_processing:
Sequenced reads were trimmed using Trimmomatic v.0.36
Trimmed reads were mapped using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2
Assembly: Homo sapiens GRCh38 reference genome available on ENSEMBL
Supplementary files format and content: The processed csv data file contains unique gene hit counts that fell within exon regions for each sample

source_name: Primary human mature monocytes

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Micro Kit (Qiagen, Hilden, Germany)
Ribosomal RNA depletion

tag: cell line

value: Primary human mature monocytes

value: HIV-infected mature monocytes

value: HIV + Methamphetamine


title: VC87.6H.MA

description: Methamphetamine treated sample 3


title: Methylation_450k_sample240

tag: race

value: African American (AA)


title: Methylation_EPIC_sample76

tag: gender

value: M


title: exp2_r2_hrs14-18_b1_L002


title: Methylation_EPIC_sample75

tag: column


title: exp2_r2_hrs14-18_b1_L003


title: IgG_KCl_0min_exp2

tag: age

value: Millipore PP64B (Lot#3229748)


title: Methylation_450k_sample239

value: F

tag: age(yrs)

tag: row


title: VC87.UNTX

description: Untreated sample 3

value: HIV


title: VC89.UNTX

description: Untreated sample 2


title: Methylation_450k_sample238

tag: plate

value: H

tag: pedigreeid


title: IgG_KCl_0min_exp1


title: Methylation_EPIC_sample74

tag: subjectid

tag: phase


title: VC88.UNTX

description: Untreated sample 1


title: exp2_r2_hrs14-18_b1_L001


title: exp2_r2_hrs12-16_b1_L004


title: 5Y_siGL2_B3

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

country: France

institute: I-Stem

description: replicate 3

data_processing:
High throughput sequencing of 125 bp paired-end reads was carried out on an Illumina HiSeq 2500 platform (Genewiz), generating an average number of 45 millions of mating pairs of reads
Mapping & QC-mapped with Tophat2 (2.0.13) & Samtools (0.1.19)
Filtering with Cutadapt
DEG analysis with DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Csv file with raw counts and raw DEG.

source_name: Neuroblastoma SH-SY5Y cell line (ECACC)

growth_protocol: SH-SY5Y cells (ECACC) were grown and transfected essentially as recommended by the supplier

extract_protocol:
Total RNA were isolated using TriPure Isolation Reagent (Roche)
Stranded RNA libraries were prepared after enrichment of polyA+ RNA.

treatment_protocol: cells were transfected with 20 nM siRNA targeting DDX5 and DDX17, or with a control siRNA (siGL2, targeting luciferase) and harvested for RNA extraction 48h post-transfection

value: Control siRNA anti-GL2


title: Methylation_450k_sample237


title: Methylation_450k_sample242


title: exp2_r2_hrs12-16_b1_L003


title: Methylation_EPIC_sample73


title: VC89.6H.MA

description: Methamphetamine treated sample 2


title: 5Y_siGL2_B2

description: replicate 2


title: Methylation_EPIC_sample71


title: Methylation_450k_sample235


title: exp2_r2_hrs12-16_b1_L002


title: Methylation_450k_sample234


title: exp2_r2_hrs12-16_b1_L001


title: Methylation_EPIC_sample70


title: 5Y_siDDX5-17_B3

description: replicate 3

value: siRNA anti-DDX5/DDX17


title: 5Y_siGL2_B1

description: replicate 1


title: Methylation_EPIC_sample69


title: 5Y_siDDX5-17_B2

description: replicate 2


title: exp2_r2_hrs10-14_b1_L004


title: Methylation_450k_sample232


title: Methylation_EPIC_sample68

value: D


title: Methylation_450k_sample236

value: G


title: 5Y_siDDX5-17_B1

description: replicate 1


title: Methylation_450k_sample231


title: exp2_r2_hrs10-14_b1_L002

value: Drosophila embryo (0-20 hrs)


title: Methylation_450k_sample230


title: Methylation_EPIC_sample67

value: C


title: shDKC1 polysomal RNA replicate 3

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

description:
rawcounts_genes.tsv
rawcounts_transcripts.tsv

data_processing:
Illumina Casava 1.8 software was used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence and low-quality nucleotides, then quantified against the Gencode v28 transcriptome using STAR (genes) and Salmon(transcripts) with default parameters
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample

source_name: MCF7 cells

growth_protocol: MCF-7 (female, estrogen-positive invasive breast ductal carcinoma derived) cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 100 U/ml penicillin, 1 mg/ml streptomycin, and 2 mM L-glutamine.

extract_protocol:
Polysomal separation was performed as follows: samples were loaded in 10-50% linear sucrose gradients, ultra-centrifuged and fractionated with an automated fraction collector. All the fractions containing subpolysomal or polysomal RNA were identified and pooled in two separate tubes. RNA was purified by extraction with 1 volume of phenol-chloroform and precipitated with isopropanol.
RNA libraries were prepared for sequencing using standard Illumina protocols: Illumina TruSeq RNA Sample Prep Kit was used with 1.5 ug of total RNA as input.

treatment_protocol: Cells were transfected with siRNAs targeting DKC1 (Invitrogen, catalog number HSS102781: 5’-AACACCUGGAAGCAUAAUCUUGGCC-3’, HSS102782: 5’-UAAACAACCAGUCACCUUGGGAUCC-3’, HSS102785: 5’-GAAGUCACAACAGAGUGCAGGCAAA-3’) and an appropriate control (Cat. N° 12935300 - Invitrogen xy) using Lipofectamine RNAiMAX reagent (Invitrogen) in OptiMEM medium (Invitrogen) according to the manufacturer’s instructions

tag: transfection

value: siRNAs targeting DKC1

tag: genotype

value: DKC1 silencing


title: exp2_r2_hrs10-14_b1_L001

tag: developmental stage


title: Methylation_EPIC_sample65

source_name: peripheral blood leukocytes


title: Methylation_EPIC_sample66

value: B


title: shDKC1 total RNA replicate 3


title: exp2_r2_hrs03-07_b2_L004


title: Methylation_450k_sample229

value: E


title: Methylation_EPIC_sample72


title: Methylation_450k_sample228


title: scramble polysomal RNA replicate 3

value: scramble control

value: wild type


title: exp2_r2_hrs03-07_b2_L003


title: Methylation_450k_sample233

value: African American (AA)


title: Methylation_450k_sample227


title: Methylation_EPIC_sample64


title: scramble total RNA replicate 3


title: exp2_r2_hrs10-14_b1_L003


title: Methylation_EPIC_sample63

value: M


title: exp2_r2_hrs03-07_b2_L002


title: Methylation_450k_sample226

value: F


title: shDKC1 polysomal RNA replicate 2


title: exp2_r2_hrs03-07_b2_L001


title: Methylation_EPIC_sample62


title: exp2_r2_hrs02-04_b2_L004


title: shDKC1 total RNA replicate 2


title: Methylation_450k_sample225


title: scramble polysomal RNA replicate 2


title: Methylation_EPIC_sample61


title: Methylation_450k_sample224


title: Methylation_EPIC_sample60


title: scramble total RNA replicate 2


title: Methylation_EPIC_sample59


title: exp2_r2_hrs02-04_b2_L003


title: Methylation_450k_sample222


title: shDKC1 polysomal RNA replicate 1


title: Methylation_450k_sample223


title: exp2_r2_hrs02-04_b2_L002


title: Methylation_EPIC_sample58

value: A


title: Methylation_450k_sample220


title: exp2_r2_hrs01-03_b2_L004


title: scramble polysomal RNA replicate 1


title: Methylation_450k_sample221


title: Methylation_EPIC_sample57

value: H


title: Methylation_EPIC_sample56


title: scramble total RNA replicate 1


title: Methylation_450k_sample219


title: exp2_r2_hrs01-03_b2_L003


title: Methylation_450k_sample217


title: Input Cytosol - replicate 5

source_name: MCF cells

extract_protocol:
RNA was purified by extraction with 1 volume of phenol-chloroform and precipitated with isopropanol.
RNA libraries were generated using the SMART-Seq Stranded Kit (Takara), using 10ng of input material for each sample.

treatment_protocol: A total amount of lysate corresponding to 500 ug of protein content from MCF7 and MDA-MB 231 cells were pre-cleaned with protein A/G Plus-Agarose beads (Santa-Cruz, sc-2003) for 1 hour at 4 °C. Five to ten percent of pre-cleaned sample was saved as input for subsequent analysis. The remainder was used in immunoprecipitation reactions with rabbit IgG (Santa Cruz, sc-2027) or rabbit polyclonal antibody against DKC1 (Genetex GTX 109000) see antibody table) with incubation overnight at 4 °C. Afterwards, anti-dyskerin interacting fraction was captured using protein A/G Plus-Agarose beads and washed several times with Wash Buffer (25 mM Tris-HCl pH 7.5, 150 mM KCl, 5 mM MgCl2, 1mM EGTA, 10 % glycerol and protease and RNAse inhibitor cocktail). Two thirds of the immunoprecipitated solution were used for RNA extraction.

tag: antibody


title: exp2_r2_hrs01-03_b2_L002


title: exp2_r2_hrs01-03_b2_L001


title: Methylation_450k_sample218


title: exp2_r2_hrs02-04_b2_L001


title: exp2_r2_hrs00-02_b2_L004


title: Methylation_EPIC_sample53


title: Methylation_450k_sample215


title: Methylation_EPIC_sample52


title: IgG Cytosol RIP - replicate 4

molecule: cytoplasmic RNA

value: rabbit IgG (Santa Cruz, sc-2027)


title: DKC1 Cytosol RIP - replicate 5

value: antibody against DKC1 (Genetex GTX 109000)


title: DKC1 Cytosol RIP - replicate 4


title: Methylation_EPIC_sample51


title: Methylation_450k_sample214


title: exp2_r2_hrs00-02_b2_L002


title: Methylation_EPIC_sample55


title: shDKC1 total RNA replicate 1


title: Methylation_450k_sample213


title: exp2_r2_GM+CH12.barnyard_b1_L004


title: Methylation_EPIC_sample54


title: Methylation_EPIC_sample48


title: exp2_r2_GM+CH12.barnyard_b1_L003


title: Methylation_EPIC_sample49


title: Methylation_450k_sample216


title: exp2_r2_hrs00-02_b2_L001


title: Input Cytosol - replicate 3


title: DKC1 Cytosol RIP - replicate 3


title: Methylation_450k_sample211


title: Methylation_450k_sample212


title: Input Cytosol - replicate 4


title: Methylation_EPIC_sample50


title: exp2_r2_hrs00-02_b2_L003


title: Methylation_450k_sample210


title: Methylation_EPIC_sample47


title: exp2_r2_GM+CH12.barnyard_b1_L002


title: IgG Cytosol RIP - replicate 5


title: Methylation_EPIC_sample46


title: exp2_r2_GM+CH12.barnyard_b1_L001


title: exp1_r2_hrs16-20_b1_L004


title: Input Cytosol - replicate 2


title: exp1_r2_hrs16-20_b1_L002


title: Methylation_450k_sample207


title: Methylation_EPIC_sample45


title: Methylation_450k_sample206


title: IgG Cytosol RIP - replicate 3


title: Methylation_450k_sample208


title: IgG Cytosol RIP - replicate 2


title: Methylation_450k_sample205


title: Methylation_EPIC_sample43


title: Methylation_EPIC_sample41


title: DKC1 Cytosol RIP - replicate 2


title: exp1_r2_hrs16-20_b1_L003


title: IgG Cytosol RIP - replicate 1


title: Methylation_450k_sample204


title: DKC1 Cytosol RIP - replicate 1


title: exp1_r2_hrs16-20_b1_L001


title: Input Cytosol - replicate 1


title: Methylation_EPIC_sample39


title: Methylation_EPIC_sample42


title: P-6388_S-8770

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

library_source: transcriptomic single cell

data_processing:
Cell Ranger (10x Genomics) was used with default parameters to demultiplex reads and align sequencing reads to the genome, distinguish cells from background, and obtain gene counts per cell.
Alignment was performed using the hg19 reference genome build, coupled with the Ensembl transcriptome (v75). In the case of snRNAseq, reads mapping to intronic regions were included.
Assembly: hg19
Supplementary files format and content: README_scRNA.md: markdown file containing information on the metadata, barcodes, features and matrix files.
Supplementary files format and content: *__features.tsv.gz, *__barcodes.tsv.gz,  *__matrix.mtx.gz: compressed filtered features, barcodes and expression matrices generated by Cell Ranger.
Supplementary files format and content: *.metadata.NG2022.tsv: Tab-separated file containing info for each cell.

source_name: tumor

extract_protocol:
Fresh tumors collected after surgery were enzymatically digested and mechanically dissociated using the papain version of the Brain Tumor Dissociation kit (Miltenyi Biotech) or the Worthington Papain dissociation kit. Red blood cells were lysed by ammonium chloride treatment for 5 min on ice. Cell viability was assessed with Trypan Blue. For samples with low viability (< 60%), dissociated cells were enriched for live cells using the Dead Cell Removal kit (Miltenyi Biotech).
Cell capture and library preparation was performed according to the Chromium Single Cell 3’ (v3) protocol.

tag: tissue

value: tumor

tag: Sex

value: male

tag: age (years)

tag: location

value: Parietal lobe

tag: diagnosis

value: high-grade glioma

tag: cellranger version(processing)

tag: technology

value: 10X Chromium Single Nuclei 3'


title: Methylation_450k_sample209

extract_protocol: genomic DNA was extracted from stored peripheral blood leukocytes using AutoGen FlexStar (AutoGen, Holliston, MA) and DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA)

tag: race

tag: gender

tag: age(yrs)

tag: column

value: G


title: exp1_r2_hrs14-16_b1_L003

value: Drosophila embryo (0-20 hrs)


title: Methylation_EPIC_sample40

tag: plate

tag: row

value: E

tag: pedigreeid

tag: subjectid


title: exp1_r2_hrs14-16_b1_L004

tag: developmental stage


title: Methylation_450k_sample202

value: C

tag: phase


title: exp1_r2_hrs14-16_b1_L002


title: P-6431_S-8842

tag: tissue

value: posterior fossa

value: Ependymoma

value: 10X Chromium Single Cell 3'


title: Methylation_450k_sample203

value: African American (AA)

value: F


title: P-6337_S-8821

tag: Sex

value: brain


title: Methylation_EPIC_sample44


title: Methylation_EPIC_sample38

value: M

value: H


title: exp1_r2_hrs14-16_b1_L001


title: Methylation_EPIC_sample37


title: P-6329_S-8673

value: tumor

tag: age (years)


title: P-6328_S-8672

value: female

tag: location


title: Methylation_450k_sample201


title: exp1_r2_hrs12-16_b1_L004


title: Methylation_450k_sample199


title: Methylation_EPIC_sample36


title: exp1_r2_hrs12-16_b1_L003


title: Methylation_450k_sample198


title: exp1_r2_hrs12-16_b1_L002


title: P-6308_S-8632

value: male

value: Parietal lobe

tag: diagnosis


title: Methylation_EPIC_sample34

value: D


title: exp1_r2_hrs12-16_b1_L001


title: exp1_r2_hrs10-14_b1_L004


title: Methylation_EPIC_sample33

value: B


title: Methylation_450k_sample196


title: exp1_r2_hrs10-14_b1_L003

value: Drosophila embryo (0-20 hrs)


title: P-6292_S-8579

tag: cellranger version(processing)


title: P-6255_S-8500

value: brainstem

value: high-grade glioma

tag: technology

value: 10X Chromium Single Nuclei 3'


title: P-6254_S-8499


title: Methylation_EPIC_sample32

tag: race

value: A


title: Methylation_EPIC_sample31

tag: gender


title: Methylation_450k_sample195

tag: age(yrs)


title: Methylation_EPIC_sample30

tag: column

value: C


title: exp1_r2_hrs10-14_b1_L001


title: Methylation_EPIC_sample35

value: African American (AA)

tag: plate

value: E


title: exp1_r2_hrs10-14_b1_L002


title: P-6253_S-8498


title: Methylation_450k_sample194

tag: row


title: P-6251_S-8496


title: Methylation_450k_sample200

value: F

tag: pedigreeid


title: exp1_r2_hrs08-12_b1_L004


title: Methylation_EPIC_sample29

value: M

tag: subjectid


title: Methylation_450k_sample197


title: P-6240_S-8628

value: brain

value: 10X Chromium Single Cell 3'


title: Methylation_450k_sample192

value: H


title: Methylation_EPIC_sample28


title: exp1_r2_hrs08-12_b1_L002

tag: developmental stage


title: Methylation_450k_sample191

tag: phase


title: P-6166_S-8321

tag: tissue

value: tumor

value: male

value: right frontal lobe


title: Methylation_EPIC_sample27


title: P-6117_S-8370

tag: Sex

value: left thalamus


title: Methylation_450k_sample190

value: G


title: Methylation_EPIC_sample26


title: P-5613_S-7162

value: female

tag: age (years)

value: right temporal lobe


title: Methylation_450k_sample189


title: exp1_r2_hrs06-10_b1_L004

value: Drosophila embryo (0-20 hrs)


title: Methylation_450k_sample188


title: Methylation_450k_sample187

value: B


title: Methylation_450k_sample193

value: C


title: Methylation_EPIC_sample24

value: African American (AA)

value: A


title: P-5099_S-6218

tag: location

value: frontal lobe

value: high-grade glioma

value: 10X Chromium Single Nuclei 3'


title: P-4198_S-4459

value: pons

tag: diagnosis


title: P-4504_S-4916

value: thalamus

tag: cellranger version(processing)


title: exp1_r2_hrs06-10_b1_L002


title: Methylation_450k_sample186

value: F


title: Methylation_EPIC_sample23

value: H


title: exp1_r2_hrs06-10_b1_L003


title: exp1_r2_hrs06-10_b1_L001


title: exp1_r2_hrs08-12_b1_L003


title: P-3407_S-3447

value: tumor

tag: technology


title: Methylation_EPIC_sample21

tag: race


title: exp1_r2_hrs04-08_b1_L004


title: P-3387_S-3411

value: left temporal lobe


title: exp1_r2_hrs04-08_b1_L003


title: Methylation_EPIC_sample20

tag: gender

value: M


title: Methylation_450k_sample183

tag: age(yrs)


title: exp1_r2_hrs08-12_b1_L001


title: P-3200_S-3254

value: male

value: left frontal lobe


title: Methylation_450k_sample185

tag: column


title: Methylation_450k_sample184

tag: plate


title: Methylation_EPIC_sample19

tag: row


title: exp1_r2_hrs04-08_b1_L002

value: Drosophila embryo (0-20 hrs)