title: MPRA1 plasmid DNA barcode reads, replicate 5

first: Yonatan

middle: Ariel

last: Cooper

address: 695 South Charles E Young Dr.  Gonda Building 2309

institute: University of California, Los Angeles

description:
MPRA barcode reads used for expression analysis
MPRA1_Plasmid_DNA_005
processed data file: MPRA1_merged_counts.txt

data_processing:
library strategy: targeted amplicon sequencing
Variant-barcode paired-end mapping reads were merged with BBMerge v9 from the bbtools software suite. All merged fastq files are presented here for both MPRA libraries. A custom python script was used to map unique barcodes to variants. This script identified the last 162 bp of merged reads for sequences perfectly matching the variants listed in the MPRA_variant_list.tsv files. The first 20 bp of each merged read were determined to be a barcode and each barcode was then mapped to the most common sequence associated with it, only retaining barcodes that appeared more than twice in merged reads. In order to identify ambiguously mapped barcodes, we generated a Levenshtein distance cut-off representing the 1st percentile of the total bootstrapped distances between all variants. Barcodes mapped to perfect variants were kept if all other variants associated with a barcode fell below this cut-off. This barcode-mapping output is the variant-barcode lookup table, indicated by MPRA1_variant_barcode_table.txt and MPRA2_variant_barcode_table.txt, and used in downstream MPRA expression analysis. Mapping script available: https://github.com/ycooper27/Tauopathy-MPRA.
MPRA barcode reads were processed using a custom python script to isolate barcode sequences from reads and determine the total count of each barcode. Briefly, the first 20 bp of each read were extracted, reverse complemented, and then mapped to the previously generated variant-barcode lookup table. Perfectly matching reads were kept and counted. Read counts from all Plasmid DNA and mRNA replicates for each experiment were merged into one count table listed here as MPRA1_merged_counts.txt and MPRA2_merged_counts.txt.
Downstream MPRA expression analysis was performed in R version 4.0.0. Merged count tables were loaded into R. A pseudocount of 1 was added, and each library was normalized to sequencing depth to create CPM which were log2 transformed. Barcodes were filtered such that barcodes with fewer than ~4 total raw counts per replicate were removed. Variants with fewer than 6 unique barcodes for either allele were removed. RNA and DNA replicates were split, and then quantile normalized using the preprocessCore (1.50.0) package. An RNA/DNA ratio was then taken representing transcriptional rate.
Supplementary_files_format_and_content: MPRA*_variant_barcode_table.txt: mapped variant-barcode lookup table
Supplementary_files_format_and_content: MPRA*_variant_list.tsv: variant ID and DNA sequence table
Supplementary_files_format_and_content: MPRA*_merged_counts.txt: combines barcode read counts from all mRNA and plasmid DNA replicates for the MPRA 1 or 2 experiment. Tab separated file has barcodes (rows) X replicate (columns)

source_name: HEK293T_MPRA1 plasmid DNA barcode reads

growth_protocol: LB

extract_protocol:
QIAprep (Qiagen, Hilden, Germany) spin miniprep kits
25 ng of plasmid were amplified for 8 cycles using NEBNext Q5 MasterMix, followed by SPRI bead cleanup. A second PCR was performed for 7 cycles in order to add P5 and P7 Illumina flow cell adapter sequences and indices. 0.5 ng was amplified for a total of 7 cycles. Bands were confirmed using Agilent’s D1000 ScreenTape and reagents (Agilent Technologies) on a 2200 Tapestation system.

tag: source

value: ATCC (CRL-3216)

tag: molecule subtype

value: Plasmid DNA


title: CD8TEM_Y1

status: Public on Dec 25 2020

type: SRA

city: Xi’an

first: Anjun

last: Jiao

state: Shaanxi

address: No. 28, Xianning West Road, Xi'an City, Shaanxi Province

country: China

institute: Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University

library_source: transcriptomic

data_processing:
The BGISEQ-500 sequencer software used for basecalling.
The double-stranded cDNA library was finished through PCR enrichment and size selection. The prepared cDNA library was sequenced with the BGISEQ-500 platform (Beijing Genomics Institute, BGI) after pooling according to its expected data volume and effective concentration.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: effector memory CD8+ T cells

growth_protocol: ZsGreen+ CD4 TEM, CD4 TCM, CD4 naïve T cells, and CD8 TEM, CD8 TCM, and CD8 naïve T cells were sorted from the spleens of TCRδCreERR26ZsGreen mice at the age of 8 weeks (Young) and 78 weeks (Old), respectively.

extract_protocol:
Total RNA was extracted using the Quick-RNA Microprep Kit (Zymo Research) according to the manufacturer’s protocol. RNA concentration was detected by the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen). After quality control using the Agilent RNA 6000 Nano Kit with the Agilent 2100 Bio analyse (Agilent Technologies). Library construction and RNA sequencing on the BGISEQ-500 platform were conducted at the Beijing Genomics Institute (BGI).
RNA libraries were prepared for sequencing according to the standard protocols provided by the Beijing Genomics Institute (BGI).

treatment_protocol: For long-term tracing experiments, TCRδCreERR26ZsGreen mice (five weeks old, n= 10) were treated with three doses of 1 mg/mouse tamoxifen intraperitoneal injection (i.p.) every other day. For short-term tracing experiments, TCRδCreERR26ZsGreen mice (five weeks old, n = 8) were treated with one dose of tamoxifen (1 mg/mouse).

tag: strain

value: TCR{delta}CreERR26ZsGreen mice

tag: tissue

value: spleen

tag: cell type

value: effector memory CD8+ T cells from the spleens of young mice (8 wks)


title: 2242-1_7_218

type: genomic

city: Los Angeles

first: Aaron

last: Gordon

state: CA

address: 695 Charles E. Young Drive South, Gonda 2306, Los Angeles, CA  90095-1761

department: Neurology

country: USA

institute: UCLA

description: cortical organoid

hyb_protocol: Hybridizatoin was performe according to manufacture's (Illumina) protocol

scan_protocol: Standard Illumina Protocol

data_processing: Data was normalized using the noob method implemented in the minfi package in R

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: human cortical spheroids

label_protocol: Labeling was performe according to manufacture's (Illumina) protocol

growth_protocol: hiPSC were cultured on inactivated mouse embryonic fibroblast feeders (EmbryoMax PMEF; Millipore) in DMEM/F12 (1:1, Life Technologies, 11330) containing 20% knockout serum (Life Technologies, 10828), 1mM non-essential amino acids (Life Technologies, 11140), 1:200 GlutaMax (Life Technologies, 35050), 0.1 mM β-mercaptoethanol (Sigma-Aldrich, M3148), 1:100 penicillin and streptomycin (Life Technologies, 15070), and 10 ng/ml FGF2 (R&D Systems, 233-FB) diluted at 0.1% BSA in DPBS (Life Technologies, 14190). hCS were generated as previously described (Pasca, 2015). Intact hiPSC cells colonies were lifted using 0.7 mg/ml dispase and transferred to ultralow-attachment plastic dishes (Corning) in hiPSC cell medium supplemented with 5 μM dorsomorphin (Sigma-Aldrich), 10 μM SB-431542 (Tocris) both of which are SMAD inhibitors, and 10 μM Y-27632 (EMD Chemicals) which is a ROCK inhibitor. From day 2 (48 hours of differentiation), the medium supplemented with dorsomorphin and SB-431542 was changed daily. From day six until day 24, neural spheroids were grown in neurobasal-A (Life Technologies, 10888) neural medium supplemented with B-27 supplement without vitamin A (Life Technologies, 12587), 1:100 GlutaMax (Life Technologies), 1:100 penicillin and streptomycin (Life Technologies) and with 20 ng/ml EGF (R&D Systems, 236-EG) and 20 ng/ml FGF2 (R&D Systems, 233-FB). From day 25 to 42, the neural medium was supplemented with 20 ng/ml BDNF (Peprotech, 450-02) and 20 ng/ml NT3 (Peprotech, 450-03) and medium was changed every other day. From day 43 onwards, hCS were maintained in unsupplemented neural medium with medium changes every four days

extract_protocol: DNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qigen, 80224

tag: Sex

value: M

tag: iPSc line

tag: differentiation

tag: differentiation day

tag: batch


title: Rat 2_Proximal Tubule_C

city: Research Triangle Park

first: Brian

last: Chorley

state: NC

address: US EPA, 109 TW Alexander Dr

institute: US EPA

description: small RNA

data_processing:
FastQ files were analyzed using the Partek Flow (version 6.0) software program (Partek, St. Louis, MO). Sequence was filtered for rRNA, tRNA, and mitochondrial DNA sequence using Bowtie 2 (v 2.2.5) using all default settings.
Remaining sequences of 18 bp or greater were retained and trimmed from both 5’ and 3’ ends if the Phred quality score was less than 20.
Samples were aligned with Bowtie version 1.0.0 to the rn6 reference index using up to a 1 base pair mismatch and seed length of 10. Samples that had less than 500,000 aligned counts were removed from further analysis (Rat 2, glomerulus).
Aligned sequences were then annotated to miRBase mature microRNAs v22 with the Partek E/M (expectation maximum) algorithm.
To identify those miRNA features with higher expression, counts were filtered out if the total raw counts for all samples were less than 100.  Raw counts were then normalized by "trimmed mean of M-values" (TMM).
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited file contains TMM normalized count values for all samples and mapped featues (excluding features <100 total counts).

organism: Rattus norvegicus

source_name: kidney_Proximal Tubule

extract_protocol:
Frozen blocks containing kidney tissue were sectioned at 8 µm and adhered to glass slides. Serial sections were stained with rabbit anti-glutathione-s-transferase, sheep anti Tamm-Horsfall protein, or rabbit anti-aquaporin-2 (all from EMD Millipore) to identify proximal tubules, the TAL of the loop of Henle, and CD, respectively using the HistoGene LCM immunofluorescence staining kit (Thermo Fisher) and Alexa Fluor 488-conjugated donkey anti-rabbit or donkey anti-sheep secondary antibodies (Life Technologies) as appropriate. Additional serial sections were stained with a histochemical stain (HistoGene LCM frozen section staining kit; Thermo Fisher) to identify glomeruli. Nephron segments of interest were identified under fluorescence or light microscopy as appropriate and collected from the stained slides using an Arcturus XT Laser Capture Microdissection instrument onto CapSure LCM Macro caps (Thermo Fisher). RNA was isolated using the RNeasy Micro kit (Qiagen).  Samples were eluted in 20 µL RNase-free water, and RNA concentrations were determined using a NanoDrop 8000 at 260 nm.  RNA quality was assessed using an Agilent Bioanalyzer and an Agilent Small RNA Analysis Kit. Samples were stored at -80C prior to small RNA-sequencing conducted at the Laboratory Corporation, Inc (Seattle, WA; acquired by Covance).
Library construction was performed according to Illumina's TruSeq small RNA sample prep protocol (Illumina, San Diego CA). Each of the twelve samples was barcoded. Library quality was assessed using the Agilent Bioanalyzer DNA chip and quantified using Ribo Green dye and standard methods. Libraries will be subjected to HiSeq analysis to ensure library quality. Sample libraries were pooled and divided across two lanes (L001 and L002, see raw files) and two flow cells (AHG5GVBCX2 [A], AHGMTHBCX2 [B], BHG5GMBCX2 [C] or BHGFVCBCX2 [D]) to reach the targeted read count. Illumina HiSeq2000 analysis was performed using 50 bp single end reads, with a targeted read depth per sample of 40 million reads.

treatment_protocol: Kidneys from 3 naïve adult male Sprague-Dawley rats, 6 months old, were collected at necropsy into Optimum Cutting Temperature (OCT) embedding medium, frozen on dry ice and isopentane, and stored at ≤ -70 °C until use. All animal studies were conducted by the participating laboratories according to the national guidelines for care and use of laboratory animals and were approved by the Institutional Animal Care and Use Committee where the study was performed.

tag: rat id

value: Rat 2

value: Sprague Dawley

value: kidney

tag: kidney region

value: Proximal Tubule

tag: age

value: 6 m

tag: exposure

value: naive

value: male


title: Rat 1_Proximal Tubule_C

description: small RNA

value: Rat 1


title: 8858-1_12_183

description: cortical organoid


title: MPRA1 plasmid DNA barcode reads, replicate 4

state: California

description:
MPRA barcode reads used for expression analysis
MPRA1_Plasmid_DNA_004
processed data file: MPRA1_merged_counts.txt

tag: cell line


title: CD8TCM_O1

source_name: central memory CD8+ T cells

value: central memory CD8+ T cells from the spleens of young mice (78 wks)


title: MPRA1 plasmid DNA barcode reads, replicate 3

description:
MPRA barcode reads used for expression analysis
MPRA1_Plasmid_DNA_003
processed data file: MPRA1_merged_counts.txt


title: CD8TCM_Y2

value: central memory CD8+ T cells from the spleens of young mice (8 wks)


title: 0307-1_1_70

description: cortical organoid


title: KO-2

city: shanghai

first: xiaoxue

last: li

address: huashan road

institute: shanghai jiaotong university

data_processing:
Illumina sequencing with paired-ends 2x150 as the sequencing mode
The clean reads were mapped to the mouse genome (assembly GRCm38) using the HISAT2 software
Gene expression levels were estimated using FPKM (fragments per kilobase of exon per million fragments mapped) by StringTie
To annotate genes with gene ontology (GO) terms, ClusterProfiler (R package) was used
Genome_build: mm10
Supplementary_files_format_and_content: This table is a file including RPKM values for each Sample

source_name: skin

extract_protocol:
skin were isolated from Setd2fl/fl and Setd2K5-KO mice . Each sample contained 3 independent repeated animals
NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) was used for the construction of sequencing libraries.

tag: genotype


title: H3K36me3-WT

library_source: genomic

data_processing:
Illumina NextSeq 500 used for sequencing
The clean reads were mapped to the mouse genome (assembly GRCm38) using the Bowtie2 (v2.2.6) software
Peak detection was performed using the MACS (v2.1.1)  peak finding algorithm with 0.01 set as the p-value cutoff.
Annotation of peak sites to gene features was performed using the ChIPseeker R package.
Genome_build: mm10
Supplementary_files_format_and_content: This table is a file obtained by annotating the peak with the ChIPseeker package in the original file WT_peaks.narrowPeak.chr.xlsx after MACS2 search.

source_name: skin primary keratinocytes

extract_protocol:
primary mouse keratinocytes were crosslinked with 1 % formaldehyde for 10 min at room temperature and quenched with 125 mM glycine. The fragmented chromatin fragments were pre-cleared and then immunoprecipitated with Protein A + G Magnetic beads coupled with anti- H3K36me3 antibodies.
The DNA libraries were amplified for 15 cycles and sequenced using Illumina NextSeq 500 with single-end 1x75 as the sequencing mode.


title: Rat 1_Collecting Duct_C

description: small RNA

source_name: kidney_Collecting Duct

value: Collecting Duct


title: CD8N_O2

source_name: naïve CD8+ T cells

value: naive CD8+ T cells from the spleens of young mice (78 wks)


title: CD8TCM_Y1


title: MPRA1 plasmid DNA barcode reads, replicate 2

description:
MPRA barcode reads used for expression analysis
MPRA1_Plasmid_DNA_002
processed data file: MPRA1_merged_counts.txt

value: ATCC (CRL-3216)

value: Plasmid DNA


title: CD8N_O1

value: TCR{delta}CreERR26ZsGreen mice

value: spleen


title: Rat 3_Glomerulus_C

description: small RNA

value: Rat 3

value: Glomerulus


title: 8858-1_2_79 2

description: cortical organoid

value: M


title: Rat 2_Thick Henle Loop_B

description: small RNA

source_name: kidney_Thick Henle Loop

value: Rat 2

value: Sprague Dawley

value: kidney

value: Thick Henle Loop


title: Rat 1_Glomerulus_C

description: small RNA

value: 6 m

value: naive

value: male


title: 2242-1_5_336

description: cortical organoid


title: CD8N_Y2

value: naive CD8+ T cells from the spleens of young mice (8 wks)


title: Rat 3_Proximal Tubule_B

description: small RNA

value: Proximal Tubule


title: MPRA1 plasmid DNA barcode reads, replicate 1

description:
MPRA barcode reads used for expression analysis
MPRA1_Plasmid_DNA_001
processed data file: MPRA1_merged_counts.txt


title: CD4TEM_O2

source_name: effector memory CD4+ T cells

value: effector memory CD4+ T cells from the spleens of young mice (78 wks)


title: 8858-1_2_79

description: cortical organoid


title: CD4TEM_O1


title: 8858-1_5_336

description: cortical organoid


title: Rat 2_Collecting Duct_B

description: small RNA

value: Collecting Duct


title: MPRA1 mRNA barcode reads, biological replicate 6

description:
MPRA barcode reads used for expression analysis
MPRA1_HEK_cDNA_006
processed data file: MPRA1_merged_counts.txt

source_name: HEK293T_MPRA1 mRNA barcode reads

growth_protocol: DMEM + GlutMAX +1% Sodium Pyruvate + 10% FBS (Thermo Fisher Scientific)

extract_protocol:
Qiagen RNeasy Mini Kits with Qiashredder and on-column DNase I digestions with Qiagen RNase-free DNase Set (Qiagen), followed by mRNA extraction with with Dynabeads mRNA purification kit (thermo fisher)
mRNA was reverse-transcribed using Superscript IV Reverse Transcriptase (Thermo Fisher Scientific) and a custom RT primer. cDNA was amplified with NEBNext Q5 Hot Start HiFi PCR Master Mix (NEB) for 8 PCR cycles, followed by SPRI bead cleanup. A second PCR was performed in order to add P5 and P7 Illumina flow cell adapter sequences and indices for 7 PCR cycles, followed by SPRI cleanup. Bands were confirmed using Agilent’s D1000 ScreenTape and reagents (Agilent Technologies) on a 2200 Tapestation system.

treatment_protocol: ~8 million HEK293T cells were subcultured onto a 10 cm culture plate. 24 hours later, cells were transfected with 10 ug of library plasmid and Lipofectamine 3000. The library was allowed to express for another 24 hrs before lysis

value: ATCC (CRL-3216)

value: mRNA


title: MPRA1 mRNA barcode reads, biological replicate 5

description:
MPRA barcode reads used for expression analysis
MPRA1_HEK_cDNA_005
processed data file: MPRA1_merged_counts.txt


title: CD4TEM_Y2

value: TCR{delta}CreERR26ZsGreen mice

value: spleen

value: effector memory CD4+ T cells from the spleens of young mice (8 wks)


title: CD4TEM_Y1


title: Rat 3_Collecting Duct_B

description: small RNA

value: Rat 3


title: MPRA1 mRNA barcode reads, biological replicate 4

description:
MPRA barcode reads used for expression analysis
MPRA1_HEK_cDNA_004
processed data file: MPRA1_merged_counts.txt


title: CD4TCM_O2

source_name: central memory CD4+ T cells

value: central memory CD4+ T cells from the spleens of young mice (78 wks)


title: CD4TCM_O1


title: CD4TCM_Y2

value: central memory CD4+ T cells from the spleens of young mice (8 wks)


title: MPRA1 mRNA barcode reads, biological replicate 3

description:
MPRA barcode reads used for expression analysis
MPRA1_HEK_cDNA_003
processed data file: MPRA1_merged_counts.txt


title: 2242-1_6_273

description: cortical organoid

value: M


title: CD4TCM_Y1


title: 8858-1_10_392

description: cortical organoid


title: 2242-1_3_614

description: cortical organoid


title: Rat 2_Proximal Tubule_B

description: small RNA

value: Rat 2

value: Sprague Dawley

value: kidney


title: CD4N_O2

source_name: naïve CD4+ T cells

value: naive CD4+ T cells from the spleens of young mice (78 wks)


title: MPRA1 mRNA barcode reads, biological replicate 2

description:
MPRA barcode reads used for expression analysis
MPRA1_HEK_cDNA_002
processed data file: MPRA1_merged_counts.txt


title: CD8TCM_O2

value: central memory CD8+ T cells from the spleens of young mice (78 wks)


title: Rat 3_Thick Henle Loop_B

description: small RNA

value: Thick Henle Loop

value: 6 m

value: naive

value: male


title: CD8N_Y1

value: naive CD8+ T cells from the spleens of young mice (8 wks)


title: 2242-1_9_423

description: cortical organoid


title: Rat 1_Thick Henle Loop_B

description: small RNA

value: Rat 1


title: MPRA1 mRNA barcode reads, biological replicate 1

description:
MPRA barcode reads used for expression analysis
MPRA1_HEK_cDNA_001
processed data file: MPRA1_merged_counts.txt

value: ATCC (CRL-3216)

value: mRNA


title: CD4N_Y2

value: TCR{delta}CreERR26ZsGreen mice

value: spleen

value: naive CD4+ T cells from the spleens of young mice (8 wks)


title: 8858-1_7_218

description: cortical organoid

value: M


title: 8858-1_6_273

description: cortical organoid


title: 2242-1_2_79

description: cortical organoid


title: CD4N_Y1


title: Rat 1_Glomerulus_B

description: small RNA

value: Glomerulus


title: Cigarette smoke and a high dose of SS-31 rep3 [SS-31H_CS_3]

city: Chengdu

first: Yongchun

last: Shen

address: Medical clinic 37 Guoxue Alley

institute: West China Hospital of Sichuan University

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by  Cutadapt (V1.9.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded  from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index  reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2(v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Genome_build: Mus musculus(GRCm38.97)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Cigarette smoke and a high dose of SS-31_lung

growth_protocol: Mice were housed in a 12-h light/dark cycle (lights on from 6:00 a.m. to 6:00 p.m.) at a constant temperature of 23°C ± 2°C with 50% ± 10% humidity.

extract_protocol:
The total RNA  from lung tissues was extracted using the Total RNA Kit I (Omega Bio-tek, Norcross, GA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
"CS" group mice were exposed to cigarette smoke for 75 min twice daily, 5 days per week for 4 weeks
“SS-31H_CS” group mice were exposed to CS and a high dose of SS-31 (5 mg/kg once daily)

value: 9-10 weeks

value: wild type

tag: treatment

value: Exposed to cigarette smoke and 5 mg/kg once daily of SS-31

value: Lung


title: shCBX8_rep6

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

data_processing:
FASTQ files were created with the Illumina supplied scripts in the BCL2FASTQ software (v2.17)
Illumina adapters trimmed with Trim Galore! v0.4.3
FASTQs aligned to the mm10 reference genome with STAR v2.5.0a using default parameters
--quantMode GeneCounts option in STAR used to count genes against the GENCODE M16 GTF annotation file
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are one tab delimited text file per sample indicating the raw counts for each gene in the GENCODE M16 GTF file with --quantMode GeneCounts option in STAR. A read is counted if it overlaps (1bp or more) with only one gene. STAR outputs read counts per gene into ReadsPerGene.out.tab file with 4 columns which correspond to different strandedness options: column 1: gene ID, column 2: counts for unstranded RNA-seq, column 3: counts for the 1st read strand aligned with RNA, column 4: counts for the 2nd read strand aligned with RNA. The TruSeq RNA libraries are 2nd stranded so column 4 is the most appropriate for gene expression analysis, though other counts may be useful for other analyses.

source_name: Regenerating adult olfactory epithelium

growth_protocol: Regenerating adult olfactory epithelium was collected 9 days after chemical lesion with methimazole. Cells were enzymatically dissocated using collagenase, dispase, DNase, and trypsin. Cells were maintaned as adherent cultures on gelatin-coated tissue culture plastic. Medium consisted of NeuroCult Basal Medium (Stemcell Tech #05700), supplemented with NeuroCult Proliferation Supplement (Stemcell Tech #05701), EGF, FGF2, Heparin, and Pen/Strep.

extract_protocol:
Total RNA was collected following manufacturer's instructions using the Quick RNA MiniPrep Kit (Zymo #R1054)
Libraries were created from 500ng of input total RNA with the Illumina TruSeq Stranded Total RNA kit (RS-122-2201)

tag: tissue source

value: Adult olfactory epithelium

tag: lentivirus treatment

value: anti-Cbx8 short hairpin


title: Rat 1_Proximal Tubule_B

description: small RNA

tag: strain

value: Sprague Dawley

value: kidney

value: Proximal Tubule

value: 6 m

value: naive


title: Cigarette smoke and a high dose of SS-31 rep1 [SS-31H_CS_1]

tag: tissue


title: Cigarette smoke rep3 [CS_3]

source_name: Cigarette smoke_lung

value: Exposed to cigarette smoke for 75 min twice daily, 5 days per week for 4 weeks


title: Cigarette smoke rep2 [CS_2]


title: 8858-1_5_336 2

description: cortical organoid


title: 2242-1_11_149

description: cortical organoid


title: Cigarette smoke rep1 [CS_1]


title: Rat 3_Glomerulus_B

description: small RNA

value: Rat 3

value: male


title: shCBX7_rep5

value: anti-Cbx7 short hairpin


title: shCTR_rep5

value: Non-targeting Scramble short hairpin


title: Cigarette smoke and a high dose of SS-31 rep2 [SS-31H_CS_2]


title: Rat 2_Thick Henle Loop_A

description: small RNA

value: Rat 2

value: Thick Henle Loop


title: shCTR_rep6


title: P54 PVCre;Ai14 plate2

city: Stockholm

first: Francois

last: Lallemend

state: Stockholm

address: Tomtebodavägen 16

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description: Very few neurons are attached by satellite glial cells. Those neuron-glia doublets could be directly discarded from analysis.

data_processing:
The samples were analyzed by first demultiplexing the fastq files using deindexer (http://github.com/ws6/deindexer) using the nextera index adapters and the 384 well layout.
Individual fastq files were then mapped to the relevant genome assembly using the STAR aligner (Dobin et al. Bioinformatics 2013) using 2-pass alignment to have improved performance of de novo splice junction reads, filtered for only uniquely mapping reads that are saved in the BAM  file.
The expression values were computed per gene as described in Ramsköld et al. (2009 PLoS Comp Biol), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo (Storvall et al. 2013 PLoS ONE).
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited files include individual counts aligning to each gene per cell

molecule: polyA RNA

source_name: dorsal root ganglion neurons

extract_protocol:
The same dissociation protocol was used for DRG of E16.5, P5 and P54 PVCre;Ai14 mice and 3 months old ChATCre;RGT mice after rabies virus infection. At each stage, DRG were dissected, cut into halves (for postnatal DRGs) and collected in L-15 medium (Life Technologies, cat#21083027) on ice. The collated DRG were incubated in 2ml DMEM-F12 medium (Life Technologies, cat#11039-021) containing 12.5 mg collagenase IV (Life Technologies, cat#17104019) and 0.8 U dispase (30min at 37°C) then transferred into 1ml 0.05% trypsin solution (15 min at 37°C) (Life Technologies, cat#25300054), and 1ml fetal bovine serum (Life Technologies, cat#10082147) was added at the end to stop the enzymatic reaction. The tissue was then spun down at 400 g for 5 min and resuspended in 1 ml L-15 medium, followed by mechanical trituration using fire polished Pasteur pipettes until the solution homogenized and filtered through 70 µm cell strainer (BD Biosciences, cat#352350). Single RFP+ cells were sorted by fluorescence-activated cell sorting (FACS) into individual wells containing lysis buffer in a 384-well plate. The plates were immediately placed on dry ice and stored at -80°C before processed for Smart-seq2 protocol. For the rabies virus traced cells, single GFP+ cells were picked with a robotic cell-picking setup, constructed in-house around an inverted Nikon microscope. Individual cells were sucked into a glass capillary attached to a CellTram syringe with visual control. By an automated x-y-z axis drive, the capillary tip was positioned in a well of a 48-well plate containing 3 μl of lysis buffer, into which the cell was released. After cell picking, the plates were immediately placed on dry ice and stored at -80°C before further procedures.
RNA libraries were prepared according to Smart-seq2 protocol.

value: dorsal root ganglia

tag: developmental stage


title: Rat 3_Proximal Tubule_A

description: small RNA

tag: Sex


title: Rat 1_Collecting Duct_B

description: small RNA

value: Rat 1

value: Collecting Duct


title: P54 PVCre;Ai14 plate1


title: Rat 2_Collecting Duct_A

description: small RNA


title: P5 PVCre;Ai14 plate1


title: P54 PVCre;Ai14 plate4


title: 8858-1_8_694

description: cortical organoid

value: M

tag: iPSc line


title: E16.5 PVCre;Ai14 plate3

description: Some neurons are attached by satellite glial cells. Glia associated genes could be easily identified by comparing glia-neuron doublets and neuron singlets, thus discarded from the analysis.


title: shCBX7_rep2

value: Adult olfactory epithelium


title: P54 PVCre;Ai14 plate3


title: shCTR_rep2


title: Rat 3_Collecting Duct_A

description: small RNA

value: Sprague Dawley


title: shCBX8_rep2

value: anti-Cbx8 short hairpin


title: P5 PVCre;Ai14 plate2


title: shCBX8_rep1


title: 2242-1_4_163

description: cortical organoid

tag: differentiation


title: MPRA2 plasmid DNA barcode reads, replicate 3

description:
MPRA barcode reads used for expression analysis
MPRA2_Plasmid_DNA_003
processed data file: MPRA2_merged_counts.txt

source_name: HEK293T_MPRA2 plasmid DNA barcode reads

extract_protocol:
QIAprep (Qiagen, Hilden, Germany) spin miniprep kits
5 ng of plasmid were amplified for 3 cycles using NEBNext Q5 MasterMix, followed by SPRI bead cleanup. A second PCR was performed for 7 cycles in order to add P5 and P7 Illumina flow cell adapter sequences and indices. 0.5 ng was amplified for a total of 7 cycles. Bands were confirmed using Agilent’s D1000 ScreenTape and reagents (Agilent Technologies) on a 2200 Tapestation system.

tag: source

value: ATCC (CRL-3216)

tag: molecule subtype

value: Plasmid DNA


title: MPRA2 plasmid DNA barcode reads, replicate 4

description:
MPRA barcode reads used for expression analysis
MPRA2_Plasmid_DNA_004
processed data file: MPRA2_merged_counts.txt


title: shCBX7_rep1


title: MPRA2 plasmid DNA barcode reads, replicate 1

description:
MPRA barcode reads used for expression analysis
MPRA2_Plasmid_DNA_001
processed data file: MPRA2_merged_counts.txt


title: Rat 2_Proximal Tubule_A

description: small RNA

tag: rat id

value: kidney

value: Proximal Tubule

value: 6 m

value: naive


title: shCTR_rep1


title: 8858-1_4_163

description: cortical organoid

source_name: human cortical spheroids

tag: differentiation day

tag: batch


title: MPRA2 mRNA barcode reads, biological replicate 6

description:
MPRA barcode reads used for expression analysis
MPRA2_HEK_cDNA_006
processed data file: MPRA2_merged_counts.txt

source_name: HEK293T_MPRA2 mRNA barcode reads

extract_protocol:
Qiagen RNeasy Mini Kits with Qiashredder and on-column DNase I digestions with Qiagen RNase-free DNase Set (Qiagen), followed by mRNA extraction with with Dynabeads mRNA purification kit (thermo fisher)
mRNA was reverse-transcribed using Superscript IV Reverse Transcriptase (Thermo Fisher Scientific) and a custom RT primer. cDNA was amplified with NEBNext Q5 Hot Start HiFi PCR Master Mix (NEB) for 3 PCR cycles, followed by SPRI bead cleanup. A second PCR was performed in order to add P5 and P7 Illumina flow cell adapter sequences and indices for 7 PCR cycles, followed by SPRI cleanup. Bands were confirmed using Agilent’s D1000 ScreenTape and reagents (Agilent Technologies) on a 2200 Tapestation system.

value: mRNA


title: MPRA2 plasmid DNA barcode reads, replicate 2

description:
MPRA barcode reads used for expression analysis
MPRA2_Plasmid_DNA_002
processed data file: MPRA2_merged_counts.txt


title: Rat 1_Thick Henle Loop_A

description: small RNA

tag: kidney region

tag: age

tag: exposure

value: male


title: MPRA2 mRNA barcode reads, biological replicate 5

description:
MPRA barcode reads used for expression analysis
MPRA2_HEK_cDNA_005
processed data file: MPRA2_merged_counts.txt

tag: cell line


title: MPRA2 mRNA barcode reads, biological replicate 3

description:
MPRA barcode reads used for expression analysis
MPRA2_HEK_cDNA_003
processed data file: MPRA2_merged_counts.txt


title: Input_5

data_processing:
FASTQ files were created with the Illumina supplied scripts in the BCL2FASTQ software (v2.17)
Illumina adapters trimmed with Trim Galore! v0.4.3
FASTQs aligned to the mm10 reference genome with bwa mem v0.7.12 using default parameters
peaks were called using MACS2 v2.1.1.20160309
for RING1B and CBX8 the narrowpeak caller was used with a q-value threshold of 0.01: RING1B_Rep1 vs Input_1, Ring1B_Rep2 vs Input_3, CBX8_Rep1 vs Input_3, CBX8_Rep2 vs Input_4
for H3K27Ac and H3K27me3 the broadpeak caller was used with a broad threshold of 0.1: H3K27me3 vs Input_1, H3K27me3_Rep2 vs Input_2, H3K27ac_Rep1 vs Input_5, H3K27ac_Rep2 vs Input_4
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are .csv files representing annotated peak calls from MACS2 and provided only for the antibody pulldown samples

source_name: Adult neural precursor

growth_protocol: Olfactory basal cells were isolated from adult olfactory epithelium on the basis of c-KIT expression (as described in Goldstein et al., 2016, Development). Cells were maintaned as adherent cultures on gelatin-coated tissue culture plastic. Medium consisted of NeuroCult Basal Medium (Stemcell Tech #05700), supplemented with NeuroCult Proliferation Supplement (Stemcell Tech #05701), EGF, FGF2, Heparin, Pen/Strep, BMP4, and SB431542.

extract_protocol:
Adherent cells were fixed in 1% formaldehyde. Cells were collected by scraping with a rubber policeman. Nuclei were isolated and sonicated by Bioruptor (Diagenode); lysates were clarified and chromatin were purified by protein-specific antibody.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs #E7103S)

tag: cell type

value: WT olfactory basal cell line 2

tag: passage

tag: chip antibody


title: H3K27ac_Rep1

tag: strain


title: E16.5 PVCre;Ai14 plate2

tag: tissue

tag: developmental stage


title: MPRA2 mRNA barcode reads, biological replicate 1

description:
MPRA barcode reads used for expression analysis
MPRA2_HEK_cDNA_001
processed data file: MPRA2_merged_counts.txt


title: Rat 1_Glomerulus_A

description: small RNA

value: Glomerulus

tag: Sex


title: Rat 1_Proximal Tubule_A

description: small RNA

source_name: kidney_Proximal Tubule


title: MPRA2 mRNA barcode reads, biological replicate 4

description:
MPRA barcode reads used for expression analysis
MPRA2_HEK_cDNA_004
processed data file: MPRA2_merged_counts.txt


title: Rat 3_Glomerulus_A

description: small RNA

value: Rat 3


title: R475C2

city: Singapore

first: Kizhakeyil

last: Atish

state: Singapore

address: Mandalay road 11

country: Singapore

institute: Nanyang Technological University

description: R475C 2 1

data_processing:
Sequenced reads were trimmed using Cutadapt to remove low quality sequence
Trimmed reads were mapped onto hg38 using STAR package
Number of reads per annotated gene was determined using featurecounts
DESeq2 was performed to determine the differential gene expression (q-value<0.05 & abs(log2FC)>1.5)
Gene Ontology & Gene Set Enrichment Analysis was executed to draw biological conclusion
Genome_build: hg38

source_name: ATCC

growth_protocol: HuT78 were grown in RPMI medium supplemeted with sodium pyruvate (100mM) and were maintained in cell T75 cm2 flask(1X10^6 cells/mL). SNK1 cells were grown in RPMI medium supplemeted with IL-2 (10 ng/mL), 10% horse serum sodium pyruvate (100mM) and were maintained in cell T75 cm2 flask(1X10^6 cells/mL).

extract_protocol:
Total RNA was isolated from the cells using RNeasy Plus Mini Kit (catalougue number 74134) according to manufacturers instructions.
Libraries were prepared according to novaseq PE150.

treatment_protocol: HuT78 and SNK1 (1X 10^6) cells were nucleofected with DDX3X siRNA (Dharmacon, L-006874-02-0005), seeded on 6 well plates and were subjected to cell lysis for total RNA extraction after 48 hrs. CRISPR DDX3X variants of  U2392 cells,  DDX3X-p41 and DDX3X-R475C (1X 10^6) cells were seeded on six plates and were lysed for RNA extraction after 48 hrs.

value: Diffused Large B cell lymphoma

tag: treatment

value: DDX3X inactive mutant


title: E16.5 PVCre;Ai14 plate1

value: dorsal root ganglia


title: H3K27ac_Rep2

value: WT olfactory basal cell line 3


title: R475C1

description: R475C 1 1


title: CBX8_Rep2


title: p412

description: p41 2 1

value: Control


title: Rat 3_Thick Henle Loop_A

description: small RNA

value: Sprague Dawley

value: Thick Henle Loop


title: Rat 1_Collecting Duct_A

description: small RNA

source_name: kidney_Collecting Duct

value: Rat 1

value: Collecting Duct


title: Input_4


title: SNK1 KD2

description: SNK1 KD 2 1

value: Natural Killer T cell Lymphoma

value: DDX3X knockdown


title: MPRA2 mRNA barcode reads, biological replicate 2

description:
MPRA barcode reads used for expression analysis
MPRA2_HEK_cDNA_002
processed data file: MPRA2_merged_counts.txt

tag: source

value: ATCC (CRL-3216)


title: Nip_scRNA-seq

city: Beijing

first: Xiaofeng

last: Gu

address: Zhongguancun south street

institute: Chinese Academy of Agricultrual Sciences

data_processing:
The raw scRNA-seq data were analyzed using the 10X CellRanger pipeline (version 2.2.0) to align reads and generate gene-cell matrices.
Genome_build: Nip-BRI and 93-11-BRI http://www.elabcaas.cn/rice/downloads.html
Supplementary_files_format_and_content: tsv: genes and barcodes, mtx: expression matrix

organism: Oryza sativa

source_name: Protoplast

growth_protocol: The rice seeds were soaked in water in the dark until germination, and then cultured in Hoagland's Complete Nutrient Solution for 3 days (28°C with 10-h-light/14-h-dark cycles, the light intensity is 300 lux).

extract_protocol:
The root tips (5 mm) of total number of 800 crown roots were cut into small pieces of about 1 mm and incubated in enzyme solution (2% cellulase RS, 0.75% macerozyme R10, 1% Hemicellulase, 0.5% Pectolyase Y-23, 10 mM MES, 0.6 M mannitol, 1 mM CaCl2, 0.1% BSA and 0.04% 2-mercapto-Ethanol) at 28°C for 30 minutes, then the mixture was placed in a 28°C incubator with 60-70 rpm for 2.5 hours to release root cell protoplasts. The protoplasts were filtered through 80-μm nylon mesh and centrifuged at 130×g for 5 min, and washed three times with 8% mannitol at room temperature, after discarded the supernatant, a small amount of 8% mannitol solution was added to resuspend the protoplasts.
The isolated protoplasts were processed through the 10X Chromium 3’ Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol. Briefly, 18,000 cells were loaded on a Single Cell Chip for library construction using Chromium Single Cell 3’ v2 Reagent Kit. The protoplasts partitioned into single-cell GEMs (gel beads in emulsion) followed by cell lysis and barcoded reverse transcription of RNA in the droplets. Quantification of DNA library was done by an Agilent 2100 Bioanalyzer. And sequencing was performed with an Illumina Hiseq X Ten sequencer.

tag: cultivar

value: Nipponbare (Nip; Japonica)

tag: Stage

value: 5mm root tip

value: Protoplast


title: SNK1 KD1

description: SNK1 KD 1 1


title: SNK1 CTL2

description: SNK1 CTL2 1


title: CBX8_Rep1

value: WT olfactory basal cell line 2


title: SNK1 CTL1

description: SNK1 CTL1 1


title: 93-11_scRNA-seq


title: RING1B_Rep2


title: Nip bulk RNA rep.2

description: 200104_X490_FCH7HGFCCX2_L5_RDWHRICjpwEAAEAA-705506

data_processing:
Sequence reads (pair-end, 150 bp) were trimmed using SOAPnuke (version 1.5.6), and aligned to the Ind/Nip reference genomes with HISAT2 (version 2.0.4). Gene expression values were calculated on uniquely mapped reads using HTSeq (version 0.11.2)
Genome_build: Nip-BRI and 93-11-BRI http://www.elabcaas.cn/rice/downloads.html
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: Nip_protoplast_bulk RNA

extract_protocol:
The root tips (5 mm) of total number of 800 crown roots were cut into small pieces of about 1 mm and incubated in enzyme solution (2% cellulase RS, 0.75% macerozyme R10, 1% Hemicellulase, 0.5% Pectolyase Y-23, 10 mM MES, 0.6 M mannitol, 1 mM CaCl2, 0.1% BSA and 0.04% 2-mercapto-Ethanol) at 28°C for 30 minutes, then the mixture was placed in a 28°C incubator with 60-70 rpm for 2.5 hours to release root cell protoplasts. The protoplasts were filtered through 80-μm nylon mesh and centrifuged at 130×g for 5 min, and washed three times with 8% mannitol at room temperature, after discarded the supernatant, a small amount of 8% mannitol solution was added to resuspend the protoplasts. Total RNA was extracted following the TRIZOL manual instruction.
Oligo(dT)-attached magnetic beads were used to mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then, first-strand cDNA was generated in First Strand reaction system by random hexamer-paired reverse transcription, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments with adapters were amplified by PCR, and the products were purified by Ampure XP Beads. The library was amplified on cBot to generate the cluster on the flowcell. And the amplified library was sequenced on HiSeq X Ten platform.


title: D3 R1

description: Day3 R1 1

value: Cutaneous T cell Lymphoma


title: Input_3


title: NS R2

description: NS R2 1


title: H3K27me3_Rep2


title: NS R1

description: NS R1 1


title: merged barcode mapping reads, MPRA2

description:
Variant-barcode paired reads used for associating barcodes with variants
MPRA2_Barcode_R1_001

organism: Escherichia coli

source_name: Escherichia Coli

extract_protocol:
QIAprep (Qiagen, Hilden, Germany) spin miniprep kits
2 ng of plasmid was amplified using primers with P5 and P7 Illumina flow cell adapter sequences for 14 cycles. Amplicons were isolated on a 2% TAE agarose gel and bands were confirmed using Agilent’s D1000 ScreenTape and reagents (Agilent Technologies) on a 2200 Tapestation system.

value: NEB 5-alpha Electrocompetent cells (#C2989K)

tag: molecule subtype

value: Plasmid DNA


title: Nip bulk RNA rep.1

description: 200104_X490_FCH7HGFCCX2_L5_RDWHRICjpwEAAAAA-701502


title: p411

description: p41 1 1

value: Diffused Large B cell lymphoma


title: Input_2


title: merged barcode mapping reads, MPRA1

description:
Variant-barcode paired reads used for associating barcodes with variants
MPRA1_Barcode_R1_001


title: 93-11 bulk RNA rep.1

description: 200104_X490_FCH7HGFCCX2_L5_RDWHRICjpwEAADAA-704505

source_name: 93-11_protoplast_bulk RNA


title: D3 R2

description: Day3 R2 1


title: 93-11 bulk RNA rep.2

description: 200104_X490_FCH7HGFCCX2_L5_RDWHRICjpwEAAHAA-708509


title: 20200414_sample_16

status: Public on Dec 24 2020

city: Solna

first: Leonard

last: Hartmanis

address: Solnavägen 9

department: Cell & Molecular Biology

description: m1_patchseq_phys_temp_exon_counts.csv.gz, m1_patchseq_phys_temp_intron_counts.csv.gz

data_processing:
Raw sequencing datawas converted to fastq files using Bcl2fastq (version 2.20)
Reads were mapped against the reference genome (mm10) using STAR (version 2.5.4b) as a part of the zUMIs pipeline version 2.5.6b (Parekh 2018)
gene expression levels were quantified using
Genome_build: mm10
Supplementary_files_format_and_content: Expression matrix gene/-sample wise for raw counts. Exonic and intronic counts are supplied.

extract_protocol:
Electrophysiological parameters were measured by patch clamping. The cytosols and nuclei of the cells were extracted and transferred to lysis buffer and converted to cDNA for sequencing
Patch-seq (Cadwell 2016)

tag: mrna type

value: L5 IT_1

value: primary mouse motor cortex

value: neurons


title: 20200414_sample_26


title: 20200414_sample_14


title: 20200414_sample_13


title: 20200414_sample_22

value: Sst Htr1a


title: 20200414_sample_18


title: 20200414_sample_27

value: Sst Calb2


title: 20200414_sample_15


title: 20200414_sample_11


title: 20200414_sample_21

value: L5/6 NP CT


title: 20200414_sample_8


title: 20200414_sample_17


title: 20200414_sample_9

value: Sst Myh8_1


title: 20200414_sample_23


title: 20200414_sample_10

value: L5 IT_3


title: 20200414_sample_25


title: 20200414_sample_7


title: 20200414_sample_19


title: 20200414_sample_24


title: 20200414_sample_12


title: 20200414_sample_5


title: CD4N_O1

extract_protocol:
Total RNA was extracted using the Quick-RNA Microprep Kit (Zymo Research) according to the manufacturer’s protocol. RNA concentration was detected by the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen). After quality control using the Agilent RNA 6000 Nano Kit with the Agilent 2100 Bio analyse (Agilent Technologies). Library construction and RNA sequencing on the BGISEQ-500 platform were conducted at the Beijing Genomics Institute (BGI).
RNA libraries were prepared for sequencing according to the standard protocols provided by the Beijing Genomics Institute (BGI).

value: TCR{delta}CreERR26ZsGreen mice

value: spleen

value: naive CD4+ T cells from the spleens of young mice (78 wks)


title: 20200414_sample_6

value: L5 IT_2


title: Area D rep4

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description: Biological replicates 4 of 4

hyb_protocol: Hybridizations were performed according to the microarray manufacturer’s instructions (Agilent Technologies). Briefly, 500 ng of labeled sample (in 22 μL) was mixed with 61 μL of hybridization master mix containing 5 μL of Cot-1 (1 mg/ml) , Applied Genetics Laboratories), 1μL of Agilent 100x Blocking Agent and 55 μL of Agilent 2× HI-RPM Hybridization Buffer (Agilent Technologies). Samples were held at 95°C for 3 min and at 37°C for 30 min followed by addition of 27 μL of Agilent-CGHBlock (final volume 110 μL). The samples were loaded onto the microarray and hybridization was carried out in a hybridization oven (Shel Lab) for 40 h at 65°C and 20 rpm. Washing was carried out according to the microarray manufacturer’s instructions

scan_protocol: Scan on a PowerScanner (Tecan) at 2um using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: The array data analysis methods and downstream analysis pipelines are described in detail in (Saadi et al., 2014). Briefly, after Loess normalization, quantile inter-array scale normalization was performed and fitted to a linear model and thus, Bayesian statistics of differential expression were obtained. Thus, differentially methylated probes were identified using linear models for microarray data (LIMMA).

organism: Sus scrofa

source_name: Blastocyst from cumulus oocyte complexes madured in coculture with porcine luteal cells

label_protocol:
amplification protocol: The methodology have been thoroughly describef in (Saadi et al., 2014). Briefly, 10ng of DNA sample and spike-in control were cut in ≈160bp fragment using MSEI restriction enzyme. MseLig 12 and MseLig 21 adapters were added to the fragmented gDNA sites. Sample were the digested using methyl sensitive restriction enzyme HpaII, HinP1I and AciI. Only unmethylated fragment have been targeted by those enzyme, leaving only one adapter on the cleaved fragment. Efficiency of the digestion was confirmed by analyzing the spike-in control added prior to the DNA fragmentation step. For the step, qPCR was performed by preparing a separate mixes containing forward and reverse primer targeting HpaII, HinP1I and AciI site. Undigested spike-in (1/1000 dilution) was used as a positive control and non-template controls were also added as negatives control. The amplification plot and the dissociation curve were evaluated for each primer set separately. The DNA fragmentation was considered successful when the threshold cycle (ct) was greater than 5 when compared to the undigested control.Fragment selection by ligation-mediated PCR After cleavage by methyl sensitive enzyme, the gDNA was purified by ethanol precipitation and dissolve in nuclease free water. Selective amplification of methylated fragments was performed using two rounds of ligation-mediated PCR (LM-PCR). The PCR products were resolved on 0.8% agarose gel to assess the quality. Then the previously added linker were removed.
For each sample, 1 μg of DNA was labeled using the Universal Linkage System (ULS) labeling kit (Kreatech Biotechnology) according to the manufacturer’s instructions with minor modifications: 1 μL of Cy-ULS dye was added per 1 μg of genomic DNA adjusted with 10× labeling buffer. The labelling mixture was then held for 30 min at 85°C in a thermocycler, followed by 3 min on ice. Non-reacted ULS-Cy3/5 was removed by purification using a QIAquick PCR Purification Kit and samples were eluted in 25 μL 1/10 Buffer EB. A 1.5 μL aliquot was used to determine DNA concentration and dye incorporation using the ND- 1000 NanoDrop.

extract_protocol: Total RNA and gDNA were extracted using the AllPrep DNA/RNA Micro Kit (Qiagen)

value: matured in coculture with porcine luteal cells

source_name: Blastocyst from cumulus oocyte complexes in control

value: none (control)


title: Area A rep1

description: Biological replicates 1 of 4

source_name: Blastocyst from cumulus oocyte complexes matured in coculture with porcine luteal cells


title: 20200414_sample_4


title: 20200413_sample_22

value: L5 PT_1


title: Area B rep2

description: Biological replicates 2 of 4

value: Blastocyst from cumulus oocyte complexes


title: 20200413_sample_23


title: 20200413_sample_9


title: 20200413_sample_21


title: 20200413_sample_11


title: 20200413_sample_20


title: 20200413_sample_15


title: 20200413_sample_16


title: 20200413_sample_13

value: L5 PT_2


title: 20200414_sample_3

value: L5 IT_1


title: 20200413_sample_19

value: L5 PT_4

value: primary mouse motor cortex


title: 20200414_sample_1

value: neurons


title: 20200413_sample_14


title: 20200413_sample_7


title: 20200413_sample_17


title: 20200413_sample_10


title: 20200414_sample_2


title: 20200413_sample_8


title: 20200413_sample_12


title: Area C rep3

description: Biological replicates 3 of 4


title: 20200413_sample_18


title: 20200413_sample_4


title: 20200413_sample_3


title: 20200413_sample_5


title: 20200413_sample_6


title: 20200413_sample_2


title: 20200410_sample_29

value: Sst Hpse


title: 20200410_sample_27


title: 20200410_sample_30

value: Sst Crhr2_1


title: 20200410_sample_24


title: 20200410_sample_28

value: Pvalb Calb1_2


title: 20200410_sample_26

value: L5 IT_3


title: 20200413_sample_1


title: 20200410_sample_23


title: 20200410_sample_20


title: 20200410_sample_11


title: 20200410_sample_13


title: 20200410_sample_21


title: 20200410_sample_22

value: Sst Myh8_1


title: 20200410_sample_14


title: 20200410_sample_18


title: 20200410_sample_15


title: 20200410_sample_8


title: 20200410_sample_6

value: L5 PT_3


title: 20200410_sample_17


title: 20200410_sample_7

value: Sst Pvalb Calb2


title: 20200410_sample_10


title: 20200410_sample_4


title: 20200410_sample_5

value: L5 IT_2


title: 20200410_sample_2

value: Sst Myh8_3


title: 20200409_sample_19


title: 20200410_sample_1


title: 20200409_sample_20


title: 20200409_sample_18


title: 20200409_sample_17


title: 20200409_sample_15

value: Sst Tac2


title: Post guadecitabine treatment

city: Urbana

first: Michael

last: Spinella

state: IL

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

description: Testicular tumor sample

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

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

data_processing: MethylationEPIC array targets 862,927 CpG sites  across the genome. All DNA methylation analysis of MethylationEPIC array was performed in R  v.3.6.2. The IDAT intensity files were analyzed in minfi R package. Raw intensity values were  normalized with minfi preprocesser Noob.

source_name: Testicular Tumor Biopsy

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was also extracted from formalin-fixed and paraffin embedded samples (FFPE) from C1D1 and C1D8 biopsies and purified using the Qiagen DNeasy Kit according to standard instructions.

value: Testicular

tag: disease state

value: Tumor


title: 20200409_sample_13

value: Sst Crhr2_2


title: 20200409_sample_10

value: Sst C1ql3_2


title: 20200409_sample_11


title: 20200409_sample_5


title: 20200409_sample_9

value: Sst Htr1a


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