title: 1067_CAP [RRBS]

city: Msida

first: Brendon

last: Scicluna

institute: University of Malta

description:
1067
RRBS
MspI digested and bisulfite sequencing.


title: 1067_CAPD28 [RRBS]

status: Public on Aug 05 2021

type: SRA

address: Msida campus

country: Malta

description:
1067_D28
RRBS
MspI digested and bisulfite sequencing.

library_source: genomic

data_processing:
Read alignment done by bs-seeker2 (version 2.1.8) and bowtie2 (version 2.3.4.3).
Methylation levels (number of C reads / [number of C + number of T]) were calculated by bs-seeker2 (version 2.1.8).
Methylation levels summarized by cgmaptools (version 0.1.8).
Genome_build: GRCh38
Supplementary_files_format_and_content: Cgmap methylation levels.

molecule: genomic DNA

organism: Homo sapiens

source_name: CD14+ monocyte

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized-blood by density-gradient centrifugation (1700 RPM for 30 min at 21°C, acceleration 1, breaks 0) using Ficoll-Paque PLUS. PMBCs were resuspended in MACS buffer (phosphate-buffered saline (PBS) having endotoxin-free 0.5% bovine serum albumin (BSA), 2mM ethylenediaminetetraacetic acid (EDTA)), containing magnetic beads coated with anti-CD14 antibodies (Miltenyi Biotec, 130-050-201), and incubated for 15 minutes on a roller bank kept at 4C. CD14+ monocytes were purified using a LS MACS column (Miltenyi Biotec, QuadroMACS) and magnetic separator (Miltenyi Biotec). Monocyte purity (CD14+ purity > 80%) was assessed by flow cytometry (FACS Canto II with FACSDiva Software; BD Biosciences). For reduced representation bisulfite sequencing (RRBS), 1 x 10^6 purified monocytes were resuspended in 350ul RNA cell protect buffer (Qiagen), and stored at -80C.

extract_protocol:
Genomic DNA was isolated using the AllPrep DNA/RNA mini kit according to the manufacturer’s instructions (Qiagen).
Libraries were prepared from 100ng genomic DNA using Diagenode Premium RRBS kits (Diagenode). Briefly, DNA was digested with the restriction enzyme MspI, which recognizes CCGG dinucleotides sites, and AMPpure XP kit (Beckman Coulter) for size selection. Samples were pooled based on concentrations (n=8 per pool) and treated with sodium bisulfite to convert the unmethylated cytosines to uracil leaving unmethylated cytosines unchanged. After bisulfite conversion samples were amplified by PCR using the following reaction setup: 20 minutes at 25°C, 10 minutes at 65°C, hold at 8°C. PCR products were cleaned using the AMPpure XP kit and sequenced on the Illumina HiSeq4000 (Illumina) instrument in single read (50) mode.

tag: diagnosis

value: Community-acquired pneumonia

tag: time point

value: After 1 month recovery

tag: cell type

value: CD14+ monocytes

tag: age

tag: gender

value: Female

tag: sequencing pool


title: RLHC4-DBS : umbilical cord blood from normal pregnancies

city: London

first: Ping

last: Yip

address: 4 Newark St

department: Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

library_source: transcriptomic

data_processing:
Illumina miseq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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.
mm9
Genome_build: 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

source_name: newborn dried blood spot

extract_protocol:
Blood was placed onto protein saver cards. 2 x 6 mm chad was hol-punched out and extracted using the MirVana miRNA isolation kit
NEB_small RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: dried blood


city: Ann Arbor

first: Sriram

last: Venneti

state: MI

address: 3520E MSRB 1, 1150 W. Medical Center Dr.

country: USA

institute: University of Michigan

description:
H3.3K27M_Mouse_neuronal stem cell_H327ac
05_03N0_00F8Michigan_K27M_H3K27Ac

data_processing:
After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end). Reads were aligned to the mouse genome (mm10) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. For active histone marks (H3K4me3, H3K27Ac), peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7.
For H3K27me3 enriched regions were identified using the SICER algorithm at a cutoff of FDR 1E-10 and a max gap parameter of 600 bp.
Spike-in of Drosophila chromatin was performed and the number of test tags were normalized by the same number of spike-in Drosophila tags for each sample.
Genome_build: mm 10

organism: Mus musculus

source_name: mouse Neuronal stem cells (p16Ink4a - /p14Arf -) with stably transduced H3.3K27M

growth_protocol: mNSC (mouse) cells were cultured in Neurobasal A supplemented with N2, B27, L-glutamine (2 mM), Pen/strep (1X), heparin (2 μg/mL), human-EGF (20 ng/mL), human-bFGF (20 ng/mL), and BSA (45 ng/ml)

extract_protocol:
H3.3WT and H3.3K27M mNSC cell lines were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara).

tag: chip antibody

value: anti-H3K27ac Chip-grade antibody (Active Motif cat#39133 Lot#20017009 4ul volume 30 ug chromatin)

value: neuronal stem cells

tag: genotype


title: H3.3K27M_Mouse_neuronal stem cell_Input

description:
H3.3K27M_Mouse_neuronal stem cell_Input
20_03DI_00F8Michigan_K27M_Input


title: 1061_CAP [RRBS]

description:
1061
RRBS
MspI digested and bisulfite sequencing.

value: Hospital admission


description:
Wildtype_h3.3__Mouse_neuronal stem cell_H3K27ac
04_03MZ_00F8Michigan_WT_H3K27Ac

source_name: mouse Neuronal stem cells (p16Ink4a - /p14Arf -) with stably transduced WTH3.3

value: wildtype H3.3


title: 1061_CAPD28 [RRBS]

description:
1061_D28
RRBS
MspI digested and bisulfite sequencing.


title: RLH28-5-DBS: moderate-severe HIE undergoing therapeutic hypothermia


description:
H3.3K27M_Mouse_neuronal stem cell_H3K4me3
02_03N6_00F8Michigan_K27M_H3K4me3

value: anti-H3K4me3 Chip-grade antibody (Active Motif cat#39159 Lot#5617005 4ul volume 30 ug chromatin)


title: RLH28-3-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: G51_B_ACT

city: Atlanta

first: Haydn

last: Kissick

address: 1462 Clifton Rd.

institute: Emory University

data_processing: Adapter trim with cutadapt, align with Hisat2, counts with subread-featurecount, differential expression between groups with DESeq2.

source_name: Blood

extract_protocol:
Cells were FACS sorted and used to generate single cell suspensions. RNA was extracted using qiagen all-prep kits.
Library construction was performed using clontech V4

tag: disease state

value: HLADR+CD38+CD8+ T cells

value: baseline


description:
Wildtype_h3.3__Mouse_neuronal stem cell_H3K4me3
01_03N5_00F8Michigan_WT_H3K4me3


title: 1060_CAP [RRBS]

description:
1060
RRBS
MspI digested and bisulfite sequencing.

value: Male


title: RLH28-1-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: 1060_CAPD28 [RRBS]

description:
1060_D28
RRBS
MspI digested and bisulfite sequencing.


title: RLH25-3-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: 1055_CAP [RRBS]

description:
1055
RRBS
MspI digested and bisulfite sequencing.


title: RLH25-1-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: 1055_CAPD28 [RRBS]

description:
1055_D28
RRBS
MspI digested and bisulfite sequencing.


title: RLH25-5-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: G49_B_ACT


title: 1054_CAP [RRBS]

description:
1054
RRBS
MspI digested and bisulfite sequencing.


title: RLH22-5-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: Vector vs FimZ_2

type: RNA

city: Koganei

first: Kaneyoshi

last: Yamamoto

state: Tokyo

address: 3-7-2 Kajinocho

department: Frontier Bioscience

country: Japan

institute: Hosei University

hyb_protocol: Each 300 ng of Cy3- and Cy5-labeled cDNA were mixed and added to 1X Blocking Buffer (Agilent) and 1X HI-RPM GE Hybridization Buffer (Agilent). After precipitation of impurities, 40 µl of the labelled-cDNA mixture was applied to theDNA chip, and the hybridization was carried out at 65°C for 17 hr. The DNA chip was washed at room temperature with Agilent Gene Expression Wash Buffer 1 (Agilent) and at 37°C with Agilent Gene Expression Wash Buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 8.1).
Agilent Feature Extraction Software (v 8.1) was used for background subtraction.

organism: Escherichia coli BW25113

source_name: Vector

label_protocol: 10 µg of total RNA were used for labeled cDNA preparation using FairPlay III Microarray Labeling kit (Agilent).

growth_protocol: E. coli strains were grown at 27°C in LB medium containing 0.2% arabinose until a stationary phase.

extract_protocol: Total RNA was extracted by a hot phenol method. Water-saturated phenol and ethanol precipitation were used, following the digestion with RNase-free DNase I (Takara Bio). Total RNA was dissolved in RNase-free water.

tag: strain

value: FimZ non-expressing strain

source_name: FimZ

value: BW25113/ pBADFimZ

value: FimZ expressing strain


title: Vector vs FimZ_1


title: Whole blood E92_1

city: Irvine

first: ABEL

last: PLAZA FLORIDO

state: California

address: 101 Academy, Suite 150 Irvine

department: Department of Pediatrics, UC Irvine School of Medicine

institute: Pediatric Exercise and Genomics Research Center (PERC)

data_processing:
The STRTprep pipeline (which is an open-source pre-processing and analysis package for STRT RNA-seq), available at https://github.com/shka/STRTprep/tree/v3dev, was used for processing raw sequencing reads, aligning to the hg19 genome, quantitating the expression levels
Genome_build: hg19 genome
Supplementary_files_format_and_content: txt

extract_protocol:
Total RNA was isolated from the blood samples that contained RNA later using RiboPureTM-Blood Kit (Thermo Fisher Scientific; Waltham, Massachusetts, USA). Subsequently, GlobinLock molecular mechanism was applied to block the high globin mRNA content of erythrocytes, which is abundant in the blood and could hamper the whole blood RNA analyses
Full transcriptome analysis was performed following the modified version of single-cell tagged reverse transcription (STRT) protocol, where 10 ng of high-quality input RNA was converted into cDNA and amplified to form an Illumina-compatible library. The STRTprep pipeline, available at https://github.com/shka/STRTprep/tree/v3dev, was used for processing raw sequencing reads, aligning to the hg19 genome, quantitating the expression levels.

treatment_protocol: 500 μL blood was collected into the tube that contained 1.3 mL RNAlater solution (Ambion Inc; Austin, Texas, USA) for transcriptome analysis and was stored at -80ºC until further processing

value: 9-11 years

tag: maturation (peak height velocity)

tag: Sex

value: female

tag: fit/unfit group

value: whole blood


title: Whole blood E88_2_1

value: male


title: RLH22-3-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: 1047_CAP [RRBS]

description:
1047
RRBS
MspI digested and bisulfite sequencing.

value: Community-acquired pneumonia

value: CD14+ monocytes


title: Whole blood E93_1


title: RLH22-1-DBS: moderate-severe HIE undergoing therapeutic hypothermia

value: dried blood


title: Whole blood E88_1_1


title: Whole blood E84_1


title: RLH19-3-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: 1045_CAP [RRBS]

description:
1045
RRBS
MspI digested and bisulfite sequencing.


title: RLH19-5-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: Whole blood E82_1


title: 1047_CAPD28 [RRBS]

description:
1047_D28
RRBS
MspI digested and bisulfite sequencing.

value: After 1 month recovery


title: 1054_CAPD28 [RRBS]

description:
1054_D28
RRBS
MspI digested and bisulfite sequencing.

value: Female


title: Whole blood E73_1


title: 1045_CAPD28 [RRBS]

description:
1045_D28
RRBS
MspI digested and bisulfite sequencing.


title: 1032_CAP [RRBS]

description:
1032
RRBS
MspI digested and bisulfite sequencing.

value: Hospital admission


title: RLH14-5-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: Whole blood E69_1


title: 1032_CAPD28 [RRBS]

description:
1032_D28
RRBS
MspI digested and bisulfite sequencing.


title: RLH14-3-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: Whole blood E68_1


title: RLH19-1-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: V0103

type: genomic

city: Hidaka

first: Masakazu

last: KOHDA

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

description: Data from patients with mental retardation

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: We identified genome-wide CNV using Affymetrix Genotyping Console (GTC), which uses a Hidden Markov Model (HMM) algorithm to calculate copy numbers.

label: Standard Affymetrix protocol

source_name: blood from affected female

label_protocol: Standard Affymetrix protocol

growth_protocol: None (Genomic DNA from blood)

extract_protocol: Standard DNA isolation Kit from whole blood

tag: trait

value: mental retardation

value: blood


title: V0099


title: 1030_CAP [RRBS]

description:
1030
RRBS
MspI digested and bisulfite sequencing.


title: RLH14-1-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: V0107


title: V0104


title: V0109

source_name: blood from affected male


title: RLH11-5-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: 1030_CAPD28 [RRBS]

description:
1030_D28
RRBS
MspI digested and bisulfite sequencing.


title: Whole blood E108_1


title: V0111


title: V0105


title: V0110


title: Whole blood E106_1


title: 1028_CAP [RRBS]

description:
1028
RRBS
MspI digested and bisulfite sequencing.


title: V0113


title: Whole blood E105_1


title: RLH11-3-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: V0101


title: RLH11-1-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: 1028_CAPD28 [RRBS]

description:
1028_D28
RRBS
MspI digested and bisulfite sequencing.


title: V0093


title: Whole blood C99_1


title: 1017_CAP [RRBS]

description:
1017
RRBS
MspI digested and bisulfite sequencing.


title: Whole blood C96_1


title: RLH9-5-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: V0097


title: V0094


title: V0091


title: Whole blood C90_1


title: 1017_CAPD28 [RRBS]

description:
1017_D28
RRBS
MspI digested and bisulfite sequencing.


title: RLH9-3-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: V0092


title: 1014_CAP [RRBS]

description:
1014
RRBS
MspI digested and bisulfite sequencing.


title: 1014_CAPD28 [RRBS]

description:
1014_D28
RRBS
MspI digested and bisulfite sequencing.


title: V0090


title: V0098


title: RLH9-1-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: Whole blood C89_1


title: V0096


title: RLH8-3-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: Whole blood C78_1


title: V0102


title: Whole blood C85_1


title: V0088


title: RLH8-5-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: V0095


title: V0089


title: 1012_CAPD28 [RRBS]

description:
1012_D28
RRBS
MspI digested and bisulfite sequencing.


title: 1010_CAP [RRBS]

description:
1010
RRBS
MspI digested and bisulfite sequencing.


title: Whole blood C74_2_1


title: 1012_CAP [RRBS]

description:
1012
RRBS
MspI digested and bisulfite sequencing.


title: RLH7-DBS: mild HIE without therapeutic hypothermia


title: V0079


title: V0080


title: EYFP_positive_RUN3

city: Amsterdam

first: Leandro

last: Moreno

address: Meibergdreef 9

country: Netherlands

institute: AmsterdamUMC

description: EYFP+ and EYFP- pancreatic cells (9 days post cerulein induced pancreatitis)

data_processing: Single cell sequencing data were aligned to the human reference genome (GRCh38) and processed using the CellRanger 2.1.0 software from 10x Genomics to generate unique molecular identifier (UMI) counts.

source_name: Pancreatic cells

extract_protocol: none provided by the submitter

tag: treatment

value: Intraperitoneal injections with cerulein (Sigma-Aldrich, C9026) in PBS (50 ug/kg) every hour 7 times a day for 2 consecutive days.

tag: background


title: RLH6-DBS: mild HIE without therapeutic hypothermia


title: Whole blood C74_1_1


title: 1010_CAPD28 [RRBS]

description:
1010_D28
RRBS
MspI digested and bisulfite sequencing.

tag: diagnosis


title: Whole blood C71_1


title: RLH5-DBS: mild HIE without therapeutic hypothermia


title: V0085


title: NN1-DBS: mild HIE without therapeutic hypothermia


title: EYFP_positive_RUN2

description: EYFP+ and EYFP- pancreatic cells (Homeostasis)


title: Whole blood C70_1


title: EYFP_positive_RUN1


title: LRP cells - scRNAseq - Rep 3

city: Pozuelo de Alarcon

first: Miguel

middle: Angel

last: Moreno-Risueno

state: Madrid

department: Biotechnology

country: Spain

institute: Center for Plant Biotechnology and Genomics

data_processing:
Base calls were performed by the Illumina real time base calling
Reads were trimmed using Trimmomatics with the following settings: Illumina clip: 2:30:10, Crop: 48, Sliding window: 4:5, Minleng: 36
Reads were mapped to the genome using Star with default settings
Transcript compilation was in Star.
Counts were calculated in Star using quantMode GeneCounts
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts values of genes in each cell (all replicates are in this file).  The 573 columns follow the order of the fastq files in the folders for replicates 1, 2 and 3, i.e first 190 columns correspond to fastq files containing H55FTAFXY in their the name and ordered as in the folder of the first replicate, subsequent 192 columns correspond to files containing H3VL5AFXY in their the name and ordered as in the folder of the second and subsequent and final 191 columns  correspond to fastq files containing H2KH2AFXY in their the name and ordered as in the folder of the third replicate.

organism: Arabidopsis thaliana

source_name: Lateral Root Primordium cells

growth_protocol: Columbia-0 seeds were surfaced-sterilized upon exposition to Cl2 gas and stratified in sterile water at 4°C in darkness during 2 days. After stratification, seeds were transferred to petri dishes containing one-half-Murashige & Skoog (MS) medium with 1% Suc and 10 g/L Plant Agar. Seedlings were grown in chambers under a 16/8 photoperiod at 22°C.

extract_protocol:
The biological samples were extracted from plants expressing the pHB53:NLS-3xmCherry construct at 5 days after germination. The sample was subjected to a protoplasting process and the resulting suspension was used to perform a Fluorescence Activated Cell Sorting (FACS), selecting mCherry-positive cells, which corresponded only to lateral root primordium cells.
Libraries were prepared using the  Nextseq 500 Mid Output 150 V2.5 kit
single-cell-RNA-seq, 150 bp SE

tag: ecotype

value: Lateral Root Primordium cells

tag: developmental stage

value: Stages I-IV

tag: replicate


title: Whole blood C28_1

tag: age


title: Whole blood C67_1


title: Whole blood C110_1


title: EYFP_negative_RUN3


title: V0078


title: EYFP_negative_RUN2


title: LRP cells - scRNAseq - Rep 1

tag: cell type


title: Whole blood C107_1

tag: tissue


title: EYFP_negative_RUN1


title: atd14-1 rep3

city: Beijing

first: Yuxin

last: Hu

address: No.20 Nanxincun, Xiangshan

department: Key Laboratory of Plant Molecular Physiology

country: China

institute: Institute of Botany, CAS

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample.
Differential expression analysis of two groups was performed using the DEseq (version 1.39.0). DEseq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value < 0.05 found by DEseq were assigned as differentially expressed.
Genome_build: Col-0 TAIR10.22
Supplementary_files_format_and_content: Tab-separated values files including AGI code, chromsomes, start, end, length, strand and RPKM values for each Sample

source_name: whole seedlings

growth_protocol: Seeds of Arabidopsis were sterilized with 75% ethanol containing 2% Triton X100, stratified in darkness at 4°C for three days, and germinated on 1/2 Murashige and Skoog (MS) medium. The seedlings and plants were grown in the growth chamber at 22°C with a 16-h-light/8-h-dark photoperiod and an illumination intensity of 80-90 mmol m-2s-1.

extract_protocol:
10-day-old seedlings were frozen with liquid nitrogen, and the total RNA was extracted with GeneJET™ Plant RNA Purification Kit
After RNA sample quality control, high-quality RNA was obtained and used for library construction. The pipeline was consisted of five main steps:  (1) Isolated mRNA from total RNA using the oligo(dT) magnetic beads;  (2) Mixed with the fragmentation buffer and fragment the mRNA randomly;  (3) Using mRNA as the template, six-base random primers (random hexamers) were used to synthesize the first strand cDNA. Then PCR buffer, dNTPs, RNase H and DNA polymerase I were added to do second strand cDNA synthesis. AMPure XP beads are used to purify cDNAs;  (4) Purified double-stranded cDNAs were resolved with EB buffer for end reparation and single nucleotide A addition. Then AMPure XP beads were used in size selection;  (5) Finally, cDNA sequencing library was obtained by PCR amplification.

treatment_protocol: No treatment applied

value: 8 day old seedlings


title: CVID3_21low

city: Freiburg

first: Baerbel

last: Keller

department: Department of Rheumatology and clinical immunology

country: Germany

institute: University Medical Center Freiburg

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina CASAVA.
Reads were aligned to hg19 using Bowtie with the parameter –m 1 (v0.12.7)
Data was analyzed using HOMER (http://homer.salk.edu/homer) (v4.9.1)
Tag directories were generated using parameter – tbp 1, which removed most of the reads arising from mitochondrial DNA.
Genome_build: hg38
Supplementary_files_format_and_content: peak file

source_name: primary cells

extract_protocol:
50000 cells pelleted by centrifugation, nuclei were prepared prior to transposition
12 cycles of PCR using indexing primers from Illumina Nextera kit

value: CD21low naive B cells

tag: health status

value: CVID patient


title: atd14-1 rep2

tag: genotype


title: CVID3_21pos

value: CD21positive naive B cells


title: Whole blood C104_1

value: 9-11 years

value: whole blood


title: atd14-1 rep1


title: LRP cells - scRNAseq - Rep 2


title: AtCXE15-OE rep3


title: CVID1_21low


title: RLH8-1-DBS: moderate-severe HIE undergoing therapeutic hypothermia


title: CVID1_21pos


title: V0076


title: V0075


title: SLE patients [S17]

city: Shanghai

first: Xiao

last: Liu

state: Shanghai

address: 12 Middle Wulumuqi Road

institute: Huashan Hospital, Fudan University

description: Gene expression of CD4+ T cells from SLE patients.

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent Technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent Technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent Technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent Technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent Technologies, Santa Clara, CA, US).

source_name: Peripheral Blood

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent Technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018, Life Technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

treatment_protocol: Fresh CD4+ T cells were isolated from peripheral blood mononuclear cells (PBMCs) of peripheral blood in SLE patients and normal controls, respectively.

value: Systemic lupus erythematosus (SLE)

value: CD4+ T cells from blood

tag: gender


title: V0060


title: AP7319

city: L'Hospitalet de Llobregat

first: ISABEL

last: FABREGAT ROMERO

state: Barcelona

address: Avinguda de la Granvia de l’Hospitalet, 199

department: Oncobell Program

institute: Bellvitge Biomedical Research Institute - IDIBELL

description: Total RNA

data_processing:
Total RNA from Mus musculus was quantified by Qubit® RNA BR Assay kit (Thermo Fisher Scientific) and the RNA integrity was estimated by using RNA 6000 Nano Bioanalyzer 2100 Assay (Agilent).
The libraries were sequenced on HiSeq 4000 (Illumina) with a read length of 2x51bp+17bp+8bp using HiSeq 4000 SBS kit (Illumina) and HiSeq 4000 PE Cluster kit (Illumina), following the manufacturer’s protocol for dual indexing.
RNA-seq reads mapped using STAR v2.5.3a with ENCODE parameters for long reads.
Annotated genes quantified by RSEM v1.3.0
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
Liver tissue was frozen in liquid nitrogen and stored at -80ºC. Small pieces of the frozen liver were mecanically fragmented with a tissue grinder and resuspended in 1mL of RNA solv-Reagent with 20 µL/mL of β-Mercaptoethanol. E.Z.N.A.® Total RNA Kit II (Omega bio-tek, Norcross, GA, USA) was used for total RNA isolation, following Manufacturer’s protocol.
The RNA-seq libraries were prepared with KAPA Stranded mRNA-Seq Illumina® Platforms Kit (Roche) following the manufacturer´s recommendations.

value: liver

tag: time after partial hepatectomy


title: V0059


title: AtCXE15-OE rep2


title: SLE patients [S16]


title: CVID2_21pos


title: AtCXE15-OE rep1


title: SLE patients [S12]


title: V0074


title: SLE patients [S13]


title: HD5_21pos

value: Healthy


title: Col-0 rep3

value: WT


title: AP7317

description: Total RNA

value: Male


title: CVID2_21low


title: HD4_21pos


title: Col-0 rep1


title: AP7316

description: Total RNA

value: Female


title: V0053

value: mental retardation

value: blood


title: Col-0 rep2


title: AP7315

description: Total RNA


title: CAMHB CIP 2

city: San Diego

first: Anand

last: Sastry

state: CA

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

data_processing:
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Comma-separated text files include log-TPM (log2-transformed Transcripts per million) for each sample

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli K12 MG1655

growth_protocol: Escherichia coli strain MG1655 was grown in three media: (1) M9 minimal medium (47.8 mM Na2HPO4, 22 mM KH2PO4, 8.6 mM NaCl, 18.7 mM NH4Cl, 2 mM MgSO4 and 0.1 mM CaCl2) supplemented with 0.2% (w/v) glucose (M9); (2) Roswell Park Memorial Institute 1640 (RPMI) (Thermo Fisher Scientific) supplemented with 10% LB (R10LB); (3) Mueller Hinton Broth (Sigma-Aldrich) supplemented with 25 mg/L Ca2+ and 12.5 mg/L Mg2+ (CA-MHB). Glycerol stocks of E. coli were streaked onto Luria Broth agar (LB Agar) and grown at 37°C overnight.

extract_protocol:
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Total RNA was sampled from duplicate cultures. Strains were cultured overnight in the respective media as described above. Mid-log phase cultures were diluted (starting OD600~0.05) into 30mL media for untreated conditions, or 30 mL media containing the MIC90 of the respective antibiotic for the respective media. Flasks were incubated for 30 min at 37C with shaking. Cell broth was centrifuged and supernatant was removed.

tag: media

value: CAMHB

tag: antibiotic

value: ciprofloxacin (16ug/mL)


title: V0054


title: SLE patients [S8]


title: HD3_21pos


title: V0058


title: AP7313

description: Total RNA

tag: Sex


title: CAMHB CIP 1


title: Normal Control [N5]

description: Gene expression of CD4+ T cells from normal controls.

value: Normal control


title: AP7314

description: Total RNA


title: AP7312

description: Total RNA


title: ABC_8

city: Madrid

first: Juana

last: Serrano Lopez

address: Avda Reyes Catolicos 2

institute: IIS-FJD

data_processing:
Raw intensity files were demultiplexed  (bcl2fastq) and fastq files for each pair were joined into a single fastq file
Joined fastq files were trimmed in paired mode (TrimGalore) prior to mapping
Mapping (TopHat) was performed against the Hg19 human reference genome
The “--library-type fr-firststrand” argument was used in TopHat to match the Illumina stranded protocol.
An average number of 25.8 million mapped reads was generated per sample (range 19 to 32 million reads)
Genome_build: Hg19
Supplementary_files_format_and_content: Raw counts of sequencing reads for the features of interest (genes) using HTSeq for each sample

source_name: DLBCL

extract_protocol:
Total DNA/RNA was harvested from three or four 10 μm thickness scrolls from FFPE blocks kept in our biobank. We used AllPrep® DNA/RNA FFPE kit (Qiagen). To determine COO of DLBCL samples we applied a digital analyzer in NanoString platform (NanoString Technologies, WA). After processing on the nCounterTM Prep Station and acquiring the gene expression data on the nCounterTM Digital Analyzer at the “high resolution” setting, raw data files were analyzed using the RUO version of the NanoString Lymphoma Subtyping Test (LST) algorithm. The Ribo-Zero RNA removal kit for Human (Illumina Inc.) was used to deplete rRNA. We prepared cDNA libraries after rRNA were depleted from samples. We used the TruSeq Stranded mRNA Library Prep (Illumina Inc.) together with the Superscript III Reverse Transcriptase (Thermo Fisher Scientific). samples indexed with compatible indices were run together on a NextSeq 500 instrument (Illumina inc.) with a 2x150 bp paired-end protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Diffuse large B-cell lymphoma (DLBCL)

tag: dlbcl subtype

value: No MYD88mut (WT_ABC)

value: Lymph nodes


title: V0045

description: Data from patients with mental retardation

tag: trait


title: ABC_7


title: V0049


title: R10LB CIP 2

value: ciprofloxacin (64ug/mL)


title: Normal Control [N6]

tag: diagnosis


title: ABC_6


title: AP7310

description: Total RNA


title: R10LB CIP 1


title: ABC_5


title: AP7309

description: Total RNA


title: SLE patients [S9]


title: GCB_4

value: GCB


title: AP7308

description: Total RNA


title: M9 CIP 1

value: ciprofloxacin (32ug/mL)


title: GA-treated WS hMSCs, rep4

first: jiang

middle: xiao

last: yu

address: 15 Datun Road Chaoyang District

institute: institute of zoology, CAS

description:
ATAC sequencing of GA-treated WS hMSCs
ATACseq_WS_hMSC_GA.bw

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human reference genome using bowtie2 software.
Genome_build: hg19 for Homo sapiens
Supplementary_files_format_and_content: bw file of RPKM normalized read cout for each 10 bp bin size for others sequencing data.

source_name: GA-treated WS hMSCs

extract_protocol: For ATAC-seq, library was amplified and purified using TruePrep DNA Library Prep Kit V2 for Illumina(Vazyme Biotech).

value: Werner syndrome (WS)

value: human mesenchymal stem cell (hMSC)

tag: treatment

value: GA

tag: passage


title: V0047


title: V0048


title: CAMHB CTR 2

value: ceftriaxone (256ug/mL)


title: M9 CIP 2


title: GA-treated WS hMSCs, rep2


title: Normal Control [N3]

value: CD4+ T cells from blood


title: V0057


title: V0046


title: GA-treated WS hMSCs, rep3


title: Normal Control [N1]

value: Female


title: Normal Control [N4]


title: V0044

value: mental retardation


title: AP7307

description: Total RNA

value: liver

value: Male


title: Normal Control [N2]


title: GA-treated WS hMSCs, rep1


title: DMSO-treated WS hMSCs, rep4

description:
ATAC sequencing of DMSO-treated WS hMSCs
ATACseq_WS_hMSC_DMSO.bw

source_name: DMSO-treated WS hMSCs

value: DMSO


title: R10LB CTR 2


title: GCB_2


title: Conditionally Immortalized Glomerular Endothelial Cell B2M-/- CIITA-/-

city: PARIS

first: Benjamin

last: SAINTPIERRE

address: 22 rue méchain

country: France

institute: Inserm

data_processing:
STAR 2.7.6a
Alignment: STAR --genomeDir $reference_dir --sjdbGTFfile $reference_GTF --runThreadN 20 --readFilesIn $fq1 $fq2 --outFileNamePrefix $sample --twopassMode Basic –sjdbOverhang 74 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped Within --outFilterType BySJout --quantMode TranscriptomeSAM
RSEM v1.3.1
Prepare reference: rsem-prepare-reference --num-threads 20 --gtf Homo_sapiens.GRCh38.101.gtf Homo_sapiens.GRCh38.dna.primary_assembly.fa Homo_sapiens.GRCh38.101-rsem-ref
Count: rsem-calculate-expression -p 20 --paired-end --bam --no-bam-output $alignedToTransciptomFile $reference_RSEM $results_RSEM
TPM data are extracted from the RSEM results
Genome_build: Ensembl release 101, Homo_sapiens.GRCh38
Supplementary_files_format_and_content: normalized count matrix

source_name: Glomerula endothelial cells

growth_protocol: CiGEnC Delta HLA cells were cultured at 33°C until 80% confluence and put in culture for 7 days at 37°C in dedicated ECMV2 medium before RNA extraction

extract_protocol:
RNEasy extraction kit (Qiagen) following supplier recommendations
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Renal microvascular cell


title: V0042

value: blood


title: CAMHB CTR 1

value: CAMHB


title: AP7306

description: Total RNA


title: GCB_3

value: Diffuse large B-cell lymphoma (DLBCL)

value: Lymph nodes


title: V0041


title: V0040


title: V0055


title: V0051


title: AP7305

description: Total RNA


title: Wild-type mouse kidneys replicate 2

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

data_processing:
Base calling was performed using bcl2fastq version 2.17.1.14.
Transcript abundance was estimated without aligning reads using Salmon against an index of coding sequences from the Ensembl GRCm38 assembly.
Transcript-level abundance was imported and count and offset matrices generated using the tximport R/Bioconductor package.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file including FPKM values for each sample.

source_name: Wild-type mouse kidneys

extract_protocol:
Dissected kidneys stored in RNA later solution (Invitrogen, Cat. AM7020). RNA was extracted with the QIAGEN's RNeasy Micro Kit (QIAGEN Cat. 74004).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

tag: strain

value: mixed

value: Wild-type (Cre negative)


title: V0043


title: V0039


title: AP7302

description: Total RNA

value: SHAM 6h


title: DMSO-treated WS hMSCs, rep1

value: Werner syndrome (WS)

tag: cell type

value: human mesenchymal stem cell (hMSC)


title: V0038

tag: tissue


title: M9 CTR 1

value: ceftriaxone (4.1mg/mL)


title: AP7303

description: Total RNA


title: Foxd1cre; Yapc/c;Tazc/c replicate 3

source_name: Foxd1cre; Yapc/c;Tazc/c mouse kidneys

value: Foxd1cre; Yapc/c;Tazc/c


title: AP7304

description: Total RNA


title: CAMHB T/S 2

value: trimethoprim-sulfamethoxazole (16mg/mL)


title: M9 CTR 2


title: Wild-type mouse kidneys replicate 1


title: R10LB CTR 1

value: ceftriaxone (256ug/mL)


title: 4F-72h-2

city: Louisville

first: Tamer

middle: M

last: Mohamed

state: KY

address: 580 S. Preston St., Baxter II Bldg., Room 122

department: Cardiology

institute: University of Louisville

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: hiPS-CMs

growth_protocol: hiPS-CMs cultured for 60 days post differentiation

extract_protocol:
RNA from hiPS-CMs were isolated using the Qiagen, miRNeasy Micro Kit, #210874, following homogenization of the tissue in QIAzol (Qiagen).
Using the Ovation RNA-seq System v2 Kit (NuGEN),

treatment_protocol: Adenovirus were added for 24, 48, or 72 hours

tag: protocol

value: 60 days post differentiation

tag: medium

value: Cellular dymnamics medium

tag: agent

value: CDK1, CDK4, CCNB, CCND (4F) adenovirus

tag: time point


title: AP7300

description: Total RNA

value: liver

tag: genotype

tag: time after partial hepatectomy

value: SHAM 48h

value: Female


title: R10LB T/S 2

tag: media

tag: antibiotic


title: Wild-type mouse kidneys replicate 3


title: AP7301

description: Total RNA

value: SHAM 72h

tag: Sex

value: Male


title: GCB_1

tag: disease state

value: Diffuse large B-cell lymphoma (DLBCL)

tag: dlbcl subtype

value: GCB

value: Lymph nodes


title: Lens, p7_EPHA2_indel722_3

city: St. Louis

last: Bennett

state: Missouri

address: 660 S Euclid Ave.

department: Ophthalmology

institute: Washington University School of Medicine

description:
Processed data file: edgeR_Eph.mutants.xlsx
Eph54.c

data_processing:
Illumina Casava software used for base calls
Fastq data was mapped to the mouse mm10 genome build using STAR  (v2.5.3a).
Aligned reads were filtered for quality using Samtools  (v1.4.1) and read counts per gene were determined using HTSeq  (v0.11.0).
The EdgeR  was used to implement the quantile-adjusted conditional maximum likelihood method to perform pairwise comparisons and p-values were adjusted using the Benjamini-Hochberg Procedure.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited Excel file containing counts, cpm, and comparative expression vs wild type with p value and FDR

molecule: polyA RNA

source_name: Lens

extract_protocol:
Lenses were removed from P7 mice and immediately frozen on dry ice. Lenses were homogenized in a Qiagen RLT Plus buffer in a Bullet Blender and RNA was extracted using using Qiagen RNEasy Plus Micro kit. RNA was analyzed using Agilent 2100 Bioanalyzer and subjected to oligo dT selection before fragmentation and adapter ligation using Illumina TruSeq RNA Library Prep Kit
PolyA plus RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lens

tag: age

value: Postnatal day 7

value: EPHA2 indel722


title: Foxd1cre; Yapc/c;Tazc/c replicate 2

value: mixed

value: Foxd1cre; Yapc/c;Tazc/c


title: AP7298

description: Total RNA

value: SHAM 24h


title: 4F-72h-1

value: 60 days post differentiation


title: AP7296

description: Total RNA

value: WT


title: R10LB T/S 1

value: trimethoprim-sulfamethoxazole (16mg/mL)


title: CAMHB T/S 1

value: CAMHB


title: AP7297

description: Total RNA

value: liver


title: AP7299

description: Total RNA

value: SHAM 48h

value: Female


title: 4F48h-3

value: Cellular dymnamics medium

value: CDK1, CDK4, CCNB, CCND (4F) adenovirus


title: Lens, p7_EPHA2_indel722_2

description:
Processed data file: edgeR_Eph.mutants.xlsx
Eph54.b


title: 4F-72h-3


title: AP7295

description: Total RNA


title: M9 T/S 1


title: 4F-24h-3


title: 4F48h-2


title: Foxd1cre; Yapc/c;Tazc/c replicate 1


title: DMSO-treated WS hMSCs, rep2

value: Werner syndrome (WS)

value: human mesenchymal stem cell (hMSC)

tag: treatment

value: DMSO

tag: passage


title: AP7294

description: Total RNA

value: Male


title: 4F48h-1


title: CAMHB MEM 2

value: meropenem (256ug/mL)


title: Lens, p7_EPHA2-Q722_2

description:
Processed data file: edgeR_Eph.mutants.xlsx
EphR722Q.b

tag: strain

value: Lens

value: Postnatal day 7

value: EPHA2 Q722 Q/Q


title: CAMHB MEM 1


title: AP7293

description: Total RNA


title: R10LB MEM 2

value: meropenem (32ug/mL)


title: M9 T/S 2


title: 4F-24h-1

value: 60 days post differentiation


title: R10LB MEM 1


title: Lens, p7_EPHA2-Q722_1

description:
Processed data file: edgeR_Eph.mutants.xlsx
EphR722Q.a


title: M9 MEM 2

value: meropenem (128ug/mL)


title: Lens, p7_EPHA2_indel722_1

description:
Processed data file: edgeR_Eph.mutants.xlsx
Eph54.a

value: EPHA2 indel722


title: LacZ-1

value: LacZ (control)


title: Lens, p7_WT_3

description:
Processed data file: edgeR_Eph.mutants.xlsx
WT.c

value: wild type


title: CAMHB control 2

value: CAMHB


title: Hyp9

city: Newark

first: Nataki

middle: C.

last: Douglas

state: NJ

address: 185 S Orange Ave, MBS E569

department: Ob-Gyn and Women's Health

institute: Rutgers-New Jersey Medical School

data_processing:
Base calling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and Alignment (Cutadapt v2.5, STAR vSTAR_2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Genome_build: GRCh37
Supplementary_files_format_and_content: Comma delimited file (csv) for differential gene expression counts via DESeq2.

source_name: HTR8 cell culture

growth_protocol: HTR-8/SVneo cells were grown in RPMI-1640 media supplemented with 5% fetal bovine serum, 5,000 units/mL penicillin and 5,000 µg/mL streptomycin and maintained in a humidified incubator under standard culture conditions (37°C, 5% CO2.)

extract_protocol:
For HTR-8/SVneo cells and chorionic villous samples, Total RNA was extracted and purified with the RNeasy Plus Mini Kit (Qiagen). 2-10 mg total RNA was sent to Novogene for mRNA enriched and library construction.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom secondstrand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the secondstrand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the doublestranded cDNA library is completed through size selection and PCR enrichment

treatment_protocol: 6x105 HTR-8/SVneo cells per well were plated on fibronectin coated 12-well dishes. After 6 hours of exposure to 21% O2 (n=3) or 2.5% O2 (n=3), cells were lysed and cell pellets were stored at -80C. For the chorionic villous samples, 5–20 mg of villous tissue was collected, snap frozen on dry ice and stored at -80C.

tag: cell line

tag: condition

value: hypoxic


title: Lens, p7_EPHA2-Q722_3

description:
Processed data file: edgeR_Eph.mutants.xlsx
EphR722Q.c

tag: tissue


title: 4F-24h-2

tag: protocol

tag: medium

value: Cellular dymnamics medium

value: CDK1, CDK4, CCNB, CCND (4F) adenovirus


title: Hyp8


title: DMSO-treated WS hMSCs, rep3

value: Werner syndrome (WS)

tag: cell type

value: human mesenchymal stem cell (hMSC)


title: AP7285

description: Total RNA

value: liver

tag: genotype

value: WT

value: Male


title: Lens, p7_WT_1

description:
Processed data file: edgeR_Eph.mutants.xlsx
WT.a

value: Lens

value: Postnatal day 7


title: Hyp7


title: AP7287

description: Total RNA

tag: time after partial hepatectomy


title: M9 MEM 1

tag: media


title: AP7291

description: Total RNA


title: R10LB control 1


title: FC3

value: normoxic


title: CAMHB control 1


title: Lens, p7_EPHA2-null_2

description:
Processed data file: edgeR_Eph.mutants.xlsx
EphKO.b

value: EPHA2 null


title: LacZ-3

value: 60 days post differentiation

tag: agent


title: AP7284

description: Total RNA

value: SHAM 6h

tag: Sex


title: AP7292

description: Total RNA

value: Female


title: LacZ-2

value: LacZ (control)


title: AP7286

description: Total RNA


title: Lens, p7_EPHA2-null_3

description:
Processed data file: edgeR_Eph.mutants.xlsx
EphKO.c


title: Lens, p7_WT_2

description:
Processed data file: edgeR_Eph.mutants.xlsx
WT.b

value: wild type


title: AP7288

description: Total RNA


title: Lens, p7_EPHA2-null_1

description:
Processed data file: edgeR_Eph.mutants.xlsx
EphKO.a


title: Foxd3_KO_rep_1

city: Pune

first: Deepika

last: Puri

state: Maharashtra

address: Ganeshkhind road

country: India

institute: National Centre for Cell Science

description: Foxd3 conditional KO cells with Tamoxifen

data_processing:
Reads were aligned to the
GRCm38 genome from Ensembl using STAR (Dobin et al., 2013) version 2.5.2b, with
settings as recommended by TEtranscripts (Jin et al., 2015). Both genes and repeats
were then quantified using TEtranscripts version 2.0.3 and differentially expressed
repeat elements and genes determined using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: bigwig

source_name: mESC

growth_protocol: Cells are grown using standard mESC culture protocols

extract_protocol:
RNA was extracted with trizol and ethanol precipitation, Dnase treated and column-purified
RNA libraries were prepared using standard TruSeq Stranded Total RNA (Gold) protocol

treatment_protocol: Foxd3 KO cells were treated with 4-OHT

value: Mouse embryonic stem cell

value: Foxd3 KO


title: AP7290

description: Total RNA


title: M9 control 2


title: Foxd3_KO_rep_2


title: R10LB control 2


title: FC1


title: AP7283

description: Total RNA

value: SHAM 48h


title: FC2


title: AP7282

description: Total RNA

value: SHAM 24h


title: CVS33

source_name: Chorionic villus sampling

value: healthy pregnancy

value: chorionic villus


title: AP7281

description: Total RNA

value: liver

value: WT


title: CVS27


title: Control_rep_2

description: Foxd3 conditional KO cells without Tamoxifen

value: Control


title: Control_rep_1


title: mESC purified eccDNA illumina

city: Boston

first: Yi

last: Zhang

state: MA

address: 200 Longwood Avenue WAB 149

department: PCMM

institute: Boston Children's Hospital / Harvard Medical School

description: eccDNA

data_processing:
Nanopore base calling and reads mapping:   The fast5 files generated by Nanopore MinION sequencer were fed to Guppy (version 3.5.2) for base calling. The parameters used for Guppy were: --flowcell FLO-MIN106 --kit SQK-LSK109 --qscore_filtering --calib_detect --trim_barcodes --trim_strategy dna --disable_pings --device auto --num_callers 16. The generated reads in fastq format were further processed by porechop (version 0.2.4) to remove adaptor sequences for each read with parameters: --extra_end_trim 0 --discard_middle. To reduce artifacts due to misalignment during reads mapping, we compiled a customized reference mouse genome (mm10combine) based on mm10 reference sequences. Then the cleaned reads were aligned to mm10combine using minimap2 (version 2.17) with parameters: -x map-ont -c --secondary=no -t 16. The alignments for each read were stored in PAF format.
Consensus eccDNA generation:   To obtain the consensus boundary and sequence of each eccDNA from the mapped RCA long reads, we developed a tool (https://github.com/icebert/eccDNA_RCA_nanopore) that uses the alignments in PAF file as input and outputs eccDNA fragments composition (chromosome, genomic start and end positions of each fragment), successive fragments coverage (number of passes) and consensus sequence derived from each RCA long read. The sub-reads of each RCA long read could be mapped to one genomic location or multiple locations. The sub-reads with mapping quality lower than 30 were discarded. This tool performed bootstrapping of successive sub-reads in each RCA long read to checks whether the order of the mapped genomic locations for each sub-read is concordant with their order in the RCA long read. Due to the inaccuracy and gap-prone property of Nanopore reads, we allowed a maximum of 20bp offset of the mapped genomic positions (start and end position, respectively) between two sub-reads to be considered as mapping to the same location. Reads with discordant sub-reads order and locations would be discarded. The exact boundaries of eccDNA fragments were determined by voting from the sub-reads’ start and end positions, respectively. The boundary positions were further refined by threading the sub-reads to ensure no gaps or overlaps between any successive sub-reads. The number of passes for each eccDNA fragment was calculated as the number of concordant sub-reads mapped to that location. Only eccDNA with at least 2 passes was kept for downstream analysis. Each eccDNA sequence was derived from the reference genome sequence where it mapped to, with sequence variants incorporated. The sequence variants were called from sub-reads mapped to the corresponding location, requiring minimum depth of 4 and minimum allele frequency of 0.75.
Genomic distribution of eccDNA:   The eccDNA fragments were piled up across the genome. To remove PCR duplicates, eccDNA fragments with the same chromosome, start and end positions were treated as duplicates and only one was retained. The coverage of unique eccDNA fragments at each base of the genome was obtained using bedtools (version 2.29.2) and stored in bigwig file.
Mapping of Illumina sequencing reads:   Raw Illumina sequence reads were preprocessed by Trimmomatic (version 0.39) to remove sequencing adaptors and low-quality reads, using parameters: ILLUMINACLIP:adapters/NexteraPE-PE.fa:2:30:10:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:75 TOPHRED33. BWA MEM (version 0.7.17) with default parameters were used to map the reads to our customized mm10combine reference genome. Duplicated reads were removed by Picard (version 2.23.4). Reads with mapping quality of at least 60 were considered as unique mapped and used for downstream analysis. The genomic coverage was calculated using bamCoverage from deeptools (version 3.5.0) with binSize 1.
Genome_build: mm10
Supplementary_files_format_and_content: For the Nanopore sequencing, the bigwig file contains the coverage of unique eccDNAs across the genome. For the Illumina sequencing, the bigwig file contains the read depth of purified eccDNA at each base of the genome.

growth_protocol: Mouse ES-E14 cells were cultured on dishes coated with 0.1% gelatin in standard LIF/serum medium containing mouse LIF (1000U/ml), 15% fetal bovine serum (FBS), 0.1 mM nonessential amino acids, 0.055mM β-mercaptoethanol (BME), 2 mM GlutaMax, 1mM sodium pyruvate and penicillin-streptomycin (PS).

extract_protocol:
Illumina sequencing library for eccDNA was prepared by Tn5-transposon-based tagmentation with Nextera® XT DNA Sample Preparation Kit according to manufactory’s instruction. Briefly, after validating the purity of eccDNAs with AFM imaging, 0.5 ng pure eccDNAs were directly tagmented with Tn5 transposase, followed by 12-14 cycles PCR amplification with Illumina sequencing adaptors. Barcoded libraries were pooled and sequenced with Illumina HiSeq 2500 in 150 PE mode.
To purify eccDNAs, cells were first dehydrate in >90% methanol before crude extrachromosomal DNA were extracted in an alkaline lysis buffer at pH11.8. After neutralization and precipitation, crude extrachromosomal DNA were bound in silica column (Qiagen) in binding buffer. Bound DNAs were eluted and digested with PacI (NEB) and Plasmid Safe ATP-dependent DNase (Lucigen) for 4-16 hours. Undigested eccDNA is then extracted with Phenol/chloroform/isoamyl alcohol (PCI) solution (25:24:1) in a Phase Lock Gel tube (QuantaBio) to minimize DNA loss. After precipitation with carrier glycogen (Roche) and 1/10 V 3M NaOAc (pH 5.5), the precipitated crude eccDNAs were resuspended in Solution P and further purified by magnetic silica beads that selectively bind to eccDNAs. The eccDNAs were then eluted with 0.1X Elution buffer (1mM Tris-HCl pH8.0) and the concentration is measured by Qubit dsDNA HS Assay kit (Thermo Fisher).
purified eccDNA seq

value: mESC


title: CVS25


title: HCT116 2-Phenylmaltol 1

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: Total RNA was used for this analysis.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: human colon cancer cell line

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Cells were cultured in Dulbecco's Eagle's medium (DMEM; Sigma) supplemented with 10% fetal bovine serum (HyClone). All cells were cultured at 37℃ in a humidified incubator under 5% CO2.

extract_protocol: Total cellular RNA was extracted using the RNeasy Minikit (Qiagen) and then was treated with Torbo DNase (Thermo Fisher Scientifc) to remove residual genomic DNA.

treatment_protocol: HeLa cells were terated 1μg/ml or 3μg/ml of 2-Phenylmaltol for 48hr. HCT116 cells were terated 5μg/ml of 2-Phenylmaltol for 48hr.

tag: concentration


title: ProB(+)_1%input-rep1

city: Isehara

first: Hiroyuki

last: Hosokawa

address: 143 Shimokasuya

department: Department of Immunology

institute: Tokai University School of Medicine

data_processing:
ChIP-seq data were mapped to the mouse genome build NCBI37/mm10 using Bowtie (v1.1.1; http://bowtie-bio.sourceforge.net/index.shtml) with “-v 3 -k 11 -m 10 -t --best –strata” settings and HOMER tagdirectories were created with makeTagDirectory and visualized in the UCSC-genome browser (http://genome.ucsc.edu) (Speir et al., 2016).  ChIP peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”.  Peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package according to ENCODE guidelines (https://sites.google.com/site/anshulkundaje/projects/idr).  Only reproducible high quality peaks, with a normalized peak score ≥ 15, were considered for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files include BED-files  All genomic coordinates are relative to mm10 mouse assembly.

source_name: ProB(+) cells

growth_protocol: A ProB(+) cell line was cultured on OP9 monolayers using OP9 medium (α-MEM, 10% FBS, 50 μM β-mercaptoethanol, Pen-Step-Glutamine) supplemented with 10 ng/ml of SCF (Pepro Tech Inc), 10 ng/ml of IL-7 (Pepro Tech Inc) and 10 ng/ml of Flt3L (Pepro Tech Inc).  Every 2-3 days, cultured cells were disaggregated, filtered through 40-um nylon mesh, and re-cultured on new OP9 monolayers with medium containing cytokines above.

extract_protocol: Ten million of ProB(+) cells were fixed with 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min at RT followed by additional 10 min with addition of formaldehyde up to 1%.  The reaction was quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed with HBSS (Gibco). Pelleted nuclei were dissolved in lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8) and PIC) and sonicated on SFX150 (Branson) for 6 cycles of 20sec sonication followed by 1min rest, with 30% amplitude.  Six ug of anti-Lmo2 Abs (a mixture of 2 ug of NB110-78626 (Novus), 2 ug of ab91652 (Abcam) and 2 ug of AF2726 (R&D systems)) were pre-bound to Dynabeads Protein A/G (Invitrogen) and then added to the diluted chromatin complexes in parallel aliquots.  The samples were incubated overnight at 4 °C, then washed and eluted for 6 h at 65 °C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, and 50 ug/ml proteinase K).  Precipitated chromatin fragments were cleaned up using PCR purification Kit (Qiagen).  ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (E6240, NEB) and sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.

value: Cultured on OP9

tag: chip (antibody)


title: CVS24


title: CVS20

value: preeclampsia pregnancy


title: ProB(+)_1%input-rep2


title: HeLa 2-Phenylmaltol 2

description: Total RNA was used for this analysis.

source_name: human cervical cancer cell line

value: HeLa


title: AP7280

description: Total RNA

value: SHAM 7days

value: Male


title: HeLa 2-Phenylmaltol 1

description: Total RNA was used for this analysis.


title: asxl1_MUT_A

status: Public on Aug 04 2021

city: Guangzhou

last: Fang

state: Guangdong

address: Guangzhou Higher Education Mega Centre, Panyu District

department: School of Medicine

institute: South China University of Technology

data_processing:
The reads were mapped onto the GRCz11 zebrafish reference genome, using STAR (Dobin et al., 2013).
Raw read counts were for each gene were calculated with Ensembl annotation by Featurecounts (Liao et al., 2014)
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited text files include feature counts for each Sample

organism: Danio rerio

source_name: 3dpf embryo's tail

growth_protocol: Zebrafish were raised and maintained under standard conditions. Embryos were raised at 28.5°C and incubated in “egg water” containing 0.002% methylene blue as a fungicide. Embryos were collected and morphologically staged as described (Kimmel et al., 1995). The mutants were based on an AB background.

extract_protocol:
3 days post fertilization (dpf) asxl1+/+ and asxl1-/- embryos from asxl1+/- intercross were collected and extract total RNA from the tails including CHT. Each sample is a pool of tails (about 20). RNA was extracted using TRIzol (Invitrogen).
Sequencing libraries were prepared from total RNA using Novogene NGS RNA Library Prep Kit.

treatment_protocol: No treatments were applied prior to RNA extraction

tag: Stage


title: asxl1_MUT_B


title: ProB(+)_anti-Lmo2_ChIP-rep1

tag: treatment

value: anti-Lmo2 Abs (a mixture of 2 ug of NB110-78626 (Novus), 2 ug of ab91652 (Abcam) and 2 ug of AF2726 (R&D systems))


title: ProB(+)_anti-Lmo2_ChIP-rep2


title: CVS32


title: asxl1_WT_B


title: HCT116 control 1

description: Total RNA was used for this analysis.

value: DMSO


title: asxl1_WT_A


title: U0126 110-cell

city: Kansas City

first: Konner

last: Winkley

state: MO

address: 2401 Gillham Road

department: Genomic Medicine Center

institute: Children's Mercy Research Institute

data_processing:
Fastq.gz files were processed using the dropSeqPipe pipeline with default parameters to produce raw Seurat objects
Genome_build: KH2012
Supplementary_files_format_and_content: Seurat files were generated using the dropSeqPipe pipeline

organism: Ciona robusta

source_name: Whole embryo

growth_protocol: Embryos developed in incubators at 18˚C

extract_protocol:
Embryos were dissociated in Calcium/Magnesium free artifical seawater and the single-cell suspension was encapsulated using the Dolomite Nadia Instrument according to standard protocols
Nextera XT, single-cell RNAseq

treatment_protocol: Embryos were treated with DMSO (1:1000 dilution) or U0126 (4 µm) from the 16-cell stage

tag: hotta stage


title: U0126 64-cell


title: DMSO 110-cell


title: DMSO Mid-gastrula


title: 9304_VEH

city: San Francisco

first: Holly

middle: A

last: Ingraham

address: 1550 4th Street, 284F

department: Cellular and Molecular Pharmacology

institute: University of California, San Francisco

data_processing:
Samples were sequenced and demultiplexed by the UCSF Center for Advanced Technology
Adapters were removed and sequences were headcropped (5bp) using Timmomatic
Sequences were mapped to the mouse genome (mm10) using HISAT2
Reads that aligned to exons were quantified using htseq-count (mode=Union, min. alignment quality=10) and the mm10 gene model
Differential gene expression was determined using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include number of exon-aligned reads for the given genes.

source_name: ventromedial hypothalamic nucleus (venotrolateral region)

extract_protocol:
VMHvl was manually microdissected and flash frozen in liquid nitrogen. RNA was isolated using the Qiagen Rneasy Micro kit with on-column Dnase digestion. Libraries were prepared using the Tecan/Nugen Trio RNA-Seq Library Preparation Kit (0357-32), using 15 ng of input RNA per sample.
Libraries were prepared according to the manufacturer's protocol. Samples were barcoded and multiplexed prior to sequencing.

treatment_protocol: 1ug estradiol benzoate (EB) or vehicle control was administered via subcutaneous injection to ovariectomized female mice. Tissue was collected 4 hours after treatment.

tag: biological sex

value: Female

tag: status

value: Ovariectomized

value: Vehicle

tag: tissue/region


title: 9305_EB

value: Estradiol Benzoate (1ug)

value: ventromedial hypothalamic nucleus (venotrolateral region)


title: 9301_VEH


title: 9309_VEH


title: HeLa control 2

description: Total RNA was used for this analysis.

tag: cell line


title: 9306_EB


title: HeLa control 1

description: Total RNA was used for this analysis.


title: 9310_EB


title: U0126 Mid-gastrula


title: PAS-seq_day-40_2

city: Stanford

first: Daniel

middle: Sunwook

last: Kim

address: 269 Campus Drive, CCSR 2150

institute: Stanford School of Medicine

description:
PAS-seq_day-40_2
primary_keratinocyte-d40.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz

data_processing:
See ENCODE RNA-seq pipeline: https://github.com/ENCODE-DCC/long-read-rna-pipeline
General protocol: https://www.encodeproject.org/documents/6354169f-86f6-4b59-8322-141005ea44eb/@@download/attachment/Long%20RNA-seq%20pipeline%20overview.pdf
Genome_build: hg19
Supplementary_files_format_and_content: Bigwigs for each timepoint; count matrices including all genes, protein coding (pc), expressed, and normalized (rlog); timeseries clustering; TPMs

source_name: Primary foreskin keratinocytes

growth_protocol: Human primary keratinocytes were cultured in 50/50 growth media and induced to differentiate for 6 days as previously describe (Zarnegar 2012), https://www.encodeproject.org/documents/6664773d-349a-492a-a63f-b7997067d53d/@@download/attachment/ggr.keratinocyte.khavari-lab.cellculture.pdf

tag: tissue

value: Skin

value: Primary foreskin keratinocyte

tag: timepoint

tag: biological replicate


title: PAS-seq_day-60_2

description:
PAS-seq_day-60_2
primary_keratinocyte-d60.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz

tag: cell type


title: PAS-seq_day-55_1

description:
PAS-seq_day-55_1
primary_keratinocyte-d55.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-55_2

description:
PAS-seq_day-55_2
primary_keratinocyte-d55.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-60_1

description:
PAS-seq_day-60_1
primary_keratinocyte-d60.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-45_1

description:
PAS-seq_day-45_1
primary_keratinocyte-d45.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-35_2

description:
PAS-seq_day-35_2
primary_keratinocyte-d35.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-45_2

description:
PAS-seq_day-45_2
primary_keratinocyte-d45.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-40_1

description:
PAS-seq_day-40_1
primary_keratinocyte-d40.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-50_2

description:
PAS-seq_day-50_2
primary_keratinocyte-d50.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-50_1

description:
PAS-seq_day-50_1
primary_keratinocyte-d50.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-30_1

description:
PAS-seq_day-30_1
primary_keratinocyte-d30.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-35_1

description:
PAS-seq_day-35_1
primary_keratinocyte-d35.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-25_2

description:
PAS-seq_day-25_2
primary_keratinocyte-d25.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: DMSO 64-cell


title: PAS-seq_day-20_2

description:
PAS-seq_day-20_2
primary_keratinocyte-d20.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: 9302_EB


title: PAS-seq_day-30_2

description:
PAS-seq_day-30_2
primary_keratinocyte-d30.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-20_1

description:
PAS-seq_day-20_1
primary_keratinocyte-d20.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-15_2

description:
PAS-seq_day-15_2
primary_keratinocyte-d15.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-15_1

description:
PAS-seq_day-15_1
primary_keratinocyte-d15.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-10_1

description:
PAS-seq_day-10_1
primary_keratinocyte-d10.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-05_2

description:
PAS-seq_day-05_2
primary_keratinocyte-d05.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-05_1

description:
PAS-seq_day-05_1
primary_keratinocyte-d05.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-10_2

description:
PAS-seq_day-10_2
primary_keratinocyte-d10.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: 56c2_H4_n2

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

description: replicate 2

data_processing:
Samples were loaded on an Ion PI v3 Chip and sequenced on the Ion Proton System using Ion PI  Hi-Q sequencing  200 kit chemistry (200 bp read length; Thermofisher Scientific)
Mapping & QC-mapped with Bowtie2 (2.3.4.1) & Samtools (0.1.19)
Genome_build: hg38
Supplementary_files_format_and_content: csv file containing raw counting reads

source_name: Myotube

growth_protocol: hiPSCs were dissociated with StemPro Accutase Cell Dissociation Reagent (Gibco®) and plated at 3000 cells per cm2 onto collagen I-coated plates (Gibco®) and maintained for 10 days in skeletal muscle induction medium (SKM01). At day 10, cells were dissociated with Trypsin-EDTA 0,05% (Gibco®), plated at 5000 cells per cm2 onto collagen I-coated plates and maintained for 6 days in skeletal myoblast medium (SKM02). At day 16, myoblasts were dissociated and cryopreserved. For terminal differentiation, cells were thawed at 10.000 cells per cm2 in SKM02 and after 2-3 days, when cells reached confluence, the medium was replaced by the myotube medium (SKM03). Cells were then maintained for 5 to 6 days in SKM03.

extract_protocol:
Total RNA was extracted using the RNeasy Micro/Mini kit (Qiagen®)
For each sample, 50 ng of total RNA was reverse transcribed using the Ion AmpliSeq Transcriptome Human Gene Expression kit following the protocol of the manufacturer (Thermofisher Scientific®). The cDNA libraries were amplified and barcoded using Ion AmpliSeq Transcriptome Human Gene Expression core panel and Ion Xpress Barcode Adapter (Thermofisher Scientific®). The amplicons were quantified using Agilent High Sensitivity DNA kit before the samples were pooled in sets of eight. Emulsion PCR and Enrichment was performed on the Ion OT2 system Instrument using the Ion PI Hi-Q OT2 200 kit (Thermofisher Scientific®). Samples were loaded on an Ion PI v3 Chip and sequenced on the Ion Proton System using Ion PI Hi-Q sequencing 200 kit chemistry (200 bp read length; Thermofisher Scientific®).

value: myotubes derived from hiPSC

tag: genotype

value: MBNL1 -/- MBNL2 -/-

tag: sample type

value: Total cells


title: 56c2_H4_n1

description: replicate 1


title: PAS-seq_day-25_1

description:
PAS-seq_day-25_1
primary_keratinocyte-d25.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-00_1

description:
PAS-seq_day-00_1
primary_keratinocyte-d00.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: PAS-seq_day-00_2

description:
PAS-seq_day-00_2
primary_keratinocyte-d00.GGR.Stanford_Khavari.PAS-seq.pooled_Signal.UniqueMultiple.nonstranded.bw
ggr.rna.counts.mat.txt.gz
ggr.rna.counts.pc.expressed.mat.txt.gz
ggr.rna.counts.pc.expressed.timeseries_adj.pooled.rlog.mat.txt.gz
ggr.rna.counts.pc.mat.txt.gz
ggr.rna.reproducible.hard.reordered.clustering.txt
ggr.rna.tpm.mat.txt.gz


title: MSK PCa20

city: New York

first: Yu

last: Chen

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA sequencing reads were 3’ trimmed for base quality 15 and adapter sequences using version 0.4.5 of TrimGalore, and then aligned to human assembly hg19 with STAR v2.6 using default parameters to generate BAM alignment files.
TPMcalculator software was to generate TPM (transcripts per million) for each gene in each BAM file.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: comma delimited text file containing TPM of genes

source_name: prostate cancer organoid

growth_protocol: Organoid culture and seeding experiments were performed as described previously (PMID: 25201529, 26797458)

extract_protocol:
RNA extraction was performed according to manufacture's instuction in PureLinkTM RNA Mini Kit (Thermo Fisher Scientific #12183025)
RNA-Seq libraries were prepared using the Illumina TruSeq stranded mRNA kit, with 10 cycles of PCR amplification, starting from 500 ng of total RNA, at the Genome Technology Center (GTC) at NYU.

tag: primary site

value: Prostate

tag: biopsy site

value: Liver


title: 56c2_WT_n1

description: replicate 1

value: WT


title: 56c2_E3_n3

description: replicate 3

value: MBNL1 -/- MBNL2 +/+


title: MSK PCa18

value: Bone


title: 56c2_E3_n2

description: replicate 2


title: M9 control 1

city: San Diego

last: Sastry

address: 9500 Gilman Dr

institute: University of California, San Diego

data_processing:
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Comma-separated text files include log-TPM (log2-transformed Transcripts per million) for each sample

source_name: E. coli K12 MG1655

extract_protocol:
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: media


title: 56c2_WT_n3

description: replicate 3


title: 61c7_DM1_n2

description: replicate 2


title: MSK PCa13

value: Lymph Node


title: MSK PCa19


title: MSK PCa15

value: Ascites


title: 61c7_DM1_n3

description: replicate 3


title: MSK PCa12


title: 56c2_H4_n3

description: replicate 3


title: MSK PCa11


title: 61c7_DM1_n1

description: replicate 1


title: 56c2_WT_n2

description: replicate 2


title: MSK PCa8


title: UN rep1 [A-45]

city: Vancouver

first: Jordan

middle: W

last: Squair

state: BC

address: 818 West 10th Avenue

country: Canada

institute: University of British Columbia

description:
A-45_S1
10x v2

data_processing:
Reads were aligned using Cellranger v.2.2.0
Exon and intron counts were tabulated using Velocyto
Data were analyzed using Seurat v3
Genome_build: mm10-1.2.0 (GRCm38.93)
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell with tab delimeters

source_name: control_Lumbar spinal cord

extract_protocol:
Single nucleus dissociation was completed with a modified protocol based on our previous work. Briefly, animals were euthanized by isoflurane inhalation and cervical dislocation. The lumbar spinal cord was rapidly dissected and frozen on dry ice. Spinal cords were dounced in 500 µl sucrose buffer (0.32 M sucrose, 10 mM HEPES [pH 8.0], 5 mM CaCl2, 3 mM Mg-acetate, 0.1 mM EDTA, 1 mM DTT) and 0.1% Triton X-100 with the Kontes Dounce Tissue Grinder. 2 mL of sucrose buffer was added and filtered through a µm cell strainer. The lysate was subsequently centrifuged at 3200 g for 10 min at 4°C. The supernatant was decanted, and 3 mL of sucrose buffer added to the pellet and incubated for 1 min. The pellet was homogenized using an Ultra-Turrax and 12.5 mL of density buffer (1 M sucrose, 10 mM HEPES [pH 8.0], 3 mM Mg-acetate, 1 mM DTT) was added below the nuclei layer. The tube was centrifuged at 3200 g at 4°C and supernatant immediately poured off. The nuclei on the bottom half of the tube wall were collected with 100 µl PBS with 0.04% BSA and 0.2 U/µl RNase inhibitor. Resuspended nuclei were filtered through a 30 µm strainer. The nuclei suspension was finally adjusted to 1000 nuclei/µl.
Library preparation was carried out with 10X Genomics Chromium Single Cell Kit Version 2. The nuclei suspension was added to the Chromium RT mix to achieve loading numbers of 5000. For downstream cDNA synthesis (13 PCR cycles), library preparation and sequencing, the manufacturer’s instructions were followed.

tag: strain

value: wild type

tag: condition

value: uninjured control

value: Lumbar spinal cord


title: NEUROG3-HA-P2A-Venus-negative#4

city: Illkirch

first: Valerie

last: SCHREIBER

address: 1 rue Laurent Fries

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were identified and mapped onto the hg38 assembly of the human genome using STAR version 2.7.5a
Quantification of gene expression was performed using HTSeq version 0.6.1 and gene annotations from Ensembl release 98.
Normalization of read counts and differential expression analysis between Venus-negative and Venus-positive samples were performed using the method implemented in the DESeq2 Bioconductor library version 1.16.1
A negative binomial GLM fit, having the condition as variable, and a Wald significance test were implemented for the differential expression analysis. Differentially expressed genes were defined as those having a Benjamini – Hochberg-adjusted Wald test P < 0.05 and a log2 Fold-Change greater than 1
Genome_build: hg38
Supplementary_files_format_and_content: Excel file showing the genes differentially expressed between NEUROG3-Venus positive and negative hiPSC line differentiated to pancreatic endocrine progenitors

source_name: Venus-negative sorted pancreatic endocrine progenitors

growth_protocol: Cells were seeded at 3x10e5 cells/cm2 on Growth Factor Reduced Matrigel (Corning)-coated 24wells in mTESR1 + 5µM Y27632 (Stem Cell Technologies). Differentiation was initiated 24 hours after and performed following exactly the protocol described by Petersen et al, Stem cell reports:1-37 (2017) until the end of Stage 5 (day 13).

extract_protocol:
Total RNA was prepared with RNeasy micro kit (Qiagen).
Full length cDNA were generated from 2 ng of total RNA using SMART-SeqX v4 UltraX Low Input RNA Kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 10 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, USA) followed by 12 cycles of library amplification. Following purification with SPRIselect beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

treatment_protocol: At day 13 of differentiation, cells were harvested with TrypLE Select (Life Technologies), quenched with 3 volumes of MCDB131-3 medium (Petersen et al (2017) Stem cell reports:1-37)  containing 5 mM Y27632 , centrifuged 4 min at 200g, resuspended at 5M/ml in MCDB131-3 medium containing 5 mM Y27632 and sorted using a FACS Fusion/Aria in 350 µl RLT buffer (RNeasy micro kit, Qiagen).

tag: differentiation stage

value: hiPSC derived pancreatic endocrine progenitors, end of stage 5 (day 13)

tag: differentiation

value: Differentiation #30

tag: number of cells

value: 100,000 sorted Venus-negative cells


title: 56c2_E3_n1

description: replicate 1


title: MSK PCa10


title: UN rep3 [A-48]

description:
A-48_S2
10x v2


title: NEUROG3-HA-P2A-Venus-negative#0

value: Differentiation #29

value: 20,000 sorted Venus-negative cells


title: NEUROG3-HA-P2A-Venus-negative#3

value: 100,000sorted Venus-negative cells


title: SCI rep2 [F-13]

description:
F-13_S2
10x v2

source_name: SCI_Lumbar spinal cord

value: SCI (severe contusion of the thoracic spinal cord)


title: NEUROG3-HA-P2A-Venus-positive#3

source_name: Venus-positive sorted pancreatic endocrine progenitors

value: 8,000 sorted Venus-positive cells


title: Total RNA from primary myoblasts CP6_AZA

city: Chicago

first: Andrea

middle: A.

last: Domenighetti

state: IL

address: 345 East Superior St

institute: Northwestern University & Rehabilitation Institute of Chicago

data_processing:
The quality of DNA reads, in fastq format, was evaluated using FastQC. Adapters were trimmed and reads of poor quality or aligning to rRNA sequences were filtered. The cleaned reads were aligned to the human genome (hg19) using STAR
Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for hg19 obtained from UCSC (University of California Santa Cruz; http://genome.ucsc.edu)
Normalization was determined using DESeq2
After normalization, the Statistics and Machine Learning Toolbox function anova2 in MATLAB was used to perform a two-way analysis of variance (ANOVA) of RNA-seq data to identify differentially regulated transcripts in CP and TD myoblasts (cell group effect), treated and non-treated with AZA (treatment effect).
Genome_build: human genome (hg19)
Supplementary_files_format_and_content: RNA_SEQ reads_normalized.csv

source_name: From contractured muscle in a child with cerebral palsy, treated with 5-azacytidine

growth_protocol: Satellite cell-derived myoblasts were cultured at 37°C in a 5% CO2 atmosphere using a high-serum medium containing Ham’s F10 (Corning) with 20% Fetal Bovine Serum (FBS, from Gibco), 10 mg/ml streptomycin and 100 units/ml penicillin (Gibco) and human recombinant bFGF (5 ng/ml) (BD). Myoblasts were seeded at ~5,000 cells/cm2 and were maintained in the same high-serum medium up to 20-30% of confluence before 5-azacytidine (AZA) treatment. Cells were treated with AZA (5 μM) (Sigma-Aldrich) for 24 hours to induce DNA demethylation, or not treated with AZA as a control. After 24h, the AZA-containing medium was removed, cells were rinsed twice with high-serum medium and then cultured until they reached 70-80% confluence in high-serum medium before RNA extraction.

extract_protocol:
Total RNA was isolated and purified from 70-80% confluent myoblast cell culture preparations (passage 4) using Trizol reagent (Ambion - Life Technologies) and a Qiagen RNeasy Mini Kit according to manufacturer's recommendations.
Total RNA examples were checked for quality using RINs generated from Agilent Bioanalyzer 2100. RNA quantity was determined using a Qubit fluorometer. The Illumina TruSeq Stranded mRNA Library Preparation Kit was used to prepare sequencing libraries from 1 ug of high-quality RNA samples (RIN>7). The Kit procedure was performed without modifications. This procedure included mRNA purification and fragmentation, cDNA synthesis, 3’ end adenylation, Illumina adapter ligation, library PCR amplification and validation. An IlluminaIllumina  NextSeq 500 sequencer was used to sequence the libraries with the production of single-end, 75 bp reads at the depth of 20-25 M reads per sample.

treatment_protocol: Cells were treated with AZA (5 μM) (Sigma-Aldrich) for 24 hours to induce DNA demethylation, or not treated with AZA as a control. After 24h, the AZA-containing medium was removed, cells were rinsed twice with high-serum medium and then cultured until they reached 70-80% confluence in high-serum medium before DNA extraction.

tag: gmfcs scale

tag: limbs

value: Diplegic

tag: gender

value: Male

tag: age

value: Hamstring muscle biopsy

value: primary myoblasts

value: contractured cerebral palsy (CP)

tag: treatment

value: AZA


title: Total RNA from primary myoblasts CP2

source_name: From contractured muscle in a child with cerebral palsy

tag: tissue

value: control


title: NEUROG3-HA-P2A-Venus - CTRL_RAM_CR

data_processing:
Library strategy: CUT&RUN
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were trimmed using cutadapt v1.9.1 with option: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -m 5 -e 0.1
Paired-end reads were mapped to Homo Sapiens genome (assembly hg38) using Bowtie2 (release 2.3.4.3, parameter: -N 1 -X 1000)
Reads overlapping with ENCODE hg38 blacklisted region V2 were removed using Bedtools
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig tracks were generated using bamCoverage from deepTools for ≤120 bp and ≥150 bp fragments separately. Tracks were normalized with RPKM method. The bin size is 20. ≤120 bp fragments for samples VLSR27, VLSR28, VLSR29. ≥150 bp fragments for samples VLSR32, VLSR41, VLSR44.

source_name: Venus+-sorted pancreatic endocrine progenitors

growth_protocol: Cells were seeded at 3x10e5 cells/cm2 on Growth Factor Reduced Matrigel (Corning)-coated 24wells- or 6wells-plates (CellBind Corning) in mTESR1 + 5µM Y27632 (Stem Cell Technologies). Differentiation was initiated 24 hours after and performed following exactly the protocol described by Petersen et al, Stem cell reports:1-37 (2017) until the end of Stage 5 (day 13).

extract_protocol:
We followed the protocol of Hainer and Fazzio (2019) Current Protocols 126 (1):e85 (2019) with minor modifications. Fresh or thawed cells were washed once with 1mL cold PBS and resuspended in nuclear extraction buffer (NE, 20mM HEPES-KOH, pH 7.9, 10mM KCl, 0.5mM Spermidine, 0.1% Triton X-100, 20% glycerol, freshly added protease inhibitors)). After 3 min spinning at 4°C at 600g, cells were resuspended in 600 μL NE buffer. Concanavalin A beads (Polysciences, 25 μL bead slurry/sample) were washed twice with ice-cold Binding buffer (20mM HEPES-KOH, pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2) and resuspended in 300 μL Binding buffer. Nuclei were added to beads with gentle vortexing and incubated for 10 min at 4°C with gentle rocking. Bead-bound nuclei were blocked with 1 mL cold Blocking buffer (20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.1% BSA, 2mM EDTA, freshly added protease inhibitors) by gentle pipetting, incubated 5 min at RT and washed in 1mL cold Wash buffer (WB, 20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.1% BSA, freshly added protease inhibitors) and resuspended in 250 μL cold WB. 250 μL of primary antibody diluted 1:100 in cold WB were added with gentle vortexing, and samples were incubated overnight with gentle rocking at 4°C. Samples were washed twice in 1 mL cold WB, and resuspended in 250 μL cold WB. When indicated, incubation with a secondary antibody (Donkey anti Sheep IgG, 1:200) was performed for 1h at 4°C in WB under gentle rocking. After 2 washes with 1 ml WB, and resuspension in 250 μl WB, 200 μL of pA-MN (diluted at 1.4 ng/mL in cold WB, in-house production using the pK19pA-MN plasmid, obtained from Ulrich Laemmli (Addgene plasmid # 86973; http://n2t.net/addgene:86973 ; RRID:Addgene_86973) was added with gentle vortexing, and samples were incubated with rotation at 4°C for 1 hour. Samples were washed twice in 1 mL cold WB and resuspended in 150 μL cold WB. Three μL of 100 mM CaCl2 was added upon gentle vortexing to activate the MN. After 30 min of digestion, reactions were stopped by addition of 150 μL 2XSTOP buffer (200mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/mL RNaseA, 40ug/mL glycogen) and DNA fragments were released by passive diffusion during incubation at 37°C for 20 min. After centrifugation for 5 min at 16,000g at +4°C to pellet cells and beads, 3 μL 10% SDS and 2.5 μL Proteinase K 20mg/ml were added to the supernatents, and samples were incubated 10 min at 70°C. DNA purification was done with phenol/chloroform/isoamyl alcohol extraction followed by chloroform extraction using MaxTract tubes (Qiagen). DNA was precipitated with ethanol after addition of 20 µg glycogene, and resuspended in 25µl 0.1XTE.
Illumina sequencing libraries were prepared at the Genomeast facility (IGBMC, Illkirch). CUT&RUN samples were purified using Agencourt SPRIselect beads (Beckman-Coulter). Libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (Diagenode) following the manufacturer's protocol with some modifications. Illumina compatible indexes were added through a PCR amplification (3 min at 72°C, 2 min at 85°C, 2 min at 98°C; [20 sec at 98°C, 10 sec at 60°C] x 13 cycles). Amplified libraries were purified and size-selected using Agencourt SPRIselect beads (Beckman Coulter) by applying the following ratio: volume of beads / volume of libraries = 1,4 / 1. The libraries were sequenced on Hiseq 4000 as Paired-End 2x100 base reads following Illumina’s instructions.

treatment_protocol: At day 13 of differentiation, cells were harvested with TrypLE Select (Life Technologies), quenched with 3 volumes of MCDB131-3 medium (Petersen et al (2017) Stem cell reports:1-37)  containing 5 mM Y27632 , centrifuged 4 min at 200g, resuspended at 5M/ml in MCDB131-3 medium containing 5 mM Y27632 and sorted using a FACS Fusion/Aria in the same medium, at +4°C. Sorted cells were either used directly for CUT&RUN or cryostored in Cryostor10 (Stem Cell Technologies) at -80°C until use.

tag: cell line

tag: cell number

value: 15,000 frozen Venus+ sorted cells

tag: cut&run antibodies (primary)

value: RAM (Bethyl, A90117A)


title: NEUROG3-HA-P2A-Venus - CTRL_DAsh_CR

value: hiPSC derived pancreatic endocrine progenitors, end of stage 5 (day 13)

value: 75,000 freshly sorted Venus+ cells

value: Donkey anti Sheep-Alexa Fluor-488 (Jackson ImmunoRes, 713-545-147)