title: MUSCLE_AGE52_F_GROUP50_64_CC_T331_Gt027_R1


title: MUSCLE_AGE51_M_GROUP50_64_CC_T289_Gt015_R1

status: Public on Jan 08 2021

type: SRA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

library_source: transcriptomic

data_processing:
Single-read sequencing was performed for 141 cycles and Real-Time Analysis (RTA) v1.18.66.3 generated the base-call files (BCL files). BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program (v2.17.1.14)
The quality of the bases was checked using FASTQC program (v11.8) before and after adapter removal and last base trimming by cutadapt program (v2.7).
The cleaned FASTQ files were aligned using STAR (v2.4.0j) using hg19 genome and Ensembl v82 annotations
The aligned files were quantifiedd  using featurecounts (v1.4.6-p5) for gene (ENSG) counts and for tracks (.bw files) using  genomeCoverageBed (v2.9.1)
The cleaned FASTQ files were used for calculating TPM values using Kallisto (v0.44) using hg19 genome and Ensembl v82 annotations
Genome_build: human hg19 genome
Supplementary_files_format_and_content: .bw

molecule: total RNA

organism: Homo sapiens

source_name: Skeletal Muscle

extract_protocol:
Total RNA was prepared by lysing cell pellet (2x106) in 700ul Qiazol and extracted using Qiagen miRNeasy mini kit according to the manufacturer’s recommendation (Qiagen Inc, CA, USA)
Samples were prepared using Nugen Ovation v2 kits and the sequencing library was prepared using Illumina ChIP-Seq kits according to manufacturer’s protocol (Illumina, San Diego, CA).

tag: tissue

value: Vastus lateralis

tag: age

tag: gender

value: M


title: MUSCLE_AGE52_M_GROUP50_64_CC_T329_Gt007_R1


title: MUSCLE_AGE72_F_GROUP65_79_CC_T296_Gt018_R1

value: F


title: MUSCLE_AGE72_M_GROUP65_79_CC_T298_Gt014_R1


title: MUSCLE_AGE73_M_GROUP65_79_CC_T565_Gt065_R1


title: CDK12nc_1

status: Public on Jan 05 2021

city: Boston

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

description:
all_TALL_samples_peaks.narrowPeak
TALL_CDK12NC_forwardRawCov.bw
TALL_CDK12NC_reverseRawCov.bw

data_processing:
Single-end 50bp reads were filtered with bbduk.sh and parameters “k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=20 minlength=75 ref=truseq_rna.fa.gz”
STAR (v2.5.1b) was used to align reads to the human genome (GRCh38) with the following parameters “--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate”.
Strand specific coverage profiles were created with the bamCoverage command (DeepTools v2.5.4) with parameters “--normalizeUsingRPKM –filterRNAstrand –bs 50".
Biological replicates were merged using "samtools merge" and processed as described for the individual replicates.
PolyA-seq peaks were called using MACS2 (v 2.1.1) and parameters “--nomodel --extsize 100 --shift 0”.
Genome_build: GRCh38
Supplementary_files_format_and_content: Combined MACS narrow peak file and bedgrap coverage files for merged replicates of each treatment condition.

molecule: polyA RNA

source_name: Jurkat cells

growth_protocol: Jurkat cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum

extract_protocol:
Biological duplicated were collected and RNA extraction was performed with TRIzol (Ambion) following the manufacturers’ instructions. Total RNA was treated with DNase I (Invitrogen).
Sequencing libraries were prepared with the RNA-seq library kit (QuantSeq 3’ mRNA Sequencing REV, Lexogen) following the manufacturers’ instructions.

treatment_protocol: Cells were incubated for 8 hours in the presence of DMSO or BSJ-4-116 (50 nM) or BSJ-4-116NC (100 nM) or THZ531 (250nM) before performing RNA extraction.

tag: treatment

tag: origin

value: T-ALL


title: MUSCLE_AGE38_M_GROUP35_49_CC_T232_Gt016_R1


title: Brg1AID/AID_Cebpb_Tir1_D-3_MLL4

status: Public on Jan 07 2021

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

library_source: genomic

data_processing:
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3);
Single-end reads of RNA-seq are aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the reads per kilobase per million (RPKM) on exonic regions as expression measurements for each gene.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: wig files were generated using in-house script and the scores represent RPKM.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each gene.

molecule: genomic DNA

organism: Mus musculus

source_name: Brown preadipocyte cell

growth_protocol: Primary brown preadipocytes were isolated from interscapular BAT of newborn Snf5f/f or Brg1AID/AID mice and immortalized with SV40T-expressing retroviruses generated from the pBabeneo-large T plasmid.

extract_protocol:
Cells were cross-linked with 1.5% formaldehyde for 10 min and quenched by 125 mM glycine for 10 min. 10 million fixed cells were resuspended in ice cold buffer containing 5mM PIPES, pH 7.5, 85mM KCl, 1% NP-40 and protease inhibitors, incubated on ice for 15 min, and centrifuged at 500 g for 5 min at 4°C. Nuclei were resuspended with 1mL buffer containing 50mM Tris-HCl, pH8.0, 10mM EDTA, 0.1% SDS and protease inhibitors, and subjected to sonication. Sheared chromatin was clarified by centrifugation at 13,000 g for 10 min at 4°C. The supernatant was transferred to a new tube and further supplemented with 1% Triton-X100, 0.1% sodium deoxycholate and protease inhibitors. 2% of the mixture was set aside as input and 20ng of spike-in chromatin (Active Motif, #53083) was added to the rest. For each ChIP, 4 - 10 µg of target antibodies and 2μg of spike-in antibody (anti-H2Av, Active Motif, #61686) were added and incubated on a rotator at 4°C overnight. ChIP samples were added with 50μL prewashed protein A Dynabeads (ThermoFisher) and incubated for 3h at 4°C. Beads were then collected on a magnetic rack and washed twice with 1mL cold RIPA buffer, twice with 1mL cold RIPA buffer containing 300mM NaCl, twice with 1mL cold LiCl buffer and once with PBS. Beads were then eluted with 100 μL buffer containing 0.1M NaHCO3, 1% SDS, and 20μg Proteinase K at 65°C overnight. Input sample volumes were adjusted to 100μL with the elution buffer. Samples were then purified using QIAquick PCR purification kit (Qiagen) and eluted in 30 μL 10mM Tris-HCl.
Libraries were prepared according to NEB (Illumina kit) instructions. DNA were used to construct libraries using NEBNext® Ultra™ II DNA Library Prep kit with AMPure XP magnetic beads (Beckman Coulter).

treatment_protocol: For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x10e6 cells per 15-cm dish 4 days before induction of adipogenesis. At D0, confluent cells were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 2 μg/ml dexamethasone, and 0.125mM indomethacin. At D2, D4, and D6, the cells were replenished with medium containing 10% FBS, 0.02 μM insulin, and 1 nM T3.

tag: cell type

value: BAT isolated brown preadipocytes

tag: stage of adipogenesis

value: Preadipocytes (D-3)

tag: chip antibody

value: anti-MLL4 (Homemade, Cho YK et al., Cell Metab, 2009)


title: MUSCLE_AGE23_M_GROUP20_34_CC_T293_Gt022_R1


title: MUSCLE_AGE42_M_GROUP35_49_AA_T297_Gt024_R1


title: MUSCLE_AGE31_M_GROUP20_34_AA_T230_Gt025_R1


title: MUSCLE_AGE45_M_GROUP35_49_AA_T325_Gt017_R1


title: CO1_r_S2_L004_R1_001

status: Public on Dec 21 2020

city: EAST LANSING

first: MARCELA

last: TABARES

state: MI

address: 567 WILSON RD

department: MMG

institute: MICHIGAN STATE UNIVERSITY

data_processing:
SPARTA pipeline https://sparta.readthedocs.io/en/latest/
raw data output file from SPARTA
raw data counts obtained in csv file were filtered base on the cuttoff parameters as follow: false discovery rate FDR< 0.05, log CPM>5, and a log2 FC<-1 (downregulated genes) or > 1 (upregulated genes) (Johnson et al., 2016).
Genome_build: ASM798v2
Supplementary_files_format_and_content: xls file with filtering steps (false discovery rate FDR<0.05, log CPM>5, and a log2 FC<-1 (downregulated genes) or >1 (upregulated genes) )
Supplementary_files_format_and_content: csv output  file give by SPARTA software

organism: Geobacter sulfurreducens PCA

source_name: WT_cobalt_exponential growth phase

growth_protocol: Anaerobic growth in liquid media without agitation

extract_protocol:
Total RNA extraction following manufacturer's recommendation for QIAGEN RNeasy kit (QIAGEN)
rRNA depletion used an Illumina TruSeq Total RNA Library Preparation kit with QIAseq FastSelect – 5S/16S/23S rRNA depletion (QIAGEN). Libraries were quantified using Qubit and Advanced Analytical Fragment Analyzer High Sensitivity DNA NGS assays. The libraries were then pooled in equimolar amounts for multiplexed sequencing and the pool was quantified using the Kapa Biosystems Illumina Library Quantification qPCR kit.

treatment_protocol: Addition of cobalt chloride into the culture media

tag: strain

value: PCA

value: with cobalt

tag: growth phase

value: Exponential


title: WT2_S1_L004_R1_001

source_name: WT_control_exponential growth phase

value: without cobalt


title: MUSCLE_AGE37_F_GROUP35_49_AA_T120_Gt037_R1


title: Snf5f/f_PPARg_GFP_D2

value: Differentiating preadipocytes (D2)

value: anti-PPARgamma (H-100, sc-7196X, Santa Cruz)


title: MUSCLE_AGE31_M_GROUP20_34_AA_T328_Gt005_R1


title: BPbrm1_RNA_Myf5Cre_D7

description: mRNA

extract_protocol:
Total RNA was subjected to mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).
Isolated mRNAs were reverse-transcribed into double stranded cDNA and subjected to sequencing library construction using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, E7770) according to the manufacturer’s instructions.

value: Mature adipocytes (D7)


title: MCF10A, WTp53 cDNA insert, 10uM Nutlin3a, Replicate 2

status: Public on Dec 18 2020

city: Boulder

first: Dylan

middle: J

last: Taatjes

state: CO

address: Campus Box 596

department: Biochemistry

institute: University of Colorado Boulder

description:
nascent RNA
nascent RNA (PRO-seq) from MCF10A cells

data_processing:
processing of all sequencing data was performed using the NascentFlow Pipeline (doi: 10.17605/OSF.IO/NDHJ2)
Genome_build: GRCh38
Supplementary_files_format_and_content: bed

source_name: MCF10A Cells

growth_protocol: MCF10A cells cultured in DMEM/F12 (Invitrogen #11330-032) media containing 5% horse serum (LifeTech #16050- 122), 20ng/mL EGF ((Peprotech #AF-100-15), 0.5μg/mL Hydrocortisone (Sigma #H0888-1g), 100ng/mL Cholera toxin (Sigma #C8052-2mg), 10μg/mL insulin (Sigma #I1882-200mg), and 1x Gibco 100x Antibiotic-Antimycotic (Fisher Sci, 15240062) penicillin-streptomycin.

extract_protocol:
After treatment, cells were washed 3x with ice cold PBS, and then treated with 10 ml (per 15 cm plate) ice-cold lysis buffer (10 mM Tris–HCl pH 7.4, 2 mM MgCl2, 3 mM CaCl2, 0.5% NP-40, 10% glycerol, 1 mM DTT, 1x Protease Inhibitors (1mM Benzamidine (Sigma B6506-100G), 1mM Sodium Metabisulfite (Sigma 255556-100G), 0.25mM Phenylmethylsulfonyl Fluoride (American Bioanalytical AB01620), and 4U/mL SUPERase-In). Cells were centrifuged with a fixed-angle rotor at 1000xg for 15 min at 4◦C. Supernatant was removed and pellet was resuspended in 1.5 mL lysis buffer to a homogenous mixture by pipetting 20-30X before adding another 8.5 mL lysis buffer. Suspension was centrifuged with a fixed-angle rotor at 1000xg for 15 min at 4◦C. Supernatant was removed and pellet was resuspended in 1 mL of lysis buffer and transferred to a 1.7 mL pre-lubricated tube (Costar cat. No. 3207). Suspensions were then pelleted in a microcentrifuge at 1000xg for 5 min at 4◦C. Next, supernatant was removed and pellets were resuspended in 500 μL of freezing buffer (50 mM Tris pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, 4U/ml SUPERase-In). Nuclei were centrifuged 2000xg for 2 min at 4◦C. Pellets were resuspended in 100 μL freezing buffer. To determine concentration, nuclei were counted from 1 μL of suspension and freezing buffer was added to generate 100 μL aliquots of 10x106 nuclei. Aliquots were flash frozen in liquid nitrogen and stored at −80◦C.
Nuclear run-on experiments were performed as described previously (Mahat, D. B., Kwak, H., Booth, G. T., Jonkers, I. H., Danko, C. G., Patel, R. K., et al. (2016). Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nature Protocols, 11(8), 1455–1476. with the following modifications: the final concentration of non-biotinylated CTP was raised from 0.25 μM to 25 μM, a clean-up and size selection was performed using 1X AMPure XP beads (1:1 ratio) (Beckman) prior to test PCR and final PCR amplification, and the final library clean-up and size selection was accomplished using 1X AMPure XP beads (1:1 ratio) (Beckman). http://doi.org/10.1093/bioinformatics/btq033) with the following modification. The final concentration of non-biotinylated CTP was raised from 0.25uM to 25uM, and the final library clean up and size selection was accomplished using 1X AMPure XP (Beckman).
PRO-seq

treatment_protocol: MCF10A WTp53 cells were seeded on three 25cm dishes (1x107 cells per dish) for each treatment 24 hours prior to the experiments ( 70% confluency at the time of the experiment). Cells were treated simultaneously with 10μM Nutlin3a or 0.1% DMSO for 1 hour.

tag: cell line

value: mammary gland; breast

value: epithelial

tag: crispr/cas9 insertion

value: 2820bp:full length p53 cDNA followed IRES expressed mCherry followed by SV40 polyA sequnece

tag: crispr/cas9 insertion location

value: 10uM Nutlin3a


title: MUSCLE_AGE45_M_GROUP35_49_AA_T292_Gt030_R1

value: Vastus lateralis

value: M


title: ChIC-seq_TCF1_ILCP_GB8022

status: Public on Dec 31 2020

first: Keji

last: Zhao

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

description: ILCP_TCF1_GB8022.150l-W100-normalized.wig.gz

data_processing:
Library strategy: small cell ChIC-seq
Basecalling by RTA 1.18.66.3, Illumina instrument run time analysis software
Sequencing reads were aligned to mouse genome (mm9) using Bowtie2 with default parameters.
Reads from replicates were merged and redundant reads were removed from further analysis.
For ChIC-seq samples, reads from replicates were merged for peak calling. Peak calling were performed using MACS2 with default parameters.
For scMNase-seq samples, reads with length between 140 and 180 bp were selected as nucleosome reads while reads with length less than 80 bp were selected as subnucleosomal reads.
Genome_build: mm9
Supplementary_files_format_and_content: For ChIC-seq and DNase-seq samples, .wig files contain normalized tag density, which can be uploaded to UCSC genome browser for visulization. For scMNase-seq samples, bed files provide genomic positions on chromosomes for nucleosomes (140-180 bp) and subnucleosomes (<80 bp).

source_name: ILCP (Innate lymphoid cell precursors)

growth_protocol: Samples were isolated by cell sorting from bone marrow single cell suspensions

extract_protocol:
Cells were fixed by adding 1:15 volume of 16%w/v formaldehyde solution (Thermo Fisher Scientific) and incubating at RT for 10 minutes. Reaction was terminated by adding 1:10 volume. 1ml RIPA buffer (10 mM Tris-Cl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.2% sodium dodecyl sulfate, 1% Triton X-100) added to each sorted 500 ALP, EILP, and ILCP cells, and incubated at room temperature for 30 minutes. Cells were rinsed with 500 μl binding buffer (10 mM Tris-Cl, 1 mM EDTA, 150 mM sodium chloride, 0.1% Triton X-100) twice and re-suspended in 50 μl binding buffer. To prepare TCF1 bounded PA-MNase (Ab+PA-MNase), TCF1 and the PA-MNase at a molecular ratio of 1:2 were pre-incubated at 4 °C for 30 minutes in 50 μl binding buffer. TCF1+PA-MNase were add to 50 μl binding buffer re-suspended cells and incubated one hour at 4 °C with rotation. Cells were washed using 200 μl wash buffer (10 mM Tris-Cl, 1 mM EDTA, 150 mM sodium chloride, 0.1%w/v SDS, 0.1%w/v sodium deoxycholate and 1%v/v Triton X-100) three times and pelleted by centrifugation at 600g for 2 minutes. Next, cells were rinsed using 200 μl rinsing buffer (10 mM Tris-Cl and 10 mM sodium chloride, 0.1%v/v Triton X-100). The MNase digestion was initiated by re-suspending the rinsed cells in 40 μl reaction solution buffer (10 mM Tris-Cl, 10 mM sodium chloride, 0.1%v/v Triton X-100, 2 mM CaCl2) and incubated at 37 °C for 3 minutes. The reaction was stopped by adding 80 μl stop buffer (20 mM Tris-Cl (pH 8.0), 10 mMethylenedioxy-bis-(ethylenenitrilo)-tetraacetic acid (EGTA), 20 mM sodium chloride, 0.2%w/v SDS) and 1 μl proteinase K (SigmaAldrich), then incubating at 65 °C for overnight. DNAs were purified by using phenol-chloroform extraction and ethanol precipitation. The purified DNA is ready for library preparation.
DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. The ligation reaction was performed by adding 2 μM Illumina's adapters to each sample and incubated at RT one hour. After adapter ligation DNA was PCR amplified with Illumina primers for 16 cycles and library fragments from 180bp to 300bp were isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Hi-seq3000 following the manufacturer's protocols.

tag: genotype/variation

value: bone marrow

tag: sorting profile

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1+ IL-7Ra+

tag: antibody name, manufacturer and catalog number

value: TCF1/TCF7 (C46C7) Rabbit mAb #2206 from CST


title: MUSCLE_AGE28_M_GROUP20_34_CC_T326_Gt001_R1


title: MCF10A, WTp53 cDNA insert, DMSO, Replicate 2


title: MCF10A, WTp53 cDNA insert, 10uM Nutlin3a, Replicate 1


title: MCF10A, WTp53 cDNA insert, DMSO, Replicate 1


title: SL96948

status: Public on Dec 08 2020

city: TUCSON

first: Roberta

last: Brinton

state: Arizona

address: 1230 N Cherry Ave, PO Box 210242

department: The Center for Innovation in Brain Science

institute: University of Arizona

data_processing:
Raw fastq data were aligned to mouse transcriptome by kallisto v0.43
Kallisto counts were imported through Tximport to get unnormalized gene expressions
Normalized counts were extracted from DESeq2
Genome_build: Rat ensembl release 90
Supplementary_files_format_and_content: csv file with unnormalized gene counts from Tximport

organism: Rattus norvegicus

source_name: Female Rat age at OVX at 9 month, data collected as 10 month

extract_protocol:
Frozen hippocampal tissues were directly homogenized in TRIzol® Reagent (Invitrogen, 15596026) using The Bullet Blender® and silicon beads. Chloroform was used to extract RNA from the homogenate at a volume ratio of 1:5 to that of the TRIzol® Reagent. Ethanol was then used to precipitate nucleic acids from the aqueous phase. RNA was further purified using PureLink™ RNA Mini Kit (Invitrogen™, 12183018A) following manufacturer’s instructions. Purelink™ DNase (Invitrogen™, 12185010) was used to eliminate DNA contamination. Purified RNA was eluded in RNase-free, diH2O. RNA concentration and quality were checked by NanoDrop™ One.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: status

value: Hippocampus

tag: Sex

value: Female


title: CO2_S4_L004_R1_001

value: PCA

value: with cobalt


title: CMFGDSS1

status: Public on Nov 24 2020

city: Beijing

first: shimeng

last: Huang

address: No. 2 Yuanmingyuan West Road, Haidian District

department: College of Animal Science and Technology

country: China

institute: China Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
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 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 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 DESeq2 were assigned as differentially expressed.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® UltraTM NA Library Prep Kit for Illumina® (NEB, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The diet with CMFG (100 mg/kg body weight (BW)/day) were pre-fed to the experimental mice for 3 weeks to investigate its prophylactic effects on alleviating DSS induced colitis (2.5% (w/v) DSS in drinking water ad libitum for 7 days). Mice in the DSS group underwent oral gavage of PBS. Colonic tissues were immediately snap-frozen in liquid nitrogen and homogenized. Total RNA recovered from two separate group include DSS and CMFGDSS.

tag: tissue

value: colon

value: CMFG+DSS

value: female

tag: age

value: 8 weeks-old


title: 29405: ICRH80

status: Public on Oct 01 2020

city: Philadelphia

first: Jonathan

last: Schug

state: Pennsylvania

address: 12-156 Smilow Ctr Trans Research

department: School of Medicine

institute: University of Pennsylvania

data_processing:
Illumina basecalling with bcl2fastq, various versions
Read alignment and expression calculation; using RUM (Grant et al. Bioinformatics  doi: 10.1093/bioinformatics/btr427)
Conversion from reads to trimmed normalized CPMs.  Briefly CPMs for genes between 25 to 75% quantiles were used to compute a normalization factor which was then applied to all CPMs.
Manual and semi-automated cell type calling. Marker genes and differentially expressed genes used to rate cell type and purity which was subsequently curated.
Genome_build: hg19
Supplementary_files_format_and_content: TSV files with raw rea counts or normalized CPMs.  Donor annotation and called cell types included as well.

extract_protocol: Fluidigm C1 single-cell RNA-Seq using 96-well chip

value: pancreas

tag: celltype

value: pancreatic islets

tag: agecategory

value: toddler

tag: healthcategory

value: control

tag: combinedcategory

value: Toddler

value: dropped


title: 29406: ICRH80


title: 29400: ICRH80


title: 29391: ICRH80


title: 29394: ICRH80


title: 29393: ICRH80


title: 29389: ICRH80

value: beta


title: 29390: ICRH80


title: 29388: ICRH80

value: mesenchyme


title: 29392: ICRH80


title: 29381: ICRH80


title: 29382: ICRH80


title: 29377: ICRH80


title: 29380: ICRH80


title: 29379: ICRH80


title: 29384: ICRH80


title: Naive 4

status: Public on Oct 30 2020

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description:
16
processed data file: naive_bampe_peaks.txt

data_processing:
The bcbio-nextgen pipeline (v. 19.03, https://github.com/bcbio/bcbio-nextgen) was used for initial computations of the analysis.
Reads were filtered for quality and aligned to the Mus musculus reference genome (mm10) using BWA (version 0.7.17-r1188).
The three alignment files of each sample were merged using samtools (version 1.9).
Peak calling was performed globally for each cell population using Macs2 (version 2.1.1) with the --broad argument.
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: *_bampe_peaks.txt: Tab-delimited text files containing the output of Macs2 --broad peaks. One file per cell population.

source_name: Naïve P14 cells

extract_protocol:
Cells were lysed in lysis buffer (NP-40)(0.1%) and crude nuclei were tagmented (TDE enzyme and buffer)(Illumina) and DNA was purified using minielute PCR Purification kit (Qiagen) according to Buenrostro et al., Curr Protoc Mol Biol (2015).
Library preparation was done using Illumina’s Unique Dual (UD) Indexes (R#20027213), and 10 PCR cycles according to Buenrostro et al., Curr Protoc Mol Biol (2015). Libraries were cleaned using Agencourt AMPure XP magnetic beads (A63880, Beckman) and sequenced on an Illumina HiSeq 4000, with paired end 150 nucleotides.

treatment_protocol: Splenocytes were enriched for CD8 T-cells using the EasySep Mouse CD8+ T Cell Isolation Kit (StemCell Technologies). Tcf7GFPhi and Tcf7GFP- P14 cells were flow sorted as CD45.2+ CD45.1- from the spleen at d8 or day28 post infection. In addition P14 cells were flow sorted from the spleen of naive mice as CD8+ CD462L+ cells (Naive).

tag: cell type

value: CD8 T cells expressing a P14 TCR

tag: genotype

tag: treatment

value: Naive


title: 29375: ICRH80


title: 29373: ICRH80


title: 29374: ICRH80


title: 29372: ICRH80


title: 29371: ICRH80


title: 29370: ICRH80

value: duct


title: 29365: ICRH80


title: 29364: ICRH80


title: 29367: ICRH80


title: 29386: ICRH80


title: 29383: ICRH80


title: 29361: ICRH80


title: 29360: ICRH80


title: 29359: ICRH80


title: 29362: ICRH80


title: 29385: ICRH80


title: 29357: ICRH80


title: 29354: ICRH80


title: 29351: ICRH80


title: 29353: ICRH80


title: 29350: ICRH80


title: 29358: ICRH80


title: 29348: ICRH80


title: 29349: ICRH80


title: 29345: ICRH80


title: 29347: ICRH80


title: 29340: ICRH80


title: 29338: ICRH80


title: 29339: ICRH80


title: 29341: ICRH80


title: 29337: ICRH80


title: 29343: ICRH80


title: WT3_S3_L004_R1_001

tag: strain

value: PCA

value: without cobalt

tag: growth phase

value: Exponential


title: 29356: ICRH80


title: 29334: ICRH80


title: 29352: ICRH80


title: 29333: ICRH80


title: 29328: ICRH80


title: 29336: ICRH80


title: 29329: ICRH80


title: 29327: ICRH80


title: 29330: ICRH80


title: 29326: ICRH80


title: 29325: ICRH80


title: 29324: ICRH80


title: 29320: ICRH80


title: 29321: ICRH80


title: 29323: ICRH80


title: 29319: ICRH80


title: RNAAtlas034_sRNA [RNA_AT040]

status: Public on Apr 15 2021

city: Badalona

first: LUCIA

last: LORENZI

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute

description:
RNAAtlas_miRNA_counts_filtered.txt
RNAAtlas_miRNA_rpm_filtered.txt

data_processing:
polyA and total RNA demultiplexed reads were mapped to the hg38 reference genome with TopHat v2.1.0 (Bowtie2 v2.2.6, parameters: --no-coverage-search option, --library-type=fr-firststrand). The Ensembl transcriptome (v86) was provided to guide the mapping of reads to known transcripts first. small RNA demultiplexed reads were processed with the FASTX-Toolkit (v0.0.14) to remove adapters, filter reads by quality (quality score of at least 20 in 80% of the sequence) and collapse non-unique reads, and then mapped to the genome with Bowtie (v1.1.2) (parameters: -n = 0, l = 25, --best, and k = 10).
Transcriptomes were assembled in each polyA and total RNA library separately using StringTie (v1.3.3). Default parameters were used and the Ensembl reference annotation (v86) was supplied to guide the assembly. All individual transcriptomes were merged together with the reference Ensembl transcriptome (v86) using StringTie merge applying a cutoff of 1 TPM and minimum transcript length of 200 nucleotides, with all other parameters set to default values. Novel miRNAs were predicted with miRDeep2 (v2.0.0.8), using mapped reads per sample and all human miRNAs in miRBase v22 as input. Novel miRNA predictions with non-zero estimated probability were aggregated across samples, retaining only the prediction with maximum counts from both mature forms in a given sample in cases of predictions with partially overlapping coordinates.
Transcripts assembled from polyA and total RNA libraries were quantified using kallisto quant (flag --rf-stranded and all other parameters set to default values) across all polyA and total RNA-sequencing libraries. Counts and TPMs were collapsed at gene level. After quantification, only protein_coding, antisense and lincRNA genes with no less than 0.1 TPM in at least one samples were retained. CircRNAs where identified from total RNA-sequencing data using two independent workflows, find_circ2 and CIRCexplorer2 using genome build hg19. Only circRNAs identified by both tools, with mean counts between tools higher than 4 in at least one sample and successfully converted to hg38 coordinates with the liftOver tool (UCSC) were retained. Reads mapped to the aggregated newly predicted miRNAs and human miRNAs from miRbase v22 were quantified across all samples. For each miRNA, counts from the canonical mature form and non-canonical mature forms (isoMiRs) were aggregated. Only miRNAs with 10 or more counts in at least one sample were retained.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data files contain abundance measurments across all samples for known and novel mRNA, antisense (asRNA) and lincRNA genes, circular RNAs and miRNAs that passed the filtering criteria. Both raw estimated counts and library-normalized values (reads per million (rpm) for circRNAs and miRNAs) or library- and gene length-normalized values (transcripts per million (TPM) for mRNAs, asRNAs and lincRNAs genes) are provided. For circRNA read counts, only reads spanning the backsplice junction (backspliced reads) are considered. Gene names and/or genome coordinates from hg38 assembly are provided as identifiers.

source_name: HOP-62 Non-Small Cell Lung cancer

extract_protocol:
RNA of individual cell types was obtained from ScienCell Research Laboratories or isolated from cell types collected at Ghent University Hospital. RNA from collected cell types and (cancer) cell lines was isolated using the miRNeasy kit (Qiagen) according to the manufacturer’s instructions. RNA samples from normal human tissues were obtained from Ambion and Biochain.
Small RNA libraries were generated using the TruSeq Small RNA library prep kit (Illumina) according to the manufacturer’s instructions, using 750 ng input RNA. Library size selection was performed using a Pippin Prep device (Sage Science). Total RNA libraries were generated using the TruSeq stranded total-RNA library prep kit with Ribo-Zero Gold (Illumina) according to the manufacturer’s instructions using 1 µg of input RNA. PolyA RNA libraries were generated using the TruSeq Stranded mRNA library prep kit (Illumina) according to the manufacturer’s instructions using 1 µg of input RNA.

tag: sample id

tag: sample id [deprecated]

tag: sample type

value: cancer cell line

tag: organ system

value: Pulmonary System


title: 29376: ICRH80


title: 29316: ICRH80


title: 29317: ICRH80


title: 29344: ICRH80


title: 29312: ICRH80


title: 26132: ICRH76


title: 29314: ICRH80


title: 26129: ICRH76


title: 26127: ICRH76

value: acinar


title: 26126: ICRH76

value: pancreas


title: 26130: ICRH76

value: pancreatic islets

value: pp


title: 26125: ICRH76

value: toddler

value: control


title: 26124: ICRH76

value: Toddler

value: dropped


title: 29315: ICRH80


title: 26120: ICRH76


title: 26123: ICRH76

value: beta


title: 26116: ICRH76


title: 26117: ICRH76


title: 26119: ICRH76


title: 26112: ICRH76


title: 29318: ICRH80


title: 26107: ICRH76


title: 26111: ICRH76


title: 26105: ICRH76


title: 26131: ICRH76

value: delta


title: 26110: ICRH76


title: 26103: ICRH76


title: 26102: ICRH76


title: 26106: ICRH76


title: 26114: ICRH76

value: alpha


title: 26099: ICRH76


title: 26104: ICRH76


title: 26109: ICRH76


title: 26100: ICRH76


title: 26097: ICRH76


title: 26122: ICRH76


title: 26098: ICRH76


title: 26093: ICRH76


title: 26096: ICRH76


title: 26094: ICRH76


title: 26091: ICRH76


title: 26088: ICRH76


title: 26095: ICRH76


title: 26086: ICRH76


title: 26092: ICRH76


title: 26083: HP-15085-01T2D

value: adult


title: 26101: ICRH76


title: 26090: ICRH76


title: 26084: HP-15085-01T2D


title: 26081: HP-15085-01T2D


title: 26087: ICRH76


title: 26080: HP-15085-01T2D


title: 26082: HP-15085-01T2D


title: 26076: HP-15085-01T2D


title: 26074: HP-15085-01T2D


title: 26078: HP-15085-01T2D


title: 26079: HP-15085-01T2D


title: 26075: HP-15085-01T2D


title: 26073: HP-15085-01T2D


title: 26069: HP-15085-01T2D

value: duct


title: 26071: HP-15085-01T2D


title: 26067: HP-15085-01T2D


title: 26065: HP-15085-01T2D


title: 26064: HP-15085-01T2D


title: 26068: HP-15085-01T2D


title: 26066: HP-15085-01T2D


title: 26077: HP-15085-01T2D


title: 26059: HP-15085-01T2D


title: 26062: HP-15085-01T2D


title: 26063: HP-15085-01T2D


title: 26061: HP-15085-01T2D


title: 26058: HP-15085-01T2D


title: 26060: HP-15085-01T2D


title: 26054: HP-15085-01T2D


title: 26055: HP-15085-01T2D


title: 26056: HP-15085-01T2D


title: 26052: HP-15085-01T2D


title: 26057: HP-15085-01T2D


title: 26053: HP-15085-01T2D


title: 26070: HP-15085-01T2D


title: 26048: HP-15085-01T2D


title: 26051: HP-15085-01T2D


title: 26049: HP-15085-01T2D


title: 26047: HP-15085-01T2D


title: 26045: HP-15085-01T2D


title: 26046: HP-15085-01T2D


title: 26044: HP-15085-01T2D


title: 26043: HP-15085-01T2D


title: 26035: HP-15085-01T2D


title: 26039: HP-15085-01T2D


title: 26038: HP-15085-01T2D


title: 26042: HP-15085-01T2D


title: 26037: HP-15085-01T2D


title: 26040: HP-15085-01T2D


title: 26041: HP-15085-01T2D


title: 26032: HP-15085-01T2D


title: 26034: HP-15085-01T2D


title: 26036: HP-15085-01T2D


title: 26031: HP-15085-01T2D


title: 26029: HP-15085-01T2D


title: 26050: HP-15085-01T2D


title: 26028: HP-15085-01T2D


title: 26027: HP-15085-01T2D


title: 26030: HP-15085-01T2D


title: 26025: HP-15085-01T2D


title: 26024: HP-15085-01T2D


title: 26021: HP-15085-01T2D


title: 26019: HP-15085-01T2D


title: 26022: HP-15085-01T2D


title: 26016: HP-15085-01T2D


title: 26033: HP-15085-01T2D


title: 26018: HP-15085-01T2D


title: 26012: HP-15085-01T2D


title: 26014: HP-15085-01T2D


title: 26015: HP-15085-01T2D


title: 26009: HP-15085-01T2D


title: 26008: HP-15085-01T2D


title: 26013: HP-15085-01T2D


title: 26026: HP-15085-01T2D


title: 26011: HP-15085-01T2D


title: 26010: HP-15085-01T2D

value: mesenchyme


title: 25993: HP-15085-01T2D


title: 25982: HP-15085-01T2D


title: 26007: HP-15085-01T2D


title: 26023: HP-15085-01T2D


title: 25992: HP-15085-01T2D


title: 25984: HP-15085-01T2D


title: 25981: HP-15085-01T2D


title: 25988: HP-15085-01T2D


title: 25986: HP-15085-01T2D


title: 25978: HP-15085-01T2D


title: 25991: HP-15085-01T2D


title: 25980: HP-15085-01T2D


title: 25989: HP-15085-01T2D


title: 25994: HP-15085-01T2D


title: 25987: HP-15085-01T2D


title: 25990: HP-15085-01T2D


title: 25976: HP-15085-01T2D


title: 25977: HP-15085-01T2D


title: 25975: HP-15085-01T2D


title: 25973: HP-15085-01T2D


title: 25974: HP-15085-01T2D


title: 25972: HP-15085-01T2D


title: 25971: HP-15085-01T2D


title: 25970: HP-15085-01T2D


title: 25969: HP-15085-01T2D


title: 25964: HP-15085-01T2D


title: 25965: HP-15085-01T2D


title: 25961: HP-15085-01T2D


title: 25966: HP-15085-01T2D


title: 25963: HP-15085-01T2D


title: 25962: HP-15085-01T2D


title: 25960: HP-15085-01T2D


title: 25979: HP-15085-01T2D


title: 25956: HP-15085-01T2D


title: 25950: HP-15085-01T2D


title: 25958: HP-15085-01T2D


title: 25946: HP-15085-01T2D


title: 25957: HP-15085-01T2D


title: 25953: HP-15085-01T2D


title: 25951: HP-15085-01T2D


title: 25952: HP-15085-01T2D


title: 25948: HP-15085-01T2D


title: 25944: HP-15085-01T2D


title: 25942: HP-15085-01T2D


title: 25940: HP-15085-01T2D


title: 25943: HP-15085-01T2D


title: 25967: HP-15085-01T2D


title: 25939: HP-15085-01T2D


title: 25938: HP-15085-01T2D


title: 25959: HP-15085-01T2D


title: 25954: HP-15085-01T2D


title: 25955: HP-15085-01T2D


title: 25937: HP-15085-01T2D


title: 23000: HP-15041


title: 22995: HP-15041


title: 22996: HP-15041


title: 25945: HP-15085-01T2D


title: 22997: HP-15041


title: 23001: HP-15041


title: 22994: HP-15041


title: 22998: HP-15041


title: 22993: HP-15041


title: 22992: HP-15041


title: 22991: HP-15041


title: 22990: HP-15041


title: 22985: HP-15041


title: 22984: HP-15041


title: 22988: HP-15041


title: 22987: HP-15041


title: 22989: HP-15041


title: 22983: HP-15041


title: 22986: HP-15041


title: 22980: HP-15041


title: 22982: HP-15041


title: 22978: HP-15041


title: 23002: HP-15041


title: 22979: HP-15041


title: 22977: HP-15041


title: 22976: HP-15041


title: 22972: HP-15041


title: 22975: HP-15041


title: 22974: HP-15041


title: 22973: HP-15041


title: 22967: HP-15041


title: 22969: HP-15041


title: 22965: HP-15041


title: 22968: HP-15041


title: 22963: HP-15041


title: 22959: HP-15041


title: 22957: HP-15041


title: 22955: HP-15041


title: 22954: HP-15041


title: 22953: HP-15041


title: 22952: HP-15041


title: 22950: HP-15041


title: 22947: HP-15041


title: 22946: HP-15041


title: 22948: HP-15041


title: 22949: HP-15041


title: 22943: HP-15041


title: 22971: HP-15041


title: 22944: HP-15041


title: 22940: HP-15041


title: 22942: HP-15041


title: 22966: HP-15041


title: 22970: HP-15041


title: 22941: HP-15041


title: 22945: HP-15041


title: 22960: HP-15041


title: 22956: HP-15041


title: 22962: HP-15041


title: 22964: HP-15041


title: 22958: HP-15041


title: 22939: HP-15041


title: 22925: HP-15041


title: 22926: HP-15041


title: 22935: HP-15041


title: 22936: HP-15041


title: 22922: HP-15041


title: 22921: HP-15041


title: 22920: HP-15041


title: 22919: HP-15041


title: 22916: HP-15041


title: 22918: HP-15041


title: 22914: HP-15041


title: 22912: HP-15041


title: 22302: ACAP236

value: Adult


title: 22907: HP-15041


title: 22938: HP-15041


title: 22300: ACAP236


title: 22909: HP-15041


title: 22301: ACAP236


title: 22299: ACAP236


title: 22303: ACAP236


title: 22298: ACAP236


title: 22292: ACAP236


title: 22294: ACAP236


title: 22291: ACAP236


title: 22295: ACAP236


title: 22289: ACAP236


title: 22297: ACAP236


title: 22293: ACAP236


title: 22287: ACAP236


title: 22286: ACAP236


title: 22290: ACAP236


title: 22288: ACAP236


title: 22285: ACAP236


title: 22284: ACAP236


title: 22283: ACAP236


title: 22282: ACAP236


title: 22304: ACAP236


title: 22280: ACAP236


title: 22281: ACAP236


title: 22278: ACAP236


title: 22277: ACAP236


title: 22274: ACAP236


title: 22276: ACAP236


title: 22268: ACAP236


title: 22270: ACAP236


title: 22273: ACAP236


title: 22267: ACAP236


title: 22272: ACAP236


title: 22264: ACAP236


title: 22269: ACAP236


title: 22263: ACAP236


title: 22262: ACAP236


title: 22265: ACAP236


title: 22261: ACAP236


title: 22266: ACAP236


title: 22257: ACAP236


title: 22260: ACAP236


title: 22259: ACAP236


title: 22256: ACAP236


title: 22255: ACAP236


title: 22254: ACAP236


title: 22252: ACAP236


title: 22258: ACAP236


title: 22248: ACAP236


title: 22275: ACAP236


title: 22251: ACAP236


title: 22250: ACAP236


title: 22246: ACAP236


title: 22247: ACAP236


title: 22245: ACAP236


title: 22243: ACAP236


title: 22242: ACAP236


title: 22239: ACAP236


title: 22235: ACAP236


title: 22253: ACAP236


title: 22240: ACAP236


title: 22237: ACAP236


title: 22236: ACAP236


title: 22230: ACAP236


title: 22233: ACAP236


title: 22231: ACAP236


title: 22238: ACAP236


title: 22229: ACAP236


title: 22234: ACAP236


title: 22226: ACAP236


title: 22232: ACAP236


title: 22227: ACAP236


title: 22228: ACAP236


title: 22222: ACAP236


title: 22220: ACAP236


title: 22223: ACAP236


title: 22225: ACAP236


title: 22218: ACAP236


title: 22244: ACAP236


title: 22224: ACAP236


title: 22221: ACAP236


title: 22217: ACAP236


title: 22216: ACAP236


title: 22215: ACAP236


title: 22209: ACAP236


title: 22213: ACAP236


title: 22214: ACAP236


title: 13791: AAJF122


title: 13794: AAJF122


title: 22211: ACAP236


title: 13788: AAJF122


title: 13784: AAJF122


title: 22210: ACAP236


title: 13785: AAJF122


title: 13796: AAJF122


title: 13783: AAJF122


title: 13782: AAJF122


title: 22219: ACAP236


title: 13789: AAJF122


title: 13780: AAJF122


title: 16180: ABAF490


title: 16178: ABAF490


title: 16177: ABAF490


title: 13778: AAJF122


title: 16179: ABAF490


title: 13779: AAJF122


title: 22212: ACAP236


title: 16175: ABAF490


title: 16174: ABAF490


title: 16171: ABAF490


title: 16166: ABAF490


title: 16169: ABAF490


title: 16170: ABAF490


title: 16173: ABAF490


title: 16163: ABAF490


title: 16165: ABAF490


title: 13781: AAJF122


title: 16164: ABAF490


title: 16155: ABAF490


title: 16154: ABAF490


title: 16167: ABAF490


title: 16162: ABAF490


title: 16159: ABAF490


title: 16161: ABAF490


title: 16158: ABAF490


title: 16152: ABAF490


title: 16153: ABAF490


title: 16144: ABAF490


title: 16150: ABAF490


title: 16151: ABAF490


title: 16147: ABAF490


title: 16176: ABAF490


title: 16148: ABAF490


title: 16140: ABAF490


title: 16145: ABAF490


title: 16141: ABAF490


title: 16142: ABAF490


title: 16136: ABAF490


title: 16132: ABAF490


title: 16139: ABAF490


title: 16126: ABAF490


title: 16133: ABAF490


title: 16134: ABAF490


title: 16127: ABAF490


title: 16119: ABAF490


title: 16129: ABAF490


title: 16124: ABAF490


title: 16135: ABAF490


title: 16130: ABAF490


title: 16118: ABAF490


title: 16116: ABAF490


title: 16115: ABAF490


title: 16120: ABAF490


title: 16111: ABAF490


title: 16143: ABAF490


title: 16125: ABAF490


title: 16112: ABAF490


title: 16113: ABAF490


title: 16110: ABAF490


title: 16117: ABAF490


title: 16108: ABAF490


title: 16107: ABAF490


title: 16106: ABAF490


title: 16104: ABAF490


title: 16102: ABAF490


title: 16105: ABAF490


title: 16103: ABAF490


title: 16099: ABAF490


title: 16095: ABAF490


title: 16097: ABAF490


title: 16098: ABAF490


title: 16089: ABAF490


title: 16096: ABAF490


title: 16109: ABAF490


title: 16088: ABAF490


title: 12776: AAJF122


title: 12772: AAJF122


title: 12773: AAJF122


title: 16086: ABAF490


title: 16087: ABAF490


title: 12769: AAJF122


title: 16114: ABAF490


title: 12771: AAJF122


title: 12770: AAJF122


title: 12774: AAJF122


title: 16085: ABAF490


title: 16101: ABAF490


title: 12767: AAJF122


title: 12764: AAJF122


title: 12768: AAJF122


title: 12765: AAJF122


title: 12763: AAJF122


title: 22279: ACAP236


title: 12762: AAJF122


title: 12759: AAJF122


title: 12761: AAJF122


title: 12757: AAJF122


title: 12758: AAJF122


title: 12753: AAJF122


title: 12755: AAJF122


title: 12775: AAJF122


title: 12756: AAJF122


title: 12752: AAJF122


title: 12751: AAJF122


title: 12749: AAJF122


title: 12747: AAJF122


title: 12745: AAJF122


title: 12750: AAJF122


title: 12742: AAJF122


title: 12738: AAJF122


title: 12744: AAJF122


title: 12739: AAJF122


title: 12737: AAJF122


title: 12748: AAJF122


title: 12743: AAJF122


title: 12740: AAJF122


title: 12731: AAJF122


title: 12736: AAJF122


title: S. cerevisiae cells - Heat Shock - rep 1

status: Public on Jul 22 2020

city: Chicago

first: Ryan

middle: Patrick

last: Dohn

state: IL

address: 5841 S. Maryland Ave.

department: Department of Medicine

institute: University of Chicago

description: Sample 5

data_processing:
A Snakemake protocol called dropRunner was used to create an expression matrix corresponding to the UMI of each gene in a cell. https://github.com/aselewa/dropseqRunner
STARsolo (STAR 2.7.0a) was used for sequence alignment to the respective yeast genomes
Genome_build: sacCer3_s288c (S. cerevisiae); A21-s02-m09-r10 (C. albicans)
Supplementary_files_format_and_content: Matrix table with raw UMI counts for every gene and every cell, cell barcode file, and gene id file.
Supplementary_files_format_and_content: Tab delimited raw count table with gene and barcode ids (Samples 3 and 4).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene (Samples 14 and 15)

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae cells

growth_protocol: Yeast cells were grown in suspension in rich YEPD media over night and diluted 4 hours prior to experiment to obtain log phase growth.

extract_protocol:
Cells encapsulation into nL droplets using a microfluidic device along with oligo poly-dT beads and zymolyase containing lysis buffer. Cells were then incubated at 37°C for 15-25 minutes for lysis. mRNA was captured by the poly-dT oligo beads.
Reverse tracnription to cDNA was performed using a template switch oligo. Beads then underwent exonuclease treatment and PCR amplification. A Illumina Nextera (cat#FC-131-1096) was used with 500-600 pg cDNA for construction of sequencing libraries.

treatment_protocol: Heat Shock Cells incubated in 42°C thermomixer for 20 minutes prior to microfluidic encapsulation.

value: 42°C Heat Shock


title: D1S7.112216

status: Public on Jun 04 2020

first: Fenna

middle: Marie

last: Krienen

state: MA

address: 77 Ave Louis Pasteur, NRB 260

department: Genetics

institute: Harvard Medical School

description:
single-nucleus gene expression data based on 3' transcript counts
adHumInt.raw.dge.txt.gz

data_processing:
Sequencing Reads were aligned against the relevant genome build using STAR
Aligned Reads within a gene were collapsed to UMI(XM)-Gene Pairs and associated with single-cells through a cell barcode (XC) shared on Read 1
A count matrix - called the digital gene expression (DGE) matrix - was output for GAD1+/GAD2+ interneurons. Columns belong to STAMPs (cells) and transcript counts (rows)
Genome_build: GRCm38.81 (mouse); MusPutFur1.0 (ferret); calJac3 (marmoset); rheMac8 (macaque); hg19 (human)
Supplementary_files_format_and_content: digital gene expression matrix; comma-delimited file with columns = cells and rows = transcript counts

source_name: Human Postmortem Brain

extract_protocol:
dx.doi.org/10.17504/protocols.io.2srged6
Drop-seq (Macosko et al. 2014 Cell)

tag: platform

value: Dropseq

value: Neocortex; Temporal lobe


title: D1S2.120816

value: Neocortex; V1


title: 12732: AAJF122

value: pancreas

value: pancreatic islets


title: 12733: AAJF122


title: 12735: AAJF122


title: 12734: AAJF122

value: acinar


title: 12730: AAJF122

value: control


title: D2S1.031317.pool1

value: Neocortex; PFC


title: RIP IGF2BP1 WT input rep2

status: Public on Aug 11 2020

city: Shanghai

first: Bi

last: Yan

address: Siping Road 1239

institute: Tongji university

description:
PolyA RNA
IGF2BP1 enrichment

data_processing:
All sequenced reads were checked for quality control by using FastQC (v0.11.7) with default parameters.
Sequenced reads was removed adapters and low-quality sequence by using trim_galore (v0.4.2 ) with the default parameters.
The processed RNA-Seq reads were mapped to hg19 genome using STAR (v0.6.0). RefSeq genes were quantified to FPKM using Stringtie.
The processed RIP-Seq reads were mapped to hg19 genome using TopHat (v2.1.1) with default parameters.
FPKM for each sample and log2 fold change were calculated by using cuffdiff (v2.1.1).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *fpkm: Tab-delimited text files include FPKM values.

source_name: pluripotent stem cells

growth_protocol: For cell culture, hiF-T were cultured in DMEM (Gibco) supplemented with 10% FBS (Gibco) and 2mM GlutaMAX (Millipore). Primed ESCs/iPSCs (pESCs/piPSCs) were cultured in hESM containing DMEM/F12 (Gibco) with 20% KnockOut SR (Gibco), 1% nonessential amino acids (Millipore), 2mM GlutaMAX (Millipore), Penicillin Streptomycin(Millipore),8 ng/ml bFGF (Peprotech). Naïve ESCs/iPSCs (nESCs/niPSCs) were cultured in 5iLAF medium containing DMEM/F12: Neurobasal (1:1) (Gibco), 1% N2 supplement (Gibco), 2% B27 supplement (Gibco), 0.5% KnockOut SR (Gibco), 1% nonessential amino acids (Millipore), 2mM GlutaMAX (Millipore), Penicillin Streptomycin(Millipore), 20ng/ml human LIF (Milipore), 8 ng/ml bFGF (Peprotech), 50 μg/ml BSA (Sigma) and the following cytokines and small molecules: PD0325901 (Selleck, 1 μM), SB590885 (Selleck, 0.5 μM), WH-4-023 (Selleck, 1 μM), Y-27632 (Selleck, 10 μM), and Activin A (Peprotech, 20 ng/ml) and passaged by Accutase (Sigma) every 4-5 days as previously reported. All hESCs were routinely cultured at 37 °C in 5% CO2, 5% O2.

extract_protocol:
For mRNA-seq, total RNAs were isolated from cells using TRizol (Invitrogen). To generate RNA sequencing libraries, KAPA Stranded mRNA-Seq Kit (KAPA) was used following the manufacturer’s instructions. For single cell RNAseq, cell clones were mechanically picked and washed with PBS supplemented with 0.5% BSA. Following the Covaris DNA shearing protocol for Smart-seq sequence library generation as previously described. Briefly, cells were lysed, RNAs with a polyadenylated tail were captured, reverse transcripted and preamplified.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: TJ-1# nESCs

tag: passages

tag: genotype/variation

value: Wild type

tag: rip antibody


title: S. cerevisiae cells - 15 minute Lysis - rep 2

description: Sample 3

value: untreated


title: RIP IGF2BP1 WT rep2

description:
PolyA RNA
IGF2BP1 enrichment


title: D1S1.120816

tag: tissue


title: Air 24h Week2 S5

status: Public on Apr 30 2020

city: Southampton

first: Emmanuel

last: Minet

address: Regents Park Road

country: United Kingdom

institute: British American Tobacco

description:
qc: pass
S5

data_processing:
Illumina Casava1.7 software used for basecalling.
Samples were QC analyzed using the arrayQualityMetrics package in Bioconductor50. Outliers were identified based on 4 parameters, maplot, boxplot, heatmap and manual inspection. The RNAseq data was preprocessed and aligned to the human genome (GRCh38) using STAR aligner and the number of mapped read-pairs per gene were quantified based on the GENCODE v25 annotation. The resulting count data for the samples was normalized using TMM (Trimmed Mean of M-value) and transformed with VOOM to log2-counts per million with associated precision weights.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file

source_name: MucilAir Bronchial donor MD046001

growth_protocol: Upon delivery MucilAir were given at least one week recovery before exposure experiments. The culture media was changed every two to three days.

extract_protocol:
The cells were lysed with QIAzol and the RNA was extracted using the QIAGEN miRNeasy Mini Kit (Hilden, Germany) and a QIACube workstation. All RNA samples had a RIN greater or equal to 8.0.
RNA libraries were prepared for sequencing using standard Illumina protocols
Sequencing was performed on an Illumina NextSeq 500 platform (Illumina, Sand Diego, CA, USA) at a depth of 40 million pair reads with 150 bp paired-end.

treatment_protocol: MucilAir™ cells were placed in exposure chambers (Adamson et al., 2011) with basal media and exposed to either vapour from the IS1(TT) prototype or to smoke from 1R6F cigarettes. Aerosols from both products were generated using a RM20S smoking machine (Borgwaldt KC, Germany). An air control was run alongside which received sterile air at an identical puffing regime to the product exposure.

tag: individual

value: Bronchial non smoker

tag: Stage

value: primary

tag: age

value: 64 yo

tag: gender

value: male

value: Air 24h post-exposure

value: in vitro primary airway cells


title: bi002.PFCdlsl01

description:
single-nucleus gene expression data based on 3' transcript counts
marm.ctx.int.DS.raw.dge.txt.gz

organism: Callithrix jacchus

source_name: Marmoset Brain

value: Dropseq


title: D1S2.122316.RB


title: D2PL.113017

value: Neocortex; Parietal Cortex


title: marm023_PFCdl_merged_corrected

description:
single-nucleus gene expression data based on 3' transcript counts
mouse.nuc.cortical_interneurons.raw.dge.txt.gz

source_name: Adult Marmoset Brain


title: marm023_Hippo_merged

description:
single-nucleus gene expression data based on 3' transcript counts
marm.hippo.int.raw.dge.txt.gz

value: Hippocampus


title: 12741: AAJF122

value: pancreas

tag: celltype

tag: agecategory

value: adult

tag: healthcategory

tag: combinedcategory

value: Adult

value: dropped


title: Anti-Ang2 + tumor-focused radiation

status: Public on May 27 2020

city: Helsinki

first: Pauliina

last: Kallio

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description: Melanoma tumor treated with Ang2 blocking antibodies + tumor-focused radiation

data_processing:
The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10
We used the Seurat R package 3.1.1 for quality control, filtering, and analysis of the data
Cells were filtered based on unique feature counts and the percentage of mitochondrial genes
Cells with more than 10-15% of mitochondrial genes were filtered out
The expression matrix was further filtered by removing genes with expression in less than three cells and cells with less than 200 expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered data was combined for CCA and further analysis, and saved as A_combined.Robj

source_name: Mouse melanoma tumor

extract_protocol:
In order to obtain single cell solution, incubated in Hanks' balanced salt solution (HBSS, 14175-053, Gibco) supplemented with 1 mg/mL collagenase type I (LS004196, Worthington), 1 mg/mL collagenase H (11074032001, Roche), 4 mg/mL dispase II (04942078001, Sigma) and 1000 U/mL benzonase (sc-202391, ChemCruz) for 30 min at +37°C with gentle shaking, followed by 15 min incubation with Trypsin-EDTA (25200056, Thermo Fisher Scientific) and red blood cell lysis buffer (ACK Lysing Buffer, A1049201, Gibco) for 10 minutes in RT. Cells were transferred into 0.04% BSA-HBSS for analysis.
Single cells were analyzed using the 10x Chromium Single-Cell 3′RNA-sequencing system (10x Genomics, Pleasanton, CA, USA) with the Reagent Kit v3 as instructed by the manufacturer. Briefly, the cells were first loaded into Chromium Single-Cell Chip v3 (10x Genomics, Pleasanton, CA, USA), followed by generation of Gel beads in EMulsion (GEM) aiming at 10 000 cell captures per sample. This was followed by cDNA purification, amplification (12 cycles), and library construction (sample index PCR 14 cycles) as instructed by the manufacturer.
The sample libraries were sequenced on an Illumina NovaSeq 6000 sequencer using read lengths of 26bp (Read 1), 8bp (i7 Index), 0 bp (i5 Index) and 91bp (Read 2). Chromium single-cell 3’ RNA-sequencing barcodes and read data were demultiplexed and converted to FASTQ files, and aligned reads and gene-cell matrices were generated using Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA, USA). Reads were aligned to mouse reference genome mm10.

treatment_protocol: Mice were treated with indicated treatments.

tag: strain

value: Mouse melanoma tumor

value: 20 weeks

tag: treatment


title: D2S2.032317.pool1

value: Neocortex; V1


title: CMs TAB

status: Public on Sep 15 2020

city: Utrecht

first: Cornelis

middle: J.

last: Boogerd

address: Uppsalalaan 8

department: Developmental Biology and Stem Cell Research

country: Netherlands

institute: Hubrecht Institute

description: TAB CM-bulk-1_AHFL7NBGX5_S2

data_processing:
Paired-end reads from Illumina sequencing were demultiplexed: The first 8 nucleotides of read 1 will match the barcodes (BC) listed in the table above. Read 2 was used for mapping to the genome, using bwa-aln.
Differential gene expression between groups was calculated using the DESeq2 package
Genome_build:GRCm38 (mm10)
Supplementary_files_format_and_content: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore. Column names indicate the sample number

source_name: cardiomyocytes from 12 ventricule samples from mice of sham, hypertrophic or failing hearts

extract_protocol:
Ventricle samples were obtained directly after sacrifice, minced and enzymatically digested. Cardiomyocytes were FACS sorted and collected into 1,5 ml eppendorf tubes containing Trizol and flash frozen on dry ice. Total RNA was extracted using standard TriZol RNA extraction.
RNA libraries were prepared according to CEL-Seq, the protocol described in Hashimshony, T., Wagner, F., Sher, N. & Yanai, I. CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification. Cell Rep. 2, 666?673 (2012)

treatment_protocol: Mouse hearts were subject to Transaortic Binding (TAB) or Sham surgey and harvested after 1week or after 8 weeks.

value: heart

tag: cell type

value: cardiomyocytes


title: S. cerevisiae cells - 20 minute Lysis - rep 2

description: Sample 4

value: untreated


title: D2S1.031317.pool2

value: Neocortex; PFC


title: SMC_17D1

status: Public on Apr 06 2020

city: Cleveland

first: Xiaoxia

last: Li

state: OH

address: 9500 Euclid Ave.

department: Inflammation & Immunity

institute: Cleveland Clinic

data_processing:
RPKM
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: hASMC

growth_protocol: Human primary ASMCs were cultured in DMEM/F-12 supplemented with 10% FCS, 100 U/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol: Total RNA extracted by NucleoSpin® RNA Plus (Takara Bio, Cat#740984) from human primary ASMCs

treatment_protocol: Human primary ASMCs were untreated and treated with IL-17A (100 ng/ml), DEX (1 µg/ml) or both for 4 hours.

tag: sample type

value: Primary cell


title: RNAseq from sorted GFP-neg subpopulation of ESC with Zscan4c promoter reporter driving expression of GFP

status: Public on Mar 22 2020

city: Stanford

first: Tomek

last: Swigut

state: CA

address: 265 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

description:
RNAseq_Con_NoGFP
Poly-A enriched mRNA

data_processing:
Basecalls performed using CASAVA.
Reads were aligned with hisat2 2.1.0 using default settings.
TPMs were obtained with StringTie 1.3.5 using GRCm38.84 gene models.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *csv: Comma-separated text files include TPM (transcripts per million).

source_name: E14 mouse ESC with stably integrated Zscan4c promoter reporter driving expression of GFP

growth_protocol: E14Tg2a male mouse ESC were maintained as previously described (Buecker et al., 2014) on 7.5μg/ml poly-l-ornithine (Sigma) and 5μg/ml laminine (Life Technologies) coated tissue culture dishes, in a serum-free N2B27-based DMEM/F12 medium supplemented with 5mg/ml BSA Albumax II, sodium pyruvate, L-glutamine, N2 Neuroplex, B27 without retinoic acid, non-essential amino acids, Beta-mercaptoethanol, penicillin/streptomycin, 0.8μM MEK inhibitor (PD0325901, Selleck Chemicals) and 3.3μM GSK3β inhibitor (CHIR99021, Selleck Chemicals).

extract_protocol:
Total RNA was extracted with TRIZOL and mRNA was purified using Oligo-dT Dynabeads mRNA purification kit (Invitrogen). mRNA was fragmented using 10X Fragmentation reagent (Thermo Fisher Scientific) and subjected to first strand synthesis with random hexamers and Superscript II (Invitrogen), and second strand synthesis with RNaseH (Invitrogen) and E. coli DNA polymerase I (NEB).
Sequencing libraries were prepared starting from ~30ng polyA enriched cDNA with NEBNext Multiplex Oligos for Illumina kit.

treatment_protocol: GFP positive 2C-like cells and GFP negative pluripotent cells were collected by FACS from each reporter line.

tag: cell line

value: Embryonic stem cells (ESC)

value: Stably integrated Zscan4c promoter reporter driving expression of GFP

tag: cell population

value: GFP negative (pluripotent cells)


title: PLAC_H3K4me3_NPC_d4_dcas9CTCF_vcan_top_rep1

status: Public on Mar 06 2020

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
fastq: Illumina's HiSeq Control Software
PLAC-seq reads were aligned as single end reads using BWA with default parameters. Uniquely mapping reads were manually paired using in an in house pipeline. PCR duplicate reads were removed using Picard MarkDuplicates.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files (pgl) were generated useing MAPS (Juric and Yu et al., 2019) and FitHiChIP (Bhattacharyya et al., 2019).

source_name: neural precursor cells

growth_protocol: Cells were grown in DMEM supplemented with 100 U/mL penicillin, 100 mg/mL streptomycin, 15% KnockOut Serum Replacement (ThermoFisher, 10828028), Glutamax (Gibco, 35050), 0.1 mM non-essential amino acid, 0.1mM beta-mercaptoethanol, and 500 U/ml LIF at 37°C and 5% CO2

extract_protocol:
PLAC-seq experiments were performed according to previous publication (Fang and Yu et al., 2014, Juric and Yu et al., 2019).
PLAC-seq library sequencing procedures were carried out as previously described according to Illumina HiSeq4000 protocols (Illumina, San Diego, CA).
PLAC-seq

treatment_protocol: To deplete CTCF, 1 ul 500 mM auxin per 1 ml medium was added, and medium with auxin was changed every 24 hours. Cells were harvested 24 or 48 hours after stating auxin treatment. Neural cell differentiation treatment was performed with or without auxin treatment, and the neural precursor cells were harvested on day 4 or 2 days after washing out auxin from the day 4 sample.

value: F123 mouse neural precursor cell


title: Human colon cancer cell line HCT116 was transfected with a control non-targeting siRNA, biological rep 2

status: Public on Feb 18 2020

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

institute: Central South University

description: Expression data for human colon cancer cell line HCT116 transfected with a control non-targeting siRNA to cells for 36 hours.

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference human genome using Tophat.
FPKM value of each gene was calculated using Hisat2, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq functions estimate Size Factors and nbinomTest. P value < 0.05 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Genome_build: human genome GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each samples

growth_protocol: The human colon cancer cell lines HCT116 were cultured in both DMEM medium supplemented with 10% fetal bovine serum, 100 units/m of penicillin and streptomycin. Cultures were incubated at 37°C in a humidified incubator at 5% CO2.

extract_protocol:
mirVana miRNA ISOlation Kit (Ambion#1561) extraction of RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Solexa protocols.

treatment_protocol: Cells were grown in DMEM medium (with 10% serum), and was transfected with a control non-targeting siRNA to cells or transfected with siRNA targeting LINC00152 for 36 hours.

value: colon cancer cell line

tag: agent

value: control siRNA(100nM)


title: scRNA_seq_B+A0

status: Public on Mar 30 2020

city: Qingdao

first: Yong

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

description: The group information is prefixed with TBA0 in the column of processed data file

data_processing:
We used CellRanger count pipeline 2.2.0 to analyze the sequencing data and generated the single cell information. To generate same number of total cells for downstream analysis, we used augments ‘--force-cells=5000 \’.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files stores normalized and log-transformed single cell expression value

extract_protocol:
Testis were isolated and washed with PBS solution supplemented with 0.04% bovine serum albumin. Then, the testis were digested with 1X TrypLE™ Express (Cat# 12605010) for 3 min to obtain single cell pellets. The single-cell Gel-Bead in Emulsions (GEMs) were then generated with Chromium 10x Genomics single-cell system by using single-cell 3’ Library and Gel Bead Kit V2 (10x Genomics, Cat#120237). Captured cells were then lysed and the released RNA were barcoded through reverse transcription in individual GEMs.
Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V2 (10x Genomics, 120237) following the manufacture’s introduction.

value: ICR

value: Testis

value: B+A 0 (busulfan alone)


title: D2S2.032317.pool2

city: Boston

tag: platform

value: Dropseq


title: High-Mg-Rep1

status: Public on Jan 29 2020

city: Calgary

first: Shawn

last: Lewenza

state: AB

address: 3330 Hospital Drive NW

department: Microbiology, Immunology & Infectious Diseases

country: Canada

institute: University of Calgary

data_processing:
SOLiD sequencing paired end 50x 35 bases
Manual removal of rRNA sequences
MarkDuplicate analysis to remove duplicate sequences
Reads were mapped to PAO1 genome using RNA-seq analysis tool (CLCbio)
DESeq performed to identify differentially regulated genes by eDNA

organism: Pseudomonas aeruginosa

source_name: Gram-negative bacteria

growth_protocol: Bacterial cultures were grown to mid-log phase in defined growth media with or without extracellular DNA (0.75%)

extract_protocol:
Total RNA extracted with the RiboPure (Ambion) bacterial kit. rRNA was depleted  with the Ribominus kit (Life Technologies)
cDNA library made using the RNA-SEQ SOLiD kit.

tag: condition

value: High Mg


title: Midbrain organoids carrying the LRRK2-G2019S mutation differentiated for 70 days

status: Public on May 01 2020

city: Maastricht

first: Silvia

last: Bolognin

state: -- None selected --

address: Universiteitssingel 40,

institute: Maastricht University

description:
org2Mu70_S1_DGE
scRNA-Seq
mRNA

data_processing:
Bcl2fastq ver 2.0 was used for the base calling.
Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Drop-seq implementation (Macosko et al., 2015), the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCh38 using STAR genome aligner - with default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw counts.

source_name: IPSC

growth_protocol: As described in Smits et al., NPJ Parkinsons Dis doi: 10.1038/s41531-019-0078-4

extract_protocol:
Single cell RNA seq using Drop-seq - 3' bead based enrichment technique, using SMART synthesis (Macosko et al., 2015 doi: 10.1016/j.cell.2015.05.002).
Libraries were prepared according to Drop-seq methods (Macosko et al., 2015 doi: 10.1016/j.cell.2015.05.002). After cDNA tagmentation, PCR amplification was performed using Illumina primers (N701, N702, A501). The purified cDNA fragments of ~600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.

treatment_protocol: No treatment was performed.

tag: tissue

value: Midbrain organoids

tag: genotype/variation

tag: differentiation time

value: 70 days

value: Astrocytes


title: High-Mg-Rep3


title: 0point75percent-DNA-rep3

value: extracellular DNA (0.75%)


title: 0point75percent-DNA-rep2


title: High-Mg-Rep2


title: R24_mushroombody

status: Public on Feb 04 2020

city: Princeton

first: Ian

middle: Michael

last: Traniello

state: NJ

address: Princeton University

department: Lewis-Sigler Insitute for Genomic Biology

institute: Princeton University

data_processing:
Align to honey bee genome build HAv3.1 and deformed wing virus reference genome with Cell Ranger 3.0 with default settings (expected cells = 3,000)
All clustering steps were performed with Seurat 3.0. We performed data normalization with default settings and combined the WB and MB datasets using the “merge” function, which generated 11 cell clusters in a tSNE plot. To identify the molecular profile of each cell population, we used the “FindAllMarkers” function in Seurat which performs a Wilcoxon Rank Sum Test to test for differentially expressed genes per tSNE cluster. We found no evidence of DWV contamination in either of our samples.
Genome_build: HAv3.1
Supplementary_files_format_and_content: 10x genomics output file for Seurat 3.0: contains barcodes.txv, genes.txv, matrix.mtx; Cell Ranger 3.0 output

organism: Apis mellifera

source_name: brain

growth_protocol: We collected two seven-day-old bees from one source colony headed by a queen instrumentally inseminated with semen from a single drone (to increase genetic similarity between the samples).

extract_protocol:
Brains were fresh-dissected in ice-cold Dulbecco’s phosphate-buffered saline (DPBS), and the MBs were dissected in one sample. Both samples were then cut into small pieces and incubated for 2 min in an Eppendorf tube containing 90 μl of DPBS and 10 μl of 0.25% Trypsin with 2.21 mM EDTA. Next, 90 μl of the solution was removed and replaced with DPBS, and brain tissue was gently triturated with a pipette tip to dissociated cells. Fixation and rehydration were carried out in accordance with 10x protocols, with a 15 min methanol fixation time on ice and storage at -20°C for less than one week before rehydration and sequencing.
scRNA-Seq libraries were constructed with the Chromium Single Cell 3’ Library and Gel Bead Kit v2 and were sequenced on a 2 x 150nt lane in a HiSeq 4000 (Illumina, San Diego, CA).

treatment_protocol: Bees were at rest, dissected at room temperature after one hour of habituation.

tag: age

value: 7 days

value: mushroom bodies

tag: colony


title: 0point75percent-DNA-rep1


title: GR MUT CTR rep3

status: Public on Dec 31 2019

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

country: Germany

institute: TU München

description:
GAR1236
C437G_DexEffect_MEFs_unfiltered_DESeq.txt

data_processing:
The reads were mapped to the mouse genome mm10 (Ensembl build 38.91) and reads per gene counted using STAR version 2.4.2a with the following settings: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 -- alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 100000 --quantMode GeneCounts.
Quality control was performed by fastQC and unsupervised sample clustering by PCA to identify outliers.
Counts were filtered for their expression strength by selecting only genes with counts above 200 as expressed. Gene count normalization and differential expression analysis was performed with DESeq2. Thresholds for genes being differential expressed were abs(log2FoldChange)>0.58 (approx. 1.5x fold-change) and an adjusted p-value < 0.05.
For gene annotation Ensembl Transcript Ids were mapped to mgi_symbol using the Bioconductor package biomaRt version 2.32.1 and information from Ensembl (build 38.91).
Genome_build: mm10
Supplementary_files_format_and_content: „_STARReadsPerGene.out“ files contain the raw read counts per transcript as determined by STAR aligner version 2.4.2.   column1 = gene ID; column2 = read counts if strandness is ignored (the sum of columns 3 and 4); column3 = read counts covering all exons of the specified gene mammping the 1st strand of the DNA (e.g: sense mRNA); column4 = read counts covering all exons of the specified gene mammping the 2nd strand of the DNA (e.g. anti-sense mRNA); „_DESeq.txt“ files contain the unfiltered results from the DESeq2 analysis for differential expression on Dex-treated vs. Vehicle-treated wild-type and GR Zn/Zn mutant MEFs or on Dex+LPS-treated vs. LPS-treated wild-type and GR Zn/Zn mutant MEFs , respectively (as indicated in the file name).

source_name: vehicle, EtOH

growth_protocol: MEFs generation: C57BL/6 male mouse embryos from either wild-type or GR Zn/Zn were harvested at 13.5 days after vaginal plug formation. Internal organs (mainly heart and liver) and head were removed and embryos were minced and digested with Trypsin 10-15min at 37°C. MEFs were cultured for 7 days in high glucose DMEM incl. 10% FBS and 1% Pen/Strep.

extract_protocol:
RNA was extracted with RNeasy minikit (Qiagen). All samples were DNAse-treated using DNaseI from the Qiagen kit.  The quality of the RNA was verified by Agilent 2100 Bioanalyzer with RNA 6000Nano Reagents (Agilent Technologies).
Library preparation and rRNA depletion was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to manufacture's manual. 500 ng RNA were used as input for each sample.

treatment_protocol: 16h EtOH (vehicle), 16h 1uM Dex in EtOH (Dex), 16h 1uM Dex in EtOH + 6h 100ng/ul LPS (Dex+LPS) or 16h EtOH + 6h 100 ng/ul LPS (LPS) as indicated in sample description

value: mouse embryonic fibroblasts (MEFs)

tag: genotype

value: GR Zn / Zn

tag: Sex

value: male


title: FG_1

last: Wang

address: 106 Nanjing Road

institute: Yellow Sea Fisheries Research Institute, Chinese Academy Fishery Science

data_processing:
After the adapters were removed from raw reads, those reads with low quality including reads with more than 10% unknown nucleotides and more than 50% low quality bases (Q-value < 20) were removed from the data set. The data were subsequently assembled with Trinity. Taken these assembled transcripts as the reference sequence, clean reads were mapping by RSEM software.
And the longest transcript in each gene-Unigene, was used for the representative of each gene. The Unigene was annotated by ways of seven database including Nr, Nt, Pfam, KOG/COG, Swiss-prot, KEGG and GO. The CDS was further predicted by Nr, Swissprot database or Estscan (3.0.3) software.
Supplementary_files_format_and_content: the sequences of the unigene

organism: Platichthys stellatus

source_name: the gonad of female Platichthys stellatus

extract_protocol:
Three samples for each tissue were used for the following experiment. A total of 24 samples named MB1-3, ML1-3, MG1-3, MM1-3, FB1-3, FL1-3, FG1-3, and FM1-3 were acquired and their total RNAs were extracted via Trizol reagent (Invitrogen, USA) and measured with the Agilent 2100 RNA 6000 Nano kit (Agilent, USA) for quality control. Twenty-four cDNA libraries were constructed using 3 μg RNA (RIN > 7.0) from each sample via the conventional protocol, and the subsequent sequencing was conducted with an Illumina HiseqTM 4000 by Novogene Co. Ltd (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gonad

value: three-year-old

tag: gender

value: female


title: R24_whole brain

value: whole brain


title: A3685

status: Public on Apr 10 2020

city: East Lansing

first: Karen

last: Liby

address: 1355 Bogue Street

department: Pharmacology&Toxicology

institute: Michigan State University

data_processing:
After removal of adaptors and low quality reads, reads were mapped to the mm10 mouse reference genome using TopHat2
Reads that mapped to genes were counted and normalized to gene length, then reported in FPKM (Fragments Per Kilo bases per Million reads)
Routine identification of differentially expressed genes was performed using DESeq2
Supplementary_files_format_and_content: FPKM

source_name: tumor

extract_protocol:
Tumors were dissected, flash frozen in liquid nitrogen. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Valencia, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tumors from Brca1Co/Co;MMTV-Cre;p53+/- mice treated with saline, free Talazoparib (i.v.), or NanoTLZ for five doses (0.33mg/kg, three times a week) were harvested. Three samples were collected for each group.

value: mammary gland tumor

value: saline


title: M-1_2

status: Public on Oct 29 2019

city: harbin

first: xu

last: yangx

address: mucai 59

institute: neau

data_processing:
Smart-Seq2 method was used to amplify the single cell sample. The reaction system for the first cDNA strand synthesis comprised the reverse transcription enzyme, buffer, TSO primers and oligo-dT primers with common sequence. For the second strand synthesis, added PCR amplification reagent and ISPCR primer with common sequence to the first strand products. The sample cDNA was fragmented into 300bp by Bioruptor®Sonication System (Diagenode Inc.), and then performed terminal repair, addition of A, and ligation of sequencing adapters, and amplified. The PCR amplification product with 350-450bp was extracted. Then, the concentration was measured by Qubit 2.0 Flurometer (Life Technologies, CA, USA). The integrity of the amplified products was detected by Agilent 2100 High Sensitivity DNA Assay Kit (Agilent Technologies, CA, USA). The libraries were sequenced by an Illumina HiSeq X Ten platform.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Sus scrofa

source_name: in vivo embryo

growth_protocol: in vivo embryos

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: morula

value: blastomere


title: 8cell-2_2


title: 8cell-3_8


title: WT_7days _long day_R1

status: Public on Oct 31 2019

city: Taipei

first: Wan-Sheng

last: Lo

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

data_processing:
The prepared library was pooled for single-end sequencing using Illumina HiSeq 2500 at YOURGENE BIOSCIENCE Co. (New Taipei City, Taiwan) with 100bp single-ended sequence read.
Reads from RNA-seq were mapped to TAIR10 genome using BLAT (http://genome.ucsc.edu/cgi-bin/hgBlat).
RPKM computation and comparison (Z score) were made using RackJ (http://rackj.sourceforge.net/).
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Whole seedling

growth_protocol: Seeds of each genotypes were grown in 1/2MS without sucrose media containing plates for 7 days in long day condition (16h light/8h dark)

extract_protocol:
Total RNA from 7day-old light grown (16h light/8h dark) and 4d dark grown Col-0 and jmj17-1 seedling was isolated using RNeasy Plant Mini Kit (QIAGEN), Cat. No. 74904
Libraries for RNA-seq were prepared using Illumina TruSeq RNA library Prep Kit (RS-122-2001, Illumina) according to the manufacturer’s protocol.

treatment_protocol: Long day(16h light/8h dark)

tag: ecotype

value: Col-0 background

value: Wild type (WT)

value: Whole seedling


title: p-T11R1

status: Public on Dec 24 2019

city: Thuwal

first: Magdalena

last: Julkowska

state: Makkah

address: KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

description:
replicate 1
batch1

data_processing:
bcl2fastq v1.8.4 for raw data processing
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR genome by Tophat, and quantified in samtools htseq-count
Reads were mapped to TAIR10 genome by TopHat (v2.0.14), with Bowtie (2.1.0.0)
Transcripts were quantified using Samtools ht-seq-count
Counts per million (cpm) were calculated and normalized by the size of the library.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Expression values of cpm (log2 transformed) for each sample.

source_name: seedling leaf tissue

growth_protocol: Plates each containing about 80 Arabidopsis Col-0 seedlings were grown inside growth chamber (Percival) with 22°C under 16h / 8h of light / dark cycle (~100 μmol m−2 s−1) with 60% relative humidity. The acclimation treatment was applied by subjecting plates with Arabidopsis seedlings into the growth chamber (Percival) with the temperature gradually rising from 22C to 45C over the course of 6 hours (starting at the beginning of the photoperiod) in the light and keep at 45C for 90 mins. Subsequently, the plates were transferred back to a growth chamber with standard (22C) temperature. For the heat shock application, the growth chamber (Percival) was pre-heated to 45C with lighting (~100 μmol m−2 s−1) and 60% relative humidity. Each plate containing 80 acclimated or non-acclimated seedlings was transferred from the control growth condition (22C) chamber to a heated growth chamber (45C) for 90 mins from 1:30 pm to 3:00 pm (7.5 - 9h after the beginning of the photoperiod).

extract_protocol:
RNA extraction was performed for each sample using RNeasy Plant Mini Kit (Qiagen)
2μg of RNA for each sample was used to construct mRNA library following the protocol of Illumina’s TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: We collected samples of 11 time-points. 11 plates each containing about 80 germinated Arabidopsis seedlings were divided into the acclimated and non-acclimated group. At each sampling time-point from the experimental design (Figure 2.2 A), all leaf tissue from the designated plate was harvested and divided into two separate Eppendorf tubes, snap-frozen in liquid nitrogen and stored at -80°C. At day 12 after seed germination, T1 samples were taken right after the start of the photoperiod and before acclimation treatment starts. Plates from acclimated group were exposed to the heat acclimation treatment and samples were taken after 3 h (T2), 6 h (T3) and 7.5 h (T4), while other plates were returned to normal growth conditions and samples were collected two days (T5) and four days (T6) after at 1:30 pm. At day 16, the remaining acclimated and all the non-acclimated plants were exposed to heat shock treatment (45°C for 90 min), and samples were taken before the heat treatment (T7 for acclimated seedlings, T9 for non-acclimated seedlings), at the end of the heat shock (T8 for acclimated seedlings, T10 for non-acclimated seedlings) and two days after the application of heat stress at 1:30pm (T9 for the acclimated seedlings, T11 for non-acclimated seedlings).

tag: time point

tag: cultivar

value: leaf

tag: sampling temperature


title: p-T4R1

description:
replicate 1
batch1


title: 0hour post infection P14 Trm rep1

status: Public on Apr 02 2020

first: Susan

last: Kaech

address: 10010 N Torrey Pines Rd

institute: Salk Institute

data_processing:
STAR Aligner
HTSeq
DESeq2
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Lung Trm cells

extract_protocol: cells were sorted based on gating strategy mentioned,directly into Trizol. RNA was isolated in combination with Qiagen RNeasy Plus Kit

tag: hours post infection

value: Lung

tag: cell type


title: p-T10R1

description:
replicate 1
batch1


title: B1.C.3

status: Public on Aug 07 2019

city: Palo Alto

first: Michael

last: Snyder

address: 3165 Porter Dr

data_processing:
Adapter trimming with Trim Galore version 0.4.1 with default setting in paired end mode
Alignment with bsmap version 2.89
Picard-tools version 1.92 MarkDuplicates to remove duplicates
Moabs version 1.3.0 used to calculate per CpG methylation values
mean CpG methylation signal over target capture regions was computed (methylated = 1, unmethylated = 0).
Genome_build: hg19
Supplementary_files_format_and_content: Bed file has CpG methyl calls (read counts) for every CpG in target capture regions with calculated ratio and breakdown for minus and plus strands, and local context

source_name: hTert-HME1 cell line

growth_protocol: Mammary Epithelial Growth Medium (Lonza) at 37degC with 5% CO2

extract_protocol:
AllPrep (Qiagen)
Agilent SureSelectXT Methyl-seq kit

treatment_protocol: siRNA transfection with RNAiMAX (Invitrogen)

tag: cell line

tag: sirna

tag: media

value: +EGF (complete)

tag: passages

tag: biological replicate

value: A


title: C2.C.3


title: B1.E.10A

value: -EGF


title: C1.C.10A


title: B2.C.3


title: SC3

status: Public on Jul 04 2019

city: Guangzhou

first: Xiang

state: Guangdong

address: 11 fengxin road, guangzhou science city

institute: Guangdong Laboratory Animals Monitoring Institute

description: SC.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Original data were filtered to remove reads with joints, indeterminate base information and low quality, followed by sequencing error rate check and GC content distribution check to obtain clean reads used in subsequent analysis.
Clean  reads were than mapped to mm10 genome with HISAT2 compares software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Heart

extract_protocol:
Total RNAs from C57BL/6J and Slit2-Tg hearts after IR or non-IR were isolated using TRIzol® Reagent(Thermo Fisher Scientific, USA). Each group contains three independent samples. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: heart


title: p-T5R1

description:
replicate 1
batch1


title: Secondary Spermatocyte

status: Public on Jun 30 2019

city: Beaverton

first: Donald

middle: F.

last: Conrad

state: OR

address: 505 NW 185th Ave

department: Division of Genetics; Oregon National Primate Research Center

institute: Oregon Health & Science University

description: FACS sorted with Hoescht (Lima et al. JoVE, 2017)

data_processing:
Base calls were performed with bcl2fastq.
Sequenced reads were tagged with molecular(UMI) and cell barcodes. Then reads with low quality scores were removed and the adaptor sequences were trimmed.
Reads were aligned to Mus_musculus.GRCm38.76 genome with STAR (v. 2.5.3a) with default configuration.
STAR aligned reads were merged with tagged SAM file to recover cell/molecular barcode information. Then the reads were annotated with exon and other annotation tags.
Digital gene expression matrix was extracted by counting the number of unique UMIs per gene within individual cell from exon-tagged bam files.
Additional step of bead synthesis error correction was performe by collapsing UMI counts when the first 11 bases of cell barcodes were the identical.
Genome_build: mm10
Supplementary_files_format_and_content: Digital Gene Expression(DGE) matrix of gene counts for each cell. Columns are cells and rows are genes.

source_name: WT_Secondary Spermatocyte

extract_protocol:
Whole testes were dissociated using two different methods, enzymatic and mechanical. Single-cell suspensions were either FACS sorted for enriching different germ cell subpopulations or directly paired to Drop-seq protocol to generate single-cell RNA sequencing libriaries.
Library preparations were perforemd with Drop-seq protocol (Macosko et al. Cell 2015)

tag: strain background

value: male

tag: genotype/variation

value: Wild-type

tag: age

value: post natal 2 months 21 days

tag: tissue/cell type

value: Secondary Spermatocyte

tag: dissociation method

value: Mechanical


title: Primary Spermatocyte

source_name: WT_Primary Spermatocyte

tag: gender

value: Primary Spermatocyte


title: Spermatid

value: Spermatid


title: Wild-type_3

value: post natal 4 months

value: Testis


title: Mlh3_1

value: post natal 3 months 22 days


title: Hormad1_2

value: post natal 4 months 3 days


title: Hormad1_1


title: Mlh3_6

value: post natal 2 months 23 days


title: Mlh3_3

value: post natal 8 months 30 days


title: Mlh3_2


title: Wild-type_11

value: post natal 7 months 21 days


title: Mlh3_4


title: Wild-type_10

value: post natal 9 months 14 days


title: Wild-type_9

value: post natal 3 months 2 days


title: Wild-type_6

value: post natal 3 months 27 days


title: Wild-type_5

value: male

value: post natal 5 months 7 days


title: Wild-type_2

value: Wild-type

value: post natal 4 months 2 days

value: Enzymatic


title: Wild-type_4

value: post natal 5 months 5 days

value: Mechanical


title: NEO16 [Patient_16_T3]

status: Public on Jul 02 2019

city: Carrington Crescent

first: Andrew

middle: H

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

description:
Patient_16_T3
processed data file: Processed_data.txt

data_processing:
All pre-processing was accomplished in fastQC for base calling, alignment, and quality control of the FASTQ files.
Expression analysis of the resultant relative expression matrix was carried out in R using limma, DEseq and edgeR packages.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Processed_data.txt: Tab-delimited text file includes raw read counts.

source_name: Breast Tissue

extract_protocol:
RNA extraction was performed via Ribo0-RNAseq performed with Life Sciences Ion AmpliSeq™ Transcriptome Human Gene Expression Kit.
Libraries were constructed according to the Ion AmpliSeq Library Kit 2.0 instructions.

tag: patient identifier

value: Breast

tag: grade

tag: histology

value: Ductal NST

value: Negative

tag: t

tag: n

tag: m

value: MX

tag: biopsy time


title: Cul4a_1

value: post natal 1 month 18 days

value: Testis


title: Spermatogonia

description: Five litter mates' testes were pooled to generated single-cell suspension and FACS sorted for GFP+ spermatogonial cells.

value: post natal 7 days

value: Spermatogonia


title: Wild-type_1

value: post natal 3 months 21 days


title: Cul4a_2

value: post natal 1 month 21 days


title: CNP_2

value: male

value: CNP eGFP BAC TRAP

value: post natal 2 months 16 days


title: CNP_1

value: post natal 2 months 14 days


title: P311_15

status: Public on Jun 18 2019

city: Freiburg

first: Nadim

last: Aizarani

address: Stübeweg 51

department: Independent group leaders

institute: MPI-IE

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The left read contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for mapping to the reference transcriptome.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.
Supplementary_files_format_and_content: Normalhumanliverdata.RData: A count table or expression matrix for all the normal human liver cells. Use readRDS function to load data in R.

source_name: Liver tissue

growth_protocol: Cells were isolated from human liver specimens obtained from surgical resections

extract_protocol:
Liver specimens were perfused and treated with collagenase followed by Percoll purifcation/clean up steps
The amplified RNA (aRNA) was reversely transcribed in order to generate libraries for sequencing. 1 µl of custom random hexamer RT primers (GCCTTGGCACCCGAGAATTCCANNNNNN) and 0.5 µl of 10mM dNTP were added to the aRNA. The samples were incubated at 65˚C for 5 min and cooled to 4˚C afterwards. Thereafter 4 µl of First Strand Reaction Mix containing SuperScript™ II Reverse Transcriptase and Buffer (Invitrogen, 18064014) and RnaseOUT™ (Invitrogen, 10777019) was added and samples were first incubated at 25˚C for 10 min followed by incubation at 42˚C for 1 hour. To every sample 2 µl of one uniquely indexed RPI index primer and 2 µl of RP1 primer (TruSeq Library Prep, sequences available from Illumina), 25 µl of Phusion® High-Fidelity PCR Master Mix with HF Buffer (NEB, M0531) and 11 µl of nuclease-free water were added. PCR was performed using 98˚C for 30 s as initial step, followed by 11 cycles of amplification (98˚C for 10 s, 60˚C for 30 s, 72˚C for 30 s) and a final extension at 72˚C for 10 min. To each sample 1 volume (50 µl) of Agencourt® AMPure XP beads (Beckman Coulter, A63881) was added and the samples were incubated at 25˚C for 15 min. The samples were incubated for 5 min on a magnetic stand (96 well format), the supernatant was removed and the beads were washed twice by adding 180 µl of 80 % ethanol and by incubating for 40 s. Ethanol was removed and beads were dried for 10 min at room temperature. DNA was eluted with 25 µl nuclease-free water and the purification was repeated with an adjusted volume of magnetic beads (25 µl). After the final step the samples were eluted in 10 µl nuclease-free water. DNA concentration and fragment size were determined using the Qubit® dsDNA HS Assay Kit (Invitrogen, Q32854) and the Agilent High Sensitivity DNA Kit for Bioanalyzer (Agilent Technologies, 5067-4627), respectively. Libraries were sequenced on an Illumina HiSeq 2500 System in high output run mode at a depth of 150000 to 200000 reads per cell.
CEL-Seq2 (Hasimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)

treatment_protocol: no treatment

value: normal liver resection specimen

tag: cause of resections

value: Colorectal cancer metastasis


title: Mlh3_5

value: post natal 2 months 22 days

value: Mechanical


title: P304_16


title: WSB WT Male Rep4

status: Public on May 22 2019

city: Farmington

first: Asli

last: Uyar

state: CT

address: 10 Discovery Dr

department: Computational Sciences

institute: The Jackson Laboratory

data_processing:
Sequenced reads were quality trimmed and filtered using Trimmomatic tool and reads passing the quality filtering were mapped to the mouse mm10 reference genome using ‘STAR’ aligner. Custom genomes were generated for CAST, PWK and WSB strains by incorporating REL-1505 variants into the reference genome.
HTSeq Python package was used to calculate raw read counts per transcript.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw read counts values for each Sample.

source_name: Whole brain

extract_protocol:
Left brain hemispheres (n=93) were snap frozen at harvest. RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher).
RNA libraries were prepared for sequencing using the KAPA mRNA HyperPrep Kit (KAPA Biosystems), according to the manufacturer’s instructions.

tag: strain/background

value: WSB

value: WT

tag: Sex

value: Male

value: 8 months

value: Left brain hemisphere