title: HepG2_Btz_50nM_S5_rep1

value: bortezomib 50nM for 10h


title: 5GB1_FM40_T20m_TR2_QC

status: Public on May 24 2021

type: SRA

city: Seattle

first: Erin

last: Wilson

state: WA

address: 185 E Stevens Way NE

department: The Paul G. Allen School of Computer Science & Engineering

country: USA

institute: University of Washington

description: Fermentor run 40, Cu transition, T20m (after Cu)

library_source: transcriptomic

data_processing:
BWA version 0.7.12-r1044 was used to align the reads to the 5GB1C genome using the BWA-MEM algorithm and default parameters
Read alignments were converted into sorted BAM files using SAMTools version 1.2-232-g87cdc4a
The htseq-count tool from the “HTSeq” framework version 0.6.1p1 was used to attribute the reads to ORFs using the “intersection-nonempty” mode, providing estimates of raw read counts
Raw counts were then normalized by sample and transcript length to reflect transcripts per million (TPM) for each genome feature.
The locus tags refer to the locus_tag field in the *M. buryatense*  genome file, available here: https://www.ncbi.nlm.nih.gov/nuccore/1678288454?report=genbank
Genome_build: NCBI: NZ_CP035467.1
Supplementary_files_format_and_content: TPM

molecule: total RNA

organism: Methylotuvimicrobium buryatense

source_name: bioreactor culture

extract_protocol:
RNA was extracted as previously described (Chu and Lidstrom, 2016).
RNA sequencing and library construction was performed by GENEWIZ (South Plainfield, NJ, USA) using Illumina HiSeq

tag: strain

value: lowCu


title: Hippocampal Astrocytes Fed Biological Sample 4

type: RNA

city: Baltimore

first: Michael

middle: J.

last: Wolfgang

state: MD

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.na32.mm9.probeset_extended.mps

label: biotin

organism: Mus musculus

source_name: Hippocampal Astrocytes Fed

label_protocol: The NuGEN Pico WTA v2 kit was used as described in the manufacturer's manual.

growth_protocol: Mouse hippocampus dissected from mice expressing a tagged ribosome specifically in astrocytes.

extract_protocol: Actively translating mRNAs were determined using translating ribosomal affinity purification based on established protocols.   Kulicke, R., Fenster, R. J., Greengard, P., Heintz, N. & Heiman, M. Cell type–specific mRNA purification by translating ribosome affinity purification (TRAP). Nature Protocols 9, 1282–1291 (2014).

treatment_protocol: Mice  were subjected to one of three dietary conditions: four weeks of normal chow diet, four weeks of ketogenic diet (high-fat, low-carbohydrate)43, or an 18-hour fast

tag: dietary challenge

value: fed

tag: tissue

value: hippocampus


title: Hippocampal Astrocytes Fed Biological Sample 2


title: B03_W4

city: Hong Kong

first: Ming

last: Yue

address: 21 Sassoon Road, Pokfulam

country: China

institute: The University of Hong Kong

description: Single-cell RNA transcriptome analysis

data_processing:
Customized Macaca mulatta reference package was created by the mkref function in Cell Ranger software (version 3.1.0) using the Macaca mulatta reference genome from Ensembl (Mmul_8.0.1, release 97)
Unique molecular identifier (UMI) counts generated by aligning raw FASTQ files to the customized reference tracscriptome using the count function of Cell Ranger (version 3.1.0)
Genome_build: Mmul 8.0.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

organism: Macaca mulatta

source_name: Outbred Chinese origin and female

extract_protocol:
The Chromium Single Cell V(D)J Reagent Kit from 10X genomics were used according to the manufacturer’s protocol.  In brief, purified CD8+ T cells were subjected to single cell encapsulation by 10X Chromium Controller, followed by barcoding, reverse transcription for cDNA synthesis, clean up and cDNA amplification and target enrichment from cDNA for subsequent library construction.
Library construction followed the protocol of 10X Chromium Single Cell V(D)J Reagent Kit

tag: gender

value: female

tag: cell type

value: Purfied peripherial CD8+ T cells

tag: treatment

value: 4 weeks post immunization of pRhPD-1-p27 DNA vaccine


title: HepG2_Btz_50nM_Nelf_20uM_S28_rep4

city: Tartu

first: Tiit

last: Örd

address: Riia 23b/2

department: Institute of Genomics

country: Estonia

institute: University of Tartu

data_processing:
Base-calling was perform during the sequencing run by RTA version 2.11.3 running under NextSeq Control Software version 4.0.1.41.
RNA-Seq reads were trimmed to remove Illumina adapter, poly(A) and low-quality bases using cutadapt (version 2.8).
The trimmed reads were processed using the nf-core RNA-Seq pipeline (version 1.4.2) with trimming disabled and with STAR selected to align the reads to the hg19 human genome. Read counts in transcripts were determined according to Ensembl GRCh37/hg19 release 87 gene annotations for protein coding, lincRNA and antisense gene biotypes.
Genome_build: hg19
Supplementary_files_format_and_content: raw count matrix (genes with zero overall counts have been removed)

organism: Homo sapiens

growth_protocol: HepG2 cells (ATCC) were maintained in Dulbecco’s Modified Eagle Medium (DMEM; 4.5 g/l D-glucose) supplemented with 10% fetal bovine serum and 1× penicillin-streptomycin at 37 °C in a 5% CO2 atmosphere (all medium components from Gibco).

extract_protocol:
Total RNA from four biological replicates per condition was extracted using the RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol for cultured cells, including on-column DNase I digestion. RNA yield and purity were measured on a NanoDrop 1000 Spectrophotometer (Thermo Scientific) to verify an A260/A280 nm ratio >1.8 and A260/A230 nm ratio ~2.
Libraries were prepared from 250 ng of total RNA per sample using the Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit for Illumina (FWD) according to the manufacturer's instructions. Libraries were quantified with the Qubit dsDNA HS assay kit (Life Technologies) and combined in equimolar ratio. The pool of libraries was sequenced at the Estonian Genome Center Core Facility using the Illumina NextSeq500 platform with 80 bp single-end reads.

treatment_protocol: To perform chemical compound treatments, the growth medium was aspirated from the cells and replaced with fresh complete growth medium (described above) supplemented with the indicated chemical compound(s) or with vehicle as control. The chemical concentrations were as follows: bortezomib 50 nM, ISRIB 50 nM and nelfinavir 20 uM. Treatment time was 10 h.

tag: cell line

value: liver cancer cell line

value: bortezomib 50nM and nelfinavir 20uM for 10h


title: A316/95_CTRL

city: Singapore

first: Michelle

middle: GK

last: Tan

address: 20 College Road

department: Clinical Translational Research

country: Singapore

institute: Singapore General Hospital

description: CTRL

hyb_protocol: Samples were hybridized to Affymetrix GeneChip HTA2.0 arrays at 45°C for 16 hours with rotation at 60rpm, then washed and stained in a Fluidics Station using the FS450_0001 fluidics protocol.

scan_protocol: Gene chips were scanned by an Affymetrix 3000 7G scanner.

data_processing:
CEL files were generated from Affymetrix GeneChip Command Console (AGCC) Software. Data was analyzed with Partek Genomics Suite 7 (http://www.partek.com/partekgs) using the exon array workflow with default conditions (Robust Multi-Chip analysis (RMA) background corrections, quantile normalization, log 2 base transformation and summarization by Median Polish).
probe_group_file: HTA-2_0.r3.pgf
meta-probeset_file: HTA-2_0.r1.Partek.mps

source_name: prefrontal cortex BA9 of control patient

label_protocol: 100ng total RNA samples was processed and labeled using GeneChip WT PLUS Reagent Kit according to manufacturer's instructions

extract_protocol: Total RNA was isolated using Trizol reagents (Invitrogen) according to the manufacturer's instructions. Microarray service was conducted by Origen Labs Inc (Singapore).

tag: age

tag: Sex

value: Male

tag: pmi


title: HLE-Maung-input

city: Portland

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

library_source: genomic

data_processing:
DATA PROCESSING STEPS TO GENERATE THE *summary.txt FILES:
Raw reads were trimmed using Trimmomatic [11] to remove adaptor sequences, as well as low quality and short reads (2:30:10:26:true SLIDINGWINDOW:4:20 TRAILING:20 LEADING:20 MINLEN:50).
We used seqtk to randomly select 2.5 million trimmed read pairs from each ChIP sample. The random subsets of reads were converted to fasta format using manual bash scripts.
Repeats in the pre-processed ChIP-seq libraries were annotated using RepeatMasker version 4.0.3. The gibbon (Hylobates sp.) 20150807 Repbase library was used for annotation.
We used a custom script to group repeats in each library based on repeat class and family in each of the read pair files, and to calculate the %count and %length (of total repeats) they constituted
Genome_build: Not applicable
Supplementary_files_format_and_content: Text files summarizing the %count and %length of each repeat, repeat family and repeat class among randomly subsampled reads from each ChIP library.
DATA PROCESSING STEPS TO GENERATE THE *contigs.fa FILES:
We used the K-mer Analysis Toolkit (KAT) to determine the optimal k-mer size and predicted genome coverage for each library.
We used RepARK for de novo assembly of reads from each ChIP-seq library.
Genome_build: not applicable
Supplementary_files_format_and_content: Fasta files representing assembled contigs obtained from each ChIP-seq library.

molecule: genomic DNA

organism: Hoolock leuconedys

source_name: Eastern hoolock gibbon (Hoolock leuconedys)

extract_protocol:
We performed ChIP-seq using the Magnify ChIP kit (Thermo Fisher Scientific) according to manufacturer’s instructions with minor modifications. Briefly, per ChIP assay we fixed 3x105 EBV transformed gibbon LCLs with 1% formaldehyde at room temperature for 10 min. Fixation was quenched with glycine, and cells were washed three times with cold 1XPBS. Cells were lysed for 10 min on ice using the Magnify Lysis buffer, in presence of Proteinase inhibitor cocktail. Lysed cells were then sonicated using the Bioruptor Pico sonicator (Diagenode) for 12 cycles (30 sec on/off) and spun down to remove cell debris. A 1% aliquot was taken from the chromatin as input, and the rest was incubated with the appropriate antibody [CENP-A (ab13939): 2ug, CENP-B (ab25734): 4ug, CENP-C (ab50974): 2ug] at 4℃, with rotation overnight. The next day we incubated samples with Dynabead protein A/G rotating at 4℃ for 2 hours, followed by bead washes, reverse-crosslink and DNA purification according to Magnify ChIP kit protocol.
All sequencing libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) for 1-5ng of starting material and without size selection. The Qubit dsDNA High Sensitivity kit (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100 were used to QC the libraries.

value: EBV-tranformed lymphocyte cell line

tag: chip antibody


title: Hippocampal Astrocytes Fed Biological Sample 1


title: HepG2_Btz_50nM_S6_rep2


title: 5GB1_FM40_T40m_TR1_QC

description: Fermentor run 40, Cu transition, T40m (after Cu)


title: HepG2_Btz_50nM_Nelf_20uM_S27_rep3


title: HLE-Maung-CENPA


title: A136/10_CTRL

description: CTRL

value: Female


title: B03_W0

description: Single-cell RNA transcriptome analysis

value: Before vaccination of pRhPD-1-p27 DNA vaccine


title: HepG2_Btz_50nM_Nelf_20uM_S26_rep2


title: B02_W12

description: Single-cell RNA transcriptome analysis

value: 12 weeks post immunization of pRhPD-1-p27 DNA vaccine


title: HepG2_Btz_50nM_S8_rep4


title: A063/10_CTRL

description: CTRL


title: 5GB1_FM40_T20m_TR2


title: 5GB1_FM40_T180m_TR1_QC

description: Fermentor run 40, Cu transition, T180m (after Cu)

value: medCu


title: HLE-Drew-CENPA


title: 5GB1_FM40_T180m_TR1


title: HepG2_Btz_50nM_S7_rep3


title: HepG2_Btz_50nM_Nelf_20uM_S25_rep1


title: HLE-ChanThar-CENPA


title: 5GB1_FM40_T150m_TR1_remake

description: Fermentor run 40, Cu transition, T150m (after Cu)


title: B02_W4

description: Single-cell RNA transcriptome analysis


title: A401/97_CTRL

description: CTRL


title: A134/00_CTRL

description: CTRL


title: HepG2_Btz_50nM_ISRIB_50nM_S24_rep4

value: bortezomib 50nM and ISRIB 50nM for 10h


title: B02_W0

description: Single-cell RNA transcriptome analysis


title: A033/96_CTRL

description: CTRL


title: HLE-Betty-input

data_processing:
DATA PROCESSING STEPS TO GENERATE THE *summary.txt FILES:
Raw reads were trimmed using Trimmomatic [11] to remove adaptor sequences, as well as low quality and short reads (2:30:10:26:true SLIDINGWINDOW:4:20 TRAILING:20 LEADING:20 MINLEN:50).
We used seqtk to randomly select 2.5 million trimmed read pairs from each ChIP sample. The random subsets of reads were converted to fasta format using manual bash scripts.
Repeats in the pre-processed ChIP-seq libraries were annotated using RepeatMasker version 4.0.3. The gibbon (Hylobates sp.) 20150807 Repbase library was used for annotation.
We used a custom script to group repeats in each library based on repeat class and family in each of the read pair files, and to calculate the %count and %length (of total repeats) they constituted
Genome_build: Not applicable
Supplementary_files_format_and_content: Text files summarizing the %count and %length of each repeat, repeat family and repeat class among randomly subsampled reads from each ChIP library.
DATA PROCESSING STEPS TO GENERATE THE *contigs.fa FILES:
We used the K-mer Analysis Toolkit (KAT) to determine the optimal k-mer size and predicted genome coverage for each library.
We used RepARK for de novo assembly of reads from each ChIP-seq library.
Genome_build: not applicable
Supplementary_files_format_and_content: Fasta files representing assembled contigs obtained from each ChIP-seq library.
DATA PROCESSING STEPS TO GENERATE THE CENP_BroadPeaks_sortedbyFE.xlsx FILE:
Raw reads were trimmed using Trimmomatic to remove adaptor sequences, as well as low quality and short reads (2:30:10:26:true SLIDINGWINDOW:4:20 TRAILING:20 LEADING:20 MINLEN:50).
Trimmed reads were aligned to the gibbon genome (Nleu3.0) using Bowtie2, with "very sensitive" paired-end settings.
Significant (q<0.01) broad peaks were identified using MACS2,while allowing maximum fof two read duplcates. Peaks were sorted based on fold enrichment.
Genome_build: Nleu3.0
Supplementary_files_format_and_content.xlsx spreadsheet containing the coordinates of all broad peaks across CENP libraries. Peaks are sorted from high fold-enrichment (FE) to low FE.


title: 5GB1_FM40_T150m_TR1_QC


title: B01_W12

description: Single-cell RNA transcriptome analysis


title: HepG2_Btz_50nM_ISRIB_50nM_S23_rep3


title: 5GB1_FM40_T10m_TR3_QC

description: Fermentor run 40, Cu transition, T10m (after Cu)


title: B01_W4

description: Single-cell RNA transcriptome analysis


title: HLE-Betty-CENPB


title: 5GB1_FM40_T10m_TR3


title: HLE-Betty-CENPC


title: HepG2_Btz_50nM_ISRIB_50nM_S21_rep1


title: B01_W0

description: Single-cell RNA transcriptome analysis


title: Hippocampal Astrocytes Fed Biological Sample 3


title: HLE-Betty-CENPA


title: A239/95_CTRL

description: CTRL


title: 5GB1_FM40_T0_TR1_QC

description: Fermentor run 40, Cu transition, T0 (before Cu)

value: NoCu


title: HLE-Betty-RNA

data_processing:
DATA PROCESSING STEPS TO GENERATE THE '*_summary.txt' FILES:
Raw reads were trimmed using Trimmomatic to remove adaptor sequences, as well as low quality and short reads (2:30:10:26:true SLIDINGWINDOW:4:20 TRAILING:20 LEADING:20 MINLEN:50).
Trimmed RNA-seq libraries were annotated using RepeatMasker version 4.0.3. The gibbon (Hylobates sp.) 20150807 Repbase library was used for annotation.
We used a custom script to group repeats in each library based on repeat class and family, and to calculate the %count and %length (of total repeats) they constituted.
Supplementary_files_format_and_content: Text files (*_summary.txt) summarizing the %count and %length of each repeat, repeat family and repeat class of the annotated RNA-seq reads.

DATA PROCESSING STEPS TO GENERATE THE '*_mapped.fasta.out_summary.txt' FILES:
The Burrow's Wheeler Aligner bwa-mem algorithm was used to map RNA-seq reads to de novo assembled contigs generated from CENP-A, CENP-B, and CENP-C ChIP-sequencing data.
Reads that successfully aligned to the de novo assemblies were extracted using SAMtools and converted to FASTA format using Bedtools and Seqtk.
Repeats in the subsequent processed FASTA files were annotated using RepeatMasker version 4.0.3. The gibbon (Hylobates sp.) 20150807 Repbase library was used for annotation.
We used a custom script to group repeats in each library based on repeat class and family, and to calculate the %count and %length (of total repeats) they constituted.
Supplementary_files_format_and_content: Text files (*_mapped.fasta.out_summary.txt) summarizing the %count and %length of each repeat, repeat family and repeat class of the annotated RNA-seq reads.

DATA PROCESSING STEPS TO GENERATE THE '*-RM-summary.txt' FILES:
RNA-seq library reads were mapped to the Nleu3.0 genome using the Burrows-Wheeler Aligner bwa-mem algorithm.
Unaligned reads, assumed to contain centromere-derived reads, were separated using SAMtools and converted to FASTA format using Bedtools and Seqtk.
Next, we used the Burrow's Wheeler Aligner bwa-mem algorithm to map the unaligned reads to de novo assembled contigs generated from CENP-A, CENP-B, and CENP-C ChIP-sequencing data.
Reads that successfully aligned to the de novo assemblies, assumed to be enriched for centromere-derived reads, were extracted using SAMtools and converted to FASTA format using Bedtools and Seqtk.
Repeats in the subsequent processed FASTA files were annotated using RepeatMasker version 4.0.3. The gibbon (Hylobates sp.) 20150807 Repbase library was used for annotation.
We used a custom script to group repeats in each library based on repeat class and family, and to calculate the %count and %length (of total repeats) they constituted.
Genome_build: Nleu3.0
Supplementary_files_format_and_content: Text files (*-RM-summary.txt) summarizing the %count and %length of each repeat, repeat family and repeat class of the annotated RNA-seq reads.

extract_protocol:
Total RNA was extracted using the mirVana™ Total RNA Isolation kit (ThermoFisher Scientific) following the manufacturer's instructions on each EBV-transformed lymphocyte cell line.
High-quality RNA was subjected to llumina Tru-seq stranded total RNA library preparation, including Ribo-depletion. The Qubit dsDNA High Sensitivity kit (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100 were used to QC the libraries.

value: EBV-transformed lymphocyte cell line


title: 5GB1_FM34_T8_TR1_QC

description: Fermentor run 34, Cu transition, T8hr (after Cu) 6.20% FAME

value: highCu


title: SNU16_dCas9_KRAB_H3K27ac_HiChIP_rep2

city: Stanford

first: Howard

middle: Y

last: Chang

state: CA

address: CCSR 2130, 269 Campus Drive

department: Center for Personal Dynamic Regulomes

institute: Stanford University

description:
H3K27ac HiChIP library
SNU16_dCas9_KRAB_H3K27ac_HiChIP.allValidPairs.hic

data_processing:
Library strategy: HiChIP
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: hg19
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.

source_name: SNU16-dCas9-KRAB cells

growth_protocol: Cells were maintained in DMEM/F12  (Gibco, #11320-082) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
HiChIP libraries were generated as described previously (PMID: 27643841).
Nextera

value: H3K27ac (Abcam ab4729)


title: 5GB1_FM34_T7_TR3_QC

description: Fermentor run 34, Cu transition, T7hr (after Cu) 6.45% FAME


title: exercised rat 24 months, biological rep 3

city: Mexico City

first: Gibrán

last: Pedraza-Vázquez

address: Av. San Rafael Atlixco #186, Colonia Vicentina, Iztapalapa

department: Ciencias de la Salud

country: Mexico

institute: Universidad Autónoma Metropolitana

description: miRNA expression from the gastrocnemius of a 24 month old exercised rat

hyb_protocol: Samples were hybridized for 16 hr at 45C on GeneChip® miRNA 4.0 Array

scan_protocol: Microarrays were scanned with GeneChip™ Scanner 3000

data_processing: Data were analyzed with Transcriptome Analysis Console 4.0.2.15

organism: Rattus norvegicus

source_name: gastrocnemius muscle, exercised, 24 months

label_protocol: Affymetrix FlashTag Biotin HSR RNA Labeling Kit was used according to the standard Affymetrix protocol

growth_protocol: Rats were housed five-per-cage in polycarbonate cages, in a room under a 12-h light/12-h dark cycle, with free access to food (standard commercial rat diet, Harlan 2018S, USA) and water.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 4 month-old rats were caged and randomly selected for sedentary conditions (no exercise) and exercised (25 cm/s, 30 min, 5 days/week on a Panlab rat treadmill). Gastrocnemius muscles were obtained at 8, 12, 18 and 24 months old for RNA extraction and hybridization on Affymetrix microarrays.

value: skeletal muscle

tag: muscle

value: gastrocnemius

tag: age (months)


title: 5GB1_FM40_T0m_TR2

description: Fermentor run 40, Cu transition, T0m before Cu)


title: SNU16_dCas9_KRAB_H3K27ac_HiChIP_rep1


title: exercised rat 24 months, biological rep 2

value: female


title: A349/08_AD

description: AD

source_name: prefrontal cortex BA9 of AD patient


title: TR14_HiC_rep3

description: Hi-C library

data_processing:
FASTQ files were processed using the Juicer pipeline v1.5.6, CPU version (PMID: 27467249), which was set up with BWA v0.7.17 (PMID: 20080505) to map short reads to reference genome hg19, from which haplotype sequences were removed and to which the sequence of Epstein-Barr virus (NC_007605.1) was added.
A threshold of MAPQ≥30 was applied for the generation of Hi-C maps with Juicer tools v1.7.5 (PMID: 27467249).
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.

source_name: TR-14 cells

growth_protocol: Cells were maintained in RPMI-1640 medium (Thermo Fisher Scientific, Inc., Waltham, MA) with 1% Penicillin/Streptomycin, and 10% FCS

extract_protocol:
Hi-C libraries were generated as described previously (PMID: 33199677).
NEBnext Ultra DNA Library Kit (NEB)


title: A371/08_AD

description: AD


title: 5GB1_FM34_T5_TR2_QC

description: Fermentor run 34, Cu transition, T5hr (after Cu) 5.75% FAME


title: exercised rat 18 months, biological rep 3

description: miRNA expression from the gastrocnemius of a 18 month old exercised rat

source_name: gastrocnemius muscle, exercised, 18 months


title: TR14_HiC_rep2

description: Hi-C library


title: 5GB1_FM34_T6_TR3_QC

description: Fermentor run 34, Cu transition, T6hr (after Cu) 5.71% FAME


title: 5GB1_FM34_T4_TR3_QC

description: Fermentor run 34, Cu transition, T4hr (after Cu) 5.12% FAME


title: TR14_HiC_rep1

description: Hi-C library


title: SNU16_ATAC_rep2

description: ATAC-seq library

data_processing:
Reads were trimmed for adaptor sequence, then aligned to the hg19 genome using Bowtie2.
Duplicate fragments were removed using Picard.
Peaks were called using Macs2 with a no-shift model.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data file is a .bed file containing all peaks merged across replicates with read counts for each replicate.

source_name: SNU16 cells

extract_protocol:
ATAC-seq libraries were prepared as described previously using the Omni-ATAC protocol (PMID: 28846090).
Nextera


title: 5GB1_FM34_T3_TR3_QC

description: Fermentor run 34, Cu transition, T3hr (after Cu) 5.49% FAME


title: exercised rat 18 months, biological rep 2


title: A267/09_AD

description: AD


title: 5GB1_FM34_T0_TR1_QC

description: Fermentor run 34, Cu transition, T0 (before Cu) 5.15% FAME


title: A076/09_AD

description: AD


title: A037/09_AD

description: AD


title: 5GB1_FM23_TR3_QC

description: Fermentor run 23, methanol

value: MeOH


title: cDNA-Rep3

first: Stephen

middle: B

last: Montgomery

state: Califonia

address: 300 Pasteur Drive, Edwards Building R248A

description: barcode sequencing of cDNA

data_processing:
Library strategy: MPRA
Barcodes were clustered using Bartender v1.1 and assigned to their parent designed oligo if perfectly matching. Bracode counts were summed across all barcodes within each oligo to generate the oligo count matrix.
Genome_build: hg19
Supplementary_files_format_and_content: Oligo count text files contain columns for the oligo specification as well as the raw oligo count in each sample. The designed library includes columns for the oligo name and the sequences used for library synthesis.

growth_protocol: Transient transfection by Neon electoporation followed by 24 hours of recovery in RPMI + 15% FBS

extract_protocol:
Standard trizol extraction followed by GFP mRNA isolation and reverse transcription
PCR amplification of oligo or barcode sequences from plasmid or cDNA samples followed by multiplexing for Illumina sequencing


title: exercised rat 12 months, biological rep 3

description: miRNA expression from the gastrocnemius of a 12 month old exercised rat

source_name: gastrocnemius muscle, exercised, 12 months


title: A092/09_AD

description: AD


title: cDNA-Rep2

description: barcode sequencing of cDNA


title: exercised rat 12 months, biological rep 2


title: N_GT_67: Normal_exosome_3rd_Trimester_38.9_weeks

city: Brisbane

first: Dominic

last: Guanzon

state: Queensland

address: Building 71/918 RBWH Herston

department: UQCCR

country: Australia

institute: University of Queensland

data_processing:
Remove index and adaptor sequences using TagCleaner (version 0.16)
Trim reads to 28 nucleotides using FASTX-Toolkit (version 0.0.14)
miRNAs were identified using the miRDeep2 program (version 2.0.0.7), using the deafult parameters with the exception of allowing for 1 mismatch and discarding read less than 16 nucleotides in length.
Raw miRNA counts were normalised and statistically anlaysed using the DESeq2 package (version 1.18.1) in R (version 3.2.2)
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited file containing raw miRNA counts

source_name: Plasma

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit and TRIzol LS Reagent for exosomes following the manufacturer's instructions.
Libraries were constructed using the TruSeq® SmallRNA Library Prep Kit, following the manufacturer’s instructions. A total of 100 to 300 ng of exosomal RNA was used as input for library construction.

value: Exosomes

tag: diagnosis

value: normal

tag: time point


title: N_GT_68: Normal_exosome_3rd_Trimester_38.6_weeks


title: exercised rat 8 months, biological rep 3

description: miRNA expression from the gastrocnemius of a 8 month old exercised rat

source_name: gastrocnemius muscle, exercised, 8 months


title: Mat Plasma GDM Control: Normal_exosome_3rd_Trimester_35.0_weeks


title: exercised rat 12 months, biological rep 1


title: SNU16_ATAC_rep1

description: ATAC-seq library


title: A108/09_AD

description: AD


title: cDNA-Rep1

description: barcode sequencing of cDNA


title: 5GB1_FM22_TR1_QC

description: Fermentor run 22, O2 limited, QC


title: NP 3rd miRNA: Normal_exosome_3rd_Trimester_33.0_weeks


title: A007/10_AD

description: AD


title: exercised rat 8 months, biological rep 2


title: A038/11_AD

description: AD


title: exercised rat 8 months, biological rep 1


title: 5GB1_FM21_TR2_UW

description: Fermentor run 21, uMax

value: uMax


title: 5GB1_FM21_TR2_QC

description: Fermentor run 21, uMax, QC


title: SporeF2

city: Aurora

first: Satyanarayan

last: Rao

state: CO

address: 12801 E 17th Ave, RC1 South

department: Biochemistry and Molecular Genetics

institute: University of Colorado, Denver | Anschutz Medical Campus

description: etana_h8_alexis_bc_03_sorted_center.bed.gz

data_processing:
DNA libraries from all samples were sequenced on  NovaSeq. Sequencing adapters were trimmed using `cutadapt` with parameters '-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGA -m 35 -l 130'.
For extracted DNA from C/PDXs plasma: the chromosomes of human (hg38; GRCh38 assembly) and mouse (mm10: GRCm38 assembly) reference genomes were first prefixed by hg38 and mm10 respectively, and then they were concatenated together to represent an in silico human + mouse genome. Paired end reads were then aligned to this concatenated genome using bowtie2 with parameters “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700”. We process the bam file using samtools to keep only mapped and properly paired reads and discards all the reads that have secondary alignment, a possibility that it may have aligned to both human and mouse genomes. To get human aligned reads we simply kept reads with hg38 prefix in reads’ chromosome name.
For DNA extracted from human plasma: Paired end reads were aligned to reference human genome (hg38; GRCh38 assembly) using bowtie2 with parameters parameters “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 500”.
For each sequenced DNA library, a bed file is generated with start and end loci representing the outer coordinates of paired end reads. With this bed file, one more version was created with mid point (start-coordinate + end-coordinate)/2  representing the centers of cfDNA fragments. These centers were mapped to regions of interest to estimate the cfDNA fragment length distribution.
Genome_build: hg38 (GRCh38), mm10 (GRCm38 assembly)
Supplementary_files_format_and_content: cfDNA center bedgz files (sorted by coordinates): Columns 1:  Chromosome, 2: mapped cfDNA fragement center coordinate, 3: Column 2 + 1, 4: cfDNA fragment length, 5: `.`, 6: mapped to strand (+/-), 7: chromosome, 8: start coordinate of mapped cfDNA fragment, 9: end coordinate of cfDNA fragment 10: length of cfDNA fragment, 11: `.` , 12:  mapped to strand (+/-)
Supplementary_files_format_and_content: bigwig files of coverage of cfDNA fragments in different length classes

source_name: cell-free DNA

growth_protocol: cfDNA is extracted from i) 250-500 ul of mouse plasma, and iii) 1-2 ml of human plasma. We extract DNA from plasma using commercially available kits and make sequencing libraries for paired-end Illumina sequencing. Since cfDNA is highly nicked, shorter fragments, which are most important for our analyses, are lost during standard library preparation, we prepared sequencing libraries from cfDNA that have been denatured into single stranded DNA – Single Strand library Protocol (SSP) (Gansauge and Meyer, 2013; Snyder et al., 2016). These libraries are subjected to paired-end sequencing in Illumina sequencers. Paired-end sequencing enables us to infer both location of fragment in the genome and the length of the fragment.

extract_protocol:
1-4 mL healthy human donor plasma (Vitalant) or 0.2-0.5 mL of mouse serum were thawed from -80ºC storage. Plasma or serum were spun at max speed (21000 rcf) at room temperature to pellet any cell debri. Supernatant was added to new tubes and cfDNA was extracted using the QIAGEN ccfMinElute kit (QIAGEN 55204). Eluates were eluted in 30 µL of nuclease-free water and directly added to the single-stranded DNA library protocol (SSP) or stored at -20ºC.
The capture of cfDNA fragments from plasma or serum was performed as in Snyder et al. 2016 and Gansauge and Meyer 2013. In brief and with the following changes, cfDNA 1-10ng was dephosphorylated using FastAP (Thermo EF0651), denatured, and incubated overnight with CircLigaseII (Lucigen CL9025K) and 0.093-0.125 µM biotinylated CL78 at 60ºC with shaking every 5 min. Captured cfDNA fragments were denatured and then bound to magnetic streptavidin M-280 beads (Invitrogen 11205D)  for 30 min at room temperature with nutation. Beads were washed and second-strand synthesis was performed using Bst 2.0 DNA polymerase (NEB M0537) with an increasing temperature gradient 15-31ºC with shaking at 1750 rpm. Beads were washed and a 3’ gap fill was performed using T4 DNA polymerase (Thermo EL0011) for 30 min at room temperature. Beads were washed and a double-stranded adapter was ligated using T4 DNA ligase (Thermo EP0062) for 2 hours at room temperature with shaking at 1750 rpm. Beads were washed and resuspended in 30 µL 10 mM TET buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 0.05% Tween-20). Beads were denatured at 95ºC for 3 min and cfDNA libraries were collected after immediate magnet separation. Quantitative real-time PCR was performed on cfDNA libraries using iTAQ Supermix (Bio-Rad 1725124) and Ct values were used to determine the number of PCR cycles needed to amplify each library. PCR was performed with KAPA HiFi DNA polymerase (Kapa Biosystems KK2502) using barcoded indexing primers adapted for Illumina sequencing on the Nova-seq. Primer dimers were removed from the libraries using 0.9X AMPure beads (Beckman Coulter A63881). Libraries were eluted in 0.1X TE and concentrations were determined using Qubit. The length distribution of each library was assessed by the Agilent Bioanalyzer using the D1000 or HSD1000 cassette. Libraries were then submitted for Illumina sequencing.

value: blood plasma

tag: disease

value: Lung Cancer (Squamous)

value: Male


title: 2043: Normal_exosome_2nd_Trimester_25.7_weeks


title: SporeB2

value: Lung Cancer (Small cell)

value: Female


title: FFF 1199: Normal_exosome_2nd_Trimester_23.7_weeks


title: exercised rat 18 months, biological rep 1


title: SporeA2

value: Lung Cancer (Non-small)


title: sedentary rat 24 months, biological rep 3

description: miRNA expression from the gastrocnemius of a 24 month old sedentary rat

source_name: gastrocnemius muscle, no exercise, 24 months


title: 5GB1_FM21_TR1_QC

description: Fermentor run 21, uMax, QC


title: 5GB1_FM20_TR3_UW

description: Fermentor run 20, uMax


title: sedentary rat 24 months, biological rep 2


title: BC03 Rep 4

description: etana_h6_alexis_bc_02_sorted_center.bed.gz

value: ER+ Breast Cancer


title: HepG2_Btz_50nM_ISRIB_50nM_S22_rep2

value: liver cancer cell line

value: bortezomib 50nM and ISRIB 50nM for 10h


title: 5GB1_FM20_TR3_QC

description: Fermentor run 20, uMax, QC


title: 1022: Normal_exosome_2nd_Trimester_22.4_weeks


title: SporeG2

value: Lung Cancer (Adenocarcinoma)


title: sedentary rat 24 months, biological rep 1

value: skeletal muscle


title: sedentary rat 18 months, biological rep 3

description: miRNA expression from the gastrocnemius of a 18 month old sedentary rat

source_name: gastrocnemius muscle, no exercise, 18 months

value: gastrocnemius


title: 2082: Normal_exosome_2nd_Trimester_26.4_weeks


title: 1048: Normal_exosome_2nd_Trimester_25.7_weeks


title: BC03 Rep 2


title: 5GB1_FM20_TR2_QC

description: Fermentor run 20, uMax

source_name: bioreactor culture


title: sedentary rat 18 months, biological rep 2

value: female


title: 5GB1_FM20_TR1_QC

description: Fermentor run 20, uMax, QC


title: 1191: Normal_exosome_2nd_Trimester_26.3_weeks


title: sedentary rat 18 months, biological rep 1


title: 5GB1_FM22_TR3_QC

description: Fermentor run 22, O2 limited, QC


title: 5GB1_FM19_TR3_QC

description: Fermentor run 19, O2 limited, QC


title: sedentary rat 12 months, biological rep 3

description: miRNA expression from the gastrocnemius of a 12 month old sedentary rat

source_name: gastrocnemius muscle, no exercise, 12 months


title: NP 2nd miRNA: Normal_exosome_2nd_Trimester_24.0_weeks


title: 5GB1_FM19_TR1_QC

description: Fermentor run 19, O2 limited, QC


title: BC03 Rep 1


title: N1 exo: Normal_exosome_1st_Trimester_11.3_weeks


title: BC03 Rep 3


title: NP 1st miRNA: Normal_exosome_1st_Trimester_14.4_weeks


title: exercised rat 24 months, biological rep 1


title: BC02 Rep 3


title: sedentary rat 12 months, biological rep 2


title: 5GB1_FM18_TR2_QC

description: Fermentor run 18, methanol

value: MeOH


title: sedentary rat 8 months, biological rep 3

description: miRNA expression from the gastrocnemius of a 8 month old sedentary rat

source_name: gastrocnemius muscle, no exercise, 8 months


title: sedentary rat 12 months, biological rep 1


title: 5GB1_FM18_TR1_QC

description: Fermentor run 18, methanol


title: Diet_GDM_60: GDM_exosome_3rd_Trimester_38.6_weeks

value: Exosomes

value: gestational diabetes mellitus (GDM)


title: BC02 Rep 1


title: N2 exo: Normal_exosome_2nd_Trimester_28.6_weeks

value: normal


title: WT_3

city: Beijing

first: Haobin

last: Hou

address: 2 Yuanmingyuan West Road, Haidian District

institute: Chinese Academy of Agricultural Sciences

data_processing:
After base calling, Cutadapt was used to remove the reads that contained adaptor contamination, low quality basea and undertermined bases.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to donkey whole genome(assembly ASM130575v1) using bowtie2 and Tophat2 with parameters Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol.
In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: assembly ASM130575v1

organism: Equus asinus

source_name: Gluteal muscle

extract_protocol:
Longissimus dorsi and gluteal muscle were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. mRNA-Seq sample preparation kit (Illumina, San Diego, USA)   TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA) were used with 10 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Wutou

value: Gluteal muscle

tag: developmental stage

value: 24 month old


title: BC02 Rep 2

value: blood plasma


title: SporeD3

value: Healthy

value: Male


title: sedentary rat 8 months, biological rep 1


title: 5GB1_FM14_TR2_QC

description: Fermentor run 14, methane limited, QC

tag: strain


title: Diet_GDM_65: GDM_exosome_3rd_Trimester_38.9_weeks

tag: tissue


title: BC02 Rep 4

value: ER+ Breast Cancer

value: Female


title: Insulin_GDM_72: GDM_exosome_3rd_Trimester_38.9_weeks


title: F05


title: WT_2


title: Insulin_GDM_63: GDM_exosome_3rd_Trimester_39.1_weeks


title: 5GB1_FM18_TR3_QC

description: Fermentor run 18, methanol


title: sedentary rat 8 months, biological rep 2

tag: gender


title: WT_1


title: F02


title: 5GB1_FM12_TR2_QC

description: Fermentor run 12, methane limited, QC


title: 2049: GDM_exosome_2nd_Trimester_25.7_weeks


title: WB_3

source_name: Longissimus dorsi muscle

value: Longissimus dorsi muscle


title: 1015: GDM_exosome_2nd_Trimester_26.4_weeks


title: UCD65 Rep 3

description:
pt65_merged_hg38-and-mm10_unique_hg38_centered_flank_30_0_79.bigwig
pt65_merged_hg38-and-mm10_unique_hg38_centered_flank_30_130_180.bigwig
pt65_merged_hg38-and-mm10_unique_hg38_sorted_center.bed.gz

source_name: Breast tumor xenograft

tag: xenograft


title: UCD65 Rep 2


title: 5GB1_FM11_TR2_QC

description: Fermentor run 11, O2 limited, QC


title: 1075: GDM_exosome_2nd_Trimester_25.7_weeks


title: WB_2


title: 5GB1_FM14_TR1_QC

description: Fermentor run 14, methane limited, QC


title: 1029: GDM_exosome_2nd_Trimester_23.7_weeks


title: ST_3

value: Sanfen


title: 5GB1_FM03_TR2_QC

description: Fermentor run 3, uMax though close to O2 limited, QC

value: uMax


title: WB_1


title: 5GB1_FM11_TR1_QC

description: Fermentor run 11, O2 limited, QC


title: 5GB1_FM03_TR1_QC


title: ST_2


title: 2001: GDM_exosome_2nd_Trimester_22.4_weeks


title: UCD4 Rep 4

description:
pt4_merged_hg38-and-mm10_unique_hg38_centered_flank_30_0_79.bigwig
pt4_merged_hg38-and-mm10_unique_hg38_centered_flank_30_130_180.bigwig
pt4_merged_hg38-and-mm10_unique_hg38_sorted_center.bed.gz


title: UCD4 Rep 3


title: 1001: GDM_exosome_2nd_Trimester_26.3_weeks


title: SSY-Karenina-input

organism: Symphalangus syndactylus

source_name: Siamang (Symphalangus syndactylus)

value: EBV-tranformed lymphocyte cell line


title: UCD4 Rep 2


title: UCD4 Rep 1


title: Mat Plasma GDM Insulin: GDM_exosome_2nd_Trimester_24.7_weeks


title: SSY-Karenina-CENPC


title: SB_3


title: Mat Plasma GDM Diet: GDM_exosome_2nd_Trimester_22.6_weeks


title: 5GB1_FM12_TR1_QC

description: Fermentor run 12, methane limited, QC


title: SB_2


title: SSY-Karenina-CENPB


title: GDM2 exo: GDM_exosome_2nd_Trimester_25.9_weeks


title: UCD65 Rep 1


title: MCF7 Rep 2

description:
mcf7_merged_hg38-and-mm10_unique_hg38_centered_flank_30_0_79.bigwig
mcf7_merged_hg38-and-mm10_unique_hg38_centered_flank_30_130_180.bigwig
mcf7_merged_hg38-and-mm10_unique_hg38_sorted_center.bed.gz

source_name: Cell line


title: SSY-Karenina-CENPA


title: SB_1


title: MCF7 Rep 1


title: GDM1 exo: GDM_exosome_1st_Trimester_11.3_weeks


title: SSY-Karenina-RNA

value: EBV-transformed lymphocyte cell line


title: ST_1


title: Newt heart

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
FastX Toolkit: fastq_quality_trimmer -t 20 -l 18: >Q20, length > 18
FastX Toolkit: fastx_collapser: remove duplicates (to accelerate analyses; still counted later)
Remove long reads: length < 29
Cluster reads which are completely included in each other or which differ by the  last 5' base only
Blastn vs. miRBase 20 miRNAs: blastn -num_alignments 15 -word_size 7 -evalue 10 -dust no -strand plus
Trim microRNA names to refer to families only
Keep only miRNA sequences with a meaningful number of counts/family (>5% of the most abundant sequence) to reduce mismatching due to sequencing errors
Keep only miRNA families with a minimum count of 5
Genome_build: miRBase 20 miRNAs
Supplementary_files_format_and_content: Tab-delimited text file with miRNA expression and clustering as generated by MIRPIPE (Kuenne et al., MIRPIPE: quantification of microRNAs in niche model organisms, Bioinformatics, 2014).   "miRNA" denotes the miRNA family that a newt read matched against (eg. bta-miR-200a, oan-miR-200a-3p, tgu-miR-200a-5p -> miR-200a).        "Expression" denotes the raw number of reads.        "Ambiguity" denotes the ratio of reads that mapped equally well to other miRNAs (1 = all reads may as well be attributed to a different miRNA).        "Cluster" denotes the cluster number.        "Primary sequence" is defined as the most abundant read for this miRNA.        "Cluster miRNAs" shows all miRNAs of this cluster. miRNAs are joined into a cluster if a read matched equally well to all of them.        "Ambiguity" denotes the ratio of reads that mapped equally well to other miRNAs (1 = all reads may as well be attributed to a different miRNA).        "Primary Sequence" is defined as the most abundant read for this miRNA.

organism: Notophthalmus viridescens

source_name: Newt heart

extract_protocol:
PureLink® miRNA Isolation Kit (Life Technologies)
Ion Total RNA-Seq Kit  (Life Technologies)
Chapter 3: Prepare Small RNA Libraries

value: adult

value: heart

tag: genotype

value: wild type


title: MCF7 Rep 3


title: long read RNA-seq from heart right ventricle (ENCLB679MMD)

status: Public on May 23 2021

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR984OAE/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_52 W76 heart right ventricle
experiment encode accession: ENCSR984OAE
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB679MMD
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens male adult (40 years) heart right ventricle tissue, preserved by flash-freezing

value: heart right ventricle

value: tissue

tag: biosample encode accession

value: male

tag: dev stage

value: 40 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Yiing Lin, MD, PhD

tag: health state

value: DM:no; HTN:yes; CAD:no

tag: link

value: ENCBS632QXG at ENCODE; https://www.encodeproject.org/ENCBS632QXG/

value: Derived from ENCODE donor ENCDO392CRK; https://www.encodeproject.org/ENCDO392CRK/


title: long read RNA-seq from lower lobe of left lung (ENCLB777FCP)

description:
https://www.encodeproject.org/experiments/ENCSR986WKB/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_39 W78 left lobe of lung
experiment encode accession: ENCSR986WKB
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB777FCP
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens male adult (60 years) lower lobe of left lung tissue, preserved by flash-freezing

value: lower lobe of left lung

tag: Sex

tag: age

value: 60 year

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: ENCBS559YLX at ENCODE; https://www.encodeproject.org/ENCBS559YLX/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: long read RNA-seq from heart left ventricle (ENCLB129YLX)

description:
https://www.encodeproject.org/experiments/ENCSR994YZY/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_53 W76 heart left ventricle
experiment encode accession: ENCSR994YZY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB129YLX
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens male adult (40 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: adult

value: ENCBS756BZF at ENCODE; https://www.encodeproject.org/ENCBS756BZF/


title: long read RNA-seq from K562 (ENCLB722DIJ)

description:
https://www.encodeproject.org/experiments/ENCSR983KDL/
***************
biological replicate number: 2
technical replicate number: 1
description: K562
experiment encode accession: ENCSR983KDL
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB722DIJ
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 0
nucleic acid starting quantity units: µg

source_name: Homo sapiens K562 cell line

tag: line

value: cell line

tag: description

value: female

value: 53 year

value: Ali Mortazavi, UCI

value: ATCC

value: chronic myelogenous leukemia (CML)

value: ENCBS657IOS at ENCODE; https://www.encodeproject.org/ENCBS657IOS/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: long read RNA-seq from PC-3 (ENCLB542NGF)

description:
https://www.encodeproject.org/experiments/ENCSR947JHA/
***************
biological replicate number: 1
technical replicate number: 1
description: PC-3 cell line
experiment encode accession: ENCSR947JHA
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB542NGF
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 6
nucleic acid starting quantity units: µg

source_name: Homo sapiens PC-3 cell line

value: male

value: 62 year

value: Mats Ljungman, UMichigan

value: grade IV, adenocarcinoma

value: ENCBS555BGE at ENCODE; https://www.encodeproject.org/ENCBS555BGE/

value: Derived from ENCODE donor ENCDO349AAA; https://www.encodeproject.org/ENCDO349AAA/


title: long read RNA-seq from GM12878 (ENCLB784FMA)

description:
https://www.encodeproject.org/experiments/ENCSR962BVU/
***************
biological replicate number: 1
technical replicate number: 1
description: GM12878 Ljungman
experiment encode accession: ENCSR962BVU
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB784FMA
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM12878 cell line

value: unknown

value: Coriell

value: ENCBS975OUN at ENCODE; https://www.encodeproject.org/ENCBS975OUN/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: long read RNA-seq from K562 (ENCLB096WLH)

description:
https://www.encodeproject.org/experiments/ENCSR983KDL/
***************
biological replicate number: 1
technical replicate number: 1
description: K562
experiment encode accession: ENCSR983KDL
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB096WLH
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 0
nucleic acid starting quantity units: µg

value: cell line

value: female

value: adult

value: ENCBS516PYE at ENCODE; https://www.encodeproject.org/ENCBS516PYE/


title: long read RNA-seq from ovary (ENCLB393KHP)

description:
https://www.encodeproject.org/experiments/ENCSR507WZC/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_72 W80 ovary
experiment encode accession: ENCSR507WZC
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB393KHP
spikeins used: Ambion mix 1 spike-ins, SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens female adult (61 years) ovary tissue, preserved by flash-freezing

value: ovary

value: tissue

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: ENCBS250FEP at ENCODE; https://www.encodeproject.org/ENCBS250FEP/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: long read RNA-seq from ovary (ENCLB194KIW)

description:
https://www.encodeproject.org/experiments/ENCSR477HHG/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_71 W73 ovary
experiment encode accession: ENCSR477HHG
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB194KIW
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Homo sapiens female adult (59 years) ovary tissue, preserved by flash-freezing

value: 59 year

value: DM:yes; HTN:yes; CAD:no

value: ENCBS756ETL at ENCODE; https://www.encodeproject.org/ENCBS756ETL/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: long read RNA-seq from Right ventricle myocardium superior (ENCLB328TYS)

description:
https://www.encodeproject.org/experiments/ENCSR899GAP/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_56 W78 right ventricle myocardium superior
experiment encode accession: ENCSR899GAP
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB328TYS
spikeins used: Ambion mix 1 spike-ins, SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Homo sapiens male adult (60 years) Right ventricle myocardium superior tissue, preserved by flash-freezing

value: Right ventricle myocardium superior

value: Superior wall of right ventricle.

value: male

value: 60 year

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: ENCBS580WTV at ENCODE; https://www.encodeproject.org/ENCBS580WTV/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: long read RNA-seq from HL-60 (ENCLB279KJK)

description:
https://www.encodeproject.org/experiments/ENCSR887LTD/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens HL-60
experiment encode accession: ENCSR887LTD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB279KJK
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Homo sapiens HL-60 cell line

value: cell line

value: Homo sapiens HL-60

value: female

value: adult

value: 36 year

value: Ali Mortazavi, UCI

value: ATCC

value: acute promyelocytic leukemia

value: ENCBS313YIM at ENCODE; https://www.encodeproject.org/ENCBS313YIM/

value: Derived from ENCODE donor ENCDO000AAM; https://www.encodeproject.org/ENCDO000AAM/


title: long read RNA-seq from HL-60 (ENCLB225HGB)

description:
https://www.encodeproject.org/experiments/ENCSR887LTD/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens HL-60
experiment encode accession: ENCSR887LTD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB225HGB
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS416JRX at ENCODE; https://www.encodeproject.org/ENCBS416JRX/


title: long read RNA-seq from endodermal cell (ENCLB042MFL)

description:
https://www.encodeproject.org/experiments/ENCSR904KAT/
***************
biological replicate number: 1
technical replicate number: 1
description: H9-derived definitive endoderm
experiment encode accession: ENCSR904KAT
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB042MFL
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Homo sapiens female embryo (5 days) endodermal in vitro differentiated cells originated from endodermal cell

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS601OTT at ENCODE; https://www.encodeproject.org/ENCBS601OTT/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: long read RNA-seq from kidney (ENCLB730SHE)

description:
https://www.encodeproject.org/experiments/ENCSR432YKA/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_42 W71 kidney
experiment encode accession: ENCSR432YKA
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB730SHE
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Homo sapiens female adult (47 years) kidney tissue, preserved by flash-freezing

value: kidney

value: tissue

value: female

value: adult

value: 47 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:yes; HTN:yes; CAD:no

value: ENCBS305JCM at ENCODE; https://www.encodeproject.org/ENCBS305JCM/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: long read RNA-seq from right cardiac atrium (ENCLB264GGI)

description:
https://www.encodeproject.org/experiments/ENCSR435UUS/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_58 W78 right cardiac atrium
experiment encode accession: ENCSR435UUS
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB264GGI
spikeins used: Ambion mix 1 spike-ins, SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline
nucleic acid starting quantity: 0
nucleic acid starting quantity units: µg

source_name: Homo sapiens male adult (60 years) right cardiac atrium tissue, preserved by flash-freezing

value: right cardiac atrium

value: male

value: 60 year

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: ENCBS271WJL at ENCODE; https://www.encodeproject.org/ENCBS271WJL/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: long read RNA-seq from GM12878 (ENCLB200YVA)

description:
https://www.encodeproject.org/experiments/ENCSR838WFC/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens GM12878 immortalized cell line
experiment encode accession: ENCSR838WFC
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-03-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB200YVA
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 6
nucleic acid starting quantity units: µg

value: cell line

value: unknown

value: Ali Mortazavi, UCI

value: Coriell

value: ENCBS496YYL at ENCODE; https://www.encodeproject.org/ENCBS496YYL/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: long read RNA-seq from GM12878 (ENCLB735WVC)

description:
https://www.encodeproject.org/experiments/ENCSR838WFC/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens GM12878 immortalized cell line
experiment encode accession: ENCSR838WFC
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-03-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB735WVC
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 6
nucleic acid starting quantity units: µg

value: female

value: adult

value: ENCBS406FCE at ENCODE; https://www.encodeproject.org/ENCBS406FCE/


title: long read RNA-seq from aorta (ENCLB327LXM)

description:
https://www.encodeproject.org/experiments/ENCSR425HFS/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_103 W73 aorta
experiment encode accession: ENCSR425HFS
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB327LXM
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Homo sapiens female adult (59 years) aorta tissue, preserved by flash-freezing

value: aorta

value: tissue

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:yes; HTN:yes; CAD:no

value: ENCBS759AII at ENCODE; https://www.encodeproject.org/ENCBS759AII/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: long read RNA-seq from HCT116 (ENCLB218VBB)

description:
https://www.encodeproject.org/experiments/ENCSR388RWE/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT 116 cell line
experiment encode accession: ENCSR388RWE
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB218VBB
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 3
nucleic acid starting quantity units: µg

source_name: Homo sapiens HCT116 cell line

value: cell line

value: male

value: 48 year

value: Mats Ljungman, UMichigan

value: ATCC

value: colorectal carcinoma

value: ENCBS375FZQ at ENCODE; https://www.encodeproject.org/ENCBS375FZQ/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: long read RNA-seq from psoas muscle (ENCLB612BYX)

description:
https://www.encodeproject.org/experiments/ENCSR803QWH/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_46 W61 psoas #2
experiment encode accession: ENCSR803QWH
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB612BYX
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 0
nucleic acid starting quantity units: µg

source_name: Homo sapiens female adult (41 years) psoas muscle tissue, preserved by flash-freezing

value: psoas muscle

value: female

value: adult

value: 41 year

value: DM:no; HTN:no; CAD:no

value: ENCBS538ZJX at ENCODE; https://www.encodeproject.org/ENCBS538ZJX/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: long read RNA-seq from MCF-7 (ENCLB192AUL)

description:
https://www.encodeproject.org/experiments/ENCSR810XLL/
***************
biological replicate number: 1
technical replicate number: 1
description: MCF-7 cell line
experiment encode accession: ENCSR810XLL
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB192AUL
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens MCF-7 cell line

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS734JMT at ENCODE; https://www.encodeproject.org/ENCBS734JMT/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: long read RNA-seq from heart right ventricle (ENCLB267ZKP)

description:
https://www.encodeproject.org/experiments/ENCSR329ZQG/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_51 W73 heart right ventricle
experiment encode accession: ENCSR329ZQG
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB267ZKP
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Homo sapiens female adult (59 years) heart right ventricle tissue, preserved by flash-freezing

value: heart right ventricle

value: tissue

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:yes; HTN:yes; CAD:no

value: ENCBS789UUH at ENCODE; https://www.encodeproject.org/ENCBS789UUH/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: long read RNA-seq from endodermal cell (ENCLB269BTC)

description:
https://www.encodeproject.org/experiments/ENCSR904KAT/
***************
biological replicate number: 2
technical replicate number: 1
description: H9-derived definitive endoderm
experiment encode accession: ENCSR904KAT
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB269BTC
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS958FWY at ENCODE; https://www.encodeproject.org/ENCBS958FWY/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: long read RNA-seq from osteocyte (ENCLB228IOV)

description:
https://www.encodeproject.org/experiments/ENCSR296PQZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H9-derived osteocytes
experiment encode accession: ENCSR296PQZ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB228IOV
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Homo sapiens female embryo (5 days) osteocyte in vitro differentiated cells originated from osteocyte

value: osteocyte

value: WA09 derived osteocytes

value: ENCBS034WOR at ENCODE; https://www.encodeproject.org/ENCBS034WOR/


title: long read RNA-seq from osteocyte (ENCLB771EIE)

description:
https://www.encodeproject.org/experiments/ENCSR296PQZ/
***************
biological replicate number: 2
technical replicate number: 1
description: H9-derived osteocytes
experiment encode accession: ENCSR296PQZ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB771EIE
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

value: ENCBS572IFJ at ENCODE; https://www.encodeproject.org/ENCBS572IFJ/


title: long read RNA-seq from left ventricle myocardium inferior (ENCLB117COA)

description:
https://www.encodeproject.org/experiments/ENCSR786FLO/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_55 W78 left ventricle myocardium inferior
experiment encode accession: ENCSR786FLO
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB117COA
spikeins used: Ambion mix 1 spike-ins, SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Homo sapiens male adult (60 years) left ventricle myocardium inferior tissue, preserved by flash-freezing

value: left ventricle myocardium inferior

value: tissue

value: Inferior wall of left ventricle.

value: male

value: adult

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: ENCBS735OAR at ENCODE; https://www.encodeproject.org/ENCBS735OAR/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: long read RNA-seq from lower lobe of left lung (ENCLB798YFL)

description:
https://www.encodeproject.org/experiments/ENCSR261GOA/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_80 W73 lower lobe of left lung
experiment encode accession: ENCSR261GOA
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB798YFL
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Homo sapiens female adult (59 years) lower lobe of left lung tissue, preserved by flash-freezing

value: lower lobe of left lung

value: female

value: 59 year

value: DM:yes; HTN:yes; CAD:no

value: ENCBS231BSF at ENCODE; https://www.encodeproject.org/ENCBS231BSF/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: long read RNA-seq from heart right ventricle (ENCLB400RGN)

description:
https://www.encodeproject.org/experiments/ENCSR782LGT/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_50 W72 heart right ventricle
experiment encode accession: ENCSR782LGT
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB400RGN
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens female adult (46 years) heart right ventricle tissue, preserved by flash-freezing

value: heart right ventricle

value: 46 year

value: DM:no; HTN:no; CAD:no

value: ENCBS238NAR at ENCODE; https://www.encodeproject.org/ENCBS238NAR/

value: Derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: long read RNA-seq from left ventricle myocardium superior (ENCLB641OJZ)

description:
https://www.encodeproject.org/experiments/ENCSR777CCI/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_54 W78 left ventricle myocardium superior
experiment encode accession: ENCSR777CCI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB641OJZ
spikeins used: Ambion mix 1 spike-ins, SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Homo sapiens male adult (60 years) left ventricle myocardium superior tissue, preserved by flash-freezing

value: left ventricle myocardium superior

value: tissue

value: Superior wall of left ventricle.

value: male

value: adult

value: 60 year

value: ENCBS165LTN at ENCODE; https://www.encodeproject.org/ENCBS165LTN/


title: long read RNA-seq from Panc1 (ENCLB962HZB)

description:
https://www.encodeproject.org/experiments/ENCSR181CES/
***************
biological replicate number: 1
technical replicate number: 1
description: Panc1 cell line
experiment encode accession: ENCSR181CES
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB962HZB
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 5
nucleic acid starting quantity units: µg

source_name: Homo sapiens Panc1 cell line

value: cell line

value: 56 year

value: Mats Ljungman, UMichigan

value: ATCC

value: pancreatic carcinoma

value: ENCBS777OZT at ENCODE; https://www.encodeproject.org/ENCBS777OZT/

value: Derived from ENCODE donor ENCDO000ABB; https://www.encodeproject.org/ENCDO000ABB/


title: long read RNA-seq from mesenteric fat pad (ENCLB350ULX)

description:
https://www.encodeproject.org/experiments/ENCSR648QZP/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_93 W73 mesenteric fat pad FLASH
experiment encode accession: ENCSR648QZP
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB350ULX
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Homo sapiens female adult (59 years) mesenteric fat pad tissue, preserved by flash-freezing

value: mesenteric fat pad

value: female

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:yes; HTN:yes; CAD:no

value: ENCBS232CCX at ENCODE; https://www.encodeproject.org/ENCBS232CCX/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: long read RNA-seq from HepG2 (ENCLB798VOD)

description:
https://www.encodeproject.org/experiments/ENCSR634AKC/
***************
biological replicate number: 1
technical replicate number: 1
description: HepG2 Ljungman
experiment encode accession: ENCSR634AKC
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB798VOD
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 3
nucleic acid starting quantity units: µg

source_name: Homo sapiens HepG2 cell line

value: male

value: child

value: 15 year

value: hepatocellular carcinoma

value: ENCBS365LJQ at ENCODE; https://www.encodeproject.org/ENCBS365LJQ/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: long read RNA-seq from posterior vena cava (ENCLB621EQT)

description:
https://www.encodeproject.org/experiments/ENCSR138TAS/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_102 W73 posterior vena cava
experiment encode accession: ENCSR138TAS
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB621EQT
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Homo sapiens female adult (59 years) posterior vena cava tissue, preserved by flash-freezing

value: posterior vena cava

value: tissue

value: adult

value: ENCBS892JRQ at ENCODE; https://www.encodeproject.org/ENCBS892JRQ/


title: long read RNA-seq from type B pancreatic cell (ENCLB292ISL)

description:
https://www.encodeproject.org/experiments/ENCSR130CIK/
***************
biological replicate number: 1
technical replicate number: 1
description: H9-derived insulin-producing beta-like cells
experiment encode accession: ENCSR130CIK
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB292ISL
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Homo sapiens female embryo (5 days) type B pancreatic in vitro differentiated cells originated from type B pancreatic cell

value: type B pancreatic cell

value: in vitro differentiated cells

value: WA09 derived insulin producing beta-like cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS779FCS at ENCODE; https://www.encodeproject.org/ENCBS779FCS/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: long read RNA-seq from heart left ventricle (ENCLB150SGW)

description:
https://www.encodeproject.org/experiments/ENCSR700XDQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_49 W72 heart left ventricle
experiment encode accession: ENCSR700XDQ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB150SGW
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Homo sapiens female adult (46 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: 46 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:no; HTN:no; CAD:no

value: ENCBS914REQ at ENCODE; https://www.encodeproject.org/ENCBS914REQ/

value: Derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: long read RNA-seq from type B pancreatic cell (ENCLB356CMQ)

description:
https://www.encodeproject.org/experiments/ENCSR130CIK/
***************
biological replicate number: 2
technical replicate number: 1
description: H9-derived insulin-producing beta-like cells
experiment encode accession: ENCSR130CIK
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB356CMQ
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

value: type B pancreatic cell

value: in vitro differentiated cells

value: ENCBS251SEQ at ENCODE; https://www.encodeproject.org/ENCBS251SEQ/


title: long read RNA-seq from IMR-90 (ENCLB085UQI)

description:
https://www.encodeproject.org/experiments/ENCSR113MEY/
***************
biological replicate number: 1
technical replicate number: 1
description: IMR90 cell line
experiment encode accession: ENCSR113MEY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB085UQI
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 3
nucleic acid starting quantity units: µg

source_name: Homo sapiens IMR-90 cell line

value: cell line

value: female

value: 16 week

value: Mats Ljungman, UMichigan

value: ATCC

value: unknown

value: ENCBS648NSQ at ENCODE; https://www.encodeproject.org/ENCBS648NSQ/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/


title: long read RNA-seq from H9 (ENCLB899PJH)

description:
https://www.encodeproject.org/experiments/ENCSR044ARQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H9 ESCs
experiment encode accession: ENCSR044ARQ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB899PJH
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Homo sapiens H9 cell line originated from H9

value: WA09 ES cells

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS713BMM at ENCODE; https://www.encodeproject.org/ENCBS713BMM/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: long read RNA-seq from H9 (ENCLB135ADH)

description:
https://www.encodeproject.org/experiments/ENCSR044ARQ/
***************
biological replicate number: 2
technical replicate number: 1
description: H9 ESCs
experiment encode accession: ENCSR044ARQ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB135ADH
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

value: ENCBS654ADT at ENCODE; https://www.encodeproject.org/ENCBS654ADT/


title: long read RNA-seq from neural crest cell (ENCLB354MHL)

description:
https://www.encodeproject.org/experiments/ENCSR056MYH/
***************
biological replicate number: 2
technical replicate number: 1
description: H9-derived neural crest cells
experiment encode accession: ENCSR056MYH
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB354MHL
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Homo sapiens female embryo (5 days) neural crest in vitro differentiated cells originated from neural crest cell

value: neural crest cell

value: in vitro differentiated cells

value: WA09 derived neural crest cells

value: ENCBS417JEU at ENCODE; https://www.encodeproject.org/ENCBS417JEU/


title: long read RNA-seq from neural crest cell (ENCLB735IIF)

description:
https://www.encodeproject.org/experiments/ENCSR056MYH/
***************
biological replicate number: 1
technical replicate number: 1
description: H9-derived neural crest cells
experiment encode accession: ENCSR056MYH
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB735IIF
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

value: female

value: ENCBS200JOD at ENCODE; https://www.encodeproject.org/ENCBS200JOD/


title: long read RNA-seq from Right ventricle myocardium inferior (ENCLB881SJQ)

description:
https://www.encodeproject.org/experiments/ENCSR591OZR/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_57 W78 right ventricle myocardium inferior
experiment encode accession: ENCSR591OZR
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB881SJQ
spikeins used: Ambion mix 1 spike-ins, SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline
nucleic acid starting quantity: 0
nucleic acid starting quantity units: µg

source_name: Homo sapiens male adult (60 years) Right ventricle myocardium inferior tissue, preserved by flash-freezing

value: Right ventricle myocardium inferior

value: tissue

value: Inferior wall of right ventricle.

value: male

value: adult

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: ENCBS705XRW at ENCODE; https://www.encodeproject.org/ENCBS705XRW/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: long read RNA-seq from adrenal gland (ENCLB699OTN)

description:
https://www.encodeproject.org/experiments/ENCSR995WKW/
***************
biological replicate number: 1
technical replicate number: 1
description: Adrenal Gland 2-1 ENTEX51
experiment encode accession: ENCSR995WKW
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-27
lab: Ali Mortazavi, UCI
library encode accession: ENCLB699OTN

source_name: Homo sapiens male adult (54 years) adrenal gland tissue

value: adrenal gland

value: Adrenal Gland

value: 54 year

value: Barbara Wold, Caltech

value: Kristin Ardlie

value: ENCBS420UOM at ENCODE; https://www.encodeproject.org/ENCBS420UOM/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: long read RNA-seq from excitatory neuron (ENCLB532XRH)

description:
https://www.encodeproject.org/experiments/ENCSR257JBF/
***************
biological replicate number: 1
technical replicate number: 2
description: excitatory cortical neurons
experiment encode accession: ENCSR257JBF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB532XRH

source_name: Homo sapiens male adult (53 years) excitatory neuron in vitro differentiated cells, preserved by cryopreservation

value: excitatory neuron

value: in vitro differentiated cells

value: PGP1 derived excitatory cortical neurons

value: 53 year

value: Bradley Bernstein, Broad

value: George Church

value: ENCBS932EVS at ENCODE; https://www.encodeproject.org/ENCBS932EVS/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: long read RNA-seq from right cardiac atrium (ENCLB918JLV)

description:
https://www.encodeproject.org/experiments/ENCSR514YQN/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_59 W72 right cardiac atrium
experiment encode accession: ENCSR514YQN
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB918JLV
spikeins used: Ambion mix 1 spike-ins, SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Homo sapiens female adult (46 years) right cardiac atrium tissue, preserved by flash-freezing

value: right cardiac atrium

value: tissue

value: female

value: adult

value: 46 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:no; HTN:no; CAD:no

value: ENCBS341KAA at ENCODE; https://www.encodeproject.org/ENCBS341KAA/

value: Derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: long read RNA-seq from heart left ventricle (ENCLB921WJD)

description:
https://www.encodeproject.org/experiments/ENCSR575LWI/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_33 W73 heart left ventricle
experiment encode accession: ENCSR575LWI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB921WJD
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Homo sapiens female adult (59 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: 59 year

value: DM:yes; HTN:yes; CAD:no

value: ENCBS692CKU at ENCODE; https://www.encodeproject.org/ENCBS692CKU/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: long read RNA-seq from progenitor cell of endocrine pancreas (ENCLB671SMF)

description:
https://www.encodeproject.org/experiments/ENCSR530BOC/
***************
biological replicate number: 1
technical replicate number: 1
description: H9-derived pancreatic progenitors
experiment encode accession: ENCSR530BOC
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB671SMF
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Homo sapiens female embryo (5 days) progenitor of endocrine pancreas in vitro differentiated cells

value: progenitor cell of endocrine pancreas

value: in vitro differentiated cells

value: WA09 derived pancreatic progenitor cells

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: healthy

value: ENCBS832MSN at ENCODE; https://www.encodeproject.org/ENCBS832MSN/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: long read RNA-seq from progenitor cell of endocrine pancreas (ENCLB767VAZ)

description:
https://www.encodeproject.org/experiments/ENCSR530BOC/
***************
biological replicate number: 2
technical replicate number: 1
description: H9-derived pancreatic progenitors
experiment encode accession: ENCSR530BOC
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB767VAZ
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Homo sapiens female embryo (5 days) progenitor of endocrine pancreas in vitro differentiated cells originated from progenitor cell of endocrine pancreas

value: female

value: ENCBS825BIV at ENCODE; https://www.encodeproject.org/ENCBS825BIV/


title: long read RNA-seq from K562 (ENCLB214YWC)

description:
https://www.encodeproject.org/experiments/ENCSR526TQU/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 Ljungman
experiment encode accession: ENCSR526TQU
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB214YWC
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 3
nucleic acid starting quantity units: µg

source_name: Homo sapiens K562 cell line

value: cell line

value: adult

value: 53 year

value: Mats Ljungman, UMichigan

value: ATCC

value: chronic myelogenous leukemia (CML)

value: ENCBS206PUV at ENCODE; https://www.encodeproject.org/ENCBS206PUV/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: long read RNA-seq from excitatory neuron (ENCLB389UCF)

description:
https://www.encodeproject.org/experiments/ENCSR257JBF/
***************
biological replicate number: 1
technical replicate number: 1
description: excitatory cortical neurons
experiment encode accession: ENCSR257JBF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB389UCF

value: excitatory neuron

value: in vitro differentiated cells

value: PGP1 derived excitatory cortical neurons

value: male

value: George Church

value: ENCBS932EVS at ENCODE; https://www.encodeproject.org/ENCBS932EVS/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: long read RNA-seq from right lobe of liver (ENCLB828NEC)

description:
https://www.encodeproject.org/experiments/ENCSR657HJW/
***************
biological replicate number: 1
technical replicate number: 1
description: W61 right lobe of liver
experiment encode accession: ENCSR657HJW
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB828NEC

source_name: Homo sapiens female adult (41 years) right lobe of liver tissue, preserved by flash-freezing

value: right lobe of liver

value: tissue

value: female

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:no; HTN:no; CAD:no

value: ENCBS823URA at ENCODE; https://www.encodeproject.org/ENCBS823URA/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: long read RNA-seq from GM23338 (ENCLB644KMO)

description:
https://www.encodeproject.org/experiments/ENCSR676IWT/
***************
biological replicate number: 1
technical replicate number: 2
description: iPSCs via Sendai-viral Yamanaka factors
experiment encode accession: ENCSR676IWT
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB644KMO

source_name: Homo sapiens GM23338 cell line, preserved by cryopreservation

value: cell line

value: PGP1 iPSCs

value: adult

value: 53 year

value: Bradley Bernstein, Broad

value: ENCBS155WDP at ENCODE; https://www.encodeproject.org/ENCBS155WDP/


title: long read RNA-seq from endothelial cell (ENCLB047SNQ)

description:
https://www.encodeproject.org/experiments/ENCSR148IIG/
***************
biological replicate number: 1
technical replicate number: 1
description: PGP1 derived endothelial-cells
experiment encode accession: ENCSR148IIG
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB047SNQ

source_name: Homo sapiens male adult (53 years) endothelial in vitro differentiated cells, preserved by cryopreservation

value: endothelial cell

value: in vitro differentiated cells

value: PGP1 derived endothelial cells

value: male

value: George Church

value: ENCBS239VAD at ENCODE; https://www.encodeproject.org/ENCBS239VAD/


title: long read RNA-seq from endothelial cell (ENCLB134MKV)

description:
https://www.encodeproject.org/experiments/ENCSR148IIG/
***************
biological replicate number: 1
technical replicate number: 2
description: PGP1 derived endothelial-cells
experiment encode accession: ENCSR148IIG
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB134MKV

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: sgRNA counts (day 18, venetoclax selection) rep2

city: Oxford

first: Thomas

last: Milne

address: MRC MHU, WIMM, John Radcliffe Hospital

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

description:
Sequencing of THP1 + Venetoclax sgRNA representation  at day 18
T6D_Venetoclax_rep2

data_processing:
Library strategy: amplicon DNA sequencing
Combine and merge Read 1 and 2 using BBMerge (quality score threshold = 30)
Count sgRNA sequences using CRISPRessoCount ("-t GTTTTAGAGCTAGAAATAGC")
MAGeCK-RRA v0.5.7 with CNV normalisation (based on THP-1 gene copy numbers derived from Affymetrix SNP6.0 arrays, downloaded from Cancer Cell Line Encyclopedia) and 10,000 permutations
MAGeCK-Flute v1.3.1 for volcano plots
Genome_build: TKOv3 sgRNA library
Supplementary_files_format_and_content: Normalized sgRNA read counts

source_name: Leukemia cell line (THP1)

growth_protocol: lentiviral pooled CRISPR screening with lentiCRISPRv2-TKOv3; cells grown in RPMI 1640 + 10% FBS and passaged every 72h

extract_protocol:
QIAamp DNA Blood Maxi Kit (Qiagen)
Sequencing libraries were prepared in two PCR steps, the first to enrich sgRNA regions from the genome, and the second to amplify sgRNA and attach sequencing adapters and indices (based on Aregger, M., Chandrashekhar, M., Tong, A. H. Y., Chan, K. & Moffat, J. in Methods Mol. Biol. 169–188 (2019). doi:10.1007/978-1-4939-8805-1_15)

treatment_protocol: half the transduced cells were continuously treated with venetoclax for 18 days (6 passages)

tag: cell line

value: Paediatric monocytic cell line derived from AML M5 with t(9;11)(q21;q23) translocation

tag: crispr sgrna library

tag: treatment

value: venetoclax


title: long read RNA-seq from GM23338 (ENCLB266AQD)

description:
https://www.encodeproject.org/experiments/ENCSR676IWT/
***************
biological replicate number: 1
technical replicate number: 1
description: iPSCs via Sendai-viral Yamanaka factors
experiment encode accession: ENCSR676IWT
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB266AQD


title: long read RNA-seq from adrenal gland (ENCLB945ZXA)

description:
https://www.encodeproject.org/experiments/ENCSR081NRO/
***************
biological replicate number: 1
technical replicate number: 1
description: Adrenal Gland 1-2 ENTEX50
experiment encode accession: ENCSR081NRO
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-27
lab: Ali Mortazavi, UCI
library encode accession: ENCLB945ZXA

source_name: Homo sapiens adrenal gland tissue male adult (37 years)

value: adrenal gland

value: tissue

value: Adrenal Gland

value: Barbara Wold, Caltech

value: 37 year

value: ENCBS636AEJ at ENCODE; https://www.encodeproject.org/ENCBS636AEJ/

value: derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: sgRNA counts (day 18, venetoclax selection) rep1

description:
Sequencing of THP1 + Venetoclax sgRNA representation  at day 18
T6D_Venetoclax_rep1


title: sgRNA counts (day zero) rep2

description:
Sequencing of THP1 sgRNA representation  at day 0
T0_control_rep2


title: long read RNA-seq from right cardiac atrium (ENCLB852BGR)

description:
https://www.encodeproject.org/experiments/ENCSR553SVP/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_36 W73 cardiac right atrium
experiment encode accession: ENCSR553SVP
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB852BGR
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Homo sapiens female adult (59 years) right cardiac atrium tissue, preserved by flash-freezing

value: right cardiac atrium

value: female

value: adult

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:yes; HTN:yes; CAD:no

value: ENCBS911SOZ at ENCODE; https://www.encodeproject.org/ENCBS911SOZ/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: 5-inactB

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the E. coli ASM75055v1 assembly genomic reference with the STAR aligner (v2.5.2b) with default alignment parameters.
Abundance estimation was performed with htseq-count (v 0.9.1)
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: Escherichia coli BW25113, Assembly ASM75055v1 (GCA_000750555.1_ASM75055v1_genomic.fna, GCA_000750555.1_ASM75055v1_genomic.gtf)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Escherichia coli BW25113

source_name: Escherichia coli BW25113 culture

growth_protocol: Isolated colonies of E. coli BW25113 harboring plasmid pKT-CNP or pKT-CNP-inact (control) were incubated in 3 mL of M9 minimal medium (supplemented with 0.4% glucose, 0.2% casamino acids, and 100 µg/mL carbenicillin) at 37°C overnight (~18 h) with shaking at 200-225 rpm. These starter cultures then were subcultured 1:100 into 10 mL of the same medium and incubated under the same conditions to a 600 nm optical density (OD600) of ~0.1-0.2. All cultures subsequently were treated with anhydrotetracycline (25 ng/mL) to induce protein expression from the pKT vector. Incubation was continued to OD600 ~0.5-0.6, at which point 2 mL of culture were harvested by centrifugation (7000 g for 5 min) for RNA-seq analysis.

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit and treated with DNase I.
Ribosomal transcripts were depleted from 2 ug of total RNA, and libraries were generated following Illumina's Scripseq V2 Complete- Bacterial library prep kits. (Epicentre, Madison, WI, USA)

tag: strain

tag: growth phase

value: logarithmic

tag: plasmid

value: pKT-CNP-inact (H73L/H152L; numbering based on catalytic domain - final 221 amino acid residues) (control)


title: 4-inactA


title: 6-inactC


title: 3-CNPC

value: pKT-CNP (Rattus norvegicus CNP gene; UniProtKB-P13233; final 221 amino acid residues; codon-optimized for E. coli)


title: 1-CNPA


title: 2-CNPB