title: hDMC (hiPSC-deerived dental mesenchymal cells)-2

data_processing:
Experimental Method(RNA QC/Library construction/sequencing)  RNA quality was assessed by analysis of rRNA band integrity on an Agilent RNA 6000 Nano  kit (Agilent Technologies, CA). Ahead of cDNA library construction, the 1ug of total RNA and magnetic beads with Oligo (dT) were used to enrich poly (A) mRNA from it. Then, the purified mRNAs were disrupted into short fragments, and the double-stranded cDNAs were immediately synthesized. The cDNAs was subjected to end-repair, poly (A) addition, and connected with sequencing adapters using the TruSeq RNA sample prep Kit (Illumina, CA). The suitable fragments automatically purified by BluePippin 2% agarose gel cassette (Sage Science, MA) were selected as templates for PCR amplification. The final library sizes and qualities were evaluated electrophoretically with an Agilent High Sensitivity DNA kit (Agilent Technologies, CA) and the fragment was found to be between 350–450 bp. Subsequently, the library was sequenced using an Illumina HiSeq2500 sequencer (Illumina, CA).
Transcriptome data analysis  Filtering  The quality of the reads were checked using fastQC (v.0.10.1) [1] , helping the understanding for the basic quality for sequence quality score, GC content, N content, length distribution and duplication level. Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose quality scores are less than 20 and reads whose average quality scores of each read is less than 20. The whole filtering process was performed using the in-house scripts.
Sequence alignment  Filtered reads were mapped to the reference genome (Ensembl release 72 [2]) using the aligner Tophat [3].
Gene expression estimation  Gene expression level was measured with Cufflinks v2.1.1 [4-5] using the  gene annotation database of Ensembl release 72. Non-coding gene region was removed with  –mask option. To improve the accuracy of measurement, multi-read-correction and fragbias-  correct options were applied. All other options were set to default values.
References  [1] Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc  [2] Flicek P. et al., (2013). “Ensembl 2013”. Nucleic Acids Res. 41(Database issue):D48-55.  [3] Trapnell C. et al., (2009). “TopHat: discovering splice junctions with RNA-Seq”,  Bioinformatics, 25(9):1105-11.  [4] Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L., (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. Mar 1;7(3):562-78.  [5] Trapnell C. et al., (2010). “Transcript assembly and quantification by RNA-Seq reveals  unannotated transcripts and isoform switching during cell differentiation”, Nat Biotechnol.  28(5):511-5.
Assembly: GRCh37-hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: mesenchymal cells

extract_protocol: hiPSC, hDECs, and hDMCs were collected and total RNA was extracted from hiPSC, hDECs, and hDMCs using TRIzol.

value: mesenchymal cells

value: WT


title: PDL205

status: Public on Dec 05 2022

type: SRA

city: Bangkok

first: Supreda

middle: Suphanatachat

last: Srithanyarat

address: 34 Henri-Dunant Rd. Pathumwan District

department: Periodontology

country: Thailand

institute: Faculty of Dentistry, Chulalongkorn University

library_source: transcriptomic

data_processing:
Illumina software used for basecalling.
Reads quality was checked, trimmed and filtered by FastQC and TrimGalore software.
Raw data fastq files were generated on NextSeq using bcl2fastq2 V2.19 software
Reads mapping with Homo sapiens UCSC hg38 using HISAT2
Transcripts quantification using HTSeq
Gene differential expression using DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

molecule: total RNA

organism: Homo sapiens

source_name: Human periodontal ligament-derived MSCs

growth_protocol: All cell types were cultured in T75 primariaTM culture flasks with  a-MEM plus 10% fetal bovine serum and 1% penicillin/streptomycin at 37 °C in a humidified 5% CO2 atmosphere. Cells from the 3rd – 6th passage were used in this study.

extract_protocol:
After treatment, total RNA was isolated using RNeasy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Human periodontal ligament-derived MSCs


title: hDEC (hiPSC-deerived dental epithelial cells)-2

city: Seoul

first: Han-Sung

last: Jung

address: 50, Yonsei-ro, Seodaemun-gu

department: Dental School

country: South Korea

institute: Yonsei University

source_name: epithelial cells

value: epithelial cells

tag: genotype


title: hDMC (hiPSC-deerived dental mesenchymal cells)-1


title: PDL203


title: hDEC (hiPSC-deerived dental epithelial cells)-1


title: PDL202


title: FLAGless, LEVO, rep3

city: Princeton

first: Juechun

last: Tang

state: NJ

address: 25 william streeet

department: Chemical and Biological Engineering

country: USA

institute: Princeton University

description:
LEVO 9
Mu_ori_MG1655.edit.fa
LEVO_sh.txt

library_source: genomic

data_processing:
Sequencing reads were trimmed using Trim Galore! (Galaxy Version 0.6.3) and mapped to Mu_origin 1 genome using BWA-MEM (version 0.7.17.1).
The resulting BAM files was filtered to retain reads that have a mapping quality >=20.
Read depth at each position was calculated using SAMtools depth taking the filtered BAM file as input. The maximum number of considered alignments was set to 100000 to prevent depth saturation with default upper boundary.
For further processing, we used GCS-seq pipeline avaialbe at (https://github.com/CathyTJC/GCS-seq/blob/main/GCS_calling.py). Briefly, we built an algorithm that searches for the 4-bp gap pattern using the sequencing coverage depth as the sole input to identify genome-wide gyrase cleavage sites
Assembly: E.coli MG1655 U00096.3 modified to incorporate the Mu sequence at designated locations. FASTA files are inlucded in the records
Supplementary files format and content: *.fasta/.fa files: file used for mapping of raw sequencing data
Supplementary files format and content: *.txt files (e.g., LEVO_Flag1.txt) contain the coverage depth at each position
Supplementary files format and content: *sh.txt/*strength.txt files contain the identified GCS genomic coordinates and assocaited cleavage strengths for each replicate

molecule: genomic DNA

organism: Escherichia coli

growth_protocol: Cells were culutred in 25ml M9 glucose media for 20 h O/N shaking at 37 ˚C to reach stationary phase.

extract_protocol:
All steps ares performed at 4˚C. The cultures were centrifuged at 4000 rpm for 10 mins at 4˚C, washed twice with 10 ml ice-cold PBS, and the cell pellet was store at -80 ˚C for at least 24 h. Cell pellet was thawed and resuspended in 2ml ChIP lysis buffer followed by incubation for ~1 h. After incubation, the samples were then sonicated for ~9-13 mins (10 sec on/10 sec off, 30% amplitude) to yield DNA fragments of ~300-500 bps using Q500 sonicator (500W, 110V with four probe horn assembly, QSONICA, Newtown, CT). Lysate was then centrifuged at 4000 rpm for 10 minutes and the cleared supernatant was kept for further processing. 20 µL supernatant was used as input controls and stored at -20˚C in low-bind tubes (Eppendorf, Enfield, CT). For each sample, 50μL Agarose Anti-FLAG M2 gel pack (Sigma-Aldrich, St. Louis, MO) was prepared by three successive washes with 1 ml TBS buffer and equilibration with 1 ml ChIP Lysis Buffer. Each wash was achieved by centrifugation at 8000xg for 30sec and removal of supernatant. 900µl supernatant was transferred to the prepared resin and incubated at 4 ˚C for 18 h on a tube rotator (Thermo Fisher Scientific, Waltham, MA). After 18 h of incubation, the samples were washed twice with 1 ml ChIP buffer and once in 1ml TE buffer at room temperature. Each wash was achieved by centrifugation at 8000 xg for 30sec and the removal of supernatant. TE buffer was added to both the ChIPped samples and thawed input controls to reach a total volume of 200 µl. 5µL of 20mg/ml proteinase K solution was added to the 200 µl sample and the sample was incubated for 3 h at 55˚C with occasional vortexing for mixing purpose. After 3 h of incubation, the samples were treated with 5 µl RNase (10 mg/ml) and further incubated for another 30 mins at 37˚C. Following the incubation, the samples were purified using Qiagen’s PCR Purification kit (Germantown, MD).
Library preparation was carried out using Accel-NGS 1S plus DNA library kit (Integrated DNA Technologies, formerly Swift Biosciences, Ann Arbor, MI) following manufacturer’s instruction. We used ~20 ng per sample for library preparation. For the clean-up steps, we used SPRI select purchased from Beckman Coulter (Indianapolis, IN). Swift Unique Dual Indexing Primers (X9096, Swift Biosciences, Ann Arbor, MI) were used for PCR indexing. The samples were mixed at equal amount (~50 ng) for a pooled library.

treatment_protocol: After 20 h incubation, the cells were treated with selected FQ (5 µg/ml LEVO or 5 µg/ml MOXI or 1 µg/ml CIP or 5 µg/ml GEMI or 5 µg/ml NOR) for 30 mins at 37˚C with shaking.

tag: strain

value: MG1655 pstS-glmS::cat-Mu gyrA-FLAG-kan

tag: chip antibody

tag: media

value: M9 glucose

tag: treatment

value: LEVO


title: ASP004_Postdose

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
FASTQ files were mapped using STAR to GRCh38 genome build
Gene counts were obtained using featureCounts on Gencodev31 annotations
Assembly: Gencodev31
Supplementary files format and content: gene_counts

source_name: PBMC

extract_protocol:
Venous blood was collected from subjects into ethylenediaminetetraacetic acid tubes.  Peripheral blood monocular cells (PBMCs) were isolated using SepMate tubes (STEMCELL Technologies) according to the manufacturer’s instructions.  Briefly, blood was diluted with phosphate buffered saline (PBS; Gibco) after plasma collection.  The diluted blood was then layered on top of Ficoll-Paque PLUS (Merck).  After centrifugation (1200 g, 10 min, brake on), the supernatant was poured into a 50 mL polypropylene tube.  Collected PBMCs were washed twice in PBS.  PBMCs were counted using a hemacytometer with trypan blue (Lonza) to determine cell viability.  Ribonucleic acid (RNA) was prepared using the PureLink RNA Mini kit (Thermo Fisher Scientific).
The total RNA was quantified using Qubit Fluorometer (ThermoFisher Scientific).  The purity was checked using NanoPhotometer spectrophotometer (Implen).  The integrity and quality of the RNA was assessed using Agilent Bioanalyzer 2100 system (Agilent Technologies) and agarose gel electrophoresis (1% agarose gel, 180 V, 16 min).  A total of 2 µg RNA from each sample was subjected to ribosomal RNA (rRNA) removal using Epicentre RiboZeroTM rRNA Removal Kit (Epicentre). The rRNA was cleaned up using ethanol precipitation method.  The Next Generation Sequencing (NGS) library was prepared using NEBNext UltraTM Directional RNA Library Prep Kit for Illumina (NEB).  In brief, the RNA were fragmented using divalent cations at 94°C in the presence of NEBNext First Strand Synthesis Reaction Buffer and Random Primers.  Subsequently, the first strand complementary deoxyribonucleic acid (cDNA) was synthesized using random hexamer and M-MulV reverse transcriptase and the second strand cDNA was synthesized using DNA Polymerase and RNAse H.  The dTTP was replaced by dUTP during the second strand cDNA synthesis. The double stranded cDNA fragment was converted to blunt end via end repair reaction and the NEBNext adapter (hairpin loop structure adapter) was ligated to the adenylated cDNA fragment using ligase.  Next, the second-strand cDNA was degraded with the aids of USER enzyme.  Size selection and sample purification was performed using AMPure XP Beads (Beckman Coulter).  Subsequently, Illumina sequencing adapter and indexes were added onto the cDNA fragment via PCR amplification (hereafter known as sequencing library).  The sequencing library was purified using Ampure XP Beads (Beckman Coulter).  The size distribution of the sequencing library was assessed using Agilent Bioanalyzer 2100 system (Agilent Technologies). The qualified sequencing library was loaded onto NovaSeq 6000 (Illumina) for sequencing using paired-end 150 sequencing strategy.  Raw data generated from the sequencer were demultiplexed and converted to FASTQ file using Illumina bcl2fastq.

tag: treatment/timpoint

value: Postdose

value: PBMC

tag: subject status

value: NIUA patient


title: FLAGless, LEVO, rep1, Input Control

description:
LEVO 10
Mu_ori_MG1655.edit.fa
LEVO_sh.txt

value: Anti-FLAG M2 gel pack (Sigma-Aldrich, St. Louis, MO)


title: hiPSC-2

source_name: Stem cell

value: Stem cell


title: FLAGless, LEVO, rep2

description:
LEVO 8
Mu_ori_MG1655.edit.fa
LEVO_sh.txt


title: PDL201


title: hiPSC-1


title: FLAGless, LEVO, rep1

description:
LEVO 7
Mu_ori_MG1655.edit.fa
LEVO_sh.txt


title: RS CRISPR mouse model 2 transplanted animal

city: Boston

first: Catherine

last: Wu

state: MA

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

description: recipient animal

data_processing:
demultiplexing of illumina BCL files with cellranger-atac mkfastq version 1.2
alignment of sequencing reads to a modified mm10 reference using cellranger-atac count version 1.2
calling of single cells using the default parameters in cellranger-atac
Assembly: mm10
Supplementary files format and content: processed fragment files from cellranger-atac count

organism: Mus

source_name: Spleen

extract_protocol:
direct harvest from murine spleens and cryopreservation in FBS + 10% DMSO
droplet-based scATAC-seq optimized for capture of mitochondrial DNA (mtscATAC-seq) as previously described (PMID 32788668, PMID 34112698)

tag: tissue

value: spleen

tag: disease state

value: CLL active disease


title: RS CRISPR mouse model 2 donor animal

description: parental animal


title: MG203

source_name: Human marginal gingival tissue-derived MSCs


title: FLAG, LEVO, rep3, Input Control

description:
LEVO 6
Mu_ori_MG1655.edit.fa
LEVO_sh.txt


title: MG202

value: Human marginal gingival tissue-derived MSCs


title: FLAG, LEVO, rep2, Input Control

description:
LEVO 5
Mu_ori_MG1655.edit.fa
LEVO_sh.txt


title: RS CRISPR mouse model transplanted animal bone marrow

description: recipient animal

source_name: Bone Marrow

value: bone marrow


title: IKZF3mut mouse model transplanted animal 2 peritoneum

description: recipient animal NSG

source_name: Peritoneum

value: peritoneum


title: FLAG, LEVO, rep1, Input Control

description:
LEVO 4
Mu_ori_MG1655.edit.fa
LEVO_sh.txt


title: FLAG, LEVO, rep3

description:
LEVO 3
Mu_ori_MG1655.edit.fa
LEVO_sh.txt


title: FLAG, LEVO, rep2

description:
LEVO 2
Mu_ori_MG1655.edit.fa
LEVO_sh.txt


title: MG205


title: MG201


title: IKZF3mut mouse model transplanted animal 2 spleen

description: recipient animal NSG


title: FLAG, LEVO, rep1

description:
LEVO 1
Mu_ori_MG1655.edit.fa
LEVO_sh.txt


title: C7_4h Dex_rep2

status: Public on Dec 04 2022

city: Farmington

first: Michael

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

description:
nascent RNA
4 hr Dex rep 2

data_processing:
Adapters trimmed with cutadapt
UMIs trimmed with fastx_trimmer
Aligned to hg38 with bowtie2
Files manipulated with samtools and seqOutBias
Assembly: hg38
Supplementary files format and content: stranded scaled bigWig counts
Library strategy: PRO-seq

extract_protocol:
Described in PMID 27492368
Described in PMID 27492368

treatment_protocol: Cells treated with 100nM Dexamethasone

tag: cell line

value: 4h Dex


title: C7_1h EtOH_rep2

description:
nascent RNA
1 hr EtOH rep 1

value: 1h EtOH


title: C7_4h Dex_rep1

description:
nascent RNA
4 hr Dex rep 1


title: C7_1h Dex_rep1

description:
nascent RNA
1 hr Dex rep 1

value: 1h Dex


title: C7_0h_rep1

description:
nascent RNA
No treatment


title: C7_1h Dex_rep2

description:
nascent RNA
1 hr Dex rep 2


title: PDL204

value: Human periodontal ligament-derived MSCs


title: Heat stress soybean flower stigma replicate 3

city: Columbia

first: Ron

last: Mittler

state: Missouri

address: University of Missouri,1201 Rollins St

department: Christopher S. Bond Life Sciences Center

institute: The Division of Plant Sciences and Technology

data_processing:
Sequencing, and bioinformatic analyses were performed by Novogene, Inc.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to G_max V2.1 whole genome using Hisat2 V2.2.1
Assembly: Glycine_max_v2.1.51
Supplementary files format and content: Matrix table FPKM values for all samples

organism: Glycine max

source_name: Stigma

growth_protocol: Soybean (Glycine max, cv Magellan) seeds were inoculated with Bradyrhizobium japonicum inoculum and germinated in Promix BX for a week in a growth chamber under short day growth condition (12-h light/12-h dark), at 28/24 ℃ day/night temperature and 500 μmol photons m-2 s-1. The temperature of the chambers was ramped from 24 to 28 °C between 6.00-8.00 AM and decreased to 24 °C from 16.00-20.00 PM. Seedlings were transplanted into pots containing 1 kg mixture of Promix BX and perlite mixed in ratio of 10:1 and soaked in 1 l of water-fertilizer mix (Zack’s classic blossom booster 10-30-20) . Plants were then grown under 28/24 ℃ day/night temperatures and 1000 μmol photons m-2 s-1 light intensity (12-h light/12-h dark photoperiod) for the next 16-18 days (until start of first open flower, R1 developmental stage) while irrigating twice a week with Zack’s classic blossom booster 10-30-20 fertilizer.

extract_protocol:
Soybean flower’s part sepal, anther, stigma and ovary were quickly separated from whole flower and immediately frozen in liquid nitrogen. The flower organs were collected from about 10-15 flowers were pooled together from 8-10 different plants for each biological repeat and total RNA was isolated using Qiagen Plant RNeasy mini kit.
RNA libraries for sequencing were prepared using standard Illumina protocols.

treatment_protocol: At R1, plants were randomly divided into control (CT), and 3 stress categories as water-deficit (WD), heat stress (HS), and combination of water-deficit and heat stress (WD+HS) in four different BDR16 growth chambers placed side-by-side in the same room. The relative humidity of chambers was maintained at about 50-60% in all chambers. The plants under WD and WD+HS treatments were irrigated with only 30% of the water available for, while plants in the CT and HS treatments were irrigated with 100% of the water available for transpiration. For HS and WD+HS treatments, temperature of chambers was maintained to 38 °C Day and 28 °C night temperature by ramping the temperature between 6.00-8.00 AM and decreasing it down to 28 °C between 16.00-20.00 PM.

value: Stigma

value: Heat stress


title: Combined water deficit and heat stress flower stigma replicate 3

value: Water deficit and heat stress


title: Combined water deficit and heat stress flower stigma replicate 2


title: Heat stress soybean flower stigma replicate 2


title: Heat stress soybean flower stigma replicate 1


title: MG204


title: Combined water deficit and heat stress flower stigma replicate 1


title: Water deficit soybean flower stigma replicate 2

value: Water deficit


title: Control soybean flower stigma replicate 3

value: No treatment


title: Water deficit soybean flower stigma replicate 3


title: Control soybean flower stigma replicate 2


title: Control soybean flower stigma replicate 1


title: Water deficit soybean flower stigma replicate 1


title: Combined water deficit and heat stress flower ovary replicate 3

source_name: Ovary

value: Ovary


title: Combined water deficit and heat stress flower ovary replicate 1


title: Heat stress soybean flower ovary replicate 1


title: Combined water deficit and heat stress flower ovary replicate 2


title: Heat stress soybean flower ovary replicate 2


title: Water deficit soybean flower ovary replicate 1


title: Water deficit soybean flower ovary replicate 2


title: Water deficit soybean flower ovary replicate 3


title: C7_1h EtOH_rep1

description:
nascent RNA
1 hr EtOH rep 1


title: Control soybean flower ovary replicate 2


title: Control soybean flower ovary replicate 3


title: Combined water deficit and heat stress flower anther replicate 1

source_name: Anther

value: Anther


title: Control soybean flower ovary replicate 1


title: Heat stress soybean flower anther replicate 3


title: Combined water deficit and heat stress flower anther replicate 3


title: Combined water deficit and heat stress flower anther replicate 2


title: Water deficit soybean flower anther replicate 3


title: Heat stress soybean flower anther replicate 2


title: Heat stress soybean flower ovary replicate 3


title: Heat stress soybean flower anther replicate 1


title: Control soybean flower anther replicate 2


title: Control soybean flower anther replicate 3


title: Combined water deficit and heat stress flower sepal replicate 3

source_name: Sepal

value: Sepal


title: Water deficit soybean flower anther replicate 1


title: Water deficit soybean flower anther replicate 2


title: Combined water deficit and heat stress flower sepal replicate 1


title: Control soybean flower anther replicate 1


title: Combined water deficit and heat stress flower sepal replicate 2


title: Heat stress soybean flower sepal replicate 2


title: Water deficit soybean flower sepal replicate 2


title: Water deficit soybean flower sepal replicate 1


title: Control soybean flower sepal replicate 1


title: Control soybean flower sepal replicate 3


title: Heat stress soybean flower sepal replicate 1


title: Water deficit soybean flower sepal replicate 3


title: Control soybean flower sepal replicate 2


title: long read RNA-seq from HL-60 (ENCLB605OTC)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR278ZPI/
***************
biological replicate number: 2
technical replicate number: 1
description: HL-60 derived M2A macrophages (12hr)
experiment encode accession: ENCSR278ZPI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB605OTC
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

source_name: Homo sapiens HL-60 cell line treated with 10 uM phorbol 13-acetate 12-myristate for 120 hours, 10 ng/mL interleukin-13 for 12 hours, 10 ng/mL interleukin-4 for 12 hours

tag: line

value: cell line

tag: description

value: HL-60 derived M2A macrophages (12hr)

tag: biosample encode accession

tag: organism

value: Homo sapiens

tag: Sex

value: female

tag: health state

value: acute promyelocytic leukemia

tag: dev stage

value: adult

tag: age

value: 36 year

tag: lab

value: Ali Mortazavi, UCI

tag: source

value: ATCC

tag: treatments

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:120; duration_units:hour; treatment_term_id:UniProtKB:P35225; treatment_term_name:interleukin-13; treatment_type:protein; duration:12; duration_units:hour; treatment_term_id:UniProtKB:P05112; treatment_term_name:interleukin-4; treatment_type:protein; duration:12; duration_units:hour;

tag: link

value: ENCBS756IEB at ENCODE; https://www.encodeproject.org/ENCBS756IEB/

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


title: long read RNA-seq from OCI-LY7 (ENCLB265DVR)

description:
https://www.encodeproject.org/experiments/ENCSR700SUP/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_503, ENC4_504 OCI-LY7 rep1 human non-Hodgkin lymphoma
experiment encode accession: ENCSR700SUP
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB265DVR
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens OCI-LY7 cell line

value: male

value: B cell lymphoma

value: 48 year

value: Mats Ljungman, UMichigan

value: DSMZ

value: ENCBS112SEO at ENCODE; https://www.encodeproject.org/ENCBS112SEO/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/


title: long read RNA-seq from HL-60 (ENCLB611DPF)

description:
https://www.encodeproject.org/experiments/ENCSR278ZPI/
***************
biological replicate number: 1
technical replicate number: 1
description: HL-60 derived M2A macrophages (12hr)
experiment encode accession: ENCSR278ZPI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB611DPF
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: cell line

value: HL-60 derived M2A macrophages (12hr)

value: Homo sapiens

value: ENCBS982BVD at ENCODE; https://www.encodeproject.org/ENCBS982BVD/


title: long read RNA-seq from mucosa of descending colon (ENCLB023HEL)

description:
https://www.encodeproject.org/experiments/ENCSR997RFW/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_77 W76 mucosa of descending colon
experiment encode accession: ENCSR997RFW
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-06-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB023HEL
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 male adult (40 years) mucosa of descending colon tissue, preserved by flash-freezing

value: mucosa of descending colon

value: tissue

value: adult

value: 40 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS105TFS at ENCODE; https://www.encodeproject.org/ENCBS105TFS/

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


title: long read RNA-seq from H1 (ENCLB519DIC)

description:
https://www.encodeproject.org/experiments/ENCSR271KEJ/
***************
biological replicate number: 2
technical replicate number: 1
description: LRGASP H1 ES
experiment encode accession: ENCSR271KEJ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-10-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB519DIC
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.

source_name: Homo sapiens H1 cell line

value: male

value: healthy

value: embryonic

value: unknown

value: Barbara Wold, Caltech

value: René Maehr

value: ENCBS872CFG at ENCODE; https://www.encodeproject.org/ENCBS872CFG/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: long read RNA-seq from H1 (ENCLB785VEF)

description:
https://www.encodeproject.org/experiments/ENCSR271KEJ/
***************
biological replicate number: 3
technical replicate number: 1
description: LRGASP H1 ES
experiment encode accession: ENCSR271KEJ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-10-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB785VEF
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.

value: cell line

value: not collected

value: ENCBS667PZC at ENCODE; https://www.encodeproject.org/ENCBS667PZC/


title: long read RNA-seq from H1 (ENCLB968WUZ)

description:
https://www.encodeproject.org/experiments/ENCSR271KEJ/
***************
biological replicate number: 1
technical replicate number: 1
description: LRGASP H1 ES
experiment encode accession: ENCSR271KEJ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-10-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB968WUZ
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.

value: ENCBS664DSZ at ENCODE; https://www.encodeproject.org/ENCBS664DSZ/


title: Heat stress soybean flower sepal replicate 3

value: Sepal

tag: treatment

value: Heat stress


title: long read RNA-seq from posterior vena cava (ENCLB065XGZ)

description:
https://www.encodeproject.org/experiments/ENCSR853YZN/
***************
biological replicate number: 1
technical replicate number: 1
description: W71 posterior vena cava ENC4_101
experiment encode accession: ENCSR853YZN
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-06-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB065XGZ
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 (47 years) posterior vena cava tissue, preserved by flash-freezing

value: posterior vena cava

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: ENCBS741WNS at ENCODE; https://www.encodeproject.org/ENCBS741WNS/

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


title: long read RNA-seq from left cardiac atrium (ENCLB284PZZ)

description:
https://www.encodeproject.org/experiments/ENCSR424QFN/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_60 W73 left cardiac atrium
experiment encode accession: ENCSR424QFN
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-06-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB284PZZ
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) left cardiac atrium tissue, preserved by flash-freezing

value: left cardiac atrium

value: 59 year

value: ENCBS034QSD at ENCODE; https://www.encodeproject.org/ENCBS034QSD/

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


title: long read RNA-seq from HL-60 (ENCLB622SOZ)

description:
https://www.encodeproject.org/experiments/ENCSR398SKD/
***************
biological replicate number: 1
technical replicate number: 1
description: HL-60 derived M1 macrophages (72hr)
experiment encode accession: ENCSR398SKD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB622SOZ
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 HL-60 cell line treated with 10 uM phorbol 13-acetate 12-myristate for 120 hours, 100 ng/mL interferon gamma for 72 hours, 100 ng/mL lipopolysaccharide for 72 hours

value: cell line

value: HL-60 derived M1 macrophages (72hr)

value: Homo sapiens

value: acute promyelocytic leukemia

value: 36 year

value: Ali Mortazavi, UCI

value: ATCC

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:120; duration_units:hour; treatment_term_id:UniProtKB:P01579; treatment_term_name:interferon gamma; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:CHEBI:16412; treatment_term_name:lipopolysaccharide; treatment_type:chemical; duration:72; duration_units:hour;

value: ENCBS013TYT at ENCODE; https://www.encodeproject.org/ENCBS013TYT/

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


title: long read RNA-seq from middle frontal area 46 (ENCLB497QJE)

description:
https://www.encodeproject.org/experiments/ENCSR462COR/
***************
biological replicate number: 1
technical replicate number: 1
description: RUSH brain E3348003
experiment encode accession: ENCSR462COR
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-04-07
lab: Ali Mortazavi, UCI
library encode accession: ENCLB497QJE
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens female adult (90 or above years) with Alzheimer's disease; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: human_brain_Rush ID_E3348003_BS71

value: female

value: adult

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS127CGY at ENCODE; https://www.encodeproject.org/ENCBS127CGY/

value: Derived from ENCODE donor ENCDO730UYW; https://www.encodeproject.org/ENCDO730UYW/


title: long read RNA-seq from left colon (ENCLB204OWG)

description:
https://www.encodeproject.org/experiments/ENCSR450GAR/
***************
biological replicate number: 1
technical replicate number: 1
description: W73 left colon ENC4_87
experiment encode accession: ENCSR450GAR
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-06-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB204OWG
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) left colon tissue, preserved by flash-freezing

value: left colon

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS908TVF at ENCODE; https://www.encodeproject.org/ENCBS908TVF/

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


title: long read RNA-seq from HL-60 (ENCLB559VQN)

description:
https://www.encodeproject.org/experiments/ENCSR930GRQ/
***************
biological replicate number: 1
technical replicate number: 1
description: HL-60 derived M2A macrophages (24hr)
experiment encode accession: ENCSR930GRQ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB559VQN
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens HL-60 cell line treated with 10 uM phorbol 13-acetate 12-myristate for 120 hours, 10 ng/mL interleukin-13 for 24 hours, 10 ng/mL interleukin-4 for 24 hours

value: cell line

value: HL-60 derived M2A macrophages (24hr)

value: Homo sapiens

value: acute promyelocytic leukemia

value: 36 year

value: Ali Mortazavi, UCI

value: ATCC

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:120; duration_units:hour; treatment_term_id:UniProtKB:P35225; treatment_term_name:interleukin-13; treatment_type:protein; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P05112; treatment_term_name:interleukin-4; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS172TZS at ENCODE; https://www.encodeproject.org/ENCBS172TZS/

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


title: long read RNA-seq from HL-60 (ENCLB825EPI)

description:
https://www.encodeproject.org/experiments/ENCSR398SKD/
***************
biological replicate number: 2
technical replicate number: 1
description: HL-60 derived M1 macrophages (72hr)
experiment encode accession: ENCSR398SKD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB825EPI
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

value: HL-60 derived M1 macrophages (72hr)

value: female

value: adult

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:120; duration_units:hour; treatment_term_id:UniProtKB:P01579; treatment_term_name:interferon gamma; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:CHEBI:16412; treatment_term_name:lipopolysaccharide; treatment_type:chemical; duration:72; duration_units:hour;

value: ENCBS807YLY at ENCODE; https://www.encodeproject.org/ENCBS807YLY/


title: long read RNA-seq from HL-60 (ENCLB101LYE)

description:
https://www.encodeproject.org/experiments/ENCSR930GRQ/
***************
biological replicate number: 2
technical replicate number: 1
description: HL-60 derived M2A macrophages (24hr)
experiment encode accession: ENCSR930GRQ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB101LYE
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: ENCBS379TMH at ENCODE; https://www.encodeproject.org/ENCBS379TMH/


title: long read RNA-seq from aorta (ENCLB084SNO)

description:
https://www.encodeproject.org/experiments/ENCSR700EBI/
***************
biological replicate number: 1
technical replicate number: 1
description: W61 aorta ENC4_88
experiment encode accession: ENCSR700EBI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-06-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB084SNO
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 (41 years) aorta tissue, preserved by flash-freezing

value: aorta

value: tissue

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS481ZAB at ENCODE; https://www.encodeproject.org/ENCBS481ZAB/

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


title: long read RNA-seq from middle frontal area 46 (ENCLB217GZS)

description:
https://www.encodeproject.org/experiments/ENCSR463IDK/
***************
biological replicate number: 1
technical replicate number: 1
description: RUSH brain E5194210
experiment encode accession: ENCSR463IDK
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-04-07
lab: Ali Mortazavi, UCI
library encode accession: ENCLB217GZS
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens female adult (79 years) middle frontal area 46 tissue

value: middle frontal area 46

value: Homo sapiens

value: 79 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS411JUI at ENCODE; https://www.encodeproject.org/ENCBS411JUI/

value: Derived from ENCODE donor ENCDO609ZOG; https://www.encodeproject.org/ENCDO609ZOG/


title: long read RNA-seq from MCF 10A (ENCLB481JDU)

description:
https://www.encodeproject.org/experiments/ENCSR813UIT/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_515, ENC4_516 MCF10A rep1 human female pre-neoplastic mammary epithelial cells
experiment encode accession: ENCSR813UIT
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB481JDU
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens MCF 10A cell line

value: MCF 10A

value: cell line

value: female

value: fibrocystic disease

value: adult

value: 36 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS863SFU at ENCODE; https://www.encodeproject.org/ENCBS863SFU/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: long read RNA-seq from A673 (ENCLB767XEK)

description:
https://www.encodeproject.org/experiments/ENCSR989ZYL/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_509 , ENC4_510 A673 rep1 human Ewing sarcoma (bone or soft tissue sarcoma)
experiment encode accession: ENCSR989ZYL
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB767XEK
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens A673 cell line

value: child

value: 15 year

value: ENCBS119CST at ENCODE; https://www.encodeproject.org/ENCBS119CST/

value: Derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/


title: long read RNA-seq from MCF 10A (ENCLB653SQB)

description:
https://www.encodeproject.org/experiments/ENCSR813UIT/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_515, ENC4_516 MCF10A rep1 human female pre-neoplastic mammary epithelial cells
experiment encode accession: ENCSR813UIT
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB653SQB
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: Homo sapiens

value: ENCBS534SPQ at ENCODE; https://www.encodeproject.org/ENCBS534SPQ/


title: long read RNA-seq from OCI-LY7 (ENCLB336XHW)

description:
https://www.encodeproject.org/experiments/ENCSR700SUP/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_503, ENC4_504 OCI-LY7 rep1 human non-Hodgkin lymphoma
experiment encode accession: ENCSR700SUP
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB336XHW
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: male

value: B cell lymphoma

value: 48 year

value: DSMZ

value: ENCBS869GJQ at ENCODE; https://www.encodeproject.org/ENCBS869GJQ/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/


title: long read RNA-seq from PC-9 (ENCLB292ZUN)

description:
https://www.encodeproject.org/experiments/ENCSR916JDV/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_501, ENC4_502 PC-9 rep1 human lung adenocarcinoma
experiment encode accession: ENCSR916JDV
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB292ZUN
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens PC-9 cell line

value: cell line

value: not collected

value: unknown

value: Sigma

value: ENCBS021NLC at ENCODE; https://www.encodeproject.org/ENCBS021NLC/

value: Derived from ENCODE donor ENCDO647UHQ; https://www.encodeproject.org/ENCDO647UHQ/


title: long read RNA-seq from PC-9 (ENCLB581JJT)

description:
https://www.encodeproject.org/experiments/ENCSR916JDV/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_501, ENC4_502 PC-9 rep1 human lung adenocarcinoma
experiment encode accession: ENCSR916JDV
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB581JJT
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: Mats Ljungman, UMichigan

value: ENCBS511ZVG at ENCODE; https://www.encodeproject.org/ENCBS511ZVG/


title: long read RNA-seq from A673 (ENCLB345FIS)

description:
https://www.encodeproject.org/experiments/ENCSR989ZYL/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_509 , ENC4_510 A673 rep1 human Ewing sarcoma (bone or soft tissue sarcoma)
experiment encode accession: ENCSR989ZYL
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB345FIS
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: female

value: child

value: 15 year

value: ATCC

value: ENCBS060KJN at ENCODE; https://www.encodeproject.org/ENCBS060KJN/

value: Derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/


title: long read RNA-seq from right cardiac atrium (ENCLB718EZY)

description:
https://www.encodeproject.org/experiments/ENCSR728TXV/
***************
biological replicate number: 1
technical replicate number: 1
description: W76 right cardiac atrium ENC4_84
experiment encode accession: ENCSR728TXV
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-06-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB718EZY
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

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

value: right cardiac atrium

value: tissue

value: male

value: adult

value: 40 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS966NKN at ENCODE; https://www.encodeproject.org/ENCBS966NKN/

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


title: long read RNA-seq from lower lobe of right lung (ENCLB922GXI)

description:
https://www.encodeproject.org/experiments/ENCSR323XND/
***************
biological replicate number: 1
technical replicate number: 1
description: W78 lower lobe of right lung ENC4_83
experiment encode accession: ENCSR323XND
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-06-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB922GXI
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

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

value: lower lobe of right lung

value: 60 year

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

value: ENCBS870VUM at ENCODE; https://www.encodeproject.org/ENCBS870VUM/

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


title: long read RNA-seq from middle frontal area 46 (ENCLB376UFG)

description:
https://www.encodeproject.org/experiments/ENCSR316ZTD/
***************
biological replicate number: 1
technical replicate number: 1
description: RUSH brain E6207143
experiment encode accession: ENCSR316ZTD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-04-07
lab: Ali Mortazavi, UCI
library encode accession: ENCLB376UFG
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: middle frontal area 46

value: Homo sapiens

value: female

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS481WHG at ENCODE; https://www.encodeproject.org/ENCBS481WHG/

value: Derived from ENCODE donor ENCDO597SRH; https://www.encodeproject.org/ENCDO597SRH/


title: long read RNA-seq from endothelial cell of umbilical vein (ENCLB017LJW)

description:
https://www.encodeproject.org/experiments/ENCSR687RWI/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_505, ENC4_506 HUVEC rep1 primary human umbilical vein endothelial cell
experiment encode accession: ENCSR687RWI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-12-13
lab: Ali Mortazavi, UCI
library encode accession: ENCLB017LJW
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens newborn endothelial of umbilical vein primary cell

value: endothelial cell of umbilical vein

value: primary cell

value: not collected

value: unknown

value: newborn

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS820SXP at ENCODE; https://www.encodeproject.org/ENCBS820SXP/

value: Derived from ENCODE donor ENCDO000AAS; https://www.encodeproject.org/ENCDO000AAS/


title: long read RNA-seq from middle frontal area 46 (ENCLB807KIT)

description:
https://www.encodeproject.org/experiments/ENCSR690QHM/
***************
biological replicate number: 1
technical replicate number: 1
description: RUSH brain E6341028
experiment encode accession: ENCSR690QHM
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-04-07
lab: Ali Mortazavi, UCI
library encode accession: ENCLB807KIT
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: middle frontal area 46

value: tissue

value: adult

value: ENCBS660AUE at ENCODE; https://www.encodeproject.org/ENCBS660AUE/

value: Derived from ENCODE donor ENCDO223NTQ; https://www.encodeproject.org/ENCDO223NTQ/


title: long read RNA-seq from middle frontal area 46 (ENCLB728VLY)

description:
https://www.encodeproject.org/experiments/ENCSR257YUB/
***************
biological replicate number: 1
technical replicate number: 1
description: RUSH brain E4368365
experiment encode accession: ENCSR257YUB
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-04-07
lab: Ali Mortazavi, UCI
library encode accession: ENCLB728VLY
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens male adult (90 or above years) with Alzheimer's disease; middle frontal area 46 tissue

value: Homo sapiens

value: male

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS644WSW at ENCODE; https://www.encodeproject.org/ENCBS644WSW/

value: Derived from ENCODE donor ENCDO197QVG; https://www.encodeproject.org/ENCDO197QVG/


title: long read RNA-seq from psoas muscle (ENCLB199XDS)

description:
https://www.encodeproject.org/experiments/ENCSR243DYK/
***************
biological replicate number: 1
technical replicate number: 1
description: W80 psoas muscle ENC4_86
experiment encode accession: ENCSR243DYK
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-06-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB199XDS
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 (61 years) psoas muscle tissue, preserved by flash-freezing

value: psoas muscle

value: female

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS326LXR at ENCODE; https://www.encodeproject.org/ENCBS326LXR/

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


title: long read RNA-seq from middle frontal area 46 (ENCLB680WQI)

description:
https://www.encodeproject.org/experiments/ENCSR697ASE/
***************
biological replicate number: 1
technical replicate number: 1
description: RUSH brain E7948794
experiment encode accession: ENCSR697ASE
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-04-07
lab: Ali Mortazavi, UCI
library encode accession: ENCLB680WQI
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: middle frontal area 46

value: tissue

value: adult

value: ENCBS422TMB at ENCODE; https://www.encodeproject.org/ENCBS422TMB/

value: Derived from ENCODE donor ENCDO470GFA; https://www.encodeproject.org/ENCDO470GFA/


title: long read RNA-seq from middle frontal area 46 (ENCLB779KWV)

description:
https://www.encodeproject.org/experiments/ENCSR169YNI/
***************
biological replicate number: 1
technical replicate number: 1
description: RUSH brain E7461192
experiment encode accession: ENCSR169YNI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-04-07
lab: Ali Mortazavi, UCI
library encode accession: ENCLB779KWV
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue

value: human_brain_Rush ID_E7461192_BS73

value: Homo sapiens

value: 90 or above year

value: Barbara Wold, Caltech

value: ENCBS086OWN at ENCODE; https://www.encodeproject.org/ENCBS086OWN/

value: Derived from ENCODE donor ENCDO218FFZ; https://www.encodeproject.org/ENCDO218FFZ/


title: long read RNA-seq from HL-60 (ENCLB054OEH)

description:
https://www.encodeproject.org/experiments/ENCSR159ICU/
***************
biological replicate number: 2
technical replicate number: 1
description: HL-60 derived M2A macrophages (72hr)
experiment encode accession: ENCSR159ICU
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB054OEH
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 HL-60 cell line treated with 10 uM phorbol 13-acetate 12-myristate for 120 hours, 10 ng/mL interleukin-13 for 72 hours, 10 ng/mL interleukin-4 for 72 hours

value: cell line

value: HL-60 derived M2A macrophages (72hr)

value: female

value: acute promyelocytic leukemia

value: 36 year

value: Ali Mortazavi, UCI

value: ATCC

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:120; duration_units:hour; treatment_term_id:UniProtKB:P35225; treatment_term_name:interleukin-13; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P05112; treatment_term_name:interleukin-4; treatment_type:protein; duration:72; duration_units:hour;

value: ENCBS538TKB at ENCODE; https://www.encodeproject.org/ENCBS538TKB/

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


title: long read RNA-seq from endothelial cell of umbilical vein (ENCLB149WJH)

description:
https://www.encodeproject.org/experiments/ENCSR687RWI/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_505, ENC4_506 HUVEC rep1 primary human umbilical vein endothelial cell
experiment encode accession: ENCSR687RWI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-12-13
lab: Ali Mortazavi, UCI
library encode accession: ENCLB149WJH
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: endothelial cell of umbilical vein

value: primary cell

value: not collected

value: newborn

value: Mats Ljungman, UMichigan

value: Lonza

value: unknown

value: ENCBS023JCN at ENCODE; https://www.encodeproject.org/ENCBS023JCN/

value: Derived from ENCODE donor ENCDO000AAS; https://www.encodeproject.org/ENCDO000AAS/


title: long read RNA-seq from HL-60 (ENCLB529IWA)

description:
https://www.encodeproject.org/experiments/ENCSR159ICU/
***************
biological replicate number: 1
technical replicate number: 1
description: HL-60 derived M2A macrophages (72hr)
experiment encode accession: ENCSR159ICU
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB529IWA
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

value: cell line

value: HL-60 derived M2A macrophages (72hr)

value: Homo sapiens

value: female

value: adult

value: ENCBS805RWS at ENCODE; https://www.encodeproject.org/ENCBS805RWS/


title: long read RNA-seq from middle frontal area 46 (ENCLB012IWP)

description:
https://www.encodeproject.org/experiments/ENCSR205QMF/
***************
biological replicate number: 1
technical replicate number: 1
description: RUSH brain E5115600
experiment encode accession: ENCSR205QMF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-04-07
lab: Ali Mortazavi, UCI
library encode accession: ENCLB012IWP
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens female adult (88 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 88 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS105DDE at ENCODE; https://www.encodeproject.org/ENCBS105DDE/

value: Derived from ENCODE donor ENCDO669IVL; https://www.encodeproject.org/ENCDO669IVL/


title: long read RNA-seq from endodermal cell (ENCLB446WHN)

description:
https://www.encodeproject.org/experiments/ENCSR127HKN/
***************
biological replicate number: 1
technical replicate number: 1
description: LRGASP H1 definitive endoderm
experiment encode accession: ENCSR127HKN
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-10-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB446WHN
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.

source_name: Homo sapiens male embryo endodermal in vitro differentiated cells

value: endodermal cell

value: in vitro differentiated cells

value: male

value: embryonic

value: not collected

value: René Maehr

value: healthy

value: ENCBS464AKI at ENCODE; https://www.encodeproject.org/ENCBS464AKI/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: long read RNA-seq from endodermal cell (ENCLB923CKD)

description:
https://www.encodeproject.org/experiments/ENCSR127HKN/
***************
biological replicate number: 2
technical replicate number: 1
description: LRGASP H1 definitive endoderm
experiment encode accession: ENCSR127HKN
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-10-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB923CKD
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.

value: ENCBS012DYC at ENCODE; https://www.encodeproject.org/ENCBS012DYC/


title: long read RNA-seq from endodermal cell (ENCLB953CWG)

description:
https://www.encodeproject.org/experiments/ENCSR127HKN/
***************
biological replicate number: 3
technical replicate number: 1
description: LRGASP H1 definitive endoderm
experiment encode accession: ENCSR127HKN
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-10-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB953CWG
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.

value: unknown

value: ENCBS971DDS at ENCODE; https://www.encodeproject.org/ENCBS971DDS/


title: long read RNA-seq from HL-60 (ENCLB268CWN)

description:
https://www.encodeproject.org/experiments/ENCSR121FDE/
***************
biological replicate number: 1
technical replicate number: 1
description: HL-60 derived M1 macrophages (12hr)
experiment encode accession: ENCSR121FDE
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB268CWN
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens HL-60 cell line treated with 10 uM phorbol 13-acetate 12-myristate for 120 hours, 100 ng/mL lipopolysaccharide for 12 hours, 100 ng/mL interferon gamma for 12 hours

value: cell line

value: HL-60 derived M1 macrophages (12hr)

value: Homo sapiens

value: female

value: acute promyelocytic leukemia

value: adult

value: 36 year

value: Ali Mortazavi, UCI

value: ATCC

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:120; duration_units:hour; treatment_term_id:CHEBI:16412; treatment_term_name:lipopolysaccharide; treatment_type:chemical; duration:12; duration_units:hour; treatment_term_id:UniProtKB:P01579; treatment_term_name:interferon gamma; treatment_type:protein; duration:12; duration_units:hour;

value: ENCBS380AKB at ENCODE; https://www.encodeproject.org/ENCBS380AKB/

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


title: long read RNA-seq from Calu3 (ENCLB814UZZ)

description:
https://www.encodeproject.org/experiments/ENCSR583KCB/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_513, ENC4_514 Calu-3 rep1 human non-small cell lung cancer (epithelial)
experiment encode accession: ENCSR583KCB
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB814UZZ
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens Calu3 cell line

value: male

value: Lung adenocarcinoma

value: 25 year

value: Mats Ljungman, UMichigan

value: ENCBS806IYJ at ENCODE; https://www.encodeproject.org/ENCBS806IYJ/

value: Derived from ENCODE donor ENCDO109DGE; https://www.encodeproject.org/ENCDO109DGE/


title: long read RNA-seq from Calu3 (ENCLB905SCM)

description:
https://www.encodeproject.org/experiments/ENCSR583KCB/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_513, ENC4_514 Calu-3 rep1 human non-small cell lung cancer (epithelial)
experiment encode accession: ENCSR583KCB
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB905SCM
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: cell line

value: ENCBS961BBX at ENCODE; https://www.encodeproject.org/ENCBS961BBX/


title: long read RNA-seq from Caco-2 (ENCLB240AAX)

description:
https://www.encodeproject.org/experiments/ENCSR580IDG/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_511, ENC4_512 Caco-2 rep1 human colorectal adenocarcinoma (epithelial)
experiment encode accession: ENCSR580IDG
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB240AAX
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens Caco-2 cell line

value: Homo sapiens

value: colorectal adenocarcinoma

value: 72 year

value: ENCBS075YII at ENCODE; https://www.encodeproject.org/ENCBS075YII/

value: Derived from ENCODE donor ENCDO000ACR; https://www.encodeproject.org/ENCDO000ACR/


title: long read RNA-seq from Caco-2 (ENCLB315YZP)

description:
https://www.encodeproject.org/experiments/ENCSR580IDG/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_511, ENC4_512 Caco-2 rep1 human colorectal adenocarcinoma (epithelial)
experiment encode accession: ENCSR580IDG
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB315YZP
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: adult

value: ATCC

value: ENCBS020DQC at ENCODE; https://www.encodeproject.org/ENCBS020DQC/


title: long read RNA-seq from middle frontal area 46 (ENCLB770MYB)

description:
https://www.encodeproject.org/experiments/ENCSR094NFM/
***************
biological replicate number: 1
technical replicate number: 1
description: RUSH brain E4368365
experiment encode accession: ENCSR094NFM
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-04-07
lab: Ali Mortazavi, UCI
library encode accession: ENCLB770MYB
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: middle frontal area 46

value: tissue

value: female

value: 90 or above year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS819UHF at ENCODE; https://www.encodeproject.org/ENCBS819UHF/

value: Derived from ENCODE donor ENCDO250PFZ; https://www.encodeproject.org/ENCDO250PFZ/


title: long read RNA-seq from upper lobe of right lung (ENCLB855HKW)

description:
https://www.encodeproject.org/experiments/ENCSR096QUP/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_82 W78 upper lobe of right lung
experiment encode accession: ENCSR096QUP
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-06-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB855HKW
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) upper lobe of right lung tissue, preserved by flash-freezing

value: upper lobe of right lung

value: male

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS496CPG at ENCODE; https://www.encodeproject.org/ENCBS496CPG/

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


title: long read RNA-seq from HL-60 (ENCLB045HKM)

description:
https://www.encodeproject.org/experiments/ENCSR546DFO/
***************
biological replicate number: 1
technical replicate number: 1
description: HL-60 derived M0 macrophages
experiment encode accession: ENCSR546DFO
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB045HKM
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 HL-60 cell line treated with 10 uM phorbol 13-acetate 12-myristate for 120 hours

value: cell line

value: HL-60 derived M0 macrophages

value: Homo sapiens

value: acute promyelocytic leukemia

value: adult

value: 36 year

value: Ali Mortazavi, UCI

value: ATCC

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:120; duration_units:hour;

value: ENCBS848YJL at ENCODE; https://www.encodeproject.org/ENCBS848YJL/

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


title: long read RNA-seq from HL-60 (ENCLB463QEM)

description:
https://www.encodeproject.org/experiments/ENCSR546DFO/
***************
biological replicate number: 2
technical replicate number: 1
description: HL-60 derived M0 macrophages
experiment encode accession: ENCSR546DFO
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB463QEM
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

value: female

value: ENCBS665LKP at ENCODE; https://www.encodeproject.org/ENCBS665LKP/


title: long read RNA-seq from cardiac septum (ENCLB530WHJ)

description:
https://www.encodeproject.org/experiments/ENCSR549ELD/
***************
biological replicate number: 1
technical replicate number: 1
description: W61 cardiac septum ENC4_92
experiment encode accession: ENCSR549ELD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-06-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB530WHJ
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 (41 years) cardiac septum tissue

value: cardiac septum

value: tissue

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS731WFT at ENCODE; https://www.encodeproject.org/ENCBS731WFT/

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


title: long read RNA-seq from adrenal gland (ENCLB748SEP)

description:
https://www.encodeproject.org/experiments/ENCSR563RLX/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_29 W61 adrenal gland
experiment encode accession: ENCSR563RLX
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB748SEP
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

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

value: adrenal gland

value: adult

value: ENCBS629ZGV at ENCODE; https://www.encodeproject.org/ENCBS629ZGV/


title: long read RNA-seq from chondrocyte (ENCLB201KID)

description:
https://www.encodeproject.org/experiments/ENCSR470HYQ/
***************
biological replicate number: 3
technical replicate number: 1
description: ENC209, ENC210, ENC211 - H9 derived chondrocytes
experiment encode accession: ENCSR470HYQ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB201KID
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

source_name: Homo sapiens female embryo (5 days) chondrocyte in vitro differentiated cells

value: chondrocyte

value: in vitro differentiated cells

value: WA09 derived chondrocytes

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS668AFC at ENCODE; https://www.encodeproject.org/ENCBS668AFC/

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


title: long read RNA-seq from chondrocyte (ENCLB165ZXK)

description:
https://www.encodeproject.org/experiments/ENCSR470HYQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC209, ENC210, ENC211 - H9 derived chondrocytes
experiment encode accession: ENCSR470HYQ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB165ZXK
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

value: female

value: ENCBS524YKH at ENCODE; https://www.encodeproject.org/ENCBS524YKH/


title: long read RNA-seq from chondrocyte (ENCLB175ASW)

description:
https://www.encodeproject.org/experiments/ENCSR470HYQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC209, ENC210, ENC211 - H9 derived chondrocytes
experiment encode accession: ENCSR470HYQ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB175ASW
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

value: ENCBS434FZQ at ENCODE; https://www.encodeproject.org/ENCBS434FZQ/


title: long read RNA-seq from WTC11 (ENCLB377SXJ)

description:
https://www.encodeproject.org/experiments/ENCSR507JOF/
***************
biological replicate number: 1
technical replicate number: 1
description: LRGASP WTC11
experiment encode accession: ENCSR507JOF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-05-04
lab: Ali Mortazavi, UCI
library encode accession: ENCLB377SXJ
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., ERCC reference spike-ins used for LRGASP. Note that this does NOT contain the SIRVs that are a part of this mix (found in ENCSR759PLA).

source_name: Homo sapiens WTC11 cell line

value: cell line

value: Induced pluripotent stem cell line derived from adult skin (leg) fibroblasts; subject clinically normal

value: male

value: 30 year

value: Barbara Wold, Caltech

value: Yiing Lin, MD, PhD

tag: passage number

value: ENCBS944CBA at ENCODE; https://www.encodeproject.org/ENCBS944CBA/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: long read RNA-seq from WTC11 (ENCLB901LCB)

description:
https://www.encodeproject.org/experiments/ENCSR507JOF/
***************
biological replicate number: 3
technical replicate number: 1
description: LRGASP WTC11
experiment encode accession: ENCSR507JOF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-05-04
lab: Ali Mortazavi, UCI
library encode accession: ENCLB901LCB
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., ERCC reference spike-ins used for LRGASP. Note that this does NOT contain the SIRVs that are a part of this mix (found in ENCSR759PLA).

value: adult

value: ENCBS474NOC at ENCODE; https://www.encodeproject.org/ENCBS474NOC/


title: long read RNA-seq from mammary epithelial cell (ENCLB325VZQ)

description:
https://www.encodeproject.org/experiments/ENCSR998KIZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_507, ENC4_508 HMEC rep1 primary human mammary epithelial cells
experiment encode accession: ENCSR998KIZ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-12-13
lab: Ali Mortazavi, UCI
library encode accession: ENCLB325VZQ
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens female mammary epithelial primary cell

value: mammary epithelial cell

value: primary cell

value: unknown

value: not collected

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS710VQU at ENCODE; https://www.encodeproject.org/ENCBS710VQU/

value: Derived from ENCODE donor ENCDO343AAA; https://www.encodeproject.org/ENCDO343AAA/


title: long read RNA-seq from K562 (ENCLB986KGX)

description:
https://www.encodeproject.org/experiments/ENCSR917JIA/
***************
biological replicate number: 2
technical replicate number: 1
description: OnT dRNA of K562
experiment encode accession: ENCSR917JIA
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-03-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB986KGX
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

source_name: Homo sapiens K562 cell line

value: cell line

value: Homo sapiens

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Ali Mortazavi, UCI

value: ATCC

value: ENCBS472HJD at ENCODE; https://www.encodeproject.org/ENCBS472HJD/

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


title: long read RNA-seq from K562 (ENCLB743TEQ)

description:
https://www.encodeproject.org/experiments/ENCSR917JIA/
***************
biological replicate number: 1
technical replicate number: 1
description: OnT dRNA of K562
experiment encode accession: ENCSR917JIA
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-03-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB743TEQ
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: adult

value: ENCBS514PFB at ENCODE; https://www.encodeproject.org/ENCBS514PFB/


title: long read RNA-seq from HL-60 (ENCLB909APR)

description:
https://www.encodeproject.org/experiments/ENCSR121FDE/
***************
biological replicate number: 2
technical replicate number: 1
description: HL-60 derived M1 macrophages (12hr)
experiment encode accession: ENCSR121FDE
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB909APR
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: HL-60 derived M1 macrophages (12hr)

value: acute promyelocytic leukemia

value: 36 year

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:120; duration_units:hour; treatment_term_id:CHEBI:16412; treatment_term_name:lipopolysaccharide; treatment_type:chemical; duration:12; duration_units:hour; treatment_term_id:UniProtKB:P01579; treatment_term_name:interferon gamma; treatment_type:protein; duration:12; duration_units:hour;

value: ENCBS887OHV at ENCODE; https://www.encodeproject.org/ENCBS887OHV/

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


title: long read RNA-seq from astrocyte (ENCLB652QMD)

description:
https://www.encodeproject.org/experiments/ENCSR071IHY/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_207, ENC4_208 - PGP1 derived astrocytes
experiment encode accession: ENCSR071IHY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB652QMD
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

source_name: Homo sapiens male adult (53 years) astrocyte in vitro differentiated cells

value: astrocyte

value: in vitro differentiated cells

value: PGP1 derived astrocytes

value: male

value: Bradley Bernstein, Broad

value: George Church

value: ENCBS372XQF at ENCODE; https://www.encodeproject.org/ENCBS372XQF/

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


title: long read RNA-seq from astrocyte (ENCLB486CFV)

description:
https://www.encodeproject.org/experiments/ENCSR071IHY/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_207, ENC4_208 - PGP1 derived astrocytes
experiment encode accession: ENCSR071IHY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB486CFV
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

value: 53 year

value: ENCBS100HNS at ENCODE; https://www.encodeproject.org/ENCBS100HNS/


title: long read RNA-seq from mammary epithelial cell (ENCLB412FYP)

description:
https://www.encodeproject.org/experiments/ENCSR998KIZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_507, ENC4_508 HMEC rep1 primary human mammary epithelial cells
experiment encode accession: ENCSR998KIZ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-12-13
lab: Ali Mortazavi, UCI
library encode accession: ENCLB412FYP
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: mammary epithelial cell

value: primary cell

value: female

value: unknown

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS996RLF at ENCODE; https://www.encodeproject.org/ENCBS996RLF/

value: Derived from ENCODE donor ENCDO343AAA; https://www.encodeproject.org/ENCDO343AAA/


title: long read RNA-seq from HepG2 (ENCLB940BIE)

description:
https://www.encodeproject.org/experiments/ENCSR724HQB/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT dRNA of HepG2
experiment encode accession: ENCSR724HQB
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-03-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB940BIE
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

source_name: Homo sapiens HepG2 cell line

value: cell line

value: Homo sapiens

value: hepatocellular carcinoma

value: child

value: 15 year

value: Ali Mortazavi, UCI

value: ATCC

value: ENCBS003ZLT at ENCODE; https://www.encodeproject.org/ENCBS003ZLT/

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


title: long read RNA-seq from HL-60 (ENCLB455DNY)

description:
https://www.encodeproject.org/experiments/ENCSR583KAF/
***************
biological replicate number: 1
technical replicate number: 1
description: HL-60 derived M1 macrophages (24hr)
experiment encode accession: ENCSR583KAF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB455DNY
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens HL-60 cell line treated with 10 uM phorbol 13-acetate 12-myristate for 120 hours, 100 ng/mL interferon gamma for 24 hours, 100 ng/mL lipopolysaccharide for 24 hours

value: HL-60 derived M1 macrophages (24hr)

value: acute promyelocytic leukemia

value: adult

value: 36 year

value: treatment_term_id:CHEBI:37537; treatment_term_name:phorbol 13-acetate 12-myristate; treatment_type:chemical; duration:120; duration_units:hour; treatment_term_id:UniProtKB:P01579; treatment_term_name:interferon gamma; treatment_type:protein; duration:24; duration_units:hour; treatment_term_id:CHEBI:16412; treatment_term_name:lipopolysaccharide; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS970MQP at ENCODE; https://www.encodeproject.org/ENCBS970MQP/

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


title: long read RNA-seq from HL-60 (ENCLB493RCQ)

description:
https://www.encodeproject.org/experiments/ENCSR583KAF/
***************
biological replicate number: 2
technical replicate number: 1
description: HL-60 derived M1 macrophages (24hr)
experiment encode accession: ENCSR583KAF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB493RCQ
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: female

value: ENCBS195FGT at ENCODE; https://www.encodeproject.org/ENCBS195FGT/


title: long read RNA-seq from HepG2 (ENCLB663CCA)

description:
https://www.encodeproject.org/experiments/ENCSR724HQB/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT dRNA of HepG2
experiment encode accession: ENCSR724HQB
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-03-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB663CCA
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: cell line

value: Homo sapiens

value: male

value: ENCBS402MPB at ENCODE; https://www.encodeproject.org/ENCBS402MPB/


title: long read RNA-seq from adrenal gland (ENCLB301TEG)

description:
https://www.encodeproject.org/experiments/ENCSR271ULH/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_217 - B6Cast F1 PND4_Female 03_Adrenals
experiment encode accession: ENCSR271ULH
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB301TEG
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

organism: Mus musculus

source_name: Mus musculus strain B6CASTF1/J female (4 days) adrenal gland tissue

value: adrenal gland

value: tissue

value: B6Cast F1 PND4 Female 03 adrenal gland for Wold core

value: unknown

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS886BLQ at ENCODE; https://www.encodeproject.org/ENCBS886BLQ/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: long read RNA-seq from adrenal gland (ENCLB766DCJ)

description:
https://www.encodeproject.org/experiments/ENCSR295PVQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_227 - B6Cast F1 PND25_Male 03_Adrenals
experiment encode accession: ENCSR295PVQ
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB766DCJ
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

source_name: Mus musculus strain B6CASTF1/J male (25 days) adrenal gland tissue

value: B6Cast F1 PND25 Male 03 adrenal gland for Wold core

value: 25 day

value: ENCBS798KOH at ENCODE; https://www.encodeproject.org/ENCBS798KOH/


title: long read RNA-seq from adrenal gland (ENCLB378BNW)

description:
https://www.encodeproject.org/experiments/ENCSR271ULH/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_217 - B6Cast F1 PND4_Female 03_Adrenals
experiment encode accession: ENCSR271ULH
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB378BNW
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: B6Cast F1 PND4 Female 04 adrenal gland for Wold core

value: female

value: ENCBS118MVG at ENCODE; https://www.encodeproject.org/ENCBS118MVG/


title: long read RNA-seq from left cerebral cortex (ENCLB407FIA)

description:
https://www.encodeproject.org/experiments/ENCSR280VKU/
***************
biological replicate number: 1
technical replicate number: 1
description: 5xFAD cortex het Female
experiment encode accession: ENCSR280VKU
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB407FIA
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Mus musculus strain B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax cerebral cortex tissue

value: left cerebral cortex

value: 5xFAD cortex het Female

value: not collected

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS172LSS at ENCODE; https://www.encodeproject.org/ENCBS172LSS/

value: Derived from ENCODE donor ENCDO835CXP; https://www.encodeproject.org/ENCDO835CXP/


title: long read RNA-seq from left cerebral cortex (ENCLB937RMU)

description:
https://www.encodeproject.org/experiments/ENCSR280VKU/
***************
biological replicate number: 2
technical replicate number: 1
description: 5xFAD cortex het Female
experiment encode accession: ENCSR280VKU
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB937RMU
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

value: tissue

value: unknown

value: ENCBS354HBB at ENCODE; https://www.encodeproject.org/ENCBS354HBB/


title: long read RNA-seq from adrenal gland (ENCLB402RPL)

description:
https://www.encodeproject.org/experiments/ENCSR698DOB/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_219 - B6Cast F1 PND10_Male 03_Adrenals
experiment encode accession: ENCSR698DOB
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB402RPL
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

source_name: Mus musculus strain B6CASTF1/J male (10 days) adrenal gland tissue

value: adrenal gland

value: B6Cast F1 PND10 Male 03 adrenal gland for Wold core

value: male

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS588OTO at ENCODE; https://www.encodeproject.org/ENCBS588OTO/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: long read RNA-seq from WTC11 (ENCLB289ECW)

description:
https://www.encodeproject.org/experiments/ENCSR507JOF/
***************
biological replicate number: 2
technical replicate number: 1
description: LRGASP WTC11
experiment encode accession: ENCSR507JOF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-05-04
lab: Ali Mortazavi, UCI
library encode accession: ENCLB289ECW
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., ERCC reference spike-ins used for LRGASP. Note that this does NOT contain the SIRVs that are a part of this mix (found in ENCSR759PLA).

value: cell line

value: Induced pluripotent stem cell line derived from adult skin (leg) fibroblasts; subject clinically normal

value: adult

value: 30 year

value: Yiing Lin, MD, PhD

value: ENCBS593PKA at ENCODE; https://www.encodeproject.org/ENCBS593PKA/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: long read RNA-seq from layer of hippocampus (ENCLB051AUO)

description:
https://www.encodeproject.org/experiments/ENCSR972DID/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_439, ENC4_440 hippocampus_B6Cast F1_2 months_male_5_ENC4_cDNA511
experiment encode accession: ENCSR972DID
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB051AUO
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Mus musculus strain B6CASTF1/J male (2 months) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: unknown

value: 2 month

value: ENCBS379YDE at ENCODE; https://www.encodeproject.org/ENCBS379YDE/


title: long read RNA-seq from adrenal gland (ENCLB928FUQ)

description:
https://www.encodeproject.org/experiments/ENCSR698DOB/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_219 - B6Cast F1 PND10_Male 03_Adrenals
experiment encode accession: ENCSR698DOB
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB928FUQ
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: adrenal gland

value: B6Cast F1 PND10 Male 04 adrenal gland for Wold core

value: male

value: 10 day

value: ENCBS368WXW at ENCODE; https://www.encodeproject.org/ENCBS368WXW/