title: muscle_notimmunized_CRC305E97042_24h

description: not immunized muscle biopsy gene expression of participant CRC305E97042 at 24 hours post immunization

value: right

value: not immunized

tag: race

tag: ethnicity


title: 38_RIt16R_CD4_Grp3_D3

status: Public on Jan 06 2020

type: SRA

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

library_source: transcriptomic

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the Rhesus macaque (MacaM v7) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

molecule: total RNA

organism: Macaca mulatta

source_name: Sorted peripheral cells

extract_protocol:
RNA was purified using QIAGEN RNeasy Micro columns, and RNA quality assessed using Agilent Bioanalyzer.
1 ng of total RNA was used as input for cDNA amplification using 5’ template-switch PCR with the Clontech SMART-Seq v4 Ultra Low Input RNA kit, according to manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual indexed bar codes using Illumina NexteraXT DNA Library Prep kits. Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled, and sequenced on an Illumina HiSeq 3000 using (101 bp SR) at an average read depth of 23 million reads/sample.

treatment_protocol: CD8 depletion administered subcutaneously to the whole animal at 50 mg/kg on day 0. N-803 was administered in four weekly subcutaneous injections of 100 µg/kg. Blood was collected in EDTA tubes and PBMCs were isolated. PBMCs were stained using fluorescent antibodies and CD4+ T cells +/- CD8+ T cells and NK cells were FACS sorted. Sorted cells were resuspended in 350 uL RLT+BME and frozen in -80.

tag: animalid

tag: group

value: ALT-803 Only=Grp3

tag: time point

tag: specific cell type

value: Bulk CD4


title: muscle_immunized_CRC305E97042_24h

type: RNA

city: London

first: David

last: Lewis

address: Du Cane Road

department: ICRF

country: United Kingdom

institute: Imperial College London

description: immunized muscle biopsy gene expression of participant CRC305E97042 at 24 hours post immunization

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented and hybridized to custom whole genome human 8 × 60K multipack microarrays (Agilent-048908) following the manufacturers instructions. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) according the manufacturers protocol.

scan_protocol: Slides were scanned immediately after washing using a high resolution DNA Microarray Scanner (G2505B, Agilent Technologies) with 3 µm resoltion and 20 bit image depth

data_processing:
The scanned microarray images were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol.
Quantile normalized signal intensity using limma 3.38.3,  read.maimages source = agilent, backgroundCorrect method= normexp, normalizeBetweenArrays method= quantile

organism: Homo sapiens

source_name: muscle,RNAlater

label_protocol: Total RNA was amplified and labeled with the low input Quick-Amp Labelling Kit (Agilent Technologies) with cyanine 3-CTP followed by precipitation, purification, and quantification.

extract_protocol: mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer

treatment_protocol: Microarray experiments were performed as single-color hybridization. Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA extracted from the whole blood in PaxGene tubes or the muscle biopsies stored in RNAlater using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

tag: protocol

tag: treatment

value: FENDRIXE

tag: injected leg

value: left

tag: day

tag: hour

tag: tissue

value: muscle

tag: biopsied leg

tag: biopsy site treatment

value: immunized

tag: biopsy comments

value: large amount of muscle

tag: participant

tag: gender

value: male

tag: age

value: white

value: hispanic or latino


title: 84_RVz15R_NK_Grp3_Pre

value: Pre

value: Bulk NK


title: 81_REf16R_NK_Grp3_Pre


title: 87_RAf16R_NK_Grp3_Pre


title: 77_RRn16R_CD8_Grp3_Pre

value: Bulk CD8


title: 73_RBn16R_CD8_Grp3_Pre


title: 69_RIt16R_CD8_Grp3_Pre


title: wholeblood__CRC305E9021_0h

description: whole blood gene expression of participant CRC305E9021 at 0 hours post immunization

source_name: whole blood,PaxGene

value: FLUADE

value: whole blood

tag: race

tag: ethnicity

value: not hispanic or latino


title: muscle_notimmunized_CRC305E9761034_24h

description: not immunized muscle biopsy gene expression of participant CRC305E9761034 at 24 hours post immunization

value: right

value: not immunized

value: very large amount of muscle


title: 65_REi16R_CD8_Grp3_Pre

tag: animalid

tag: group

value: ALT-803 Only=Grp3


title: 61_RAf16R_CD8_Grp3_Pre

tag: time point

tag: specific cell type


title: 58_RVz15R_CD8_Grp3_Pre


title: OrgDuo_3

city: Boston

first: Magdalena

last: Kasendra

state: MA

address: 27 Drydock avenue

institute: Emulate Inc.

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted
FPKMs were calculated using the hit counts and the corresponding gene lengths (using R, DESeq2, fpkm()).
Genome_build: GRCh38
Supplementary_files_format_and_content: text and comma-separated values files are generated to contain the hit counts and FPKM values

source_name: Epithelial cells from Duodenal Organoids

growth_protocol: Duodenum Intestine-Chips were seeded with intestinal epithelial cells obtained from dissociation of duodenal organoids (introduced in the top channel of Organ-on-Chip device) and Human Intestinal Microvascular Endothelial Cells (HIMEC) (intoduced in the bottom channel of Organ-on-Chip device) .The chips were maintained under constant perfusion of fresh media at 30 µl/hr through top (expansion medium till day 6, followed by the switch to differentiation medium) and bottom channels (EGM2-MV medium) and  peristalsis-like deformations of tissue attached to the membrane (10% strain; 0.2 Hz). Duodenal Organoids were grown embedded in Matrigel and in the presence of expansion medium until day 6, followed by the switch to differenctiation media.

extract_protocol:
RNA was extracted using TRIzol (Life Technologies) according to manufacturer’s guidelines
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Duodenal Epithelial Cells

tag: donor

value: Donor 3

tag: timepoint

value: Day 8

tag: applied mechanostimulation


title: muscle_immunized_CRC305E95016_24h

description: immunized muscle biopsy gene expression of participant CRC305E95016 at 24 hours post immunization

tag: protocol

tag: treatment

value: PLACEBOE

tag: injected leg

value: left

tag: day

tag: hour

tag: tissue

value: muscle

value: immunized

value: clean adequate muscle tissue obtaned.


title: OrgDuo_2

value: Donor 2


title: muscle_notimmunized_CRC305E95729_24h

description: not immunized muscle biopsy gene expression of participant CRC305E95729 at 24 hours post immunization

tag: biopsied leg

tag: biopsy site treatment

tag: biopsy comments

value: muscle tissue++

tag: participant

tag: gender

value: male

tag: age

value: white


title: muscle_notimmunized_CRC305E95016_24h

description: not immunized muscle biopsy gene expression of participant CRC305E95016 at 24 hours post immunization

tag: race

tag: ethnicity

value: not hispanic or latino


title: muscle_immunized_CRC305E95227_120h

description: immunized muscle biopsy gene expression of participant CRC305E95227 at 120 hours post immunization

value: FENDRIXE

value: right


title: 55_REf16R_CD8_Grp3_Pre

tag: animalid

tag: group

tag: time point

value: Pre

tag: specific cell type

value: Bulk CD8


title: muscle_notimmunized_CRC305E95227_120h

description: not immunized muscle biopsy gene expression of participant CRC305E95227 at 120 hours post immunization

tag: protocol

tag: treatment

value: not immunized


title: muscle_notimmunized_CRC305E96536_3h

description: not immunized muscle biopsy gene expression of participant CRC305E96536 at 3 hours post immunization

tag: injected leg

tag: day

value: muscle tissue ++ and blood


title: muscle_notimmunized_CRC305E94341_3h

description: not immunized muscle biopsy gene expression of participant CRC305E94341 at 3 hours post immunization

tag: hour

tag: tissue

value: good amounts of muscle. small amount of adipose


title: muscle_immunized_CRC305E94341_3h

description: immunized muscle biopsy gene expression of participant CRC305E94341 at 3 hours post immunization

tag: biopsied leg

tag: biopsy site treatment

value: good amount of muscle. small amount of adipose


title: muscle_notimmunized_CRC305E94819_120h

description: not immunized muscle biopsy gene expression of participant CRC305E94819 at 120 hours post immunization

value: left

tag: biopsy comments

tag: participant


title: ChipDuo_3

source_name: Epithelial cells from Duodenum Intestine-Chip

tag: cell type

value: Duodenal Epithelial Cells

tag: donor

value: Donor 3

tag: timepoint

value: Day 8

tag: applied mechanostimulation

value: flow (30 ul/hr) and stretch 10%


title: muscle_immunized_CRC305E95124_168h

description: immunized muscle biopsy gene expression of participant CRC305E95124 at 168 hours post immunization

value: muscle

value: immunized

value: muscle tissue ++

tag: gender

tag: age

tag: race

tag: ethnicity


title: OrgDuo_1

value: Donor 1


title: muscle_notimmunized_CRC305E96637_168h

description: not immunized muscle biopsy gene expression of participant CRC305E96637 at 168 hours post immunization

tag: protocol

tag: treatment

value: FENDRIXE

value: muscle tissue+++

value: male

value: white

value: not hispanic or latino


title: muscle_immunized_CRC305E95426_168h

description: immunized muscle biopsy gene expression of participant CRC305E95426 at 168 hours post immunization

tag: injected leg

tag: day


title: muscle_notimmunized_CRC305E95124_168h

description: not immunized muscle biopsy gene expression of participant CRC305E95124 at 168 hours post immunization

tag: hour

tag: tissue

value: right

value: not immunized


title: muscle_immunized_CRC305E96637_168h

description: immunized muscle biopsy gene expression of participant CRC305E96637 at 168 hours post immunization

tag: biopsied leg

tag: biopsy site treatment


title: muscle_notimmunized_CRC305E95426_168h

description: not immunized muscle biopsy gene expression of participant CRC305E95426 at 168 hours post immunization

tag: biopsy comments

tag: participant


title: ChipDuo_2

tag: cell type

tag: donor

value: Donor 2


title: muscle_immunized_CRC305E96536_3h

description: immunized muscle biopsy gene expression of participant CRC305E96536 at 3 hours post immunization

value: left

value: muscle tissue++


title: muscle_immunized_CRC305E94819_120h

description: immunized muscle biopsy gene expression of participant CRC305E94819 at 120 hours post immunization


title: 35_RIt16R_CD4_Grp3_Pre

tag: animalid

tag: group

value: ALT-803 Only=Grp3

tag: time point

value: Pre

tag: specific cell type

value: Bulk CD4


title: muscle_immunized_CRC305E9448_24h

description: immunized muscle biopsy gene expression of participant CRC305E9448 at 24 hours post immunization

value: muscle

tag: gender

tag: age

tag: race

tag: ethnicity


title: ChipDuo_1

value: Duodenal Epithelial Cells

tag: timepoint

value: Day 8

tag: applied mechanostimulation

value: flow (30 ul/hr) and stretch 10%


title: muscle_notimmunized_CRC305E9448_24h

description: not immunized muscle biopsy gene expression of participant CRC305E9448 at 24 hours post immunization

tag: protocol

tag: treatment

value: FENDRIXE

tag: injected leg

tag: day

tag: hour

tag: tissue


title: 27_REi16R_CD4_Grp3_Pre


title: muscle_immunized_CRC305E95335_3h

description: immunized muscle biopsy gene expression of participant CRC305E95335 at 3 hours post immunization

value: PLACEBOE

tag: biopsied leg

tag: biopsy site treatment

value: immunized

tag: biopsy comments

value: muscle tissue ++

tag: participant


title: muscle_notimmunized_CRC305E95335_3h

description: not immunized muscle biopsy gene expression of participant CRC305E95335 at 3 hours post immunization

value: small sample muscle and blood

value: male

value: white

value: not hispanic or latino


title: muscle_immunized_CRC305E93614_168h

description: immunized muscle biopsy gene expression of participant CRC305E93614 at 168 hours post immunization

value: FLUADE

value: left

value: 1st attempt:all muscle but small amounts. 2nd attempt:large amount of muscle with some blood clots

value: hispanic or latino


title: muscle_immunized_CRC305E93817_168h

description: immunized muscle biopsy gene expression of participant CRC305E93817 at 168 hours post immunization

value: right

value: muscle tissue +++

value: asian


title: muscle_notimmunized_CRC305E93817_168h

description: not immunized muscle biopsy gene expression of participant CRC305E93817 at 168 hours post immunization

value: muscle

value: not immunized

value: muscle tissue and clots


title: muscle_notimmunized_CRC305E93011_120h

description: not immunized muscle biopsy gene expression of participant CRC305E93011 at 120 hours post immunization

value: all muscle


title: muscle_notimmunized_CRC305E9229_120h

description: not immunized muscle biopsy gene expression of participant CRC305E9229 at 120 hours post immunization

value: large amount of muscle


title: 19_RAf16R_CD4_Grp3_Pre

tag: animalid

tag: group

value: ALT-803 Only=Grp3

tag: time point

value: Pre

tag: specific cell type

value: Bulk CD4


title: Donor 3 Day 28

city: Cleveland

first: Daniel

middle: Joseph

last: Vail

state: OH

address: BRB 647C 2109 Adelbert Road

department: Genetics

institute: Case Western Reserve University

description: Donor 3 Day 28

data_processing:
FASTQ files are aligned to human transcriptome (ENSEMBL GRCh38 cdna.all combined with ncrna, both v93) and quantified by TPM (transcripts per million) and estimated read counts with Salmon v 0.92
Transcripts are associated with gene according to biomart/ENSEMBL v93 "Transcript Stable ID version" and "Gene stable ID"
DESeq2 was used for  differential expression analysis data annotated in "supplementary file 1.csv"
Resulting DESeqDataSet was trimmed by requirement of all sample row counts >= 10 in order to eliminate non-expressed genes from the dataset
Genome_build: GRCh38
Supplementary_files_format_and_content: NumReads, TPMs

source_name: Bone marrow derived mesenchymal stem cells undergoing chondrogenic pellet culture

growth_protocol: MSCs were extracted from whole bone marrow donations and plated, passaged twice in low glucose DMEM treated with recombinant FGF2 and 10%FBS

extract_protocol:
[Homogenization method]  static rotor homogenization for 5 min in trizol
All samples underwent trizol phase separation of nucleic acids followed by QIAGEN column RNA purification (catalog number 74194)
Strand specific cDNA (250-300bp) libraries constructed using the NEBNext Ultra Kit for low input (5ng-1000ng) following poly-T oligo-attached magnetic bead purification. Quality assessed by insert size (Agilent 2100).
RNA-seq (low input)

treatment_protocol: Passage 2 MSCs are plated in conical wells in chondrogenic media (low glucose DMEM with 1% ITS+, 100uM dexamethasone, 1mM sodium pyruvate, 120uM ascorbic acid-2 phosphate, 100uM non-essential amino acids)  and cetrifuged to form a pellet. Media is changed 3x per week. Pellets harvested by addition into trizol. 3-4 pellets per sample.

tag: sample provider

value: Human donor CWRU Tissue Procurement

tag: pre-process shipping and storage

value: fresh / n/a

value: BM-derived MSCs undergoing chondrogenic pellet culture

tag: Cause of death

tag: gender

value: M

tag: race

value: UNK

tag: age


title: Donor 2 Day 28

description: Donor 2 Day 28


title: 11_RVz15R_CD4_Grp3_Pre


title: Donor 1 Day 28

description: Donor 1 Day 28

value: F


title: 3_REf16R_CD4_Grp3_Pre


title: 49_RVe16R_CD4_Grp2_Pre

value: CD8 depletion Only=Grp2


title: Donor 3 Day 21

description: Donor 3 Day 21


title: Donor 2 Day 21

description: Donor 2 Day 21


title: Donor 1 Day 21

description: Donor 1 Day 21


title: 42_RSt15R_CD4_Grp2_Pre


title: 34_REs16R_CD4_Grp2_Pre


title: muscle_immunized_CRC305E94223_120h

description: immunized muscle biopsy gene expression of participant CRC305E94223 at 120 hours post immunization

tag: protocol

tag: treatment

value: FLUADE

tag: injected leg

value: left

tag: day

value: immunized

value: sample:all muscle

value: male

value: other

tag: ethnicity

value: not hispanic or latino


title: Donor 3 Day 14

description: Donor 3 Day 14

tag: tissue


title: 26_RRb16R_CD4_Grp2_Pre


title: muscle_notimmunized_CRC305E94223_120h

description: not immunized muscle biopsy gene expression of participant CRC305E94223 at 120 hours post immunization

value: right

tag: hour

value: muscle

tag: biopsied leg

tag: biopsy site treatment

value: not immunized

tag: biopsy comments

value: sample:all muscle large amounts

tag: participant


title: muscle_notimmunized_CRC305E93921_24h

description: not immunized muscle biopsy gene expression of participant CRC305E93921 at 24 hours post immunization

value: 2 good pieces of muscle tissue obtained at depth of approx 3cm. no other tissue in sample.

value: white


title: imb_koenig_2018_06_rep_05

city: Mainz

first: Annabelle

last: Dold

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology, IMB

data_processing:
Sequencing qualities were checked for all reads using FastQC (version 0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Afterwards, reads were filtered based on sequencing qualities (Phred score) of the barcode region. Reads with more than one position with a Phred score < 20 in the experimental barcode (positions 4 to 7 of the reads) or any position with a Phred score < 17 in the random barcode (positions 1 to 3 and 8 to 9) were excluded from subsequent analysis. Remaining reads were de-multiplexed based on the experimental barcode (positions 4 to 7) using Flexbar (version 3.0.0, Dodt et al., 2012) without allowing any mismatch.
All following steps of the analysis were performed on the individual samples after de-multiplexing. Remaining adapter sequences were removed from the read ends using Flexbar (version 3.0.0) with a maximal error rate of 0.1 and a minimal overlap of 1 nt between the beginning of the adapter and the end of the read. Following adapter trimming, the first 9 nt of each read containing the experimental and random barodes were trimmed off and added to the read name in the fastq files in order to keep this information for downstream analysis. Reads shorter than 15 nt were removed from further analysis.
Trimmed and filtered reads were mapped to the Drosophila melanogaster genome (Ensembl genome assembly version BDGP6) and its annotation (Ensembl release 90, Bronwen et al., 2017) using STAR (version 2.5.2b, Dobin et al., 2013). When running STAR, up to two mismatches were allowed, soft-clipping was prohibited and only uniquely mapping reads were kept for further analysis. For further analysis, only unspliced reads were kept and analyzed.
Following mapping, duplicate reads were marked using the dedup function of bamUtil (version 1.0.13), which defines duplicates as reads whose 5' ends map to the same position in the genome (https://github.com/statgen/bamUtil). Subsequently, marked duplicates with identical random barcodes were removed since they are considered technical duplicates, while biological duplicates showing unequal random barcodes were kept.
Genome_build: Ensembl BDGP6
Supplementary_files_format_and_content: Resulting bam files were sorted and indexed using SAMtools (version 1.3.1, Li et al., 2009). Afterwards, bedgraph files were created based on bam files, using bamToBed of the BEDTools suite (version 2.25.0, Quinlan and Hall, 2010), considering only the position upstream of the 5' mapping position of the read, since this nucleotide is considered as the crosslinked nucleotide. Using bedGraphToBigWig of the UCSC tool suite (Kent et al., 2010), all bedgraph files were converted into bigWig files. The counts of all Mkrn1 iCLIP experiments were combined in one file.

organism: Drosophila melanogaster

source_name: S2R+ cell culture

extract_protocol:
The iCLIP protocol was from (Sutandy et al., 2016) with the following adaptations. Cells were crosslinked with 150 mJ/cm2 of UV light and subsequently harvested. Cells were lysed in urea cracking buffer (50 mM Tris pH 7.5, 6 M urea, 1% SDS, 25% PBS) and sonicated using 2 cycles with 30 sec “ON”/“OFF” at low setting. Remaining cell debris was removed by centrifugation at 21,000 x g for 10 min at 4°C. Lysate was diluted 1:5 in IP buffer (150 mM NaCl, 50 mM Tris pH 7.5, 0.5% Tween-20, 0.1 mM EDTA) and incubated with 2 µg of anti-FLAG M2® antibody (Sigma-Aldrich) pre-coupled to 40 µl of protein G Dynabeads® (ThermoFisher Scientific) for 2 h at 4°C. The beads were washed 3x with high salt buffer and 3x with PNK buffer before Turbo DNase (Ambion) and RNase I (Ambion) treatment was performed. Beads were washed again 3x with high-salt buffer and 3x with PNK buffer to remove residual enzymes.
For high-throughput sequencing, libraries of 6 technical replicates for FLAG-Mkrn1 and 1 replicate for FLAG-GFP (control) were prepared as described before (Huppertz et al., 2014). Multiplexed iCLIP libraries were sequenced as 75-nt single-end reads on an Illumina MiSeq sequencing system.

tag: technique

value: iCLIP

tag: cell line

tag: genotype

value: Flag-tagged Mkrn1


title: imb_koenig_2018_06_rep_06


title: muscle_immunized_CRC305E9229_120h

description: immunized muscle biopsy gene expression of participant CRC305E9229 at 120 hours post immunization

value: all muscle

tag: gender


title: muscle_immunized_CRC305E93921_24h

description: immunized muscle biopsy gene expression of participant CRC305E93921 at 24 hours post immunization

value: 2 good muscle samples obtained at depth of approx 3cm. no other tissue in sample.

tag: race


title: muscle_immunized_CRC305E93728_72h

description: immunized muscle biopsy gene expression of participant CRC305E93728 at 72 hours post immunization

value: PLACEBOE

value: muscle tisssue

tag: age


title: muscle_immunized_CRC305E91030_3h

description: immunized muscle biopsy gene expression of participant CRC305E91030 at 3 hours post immunization

tag: protocol

value: left

value: immunized

value: muscle tissue

value: asian


title: muscle_notimmunized_CRC305E93728_72h

description: not immunized muscle biopsy gene expression of participant CRC305E93728 at 72 hours post immunization

tag: treatment

value: small sample muscle tissue

value: male

value: not hispanic or latino


title: muscle_immunized_CRC305E93544_168h

description: immunized muscle biopsy gene expression of participant CRC305E93544 at 168 hours post immunization

tag: injected leg

value: right

value: muscle

value: hispanic or latino


title: muscle_notimmunized_CRC305E9285_168h

description: not immunized muscle biopsy gene expression of participant CRC305E9285 at 168 hours post immunization

value: FLUADE

tag: day

value: not immunized

value: small amount muscle tissue

value: white


title: muscle_notimmunized_CRC305E93544_168h

description: not immunized muscle biopsy gene expression of participant CRC305E93544 at 168 hours post immunization

tag: ethnicity


title: muscle_immunized_CRC305E9285_168h

description: immunized muscle biopsy gene expression of participant CRC305E9285 at 168 hours post immunization

tag: tissue

value: muscle tissue+++


title: muscle_notimmunized_CRC305E91030_3h

description: not immunized muscle biopsy gene expression of participant CRC305E91030 at 3 hours post immunization

value: PLACEBOE

tag: hour


title: Donor 2 Day 14

description: Donor 2 Day 14

tag: sample provider

value: Human donor CWRU Tissue Procurement

tag: pre-process shipping and storage

value: fresh / n/a

value: BM-derived MSCs undergoing chondrogenic pellet culture

tag: Cause of death

value: M

value: UNK


title: 43_RBn16R_CD4_Grp3_Pre

tag: animalid

tag: group

value: ALT-803 Only=Grp3

tag: time point

value: Pre

tag: specific cell type

value: Bulk CD4


title: imb_koenig_2018_06_rep_04

tag: technique

value: iCLIP

tag: cell line

tag: genotype

value: Flag-tagged Mkrn1


title: muscle_immunized_CRC305E93439_120h

description: immunized muscle biopsy gene expression of participant CRC305E93439 at 120 hours post immunization

tag: protocol

value: right

value: muscle

tag: biopsied leg

tag: biopsy site treatment

value: immunized

tag: biopsy comments

value: muscle tissue

tag: participant

tag: gender

value: male

tag: age

tag: race

value: not hispanic or latino


title: 18_RKs15R_CD4_Grp2_Pre

value: CD8 depletion Only=Grp2


title: Donor 1 Day 14

description: Donor 1 Day 14

tag: sample provider

value: Human donor CWRU Tissue Procurement

tag: pre-process shipping and storage

tag: tissue

value: F


title: imb_koenig_2018_06_rep_03


title: 10_ROr15R_CD4_Grp2_Pre

tag: animalid

tag: group


title: imb_koenig_2018_06_rep_02


title: 2_RNz15R_CD4_Grp2_Pre

tag: time point

tag: specific cell type


title: 48_REu16R_CD4_Grp1_Pre

value: CD8 depletion + early ALT-803= Grp1


title: imb_koenig_2018_06_rep_01

tag: technique

tag: cell line


title: muscle_notimmunized_CRC305E93439_120h

description: not immunized muscle biopsy gene expression of participant CRC305E93439 at 120 hours post immunization

tag: protocol

tag: treatment

value: PLACEBOE

tag: injected leg

value: left

tag: day

tag: hour

value: not immunized

value: white

tag: ethnicity


title: muscle_immunized_CRC305E92633_168h

description: immunized muscle biopsy gene expression of participant CRC305E92633 at 168 hours post immunization

tag: biopsied leg

tag: biopsy site treatment

tag: biopsy comments

tag: participant

tag: gender

tag: age


title: Donor 3 Day 3

description: Donor 3 Day 3

tag: sample provider

tag: pre-process shipping and storage

value: fresh / n/a

tag: tissue

value: BM-derived MSCs undergoing chondrogenic pellet culture

tag: Cause of death

value: M

tag: race

value: UNK


title: Donor 1 Day 7

description: Donor 1 Day 7


title: 33_RAu15R_CD4_Grp1_Pre

tag: animalid

tag: group

tag: time point

value: Pre

tag: specific cell type

value: Bulk CD4


title: imb_koenig_2018_06_control

tag: technique

value: iCLIP

tag: cell line

tag: genotype

value: Flag-tagged GFP


title: 41_RNa16R_CD4_Grp1_Pre


title: Donor 3 Day 7

description: Donor 3 Day 7


title: muscle_notimmunized_CRC305E91420_72h

description: not immunized muscle biopsy gene expression of participant CRC305E91420 at 72 hours post immunization

tag: protocol

tag: treatment

value: FLUADE

tag: injected leg

tag: day

tag: hour

value: muscle

tag: biopsied leg

value: right

tag: biopsy site treatment

value: good amount. all muscle.

value: male

value: other

tag: ethnicity

value: hispanic or latino


title: muscle_notimmunized_CRC305E91922_72h

description: not immunized muscle biopsy gene expression of participant CRC305E91922 at 72 hours post immunization

value: PLACEBOE

value: left

tag: tissue

value: not immunized

tag: biopsy comments

value: good amount. all muscle

tag: participant

tag: gender

tag: age


title: muscle_immunized_CRC305E9761034_24h

description: immunized muscle biopsy gene expression of participant CRC305E9761034 at 24 hours post immunization

value: FENDRIXE

value: immunized

value: large amount of muscle

tag: race

value: white


title: Donor 2 Day 3

description: Donor 2 Day 3

tag: sample provider

value: Human donor CWRU Tissue Procurement

tag: pre-process shipping and storage

value: fresh / n/a

value: BM-derived MSCs undergoing chondrogenic pellet culture

tag: Cause of death

value: M

value: UNK


title: Hi-C_CTCF Y226A, F228A 2.2

city: Amsterdam

first: Angela

last: Sedeno Cacciatore

state: Noord-Holland

address: Plesmanlaan 121

department: Gene regulation

country: Netherlands

institute: Netherlands Cancer Institute

description: HiC_CTCF.Y226A.F228A_merged_allValidPairs.gz

library_source: genomic

data_processing:
Raw sequence data was mapped and processed using HiC-Pro v2.9.0 (Servant et al., 2015).
After confirming high similarity between the different library preparations (1 and 2), the contact information was pooled together and processed to obtain merged contact matrices.
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C summary files contain the genomic position and strand of the two pairs of a Hi-C ligation

molecule: genomic DNA

growth_protocol: HAP1 cells (Carette et al., 2011) were cultured in IMDM (Invitrogen) supplemented with 10% FCS (Clontech), 1% Penicillin-Streptomycin (Invitrogen) and 0.5% Ultraglutamin (Lonza).

extract_protocol:
Hi-C was performed essentially as previously described (Rao et al., 2014). Briefly, for each template roughly 10 million cells were crosslinked using 2% formaldehyde. In nucleus restriction was performed using MboI. Restriction overhangs were filled in with biotinylated nucleotides followed by blunt-end ligation. A streptavidin pull-down was performed to enrich for ligated sequences.
Pulled-down DNA was end-repaired and an A-overhang was added. Sequencing adapters were ligated to the DNA samples to create sequencing libraries.

treatment_protocol: gRNA targeting exon 1 of CTCF were designed and annealed into pX330 (primer: 5’- CGATTTTGAGGAAGAACAGC-3’). To modify the targeted locus we co-transfected a 120 basepair repair oligo containing the desired mutation and a silent mutation (repair oligo: 5’ – CCAAAAAGAGCAAACTGCGTTATACAGAGGAGGGCAAAGATGTAGATGTGTCTGTCGCCGATGCTGAAGAAGAACAGCAGGAGGGTCTGCTATCAGAGGTTAATGCAGAGAAAGTGGTTG-3’). pBabePuro was co-transfected in a 10:1 ratio to the pX330. Transfected clones were selected using 2 µg/µl puromycin for 2 days. gDNA of clones was isolated and send for Sanger sequencing to check for the desired mutation.

tag: cell line

tag: genotype

value: CTCF Y226A, F228A


title: Donor 1 Day 3

description: Donor 1 Day 3

value: F


title: 25_RUa16R_CD4_Grp1_Pre

tag: animalid

tag: group

value: CD8 depletion + early ALT-803= Grp1

tag: time point

value: Pre

tag: specific cell type

value: Bulk CD4


title: Donor 2 Day 7

description: Donor 2 Day 7


title: Hi-C_WT 2.2

value: Wild-Type


title: muscle_notimmunized_CRC305E9091012_24h

description: not immunized muscle biopsy gene expression of participant CRC305E9091012 at 24 hours post immunization

tag: protocol

tag: treatment

value: FLUADE

tag: injected leg

value: left

tag: day

tag: hour

value: muscle

tag: biopsied leg

value: right

tag: biopsy site treatment

value: not immunized

value: good amount. all muscle.

value: male

value: not hispanic or latino


title: MM_8dpi_B3

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

country: China

institute: Northeast Agricultural University

data_processing:
BGI500 own software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2 with parameters v1.5.2, then mapped to Gallus_gallus-5.0 genome using bowtie2 v2. 2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: NCBI_GCF_000188115.3_SL2.50
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Solanum lycopersicum

growth_protocol: Ontario7816 and Moneymaker were sown into pots filled with soil and grown under controlled conditions (16h light, 25℃ and 95% ambient humidity) in a greenhouse at the Horticultural station of Northeast Agricultural University (Harbin, China).

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard BGI500 protocols

treatment_protocol: At the four-six leaf stage, the abaxial leaf surfaces of 40 plants per line were inoculated with a suspension of C. fulvum (Race 1.2.3.4) at 1 × 10^7 sporangia per mL, mock-treat plants of each lines were sprayed with sterilized water under the same conditions.

tag: tomato line

value: Moneymaker

tag: phenotype

value: C. fulvum-susceptible


title: Donor 3 Day 0

description: Donor 3 Day 0

source_name: Bone marrow derived mesenchymal stem cells at passage 2

extract_protocol:
[Homogenization method]  n/a
All samples underwent trizol phase separation of nucleic acids followed by QIAGEN column RNA purification (catalog number 74194)
Strand specific cDNA (250-300bp) libraries constructed using the NEBNext Ultra Kit for low input (5ng-1000ng) following poly-T oligo-attached magnetic bead purification. Quality assessed by insert size (Agilent 2100).
RNA-seq (low input)

tag: sample provider

value: Human donor CWRU Tissue Procurement

tag: pre-process shipping and storage

value: fresh / n/a

tag: tissue

value: BM-derived MSCs at passage 2

tag: gender

value: M

tag: race

value: UNK

tag: age


title: 9_RHv15R_CD4_Grp1_Pre

tag: animalid

tag: group

value: CD8 depletion + early ALT-803= Grp1

tag: time point

value: Pre

value: Bulk CD4


title: muscle_notimmunized_CRC305E93614_168h

description: not immunized muscle biopsy gene expression of participant CRC305E93614 at 168 hours post immunization

tag: protocol

tag: treatment

value: FLUADE

value: left

tag: biopsy comments

value: large amount of muscle

tag: participant

value: white

tag: ethnicity

value: hispanic or latino


title: MM_8dpi_B2


title: Donor 2 Day 0

description: Donor 2 Day 0

tag: Cause of death


title: 1_RJt15R_CD4_Grp1_Pre

tag: specific cell type


title: Donor 1 Day 0

description: Donor 1 Day 0

value: F


title: muscle_immunized_CRC305E91218_3h

description: immunized muscle biopsy gene expression of participant CRC305E91218 at 3 hours post immunization

tag: injected leg

value: right

tag: day

tag: hour

value: muscle

tag: biopsied leg

tag: biopsy site treatment

value: immunized

value: muscle tissue

value: male

value: not hispanic or latino


title: muscle_immunized_CRC305E93011_120h

description: immunized muscle biopsy gene expression of participant CRC305E93011 at 120 hours post immunization

tag: tissue

value: all muscle

tag: gender

tag: race


title: muscle_notimmunized_CRC305E91218_3h

description: not immunized muscle biopsy gene expression of participant CRC305E91218 at 3 hours post immunization

value: not immunized

tag: age


title: MM_8dpi_B1

tag: tomato line

value: Moneymaker

tag: phenotype

value: C. fulvum-susceptible

tag: time point


title: MM_4dpi_A3

tag: treatment


title: 17_106_13R_CD4_Grp1_Pre

tag: animalid

tag: group

value: CD8 depletion + early ALT-803= Grp1

value: Pre

value: Bulk CD4


title: muscle_immunized_CRC305E91922_72h

description: immunized muscle biopsy gene expression of participant CRC305E91922 at 72 hours post immunization

tag: protocol

value: PLACEBOE

tag: biopsy comments

value: need 2 attempts. first biopsy:small amounts with connective tissue. second biopsy:good amounts all muscle.

tag: participant

value: other

tag: ethnicity


title: Neonate 3

source_name: articular cartilage of the femoral condyle and/or tibial plateau

extract_protocol:
[Homogenization method] Liquid nitrogen snap freeze, mechanical crushing, then static rotor homogenization for 5 min in trizol
All samples underwent trizol phase separation of nucleic acids followed by QIAGEN column RNA purification (catalog number 74194)
Strand specific cDNA (250-300bp) libraries constructed using the NEBNext Ultra Kit for low input (5ng-1000ng) following poly-T oligo-attached magnetic bead purification. Quality assessed by insert size (Agilent 2100).
RNA-seq (low input)

tag: sample provider

value: Allosource LLC

tag: pre-process shipping and storage

value: fresh / wet ice

value: neonatal cartilage

tag: Cause of death

value: UNK

value: M


title: Hi-C_CTCF Y226A, F228A 2.1

tag: cell line

tag: genotype

value: CTCF Y226A, F228A


title: Neonate 2

tag: tissue

tag: gender

tag: race


title: MM_4dpi_A2

tag: tomato line

tag: phenotype


title: Hi-C_WT 2.1

value: Wild-Type


title: MM_4dpi_A1

tag: treatment

tag: time point


title: Neonate 1

tag: age


title: Adult 3

value: Articular Engineering, LLC

value: snap frozen / dry ice

value: adult cartilage

value: Gun shot wound

value: Hispanic


title: long read RNA-seq from HFFc6 (ENCLB794WCT)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR902GAF/
***************
biological replicate number: 2
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF parental line
experiment encode accession: ENCSR902GAF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2019-12-05
lab: Ali Mortazavi, UCI
library encode accession: ENCLB794WCT

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

source_name: Homo sapiens HFFc6 cell line

tag: line

value: cell line

tag: description

tag: biosample encode accession

tag: Sex

value: male

tag: health state

value: normal

tag: dev stage

value: newborn

value: 0 year

tag: lab

value: Ali Mortazavi, UCI

tag: source

value: Job Dekker

tag: link

value: ENCBS109KQW at ENCODE; https://www.encodeproject.org/ENCBS109KQW/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: Hi-C_WT 1

tag: cell line

tag: genotype


title: Hi-C_CTCF Y226A, F228A 1


title: CK_MM_8dpi_B3

value: Moneymaker

value: C. fulvum-susceptible

value: mock-infected


title: CK_MM_8dpi_B2


title: muscle_immunized_CRC305E9091012_24h

description: immunized muscle biopsy gene expression of participant CRC305E9091012 at 24 hours post immunization

tag: protocol

value: FLUADE

tag: injected leg

value: right

tag: day

tag: hour

tag: tissue

value: muscle

tag: biopsied leg

tag: biopsy site treatment

value: immunized

tag: biopsy comments

value: good amount. all muscle.

tag: participant

tag: gender

tag: race

value: white

tag: ethnicity

value: not hispanic or latino


title: Adult 2

tag: sample provider

value: Articular Engineering, LLC

tag: pre-process shipping and storage

value: snap frozen / dry ice

value: adult cartilage

tag: Cause of death

value: Xanax overdose

value: M

value: Hispanic

tag: age


title: CK_MM_8dpi_B1

tag: tomato line

tag: phenotype

tag: treatment

tag: time point


title: long read RNA-seq from HFFc6 (ENCLB952ETR)

description:
https://www.encodeproject.org/experiments/ENCSR902GAF/
***************
biological replicate number: 3
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF parental line
experiment encode accession: ENCSR902GAF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2019-12-05
lab: Ali Mortazavi, UCI
library encode accession: ENCLB952ETR

tag: line

value: cell line

tag: description

tag: biosample encode accession

tag: Sex

value: male

tag: health state

value: normal

tag: dev stage

value: newborn

value: 0 year

tag: lab

value: Ali Mortazavi, UCI

tag: source

value: Job Dekker

tag: link

value: ENCBS793IWN at ENCODE; https://www.encodeproject.org/ENCBS793IWN/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: CK_MM_4dpi_A3

value: Moneymaker

value: C. fulvum-susceptible

value: mock-infected


title: long read RNA-seq from HFFc6 (ENCLB678ULN)

description:
https://www.encodeproject.org/experiments/ENCSR902GAF/
***************
biological replicate number: 1
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF parental line
experiment encode accession: ENCSR902GAF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2019-12-05
lab: Ali Mortazavi, UCI
library encode accession: ENCLB678ULN

value: ENCBS974NEC at ENCODE; https://www.encodeproject.org/ENCBS974NEC/


title: muscle_immunized_CRC305E92725_3h

description: immunized muscle biopsy gene expression of participant CRC305E92725 at 3 hours post immunization

tag: protocol

value: FLUADE

tag: injected leg

value: right

tag: day

tag: hour

tag: tissue

value: muscle

tag: biopsied leg

tag: biopsy site treatment

value: immunized

tag: biopsy comments

value: muscle tissue

tag: participant

tag: gender

tag: race

value: white

tag: ethnicity

value: not hispanic or latino


title: CK_MM_4dpi_A2

tag: tomato line

tag: phenotype

tag: treatment

tag: time point


title: 50_RRn16R_CD4_Grp3_Pre

tag: animalid

tag: group

value: ALT-803 Only=Grp3

value: Pre

tag: specific cell type

value: Bulk CD4


title: SH-SY5Y SNAI2 gRNA2 #3

city: Utrecht

first: Kirsten

last: Vrenken

address: Heidelberglaan 25

institute: Princess Máxima Center for Pediatric Oncology

description:
Control-v-gRNA2.tab
gRNA1-v-gRNA2.tab

data_processing:
Primary data analysis - Image analyses, base calling, and quality check was performed using the Illumina data analysis pipeline RTA v2.7.7 and Bcl2fastq v2.17 (Illumina).
Adapter clipping - Prior to alignment, reads were trimmed for adapter sequences using Trimmomatic v0.30. Presumed adapter sequences were removed from the read when the bases matched a sequence in the adapter sequence set (TruSeq adapters) with 2 or less mismatches and an alignment score of at least 12. All forward and reverse reads were pooled for each sample after trimming.
Mapping of reads - Reads were mapped to the reference sequence, Hg19 reference for Homo sapiens, using a short read aligner based on the Burrows‑Wheeler Transform. The default mismatch rate of 2% was used. Frequency of reads mapping to a transcript was determined based on the mapped locations.
Differential expression analysis was performed with the read counts using the DESeq package v 1.10.1 on the R platform v2.15.3.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files providing GeneID, mean coverage count/gene; base mean counts per gene/per group; fold change between the groups; log2 fold change; P-value of log2 fold change; adjusted P-value (Benjamini-Hochberg); rank based on corrected P-value; Gene symbol

molecule: polyA RNA

source_name: Neuroblastoma cell line

extract_protocol:
Total RNA was isolated using an RNAeasy minikit (#74106, Qiagen) with on column Dnase (#79254, Qiagen) treatment according to manufacturer's protocol. Quality and integrity of the RNA was determined using Fragment AnalyzerTM (Advanced Analytical Technologies).
Samples were processed using the NEBNext® UltraTM Directional RNA Library Prep kit for Illumina® (#E7420S, NEB) according to manufactures instructions. In short, after isolation of mRNA from total RNA using the oligo dT magnetic beads, mRNA was fragmented and cDNA synthesis was performed for ligation with the sequencing adapters and PCR amplification of the resulting product.

treatment_protocol: Cells were lentivirally transduced with pLentiCRISPRv1 containing either control or SNAI2 gRNA sequences and selected using 1 ug/mL puromycin. Efficient CRISPR/CAS9 targeting at position of interest was determined by sequencing, and significant loss of SNAI2 protein on protein level as determined by Western blot. Three independent experiments were carried out, where 0.5 x 10^6 cells/cell line were seeded in 6 wells plates and allowed to adhere o/n in a humidified incubator at 37°C and 5% CO2. Subsequently, RNA samples of SH-SY5Y SNAI2 control and gRNA cells were prepared and analyzed as three independent experiments.

tag: cell line

tag: genotype

value: SNAI2 gRNA#2


title: muscle_notimmunized_CRC305E92633_168h

description: not immunized muscle biopsy gene expression of participant CRC305E92633 at 168 hours post immunization

tag: protocol

value: PLACEBOE

tag: injected leg

value: left

tag: day

tag: hour

tag: tissue

value: not immunized

value: good amount muscle tissue

value: male

tag: age


title: muscle_immunized_CRC305E92432_120h

description: immunized muscle biopsy gene expression of participant CRC305E92432 at 120 hours post immunization

tag: biopsied leg

tag: biopsy site treatment

tag: biopsy comments

value: small sample. muscle with 1 strand of connective tissue

tag: participant

tag: gender

tag: race

value: asian


title: muscle_immunized_CRC305E91420_72h

description: immunized muscle biopsy gene expression of participant CRC305E91420 at 72 hours post immunization

tag: treatment

value: FLUADE

value: right

value: good amount. all muscle.

value: other

tag: ethnicity

value: hispanic or latino


title: muscle_notimmunized_CRC305E92432_120h

description: not immunized muscle biopsy gene expression of participant CRC305E92432 at 120 hours post immunization

value: muscle

value: 2 attempts. in total adequate sample. all muscle.

value: not hispanic or latino


title: long read RNA-seq from HepG2 (ENCLB443KZB)

description:
https://www.encodeproject.org/experiments/ENCSR834DQL/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens HepG2 immortalized cell line
experiment encode accession: ENCSR834DQL
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2019-06-28
lab: Ali Mortazavi, UCI
library encode accession: ENCLB443KZB

source_name: Homo sapiens HepG2 cell line

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

tag: health state

value: hepatocellular carcinoma

tag: dev stage

value: child

value: 15 year

tag: lab

value: Ali Mortazavi, UCI

tag: source

value: ATCC

tag: link

value: ENCBS440MJL at ENCODE; https://www.encodeproject.org/ENCBS440MJL/

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


title: long read RNA-seq from mucosa of descending colon (ENCLB620TRY)

description:
https://www.encodeproject.org/experiments/ENCSR803XXZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_78 W80 mucosa of descending colon
experiment encode accession: ENCSR803XXZ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2019-12-19
lab: Ali Mortazavi, UCI
library encode accession: ENCLB620TRY

source_name: Homo sapiens female adult (61 year) mucosa of descending colon tissue, preserved by flash-freezing

value: mucosa of descending colon

value: tissue

value: female

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

value: adult

tag: age

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS825BLU at ENCODE; https://www.encodeproject.org/ENCBS825BLU/

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


title: SH-SY5Y SNAI2 gRNA2 #2

description:
Control-v-gRNA2.tab
gRNA1-v-gRNA2.tab

tag: cell line

tag: genotype

value: SNAI2 gRNA#2


title: SH-SY5Y SNAI2 gRNA1 #3

description:
Control-v-gRNA1.tab
gRNA1-v-gRNA2.tab

value: SNAI2 gRNA#1


title: SH-SY5Y SNAI2 gRNA2 #1

description:
Control-v-gRNA2.tab
gRNA1-v-gRNA2.tab


title: Cf16_8dpi_B3

tag: tomato line

tag: phenotype

value: C. fulvum-resistant

tag: time point


title: Cf16_8dpi_B2


title: long read RNA-seq from left lung (ENCLB849DQR)

description:
https://www.encodeproject.org/experiments/ENCSR746ITG/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_79 W62 left lung
experiment encode accession: ENCSR746ITG
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2019-12-19
lab: Ali Mortazavi, UCI
library encode accession: ENCLB849DQR

source_name: Homo sapiens female child (16 years) left lung tissue, preserved by flash-freezing

value: left lung

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

value: child

value: 16 year

value: ENCBS725WGH at ENCODE; https://www.encodeproject.org/ENCBS725WGH/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: Adult 1

tag: sample provider

value: Articular Engineering, LLC

tag: pre-process shipping and storage

value: snap frozen / dry ice

tag: tissue

value: adult cartilage

tag: Cause of death

value: APAP overdose

tag: gender

value: F

tag: race

value: Caucasian


title: muscle_notimmunized_CRC305E91110_72h

description: not immunized muscle biopsy gene expression of participant CRC305E91110 at 72 hours post immunization

tag: protocol

tag: treatment

value: FLUADE

tag: injected leg

value: right

tag: day

tag: hour

value: muscle

tag: biopsied leg

value: left

tag: biopsy site treatment

value: not immunized

tag: biopsy comments

value: large sample. almost all muscle. small strip of connective tissue

tag: participant

value: male

value: white

tag: ethnicity

value: not hispanic or latino


title: muscle_notimmunized_CRC305E92725_3h

description: not immunized muscle biopsy gene expression of participant CRC305E92725 at 3 hours post immunization

value: muscle tissue

tag: age


title: long read RNA-seq from HepG2 (ENCLB572FVU)

description:
https://www.encodeproject.org/experiments/ENCSR834DQL/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens HepG2 immortalized cell line
experiment encode accession: ENCSR834DQL
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2019-06-28
lab: Ali Mortazavi, UCI
library encode accession: ENCLB572FVU

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

tag: health state

value: hepatocellular carcinoma

tag: dev stage

value: child

value: 15 year

tag: lab

value: Ali Mortazavi, UCI

tag: source

value: ATCC

tag: link

value: ENCBS667GKM at ENCODE; https://www.encodeproject.org/ENCBS667GKM/

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


title: muscle_notimmunized_CRC305E91513_72h

description: not immunized muscle biopsy gene expression of participant CRC305E91513 at 72 hours post immunization

tag: protocol

tag: treatment

value: FENDRIXE

tag: injected leg

value: right

tag: tissue

value: sample - some blood good amount of muscle 1 small streak of connective tissue

tag: gender

tag: race


title: muscle_immunized_CRC305E91110_72h

description: immunized muscle biopsy gene expression of participant CRC305E91110 at 72 hours post immunization

value: FLUADE

value: left

tag: day

tag: hour

value: muscle

tag: biopsied leg

tag: biopsy site treatment

value: immunized

tag: biopsy comments

value: almost all muscle. very small amount of adipose tissue

tag: participant


title: CK_MM_4dpi_A1

tag: tomato line

value: Moneymaker

tag: phenotype

value: C. fulvum-susceptible

value: mock-infected

tag: time point


title: muscle_notimmunized_CRC305E9077_3h

description: not immunized muscle biopsy gene expression of participant CRC305E9077 at 3 hours post immunization

value: not immunized

value: muscle tissue

value: male

tag: age

value: white

tag: ethnicity

value: not hispanic or latino


title: SH-SY5Y SNAI2 gRNA1 #2

description:
Control-v-gRNA1.tab
gRNA1-v-gRNA2.tab

tag: cell line

tag: genotype

value: SNAI2 gRNA#1


title: long read RNA-seq from GM12878 (ENCLB027JID)

description:
https://www.encodeproject.org/experiments/ENCSR706ANY/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens GM12878 immortalized cell line
experiment encode accession: ENCSR706ANY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2019-06-28
lab: Ali Mortazavi, UCI
library encode accession: ENCLB027JID

source_name: Homo sapiens GM12878 cell line originated from GM12878

tag: line

value: cell line

tag: description

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: unknown

tag: dev stage

value: adult

tag: lab

value: Ali Mortazavi, UCI

tag: source

value: Coriell

tag: link

value: ENCBS229YYL at ENCODE; https://www.encodeproject.org/ENCBS229YYL/

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


title: Cf16_8dpi_B1

value: C. fulvum-resistant

tag: treatment


title: muscle_immunized_CRC305E91513_72h

description: immunized muscle biopsy gene expression of participant CRC305E91513 at 72 hours post immunization

tag: protocol

value: FENDRIXE

tag: injected leg

value: left

tag: day

tag: hour

tag: tissue

value: muscle

tag: biopsied leg

tag: biopsy site treatment

value: immunized

tag: biopsy comments

value: sample - all muscle

tag: participant

tag: gender

tag: race


title: Cf16_4dpi_A3

tag: tomato line

tag: phenotype

tag: time point


title: long read RNA-seq from GM12878 (ENCLB713XRP)

description:
https://www.encodeproject.org/experiments/ENCSR706ANY/
***************
biological replicate number: 3
technical replicate number: 1
description: Homo sapiens GM12878 immortalized cell line
experiment encode accession: ENCSR706ANY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2019-06-28
lab: Ali Mortazavi, UCI
library encode accession: ENCLB713XRP

tag: line

tag: description

tag: biosample encode accession

tag: Sex

tag: health state

tag: dev stage

tag: age

tag: lab

tag: source

value: ENCBS694MFZ at ENCODE; https://www.encodeproject.org/ENCBS694MFZ/


title: muscle_immunized_CRC305E92315_3h

description: immunized muscle biopsy gene expression of participant CRC305E92315 at 3 hours post immunization

tag: protocol

tag: treatment

value: PLACEBOE

tag: injected leg

tag: day

tag: hour

tag: tissue

tag: biopsied leg

tag: biopsy site treatment

value: muscle tissue with small amount of adipose

value: male

value: white

tag: ethnicity

value: not hispanic or latino


title: muscle_immunized_CRC305E9077_3h

description: immunized muscle biopsy gene expression of participant CRC305E9077 at 3 hours post immunization

value: FLUADE

tag: biopsy comments

value: muscle tissue

tag: participant

tag: gender

tag: race


title: SH-SY5Y control #2

description:
Control-v-gRNA1.tab
Control-v-gRNA2.tab

tag: cell line

tag: genotype

value: Control


title: Cf16_4dpi_A2

tag: tomato line

tag: phenotype

tag: time point


title: SH-SY5Y control #3

description:
Control-v-gRNA1.tab
Control-v-gRNA2.tab


title: SH-SY5Y SNAI2 gRNA1 #1

description:
Control-v-gRNA1.tab
gRNA1-v-gRNA2.tab

value: SNAI2 gRNA#1


title: long read RNA-seq from GM12878 (ENCLB521AXX)

description:
https://www.encodeproject.org/experiments/ENCSR706ANY/
***************
biological replicate number: 4
technical replicate number: 1
description: Homo sapiens GM12878 immortalized cell line
experiment encode accession: ENCSR706ANY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2019-06-28
lab: Ali Mortazavi, UCI
library encode accession: ENCLB521AXX

tag: line

value: cell line

tag: description

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: unknown

tag: dev stage

value: adult

tag: age

tag: lab

value: Ali Mortazavi, UCI

tag: source

value: Coriell

tag: link

value: ENCBS844IZD at ENCODE; https://www.encodeproject.org/ENCBS844IZD/

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


title: Cf16_4dpi_A1

value: C. fulvum-resistant

tag: treatment


title: SH-SY5Y control #1

description:
Control-v-gRNA1.tab
Control-v-gRNA2.tab


title: long read RNA-seq from GM12878 (ENCLB133UBC)

description:
https://www.encodeproject.org/experiments/ENCSR706ANY/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens GM12878 immortalized cell line
experiment encode accession: ENCSR706ANY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2019-06-28
lab: Ali Mortazavi, UCI
library encode accession: ENCLB133UBC

value: ENCBS657BPX at ENCODE; https://www.encodeproject.org/ENCBS657BPX/


title: CK_Cf16_8dpi_B3

value: mock-infected


title: GDNF 3

city: Melbourne

first: Christopher

last: Bye

state: Victoria

address: University of Melbourne

country: Australia

institute: The Florey Institute of Neuroscience and Mental Health

data_processing:
Align reads to Human Genome and Output concordant aligned reads as fastq - HiSat2  (v2.0.3) : hisat2  -x "UCSC_hg38"  --al-conc  "output"  --rna-strandness R  --no-mixed --no-discordant.
Align concordant human aligned reads to Mouse Genome and output unaligned reads as fastq - HiSat2  (v2.0.3) : hisat2  -x "UCSC_mm10" --un-conc "output"   --rna-strandness R  --no-mixed --no-discordant.
Align Human Specific Reads to Human Genome and output concordant aligned reads as BAM - HiSat2  (v2.0.3) : hisat2  -x "UCSC_hg38"  --rna-strandness R  --no-mixed --no-discordant. Output concordant aligned reads as BAM
Generate Human specific read counts for each gene - HTSeq-count  (v0.6.1) : htseq-count --mode=union --stranded=reverse --minaqual=255 --type='exon'
Differential Expression Analysis - DESeq2 (v1.12.4) : DESeq  (test = "Wald", fitType= "parametric")
Genome_build: Homo_sapiens_UCSC_hg38 & Mus_musculus_UCSC_mm10
Supplementary_files_format_and_content: tab-delimited text files containing feature counts (htCount)

organism:
Homo sapiens
Mus musculus

source_name: hES cell graft in rodent brain

growth_protocol: Human PSCs were seeded on Laminin-521 (10ug/ml; StemCell Technologies) in the presence of dual SMAD inhibitors (SB431542, 10uM, 0-5 days in vitro (DIV), R&D systems; and LDN193189, 200nM, 0-11DIV, Stemgent) to promote neural induction. Sonic hedgehog C25II (100ng/ml; R&D systems) and Purmorphamine (2uM; Stemgent) were supplemented into the media from day 1-7DIV to promote ventralisation, in addition to the caudalizing Wnt agonist, CHIR 99021 (3uM; Stemgent, 3-11DIV). From 13DIV, cells were cultured in a ‘maturation media’ consisting of NBB27 supplemented with GDNF (20ng/ml; R&D systems), BDNF (20ng/ml, R&D system), TGFβ3 (1 ng/ml; PeproTech), DAPT (10 μM, Sigma-Aldrich), ascorbic acid (200nM; Sigma-Aldrich) and dibutyryl cAMP (0.05mM; Tocris Bioscience). At 21 DIV differentiating cultures were dissociated in Accutase (Innovative Cell Technologies) to a single-cell suspension and fluorescent activated cell sorting (FACS) performed on a MoFlo cell sorter (Beckman Coulter, MoFlo to isolate LMX1A-GFP expressing progenitors, as previously described (de Luzy et al., 2018). The FACS-isolated cell fraction was resuspended at 100,000 cells/µL in maturation media containing ROCK inhibitor (Y27632, 40uM, Sigma) and stored on ice until the time of implantation.

extract_protocol:
The striatum (containing the transplant) were rapidly dissected from the host brain and flash frozen. The isolated tissue was homogenised using a TissueLyser LT (Qiagen) and total RNA extracted using the RNeasy Mini Kit (Qiagen) including DNase treatment.
Mixed species cDNA libraries were prepared using TruSeq stranded mRNA sample preparation kit (Illumina).

treatment_protocol: Intrastriatal injections of adeno-associated viral vector carrying GDNF (AAV-GDNF) into the striatum 3 weeks prior to, or after 3 weeks after transplantation.

tag: graft type

value: Ventral midbrain

value: GDNF

tag: host

value: Athymic (Foxn1nu) nude mice


title: long read RNA-seq from K562 (ENCLB846KPV)

description:
https://www.encodeproject.org/experiments/ENCSR589FUJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Homo sapiens K562 immortalized cell line
experiment encode accession: ENCSR589FUJ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2019-06-28
lab: Ali Mortazavi, UCI
library encode accession: ENCLB846KPV

source_name: Homo sapiens K562 cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

value: ENCBS203BUH at ENCODE; https://www.encodeproject.org/ENCBS203BUH/

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


title: CK_Cf16_8dpi_B2


title: long read RNA-seq from K562 (ENCLB095ZGG)

description:
https://www.encodeproject.org/experiments/ENCSR589FUJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Homo sapiens K562 immortalized cell line
experiment encode accession: ENCSR589FUJ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2019-06-28
lab: Ali Mortazavi, UCI
library encode accession: ENCLB095ZGG

value: cell line

value: female

value: ENCBS859NNO at ENCODE; https://www.encodeproject.org/ENCBS859NNO/


title: GDNF 2


title: muscle_immunized_CRC305E9086_168h

description: immunized muscle biopsy gene expression of participant CRC305E9086 at 168 hours post immunization

tag: protocol

value: PLACEBOE

tag: injected leg

value: left

tag: day

tag: hour

tag: tissue

value: muscle

tag: biopsied leg

tag: biopsy site treatment

value: immunized

tag: biopsy comments

value: appearance of muscle tissue in two pieces; sample taken at a depth of 3 cm.

tag: participant

tag: gender

value: male

tag: race

value: black or african american

tag: ethnicity

value: not hispanic or latino


title: CK_Cf16_8dpi_B1

tag: tomato line

tag: phenotype

value: C. fulvum-resistant

value: mock-infected

tag: time point


title: long read RNA-seq from ovary (ENCLB995ZQY)

description:
https://www.encodeproject.org/experiments/ENCSR587WPR/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_35 W61 ovary
experiment encode accession: ENCSR587WPR
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2019-12-19
lab: Ali Mortazavi, UCI
library encode accession: ENCLB995ZQY

source_name: Homo sapiens female adult (41 year) ovary tissue, preserved by flash-freezing

value: ovary

value: tissue

tag: biosample encode accession

tag: Sex

tag: health state

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

tag: dev stage

value: adult

tag: age

value: 41 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS472VJA at ENCODE; https://www.encodeproject.org/ENCBS472VJA/

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


title: GDNF 1

tag: graft type

value: Ventral midbrain

tag: treatment

value: GDNF

tag: host

value: Athymic (Foxn1nu) nude mice


title: Untreated 3

value: Undifferentiated

value: Untreated


title: CK_Cf16_4dpi_A2


title: CK_Cf16_4dpi_A3


title: muscle_notimmunized_CRC305E92315_3h

description: not immunized muscle biopsy gene expression of participant CRC305E92315 at 3 hours post immunization

source_name: muscle,RNAlater

tag: protocol

value: PLACEBOE

tag: injected leg

value: right

tag: day

tag: hour

tag: tissue

value: muscle

tag: biopsied leg

value: left

tag: biopsy site treatment

value: not immunized

tag: biopsy comments

value: muscle tissue+++

tag: participant

tag: gender

value: male

value: white

value: not hispanic or latino


title: Untreated 2


title: long read RNA-seq from heart left ventricle (ENCLB452TKV)

description:
https://www.encodeproject.org/experiments/ENCSR194YUY/
***************
biological replicate number: 1
technical replicate number: 1
description: ENTEX105 Heart - Left Ventricle 3-1
experiment encode accession: ENCSR194YUY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2019-12-05
lab: Ali Mortazavi, UCI
library encode accession: ENCLB452TKV

source_name: Homo sapiens heart left ventricle tissue female adult (53 years)

value: heart left ventricle

value: tissue

tag: description

value: Heart - Left Ventricle

tag: biosample encode accession

tag: age

value: 53 year

tag: dev stage

value: adult

tag: Sex

value: female

value: Barbara Wold, Caltech

value: ENCBS504IQD at ENCODE; https://www.encodeproject.org/ENCBS504IQD/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: iOL_HA-PPAR_Input

status: Public on Jan 05 2020

city: Shanghai

first: Chenxi

last: He

address: 131 Dong'an Rd, Mingdao Bldg, Rm 512

institute: Fudan University

data_processing:
Basecalls performed using bcl2fastq (v2.19.1.403)
ChIP-seq reads (only R1) were trimmed by trim_galore(v0.4.4_dev)
Trimmed reads were aligned to the mm10 genome assembly using bowtie (v1.2.2) with the following setting: bowtie -M 1 --best --strata --sam
Bam files were generated and removed duplicates by samtools (v1.8)
Tag directories were generated using homer (v4.10.1) with the following setting: makeTagDirectory ./Sample_tag Sample.bam
peaks were called using homer (v4.10.1) with the following setting: findPeaks Sample_tag -style factor -o Sample_peaks.txt -size auto -minDist default -i Input_tag -fdr 0.001
Genome_build: mm10
Supplementary_files_format_and_content: peak files called by homer (v4.10.1)

organism: Mus musculus

source_name: differentiated oligodendrocyte

growth_protocol: neural stem cells were differentiated in Neurobasal medium containing B-27, 2 mM GlutaMAX-I, 100 ng/mL insulin-like growth factor 1 (IGF-1), and 50 ng/mL 3,3',5-Triiodo-L-thyronine (T3)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complex were isolated with Qki-5, PPARb, HA, and Pol II antibodies.
Libraries were prepared by VAHTS Universal DNA Library Prep Kit (Vazyme, ND607)

tag: strain

value: FvB/C57BL6 hybrid

tag: cell type

value: differentiated oligodendrocyte from neural stem cell with ectopic expression of PPARb

tag: passages

tag: chip antibody


title: iOL_HA-PPAR_Pol2_ChIPseq

value: RNA polymerase II CTD repeat YSPTSPS (Abcam, Cat# ab817)


title: irCLIP in HeLa-ActD of Ku80 bioRep 2

first: Ryan

middle: Alexander

last: Flynn

address: 380 Roth Way, Room 265

institute: Stanford University

description:
processed data file:
HS_HeLa_Ku80_ActD_plus.norm.bw
HS_HeLa_Ku80_ActD_minus.norm.bw

data_processing:
library strategy: irCLIP
Sequencing reads were trimmed of 3' adaptors, collapsed for PCR duplicates, stripped of the 5' barcode, and mapped to the human (hg38) genome using bowtie2
RT stop identificaiton, gene assignment, and peak calling was performed as in FAST-iCLIP (PMID: 25411354)
Genome_build: hg38
Supplementary_files_format_and_content: bigWig file containing unique RT stops from the high confidence intersection of biological replicates of Ku80 irCLIP

source_name: irCLIP in HeLa-ActD of Ku80

growth_protocol: HeLa cells were grown in DMEM with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Lysates were sonicated, DNA-PKcs-RNA complexes were isolated with an anti-Ku80 (Bethyl A302-627A) antibody.
Libraries were prepared according to the irCLIP protocol (PMID: 27111506)

treatment_protocol: Cells were treated with DMSO or actinomycin D (1ug/mL) for 1 hour at 37C. Cells were then UV crosslinked at 254nm for 0.3J/cm^2 to in vivo fix RNA-RBP interactions.

tag: cell line

value: HeLa

tag: cell line source gender

tag: treatment

value: Actinomycin D treated

tag: rip antibody

value: anti-Ku80 (Bethyl A302-627A)

tag: molecule subtype

value: Protein enriched RNA


title: iOL_HA-PPAR_HA_ChIPseq

value: HA (Cell Signaling Technology, #3724S)


title: muscle_immunized_CRC305E9064_3h

description: immunized muscle biopsy gene expression of participant CRC305E9064 at 3 hours post immunization

tag: protocol

value: FENDRIXE

tag: injected leg

value: right

tag: day

tag: hour

tag: tissue

value: muscle

tag: biopsied leg

tag: biopsy site treatment

value: immunized

tag: biopsy comments

value: no comments recorded

value: male

tag: race

value: asian

tag: ethnicity

value: not hispanic or latino


title: long read RNA-seq from left lung (ENCLB355PRN)

description:
https://www.encodeproject.org/experiments/ENCSR426KOP/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_81 W76 left lung
experiment encode accession: ENCSR426KOP
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2019-12-19
lab: Ali Mortazavi, UCI
library encode accession: ENCLB355PRN

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

value: left lung

value: tissue

tag: biosample encode accession

tag: Sex

tag: health state

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

tag: dev stage

value: adult

tag: age

value: 40 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS420JRY at ENCODE; https://www.encodeproject.org/ENCBS420JRY/

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


title: irCLIP in HeLa-ActD of Ku80 bioRep 1

tag: cell line

value: HeLa

tag: cell line source gender

value: female

tag: treatment

value: Actinomycin D treated

tag: rip antibody

value: anti-Ku80 (Bethyl A302-627A)

tag: molecule subtype

value: Protein enriched RNA


title: muscle_notimmunized_CRC305E9086_168h

description: not immunized muscle biopsy gene expression of participant CRC305E9086 at 168 hours post immunization

tag: protocol

value: PLACEBOE

tag: injected leg

value: right

tag: day

tag: hour

tag: tissue

value: muscle

tag: biopsied leg

value: left

tag: biopsy site treatment

value: not immunized

value: appearance of muscle tissue with blood in one piece taken at a depth slightly shallower than 3 cm.

tag: participant

tag: gender

value: male

value: black or african american


title: muscle_immunized_CRC305E9042_24h

description: immunized muscle biopsy gene expression of participant CRC305E9042 at 24 hours post immunization

value: FLUADE

value: immunized

tag: biopsy comments

value: good muscle biopsy taken.

tag: age

tag: race

value: white

tag: ethnicity

value: not hispanic or latino


title: muscle_immunized_CRC305E9053_120h

description: immunized muscle biopsy gene expression of participant CRC305E9053 at 120 hours post immunization

value: adequate sample. all muscle. no connective or adipose tissue.


title: muscle_notimmunized_CRC305E9064_3h

description: not immunized muscle biopsy gene expression of participant CRC305E9064 at 3 hours post immunization

value: FENDRIXE

value: no comments recorded

value: asian


title: muscle_immunized_CRC305E9021_72h

description: immunized muscle biopsy gene expression of participant CRC305E9021 at 72 hours post immunization

value: all muscle no connective tissue or adipose seen.


title: irCLIP in HeLa-DMSO of Ku80 bioRep 2

description:
processed data file:
HS_HeLa_Ku80_DMSO_plus.norm.bw
HS_HeLa_Ku80_DMSO_minus.norm.bw

source_name: irCLIP in HeLa-DMSO of Ku80

tag: cell line

value: HeLa

tag: cell line source gender

value: female

value: DMSO treated

value: anti-Ku80 (Bethyl A302-627A)

value: Protein enriched RNA


title: muscle_notimmunized_CRC305E9053_120h

description: not immunized muscle biopsy gene expression of participant CRC305E9053 at 120 hours post immunization

tag: treatment

value: PLACEBOE

value: right

value: muscle

value: left

value: not immunized

value: male


title: long read RNA-seq from right lobe of liver (ENCLB904ZJV)

description:
https://www.encodeproject.org/experiments/ENCSR293MOX/
***************
biological replicate number: 1
technical replicate number: 1
description: W62 right lobe of liver
experiment encode accession: ENCSR293MOX
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2019-12-05
lab: Ali Mortazavi, UCI
library encode accession: ENCLB904ZJV

source_name: Homo sapiens female child (16 years) right lobe of liver tissue

value: right lobe of liver

value: tissue

tag: biosample encode accession

tag: Sex

tag: health state

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

tag: dev stage

value: child

value: 16 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS437TFK at ENCODE; https://www.encodeproject.org/ENCBS437TFK/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: iOL_HA-PPAR_PPARbeta_ChIPseq

tag: strain

value: FvB/C57BL6 hybrid

tag: cell type

value: differentiated oligodendrocyte from neural stem cell with ectopic expression of PPARb

tag: passages

tag: chip antibody

value: PPARb (Thermo Fisher, Cat# PA1-823A)


title: iOL_HA-PPAR_Qki-5_ChIPseq

value: Qki-5 (home-made)


title: CK_Cf16_4dpi_A1

tag: tomato line

tag: phenotype

value: C. fulvum-resistant

value: mock-infected

tag: time point


title: Untreated 1

tag: graft type

value: Ventral midbrain

value: Untreated

tag: host

value: Athymic (Foxn1nu) nude mice


title: irCLIP in HeLa-ActD of DNA-PKcs bioRep 1

description:
Protein enriched RNA
irCLIP_HeLa_ActD_DNA-PKcs_norm_minusStrand.bw
irCLIP_HeLa_ActD_DNA-PKcs_norm_plusStrand.bw

data_processing:
Sequencing reads were trimmed of 3' adaptors, collapsed for PCR duplicates, stripped of the 5' barcode, and mapped to the human (hg38) genome using bowtie2
RT stop identification, gene assignment, and peak calling was performed as in FAST-iCLIP (PMID: 25411354)
Genome_build: hg38
Supplementary_files_format_and_content: bigWig file containing unique RT stops from the high confidence intersection of biological replicates of DNA-PKcs irCLIP

source_name: HeLa cells

extract_protocol:
Lysates were sonicated, DNA-PKcs-RNA complexes were isolated with an anti-DNA-PKCs (Bethyl A303-967A) antibody.
Libraries were prepared according to the irCLIP protocol (PMID: 27111506)

tag: cell line

value: HeLa

tag: treatment

value: Actinomycin D treated

tag: gender

value: female


title: irCLIP in HeLa-ActD of DNA-PKcs bioRep 2


title: irCLIP in HeLa-DMSO of DNA-PKcs bioRep 2

description:
Protein enriched RNA
irCLIP_HeLa_DMSO_DNA-PKcs_norm_minusStrand.bw
irCLIP_HeLa_DMSO_DNA-PKcs_norm_plusStrand.bw

value: DMSO treated


title: mOL_Input

source_name: oligodendrocyte

value: oligodendrocyte freshly isolated from mouse brain


title: Cnp1T7_ChiP-Nexus

city: Edinburgh

first: Robin

last: Allshire

state: Midlothian

address: Max Born Cresent

institute: The University of Edinburgh

data_processing:
Library strategy: ChIP-Nexus
ChIP-seq reads were aligned to ASM294v2.20 build using Bowtie2, trimmed first 15bp;
Data were analysis using MACE
Genome_build: ASM294v2.20
Supplementary_files_format_and_content: bigwig files were generated using bedtools and wigToBigWig from UCSC

organism: Schizosaccharomyces pombe

source_name: cell

growth_protocol: Schizosaccharomyces pombe cell were gwon in rich medium (1X YES).

extract_protocol:
Lysates were prepared using standard bead beating procedure, sonicated to achieve fragmements of 200-400bp andclarified by centrifugation at 17000g.
ChIP-Nexus libraries were prepared essentially as described in He et al., 2015, Briefly, protein G-dynabeads bound DNA-protein-complexes were affinity selected using specific antibodies . DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment and T4 polynucleotide kinase. A single 3'-A overhang was added using Klenow 3'-5' exo- polymerase. Adapters were ligated and blunted again by Klenow 3'-5' exo- polymerase to fill in the 5’ overhang first and then by T4 DNA polymerase to trim possible 3’ overhangs. Blunted DNA was then sequentially digested by lambda exonuclease and RecJf. Digested single strand DNA was then eluted, reverse cross-linked and phenol-chloroform purified. Fragments were  then self-circularized by Circligase. An oligonucleotide was hybridized to circularized single DNA for subsequent BamHI digestion in order to linearize the DNA. This linearized single strand DNA was then PCR-amplified using adapter sequences and library was purified and size selected using Ampure XP beads. The sequencing libraries were sequenced following Illumina's work flow.

tag: genotype

value: wildtype


title: ischemia + exercise

city: Tokyo

first: Momoko

last: Ogitani

address: 1-2-58, Hiromachi, Shinagawa-ku

department: Research and Development Division

country: Japan

institute: Daiichi Sankyo Co., Ltd.

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C onAffymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Rattus norvegicus

source_name: skeletal muscle

label_protocol: Biotinylated cRNA were prepared using GeneChip 3' IVT Express Kit (Affymetrix, CA, USA).

extract_protocol: RNA isolation was performed using RNeasy Fibrous Tissue Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s description.

tag: excerise group

value: ischemia + exercise


title: ischemia + ES

value: ischemia + ES


title: irCLIP in HeLa-DMSO of DNA-PKcs bioRep 1


title: mOL_Qki-5_ChIPseq


title: sham

value: sham


title: Qk-KO rep2

status: Public on Jan 04 2020

city: Houston

last: Hu

state: Texas

address: 1881 East Rd

department: Department of Cancer Biology, Division of Basic Sciences

institute: The University of Texas MD Anderson Cancer Center

data_processing:
FastQC is used to check the read quality
Tophat2 2.0.14 (-a 6 --microexon-search -m 2) was used to map the reads to mouse genome (mm10) with transcription annotations (GENCODE vM8 basic).
featureCounts was used to count the gene level reads numbers.
DESeq2 was used to do the differential gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 result in text format

source_name: freshly isolated oligodendrocyte

growth_protocol: freshly isolated oligodendrocytes without further culture

extract_protocol:
Total RNAs were extracted with Rnasey kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Plp-CreERT2;QKLoxP/LoxP (Qk-KO) mice and control mice were injected with tamoxifen at 8-week, and brains were collected 4 days after tamoxifen injection to isolate oligodendrocyte freshly.

value: FvB/C57BL6 hybrid

tag: tissue

value: brain

tag: age

value: freshly isolated oligodendrocyte

tag: passage


title: Qk-KO rep1

tag: strain


title: WT rep3

value: WT

tag: cell type


title: WT rep1


title: WT rep2


title: oligodendrocyte_WT rep3

data_processing:
FastQC is used to check the read quality
Tophat2 2.0.14 (-a 6 --microexon-search -m 2) was used to map the reads to mouse genome (mm10) with transcription annotations (GENCODE vM8 basic).
featureCounts was used to count the gene level reads numbers.
DESeq2 was used to do the differential gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 result in text files.
Lplus_LL_DESeq2_AllSample.tsv.gz: Corpus callosum samples
Project_JH_QK-NSC-1T_Nu109_DESeq2.tsv.gz: oligodendrocyte samples

growth_protocol: WT or Qk-KO neural stem cells were differntiated in Neurobasal medium containing B-27, 2 mM GlutaMAX-I, 100 ng/ml insulin-like growth factor 1 (IGF-1), and 50 ng/ml 3,3',5-Triiodo-L-thyronine (T3)

treatment_protocol: Plp-CreERT2;QKLoxP/LoxP (Qk-KO) and Plp-CreERT2;QKLoxP/+ (WT) mice were injected with tamoxifen at 8-week, and corpus callosum were collected 4 days after tamoxifen injection.

value: differentiated oligodendrocyte from NSC


title: oligodendrocyte_Qk-KO rep1


title: oligodendrocyte_WT rep1


title: oligodendrocyte_WT rep2


title: oligodendrocyte_Qk-KO rep3


title: oligodendrocyte_Qk-KO rep2


title: corpus callosum_WT rep4

source_name: corpus callosum

tag: brain region

value: corpus callosum


title: corpus callosum_Qk-KO rep4


title: corpus callosum_WT rep3


title: Qk-KO rep3


title: corpus callosum_Qk-KO rep3


title: corpus callosum_WT rep2


title: ischemia

value: ischemia


title: corpus callosum_WT rep1


title: corpus callosum_Qk-KO rep2


title: CCs with VIP vs. CCs without VIP

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: CCs without VIP vs. CCs with VIP.

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

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

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: mCC VIP- #2

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

growth_protocol: Dlk+ hepatoblasts were isolated from E13.5 fetal livers by magnetic sorting, followed by two dimensional pre-culture on type1 collagen-coated dishes. The cells were cultured in hepatocyte culture media (DMEM supplemented with 10% FCS, 2 mM L-glutamine, 1× insulin/transferrin/selenium, 1× nonessential amino acid, 100 U/mL penicillin, 100 μg/mL streptomycin, and 10e−7 M dexamethasone). After the 7-day culture, the cells were subjected to three dimensional (3D) culture in gel consisting of a mixture of 50% biliary culture media, 40% EHS gel and 10% type I collagen gel. The biliary culture media were DMEM/F-12 supplemented with 1×insulin/transferrin/selenium, 12.5mM nicotinamide, 2.5mM HEPES, 1× nonessential amino acid, 2% B27 supplement, 0.25 μM A-83-01, 10 μM Y-27632, 20 ng/ml recombinant epidermal growth factor, 100 ng/ml recombinant R-spondin1, 100 U/mL penicillin, 100 μg/mL streptomycin, and 10e−7 M dexamethasone.

extract_protocol: Total RNA was extracted from CCs on the 12th day of 3D culture by using RNeasy Mini kit (QIAGEN).

treatment_protocol: CCs with VIP: 10-7 M VIP was added to the biliary culture media from the initiation of 3D culture. CCs without VIP: cells were treated by vehicle instead.

tag: strain/background

tag: genotype/variation

tag: developmental stage

value: Cholangiocytic cysts (CCs)

value: Vehicle

source_name: mCC VIP+ #2

value: Vasoactive intestinal peptide (VIP)


title: corpus callosum_Qk-KO rep1


title: MMP-14 WT vs. MMP-14 KO liver mesenchymal cells

description: E16.5 MMP14-WT liver mesenchymal cells vs. E16.5 MMP14-KO liver mesenchymal cells.

source_name: E16 MMP14 WT

growth_protocol: Systemic MMP-14 KO mice and WT littermates were obtained by crossbreeding MMP-14 heterozygous mice with a C57B/6J background. Embryos were collected from pregnant mice on E16 and subjected to genotyping.

extract_protocol: Total RNA was directly extracted from the sorted cells using RNeasy Mini kit (QIAGEN).

treatment_protocol: Liver samples were collected from E16.5 MMP14-WT and -KO mice and dissociated by collagenase treatment, followed by purification of CD45-Ter119-p75NTR+ liver mesenchymal cells using FACS.

value: liver mesenchymal cells

source_name: E16 MMP14 KO


title: Cnp1HA_ChiP-Nexus

tag: chip antibody

value: HA


title: mOL_PPARbeta_ChIPseq

value: oligodendrocyte freshly isolated from mouse brain

tag: passages

value: PPARb (Thermo Fisher, Cat# PA1-823A)


title: irCLIP in HeLa-DMSO of Ku80 bioRep 1

value: HeLa

tag: cell line source gender

value: female

value: DMSO treated

tag: rip antibody

value: anti-Ku80 (Bethyl A302-627A)

tag: molecule subtype

value: Protein enriched RNA


title: 9234921140_J: PR Patient_CODE22 - T1

city: Bari

first: Vincenzo

middle: Ostilio

last: Palmieri

address: P.za Giulio Cesare

department: Biomedical Sciences and Human Oncology

country: Italy

institute: University of Bari

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization (background was not subtracted) with Illumina Genome Studio Software; items with detection p values >0.001 or AVG Signal <120 in more than 1 group were excluded. Data were analyzed with non parametric analysis plus False Discovery Rate, FDR.

source_name: PBMCs

label_protocol: Standard Illumina Protocol

extract_protocol: Total RNA was extracted using the QIAzol® Lysis Reagent, according to the manufacturer’s instructions. Quality control was performed with Biorad Experion.

value: PBMCs

tag: disease state

value: hepatocarcinoma


title: 8803828080_H: CR Patient_CODE24 - T1

description: replicate 1


title: 9273370138_H: PR Patient_CODE23 - T1

description: replicate 1


title: 9273370138_F: CR Patient_CODE18 - T1

description: replicate 1


title: 9252621035_J: PR Patient_CODE20 - T1

description: replicate 1


title: 9273370138_A: PR Patient_CODE17 - T1

description: replicate 1


title: 9252621019_L: PR Patient_CODE19 - T1

description: replicate 1


title: 9252621035_F: PR Patient_CODE15 - T1

description: replicate 1


title: 9234921140_H: PR Patient_CODE9 - T1

description: replicate 1


title: 9252621019_D: CR Patient_CODE16 - T1

description: replicate 1


title: 9252621019_F: CR Patient_CODE21 - T1

description: replicate 1


title: 9234921140_F: PR Patient_CODE6 - T1

description: replicate 1


title: 9273370138_L: CR Patient_CODE5 - T1

description: replicate 1


title: 9273370138_J: PR Patient_CODE10 - T1

description: replicate 1


title: 9273370139_B: PR Patient_CODE14 - T1

description: replicate 1


title: 9273370138_G: PR Patient_CODE23 - T0

description: replicate 1


title: 9252621019_K: PR Patient_CODE19 - T0

description: replicate 1


title: 9234921140_B: CR Patient_CODE13 - T1

description: replicate 1


title: 9273370138_C: CR Patient_CODE24 - T0

description: replicate 1


title: 9273370139_F: PR Patient_CODE22 - T0

description: replicate 1


title: 9273370139_H: PR Patient_CODE11 - T1

description: replicate 1


title: 9252621035_D: CR Patient_CODE7 - T1

description: replicate 1


title: 9273370139_D: PR Patient_CODE4 - T1

description: replicate 1


title: 8803828080_F: CR Patient_CODE8 - T1

description: replicate 1


title: 9234921140_D: CR Patient_CODE2 - T1

description: replicate 1


title: 9252621035_I: PR Patient_CODE20 - T0

description: replicate 1


title: 9273370139_J: CR Patient_CODE3 - T1

description: replicate 1


title: 9252621019_E: CR Patient_CODE21 - T0

description: replicate 1


title: 9252621035_B: CR Patient_CODE12 - T1

description: replicate 1


title: 9273370138_E: CR Patient_CODE18 - T0

description: replicate 1


title: 9273370139_G: PR Patient_CODE11 - T0

description: replicate 1


title: 9252621035_A: CR Patient_CODE12 - T0

description: replicate 1


title: 9252621035_E: PR Patient_CODE15 - T0

description: replicate 1


title: 9252621019_A: PR Patient_CODE14 - T0

description: replicate 1


title: nSyb_48h_ORN (N510Barcode_706-521)

first: Hongjie

last: Li

state: TX

address: one Baylor Plaza

institute: Baylor College of Medicine

description:
Single cell
df_libs.csv, htseq.tab

data_processing:
library strategy: 5’ RACE RNA-seq
alignment (STAR 2.4.2a, ENCODE standard options, except --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --  outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04)
gene count (HTSeq-count 0.7.1, default options, except -m intersection-strict)
Genome_build: Dmel r6.10
Supplementary_files_format_and_content: df_htseq_ORN.csv, df_libs_ORN.csv

source_name: in house

extract_protocol:
None
Modified SMART-seq2 (Li et al. 2017)

tag: genotype

tag: number of cells

tag: orn type

value: labels 44 ORN types


title: nSyb_48h_ORN (N509Barcode_721-521)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N543Barcode_702-516)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_702-515)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_727-511)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_724-521)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_714-518)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_705-503)

description:
Single cell
df_libs.csv, htseq.tab


title: 9252621019_C: CR Patient_CODE16 - T0

description: replicate 1

tag: age

tag: tissue


title: 9252621035_G: PR Patient_CODE17 - T0

description: replicate 1


title: 9234921140_A: CR Patient_CODE13 - T0

description: replicate 1


title: 9234921140_G: PR Patient_CODE9 - T0

description: replicate 1


title: 9252621035_C: CR Patient_CODE7 - T0

description: replicate 1


title: 9273370138_I: PR Patient_CODE10 - T0

description: replicate 1


title: 8803828080_E: CR Patient_CODE8 - T0

description: replicate 1


title: 9252621019_G: CR Patient_CODE5 - T0

description: replicate 1


title: nSyb_48h_ORN (N543Barcode_707-516)

description:
Single cell
df_libs.csv, htseq.tab


title: 9234921140_E: PR Patient_CODE6 - T0

description: replicate 1


title: Control

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: pooled samples

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60°C and hybridized on to a Agilent's Human Gene Expression  8x60k Array (AMADID: 039494). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the quantile normalization method .Gene based analysis was performed.

source_name: Corneal epithelium

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Corneal epithelium were collected after the surgical procedures of photorefractive keratectomy (PRK)

extract_protocol: RNA extraction was perforemd by using Qiagen Rneasy mini kit with Dnase Treatment.

treatment_protocol: Corneal epithelium were stored in -80°C deep freezer for downstream process

tag: subject

value: control

value: corneal epithelium


title: Haze predisposed

description: pooled samples

value: haze predisposed


title: 9273370139_I: CR Patient_CODE3 - T0

description: replicate 1


title: 9273370139_C: PR Patient_CODE4 - T0

description: replicate 1


title: 9273370139_E: CR Patient_CODE2 - T0

description: replicate 1


title: 9252621035_K: PR Patient_CODE1 - T0

description: replicate 1


title: nSyb_48h_ORN (N510Barcode_706-520)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_711-510)

description:
Single cell
df_libs.csv, htseq.tab


title: 85A10_48h_ORN (N543Barcode_714-508)

description:
Single cell
df_libs.csv, htseq.tab

value: labels 5 ORN types


title: nSyb_48h_ORN (N509Barcode_705-502)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_720-508)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_711-511)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_721-520)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_716-516)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N543Barcode_707-505)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_727-510)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_702-513)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N543Barcode_702-505)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_714-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_724-520)

description:
Single cell
df_libs.csv, htseq.tab


title: Am29_48h_ORN (N543Barcode_729-513)

description:
Single cell
df_libs.csv, htseq.tab

value: labels 2 ORN types


title: 85A10_48h_ORN (N543Barcode_723-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_724-518)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_704-522)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_707-510)

description:
Single cell
df_libs.csv, htseq.tab


title: 85A10_48h_ORN (N543Barcode_714-518)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_727-518)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_711-522)

description:
Single cell
df_libs.csv, htseq.tab


title: Am29_48h_ORN (N543Barcode_729-508)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_722-508)

description:
Single cell
df_libs.csv, htseq.tab


title: 9252621035_L: PR Patient_CODE1 - T1

description: replicate 1


title: 85A10_48h_ORN (N543Barcode_723-511)

description:
Single cell
df_libs.csv, htseq.tab


title: 85A10_48h_ORN (N543Barcode_715-515)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N543Barcode_707-510)

description:
Single cell
df_libs.csv, htseq.tab


title: 85A10_48h_ORN (N543Barcode_720-505)

description:
Single cell
df_libs.csv, htseq.tab


title: Am29_48h_ORN (N543Barcode_729-502)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_720-520)

description:
Single cell
df_libs.csv, htseq.tab


title: 85A10_48h_ORN (N543Barcode_720-515)

description:
Single cell
df_libs.csv, htseq.tab


title: 85A10_48h_ORN (N543Barcode_723-521)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_702-520)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N543Barcode_702-520)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_711-521)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_726-508)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_705-513)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_722-507)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N543Barcode_702-510)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_726-510)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N543Barcode_707-520)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_715-503)

description:
Single cell
df_libs.csv, htseq.tab


title: Am29_48h_ORN (N543Barcode_729-518)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_720-518)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_702-518)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_727-516)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_707-508)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_722-506)

description:
Single cell
df_libs.csv, htseq.tab


title: 85A10_48h_ORN (N543Barcode_715-513)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N543Barcode_707-508)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_711-520)

description:
Single cell
df_libs.csv, htseq.tab


title: 85A10_48h_ORN (N543Barcode_720-503)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N543Barcode_702-508)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_726-507)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_705-511)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_727-517)

description:
Single cell
df_libs.csv, htseq.tab


title: 85A10_48h_ORN (N543Barcode_715-503)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_720-507)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_716-515)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_711-508)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_714-516)

description:
Single cell
df_libs.csv, htseq.tab


title: 85A10_48h_ORN (N543Barcode_719-521)

description:
Single cell
df_libs.csv, htseq.tab


title: 85A10_48h_ORN (N543Barcode_714-507)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_702-507)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_714-510)

description:
Single cell
df_libs.csv, htseq.tab