title: FAIRE_STARR_RA_rep2

status: Public on Oct 21 2021

city: Berlin

first: Laura

middle: V

last: Glaser

address: Ihnestraße 63-73

department: Computational Molecular Biology

institute: Max Planck Institute for Molecular Genetics

description:
STARR-seq
FAIRE_STARR_RAvsInp_RPGC_subtract.bw
FAIRE_STARR_RAvsInp_RPGC_log2.bw
FAIRE_STARR_enh_RAind.bed

data_processing:
FAIRE-STARR-seq: Sequencing reads were aligned to the mouse genome (mm9) using Bowtie2 (Langmead and Salzberg, 2012)(-X 800 --fr --very-sensitive). UMI-tools (Smith, Heger and Sudbery, 2017) was used for UMI-aware removal of PCR duplicates. SAMtools (Li et al., 2009) was used to filter reads for proper pairs, alignment and quality scores (-h -b -f 3 -F 780 -q 5), to select reads mapping only to regular chromosomes (chr1-19, chrX and chrY), and to remove reads mapping to blacklisted regions (ENCFF547MET).
ChIP-seq: Paired-end ChIP-seq reads were mapped to the mm9 reference genome using Bowtie2 (Langmead and Salzberg, 2012)(--sensitive), and if applicable, mapped reads from the same experiment but different sequencing runs were first merged and then samtools (Li et al., 2009) was used to filter for proper pairs, alignment and quality scores (-h -b -f 3 -F 780 -q 10), to select reads mapping only to regular chromosomes (chr1-19, chrX and chrY), and to remove reads mapping to blacklisted regions (ENCFF547MET).
Genome_build: mm9
Supplementary_files_format_and_content: FAIRE-STARR-seq: Sequencing reads were demultiplexed for p5 (sample barcode) and writen into three fastq files: R1 and R3 containing read pairs and R2 containing the UMI (read from p7). Then reads were aligned to the mouse genome (mm9) using Bowtie2 (Langmead and Salzberg, 2012)(-X 800 --fr --very-sensitive). UMI-tools (Smith, Heger and Sudbery, 2017) was used for UMI-aware removal of PCR duplicates. SAMtools (Li et al., 2009) was used to filter reads for proper pairs, alignment and quality scores (-h -b -f 3 -F 780 -q 5), to select reads mapping only to regular chromosomes (chr1-19, chrX and chrY), and to remove reads mapping to blacklisted regions (ENCFF547MET).
Supplementary_files_format_and_content: FAIRE-STARR-seq: Significantly active enhancers, using the input library as control, were called using MACS2. The analysis was performed for each biological STARR-seq replicate individually, as well as for the merged reads from all replicates. Peaks were counted as active STARR-seq enhancers when they were called for the merged reads and for at least two of three biological replicates and are covered by at least three individual fragments.To score the FAIRE-STARR-seq enhancers, the computeMatrix tool of the deepTools package was used, this time to obtain the average enhancer activity signal (input and read depth normalized tracks by bigwigCompare, see above (--operation log2)) over the size-scaled regions (scaleregions mode).
Supplementary_files_format_and_content: ChIP-seq: Input and sequencing depth normalized signal tracks were computed with bamCompare (-of bigwig --operation subtract -bs 25 --smoothLength 50 -e --normalizeUsing RPKM --ignoreDuplicates) (Ramírez et al., 2016). Significant RARα binding sites were identified using MACS2 (Zhang et al., 2008) normalizing RARα ChIP to input sample.

source_name: Embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured under feeder-free conditions and routinely passaged every two days in ES medium plus LIF: Glasgow Minimum Essential Medium (Sigma-Aldrich) supplemented with 17% FBS (HycloneTM, SV30160.03, GE Healthcare), 2 mM GlutaMAXTM (Gibco), 100 U/ml Penicillin-Streptomycin (Gibco), 1x MEM Non-Essential Amino Acid Solution (Gibco), 1 mM Sodium Pyruvate (Gibco), 0.5 mM 2-Mercaptoethanol (Gibco), and recombinantly expressed LIF.

extract_protocol:
As input material for the reporter screen, DNA fragments representing accessible chromatin from E14 mESCs were used. Prior to DNA isolation, the cells were treated with retinoic acid (RA, Sigma, #R2625) for 4h. Accessible DNA was isolated by formaldehyde-assisted isolation of regulatory elements (FAIRE, Giresi et al., 2007) and subsequently cloned into the STARR-seq screening vector (Addgene #71509) following the protocol described in Arnold et al., 2013. E14 cells were transfected with this plasmid library using a NucleofectorTM 2b device applying the Mouse ES Cell Nucleofector Kit (Lonza, VAPH-1001). For each of the three biological replicates, four individual transfections, each with 5 µg plasmid library and 5x10e6 cells, were performed. The medium was changed 12 h after transfection and to half of the cells either LIF or 1 µM RA was added. After an additional 4 h of incubation, RNA was isolated from the combined transfections (of the same treatment) using the RNeasy Midi kit (Qiagen). The polyA RNA fraction was enriched using DnyabeadsTM Oligo(dT)25 (Invitrogen), residual DNA was digested using Turbo DNase (Invitrogen), and finally RNA was cleaned-up with Agencourt® RNAClean® XP beads (Beckman Coulter). cDNA was synthesized using SuperScriptTM III Reverse Transcriptase (Invitrogen) according to the manufacturer’s protocol, applying a reporter transcript-specific primer. This primer also includes the sequence of the Illumina PCR Primer 2.0 as overhang as well as eight randomly generated nucleotides that serves as unique-molecular identifier (UMI) to each cDNA molecule (CAAGCAGAAGACGGCATACGAGAT[N]8GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT).  cDNA was further amplified as described in Arnold et al., 2013, using adjusted reporter-specific primers based on Illumina’s TruSeq dual index system (universal: CAAGCAGAAGACGGCATACGA, sample specific: AATGATACGGCGACCACCGAGATCTACAC[barcode, n=6]ACACTCTTTCCCTACACGACGCTC).  As input control for FAIRE-STARR-seq, the input plasmid library was sequenced as well. To this end, the plasmid library was used for a pseudo “cDNA synthesis”, using the random-UMI primer and the KAPA HiFi HotStart ReadyMix (Roche) for 4 cycles with a prolonged synthesis step (70 sec) to individually label input fragments.
Input and FAIRE-STARR-seq libraries were amplified with Illumina’s TruSeq dual index based universal and barcoded primers applying the KAPA HiFi HotStart ReadyMix (Roche) for 12 PCR cycles.

treatment_protocol: E14 mESC cells were cultured in the presence of leukemia inhibitory factor (LIF) in order to maintain the pluripotent state of the cells. To exit from pluripotency and push the cells towards differentiation, LIF was withdrawn and retinoic acid (RA, Sigma, R2625) was added to the medium to a final concentration of 1 µM. For all experiments, 4h prior to harvest, cell culture medium was removed, cells washed twice with PBS and fresh ES medium was added containing either LIF or RA.

value: E14 ES cells

tag: treatment

value: RA


title: FAIRE_STARR_RA_rep3

type: SRA

country: Germany

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: cell line


title: FAIRE_STARR_LIF_rep3

description:
STARR-seq
FAIRE_STARR_LIFvsInp_RPGC_subtract.bw
FAIRE_STARR_LIFvsInp_RPGC_log2.bw
FAIRE_STARR_enh_mESC.bed
FAIRE_STARR_enh_LIFdep.bed
FAIRE_STARR_enh_mESC_scored.tab

value: LIF


title: E2.75_embryo_male_wt1_RNA

status: Public on Oct 24 2021

city: Heidelberg

first: Quentin

last: Gouil

state: VIC

address: Studley Road

country: Australia

institute: Olivia Newton-John Cancer Research Institute

description:
single-embryo RNA-seq
seRNA_seq_raw_counts.tsv
single_embryo_Control_Plate1_Collected_20190513_A2_RNA

data_processing:
as described in Wanigasuriya, Gouil et al. 2020 (https://doi.org/10.7554/eLife.55529)
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: gene counts matrices. RRBS/WGBS: bismark coverage reports of mC and C counts (total and by allele)

source_name: E2.75 embryo

tag: strain

tag: mating

value: B6 SMCH/MMTV-Cre ♀ (FL/FL, +/+) X Cast ♂

tag: Sex

value: male

tag: age

tag: tissue

value: embryo

tag: genotype

value: wt


title: RARA_Input

library_source: genomic

molecule: genomic DNA

extract_protocol:
6x10e5 low passage (< 10) E14 cells were plated per 15 cm culture dish and cultivated for 48 h in regular ES medium containing LIF. 4 h prior to cross-link cells were treated with RA as described in the treatment protocol. Then cells were washed with PBS, trypsinized and gently but thoroughly resuspended in ES medium to obtain a single cell suspension of  12x106 cells in 10 ml medium. Cells were cross-linked adding 1% formaldehyde for 5 min and the reaction was quenched using 125 mM glycine for another 5 min. After two wash steps with PBS, nuclei were prepared by washing twice with ice-cold Lysis Buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40, 1x proteinase inhibitor cocktail (PIC, Roche)), and finally cell pellets were resuspended in 100 µl Sonication Buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA pH 8.0, 1% Triton X-100, 150 mM NaCl, 0.1% SDS, 1x PIC) per 2x106 cells, incubated for 20 min on ice, homogenized 10 times with a 27G needle, and chromatin was sheared by sonication applying a Bioruptor Pico (Diagenode) device for 40 cycles (30 sec pulse, 30 sec pause). Cell debris was removed by centrifugation at maximum speed for 10 min at 4°C and chromatin containing supernatants were used for IP. To prepare input DNA, 30 μl aliquots (1/10 of the amount used per IP) were saved at -20°C. For IPs 300 μl chromatin (equals 6x 106 cells) were incubated with 4 μl of RAR antibody (Diagenode C15310155, polyclonal rabbit IgG, Lot # A704-001) at 4°C overnight under rotation. Protein-A/-G agarose (sc-2003) was equilibrated with sonication buffer, 30 µl 1:1 slurry was added to each sample and incubated at 4°C for 4 h under constant rotation. Beads were extensively washed with: 1x Wash Buffer I (20 mM Tris-HCl, pH 8.0, 2 mM EDTA, pH 8.0, 1% Triton X-100, 150 mM NaCl, 0.1% SDS, 1x PIC), 1x Wash Buffer II (20 mM Tris-HCl, pH 8.0, 2 mM EDTA, pH 8.0, 1% Triton X-100, 500 mM NaCl, 0.1% SDS, 1x PIC), 1x Wash Buffer III (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1x PIC) for 5 min under rotation, and 2x with TE (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0) for 1 min. Protein-DNA complexes were eluted with 100 μl Elution Buffer (25 mM Tris-HCl, pH 7.5, 10 mM EDTA, pH 8.0, 1% SDS, 100 mM NaCl). Input samples were adjusted to 100 μl with Elution Buffer. Eluates and input samples were first incubated with RNase A (100 µg/ml final) for 1 h at 37°C and then with Proteinase K (200 µg/ml final, Ambion) for 1 h at 50°C. Cross-linking was reversed by incubation at 65°C overnight. DNA was recovered using Zymo ChIP DNA clean & concentrator kit (D5202).
Sequencing libraries for RAR ChIP and Input fragments were prepared using the KAPA Hyper Prep Kit (Roche).

tag: chip antibody


title: FAIRE_STARR_LIF_rep1


title: FAIRE_STARR_Input

description:
STARR-seq
plasmid DNA

molecule: other


title: RARA_ChIP


title: NPC G4 CUT&Tag Rep1 Batch5

status: Public on Oct 13 2021

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Library strategy: CUT&TAG
read alignment: reads were aligned with bowtie2 (v.2.3.5.1) using --fast-local and samtools (v1.10).
deduplication: BAM files were deduplicated with picard (v2.23.4) MarkDuplicates
blacklist: Blacklisted regions were removed from the BAM file with bedtools (v2.29.2) intersect using ENCODE blacklist bed files for mm9 or hg19
genome coverage: Normalized (RPGC, 1x Genome Coverage) coverage tracks were generated using deepTools (v3.3.2) bamCoverage using parameters -binSize 5 --normalizeUsing RPGC
Genome_build: mm9, hg19
Supplementary_files_format_and_content: Normalized Ggenomic tracks in bigwig format

source_name: NPC

growth_protocol: Mouse neural progenitor cells were cultured in 1:1 mixed DMEM/F12 medium (Gibco, 31330-038) and neurobasal medium (Gibco, 21103-049) supplemented with 2mM L-Glutamine (Thermo fisher, 25030081), 0.5X B27 (Gibco, 17504-044), 1X N2 (Millipore, SCM012), 0.1mM β-mercaptoethanol (Sigma, M3148), 10ng/ml EGF (Peprotech, 315-09), 10ng/ml FGF-basic (Peprotech, 100-18C), on 0.1% gelatin-coated flasks.

extract_protocol:
CUT&Tag experiment was performed as described previously (Kaya-Okur et al. 2019) with minor modifications" Briefly, 1x10e5 cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Bangs Laboratories, BP531) with incubation at room temperature for 10min. The beads-bound cells were incubated in 200μl of primary antibody buffer (wash buffer with 2mM EDTA and 0.05% digitonin) with 1:100 BG4 antibody or S9.6 (Millipore, MABE1095) antibody dilution at 4℃ by rotating overnight. The next day, the primary antibody buffer was removed and cells were washed with 800μl of dig-wash buffer (wash buffer with 0.05% digitonin) three times. After washing, BG4 antibody-incubated cells were resuspended with 200ul of dig-wash buffer with 1:100 dilution of anti-FLAG antibody (Sigma, F1804) and incubated at room temperature for 1 hour by rotating. Cells were washed with 800μl of dig-wash buffer briefly three times to remove unbound antibodies. S9.6-treated or anti-FLAG treated cells were incubated with 1:100 dilution of anti-mouse antibody (Sigma, M7023) in 200μl of dig-wash buffer at room temperature for 1 hour by rotating. After brief wash with dig-wash buffer, cells were resuspended in 200ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:200 dilution of pA-Tn5 adapter complex and incubated at room temperature for 1 hour by rotating. pA-Tn5-bound cells were washed with 800ul of dig-300 buffer three times, followed by tagmentation in 200ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 15mM  EDTA, 500μg/ml proteinase K and 0.1% SDS were added and further incubated at 63℃ for another 1 hour to stop tagmentation and digest protein.
Genomic DNA was extracted and purified with DNA Clean & Concentrator-5 (Zymo research, D4013).
To generate G4 or R-loop libraries, purified genomic DNA were mixed with the universal i5 primer and barcoded i7 primer, and amplified with NEBNext Ultra II Q5 Master Mix (NEB, M0544). The library PCR products were cleaned up with Agencourt AMPure XP beads (Beckman Coulter, A63881) and sequenced with Illumina Nextseq 500 instrument.

tag: cell type

value: mouse neural progenitor cells

tag: antibody


title: mES S9.6 CUT&Tag mock Batch6

source_name: mES

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured feeder-free in 0.1% gelatin-coated flasks (Sigma, G1890) under standard conditions (10% CO2, 90% humidity, 37 °C) in KnockOut DMEM (LifeTechnologies, 10829018), 2 mM Alanyl-glutamine (Sigma, G8541), 0.1 mM non-essential amino acids (Sigma, M7145) 15% fetal bovine serum (FBS) (Sigma, F7524), 0.1 mM β-mercaptoethanol (Sigma, M3148), ESGRO Leukemia Inhibitory Factor (LIF) (Millipore, ESG1107), Penicillin-Streptomycin (Sigma, P4333).

value: mouse embryonic stem cells

value: Cells were mock treated with nuclease digestion buffer at 30C for 30min before BG4 antibody incubation


title: mES G4 CUT&Tag triptolide Rep2 Batch4

value: Triptolide


title: NPC G4 CUT&Tag Rep2 Batch5


title: mES G4 CUT&Tag Rep1 Batch5


title: mES G4 CUT&Tag Rep2 Batch5


title: mES G4 CUT&Tag DRB Rep2 Batch4

value: DRB


title: mES G4 CUT&Tag mock Rep2 Batch4

value: DMSO


title: mES G4 CUT&Tag DRB Rep1 Batch4


title: mES G4 CUT&Tag triptolide Rep1 Batch4


title: mES G4 CUT&Tag mock Rep1 Batch4

extract_protocol:
CUT&Tag experiment was performed as described previously (Kaya-Okur et al. 2019) with minor modifications Briefly, 1x10e5 cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Bangs Laboratories, BP531) with incubation at room temperature for 10min. The beads-bound cells were incubated in 200μl of primary antibody buffer (wash buffer with 2mM EDTA and 0.05% digitonin) with 1:100 BG4 antibody or S9.6 (Millipore, MABE1095) antibody dilution at 4℃ by rotating overnight. The next day, the primary antibody buffer was removed and cells were washed with 800μl of dig-wash buffer (wash buffer with 0.05% digitonin) three times. After washing, BG4 antibody-incubated cells were resuspended with 200ul of dig-wash buffer with 1:100 dilution of anti-FLAG antibody (Sigma, F1804) and incubated at room temperature for 1 hour by rotating. Cells were washed with 800μl of dig-wash buffer briefly three times to remove unbound antibodies. S9.6-treated or anti-FLAG treated cells were incubated with 1:100 dilution of anti-mouse antibody (Sigma, M7023) in 200μl of dig-wash buffer at room temperature for 1 hour by rotating. After brief wash with dig-wash buffer, cells were resuspended in 200ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:200 dilution of pA-Tn5 adapter complex and incubated at room temperature for 1 hour by rotating. pA-Tn5-bound cells were washed with 800ul of dig-300 buffer three times, followed by tagmentation in 200ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 15mM EDTA, 500μg/ml proteinase K and 0.1% SDS were added and further incubated at 63℃ for another 1 hour to stop tagmentation and digest protein.
Genomic DNA was extracted and purified with DNA Clean & Concentrator-5 (Zymo research, D4013).
To generate G4 or R-loop libraries, purified genomic DNA were mixed with the universal i5 primer and barcoded i7 primer, and amplified with NEBNext Ultra II Q5 Master Mix (NEB, M0544). The library PCR products were cleaned up with Agencourt AMPure XP beads (BeckmaGenomic DNA was extracted and purified with DNA Clean & Concentrator-5 (Zymo research, D4013).
To generate G4 or R-loop libraries, purified genomic DNA were mixed with the universal i5 primer and barcoded i7 primer, and amplified with NEBNext Ultra II Q5 Master Mix (NEB, M0544). The library PCR products were cleaned up with Agencourt AMPure XP beads (Beckman Coulter, A63881) and sequenced with Illumina Nextseq 500 instrument.


title: JFH-EYFP+P

status: Public on Oct 09 2021

city: Taichung

first: Wei-Chung

last: Cheng

address: No.91, Hsueh-Shih Road

country: Taiwan

institute: China Medical University

description: JFH1 infected Huh7.5.1 cells were gated high FITC intensity (Log 10^2.5–Log 10^5) as defined as high-viral-load cells (JFH-EYFP+P)

data_processing:
RNA-Seq libraries were prepared Illumina® TruSeq RNA Library Prep Kit v2 and were sequenced using Illumina® Hiseq2500 to obtain 150-bp paired-end reads.
The sequencing depth for each sample was >20 million reads. The reads were aligned with TopHat 2.0.13 to GRCh37 with default parameters and then were assembled by Cufflink 2.2.1,
using Ensembl v79 annotations. Transcript abundance was measured in fragments per kb of exon per million fragments mapped (FPKM).
Genome_build: GRCh37
Supplementary_files_format_and_content: genes_fpkm_table.txt

molecule: total RNA

organism: Homo sapiens

source_name: JFH1 infectious Huh751 cells

growth_protocol: Huh7.5.1 cells in medium were infected by incubation with HCV JFH1-EYFP labelled (HCV cc, developed by Dr. Machi Yamamoto) for 6 hours after which the medium was replaced with fresh medium and cells were incubated for 5 days.

extract_protocol:
Total RNA was extracted using TRIzol reagent. The quality of total RNA was analyzed by the Agilent 2100 bioanalyzer with the RNA 6000 Nano LabChip kit.
RNA-seq libraries were prepared using Illumina® TruSeq RNA Library Prep Kit v2 and were sequenced using Illumina® Hiseq2500 to obtain 150-bp paired-end reads.

treatment_protocol: HCV JFH1-EYFP infections cells were distinguishable into two cell populations with low-viral loads (R1 region, 28% of infectious cells) and high-viral loads (R2 region, 26% of infectious cells) by fluorescence intensity after 5 days infection. Low-viral load cells here on referred to as “early long-term HCV (eL-HCV)” and high-viral load cells here on referred to as “short-term HCV (S-HCV)". eL-HCV cells of Day 5 were cultured to day 30 and sorted low-viral loads cells and confirmed to be a distinct population of long-term-HCV (L-HCV) cells referred to as long-term HCV (L-HCV) by FACS.

tag: viral load

value: High viral loads

tag: time

value: 5 culture days

tag: sample type

value: S-HCV


title: JFH-EYFP-N

description: JFH1 infected Huh7.5.1 cells were gated  low FITC intensity (10^0–Log 10^1.5) as defined as low-viral-load cells (JFH-EYFP-N)

value: Low viral loads

value: eL-HCV


title: mES S9.6 CUT&Tag Mungbean-100U Batch6

value: Cells were treated with 100 units Mung Bean nuclease at 30C for 30min before BG4 antibody incubation


title: RNASeq_Ubc9-WT_replicate1

status: Public on Oct 22 2021

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
Analysis of RNA-seq data was carried out in User-friendly Transcriptome Analysis Pipeline UTAP 27. In short, reads were trimmed using ‘cutadapt’ function.
Reads were then mapped to the mouse genome mm10 using STAR method. Followed by quantification with RefSeq annotated genes. Counting was performed using HTSeq.
Normalization of the counts was done using DESeq2. Raw P-values were adjusted for multiple testing using Benjamini and Hochberg.
Genome_build: mm10
Supplementary_files_format_and_content: csv matrix file containing raw + normalized counts per gene, and KO/WT FoldChange and p-value

source_name: mouse embryonic stem cells

growth_protocol: Cells were grown in 2i/LIF for 3-4 passages.

extract_protocol:
Total RNA was extracted from cells using Trizol (Ambion Life Technologies) and chloroform, followed by washes with isopropanol and 70% ethanol. 1 mg of extracted RNA was used as an input for mRNA isolation using PolyA beads.
For H1-TKO RNA-seq: Libraries preparation was carried out using Lexogen's SENSETM mRNA-Seq Kit V2 according to manufacturer’s instruction.
For Ubc9-depletion RNA-seq: Libraries preparation was carried out using ScriptSeq v2 RNA-seq library preparation kit according to manufacturer’s instruction.

treatment_protocol: For Ubc9 depletion, DOX was added for 72 hours.


title: LVL_S2

description: JFH1 infected Huh7.5.1 cells were gated and defined as low-viral-load cells for 30 days cell culture.

value: over 30 culture days

value: L-HCV


title: JFH-72H-2

description: JFH1 infectious Huh751 cells for 6 hr with viral particles then change medium for 72 hr.

value: HCV normal viral laods


title: 751-2

description: Hepatocellular carcinoma cell line

source_name: Hepatocellular carcinoma cell line

value: Non viral infected


title: LbaCas12a, SauCas9, SpyCas9 edited embryo 34 [ALL34]

status: Public on Oct 25 2021

city: Salt Lake City

first: James

middle: A

last: Gagnon

state: UT

address: 1390 Presidents Circle, Crocker Science Center Receiving

country: USA

institute: University of Utah

data_processing:
library strategy: Amplicon-seq
Following the GESTALT pipeline (Mckenna Science 2016), low quality bases were removed with Trimmomatic
Paired reads were merged using FLASH
Merged reads were aligned to unedited barcode sequence using NEEDLEALL with gap open penalty 10 and gap extension penalty 0.5
Reads were required to have >85% matching bases, and match at least 90 bases of the reference
Target sites were deemed edited if there was an insertion or deletion event present within 3 bases of the predicted cut site (4 nucleotides 5' of the SpyCas9 PAM, 3 nucleotides 5' of SauCas9 PAM, 21 nucleotides 3' of LbaCas12a PAM), or if a deletion spanned the site entirely.
An edited barcode was then defined as the complete list of insertion and deletion events (i.e. ‘editing events’) within the consensus sequence
Genome_build: N/A
Supplementary_files_format_and_content: event - string of insertion and deletions within a barcode; array - index of barcode after sorting for descending abundance; count - number of reads mapped to a given barcode; proportion - proportion of total reads mapped to a given barcode within a sample

organism: Danio rerio

source_name: whole embryo

growth_protocol: Embryos were grown at 28.5C for 2 days

extract_protocol:
Genomic DNA was prepared using HoTSHOT lysis
Libraries were prepared using two rounds of PCR to add Illumina adapters and 8 bp dual indexes for multiplexing.

treatment_protocol: SpyCas9 editing was induced by heat shock at 37C for 30 minutes

tag: developmental stage

value: 2 dpf embryo

tag: strain background

value: TU wild type

tag: sample group

value: LbaCas12a, SauCas9, SpyCas9 edited


title: FAIRE_STARR_RA_rep1

value: E14 ES cells

tag: treatment

value: RA


title: FAIRE_STARR_LIF_rep2

tag: cell line

value: LIF


title: Old_D3_5_C

status: Public on Sep 29 2021

city: Ithaca

first: Lauren

middle: D

last: Walter

state: NY

address: 161 Weill Hall

department: Biomedical Engineering

institute: Cornell University

data_processing:
Libraries were sequenced on Illumina NextSeq 500 using paired-end 26 + 8 + 58 (according to 10X Chromium Single Cell 3' protocol)
Sequences were aligned to mm10 using cellranger v3.1.0 pipeline
Ambient RNA content was removed using SoupX v1.4.5
Gene expression data was processed with Seurat v3.1.5
Initial data filtering (minimum cells to express an included gene = 3, minium genes to be expressed in an included cell = 500)
Filtering by percent mitochondiral genes in included cells (maximum 30%), number of UMIs in included cells (minimum 1000)
Log-normalization of expression data
Cell annotations in metadata derived from shared nearest neighbor clustering
Genome_build: mm10
Supplementary_files_format_and_content: zipped, market exchange format (MEF) for raw, filtered, and scrubbed (SoupX) transcript count matrices; .csv files of single-cell metadata information

source_name: Tibialis anterior muscle

extract_protocol:
Single-cell RNA-sequencing libraries were prepared using a Chromium Single Cell 3' Reagent Kit (10X Genomics, v3 kit) following the directions of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: 20 months

value: F

value: Tibialis anterior muscle

tag: injury

value: Notexin injury (Day 3.5)


title: mES S9.6 CUT&Tag Mungbean-150U Batch6

value: mouse embryonic stem cells

value: Cells were treated with 150 units Mung Bean nuclease at 30C for 30min before BG4 antibody incubation


title: Old_D1_D

tag: Sex

value: Notexin injury (Day 1)


title: Old_D1_C

tag: age


title: Old_D7_B

tag: tissue

value: Notexin injury (Day 7)


title: Old_D5_C

value: Notexin injury (Day 5)


title: Old_D7_A


title: Old_D3_5_B


title: Old_D5_B


title: Old_D3_5_A


title: Old_D1_B


title: Old_D2_B

value: Notexin injury (Day 2)


title: Old_D0_C

value: Uninjured


title: Old_D2_C


title: Old_D0_D


title: Patient 2 left lymph node

status: Public on Sep 19 2021

city: Shanghai

first: Yulong

last: Wang

state: Shanghai

address: 270 Dongan Road, Shanghai

department: Department of Head and Neck Surgery

country: China

institute: Fudan University Shanghai Cancer Center

description: left lymph node patient 2

data_processing:
Cell Ranger (v3.0.1, 10X Genomics)
Genome_build: GRCh38
Supplementary_files_format_and_content: Filtered single-cell gene expression matrix and associated cell barcodes and gene features

source_name: lymph node metastase

extract_protocol: The cell suspension of each sample was subjected to the Gel Bead Kit V3 (10x Genomics, Pleasanton, CA) for library preparation according to the standard protocols.

treatment_protocol: Fresh samples were resected and washed twice with 1x PBS (Gibco). Each sample was cut into approximately 1 mm3 pieces and enzymatically digested with 10 mL digestion medium containing 1 mg/mL collagenase and 1 U/mL Dispase II (Gibco). These samples were subsequently incubated at 37 ℃ for 50 min and were triturated with pipette per 15 min. The suspended cells were washed with 20% fetal bovine serum (FBS) in Dulbecco’s Modified Eagle Medium (DMEM) and filtered through a 40-µm Cell-Strainer nylon mesh (BD) and centrifuged at 700 × g for 10 min. After removing the supernatant, the cell pellet was washed twice with MACS buffer (PBS containing 1% FBS, 0.5% EDTA, and 0.05% gentamycin) and then re-suspended in the sorting buffer (PBS supplemented with 1% FBS).  Subsequently, the suspended cells were stained with DRAQ5 and DAPI (Sigma) to harvest nucleated living cells. After antibody incubation, the cells were washed twice with cold PBS and reconstituted in DMEM with 20% FBS. Cell sorting was performed with a MoFlo Astrios EQ Cell Sorter (Beckman Coulter). Unstained cells were routinely used to define FACS gating parameters and sorted into DMEM media supplemented with 20% FBS.

tag: patient id

value: Patient 2

value: lymph node

value: lymph node metastase

value: No treatment


title: Patient 2 tumor

description: tumor patient 2

source_name: thyroid tumor

value: thyroid gland

value: thyroid tumor


title: Patient 1 paratumor

description: paratumor patient 1

source_name: thyroid paratumor

value: Patient 1

value: thyroid paratumor


title: Old_D1_A

value: 20 months

value: F

value: Tibialis anterior muscle


title: Old_D0_B


title: Old_D3_5_D

value: Notexin injury (Day 3.5)


title: DRG cells - spared nerve injury (SNI), day 14

status: Public on Sep 01 2021

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

data_processing: The FASTQ files were mapped to refdata-cellranger-mm10 reference by cellranger count (cellranger-3.0.2) and the feature-barcode matrices were stored in the Market Exchange Format (MEX).

source_name: Dorsal root ganglion cells

growth_protocol: Male C57bl/6J mice (Janvier Labs, France) were housed in pairs of 2 littermates with water and chow (Altromin 1342, Brogaarden, Denmark) available ad libitum and with a 12-hour light/dark cycle. Small-grained bedding after spared nerve injury.

extract_protocol:
Mice were anesthetized and perfused prior to dissection of dorsal root ganglions (DRGs, L3 + L4 from both sides). Whole DRGs were subsequently enzymatically (collagenase, dispase) and mechanically dissociated to a single cell suspension and passed through a 40-micron cell strainer.
The 3’ expression library was generated with Chromium Single Cell 3’ Library, Gel Dead & multiplex kit and Chip Kit (v3, 10x Genomics).

value: Dorsal root ganglion, lumbar, L3 + L4

value: postnatal week 13

value: Spared nerve injury (double sided), 14 days

value: Male


title: Patient 1 tumor

description: tumor patient 1


title: DRG cells - spared nerve injury (SNI), day 7

value: Spared nerve injury (double sided), 7 days


title: SarCMSK3

status: Public on Aug 26 2021

city: Tucson

first: Jared

last: Churko

state: Arizona

address: 1501 N CAMPBELL AVE LSN 461

department: CMM

institute: University of Arizona

data_processing:
RNA-seq: reads were mapped to reference Ensembl GRCh38 genome using STAR and RPKM values were obtained using AltAnalyze
Genome_build: GRCh38
Supplementary_files_format_and_content: RPKM values

growth_protocol: hPSCs were grown in E8 media on Matrigel, primarly endothelial cells were grown in endothelial cell media (DMEM supplemented with 5ng/mL VEGF, 5 ng/mL EGF, 5 ng/mL FGF basic, 15 ng/mL IGF-1, 10 mM glutamine, 0.75 Units/mL heparin sulfate, 1 µg/mL hydrocortisone, 50 µg/mL ascorbic acid, and 2% fetal bovine serum).

extract_protocol:
Direct-zol RNA Miniprep Plus kit (Zymo Research).
Zymo-Seq RiboFree Total RNA Library Kit for SARS-CoV-2, NEB  Next  Ultra  II  non-directional  kit for   lisinopril  and  losartan  treated  cells
Libraries were generated at Novogene

treatment_protocol: 5 µM lisinopril (Cayman Chemical Co.), 10 µM losartan carboxylic acid (a potent active metabolite of losartan) (Cayman Chemical Co.), or DMSO (Sigma-Aldrich)

tag: infection

value: No Treatment


title: SarCMSK2

tag: cell type


title: Old_D7_C

value: Notexin injury (Day 7)


title: DRG cells - naïve

value: Naïve (untreated)


title: SarCMSK1


title: losCMSK3

value: Uninfected

value: Losartan


title: losCMSK2


title: Old_D5_A

value: Notexin injury (Day 5)


title: Old_D2_A

value: Notexin injury (Day 2)


title: lisCMSK3

value: Lisinopril


title: lisCMSK2


title: lisCMSK1


title: losCMSK1


title: Patient 2 paratumor

description: paratumor patient 2

value: Patient 2

value: thyroid gland

value: thyroid paratumor

value: No treatment


title: EC46los

source_name: Primary endothelial

value: hEC


title: EC46cnt


title: 46EClos


title: ConCMSK2

description:
GEO_SAR.txt
GEO_CM_RPKM.txt


title: EC46lis


title: 37EClos


title: 46EClis


title: 46ECcnt


title: CMH7lis


title: ConCMSK1

description:
GEO_SAR.txt
GEO_CM_RPKM.txt


title: CMH7cnt


title: MultiplexedPBMC

status: Public on Aug 11 2021

city: Farmington

first: Duygu

last: Ucar

state: Connecticut

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
snATAC-seq reads were processed by using 10x's cellranger-atac software, version 1.2.0, with default parameters. Hg19 was used as the reference genome.
Doublet cells were identified by using the novel AMULET method.
Genome_build: hg19
Supplementary_files_format_and_content: snATAC-seq peaks, cell barcodes and matrix showing the number of reads for a particular cell at a particular peak, aggregate reads for the clusters identified on the same peaks, aligned and sorted reads in BAM format, single cell barcode information from cellranger atac output, processed seurat object in R data format.
Supplementary_files_format_and_content: control_fragment_files.tar includes the processed fragment files.

source_name: PBMC

extract_protocol:
Cryopreserved PBMCs isolated from three healthy unrelated donors were obtained from Hemacare (Los Angeles, CA, USA).
PBMCs were thawed and cultured in RPMI 1640 with GlutaMax and HEPES (ThermoFisher, cat#72400047) supplemented with 10% FBS and 1% pen/strep overnight on ultra low-attachment 10cm dishes (Corning, cat#3262). Following overnight culture, suspension PBMCs were transferred to a 50mL conical tube and placed on ice. Adherent PBMCs were lifted using TrypLE and pooled with the suspension PBMCs. The cells were then washed twice with ice-cold PBS before nuclei isolation according to the “Nuclei Isolation for Single Cell ATAC Sequencing” protocol from 10x Genomics. Isolated nuclei were then resuspended in ice-cold 10x Genomics diluted nuclei buffer and counted. 15,000 nuclei from each PBMC donor were then subjected to transposition according to the “Chromium Next GEM Single Cell ATAC Reagent Kits v1.1” protocol from 10x Genomics. After transposition, nuclei from each donor were pooled, pelleted, resuspended in 10x Genomics ATAC Buffer B, and counted prior to microfluidic capture (targeting ~10,000 recovered nuclei). Next-generation sequencing library preparation was then performed according to supplier recommendations before sequencing on a single lane of a Illumina NovaSeq SP100 flow cell.

value: PBMC

tag: diagnosis

value: Healthy


title: 37EClis


title: naive.positive.id_12

status: Public on Aug 03 2021

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Reads were aligned to the mouse genome (UCSC version mm10) with STAR (version 2.7.0c) using the multi-map settings '-outFilterMultimapNmax 10 --outSAMmultNmax 1'.
Mapped reads were assigned to genes based on the ENSEMBL (version 94) using featureCounts and extra options ‘-O --read2pos 5 –M –s 2 –p -B’.
Genes were filtered for a log-CPM>0 in at least 2 samples (n=12251 genes).
Genome_build: mm10
Supplementary_files_format_and_content: counts.tsv; tab-separated values text file with columns: 1. Ensembl gene Id, 2. Entrez gene id, 3. gene symbol, 4. gene name, 5. gene length (exon-union model), 6. - 24. counts per sample

source_name: primary hepatocytes

extract_protocol:
Animals were euthanized with CO2 followed by  perfusion of the liver with HBSS (0.5mM EGTA) and subsequent digestion with digestion medium (L15 medium, 40 mg/L Liberase (Roche)). Hepatocytes were sorted into TRI Reagent LS (Sigma-Aldrich) and RNA was extracted using the Direct-zol RNA MicroPrep kit (Zymo Research).
TruSeq Stranded mRNA Library Kit (Cat# 20020595, Illumina, San Diego, CA, USA) and the TruSeq RNA UD Indexes (Cat# 20022371, Illumina, San Diego, CA, USA) were used for library preparation

tag: background strain

value: primary hepatocytes

value: naive

tag: rfp status

value: positive

tag: animal id

value: female


title: naive.positive.id_11


title: naive.negative.id_8

value: negative

value: male


title: naive.positive.id_13


title: naive.negative.id_9


title: naive.negative.id_10


title: naive.negative.id_7


title: infected.negative.id_1

value: infected


title: ConCMSK3

description:
GEO_SAR.txt
GEO_CM_RPKM.txt

value: Uninfected

value: No Treatment


title: CMH7los

value: Losartan


title: infected.positive.id_4


title: infected.negative.id_4


title: infected.positive.id_5


title: infected.negative.id_5


title: infected.negative.id_6


title: infected.positive.id_1


title: infected.positive.id_6


title: infected.positive.id_3


title: infected.positive.id_2


title: 37ECcnt


title: LDER_Nor_Pan_scRNA2

status: Public on Jul 29 2021

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

institute: Frederick National Labroatory for Cancer Research

data_processing:
Basecalling was using Illumina RTA v2.4.11
Demultiplex was using BCL2FASTQ v2.17 and allowing I mismatch in barcodes.
Aslignment, initial gene and transcript counting and clustering analysis were done using Cellranger v3.1.0
Seurat v2.3.4 was used for initial data filtering, normalizaiton and clustering  analysis.
SingleR  (v1.0) was used for cell type classfication and DigitalCellSorter was used for subpopulation identification  based on known marker genes
Genome_build: mm10
Supplementary_files_format_and_content: gene matrix .h5 file

source_name: mouse pancreas

extract_protocol:
extraction protocol per the manufacturer guidelines (10X Genomics, Pleasanton, CA)
10x Genomics Chromium Single Cell 5' v2 Dual Index Gene Expression

value: Nomal pancreas

value: KPC mouse model


title: LDER_Nor_Pan_scRNA3


title: LDER_Nor_Pan_scRNA5


title: LDER_Nor_Pan_scRNA6


title: Un_Nor_P2_WTS


title: Un_Nor_P3_WTS


title: Pancreas_A7_050318


title: Pancreas


title: LDER_tumor_scRNA5

value: pancreatic tumors


title: LDER_tumor_scRNA6


title: Un_Nor_P1_WTS


title: LDER_tumor_scRNA4


title: LDER_tumor_scRNA3


title: LDER_tumor_scRNA1


title: Un_Tum_P4_WTS


title: Un_Tum_P2_WTS


title: Un_Tum_P3_WTS


title: Tumor_A7_050318


title: infected.negative.id_3


title: Tumor_A2_050318


title: Un_Tum_P1_WTS


title: LDER_Nor_Pan_scRNA4


title: LDER_tumor_scRNA2


title: LDER_Nor_Pan_scRNA1


title: Primary_Tumor_050118


title: Primary_Tumor


title: Mouse_Tumor_1_10mM


title: infected.negative.id_2


title: ATAC HH24 replicate 2

data_processing:
Samples were mapped to the chicken genome (UCSC version galGal4) with the qAlign function of the R/Bioconductor package QuasR (version 1.8.2) using options '-m 1 --best --strata --maxins 2000'.
Coverage tracks per sample were generated by tiling the genome in 10 bp windows, counting the number of 5'-ends per window using the function bamCount from the bioconductor package bamsignals (bioconductor version 3.6) and exporting these window counts in bigWig format using the export function of the bioconductor package rtracklayer.
Supplementary_files_format_and_content: bigWig files with scores representing RPKM values (within 10 bp windows)

organism: Gallus gallus

source_name: wing bud

growth_protocol: Fertilized chicken White Leghorn eggs were purchased from a local supplier, incubated at 38ºC and staged according to Hamburger and Hamilton (1951).

extract_protocol:
Per biological replicate, dissected left and right wing buds from one embryo at the desired stage were pooled and dissociated in PBS (Gibco 14040-117) at 4ºC using a 2ml glass tissue grinder (Sigma-Aldrich D8938; 20 strokes with pestle A followed by 20 strokes with pestle B).
75'000 cells were processed per sample for ATAC-Seq as described in Buenrostro et al., 2015. Curr Protoc Mol Biol. 2015 Jan 5;109:21.29.1-9. doi:10.1002/0471142727.mb2129s109

value: wing buds

tag: developmental stage

value: White Leghorn


title: Un_Nor_P4_WTS


title: H3K27Ac ChIP-Seq, fore limb, E10.5, input

data_processing:
Reads were aligned with bowtie2 (version 2.3.2) to the mouse genome (UCSC version mm10).
The output was sorted and indexed with samtools (version 1.3.1). Duplicated reads were marked with picard (version 2.9.2).
Regions listed in the ENCODE blacklist for mm10 (version 2014) were excluded.
Narrow peaks where called for each replicate seperately with macs2 (version 2.1.1.20160309) using the option '-q 0.01 -g 2652783500 --keep-dup all'. Called peaks were additionally filter for logFC>1.5 and merged across biological replicates. The maximal peak distance for merging was set to the average fragment size (164 bases).
The resulting merged and filtered peaks were converted to bigBed format using the UCSC command line tool "bedToBigBed".
Coverage tracks were generated with macs2 and options "-B --SPMR". The resulting bedGraph files were converted to bigWig format using the UCSC command line tools "bedSort" and "bedGraphToBigWig".
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files with fragment pileups; bigBed file with merged peak regions

source_name: forelimb

extract_protocol:
Embryos were cross linked with 1%formaldehyde and chromatin immunoprecipitation was performed according to Sheth et 2016.
 Libraries were prepared with MicroPlex Library preparation kit V2 (Diagenode) according to the manufactures instructions

value: forelimb

tag: antibody

value: input


title: H3K27Ac ChIP-Seq, fore limb, E10.5, replicate 2


title: ATAC HH24 replicate 1


title: ChIP Input fore limb HP E11.5

description: CHIP_H3K27Ac_FL_HP_E11.5_mergedPeaks.bigBed

data_processing:
Reads were aligned with bowtie2 (version 2.3.2) to the mouse genome (UCSC version mm10).
The output was sorted and indexed with samtools (version 1.3.1). Duplicated reads were marked with picard (version 2.9.2).
Regions listed in the ENCODE blacklist for mm10 (version 2014) were excluded.
Narrow peaks where called for each replicate seperately with macs2 (version 2.1.1.20160309) using the option '-q 0.01 -g 2652783500 --keep-dup all'. Called peaks were additionally filter for logFC>1.5 and merged across biological replicates. The maximal peak distance for merging was set to the average fragment size (164 bases).
The resulting merged and filtered peaks were converted to bigBed format using the UCSC command line tool bedToBigBed.
Coverage tracks were generated with macs2 and options "-B --SPMR". The resulting bedGraph files were converted to bigWig format using the UCSC command line tools bedSort and bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files with fragment pileups; bigBed file with called peak regions

source_name: fore limb buds

extract_protocol:
Embryos were cross linked with 1%formaldehyde and chromatin immunoprecipitation was performed according to Sheth et 2016.
Libraries were prepared with MicroPlex Library preparation kit V2 (Diagenode) according to the manufactures instructions

value: fore limb


title: H3K27Ac ChIP-Seq, fore limb, E10.5, replicate 1


title: ChIP H3K27Ac fore limb HP E11.5 replicate 2


title: ATAC fore limb E9.75 replicate 2

data_processing:
Samples were mapped to the mouse genome (UCSC version mm10) with the qAlign function of the R/Bioconductor package QuasR (version 1.8.2) using options '-m 1 --best --strata --maxins 2000'.
Coverage tracks per sample were generated by tiling the genome in 10 bp windows, counting the number of 5'-ends per window using the function bamCount from the bioconductor package bamsignals (bioconductor version 3.6) and exporting these window counts in bigWig format using the export function of the bioconductor package rtracklayer.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files with scores representing RPKM values (within 10 bp windows)

source_name: forelimb buds

growth_protocol: Wild-type NMRI mice were maintained in the animal facility under normal conditions. Date of vaginal plug was scored as embryonic day (E) 0.5 and pregnancy was confirmed by palpation.

extract_protocol:
Per biological replicate, dissected left and right forelimb buds from three embryos at the same stage were pooled and dissociated in PBS (Gibco 14040-117) at 4ºC using a 2ml glass tissue grinder (Sigma-Aldrich D8938; 20 strokes with pestle A followed by 20 strokes with pestle B).
75'000 cells were processed per sample for ATAC-Seq as described in Buenrostro et al., 2015. Curr Protoc Mol Biol. 2015 Jan 5;109:21.29.1-9. doi:10.1002/0471142727.mb2129s109

value: forelimb buds

value: NMRI


title: ChIP H3K27Ac fore limb HP E11.5 replicate 1


title: PC3_Ctrl

status: Public on Jul 21 2021

data_processing:
RNA-Seq libraries were prepared Illumina® TruSeq RNA Library Prep Kit v2 and were sequenced using Illumina® Hiseq2500 to obtain 150-bp paired-end reads.
The sequencing depth for each sample was >20 million reads. The reads were aligned with TopHat 2.0.13 to GRCh37 with default parameters and then were assembled by Cufflink 2.2.1,
using Ensembl v75 annotations. Transcript abundance was measured in fragments per kb of exon per million fragments mapped (FPKM).
Genome_build: GRCh37
Supplementary_files_format_and_content: txt

source_name: Prostate cancer cells (PC3)

growth_protocol: LNCaP cells were cultured in RPMI medium, whereas PC3 cells were cultured in F12 medium. All media were supplemented with 10% heat-inactivated fetal bovine serum, 100 U/mL penicillin and 0.1 mg/mL streptomycin.

treatment_protocol: LNCaP and PC3 cells were treated with or without 50 Μm 3-BP for 6 hr.

tag: dose

value: 0 μM


title: PC3_3BP50

tag: treatment

value: 50 μM


title: LNCaP_3BP50

source_name: Prostate cancer cells (LNCaP)

tag: cell line

value: LNCaP


title: Mouse_Tumor_2_1p5mM

tag: strain


title: PC-FTAZ:IT-M-1

status: Public on Jul 17 2021

city: Raleigh

first: Heike

last: Sederoff

state: NC

address: 851 Main Campus Dr

department: Plant & Microbial Biology

institute: North Carolina State University

data_processing:
QC metrics were obtained using FastQC and high-quality (Q>30) read pairs were mapped to Lsat_Salinas_v7 genome assembly using HISAT2 with default parameter settings
Aligned reads were assigned genomic features according to Lsat_Salinas_v7 annotations using featureCounts and read abundances quantified at the gene-level with default parameter settings
Raw counts were filtered for zero and low counts (<2) and library normalization was performed using DESeq2 size factor estimates
Genome_build: GCA_002870075.2_Lsat_Salinas_v7
Supplementary_files_format_and_content: Text files with counts for each of the 32 samples by gene

organism: Lactuca sativa

source_name: leaf

growth_protocol: 16 plants were grown per box, 2 plants per pot until "transplant" harvest at 3 weeks, 8 plants were grown to final harvest at 5 weeks, water and fertilizer were provided with automated irrigation system, pots were rotated every 2 days to prevent positional effects; leaf tissue was collected from 4 plants per treatment

extract_protocol:
TRIzol + PureLink RNA Mini kit, on-column DNAse and DNAse I treatment
Library was prepared by BGI Genomics Co., Ltd., poly A selection with oligo dT library, all 32 samples were pooled and loaded into all 3 lanes

treatment_protocol: Ceramic metal halide and incandescent lighting filtered through either 1 OPV filter or clear glass control, adjusted for light intensity (PAR controlled) or not adjusted for light intensity (Height Controlled)

tag: intensity experiment

value: PAR Controlled

tag: opv filter

value: leaf


title: hnRNPC_ADAR_cyto_2

status: Public on Jul 16 2021

city: Biberach a.d. Riß

first: Anna-Maria

last: Herzner

address: Birkendorfer Str 65

institute: Boehringer Ingelheim

description:
LIB5420101_SAM24363877
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv

data_processing:
Reads were aligned to GrCH37 v13 using STAR (V2.5.4a) with the basic two-pass mode allowing for a maximum number of multiple alignments of 1000 and 999 mismatches per read (--outFilterMultimapNmax 1000 --outFilterMismatchNmax 999), however 10% mismatches per read pair using --outFilterMismatchNoverReadLmax 0.1 to increase the detection of A-to-I editing sites. In addition, we allowed introns to be 20-1000000 nt and a 1000000 nt distance between read pair mates.
Aligned reads were summarized to gene level using the R Rsubread package featureCounts function in paired end mode (isPairedEnd=TRUE) based on the GrCH37 gencode V19 GTF annotation, using the default exons as features for counting and genes as meta-features (GTF.featureType="exon" and GTF.attrType="gene_id"). We only allowed uniquely mapping reads by setting the read-quality filter to 255 (minMQS=255).
To quantify introns, we first extracted intron ranges from appris annotation based on https://davetang.org/muse/2013/01/18/defining-genomic-regions/ from the GrCH37 gencode V19 GTF file using awk to filter for appris annotated transcripts (awk ’BEGIN’{OFS=”\t”;} /appris/ {print}’). Exons were extracted from the appris annotated transcripts into bed format using awk ('BEGIN{OFS="\t";} $3=="exon" {print $1,$4-1,$5,$10,$3}'), sorted using bedtools2 sortBed and overlapping exons merged with bedtools2 mergeBed. Next, unique genes of appris-annotated transcripts were extracted using awk as described above, their annotations extracted from the original GTF file, sorted and the merged appris-annotated exons subtracted from genes using bedtools2 subtractBed to yield introns delineated from appris annotated transcripts, saved in bed format for later quantification.
Reads mapping to intron- and editing-cluster-rich-region- features were counted using the R Rsubread package featureCounts function after converting bed files to SAF format, as described for gene quantification, not using the meta-feature flag.
Editing sites were discovered using the SAILOR pipeline (https://github.com/YeoLab/sailor). Total or G counts (indicating adenosine-to-inosine editing) were extracted from *.sorted.rmdup.readfiltered.bam intermediate files generated by the SAILOR pipeline using flags -B -d10000000 -t DPR,INFO/DPR,DP4 -uf, using the -l flag with a bed annotation of the primary selection of editing sites. INFO/DPR counts were used to determine nucleotide counts. T and C counts for sense or A and G counts for antisense reads, respectively, were considered sequencing errors and added to reference counts.
Genome_build: GrCH37 v13
Supplementary_files_format_and_content: Raw gene counts, comma separated values
Supplementary_files_format_and_content: Raw intron counts, comma separated values
Supplementary_files_format_and_content: Raw counts of regions rich in RNA editing clusters (ECR), comma separated values
Supplementary_files_format_and_content: Raw G counts at unfiltered, putative editing sites, comma separated values
Supplementary_files_format_and_content: Raw total (G+H) counts at unfiltered, putative editing sites, comma separated values

growth_protocol: THP-1 were grown in RPMI, 10% FBS, 1x glutamax and 1x Pen/Strep at 37°C and 5% CO2

extract_protocol:
Cells were precipitated by centrifugation and either directly subjected to RNA extraction or separated into cytosolic vs nuclear/mitochondrial fractions as described in Baghirova et al, 2015 (PMID 26740924), using an increased digitonin concentration of 300 µg/mL. RNA extraction was performed using the Qiagen RNeasy Mini Kit including on-column DNase digest.
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold kit (Illumina).

treatment_protocol: THP-1 were nucleofected with 2 ul of each gRNA (annealed crRNA:tracrRNA, idt) as described in Cuellar et al, 2017 (PMID 28887438).

value: monocytic cell line

tag: background genotype

value: WT, cas9 transgenic

tag: grna #1

value: hnRNPC

tag: grna #2

value: ADAR

value: medium

tag: time point

value: day 4

tag: compartment

value: digitonin soluble compartment (cytosolic enriched)

tag: replicate


title: hnRNPC_CTRL_nuc_1

description:
LIB5420102_SAM24363878
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv

tag: cell type

value: digitonin insoluble compartment (nuclear/mitochondria enriched)


title: hnRNPC_CTRL_nuc_2

description:
LIB5420103_SAM24363879
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv


title: PC-FTAZ:IT-M-4

tag: tissue


title: CTRL_ADAR_cyto_1

description:
LIB5420098_SAM24363874
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv


title: hnRNPC_CTRL_cyto_2

description:
LIB5420097_SAM24363873
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv


title: hnRNPC_ADAR_total_2

description:
LIB5420093_SAM24363869
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv

value: total RNA/whole cell


title: CTRL_ADAR_cyto_2

description:
LIB5420099_SAM24363875
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv


title: hnRNPC_ADAR_total_1

description:
LIB5420092_SAM24363868
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv


title: CTRL_ADAR_total_2

description:
LIB5420091_SAM24363867
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv


title: hnRNPC_CTRL_cyto_1

description:
LIB5420096_SAM24363872
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv


title: CTRL_CTRL_cyto_1

description:
LIB5420094_SAM24363870
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv


title: CTRL_ADAR_total_1

description:
LIB5420090_SAM24363866
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv


title: LNCaP_Ctrl


title: hnRNPC_CTRL_total_2

description:
LIB5420089_SAM24363865
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv


title: CTRL_CTRL_cyto_2

description:
LIB5420095_SAM24363871
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv


title: hnRNPC_ADAR_cyto_1

description:
LIB5420100_SAM24363876
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv


title: ATAC fore limb E9.75 replicate 1


title: CTRL_CTRL_total_1

description:
LIB5420086_SAM24363862
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv


title: CTRL_CTRL_total_2

description:
LIB5420087_SAM24363863
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv


title: hnRNPC_CTRL_total_1

description:
LIB5420088_SAM24363864
part_2_genes_counts.csv
part_2_ECR_counts.csv
part_2_editingsites_total_counts.csv
part_2_editingsites_G_counts.csv


title: RRBS_WT_5dpf_Livers_1

status: Public on Jul 07 2021

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

description:
"ATAC-seq: Protocol as described in Buenrostro et al (2015): doi:10.1002/0471142727.mb2129s109, using illumina barcoded primers for sequencing.
RRBS: DNA quantitiy and quality was assesed by Qbit and BioAnalyzer. 50-150ng of DNA was used for library prep. Libraries were prepared according to Garrett-Bakelman et al., 2015 with some modifications. To avoid loss of gDNA, after MspI digestion, end repair and A-tailing the reactions were stopped by heat inactivation. The adaptors used for multiplexing were purchased separately (Next Multiplex Methylated Adaptors - New England Biolabs). Libraries were size-selected by dual-step purification with Ampure XP Magnetic Beads (Beckman Coulter, Agencourt) to specifically select a region of fragments from 175 bp to 670 bp. Bisulfite conversion was performed with Lightning Methylation Kit (ZYMO Research) by following the manufacturer’s instructions. Libraries were amplified using KAPA HiFi HotStart Uracil+ Taq polymerase (Roche) and purified with Ampure XP Magnetic Beads (Beckman Coulter, Agencourt) before sequencing."

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw reads were quality assessed using FastQC  v0.11.5, then quality trimmed using Trimmomatic. were “trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36”
For ATACseq, reads that passed quality control were aligned to reference genome GRCz10 using bwa-mem. In RRBS, Qualified reads were aligned to the genome reference GRCz10 by Bismark-0.22.3 with default parameters ,  while calling CpG methylation
In ATAC-seq, the resulting BAM alignments were then processed through PICARD tools to clean, sort and deduplicate
For ATACseq peaks calling,  MACs2 was adopted with -f BAMPE, q-vaule 0.05
In RRBS,  Bismark_methylation_extractor extracted CpG methylation as .bed files from aligned files
Genome_build: GRCz10
Supplementary_files_format_and_content: bed files provides called peaks from concatenated bam files and methylation of each called CpG site

source_name: 5 dpf Livers

growth_protocol:
"ATACseq: Zebrafish larvae of fabp10:CAAX-EGFP in ABNYU background derivied from incross heterozygous adults (ABNYU backgoround) were kept in 10 cm petri dish at a density of 60 larvae/plate (30ml) in a 10:14 light/dark cycle.
For RRBS: WT zebrafish larvae with no transgene and unknown background were generated as described for ATACseq"

extract_protocol:
"For ATACseq: 10 or 20 wildtype 5 dpf (120 hpf) zebrafish embryo livers were manually dissected, pooled per library preparation. ATAC-seq: Protocol as described in Buenrostro et al (2015): doi:10.1002/0471142727.mb2129s109, with the exception of dissociating the livers to get cell suspension was obtained using trypsin at 37 degree for 30 minutes.
For RRBS: Genomic DNA was extracted from 40 dissected livers by using a DNA extraction buffer (10mM Tris-HCl pH9, 10mM EDTA, 200mM NaCl, 0.5% DSD, 200µg/ml proteinase K) as previously described (Chernyavskaya et al., 2017). DNA was resuspended in water and quantified by Qubit dsDNA High Sensitivity kit."

treatment_protocol: Zebrafish larvae were anethetized in tricaine and the liver was dissected out between 120 and 122 hpf.

tag: age

value: 120 hpf; 40 pooled livers

value: WT


title: RRBS_WT_5dpf_Livers_2

value: 120 hpf


title: 120hpf_wildtype embryo_20 livers_ATAC 3

source_name: larval liver

value: 120 hpf;Pool of 20 livers

value: ABNYU


title: 120hpf_wildtype embryo_10 livers_ATAC 2

source_name: embryo liver


title: PC-FTAZ:IT-M-2


title: PC-FTAZ:IT-M-3


title: 120hpf_wildtype embryo_10 livers_ATAC 1

extract_protocol:
"For ATACseq: 10 or 20 wildtype 5 dpf (120 hpf) zebrafish embryo livers were manually dissected, pooled per library preparation. ATAC-seq: Protocol as described in Buenrostro et al (2015): doi:10.1002/0471142727.mb2129s109, with the exception of dissociating the livers to get cell suspension, was obtained using trypsin at 37 degree for 30 minutes.
For RRBS: Genomic DNA was extracted from 40 dissected livers by using a DNA extraction buffer (10mM Tris-HCl pH9, 10mM EDTA, 200mM NaCl, 0.5% DSD, 200µg/ml proteinase K) as previously described (Chernyavskaya et al., 2017). DNA was resuspended in water and quantified by Qubit dsDNA High Sensitivity kit."


title: Nsun2 KO 1- cortex

status: Public on Jul 01 2021

city: New York

first: Jennifer

last: Blaze

state: New York

address: 1470 Madison Ave 9-202

institute: Icahn School of Medicine at Mount Sinai

data_processing:
After paired-end sequencing, samples were mapped to mouse (GRCm38.p5_M13) with STAR (v2.5.3a) using a two-method step protocol following tool specifications
Genome_build: GRCm38.p5_M13
Supplementary_files_format_and_content: tdf

source_name: Mouse cortex

extract_protocol:
total RNA was extracted from Nsun2 KO or WT cortex using the Directzol RNA MiniPrep Kit (Zymo Research) including on-column DNase treatment and quantity was measured on Qubit fluorometer.  Quality of total RNA was checked on the Agilent Bioanalyzer using the RNA 6000 Pico Kit
5ug of total RNA was rRNA depleted using the Illumina RiboZero Gold rRNA depletion kit according to manufacturer’s instructions.  We then used 40-50ng rRNA-depleted RNA samples as input for the Smartr Stranded RNAseq kit (Takara Biosystems) following the manufacturer’s instructions for library prepraration and amplifying libraries with 11 PCR cycles.  4 libraries (2 KO, 2 WT) were then pooled at equimolar concentrations in one lane for sequencing on the Illumina HiSeq at the New York Genome Center

tag: tissue type

value: Cortex

value: Nsun2 floxed, Camk2a-Cre pos.

tag: developmental stage

value: Adult


title: Nsun2 KO 2- cortex


title: wild type 1- cortex

value: Nsun2 floxed, Camk2a-Cre neg.


title: LTi cells, Ctrl_rep2

status: Public on Jun 28 2021

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Reads were aligned to mouse genome (mm10) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Genome_build: mm10
Supplementary_files_format_and_content: GATA3.rpkm.count.gs.txt  (First column: entrez ID; second column: gene symbol; columns thereafter: RPKMs for each sample in log2 scale)

extract_protocol:
Total RNA was extracted with miRNeasy Micro kit (50) (1071023; Qiagen)
RNA-Seq libraries were prepared through the Smart-seq2 method (PMID: 24385147) as previously described (PMID: 29466755).

tag: genotype

value: Ctrl

value: small intestine lamina propria


title: LTi cells, Gata3-KO_rep1_

source_name: Gata3fl/fl-VavCre #1


title: MEF - c9ROW38

status: Public on Jun 16 2021

city: Shenzhen

first: Wenfei

last: Jin

state: Guangdong

address: 1088 Xueyuan Rd #faculty research building 1

department: Department of Biology

institute: Southern University of Science and Technology

data_processing:
Basecalling was performed with CASAVA v1.7 from Illumina.
Each column was demultiplexed to single cells using a script provided by Fluidigm (mRNASeqHT_demultiplex.pl).
Reads were filtered and trimmed using Trim Galore version 0.6.1.
Reads from each cell were mapped to human reference genome (hg19) or mouse GRCm38  by STAR version 2.5.2b.
Gene expression level was quantified by htseq-count version 0.11.2.
Genome_build: hg19 for human; GRCm38 for mouse
Supplementary_files_format_and_content: Counts matrix are tab-delimited files containing raw counts of each cell. Each column represents a sample/cell and each row represents a gene.

source_name: MEF

extract_protocol:
Single cell RNA libraries were prepared by Fluidigm C1 Single-Cell Autoprep System.
We started scPolyA-seq library preparation by cell lysis. Then we added primers containing polyT and cell barcode for labeling the 3’ end of transcripts. Full-length cDNA was synthesized by template-switching reverse transcription, amplification and tagmentation with Tn5 transposases. Nextera XT DNA Library Preparation Kit (Ilumina) was applied to construct scPolyA-seq library. DNA fragments at the 3’ end of the cDNA were captured by targeted PCR, and sequencing indexes were added for amplification. The quality of library was examined by Qubit 3.0 Fluorometer and Agilent 2100 Bioanalyzer. Libraries separated by columns were pooled together and sequenced on Illumina HiSeq2500 to obtain 150-bp paired-end reads.

value: MEF


title: MEF - c9ROW39


title: MEF - c9ROW37


title: MEF - c9ROW35


title: MEF - c9ROW31


title: MEF - c9ROW30


title: MEF - c9ROW32


title: MEF - c9ROW27


title: MEF - c9ROW28


title: MEF - c9ROW34


title: MEF - c9ROW21


title: MEF - c9ROW26


title: MEF - c9ROW33


title: MEF - c9ROW25


title: MEF - c9ROW23


title: MEF - c9ROW19


title: MEF - c9ROW20


title: MEF - c9ROW40


title: wild type 2- cortex


title: MEF - c9ROW17


title: MEF - c9ROW18


title: MEF - c9ROW36


title: MEF - c9ROW22


title: MEF - c9ROW24


title: MEF - c9ROW12


title: MEF - c9ROW13


title: MEF - c9ROW16


title: MEF - c9ROW10


title: MEF - c9ROW11


title: MEF - c9ROW06


title: MEF - c9ROW05


title: MEF - c9ROW03


title: MEF - c8ROW39


title: MEF - c8ROW38


title: MEF - c8ROW37


title: MEF - c8ROW40


title: MEF - c9ROW01


title: MEF - c8ROW36


title: MEF - c8ROW35


title: MEF - c8ROW32


title: MEF - c8ROW33


title: MEF - c8ROW28


title: MEF - c8ROW34


title: MEF - c8ROW29


title: MEF - c8ROW30


title: MEF - c8ROW31


title: MEF - c9ROW29


title: MEF - c8ROW23


title: MEF - c8ROW24


title: MEF - c8ROW25


title: MEF - c8ROW27


title: MEF - c8ROW21


title: MEF - c8ROW20


title: MEF - c8ROW18


title: MEF - c8ROW22


title: MEF - c9ROW09


title: MEF - c8ROW19


title: MEF - c8ROW26


title: MEF - c8ROW17


title: MEF - c8ROW15


title: MEF - c8ROW14


title: MEF - c8ROW13


title: MEF - c8ROW11


title: MEF - c8ROW07


title: MEF - c8ROW08


title: MEF - c8ROW06


title: MEF - c8ROW05


title: MEF - c8ROW02


title: MEF - c8ROW01


title: MEF - c7ROW37


title: MEF - c7ROW39


title: MEF - c8ROW04


title: MEF - c7ROW38


title: MEF - c7ROW34


title: MEF - c7ROW33


title: MEF - c7ROW32


title: MEF - c7ROW31


title: MEF - c7ROW36


title: MEF - c7ROW29


title: MEF - c7ROW35


title: MEF - c8ROW10


title: MEF - c7ROW26


title: MEF - c7ROW28


title: MEF - c7ROW23


title: MEF - c7ROW24


title: MEF - c7ROW22


title: MEF - c7ROW25


title: MEF - c8ROW09


title: MEF - c7ROW21


title: MEF - c7ROW19


title: MEF - c7ROW20


title: MEF - c7ROW17


title: MEF - c7ROW40


title: MEF - c7ROW16


title: MEF - c7ROW18


title: MEF - c7ROW15


title: MEF - c7ROW13


title: MEF - c7ROW14


title: MEF - c7ROW11


title: MEF - c7ROW10


title: MEF - c7ROW30


title: MEF - c7ROW06


title: MEF - c7ROW08


title: MEF - c7ROW05


title: MEF - c7ROW03


title: MEF - c7ROW07


title: MEF - c7ROW01


title: MEF - c6ROW38


title: MEF - c6ROW40


title: MEF - c6ROW34


title: MEF - c6ROW39


title: MEF - c7ROW02


title: MEF - c7ROW09


title: MEF - c6ROW37


title: MEF - c6ROW35


title: MEF - c8ROW16


title: MEF - c6ROW26


title: MEF - c6ROW32


title: MEF - c6ROW29


title: MEF - c6ROW31


title: MEF - c6ROW27


title: MEF - c6ROW25


title: MEF - c6ROW24


title: MEF - c6ROW20


title: MEF - c6ROW23


title: MEF - c6ROW36


title: MEF - c6ROW22


title: MEF - c7ROW04


title: MEF - c6ROW21


title: MEF - c6ROW14


title: MEF - c6ROW12


title: MEF - c6ROW15


title: MEF - c6ROW18


title: MEF - c6ROW17


title: MEF - c6ROW28


title: MEF - c6ROW09


title: MEF - c6ROW16


title: MEF - c6ROW10


title: MEF - c6ROW30


title: MEF - c6ROW08


title: MEF - c6ROW13


title: MEF - c6ROW33


title: MEF - c6ROW11


title: MEF - c6ROW06


title: MEF - c6ROW02


title: MEF - c6ROW07


title: MEF - c6ROW01


title: MEF - c6ROW03


title: MEF - c3ROW40


title: MEF - c6ROW05


title: MEF - c3ROW30


title: MEF - c6ROW19


title: MEF - c3ROW27


title: MEF - c3ROW25


title: MEF - c3ROW24


title: MEF - c6ROW04


title: MEF - c3ROW38


title: MEF - c3ROW19


title: MEF - c3ROW37


title: MEF - c3ROW39


title: MEF - c3ROW18


title: MEF - c3ROW36


title: MEF - c3ROW17


title: MEF - c3ROW26


title: MEF - c3ROW34


title: MEF - c3ROW33


title: MEF - c3ROW32


title: MEF - c3ROW31


title: MEF - c3ROW29


title: MEF - c3ROW22


title: MEF - c3ROW28


title: MEF - c3ROW23


title: MEF - c3ROW06


title: MEF - c3ROW16


title: MEF - c3ROW21


title: MEF - c3ROW20


title: MEF - c3ROW15


title: MEF - c3ROW05


title: MEF - c3ROW14


title: MEF - c3ROW13


title: MEF - c3ROW12


title: MEF - c3ROW11


title: MEF - c2ROW39


title: MEF - c2ROW35


title: MEF - c3ROW09


title: MEF - c3ROW01


title: MEF - c2ROW34


title: MEF - c2ROW40


title: MEF - c2ROW37


title: MEF - c2ROW36


title: MEF - c3ROW10


title: MEF - c2ROW32


title: MEF - c3ROW08


title: MEF - c2ROW30


title: MEF - c2ROW29


title: MEF - c2ROW27


title: MEF - c3ROW07


title: MEF - c2ROW28


title: MEF - c2ROW31


title: MEF - c2ROW26


title: MEF - c2ROW25


title: MEF - c2ROW24


title: MEF - c2ROW38


title: MEF - c3ROW03


title: MEF - c2ROW21


title: MEF - c2ROW17


title: MEF - c2ROW18


title: MEF - c2ROW16


title: MEF - c2ROW20


title: MEF - c2ROW33


title: MEF - c2ROW14


title: MEF - c2ROW11


title: MEF - c2ROW13


title: MEF - c2ROW08


title: MEF - c2ROW12


title: MEF - c2ROW07


title: MEF - c2ROW01


title: MEF - c10ROW40


title: MEF - c10ROW38


title: MEF - c2ROW03


title: MEF - c10ROW39


title: MEF - c10ROW36


title: MEF - c10ROW37


title: MEF - c2ROW23


title: MEF - c10ROW35


title: MEF - c10ROW29


title: MEF - c10ROW33


title: MEF - c10ROW32


title: MEF - c10ROW27


title: MEF - c10ROW26


title: MEF - c10ROW25


title: MEF - c10ROW21


title: MEF - c10ROW24


title: MEF - c10ROW22


title: MEF - c2ROW22


title: MEF - c10ROW23


title: MEF - c10ROW17


title: MEF - c10ROW14


title: MEF - c05ROW40


title: MEF - c05ROW36


title: MEF - c05ROW37


title: MEF - c05ROW39


title: MEF - c05ROW38


title: MEF - c05ROW35


title: MEF - c05ROW32


title: MEF - c05ROW29


title: MEF - c05ROW34


title: MEF - c05ROW30


title: MEF - c10ROW31


title: MEF - c05ROW27


title: MEF - c05ROW28


title: MEF - c05ROW25


title: MEF - c05ROW24


title: MEF - c05ROW23


title: MEF - c05ROW26


title: MEF - c05ROW22


title: MEF - c05ROW20


title: MEF - c05ROW17


title: MEF - c10ROW16


title: MEF - c05ROW12


title: MEF - c05ROW15


title: MEF - c05ROW21


title: MEF - c05ROW11


title: MEF - c05ROW16


title: MEF - c05ROW08


title: MEF - c05ROW09


title: MEF - c05ROW07


title: MEF - c05ROW05


title: MEF - c05ROW04


title: MEF - c05ROW03


title: MEF - c05ROW01


title: MEF - c04ROW40


title: MEF - c04ROW39


title: MEF - c04ROW36


title: MEF - c04ROW37


title: MEF - c04ROW38


title: MEF - c04ROW34


title: MEF - c05ROW18


title: MEF - c05ROW13


title: MEF - c04ROW30


title: MEF - c04ROW32


title: MEF - c05ROW10


title: MEF - c04ROW28


title: MEF - c04ROW24


title: MEF - c04ROW35


title: MEF - c04ROW22


title: MEF - c04ROW27


title: MEF - c04ROW21


title: MEF - c04ROW20


title: MEF - c05ROW06


title: MEF - c04ROW19


title: MEF - c04ROW26


title: MEF - c04ROW18


title: MEF - c04ROW17


title: MEF - c04ROW16


title: MEF - c04ROW11


title: MEF - c04ROW33


title: MEF - c04ROW12


title: MEF - c04ROW13


title: MEF - c04ROW31


title: MEF - c04ROW09


title: MEF - c04ROW05


title: MEF - c04ROW07


title: MEF - c04ROW23


title: MEF - c01ROW39


title: MEF - c01ROW40


title: MEF - c01ROW36


title: MEF - c01ROW34


title: MEF - c04ROW29


title: MEF - c04ROW03


title: MEF - c01ROW33


title: MEF - c01ROW32


title: MEF - c01ROW28


title: MEF - c01ROW27


title: MEF - c01ROW38


title: MEF - c01ROW29


title: MEF - c01ROW26


title: MEF - c01ROW25


title: MEF - c04ROW15


title: MEF - c01ROW21


title: MEF - c01ROW20


title: MEF - c01ROW23


title: MEF - c01ROW22


title: MEF - c01ROW19


title: MEF - c01ROW18


title: MEF - c01ROW17


title: MEF - c01ROW16


title: MEF - c01ROW37


title: MEF - c01ROW15


title: MEF - c01ROW13


title: MEF - c01ROW14


title: MEF - c01ROW08


title: MEF - c01ROW11


title: MEF - c01ROW04


title: MEF - c01ROW06


title: MEF - c01ROW03


title: Sample a43973 (Lung, Female), Tumor

status: Public on Jun 15 2021

type: RNA

city: London

first: William

last: Cookson

address: Dovehouse Street

country: United Kingdom

institute: Imperial College London

description: Gene expression from surgically resected lung tissue in lung cancer patients.

hyb_protocol: Hybridization was performed for 16 h on GeneTitanTM Instrument.

scan_protocol: GeneChips were scanned on a GeneTitan system (Affymetrix Ltd.).

data_processing: Gene expression data from the Affymetrix HuGene 1.1 ST array were available for a total of 123 samples from 69 patients with either adenocarcinoma or squamous cell carcinoma. Data were RMA-treated using Oligo (1.38.0) as part of a larger study and filtered. Specifically, transcript cluster intensity was required to exceed the data set median in 1 or more sample (genefilter 1.56.0), and be designated within the Affymetrix annotation (netaffx build 36) with a cross-hybridisation potential of 1 (unique), a non-missing mRNA assignment and as part of the main design probe set category.

label: Biotin

source_name: Lung

label_protocol: Total RNA was converted to labelled cDNA for hybridization onto the gene expression chips using the AmbionTM WT Expression Kit. The single-stranded DNA was fragmented and labelled using Affymetrix GeneChipTM WT Terminal Labelling Kit.

extract_protocol: RNA was extracted using the Qiagen RNeasy mini kit (Qiagen, Crawley, UK).

tag: diagnosis

value: Lung cancer

tag: gender

value: Female

value: Tumor

tag: patient id


title: Sample a43446 (Lung, Male), Tumor

value: Male


title: Sample a43446 (Lung, Male), Normal

value: Normal


title: Sample a43567 (Lung, Male), Normal


title: Sample a43567 (Lung, Male), Tumor


title: Sample a42934 (Lung, Female), Normal


title: Sample a42761 (Lung, Female), Normal


title: Sample a41335 (Lung, Female), Tumor


title: Sample a41820 (Lung, Male), Normal


title: Sample a42677 (Lung, Female), Normal


title: Sample a42761 (Lung, Female), Tumor


title: Sample a42934 (Lung, Female), Tumor


title: Sample n1163 (Lung, Male), Tumor


title: Sample a41335 (Lung, Female), Normal


title: Sample a40648 (Lung, Male), Tumor


title: Sample a41820 (Lung, Male), Tumor


title: Sample a41754 (Lung, Female), Normal


title: Sample a40648 (Lung, Male), Normal


title: Sample a35365 (Lung, Male), Tumor


title: Sample n1177 (Lung, Male), Tumor


title: Sample a35365 (Lung, Male), Normal


title: Sample a41136 (Lung, Female), Tumor


title: Sample a40342 (Lung, Female), Normal


title: Sample a37712 (Lung, Male), Tumor


title: Sample a41136 (Lung, Female), Normal


title: Sample a35337 (Lung, Male), Tumor


title: Sample a37712 (Lung, Male), Normal


title: Sample a37668 (Lung, Female), Tumor


title: Sample a38814 (Lung, Female), Tumor


title: Sample a37278 (Lung, Male), Normal


title: Sample a39605 (Lung, Male), Tumor


title: Sample a39605 (Lung, Male), Normal


title: Sample a37668 (Lung, Female), Normal


title: Sample a35329 (Lung, Male), Tumor


title: Sample a40342 (Lung, Female), Tumor


title: Sample a42677 (Lung, Female), Tumor


title: Sample a34541 (Lung, Female), Normal


title: Sample a37278 (Lung, Male), Tumor


title: Sample a41754 (Lung, Female), Tumor


title: Sample a34541 (Lung, Female), Tumor


title: Sample a12047 (Lung, Female), Tumor


title: Sample a38814 (Lung, Female), Normal


title: Sample a12047 (Lung, Female), Normal


title: Sample a27805 (Lung, Female), Tumor


title: Sample a37558 (Lung, Female), Tumor


title: Sample n1223 (Lung, Male), Tumor


title: Sample a33061 (Lung, Female), Tumor


title: Sample a37558 (Lung, Female), Normal


title: Sample a37644 (Lung, Male), Normal


title: Sample a35267 (Lung, Male), Tumor


title: Sample n1200 (Lung, Female), Tumor


title: Sample n1209 (Lung, Female), Tumor


title: Sample a33061 (Lung, Female), Normal


title: Sample n1211 (Lung, Female), Tumor


title: Sample a35329 (Lung, Male), Normal


title: Sample a35267 (Lung, Male), Normal


title: Sample n1206 (Lung, Female), Normal


title: Sample a29662 (Lung, Male), Tumor


title: Sample n1202 (Lung, Female), Tumor


title: Sample n1208 (Lung, Male), Normal


title: Sample n1202 (Lung, Female), Normal


title: Sample a29662 (Lung, Male), Normal


title: Sample a37644 (Lung, Male), Tumor


title: Sample n1199 (Lung, Male), Tumor


title: Sample a27805 (Lung, Female), Normal


title: Sample n1199 (Lung, Male), Normal


title: Sample n1196 (Lung, Male), Tumor


title: Sample n1209 (Lung, Female), Normal


title: Sample n1223 (Lung, Male), Normal


title: Sample n1200 (Lung, Female), Normal


title: Sample n1211 (Lung, Female), Normal


title: Sample n1198 (Lung, Female), Tumor


title: Sample n1208 (Lung, Male), Tumor


title: Sample n1196 (Lung, Male), Normal


title: Sample n1198 (Lung, Female), Normal


title: Sample n1189 (Lung, Male), Tumor


title: Sample n1187 (Lung, Male), Normal


title: Sample n1186 (Lung, Female), Normal


title: Sample n1187 (Lung, Male), Tumor


title: Sample n1189 (Lung, Male), Normal


title: Sample n1186 (Lung, Female), Tumor


title: Sample n1181 (Lung, Female), Tumor


title: Sample n1184 (Lung, Male), Normal


title: Sample n1179 (Lung, Male), Tumor


title: Sample n1121 (Lung, Male), Normal


title: Sample n1119 (Lung, Male), Tumor


title: Sample n1163 (Lung, Male), Normal


title: Sample n1182 (Lung, Female), Tumor


title: Sample n1103 (Lung, Male), Tumor


title: Sample n1181 (Lung, Female), Normal


title: Sample n1175 (Lung, Male), Normal


title: Sample n1182 (Lung, Female), Normal


title: Sample n1177 (Lung, Male), Normal


title: Sample n1121 (Lung, Male), Tumor


title: Sample n1167 (Lung, Male), Normal


title: Sample n1146 (Lung, Female), Normal


title: Sample n1167 (Lung, Male), Tumor


title: Sample n1052 (Lung, Female), Tumor


title: Sample n1175 (Lung, Male), Tumor


title: Sample n1114 (Lung, Female), Tumor


title: Sample n1119 (Lung, Male), Normal


title: Sample n1089 (Lung, Female), Tumor


title: Sample n1103 (Lung, Male), Normal


title: Sample n1114 (Lung, Female), Normal


title: Sample n1059 (Lung, Male), Normal


title: Sample n1088 (Lung, Female), Normal


title: Sample n1089 (Lung, Female), Normal


title: Sample n1094 (Lung, Male), Tumor


title: Sample n1088 (Lung, Female), Tumor


title: Sample n1146 (Lung, Female), Tumor


title: Sample n1094 (Lung, Male), Normal


title: Sample n1049 (Lung, Female), Normal


title: Sample n1051 (Lung, Female), Normal


title: Sample n1065 (Lung, Male), Normal


title: Sample n1031 (Lung, Male), Tumor


title: Sample n1017 (Lung, Male), Tumor


title: Sample n1052 (Lung, Female), Normal


title: Sample n1016 (Lung, Male), Tumor


title: Sample n1020 (Lung, Female), Tumor


title: Sample n1035 (Lung, Female), Tumor


title: Sample 00405 (Lung, Normal)

description:
H7_00405_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.

data_processing: Raw expression data for these 237 samples were RMA-treated using Oligo (1.38.0) as part of a larger study and filtered. Specifically, transcript cluster intensity was required to exceed the data set median in 1 or more sample (genefilter 1.56.0), and be designated within the Affymetrix annotation (netaffx build 36) with a cross-hybridisation potential of 1 (unique), a non-missing mRNA assignment and as part of the main design probe set category.


title: Sample n1019 (Lung, Male), Tumor


title: Sample 480 (Lung, Tumor)

description:
C7_480_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00324 (Lung, Normal)

description:
H5_00324_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 622 (Lung, Tumor)

description:
G9_622_T_RERUN
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample n1042 (Lung, Male), Tumor


title: Sample 642 (Lung, Normal)

description:
H9_642_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 674 (Lung, Normal)

description:
H9_674_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1301 (Lung, Tumor)

description:
A7_1301_T_rerun
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample n1049 (Lung, Female), Tumor


title: Sample 423 (Lung, Normal)

description:
H9_423_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00314 (Lung, Tumor)

description:
H9_00314_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 469 (Lung, Normal)

description:
B7_469_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00301 (Lung, Normal)

description:
H9_00301_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 834 (Lung, Tumor)

description:
H5_834_T_rerun
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1251 (Lung, Tumor)

description:
H7_H7_1251_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 247 (Lung, Tumor)

description:
B7_247_T_rerun
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 889 (Lung, Tumor)

description:
F9_889_T_RERUN
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 934 (Lung, Normal)

description:
H7_934_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 951 (Lung, Normal)

description:
H9_951_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 853 (Lung, Normal)

description:
H7_853_N_rerun
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 21 (Lung, Normal)

description:
H9_21-N-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 617 (Lung, Normal)

description:
H7_617_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1002 (Lung, Normal)

description:
H7_1002_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 629 (Lung, Normal)

description:
H7_629_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 82 (Lung, Normal)

description:
H7_82-N-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00355 (Lung, Normal)

description:
H7_00355_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 886 (Lung, Normal)

description:
H5_886_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00434 (Lung, Normal)

description:
H7_00434_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1291 (Lung, Normal)

description:
H5_1291_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 223 (Lung, Normal)

description:
H5_223-N-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 969 (Lung, Normal)

description:
H5_969_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1299 (Lung, Normal)

description:
H5_1299_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 35 (Lung, Normal)

description:
H5_35-N-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 689 (Lung, Normal)

description:
H5_689_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1274 (Lung, Normal)

description:
H5_1274_N2_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 951 (Lung, Tumor)

description:
G9_951_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 24 (Lung, Normal)

description:
H5_24-N-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 52 (Lung, Normal)

description:
H5_52-N-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 423 (Lung, Tumor)

description:
G9_423_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 934 (Lung, Tumor)

description:
G7_934_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 21 (Lung, Tumor)

description:
G9_21-T-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 642 (Lung, Tumor)

description:
G9_642_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1286 (Lung, Normal)

description:
G7_G7_1286_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 688 (Lung, Normal)

description:
H5_688_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 629 (Lung, Tumor)

description:
G7_629_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 202 (Lung, Normal)

description:
G7_202_N_rerun
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 82 (Lung, Tumor)

description:
G7_82-T-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 674 (Lung, Tumor)

description:
G9_674_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00301 (Lung, Tumor)

description:
G9_00301_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 617 (Lung, Tumor)

description:
G7_617_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1002 (Lung, Tumor)

description:
G7_1002_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 93 (Lung, Tumor)

description:
G5_G5_93_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1299 (Lung, Tumor)

description:
G5_1299_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 969 (Lung, Tumor)

description:
G5_969_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 689 (Lung, Tumor)

description:
G5_689_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1306 (Lung, Tumor)

description:
G7_1306_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 223 (Lung, Tumor)

description:
G5_223-T-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1274 (Lung, Tumor)

description:
G5_1274_T2_rerun
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00405 (Lung, Tumor)

description:
G7_00405_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 688 (Lung, Tumor)

description:
G5_688_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 886 (Lung, Tumor)

description:
G5_886_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1291 (Lung, Tumor)

description:
G5_1291_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00355 (Lung, Tumor)

description:
G7_00355_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 24 (Lung, Tumor)

description:
G5_24-T-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 635 (Lung, Normal)

description:
F9_635_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00324 (Lung, Tumor)

description:
G5_00324_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 35 (Lung, Tumor)

description:
G5_35-T-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 76 (Lung, Tumor)

description:
F9_76_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00434 (Lung, Tumor)

description:
G7_00434_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1286 (Lung, Tumor)

description:
F7_F7_1286_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 52 (Lung, Tumor)

description:
G5_52-T-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 977 (Lung, Normal)

description:
F9_977_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 809 (Lung, Normal)

description:
F7_809_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 627 (Lung, Normal)

description:
F9_627_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 931 (Lung, Normal)

description:
F7_931_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 421 (Lung, Normal)

description:
F9_421_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 618 (Lung, Normal)

description:
F7_618_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00282 (Lung, Normal)

description:
F9_00282_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 921 (Lung, Normal)

description:
F7_921_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1285 (Lung, Normal)

description:
F7_1285_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00271 (Lung, Normal)

description:
F7_00271_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 681 (Lung, Normal)

description:
F5_681_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 395 (Lung, Normal)

description:
F7_395_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 822 (Lung, Normal)

description:
F5_822_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00363 (Lung, Normal)

description:
F7_00363_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 612 (Lung, Normal)

description:
F7_612_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00354 (Lung, Normal)

description:
F7_00354_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 493 (Lung, Normal)

description:
F5_493_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 359 (Lung, Normal)

description:
F5_359_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1246 (Lung, Normal)

description:
F5_1246_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 208 (Lung, Normal)

description:
F5_208-N-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1022 (Lung, Normal)

description:
F5_1022_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 279 (Lung, Tumor)

description:
E9_279_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 635 (Lung, Tumor)

description:
E9_635_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 395 (Lung, Tumor)

description:
E7_395_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 421 (Lung, Tumor)

description:
E9_421_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 612 (Lung, Tumor)

description:
E7_612_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 977 (Lung, Tumor)

description:
E9_977_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1012 (Lung, Normal)

description:
F5_1012_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 627 (Lung, Tumor)

description:
E9_627_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 921 (Lung, Tumor)

description:
E7_921_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00282 (Lung, Tumor)

description:
E9_00282_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 243 (Lung, Normal)

description:
F5_243-N-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00319 (Lung, Normal)

description:
F5_00319_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 202 (Lung, Tumor)

description:
E9_202-T-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 931 (Lung, Tumor)

description:
E7_931_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 618 (Lung, Tumor)

description:
E7_618_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 809 (Lung, Tumor)

description:
E7_809_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 359 (Lung, Tumor)

description:
E7_359_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00271 (Lung, Tumor)

description:
E7_00271_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1022 (Lung, Tumor)

description:
E5_1022_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 853 (Lung, Tumor)

description:
E5_853_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1285 (Lung, Tumor)

description:
E7_1285_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 243 (Lung, Tumor)

description:
E5_243-T-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1246 (Lung, Tumor)

description:
E5_1246_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 681 (Lung, Tumor)

description:
E5_681_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 493 (Lung, Tumor)

description:
E5_493_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1012 (Lung, Tumor)

description:
E5_1012_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00363 (Lung, Tumor)

description:
E7_00363_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00354 (Lung, Tumor)

description:
E7_00354_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1011 (Lung, Normal)

description:
D9_1011_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 937 (Lung, Normal)

description:
D9_937_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 988 (Lung, Normal)

description:
D7_988_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 224 (Lung, Tumor)

description:
D9_224_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00319 (Lung, Tumor)

description:
E5_00319_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00362 (Lung, Normal)

description:
D9_00362_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 413 (Lung, Normal)

description:
D9_413_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 634 (Lung, Normal)

description:
D9_634_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 999 (Lung, Tumor)

description:
D7_999_T_rerun
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 822 (Lung, Tumor)

description:
E5_822_T_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 878 (Lung, Normal)

description:
D7_878_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 925 (Lung, Normal)

description:
D7_925_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 208 (Lung, Tumor)

description:
E5_208-T-RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 380 (Lung, Normal)

description:
D7_380_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 622 (Lung, Normal)

description:
D9_622_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 806 (Lung, Normal)

description:
D7_806_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 615 (Lung, Normal)

description:
D7_615_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 687 (Lung, Normal)

description:
D5_687_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 00345 (Lung, Normal)

description:
D7_00345_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.


title: Sample 1241 (Lung, Normal)

description:
D7_1241_N_RL
Gene expression from surgically resected lung tissue in lung cancer patients.