title: 3805_OM1B_1-2-K15-L4

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-L3

status: Public on Dec 11 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

description: nuclear RNA + genomic DNA

library_source: transcriptomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM file were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmCT-seq

molecule: nuclear RNA

organism: Homo sapiens

source_name: OM1B human BA46

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age

tag: Sex

value: Male


title: 3805_OM1B_1-2-K15-K16

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-L16

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-K15

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-K4

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-K3

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-L15

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-J4

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-J16

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-I4

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-J3

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-J15

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-M4

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-I16

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-I3

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-H16

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-G4

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-H4

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-G3

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-H15

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-I15

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-H3

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-G15

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-F4

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-F3

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-F16

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-G16

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-F15

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-E4

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-E3

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-E16

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-D16

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-E15

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-D3

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-C4

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-D4

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-D15

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-C3

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-C15

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-B3

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-B4

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-B16

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-A16

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-A3

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-A4

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-A15

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-P2

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-P1

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-B15

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-P13

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-O13

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-O14

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-N14

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-N1

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-N13

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-O1

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-2-K15-C16

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-M2

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-M14

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-L2

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-L1

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-L13

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-L14

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-K13

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-P14

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-K1

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-O2

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-K2

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-J1

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-J2

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-J14

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-J13

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-K14

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-I1

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-I13

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-I14

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-H2

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-N2

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-I2

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-G1

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-G2

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-M1

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-H13

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-G14

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-M13

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-F14

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-G13

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-F1

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-F2

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-F13

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-E2

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-E1

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-E14

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-D13

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-D14

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-D2

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-E13

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-C1

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-H14

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-D1

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-H1

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-C2

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-C14

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-B2

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-B13

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-C13

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-A1

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-A14

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-B14

description: nuclear RNA + genomic DNA


title: 3805_OM1B_1-1-K15-A13

description: nuclear RNA + genomic DNA


title: untreated ALI S2,D21

city: Guangzhou

first: Danni

last: FENG

state: Guangdong

address: No. 58, Zhong Shan 2nd Street, Guangzhou, China, 510080

department: Department of Otolaryngology, Department of Allergy

country: China

institute: The First Affiliated Hospital, Sun Yat-sen University

description:
ALI_readcount.txt
S2.D21.ALI

data_processing:
The signals of transcripts from RNA-seq data were quantified by Kallisto program(kallisto 0.46.2 version),read counts were  performed using tximport program(tximport_1.28.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited texfile includes read counts for each Sample

molecule: total RNA

source_name: nasal polyps

growth_protocol: The concentrations of organoids gel components were 3 mg/ml collagen, 5 mg/ml 626 alginate, and 1 mg/ml hyaluronic acid. The premixed solution (250 μl per dish) with  hNEPC suspension was adjusted to neutral pH, cross-linked with 3.75 mM CaCl2 (Sigma-Aldrich) and then was gently placed in a 15mm glass bottom cell culture dish  (Nest Biotechnology, Wuxi, China).The organoids were maintained in growth media (500 μl) covered the gel and the cultures were  incubated at 37°C with 5% CO2. The ALI were maintained in growth media (1500 μl) incubated at 37°C with 5% CO2.

extract_protocol:
RNA was harveted using trizol.1.0 ug of total RNA was used for the construction of sequencing libraries
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: tissue

value: nasal polyps

tag: cell type

value: airway epithelial

tag: treatment

value: untreated


title: untreated ALI S2,D14

description:
ALI_readcount.txt
S2.D14.ALI


title: untreated ALI S2,D7

description:
ALI_readcount.txt
S2.D7.ALI


title: act-treated organoids S3,D24

description:
organoids_readcount.txt
S3.D24.Act

value: act-treated


title: untreated ALI S1,D14

description:
ALI_readcount.txt
S1.D14.ALI


title: untreated organoids S3,D24

description:
organoids_readcount.txt
S3.D24


title: untreated ALI S3,D14

description:
ALI_readcount.txt
S3.D14.ALI


title: untreated ALI S3,D7

description:
ALI_readcount.txt
S3.D7.ALI


title: untreated organoids S3,D17

description:
organoids_readcount.txt
S3.D17


title: untreated ALI S1,D7

description:
ALI_readcount.txt
S1.D7.ALI


title: untreated ALI S1,D21

description:
ALI_readcount.txt
S1.D21.ALI


title: untreated ALI S3,D21

description:
ALI_readcount.txt
S3.D21.ALI


title: act-treated organoids S3,D17

description:
organoids_readcount.txt
S3.D17.Act


title: untreated organoids S3,D10

description:
organoids_readcount.txt
S3.D10


title: act-treated organoids S1,D24

description:
organoids_readcount.txt
S1.D24.Act


title: act-treated organoids S2,D17

description:
organoids_readcount.txt
S2.D17.Act


title: 3805_OM1B_1-1-K15-A2

description: nuclear RNA + genomic DNA


title: untreated organoids S2,D10

description:
organoids_readcount.txt
S2.D10


title: untreated organoids S2,D17

description:
organoids_readcount.txt
S2.D17


title: untreated organoids S2,D24

description:
organoids_readcount.txt
S2.D24


title: act-treated organoids S2,D24

description:
organoids_readcount.txt
S2.D24.Act


title: act-treated organoids S1,D17

description:
organoids_readcount.txt
S1.D17.Act


title: untreated organoids S1,D10

description:
organoids_readcount.txt
S1.D10


title: untreated organoids S1,D24

description:
organoids_readcount.txt
S1.D24


title: 3805_OM1B_1-1-K15-B1

description: nuclear RNA + genomic DNA


title: ADAM9i_PDAC103P

city: Taichung

first: Wei-Chung

last: Cheng

address: No. 91, Hsueh-Shih Road

department: Research Center for Tumor Medical Science

country: Taiwan

institute: China Medical University

data_processing:
1. trim adapter: trimmomatic
2. Alignment: Hisat2
3. Expression profiling: stringtie
Assembly: Homo_sapiens.GRCh38
hisat2_index: V97

source_name: PDAC103P cell

extract_protocol:
RNA was harvested using TRIzol (Invitrogen)
The library synthesis was using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer's protocols

treatment_protocol: with or without ADAM9i for 48 hours under serum starvation

tag: cell line

value: PDAC103P cell

value: Pancreatic cancer cell

tag: genotype

value: KRAS wild-type


title: Vehicle_PDAC103P


title: PM00342

city: Trento

first: Gian Marco

last: Franceschini

state: Trentino Alto Adige

address: via Sommarive 9, Povo

department: CIBIO

country: Italy

institute: University of Trento

library_source: genomic

data_processing:
nextflow run nf-core/methylseq -r 1.6 -profile docker --aligner bismark --input $FASTQ_PATH --genome hg19 --accel
bam files were subject to deduplication and sensible genomic variation was removed using a custom method (https://github.com/GMFranceschini/dataprivacy_bisulfite)
Assembly: hg19
Supplementary files format and content: bismark .cov files reporting CpG level DNA methylation values
Supplementary files format and content: bismark .CpG_OT and CpG_OB read level DNA methylation calls

molecule: genomic DNA

source_name: Plasma cell-free DNA

growth_protocol: Cell lines have been grown following the standard recommendation from vendors.

extract_protocol:
Plasma was separated from whole blood with a standard double spin protocol and stored at -80°C. The input plasma volume ranged between 1mL and 2mL depending on the cohort.  For cfDNA extraction of samples processed in Trento, plasma was thawed at RT and immediately processed with the QIAamp Circulating Nucleic Acid Kit (QIAGEN) according to the manufacturer's protocol. The extracted cfDNA was eluted in 30 µL Tris HCl 10mM pH8 and quantified with Qubit dsDNA High Sensitivity Assay (Invitrogen); the quality was assessed using the Bioanalyzer High Sensitivity DNA Kit (Agilent). For samples processed at Weill Cornell Medicine (WCM, DFCI, and Alisertib trial) cfDNA was extracted from plasma using the NeoGeneStar Cell-Free DNA Purification kit per manufacturer’s instructions. Briefly, for 2ml plasma samples, cfDNA was isolated via proteolytic digestion with 1μg of RNA carrier at 55°C for 30 minutes. cfDNA capture on the superparamagnetic particles was accomplished via the addition of 3 volumes (6mL) of LYS buffer, 0.8mL isopropanol, and 30μL NGSTM Beads. The capture of cfDNA was carried out via 30-minute room temperature incubation, 2x wash and 2x 80% EtOH, air drying, and elution in 30μL 10mM Tris, 0.1mM EDTA (pH 8.5). For PDX samples, 20-25 5µm slides of fresh-frozen tissue were cut using the HM525 NX cryostat (Thermo Scientific) and used for subsequent gDNA extraction. gDNA from PDX was extracted using the DNeasy Blood & Tissue Kit (QIAGEN), and gDNA from cell lines was extracted using the NucleoSpin Tissue Kit (Macherey-Nagel) according to the manufacturer's instructions and eluted in 100 µL Tris HCl 10mM pH 8. The gDNA was quantified using the Qubit dsDNA High Sensitivity Assay (Invitrogen). gDNA for libraries preparation was fragmented to a target size of 350 bp using the Covaris focused ultrasonicator M220.
Based on the manufacturer's instructions, bisulfite conversion was performed on 5-25 ng of cfDNA and 200 ng of fragmented gDNA using the EZ DNA Methylation-Lightning Kit (Zymo). gDNA was re-quantified after bisulfite conversion using Qubit ssDNA High Sensitivity Assay (Invitrogen) and 100 ng of converted gDNA was used as input, whereas the whole converted cfDNA was used for libraries preparation for target sequencing with xGen Methyl-Seq DNA Library Prep Kit (IDT), following the kit's protocol with few modifications. All indexing PCR reagents were substituted with the HiFi HotStart Uracil+ ReadyMix (KAPA), and 11-12 PCR cycles were performed to achieve library yields higher than 500 ng for downstream experiments. For probes hybridization, 500 ng of each library of up to 12 samples were pooled together and captured using the xGen Hybridization and Wash Kit (IDT) following the xGen hybridization capture of DNA libraries protocol (version 4). The multiplexed libraries were dried together with the custom xGen Blocking Oligos and Human Cot DNA. Probes hybridization occurred during overnight incubation with custom xGen Lockdown Probes at 65°C. The captured DNA was amplified for 11 PCR cycles according to the panel size. Pre- and post-capture libraries were quantified using Qubit dsDNA High Sensitivity Assay (Invitrogen), and the quality was assessed with the Bioanalyzer High Sensitivity DNA Kit (Agilent). Libraries were sequenced on Illumina NovaSeq 6000 or MiSeq sequencing machines, with variable nominal depth based on the run and sample type (~100X for genomic DNA, ~1000X for cfDNA samples).
Targeted Bisulfite-Seq

value: Plasma cell-free DNA


title: PM00170


title: PM00175


title: dil_75_25_PM00126


title: PM00196


title: dil_50_50_PM00126


title: HD1


title: HD2


title: PM00126


title: PM00557


title: untreated organoids S1,D17

description:
organoids_readcount.txt
S1.D17


title: PM00387


title: PM00459


title: PM00265


title: PM00382


title: PM00306


title: PM00329


title: PM00354


title: PM00310


title: PM00134


title: PM00231


title: PM00210


title: PM00192


title: HD3


title: PM00102


title: PM00552


title: PM00454


title: PM00120


title: lc96CR

source_name: Solid tissue

value: Solid tissue


title: lc93


title: lc77CR


title: lc173_2A_2270


title: lc176


title: lc49


title: lc243


title: lc78CR


title: PM00124


title: lc145_1


title: lc173_1


title: PM00194


title: PM01073_cfDNA


title: PM01072_cfDNA


title: PM01076_cfDNA


title: PM01074_cfDNA


title: PM01075_cfDNA


title: PM01071_cfDNA


title: PM01067_cfDNA


title: lc105CR


title: PM01066_cfDNA


title: PM01068_cfDNA


title: PM01069_cfDNA


title: PM01063_cfDNA


title: lc173_2A_6712


title: PM01061_cfDNA


title: PM01065_cfDNA


title: PM01057_cfDNA


title: PM01060_cfDNA


title: PM01056_cfDNA


title: PM01055_cfDNA


title: PM01051_cfDNA


title: PM01050_cfDNA


title: PM01054_cfDNA


title: PM01053_cfDNA


title: PM01048_cfDNA


title: PM01049_cfDNA


title: PM01046_cfDNA


title: PM01047_cfDNA


title: PM01041_cfDNA


title: PM01045_cfDNA


title: PM01044_cfDNA


title: PM01042_cfDNA


title: PM01039_cfDNA


title: PM01037_cfDNA


title: PM01038_cfDNA


title: PM01040_cfDNA


title: PM01034_cfDNA


title: PM01036_cfDNA


title: PM01033_cfDNA


title: PM01032_cfDNA


title: PM01031_cfDNA


title: PM01027_cfDNA


title: PBMCs_Pool_2

source_name: Cell culture

value: Cell culture


title: PM01028_cfDNA


title: PM01030_cfDNA


title: WCM155_P


title: WCM154_P


title: 22Rv1


title: RWPE-1


title: VCaP


title: WCM155_LNCaP_99


title: DU145


title: LNCaP


title: LNCaP_Pool1_999


title: WCM155_LNCaP_50


title: WCM155_LNCaP_75


title: LNCaP_Pool1_99


title: WCM155_LNCaP_999


title: WCM155_LNCaP_98


title: LNCaP_Pool1_95


title: WCM981_Progression_SP29-33_cfDNA


title: LNCaP_Pool1_50


title: PBMCs_Pool_1


title: LNCaP_Pool1_90


title: PBMCs_Pool_3


title: WCM733_C1D1_E1-6_cfDNA


title: WCM886_C1D1_EP7-10_cfDNA


title: WCM779_Progression_SP89-93_cfDNA


title: WCM155_LNCaP_90


title: WCM78_C1D8_EP10_cfDNA


title: WCM7_C1D1_P22-27_5_cfDNA


title: WCM155_LNCaP_95


title: LNCaP_Pool1_98


title: WCM688_Screening_SP1-2_cfDNA


title: WCM89_Progression_P110-119_cfDNA


title: WCM6_C1D1_P4-10_22-25_cfDNA


title: WCM698_Progression_SP58-62_cfDNA


title: WCM664_C1D1_EP1-6_cfDNA


title: WCM665_C1D1_EP1-6_cfDNA


title: WCM661_C1D1_EP1-4_cfDNA


title: WCM663_C1D1_EP1-6_cfDNA


title: WCM668_C1D1_EP7-11_cfDNA


title: WCM666_C1D1_EP1_4-7_9_cfDNA


title: WCM662_C1D1_EP1_X_cfDNA


title: WCM658_C1D1_EP1_cfDNA


title: WCM946_Progression_SP45-49_cfDNA


title: WCM657_C1D1_EP1-2_cfDNA


title: WCM656_C1D1_EP1-2_cfDNA


title: WCM655_C1D1_EP1-2_cfDNA


title: WCM652_C1D1_EP1-2_cfDNA


title: WCM653_C1D1_EP1-2_cfDNA


title: WCM649_C1D1_EP1-2_cfDNA


title: WCM651_C1D1_EP1-2_cfDNA


title: WCM63_Progression_SP159_cfDNA


title: WCM646_C1D1_EP1_cfDNA


title: WCM639_Progression_SP21-25_cfDNA


title: WCM620_Progression_SP46-50_cfDNA


title: WCM654_C1D1_EP1-2_cfDNA


title: WCM573_C1D1_EP3-6_X_cfDNA


title: WCM556_C1D1_EP3-2_cfDNA


title: WCM559_C1D1_EP1-5_cfDNA


title: WCM555_C1D1_EP1-4_cfDNA


title: WCM557_C1D1_EP1-4_cfDNA


title: WCM558_C1D1_EP3-5_X_cfDNA


title: WCM428_Progression_SP116-120_cfDNA


title: WCM509_C1D1_EP8-13_cfDNA


title: WCM572_C1D1_EP1_4_cfDNA


title: WCM554_C1D8_EP1_5_cfDNA


title: WCM423_C1D1_EP3-7_cfDNA


title: WCM648_C1D8_EP1-2_cfDNA


title: WCM404_C1D1_EP3-6_cfDNA


title: WCM405_C1D1_EP3-8_cfDNA


title: WCM647_C1D1_EP1_cfDNA


title: WCM399_Progression_SP55-59_cfDNA


title: WCM393_Progression_SP45-49_cfDNA


title: WCM369_Progression_SP101-105_cfDNA


title: WCM370_Progression_SP1-10_cfDNA


title: WCM367_C1D1_EP1-6_cfDNA


title: WCM343_C1D8_EP1-5_X_cfDNA


title: WCM341_C1D1_EP1_4_5_X_cfDNA


title: WCM342_C1D1_EP3-5_X_cfDNA


title: WCM253_C1D8_EP1-6_cfDNA


title: WCM258_Progression_SP113-116_cfDNA


title: WCM252_C1D1_SP7-9_cfDNA


title: WCM406_C1D1_EP1-2_cfDNA


title: WCM239_Progression_SP50-54_cfDNA


title: WCM212_C1D1_EP2_cfDNA


title: WCM213_C1D1_EP11-16_cfDNA


title: WCM221_C1D1_EP1_cfDNA


title: WCM199_C1D1_EP1-2_cfDNA


title: WCM207_C1D8_EP11_13_15-16_cfDNA


title: WCM198_C1D1_EP1-2_cfDNA


title: WCM185_Progression_SP174-178_cfDNA


title: WCM192_C1D1_EP10_SPx_cfDNA


title: WCM373_C1D1_EP1-2_3_6_cfDNA


title: WCM161_C1D1_EP13-16_cfDNA


title: WCM15_C1D1_EP3_6_7_8_9_cfDNA


title: WCM156_C1D1_C1D8_EP1-2_cfDNA


title: WCM160_Progression_SP21-26_28-31_cfDNA


title: WCM340_C1D1_EP1-2_5_cfDNA


title: WCM155_C1D8_EP10-14_cfDNA


title: PM00205


title: PM00123


title: WCM14_Progression_SP121-125_cfDNA


title: WCM1388_Progression_SP9-10_cfDNA


title: WCM1262_Progression_SP12-16_cfDNA


title: WCM1344_Progression_SP17-21_cfDNA


title: WCM1138_Progression_SP19-20_cfDNA


title: WCM210_C1D1_EP1-2_cfDNA


title: WCM10_C1D1_SP1-8_13-20_cfDNA


title: WCM1088_Progression_SP1-5_cfDNA


title: DFCI-HB-011


title: DFCI-HB-010


title: DFCI-HB-008


title: DFCI-HB-007


title: DFCI-HB-009


title: DFCI-HB-006


title: DFCI-HB-004


title: DFCI-HB-005


title: 12-mt2-K27me3

city: Clayton

first: Evan

last: Healy

state: VIC

address: 23 Innovation Way, Building 77,, Monash University

country: Australia

institute: Monash University

data_processing:
Reads were aligned to the human reference genome (hg38) and the relevant spike-in genome (mm10) using bowtie2. Bigwig files were generated at a resolution of 10bp using bamCoverage. Tracks were normalised using spike-in derived normalisation factors.
Assembly: hg38 & mm10
Supplementary files format and content: bigWig

growth_protocol: K562 cells were cultured in RPMI-1640 (Merck #R8758) growth medium supplemented with 10% FBS (Cellsera AU-FBS/SF) and 1% (v/v) penicillin-streptomycin (Thermo Scientific #15140122) and were incubated at 37 °C with 5% CO2. Mouse embryonic stem cells (mESC) were cultured on 0.1% gelatin-coated dishes in DMEM medium supplemented with 20% FBS, 1% (v/v) penicillin-streptomycin, 50 µM β-mercaptoethanol, 1:100 GlutaMAX (Thermo #35050061), 1:100 MEM Non-Essential Amino Acids (Thermo # 11140076), 1:100 Sodium Pyruvate (Thermo #11360070), 1:1000 leukaemia inhibitory factor (LIF; produced in-house), 3 µM CHIR99021 (STEMCELL #72054) and 1 µM PD0325901 (STEMCELL #72184). HEK293T cells (for lentiviral production) were cultured in DMEM medium supplemented with 10% FBS, 1% (v/v) penicillin-streptomycin.

extract_protocol:
Cells were collected, counted and washed once with PBS before crosslinking for 10 minutes with PBS containing 1 % formaldehyde (Sigma). Cells were crosslinked in 15 mL falcon tubes at a density of ~5x106 cells/mL. Crosslinking was quenched with 0.125 M Glycine prior to two PBS washes. Crosslinked cells were then snap-frozen on liquid nitrogen and stored at -80ºC. Crosslinked cells were thawed on ice and lysed in 5 mL of SDS-Lysis buffer (100 mM NaCl, 50 mM Tris pH 8.1, 5 mM EDTA pH 8.0, 0.5 % SDS, 1X protease inhibitor cocktail [Sigma; P8340]). Nuclei and chromatin were pelleted by centrifugation at 1200 rpm for 6 min at room temperature. The supernatant was then discarded, and the pellet was resuspended in 2 mL of ChIP buffer (33 mM Tris-HCl pH 8, 100 mM NaCl, 5 mM EDTA, 0.33% SDS, 1.67% Triton X-100, 1X protease inhibitor cocktail [Sigma; P8340]). Chromatin was sheared to approximately 200 bp to 500 bp fragments by sonication using a Bioruptor Plus (Diagenode) at high power. Total sonication time (i.e. cumulative “on” time) was 15min with 30 sec on/off pulses. Sonicated chromatin was incubated overnight with antibody while rotating at 4 ºC.
Following ChIP experiments, the precipitated DNA was quantified using the Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Q32854). A total of 1-10 ng of DNA from each ChIP experiment was used for library preparation using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) and NEBNext Multiplex Oligos for Illumina (Set#1 & #2; E7335 & E7500). Following adaptor ligation, DNA was PCR amplified for 4-10 cycles, depending on the amount of the input DNA. DNA purification was then performed using NEBNext Sample Purification Beads (E7767S). The quality and size distributions of DNA libraries were ascertained on a TapeStation (Agilent) using High Sensitivity D1000 ScreenTape assay reagents (Agilent; 5067-5585). The resulting libraries were then used for cluster generation and sequencing on an Illumina-based platform with a 150 bp paired-end read format (2-3x107 reads per sample).

tag: chip antibody

value: anti-H3K27me3 (CST - C36B11)


title: 6-WT-EZH2

value: anti-EZH2 (CST - D2C9)


title: 13-dEZH2-K27me3


title: 11-mt1-K27me3


title: 4-mt2-SUZ12

value: anti-SUZ12 (CST - D39F6)


title: 3-mt1-SUZ12


title: 5-dEZH2-SUZ12


title: 10-WT-K27me3


title: 9-dEZH2-EZH2


title: 7-mt1-EZH2


title: 8-mt2-EZH2


title: 2-WT-SUZ12


title: 1-K562-IN

value: INPUT


title: CAG59_hCO_3, HD, Day60

city: Shanghai

first: Lixiang

last: Ma

address: Dong'an road No.130

department: School of Basic Medical Sciences

institute: Fudan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software
Trimmed sequence reads were mapped to GRCh38.p13 human genome
Read count extraction and normalization were performed using STAR software
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: brain organoid

growth_protocol: in vitro culture

extract_protocol:
RNA was harvested using Rneasy mini plus kit (VZ6). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: brain organoid

value: induced pluripotent stem cells

value: HD

value: cortical organoid differentiation

tag: time


title: CAG55_hCO_3, HD, Day60


title: CAG55_hCO_2, HD, Day60


title: CAG55_hCO_1, HD, Day60


title: CAG59_hCO_2, HD, Day60


title: H9_hCO_2, control, Day60

value: human embryonic stem cells

value: WT


title: CAG19_hCO_3, control, Day60


title: CAG19_hCO_1, control, Day60


title: CAG59_hCO_3, HD, Day30


title: CAG59_hCO_1, HD, Day60


title: H9_hCO_3, control, Day60


title: CAG19_hCO_2, control, Day60


title: CAG59_hCO_1, HD, Day30


title: H9_hCO_1, control, Day60


title: CAG55_hCO_3, HD, Day30


title: CAG55_hCO_1, HD, Day30


title: CAG55_hCO_2, HD, Day30


title: H9_hCO_2, control, Day30


title: 02-012_C1D8_EP1-2_cfDNA


title: H9_hCO_1, control, Day30


title: CAG19_hCO_2, control, Day30


title: CAG19_hCO_3, control, Day30


title: CAG19_hCO_1, control, Day30


title: KO-dEZH2_RNAseq_rp4

first: Qi

last: Zhang

address: 23 Innovation Walk

description:
EZH2 KO/Rescue RNAseq-rp4
H6-LDG1736_L1.sf

data_processing:
rChIP-seq: short reads were aligned using bowtie with the following flags: --best --chunkmbs 256 -m 1 -n 1 -q. SAM files were converted to BAM files and then bigwig files using samtools and deepTools.
CUT&Tag: First, the --local flag was used for bowtie alignment in order to remove adapter sequences used during the experimental protocol. Second, potential duplicates were removed from the BAM files using the MarkDuplicates function from the Picard toolkit, with these BAM filles were then used to calculate scaling factors for H3K27me3 and H3K27ac datasets using the ChIPseqSpikeInFree R package. These scaling factors were used to generate bigwig files for heatmap, enrichment profiles, and genome browser tracks.
RNAseq: RNA-seq reads were obtained in FASTQ format and were quantified against the hg38 transcriptome index using Salmon (version 0.14.1) with the --gcBias flag. These transcript-level quantifications were then imported into R using the R packages DESeq2 and tximport. Batch effect removal was done with limma, using the function removeBatchEffect().
Assembly: hg38 and mm9
Supplementary files format and content: bigWig
Supplementary files format and content: abundance measurements

growth_protocol: K562 cells were cultured in RPMI-1640 (Merck #R8758) growth medium supplemented with 10% FBS (Cellsera AU-FBS/SF) and 1% (v/v) penicillin-streptomycin (Thermo Scientific #15140122) and were incubated at 37 °C with 5% CO2. J1 mouse embryonic stem cells (mESCs) were cultured at 37°C with 5% CO2 in DMEM growth medium, supplemented with 10% FBS (Moregate Biotech), 2% penicillin-streptomycin (Thermo Scientific 15140122), EmbryoMax® Nucleosides (Merck ES-008-D), MEM Non-Essential Amino Acids Solution (Thermo Scientific 11140050), Glutamax™ Supplement (Thermo Scientific 35050061), EmbryoMax® 2-Mercaptoethanol (Merck ES-007-E), 0.01% Plasmocin® (Invivogen ant-mpt) and ESGRO® Recombinant Mouse LIF Protein (Merck ESG1107). All tissue culture plates were first incubated with 0.1% gelatin (Sigma G1393) for >10 minutes at 37°C.

extract_protocol:
CUT&TAG was performed according to Bench top CUT&Tag V.3 (protocols.io, Kaya-Okur & Henikoff). RNA was extracted from 1 million cells using RNeasy kit (QIAGEN #74004) as per manufacturer’s instructions. For rChIP, cell lysates were clarified from sonicated nuclei and DNA were isolated with EZH2 (CST #5246) and H3K27me3 (CST #9733 and Millipore #07-449) antibodies w/o RNase A treatment.
Libraries were constructed according to Bench top CUT&Tag V.3 (protocols.io, Kaya-Okur & Henikoff) using PCR primers described in Buenrostro et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature  (2015). DNA (ChIP) and RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For EZH2 depletion and rescue experiments, 3x104 K562 cells were transduced in RPMI and 8 µg/mL polybrene using 200 µL of either EZH2 gRNA or AAVS1 gRNA lentivirus, and 200 µL of rescue or empty vector lentivirus to a final volume of 700 µl in a treated 24-well plate (day 0). On the second day 50% of the media was replaced with fresh RPMI, and on the third day the cell suspension was moved to a 10 cm dish with puromycin added to a final concentration of 10 µg/mL. On day 7, cells were sorted by flow cytometry based on EGFP signal, and seeded into a 10 cm dish. On day 14, cells were trypsinized and washed twice with PBS by centrifugation at 500 x rcf for 5 minutes, resuspended in PBS to 1 million/mL before aliquoting them to the downstream applications.

value: EZH2 KO/Rescue dEZH2

tag: antibody


title: KO-mt1_RNAseq_rp4

description:
EZH2 KO/Rescue RNAseq-rp4
H5-LDG1735_L1.sf

value: EZH2 KO/Rescue mt1


title: KO-mt2_RNAseq_rp4

description:
EZH2 KO/Rescue RNAseq-rp4
H4-LDG1734_L1.sf

value: EZH2 KO/Rescue mt2


title: KO-WT_RNAseq_rp4

description:
EZH2 KO/Rescue RNAseq-rp4
H3-LDG1733_L1.sf

value: EZH2 KO/Rescue WT


title: KO-Ctrl_RNAseq_rp4

description:
EZH2 KO/Rescue RNAseq-rp4
H2-LDG1732_L1.sf

value: EZH2 KO/Rescue Ctrl


title: CAG59_hCO_2, HD, Day30


title: Ctrl-Ctrl_RNAseq_rp4

description:
EZH2 KO/Rescue RNAseq-rp4
H1-LDG1731_L1.sf

value: KO Ctrl/Rescue Ctrl


title: KO-dEZH2_RNAseq_rp3

description:
EZH2 KO/Rescue RNAseq-rp3
G6-LDG1730_L3.sf


title: KO-WT_RNAseq_rp3

description:
EZH2 KO/Rescue RNAseq-rp3
G3-LDG1727_L3.sf


title: KO-mt2_RNAseq_rp3

description:
EZH2 KO/Rescue RNAseq-rp3
G4-LDG1728_L1.sf


title: Ctrl-Ctrl_RNAseq_rp3

description:
EZH2 KO/Rescue RNAseq-rp3
G1-LDG1725_L1.sf


title: KO-dEZH2_RNAseq_rp2

description:
EZH2 KO/Rescue RNAseq-rp2
F6-LDG1748_L1.sf


title: KO-Ctrl_RNAseq_rp3

description:
EZH2 KO/Rescue RNAseq-rp3
G2-LDG1726_L1.sf


title: H9_hCO_3, control, Day30


title: KO-mt1_RNAseq_rp2

description:
EZH2 KO/Rescue RNAseq-rp2
F5-LDG1747_L1.sf


title: KO-WT_RNAseq_rp2

description:
EZH2 KO/Rescue RNAseq-rp2
F3-LDG1745_L3.sf


title: KO-mt1_RNAseq_rp1

description:
EZH2 KO/Rescue RNAseq-rp1
E5-LDG1741_L3.sf


title: KO-mt2_RNAseq_rp2

description:
EZH2 KO/Rescue RNAseq-rp2
F4-LDG1746_L1.sf


title: KO-Ctrl_RNAseq_rp2

description:
EZH2 KO/Rescue RNAseq-rp2
F2-LDG1744_L3.sf


title: Ctrl-Ctrl_RNAseq_rp2

description:
EZH2 KO/Rescue RNAseq-rp2
F1-LDG1743_L1.sf


title: KO-mt2_RNAseq_rp1

description:
EZH2 KO/Rescue RNAseq-rp1
E4-LDG1740_L3.sf


title: KO-Ctrl_RNAseq_rp1

description:
EZH2 KO/Rescue RNAseq-rp1
E2-LDG1738_L3.sf


title: KO-mt1_RNAseq_rp3

description:
EZH2 KO/Rescue RNAseq-rp3
G5-LDG1729_L3.sf


title: KO-dEZH2_H3K27me3_cuttag_rp3

description: EZH2 KO/Rescue CUT&TAG-rp3

data_processing:
Library strategy: CUT&TAG
rChIP-seq: short reads were aligned using bowtie with the following flags: --best --chunkmbs 256 -m 1 -n 1 -q. SAM files were converted to BAM files and then bigwig files using samtools and deepTools.
CUT&Tag: First, the --local flag was used for bowtie alignment in order to remove adapter sequences used during the experimental protocol. Second, potential duplicates were removed from the BAM files using the MarkDuplicates function from the Picard toolkit, with these BAM filles were then used to calculate scaling factors for H3K27me3 and H3K27ac datasets using the ChIPseqSpikeInFree R package. These scaling factors were used to generate bigwig files for heatmap, enrichment profiles, and genome browser tracks.
CUT&Tag: CUT&Tag peaks of H3K27me3 were calculated using SEACR (PMID: 31300027) as previously described (dx.doi.org/10.17504/protocols.io.bjk2kkye; PMID: 33191916)
RNAseq: RNA-seq reads were obtained in FASTQ format and were quantified against the hg38 transcriptome index using Salmon (version 0.14.1) with the --gcBias flag. These transcript-level quantifications were then imported into R using the R packages DESeq2 and tximport. Batch effect removal was done with limma, using the function removeBatchEffect().
Assembly: hg38 and mm9
Supplementary files format and content: bed
Supplementary files format and content: bigWig
Supplementary files format and content: abundance measurements


title: Ctrl-Ctrl_RNAseq_rp1

description:
EZH2 KO/Rescue RNAseq-rp1
E1-LDG1737_L1.sf


title: KO-dEZH2_H3K27ac_cuttag_rp3

description: EZH2 KO/Rescue CUT&TAG-rp3

data_processing:
Library strategy: CUT&TAG
rChIP-seq: short reads were aligned using bowtie with the following flags: --best --chunkmbs 256 -m 1 -n 1 -q. SAM files were converted to BAM files and then bigwig files using samtools and deepTools.
CUT&Tag: First, the --local flag was used for bowtie alignment in order to remove adapter sequences used during the experimental protocol. Second, potential duplicates were removed from the BAM files using the MarkDuplicates function from the Picard toolkit, with these BAM filles were then used to calculate scaling factors for H3K27me3 and H3K27ac datasets using the ChIPseqSpikeInFree R package. These scaling factors were used to generate bigwig files for heatmap, enrichment profiles, and genome browser tracks.
RNAseq: RNA-seq reads were obtained in FASTQ format and were quantified against the hg38 transcriptome index using Salmon (version 0.14.1) with the --gcBias flag. These transcript-level quantifications were then imported into R using the R packages DESeq2 and tximport. Batch effect removal was done with limma, using the function removeBatchEffect().
Assembly: hg38 and mm9
Supplementary files format and content: bigWig
Supplementary files format and content: abundance measurements


title: KO-mt1_H3K27ac_cuttag_rp3

description: EZH2 KO/Rescue CUT&TAG-rp3


title: KO-mt2_H3K27ac_cuttag_rp3

description: EZH2 KO/Rescue CUT&TAG-rp3


title: KO-mt1_H3K27me3_cuttag_rp3

description: EZH2 KO/Rescue CUT&TAG-rp3


title: KO-mt1_IgG_cuttag_rp3

description: EZH2 KO/Rescue CUT&TAG-rp3

value: IgG


title: KO-mt2_H3K27me3_cuttag_rp3

description: EZH2 KO/Rescue CUT&TAG-rp3


title: KO-WT_H3K27me3_cuttag_rp3

description: EZH2 KO/Rescue CUT&TAG-rp3


title: KO-Ctrl_H3K27ac_cuttag_rp3

description: EZH2 KO/Rescue CUT&TAG-rp3


title: KO-WT_IgG_cuttag_rp3

description: EZH2 KO/Rescue CUT&TAG-rp3


title: KO-dEZH2_RNAseq_rp1

description:
EZH2 KO/Rescue RNAseq-rp1
E6-LDG1742_L3.sf


title: KO-Ctrl_IgG_cuttag_rp3

description: EZH2 KO/Rescue CUT&TAG-rp3


title: KO-Ctrl_H3K27me3_cuttag_rp3

description: EZH2 KO/Rescue CUT&TAG-rp3


title: Ctrl-Ctrl_H3K27me3_cuttag_rp3

description: EZH2 KO/Rescue CUT&TAG-rp3


title: Ctrl-Ctrl_H3K27ac_cuttag_rp3

description: EZH2 KO/Rescue CUT&TAG-rp3


title: Ctrl-Ctrl_IgG_cuttag_rp3

description: EZH2 KO/Rescue CUT&TAG-rp3


title: KO-WT_RNAseq_rp1

description:
EZH2 KO/Rescue RNAseq-rp1
E3-LDG1739_L3.sf


title: KO-dEZH2_IgG_cuttag_rp3

description: EZH2 KO/Rescue CUT&TAG-rp3


title: 5679_YM3B_8-6-D8-P12

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

source_name: YM3B human BA46

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Male

tag: molecule subtype

value: nuclear RNA + genomic DNA


title: 5679_YM3B_8-6-D8-N23


title: 5679_YM3B_8-6-D8-O11


title: 5679_YM3B_8-6-D8-O23


title: 5679_YM3B_8-6-D8-P11


title: 5679_YM3B_8-6-D8-O24


title: 5679_YM3B_8-6-D8-P23


title: 5679_YM3B_8-6-D8-N24


title: 5679_YM3B_8-6-D8-P24


title: 5679_YM3B_8-6-D8-N12


title: 5679_YM3B_8-6-D8-N11


title: KO-mt2_IgG_cuttag_rp3

description: EZH2 KO/Rescue CUT&TAG-rp3


title: 5679_YM3B_8-6-D8-M12


title: 5679_YM3B_8-6-D8-M11


title: 5679_YM3B_8-6-D8-L23


title: 5679_YM3B_8-6-D8-L24


title: 5679_YM3B_8-6-D8-L12


title: 5679_YM3B_8-6-D8-L11


title: 5679_YM3B_8-6-D8-K12


title: 5679_YM3B_8-6-D8-K24


title: 5679_YM3B_8-6-D8-K11


title: 5679_YM3B_8-6-D8-J23


title: 5679_YM3B_8-6-D8-J24


title: 5679_YM3B_8-6-D8-J12


title: 5679_YM3B_8-6-D8-J11


title: 5679_YM3B_8-6-D8-I24


title: 5679_YM3B_8-6-D8-M23


title: 5679_YM3B_8-6-D8-I23


title: 5679_YM3B_8-6-D8-M24


title: 5679_YM3B_8-6-D8-G23


title: 5679_YM3B_8-6-D8-H23


title: 5679_YM3B_8-6-D8-H12


title: 5679_YM3B_8-6-D8-H11


title: 5679_YM3B_8-6-D8-G24


title: 5679_YM3B_8-6-D8-H24


title: 5679_YM3B_8-6-D8-I11


title: 5679_YM3B_8-6-D8-G11


title: 5679_YM3B_8-6-D8-G12


title: 5679_YM3B_8-6-D8-I12


title: 5679_YM3B_8-6-D8-F12


title: 5679_YM3B_8-6-D8-F23


title: 5679_YM3B_8-6-D8-K23


title: 5679_YM3B_8-6-D8-F11


title: 5679_YM3B_8-6-D8-E23


title: 5679_YM3B_8-6-D8-E24


title: 5679_YM3B_8-6-D8-E11


title: 5679_YM3B_8-6-D8-D24


title: 5679_YM3B_8-6-D8-D12


title: 5679_YM3B_8-6-D8-D11


title: 5679_YM3B_8-6-D8-C24


title: 5679_YM3B_8-6-D8-F24


title: 5679_YM3B_8-6-D8-C23


title: 5679_YM3B_8-6-D8-C12


title: 5679_YM3B_8-6-D8-B23


title: 5679_YM3B_8-6-D8-B24


title: 5679_YM3B_8-6-D8-C11


title: 5679_YM3B_8-6-D8-B12


title: 5679_YM3B_8-6-D8-A24


title: 5679_YM3B_8-5-D8-O9


title: 5679_YM3B_8-5-D8-P22


title: 5679_YM3B_8-6-D8-D23


title: 5679_YM3B_8-6-D8-B11


title: 5679_YM3B_8-5-D8-O10


title: 5679_YM3B_8-6-D8-E12


title: 5679_YM3B_8-5-D8-O22


title: 5679_YM3B_8-6-D8-A12


title: 5679_YM3B_8-6-D8-A11


title: 5679_YM3B_8-5-D8-N9


title: 5679_YM3B_8-5-D8-P10


title: 5679_YM3B_8-5-D8-O21


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title: 5679_YM3B_2-2-J11-A4


title: 5679_YM3B_2-2-J11-A16


title: 5679_YM3B_2-2-J11-B16


title: 5679_YM3B_2-1-J11-O1


title: 5679_YM3B_2-2-J11-A3


title: 5679_YM3B_2-1-J11-O13


title: 5679_YM3B_2-1-J11-P2


title: 5679_YM3B_2-1-J11-M2


title: 5679_YM3B_2-1-J11-N2


title: 5679_YM3B_2-2-J11-B15


title: 5679_YM3B_2-1-J11-M1


title: 5679_YM3B_2-1-J11-M13


title: 5679_YM3B_2-1-J11-O2


title: 5679_YM3B_2-1-J11-P14


title: 5679_YM3B_2-1-J11-O14


title: RPE-19 cells treated with 200 µg/mL GPE and stressed with 500 µM H2O2 36

type: RNA

city: Bundoora

first: Dao

last: Nguyen

state: Victoria

address: 289 McKimmies Rd

department: School of Science and Health and Biomedical Science

institute: Royal Melbourne Institute of Technology

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://rotor-gene-q.software.informer.com/2.3/
For the normalization it uses housekeeping gene: GAPDH.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]

label: SYBR Green

source_name: Human retinal pigment epithelium (RPR-19) cell, CRL-2502

label_protocol: The qPCR was performed on a Qiagen Rotor-Gene Q (Qiagen, Germany) and analysed with inbuilt software (version 2.3.1.49). The thermal cycling conditions were as follows: initial activation at 95°C for 2 min, 45 cycles of 95°C 5 s, 60°C for 10 s, 72°C for 15 s, and melting curve from 65°C to 95°C

extract_protocol: Total RNA was extracted using TRIzol™ Reagent (Life Technologies, Melbourne, Australia) as per the manufacturer’s protocol

value: Spontaneously immortalized cell line

tag: activation agent

value: Gac peel extract

tag: treatment time


title: RPE-19 cells treated with 100 µg/mL GPE and stressed with 500 µM H2O2 35

description: Test


title: 5679_YM3B_2-1-J11-P1


title: 5679_YM3B_2-1-J11-L2


title: 5679_YM3B_2-1-J11-P13


title: 5679_YM3B_2-2-J11-C3


title: 5679_YM3B_2-1-J11-N1


title: 5679_YM3B_2-1-J11-N14


title: 5679_YM3B_2-1-J11-N13


title: RPE-19 cells treated with 10 µg/mL GPE and stressed with 500 µM H2O2 34

description: Test


title: RPE-19 cells treated with 1 µg/mL GPE and stressed with 500 µM H2O2 33

description: Test


title: 5679_YM3B_2-1-J11-L1


title: 5679_YM3B_2-1-J11-L14


title: 5679_YM3B_2-1-J11-M14


title: 5679_YM3B_2-1-J11-L13


title: RPE-19 cells stressed with 500 µM H2O2 29

description: Test

value: Hydro peroxide


title: RPE-19 cells treated with 50 µg/mLTrolox and stressed with 500 µM H2O2 30

description: Test

value: Trolox


title: 5679_YM3B_2-1-J11-K13


title: RPE-19 cells treated with 10 µg/mL lutein and stressed with 500 µM H2O2 31

description: Test

value: Lutein


title: Untreated and unstressed RPE-19 cells 28

description: Control

value: Control (untreated and unstressed)


title: 5679_YM3B_2-1-J11-I14


title: RPE-19 cells treated with 100 µg/mL GPE and stressed with 500 µM H2O2 26

description: Test


title: 5679_YM3B_2-1-J11-J1


title: 5679_YM3B_2-1-J11-K2


title: 5679_YM3B_2-1-J11-J2


title: RPE-19 cells treated with 10 µg/mL GPE and stressed with 500 µM H2O2 25

description: Test


title: RPE-19 cells treated with 1 µg/mL GPE and stressed with 500 µM H2O2 24

description: Test


title: 5679_YM3B_2-1-J11-K1


title: RPE-19 cells treated with 200 µg/mL GPE and stressed with 500 µM H2O2 27

description: Test


title: 5679_YM3B_2-1-J11-I2


title: RPE-19 cells treated with 10 µg/mL lutein and stressed with 500 µM H2O2 22

description: Test


title: 5679_YM3B_2-1-J11-J14


title: RPE-19 cells treated with 0.1 µg/mL GPE and stressed with 500 µM H2O2 23

description: Test


title: 5679_YM3B_2-1-J11-J13


title: RPE-19 cells treated with 50 µg/mLTrolox and stressed with 500 µM H2O2 21

description: Test


title: RPE-19 cells stressed with 500 µM H2O2 20

description: Test


title: 5679_YM3B_2-1-J11-H2


title: RPE-19 cells treated with 200 µg/mL GPE and stressed with 500 µM H2O2 18

description: Test


title: RPE-19 cells treated with 0.1 µg/mL GPE and stressed with 500 µM H2O2 32

description: Test


title: 5679_YM3B_2-1-J11-H1


title: 5679_YM3B_2-1-J11-K14


title: 5679_YM3B_2-1-J11-H14


title: RPE-19 cells treated with 100 µg/mL GPE and stressed with 500 µM H2O2 17

description: Test


title: 5679_YM3B_2-1-J11-I1


title: 5679_YM3B_2-1-J11-H13


title: RPE-19 cells treated with 1 µg/mL GPE and stressed with 500 µM H2O2 15

description: Test


title: 5679_YM3B_2-1-J11-I13


title: RPE-19 cells treated with 10 µg/mL lutein and stressed with 500 µM H2O2 13

description: Test


title: RPE-19 cells treated with 0.1 µg/mL GPE and stressed with 500 µM H2O2 14

description: Test


title: RPE-19 cells stressed with 500 µM H2O2 11

description: Test


title: RPE-19 cells treated with 50 µg/mLTrolox and stressed with 500 µM H2O2 12

description: Test


title: 5679_YM3B_2-1-J11-F14


title: 5679_YM3B_2-1-J11-G13


title: 5679_YM3B_2-1-J11-F1


title: 5679_YM3B_2-1-J11-G14


title: Untreated and unstressed RPE-19 cells 10

description: Control


title: 5679_YM3B_2-1-J11-F2


title: Untreated and unstressed RPE-19 cells 19

description: Control


title: RPE-19 cells treated with 200 µg/mL GPE and stressed with 500 µM H2O2 9

description: Test


title: 5679_YM3B_2-1-J11-E2


title: RPE-19 cells treated with 100 µg/mL GPE and stressed with 500 µM H2O2 8

description: Test


title: RPE-19 cells treated with 10 µg/mL GPE and stressed with 500 µM H2O2 7

description: Test


title: RPE-19 cells treated with 0.1 µg/mL GPE and stressed with 500 µM H2O2 5

description: Test


title: 5679_YM3B_2-1-J11-F13


title: RPE-19 cells treated with 1 µg/mL GPE and stressed with 500 µM H2O2 6

description: Test


title: 5679_YM3B_2-1-J11-E1


title: RPE-19 cells treated with 10 µg/mL GPE and stressed with 500 µM H2O2 16

description: Test


title: RPE-19 cells treated with 10 µg/mL lutein and stressed with 500 µM H2O2 4

description: Test


title: 5679_YM3B_2-1-J11-G2


title: 5679_YM3B_2-1-J11-D2


title: 5679_YM3B_2-1-J11-E14


title: 5679_YM3B_2-1-J11-G1


title: 5679_YM3B_2-1-J11-D14


title: 5679_YM3B_2-1-J11-D1


title: RPE-19 cells stressed with 500 µM H2O2 2

description: Test


title: Untreated and unstressed RPE-19 cells 1

description: Control


title: RPE-19 cells treated with 50 µg/mLTrolox and stressed with 500 µM H2O2 3

description: Test


title: 5679_YM3B_2-1-J11-C2


title: 5679_YM3B_2-1-J11-E13


title: 5679_YM3B_2-1-J11-C14


title: UY031, water, biol rep 2

city: Cerdanyola del Valles

first: Marc

last: Valls

email: marcvalls@ub.edu, mercerf93@gmail.com

state: Barcelona

address: CRAG Building - Campus UAB

country: Spain

institute: CRAG

data_processing:
Samples were trimmed with trimGalore (v.0.6.1) (Moskvin et al., 2011) with the paired (--paired) option to remove adaptors and low quality reads from the analysis
Trimmed libraries were searched for potential contaminants using the software SortMeRNA (v.4.2.0) (Kopylova, Noé and Touzet, 2012) with the default parameters and contaminant libraries
Filtered sequenced reads were mapped to UY031 genome with Bowtie2 (v. 2.4.4) (Langmead and Salzberg, 2013) with deafault parameters.
Raw counts were extracted from alinged files using the prokaryote counting software FADU (Feature Aggregate Depth Utility) (v. 1.8) (Fraser et al., 2021)
Assembly: GCF_001299555.1_ASM129955v1
Supplementary files format and content: Excel file includes raw counts for each sample
Supplementary files format and content: Excel file includes Deseq2 normalized counts for each sample

organism: Ralstonia solanacearum

growth_protocol: For the soil samples, a natural soil (Table S2) was autoclaved three times (∼3 h),  200 g of soil was added to pots without plants and incubated for 3 days at plant infection conditions. Finally, 5 g soil samples were sampled.  For the water samples, bacteria were recovered 48 h after growth in rich B medium plates, washed and resuspended in sterile mineral water (Water A - Table S1) to a final concentration of ∼107 CFU/mL in 250 mL. The suspension was incubated at 28 °C for 6 hours, centrifuged at 4 ºC, and the pellet frozen in liquid nitrogen.

extract_protocol:
Total RNA from bacterial pellets grown in water was extracted using the SV Total RNA Isolation System kit (Promega
Total RNA was extracted using the SV Total RNA Isolation System kit (Promega) for water samples and the RNA PowerSoil® Total RNA Isolation Kit (MO BIO) followed with a rigorous DNAse treatment with the TURBO DNA-free kit (Life Technologies) for soil samples.
Bacterial rRNA was removed using NEBNext rRNA Depletion kit (Bacteria) (NEB). Libraries were independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit

tag: strain

value: wt

tag: condition

value: water


title: UY031, soil, biol rep 3

extract_protocol:
RNA PowerSoil® Total RNA Isolation Kit (MO BIO) was used supplemented with a Rigurous DNAse treatment using the TURBO DNA-free kit (Life Technologies, Ambion)
Total RNA was extracted using the SV Total RNA Isolation System kit (Promega) for water samples and the RNA PowerSoil® Total RNA Isolation Kit (MO BIO) followed with a rigorous DNAse treatment with the TURBO DNA-free kit (Life Technologies) for soil samples.
Bacterial rRNA was removed using NEBNext rRNA Depletion kit (Bacteria) (NEB). Libraries were independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit

value: soil


title: 5679_YM3B_2-1-J11-C13


title: 5679_YM3B_2-1-J11-C1


title: UY031, soil, biol rep 2


title: 5679_YM3B_2-1-J11-B2


title: UY031, water, biol rep 1


title: UY031, water, biol rep 3


title: UY031, soil, biol rep 1


title: 5679_YM3B_2-1-J11-B1


title: 5679_YM3B_2-1-J11-B14


title: 5679_YM3B_2-1-J11-B13


title: ans-lmi1, rep 2

city: Yangling

first: Liping

last: Guo

address: Taicheng Road

institute: Northwest A&F University

data_processing:
Raw reads were filtered by removing adaptor sequences and low quality sequences to obtain high-quality reads
The clean reads were assembled into transcript using Trinity after the adaptors and the low quality reads were removed
The clean reads were separately mapped to the reference transcriptome by TopHat2
Fragments per kilobase per million mapped reads (FPKM) values were calculated using RSEM
Assembly: For de novo transcriptome analysis, RNA-seq reads were assembled into transcripts using the Trinity software.
Supplementary files format and content: Tab-delimited text file includes reads counts for each sample

organism: Delphinium anthriscifolium

source_name: Lateral non-spurred sepals

extract_protocol:
RNA was extracted using the RNAprep Pure Plant Kit (TIANGEN)
Construction of an RNA sequencing library was uising Fast RNA-seq Lib Prep Kit V2

value: Lateral non-spurred sepals

value: LMI2 knockdown


title: ans, rep 2

value: ans


title: 5679_YM3B_2-1-J11-A2


title: ans, rep 1


title: ans-lmi1, rep 1

value: LMI1 knockdown


title: 5679_YM3B_2-1-J11-A1


title: 5679_YM3B_2-1-J11-A14


title: Carpels, S16, rep 3

source_name: Carpels

value: Carpels

value: WT


title: Carpels, S16, rep 2


title: 5679_YM3B_2-1-J11-D13

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Male


title: 5679_YM3B_2-1-J11-A13

value: nuclear RNA + genomic DNA


title: Carpels, S16, rep 1


title: 5679_YM3B_1-6-B11-P24


title: Carpels, S12, rep 3


title: 5679_YM3B_1-6-B11-P23


title: 5679_YM3B_1-6-B11-P12


title: 5679_YM3B_1-6-B11-P11


title: Carpels, S12, rep 2


title: 5679_YM3B_1-6-B11-O24


title: Carpels, S10, rep 3


title: 5679_YM3B_1-6-B11-O23


title: Carpels, S10, rep 1


title: 5679_YM3B_1-6-B11-O11


title: Carpels, S10, rep 2


title: 5679_YM3B_1-6-B11-O12


title: 5679_YM3B_1-6-B11-N24


title: Carpels, S9, rep 1


title: 5679_YM3B_1-6-B11-N23


title: Stamens, S16, rep 3

source_name: Stamens

value: Stamens


title: Stamens, S16, rep 1


title: Stamens, S16, rep 2


title: Stamens, S12, rep 3


title: 5679_YM3B_1-6-B11-N11


title: 5679_YM3B_1-6-B11-M24


title: Stamens, S12, rep 2


title: 5679_YM3B_1-6-B11-N12


title: Stamens, S12, rep 1


title: 5679_YM3B_1-6-B11-M23


title: 5679_YM3B_1-6-B11-M11


title: 5679_YM3B_1-6-B11-M12


title: Carpels, S12, rep 1


title: 5679_YM3B_1-6-B11-L24


title: Stamens, S10, rep 2


title: Carpels, S9, rep 2


title: 5679_YM3B_1-6-B11-L23


title: 5679_YM3B_1-6-B11-L12


title: Stamens, S9, rep 2


title: Stamens, S10, rep 1


title: 5679_YM3B_1-6-B11-L11


title: Lateral non-spurred petals, S16, rep 3

source_name: Lateral non-spurred petals

value: Lateral non-spurred petals


title: 5679_YM3B_1-6-B11-K24


title: Stamens, S9, rep 1


title: Lateral non-spurred petals, S16, rep 2


title: Lateral non-spurred petals, S16, rep 1


title: 5679_YM3B_1-6-B11-K12


title: 5679_YM3B_1-6-B11-J24


title: Lateral non-spurred petals, S12, rep 3


title: 5679_YM3B_1-6-B11-K11


title: Stamens, S10, rep 3


title: Lateral non-spurred petals, S12, rep 2


title: Lateral non-spurred petals, S10, rep 3


title: Lateral non-spurred petals, S12, rep 1


title: Lateral non-spurred petals, S10, rep 1


title: 5679_YM3B_1-6-B11-J23


title: 5679_YM3B_1-6-B11-J12


title: 5679_YM3B_1-6-B11-I24


title: 5679_YM3B_1-6-B11-J11


title: Lateral non-spurred petals, S10, rep 2


title: 5679_YM3B_1-6-B11-I23


title: Lateral non-spurred petals, S9, rep 1


title: Lateral non-spurred petals, S9, rep 2


title: 5679_YM3B_1-6-B11-I12


title: Dorsal spurred petals, S16, rep 3

source_name: Dorsal spurred petals

value: Dorsal spurred petals


title: 5679_YM3B_1-6-B11-I11


title: Dorsal spurred petals, S16, rep 2


title: 5679_YM3B_1-6-B11-H24


title: 5679_YM3B_1-6-B11-K23


title: Dorsal spurred petals, S12, rep 2


title: 5679_YM3B_1-6-B11-H23


title: Dorsal spurred petals, S16, rep 1


title: Dorsal spurred petals, S12, rep 3


title: 5679_YM3B_1-6-B11-H12


title: 5679_YM3B_1-6-B11-H11


title: 5679_YM3B_1-6-B11-G24


title: Dorsal spurred petals,  S10, rep 3


title: Dorsal spurred petals,  S10, rep 2


title: 5679_YM3B_1-6-B11-G23


title: Dorsal spurred petals,  S10, rep 1


title: 5679_YM3B_1-6-B11-G12


title: 5679_YM3B_1-6-B11-G11


title: Dorsal spurred petals, S9, rep 2


title: 5679_YM3B_1-6-B11-F24


title: Dorsal spurred petals, S9, rep 1


title: Ventral  non-spurred sepals, S16, rep 3

source_name: Ventral  non-spurred sepals

value: Ventral  non-spurred sepals


title: Ventral  non-spurred sepals, S16, rep 2


title: 5679_YM3B_1-6-B11-F12


title: 5679_YM3B_1-6-B11-F11


title: 5679_YM3B_1-6-B11-F23


title: Ventral  non-spurred sepals, S12, rep 2


title: Ventral  non-spurred sepals, S16, rep 1


title: 5679_YM3B_1-6-B11-E24


title: 5679_YM3B_1-6-B11-E23


title: 5679_YM3B_1-6-B11-E12


title: Ventral  non-spurred sepals, S10, rep 3


title: Dorsal spurred petals, S12, rep 1


title: Ventral  non-spurred sepals, S12, rep 3


title: Ventral  non-spurred sepals, S10, rep 2


title: 5679_YM3B_1-6-B11-D12


title: 5679_YM3B_1-6-B11-D23


title: 5679_YM3B_1-6-B11-E11


title: 5679_YM3B_1-6-B11-D24


title: Ventral non-spurred sepals, S9, rep 2

source_name: Ventral non-spurred sepals

value: Ventral non-spurred sepals


title: 5679_YM3B_1-6-B11-D11


title: Ventral non-spurred sepals, S9, rep 1


title: 5679_YM3B_1-6-B11-C24


title: 5679_YM3B_1-6-B11-C23


title: Lateral non-spurred sepals, S16, rep 3


title: 5679_YM3B_1-6-B11-C12


title: Lateral non-spurred sepals, S16, rep 1


title: Lateral non-spurred sepals, S16, rep 2


title: 5679_YM3B_1-6-B11-C11


title: Lateral non-spurred sepals, S12, rep 3


title: Lateral non-spurred sepals, S12, rep 2


title: 5679_YM3B_1-6-B11-B23


title: 5679_YM3B_1-6-B11-B24


title: Ventral  non-spurred sepals, S10, rep 1


title: Ventral  non-spurred sepals, S12, rep 1


title: Lateral non-spurred sepals, S10, rep 3


title: 5679_YM3B_1-6-B11-B12


title: 5679_YM3B_1-6-B11-A24


title: 5679_YM3B_1-6-B11-A23


title: Lateral non-spurred sepals, S10, rep 2


title: 5679_YM3B_1-6-B11-B11


title: Lateral non-spurred sepals, S9, rep 2


title: 5679_YM3B_1-6-B11-A11


title: 5679_YM3B_1-6-B11-A12


title: Lateral non-spurred sepals, S10, rep 1


title: Dorsal spurred sepals, S16, rep 3

source_name: Dorsal spurred sepals

value: Dorsal spurred sepals


title: 5679_YM3B_1-5-B11-P9


title: 5679_YM3B_1-5-B11-P21


title: Dorsal spurred sepals, S16, rep 1


title: 5679_YM3B_1-5-B11-P22


title: Dorsal spurred sepals, S12, rep 3


title: 5679_YM3B_1-5-B11-P10


title: 5679_YM3B_1-5-B11-O9


title: Dorsal spurred sepals, S12, rep 1


title: Dorsal spurred sepals, S12, rep 2


title: Lateral non-spurred sepals, S12, rep 1


title: 5679_YM3B_1-5-B11-O21


title: Dorsal spurred sepals,  S10, rep 2


title: 5679_YM3B_1-5-B11-O10


title: Lateral non-spurred sepals, S9, rep 1


title: Dorsal spurred sepals,  S10, rep 1


title: Dorsal spurred sepals, S9, rep 2


title: 5679_YM3B_1-5-B11-N21


title: 5679_YM3B_1-5-B11-N22


title: 5679_YM3B_1-5-B11-N9


title: Bracts, rep 4

source_name: Bracts

value: Bracts


title: 5679_YM3B_1-5-B11-N10


title: Dorsal spurred sepals, S16, rep 2


title: 5679_YM3B_1-5-B11-M22


title: 5679_YM3B_1-5-B11-M21


title: Bracts, rep 3


title: Bracts, rep 1


title: Dorsal spurred sepals,  S10, rep 3


title: 5679_YM3B_1-5-B11-M10


title: Leaves, rep 3

source_name: Leaves

value: Leaves


title: 5679_YM3B_1-5-B11-O22


title: Leaves, rep 1


title: Bracts, rep 2


title: 5679_YM3B_1-5-B11-L21


title: Nasal swab, COVID19+, Patient 10

city: Bedford Park

first: Jonathan

last: Gleadle

state: SA

address: 3D226 Renal Lab, Flinders Medical Centre, Flinders Drive

department: College of Medicine and Public Health

institute: Flinders University

description: MM-C_10 column in coverage_all_samples_hsa_un_COVID_al.txt

data_processing:
FastQC (Andrews, 2010) was used to quality check the smRNAseq sequencing reads.
Cutadapt version 2.3 (Martin, 2011) was used to trim reads with adaptors (AAGATCGGAAGAGCACACGTCT), remove low quality reads and remove reads with a length less than 18bp.
The cleaned reads were first aligned to the Homo sapiens genome (GRCh38, Gencode) using Bowtie2 with the following parameters: -q -D 20 -R 3 -N 0 -L 18 -i S,1,0.50.
The unaligned reads were then aligned to SARS-CoV-2 genome (NC_045512.2, NCBI) using Bowtie2 with the following parameters: -q -D 20 -R 3 -N 0 -L 18 -i S,1,0.50.
The whole read coverage was visualised as a circos plot using the Circlize package in R (Gu et al., 2014) with mapped reads divided into different bins and distribution calculated at each position to produce smooth and uniform coverage.
The alignment process was repeated with 18 to 26 nucleotides size selected reads using awk command. The size distribution of SARS CoV-2 mapped reads and the overrepresented smRNAseq patient reads were determined.
Assembly: hg39, SARS-CoV-2
Supplementary files format and content: bigwig files; BAM files generated from unalignment to human followed alignment to COVID-19. It was then filtered for 18-26 nt and normalized to CPM with a bin size of 1 into bigwig format for visualisation. Patient 6 has not alignment to COVID-19.
Supplementary files format and content: txt files; BAM files generated from unalignment to human followed alignment to COVID-19. Coverage for individual genes for each patients were calculated and then normalize for CIRCOS plot

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: Nasopharyngeal swab

extract_protocol:
RNA was isolated from 0.5 mL of viral transport fluid using 1.5 mL of Trizol LS (Thermo Fisher Scientific) and chloroform as per the manufacturer’s recommendations. RNA was precipitated with isopropanol supplemented with 20 µg of glycogen (Thermo Fisher Scientific) as a carrier. RNA pellets were washed with 75% ethanol and resuspended in 30 µL 0.1mM nuclease-free EDTA (Thermo Fisher Scientific). RNA concentration was determined using a NanoDrop 8000 Spectrophotometer (Thermo Fisher Scientific) and Qubit Fluorometer (Thermo Fisher Scientific), and LabChip GX Touch 24 (Perkin Elmer) for quality assessment.
Libraries were prepared from nasopharyngeal RNA from SARS-CoV-2 positive patients using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England Biolabs) as per the manufacturer’s protocol. PCR amplification was performed using 15 cycles and size selection was performed using AMPureXP beads (Beckman Coulter) according to the manufacturer’s protocol. Libraries were QC checked for quality and quantitation of RNA on the Lab Chip (Perkin Elmer). Pooled libraries were sequenced on the Illumina NextSeq 500 1 x 75 cycle High Output kit.

value: Nasopharyngeal swab

tag: disease

value: COVID19 positive

tag: diagnostic ct


title: 5679_YM3B_1-5-B11-K9

tag: brain region

tag: age


title: Nasal swab, COVID19+, Patient 9

description: MM-C_09 column in coverage_all_samples_hsa_un_COVID_al.txt

tag: tissue


title: 5679_YM3B_1-5-B11-L10

tag: Sex


title: Dorsal spurred sepals, S9, rep 1


title: 5679_YM3B_1-5-B11-L9


title: 5679_YM3B_1-5-B11-L22


title: 5679_YM3B_1-5-B11-M9


title: 5679_YM3B_1-5-B11-K22


title: Nasal swab, COVID19+, Patient 8

description: MM-C_08 column in coverage_all_samples_hsa_un_COVID_al.txt


title: 5679_YM3B_1-5-B11-K21


title: Nasal swab, COVID19+, Patient 6

description: MM-C_06 column in coverage_all_samples_hsa_un_COVID_al.txt


title: Nasal swab, COVID19+, Patient 5

description: MM-C_05 column in coverage_all_samples_hsa_un_COVID_al.txt


title: 5679_YM3B_1-5-B11-K10


title: 5679_YM3B_1-5-B11-J9


title: Nasal swab, COVID19+, Patient 7

description: MM-C_07 column in coverage_all_samples_hsa_un_COVID_al.txt


title: Leaves, rep 4