title: WT Cortex male ZT3 mRNA rep4

description:
331380_CRM114
331380_CRM114_WT_CTXR_26WKS_M_ZT3_L7
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT3 mRNA rep3

status: Public on Jul 14 2020

type: SRA

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

country: USA

institute: CHDI

description:
331345_CRM110
331345_CRM110_WT_CTXR_26WKS_M_ZT3_L8.D705
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

library_source: transcriptomic

data_processing:
Libraries for RNA-seq were sequenced using an Illumina HiSeq 2000.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.3a with default parameter settings.
Raw counts were obtained with HTSeq 0.10.0 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Genome_build: Genome version Mouse GRCm38 (mm10)
Supplementary_files_format_and_content: *-FPKM.csv: Comma-separated text files include FPKM values for each Sample.
Supplementary_files_format_and_content: *-counts.csv: Comma-separated text files include count values for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: Cortex right hemisphere

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: Cerebral Cortex

tag: genotype

value: Wild type

tag: strain/background

tag: age

value: 26 weeks

tag: Sex

value: male

tag: zt group

value: 3 hrs

tag: time point

value: 27 hrs


title: NMD screen_sorted_PTC231-2

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

description: sgRNA sequence amplified out of genomic DNA

library_source: genomic

data_processing:
Reads were mapped to Brunello library sgRNA reference files.
Normalized read counts were calculated as described in Shalem et al., Science, 2014.
MAGeCK (Li et al., Genome Biology, 2014) was used to assign significance to each gene targeted by the sgRNAs in the Brunello library.
Genome_build: Brunello library sgRNA reference files obtained from Addgene
Supplementary_files_format_and_content: A table of normalized read counts for each sgRNA in each sample is provided.

molecule: genomic DNA

organism: Homo sapiens

source_name: HCT116 colon cancer cell line

growth_protocol: Fluorescent-reporter coupled CRISPR/Cas9-mediated loss of function screening was carried out as described in Golden et al., Nature, 2017, except for the Brunello library (Addgene #73179) but not the GeCKO V2 libarary was used, in both NMD EGFP reporter and control EGFP reporter cell lines. Reporter cell line generation and more information about the screen are described in the manuscript.

extract_protocol:
Genomic DNA was extracted from cell pellets using either a gDNA isolation method that has been previously described Golden et al., Nature, 2017 for the sorted cells or the MasterPureTM Complete DNA Purification Kit (Lucigen) for the unsorted cells.
PCR amplicon libraries were generated as described in the manuscript.
CRISPR/Cas9-mediated loss of function screening.

treatment_protocol: N/A.

tag: experiment

value: NMD screen

tag: lentiviral library received

value: Brunello library

tag: reporter cell line

value: NMD reporter


title: WT Cortex male ZT3 mRNA rep2

description:
331312_CRM15
331312_CRM15_WT_CTXR_26WKS_M_ZT3_L2.D708
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: NMD screen_sorted_PTC231-1


title: WT Cortex male ZT3 mRNA rep1

description:
331311_CRM62
331311_CRM62_WT_CTXR_26WKS_M_ZT3_L2.D707
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT21 mRNA rep4

description:
331459_CRM44
331459_CRM44_WT_CTXR_26WKS_M_ZT21_L6.D709
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: 21 hrs


title: WT Cortex male ZT21 mRNA rep6

description:
331509_CRM103
331509_CRM103_WT_CTXR_26WKS_M_ZT21_L6.D704
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT21 mRNA rep5

description:
331466_CRM72
331466_CRM72_WT_CTXR_26WKS_M_ZT21_L7.D704
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT21 mRNA rep2

description:
331328_CRM73
331328_CRM73_WT_CTXR_26WKS_M_ZT21_L5.D712
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT21 mRNA rep3

description:
331338_CRM106
331338_CRM106_WT_CTXR_26WKS_M_ZT21_L7.D710
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT18 mRNA rep4

description:
331413_CRM71
331413_CRM71_WT_CTXR_26WKS_M_ZT18_L5.D711
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: 18 hrs


title: NMD screen_unsorted_PTC35-1

value: Control reporter


title: Rodasen-47 (Sweden) high light, warm biological replicate 2

city: Berkeley

first: christopher

middle: r

last: baker

state: CA

address: Koshland Hall

department: PMB

institute: UC-Berkeley

description:
rRNA depleted RNA
KN_CB_005

data_processing:
preliminary differential expression analysis was conducted using HISAT and StringTie
Differential expression analysis was conducted using DESeq2 as well as the calculation of adjusted p-values
Genome_build: TAIR10
Supplementary_files_format_and_content: DESeq2 FPKM values

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis thaliana ecotypes IT (Castelnuovo-12 [ABRC stock number: CS98761], sub-line 24) and SW (Rodasen-47 [ABRC stock number: CS98762], sub-line 29) were grown from seed in Conviron E15 and then in Percival Scientific E36-HID chambers.

extract_protocol:
Two flash-frozen leaf discs of 0.73 cm2 collected at the end of the 15-h dark period were homogenized in liquid nitrogen by bead beating, and RNA was extracted and DNase-treated using the Qiagen RNeasy Plant Mini Kit
Barcoded cDNA libraries were generated from our rRNA-depleted RNA samples using the TruSeq RNA library preparation kit

treatment_protocol: Low light, warm temperatures (LLW; 9-h photoperiods of 100 µmol photons m−2 s−1 and 25°C/20°C [light/dark] leaf temperatures), low light, cool temperatures (LLC; 9-h photoperiods of 100 µmol photons m−2 s−1 and 16°C/12.5°C [light/dark] leaf temperatures), high light, warm temperatures (HLW; 9-h photoperiods of 1000 µmol photons m−2 s−1 and 25°C/20°C [light/dark] leaf temperatures), and high light, cool temperatures (HLC; 9-h photoperiods of 1000 µmol photons m−2 s−1 and 14°C/12.5°C [light/dark] leaf temperatures)

value: Youngest fully developed leaf

tag: ecotype

value: Rodasen-47 (Sweden)

tag: growth state

value: vegatative


title: Rodasen-47 (Sweden) high light, warm biological replicate 3

description:
rRNA depleted RNA
KN_CB_006


title: WT Cortex male ZT18 mRNA rep5

description:
331441_CRM25
331441_CRM25_WT_CTXR_26WKS_M_ZT18_L2.D703
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: Rodasen-47 (Sweden) high light, warm biological replicate 1

description:
rRNA depleted RNA
KN_CB_004


title: WT Cortex male ZT18 mRNA rep2

description:
331363_CRM81
331363_CRM81_WT_CTXR_26WKS_M_ZT18_L4.D711
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: Castelnuovo-12 (Italy) high light, warm biological replicate 2

description:
rRNA depleted RNA
KN_CB_011

value: Castelnuovo-12 (Italy)


title: WT Cortex male ZT18 mRNA rep6

description:
331493_CRM80
331493_CRM80_WT_CTXR_26WKS_M_ZT18_L3.D702
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT18 mRNA rep1

description:
331334_CRM48
331334_CRM48_WT_CTXR_26WKS_M_ZT18_L6.D706
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT18 mRNA rep3

description:
331384_CRM76
331384_CRM76_WT_CTXR_26WKS_M_ZT18_L7.D706
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: Castelnuovo-12 (Italy) high light, warm biological replicate 1

description:
rRNA depleted RNA
KN_CB_010


title: WT Cortex male ZT15 mRNA rep5

description:
331496_CRM22
331496_CRM22_WT_CTXR_26WKS_M_ZT15_L4.D705
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: 15 hrs


title: Castelnuovo-12 (Italy) high light, warm biological replicate 3

description:
rRNA depleted RNA
KN_CB_012


title: WT Cortex male ZT15 mRNA rep6

description:
331528_CRM30
331528_CRM30_WT_CTXR_26WKS_M_ZT15_L1.D708
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: Cerebral Cortex


title: WT Cortex male ZT15 mRNA rep1

description:
331340_CRM70
331340_CRM70_WT_CTXR_26WKS_M_ZT15_L7.D712
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: Wild type


title: WT Cortex male ZT21 mRNA rep1

description:
331316_CRM83
331316_CRM83_WT_CTXR_26WKS_M_ZT21_L21
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: 26 weeks


title: WT Cortex male ZT12 mRNA rep12

description:
331521_CRM52
331521_CRM52_WT_CTXR_26WKS_M_ZT12_L8.D701
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: male

value: 12 hrs


title: WT Cortex male ZT15 mRNA rep4

description:
331401_CRM45
331401_CRM45_WT_CTXR_26WKS_M_ZT15_L2.D710
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: BIC1-YFP rep3

city: Beijing

first: zongju

last: Yang

address: 12 Zhongguancun South Street

country: China

institute: Chinese Academy of Agriculture Science

description: biological replicate 3

data_processing:
Libraries were constructed and further sequenced on Illumina HiSeq. 2000 platform (Illumina Inc., USA)
After screening and trimming, clean reads were mapped to the Arabidopsis thaliana genome (TAIR10, www.arabidopsis.org).
Cufflinks methods were used for determination of expression values.
Genome_build: tair 10
Supplementary_files_format_and_content: BIC1-VS-Col-0.GeneDiffExp.txt: tab-delimited text files include a list of the results of the difference analysis of all genes of the samples compared with each other

source_name: seedling

growth_protocol: WT, BIC1-YFP seedlings grown in 1/2 MS plates under long-day conditions chamber for 10 days and were collected.

extract_protocol:
RNA was extracted using an ethanol precipitation protocol and Trizol (Invitrogen) reagent.
Libraries were constructed and further sequenced on Illumina HiSeq. 2000 platform (Illumina Inc., USA) with three independent biological replications for each sample.

value: seedling

value: Columbia

tag: development stage

value: 10-d-old seedling


title: Rodasen-47 (Sweden) Low light, cool biological replicate 2

description:
rRNA depleted RNA
KN_CB_002


title: WT Cortex male ZT15 mRNA rep3

description:
331392_CRM18
331392_CRM18_WT_CTXR_26WKS_M_ZT15_L2
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT12 mRNA rep10

description:
331475_CRM111
331475_CRM111_WT_CTXR_26WKS_M_ZT12_L8.D709
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: 36 hrs


title: WT Cortex male ZT12 mRNA rep11

description:
331501_CRM117
331501_CRM117_WT_CTXR_26WKS_M_ZT12_L4.D707
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: Rodasen-47 (Sweden) Low light, cool biological replicate 1

description:
rRNA depleted RNA
KN_CB_001


title: BIC1-YFP rep2

description: biological replicate 2


title: Castelnuovo-12 (Italy) Low light, cool biological replicate 3

description:
rRNA depleted RNA
KN_CB_009


title: WT Cortex male ZT12 mRNA rep6

description:
331373_CRM75
331373_CRM75_WT_CTXR_26WKS_M_ZT12_L5.D708
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT12 mRNA rep8

description:
331422_CRM84
331422_CRM84_WT_CTXR_26WKS_M_ZT12_L8
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT rep2

description: biological replicate 2

value: WT


title: WT Cortex male ZT12 mRNA rep9

description:
331473_CRM56
331473_CRM56_WT_CTXR_26WKS_M_ZT12_L8.D707
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT rep3

description: biological replicate 3


title: WT Cortex male ZT12 mRNA rep5

description:
331366_CRM67
331366_CRM67_WT_CTXR_26WKS_M_ZT12_L4.D702
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT12 mRNA rep4

description:
331355_CRM92
331355_CRM92_WT_CTXR_26WKS_M_ZT12_L2.D703
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT15 mRNA rep2

description:
331375_CRM27
331375_CRM27_WT_CTXR_26WKS_M_ZT15_L6.D710
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: Rodasen-47 (Sweden) Low light, cool biological replicate 3

description:
rRNA depleted RNA
KN_CB_003


title: Castelnuovo-12 (Italy) Low light, cool biological replicate 2

description:
rRNA depleted RNA
KN_CB_008


title: BIC1-YFP rep1

description: biological replicate 1


title: WT Cortex male ZT12 mRNA rep1

description:
331310_CRM87
331310_CRM87_WT_CTXR_26WKS_M_ZT12_L1.D706
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: Rodasen-47 (Sweden) High light, cool biological replicate 2

description:
rRNA depleted RNA
KN_CB001B


title: WT Cortex male ZT12 mRNA rep3

description:
331351_CRM49
331351_CRM49_WT_CTXR_26WKS_M_ZT12_L1.D711
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: Rodasen-47 (Sweden) High light, cool biological replicate 3

description:
rRNA depleted RNA
KN_CB001H


title: WT Cortex male ZT12 mRNA rep2

description:
331314_CRM119
331314_CRM119_WT_CTXR_26WKS_M_ZT12_L2.D710
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT0 mRNA rep12

description:
331529_CRM118
331529_CRM118_WT_CTXR_26WKS_M_ZT0_L1.D709
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: 0 hr

value: 24 hrs


title: WT Cortex male ZT0 mRNA rep11

description:
331523_CRM115
331523_CRM115_WT_CTXR_26WKS_M_ZT0_L8.D703
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT0 mRNA rep10

description:
331522_CRM46
331522_CRM46_WT_CTXR_26WKS_M_ZT0_L8.D702
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: 0 hrs


title: Pe day3 rep2

city: Minneapolis

first: Hiroshi

last: Nakato

state: MN

address: 515 Delaware Street SE

department: Genetics, Cell Biology, and Development

institute: University of Minnesota

data_processing:
Illumina CASAVA v1.8 was used for basecalling.
Sequenced reads were filtered by fastp v0.19.5 with default settings.
Transcript abundance was estimated by the quasi-mapping mode of salmon v0.11.3.
Differential gene expression analysis was performed using DESeq2 v1.22.0.
Genome_build: Ensembl BDGP6
Supplementary_files_format_and_content: CSV files including log2 fold changes for each gene

organism: Drosophila melanogaster

source_name: Adult midgut

extract_protocol:
Total RNA was extracted using TRIzol Reagent. Illumina TruSeq RNA Library Preparation Kit v2 was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Oregon-R

value: Adult midgut

value: day 7-8

value: wild type

tag: treatment

value: Pe


title: Castelnuovo-12 (Italy) Low light, cool biological replicate 1

description:
rRNA depleted RNA
KN_CB_007

value: Youngest fully developed leaf

value: Castelnuovo-12 (Italy)

value: vegatative


title: Pe day3 rep1


title: WT Cortex male ZT0 mRNA rep8

description:
331460_CRM47
331460_CRM47_WT_CTXR_26WKS_M_ZT0_L6.D710
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: Cerebral Cortex

value: Wild type

value: 26 weeks

value: male


title: Pe day0 rep2

value: day 4-5


title: Castelnuovo-12 (Italy) High light, cool biological replicate 2

description:
rRNA depleted RNA
KN_CB001G


title: WT Cortex male ZT0 mRNA rep6

description:
331435_CRM61
331435_CRM61_WT_CTXR_26WKS_M_ZT0_L1.D709
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv


title: WT Cortex male ZT12 mRNA rep7

description:
331396_CRM107
331396_CRM107_WT_CTXR_26WKS_M_ZT12_L2.D705
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: 12 hrs

value: 36 hrs


title: Castelnuovo-12 (Italy) High light, cool biological replicate 3

description:
rRNA depleted RNA
KN_CB001I


title: WT Cortex male ZT0 mRNA rep5

description:
331430_CRM54
331430_CRM54_WT_CTXR_26WKS_M_ZT0_L8.D704
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: 0 hr


title: WT Cortex male ZT0 mRNA rep3

description:
331398_CRM102
331398_CRM102_WT_CTXR_26WKS_M_ZT0_L2.D707
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: 24 hrs


title: Castelnuovo-12 (Italy) High light, Cool biological replicate 1

description:
rRNA depleted RNA
KN_CB001F


title: WT rep1

description: biological replicate 1

value: seedling

value: Columbia

value: 10-d-old seedling

value: WT


title: Mock day0 rep2

value: Oregon-R

value: Adult midgut

value: wild type

value: Sucrose


title: WT Cortex male ZT0 mRNA rep2

description:
331337_CRM101
331337_CRM101_WT_CTXR_26WKS_M_ZT0_L7.D709
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: Cerebral Cortex


title: WT Cortex male ZT0 mRNA rep1

description:
331308_CRM55
331308_CRM55_WT_CTXR_26WKS_M_ZT0_L1.D704
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: Wild type

value: 0 hrs


title: Mock day0 rep1


title: Rodasen-47 (Sweden) Low light, warm biological replicate 3

description:
rRNA depleted RNA
KN_CB001E

value: Youngest fully developed leaf

value: Rodasen-47 (Sweden)

value: vegatative


title: WT Cortex male ZT0 mRNA rep9

description:
331465_CRM113
331465_CRM113_WT_CTXR_26WKS_M_ZT0_L7.D703
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

value: 26 weeks

value: male


title: Rodasen-47 (Sweden) High light, cool biological replicate 1

description:
rRNA depleted RNA
KN_CB001A


title: YAP1 ON Mouse. Tumor 2 [WX6010_T2]

city: Worcester

first: Tomas

middle: Christopher

last: Rodriguez

state: MA

address: 55 N Lake Ave, AS5-2005

department: RNA Therapeutic Institute

institute: University of Massachusetts Medical School

data_processing:
Demultiplexed using Illumina bcl2fastq software
Pseudoaligned to latest ensembl cDNA FASTA (Mouse GRCm38.p6) using  kallisto v0.45.0. Options: -b 100.
Abundance h5 file output used for gene-level aggregation and quantification using the R Sleuth package.
Genome_build: Ensembl cDNA transcriptome
Supplementary_files_format_and_content: CSV; combined sample scaled-base-per-read counts for all genes

source_name: YAP1 ON Mouse. Tumor

growth_protocol: All liver was extracted during post-mortem examination and used immediately for RNA extraction or flash frozen

extract_protocol:
RNA was extracted from fresh or flash frozen liver with a standard Trizol, Chloroform extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

tag: tissue/cell type

value: hepatoblastoma tumor, on doxycycline

value: liver


title: Rodasen-47 (Sweden) Low light, warm biological replicate 1

description:
rRNA depleted RNA
KN_CB001C

tag: tissue


title: WT Cortex male ZT0 mRNA rep7

description:
331458_CRM63
331458_CRM63_WT_CTXR_26WKS_M_ZT0_L5.D708
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

tag: genotype

value: 0 hr


title: Castelnuovo-12 (Italy) Low light, warm biological replicate 3

description:
rRNA depleted RNA
KN_CB001L

value: Castelnuovo-12 (Italy)


title: YAP1 OFF Mouse Day6, Tumor 3 [WX6002_T3]

source_name: YAP1 OFF Mouse Day6, Tumor

value: hepatoblastoma tumor, off doxycycline


title: YAP1 ON Mouse. Tumor 1 [WX6010_T1]


title: YAP1 ON Mouse. Tumor 3 [WX6010_T3]


title: YAP1 OFF Mouse Day6, Tumor 4 [WX6002_T4]


title: YAP1 OFF Mouse Day6, Tumor 2 [WX6002_T2]


title: Pe day0 rep1

value: Oregon-R

value: day 4-5

value: Pe


title: YAP1 OFF Mouse Day6, Tumor 1 [WX6002_T1]


title: Castelnuovo-12 (Italy) Low light, warm biological replicate 1

description:
rRNA depleted RNA
KN_CB001J


title: Castelnuovo-12 (Italy) Low light, warm biological replicate 2

description:
rRNA depleted RNA
KN_CB001K


title: WT Cortex male ZT0 mRNA rep4

description:
331406_CRM105
331406_CRM105_WT_CTXR_26WKS_M_ZT0_L3.D704
mRNA
processed data file: Cortex-FPKM.csv
processed data file: Cortex-counts.csv

tag: strain/background

value: 24 hrs


title: WT FAH DeltaExon 5 Mouse on NTBC, Biological Replicate 3 [WT-FAH-DeltaExon5-3]

source_name: WT FAH DeltaExon 5 Mouse on NTBC

value: FAH Delta Exon 5

value: FAH +NTBC hepatocyte


title: WT FAH DeltaExon 5 Mouse on NTBC, Biological Replicate 2 [WT-FAH-DeltaExon5-2]


title: WT FAH DeltaExon 5 Mouse on NTBC, Biological Replicate 1 [WT-FAH-DeltaExon5-1]


title: hbHep Mouse #3 [EM2788-1]

source_name: hbHep Mouse

value: hbHep Day 117


title: hbHep Mouse #3, technical replicate  [EM2788-2]


title: Rodasen-47 (Sweden) Low light, warm biological replicate 2

description:
rRNA depleted RNA
KN_CB001D

value: Youngest fully developed leaf


title: hbHep Mouse #2, technical replciate  [EM2787-2]

value: hbHep Day 114


title: YAP1 ON Mouse. Tumor 4 [WX6010_T4]


title: hbHep Mouse #1, technical replicate [EM2783-2]

value: hbHep Day 121


title: hbHep Mouse #1 [EM2783-1]


title: hbHep Mouse #2 [EM2787-1]


title: WT_day_4

city: Madrid

first: Maria

last: Salazar

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

country: Spain

institute: CNIO

description: Strand-specific RNA-seq (dUTP)

data_processing:
RNA-seq processing:
Reads were quality-checked with FastQC, and aligned to the mouse genome (GRCm38/mm10) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.16), allowing 2 mismatches and 5 multihits
Transcripts quantification and differential expression were calculated with Cufflinks 2.2.1, using the Mus musculus GRCm38.75 transcript annotation from Ensembl
Genome_build: GRCm38/mm10 reference sequence and Mus musculus GRCm38.75 transcript annotation
Supplementary_files_format_and_content: FPKM values calculated with Cufflinks

source_name: miR-203 WT_day 4

growth_protocol: miR-203 animal models were crossed with the OSKM (Oct4, Sox2, Klf4, cMyc) transgenic mice, in order to generate reprogramable mice in which the expression of miR-203 could also be modulated by Dox (see "Abad et al, Nature 2013" for specific reference to the OSKM model). MEFs were extracted from those animals and were reprogrammed in vitro using Doxycycline 1ug/ml (to induce the OSKM cassette and miR-203 in the case of KI MEFs) and the appropiate iPSCs media. After aproximately two weeks of reprogramming, iPSCs colonies were visible and detectable.

extract_protocol:
RNA was extracted at different time points using the miRVana RNA isolation Kit, form Thermo Fisher Scientific
1 µg of total RNA sample was used. RNA Integrity Numbers were in the range 9.7-10.0 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: (miR-203;OSKM) MEFs were treated with 1ug/ml Dox during the whole reprogramming process, which takes aproximately 2 weeks.

tag: cell type

value: Mouse embryonic cells (MEFs)

tag: source animal model

value: miR-203 WT; OSKM

value: DOX treatment during 2 weeks


title: WT_day_7

description: Strand-specific RNA-seq (dUTP)

source_name: miR-203 WT_day 7


title: WT_day_6

description: Strand-specific RNA-seq (dUTP)

source_name: miR-203 WT_day 6


title: miR203_KO_day6

description: Strand-specific RNA-seq (dUTP)

source_name: miR-203 KO_day 6

value: miR-203 KO; OSKM


title: WT_day_0

description: Strand-specific RNA-seq (dUTP)

source_name: miR-203 WT_day 0


title: fibro_target_rna-seq_mir-ns_2

city: Saint Louis

first: Kitra

last: Cates

state: MO

address: 4523 Clayton Ave, MCD SCI 361

department: Developmental Biology

institute: Washington University in St. Louis

data_processing:
Raw reads were aligned to human reference genome (GRCh38) by STAR (Dobin and Gingeras, 2015).
Gene counts were derived from the number of uniquely aligned reads by Subread:featureCounts (Liao et al., 2014).
Counts were normalized by trimmed mean of M-values (TMM) using edgeR (Robinson et al., 2010).
EdgeR (v3.11; Robinson et al., 2010; McCarthy, Chen, and Smyth, 2012) and limma (Ritchie et al., 2015) were used to identify differentially expressed genes.
Differentially expressed genes were sorted by the following thresholds: adj.p<0.05, log2FC=<-0.5 and matched to AGO-HITS-CLIP targets that met the following criteria: basemean>20, adj.p<0.001, log2FC=<-1.
Genome_build: hg38
Supplementary_files_format_and_content: count matrix; differentially expressed genes with adjusted p-values, log fold change, and CPM for each sample

source_name: Dermal fibroblasts

growth_protocol: Direct neuronal reprogramming of human fibroblasts to neurons was performed as previously described (Abernathy et al., 2017; Richner et al., 2015).

extract_protocol:
Day 7 cells were harvested for HITS-CLIP following the published protocol (Moore et al., 2014) with modifications. Briefly, cross-linked cells came from 3 dishes were lysed in lysis buffer, digested with RQ1 DNase (Promega, Madison, WI) and diluted (1:1000) RNAseA (Thermo, Waltham, MA) respectively, and then the RISC complex containing bound miRNAs and mRNAs (ternary complex) was immunoprecipitated overnight at 4 oC with mouse anti-Ago1/2/3 antibody 2A8 (Active Motif, Carlsbad, CA). The ternary complex was labelled 32P by ligating miRNA with 32P-labelled 3’-linker and then separated by NuPAGE™ gel (Thermo, Waltham, MA). The 130 kDa bands on the nitrocellulose membrane corresponding to ternary complex containing Ago:miRNA:mRNA were excised and used to extract RNA for sequencing library prep.
RNA was prepared for sequencing using TruSeq Small RNA Library Preparation Kits (San Diego, CA).

tag: cell line

value: Sciencell, Catalog #2310

tag: overexpression 1

value: miR-NS

tag: overexpression 2


title: fibro_target_rna-seq_mir-9124_3


title: fibro_target_rna-seq_mir-9124_1


title: fibro_target_rna-seq_mir-9124_2


title: fibro_target_rna-seq_mir-ns_3


title: miR203_KO_day7

description: Strand-specific RNA-seq (dUTP)

source_name: miR-203 KO_day 7


title: fibro_target_rna-seq_mir-ns_1


title: RNA PAT fibroblast IMDM Biological rep 4

type: RNA

city: Liverpool

first: Eithne

last: Costello

address: Ashton Street

department: Department of Molecular and Clinical Cancer Medicine

country: United Kingdom

institute: University of Liverpool

description: Gene expression from disese-associated cultured fibroblasts

hyb_protocol: The SPIA amplified cDNA was purified using the Qiagen QIAquick PCR Purification system. Utilising the Encore Biotin Module 5ug of amplified cDNA was fragmented and Biotin-labelled before hybridisation on Affymetrix GeneChip Human Transcriptome 2.0 arrays (HTA_2.0) (Affymetrix, Inc.). Arrays were hybridised for 17 hours at 45˚C and 60rpm in an Affymetrix GeneChip hybridisation oven 645.

scan_protocol: Following hybridisation the arrays were washed and stained on an Affymetrix GeneChip Fluidics Station 450 using a FS450_0001 script and scanned in an Affymetrix Genechip Scanner 3000G.

data_processing: Data were RMA normalised in Partek Genomics Suite

label: Bioitin

source_name: Cultured human fibroblasts from PAT

label_protocol: 50ng of total RNA (free from DNA) was labelled using the Ovation Pico WTA system V2 (NuGen Technologies, Inc.). This kit prepares amplified cDNA for gene expression analysis. Following second strand synthesis the cDNA was purified using Agencourt RNAClean XP beads prior to SPIA amplification.

growth_protocol: Disease-associated fibroblasts from PDAC, CP and PAT were isolated using the outgrowth method, these cells were grown in IMDM supplemented with 10% FBS, 2% L-glutamine, 1% penicillin-streptomycin. In addition, normal PSCs were isolated using the density gradient method  and cultured in the same media.These normal PSC were expanded in culture for more than 15 days to achieve adequate yield and purity and referred to as normal-activated (NA) fibroblast. Samples used for array experiments were used from early passages (P1 or P2). Commercial normal fibroblasts (NF) were grown using low serum medium (LSM) (MSC-GRO, Vitro Biopharma) and IMDM supplemented with 10% FBS, 2% L-glutamine, 1% penicillin-streptomycin.

extract_protocol: RNA was isolated using the high pure miRNA isolation kit (one-column protocol) (Qiagen) for the isolation of total RNA (containing small RNAs) following the manufacturer’s instructions. Purified total RNA was cleaned from genomic DNA using the DNA-freeTM DNA removal kit (ThermoFisher Scientific) following the manufacturer’s instruction.

value: PAT

tag: media

value: IMDM


title: fibro_target_hits-clip-seq_mir-9124_3

data_processing:
Library strategy: HITS-CLIP-Seq
Reads were trimmed using Trimmomatic (v0.33) to remove primer and adapter sequences (Bolger et al., 2014).
Trimmed reads were aligned to human genome hg38 using STAR (v2.4.2a) with default parameters (Dobin and Gingeras, 2015).
Reads uniquely aligning to genomic features (phred score ≥ 10) were quantified using featureCounts (v1.4.6-p4) from the Subread package with gencode v23 annotations (Liao et al., 2013).
In-house software was used to divide the UTRs or CDs from the gencode annotations into continuous 100bp bins. For each feature, two sets of bins were formed such that the second set of bins was offset by 50bp from the first set of bins.
Reads aligning to bins were quantified using featureCounts.
Differentially associated features or bins were determined by using DESeq2 (Love et al., 2014) in the negative binomial distribution model with a cutoff of adjusted p-value <0.001 and fold change >2. A UTR or CD was considered to have differential association if one or more bins from that UTR or CD was called as differentially associated by DESeq2.
Reads Per Kilobase per Millions mapped reads, RPKM, of features or bins were determined by quantifying uniquely aligned reads.
Wiggle and bigwig files were created from bam files using igvtools (v2.3.60) (https://software.broadinstitute.org/software/igv/igvtools) and wigToBigWig (v4) (Kent et al., 2010).
Genome_build: hg38


title: RNA PAT fibroblast IMDM Biological rep 3


title: RNA PAT fibroblast IMDM Biological rep 2


title: RNA PAT fibroblast IMDM Biological rep 1


title: RNA PAT fibroblast IMDM Biological rep 5


title: miR203_KO_day4

description: Strand-specific RNA-seq (dUTP)

source_name: miR-203 KO_day 4


title: miR203_KI_day7

description: Strand-specific RNA-seq (dUTP)

source_name: miR-203 KI_day 7

value: ColA1_miR203; Rosa26rtTA; OSKM


title: miR203_KO_day0

description: Strand-specific RNA-seq (dUTP)

source_name: miR-203 KO_day 0


title: fibro_target_hits-clip-seq_mir-9124_2


title: miR203_KI_day6

description: Strand-specific RNA-seq (dUTP)

source_name: miR-203 KI_day 6


title: miR203_KI_day0

description: Strand-specific RNA-seq (dUTP)

source_name: miR-203 KI_day 0


title: MEFs_WT

description: Strand-specific RNA-seq (dUTP)

source_name: miR-203 WT MEFs


title: miR203_KI_day4

description: Strand-specific RNA-seq (dUTP)

source_name: miR-203 KI_day 4


title: MEFs_miR203_KO

description: Strand-specific RNA-seq (dUTP)

source_name: miR-203 KO MEFs


title: fibro_target_hits-clip-seq_mir-9124_1


title: fibro_target_hits-clip-seq_mir-ns_3


title: MEFs_miR203_KI

description: Strand-specific RNA-seq (dUTP)

source_name: miR-203 KI MEFs


title: iPS_WT

description: Strand-specific RNA-seq (dUTP)

source_name: miR-203 WT iPSC

value: iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs)


title: fibro_target_hits-clip-seq_mir-ns_1


title: fibro_target_hits-clip-seq_mir-ns_2


title: RNA PDAC fibroblast IMDM Biological rep 5

source_name: Cultured human fibroblasts from PDAC

value: PDAC


title: RNA PDAC fibroblast IMDM Biological rep 4


title: RNA PDAC fibroblast IMDM Biological rep 3


title: RNA PDAC fibroblast IMDM Biological rep 6


title: NSCLC biopsy_Patient 143_Diagnosis

city: Bern

first: Adian

middle: F

last: Ochaenbein

address: Murtenstrasse 35

department: Department of Biomedical Research

country: Switzerland

institute: University and University Hopsital of Bern

hyb_protocol: 100 ng RNA were incubated over night at 65°C with Nanostring probe sets

scan_protocol: Scanned with NanoString Digital analyzer with 1155 FOV

data_processing: Briefly, the negative control averages plus 2 SD were subtracted to correct for background noise and values below 0 were set to 1.  Then, the geNorm method was used to select adequate genes for normalization from the included set of 6 candidates based on their relative stability.For the final normalization, the geometric mean of the selected normalization genes was calculated and used as normalization factor. Normalized expression values were log2 transformed and samples where >50% of the probes were not detectable were removed from further analysis.

source_name: NSCLC biopsy

label_protocol: RNA species were identified and counted using a custom probe code set consisting of 201 genes

growth_protocol: Human Samples

extract_protocol: Total RNA was extracted from microdissected tumor tissue using the FFPE Tissue RNA Extraction Kit from amsbio, (Bioggio-Lugano, Switzerland), according to the manufacturers protocol. RNA quantity was assessed on a Nanodrop and quality was assessed on a Bioanalyzer

treatment_protocol: At time of diagnosis and at progression

tag: patient id

tag: treatment cohort

value: P

tag: timepoint

value: Diagnosis


title: NSCLC biopsy_Patient 140_Diagnosis


title: NSCLC biopsy_Patient 138_Progression

value: Progression


title: NSCLC biopsy_Patient 145_Diagnosis


title: NSCLC biopsy_Patient 145_Progression


title: NSCLC biopsy_Patient 133_Diagnosis


title: NSCLC biopsy_Patient 134_Diagnosis


title: NSCLC biopsy_Patient 133_Progression


title: NSCLC biopsy_Patient 136_Diagnosis


title: NSCLC biopsy_Patient 138_Diagnosis


title: NSCLC biopsy_Patient 135_Progression


title: RNA PDAC fibroblast IMDM Biological rep 2


title: iPS_KO

description: Strand-specific RNA-seq (dUTP)

source_name: miR-203 KO iPSC

value: miR203 KO; OSKM


title: RNA Normal Fibro IMDM Technical rep 3

description: Gene expression from commercial cultured fibroblasts IMDM

source_name: Commercial cultured human fibroblasts from non-disease pancreas

value: NormalFibro


title: NSCLC biopsy_Patient 132_Diagnosis


title: NSCLC biopsy_Patient 132_Progression


title: RNA PDAC fibroblast IMDM Biological rep 1


title: RNA Normal Fibro LSM Technical rep 3

description: Gene expression from commercial cultured fibroblasts Low serum media

value: LSM


title: NSCLC biopsy_Patient 131_Diagnosis


title: CHMI4.d0

city: Smithfield

first: Matt

last: Field

address: 14-88 Macgregor Road

country: Australia

institute: James Cook University

data_processing:
Transcriptome data were analysed using a modified version of an existing variant detection pipeline consisting of software STAR aligner, samtools, HTSeq, and DESeq2.
Reads were first aligned to human reference genome GRCh38 using STAR with the gene model set to ensembl v95 annotation and quantmode set to TranscriptomeSAM.
The alignment files were sorted with samtools and the resultant reads input to HTSeq to generate raw read counts using the union overlap resolution mode.
Read counts were input to DESeq2 and a paired analysis performed for the all participants with acute infection and baseline or convalescence data.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each sample.

source_name: PBMC

extract_protocol:
MACs beads negative selection
Conducted by Macrogen© (Seoul, Korea) using the Illumina TruSeq stranded mRNA LT sample kit and the HiSeq 2500 instrument

treatment_protocol: Thawed cryopreserved PBMCs

value: monocyte

tag: age

value: Adult

tag: day

value: Baseline

tag: cohort

value: CHMI


title: RNA Normal Fibro IMDM Technical rep 2


title: CHMI4.doA

value: Peak-infection


title: CHMI5.doA


title: RNA Normal Activated fibroblast IMDM Biological rep 5

description: Gene expression from non-disease cultured fibroblasts

source_name: Cultured human fibroblasts from normal pancreas

value: NormActivated


title: CHMI5.d0


title: RNA Normal Fibro IMDM Technical rep 1


title: NSCLC biopsy_Patient 129_Diagnosis


title: RNA Normal Fibro LSM Technical rep 1


title: RNA Normal Activated fibroblast IMDM Biological rep 3


title: RNA Normal Fibro LSM Technical rep 2


title: RNA Normal Activated fibroblast IMDM Biological rep 4


title: NSCLC biopsy_Patient 126_Diagnosis


title: NSCLC biopsy_Patient 128_Diagnosis


title: NSCLC biopsy_Patient 125_Progression


title: CHMI3.doA


title: NSCLC biopsy_Patient 124_Progression


title: NSCLC biopsy_Patient 124_Diagnosis


title: CHMI3.d0


title: RNA Normal Activated fibroblast IMDM Biological rep 2


title: NSCLC biopsy_Patient 127_Diagnosis


title: NSCLC biopsy_Patient 123_Diagnosis


title: RNA Normal Activated fibroblast IMDM Biological rep 1


title: NSCLC biopsy_Patient 121_Diagnosis


title: CHMI2.doA


title: NSCLC biopsy_Patient 120_Diagnosis


title: CHMI2.d0


title: RNA CP fibroblast IMDM Biological rep 5

source_name: Cultured human fibroblasts from CP

value: CP


title: CHMI1.d0A


title: NSCLC biopsy_Patient 119_Diagnosis


title: CHMI1.d0


title: NSCLC biopsy_Patient 118_Diagnosis


title: NSCLC biopsy_Patient 121_Progression


title: NSCLC biopsy_Patient 114_Progression


title: NSCLC biopsy_Patient 117_Progression


title: NSCLC biopsy_Patient 115_Diagnosis


title: TESA Sperm Total RNA KG8-12

city: Zürich

first: Deepak

last: Tanwar

state: ZH

address: Winterthurerstrasse 190

institute: ETH Zürich

data_processing:
For long RNA sequencing, quality and adapter trimming was performed with Trim Galore 1.16 with -q 30 --length 30, and filtered reads were pseudo-aligned with Salmon 0.11.2 (-l SR) on a transcriptome index prepared with 1) the GENCODE annotation M18, 2) piRNA precursors, and 3) transposable elements (TEs) from repeat masker (concatenated by family).
For short RNA sequencing, reads were trimmed of adapter sequences using cutadapt v1.14 with a 5% error rate and collapsed to unique sequences. Only sequences with a count greater than 1 in more than one sample are reported in the processed files.
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene count matrices and, for short RNA, counts for unique sequences

source_name: Sperm

extract_protocol: TruSeq + RiboZero Gold

tag: condition

value: TESA

tag: time from last injection

value: 46 days


title: NSCLC biopsy_Patient 117_Diagnosis


title: NSCLC biopsy_Patient 114_Diagnosis


title: Child8.day0

value: Child

value: Acute

value: Clinical Malaria


title: NSCLC biopsy_Patient 113_Diagnosis

value: P

value: Diagnosis


title: TESA Sperm Total RNA KG8-11


title: RNA CP fibroblast IMDM Biological rep 4

value: IMDM


title: CTRL Sperm Total RNA KG8-14

value: CTRL


title: Child7.day28

value: Convalescence


title: NSCLC biopsy_Patient 112_Diagnosis


title: NSCLC biopsy_Patient 111_Diagnosis


title: RNA CP fibroblast IMDM Biological rep 3


title: NSCLC biopsy_Patient 110_Diagnosis


title: RNA CP fibroblast IMDM Biological rep 2


title: CTRL Sperm Total RNA KG8-13


title: RNA CP fibroblast IMDM Biological rep 1


title: NSCLC biopsy_Patient 109_Diagnosis


title: CTRL Sperm Total RNA KG8-10


title: NSCLC biopsy_Patient 113_Progression

value: Progression


title: Child8.day28

value: monocyte


title: Child7.day0


title: CTRL Sperm Total RNA KG8-09


title: Child6.day28


title: NSCLC biopsy_Patient 103_Diagnosis


title: NSCLC biopsy_Patient 107_Progression


title: CTRL Sperm Total RNA KG8-07


title: Child5.day28


title: NSCLC biopsy_Patient 81_Progression

value: PB


title: NSCLC biopsy_Patient 101_Progression


title: Child5.day0


title: TESA Sperm Total RNA KG8-05


title: CTRL Sperm Total RNA KG8-06


title: Child6.day0


title: Child4.day28


title: NSCLC biopsy_Patient 63_Diagnosis


title: NSCLC biopsy_Patient 58_Diagnosis


title: NSCLC biopsy_Patient 78_Progression


title: NSCLC biopsy_Patient 54_Diagnosis


title: Child4.day0


title: NSCLC biopsy_Patient 107_Diagnosis


title: TESA Sperm Total RNA KG8-03


title: NSCLC biopsy_Patient 106_Diagnosis


title: Child3.day28


title: NSCLC biopsy_Patient 108_Diagnosis


title: NSCLC biopsy_Patient 105_Diagnosis


title: NSCLC biopsy_Patient 101_Diagnosis


title: NSCLC biopsy_Patient 104_Diagnosis


title: NSCLC biopsy_Patient 102_Diagnosis


title: CTRL Sperm Total RNA KG8-08


title: TESA Sperm Total RNA KG8-02


title: NSCLC biopsy_Patient 91_Diagnosis


title: NSCLC biopsy_Patient 77_Progression


title: TESA Sperm Total RNA KG8-04


title: Child3.day0


title: Child2.day0


title: Mut3

city: Tucson

first: Martha

last: Bhattacharya

state: AZ

address: 1040 E 4th Street

department: Neuroscience

institute: University of Arizona

data_processing:
Alignment to mouse genome using Salmon (salmon-0.11.1-linux_x86_64) for single end reads.
Trim first column of Salmon output data to contain ENSMUST transcript identifiers. This was done using the Galaxy platform.
Created a file to convert ENSMUST identifiers to GeneID using Galaxy
Normalize count values and idnetify differentially expressed genes using DeSeq2. This was done using the Galaxy Platform.
Export Data and evaluate in R to create visuals.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft excel files containing TPM data and other identifying information for each sample outputted from Salmon

source_name: adult dorsal root ganglia

extract_protocol:
Qiagen Rneasy Micro kit was used to isolate total RNA
Single end 150 according to Illumina instructions.

value: 6 months

value: Tmem184b gene trap homozygous (C57BL/6 background)

tag: tissue

value: dorsal root ganglia


title: Child2.day28


title: Mut4

tag: genotype


title: NSCLC biopsy_Patient 82_Diagnosis


title: NSCLC biopsy_Patient 85_Progression


title: NSCLC biopsy_Patient 80_Diagnosis


title: Child1.day28


title: Child1.day0


title: NSCLC biopsy_Patient 80_Progression


title: Mut2


title: NSCLC biopsy_Patient 84_Diagnosis


title: Adult10.day28

value: Adult


title: NSCLC biopsy_Patient 81_Diagnosis


title: NSCLC biopsy_Patient 75_Diagnosis


title: NSCLC biopsy_Patient 79_Diagnosis


title: WT4


title: NSCLC biopsy_Patient 78_Diagnosis


title: TESA Sperm Total RNA KG8-01

value: TESA


title: NSCLC biopsy_Patient 74_Diagnosis


title: Mut1


title: NSCLC biopsy_Patient 77_Diagnosis


title: WT8


title: Adult9.day28


title: Adult10.day0


title: NSCLC biopsy_Patient 73_Diagnosis


title: NSCLC biopsy_Patient 72_Progression


title: NSCLC biopsy_Patient 72_Diagnosis


title: NSCLC biopsy_Patient 71_Diagnosis


title: Adult8.day0


title: WT3


title: BglC_8h2

city: Campinas

first: Gabriela

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

description: recombinant strain producing a heterologous GH3 beta-glucosidase

data_processing:
Base calls and demultiplexing was performed with Illumina bcl2fastq version 1.8.4
The Illumina HiSeq 2500 system was used to sequence the transcriptome of Aspergillus nidulans strains, yielding approximately 10 million 100-bp paired-end reads per sample. These sequences were firstly quality checked and filtered using FASTQC and Trimommatic v.0.32 (Bolger, et al, 2014).
Trimmed reads were mapped to the Aspergillus nidulans reference genome available at AspGD database using Tohat2 v2.0.4 (Kim et al, 2013), allowing two mismatches and only unique alignments.
Samtools version 0.1.18 (Li et al., 2009) was used to process the alignments files which were visualized using the Integrative Genomics Viewer (Thorvaldsdottir et al., 2012).
Aligned reads were quantified using htseq-count v0.6.0 (Anders et al 2015) with Aspergillus nidulans gene modes, that includes 10778 genes models.
For differential expression analysis, pairwise comparisons between each strain and the control strain A. nidulansA773 were performed using Bioconductor DESeq2 package version v 1.6.3 (Love et al, 2014) applying a  log2 fold change ≥ 2 or ≤ -2 and adjusted p-value ≤ 0.01 as thresholds.
Supplementary_files_format_and_content: Processed data files are presented as tab delimited txt format. Raw count, FPKM and TPM data are provided, being expressed as “gene ID” “Sample ID”
Supplementary_files_format_and_content: Gene expression results are expressed as Log 2 Fold Change between indicated samples and the respective adjusted p-value calculated by DESeq2.

organism: Aspergillus nidulans

source_name: mycelia

growth_protocol: Vegetative cultures and spore production were prepared by inoculation of conidia in minimal medium as described by Clutterbuck and Pontecorvo. All of the strains of A. nidulans were cultivated in the minimal medium contained 5 % of 20× Clutterbuck salts, 0.1 % of 1000× vitamins, 0.1 % of 1000× trace elements, pH 6.5 and supplemented with pyridoxine (1 mg/L), uracil/uridine (2.5 mg/L each) or as needed. Minimal medium was supplemented with 1% of glucose for mycelium growth (growth medium) or with 2 % of maltose and 250 mM of HEPES (Sigma–Aldrich) for promoter activation and recombinant protein production (induction medium). Incubation temperature was always at 37 oC.

extract_protocol:
Total RNA were extracted from frozen mycelium using the Quick-RNA™ MiniPrep kit (Zymo Research) according to manufacturer's instructions. The integrity of extracted RNA was evaluated (RIN ≥ 8) on the Agilent Bioanalyzer 2100 and quantified using an ND-1000 NanoDrop (Thermo Scientific) spectrophotometer.
For RNA-seq sample preparation, the total RNA from four A. nidulans strains (three recombinant strains and the parental strain) cultivated in 2 and 8 hours in biological triplicates, resulted in twenty-four samples for library preparation, using TruSeq Stranded mRNA Library Prep Kit v2 (Illumina) according to manufacturer's instructions.

treatment_protocol: Three A. nidulans recombinant strains producing the following heterologous proteins: alpha-arabinofuranosidase (AbfA), beta-glucosidase (BglC) and thermophilic mannanase (1542) and the parental strain A. nidulansA773 (pyrG89;wA3;pyroA4) were cultivated on minimal medium supplemented with 2% maltose for promoter activation for 2 and 8 hours.

tag: strain

value: BglC


title: Adult9.day0

tag: cell type


title: NSCLC biopsy_Patient 64_Diagnosis


title: NSCLC biopsy_Patient 45_Progression


title: NSCLC biopsy_Patient 70_Diagnosis


title: BglC_8h1


title: BM_DN2a_Bcl11b+_dll1

city: Pasadena

first: Boyoung

last: Shin

state: California

address: 1200 E. California Blvd

institute: Californial Institute of Technology

description:
Bulk RNA-seq
OP9Dll1_DN_count.txt, OP9Dll1_DN_rpkm.txt

data_processing:
Basecalls performed using RTA 1.13.48.0 and converted to Fastq files using bcl2fastq 1.8.4.
ChIP-seq reads were aligned to the GRCm38/mm10 using Bowtie (v1.1.1).
Reproducible peak calling from ChIP-seq was performed using a HOMER (Heinz et al., 2010) adaptation of the Irreproducibility Discovery Rate (IDR) tool according to ENCODE guideline.  For downstream analysis, peaks with a normalized peak score >= 15 were considered.
RNA-seq reads were aligned to the mouse reference genome GRCm38/mm10 using STAR (v2.4.0).
Gene expression from RNA-seq was calculated with RSEM(v1.2.25) by following the ENCODE RNA-seq pipelines.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: peak file (txt) for ChIP-seq, Count table and RPKM table (txt) for RNA-seq

source_name: BM progenitor-derived T  progenitor cells (DNs)

growth_protocol: Multipotent bone marrow progenitor cells were cultured with OP9-Dll1 cells in  OP9 medium(20% FBS, 2mM glutamine, 100 IU/ml penicillin, 100 mg/ml streptomycin, and 50 µM β-ME in α-MEM).   Cells were supplemented with  IL-7, Flt3-ligand  (10 ng/ml each from day0 - day7, 5 ng/ml each from day7 - day10, and 1 ng/ml each after day10) under 37 °C, 7% CO2 environment.

extract_protocol:
Zymo ChIP DNA Clean & Concentrator was used to clean eluted DNA after ChIP.  For total RNA extraction, the RNeasy Micro Kit (QIAGEN) was used.
Sequencing libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB)

treatment_protocol: For sgRNA delivery, pro-T cells from OP9-Dll1 culture on day2 (for Phase1) or on day10 (for Phase2) were detached from the OP9-Dll1 stromal cells and sgRNA was deliverered by retroviral transduction.  After infection, cells were removed from the viral particles and cultured with OP9-Dll1 for 3 days.

tag: treatment

value: Cultured on OP9DL1

value: B6. Bcl11byfp/yfp

tag: developmental stage

value: Day6 cKit high CD25+ YFP(Bcl11b)+


title: BglC_8h3


title: BM_ETP_dll1_rep2

value: Day4 cKit high CD25+ YFP(Bcl11b)-


title: BM_DN2a_Bcl11b-_dll1_rep1

value: Day6 cKit high CD25- YFP(Bcl11b)-


title: NSCLC biopsy_Patient 67_Diagnosis

value: Diagnosis


title: NSCLC biopsy_Patient 61_Progression


title: BM_DN2a_Bcl11b-_dll1_rep2

value: Day6 cKit high CD25+ YFP(Bcl11b)-


title: NSCLC biopsy_Patient 62_Diagnosis


title: Adult7.day0

value: Acute

value: Clinical Malaria


title: NSCLC biopsy_Patient 68_Diagnosis


title: WT1


title: Phase2_sgRunx1+sgRunx3 rep2

description:
Bulk RNA-seq on day3 post sgRNAs delivery
Phase2_perturbation_count.txt, Phase2_perturbation_rpkm.txt

value: B6. CRISPR-Cas9/Bcl2

value: Phase2 perturbation

tag: time

value: day3 post sgRNAs delivery


title: BM_ETP_dll1_rep1

value: Day4 cKit high CD25- YFP(Bcl11b)-


title: BglC_2h3


title: BglC_2h2


title: Adult8.day28

value: monocyte

value: Convalescence


title: NSCLC biopsy_Patient 69_Diagnosis

value: PB


title: Adult6.day0

value: Adult


title: NSCLC biopsy_Patient 61_Diagnosis


title: Adult7.day28


title: Adult5.day28


title: BglC_2h1

value: BglC


title: NSCLC biopsy_Patient 60_Diagnosis


title: Phase2_sgRunx1+sgRunx3_rep1

value: Cultured on OP9DL1


title: Adult6.day28


title: AbfA_8h3

description: recombinant strain producing a heterologous GH51 alpha-arabinofuranosidase

value: AbfA


title: Phase2_sgRunx3_rep3


title: Adult4.day28


title: Adult5.day0


title: AbfA_8h2


title: NSCLC biopsy_Patient 59_Diagnosis


title: NSCLC biopsy_Patient 44_Diagnosis


title: Phase2_sgRunx3_rep2


title: AbfA_8h1


title: Phase2_sgRunx3_rep1


title: Adult4.day0


title: Adult3.day28


title: NSCLC biopsy_Patient 57_Diagnosis


title: Adult3.day0


title: AbfA_2h2


title: NSCLC biopsy_Patient 56_Diagnosis


title: NSCLC biopsy_Patient 55_Diagnosis


title: Phase2_sgRunx1_rep3


title: AbfA_2h3


title: Adult1.day28


title: NSCLC biopsy_Patient 43_Diagnosis


title: Adult2.day28


title: NSCLC biopsy_Patient 55_Progression

value: Progression


title: NSCLC biopsy_Patient 52_Progression


title: A773_8h2

description: wild type strain

value: WT


title: AbfA_2h1


title: Phase2_sgRunx1_rep1


title: Adult1.day0


title: A773_8h1

description: wild type strain


title: Phase2_sgRunx1_rep2


title: NSCLC biopsy_Patient 52_Diagnosis

value: Diagnosis


title: A773_8h3

description: wild type strain


title: Phase2_sgControl_rep3


title: A773_2h3

description: wild type strain


title: Phase2_sgControl_rep1


title: Phase1_sgRunx1+sgRunx3_rep2

description:
Bulk RNA-seq on day3 post sgRNAs delivery
Phase1_perturbation_count.txt, Phase1_perturbation_rpkm.txt

value: Phase1 perturbation


title: NSCLC biopsy_Patient 50_Diagnosis


title: NSCLC biopsy_Patient 51_Diagnosis


title: Phase1_sgRunx1+sgRunx3_rep1


title: NSCLC biopsy_Patient 49_Diagnosis


title: PC3_FOXA2_VEH_L002

city: Boston

first: Changmeng

last: Cai

state: Massachusetts

address: 100 William T. Morrissey Blvd.

institute: University of Massachusetts Boston

description:
technical replicate for ATAC-seq after treated with vehicle control
PC3_FOXA2_S10_peaks.narrowPeak
PC3_FOXA2_S10.bw

data_processing:
Raw reads were aligned to hg19 using bwa (version 0.7.2)
sam files are converted to bam with samtools (version 0.1.18 )
MACS2 (version 2.1.2) was used to call peak on the bam files
bedGraph files containing signal per million reads produced from MACS2 was converted to bigwig files with ucsctool kit (315)
Genome_build: GRCh37
Supplementary_files_format_and_content: bigWig and narrowPeak files containing normalized signal and peak intervals

growth_protocol: PC-3 cells were maintained in RPMI-1640 with 10% FBS

extract_protocol: Libraries construction was performed using ThruPLEX DNA-seq 48D Kit (Rubicon Genomics)

treatment_protocol: PC-3 cells grown in RPMI1640 with 5% CSS were treated with 50μM GSK2879552 for 4 hours

value: prostate cancer cell

tag: cell line

tag: agent

value: vehicle


title: PC3_FOXA2_VEH_L001


title: 1542_8h3

description: recombinant strain producing a heterologous GH5 thermophilic mannanase


title: Adult2.day0

value: Acute

value: Clinical Malaria


title: Phase1_sgRunx3_rep2

value: B6. CRISPR-Cas9/Bcl2

value: day3 post sgRNAs delivery


title: A773_2h1

description: wild type strain


title: NSCLC biopsy_Patient 47_Progression

tag: patient id


title: Phase1_sgRunx1_rep2


title: NSCLC biopsy_Patient 48_Diagnosis

tag: treatment cohort


title: 1542_8h1


title: PC3_FOXA2_GSK_S11_L001

description:
technical replicate for ATAC-seq after treated with GSK
PC3_FOXA2_GSK_S11_peaks.narrowPeak
PC3_FOXA2_GSK_S11.bw


title: Phase1_sgRunx1_rep1


title: Phase1_sgRunx3_rep1


title: Phase2_sgControl_rep2

value: Phase2 perturbation


title: 1542_8h2


title: A773_2h2

description: wild type strain


title: PC3_FOXA2_GSK_S11_L002


title: LN_HOXB13_VEH_S5_L002

description:
technical replicate for HOXB13 ChIP-Seq after treated with vehicle control
LN_HOXB13_VEH_S5_peaks.narrowPeak
LN_HOXB13_VEH_S5.bw

source_name: LNCaP

growth_protocol: LNCaP cells were maintained in RPMI-1640 with 10% FBS

treatment_protocol: LNCaP cells grown in RPMI1640 with 5% CSS were treated with 50μM GSK2879552 for 4 hours

tag: antibody

value: LNCaP


title: LN_HOXB13_VEH_S5_L001


title: LN_HOXB13_GSK_S6_L002

description:
technical replicate for HOXB13 ChIP-Seq after treated with GSK
LN_HOXB13_GSK_S6_peaks.narrowPeak
LN_HOXB13_GSK_S6.bw


title: 1542_2h3


title: LN_HOXB13_GSK_S6_L001


title: Phase1_sgControl_rep2


title: NSCLC biopsy_Patient 39_Diagnosis

value: PB

tag: timepoint


title: 1542_2h1


title: Phase1_sgControl_rep1


title: LN_ATAC_VEH_S1_L002

description:
technical replicate for ATAC-seq after treated with vehicle control
LN_ATAC_VEH_S1_peaks.narrowPeak
LN_ATAC_VEH_S1.bw

extract_protocol: Libraries construction was performed Tagment DNA TDE1 Enzyme and Buffer Kit(Illumina)


title: LN_ATAC_VEH_S1_L001


title: Phase2_cKit_low_CD25+_1%_input_rep2

description: 1% input for Runx3 ChIP-seq

source_name: BM progenitor-derived T  progenitor cells (DNs) in Phase2

value: cKit_low_CD25+Phase2 stage

tag: chip antibody


title: Phase2_cKit_low_CD25+_1%_input_rep1

description: 1% input for Runx3 ChIP-seq


title: LN_ATAC_GSK_S2_L002

description:
technical replicate for ATAC-seq after treated with GSK
LN_ATAC_GSK_S2_peaks.narrowPeak
LN_ATAC_GSK_S2.bw


title: Phase2_cKit_low_CD25+_Runx3_rep2

description:
Runx3 ChIP-seq
Phase2_Runx3_IDR_peaks.txt

value: Rabbit anti-Runx3 (provided from Dr. Levanon and Dr. Groner, Levanon et al., 2014)


title: NSCLC biopsy_Patient 47_Diagnosis


title: LN_ATAC_GSK_S2_L001


title: NSCLC biopsy_Patient 35_Progression


title: NSCLC biopsy_Patient 46_Diagnosis


title: Phase2_cKit_low_CD25+_Runx3_rep1

value: Cultured on OP9DL1


title: miRNA PAT fibroblast IMDM Biological remiRNA P 5

description: Gene expression from disese-associated cultured fibroblasts

hyb_protocol: Biotin-labelled samples and controls were added to a hybridisation mix and hybridized to Affymetrix GeneChip miRNA 4.0 arrays for 18 hours at 48˚C and 60rpm in an Affymetrix GeneChip hybridisation oven 645.

scan_protocol: Following hybridisation the arrays were washed and stained on an Affymetrix GeneChip Fluidics Station 450 using a FS450_0002 script and scanned in an Affymetrix Genechip Scanner 3000G.

source_name: Cultured human fibroblasts from PAT

label_protocol: 130ng of total RNA (free from DNA) was labelled using the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix). This process begins with a brief tailing reaction followed by ligation of the biotinylated signal molecule to the target RNA sample.

value: PAT

tag: media

value: IMDM


title: 1542_2h2


title: NSCLC biopsy_Patient 44_Progression

value: Progression


title: NSCLC biopsy_Patient 42_Progression


title: miRNA PAT fibroblast IMDM Biological remiRNA P 3


title: RE90

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ssc10.2 whole genome using tophat2  with parameters -a 8 -m 0 -i 50 -I 500000 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments --b2-N 1 --read-edit-dist 4 -N 4
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Ssc10.2
Supplementary_files_format_and_content: tab-delimited excel files include reads and RPKM values for each Sample

molecule: polyA RNA

organism: Sus scrofa

source_name: longissimus muscles

extract_protocol:
Musucle samples were harvested, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sows were fed with a normal or calorie-restricted diet after mating

value: embryo

tag: diet

value: calorie-restricted diet during the gestation

tag: time point

value: 90 days of gestation

value: longissimus muscles


title: miRNA PAT fibroblast IMDM Biological remiRNA P 4


title: NE55

value: normal diet during the gestation

value: 55 days of gestation

tag: tissue


title: NSCLC biopsy_Patient 42_Diagnosis

value: Diagnosis


title: NSCLC biopsy_Patient 41_Diagnosis


title: Phase1_cKit_high_CD25-_Runx3_rep2

description:
Runx3 ChIP-seq
Phase1_Runx3_IDR_peaks.txt

source_name: BM progenitor-derived T  progenitor cells (DNs) in Phase1

value: cKit high CD25- Phase1 stage


title: RE35

value: 35 days of gestation


title: NSCLC biopsy_Patient 45_Diagnosis


title: NSCLC biopsy_Patient 38_Progression


title: NSCLC biopsy_Patient 38_Diagnosis


title: Phase1_cKit_high_CD25-_1%_input_rep2

description: 1% input for Runx3 ChIP-seq


title: JLAVC006F

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

country: Canada

institute: University of British Columbia

data_processing:
All fastq files were trimmed using trimmomatic (version 0.38) to remove paired end adapters, minimum MAPQ score of 30, leading and trailing 3bp, and to a minimum length of 15bp. Trimmed fastq files were then aligned to either the mm10 genome or a modified mm10 that incorporated BTBR genetic changes using bowtie232 with mmarge30 with default settings for paired end data. BTBR aligned data were then shifted back to mm10 standard genome coordinates using MMARGE.pl shift30. For all samples aligned reads were then filtered using samtools (version 1.8) to remove PCR duplicates, unpaired reads, unmapped reads, and secondary alignments. To assess transposition efficiency and the proportion of nucleosome free reads compared to mono and di- nucleosomes, histograms of the distribution of insert sizes was created using picard-tools (version 2.18.4) CollectInsertSizeMetrics. The filtered reads were then shifted to account for the Tn5 insertions site (+4bp to positive strand and -5bp from negative strand) using the perl script ATAC_BAM_shifter_gappedAlign.pl (https://github.com/TheJacksonLaboratory/ATAC-seq/blob/master/auyar/). Shifted reads were filtered for nucleosome free regions (read length < 147bp) and to remove mitochondrial reads using samtools.
Filtered reads were then used for peak calling with HOMER (-style factor -center -F 0 -L 0 -C 0 -fdr 0.01 -minDist 200 -size 200). The resulting peak files were then filtered to remove mm10 blacklist regions using bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: bed files of HOMER peaks

source_name: BTBR T+ Itpr3tf/J_BMDM_two doses LPS

growth_protocol: Bone marrow cells were isolated from postnatal day 28 BTBR (BTBR T+ Itpr3tf/J, Jax 002282) and C57BL6/J (Jax 000664) male mice.  Isolated cells were cultured for seven days to generate bone marrow derived macrophages (BMDM) in DMEM/F12 media supplemented with 10% fetal bovine serum and 1% Penicillin-Streptomycin (base media). BMDM were then reseeded at a density of 5x105 cells per well of a 6 well plate and incubated overnight.

extract_protocol:
ATACseq was performed as described in(Buenrostro, et al., 2015).  Briefly, cultures of 50,000 BMDM were washed once in ice cold 1xPBS and then resuspended gently in 100ul ATACseq lysis buffer (1 mM Tris·Cl, pH 7.4, 1 mM NaCl= 500ul 1M NaCl, 0.3 mM MgCl2, and 0.01% (v/v) Triton-X 100) to release nuclei. Nuclei were then pelleted (1,000xg, 10min, 4C) and transposed in 2.5ul Tn5 (Nextera Tn5 transposase, Illumina), 12.5ul TD reaction buffer and 10.5ul water for 40min at 37C with rotation. Following transposition, DNA was purified (MinElute PCR Purification Kit, Qiagen) and stored at -80C.
Samples were then thawed on ice and unique barcodes(Buenrostro, et al., 2015) were added to each sample using 5 cycles of PCR(Buenrostro, et al., 2015).  A side PCR reaction was then taken and used as input for qPCR for an additional 20 cycles to assess determine the optimal number of additional PCR cycles for each library (the cycle number that corresponds to one-third of the maximum fluorescent intensity). Each sample was then amplified by the determined number of PCR cycles and then purified (MinElute PCR Purification Kit, Qiagen).  Final libraries were then size selected for fragments between 100-1000bp using AMPure XP beds (Beckman Coulter) and quality was checked by DNA High Sensitivity bioanalyzer.
Libraries were pooled (6 per pool) and sequenced across four lanes of the HiSeq2500 to generate 50bp paired end reads.

treatment_protocol: There were three treatment conditions: media, one dose LPS (LPSx1) or two doses of LPS (LPSx2).  BMDM were treated with media (media or LPSx1) or 100ng LPS/ml for four hours (LPSx2). Cultures were then washed twice with HBSS and incubated overnight in base media. Twenty hours later cultures were treated with media (media) or 100ng LPS/ml for 24 hours (LPSx1 and LPSx2).

value: BTBR T+ Itpr3tf/J

tag: Sex

value: male

tag: age (years)

value: postnatal day 28

value: bone marrow derived macrophage (BMDM)

tag: biological replicate

value: two doses LPS

tag: additional pcr cycles

tag: sequencing lane

tag: barcode

value: Index 2.6 5' TAGGCATG 3'

tag: molecule subtype

value: Tn5 Transposase treated DNA


title: NSCLC biopsy_Patient 85_Diagnosis

value: PB


title: JLAVC006E

source_name: BTBR T+ Itpr3tf/J_BMDM_one dose LPS

tag: strain

tag: cell type

tag: treatment

value: one dose LPS

value: Index 2.5 5' GGACTCCT 3'


title: NE35

tag: developmental stage

value: embryo


title: NE90

value: 90 days of gestation

value: longissimus muscles


title: shoot 7dpt pa23 s2

city: Winnipeg

first: Joey

middle: C

last: Wan

address: 50 Sifton Road

institute: University of Manitoba

data_processing:
Quality control with FastQC reports
Trimming with Trimmomatic
Aligned to B napus genome with Tophat2
Cuffquant used to quantify aligned reads
cuffdiff to determine differential expression
Genome_build: B napus reference annotation v.5.0
Supplementary_files_format_and_content: cuffquant files (.cxb files)

organism: Brassica napus

source_name: shoot

growth_protocol: Grown in Conviron Growth chambers with a 16-8 light dark cycle. Light settings at 150 umol/m^2/s

extract_protocol:
Tissue homogenized in liquid nitrogen, extracted with Invitrogen Plant Extraction Reagent. DNA removed with Ambion Turbo DNAse. Quality and quantity confirmed with nanodrop and Agilent bioanalyzer
Ravi et al 2012 – PLOS One

treatment_protocol: Biological drench of PA23 for treated samples and control treatment of LB broth

value: shoot

tag: time poit

value: 7 days

value: Pseudomonas chlororaphis PA23


title: Phase1_cKit_high_CD25-_1%_input_rep1

description: 1% input for Runx3 ChIP-seq

value: Cultured on OP9DL1

value: cKit high CD25- Phase1 stage

tag: chip antibody


title: RE55

value: calorie-restricted diet during the gestation

value: 55 days of gestation


title: NSCLC biopsy_Patient 33_Diagnosis

source_name: NSCLC biopsy

tag: patient id

tag: treatment cohort

tag: timepoint

value: Diagnosis


title: shoot 7dpt pa23 s1

tag: tissue


title: JLAVC006D

source_name: BTBR T+ Itpr3tf/J_BMDM_media

value: BTBR T+ Itpr3tf/J

tag: Sex

value: male

value: postnatal day 28

value: bone marrow derived macrophage (BMDM)

value: media

value: Index 2.4 5' TCCTGAGC 3'


title: NSCLC biopsy_Patient 32_Diagnosis

value: PB


title: JLAVC006C

source_name: C57BL6/J_BMDM_two doses LPS

tag: age (years)

value: two doses LPS

value: Index 2.3 5' AGGCAGAA 3'

value: Tn5 Transposase treated DNA


title: miRNA PDAC fibroblast IMDM Biological remiRNA P 4

source_name: Cultured human fibroblasts from PDAC

tag: cell line

value: PDAC

tag: media

value: IMDM


title: miRNA PAT fibroblast IMDM Biological remiRNA P 1

value: PAT


title: miRNA PDAC fibroblast IMDM Biological remiRNA P 5


title: miRNA PDAC fibroblast IMDM Biological remiRNA P 2


title: miRNA PDAC fibroblast IMDM Biological remiRNA P 3


title: miRNA PAT fibroblast IMDM Biological remiRNA P 2


title: shoot 7dpt ctrl s2

value: shoot

value: 7 days

value: Control


title: NSCLC biopsy_Patient 31_Diagnosis

value: Diagnosis


title: miRNA PDAC fibroblast IMDM Biological remiRNA P 6


title: JLAVC006B

source_name: C57BL6/J_BMDM_one dose LPS

tag: biological replicate

value: one dose LPS

tag: additional pcr cycles

tag: sequencing lane

value: Index 2.2 5' CGTACTAG 3'


title: miRNA PDAC fibroblast IMDM Biological remiRNA P 1


title: NSCLC biopsy_Patient 35_Diagnosis


title: shoot 7dpt ctrl s1


title: NSCLC biopsy_Patient 30_Diagnosis


title: shoot 24hpt pa23 s1

value: 24 hours

value: Pseudomonas chlororaphis PA23


title: miRNA Normal Fibro IMDM Technical rep 3

description: Gene expression from commercial cultured fibroblasts IMDM

source_name: Commercial cultured human fibroblasts from non-disease pancreas

value: NormalFibro


title: JLAVC006A

tag: strain

value: male

value: postnatal day 28

value: bone marrow derived macrophage (BMDM)

value: media

tag: barcode

value: Index 2.1 5' TAAGGCGA 3'

tag: molecule subtype


title: JLAVC005F

tag: cell type

tag: treatment

value: two doses LPS

value: Index 2.6 5' TAGGCATG 3'

value: Tn5 Transposase treated DNA


title: NSCLC biopsy_Patient 22_Diagnosis

value: PB


title: JLAVC005E

value: Index 2.5 5' GGACTCCT 3'


title: shoot 24hpt pa23 s2

value: shoot

tag: time poit


title: shoot 24hpt ctrl s2

value: Control


title: NSCLC biopsy_Patient 24_Diagnosis

tag: patient id

value: Diagnosis


title: NSCLC biopsy_Patient 21_Diagnosis

tag: treatment cohort


title: miRNA Normal Fibro LSM Technical rep 3

description: Gene expression from commercial cultured fibroblasts Low serum media

value: LSM


title: JLAVC005D

value: Index 2.4 5' TCCTGAGC 3'


title: shoot 24hpt ctrl s1

value: 24 hours


title: JLAVC005C

value: BTBR T+ Itpr3tf/J

value: Index 2.3 5' AGGCAGAA 3'


title: root 7dpt pa23 r2

source_name: root

value: root

value: 7 days

value: Pseudomonas chlororaphis PA23


title: NSCLC biopsy_Patient 15_Diagnosis

tag: timepoint


title: NSCLC biopsy_Patient 18_Diagnosis


title: miRNA Normal Fibro IMDM Technical rep 1

value: NormalFibro

value: IMDM


title: root 7dpt pa23 r1

tag: tissue


title: miRNA Normal Fibro LSM Technical rep 2


title: JLAVC005A

tag: Sex

value: male

value: postnatal day 28

value: bone marrow derived macrophage (BMDM)

value: media

value: Index 2.1 5' TAAGGCGA 3'


title: miRNA Normal Fibro IMDM Technical rep 2


title: root 7dpt ctrl r2

value: Control


title: NSCLC biopsy_Patient 14_Diagnosis

value: PB

value: Diagnosis


title: NSCLC biopsy_Patient 13_Progression

value: Progression


title: miRNA Normal Activated fibroblast IMDM Biological rep 5

description: Gene expression from non-disease cultured fibroblasts

source_name: Cultured human fibroblasts from normal pancreas

value: NormActivated


title: root 7dpt ctrl r1


title: JLAC004E

tag: age (years)

value: one dose LPS

value: Index 2.5 5' GGACTCCT 3'

value: Tn5 Transposase treated DNA


title: miRNA Normal Activated fibroblast IMDM Biological rep 3

tag: cell line


title: NSCLC biopsy_Patient 12_Diagnosis


title: root 24hpt pa23 r2

value: root

value: 24 hours


title: JLAVC005B

value: BTBR T+ Itpr3tf/J

value: Index 2.2 5' CGTACTAG 3'


title: JLAC004D

value: male

value: Index 2.4 5' TCCTGAGC 3'


title: miRNA Normal Activated fibroblast IMDM Biological rep 4

tag: media

value: IMDM


title: root 24hpt pa23 r1

value: Pseudomonas chlororaphis PA23


title: miRNA Normal Activated fibroblast IMDM Biological rep 2


title: JLAC004C

value: postnatal day 28

value: bone marrow derived macrophage (BMDM)

tag: biological replicate

value: two doses LPS

value: Index 2.3 5' AGGCAGAA 3'


title: NSCLC biopsy_Patient 10_Diagnosis

value: PB

value: Diagnosis


title: miRNA Normal Fibro LSM Technical rep 1

value: NormalFibro

value: LSM


title: NSCLC biopsy_Patient 8_Diagnosis


title: root 24hpt ctrl r2

value: Control


title: NSCLC biopsy_Patient 13_Diagnosis


title: root 24hpt ctrl r1

value: root


title: JLAC004A

value: media

tag: additional pcr cycles

value: Index 2.1 5' TAAGGCGA 3'

value: Tn5 Transposase treated DNA


title: JLAC003F

value: BTBR T+ Itpr3tf/J

value: male

tag: sequencing lane

value: Index 2.6 5' TAGGCATG 3'


title: JLAC004F

tag: strain


title: miRNA CP fibroblast IMDM Biological rep 4

source_name: Cultured human fibroblasts from CP

value: CP

value: IMDM


title: NSCLC biopsy_Patient 7_Progression

value: Progression


title: miRNA CP fibroblast IMDM Biological rep 5


title: miRNA CP fibroblast IMDM Biological rep 3


title: JLAC003E

value: postnatal day 28

value: bone marrow derived macrophage (BMDM)

value: one dose LPS

tag: barcode

value: Index 2.5 5' GGACTCCT 3'


title: NSCLC biopsy_Patient 6_Diagnosis

value: PB

value: Diagnosis


title: MSUS Serum small RNA sample8

source_name: Serum

extract_protocol: TruSeq small RNA Kit

tag: condition

value: MSUS

tag: time from last injection


title: BAQ12O-3

city: Sacramento

first: Zhao

last: Ma

address: 2700 Stockton Blvd, 2301

department: Biochemistry and Molecular Medicine

institute: University of California, Davis

data_processing:
Raw sequence data (FASTQ) was processed with the QuantSeq FWD-UMI Analysis Pipeline for Read QC and trimming, followed by alignment to the reference human genome assembly (GRCh38/hg38) with the STAR Aligner. PCR duplicates were removed by collapsing reads with identical mapping coordinates and UMI sequences.
Gene-level read counts were then generated from BAM alignment files with HTSeq using the Ensembl gene annotation for human version 77.
Count data was brought into DESeq2 for normalization.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Tab-delimited text files include Ensembl ID and gene-level read counts for each transcript.

source_name: pancreas

extract_protocol:
Total RNA was extracted by the RNeasy Mini Kit (Qiagen, Germany) from MIA PaCa-2 cells after treatments.
Sequencing libraries were prepared with the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexgen) according to the manufacturer's protcol.
RNA-Seq (3'Tag-Seq)

tag: agent

tag: cell type

value: epithelial cell

value: MIA PaCa-2


title: BAQ12O-2


title: miRNA Normal Activated fibroblast IMDM Biological rep 1

value: NormActivated


title: BAQ12O-1


title: BAQ13-3


title: miRNA CP fibroblast IMDM Biological rep 2


title: NSCLC biopsy_Patient 5_Diagnosis

tag: patient id


title: JLAC003D

tag: treatment

value: media

value: Index 2.4 5' TCCTGAGC 3'

tag: molecule subtype

value: Tn5 Transposase treated DNA


title: JLAC003C

value: male

value: two doses LPS

value: Index 2.3 5' AGGCAGAA 3'


title: NSCLC biopsy_Patient 4_Progression

tag: treatment cohort

tag: timepoint

value: Progression


title: NSCLC biopsy_Patient 4_Diagnosis


title: BAQ13-2


title: MSUS Serum small RNA sample6


title: JLAC003B

tag: Sex

tag: age (years)

value: postnatal day 28

value: Index 2.2 5' CGTACTAG 3'


title: NSCLC biopsy_Patient 7_Diagnosis


title: CTRL Serum small RNA sample5

value: CTRL


title: JLAC003A

value: bone marrow derived macrophage (BMDM)

value: Index 2.1 5' TAAGGCGA 3'


title: NSCLC biopsy_Patient 3_Progression

value: PB


title: BAQ13-1

tag: cell line


title: BAQ12-3


title: CTRL Serum small RNA sample3


title: NSCLC biopsy_Patient 3_Diagnosis

value: Diagnosis


title: LN_FOXA1_G_veh_S7_L002

description:
technical replicate for FOXA1 ChIP-Seq after treated with vehicle control
LN_FOXA1_G_S7_peaks.narrowPeak
LN_FOXA1_G_S7.bw

source_name: LNCaP

value: prostate cancer cell

tag: antibody

value: LNCaP

value: vehicle


title: BAQ12-2

value: epithelial cell

value: MIA PaCa-2


title: LN_FOXA1_G_veh_S7_L001


title: BAQ12-1


title: LN_FOXA1_G_GSK_S8_L002

description:
technical replicate for FOXA1 ChIP-Seq after treated with GSK
LN_FOXA1_G_GSK_S8_peaks.narrowPeak
LN_FOXA1_G_GSK_S8.bw


title: CTRL Serum small RNA sample1


title: NSCLC biopsy_Patient 2_Diagnosis


title: MSUS Serum small RNA sample10

value: MSUS


title: Lys05-3


title: CTRL Sperm polyA RNA ai_8

source_name: Sperm

extract_protocol: TruSeq Stranded RNA Kit


title: NSCLC biopsy_Patient 1_Progression


title: Lys05-1


title: TESA Sperm polyA RNA ai_7

value: TESA


title: Ctrl-3

value: Ctrl


title: CTRL Sperm polyA RNA ai_6


title: miRNA CP fibroblast IMDM Biological rep 1

value: CP

tag: media

value: IMDM


title: TESA Sperm polyA RNA ai_5


title: Ctrl-2


title: Ctrl-1


title: CTRL Serum small RNA sample2


title: CTRL Sperm polyA RNA ai_4


title: TESA Sperm polyA RNA ai_3


title: NSCLC biopsy_Patient 1_Diagnosis


title: Lys05-2


title: HEK293_mRNAseq_replicate 2

city: Cambridge

first: Ramanujan

last: Hegde

address: Francis Crick Ave

institute: MRC Laboratory of Molecular Biology

data_processing:
Trimmomatic ILLUMINACLIP 2:30:10 (TruSeq3-PE adapters) SLIDINGWINDOW:5:20 and MINLEN:35
TopHat2 2.2.5
HTSeq 0.11.2
Genome_build: hg38
Supplementary_files_format_and_content: raw counts from HTSeq

growth_protocol: HEK293 were maintained in Dulbecco’s Modified Eagles’s Medium (DMEM) supplemented with 10% fetal calf serum.

extract_protocol:
Total RNA from cells were extracted with TRIzol (Life Technologies, 15596018). 2.5 µg of total extracted RNA was used as input for rRNA depletion using Ribo-Zero rRNA Removal Kit (illumina). Subtracted RNAs were purified by ethanol precipitation. according to the manufacturer’s instruction.
Depleted RNA was used as input for library preparation using NEBNext® Ultra™ Directional RNA Library Prep Kit according to the manufacturer's instructions.


title: CTRL Sperm polyA RNA ai_2


title: HEK293_mRNAseq_replicate 3


title: LN_FOXA1_G_GSK_S8_L001


title: HEK293_mRNAseq_replicate 1


title: TESA Sperm polyA RNA ai_1


title: HE_ALA_replicate3

city: chengdu

first: Yong

last: Dong

state: sichuan

address: Xindu road 783, Xindu district

department: Immunology

institute: Chengdu medical college

data_processing:
The clean fastq files were provied by Novogene company. All the fastq files were mapped to human genomic hg38 by Hisat2 program to generate .sam files. FeatureCounts program was used to calculate the gene expression raw counts.
The gene expression raw counts were normalized by DESeq2 R package.
Supplementary_files_format_and_content: The gene expression raw counts were provided in the HE_data_raw.csv file.

source_name: Hemogenic endothelial cells differentiated from human embronic stem cell (H1)

growth_protocol: Human embryonic stem cells (H1) were induced into hematopoietic cells by co-culturing with AGM-S3 stroma cells as previouly reported(PMID: 27720903, 31178416). CD34+CD43-KDR+CD144+ hemogenic endothelial cells were sorted at day8.

extract_protocol:
1000 of CD34+CD43-KDR+CD144+ hemogenic endothelium cells were sorted separately into 200 µL DPBS-BSA buffer (0.5% BSA) using a 1.5 mL Eppendorf tube. The cDNA of sorted 1000-cell aliquots were generated and amplified, as described previously(PMID:29434353, 31443434)
Then qualities of the amplified cDNA were examined by qPCR analysis of housekeeping genes (B2m, Actb, Gapdh). Samples that passed quality control were used for subsequent sequencing library preparation, 1ng of dsDNA was used to generate the library using Vazyme TruePrepTM DNA library Prep Kit V2 for Illumina (TD-503). All libraries were sequenced by Illumina Novaseq6000 system (Novogene Co., Ltd. ).

treatment_protocol: The hematopoietic inducing culture medium were added with 100ug/ml alpha lipoic acid (ALA) or not(Ctrl).

value: Lipoic acid (ALA)


title: HE_ALA_replicate2


title: CG6967-ADARcd rep2

city: Minneapolis

first: Hiroshi

last: Nakato

address: 515 Delaware Street SE

institute: University of Minnesota

data_processing:
Illumina CASAVA v1.8 was used for basecalling.
Sequenced reads were filtered by fastp v0.19.5 with default settings.
Sequence reads were mapped to the UCSC dm6 genome using STAR v2.6.1c.
Duplicated reads were marked using Picard v2.18.20 and ignored in the downstream analysis.
A-to-G variants were detected using JACUSA v1.2.4.
Genome_build: UCSC dm6
Supplementary_files_format_and_content: Text files including single nucleotide variant information generated by JACUSA in the biological replicate 1
Supplementary_files_format_and_content: Text files including single nucleotide variant information generated by JACUSA in the biological replicate 2
Supplementary_files_format_and_content: CSV files including genes that have TRIBE sites in the biological replicate 1
Supplementary_files_format_and_content: CSV files including genes that have TRIBE sites in the biological replicate 2

source_name: Adult midgut

extract_protocol:
Total RNA was extracted using TRIzol Reagent. Illumina TrueSeq Stranded mRNA Library Prep Kit was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: Adult midgut

tag: age

value: day 7-8

tag: genotype

value: esg[ts] F/O > CG6967-ADARcd-V5


title: Pe day3 rep2 [miRNA]

data_processing:
Reads per million (RPM) were calculated using miRge v2.0.
Differential expression analysis was performed using DESeq2 v1.22.0.
Genome_build: miRBase v22
Supplementary_files_format_and_content: Reads per million (RPM) for each miRNA
Supplementary_files_format_and_content: CSV files including log2 fold changes for each miRNA

extract_protocol:
Total RNA was extracted using TRIzol Reagent. Illumina TruSeq Small RNA Library Preparation Kit was used with 2 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Oregon-R

value: wild type

value: Pe


title: MSUS Serum small RNA sample7

tag: condition

tag: time from last injection


title: CG6967-ADARcd rep1


title: HE_ALA_replicate1

tag: agent


title: HE_Ctrl1_replicate3


title: Pe day3 rep1 [miRNA]


title: Pe day0 rep3 [miRNA]

value: day 4-5


title: ADARcd control rep2

value: esg[ts] F/O > ADARcd-V5


title: Male_12LFD_Adipose_biological replicate 1

city: New York City

first: Dimitris

last: Nasias

state: New York

address: 550 1st Avenue

department: Langone Medical School

institute: New York University

hyb_protocol: as per Affymetrix instructions

scan_protocol: GeneChip® Scanner 3000 7G (Affymetrix/ThermoFisher Scientific)

data_processing: Affymetrix Transcriptome Analysis Console (TAC) Software Version 4.0.2 was used first for the normalization, summarization and quality control of the microarray data. In the next step, TAC was used for the determination of the differentially expressed genes by performing p-value and fold change thresholds (Two Way Analysis of Variance (Two-Way ANOVA): p-value <0.05 and absolute fold change >1.5).

label: biotin

source_name: Male mouse, LFD, 12 weeks, Adipose, biological replicate 1

label_protocol: The aRNA was purified, reverse transcribed and the resulting cDNA was fragmented, labelled and hybridized overnight to GeneChip™ Mouse Gene 2.0 ST Affymetrix expression arrays.

growth_protocol: ApoE3Leiden and hCETP transgenic mice were obtained from TNO Leiden (Leiden, The Netherlands). All mice were bred at the animal facility of the Institute of Molecular Biology and Biotechnology of Heraklion, Greece under pathogen free conditions on a 12h light/dark cycle with free access to food and water. Heterozygous male apoE3L.CETP mice were included in the experiments.

extract_protocol: PureLink® RNA Mini Kit (ThermoFisher Scientific) was used for RNA isolation according to the manufacturer's instructions. Sample processing was performed using the GeneChip WT PLUS Reagent Kit (Affymetrix/ThermoFisher Scientific).Starting from total RNA, first and second strand cDNA synthesis was performed. The double stranded cDNA was transcribed to aRNA (amplified RNA) during in vitro transcription (IVT).

treatment_protocol: Starting at the age of 12 weeks, heterozygous male apoE3L.CETP mice were randomized based on body weight and were fed for 4, 8 and 12 weeks with either a low fat diet (LFD) (D12450B, Research diets, New Brunswick, USA) containing 20% protein, 70% carbohydrate and 10% fat (LFD) or a high fat diet (HFD) (D14010701, Research diets, New Brunswick, USA) containing 20% protein, 20% carbohydrate, 60% fat and 0,25% cholesterol (HFD, n=6-7 mice per group). All animals were anesthetized with isoflurane and euthanized by cardiac puncture at the end of diet administration. All experimental protocols in mice were in accordance with institutional guidelines and were approved by the Greek Federal Veterinary Office (License #8595/2015).  Clinical measurements in mice have been previously described (doi: 10.1002/jcp.28649).

value: adipose

value: 34 weeks

tag: diet

value: LFD, 12 weeks

tag: gender

value: male


title: HE_Ctrl1_replicate2


title: ADARcd control rep1


title: Pe day0 rep2 [miRNA]

tag: treatment


title: Male_12LFD_Adipose_biological replicate 3

source_name: Male mouse, LFD, 12 weeks, Adipose, biological replicate 3


title: GW10-Hy

city: Beijing

first: Xin

last: Zhou

address: 15 Datun Road

department: State key laboratory of Brain and Cognitive Science

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Cell ranger 2.0.1 was used to perform quality control and read counting of Ensemble genes with default parameter (v2.0.1) by mapping to the hg19 human genome.
Poor quality cells after the gene-cell data matrix was generated by cell ranger software using the Seurat package (v2.1.0) in Bioconductor.
The data were natural log transformed and normalized for scaling the sequencing depth to a total of 1e4 molecules per cell, followed by regressing-out the number of UMI using Seurat package.
Genome_build: hg19
Supplementary_files_format_and_content: TSV and MTX

source_name: hypothalamus

extract_protocol:
Hypothalamic tissues were dissected under dissection microscope and subjected to tissue dissociation. The tissue was dissociated into single-cell suspension using a papain-based dissociation protocol. Single cells were partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) by 10x GemCode™ Technology. The cDNA libraries were generated with Single Cell 3’ Reagent Kits, according to the manufacturer’s protocol. The library was sequenced with 150bp pair-end reads using an Illumina HiSeq4000.
Illumina HiSeq4000

tag: embryonic stage

tag: brain structure

value: hypothalamus


title: HE_Ctrl1_replicate1


title: Male_12LFD_Adipose_biological replicate 4

source_name: Male mouse, LFD, 12 weeks, Adipose, biological replicate 4


title: Male_12HFD_Adipose_biological replicate 3

source_name: Male mouse, HFD, 12 weeks, Adipose, biological replicate 3

value: HFD, 12 weeks


title: Male_12HFD_Adipose_biological replicate 4

source_name: Male mouse, HFD, 12 weeks, Adipose, biological replicate 4


title: Pe day3 rep3 [miRNA]


title: Male_12LFD_Adipose_biological replicate 2

source_name: Male mouse, LFD, 12 weeks, Adipose, biological replicate 2


title: Male_12HFD_Adipose_biological replicate 2

source_name: Male mouse, HFD, 12 weeks, Adipose, biological replicate 2


title: Male_12HFD_Adipose_biological replicate 1

source_name: Male mouse, HFD, 12 weeks, Adipose, biological replicate 1


title: Male_8LFD_Adipose_biological replicate 2

source_name: Male mouse, LFD, 8 weeks, Adipose, biological replicate 2

value: 20 weeks

value: LFD, 8 weeks


title: Pe day0 rep1 [miRNA]


title: Mock day0 rep3 [miRNA]

value: Sucrose


title: Male_8LFD_Adipose_biological replicate 4

source_name: Male mouse, LFD, 8 weeks, Adipose, biological replicate 4


title: Male_8LFD_Adipose_biological replicate 1

source_name: Male mouse, LFD, 8 weeks, Adipose, biological replicate 1


title: Male_8LFD_Adipose_biological replicate 3

source_name: Male mouse, LFD, 8 weeks, Adipose, biological replicate 3


title: Hidbrain hypoxic rep2

city: Safed

first: Bodhisattwa

last: Banerjee

address: 8 Henrietta Szold Street

department: Faculty of Medicine

country: Israel

institute: Bar-Ilan University

description:
Hb_novel_lnc_raw_counts.txt
Hbt2

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads with Q≥30 were selected for the downstream analysis. The raw reads were aligned to the latest zebrafish genome (GRCz11) from Ensembl using STAR v2.7.3 and transcripts were assembled by StringTie using the reference annotation from Ensembl.
The expression level of each transcript was calculated and normalized as transcripts per million (TPM).
Genome_build: GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: Brain

extract_protocol:
A total of 18 fish (9 hypoxic and 9 normoxic) were sacrificed after anesthetizing with 0.03% tricaine (Sigma-Aldrich, Germany), and brains were separated and placed in ice-cold HBSS (1X Hank’s basal salt solution, 2.5 mM HEPES-KOH, pH 7.4, 35 mM glucose). Three sub-regions of the brain were dissected, and RNA was isolated using the NucleoSpin RNA XS kit (Macherey-Nagel, Germany) following the manufacture’s protocol. The RNA quality and concentration were measured in the QIAxcel Advanced system (Qiagen, Germany) using QIAxcel RNA QC Kit v2.0 (Qiagen) and Qubit 3.0 fluorometer (Thermo Fisher Scientific, USA). The RNA samples with an RNA integrity score (RIS) value of more than eight were used in further processing.
Ribosomal RNA was depleted from the total RNA using the Ribo-Zero Gold rRNA removal kit (Human/Mouse/Rat) (Illumina, USA). The ribo-depleted RNA was used to create a strand-specific RNA sequencing (ssRNA-seq) library, according to the TruSeq® Stranded Total RNA sample preparation guide.

treatment_protocol: A group of zebrafish was exposed to hypoxic conditions (1.15±0.6 mg/l of dissolved oxygen)

value: hindbrain

tag: developmental stage

value: adult

value: hypoxia


title: Hidbrain hypoxic rep1

description:
Hb_novel_lnc_raw_counts.txt
Hbt1


title: Hindbrain control rep3

description:
Hb_novel_lnc_raw_counts.txt
Hbc3

value: control


title: ST02_Biofilm_PTL_ME

city: Ottawa

first: Basit

last: Yousuf

state: ON

address: 2035, Othello Avenue, Ottawa

institute: University of Ottawa

description: ST02_Biofilm_PTL_ME.MPS12302030-G01.3171.5

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were subjected to trimming to remove adaptor and low quality sequences
The transcriptome of each strain has been assembled on normalized reads using the Trinity assembler (Garber et al., 2011). Transcripts were subjected to trinotate annotation and additionally BLAT against the fully sequenced reference genome, S. epidermidis genomes RP62A.
Differential exploratory analysis was applied to the gene expression levels, quantified by the counts-per-million reads by the RSEM log2(CPM) (counts-per-million reads). Differential expression analysis was done using DESeq (Anders & Huber, 2010)
Genome_build: S. epidermidis RP62A genome (GenBank accession number: CP000029.1)
Supplementary_files_format_and_content: logCPM values; normalized raw gene counts for every gene and every sample

organism: Staphylococcus epidermidis

growth_protocol: Staphylococcus epidermiis strains (AZ22, AZ39 and ST02) were routinely cultured on Trypticase Soy Agar (TSA) or in Trypticase Soy Broth (TSB) incubated aerobically overnight at 37°C. Biofilms of staphylococcal strains were grown in TSB supplemented with 0.5% glucose (TSBg) for 24 h at 37°C.

extract_protocol:
Total RNA was isolated from the mature biofilms of S. epidermidis strains grown in TSBg or PCs using FastRNA Pro Blue (MP Biomedicals, Irvine, CA, US). All RNA samples were treated with AmbionTM DNase I (Thermo Fisher Scientific) to digest genomic DNA. Samples exposed to PCs were further treated to remove contaminating eukaryotic RNA using MICROBEEnrichTM kit (Ambion).
Ribosomal RNA (rRNA) was removed using Ribo-ZeroTM Meta-Bacteria kit (Epicentre) and strand-specific sequencing libraries were constructed using TruSeq kits (Epicentre). The generation of the cluster was performed using standard Illumina protocols with sequencing performed using an Illumina HiSeq 2500 sequencer from paired-end reads with a target read length of 100 nucleotides.

treatment_protocol: S. epidermidis strains were introduced into Platelet Concentrates and incubated for 5 days at 20-24°C with agitation in a platelet incubator. Initial bacterial concentration of ~107 CFU/ml in a final volume of 50 ml was used.

tag: genotype/variation

value: PIA+ biofilm positive

tag: sample type

value: Mature biofilm in PC


title: ST02_Biofilm2_PTL2_ME

description: ST02_Biofilm2_PTL2_ME.MPS12302030-E02.3171.7


title: ST02_Biofilm2_TSB2

description: ST02_Biofilm2_TSB2.MPS12302030-D02.3171.7

value: Mature biofilm in TSBg


title: Hindbrain control rep2

description:
Hb_novel_lnc_raw_counts.txt
Hbc2


title: ST02_Biofilm_TSB


title: Male_8HFD_Adipose_biological replicate 4

source_name: Male mouse, HFD, 8 weeks, Adipose, biological replicate 4

value: HFD, 8 weeks


title: Mock day0 rep2 [miRNA]

value: Oregon-R

value: Adult midgut

value: day 4-5

value: wild type


title: Hindbrain control rep1

description:
Hb_novel_lnc_raw_counts.txt
Hbc1


title: AZ39_PC4_Biofilm

value: PIA- biofilm positive


title: Midbrain hypoxic rep2

description:
Mb_novel_lnc_raw_counts.txt
Mbt2

value: midbrain


title: Male_8HFD_Adipose_biological replicate 3

source_name: Male mouse, HFD, 8 weeks, Adipose, biological replicate 3

value: adipose

value: 20 weeks

value: male


title: Mock day0 rep1 [miRNA]

source_name: Adult midgut

value: Sucrose


title: Midbrain hypoxic rep1

description:
Mb_novel_lnc_raw_counts.txt
Mbt1

value: adult


title: Phase1_cKit_high_CD25-_Runx3_rep1

source_name: BM progenitor-derived T  progenitor cells (DNs) in Phase1

extract_protocol:
Zymo ChIP DNA Clean & Concentrator was used to clean eluted DNA after ChIP.  For total RNA extraction, the RNeasy Micro Kit (QIAGEN) was used.
Sequencing libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB)

value: Cultured on OP9DL1

value: cKit high CD25- Phase1 stage

tag: chip antibody

value: Rabbit anti-Runx3 (provided from Dr. Levanon and Dr. Groner, Levanon et al., 2014)


title: AZ39_PC6_Biofilm

value: Mature biofilm in PC


title: Hela-porf5

city: Hengyang

first: Yating

last: Wen

state: Hunan

address: No. 28, Changsheng West Road

institute: University of South China

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: HeLa cells

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: HeLa cells were cultured and maintained in DMEM (Dulbecco’s Modified Eagle Medium; Gibco, Karlsruhe, Germany) supplemented with 10% (v/v) fetal bovine serum (FBS; Gibco) at 37℃ in 5% atmosphere.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: The pORF5 gene was cloned into pHBLV-CMV-MCS-3FLAG-EF1-ZsGreen-T2A-PURO vector using HB-infusionTM (HanBio Biotechnology CO.LTD, Shanghai, China) according to the instructions of manufacturer. When cells fused about 70%-80% in 100 mm plates, the cells were co-transfected with pHBLV-CMV-MCS-3FLAG-EF1-ZsGreen-T2A-PURO-pORF5 plasmid (or the pHBLV-CMV-MCS-3FLAG-EF1-ZsGreen-T2A-PURO control plasmid), the lentiviral packaging plasmid pSPAX2 and lentiviral envelope plasmid pMD2G. The fresh medium was added to incubate 2 days follow six-hour incubation. The medium was harvested at 72h post-transfection and centrifugation for harvest the lentivirus vector. Stable clones were selected in DMEM medium containing puromycin (2μg/ml) and 10% (v/v) FBS for 5 days.

tag: transfected with

tag: cell line

value: HeLa

value: Cervical epithelium

tag: Sex

value: Female


title: Male_8HFD_Adipose_biological replicate 2

source_name: Male mouse, HFD, 8 weeks, Adipose, biological replicate 2

tag: tissue

tag: age

tag: genotype

value: HFD, 8 weeks


title: Male_4LFD_Adipose_biological replicate 3

source_name: Male mouse, LFD, 4 weeks, Adipose, biological replicate 3

value: 16 weeks

value: LFD, 4 weeks


title: Hela-gfp

value: GFP


title: Male_8HFD_Adipose_biological replicate 1

source_name: Male mouse, HFD, 8 weeks, Adipose, biological replicate 1


title: JLAC004B

source_name: BTBR T+ Itpr3tf/J_BMDM_one dose LPS

tag: strain

value: BTBR T+ Itpr3tf/J

tag: age (years)

value: postnatal day 28

tag: cell type

value: bone marrow derived macrophage (BMDM)

tag: biological replicate

value: one dose LPS

tag: additional pcr cycles

tag: sequencing lane

tag: barcode

value: Index 2.2 5' CGTACTAG 3'

tag: molecule subtype

value: Tn5 Transposase treated DNA


title: Male_4LFD_Adipose_biological replicate 4

source_name: Male mouse, LFD, 4 weeks, Adipose, biological replicate 4

value: adipose

tag: diet

tag: gender

value: male