title: D283_1_rep2


title: RNAseq_0hr_rep2

status: Public on Oct 23 2019

type: SRA

city: Berkeley

first: Anat

last: Kreimer

state: CA

address: 378 Stanley Hall

country: USA

institute: University of California, Berkeley

library_source: transcriptomic

data_processing:
Reads were aligned to the hg19 human genome assembly with Tophat2 (Version 2.1.1; (Kim et al., 2013)), and low quality reads were removed with Trimmomatic (Version 0.3.2; (Bolger et al., 2014)). Reads that aligned to more than one gene as well as chimeric fragments were excluded.
We also removed genes that failed to be quantified in at least one sample by Cufflinks (Trapnell et al., 2010). We implemented a quality control (QC) pipeline that computes an extensive set of quality metrics, relying in part on FASTQC (Version 0.3.2; Babraham Bioinformatics) and the PICARD suite of alignment metrics (Version 2.5.0 with samtools 1.3.1).
Transcript levels were determined using RefSeq transcript annotations, and counting the number of reads aligning to every gene (defined as the union of all splice forms) with featureCounts (Version 1.5.0-p3; (Liao et al., 2014)).
Genome_build: hg19
Supplementary_files_format_and_content: featureCountsTable

molecule: total RNA

organism: Homo sapiens

source_name: Neural progenitor cells

growth_protocol: H1 hESCs were culture in mTeSR1 media on matrigel coated dishes.

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen).
Library construction was done using Illumina TruSeq Stranded Total RNA Kit.

treatment_protocol: Neural induction was performed according to dual-Smad inhibition protocol (Chambers et al., 2009) for up to 72 hours.

tag: cell type

value: H1 hESC-derived neural progenitor cells


title: Non-malignant lung 05L7_N

type: genomic

city: Vancouver

first: Katey

middle: SS

last: Enfield

state: BC

address: 675 West 10th Ave

country: Canada

institute: BC Cancer Research Centre

description: Fresh frozen non-malignant lung sample

hyb_protocol: DNA was hybridized according to manufacturer's instructions

scan_protocol: Arrays were scanned according to manufacturer's instructions

data_processing: Probe intensity files were processed in Partek Genomics Suite (Partek Incorporated, Missouri, USA). Probe sequencing, GC content, fragment length, and background adjustments were applied to correct for biases in signal intensities. DNA copy number profiles were generated in the Copy Number, Paired Analysis Workflow using patient-matched non-malignant lung as a baseline for each lung tumour sample. Segmentation was applied using stringent significance thresholds to identify regions of copy number gain and loss (signal to noise >0.3, minimum of 50 markers per segment, p-value < 10-7). Segments were merged using a 1 Mbp windown. Genomic mapping was based on the hg18 genomic build.

label: biotin

molecule: genomic DNA

source_name: Non-malignant lung

label_protocol: DNA was labeled according to manufacturer's instructions

growth_protocol: Fresh frozen tissue

extract_protocol: DNA was extracted using standard phenol:chloroform procedures

tag: tissue

value: Non-malignant lung

tag: patient

tag: sample

value: Normal

tag: age (years)

tag: Sex

value: Male

tag: race

value: Asian

tag: smoking history

value: Never

tag: pack-years

tag: Stage

tag: egfr mutation

tag: kras mutation


title: Patients_39_Training_P_39

type: RNA

city: Daejeon

first: Jin Young

last: Park

address: 24,Techno 11-ro, Yuseong-gu

country: South Korea

institute: CbsBioscience

description: 6 positive controls  and 8 negative controls were contained NanoString panel

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing: The raw data were numerical counts of each reporter barcode that hybridized with target RNA. The raw data were normalized through NanoString nSolver software. Training cohort and validation cohort normalization were separately conducted.

source_name: Locally Advanced Rectal Cancer

extract_protocol: Total RNA was extracted from FFPE tissues (n = 156) using the RNeasy FFPE kit (Qiagen, Hilden, Germany) with Deparaffinization Solution (Qiagen) and DNase I treatment (Qiagen).

tag: histology

value: Good-Response


title: RNAseq_72hr_rep1


title: D283_21_rep3

city: Liverpool

first: Sophie

last: Cowman

address: Crown Street

department: Institute of Integrative Biology

country: United Kingdom

institute: University of Liverpool

hyb_protocol: 20ug of total RNA was used in hybridisation reactions following the manufacturers protocol.

data_processing: Data was processed and analysed usung nSolverTM Analysis Software (3.0) with nCounter® Advanced Analysis plug-in (2.0.115).

source_name: D283-MED cells incubated in 21% O2 for 5 days

extract_protocol: Total RNA was extracted using a spin column based kit

treatment_protocol: Cells were incubated in 21%, 1% or 0.1% oxygen for 5 days before RNA extraction

tag: tumour type

value: Medulloblastoma

tag: oxygen percentage


title: Patients_38_Training_P_38

value: Non-Response


title: RNAseq_48hr_rep1


title: Patients_37_Training_P_37


title: RNAseq_24hr_rep1


title: D283_21_rep1


title: Lung adenocarcinoma 05L6_T

description: Fresh frozen non-malignant lung sample

source_name: Lung adenocarcinoma

value: Lung adenocarcinoma

value: Tumor

value: Female

value: IB

value: WT


title: RNAseq_12hr_rep1


title: Patients_35_Training_P_35


title: T98_0.1_rep2

source_name: T98G cells incubated in 0.1% O2 for 5 days

value: Glioblastoma


title: Lung adenocarcinoma 05L54_T

description: Fresh frozen non-malignant lung sample

value: IA

value: MUT


title: RNAseq_6hr_rep1

value: H1 hESC-derived neural progenitor cells


title: Non-malignant lung 05L6_N

description: Fresh frozen non-malignant lung sample

value: Non-malignant lung


title: T98_0.1_rep3


title: D283_21_rep2


title: Patients_34_Training_P_34


title: T98_0.1_rep1


title: Patients_33_Training_P_33


title: Non-malignant lung 05L54_N

description: Fresh frozen non-malignant lung sample

value: Normal


title: T98_1_rep3

source_name: T98G cells incubated in 1% O2 for 5 days


title: RNAseq_0hr_rep1


title: Patients_36_Training_P_36


title: RNAseq_6hr_rep2


title: Lung adenocarcinoma 05L7_T

description: Fresh frozen non-malignant lung sample

value: Male


title: Non-malignant lung 05L52_N

description: Fresh frozen non-malignant lung sample

value: Caucasian

value: Current


title: T98_1_rep2


title: 88_M: E16 Low Protein Male

city: Calgary

first: Malcolm

last: Eaton

state: AB

address: 3330 Hospital Drive NW

department: Medicine

institute: University of Calgary

description: Pooled n=3 litter mates

data_processing:
Transcripts were quantified with Kallisto 0.43.1 using Mus muluscus GRCh38 (Ensembl release 90) cDNA, with sequence bias correction turned on and 50 bootstraps
Genome_build: Mus muluscus GRCh38 (Ensembl release 90)
Supplementary_files_format_and_content: estimated transciprt counts for each sample, output from kallisto, tab-delimited.  Rows are Ensmbl transcript IDs and columns are samples

organism: Mus musculus

source_name: whole placenta

extract_protocol:
Placentas were removed, sonicated in Trizol reagent and stored at -80.
Illumina TruSeq Standed mRNA was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: strain

value: Placenta

tag: age

value: Embryonic Day 16.5

tag: diet

value: Low Protein


title: Non-malignant lung 05L49_N

description: Fresh frozen non-malignant lung sample

tag: tissue

value: Asian

value: Never


title: Patients_32_Training_P_32

value: Good-Response


title: 88_F: E16 Low Protein Female

description: Pooled n=3 litter mates

value: Female


title: T98_1_rep1


title: Patients_31_Training_P_31


title: Non-malignant lung 05L47_N

description: Fresh frozen non-malignant lung sample

tag: patient


title: Patients_30_Training_P_30

value: Non-Response


title: T98_21_rep3

source_name: T98G cells incubated in 21% O2 for 5 days

value: Glioblastoma


title: Non-malignant lung 06L10_N

description: Fresh frozen non-malignant lung sample

tag: sample


title: RNAseq_3hr_rep1

tag: cell type


title: 87_M: E16 Low Protein Male

description: Pooled n=3 litter mates

tag: Sex


title: 87_F: E16 Low Protein Female

description: Pooled n=3 litter mates


title: T98_21_rep2


title: Patients_29_Training_P_29


title: Patients_28_Training_P_28


title: Non-malignant lung 05L9_N

description: Fresh frozen non-malignant lung sample

tag: age (years)

tag: race


title: 86_M: E16 Low Protein Male

description: Pooled n=3 litter mates


title: Lung adenocarcinoma 05L52_T

description: Fresh frozen non-malignant lung sample

value: Lung adenocarcinoma

value: Tumor

tag: smoking history

tag: pack-years

value: IB

value: WT


title: T98_21_rep1


title: Non-malignant lung 05L45_N

description: Fresh frozen non-malignant lung sample

value: Non-malignant lung

value: Normal

tag: Stage

tag: egfr mutation


title: 86_F: E16 Low Protein Female

description: Pooled n=3 litter mates


title: Patients_27_Training_P_27

tag: histology


title: D566_0.1_rep3

source_name: D566-MG cells incubated in 0.1% O2 for 5 days

tag: tumour type


title: Patients_26_Training_P_26


title: 84_M: E16 Low Protein Male

description: Pooled n=3 litter mates

value: Male


title: Lung adenocarcinoma 05L47_T

description: Fresh frozen non-malignant lung sample

value: IIB

tag: kras mutation


title: Lung adenocarcinoma 05L49_T

description: Fresh frozen non-malignant lung sample


title: Lung adenocarcinoma 05L45_T

description: Fresh frozen non-malignant lung sample

value: IA


title: D566_0.1_rep2

tag: oxygen percentage


title: Non-malignant lung 05L40_N

description: Fresh frozen non-malignant lung sample


title: D566_1_rep3

source_name: D566-MG cells incubated in 1% O2 for 5 days


title: Patients_24_Training_P_24


title: Non-malignant lung 05L46_N

description: Fresh frozen non-malignant lung sample

value: Caucasian

value: Former


title: 83_M: E16 Low Protein Male

description: Pooled n=3 litter mates

tag: strain

value: Placenta

tag: age

value: Embryonic Day 16.5

value: Low Protein


title: Lung adenocarcinoma 05L43_T

description: Fresh frozen non-malignant lung sample

tag: tissue

value: Female

value: Current

value: MUT


title: Patients_25_Training_P_25

value: Non-Response


title: D566_0.1_rep1

value: Glioblastoma


title: Patients_23_Training_P_23


title: D566_1_rep2


title: Non-malignant lung 05L43_N

description: Fresh frozen non-malignant lung sample

tag: patient


title: 30_M: E16 Control Male

description: Pooled n=3 litter mates

tag: diet

value: Control


title: 83_F: E16 Low Protein Female

description: Pooled n=3 litter mates


title: Lung adenocarcinoma 05L40_T

description: Fresh frozen non-malignant lung sample

value: Lung adenocarcinoma

tag: sample

value: Tumor

value: Asian

value: Never

value: WT


title: Patients_22_Training_P_22


title: D566_1_rep1


title: Lung adenocarcinoma 05L4_T

description: Fresh frozen non-malignant lung sample

tag: Sex

value: IIB


title: Patients_21_Training_P_21


title: D566_21_rep3

source_name: D566-MG cells incubated in 21% O2 for 5 days


title: 30_F: E16 Control Female

description: Pooled n=3 litter mates


title: Lung adenocarcinoma 05L39_T

description: Fresh frozen non-malignant lung sample

tag: age (years)

value: IB


title: 29_M: E16 Control Male

description: Pooled n=3 litter mates

value: Male


title: Patients_20_Training_P_20

value: Good-Response


title: 29_F: E16 Control Female

description: Pooled n=3 litter mates

value: Placenta

value: Embryonic Day 16.5


title: Patients_19_Training_P_19


title: Non-malignant lung 05L4_N

description: Fresh frozen non-malignant lung sample

value: Non-malignant lung

value: Normal

value: Female

tag: race


title: D566_21_rep1


title: D566_21_rep2


title: 28_M: E16 Control Male

description: Pooled n=3 litter mates


title: Patients_18_Training_P_18


title: 84_F: E16 Low Protein Female

description: Pooled n=3 litter mates

value: Low Protein


title: U251_0.1_rep3

source_name: U251-MG cells incubated in 0.1% O2 for 5 days

value: Glioblastoma


title: Patients_17_Training_P_17

value: Non-Response


title: U251_0.1_rep2


title: 28_F: E16 Control Female

description: Pooled n=3 litter mates

value: Control


title: Lung adenocarcinoma 05L38_T

description: Fresh frozen non-malignant lung sample

value: Lung adenocarcinoma

value: Tumor

value: Caucasian

tag: smoking history

value: Former

value: IV

value: MUT


title: 27_M: E16 Control Male

description: Pooled n=3 litter mates

value: Male


title: Patients_16_Training_P_16

value: Good-Response


title: U251_0.1_rep1


title: Patients_15_Training_P_15


title: U251_1_rep3

source_name: U251-MG cells incubated in 1% O2 for 5 days


title: NF66_3

city: Ann Arbor

first: Robert

middle: J

last: Denver

state: Michigan

address: 1105 North University Ave

department: MCDB

institute: University of Michigan

description: NF66 MethylCap

library_source: genomic

data_processing:
Raw reads were quality processed (quality trimming, adapter removal, duplicate removal) using bbduk.sh.
Qualtiy processed reads were aligned to the X. tropicalis genome (v4.1) with Hisat2 (v2.1.0) and the --dta option, with all other defaults.
Sharp and broad peaks were called from aligned and indexed reads using PePr (v1.1.18).
Differentially bound regions were identified using PePr by using the --diff flag and setting the --normalization flag to inter-group
Sharp and broad peaks were combined using the bedops (v2.4.34) -not-element-of-1 command to add all sharp  peaks that were not partially contained within broad peaks and combine them with the  broad peaks
Sharp and broad differentially bound regions were combined as above
Genome_build: X. tropicalis genome (v4.1)
Supplementary_files_format_and_content: *peaks.bed: Called peaks from PePr, BED
Supplementary_files_format_and_content: *DMR.bed: Differentially bound peaks from PePr, BED

organism: Xenopus tropicalis

source_name: Brain (POA/hypothalamus/thalamus)

growth_protocol: We obtained wildtype (WT) Xenopus tropicalis frogs from NASCO and reared them in dechlorinated tap water at 25C under a 13L:11D photoperiod, and fed them frog brittle (NASCO, Fort Atkinson, WI) or Sera Micron plankton food (tadpoles only).

extract_protocol:
We isolated genomic DNA from tadpole brain using the We isolated genomic DNA using the DNeasy Blood and Tissue kit (Qiagen), and sonicated the DNA to an average size of 400 bp using a Covaris S2 sonicator (Covaris, Woburn, MA).
The sequencing libraries were constructed on the Apollo instrument (an automated system) using IntegenX reagents (now Wafergen, Fremont, CA) at the University of Michigan DNA sequencing core. We sequenced the libraries on Illumina HiSeq 2000 using High Output mode (50 bp, single-end).

tag: genotype

value: Wild type

value: middle brain region containing preoptic area/hypothalamus/thalamus

tag: developmental stage


title: NF66_2

description: NF66 MethylCap


title: U251_1_rep1


title: Non-malignant lung 05L38_N

description: Fresh frozen non-malignant lung sample

value: Non-malignant lung

tag: pack-years

tag: Stage

tag: egfr mutation


title: NF66_1

description: NF66 MethylCap


title: Patients_14_Training_P_14

tag: histology


title: 25_F: E16 Control Female

description: Pooled n=3 litter mates

value: Placenta

value: Embryonic Day 16.5


title: Patients_12_Training_P_12


title: Patients_13_Training_P_13


title: U251_21_rep3

source_name: U251-MG cells incubated in 21% O2 for 5 days

tag: tumour type

tag: oxygen percentage


title: 25_M: E16 Control Male

description: Pooled n=3 litter mates

tag: strain

tag: age


title: PA14T3

city: Geneva

first: Thilo

last: Kohler

address: 1, rue Michel Servet

department: Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva

data_processing:
sequencing quality was assessed using FastQC v.0.11.5
average mapping rate: 98.4%
The differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR v. 3.26.4
The differentially expressed genes p-values are corrected for multiple testing error with a 5% FDR (false discovery rate).
The correction used is Benjamini-Hochberg (BH)
Genome_build: The reads were mapped with BWA aligner v.0.7.17 (mem) to the NCBI NC_008463.1 PA14 reference genome
Supplementary_files_format_and_content: dtata files are excel spread sheets with fold-change values: one spreadsheet each for for treatment with Pmx-B, G3KL or T7

organism: Pseudomonas aeruginosa PA14

source_name: in vitro grown bacterial cells

growth_protocol: MHB medium

extract_protocol:
RNA was extracted after 16 h growth at 37 oC in microtiter plates using the RNAeasy kit (Qiagen)
SR100 – libraries Truseq HT, ribodepleted stranded RNA
ribo depletion was performed with Ribo-Zero (Epicenter)

treatment_protocol: presence or absence of 0.25 x the MIC of either Polymyxin B, dendrimer G3KL or dendrimer T7

tag: treatment

value: treated with 0.25 x MIC T7

tag: replicate

tag: molecule

value: ribo-depleted total RNA


title: Non-malignant lung 05L39_N

description: Fresh frozen non-malignant lung sample

tag: tissue

tag: patient

tag: sample

value: Normal

tag: Sex

value: Female

value: Asian

value: Never

tag: kras mutation


title: Patients_11_Training_P_11

value: Non-Response


title: NF62_2

description: NF62 MethylCap

tag: genotype

tag: developmental stage


title: PA14T2


title: Patients_10_Training_P_10


title: U251_21_rep2

value: Glioblastoma


title: 27_F: E16 Control Female

description: Pooled n=3 litter mates

tag: diet

value: Control


title: Lung adenocarcinoma 05L33_T

description: Fresh frozen non-malignant lung sample

value: Lung adenocarcinoma

value: Tumor

tag: age (years)

tag: race

value: Caucasian

tag: smoking history

value: Former

tag: pack-years

tag: Stage

value: IB

tag: egfr mutation

value: WT

value: MUT


title: NF62_1

description: NF62 MethylCap

value: Wild type

value: middle brain region containing preoptic area/hypothalamus/thalamus


title: U251_1_rep2

tag: tumour type

tag: oxygen percentage


title: Lung adenocarcinoma 05L46_T

description: Fresh frozen non-malignant lung sample

value: IIB


title: NF62_3

description: NF62 MethylCap


title: Patients_9_Training_P_9

tag: histology


title: U87_0.1_rep3

source_name: U87-MG cells incubated in 0.1% O2 for 5 days


title: NF56_3

description: NF56 MethylCap

tag: tissue


title: Non-malignant lung 05L34_N

description: Fresh frozen non-malignant lung sample

source_name: Non-malignant lung

value: Non-malignant lung

tag: patient

value: Normal


title: PA14G2

tag: treatment

value: treated with 0.25 x MIC G3KL

tag: replicate

tag: molecule

value: ribo-depleted total RNA


title: PA14G3


title: NF56_2

description: NF56 MethylCap

tag: genotype


title: U87_0.1_rep2


title: Patients_8_Training_P_8

source_name: Locally Advanced Rectal Cancer

value: Non-Response


title: NF56_1

description: NF56 MethylCap

tag: developmental stage


title: PA14T1

value: treated with 0.25 x MIC T7


title: PA14G1


title: U87_0.1_rep1

value: Glioblastoma


title: PA14P3

value: treated with 0.25 x MIC of polymyxin B


title: NF50_3

description: NF50 MethylCap


title: Patients_6_Training_P_6

value: Good-Response


title: Non-malignant lung 05L27_N

description: Fresh frozen non-malignant lung sample

tag: sample

tag: Sex

value: Female

value: Asian

value: Never

tag: kras mutation


title: NF50_2

description: NF50 MethylCap


title: Patients_5_Training_P_5


title: Non-malignant lung 05L33_N

description: Fresh frozen non-malignant lung sample

tag: age (years)

value: Male

tag: race

value: Caucasian

tag: smoking history

value: Former


title: NF50_1

description: NF50 MethylCap

value: Wild type

value: middle brain region containing preoptic area/hypothalamus/thalamus


title: U87_1_rep2

source_name: U87-MG cells incubated in 1% O2 for 5 days


title: Non-malignant lung 05L32_N

description: Fresh frozen non-malignant lung sample

value: Non-malignant lung

value: Current

tag: pack-years

tag: Stage

tag: egfr mutation


title: U87_1_rep1

tag: tumour type

tag: oxygen percentage


title: Patients_3_Training_P_3

tag: histology


title: Lung adenocarcinoma 05L27_T

description: Fresh frozen non-malignant lung sample

source_name: Lung adenocarcinoma

tag: tissue

value: Lung adenocarcinoma

tag: patient

value: Tumor

value: IIB

value: MUT

value: WT


title: Patients_7_Training_P_7

value: Non-Response


title: U87_1_rep3

value: Glioblastoma


title: PA14P1

tag: treatment

value: treated with 0.25 x MIC of polymyxin B

tag: replicate

tag: molecule

value: ribo-depleted total RNA


title: Lung adenocarcinoma 05L34_T

description: Fresh frozen non-malignant lung sample

tag: sample

value: Female

value: Asian

value: Never

value: IB


title: Non-malignant lung 05L13_N

description: Fresh frozen non-malignant lung sample

value: Normal

tag: Sex

value: Male


title: PA14P2


title: PA14C2

value: untreated


title: Input_2

description: NF56 Input

tag: genotype

value: Wild type

value: middle brain region containing preoptic area/hypothalamus/thalamus

tag: developmental stage


title: U87_21_rep2

source_name: U87-MG cells incubated in 21% O2 for 5 days


title: Non-malignant lung 05L19_N

description: Fresh frozen non-malignant lung sample

value: Non-malignant lung

tag: age (years)

tag: race

value: Caucasian

value: Current

tag: kras mutation


title: Lung adenocarcinoma 05L19_T

description: Fresh frozen non-malignant lung sample

value: Lung adenocarcinoma

value: Tumor

tag: smoking history

tag: pack-years

tag: Stage

value: IV

value: WT


title: Input_1

description: NF50 Input


title: PA14C1

value: ribo-depleted total RNA


title: U251_21_rep1

tag: tumour type

value: Glioblastoma

tag: oxygen percentage


title: U87_21_rep1


title: Patients_2_Training_P_2

tag: histology

value: Non-Response


title: Non-malignant lung 05L10_N

description: Fresh frozen non-malignant lung sample

tag: tissue

tag: patient

value: Female

value: Former

tag: egfr mutation


title: rBEL Low GC 2

status: Public on Oct 22 2019

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

description:
Distal biopsy sample from right lateral lobe (same rBEL constuct as "rBEL Low GC 1")
Core Sample ID:
19053008169_2_2_14
sample name:
CP #2

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: reendothelialized bioengineered liver contructs (rBELs)

extract_protocol:
RNA was extracted using the solution indicated with each samples. mRNA isolation for all samples was performed using the Direct-zol RNA Miniprep Kit (Zymo Research).
mRNA version 2 library prep kit (Illumina)

tag: culture format

value: 3D (Perfusion Bioreactor)

tag: rna extraction solution

value: RNA Later

tag: glucose consumption phase

value: low


title: rBEL High GC 6 (HUVEC)

description:
Mid section biopsy.
Core Sample ID:
19053008183_16_2_14
sample name:
CP #16

value: RNA Later/Trizol

value: reendothelialized bioengineered liver contructs (rBELs)

value: high


title: rBEL High GC 5 (HUVEC)

description:
Mid section biopsy.
Core Sample ID:
19053008178_11_2_14
sample name:
CP #11


title: rBEL High GC 4 (HUVEC)

description:
Mid section biopsy.
Core Sample ID:
19053008175_8_2_14
sample name:
CP #8


title: HLSEC

description:
Core Sample ID:
19053008180_13_2_14
sample name:
CP #13

source_name: Human liver tissue (Cell Systems ACBRI 566)

value: 2D (Standard cell culture plastic)

value: human liver sinusoidal endothelial cells (HLSECs)


title: rBEL Low GC 1

description:
Proximal biopsy sample from right lateral lobe (same rBEL constuct as "rBEL Low GC 2")
Core Sample ID:
19053008168_1_2_14
sample name:
CP #1


title: rBEL High GC 1 (HUVEC)

description:
Proximal biopsy sample from right lateral lobe (same rBEL contruct as "rBEL High GC 2")
Core Sample ID:
19053008172_5_2_14
sample name:
CP #5


title: rBEL High GC 3 (HUVEC)

description:
Mid section biopsy.
Core Sample ID:
19053008174_7_2_14
sample name:
CP #7


title: Lung adenocarcinoma 05L32_T

description: Fresh frozen non-malignant lung sample

value: Lung adenocarcinoma

tag: sample

tag: Sex

value: Male

value: Caucasian

value: Current

value: IIB


title: HUVEC

description:
Core Sample ID:
19053008179_12_2_14
sample name:
CP #12

source_name: Human umbilical vein

value: Human umbilical vein (HUVEC)


title: Patients_1_Training_P_1

value: Non-Response


title: GCNA-2

city: Dallas

first: Michael

last: Buszczak

state: Texas

address: 5323 Harry Hines Boulevard

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

description:
GCNA-/-
total RNA including small RNA species (18 nt upwards)

data_processing:
Basecalls were performed using CASAVA (v. 1.8.2)
Reads were aligned to dm6 geneome assembly and transcript assembly was performed using STAR (v.2.5)
Normalized expression calculation and differential expression analysis was performed using DESeq2
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each sample …

organism: Drosophila melanogaster

source_name: GCNA-/-

extract_protocol:
Used standard protocol from Qiagen miRNEasy kit with on columnb Qiagen DNAse digest to remove and contaminating DNA species.
From the NGS core at UTSouthwestern: Total RNA is depleted of its rRNA and fragmented before strand specific cDNA synthesis. cDNA are then a-tailed and indexed adapters are ligated. After adapter ligation, samples are PCR amplified and purified with Ampure XP beads, then validated again on the Agilent 2100 Bioanalyzer. Samples are quantified by Qubit before being normalized and pooled, then run on the Illumina HiSeq 2500 using SBS v3 reagents.

treatment_protocol: 0-2 day old Drosophila females were collected from actively growing stocks of wildtype or GCNAKO and fed on wet yeast for 24 hours before dissection, collection of ovaries and RNA extraction.  All stocks were maintained at room temperature (25°C) and fed on standard feed.

tag: strain

value: GCNA null, generated by knockin-knockout CRISPR construct-outcrossed to wBerlin for 10 generations

value: ovary

tag: age

value: 1-3 days old


title: rBEL High GC 2 (HUVEC)

description:
Distal biopsy sample from right lateral lobe (same rBEL contruct as "rBEL High GC 1")
Core Sample ID:
19053008173_6_2_14
sample name:
CP #6

value: 3D (Perfusion Bioreactor)


title: PA14C3

tag: treatment

value: untreated

tag: replicate

tag: molecule

value: ribo-depleted total RNA


title: GCNA-1


title: WT-3

description:
wildtype
total RNA including small RNA species (18 nt upwards)

source_name: wildtype

value: wBerlin


title: WT-1


title: WT-2


title: Lung adenocarcinoma 05L13_T

description: Fresh frozen non-malignant lung sample

value: Tumor

tag: age (years)

tag: race

value: Asian

tag: smoking history

value: Never

tag: pack-years

tag: Stage

value: IB

value: MUT

tag: kras mutation

value: WT


title: Non-malignant lung 05L12_N

description: Fresh frozen non-malignant lung sample

tag: tissue

value: Non-malignant lung

tag: patient

value: Normal

value: Male

tag: egfr mutation


title: Lung adenocarcinoma 05L10_T

description: Fresh frozen non-malignant lung sample

value: Lung adenocarcinoma

value: Female

value: Caucasian

value: Former

value: IA


title: P1_Maternal_CD45neg_1

city: Singapore

first: Vipin

last: Narang

address: Immunos #04-01, 8A Biomedical Grove, Singapore-138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

description:
PolyA RNA
processed data file: gene_abundances_rawcounts.txt
processed data file: gene_abundances_TPM.txt

data_processing:
Quality assessment of the RNA sequencing reads was performed using FASTQC (version 0.11.5; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Cutadapt (version 1.2.1) was used to remove Illumina adapter sequences with option -O 3 so that the 3' end of any reads that matched the adapter sequence for ≥3 bp were trimmed. The reads were further trimmed using Sickle (version 1.20; https://github.com/najoshi/sickle) with a minimum window quality score of 20. Reads <10 bp after trimming were removed.
The resulting clean, paired-end reads were mapped to human transcript sequences obtained from Gencode (version 27) using Salmon (version 0.9.1). Transcript abundances quantified by Salmon were summarized to gene-level counts and normalized gene-level abundances in transcript per million (TPM) units using the tximport R/Bioconductor package (version 1.2.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: The processed data files are in tab-delimited text format and contain (i) a matrix of gene-level counts, and (ii) a matrix of normalized gene-level abundances in transcript per million (TPM) units.

source_name: Placenta disc

growth_protocol: Placenta was separated into the foetal membrane (chorion and amnion) and placenta disc (chorionic villi) layers. The tissues were finely diced in a digestion medium containing collagenase type 4 (0.2mg/ml) and DNase (0.05mg/ml) prepared in Roswell Park Memorial Institute medium (GE Healthcare Life Sciences, Pittsburgh, PA, USA) containing 10% Fetal Bovine Serum (ThermoFisher Scientific, Waltham, MA, USA). The foetal membranes were incubated in digestion medium for 3 h in a 37°C incubator supplemented with 5% CO2. The foetal cells were then centrifuged (400 g, 5 min) and repeatedly washed with PBS to remove traces of digestion medium before red blood cell (RBC) lysis. Lysis was done with in-house RBC lysing solution containing 155 mM NH4C1 (Sigma Aldrich), 10 mM KHCO3 (Sigma Aldrich) and 0.1 mM EDTA (ThermoFisher Scientific). Lysed cells were then enumerated and used for downstream procedures. The placenta disc was incubated in digestion medium for 1 h, and then the digestion medium was carefully overlaid on Ficoll-Paque Plus (GE Healthcare Life Sciences) at a ratio of 2:1, respectively. The samples were then centrifuged at 1,600 g for 20 min (with minimal acceleration and deceleration) to isolate the "buffy coat" containing leucocytes. The leucocytes were carefully removed and traces of RBCs were subsequently lysed. The cells were enumerated and used for downstream procedures. In both cases, the digestion medium was filtered through a 100μM filter unit after digestion to remove any undigested tissues. The volume of medium used was adjusted according to the size of the tissue being digested. Antibodies were used to identify CD45+ leucocytes (mouse anti-human CD45, Biolegend, California, CA, USA) for acquisition on a LSR Fortessa (BD Biosciences).

extract_protocol:
RNA samples, extracted from the fractions of isolated placental cells, were treated with DNase using an Ambion Turbo DNA-free Kit (ThermoFisher Scientific), and then purified using Ampure XP beads (Beckman Coulter). The DNase-treated RNA (2 μg) was treated with Ribo-Zero using an Epicentre Ribo-Zero Gold Kit (Human/Rat/Mouse) (Illumina, San Diego, CA, USA) and re-purified on Ampure XP beads. Successful RNA depletion was verified using a Qubit (ThermoFisher Scientific) and an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA) and all depleted RNA was used as input material for the ScriptSeq v2 RNA-Seq Library Preparation protocol.
RNA was amplified for 14 cycles and the libraries were purified on Ampure XP beads. Each library was quantified using a Qubit and the size distribution was assessed using an AATI Fragment Analyser (Agilent); the final libraries were pooled in equimolar amounts. The quantity and quality of each pool was assessed using a Fragment Analyser and by qPCR using an Illumina Library Quantification Kit (KAPA Biosystems, Wilmington, Massachusetts, USA) on a Light Cycler LC480II (Roche, Basel, Switzerland), according to manufacturer's instructions. The template DNA was denatured according to the protocol described in the Illumina cBot User guide and loaded at a 12 pM concentration. Sequencing was carried out on three lanes of an Illumina HiSeq 2500 with version 4 chemistry, generating 2 × 125 bp paired-end reads.

tag: condition

value: Zika (Trimester 1)

value: Maternal CD45-

tag: individual


title: P1_Maternal_CD45neg_2


title: P2_Fetal_3

source_name: Foetal membrane of placenta

value: Zika (Trimester 2)

value: Fetal membrane


title: P2_Maternal_CD45neg_2


title: P2_Maternal_CD45neg_1


title: P1_Maternal_CD45pos_1

value: Maternal CD45+


title: P2_Maternal_CD45pos_3


title: P2_Maternal_CD45neg_3


title: P3_Fetal_All

value: Zika (Trimester 3)


title: P1_Maternal_CD45pos_2


title: P1_Fetal_3


title: P3_Maternal_CD45neg_All


title: P1_Maternal_CD45pos_3


title: P2_Maternal_CD45pos_1


title: P2_Fetal_1


title: P3_Maternal_CD45pos_All


title: P2_Maternal_CD45pos_2


title: P2_Fetal_2


title: P1_Fetal_1


title: P1_Fetal_2


title: P1_Maternal_CD45neg_3


title: H2_Maternal_CD45pos_3

value: Healthy


title: U87_21_rep3

tag: tumour type

value: Glioblastoma

tag: oxygen percentage


title: H2_Maternal_CD45pos_2


title: H2_Maternal_CD45pos_1


title: Lung adenocarcinoma 05L12_T

description: Fresh frozen non-malignant lung sample

tag: sample

value: Tumor

tag: Sex

value: Asian

value: Never

value: IIIA

value: MUT

value: WT


title: H2_Maternal_CD45neg_3


title: H1_Maternal_CD45pos_All


title: H2_Maternal_CD45neg_2


title: H1_Maternal_CD45neg_All


title: H2_Fetal_3


title: H2_Maternal_CD45neg_1


title: H2_Fetal_1


title: 5B CBFB KO Selumetinib 3912_10_TS10_TAGCTTA

city: Amsterdam

first: Evert

last: Bosdriesz

address: De Boelelaan 1111

department: Computer Science

country: Netherlands

institute: VU University Amsterdam

description:
CBFB-B_Sel
processed data file: readcounts-lovo-b9.tsv

data_processing:
DESeq2 was used for RNA-seq data normalization.
The differential expression was based on the ratio of normalized read counts (FPKM, after library size correction).
An absolute fold-change threshold of 2 was used. Genes with a coverage <50 in both conditions were excluded from the analyses to prevent spurious results.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: readcounts-lovo-b9.tsv: Tab-separated text file includes gene counts and gene annotation for all samples.

source_name: LoVo ERN1 knockout cells (5B)

growth_protocol: LoVo ERN1 knockout cells harboring CRISPR constructs were cultured in RPMI (+10% FBS, +1% pen/strep) at 37C in 5% CO2.

extract_protocol:
RNA extraction using Trizol.
Stranded RNA libraries were prepared for sequencing according to Illumina instructions.

treatment_protocol: Cells were plated (1 million cells / 10cm dish) in RPMI (+10% FBS, +1% pen/strep) at 37C in 5% CO2. The following day, selumetinib (1 uM) or vehicle was added, and cells were cultured for 2 days before harvesting using Trizol.

tag: cell line

value: LoVo

tag: cell type

value: Colorectal cancer cells

tag: genotype/variation

value: ERN1/CBFB double KO

tag: treatment

value: Selumetinib


title: 5B RUNX2 Selumetinib 3912_6_TS6_ACTTGAA

description:
RUNX2-A_Sel
processed data file: readcounts-lovo-b9.tsv

value: ERN1/RUNX2 double KO


title: H1_Fetal_All


title: 5B Selumetinib 3912_4_TS4_ATCACGA

description:
5B_Sel
processed data file: readcounts-lovo-b9.tsv

value: ERN1 KO


title: H2_Fetal_2

value: Fetal membrane


title: 5B RUNX2 vehicle control 3912_5_TS5_TTAGGCA

description:
RUNX2-A_UT
processed data file: readcounts-lovo-b9.tsv

value: Vehicle


title: 5B vehicle control 3912_3_TS3_GTGAAAC

description:
5B_UT
processed data file: readcounts-lovo-b9.tsv


title: 5B CBFB KO vehicle control 3912_9_TS9_GATCAGA

description:
CBFB-B_UT
processed data file: readcounts-lovo-b9.tsv


title: B7M LO

city: Durham

first: Kevin

middle: Matthew

last: Byrd

state: North Carolina

address: 4134 Brenmar Lane

department: Pathology and Laboratory Medicine

institute: The University of North Carolina

data_processing:
Illumina output data was first processed using Illumina’s bcl2fastq pipeline (v.2.20.0). Quality control of the samples was performed using FastQC.
RNA-seq fastq files were trimmed and aligned to the latest mouse genome, mm10 (GRCm38/GCA_000001635.2) using BBMap
A matrix of the data was generated using featureCounts. RNAseq data was analyzed with DESeq2 (Love et al., 2014),
All statistical analyses were performed using R version 3.4.1 and RStudio version 1.0.143.
Genome_build: mm10

source_name: K5-tTA; tetO-H2B-GFP (GFP-LO)

extract_protocol:
Hard palates (rugae 1-8) were microdissected and immediately transferred to 12-well plates with 1 mL of PBS and kept on ice. 500 µL 1x dispase (Life Technologies) was added to each palate and incubated for 1 hour at 37°C. Dissecting forceps (Roboz) were used to peel the epithelia from the underlying lamina propria and scissors/forceps were used to physically separate the epithelia into smaller pieces. Further isolation of basal palatal cells was adapted from the epidermal method of (Nowak and Fuchs, 2009). Palatal epithelia were transferred to a new 12-well plate with 0.25% Trypsin-EDTA. After 60 min incubation at 37°C with vigorous shaking, samples were triturated with P1000 pipette tips precoated with FACS buffer (PBS + 1% FBS) several times to suspend basal epithelial cells. Single cells were isolated using a 35 μm Falcon cell strainer (Thermo Fisher), rinsed with 2 mL of epidermal low calcium medium (E low Ca2+, and then centrifuged for 5 minutes at RT/300x g. The cell pellet was resuspended in FACS buffer and stored on ice. To isolate basal cells by FACS, Rat anti-CD49f-Alexa Fluor® 647 (α6-Integrin, BioLegend) was added to cells and incubated for 60 min on ice. Sytox® Dead Cell Stain (Thermo Fisher, 1:1000) was added 5 minutes before FACS to evaluate cell viability. FACS was performed on a Sony SH800S Cell Sorter, with the following single-channel compensation controls: unchased GFP palatal epithelial cells, anti-CD49f:Alexa Fluor® 647 negative, and Sytox® Dead Cell Stain negative cell suspensions
RNA was isolated from 200-1000 cells and libraries prepared using the SoLo RNA-Seq library preparation kit (NuGEN).

value: Palatal Basal Epithelial Stem Cells

tag: strain

value: FVB

value: palate

tag: age

tag: genotype

tag: type

value: GFP-LO (Frequently Dividing Cells)


title: B3M LO

tag: tissue


title: B4M HI

source_name: K5-tTA; tetO-H2B-GFP (GFP-HI)

value: GFP-HI (Infrequently Dividing Cells)


title: B3M HI


title: B1M HI


title: B5M HI


title: B7M HI


title: B5M LO


title: B7F HI


title: B4M LO


title: B7F LO


title: WT AsiSI MEFS ENDseq rep2

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

country: China

data_processing:
Library strategy: END-seq
mouse reads were aligned to the GRCm38p2/mm10.Alignment done using bowtie version 1.1.2, with the parameters: -l 50 -n 3 -k 1.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were made for plus (*.plus.bw) and minus (*.neg.bw) strand separately using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Cells are grown in DMEM containing 10% FBS and 1% P/S

extract_protocol:
MEFs were harvested and 9 million cells were embedded in agarose plugs,  after which END-seq was performed as previously described (Canela et al., 2016)
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).  libraries were prepared and sequenced following standard Illumina protocols

treatment_protocol: Exponentially AsiSI-expressing MEFs were treated with 1uM doxocyclin (DOX) for 24 hours and then, for 5 hours with 4-OHT, resulting in the nuclear translocation of AsiSI

value: Mouse Embryonic Fibroblasts

tag: expression

value: AsiSI


title: BRCA1-/- AsiSI MEFS ENDseq rep2

institute: Center for Excellence in Molecular Cell Science


title: B1M LO


title: 53BP1-/- AsiSI MEFS ENDseq


title: WT AsiSI MEFS Rad51 ChIP-seq without FHA-PALB2

data_processing:
adapters was removed by trimmomatic version 0.36
mouse reads were aligned to the GRCm38p2/mm10.Alignment done using bowtie version 1.1.2, with the parameters: -l 50 -n 2 -m 1.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were made for plus (*.plus.bw) and minus (*.neg.bw) strand separately using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

extract_protocol:
Twenty million cells were harvested for chromatin immunoprecipitation (ChIP) using an anti-RAD51 (10ug/sample) or anti-RPA antibody (10ug/sample).  ssDNA that spontaneously forms hairpins after heat renaturation was then enriched and sequenced as described (Brick et al., 2018)
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).  libraries were prepared and sequenced following standard Illumina protocols

tag: chip antibody


title: 53BP1_S25A AsiSI MEFS ENDseq


title: WT AsiSI MEFS ENDseq rep1


title: BRCA1-/- AsiSI MEFS ENDseq rep1


title: BRCA1-/- 53BP1-/- AsiSI MEFS ENDseq


title: BRCA1-/- 53BP1_S25A AsiSI MEFS ENDseq


title: BRCA1-/- 53BP1_S25A AsiSI MEFS Rad51 ChIP-seq without FHA-PALB2


title: 53BP1-/- AsiSI MEFS RPA ChIP-seq

value: RPA Abcam #10359


title: WT AsiSI MEFS Rad51 ChIP-seq with FHA-PALB2

value: WT


title: BRCA1-/- AsiSI MEFS RPA ChIP-seq


title: BRCA1-/- 53BP1_S25A AsiSI MEFS Rad51 ChIP-seq with FHA-PALB2


title: BRCA1-/- AsiSI MEFS Rad51 ChIP-seq with FHA-PALB2


title: WT AsiSI MEFS RPA ChIP-seq


title: BRCA1-/- AsiSI MEFS Rad51 ChIP-seq without FHA-PALB2


title: mpUL3NCBC30

city: Cambridge

first: David

middle: Michael

last: Mauger

state: MA

address: 200 Technology Square

department: Platform Research

institute: Moderna, Inc.

data_processing:
Library strategy: SHAPE-MaP
Reads from SHAPE-MaP libraries were processed with default settings in SHAPEMapper pipeline version 1.2:
1. Reads from 'DEN', 'MOD', and 'NC' samples are mapped to the reference transcripts in Bowtie2
2. Mutation frequencies are calculated for each base in the samples
3. SHAPE reactivities are calculated form 'p', 'm', and 'd' mutational fre
Genome_build: Custom
Supplementary_files_format_and_content: .tab.txt files include the read depths, standard errors and SHAPE reactivity of each base. Column "Normalized reactivity" is the SHAPE reactivity.

organism: synthetic construct

source_name: Luciferase mRNA L3 with pmU

extract_protocol:
Treated RNAs were purified with Ampure beads
SHAPE-MaP reverse transcript, NEBnext Ultra II RNA library prep kit for illumina

treatment_protocol: RNA were treated as described

tag: nucleotide chemistry

value: RNA contains 1-methyl-psuedouridine

value: RNA treated with DMSO


title: mpUL8DENBC22

source_name: Luciferase mRNA L8 with pmU

value: RNA heat denatured at 95C and treated with 1M6 in DMSO


title: mpUL38NCBC154

source_name: Luciferase mRNA L38 with pmU


title: mpUL4MODBC176

source_name: Luciferase mRNA L4 with pmU

value: Folded RNA treated with 1M6 in DMSO at 37C


title: mpUL6DENBC23

source_name: Luciferase mRNA L6 with pmU


title: mpUL7DENBC19

source_name: Luciferase mRNA L7 with pmU


title: mpUL39NCBC22

source_name: Luciferase mRNA L39 with pmU


title: mpUL5NCBC32

source_name: Luciferase mRNA L5 with pmU


title: mpUL7NCBC17


title: mpUL9NCBC3

source_name: Luciferase mRNA L9 with pmU


title: mpUL5MODBC177


title: mpUL39DENBC24


title: mpUL3MODBC175


title: mpUL6NCBC33


title: mpUL39MODBC23


title: mpUL8MODBC21


title: mpUL3DENBC20


title: mpUL7MODBC18


title: mpUL4DENBC21


title: mpUL8NCBC20


title: mpUL5DENBC22


title: mpUL9MODBC4


title: mpUL4NCBC31


title: mpUL9DENBC5


title: mpUL6MODBC178


title: mpUL38DENBC204


title: Input_3

description: NF62 Input

source_name: Brain (POA/hypothalamus/thalamus)

value: Wild type

value: middle brain region containing preoptic area/hypothalamus/thalamus

tag: developmental stage


title: mpUL38MODBC69


title: mpUL36MODBC20

source_name: Luciferase mRNA L36 with pmU


title: mpUL36NCBC19


title: mpUL37DENBC29

source_name: Luciferase mRNA L37 with pmU


title: mpUL35MODBC182

source_name: Luciferase mRNA L35 with pmU


title: mpUL35DENBC27


title: mpUL34MODBC68

source_name: Luciferase mRNA L34 with pmU


title: mpUL37MODBC184


title: mpUL35NCBC37


title: mpUL30MODBC67

source_name: Luciferase mRNA L30 with pmU


title: mpUL31MODBC180

source_name: Luciferase mRNA L31 with pmU


title: mpUL32MODBC181

source_name: Luciferase mRNA L32 with pmU


title: mpUL34NCBC153


title: mpUL2NCBC14

source_name: Luciferase mRNA L2 with pmU


title: mpUL33MODBC17

source_name: Luciferase mRNA L33 with pmU


title: mpUL36DENBC21


title: mpUL32DENBC26


title: mpUL31NCBC35


title: mpUL33DENBC18


title: mpUL32MODBC39


title: mpUL32NCBC36


title: mpUL32DENBC40


title: GCNA-3

source_name: GCNA-/-

value: GCNA null, generated by knockin-knockout CRISPR construct-outcrossed to wBerlin for 10 generations

value: ovary

value: 1-3 days old


title: mpUL31DENBC25


title: mpUL30DENBC202


title: Patients_4_Training_P_4

description: 6 positive controls  and 8 negative controls were contained NanoString panel

source_name: Locally Advanced Rectal Cancer

tag: histology

value: Non-Response


title: mpUL37NCBC39


title: mpUL32NCBC38


title: mpUL33NCBC16


title: mpUL34DENBC203


title: mpUL30NCBC152


title: mpUL2MODBC15


title: mpUL29NCBC35

source_name: Luciferase mRNA L29 with pmU


title: mpUL29MODBC36


title: mpUL29DENBC37


title: mpUL28NCBC150

source_name: Luciferase mRNA L28 with pmU


title: mpUL28MODBC65


title: mpUL27MODBC11

source_name: Luciferase mRNA L27 with pmU


title: mpUL26NCBC149

source_name: Luciferase mRNA L26 with pmU


title: mpUL26MODBC64


title: mpUL27NCBC10


title: mpUL26DENBC9


title: mpUL26NCBC7


title: mpUL25NCBC148

source_name: Luciferase mRNA L25 with pmU


title: mpUL27DENBC12


title: mpUL26MODBC8


title: mpUL25DENBC198


title: mpUL24NCBC27

source_name: Luciferase mRNA L24 with pmU


title: mpUL24MODBC33


title: mpUL25MODBC63


title: mpUL24MODBC28


title: mpUL24DENBC29


title: mpUL23NCBC147

source_name: Luciferase mRNA L23 with pmU


title: mpUL2DENBC16


title: mpUL23DENBC197


title: mpUL22NCBC29

source_name: Luciferase mRNA L22 with pmU


title: mpUL23MODBC62


title: mpUL28DENBC200


title: mpUL22MODBC30


title: mpUL22DENBC31


title: mpUL26DENBC199


title: mpUL21NCBC6

source_name: Luciferase mRNA L21 with pmU


title: mpUL21MODBC7


title: mpUL20NCBC9

source_name: Luciferase mRNA L20 with pmU


title: mpUL24NCBC32


title: mpUL20DENBC11


title: mpUL1NCBC11

source_name: Luciferase mRNA L1 with pmU


title: mpUL20MODBC10


title: mpUL19NCBC24

source_name: Luciferase mRNA L19 with pmU


title: mpUL1DENBC13


title: mpUL18NCBC26

source_name: Luciferase mRNA L18 with pmU


title: mpUL18DENBC28


title: mpUL24DENBC34


title: mpUL19MODBC25


title: mpUL17MODBC5

source_name: Luciferase mRNA L17 with pmU


title: mpUL1MODBC12


title: mpUL17NCBC4


title: mpUL16NCBC21

source_name: Luciferase mRNA L16 with pmU


title: mpUL16MODBC22


title: mpUL16DENBC23


title: mpUL15NCBC23

source_name: Luciferase mRNA L15 with pmU


title: mpUL15MODBC24


title: mpUL15NCBC34


title: mpUL15DENBC24


title: mpUL15MODBC179


title: mpUL21DENBC8


title: mpUL15DENBC25


title: mpUL14MODBC19

source_name: Luciferase mRNA L14 with pmU


title: mpUL14NCBC18


title: mpUL13NCBC12

source_name: Luciferase mRNA L13 with pmU


title: mpUL14DENBC20


title: mpUL13MODBC13


title: mpUL18MODBC27


title: mpUL19DENBC26


title: mpUL12MODBC16

source_name: Luciferase mRNA L12 with pmU


title: mpUL13DENBC14


title: mpUL12DENBC17


title: mpUL11DENBC196

source_name: Luciferase mRNA L11 with pmU


title: mpUL12NCBC15


title: mpUL10MODBC2

source_name: Luciferase mRNA L10 with pmU


title: mpUL11NCBC146


title: mpUL10DENBC3


title: moUL9NCBC40

source_name: Luciferase mRNA L9 with moU

value: RNA contains 5-methoxyuridine


title: moUL9MODBC10


title: mpUL11MODBC61


title: mpUL17DENBC6


title: mpUL10NCBC1


title: moUL9DENBC88


title: moUL8NCBC30

source_name: Luciferase mRNA L8 with moU


title: moUL7NCBC27

source_name: Luciferase mRNA L7 with moU


title: moUL8DENBC32


title: moUL7MODBC28


title: moUL8MODBC31


title: moUL6NCBC12

source_name: Luciferase mRNA L6 with moU


title: moUL7DENBC29


title: moUL6DENBC14


title: moUL6MODBC13


title: moUL5DENBC17

source_name: Luciferase mRNA L5 with moU


title: moUL5MODBC16


title: moUL3NCBC9

source_name: Luciferase mRNA L3 with moU


title: moUL4MODBC19

source_name: Luciferase mRNA L4 with moU


title: moUL4DENBC20


title: moUL3MODBC10


title: moUL3DENBC11


title: moUL39DENBC107

source_name: Luciferase mRNA L39 with moU


title: moUL38NCBC193

source_name: Luciferase mRNA L38 with moU


title: moUL39NCBC194


title: moUL37NCBC24

source_name: Luciferase mRNA L37 with moU


title: moUL38DENBC106


title: moUL38MODBC58


title: moUL36MODBC19

source_name: Luciferase mRNA L36 with moU


title: moUL35NCBC192

source_name: Luciferase mRNA L35 with moU


title: moUL36NCBC49


title: moUL35MODBC57


title: moUL36DENBC97


title: moUL35DENBC105


title: moUL34NCBC48

source_name: Luciferase mRNA L34 with moU


title: moUL34MODBC18


title: moUL4NCBC18


title: moUL33MODBC28

source_name: Luciferase mRNA L33 with moU


title: moUL34DENBC96


title: moUL33NCBC27


title: moUL33DENBC29


title: moUL32MODBC49

source_name: Luciferase mRNA L32 with moU


title: moUL39MODBC59


title: moUL31DENBC26

source_name: Luciferase mRNA L31 with moU


title: moUL31NCBC24


title: moUL30NCBC47

source_name: Luciferase mRNA L30 with moU


title: moUL37DENBC26


title: moUL32DENBC50


title: moUL31MODBC25


title: moUL37MODBC25


title: moUL30MODBC17


title: moUL2NCBC24

source_name: Luciferase mRNA L2 with moU


title: moUL2MODBC25


title: moUL29NCBC45

source_name: Luciferase mRNA L29 with moU


title: moUL2DENBC26


title: moUL29MODBC46


title: moUL28NCBC190

source_name: Luciferase mRNA L28 with moU


title: moUL29DENBC47


title: moUL5NCBC15


title: moUL28MODBC55


title: WT_LLC

city: La Jolla

first: Judith

middle: Anne

last: Varner

address: Center for Novel Therapeutics 9310 Athena Circle 9310 Athena Circle

department: Pathology

institute: University of California, San Diego

description: Targeted RNA-Seq

data_processing:
Filtering, alignment, annontation of reads, and cell calling, were performed using the BD Rhapsody Analysis Pipeline v1.02
R1 contains only barcode sequence in the following orientation from 5' to 3':
barcode CLS1 (bp 1-9), linker (12 bp), barbode CLS2 (bp 22-30), linker (13 bp), CLS3 (bp 44-42), UMI (bp 53-60). polyT (18 bp)
R2 contains the biological transcript.
Genome_build: Data were aligned to custom set of gene sequences. FASTA used for alignment is available on the series record.
Supplementary_files_format_and_content: csv file with raw counts per gene per cell. Barcode IDs with associated barcode sequence are available in a supplementary file on the series record.

source_name: Tumor cells

growth_protocol: Wild-type male syngeneic C57Bl/6J mice were implanted with 10^6 murine LLC lung cancer tumor cells by subcutaneous injection

extract_protocol: Tumors were isolated on day 18 and the single cell suspension was prepared. The cells were unsorted and include all cell types in the tumor when it was isolated.  Single cells were loaded onto a BD Rhapsody cartridge for single-cell RNA capture on BD Rhapsody beads. Cells were lysed, beads recovered and subjected to cDNA synthesis using a customized BD Rhapsody Immune Response Targeted Panel (Mouse).

value: Cells isolated from mouse subcutanous lung tumors

value: wild type

value: male


title: moUL32NCBC48


title: vip3 RNA-Seq - replicate 1

city: Lyon

first: Christophe

last: TREHIN

address: 46, Allée d'Italie

department: Biology

country: France

institute: ENS Lyon

data_processing:
HiSeq Control Software HD 3.4.0.38.
Adapter trimming: Trimmomatic (Bolger et al., 2014)
Mapping: Bowtie 2.0.5 (Langmead et al., 2009)
Tophat 2.0.6 (Kim et al., 2013).
SAMTools 1.2 (Li et al., 2009).
Expression estimation, normalization and differential analysis: Cufflinks v2.1.1 (Trapnell et al., 2012)
Genome_build: Arabidopsis thaliana TAIR10 (Lamesch et al., 2011)
Supplementary_files_format_and_content: Fal_et_al_TAIR10_genes-countsMatrix.txt: Tab-delimited text file includes read raw counts per gene.
Supplementary_files_format_and_content: Fal_et_al_TAIR10_genes-fpkmsMatrix.txt: Tab-delimited text file includes normalized expression of genes, in FPKM (Fragments Per Kilobase of exon per Million reads).
Supplementary_files_format_and_content: Fal_et_al_TAIR10_gene_exp_diff_filt.txt: Tab-delimited text file includes differential analysis of gene expression between WT and vip3-1 mutant.

organism: Arabidopsis thaliana

source_name: dissected shoot apices

growth_protocol: Material for the RNA-seq was collected from the primary inflorescence of vip3-1 and Col-0 shoot apices (from plants grown in short day 21°C then continuous light 16°C conditions).

extract_protocol:
RNA extraction was performed using the PicoPure RNA Isolation kit Arcturus (ThermoFisher, KIT0204) with an on column DNase treatment (Qiagen, catalog#79254). After elution, 2 samples were combined together, obtaining the final technical triplicates for each genotype. Isolated RNA was subjected to high throughput sequencing analyses to identify differentially expressed transcripts.
Illumina standard library construction protocol, performed by Fasteris sequencing provider (Plan-les-Ouates, Switzerland; https://www.fasteris.com/dna/).

treatment_protocol: Apices were dissected, by removing flower older than stage 4. Samples were collected into liquid nitrogen-cooled eppendorf tubes directly after dissection, each tube containing between 30 and 35 apices, 6 samples for each genotype.

tag: ecotype/background

value: vip3-1 null

value: Primary inflorescence of shoot apices


title: WT RNA-Seq - replicate 2

value: WT


title: vip3 RNA-Seq - replicate 3


title: WT RNA-Seq - replicate 1


title: WT RNA-Seq - replicate 3


title: moUL28DENBC103


title: vip3 RNA-Seq - replicate 2


title: moUL27NCBC21

source_name: Luciferase mRNA L27 with moU


title: moUL27MODBC22


title: moUL30DENBC95


title: moUL26NCBC27

source_name: Luciferase mRNA L26 with moU


title: moUL26MODBC28


title: moUL26DENBC29


title: moUL25NCBC46

source_name: Luciferase mRNA L25 with moU


title: moUL25MODBC16


title: Ctr9.ES.6

first: Byungkuk

last: Min

address: 125 Gwahak-ro, Yuseong-gu

department: Development and Differentiation Research Center

institute: KRIBB

description: amplicon-seq

data_processing:
Raw sequencing reads were groomed to remove the adapter and low quality bases. using ‘Trim_galore’
Since each read was too short to cover the whole amplicon, overwrapping sequences of each read pairs waere merged to generate full-length amplicon sequences using ‘PANDAseq’.
The merged reads were aligned on wild type amplicon sequences by ‘ncbi-blastn’.
For INDEL assessments, frequency of reads with unique INDEL patterns were quantified by compiling hits and gaps information in ‘blastn’ results using a home-made bash script.
Genome_build: mm10
Supplementary_files_format_and_content: EXCEL file containing the IDEL frequencies detected in high-throughput sequencing reads and reference sequences used for read alignment.

source_name: ESCs

extract_protocol: Using genomic DNA from Brca2 or Ctr9 edited mouse embryos or ES cells by the CRISPR/Cas9 system, target regions were amplified. The amplicons were end-repaired/3'-A tailed and finally Illumina specific adapters were ligated. The ligates were amplified by p5/p7 primers to generate libraries. The libraries were pooled for the high-throughput sequencing technology.

value: ESCs


title: Ctr9.ES.5

description: amplicon-seq


title: moUL24NCBC42

source_name: Luciferase mRNA L24 with moU

value: RNA treated with DMSO


title: CAP-seq_RNAseH1oe

city: Oxford

first: Nicholas

last: Proudfoot

address: South Parks Road

institute: Sir William Dunn School of Pathology,  University of Oxford

data_processing:
Library strategy: CAP-seq
For chrRNA-seq, adaptors were trimmed using Cutadapt. Paired-end reads for each sample were mapped to human genome reference assembly GRh37/hg19 (build 37.2, February 2009) with Tophat v. 2.0.13 with parameters -g 1 -r 3000 --no-coverage-search.
RR-ChIP-seq reads were demultiplexed and aligned to reference genome hg19/GRCh37 using Bowtie2 alignment software.Plus and minus strand were assigned to mapped reads using SAMtools. RR-ChIP-seq peaks were called using MACS2 algorithm with default options
Genome_build: hg19
Supplementary_files_format_and_content: BigWig file containing read densities from RNA-seq experiments.

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10%FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and 1) RNA:DNA hybrids were isolated with S9.6 antibody for RDIP-seq 2) RNA:DNA hybrids were isolated with GFP antibody for RR-ChIP-seq
For the RDIP-seq and RR-ChIP-seq, the RNA component of the R-loop was used to prepare the library using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, (E7760S) according to manufacturer's guidelines. For the ChrRNA-seq and ChrCAP-seq, chromatin associated RNA was used for library prepration as for RDIP-seq.

treatment_protocol: Lipofectamine 2000 was used to deliver RNAseH1 over-expressing plasmid (pRNH1-GFP), RNaseH1 catalytically dead mutant (pRNH1-D210N-GFP) Rnase H1 non binding ctalytically dead mutant (pRNH1-WKKD-GFP) and pGFP.  For RDIP-seq experiments recombinant RNase H was added the sonicated HeLa cells before S9.6 immunoprecipitation. All HeLa cells used in Chromatin associated RNA-seq and ChrCAP-seq were GFP FACs sorted. For ChrCAP-seq, chromatin RNA were treated with Terminator exonuclease followed by calf intestine phosphatase before CAP-CLIP (5' pyrophosphatase) treatment.

value: cervical cancer cells


title: moUL25DENBC94

value: RNA heat denatured at 95C and treated with 1M6 in DMSO


title: CAP-seq_WT


title: moUL24MODBC43

value: Folded RNA treated with 1M6 in DMSO at 37C


title: Ctr9.ES.3

description: amplicon-seq


title: Ctr9.ES.2

description: amplicon-seq


title: Ctr9.8cell.9

description: amplicon-seq

source_name: embryos

value: embryos


title: Ctr9.8cell.8

description: amplicon-seq


title: Ctr9.8cell.7

description: amplicon-seq


title: moUL23NCBC189

source_name: Luciferase mRNA L23 with moU


title: Ctr9.8cell.6

description: amplicon-seq


title: moUL24DENBC44


title: Ctr9.8cell.5

description: amplicon-seq


title: moUL22NCBC45

source_name: Luciferase mRNA L22 with moU


title: moUL23DENBC102


title: moUL23MODBC54


title: moUL22NCBC39


title: moUL27DENBC23


title: moUL22MODBC40


title: Ctr9.8cell.3

description: amplicon-seq


title: Ctr9.8cell.1

description: amplicon-seq


title: moUL22DENBC93


title: moUL22MODBC14


title: Ctr9.8cell.2

description: amplicon-seq


title: Ctr9.ES.4

description: amplicon-seq


title: moUL22DENBC41


title: moUL21NCBC188

source_name: Luciferase mRNA L21 with moU


title: Ctr9.5cell.4

description: amplicon-seq


title: Ctr9.5cell.3

description: amplicon-seq


title: moUL21DENBC101


title: Ctr9.4cell.9

description: amplicon-seq


title: Ctr9.5cell.2

description: amplicon-seq


title: moUL20NCBC21

source_name: Luciferase mRNA L20 with moU


title: Ctr9.8cell.4

description: amplicon-seq


title: moUL20MODBC22


title: moUL20DENBC23


title: moUL21MODBC53


title: moUL1MODBC22

source_name: Luciferase mRNA L1 with moU


title: Ctr9.5cell.1

description: amplicon-seq


title: Ctr9.4cell.7

description: amplicon-seq


title: Ctr9.4cell.8

description: amplicon-seq


title: Ctr9.4cell.6

description: amplicon-seq


title: Ctr9.4cell.5

description: amplicon-seq


title: moUL19NCBC18

source_name: Luciferase mRNA L19 with moU


title: moUL1NCBC21


title: Brca2.ES.4

description: amplicon-seq


title: moUL1DENBC23


title: Brca2.ES.5

description: amplicon-seq


title: moUL19MODBC19


title: moUL19DENBC20


title: Brca2.ES.1

description: amplicon-seq


title: moUL18NCBC36

source_name: Luciferase mRNA L18 with moU


title: Brca2.8cell.8

description: amplicon-seq


title: moUL18MODBC37


title: Brca2.8cell.9

description: amplicon-seq


title: moUL18DENBC38


title: moUL17NCBC187

source_name: Luciferase mRNA L17 with moU


title: Brca2.8cell.7

description: amplicon-seq


title: moUL17DENBC100


title: moUL17MODBC52


title: Brca2.8cell.6

description: amplicon-seq


title: Brca2.8cell.5

description: amplicon-seq


title: moUL16NCBC44

source_name: Luciferase mRNA L16 with moU


title: Brca2.8cell.4

description: amplicon-seq


title: Brca2.8cell.2

description: amplicon-seq


title: moUL16DENBC92


title: Brca2.8cell.1

description: amplicon-seq


title: moUL15MODBC34

source_name: Luciferase mRNA L15 with moU


title: Brca2.7cell.10

description: amplicon-seq


title: moUL15DENBC35


title: moUL14NCBC43

source_name: Luciferase mRNA L14 with moU


title: moUL15NCBC33


title: Brca2.6cell.12

description: amplicon-seq


title: Brca2.4cell.13

description: amplicon-seq


title: Brca2.4cell.14

description: amplicon-seq


title: moUL14MODBC11


title: 2mo-het-3

city: Nanjing

first: Guoqiang

last: Wan

address: 12 Xuefu Road

institute: Nanjing University

data_processing:
Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
The sequences were processed and analyzed by GENEWIZ. Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. The estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were set < 0.05 to detect differential expressed ones.
Genome_build: mm8
Supplementary_files_format_and_content: speadsheet files include RPKM values for each Sample

extract_protocol:
Total RNA of cochleae from 2 months old wildtype and Pou4f3(Δ/+) mice was extracted using RNAiso plus kit (TaKaRa, Japan). Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA), NanoDrop (Thermo Fisher Scientific, USA) and 1% agarose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified doublestranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dAtailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptorligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using a Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, CA, USA). Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA).

tag: strain background

value: 2 months

value: Cochlea


title: moUL13NCBC15

source_name: Luciferase mRNA L13 with moU


title: Brca2.ES.2

description: amplicon-seq


title: moUL14DENBC91


title: 2mo-het-1


title: 2mo-het-2


title: 2mo-wt-4

value: wildtype


title: moUL12NCBC186

source_name: Luciferase mRNA L12 with moU


title: 2mo-wt-5


title: Brca2.8cell.3

description: amplicon-seq


title: moUL12DENBC99


title: 2mo-wt-3


title: moUL11NCBC42

source_name: Luciferase mRNA L11 with moU


title: moUL11MODBC15


title: moUL10NCBC41

source_name: Luciferase mRNA L10 with moU


title: FoxG1creplus_hippocampus6wk_Rep1

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 17

department: Institute for Anatomy and Cell Biology

country: Germany

institute: University of Freiburg

data_processing:
 Adapters and low-quality ends were trimmed using TrimGalore version 0.2.8 with parameters --quality 28 --stringency 12  -e 0.1 --length 25 –paired
Trimmed reads were aligned to reference genome build mm10 using TopHat v2.0.9 with the parameter setting --num-threads 4 --library-type fr-firststrand  -G ensGene.Mus_musculus.GRCm38.79.gtf –no-coverage-search -r -3 –mate-std-dev=88. Gene model annotation supplied for mapping was downloaded from Ensembl FTP ftp://ftp.ensembl.org/pub/release-79/gtf/mus_musculus/
 htseq-count v0.6.0 was used to count reads per genomic features with parameters --mode=union --stranded=reverse
Significantly differentially expressed genes were obtained on application DESeq2 version 1.6.1 on the count data with an adjusted p-value threshold of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: The htseq-count processed files are 2 column tab separated, with the first column as gene id and the second column as the number of reads.

extract_protocol:
total RNA was isolated using the Qiagen Rneasy Minikit according to the manufacturers protocol. An on-column DNAse digestion was performed.
5 - TruSeq stranded total RNA sample preparation GOLD (RS-122-2301), total RNA was depleted of rRNA using the Ribo Gold kit (Illumina)

tag: strain  background

value: 6 weeks

tag: Sex

value: hippocampus


title: FoxG1pluplus_hippocampus6wk_Rep2

value: WT; FoxG1+/+


title: moUL11DENBC90

value: RNA contains 5-methoxyuridine


title: FoxG1plusplus_hippocampus6wk_Rep3

value: male


title: moUL13MODBC16


title: FoxG1creplus_hippocampus6wk_Rep2


title: FoxG1creplus_hippocampus6wk_Rep3


title: moUL10MODBC13


title: moUL10DENBC89


title: UL9MODBC5

source_name: Luciferase mRNA L9 with U

value: RNA contains Uracil


title: H_2412_70A

city: Guelph

first: Angela

last: Cánovas

state: ON

address: 50 Stone Road East

department: Animal Biosciences

institute: University of Guelph

data_processing:
CLC genomics workbench (CLC Bio, Aarhus, Denmark) was used to map the genes to the annoated UMD3.1 bovine reference genome (release 90)
Transcript levels were quantified in reads per kilo base per million mapped reads (RPKM). By normalizing the data for transcript length and total reads in each gene for each sample, the RPKM measure facilitated comparisons of transcript levels between both groups.
Genome_build: UMD3.1
Supplementary_files_format_and_content: RPKM values normalized per gene and sample.

molecule: polyA RNA

organism: Bos taurus

source_name: Healthy_milk somatic cells

extract_protocol:
Milk samples were collected using a 3 cm plastic cannula to ensure no bacteria contaminated the sample. Milk was kept on ice and immediately processed for RNA extraction using Trizol reagent to preserve the integrity of RNA.
Library construction was performed using the Illumina TruSeq RNA sample preparation kit

tag: breed

value: Holstein

tag: group

value: Healthy

tag: lactation number

tag: dim

tag: cell type

value: Milk somatic cells


title: H_2457_70E


title: M_2412_70C

source_name: Mastitic_milk somatic cells

value: Mastitic


title: M_2457_70G


title: moUL12MODBC51

tag: treatment


title: moUL13DENBC17


title: M_2339_50H


title: UL8MODBC11

source_name: Luciferase mRNA L8 with U


title: UL8DENBC12


title: UL8NCBC10

value: RNA treated with DMSO


title: M_2301_50F


title: H_2339_50G


title: H_2301_50E


title: UL7MODBC8

source_name: Luciferase mRNA L7 with U


title: H_2360_50C


title: M_2360_50D


title: H_2252_50A


title: UL7DENBC9

value: RNA heat denatured at 95C and treated with 1M6 in DMSO


title: UL7NCBC7


title: UL6NCBC1

source_name: Luciferase mRNA L6 with U


title: UL9NCBC4


title: M_2252_50B


title: UL6MODBC2

value: Folded RNA treated with 1M6 in DMSO at 37C


title: UL6DENBC3


title: UL5NCBC72

source_name: Luciferase mRNA L5 with U


title: UL9DENBC6


title: UL5MODBC138


title: UL4NCBC71

source_name: Luciferase mRNA L4 with U


title: UL5DENBC207


title: Replicate1, RDIP pRNH1-GFP

description:
chromatin RNA
RDIP_pRNH1-GFP.peaks.txt

data_processing:
Library strategy: RDIP-seq
For chrRNA-seq, adaptors were trimmed using Cutadapt. Paired-end reads for each sample were mapped to human genome reference assembly GRh37/hg19 (build 37.2, February 2009) with Bowtie2 alignment software. Uniquely mapped reads with no more than two mismatches were retained for further analysis.
Raw reads from RNA-DIP-seq were aligned to reference genome hg19/GRCh37 using bowtie2. Uniquely mapped reads with no mismatches were retained for further analysis. Plus and minus strand were assigned to mapped reads using SAMtools.
RNA-DIP-seq peaks were called using MACS2 algorithm with default options.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig file containing read densities from RNA-seq experiments.

source_name: HeLa cells

value: cervical cancer cells

tag: genotype/variation

value: RnaseH1 over-expression


title: Replicate1, RR-ChIP pRNH1-GFP

description:
chromatin RNA
RR-ChIP_pRNH1-GFP.peaks.txt

data_processing:
Library strategy: RR-ChIP-seq
For chrRNA-seq, adaptors were trimmed using Cutadapt. Paired-end reads for each sample were mapped to human genome reference assembly GRh37/hg19 (build 37.2, February 2009) with Bowtie2 alignment software. Uniquely mapped reads with no more than two mismatches were retained for further analysis.
Raw reads from RNA-DIP-seq were aligned to reference genome hg19/GRCh37 using bowtie2. Uniquely mapped reads with no mismatches were retained for further analysis. Plus and minus strand were assigned to mapped reads using SAMtools.
RNA-DIP-seq peaks were called using MACS2 algorithm with default options.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig file containing read densities from RNA-seq experiments.


title: Replicate2, RDIP pRNH1-GFP

description:
chromatin RNA
RDIP_pRNH1-GFP.peaks.txt


title: Replicate2, RR-ChIP pRNH1-GFP


title: UL4MODBC137


title: Replicate2, chrRNA-seq WildType

data_processing:
Library strategy: chrRNA-seq
For chrRNA-seq, adaptors were trimmed using Cutadapt. Paired-end reads for each sample were mapped to human genome reference assembly GRh37/hg19 (build 37.2, February 2009) with Tophat v. 2.0.13 with parameters -g 1 -r 3000 --no-coverage-search.
RR-ChIP-seq reads were demultiplexed and aligned to reference genome hg19/GRCh37 using Bowtie2 alignment software.Plus and minus strand were assigned to mapped reads using SAMtools. RR-ChIP-seq peaks were called using MACS2 algorithm with default options
Genome_build: hg19
Supplementary_files_format_and_content: BigWig file containing read densities from RNA-seq experiments.

value: wild type


title: UL3NCBC70

source_name: Luciferase mRNA L3 with U


title: Replicate1, chrRNA-seq RnaseH1_oversxpression

description:
chrRNA-seq
chromatin RNA


title: UL3MODBC136


title: Replicate1,chrRNA-seq WildType

description:
chrRNA-seq
chromatin RNA


title: UL39NCBC78

source_name: Luciferase mRNA L39 with U


title: UL3DENBC205


title: Unsorted treated with E2 replicate 4

city: Fort Collins

first: Colin

middle: M

last: Clay

state: CO

address: 1683 Campus Delivery Mail

department: Biomedical Sciences

institute: Colorado State University

description:
e2-unsorted-4
processed data file: raw_counts_unsorted_E2.txt
processed data file: edgeR_unsorted_E2.txt

data_processing:
Sequenced reads were trimmed to remove adaptor sequence, then mapped to Oar-v3.1 whole genome using gsnap version 2017-06-20 with parameters --use-snps --use splicing, max-mismatches = 0.06, -i2, -n2.
Reads count per gene were extracted using featureCounts software version 1.5.1.
Genome_build: Oar v3.1
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample.
Supplementary_files_format_and_content: Three separate analyses: sorted controls versus unsorted controls, sorted controls versus sorted E2 samples, and unsorted controls versus E2 unsorted.

organism: Ovis aries

source_name: dissociated pituitary cells

growth_protocol: Pituitaries were harvested from exsanguinated ewes and mechanically and enzymatically dispersed. Cells were then cultured on plastic dishes for the remainder of the experiment.

extract_protocol:
RNA was harvested with an RNeasy Kit (Qiagen). An Illumina TruSeq RNA Sample Prep Kit was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 24 hours following cell dispersal, cells were infected with adenovirus transcriptionally targeting GFP expression to gonadotropes. Three days following infection, cells were treated with vehicle (ethanol) or 10 nM of estradiol E2 for 6 hours and sorted by FACS.

value: Western white faced

tag: animal used

value: ovariectomized ewe

tag: tissue

value: pituitary

value: anterior pituitary cells (unsorted)

value: 10 nM E2


title: Unsorted treated with E2 replicate 3

description:
e2-unsorted-3
processed data file: raw_counts_unsorted_E2.txt
processed data file: edgeR_unsorted_E2.txt


title: Unsorted treated with E2 replicate 5

description:
e2-unsorted-5
processed data file: raw_counts_unsorted_E2.txt
processed data file: edgeR_unsorted_E2.txt


title: UL39DENBC213


title: UL38NCBC126

source_name: Luciferase mRNA L38 with U


title: Unsorted treated with E2 replicate 2

description:
e2-unsorted-2
processed data file: raw_counts_unsorted_E2.txt
processed data file: edgeR_unsorted_E2.txt


title: UL38MODBC164


title: Unsorted treated with E2 replicate 1

description:
e2-unsorted-1
processed data file: raw_counts_unsorted_E2.txt
processed data file: edgeR_unsorted_E2.txt


title: Sorted treated with E2 replicate 6

description:
e2-sorted-6
processed data file: raw_counts_sorted_E2.txt
processed data file: edgeR_sorted_E2.txt

value: gonoadotropes (sorted)


title: UL38DENBC174

value: RNA contains Uracil


title: Sorted treated with E2 replicate 5

description:
e2-sorted-5
processed data file: raw_counts_sorted_E2.txt
processed data file: edgeR_sorted_E2.txt


title: Sorted treated with E2 replicate 3

description:
e2-sorted-3
processed data file: raw_counts_sorted_E2.txt
processed data file: edgeR_sorted_E2.txt


title: UL37NCBC77

source_name: Luciferase mRNA L37 with U


title: UL37DENBC212


title: Sorted treated with E2 replicate 4

description:
e2-sorted-4
processed data file: raw_counts_sorted_E2.txt
processed data file: edgeR_sorted_E2.txt


title: UL4DENBC206


title: UL36NCBC76

source_name: Luciferase mRNA L36 with U


title: Sorted treated with E2 replicate 1

description:
e2-sorted-1
processed data file: raw_counts_sorted_E2.txt
processed data file: edgeR_sorted_E2.txt


title: UL39MODBC144


title: Unsorted treated with E2 replicate 6

description:
e2-unsorted-6
processed data file: raw_counts_unsorted_E2.txt
processed data file: edgeR_unsorted_E2.txt


title: Unsorted replicate 6

description:
cont-unsorted-6
processed data file: raw_counts_sorted_unsorted_controls.txt
processed data file: edgeR_sorted_unsorted_controls.txt

value: control


title: moUL16MODBC12

source_name: Luciferase mRNA L16 with moU

value: RNA contains 5-methoxyuridine


title: Unsorted replicate 4

description:
cont-unsorted-4
processed data file: raw_counts_sorted_unsorted_controls.txt
processed data file: edgeR_sorted_unsorted_controls.txt


title: Unsorted replicate 5

description:
cont-unsorted-5
processed data file: raw_counts_sorted_unsorted_controls.txt
processed data file: edgeR_sorted_unsorted_controls.txt


title: Unsorted replicate 3

description:
cont-unsorted-3
processed data file: raw_counts_sorted_unsorted_controls.txt
processed data file: edgeR_sorted_unsorted_controls.txt


title: UL35DENBC173

source_name: Luciferase mRNA L35 with U


title: Unsorted replicate 2

description:
cont-unsorted-2
processed data file: raw_counts_sorted_unsorted_controls.txt
processed data file: edgeR_sorted_unsorted_controls.txt


title: UL34MODBC116

source_name: Luciferase mRNA L34 with U


title: Unsorted replicate 1

description:
cont-unsorted-1
processed data file: raw_counts_sorted_unsorted_controls.txt
processed data file: edgeR_sorted_unsorted_controls.txt


title: Sorted replicate 6

description:
cont-sorted-6
processed data file: raw_counts_sorted_unsorted_controls.txt
processed data file: edgeR_sorted_unsorted_controls.txt


title: UL36DENBC211


title: UL36MODBC142


title: UL37MODBC143


title: UL35NCBC125


title: Sorted treated with E2 replicate 2

description:
e2-sorted-2
processed data file: raw_counts_sorted_E2.txt
processed data file: edgeR_sorted_E2.txt


title: Sorted replicate 5

description:
cont-sorted-5
processed data file: raw_counts_sorted_unsorted_controls.txt
processed data file: edgeR_sorted_unsorted_controls.txt


title: UL33NCBC86

source_name: Luciferase mRNA L33 with U


title: UL34NCBC87


title: UL33MODBC115


title: UL33DENBC134


title: Sorted replicate 1

description:
cont-sorted-1
processed data file: raw_counts_sorted_unsorted_controls.txt
processed data file: edgeR_sorted_unsorted_controls.txt


title: Sorted replicate 3

description:
cont-sorted-3
processed data file: raw_counts_sorted_unsorted_controls.txt
processed data file: edgeR_sorted_unsorted_controls.txt


title: Sorted replicate 2

description:
cont-sorted-2
processed data file: raw_counts_sorted_unsorted_controls.txt
processed data file: edgeR_sorted_unsorted_controls.txt


title: UL32NCBC28

source_name: Luciferase mRNA L32 with U


title: Replicate2, chrRNA-seq RnaseH1_oversxpression


title: UL35MODBC163


title: 9867_High_AS_Control_Diet

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

data_processing:
Illumina Casava1.7 software used for basecalling.
Trimmomatic v.0.33 - trimming for bad reads by standard parameters: PE -phred33 \ ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Cutadapt v.1.8.1 - trimming for adapter sequences: -a TACACTCTTTCCCTACACGACGCTCTTCCGATCT -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -a GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT -A AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \ -e 0.1 -O 5 -m 15 --minimum-length 1 STAR aligner v. 020201 - aligned by parameters: --runThreadN 10 --outFilterMultimapNmax 3 --outFilterMismatchNmax 8 --readFilesCommand zcat --outSAMunmapped Within --outReadsUnmapped Fastx >> output.log
samtools v. 1.3.1 by parameters: view -h -F 1792
HT-seq count v. 0.6.0 - genes counted by parameters: -m intersection-nonempty -s reverse -r pos -f sam -a 10 -t exon
Genome_build: Sus scrofa 10.2.87
Supplementary_files_format_and_content: HT-seq count file (.txt) - raw gene counts

organism: Sus scrofa

growth_protocol: Male pigs, Crossbred Duroc X Landrace/Yorkshire slaughtered at around 100 kg weight

extract_protocol:
Qiagen RNA Minikit
TruSeq stranded mRNA (Illumina, San Diego, USA) kit following instructions of the manufacturer

treatment_protocol: Fed either a control or chicory (15%) additive three days before slaughter. All androstenone, skatole and indole concentrations measured by spectrophotometry.

tag: sow id

value: Danish crossbred Duroc X Landrace/Yorkshire

tag: diet (control or chicory additive (15%))

value: Control

tag: androstenone and skatole [as] group

tag: androstenone concentration (mg/kg)

tag: skatole concentration (mg/kg)

tag: indole concentration (mg/kg)

tag: estimated breeding values of sire for androstenone

tag: carcass weight (kg)

value: testis


title: UL32MODBC29

tag: nucleotide chemistry


title: 9859_NA_chicory

tag: breed

value: Chicory


title: UL31NCBC75

source_name: Luciferase mRNA L31 with U

value: RNA treated with DMSO


title: UL32DENBC30

value: RNA heat denatured at 95C and treated with 1M6 in DMSO


title: UL34DENBC135


title: 8095_High_AS_Chicory_Diet


title: UL31MODBC141

value: Folded RNA treated with 1M6 in DMSO at 37C


title: 8094_Low_AS_Control_Diet


title: UL31DENBC210


title: UL30MODBC114

source_name: Luciferase mRNA L30 with U


title: Sorted replicate 4

description:
cont-sorted-4
processed data file: raw_counts_sorted_unsorted_controls.txt
processed data file: edgeR_sorted_unsorted_controls.txt


title: 8086_Low_AS_Chicory_Diet


title: 8080_Low_AS_Chicory_Diet


title: UL30DENBC133


title: UL2NCBC4

source_name: Luciferase mRNA L2 with U


title: UL2MODBC5


title: 8077_Low_AS_Chicory_Diet


title: 8078_High_AS_Chicory_Diet


title: UL29NCBC25

source_name: Luciferase mRNA L29 with U


title: 7869_High_AS_Control_Diet


title: 8072_Low_AS_Chicory_Diet


title: UL2DENBC6


title: 7864_Low_AS_Control_Diet


title: UL29MODBC26


title: 7863_High_AS_Control_Diet


title: 7859_High_AS_Control_Diet


title: UL29DENBC27


title: UL28NCBC83

source_name: Luciferase mRNA L28 with U


title: 7858_High_AS_Control_Diet


title: UL28MODBC112


title: UL30NCBC85


title: 7005_High_AS_Control_Diet


title: UL28DENBC131


title: 5995_Low_AS_Chicory_Diet


title: UL27NCBC82

source_name: Luciferase mRNA L27 with U


title: UL27MODBC111


title: 5990_High_AS_Control_Diet


title: 8079_Low_AS_Chicory_Diet


title: UL27DENBC130


title: UL26NCBC124

source_name: Luciferase mRNA L26 with U


title: 5986_Low_AS_Control_Diet


title: 5985_High_AS_Chicory_Diet


title: UL26DENBC172


title: 5983_Low_AS_Chicory_Diet


title: 5982_Low_AS_Control_Diet


title: UL25DENBC129

source_name: Luciferase mRNA L25 with U


title: UL25MODBC110


title: UL26MODBC162


title: UL25NCBC81


title: FoxG1plusplus_hippocampus6wk_Rep1

tag: strain  background

value: WT; FoxG1+/+

tag: age

value: 6 weeks

tag: Sex

value: male

value: hippocampus


title: 5980_High_AS_Chicory_Diet


title: 5976_Low_AS_Control_Diet


title: UL24NCBC22

source_name: Luciferase mRNA L24 with U

tag: treatment


title: UL24MODBC23


title: 5974_High_AS_Chicory_Diet


title: 5973_High_AS_Chicory_Diet


title: 3923_Low_AS_Control_Diet


title: UL24DENBC24


title: 5988_Low_AS_Control_Diet


title: 3920_High_AS_Chicory_Diet


title: UL23DENBC171

source_name: Luciferase mRNA L23 with U


title: 5991_High_AS_Control_Diet


title: UL22NCBC19

source_name: Luciferase mRNA L22 with U


title: UL23NCBC123


title: 3908_High_AS_Control_Diet


title: UL22MODBC20


title: UL22DENBC21


title: DAC2_rep2

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

data_processing:
Sequencing reads were cleaned with Trim Galore v0.5.0,  including removing bases with low quality score (<20)  and cutting sequencing adaptors followed by filtering short reads.
Paired-end reads were mapped to the Arabidopsis thaliana genome (TAIR10) using STAR v2.7.2b. RSEM v1.3.2 was used to quantify transcript abundance.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include TPM for each genes

source_name: Arabidopsis thaliana seedings

growth_protocol: Arabidopsis thaliana Col-0 seeds were grown on 1/2 MS medium with sucrose at 22 °C under a 16-h light/8-h dark photoperiod.

extract_protocol:
The wounded region were harvested and frozen in liquid nitrogen, RNA was extracted using TRIzol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Detached leaf explants with partial petiole from 12-day-old seedlings were cultured on B5 medium with sucrose at 22 °C under dark conditions for 0 (time 0) or 2 days (2 DAC). The wounded region (including the partial petiole and some surrounding tissues), which comprises regeneration-competent cells, was separated and collected for RNA extraction.

value: wounded region of detached leaf explants with partial petiole

tag: ecotype

value: wild type Col-0

value: 12-day-old seedlings

tag: time

value: 2 day after culture


title: UL21NCBC74

source_name: Luciferase mRNA L21 with U

value: RNA contains Uracil


title: UL21MODBC140


title: UL21DENBC209


title: DAC2_rep1

tag: tissue


title: T0_rep2

value: before culture


title: UL20NCBC73

source_name: Luciferase mRNA L20 with U


title: T0_rep1


title: heso1-2

city: Nanchang

first: Jianbo

last: Song

state: Jiang Xi

address: Department of Biochemistry and Molecular Biology, College of Science, Jiang Xi Agricultural University, Nanchang 330045, China

institute: Jiang Xi Agricultural University

data_processing:
Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was applied for adapter trimming as well as quality control.
The remaining reads were mapped to the genome with hisat2 allowing 3’ soft clipping (Daehwan et al., 2015).
The reads that mapped to multiple loci were removed. Reads that mapped within 50 bp of annotated pre-miRNAs (miRBase release 21) (Ana and Sam, 2014) were retained.
Genome_build: ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/
Supplementary_files_format_and_content: The map file contains the pre-miRNA alignment information and the non-templated sequence information statistics.

growth_protocol: Plants were grown under long day (16 h light/ 8 h darkness) conditions at 22°C

extract_protocol:
Arabidopsis seedlings were collected, frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
Total RNAs from 14-day-old seedlings were resolved on a 15% denaturing polyacrylamide gel and RNAs of 40-400 nt were recovered from the gel. The size-fractionated RNAs were ligated to a 3’ adaptor using T4 RNA ligase 2, truncated (NEB). The 3’ adaptor-ligated RNAs were resolved on a 15% denature polyacrylamide gel and RNAs of 60-420 nt were recovered. The size-fractionated RNAs were reverse-transcribed with an RT primer that is complementary to the 3’ adaptor using SuperScript III (Life Technologies), followed by two-step PCR amplification. The cDNA was first amplified with the RT primer and a mixture of pre-miRNA-specific forward primers for 10 cycles and secondly amplified for 16 cycles with the 2nd PCR forward and reverse primers using Phusion DNA polymerase (NEB).  The PCR products were resolved on a 12% native polyacrylamide gel, and DNAs of 150-230 bp were recovered from the gel as the pre-miRNA 3’ RACE-seq library. The library was sequenced on Illumina HiSeq3000.

tag: ecotype background

value: Landsberg

tag: genotype

value: 3 weeks

value: Seeding


title: UL20MODBC139


title: UL23MODBC161


title: 3918_High_AS_Control_Diet

tag: sow id

value: Danish crossbred Duroc X Landrace/Yorkshire

tag: diet (control or chicory additive (15%))

value: Control

tag: androstenone and skatole [as] group

value: testis


title: Ler rep2

source_name: wild type_seedilng

value: wild type


title: MiR200-OE_A_3_S29_Rep2

data_processing:
Reads were mapped to the reference genome build mm10 using TopHat v2.0.9 with option -G ensGene.Mus_musculus.GRCm38.79.gtf –no-coverage-search.  Gene model annotation supplied for mapping was downloaded from Ensembl FTP ftp://ftp.ensembl.org/pub/release-79/gtf/mus_musculus/
htseq-count v0.6.0 was used to count reads per genomic features with default parameters.
DESeq2 version 1.6.1 was used on the count data to assess the differentially expressed genes. Genes with an adjusted p-value of 0.05 or less are considered as significantly differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: The htseq-count files contain tab separated data with gene ids in the first column and their corresponding read counts in the second column.

source_name: Neuro2a_miR200 overexpression

extract_protocol:
total RNA was isolated using the Qiagen miRNeasy kit according to the manufacturers protocol. An on-column DNAse digestion was performed.
5 - TruSeq stranded total RNA sample preparation GOLD (RS-122-2301), total RNA was depleted of rRNA using the Ribo Gold kit (Illumina)

treatment_protocol: Neuro2A cells were either transfected with a pCX-miR200 overexpression plasmid or a miR200 sponge plasmid and kept for 48 housr in culture

tag: cell line

tag: cell type

value: mouse neuroblastoma cells

tag: genotype/variation

value: miR200 overexpression


title: SAMPLE 2_S100A4-positive cells

city: Fukuoka

first: Takehito

last: Uruno

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Immunobiology and Neuroscience

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: Peyer's patch_S100A4-positive cells

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using ISOGEN (Nippon Gene).

treatment_protocol: Peyer's patches were dissected from small intestine, cut into pieces and incubated for 60 min at 37 °C with fresh DMEM containing dispase II, collagenase D and DNase I. Every 15 min, tissues were washed with warm DMEM and reincubated with fresh medium containing dispase II, collagenase D and DNase I. The supernatant was collected at each step.

tag: strain

value: S100A4-GFP transgenic

value: Small intestine

value: S100A4-positive cells


title: UL1NCBC1

data_processing:
Library strategy: SHAPE-MaP
Reads from SHAPE-MaP libraries were processed with default settings in SHAPEMapper pipeline version 1.2:
1. Reads from 'DEN', 'MOD', and 'NC' samples are mapped to the reference transcripts in Bowtie2
2. Mutation frequencies are calculated for each base in the samples
3. SHAPE reactivities are calculated form 'p', 'm', and 'd' mutational fre
Genome_build: Custom
Supplementary_files_format_and_content: .tab.txt files include the read depths, standard errors and SHAPE reactivity of each base. Column "Normalized reactivity" is the SHAPE reactivity.

source_name: Luciferase mRNA L1 with U

tag: nucleotide chemistry

value: RNA treated with DMSO


title: MiR200-sponge_B_4_S34_Rep3

source_name: Neuro2a_miR200 sponge

value: miR200 sponge


title: Ler rep1


title: miR200-OE_A_2_S28_Rep1


title: UL1MODBC2

value: Folded RNA treated with 1M6 in DMSO at 37C


title: heso1-1 rep6


title: UL1DENBC3

value: RNA contains Uracil

value: RNA heat denatured at 95C and treated with 1M6 in DMSO


title: miR200-sponge_B_2_S32_Rep2


title: MiR200-sponge_B_1_S31_Rep1


title: heso1-1+pHESO1-HESO1 rep2


title: heso1-1+pHESO1-HESO1 rep1


title: UL19NCBC122

source_name: Luciferase mRNA L19 with U


title: UL19MODBC160


title: Ler rep3

value: Landsberg


title: UL20DENBC208


title: UL19DENBC170


title: Col-0 rep6

value: 3 weeks


title: ntp2-1ntp6-1ntp7-1 rep2

value: Seeding


title: UL18NCBC16

source_name: Luciferase mRNA L18 with U


title: Brca2.ES.3

city: Daejeon

description: amplicon-seq

source_name: ESCs

value: ESCs


title: UL18MODBC17


title: ntp6-1ntp7-1 rep2


title: UL18DENBC18


title: SAMPLE 1_S100A4-negative cells

source_name: Peyer's patch_S100A4-negative cells

value: S100A4-negative cells


title: exposed to 100 ug/L of TCS 100_5

city: Namur

first: Elodie

last: Falisse

address: rue de Bruxelles 61

country: Belgium

institute: University of Namur

data_processing:
DNA from 12 RRBS were sequenced in Illumina HiSeq Machines, Base-calling perfromed using RTA software and demultiplexed to obtain individual Fastq files.
DNA methylation analysis was perfromed using a fragment based approach using our own in house developed pipeline called DMAP (Stockwell et al Bioinformatics, 2014).
Unix scripts and Epiexplorer ( for overlapping ENCODE data) was used for further processing of data.
Genome_build: Zv9
Supplementary_files_format_and_content: Excel file contains variably methylated fragment details (excel)

organism: Danio rerio

source_name: pool of 7dpf larvae

growth_protocol: zebrafish were maintained individually in 24-well microplates, at 26.5 °C under a 12:12 light/dark photoperiod cycle in a climate chamber during all the experiment.

extract_protocol:
Genomic DNA from each pooled larvae sample was extracted using DNeasy Blood & Tissue Kit (Qiagen) following the manufacturer's protocol.
Reduced representation bisulfite sequencing libraries were prepared based on published protocols. Briefly, 12 RRBS libraries were prepared, 4 libraries per condition, each library containing a pool of 24 larvae. Genomic DNA was digested with MspI (New England Biolabs, Ipswich, MA) followed by end repair, addition of 3′ A overhangs and addition of methylated adaptors (Illumina, San Diego, CA) to the digested fragments. Following adaptor ligation, DNA fragments ranging from 40–220 bp (pre-ligation size) were cut from a 3% (w/v) NuSieve GTG agarose gel (Lonza, Basel, Switzerland) and subsequently bisulfite converted using the EZ DNA methylation kit (Zymo Research, Irvine, CA) with an extended incubation time of 18–20 h. Bisulfite converted libraries were amplified by PCR reactions and sequenced (100-bp single ended reads) by New Zealand Genomics Limited (University of Otago, New Zealand) on an Illumina HiSeq2000 sequencer.

treatment_protocol: zebrafsih were exposed to 2 sublethal concentrations of tCS: 50 and 100 µg/L. 50% of the solution were renewed every day.

value: AB strain

value: exposed to 100 ug/L of TCS


title: ntp10-1 rep2


title: HEK293-TLR5_Mock_biological_rep3

city: Erlangen

first: Pachathundikandi

last: Suneesh Kumar

state: Bayern

address: Staudtstrasse 5

department: Chair of Microbiology

institute: FAU Erlangen-Nuremberg

hyb_protocol: 0.6 μg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 8x60K V2 using Agilent’s recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).

source_name: Embryonic kidney_TLR5_mock

label_protocol: Cyanine-3(Cy3) labelled cRNA was prepared by linear T7 based amplification step, 0.1 µg RNA (Nanodrop-1000 spectrophotometer/ND-1000) were amplified and labeled using Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies, USA) following the protocol. cRNA yield and dye incorporation rate were quantified by ND-1000 spectrophotometer.

growth_protocol: Parental (HEK293 Blue Null) cells were maintained in DMEM medium with 1% sigma antibiotic-antimycotic solution and selected with 100  µg/ml Zeocin. TLR5+ (HEK293 Blue TLR5) cells were maintained in the same base medium and additionally selected using 100  µg/ml Blasticidin. Before experiment cells were grown in culture plates and washed with PBS for two times and maintained in antibiotics free media.

extract_protocol: RNA was prepared using Qiazol lysis reagent and miRNA easy kit (Qiagen, Germany) as per the manufacturer's protocol. The RNA quality was analyzed using Agilent 2100 Bioanalyzer and the samples had RIN value between 9.3 and 10.

treatment_protocol: Both cell lines in antibiotic free media were infected with H. pylori or mock infected for 6h at 37°C in a humidified CO2 incubator.

value: HEK293 Blue Null

value: TLR5 overexpression


title: ntp9-1 rep2


title: exposed to 100 ug/L of TCS 100_4


title: HEK293-TLR5_H. Pylori_biological_rep3

source_name: Embryonic kidney_TLR5_H.pylori


title: UL17NCBC121

source_name: Luciferase mRNA L17 with U


title: ntp8-1 rep2


title: HEK293-TLR5_Mock_biological_rep1


title: HEK293-TLR5_H. Pylori_biological_rep2


title: HEK293-TLR5_H. Pylori_biological_rep1


title: exposed to 100 ug/L of TCS 100_1


title: HEK293 _Mock_biological_rep3

source_name: Embryonic kidney_mock

value: parental wildtype


title: HEK293 _Mock_biological_rep2


title: UL17MODBC159


title: HEK293 _Mock_biological_rep1


title: HEK293 _H. Pylori_biological_rep1

source_name: Embryonic kidney_H.pylori-infected


title: HEK293-TLR5_Mock_biological_rep2


title: exposed to 50 ug/L of triclosan 50_6

value: exposed to 50 ug/L of triclosan


title: HEK293 _H. Pylori_biological_rep2


title: exposed to 50 ug/L of triclosan 50_4


title: ntp7-1 rep2


title: exposed to 50 ug/L of triclosan 50_3


title: UL17DENBC169


title: ntp6-1 rep2


title: exposed to 50 ug/L of triclosan 50_2


title: UL16NCBC120

source_name: Luciferase mRNA L16 with U