title: Crohn's disease patient 100

city: Seoul

first: Seulgi

last: Jung

address: 88 Olympic-ro 43-gil

department: Department of Biochemistry and Molecular Biology

country: South Korea

institute: University of Ulsan College of Medicine

data_processing:
Paired-end RNA sequencing of 2 × 101 bp reads was performed using Illumina HiSeq 2500 platform.
GC percent (46 − 56%), raw read counts > 93 million and  read quality check (average Phred quality score > 36) using FastQC v0.11.7.
The adapter sequences and reads with low quality were excluded using cutadapt applying the quality Phred score cut-off < 33 and read length cut-off < 20 bp.
Alignment for the trimmed reads using STAR and GRCh37 reference genome in GENCODE release 19.
Estimation of the transcript abundance, expected read counts, and transcripts per million reads (TPM) for each gene by selecting the uniquely mapped reads with a mapping quality > 255, and ≤6 mismatched bases.
Genome_build: Hg19
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample.

source_name: Peripheral blood

extract_protocol:
The total RNA was extracted using the PAXgene Blood RNA kit, following the manufacturer’s instructions.
Sequencing libraries were prepared with the Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-ZeroTM Globin (Illumina, CA, USA)

value: Peripheral blood

value: Male

tag: age

tag: disease state

value: Crohn's disease


title: Crohn's disease patient 98

status: Public on Jan 14 2020

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: Sex


title: Crohn's disease patient 97

value: Female


title: Crohn's disease patient 96


title: Crohn's disease patient 99


title: Crohn's disease patient 101


title: E2_S13_Human 4hrs untreated

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

data_processing:
Poor quality reads/bases or technical sequences such as adapters are removed from the paired end reads using Trimmomatic v0.32
Trimmed RNA-seq reads were aligned to the Ensembl release 84-GRCh38 genome assembly using using STAR aligner (STAR_2.5.2a) with default options.
Transcript abundance and differential expression was performedusing Cufflinks v2.2.1 and Cuffdiff v2.2.1 respectively.
Genome_build: Ensembl release 84-GRCh38

source_name: Human 4hrs untreated

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS, 1% sterptomycin/penicillin + 1% L-Glutamine at 37 ºC with 5 % CO2.

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen) as indicated by the manufacturer followed by reverse transcription using the iScript cDNA Synthesis Kit (Biorad).RNA quality and quantity was analyzed on an Agilent Bioanalyzer nano chip.
RNAseq libraries were prepared using the stranded TruSeq mRNA kit (Illumina), starting from 500 ng of DNAse I (Qiagen) treated total RNA, following the manufacturer’s protocol. The amplified libraries (10 PCR cycles) were purified using AMPure beads (Beckman Coulter), quantified by Qubit 2.0 fluorometer (Life Technologies), and visualized in an Agilent Tapestation 2200. The libraries were pooled equimolarly, and loaded on an S1100 flow cell, and run as paired-end 50 nucleotide reads on a NovaSeq 6000.  Raw paired-end sequencing reads from both human and mouse samples were quality co

treatment_protocol: Treated cells were kept on the same growth medium but were suplemented with 1 mM NaF for 24 hours before RNA isolation in 6 x well plates at a density of ~80%. Four NaF-treated and four untreated samples per cells type were used.

tag: cell line

tag: treatment

value: Untreated for 4hrs


title: Crohn's disease patient 94


title: Crohn's disease patient 95


title: Crohn's disease patient 93


title: Crohn's disease patient 91


title: Crohn's disease patient 92


title: 4OHT_Zbtb11KO_48h_RNASeq_Rep1

city: London

first: Vlad

middle: Cezar

last: Seitan

address: Guy's Hospital

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

description: total RNA (rRNA-depleted)

data_processing:
ChIP-seq: Reads were trimmed and filtered using Cutadapt applying a Phred quality threshold of 25 and a minimal read length of 25 bases. Filtered reads were aligned to the mouse genome (NCBI37/mm9 assembly) with Bowtie 1.1.2 keeping only uniquely aligned reads while allowing a maximum of 2 mismatches (-v 2 -m 1). MACS2 was set to discard PCR/optical duplicates and was used as peak caller within the Irreproducibility Discovery Rate (IDR) pipeline implemented by the ENCODE consortium. The final set of peaks was considered the conservative set for IDR <0.02. From this set we removed blacklisted sites. Peak overlap analysis was carried out in R and normalised read coverage values were obtained using the DiffBind Bioconductor package.
RNA-seq: Bases with a Phred quality score lower than 25 were trimmed from read ends with Cutadapt, and polyA tails were removed using PRINSEQ. Filtered reads were aligned to the mouse transcriptome with STAR using 2-pass mapping, and gene-level counts were generated with HTSeq. Differential gene expression analysis was carried out using the Bioconductor package EdgeR.
Genome_build: mm9

organism: Mus musculus

source_name: Embryonic Stem Cells

growth_protocol: Mouse embryonic stem cells were maintained in feeder-free conditions, on gelatin-coated plates, in KO DMEM supplemented with 10% foetal bovine serum, LIF, L-Glutamine, 2-mercaptoethanol, non-essential amino acids, penicillin and streptomycin

extract_protocol:
1μg total RNA was used as starting material for each library. rRNA was depleted using the NEBNext rRNA Depletion Kit (E6310, New England Biolabs)
Directional RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420, New England Biolabs).

tag: parental esc line

tag: zbtb11 locus genotype

tag: rosa26 locus genotype

value: 4-hydorxytamoxifen (250nM)

tag: treatment protocol

value: To induce Zbtb11 KO, growth media was supplemented with 4-hydroxytamoxifen (4OHT) pre-slubilised in ethanol. 4OHT was added to a final concentration of 250nM from a 1000x stock solution. As control, Zbtb11lox/lox Rosa26ERt2-Cre were treated with the carrier ethanol, or Zbtb11WT/WT Rosa26WT were treated with 4OHT.

tag: antibody


title: Crohn's disease patient 90


title: Crohn's disease patient 89


title: Crohn's disease patient 88


title: Crohn's disease patient 87


title: Crohn's disease patient 86


title: MSS_FFPE_Spleen [ID_28]

type: RNA

city: Oslo

first: Berit

middle: Sletbakk

last: Brusletto

address: Kirkeveien 166

department: Oslo University Hospital

country: Norway

institute: Medical Biochemisty

description:
ID_28
Gene expression data from MSS patient.

hyb_protocol: Fragmented and labeled sense strand DNA was hybridized to the GeneChip Human Transcriptome 2.0 Arrays (Affymetrix, Santa Clara, CA). The arrays were washed and stained using FS-450 fluidics station (Affymetrix).

scan_protocol: Fluorescent images were scanned by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA). The scanned images were then analyzed using Affymetrix GeneChip Command Console.

data_processing: The CEL files were imported into Partek Genomics Suite software (Partek, Inc., St. Louis, MO). Robust microarray analysis (RMA) was applied for normalization.

label: biotin

label_protocol: Total RNA was subjected to the Sensation Plus FFPE Amplification and WT Labeling Kit, following the manufacturer’s protocol for whole-genome gene expression analysis (Affymetrix).

extract_protocol: Total RNA from FFPE tissue was isolated using Qiagen miRNeasy FFPE kit (Qiagen, Hilden, Germany) according to manufacturer’s protocol. Total RNA from FF tissue was isolated using the miRNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: FFPE and FF tissue samples from patients with meningococcal septic shock and multiple organ failure and control patients with acute non-infectious death.

tag: patients id nr

value: Nr 2

tag: diagnosis

value: Meningococcal septic shock (MSS)

tag: type of storage tissue

value: FFPE

value: Spleen

tag: age of tissue sample at rna isolation timepoint (years)


title: MSS_FF_Spleen [ID_36]

description:
ID_36
Gene expression data from MSS patient.

value: Nr 4

value: FF


title: Crohn's disease patient 84


title: Crohn's disease patient 83


title: Control_FFPE_Spleen [ID_33]

description:
ID_33
Gene expression data from control patient.

value: Nr 7

value: Acute non-infectious death


title: MSS_FFPE_ Spleen [ID_2]

description:
ID_2
Gene expression data from MSS patient.

value: Nr 3


title: MSS_FFPE_Spleen [ID_7]

description:
ID_7
Gene expression data from MSS patient.

value: Nr 1


title: Crohn's disease patient 81

value: Peripheral blood


title: Crohn's disease patient 82


title: MSS_FF_Spleen [ID_18]

description:
ID_18
Gene expression data from MSS patient.


title: Crohn's disease patient 80

value: Male


title: MSS_FFPE_Lungs [ID_49]

description:
ID_49
Gene expression data from MSS patient.

value: Nr 5

value: Lungs


title: MSS_FFPE_Lungs [ID_4]

description:
ID_4
Gene expression data from MSS patient.


title: Crohn's disease patient 85

value: Crohn's disease


title: Crohn's disease patient 79

value: Female


title: MSS_FFPE_Lungs [ID_25]

description:
ID_25
Gene expression data from MSS patient.


title: MSS-FF_Lungs [ID_17]

description:
ID_17
Gene expression data from MSS patient.


title: MSS_FF_Lungs [ID_44]

description:
ID_44
Gene expression data from MSS patient.


title: MSS_FFPE_Lungs [ID_10]

description:
ID_10
Gene expression data from MSS patient.


title: MSS_FFPE_Lungs [ID_21]

description:
ID_21
Gene expression data from MSS patient.


title: MSS_FFPE_Spleen [ID_48]

description:
ID_48
Gene expression data from MSS patient.


title: Control_FFPE_Lungs [ID_30]

description:
ID_30
Gene expression data from control patient.


title: MSS_FF_Lungs [ID_15]

description:
ID_15
Gene expression data from MSS patient.


title: Control_FFPE_Lungs [ID_12]

description:
ID_12
Gene expression data from control patient.

value: Nr 6


title: Crohn's disease patient 78


title: Crohn's disease patient 77


title: Crohn's disease patient 75


title: Crohn's disease patient 73


title: Crohn's disease patient 72


title: Crohn's disease patient 71


title: MSS_FFPE_Liver [ID_6]

description:
ID_6
Gene expression data from MSS patient.

value: Liver


title: Crohn's disease patient 76


title: MSS_FFPE_Liver  [ID_27]

description:
ID_27
Gene expression data from MSS patient.

value: Nr 2

value: Meningococcal septic shock (MSS)


title: MSS_FFPE_Liver [ID_23]

description:
ID_23
Gene expression data from MSS patient.

value: FFPE


title: Crohn's disease patient 70


title: Crohn's disease patient 69


title: MSS_FF_Liver [ID_35]

description:
ID_35
Gene expression data from MSS patient.

value: Nr 4


title: MSS_FF_Lungs [ID_104]

description:
ID_104
Gene expression data from MSS patient.

value: FF


title: Control_FFPE_Liver [ID_31]

description:
ID_31
Gene expression data from control patient.

value: Nr 7


title: MSS_FFPE_Kidneys [ID_9]

description:
ID_9
Gene expression data from MSS patient.

value: Kidneys


title: Crohn's disease patient 68


title: MSS_FFPE_Liver [ID_1]

description:
ID_1
Gene expression data from MSS patient.

value: Nr 3


title: Crohn's disease patient 74


title: Control_FFPE_Kidneys [ID_32]

description:
ID_32
Gene expression data from control patient.

value: Acute non-infectious death


title: Crohn's disease patient 65

value: Peripheral blood


title: Crohn's disease patient 67


title: Crohn's disease patient 66

value: Male


title: MSS_FFPE_Kidneys [ID_26]

description:
ID_26
Gene expression data from MSS patient.


title: MSS_FF_Liver [ID_47]

description:
ID_47
Gene expression data from MSS patient.

value: Nr 5


title: Control_FFPE_Kidneys [ID_14]

description:
ID_14
Gene expression data from control patient.


title: MSS_FF_Kidneys [ID_46]

description:
ID_46
Gene expression data from MSS patient.


title: Crohn's disease patient 63


title: Crohn's disease patient 62


title: Crohn's disease patient 60


title: Crohn's disease patient 61


title: MSS_FFPE_Kidneys [ID_22]

description:
ID_22
Gene expression data from MSS patient.


title: Crohn's disease patient 59


title: MSS_FF_Kidneys [ID_37]

description:
ID_37
Gene expression data from MSS patient.


title: Crohn's disease patient 57


title: MSS_FFPE_Heart [ID_3]

description:
ID_3
Gene expression data from MSS patient.

value: Heart


title: MSS_FFPE_Kidneys [ID_5]

description:
ID_5
Gene expression data from MSS patient.


title: Crohn's disease patient 58

value: Crohn's disease


title: MSS_FF_Kidneys [ID_19]

description:
ID_19
Gene expression data from MSS patient.


title: Crohn's disease patient 54


title: MSS_FFPE_Heart [ID_43]

description:
ID_43
Gene expression data from MSS patient.


title: Crohn's disease patient 55


title: Crohn's disease patient 53

value: Female


title: Crohn's disease patient 56


title: MSS_FFPE_Heart [ID_24]

description:
ID_24
Gene expression data from MSS patient.


title: MSS_FFPE_Heart [ID_20]

description:
ID_20
Gene expression data from MSS patient.


title: Crohn's disease patient 51


title: MSS_FFPE_Heart [ID_105]

description:
ID_105
Gene expression data from MSS patient.

value: Nr 1


title: MSS_FF_Heart [ID_45]

description:
ID_45
Gene expression data from MSS patient.


title: Crohn's disease patient 64


title: MSS_FF_Heart [ID_34]

description:
ID_34
Gene expression data from MSS patient.


title: Control_FFPE_Heart [ID_29]

description:
ID_29
Gene expression data from control patient.


title: Crohn's disease patient 50


title: MSS_FF_Heart [ID_16]

description:
ID_16
Gene expression data from MSS patient.


title: Crohn's disease patient 52


title: Control_FFPE_Heart [ID_11]

description:
ID_11
Gene expression data from control patient.

value: Nr 6


title: Crohn's disease patient 49


title: Human_lung_P55

city: Columbus

first: Daniel

middle: Yui

last: Weng

state: OH

address: 420 W. 12th Ave. Room 390

department: Comprehensive Cancer Center

country: USA

institute: The Ohio State University

description: Gene expression data

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), Eukaryotic Hybridization Controls (Affymetrix). Heat 65C for 5 minutes, 99C for 5 minutes, 45C for 5 minutes centrifuge top speed for 5 minutes. Hybridize 16 hours at 45°C at 60rpm. Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G using AGCC (Affymetrix GeneChip Command Console)

data_processing: The data were analyzed with Partek Genomics Suite using GC-RMA as normalization method and applied batch remove.

source_name: Bronchial epithelial cells

label_protocol: 5.5 ug of single stranded cDNA were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Total RNA was extracted using the TriplePure High Impact Zirconium beads and AllPrep DNA/RNA Mini Kit according to the manufacturer's instructions.

value: lung

tag: week

tag: trial group

value: E-cig


title: Human_lung_P57

description: Gene expression data

tag: age


title: Human_lung_P58

description: Gene expression data


title: Human_lung_P56

description: Gene expression data


title: Crohn's disease patient 48

tag: disease state


title: Human_lung_P49

description: Gene expression data

tag: tissue


title: Human_lung_P50

description: Gene expression data


title: Crohn's disease patient 47

tag: Sex


title: Human_lung_P47

description: Gene expression data


title: Crohn's disease patient 46


title: Human_lung_P48

description: Gene expression data


title: Crohn's disease patient 45


title: Human_lung_P38

description: Gene expression data


title: dbR2

city: Shanghai

first: Liwen

last: Zhang

address: 197 Ruijin Er Road

country: China

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
FASTQ raw reads were firstly processed through in-house Perl scripts to obtain clean reads.
Clean reads were aligned with the Ensembl reference mouse transcriptome (GRCm38.p2) using TopHat v2.0.9.
The resulting mapped reads for each sample were assembled using Scripture Beta2 and Cufflinks (v2.1.1) in a reference-based approach.
Cufflinks was used to calculate fragments per kilobase of exon per million mapped reads (FPKMs) for the lncRNAs and coding genes identified in each sample that mapped to a specific fragment. Gene FPKMs were computed by adding the transcript FPKMs in each gene group.
Genome_build: Ensembl reference mouse transcriptome (GRCm38.p2)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of mRNAs or annotated lncRNAs for each Sample, and information as well as FPKM values of novel lncRNAs for each Sample.

source_name: Renal cortex

extract_protocol:
Total RNA was extracted from the renal cortex of each mouse (n = 3 for each group) using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations.
Ribosomal RNA was removed with an Epicentre Ribo-zero™ rRNA removal kit (Epicenter, USA) according to manufacturer’s instructions. Sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library prep kit from Illumina® (NEB, USA).

tag: phenotype

value: Type 2 diabetic with rosiglitazone treated

tag: genotype

value: homozygous mutation in Leptin receptor (db)

value: 15 weeks

value: Renal cortex


title: Crohn's disease patient 44


title: Human_lung_P37

description: Gene expression data


title: dbR1


title: Human_lung_P36

description: Gene expression data


title: dbdb3

value: Type 2 diabetic


title: Crohn's disease patient 43


title: Crohn's disease patient 42


title: Human_lung_P28

description: Gene expression data


title: dbdb2


title: Human_lung_P35

description: Gene expression data


title: Human_lung_P27

description: Gene expression data


title: Crohn's disease patient 41


title: Human_lung_P24

description: Gene expression data


title: dbdb1


title: 202259490134_R02C01

type: genomic

description: normal lung

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850 Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Genome Studio 1.9.0 and Partek Genomics Suite 6.6 (Partek Inc., St. Louis, MO) and normalized using the Subset-quantile Within Array Normalization (SWAN)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: lung tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from human bronchial epithelial cells using the Triple High Impact Zirconium beads and AllPrep DNA/RNA Mini Kit according to standard instructions.

tag: patient order

value: Control


title: Human_lung_P23

description: Gene expression data


title: Crohn's disease patient 40


title: dbR3


title: 202225190117_R01C01

description: normal lung


title: 202232360213_R04C01

description: normal lung


title: 202262730064_R04C01

description: normal lung


title: 202225190007_R01C01

description: normal lung


title: Control2

value: non-diabetic, normal control

value: heterozygous mutation in Leptin receptor (db)


title: 202232360213_R03C01

description: normal lung


title: 202232360213_R06C01

description: normal lung


title: 202259490134_R01C01

description: normal lung


title: Human_lung_P22

description: Gene expression data


title: Crohn's disease patient 39

value: Peripheral blood

value: Male


title: 202225190117_R02C01

description: normal lung


title: 202225190140_R05C01

description: normal lung


title: 202225190116_R05C01

description: normal lung


title: 202225190140_R04C01

description: normal lung


title: Crohn's disease patient 38


title: 202262730064_R03C01

description: normal lung


title: 202225190007_R06C01

description: normal lung


title: 202232360101_R02C01

description: normal lung


title: Crohn's disease patient 37


title: M3: Axin2+ endometrial epithelial cells ovariectomized mice

city: Callaghan

first: Shafiq

middle: Mukhtar

last: Syed

state: NSW

address: University Drive, Callaghan-2308

department: School of Biomedical Sciences and Pharmacy

country: Australia

institute: University of Newcastle

data_processing:
Primary sequence data was generated using the Illumina bcl2fastq 2.20.0.422 pipeline. The primary bioinformatics analysis involved demultiplexing and quality control (QC).
The data was then processed through RNA-seq expression analysis workflow, which included alignment, transcript assembly, quantification, normalization and differential expression analysis.
The cleaned sequence reads were aligned against the Mus musculus genome (Build version mm10).
The STAR aligner (v2.5.3a) was used to map reads to the genomic sequences. Raw gene counts were summarized at gene level using the featureCounts v1.5.3 utility of the subread package (http://subread.sourceforge.net/).
The transcripts were assembled with the Stringtie tool v1.3.3 (http://ccb.jhu.edu/software/stringtie/) utilizing the reads alignment with M6 and reference annotation-based assembly option (RABT).
Differential gene expression analysis was performed using edgeR (version 3.22.5) tool. The default TMM normalization method of edgeR was used to normalize the counts between samples. A generalized linear model was used to quantify the differential expression between the groups (n=3 mutant and control groups each).
Genome_build: mm10
Supplementary_files_format_and_content: features_summary.csv: provides overall mapping rate with the genome and genome feature
Supplementary_files_format_and_content: gene_counts.txt: Provides counts of reads mapping to each known gene
Supplementary_files_format_and_content: M.VS.C-top1000_genes.txt: Top 1000 differentially expressed genes
Supplementary_files_format_and_content: M.VS.C-all_genes.txt: Total differentially expressed genes

extract_protocol:
Endometrial epithelial cells were isolated, digested into single cell suspension and Axin2+ (GFP+) and Axin2- (GFP-) cells were FACS sorted. The respective Axin2+ and Axin2- cells from each of the three mice used in this experiment were pooled together ( Axin2- cells = C1, C2, C3; Axin2+ cells = M1, M2, M3, Arabic numeral represents the mouse number ). Total RNA was isolated using RNeasy Micro kit (Qiagen) as per manufacturer instructions. RNA quality and concentration were determined using Nanodrop ND-1000 Spectrophotometer.
RNA libraries were prepared using Illumina's Ribo-zero Gold protocol.

treatment_protocol: Axin2rtTA; tetOH2BJGFP mice were ovariectomized at 4 weeks age. After 2 weeks of rest, H2BJGFP was induced in Axin2+ cells by doxycycline administration and uteri were collected 4 days post-doxycycline administration.

tag: strain

value: Axin2rtTA; tetOH2BJGFP

value: uterus

value: 6 weeks

tag: genotype/variation


title: Crohn's disease patient 36

value: Female

value: Crohn's disease


title: Control1


title: Human_lung_P21

description: Gene expression data

value: lung


title: 202225190116_R01C01

description: normal lung


title: M1: Axin2+ endometrial epithelial cells ovariectomized mice


title: 202225190116_R02C01

description: normal lung


title: 202225190116_R06C01

description: normal lung


title: Crohn's disease patient 35


title: C3: Axin2- endometrial epithelial cells ovariectomized mice


title: Human_lung_P20

description: Gene expression data

value: E-cig


title: Crohn's disease patient 34


title: Human_lung_P19

description: Gene expression data


title: 202232360211_R04C01

description: normal lung


title: 202232360101_R03C01

description: normal lung


title: Control3


title: C2: Axin2- endometrial epithelial cells ovariectomized mice


title: C1: Axin2- endometrial epithelial cells from ovariectomized mice


title: Crohn's disease patient 32


title: Human_lung_P15

description: Gene expression data


title: Crohn's disease patient 31


title: Tb_VA_pTet_B

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
Raw reads were trimmed with the default settings of fastp (v0.19.5)
alignment: Bowtie2 v2.3.4.1 using sensitive local alignment mode
sorting: Samtools v1.2 using default parameters
gene tag counts: HTSeq count
Genome_build: Trypanosoma brucei Lister 427 (v9.0 from TriTrypDB.org)
Supplementary_files_format_and_content: tab-delimited text file, see metafile for column headers

molecule: polyA RNA

organism: Trypanosoma brucei

source_name: VAa RNAi parasite

growth_protocol: Bloodstream form T. brucei cells were grown as described in Hirumi et al. (1980).  Parasitology 80, 371–382.

extract_protocol: Total RNA was isolated from T. brucei cultures using TriPure, according to the manufacturer’s instructions. 5x107 cells were used for each prep.

treatment_protocol: RNAi was induced by supplementing media with 1 ug/ml tetracyclin for 2 days in T. brucei

tag: strain, lifestage

value: Blood Stream Form Single Marker Cell line

value: Trypanosoma brucei cell line

tag: treatment

value: +tet


title: Crohn's disease patient 33


title: Tb_VA_mTet_B

value: -tet


title: 202232360101_R07C01

description: normal lung


title: Crohn's disease patient 30


title: 202232360211_R03C01

description: normal lung


title: Human_lung_P11

description: Gene expression data


title: Human_lung_P14

description: Gene expression data


title: Human_lung_P13

description: Gene expression data


title: 202232360213_R05C01

description: normal lung


title: Crohn's disease patient 29


title: Human_lung_P12

description: Gene expression data


title: Tb_VA_mTet_A


title: Crohn's disease patient 28


title: Tb_VA_pTet_A


title: Tb_PNUTS_pTet_C

source_name: PNUTS RNAi parasite


title: Human_lung_P10

description: Gene expression data


title: Crohn's disease patient 27


title: 202225190007_R02C01

description: normal lung


title: Tb_PNUTS_mTet_C


title: Human_lung_P4

description: Gene expression data


title: Tb_PNUTS_pTet_B


title: Crohn's disease patient 25


title: M2: Axin2+ endometrial epithelial cells ovariectomized mice


title: Tb_PNUTS_mTet_B


title: Crohn's disease patient 24


title: Human_lung_P54

description: Gene expression data


title: Human_lung_P3

description: Gene expression data


title: Crohn's disease patient 26


title: Human_lung_P53

description: Gene expression data


title: Human_lung_P16

description: Gene expression data


title: Tb_PNUTS_pTet_A


title: 202232360211_R06C01

description: normal lung


title: 202232360211_R05C01

description: normal lung


title: Tb_PNUTS_mTet_A


title: 202225190007_R03C01

description: normal lung


title: Crohn's disease patient 21


title: Human_lung_P52

description: Gene expression data


title: 202225190117_R04C01

description: normal lung


title: Human_lung_P51

description: Gene expression data


title: 202225190117_R05C01

description: normal lung


title: Crohn's disease patient 23


title: Crohn's disease patient 19


title: Human_lung_P46

description: Gene expression data


title: Ab-3A3L (WT)

city: Stuttgart

first: Albert

last: Jeltsch

address: Allmandring 31

department: Institute of Biochemistry and Technical Biochemistry

country: Germany

institute: University Stuttgart

library_source: genomic

data_processing:
Files received in FASTQ format and processed on the European Galaxy platform
Quality of reads checked with FastQC
Mapping of reads on Hg19/GRCh37 using bowtie2 with default settings to obtain BAM files
BigWig files obtained using the bamCoverage tool (25 bp bins, RPKM normalization) from Deeptools. Internal re-normalization performed as follows: Signals in CpG islands (CGIs) (from UCSC Table Browser) were quantified using the multiBigwigSummary tool. The 1000 highest methylated CGIs in 'Untreated cells' were selected, mean signals in these CGIs were calculated and the relative value to "Untreated cells" served as scaling factor. New bigWig files were created (25 bp bins, RPKM normalization) with the scaling factor included using the bamCoverage Tool.
New peaks for 3A3L(WT) were called using the MACS2 tool by using 'Untreated cells' as control file (10 - 100 mfold bounds, q-value = 0.01)
Genome_build: Hg19/GRCh37
Supplementary_files_format_and_content: bigWig

source_name: HEK293 cell line

extract_protocol:
Genomic DNA (gDNA) was isolated from 0.5 - 1 x 106 cells using the QIAmp Mini Kit (Qiagen) according to the manufacturer's protocol and fragmented (200 - 1000 bp) with a EpiShear probe sonicator (Active Motif).
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer's protocol.

tag: binding protein

value: Ab-3A3L (WT)


title: Ab-3A3L (R887E)


title: Human_lung_P45

description: Gene expression data

value: Control


title: 202259490134_R07C01

description: normal lung


title: Ab-3A3L (K844E)


title: Human_lung_P44

description: Gene expression data


title: 202225190140_R07C01

description: normal lung


title: Human_lung_P9

description: Gene expression data


title: Untreated cells

value: Untreated cells


title: Crohn's disease patient 18


title: 202225190007_R07C01

description: normal lung


title: HS_2KO_rep4

city: Turku

first: Jenny

middle: Maaria

last: Joutsen

state: Varsinais-Suomi

address: Tykistökatu 6A

department: Cell Biology

country: Finland

institute: Åbo Akademi University

description: sequencing run made in 3 lanes

data_processing:
The base calling was done using bcl2fastq (v. 1.8.4)
Read alignment was done using Tophat (v2.1.0) to  human hg38 genome
Genewise read counts were calculated using subreads package (v. 1.5.1)
Genome_build: human hg38
Supplementary_files_format_and_content: files are tab delimited text files containing the genewise read counts for each sample

source_name: cell

growth_protocol: CRISPR-Cas9 modified U2OS cells (control, HSF1 KO, HSF2 KO) were cultured in DMEM (Dulbecco’s Modified Eagle’s media, D6171, Sigma-Aldrich), supplemented with 10% fetal calf serum, 2 mM L-glutamine and 100 μg/ml penicillin-streptomycin and grown in 5% CO2 at 37°C.

extract_protocol:
After treatments, cells were washed with PBS, collected, and the total RNA was purified with AllPrep DNA/RNA/miRNA Universal Kit (80224, Qiagen) according to manufacturer´s instructions. Genomic DNA was removed with DNAse I treatment according to the AllPrep protocol and the samples were sent to the Finnish Microarray and Sequencing Centre (Turku, Finland) for further processing.
Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047):

treatment_protocol: 2 x 10^6 U2OS WT, HSF1 KO and HSF2 KO cells were plated and cultured o/n. Following day, cells were treated with 25 nM Bortezomib for 6 or 10 h or heat shocked at 42 degrees for 1 h. Control cells were treated with DMSO.

tag: cell line

tag: disease

value: osteosarcoma

value: heat shock farctor 2 KO

value: heat shock 1 h in 42 degrees


title: Crohn's disease patient 17

value: Peripheral blood

value: Male


title: Crohn's disease patient 22


title: 10h_2KO_rep4

description: sequencing run made in 3 lanes

value: treated with Bortezomib for 10 h


title: 202262730064_R01C01

description: normal lung


title: 202259490134_R06C01

description: normal lung


title: 202262730064_R06C01

description: normal lung


title: Crohn's disease patient 15

value: Female


title: 6h_2KO_rep4

description: sequencing run made in 3 lanes

value: treated with Bortezomib for 6 h


title: Crohn's disease patient 20

value: Crohn's disease


title: Human_lung_P41

description: Gene expression data

value: lung


title: Human_lung_P43

description: Gene expression data


title: C_2KO_rep4

description: sequencing run made in 3 lanes

value: control


title: 202262730064_R02C01

description: normal lung

value: E-cig


title: Human_lung_P42

description: Gene expression data


title: HS_1KO_rep4

description: sequencing run made in 3 lanes

value: heat shock farctor 1 KO


title: Crohn's disease patient 14


title: Human_lung_P40

description: Gene expression data


title: 202232360211_R08C01

description: normal lung


title: 202225190140_R08C01

description: normal lung


title: Crohn's disease patient 12


title: 10h_1KO_rep4

description: sequencing run made in 3 lanes


title: Human_lung_P39

description: Gene expression data


title: 6h_1KO_rep4

description: sequencing run made in 3 lanes


title: Human_lung_P34

description: Gene expression data


title: Human_lung_P33

description: Gene expression data


title: Crohn's disease patient 11


title: C_1KO_rep4

description: sequencing run made in 3 lanes


title: 202225190117_R06C01

description: normal lung


title: Crohn's disease patient 10


title: Human_lung_P32

description: Gene expression data


title: Crohn's disease patient 9


title: 202232360101_R08C01

description: normal lung


title: HS_WT_rep4

description: sequencing run made in 3 lanes

value: wild type


title: 10h_WT_rep4

description: sequencing run made in 3 lanes


title: Crohn's disease patient 8


title: Human_lung_P31

description: Gene expression data


title: 202225190117_R07C01

description: normal lung


title: 6h_WT_rep4

description: sequencing run made in 3 lanes


title: 202259490134_R03C01

description: normal lung


title: Human_lung_P29

description: Gene expression data


title: Human_lung_P30

description: Gene expression data


title: Crohn's disease patient 7


title: 202259490134_R04C01

description: normal lung


title: Crohn's disease patient 6


title: Crohn's disease patient 16


title: Crohn's disease patient 13


title: HS_2KO_rep3

description: sequencing run made in 3 lanes


title: Human_lung_P26

description: Gene expression data


title: 202262730064_R07C01

description: normal lung


title: 202225190116_R07C01

description: normal lung


title: U4_6_core_domain

city: Cambridge

first: Silvi

last: Rouskin

state: MA

address: 455 Main Street

institute: Whitehead Institute

data_processing:
Library strategy: DMS-MaPseq
Alignment with bowtie2 (2.3.4.1)
Read trimming (TrimGalore v0.4.1) and QC (FastQCv0.11.8)
DREEM Clustering (custom code available at https://gitlab.com/Corbin-Rouskin/RNA_structure/tree/gpu)
RNAstructure(v6.0.1) folding and VARNA (v3.93) visualization
Genome_build: Adenosine deaminase (add) riboswitch corresponds to nucleotides 1590535-1590663 of V.vulnificus strain (Genbank Accession code CP037932.1). The U4/6 core-domain RNA construct is based on the interface of the U4 and U6 snRNA (Genbank accession code 2N7M_X).
Supplementary_files_format_and_content: _Mu.txt files produced by DREEM clustering algorithm

growth_protocol: In vitro transcribed and DMS modified RNA

extract_protocol:
DMS-treated cells were pelleted and resuspended in 1 mL Trizol, RNA was extracted by chloroform extraction and isopropanol precipitation.
3'Phosphorylation with rSAP, linker ligation with T4 RNA ligase truncated KQ, excess linker degraded with RecJ and 5'Deadenylase. rRNA was subtracted with RiboZero, and RT was performed with TGIRT-III. cDNAs were isolated by gelextraction on a 10% TBE-Urea gel and extracted by isopropanol precipitation. cDNAs were circularized with circLigase and amplified by PCR with phusion polymerase. PCR products were purified by gel extraction from an 8% TBE gel and isopropanol precipitation. Samples were quantified by Bioanalyzer.

treatment_protocol: DMS-treatment for RNA secondary structure analysis, between 0.2-2% DMS at 37C for 5 minutes

tag: sample type

value: In vitro transcribed RNA

tag: molecule subtype

value: DMS-modified RNA


title: Crohn's disease patient 5


title: 10h_2KO_rep3

description: sequencing run made in 3 lanes


title: Crohn's disease patient 4


title: Human_lung_P17

description: Gene expression data

tag: week

tag: trial group

value: Control


title: Crohn's disease patient 3

tag: age

tag: disease state


title: Human_lung_P25

description: Gene expression data

tag: tissue


title: Human_lung_P18

description: Gene expression data


title: 202225190116_R08C01

description: normal lung


title: 202232360211_R07C01

description: normal lung


title: 202225190007_R05C01

description: normal lung


title: 6h_2KO_rep3

description: sequencing run made in 3 lanes

value: osteosarcoma


title: 202232360101_R05C01

description: normal lung


title: Crohn's disease patient 2

tag: Sex


title: 202232360211_R01C01

description: normal lung


title: 16_Org_CUL4B

city: Jinan

first: Yanjun

last: Li

address: 44 Wenhua West Road

institute: Shandong university

description:
Org_CUL4B and Org_con_TPM.txt
Org_2_4B

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and  python  scripts.  In  this  step,  clean  datas(clean  reads)  were  obtained  by removing  reads  containing  ploy-N,  with  5’  adapter  contaminants,  without  3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from  raw  data.  At  the  same  time,  Q20,  Q30,  and  GC-content  of  the  raw  datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels. The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Genome_build: hg18
Supplementary_files_format_and_content: Org_sh and Org_NC_gene_fpkm.txt, Org_CUL4B and Org_con_TPM.txt

source_name: Overexpression of CUL4B, colorectal cancer organoids

growth_protocol: Briefly, isolated tissues were shortly incubated in 10ml Ad-F+++ in Falcon tube. Advanced DMEM/F12 was supplemented with penicillin/streptomycin, 10 mM HEPES, 2 mM GlutaMAX . The tissue was cut into small pieces, washed with ice-cold type I solution at least five times, and subsequently digested with 500mM EDTA for 25 min on the shaker. The supernatant was filtered, collected and centrifuged. The cell pellet was suspended with matrigel and dispensed into two 24-well culture plates. The basal culture medium for organoids was prepared as following(50ml): Ad-F+++ was supplemented with 1ml B27, 500 μl N2, 10 nM gastrin I, and 1.25 mM N-acetylcysteine, 50 ng/ml recombinant EGF, 15% Noggin conditioned medium, 30% R-spondin-1 conditioned medium, 50% Wnt-3A conditioned medium, 500 nM A83-01, 3mM SB202190, and 10nM Y-27632 2HCl.

extract_protocol:
Total RNA was extracted with Trizol reagents (Thermo) following the manufacturer's instructions.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLVReverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.    A total amount of 3 μg total RNA per sample was used as input material for the  small  RNA  library.  Sequencing  libraries  were  generated  using  NEBNext® Multiplex  Small  RNA  Library  Prep  Set  for  Illumina® (NEB,  USA.) following manufacturer’s  recommendations  and  index  codes  were  added  to  attribute sequences  to  each  sample.  Briefly,  NEB  3'  SR  Adaptor  was  directly,  and  specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation  reaction,  the  SR  RT  Primer  hybridized  to  the  excess  of  3'  SR  Adaptor  (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA  adaptor  into  a  double-stranded  DNA  molecule.  This  step  is  important  to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5´  SR Adaptor in the subsequent ligation step. 5´ends adapter was ligated to 5´ends of miRNAs,  siRNA  and  piRNA.  Then  first  strand  cDNA  was  synthesized  using  M-MuLV  Reverse  Transcriptase  (RNase  H–).  PCR  amplification  was  performed  using  LongAmp  Taq  2X  Master  Mix,  SR  Primer  for  illumina  and  index  (X)  primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA  fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.

treatment_protocol: No treatment

value: Colorectal cancer organoids

tag: genotype


title: 6h_1KO_rep3

description: sequencing run made in 3 lanes


title: Human_lung_P8

description: Gene expression data


title: C_2KO_rep3

description: sequencing run made in 3 lanes

value: heat shock farctor 2 KO


title: 202232360102_R03C01

description: normal lung

tag: patient order


title: 23_Org_sh

description:
Org_sh and Org_NC_gene_fpkm.txt
Org_3_sh

source_name: Knock down CUL4B, colorectal cancer organoids


title: HS_1KO_rep3

description: sequencing run made in 3 lanes

value: heat shock 1 h in 42 degrees


title: Crohn's disease patient 1

value: Peripheral blood

value: Male


title: C_1KO_rep3

description: sequencing run made in 3 lanes


title: 10h_1KO_rep3

description: sequencing run made in 3 lanes

value: treated with Bortezomib for 10 h


title: 16_Org_con

description:
Org_CUL4B and Org_con_TPM.txt
Org_2_WT

source_name: control, colorectal cancer organoids

value: con


title: HS_WT_rep3

description: sequencing run made in 3 lanes


title: 202232360211_R02C01

description: normal lung


title: Human_lung_P6

description: Gene expression data


title: bulk_RNA-seq_HS1_day_16_replicate_2_re-used

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17, building A11

country: Sweden

institute: Lund University

description:
Re-used GSM3633228
GSE131697_GSE127253_hg38.s2.multi.Gencode27.Exon.sjdb.v2.txt.gz

data_processing:
bcl2fastq (Illumina) was used for base-calling.
The reads were aligned to the human genome (GRCh38) with STAR aligner v2.5.0a, allowing for 0.03 mismatches per base and multimapping at up to 10 loci.
Reads overlapping Gencode v27 gene annotations were quantified using the Subread package FeatureCounts.
Genome_build: GRCh38

source_name: forebrain neural progenitors

growth_protocol: Human ES and iPS cells were differentiated into forebrain progenitor cells and RNA was extracted for sequencing at four time points (day 13, 14, 15, and 16 of differentiation). At the start of differentiation, the ES/iPS cells were plated at a density of 10.000 cells/cm2 on LN111 coated Nunc delta multidishes (1.14 µg/cm2; Biolamina). The cells were plated in N2 medium (1:1 DMEM/F-12 (21331-020; Gibco) and Neurobasal (21103-049; Gibco) supplemented with 1% N2 (Gibco), 2 mM L-glutamine (Gibco), and 0.2% penicillin/streptomycin) with dual SMAD-inhibition (10 µM SB431542 (Axon) and 100 ng/ml noggin (Miltenyi)) and 10 µM Y27632. The cells were maintained in this medium (without further addition of Y27632)  up until day 9 of differentiation, at which point N2 medium without SMAD inhibitors was added. On day 11, cells were replated as follows. The cells were washed twice with DPBS and dissociated with StemPro accutase (75 µl/cm2; Gibco) for 10-20 minutes at 37 degrees Celsius. The cells were then collected in a tube with 10 ml wash medium (9.5 ml DMEM/F-12 (31330-038; Gibco) and 0.5 ml knockout serum replacement (Gibco)) and spun at 400 x g for 5 minutes after which they were resuspended in B27 (Neurobasal supplemented with 1% B27 without vitamin A (Gibco), 2 mM L-glutamine and 0.2% penicillin/streptomycin) and replated at 800.000 cells/cm2 on LN111-coated plastic. The medium was supplemented with Y27632 (10 µM), BDNF (20 ng/ml; R&D), and L-ascorbic acid (0.2 mM; Sigma-Aldrich). The cells were maintained in this medium until day 14, after which fresh B27 medium was added.

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen)
Librares were prepared with TruSeq RNA library prep kit v2 (Illumina)

tag: cell type

value: iPSC-derived forebrain neural progenitors

value: RBRC-HPS0328 606A1 from RIKEN


title: 202232360102_R02C01

description: normal lung


title: Human_lung_P7

description: Gene expression data

value: lung


title: Human_lung_P5

description: Gene expression data


title: C_WT_rep4

description: sequencing run made in 3 lanes

value: control


title: Human_lung_P2

description: Gene expression data


title: 202232360101_R06C01

description: normal lung


title: bulk_RNA-seq_HS1_day_16_replicate_1_re-used

description:
Re-used GSM3633227
GSE131697_GSE127253_hg38.s2.multi.Gencode27.Exon.sjdb.v2.txt.gz


title: 09_Org_NC

description:
Org_sh and Org_NC_gene_fpkm.txt
Org_2_WT

source_name: Knock down control, colorectal cancer organoids

value: NC


title: 09_Org_sh

description:
Org_sh and Org_NC_gene_fpkm.txt
Org_2_sh


title: 10h_WT_rep3

description: sequencing run made in 3 lanes

value: wild type


title: 23_Org_NC

description:
Org_sh and Org_NC_gene_fpkm.txt
Org_3_WT


title: 02_Org_NC

description:
Org_sh and Org_NC_gene_fpkm.txt
Org_1_WT


title: 02_Org_sh

description:
Org_sh and Org_NC_gene_fpkm.txt
Org_1_sh


title: 6h_WT_rep3

description: sequencing run made in 3 lanes

value: treated with Bortezomib for 6 h


title: Human_lung_P1

description: Gene expression data


title: bulk_RNA-seq_HS1_day_15_replicate_2_re-used

description:
Re-used GSM3633226
GSE131697_GSE127253_hg38.s2.multi.Gencode27.Exon.sjdb.v2.txt.gz


title: bulk_RNA-seq_HS1_day_15_replicate_1_re-used

description:
Re-used GSM3633225
GSE131697_GSE127253_hg38.s2.multi.Gencode27.Exon.sjdb.v2.txt.gz


title: 10h_2KO_rep2

description: sequencing run made in 3 lanes


title: bulk_RNA-seq_HS1_day_14_replicate_2_re-used

description:
Re-used GSM3633224
GSE131697_GSE127253_hg38.s2.multi.Gencode27.Exon.sjdb.v2.txt.gz


title: Cyst 8 from an ADPKD kidney

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

data_processing:
DNA from 8 libraries were sequenced in Illumina HiSeq machines, base-calling performed using RTA software and demultiplexed to obtain individual Fastq files.
Alignment was done using Bismark program.
UNIX scripts and our in-house developed tool DMAP (Chatterjee et al. 2012, Nucleic Acids Research) was used for post processing of the data.
DNA methylation analysis was performed using a fragment based approach using our own in house developed pipeline called DMAP (Stockwell et al. Bioinformatics, 2014).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: .csv file of chi square analysis between all eight cysts (fragments required to be in at least six of the eight cysts to be included in analysis) and the corresponding methylation values of each cyst sample at each analysed fragment.

source_name: Single ADPKD cyst

extract_protocol:
Genomic DNA was extracted from formalin-fixed sections of ADPKD cyst walls using the QIAmp DNA FFPE Mini Kit (Qiagen), following manufacturer's instruction, excluding paraffin melting steps
Libraries were prepared from 500 ng of genomic DNA. DNA was digested with MspI (New England Biolabs, Ipswich, MA), followed by end repair and the addition of 30 A overhangs. Methylated adaptors (Illumina, San Diego, CA) with a 30 T overhang were then ligated to the generated fragments. Fragments were bisulfite modified using the MethylCode DNA Methylation kit (Invitrogen, Carlsbad, CA) and amplified by PCR before selecting fragments between 40 and 220 bp on a 3% (w/v) NuSieve GTG Agarose gel (Lonza, Basel, Switzerland) and AMPure XP Bead Purification (New England Biolabs, Ipswich, MA). The resulting library was sequenced on an Illumina platform with a single-ended 100 bp run.

treatment_protocol: Kidney was treated with formalin prior to macrodissection and DNA extraction

value: kidney cyst

value: Autosomal Dominant Polycystic Kidney Disease


title: 202225190140_R02C01

description: normal lung

value: Control


title: 202232360102_R07C01

description: normal lung

value: E-cig


title: Cyst 7 from an ADPKD kidney


title: HS_2KO_rep2

description: sequencing run made in 3 lanes

value: osteosarcoma

value: heat shock farctor 2 KO


title: 202225190140_R03C01

description: normal lung


title: bulk_RNA-seq_HS1_day_13_replicate_2_re-used

description:
Re-used GSM3633222
GSE131697_GSE127253_hg38.s2.multi.Gencode27.Exon.sjdb.v2.txt.gz


title: 6h_2KO_rep2

description: sequencing run made in 3 lanes


title: C_2KO_rep2

description: sequencing run made in 3 lanes


title: bulk RNA-seq hiPS10 day 16 replicate 2

description:
sample name in processed data file:
S8Aligned.out.bam
hg38.s2.multi.Gencode27.Exon.sjdb.191007.txt

value: RBRC-HPS0331 610B1 from RIKEN


title: bulk_RNA-seq_HS1_day_14_replicate_1_re-used

description:
Re-used GSM3633223
GSE131697_GSE127253_hg38.s2.multi.Gencode27.Exon.sjdb.v2.txt.gz


title: bulk_RNA-seq_HS1_day_13_replicate_1_re-used

description:
Re-used GSM3633221
GSE131697_GSE127253_hg38.s2.multi.Gencode27.Exon.sjdb.v2.txt.gz


title: HS_1KO_rep2

description: sequencing run made in 3 lanes

value: heat shock farctor 1 KO

value: heat shock 1 h in 42 degrees


title: Cyst 5 from an ADPKD kidney


title: 202232360102_R08C01

description: normal lung


title: Cyst 6 from an ADPKD kidney


title: 6h_1KO_rep2

description: sequencing run made in 3 lanes


title: Cyst 4 from an ADPKD kidney


title: C_WT_rep3

description: sequencing run made in 3 lanes


title: bulk RNA-seq hiPS10 day 16 replicate 1

description:
sample name in processed data file:
S4Aligned.out.bam
hg38.s2.multi.Gencode27.Exon.sjdb.191007.txt


title: Cyst 3 from an ADPKD kidney


title: C_1KO_rep2

description: sequencing run made in 3 lanes


title: 10h_1KO_rep2

description: sequencing run made in 3 lanes

value: treated with Bortezomib for 10 h


title: bulk RNA-seq hiPS10 day 15 replicate 1

description:
sample name in processed data file:
S3Aligned.out.bam
hg38.s2.multi.Gencode27.Exon.sjdb.191007.txt

value: iPSC-derived forebrain neural progenitors


title: bulk RNA-seq hiPS10 day 14 replicate 2

description:
sample name in processed data file:
S6Aligned.out.bam
hg38.s2.multi.Gencode27.Exon.sjdb.191007.txt


title: HS_WT_rep2

description: sequencing run made in 3 lanes


title: Cyst 1 from an ADPKD kidney


title: TAU_WT_Y_11

city: Leuven

first: Bart

last: De Strooper

address: O&N4 Herestraat 49

department: Centre for Brain and Disease research

country: Belgium

institute: VIB - KU Leuven

description: nm.mRNA.mmu.txt

data_processing:
Reads were pre-processed and mapped using BaseSpace SecondaryAnalysis (version 2.4.19.6, basespace.illumina.com), filtering out abundant sequences and trimming 2bp from the 5’ end. Reads were aligned against the mm10/GRCm38 Mus musculus reference genome by Tophat2 (version 2.0.7).
We found in 2 of the 12 APPtg-O mice a 46% lower expression levels of hsa-APPswe, a 26% lower expression of hsa-Psen1L166p and a 24% reduction in mmu-Thy1 gene, which drives the expression of the transgenes (see Suppl. Fig.1). In the absence of an explanation for this phenomenon, these two mice were excluded from all further analyses.
mRNAs with average raw read counts ≤ 5 in 10 out of 96 samples were discarded, leaving 15824 mRNAs for differential expression (DE) analysis. Non-biological variation due to library preparation technicalities (i.e. effects for library prep batch, RNA extraction group and RNA concentration) was removed by the removeBatchEffect function from limma package 3.22.7 Bioconductor/R (3). DE analysis was conducted using a 2-way interaction model (age, genotype, age*genotype) and performing Benjamini-Hochberg p-value adjustment for multiple testing.
Genome_build: mm10/GRCm38 Mus musculus reference genome
Supplementary_files_format_and_content: tab-delimited text file containing read counts after Limma Voom normalisation for all Samples

source_name: hippocampus

growth_protocol: Mice were co-housed and had ad libitum access to food and water.

extract_protocol:
Total RNA was extracted by homogenizing the left hippocampus in TRIzol (Invitrogen, Carlsbad, CA, USA) using 1ml syringes and 22G/26G needles and purified on mirVana spin columns according to the manufacturer’s instructions (Ambion, Austin, TX, USA). RNA purity (260/280 and 260/230 ratios) and integrity was assessed using  Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer with High Sensitivity chips (Agilent Technologies, Inc., Santa Clara, CA, USA) and Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, USA), respectively.
Library preparation and sequencing was performed at the VIB Nucleomics Core (Leuven, Belgium) using 1 μg of total RNA per sample. Poly-A containing mRNA molecules were purified using Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version 15031047 Rev.E) and poly-T oligo-attached magnetic beads. After reverse transcription with random primers, different barcodes were introduced to each sample by ligating a single ‘A’ base to the 3’ ends of the blunt-ended cDNA fragments and multiple indexing adapters and 10 cycles of PCR amplification were performed. 96 libraries were pooled and sequenced in 4 runs using NextSeq 500 High75 Output kits on an Illumina NextSeq 500 instrument (Illumina, San Diego, CA, USA).

treatment_protocol: Mice were sacrificed by cervical dislocation and the hippocampus was microdissected. Brain samples were snap frozen in liquid nitrogen and stored in -80°C until use.

value: hippocampus

tag: strain

tag: age (month)

value: Wildtype


title: bulk RNA-seq hiPS10 day 15 replicate 2

description:
sample name in processed data file:
S7Aligned.out.bam
hg38.s2.multi.Gencode27.Exon.sjdb.191007.txt


title: bulk RNA-seq hiPS10 day 13 replicate 2

description:
sample name in processed data file:
S5Aligned.out.bam
hg38.s2.multi.Gencode27.Exon.sjdb.191007.txt


title: x1_48h_1

city: Paris

first: Dominika

last: Foretek

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: HCT116 cell line with inducible shRNA against Xrn1 doxocyclin induced for 48h

data_processing:
Reads were mapped with tophat version 2.0.6, with the following parameters : -N 3 --read-edit-dist 3 -r 155 --mate-std-dev 80 --no-coverage-search -x 1 -M -p 12 --library-type fr-firststrand -g 1
Only unique mapped reads were kept for further analysis.
Read counting on the annotation gencode19 was performed using htseq-count version 0.6.0, with the following parameters : -f bam -q --mode=intersection-nonempty -r name --stranded=reverse -t gene -i ID
Differential expression analysis was performed by Deseq2 version 1.18.1, with default options (genes with 0 count in all samples were preliminarly removed, then a pseudocount of “1” was added).
Genome_build: hg19
Supplementary_files_format_and_content: For each sample, tab-delimited text file of raw counts (the first column is the gene ID, and the second column is the count value)

source_name: HCT116 cell line

growth_protocol: HCT116 cell line was grown in McCoy's 5A Modified medium, supplemented with FBS, non-essential amino-acids and sodium pyruvate, at 37°C, 5% CO2.

extract_protocol:
RNA used for shRNA Xrn1 experiment was isolated using Quiazol and miRNase Mini Kit (Quiagen), next subjected to DNase treatement (Quiagen) and quality control with Bioanalyzer.
Total RNA-seq libraries were prepared with TruSeq Stranded Total RNA Sample Prep Kit (RS-122-2201, Illumina)

treatment_protocol: doxocyline was added to cells in concentration of 1ug/ml for 48h

tag: treatment

value: Xrn1 silencing


title: x1_48h_2


title: bulk RNA-seq hiPS10 day 14 replicate 1

description:
sample name in processed data file:
S2Aligned.out.bam
hg38.s2.multi.Gencode27.Exon.sjdb.191007.txt


title: ns_48h_2

description: HCT116 control cell line with non-silencing shRNA doxocyclin induced for 48h

value: non-silencing


title: C_WT_rep2

description: sequencing run made in 3 lanes

value: wild type

value: control


title: 6h_2KO_rep1

description: sequencing run made in 3 lanes

value: treated with Bortezomib for 6 h


title: HS_h9_d15_276: bulk RNA-seq H9 day 15 replicate 2

value: ESC-derived forebrain neural progenitors


title: 6h_WT_rep2

description: sequencing run made in 3 lanes


title: HS_h9_d16_267: bulk RNA-seq H9 day 16 replicate 1


title: 10h_WT_rep2

description: sequencing run made in 3 lanes


title: 10h_2KO_rep1

description: sequencing run made in 3 lanes


title: ns_48h_1


title: C_2KO_rep1

description: sequencing run made in 3 lanes


title: TAU_WT_Y_07

description: nm.mRNA.mmu.txt


title: TAU_WT_Y_09

description: nm.mRNA.mmu.txt


title: TAU_WT_Y_08

description: nm.mRNA.mmu.txt


title: HS_h9_d14_273: bulk RNA-seq H9 day 14 replicate 2


title: HS_h9_d15_264: bulk RNA-seq H9 day 15 replicate 1


title: Cyst 2 from an ADPKD kidney

value: kidney cyst

value: Autosomal Dominant Polycystic Kidney Disease


title: RNA_12_Calu6_4_G418_B

city: Baltimore

first: Rachel

last: Green

state: MD

address: 725 N Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: Total RNA

data_processing:
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Linker sequence (For ribosome proifling: NNNNNNCACTCGGGCACCAAGGAC, For RNA-seq: FW=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, RV=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA) was trimmed using Skewer
reads aligning to non-coding RNA sequences including rRNA and tRNA were depleted using STAR
remaining reads were aligned to the human genome using STAR
Genome_build: GRCh38 (hg38), Gencode release 30
Supplementary_files_format_and_content: Count tables for ribosome profiling samples

source_name: G418 500 ug/mL RNA-seq B

growth_protocol: Cells were grown in DMEM with 10% FBS to ~75% confluency before harvest

extract_protocol:
Cells were lysed on ice in the presence of cycloheximide. Lysates were clarified by centrifugation. For ribosome profiling, monosomes were generated by RNaseI digest followed by ultracentrifugation. For RNAseq, total RNA was extracted using Trizol, and sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Gold (20020598) kit.
For ribosome profiling, fragments ranging from 26-35 nt were gel purified. Upon dephosphorylation of sample RNA, linker was ligated and this product and and rRNA was depleted using Ribo-Zero Gold from Illumina. This was followed by reverse transcription and gel purification. Libraries were then circularized, PCR-amplified, and gel-purified cDNA was submitted for sequencing.

treatment_protocol: Aminoglycosides were added to cells, and treated for 24 hours

value: Calu-6 cells

tag: concentration

value: 500 ug/mL

tag: duration

value: 24 hours

tag: adapter


title: RNA_10_Calu6_2_Untr_B

description: Total RNA

source_name: Untreated RNA-seq B

tag: cell line

value: Untreated

value: 0 ug/mL


title: RNA_11_Calu6_3_G418_A

description: Total RNA

source_name: G418 500 ug/mL RNA-seq A


title: TAU_WT_Y_10

description: nm.mRNA.mmu.txt


title: HS_2KO_rep1

description: sequencing run made in 3 lanes

tag: disease

value: osteosarcoma

value: heat shock farctor 2 KO

value: heat shock 1 h in 42 degrees


title: HS_h9_d16_279: bulk RNA-seq H9 day 16 replicate 2


title: TAU_WT_Y_12

description: nm.mRNA.mmu.txt

value: hippocampus

value: Wildtype


title: bulk RNA-seq hiPS10 day 13 replicate 1

description:
sample name in processed data file:
S1Aligned.out.bam
hg38.s2.multi.Gencode27.Exon.sjdb.191007.txt

value: iPSC-derived forebrain neural progenitors

value: RBRC-HPS0331 610B1 from RIKEN


title: TAU_WT_Y_06

description: nm.mRNA.mmu.txt


title: RNA_9_Calu6_1_Untr_A

description: Total RNA

source_name: Untreated RNA-seq A


title: HS_1KO_rep1

description: sequencing run made in 3 lanes

value: heat shock farctor 1 KO


title: HS_h9_d13_258: bulk RNA-seq H9 day 13 replicate 1


title: 6h_1KO_rep1

description: sequencing run made in 3 lanes

value: treated with Bortezomib for 6 h


title: HS_h9_d14_261: bulk RNA-seq H9 day 14 replicate 1

value: ESC-derived forebrain neural progenitors


title: TAU_WT_Y_05

description: nm.mRNA.mmu.txt


title: RPF_29_Calu6_2_G418_A

description: Ribosome Protected mRNA (26-35 nt)

source_name: G418 500 ug/mL ribosome profiling A

value: CTGTAGGCACCATCAAT


title: TAU_WT_Y_04

description: nm.mRNA.mmu.txt


title: RPF_28_Calu6_1_Untr_A

description: Ribosome Protected mRNA (26-35 nt)

source_name: Untreated ribosome profiling A


title: 10h_1KO_rep1

description: sequencing run made in 3 lanes

value: treated with Bortezomib for 10 h


title: RPF_27_G418rep3_2_G418_A

description: Ribosome Protected mRNA (15-35 nt)

data_processing:
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Deduplication of PCR duplicates using Tally
5 prime ends of reads were trimmed using seqtk removing 4 nucleotides of degenerate RT primer sequence (RNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSP18/TTCAGACGTGTGCTCTTCCGATCTGTCCTTGGTGCCCGAGTG)
Linker sequence (NNNNNNCACTCGGGCACCAAGGAC) was trimmed using Skewer
reads aligning to non-coding RNA sequences including rRNA and tRNA were depleted using STAR
remaining reads were aligned to the human genome using STAR
Genome_build: GRCh38 (hg38), Gencode release 30
Supplementary_files_format_and_content: Count tables for ribosome profiling samples

source_name: G418 ribosome profiilng A

extract_protocol:
Cells were lysed on ice in the presence of cycloheximide. Lysates were clarified by centrifugation. For ribosome profiling, monosomes were generated by RNaseI digest followed by ultracentrifugation.
For ribosome profiling, fragments ranging from 15-35 nt were gel purified. Upon dephosphorylation of sample RNA, linker was ligated and this product and and rRNA was depleted using Ribo-Zero Gold from Illumina. This was followed by reverse transcription and gel purification. Libraries were then circularized, PCR-amplified, and gel-purified cDNA was submitted for sequencing.

value: HEK293T cells

value: NNNNNNCACTCGGGCACCAAGGAC


title: HS_h9_d13_270: bulk RNA-seq H9 day 13 replicate 2


title: 10h_WT_rep1

description: sequencing run made in 3 lanes

value: wild type


title: 6h_WT_rep1

description: sequencing run made in 3 lanes


title: HS_WT_rep1

description: sequencing run made in 3 lanes


title: RPF_24_G418rep2_2_Untr_B

description: Ribosome Protected mRNA (26-35 nt)

data_processing:
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Linker sequence (NNNNNNCACTCGGGCACCAAGGAC) was trimmed using Skewer
reads aligning to non-coding RNA sequences including rRNA and tRNA were depleted using STAR
remaining reads were aligned to the human genome using STAR
Genome_build: GRCh38 (hg38), Gencode release 30
Supplementary_files_format_and_content: Count tables for ribosome profiling samples

source_name: Untreated ribosome profiling B

extract_protocol:
Cells were lysed on ice in the presence of cycloheximide. Lysates were clarified by centrifugation. For ribosome profiling, monosomes were generated by RNaseI digest followed by ultracentrifugation.
For ribosome profiling, fragments ranging from 26-35 nt were gel purified. Upon dephosphorylation of sample RNA, linker was ligated and this product and and rRNA was depleted using Ribo-Zero Gold from Illumina. This was followed by reverse transcription and gel purification. Libraries were then circularized, PCR-amplified, and gel-purified cDNA was submitted for sequencing.

value: Untreated

value: 24 hours


title: C_WT_rep1

description: sequencing run made in 3 lanes

source_name: cell

value: osteosarcoma

value: control


title: RPF_25_G418rep2_3_G418_A

description: Ribosome Protected mRNA (26-35 nt)

value: 500 ug/mL


title: C_1KO_rep1

description: sequencing run made in 3 lanes


title: TAU_WT_Y_01

description: nm.mRNA.mmu.txt

value: hippocampus


title: TAU_WT_O_13

description: nm.mRNA.mmu.txt

value: Wildtype


title: TAU_WT_O_12

description: nm.mRNA.mmu.txt


title: RPF_23_G418rep2_1_Untr_A

description: Ribosome Protected mRNA (26-35 nt)

value: 0 ug/mL


title: RPF_22_G418rep1_4_G418_B

description: Ribosome Protected mRNA (15-35 nt)

source_name: G418 500 ug/mL ribosome profiling B


title: TAU_WT_O_11

description: nm.mRNA.mmu.txt


title: BRD 5 [S_76]

city: Canyon

first: Matthew

middle: Adam

last: Scott

state: TX

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

institute: Texas A&M University

data_processing:
Illumina RTA v2 software was used for base calling.
Read quality was assessed in FastQC v0.11.8
Read trimming was performed with Trimmomatic v0.38 with parameters ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Read mapping and indexing was performed with HISAT2 v2.1.0, using the bovine whole genome assembly ARS-UCD1.2; parameters -p 8 --dta -x GCF_002263795.1_ARS-UCD1.2_genomic
Read assembly and quantification was performed with StringTie v1.3.4 with parameters -p 8 -G ref_ARS-UCD1.2_top_level, followed by ./stringtie --merge -p 8 -G ref_ARS-UCD1.2_top_level, and /stringtie -e -p 8 -G stringtie_merge.gtf -o. A read count matrix was generated with prepDE.py with parameters python2.7 ./prepDE.py -i mergelist.txt. Differential expression analysis was performed with edgeR v3.24.3 and DESeq2 v1.22.2.
Genome_build: GCF_002263795.1
Supplementary_files_format_and_content: tab-delimited text file of gene counts for each sample

organism: Bos taurus

source_name: BRD_whole blood

extract_protocol:
RNA purification and extraction was performed with the Tempus Spin RNA Isolation kit (Applied Biosystems), per product instructions. RNA concentration and quality was measured with an Agilent 2100 (Agilent).
Paired end libraries were prepared using the TruSeq stranded mRNA kit. All samples were generated in 2 x 150 base pair lengths, in 2 lanes, at 80 million reads per sample.

treatment_protocol: All blood samples were collected in Tempus blood tubes (Applied Biosystem). Samples were stored per product recommendation.

tag: arrival weight (lbs.)

tag: disease status

value: bovine respiratory disease (BRD)

value: whole blood


title: RPF_19_G418rep1_1_Untr_A

description: Ribosome Protected mRNA (15-35 nt)


title: RPF_20_G418rep1_2_Untr_B

description: Ribosome Protected mRNA (15-35 nt)


title: RPF_21_G418rep1_3_G418_A

description: Ribosome Protected mRNA (15-35 nt)


title: BRD 6 [S_85]


title: RNA_8_allAG_18_G418_10min_B

description: Total RNA

data_processing:
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Deduplication of PCR duplicates using Tally
5 prime ends of reads were trimmed using seqtk removing 4 nucleotides of degenerate RT primer sequence (RNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSP18/TTCAGACGTGTGCTCTTCCGATCTGTCCTTGGTGCCCGAGTG)
Linker sequence (NNNNNNCACTCGGGCACCAAGGAC) was trimmed using Skewer
reads aligning to non-coding RNA sequences including rRNA and tRNA were depleted using STAR
remaining reads were aligned to the human genome using STAR
Genome_build: GRCh38 (hg38), Gencode release 30
Supplementary_files_format_and_content: Count tables for ribosome profiling and RNA-seq samples

source_name: G418 500 ug/mL 10-min RNAseq B

extract_protocol:
Cells were lysed on ice in the presence of cycloheximide. Lysates were clarified by centrifugation. For ribosome profiling, monosomes were generated by RNaseI digest followed by ultracentrifugation. For RNAseq, total RNA was extracted using Trizol, and sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Gold (20020598) kit.
For ribosome profiling, fragments ranging from 15-34 nt were gel purified. Upon dephosphorylation of sample RNA, linker was ligated and this product and and rRNA was depleted using Ribo-Zero Gold from Illumina. This was followed by reverse transcription and gel purification. Libraries were then circularized, PCR-amplified, and gel-purified cDNA was submitted for sequencing. RNA-seq samples were prepared from 1 ug of total RNA following the Truseq protocol.

treatment_protocol: Aminoglycosides were added to cells, and treated for either 10 minutes or 24 hours

value: 10 minutes


title: TAU_WT_Y_02

description: nm.mRNA.mmu.txt


title: Healthy 5 [S_55]

source_name: healthy_whole blood

value: healthy


title: TAU_WT_O_09

description: nm.mRNA.mmu.txt


title: TAU_WT_O_08

description: nm.mRNA.mmu.txt


title: TAU_WT_O_06

description: nm.mRNA.mmu.txt


title: TAU_WT_O_10

description: nm.mRNA.mmu.txt


title: RPF_26_G418rep3_1_Untr_A

description: Ribosome Protected mRNA (15-35 nt)


title: TAU_WT_Y_03

description: nm.mRNA.mmu.txt


title: BRD 4 [S_75]


title: BRD 3 [S_52]


title: Healthy 6 [S_72]


title: TAU_WT_O_05

description: nm.mRNA.mmu.txt


title: TAU_WT_O_04

description: nm.mRNA.mmu.txt


title: BRD 2 [S_51]


title: TAU_WT_O_03

description: nm.mRNA.mmu.txt


title: BRD 1 [S_33]


title: Healthy 4 [S_28]


title: RNA_4_allAG_4_G418_500_B

description: Total RNA

source_name: G418 500 ug/mL RNAseq B


title: TAU_WT_O_02

description: nm.mRNA.mmu.txt


title: RNA_5_allAG_5_G418_2000_A

description: Total RNA

source_name: G418 2000 ug/mL RNAseq A


title: RNA_6_allAG_6_G418_2000_B

description: Total RNA

source_name: G418 2000 ug/mL RNAseq B


title: Healthy 3 [S_12]


title: RNA_3_allAG_3_G418_500_A

description: Total RNA

source_name: G418 500 ug/mL RNAseq A


title: RNA_7_allAG_17_G418_10min_A

description: Total RNA

source_name: G418 500 ug/mL 10-min RNAseq A


title: RNA_2_allAG_2_Untr_B

description: Total RNA

source_name: Untreated RNAseq B


title: TAU_TG_Y_11

description: nm.mRNA.mmu.txt

source_name: hippocampus

value: Transgenic


title: Healthy 1 [S_5]


title: crz1hog1_FK506_60min_rep2

city: Worcester

first: Jennifer

last: Benanti

address: 364 Plantation St., LRB 525

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

description:
D-60
FCHKJF7BBXX_L6_HKRDBUDwuvRAAPRAAPEI-207

data_processing:
RNA-seq reads were aligned to the reference genome sacCer3 by using TopHat2 (version 2.1.1) with the maximal intron length set as 100 kb
A gene-level count summary table per sample was generated by using featureCounts (in subread 1.5.3)
Genome_build: sacCer3
Supplementary_files_format_and_content: A tab-delimited txt file for all samples: column 1 is yeast gene ID; other columns are the raw read count at the gene level generated by featureCounts

organism: Saccharomyces cerevisiae

growth_protocol: All strains are in the BY4741 background and were grown in synthetic media with ammonium chloride as a nitrogen source.

extract_protocol:
Total RNA was purified using an acid-phenol extraction protocol.
For each sample Ribo-Zero™ Kits were used to remove rRNA and the remaining RNA fragmented using Ambion Fragmentation Solution. First-strand cDNA was synthesized by random-hexamer priming via the standard Illumina solexa transcriptome sequencing protocol. Fragments were purified with QiaQuick PCR extraction kit then end repaired and A-tailed before ligating to sequencing adaptors. UNG was added before synthesizing the second cDNA strand. After the second strand was degraded, dUTP was converted to dTTP and Y-adaptors added. Samples were enriched by PCR and suitable fragments purified by agarose gel electrophoresis.

treatment_protocol: Yeast cells were pre-treated with ET buffer or 1μg/ml FK506 for 15 minutes prior to the addition of 200mM CaCl2. Samples were collected at intervals following CaCl2 addition for RNA isolation.

tag: strain name

tag: strain information

value: MATa ura3∆0 leu2∆0 his3∆0 met15∆0 crz1∆::KanMx Hcm1-3HA-HIS3 hog1∆::LEU2

tag: pre-treatment

tag: time point

value: 60 minutes


title: TAU_TG_Y_10

description: nm.mRNA.mmu.txt

tag: tissue

tag: genotype


title: TAU_TG_Y_12

description: nm.mRNA.mmu.txt


title: TAU_TG_Y_08

description: nm.mRNA.mmu.txt


title: TAU_TG_Y_09

description: nm.mRNA.mmu.txt


title: TAU_TG_Y_07

description: nm.mRNA.mmu.txt


title: crz1hog1_FK506_10min_rep2

description:
D-10
FCHKJF7BBXX_L6_HKRDBUDwuvRAANRAAPEI-205


title: crz1hog1_FK506_0min_rep2

description:
D-0
FCHKJF7BBXX_L6_HKRDBUDwuvRAAMRAAPEI-202

value: 0 minutes


title: crz1hog1_ET_30min_rep2

description:
C-30
FCHKJF7BBXX_L6_HKRDBUDwuvRAAKRAAPEI-225

value: ET buffer

value: 30 minutes


title: TAU_TG_Y_06

description: nm.mRNA.mmu.txt


title: RNA_1_allAG_1_Untr_A

description: Total RNA

source_name: Untreated RNAseq A

value: HEK293T cells

value: Untreated

value: 24 hours


title: RPF_18_allAG_18_G418_500_10min_B

description: Ribosome Protected mRNA (15-35 nt)

source_name: G418 500 ug/mL 10-min ribosome profiling B

value: 500 ug/mL

value: NNNNNNCACTCGGGCACCAAGGAC


title: RPF_15_allAG_15_Amik_A

description: Ribosome Protected mRNA (15-35 nt)

source_name: Amikacin ribosome profiling A

value: Amikacin


title: TAU_TG_Y_05

description: nm.mRNA.mmu.txt

value: hippocampus


title: TAU_TG_Y_04

description: nm.mRNA.mmu.txt


title: RPF_13_allAG_13_Tobra_A

description: Ribosome Protected mRNA (15-35 nt)

source_name: Tobramycin ribosome profiling A

value: Tobramycin


title: siXRN1-2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

data_processing:
Mapping with STAR_2.4.0a versus hg19 folowing Encode RNA-seq options.
Counting with featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M -C" options.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix text file with raw read count, rows are genes, columns are samples

source_name: Hela cells

growth_protocol: Cells were plated at 200 000 cells/well in 6-well plates. After 24 h, cells were transfected with siRNA negative Control or Silencer Pre-designed siRNA XRN1 at 50 nM using Lipofectamine RNAiMAX (Life Technologies) according to the manufacturer’s instructions. Forty-eight hours after transfection, cells were lysed for RNA analysis as described below.

extract_protocol:
Total RNA extraction was performed using TRI-Reagent (Sigma-Aldrich) and QIAGEN RNAeasy kit. Isolation of RNA from cultured cells or human samples was performed as described previously (15,16). The RNA concentration was measured by NanoDrop 2000 (Thermo Fisher Scientific), the purity (A260/A280) of RNA was around 2.0 and the yield was in a range of 200–500 ng/ l. Then, mRNA were analyzed on a Bioanalyzer (Agilent) and only samples with RIN > 9 were used for further experiments.
Paired-end 2x75b reads

value: Hela


title: crz1hog1_FK506_30min_rep2

description:
D-30
FCHKJF7BBXX_L6_HKRDBUDwuvRAAORAAPEI-206


title: TAU_WT_O_01

description: nm.mRNA.mmu.txt

value: Wildtype


title: RPF_17_allAG_17_G418_500_10min_A

description: Ribosome Protected mRNA (15-35 nt)

source_name: G418 500 ug/mL 10-min ribosome profiling A

value: 10 minutes


title: crz1hog1_ET_0min_rep2

description:
C-0
FCHKJF7BBXX_L6_HKRDBUDwuvRAAIRAAPEI-222


title: TAU_TG_Y_03

description: nm.mRNA.mmu.txt

value: Transgenic


title: RPF_16_allAG_16_Amik_B

description: Ribosome Protected mRNA (15-35 nt)

source_name: Amikacin ribosome profiling B

value: Amikcain


title: RPF_11_allAG_11_Neo_A

description: Ribosome Protected mRNA (15-35 nt)

source_name: Neomycin ribosome profiling A

value: Neomycin


title: siXRN1-1


title: crz1hog1_ET_60min_rep2

description:
C-60
FCHKJF7BBXX_L6_HKRDBUDwuvRAALRAAPEI-227

value: MATa ura3∆0 leu2∆0 his3∆0 met15∆0 crz1∆::KanMx Hcm1-3HA-HIS3 hog1∆::LEU2

value: 60 minutes


title: crz1hog1_FK506_60min_rep1

description:
B-60
FCHKJF7BBXX_L6_HKRDBUDwuvRAAHRAAPEI-221


title: crz1hog1_ET_10min_rep2

description:
C-10
FCHKJF7BBXX_L6_HKRDBUDwuvRAAJRAAPEI-223

value: ET buffer


title: RPF_12_allAG_12_Neo_B

description: Ribosome Protected mRNA (15-35 nt)

source_name: Neomycin ribosome profiling B

value: HEK293T cells


title: siCTL-2


title: RPF_14_allAG_14_Tobra_B

description: Ribosome Protected mRNA (15-35 nt)

source_name: Tobramycin ribosome profiling B


title: crz1hog1_FK506_30min_rep1

description:
B-30
FCHKJF7BBXX_L6_HKRDBUDwuvRAAGRAAPEI-220

value: 30 minutes


title: TAU_TG_Y_02

description: nm.mRNA.mmu.txt


title: TAU_TG_Y_01

description: nm.mRNA.mmu.txt


title: siCTL-1


title: crz1hog1_FK506_10min_rep1

description:
B-10
FCHKJF7BBXX_L6_HKRDBUDwuvRAAFRAAPEI-219


title: TAU_TG_O_13

description: nm.mRNA.mmu.txt


title: crz1hog1_FK506_0min_rep1

description:
B-0
FCHKJF7BBXX_L6_HKRDBUDwuvRAAERAAPEI-218

value: 0 minutes


title: TAU_TG_O_12

description: nm.mRNA.mmu.txt


title: crz1hog1_ET_60min_rep1

description:
A-60
FCHKJF7BBXX_L6_HKRDBUDwuvRAADRAAPEI-216


title: RPF_8_allAG_8_Genta_B

description: Ribosome Protected mRNA (15-35 nt)

source_name: Gentamicin ribosome profiling B

value: Gentamicin

value: 500 ug/mL

value: 24 hours


title: RPF_7_allAG_7_Genta_A

description: Ribosome Protected mRNA (15-35 nt)

source_name: Gentamicin ribosome profiling A

value: NNNNNNCACTCGGGCACCAAGGAC


title: Healthy 2 [S_6]

source_name: healthy_whole blood

value: healthy

value: whole blood


title: anti-Dll4 3

city: Daejeon

first: Injune

last: Kim

address: Daehak-ro 291, Biomedical Building (E7) 8102

department: Graduate School of Medical Science and Engineering

institute: Korea Advanced Institute of Science and Technology

description: EC-specific ribosome-bound mRNA

data_processing:
Reads were trimmed based on sequencing quality using Sickle.
Adaptor contents were removed using Cutadapt.
Trimmed reads were aligned on a human reference sequence (hg19) using Tophat2.
The number of mapped reads on the 3’ end of each gene was calculated using Bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: Raw read count

source_name: Retina

extract_protocol:
Fresh retinas were dissected, snap-frozen into liquid nitrogen, homogenized in polysome buffer (50 mM Tris pH 7.5, 100 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1 mM DTT, 200 U/ml RNase inhibitor, protease inhibitor cocktail (P2714, Sigma), 1 mg/ml heparin, and 100 mg/ml cycloheximide) with pellet pestles, and centrifuged at 4°C for 10 min with 12,000 g. Ten% of supernatant was reserved as an ‘input’ and immediately stored at -80°C. The remaining supernatant was incubated with magnetic beads with anti-HA antibody (M180-9, MBL) at 4°C. After the supernatant was aspirated, the beads were washed with high salt buffer (50 mM Tris pH 7.5, 300 mM KCl, 12 mM MgCl2, 1 mM DTT, and 100 mg/ml cycloheximide) and re-suspended with supplemented RLT buffer (400 µl, with β-mercaptoethanol, Qiagen). The suspensions were used for ‘HA-enriched’ RNA extraction. RNAs from both ‘input’ and ‘HA enrichment’ were extracted using RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s instruction.
Total RNA quality was assessed with the Agilent 2100 Bioanalyzer System. Extracted RNA samples were processed using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Vienna) and sequenced on an Illumina NextSeq 500. A median 2.0x107 (range 1.7x107 to 2.4x107) single-end reads with 75 bp were generated.

tag: cell type

value: Retinal endothelial cell

value: Retina

tag: age

value: adult

value: Cdh5-CreERT2 Rpl22 tm1.1Psam


title: anti-Dll4 4

description: EC-specific ribosome-bound mRNA

tag: strain


title: RPF_6_allAG_6_G418_2000_B

description: Ribosome Protected mRNA (15-35 nt)

source_name: G418 2000 ug/mL ribosome profiling B

tag: treatment


title: TAU_TG_O_11

description: nm.mRNA.mmu.txt

value: hippocampus

tag: age (month)

value: Transgenic


title: RPF_10_allAG_10_Parom_B

description: Ribosome Protected mRNA (15-35 nt)

source_name: Paromomycin ribosome profiling B

value: Paromomycin

tag: concentration

tag: duration


title: anti-Dll4 2

description: EC-specific ribosome-bound mRNA


title: crz1hog1_ET_30min_rep1

description:
A-30
FCHKJF7BBXX_L6_HKRDBUDwuvRAACRAAPEI-214

value: MATa ura3∆0 leu2∆0 his3∆0 met15∆0 crz1∆::KanMx Hcm1-3HA-HIS3 hog1∆::LEU2

value: ET buffer


title: RPF_5_allAG_5_G418_2000_A

description: Ribosome Protected mRNA (15-35 nt)

source_name: G418 2000 ug/mL ribosome profiling A

tag: cell line

value: HEK293T cells

tag: adapter


title: RPF_9_allAG_9_Parom_A

description: Ribosome Protected mRNA (15-35 nt)

source_name: Paromomycin ribosome profiling A


title: TAU_TG_O_08

description: nm.mRNA.mmu.txt

source_name: hippocampus


title: RPF_4_allAG_4_G418_500_B

description: Ribosome Protected mRNA (15-35 nt)

source_name: G418 500 ug/mL ribosome profiling B


title: crz1hog1_ET_10min_rep1

description:
A-10
FCHKJF7BBXX_L6_HKRDBUDwuvRAABRAAPEI-213

value: 10 minutes


title: crz1hog1_ET_0min_rep1

description:
A-0
FCHKJF7BBXX_L6_HKRDBUDwuvRAAARAAPEI-212

value: 0 minutes


title: Control IgG 4

description: EC-specific ribosome-bound mRNA

value: control IgG


title: RPF_3_allAG_3_G418_500_A

description: Ribosome Protected mRNA (15-35 nt)

source_name: G418 500 ug/mL ribosome profiling A

value: 500 ug/mL

value: 24 hours


title: crz1hcm1dP_ET_90min_rep2

data_processing:
RNA-seq reads were aligned to the reference genome sacCer3 by using TopHat2 (version 2.1.1) with the maximal intron length set as 100 kb
A gene-level count summary table per sample was generated by using htseq-count (version 0.8.0)
Genome_build: sacCer3
Supplementary_files_format_and_content: A tab-delimited txt file for each sample: column 1 is yeast gene ID; column 2 is the raw read count at gene level generated by htseq-count

extract_protocol:
Total RNA was purified using an acid-phenol extraction protocol.
Ribo-Zero™ Magnetic Kit is used to remove RNA, remained RNA is then retrieved by ethonal precipitation. The retrieved RNA is fragmented using Ambion Fragmentation Solution. And according to Illumina solexa transcriptome sequencing protocol, random hexamer-primer was used to synthesize the first-strand cDNA. The second-strand cDNA is synthesized using buffer, dNTPs, RNase H and DNA polymerase I. Fragments are purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding A at 3’ end. After that, the fragments are ligated with sequencing adaptors. UNG is added before synthesizing the second cDNA strand. After the second strand degraded, dUTP is then converted to dTTP. Y-adaptor is added afterwards. Suitable fragments are selected as templates according to the agarose gel electrophoresis results for PCR amplification.

treatment_protocol: Yeast cells were pre-treated with ET buffer or 1μg/ml FK506 for 15 minutes prior to the addition of 200mM CaCl2. Samples were collected at 10-30 minute intervals following CaCl2 addition for RNA isolation.

value: MATa ura3∆0 leu2∆0 his3∆0 met15∆0 crz1∆::KanMx Hcm1-∆PSIEIQ-3HA-HIS3

value: 90 minutes


title: TAU_TG_O_06

description: nm.mRNA.mmu.txt


title: RPF_2_allAG_2_Untr_B

description: Ribosome Protected mRNA (15-35 nt)

source_name: Untreated ribosome profiling B

value: Untreated

value: 0 ug/mL

value: NNNNNNCACTCGGGCACCAAGGAC


title: Control IgG 15

description: EC-specific ribosome-bound mRNA

value: Retinal endothelial cell

value: Retina

value: adult

value: Cdh5-CreERT2 Rpl22 tm1.1Psam


title: Control IgG 3

description: EC-specific ribosome-bound mRNA


title: crz1hcm1dP_ET_60min_rep2

value: 60 minutes


title: RPF_1_allAG_1_Untr_A

description: Ribosome Protected mRNA (15-35 nt)

source_name: Untreated ribosome profiling A


title: MSK_LX701_METASTASIS

city: NEW YORK

first: Ashley

middle: M

last: Laughney

state: New York

address: 413 East 69th Street

department: Physiology, Biophysics and Systems Biology

institute: Weill Cornell Medicine

description: Barcoded single cells

data_processing:
The Sequence Quality Control (SEQC) package18 was utilized for de-multiplexing, STAR alignment, implementation of cell barcode and multi-alignment correction, and the generation of a raw digital expression matrix by collapsing groups of reads with the same unique molecular identifier (UMI), cell barcode and gene annotation. Alignment to the hg38 annotation was restricted to transcribed, polyadenylated RNA of length > 200 nucleotides (gene biotypes accessible by 3’ mRNA sequencing technologies) to increase mapping specificity.
Genome_build: hg38 annotation restricted to transcribed, polyadenylated RNA of length > 200 nucleotides
Supplementary_files_format_and_content: csv of cells x genes unnormalized

source_name: Patient primary lung adenocarcinoma metastasis to BRAIN

extract_protocol:
Non-involved lung, tumour tissues, and metastatic lesions were obtained from patients with lung adenocarcinoma undergoing resection surgery at Memorial Sloan Kettering Cancer Center (MSKCC, New York, NY) after obtaining informed consent. Tissue samples were immediately placed in RPMI media (Corning) or Hypothermosol on ice and dissociated using both mechanical and enzymatic digestion (Human Tumour Dissociation Kit #130-095-929, Miltenyi Biotec), generally within 1 h of surgical resection. Tissues were minced with a razor blade in the Miltenyi enzyme mix according to the manufacturer’s specifications and transferred to a Gentle MACS Octo Dissociator with heaters (# 30-096-427, 37°C) for further mechanical dissociation. Upon completion, cell suspensions were passed through a 70 µm filter and washed twice with FACS buffer (2% heat-inactivated FBS, 1 mM EDTA and Pen/Strep in PBS without Ca or Mg). Red blood cells were lysed in Red Blood Cell Lysis Solution (ACK lysis buffer) once or twice depending on red blood cell content, and final single-cell suspensions were made in Hanks’ Balanced Salt Solution (HBSS). For scRNA-seq, the remaining cell suspensions were subsequently flow sorted with a BD FACSAria II cell sorter fitted with a 100 µM nozzle to enrich for viable, single cells according to forward and side scattering, and DAPI exclusion. Cells were sorted directly into RPMI media with 10% FBS, washed thrice and re-suspend in PBS with 0.04% BSA for single cell encapsulation.
The 10X Genomics Chromium Platform was used to generate a targeted 5000 single cell Gel Bead-In-Emulsions (GEMs) per sample, loaded with an initial cell viability of ~90%. scRNA-seq libraries were prepared following the 10X Genomics user guide (Single Cell 3′ Reagent Kits User Guide PN-120233, 10X Genomics).
Single cell barcoded 3' mRNA

tag: Stage

value: IV

tag: diagnosis

value: Lung Adenocarcinoma

tag: chemotherapy

value: Yes


title: crz1hcm1dP_ET_45min_rep2

tag: strain name

tag: strain information

value: ET buffer

value: 45 minutes


title: crz1hcm1dP_ET_30min_rep2

tag: pre-treatment

tag: time point

value: 30 minutes


title: MSK_LX699_METASTASIS

description: Barcoded single cells

source_name: Patient primary lung adenocarcinoma metastasis to ADRENAL

tag: tissue


title: MSK_LX685_NORMAL

description: Barcoded single cells

source_name: Patient adjacent non-tumour involved lung

value: non-tumour involved lung

value: No


title: anti-Dll4 1

description: EC-specific ribosome-bound mRNA

tag: cell type

tag: genotype


title: crz1hcm1dP_ET_20min_rep2

value: MATa ura3∆0 leu2∆0 his3∆0 met15∆0 crz1∆::KanMx Hcm1-∆PSIEIQ-3HA-HIS3

value: 20 minutes


title: TAU_TG_O_04

description: nm.mRNA.mmu.txt

value: hippocampus

tag: strain

value: Transgenic


title: TAU_TG_O_05

description: nm.mRNA.mmu.txt


title: TAU_TG_O_03

description: nm.mRNA.mmu.txt


title: 918 smn 0hr

city: Tsukuba

first: Fuminori

last: Takahashi

state: Ibaraki

address: 3-1-1 Koyadai

country: Japan

institute: RIKEN

data_processing:
CLC Genomics Workbench ver.9.0
Genome_build: TAIR10
Supplementary_files_format_and_content: bam files were generated using CLC Genomic Workbench

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Plants were grown for 14days on GM medium at 22oC.

extract_protocol:
Samples were frozen in liquid nitrogen, and total RNA was extracted from whole seedlings and prepared with NucleoSpin® RNA Plant (MACHEREY-NAGEL) according to the manufacturer’s instructions.
Dynabeads mRNA Purification Kit and Ion Total RNA-Seq Kit v2

treatment_protocol: Seedlings were treated with 0.1μM flg22 for 0hr or 4hr.

value: Landsberg erecta

tag: age

value: 14 days

tag: treatment

value: 0.1μM flg22 for 0hr

value: seedling


title: 918 smn 4hr

value: 0.1μM flg22 for 4hr


title: MSK_LX684_NORMAL

description: Barcoded single cells

value: Patient adjacent non-tumour involved lung


title: crz1hcm1dP_ET_0min_rep2

value: 0 minutes


title: crz1hcm1dP_ET_10min_rep2

value: 10 minutes


title: MSK_LX684_PRIMARY_TUMOUR

description: Barcoded single cells

source_name: Patient primary lung adenocarcinoma

value: Patient primary lung adenocarcinoma

value: IA

value: Lung Adenocarcinoma


title: APP_WT_Y_12

description: nm.mRNA.mmu.txt

tag: age (month)

value: Wildtype


title: TAU_TG_O_01

description: nm.mRNA.mmu.txt


title: TAU_TG_O_02

description: nm.mRNA.mmu.txt


title: 918 WT 4hr

value: wild-type


title: crz1_FK506_90min_rep2

value: MATa ura3∆0 leu2∆0 his3∆0 met15∆0 crz1∆::KanMx Hcm1-3HA-HIS3

value: 90 minutes


title: TAU_TG_O_09

description: nm.mRNA.mmu.txt

value: hippocampus


title: MSK_LX682_NORMAL

description: Barcoded single cells

value: non-tumour involved lung

value: No


title: APP_WT_Y_11

description: nm.mRNA.mmu.txt


title: Baseline0707

city: Okayama

first: Yukihide

last: Maeda

address: 2-5-1 Shikata, Kita-Ku

department: Department of Otolaryngology-, Head and Neck Surgery

institute: Okayama University Hospital

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes following the manufacturer’s instructions. On completion of the fragmentation reaction, Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Microarray ver 2 (G4853B) according to the manufacturer's instructions.

scan_protocol: Slides were scanned after washing on the Agilent DNA Microarray Scanner  using one color scan setting for 8x60k array slides.

data_processing: The scanned images were quantified using Feature Extraction software (Agilent). The data was analyzed with GeneSpring GX software. 14.9.1(Agilent). Using GeneSpringGX, intensity of each probe was normalized to 75th percentile, and represented the expression levels of each genes.

source_name: Cochlear tissue without noise exposure

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.１ ug RNA using the One-Color Low Input Quick amp labeling kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using miReasy column (Qiagen) following the manufacturer's recommendations.

treatment_protocol: Mice were exposed to intense noise for 2h. At 3 hours following noise exposure, mice were deeply anesthetized and the cochlear tissue was dissected in RNA later (Qian, Valencia, CA). Cochlear tissues from mice without noise exposure served as controls.

tag: Sex

value: female

value: 7 weeks

value: cochlea

value: without noise exposure


title: MSK_LX682_PRIMARY_TUMOUR

description: Barcoded single cells

value: IB


title: Noise3h

source_name: Cochlear tissue at 3h post-noise exposure

value: at 3h post-noise exposure


title: APP_WT_Y_10

description: nm.mRNA.mmu.txt


title: 910 smn 4hr

value: Landsberg erecta

value: 14 days

value: 0.1μM flg22 for 4hr

value: seedling


title: crz1_FK506_60min_rep2

value: 60 minutes


title: crz1_FK506_45min_rep2

value: 45 minutes


title: MSK_LX681_METASTASIS

description: Barcoded single cells

value: Patient primary lung adenocarcinoma metastasis to BRAIN

value: IV

value: Lung Adenocarcinoma

value: Yes


title: 910 WT 4hr

value: wild-type


title: APP_WT_Y_08

description: nm.mRNA.mmu.txt

value: hippocampus

value: Wildtype


title: crz1_FK506_30min_rep2

value: MATa ura3∆0 leu2∆0 his3∆0 met15∆0 crz1∆::KanMx Hcm1-3HA-HIS3

value: 30 minutes


title: 910 WT 0hr

value: 0.1μM flg22 for 0hr


title: APP_WT_Y_09

description: nm.mRNA.mmu.txt


title: MSK_LX680_PRIMARY_TUMOUR

description: Barcoded single cells

value: Patient primary lung adenocarcinoma

value: IB

value: Lung Adenocarcinom + Large Cell Neuroendocrine Carcinoma

value: No


title: 918 WT 0hr

value: Landsberg erecta

value: 14 days

value: seedling


title: APP_WT_Y_06

description: nm.mRNA.mmu.txt


title: MSK_LX255B_METASTASIS

description: Barcoded single cells

value: Patient primary lung adenocarcinoma metastasis to BRAIN


title: crz1_FK506_10min_rep2

value: 10 minutes


title: crz1_FK506_20min_rep2

value: 20 minutes


title: MSK_LX676_PRIMARY_TUMOUR

description: Barcoded single cells

value: Lung Adenocarcinoma


title: APP_WT_Y_07

description: nm.mRNA.mmu.txt


title: APP_WT_Y_05

description: nm.mRNA.mmu.txt


title: MSK_LX679_PRIMARY_TUMOUR

description: Barcoded single cells

value: IIA

value: Yes


title: crz1_FK506_0min_rep2

value: 0 minutes


title: MSK_LX675_NORMAL

description: Barcoded single cells

value: Patient adjacent non-tumour involved lung

value: non-tumour involved lung


title: 910 smn 0hr

value: 0.1μM flg22 for 0hr


title: APP_WT_Y_04

description: nm.mRNA.mmu.txt

value: hippocampus

value: Wildtype


title: crz1_ET_60min_rep2

value: MATa ura3∆0 leu2∆0 his3∆0 met15∆0 crz1∆::KanMx Hcm1-3HA-HIS3

value: ET buffer

value: 60 minutes


title: crz1_ET_90min_rep2

value: 90 minutes


title: TAU_TG_O_07

description: nm.mRNA.mmu.txt

value: Transgenic


title: MSK_LX675_PRIMARY_TUMOUR

description: Barcoded single cells

value: Patient primary lung adenocarcinoma

value: IV

value: No


title: APP_WT_Y_03

description: nm.mRNA.mmu.txt


title: MSK_LX666_METASTASIS

description: Barcoded single cells

source_name: Patient primary lung adenocarcinoma metastasis to BONE

value: Lung Adenocarcinoma


title: crz1_ET_45min_rep2

value: 45 minutes


title: APP_WT_Y_01

description: nm.mRNA.mmu.txt


title: Xylose rep 3

city: Richland

first: Daniel

middle: Torres

last: Naylor

state: WA

address: 3300 Stevens Drive, MSIN. J4-18

department: Biological Systems Division

institute: Pacific Northwest National Laboratory

description: Enrichment of Prosser, WA soil microbes in liquid culture of M9 + xylose, rep. 3.

data_processing:
Raw reads from all samples were aligned to a previously obtained soil metagenome using the Burrows Wheeler Aligner.
Resulting reads were converted to raw counts using HTSeq.
Only transcripts with at least 75 cumulative counts across the 15 samples, and with no more than 3 zero counts, were retained for downstream analysis.
The dataset was normalized using DESeq.
Statistical analyses were conducted using R.
Genome_build: Prosser soil metagenome, NCBI Bioproject PRJNA597444
Supplementary_files_format_and_content: tab-delimited text files include raw counts and variance-stabilized normalized counts for full dataset, as well as HTSeq output (raw counts) for each sample

organism: soil metagenome

source_name: Soil

extract_protocol:
Microbial cultures of a liquid culture were pelleted, flash frozen using liquid N2, and RNA was harvested using Trizol reagent. Ambien Turbo DNase was used to remove DNA, and MicrobExpress kit was used to deplete rRNA species before sending the purified mRNA to GENEWIZ for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: replicate

tag: enrichment type

value: xylose


title: Xylose rep 2

description: Enrichment of Prosser, WA soil microbes in liquid culture of M9 + xylose, rep. 2.


title: Pectin rep 8

description: Enrichment of Prosser, WA soil microbes in liquid culture of M9 + pectin, rep 8.

value: pectin


title: APP_WT_Y_02

description: nm.mRNA.mmu.txt


title: Xylan rep 15

description: Enrichment of Prosser, WA soil microbes in liquid culture of M9 + xylan, rep. 15.

value: xylan


title: Xylan rep 13

description: Enrichment of Prosser, WA soil microbes in liquid culture of M9 + xylan, rep. 13.


title: Xylose rep 4

description: Enrichment of Prosser, WA soil microbes in liquid culture of M9 + xylan, rep. 4.


title: Xylan rep 11

description: Enrichment of Prosser, WA soil microbes in liquid culture of M9 + xylan, rep. 11.


title: MSK_LX661_PRIMARY_TUMOUR

description: Barcoded single cells

tag: Stage


title: crz1_ET_30min_rep2

value: 30 minutes


title: crz1_ET_20min_rep2

value: 20 minutes


title: MSK_LX653_PRIMARY_TUMOUR

description: Barcoded single cells

tag: diagnosis


title: APP_WT_O_11

description: nm.mRNA.mmu.txt

value: hippocampus


title: crz1_ET_0min_rep2

value: 0 minutes


title: crz1_ET_10min_rep2

value: MATa ura3∆0 leu2∆0 his3∆0 met15∆0 crz1∆::KanMx Hcm1-3HA-HIS3

value: 10 minutes


title: Pectin rep 4

description: Enrichment of Prosser, WA soil microbes in liquid culture of M9 + pectin, rep 4.