title: 387_Hypoxia

description: 387_Hypoxia_vs_Normoxia_RNAseq_Processed.xlsx

data_processing:
FASTQ sequencing files were trimmed and then aligned to the hg19 human genome using the STAR aligner (Dobin et al., 2013).
Differential expression analysis was performed using CuffDiff (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/).
ALKBH1 Knockdown in HYPOXIA: FASTQ sequencing reads were trimmed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)  and transcript quantification was performed using Salmon in the quasi-mapping mode (Patro et al., 2017).
ALKBH1 Knockdown in HYPOXIA: Salmon “quant” files were converted using Tximport (https://bioconductor.org/packages/release/bioc/html/tximport.html) and differential expression analysis was performed using DESeq2 (Love et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: TPM Abundance values from Salmon and FPKM from CuffDiff are provided in Excel Tables

growth_protocol: 387 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocompromised NSG mouse and allowed to grow into a tumor. Cells were dissociated and passaged in vitro. Cells were grown in 1% oxygen

extract_protocol:
Cells were collected and lysed in trizol. Cellular RNA was extracted using the Qiagen miRNeasy Mini Kit.
RNA was extracted with TRIzol (Invitrogen), Cellular RNA was extracted using the Qiagen miRNeasy Mini Kit (catalog number 217004) according to the manufacturers instructions.
Total RNA was prepared for sequencing using the Illumina TruSeq Stranded Total RNA Library Prep Kit according to the manufacturers instructions

tag: agent

value: Cells were grown in 1% oxygen

tag: condition

value: Hypoxia


title: vivo12hr_rep1

status: Public on Nov 01 2018

type: SRA

city: Irvine

first: Ali

last: Mortazavi

address: 2300 E biological science 3

country: USA

institute: University of California Irvine

library_source: transcriptomic

data_processing:
Unstranded, paired-end 43 bp RNA-seq reads for each worm were mapped to the S. feltiae transcriptome downloaded from WormBase ParaSite (WS263) using Bowtie 1.0.0 with the following options: -X 1500 -a -m 200 --S -- seedlen 25 -n 2 --offrate 1 -p 64 -v 3  (Langmead et al. 2009). After Bowtie, gene expression was quantified with RSEM with the following options: rsem-calculate-expression -- bam -- paired-end. Gene expression for S. carpocapsae were performed as previously described (Lu et al. 2017) and reported in Transcripts Per Million (TPM). We used counts for differential gene expression analysis.
The Transcript per million (TPM) generated by rsem-calculate-expression for S. feltiae samples were normalized according to groups using the R package limma (Ritchie et al., 2015) because samples were collected, processed and sequenced in different batches. Samples were batched corrected between 3 and 9 hours in vitro to 6 hours in vitro, 3,6,9,12,15 in vivo with edgeR package removebatcheffects with log2 of TPM matrix.
Genome_build: S_felt_v1

molecule: total RNA

organism: Steinernema feltiae

source_name: activated in a live waxworm

growth_protocol: As described in Serra L., Chang D., Macchietto M., Williams K., Murad R., Lu D., *Dillman A.R., & *Mortazavi A. 2018. Adapting the Smart-seq2 protocol for robust single worm RNA-seq. Bio-protocol 8(4): e2729.

extract_protocol:
as described in Serra L., Chang D., Macchietto M., Williams K., Murad R., Lu D., *Dillman A.R., & *Mortazavi A. 2018. Adapting the Smart-seq2 protocol for robust single worm RNA-seq. Bio-protocol 8(4): e2729.
as described in Serra L., Chang D., Macchietto M., Williams K., Murad R., Lu D., *Dillman A.R., & *Mortazavi A. 2018. Adapting the Smart-seq2 protocol for robust single worm RNA-seq. Bio-protocol 8(4): e2729.
PolyA RNA  unstranded, paired-end, read_length= 43 bp

tag: strain

value: SN

tag: genotype

value: wildtype

tag: developmental stage

value: Infective Juvenile (IJ)

tag: treatment

value: in vivo activated

tag: time point

tag: tissue

value: whole body


title: Hep-Ethanol-0 hr-14

type: RNA

city: Philadelphia

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1020 Locust Street

department: Pathology, Anatomy and Cell Biology

institute: Thomas Jefferson University

description: SAMPLE 138

data_processing:
The data were normalized using the -ΔΔCt scheme. Expression values within samples were normalized using the median expression of 55 high performing genes (Ct_reaction - Ct_median_across_55_genes). Expression values within genes were scaled to the median using (Ct_median_across_all_samples - Ct_reaction)
Missing values were imputed using the k-nearest neighbors imputation after normalization

label: SYBR Green

organism: Rattus norvegicus

source_name: Ethanol-0 hr

extract_protocol: Single hepatocytes extracted using laser capture microdissection were lysed and directly processed for reverse transcription followed by targeted pre-amplification. Pre-amplification of cDNA samples was performed for 22 cycles using TaqMan PreAmp Master Mix as per the manufacturer’s protocol. Primers for the 84 genes tested were custom designed. qPCR was performed on BioMark 96.96 Dynamic Array for 30 cycles.

treatment_protocol: Lieber-De Carli feeding protocol

tag: cell type

value: Hepatocyte

value: liver

tag: diet

value: Ethanol

tag: time after partial hepatectomy

value: 0 hr


title: 387_Normoxia

city: San Diego

first: Jeremy

last: Rich

state: CA

address: 9500 Gilman Drive #0695

institute: University of California, San Diego

organism: Homo sapiens

source_name: Patient Derived Glioblastoma Stem Cell

value: Cells were grown in 20% oxygen

value: Normoxia


title: AWC

city: New York

first: Bhama

last: Ramkhelawon

state: NY

address: 435 East 30th - Science Building 416

department: Surgery

institute: NYU Langone Medical Center

description: RNAseq

data_processing:
FASTQ files were aligned to the MM9 Mus musculus reference genome using Tophat (version 2.0.9) with 2 mismatches allowed
The resulting read counts were extracted using the Featurecounts program from binary alignment map (BAM) files
Differential gene expression analysis was conducted using the DESEQ2 package from the BioconductR repository using the open source R statistical programming environment
P values attained from differential gene expression analysis were adjusted for multiple testing by controlling for false discovery using the Benjamini-Hochberg method and genes with adjusted p values <0.05 were flagged as differentially expressed then used for Gene Set Enrichment Analysis (GSEA)
GSEA was performed using the DAVID Bioinformatics Resource (version 6.8) to elucidate relevant biological significance.
Genome_build: mm9
Supplementary_files_format_and_content: AN_vs_AW file contains Gene name, base mean, log2Fold Change, IfcSE, stat, pvalue, adjusted p value, ensemble ID , description of 23420 genes in ANA, ANB, ANC, AND, AWA, AWB, AWC and AWB samples
Supplementary_files_format_and_content: AN_vs_AW_pathway contains in sheet 1 the Ingenuity Canonical Pathways, -log(p-value), Ratio, z-score and Molecules result of DAVID pathway analysis. Sheet 2 "genes" contains the gene name, log2 fold change and adjusted p value of the 951 significantly changed genes

organism: Mus musculus

source_name: Aortic tissue

extract_protocol:
RNA was extracted from aortas using the RNEasy fibrous tissue kit as per manufacturer’s instructions (74704, Qiagen)
The samples were run on a HiSeq (Illumina) as single-end reads, 50 nucleotides in length

value: Abdominal aortic aneurysm

tag: genotype/variation

value: Apolipoprotein E deficient (ApoE-/-) reconstituted with wild type hematopietic stem cells

tag: protocol

value: Angiotensin II perfusion 28 days


title: AWD

description: RNAseq


title: PB-iNSC_82b-3-SC

city: Aachen

first: Qiong

last: Lin

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization standard Illumina protocol

scan_protocol: Direct Hyb

data_processing: The data were pre-processed and normalised using quantile normalisation with illuminaio and limma in R.

label: biotin

source_name: R330: PB-iNSC

label_protocol: Ambion/LifeTechnologies Illumina TotalPrep-96 RNA Amplification Kit

growth_protocol: Adult human peripheral blood cells are cultured using a published protocol (van den Akker et al., 2010). Neonatal human cord blood cells are cultured in DMEM/F12 medium supplemented with FCS, SCF, TPO, Flt-3 ligand, and IL-6. All the iNSCs are cultured in N2B27 medium supplemented with CHIR99021, purmorphamine, A83-01, and human LIF. All the smNPCs are cultured as described previously (Reinhardt et al., 2013) and all the lt-NES are cultured as described previously ((Koch et al., 2009).

extract_protocol: Total RNA was isolated from cell cultures using RNeasy mini kit (Qiagen)

treatment_protocol: Cells are washed by DPBS before collection

tag: subject status

value: healthy

tag: gender

value: female

tag: age

value: brain

value: peripheral blood cell-derived iNSC (PB-iNSC) line


title: 387_shALKBH1.1551_Normoxia

description: Normoxia_ALKBH1_Knockdown_RNAseq_Processed.xlsx

growth_protocol: 387 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocompromised NSG mouse and allowed to grow into a tumor. Cells were dissociated and passaged in vitro. Cells were grown in 20% oxygen

tag: shRNA

value: Cells were treated with an shRNA targeting ALKBH1


title: CBC

source_name: R327: CBC

value: male

value: neonatal

value: cord blood

value: neonatal cord blood cell


title: vivo12hr_rep2

value: SN

value: wildtype

value: Infective Juvenile (IJ)

value: in vivo activated

value: whole body


title: PB-iNSC_82b-1-SC

source_name: R328: PB-iNSC


title: vivo9hr_rep2


title: Hep-Ethanol-0 hr-11

description: SAMPLE 135

value: Hepatocyte

value: liver

value: Ethanol

value: 0 hr


title: AWA

description: RNAseq

value: Abdominal aortic aneurysm

value: Apolipoprotein E deficient (ApoE-/-) reconstituted with wild type hematopietic stem cells

value: Angiotensin II perfusion 28 days


title: 387_shALKBH1.1008_Normoxia

value: Cells were treated with an shRNA targeting ALKBH1

value: Normoxia


title: AWB

description: RNAseq


title: iPSC_lt-NES

source_name: R347: lt-NES

value: healthy

value: female

value: brain

value: hPSC-derived long-term neuroepithelium stem cell (lt-NES) line


title: vivo9hr_rep3

value: SN

value: wildtype


title: ANC

description: RNAseq

value: Apolipoprotein E deficient (ApoE-/-) reconstituted with Netrin-1 deficient hematopietic stem cells


title: vivo6hr_rep3

value: Infective Juvenile (IJ)

value: in vivo activated

value: whole body


title: Hep-Ethanol-0 hr-13

description: SAMPLE 137

value: Hepatocyte

value: liver

value: Ethanol


title: Hep-Ethanol-0 hr-15

description: SAMPLE 139

value: 0 hr


title: vivo9hr_rep1


title: Hep-Ethanol-0 hr-12

description: SAMPLE 136


title: Gastric cancer 80

city: Goyang

first: Hark

middle: K

last: Kim

state: Gyeonggi

address: 323 Ilsanro, Ilsan

country: South Korea

institute: National Cancer Center

description: Fastq contains personal confidential information that is controlled-access only

data_processing:
Reads that passed the chastity filter of the Illumina BaseCall software were used for subsequent analyses.
Using BWA aln & sampe (version 0.5.7), we aligned all reads to a human reference genome consisting of hg19/GRCh37-lite and exon-exon junction sequences that were constructed from known transcript models in EnsEMBL, RefSeq and UCSC genes. Default BWA parameters were used for alignments, with the exception of the -s sampe option which was included to disable Smith-Waterman rescue of unmapped mates as this feature was not designed to handle the insert size distribution that occurs in paired-end RNA sequencing data. After BWA alignment, a post-alignment process was performed to reposition the read alignments that spanned across the exon-exon junctions and transform them into large-gapped genomic alignments.
Genome_build: hg19/GRCh37-lite
Supplementary_files_format_and_content: The Reads Per Kilobase Of Exon Per Million Mapped Reads (RPKM) values of exons and genes were calculated. GENCODE V3 was used in the quantification process.

source_name: Gastric cancer (frozen)

extract_protocol:
AllPrep and mirVana
Transcriptome libraries were prepared following Illumina’s TruSeq mRNA kit protocol using 1–2 μg of total RNA obtained from 80 tumors obtained from patients with diffuse gastric cancer. Poly(A)+ RNA was isolated using AMPure XP beads (BECKMAN COULTER, Brea, CA) and fragmented using an Ambion Fragmentation Reagents kit (Thermo Fisher Scientific). cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina-indexed adapters were performed according to Illumina protocols. Libraries were size-selected for 250–300 bp cDNA fragments on a 3% Nusieve 3:1 (Lonza, Basel, Switzerland) agarose gel, recovered using QIAEX II gel extraction reagents (Qiagen), and PCR-amplified using Phusion DNA polymerase (New England Biolabs) for 14 PCR cycles. The amplified libraries were purified using AMPure XP beads. Library quality was measured on an Agilent 2100 Bioanalyzer to determine the product size and concentration. Paired-end libraries were sequenced using an Illumina HiSeq 2000 instrument (2×100 nucleotide read length).

value: M

value: Gastric cancer (frozen)

tag: histology

value: Non-signet ring cell diffuse

tag: recurrent fusion

tag: location

value: Distal 1/3

tag: surgery

value: Distal gastrectomy

tag: ajcc stage

value: IIIA


title: AND

description: RNAseq

value: Abdominal aortic aneurysm

value: Angiotensin II perfusion 28 days


title: vivo6hr_rep2

tag: strain

value: SN

tag: genotype

value: wildtype

tag: developmental stage

tag: treatment


title: ANB

description: RNAseq

tag: tissue

value: Apolipoprotein E deficient (ApoE-/-) reconstituted with Netrin-1 deficient hematopietic stem cells


title: Hep-Ethanol-0 hr-10

description: SAMPLE 134

tag: cell type

tag: diet

tag: time after partial hepatectomy


title: Gastric cancer 79


title: Hep-Ethanol-0 hr-9

description: SAMPLE 133


title: PBC

source_name: R319: PBC

tag: subject status

value: healthy

value: female

value: peripheral blood

value: adult peripheral blood cell


title: vivo6hr_rep1

value: Infective Juvenile (IJ)

value: in vivo activated

tag: time point

value: whole body


title: 387_shCONT_Normoxia

value: Cells were treated with a non-targeting shRNA (shCONT)

tag: condition

value: Normoxia


title: ANA

description: RNAseq

tag: genotype/variation

tag: protocol


title: Hep-Ethanol-0 hr-8

description: SAMPLE 132

value: Hepatocyte

value: liver

value: Ethanol

value: 0 hr


title: Gastric cancer 78

tag: gender

value: M

value: Gastric cancer (frozen)

tag: histology

value: Non-signet ring cell diffuse

tag: recurrent fusion

value: Middle 1/3

value: Total gastrectomy

value: IIA


title: vivo3hr_rep3

value: SN

value: wildtype


title: Gastric cancer 77

tag: location

value: Proximal 1/3

tag: surgery

tag: ajcc stage

value: IIIB


title: Hep-Ethanol-0 hr-7

description: SAMPLE 131


title: Gastric cancer 76

value: Distal 1/3

value: Distal gastrectomy


title: Gastric cancer 75

value: F


title: Hep-Ethanol-0 hr-6

description: SAMPLE 130

value: Hepatocyte


title: Gastric cancer 74

value: IB


title: vitro9hr_rep2

source_name: activated in waxworm homogenate

tag: strain

tag: genotype

tag: developmental stage

value: Infective Juvenile (IJ)

value: in vitro activated

value: whole body


title: vivo3hr_rep1

tag: treatment

value: in vivo activated

tag: tissue


title: vivo3hr_rep2


title: vitro9hr_rep3


title: Hep-Ethanol-0 hr-4

description: SAMPLE 128

tag: cell type

value: liver

tag: diet

value: Ethanol

tag: time after partial hepatectomy

value: 0 hr


title: Hep-Ethanol-0 hr-5

description: SAMPLE 129


title: Hep-Ethanol-0 hr-3

description: SAMPLE 127


title: EnMt X LMEB3 replicate 3

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
The primary sequence data was generated using the Illumina bcl2fastq 1.8.4 pipeline.
Reads were trimmed for quality using a minimum phred value of 20 and minimum length of 18 using Skewer version 0.2.2 (Jiang 2014)
Reads were mapped with STAR (Dobin 2013) to the Ensembl mouse reference genome (GRCm38)
FeatureCounts (Liao 2014) was used to count reads mapped to exons of genes with a minimum mapping quality of 20 using Ensembl genome annotation (Mus musculus.GRCm38.77.gtf) to generate a count matrix. Genes with an average of 10 reads or less per sample across  the experiment were excluded from downstream analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression count matrix

source_name: Xenomitochondrial cybrid line

growth_protocol: Xenomitochondrial cybrid cell lines harbouring nuclear DNA from Mus musculus domesticus and mtDNA from Mus musculus domesticus (MusMus; control), or mtDNA from Mus spretus (MusSpretus), Mus terricolor (MusTerricolor), Mus caroli (MusCar), Mus pahari (MusPahari), Rattus norvegicus (MusRattus) or Otomys irroratus (MusOtomys) were generated as described previously (McKenzie 2000 and McKenzie 2003). mtDNA D-loop sequences of each xenomitochondrial construct were compared to the reference sequence of each rodent (Mus musculus domesticus NC_005089.1; Mus spretus NC_025952.1; Mus terricolor (also known as Mus dunni) NC_001665.2; Rattus norvegicus NC_001665.2) by PCR as described previously (McKenzie 2014) using previously published primers (McKenzie 2000). Full mtDNA sequences were generated for Mus caroli and Otomys irroratus as they were not previously available. Xenomitochondrial cybrid cell lines were maintained in RPMI-1640 medium (Cat. #11875-093, Life Technologies) supplemented with 25 mM D-glucose (final concentration), 0.2 mM uridine, 1 mM pyruvate, 10% fetal bovine serum, 100 units/mL penicillin, and 100 µg/mL streptomycin in a humidified incubator (37°C; 5% CO2). Prior to experimental procedures, cells were incubated in glucose-free RPMI-1640 medium (Cat. #11879-020, Life Technologies) supplemented with 5.5 mM D-glucose, 0.2 mM uridine, 1 mM pyruvate, 10% fetal bovine serum, 100 units/mL penicillin, and 100 µg/mL streptomycin for 48 h in a humidified incubator (37°C; 5% CO2).

extract_protocol:
Total RNA was extracted from three independent biological replicates from each xenomitochondrial cybrid cell line using a miRNeasy RNA extraction kit (Qiagen, Cat. #217004) with an on-column DNase I (Qiagen) treatment to eliminate contaminating genomic DNA, according to manufacturer’s instructions.
Transcriptome-wide mRNA sequencing was performed by the Australian Genome Research Facility (Melbourne, Australia). RNA purity and integrity were confirmed by BioAnalyser (Agilent, CA). Libraries were created with TruSeq RNA v2 kit (Illumina), barcoded and sequenced on a HiSeq 2000 sequencer (Illumina), producing 100bp single-end reads, with a depth of 10 million reads per sample.

tag: mtdna origin

value: Mus terricolor


title: Gastric cancer 72

value: M

value: Gastric cancer (frozen)

value: Signet ring cell carcinoma

value: Middle 1/3

value: IIB


title: Gastric cancer 73

value: Proximal 1/3

value: Total gastrectomy

value: IIIC


title: vitro9hr_rep1

value: SN

value: wildtype

tag: time point


title: Hep-Ethanol-0 hr-2

description: SAMPLE 126

value: Hepatocyte


title: EnMt X LMEB3 replicate 2


title: EnMt X LMEB3 replicate 1


title: EnOi X LMEB3 replicate 2

value: Otomys irroratus


title: EnOi X LMEB3 replicate 1


title: Hep-Ethanol-0 hr-1

description: SAMPLE 125


title: EnOi X LMEB3 replicate 3


title: vitro6hr_rep3

value: Infective Juvenile (IJ)

value: in vitro activated

value: whole body


title: vitro6hr_rep2


title: Gastric cancer 71

value: Non-signet ring cell diffuse

value: Distal 1/3


title: Gastric cancer 70

value: F


title: Hep-Carbohydrate-24 hr-55

description: SAMPLE 124

source_name: Carbohydrate-24 hr

value: liver

value: Carbohydrate

value: 24 hr


title: EnRn X LMEB3 replicate 2

value: Rattus norvegicus


title: EnRn X LMEB3 replicate 1


title: Hep-Carbohydrate-24 hr-54

description: SAMPLE 123


title: Gastric cancer 68

value: Gastric cancer (frozen)

value: Signet ring cell carcinoma

value: Distal gastrectomy

value: IIIA


title: Gastric cancer 67

value: M

value: Total gastrectomy

value: IIIC


title: Gastric cancer 69

value: Middle 1/3

value: IIB


title: vitro3hr_rep2

value: SN

value: wildtype

value: Infective Juvenile (IJ)

value: in vitro activated

value: whole body


title: vitro3hr_rep3


title: Hep-Carbohydrate-24 hr-53

description: SAMPLE 122

value: Hepatocyte

value: liver

value: Carbohydrate


title: Hep-Carbohydrate-24 hr-52

description: SAMPLE 121

value: 24 hr


title: EnMs X LMEB3 replicate 3

value: Mus spretus


title: EnRn X LMEB3 replicate 3

value: Rattus norvegicus


title: naïve_rep3

source_name: not activated Infective Juvenile(IJ)

value: nonactivated


title: Hep-Carbohydrate-24 hr-51

description: SAMPLE 120


title: naïve_rep2


title: EnMs X LMEB3 replicate 1


title: EnMc X LMEB3 replicate 3

value: Mus caroli


title: EnMs X LMEB3 replicate 2


title: vitro6hr_rep1


title: Gastric cancer 65

value: F

value: Gastric cancer (frozen)

value: Non-signet ring cell diffuse

value: Total gastrectomy

value: IIIB


title: EnMc X LMEB3 replicate 2


title: EnMc X LMEB3 replicate 1


title: Gastric cancer 64

value: M

value: Signet ring cell carcinoma

value: Middle 1/3


title: naïve_rep1

value: SN

value: wildtype

value: Infective Juvenile (IJ)

value: whole body


title: Hep-Carbohydrate-24 hr-49

description: SAMPLE 118

value: Hepatocyte

value: liver

value: Carbohydrate

value: 24 hr


title: Hep-Carbohydrate-24 hr-50

description: SAMPLE 119


title: Hep-Carbohydrate-24 hr-48

description: SAMPLE 117


title: Gastric cancer 63

value: Distal 1/3

value: Distal gastrectomy

value: IIIC


title: ZT14_fed_lean_RNA rep3

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description:
ZT14 fed, chow diet, single mouse, rep3
RNAseq_RPKM.txt
SM2768

data_processing:
RNA-seq, DNase-seq and ChIP-seq sequencing data was aligned to mm9 using STAR
Differential RNA expression and H3K27 acetylation was analysed by DESeq2
Bedgraph files were generated using HOMER
Nomilized tag counts were optained using HOMER
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraphs and text files with log2FC and FDR

source_name: Liver

extract_protocol:
Approximately 5 mg of liver tissue were homogenized using Ultra-Thorax and RNA was purified using TRIzol-RNA lysis reagent (ThermoFisher) in EconoSpin columns (Epoc Life) according to manufacturer’s instructions.
Total RNA (1000 ng) was prepared for sequencing using ribosome depletion followed by random primed cDNA synthesis or polydT-mediated cDNA synthesis according to the manufacturer´s (Illumina) instructions. Subsequent library preparation was performed using the NEBNext RNA library preparation kit for Illumina.

value: Liver

value: wild type

tag: molecule enrichment protocol

value: RNA-seq, PolyA enriched RNA

value: 10 weeks chow ad libitum followed by four days night restricted feeding


title: vitro3hr_rep1

value: in vitro activated


title: EnMp X LMEB3 replicate 3

value: Mus pahari


title: Hep-Carbohydrate-24 hr-47

description: SAMPLE 116


title: Gastric cancer 61

tag: gender

value: F

value: Gastric cancer (frozen)

value: Signet ring cell carcinoma

value: Proximal 1/3

value: Total gastrectomy

value: IIB


title: ZT14_fed_lean_RNA rep1

description:
ZT14 fed, chow diet, single mouse, rep1
RNAseq_RPKM.txt
SM2766


title: Gastric cancer 66

value: M

tag: histology

value: Non-signet ring cell diffuse

value: Middle 1/3

value: IIA


title: Hep-Carbohydrate-24 hr-46

description: SAMPLE 115

value: Hepatocyte

value: liver

value: Carbohydrate

value: 24 hr


title: Gastric cancer 60

tag: recurrent fusion

value: Distal gastrectomy


title: EnMp X LMEB3 replicate 1


title: ZT14_fed_DIO_RNA rep3

description:
ZT14 fed, HFD, single mouse, rep3
RNAseq_RPKM.txt
SM2765

value: Liver

value: wild type

value: RNA-seq, PolyA enriched RNA

value: 10 weeks HFD ad libitum followed by four days night restricted feeding


title: EnMm X LMEB3 replicate 3

value: Mus musculus


title: ZT14_fed_DIO_RNA rep2

description:
ZT14 fed, HFD, single mouse, rep2
RNAseq_RPKM.txt
SM2764


title: Gastric cancer 59

value: Gastric cancer (frozen)

tag: location

value: Distal 1/3

value: IIIB


title: Gastric cancer 58

value: F

value: Proximal 1/3

tag: surgery

value: Total gastrectomy

value: IIIC


title: Hep-Carbohydrate-24 hr-44

description: SAMPLE 113

value: Hepatocyte


title: Hep-Carbohydrate-24 hr-43

description: SAMPLE 112

value: liver


title: ZT14_fed_DIO_RNA rep1

description:
ZT14 fed, HFD, single mouse, rep1
RNAseq_RPKM.txt
SM2763


title: Gastric cancer 56

value: Non-signet ring cell diffuse

value: Middle 1/3

tag: ajcc stage

value: IA


title: Hep-Carbohydrate-24 hr-42

description: SAMPLE 111

value: Carbohydrate

value: 24 hr


title: EnMp X LMEB3 replicate 2

value: Mus pahari


title: Hep-Carbohydrate-24 hr-41

description: SAMPLE 110


title: Gastric cancer 57

value: Distal gastrectomy


title: EnMm X LMEB3 replicate 1

value: Mus musculus


title: ZT14_unfed_lean_RNA rep3

description:
ZT14 unfed, chow diet, single mouse, rep3
RNAseq_RPKM.txt
SM2762

tag: strain

value: Liver

value: wild type

value: RNA-seq, PolyA enriched RNA

value: 10 weeks chow ad libitum followed by four days night restricted feeding


title: ZT14_fed_lean_RNA rep2

description:
ZT14 fed, chow diet, single mouse, rep2
RNAseq_RPKM.txt
SM2767

tag: genotype


title: Gastric cancer 62

value: F

value: Gastric cancer (frozen)

value: IIIB


title: ZT14_unfed_lean_RNA rep2

description:
ZT14 unfed, chow diet, single mouse, rep2
RNAseq_RPKM.txt
SM2761


title: Hep-Carbohydrate-24 hr-40

description: SAMPLE 109

value: Hepatocyte


title: Gastric cancer 55

value: Signet ring cell carcinoma

value: Distal 1/3

value: Total gastrectomy

value: IIIA


title: OB-CM3

city: Aurora

first: Stephen

middle: William

last: Santoro

state: Colorado

department: Department of Pediatrics, Section of Developmental Biology

institute: University of Colorado Denver - Anschutz Medical Campus

description: OB_sample_differential_gene expression

data_processing:
RNA-seq data were analyzed using the Galaxy platform (https://usegalaxy.org)
Fastq files from each sequencing lane (L1, L2) and corresponding to each fragment end (R1, R2) were concatenated into a single file to generate 2 fastq files (R1, R2) per biological replicate.
For each sample, sequence pairs were aligned to the mm9 genome using Tophat2 (V2.1.0) with default parameters.
A GTF file for each biological replicate was generated using Cufflinks (V2.2.1.0) with default parameters.
Cufflinks GTF files were merged using CuffMerge (V2.2.1.0) with the mouse Refseq reference annotation and default parameters.
Gene-level analyses of differential expression were performed using CuffDiff with bias correction and a minimum alignment count of 5 fragments. All other parameters were default.
Genome_build: mm9
Supplementary_files_format_and_content: Gene expression measurement files (output from Cufflinks) are tab-delimited text files with gene-level FPKM values for each sample. Differential gene expression files (output from Cuffdiff) contain mean gene-level FPKM values for each sample group and information regarding differential gene expression between groups.

source_name: olfactory bulb (OB)

growth_protocol: Mice were weaned at 3 weeks of age and then housed under either sex-separated or sex-combined conditions at a density of four animals per cage until six months of age, at which time they were euthanized and their olfactory tissues were dissected and flash-frozen.

extract_protocol:
RNA samples were prepared via mechanical homogenization of frozen tissues in Trizol Reagent (Life Technologies) following the manufacturer’s protocol. Trizol-purified RNA samples were further purified using an RNeasy Plus Mini Kit (Qiagen).
The TruSeq Stranded Total RNA with Ribo-Zero Gold Kit (Illumina) was used to deplete each RNA sample of ribosomal RNA and prepare a library tagged with a unique barcode. Libraries were paired-end sequenced (2 x 50 bases) to a depth of ~40 million reads/replicate (~20 million fragments/replicate) using a HighSeq 2000 instrument (Illumina). Each library was sequenced on two lanes, generating a total of four fastq files.

tag: age

value: 6 months

tag: Sex

value: male

tag: condition

value: sex-combined


title: OB-CM2

description: OB_sample_differential_gene expression


title: Hep-Carbohydrate-24 hr-45

description: SAMPLE 114

tag: cell type

tag: tissue

value: liver

value: Carbohydrate

value: 24 hr


title: OB-CM1

description: OB_sample_differential_gene expression


title: OB-CF2

description: OB_sample_differential_gene expression

value: female


title: Hep-Carbohydrate-24 hr-39

description: SAMPLE 108

tag: diet

tag: time after partial hepatectomy


title: ZT14_unfed_DIO_RNA rep3

description:
ZT14 unfed, HFD single mouse, rep3
RNAseq_RPKM.txt
SM2759

value: Liver

value: wild type

value: RNA-seq, PolyA enriched RNA

tag: treatment

value: 10 weeks HFD ad libitum followed by four days night restricted feeding


title: cw2386plus_N6mA_DIPseq

description: N6-mA DIP-seq from patient derived glioblastoma specimens

library_source: genomic

data_processing:
Library strategy: DIP-seq
FASTQ files were trimmed with Trim Galore and aligned to the hg19 genome using BWA (for ChIPseq) or Bowtie2 (for N6mA DIPseq) as described in the methods.
SAM files were sorted and duplicates were removed using PicardTools as described in the methods
Bigwigs were generated from BAM files using DeepTools
Peaks were called using the EPIC implementation of the SICER algorithm as described in the methods. For differential peak calling, the Non-targeting shRNA file was used as the input, as described in the methods.
See methods section in manuscript for complete data processing details for ChIP, DIP, and Bisulfite sequencing analysis
Genome_build: hg19
Supplementary_files_format_and_content: BIGWIG and BED files

molecule: genomic DNA

growth_protocol:
Cells from a primary patient derived GBM tumor
Cells were grown in neurobasal media supplemented with sodium pyruvate, B27, glutamax, EGF/FGF, and penicillin/streptomycin as described in more detail in the methods. Cells were treated with the indicated shRNA.

extract_protocol:
DNA extraction protocol is described in the method section
For ChIP-seq and N6-mA DIPseq, NEB NEBNext® Ultra™ DNA Library Prep Kit

treatment_protocol:
For N6mA DIPseq, Rabbit polyclonal antibody to N6-mA (Synaptic Systems, Cat#202-003) was used.
For H3K9me3 ChIPseq, rabbit polyclonal antibody to Histone H3K9me3 (Abcam,Cat#ab8898) was used
For H3K27me3 ChIPseq, rabbit polyclonal antibody to Histone H3K27me3 , (Active Motif, Cat#39155) was used
For H3K4me3 ChIPseq, rabbit polyclonal antibody to Histone H3K4me3 (Abcam,Cat#8580)
For ALKBH1 ChIPseq, rabit polyclonal antibody to ALKBH1 (Abcam, Cat#ab126596) was used
Chromatin Immunoprecipitation (ChIP) was performed as previously described. Briefly, formaldehyde-fixed cells were lysed and sheared (Branson S220) on wet ice. The sheared chromatin was cleared and incubated overnight at 4  C with 5  mg H3K9me3 antibody (Abcam, ab8898), H3K27me3 (active motif, 39155), or H3K4me3 (Abcam) respectively. Antibody-chromatin complexes were immunoprecipitated with protein G magnetic Dynal beads (Life Technologies), washed, eluted, reverse crosslinked, and treated with RNAse A followed by proteinase K. ChIP DNA was purified using Ampure XP beads (Beckmann Coulter) and then used to prepare sequencing libraries by NEB NEBNext   Ultra    DNA Library Prep Kit for Illumina for sequencing.
For N6mA DIPsequencing, briefly, genomic DNA from patient-derived glioblastoma stem cell models was purified with a DNeasy kit (QIAGEN, 69504). For each sample, 5   g DNA was sonicated to 200   300 bp with Bioruptor. Then, adaptors were ligated to genomic DNA fragments following the Illumina protocol. The ligated DNA fragments were denatured at 95 degree for 5 minutes. Then, the single-stranded DNA fragments were immunoprecipitated with N6-mA antibodies (5   g for each reaction, 202-003, Synaptic Systems) overnight at 4  C. N6-mA enriched DNA fragments were purified according to the Active Motif hMeDIP protocol. IP DNA and input DNA were PCR amplified with NEBNext indexing primers, and were then subjected to multiplexed library construction and sequencing with Illumina HiSeq sequencing

tag: cell treatment

value: No Treatment


title: EnMm X LMEB3 replicate 2

tag: mtdna origin

value: Mus musculus


title: Gastric cancer 54

tag: gender

value: F

value: Gastric cancer (frozen)

tag: histology

value: Non-signet ring cell diffuse

value: Middle 1/3

value: Distal gastrectomy

value: IIB


title: OB-CF3

description: OB_sample_differential_gene expression

value: 6 months

value: sex-combined


title: Gastric cancer 52

value: Signet ring cell carcinoma

tag: recurrent fusion

tag: location

value: Proximal 1/3

value: Total gastrectomy

value: IIIA


title: ZT14_unfed_DIO_RNA rep2

description:
ZT14 unfed, HFD single mouse, rep2
RNAseq_RPKM.txt
SM2758

value: Liver

value: wild type

tag: molecule enrichment protocol


title: ZT14_unfed_DIO_RNA rep1

description:
ZT14 unfed, HFD single mouse, rep1
RNAseq_RPKM.txt
SM2757

tag: strain

value: RNA-seq, PolyA enriched RNA

value: 10 weeks HFD ad libitum followed by four days night restricted feeding


title: Hep-Carbohydrate-24 hr-37

description: SAMPLE 106

value: Hepatocyte

value: liver

value: Carbohydrate

value: 24 hr


title: Gastric cancer 53

value: F

value: Gastric cancer (frozen)

value: Non-signet ring cell diffuse

value: Distal 1/3

tag: surgery

tag: ajcc stage

value: IIIC


title: Hep-Carbohydrate-24 hr-36

description: SAMPLE 105


title: ZT14_unfed_lean_RNA rep1

description:
ZT14 unfed, chow diet, single mouse, rep1
RNAseq_RPKM.txt
SM2760

tag: genotype

value: 10 weeks chow ad libitum followed by four days night restricted feeding


title: Gastric cancer 51

value: M

value: Middle 1/3

value: IIIB


title: ZT14_fed_IRSdKO_RNA rep4

description:
ZT14 fed Dex (1mg/kg), single mouse, L-IRS1/2 dKO, rep4
RNAseq_RPKM.txt
SM2423

value: Irs1 (fl/fl), Irs2 (fl/fl), Alb-Cre, C57BL/6 background

value: Liver

value: Liver specific IRS1 and IRS2 knockout

value: Night restricted feeding, pre-prandial injection with 1mg/kg dex


title: OB-CF1

description: OB_sample_differential_gene expression

tag: age

value: 6 months

tag: Sex

value: female

tag: condition

value: sex-combined


title: Gastric cancer 50

tag: tissue

value: Proximal 1/3

value: Total gastrectomy


title: Gastric cancer 49

value: F

value: Gastric cancer (frozen)

value: Distal gastrectomy


title: Hep-Carbohydrate-24 hr-34

description: SAMPLE 103

tag: cell type

value: Hepatocyte

value: liver

tag: diet

value: Carbohydrate

tag: time after partial hepatectomy

value: 24 hr


title: Hep-Carbohydrate-24 hr-35

description: SAMPLE 104


title: OB-SM3

description: OB_sample_differential_gene expression

value: male

value: sex-separated


title: ZT14_fed_IRSdKO_RNA rep2

description:
ZT14 fed Dex (1mg/kg), single mouse, L-IRS1/2 dKO, rep2
RNAseq_RPKM.txt
SM2421

value: Irs1 (fl/fl), Irs2 (fl/fl), Alb-Cre, C57BL/6 background

value: Liver

value: RNA-seq, PolyA enriched RNA

tag: treatment


title: OB-SM1

description: OB_sample_differential_gene expression

value: 6 months


title: Gastric cancer 48

tag: gender

value: Non-signet ring cell diffuse

value: IV


title: OB-SM2

description: OB_sample_differential_gene expression


title: ZT14_fed_IRSdKO_RNA rep3

description:
ZT14 fed Dex (1mg/kg), single mouse, L-IRS1/2 dKO, rep3
RNAseq_RPKM.txt
SM2422

value: Liver specific IRS1 and IRS2 knockout

value: Night restricted feeding, pre-prandial injection with 1mg/kg dex


title: ZT14_fed_IRSdKO_RNA rep1

description:
ZT14 fed Dex (1mg/kg), single mouse, L-IRS1/2 dKO, rep1
RNAseq_RPKM.txt
SM2420


title: Hep-Carbohydrate-24 hr-33

description: SAMPLE 102


title: Hep-Carbohydrate-24 hr-38

description: SAMPLE 107


title: Hep-Carbohydrate-24 hr-32

description: SAMPLE 101


title: OB-SF3

description: OB_sample_differential_gene expression

value: female


title: OB-SF2

description: OB_sample_differential_gene expression


title: Gastric cancer 47

description: Fastq contains personal confidential information that is controlled-access only

value: M

value: Gastric cancer (frozen)

tag: histology

value: Proximal 1/3

value: Total gastrectomy

value: IIB


title: Gastric cancer 46

tag: recurrent fusion

value: Distal 1/3

value: Distal gastrectomy


title: Gastric cancer 45

tag: location


title: OB-SF1

description: OB_sample_differential_gene expression

value: sex-separated


title: ZT14_fed_IRSfl_RNA rep3

description:
ZT14 fed Dex (1mg/kg), single mouse, WT, rep3
RNAseq_RPKM.txt
SM2418

value: Irs1 (fl/fl), Irs2 (fl/fl), C57BL/6 background

value: wild type

tag: molecule enrichment protocol


title: ZT14_fed_IRSfl_RNA rep4

description:
ZT14 fed Dex (1mg/kg), single mouse, WT, rep4
RNAseq_RPKM.txt
SM2419

tag: strain

value: Liver

value: RNA-seq, PolyA enriched RNA


title: Gastric cancer 44

value: F

value: Non-signet ring cell diffuse

tag: surgery


title: ZT14_fed_IRSfl_RNA rep2

description:
ZT14 fed Dex (1mg/kg), single mouse, WT, rep2
RNAseq_RPKM.txt
SM2417


title: Hep-Carbohydrate-24 hr-31

description: SAMPLE 100

value: Hepatocyte

value: liver

value: Carbohydrate

value: 24 hr


title: Hep-Carbohydrate-24 hr-30

description: SAMPLE 99


title: Hep-Carbohydrate-24 hr-29

description: SAMPLE 98


title: Hep-Carbohydrate-24 hr-28

description: SAMPLE 97


title: Gastric cancer 43

value: M

value: Gastric cancer (frozen)

tag: ajcc stage


title: ZT14_unfed_GRfl_CRE_RNA rep4

description:
ZT14 unfed, single mouse (GR fl/fl), AAV-CRE, rep4
RNAseq_RPKM.txt
SM3210

value: Nr3c1 (fl/fl), C57BL/6 background

tag: genotype

value: Liver specific GR knockout

value: AAV-CRE injection two weeks before night restricted feeding


title: Gastric cancer 42

value: Distal 1/3

value: Distal gastrectomy

value: IIB


title: VNO-CM3

description: VNO_sample_differential_gene expression

source_name: vomeronasal organ (VNO)

tag: age

value: 6 months

value: male

value: sex-combined


title: VNO-CF3

description: VNO_sample_differential_gene expression

tag: Sex

value: female


title: VNO-CM2

description: VNO_sample_differential_gene expression

tag: condition


title: Hep-Carbohydrate-24 hr-27

description: SAMPLE 96

tag: tissue


title: VNO-CM1

description: VNO_sample_differential_gene expression


title: ZT14_unfed_GRfl_CRE_RNA rep3

description:
ZT14 unfed, single mouse (GR fl/fl), AAV-CRE, rep3
RNAseq_RPKM.txt
SM3209

value: Liver

value: RNA-seq, PolyA enriched RNA


title: Gastric cancer 41

value: F

value: Non-signet ring cell diffuse

value: Middle 1/3

value: IIA


title: ZT14_unfed_GRfl_CRE_RNA rep2

description:
ZT14 unfed, single mouse (GR fl/fl), AAV-CRE, rep2
RNAseq_RPKM.txt
SM3208


title: Hep-Carbohydrate-24 hr-26

description: SAMPLE 95

tag: cell type

value: Hepatocyte

value: liver

value: Carbohydrate

value: 24 hr


title: VNO-CF2

description: VNO_sample_differential_gene expression


title: Gastric cancer 40

value: Gastric cancer (frozen)

value: Total gastrectomy


title: ZT14_unfed_GRfl_CRE_RNA rep1

description:
ZT14 unfed, single mouse (GR fl/fl), AAV-CRE, rep1
RNAseq_RPKM.txt
SM3207

value: Nr3c1 (fl/fl), C57BL/6 background

value: Liver specific GR knockout

value: AAV-CRE injection two weeks before night restricted feeding


title: ZT14_unfed_GRfl_GFP_RNA rep4

description:
ZT14 unfed, single mouse (GR fl/fl), AAV-GFP, rep4
RNAseq_RPKM.txt
SM3206

value: wild type

value: AAV-GFP injection two weeks before night restricted feeding


title: Gastric cancer 39

value: IIIB


title: VNO-CF1

description: VNO_sample_differential_gene expression

value: 6 months

value: female

value: sex-combined


title: ZT14_unfed_GRfl_GFP_RNA rep3

description:
ZT14 unfed, single mouse (GR fl/fl), AAV-GFP, rep3
RNAseq_RPKM.txt
SM3205

value: Liver

value: RNA-seq, PolyA enriched RNA


title: Gastric cancer 38

value: F

value: Non-signet ring cell diffuse

value: Middle 1/3


title: Gastric cancer 37

value: M

value: Distal 1/3

value: Distal gastrectomy

value: IIA


title: Hep-Carbohydrate-24 hr-24

description: SAMPLE 93

value: Hepatocyte

value: liver

tag: diet

value: Carbohydrate

value: 24 hr


title: VNO-SM3

description: VNO_sample_differential_gene expression

value: male

value: sex-separated


title: Hep-Carbohydrate-24 hr-25

description: SAMPLE 94

tag: time after partial hepatectomy


title: VNO-SM2

description: VNO_sample_differential_gene expression

value: 6 months


title: Gastric cancer 36

value: Gastric cancer (frozen)

value: Proximal 1/3

value: Total gastrectomy

value: IIB


title: ZT14_unfed_GRfl_GFP_RNA rep1

description:
ZT14 unfed, single mouse (GR fl/fl), AAV-GFP, rep1
RNAseq_RPKM.txt
SM3203

value: Nr3c1 (fl/fl), C57BL/6 background

value: Liver

value: wild type

value: RNA-seq, PolyA enriched RNA

tag: treatment

value: AAV-GFP injection two weeks before night restricted feeding


title: Hep-Carbohydrate-24 hr-22

description: SAMPLE 91


title: ZT14_unfed_GRfl_GFP_RNA rep2

description:
ZT14 unfed, single mouse (GR fl/fl), AAV-GFP, rep2
RNAseq_RPKM.txt
SM3204


title: Hep-Carbohydrate-24 hr-21

description: SAMPLE 90


title: ZT14_unfed_PBS_RNA rep4

description:
ZT14 unfed PBS, single mouse, rep4
RNAseq_RPKM.txt
SM2297

value: Night restricted feeding, pre-prandial injection with vehicle


title: Hep-Carbohydrate-24 hr-20

description: SAMPLE 89

value: Hepatocyte


title: Gastric cancer 35

tag: gender

value: F

value: Signet ring cell carcinoma

value: Middle 1/3


title: Gastric cancer 34

value: M

tag: histology

value: Non-signet ring cell diffuse

value: Distal gastrectomy

value: IIA


title: ZT14_unfed_PBS_RNA rep3

description:
ZT14 unfed PBS, single mouse, rep3
RNAseq_RPKM.txt
SM1995


title: VNO-SF3

description: VNO_sample_differential_gene expression

value: 6 months

value: female

value: sex-separated


title: VNO-SF2

description: VNO_sample_differential_gene expression


title: Hep-Carbohydrate-24 hr-19

description: SAMPLE 88

value: liver

value: Carbohydrate

value: 24 hr


title: ZT14_fed_IRSfl_RNA rep1

description:
ZT14 fed Dex (1mg/kg), single mouse, WT, rep1
RNAseq_RPKM.txt
SM2416

value: Irs1 (fl/fl), Irs2 (fl/fl), C57BL/6 background

value: Liver

value: wild type

value: RNA-seq, PolyA enriched RNA

value: Night restricted feeding, pre-prandial injection with 1mg/kg dex


title: VNO-SF1

description: VNO_sample_differential_gene expression


title: Hep-Carbohydrate-24 hr-18

description: SAMPLE 87

value: Hepatocyte


title: Gastric cancer 33

value: F

value: Gastric cancer (frozen)

tag: recurrent fusion

value: Middle 1/3

value: IV


title: Gastric cancer 32

value: Signet ring cell carcinoma

tag: location

value: Proximal 1/3

value: Total gastrectomy

value: IIIB


title: ZT14_unfed_PBS_RNA rep2

description:
ZT14 unfd PBS, single mouse, rep2
RNAseq_RPKM.txt
SM1994

tag: molecule enrichment protocol

value: Night restricted feeding, pre-prandial injection with vehicle


title: Hep-Carbohydrate-24 hr-23

description: SAMPLE 92

value: liver

value: Carbohydrate


title: ZT14_unfed_PBS_RNA rep1

description:
ZT14 unfed PBS, single mouse, rep1
RNAseq_RPKM.txt
SM1993

tag: strain


title: Hep-Carbohydrate-24 hr-17

description: SAMPLE 86

value: 24 hr


title: MOE-CM3

description: MOE_sample_differential_gene expression

source_name: main olfactory epithelium (MOE)

value: 6 months

value: male

value: sex-combined


title: MOE-CM2

description: MOE_sample_differential_gene expression


title: ZT14_fed_DEX_S961_RNA rep4

description:
ZT14 fed S961 (44 nM/mouse) + Dex (1mg/kg), single mouse, rep4
RNAseq_RPKM.txt
SM2296

value: Liver

value: wild type

value: RNA-seq, PolyA enriched RNA

value: Night restricted feeding, pre-prandial injection with 44nM/mouse S965 and 1mg/kg dex


title: VNO-SM1

description: VNO_sample_differential_gene expression

value: sex-separated


title: MOE-CM1

description: MOE_sample_differential_gene expression


title: Gastric cancer 30

description: Fastq contains personal confidential information that is controlled-access only

value: F

value: Gastric cancer (frozen)

value: Non-signet ring cell diffuse

tag: surgery

value: IIB


title: Hep-Carbohydrate-24 hr-15

description: SAMPLE 84

value: Hepatocyte


title: Hep-Carbohydrate-24 hr-16

description: SAMPLE 85


title: ZT14_fed_DEX_S961_RNA rep3

description:
ZT14 fed S961 (44 nM/mouse) + Dex (1mg/kg), single mouse, rep3
RNAseq_RPKM.txt
SM1992


title: Hep-Carbohydrate-24 hr-14

description: SAMPLE 83


title: ZT14_fed_DEX_S961_RNA rep2

description:
ZT14 fed S961 (44 nM/mouse) + Dex (1mg/kg), single mouse, rep2
RNAseq_RPKM.txt
SM1991


title: ZT14_fed_DEX_S961_RNA rep1

description:
ZT14 fed S961 (44 nM/mouse) + Dex (1mg/kg), single mouse, rep1
RNAseq_RPKM.txt
SM1990


title: Gastric cancer 28

value: Distal 1/3

value: Distal gastrectomy

tag: ajcc stage


title: Gastric cancer 29

value: Middle 1/3

value: IB


title: Hep-Carbohydrate-24 hr-13

description: SAMPLE 82

value: liver

value: Carbohydrate

value: 24 hr


title: MOE-CF1

description: MOE_sample_differential_gene expression

value: 6 months

value: female

value: sex-combined


title: Gastric cancer 27

value: Signet ring cell carcinoma

value: IIIB


title: Gastric cancer 26

value: M

value: IA


title: ZT14_fed_S961_RNA rep4

description:
ZT14 fed S961 (44 nM/mouse), single mouse, rep4
RNAseq_RPKM.txt
SM2295

value: Liver

tag: genotype

value: wild type

value: RNA-seq, PolyA enriched RNA

value: Night restricted feeding, pre-prandial injection with 44nM/mouse S964


title: MOE-CF2

description: MOE_sample_differential_gene expression

tag: age


title: ZT14_fed_S961_RNA rep3

description:
ZT14 fed S961 (44 nM/mouse), single mouse, rep3
RNAseq_RPKM.txt
SM1989

value: Night restricted feeding, pre-prandial injection with 44nM/mouse S963


title: Gastric cancer 31

value: F

value: Gastric cancer (frozen)

value: Middle 1/3

value: Distal gastrectomy

value: IIIA


title: Hep-Carbohydrate-24 hr-11

description: SAMPLE 80

value: Hepatocyte

value: liver

value: Carbohydrate

value: 24 hr


title: MOE-SM2

description: MOE_sample_differential_gene expression

value: 6 months

tag: Sex

value: male

value: sex-separated


title: Hep-Carbohydrate-24 hr-10

description: SAMPLE 79


title: Gastric cancer 24

value: Signet ring cell carcinoma

value: Distal 1/3

value: IIA


title: ZT14_fed_S961_RNA rep1

description:
ZT14 fed S961 (44 nM/mouse), single mouse, rep1
RNAseq_RPKM.txt
SM1987

value: Liver

value: wild type

value: RNA-seq, PolyA enriched RNA

value: Night restricted feeding, pre-prandial injection with 44nM/mouse S961


title: Hep-Carbohydrate-24 hr-12

description: SAMPLE 81


title: MOE-SM3

description: MOE_sample_differential_gene expression

tag: condition


title: Gastric cancer 25

value: M

tag: tissue

value: Gastric cancer (frozen)

value: Proximal 1/3

value: Total gastrectomy

value: IIIB


title: Hep-Carbohydrate-24 hr-9

description: SAMPLE 78

tag: cell type

value: Hepatocyte

value: liver

value: Carbohydrate


title: MOE-SF3

description: MOE_sample_differential_gene expression

value: 6 months

value: female


title: MOE-CF3

description: MOE_sample_differential_gene expression

value: sex-combined


title: Hep-Carbohydrate-24 hr-8

description: SAMPLE 77

tag: diet

value: 24 hr


title: ZT14_fed_DEX_RNA rep4

description:
ZT14 fed Dex (1mg/kg), single mouse, rep4
RNAseq_RPKM.txt
SM2294

value: Night restricted feeding, pre-prandial injection with 1mg/kg dex


title: Gastric cancer 23

value: F

value: Non-signet ring cell diffuse

value: Middle 1/3

value: IIA


title: Hep-Carbohydrate-24 hr-7

description: SAMPLE 76

tag: time after partial hepatectomy


title: MOE-SF2

description: MOE_sample_differential_gene expression

value: sex-separated


title: Gastric cancer 22

value: Gastric cancer (frozen)


title: MOE-SF1

description: MOE_sample_differential_gene expression


title: Gastric cancer 21

value: IV


title: ZT14_fed_DEX_RNA rep3

description:
ZT14 fed Dex (1mg/kg), single mouse, rep3
RNAseq_RPKM.txt
SM1986

value: Liver

value: wild type

value: RNA-seq, PolyA enriched RNA

tag: treatment


title: Hep-Carbohydrate-24 hr-6

description: SAMPLE 75

value: Hepatocyte

value: liver


title: Gastric cancer 20

tag: gender

value: M

value: Entire stomach

value: Total gastrectomy


title: ZT14_fed_S961_RNA rep2

description:
ZT14 fed S961 (44 nM/mouse), single mouse, rep2
RNAseq_RPKM.txt
SM1988

value: Night restricted feeding, pre-prandial injection with 44nM/mouse S962


title: ZT14_fed_DEX_RNA rep1

description:
ZT14 fed Dex (1mg/kg), single mouse, rep1
RNAseq_RPKM.txt
SM1984

value: Night restricted feeding, pre-prandial injection with 1mg/kg dex


title: Gastric cancer 19

value: F

tag: histology

value: Distal gastrectomy

value: IIB


title: Hep-Carbohydrate-24 hr-5

description: SAMPLE 74

value: Carbohydrate

value: 24 hr


title: ZT14_fed_PBS_RNA rep4

description:
ZT14 fed PBS, single mouse, rep4
RNAseq_RPKM.txt
SM2293

value: Night restricted feeding, pre-prandial injection with vehicle


title: ZT14_fed_PBS_RNA rep3

description:
ZT14 fed PBS, single mouse, rep3
RNAseq_RPKM.txt
SM1983


title: Gastric cancer 18

value: Gastric cancer (frozen)

value: Non-signet ring cell diffuse

tag: recurrent fusion

value: IIIC


title: MOE-SM1

description: MOE_sample_differential_gene expression

value: 6 months

value: male

value: sex-separated


title: ZT14_fed_PBS_RNA rep2

description:
ZT14 fed PBS, single mouse, rep2
RNAseq_RPKM.txt
SM1982

value: Liver

value: wild type

value: RNA-seq, PolyA enriched RNA


title: Hep-Carbohydrate-24 hr-2

description: SAMPLE 71

value: Hepatocyte

value: liver


title: ZT14_fed_DEX_H3K27Ac rep2

description:
ZT14 Fed Dex (1mg/kg), liver pooled from 3-4 mice, rep2
SM2243

extract_protocol:
Crosslinked sonicated chromatin was IP'ed using antibodies against H3K27Ac, GR or FOXO1. DNA was extracted by phenol/choloroform.
ChIP-seq and DHS-seq libraries were constructed using the NEBNext Library prep kit according to manufacturer´s (NEB) instructions.

value: H3K27Ac ChIP-seq,  Ab4729 (Abcam)

value: Night restricted feeding, pre-prandial injection with 1mg/kg dex


title: Gastric cancer 16

value: M

value: Signet ring cell carcinoma

tag: location

value: Proximal 1/3

value: Total gastrectomy

value: IV


title: Hep-Carbohydrate-24 hr-3

description: SAMPLE 72

value: Carbohydrate

value: 24 hr


title: Gastric cancer 17

value: F

value: Gastric cancer (frozen)

value: Non-signet ring cell diffuse

value: IIIA


title: Gastric cancer 15

value: Middle 1/3

value: Distal gastrectomy


title: ZT14_fed_PBS_RNA rep1

description:
ZT14 fed PBS, single mouse, rep1
RNAseq_RPKM.txt
SM1981

value: Liver

value: wild type

tag: molecule enrichment protocol

value: RNA-seq, PolyA enriched RNA

value: Night restricted feeding, pre-prandial injection with vehicle


title: Hep-Carbohydrate-0 hr-69

description: SAMPLE 69

source_name: Carbohydrate-0 hr

value: Hepatocyte

value: liver

value: 0 hr


title: Hep-Carbohydrate-0 hr-68

description: SAMPLE 68


title: Hep-Carbohydrate-24 hr-1

description: SAMPLE 70


title: Gastric cancer 13

value: M

value: Signet ring cell carcinoma

value: IIIC


title: ZT14_fed_PBS_H3K27Ac rep2

description:
ZT14 fed PBS, liver pooled from 3-4 mice, rep2
SM2242

tag: strain

value: H3K27Ac ChIP-seq,  Ab4729 (Abcam)


title: ZT14_fed_DEX_RNA rep2

description:
ZT14 fed Dex (1mg/kg), single mouse, rep2
RNAseq_RPKM.txt
SM1985

value: Night restricted feeding, pre-prandial injection with 1mg/kg dex


title: Gastric cancer 12

description: Fastq contains personal confidential information that is controlled-access only

value: Gastric cancer (frozen)

value: Proximal 1/3

tag: surgery

value: Total gastrectomy

value: IIB


title: Hep-Carbohydrate-24 hr-4

description: SAMPLE 73

value: Carbohydrate

value: 24 hr


title: Hep-Carbohydrate-0 hr-66

description: SAMPLE 66


title: ZT14_fed_DEX_H3K27Ac rep1

description:
ZT14 Fed Dex (1mg/kg), liver pooled from 3-4 mice, rep1
SM1624

value: Liver

value: wild type


title: ZT14_fed_PBS_H3K27Ac rep1

description:
ZT14 fed PBS, liver pooled from 3-4 mice, rep1
SM1622

value: Night restricted feeding, pre-prandial injection with vehicle


title: Hep-Carbohydrate-0 hr-65

description: SAMPLE 65

value: Hepatocyte


title: ZT14_unfed_PBS_H3K27Ac rep1

description:
ZT14 unfed PBS, liver pooled from 3-4 mice, rep1
SM1621


title: Gastric cancer 11

value: Non-signet ring cell diffuse

value: Middle 1/3

value: Distal gastrectomy

tag: ajcc stage

value: IV


title: Hep-Carbohydrate-0 hr-64

description: SAMPLE 64

value: liver

value: 0 hr


title: ZT14_fed_DEX_GR

description:
ZT14 Fed Dex (1mg/kg), liver pooled from 3-4 mice, rep1
SM1620

tag: genotype

value: GR ChIP-seq, MA1-510 (ThermoFischer), PA1-511a (ThermoFischer), SC-1003 (Santa Cruz)

value: Night restricted feeding, pre-prandial injection with 1mg/kg dex


title: Hep-Carbohydrate-0 hr-63

description: SAMPLE 63


title: ZT14_fed_PBS_GR

description:
ZT14 Fed PBS, liver pooled from 3-4 mice, rep1
SM1618


title: Gastric cancer 9

value: F

value: Gastric cancer (frozen)

value: Proximal 1/3


title: Gastric cancer 8

value: Total gastrectomy


title: Hep-Carbohydrate-0 hr-62

description: SAMPLE 62

value: Carbohydrate


title: ZT14_unfed_PBS_GR

description:
ZT14 unfed PBS, liver pooled from 3-4 mice, rep1
SM1617

value: Liver


title: Gastric cancer 14

value: M

value: Distal 1/3

value: IIB


title: ZT14_fed_FOXO1 rep2

description:
ZT14 fed, liver pooled from 3 mice, rep2
SM1924

value: wild type

value: FoxO1 ChIP-seq, sc-11350 (Santa Cruz)

value: Night restricted feeding


title: Gastric cancer 7

value: Signet ring cell carcinoma

value: IV


title: ZT14_unfed_PBS_H3K27Ac rep2

description:
ZT14 unfed PBS, liver pooled from 3-4 mice, rep2
SM2246

value: H3K27Ac ChIP-seq,  Ab4729 (Abcam)

value: Night restricted feeding, pre-prandial injection with vehicle


title: Hep-Carbohydrate-0 hr-60

description: SAMPLE 60

value: Hepatocyte

value: liver

value: 0 hr


title: Hep-Carbohydrate-0 hr-61

description: SAMPLE 61


title: Gastric cancer 5

value: F

value: Gastric cancer (frozen)

value: Distal gastrectomy


title: Gastric cancer 4


title: ZT14_fed_FOXO1 rep1

description:
ZT14 fed, liver pooled from 3 mice, rep1
SM1923

value: Liver


title: Hep-Carbohydrate-0 hr-67

description: SAMPLE 67

value: Carbohydrate


title: Gastric cancer 10

value: Non-signet ring cell diffuse

value: Middle 1/3


title: Gastric cancer 3

value: Proximal 1/3

value: Total gastrectomy

value: IIIB


title: ZT14_unfed_FOXO1 rep1

description:
ZT14 unfed, liver pooled from 3 mice, rep1
SM1921

value: wild type

value: FoxO1 ChIP-seq, sc-11350 (Santa Cruz)

value: Night restricted feeding


title: Hep-Carbohydrate-0 hr-57

description: SAMPLE 57


title: Hep-Carbohydrate-0 hr-56

description: SAMPLE 56


title: Gastric cancer 1

value: M

value: IIIC


title: ZT14_fed_input

description:
ZT14 fed, liver pooled from 3-4 mice, rep2
SM1063

value: ChIP input


title: ZT14_unfed_input

description:
ZT14 unfed, liver pooled from 3-4 mice, rep1
SM1062


title: Gastric cancer 6

value: Distal 1/3


title: Hep-Carbohydrate-0 hr-55

description: SAMPLE 55

value: Hepatocyte

value: liver

value: 0 hr


title: ZT14_fed_GR rep2

description:
ZT14 fed, liver pooled from 3-4 mice, rep2
SM1201

value: Liver

value: GR ChIP-seq, MA1-510 (ThermoFischer), PA1-511a (ThermoFischer), SC-1003 (Santa Cruz)


title: ZT14_unfed_GR rep2

description:
ZT14 unfed, liver pooled from 3-4 mice, rep2
SM1200


title: Hep-Carbohydrate-0 hr-59

description: SAMPLE 59

value: Carbohydrate


title: ZT14_fed_GR rep1

description:
ZT14 fed, liver pooled from 3-4 mice, rep1
SM1061


title: Hep-Carbohydrate-0 hr-54

description: SAMPLE 54


title: Hep-Carbohydrate-0 hr-51

description: SAMPLE 51


title: ZT14_unfed_GR rep1

description:
ZT14 unfed, liver pooled from 3-4 mice, rep1
SM1060


title: Hep-Carbohydrate-0 hr-50

description: SAMPLE 50


title: ZT14_unfed_FOXO1 rep2

description:
ZT14 unfed, liver pooled from 3 mice, rep2
SM1922


title: ZT14_fed_80U rep2

description:
ZT14 fed, liver pooled from 3-4 mice, rep2
SM929

extract_protocol:
Nuclei purified from liver tissue was treated with 60U or 80U of DNase I. DNA fragments below 1000 bp were isolated using a sucrose gradeint and purified by phenol/chloroform extraction
ChIP-seq and DHS-seq libraries were constructed using the NEBNext Library prep kit according to manufacturer´s (NEB) instructions.

value: DNase-seq, 80U Dnase


title: Hep-Carbohydrate-0 hr-58

description: SAMPLE 58


title: Hep-Carbohydrate-0 hr-53

description: SAMPLE 53


title: ZT14_unfed_80 rep2

description:
ZT14 unfed, liver pooled from 3-4 mice, rep2
SM927


title: ZT14_fed_60U rep2

description:
ZT14 fed, liver pooled from 3-4 mice, rep2
SM928

value: DNase-seq, 60U Dnase


title: Hep-Carbohydrate-0 hr-52

description: SAMPLE 52


title: ZT14_unfed_60U rep2

description:
ZT14 unfed, liver pooled from 3-4 mice, rep2
SM926


title: Hep-Carbohydrate-0 hr-48

description: SAMPLE 48


title: ZT14_fed_80U rep1

description:
ZT14 fed, liver pooled from 3-4 mice, rep1
SM894


title: Hep-Carbohydrate-0 hr-47

description: SAMPLE 47


title: Hep-Carbohydrate-0 hr-49

description: SAMPLE 49


title: Hep-Carbohydrate-0 hr-46

description: SAMPLE 46


title: Gastric cancer 2

description: Fastq contains personal confidential information that is controlled-access only

value: Gastric cancer (frozen)

value: Non-signet ring cell diffuse

value: Distal gastrectomy

value: IV


title: ZT14_fed_60U rep1

description:
ZT14 fed, liver pooled from 3-4 mice, rep1
SM893

value: wild type

value: Night restricted feeding


title: ZT14_unfed_80 rep1

description:
ZT14 unfed, liver pooled from 3-4 mice, rep1
SM892


title: ZT14_unfed_60U rep1

description:
ZT14 unfed, liver pooled from 3-4 mice, rep1
SM891


title: Hep-Carbohydrate-0 hr-45

description: SAMPLE 45


title: ZT14_fed_H3K27Ac rep3

description:
ZT14 fed, single mouse, rep3
SM1102

value: H3K27Ac ChIP-seq,  Ab4729 (Abcam)


title: Hep-Carbohydrate-0 hr-43

description: SAMPLE 43


title: Hep-Carbohydrate-0 hr-42

description: SAMPLE 42


title: ZT14_fed_H3K27Ac rep2

description:
ZT14 fed, single mouse, rep2
SM1101


title: Hep-Carbohydrate-0 hr-41

description: SAMPLE 41


title: ZT14_fed_H3K27Ac rep1

description:
ZT14 fed, single mouse, rep1
SM1100


title: ZT14_unfed_H3K27Ac rep3

description:
ZT14 unfed, single mouse, rep3
SM1099


title: ZT14_unfed_H3K27Ac rep2

description:
ZT14 unfed, single mouse, rep2
SM1098


title: ZT14_unfed_H3K27Ac rep1

description:
ZT14 unfed, single mouse, rep1
SM1097


title: ZT10_unfed_H3K27Ac rep3

description:
ZT10 unfed, single mouse, rep3
SM1096


title: ZT10_unfed_H3K27Ac rep1

description:
ZT10 unfed, single mouse, rep1
SM1094

value: H3K27Ac ChIP-seq, Ab4729 (Abcam)


title: Hep-Carbohydrate-0 hr-39

description: SAMPLE 39


title: Hep-Carbohydrate-0 hr-40

description: SAMPLE 40


title: Hep-Carbohydrate-0 hr-38

description: SAMPLE 38


title: ZT10_unfed_H3K27Ac rep2

description:
ZT10 unfed, single mouse, rep2
SM1095


title: Hep-Carbohydrate-0 hr-34

description: SAMPLE 34


title: Hep-Carbohydrate-0 hr-36

description: SAMPLE 36


title: ZT14_fed_RNA rep1

description:
ZT14 fed, single mouse, rep1
RNAseq_RPKM.txt
SM938c

value: RNA-seq, RNA ribo zero


title: ZT14_fed_RNA rep2

description:
ZT14 fed, single mouse, rep2
RNAseq_RPKM.txt
SM939c


title: ZT14_unfed_RNA rep2

description:
ZT14 unfed, single mouse, rep2
RNAseq_RPKM.txt
SM937c


title: Hep-Carbohydrate-0 hr-35

description: SAMPLE 35

value: Hepatocyte


title: Hep-Carbohydrate-0 hr-33

description: SAMPLE 33

value: liver


title: Hep-Carbohydrate-0 hr-37

description: SAMPLE 37

value: 0 hr


title: Hep-Carbohydrate-0 hr-44

description: SAMPLE 44


title: Hep-Carbohydrate-0 hr-30

description: SAMPLE 30


title: Hep-Carbohydrate-0 hr-31

description: SAMPLE 31


title: ZT10_unfed_RNA rep2

description:
ZT10 unfed, single mouse, rep2
RNAseq_RPKM.txt
SM935c

value: Liver


title: Hep-Carbohydrate-0 hr-29

description: SAMPLE 29


title: ZT10_unfed_RNA rep1

description:
ZT10 unfed, single mouse, rep1
RNAseq_RPKM.txt
SM934c


title: Hep-Carbohydrate-0 hr-28

description: SAMPLE 28


title: Hep-Carbohydrate-0 hr-27

description: SAMPLE 27


title: ModA9 OFF 3

city: Gold Coast

first: John

middle: Michael

last: Atack

state: QLD

address: Gold Coast Campus

department: Institute for Glycomics

institute: Griffith University

data_processing:
Illumina bcl2fastq  2.20.0.422 pipeline
bowtie aligner (2.3.2) was used to map reads to the C486 genomic DNA sequence; accession number CP007471
edgeR version 3.18.1 was used to perform differential expression analysis.
Supplementary_files_format_and_content: .txt files - abundance measurements and expression differences modA9 ON vs modA9OFF

organism: Haemophilus influenzae

source_name: non-typeable Haemophilus influenzae strain 1209

growth_protocol: mid-log cultures in supplemented BHI (sBHI; containing haemin and NAD)

extract_protocol:
RNA was isolated using Trizol according to manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina RiboZero Gold protocols

tag: genotype/variation

value: ModA9 OFF

value: methyltransferase absent


title: ModA9 OFF 2


title: ModA9 OFF 1


title: tma20tma64_sd_ribo

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

description: Ribosome-bound RNA

data_processing:
Library strategy: Ribosome profiling
Adapter sequences were trimmed with cutadapt v1.18 (-a CTGTAGGCACCATCAAT -a GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC -O 4 -n 4 --minimum-length 20).
Read mapping and counting was performed with STAR v2.5.3a.
Genome_build: Ensembl Saccharomyces_cerevisiae.R64-1-1.90 (genome-build-accession GCA_000146045.2, UCSC sacCer3)
Supplementary_files_format_and_content: Tab-separated text files containing read counts per gene as estimated by STAR.

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: The cells were grown in YPD (2% glucose, 2% peptone, 1% yeast extract) or SD (0,67% YNB w/o amino acids, 2% glucose) at 30C and 220 rpm to exponential growth stage.

extract_protocol:
Cells were resuspended in polysome lysis bufer (20 mM Tris pH 8.0, 140 mM KCl, 1.5 mM MgCl2, 100  g/ml cycloheximide, 1% Triton), flash frozen in liquid nitrogen and homogenyzed by grinding. Part of the cell lysates was used for mRNA isolation, another part was treated with ribonuclease I for polysome disassembly and applied to sucrose gradient fractionation with subsequent isolation of ribosome-bound RNA fragments from monosome fraction. mRNA was isolated using Oligo(dT) beads  and ribosome-bound RNA was isolated using acidic-phenol extraction.
cDNA libraries for Ribo-Seq and RNA-Seq were constructed in parallel using standard ribosomal profiling library construction protocol (described in Ingolia NT et al., 2009, Science).

treatment_protocol: Cycloheximide was added to yeast media to final concentration 100µg/ml and growth was continued for 3 minutes then cells were harvested by filtration.

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 tma64delta::HygMX4 tma20delta::KanMX4

tag: growth media

value: SD


title: tma20tma64_sd_rna

description: Total RNA

data_processing:
Adapter sequences were trimmed with cutadapt v1.18 (-a CTGTAGGCACCATCAAT -a GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC -O 4 -n 4 --minimum-length 20).
Read mapping and counting was performed with STAR v2.5.3a.
Genome_build: Ensembl Saccharomyces_cerevisiae.R64-1-1.90 (genome-build-accession GCA_000146045.2, UCSC sacCer3)
Supplementary_files_format_and_content: Tab-separated text files containing read counts per gene as estimated by STAR.


title: Hep-Carbohydrate-0 hr-32

description: SAMPLE 32

value: Carbohydrate


title: tma20tma64_rna

description: Total RNA

value: YPD


title: Hep-Carbohydrate-0 hr-25

description: SAMPLE 25


title: ModA5 OFF 3

data_processing:
Illumina bcl2fastq  2.20.0.422 pipeline
bowtie aligner (2.3.2) was used to map reads to the C486 genomic DNA sequence; accession number CP007471
edgeR version 3.18.1 was used to perform differential expression analysis.
Supplementary_files_format_and_content: .txt files - abundance measurements and expression differences modA5 ON vs modA5 OFF

source_name: non-typeable Haemophilus influenzae strain477

value: ModA5 OFF


title: ModA9 ON 3

value: ModA9 ON

value: methyltransferase present


title: ModA9 ON 2


title: ZT14_unfed_RNA rep1

description:
ZT14 unfed, single mouse, rep1
RNAseq_RPKM.txt
SM936c

value: wild type

value: Night restricted feeding


title: Hep-Carbohydrate-0 hr-24

description: SAMPLE 24


title: Hep-Carbohydrate-0 hr-23

description: SAMPLE 23


title: ModA9 ON 1


title: Hep-Carbohydrate-0 hr-22

description: SAMPLE 22


title: tma20tma64_ribo

description: Ribosome-bound RNA


title: tma64_sd_rna

description: Total RNA

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 tma64delta::KanMX4


title: tma64_sd_ribo

description: Ribosome-bound RNA


title: ModA5 OFF 2


title: tma64_rna

description: Total RNA


title: ModA5 OFF 1


title: tma64_ribo

description: Ribosome-bound RNA


title: Hep-Carbohydrate-0 hr-20

description: SAMPLE 20


title: Hep-Carbohydrate-0 hr-21

description: SAMPLE 21


title: Hep-Carbohydrate-0 hr-19

description: SAMPLE 19


title: ModA5 ON 3

source_name: non-typeable Haemophilus influenzae strain 477

value: ModA5 ON


title: Hep-Carbohydrate-0 hr-18

description: SAMPLE 18

value: Hepatocyte


title: Hep-Carbohydrate-0 hr-26

description: SAMPLE 26

value: liver


title: tma20_sd_rna

description: Total RNA

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 tma20delta::KanMX4


title: tma20_sd_ribo

description: Ribosome-bound RNA


title: Hep-Carbohydrate-0 hr-17

description: SAMPLE 17

value: 0 hr


title: ModA5 ON 2


title: tma20_rna

description: Total RNA


title: ModA5 ON 1


title: Hep-Carbohydrate-0 hr-16

description: SAMPLE 16


title: ModA4 OFF 3

data_processing:
Illumina bcl2fastq  2.20.0.422 pipeline
bowtie aligner (2.3.2) was used to map reads to the C486 genomic DNA sequence; accession number CP007471
edgeR version 3.18.1 was used to perform differential expression analysis.
Supplementary_files_format_and_content: .txt files - abundance measurements and expression differences modA4 ON vs modA4 OFF

source_name: non-typeable Haemophilus influenzae strain C486

extract_protocol:
RNA was isolated using Trizol according to manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols

value: ModA4 OFF


title: tma20_ribo

description: Ribosome-bound RNA


title: wt_sd_rna

description: Total RNA

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0

value: WT


title: Hep-Carbohydrate-0 hr-15

description: SAMPLE 15


title: wt_sd_ribo

description: Ribosome-bound RNA

value: SD


title: ModA4 OFF 1

value: methyltransferase absent


title: wt2_rna

description: Total RNA

value: YPD


title: ModA4 ON 3

value: ModA4 ON


title: wt2_ribo

description: Ribosome-bound RNA


title: ModA4 ON 1


title: wt1_rna

description: Total RNA


title: Hep-Carbohydrate-0 hr-11

description: SAMPLE 11

value: Carbohydrate


title: Hep-Carbohydrate-0 hr-12

description: SAMPLE 12


title: Hep-Carbohydrate-0 hr-10

description: SAMPLE 10


title: wt1_ribo

description: Ribosome-bound RNA


title: Hep-Carbohydrate-0 hr-9

description: SAMPLE 9


title: ModA4 OFF 2


title: Hep-Carbohydrate-0 hr-14

description: SAMPLE 14


title: L1-DR-C

city: Eugene

first: Amy

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

data_processing:
Bowtie version 1.1.2 was used to map reads to the WS210  version of the genome.
Count files were generated with HTSeq using the GTF file used in Maxwell et al., 2012. This file includes features of the WS210 genome in addition to features of WS220 mapped back to WS210.
edgeR exact test was used on normalized count tables for differential expression analysis. Genes with counts per million (CPM) >1 in at least 3 libraries were included in the analysis.
Genome_build: WS210
Supplementary_files_format_and_content: Count files include the sequence identifier for each gene and the number of counts mapping to that gene (not normalized across libraries).

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: The wild-type N2 strain was maintained well-fed at 20C on E. coli OP50 on standard NGM plates prior to setting up the experiment. Worms were then bleached, and embryos were placed in liquid culture at 1 embryo/ 100 uL under AL (25 mg/mL HB101) or DR (3.1 ml/mL HB101) conditions with S-complete. After 96 hr, AL/DR adults were bleached and embryos were resuspended in S-basal at 1 embryo / uL.

extract_protocol:
Total RNA was extracted using TRIzol with minor modifications to the manufacturer's protocol. 1mL of TRIzol was used per sample. Samples were homogenized using 100uL of acid-washed sand.
Libraries were prepared using the NEB Next Ultra Non-directional mRNA-seq Kit. 12 cycles of PCR were used to amplify libraries.

treatment_protocol: After 24 hr, L1 larvae were collected. Samples were flash frozen in liquid nitrogen and stored at -80C until RNA extraction.

tag: parental diet

value: DR


title: L1-DR-D


title: pMN Meg3KD-H6

city: Taipei

first: Ya-Ping

last: Yen

address: 128 Academia Road, Section 2, Nankang

department: Institute of molecular biology

country: Taiwan

institute: Academia Sinica

hyb_protocol: 825 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray (G4858A-028005) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software10.5.1 (Agilent) using default parameters (protocol GE1-105_D08 and Grid: 028005_D_F_20110711) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Meg3KD projenitor motor neuron after two day RA induction

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA isolation by Trizol, DNase treated by TURBO DNA-free Kit (Life Technology), and checked with Bioanalyzer 2100 (Agilent) for RIN > 9.

treatment_protocol: To get the time series samples from ES cell to motor neurons, RA/Shh were applied from day 2 to day 5 during the differention process.

tag: tissue

value: embryoid bodies

value: male


title: Hep-Carbohydrate-0 hr-13

description: SAMPLE 13

tag: cell type


title: Hep-Carbohydrate-0 hr-7

description: SAMPLE 7

tag: diet


title: ModA4 ON 2

value: methyltransferase present


title: L1-DR-A


title: Day7MN MegKD-K4

source_name: MN after five day RA induction


title: Day7MN-Meg3KD-H6-R1

source_name: Meg3KD motor neuron after five day RA induction (replicate1)


title: Hep-Carbohydrate-0 hr-6

description: SAMPLE 6

tag: time after partial hepatectomy


title: Day7MN-Meg3KD-H6-R2

source_name: Meg3KD motor neuron after five day RA induction (replicate2)


title: ES Meg3KD-H6

source_name: Meg3KD ESC

value: embryonic stem cell


title: Hep-Carbohydrate-0 hr-5

description: SAMPLE 5

value: Hepatocyte


title: Day7MN-IG-DMR mat KOA-R2

source_name: IG-DMR materlal deletion motor neuron after five day RA induction (replicate2)


title: L1-AL-C

value: AL


title: L1-AL-B


title: spt6-1004 37C NET-seq 2

city: Boston

first: Fred

last: Winston

state: MA

address: 77 Avenue Louis Pasteur, Room 239

department: Genetics

institute: Harvard Medical School

description: Native Elongating Transcript Sequencing (NET-seq) of the spt6-1004 S. cerevisiae strain grown at 30ºC and shifted to 37ºC for 80 minutes.

data_processing:
Library strategy: NET-seq
The Snakemake pipeline used to process NET-seq libraries is available at github.com/winston-lab. Removal of adapter sequences from the 3’ end of the read and 3’ quality trimming were performed using cutadapt. Reads were aligned to the S. cerevisiae genome using Tophat2 without a reference transcriptome, and uniquely mapping reads were selected using SAMtools. Coverage of the 5’-most base of the read, corresponding to the 3’-most base of the nascent RNA and the active site of elongating RNA polymerase, was extracted using bedtools genomecov and normalized to the total number of uniquely mapped reads.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: TSS-seq “plus” and “minus” files are bigWig files of spike-in normalized S. cerevisiae transcription start sites on the positive and negative strands, respectively. ChIP-nexus “plus” and “minus” files are bigWig files of library-size normalized S. cerevisiae coverage of the points of crosslinking on the positive and negative strand, respectively. ChIP-nexus “midpoint” and “protection” files are library-size normalized S. cerevisiae coverage of either the midpoint of the fragment predicted to be protected by the ChIP’ed factor by MACS2, or the entire fragment. NET-seq “plus” and “minus” files are bigWig files of library-size normalized S. cerevisiae coverage of the positions of transcribing RNA polymerase II on the positive and negative strands, respectively. MNase-seq “midpoint” files are bigWig files of spike-in normalized S. cerevisiae dyad coverage determined by taking the midpoint of each sequenced fragment. MNase-seq “midpoint_smoothed” files are bigWig files of the same spike-in normalized dyad coverage, smoothed with a Gaussian kernel of 20bp bandwidth. MNase-seq “wholefrag” files are bigWig files of spike-in normalized S. cerevisiae  coverage of the entire fragment protected from MNase digestion.

source_name: log phase S. cerevisiae

growth_protocol: Cells were grown in YPD at 30ºC to approximately 1x107 cells/ml (OD600=0.6), at which point an equal volume of YPD medium pre-warmed to 44ºC was added, and the cultures were shifted to 37C for an additional 80 minutes.

extract_protocol:
RNA was extracted as previously described (Churchman, 2011).
NET-seq library construction was done as previously described (Churchman, 2011)

tag: temperature

value: log phase S. cerevisiae

tag: experiment type

tag: target molecule

value: nascent RNA


title: Hep-Carbohydrate-0 hr-4

description: SAMPLE 4

value: liver

value: 0 hr


title: Day7MN-shScr-E5

source_name: scramble motor neuron after five day RA induction

tag: gender


title: spt6-1004 37C NET-seq 1

value: Native Elongating Transcript Sequencing (NET-seq)


title: E18.5 Myf5-/-:MyoD-/- mouse esophagus

city: Halifax

first: Boris

last: Kablar

state: Nova Scotia

address: 5850 College Street

department: Medical Neuroscience

country: Canada

institute: Dalhousie University

description: Gene expression data from double knock-out (MyoD-/-:Myf5-/-) fetal esophagus.

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: E18.5 mouse esophagus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: fetal esophagus

value: BALB/c Myf5:Myod null

tag: age


title: E18.5 WT mouse esophagus

description: Gene expression data from wild-type fetal esophagus.

value: BALB/c


title: Day7MN-IG-DMR mat KOA-R1

source_name: IG-DMR materlal deletion motor neuron after five day RA induction (replicate1)


title: L1-AL-A


title: L1-DR-B


title: Hep-Carbohydrate-0 hr-3

description: SAMPLE 3

data_processing:
The data were normalized using the -ΔΔCt scheme. Expression values within samples were normalized using the median expression of 55 high performing genes (Ct_reaction - Ct_median_across_55_genes). Expression values within genes were scaled to the median using (Ct_median_across_all_samples - Ct_reaction)
Missing values were imputed using the k-nearest neighbors imputation after normalization

source_name: Carbohydrate-0 hr

extract_protocol: Single hepatocytes extracted using laser capture microdissection were lysed and directly processed for reverse transcription followed by targeted pre-amplification. Pre-amplification of cDNA samples was performed for 22 cycles using TaqMan PreAmp Master Mix as per the manufacturer’s protocol. Primers for the 84 genes tested were custom designed. qPCR was performed on BioMark 96.96 Dynamic Array for 30 cycles.


title: spt6-1004 30C NET-seq 1

description: Native Elongating Transcript Sequencing (NET-seq) of the spt6-1004  S. cerevisiae strain grown at 30ºC.

growth_protocol: Cells were grown in YPD at 30ºC to approximately 1x107 cells/ml (OD600=0.6).


title: Hep-Carbohydrate-0 hr-2

description: SAMPLE 2


title: wild-type 37C NET-seq 2

description: Native Elongating Transcript Sequencing (NET-seq) of a wild-type S. cerevisiae strain grown at 30ºC and shifted to 37ºC for 80 minutes.

growth_protocol: Cells were grown in YPD at 30ºC to approximately 1x107 cells/ml (OD600=0.6), at which point an equal volume of YPD medium pre-warmed to 44ºC was added, and the cultures were shifted to 37ºC for an additional 80 minutes.


title: Hep-Carbohydrate-0 hr-1

description: SAMPLE 1


title: Hep-Carbohydrate-0 hr-8

description: SAMPLE 8


title: wild-type 37C NET-seq 1


title: Mock_24hr_rep1

city: Frederick

first: Catherine

middle: E

last: Arnold

state: MD

address: 1425 Porter St

department: Diagnostic Systems Division

institute: US Army Medical Research Institute of Infectious Diseases

data_processing:
dual index filter: in house software (raw reads index filtered to Q30 cutoff)
trimming : Trimmomatic-0.33 (leading:3, trailing:3, sliding window:4:15, minlen: 80, Q30 cutoff)
alignment and normalization: kallisto 0.43.0 (bootstraps: 100, default parameters)
Genome_build: Raegyp2.0
Supplementary_files_format_and_content: abundance files: h5 (contains transcript_id, length, eff_length (effective length), est_counts (estimated counts) and tpm (transcripts per million) for each gene in the transcriptome, includes bootstrap values (each h5 contains 100 bootstraps that are used for downstream differential gene expression).  length, eff_length, est_counts used to calculate tpm.  )
Supplementary_files_format_and_content: annotation: gff (contains gene identifiers used in h5 files, genome coordinates, Ensembl IDs, gene symbols, etc)

organism: Rousettus aegyptiacus

growth_protocol: 10% FBS DMEM, 5% CO2 and 37C

extract_protocol:
Harvested in 1x RNA Lysis/Binding Solution Concentrate (Thermo Fisher Scientific) at 3hr, 8hr and 24hr post-infection, followed by magnetic bead purification and TURBO DNase treatment using the MagMAX-96 Total RNA Isolation Kit (Ambion) according to manufacturer guidelines. RNA extractions were performed on a MagMAX Express 96 Magnetic Particle Processor (Applied Biosystems)
Libraries were generated on the Sciclone G3 Liquid Handling Robot (PerkinElmer) using the TruSeq Stranded Total RNA Library Prep Kit (Illumina). Library quality was evaluated on the Agilent 2200 TapeStation 2200 and quantified by qPCR using the KAPA Complete (Universal) qPCR kit (Kapa Biosystems) for Illumina libraries. Libraries were diluted to 12 pM and cluster generation was performed on the Illumina cBot. Libraries were sequenced on the Illumina HiSeq 2500 using the paired end 2x125 bp, dual-index format.

treatment_protocol: MOI 1.0 of Sendai (Cantell, Charles River), MARV371bat, MARV371-R301A, or mock (DMEM media alone), media changed afer 1 hour of absorption and cells incubated at 5% CO2 and 37C

value: RoNi7.1 (fibroblast like kidney derived)

tag: infection

value: mock

tag: time

tag: passage

value: 4 to 6


title: Mock_8hr_rep3


title: Mock_24hr_rep3


title: spt6-1004 37C TFIIB ChIP-nexus 2

description: ChIP-nexus of TFIIB in the spt6-1004  S. cerevisiae strain grown at 30ºC and shifted to 37ºC for 80 minutes.

data_processing:
The Snakemake pipeline used to process ChIP-nexus libraries is available at github.com/winston-lab. Filtering for reads containing the constant region of the adapter on the 5’ end of the read, 3’ adapter removal, and 3’ quality trimming were performed using cutadapt. The random pentamer molecular barcode on the 5’ end of the read was then removed and processed using a custom Python script. Reads were aligned to the combined S. cerevisiae and S. pombe genomes using Bowtie2, and uniquely mapping reads were selected using SAMtools. Reads mapping to the same location as another read with the same molecular barcode were identified as PCR duplciates and removed using a custom Python script. Coverage of the 5’-most base, corresponding to the point of crosslinking, was extracted using bedtools genomecov. The median fragment size estimated by MACS2 over all ChIP-nexus samples for the same factor was used to generate coverage of factor protection and fragment midpoints, by extending reads to the fragment size, or by shifting reads by half the fragment size, respectively. Coverage was normalized to the total number of reads uniquely mapping to S. cerevisiae.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: TSS-seq “plus” and “minus” files are bigWig files of spike-in normalized S. cerevisiae transcription start sites on the positive and negative strands, respectively. ChIP-nexus “plus” and “minus” files are bigWig files of library-size normalized S. cerevisiae coverage of the points of crosslinking on the positive and negative strand, respectively. ChIP-nexus “midpoint” and “protection” files are library-size normalized S. cerevisiae coverage of either the midpoint of the fragment predicted to be protected by the ChIP’ed factor by MACS2, or the entire fragment. NET-seq “plus” and “minus” files are bigWig files of library-size normalized S. cerevisiae coverage of the positions of transcribing RNA polymerase II on the positive and negative strands, respectively. MNase-seq “midpoint” files are bigWig files of spike-in normalized S. cerevisiae dyad coverage determined by taking the midpoint of each sequenced fragment. MNase-seq “midpoint_smoothed” files are bigWig files of the same spike-in normalized dyad coverage, smoothed with a Gaussian kernel of 20bp bandwidth. MNase-seq “wholefrag” files are bigWig files of spike-in normalized S. cerevisiae  coverage of the entire fragment protected from MNase digestion.

extract_protocol:
Cultures were cooled to 25ºC with medium pre-chilled to 4ºC before cross-linking in 1% formaldehyde while shaking at 25ºC for 30 minutes. Chromatin was extracted using standard methods (DeGennaro, 2013) and sheared in a QSONICA sonicating water bath. 2.5-3 mg of S. cerevisiae chromatin containing 5% S. pombe spike-in chromatin by mass was affinity purified using 100μL Pan Mouse IgG Dynabeads (Invitrogen).
Library construction for Illumina sequencing was performed essentially as previously described (He, 2017), except buffers were optimized for yeast: Buffer A (10 mM TE, 0.1% Triton X), Buffer B (50mM HEPES.KOH pH 7.4, 140mM NaCl, 1mM EDTA, 1% Triton-X, 0.1% sodium deoxycholate), Buffer C (Buffer B with 250mM NaCl), Buffer D (10mM Tris pH 7.5, 250mM LiCl, 10mM EDTA, 0.5% IGEPAL CA-360, 0.1% sodium deoxycholate).

tag: strain

value: ChIP-nexus of TFIIB

value: genomic DNA


title: Mock_8hr_rep2


title: S6RM1

city: Tokushima

first: Taigo

last: Horiguchi

address: 3-18-15, Kuramoto-Cho

country: Japan

institute: Tokushima University

description: Gene expression

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4858A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028282_D_F_20110531) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Sedentary SPORTS rat, muscle

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Valencia CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: skeletal muscle

value: male


title: spt6-1004 30C NET-seq 2


title: spt6-1004 37C TFIIB ChIP-nexus 1


title: imMKCL_TA316_11days

city: Shiraoka

first: Ayako

last: Otani

state: Saitama

address: 1470 Shiraoka

department: Medical Materials group

institute: Nissan Chemical Industries

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G system.

data_processing: The data were analyzed with Affimetrix Expression Console Softwere ver.1.3.0 using RMA-Sketch (RMA-Gene-Default) algorithm.

source_name: human iPSCs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: imMKCLs were cultured in 15 % fetal bovine serum/EBM medium (IMDM containing 292 ug/mL L-Glutamine, 100 U/mL penicillin, 100 ug/mL streptomyci, 0.05 mg/mL ascorbic acid, 0.45 mM 1-thioglycerol , 1 % Insulin-Transferrin-Selenium supplement) supplemented with 50 ng/mL recombinant human SCF (rhSCF), 50 ng/mL recombinant human TPO (rhTPO), and 1ug/mL doxycycline(Dox). Cells were seeded on 0.1 % gelatin coated 6-well plates with mitomycin C treated C3H 10T1/2 cells. Cells were cultured in a humidified incubator at 37 C and 5 % CO2 and passaged every 3-4 days.

extract_protocol: Extraction of total RNA was performed with Quiagen RNeasy mini kit according to the manufacturer's instructions.

treatment_protocol: imMKCLs were cultured for 11 days with rhSCF and Dox, in the presense of 50 ng/mL rhTPO or 200 ng/mL TA-316.

tag: cell line

value: imMKCLs

value: immortalized megakaryocyte progenitor cell lines (imMKCLs)

tag: cultured with

value: 200 ng/mL TA-316 for 11 days


title: imMKCL_TPO_11days

description: TPO

value: 50 ng/mL recombinant human TPO (rhTPO) for 11 days


title: Mock_8hr_rep1


title: Mouse 12.5

city: Edinburgh

first: Liam

last: Morrison

state: Midlothian

address: Easter Bush

country: United Kingdom

institute: The Roslin Institute, The University of Edinburgh

description:
cDNA Amplicon
VSG transcripts were enriched by carrying out PCR with oligonucleotide primers specific to the T. brucei spliced leader sequence (TbSL) and a reverse primers complementary to a 13 base pair conserved region in VSG 3’ untranslated regions (3'UTR)
balbc_12_5

data_processing:
Library strategy: cDNA Amplicon sequencing
Pacbio raw data was initially processed using the Pacbio SMRT analysis protocol (v2.3)
Raw data was converted into a fastq file using read_of_insert protocol with the following parameter selections: minimum 1 full pass, minimum predicted accuracy of 90%.
Based on the read length distribution and predicted gene length, a range of 1400-2000bp was used to filter the sequenced reads for downstream VSG analysis in fasta format
VSG variant distribution was determined by locally aligning the reads to TREU927 reference transcripts annotated to ‘VSGs’ using custom workflows
Genome_build: TREU927 genome (v26) on www.tritrypdb.org
Supplementary_files_format_and_content: the VSG transcript counts for the aligned reads are presented in the tab-seperated ".txt" file

organism: Trypanosoma brucei brucei

source_name: Infected mouse blood

extract_protocol:
Mice were maintained for 12 days post-infection, and groups of 5 mice were euthanased at 3, 6, 10 and 12 days post-infection. At each sampling day, RNA was extracted from 200 µl infected blood using the Qiagen RNeasy kit. Approximately 1 µg RNA was treated with DNase Turbo and cDNA was generated via reverse transcription. VSG transcripts were enriched by carrying out PCR with oligonucleotide primers specific to the T. brucei spliced leader sequence (TbSL) and a reverse primers complementary to a 13 base pair conserved region in VSG 3’ untranslated regions (3UTR).
DNA was purified with 1x cleaned Ampure beads (Agencourt) and the quantity and quality was assessed using Nanodrop and Qubit assay. Fragment Analyser (using a high sensitivity genomic kit) was used to determine the average size of the DNA and the extent of degradation. DNA was treated with Exonuclease V11 at 37 °C for 15 minutes. The ends of the DNA were repaired as described by the Pacific Biosciences protocol. Samples were incubated for 20 minutes at 37 °C with damage repair mix supplied in the SMRTbell library kit (Pacific Biosciences). This was followed by a 5 minute incubation at 25 °C with end repair mix. DNA was cleaned using 0.5x Ampure beads and 70% ethanol washes. DNA was ligated to adapter overnight at 25 °C. Ligation was terminated by incubation at 65°C for 10 minutes followed by exonuclease treatment for 1 hour at 37°C. The SMRTbell libraries were purified with 0.5x Ampure beads. The quantity of library and therefore the recovery was determined by Qubit assay and the average fragment size determined by Fragment Analyser. SMRTbell libraries were then annealed to the sequencing primer at values predetermined by the Binding Calculator (Pacific Biosciences) and a complex made with the DNA Polymerase (P4/C2chemistry). The complex was bound to Magbeads and this was used to set up 20 SMRT cells for sequencing. Sequencing was done using 180 minute movie times.

treatment_protocol: Mice were inoculated with 1 x 10^5 Trypanosoma brucei brucei TREU927 via the intraperitoneal route.

tag: host organism

value: Mus musculus BALB/c


title: C1RM2

description: Gene expression

source_name: Wild type, muscle


title: wild-type 37C TFIIB ChIP-nexus 2

description: ChIP-nexus of TFIIB in a wild-type S. cerevisiae strain grown at 30ºC and shifted to 37ºC for 80 minutes.

value: log phase S. cerevisiae


title: Mouse 12.4

description:
cDNA Amplicon
VSG transcripts were enriched by carrying out PCR with oligonucleotide primers specific to the T. brucei spliced leader sequence (TbSL) and a reverse primers complementary to a 13 base pair conserved region in VSG 3’ untranslated regions (3'UTR)
balbc_12_4


title: S1RM1

description: Gene expression

source_name: Exercised SPORTS rat, muscle


title: Mock_3hr_rep3


title: Mock_24hr_rep2


title: wild-type 37C TFIIB ChIP-nexus 1


title: Mock_3hr_rep2


title: Mouse 12.3

description:
cDNA Amplicon
VSG transcripts were enriched by carrying out PCR with oligonucleotide primers specific to the T. brucei spliced leader sequence (TbSL) and a reverse primers complementary to a 13 base pair conserved region in VSG 3’ untranslated regions (3'UTR)
balbc_12_3


title: Mouse 12.2

description:
cDNA Amplicon
VSG transcripts were enriched by carrying out PCR with oligonucleotide primers specific to the T. brucei spliced leader sequence (TbSL) and a reverse primers complementary to a 13 base pair conserved region in VSG 3’ untranslated regions (3'UTR)
balbc_12_2


title: Mock_3hr_rep1