title: ChIP-seq from A549 (ENCLB649DCK)

description:
https://www.encodeproject.org/experiments/ENCSR676MJK/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR676MJK
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR701MJQ
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB649DCK
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS307SRO at ENCODE; https://www.encodeproject.org/ENCBS307SRO/


title: ChIP-seq from A549 (ENCLB670NYD)

status: Public on Apr 20 2018

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR956LGB/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR956LGB
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR560DEL
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB670NYD
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 1 hour

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 58 year

tag: lab

value: Tim Reddy, Duke

tag: treatments

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_100nM;

tag: link

value: ENCBS222WNL at ENCODE; https://www.encodeproject.org/ENCBS222WNL/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB926NQQ)

description:
https://www.encodeproject.org/experiments/ENCSR247LSH/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR247LSH
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR088SOR
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB926NQQ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 2 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:2; duration_units:hour;

value: ENCBS643ZJW at ENCODE; https://www.encodeproject.org/ENCBS643ZJW/


title: ChIP-seq from A549 (ENCLB246FOK)

description:
https://www.encodeproject.org/experiments/ENCSR760NPX/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 hours.
experiment encode accession: ENCSR760NPX
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR565ZHQ
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB246FOK
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 5 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:5; duration_units:hour;

value: ENCBS823UOD at ENCODE; https://www.encodeproject.org/ENCBS823UOD/


title: ChIP-seq from A549 (ENCLB209IZE)

description:
https://www.encodeproject.org/experiments/ENCSR944ZCT/
***************
biological replicate number: 1
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 3 hours.
experiment encode accession: ENCSR944ZCT
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR266YIS
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB209IZE
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 3 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:3; duration_units:hour;

value: ENCBS776MHF at ENCODE; https://www.encodeproject.org/ENCBS776MHF/


title: ChIP-seq from A549 (ENCLB777UXM)

description:
https://www.encodeproject.org/experiments/ENCSR748MVX/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR748MVX
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR748SVE
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB777UXM
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 4 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS514LZY at ENCODE; https://www.encodeproject.org/ENCBS514LZY/


title: ChIP-seq from A549 (ENCLB704PDV)

description:
https://www.encodeproject.org/experiments/ENCSR895JMI/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR895JMI
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR216DMN
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB704PDV
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 30 minutes

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:30; duration_units:minute;

value: ENCBS108SYG at ENCODE; https://www.encodeproject.org/ENCBS108SYG/


title: ChIP-seq from A549 (ENCLB516HHO)

description:
https://www.encodeproject.org/experiments/ENCSR193NSH/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR193NSH
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR139PCE
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB516HHO
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line

value: cell line

value: male

value: ENCBS633IMH at ENCODE; https://www.encodeproject.org/ENCBS633IMH/


title: ChIP-seq from A549 (ENCLB527XBY)

description:
https://www.encodeproject.org/experiments/ENCSR330ELC/
***************
biological replicate number: 1
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR330ELC
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR328BXP
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB527XBY
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 10 hours

value: adult

value: 58 year

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:10; duration_units:hour;

value: ENCBS077ELW at ENCODE; https://www.encodeproject.org/ENCBS077ELW/


title: ChIP-seq from A549 (ENCLB816SMA)

description:
https://www.encodeproject.org/experiments/ENCSR853VWZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR853VWZ
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR366VPA
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB816SMA
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 6 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS386HKI at ENCODE; https://www.encodeproject.org/ENCBS386HKI/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB996SOI)

description:
https://www.encodeproject.org/experiments/ENCSR150EFU/
***************
biological replicate number: 2
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR150EFU
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR139PCE
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB996SOI
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS359PKV at ENCODE; https://www.encodeproject.org/ENCBS359PKV/


title: Sample_69378

status: Public on Apr 18 2018

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

description:
G= GnRH RNA; M = Male; I=Intact; 3=Biological Replicate
Moenter-27

library_source: transcriptomic

data_processing:
QC: We checked the quality of the raw reads data for each sample using FastQC [1] (version 0.10.1) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content, etc.).
Aligment: We used the software package Tuxedo Suite for alignment, differential expression analysis, and post-analysis diagnostics [2, 3, 4]. Briefly, we aligned reads to the reference transcriptome including both mRNAs and lncRNSs (UCSC mm10) [5] using TopHat (version 2.0.9) and Bowtie (version 2.1.0.). We used default parameter settings for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments.
QC: We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
Normalization and Quantitation: We used Cufflinks/CuffDiff (version 2.1.1) for expression quantitation, normalization, and differential expression analysis, using UCSC mm10.fa as the reference genome sequence. For this analysis, we used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package.
Differential Expression: We used locally developed scripts to format and annotate the differential expression data output from CuffDiff. Briefly, we identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR < 0.05 and fold change ≥ ± 1.5.
Annotation: We annotated genes and isoforms with NCBI Entrez GeneIDs and text descriptions. We further annotated differentially expressed genes with Gene Ontology (GO) [6] terms using NCBI annotation.
Enrichment Testing: We used DAVID (version 6.7) [7] for enrichment analysis of the set of differentially expressed genes to identify significantly enriched functional categories.
Genome_build: MM10
Supplementary_files_format_and_content: Text file with mapped read counts (not normalized) for each gene in each sample

molecule: total RNA

organism: Mus musculus

growth_protocol: GnRH CRE (homozygote) male mice were bred to floxed-stop-floxed  L10a-GFP (homozygote) female mice to generate offspring that express GFP tagged ribosomal protein L10a in GnRH neurons.

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (Qiagen; 74004) with on column DNasing and assessed for quantity and quality using the Pico or Nano Chip (Agilent).
Total RNA was first amplified using the SMARTer technology (SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing; Clonetech 634888 and 634889) with cDNA as the output.
The cDNA was input into the Low Input DNA Library Prep Kits for Illumina (Clonetech 634899) it was end repaired A tailed and Illumina adapters were ligated.
The resultant library was PCR amplified to generate sufficient material for sequencing.
Libraries were clustered on the cBot (illumina) and sequenced on 4 lanes of a 50-cycle
paired end HiSeq 4000. HiSeq Control Software version 3.3.52 was used according to manufacturer’s protocols. Demultiplexing and Fastq file generation was done using bcl2fastq version 2.17.1.14.

treatment_protocol:
Preoptic Area hypothalamic punches were collected from adult (55-165 days) female (diestrous), male, ovariectomized females and orchidecomized male mice. Steroid bioavailability, or lack thereof, was confirmed by measuring uterine mass in females and serum LH from trunk blood collected at the time of tissue collection from both sexes.
GnRH neuron enriched RNA was generated by Translating Ribosome Affinity Purification. This technique generates two RNAs per sample one enriched for GnRH neurons (immunoprecipitant) and one depleted for GnRH neurons (supernatant).

tag: genotype/variation

value: GnRH CRE x Floxed L10a-GFP

value: Male

tag: treatment

value: Intact

tag: trap lysate

value: GnRH Enriched Immunoprecipitant

tag: alternative sample id

tag: # mice pooled per sample

tag: tissue

value: Preoptic area of the hypothalamus


title: Sample_69380

description:
G= GnRH RNA; M = Male; G=Gonadectomized; 1=Biological Replicate
Moenter-29

value: Orchidectomized


title: ChIP-seq from A549 (ENCLB005DYK)

description:
https://www.encodeproject.org/experiments/ENCSR495WGO/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR495WGO
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR328BXP
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB005DYK
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: cell line

value: male

value: ENCBS083ZIM at ENCODE; https://www.encodeproject.org/ENCBS083ZIM/


title: ChIP-seq from A549 (ENCLB035IXC)

description:
https://www.encodeproject.org/experiments/ENCSR501LQA/
***************
biological replicate number: 1
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR501LQA
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR366VPA
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB035IXC
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: 58 year

value: ENCBS620RRT at ENCODE; https://www.encodeproject.org/ENCBS620RRT/


title: Sample_69376

description:
G= GnRH RNA; F = Female; G=Gonadectomized; 2=Biological Replicate
Moenter-25

value: Female

value: Ovariectomized


title: ChIP-seq from A549 (ENCLB534SJA)

description:
https://www.encodeproject.org/experiments/ENCSR217ELF/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR217ELF
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR382EJS
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB534SJA
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 12 hours

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:12; duration_units:hour;

value: ENCBS503WAV at ENCODE; https://www.encodeproject.org/ENCBS503WAV/


title: ChIP-seq from A549 (ENCLB676XEU)

description:
https://www.encodeproject.org/experiments/ENCSR199XBQ/
***************
biological replicate number: 1
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 8 hours.
experiment encode accession: ENCSR199XBQ
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR233BJW
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB676XEU
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 8 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:8; duration_units:hour;

value: ENCBS479IGH at ENCODE; https://www.encodeproject.org/ENCBS479IGH/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB494WFM)

description:
https://www.encodeproject.org/experiments/ENCSR150EFU/
***************
biological replicate number: 1
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR150EFU
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR139PCE
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB494WFM
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS781DZW at ENCODE; https://www.encodeproject.org/ENCBS781DZW/


title: ChIP-seq from A549 (ENCLB227CIB)

description:
https://www.encodeproject.org/experiments/ENCSR335RKQ/
***************
biological replicate number: 1
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR335RKQ
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR748SVE
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB227CIB
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS695NLF at ENCODE; https://www.encodeproject.org/ENCBS695NLF/


title: ChIP-seq from A549 (ENCLB509MQC)

description:
https://www.encodeproject.org/experiments/ENCSR768DOX/
***************
biological replicate number: 1
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR768DOX
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR560DEL
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB509MQC
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: cell line

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_100nM;

value: ENCBS928VYM at ENCODE; https://www.encodeproject.org/ENCBS928VYM/


title: Sample_69379

description:
G= GnRH RNA; M = Male; G=Gonadectomized; 0=Biological Replicate
Moenter-28

value: GnRH CRE x Floxed L10a-GFP

value: Male

value: Orchidectomized

value: GnRH Enriched Immunoprecipitant

value: Preoptic area of the hypothalamus


title: Sample_69381

description:
G= GnRH RNA; M = Male; G=Gonadectomized; 2=Biological Replicate
Moenter-30


title: Sample_69375

description:
G= GnRH RNA; F = Female; G=Gonadectomized; 1=Biological Replicate
Moenter-24

value: Female

value: Ovariectomized


title: Sample_69374

description:
G= GnRH RNA; F = Female; G=Gonadectomized; 0=Biological Replicate
Moenter-23


title: Sample_69377

description:
G= GnRH RNA; M = Male; I=Intact; 2=Biological Replicate
Moenter-26

value: Intact


title: Sample_69372

description:
G= GnRH RNA; F = Female; I=Intact; 2=Biological Replicate
Moenter-21

value: Intact, Diestrus


title: Sample_69371

description:
T= Total RNA; M = Male; G=Gonadectomized; 2=Biological Replicate
Moenter-20

value: GnRH Depleted Supernatant


title: Sample_69369

description:
T= Total RNA; M = Male; G=Gonadectomized; 0=Biological Replicate
Moenter-18


title: Sample_69370

description:
T= Total RNA; M = Male; G=Gonadectomized; 1=Biological Replicate
Moenter-19


title: Sample_69368

description:
T= Total RNA; M = Male; I=Intact; 3=Biological Replicate
Moenter-17

source_name: Male_Intact_GnRH Depleted Supernatant


title: Sample_69365

description:
T= Total RNA; F = Female; G=Gonadectomized; 1=Biological Replicate
Moenter-14


title: Sample_69367

description:
T= Total RNA; M = Male; I=Intact; 2=Biological Replicate
Moenter-16


title: Sample_69364

description:
T= Total RNA; F = Female; G=Gonadectomized; 0=Biological Replicate
Moenter-13


title: Sample_69359

description:
G= GnRH RNA; F = Female; I=Intact; 1=Biological Replicate
Moenter-08


title: Wild-type replicate 4

city: New Haven

first: Byoung-Il

last: Bae

state: CT

address: Department of Neurosurgery, School of Medicine, Yale University

institute: Yale University

description:
Drop-seq
excluded from analysis (outlier)
see Macosko et al. 2015 for the Drop-seq library strategy. Briefly, paired end libraries include a sample (biological replicate) barcode and a unique molecular identifier on read 1 (R1) and a 50-base read from the 3'-end of the captured cDNA molecule on read 2 (R2).
As per dropseq protocol, R1 are barcodes and molecular identifiers, and R2 is the sequence, so paired reads do nor represent two reads with an insert

data_processing:
Tophat alignment version 2.1.1 of paired end raw bulk data
Transcriptome assembly with cufflinks version 2.2.1
The assembled transcriptome and the Ensembl reference transcriptome version 1.0.85 were merged using cuffmerge  from cufflinks 2.2.1, this merged reference file was then used for the single cell RNA-seq analysis in the Drop-Seq pipeline.
Single Cell Fastq reads were converted to BAM using the “FastqToSam” command in Picard version 1.130
For the single cell raw data, the Drop-Seq Core Computational Protocol version 1.0.1 was followed to obtain the Digital Gene Expression Matrix. Read pairs where more than one base in the barcode had a quality below 10 were discarded. Adapter sequences were trimmed from the 5’ end of the read, along with polyA tails. Star-2.5.2 was used to map reads to the custom transcriptome reference. The digital gene expression matrix was extracted using the “DigitalExpression” program of the Drop-seq protocol, keeping only cells with at least 200 reads per cell for clustering analysis.
Genome_build: MusPutFur1.0, transcript annotation version MusPutFur1.0.85
Supplementary_files_format_and_content: The SAMPLE_out_gene_exon_tagged.dge.txt.gz files are the Digital Gene Expression Matrices obtained from the Drop-Seq Core Computational process and are ready to be normalized, filtered, and analyzed. We do not provide the DGE of the sample which was not included in the analysis due to it being an outlier when clustering, but we have included the raw single cell sequencing data for that sample.
Supplementary_files_format_and_content: The CufflinksID_coordinates.txt is a text file with the ferret genome coordinates of some of the genes that we detected in bulk sequencing experiment and added to the reference transcriptome of the ferret, since these genes are not annotated in the current ferret reference transcriptome. These can be used along with the Digital Gene Expression files for genes that do not have annotation to look up their position in the ferret genome. In some cases it is then possible to infer which gene it might be based on conservation with other species that have this gene annotated.

organism: Mustela putorius furo

source_name: embryonic ferret forebrain

extract_protocol:
embryos removed from anesthetized jill, forebrains dissected out in cold HBSS, minced and cryopreserved (gradually frozen in HBSS w/ 10%DMSO & stored at -80); shipped on dry ice then thawed and dissociated using trypsin to a single-cell suspension on the day of Droplet capture
standard Illumina paired-end library

tag: dropseq batch

tag: aspm genotype

value: wildtype

tag: litter


title: Sample_69360

description:
G= GnRH RNA; M = Male; I=Intact; 0=Biological Replicate
Moenter-09


title: Sample_69355

description:
T= Total RNA; M = Male; I=Intact; 0=Biological Replicate
Moenter-04


title: Sample_69356

description:
T= Total RNA; M = Male; I=Intact; 1=Biological Replicate
Moenter-05


title: Wild-type replicate 3

description:
Drop-seq
see Macosko et al. 2015 for the Drop-seq library strategy. Briefly, paired end libraries include a sample (biological replicate) barcode and a unique molecular identifier on read 1 (R1) and a 50-base read from the 3'-end of the captured cDNA molecule on read 2 (R2).
As per dropseq protocol, R1 are barcodes and molecular identifiers, and R2 is the sequence, so paired reads do nor represent two reads with an insert


title: Sample_69366

description:
T= Total RNA; F = Female; G=Gonadectomized; 2=Biological Replicate
Moenter-15


title: Bulk neurons replicate 1

description:
bulk RNA-seq used only to generate reference transcriptome
CufflinksID_coordinates.txt
Illumina TrueSeq v2

source_name: newborn ferret forebrain

value: not applicable


title: Sample_69352

description:
T= Total RNA; F = Female; I=Intact; 0=Biological Replicate
Moenter-01

source_name: Female_Intact_GnRH Depleted Supernatant


title: Wild-type replicate 1

value: heterozygous


title: Knockout replicate 4

value: knockout


title: Wild-type replicate 2


title: Sample_69354

description:
T= Total RNA; F = Female; I=Intact; 1=Biological Replicate
Moenter-03


title: Sample_69362

description:
T= Total RNA; F = Female; I=Intact; 2=Biological Replicate
Moenter-11


title: Bulk progenitors replicate 2


title: Bulk progenitors replicate 1


title: Knockout replicate 2


title: Bulk neurons replicate 2


title: Knockout replicate 1


title: Sample_69357

description:
G= GnRH RNA; F = Female; I=Intact; 0=Biological Replicate
Moenter-06


title: Sample_69361

description:
G= GnRH RNA; M = Male; I=Intact; 1=Biological Replicate
Moenter-10


title: Knockout replicate 3


title: donor 1 siControl time point 2

status: Public on Apr 12 2018

city: Geneva

first: Cedric

last: Howald

state: Geneva

address: Campus Biotech, Chemin des Mines 9

country: Switzerland

institute: Health2030 Genome Center

description: Sample name: donor1_siCtrl_3_140505_2

data_processing:
Demultiplexing was done using bcl2fastq software
Paired-end reads were mapped to the Homo sapiens genome (GRCh37) using GEMtools (http://gemtools.github.io/) and the GENCODE v19 annotation to define splice sites
The gene-level quantification and normalization (RPKM values) were performed with an in-house script using GENCODE v19 as reference. Only reads having a mapping quality score of 150 or above, in proper orientation and having not more than 5 mismatches in both ends together were kept for quantification.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: polyA RNA

source_name: human primary myotube cells

growth_protocol: Biopsies from the Gluteus maximus muscles were derived from donors not diagnosed for type 2 diabetic (T2D), neoplasia or chronic inflammatory diseases, and not doing shift work. Primary skeletal myoblasts were purified and differentiated into myotubes according to the previously described procedure (Agley et al. 2015; Perrin et al. 2015). After reaching confluence, myoblasts were differentiated into myotubes during 7-10 days in DMEM supplemented with 2% FBS.

extract_protocol:
Total RNA was prepared using RNeasy® Mini kit (Qiagen).
Sequencing libraries were prepared from 300 ng of polyA+ RNA using the TruSeq RNA sample prep kit v2 (Illumina). The quality of the libraries were assessed by Bioanalyzer and TapeStation. The sequencing was perforemed with a Illumina HiSeq2000 sequencer

treatment_protocol: Cells were transfected 24 h (RNA-seq) or 72 h (western blot, glucose uptake) prior to experiment with 20 nM siRNA targeting CLOCK (siCLOCK), or with non-targeting siControl (Dharmacon), using HiPerFect transfection reagent (Qiagen) following the manufacturer's protocol. Primary myotubes were synchronized with 10 µM forskolin (Sigma) for 60 min at 37°C in a cell culture incubator, then the medium was changed, and cells from 6 cm dishes were collected every 2 hours during 48 hours from siControl and siClock samples from two cell cultures established from two donors.

value: primary human skeletal myotube cells

tag: time

value: 2 h following synchronization


title: donor 2 siClock time point 26

description: Sample name: donor2_siClock_77_140505_2

value: 26 h following synchronization


title: donor 1 siClock time point 44

description: Sample name: donor1_siClock_95_140505_2

value: 44 h following synchronization


title: donor 2 siControl time point 46

description: Sample name: donor2_siCtrl47_140313_1

value: 46 h following synchronization


title: donor 1 siClock time point 42

description: Sample name: donor1_siClock93_140313_2

value: 42 h following synchronization


title: donor 2 siClock time point 12

description: Sample name: donor2_siClock63_140313_3

value: 12 h following synchronization


title: donor 1 siClock time point 26

description: Sample name: donor1_siClock77_140313_3


title: donor 2 siControl time point 20

description: Sample name: donor2_siCtrl_21_140505_1

value: 20 h following synchronization


title: donor 2 siClock time point 32

description: Sample name: donor2_siClock83_140313_2

value: 32 h following synchronization


title: donor 2 siControl time point 28

description: Sample name: donor2_siCtrl29_140313_3

value: 28 h following synchronization


title: donor 2 siControl time point 30

description: Sample name: donor2_siCtrl31_140313_1

value: 30 h following synchronization


title: donor 2 siClock time point 42

description: Sample name: donor2_siClock93_140313_2


title: donor 2 siClock time point 2

description: Sample name: donor2_siClock53_140313_1


title: donor 1 siClock time point 6

description: Sample name: donor1_siClock57_140313_1

value: 6 h following synchronization


title: donor 2 siControl time point 6

description: Sample name: donor2_siCtrl7_140313_3


title: donor 2 siControl time point 36

description: Sample name: donor2_siCtrl37_140313_3

value: 36 h following synchronization


title: donor 1 siClock time point 32

description: Sample name: donor1_siClock83_140313_3


title: donor 2 siControl time point 8

description: Sample name: donor2_siCtrl9_140313_3

value: 8 h following synchronization


title: donor 2 siControl time point 24

description: Sample name: donor2_siCtrl25_140313_2

value: 24 h following synchronization


title: donor 2 siClock time point 48

description: Sample name: donor2_siClock99_140313_3

value: 48 h following synchronization


title: donor 2 siClock time point 40

description: Sample name: donor2_siClock91_140313_4

value: 40 h following synchronization


title: donor 2 siClock time point 46

description: Sample name: donor2_siClock97_140313_2

value: primary human skeletal myotube cells


title: donor 2 siControl time point 22

description: Sample name: donor2_siCtrl23_140313_2

value: 22 h following synchronization


title: donor 2 siClock time point 36

description: Sample name: donor2_siClock87_140313_2


title: donor 1 siControl time point 22

description: Sample name: donor1_siCtrl23_140313_2


title: donor 2 siControl time point 14

description: Sample name: donor2_siCtrl15_140313_2

value: 14 h following synchronization


title: donor 1 siClock time point 34

description: Sample name: donor1_siClock85_140313_1

value: 34 h following synchronization


title: donor 2 siControl time point 12

description: Sample name: donor2_siCtrl13_140313_1


title: donor 2 siClock time point 4

description: Sample name: donor2_siClock55_140313_1

value: 4 h following synchronization


title: donor 2 siClock time point 24

description: Sample name: donor2_siClock75_140313_3


title: donor 2 siClock time point 28

description: Sample name: donor2_siClock79_140313_4


title: donor 2 siControl time point 44

description: Sample name: donor2_siCtrl45_140313_1

value: 44 h following synchronization


title: donor 2 siClock time point 16

description: Sample name: donor2_siClock67_140313_4

value: 16 h following synchronization


title: donor 2 siControl time point 2

description: Sample name: donor2_siCtrl3_140313_4

value: 2 h following synchronization


title: donor 2 siClock time point 18

description: Sample name: donor2_siClock69_140313_1

value: 18 h following synchronization


title: donor 2 siClock time point 44

description: Sample name: donor2_siClock95_140313_3


title: donor 2 siClock time point 14

description: Sample name: donor2_siClock65_140313_2


title: donor 2 siControl time point 26

description: Sample name: donor2_siCtrl27_140313_1

value: 26 h following synchronization


title: donor 2 siControl time point 32

description: Sample name: donor2_siCtrl33_140313_4

value: 32 h following synchronization


title: donor 2 siClock time point 22

description: Sample name: donor2_siClock73_140313_1


title: donor 2 siControl time point 0

description: Sample name: donor2_siCtrl1_140313_8

value: 0 h following synchronization


title: donor 1 siControl time point 44

description: Sample name: donor1_siCtrl45_140313_7


title: donor 2 siControl time point 48

description: Sample name: donor2_siCtrl49_140313_3


title: donor 1 siClock time point 18

description: Sample name: donor1_siClock69_140313_7


title: donor 2 siClock time point 20

description: Sample name: donor2_siClock71_140313_4

value: 20 h following synchronization


title: donor 2 siControl time point 34

description: Sample name: donor2_siCtrl35_140313_2


title: donor 2 siControl time point 10

description: Sample name: donor2_siCtrl11_140313_1

value: 10 h following synchronization


title: donor 2 siClock time point 6

description: Sample name: donor2_siClock57_140313_2

value: 6 h following synchronization


title: donor 1 siClock time point 0

description: Sample name: donor1_siClock51_140313_4


title: donor 2 siClock time point 30

description: Sample name: donor2_siClock81_140313_3

value: 30 h following synchronization


title: donor 2 siClock time point 34

description: Sample name: donor2_siClock85_140313_8


title: donor 2 siControl time point 42

description: Sample name: donor2_siCtrl43_140313_4

value: 42 h following synchronization


title: donor 1 siClock time point 40

description: Sample name: donor1_siClock91_140313_5

value: primary human skeletal myotube cells

value: 40 h following synchronization


title: donor 1 siControl time point 26

description: Sample name: donor1_siCtrl27_140313_6


title: donor 1 siControl time point 34

description: Sample name: donor1_siCtrl35_140313_5


title: donor 1 siControl time point 18

description: Sample name: donor1_siCtrl19_140313_8


title: donor 1 siControl time point 10

description: Sample name: donor1_siCtrl11_140313_7


title: donor 1 siClock time point 10

description: Sample name: donor1_siClock61_140313_8


title: donor 1 siClock time point 4

description: Sample name: donor1_siClock55_140313_6


title: donor 1 siClock time point 8

description: Sample name: donor1_siClock59_140313_8

value: 8 h following synchronization


title: donor 1 siClock time point 20

description: Sample name: donor1_siClock71_140313_5


title: donor 1 siControl time point 14

description: Sample name: donor1_siCtrl15_140313_5

value: 14 h following synchronization


title: donor 2 siControl time point 16

description: Sample name: donor2_siCtrl17_140313_4


title: donor 1 siClock time point 48

description: Sample name: donor1_siClock99_140313_7

value: 48 h following synchronization


title: donor 1 siClock time point 38

description: Sample name: donor1_siClock89_140313_7

value: 38 h following synchronization


title: donor 1 siClock time point 30

description: Sample name: donor1_siClock81_140313_8


title: donor 2 siControl time point 4

description: Sample name: donor2_siCtrl5_140313_8

value: 4 h following synchronization


title: donor 1 siControl time point 42

description: Sample name: donor1_siCtrl43_140313_5


title: donor 1 siClock time point 28

description: Sample name: donor1_siClock79_140313_7

value: 28 h following synchronization


title: donor 2 siClock time point 8

description: Sample name: donor2_siClock59_140313_4


title: donor 1 siControl time point 46

description: Sample name: donor1_siCtrl47_140313_7

value: 46 h following synchronization


title: donor 1 siControl time point 12

description: Sample name: donor1_siCtrl13_140313_6

value: 12 h following synchronization


title: donor 1 siClock time point 16

description: Sample name: donor1_siClock67_140313_7

value: 16 h following synchronization


title: donor 2 siClock time point 10

description: Sample name: donor2_siClock61_140313_7


title: donor 1 siClock time point 24

description: Sample name: donor1_siClock75_140313_7

value: 24 h following synchronization


title: donor 1 siControl time point 36

description: Sample name: donor1_siCtrl37_140313_5

value: 36 h following synchronization


title: donor 1 siControl time point 48

description: Sample name: donor1_siCtrl49_140313_6


title: donor 2 siControl time point 38

description: Sample name: donor2_siCtrl39_140313_8


title: donor 1 siClock time point 12

description: Sample name: donor1_siClock63_140313_6


title: donor 1 siControl time point 32

description: Sample name: donor1_siCtrl33_140313_8

value: 32 h following synchronization


title: donor 2 siClock time point 0

description: Sample name: donor2_siClock51_140313_8

value: 0 h following synchronization


title: donor 1 siControl time point 8

description: Sample name: donor1_siCtrl9_140313_5


title: donor 1 siClock time point 14

description: Sample name: donor1_siClock65_140313_6


title: donor 2 siControl time point 18

description: Sample name: donor2_siCtrl19_140313_6

value: 18 h following synchronization


title: STAR_51hr_3

status: Public on Mar 30 2018

city: Raleigh

first: Heike

last: Sederoff

state: NC

address: 851 Main Campus Dr

department: Plant & Microbial Biology

institute: North Carolina State University

data_processing:
Quality control, filtering, and trimming were performed using FastQC and the FAST-X toolkit and resulted in an average loss of 3% of reads
Reads from each sample were mapped to the previously de novo assembled reference transcriptome of Dunaliella viridis strain dumsii (Srirangan et al., 2015) using the RNA-Seq Analysis module of the CLC Genomics Workbench version 10.0 (https://www.qiagenbioinformatics.com/). The RNA-Seq Analysis module, which uses an expectation -maximization (EM) algorithm like RSEM (B. Li and Dewey, 2011), was run with default parameters (mismatch cost = 2; insertion cost = 3, deletion cost = 3; length fraction = 0.8; similarity fraction = 0.8), but strand specificity was ignored. Since putative alternate splice transcripts are represented individually in the reference transcriptome, the “maximum number of hits for a read” was increased to 30 so that reads that matched the multiple transcripts were not discarded.
As putative transcripts are only predicted and not verified for D. viridis, gene counts are preferable to transcript differences.  To obtain gene specific data, raw counts and TPM (transcripts per million) values for each transcript were exported from the CLC Genomics Workbench, and the counts and TPM values for each putative transcript of each gene were summed to give a total raw read count per gene and a separate summed TPM value per gene.
Differential expression analysis was used to determine transcriptional differences between the four nitrogen sources (NO3, STAR, GLU, GLN) at each of the three time points (0 h, 24 h, and 48 h).  Comparisons were also made between the time points within each nitrogen source to determine transcriptional differences over time for a single nitrogen source.  All samples were also compared to the inoculum culture (PAR) to provide a common comparison point (Figure 3.1).  Differential expression was performed using the “Empirical analysis of DGE” tool in CLC, which utilizes the edgeR version 3.4.0 implementation of Fisher’s Exact Test for two-group comparisons (Robinson et al., 2010).  Only genes that had a total number of read counts >5 within each comparison group were used to estimate tagwise dispersions, and counts from biological replicates were averaged together.  Initial analysis showed all comparisons between the GLU and STAR conditions were not statistically different, and thus all comparisons were regenerated without GLU data.  Differential expression was considered significant based on the following parameters: False Discovery Rate (FDR) corrected p-value ≤ 0.05, Log2 fold change ≥ |2|, and the total read count for the gene within the comparison was > 75.
Genome_build: Dunaliella_viridis_annotated_transcripts.fasta
Supplementary_files_format_and_content: Raw_Read_Counts.txt:  The matrix file contains the raw read counts for each sample (sample title) for each gene.  The read count for each transcript of each gene have already been summed to give the gene read count.  This is the data that was analyzed with the “Empirical analysis of DGE” tool in CLC, which utilizes the edgeR version 3.4.0 implementation of Fisher’s Exact Test for two-group comparisons (Robinson et al., 2010) for differential expression analysis.   Dunaliella_viridis_annotated_transcripts.fasta:  The file contains the annotated fasta sequences of the reference transcriptome used for mapping of reads.  The original transcriptome annotations for D. viridis strain dumsii were derived from a 2012 Blast2GO annotation run (Srirangan et al., 2015).  Since the Dunaliella salina CCAP 19/18 genome is available through Phytozome (Polle et al., 2017), a decision was made to re-annotate based upon similarity of D. viridis transcripts to D. salina proteins.  The D. salina proteome was obtained from Phytozome on June 11, 2017 and converted to a Blast database within the CLC Genomics Workbench version 10.0 (https://www.qiagenbioinformatics.com/).  Blastx was used to extract the best protein hit for each D. viridis transcript using the following parameters: maximum number of blast hits = 1; e-value cutoff = 10-1; low complexity filter = off.  D. salina annotations were then ascribed to the D. viridis transcripts.  Previous manual annotations were kept as they had already been confirmed.  This rough annotation increased the number of annotated genes in D. viridis strain dumsii from 9400 to 13273.  The annotation of each sequence is a combination of the original Blast2GO annotation, the name of the Arabidopsis hit and then the Chlamydomonas hit from the Dunaliella salina proteome.  Names are separated by **.
Supplementary_files_format_and_content: TPM_values.txt

organism: Dunaliella viridis

source_name: whole cells

growth_protocol: Dunaliella viridis strain dumsii was grown in a modified Ben-Amotz medium as reported (Murphree et al., 2017).  Experiments were performed in a Percival E-36L growth chamber under continuous cool white fluorescent light (~125 µmol photons m2/s) at a temperature of 23.5 °C.

extract_protocol:
Total RNA was extracted from the 30 ml frozen pellets of the 39 samples using the RNeasy Plant Mini Kit (Qiagen) following standard procedures for use with a QIAcube.  DNA was removed from total RNA using RNase-Free DNase (Qiagen), and rRNA was depleted from the samples using the Ribo-Zero™ Magnetic Kit (Plant Leaf) (Epicentre Cat. No. MRZPL1224).  After each processing step, RNA quality was confirmed using a Bioanalyzer RNA Pico Chip (Agilent)
Strand specific cDNA libraries with 300–450 bp inserts were generated with the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England BioLabs).  Sample libraries were barcoded using the TruSeq DNA LT Sample Prep Kit, Indexed Adapter Sequences (Illumina).  Final quality of the libraries was confirmed using a Bioanalyzer DNA high sensitivity chip (Agilent).  Libraries were split into 2 groups and submitted for single end 125 bp Illumina HiSeq 2500 sequencing runs in 2 flow cells at the North Carolina State University Genome Sciences Laboratory (GSL).

treatment_protocol: Four experimental media were created with nitrogen sources of 5 mM KNO3, 5 mM L-glutamine (Sigma-Aldrich), 5 mM L-glutamate (Sigma-Aldrich), or no addition of KNO3 (Figure 3.1).  The L-glutamate condition was used to control for nitrogen starvation in the presence of an unused and stable amino acid (Murphree et al., 2017).  Cultures for inoculation were grown for a week in experimental conditions and were harvested by centrifugation (3500 g, 6 min.) in mid-logarithmic phase for use as inoculum.  Cells were suspended in 450 ml of the proper experimental media in 1 liter narrow-necked Erlenmeyer flasks to a concentration of 1 million cells/ml.  Each of the 4 experimental cultures was duplicated to give 2 technical replicates and the entire experiment was repeated 3 times to provide 3 biological replicates.  The first set of samples (T0) were taken three hours after inoculation in an attempt to decrease effects seen from transfer shock and to detect quicker transcriptional changes.  Two more collections were taken at 24 hours (T24) and 48 hours (T48) after the first collection.  In addition to the samples taken from the experimental cultures, half volume samples were taken in duplicate from the inoculum at the point of inoculation (T-3).  Sample collection consisted of aliquots taken for cell density/diameter/pH measurements (1 ml), RNA extraction (30 ml), neutral lipid fluorescence assay (5 ml), carbohydrate/starch detection (100 ml), soluble protein assay (5 ml), and chlorophyll content measurement (1 ml).  The aliquots for RNA, carbohydrate/starch, and protein were pelleted and flash frozen in liquid nitrogen for bulk processing.

tag: strain

value: dumsii

tag: biological replicate

tag: nitrogen source

tag: hours after inoculation

tag: run


title: donor 1 siControl time point 0

description: Sample name: donor1_siCtrl1_140313_6

value: primary human skeletal myotube cells


title: donor 1 siControl time point 28

description: Sample name: donor1_siCtrl29_140313_5


title: BAT_3

status: Public on Apr 02 2018

city: Neuherberg

first: Yiming

last: Cheng

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Munich

data_processing:
Sequenced reads were trimmed for adaptor sequence with trim-galore and aligned with tophat softare
Genome_build: Ensembl release 81
Supplementary_files_format_and_content: tab-delimited text files include raw read count per sample

extract_protocol:
RNA molecules were poly(A) selected, fragmented, and reverse transcribed with the Elute, Prime, Fragment Mix (EPF, Illumina)
End repair, A-tailing, adaptor ligation, and library enrichment were performed as described in the Low Throughput protocol of the TruSeq RNA Sample Prep Guide (Illumina).

treatment_protocol: All mice were bred, born and weaned at 30°C. At the age of 10-12 weeks, half of the mice were transferred to a temperature-controlled (+/- 0.5°C) climate chamber and kept for two weeks at 18°C followed by 3 weeks at 5°C. Afterwards, mice kept at 30°C and 5°C were euthanized after 2-3 hours food withdrawal, and serum and tissue samples were collected.

value: wild type

tag: gender

value: female

tag: age

tag: kept at

value: Inguinal BAT


title: donor 1 siControl time point 20

description: Sample name: donor1_siCtrl21_140313_6

value: 20 h following synchronization


title: BAT_4

tag: genotype/variation


title: donor 1 siClock time point 2

description: Sample name: donor1_siClock53_140313_7

value: 2 h following synchronization


title: donor 1 siControl time point 40

description: Sample name: donor1_siCtrl41_140313_5

value: 40 h following synchronization


title: donor 1 siControl time point 38

description: Sample name: donor1_siCtrl39_140313_5

value: 38 h following synchronization


title: donor 1 siControl time point 30

description: Sample name: donor1_siCtrl31_140313_7

value: 30 h following synchronization


title: donor 1 siControl time point 16

description: Sample name: donor1_siCtrl17_140313_6


title: donor 1 siClock time point 46

description: Sample name: donor1_siClock97_140313_8

value: 46 h following synchronization


title: donor 2 siControl time point 40

description: Sample name: donor2_siCtrl41_140313_4


title: BAT_cold_1

source_name: BAT


title: donor 1 siClock time point 36

description: Sample name: donor1_siClock87_140313_8


title: donor 1 siControl time point 6

description: Sample name: donor1_siCtrl7_140313_5

value: 6 h following synchronization


title: donor 1 siClock time point 22

description: Sample name: donor1_siClock73_140313_5

value: 22 h following synchronization


title: STAR_27hr_3


title: STAR_3hr_3


title: STAR_27hr_2


title: STAR_51hr_2


title: STAR_3hr_2


title: donor 2 siClock time point 38

description: Sample name: donor2_siClock89_140313_4


title: donor 1 siControl time point 24

description: Sample name: donor1_siCtrl25_140313_6

value: 24 h following synchronization


title: donor 1 siControl time point 4

description: Sample name: donor1_siCtrl5_140313_6

value: 4 h following synchronization


title: BAT_cold_2


title: STAR_51hr_1


title: GLN_3hr_1

value: Glutamine


title: GLU_51hr_3

value: Glutamate


title: GLN_27hr_1

value: dumsii


title: GLU_27hr_3


title: GLU_3hr_1


title: KNO3_3hr_1

value: Nitrate


title: GLN_3hr_2


title: KNO3_51hr_3


title: GLN_27hr_2


title: KNO3_3hr_2


title: KNO3_51hr_2


title: KNO3_27hr_3


title: GLN_51hr_2


title: GLN_3hr_3


title: GLN_27hr_3


title: KNO3_51hr_1


title: STAR_27hr_1


title: KNO3_3hr_3


title: KNO3_27hr_1


title: KNO3_27hr_2


title: STAR_3hr_1


title: GLN_51hr_1


title: GLN_51hr_3


title: GLU_3hr_3


title: GLU_51hr_2


title: GLU_27hr_2


title: GLU_27hr_1


title: GLU_3hr_2


title: GLU_51hr_1


title: Long-lived merozoite Plasmodium falciparum, schizont stage rep 3

status: Public on Feb 14 2018

type: RNA

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from long-lived merozoite Plasmodium falciparum, schizont stage rep 3.

hyb_protocol: Samples were hybridized onto Affymetrix GeneChip Plasmodium/Anopheles arrays according to manufacturer's recommendations.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with Expression Console (EC) 1.4 using Affymetrix default analysis with a Scale factor normalization method (mas5).

label: biotin

organism: Plasmodium falciparum

label_protocol: Labeling was performed using the Ovation Pico WTA system (Nugen Inc., San Carlos, CA).

growth_protocol: Merozoites were passed through a 5% sucrose cushion at 1500 x g for 7 mins, followed by a PBS wash at 5000 x g for 10 mins.

extract_protocol: RNA was extracted using the RNeasy 96 kit according to manufacturer's recommendations.

treatment_protocol: WT vs. LLM.

tag: strain/background

value: LLM

tag: phenotype

value: long-lived merozoite

tag: developmental stage

value: schizont


title: 309-2216

status: Public on Mar 01 2018

city: Houston

first: Zhiqiang

last: Wang

state: Texas

address: 7455 Fannin St.

department: Lymphoma and Myeloma

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader.

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

label: Biotin

source_name: Primary tumor cell line

label_protocol: 100 ng of total RNA was reverse-transcribed, biotinylated, and amplified by standard Eberwine labeling with the Illumina TotalPrep RNA Amplification Kit.

growth_protocol: Primary melanoma tumor cell lines were maintained in RPMI 1640 complete medium supplemented with 10% heat-inactivated fetal bovine serum and normocin.

extract_protocol: Total RNA was isolated from harvested cells with RNA mini isolation kits (Qiagen) with subsequent RNA quality assessment using an Agilent 2100 Bioanalyzer.

treatment_protocol: No treatment was given prior to harvest for gene expression analysis.

tag: ecar level (1-4 = low-high)

tag: act response (2 = responder, 1 = non-responder)


title: 209-2654


title: 202-2379


title: 311-2153


title: Long-lived merozoite Plasmodium falciparum, schizont stage rep 4

description: Gene expression data from long-lived merozoite Plasmodium falciparum, schizont stage rep 4.


title: Long-lived merozoite Plasmodium falciparum, schizont stage rep 5

description: Gene expression data from long-lived merozoite Plasmodium falciparum, schizont stage rep 5.


title: 211-2510


title: 310-2247


title: 210-2373


title: Long-lived merozoite Plasmodium falciparum, schizont stage rep 1

description: Gene expression data from long-lived merozoite Plasmodium falciparum, schizont stage rep 1.


title: Wild type Plasmodium falciparum, schizont stage rep 4

description: Gene expression data from wild type Plasmodium falciparum, schizont stage rep 4.

value: wild type


title: 203-2596


title: Long-lived merozoite Plasmodium falciparum, schizont stage rep 2

description: Gene expression data from long-lived merozoite Plasmodium falciparum, schizont stage rep 2.


title: 204-2765


title: 308-2549

value: not available


title: 207-2508


title: 312-2173


title: 212-2661


title: 205-2338


title: Wild type Plasmodium falciparum, schizont stage rep 1

description: Gene expression data from wild type Plasmodium falciparum, schizont stage rep 1.


title: Wild type Plasmodium falciparum, schizont stage rep 5

description: Gene expression data from wild type Plasmodium falciparum, schizont stage rep 5.


title: Long-lived merozoite Plasmodium falciparum rep 10

description: Gene expression data from long-lived merozoite Plasmodium falciparum, merozoite stage rep 10.

value: merozoite


title: Long-lived merozoite Plasmodium falciparum rep 8

description: Gene expression data from long-lived merozoite Plasmodium falciparum, merozoite stage rep 8.


title: Wild type Plasmodium falciparum, schizont stage rep 3

description: Gene expression data from wild type Plasmodium falciparum, schizont stage rep 3.


title: CB_p52

status: Public on Feb 09 2018

city: CABA

first: Stella

last: Ranuncolo

state: Buenos Aires

address: Potosí 4240

country: Argentina

institute: Instituto Universitario del Hospital Italiano (IUHI)

description: Immunoprecipitated  genomic DNA

data_processing:
Images acquired from the sequencer were processed through the bundled Solexa image extraction pipeline which identified colonies positions, performed base-calling and generated quality controls statistics.
Sequences were aligned using the bundled ELAND software
Only sequences perfectly and uniquely mapping to the genome were used.
Genome_build: The human genome NCBI build 37 as the reference genome.
Supplementary_files_format_and_content: wig files are on each sample record. A tar archive with peak data is available on the series record. Peaks were called by MACS.

source_name: Primary germinal center B cells isolated from human tonsil

growth_protocol: U-H01 HL and BJAB GCB-Like DLBCL cell lines growth in RPMI 1640 medium + ATB + 20% FBS. HBL-1 ABC-Like DLBCL cell line growths in DMEM + ATB + 10% FSB. Centroblasts were isolated from human tonsils.

extract_protocol:
ChIP was performed for Rel-A, Rel-B, cRel, p50 and p52.  Thirty million U-H01, BJAB and HBL-1 cells and centroblasts were treated with formaldehyde 1% during 15 minutes at RT. Crosslinking was stopped by glycine 0.125M for 10 minutes at RT. Cells were resuspended in Lysis Buffer (50 mM Hepes pH 8,0, 150 mM NaCl, 1% Triton-X 100, 0.1% Na-deoxycholate, 1 mM EDTA, protease inhibitors). DNA was shared by sonication in a Bioruptor (high energy 30 seconds on-30 seconds off during 30 minutes). Precipitation of DNA fragments were performed using Protein G-magnetic-beads (Dynal/Invitrogen). 10 ug of antibody and normal rabbit serum were pre-bound to 50 ul of washed beads in 100 ul of binding buffer (0.1M NaOAc, 0.2% Tween-20, 0.2% BSA) rotating during 3 hours at 4°C.  Immunoprecipitation was performed by incubating lysate (5 x 106 cells) with antibody bounded-beads rotating ON at 4°C. Unprocessed lysate (10%) was used as “input”.  DNA was recovered using 100 ml Chelex-100 (BioRad 142-1253) at boiling temperature during 10 minutes. Samples were incubated with Proteinase K (10 mg/ml) at 55°C-30 minutes and 100°C-10 minutes. Samples were cleaned up using the QIAquick Spin columns (QIAGEN) according to manufacturer’s recommendation and eluted in 40 ml of Elution Buffer (EB).
DNA ChIP fragments were repaired generating phosphorylated blunt ends using T4 DNA Polymerase, Klenow DNA polymerase and T4 polynucleotide kinase. The 3’-5’-exonuclease activity removed the 3’-overhangs and the polymerase activity filled-in the 5’ ones. A single adenine nucleotide was added to the 3’-end of the blunt phosphorylated fragments allowing for directional ligation of the Solexa adapters (single T-overhanging at their 3'-ends).  Samples were run on a 2% agarose gel with ethidium bromide for the library size selection (200 ± 25 bp range). DNA purification was performed using the QIAGEN Gel Extraction kit following the manufacturer’s instructions. The DNA was amplified by PCR to enrich for the adapter-modified DNA fragments. PCR products were cleaned on a QIAGEN MinElute purification column. DNA was diluted to 10 nM in Qiagen EB with 0.1% Tween-20. To prepare for cluster generation, 1-4 pM DNA was used, leading to a 120-150.000 clusters/tile density. DNA was denatured with NaOH to 0.5 nM.

tag: tissue

value: tonsil

tag: cell type

value: Primary germinal center B cells

tag: chip antibody

tag: concentration

tag: chip antibody manufacturer

value: Santa Cruz Biotech


title: CB_Rabbit_IgG

description: Immunoprecipitated  genomic DNA

treatment_protocol: ChIP was performed for Rel-A, Rel-B, cRel, p50 and p52.  Thirty million U-H01, BJAB and HBL-1 cells and centroblasts were treated with formaldehyde 1% during 15 minutes at RT. Crosslinking was stopped by glycine 0.125M for 10 minutes at RT. Cells were resuspended in Lysis Buffer (50 mM Hepes pH 8,0, 150 mM NaCl, 1% Triton-X 100, 0.1% Na-deoxycholate, 1 mM EDTA, protease inhibitors). DNA was shared by sonication in a Bioruptor (high energy 30 seconds on-30 seconds off during 30 minutes). Precipitation of DNA fragments were performed using Protein G-magnetic-beads (Dynal/Invitrogen). 10 ug of antibody and normal rabbit serum were pre-bound to 50 ul of washed beads in 100 ul of binding buffer (0.1M NaOAc, 0.2% Tween-20, 0.2% BSA) rotating during 3 hours at 4°C.  Immunoprecipitation was performed by incubating lysate (5 x 106 cells) with antibody bounded-beads rotating ON at 4°C. Unprocessed lysate (10%) was used as “input”.  DNA was recovered using 100 ml Chelex-100 (BioRad 142-1253) at boiling temperature during 10 minutes. Samples were incubated with Proteinase K (10 mg/ml) at 55°C-30 minutes and 100°C-10 minutes. Samples were cleaned up using the QIAquick Spin columns (QIAGEN) according to manufacturer’s recommendation and eluted in 40 ml of Elution Buffer (EB).

value: Normal Rabbit IgG


title: CB_p50

description: Immunoprecipitated  genomic DNA

value: NFkB p50 (NLS)


title: CB_c_REL

description: Immunoprecipitated  genomic DNA

value: c-REL (C)


title: 201-2357


title: Long-lived merozoite Plasmodium falciparum rep 6

description: Gene expression data from long-lived merozoite Plasmodium falciparum, merozoite stage rep 6.


title: Long-lived merozoite Plasmodium falciparum rep 1

description: Gene expression data from long-lived merozoite Plasmodium falciparum, merozoite stage rep 1.


title: CB_REL_B

description: Immunoprecipitated  genomic DNA


title: Wild type Plasmodium falciparum rep 6

description: Gene expression data from wild type Plasmodium falciparum, merozoite stage rep 6.


title: Wild type Plasmodium falciparum, schizont stage rep 2

description: Gene expression data from wild type Plasmodium falciparum, schizont stage rep 2.


title: Long-lived merozoite Plasmodium falciparum rep 7

description: Gene expression data from long-lived merozoite Plasmodium falciparum, merozoite stage rep 7.


title: Wild type Plasmodium falciparum rep 9

description: Gene expression data from wild type Plasmodium falciparum, merozoite stage rep 9.


title: Wild type Plasmodium falciparum rep 2

description: Gene expression data from wild type Plasmodium falciparum, merozoite stage rep 2.


title: Wild type Plasmodium falciparum rep 4

description: Gene expression data from wild type Plasmodium falciparum, merozoite stage rep 4.


title: Long-lived merozoite Plasmodium falciparum rep 2

description: Gene expression data from long-lived merozoite Plasmodium falciparum, merozoite stage rep 2.


title: Long-lived merozoite Plasmodium falciparum rep 9

description: Gene expression data from long-lived merozoite Plasmodium falciparum, merozoite stage rep 9.


title: CB_p65_RELA

description: Immunoprecipitated  genomic DNA

value: REL-A NFkB p65 (C-20)


title: Long-lived merozoite Plasmodium falciparum rep 3

description: Gene expression data from long-lived merozoite Plasmodium falciparum, merozoite stage rep 3.


title: HBL_1_Rabbit_IgG

description: Immunoprecipitated  genomic DNA

source_name: ABC-Like DLBCL cell line

tag: cell line

value: ABC-Like DLBCL cell line


title: Long-lived merozoite Plasmodium falciparum rep 4

description: Gene expression data from long-lived merozoite Plasmodium falciparum, merozoite stage rep 4.


title: Long-lived merozoite Plasmodium falciparum rep 11

description: Gene expression data from long-lived merozoite Plasmodium falciparum, merozoite stage rep 11.


title: Long-lived merozoite Plasmodium falciparum rep 12

description: Gene expression data from long-lived merozoite Plasmodium falciparum, merozoite stage rep 12.


title: Long-lived merozoite Plasmodium falciparum rep 5

description: Gene expression data from long-lived merozoite Plasmodium falciparum, merozoite stage rep 5.


title: Wild type Plasmodium falciparum rep 7

description: Gene expression data from wild type Plasmodium falciparum, merozoite stage rep 7.


title: HBL_1_REL_B

description: Immunoprecipitated  genomic DNA


title: Wild type Plasmodium falciparum rep 3

description: Gene expression data from wild type Plasmodium falciparum, merozoite stage rep 3.


title: HBL_1_p50

description: Immunoprecipitated  genomic DNA


title: Wild type Plasmodium falciparum rep 8

description: Gene expression data from wild type Plasmodium falciparum, merozoite stage rep 8.


title: Wild type Plasmodium falciparum rep 10

description: Gene expression data from wild type Plasmodium falciparum, merozoite stage rep 10.


title: Wild type Plasmodium falciparum rep 1

description: Gene expression data from wild type Plasmodium falciparum, merozoite stage rep 1.


title: Wild type Plasmodium falciparum rep 5

description: Gene expression data from wild type Plasmodium falciparum, merozoite stage rep 5.


title: HBL_1_p52

description: Immunoprecipitated  genomic DNA


title: BJAB_Rabbit_IgG

description: Immunoprecipitated  genomic DNA

source_name: GCB-Like DLBCL cell line

value: BJAB

value: GCB-Like DLBCL cell line


title: HBL_1_p65_RELA

description: Immunoprecipitated  genomic DNA


title: BJAB_p52

description: Immunoprecipitated  genomic DNA


title: HBL_1_c_REL

description: Immunoprecipitated  genomic DNA


title: BJAB_p50

description: Immunoprecipitated  genomic DNA


title: BJAB_c_REL

description: Immunoprecipitated  genomic DNA


title: BJAB_p65_RELA

description: Immunoprecipitated  genomic DNA


title: U_H01_Rabbit_IgG

description: Immunoprecipitated  genomic DNA

source_name: Hodgkin Lymphoma cell line

value: Hodgkin Lymphoma cell line


title: U_H01_c_REL

description: Immunoprecipitated  genomic DNA


title: BJAB_REL_B

description: Immunoprecipitated  genomic DNA


title: U_H01_p52

description: Immunoprecipitated  genomic DNA


title: U_H01_REL_B

description: Immunoprecipitated  genomic DNA


title: U_H01_p65_RELA

description: Immunoprecipitated  genomic DNA


title: U_H01_p50

description: Immunoprecipitated  genomic DNA


title: e13.5 Sox9+ cells from developing digits

status: Public on Feb 08 2018

city: Hong Kong S.A.R.

first: Kathryn

last: Cheah

state: Hong Kong

address: 3/F, Laboratory Block, 21 Sassoon Road, Pokfulam, Hong Kong

department: School of Biomedical Sciences

country: China

institute: University of Hong Kong

description: e13.5,  digit, Sox9+, Sox9-eGFP mouse

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 with default parameter setting.
Fragment Per Kilobase of exon per Megabase of library size value for each gene was calculated by using the Gencode mouse annotation file version 16. Cufflink program was used to normalize the gene expression levels with default parameter setting.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_FPKM.txt: Tab-delimited text files include FPKM values for each Sample.

growth_protocol: All mice were kept in the Minimal Disease Area in the Laboratory Animal Unit, the University of Hong Kong, a member of the Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC).

extract_protocol:
Digested in a mixture of TrypLE Express (Gibco) and 0.1% (w/v) DNase I for 20 min. The isolated cells were filtered through 40μm cell strainer.
cDNA libraries were constructed with 10ng of total RNA using SMARTer Ultra Low Input RNA Kit for Sequencing (v3, Illumina).


title: Organoid 2

status: Public on Jan 09 2018

city: Parkville

first: Luke

last: Zappia

address: 50 Flemington Road

country: Australia

institute: Murdoch Childrens Research Institute

data_processing:
The 10x Genomics Cell Ranger pipeline (v1.3.1) was used to align, filter and de-duplicate reads before counting those overlapping genes to produce count matrices for each sample.
Count matrics from the kidney samples were combined using cellranger aggr with no normalisation, as were those from the organoid samples. The resulting datasets consist of matrix files (kid_matrix.mtx, org_matrix.mtx) containing the UMI count values, barcode files (kid_barcodes.tsv, org_matrix.tsv) containing the detected cell barcodes and genes files (kid_genes.tsv, org_genes.tsv) containing the ENSEMBL ids of the detected genes. These have been converted to dense matrices in CSV format (kidney_counts.csv, org_counts.csv).
Genome_build: mm10 / hg38
Supplementary_files_format_and_content: CSV files containing raw count matrices.

source_name: C32 human embryonic stem cell

growth_protocol: Kidney organoids were made according to a published protocol (Takasata et al., Generation of kidney organoids from human pluripotent stem cells, Nature protocols 2016, PMID:27560173.

extract_protocol:
Mouse kidneys were dissected into ice cold PBS then digested over 15 minutes at 37C in Accutase, with manual dissociation via pippetting through a P1000 tip every 5 minutes. Following dissociation, cells were passed through a 30 micron filter and stored on ice in 50% PBS, 50% DMEM with 10% FCS. Human kidney organoids were dissociated via a similar protocol using Trypsin instead of Accutase and stored on ice in APEL media.
Chromium Single Cell Library kit V2
Illumina HiSeq HT chemistry- 100bp paired end sequencing

value: ES-derived kidney organoid

tag: day of differentiation


title: Organoid 3


title: Organoid 1


title: Host_60 min_rep2

status: Public on Jan 20 2018

city: Xiamen

first: Yunlan

last: Yang

address: Zhourong quan BLV 2-306, Xiamen University, Xianan, Xiamen

institute: Xiamen university

description: isolation environment: Marine

hyb_protocol: Labeled cDNA in hybridization solution (50% formamide, 1 × hybridization buffer; Amersham Biosciences) was denatured prior to loading onto a microarray. The arrays were hybridized overnight at 42°C and washed with two consecutive solutions (0.2% SDS, 2× saline-sodium citrate (SSC) for 5 min at 42°C, and 0.2× SSC for 5 min at room temperature)

scan_protocol: The array image was acquired by a Agilent G2565CA Microsrrat scanner (Agilent)

data_processing: Summarization of expressed genes was performed using the GeneSpring software V12 (CapitalBio, Beijing, China). Normalization and quality control of the signal intensity were processed using the Limma package in R. The normalized data were log2-transformed and the statistically significant differences of expressed genes between each two treatments were calculated using empirical Bayes method. Thereafter, the p-value was adjusted by false discovery ratio method.

organism: Dinoroseobacter shibae

source_name: Gene expression of uninfected host at 60 min

label_protocol: As templates, the cRNAs were reversed transcription using CbcScript Ⅱ reverse transcriptase, and then labeled with fluorescent dyes (Cy3-dCTP, GE Healthcare) using Eberwine’s linear RNA amplification method and subsequent enzymatic reaction

growth_protocol: D.shibae DFL12T was maintained in RO medium (yeast extract 1 g•L−1, peptone 1 g•L−1, sodium acetate 1 g•L−1, artificial seawater 1 L, pH 7.4-7.8) at room temperature. Constant bubbling (aeration rate 0.16 L h-1) was used to prevent settling on the bottom during the incubation.

extract_protocol: Total RNA was extracted and purified from the pellets with Ambion RiboPureTM-Bacteria Kit (Ambion, Austin, TX, USA). To ensure the quality of RNA, the concentration and purify of RNA were detected using spectrophotometer (NanoDrop ND-1000) and the integrity of RNA was determined by 1% formaldehyde denaturing gel electrophoresis. Only RNA extracts with integrity number values ≥ 6, purity determined from A260/280 ≥ 1.80 and concentration ≥ 1 μg underwent in further analysis. In the presence of poly(A) polymerase, poly(A) tails were added to the total RNAs. The total RNAs were reverse transcribed to double-strand cDNAs using the CbcScript reverse transcriptase with cDNA synthesis system according to the manufacturer’s protocol (Capitalbio) with the T7 Oligo (dT). The double-stranded DNA products were purified using a PCR purification kit (Macherey-Nagel, Düren, Germany) and kept in elution buffer. After completion of cRNA synthesis using T7 Enzyme Mix, the amplified cRNA was purified using the RNA Clean-up Kit (Macherey-Nagel, Düren, Germany). The cRNAs were reversed transcription using CbcScript Ⅱ reverse transcriptase

treatment_protocol: About 2 mL culture was spun down at 10,000 g for 5 min at 4 ºC, cell pellets were flash frozen in liquid nitrogen and stored at -80 ºC until RNA extraction

tag: time

value: Sampled at 60 min

tag: infection

value: cultured without phage R2C

tag: strain


title: Host_60 min_rep1

description: isolation environment: Marine


title: Host+V_60 min_rep2

description: isolation environment: Marine

source_name: Gene expression of infected host at 60 min

value: cultured with phage R2C


title: Host_140 min_rep1

description: isolation environment: Marine

source_name: Gene expression of uninfected host at 140 min

value: Sampled at 120 min


title: Host+V_140 min_rep1

description: isolation environment: Marine

source_name: Gene expression of infected host at 140 min


title: Host+V_140 min_rep2

description: isolation environment: Marine


title: Host+V_60 min_rep1

description: isolation environment: Marine


title: Host_140 min_rep2

description: isolation environment: Marine


title: long_survival stage IIB [7018852019_K]

status: Public on Oct 04 2017

city: valencia

first: Ana Barbara

last: Garcia

state: valencia

address: menendez pelayo 4acc

country: Spain

institute: CIBERDEM-INCLIVA

description:
7018852019_K
survival > 24 months

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: The Illumina HiScan was used to scan the arrays.

data_processing: The data were normalised using quantile normalisation with BeadArray in R.

source_name: ductal adenocarcinoma, stage IIB, long survival

label_protocol: TotalPrep™-96 RNA Amplification Kit (Ambion™) was used to prepare samples.

extract_protocol: Total RNA was extracted with High Pure FFPE RNA Micro kit (Roche) following instructions given by the manufacturer. RNA from each sample was proportionally amplified with a Sensation TM RNA Amplification kit (Genisphere).

value: pancreatic ductal adenocarcinoma

value: IIB


title: long_survival stage IIB [7196798004_J]

description:
7196798004_J
survival > 24 months


title: short_survival stage IIB [7196780088_A]

description:
7196780088_A
survival < 24 months

source_name: ductal adenocarcinoma, stage IIB, short survival


title: short_survival stage IIB [7196798004_D]

description:
7196798004_D
survival < 24 months


title: long_survival stage I-IIA [7018852019_L]

description:
7018852019_L
survival > 24 months

source_name: ductal adenocarcinoma, stage IA, long survival

value: IA


title: short_survival stage I-IIA [7196780085_K]

description:
7196780085_K
survival < 24 months

source_name: ductal adenocarcinoma, stage IB, short survival

value: IB


title: long_survival stage IIB [7196780086_H]

description:
7196780086_H
survival > 24 months


title: short_survival stage I-IIA [7196780088_B]

description:
7196780088_B
survival < 24 months


title: long_survival stage I-IIA [7196780088_E]

description:
7196780088_E
survival > 24 months

source_name: ductal adenocarcinoma, stage IIA, long survival

value: IIA


title: short_survival stage IIB [7196798004_K]

description:
7196798004_K
survival < 24 months


title: short_survival stage IIB [7196780086_E]

description:
7196780086_E
survival < 24 months


title: long_survival stage IIB [7196780088_C]

description:
7196780088_C
survival > 24 months


title: short_survival stage IIB [7018852019_J]

description:
7018852019_J
survival < 24 months


title: short_survival stage I-IIA [7018852019_G]

description:
7018852019_G
survival < 24 months

source_name: ductal adenocarcinoma, stage IIA, short survival


title: short_survival stage I-IIA [7196780085_A]

description:
7196780085_A
survival < 24 months


title: short_survival stage I-IIA [7196780085_E]

description:
7196780085_E
survival < 24 months


title: short_survival stage I-IIA [7018852019_F]

description:
7018852019_F
survival < 24 months


title: short_survival stage IIB [7196780085_F]

description:
7196780085_F
survival < 24 months


title: long_survival stage IIB [7018852019_I]

description:
7018852019_I
survival > 24 months


title: long_survival stage I-IIA [7196780085_L]

description:
7196780085_L
survival > 24 months


title: short_survival stage IIB [7196780085_H]

description:
7196780085_H
survival < 24 months


title: long_survival stage I-IIA [7196780086_D]

description:
7196780086_D
survival > 24 months


title: short_survival stage IIB [7196780086_J]

description:
7196780086_J
survival < 24 months


title: short_survival stage I-IIA [7018852019_B]

description:
7018852019_B
survival < 24 months


title: short_survival stage IIB [7018852019_E]

description:
7018852019_E
survival < 24 months


title: short_survival stage IIB [7018852016_L]

description:
7018852016_L
survival < 24 months


title: long_survival stage I-IIA [7018852019_D]

description:
7018852019_D
survival > 24 months

source_name: ductal adenocarcinoma, stage IB, long survival


title: long_survival stage IIB [7018852016_K]

description:
7018852016_K
survival > 24 months


title: long_survival stage I-IIA [7018852019_H]

description:
7018852019_H
survival > 24 months


title: long_survival stage I-IIA [7018852019_A]

description:
7018852019_A
survival > 24 months


title: Hypoxia+ketamine replicate 2 (HK2)

status: Public on Jul 31 2017

city: GAINESVILLE

first: Charles

middle: Evans

last: Wood

state: Florida

address: 1345 Center Drive/Room M552

department: Physiology and Functional Genomics

institute: University of Florida

description:
Fetal sheep
Fetal hypothalamus 24 hours after onset of 30 min hypoxia and intravenous injection of ketamine.
HK2

hyb_protocol: Hybridization was performed following protocols from Agilent. Briefly, 600 ng of each labeled cRNA was fragmented and then mixed with hybridization buffer using the Agilent gene expression hybridization kit. These were applied to a sheep 8 x 15 K array slide (Agilent-019921), containing 8 arrays with 15,744 oligomers with a length of 60 bases corresponding to 15,208 ovine genetic sequences published in the NCBI data base plus 500+ quality control probes provided by Agilent and hybridized at 65oC for 17 h at 10 rpm.

scan_protocol: The arrays were hybridized, washed, dried, stabilized, and scanned at 5 μm at both 10 and 100 PMT with an Agilent G2505B Microarray scanner at the Interdisciplinary Center for Biotechnology Research at the University of Florida. Features were extracted with Agilent Feature extraction 9.1 software. Features flagged as Feature Non-uniform outliers were excluded from further analysis.

data_processing: Transcript levels were normalized to the chip median and log-transformed, in order to obtain more power in discovering differences between groups and compensate for systematic differences between the arrays. To identify the genes that were differentially regulated (DR) between the treated and control fetuses, the normalized and transformed intensities were analyzed by one-way ANOVA (p<0.01). All the statistical procedures were carried out using JMP Genomics 5 software (SAS Institute Inc, Cary, NC, USA).

organism: Ovis aries

source_name: fetal hypothalamus, hypoxia plus ketamine

label_protocol: Five hundred ng of the DNase-treated RNA was labeled with Cyanine 3 (Cy3) CTP with the Agilent Quick Amp kit (5190-0442, New Castle, DE) according to their methodology, purified with the Qiagen RNeasy kit (Valencia, CA) according to Agilent's revision of the Qiagen protocol as shown in the Quick Amp kit protocol except that the microcentrifugation was performed at room temperature instead of 4oC. The resulting labeled cRNA was analyzed with the NanoDrop spectrophotometer, and the specific activities and the yields of the cRNAs were calculated; these ranged from 9.0 to 12.8 pmol Cy3/µg RNA and from 4.29 to 10.38 µg, respectively. The labeled cRNA was stored at -80oC until use.

extract_protocol: RNA was extracted from the hypothalamus using Trizol (Invitrogen, Carlsbad, CA), followed by RNeasy+ kits with on-column DNase treatment (Qiazol, Valencia, CA). The RNA concentration was determined with a NanoDrop spectrophotometer (ND-1000, ThermoFisher, Wilmington, DE) and the integrity of the RNA was measured using an Agilent Bioanalyzer, 2100 model. RNA Integrity Number (RIN) values ranged from 7.4 to 8.4.

treatment_protocol: Chronically catheterized late-gestation fetal sheep were subjected to transient (30 min) maternal ventilatory hypoxia following saline (n=5) or ketamine (n=4) intravenous injection or to normoxia following saline (n=3) or ketamine (n=4) intravenous injection, followed by 23.5 hours normoxia. Hypothalami were collected at the end of the normoxia recovery period and group comparisons were performed.

tag: breed

value: Suffolk

value: late-gestation fetus

value: hypothalamus

tag: treatment

tag: time point


title: Hypoxia+ketamine replicate 3 (HK3)

description:
Fetal sheep
Fetal hypothalamus 24 hours after onset of 30 min hypoxia and intravenous injection of ketamine.
HK3


title: Normoxia+Ketamine replicate 1 (NK1)

description:
Fetal sheep
Fetal hypothalamus 24 hours after onset of 30 min normoxia and intravenous injection of ketamine.
NK1

source_name: fetal hypothalamus, normoxia plus ketamine


title: Hypoxia replicate 5 (HC5)

description:
Fetal sheep
Fetal hypothalamus 24 hours after onset of 30 min hypoxia.
HC5

source_name: fetal hypothalamus, hypoxia

value: 30 min hypoxia


title: Normoxia+Ketamine replicate 4 (NK4)

description:
Fetal sheep
Fetal hypothalamus 24 hours after onset of 30 min normoxia and intravenous injection of ketamine.
NK4


title: Normoxia replicate 2 (NC2)

description:
Fetal sheep
Fetal hypothalamus 24 hours after onset of 30 min normoxia.
NC2

source_name: fetal hypothalamus, normoxia

value: 30 min normoxia


title: Hypoxia replicate 2 (HC2)

description:
Fetal sheep
Fetal hypothalamus 24 hours after onset of 30 min hypoxia.
HC2


title: Hypoxia+ketamine replicate 1 (HK1)

description:
Fetal sheep
Fetal hypothalamus 24 hours after onset of 30 min hypoxia and intravenous injection of ketamine.
HK1


title: Normoxia+Ketamine replicate 2 (NK2)

description:
Fetal sheep
Fetal hypothalamus 24 hours after onset of 30 min normoxia and intravenous injection of ketamine.
NK2


title: Normoxia replicate 3 (NC3)

description:
Fetal sheep
Fetal hypothalamus 24 hours after onset of 30 min normoxia.
NC3


title: Hypoxia replicate 3 (HC3)

description:
Fetal sheep
Fetal hypothalamus 24 hours after onset of 30 min hypoxia.
HC3


title: Hypoxia replicate 4 (HC4)

description:
Fetal sheep
Fetal hypothalamus 24 hours after onset of 30 min hypoxia.
HC4


title: Hypoxia replicate 1 (HC1)

description:
Fetal sheep
Fetal hypothalamus 24 hours after onset of 30 min hypoxia.
HC1


title: Normoxia replicate 1 (NC1)

description:
Fetal sheep
Fetal hypothalamus 24 hours after onset of 30 min normoxia.
NC1


title: Normoxia+Ketamine replicate 3 (NK3)

description:
Fetal sheep
Fetal hypothalamus 24 hours after onset of 30 min normoxia and intravenous injection of ketamine.
NK3


title: WT-hippocampus, animal 2

status: Public on Apr 26 2017

city: Salamanca

first: Carmela

last: Gómez

state: Salamanca

address: Paseo Universidad de Coimbra, Salamanca, España

institute: CSIC

description: Gene expression data from WT hippocampus.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Washing and scanning were performed using GeneChip System of Affymetrix (Affymetrix GeneChip Mouse Gene 1.0 ST Array).

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing: The RMA function provided by the package oligo from R/Bioconductor was applied to the raw expression data.

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Ambion).

growth_protocol: Animals were housed in conventional facility and they have been exposed to common pathogens.

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

treatment_protocol: Not applicable.

tag: strain/background

tag: genotype/variation

value: WT

value: Hippocampus

tag: age

value: Adult


title: GRF2KO-olfactory bulb, animal 5

description: Gene expression data from G2-KO olfactory bulb.

value: GRF2 KO

value: Olfactory Bulb


title: GRF2KO-hippocampus, animal 4

description: Gene expression data from G2-KO hippocampus.


title: GRF2KO-hippocampus, animal 5


title: GRF2KO-hippocampus, animal 6


title: WT-olfactory bulb, animal 2

description: Gene expression data from WT olfactory bulb.


title: GRF2KO-olfactory bulb, animal 4


title: GRF2KO-olfactory bulb, animal 6


title: WT-olfactory bulb, animal 3


title: WT-olfactory bulb, animal 1


title: WT-hippocampus, animal 1


title: WT-hippocampus, animal 3


title: AEC methylation data_36b7_4822

status: Public on Jan 06 2017

type: genomic

city: Chicago

first: Carole

last: Ober

state: IL

address: 920 E 58TH ST

department: Human Genetics

institute: The University of Chicago

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

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

data_processing: minfi protocol

label: Cy3 and Cy5

source_name: airway epithelial cells

label_protocol: Standard Illumina Protocol

extract_protocol: AECs were harvested via bronchial brushing and DNA/RNA was extracted consecutively using the AllPrep kit from QIAgen

value: airway epithelial cells

tag: disease status

value: Asthma

tag: gender

value: Female

tag: ethnicity

value: AA

tag: ChIP

tag: well


title: AEC methylation data_02d9_41bc

tag: cell type

value: EA


title: AEC methylation data_3348_4c75

value: Control


title: AEC methylation data_411a_4fba

value: Other


title: AEC methylation data_e549_49d1

value: Male


title: AEC methylation data_cd0c_4cca


title: AEC methylation data_1586_4591


title: AEC methylation data_f964_47ea


title: AEC methylation data_a8b2_474d


title: AEC methylation data_ede5_46de


title: AEC methylation data_767f_4e2a


title: AEC methylation data_87f0_42ad


title: AEC methylation data_b75e_4b56


title: AEC methylation data_acb6_4308


title: AEC methylation data_107e_4776


title: AEC methylation data_2cfc_42e1


title: AEC methylation data_486a_4466


title: Hypoxia+ketamine replicate 4 (HK4)

description:
Fetal sheep
Fetal hypothalamus 24 hours after onset of 30 min hypoxia and intravenous injection of ketamine.
HK4

value: Suffolk

tag: developmental stage

value: late-gestation fetus

tag: tissue


title: AEC methylation data_29ed_4409


title: AEC methylation data_1f64_4727


title: AEC methylation data_d93e_43a4


title: AEC methylation data_86b9_4119


title: AEC methylation data_ce47_4b11


title: AEC methylation data_179c_43ec


title: AEC methylation data_154f_455f


title: DNA methylation in iAsT cells_ Replicate 2

status: Public on Jun 23 2017

city: Grand Rapids

first: Yvonne

middle: Nsokika

last: Fondufe-Mittendorf

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC BeadChip using standard Illumina EPIC protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina HiScan.

data_processing: Minfi preprocessFunNorm.

label: unknown

source_name: Cervical carcinoma

label_protocol: Standard Illumina Protocol.

growth_protocol: Cell cultures were incubated at 37 degree with humidified air and 5% CO2. Cells were harvested after each treatment. Cells were grown ensuring that 95% of the cells were viable. Harvested cells were centrifuged for five minutes at 200 X g.

extract_protocol: Genomic DNA was extracted using Qiagen DNeasy kit according to manufacturer's instructions.

treatment_protocol: iAsT cells were treated with 0.5 uM Sodium Arsenite for 36 days; iAsT-rev cells were treated with 0.5 uM Sodium Arsenite for 36 days and were then treated with dI water, cells were harvested 10 days after reversal of treatment.

tag: cell line

value: HeLa

value: cervical carcinoma cell line

value: inorganic arsenic (iAs)


title: DNA methylation in NT cells_ Replicate 2

value: nontreated


title: AEC methylation data_4ca1_4174


title: AEC methylation data_f868_4cba


title: AEC methylation data_e089_4cc0


title: AEC methylation data_39e9_4475


title: AEC methylation data_8cd5_4d95


title: DNA methylation in iAs-rev cells_ Replicate 2

value: inorganic arsenic (iAs), then reverse treated


title: AEC methylation data_3a8f_4120


title: AEC methylation data_fc49_47bc


title: AEC methylation data_74f3_4f8a


title: AEC methylation data_fb20_4736


title: AEC methylation data_efe7_4deb


title: AEC methylation data_7a9e_4793


title: AEC methylation data_3b7f_4689


title: AEC methylation data_3332_4c70


title: AEC methylation data_502d_4e7d


title: AEC methylation data_2239_4ef1


title: AEC methylation data_06f5_4503


title: AEC methylation data_6ebc_47ef


title: AEC methylation data_53ff_4183


title: AEC methylation data_6ef2_465c


title: AEC methylation data_48e6_48a0


title: AEC methylation data_e436_4a93


title: AEC methylation data_44df_487e


title: AEC methylation data_0d7e_4fec


title: AEC methylation data_0e79_441c


title: AEC methylation data_1ba9_4d79


title: AEC methylation data_6132_4c18


title: AEC methylation data_a63f_4b28


title: AEC methylation data_9975_489b


title: AEC methylation data_442a_4ee4


title: AEC methylation data_b3c4_45a5


title: AEC methylation data_ad5c_4ce5


title: AEC methylation data_9c8b_4a61


title: AEC methylation data_fff9_43b1


title: AEC methylation data_9c18_4eb2


title: AEC methylation data_ae28_4608


title: AEC methylation data_e380_4917


title: AEC methylation data_cf2d_4e5f


title: AEC methylation data_22ea_40a1


title: AEC methylation data_b866_4952


title: AEC methylation data_1299_419b


title: AEC methylation data_7bfd_4bf0


title: AEC methylation data_86aa_4206


title: AEC methylation data_4ba3_4efe


title: AEC methylation data_8d33_4312


title: AEC methylation data_6e3d_4718


title: AEC methylation data_2d00_4023


title: AEC methylation data_307c_4037


title: AEC methylation data_e207_4fcd


title: AEC methylation data_1ca9_4a88


title: AEC methylation data_84e5_4094


title: AEC methylation data_0447_47e4


title: AEC methylation data_76d1_4b02


title: AEC methylation data_0607_495d


title: AEC methylation data_b9fb_4080


title: AEC methylation data_f4fe_4560


title: AEC methylation data_c0cb_47ed


title: AEC methylation data_4c83_4965


title: AEC methylation data_c9c6_408f


title: AEC methylation data_1c7d_4407


title: AEC methylation data_867b_4bae


title: AEC methylation data_2c3e_4a40


title: AEC methylation data_78d1_4946


title: AEC methylation data_89c9_4f13


title: AEC methylation data_0a57_4360


title: AEC methylation data_ed81_42cb


title: AEC methylation data_273e_4084


title: AEC methylation data_c853_412c


title: AEC methylation data_5e70_4f6c


title: AEC methylation data_3d3b_40f5


title: AEC methylation data_b3ae_412f


title: AEC methylation data_8d5d_424a


title: AEC methylation data_2800_4691


title: AEC methylation data_a6d0_4327


title: AEC methylation data_545c_49f9


title: AEC methylation data_12b2_42c4


title: AEC methylation data_dd18_4326


title: AEC methylation data_c3df_4109


title: Icat expressing, biological rep3

status: Public on Dec 01 2016

city: Worcester

first: Brian

last: Lewis

state: MA

address: 364 Plantation Street, LRB 521

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

description:
Icat_3
170#3 cell line (Morton et al., PNAS 104: 5103-8, 2007)

hyb_protocol: GeneChip Hybridization Oven 320.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: RMA method in Affy package from Bioconductor was used in R to summarize the probe level data and normalize.

source_name: pancreatic cancer cells, Icat expressing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol with Affymetrix 3' IVT Express Kit.

growth_protocol: Pancreatic cancer cells were grown in DMEM medium with 10% FBS.

treatment_protocol: Cells were grown in monolayer culture.

value: mixed (C57BL6 x FVB x 129Sv)

value: pancreatic cancer

tag: stable transfection

value: ICAT


title: Icat expressing, biological rep2

description:
Icat_2
170#3 cell line (Morton et al., PNAS 104: 5103-8, 2007)


title: AEC methylation data_f9c8_4025

value: airway epithelial cells

value: Asthma


title: control, biological rep1

description:
control_1
170#3 cell line (Morton et al., PNAS 104: 5103-8, 2007)

source_name: pancreatic cancer cells, control

value: control


title: beta-catenin expressing, biological rep2

description:
beta-catenin_2
170#3 cell line (Morton et al., PNAS 104: 5103-8, 2007)

source_name: pancreatic cancer cells, beta-catenin expressing

value: beta-catenin


title: Icat expressing, biological rep1

description:
Icat_1
170#3 cell line (Morton et al., PNAS 104: 5103-8, 2007)


title: beta-catenin expressing, biological rep1

description:
beta-catenin_1
170#3 cell line (Morton et al., PNAS 104: 5103-8, 2007)


title: beta-catenin expressing, biological rep3

description:
beta-catenin_3
170#3 cell line (Morton et al., PNAS 104: 5103-8, 2007)


title: AEC methylation data_b65a_44b4

value: Female

value: AA


title: AEC methylation data_7ed8_4eff


title: AEC methylation data_f5d3_41dd


title: AEC methylation data_07f4_4e79

value: Male


title: control, biological rep2

description:
control_2
170#3 cell line (Morton et al., PNAS 104: 5103-8, 2007)


title: control, biological rep3

description:
control_3
170#3 cell line (Morton et al., PNAS 104: 5103-8, 2007)


title: Hypertrophic Cell Layer, biological rep3

status: Public on Oct 05 2016

city: Boston

first: Shigeki

last: Nishimori

address: 50 Blossom Street, Thier 1101

department: Medicine

institute: Massachusetts General Hospital

description: Gene expression data from the hypertrophic cell layer in the growth plate.

hyb_protocol: Following fragmentation, 15 μg of cRNA were hybridized on GeneChip Mouse Genome Array for 16 hr at 45 °C in Hybridization Oven. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Affymetrix Expression Console Software using MAS5 (Microarray Suite version 5.0) algorithm. We used Affymetrix default analysis settings and global scaling as normalization method.

source_name: Newborn mouse, tibia growth plate, hypertrophic cell layer

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix One-Cycle Target Labeling protocol from 2.7 to 4.6 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The newborn pups were euthanized after the delivery. To obtain enough yield of total RNA, we used litters with 9 to 10 pups.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen) with on-column DNase I digestion according to the manufacturer's instructions.

treatment_protocol: The hind limbs were dissected and frozen immediately by Dryice in OCT compound media without fixation. From cryosections of the hind limbs on the glass slide, we manually dissected each layer of the growth plate under a dissecting microscope. We collected the pieces of sections in Qiagen Buffer RLT and stored at -80 °C prior to RNA extraction. To prepare one sample, we dissected 18 to 20 tibiae from the same litter.

value: Black Swiss

value: Wild type

value: Newborn (P0)

value: Growth plate in the proximal tibia

tag: growth plate layer

value: Hypertrophic cell layer


title: rnh1∆rnh201∆_rep1

status: Public on Oct 28 2016

city: Canberra

first: Tamas

last: Fischer

state: ACT

address: Building 131, Garran Rd

department: The John Curtin School of Medical Research

institute: The Australian National University

hyb_protocol: Hybridization, blocking, and washing was performed following the Agilent instructions.

scan_protocol: Scanning of arrays was performed using Agilent DNA Microarray Scanner and Agilent Scan control software (v A.8.4.1.).

data_processing:
Agilent Feature Extraction Software (v 10.7.3.1) Protocol: GE2_107_Sep09 with modifications; Background Subtraction Method - Local Background; Detrend on Replicates Only - False; Robust Neg Ctrl Stats? - True; Choose universal error, or the most conservative - Use Universal Error Model; Dye Normalization Probe Selection Method/Variable Rank Tolerance - True; Max Number Ranked Probes - -1; Normalization Correction Method - Lowess Only; Spikein Target Used - False p-value filtering (p<=0.05) and background filtering (BG=median of negative control probes for green channel and red channel, probes with gProcessedSignal < 2x gBG AND rProcessedSignal < 2x rBG are filtered out) Filtered probes value set to 1.
The bedGraph files were generated in R, using custom scripts. They contain the final, normalized values that are included in the Sample data tables.

organism: Schizosaccharomyces pombe

source_name: poly(A) selected RNA of rnh1∆rnh201∆

label_protocol: The cDNAs from WT and mutant strains were labeled with Cy3 (WT or OFF state) and Cy5 (mutant or ON state) (GE Healthcare).

growth_protocol: 30ºC liquid cultures grown to log phase in full media (YEA) for the WT and rnh1∆rnh201∆ samples, and in SCD-Th for Pnmt::rnh1 ON and SDC+Th for Pnmt::rnh1 OFF.

extract_protocol: The samples were reverse transcribed to cDNA using the SuperScriptTM Indirect cDNA labeling system (Life Technologies) with anchored oligo(dT)20.

treatment_protocol: RNA was isolated from the strains using TRI Reagent (Sigma Aldrich) following the manufacturer's instructions.

tag: strain

source_name: poly(A) selected RNA of wildtype

value: wildtype


title: AEC methylation data_8ebb_4e23


title: Flat Cell Layer, biological rep3

description: Gene expression data from the flat cell layer in the growth plate.

source_name: Newborn mouse, tibia growth plate, flat cell layer

value: Flat cell layer


title: Pnmt::rnh1_rep2

description: ON state induced by SDC-Th media.

source_name: poly(A) selected RNA of Pnmt::rnh1 ON

value: Pnmt::rnh1 ON

source_name: poly(A) selected RNA of Pnmt::rnh1 OFF

value: Pnmt::rnh1 OFF


title: Pnmt::rnh1_rep1

description: ON state induced by SDC-Th media.


title: Round Cell Layer, biological rep3

description: Gene expression data from the round cell layer in the growth plate.

source_name: Newborn mouse, tibia growth plate, round cell layer

value: Round cell layer


title: rnh1∆rnh201∆_rep2


title: Flat Cell Layer, biological rep2


title: AEC methylation data_ed3a_48b6

value: airway epithelial cells


title: Round Cell Layer, biological rep2


title: AEC methylation data_f0b3_4ef4

value: Asthma


title: AEC methylation data_9baa_4554

value: Control