title: Venous blood sample MM0018_2

description: Ion Torrent, Ion Proton System


title: Venous blood sample MM0027_3

status: Public on Sep 13 2019

type: SRA

city: Riga

first: Monta

last: Brīvība

address: Ratsupites 1

country: Latvia

institute: Latvian Biomedical Research and Study Centre

description: Ion Torrent, Ion Proton System

library_source: transcriptomic

data_processing:
The reads were trimmed with Trimmomatic 0.36 using window size 5 and quality threshold 10.
Sequencing reads were mapped against human reference genome GRCh38 release 90 and read counts were calculated with STAR 2.5.3a.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text file containing RNA-Seq read counts per gene for all samples claculated with STAR 2.5.3a.

molecule: total RNA

organism: Homo sapiens

source_name: Venous blood sample

extract_protocol:
Total RNA isolation was performed with PerfectPure RNA Blood Kit (5Prime GmbH, Germany), according to the manufacturer's instructions.
Ribosomal RNA depletion was done with Low Input RiboMinus™ Eukaryote System v2 (Thermo Fisher Scientific, USA) by processing 500ng of total RNA from each sample. For cDNA library preparation we used Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific, USA), sequencing was done on Ion Proton™ System and Ion PI™ Chip (Thermo Fisher Scientific, USA), following the manufacturer’s instructions.

treatment_protocol: Venous blood samples were collected in Tempus™ Blood RNA Tubes (ThermoFisher Scientific), containing Stabilizing Reagent.

tag: tissue

value: Venous blood sample

tag: time point of blood collcetion regarding metformin intervention

value: after 7 days long metformin course

tag: time point of blood collection regarding

value: morning, fasting state

tag: intervention

value: 850mg dose of metformin hydrochloride (Metforal 850mg, Berlin‑Chemie AG)


title: S1263-00161

type: RNA

city: Kansas City

first: Priyanka

last: Sharma

address: 3901 Rainbow Boulevard

country: USA

institute: University of Kansas Medical Center

hyb_protocol: Labelled cDNA was combined with dimethyl sulfoxide, hybridization buffer and nuclease free water and hybridised onto an Almac Xcel Array for 18hrs at 40oC.  Following hybridization, all arrays were washed using buffers of varying salt concentrations and stained with streptavidin-phycoerythrin conjugate (SAPE) .    All reaction components are contained within the hybridization, wash and stain kit (ThermoFisher).

scan_protocol: The arrays were scanned on the GeneChip scanner system (Thermofisher) using an epiflourescent, confocal microscope.  A solid-state laser contained within the GeneChip system was used to excite fluorophores bound to the hybridized cDNA molecules. The fluorescent values were firstly converted into an electronic signal and then to a numerical value representing the fluorescent intensity.

data_processing: CEL file intensities have been normalised to probeset level using Robust Multichip Average (RMA) consisting background adjustment, quantile normalisation and summarisation pre-processing (Bolstad et al, 2003).

label: Biotin

source_name: Triple Negative Breast Cancer

label_protocol: 3.5 µg of cDNA was first enzymatically fragmented by DNase at 37oC for 30min followed by labelling with a terminal deoxynucleotidyl transferase (TdT) and biotin at 37oC for 60min.  All reaction components are contained within the  Encore Biotin Module (NuGEN Inc).

extract_protocol: RNA was extracted from FFPE breast tissue sections using the Roche HighPure RNA Paraffin Extraction Kit.

tag: treatment group

value: Combined AC

tag: nodal status

value: Positive

tag: tumour size

value: greater than 2 cm and less than or equal to 5 cm


title: mRNA_endometrialCancer_rep7

city: Koto

first: Akihisa

last: Takahara

state: Tokyo

country: Japan

institute: Japanese Foundation For Cancer Research

hyb_protocol: After fragmentation, RNA was hybridized with Affymetrix Hybridization, Wash, and Stain Kit on Affymetrix HG-U133 plus2.0 Array following manufactuer's instruction.

scan_protocol: GeneChip was scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data was processed with RMA-dabg using Affymetrix Expression Console software.

source_name: endometrial Cancer tissue.

label_protocol: Biotinylated cRNA was prepared with Affymetrix GeneChip 3'IVT Plus kit according to the manufactuer's instruction.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy Micro Kit following manufacturer's instruction.

value: endometrial cancer

tag: Sex

value: F

tag: age


title: mRNA_endometrialCancer_rep9


title: mRNA_endometrialCancer_rep6


title: Venous blood sample MM0027_2

description: Ion Torrent, Ion Proton System

value: 10 hours after the first metformin intake

value: evening


title: Venous blood sample MM0027_1

description: Ion Torrent, Ion Proton System

value: before administration of metformin


title: mRNA_endometrialCancer_rep5


title: S1263-00158

value: Negative


title: HeLa_014_WT_new

city: SAINT LOUIS

first: Xiaoxin

last: Liu

state: MO

address: ONE BROOKINGS DRIVE

department: Computer Science & Engineering

institute: WASHINGTON UNIVERSITY IN ST LOUIS

description:
Total RNA--RiboZero--3' biotin--RNase R--Rnase III
strand specific

data_processing:
The raw sequences are aligned to GRCh38 with Bowtie2.
The unmapped reads are split into left and right anchors and remapped to GRCh38 genome.
The candidate circRNAs are identified by our in-house method.
Genome_build: GRCh38
Supplementary_files_format_and_content: Bed file includes all the canonical circRNAs, i-circRNAs and intergenic circRNAs.

source_name: HeLa cell

extract_protocol:
see Ion Total RNA-Seq Kit v2, 12-Reaction Kit (Life technologies, Cat. no. 4475936)
Libraries were prepared according to Ion Total RNA-Seq Kit v2, 12-Reaction Kit (Life technologies, Cat. no. 4475936)

tag: cell line

value: HeLa


title: HeLa_013_WT_old

description:
Total RNA--RiboZero--RNase R--Rnase III
strand specific


title: TRAP-seq 2R Rep #3

city: La Jolla

first: Travis

middle: Andrew

last: Lee

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

description:
TRAP-2R-3_S34_L003
processed data file: supplemental_RPKM.txt

data_processing:
library strategy: TRAP-seq
Adapter trimming and quality filtering was performed with fastx_toolkit
Reads were aligned to the tair10 genome with Bowtie 2/Tophat2
Read pileup was quantified for entire transcripts and reads per kilobase per million reads (RPKM) were calculated using the GenomicFeatures R package
Peak calling for ATAC-seq and HRE2 ChIP-seq data was performed using the Homer findPeaks command with the following specifications: -gsize 1.118e8 -minDist 150 -region.  Read pileup for each peak was quantified and counts per million of reads (CPM) was calculated using the GenomicRanges R package
Genome_build: Ararport 11 201606
Supplementary_files_format_and_content: supplemental_RPKM.txt

organism: Arabidopsis thaliana

source_name: TRAP-seq 2R

growth_protocol: 7 day-old seedlings grown in long day conditions (16 h light / 8 h dark) on 1 x MS, 1% sucrose plated media

extract_protocol:
Ribosome associated mRNA was purified by TRAP.  TRAP-mRNA was extracted by lysis/binding buffer and polyA mRNA was purified by use of biotinylated oligoDT
RNA-seq library preparation for nRNA, polyA, and TRAP RNA was performed as described in Kumar et al., 2012.  In brief, RNA was fragmented and primed for first strand synthesis with random hexamers (Invitrogen).  First strand synthesis was performed, followed by second strand synthesis, end repair, and A-tailing. Universal sequencing adapters were ligated to cDNA molecules.  An initial enrichment and adapter extension PCR was first performed on 0.25x volume of the ligated products for each sample to determine amplification cycle number to prevent overamplification of sequencing libraries.  A final enrichment and adapter extension PCR was performed with 0.25x starting volume for the specified cycle number (13-15 cycles) for each sample. Following enrichment, purification, size selection of libraries, and sequencing was performed as described for ChIP-seq.

treatment_protocol: Hypoxia stressed seedlings were placed into a sealed hypoxia chamber.  Argon was bubbled into the chamber for the specified length prior to harvest.

tag: genotype/variation

tag: condition

value: 2R (2h hypoxic stress + 2h reoxygenation)

value: 7 day-old whole seedling tissue

tag: chip antibody

value: FLAG (F1804, Sigma)

tag: ribosomal rna removal method

value: OligoDT selection

tag: molecule subtype

value: Ribosome associated mRNA


title: mRNA_endometrialCancer_rep3


title: S1263-00155_F1


title: TRAP-seq 2R Rep #2

description:
TRAP-2R-2_S28_L003
processed data file: supplemental_RPKM.txt


title: S1263-00157_F1


title: S1263-00154


title: HeLa_011_WT_old


title: S1263-00159

value: less than or equal to 2 cm


title: HeLa_010_WT_new

description:
Total RNA--RiboZero--RNase R--3' biotin--Rnase III
strand specific


title: S1263-00153


title: S1263-00150


title: mRNA_endometrialCancer_rep2


title: mRNA_endometrialCancer_rep1


title: S1263-00151_F1

value: Sequential AC


title: S1263-00146

value: Combined AC


title: mRNA-seq 1R Rep #3

description:
Tot-mRNA-R-3_S14_L002
processed data file: supplemental_RPKM.txt

data_processing:
Adapter trimming and quality filtering was performed with fastx_toolkit
Reads were aligned to the tair10 genome with Bowtie 2/Tophat2
Read pileup was quantified for entire transcripts and reads per kilobase per million reads (RPKM) were calculated using the GenomicFeatures R package
Peak calling for ATAC-seq and HRE2 ChIP-seq data was performed using the Homer findPeaks command with the following specifications: -gsize 1.118e8 -minDist 150 -region.  Read pileup for each peak was quantified and counts per million of reads (CPM) was calculated using the GenomicRanges R package
Genome_build: Ararport 11 201606
Supplementary_files_format_and_content: supplemental_RPKM.txt

source_name: mRNA-seq 1R

extract_protocol:
Total RNA was extracted with Trizol and precipitated with standard phenol/chloroform.  PolyA mRNA was purified by use of dynabeads oligoDT
RNA-seq library preparation for nRNA, polyA, and TRAP RNA was performed as described in Kumar et al., 2012.  In brief, RNA was fragmented and primed for first strand synthesis with random hexamers (Invitrogen).  First strand synthesis was performed, followed by second strand synthesis, end repair, and A-tailing. Universal sequencing adapters were ligated to cDNA molecules.  An initial enrichment and adapter extension PCR was first performed on 0.25x volume of the ligated products for each sample to determine amplification cycle number to prevent overamplification of sequencing libraries.  A final enrichment and adapter extension PCR was performed with 0.25x starting volume for the specified cycle number (13-15 cycles) for each sample. Following enrichment, purification, size selection of libraries, and sequencing was performed as described for ChIP-seq.

value: pUBQ10:NTF pACT2:BirA

value: 1R (2h hypoxic stress + 1h reoxygenation)

value: Poly(A)+ mRNA


title: S1263-00143

value: Positive

value: greater than 5 cm


title: S1263-00144

value: greater than 2 cm and less than or equal to 5 cm


title: S1263-00148_F1


title: S1263-00142


title: mRNA-seq 1R Rep #2

description:
Tot-mRNA-R-2_S9_L002
processed data file: supplemental_RPKM.txt


title: mRNA-seq 1R Rep #1

description:
Tot-mRNA-R-1_S4_L002
processed data file: supplemental_RPKM.txt


title: S1263-00141


title: S1263-00139_F1


title: S1263-00137


title: S1263-00147


title: S1263-00136


title: Nuclear RNA-seq 1R Rep #2

description:
nuc-RNA-R-2_S19_L002
processed data file: supplemental_RPKM.txt

source_name: Nuclear RNA-seq 1R

extract_protocol:
Nuclei were purified by INTACT and RNA was extracted by use of Qiagen Rneasy micro
RNA-seq library preparation for nRNA, polyA, and TRAP RNA was performed as described in Kumar et al., 2012.  In brief, RNA was fragmented and primed for first strand synthesis with random hexamers (Invitrogen).  First strand synthesis was performed, followed by second strand synthesis, end repair, and A-tailing. Universal sequencing adapters were ligated to cDNA molecules.  An initial enrichment and adapter extension PCR was first performed on 0.25x volume of the ligated products for each sample to determine amplification cycle number to prevent overamplification of sequencing libraries.  A final enrichment and adapter extension PCR was performed with 0.25x starting volume for the specified cycle number (13-15 cycles) for each sample. Following enrichment, purification, size selection of libraries, and sequencing was performed as described for ChIP-seq.

value: Ribo-zero

value: Nuclear RNA


title: Nuclear RNA-seq 1R Rep #3

description:
nuc-RNA-R-3_S24_L002
processed data file: supplemental_RPKM.txt


title: Nuclear RNA-seq 1R Rep #1

description:
nuc-RNA-R_S190_L008
processed data file: supplemental_RPKM.txt


title: S1263-00138_F1

value: Negative


title: S1263-00134


title: S1263-00131


title: S1263-00133


title: EM_PCOS_3

city: Shanghai

first: Jieying

last: Xu

address: 845 Lingshan Road

department: Renji Hospital, School of medicine

country: China

institute: Shanghai Jiao Tong university

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

data_processing: The data were analyzed by the Expression Console software of Affymetrix at gene level and exon level respectively.

label: biotin

source_name: endometrium of PCOS patients

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix® WT PLUS Reagent Kit(Cat#902280，Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: The endometrial biopsy was obtained seven days after the LH surge.

extract_protocol: Total RNA was extracted using Takara RNAiso Plus Kit (Cat#9109, Takara, DaLian, LiaoNing, CN)following the manufacturer’s instruction.

treatment_protocol: Endometrial samples were immersed in RNA Later solution (Invitrogen™, USA), snap frozen and stored at –80°C for RNA extraction.

tag: subject status

value: Polycystic Ovary Syndrome (PCOS) Patient

tag: gender

value: female

value: endometrium (during the window of implantation)

tag: diagnosis

value: PCOS


title: EM_NM_2

source_name: endometrium of non-PCOS patients

value: normal control

tag: tissue

value: Normal


title: EM_PCOS_1


title: EM_PCOS_2


title: S1263-00129

value: less than or equal to 2 cm


title: S1263-00126

value: Sequential AC


title: S1263-00132


title: S1263-00125


title: ATAC-seq 1R Rep #2

description:
INATACR3_S41_L004
processed data file: S1_Supplemental peak file.xls

library_source: genomic

molecule: genomic DNA

source_name: ATAC-seq 1R

extract_protocol:
Nuclei were purified by INTACT, transposition was performed by incubation with Tn5, and DNA was extracted by use of Qiagen Minelute
ATAC-seq library preparation was performed according to (Buenrostro et al., 2013).  Briefly, a reaction was prepared to amplify the sample in a two step process. The reaction was assembled containing transposed DNA (10 µL), 5 µM Ad1.1 and an indexing primer (Buenrostro, Giresi, Zaba, Chang, & Greenleaf, 2013), 1X NEBNext High Fidelity PCR mix and cycled in the following program: 72oC 5 min; 98oC 30 s; 3 cycles of 98oC 10 s, 63oC 30s, 72oC 1 min; 4oC and the samples were placed on ice.  Then a qPCR was performed using an aliquot of the amplified library with the following program: 98oC for 30 s; 20 cycles of 98oC for 10 s, 63oC for 30 s, 72oC for 1 min.  The original PCR reaction was resumed for n additional cycles, where n is the cycle at which the qPCR reaction was at 1/3 of its maximum fluorescence intensity.  Amplified DNA was then purified with Qiagen MinElute PCR purification columns and eluted in 20 µL of EB. Amplified libraries were purified and size selected for fragments between 200 to 600 bp using SPRI AMPure XP beads (Beckman).  AMPure XP beads were added at a 0.55:1.0 bead to sample ratio, and the remaining DNA was recovered by the addition of AMPure XP beads at a 1.55:1.0 bead to sample ratio and eluted in 13 µL of EB. Library concentration was determined using the NEBNext (New England Biolabs) library quantification kit.  Final libraries were multiplexed to >5 nM final concentration and sequenced on the HiSeq 3000/4000

value: pUBQ10:NTF pACT2:BirA

value: 7 day-old seedling root tissue


title: ATAC-seq 1R Rep #1

description:
INATACR2_S36_L004
processed data file: S1_Supplemental peak file.xls

value: 1R (2h hypoxic stress + 1h reoxygenation)


title: S1263-00140_F1


title: S1263-00127_F1

value: Positive


title: TRAP-seq 2HS Rep #3

description: Ribosome associated mRNA

data_processing:
Library strategy: TRAP-seq
Adapter trimming and quality filtering was performed with fastx_toolkit
Reads were aligned to the tair10 genome with Bowtie 2/Tophat2
Read pileup was quantified for entire transcripts and reads per kilobase per million reads (RPKM) were calculated using the GenomicFeatures R package
Peak calling for ATAC-seq and HRE2 ChIP-seq data was performed using the Homer findPeaks command with the following specifications: -gsize 1.118e8 -minDist 150 -region.  Read pileup for each peak was quantified and counts per million of reads (CPM) was calculated using the GenomicRanges R package
Genome_build: Ararport 11 201606

source_name: 7 day-old whole seedling tissue

value: whole seedling

value: 7-day-old seedling

tag: genotype

tag: immunoprecipitation antibody

value: FLAG (F1804, Sigma)

value: OligoDT selection


title: TRAP-seq 2NS Rep #3

description: Ribosome associated mRNA


title: S1263-00122

tag: treatment group

value: Combined AC

value: Negative

value: greater than 2 cm and less than or equal to 5 cm


title: T8

city: Budapest

first: Wichmann

last: Barna

address: Szentkirály

country: Hungary

institute: SOTE

description: Whole transcriptome expression data from biopsy sample

hyb_protocol: For sscDNA synthesis 15 µg cRNA was used and 5.5 µg fragmented and labeled sscDNA sample was hybridized to HTA 2.0 microarrays (Affymetrix) for 16 hours at 45°C with 60 rpm rotation in the Hybridization Oven (Affymetrix).

scan_protocol: Scanning was performed with GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were preprocessed by the function RMA-Sketch by Gene Expression Console

source_name: Human biopsy sample

label_protocol: Not provided

extract_protocol: 100 ng input total RNA samples were applied as staring material according to the manufacturer instructions

value: Colorectal adenocarcinoma biopsy, Dukes D


title: S1263-00121

tag: nodal status


title: S1263-00123

tag: tumour size


title: T9


title: TRAP-seq 2NS Rep #2

description: Ribosome associated mRNA


title: T1

value: Colorectal adenocarcinoma biopsy, Dukes C2


title: S1263-00120_F1


title: TRAP-seq 2HS Rep #2

description: Ribosome associated mRNA


title: TRAP-seq 2HS Rep #1

description: Ribosome associated mRNA


title: S1263-00115


title: S1263-00117_F1


title: S1263-00118_F1


title: T6

value: Colorectal adenocarcinoma biopsy, Dukes C


title: S1263-00112


title: S1263-00114


title: S1263-00113


title: T7

value: Colorectal adenocarcinoma biopsy, Dukes B2


title: T4


title: mRNA-seq 9HS Rep #3

data_processing:
Adapter trimming and quality filtering was performed with fastx_toolkit
Reads were aligned to the tair10 genome with Bowtie 2/Tophat2
Read pileup was quantified for entire transcripts and reads per kilobase per million reads (RPKM) were calculated using the GenomicFeatures R package
Peak calling for ATAC-seq and HRE2 ChIP-seq data was performed using the Homer findPeaks command with the following specifications: -gsize 1.118e8 -minDist 150 -region.  Read pileup for each peak was quantified and counts per million of reads (CPM) was calculated using the GenomicRanges R package
Genome_build: Ararport 11 201606

molecule: polyA RNA


title: S1263-00111_F1


title: mRNA_endometrialCancer_rep4

value: endometrial cancer

tag: Sex

value: F


title: EM_NM_3

value: normal control

value: female

value: endometrium (during the window of implantation)

value: Normal


title: TRAP-seq 2NS Rep #1

description: Ribosome associated mRNA

value: whole seedling

tag: age


title: T2


title: T3


title: S1263-00103_F1


title: S1263-00105

value: Sequential AC

value: greater than 5 cm


title: S1263-00109_F1


title: S1263-00108

value: Positive

value: less than or equal to 2 cm


title: S1263-00104_F1

value: Combined AC

value: Negative


title: S1263-00106

value: greater than 2 cm and less than or equal to 5 cm


title: S1263-00107_F1


title: T5

value: Colorectal adenocarcinoma biopsy, Dukes D


title: mRNA-seq 9NS Rep #3

value: 7-day-old seedling

value: pUBQ10:NTF pACT2:BirA

value: OligoDT selection


title: mRNA-seq 2NS Rep #3


title: S1263-00101


title: S1263-00130_F1


title: S1263-00102


title: mRNA-seq 9HS Rep #2


title: T19

value: Colorectal adenocarcinoma biopsy, Dukes B1


title: T20

value: Colorectal adenocarcinoma biopsy, Dukes C


title: S1263-00100


title: mRNA-seq 2HS Rep #3


title: mRNA-seq 9NS Rep #2


title: mRNA-seq 2HS Rep #2


title: T18


title: T17

value: Colorectal adenocarcinoma biopsy, Dukes B2


title: mRNA-seq 9HS Rep #1


title: T16


title: mRNA-seq 9NS Rep #1


title: mRNA-seq 2NS Rep #2


title: T15

value: Colorectal adenocarcinoma biopsy, unknown


title: S1263-00097_F1


title: TRAP-seq 2R Rep #1

description:
TRAP-2R-1_S22_L003
processed data file: supplemental_RPKM.txt

value: 2R (2h hypoxic stress + 2h reoxygenation)

value: 7 day-old whole seedling tissue

value: FLAG (F1804, Sigma)

value: Ribosome associated mRNA


title: S1263-00091


title: S1263-00094

value: Sequential AC


title: T13


title: mRNA-seq 2HS Rep #1

value: whole seedling


title: T14


title: S1263-00090


title: S1263-00092

value: less than or equal to 2 cm


title: S1263-00095

value: Combined AC

value: Positive

value: greater than 5 cm


title: S1263-00099_F1


title: S1263-00089_F1

value: Negative

value: greater than 2 cm and less than or equal to 5 cm


title: EM_NM_1

value: normal control

value: female

value: endometrium (during the window of implantation)

value: Normal


title: S1263-00087_F1


title: T11

value: Colorectal adenocarcinoma biopsy, Dukes C


title: T12

value: Colorectal adenocarcinoma biopsy, Dukes B1


title: S1263-00119_F1


title: S1263-00088_F1


title: S1263-00098


title: S1263-00083


title: S1263-00124


title: S1263-00085


title: Nuclear RNA-seq 9NS Rep #3

molecule: nuclear RNA

value: 7-day-old seedling

value: pUBQ10:NTF pACT2:BirA

value: Ribo-zero


title: Nuclear RNA-seq 9HS Rep #3


title: mRNA-seq 2NS Rep #1

value: OligoDT selection


title: S1263-00081

value: Sequential AC


title: Nuclear RNA-seq 2HS Rep #3

value: whole seedling


title: Nuclear RNA-seq 2NS Rep #3


title: S1263-00082

value: less than or equal to 2 cm


title: S1263-00079

value: Combined AC


title: S1263-00078


title: S1263-00080


title: T10

value: Colorectal adenocarcinoma biopsy, Dukes B2


title: N9

value: healthy colon biopsy


title: S1263-00077

value: Positive

value: greater than 2 cm and less than or equal to 5 cm


title: Nuclear RNA-seq 9HS Rep #2


title: N1


title: N8


title: S1263-00076

value: Negative


title: Nuclear RNA-seq 9NS Rep #2


title: S1263-00073_F1


title: S1263-00075_F1


title: S1263-00072


title: N6


title: Nuclear RNA-seq 2HS Rep #2


title: S1263-00070_F1


title: S1263-00074


title: S1263-00069


title: S1263-00128_F1


title: Nuclear RNA-seq 9HS Rep #1


title: Nuclear RNA-seq 2NS Rep #2


title: N5


title: S1263-00068


title: S1263-00067


title: S1263-00071_F1


title: S1263-00066


title: N4


title: N7


title: Nuclear RNA-seq 9NS Rep #1


title: N20


title: N2


title: Nuclear RNA-seq 2HS Rep #1


title: Nuclear RNA-seq 2NS Rep #1


title: RNA-seq in RWPE1 rep3

city: Los Angeles

first: Suhn

middle: K

last: Rhie

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

data_processing:
The quality of each in situ Hi-C library was checked with FastQC and HIC-Pro version 2.8.0. Raw fastq files were processed through the HiC-Pro version 2.8.0 to make the raw contact count matrices for multiple resolutions. The matrices were normalized using the iterative correction method (iced python library). To increase the sequencing depth, replicates were pooled and processed as above described.
Each ChIP-seq experiment was performed in duplicate and ChIP-seq libraries were sequenced on an Illumina Hiseq machine. All ChIP-seq data were mapped to hg19 and peaks were called using MACS245 after preprocessing data with the ENCODE3 ChIP-seq pipeline (https://www.encodeproject.org/chip-seq/). To call reproducible peaks from two replicates, the naïve overlap tool for histone mark datasets was used, as suggested in the ENCODE3 ChIP-seq standards document (https://www.encodeproject.org/pages/pipelines/) and previously described.
For RNA-seq, reads were mapped to hg19 GENCODE version 19 using STAR 2.4.1d49 and aligned reads were quantified at the gene level using Partek® Flow® software Quantify to annotation model  (Partek Inc., St. Louis, MO, USA). The RPKM normalization method was used and log2 transformed. Differentially expressed genes between normal and cancer cells were selected by using the Gene Specific Algorithm from Partek® Flow® software using the upper quartile normalization method (Partek Inc., St. Louis, MO, USA) (FDR <0.05).
For NOMe-seq, the fastq files were aligned to a bisulfite-converted genome using the BSMAP, and the Bis-SNP was used to call methylation sites. NDR was called using the findNDRs function from the aaRon R package (https://github.com/astatham/aaRon) (P-value cutoff, 1e-8).
Genome_build: GRCh37
Supplementary_files_format_and_content:
For in situ Hi-C, text files include contact count matrices at 10kb and 40kb, respectively
For ChIP-seq, tab-delimited text files include location of peaks
For RNA-seq, tab-delimited text files include log2(RPKM+1) for each gene.
For NOMe-seq, tab-delimited text files include location of nucleosome depleted regions

source_name: RNA-seq in RWPE1

growth_protocol: The human prostate cancer C42B cells were obtained from ViroMed Laboratories (Minneapolis, MN, USA) whereas the human prostate cancer 22Rv1 (ATCC # CRL-2505) and normal prostate RWPE1 (ATCC # CRL-11609) cells were obtained from ATCC (https://www.atcc.org/). Cells were grown at 37ºC in 5% CO2; the corresponding culture medium for each cell line (RPMI 1640 for C42B and 22Rv1 and Keratinocyte Serum Free Medium for RWPE-1) was supplemented with 10% fetal bovine serum (Gibco by Thermo Fisher Scientific, Waltham, MA, USA) and 1% penicillin and streptomycin. All cell stocks were authenticated at the USC Norris Cancer Center cell culture facility by comparison to the ATCC and/or published genomic criteria for that specific cell line; all cells were documented as free of mycoplasma.

extract_protocol:
In situ Hi-C experiments were performed following the original protocol by Rao et al with minor modifications. In situ Hi-C was performed in duplicate and 5 x 106 cells were used for each experiment. 100U of MboI restriction enzyme (NEB, R0147) was used to digest chromatin. For ligation, 2000U T4 DNA Ligase (NEB, M0202) was added and incubated at room temperature for 4 hours with slow rotation. Hi-C material was sheared to a size of 300-500bp using a Covaris instrument (Covaris S2, Woburn, MA). Biotin-tagged DNA was pulled down using Dynabeads MyOne Streptavidin C1 beads (Life technologies, 65002) with 2X Binding Buffer (2X BB: 10mM Tris-HCl (pH 7.5), 1nM EDTA, 2M NaCl).
ChIP assays were performed in C42B, 22Rv1 and RWPE1 cells using H3K9me3 (Cat# 13969 Lot# 1, Cell Signaling and Technology, Inc.), H3K27me3 (Cat# 9733 Lot# 8, Cell Signaling and Technology, Inc.), and H3K36me3 (Cat# 2901 Lot# 3, Cell Signaling and Technology, Inc.) antibodies, according to ENCODE standards (https://www.encodeproject.org/data-standards/).
RNA-seq was performed in triplicate for RWPE1, C42B, and 22Rv1 cells.  RNA was extracted using Trizol reagent (Cat # 15596-018, Thermo Fisher Scientific, NY, USA) and the quality of RNA was assessed using a 2100 Bioanalyzer instrument (Cat # G2939AA, Agilent technologies), as described previously.
For NOMe-seq, after isolating nuclei from the cells, M.CviPI was treated to methylate accessible GpCs. After purifying M.CvPI-treated DNA, sonication was performed. Bisulfite treatment of M.CviPI-methylated DNA resulted to convert all unmethylated Cs to Ts.
In situ Hi-C ibraries were prepared using Kapa Hyper prep kit (Kapa #KK8503) according to the provided protocol. Library was amplified with PCR using Illumina primers.
ChIP-seq: Libraries were barcoded (NEXTflex™ DNA Barcodes) (Bio Scientific, Austin, TX).
RNA-seq libraries were made using KAPA Stranded mRNA-Seq Kit with KAPA mRNA Capture Beads (KK8420) (Kapa Biosystems, Woburn, MA).
NOMe-seq: Libraries were generated using the Accel-NGS Methyl-Seq DNA Library Kit for Illumina Platforms.

tag: cell line

tag: cell type

value: Human normal prostate cell line


title: S1263-00065


title: S1263-00062_F1


title: S1263-00061


title: RNA-seq in RWPE1 rep2


title: S1263-00060


title: N3


title: S1263-00063


title: ATAC-seq 9HS Rep #2

source_name: 7 day-old seedling root tissue

value: root

tag: condition


title: ATAC-seq 9NS Rep #2


title: RNA-seq in 22Rv1 rep3

source_name: RNA-seq in 22Rv1

value: Human prostate cancer cell line


title: RNA-seq in RWPE1 rep1


title: ATAC-seq 9HS Rep #1


title: ATAC-seq 2HS Rep #2


title: RNA-seq in 22Rv1 rep2


title: H3K36me3 ChIP-seq in C42B rep1

source_name: H3K36me3 ChIP-seq in C42B

tag: chip antibody


title: H3K36me3 ChIP-seq in C42B rep2


title: ATAC-seq 2HS Rep #1

tag: ribosomal rna removal method


title: ATAC-seq 2NS Rep #2


title: RNA-seq in 22Rv1 rep1


title: ATAC-seq 9NS Rep #1


title: N18


title: S1263-00057


title: S1263-00058


title: N15


title: S1263-00059


title: S1263-00056


title: S1263-00054_F1


title: N13


title: N12


title: N14


title: S1263-00048_F1


title: N16


title: H3K27me3 ChIP-seq in C42B rep2

source_name: H3K27me3 ChIP-seq in C42B


title: N17


title: S1263-00046_F1


title: C2A HRE2 ChIP-seq Rep #2

extract_protocol:
Chromatin lysates were clarified from sonicated nuclei and protein-DNA complexes were purified by use of specific antibody
Library preparation for short-read sequencing (ChIP-seq) with tagmentation was performed according to (Schmidl, Rendeiro, Sheffield, & Bock, 2015), with minor modifications. Final library enrichment was performed in a 50 µL reaction containing 12 µL ChIP DNA, 0.75 µM primers, and 25 µL 2X NEBNext PCR Master Mix.  To determine the appropriate amplification cycle number, a qPCR reaction was performed on 1 µL of tagmented ChIP DNA in a 10 µL reaction volume containing 0.15 µM primers, 1X SybrGreen (ThermoFisher), and 5 µL 2X NEBNext PCR Master Mix (New England Biolabs) with the following program: 72oC for 5 min, 98oC for 30 s, 24 cycles of 98oC for 10 s, 63oC for 30 s, 72oC for 30 s, and a final elongation at 72oC for 1 min.  Libraries were amplified for n cycles, where n is equal to the rounded up Cq value determined in the qPCR reaction.  Amplified libraries were purified and size selected using SPRI AMPure XP beads (Beckman).  AMPure XP beads were added at a 0.7:1.0 bead to sample ratio, and the remaining DNA was recovered by the addition of AMPure XP beads at a 2.0:1.0 bead to sample ratio and eluted in 13 µL of EB.  Quantification of the final libraries was performed with Quant-iT PicoGreen (ThermoFisher), and library fragment distribution was evaluated by use of the the Agilent 2100 Bioanalyzer using the high sensitivity DNA chip.  Final libraries were multiplexed to >5 nM final concentration and sequenced on the HiSeq 3000/4000.

value: p35S:C2A HRE2-HA

value: HA (h3663, Sigma)


title: H3K9me3 ChIP-seq in C42B rep2

source_name: H3K9me3 ChIP-seq in C42B


title: S1263-00050_F1

source_name: Triple Negative Breast Cancer


title: S1263-00044_F1


title: N11


title: S1263-00047

value: greater than 5 cm


title: N19


title: S1263-00053_F1


title: S1263-00049


title: ATAC-seq 2NS Rep #1

value: 7-day-old seedling

value: pUBQ10:NTF pACT2:BirA


title: C2A HRE2 ChIP-seq Rep #1


title: RNAP II Ser2P ChIP-seq 2HS Rep #3

value: p-CTD RNA Polymerase II (ab5095, Abcam)


title: H3K9me3 ChIP-seq in C42B rep1


title: H3K36me3 ChIP-seq in RWPE1 rep2

source_name: H3K36me3 ChIP-seq in RWPE1


title: H3K36me3 ChIP-seq in RWPE1 rep1


title: RNAP II Ser2P ChIP-seq 2NS Rep #3

value: whole seedling


title: RNAP II Ser2P ChIP-seq 2HS Rep #2


title: H3K27me3 ChIP-seq in RWPE1 rep2

source_name: H3K27me3 ChIP-seq in RWPE1


title: RNAP II Ser2P ChIP-seq 2NS Rep #2


title: H3K27me3 ChIP-seq in RWPE1 rep1


title: S1263-00043


title: S1263-00041

value: Sequential AC


title: H3K9me3 ChIP-seq in RWPE1 rep1

source_name: H3K9me3 ChIP-seq in RWPE1


title: H3K9me3 ChIP-seq in RWPE1 rep2


title: AD8

value: Villous / tubulovillous adenoma biopsy, low-grade


title: AD9

value: Tubulovillous adenoma biopsy, low-grade


title: AD7

value: Tubulovillous adenoma biopsy, low-grade biopsy sample


title: AD6

value: Tubular adenoma biopsy, low-grade


title: S1263-00038

value: Combined AC

value: greater than 2 cm and less than or equal to 5 cm


title: H2A.Z ChIP-seq 2HS Rep #2

value: FLAG (F1804, Sigma)


title: RNAP II Ser2P ChIP-seq 2NS Rep #1


title: RNAP II Ser2P ChIP-seq 2HS Rep #1


title: H3K36me3 ChIP-seq in 22Rv1 rep2

source_name: H3K36me3 ChIP-seq in 22Rv1


title: H3K36me3 ChIP-seq in 22Rv1 rep1


title: H2A.Z ChIP-seq 2NS Rep #2


title: AD5

value: Tubulovillous adenoma biopsy, high-grade


title: S1263-00040_F1

value: Negative


title: S1263-00035


title: S1263-00036_F2

value: Positive

value: less than or equal to 2 cm


title: S1263-00039


title: AD20


title: AD4


title: AD3


title: S1263-00034


title: S1263-00032


title: H3K27me3 ChIP-seq in 22Rv1 rep2

source_name: H3K27me3 ChIP-seq in 22Rv1

value: Human prostate cancer cell line


title: S1263-00033_F1


title: S1263-00031

value: greater than 5 cm


title: H3K27me3 ChIP-seq in 22Rv1 rep1


title: AD1


title: H3K14ac ChIP-seq 9HS Rep #2

value: 7-day-old seedling

value: H3K14ac (ab52946, Abcam)


title: H3K9me3 ChIP-seq in 22Rv1 rep2

source_name: H3K9me3 ChIP-seq in 22Rv1


title: H3K14ac ChIP-seq 9NS Rep #2

value: whole seedling


title: H2A.Z ChIP-seq 2HS Rep #1


title: H3K9me3 ChIP-seq in 22Rv1 rep1


title: H2A.Z ChIP-seq 2NS Rep #1


title: H3K14ac ChIP-seq 2HS Rep #2


title: AD2


city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

description: Knee-joint at E14.5 single-cell RNAseq by 10X Genomics.

data_processing:
Using software from Illumina (bcl2fastq), sequencing reads were assigned into individual samples. An average of 72% of the bases achieved a quality score1 of Q30 where Q30 denotes the accuracy of a base call to be 99.9%.
The demultiplexed FASTQ files were then processed with cellranger-2.1.0 (10X Genomics, Inc), a proprietary pipeline that perform alignment, quantification, and light-weight analyses in one go.
R1 contains barcode (bp 1-16) and UMI (bp 11-26).
Genome_build: Grcm38(mm10)
Supplementary_files_format_and_content: space-delimited text files containing gene expression table of the cells in sparse format (gene-id, cell-id, number-of-UMIs)
barcodes.tsv: cell barcodes for cells that pass non-background cutoff
genes.tsv: a list of all genes
matrix.mtx: gene expression table in sparse format

organism: Mus musculus

source_name: Lgr5-EGFP-IRES-creERT2/+ heterozygous embryos, GFP expressed in Lgr5+ cells in the forming knee joint

growth_protocol: Lgr5GFP/+ (c57bl6) mice were crossed with c57bl6 wt mice to generate the embryos

extract_protocol:
Tissue was digested with 0.2% Collagenase II, 0.1% Dispase and 0.1% Hyaluronidase. Cells were washed twice with HBSS, and filtered through 40um cell strainer twice before loading onto the 10x genomics machine.
Single cell encapsulation and cDNA libraries were prepared by Chromium™ Single Cell 3’ Reagent Kits v2 and Chromium™ Single Cell A Chip Kit. Cells in suspension are counted and loaded into individual wells of 10X Chromium Single Cell chip. Single cells are then encapsulated into Gel in-beads emulsions (GEM) by 10X Chromium Controller. Single Cell 3’ Reagent Kits v2 is used to perform downstream steps, in brief as follows: reverse transcription is performed on GEMs, followed by cDNA clean up and amplification. The double-stranded cDNA will then go through enzymatic fragmentation, adapter ligation, index PCR and SPRIselect size selection per manufacturer’s protocol. Library size and concentration is determined by Qubit and Bioanalyzer assays. The libraries are denatured and diluted to optimal concentration. Cluster generation is performed on the flow cell with HiSeq PE Cluster Kit v4 by cbot. Illumina HiSeq SBS Kit v4 is used for sequencing run at 100 bp for read 1 and read 2.

value: Lgr5-EGFP-IRES-creERT2/+ heterozygous

tag: developmental stage

tag: strain background


title: H3K14ac ChIP-seq 2NS Rep #2


title: N10

value: healthy colon biopsy


title: C9: Control No.9

city: Piscataway

first: Hong

last: Wang

state: NJ

address: 164 Frelinghuysen

department: Chemical Biology

institute: Rutgers the State Univesrity of New Jersey

description: Adjacent non-cancerous colon tissue of colon cancer No.9

data_processing:
Firstly, we filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads. We mapped clean reads to reference using Bowtie2 and then calculate gene expression level with RSEM. Finally, we identify DEGs (differentially expressed genes) between samples.
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step
Genome_build: hg38

source_name: Colon

extract_protocol:
RNA was extracted from the de-identified frozen colon cancer and adjacent non-cancerous tissue samples using Qiagen Rneasy kit.  These tissue samples were ontained from the Biospecimen Repository and Histopathology Service of the Rutgers Cancer Institute of New Jersey (approved by IRB).
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification.  We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process.

value: Adjacent non-cancerous colon tissue

tag: histology

value: Normal colon epithelium


title: H3K14ac ChIP-seq 9HS Rep #1

source_name: 7 day-old whole seedling tissue


title: S1263-00030_F1

value: Sequential AC


title: S1263-00029


title: T9: Colon cancer No.9

description: Colon cancer No.9

value: Primary colon cancer

value: Adenocarcinoma


title: AD17

source_name: Human biopsy sample

value: Tubular adenoma biopsy, low-grade


title: AD15


title: S1263-00028

value: greater than 2 cm and less than or equal to 5 cm


title: AD16


title: AD19

value: Tubulovillous adenoma biopsy, low-grade


title: AD14


title: S1263-00027_H

value: Positive


title: C8: Control No.8

description: Adjacent non-cancerous colon tissue of colon cancer No.8


title: AD18


title: H3K14ac ChIP-seq 2HS Rep #1


title: H3K27me3 ChIP-seq in C42B rep1


title: T8: Colon cancer No.8

description: Colon cancer No.8


title: S1263-00026

value: Negative


title: AD13


title: C7: Control No.7

description: Adjacent non-cancerous colon tissue of colon cancer No.7


title: S1263-00025


title: H3K14ac ChIP-seq 2NS Rep #1


title: H3K27me3 ChIP-seq 2NS Rep #2

value: H3K27me3 (07-449, Millipore)


title: H3K9ac ChIP-seq 9HS Rep #2

value: H3K9ac (ab4441, Abcam)


title: T7: Colon cancer No.7

description: Colon cancer No.7


title: H3K14ac ChIP-seq 9NS Rep #1

value: 7-day-old seedling


title: H3K9ac ChIP-seq 9NS Rep #2


title: AD12


title: H3K27me3 ChIP-seq 2NS Rep #1


title: C6: Control No.6

description: Adjacent non-cancerous colon tissue of colon cancer No.6


title: S1263-00024_F1

value: less than or equal to 2 cm


title: H3K9ac ChIP-seq 2HS Rep #2

value: whole seedling


title: AD11


title: T6: Colon cancer No.6

description: Colon cancer No.6


title: S1263-00023_F1

value: Combined AC


title: H3K4me3 ChIP-seq 2NS Rep #2

value: H3K4me3 (ab8580, Abcam)


title: H3K4me3 ChIP-seq 2HS Rep #2


title: AD10


title: H3K9ac ChIP-seq 2NS Rep #2


title: H3K4me3 ChIP-seq 2NS Rep #1


title: S1263-00022_F1


title: C5: Control No.5

description: Adjacent non-cancerous colon tissue of colon cancer No.5

value: Adjacent non-cancerous colon tissue


title: S1263-00021


title: S1263-00020


title: S1263-00019


title: RNA-seq in C42B rep3

source_name: RNA-seq in C42B

value: Human prostate cancer cell line


title: RNA-seq in C42B rep2


title: T4: Colon cancer No.4

description: Colon cancer No.4


title: H3K9ac ChIP-seq 2NS Rep #1


title: H3K9ac ChIP-seq 9HS Rep #1


title: RNA-seq in C42B rep1


title: H3K9ac ChIP-seq 2HS Rep #1


title: H3K9ac ChIP-seq 9NS Rep #1


title: C4: Control No.4

description: Adjacent non-cancerous colon tissue of colon cancer No.4

value: Normal colon epithelium


title: H3K27me3 ChIP-seq 2HS Rep #2


title: T5: Colon cancer No.5

description: Colon cancer No.5

value: Primary colon cancer


title: Leaf, STV-infected, rep2

city: Kusatsu, Shiga

first: Midori

last: Tabara

address: 1-1-1, Noji-Higashi

institute: Ritsumeikan University

description: Sample 412

data_processing:
Illumina Casava ver.1.8.2 software was used for base calling.
Sequenced reads were mapped to the tomato genome (Tomato SL2.50 ITAG2.4; Sol Genomic Network https://solgenomics.net/) using TopHat ver. 2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19 (Trapnell et al., 2009).
The number of fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm ver. 2.2.1 (Trapnell et al., 2010).
Genome_build: Tomato SL2.50 ITAG2.4; Sol Genomic Network https://solgenomics.net/
Supplementary_files_format_and_content: FPKM, Processed Signal, count

organism: Solanum lycopersicum

source_name: leaf

extract_protocol:
Total RNAs were extracted by using the Trizol reagent following the manufacturer’s protocol (Thermo Fisher Scientific, Japan).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

tag: cultivar

tag: virus infection

value: STV-infected

value: leaf


title: S1263-00017

value: greater than 2 cm and less than or equal to 5 cm


title: Leaf, STV-infected, rep3

description: Sample 422

tag: tissue


title: H3K27me3 ChIP-seq 2HS Rep #1

tag: genotype

tag: immunoprecipitation antibody


title: S1263-00013

tag: treatment group

tag: nodal status


title: S1263-00015

value: Sequential AC

tag: tumour size


title: S1263-00009_F1


title: S1263-00008


title: H3K4me3 ChIP-seq 2HS Rep #3

tag: age


title: S1263-00012_F1


title: S1263-00011


title: Leaf, STV-infected, rep1

description: Sample 22


title: C3: Control No.3

description: Adjacent non-cancerous colon tissue of colon cancer No.3


title: H3K4me3 ChIP-seq 2NS Rep #3


title: T3: Colon cancer No.3

description: Colon cancer No.3

value: Adenocarcinoma


title: Leaf, STV-free, rep2

description: Sample 432

value: STV-free


title: H3K4me3 ChIP-seq 2HS Rep #1


title: Leaf, STV-free, rep1

description: Sample 12


title: Leaf, STV-free, rep3

description: Sample 433


title: T2: Colon cancer No.2

description: Colon cancer No.2


title: C1: Control No.1

description: Adjacent non-cancerous colon tissue of colon cancer No.1


title: S1263-00007_F1

value: Negative


title: T1: Colon cancer No.1

description: Colon cancer No.1


title: C2: Control No.2

description: Adjacent non-cancerous colon tissue of colon cancer No.2


title: S1263-00005


title: S1263-00006


title: Sputum Asthma_11259

status: Public on Sep 12 2019

city: New Lambton Heights

first: Katie

last: Baines

state: NSW

address: Lot 1 Kookaburra Circuit

department: Respiratory and Sleep Medicine

country: Australia

institute: University of Newcastle

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log transformed, normalized and baseline converted to the median of all samples.

source_name: Induced sputum

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification kit for Illumina arrays

extract_protocol: RNA was extracted from sputum samples using the Rneasy Mini Kit (Qiagen) as per manufacturers instructions.

tag: condition (severity group)

value: Uncontrolled Asthma

tag: inflammatory phenotype

value: Mixed Granulocytic Asthma

tag: gender

value: Male

tag: sample type

value: Induced sputum


title: Sputum Asthma_15857


title: Sputum Asthma_13208

value: Paucigranulocytic Asthma

value: Female


title: S1263-00002_F1

value: Combined AC

value: less than or equal to 2 cm


title: Sputum Asthma_16996


title: S1263-00001


title: Sputum Asthma_6507

value: Neutrophilic Asthma


title: Sputum Asthma_14627


title: Sputum Asthma_11000


title: Sputum Asthma_17093


title: Sputum Asthma_16385

value: Eosinophilic Asthma


title: Sputum Asthma_18437


title: Sputum Asthma_16739


title: Sputum Asthma_18090


title: Sputum Asthma_17225


title: Sputum Asthma_11756


title: Sputum Asthma_15079


title: Sputum Asthma_11309


title: Sputum Asthma_16566


title: Sputum Asthma_10978


title: Sputum Asthma_9938


title: Sputum Asthma_11312

value: Severe Asthma


title: Sputum Asthma_13686


title: Sputum Asthma_13333


title: Sputum Asthma_16619


title: Sputum Asthma_15041


title: ERBOE_Eutopic Endometrium_2

city: HOUSTON

first: Sang

middle: Jun

last: Han

state: Texas

address: One Baylor Plaza

department: Molecular Cellular Biology

institute: Baylor College of Medicine

hyb_protocol: Approximately 480ng of fragmented cRNA samples were loaded onto each of the Mouse G3 v2 8x60K Expression arrays. The arrays were hybridized in an Agilent Hybridization Chamber for 17 hours at 65C with rotation at 10rpm. The arrays were washed using the Agilent Expression Wash Buffers One and Two, followed by acetonitrile, as per the Agilent protocol.

scan_protocol: Once dry, the slides were scanned with the Agilent Scanner (G2565BA) using Scanner Version C and Scan Control software version A.8.3.1. Data extraction and quality assessment of the microarray data was completed using Agilent Feature Extraction Software Version 11.0.1.1.

data_processing: 1. Place Grid – this algorithm finds the grid to define the nominal positions of the spots on the microarray.  2. Optimize Grid Fit – this algorithm improves the grid fit. It leverages from the Spot Finder algorithm and examines the spots in the four corners of the microarray and iteratively adjusts the grid for a better fit.  3. Find Spots – this algorithm locates the exact size and centroid of each spot on the scanned microarray, and the feature for each spot is defined. The software defines the local background for each spot. Outlier pixels are omitted from further calculations (this is the only point where data is omitted). Feature extraction calculates the following values from the inlier pixels: mean, median, standard deviation, normalized IQR, and number of inlier pixels.  4. Flag Outliers – this algorithm flags anomalous features and local backgrounds as non-uniformity outliers and/or population outliers. This flagging is based on population statistics and replicate features on the microarray.  5. Compute Background, Bias and Error – this algorithm applies background subtraction to each feature to yield the background-subtracted intensity.   6. Correct Dye Biases – Not applicable for 1-color experiments.  7. Compute Ratios – Not applicable for 1-color experiments.  8. Calculate Metrics – this algorithm calculates all QC metrics for the analysis, including gridding test.

source_name: Eutopic endometrium of ERBOE mice without endometriosis

label_protocol: Twenty-five nanograms of total RNA combined with RNA spike mix were reverse transcribed using a T7 Primer Mix to produce cDNA. The cDNA product was transcribed using T7 RNA Polymerase, producing cyanine-3-labeled cRNA. The labeled cRNA was purified using a Qiagen RNeasy Mini Kit. Purified products were quantified using the NanoDrop spectrophotometer for yield and dye incorporation, and tested for integrity on the Agilent Bioanalyzer. Six hundred nanograms of the labeled cRNA was fragmented.

extract_protocol: Total RNA was isolated from each type of endometrium by using Trizol reagent and then total RNA was purified using the RNeasy kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Endometriosis was surgically induced to ERBOE and PRCre mice

value: Eutopci Endometrium

value: female


title: ERBOE_Eutopic Endometrium_1


title: ERBOE_Eutopic Endometrium_3


title: Sputum Asthma_17969


title: Sputum Asthma_8220


title: Sputum Asthma_11669


title: PRCre_Eutopic Endometrium_3

source_name: Eutopic  endometrium of PRCre mice with endometriosis

value: Eutopic Endometrium


title: Sputum Asthma_14907


title: Sputum Asthma_12529


title: Sputum Healthy_19458

value: Healthy Control


title: Sputum Healthy_11803


title: ERBOE_Ectopic Lesions_3

source_name: Ectopic lesions of ERBOE mice without endometriosis

value: Ectopic lesions


title: PRCre_Ectopic Lesions_2

source_name: Ectopic lesions of PRCre mice with endometriosis


title: Sputum Asthma_16719


title: Sputum Asthma_8551


title: Sputum Asthma_16466


title: Sputum Healthy_19518


title: PRCre_Ectopic Lesions_3


title: PRCre_Eutopic Endometrium_1


title: Sputum Asthma_16841


title: Sputum Healthy_19556


title: PRCre_Ectopic Lesions_1


title: ERBOE_Uterus_3

source_name: Uterus of ERBOE mice without endometriosis

value: Uterus


title: ERBOE_Ectopic Lesions_1


title: ERBOE_Uterus_1


title: ERBOE_Ectopic Lesions_2


title: Sputum Healthy_19513


title: Sputum Healthy_19451


title: ERBOE_Uterus_2


title: PRCre_Eutopic Endometrium_2


title: PRCre_Uterus_2

source_name: Uterus of PRCre mice without endometriosis


title: PRCre_Uterus_3


title: PRCre_Uterus_1


title: Sputum Healthy_11806


title: 3668-SH-3_FOXO1_input

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

data_processing:
adapter sequences were trimmed with Trimmomatic-0.32 (ILLUMINACLIP:adaptor.txt:2:30:7)
alignment to hg19 genome build with Bowtie default settings
peak calling for FOXO1 with MACS2 version 2.0.10; q=0.005
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph alignments; FOXO1 peak file

source_name: OCI-LY1 cells

growth_protocol: cells were cultured in IMDM +10%FBS +1%L-glut +1%Pen/Strep

extract_protocol:
cells were cross-linked with 1% formaldehyde, quenched with glycine, washed 2x with PBS. Cells were lysed and nuclei harvested and resuspended in ChIP lysis buffer (25 mM tris, ph 8.0; 150 mM NaCl; 2mM EDTA, 1% Triton x-100; 0.25% SDS; protease inhibitors) prior to sonication on Biorupter (Diagenode). Samples were diluted  two times in buffer without SDS and IP carried out with 5 μg antibody for 2 hours and pulled down with 15 μl 1:1 Prot A:Prot G Dynabeads
first steps of library construction were carried out on beads including- polishing, A-tailing, P7 adapter ligation, Phi29 nick repair, PNK, lambda exonuclease treatnent, and RecJf nuclease treatment prior to elution and cross-link reversal. Library construction was completed by P7 primer extension and P5 adaptor ligation followed by AMPure purification and library amplification

treatment_protocol: For H3K27ac, cells were treated with 10 μM RGFP966 or DMSO control for 3 hours prior to formaldehyde cross-linking. For FOXO1, cells were untreated.

tag: growth media

value: IMDM +10%FBS

tag: treatment

value: untreated


title: 3668-SH-1_FOXO1-IP

tag: antibody


title: 3620-SH-11_966_input-2

value: 3 hours RGFP966


title: Sputum Healthy_11557

value: Induced sputum


title: Sputum Healthy_12578

value: Male


title: Sputum Healthy_12152


title: Sputum Asthma_17289

value: Controlled Asthma

value: Mixed Granulocytic Asthma

value: Female


title: W_T_rep2

city: New Delhi

first: Nandula

last: Raghuram

email: raghuram98@hotmail.com, ravipathak@aol.in, pathakster@gmail.com, navjyoti.chakraborty@gmail.com

state: Delhi

address: Dwarka, Sector -16C

department: School of Biotechnology

country: India

institute: Guru Gobind Singh Indraprastha University

description:
Wildtype treated 2
WT_T_2
Oryza sativa wild type japaonica 30 day old seedlings treated with 120mM of KNO3 90 minutes

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5188-6420; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327). The hybridized, washed microarray slides were then scanned on a G2600D scanner (Agilent Technologies)

scan_protocol: Microarray slides were then scanned on a G2600D scanner (Agilent Technologies)

data_processing: Images were quantified using Agilent Feature Extraction Software and  Normalization of the data was done in GeneSpring GX using the 75th percentile shift (Percentile shift normalization)

organism: Oryza sativa Japonica Group

source_name: Shoot tissue

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0424). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

growth_protocol: Oryza sativa japonica Wildtype and G-alpha subunit mutant (daikoku1) were grown at 27 degrees celsius with a light intensity of 3 kilolux and a photoperiod 12hr light/12hr dark for 30 days

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

treatment_protocol: The plants were grown in Arnon Hoagland media for a month and then for the next two days grown in Arnon Hoagland media without Nitrogen.The shoots were excised and floated in 120mM of KCl (Control) and KNO3(Treatment) for 90 minutes before harvesting.

tag: genotype/variation

value: Wild type

tag: agent


title: Sputum Healthy_14981


title: Sputum Asthma_13083


title: Sputum Asthma_18495

value: Paucigranulocytic Asthma


title: Sputum Healthy_12443


title: M_T_rep2

description:
Mutant treated 2
MT_T_2
Oryza sativa G-alpha subunit (daikoku1) mutant japaonica 30 day old seedlings treated with 120mM of KNO3 for 90 minutes

value: G-alpha subunit mutant


title: 3620-SH-10_DMSO_input-2

value: 3 hours DMSO


title: M_T_rep1

description:
Mutant treated 1
MT_T_1
Oryza sativa G-alpha subunit (daikoku1) mutant japaonica 30 day old seedlings treated with 120mM of KNO3 for 90 minutes


title: Sputum Asthma_15874


title: W_T_rep1

description:
Wildtype treated 1
WT_T_1
Oryza sativa wild type japaonica 30 day old seedlings treated with 120mM of KNO3 for 90 minutes


title: Sputum Asthma_11483


title: Sputum Healthy_11944


title: Sputum Asthma_11407


title: Sputum Healthy_11384


title: W_T_rep3

description:
Wildtype treated 3
WT_T_3
Oryza sativa wild type japaonica 30 day old seedlings treated with 120mM of KNO3 for 90 minutes


title: Sputum Healthy_12554


title: M_C_rep1

description:
Mutant control 1
MT_C_1
Oryza sativa G-alpha subunit (daikoku1) mutant japaonica 30 day old seedlings treated with 120mM of KCl for 90 minutes

value: KCl


title: 3620-SH-8_966_input-1


title: W_C_rep3

description:
Wildtype control 3
WT_C_3
Oryza sativa wild type japaonica 30 day old seedlings treated with 120mM of KCl for 90 minutes


title: Sputum Asthma_14888


title: W_C_rep2

description:
Wildtype control 2
WT_C_2
Oryza sativa wild type japaonica 30 day old seedlings treated with 120mM of KCl for 90 minutes


title: M_C_rep2

description:
Mutant control 2
MT_C_2
Oryza sativa G-alpha subunit (daikoku1) mutant japaonica 30 day old seedlings treated with 120mM of KCl for 90 minutes


title: 3620-SH-7_DMSO_input-1


title: Sputum Asthma_11348


title: M_T_rep3

description:
Mutant treated 3
MT_T_3
Oryza sativa G-alpha subunit (daikoku1) mutant japaonica 30 day old seedlings treated with 120mM of KNO3 for 90 minutes


title: M_C_rep3

description:
Mutant control 3
MT_C_3
Oryza sativa G-alpha subunit (daikoku1) mutant japaonica 30 day old seedlings treated with 120mM of KCl for 90 minutes


title: W_C_rep1

description:
Wildtype control 1
WT_C_1
Oryza sativa wild type japaonica 30 day old seedlings treated with 120mM of KCl for 90 minutes


title: 3620-SH-5_966_H3K27ac-2


title: 3620-SH-2_966-H3K27ac-1


title: 655-KS-5_SUDHL4_DMSO-2

data_processing:
Library strategy: PRO-seq
Trimmomatic-0.32: trim adapter sequences and trailing 15 and minimum read length
fastx_reverse_complement: generate reverse complemented reads
Bowtie2: read alignment to hg19 + spikein (Luciferase, Gal4, NeoR, GFP)
samtools: filter out low quality alignments
spikein removal: grep -vwE "("Luciferase|Gal4|NeoR|GFP)" in.sam > out.spikeinrm.sam
NRSA: pause_PROseq.pl
NRSA: eRNA.pl
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph alignments

source_name: B cell lymphoma cell line

extract_protocol:
Nuclear run-on assays were performed with ATP, UTP, GTP, and biotin-11-CTP or with all 4 biotin-11-NTPs. Nuclei were lyzed with TRIzol, nuclear RNA was extracted and fragmented, and biotinylated RNA was purified with strepavidin magnetic beads
Library construction included 3' adaptor ligation, 5' repair, 5' adaptor ligation, reverse transcription, and PCR full-scale amplification.

tag: cell line

value: RPMI + 10%FBS +1% L-glutamine and Pen/Strep

value: DMSO control (3hrs)


title: 655-KS-7_NUDUL1_DMSO-2


title: 3620-SH-1_DMSO-H3K27ac-1


title: 655-KS-8_NUDUL1_966-2

value: 10 uM RGFP966 (3hrs)


title: 655-KS-3_NUDUL1_DMSO-1


title: 655-KS-6_SUDHL4_966-2


title: 655-KS-4_NUDUL1_966-1


title: Oligo2

city: Heidelberg

first: Ruslan

last: Al-Ali

state: Baden Wurttemberg

address: INF 400

country: Germany

institute: University Hospital Heidelberg

description: Open chromatin from nuclei

data_processing:
deduplicate fastq files with clumpify
remove leaking reads (python script)
align with bowtie2
deduplicate, sorted, non-standard chromosomes were removed and bam files were indexed using Samtools
Call peaks with HOMER v4.10/findPeaks
peaks converted to bed using pos2bed.pl
Genome_build: GRCh37.p13 / hg19
Supplementary_files_format_and_content: bed files for open chromatin peaks called in each single nuclei

source_name: Oligodendroglioma

extract_protocol:
Following surgical resection, fresh tumor samples were separated into a single cell suspensions via mechanical and collagenase enzymatic dissociation. Debris was removed using tubes with strainer cap. Nuclei were obtained using Nuclei EZ Prep. The single nucleus ATAC-Seq protocol performed on HT IFC microfluidics system (Fluidigm) and HiSeq 2000 sequencing technologies.
Nuclei were obtained using Nuclei EZ Prep (Sigma-Aldrich, USA-MO). The single nucleus ATAC-Seq protocol performed on HT IFC microfluidics system (Fluidigm, USA-CA) and HiSeq 2000 sequencing technologies (Illumina, USA-CA) with an adapted protocol. Nuclei were incubated with Tn5 off-chip. The reaction was stopped with EDTA and the nuclei are loaded on the C1 HT IFC. During the amplification in the IFC the first barcode was added to the library which allows pooling per column. After harvesting the PCR products were purified with Ampure beads at a 1.4x ratio. The second barcode was then introduced by a second PCR off-chip and the libraries were size selected with AMPure beads (Beckman Coulter, Brea, CA). Each pool was subjected to quality control using Qubit (ThermoFischer, USA-MA) and TapeStation 4200 (Agilent, USA-CA).

tag: tissue

value: Oligodendroglioma

tag: idh mutation

value: IDH1 R132H

tag: grade

value: Grade II


title: 655-KS-2_SUDHL4_966-1


title: Oligo1

description: Open chromatin from nuclei


title: Sputum Asthma_14865

value: Neutrophilic Asthma


title: Astro3

description: Open chromatin from nuclei

source_name: Astrocytoma

value: Astrocytoma


title: Sputum Asthma_13107

value: Eosinophilic Asthma

value: Male

value: Induced sputum


title: Sputum Asthma_6298

value: Controlled Asthma


title: Astro2

description: Open chromatin from nuclei


title: Sputum Asthma_10904

value: Female


title: Sputum Asthma_10434


title: Sputum Asthma_12140

value: Paucigranulocytic Asthma


title: Sputum Asthma_15830


title: Sputum Asthma_11341


title: U87 control polyA replicate 2

city: Santa Cruz

first: Todd

last: Lowe

address: 1156 High Street

department: Biomolecular Engineering and Bioinformatics

institute: University of California Santa Cruz

data_processing:
Reads were mapped to the gencode hg19 release 28 genome using STAR v2.5.2b using the following parameters --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax .3 --outFilterMismatchNoverReadLmax .2 --outFilterMultimapNmax 1
featureCounts v1.5.2 was used to assign reads to genes for differential expression; for intron vs exon the following parameters were used [-p –s 2 –O –M –fraction –fracOverlap 0.51]
differential expression analysis to determine bound targets in the RIP was performed using a log ratio test in DESeq2
variants were called in the polyA dataset using samtools(v1.3.1) mpileup [-u -t DP4 -v  -l], the DP4 field was then used to determine read coverage and editing percentage, known SNPs were filtered out using a comprehensive list of SNPs from the dbSNP database build 151.
sailor was run on the polyA dataset to determine editing sites
Genome_build: gencode hg19 release 28
Supplementary_files_format_and_content: tab delimeted text files of read counts at each gene were generated using featureCounts v1.5.2; tab delimeted text files of differentially expressed genes were generated using DESeq2; bed files of called editing sites were generated using SAILOR; vcf files containing variants were generated using samtools mpileup

source_name: U87 cells

growth_protocol: U87 cells were maintained in  Dulbecco’s modified Eagle’s medium (DMEM)  (Mediatech) supplemented with 10% fetal bovine  serum (FBS) (Sigma), 100ug/ml penicillin and 100  units/ml streptomycin (MediaTech).

extract_protocol:
RNA was isolated using Trizol (Invitrogen), purified by treatment with TURBO DNAase (Ambion) and isolated using the RNeasy Extraction Kit (Qiagen).
The RNA libraries were prepared using the Clontech pico v2 kit stranded-RNA library preparation kit according the manufacturer’s instructions. The samples were sequenced on a NextSeq500 as paired ends reads of 75 bp according to the manufacturer’s instructions.

treatment_protocol: Cells subjected to to 150mj/cm2 of UV radiation using  the Spectrolinker (Spectronic Corp) and sonciated.

tag: expression plasmid

value: empty vector (neomycin)

tag: rna source

value: RNA from whole cell lysate


title: U87 ADAR3 polyA replicate 3

value: 3X-FLAG ADAR3 (neomycin)


title: Sputum Asthma_10727


title: U87 control polyA replicate 3


title: Sputum Asthma_15933


title: U87 ADAR3 polyA replicate 2


title: Astro1

description: Open chromatin from nuclei

value: IDH1 R132S


title: U87 ADAR3 polyA replicate 1


title: U87 control polyA replicate 1


title: 655-KS-1_SUDHL4_DMSO-1

value: RPMI + 10%FBS +1% L-glutamine and Pen/Strep

value: DMSO control (3hrs)


title: 3620-SH-4_DMSO-H3K27ac-2

value: IMDM +10%FBS

value: 3 hours DMSO


title: U87 ADAR3 input RNA 11.14

description:
ribosomal depleted RNA
412_input_11-14


title: U87 ADAR3 IP RNA 11.14

description:
ribosomal depleted RNA
412_RIP_11-14

value: Immunoprecipitated RNA


title: U87 control input RNA 11.14

description:
ribosomal depleted RNA
338_input_11-14


title: U87 ADAR3 IP RNA 10.26

description:
ribosomal depleted RNA
412_RIP_10-16


title: Sputum Asthma_11472


title: 3216-SH-6_OCILY1_966-1

value: IMDM + 10%FBS +1% L-glutamine and Pen/Strep

value: 10 uM RGFP966 (3hrs)


title: U87 control IP RNA 10.26

description:
ribosomal depleted RNA
338_RIP_10-26


title: U87 ADAR3 input RNA 10.26

description:
ribosomal depleted RNA
412_input_10-26


title: 3216-SH-7_OCILY1_966-2


title: 3216-SH-5_OCILY1_DMSO-2


title: 3216-SH-4_OCILY1_DMSO-1


title: U87 control IP RNA 11.14

description:
ribosomal depleted RNA
338_RIP_11-14


title: MRC5 fibroblasts, dUL26_3_48hpi_R1

city: Rochester

first: Joshua

last: Munger

state: New York

address: 601 Elmwood Ave, Room 3-8828

department: Biochemistry & Biophysics

institute: University of Rochester

data_processing:
Raw read counts were obtained using featurecounts from the subread1.5.0p3 package and gencode 25 human gene annotations using only uniquely aligned reads (default) and including multi-mapping reads (-M)
Sequence reads were cleaned and adapter trimmed using trimmomatic-0.36
Each sample was mapped individually to the human reference genome (GRCh38.p7, primary assembly + gencode 25 annotation) with STAR2.5.2b
DESeq2-1.14.1 within R-3.3.2 was used to perform data normalization and differential expression analysis with a false-discovery rate adjusted p-value threshold of 0.05 on each set of raw expression measures.
Genome_build: GRCh38.p7, primary assembly + gencode 25 annotation
Supplementary_files_format_and_content: predeSeq2_counts.txt containing raw expression measures.  deSeq2_Ad_vs_dUL26.xlsx containing gene names, abundance values, log2 fold changes, and significance scores (p-values).

source_name: Human Lung Fibroblasts

growth_protocol: MRC5 fibroblasts (ATCC CCL-171) were cultured in Dulbecco’s modified Eagle serum (DMEM; Invitrogen) supplemented with 10% (vol/vol) FBS, 4.5 g/liter glucose, and 1% penicillin-streptomycin (Life Technologies) at 37oC in a 5% (vol/vol) CO2 atmosphere.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) according to manufacturer's instructions.
TruSeq Stranded mRNA Sample Preparation Kit (Illumina) was used for next generation sequencing library construction per manufacturer's protocols

treatment_protocol: Cells were infected for 2 hrs with each indicated virus and then allowed to grow in fresh, serum-free DMEM for 48 hrs.

tag: cell type

value: MRC5 fibroblasts

tag: infection

value: HCMV strain AD169ΔUL26 (UL26dbMet)


title: U87 control input RNA 10.26

description:
ribosomal depleted RNA
338_input_10-26


title: MRC5 fibroblasts, dUL26_2_48hpi_R1


title: MRC5 fibroblasts, dUL26_1_48hpi_R1


title: U87 ADAR3 IP RNA 10.16

description:
ribosomal depleted RNA
412_RIP_10-16


title: U87 control input RNA 10.16

description:
ribosomal depleted RNA
338_input_10-16


title: SRT #07

city: Kanazawa

first: Hiro

last: Takahashi

state: Ishikawa

address: Kakuma-machi

institute: Kanazawa University

description:
TR_5253.genes.fpkm_table3.txt
TR_5253_009_R1

data_processing:
Illumina HiSeq2500 pipeline ver. 1.8 used for basecalling.
Adapter and low-quality sequences were removed by cutadapt (v1.2.1). After quality control, poly-A/T sequences were also removed by PRINSEQ (v0.19.2).
The trimmed reads were mapped to the reference human genome (GRCh37/hg19) using TopHat (v2.0.13).
Mapped reads were assembled by Cufflinks (v2.2.1), and the transcripts across all samples were merged by Cuffmerge. The fragments per kilo base per million map reads (FPKM) was calculated with Cuffquant. Cuffquant and Cuffdiff are programs involved in the Cufflinks package.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Lung

growth_protocol: Lung cancer tumor specimens were divided into small pieces (3-5 mm) and implanted into the subcutaneous flank tissue of female SHO mice.

extract_protocol:
Total RNA of PDXs and SRTs was extracted using Nucleo Spin RNA kits (Takara Bio, Shiga, Japan). Each total RNA sample (0.5 µg), extracted from six paired samples of PDXs and SRTs, was converted into a RNA-seq library of template molecules suitable for subsequent cluster generation using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Surgically resected tumor

tag: egfr mutation

value: Exon 19 deletion


title: SRT #10

description:
TR_5253.genes.fpkm_table3.txt
TR_5253_010_R1

value: Wild type


title: SRT #11

description:
TR_5253.genes.fpkm_table3.txt
TR_5253_011_R1

value: Exon 21 L858R


title: SRT #05

description:
TR_5253.genes.fpkm_table3.txt
TR_5253_008_R1


title: SRT #16

description:
TR_5253.genes.fpkm_table3.txt
TR_5253_012_R1


title: Sputum Asthma_11344

tag: condition (severity group)

value: Controlled Asthma

tag: inflammatory phenotype

value: Paucigranulocytic Asthma

value: Female

tag: age

value: Induced sputum


title: SRT #02

description:
TR_5253.genes.fpkm_table3.txt
TR_5253_007_R1


title: Ectopic-lesions_FLAG-ER beta_ChIP-Seq

description: Genome-Wide ER beta binding locus in ectopic lesions.

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the mouse genome (mm10) using the BWA algorithm (v0.7.12, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of pvalue = 1E-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: mm10
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)

source_name: Endometriotic Lesions

extract_protocol:
Tissue was submersed in PBS + 1% formaldehyde, cut into small pieces and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine. The tissue pieces were then treated with a TissueTearer and spun down and washed 2x in PBS. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. For each ChIP reaction, 50 ug of precleared chromatin was mixed with Flag M2 Agarose and incubated for 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.

tag: strain

tag: gender

value: lesion

tag: chip antibody

value: FLAG M2 agarose (Sigma, A2220)


title: Pooled_Input

description: Input DNA

source_name: Endometrium


title: Eutopic-endometrium_FLAG-ER beta_ChIP-Seq

description: Genome-Wide ER beta binding locus in eutopic endometrium

source_name: Eutopic Endometrium

value: endometrium


title: IntS9_rep3

city: Philadelphia

first: Jeremy

middle: E.

last: Wilusz

state: PA

address: 363 Clinical Research Building, 415 Curie Boulevard

department: Department of Biochemistry & Biophysics

institute: University of Pennsylvania Perelman School of Medicine

description: ribo-depleted total RNA isolated from Drosophila DL1 cells treated with IntS9 dsRNA for 3 days and induced with CuSO4 for the final 14h

data_processing:
RNA-seq reads were filtered to remove low quality bases and adaptor sequences with fastp.
Filtered reads were mapped to dm6 by Tophat2 with default parameters.
Raw reads mapped to each gene were counted by htseq-count.
Differentially expressed genes were identified by using DESeq2.
Genome_build: dm6 (BDGP6.22)
Supplementary_files_format_and_content: bedGraph files contain the bedGraph data for Genome Browser visualization

organism: Drosophila melanogaster

source_name: Drosophila DL1 cells

growth_protocol: Drosophila DL1 cells were cultured at 25°C in Schneider’s Drosophila medium (Thermo Fisher Scientific 21720024), supplemented with 10% (v/v) fetal bovine serum (HyClone SH30910.03), 1% (v/v) penicillin-streptomycin (Thermo Fisher Scientific 15140122), and 1% (v/v) L-glutamine (Thermo Fisher Scientific 35050061).

extract_protocol:
RNAseq experiments: total RNA was extracted with TRIzol Reagent (Thermo Fsher Scientific), DNase I treated (Qiagen) and purified with the RNeasy Mini kit (Qiagen) following manufacturer's instructions.
TruSeq RNA Library Preparation Kit v2

treatment_protocol: RNAseq experiments: Three independent biological replicates were generated for Control (treated with  B-galactosidase [Bgal] dsRNA for 3 days) and IntS9 depletion (treated with IntS9 dsRNA for 3 days) in DL1 cells. All samples were treated with 500 μM CuSO4 for the final 14 h.

value: DL1 cells

tag: treatment

value: IntS9 dsRNA


title: U87 control IP RNA 10.16

description:
ribosomal depleted RNA
338_RIP_10-16

value: empty vector (neomycin)

value: Immunoprecipitated RNA


title: U87 ADAR3 input RNA 10.16

description:
ribosomal depleted RNA
412_input_10-16

value: 3X-FLAG ADAR3 (neomycin)

value: RNA from whole cell lysate


title: PDX #16

description:
TR_5253.genes.fpkm_table3.txt
TR_5253_006_R1

value: Patient-derived xenograft tumor

tag: number of pdx passage

value: 4 passaged


title: IntS9_rep2

tag: cell line


title: PDX #11

description:
TR_5253.genes.fpkm_table3.txt
TR_5253_005_R1

tag: tissue

value: 3 passaged


title: Bgal_rep3

description: ribo-depleted total RNA isolated from Drosophila DL1 cells treated with Bgal dsRNA for 3 days and induced with CuSO4 for the final 14h

value: βgal dsRNA


title: IntS9_rep1


title: Bgal_rep2


title: PDX #07

description:
TR_5253.genes.fpkm_table3.txt
TR_5253_003_R1

value: Exon 19 deletion

value: 6 passaged


title: Bgal_rep1


title: Hi-C ZF10d Rescue

city: New York

first: Ricardo

last: Saldana-Meyer

state: NY

address: 522 First Avenue

department: Biochemistry and Molecular Pharmacology

institute: NYUMC - HHMI

data_processing:
Library strategy: Hi-C
HiC-Bench (Lazaris et al., 2017) was used to align and filter the Hi-C data, identify TADs, and generate Hi-C heatmaps.  To generate Hi-C filtered contact matrices, the Hi-C reads were aligned against the mouse reference genome (GRCm38/mm10) by bowtie2 (Langmead and Salzberg, 2012) (version 2.3.1). Mapped read pairs were filtered by the GenomicTools (Tsirigos et al., 2012) tools-hic filter command integrated in HiC-bench for known artifacts of the Hi-C protocol. The filtered reads include multi-mapped reads (‘multihit’), read-pairs with only one mappable read (‘single sided’), duplicated read-pairs (‘ds.duplicate’), low mapping quality reads (MAPQ < 20), read-pairs resulting from self-ligated fragments, and short-range interactions resulting from read-pairs aligning within 25kb (‘ds.filtered’). For the downstream analyses, all the accepted intra-chromosomal read-pairs (‘ds.accepted intra’) were used. The Hi-C filtered contact matrices were corrected using the ICE “correction” algorithm (Imakaev et al., 2012)  built into HiC-bench. TADs and boundaries were called using Crane insulation scores (Crane et al., 2015) (‘ratio’ index) at 40 kb bin resolution with an insulating window of 500kb. HiC heatmaps for regions of interest were generated using the ICE corrected contact matrices through the ‘hic-plotter-diff’ pipeline step integrated in HiC-bench. Additionally, fastq files were also analyzed using the HiCPro 2.11.1 pipeline (Servant et al., 2015). Mapping was done against the mm10 genome with Bowtie2 (v 2.3.1). Using the same number of valid pairs for all samples we identified TADs using the Insulation Score (IS) metric implemented in TADtool (Kruse et al., 2016) using a resolution of 40kb bins and a window given by default at that resolution of 102,353 bp.  The cutoff value for boundary identification through IS, was adjusted using the WT sample (cutoff=50) and applied to all samples (WT, ZF1 and ZF10) for comparison.
supplementary_files_format_and_content:TADs and boundaries called using two different metrics in bed file format
Genome_build: mm10

growth_protocol: E14Tga2 ESCs were grown in standard medium supplemented with LIF, 1 μM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 μM GSK3 inhibitor (CHIR99021, Stemgent)

extract_protocol:
Cells were fixed with 2% Formaldehyde.
Arima Hi-C Kit following the manufacturer’s instructions

treatment_protocol: Rescue cell lines were also grown with 500mM of indole-3-acetic acid (IAA, chemical analog of auxin) in the medium.

tag: genotype

value: embryonic stem cells


title: Hi-C ZF1d Rescue


title: Hi-C WT Rescue


title: PDX #10

description:
TR_5253.genes.fpkm_table3.txt
TR_5253_004_R1

value: Wild type

value: 5 passaged


title: PDX #02

description:
TR_5253.genes.fpkm_table3.txt
TR_5253_001_R1

value: 2 passaged


title: scRNA-Seq WT Rescue

description: Rescues.cloupe

data_processing:
Sequencing data was demultiplexed using the 10X Genomics Cell Ranger software (version 2.0.0) and aligned to the mm10 transcriptome. Unique molecular identifiers were collapsed into a gene-barcode matrix representing the counts of molecules per cell as determined and filtered by Cell Ranger using default parameters. Normalized expression values were generated using Cell Ranger using the default parameters.
supplementary_files_format_and_content:Processed .cloupe file to browse all data in Cell Ranger Software
For scRNA-seq data R1 and R2 files are the biological mapping data, I1 files are the barcode information. The first 26 bp of Read1 includes the 10X cell barcodes (16bp) + UMI (10bp)
Genome_build: mm10

extract_protocol:
Total RNA from ESCs was isolated with TRIzol (Life Technologies). Stranded libraries were prepared using TruSeq Stranded Total RNA kits.
10X Genomics


title: scRNA-Seq ZF10d Rescue

description: Rescues.cloupe

data_processing:
Sequencing data was demultiplexed using the 10X Genomics Cell Ranger software (version 2.0.0) and aligned to the mm10 transcriptome. Unique molecular identifiers were collapsed into a gene-barcode matrix representing the counts of molecules per cell as determined and filtered by Cell Ranger using default parameters. Normalized expression values were generated using Cell Ranger using the default parameters.
supplementary_files_format_and_content:Processed .cloupe file to browse all data in Cell Ranger Software
Genome_build: mm10
For scRNA-seq data R1 and R2 files are the biological mapping data, I1 files are the barcode information. The first 26 bp of Read1 includes the 10X cell barcodes (16bp) + UMI (10bp)


title: RNA-Seq ZF10d

data_processing:
Raw sequencing files were aligned against the mouse reference genome (GRCm38/mm10) using tophat 2.1.1 and differentially expressed genes were called using DESeq2 with adjusted p-values 0.05 and 0.001.
supplementary_files_format_and_content:Differentially expresed genes called by DESeq2 in a text file
Genome_build: mm10

extract_protocol:
Total RNA from ESCs was isolated with TRIzol (Life Technologies). Stranded libraries were prepared using TruSeq Stranded Total RNA kits.
TruSeq Stranded Total RNA kit following the manufacturer’s instructions


title: RNA-Seq ZF1d


title: scRNA-Seq ZF1d Rescue

description: Rescues.cloupe


title: PDX #05

description:
TR_5253.genes.fpkm_table3.txt
TR_5253_002_R1


title: Sputum Asthma_11005

source_name: Induced sputum

value: Controlled Asthma

value: Paucigranulocytic Asthma

value: Male

tag: sample type

value: Induced sputum


title: RNA-Seq 24h Auxin

treatment_protocol: Cells were incubated with 500mM of indole-3-acetic acid (IAA, chemical analog of auxin) in the medium for 24 or 48 hours


title: RNA-Seq 48 h Auxin


title: Cont_2GM [RNA-seq]

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description:
PolyA
mRNA-seq

data_processing:
Raw reads data were converted into FASTQ format and quality control was performed using the FASTQC software (Babraham Bioinformatics).
After trimming for adapters using trim_galore (Babraham Bioinformatics), mapping of the reads was obtained using the STAR program against human genome (hg38) and the quantification of genes and transcripts was done with the RSEM program using GENCODE v26.
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non-biological variability.
Genome_build: Human genome hg38 (GRCh38)
Supplementary_files_format_and_content: *.tsv: RSEM expected counts

source_name: Human peripheral blood monocytes

growth_protocol: Monocytes were cultured in RPMI medium (Life Technologies) supplemented with 10% FCS (ThermoFisher Scientific).

extract_protocol:
RNAqueous-Micro kit (Ambion).
TruSeq Stranded mRNA Sample Preparation Guide (Part # 15031047 Rev. E).

treatment_protocol: Monocytes were incubated with GM-CSF (1000 U/ml, PeproTech) or M-CSF (10 ng/ml, PeproTech) for 12h. Monocytes treated with GM-CSF were also treated with wortmannin (250 nM), trametinib (75 nM) or ruxolitinib (600 nM) (Selleck Chemicals).

value: Monocyte CD14+

tag: differentiation treatment

value: GM-CSF

tag: inhibitor treatment


title: Wort_2GM [RNA-seq]

description:
PolyA
mRNA-seq

tag: cell type

value: Wortmannin


title: Rux_2GM [RNA-seq]

description:
PolyA
mRNA-seq

value: Ruxolitinib


title: 5C_Rnase_Treatment

data_processing:
Library strategy: 5C
Genome was constructed from all possible forward-reverse primer concatenated sequence pairs. Bowtie v1 was used to align reads to reference genome of concatenated primer sequences. Data was normalized according to sequencing depth.
supplementary_files_format_and_content:Matrixes with all possible primer combinations in a text file
Genome_build: mm10

extract_protocol: Cells were fixed with 2% Formaldehyde


title: RNA-Seq 0h Auxin


title: 5C_Transcriptional_Inhibition, DMSO


title: Cont_2M [RNA-seq]

description:
PolyA
mRNA-seq

value: M-CSF


title: 5C_Transcriptional_Inhibition, TI


title: Mo2 [RNA-seq]

description:
PolyA
mRNA-seq


title: cTreg cells, stimulated (20hr), PP242-treated, replicate 3

city: Memphis

first: Geoffrey

last: Neale

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Mouse Gene 2.0 ST GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.6

source_name: Foxp3-YFP+CD4+CD62L+CD44- cTreg cells, activated (20hr) in presence of PP242

label_protocol: Five hundred picograms (500 pg) of total RNA were converted into biotinylated cDNA using the Affymetrix GeneChip WT Pico protocol (Applied Biosystems P/N 902623)

growth_protocol: Lymphocytes were isolated from spleen and peripheral lymph nodes, that included inguinal, auxiliary and cervical lymph nodes, and cTreg cells (YFP+CD4+CD62LhiCD44lo) were sorted on a MoFlow (Beckman-Coulter) or Reflection (i-Cyt).

extract_protocol: RNA was extracted using Qiagen's RNAeasy kit, with on-column DNase digestion included.

treatment_protocol: Sort-purified cTreg cells were activated in cell culture using anti-CD3 and anti-CD28 antibodies in the presence of recombinant IL-2 for 20h. During this activation period, cells were treated with vehicle (DMSO) or with the mTOR inhibitors Torin 1 (50 nM) or PP242 (500 nM).

value: Foxp3-YFP+ transgenic backcrossed on C57BL/6 background

value: cTreg cells

value: activated in presence of PP242


title: Rux_1GM [RNA-seq]

description:
PolyA
mRNA-seq


title: Input DNA

data_processing:
Raw sequencing files were aligned against the mouse reference genome (GRCm38/mm10) using Bowtie2 (version 2.3.4.1) (parameters: -N 1 -k 1 -q -x). Ambiguous reads were filtered to use uniquely mapped reads in the downstream analysis. PCR duplicates were removed using Picard-tools (version 1.88). MACS version 2.0.10 was used to call narrow peaks (parameters: -g 1.87e9 --qvalue 0.01).
supplementary_files_format_and_content:bigWigs or peaks called by MACS on bed format
Genome_build: mm10

extract_protocol:
Cells were fixed with 1% Formaldehyde. Nuclei were isolated and chromatin was fragmented. Chromatin immunoprecipitation (ChIP) was performed and the libraries were prepared using the eluted DNA from ChIP
Kapa Library Prep Kit following the manufacturer’s instructions

treatment_protocol: Nuclei were permeabilized with 0.05% Tween-20 in PBS for 10 min at 4C, washed once and resuspended in PBS and finally incubated with RNase A (1 mg/ml) or a mock reaction for 30 minutes


title: Tram_1GM [RNA-seq]

description:
PolyA
mRNA-seq

value: Trametinib


title: cTreg cells, stimulated (20hr), PP242-treated, replicate 2


title: Wort_1GM [RNA-seq]

description:
PolyA
mRNA-seq


title: 5C_Mock_Treatment

value: embryonic stem cells


title: cTreg cells, stimulated (20hr), Torin 1-treated, replicate 2

source_name: Foxp3-YFP+CD4+CD62L+CD44- cTreg cells, activated (20hr) in presence of Torin 1

value: activated in presence of Torin 1


title: Cont_1GM [RNA-seq]

description:
PolyA
mRNA-seq


title: Cont_1M [RNA-seq]

description:
PolyA
mRNA-seq


title: cTreg cells, stimulated (20hr), PP242-treated, replicate 1


title: cTreg cells, stimulated (20hr), Torin 1-treated, replicate 3


title: cTreg cells, stimulated (20hr), DMSO-treated, replicate 1

source_name: Foxp3-YFP+CD4+CD62L+CD44- cTreg cells, activated (20hr) in presence of DMSO

value: activated in presence of DMSO


title: cTreg cells, unstimulated (0hr), DMSO-treated, replicate 3

source_name: Foxp3-YFP+CD4+CD62L+CD44- cTreg cells, unactivated (0hr) in presence of DMSO

value: unactivated in presence of DMSO


title: Mo1 [RNA-seq]

description:
PolyA
mRNA-seq


title: cTreg cells, stimulated (20hr), DMSO-treated, replicate 3


title: cTreg cells, stimulated (20hr), DMSO-treated, replicate 2


title: FUBP1clone3

city: Boston

first: Jessica

middle: Sarah

last: Elman

state: MA

address: 150 Harrison Ave

department: DMCB

institute: Tufts University

description:
processed data file:
JE_FUBP_isoform.matrix.results.DEhigherthresh
JE_FUBP_genes.matrix.results.Dehigherthresh

data_processing:
STAR version 2.6 for alignment
rMATS 4.0.1 for alternative splice analysis
RSEM (using bowtie2 for alignment)
EBSeq for differential gene expression
Genome_build: hg38
Supplementary_files_format_and_content: JE_FUBP_*.matrix.results.DEhigherthresh  = text files with isoform or gene expression
Supplementary_files_format_and_content: *.MATS.JCEC.txt = tab-delimited text file with a3ss, a5ss, mxe, se, ri splice events, as indicated in the file names.
Supplementary_files_format_and_content: more details in the readme.txt

source_name: MCF10F cells

growth_protocol: Cells were grown at 37°C with 5% CO2 and cultured in DMEM/F12 supplemented with 5% horse serum, 100ng/ml cholera toxin, 5μg/ml insulin, 0.5μg/ml hydrocortisone, 50ng/ml EGF, and 1% antibiotic/antimycotic (Corning, Corning, NY).

extract_protocol:
Total RNA was extracted from MCF10F cells using the RNeasy Maxi Kit (Qiagen).
Library was prepared with the TruSeq Stranded mRNA kit and samples were sequenced by the Illumina HiSeq 2500 system using the Rapid PE150 flow cell.

value: mammary epithelial cells

tag: genotype/variation

value: clonal FUBP1 knockout


title: FUBP1polyclonal

description:
processed data file:
JE_FUBP_isoform.matrix.results.DEhigherthresh
JE_FUBP_genes.matrix.results.Dehigherthresh
A3SS.MATS.JCEC.txt
A5SS.MATS.JCEC.txt
MXE.MATS.JCEC.txt
SE.MATS.JCEC.txt
RI.MATS.JCEC.txt

value: polyclonal FUBP1 knockout


title: FUBP1clone9


title: cTreg cells, unstimulated (0hr), DMSO-treated, replicate 2


title: cTreg cells, unstimulated (0hr), DMSO-treated, replicate 1


title: Jos6019(1X)(12)

first: Grace

last: Daher

address: 1 Joslin Place

institute: Joslin Diabetes Center

description: primary muscle cells_standard media_undernourished_primary muscle cells_standard_undernourished_1x

hyb_protocol: 15ug cRNA was used to make 300ul hyb cocktail, of which 200ul were injected into GeneChip Mouse Gene  2.0 ST arrays and hybridized for 16 hours at 45C. Arrays were washed and stained using Affymetrix Fluidics Station 450 with reagents from Affymetrix.

scan_protocol: Microarrays were scanned using the GeneChip Scanner 3000 system from Affymetrix.

data_processing: Data were normalized using RMA (Expression Console from Affymetrix)

source_name: primary muscle cells from quadruceps,standard media,undernourished

label_protocol: Biotin labeling via WT PLUS Protocol

growth_protocol: Pregnant mice were housed individually with ad libitum access to standard rodent chow (T.2018, Harlan Teklad, Indianapolis, IN, USA). On day 12.5 of pregnancy, dams were randomly assigned to either a control or undernutrition group. In the undernutrition group, food was restricted to 50% that of gestational day -matched controls for the remainder of pregnancy. After delivery, mothers were given ad libitum access to chow and 24 hours after birth, litters were equalized to eight. We studied mice from 2 groups: in utero undernourished offpring (U) and control offspring (C). . Isolated primary muscle cells were grown on Matrigel coated flasks in low glucose (5.5 mmol/L) Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 20% FBS, 1X antibiotic-antimycotic, 2.5μg/ml gentamycin and 2.5ng/ml basic fibroblast growth factor.

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

treatment_protocol: On day 12.5 of pregnancy, dams were randomly assigned to either a control or undernutrition group. In the undernutrition group, food was restricted to 50% that of gestational day -matched controls for the remainder of pregnancy. Primary muscle cells were collected from offspring.  When cells reached approximately 90% confluency, they were differentiated in low glucose DMEM supplemented with 2% FBS, 1X antibiotic-antimycotic, and 2.5μg/ml gentamycin. Other cells were cultured overnight in substrate limited medium (glucose and glutamine free DMEM supplemented with 0.5mM glucose, 1mM glutamine, 0.5mM carnitine and 1% (v/v) FBS; pH 7.4).

value: primary muscle cells from quadruceps

value: ICR


title: Jos6018(1T)(11)

description: primary muscle cells_limited media_undernourished_primary muscle cells_limited_undernourished_1t

source_name: primary muscle cells from quadruceps,limited media,undernourished


title: cTreg cells, stimulated (20hr), Torin 1-treated, replicate 1


title: Jos6013(12X)(6)

description: primary muscle cells_standard media_undernourished_primary muscle cells_standard_undernourished_12x


title: Jos6020(20T)(13)

description: primary muscle cells_limited media_undernourished_primary muscle cells_limited_undernourished_20t


title: Jos6021(20x)(14)

description: primary muscle cells_standard media_undernourished_primary muscle cells_standard_undernourished_20x


title: PM_B

first: Lauren

last: Bayer Horowitz

address: 540 1st Ave

department: Cell Biology

institute: NYU School of Medicine

description:
pmk-3 mutant BAG cells replicate 2
PM-B

data_processing:
fastq files were aligned to the Caenorhabditis elegans genome and transcriptome (Wormbase WS243) using the STAR software package (Dobin et al., 2013).
Gene expression quantification was performed on the resulting BAM files using HTSeq (Anders et al., 2014)
Differential expression analysis was done using the DeSeq2 software package (Love et al., 2014) in R.
Tiled-data files (TDF) were generated from the genomic alignments (BAM files) using Integrative Genomics Viewer (Thorvaldsdottir et al., 2013) and used to generate read coverage histograms.
Genome_build: version 243 of the Caenorhabditis elegans reference genome from Wormbase, WS243
Supplementary_files_format_and_content: comma-separated file of the normalized read counts in the different cell populations sequenced;  TDF files for the different cell-populations sequenced.

organism: Caenorhabditis elegans

source_name: C. elegans fluorescent BAG cells

growth_protocol: Embryonic cell cultures were prepared as previously described (Christensen et al., 2002, Zhang et al., 2002) from wild-type and pmk-3(wz31) mutant animals expressing the BAG-specific and pmk-3 independent marker wzIs113[Pgcy-9::GFP].In brief, embryos were isolated from synchronized populations of hypochlorite treated hermaphrodites, and dissociated into single cells by chitinase treatment. Cells were resuspended in L-15 medium supplemented with 10% FBS (Sigma) and antibiotics, and passed through a 5 um syringe filter (Millipore). Cells were plated onto poly-D-lysine coated single-well chambered cover glasses (Lab-Tek II) and incubated overnight at 25degC.

extract_protocol:
GFP-labeled BAG neurons were isolated approximately 24 hours after dissociation using Fluorescence Activated Cell Sorting (FACS); sorted cells were confirmed to be >90% GFP positive by direct inspection on a fluorescent microscope. Non-fluorescent, ‘non-BAG’, cells were also collected. Dead cells were marked with propidium-iodide and excluded from sorted cells. Sorting was performed on a FACSAria Ilu SORP cell sorter using a 70 um nozzle. Cells were sorted directly into RNA Extraction Buffer (10,000 cells/100 uL buffer), and RNA was purified using the Arcturus PicoPure RNA Isolation Kit (Thermo Fisher). RNA integrity and concentration were evaluated using an Agilent Bioanalyzer. RNA samples had an RNA Integrity score of at least 8, indicating that all samples were of high quality.
cDNA libraries were prepared from RNA (1-2 ng) using the Ovation RNA-Seq System V2 (NuGEN), multiplexed, and sequenced as 100 base pair paired end reads using the HiSeq 2500 (Illumina).

value: wzIs113[Pgcy-9::GFP]; pmk-3(wz31)

tag: developmental stage

value: embryonic


title: Jos6012(12T)(5)

description: primary muscle cells_limited media_undernourished_primary muscle cells_limited_undernourished_12t