title: SHI1 input

city: Singapore

first: Jia

last: Li

address: 8 College Road

country: Singapore

institute: Duke-NUS

data_processing:
ChIP-Seq reads aligned to hg19 genome using BWA  (version 0.7.12).
ChIP-Seq peaks with q<0.05 and fold-enrichment between 5 to 50 were called by MACS (version 2.1).
Bigwig generated after normalization.
Genome_build: Hg19
Supplementary_files_format_and_content: Bigwig

source_name: Commercially available cell line

growth_protocol: SHI1 cells were maintained in RPMI 1640 supplemented with 10% FBS.

extract_protocol:
ChIP were performed as described in (Milne et al., 2009) with the following modifications: The cells were fixed using a 1% formaldehyde (FA) fixation protocol for 10 min, while a 45 min, 2mM disuccinimidyl glutarate (DSG) and a 30 min 1% FA double fixation protocol was used for all other antibodies. The antibodies used included SHARP1 (a mixture of H-72 Santa-Cruz, 12688-1-AP Proteintech, and ab175544 Abcam), H3K79me2 (Millipore, 04-835), H3K79me3 (Diagenode, pAb-068-050), MLL1 (Bethyl, A300-086A), H3K4me3 (Active Motif, 39159), H3K27me3 (Millipore, 07-499), H3K27ac (Millipore, 07-360), LEDGF (Bethyl, A300-848A), MEN1 (Bethyl, A300-105A). Fixed chromatin samples were fragmented using a Bioruptor sonicator (Diagenode) for 30 min at high in a constantly circulating 4C water bath to an average size of 200-500bps. Antibody:chromatin complexes were collected with a mixture of protein A and Protein G Dynabeads (Life Technologies) collected with a magnet, and washed 2X with a solution of 50mM HEPES-KOH, pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, and 0.7% Na-Deoxycholate. After a TE wash, samples were eluted, RNase and Proteinase K treated, and purified using a QIAGEN PCR purification kit. RNA was extracted using RNeasy kit (QIAGEN).
ChIP-seq libraries were prepared using Next ChIP-Seq library prep reagent set (New England Biolabs), and multiplexed (New England Biolabs). RNA-seq libraries were prepared using Illumina Tru-Seq Stranded Total RNA with Ribo-Zero Gold kit protocol, according to the manufacturer’s instructions (Illumina, San Diego, California, USA).

value: Human leukemia cell


title: SHI1 MLL

status: Public on Apr 26 2018

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: chip antibody

value: MLL1 (Bethyl, A300-086A)


title: pDCs no culture repeat 3

type: RNA

city: CLEVELAND

first: ENGUANG

last: BI

state: OH

address: 9500 EUCLID AVE

department: CANCER BIOLOGY

country: USA

institute: CLEVELAND CLINIC LERNER RESEARCH INSTITUTE

description:
9269325019_K
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: biotin

molecule: total RNA

source_name: Freshly isolated pDCs without any treatment

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Cells were cultured in RPMI1640 with 10% FCS.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: PDCs were treated with CpG (0.15 mM) for 12 hours with or without coculture with ARP1. Transwells were used in some cultures. In some condition, to avoid the two types of cells ARP1 and pDCs to contact directly, we cultured pDCs in transwell, a polycarbonate membrane cell culture inserts and ARP1 in the well. The soluble factors from ARP1 can still affect pDCs through the transwell membrane.

tag: tissue

value: blood

value: pDCs


title: Liver_Exercise_VitE_rep5

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description:
Run_VitE_2423
Gene expression data from liver tissue from mice after treadmill run fed with vitamin E-enriched diet, biological replicate 5.

hyb_protocol: According to the Affymetrix expression protocol (HWS kit) including minor changes as suggested by the Encore Biotin protocol.

scan_protocol: According to the Affymetrix expression protocol (GeneChip Scanner 3000 7G).

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (build 1.4.1.46) including median polish and Sketch-Quantile normalisation.

organism: Mus musculus

source_name: Liver tissue from mice after treadmill run fed with vitamin E-enriched diet

label_protocol: Ovation Pico WTA System V2 and Encore Biotin Module (Nugen).

extract_protocol: RNeasy Fibrous Tissue Kit (Qiagen) including DNase digestion.

treatment_protocol: As described in the paper. Briefly, mice were assigned to either a diet supplemented with 100 mg/kg vitamin C and 2,000 IU/kg vitamin E (as α-tocopheryl acetate) or to control diet (0 mg/kg vitamin C, 149 IU/kg vitamin E) based on the purified diet C1000 (Altromin, Lage, Germany). After 4 weeks of feeding, at an age of 11-12 weeks, the animals were subjected to an acute bout of exercise (60 min at 13 m/min and 14° inclination) on a treadmill as described previously (Hoene et al., 2010). Mice remaining in their cages, but in close proximity to the treadmill, served as controls and were deprived of food for the last 60 min before they were killed, to align with the feeding state of the exercised group.

tag: strain/background

tag: age

value: 11-12 weeks

tag: gender

value: Male

value: Liver

tag: diet

value: vitamin E enriched

tag: exercise

value: treadmill run


title: H3K27ac ChIP-seq in WT

city: Irvine

first: Jiejun

last: Shi

state: CA

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie v1.1.0
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.4.2; Scores represent the ChIP-seq tag numbers

source_name: HeLa_WT H3.3

growth_protocol: Hela cells were maintained in DMEM media [Dulbecco’s modified Eagle’s medium (DMEM, Cellgro) supplemented with 10% Fetal Bovine Serum (Sigma), 100 U/ml penicillin, 100 µg/ml streptomycin, 292 µg/ml L-glutamine]. Media was changed every other day.

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_24.
ChIP analysis was performed as described previously (Li et al., 2014) with minor modification. In brief, cells were cross-linked with 1% formaldehyde for 10 min and stopped with 125 mM glycine for 5 min. Fixed cells were scraped from dishes and washed with PBS for 2 times. Cell pellets were resuspended with cell lysis buffer (5 mM PIEPES pH 8.0, 85 mM KCl, 1% NP-40) with protease inhibitor cocktail (Roche) and 10 mM phenylmethanesulfonyl fluoride (PMSF). After 20 min rotation in 4 °C, cell nuclei were pelleted by centrifugation. The nuclei were resuspended with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors and sonicated using Bioruptor Sonicator (Diagenode). Length of most sheared DNA fragments were between 100-400 base pairs. Sonicated chromatin contains approximately 20 μg of DNA were diluted 4 fold with dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.01% SDS) and were subjected to immunoprecipitation with 2 μg of antibodies overnight at 4 °C. Protein A/G beads (Millipore) were then added and incubated for 1 hr. The immunoprecipitates were washed twice with low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and then once with LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na-Deoxycholate). DNA was eluted with vigorously shaking in elution buffer (50 mM NaHCO3, 1% SDS) for 15 min and then reverse crosslink in the presence of 0.3M NaCl at 67 °C for 12 hr. DNA was purified using PCR purification kit (Qiagen) and analyzed by quantitative real-time PCR on the ABI 7500-FAST System using the Power SYBR Green PCR Master Mix (Applied Biosystems).
For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using single-end sequencing technology on Illumina HiSeq 3000 platform.

treatment_protocol: For infections, Hela cells were incubated with viral supernatants in the presence of 8 µg/ml polybrene for 14 hr. After 48 hr, the infected cells were selected with blasticidin (5 µg/ml) for overexpression experiments.

value: HeLa

tag: genotype/variation

value: stably expressing WT or mutant (G34L/G34W) H3.3

tag: chip antibody vendor/cat.#

value: Abcam, Ab4729


title: H3K36me3 ChIP-seq in G34L

source_name: HeLa_G34L H3.3

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.
ChIP analysis was performed as described previously (Li et al., 2014) with minor modification. In brief, cells were cross-linked with 1% formaldehyde for 10 min and stopped with 125 mM glycine for 5 min. Fixed cells were scraped from dishes and washed with PBS for 2 times. Cell pellets were resuspended with cell lysis buffer (5 mM PIEPES pH 8.0, 85 mM KCl, 1% NP-40) with protease inhibitor cocktail (Roche) and 10 mM phenylmethanesulfonyl fluoride (PMSF). After 20 min rotation in 4 °C, cell nuclei were pelleted by centrifugation. The nuclei were resuspended with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors and sonicated using Bioruptor Sonicator (Diagenode). Length of most sheared DNA fragments were between 100-400 base pairs. Sonicated chromatin contains approximately 20 μg of DNA were diluted 4 fold with dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.01% SDS) and were subjected to immunoprecipitation with 2 μg of antibodies overnight at 4 °C. Protein A/G beads (Millipore) were then added and incubated for 1 hr. The immunoprecipitates were washed twice with low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and then once with LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na-Deoxycholate). DNA was eluted with vigorously shaking in elution buffer (50 mM NaHCO3, 1% SDS) for 15 min and then reverse crosslink in the presence of 0.3M NaCl at 67 °C for 12 hr. DNA was purified using PCR purification kit (Qiagen) and analyzed by quantitative real-time PCR on the ABI 7500-FAST System using the Power SYBR Green PCR Master Mix (Applied Biosystems).
For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using single-end sequencing technology on Illumina HiSeq 3000 platform.

value: stably expressing mutant (G34L)  H3.3

value: Abcam, Ab9050


title: Flag-H3.3 ChIP-seq in K36M

source_name: HeLa_K36M H3.3

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_23.
ChIP analysis was performed as described previously (Li et al., 2014) with minor modification. In brief, cells were cross-linked with 1% formaldehyde for 10 min and stopped with 125 mM glycine for 5 min. Fixed cells were scraped from dishes and washed with PBS for 2 times. Cell pellets were resuspended with cell lysis buffer (5 mM PIEPES pH 8.0, 85 mM KCl, 1% NP-40) with protease inhibitor cocktail (Roche) and 10 mM phenylmethanesulfonyl fluoride (PMSF). After 20 min rotation in 4 °C, cell nuclei were pelleted by centrifugation. The nuclei were resuspended with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors and sonicated using Bioruptor Sonicator (Diagenode). Length of most sheared DNA fragments were between 100-400 base pairs. Sonicated chromatin contains approximately 20 μg of DNA were diluted 4 fold with dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.01% SDS) and were subjected to immunoprecipitation with 2 μg of antibodies overnight at 4 °C. Protein A/G beads (Millipore) were then added and incubated for 1 hr. The immunoprecipitates were washed twice with low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and then once with LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na-Deoxycholate). DNA was eluted with vigorously shaking in elution buffer (50 mM NaHCO3, 1% SDS) for 15 min and then reverse crosslink in the presence of 0.3M NaCl at 67 °C for 12 hr. DNA was purified using PCR purification kit (Qiagen) and analyzed by quantitative real-time PCR on the ABI 7500-FAST System using the Power SYBR Green PCR Master Mix (Applied Biosystems).
For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using single-end sequencing technology on Illumina HiSeq 3000 platform.

value: Sigma, F1804


title: Liver_Exercise_VitE_rep9

description:
Run_VitE_2719
Gene expression data from liver tissue from mice after treadmill run fed with vitamin E-enriched diet, biological replicate 9.


title: H3K36me2 ChIP-seq in G34L

value: Abcam, Ab9049


title: pDCs no culture repeat 1

description:
9269325018_E
replicate 1


title: pDCs-CpG repeat 2

description:
9269325019_E
replicate 2

source_name: pDCs were stimulated with CpG for 12 hours


title: H3.3 ChIP-seq in G34L

value: Millipore, 09-838


title: Liver_Exercise_VitE_rep2

description:
Run_VitE_2420
Gene expression data from liver tissue from mice after treadmill run fed with vitamin E-enriched diet, biological replicate 2.


title: Liver_Exercise_VitE_rep1

description:
Run_VitE_2419
Gene expression data from liver tissue from mice after treadmill run fed with vitamin E-enriched diet, biological replicate 1.


title: Liver_Exercise_VitE_rep4

description:
Run_VitE_2422
Gene expression data from liver tissue from mice after treadmill run fed with vitamin E-enriched diet, biological replicate 4.


title: pDCs-CpG repeat 3

description:
9269325019_J
replicate 3


title: H3K27me3 ChIP-seq in G34L

value: Millipore, 07-449


title: pDCs-CpG repeat 1

description:
9269325018_I
replicate 1


title: Liver_Exercise_Control_rep12

description:
Run_Ctrl_2711
Gene expression data from liver tissue from mice after treadmill run fed with control diet, biological replicate 12.

source_name: Liver tissue from mice after treadmill run fed with control diet

value: control


title: H3K27ac ChIP-seq in G34L


title: pDCs no culture repeat 2

description:
9269325018_F
replicate 2

value: blood


title: ARP1 Transwell repeat 2

description:
9269325019_A
replicate 2

source_name: This sample includes only ARP1 cells from outside the transwell insert. pDCs were inside transwell. Co-culture  was treated with CpG for 12 hours.


title: M. tuberculosis exposed to Ax-35 at 30x MIC, replicate 1

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

library_source: transcriptomic

data_processing:
Reads were adapter- and quality-trimmed with Trimmomatic v0.33 and mapped onto the M. tuberculosis H37Rv reference genome (RefSeq NC_000962.3) using Bowtie2 v2.2.5.
Counting reads over features was done with featureCounts from the Subread package v1.4.6.
DESeq2 was used to infer differentially expressed genes.
Genome_build: NC_000962.3

organism: Mycobacterium tuberculosis

source_name: cell culture

growth_protocol: Wild-type H37Rv cultures were grown to mid-log phase at 37°C.

extract_protocol:
Cells were harvested by centrifugation and pellets were stored with 1 ml of TRIzol reagent (Thermo Fisher Scientific) at -80oC until further processed. Cells were lysed by bead-beating and total RNA was extracted by phenol-chloroform with DNAse treatment (RQ1 RNase–free DNase, Promega).
Library preparation was done using the Ribo-zero rRNA removal kit (Illumina) for Gram-positive bacteria.

treatment_protocol: Cells were exposed to DMSO (vehicle control) or AX-35 compound for 4 h at 37°C.

tag: strain

tag: treatment

value: Ax-35 at 30x MIC


title: M. tuberculosis exposed to Ax-35 at 30x MIC, replicate 2


title: Liver_Exercise_VitE_rep3

description:
Run_VitE_2421
Gene expression data from liver tissue from mice after treadmill run fed with vitamin E-enriched diet, biological replicate 3.

value: 11-12 weeks


title: ARP1 Transwell repeat 3

description:
9269325019_I
replicate 3


title: Liver_Exercise_Control_rep11

description:
Run_Ctrl_2710
Gene expression data from liver tissue from mice after treadmill run fed with control diet, biological replicate 11.

value: Male


title: ARP1 Transwell repeat 1

description:
9269325018_C
replicate 1


title: Liver_Exercise_Control_rep6

description:
Run_Ctrl_2412
Gene expression data from liver tissue from mice after treadmill run fed with control diet, biological replicate 6.

value: Liver


title: Liver_Exercise_Control_rep9

description:
Run_Ctrl_2708
Gene expression data from liver tissue from mice after treadmill run fed with control diet, biological replicate 9.


title: Liver_Exercise_Control_rep10

description:
Run_Ctrl_2709
Gene expression data from liver tissue from mice after treadmill run fed with control diet, biological replicate 10.


title: ARP1 no culture repeat 2

description:
9269325018_D
replicate 2

source_name: ARP1 cells without any treatment


title: ARP1 no culture repeat 3

description:
9269325017_E
replicate 3


title: Liver_Exercise_Control_rep8

description:
Run_Ctrl_2707
Gene expression data from liver tissue from mice after treadmill run fed with control diet, biological replicate 8.


title: M. tuberculosis exposed to Ax-35 at 10x MIC, replicate 1

value: Ax-35 at 10x MIC


title: ARP1 CpG repeat 3

description:
9269325018_B
replicate 3

source_name: ARP1 cells treated with CpG for 12 hours


title: ARP1 no culture repeat 1

description:
9269325019_C
replicate 1


title: M. tuberculosis wild-type, replicate 2

value: wild type


title: M. tuberculosis wild-type, replicate 1


title: ARP1 CpG repeat 2

description:
9269325017_L
replicate 2


title: ARP1 CpG repeat 1

description:
9269325017_K
replicate 1


title: M. tuberculosis exposed to Ax-35 at 10x MIC, replicate 2


title: Donor E-ctrl

city: Saint Louis

first: Miriam

last: Kim

state: Missouri

address: 660 S. Euclid Ave

institute: Washington University in St Louis

data_processing:
Sequencing reads were aligned to the human genome (hg19) using RUM
Differential expression was analyzed using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: single excel file with RPKM values for each sample

source_name: In vitro differentiated human CD34+ cells

growth_protocol: Cells were cultured in IMDM+10% FBS and the following human cytokines: SCF 100ng/ul, Flt3 ligand 100ng/ul, TPO 50ng/ul, IL-6 50ng/ul, GM-CSF 100ng/ul, IL-3 10ng/ul (all purchased from Peprotech). Cells were maintained at 0.5-1x106 cells/ml for 5-7 days prior to analysis.

extract_protocol:
RNA was isolated from 5 matched samples of in vitro differentiated control/CD33 KO human HSPCs using Ambion RiboPure RNA purification kit (ThermoFisher Scientific, AM1924).
RNA-seq libraries were generated using TruSeq RNA library prep kit (Illumina, RS-122-2001/2) per the manufacturer’s instructions

treatment_protocol: CD34+ cells were washed and resuspended in Opti-MEM and electroporated with the Cas9 ribonucleoprotein complex using the BTX ECM 830 Square Wave Electroporation System (Harvard Apparatus) with a single pulse of 400V and 5msec.

tag: donor

value: E

value: wt


title: Donor E-KO

value: CD33 KO


title: Liver_Exercise_Control_rep7

description:
Run_Ctrl_2706
Gene expression data from liver tissue from mice after treadmill run fed with control diet, biological replicate 7.

value: treadmill run


title: Donor D-KO

value: D


title: Liver_Exercise_Control_rep3

description:
Run_Ctrl_2409
Gene expression data from liver tissue from mice after treadmill run fed with control diet, biological replicate 3.


title: Donor D-ctrl


title: Liver_Exercise_Control_rep4

description:
Run_Ctrl_2410
Gene expression data from liver tissue from mice after treadmill run fed with control diet, biological replicate 4.


title: E3

city: Ningbo

first: Mingyue

last: Cao

state: Zheijang

address: 818, Fenghua Rod, Jiangbei District

country: China

institute: Ningbo University

description: miRNADiffExp.Expdiff.txt

data_processing:
Basecalls performed using miRbase v20 .
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence to bulid gene library, and then detect quality & productivety by using Agilent 2100 Bioanalyzer & ABI StepOnePlus Real-Time PCR System.
Data were filtered using the following specification such as gene 3'UTR sequences, diveristies of expression for muscle.
Get the credible target sequences by Bioinformatics Analysis with the following database miRbase v20.
Targetscan and miRanda are two online softwares used in this study.
Genome_build: GCA_000972845.1 L_crocea_1.0
Supplementary_files_format_and_content: Tab-delimited text files include match values for each Sample, some are formed as text ("UN" means unknown microRNAs which aren't identified in present database, but can be found in results of Hi-seq detecting; non''UN'' means can be found in both database and Hi-seq results).

organism: Larimichthys crocea

source_name: muscle, fasting

extract_protocol:
Muscles were frozen on Liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Dai Qu Ocean large yellow crocea

value: muscle

tag: stress

value: 21d fasting


title: C3

description: miRNADiffExp.Expdiff.txt

source_name: muscle, control


title: Donor B-KO

value: B


title: Donor B-ctrl


title: Input chromatin ChIPseq

city: Storrs

first: Thomas

last: Heider

address: 181 Auditorium Road, Unit 3197

institute: University of Connecticut

data_processing:
Reads were adapter clipped and trimmed with Trimmomatic 0.36 PE.
Surviving paired reads were mapped to the koala genome (phaCin_unsw_v4.1) with bowtie 2 using the “very sensitive, paired end” parameters.
Peaks were called by MACS2 (version 2.0.10.20131216) using the following parameters: –broad –keep-dup 2 –B –q 0.01
Surviving paired read files were converted to fasta files. The fasta files were broken up into smaller files of 1 million reads each. A single 1 million read fasta file from each pair was repeat masked with RepeatMasker 4.0.3 using the marsupial database as well as a koala denovo database. Repeat class and type was summarized using the buildSummary.pl script in the RepeatMasker utility script folder. The number of reads for each repeat in the RepeatMasker output file was normalized to the total number of repeats detected by RepeatMasker to obtain a frequency of detection for each repeat type.
Genome_build: phaCin_unsw_v4.1
Supplementary_files_format_and_content: BED files

organism: Phascolarctos cinereus

source_name: koala tissue (endometrium)

extract_protocol:
Following tissue homogenization by mortar and pestle while submerged in liquid nitrogen, 10 ug of custom Meu anti-CenpA (rabbit) or human anti-centromere protein IgG (Antibodies incorporated) and 1 ug of negative control antibody (Invitrogen Rabbit IgG or Rb pAb to human IgG, Abcam ab2410, respectively) was employed in ChIP samples.
To characterize the centromeric regions of the genome assembly, chromatin immunoprecipitation (ChIP) was performed on koala endometrium tissue using the Invitrogen MAGnify Chromatin Immunoprecipitation System (Revision 6). Following tissue homogenization by mortar and pestle while submerged in liquid nitrogen, 10 ug of custom Meu anti-CenpA (rabbit) or human anti-centromere protein IgG (Antibodies incorporated) and 1 ug of negative control antibody (Invitrogen Rabbit IgG or Rb pAb to human IgG, Abcam ab2410, respectively) was employed in ChIP samples. Antibodies were coupled to beads for 6 hours at 4˚C. Chromatin was sheared using the Covaris S2 from a total of 100,000 cells per IP.  Following overnight IP and DNA isolation, quantification was performed on all samples using QuBit. While no detectable DNA was obtained from negative control antibody IPs, 1 ng of DNA was used from CENP-A IP, CREST IP, and input DNA for library preparation using the Swift Biosciences Accel NGS 2S Plus DNA Library Kit. Library amplification was performed at the recommended number of cycles. Following QA/QC, Illumina libraries were pooled and were run on Illumina Next Seq 500 using the Mid Output Flow Cell Cartridge v2 (paired end 300 cycles).

value: koala tissue (endometrium)


title: CREST ChIPSeq

value: CREST:human anti-centromere protein IgG (Antibodies incorporated), cat# 15-235, lot:441.20BK.82


title: Donor A-KO

value: A


title: Donor C-KO

value: C


title: Liver_Exercise_Control_rep1

description:
Run_Ctrl_2407
Gene expression data from liver tissue from mice after treadmill run fed with control diet, biological replicate 1.

value: 11-12 weeks

value: Male

value: control


title: Liver_Exercise_Control_rep2

description:
Run_Ctrl_2408
Gene expression data from liver tissue from mice after treadmill run fed with control diet, biological replicate 2.

value: Liver


title: CENP-A ChIPseq

value: Macropus eugenii anti-CenpA (rabbit) (derived by Biosynthesis), lot:AB1035-1


title: Donor C-ctrl

value: wt


title: Spred1 KO_1

city: Kanazawa

first: Yuko

last: Tadokoro

address: Kakuma

department: Cancer Research Institute

country: Japan

institute: Kanazawa University

hyb_protocol: Hybridization was performed using Gene Expression Hybridization Kit (Agilent Technologies) according to the manufacturer's protocol. The slides were washed using Gene Expression Wash Buffer (Agilent Technologies).

scan_protocol: Images were scanned using Agilent Technologies Microarray Scanner (Scan Resolution; 3μm, TIFF file dynamic range; 20bit).

data_processing: The scanned images of the microarray were digitalized using Agilent Feature Extraction 10.7.3.1. The raw digitalized signal values were imported into GeneSpring GX software (Agilent Technologies) and normalized to shift to the 75th percentile.

source_name: Mouse bone marrow

label_protocol: The RNA samples were labeled using Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: CD48-KSL cells were sorted directly into Trizol Reagent (Invitrogen) and total RNA was isolated according to the manufacturer’s protocol. RNA quality was confirmed using Nanodrop (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: genotype

value: Spred1 KO

value: bone marrow

value: HSCs/progenitor cells

tag: cell markers


title: Spred1 KO_3


title: Donor A-ctrl


title: BJAB treated by APRIL replicate 2

city: Montpellier

first: Jerome

last: Moreaux

address: 80 Av. Augustin Fliche

department: Biological Hematology

country: France

institute: CHRU Montpellier

description:
BH8
RNA expression data from BJAB treated by APRIL

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing:
Data obtained for the whole set of samples were normalized by RMA.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: BJAB treated by APRIL

label_protocol: Standard Affymetrix procedures

growth_protocol: BJAB and HBL-1 cell lines were cultured in RPMI1640 medium and 10% FCS.

extract_protocol: Total RNAs were purified from cells with the RNeasy Qiagen purification kit following manufacturer's instructions including an on-column DNase I treatment step to remove any residual contaminant DNA.

treatment_protocol: BJAB and HBL-1 cell lines were stimulated for 6 hours with recombinant purified APRIL (1µg/ml) or with EDA (1µg/ml)  as control.

tag: cell line

value: BJAB

value: B Lymphoma cell line

tag: treated with

value: recombinant purified APRIL (1µg/ml) for 6hrs


title: V3OE UT

city: Salt Lake City

first: Christopher

middle: A

last: Reilly

state: UT

address: 30 S 2000 E, Room 201 Skaggs Hall

department: Pharmacology and Toxicology

institute: University of Utah

data_processing:
Reads were aligned to human genome from Ensembl release 87 using STAR.
Reads mapping uniquely to features in the Ensembl human GTF were counted using featureCounts.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2
Genome_build: Ensembl release 87
Supplementary_files_format_and_content: text file with read counts

source_name: BEAS-2B TRPV3-OE

growth_protocol: all BEAS-2B cells were grown in LHC-9 (lifetechnologies) and sub cultured before reaching confluence using trypLE.  Plate coat consisiting of collagen and fibronectin was used.

extract_protocol: At confluence, cell culture medium was removed and cells were snap frozen.  RNA was extracted using Rneasy kit (qiagen) with on column Dnase I digestion.

treatment_protocol: Cells were plated at equal densities into 6-well plates and harvested at confluence.

tag: cell type

value: lung epithelium

tag: passage

value: between 4 and 8


title: BJAB treated by EDA replicate 2

description:
BH6
RNA expression data from BJAB treated by EDA

source_name: BJAB treated by EDA

value: EDA (1µg/ml) for 6hrs


title: Spred1 KO_2

tag: tissue


title: Liver_Exercise_Control_rep5

description:
Run_Ctrl_2411
Gene expression data from liver tissue from mice after treadmill run fed with control diet, biological replicate 5.

tag: strain/background

tag: age

value: treadmill run


title: BJAB treated by APRIL replicate 1

description:
BH7
RNA expression data from BJAB treated by APRIL


title: HBL-1 treated by EDA replicate 2

description:
BH2
RNA expression data from HBL-1 treated by EDA

source_name: HBL-1 treated by EDA


title: HBL-1 treated by EDA replicate 1

description:
BH1
RNA expression data from HBL-1 treated by EDA


title: HBL-1 treated by APRIL replicate 1

description:
BH3
RNA expression data from HBL-1 treated by APRIL

source_name: HBL-1 treated by APRIL


title: BJAB treated by EDA replicate 1

description:
BH5
RNA expression data from BJAB treated by EDA


title: HBL-1 treated by APRIL replicate 2

description:
BH4
RNA expression data from HBL-1 treated by APRIL


title: Spred1 WT_1

value: wildtype


title: RRas2-deficient GC cells, biological replicate 2

status: Public on Apr 25 2018

city: Madrid

first: Balbino

last: Alarcon

state: Madrid

address: Nicolas Cabrera 1

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa

description: B220+CD95+GL7+B cells collected from Rras-deficient mice 7 days after immunization with sheep red blood cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

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

source_name: Germinal center B cells FACS-sorted from immunized RRas2-deficient mice

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

growth_protocol: All mice were maintained in ventilated filter cages under specific-pathogen-free (SPF) conditions and were fed ad libitum.

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

treatment_protocol: All mice were immunized with sheep red blood cellls 7 days before extraction of spleen cells

value: spleen

value: germinal center B cells


title: RRas2-deficient GC cells, biological replicate 1


title: Spred1 WT_2


title: WT GC cells, biological replicate 2

description: B220+CD95+GL7+B cells collected from wild type mice 7 days after immunization with sheep red blood cells

source_name: Germinal center B cells FACS-sorted from immunized wild type mice

value: Wild-type


title: uMT_Ca_d42_3

city: Kurume

first: Hiroki

last: Aoki

state: Fukuoka

address: 67 Asahimachi

department: Cardiovascular Research Institute

institute: Kurume University

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

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

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

source_name: uMT, Ca, day42, replicate3

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

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: abdominal aortic aneurysm

value: uMT

tag: condition

value: Ca, day42


title: uMT_sham_d42_3

source_name: uMT, sham, day42, replicate3

value: sham, day42


title: uMT_Ca_d42_1

source_name: uMT, Ca, day42, replicate1


title: uMT_sham_d42_2

source_name: uMT, sham, day42, replicate2


title: WT GC cells, biological replicate 4


title: uMT_Ca_d7_2

source_name: uMT, Ca, day7, replicate2

value: Ca, day7


title: Spred1 WT_3

value: bone marrow

value: HSCs/progenitor cells


title: uMT_Ca_d7_1

source_name: uMT, Ca, day7, replicate1


title: uMT_Ca_d7_3

source_name: uMT, Ca, day7, replicate3


title: WT GC cells, biological replicate 1


title: RRas2-deficient GC cells, biological replicate 3


title: WT GC cells, biological replicate 3


title: uMT_pre_2

source_name: uMT, pre, replicate2

value: pre


title: uMT_sham_d7_3

source_name: uMT, sham, day7, replicate3

value: sham, day7


title: uMT_Ca_d42_2

source_name: uMT, Ca, day42, replicate2


title: 12_DexMif

city: Chicago

first: Suzanne

middle: D

last: Conzen

state: IL

address: KCBD 8th Floor Conzen Lab, 900 E 57th Street

department: Medicine

institute: The University of Chicago

description: RMA-normalized by University of Chicago Genomics Core Facility

hyb_protocol: The University of Chicago Genomics Core facility carried out the reverse transcription on the samples, followed by hybridization and microarray analysis using the Affymetrix Human U133 Plus 2.0 platform

data_processing:
RMA normalization and expression fold-change over vehicle control was calculated.
Application of a cut-off of at least +/- 1.3-fold change difference in expression for each treatment group versus vehicle, the genes became candidates for further analysis when their expression was altered significantly by Dex, and inhibited commonly by Mif and C297 (within the same time point as Dex) by at least 25%, in any treatment group.

source_name: triple-negative breast cancer cell line MDA-MB-231 treated for 12 hours with 100nM dexamethasone + 100nM mifepristone

growth_protocol: MDA-MB-231 cells were grown to 80% confluence in 15-cm dishes in DMEM with 10% FBS. After culturing cells for 48h in DMEM with 2.5% charcoal-stripped FBS, 2 x 10^7 cells (per condition) were treated.

extract_protocol: Following compound exposure, cells were washed in PBS, and lysed in RNA lysis buffer (Qiagen overnight at -80°C. RNA extraction, with accompanying DNase treatment, was performed using the RNeasy kit (Qiagen) following the manufacturer’s protocol

treatment_protocol: Treatments include either Vehicle, 100 nM Dex +/- 100 nM C297 or 100 nM Mif for 4, 8, and 12h. )


title: uMT_pre_3

source_name: uMT, pre, replicate3


title: 8h_DexMif

scan_protocol: The University of Chicago Genomics Core facility carried out the reverse transcription on the samples, followed by hybridization and microarray analysis using the Affymetrix Human U133 Plus 2.0 platform

source_name: triple-negative breast cancer cell line MDA-MB-231 treated for 8 hours with 100nM dexamethasone + 100nM mifepristone


title: wild_Ca_d42_3

source_name: wild type, Ca, day42, replicate3

value: wild type


title: 12h_Veh

source_name: triple-negative breast cancer cell line MDA-MB-231 treated for 12 hours with vehicle

label_protocol: The University of Chicago Genomics Core facility carried out the reverse transcription on the samples, followed by hybridization and microarray analysis using the Affymetrix Human U133 Plus 2.0 platform


title: uMT_sham_d7_2

source_name: uMT, sham, day7, replicate2


title: uMT_sham_d7_1

source_name: uMT, sham, day7, replicate1


title: uMT_pre_1

source_name: uMT, pre, replicate1


title: 12h_DexVeh

source_name: triple-negative breast cancer cell line MDA-MB-231 treated for 12 hours with 100nM dexamethasone


title: 8h_DexVeh

source_name: triple-negative breast cancer cell line MDA-MB-231 treated for8  hours with 100nM dexamethasone


title: wild_Ca_d42_1

source_name: wild type, Ca, day42, replicate1


title: 8h_Dex297

source_name: triple-negative breast cancer cell line MDA-MB-231 treated for 8 hours with 100nM dexamethasone + 100nM CORT108297


title: wild_Ca_d7_2

source_name: wild type, Ca, day7, replicate2


title: wild_Ca_d42_2

source_name: wild type, Ca, day42, replicate2


title: 4h replicate dexmif

description: RMA-normalized by the BiocLite(Affy) package in R

source_name: triple-negative breast cancer cell line MDA-MB-231 treated for 4 hours with 100nM dexamethasone + 100nM mifepristone


title: 8h_Veh

source_name: triple-negative breast cancer cell line MDA-MB-231 treated for 8 hours with vehicle


title: 4h replicate dex

source_name: triple-negative breast cancer cell line MDA-MB-231 treated for 4 hours with 100nM dexamethasone


title: wild_sham_d42_1

source_name: wild type, sham, day42, replicate1


title: 12h_Dex297

source_name: triple-negative breast cancer cell line MDA-MB-231 treated for 12 hours with 100nM dexamethasone + 100nM CORT108297


title: wild_Ca_d7_1

source_name: wild type, Ca, day7, replicate1


title: wild_sham_d42_2

source_name: wild type, sham, day42, replicate2


title: wild_sham_d7_3

source_name: wild type, sham, day7, replicate3


title: wild_sham_d7_1

source_name: wild type, sham, day7, replicate1


title: wild_pre_3

source_name: wild type, pre, replicate3


title: 4h_Veh

source_name: triple-negative breast cancer cell line MDA-MB-231 treated for 4 hours with vehicle


title: 4h_DexMif


title: wild_pre_1

source_name: wild type, pre, replicate1


title: 4h replicate veh


title: wild_sham_d42_3

source_name: wild type, sham, day42, replicate3


title: wild_Ca_d7_3

source_name: wild type, Ca, day7, replicate3


title: wild_sham_d7_2

source_name: wild type, sham, day7, replicate2


title: B2B UT

value: lung epithelium

value: WT

value: between 20 and 30


title: placebo_b; 256HV

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Samples were hybridized to Affymetrix GeneChip Human Gene 1.1 ST array plates (Santa Clara, CA) according to manufacturer's instructions.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.36.1).

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 256

label_protocol: One hundred nanogram of total RNA was used for whole transcript cDNA synthesis with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Apparently healthy men and women aged 40–80 y were recruited from Wageningen and surroundings, in The Netherlands. Eligible for participation were nonsmoking men and women, with a BMI (in kg/m2) between 20 and 40 and systolic blood pressure (SBP) between 125 and 160 mm Hg on 2 separate occasions. Exclusion criteria included the presence of diabetes mellitus; cardiovascular, gastrointestinal, or liver disease; usage of antihypertensive or cholesterol-lowering medication or corticosteroids; adherence to a prescribed diet; unstable weight in the past 2 mo; ≥10 h/wk moderate to vigorous physical activity (≥3 metabolic equivalent tasks); and pregnancy or lactation. All subjects gave written informed consent for participation in this study, which was reviewed and approved by the local Medical Ethical Committee of Wageningen University. All procedures were executed according to the declaration of Helsinki. This study was registered at clinicaltrials.gov as NCT01691404.

extract_protocol: RNA was isolated (RNeasy Micro kit, Qiagen, Venlo, the Netherlands), quantified (Nanodrop ND 1000, Nanodrop technologies, Wilmington, Delaware USA) and integrity was checked by an Agilent 2100 Bioanalyser with RNA 6000 microchips (Agilent Technologies, South Queensferry, UK). Samples were included for microarray analysis if the RNA integrity number (RIN) was > 7.

treatment_protocol: The study was a randomized, double blind, placebo-controlled, cross-over trial in which subjects received two 4-week interventions; epicatechin (100mg/day) or placebo (microcrystalline cellulose). Details of the study have been previously described (Dower et al., 2015; PMID: 25934864). In brief, subjects received both interventions in random order with a wash-out period of 4-week between both interventions. Subjects consumed 2 capsules per day with a glass of water: one during breakfast and one during dinner. Subjects were asked to avoid consumption of epicatechin-rich foods throughout the study. Fasting peripheral blood mononuclear cells (PBMC) were collected before (T0) and after each intervention period (T4) using BD Vacutainer Cell Preparation Tubes. On the day prior to each study day, subjects received a standardized evening meal, refrained from alcohol consumption and strenuous exercise, and were not allowed to eat or drink anything except water after 10.00 pm.

value: placebo

tag: subjectid

tag: before/after supplementation

value: before


title: wild_pre_2

source_name: wild type, pre, replicate2


title: epi_e; 256HV

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 256

value: epicatechin (100mg/d)

value: after


title: 4h_Dex


title: uMT_Ca+IgG#2

source_name: uMT, Ca+IgG, replicate2

value: abdominal aorta

value: Ca+IgG


title: uMT_Ca#2

source_name: uMT, Ca, replicate2

value: uMT

value: Ca


title: total RNA from bone marrow 27

city: Houston

first: Koichi

last: Takahashi

state: TX

address: 1881 East Road

institute: UT MD Anderson Cancer Center

data_processing:
Raw sequencing data from Illumina platform were converted to fastq files and aligned to the reference genome (hg19) using the Spliced Transcripts Alignment to a Reference (STAR) algorithm.
HTSeq-count was then utilized to generate the raw counts for each gene.
Raw counts were then analyzed by DESeq2 for data processing, normalization and differential expression analysis following standard procedures.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include normalized counts for each sample

source_name: bone marrow

extract_protocol: After extraction of total RNA, we used Ribo-SPIA Technology (Nugen, CA) for cDNA synthesis as per the manufacture’s instruction. Synthesized cDNA library was sequenced by Illumina’s HiSeq 2000 platform.

tag: disease state

value: adult mixed phenotype acute leukemia


title: uMT_Ca#3

source_name: uMT, Ca, replicate3

tag: strain


title: placebo_e; 256HV

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 256

tag: treatment


title: placebo_e; 255HB

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 255


title: total RNA from bone marrow 25

value: bone marrow


title: uMT_Ca+IgG#3

source_name: uMT, Ca+IgG, replicate3


title: uMT_Ca+IgG#1

source_name: uMT, Ca+IgG, replicate1


title: placebo_b; 255HB

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 255


title: epi_b; 255HB

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 255


title: epi_e; 255HB

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 255


title: uMT_sham#2

source_name: uMT, sham, replicate2

value: sham


title: uMT_Ca#1

source_name: uMT, Ca, replicate1


title: epi_b; 256HV

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 256


title: epi_b; 251AD

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 251


title: placebo_e; 251AD

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 251


title: placebo_b; 251AD

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 251


title: total RNA from bone marrow 24


title: uMT_sham#1

source_name: uMT, sham, replicate1


title: total RNA from bone marrow 23


title: uMT_sham#3

source_name: uMT, sham, replicate3


title: epi_b; 250JB

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 250


title: placebo_e; 250JB

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 250


title: epi_e; 250JB

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 250


title: epi_e; 251AD

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 251


title: total RNA from bone marrow 22

source_name: bone marrow


title: total RNA from bone marrow 21


title: total RNA from bone marrow 20


title: total RNA from bone marrow 19


title: placebo_b; 250JB

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 250


title: placebo_e; 242BG

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 242


title: total RNA from bone marrow 17


title: placebo_b; 242BG

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 242


title: uMT_sham_d42_1

source_name: uMT, sham, day42, replicate1

value: abdominal aortic aneurysm

value: sham, day42


title: total RNA from bone marrow 16


title: total RNA from bone marrow 15


title: total RNA from bone marrow 14


title: total RNA from bone marrow 13


title: total RNA from bone marrow 10


title: total RNA from bone marrow 11


title: total RNA from bone marrow 12


title: epi_b; 242BG

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 242


title: total RNA from bone marrow 9


title: total RNA from bone marrow 8


title: epi_e; 240GJ

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 240


title: epi_e; 242BG

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 242


title: placebo_e; 241WV

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 241


title: epi_e; 241WV

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 241


title: total RNA from bone marrow 6


title: total RNA from bone marrow 5


title: total RNA from bone marrow 4


title: placebo_b; 240GJ

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 240


title: total RNA from bone marrow 2


title: placebo_b; 241WV

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 241


title: epi_b; 240GJ

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 240


title: epi_b; 241WV

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 241


title: epi_e; 239SS

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 239


title: 554 RNA-Seq

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

institute: CNIO

description: Strand-specific RNA-seq (dUTP)

data_processing:
RNA-seq analysis:
RNA-seq data was analysed with the nextpresso (http://bioinfo.cnio.es/nextpresso/) pipeline as follows:
Directional RNA-seq libraries were sequenced in paired-end format in two different rounds (Illumina HiSeq2000), leading to 50bp and 76bp reads (the latter were trimmed to 50bp). RNA-seq reads were aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10[1] (using Bowtie 1.0.0 and Samtools 0.1.19) allowing two mismatches and five multihits. Transcripts assembly, estimation of their abundances were calculated with Cufflinks 2.2.1, using the Ensembl GRCh37.74 annotation for human.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM values calculated with Cuffnorm

molecule: polyA RNA

source_name: tumor

growth_protocol: No cultered cells were used.

extract_protocol:
Total RNA was obtained using TriPure Reagent (Roche Applied Science, Indianapolis, IN, USA), following manufacturer’s instructions.
1 µg of total sample RNA was used. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina HiSeq2000 sequencer by following manufacturer's protocols.
Strand-specific RNA-Seq (dUTP)

treatment_protocol: No treatment was used

value: T-cell lymphoblastic lymphoma


title: 840 RNA-Seq

description: Strand-specific RNA-seq (dUTP)


title: epi_e; 238GG

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 238


title: placebo_e; 239SS

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 239


title: epi_b; 239SS

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 239


title: 521 RNA-Seq

description: Strand-specific RNA-seq (dUTP)


title: placebo_e; 240GJ

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 240


title: 460 RNA-Seq

description: Strand-specific RNA-seq (dUTP)


title: total RNA from bone marrow 3

source_name: bone marrow


title: 408 RNA-Seq

description: Strand-specific RNA-seq (dUTP)


title: total RNA from bone marrow 1


title: placebo_e; 237EH

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 237


title: 404 RNA-Seq

description: Strand-specific RNA-seq (dUTP)

source_name: control

value: control thymus


title: 346 RNA-Seq

description: Strand-specific RNA-seq (dUTP)


title: 405 RNA-Seq

description: Strand-specific RNA-seq (dUTP)


title: 238 RNA-Seq

description: Strand-specific RNA-seq (dUTP)


title: placebo_b; 237EH

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 237


title: placebo_b; 239SS

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 239


title: epi_e; 237EH

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 237


title: epi_e; 236JK

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 236


title: epi_b; 236JK

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 236


title: epi_b; 237EH

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 237


title: placebo_e; 235JV

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 235


title: placebo_b; 236JK

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 236


title: placebo_e; 236JK

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 236


title: 192 RNA-Seq

description: Strand-specific RNA-seq (dUTP)

source_name: tumor


title: placebo_b; 235JV

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 235


title: 4h_Dex297

source_name: triple-negative breast cancer cell line MDA-MB-231 treated for 4 hours with 100nM dexamethasone + 100nM CORT108297


title: epi_e; 232WD

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 232


title: epi_b; 232WD

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 232


title: epi_e; 231CC

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 231


title: placebo_e; 233GM

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 233


title: placebo_b; 231CC

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 231


title: epi_e; 230FC

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 230


title: epi_b; 235JV

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 235


title: epi_e; 235JV

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 235


title: placebo_b; 232WD

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 232


title: placebo_e; 229TV

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 229


title: placebo_e; 231CC

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 231


title: placebo_e; 232WD

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 232


title: placebo_b; 233GM

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 233


title: epi_e; 233GM

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 233


title: epi_b; 231CC

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 231


title: epi_b; 233GM

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 233


title: epi_e; 229TV

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 229


title: epi_b; 230FC

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 230


title: RNA13_Male_KO_3months

first: Grant

middle: D.

last: Barish

address: 303 E Superior Street

institute: Northwestern University

data_processing:
Alignment:  Sequenced reads were aligned to the mm10 reference mouse genome using STAR
Differenial Expression Analysis: differentially expressed RNAs were identified using DESeq2 (FDR-adjusted p-value <0.01, fold change>±1.5).  STAR alignment and DESeq2 analysis were executed through the RNA Express BaseSpace application (Illumina).
Visualization: bedGraph files were generated from aggregated male and female sequencing data (mice at 3 weeks of age) using HOMER which were viewed on the UCSC genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text (txt) file with differential expression and bed graphs for RNA-seq visualization.

source_name: female ERRg knockout  kidney (3 months) sample 13 mRNA

extract_protocol:
Total RNA from Cre- (control) and Cre+ (ERRg KO) 3-week-old or 3-month old male or female littermate mouse kidneys were purified.  RNA quality was assessed using a Bioanalyzer (Agilent).
TruSeq Stranded mRNA sample prep kit (Illumina).

value: kidney

value: ERRg fl/fl;Sim1-Cre

tag: Sex

value: male

value: 3 months


title: epi_e; 223KH

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 223

value: epicatechin (100mg/d)


title: RNA15_Male_KO_3months

source_name: female ERRg knockout  kidney (3 months) sample 15 mRNA


title: RNA14_Male_KO_3months

source_name: female ERRg knockout  kidney (3 months) sample 14 mRNA


title: epi_b; 229TV

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 229

value: before


title: placebo_b; 223KH

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 223

value: placebo


title: epi_b; 223KH

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 223


title: epi_b; 219SA

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 219


title: epi_e; 228TG

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 228

value: after


title: placebo_e; 228TG

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 228


title: placebo_e; 223KH

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 223


title: placebo_b; 229TV

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 229


title: placebo_b; 216NR

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 216


title: placebo_e; 216NR

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 216


title: epi_b; 228TG

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 228


title: epi_e; 218AK

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 218


title: placebo_b; 218AK

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 218


title: epi_e; 219SA

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 219


title: epi_b; 216NR

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 216


title: placebo_b; 219SA

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 219


title: RNA12_Male_WT_3months

source_name: male wild type kidney (3 months) sample 12 mRNA

value: ERRg fl/fl


title: placebo_e; 218AK

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 218


title: placebo_b; 228TG

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 228


title: epi_b; 218AK

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 218


title: placebo_b; 214TV

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 214


title: placebo_e; 219SA

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 219


title: placebo_e; 214TV

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 214


title: epi_e; 216NR

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 216


title: RNA11_Male_WT_3months

source_name: male wild type kidney (3 months) sample 11 mRNA


title: RNA9_Female_KO_3wks

source_name: female ERRg knockout  kidney (3 weeks) sample 9 mRNA

value: female

value: 3 weeks


title: RNA10_Male_WT_3months

source_name: male wild type kidney (3 months) sample 10 mRNA


title: RNA8_Female_KO_3wks

source_name: female ERRg knockout  kidney (3 weeks) sample 8 mRNA


title: RNA7_Female_WT_3wks

source_name: female wild type kidney (3 weeks) sample 7 mRNA


title: RNA5_Male_KO_3wks

source_name: male ERRg knockout  kidney (3 weeks) sample 5 mRNA


title: RNA6_Female_WT_3wks

source_name: female wild type kidney (3 weeks) sample 6 mRNA


title: RNA3_Male_KO_3wks

source_name: male ERRg knockout  kidney (3 weeks) sample 3 mRNA


title: RNA2_Male_WT_3wks

source_name: male wild type kidney (3 weeks) sample 2 mRNA


title: RNA4_Male_KO_3wks

source_name: male ERRg knockout  kidney (3 weeks) sample 4 mRNA


title: RNA1_Male_WT_3wks

source_name: male wild type kidney (3 weeks) sample 1 mRNA


title: epi_e; 213JJ

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 213


title: Liver_SoyEnrichedDiet [SED_L2_NGS]

city: Timisoara

first: Edward

last: Seclaman

state: Timis

address: Burebista

country: Romania

institute: University Of Medicine and Pharmacy Timisoara

data_processing:
Sequencing reads were processed using Cobra, Biogazelle’s proprietary small RNA sequencing pipeline for read QC, adapter trimming, read mapping and read annotation.
Data were filtered using a cut-off of 4 reads. Reads up to 25 nucleotides were mapped with no mismatches.
Mapped reads were annotated based on miRBase 21.
miRNA expression data were normalized based on the total read count per sample. Read count for each sample was divided by total read count in that sample and multiplied by the total read count across all samples.
Supplementary_files_format_and_content: XLS files containing read counts and miRNA expression

extract_protocol:
RNA was isolated using the miRNeasy Mini Kit (Qiagen). On-column DNase digestion was performed during the RNA extraction.
TruSeq Small RNA Sample kit followed by Illumina single-end sequencing with read length of 75 bp on the NextSeq 500 Sequencing System (Illumina)

tag: strain backgroudn

value: mixed

value: 12 weeks

tag: food type

value: 75% granulated regular food, 25% soy bean powder

value: liver


title: Liver_SoyEnrichedDiet [SED_L3_NGS]


title: Liver_SoyEnrichedDiet [SED_L1_NGS]


title: epi_b; 238GG

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 238


title: epi_e; 214TV

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 214


title: epi_e; 212LT

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 212


title: epi_b; 209JK

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 209


title: epi_e; 208JS

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 208


title: placebo_b; 209JK

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 209


title: placebo_e; 209JK

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 209


title: Liver_RegularDiet [CTR_L2_NGS]

value: 100% granulated regular food


title: Liver_RegularDiet [CTR_L3_NGS]


title: epi_b; 214TV

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 214


title: epi_b; 213JJ

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 213


title: placebo_e; 213JJ

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 213


title: placebo_b; 212LT

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 212


title: Liver_RegularDiet [CTR_L1_NGS]


title: placebo_b; 213JJ

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 213


title: epi_b; 212LT

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 212


title: placebo_e; 212LT

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 212


title: epi_e; 209JK

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 209


title: epi_b; 208JS

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 208


title: 3T3_parental_dTAG47_rep3

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
Processed file sample name: 3T3_parental_dTAG47_rep_2
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt

data_processing:
Fastq files were aligned to mouse genome build mm9 using HiSat with default parameters.
Transcripts were assembled and FPKM values were generated using cuff quant and cuffnorm from the cufflinks pipeline (Trapnell et al., Nat. Biotechnol. 28, 511-515, 2010).
FPKM values were then normalized to synthetic ERCC spike-in RNAs as described previously (Loven et al., Cell 151, 476-482, 2012).
Genome_build: mm9
Supplementary_files_format_and_content: dTAG_parental_control_all_fpkm_exprs_norm.txt: Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript

growth_protocol: NIH/3T3 cells (ATCC, DMEM supplemented with 10% bovine serum, 100 U/mL penicillin, 100 μg/mL streptomycin) cells were cultured at 37 ºC and 5% CO2. Cells that were transduced with lentivirus were additionally cultured with 2 mg/mL puromycin.

extract_protocol:
NIH/3T3 cells were treated in triplicate with DMSO, 1 μM dTAG-13, 1 μM ortho-AP1867, 1 μM AP1867, 1 μM Thalidomide, 500 nM dBET6, and 1 μM dTAG-47 for four hours, lysed, homogenized using Qiashredder columns (Qiagen), and RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. Cell count normalized RNA samples were mixed with the ERCC RNA Spike-In Mix #1 (Life Technologies) prior to library preparation.
Libraries for Illumina sequencing were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) and equimolar multiplexed libraries were sequenced on an Illumina NextSeq 500 (single end 75 bp reads) .

treatment_protocol: Cells were treated with DMSO, 1 μM dTAG-13, 1 μM ortho-AP1867, 1 μM AP1867, 1 μM Thalidomide, 500 nM dBET6, and 1 μM dTAG-47 for four hours.

tag: associated experiment

value: Control-related experiment

tag: stable transduction

value: Untransduced control

tag: culture condition

value: DMEM + 10% Bovine Serum + 1% Pen/Strep

value: 1 μM dTAG-47 for 4 hours


title: 3T3_parental_dTAG47_rep1

description:
Processed file sample name: 3T3_parental_dTAG47_rep_0
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt

tag: cell line


title: 3T3_parental_dTAG47_rep2

description:
Processed file sample name: 3T3_parental_dTAG47_rep_1
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt


title: 3T3_parental_dBET6_rep3

description:
Processed file sample name: 3T3_parental_dBET6_rep_2
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt

value: 0.5 μM dBET6 for 4 hours


title: 3T3_parental_dBET6_rep2

description:
Processed file sample name: 3T3_parental_dBET6_rep_1
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt


title: placebo_b; 206TD

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 206


title: placebo_e; 206TD

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 206


title: 3T3_parental_thalidomide_rep3

description:
Processed file sample name: 3T3_parental_thalidomide_rep_2
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt

value: 1 μM Thalidomide for 4 hours


title: 3T3_parental_thalidomide_rep2

description:
Processed file sample name: 3T3_parental_thalidomide_rep_1
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt


title: 3T3_parental_thalidomide_rep1

description:
Processed file sample name: 3T3_parental_thalidomide_rep_0
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt


title: 3T3_parental_dBET6_rep1

description:
Processed file sample name: 3T3_parental_dBET6_rep_0
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt


title: placebo_e; 204GK

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 204


title: 3T3_parental_AP1867_rep3

description:
Processed file sample name: 3T3_parental_AP1867_rep_2
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt

value: 1 μM AP1867 for 4 hours


title: 3T3_parental_orthoAP1867_rep3

description:
Processed file sample name: 3T3_parental_orthoAP1867_rep_2
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt

value: 1 μM ortho-AP1867 for 4 hours


title: placebo_e; 208JS

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 208

value: placebo

value: after


title: epi_e; 206TD

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 206

value: epicatechin (100mg/d)


title: placebo_b; 208JS

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 208

value: before


title: placebo_b; 204GK

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 204


title: 3T3_parental_AP1867_rep1

description:
Processed file sample name: 3T3_parental_AP1867_rep_0
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt


title: 3T3_parental_orthoAP1867_rep2

description:
Processed file sample name: 3T3_parental_orthoAP1867_rep_1
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt


title: 3T3_parental_orthoAP1867_rep1

description:
Processed file sample name: 3T3_parental_orthoAP1867_rep_0
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt


title: epi_e; 204GK

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 204


title: epi_b; 206TD

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 206


title: epi_e; 203LK

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 203


title: epi_b; 204GK

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 204


title: 3T3_parental_dTAG13_rep3

description:
Processed file sample name: 3T3_parental_dTAG13_rep_2
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt

value: 1 μM dTAG-13 for 4 hours


title: 3T3_parental_dTAG13_rep1

description:
Processed file sample name: 3T3_parental_dTAG13_rep_0
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt


title: 3T3_parental_DMSO_rep3

description:
Processed file sample name: 3T3_parental_DMSO_rep_2
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt

value: DMSO for 4 hours


title: 3T3_parental_AP1867_rep2

description:
Processed file sample name: 3T3_parental_AP1867_rep_1
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt


title: 3T3_parental_DMSO_rep1

description:
Processed file sample name: 3T3_parental_DMSO_rep_0
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt


title: 3T3_parental_dTAG13_rep2

description:
Processed file sample name: 3T3_parental_dTAG13_rep_1
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt


title: 3T3_parental_DMSO_rep2

description:
Processed file sample name: 3T3_parental_DMSO_rep_1
Processed data file: dTAG_parental_control_all_fpkm_exprs_norm.txt


title: 3362-ACP-0012

city: Nashville

first: Nathaniel

last: Hart

state: TN

address: 7465 Medical Research Building IV, 2215 Garland Ave.

institute: Vanderbilt University Medical Center

data_processing:
Following RNA sequencing, raw reads were mapped to reference mouse or human genome as appropriate using TopHat v2.0. Aligned reads were imported onto the Avadis NGS data analysis platform (Strand Scientific Intelligence, Bengalor). Reads were first filtered on their quality metrics, and then duplicate reads were removed. Normalized gene expression was quantified using the TMM (Trimmed Mean of M-values) algorithm. The transcriptional profile from each sample group was compared by principle component analysis (PCA) and hierarchal clustering analysis to determine the layout and spread of the samples. Differential expression between conditions was calculated on the basis of fold change (cutoff ≥ 2.0) and the p-value was estimated by z-score calculations (cutoff 0.05) as determined by the Benjamini Hochberg false discovery rate (FDR) method. Differentially expressed genes underwent gene set enrichment analysis (GSEA), gene ontology (GO) analysis, and pathway analysis using DAVID and Ingenuity Pathway Analysis.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: Excel files include expression values for each Sample

extract_protocol:
RNAqueous Micro-Total RNA Isolation Kit (Ambion/Invitrogen). Trace contaminating DNA was removed with TURBO DNA-free (Ambion/Invitrogen).
Both murine and human islets were handpicked under microscope guidance, washed with PBS, and immediately frozen at -80 ºC. Islet RNA was extracted using the RNAqueous Micro-Total RNA Isolation Kit (Ambion/Invitrogen). Trace contaminating DNA was removed with TURBO DNA-free (Ambion/Invitrogen). RNA quality control quantification was performed using a Qubit Fluorometer (Invitrogen) and an Agilent 2100 Bioanalyzer. All RNA samples had an RNA integrity number (RIN) ≥6.0. RNA was amplified using the NuGEN Technologies Ovation RNA amplification kit optimized for RNA sequencing. Following amplification, the resulting cDNA was sheared to an average insert size of 300bp and used for library preparation. Sequencing was performed using standard Illumina methods.

tag: subject

value: Donor 7

tag: diagnosis

value: Cystic fibrosis

value: Pancreas

value: 42 year old

tag: gender

value: female

tag: cell type

value: Islet of Langerhans


title: 3362-ACP-0013

value: Donor 2

tag: tissue

tag: age

value: 22 year old


title: 3632-ACP-0014

value: Donor 3

value: 34 year old


title: 3632-ACP-0015

value: Donor 4

value: 24 year old

value: male


title: 3362-ACP-0011

value: Donor 1

value: 25 year old


title: 3351-ACP-0036

source_name: Normal

value: Donor 24

value: Normal

value: 50 year old


title: placebo_b; 203LK

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 203

value: placebo

tag: subjectid

tag: before/after supplementation

value: before


title: epi_b; 203LK

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 203

value: epicatechin (100mg/d)


title: Sox9CreErt2:TdTomato collection 1 TdTomato-

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

description: Sorted TdTomato negative cells

data_processing:
Sequence reads were mapped by the Star aligner
Mapped sequence reads were quantified within the Partek Genomics Suite software (http://www.partek.com) to identify differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: text file with statistical analysis

source_name: hind limb

growth_protocol: Double heterozygous mice, carrying one allele of Sox9CreErt2 driver and one allele of Td-Tomato reporter, were generated by crossing heterozygous Sox9CreErt2 (Sox9tm1(cre/ERT2)Haak) with homozygous Td-Tomato (Gt(ROSA)26Sortm14(CAG-tdTomato)Hze) mice.

extract_protocol:
Femoral diaphyses were digested in a liberase solution (100ug/mL in PBS) for 2 hours in a fast shaking rocker at 37 oC, 100 rpm to obtain diaphyseal periosteum cells. Digested cells were filtered and single cell suspensions were subjected to FACS sorting to collect Td-Tomato positive and negative cells. About 10,000 Td-Tomato positive cells and 10,000 Td-Tomato negative control cells were isolated after two collections from 18 femora (9 mice). Total RNA was extracted from each cell population separately with Qiagen RNAasy micro kit with DNaseI digestion according to the manufacturer’s instructions.
Duplicated experimental RNA sequencing libraries were made with a SMARTer Universal Low Input RNA Kit

treatment_protocol: The mice received 3 intraperitoneal injections of 100µL tamoxifen (TM) solution (20 mg/mL diluted in corn oil), at 48-hour intervals. Intact mouse femora were harvested 2 weeks after the last tamoxifen injection and analyzed with RNA sequencing to determine the gene expression profile of periosteal cells of the femur.

value: periosteum

tag: strain

tag: facs

value: TdTomato-


title: Sox9CreErt2:TdTomato collection 1 TdTomato+

description: Sorted TdTomato postive cells

value: TdTomato+


title: Sox9CreErt2:TdTomato collection 2 TdTomato+

description: Sorted TdTomato postive cells


title: 3351-ACP-0017

value: Donor 21

value: Pancreas

value: 26 year old

value: female

tag: treatment

value: Islet of Langerhans


title: placebo_e; 202RK

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 202

value: after


title: epi_b; 202RK

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 202


title: placebo_e; 203LK

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 203


title: epi_e; 202RK

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 202


title: epi_e; 201BB

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, after intervention, subject 201


title: epi_b; 201BB

source_name: Peripheral blood mononuclear cells, epicatechin (100mg/d) treatment, before  intervention, subject 201


title: placebo_e; 201BB

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 201


title: TFAP2C-/- Line 1 5iLAF 5% O2 SSEA4 Minus Reversion 1 [ATAC-Seq]

city: Montreal

first: William

middle: Abraham

last: Pastor

state: QC

address: 3655 Promenade Sir William Osler

department: Biochemistry

institute: McGill University

description:
DNA (open chromatin enriched)
TFAP2C-/- UCLA1 line 1, cultured for five passages (34d) in 5iLAF in 5% O2. TRA-1-85+ cells (human) were then sorted into SSEA4 negative and positive cell populations.

data_processing:
RNA-seq: RNA-seq reads were first aligned to the hg19 or mm9 gene annotation using Tophat, and reads that did not map to the gene annotation were mapped to the genome as a whole. Default parameters were used, except that the --no-coverage-search parameter was used. Readcounts for each gene were calculated using HTseq with default parameters, mapping to the UCSC hg19 (human) or mm9 Ensembl (mouse) annotations.
ATAC-seq: ATAC-seq reads were aligned to hg19 or mm9 using Bowtie with the parameters -X 2000 -m 1 -p 4 -S. All reads aligned to the + strands were offset by +4bp, and all reads aligned to the – strands were offset by -5bp to account for the pattern of primer insertion by the Tn5 transposase. The SAM files were converted to BAM using samtools and duplicated reads were removed with the samtools rmdup function. Processed bigwig files were generated using Deeptools with default settings.
ChIP-seq: ChIP-seq data was mapped using Bowtie2 with default settings and clonal reads were removed using samtools rmdup. Processed bigwig files were generated using Deeptools with default settings.
Genome_build: hg19/GRCh37 (human)
Genome_build: mm9/MGSCv37 (mouse)
Supplementary_files_format_and_content: RNA-seq: *_readsCount.txt: Readcount by gene.
Supplementary_files_format_and_content: ATAC-seq and ChIP-seq: *.bw: bigwig

extract_protocol:
FACS collected cells were spun 500g x 5 minutes at 4°C. Cells were resuspended in 50μL lysis buffer (10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 1x Complete Protease Inhibitor(Roche)) and spun 10 minutes 500g 4°C to collect nuclei. The nuclei were resuspended in 50μL Transposase reaction (25μL 2xTagmentation buffer, 22.5μL water, 2.5μL Tn5 Transposase enzyme) and reacted for 30 minutes at 37°C on a PCR machine. The material was purified using a Qiagen MinElute protocol, eluting with 14μL EB.
The eluted material was amplified in 50μL volume using 1.25μM primer concentration and a 1x concentration NEBNext High-Fidelity Master-Mix (NEB) (Program: 72°C 5:00, 98°C 30s, 5x (98°C 10s, 63°C 30s, 72°C 1 minute), 4°C hold). After these 5 cycles of amplification, the tube was kept on ice. A 5μL aliquot was then removed and used to perform a 15 μL side reaction with identical concentrations of primer and enzyme, except that 0.6x SYBR Green (Invitrogen S-7563) was included to monitor amplification. This side reaction was amplified on a Stratagene Mx3005p qPCR (Agilent) system with the following amplification conditions (98°C 30s, 20x (98°C 10s, 63°C 30s, 72°C 1:00)). The number of additional cycles ‘N’ required to reach ¼ maximum fluorescence was observed. The remaining 45μL of the reaction was then further amplified (98°C 30s, N x (98°C 10s, 63°C 30s, 72°C 1:00), 4°C) and the libraries were purified by a Qiagen MinElute kit eluting with 20 μL volume.

tag: passage number

tag: library type

value: Nextera ATAC-seq


title: placebo_b; 202RK

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 202


title: Control Line 1 5iLAF 5% O2 SSEA4 Plus Reversion 1 [ATAC-Seq]

description:
DNA (open chromatin enriched)
Control nucleofected UCLA1 line cultured for five passages (34d) in 5iLAF in 5% O2. TRA-1-85+ cells (human) were then sorted into SSEA4 negative and positive cell populations.


title: placebo_b; 201BB

source_name: Peripheral blood mononuclear cells, placebo treatment, before  intervention, subject 201


title: 3351-ACP-0027

value: Donor 23

value: 35 year old


title: Control Line 1 5iLAF 5% O2 SSEA4 Minus Reversion 1 [ATAC-Seq]

source_name: Control nucleofected UCLA1 line cultured for five passages (34d) in 5iLAF in 5% O2. TRA-1-85+ cells (human) were then sorted into SSEA4 negative and positive cell populations.


title: Primed Control for 5% O2 samples Reversion 1 [ATAC-Seq]

description:
DNA (open chromatin enriched)
Primed SSEA4+ UCLA1 hESCs

source_name: Primed SSEA4+ UCLA1 hESCs


title: 3351-ACP-0020

value: Donor 22

value: Normal

value: 55 year old

value: male


title: 3351-ACP-0005

value: Donor 17

value: 24 year old


title: TFAP2C-/- Line 2 5iLAF 5% O2 SSEA4 Plus Reversion 1 [ATAC-Seq]

source_name: TFAP2C-/- UCLA1 line 1, cultured for five passages (34d) in 5iLAF in 5% O2. TRA-1-85+ cells (human) were then sorted into SSEA4 negative and positive cell populations.


title: TFAP2C-/- Dox withdrawn 5iLAF SSEA4 Plus [ATAC-Seq]

description:
DNA (open chromatin enriched)
TFAP2C-/- UCLA1 hESCs transduced with a construct that allows doxycycline inducible expression of TFAP2C. These cells were treated for 15 days with 5iLAF media and 0.25μg/mL doxycycline, then 12 days with 5iLAF media only. Cells were then harvested and  TRA-1-85+ (human) cells were subsorted into SSEA4 positive and negative populations

source_name: TFAP2C-/- UCLA1 hESCs transduced with construct allowing dox inducible expression of TFAP2C; cells treated 15d with 5iLAF media & 0.25μg/mL dox, then 12d with 5iLAF media only; cells harvested and TRA-1-85+ cells subsorted into SSEA4 + and - populations


title: TFAP2C-/- Dox withdrawn 5iLAF SSEA4 Minus [ATAC-Seq]


title: TFAP2C-/- Dox Induc 5iLAF SSEA4 Minus [ATAC-Seq]

description:
DNA (open chromatin enriched)
TFAP2C-/- UCLA1 hESCs transduced with a construct that allows doxycycline inducible expression of TFAP2C. These cells were treated for five passages (27 days) with 5iLAF media and 0.25μg/mL doxycycline, then TRA-1-85+ (human) cells were subsorted into SSEA4 positive and negative populations

source_name: TFAP2C-/- UCLA1 hESCs transduced with construct allowing doxycycline inducible expression of TFAP2C; cells treated for 5 passages (27 days) with 5iLAF media and 0.25μg/mL doxycycline, then TRA-1-85+ (human) cells subsorted into SSEA4 + and - populations

value: TFAP2C-/- Dox Induc 5iLAF SSEA4 Minus


title: Primed Control for Withdrawal Experiment [ATAC-Seq]


title: L363-ELL2-knockout cells_Empty 4

city: Lund

first: Björn

last: Nilsson

address: BMC

department: Hematology and Transfusion Medicine

country: Sweden

institute: Lund University

data_processing:
Sequence alignment to hg38 genome assembly uing TopHat v2.1.1 and Bowtie 2.2.6.0
Estimation of gene expresion values uing CuffLinks 2.2.1
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text with gene expression values (FPKM)

extract_protocol:
Cultured cells were harvested and total RNA was prepared using Rneasy mini kit from QIAGEN
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Blood

tag: disease state

value: Multiple Myeloma

value: Empty


title: L363-ELL2-knockout cells_Empty 6


title: L363-ELL2-knockout cells_Empty 5


title: L363-ELL2-knockout cells_Empty 3


title: Untransfected cells, 5d 5iLAF treatment ATAC [ATAC-Seq]

data_processing:
ATAC-seq: ATAC-seq reads were aligned to hg19 or mm9 using Bowtie with the parameters -X 2000 -m 1 -p 4 -S. All reads aligned to the + strands were offset by +4bp, and all reads aligned to the – strands were offset by -5bp to account for the pattern of primer insertion by the Tn5 transposase. The SAM files were converted to BAM using samtools and duplicated reads were removed with the samtools rmdup function. Processed bigwig files were generated using Deeptools with default settings.
Genome_build: hg19 (human); mm9 (mouse)

source_name: Untransfected UCLA1 hESCs cultured for 5 days in 5iLAF


title: TFAP2C-/- Line 2 5d 5iLAF treatment ATAC [ATAC-Seq]

source_name: TFAP2C knockout line 2 UCLA hESCs cultured for 5 days


title: TFAP2C-/- Line 1 5d 5iLAF treatment ATAC [ATAC-Seq]

source_name: TFAP2C knockout line 1 UCLA hESCs cultured for 5 days


title: Control transfected cells, 5d 5iLAF treatment ATAC [ATAC-Seq]

source_name: Control transfected UCLA1 hESCs cultured for 5 days in 5iLAF


title: L363-ELL2-knockout cells_Empty 2


title: Naïve hESCs Replicate 3 ATAC [ATAC-Seq]

source_name: SSEA4- 5iLAF cultured UCLA1 hESCs

value: SSEA4- 5iLAF cultured UCLA1 hESCs


title: Eight Blastocysts ATAC [ATAC-Seq]

source_name: Eight day

extract_protocol:
Embryos were resuspended in 50μL lysis buffer (10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 1x Complete Protease Inhibitor(Roche)) and incubated for ten minutes, during which they were vortexed in 10s bursts every three to four minutes, then spun 10 minutes 500g 4°C to collect nuclei. The nuclei were resuspended in 50μL Transposase reaction (25μL 2xTagmentation buffer, 22.5μL water, 2.5μL Tn5 Transposase enzyme) and reacted for 30 minutes at 37°C on a PCR machine. The material was purified using a Qiagen MinElute protocol, eluting with 14μL EB.
The eluted material was amplified in 50μL volume using 1.25μM primer concentration and a 1x concentration NEBNext High-Fidelity Master-Mix (NEB) (Program: 72°C 5:00, 98°C 30s, 5x (98°C 10s, 63°C 30s, 72°C 1 minute), 4°C hold). After these 5 cycles of amplification, the tube was kept on ice. A 5μL aliquot was then removed and used to perform a 15 μL side reaction with identical concentrations of primer and enzyme, except that 0.6x SYBR Green (Invitrogen S-7563) was included to monitor amplification. This side reaction was amplified on a Stratagene Mx3005p qPCR (Agilent) system with the following amplification conditions (98°C 30s, 20x (98°C 10s, 63°C 30s, 72°C 1:00)). The number of additional cycles ‘N’ required to reach ¼ maximum fluorescence was observed. The remaining 45μL of the reaction was then further amplified (98°C 30s, N x (98°C 10s, 63°C 30s, 72°C 1:00), 4°C) and the libraries were purified by a Qiagen MinElute kit eluting with 20 μL volume.

value: Eight day


title: Naïve hESCs Replicate 4 ATAC [ATAC-Seq]


title: Naïve hESCs Replicate 2 ATAC [ATAC-Seq]


title: TFAP2C-/- Dox Induc 5iLAF SSEA4 Plus [ATAC-Seq]

value: TFAP2C-/- Dox Induc 5iLAF SSEA4 Plus


title: Control Line 1 5iLAF SSEA4 Minus [ATAC-Seq]

description:
DNA (open chromatin enriched)
Control nucleofected UCLA1 line cultured for five passages (27d) in LAF. Tra-1-85 positive (human) cells were sorted into positive and negative populations

value: Control Line 1 5iLAF SSEA4 Minus


title: Naïve hESCs Replicate 1 ATAC [ATAC-Seq]

value: Nextera ATAC-seq


title: Control Line 1 5iLAF SSEA4 Plus [ATAC-Seq]

source_name: Control nucleofected UCLA1 line cultured for five passages (27d) in LAF. Tra-1-85 positive (human) cells were sorted into positive and negative populations

value: Control Line 1 5iLAF SSEA4 Plus


title: L363-ELL2-knockout cells_ELL2 rescue 4


title: L363-ELL2-knockout cells_ELL2 rescue 5


title: L363-ELL2-knockout cells_Empty 8


title: L363-ELL2-knockout cells_Empty 7


title: Primed hESCs Replicate 4 ATAC [ATAC-Seq]

value: Primed SSEA4+ UCLA1 hESCs


title: L363-ELL2-knockout cells_ELL2 rescue 3


title: Primed hESCs Replicate 3 ATAC [ATAC-Seq]


title: L363-ELL2-knockout cells_ELL2 rescue 2


title: L363-ELL2-knockout cells_ELL2 rescue 1


title: Primed hESCs Replicate 2 ATAC [ATAC-Seq]


title: PACEIIW

tag: genotype

value: ELL2 knock-out

value: Multiple Myelom


title: Primed hESCs Replicate 1 ATAC [ATAC-Seq]


title: L363-ELL2-knockout cells_Empty 1


title: L363-ELL2-knockout cells_ELL2 rescue 7


title: PACEIIU


title: PACEIIT

value: wildtype


title: PACEIIS


title: PACEIIQ


title: (Cre-)_inp_3

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

description:
input RNA
Complete_genelist_wtPD_vs_input.csv

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to mm10 using STAR2.4.0
Count read using HT-seq0.6.1 using mm10 RefSeq as reference
Normalization (TMM), and differential expression analysis using EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: csv file with statistical analysis, normalized count and  raw read counts

growth_protocol: Dorsal root ganglion neurons (all ganglia) from adult male mice were isolated using density purification on a 20% Percoll cushion to  separate neurons from myelin debris and contaminating glial cells.  Neurons were grown in 12-well dishes coated with poly-L-lysine (P4832, Sigma) and laminin (5 µg/mL), in F12 medium supplemented with 10% fetal bovine serum and Primocin (Invivogen). Neurons from one mouse were seeded on 4 wells, five mice per genotype were used to generate one sample.  After 24h cells were washed with PBS and snap-frozen in liquid nitrogen.

extract_protocol:
Ribosome-associated RNA was immunoprecipitated using 5 µg of rat anti-HA antibody (clone 12CA5, Roche) per sample and purified using  RNeasy Micro kit (Qiagen). On-column DNA digestion was performed using the RNase-Free Dnase Set (Qiagen). Integrity of the isolated RNA was analyzed using a 2100 Bioanalyzer (Agilent, RNA Pico chip).
Nugen Ovation RNA Ultra Low Input (500 pg) +Kapa Hyper kit

value: 3-6 months

tag: Sex

value: male

value: Rpl22HA/HA Runx3-Cre-

tag: rna sample type

value: pre-immunoprecipitation input


title: (Cre-)_inp_2

source_name: Dorsal root ganglion neurons (all ganglia)


title: (Cre-)_PD_2

description:
Immunoprecipitated RNAs
Complete_genelist_wtPD_vs_input.csv

value: Dorsal root ganglion neurons (all ganglia)

value: HA immunoprecipitation


title: (Cre-)_PD_1


title: Runx3_PD_1

description:
Immunoprecipitated RNAs
Complete_genelist_CrePD_vs_input.csv

value: Rpl22HA/HA Runx3-Cre+


title: Runx3_PD_3


title: Runx3_inp_2

description:
input RNA
Complete_genelist_CrePD_vs_input.csv


title: TFAP2A-/- TFAP2C-/- Line 2 2i+LIF Replicate 3 RNA [RNA-Seq]

description: RNA (polyA enriched)

data_processing:
RNA-seq: RNA-seq reads were first aligned to the mm9 or hg19 gene annotation using Tophat, and reads that did not map to the gene annotation were mapped to the genome as a whole. Default parameters were used, except that the --no-coverage-search parameter was used. Readcounts for each gene were calculated using HTseq with default parameters, mapping to the UCSC hg19 (human) or mm9 Ensembl (mouse) annotations.
Genome_build: hg19 (human); mm9 (mouse)

source_name: TFAP2A/2C doubly deficient mESCs cultured for eight passages in 2i+LIF

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and quantified using the Qubit RNA HS Assay kit (Thermo Scientific)
5ng to 50ng total RNA input was used to generate sequencing libraries using the Ovation Ultralow Library System V2 (Nugen) and then Ovation Rapid Library System (Nugen) protocols.

value: Ovation RNASeq System V2


title: Runx3_inp_3


title: Male pravastatin treatment, biological replicate 3.

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

data_processing:
Reads were aligned to the GRCm38 genome using Tophat v 2.1.1 (default parameters)
Gene expression values were quantified using HTSeq with the union method
Differential expression was performed for genes with >1 CPM in at least 3 samples
Genome_build: GRCm38
Supplementary_files_format_and_content: Xlsx file contains results for all genes from three differential expression analyses: male pravastatin vs male vehicle, female pravastatin vs female vehicle, and all (male+female) pravastatin vs all (male+female) vehicle

source_name: cerebral cortical neurosphere culture

growth_protocol: Cortex dissected from embryonic day 14.5 fetal mouse brain were dissociated into single cells and then cultured as neurospheres

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions
The Ilumina Stranded Total RNA-Seq Kit was used to construct the library according to the manufacturer's instructions

treatment_protocol: Neurospheres at third passage were treated with 10 uM pravastatin or equivalent volumes of vehicle for 24 hours

value: embryonic day E14.5

value: Male

value: Pravastatin

value: brain

tag: brain region

value: Cortex


title: Serial Control Transfection Line 1 2i+LIF Replicate 3 RNA [RNA-Seq]

description: RNA (polyA enriched)

source_name: Control transfected (twice) V6.5 mESCs cultured for eight passages in 2i+LIF media


title: Runx3_inp_1


title: L363-ELL2-knockout cells_ELL2 rescue 6

value: Blood

value: Multiple Myeloma

tag: cell line


title: Runx3_PD_2


title: (Cre-)_inp_1


title: TFAP2A-/- TFAP2C-/- Line 1 2i+LIF Replicate 3 RNA [RNA-Seq]

description: RNA (polyA enriched)

value: TFAP2A/2C doubly deficient mESCs cultured for eight passages in 2i+LIF


title: Serial Control Transfection Line 2 2i+LIF Replicate 3 RNA [RNA-Seq]

description: RNA (polyA enriched)

value: Control transfected (twice) V6.5 mESCs cultured for eight passages in 2i+LIF media


title: TFAP2A-/- TFAP2C-/- Line 2 2i+LIF Replicate 2 RNA [RNA-Seq]

description: RNA (polyA enriched)

source_name: TFAP2A/2C doubly deficient mESCs cultured for seven passages in 2i+LIF


title: PACEIIP

value: wildtype

value: Multiple Myelom


title: TFAP2A-/- TFAP2C-/- Line 1 2i+LIF Replicate 2 RNA [RNA-Seq]

description: RNA (polyA enriched)

value: TFAP2A/2C doubly deficient mESCs cultured for seven passages in 2i+LIF


title: (Cre-)_PD_3

value: 3-6 months

value: male

value: Rpl22HA/HA Runx3-Cre-


title: Serial Control Transfection Line 2 2i+LIF Replicate 2 RNA [RNA-Seq]

description: RNA (polyA enriched)

source_name: Control transfected (twice) V6.5 mESCs cultured for seven passages in 2i+LIF media