title: 11C_TP5C_074031_Cycle2

city: Singapore

first: Frances Maureen

middle: Casica

last: Rocamora

state: Singapore

address: 60 Nanyang Drive Nanyang Technological University

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Hybridizations were performed for 20 hours at 65°C in a rotating hybridization oven at 10rpm.

scan_protocol: Microarray scanning was done using PowerScanner (Tecan, Austria) at 10uM resolution and with autogain PMT adjustments for both channels. Data was acquired using GenePix Pro v6.0 software (Axon Instruments, USA) as described in Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391.

data_processing: Features with flag>0 and with median foreground intensity greater than 1.5 fold median background intensity for either channel were accepted. Log2 ratios were background corrected using a normexp method, followed by loess normalization within arrays, and subsequently with quantile normalization between arrays. Post processing was performed using the Linear Models for Microarray (LIMMA) package for R.

organism: Plasmodium falciparum

source_name: P. falciparum, 11C clone, 18 HPI

label_protocol: Equal amounts of sample cDNA and reference cDNA generated from a 3D7 reference strain were labelled with Cy5 and Cy3, respectively, for 4 hours. Labelled products were subsequently purified and hybridized on the microarray chip using the Agilent hybridization system.

growth_protocol: Synchronized P. falciparum parasites were grown at 1% parasitemia, 2% hematocrit, and synchronized using 5% sorbitol treatment at 4 HPI

extract_protocol: Total RNA was extracted from tightly synchronized parasite cultures using TRIZol-Chloroform method as  previously described in detail in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

treatment_protocol: Parasites were grown in vitro in the absence of any drug treatment

tag: sample type

value: In vitro culture (derived fromn 3D7 strain) harvested at 18 hours post invasion during the parasite's intraerythrocytic life cycle

source_name: P. falciparum 3D7 RNA reference pool

value: In vitro culture, asexual blood stage, laboratory strain 3D7, mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle


title: D1F7A61E

status: Public on Mar 22 2018

type: genomic

city: Paris

first: Nathalie

last: Clément

address: 26 rue d'Ulm

country: France

institute: Institut Curie

hyb_protocol: For each sample, 700 ng of tumor and normal DNA were labeled and co-hybridized to the NimbleGen arrays according to the manufacturer’s protocol.  After ethanol-coprecipitation with 210µg of Human Cot-1 DNA (Invitrogen, Cergy (Invitrogen, Cergy Pontoise, France), resuspension in hybridization buffer (50% formamide), denaturation at 95°C for 10 minutes and pre-hybridization at 37°C for 90 minutes, probes were cohybridized on aCGH. The aCGH slide was previously preblocked with a buffer containing 2.6mg succinic anhydride/118ml N-methyl-2-pyrrolidinone/32ml sodium tetraborate decahydrate, pH 8.0 for BAC array.       .

scan_protocol: Arrays were washed and then scanned on a GenePix 4000B scanner using GenePix 6.0 Software for Nimblegen array.  The aCGH developed in the laboratory contains 3342 sequence-validated BACs including 340 localized on 1p and 29 on 19q. After washing, arrays were scanned using a 4000B scan.

data_processing:
Raw data in .pair file format were normalized and processed using the NimbleScan v2.5 Software (Roche NimbleGen) to obtain data with a resolution of 100 kb. The data were then visualized with SignalMap v1.9 (Roche NimbleGen) before analysis. For .gpr files, image analysis was performed with Genepix 5.1 software (Axon) and ratios of Cy5/Cy3 signals were determined for BAC array.
The data included in the processed data files (.txt files) are: normalized log2 ratio (Cy5/Cy3) representing test/reference. The Log2 ratio values can also be found in the .gpr files in the column "Log Ratio (635/532). The  "RATIO_CORRECTED" column in the processed data for the Nimblegen arrays is identical to the "RATIO_CORRECTED" column in the *raw.txt files.

molecule: genomic DNA

organism: Homo sapiens

source_name: tumor DNA

label_protocol: For each sample, 700 ng of tumor and normal DNA  (from normal tissue from healthy donor) were labeled and co-hybridized to the NimbleGen arrays according to the manufacturer’s protocol. Tumor DNAs were labeled by the random priming method with cyanine-5 and using the same procedure, we labeled control DNAs (from control tissue from healthy donor)with cyanine-3  for homemade bacterial artificial chromosome (BAC)-arrays.

extract_protocol: Total DNA extracted using Trizol following manufacturer's instructions

tag: tissue

value: Neuroblastoma

tag: tumor inss stage

tag: tumor inrg stage

tag: gender (1=male; 2=female)

tag: mycn status (0=non amplified, 1= amplified)

tag: age (days) at diagnosis

tag: relapse/progression (0=no, 1= yes)

tag: time from diagnosis to event or last follow up (days)

tag: patient status (0=alive, 1= dead)

tag: time from diagnosis to death or last follow up (days)

source_name: Normal reference DNA

tag: control type

value: normal tissue (blood) from healthy donor


title: 90B89789


title: 11C-R_TP4C_074045_Cycle2

type: RNA

molecule: total RNA

source_name: P. falciparum, 11C-R clone, 16 HPI

value: In vitro culture (derived fromn 3D7 strain) harvested at 16 hours post invasion during the parasite's intraerythrocytic life cycle


title: 11C_TP6C_074053_Cycle2

source_name: P. falciparum, 11C clone, 20 HPI

value: In vitro culture (derived fromn 3D7 strain) harvested at 20 hours post invasion during the parasite's intraerythrocytic life cycle


title: 11C_TP4C_074054_Cycle2

source_name: P. falciparum, 11C clone, 16 HPI


title: 11C_TP0_074028_Cycle1

source_name: P. falciparum, 11C clone, 10 HPI

value: In vitro culture (derived fromn 3D7 strain) harvested at 10 hours post invasion during the parasite's intraerythrocytic life cycle


title: 7243F659


title: 11C-R_TP5C_074047_Cycle2

source_name: P. falciparum, 11C-R clone, 18 HPI


title: 11C-R_TP6C_074033_Cycle2

source_name: P. falciparum, 11C-R clone, 20 HPI


title: 11C-R_TP0_074028_Cycle2

source_name: P. falciparum, 11C-R clone, 10 HPI


title: 149948C3


title: 1BB1B1D3


title: 3E5EE0D3


title: FEF0A7D7


title: ED040B53


title: 6A_TP4C_074026_Cycle2

source_name: P. falciparum, 6A clone, 16 HPI


title: 6A_TP6C_074046_Cycle2

source_name: P. falciparum, 6A clone, 20 HPI


title: 6A-R_TP6C_074049_Cycle2

source_name: P. falciparum, 6A-R clone, 20 HPI


title: 6A-R_TP5C_074051_Cycle2

source_name: P. falciparum, 6A-R clone, 18 HPI


title: F1

type: SRA

city: Los Angeles

first: Samuel

middle: A

last: Sances

state: CA

address: 8500 Beverly Blvd

department: Regenerative Medicine Institute

country: USA

institute: Cedars Sinai

library_source: transcriptomic

data_processing:
RNAseq libraries were generated using Illumina TruSeq Kit, sequenced on Nextseq500 by 75bp single readsand aligned to hg19 using Tophat2 25 million
Rseqtools was used to quntify UCSC annotated transcripts to RPKM.
Duplicate genes were filtered out by eliminating the low expressed transcript in each sample. (gmax)
Genome_build: hg19

source_name: ipsc-derived motor neuron

growth_protocol: Day 12 spMN progenitors were cultured for 6 days in each condition.

extract_protocol:
Cells were dissociated, pelleted and extracted using magNA Pure
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: Day 12 spMN progenitors

value: spinal motor neuron


title: E3

value: Chip + BMEC


title: F2


title: 6A_TP0_074027_Cycle1

source_name: P. falciparum, 6A clone, 10 HPI


title: F3


title: 6A-R_TP0_074027_Cycle2

source_name: P. falciparum, 6A-R clone, 10 HPI


title: 6A-R_TP4C_074050_Cycle2

source_name: P. falciparum, 6A-R clone, 16 HPI

source_name: P. falciparum 3D7 RNA reference pool


title: E2


title: 082011_Cycle2_11C_TP3

source_name: P. falciparum, 11C clone, sampling interval 3

label_protocol: Equal amounts (4 µg) of sample cDNA and reference cDNA generated from a 3D7 reference strain were labelled with Cy5 and Cy3, respectively, for 4 hours. Labelled products were subsequently purified and hybridized on the microarray chip using the Agilent hybridization system.

growth_protocol: Synchronized P. falciparum parasites were grown at 5% parastemia, 1% hematocrit. Prior to harvesting the first sampling interval, all parasite lines were tighty synchronized 5 times over 2 generations using treatment with 5% sorbitol.

value: In vitro culture (derived from 3D7 strain) harvested at 20 HPI during the parasite's intraerythrocytic life cycle


title: 082008_Cycle2_11C_TP1

source_name: P. falciparum, 11C clone, sampling interval 1

value: In vitro culture (derived from 3D7 strain) harvested at 4 HPI during the parasite's intraerythrocytic life cycle


title: E1


title: 082029_Cycle2_11C_TP5

source_name: P. falciparum, 11C clone, sampling interval 5

value: In vitro culture (derived from 3D7 strain) harvested at 36 HPI during the parasite's intraerythrocytic life cycle


title: 081006_Cycle2_11C_TP6

source_name: P. falciparum, 11C clone, sampling interval 6

value: In vitro culture (derived from 3D7 strain) harvested at 44 HPI during the parasite's intraerythrocytic life cycle


title: 082017_Cycle2_11C_TP4

source_name: P. falciparum, 11C clone, sampling interval 4

value: In vitro culture (derived from 3D7 strain) harvested at 28 HPI during the parasite's intraerythrocytic life cycle


title: 082029_Cycle1_11C-R_TP5

source_name: P. falciparum, 11C-R clone, sampling interval 5


title: 6A_TP5C_074029_Cycle2

source_name: P. falciparum, 6A clone, 18 HPI


title: 082009_Cycle1_11C-R_TP2

source_name: P. falciparum, 11C-R clone, sampling interval 2

value: In vitro culture (derived from 3D7 strain) harvested at 12 HPI during the parasite's intraerythrocytic life cycle


title: 082009_Cycle2_11C_TP2

source_name: P. falciparum, 11C clone, sampling interval 2


title: 081003_Cycle2_11C-R_TP6

source_name: P. falciparum, 11C-R clone, sampling interval 6


title: 082017_Cycle1_11C-R_TP4

source_name: P. falciparum, 11C-R clone, sampling interval 4


title: 082008_Cycle1_11C-R_TP1

source_name: P. falciparum, 11C-R clone, sampling interval 1


title: D3

source_name: ipsc-derived motor neuron

value: Chip


title: 082011_Cycle1_11C-R_TP3

source_name: P. falciparum, 11C-R clone, sampling interval 3


title: 081006_Cycle1_6A_TP6

source_name: P. falciparum, 6A clone, sampling interval 6


title: D2


title: 082016_Cycle2_6A_TP5

source_name: P. falciparum, 6A clone, sampling interval 5


title: C2

value: 96-well plate + conditioned media


title: C3


title: C1


title: D1


title: 081003_Cycle1_6A-R_TP6

source_name: P. falciparum, 6A-R clone, sampling interval 6

source_name: P. falciparum 3D7 RNA reference pool

value: In vitro culture, asexual blood stage, laboratory strain 3D7, mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle


title: 081008_Cycle2_6A_TP2

source_name: P. falciparum, 6A clone, sampling interval 2


title: SI_conventional_FOS_rep4

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

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

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.38.0).

label: biotin

organism: Mus musculus

source_name: terminal ileum from conventional-raised mouse, short-chain β2→1-fructan

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Specified pathogen-free (SPF) conventional C57BL/6OlaHsd males of 8 weeks old were purchased from a commercial supplier (Envigo, Horst, The Netherlands) and C57BL/6OlaHsd male 8-week-old germ-free mice were obtained from a breeding colony at the animal facility of the Radboud University (Nijmegen, The Netherlands). Samples derived from germ-free mice were routinely screened once every two weeks on sterility. In addition, samples from germ-free mice the day before the end of the experiment were tested on sterility. All samples were screened on sterility by QM diagnostics (Nijmegen, The Netherlands) and confirmed to be sterile. At least 2 weeks before the start of β2→1-fructans treatment, all animals were receiving a D12450B diet (10% fat, Research Diet Services, Wijk bij Duurstede, The Netherlands). The mice were kept on this diet throughout the experiment. All experiments were approved by the animal ethics committee of the University of Groningen (Dierenexperimentencommissie Rijksuniversiteit Groningen, DEC-RUG).

extract_protocol: Total RNA was purified using TRIzol (Life Technologies, Calsbad, CA, USA) followed by an additional round of purification with RNeasy Microkit columns (Qiagen, Venlo, The Netherlands). RNA quality was assessed using RNA 6000 nanochips on the Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands). RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Fructans were dissolved in sterile water and given to the conventional mice by oral gavage. In addition, to ensure sterility of these solutions before administration to germ-free mice, short-chain β2→1-fructans were filtered with a 0.2 micron filter and long-chain β2→1-fructans were irradiated with 25 kGy (Synergy Health, Ede, The Netherlands), as it was too viscous for sterilization by filtration. Irradiation induced some degradation of higher DP oligomers, but still significant amounts of oligomers up to DP30 were present. Sterility of the fructans after filtration or irradiation was tested by QM diagnostics (Nijmegen, The Netherlands) and confirmed to be sterile. Mice received 10 mg of these fibers or water only as a negative control by oral gavage once a day for 5 days in a row. At the end of the experiment, mice were anesthetized and a part of the terminal ileum from each mouse was snap frozen in liquid nitrogen and stored at -80 °C.

tag: strain/background

tag: Sex

value: male

tag: mouse type

value: conventional

value: terminal ileum

value: oligofructose treatment (FOS)


title: SI_germ-free_IN_rep2

source_name: terminal ileum from germ free-raised mouse, long-chain β2→1-fructan

value: germ-free

value: inulin treatment (IN)


title: 082015_Cycle2_6A_TP4

source_name: P. falciparum, 6A clone, sampling interval 4


title: 081004_Cycle2_6A_TP3

source_name: P. falciparum, 6A clone, sampling interval 3


title: 081007_Cycle2_6A_TP1

source_name: P. falciparum, 6A clone, sampling interval 1


title: B2

value: 96-well plate + neural media

value: spinal motor neuron


title: B1


title: SI_germ-free_water_rep1

source_name: terminal ileum from germ free-raised mouse, control treatment

value: control treatment (vehicle [water])


title: B3


title: SI_germ-free_water_rep4


title: 081004_Cycle1_6A-R_TP3

source_name: P. falciparum, 6A-R clone, sampling interval 3

value: In vitro culture (derived from 3D7 strain) harvested at 20 HPI during the parasite's intraerythrocytic life cycle


title: SI_germ-free_IN_rep4


title: SI_germ-free_water_rep3


title: SI_conventional_FOS_rep3


title: SI_conventional_IN_rep4

source_name: terminal ileum from conventional-raised mouse, long-chain β2→1-fructan


title: 082015_Cycle1_6A-R_TP4

source_name: P. falciparum, 6A-R clone, sampling interval 4


title: SI_germ-free_IN_rep1


title: 081008_Cycle1_6A-R_TP2

source_name: P. falciparum, 6A-R clone, sampling interval 2


title: 082016_Cycle1_6A-R_TP5

source_name: P. falciparum, 6A-R clone, sampling interval 5

value: In vitro culture (derived from 3D7 strain) harvested at 36 HPI during the parasite's intraerythrocytic life cycle


title: SI_conventional_FOS_rep2


title: SI_conventional_water_rep3

source_name: terminal ileum from conventional-raised mouse, control treatment


title: SI_conventional_IN_rep3


title: SI_germ-free_FOS_rep4

source_name: terminal ileum from germ free-raised mouse, short-chain β2→1-fructan


title: SI_conventional_water_rep4


title: 081007_Cycle1_6A-R_TP1

source_name: P. falciparum, 6A-R clone, sampling interval 1

value: In vitro culture (derived from 3D7 strain) harvested at 4 HPI during the parasite's intraerythrocytic life cycle


title: SI_germ-free_IN_rep3


title: SI_germ-free_FOS_rep2


title: SI_conventional_water_rep2


title: SI_germ-free_water_rep2


title: SI_conventional_FOS_rep1


title: SI_germ-free_FOS_rep3


title: SI_germ-free_FOS_rep1


title: SI_conventional_IN_rep2


title: 11C_TP3C_074036_Cycle2

source_name: P. falciparum, 11C clone, exposed to DMSO (control) for 4hrs

extract_protocol: Total RNA was extracted from parasite cultures using TRIZol-Chloroform method as  previously described in detail in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

treatment_protocol: Synchronized parasites were exposed to 900 nM ART for 4 hrs, starting from 10 HPI

value: In vitro culture (derived fromn 3D7 strain), harvested after 4hrs of exposure to DMSO (initiated at 10 HPI)


title: 11C_TP1C_074048_Cycle2

source_name: P. falciparum, 11C clone, exposed to DMSO (control) for 1hr

value: In vitro culture (derived fromn 3D7 strain), harvested after 1hr of exposure to DMSO (initiated at 10 HPI)

source_name: P. falciparum 3D7 RNA reference pool


title: 11C_TP2C_074043_Cycle2

source_name: P. falciparum, 11C clone, exposed to DMSO (control) for 2hrs

value: In vitro culture (derived fromn 3D7 strain), harvested after 2hrs of exposure to DMSO (initiated at 10 HPI)


title: SI_conventional_IN_rep1


title: 11C-R_TP1ART_074024_Cycle2

source_name: P. falciparum, 11C-R clone, exposed to 900 nM ART for 1hr

value: In vitro culture (derived fromn 3D7 strain), harvested after 1hr of exposure to 900 nM ART (initiated at 10 HPI)


title: 11C_TP2ART_074043_Cycle1

source_name: P. falciparum, 11C clone, exposed to 900 nM ART for 2hrs

value: In vitro culture (derived fromn 3D7 strain), harvested after 2hrs of exposure to 900 nM ART (initiated at 10 HPI)

value: In vitro culture, asexual blood stage, laboratory strain 3D7, mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle


title: SI_conventional_water_rep1

value: male

value: conventional


title: 11C_TP3ART_074036_Cycle1

source_name: P. falciparum, 11C clone, exposed to 900 nM ART for 4hrs

value: In vitro culture (derived fromn 3D7 strain), harvested after 4hrs of exposure to 900 nM ART (initiated at 10 HPI)


title: 11C_TP1ART_074048_Cycle1

source_name: P. falciparum, 11C clone, exposed to 900 nM ART for 1hr


title: shDYRK1A VEGF 1h CsA, replicate 1

city: Barcelona

first: Chiara

last: Di Vona

state: Spain

address: Carrer Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: CRG

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).   Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: shDYRK1A VEGF 1h CsA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit - Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human umbilical vein endothelial cells (HUVEC) were grown in EGM-2 BulletKit complete Medium (Lonza). Cells were maintained at 37 °C under 5% CO2.

extract_protocol: Total RNA was isolated with the RNeasy extraction Kit (Qiagen), and then treated with DNase I, according to the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Cells were kept in basal EBM-2 medium (Lonza) supplemented with 0.5% FCS for 6 h before VEGF-A stimulation; CsA was added for 30 min before treatment and maintained during stimulation.

value: VEGF 1h + CsA

tag: cell type

value: HUVEC

tag: condition


title: 11C-R_TP1C_074024_Cycle1

source_name: P. falciparum, 11C-R clone, exposed to DMSO (control) for 1hr

tag: sample type


title: shDYRK1A VEGF 1h, replicate 2

source_name: shDYRK1A VEGF 1h

value: VEGF 1h


title: 11C-R_TP2ART_074037_Cycle2

source_name: P. falciparum, 11C-R clone, exposed to 900 nM ART for 2hrs


title: shDYRK1A VEGF 1h CsA, replicate 3


title: shDYRK1A VEGF 1h, replicate 3


title: 11C-R_TP3ART_074044_Cycle2

source_name: P. falciparum, 11C-R clone, exposed to 900 nM ART for 4hrs


title: 6A_TP3C_074032_Cycle2

source_name: P. falciparum, 6A clone, exposed to DMSO (control) for 4hrs


title: 11C-R_TP2C_074037_Cycle1

source_name: P. falciparum, 11C-R clone, exposed to DMSO (control) for 2hrs


title: 11C-R_TP3C_074044_Cycle1

source_name: P. falciparum, 11C-R clone, exposed to DMSO (control) for 4hrs


title: shControl VEGF 1h CsA, replicate 3

source_name: shControl VEGF 1h CsA

value: shControl


title: shControl VEGF 1h CsA, replicate 2


title: shDYRK1A basal, replicate 1

source_name: shDYRK1A basal


title: shControl VEGF 1h CsA, replicate 1


title: shControl VEGF 1h, replicate 3

source_name: shControl VEGF 1h


title: shDYRK1A basal, replicate 3


title: 6A_TP2C_074030_Cycle2

source_name: P. falciparum, 6A clone, exposed to DMSO (control) for 2hrs

source_name: P. falciparum 3D7 RNA reference pool


title: shDYRK1A VEGF 1h, replicate 1


title: shControl VEGF 1h, replicate 2


title: shDYRK1A VEGF 1h CsA, replicate 2


title: shDYRK1A basal, replicate 2


title: D186_HIV_RAL_40h

city: Seattle

first: Jarrod

middle: S

last: Johnson

state: Washington

address: 307 Westlake Ave, Suite 500

institute: Center for Infectious Disease Research

description: Gene expression of human monocyte-derived DCs 40 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx, with Raltegravir

hyb_protocol: 600ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 8x60K Microarrays using the Agilent hybridization chambers. The hybridization was allowed to run for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by compressed air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area  61mmx21.6mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid:039494_D_F_20120628. Probe sequences were mapped against the Ensembl transcript database (ensembl.org, GRCh37.74). Only sequences that matched with at most 5 mismatches and were best matches were retained. Sequences that mapped to more than one gene were removed for a  total of 37,623 unique probe sequences. Probe-specific logarithmically transformed expression was quantile-normalized. Duplicate probe sequences were averaged.

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 40, drug: Raltegravir, donor: D186

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100-200ng total RNA using Agilent’s Low Input Quick Amp One-Color Labeling Kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: To generate monocyte-derived dendritic cells, CD14+ monocytes from PBMC buffy coats were isolated with anti-human CD14 magnetic beads (Miltenyi) and cultured in RPMI containing 10% heat-inactivated fetal bovine serum (FBS), 50 U/ml penicillin, 50 ug/ml streptomycin (P/S), 10 mM HEPES, beta mercaptoethanol, and 2 mM glutamine, in the presence of recombinant human GM-CSF at 10 ng/ml and IL-4 at 50 ng/ml (Peprotech). To overcome restriction to HIV-1 reverse transcription, virus-like particles packaging Vpx were added to isolated cells on day 0.  Fresh media and cytokines were added to cells (40% by volume) on day 1. On day 4, cells were collected, resuspended in fresh media with cytokines used for infection.

extract_protocol: Total RNA was isolated with TRIzol (ThermoFisher) according to the manufacturer's instructions using two sequential chloroform extractions and adding Glycoblue as carrier prior to precipitation.

treatment_protocol: Monocyte-derived dendritic cells that had been treated with virus-like particles packaging Vpx were infected with HIV-GFP in the presence or absence of Raltegravir (25 uM) in a time course according to the following protocol:  On day 4 after differentiation from monocytes, dendritic cells were counted and resuspended at 800,000 cell per ml in fresh DC medium with GM-CSF, IL-4, and polybrene (1 ug/ml) and then plated into round bottom 96 well plates with 75 ul per well. Cells were mock-treated or treated with Raltegravir and then infections were performed by diluting virus in fresh medium (without cytokines or polybrene) to a final volume normalized to controls (160 ul per well).  The time course was performed in reverse order such that all samples were harvested at the same time on day 6 after DC differentiation.  Mock-infected samples were treated with Vpx and DC media in parallel with samples that received HIV-GFP for 40 hours.

tag: tissue

value: monocyte-derived dendritic cells


title: 6A-R_TP3C_074042_Cycle2

source_name: P. falciparum, 6A-R clone, exposed to DMSO (control) for 4hrs


title: 6A_TP2ART_074030_Cycle1

source_name: P. falciparum, 6A clone, exposed to 900 nM ART for 2hrs


title: shControl VEGF 1h, replicate 1


title: 6A_TP1C_074025_Cycle2

source_name: P. falciparum, 6A clone, exposed to DMSO (control) for 1hr


title: 6A_TP3ART_074032_Cycle1

source_name: P. falciparum, 6A clone, exposed to 900 nM ART for 4hrs


title: 6A_TP1ART_074025_Cycle1

source_name: P. falciparum, 6A clone, exposed to 900 nM ART for 1hr


title: D186_HIV_RAL_32h

description: Gene expression of human monocyte-derived DCs 32 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx, with Raltegravir

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 32, drug: Raltegravir, donor: D186


title: shControl basal, replicate 3

source_name: shControl basal


title: D187_HIV_RAL_32h

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 32, drug: Raltegravir, donor: D187


title: shControl basal, replicate 1


title: untreated VEGF 1h CsA, replicate 3

source_name: untreated VEGF 1h CsA

value: basal


title: untreated VEGF 1h CsA, replicate 1


title: shControl basal, replicate 2


title: D186_HIV_RAL_28h

description: Gene expression of human monocyte-derived DCs 28 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx, with Raltegravir

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 28, drug: Raltegravir, donor: D186


title: untreated VEGF 1h, replicate 3

source_name: untreated VEGF 1h


title: D187_HIV_RAL_40h

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 40, drug: Raltegravir, donor: D187


title: untreated VEGF 1h, replicate 2


title: D187_HIV_RAL_28h

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 28, drug: Raltegravir, donor: D187


title: D187_HIV_RAL_24h

description: Gene expression of human monocyte-derived DCs 24 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx, with Raltegravir

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 24, drug: Raltegravir, donor: D187


title: 6A-R_TP1C_074038_Cycle2

source_name: P. falciparum, 6A-R clone, exposed to DMSO (control) for 1hr


title: untreated basal replicate 3

source_name: untreated basal


title: 6A-R_TP2C_074039_Cycle2

source_name: P. falciparum, 6A-R clone, exposed to DMSO (control) for 2hrs

source_name: P. falciparum 3D7 RNA reference pool


title: D187_HIV_RAL_20h

description: Gene expression of human monocyte-derived DCs 20 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx, with Raltegravir

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 20, drug: Raltegravir, donor: D187


title: untreated VEGF 1h CsA, replicate 2


title: D186_HIV_RAL_24h

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 24, drug: Raltegravir, donor: D186


title: untreated VEGF 1h, replicate 1


title: D186_HIV_RAL_20h

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 20, drug: Raltegravir, donor: D186


title: D186_HIV_RAL_8h

description: Gene expression of human monocyte-derived DCs 8 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx, with Raltegravir

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 8, drug: Raltegravir, donor: D186


title: 970715A4

source_name: tumor DNA

value: Neuroblastoma

tag: tumor inss stage

tag: tumor inrg stage

source_name: Normal reference DNA

value: normal tissue (blood) from healthy donor


title: 91EFF429

tag: gender (1=male; 2=female)

tag: mycn status (0=non amplified, 1= amplified)


title: 6A-R_TP2ART_074039_Cycle1

source_name: P. falciparum, 6A-R clone, exposed to 900 nM ART for 2hrs


title: D187_HIV_RAL_16h

description: Gene expression of human monocyte-derived DCs 16 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx, with Raltegravir

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 16, drug: Raltegravir, donor: D187


title: 6A-R_TP1ART_074038_Cycle1

source_name: P. falciparum, 6A-R clone, exposed to 900 nM ART for 1hr


title: D187_HIV_RAL_8h

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 8, drug: Raltegravir, donor: D187


title: D186_VLP_mock_RAL

description: Gene expression of human monocyte-derived DCs 40 hours after mock infection in the presence of virus-like particles packaging Vpx, with Raltegravir

source_name: monocyte-derived dendritic cells with mock infection in the presence of Vpx, time (hours): 40, drug: Raltegravir, donor: D186


title: D186_HIV_RAL_16h

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 16, drug: Raltegravir, donor: D186


title: untreated basal replicate 2


title: U2OS-tet p63 T46/281A#1 Dox

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: Dox (+) condition in Tet-ON inducible Myc-TAp63-T46A/T281A cells

hyb_protocol: Before hybridization, 1650 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Data were analyzed using the bioinformatics software GeneSpring 13.0 (Agilent)

label_protocol: 200 ng of total RNAs were independently reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and AffinityScript, RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham Pharmacia Biotech, Piscataway, NJ) using a Low input Quick-Amp Labeling Kit (Agilent Technologies).

growth_protocol: U2OS cells, purchased from the American Type Culture Collection, were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM; Sigma-Aldrich, D5796) supplemented with 10% fetal bovine serum (FBS) (HyClone, SV30014.03) with 100 U/mL penicillin and 100 μg/mL streptomycin (Nacalai Tesque, #26253-84). For preparation of Dox-inducible U2OS advanced cells, pTet-On advanced plasmid vector (Clontech) was transfected into cells. The cells were incubated in DMEM supplemented with 10% FBS, penicillin/streptomycin, and 0.2 mg/mL G418 disulfate aqueous solution (Nacalai Tesque, #16513-26), from which several single colonies were selected for preparation of Tet-ON inducible cell lines. For culture of pTet-On_advanced cells, 0.2 mg/mL G418 was added to the medium.

extract_protocol: Total RNA was extracted from cells using an miRNeasy Mini kit according to the manufacturer’s instructions (Qiagen). The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit on the Agilent 2100 Bioanalyzer (Agilent).

tag: cell line

tag: genotype/variation

value: doxycycline


title: 6A-R_TP3ART_074042_Cycle1

source_name: P. falciparum, 6A-R clone, exposed to 900 nM ART for 4hrs


title: untreated basal replicate 1


title: D186_HIV_28h

description: Gene expression of human monocyte-derived DCs 28 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 28, drug: none, donor: D186


title: D186_HIV_40h

description: Gene expression of human monocyte-derived DCs 40 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 40, drug: none, donor: D186


title: D186_HIV_32h

description: Gene expression of human monocyte-derived DCs 32 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 32, drug: none, donor: D186


title: U2OS-tet p63 wild type#7 non-treated

description: Dox (-) condition in Tet-ON inducible Myc-TAp63-WT cells

value: wild type

value: non-treated


title: D187_VLP_mock_RAL

source_name: monocyte-derived dendritic cells with mock infection in the presence of Vpx, time (hours): 40, drug: Raltegravir, donor: D187


title: D187_HIV_28h

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 28, drug: none, donor: D187


title: U2OS-tet p63 T46/281A#1 non-treated

description: Dox (-) condition in Tet-ON inducible Myc-TAp63-T46A/T281A cells


title: D187_HIV_32h

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 32, drug: none, donor: D187


title: D187_HIV_24h

description: Gene expression of human monocyte-derived DCs 24 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 24, drug: none, donor: D187


title: D187_HIV_20h

description: Gene expression of human monocyte-derived DCs 20 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 20, drug: none, donor: D187


title: HaCaT AKBA H3K27me3 ChIP

city: Shanghai

first: Hong

middle: Lin

last: Wang

address: 280 Chongqing South Road

country: China

institute: Shanghai Jiao Tong University

description: AKBA H3K27me3 ChIP

library_source: genomic

data_processing:
Basecalls for ChIP-seq were performed using Illumina pipeline software v1.8 Adapter sequences were trimmed (FASTQ Quality Trimmer) then mapped to hg19 using BWA (ChIP-seq) or STAR (RNA-seq) using the default parameters.
MACS2 was used to call peaks from ChIP-seq data using the following parameters: -t[experimental file] -c[input file] -n[output file name] -f BAM -g hs -q 0.01 --browd-cutoff 0.1.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq: bigwig files, text files are output from MACS2 and columns include: chr, start, end, length, abs_summit,pileup, -log10.pvalue, fold enrichment, and -log10.qvalue.

source_name: HaCaT

extract_protocol:
Cells grown on 10cm plates were crosslinked with 1% formaldyhyde in culture media. Cross-linked chromatin was collected and flash frozen before sonication with the Ultrasonic Cell Crusher. Lysates were clarified and protein-DNA complexes were immunoprecipitated with H3K27me3 antibody. Libraries were prepared according to standard Illumina protocols.
Libraries were prepared according to NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E.coli DNA Pol I Large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenowfragment (32 to 52 exominus) and dATP to yield a protruding 3-'A' base forligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200-500bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was capturedon an Illumina flowcell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: HaCaT

value: Human immortalized keratinocytes

tag: chip antibody

value: Anti-H3K27me3(Millipore #07-449)

tag: culture media

value: +AKBA


title: HaCaT DMSO Input DNA

description: DMSO Input DNA

value: +DMSO


title: Placenta_E19.5d_rep3

first: Zhihui

last: Dai

address: Xiangyin Road 800

institute: placenta

description: Gene expression in E19.5d placenta tissue of mouce

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 9 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: Placenta tissue,E19.5d,replicate 3

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

treatment_protocol: Three female mice in the estrous period, which were verified by detecting vaginal secretions, were mated with one male mouse. Timing of pregnancy was determined by visual inspection of the vaginal plug, which was defined as 0.5 days post-conception (E0.5 d). On the day E7.5 d (group A), E14.5 d (group B) and E19.5 d (group C) mice were killed. The placentas were removed and washed by preheated PBS buffer. Then the placental tissue were preserved in liquid nitrogen for further study.Three samples were repeated at each time point.

tag: gender

value: female

tag: age

value: 8 week


title: HaCaT AKBA Input DNA

description: AKBA Input DNA


title: Placenta_E19.5d_rep1

source_name: Placenta tissue,E19.5d,replicate 1


title: HaCaT DMSO H3K27me3 ChIP

description: DMSO H3K27me3 ChIP


title: 8CD0F72E

source_name: tumor DNA

tag: age (days) at diagnosis

tag: relapse/progression (0=no, 1= yes)

tag: time from diagnosis to event or last follow up (days)

tag: patient status (0=alive, 1= dead)

tag: time from diagnosis to death or last follow up (days)

source_name: Normal reference DNA

tag: control type


title: U2OS-tet p63 wild type#7 Dox

description: Dox (+) condition in Tet-ON inducible Myc-TAp63-WT cells

tag: treatment


title: 888CFF5F

tag: tissue

tag: tumor inss stage


title: F2F5F85B

tag: tumor inrg stage

tag: gender (1=male; 2=female)


title: D186_HIV_24h

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 24, drug: none, donor: D186


title: mature leaf

city: Thalassery

first: Anu

last: Augustine

state: Kerala

address: Kannur University, Thalassery Campus, Palayad P O

department: Department of Biotechnology and Microbiology

country: India

institute: Kannur University

data_processing:
The adapter sequences added prior to sequencing were trimmed using Cutadapt v1.9.
Based on quality report of fastq files, sickle v1.33 programme was used to filter out all low quality (Q<20) and low read length (Read length < 30 bases) data
The quality filtered data was then normalized using BBNORM tool for assembly
The cleaned reads were assembled using Trinity with default settings (version trinityrnaseq_r20 140717)
The trimmed reads were aligned to the assembled transcriptome using Bowtie2 program (version 2.2.2)
Genome_build: De novo transcritome
Supplementary_files_format_and_content: anuaugustine_kscste.txt containing three columns for contig id, accession number and fpkm value respectively

organism: Rhizophora mucronata

source_name: Leaf

extract_protocol:
Total RNA from the leaves of Rhizophora mucronata were isolated by LiCl cold extraction method developed for tissues rich in polyphenols and polysaccharides of mangrove plants as described over here (Rubio Pina and Perez 2011). About 200 mg of each sample tissue were ground to a fine powder using liquid nitrogen and transferred into a 2 ml centrifuge tubes. 900 µl of extraction buffer 1 and 100 µl of β-mercaptoethanol were added. The mixture was shaken for 30 sec and then incubated at 65ºC for 10 min, inverting the tube 3-4 times every now and then during incubation. Then, 800 µl of chloroform were added. The mixture was shaken for 30 sec. Later the mixture was centrifuged at 10,000 rpm for 10 min at 4ºC. The supernatant was transferred to a new tube. Next, 800 µl of phenol/chloroform (1:1) were added and shaken for 30 sec. Later the mixture was centrifuged at 10,000 rpm for 10 min at 4ºC. The supernatant was transferred to a new tube and an equal volume of chloroform/ isoamyl alcohol (24:1) was added. Samples were shaken for 30 sec and centrifuged at 10,000 rpm for 10 min at 4ºC. The final supernatant was transferred to new tube containing 1/3 volume of LiCl (8 M) and kept at -200C for at least 4 hrs. Next, the samples were centrifuged at 10,000 rpm for 20 min at 40C. The pellets were successively washed with 100% and 70% ethanol. After a short drying time at room temperature, the pellets were dissolved in 50 µl of DEPC water.
Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments was used to synthesize first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments were then gone through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were purified and enriched with PCR to create the final cDNA library (llumina’s TrueSeq RNA sample preparation kit)

value: Leaf

tag: developmental stage

value: Mature leaves


title: D187_HIV_40h

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 40, drug: none, donor: D187


title: D186_HIV_20h

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 20, drug: none, donor: D186


title: D186_HIV_16h

description: Gene expression of human monocyte-derived DCs 16 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 16, drug: none, donor: D186


title: Placenta_E19.5d_rep2

source_name: Placenta tissue,E19.5d,replicate 2


title: Placenta_E14.5d_rep2

description: Gene expression in E14.5d placenta tissue of mouce

source_name: Placenta tissue,E14.5d,replicate 2


title: Placenta_E14.5d_rep3

source_name: Placenta tissue,E14.5d,replicate 3


title: D187_HIV_16h

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 16, drug: none, donor: D187


title: Placenta_E14.5d_rep1

source_name: Placenta tissue,E14.5d,replicate 1


title: D187_HIV_8h

description: Gene expression of human monocyte-derived DCs 8 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 8, drug: none, donor: D187


title: MS_NORM_32 MS_NORM_32_C8078ANXX_CTTGTA_L008

status: Public on Mar 21 2018

city: Parkville

first: CSL

last: Research

state: VIC

address: 30 Flemington Rd

country: Australia

institute: CSL Limited / bio21 Institute

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_32 donor blood

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.58 and Real Time Analysis (RTA) v1.18.64, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 1.8.4 pipeline was used to generate the sequence data.
Reads were mapped to Homo sapiens GRCh37.p10 genome, using TopHat2 (TopHat v2.0.12, bowtie v2.2.5; Trapnell et al.,2009).
Mapped reads were summaried on a gene level using Ensembl ID gene annotation (Ensembl Release 70 based on GRCh37.p10 genome build) and featureCounts (v1.4.6; Liao et al., 2014) software.
Summarised read counts in this submission were NOT normalised nor filtered. We recommend using Bioconductor edgeR package functions: i) calcNormFactors (TMM method) to normalise between samples based on library sizes,  and ii) rpkm function to normalise between genes within a sample based on gene lengths.
Genome_build: GRCh37.p10
Supplementary_files_format_and_content: All processed data files are in a tab delimited file format. They contain raw read counts summarised on a gene level according to Ensembl Release 70 annotation.

source_name: RNA from lysed whole blood cells

extract_protocol:
RNA was extracted from PaxGene tubes using an PaxGene blood RNA kit (Qiagen, catalog number 762174)
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: blood

tag: donor

value: F

tag: ancestry

value: Caucasian

tag: phenotype

value: Healthy


title: Placenta_E7.5d_rep3

description: Gene expression in E7.5d placenta tissue of mouce

source_name: Placenta tissue,E7.5d,replicate 3

tag: gender


title: MS_NORM_32 MS_NORM_32_C8078ANXX_CTTGTA_L007

tag: age


title: Placenta_E7.5d_rep1

source_name: Placenta tissue,E7.5d,replicate 1


title: Lim_030

city: Ann Arbor

first: Celine

middle: C

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description: Gene expression data from human limited systemic sclerosis keratinocytes

hyb_protocol: Biotin labeled cDNA was fragmented and hybridized to Affymetrix Human Gene 2.1  ST arrays (Santa Clara, CA) according to the manufacturer protocol.

scan_protocol: GeneChip arrays were scanned by using the Affymetrix GeneTitan system (software version 3.2.4.1515) according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were analyzed using ChipInspector software from Genomatix (www.genomatix.de). One class of exhaustive matching was used to detect the differentially regulated genes in the keratinocytes from diffuse fibrosis and limited skin disease compared to normal. A false discovery rate of <1% was applied on all datasets to detect the significantly regulated genes.  Supplementary files on the series record contain fold-change values. ChipInspector software does not produce the normalized values.

source_name: Keratinocytes from limited systemic sclerosis

label_protocol: Biotinylated cRNA were prepared using the NuGEN Encore Biotin Module (Encore Biotin Module Manual, P/N M01111 v6) following the manufacturer's protocol.

extract_protocol: Total RNA was isolated using the Direct-Zol RNA kit (Zymo Research, Irvine, CA) following manufacturer’s instructions.

treatment_protocol:
culture protocol: To isolate keratinocytes, the epidermis was separated from the dermis and incubated at 37ºC in basal media containing 0.17% trypsin for two hours.  Keratinocytes were initially selected in growth medium (EpiLife, Life Technologies, Grand Island, NY) with keratinocyte growth factor supplementation (Life Technologies) and 2% fetal bovine serum (FBS,Sigma, St. Louis, MO).
After three days, keratinocytes switched to keratinocyte growth medium without FBS to prevent epithelialization.  To ensure purity of the keratinocyte population we grew the cells in serum free media, a process that represses fibroblast growth. Keratinocyte purity was confirmed via cellular morphology.  At passage 2, conditioned media was collected and stored at -80ºC and 5x105 cells will be saved for RNA in Tripure (Roche).

value: skin

tag: cell type

value: Keratinocytes

tag: disease state

value: limited systemic sclerosis


title: D186_VLP_mock

description: Gene expression of human monocyte-derived DCs after mock infection in the presence of virus-like particles packaging Vpx

source_name: monocyte-derived dendritic cells with mock infection in the presence of Vpx, time (hours): 0, drug: none, donor: D186

value: monocyte-derived dendritic cells


title: Lim_016


title: Placenta_E7.5d_rep2

source_name: Placenta tissue,E7.5d,replicate 2


title: D186_HIV_8h

source_name: monocyte-derived dendritic cells infected with HIV-GFP in the presence of Vpx, time (hours): 8, drug: none, donor: D186


title: MS_NORM_31 MS_NORM_31_C8078ANXX_GGCTAC_L008

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_31 donor blood


title: weeping peach tree 4

city: East Lansing

first: Courtney

last: Hollender

address: 1066 Bogue St

department: Dept. of Horticulture

institute: Michigan State University

description:
Sequencing data from the shoot tips of one weeping peach branch. This is a biolical replicate. It is from a weeping tree that we call #4
These peach trees were from a segregating F2 population from a cross between  parents used only for breeding purposes. The  trees sequenced here are not cultivar varieties. Lengthy detail on their origin can be found in the supplementary section of the  paper Hollender et al (2018) PNAS.

data_processing:
Barcodes were removed from Raw Reads and then the sequences were trimmed based on qualtiy and ambiguity using CLC Genomics workbench 9.5.3
The remaining reads were aligned against the Peach Genome Version 1 using CLC Genomics workbench 9.5.3
Differential expression analysis was perfuormed using CLC Genomics workbench 9.5.3 "Transcriptomics Analysis" function
Genome_build: https://www.rosaceae.org/organism/Prunus/persica
Supplementary_files_format_and_content: Excel file of CLC genomics workbench output of the differential expression analysis

organism: Prunus persica

source_name: Lateral shoot (branch) tips of trees

growth_protocol: Trees were grown in a field at the USDA ARS Appalachian Fruit Research Station

extract_protocol:
RNA was extracted using the Omega SQ total RNA kit with the addition of 2% PVP to the lysis buffer
50 bp Illumina Truseq uppaired libraries were constructed at the gemoics resources core facility at Weill Cornell College of Medicine

value: Mature tree

value: branch tip

tag: growth habit

value: weeping growth habit


title: Standard Peach Tree 10

description:
Sequencing data from the shoot tips of one standard peach branch. This is a biolical replicate. It is from a standard tree that we call #10)
These peach trees were from a segregating F2 population from a cross between  parents used only for breeding purposes. The  trees sequenced here are not cultivar varieties. Lengthy detail on their origin can be found in the supplementary section of the  paper Hollender et al (2018) PNAS.

value: standard growth habit


title: Standard Peach Tree 9

description:
Sequencing data from the shoot tips of one standard peach branch. This is a biolical replicate. It is from a standard tree that we call #9
These peach trees were from a segregating F2 population from a cross between  parents used only for breeding purposes. The  trees sequenced here are not cultivar varieties. Lengthy detail on their origin can be found in the supplementary section of the  paper Hollender et al (2018) PNAS.


title: weeping peach tree 1

description:
Sequencing data from the shoot tips of one weeping peach branch. This is a biolical replicate. It is from a weeping tree that we call #1)
These peach trees were from a segregating F2 population from a cross between  parents used only for breeding purposes. The  trees sequenced here are not cultivar varieties. Lengthy detail on their origin can be found in the supplementary section of the  paper Hollender et al (2018) PNAS.


title: weeping peach tree 2

description:
Sequencing data from the shoot tips of one weeping peach branch. This is a biolical replicate. It is from a weeping tree that we call #2
These peach trees were from a segregating F2 population from a cross between  parents used only for breeding purposes. The  trees sequenced here are not cultivar varieties. Lengthy detail on their origin can be found in the supplementary section of the  paper Hollender et al (2018) PNAS.


title: Standard Peach Tree 8

description:
Sequencing data from the shoot tips of one standard peach branch. This is a biolical replicate. It is from a standard tree that we call #8
These peach trees were from a segregating F2 population from a cross between  parents used only for breeding purposes. The  trees sequenced here are not cultivar varieties. Lengthy detail on their origin can be found in the supplementary section of the  paper Hollender et al (2018) PNAS.


title: Standard Peach Tree 7

description:
Sequencing data from the shoot tips of one standard peach branch. This is a biolical replicate. It is from a standard tree that we call #7
These peach trees were from a segregating F2 population from a cross between  parents used only for breeding purposes. The  trees sequenced here are not cultivar varieties. Lengthy detail on their origin can be found in the supplementary section of the  paper Hollender et al (2018) PNAS.


title: Lim_015


title: weeping peach tree 3

description:
Sequencing data from the shoot tips of one weeping peach branch. This is a biolical replicate. It is from a weeping tree that we call #3
These peach trees were from a segregating F2 population from a cross between  parents used only for breeding purposes. The  trees sequenced here are not cultivar varieties. Lengthy detail on their origin can be found in the supplementary section of the  paper Hollender et al (2018) PNAS.


title: MS_NORM_31 MS_NORM_31_C8078ANXX_GGCTAC_L007


title: Lim_014


title: MS_NORM_30 MS_NORM_30_C8078ANXX_TAGCTT_L008

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_30 donor blood


title: Lim_012


title: MS_NORM_30 MS_NORM_30_C8078ANXX_TAGCTT_L007


title: Diff_008

description: Gene expression data from human diffuse systemic sclerosis keratinocytes

source_name: Keratinocytes from diffuse systemic sclerosis

value: diffuse systemic sclerosis


title: Lim_010


title: Diff_006


title: MS_NORM_27 MS_NORM_27_C8078ANXX_ACTTGA_L008

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_27 donor blood


title: MS_NORM_28 MS_NORM_28_C8078ANXX_GATCAG_L007

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_28 donor blood


title: MS_NORM_27 MS_NORM_27_C8078ANXX_ACTTGA_L007


title: Diff_005


title: MS_NORM_26 MS_NORM_26_C8078ANXX_CAGATC_L007

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_26 donor blood


title: D187_VLP_mock

source_name: monocyte-derived dendritic cells with mock infection in the presence of Vpx, time (hours): 0, drug: none, donor: D187


title: MS_NORM_26 MS_NORM_26_C8078ANXX_CAGATC_L008


title: Diff_004


title: Norm_024

description: Gene expression data from human normal keratinocytes

source_name: Keratinocytes from normal skin

value: healthy


title: MS_NORM_23 MS_NORM_23_C8078ANXX_TGACCA_L008

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_23 donor blood


title: Norm_032


title: MS_NORM_24 MS_NORM_24_C8078ANXX_ACAGTG_L007

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_24 donor blood


title: MS_NORM_24 MS_NORM_24_C8078ANXX_ACAGTG_L008


title: Norm_019


title: Norm_028


title: MS_NORM_25 MS_NORM_25_C8078ANXX_GCCAAT_L008

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_25 donor blood


title: Lim_011

description: Gene expression data from human limited systemic sclerosis keratinocytes


title: Norm_022


title: MS_NORM_25 MS_NORM_25_C8078ANXX_GCCAAT_L007


title: MS_NORM_23 MS_NORM_23_C8078ANXX_TGACCA_L007


title: MS_NORM_28 MS_NORM_28_C8078ANXX_GATCAG_L008


title: MS_NORM_22 MS_NORM_22_C8078ANXX_TTAGGC_L008

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_22 donor blood


title: Diff_007


title: Norm_018


title: MS_NORM_22 MS_NORM_22_C8078ANXX_TTAGGC_L007


title: MS_NORM_20 MS_NORM_20_C8078ANXX_ATCACG_L007

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_20 donor blood


title: Norm_021


title: MS_NORM_21 MS_NORM_21_C8078ANXX_CGATGT_L007

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_21 donor blood


title: MS_NORM_18 MS_NORM_18_C8078ANXX_ACTGAT_L006

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_18 donor blood


title: MS_NORM_21 MS_NORM_21_C8078ANXX_CGATGT_L008


title: MS_NORM_19 MS_NORM_19_C8078ANXX_ATTCCT_L006

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_19 donor blood

value: Asian


title: MS_NORM_19 MS_NORM_19_C8078ANXX_ATTCCT_L005


title: MS_NORM_17 MS_NORM_17_C8078ANXX_GAGTGG_L006

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_17 donor blood


title: MS_NORM_18 MS_NORM_18_C8078ANXX_ACTGAT_L005


title: MS_NORM_17 MS_NORM_17_C8078ANXX_GAGTGG_L005


title: MS_NORM_16 MS_NORM_16_C8078ANXX_CGTACG_L006

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_16 donor blood


title: Norm_017


title: MS_NORM_16 MS_NORM_16_C8078ANXX_CGTACG_L005


title: MS_NORM_15 MS_NORM_15_C8078ANXX_GTTTCG_L005

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_15 donor blood

value: M


title: MS_NORM_14 MS_NORM_14_C8078ANXX_GTGGCC_L006

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_14 donor blood


title: MS_NORM_20 MS_NORM_20_C8078ANXX_ATCACG_L008


title: MS_NORM_14 MS_NORM_14_C8078ANXX_GTGGCC_L005


title: MS_NORM_15 MS_NORM_15_C8078ANXX_GTTTCG_L006


title: MS_NORM_11 MS_NORM_11_C8078ANXX_GTCCGC_L006

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_11 donor blood


title: MS_NORM_13 MS_NORM_13_C8078ANXX_GTGAAA_L006

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_13 donor blood


title: MS_NORM_11 MS_NORM_11_C8078ANXX_GTCCGC_L005


title: MS_NORM_13 MS_NORM_13_C8078ANXX_GTGAAA_L005


title: MS_NORM_10 MS_NORM_10_C8078ANXX_CCGTCC_L006

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_10 donor blood


title: MS_NORM_10 MS_NORM_10_C8078ANXX_CCGTCC_L005


title: MS_NORM_08 MS_NORM_08_C8078ANXX_ATGTCA_L006

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_08 donor blood


title: MS_NORM_08 MS_NORM_08_C8078ANXX_ATGTCA_L005


title: MS_NORM_07 MS_NORM_07_C8078ANXX_AGTTCC_L006

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_07 donor blood


title: MS_NORM_06 MS_NORM_06_C8078ANXX_AGTCAA_L005

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_06 donor blood


title: MS_NORM_05 MS_NORM_05_C8078ANXX_CTTGTA_L004

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_05 donor blood


title: MS_NORM_07 MS_NORM_07_C8078ANXX_AGTTCC_L005


title: MS_NORM_06 MS_NORM_06_C8078ANXX_AGTCAA_L006


title: MS_NORM_05 MS_NORM_05_C8078ANXX_CTTGTA_L003


title: BM06-P4-FS20

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

description: BM06-P4-FS20 20% FBS

hyb_protocol: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit and subsequently mixed with Universal Human Reference RNA (Stratagene, Santa Clara, CA, USA) and cohybridized to Agilent Chip Whole Human genome, 4x44k slides according to the protocol provided by Agilent.

scan_protocol: The slides were incubated for 17h at 65°C and then the scanned using the Agilent B Scanner.

data_processing: Raw images were obtained by scanning the slides with an Agilent Scan G2505B and Agilent Scan Control software (version 9.5). The images were extracted using the Feature Extraction Software (Agilent Technologies). Partek Genomic Suite 6.4 (Partek Inc., St. Louis, MO, USA) was used for data visualization, identification of differentially expressed transcripts and hierarchical cluster analysis. We transformed the fluorescence intensity data to log2 ratios of each sample versus the universal human RNA reference (Stratagene, Santa Clara, CA, USA).

growth_protocol: BMSCs were isolated at Department of Transfusion Medicine, Clinical Center, NIH, Bethesda, Maryland. These cells were expanded and characterized as described in our previous work. Briefly, cells from the bone marrow aspirates were seeded in complete media (α-minimal essential medium [α-MEM], 2mM glutamine, 10µg/ml gentamicin and 20% fetal bovine serum) for 24 hours, and the non-adherent cells were removed. The adherent cells were expanded until 70-80% confluence was reached. Cells were sub-cultured and kept in complete media. These BMSCs were >70% viable and expressed CD73, CD90, CD105 and CD146 but not CD11b, CD14, CD19, CD34 or CD45.

extract_protocol: Total RNA from BMSC samples were isolated and purified by using miRNeasyKit (Qiagen, Germantown, MD, USA). The RNA concentration was determined using Nano Drop ND-1000 Spectrophotometer (Nano Drop Technologies, Wilmington, DE, USA) and RNA quality was assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Marrow aspirates from 5 healthy subjects were cultured for 4 passages in 10% HPGF-C18 or 20% FBS and were analyzed for global gene expression.

tag: donor id

tag: passage

value: Bone Marrow Stromal Cells (BMSC)

source_name: universal human reference RNA

value: pooled whole human RNA


title: MS_NORM_04 MS_NORM_04_C8078ANXX_GGCTAC_L004

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_04 donor blood

value: blood

value: F


title: MS_NORM_04 MS_NORM_04_C8078ANXX_GGCTAC_L003

value: Caucasian

value: Healthy


title: MS_NORM_03 MS_NORM_03_C8078ANXX_TAGCTT_L004

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_03 donor blood


title: MS_NORM_03 MS_NORM_03_C8078ANXX_TAGCTT_L003


title: MS_NORM_02 MS_NORM_02_C8078ANXX_GATCAG_L004

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_02 donor blood


title: BM07-P4-FS20

description: BM07-P4-FS20 20% FBS

label_protocol: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit and subsequently mixed with Universal Human Reference RNA (Stratagene, Santa Clara, CA, USA)

tag: control type


title: MS_NORM_02 MS_NORM_02_C8078ANXX_GATCAG_L003


title: BM06-P2-PF10

description: BM06-P2-PF10 10% HPGF


title: BM04-P3-FS20

description: BM04-P3-FS20 20% FBS


title: MS_NORM_01 MS_NORM_01_C8078ANXX_ACTTGA_L004

description:
Total RNA with Ribo Zero and Globin Depletion
NORM_01 donor blood


title: BM06-P3-PF10

description: BM06-P3-PF10 10% HPGF


title: BM04-P3-PF10

description: BM04-P3-PF10 10% HPGF


title: BM06-P3-FS20

description: BM06-P3-FS20 20% FBS


title: BM06-P4-PF10

description: BM06-P4-PF10 10% HPGF


title: BM03-P3-FS20

description: BM03-P3-FS20 20% FBS


title: BM06-P2-FS20

description: BM06-P2-FS20 20% FBS


title: BM01-P4-PF10

description: BM01-P4-PF10 10% HPGF


title: BM04-P4-PF10

description: BM04-P4-PF10 10% HPGF


title: MON_SLE_34_01 MON_SLE_34_01_C8078ANXX_CAGATC_L004

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_34 donor blood

value: SLE


title: BM07-P4-PF10

description: BM07-P4-PF10 10% HPGF


title: MON_SLE_33_01 MON_SLE_33_01_C8078ANXX_GCCAAT_L004

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_33 donor blood


title: BM03-P3-PF10

description: BM03-P3-PF10 10% HPGF


title: BM04-P4-FS20

description: BM04-P4-FS20 20% FBS


title: SHC2

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were first discarded if containing more than 2-N bases, then reads were processed by clipping adaptor, removing low quality bases, and discarding too short reads (less than 16nt). FASTX-Toolkit (Version 0.0.13) was used to get the clean reads.
After that, clean reads were aligned to the Rattus norvegicus (Rnor 5.0) by tophat2 (Kim et al., 2013). Aligned reads with more than one genome location were discarded due to their ambiguous location.
Uniquely localized reads were used to calculate reads number and RPKM value (RPKM represents reads per kilobase and per million) for each gene according to reads and genes genome location. Other statistical results, such as gene coverage and depth, reads distribution around start codon and stop codon, were also obtained.
After getting the Expression level of all genes in all samples, differentially expressed genes were analyzed by using edgeR(Robinson et al., 2010), one of R packages.
Genome_build: Rnor 5.0
Supplementary_files_format_and_content: tabular data of  txt , the RPKM of expressed genes

molecule: polyA RNA

organism: Rattus norvegicus

source_name: SH colon 2

extract_protocol:
Total RNA was extracted from 30 mg of ground tissue by using hot phenol method. The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1DNase (Promega) to remove DNA. The quality and quantity of the purified RNA we redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad).
For each sample, 10 μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen) before used for directional RNA-seq library preparation. The purified mRNAs were then iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer.

value: colon


title: SHH2

source_name: SH thalamus 2

value: hypothalamus


title: MON_SLE_33_01 MON_SLE_33_01_C8078ANXX_GCCAAT_L003


title: SHC1

source_name: SH colon 1


title: BM03-P4-PF10

description: BM03-P4-PF10 10% HPGF


title: BM01-P4-FS20

description: BM01-P4-FS20 20% FBS


title: SHH1

source_name: SH thalamus 1


title: MON_SLE_32_01 MON_SLE_32_01_C8078ANXX_ACAGTG_L003

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_32 donor blood


title: MS_NORM_01 MS_NORM_01_C8078ANXX_ACTTGA_L003


title: MON_SLE_31_01 MON_SLE_31_01_C8078ANXX_TGACCA_L004

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_31 donor blood


title: BM01-P3-PF10

description: BM01-P3-PF10 10% HPGF


title: BM01-P2-PF10

description: BM01-P2-PF10 10% HPGF


title: BM03-P4-FS20

description: BM03-P4-FS20 20% FBS


title: BM01-P2-FS20

description: BM01-P2-FS20 20% FBS


title: BM01-P3-FS20

description: BM01-P3-FS20 20% FBS


title: Patient 1

city: Vancouver

first: Lindsay

last: Brown

address: 4480 Oak St

country: Canada

institute: BC Children's and Woman's Health Centre of BC

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: CytoScan array CEL files are processed and copy number analyzed in ChAS software

source_name: Peripheral blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood using the QIAcube according to the manufacturer's instructions

tag: Sex

value: Female

value: Peripheral blood

tag: diagnosis

value: Vitamin D deficiency


title: MON_SLE_34_01 MON_SLE_34_01_C8078ANXX_CAGATC_L003

source_name: RNA from lysed whole blood cells

tag: tissue


title: MON_SLE_30_01 MON_SLE_30_01_C8078ANXX_TTAGGC_L004

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_30 donor blood


title: MON_SLE_29_01 MON_SLE_29_01_C8078ANXX_CGATGT_L004

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_29 donor blood


title: MON_SLE_29_01 MON_SLE_29_01_C8078ANXX_CGATGT_L003


title: wago-4_F1_oma-1_replicate2

city: Boston

first: Scott

last: Kennedy

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: 5' barcode CGTC

data_processing:
fastx_clipper to trim 3' adaptor (CTGTAGCCAGCATCAATAGATCGGAAGAGCAC), -Q33, reads>14nt were kept
covert fastq to fasta
remove 5' barcode with customed python script
map to the c. elegans genome (WS220) using bowtie
samtool view and sort.
Genome_build: WS220
plot using customed python script
Supplementary_files_format_and_content: bed

organism: Caenorhabditis elegans

source_name: larve L4 animals

growth_protocol: Embryos were collected via hypochlorite treatment and placed ontoHT115 bacteria expressing dsRNA against oma-1. Animals were grown to L4 stage(about 48h growth on bacteria) befoere collected)

extract_protocol:
Animals were flash frozen in liquid nitrogen, extract with Trizol, 20ug total RNAs were separated with 15% Urea gel.
Small RNA from about 18 nt to 35 nt were cut from gel.  Small RNAs were ligated to a 3' end linker(/5rApp/CTG TAG GCA CCA TCA AT/3ddC/), 5' end were treated with antarctic phosphatase and T4 PNK, result RNAs were ligated to 5' end linker (/5AmMC6/ ACG CTC TTC CGA TCT rArGrCrG or /5AmMC6/ ACG CTC TTC CGA TCT rCrGrUrC), RNAs with linkers were reverse transcribed using GGAGTTCAGACGTGTGCTCTTCCGATCT ATTGATGCTGGCTACAG as primer, PCR libraries were amplified.

tag: genotype

tag: generations

tag: 5' adaptor

value: /5AmMC6/ ACG CTC TTC CGA TCT rCrGrUrC


title: MON_SLE_32_01 MON_SLE_32_01_C8078ANXX_ACAGTG_L004

tag: donor


title: wago-4_F1_oma-1_replicate1

description: 5' barcode CGTC


title: znfx-1_F1_oma-1_replicate2

description: 5' barcode CGTC


title: MON_SLE_31_01 MON_SLE_31_01_C8078ANXX_TGACCA_L003

tag: ancestry


title: MON_SLE_27_01 MON_SLE_27_01_C8078ANXX_ATTCCT_L002

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_27 donor blood

tag: phenotype


title: MON_SLE_27_01 MON_SLE_27_01_C8078ANXX_ATTCCT_L001

tag: gender


title: znfx-1_P0_oma-1_replicate2

description: 5' barcode AGCG

value: /5AmMC6/ ACG CTC TTC CGA TCT rArGrCrG


title: znfx-1_F1_oma-1_replicate1

description: 5' barcode CGTC


title: wago-4_P0_oma-1_replicate1

description: 5' barcode AGCG


title: WT_F1_oma-1_replicate2

description: 5' barcode CGTC

value: WT


title: MON_SLE_28_01 MON_SLE_28_01_C8078ANXX_ATCACG_L003

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_28 donor blood

tag: age


title: MON_SLE_26_01 MON_SLE_26_01_C8078ANXX_ACTGAT_L002

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_26 donor blood


title: WT_P0_oma-1_replicate2

description: 5' barcode AGCG


title: znfx-1_P0_oma-1_replicate1

description: 5' barcode AGCG


title: wago-4_P0_oma-1_replicate2

description: 5' barcode AGCG


title: WT_F1_oma-1_replicate1

description: 5' barcode CGTC


title: MON_SLE_28_01 MON_SLE_28_01_C8078ANXX_ATCACG_L004


title: MON_SLE_25_01 MON_SLE_25_01_C8078ANXX_GAGTGG_L002

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_25 donor blood


title: MON_SLE_24_01 MON_SLE_24_01_C8078ANXX_CGTACG_L002

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_24 donor blood


title: MON_SLE_26_01 MON_SLE_26_01_C8078ANXX_ACTGAT_L001


title: WT_P0_oma-1_replicate1

description: 5' barcode AGCG


title: MON_SLE_24_01 MON_SLE_24_01_C8078ANXX_CGTACG_L001


title: MON_SLE_30_01 MON_SLE_30_01_C8078ANXX_TTAGGC_L003

value: Asian


title: Ctrl-input-CSE1L

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

data_processing:
Basecalls performed by BGI, Shenzhen.
Data were filtered using samtools to remove potential PCR duplicates
MeDIP sequencing reads were mapped to the Human genome (hg19) using Bowtie2.
Sequencing qualities were evaluated with FASTQC software and then the reads were aligned to hg19 genome sequences with a maximum of 2 mismatches allowed. Only the uniquely mapped reads were kept, and duplicate reads were removed. Mapped reads were extended to the average fragment sizes. Genome profile files were generated with IGV tools and linearly normalized to the same depth of 10 million reads.
RNA-Seq data were mapped by TopHat and quantitified by Crosslinks.
Genome_build: hg19
Supplementary_files_format_and_content: The transcription levels (RPKM) were quantified with Cufflinks (v2.0.2) software. Bigwig files were generated with IGV tools followed by UCSC utilities.

extract_protocol:
Genomic DNA was isolated by conventional phenol extraction and proteinase K treatment. For sperm samples, 40 mM DTT were added during cell lysis.
According to standard protocols provided by Illumina Kits.

tag: parental cell line

value: HEK-293 cell line

tag: cell line

tag: cell type

value: somatic cell line

tag: genotype/variation

value: embryonic kidney

tag: developmental stage

value: fetus


title: Ctrl-ChIP-CSE1L


title: MON_SLE_23_01 MON_SLE_23_01_C8078ANXX_GTTTCG_L002

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_23 donor blood

value: blood

value: F


title: Input-bioCSE1L


title: MON_SLE_23_01 MON_SLE_23_01_C8078ANXX_GTTTCG_L001


title: MON_SLE_25_01 MON_SLE_25_01_C8078ANXX_GAGTGG_L001

value: Caucasian


title: ChIPseq-bioCSE1L


title: MON_SLE_22_01 MON_SLE_22_01_C8078ANXX_GTGGCC_L001

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_22 donor blood

value: SLE


title: MON_SLE_21_01 MON_SLE_21_01_C8078ANXX_GTGAAA_L002

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_21 donor blood


title: MON_SLE_20_01 MON_SLE_20_01_C8078ANXX_GTCCGC_L001

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_20 donor blood


title: MON_SLE_22_01 MON_SLE_22_01_C8078ANXX_GTGGCC_L002


title: MON_SLE_21_01 MON_SLE_21_01_C8078ANXX_GTGAAA_L001


title: MON_SLE_19_01 MON_SLE_19_01_C8078ANXX_CCGTCC_L002

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_19 donor blood


title: MON_SLE_18_01 MON_SLE_18_01_C8078ANXX_ATGTCA_L002

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_18 donor blood


title: MON_SLE_18_01 MON_SLE_18_01_C8078ANXX_ATGTCA_L001


title: Spleen classical dendritic cells, biological rep 3

city: St. Louis

first: Daniel

last: Link

state: MO

address: 660 South Euclid Avenue

department: Internal Medicine

institute: Washington University in St Louis

description: 905 Sp

hyb_protocol: Following fragmentation and labeling, 2.5 ug of cDNA were hybridized onto the Gene 1.0 ST arrays and placed in GeneChip Hybridization Oven 640 for 18 hr at 45C. Gene Chip’s were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: The data were analyzed with Affymetrix Expression Console 1.4 using default analysis settings

source_name: FACS sorted classical dendritic cells from mouse spleen

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Pico reagent kit from 100pg-2ng total RNA.

growth_protocol: Mice were kept in regular mouse facility, standard mouse food and water were provided

extract_protocol: FACS sorted cells were directly collected in RLT lysis buffer and total RNA were extracted using Qiagen Rnesay Micro Kit (Cat# 74004, Qiagen)

treatment_protocol: Mice were killed using CO2 chamber, bone marrow were then harvested from femur and tibia.

value: 8 weeks after birth

value: Spleen

value: spleen classical dendritic cells


title: MON_SLE_17_01 MON_SLE_17_01_C8078ANXX_AGTTCC_L001

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_17 donor blood


title: Bone marrow myeloid dendritic cells, biological rep 3

description: 905 BM

source_name: FACS sorted myeloid cells from mouse bone marrow

value: Bone marrow

value: myeloid dendritic cells


title: B-CaM-teto_130_Mut__Rep_1

city: Ulm

first: Ruth

last: Simon

address: Albert-Einstein-Allee 11

department: Institute of Molecular and Cellular Anatomy

country: Germany

institute: University of Ulm

description: Gene expression data from adult DG granule cells

hyb_protocol: according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Affymetrix® Expression Console™ Software for RMA normalization, BRB Array Tools for statistical analysis

source_name: DG granule cells of Bcl11b mutant mice

growth_protocol: Mice were administered doxycycline with the drinking water throughout embryogenesis up to 2 months of age. Animals were sacrificed at 4 weeks after removal of doxycycline, the brain dissected and cryo sections prepared.

extract_protocol: RNA was isolated by using RNeasy Minikit (Qiagen) according to the manufacture's protocol.

treatment_protocol: Cryo sectios were stained with cresyl violet and DG granule dells were isolated by laser capture microdissection.

value: Dentate gyrus granule cells


title: B-CaM-teto_131_Mut__Rep_2

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay


title: Spleen classical dendritic cells, biological rep 2

description: 904 Sp


title: Bone marrow myeloid dendritic cells, biological rep 2

description: 904 BM


title: B-CaM-teto_133_Mut__Rep_3


title: Spleen classical dendritic cells, biological rep 4

description: 906 Sp


title: B-CaM-teto_126_Control_Rep_1

source_name: DG granule cells of Bcl11b control mice


title: Bone marrow myeloid dendritic cells, biological rep 1

description: 901 BM


title: Spleen classical dendritic cells, biological rep 1

description: 901 Sp


title: B-CaM-teto_156_Control_Rep_3


title: MON_SLE_16_01 MON_SLE_16_01_C8078ANXX_AGTCAA_L002

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_16 donor blood


title: MON_SLE_20_01 MON_SLE_20_01_C8078ANXX_GTCCGC_L002


title: MON_SLE_17_01 MON_SLE_17_01_C8078ANXX_AGTTCC_L002


title: MON_SLE_15_01 MON_SLE_15_01_C7JK7ANXX_CTTGTA_L008

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_15 donor blood


title: B-CaM-teto_142_Control_Rep_2


title: MON_SLE_16_01 MON_SLE_16_01_C8078ANXX_AGTCAA_L001


title: MON_SLE_15_01 MON_SLE_15_01_C7JK7ANXX_CTTGTA_L007


title: MON_SLE_19_01 MON_SLE_19_01_C8078ANXX_CCGTCC_L001


title: Bone marrow myeloid dendritic cells, biological rep 4

description: 906 BM


title: MON_SLE_14_01 MON_SLE_14_01_C7JK7ANXX_GGCTAC_L007

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_14 donor blood


title: STRT 10ug Replicate 2

city: Cambridge

first: Joshua

last: Levin

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

description: STRT

data_processing:
Fastq files were hard clipped and de-multiplexed for each method requiring it (see manuscript for details).
Fastq files for Five-Prime methods were mapped to hg19 with STAR (version 2.4.2a) using two-pass mode, and the softclip option to trim reads and otherwise default parameters.
For standard RNA-Seq data, we aligned untrimmed reads with Tophat (version v1.4.1) using default parameters except mate-inner-dist set to 300 and mate-std-diff set to 500, followed by Cufflinks (v2.2.1) using the default settings.
Aligned reads were downsampled (to 20 million unique reads for the non-replicate samples (except for NanoCAGEXL), to 7 million for CAGE replicates, and to 5 million for the remaining replicates)
Peaks were called with Paraclu
Peaks were filtered for CAGE/RAMPAGE/NanoCAGE-XL/STRT with Capfilter
Genome_build: hg19
Supplementary_files_format_and_content: Bed files, containing called peaks (putative TSSs) and normalized scores for each peak.

source_name: Chronic Myeloid Leukemia cell line K-562 grown in tissue culture (Ambion)

extract_protocol: From Ambion (Thermo Fisher Scientific). Prepared from cells homogenized in ToTALLY RNA™ Lysis/Denaturation  Solution (Part no. AM8540G), flash-frozen in liquid nitrogen, and stored at –80°C until use. RNA isolated using  Ambion® RNA isolation reagents. Purified RNA underwent a stringent DNase treatment.

tag: total rna input


title: STRT 10ug Replicate 1

description: STRT


title: MON_SLE_13_01 MON_SLE_13_01_C7JK7ANXX_TAGCTT_L008

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_13 donor blood


title: MON_SLE_13_01 MON_SLE_13_01_C7JK7ANXX_TAGCTT_L007


title: MON_SLE_14_01 MON_SLE_14_01_C7JK7ANXX_GGCTAC_L008


title: STRT 5ug Replicate 2

description: STRT


title: MON_SLE_11_01 MON_SLE_11_01_C7JK7ANXX_GATCAG_L007

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_11 donor blood

value: M


title: STRT 5ug Replicate 1

description: STRT


title: STRT 1ug Replicate 1

description: STRT


title: MON_SLE_10_01 MON_SLE_10_01_C7JK7ANXX_ACTTGA_L008

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_10 donor blood


title: MON_SLE_10_01 MON_SLE_10_01_C7JK7ANXX_ACTTGA_L007


title: MON_SLE_09_01 MON_SLE_09_01_C7JK7ANXX_CAGATC_L007

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_09 donor blood

value: Maori


title: MON_SLE_07_01 MON_SLE_07_01_C7JK7ANXX_ACAGTG_L008

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_07 donor blood

value: Asian


title: MON_SLE_09_01 MON_SLE_09_01_C7JK7ANXX_CAGATC_L008


title: STRT 10ng

description: STRT


title: MON_SLE_08_01 MON_SLE_08_01_C7JK7ANXX_GCCAAT_L008

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_08 donor blood


title: MON_SLE_08_01 MON_SLE_08_01_C7JK7ANXX_GCCAAT_L007


title: MON_SLE_07_01 MON_SLE_07_01_C7JK7ANXX_ACAGTG_L007


title: MON_SLE_02_01 MON_SLE_02_01_C7JK7ANXX_CGATGT_L008

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_02 donor blood


title: MON_SLE_04_01 MON_SLE_04_01_C7JK7ANXX_TGACCA_L007

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_04 donor blood


title: MON_SLE_02_01 MON_SLE_02_01_C7JK7ANXX_CGATGT_L007


title: MON_SLE_03_01 MON_SLE_03_01_C7JK7ANXX_TTAGGC_L008

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_03 donor blood


title: MON_SLE_03_01 MON_SLE_03_01_C7JK7ANXX_TTAGGC_L007


title: MON_SLE_04_01 MON_SLE_04_01_C7JK7ANXX_TGACCA_L008


title: MON_SLE_01_01 MON_SLE_01_01_C7JK7ANXX_ATCACG_L008

description:
Total RNA with Ribo Zero and Globin Depletion
SLE_01 donor blood


title: normal esophageal tissue

city: Shantou

first: Qian

last: Yang

state: Guangdong

address: Xinling 22 Road

institute: Medical College of Shantou University

data_processing:
Tophat V2.0.6
easyRNAseq V1.6.0
Genome_build: hg19
Supplementary_files_format_and_content: text file with FPKM for Ensembl Gene IDs

source_name: adult male normal esophagus tissue

extract_protocol:
Total RNA was isolated using an RNeasy mini kit and analyzed on 1% formaldehyde-denatured agarose gels to ensure there was no degradation.
Paired-end libraries were synthesized by using the TruSeq(tm) RNA Sample Preparation Kit following the TruSeq(tm) RNA Sample Preparation Guide. Briefly, poly-A containing mRNA was purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented into small pieces by using divalent cations at 94oC for 8 min. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments then underwent an end repair process, the addition of a single 'A' base, and then ligation of the adapters. Products were then purified and enriched by PCR to create the final cDNA library. Purified libraries were quantified using a Qubit(r) 2.0 Fluorometer, and validated with a Agilent 2100 bioanalyzer to confirm the insert size and calculate the mole concentration. A cluster was generated by cBot, with the library diluted to 10 pM,, and then inserts were sequenced on the Illumina HiSeq 2500. Library construction and sequencing was performed at the Shanghai Biotechnology Corporation.

value: esophagus

value: normal esophageal tissue

tag: Sex

value: male


title: MON_SLE_01_01 MON_SLE_01_01_C7JK7ANXX_ATCACG_L007


title: MON_SLE_11_01 MON_SLE_11_01_C7JK7ANXX_GATCAG_L008


title: STRT 1ug Replicate 2

description: STRT


title: GRO-seq in siCTL and with no FCCP treatment of 3T3-L1 cells

first: Valentina

last: Perissi

address: 72 E. Concord St

institute: Boston University

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to mm8 by using bowtie aligner. 4.2 milions reads were randomly extracted from each sample in order to have the same number of reads across the samples for the downstream analyses and for the visualization in the browser at UCSC.
The bedgraph files were generated by using HOMER (http://homer.salk.edu/homer/).
Genome_build: mm8
Supplementary_files_format_and_content: bedgraph files displaying the continuous-valued data, as computed by HOMER (homer.salk.edu).

growth_protocol: 3T3-L1 cells were grown in 10% BCS/DMEM supplemented with 0.1 mM MEM non-essential aminoacids, 2mM L-glutamine, 1mM sodium pyruvate

extract_protocol:
The experiments were performed as previously described (Cardamone et al, Cell Reports 2014).
The library construction protocol followed the manufacturer’s instructions.

treatment_protocol: 3T3-L1 cells were treated with FCCP. The siRNAs specific for GPS2 were purchased from Invitrogen (Silencer Select siRNAs).

value: control

tag: treatment

value: no FCCP


title: GRO-seq in siGPS2 and with no FCCP treatment of 3T3-L1 cells

value: knock-down of GPS2


title: GRO-seq in siGPS2 and after 3 hours of FCCP treatment  of 3T3-L1 cells

value: FCCP


title: GRO-seq in siCTL and after 3 hours of FCCP treatment of 3T3-L1 cells


title: input DNA in MALE WT BAT (brown adipose tissue)

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to mm8 by using Bowtie2 aligner.
The bedgraph files were generated by using HOMER (http://homer.salk.edu/homer/).
Genome_build: mm8

source_name: mouse brown adipose tissue (BAT)

growth_protocol: Fat-specific GPS2 knockout mice (GPS2-AKO) were generated using a cre/lox approach and maintained on a mixed 129sv/C57BL6J background. The conditional Gps2 floxed mice were generated by inGenious Targeting Laboratory and adipose tissue specific deletion was achieved by crossing Gps2flox/flox mice with heterozygous Adipoq-Cre C57BL/6J transgenic mice expressing Cre recombinase under control of the adiponectin promoter. Male mice and littermate controls were used for all experiments.

extract_protocol:
Tissue was minced with curved scissors (slurry like) and put in 10ml tubes containing PBS 1% formaldehyde for crosslink for 15 min at RT and neutralized with 0.125 M glycine. Tissue was then shredded in Lysis Buffer using a Bullet Blender Homogenizer at max power for 5 min 4°C. After sonication, chromatin was incubated with 2¬μg of antibody at 4 °C overnight. Immunoprecipitated complexes were collected using sepharose beads A (Life Technologies). After extensive washes the DNA was extracted and purified by phenol/chloroform extraction.
The library construction protocol followed  the manufacturer’s instructions.

treatment_protocol: Brown Adipose Tissue was isolated from GPS2-WT and GPS2-KO mice.

tag: background strain

value: GPS2 wildtype

value: Male

tag: tissue

value: mouse brown adipose tissue (BAT)


title: input DNA in MALE KO BAT (brown adipose tissue)

value: GPS2 knockout


title: H3K9me3 ChIP-seq in MALE WT BAT (brown adipose tissue)


title: H3K9me3 ChIP-seq in FEMALE KO BAT (brown adipose tissue)

value: Female


title: input DNA in FEMALE KO BAT (brown adipose tissue)


title: H3K9me3 ChIP-seq in FEMALE WT BAT (brown adipose tissue)


title: input DNA in FEMALE WT BAT (brown adipose tissue)


title: esophageal squamous cell carcinoma

source_name: adult male esophagus cancer tissue

value: fibrosarcoma with esophageal squamous cell carcinoma


title: GPS2 ChIP-seq in minus (no) FCCP treatment of 3T3-L1 cells

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to mm8 by using Bowtie2 aligner.
The bedgraph files were generated by using HOMER (homer.salk.edu/homer/), after combining the replicates in -FCCP and +FCCP experiments, and keeping 1copy/read, shall a read have multiple copies.
The peaks were called by using HOMER (homer.ucsd.edu/homer/).
Genome_build: mm8

source_name: 3T3-L1 cells

extract_protocol:
The experiments were performed as previously described (Cardamone et al, Cell Reports 2014)
The library construction protocol followed  the manufacturer’s instructions.

treatment_protocol: 3T3-L1 cells were treated with FCCP.


title: GPS2 ChIP-seq in plus (with) FCCP treatment of 3T3-L1 cells


title: GPS2 ChIP-seq in MALE WT BAT (brown adipose tissue)

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to mm8 by using Bowtie2 aligner.
The bedgraph files were generated by using HOMER (http://homer.salk.edu/homer/).
The peak files were generated by using HOMER on WT sample having KO sample as background.
Genome_build: mm8


title: GPS2 ChIP-seq in FEMALE WT BAT (brown adipose tissue)


title: GPS2 ChIP-seq in FEMALE KO BAT (brown adipose tissue)


title: H3K9me3 ChIP-seq in MALE KO BAT (brown adipose tissue)


title: GPS2 ChIP-seq in MALE KO BAT (brown adipose tissue)


title: 143B rho+ - rep 3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from 143B rho+ -

hyb_protocol: 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console and Expression Console Software (AGCC; Version 3.2 and Expression Console; Version 1.2) using the MAS5 algorithm to generate .CHP files.

source_name: control

label_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Plus kit protocol.

growth_protocol: all cells were grown in DMEM high glucose medium supplemented with uridine and pyruvate.

extract_protocol: RNA was isolated using the qiagen mini kits and the Qiashredder

treatment_protocol: HEK293 were exposed to doxycycline to induce the DN-POLG transgene

value: 143B osteosarcoma


title: H3K9me3 ChIP-seq in siGPS2

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to mm8 by using bowtie aligner. 19 milions reads were randomly extracted from each sample for downstream analyses.
The bedgraph files were generated by using HOMER (http://homer.salk.edu/homer/).
Genome_build: mm8

extract_protocol: The library construction protocol followed  the manufacturer’s instructions.

treatment_protocol: siRNAs specific for GPS2 were purchased from Invitrogen (Silencer Select siRNAs).

tag: chip antibody

value: H3K9me3 (6f12-h4-Enzo Life Sciences)


title: POL2 ChIPseq in siCTL

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to mm8 by using bowtie aligner. 9 milions reads were randomly extracted from each sample for downstream analyses.
The bedgraph files were generated by using HOMER (http://homer.salk.edu/homer/).
Genome_build: mm8

value: Pol2 (ac-055-100-adgenode mouse)


title: POL2 ChIPseq in siGPS2


title: 143B rho+ - rep 2

description: Gene expression from 143B rho+ -


title: AOX/NDI1 - day 0 rep 3

description: Gene expression from AOX/NDI1 - day 0

source_name: control + ectopic NADH oxidation


title: 143B rho0 - rep 2

description: Gene expression from 143B rho0 -

source_name: chronically mtDNA depleted


title: AOX/NDI1 - day 9 rep 3

description: Gene expression from AOX/NDI1 - day 9

source_name: mtDNA depleted + ectopic NADH oxidation


title: 143B rho+ - rep 1

description: Gene expression from 143B rho+ -


title: 143B rho0 - rep 3

description: Gene expression from 143B rho0 -


title: 143B rho0 - rep 1

description: Gene expression from 143B rho0 -


title: AOX/NDI1 - day 0 rep 3_methylation

first: Janine

last: Santos

address: 111 TW Alexander drive

department: GISBL

description: AOX/NDI1 - day 0

hyb_protocol: Illumina InfiniumHD Methylation Protocol.

scan_protocol: Slides were scanned with an Illumina BeadArray Reader with BeadScan (version 3).

data_processing: Data obtained using Illumina GenomeStudio software (V2011.1).

label: Cy3 and Cy5

extract_protocol: DNA was isolated using the qiagen 20G kit and bisulfite converted using the Zymoresearch kit


title: 143B rho+ - rep 3_methylation

description: 143B rho+ -

label_protocol: Illumina InfiniumHD Methylation Protocol.


title: AOX/NDI1 - day 9 rep 2_methylation

description: AOX/NDI1 - day 9


title: 143B rho+ - rep 2_methylation

description: 143B rho+ -


title: AOX/NDI1 - day 0 rep 2_methylation

description: AOX/NDI1 - day 0


title: H3K9me3 ChIP-seq in siCTL


title: 143B rho0 - rep 2_methylation

description: 143B rho0 -


title: AOX/NDI1 - day 9 rep 1

description: Gene expression from AOX/NDI1 - day 9


title: 143B rho0 - rep 3_methylation

description: 143B rho0 -


title: STRT 100ng

description: STRT


title: 143B rho0 - rep 1_methylation

description: 143B rho0 -


title: 143B rho+ - rep 1_methylation

description: 143B rho+ -


title: AOX/NDI1 - day 9 rep 1_methylation

description: AOX/NDI1 - day 9


title: AOX/NDI1 - day 0 rep 2

description: Gene expression from AOX/NDI1 - day 0


title: AOX/NDI1 - day 9 rep 3_methylation

description: AOX/NDI1 - day 9


title: DN-POLG - day 0 rep 3_methylation

description: DN-POLG - day 0