title: MGAS29162

value: Subclade1B (SC1B)

tag: growth phase


title: Mother_P174

status: Public on Dec 31 2018

type: genomic

city: Maastricht

first: Masoud

last: Zamani Esteki

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

description: DNA extracted from peripheral venous blood of the mother.

hyb_protocol: According to the manual of Infinium II Assay (Illumina, USA).

scan_protocol: The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA)

data_processing:
The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. We subsequently fed these data into siCHILD algorithm, which is equipted with haplarithmisis (Zamani Esteki et al. 2015, AJHG).
Image data was analyzed using Genomestudio with genotyping module (Illumina).

label: Cy5, Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood

label_protocol: The samples were not labelled before the hybridization. The staining is based on post-hybridization Cy5/Cy3 labelling by extension, according to the manual of Infinium II Assay (Illumina, USA).

extract_protocol: A total of 9 mL of peripheral venous blood from parents and 4 mL of umbilical cord blood were collected into ethylenediaminetetraacetic acid-containing tubes (BD Vacutainer, Becton, Dickinson and Co) for DNA extraction. DNA was isolated from blood and the placental tissue using PureLink® Genomic DNA Kit (Invitrogen, Life Technologies™) according to manufacturer’s protocol. DNA samples were eluted with 200 µL of PureLink® Genomic Elution Buffer (10 mM Tris-HCl, pH 9.0, 0.1 mM EDTA) and stored at -20 °C until analysis. NanoDrop 2000 (Thermo Fisher Scientific Inc.) was used to assess DNA concentration and purity.

treatment_protocol: Full-thickness placental blocks of around 1 cm were taken from the placenta and stored at -80 °C for subsequent DNA extraction. The maturity and health of the term placenta were confirmed by histological examination.

tag: dna sample

value: multi cells

tag: quartet

tag: conception method

value: IVF

tag: tissue

value: Peripheral blood

tag: birthweight at delivery

value: AGA


title: Male_Achl_RNAi_CT30

type: SRA

city: Saint Louis

first: Jiajia

last: Li

state: MO

address: 9952 CSRB, 4939 Children's Place.

department: Department of Medicine

country: USA

institute: Washington University in St. Louis

library_source: transcriptomic

data_processing:
STAR was used to align raw reads to the reference Drosophila genome and transcriptome, RSEM was used to quantify the expression.
Genome_build: dm6
Supplementary_files_format_and_content: STAR-RSEM-generated TPM per gene per sample

molecule: total RNA

organism: Drosophila melanogaster

source_name: heads

growth_protocol: 3-5 day old adult flies were collected. Flies were maintained on standard food at 25 degrees under 12hr:12hr light:dark condition. The incubator light scheme was adjusted to constant darkness 24 hours before collection starts and maintained under constant darkness duringt the enitire collection period.

extract_protocol:
fly heads were manually dissected in PBS and homogenized in Ttizol (Life Technologies), total RNAs were collected using Phase lock gels (5Prime) and RNeasy mini kit (Qiagen)
libraries were prepared with 200ng total RNA per sample using TruSeq Stranded mRNA LT prep kit (Illumina)

tag: gender

value: Male

tag: genotype

tag: time

value: heads


title: REC#3

city: DAEGU

first: JAE

middle: HO

last: LEE

address: 333, Techno jungang-daero, Hyeonpung-myeon, Dalseong-gun

department: NewBiology

country: South Korea

institute: DGIST

data_processing:
Illumina HiSeq generated raw images using HiSeq Control Software v2.2 for the system control and base calling using Real Time Analysis v1.18-integrated primary analysis software.
The BCL (base calls) binary files were converted into FASTQ format using Illumina package bcl2fastq (v1.8.4).
Quality control and preprocessing of metagenomic data were performed using FastQC (v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapters and low quality sequences were filtered out with Trimmomatic v0.32.3 (Bolger et al., 2014), and alignment was performed using the Arabidopsis TAIR10 genome (ENSEMBL annotation) and TopHat 2.0.9 (Trapnell et al., 2009). PCR duplication was removed using Picard (v1.119; http://broadinstitute.github.io/picard/), and only uniquely mapped reads were counted using HTSeq v0.6.1 (Anders et al., 2015).
A differential gene expression analysis was performed using DESeq2 (Love et al., 2014). P-values were adjusted via the Benjamini–Hochberg method (Benjamini and Hochberg, 1995), and differentially expressed genes with false discovery rates (FDR) < 0.05 were considered significant.
Genome_build: Arabidopsis_thaliana.TAIR10
Supplementary_files_format_and_content: tab-delimited text file including read counts processed by HTSeq-count.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana, floral abscission zone (REC), 16 stage

growth_protocol: Arabidopsis plants were grown in soil in growth chambers at 22°C ± 2°C. The photoperiod was 16-h light/8-h dark (110 μmol m−2 s−1).

extract_protocol:
Total RNA from the protoplasts was extracted using the RNeasy™ Micro Kit (QIAGEN) according to the manufacturer’s instructions. RNA was eluted in 14-μl water, and RNA quality was monitored using a Bioanalyzer Pico chip (Agilent Technologies).
cDNA was generated using SMART-Seq V4 Ultra Low Input RNA Kit (Clontech) with 18 amplification cycles, and RNA-seq libraries were generated using the TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s manual. The libraries were qualitatively and quantitatively verified and then loaded onto a flow cell for cluster generation using cBot and TruSeq PE Cluster Kit v3 (Illumina).

value: REC (abscission zone of receptacle)


title: MGAS29161

city: Houston

first: Priyanka

last: Kachroo

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

data_processing:
Multiplexed SE libraries were sequenced on an Illumina NextSeq 500 instrument. Reads from each pool were demultiplexed into separate fastq files corresponding to individual samples based on the inline barcodes using FASTX-toolkit.
RNAtag-seq reads from all strains were mapped to reference strain MGAS6180 (GenBank accession number CP000056), using Edge-pro v1.3.1 (Estimated Degree of Gene Expression for Prokaryotes).
Low-expressed genes and genes encoding ribosomal RNAs and tRNAs were filtered out prior to running differential expression analyses
Differential expression analysis was perfomed using DESeq2 v1.6.3 and NOISeq-sim (NOISeq package) running in R version 3.4.0. Differentially expressed genes were identified in each of the 441 strains compared to a common reference strain (MGAS28737).
Genome_build: reference strain MGAS6180 (GenBank accession number CP000056)
Supplementary_files_format_and_content: normalized counts

organism: Streptococcus pyogenes

source_name: cell pellet

growth_protocol: Cells were grown in Todd-Hewitt broth supplemented with yeast extract (THY media) at 37 C in atmosphere supplemented with 5% CO2

extract_protocol:
Pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using Turbo DNA-free (Ambion), and rRNA was depleted using Ribo-Zero (Illumina)
Resultant RNAs were tagged and pooled, reverse transcribed to cDNA, tagged a second time, pooled into superpools and sequenced

treatment_protocol: At the desired growth stage, early-stationary (OD 600nm 1.65), the culture was treated with RNAprotect Bacteria Reagent and cells were harvested by centrifugation

tag: subclade

tag: site of isolation

value: invasive infection isolate

value: Early-stationay (ES, OD600nm=1.65)


title: Male_Achl_RNAi_CT24


title: Female_Control_CT70

value: Female

value: Control


title: MGAS29143


title: Mother_P169


title: Female_Control_CT68


title: Father_P169

description: DNA extracted from peripheral venous blood of the father.


title: MGAS29140


title: MGAS29138


title: Female_Control_CT64


title: Umbilicalcord_P169

description: DNA extracted from umbilical cord blood of the newborn.

source_name: Cord blood

value: Cord blood


title: Male_Achl_RNAi_CT26


title: Placenta_P169

description: DNA extracted from placenta tissue.

source_name: Placenta tissue

value: Placenta tissue


title: Male_Achl_RNAi_CT28


title: MGAS29133


title: Female_Control_CT62


title: MGAS29147


title: Female_Control_CT60


title: MGAS29127


title: MGAS29125


title: Mother_P164


title: Female_Control_CT58


title: MGAS29124


title: Umbilicalcord_P164


title: Female_Control_CT66


title: Female_Control_CT54


title: GpatHF-HF 44L

type: RNA

city: Stockholm

first: Thais

last: de Castro Barbosa

state: Stockholm

address: von Eulers väg 4a

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Affymetrix GeneTitan instruments were used for hybridization, wash, stain and scanning of Rat Gene 1.1 ST Array Plates

scan_protocol: Arrays were scanned in a Affymetrix GeneTitan Scanner

data_processing: Generated CEL files were preprocessed using Affymetrix Expression Console using the Probe Logarithmic Intensity Error (PLIER) method for summarization, PM-GCBG for background correction and Global Median for normalization.

label: Biotin

organism: Rattus norvegicus

source_name: Rat liver - Grandpaternal HFD on HFD

label_protocol: 200 ng of total RNA was used as input to generate sense-strand cDNA with  Ambion® WT Expression kit (Life Technologies: PN 4425209). The generated sense-strand cDNA was fragmented and biotin labelled using Affymetrix® GeneChip WT Terminal Labeling Kit (Affymetrix: PN 900671).

growth_protocol: Sprague-Dawley female rats were maintaned under a temperature-controlled environment and 12:12-h light:dark cycle. Adult females were fed either a control chow diet or a high-fat diet (42/45% energy from fat) for 12 weeks. Gonadal white adipose tissue was dissect and store at -80C until use.

extract_protocol: Total RNA was extracted using the RNeasy Lipid Tissue kit from Qiagen according to manufacturer’s instructions.  RNA quality was confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies), and RNA concentration was measured on a NanoDrop (Thermo Scientific).

treatment_protocol: Not applicable.

tag: strain

value: Sprague-Dawley

value: Liver


title: GpatHF-HF 47L


title: GpatHF-HF 46L


title: MGAS29109


title: MGAS29108


title: Female_Control_CT52


title: Mother_P163


title: Father_P164


title: GpatHF-HF 45L


title: GpatHF-CD 42L

source_name: Rat liver - Grandpaternal HFD on Chow diet


title: GpatHF-CD 41L


title: GpatHF-HF 24L


title: Placenta_F1801

description:
Sample 269
DNA extracted from placenta tissue.

data_processing: The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. We subsequently fed these data into siCHILD algorithm, which is equipted with haplarithmisis (Zamani Esteki et al. 2015, AJHG). Image data was analyzed using Genomestudio with genotyping module (Illumina).

value: Multi cell

tag: conception


title: Umbilicalcord_P163


title: MGAS29105

value: Subclade1B (SC1B)


title: Female_Control_CT56


title: GpatHF-CD 40L


title: Female_Control_CT48


title: Placenta_P163

description: DNA extracted from placenta tissue.

value: multi cells


title: Female_Control_CT46


title: Placenta_P164

description: DNA extracted from placenta tissue.

value: IVF


title: MGAS29117


title: GpatHF-CD 39L


title: GpatHF-CD 38L


title: MGAS29095


title: MGAS29094


title: Mother_P161

value: Peripheral blood


title: GpatHF-CD 37L


title: Father_P163

value: AGA


title: Female_Control_CT50


title: MGAS29088


title: Father_P161


title: Female_Control_CT42


title: MGAS29086


title: Female_Control_CT40


title: MGAS29080


title: Umbilicalcord_P161


title: GpatCD-HF 35L

source_name: Rat liver - Grandpaternal Chow on HFD


title: Female_Control_CT38


title: GpatCD-HF 34L


title: MGAS29076


title: Female_Control_CT36


title: Placenta_P161

description: DNA extracted from placenta tissue.


title: Father_P135


title: MGAS29075


title: Female_Control_CT34


title: Female_Control_CT44


title: MGAS29074


title: Umbilicalcord_P135


title: Female_Control_CT32


title: GpatCD-HF 33L


title: MGAS29073


title: GpatCD-HF 22L


title: Placenta_P135

description: DNA extracted from placenta tissue.


title: GpatCD-CD 30L

source_name: Rat liver - Grandpaternal Chow on Chow diet


title: Female_Control_CT30


title: MGAS29069


title: Mother_P128


title: GpatCD-CD 29L


title: Female_Control_CT28


title: Mother_P135


title: Umbilicalcord_P128


title: Father_P128


title: Female_Control_CT26


title: MGAS29061


title: Placenta_P128

description: DNA extracted from placenta tissue.


title: MGAS29054


title: GpatCD-CD 28L


title: Female_Control_CT24


title: GpatCD-HF 31L


title: Female_Achl_RNAi_CT70


title: GpatCD-HF 32L


title: Mother_P124


title: Female_Achl_RNAi_CT68


title: MGAS29051


title: GpatCD-CD 27L


title: Father_P124


title: MGAS29050


title: Female_Achl_RNAi_CT66


title: MGAS29045


title: Female_Achl_RNAi_CT64


title: MGAS29068


title: Umbilicalcord_P124


title: MGAS29043


title: Placenta_P124

description: DNA extracted from placenta tissue.


title: Mother_P116


title: Female_Achl_RNAi_CT62


title: MGAS29041


title: Father_P116


title: Female_Achl_RNAi_CT58


title: MGAS28935


title: Umbilicalcord_P116


title: MGAS28924


title: GpatCD-CD 21L


title: Female_Achl_RNAi_CT56


title: GpatCD-CD 26L


title: MGAS28921


title: Placenta_P116

description: DNA extracted from placenta tissue.


title: Female_Achl_RNAi_CT54


title: MGAS28916


title: Female_Achl_RNAi_CT52


title: Mother_P114


title: GpatCD-CD 25L


title: Father_P114


title: Female_Achl_RNAi_CT60


title: MGAS28904


title: Female_Achl_RNAi_CT50


title: MGAS28880


title: Umbilicalcord_P114


title: BAL_HV20

city: Hannover

first: Antje

last: Prasse

address: Carl-Neubergstrasse 1

department: Pneumology

country: Germany

institute: Medical School Hannover

description: HUGENE-1_0-ST-V1 HV_20

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Whole-Transcript Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using a CGS30007G scanner (serialnumber 54713600)

data_processing: Raw CEL files were RMA normalized using the R/Bioconductor package oligo (V.1.32.0) with default settings.  Gene expression data was normalized to the geometric mean of all samples using quantile normalization and expression levels were summarized.

label: biotin

source_name: Healthy Volunteer_BAL cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA

extract_protocol:
Isolation protocol: BAL cells were obtained by bronchoscopy, immediately isolated and 1 ml of TRIzol was added to the cell pellet, which was then immediately snap frozen in -80 celsius.
Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: diagnosis

value: Healthy Volunteer

tag: cohort

value: Freiburg

tag: age (yrs)

tag: gender (male=1)

tag: cell type

value: bronchoalveolar lavage (BAL) cells


title: Female_Achl_RNAi_CT48

value: heads


title: MGAS28825

value: invasive infection isolate

tag: growth phase

value: Early-stationay (ES, OD600nm=1.65)


title: BAL_HV18

description: HUGENE-1_0-ST-V1 HV_18


title: BAL_HV19

description: HUGENE-1_0-ST-V1 HV_19


title: MGAS28822


title: BAL_HV15

description: HUGENE-1_0-ST-V1 HV_15


title: Placenta_P114

description: DNA extracted from placenta tissue.

tag: dna sample

tag: quartet


title: Female_Achl_RNAi_CT44

value: Female

tag: tissue


title: Father_P106

tag: conception method

tag: birthweight at delivery


title: MGAS28811


title: BAL_HV12

description: HUGENE-1_0-ST-V1 HV_12


title: Female_Achl_RNAi_CT42

tag: gender

tag: genotype


title: BAL_HV17

description: HUGENE-1_0-ST-V1 HV_17


title: Mother_P106


title: BAL_HV14

description: HUGENE-1_0-ST-V1 HV_14


title: MGAS28772

tag: subclade


title: Female_Achl_RNAi_CT40

tag: time


title: BAL_HV16

description: HUGENE-1_0-ST-V1 HV_16


title: Umbilicalcord_P106

value: Cord blood


title: MGAS28766

tag: site of isolation


title: BAL_HV13

description: HUGENE-1_0-ST-V1 HV_13


title: PlacentaBiopsy3_P106

description: DNA extracted from placenta tissue.

value: Placenta tissue


title: Female_Achl_RNAi_CT38


title: Female_Achl_RNAi_CT46


title: MGAS28764


title: PlacentaBiopsy2_P106

description: DNA extracted from placenta tissue.


title: Female_Achl_RNAi_CT36


title: PlacentaBiopsy1_P106

description: DNA extracted from placenta tissue.


title: MGAS28747


title: Female_Achl_RNAi_CT34


title: BAL_HV11

description: HUGENE-1_0-ST-V1 HV_11


title: MGAS28737


title: Mother_P105


title: Female_Achl_RNAi_CT32


title: Father_P105


title: MGAS28724


title: Female_Achl_RNAi_CT30


title: Umbilicalcord_P105


title: BAL_HV7

description: HUGENE-1_0-ST-V1 HV_7


title: BAL_HV8

description: HUGENE-1_0-ST-V1 HV_8


title: MGAS28718


title: Placenta_P105

description: DNA extracted from placenta tissue.


title: BAL_HV6

description: HUGENE-1_0-ST-V1 HV_6


title: BAL_HV5

description: HUGENE-1_0-ST-V1 HV_5


title: Female_Achl_RNAi_CT26


title: BAL_HV9

description: HUGENE-1_0-ST-V1 HV_9


title: MGAS28716


title: Female_Achl_RNAi_CT28


title: Mother_P095


title: MGAS28710


title: Female_Achl_RNAi_CT24


title: MGAS28707


title: Father_P095


title: MGAS28688


title: Umbilicalcord_P095


title: MGAS28673


title: Placenta_P095

description: DNA extracted from placenta tissue.


title: MGAS28661


title: Mother_P091


title: Father_P091


title: MGAS28653


title: Umbilicalcord_P091


title: MGAS28654


title: MGAS28645


title: MGAS28622


title: BAL_HV4

description: HUGENE-1_0-ST-V1 HV_4


title: BAL_HV3

description: HUGENE-1_0-ST-V1 HV_3


title: Father_P077


title: BAL_HV2

description: HUGENE-1_0-ST-V1 HV_2


title: BAL_HV1

description: HUGENE-1_0-ST-V1 HV_1


title: BAL_SARC_25

description: HUGENE-1_0-ST-V1 SARC_25

source_name: SARC_BAL cells

value: SARC


title: MGAS28566


title: MGAS28657


title: Umbilicalcord_P077


title: Placenta_P091

description: DNA extracted from placenta tissue.


title: BAL_SARC_26

description: HUGENE-1_0-ST-V1 SARC_26


title: Mother_P075


title: MGAS28544


title: Placenta_P077

description: DNA extracted from placenta tissue.


title: MGAS28557


title: BAL_SARC_24

description: HUGENE-1_0-ST-V1 SARC_24


title: Father_P075


title: MGAS28530


title: BAL_SARC_16

description: HUGENE-1_0-ST-V1 SARC_16


title: BAL_SARC_18

description: HUGENE-1_0-ST-V1 SARC_18


title: BAL_SARC_17

description: HUGENE-1_0-ST-V1 SARC_17


title: MGAS28508


title: BAL_SARC_23

description: HUGENE-1_0-ST-V1 SARC_23


title: BAL_SARC_22

description: HUGENE-1_0-ST-V1 SARC_22


title: Umbilicalcord_P075


title: BAL_SARC_20

description: HUGENE-1_0-ST-V1 SARC_20


title: BAL_SARC_19

description: HUGENE-1_0-ST-V1 SARC_19


title: MGAS28505


title: Placenta_P075

description: DNA extracted from placenta tissue.


title: Mother_P072


title: BAL_SARC_21

description: HUGENE-1_0-ST-V1 SARC_21


title: Father_P072


title: MGAS28480


title: BAL_SARC_14

description: HUGENE-1_0-ST-V1 SARC_14


title: BAL_SARC_15

description: HUGENE-1_0-ST-V1 SARC_15


title: MGAS28473


title: Mother_P077


title: Umbilicalcord_P072


title: B16F12_Input

city: Shanghai

first: Fei

last: Lan

address: 130 Dong An Road

country: China

institute: Fudan university

library_source: genomic

data_processing:
base_calling: CASAVA package (Illumina v1.6)
alignment: Bowtie 2 (version 2.2.5) with -p 8 -k 1 -X 1000 and other default parameters
peak_calling: macs2 (version 2.1.1.20160309) with -p 0.00001 --nomodel
Genome_build: mm10
Supplementary_files_format_and_content: bed files including peak locations

organism: Mus musculus

source_name: mouse melanoma cell

extract_protocol:
Chromatin samples were incubated with specific antibodies in ChIP Lysis buffer (50mM HEPES pH7.5, 500mM NaCl, 1mM EDTA, 1%Triton, 0.1%Na-deoxylcholate, 0.3% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on protein A/G beads (10μl per reaction). The bound fractions were washed 3 times with Lysis buffer, and 3 times with RIPA buffer (50mM Hepes, 300mM LiCl, 1mM EDTA, 0.5%NP-40, 0.7%Nadeoxylcholate), and once with TE. Elution and Reverse crosslinking were carried out in Elution buffer (50mM Tris, PH8.0, 1mM EDTA, 1% SDS) 65℃ for 6 hours. After RNase A and protease K digestion, DNA fraction was purified using PCR extraction kit (QIAGEN).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: melanoma cell line B16-F12

tag: chip antibody


title: BAL_SARC_12

description: HUGENE-1_0-ST-V1 SARC_12

tag: diagnosis

tag: cohort


title: BAL_SARC_11

description: HUGENE-1_0-ST-V1 SARC_11

tag: age (yrs)

tag: gender (male=1)


title: Placenta_P072

description: DNA extracted from placenta tissue.


title: MGAS28295

tag: growth phase


title: Mother_P067

tag: dna sample

value: SGA


title: MGAS28273

value: Subclade1B (SC1B)


title: BAL_HV10

description: HUGENE-1_0-ST-V1 HV_10

tag: cell type


title: MGAS28455


title: BAL_SARC_9

description: HUGENE-1_0-ST-V1 SARC_9


title: Father_P067

value: multi cells

tag: quartet

tag: tissue


title: Umbilicalcord_P067

tag: conception method

value: IVF

tag: birthweight at delivery


title: MGAS28268


title: Placenta_P067

description: DNA extracted from placenta tissue.


title: MGAS28241


title: MGAS28481


title: B16F12_H3K14me3

value: H3K14me3 (homemade)


title: BAL_SARC_8

description: HUGENE-1_0-ST-V1 SARC_8


title: MGAS28208


title: BAL_SARC_10

description: HUGENE-1_0-ST-V1 SARC_10


title: BAL_SARC_13

description: HUGENE-1_0-ST-V1 SARC_13


title: Father_P064

value: Peripheral blood

value: AGA


title: MGAS28142


title: MGAS28108


title: Placenta_P064

description: DNA extracted from placenta tissue.


title: Control Myoblasts,D48 hours,Replicate1

city: Hyderabad

first: Nisha

last: Venugopal

state: Telangana

address: Habsiguda, Uppal Road

country: India

institute: CCMB

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChipMouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

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

data_processing: All the CEL (cell intensity) files generated by the  Affymetrix Gene Chip operating software (GCOS) Expression Console were loaded into the R Bioconductor affy package for microarray analysis,normalized using Loess Normalization method

source_name: Control siRNA treated C2C12 myoblasts in adherant culture with differentiation medium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Control and IFT88KD C2C12 myoblasts were cultured in different conditions to achieve different cell cycle states (Proliferating myoblasts (MB):Adherent culture, full growth medium (DMEM+20% FBS); Quiescent myoblasts (G0): Suspension culture, full growth medium (DMEM+20% FBS); Reactivated myoblasts (R2): G0 myoblasts replated after suspenion culture, full growth medium (DMEM+20% FBS); Differentiating myoblasts (D48): 80% confluent myoblasts in adherent culture cultured in Differentiation medium (DMEM +2% NHS) for 48 hours.)

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

treatment_protocol: Cells collected from different conditions were washed in ice cold PBS and lysed in TRIZol  solution

value: skeletal muscle myoblasts


title: Umbilicalcord_P064


title: Control Myoblasts,D48 hours,Replicate2


title: BAL_SARC_6

description: HUGENE-1_0-ST-V1 SARC_6

value: Freiburg

value: bronchoalveolar lavage (BAL) cells


title: BAL_SARC_7

description: HUGENE-1_0-ST-V1 SARC_7


title: MGAS28081

value: invasive infection isolate


title: BAL_SARC_5

description: HUGENE-1_0-ST-V1 SARC_5


title: IFT88KD Myoblasts,D48 hours,Replicate1

source_name: IFT88 siRNA treated C2C12 myoblasts in adherant culture with differentiation medium


title: IFT88KD Myoblasts,D48 hours,Replicate3


title: Mother_P064


title: Mother_P047


title: Father_P047


title: Control Myoblasts,R2 hours,Replicate3

source_name: Control siRNA treated C2C12 myoblasts 2 hours after replating after suspension culture with growth medium


title: Control Myoblasts,R2 hours,Replicate2


title: IFT88KD Myoblasts,D48 hours,Replicate2


title: Umbilicalcord_P047


title: MGAS28049

value: Early-stationay (ES, OD600nm=1.65)


title: BAL_SARC_1

description: HUGENE-1_0-ST-V1 SARC_1


title: MGAS28106


title: BAL_SARC_3

description: HUGENE-1_0-ST-V1 SARC_3


title: Control Myoblasts,D48 hours,Replicate3


title: BAL_SARC_2

description: HUGENE-1_0-ST-V1 SARC_2


title: 14286399 - Brassica_Benzene vs Brassica_Ctrl

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Improving the knowledge of the metabolic pathways of benzene in higher plants.

hyb_protocol: Brassica_Ctrl Cy5 / Brassica_Benzene Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Brassica napus

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: caulin leaf - Media=Compost Temperature=20°C

extract_protocol: Brassica_Ctrl:3ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: harvest date

tag: treatment

treatment_protocol: Name:Benzene - environmental treatment - abiotic stress,benzene:time 24hour . 2 months old cabbages are exposed to 3ppm of atmospheric benzene in a 300 liters hermetic chamber. Exposures were conducted over periods of 1h, 3h and 24h. We made biological replicates of exposures of 1h and 3h. As controls, non-exposed plants are located next the exposure chamber for each experiment. At the end of the exposure, pieces of leaves from 3 different plants were pooled and immediatly flash-frozen with liquid nitrogen and stored at -80°C until RNA extraction.

value: benzene


title: MGAS28048

tag: subclade


title: MGAS28059

tag: site of isolation


title: Mother_P042


title: MGAS28046


title: Father_P042


title: MGAS28032


title: 14286398 - Brassica_Ctrl vs Brassica_Benzene

hyb_protocol: Brassica_Benzene Cy5 / Brassica_Ctrl Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Control Myoblasts,R2 hours,Replicate1


title: MGAS27990


title: Umbilicalcord_P042

value: Cord blood


title: IFT88KD Myoblasts,R2 hours,Replicate2

source_name: IFT88 siRNA treated C2C12 myoblasts 2 hours after replating after suspension culture with growth medium


title: IFT88KD Myoblasts,R2 hours,Replicate3


title: Placenta_P042

description: DNA extracted from placenta tissue.

value: Placenta tissue


title: Placenta_P047

description: DNA extracted from placenta tissue.


title: MGAS27970


title: MGAS27967


title: IFT88KD Myoblasts,R2 hours,Replicate1


title: Control Myoblasts,Quiescence conditions,Replicate2

source_name: Control siRNA treated C2C12 myoblasts in suspension culture with growth medium


title: Father_P040

source_name: Peripheral blood


title: Mother_P040


title: BAL_SARC_4

description: HUGENE-1_0-ST-V1 SARC_4

value: SARC


title: Umbilicalcord_P040


title: MGAS27895


title: Placenta_P040

description: DNA extracted from placenta tissue.


title: Control Myoblasts,Quiescence conditions,Replicate3


title: Mother_P038


title: Control vs TNF-a stimulation+Doxycycline addition (NICD overexpression)

city: Tokyo

first: Ryuichi

last: Okamoto

state: Please Select

address: Tokyo Medical and Dental University

country: Japan

institute: Tokyo Medical and Dental University

hyb_protocol: Hybridization was done using 1μg of Cy5-labeled aRNA (Contol) and 1μg of Cy3-labeled aRNA (test) in the Hybridization Chamber (Takara Bio) for 16h, 37℃. After hybridization, slides were washed sequentially.

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal.Global normalized, background subtracted data were obtained from log2 of processed Green signal/processed Red signal.

source_name: Non-treated control of LS174T-tetON-NICD cells

label_protocol: First and 2nd strand cDNA synthesis, and synthesis of aRNA was done by Amino Allyl aRNA kit (Ambion, using 1μg of total RNA as a starting material. 10μg of aRNA were subsequently labeled either by Cy5 Mono-reactive Dye (Amersham) or Cy3 Mono-reactive Dye (Amersham).

growth_protocol: LS174T cells were maintained in minimum essential medium supplemented with 10% fetal calf serum, 1% penicillin-streptomycin, and 4 mM L-glutamine.

extract_protocol: Total RNA extracted using RNA Bee Reagent (Tel Test Inc) following manufacturer's instructions

treatment_protocol: un-treated control

tag: cell line background

tag: genotype/variation

value: un-treated control

source_name: LS174T-tetON-NICD cells, TNF-a and Doxycycline for 24h

treatment_protocol: Human recombinant TNF-a was added at a concentration of 50ng/ml for 24h. Doxycycline was added at a concentration of 100ng/ml for 24 h.

value: Stimulated with TNF-a (50ng/ml) for 24h and induced with Doxycycline (100ng/ml) for 24 h.


title: MGAS27865

source_name: cell pellet

value: Subclade1B (SC1B)


title: MGAS27848


title: MGAS27956


title: Umbilicalcord_P038

source_name: Cord blood

value: multi cells


title: MGAS27813


title: MGAS27846


title: IFT88KD Myoblasts,Quiescence conditions,Replicate1

source_name: IFT88 siRNA treated C2C12 myoblasts in suspension culture with growth medium


title: IFT88KD Myoblasts,Quiescence conditions,Replicate2


title: IFT88KD Myoblasts,Quiescence conditions,Replicate3


title: 5hmC_HK_466_rep2

type: protein

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

description: Array 466, 5hmC

hyb_protocol: The double-stranded arrays were blocked with 4% milk for 1 hour and washed with 0.1% Tween-20 in 1x PBS.  Freshly synthesized protein (25 µL) was mixed with 125 µL of protein binding reaction mixture consisting of 4% milk in 1x PBS, 50 ng of salmon testes DNA and 0.2 µg/µL bovine serum albumin and added to double-stranded array.  The protein binding reactions were carried out in hydration chamber for 1 hour followed by one wash with 0.5% Tween-20 in 1xPBS.  The protein bound array was incubated with Alexa Fluor 647 conjugated Anti-GST antibody for 1 hour, followed by three washes with 0.05 % Tween-20.  Finally array slides were washed and dried in 1x PBS and scanned using an Agilent Sure Scan II scanner.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 micron resolution. Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low). The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used. Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: For all possible 65,536 8-mers, a transformed 8-mer median intensity (Z-score) was calculated from the average signal intensity across array probes containing each 8-mer.  For the dsDNA data sets 8-mer Z-scores of the nascent strand (the reverse complement of the array probe sequence) were used for downstream analyses.

molecule: protein

label_protocol: 180 ng of plasmid containing DNA binding domains of Zta or CEBPB or cJun|cFos were used to express proteins using PureExpress in-vitro transcription translation kit (NEB) in 25 µL reaction volume as per manufacturer’s instructions.

extract_protocol: DBD sequences along with 15 amino acid residues on either side of the DBD in the native protein were cloned as NcoI-SacI fragments into a T7-driven C-terminal GST expression vector (Sharrocks 1994, Gene:138, 105-108).

treatment_protocol: The 16 grids of the Agilent HK design 44K DNA microarray was divided into four chambers containing four grids each using a gasket slide from Agilent.  One chamber was left as single-stranded DNA (ssDNA), and the three other sectors were double stranded using either cytosine, 5-methylcytosine (5mC, NEB)  , or 5hmC (5hmC, Zymo Research)by primer extension as described in Badis et al. Science (2009).  NFATc2 was bound to two grids in each of the four sectors.   The resulting double-stranded DNA on the array thus contained probes with either cytosine in both strands or modified cytosine (5mC/5hmC) in one strand and cytosine in the second strand.

tag: dbd

value: REL

tag: protein

tag: double-stranding treatment


title: Control Myoblasts,Quiescence conditions,Replicate1


title: 5hmC_HK_463_rep2

description: Array 463, 5hmC


title: 5hmC_HK_466_rep1

description: Array 466, 5hmC


title: Placenta_P038

description: DNA extracted from placenta tissue.

source_name: Placenta tissue

value: IVF


title: Control vs Doxycycline addition (NICD overexpression)

source_name: LS174T-tetON-NICD cells, Doxycycline for 24h

value: Induced with Doxycycline (100ng/ml) for 24 h.


title: Control Myoblasts,Proliferating condition,Replicate3

source_name: Control siRNA treated C2C12 myoblasts in adherant culture with growth medium


title: MGAS27767


title: Mother_P036

value: Peripheral blood

value: AGA


title: Father_P038


title: MGAS27787


title: Control Myoblasts,Proliferating condition,Replicate2

value: skeletal muscle myoblasts


title: 5hmC_HK_463_rep1

description: Array 463, 5hmC


title: Control Myoblasts,Proliferating condition,Replicate1


title: MGAS27754


title: IFT88KD Myoblasts,Proliferating condition,Replicate3

source_name: IFT88 siRNA treated C2C12 myoblasts in adherant culture with growth medium


title: Umbilicalcord_P036


title: MGAS12248


title: IFT88KD Myoblasts,Proliferating condition,Replicate2


title: 5hmC_HK_461_rep1

description: Array 461, 5hmC


title: Control vs TNF-a stimulation

source_name: LS174T-tetON-NICD cells, TNF-a for 24h

value: Stimulated with TNF-a  (50ng/ml) for 24h


title: MGAS11149

value: invasive infection isolate


title: Placenta_P036

description: DNA extracted from placenta tissue.


title: 5hmC_HK_461_rep2

description: Array 461, 5hmC


title: 5mC_HK_466_rep1

description: Array 466, 5mC


title: 5mC_HK_466_rep2

description: Array 466, 5mC


title: C_HK_466_rep2

description: Array 466, cytosine

value: Cytosine


title: C_HK_466_rep1

description: Array 466, cytosine


title: ssDNA_HK_466_rep2

description: Array 466, ssDNA


title: Father_P025


title: Mother_P025


title: MGAS11140

value: Early-stationay (ES, OD600nm=1.65)


title: Father_P036


title: MGAS11128


title: MGAS11123


title: MGAS11121


title: Umbilicalcord_P025

value: Cord blood


title: Mother_P019


title: Placenta_P025

description: DNA extracted from placenta tissue.

value: Placenta tissue


title: MGAS11113


title: MGAS11100


title: Umbilicalcord_P019


title: Father_P019


title: Placenta_P019

description: DNA extracted from placenta tissue.


title: MGAS11087


title: MGAS11138


title: MGAS11098


title: Mother_P177

value: Natural

value: SGA


title: MGAS8365


title: MGAS7982


title: Father_P177


title: TP3_control

city: Washington

first: Zhenzhi

state: DC

address: 3900 reservoir rd nw

department: Biochemistry and Molecular Biology

institute: Georgetown University

scan_protocol: Arrays were scanned by HiScan 2000 (Illumina) following its protocol.

data_processing: Illumina Genome Studio software (Illumina) was used to extract signal intensities for each probe and to perform initial control quality  checks.BSMAP was used to map raw reads to GRCh37 genome build, methyratui.py from BSMAP was used to compute number of converted/uncoverted Cytosine

label: Cy3, Cy5

source_name: twin pair 3 control

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from whole blood using the QIAamp DNA Mini Kit (Qiagen, Darmstadt, German), and assessed for integrity, quantity, purity and concentration by electrophoresis in a 1% agarose gel and Nanodrop2000 spectrophotometer.Bisulfite conversion of 500 ng of genomic DNA was performed using EZ 96-DNA methylation kit (Zymo Research, Irvine, CA, USA) following manufacturer’s standard protocol.

value: whole blood

tag: disease

value: normal control


title: ssDNA_HK_463_rep2

description: Array 463, ssDNA


title: ssDNA_HK_466_rep1

description: Array 466, ssDNA


title: ssDNA_HK_463_rep1

description: Array 463, ssDNA


title: MGAS7921

value: Subclade1B (SC1B)

tag: growth phase


title: Placenta_P177

description: DNA extracted from placenta tissue.

tag: dna sample

value: multi cells


title: TP1_control

source_name: twin pair 1 control


title: MGAS29608

value: Subclade1A (SC1A)


title: Mother_P172


title: MGAS29538


title: Father_P172


title: MGAS29393


title: MGAS28949


title: Umbilicalcord_P177


title: PlacentaBiopsy3_P172

description: DNA extracted from placenta tissue.


title: MGAS28907


title: PlacentaBiopsy2_P172

description: DNA extracted from placenta tissue.


title: Umbilicalcord_P172


title: PlacentaBiopsy1_P172

description: DNA extracted from placenta tissue.


title: MGAS28900


title: Mother_P162


title: MGAS28879


title: MGAS28845


title: Father_P162


title: TP2_control

source_name: twin pair 2 control


title: TP3_case

source_name: twin pair 3 case

value: autism spectrum disorder


title: MGAS28840


title: MGAS28804


title: TP2_case

source_name: twin pair 2 case


title: Placenta_P162

description: DNA extracted from placenta tissue.


title: Umbilicalcord_P162


title: Med1 knowkout (KO)

city: San Francisco

first: Yuko

last: Oda

state: CA

address: 111N-MB 360 1700 Owens St, Suite 360

department: Endocrine Research

institute: VA Medical Center UCSF

description:
KO incisor forms ectopic hair
3998333007_F

hyb_protocol: Standard Illumina hybridization protocol done by UCLA neuroscience genomics core

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalized by using quantile method in Genome studio V2011.1

source_name: Dental epithelial stem cells

label_protocol: Standard Illumina hybridization protocol cDNA labeled by Biotin and detected by Cy3-streptoavidin

growth_protocol: Med1 is removed from keratin 14 (K14) expressing dental epithelia including epithelial stem cells (DESC) by using Crelox stragety

extract_protocol: Total RNA was isolated from cultured DESC using Pico Pure RNA purification kit (ABI).

treatment_protocol:
Dental epithelial stem cells (DESC) were isolated according to the method previously described (Chavez MG, Hu J, Seidel K, Li C, Jheon A, Naveau A, Horst O, Klein OD. J Vis Exp. 2014, 87). Briefly, labial cervical loop tissues containing DESC were micro-dissected from lower hemi-mandibles of Med1 KO mice (3 months old) and their littermate control mice (n=3). Cells were isolated by cell detachment solution, and were plated in low density so that only stem cells are able to grow as a single colony.  Cells were maintained in DESC media containing DMEM/F12 with recombinant EGF and FGF for 7 days. RNA was isolated from primary culture of DESC without passage.
plated in low density so that only stem cells are able to grow as a single colony.  Cells were maintained in DESC media containing DMEM/F12 with recombinant EGF and FGF for 7 days. RNA was isolated from primary culture of DESC without passage.

tag: strain

tag: age

value: Cells derived from 3 month old mice

tag: genotype

value: Med1 fl/fl Krt14 driven Cre

value: keratinocyte isolated from cervical loop of tooth


title: TP1_case

source_name: twin pair 1 case

tag: tissue


title: Control (CON)

description:
CON incisor generates enamel
3998333007_E

value: Med1 fl/fl


title: MGAS28739

value: invasive infection isolate


title: Fmod_liver_rep2

city: Los Angeles

first: Xia

last: Yang

address: 610 Charles E. Young Dr. East

institute: UCLA

description: F

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using a robust spline normalization (RSN) with lumi (v2.10.0) in R (v2.15.0)

label_protocol: Standard Illumina label protocol

extract_protocol: RNA was extracted with QIAGEN RNeasy Mini Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain background

tag: gender

value: male

value: Fmod knockout

value: 13 weeks

value: liver


title: Fmod_liver_rep1

description: E


title: Fmod_liver_rep3

description: G


title: Fmod_hypo_rep4

description: D

value: hypothalamus


title: MGAS28708

value: Early-stationay (ES, OD600nm=1.65)


title: Father_P157

source_name: Peripheral blood

tag: quartet

tag: conception method

value: Natural

value: Peripheral blood

tag: birthweight at delivery

value: SGA


title: IFT88KD Myoblasts,Proliferating condition,Replicate1

tag: cell type

value: skeletal muscle myoblasts


title: Cold_T48_10_Rep C

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

description:
30_c_28_48_ATTCCT_L008
10_Cold_T48_C (fpkm)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,
Mapping with RSEM
Differential Expression Calling with EdgeR
Genome_build: PRJNA13023; ASM34128v1
Supplementary_files_format_and_content: fpkm, logFC, raw counts etc. per gene

organism: Galdieria sulphuraria

source_name: Batch Culture - Biological Replicate C - Autorophic - 2xAllen Medium

growth_protocol: 42°C/28°C, constant illumination (90 μE) and constant shaking (160 rpm) in photoautotrophic conditions using 2xGS Medium (M. B. Allen (1959). Studies with cyanidium caldarium, an anomalously pigmented chlorophyte. Archiv für Mikrobiologie, vol. 32, no. 3, p. 270–277.)

extract_protocol:
RNA was extracted using Roboklon’s Universal RNA Purification Kit by following the “plant tissue samples” protocol (Roboklon, Berlin - Germany). RNA quality and concentration was assessed using a Nanodrop photospectrometer ND-1000 (Peqlab Biotechnologie GmbH, Erlangen -Germany).
The samples were synthetized to Illumina HiSeq2000 compatible RNA-Seq libraries strictly following "Illumina TruSeq RNA Sample Prep v2 LS Protocol" (Illumina, San Diego - USA). All reagents were scaled by 2/3 to the volume proposed in the protocol. The quality of all libraries was assessed using the Bioanalyzer (Agilent Technologies, Santa Clara - USA).
The quality of all libraries was assessed using the Bioanalyzer (Agilent Technologies, Santa Clara - USA). The libraries were sequenced in paired-end mode (2x100bp) on two lanes with an Illumina HiSeq2000 sequencer at the BMFZ (Biologisch-Medizinisches Forschungszentrum, Düsseldorf - Germany).

tag: genotype/variation

value: wild type

tag: temperature (°c)

tag: truseq adapter sequence

value: ATTCCT


title: Mother_P157

value: multi cells


title: Cold_T48_10_Rep A

description:
28_a_28_48_GTGAAA_L007
10_Cold_T48_A (fpkm)

source_name: Batch Culture - Biological Replicate A - Autorophic - 2xAllen Medium

value: GTGAAA


title: Fmod_hypo_rep3

description: C


title: Cold_T12_9_Rep C

description:
27_c_28_12_ACTGAT_L008
09_Cold_T12_C (fpkm)

value: ACTGAT


title: MGAS28640

source_name: cell pellet

tag: subclade

value: Subclade1A (SC1A)

tag: site of isolation


title: Placenta_P157

description: DNA extracted from placenta tissue.

value: Placenta tissue


title: Umbilicalcord_P157

source_name: Cord blood

value: Cord blood


title: MGAS28477

value: invasive infection isolate

tag: growth phase


title: Fmod_hypo_rep2

description: B

value: male

value: Fmod knockout

value: 13 weeks


title: Mother_P154

tag: dna sample

value: AGA


title: Cold_T12_9_Rep B

description:
26_b_28_12_GTCCGC_L008
09_Cold_T12_B (fpkm)

source_name: Batch Culture - Biological Replicate B - Autorophic - 2xAllen Medium

tag: strain

value: GTCCGC


title: Cold_T12_9_Rep A

description:
25_a_28_12_GTCCGC_L007
09_Cold_T12_A (fpkm)


title: BGN_DHA_5

description: H

value: BGN knockout

tag: age

tag: treated with

value: DHA

value: hypothalamus


title: MGAS28449

value: Early-stationay (ES, OD600nm=1.65)


title: Father_P154

value: Natural

tag: tissue

value: Peripheral blood


title: Cold_T3_8_Rep C

description:
24_c_28_3_GAGTGG_L008
08_Cold_T3_C (fpkm)

value: wild type

value: GAGTGG


title: Umbilicalcord_P154

value: multi cells


title: MGAS28430

value: Subclade1A (SC1A)


title: MGAS28425


title: Placenta_P154

description: DNA extracted from placenta tissue.

source_name: Placenta tissue

value: Placenta tissue


title: Cold_T3_8_Rep B

description:
23_b_28_3_CCGTCC_L008
08_Cold_T3_B (fpkm)

value: CCGTCC


title: Cold_T3_8_Rep A

description:
22_a_28_3_CCGTCC_L007
08_Cold_T3_A (fpkm)


title: MGAS28415

value: invasive infection isolate


title: Mother_P142


title: BGN_3

description: C

tag: strain background

value: male

value: none (untreated control)


title: BGN_DHA_3

description: F

tag: gender

value: 13 weeks


title: MGAS28648


title: BGN_DHA_2

description: E


title: BGN_DHA_4

description: G


title: BGN_1

description: A


title: BGN_DHA_1

description: D


title: Father_P142

tag: quartet

value: AGA


title: Hot_T48_7_Rep C

description:
21_c_46_48_CGTACG_L008
07_Hot_T48_C (fpkm)

value: CGTACG


title: Hot_T48_7_Rep A

description:
19_a_46_48_ATGTCA_L007
07_Hot_T48_A (fpkm)

value: ATGTCA


title: MGAS28403


title: Fmod_hypo_rep1

description: A

value: Fmod knockout

value: hypothalamus


title: Umbilicalcord_P142

tag: conception method

value: Natural

value: Cord blood


title: MGAS28411

value: Early-stationay (ES, OD600nm=1.65)


title: Hot_T12_6_Rep B

description:
17_b_46_12_AGTTCC_L008
06_Hot_T12_B (fpkm)

value: wild type

value: AGTTCC


title: Placenta_P142

description: DNA extracted from placenta tissue.

value: multi cells

tag: birthweight at delivery


title: MGAS28397

value: Subclade1A (SC1A)


title: gLBD16-GR_NAA+DEX+CHX_rep2

city: Kobe

first: Hidehiro

last: Fukaki

state: Hyogo

address: Rokko-dai 1-1

institute: Kobe University

description: Gene expression data from 5-day-old gLBD16-GR roots NAA DEX CHX treatment (4h) rep2

hyb_protocol: Hybridization, washing, staining procedures were run on Fluidics Station 450 (Affymetrix) with GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G.

data_processing: Data procession was performed with Expression Console Version 1.3 (Affymetrix).

source_name: Arabidopsis 5-day-old root

label_protocol: Biotinylated cRNA was prepared from total RNA with GeneChip One-Cycle Target Labeling and Control Reagents (Arab-0018 to Arab-0054) or GeneChip 3' IVT Expression Kit (Arab-113-2 to Arab-124) (Affymetrix).

growth_protocol: Arabidopsis seedlings of gLBD16:GR lbd16 lbd18 lbd33 were grown for 5 days on 1x MS agar plate under continuous light condition.

extract_protocol: Total RNA was extracted with RNeasy Plant Mini Kit (QIAGEN).

treatment_protocol: 5-day-old seedlins of gLBD16:GR lbd16 lbd18 lbd33 were treated with/without 2 µM DEX, 10 µM CHX and 1µM NAA for 4 hours

tag: genotype

value: 5-day-old root

tag: treatment

value: 1 µM NAA, 2 µM DEX and 10 µM CHX treatment for 4 hours


title: gLBD16-GR_NAA+DEX+CHX_rep1

description: Gene expression data from 5-day-old gLBD16-GR roots NAA DEX CHX treatment (4h) rep1


title: Hot_T12_6_Rep A

description:
16_a_46_12_AGTTCC_L007
06_Hot_T12_A (fpkm)

tag: genotype/variation

tag: temperature (°c)


title: Mother_P141

description: DNA extracted from peripheral venous blood of the mother.

data_processing:
The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. We subsequently fed these data into siCHILD algorithm, which is equipted with haplarithmisis (Zamani Esteki et al. 2015, AJHG).
Image data was analyzed using Genomestudio with genotyping module (Illumina).

value: Peripheral blood

value: SGA


title: Hot_T3_5_Rep C

description:
15_c_46_3_AGTCAA_L008
05_Hot_T3_C (fpkm)

tag: truseq adapter sequence

value: AGTCAA


title: MGAS28374

tag: subclade

tag: site of isolation

value: invasive infection isolate


title: Father_P141

description: DNA extracted from peripheral venous blood of the father.

tag: dna sample


title: Umbilicalcord_P141

description: DNA extracted from umbilical cord blood of the newborn.


title: Hot_T3_5_Rep A

description:
13_a_46_3_AGTCAA_L007
05_Hot_T3_A (fpkm)

tag: strain


title: Cold_T48_4_Rep C

description:
12_c_28_48_GTTTCG_L008
04_Cold_T48_C (fpkm)

value: GTTTCG


title: gLBD16-GR_NAA+CHX_rep2

description: Gene expression data from 5-day-old gLBD16-GR roots NAA CHX treatment (4h) rep2

value: 1 µM NAA and 10 µM CHX treatment for 4 hours


title: MGAS28367

tag: growth phase


title: Placenta_P141

description: DNA extracted from placenta tissue.

value: Placenta tissue


title: MGAS28338


title: gLBD16-GR_NAA+CHX_rep1

description: Gene expression data from 5-day-old gLBD16-GR roots NAA CHX treatment (4h) rep1


title: Cold_T48_4_Rep B

description:
11_b_28_48_CTTGTA_L008
04_Cold_T48_B (fpkm)

value: CTTGTA


title: gLBD16-GR_NAA+DEX_rep1

description: Gene expression data from 5-day-old gLBD16-GR roots NAA DEX treatment (4h) rep1

value: 1 µM NAA and 2 µM DEX treatment for 4 hours


title: MGAS28334


title: gLBD16-GR_NAA+DEX_rep2

description: Gene expression data from 5-day-old gLBD16-GR roots NAA DEX treatment (4h) rep2


title: Mother_P137

value: Natural

value: AGA


title: Cold_T48_4_Rep A

description:
10_a_28_48_CTTGTA_L007
04_Cold_T48_A (fpkm)

value: wild type

value: GTGGCC


title: Father_P137

value: multi cells


title: MGAS28317

value: Subclade1A (SC1A)

value: Early-stationay (ES, OD600nm=1.65)


title: Fmod_liver_rep4

description: H

value: male

value: Fmod knockout

tag: age

value: 13 weeks

value: liver


title: gLBD16-GR_NAA_rep2

description: Gene expression data from 5-day-old gLBD16-GR roots NAA treatment (4h) rep2

tag: tissue

value: 5-day-old root

value: 1 µM NAA treatment for 4 hours


title: Cold_T12_3_Rep C

description:
9_c_28_12_GTGGCC_L008
03_Cold_T12_C (fpkm)


title: MGAS28315

value: invasive infection isolate


title: Umbilicalcord_P137

value: Cord blood


title: HSR-GBM1 tumour -0.2% mtDNA rep3

city: Clayton

first: Justin

middle: C

last: St. John

state: Vic

address: 27-31 Wright St

department: Centre for Genetic Diseases

country: Australia

institute: Hudson Institute of Medical Research

description: Genomic DNA extracted from HSR-GBM1 tumors formed from cells with 100%, 50%, 3% or 0.2% mtDNA content were genotyped using Infinium Global Screening Array-24 (Illumina).

hyb_protocol: The fragmented, resuspended DNA was loaded onto a BeadChip and incubated for 18 hours at 48°C. After incubation, single-base extension and allele-specific staining was performed on a Te-Flow Chamber Rack (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining, the BeadChip was coated with XC4/EtOH, dried in a vacuum desiccator for approximately 1 hour and scanned on an iScan System (Illumina) using the Infinium LCG scan setting.

data_processing: DNA samples were genotyped using Infinium Global Screening Array-24 (Illumina). Data were analyzed using GenomeStudio 2.0 Genotyping Module (Illumina).

label: C-Bio and A-DNP

source_name: Glioblastoma

label_protocol: Approximately 200ng of genomic DNA was whole-genome amplified using neutralisation mix (MA2) and amplification master mix (MSM) and incubated for 22 hours at 37°C. After incubation, the amplified DNA was fragmented with fragmentation solution (FMS), precipitated with precipitation solution (PM1) and 2-propanol and resuspended in resuspension/hybridisation solution (RA1).

growth_protocol: HSR-GBM1 cells were cultured as neurospheres on ultra-low attachment plates (Sigma) in Dulbecco's Modified Eagle Medium /Nutrient Mixture (DMEM/F-12) Media (Gibco) containing 2% StemPro neural supplement (Invitrogen Life Technologies), 20 ng/ml basic fibroblast growth factor (bFGF; Millipore) and 20 ng/ml epidermal growth factor (EGF; Millipore) at 37 °C, 5% CO2 and 95% humidity.

extract_protocol: Total genomic DNA were extracted from cultured cell pellets using the ISOLATE II Genomic DNA Kit (Bioline) according to manufacturer’s protocols . The DNA samples were treated with 3 μL of RNase solution (Qiagen) and Proteinase K Solution (20 μg/μL; Qiagen) at 65 °C for 10 minutes.

treatment_protocol: MtDNA depletion was performed by the addiotion of 10ug/mL of 2',3'-dideoxycytidine in the presence of 50ug/mL of urindine. Bagg albino nude mice received right flank injections pf 1*10^6 cells per mouse in 200uL OF 1:1 mixed cell suspension and Matrigel (WTY Lee et al (2016), Cell Death Discovery)

value: Male

value: Brain tumor

tag: disease state

value: Glioblastoma

tag: cell line


title: Placenta_P137

city: Maastricht

first: Masoud

address: P. Debyelaan 25

institute: Maastricht University Medical Center

description: DNA extracted from placenta tissue.

extract_protocol: A total of 9 mL of peripheral venous blood from parents and 4 mL of umbilical cord blood were collected into ethylenediaminetetraacetic acid-containing tubes (BD Vacutainer, Becton, Dickinson and Co) for DNA extraction. DNA was isolated from blood and the placental tissue using PureLink® Genomic DNA Kit (Invitrogen, Life Technologies™) according to manufacturer’s protocol. DNA samples were eluted with 200 µL of PureLink® Genomic Elution Buffer (10 mM Tris-HCl, pH 9.0, 0.1 mM EDTA) and stored at -20 °C until analysis. NanoDrop 2000 (Thermo Fisher Scientific Inc.) was used to assess DNA concentration and purity.

tag: quartet

value: Natural

value: Placenta tissue

value: AGA


title: HSR-GBM1 tumour -3% mtDNA rep2

tag: gender


title: MGAS28287


title: gLBD16-GR_DEX+CHX_rep2

description: Gene expression data from 5-day-old gLBD16-GR roots DEX+CHX treatment (4h) rep2

value: 2 µM DEX and 10 µM CHX treatment for 4 hours


title: MGAS28400

value: Subclade1A (SC1A)


title: Cold_T12_3_Rep B

description:
8_b_28_12_GGCTAC_L008
03_Cold_T12_B (fpkm)

value: wild type

value: GGCTAC


title: MGAS28254

value: Early-stationay (ES, OD600nm=1.65)


title: gLBD16-GR_NAA_rep1

description: Gene expression data from 5-day-old gLBD16-GR roots NAA treatment (4h) rep1


title: Mother_P136

description: DNA extracted from peripheral venous blood of the mother.

value: multi cells

tag: conception method

value: Peripheral blood

tag: birthweight at delivery


title: gLBD16-GR_DEX+CHX_rep1

description: Gene expression data from 5-day-old gLBD16-GR roots DEX+CHX treatment (4h) rep1

tag: genotype

value: 5-day-old root

tag: treatment


title: Cold_T12_3_Rep A

description:
7_a_28_12_CAGATC_L007
03_Cold_T12_A (fpkm)

tag: genotype/variation

tag: temperature (°c)

value: CAGATC


title: Cold_T3_2_Rep C

description:
6_c_28_3_GATCAG_L008
02_Cold_T3_C (fpkm)

tag: truseq adapter sequence

value: GATCAG


title: HSR-GBM1 tumour -3% mtDNA rep3


title: gLBD16-GR_CHX_rep2

description: Gene expression data from 5-day-old gLBD16-GR roots CHX treatment (4h) rep2

value: 10 µM CHX treatment for 4 hours


title: MGAS28225

tag: subclade

tag: site of isolation

value: invasive infection isolate


title: Father_P136

description: DNA extracted from peripheral venous blood of the father.

tag: dna sample


title: Cold_T3_2_Rep B

description:
5_b_28_3_TAGCTT_L008
02_Cold_T3_B (fpkm)

tag: strain

value: TAGCTT


title: MGAS28217

tag: growth phase


title: Umbilicalcord_P136

description: DNA extracted from umbilical cord blood of the newborn.

tag: tissue

value: Cord blood


title: HSR-GBM1 tumour -50% mtDNA rep1

value: Male

value: Brain tumor

tag: disease state

value: Glioblastoma


title: Cold_T3_2_Rep A

description:
4_a_28_3_GCCAAT_L007
02_Cold_T3_A (fpkm)

value: GCCAAT


title: MGAS28204

value: Subclade1A (SC1A)


title: HSR-GBM1 tumour -3% mtDNA rep1

tag: cell line


title: gLBD16-GR_DEX_rep2

description: Gene expression data from 5-day-old gLBD16-GR roots DEX treatment (4h) rep2

value: 2 µM DEX treatment for 4 hours


title: Placenta_P136

description: DNA extracted from placenta tissue.

tag: quartet

value: Natural

value: Placenta tissue

value: AGA


title: Mother_P109

value: multi cells

value: Peripheral blood

value: SGA


title: Hot_T48_1_Rep C

description:
3_c_42_n_GCCAAT_L008
01_Hot_T48_C (fpkm)

value: wild type


title: MGAS28201

value: Early-stationay (ES, OD600nm=1.65)


title: Hot_T48_1_Rep B

description:
2_b_42_n_CGATGT_L008
01_Hot_T48_B (fpkm)

value: CGATGT


title: gLBD16-GR_CHX_rep1

description: Gene expression data from 5-day-old gLBD16-GR roots CHX treatment (4h) rep1

value: 5-day-old root

value: 10 µM CHX treatment for 4 hours


title: HSR-GBM1 tumour -50% mtDNA rep2

description: Genomic DNA extracted from HSR-GBM1 tumors formed from cells with 100%, 50%, 3% or 0.2% mtDNA content were genotyped using Infinium Global Screening Array-24 (Illumina).

tag: gender

value: Male


title: HSR-GBM1 tumour -100% mtDNA rep2

value: Brain tumor


title: Umbilicalcord_P109

tag: conception method

value: Cord blood


title: MGAS28185

value: invasive infection isolate


title: MGAS28164

value: Subclade1A (SC1A)


title: Father_P109

tag: birthweight at delivery


title: HSR-GBM1 tumour -50% mtDNA rep3

value: Glioblastoma


title: gLBD16-GR_DEX_rep1

description: Gene expression data from 5-day-old gLBD16-GR roots DEX treatment (4h) rep1

tag: genotype

value: 2 µM DEX treatment for 4 hours


title: HSR-GBM1 tumour -0.2% mtDNA rep2


title: MGAS28138


title: gLBD16-GR_mock_rep2

description: Gene expression data from 5-day-old gLBD16-GR roots mock treatment (4h) rep2

tag: treatment

value: Mock (0.1% DMSO) treatment for 4 hours


title: HSR-GBM1 tumour -100% mtDNA rep1


title: Placenta_P109

description: DNA extracted from placenta tissue.

value: Natural

value: Placenta tissue


title: MGAS28118


title: MGAS28041


title: MGAS28035


title: HSR-GBM1 tumour -100% mtDNA rep3


title: MGAS27983


title: MGAS27962


title: Mother_P102

value: multi cells

value: Peripheral blood


title: Umbilicalcord_P102

value: SGA


title: Placenta_P102

description: DNA extracted from placenta tissue.


title: Father_P102


title: Mother_P100

value: AGA


title: HSR-GBM1 tumour -0.2% mtDNA rep1


title: Father_P100


title: MGAS27951

value: Early-stationay (ES, OD600nm=1.65)


title: MGAS27946


title: MGAS12250


title: Umbilicalcord_P100


title: Placenta_P100

description: DNA extracted from placenta tissue.


title: MGAS12247


title: Mother_P088


title: colon adenocarcinoma, replicate 9

city: Singapore

first: bin

last: zhang

address: 14 Medical Drive, #12-01

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

description: Gene expression data from COAD

hyb_protocol: Clariom D array

scan_protocol: Affymetrix Model 450 Fluidics Station and Affymetrix Model 3000 7G

data_processing: Expression Console software (Affymetrix)

source_name: COAD tumor

label_protocol: Affymetrix WT plus kit

growth_protocol: no culture

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

tag: disease

value: COAD tumor


title: colon adenocarcinoma, replicate 6

description: Gene expression data from COAD


title: gLBD16-GR_mock_rep1

description: Gene expression data from 5-day-old gLBD16-GR roots mock treatment (4h) rep1

value: 5-day-old root


title: MGAS12231

data_processing:
Multiplexed SE libraries were sequenced on an Illumina NextSeq 500 instrument. Reads from each pool were demultiplexed into separate fastq files corresponding to individual samples based on the inline barcodes using FASTX-toolkit.
RNAtag-seq reads from all strains were mapped to reference strain MGAS6180 (GenBank accession number CP000056), using Edge-pro v1.3.1 (Estimated Degree of Gene Expression for Prokaryotes).
Low-expressed genes and genes encoding ribosomal RNAs and tRNAs were filtered out prior to running differential expression analyses
Differential expression analysis was perfomed using DESeq2 v1.6.3 and NOISeq-sim (NOISeq package) running in R version 3.4.0. Differentially expressed genes were identified in each of the 441 strains compared to a common reference strain (MGAS28737).
Genome_build: reference strain MGAS6180 (GenBank accession number CP000056)
Supplementary_files_format_and_content: normalized counts


title: Umbilicalcord_P088

last: Zamani Esteki


title: MGAS12226


title: colon adenocarcinoma, replicate 8

description: Gene expression data from COAD


title: MOT.RNASeq Rep 3

city: Nottingham

first: Richard

middle: D

last: Emes

state: Nottinghamshire

department: School of Veterinary Medicine and Sciences.

country: United Kingdom

institute: University of Nottingham

data_processing:
Genome_build:AgamP4.4
Genome index was built using hisat2-build (version 2.1.0)
Reads trimmed using scythe and Tru-seq adapters (version 0.981)
Alignment of reads using hisat2 (version 2.1.0)
Assemble GTF using stringtie (version 1.2.3)
Generate normalized transcript abundances using stringtie (version 1.2.3)
Genome_build: www.vectorbase.org
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Anopheles coluzzii

source_name: Testes

growth_protocol: All the mosquito stocks were obtained from the Malaria Research and Reference Reagent Resource Center (MR4) in Atlanta (https://www.beiresources.org/Catalog/BEIVectors/MRA-762.aspx).

extract_protocol: Preparation of Illumina libraries  The total RNA libraries were prepared in accordance with the Illumina TruSeq RNA sample preparation  v2 guide (Part # 15026495, rev.D, September 2012) for Illumina Paired-End Indexed Sequencing.  Step 1: RNA purification and fragmentation  According to the Illumina mRNA libraries preparation protocol, poly-A mRNA in the tRNA samples  were first purified using Illumina poly-T oligo-attached magnetic beads and two rounds of purification.  During the second elution of the poly-A-RNA, the mRNA was also fragmented and primed with random  hexamers for cDNA synthesis.  Step2: Generation of double-stranded cDNA  Cleaved mRNAs were reverse transcribed into first strand cDNA using reverse transcriptase and  random primers. The RNA template was then removed and a replacement strand synthesized to  generate double-stranded cDNA.  Step 3: Preparation of ds cDNA samples for Indexed paired-end sequencing  Following the standard protocol, after the first and second strand cDNA synthesis, ends were repaired,  dA base added, and Illumina indexing adapters were ligated. Finally, cDNA fragments that have  adapter molecules on both ends underwent 15 cylcles of PCR to amplify the amount of prepared  material.

value: Testes


title: MOT.RNASeq Rep 2

address: School of Veterinary Medicine and Science


title: colon adenocarcinoma, replicate 7

description: Gene expression data from COAD


title: Placenta_P088

description: DNA extracted from placenta tissue.


title: MGAS11103

city: Houston

first: Priyanka

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

extract_protocol:
Pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using Turbo DNA-free (Ambion), and rRNA was depleted using Ribo-Zero (Illumina)
Resultant RNAs were tagged and pooled, reverse transcribed to cDNA, tagged a second time, pooled into superpools and sequenced


title: colon adenocarcinoma, replicate 1

description: Gene expression data from COAD


title: MOT.RNASeq Rep 1


title: MGAS10827


title: colon adenocarcinoma, replicate 3

description: Gene expression data from COAD


title: colon adenocarcinoma, replicate 10

description: Gene expression data from COAD


title: normal colon, replicate 10

description: Gene expression data from normal colon tissue

source_name: normal colon tissue

value: normal


title: colon adenocarcinoma, replicate 4

description: Gene expression data from COAD


title: Mother_P084

description: DNA extracted from peripheral venous blood of the mother.


title: Father_P084


title: Father_P088


title: MGAS10824


title: MOM.RNASeq Rep 3

source_name: Male Acessory Glands (MAGs)

value: Male Acessory Glands (MAGs)


title: colon adenocarcinoma, replicate 5

description: Gene expression data from COAD


title: colon adenocarcinoma, replicate 2

description: Gene expression data from COAD


title: normal colon, replicate 8


title: normal colon, replicate 7


title: normal colon, replicate 9


title: normal colon, replicate 6


title: MOM.RNASeq Rep 2


title: Placenta_P084

description: DNA extracted from placenta tissue.


title: Umbilicalcord_P084

value: Cord blood


title: MOM.RNASeq Rep 1


title: MGAS10819

value: Subclade1A (SC1A)

value: invasive infection isolate


title: MGAS10817


title: MGAS10820


title: Father_P079


title: nox1OEvsFOC4_AC3

city: Nanjing

first: Youzhi

last: Miao

address: WeiGang NO.1

institute: Nanjing Agricultural University

description:
all_samples_NJAU4742.xlsx,all_samples_FOC4.xlsx
T. guizhouense + F. oxysporum

data_processing:
quality control(adaptor trimming, masking of low-complexity or low-quality sequence)
reads alignment and sample comparisons using TopHat 2.0
RPKM is used for normalization
Genome_build: NJAU4742 and FOC4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each gene in each sample

organism:
Fusarium oxysporum
Trichoderma guizhouense

source_name: hypha

growth_protocol: Different mutants or wide type of NJAU4742 were seprately incubated together with FOC4 on the confrontation 9 mm plates with GSM medium in darkness at 28℃.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the samples of Before contact were scraped from the plates in the time when the distance between two different stains was equal to 1 cm; the samples of After contact were scrapted from the plates in 30 h later after contact of two different strains, and the sampling regions should contain both hypha.

value: mixture(NJAU4742 and FOC4)

value: nox1OE(NJAU4742)+wild type(FOC4)

tag: condition

value: After contact in condition of nox1OE vs FOC4


title: MGAS10815

last: Kachroo


title: Mother_P079

value: Natural


title: 6dpg  rep1

city: Shijiazhuang

first: Yanmin

last: Zou

state: Hebei

address: 286 Huaizhong Road

department: Center for Agricultural Resources Research

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

description:
day6vsday2 gene description.txt
transcription_factor.txt

data_processing:
Illumina Casava 1.8 software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using Bowtie v2.2.3 and  paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We  selected TopHat as the mapping tool for that TopHat can generate a database of splice  junctions based on the gene model annotation file and thus a better mapping result than  other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0).
Genome_build: Arabidopsis thaliana
Supplementary_files_format_and_content: tab-delimited text files include reads and FPKM values for each Sample

source_name: seedling

growth_protocol: Seeds were surface-sterilized with 50% (v/v) bleach for 5 min and washed at least four times with sterile water. Sterile seeds were germinated and grown on 1/2 Murashige and Skoog (MS) plates supplemented with 0.5% sucrose. The plates were kept for 2 days in the dark at 4°C to break dormancy (stratification) and transferred thereafter to a growth room at 22°C, with a 12-h photoperiod.

extract_protocol:
Total RNA for transcriptome sequencing was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: 2-, or 6-d-old plants grown in1/2 Murashige and Skoog (MS) medium were collected.

tag: age

value: 6 day after germination

value: wild type

tag: genetic background ecotype

value: seedling


title: 6dpg  rep2


title: 2dpg  rep1

value: 2 day after germination


title: MGAS10802

tag: subclade

tag: site of isolation

value: Early-stationay (ES, OD600nm=1.65)


title: normal colon, replicate 4


title: nox1OEvsFOC4_AC2

tag: strain


title: normal colon, replicate 5


title: 2dpg  rep2


title: normal colon, replicate 3


title: Placenta_P079

description: DNA extracted from placenta tissue.

tag: dna sample

value: multi cells

value: Placenta tissue

value: SGA


title: normal colon, replicate 2

value: normal


title: Umbilicalcord_P079

tag: tissue


title: nox1OEvsFOC4_AC1


title: ∆nox1vsFOC4_AC3

value: <delta>nox1(NJAU4742)+wild type(FOC4)

value: After contact in condition of <delta>nox1 vs FOC4


title: MGAS10799

value: Subclade1A (SC1A)

tag: growth phase


title: ∆nox1vsFOC4_AC2


title: Father_P074

value: Peripheral blood

value: AGA


title: Mother_P074


title: MGAS10807

value: invasive infection isolate


title: MGAS10757


title: WTvsFOC4_AC2

value: mixture(NJAU4742 and FOC4)

value: After contact in condition of NJAU4742 vs FOC4


title: WTvsFOC4_AC3


title: MGAS10771


title: Mother_P073

value: Natural


title: ∆nox1vsFOC4_AC1


title: MGAS10761


title: Placenta_P074

description: DNA extracted from placenta tissue.


title: normal colon, replicate 1


title: Umbilicalcord_P074

value: Cord blood


title: MGAS10764


title: WTvsFOC4_AC1

value: wild type


title: Umbilicalcord_P073


title: MGAS8417


title: MGAS8447


title: Father_P073


title: Mother_P070


title: Placenta_P073

description: DNA extracted from placenta tissue.


title: MGAS8374


title: MGAS8358


title: KT_2_Myr_Exp

city: Sevilla

first: Lorena

middle: Jiménez

last: Díaz

state: Sevilla

address: Energia Solar s/n

department: Biotechnology

country: Spain

institute: Abengoa Research

description:
genes FPKM.txt
10033956.1KT_Glu_Exp%KT_Myr_Exp.toptags_edgeR.csv

data_processing:
The alignment of the sequence with the annotated P. putida KT2440 (NC_002947) reference genomes was performed using Tophat (http://tophat.cbcb.umd.edu/) in conjunction with Bowtie (http://bowtie-bio.sourceforge.net/index.shtml).
Gene counts and expression values were obtained using Cufflinks (http://cufflinks.cbcb.umd.edu/).
For differential expression, the edgeR R Bioconductor (http://bioconductor.org/packages/release/bioc/html/edgeR.html) was used with the use of the easyRNASeq (https://bioconductor.org/packages/release/bioc/html/easyRNASeq.html)
Predictions for sub-cellular localization, clusters of orthologous groups (COG) number and COG functional category were obtained from the Pseudomonas Genome Database
Genome_build: NC_002947
Supplementary_files_format_and_content: File genes_FPKM.txt includes FPKM values for each Sample.
File 10033956.1KT_Glu_Exp%KT_Myr_Exp.toptags_edgeR.csv includes differential expression between two assayed conditions.

organism: Pseudomonas putida KT2440

source_name: Complete bacteria

growth_protocol: For RNA purification, single colonies of P. putida KT2440 were grown overnight in M9 minimal medium with glucose 0.5% (p/v) at 30ºC and the following day were diluted to OD660nm of 0.1 in M9 minimal medium with glucose 0.5% (v/v) or myristic acid 0.25% (v/v) and incubated at 30ºC with shaking. The cells were collected when the culture reached OD660nm of 0.8

extract_protocol:
RNA isolation was performed using RNeasy Mini Kit (QIAGEN) according to the specifications of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: carbon source

value: myristic acid


title: KT_3_Glu_Exp

value: glucose


title: KT_3_Myr_Exp


title: 257864010007_1_4_SALS2

city: Catania

first: Sebastiano

last: Cavallaro

address: Via Paolo Gaifami, 18

country: Italy

institute: IRIB-CNR

description: Sample 40

hyb_protocol: After probe denaturation and pre-annealing with Cot-1 DNA, hybridization was performed at 65°C with rotation for 24 hr.

scan_protocol: After two washing steps, arrays were scanned at 3 µm resolution using an Agilent G4900DA SureScan Microarray Scanner System.

data_processing:
aCGH image data were processed using Agilent’s Feature Extraction software to assess the array spot quality as well as check signal and background intensity statistics in default setting.Feature extracted raw data was normalized, analyzed and visualized using Agilent CytoGenomics v. 4.0.3.12 and Genomic Workbench v. 7.0.4.0 software (Agilent Technologies, Santa Clara, CA, USA). Briefly, after filtering for saturated and non-uniform probes, data were normalized by GC correction with a window size of 2 kb and Diploid Peak Centralization. The Centralization Normalization Algorithm with a threshold of 6.0 and a bin size of 10 was also used for detecting aberrant regions or regions of constant CNVs. Aberrations were detected by the Aberration Detection Method II algorithm (ADM-2), with a sensitivity threshold of 6.0 and moving average window of 2Mb, which permits to identify all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score. For chromosome X, only females were used and for chromosome Y only males were used.  An aberration filter was applied for identifying copy number alterations, changes were considered as true positive events with a minimum log2ratio test/control of ±0.5 and a minimum of 3 consecutive probes. Positive statistical score meant amplification, while negative score indicated deletion. Human reference sequence hg19 assembly was used to define the genomic coordinates of detected CNVs.
Normalized log2ratio (Cy5/Cy3) representing test/reference. Changes were considered as true positive events with a minimum log2ratio test/control of ±0.5 and a minimum of 3 consecutive probes.

source_name: patients with clear SALS diagnosis

label_protocol: DNA test and a reference of the same sex (Euro Reference, Agilent Technologies, Santa Clara, CA), both at the concentration of 500 ng, were double digested with RsaI and AluI for 2 hours at 37°C. After heat inactivation of the enzymes at 65°C for 20 min, each digested sample was labeled by random priming by using the genomic DNA Enzymatic Labelling Kit (Agilent Technologies, Santa Clara, CA) for 2 hours using Cy5-dUTP for patient DNAs and Cy3-dUTP for reference DNAs. Labeled products were column purified by using the SureTag DNA Labeling Kit Purification Columns (Agilent Technologies, Santa Clara, CA).

extract_protocol: DNA extractions from frozen brain tissues and whole-blood samples were performed using standard procedures.Individual slices of 10 μm were produced from tissue samples at -20°C by a Leica CM1510S cryostat (Leica Microsystems) and stored at -80°C until further processing. Two slices per sample were stained by hematoxylin/eosin staining (Bio Optica) and for Nissl substance (with a microfiltered solution of cresyl violet, Sigma-Aldrich), respectively, to assess integrity of cellular and tissue morphology. Ten adjacent slices per sample were pooled and dissolved in SE buffer (750 m NaCl (pH 8), 250 m EDTA, 1% SDS) containing Proteinase K for DNA isolation. The extracted genomic DNA was quantified by ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA), and assessed for quality by microcapillary electrophoresis on 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: Sex

value: male

tag: age at death (in years)

tag: disease state

value: Sporadic Amyotrophic Lateral Sclerosis

tag: survival characteristics

value: short term survival up to 24 months

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

value: caucasian

tag: location of onset

value: trunk onset

tag: occupation (job)

value: Assistent export manager in office product supplies. At the age of 16 suffered a heavy blow on his head

tag: smoker or non smoker

value: smoker

tag: alchool use or not

value: moderate use of alcohol ( 2/d men, 1/d women, elderly)

tag: other pathologies

value: malaria since 1991 (New-Guinea). Sincs 1990 diabetes type II. 1986 cholecystectomie, 1987 period with hypertension

tag: therapy used

value: antidiabetics, Rastinon, glucophage

tag: vaccination boost

tag: familial anamnesis

source_name: Euro Reference, Agilent Technologies


title: 257864010004_2_3_SALS2

description: Sample 39

value: leg onset

value: occupation not known, however patient had been exposed to toxic substances


title: 257864010004_1_1_SALS2

description: Sample 41

value: In 1976 operated for aneurysma. Post-operational abducensparesis. in 1981 dogbite upperlip. 1983 angina complaints

value: Legendal, Tryptizol


title: 257864010004_1_3_SALS2

description: Sample 38

value: medium term survival up to 6 yrs

value: In the past contact with lead damps, and dental protheses with 9 amalgam fillings

value: Acetyl cyst.


title: 257864010009_2_3_SALS2

description: Sample 37

value: female

value: housewife, previously worked in a taylorshop, wife of painter,/decorator

value: non smoker

value: known with hypertension since 1960. Hypercholesterolemia and ECG with signs of anteroseptal infarct.

value: Participated in the Acetyl cyst. trial

value: father died at the age of 49 of hart disease and mother suffered of hypertension


title: 257864010004_2_1_SALS2

description: Sample 36

value: Sporadic Amyotrophic Lateral Sclerosis

value: caucasian

value: housewife

value: Possible leasion of periferic and central motoric neuron at the spinal level. Known with hypertension

value: Selokeen, vit C, vit E, Coenzyme q10, vitamax, vit. B complex, superoxyde dismutase.


title: 257864010008_1_3_SALS2

description: Sample 35

value: trunk onset

value: Adipositas, diabetes mellitus, arthrosis. Amamnesis:womb operaion, and knees and ankles due to arthrosis

value: Tolbutamide, magnesiumsulfate (for cramps), Rilutec, Fluimicil, etc


title: MGAS8350

tag: subclade

value: Subclade1A (SC1A)

tag: site of isolation

value: invasive infection isolate

tag: growth phase

value: Early-stationay (ES, OD600nm=1.65)


title: KT_2_Glu_Exp

tag: carbon source

value: glucose

tag: genotype

value: wild type


title: MGAS8345


title: Father_P070

description: DNA extracted from peripheral venous blood of the father.

source_name: Peripheral blood

tag: dna sample

value: multi cells

tag: quartet

tag: conception method

value: Natural

tag: tissue

value: Peripheral blood

tag: birthweight at delivery

value: SGA


title: MGAS8015


title: KT_1_Glu_Exp


title: Placenta_P070

description: DNA extracted from placenta tissue.

value: Placenta tissue


title: KT_1_Myr_Exp

value: myristic acid


title: MGAS8375


title: 257864010008_1_1_SALS2

description: Sample 31

tag: Sex

value: female

tag: age at death (in years)

tag: disease state

value: Sporadic Amyotrophic Lateral Sclerosis

tag: survival characteristics

value: medium term survival up to 6 yrs

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

value: caucasian

tag: location of onset

value: leg onset

tag: occupation (job)

value: In the past frequent migrain headaches.Osteopenia and hypercholesterolemy. Trismus.

value: Trismus treated with botox injections and irradiation of parotids for excessive saliva


title: 257864010007_1_1_SALS2

description: Sample 33

tag: smoker or non smoker

value: smoker

tag: alchool use or not

value: moderate use of alcohol ( 2/d men, 1/d women, elderly)

tag: other pathologies

value: Injured nose (with nosebleeds), due to violent ex-partner. Very stressed due to personal situation, divorce. Previous womb operation.

tag: therapy used

value: Participated in the n-acetylcysteine trial. Ozazepap when needed

tag: vaccination boost

tag: familial anamnesis

value: Mother died of cancer, father of consequences tentamen suicidii


title: 257864010007_2_4_SALS2

description: Sample 34

value: male

value: trunk onset

value: Known with hypertension

value: Renitec (hypertension). participated in the n-acetylcysteine trial


title: Mother_P062

tag: dna sample

value: multi cells

tag: quartet

tag: conception method

value: Natural

tag: tissue

value: Peripheral blood

value: AGA


title: WTCu(2) R5A

city: OVIEDO

first: Paula

last: Yagüe

state: ASTURIAS

address: JULIAN CLAVERIA SN

department: Biologia funcional

institute: Universidad de Oviedo

data_processing:
lllumina Hiseq 2500 platform, using 100bp paired-end sequencing reads
sequence reads were not trimmed due to its high quality, then they were mapped to Streptomyces coelicolor M145 whole genome.fa (8.6 kb) using Tophat Bowtie2 (V2.1.0)
differential gene expression was analyzed with Cuffdiff using Streptomyces coelicolor M145 whole genome.gff and the tophat results (accepted_hits.bam) from each sample
The results gene_express.diff were analyzed using Microsoft Excell
Genome_build: Streptomyes coelicolor accession number AL645882
Supplementary_files_format_and_content: The format of the processed data files is .txt in which the column "value 1" corresponds to the average readings of each gene in the mutant strain (M110 or WTCu) and "value 2" corresponds to the avearge readings of each gene in the wild type strain (S.coelicolor M145)

organism: Streptomyces coelicolor

source_name: WTCu(2) R5A

growth_protocol: 50 mL sucrose-free R5A cultures (1.107 espores/mL) were grown at 30ºC and 200 rpm in 250 mL baffled flasks.

extract_protocol:
Total RNA samples from cultures stabilized with Bacteria RNA protect (Qiagen) were isolated using RNeasy Mini spin columns and treated with DNase I (Qiagen).
cDNA library construction was carried out using TruSeq Stranded mRNA Library Preparation Kit (Illumina) following standard Illumina protocol.

tag: genotype

tag: treatment

value: sporulated in media with 80µM CuSO4

tag: culture medium

value: Sucrose free R5A

tag: time

value: 10 culture hours


title: 257864010009_1_4_SALS2

description: Sample 32

tag: Sex

value: female

tag: age at death (in years)

tag: disease state

value: Sporadic Amyotrophic Lateral Sclerosis

tag: survival characteristics

value: medium term survival up to 6 yrs

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

value: caucasian

value: leg onset

value: Participated in the n-acetylcysteine trial. Amytriptiline, Scopoderm plasters, Oxygen


title: Father_P062

tag: birthweight at delivery


title: Umbilicalcord_P070

value: Cord blood

value: SGA


title: WTCu(1) R5A

source_name: WTCu(1) R5A


title: MGAS8009

source_name: cell pellet

tag: subclade

value: Subclade1A (SC1A)

tag: site of isolation

value: invasive infection isolate

tag: growth phase

value: Early-stationay (ES, OD600nm=1.65)


title: MGAS8007


title: 257864010008_2_3_SALS2

description: Sample 30

value: male

value: long term survival more than 6 yrs

tag: location of onset

value: trunk onset

tag: occupation (job)

value: employed in administration

tag: smoker or non smoker

value: non smoker

tag: alchool use or not

value: moderate use of alcohol ( 2/d men, 1/d women, elderly)

tag: other pathologies

tag: therapy used

value: vit-B complex, vitamine C

tag: vaccination boost

value: polio vaccine (1992)

tag: familial anamnesis

value: sister with morbus Reckinhhausen


title: Placenta_P062

description: DNA extracted from placenta tissue.

tag: dna sample

value: multi cells

tag: quartet

tag: conception method

value: Natural

tag: tissue

value: Placenta tissue

value: AGA


title: 257864010001_2_4_SALS2

description: Sample 29

tag: Sex

value: female

tag: age at death (in years)

tag: disease state

value: Sporadic Amyotrophic Lateral Sclerosis

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

value: caucasian

value: arm onset

value: Stressful experiences in her life, such as traumatic birth of her son.

value: Mother died of cancer


title: Umbilicalcord_P062

source_name: Cord blood

value: Cord blood

tag: birthweight at delivery


title: M110(1) R5A

tag: genotype

tag: culture medium

value: Sucrose free R5A

tag: time

value: 20 culture hours


title: MGAS7995

tag: subclade

value: Subclade1A (SC1A)

tag: site of isolation

value: invasive infection isolate

tag: growth phase

value: Early-stationay (ES, OD600nm=1.65)


title: MGAS7994


title: WT(2) R5A

source_name: WT(2) R5A

value: 10 culture hours


title: WT(1) R5A

source_name: WT(1) R5A


title: Father_P059

tag: dna sample

value: multi cells

tag: quartet

value: Peripheral blood


title: 257864010001_2_1_SALS1

description: Sample 27

value: male

value: short term survival up to 24 months

tag: location of onset

value: leg onset

tag: occupation (job)

value: computer operator, worked also with chemical substances

tag: smoker or non smoker

value: non smoker

tag: alchool use or not

value: abstinent

tag: other pathologies

value: psoriasis. Motor and car-accident

tag: therapy used

value: Rilutek, cream for psoriasis

tag: vaccination boost

tag: familial anamnesis


title: Mother_P059

tag: conception method

value: Natural

tag: tissue

tag: birthweight at delivery

value: AGA


title: 257864010004_2_2_SALS1

description: Sample 26

tag: Sex

value: female

tag: age at death (in years)

tag: disease state

value: Sporadic Amyotrophic Lateral Sclerosis

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

value: caucasian

value: trunk onset

value: smoker

value: moderate use of alcohol ( 2/d men, 1/d women, elderly)

value: Colic pains left side of abdomen, had previously been operated 13 times for similar problem. Suffered hypertension

value: Carbamazepine divitabs, sinaspril, clonazepam, importal, microlax

value: Husband died in 13-03-1986 in Switserland of ALS. A nephew of mother's side was paralyzed


title: MGAS7987

tag: subclade

value: Subclade1A (SC1A)

tag: site of isolation

value: invasive infection isolate

tag: growth phase

value: Early-stationay (ES, OD600nm=1.65)


title: MGAS7976


title: MGAS7973


title: M110(2) R5A

tag: genotype

tag: culture medium

value: Sucrose free R5A

tag: time

value: 20 culture hours


title: Umbilicalcord_P059

tag: dna sample

value: multi cells

tag: quartet

value: Cord blood


title: 257864010007_2_2_SALS1

description: Sample 24

value: male

value: short term survival up to 24 months

tag: location of onset

value: leg onset

tag: occupation (job)

value: Ex-metal- bank employee

tag: smoker or non smoker

tag: alchool use or not

tag: other pathologies

value: Suffered a heart attack after which he had probmlems of communication. August 1989 operated intestinal carcinoma (stoma was closed in november 1989)

tag: therapy used

tag: vaccination boost

tag: familial anamnesis


title: MGAS7972


title: 257864010001_2_2_SALS1

description: Sample 22

tag: Sex

tag: age at death (in years)

tag: disease state

value: Sporadic Amyotrophic Lateral Sclerosis

tag: survival characteristics

value: medium term survival up to 6 yrs

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

value: caucasian

value: arm onset

value: employed in management with stressful job (self report)

value: smoker

value: abuse of acohol

value: Raynaud's attacks

value: rilutek, vit E, Oxazepam, amitriptyline-chloride, acetyl cyst.

value: father died in 1987 of brain tumor and had spinal cord tumors and intestine polyps


title: 257864010009_1_2_SALS1

description: Sample 23

value: employed in administration in woodfactory and in past worked as barman

value: more than moderate (3 /d men, 2/d women, elderly)

value: transposition of n. ulnaris (1988)/in the past suffered some epileptic attacks/ spondylarthrosis deform. C4-C6

value: Acetyl cyst.

value: brother MS, daughter handicapped


title: 257864010009_1_3_SALS1

description: Sample 21

value: female

value: leg onset

value: housewife and nurse in old people's nursing home untill 1987

value: non smoker

value: moderate use of alcohol ( 2/d men, 1/d women, elderly)

value: Had bronchitis untill 1945, had a period of hypertension during the use of the pill

value: A sister of her mother had MS and died after an ilness period of 10 years at the age of 68


title: 257864010007_1_3_SALS1

description: Sample 20

value: Sporadic Amyotrophic Lateral Sclerosis

value: medium term survival up to 6 yrs

value: caucasian

value: arm onset

value: Begin 1990,hallucinations with signs of daementia, change in personality, planning capacity and disorienation. 1990 diagnosis:schizofrenia simplex with loss of intelligence and frontal, cortical atrophy


title: MGAS7959

tag: subclade

value: Subclade1A (SC1A)

tag: site of isolation

value: invasive infection isolate

tag: growth phase

value: Early-stationay (ES, OD600nm=1.65)


title: Umbilicalcord_P050

tag: dna sample

value: multi cells

tag: quartet

tag: conception method

value: Natural

tag: tissue

value: Cord blood

tag: birthweight at delivery

value: SGA


title: 257864010009_2_2_SALS1

description: Sample 25

value: male

value: short term survival up to 24 months

tag: location of onset

tag: occupation (job)

tag: smoker or non smoker

tag: alchool use or not

tag: other pathologies

tag: therapy used

tag: vaccination boost


title: adjacent tissues-4P

city: NanJing

first: Zhengdong

last: Zhang

address: 101 Longmian Avenue

department: Department of Environmental Genomics, School of Public Health

institute: Nanjing Medical University

description: Gene expression of lncRNA and mRNA in gastric cancer adjacent tissues

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner.

data_processing: Data was extracted using Agilent Feature Extraction software.Normalization was performed using the Agilent GeneSpring GX v11.5.1.

source_name: gastric tumor adjacent tissues-4P

label_protocol: Agilent Quick Amp Labeling Kit was used for sample labeling.

extract_protocol: The total RNA was extracted from fresh tissues and cells using TRIzol reagent (Invitrogen, CA, USA). The quantity of RNA was assessed by NanoDrop ND-2000, and the RNA integrity was tested by standard denaturing agarose gel electrophoresis. RNA from the 5 paired tissues was used for microarray analysis by Arraystar Human lncRNA microarray V2.0 (Agilent, USA).

treatment_protocol: None of the patients received radiotherapy and chemotherapy before the surgery.

value: gastric tissue

tag: gender


title: MGAS7946


title: Mother_P039

value: Peripheral blood

value: AGA


title: Father_P050


title: Placenta_P050

description: DNA extracted from placenta tissue.

source_name: Placenta tissue

value: Placenta tissue


title: MGAS7960


title: MGAS7956


title: MGAS7935


title: Father_P039


title: Placenta_P059

description: DNA extracted from placenta tissue.


title: Mother_P050


title: MGAS7932


title: Umbilicalcord_P039

description: DNA extracted from umbilical cord blood of the newborn.


title: 257864010007_2_3_SALS1

description: Sample 14

tag: Sex

tag: age at death (in years)

tag: disease state

value: Sporadic Amyotrophic Lateral Sclerosis

tag: survival characteristics

value: medium term survival up to 6 yrs

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

value: Employed in bike club as secretary. Sportive type, cycled 150 km a day up unill 1994.

value: smoker

value: moderate use of alcohol ( 2/d men, 1/d women, elderly)

value: Suffered atopic eczema as a child (age 2 yrs). 1969 pneumonia. Chronic aspecific respiratory disease

tag: familial anamnesis

value: Father died of heart attack.


title: gastric tumor-3Ca

description: Gene expression of lncRNA and mRNA in gastric cancer

source_name: gastric tumor-3Ca

tag: tissue


title: gastric tumor-5Ca

source_name: gastric tumor-5Ca


title: adjacent tissues-12P

source_name: gastric tumor adjacent tissues-12P


title: 257864010008_1_4_SALS1

description: Sample 17

value: caucasian

tag: location of onset

value: leg onset

value: Head constable of the policeforce in Haarlem

value: non smoker

value: abstinent

value: A lot of stress due to loss of family members/ friends and difficult contact with eldest son

value: Vitamin B, Tryptizol, Prednison/Lactulose, Normison and lactulose when needed

value: Several cases of Alzheimer in his mother's family


title: 257864010001_1_3_SALS1

description: Sample 16

value: male

tag: occupation (job)

value: Administrator in gardening company, sportive man, Up until 1975 lived with his parents in gardening company and came into contact with different pesticides

value: more than moderate (3 /d men, 2/d women, elderly)

value: Back pain underwent a laminectomy (L4-L5).As a child also suffered kidney disease during a cold. Bad acn?, rontgen treatment of torax and face. In 1990 facial and bottom cheak infection

value: In 1990 infections treated with different antibiotics and a mushroom extract. Vit B injections

value: A son with asthma bronchiale. Brother with back problems.


title: Placenta_P039

description: DNA extracted from placenta tissue.

tag: dna sample

value: multi cells

tag: quartet

tag: conception method

value: Natural

value: Placenta tissue

tag: birthweight at delivery

value: AGA


title: gastric tumor-4Ca

source_name: gastric tumor-4Ca

value: gastric tissue


title: adjacent tissues-3P

source_name: gastric tumor adjacent tissues-3P


title: adjacent tissues-5P

source_name: gastric tumor adjacent tissues-5P


title: MGAS7927

tag: subclade

value: Subclade1A (SC1A)

tag: site of isolation

value: invasive infection isolate

tag: growth phase

value: Early-stationay (ES, OD600nm=1.65)