title: EV

city: Guangzhou

first: Jindong

last: Zhang

address: Zhongshan road 74#

institute: Sun Yat-sen University

description: Gene expression data from normal human thalamencephalon

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

source_name: U251 cells trunsduced with empty vector

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: U251 cells were transduced with TRIM45 or empty vevtor using lentivirus and cultured in DMEM supplemented with 10% fetal bovine serum (Gibco) and 1 mM Glutamine.

extract_protocol: Total RNA of parietal cortex of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: No treatment.

tag: tissue

value: brain


title: BAL_IPF_Leuven_63

status: Public on Dec 31 2018

type: RNA

city: Hannover

first: Antje

last: Prasse

address: Carl-Neubergstrasse 1

department: Pneumology

country: Germany

institute: Medical School Hannover

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x GEx Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays, 4x44K (Freiburg and Siena) or  8 x 60K (Leuven) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA High Resolution Microarray Scanner (G2505C US45102918) using one color scan setting for 8 x 60K array slides (Freiburg and Siena) and  8 x 60K array slides (Leuven). Scan Area 61x21.6 mm, Scan resolution 5 μm, Tiff 20 bit, Dye channel is set to Green.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Gene expression data was normalized to the geometric mean of all the IPF samples and controls using quantile normalization. Non-expressed and invariant transcripts were removed.  For statiscal analysis we used the average gene expression values of the replicated probes. After merging the datasets of the 3 cohorts we obtained a final dataset of 20330 transcript measurements across the 176 IPF samples and 20 healthy donor samples.

molecule: total RNA

organism: Homo sapiens

source_name: BAL cells

label_protocol: Labeling reactions were performed for each sample using Agilent Low Input Quick Amp Labeling, One-Color (Agilent Technologies, Santa Clara, CA). Briefly, with a starting concentration of 100 nanograms of total RNA, an initial cDNA strand was synthesized using a oligo(dT)24 primer containing a T7 RNA polymerase, this cDNA was then used as a template to generate Cy3 labeled cRNA by a reverse transcriptase enzyme. After the cRNA was obtained a purification step was performed using RNeasy Mini Kit (74104, Qiagen, Valencia, CA) followed by measurement of the yield and specific activity of each sample

extract_protocol:
[Isolation protocol] BAL cells were obtained by bronchoscopy, immediately isolated and 1 ml of TRIzol (15596018, life technologies, Darmstadt, Germany) was added to the cell pellet, which was then immediately snap frozen in -80 celsius.
Total RNA of TRIzol samples was extracted and purified using the RNeasy Mini Kit (217004, Qiagen, Valencia, CA), under fully automated sample preparation by the assistance of the QIAcube device (9001292, Qiagen, Valencia CA) following the manufacturer’s protocol. After extraction, total RNA yield and quality were evaluated using NanoDrop at 260 nm and the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

tag: cell type

value: bronchoalveolar lavage (BAL) cells

tag: diagnosis

value: IPF

tag: cohort

value: LEUVEN

tag: age

tag: sex (0=female, 1=male)

tag: time to death (days)

tag: survival status, 0 = censored, 1 = death

tag: gap


title: BAL_IPF_Leuven_59


title: MGAS28776

type: SRA

city: Houston

first: Priyanka

last: Kachroo

address: 6670 Bertner Avenue

country: USA

institute: Houston Methodist Research Institute

library_source: transcriptomic

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

value: Subclade2A (SC2A)

tag: site of isolation

value: invasive infection isolate

tag: growth phase

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


title: BAL_IPF_Leuven_62


title: TRIM45

country: China

description: Gene expression data from patient thalamencephalon

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

label: biotin

source_name: U251 cells trunsduced with TRIM45


title: BAL_HV_25

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with RMA default analysis settings and quantile normalisation as normalization method (R v.1.9; affy package v.1.4).

source_name: BAL_healthy volunteer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol:
Isolation protocol: BAL cells were obtained by bronchial lavage immediately isolated and 0.6 ml of Qiagens RLT buffer was added to the cell pellet and lysed, which was then immediately snap frozen in -80 celsius
Qiagen RNeasy Mini extraction of total RNA was performed according to the manufacturer's instructions

value: BAL cells

value: Healthy Volunteer

value: Hannover


title: BAL_HV_28


title: BAL_HV_27


title: BAL_HV_26


title: BAL_HV_24


title: MGAS28760


title: Mother_P178

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:
Sample 436
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

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 cell

tag: quartet

tag: conception

value: IVF

tag: birthweight at delivery

value: AGA


title: BAL_IPF_Leuven_58


title: Father_P178

description:
Sample 435
DNA extracted from peripheral venous blood of the father.


title: BAL_HV_23


title: MGAS28752


title: BAL_IPF_Leuven_56


title: BAL_IPF_Leuven_57


title: UmbilicalCord_P178

description:
Sample 434
DNA extracted from umbilical cord blood of the newborn.

source_name: Cord blood


title: MGAS28751


title: Placenta_P178

description:
Sample 433
DNA extracted from placenta tissue.

source_name: Placenta tissue


title: MGAS28748


title: Mother_P176

description:
Sample 432
DNA extracted from peripheral venous blood of the mother.


title: MGAS28744


title: MGAS28728


title: MGAS28731


title: UmbilicalCord_P176

description:
Sample 430
DNA extracted from umbilical cord blood of the newborn.


title: Father_P176

description:
Sample 431
DNA extracted from peripheral venous blood of the father.


title: BAL_IPF_Leuven_55


title: BAL_HV_21


title: MGAS28727


title: MGAS28722


title: BAL_HV_19


title: BAL_HV_22


title: Mother_P168

description:
Sample 428
DNA extracted from peripheral venous blood of the mother.

value: NAT


title: BAL_IPF_Leuven_52


title: BAL_IPF_Leuven_53


title: Father_P168

description:
Sample 427
DNA extracted from peripheral venous blood of the father.


title: MGAS28715


title: BAL_HV_17


title: BAL_IPF_Leuven_50


title: BAL_IPF_Leuven_51


title: BAL_HV_20


title: BAL_HV_16


title: BAL_IPF_Leuven_49


title: MGAS28687


title: BAL_HV_18


title: UmbilicalCord_P168

description:
Sample 426
DNA extracted from umbilical cord blood of the newborn.


title: Placenta_P176

description:
Sample 429
DNA extracted from placenta tissue.


title: BAL_IPF_Leuven_47


title: BAL_IPF_Leuven_54


title: BAL_IPF_Leuven_48


title: MGAS28670


title: BAL_IPF_Leuven_46


title: BAL_HV_15


title: Placenta_P168

description:
Sample 425
DNA extracted from placenta tissue.


title: BAL_HV_13


title: MGAS28662


title: Mother_P156

description:
Sample 424
DNA extracted from peripheral venous blood of the mother.


title: MGAS28633


title: Father_P156

description:
Sample 423
DNA extracted from peripheral venous blood of the father.


title: BAL_HV_12


title: MGAS28630


title: BAL_IPF_Leuven_44


title: UmbilicalCord_P156

description:
Sample 422
DNA extracted from umbilical cord blood of the newborn.


title: MGAS28626


title: Placenta_P156

description:
Sample 421
DNA extracted from placenta tissue.


title: Mother_P155

description:
Sample 420
DNA extracted from peripheral venous blood of the mother.


title: BAL_IPF_Leuven_45


title: MGAS28612


title: BAL_HV_14


title: BAL_HV_11


title: Father_P155

description:
Sample 419
DNA extracted from peripheral venous blood of the father.


title: MGAS28609


title: MGAS28596


title: UmbilicalCord_P155

description:
Sample 418
DNA extracted from umbilical cord blood of the newborn.


title: BAL_HV_9


title: BAL_IPF_Leuven_42


title: Placenta_P155

description:
Sample 417
DNA extracted from placenta tissue.


title: BAL_HV_8


title: MGAS28589


title: BAL_IPF_Leuven_43


title: Mother_P140

description:
Sample 416
DNA extracted from peripheral venous blood of the mother.


title: MGAS28585


title: BAL_HV_10


title: BAL_HV_6


title: Father_P140

description:
Sample 415
DNA extracted from peripheral venous blood of the father.


title: MGAS28576


title: BAL_HV_7


title: BAL_IPF_Leuven_38


title: BAL_IPF_Leuven_39


title: BAL_IPF_Leuven_40


title: BAL_HV_4


title: BAL_IPF_Leuven_37


title: BAL_IPF_Leuven_41


title: MGAS28562


title: BAL_IPF_Leuven_35


title: BAL_IPF_Leuven_34


title: BAL_HV_2


title: BAL_HV_5


title: BAL_COPD_29

value: COPD


title: BAL_IPF_Leuven_36


title: Mother_P132

description:
Sample 412
DNA extracted from peripheral venous blood of the mother.

value: SGA


title: BAL_HV_3


title: Placenta_P140

description:
Sample 413
DNA extracted from placenta tissue.


title: UmbilicalCord_P140

description:
Sample 414
DNA extracted from umbilical cord blood of the newborn.


title: MGAS28567


title: MGAS28549


title: BAL_IPF_Leuven_32


title: BAL_IPF_Leuven_31


title: MGAS28550


title: BAL_HV_1


title: Placenta_P132

description: Sample 409


title: Father_P132

description:
Sample 411
DNA extracted from peripheral venous blood of the father.


title: BAL_IPF_Leuven_33


title: UmbilicalCord_P132

description:
Sample 410
DNA extracted from umbilical cord blood of the newborn.


title: BAL_COPD_28


title: MGAS28543


title: Mother_P130

description:
Sample 408
DNA extracted from peripheral venous blood of the mother.


title: MGAS28536


title: BAL_COPD_27


title: BAL_COPD_26


title: BAL_IPF_Leuven_29


title: UmbilicalCord_P130

description:
Sample 406
DNA extracted from umbilical cord blood of the newborn.


title: MGAS28523


title: MGAS28513


title: BAL_IPF_Leuven_30


title: MGAS28512


title: Placenta_P130

description:
Sample 405
DNA extracted from placenta tissue.


title: MGAS28510


title: Father_P130

description:
Sample 407
DNA extracted from peripheral venous blood of the father.


title: Father_P113

description:
Sample 403
DNA extracted from peripheral venous blood of the father.


title: BAL_COPD_24


title: BAL_IPF_Leuven_27


title: BAL_COPD_23


title: Mother_P113

description:
Sample 404
DNA extracted from peripheral venous blood of the mother.


title: BAL_COPD_25


title: BAL_IPF_Leuven_25


title: UmbilicalCord_P113

description:
Sample 402
DNA extracted from umbilical cord blood of the newborn.


title: BAL_COPD_22


title: MGAS28501


title: Placenta_P113

description: Sample 401


title: BAL_COPD_21


title: BAL_IPF_Leuven_24


title: MGAS28484


title: BAL_IPF_Leuven_28


title: MGAS28482


title: BAL_IPF_Leuven_23


title: MGAS28504


title: BAL_COPD_20


title: Mother_P111

description:
Sample 400
DNA extracted from peripheral venous blood of the mother.


title: BAL_COPD_18


title: BAL_COPD_19


title: MGAS28479


title: Father_P111

description:
Sample 399
DNA extracted from peripheral venous blood of the father.


title: BAL_IPF_Leuven_26


title: BAL_IPF_Leuven_21


title: BAL_IPF_Leuven_20


title: BAL_IPF_Leuven_22


title: BAL_COPD_16


title: BAL_COPD_15


title: BAL_COPD_17


title: BAL_COPD_13


title: MGAS28463


title: UmbilicalCord_P111

description:
Sample 398
DNA extracted from umbilical cord blood of the newborn.


title: Placenta_P111

description:
Sample 397
DNA extracted from placenta tissue.


title: Mother_P108

description:
Sample 396
DNA extracted from peripheral venous blood of the mother.


title: MGAS28467


title: BAL_COPD_14


title: MGAS28462


title: Father_P108

description:
Sample 395
DNA extracted from peripheral venous blood of the father.


title: MGAS28461


title: UmbilicalCord_P108

description:
Sample 394
DNA extracted from umbilical cord blood of the newborn.


title: BAL_IPF_Leuven_19


title: BAL_IPF_Leuven_17


title: BAL_IPF_Leuven_16


title: BAL_COPD_11


title: BAL_IPF_Leuven_18


title: BAL_IPF_Leuven_15


title: BAL_COPD_10


title: BAL_COPD_12


title: MGAS28447


title: BAL_COPD_9


title: Placenta_P108

description:
Sample 393
DNA extracted from placenta tissue.


title: BAL_IPF_Leuven_14


title: Mother_P082

description:
Sample 392
DNA extracted from peripheral venous blood of the mother.


title: MGAS28446


title: Father_P082

description:
Sample 391
DNA extracted from peripheral venous blood of the father.


title: MGAS28443


title: BAL_IPF_Leuven_13


title: MGAS28441


title: UmbilicalCord_P082

description:
Sample 390
DNA extracted from umbilical cord blood of the newborn.


title: BAL_COPD_8


title: Placenta_P082

description:
Sample 389
DNA extracted from placenta tissue.


title: MGAS28440


title: BAL_COPD_7


title: BAL_IPF_Leuven_12


title: MGAS28429


title: BAL_COPD_5


title: BAL_IPF_Leuven_11


title: Mother_P080

description:
Sample 388
DNA extracted from peripheral venous blood of the mother.


title: BAL_COPD_4


title: BAL_COPD_6


title: Father_P080

description:
Sample 387
DNA extracted from peripheral venous blood of the father.


title: MGAS28424


title: UmbilicalCord_P080

description:
Sample 386
DNA extracted from umbilical cord blood of the newborn.


title: MGAS28418


title: BAL_COPD_3


title: BAL_IPF_Leuven_9


title: MGAS28402


title: Placenta_P080

description:
Sample 385
DNA extracted from placenta tissue.


title: Mother_P054

description:
Sample 384
DNA extracted from peripheral venous blood of the mother.


title: BAL_IPF_Leuven_8


title: MGAS28362


title: BAL_IPF_Leuven_10


title: Father_P054

description:
Sample 383
DNA extracted from peripheral venous blood of the father.


title: MGAS28356


title: BAL_IPF_Leuven_4


title: UmbilicalCord_P054

description:
Sample 382
DNA extracted from umbilical cord blood of the newborn.


title: Placenta_P054

description:
Sample 381
DNA extracted from placenta tissue.


title: BAL_IPF_Leuven_5


title: BAL_IPF_Leuven_6


title: MGAS28553


title: BAL_COPD_1


title: BAL_COPD_2


title: Mother_P052

description:
Sample 380
DNA extracted from peripheral venous blood of the mother.


title: MGAS28347


title: MGAS28363


title: MGAS28341


title: BAL_IPF_Leuven_7


title: HEK293 10 mM INAM treated - Batch 3

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

country: Australia

institute: The Westmead Institute for Medical Research

description: HEK293 cells treated with 10 mM INAM

hyb_protocol: The Affymetrix arrays were hybridized and washed using the manufacturer's protocol. The arrays were then stained with streptavidin-phycoerythrin using the standard antibody amplification protocol. Please refer to Expression Analysis Technical Manual available from Affymetrix website (GeneChip® Expression Manual, Affymetrix, Inc., Santa Clara, CA)

scan_protocol: Affymetrix arrays were scanned with the Affymetrix GeneArray scanner. Please refer to Expression Analysis Technical Manual available from Affymetrix website (GeneChip® Expression Manual, Affymetrix, Inc., Santa Clara, CA)

data_processing: The images were analyzed using Microarray Suite 5.0 software (MAS5.0; Affymetrix Inc., Santa Clara, CA). Expression ratios were computed by comparative analysis of MAS5 values. The data were filtered using MAS5's signal detection and change calls generated at recommended default settings. The ratios included were those that had present calls for signal detection or an increase or decrease call associated with the ratio

source_name: Human embryonic kidney 293 (HEK293) cells (Batch 3), treated with 10 mM isonicotinamide (INAM) for 24 hours

label_protocol:
cRNA targets for the Affymetrix arrays were synthesized, labeled, and purified according to vendor's (Affymetrix) instructions.
Please refer to Expression Analysis Technical Manual available from Affymetrix website
(GeneChip® Expression Manual, Affymetrix, Inc., Santa Clara, CA)

growth_protocol:
Cells were cultured at 5% CO2, 37ºC and 93% relative humidity in complete minimum essential medium (cMEM), which contained per 565 ml: 500 ml MEM with Earle’s salts and L-glutamine, 50 ml fetal bovine
serum, 5 ml sodium pyruvate solution (100 mM), 5 ml MEM non-essential amino acids solution (10 mM), and 5 ml penicillin-streptomycin solution (10,000 U/ml each). Transfer to fresh medium was performed when confluence was ~ 70% and an approximate of 5 X 10^5 cells/ml density was maintained for routine growth. Cell counts were obtained by
resuspension in cMEM following trypsinization. For all experiments, confluent cultures at passage number below 9 were used. Cells seeded from a single vial of stock frozen in cMEM and 10% dimethyl sulfoxide (DMSO) were used in each experiment.

extract_protocol:
Total RNA from the cultured cell samples was collected by replacing media with 2 ml of TRIzol® Reagent. Cells suspended in TRIzol® reagent were disrupted by repeated pipetting and then transferred into microfuge tubes. This protocol was modified from manufacturer’s instructions and is described here. The lysate was further homogenized using syringe and needle for 30 s and incubated at room temperature (~21ºC) for 5 min, and 200 l of chloroform was added. The tubes were shaken vigorously μ for 15 s to mix the
phases and incubated for 3 min at room temperature. The phases were separated by centrifugation at 12,000 x g for 15 min at 4ºC. The upper aqueous phase was transferred into a fresh microfuge tube and 500 μl of ice cold isopropanol added to precipitate the RNA. The contents were mixed by gentle inversion and then incubated for 10 min at room
temperature. The RNA was recovered by centrifugation at 12,000 x g for 10 min at 4ºC. A gelatinous pellet was left on the side of the tube after removal of the supernatant. The RNA pellet was washed with 1 ml of 75% ethanol and the tube was vortexed briefly to resuspend
the pellet. The RNA was recovered by centrifugation at 7,500 x g for 5 min at 4ºC. This washing step was repeated twice. After removal of the supernatant, the RNA pellet was airdried briefly and then resuspended in 20 μl Nuclease-free H2O and stored in -80ºC for further processing.

treatment_protocol: Cells at a density of approximately 5 X 10^5 cells/ml were split equally into 25 cm3 flasks (NuncTM, Roskilde, Denmark) supplemented with fresh complete minimum essential medium (cMEM) 24 hr before the commencement of treatment. INAM stock solutions (50 mM) were prepared in fresh MEM and then filter-sterilized. After 24 hr, cells were checked to have reached 50-60 % confluence and the medium was supplemented with fresh MEM with INAM stock solution added to a final concentration of 5 mM. Total RNA from the cells were extracted at 24 hr following the treatment.

tag: Designations

value: 293 [HEK-293] Organism:Homo sapiens (human) Source organ:kidney Growth properties:adherent This is a hypotriploid human cell line. The modal chromosome number was 64, occurring in 30% of cells. Please refer to www.atcc.org for further information.


title: BAL_IPF_Leuven_2


title: BAL_IPF_Leuven_3


title: HEK293 10 mM INAM treated - Batch 2

description: HEK293 cells treated with 10 mM INAM

source_name: Human embryonic kidney 293 (HEK293) cells (Batch 1), treated with 10 mM isonicotinamide (INAM) for 24 hours


title: Father_P052

description:
Sample 379
DNA extracted from peripheral venous blood of the father.


title: MGAS28331


title: Placenta_P052

description:
Sample 377
DNA extracted from placenta tissue.


title: MGAS28321


title: Father_P043

description:
Sample 376
DNA extracted from peripheral venous blood of the father.


title: MGAS28305


title: MGAS28307


title: MGAS28296


title: BAL_IPF_Leuven_1


title: UmbilicalCord_P043

description:
Sample 375
DNA extracted from umbilical cord blood of the newborn.


title: PHH_WO_MD_exp3 [mRNA]

first: Linda

last: Rieswijk

address: Universiteitssingel 50

department: Toxicogenomics

institute: Maastricht University

description: BrainArray custom CDF v15.1.0

hyb_protocol: Amplified, biotinylated and fragmented targets were then hybridized on to the arrays.

scan_protocol: After hybridization, arrays were washed and stained using an Affymetrix fluidics station and scanned by use of an Affymetrix GeneArray scanner. A total of 6 RNA samples was prepared and analyzed on GeneChip arrays (treated and control samples from each time point were at least in triplicate). Normalization quality controls, including scaling factors, average intensities, present calls, background intensities, noise, and raw Q values, appeared to be within acceptable limits for all chips. Hybridization controls BioB, BioC, BioD, and CreX were called present on all chips and yielded the expected increases in intensities.

data_processing: The Arrayanalysis.org web service was used for quality control (27) and all microarrays except one were of high quality which was omitted from the analyses. CEL files were imported into R v2.15.3 (http://www.r-project.org) using the “affy” library (28) within BioConductor (v2.9) (29). Probe re-annotation, normalization and data filtering was performed as previously described (30).

label: Biotin

label_protocol: High-density oligonucleotide GeneChips from Affymetrix were used to measure gene expression levels (Human Genome U133 Plus 2.0 array (604,258 probes)). Targets for these arrays were prepared, hybridized and scanned according to the Affymetrix protocol (Affymetrix).Normalization quality controls appeared to be within acceptable limits for almost all chips.

growth_protocol: Cryopreserved primary human hepatocytes (PHH) were purchased from Life Technologies. Cells were cultured in pre-coated 24-well and 6-well plates (700,000 cells/ml) in a 2-layer collagen sandwich (A11428-02, Gibco), according to the supplier’s protocol (Invitrogen, 2012). The following culture media were used: Hepatocyte Thawing Medium (HTM) for thawing (CM7500, Gibco), Williams’ Medium E (1x, no phenol red) (A1217601, Gibco) + Cell Maintenance supplement B kit (CM4000, Gibco) for plating and incubation.

extract_protocol: Cells were cultured in triplicate in 24 wells (RNA) or 6 wells (DNA) in a collagen sandwich layer. Following 5 days of repetitive daily exposure the treatment was removed for 3 days (washout period), then cells lysates were harvested for DNA and total RNA isolation. At the end of washout, medium was removed and PHH were harvested in Qiazol (Qiagen). Total RNA was isolated using a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and followed by DNase I (Qiagen) treatment. Upon purification, RNA concentrations were measured by means of a NanoDrop® ND-1000 spectrophotometer (Thermo Scientific) at 260 and 280 nm. RNA quality and integrity were assessed by using automated gel electrophoresis on an Agilent 2100 Bioanalyzer system (Agilent Technologies). Only RNA samples which showed clear 18S and 28S peaks and with an RNA integrity number (RIN) higher than 8, were used. Samples were stored at -80ºC until RNA hybridization.

treatment_protocol: After quick thawing in a water bath at 37°C, viability of the cells was checked by a Trypan blue (CAS no. 72-57-1, Sigma–Aldrich) exclusion test as instructed in the supplier’s protocol (Invitrogen, 2012). All viability scores after thawing were in agreement with those listed by the supplier. Before AFB1 treatment, cells were allowed to acclimatize for 48 hours. This is needed for the hepatocytes to restore an in vivo like cellular configuration and enzyme expression levels as optimally as possible.AFB1 doses causing moderate (IC40) cytotoxicity after 5 days of repetitive daily exposure were established by means of the MTT assay (23). Furthermore, crucial liver function enzymes such as lactate dehydrogenase (LDH) and alanine transaminase (ALT) were measured. LDH and ALT were spectrophotometrically determined on a Cobas 8000 Modular Analyser (Roche Diagnostics, Basel, Switzerland). Based on this data,  1 µM of AFB1, was selected for the main experiment.

value: primary human hepatocytes

tag: main source

value: liver

tag: study type

value: Wash out effect

tag: assay type

value: ex vivo

tag: strain

tag: agent

value: aflatoxin B1

tag: dose

tag: dose unit

value: uM

tag: dose duration

tag: duration unit

value: days

tag: dose frequency

value: daily

tag: vehicle

value: DMSO

tag: route

value: medium


title: HEK293 0 mM INAM treated - Batch 1

description: HEK293 cells treated with 0mM INAM

source_name: Human embryonic kidney 293 (HEK293) cells (Batch 1), treated with 0 mM isonicotinamide (INAM) for 24 hours


title: PHH_WO_MD_exp1 [mRNA]

description: BrainArray custom CDF v15.1.0

tag: cell type


title: PHH_WO_MD_exp2 [mRNA]

description: BrainArray custom CDF v15.1.0


title: HEK293 10 mM INAM treated - Batch 1

description: HEK293 cells treated with 10 mM INAM


title: HEK293 0 mM INAM treated - Batch 3

description: HEK293 cells treated with 0mM INAM

source_name: Human embryonic kidney 293 (HEK293) cells (Batch 3), treated with 0 mM isonicotinamide (INAM) for 24 hours


title: PHH_WO_MD_control_exp2 [mRNA]

description: BrainArray custom CDF v15.1.0


title: HEK293 0 mM INAM treated - Batch 2

description: HEK293 cells treated with 0mM INAM

source_name: Human embryonic kidney 293 (HEK293) cells (Batch 2), treated with 0 mM isonicotinamide (INAM) for 24 hours


title: MGAS28265

tag: subclade

value: Subclade2A (SC2A)

tag: site of isolation

value: invasive infection isolate

tag: growth phase

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


title: Placenta_P043

description:
Sample 374
DNA extracted from placenta tissue.

tag: dna sample

value: Multi cell

tag: quartet

tag: conception

value: NAT

tag: birthweight at delivery

value: AGA


title: MGAS28261


title: UmbilicalCord_P052

description:
Sample 378
DNA extracted from umbilical cord blood of the newborn.


title: Mother_P043

description:
Sample 373
DNA extracted from peripheral venous blood of the mother.


title: HEK293 5 mM INAM treated - Batch 2

description: HEK293 cells treated with 5mM INAM

source_name: Human embryonic kidney 293 (HEK293) cells (Batch 2), treated with 5 mM isonicotinamide (INAM) for 24 hours

tag: Designations

value: 293 [HEK-293] Organism:Homo sapiens (human) Source organ:kidney Growth properties:adherent This is a hypotriploid human cell line. The modal chromosome number was 64, occurring in 30% of cells. Please refer to www.atcc.org for further information.


title: HEK293 5 mM INAM treated - Batch 3

description: HEK293 cells treated with 5mM INAM

source_name: Human embryonic kidney 293 (HEK293) cells (Batch 3), treated with 5 mM isonicotinamide (INAM) for 24 hours


title: MGAS28259


title: Father_P041

description:
Sample 371
DNA extracted from peripheral venous blood of the father.

value: IVF


title: MGAS28255


title: HEK293 5 mM NAM treated - Batch 2

description: HEK293 cells treated with 5 mM NAM

source_name: Human embryonic kidney 293 (HEK293) cells (Batch 2), treated with 5 mM nicotinamide (NAM) for 24 hours

growth_protocol:
Cells were cultured at 5% CO2, 37ºC and 93% relative humidity in complete minimum essential medium (cMEM), which contained per 565 ml: 500 ml MEM with Earle’s salts and L-glutamine, 50 ml fetal bovine
serum, 5 ml sodium pyruvate solution (100 mM), 5 ml MEM non-essential amino acids solution (10 mM), and 5 ml penicillin-streptomycin solution (10,000 U/ml each). Transfer to fresh medium was performed when confluence was ~ 70% and an approximate of 5 X 10^5 cells/ml density was maintained for routine growth. Cell counts were obtained by
resuspension in cMEM following trypsinization. For all experiments, confluent cultures at passage number below 15 were used. Cells seeded from a single vial of stock frozen in cMEM and 10% dimethyl sulfoxide (DMSO) were used in each experiment.

treatment_protocol:
Cells at a density of approximately 5 X 10^5 cells/ml were split equally into 25 cm3 flasks (NuncTM, Roskilde, Denmark) supplemented with fresh complete minimum essential medium (cMEM) 24 hr before the commencement of treatment. NAM stock solutions (50 mM) were prepared in fresh MEM and then filter-sterilized. After 24 hr, cells were checked to have reached 50-60 % confluence and the medium was supplemented with fresh MEM with NAM stock solution added to a
final concentration of 5 mM. Total RNA from the cells were extracted at 24 hr following the treatment.

tag: Organism

value: Homo sapiens (human)

tag: Source organ

value: kidney

tag: Growth properties

value: adherent

tag: This is a hypotriploid human cell line. The modal chromosome number was 64, occurring in 30% of cells.

tag: Please refer to www.atcc.org for further information.


title: HEK293 5 mM NAM treated - Batch 3

description: HEK293 cells treated with 5 mM NAM

source_name: Human embryonic kidney 293 (HEK293) cells (Batch 3), treated with 5 mM nicotinamide (NAM) for 24 hours


title: MGAS28249


title: HEK293 5 mM INAM treated - Batch 1

description: HEK293 cells treated with 5mM INAM

source_name: Human embryonic kidney 293 (HEK293) cells (Batch 1), treated with 5 mM isonicotinamide (INAM) for 24 hours


title: MGAS28232


title: MGAS28471


title: UmbilicalCord_P041

description:
Sample 370
DNA extracted from umbilical cord blood of the newborn.


title: MGAS28248


title: Ab42.26.2

city: Duarte

first: Paul

middle: M.

last: Salvaterra

state: CA

address: 1500 E. Duarte Rd.

department: Stem Cell and Developmental Biology

institute: Beckman Research Institute of the City of Hope

description: RNA-Seq data, TALEN Editied Ab42, Clone 42-26, Replicate 2

data_processing:
Illumina RTA was used to create .bcl files, and bcl2fastq 1.8 software was used for base calling (for samples split between flowcells and later merged per run)
Reads aligned using TopHat2 (v2.0.14), with --no-coverage-search (with --library-type fr-firststrand for stranded library samples)
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Hsapiens.UCSC.hg19.knownGene (Bioconductor annotations, downloaded 6/8/2016), with strand was set to "reverse"
Genome_build: hg19
Supplementary_files_format_and_content: FPKM normalized expression (using quantified reads and TxDb annotations in R) and read counts (calculated using htseq-count).  Log2(FPKM+0.1) values are anti-logged to provide linear values (with low FPKM values appearing as 0)

growth_protocol: Amoroso et al. (2013) J. Neurosci. 33:574-586. This neural differentiation protocol was originally designed for motor neuron enrichment.

extract_protocol:
Total RNA was extracted using Amsbio RNA Stat-60 RNA extraction reagent according to the manufacturers directions.
KAPA stranded mRNA kit

treatment_protocol: Differentiating neuronal cultures were treated with BrdU weekly up to ~7-9 weeks to control rapidly dividing cells.

value: WiCell WA09 human embryonic stem cells

tag: treatment

tag: clone

tag: batch


title: Placenta_P041

description:
Sample 369
DNA extracted from placenta tissue.


title: HEK293 0 mM NAM treated - Batch 3

description: HEK293 cells treated with 0 mM NAM

source_name: Human embryonic kidney 293 (HEK293) cells (Batch 3), treated with 0 mM nicotinamide (NAM) for 24 hours

treatment_protocol: Cells at a density of approximately 5 X 10^5 cells/ml were split equally into different 25 cm3 flasks supplemented with fresh complete minimum essential medium (cMEM) 24 hr before the commencement of treatment. After 24 hr, cells were checked to have reached 50-60 % confluence and the medium was supplemented with 2 ml of fresh MEM, i.e. 0 mM NAM, to serve as a control. Total RNA from the cells were extracted at 24 hr following the treatment.


title: PHH_WO_MD_control_exp3 [mRNA]

description: BrainArray custom CDF v15.1.0

tag: cell type

value: primary human hepatocytes

tag: main source

value: liver

tag: study type

value: Wash out effect

tag: assay type

value: ex vivo

tag: strain

tag: agent

tag: dose

tag: dose unit

tag: dose duration

tag: duration unit

tag: dose frequency

tag: vehicle

tag: route


title: Mother_P033

description:
Sample 368
DNA extracted from peripheral venous blood of the mother.

tag: dna sample

tag: quartet

tag: conception

tag: birthweight at delivery


title: UmbilicalCord_P033

description:
Sample 366
DNA extracted from umbilical cord blood of the newborn.


title: MGAS28209

source_name: cell pellet

tag: subclade

tag: site of isolation

tag: growth phase


title: HEK293 0 mM NAM treated - Batch 2

description: HEK293 cells treated with 0 mM NAM

source_name: Human embryonic kidney 293 (HEK293) cells (Batch 2), treated with 0 mM nicotinamide (NAM) for 24 hours

tag: Designations

tag: Organism

tag: Source organ

tag: Growth properties

tag: This is a hypotriploid human cell line. The modal chromosome number was 64, occurring in 30% of cells.

tag: Please refer to www.atcc.org for further information.


title: MGAS28230


title: Father_P033

description:
Sample 367
DNA extracted from peripheral venous blood of the father.


title: MGAS28207


title: Ab40.31.2

description: RNA-Seq data, TALEN Editied Ab40, Clone 40-31

source_name: TALEN Editied Ab40, Clone 40-31

tag: cell type

tag: treatment

tag: clone

tag: batch


title: HEK293 15 mM NAM treated - Batch 1

description: HEK293 cells treated with 15mM NAM

source_name: Human embryonic kidney 293 (HEK293) cells (Batch 1), treated with 15 mM nicotinamide (NAM) for 24 hours

treatment_protocol: Cells at a density of approximately 5 X 10^5 cells/ml were split equally into 25 cm3 flasks (NuncTM, Roskilde, Denmark) supplemented with fresh complete minimum essential medium (cMEM) 24 hr before the commencement of treatment. NAM stock solutions (50 mM) were prepared in fresh MEM and then filter-sterilized. After 24 hr, cells were checked to have reached 50-60 % confluence and the medium was supplemented with fresh MEM with NAM stock solution added to a final concentration of 15 mM. Total RNA from the cells were extracted at 24 hr following the treatment.


title: HEK293 10 mM NAM treated - Batch 1

description: HEK293 cells treated with 10mM NAM

source_name: Human embryonic kidney 293 (HEK293) cells (Batch 1), treated with 10 mM nicotinamide (NAM) for 24 hours

treatment_protocol: Cells at a density of approximately 5 X 10^5 cells/ml were split equally into 25 cm3 flasks (NuncTM, Roskilde, Denmark) supplemented with fresh complete minimum essential medium (cMEM) 24 hr before the commencement of treatment. NAM stock solutions (50 mM) were prepared in fresh MEM and then filter-sterilized. After 24 hr, cells were checked to have reached 50-60 % confluence and the medium was supplemented with fresh MEM with NAM stock solution added to a final concentration of 10 mM. Total RNA from the cells were extracted at 24 hr following the treatment.


title: HEK293 20 mM NAM treated - Batch 1

description: HEK293 cells treated with 20mM NAM

source_name: Human embryonic kidney 293 (HEK293) cells (Batch 1), treated with 20 mM nicotinamide (NAM) for 24 hours

treatment_protocol: Cells at a density of approximately 5 X 10^5 cells/ml were split equally into 25 cm3 flasks (NuncTM, Roskilde, Denmark) supplemented with fresh complete minimum essential medium (cMEM) 24 hr before the commencement of treatment. NAM stock solutions (50 mM) were prepared in fresh MEM and then filter-sterilized. After 24 hr, cells were checked to have reached 50-60 % confluence and the medium was supplemented with fresh MEM with NAM stock solution added to a final concentration of 20 mM. Total RNA from the cells were extracted at 24 hr following the treatment.


title: Mother_P041

description:
Sample 372
DNA extracted from peripheral venous blood of the mother.

source_name: Peripheral blood

tag: dna sample


title: HEK293 5 mM NAM treated - Batch 1

description: HEK293 cells treated with 5 mM NAM

source_name: Human embryonic kidney 293 (HEK293) cells (Batch 1), treated with 5 mM nicotinamide (NAM) for 24 hours

treatment_protocol: Cells at a density of approximately 5 X 10^5 cells/ml were split equally into 25 cm3 flasks (NuncTM, Roskilde, Denmark) supplemented with fresh complete minimum essential medium (cMEM) 24 hr before the commencement of treatment. NAM stock solutions (50 mM) were prepared in fresh MEM and then filter-sterilized. After 24 hr, cells were checked to have reached 50-60 % confluence and the medium was supplemented with fresh MEM with NAM stock solution added to a final concentration of 5 mM. Total RNA from the cells were extracted at 24 hr following the treatment.


title: Ab42.14.2

description: RNA-Seq data, TALEN Editied Ab42, Clone 42-14, Replicate 2


title: Placenta_P033

description:
Sample 365
DNA extracted from placenta tissue.

source_name: Placenta tissue

tag: quartet


title: HEK293 0 mM NAM treated - Batch 1

description: HEK293 cells treated with 0 mM NAM to serve as controls

source_name: Human embryonic kidney 293 (HEK293) cells (Batch 1), treated with 0mM nicotinamide (NAM) for 24 hours

treatment_protocol:
Cells at a density of approximately 5 X 10^5 cells/ml were split equally into different 25 cm3 flasks supplemented with fresh complete minimum essential medium (cMEM) 24 hr before the commencement of treatment. After 24 hr, cells were checked to have reached 50-60 %
confluence and the medium was supplemented with 2 ml of fresh MEM, i.e. 0 mM NAM, to serve as a control. Total RNA from the cells were extracted at 24 hr following the treatment.


title: H9.3

description: RNA-Seq data, Unmodified H9 Cells, Replicate 3

source_name: Unmodified H9 Cells, Replicate 3

value: WT H9

value: WT


title: MGAS28172

value: Subclade2A (SC2A)

value: invasive infection isolate


title: MGAS28131

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


title: Ab42.26.1

description: RNA-Seq data, TALEN Editied Ab42, Clone 42-26, Replicate 1


title: MGAS28127


title: Ab42.14.1

description: RNA-Seq data, TALEN Editied Ab42, Clone 42-14, Replicate 1


title: UmbilicalCord_P032

description:
Sample 362
DNA extracted from umbilical cord blood of the newborn.

source_name: Cord blood

value: Multi cell

tag: conception

value: NAT


title: Father_P032

description:
Sample 363
DNA extracted from peripheral venous blood of the father.

tag: birthweight at delivery

value: AGA


title: Mother_P032

description:
Sample 364
DNA extracted from peripheral venous blood of the mother.


title: Ab40.41.1

description: RNA-Seq data, TALEN Editied Ab40, Clone 40-41

source_name: TALEN Editied Ab40, Clone 40-41


title: Placenta_P032

description:
Sample 361
DNA extracted from placenta tissue.


title: MGAS28121

tag: subclade


title: Mother_P029

description:
Sample 360
DNA extracted from peripheral venous blood of the mother.


title: H9.2

description: RNA-Seq data, Unmodified H9 Cells, Replicate 2

source_name: Unmodified H9 Cells, Replicate 2


title: MGAS28117

tag: site of isolation


title: MGAS28115

tag: growth phase


title: Father_P029

description:
Sample 359
DNA extracted from peripheral venous blood of the father.


title: H9.1

description: RNA-Seq data, Unmodified H9 Cells, Replicate 1

source_name: Unmodified H9 Cells, Replicate 1


title: MGAS28107


title: UmbilicalCord_P029

description:
Sample 358
DNA extracted from umbilical cord blood of the newborn.


title: HEK293T_Input

city: Shanghai

first: Fei

last: Lan

address: 130 Dong An Road

institute: Fudan university

library_source: genomic

data_processing:
base_calling: CASAVA package (Illumina v1.6)
alignment: Bowtie (version 1.2.1.1) with -m 1 and other default parameters
peak_calling: macs14 (1.4.2 20120305) with -p 0.00001 --nomodel
Genome_build: hg19
Supplementary_files_format_and_content: bed files including peak locations

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: embryonic kidney cell line HEK293T

tag: chip antibody


title: Placenta_P029

description:
Sample 357
DNA extracted from placenta tissue.


title: Mother_P028

description:
Sample 356
DNA extracted from peripheral venous blood of the mother.


title: hES_Input

source_name: human ESC

value: ESC


title: HEK293T_H3K14me3

value: H3K14me3 (homemade)


title: hES_H3K14me3


title: Father_P028

description:
Sample 355
DNA extracted from peripheral venous blood of the father.


title: MGAS28082


title: MGAS28074


title: MGAS28065


title: Sample_Si

city: Changsha

first: Zhen

middle: zi

last: Peng

state: Hunan

address: Xiangya Road 87th

institute: Xiangya hospital

data_processing:
Raw data (raw reads) were processed using NGS QC Toolkit. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference P. trichocarpa genome using bowtie2 or Tophat (http://tophat.cbcb.umd.edu/).
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: lung adenocarcinoma cell

growth_protocol: The base medium for this cell line is RPMI-1640 Medium. Add fetal bovine serum to a final concentration of 10%.  Cells were harvest as 90% confluent in a T75 flask.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
The libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or Illumina HiSeq X Ten) and 125bp/150bp paired-end reads were generated.

treatment_protocol: The siRNAs were transfected into cells with Lipofectamine 3000 (Invitrogen) as the manufacturer’s protocol. Cells were harvested for analysis at 48hrs after transfection. Lentiviral vectors for LINC00312 overexpression and negative control were constructed by Shanghai Genechem. After lentivirus transduction, cells were selected on 2 μg /ml puromycin to establish stable cell lines.

tag: genotype

value: LINC00312- Kockdown


title: Sample_Wt

value: Wild type


title: MGAS28058

source_name: cell pellet


title: MGAS28031


title: GCM_3

city: Philadelphia

first: Yi

last: Fan

state: PA

address: 3400 Civic Center Blvd

department: Department of Radiation Oncology

institute: University of Pennsylvania Perelman School of Medicine

description: processed data file: FPKM.xlsx

data_processing:
The sequences were aligned to the UCSC hg38 reference genome using RNA-Star (v2.4.2a) (https://github.com/alexdobin/STAR). The gene expression was normalized and calculated as FPKM (Fragments Per Kilobase Million) values by Cufflinks (v2.2.1) (http://cole-trapnell-lab.github.io/cufflinks/releases/v2.2.1/) with Gencode v22 gene annotations (https://www.gencodegenes.org/releases/22.html). Gene expression was expressed as FPKM values.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: FPKM.xlsx: Excel file includes abundance measurements.

source_name: Treated normal human brain microvascular endothelial cells #3

growth_protocol: ECs were cultured in Endothelial Cell Medium (ECM, ScienCell) with 5% CO2.

extract_protocol:
2 x 10e6 cells were lysed in 1 ml TRIzol (Thermo Fisher), followed by RNA extraction. The isolated RNA was purified by using an RNeasy Plus Mini Kit (Qiagen).
Library was constructed by using a TruSeq protocol with TapeStation (Agilent), and subjected to deep sequencing (100 PE, about 10 megabyte reads for each sample, Illumina sequencer 2500) in the Children’s Hospital of Philadelphia/Beijing Genomics Institute core facility (CHOP/BGI).

treatment_protocol: Human brain microvascular ECs were treated with glioma-CM for 2 days. After changing medium, cells were cultured in DMEM/F-12 medium for 1 day.

value: Normal human brain microvascular endothelial cells

value: glioma-conditioned medium


title: GCM_2

description: processed data file: FPKM.xlsx

source_name: Treated normal human brain microvascular endothelial cells #2


title: Mother_P027

description:
Sample 352
DNA extracted from peripheral venous blood of the mother.


title: UmbilicalCord_P027

description:
Sample 350
DNA extracted from umbilical cord blood of the newborn.


title: MGAS28086


title: GCM_1

description: processed data file: FPKM.xlsx

source_name: Treated normal human brain microvascular endothelial cells #1


title: MGAS28085


title: MGAS28029


title: Placenta_P027

description:
Sample 349
DNA extracted from placenta tissue.


title: Ctr_3

description: processed data file: FPKM.xlsx

source_name: Normal human brain microvascular endothelial cells #3

value: control


title: MGAS28022


title: HCC serum severe (D49)

city: Kaohsiung

first: I-Hsuan

middle: Ann

last: Chen

address: 123 Ta-Pei Rd., Niao-Sung

country: Taiwan

institute: CGMH

description: Gene expression after injection on D49

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: HCC serum severe (D49)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: serum exosomes  RNA extracted according to SBI exosome extraction kit protocol

treatment_protocol: HCC cell line were injected to Rat and havested the serum from D 35 and Day 49.

tag: sample type

value: serum

tag: gender

value: male


title: HCC serum moderate (D49)

description: Gene expression after injection on D49

source_name: HCC serum moderate (D49)


title: UmbilicalCord_P028

description:
Sample 354
DNA extracted from umbilical cord blood of the newborn.


title: Ctr_2

description: processed data file: FPKM.xlsx

source_name: Normal human brain microvascular endothelial cells #2


title: PHH_WO_MD_control_exp1 [mRNA]

description: BrainArray custom CDF v15.1.0

value: primary human hepatocytes

tag: main source

value: liver

tag: study type

value: Wash out effect

tag: assay type

value: ex vivo

tag: strain

tag: agent

value: DMSO

tag: dose

tag: dose unit

tag: dose duration

tag: duration unit

value: days

tag: dose frequency

value: daily

tag: vehicle

tag: route

value: medium


title: Placenta_P028

description:
Sample 353
DNA extracted from placenta tissue.

source_name: Placenta tissue

tag: dna sample

value: Multi cell

tag: quartet

tag: conception

value: NAT

tag: birthweight at delivery

value: AGA


title: Sample_OE

tag: cell type

tag: genotype

value: LINC00312- Overexpress


title: HCC serum light(D35)

description: Gene expression after injection on D35

source_name: HCC serum light(D35)

tag: sample type

tag: gender


title: Naïve

description: Gene expression w/o injection

source_name: Naïve


title: MGAS28047

tag: subclade

value: Subclade2A (SC2A)

tag: site of isolation

value: invasive infection isolate

tag: growth phase

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


title: Father_P027

description:
Sample 351
DNA extracted from peripheral venous blood of the father.

source_name: Peripheral blood


title: Ctr_1

description: processed data file: FPKM.xlsx

source_name: Normal human brain microvascular endothelial cells #1

tag: treatment

value: control


title: MGAS28008


title: UmbilicalCord_P026

description:
Sample 346
DNA extracted from umbilical cord blood of the newborn.

source_name: Cord blood


title: MGAS28007


title: Mother_P026

description:
Sample 348
DNA extracted from peripheral venous blood of the mother.


title: Mother_P020

description:
Sample 344
DNA extracted from peripheral venous blood of the mother.


title: MGAS28004


title: maize endosperm 15 DAP - dek33

city: Gainesville

first: Dawei

last: Dai

state: Florida

address: 2550 Hull Rd

department: Horticultural Sciences

institute: University of Florida

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B73 RefGen_v3 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Ensembl plants release-37 zea_mays
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

organism: Zea mays

source_name: kernel

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: endosperm

tag: age

value: 15 DAP


title: ∆IMP1_RPF

city: Piscataway

first: Premal

last: Shah

state: NJ

address: 145 Bevier Road, Rm 326

department: Genetics

institute: Rutgers University

data_processing:
RNA-seq and footprinting reads were mapped to the human transcriptome using the riboviz pipeline (Carja et al., BMC Bioinformatics 2017). Sequencing adapters were trimmed from reads using Cutadapt 1.10 (--trim-n -O 1 –minimum-length 5).
The reads from different samples were separated based on the barcodes in their 3’ linkers using fastx_barcode_splitter (FASTX toolkit, Hannon lab) with utmost one mismatch allowed. UMI and barcodes were removed from reads in each sample using Cutadapt (--trim-n -m 10 -u 4 -u -10)
Trimmed reads that aligned to human/mouse rRNA were removed using Bowtie v1.1.2 . Remaining reads were mapped to a set of 19,192 principal transcripts for each gene in the APPRIS database (using HISAT2 v2.1.0). Only reads that mapped uniquely were used for all downstream analyses. For genes with multiple principal transcripts, the first one in the list was chosen.
All analyses of ribosome profiling datasets were performed in R. We restricted analyses to genes with at least one dataset (RNA-seq or footprinting across conditions) with 64 mapped reads and genes with 0 read counts in any dataset were ignored unless the mean read counts across all 8 datasets was above 64.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include count values for each sample

source_name: SW480 cell lines

extract_protocol:
Ribosome profiling libraries from 3 pooled cell culture plates were prepared using a standard protocol (McGlincy and Ingolia, Methods 2017), with minor modifications.
Separate 5’ and 3’ linkers were ligated to the RNA-fragment instead of 3’ linker followed by circularization (Subtelny et al, Nature 2014). 5’ linkers contained 4 random nt unique molecular identifier (UMI) similar to a 5 nt UMI in 3’ linkers. During size-selection, we restricted the footprint lengths to 18-34 nts. Matched RNA-seq libraries were prepared using RNA that was randomly fragmentation by incubating for 15 min at 95C with in 1 mM EDTA, 6 mM Na2CO3, 44 mM NaHCO3, pH 9.3. RNA-seq fragments were restricted to 18-50 nts. Ribosomal rRNA were removed from pooled RNA-seq and footprinting samples using RiboZero (Epicenter MRZH116). cDNA for the pooled library were PCR amplified for 15 cycles.

tag: cell line

value: intestinal epithelial

tag: library type

value: Ribosome-protected fragments


title: Father_P020

description:
Sample 343
DNA extracted from peripheral venous blood of the father.


title: WT RNA

value: wild type

value: Total RNA


title: MGAS27993


title: MGAS28020


title: UmbilicalCord_P020

description:
Sample 342
DNA extracted from umbilical cord blood of the newborn.


title: Father_P026

description:
Sample 347
DNA extracted from peripheral venous blood of the father.


title: WT RPF


title: MGAS27981


title: maize endosperm 15 DAP - wild type


title: MGAS27979


title: Placenta_P020

description:
Sample 341
DNA extracted from placenta tissue.


title: 6con

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

data_processing:
FASTQ files were uploaded to an Oasis 1.0 sRNA Detection Pipeline (Capece et al. 2015). The FASTQ files were subsequently trimmed with cutadapt 1.7.1 ((http://code.google.com/p/cutadapt/). This enabled the removal of the adapter sequences (TGGAATTCTCGGGTGCCAAGG) and nucleotides with phred scores below 20.   A cut-off between 15-32 nucleotides was set to limit the minimum and maximum sequence length. Following trimming, the FASTQ sequences were aligned with STAR Aligner (Dobin et al. 2013) against the following databases: snoRNAEnsembl: Human s. version GRCh38.74, Mirbase version 20; release date: 2013-10-1, snRNA: Ensembl: Human s. version GRCh38.74; rRNA: Ensembl: Human s. version GRCh38.74. For a successful alignment, the total number of mismatches was set to 5% of sequence length. Counts per small RNA (feature) were evaluated applying feature Counts (Liao et al. 2014). The differential expression of the snoRNAs was estimated by DESeq2 (Love et al. 2014).
To normalize the raw read counts, we first converted the read counts of each small RNAs into “reads per million” (RPM) applying the formula: normalized expression = reads assigned to a unique sequence in a library/total number of reads identified by all sequences in that library x 1,000,000 (Motameny et al. 2010). The snoRNAs were then filtered from other small non-coding RNAs (microRNAs, piRNAs, rRNAs and novelmiRNAs,). This yielded a total of 271 snoRNA sequences. Next, an arbitrary filter of RPM values ≥ 30 in at least two out of 6 libraries screened was applied. This gave us a total 120 expressed snoRNAs in CCM compared to the healthy brain.
Genome_build: GRCh38.74, Mirbase version 20
Supplementary_files_format_and_content: RPM, reads per million

source_name: brain

extract_protocol:
mirVana miRNA isolation Kit (AM1560; Ambion) was used to isolate total RNA containing small RNA from the tissue specimens. The eluted RNA underwent DNase I treatment in solution for 10 min at RT by adding 10 µl of buffer RDD and 2.5 µl of DNase I, both extracted from RNeasy Micro Kit (74004; Qiagen). Thereafter, 10 µl of 5 M NaCl and 152 µl of 100% Ethanol were added and were thoroughly mixed followed by loading into the RNeasy column for end point elution. Total RNA was then eluted with 14 µl of RNase-free water. Quantification and quality of total RNA was carried out with the NanoDrop ND-1000 spectrophotometer (Peqlab). RNA integrity was detected with an Agilent Bioanalyzer 2100 using the RNA 6000 Nano Assay (5067-1511; Agilent Technologies). Only RNA extracts with a RNA integrity number (RIN) values ≥ 7 underwent further deep sequencing analysis.
A starting material of 50-100 ng total RNA was used to generate RNA sequencing library using the TruSeq® Small RNA Library Prep Kits v2 (Illumina). The libraries were sequenced on Illumina HiSeq2500 using TruSeq SBS Kit v3-HS (50 cycles, single ended run) with an average of 10 x106 reads per RNA sample.

treatment_protocol: Surgical resection of brainstem cavernous malformations is more challenging than CCM at other areas due to the surrounding delicate structures and its intricate location. Considering its high rate of hemorrhagic risks and higher operative morbidity with respect to superficially located CCM, we therefore, conducted this study on 3 CCM patients. Biopsy samples were dissected intraoperatively from patients (C1, C2 and C3) suffering due to CCM within the brainstem regions, snap-frozen in liquid nitrogen and stored at -800C until further usage. Commercially available Human Brain Reference Total RNA (Amsbio) isolated from 3 healthy adult brains (N1, N2 and N3) was used as corresponding controls. The patient clinical diagnosis and their histopathological assessment were based as previously described (Bertalanffy et al. 2002). Each patient underwent at least one or more clinical episodes manifested by seizures, hemorrhage and focal neurological deficits.

value: brain

tag: phenotype


title: MGAS27937

source_name: cell pellet


title: 5con


title: Mother_P018

description:
Sample 340
DNA extracted from peripheral venous blood of the mother.

tag: dna sample


title: ∆IMP1_RNA


title: Placenta_P026

description:
Sample 345
DNA extracted from placenta tissue.

tag: quartet


title: 4con


title: MGAS12254


title: Father_P018

description:
Sample 339
DNA extracted from peripheral venous blood of the father.

tag: conception


title: 3cav

value: Cerebral cavernous malformations


title: MGAS10793


title: UmbilicalCord_P018

description:
Sample 338
DNA extracted from umbilical cord blood of the newborn.

tag: birthweight at delivery


title: 2cav


title: Placenta_P018

description:
Sample 337
DNA extracted from placenta tissue.


title: 1cav


title: MGAS8012


title: Mother_P017

description:
Sample 336
DNA extracted from peripheral venous blood of the mother.


title: Father_P017

description:
Sample 335
DNA extracted from peripheral venous blood of the father.


title: MGAS7918


title: MGAS29633

value: Subclade1B (SC1B)


title: 48h_PG2, tech rep2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: 2000 ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Agilent Microarray Gene expression 8x15k Array (AMADID: 020941). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift .Gene based analysis was performed.

organism: Bacillus subtilis

source_name: 48h Bac cul_presence of glutamic acid, tech rep2

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligodT primer with T7 polymerase promoter converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: 37°C till 48 h, at 170 RPM

extract_protocol: RNA extraction was performed using Qiagen RNeasy Mini kit (Cat. No. 74106) as per the manufacturer's recommendations.

treatment_protocol: Organism was grown in 3 different conditions, in presence of glucose, glutamic acid and glucose and glutamic acid both (in 50 ml scale in the base media Urea 3gpl; Yeast extract 0.5 gpl; Peptone 1.5 gpl; Dipotassium phosphate 0.2 gpl). Till 48 h, followed by RNA ectraction.

tag: bacterial culture

value: cells

value: glutamic acid


title: 12_FHK124-CSA-18H

city: Seattle

first: Ying

last: Zheng

state: WA

address: 850 Republican

department: Bioengineering

institute: University of Washington

data_processing:
Base calling was performed using Illumina's Real-Time Analysis software v1.18.66.3 (https://support.illumina.com/sequencing/sequencing_software/real-time_analysis_rta.html), using the default settings.
Reads that didn't pass Illumina's base call quality filter were discarded, followed by using Cutadapt v1.11 to trim adapter sequence, discarding paired reads where either read in the pair has a length < 25
Generated counts for each gene using htseq-count v0.6.1p1 (using the "intersection-strict" overlapping mode)
Alignments were performed using TopHat v2.1.0, using the default parameters, with the exceptions of:  --mate-inner-dist = 80  --library-type = fr-firststrand  --no-coverage-search
Normalized data and performed significance testing using the GLM method in edgeR v3.18.1
Genome_build: Reads were aligned using UCSC assembly hg38
Supplementary_files_format_and_content: edgeR results files are in tab-delimited text format and contain columns for logFC(log2 ratio), logCPM(average log2 counts per million), sig (a value of 1 if |logFC| >= 0.585 & FDR 5% , otherwise 0), normalized gene counts, raw gene counts, as well annotation. Ratio formulation can be determined by the file naming convention, where the sample in the numerator comes first (e.g., x-y.txt would contain data where ratios were calculated as log2(x/y)

source_name: cultured HKMEC from donor

extract_protocol:
Total RNA was extracted from endothelial cells cultured in 6-well dishes using RNeasy kit (Qiagen). RNA was purified to reach 400ng at concentration above 50ng/mL for RNA-seq
RNA libraries were prepared for sequencing using standard Illumina protocols

value: exposed to CsA, 18 hrs

value: Kidney

tag: cell type

value: Human kidney peritubular microvascular endothelial cell


title: 13_FHK133-CSA-18H


title: UmbilicalCord_P017

description:
Sample 334
DNA extracted from umbilical cord blood of the newborn.

value: Multi cell

value: NAT

value: AGA


title: 48h_PG1 tech rep3

source_name: 48h Bac cul_presence of glucose, tech rep3

value: glucose


title: 48h_PG2, tech rep3

source_name: 48h Bac cul_presence of glutamic acid, tech rep3


title: 48h_PG2, tech rep1

source_name: 48h Bac cul_presence of glutamic acid, tech rep1


title: 48h_PG1 tech rep1

source_name: 48h Bac cul_presence of glucose, tech rep1


title: 48h_PG1 tech rep2

source_name: 48h Bac cul_presence of glucose, tech rep2


title: 48h_PG3, tech rep2

source_name: 48h Bac cul_presence of glucose & glutamic acid both, tech rep2

value: glucose & glutamic


title: MGAS29620

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

value: invasive infection isolate

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


title: Placenta_P017

description:
Sample 333
DNA extracted from placenta tissue.

source_name: Placenta tissue

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.


title: 48h_PG3, tech rep1

source_name: 48h Bac cul_presence of glucose & glutamic acid both, tech rep1


title: 10_FHK133-CTRL-18H

value: control


title: MGAS29617


title: 48h_PG3, tech rep3

source_name: 48h Bac cul_presence of glucose & glutamic acid both, tech rep3


title: Mother_F441

description:
Sample 332
DNA extracted from peripheral venous blood of the mother.

source_name: Peripheral blood


title: MGAS29613


title: Father_F441

description:
Sample 331
DNA extracted from peripheral venous blood of the father.


title: MGAS7980

value: Subclade2A (SC2A)


title: 8_FHK124-CTRL-18H


title: MGAS29611


title: UmbilicalCord_F441

description:
Sample 330
DNA extracted from umbilical cord blood of the newborn.

source_name: Cord blood


title: MGAS29599


title: TP5_control

city: Washington

first: Zhenzhi

last: Li

state: DC

address: 3900 reservoir rd nw

department: Biochemistry and Molecular Biology

institute: Georgetown University

data_processing:
Illumina Genome Studio software (Illumina) was used to extract signal intensities for each probe and to perform initial control quality checks
ChAMP pipeline was used to normalize and batch correct methylation array data
Probes that ambiguously mapped or had a high detection P value (>0.01), low bead count (<3 beads), and a low success rate (missing in >95% of the samples) were set to missing.
Probes with SNPs (MAF≥ 0.05 in 1000 Genomes Project) at CpG sites were excluded to avoid SNP (single-nucleotide polymorphism) effects on methylation measurement.
Genome_build: GRCh37
Supplementary_files_format_and_content: txt files with chromosome, positition of CpG site, percent methylation on each column

source_name: whole blood from ASD-discordant MZ twins

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.
5μg of genomic DNA was digested overnight with 4 μl MspI (New England Biolabs, Ipswich, MA) to ensure complete digestion and purified by phenol-chloroform extraction. After end repair and addition of 3’A overhangs, methylated-adaptors were ligated according to the manufacturer’s protocol and purified with AMPure beads (Agencourt Bioscience, Beverly, MA). Two ranges of 150-175bp and 175-225bp adapter-ligated fractions were excised from a 2% agarose gel, respectively. Bisulfite conversion was conducted using the reagents and protocol of EpiTect Bisulfite Kit (Qiagen, Darmstadt, Germany). Subsequently, the bisulfite-converted DNA was amplified by PCR with PfuTurbo Cx Hotstart DNA polymerase to build the PCR-amplified RRBS libraries, which were analyzed by Illumina HiSeq2500 (Illumina).

value: whole blood

tag: cohort

value: ASD-discordant MZ twin pair 5_control

tag: disease

value: healthy control


title: 11_FHK132-CSA-18H


title: TP4_control

value: ASD-discordant MZ twin pair 4_control


title: MGAS29594

tag: subclade

value: Subclade1B (SC1B)


title: TP5_case

value: ASD-discordant MZ twin pair 5_case

value: case


title: TP4_case

value: ASD-discordant MZ twin pair 4_case


title: Placenta_F415

description:
Sample 325
DNA extracted from placenta tissue.

value: Multi cell


title: UmbilicalCord_F415

description:
Sample 326
DNA extracted from umbilical cord blood of the newborn.

value: NAT


title: MGAS29588

tag: site of isolation


title: MGAS29583

tag: growth phase


title: MGAS29570


title: MGAS29587


title: Father_F415

description:
Sample 327
DNA extracted from peripheral venous blood of the father.

value: AGA


title: Mother_F414

description:
Sample 324
DNA extracted from peripheral venous blood of the mother.


title: 9_FHK132-CTRL-18H

tag: treatment

value: Kidney

value: Human kidney peritubular microvascular endothelial cell


title: MGAS29582

value: invasive infection isolate


title: Father_F414

description:
Sample 323
DNA extracted from peripheral venous blood of the father.


title: MGAS29564

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


title: UmbilicalCord_F414

description:
Sample 322
DNA extracted from umbilical cord blood of the newborn.


title: Placenta_F414

description:
Sample 321
DNA extracted from placenta tissue.


title: Mother_F411

description:
Sample 320
DNA extracted from peripheral venous blood of the mother.


title: MGAS29556


title: MGAS29559


title: MGAS29548


title: UmbilicalCord_F411

description:
Sample 318
DNA extracted from umbilical cord blood of the newborn.


title: Placenta_F411

description:
Sample 317
DNA extracted from placenta tissue.


title: Placenta_F441

description:
Sample 329
DNA extracted from placenta tissue.


title: MGAS29542


title: Mother_F415

description:
Sample 328
DNA extracted from peripheral venous blood of the mother.


title: MGAS29546


title: Mother_F404

description:
Sample 316
DNA extracted from peripheral venous blood of the mother.


title: MGAS29537


title: Father_F404

description:
Sample 315
DNA extracted from peripheral venous blood of the father.


title: MGAS29536


title: MGAS29569


title: UmbilicalCord_F404

description:
Sample 314
DNA extracted from umbilical cord blood of the newborn.


title: MGAS29534


title: Placenta_F404

description:
Sample 313
DNA extracted from placenta tissue.


title: Father_F390

description:
Sample 311
DNA extracted from peripheral venous blood of the father.


title: Mother_F390

description:
Sample 312
DNA extracted from peripheral venous blood of the mother.


title: MGAS29525


title: Father_F411

description:
Sample 319
DNA extracted from peripheral venous blood of the father.


title: MGAS29522


title: MGAS29517


title: UmbilicalCord_F390

description:
Sample 310
DNA extracted from umbilical cord blood of the newborn.


title: Placenta_F390

description:
Sample 309
DNA extracted from placenta tissue.


title: MGAS29510


title: Father_F386

description:
Sample 307
DNA extracted from peripheral venous blood of the father.


title: Mother_F386

description:
Sample 308
DNA extracted from peripheral venous blood of the mother.


title: UmbilicalCord_F386

description:
Sample 306
DNA extracted from umbilical cord blood of the newborn.


title: MGAS29507


title: MGAS29504


title: Placenta_F386

description:
Sample 305
DNA extracted from placenta tissue.


title: MGAS29508


title: Mother_F382

description:
Sample 304
DNA extracted from peripheral venous blood of the mother.


title: MGAS29501


title: Father_F382

description:
Sample 303
DNA extracted from peripheral venous blood of the father.


title: MGAS29494


title: UmbilicalCord_F382

description:
Sample 302
DNA extracted from umbilical cord blood of the newborn.


title: MGAS29528


title: MGAS29491


title: MGAS29511


title: Mother_F368

description:
Sample 300
DNA extracted from peripheral venous blood of the mother.


title: MGAS29488


title: RPMI72SB

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description:
Gene expression data from human myeloma cell lines.
SAMPLE 16

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip Gene 1.0 ST array, according to the standard Affymetrix protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning  of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Log2-transformed expression values were extracted from CEL files raw data and normalized using RMA procedure in the affy package for Bioconductor and the Transcript Cluster Annotations included in the cdf definition files version 19 available at the Brainarray portal at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/19.0.0/version.html

source_name: RPMI-8226_gapmer scramble_72h post silencing

label_protocol: Biotinylated single stranded cDNA samples were prepared starting from 100 nanograms of purified total RNA, according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).

value: human myeloma cell line

tag: treated with

value: gapmer scramble

tag: time point

value: 72h post silencing


title: MGAS29486

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

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: RPMI72MB

description:
Gene expression data from human myeloma cell lines.
SAMPLE 14

source_name: RPMI-8226_gapmer MALAT1_72h post silencing

tag: cell line

value: gapmer MALAT1


title: Father_F368

description:
Sample 299
DNA extracted from peripheral venous blood of the father.


title: UmbilicalCord_F368

description:
Sample 298
DNA extracted from umbilical cord blood of the newborn.


title: MGAS29476

source_name: cell pellet


title: Placenta_F368

description:
Sample 297
DNA extracted from placenta tissue.


title: MGAS29485


title: RPMI72SA

description:
Gene expression data from human myeloma cell lines.
SAMPLE 15


title: MGAS29474


title: Mother_F359

description:
Sample 296
DNA extracted from peripheral venous blood of the mother.


title: Father_F359

description:
Sample 295
DNA extracted from peripheral venous blood of the father.


title: MGAS29464


title: MGAS29447


title: RPMI48SA

description:
Gene expression data from human myeloma cell lines.
SAMPLE 11

source_name: RPMI-8226_gapmer scramble_48h post silencing

value: 48h post silencing


title: UmbilicalCord_F359

description:
Sample 294
DNA extracted from umbilical cord blood of the newborn.


title: Placenta_F382

description:
Sample 301
DNA extracted from placenta tissue.


title: RPMI72MA

description:
Gene expression data from human myeloma cell lines.
SAMPLE 13


title: RPMI48MA

description:
Gene expression data from human myeloma cell lines.
SAMPLE 9

source_name: RPMI-8226_gapmer MALAT1_48h post silencing


title: RPMI48MB

description:
Gene expression data from human myeloma cell lines.
SAMPLE 10


title: MGAS29444


title: MM1S72SA

description:
Gene expression data from human myeloma cell lines.
SAMPLE 7

source_name: MM.1S_gapmer scramble_72h post silencing


title: MM1S72SB

description:
Gene expression data from human myeloma cell lines.
SAMPLE 8


title: Mother_F357

description:
Sample 292
DNA extracted from peripheral venous blood of the mother.


title: RPMI48SB

description:
Gene expression data from human myeloma cell lines.
SAMPLE 12


title: MGAS29429


title: Placenta_F359

description:
Sample 293
DNA extracted from placenta tissue.


title: Father_F357

description:
Sample 291
DNA extracted from peripheral venous blood of the father.


title: MGAS29426


title: UmbilicalCord_F357

description:
Sample 290
DNA extracted from umbilical cord blood of the newborn.


title: MGAS29423


title: MGAS29416


title: Placenta_F357

description:
Sample 289
DNA extracted from placenta tissue.


title: MGAS29412


title: MM1S48SA

description:
Gene expression data from human myeloma cell lines.
SAMPLE 3

source_name: MM.1S_gapmer scramble_48h post silencing


title: MM1S72MA

description:
Gene expression data from human myeloma cell lines.
SAMPLE 5

source_name: MM.1S_gapmer MALAT1_72h post silencing


title: Mother_F351

description:
Sample 288
DNA extracted from peripheral venous blood of the mother.


title: MM1S48SB

description:
Gene expression data from human myeloma cell lines.
SAMPLE 4


title: MM1S72MB

description:
Gene expression data from human myeloma cell lines.
SAMPLE 6


title: Father_F351

description:
Sample 287
DNA extracted from peripheral venous blood of the father.


title: MGAS29406


title: MM1S48MA

description:
Gene expression data from human myeloma cell lines.
SAMPLE 1

source_name: MM.1S_gapmer MALAT1_48h post silencing


title: MM1S48MB

description:
Gene expression data from human myeloma cell lines.
SAMPLE 2


title: MGAS29404


title: UmbilicalCord_F351

description:
Sample 286
DNA extracted from umbilical cord blood of the newborn.


title: Placenta_F351

description:
Sample 285
DNA extracted from placenta tissue.


title: Mother_F337

description:
Sample 284
DNA extracted from peripheral venous blood of the mother.


title: MGAS29387


title: MGAS29402


title: Father_F337

description:
Sample 283
DNA extracted from peripheral venous blood of the father.


title: MGAS29384


title: UmbilicalCord_F337

description:
Sample 282
DNA extracted from umbilical cord blood of the newborn.


title: MGAS29382


title: Placenta_F337

description:
Sample 281
DNA extracted from placenta tissue.


title: MGAS29381


title: Father_F3010

description:
Sample 279
DNA extracted from peripheral venous blood of the father.

value: IVF


title: Placenta_F3010

description:
Sample 280
DNA extracted from placenta tissue.


title: MGAS29372

value: Subclade1B (SC1B)


title: MGAS29377


title: UmbilicalCord_F3010

description:
Sample 277
DNA extracted from umbilical cord blood of the newborn.


title: MGAS29394


title: MGAS29371


title: Mother_F3005

description:
Sample 276
DNA extracted from peripheral venous blood of the mother.


title: MGAS29360


title: MGAS29357


title: Father_F3005

description:
Sample 275
DNA extracted from peripheral venous blood of the father.


title: UmbilicalCord_F3005

description:
Sample 274
DNA extracted from umbilical cord blood of the newborn.


title: MGAS29351


title: Placenta_F3005

description:
Sample 273
DNA extracted from placenta tissue.


title: MGAS29347


title: Mother_F3010

description:
Sample 278
DNA extracted from peripheral venous blood of the mother.


title: Male_Control_CT66

city: Saint Louis

first: Jiajia

state: MO

address: 9952 CSRB, 4939 Children's Place.

department: Department of Medicine

institute: Washington University in St. Louis

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

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

value: Control

tag: time

tag: tissue

value: heads


title: Male_Control_CT70


title: Male_Control_CT68


title: Male_Control_CT62


title: MGAS29342

first: Priyanka

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute


title: Mother_F1801

first: Masoud

address: P. Debyelaan 25

institute: Maastricht University Medical Center

description:
Sample 272
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).

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: dna sample

value: Multi cell

tag: quartet

tag: conception


title: Male_Control_CT60


title: [6_cnt, Control]

city: Barcelona

first: Luis

last: Hernandez

address: Rossello 153, CEK building

department: Molecular Pathology

country: Spain

institute: IDIBAPS

description: T-UCR and related gene expression after 18h of mock treatment

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

scan_protocol: Slides were scanned with the Agilent DNA Microarray Scanner

data_processing: Data was extracted using Agilent Feature Extraction software. Normalization was performed using Agilent GeneSpring GX v11.5.1 software. Further data analysis was performed using GeneSpring GX v11.5.1 and a signal processing algorithm termed Otsu’s method.

source_name: negatively-selected CLL cells after 18h of mock treatment

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

growth_protocol: Freshly isolated negatively-selected CLL cells were cultured (1 × 107 cells/ml) in RPMI-1640 supplemented with 10% heat-inactivated fetal bovine serum, 100 U/ml penicillin, 0.1 mg/ml streptomycin, 2 mM L-glutamine and 1 mM sodium pyruvate (Invitrogen, Carlsbad, CA, USA)

extract_protocol: mRNAs and LncRNAs were purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre)

treatment_protocol: Treated cells were grown in the presence of 7.5 μg/ml complete phosphorothioate CpG-ODN oligonucleotide 2006 (5′-TCG TCG TTT TGT CGT TTT GTC GTT-3′; Microsynth, Balgach, Switzerland; hereafter CpG) for 18 hours

value: male

tag: age


title: MGAS29338

city: Houston

last: Kachroo


title: [4_cpg, Treated]

description: T-UCR and related gene expression after 18h of CpG ODN treatment

source_name: negatively-selected CLL cells after 18h of CpG ODN treatment

value: female


title: [6_cpg, Treated]


title: [1_cnt, Control]


title: Father_F1801

city: Maastricht

last: Zamani Esteki

description:
Sample 271
DNA extracted from peripheral venous blood of the father.

tag: birthweight at delivery

value: AGA


title: Male_Control_CT58


title: [2_cpg, Treated]


title: [5_cpg, Treated]


title: [3_cnt, Control]


title: [3_cpg, Treated]


title: [1_cpg, Treated]


title: [4_cnt, Control]


title: [5_cnt, Control]


title: UmbilicalCord_F1801

description:
Sample 270
DNA extracted from umbilical cord blood of the newborn.


title: Male_Control_CT56


title: Male_Control_CT64


title: [2_cnt, Control]


title: MGAS29330


title: Male_Control_CT54


title: Male_Control_CT52


title: MGAS29331


title: Father_F1039

description:
Sample 267
DNA extracted from peripheral venous blood of the father.


title: Mother_F1039

description:
Sample 268
DNA extracted from peripheral venous blood of the mother.


title: Male_Control_CT50


title: MGAS29336


title: MGAS29325


title: UmbilicalCord_F1039

description:
Sample 266
DNA extracted from umbilical cord blood of the newborn.


title: Male_Control_CT48


title: MGAS29324


title: Placenta_F1039

description:
Sample 265
DNA extracted from placenta tissue.

source_name: Placenta tissue


title: MGAS29323


title: Male_Control_CT46


title: MGAS29321


title: Mother_F1036

description:
Sample 264
DNA extracted from peripheral venous blood of the mother.


title: Male_Control_CT44


title: MGAS29314


title: MGAS29310


title: Father_F1036

description:
Sample 263
DNA extracted from peripheral venous blood of the father.


title: Male_Control_CT42


title: Male_Control_CT40


title: UmbilicalCord_F1036

description:
Sample 262
DNA extracted from umbilical cord blood of the newborn.


title: Placenta_F1036

description:
Sample 261
DNA extracted from placenta tissue.


title: MGAS29305


title: Mother_F1034

description:
Sample 260
DNA extracted from peripheral venous blood of the mother.


title: MGAS29300


title: Male_Control_CT38


title: MGAS29299


title: Male_Control_CT34


title: Male_Control_CT36


title: Father_F1034

description:
Sample 259
DNA extracted from peripheral venous blood of the father.


title: Male_Control_CT32


title: Placenta_F1034

description:
Sample 257
DNA extracted from placenta tissue.


title: Male_Control_CT30


title: MGAS29286


title: MGAS29292


title: Mother_F1030

description:
Sample 256
DNA extracted from peripheral venous blood of the mother.


title: Father_F1030

description:
Sample 255
DNA extracted from peripheral venous blood of the father.


title: MGAS29281


title: Male_Control_CT28


title: Male_Control_CT26


title: MGAS29277


title: Placenta_F1030

description:
Sample 253
DNA extracted from placenta tissue.


title: Male_Control_CT24


title: MGAS29268


title: Male_Achl_RNAi_CT70


title: MGAS29276


title: Mother_F1027

description:
Sample 252
DNA extracted from peripheral venous blood of the mother.


title: Male_Achl_RNAi_CT68


title: Father_F1027

description:
Sample 251
DNA extracted from peripheral venous blood of the father.


title: MGAS29258


title: Male_Achl_RNAi_CT66


title: UmbilicalCord_F1034

description:
Sample 258
DNA extracted from umbilical cord blood of the newborn.


title: MGAS29263


title: MGAS29254


title: Male_Achl_RNAi_CT62


title: Placenta_F1027

description:
Sample 249
DNA extracted from placenta tissue.


title: MGAS29253


title: MGAS29293


title: Mother_F1025

description:
Sample 248
DNA extracted from peripheral venous blood of the mother.


title: Male_Achl_RNAi_CT64


title: Father_F1025

description:
Sample 247
DNA extracted from peripheral venous blood of the father.


title: Male_Achl_RNAi_CT60


title: Male_Achl_RNAi_CT58


title: MGAS29240


title: MGAS29243


title: UmbilicalCord_F1025

description:
Sample 246
DNA extracted from umbilical cord blood of the newborn.


title: UmbilicalCord_F1030

description:
Sample 254
DNA extracted from umbilical cord blood of the newborn.


title: Male_Achl_RNAi_CT56


title: Placenta_F1025

description:
Sample 245
DNA extracted from placenta tissue.


title: MGAS29233


title: MGAS29230


title: Male_Achl_RNAi_CT54


title: Male_Achl_RNAi_CT52


title: UmbilicalCord_F1027

description:
Sample 250
DNA extracted from umbilical cord blood of the newborn.


title: Father_F1023

description:
Sample 243
DNA extracted from peripheral venous blood of the father.


title: Male_Achl_RNAi_CT50


title: UmbilicalCord_F1023

description:
Sample 242
DNA extracted from umbilical cord blood of the newborn.


title: Male_Achl_RNAi_CT48


title: MGAS29214


title: MGAS29221


title: Placenta_F1023

description:
Sample 241
DNA extracted from placenta tissue.


title: Male_Achl_RNAi_CT46


title: Mother_F1021

description:
Sample 240
DNA extracted from peripheral venous blood of the mother.


title: Father_F1021

description:
Sample 239
DNA extracted from peripheral venous blood of the father.


title: MGAS29209


title: Male_Achl_RNAi_CT42


title: UmbilicalCord_F1021

description:
Sample 238
DNA extracted from umbilical cord blood of the newborn.


title: Male_Achl_RNAi_CT40


title: MGAS29212


title: Male_Achl_RNAi_CT44


title: MGAS29188


title: MGAS29238


title: MGAS29201


title: SEC#1

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 (SEC), 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: SEC (abscission zone of separated floral organs)


title: SEC#2


title: Mother_F1023

description:
Sample 244
DNA extracted from peripheral venous blood of the mother.

source_name: Peripheral blood


title: SEC#3


title: Male_Achl_RNAi_CT38


title: MGAS29186

value: invasive infection isolate


title: REC#2

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

value: REC (abscission zone of receptacle)


title: MGAS29181

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


title: Male_Achl_RNAi_CT36


title: MGAS29180


title: REC#1


title: Male_Achl_RNAi_CT34


title: Male_Achl_RNAi_CT32


title: Father_P174

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

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 cells

tag: conception method

value: Peripheral blood


title: Umbilicalcord_P174

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

source_name: Cord blood

value: Cord blood


title: MGAS29170

tag: subclade


title: MGAS29164

tag: site of isolation


title: Mother_P171

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


title: Placenta_P174

description: DNA extracted from placenta tissue.

value: Placenta tissue


title: Father_P171

value: IVF


title: Placenta_F1021

description:
Sample 237
DNA extracted from placenta tissue.


title: Placenta_P171

description: DNA extracted from placenta tissue.


title: Umbilicalcord_P171