title: US84403582_252680610467_S01_GE1_107_Sep09_1_1_Anhui1_Old_Lung_day 6_5


title: US84403582_252680610514_S01_GE1_107_Sep09_1_3_Anhui1_Old_Lung_day 6_5

status: Public on Jun 13 2020

type: RNA

city: Tokyo

first: Yoshihiro

last: Kawaoka

address: 4-6-1, Shirokanedai, Minato-ku

department: Department  of  Microbiology  and  Immunology

country: Japan

institute: University of Tokyo

hyb_protocol: hybridized  to  the   Rhesus  Macaque   Gene Expression    Microarray

scan_protocol: Specific antigen–antibody reactions were  visualized with  DAB staining  by  using  the  DAKO  Envision  system

data_processing: Statistical analysis was performed using the  LIMMA  package.  The  log2of  the  intensity  of  each  probe  was  background  corrected  and normalized   between   arrays   (using   the   quantile   method).   Duplicate   probes   were   averaged. Hierarchical  clustering  was  used  to  review  biological  replicate  quality.  One-way  or  two-way ANOVA were  constructed  and  the  moderated  t-statistic  was  calculated  to  determine  the  significance between  the  means.  The  duplicateCorrelation  function  was  used  to  control  for  multiple  samples from  the  same  animal.  All pvalues  were  Benjamini-Hochberg  (BH)  corrected  to  control  the  false discovery rate (FDR). Probes were considered differentially expressed (DE) if they had a fold change ≥ 2 and an FDR < 0.01.

molecule: total RNA

organism: Macaca fascicularis

source_name: Lung

label_protocol: Total  RNA  was  extracted  from  lung  samples  and  blood  by  using  the  RNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol. RNA was labeledwith Cy3 dye with the QuickAmplabelingkit(Agilent  Technologies)

growth_protocol: Aged (20–26 years) and young (2–3 years) female cynomolgus   macaques   (Macaca   fascicularis)   were   obtained from the   National   Institute   of Biomedical Innovation (NIBIO, Ibaraki, Japan),JapanLaboratoryAnimal Inc. (Tokyo, Japan)and SNBL, and    tested    to    ensure    that    they    were    serologically    negative    byneutralization    against A/Osaka/1365/2009   (H1N1pdm09),   A/Kawasaki/UTK-4/2009   (seasonal   H1N1),   A/Kawasaki/UTK-20/2008  (H3N2),  B/Tokyo/UT-E2/2008  (type  B),  and  A/duck/Hong  Kong/301/78  (H7N2)  viruses.  In this study

extract_protocol: Excised  macaque  tissues  were  preserved  in  10%  phosphate-buffered  formalin.  The  tissues  were  then  processed  for  paraffin embedding  and  cut  into  3-μm-thick  sections.  The  sections  of  each  tissue  sample  were  stained  using  a  standard hematoxylin and eosin procedure. Each serial section was processed  for  immunohistological staining  with  a  mouse  monoclonal  antibody  for  type  A  influenza  nucleoprotein  antigen (prepared  in our  laboratory)

treatment_protocol: macaques   were   intramuscularly anesthetized  with  ketamine  and  xylazine  or  medetomidine  and  inoculated  with  a  suspension containing 107plaque-forming units (pfu)/ml of Anhui/1through a combination of the intratracheal (4.5 ml), intranasal (0.5 ml per nostril), ocular (0.1 ml per eye) and oral (1 ml) routes, resulting in a total  infectious  dose  of  107.8pfu

tag: tissue

value: lung

tag: lobe

value: Right Lower

tag: concentration (ng/ul)

tag: rin

tag: strain

tag: day

value: day 6

tag: death

value: No

tag: age

value: Old

tag: animal number


title: US84403582_252680610470_S01_GE1_107_Sep09_1_1_Anhui1_Old_Lung_day 4_4

value: Left Upper

value: day 4

value: Yes (4dpi)


title: US84403582_252680610517_S01_GE1_107_Sep09_1_3_Anhui1_Old_Lung_day 3_2

value: day 3


title: US84403582_252680610495_S01_GE1_107_Sep09_1_3_Anhui1_Old_Lung_day 3_2


title: mTOR Tg rep1

type: SRA

first: Minako

last: Saito

address: 7-3-1, Hongo, Bunkyo-ku

institute: The University of Tokyo

library_source: transcriptomic

data_processing:
RNA-sequencing (RNA-seq) reads were analyzed using CLC Genomics workbench software (Qiagen, Hilden, Germany) .
Read mapping was carried out using HISAT2 against mouse genome mm10.
Differential expression analysis was performed using edgeR Bioconductor package.
Genome_build: mm10
Supplementary_files_format_and_content: a text file include normalized values for each sample

organism: Mus musculus

source_name: alveolar epithelial type II cells

extract_protocol:
Rneasy Mini (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Sftpc-mTOR transgenic mice

tag: cell type

value: alveolar epithelial type II cells


title: mTOR Tg rep2


title: US84403582_252680610514_S01_GE1_107_Sep09_1_4_Anhui1_Old_Lung_day 6_6


title: WT rep2

value: wild type


title: US84403582_252680610513_S01_GE1_107_Sep09_1_4_Anhui1_Old_Lung_day 3_2


title: US84403582_252680610495_S01_GE1_107_Sep09_1_2_Anhui1_Old_Lung_day 3_1


title: US84403582_252680610514_S01_GE1_107_Sep09_1_2_Anhui1_Old_Lung_day 4_4


title: US84403582_252680610499_S01_GE1_107_Sep09_1_2_Anhui1_Young_Blood_day 6_16

source_name: Blood

value: blood

value: Young


title: US84403582_252680610466_S01_GE1_107_Sep09_1_1_Anhui1_Old_Lung_day 3_1


title: US84403582_252680610490_S01_GE1_107_Sep09_1_1_Naive_Young_Blood_day 0_16

value: Naive

value: day 0


title: WT rep1


title: US84403582_252680610514_S01_GE1_107_Sep09_1_1_Anhui1_Old_Lung_day 3_3


title: US84403582_252680610490_S01_GE1_107_Sep09_1_2_Anhui1_Young_Blood_day 6_16


title: US84403582_252680610499_S01_GE1_107_Sep09_1_1_Naive_Young_Blood_day 0_16


title: US84403582_252680610513_S01_GE1_107_Sep09_1_3_Anhui1_Old_Lung_day 3_1


title: US84403582_252680610517_S01_GE1_107_Sep09_1_2_Anhui1_Old_Lung_day 3_1


title: US84403582_252680610466_S01_GE1_107_Sep09_1_2_Anhui1_Old_Lung_day 3_2


title: US84403582_252680610498_S01_GE1_107_Sep09_1_4_Anhui1_Young_Blood_day 6_15


title: Empty Vector Rep3 Batch3

city: Urbana

first: Matthew

middle: D.

last: Brooks

state: Illinois

address: 1201 W Gregory Drive

department: GCPRU

country: USA

institute: USDA

data_processing:
Raw reads were trimmed to remove low quality bases (q<14), adapter contamination and short reads using the BBDuk tool within the BBTools (v37.48) package.
Gene expression levels were determined by aligning reads to the Arabidopsis thaliana genome (TAIR10) using the HISAT2 (v2.0.5) package and estimating read counts by the GenomicFeatures(v1.28.5)/GenomicAlignments(v1.12.2) packages.
Genes responding significantly (FDR adjusted p-val <0.05) to each of the TFs relative to the empty vector control were identified using DESeq2 (v1.22.1) with a ~TF+Batch model.
Genome_build: TAIR10
Supplementary_files_format_and_content: Read counts output from GenomicFeatures/GenomicAlignments packages

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: root protoplasts

growth_protocol: Arabidopsis seedlings grown on vertical plates containing 1/2X MS basal media

extract_protocol:
Approximately 10,000-20,000 cells were FACS sorted into RLT buffer and frozen. Total RNA was extracted using the RNeasy Micro Kit (Qiagen) with on-column DNase treatment. mRNA was purified using Dynabeads Oligo (dT).
Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina. Final quantity was determined using the DNA TapeStation and KAPA Library Quant qPCR.

treatment_protocol: Protoplasts were isolated from root tissue and transfected with expression vector. The following morning protoplasts were treated with 35 uM cycloheximide and 10uM dexamethasone

value: root protoplasts

tag: ecotype

tag: treatments

value: Cycloheximide, Dexamethasone

value: 10 days


title: AT1G51140 FBH3 Rep2 Batch3


title: US84403582_252680610489_S01_GE1_107_Sep09_1_4_Anhui1_Young_Blood_day 6_15

value: day 6


title: US84403582_252680610508_S01_GE1_107_Sep09_1_2_Anhui1_Young_Lung_day 3_12

value: lung

value: Right Lower

value: No


title: AT2G46270 GBF3 Rep2 Batch3


title: US84403582_252680610511_S01_GE1_107_Sep09_1_1_Anhui1_Young_Lung_day 3_11

value: Left Upper


title: US84403582_252680610489_S01_GE1_107_Sep09_1_2_Anhui1_Young_Blood_day 6_14


title: Huh-7_NC_2

city: Nanjing

first: CHANG

last: ZHENG

address: 22 Hankou Road

country: China

institute: Nanjing University

description: Gene expression in Huh7 cell line

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: Homo sapiens

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: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell line

tag: genotype/variation

value: negative control


title: AT2G46680 HB7 Rep2 Batch3


title: US84403582_252680610489_S01_GE1_107_Sep09_1_3_Naive_Young_Blood_day 0_15


title: Huh-7_NC_1

description: Gene expression in Huh7 cell line


title: US84403582_252680610498_S01_GE1_107_Sep09_1_3_Naive_Young_Blood_day 0_15


title: US84403582_252680610498_S01_GE1_107_Sep09_1_1_Naive_Young_Blood_day 0_14


title: AT5G05410 DREB2A Rep2 Batch3


title: Huh-7_R-spodin2_OE_1

description: Gene expression after R-spodin2 overexpression in Huh7 cell line

source_name: Huh7_R-spodin2 overexpression


title: Empty Vector Rep2 Batch3


title: US84403582_252680610498_S01_GE1_107_Sep09_1_2_Anhui1_Young_Blood_day 6_14


title: US84403582_252680610488_S01_GE1_107_Sep09_1_4_Anhui1_Young_Blood_day 3_13

value: day 3


title: US84403582_252680610488_S01_GE1_107_Sep09_1_3_Naive_Young_Blood_day 0_13


title: Huh-7_R-spodin2_OE_2


title: US84403582_252680610496_S01_GE1_107_Sep09_1_4_Anhui1_Young_Blood_day 3_13


title: AT1G51140 FBH3 Rep1 Batch3


title: AT4G01120 GBF2 Rep2 Batch3


title: US84403582_252680610489_S01_GE1_107_Sep09_1_1_Naive_Young_Blood_day 0_14


title: AT4G34000 ABF3 Rep2 Batch3


title: US84403582_252680610500_S01_GE1_107_Sep09_1_4_Anhui1_Young_Blood_day 3_12


title: US84403582_252680610496_S01_GE1_107_Sep09_1_2_Anhui1_Young_Blood_day 3_12


title: AT2G46270 GBF3 Rep1 Batch3


title: US84403582_252680610487_S01_GE1_107_Sep09_1_4_Naive_Young_Blood_day 0_12


title: US84403582_252680610496_S01_GE1_107_Sep09_1_3_Naive_Young_Blood_day 0_13


title: AT2G46680 HB7 Rep1 Batch3


title: AT5G05410 DREB2A Rep1 Batch3


title: US84403582_252680610496_S01_GE1_107_Sep09_1_1_Naive_Young_Blood_day 0_12


title: Empty Vector Rep1 Batch3


title: AT1G51140 FBH3 Rep3 Batch3


title: US84403582_252680610488_S01_GE1_107_Sep09_1_1_Naive_Young_Blood_day 0_11


title: AT4G34000 ABF3 Rep1 Batch3


title: US84403582_252680610488_S01_GE1_107_Sep09_1_2_Anhui1_Young_Blood_day 3_11


title: AT2G46270 GBF3 Rep3 Batch3


title: AT4G01120 GBF2 Rep3 Batch3


title: US84403582_252680610492_S01_GE1_107_Sep09_1_4_Anhui1_Young_Blood_day 3_11


title: AT5G05410 DREB2A Rep3 Batch3


title: AT2G46680 HB7 Rep3 Batch3


title: AT2G38470 WRKY33 Rep2 Batch2


title: TgGRK5-MI.4: cardiomyocytes from Grk5 transgenic mouse, replicate 4

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-seq data was aligned using bowtie2 against mm10 version of the human genome and RSEM v1.2.31 software was used to estimate raw read counts and FPKM values using transcriptome information from Ensemble v84 set
DESeq2 was used to estimate significance of differential expression between groups
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene as estimated by RSEM

source_name: cardiomyocytes

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen) according to the manufacturer's instruction from cardiomyocytes were extracted 4 days after myocardial infraction
Total RNA libraries were prepared using Illumina TruSeq RNA Library Prep Kit v2 library preparation kit

value: cardiomyocytes

value: cardiomyocyte-specific GRK5 transgenic

tag: timepoint

value: 4 days after myocardial infraction (MI)

tag: replicate


title: AT5G67300 MYBR1 Rep2 Batch2

tag: tissue


title: US84403582_252680610504_S01_GE1_107_Sep09_1_4_Anhui1_Old_Blood_day 3_7

value: blood

tag: lobe

value: Yes (3dpi, euthanasia)

value: Old


title: AT4G01120 GBF2 Rep2 Batch2


title: US84403582_252680610476_S01_GE1_107_Sep09_1_3_Anhui1_Old_Blood_day 3_7

tag: concentration (ng/ul)


title: TgGRK5-MI.2: cardiomyocytes from Grk5 transgenic mouse, replicate 2


title: US84403582_252680610476_S01_GE1_107_Sep09_1_1_Anhui1_Old_Blood_day 6_6

tag: rin


title: US84403582_252680610504_S01_GE1_107_Sep09_1_1_Naive_Old_Blood_day 0_6

tag: strain

value: Naive

value: day 0


title: TgGRK5-MI.1: cardiomyocytes from Grk5 transgenic mouse, replicate 1


title: US84403582_252680610504_S01_GE1_107_Sep09_1_3_Naive_Old_Blood_day 0_7

tag: day


title: AT5G04760 DIV2 Rep2 Batch2

value: root protoplasts

value: Cycloheximide, Dexamethasone


title: US84403582_252680610476_S01_GE1_107_Sep09_1_2_Naive_Old_Blood_day 0_7

tag: death


title: US84403582_252680610492_S01_GE1_107_Sep09_1_3_Naive_Young_Blood_day 0_11

tag: age

value: Young


title: US84403582_252680610475_S01_GE1_107_Sep09_1_3_Anhui1_Old_Blood_day 6_5

value: day 6

tag: animal number


title: US84403582_252680610475_S01_GE1_107_Sep09_1_4_Naive_Old_Blood_day 0_6


title: NLC-MI.4: cardiomyocytes from Grk5 non-transgenic mouse, replicate 4

value: non-transgenic littermate control


title: US84403582_252680610504_S01_GE1_107_Sep09_1_2_Anhui1_Old_Blood_day 6_6

value: No


title: US84403582_252680610463_S01_GE1_107_Sep09_1_4_Anhui1_Young_Lung_day 3_12

value: lung

value: Left Upper


title: NLC-MI.3: cardiomyocytes from Grk5 non-transgenic mouse, replicate 3


title: NLC-MI.5: cardiomyocytes from Grk5 non-transgenic mouse, replicate 5


title: AT1G22640 MYB3 Rep2 Batch2

value: 10 days


title: TgGRK5-MI.3: cardiomyocytes from Grk5 transgenic mouse, replicate 3

value: cardiomyocytes


title: TgGRK5-MI.5: cardiomyocytes from Grk5 transgenic mouse, replicate 5

value: cardiomyocyte-specific GRK5 transgenic


title: NLC-MI.1: cardiomyocytes from Grk5 non-transgenic mouse, replicate 1

value: 4 days after myocardial infraction (MI)


title: Empty Vector Rep2 Batch2


title: AT5G43840 HSFA6A Rep1 Batch2


title: NLC-MI.2: cardiomyocytes from Grk5 non-transgenic mouse, replicate 2


title: AT2G38470 WRKY33 Rep1 Batch2


title: AT5G67300 MYBR1 Rep1 Batch2


title: US84403582_252680610475_S01_GE1_107_Sep09_1_2_Naive_Old_Blood_day 0_5

value: blood


title: AT4G01120 GBF2 Rep1 Batch2


title: US84403582_252680610503_S01_GE1_107_Sep09_1_4_Anhui1_Old_Blood_day 6_5


title: US84403582_252680610503_S01_GE1_107_Sep09_1_3_Naive_Old_Blood_day 0_5


title: AT1G22640 MYB3 Rep1 Batch2


title: US84403582_252680610475_S01_GE1_107_Sep09_1_1_Naive_Old_Blood_day 0_4

value: Yes (4dpi)


title: 621: Uterus - Arg260_PLB - Rep4

city: Toulouse

first: Francoise

middle: B.

last: LENFANT

address: 1 avenue J. Poulhès

department: Team 9- I2MC

country: France

institute: INSERM U1048

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarray (8X60K, Design 028005  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20120201). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 13 out of 16 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 40544 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 37585 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Uterus

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: mice were ovariectomized at 4 weeks of age and maintained in animal facility 2-3 weeks before treatment on normal chow diet.

extract_protocol: RNA was prepared using the GenElute Mammalian Total RNA kit (Sigma) in Trizol following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: ovariectomized mice were treated 6 hours with 0 or 8µg/kg of 17b-estradiol injected subcutaneously in castor oil.

value: Uterus

tag: genotype

tag: treatment

value: PLB

tag: ovariectomy

value: 4 sem

tag: deprivation

value: 2 sem

value: 0µg/kg/day, 6h


title: Empty Vector Rep1 Batch2

value: root protoplasts

tag: ecotype

tag: treatments

value: Cycloheximide, Dexamethasone


title: AT5G04760 DIV2 Rep1 Batch2


title: 691: Uterus - WT_E2 - Rep2

value: WT

value: 8µg/kg/days, 6h


title: 668: Uterus - Arg260_E2 - Rep2


title: 611: Uterus - Arg260_E2 - Rep3


title: US84403582_252680610503_S01_GE1_107_Sep09_1_1_Naive_Old_Blood_day 0_3

value: Naive

value: day 0

value: No

value: Old


title: US84403582_252680610474_S01_GE1_107_Sep09_1_4_Anhui1_Old_Blood_day 3_3

value: day 3


title: US84403582_252680610474_S01_GE1_107_Sep09_1_3_Naive_Old_Blood_day 0_3


title: 669: Uterus - Arg260_PLB - Rep1


title: AT5G43840 HSFA6A Rep3 Batch2

value: 10 days


title: 626: Uterus - WT_E2 - Rep4


title: 644: Uterus - Arg260_E2 - Rep4


title: 671: Uterus - WT_PLB - Rep2


title: 610: Uterus - WT_E2 - Rep3


title: US84403582_252680610501_S01_GE1_107_Sep09_1_4_Naive_Old_Blood_day 0_4

value: blood


title: US84403582_252680610474_S01_GE1_107_Sep09_1_2_Anhui1_Old_Blood_day 3_2


title: 599: Uterus - WT_PLB - Rep3


title: US84403582_252680610503_S01_GE1_107_Sep09_1_2_Anhui1_Old_Blood_day 3_3


title: 619: Uterus - Arg260_PLB - Rep3


title: AT2G38470 WRKY33 Rep3 Batch2


title: 601: Uterus - Arg260_PLB - Rep2


title: ND523-aCD3aCD28-48hrs

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

institute: University of Pennsylvania

data_processing:
fastq.gz reads trimmed with bbduk to remove low-quality base calls and library adaptor sequences (reads <35nt discarded)
For expression analyses, reads mapped to hg38 transcripts with Salmon to calculate transcripts per million
For splicing analyses, reads mapped to hg38 genome with STAR, then alternative splicing quantified with MAJIQ
Genome_build: hg38
Supplementary_files_format_and_content: Salmon's quant.sf files are tab-separated with effective counts, effective gene lengths, and TPMs. See: salmon.readthedocs.io/en/latest/file_formats.html

growth_protocol: RPMI complete

extract_protocol:
Total RNA isolated with RNA-bee (Tel-Test) protocol
GeneWiz RNA library preparation with polyA selection

treatment_protocol: No treatment, and different combinatons of 10 IU/mL IL-2, anti-CD3, and anti-CD28

tag: Sex

value: Female

tag: donor age

tag: cell type

value: PBMC

tag: cell subtype

value: naïve CD4+ T cells

tag: in vitro culture conditions

value: RPMI complete, 10 IU/mL IL-2, anti-CD3, anti-CD28


title: ND535-aCD3aCD28-48hrs

value: Male

tag: rin


title: 675: Uterus - WT_PLB - Rep4

tag: tissue

value: Uterus

value: PLB

value: 4 sem

value: 2 sem

value: 0µg/kg/day, 6h


title: 629: Uterus - WT_E2 - Rep1

value: WT

value: 8µg/kg/days, 6h


title: 678: Uterus - Arg260_E2 - Rep1


title: ND307-aCD3aCD28-48hrs


title: 618: Uterus - WT_PLB - Rep1


title: US84403582_252680610502_S01_GE1_107_Sep09_1_4_Anhui1_Old_Blood_day 3_2

tag: lobe

tag: concentration (ng/ul)

tag: strain

tag: day

value: No


title: AT5G67300 MYBR1 Rep3 Batch2

value: root protoplasts

value: Cycloheximide, Dexamethasone

tag: age


title: US84403582_252680610474_S01_GE1_107_Sep09_1_1_Naive_Old_Blood_day 0_2

value: Naive

value: day 0

tag: death

value: Old

tag: animal number


title: AT4G01120 GBF2 Rep3 Batch2

value: 10 days


title: ND535-aCD3aCD28-8hrs

value: PBMC

value: naïve CD4+ T cells

tag: treatment


title: ND523-aCD3aCD28-8hrs

value: Female

value: RPMI complete, 10 IU/mL IL-2, anti-CD3, anti-CD28


title: ND307-aCD3aCD28-8hrs

value: Male


title: US84403582_252680610502_S01_GE1_107_Sep09_1_3_Naive_Old_Blood_day 0_2

value: blood


title: ND523-aCD3-48hrs

value: RPMI complete, 10 IU/mL IL-2, anti-CD3


title: AT5G04760 DIV2 Rep3 Batch2

tag: ecotype


title: ND307-aCD3-48hrs


title: ND523-aCD3-8hrs


title: AT1G22640 MYB3 Rep3 Batch2

tag: treatments


title: Empty Vector Rep3 Batch2


title: ND535-aCD3-48hrs

tag: Sex


title: ND535-aCD3-8hrs

tag: donor age


title: ND307-aCD3-8hrs

tag: cell type


title: US84403582_252680610502_S01_GE1_107_Sep09_1_2_Anhui1_Old_Blood_day 3_1

value: day 3


title: M100_DC_CD11bSP_r2

city: Shinjuku-ku

first: Yohei

last: Mikami

state: Tokyo

address: Shinanomachi 35

institute: Keio University School of Medicine

data_processing:
Real Time Analysis 2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using kallisto v0.44.0 with parameters -b 100; pachterlab.github.io/kallisto/
Transcripts Per Kilobase Million (TPM) were calculated using sleuth.
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated values files includes pseudocount matrix for each sample.

extract_protocol:
RNA was harvested using Trizol reagent. RNA was prepared from approximately 20,000–50,000 cells by using TRIzol (Thermo Fisher Scientific Inc.). Total RNAs were subsequently processed to generate an mRNA-seq library using a NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490S), NEBNext Ultra II Directional RNA Library Prep with Sample Purification Beads (NEB, E7765S) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and 2) (NEB, E7335S and E7550S).
RNA libraries were prepared for sequencing using standard NEB protocols

value: DC/MNP


title: US84403582_252680610473_S01_GE1_107_Sep09_1_4_Anhui1_Old_Blood_day 3_1


title: ND535-aCD28-48hrs

tag: cell subtype

value: RPMI complete, 10 IU/mL IL-2, anti-CD28


title: M099_DC_DP_r2


title: AT4G01120 GBF2 Rep1 Batch3


title: M098_DC_CD11cSP_r2


title: ND307-aCD28-48hrs

tag: in vitro culture conditions


title: ND523-aCD28-48hrs

tag: rin


title: AT1G51140 FBH3 Rep2 Batch1

tag: tissue


title: Empty Vector Rep3 Batch1


title: M097_DC_CD11bSP_r1


title: AT5G43840 HSFA6A Rep2 Batch1


title: ND523-Naïve-48hrs

value: RPMI complete, 10 IU/mL IL-2


title: ND523-Naïve-8hrs


title: ND307-Naïve-48hrs


title: ND535-Naïve-48hrs


title: AT5G43840 HSFA6A Rep2 Batch2

value: root protoplasts


title: M095_DC_CD11cSP_r1


title: US84403582_252680610473_S01_GE1_107_Sep09_1_3_Naive_Old_Blood_day 0_1

tag: lobe

value: No


title: AT5G04340 ZAT6 Rep2 Batch1

value: Cycloheximide, Dexamethasone


title: M084_DC_MHCSp_r1

value: APC


title: ND523-Naïve-0hrs

value: RPMI complete


title: AT1G49720 ABF1 Rep2 Batch1

value: 10 days


title: Empty Vector Rep2 Batch1


title: ND523-aCD28-8hrs

value: PBMC


title: M083_DC_MHCSp_r1


title: US84403582_252680610510_S01_GE1_107_Sep09_1_3_Naive_Old_Blood_day 0_1

tag: concentration (ng/ul)

value: Naive

value: day 0

value: Old


title: ND535-Naïve-0hrs

value: Male

value: naïve CD4+ T cells


title: AT1G51140 FBH3 Rep1 Batch1


title: ND307-Naïve-8hrs


title: M082_DC_MHCLI_r2

tag: strain


title: M096_DC_DP_r1


title: ND307-aCD28-8hrs


title: Slyc_T24h_P1

city: SAN LUIS POTOSI

first: Cesaré

last: Ovando-Vázquez

state: SAN LUIS POTOSI

address: Camino a la Presa de San José 2055. Lomas 4 sección

department: CNS

country: Mexico

institute: CONACyT IPICyT

data_processing:
Methodology 01, Mapping to the ITAG3.2 genome: Sequence reads were mapped to ITAG3.2 genome using Hisat 2 with parameters --non-deterministic; quantifications to each exon per gene was performed with FeatureCounts from SubRead package witch parameters -p -T $n -J -M --fraction --largestOverlap --fracOverlap 0.75.
Methodology 02, Mapping to the semi-de-novo transcriptome: Sequence reads were mapped and quantified to the semi-de-novo transcriptome (ITAG3.2 transcriptomes plus a Trinity transcritome with thos sequence reads un-mapped to ITAG3.2 genome) using Kallisto with default parameters.
Methodology 01, Mapping to the de-novo transcriptome: Sequence reads were mapped and quantified to the de-novo transcriptome (generated with Trinity using all sequence reads) using kallisto with default parameters.
Normalized coutns were obtained with the cpm() function from edgeR R package.
Genome_build: ITAG3.2, Sollanum Lycopersicum
Supplementary_files_format_and_content: Matrix tables with raw transcript counts and cpms for every sample in each methdology: mapping to ITAG3.2 genome, mapping to semi-de-novo transcriptome, and mapping to de-novo transcriptome.

organism: Solanum lycopersicum

source_name: Leaves

growth_protocol: All experiments were carried out in controlled conditions, as described below, and plant residues were sterilized. Before germination, all tomato seeds were sterilized in a 10% extran solution for 15 min. Subsequently, three washes with deionized water and one wash with 70% ethanol solution were performed, followed by a 10% bleach solution wash for 10 min and rinsing three times in deionized water. Tomato seeds were germinated in a commercial mix substrate (Sunshine Mix #3, Sun Grow Horticulture, Vancouver, BC, CA) in a bioclimatic chamber at 25°C and 16/8 h light and dark period. Two weeks later, plants were transferred to greenhouse conditions with a controlled temperature max 28°C, min 20°C and humidity of 55-60%

extract_protocol:
The 18 samples (nine each of S. lycopersicum and S. arcanum) were processed and sequenced by BGI Hong Kong (Beijing Genome Institute, https://www.bgi.com/global/) as follows. RNA quality of the samples (OD 260/280 & 260/230) was tested by NanoDropTM after total RNA extraction. Total RNA samples concentration, RIN, 28S/18S, was determined by using the Agilent 2100 Bioanalyzer (https://www.agilent.com/). According to the TruSeq RNA Sample Prep Kit v2 (Illumina), mRNA molecules were purified using poly-T oligo attached magnetic beads. Following purification, for each sample mRNA was fragmented into small pieces using divalent cations at 94°C. The purified RNA was used as template for cDNA synthesis.
RNA libraries prepared for sequencing using standard Illumina protocols

treatment_protocol: Forty days after germination of both plant tomato species were infected with the pathogenic strain Cmm 1569. The bacterial cells were propagated in 802 medium culture (2g/L yeast extract, 1g/L polypeptone and 0.92 g/L magnesium sulfate). For inoculation, three biological replicates per each tomato species (S. lycopersicum and S. arcanum) were inoculated in the first proximal internode above ground of each plant with an insulin syringe with a concentration of 5x10⁷ CFU (OD = 0.2). After inoculation, tomato plants were sampled (true leaves next to inoculation site) at 0, 8 and 24 h post inoculation. Biological samples were immediately frozen in liquid nitrogen and stored at -80°C.

tag: cultivar

value: Ailsa Craig

value: leaves

tag: hpi

value: Infection with pathogenic strain Cmm 156


title: AT1G49720 ABF1 Rep1 Batch1

tag: age


title: ND535-aCD28-8hrs

value: RPMI complete, 10 IU/mL IL-2, anti-CD28


title: M081_DC_MHCLI_r1


title: Slyc_T24h_P2


title: Slyc_T24h_P3


title: AT5G04340 ZAT6 Rep1 Batch1


title: AT5G43840 HSFA6A Rep1 Batch1


title: Slyc_T8h_P2


title: ND307-Naïve-0hrs


title: brainstem_10x

city: Horn

first: Joachim

last: Luginbuehl

address: Bürgerstrasse

country: Switzerland

institute: RIKEN

data_processing:
Raw sequencing data from the organoid was preprocessed using the Cell Ranger (v 2.2.0, 10X Genomics) software
Reads were aligned to the GRCh38 human reference genome using STAR
The scRNA-seq data was analyzed using the Seurat package (version 3.0.0) in R (version 3.6.0).
Cells with more than 8000 or less than 750 detected genes, as well as cells expressing more than 5% mitochondrial genes were excluded. Genes expressed in less than 3 cells were excluded. We collected a total of 2345 cells expressing a total of 19454 genes.
The data was log normalized and scaled. The dimention reduction was performed by principal component analysis (PCA).
Clustering was performed based on the top 45 principal components using the shared nearest neighbor (SNN) modularity optimization.
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated values files contain raw counts and counts per million (CPM) values after quality control.

source_name: Brainstem organoids from human pluripotent stem cells containing neural crest population

growth_protocol: Human iPSCs/ESCs were gently dissociated by 10 minutes of treatment with 50% Accutase in PBS. Detached cells were transferred to 6-well plates at the density of 4 million cells in 5ml mTESRTM1 medium with 5µM ROCK inhibitor, 1mM dorsomorphin and 10mM SB431542 per one well in six-well plates on the orbit shaker to keep the cells under suspension. For neural induction from day 3, media was switched to one composed of Neurobasal media and 2x Gem21NeuroPlex, 1x NEAA, 1x Glutamax, 1mM dorsomorphin, 10mM SB431542, 10 µM Transferrin, 5mg/l human Insulin, and 0.063mg/l Progesterone. After nine days of exposure to dorsomorphin and SB431542, we treated the cells with 20ng/ml bFGF to induce NPC proliferation in the presence of Neurobasal-A media, supplemented with 2x Gem21NeuroPlex, 1x NEAA, 1x Glutamax, 10 µM Transferrin, 5mg/l human Insulin, and 0.063mg/l Progesterone till day 16. Cells were then kept in the same media containing not only 20ng/ml bFGF, but also 20ng/ml EGF until day 22. After day 22, EGF and bFGF were replaced by Ascorbic acid, cAMP, BDNF, GDNF, and NT-3. After day 28, cells were cultivated without any growth factors for neuronal maturation.

extract_protocol:
To dissociate brainstem organoids into single cells, they were incubated for ~30min in Accutase (STEMCELL TECHNOLOGIES) at 37°C.
Droplet-based scRNA-seq libraries were generated using the ChromiumTM Single Cell 3’ Reagent kits V2 (10x Genomics). Briefly, cell number and cell viability were assessed using the Countess II Automated Cell Counter (ThermoFisher). Thereafter, cells were mixed with the Single Cell Master Mix and loaded together with Single Cell 3’ Gel beads and Partitioning Oil into a Single Cell 3’ Chip. RNA transcripts were uniquely barcoded and reverse-transcribed in droplets. cDNAs were pooled and amplified according to the manufacturer’s protocol. Libraries were quantified by High Sensitivity DNA Reagents (Agilent Technologies) and the KAPA Library Quantification kit (KAPA BIOSYSTEMS). Libraries then were sequenced by Illumina Hiseq 2500 in rapid mode.

treatment_protocol: No treatment

value: hESC-derived brainstam neurons

value: 1 month


title: KSHV-83NS

city: Daejeon

first: Hyungtaek

last: Jeon

address: 77 GYERYONG-RO 771BEON-GIL, JUNG-GU

department: school of medicine, Dept. of microbiology and immunology

country: South Korea

institute: Eulji University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Human glioma stem like cells

growth_protocol: All GSCs were cultured in DMEM/F-12 supplemented with, B27, EGF and bFGF.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Hygromycin B was treated in KSHV infected cell for 1 months because of the selection of the KSHV genes.

value: Human glioma stem like cells

tag: virus

value: KSHV infected


title: Empty Vector Rep1 Batch1

value: root protoplasts

value: Cycloheximide, Dexamethasone


title: MCF7 pH7.6 rep2

city: Copenhagen

first: Jiayi

last: Yao

state: Copenhangen

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen

data_processing:
GRCh38 transcriptome and genome reference file were concatenated for Salmon indexing
Sequenced reads were quantified to transcipt level using Salmon v1.1.0 (Patro, R., Duggal, G., Love, M. et al. Nat Methods 14, 417–419 (2017)) with parameter --validateMappings
The quantification result was summarized to gene-level by GRCh38.p13 comprehensive gene annotation
Genome_build: GRCh38.p13 transcriptome and genome
Supplementary_files_format_and_content: tab-delimited text file include TPM values for every gene and every sample

source_name: Human luminal A breast cancer

growth_protocol: MDA-MB-231, MCF-7 S9, and Panc-1 cells were cultured in RPMI medium supplemented with 10 mM Glucose, 5% fetal bovine serum (FBS, Sigma-Aldrich, F9665) and 1% Penicillin/Streptomycin. Cells were cultured at 37 °C, 5% CO2 and passaged at a confluence of ~70-80%.

extract_protocol:
Total RNA was isolated using NucleoSpin® RNA II (Macherey-Nagel, Germany) according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To adjust pH to 7.6 or 6.5 while maintaining osmolarity, medium was prepared with 0 or 35 mM NaCl and 38 or 3 mM NaHCO3-, respectively.

tag: treatment

value: Grown at pH 7.6 for 1-2 months


title: MCF7 pH7.6 rep1


title: 83NS

value: mock infected


title: MCF7 pH7.6 rep3


title: Slyc_T0h_P2


title: AT1G51140 FBH3 Rep3 Batch1

tag: ecotype

value: 10 days


title: Slyc_T0h_P3


title: MCF7 pH6.5 rep3

value: Grown at pH 6.5 for 1-2 months


title: AT1G49720 ABF1 Rep3 Batch1

tag: treatments


title: MCF7 pH6.5 rep2


title: Slyc_T0h_P1


title: pUTE1056 (acpB complementation) Rep3

city: Houston

first: Theresa

middle: Marie

last: Koehler

state: Texas

address: 6431 Fannin Street, MSB 1.508

department: Microbiology and Molecular Genetics

institute: McGovern Medical School

description:
pUTE1056.vs.pUTE657.txt
pUTE1056.vs.Ames.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
The quality of the reads was assessed using FastQC (Andrews, 2010).
Reads were aligned to the B. anthracis strain ‘Ames Ancestor’, NCBI accession AE017334.2, using bowtie2 version 2.2.5 (Langmead and Salzberg, 2012) with default parameters.
The bedtools genomeCoverageBed command (Quinlan and Hall, 2010) was used to create bedgraph files from the aligned read files in BAM format. The IGVtools function of IGV (Thorvaldsdόttir et al., 2013) was used to convert the bedgraph files to tdf format files for use in IGV.
For differential gene expression analysis, sequencing files (BAM format) were imported into the Cufflinks pipeline. Triplicate sequencing results of each strain were compared to calculate Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) changes using the default setting. CuffDiff calculated log2(fold-change) in FPKM expression of genes between strains.
Genome_build: GCF_000008445.1_ASM844v1
Supplementary_files_format_and_content: Tab-delimited text files showing log2(fold-change) in expression between indicated strains for the complete Ames genome
Supplementary_files_format_and_content: tdf files showing genome coverage of reads along the genome per strain.

organism: Bacillus anthracis

source_name: B. anthracis cell culture

growth_protocol: Bacillus anthracis strains were cultivated at 37◦C in casamino acid medium containing 0.8% sodium bicarbonate (CA CO3). CA broth cultures were shaken at 200 r.p.m. in 5% atmospheric CO2. For strains harboring atxA, acpA, and acpB alleles under control of the hyperspank promoter (Phyperspank) (Britton 2002), expression was induced with isopropyl b-D-thiogalactoside (IPTG) during early exponential phase at 2 h and harvested at early stationary phase at 4 h. Optical densities for early exponential phase cultures ranged from OD600 0.25 to 0.35, and early stationary phase cultures ranged from 1.2 to 1.7.

extract_protocol:
Four ml samples were harvested at early stationary phase (OD600 5 1.2–1.7). Samples were centrifuged at 10,000 X g at 48◦C, and resulting pellets were resuspended in 500 μl of CACO3. An equivalent volume of saturated acid phenol (pH 4.3; Fisher Bioreagents, Fair Lawn, NJ) at 65◦C was added to each sample and transferred to screw top tubes containing 400 μl of 0.1 mm zirconia/silica beads (BioSpec Products, Bartlesville, OK). Samples were lysed mechanically for 1 min, incubated for 5 min at 65◦C and subsequently lysed for an additional 1 min followed by centrifugation at 3000 X g at 48◦C. Supernates were transferred to 500 μl of saturated acid phenol at 65◦C. Samples were vortexed, incubated at room temperature (RT) for 5 min and centrifuged at 16,000 X g for 3 min at 48◦C. One-third volume of chloroform was added to the aqueous phase. Following incubation for 10 min at RT, samples were centrifuged at 16,000 X g for 15 min at 48◦C. The aqueous phase was transferred to a new tube, and RNA was precipitated by the addition of one-half volume diethyl-pyrocarbonate (DEPC)-treated water and one total volume (aqueous phase + DEPC-treated water) of isopropanol followed by incubation at RT for 10 min. Samples were centrifuged at 16,000 X g for 15 min at 48◦C, and pellets containing precipitated RNA were washed with 75% ethanol. Following the removal of ethanol, pellets were air dried and finally resuspended in DEPC-treated water.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Ames ancestor

tag: genotype

value: atxA-null, acpA-null, acpB-null, pUTE1056 (acpB complementation)


title: pUTE1056 (acpB complementation) Rep2


title: AT5G43840 HSFA6A Rep3 Batch1


title: pUTE1056 (acpB complementation) Rep1


title: MCF7 pH6.5 rep1


title: Slyc_T8h_P1


title: Panc1 pH7.6 rep3

source_name: Human pancreatic adenocarinoma


title: AT5G04340 ZAT6 Rep3 Batch1


title: Slyc_T8h_P3


title: Wis 2

city: Belo Horizonte

first: Samara

last: Damasceno

state: MG

address: Avenida Antonio Carlos 6627

department: General Biology

country: Brazil

institute: Universidade Federal de Minas Gerais

data_processing:
Raw sequence reads were assessed for sequencing quality using FastQC (version 0.11.5), which attributes values of the identification of the sequences according to the error rate using the Phred quality score (0-40).
The data were submitted for trimming by the software Cutadapt, which removes the sequences of the adapters and excludes reads with Phred values < 25
The reference genome sequence Rattus novergicus (R.nor 6.0) was obtained from the NCBI database and the filtered reads were mapped using the software Bowtie2 (version 2.2.4.0)
The identification of differentially regulated genes was performed using different types of software.
The genes were counted using the software HTseq and featureCounts, and the differential expression between the two groups was calculated using the software DESeq and EdgeR
Genes presenting False discovery rate (FDR) ≤ 0.05 were considered differentially expressed
Genome_build: R.nor 6.0
Supplementary_files_format_and_content: Tab-delimited text files include reads counts, p value, FDR,... for each sample

organism: Rattus norvegicus

source_name: mRNA of the corpus quadrigeminum

extract_protocol:
RNA extraction was performed according to the TRIzol Reagent protocol (Invitrogen).
RNA libraries were prepared according to the TruSeq RNA Sample Preparation kit v2 Guide (Illumina)

value: Wistar

value: wild type

value: post natal day 70


title: Wis 1


title: Panc1 pH7.6 rep2


title: uterine body LPS+CsA 2

city: Chengdu

first: Ling

last: xu

state: Sichuan

address: No. 211 Huimin road

department: College of animal science and technology

institute: Sichuan Agricultural University

data_processing:
Clean Reads was sequenced to the reference genome using TopHat2
The Mapped notes were pieced together using Cufflinks software and compared with the original genome annotation information to search for previously unannotated transcriptional areas and to excavate new transcripts and new genes of the species to complement and refine the original genome annotation information.
Cuffquant and Cuffnorm used FPKM (Fragments Per Kilobase of transcript Per Million Fragments mapped) as an indicator to measure transcription or gene expression level.
The set of genes obtained by differential expression analysis is called differential expression gene set and is named "A_vs_B".Differentially expressed genes can be classified into up-regulated and down-regulated genes, depending on the relative level of expression between the two samples.
Genome_build: ftp://ftp.ensembl.org/pub/release-84/fasta/oryctolagus_cuniculus/dna/

organism: Oryctolagus cuniculus

source_name: rabbit uterine body

growth_protocol: All rabbits were fed in individual cages under a 14-h light and 10-h dark regimen and at temperatures ranging from 16°C to 25°C. All animals were fed ad libitum on a standard diet.

extract_protocol:
uterine body were removed, flash frozen on  liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina  Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After synchronization of estrus and ovulation cycles using eCG and hCG-induction, the animals were randomly divided into four groups (n = 3). Half (n = 6) were intravaginally infused with saline, the LPS vehicle, and half (n = 6) with 4 mg/kg of LPS (055: B5, Sigma-Aldrich, USA). Three animals from the saline (n = 3) and three from the LPS (n = 3) group were intramuscularly injected with 20 mg/kg of CsA (BBI Life Sciences, UK), and the remaining three animals in each group were injected i.m. with saline three hours after infusion. After 3 hours of treatment tissue samples were taken from the uterine body.

value: uterine body

tag: breed

value: New Zealand White

tag: body weight


title: WAR 1

value: Wistar Audiogenic Rat (WAR)

value: isogenic


title: pUTE1054 (acpA complementation) Rep2

description:
pUTE1054.vs.pUTE657.txt
pUTE1054.vs.Ames.txt

value: atxA-null, acpA-null, acpB-null, pUTE1054 (acpA complementation)


title: pUTE1054 (acpA complementation) Rep3


title: Panc1 pH7.6 rep1


title: Arcanum_T24h_P3

organism: Solanum arcanum

value: leaves

value: Infection with pathogenic strain Cmm 156


title: pUTE1054 (acpA complementation) Rep1


title: Panc1 pH6.5 rep2


title: pUTE992 (atxA complementation) Rep3

description:
pUTE992.vs.pUTE657.txt
pUTE992.vs.Ames.txt

value: atxA-null, acpA-null, acpB-null, pUTE992 (atxA complementation)


title: pUTE992 (atxA complementation) Rep2


title: uterine body CsA 2


title: Panc1 pH6.5 rep1


title: Arcanum_T24h_P1


title: pUTE992 (atxA complementation) Rep1


title: uterine body CsA 1


title: Arcanum_T8h_P3


title: WAR 2


title: MDA-MB-231 pH7.6 rep3

source_name: Human triple-negative breast cancer

value: Grown at pH 7.6 for 1-2 months


title: uterine body LPS+CsA 3


title: Arcanum_T8h_P2


title: pUTE657 (atxAacpAacpB-null) Rep3

value: atxA-null, acpA-null, acpB-null, pUTE657 (empty vector)


title: pUTE657 (atxAacpAacpB-null) Rep2


title: MDA-MB-231 pH7.6 rep2


title: uterine body LPS 3


title: uterine body LPS 2


title: Panc1 pH6.5 rep3


title: MDA-MB-231 pH7.6 rep1


title: pUTE657 (atxAacpAacpB-null) Rep1


title: uterine body LPS 1


title: Arcanum_T0h_P3


title: MDA-MB-231 pH6.5 rep3


title: Ames (Parent) Rep3

value: Parent


title: uterine body CsA 3


title: uterine body control 3


title: Arcanum_T0h_P2


title: Ames (Parent) Rep2


title: MDA-MB-231 pH6.5 rep2

value: Grown at pH 6.5 for 1-2 months


title: uterine body control 2


title: Arcanum_T0h_P1


title: Ames (Parent) Rep1

value: Ames ancestor


title: MDA-MB-231 pH6.5 rep1


title: Thymus 1 CD34+

status: Public on Jun 12 2020

city: Los Angeles

first: chintan

last: parekh

state: CA

address: 4650 sunset blvd, mail stop 54, mail stop 54

institute: CHLA

data_processing:
Conversion of fastq to UMI counts
Cellranger (10x genomics, thymus 1), BD™ Precise WTA Analysis v2.0 (thymus 2, Seven Bridges Genomics, RSEC adjusted UMI counts), or Indrops (https://github.com/indrops/indrops) (thymuses 3, 4) pipelines. For thymus 1, the data from libraries from CD34+ cells and CD34- cells (n=2 libraries) was aggregated using the cellranger aggr function with normalize=mapped (the two libraries were normalized for sequencing depth) to generate a combined gene expression matrix for CD34+ and CD34- cells. The combined matrix was split to provide expression data for each cell type (CD34+ or CD34-)  as a separate file.  The indrops v3 library analysis pipeline was used for thymus 3, where FASTQ files generated from basecall files are demultiplexed to generate single composite filtered fastq files that include cell and UMI barcodes  in the read headers and are filtered to only include reads with the correct barcode structure that survive trimommatic trimming and a low complexity filter. The composite FASTQ file for thymus 3 is deposited in the NCBI SRA and can seve as the input data for the indrops analysis pipeline at  the "Identify abundant barcodes" step (https://github.com/indrops/).The indrops v2 library analysis pipeline was used for thymus 4. We excluded barcodes with reads <1000 and reads <10000 for thymus 3 and thymus 4 respectively. Default values were used for all other parameters in the indrops analysis pipeline. The refdata-cellranger-GRCh38-1.2.0 (thymus 1) , gencode.v19.annotation.gtf (thymus 2), and GRCh38.85.gtf (thymuses 3,4) transcriptome annotation files were used.
Genome_build: hg38 for thymuses 1,3,4 and hg19 for thymus 2
Supplementary_files_format_and_content: Thymus1counts_34*.txt: gene expression counts
Supplementary_files_format_and_content: Thymus2counts.csv:  gene expression counts (RSEC adjusted UMI counts generated by the Seven Bridges  BD™ Precise WTA Analysis v2.0  pipeline); "_P1" indicates cells from plate 1. Cell names without suffix refer to cells from plate 2.
Supplementary_files_format_and_content: Thymus3counts.csv, Thymus4counts.csv: gene expression counts (from .TSV output file of UMIFM counts generated by the indrops pipeline)
Supplementary_files_format_and_content: Thymus2Celltypebasedonfacs.csv: cell type information based on index FACS; "_P1" indicates cells from plate 1. Cell names without suffix refer to cells from plate 2.

source_name: CD34+ thymic progenitor cells

extract_protocol:
Single cells were captured into barcoded hydrogels using the 10X (thymus 1) or Indrops (Thymuses 3,4) microfluidics platforms. For thymus 2, single cells were index sorted into a 96 well plate (two 96 well plates, 1 cell/ well) containing RNA extraction buffer (BD Precise WTA Single Cell Kit (BD Genomics, PN 634100, 96 well plates). Cell type information based on FACS for thymus 2 is provided as a csv file. Cell barcodes used for sequencing are provided as csv files for plate 1 (S1) and plate 2 (S2)
Single cell RNA-Seq libraries were prepared using the 10x Genomics Chromium Single Cell v2 kit (thymus 1), the BD Precise WTA Single Cell Kit (BD Genomics, PN 634100, thymus 2), or the Indrops protocol (Zilionis et al, Nature Protocols, 2017)(thymuses 3,4). The indrops v3 and v2 protocols were used for Thymus 3 and thymus 4 respectively.
Illumina Hiseq (Thymus 1, 150bp paired end) or Nextseq500 (thymuses 2-4). The Nextseq mid output kit (150 cycles,  75 base pair paired end) and the the Nextseq high output kit (75 cycles) were used for thymus 2 and thymuses3,4 respectively. For thymus 3 cycles were distributed as read 1 (61 cycles, biological read), read 2 (8 cycles, first half of the gel barcode), read 3  (8 cycles, library index ), and  read 4 (14 cycles, the second half of the gel barcode, the UMI and a fraction of the polyA tail) (indrops v3). For thymus 4 cycles were distributed as read 1 (37 cycles, biological read), read 2 (51 cycles, metadata read),  and index read (6 cycles, library index) (indrops v2).

tag: donor sex

value: male

tag: donor age

value: 19 months

value: Thymus

tag: cell type

value: CD34+ thymic progenitor cells


title: Thymus 1 CD34-

source_name: CD34- thymic cells

tag: tissue

value: CD34- thymic cells


title: Arcanum_T8h_P1


title: 4280

city: London

first: Findlay

last: Bewicke-Copley

address: John Vane Science Centre, Barts Cancer Institute

country: United Kingdom

institute: Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London

data_processing:
Reads were aligned to the genome using HISAT2
Reads overlapping exons were counted using HTSeq
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: WT

extract_protocol:
RNA was extracted using the RNA blood kit (Qiagen) following manufacturer’s instructions
NEBNext Ultra II RNA Library Prep Kit for Illumina with optional mRNA enrichment and NEBNext multiplexing oligos using the manufacturer’s protocol

value: Whole Blood

value: WT


title: 4281

source_name: SP1 mutant

value: SP1 mutant


title: 4279


title: 4280a


title: 4277


title: Subject K day 8 replicate 1 [K_d8_L4]

city: Burlington

first: Korin

last: Eckstrom

state: VT

address: 89 Beaumont Ave

institute: University of Vermont

data_processing:
Illumina bcl2fastq used for basecalling
Sequences were trimmed of adaptor sequences, bases <Q15, and length >60bp using Trimmomatic
Reads passing QC were mapped to the human genome (GRCh37, version 17, Ensembl 72)  using hisat2 (v 2.1.0) with the parameters -p 8 -k 1 -q
Mapped reads were assembled into transcripts using StringTie (v 1.3.4) with the parameters -e -B -p 8. StringTie output for each sample was merged to create a uniform annotation and counts to this carried forward.
Counts at the transcript level were extracted using Ballgown and differential expression was calculated using edgeR. Counts were normalized by library size and adjusted using TMM. Transcripts with counts less than 2 cpm in at least 3 samples were removed from further analysis.
For deconvolution analysis, replicate bam files for each subject were merged by timepoint and a counts were extracted using featureCounts.
Genome_build: GRCh37 version 17 Ensembl 72
Supplementary_files_format_and_content: comma-separated file with the raw counts at the transcript level or at the gene level merged across replicates

source_name: Subject K day 8_whole blood

extract_protocol:
Whole blood was collected from test subjects using PAXgene Blood RNA tubes containing 6.9 mL of additive on days 0, 8, and 28 post challenge. Total RNA was extracted using PAXgene Blood kit equipped with RNA spin column , then protected by adding Ribolock RNase inhibitor. (ThermoFisher, Waltham, MA USA, Cat. EO0381) to a final concentration of 0.25 U/µL of RNA.
Libraries were constructed using the NuGEN Ovation Universal RNA reagent with ribosomal RNA and globin depletion.

tag: subject status

value: healthy flavivirus-naive volunteers infected with the live attenuated dengue serotype 2 challenge virus (rDEN2delta30)

tag: subject id

value: Subject K

tag: time point

value: day 8


title: Subject K day 8 replicate 2 [K_d8_L5]


title: Subject K day 28 replicate 3 [K_d28_L6]

source_name: Subject K day 28_whole blood

value: day 28


title: Subject K day 8 replicate 3 [K_d8_L6]


title: Subject K day 0 replicate 2 [K_d0_L5]

source_name: Subject K day 0_whole blood

value: day 0


title: Subject K day 0 replicate 3 [K_d0_L6]


title: Subject K day 0 replicate 1 [K_d0_L4]


title: Subject J day 28 replicate 3 [J_d28_L6]

source_name: Subject J day 28_whole blood

value: Subject J


title: uterine body control 1

value: uterine body

value: New Zealand White


title: Subject J day 28 replicate 2 [J_d28_L5]


title: Subject J day 28 replicate 1 [J_d28_L4]


title: Subject J day 8 replicate 2 [J_d8_L5]

source_name: Subject J day 8_whole blood


title: 4275


title: Subject J day 8 replicate 1 [J_d8_L4]


title: Subject K day 28 replicate 2 [K_d28_L5]


title: Subject K day 28 replicate 1 [K_d28_L4]


title: Subject J day 0 replicate 3 [J_d0_L6]

source_name: Subject J day 0_whole blood


title: Subject J day 8 replicate 3 [J_d8_L6]


title: Subject I day 28 replicate 3 [I_d28_L6]

source_name: Subject I day 28_whole blood

value: Subject I


title: Subject J day 0 replicate 1 [J_d0_L4]


title: Subject I day 28 replicate 2 [I_d28_L5]


title: Subject J day 0 replicate 2 [J_d0_L5]


title: Subject I day 8 replicate 2 [I_d8_L5]

source_name: Subject I day 8_whole blood


title: Subject I day 28 replicate 1 [I_d28_L4]


title: Subject I day 8 replicate 1 [I_d8_L4]


title: Subject I day 0 replicate 3 [I_d0_L6]

source_name: Subject I day 0_whole blood


title: Subject I day 8 replicate 3 [I_d8_L6]


title: uterine body LPS+CsA 1


title: ND535-Naïve-8hrs

tag: Sex

value: Male

value: PBMC

tag: cell subtype

value: naïve CD4+ T cells

tag: in vitro culture conditions

value: RPMI complete, 10 IU/mL IL-2

tag: rin


title: Subject I day 0 replicate 2 [I_d0_L5]


title: Subject I day 0 replicate 1 [I_d0_L4]


title: Subject H day 28 replicate 3 [H_d28_L6]

source_name: Subject H day 28_whole blood

value: Subject H


title: PB-ip-8_Hp

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.5.4b, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Mus Musculus, UCSC, mm10
Supplementary_files_format_and_content: tad-delimited, raw counts

source_name: Hippocampus

growth_protocol: Mice were kept in a conventional hygienic grade facility and sacrificed at the indicated time point.

extract_protocol:
RNA was extracted from snap frozen brain areas (both hemispheres for hippocampus) using the RNeasy Plus Universal Kit (QIAGEN), following manufacturer’s instructions.
TruSeq RNA stranded protocol, 76-151 bp paired end

tag: age of inoculation

value: 6 weeks

tag: type of inoculation

value: intraperitoneal

value: PrP present

tag: date of sacrifice

value: 8 wpi

tag: treatment

value: non-infectious brain homogenate

value: Hippocampus


title: PB-ip-28_Hp

tag: genotype

value: terminal


title: PB-ip-16_Hp

value: 12 wpi


title: PB-ip-12_Hp

value: RML6 prions


title: PB-ip-17_Hp


title: PB-ip-11_Hp


title: PB-ip-26_Hp


title: PB-ip-3_Hp


title: PB-ip-21_Hp


title: PB-ip-1_Hp


title: PB-ip-24_Hp


title: PB-ip-27_Hp


title: PB-ip-2_Hp


title: PB-ip-6_Hp


title: PB-ip-23_Hp


title: PB-ip-18_Hp


title: PB-ip-7_Hp


title: PB-ip-13_Hp


title: Tam-R MCF-7- ELOVL2 ORF 2

city: Goyang

first: Dawoon

last: Jeong

address: 32 Dongguk-ro, Ilsan Dong-gu

department: Life Science

institute: Dongguk University

description: Gene expression after infection uisng lentiviral particles with human ELOVL2 ORF clone in tamoxifen-resistant breast cancer cell

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing:
Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1
Array probes that have Flag A in samples were filtered out. Selected gProcessedSignal value was transformed by logarithm and normalized by quantile method.

source_name: Mammary Gland; Breast

label_protocol: Cy3 labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: RNA was extracted and purified from Tam-R MCF-7 using ZR Dyet DNA/RNA kit (Zymo research) according to standard instructions

tag: cell line

value: tamoxifen-resistant MCF-7 (Tam-R MCF-7)

value: breast epithelial

tag: disease

value: adenocarcinoma

tag: genotype/variation


title: Tam-R MCF-7- ELOVL2 ORF 1

tag: cell type


title: Tam-R MCF-7- control 1

description: Gene expression after infection uisng lentiviral particles with control clone in tamoxifen-resistant breast cancer cell

value: control


title: Arcanum_T24h_P2

source_name: Leaves

tag: cultivar

tag: tissue

value: leaves

tag: hpi

value: Infection with pathogenic strain Cmm 156


title: Subject H day 28 replicate 1 [H_d28_L4]

tag: subject status

value: healthy flavivirus-naive volunteers infected with the live attenuated dengue serotype 2 challenge virus (rDEN2delta30)

tag: subject id

tag: time point

value: day 28

value: Whole Blood


title: Subject H day 8 replicate 2 [H_d8_L5]

source_name: Subject H day 8_whole blood

value: Subject H

value: day 8


title: Subject H day 0 replicate 3 [H_d0_L6]

source_name: Subject H day 0_whole blood

value: day 0


title: Subject H day 8 replicate 3 [H_d8_L6]


title: Subject H day 28 replicate 2 [H_d28_L5]


title: Subject H day 0 replicate 2 [H_d0_L5]


title: lambda_4h_repeat 3

first: Andreas

last: Wack

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
Adaptor removal and quality trimming done with Trimmomatic v 0.36
Read alingment and gene counts was performed with RSEM v 1.2.31 and STAR v 2.5.2a
Differential expression analysis was carried out with DESeq2 package ( version 1.20.0 ) with R version 3.5.1
Genome_build: Ensembl GRCm38 release 89
Supplementary_files_format_and_content: Tab-delimited text include normalized counts per gene and per sample (generated by DESeq2).

source_name: airway epithelia (AEC)

growth_protocol: Primary cells isolated from tracheas by enzymatic treatment were seeded onto 0.4 μm pore size clear polyester membrane  coated with a collagen solution. At confluence, media was removed from the upper chamber to establish an air- liquid interface (ALI). Fully differentiated, 10-14 days-old AEC cultures were routinely used for experiments.

extract_protocol:
RNA was isolated from AEC cultures by directly lysing the cells in the transwells, using the Qiagen RNeasy mini kit
library was prepared using polyA KAPA mRNA Hyper Prep kit  following manufacturer’s protocols

treatment_protocol: AEC were either mock treated or treated with IFN alpha , IFN beta, or IFN Lambda

value: airway epithelia (AEC)

tag: strain

value: wt

tag: passage

value: primary

value: 4 hour IFN-λ treatment 5ng/ml


title: lambda_4h_repeat 1


title: Subject H day 0 replicate 1 [H_d0_L4]


title: lambda_4h_repeat 2


title: Subject G day 28 replicate 2 [G_d28_L5]

source_name: Subject G day 28_whole blood

value: Subject G


title: alpha_4h_repeat 3

value: 4 hour IFN-α treatment 600U/ml


title: beta_4h_repeat 2

value: 4 hour IFN-β treatment 1000U/ml


title: beta_4h_repeat 1


title: lambda_day5_repeat 3

value: 5 day IFN-λ treatment 5ng/ml


title: Subject G day 28 replicate 1 [G_d28_L4]


title: beta_4h_repeat 3


title: alpha_4h_repeat 1


title: Tam-R MCF-7- control 2

value: tamoxifen-resistant MCF-7 (Tam-R MCF-7)

value: breast epithelial

value: adenocarcinoma

value: control


title: Subject H day 8 replicate 1 [H_d8_L4]

value: healthy flavivirus-naive volunteers infected with the live attenuated dengue serotype 2 challenge virus (rDEN2delta30)


title: lambda_day5_repeat 1


title: Subject G day 28 replicate 3 [G_d28_L6]

value: day 28

value: Whole Blood


title: alpha_4h_repeat 2


title: Subject G day 0 replicate 3 [G_d0_L6]

source_name: Subject G day 0_whole blood


title: Subject G day 8 replicate 1 [G_d8_L4]

source_name: Subject G day 8_whole blood

value: day 8


title: Subject G day 8 replicate 3 [G_d8_L6]


title: Subject G day 0 replicate 2 [G_d0_L5]

value: day 0


title: Subject G day 8 replicate 2 [G_d8_L5]


title: Subject G day 0 replicate 1 [G_d0_L4]


title: Subject F day 28 replicate 3 [F_d28_L6]

source_name: Subject F day 28_whole blood

value: Subject F


title: Subject F day 28 replicate 2 [F_d28_L5]


title: beta_day5_repeat 2

value: airway epithelia (AEC)

value: wt

value: 5 day IFN-β treatment 1000U/ml


title: Subject F day 28 replicate 1 [F_d28_L4]


title: Subject F day 8 replicate 3 [F_d8_L6]

source_name: Subject F day 8_whole blood


title: beta_day5_repeat 1

value: primary


title: alpha_day5_repeat 3

value: 5 day IFN-α treatment 600U/ml


title: alpha_day5_repeat 2


title: lambda_day5_repeat 2


title: mock_day5/4h_repeat 3

value: 4 hour/5 day mock treatment


title: mock_day5/4h_repeat 1


title: lambda_day3_repeat 3

value: 3 day IFN-λ treatment 5ng/ml


title: Subject F day 8 replicate 2 [F_d8_L5]


title: alpha_day5_repeat 1


title: Subject E day 28 replicate 3 [E_d28_L3]

source_name: Subject E day 28_whole blood

value: Subject E


title: Subject F day 0 replicate 2 [F_d0_L5]

source_name: Subject F day 0_whole blood


title: Subject F day 0 replicate 1 [F_d0_L4]


title: Subject F day 8 replicate 1 [F_d8_L4]


title: Subject F day 0 replicate 3 [F_d0_L6]


title: Subject E day 28 replicate 1 [E_d28_L1]


title: Subject E day 28 replicate 2 [E_d28_L2]


title: lambda_day3_repeat 1


title: lambda_day3_repeat 2


title: Subject E day 8 replicate 3 [E_d8_L3]

source_name: Subject E day 8_whole blood


title: Subject E day 8 replicate 2 [E_d8_L2]


title: beta_day3_repeat 3

value: 3 day IFN-β treatment 1000U/ml


title: beta_day5_repeat 3


title: beta_day3_repeat 1


title: alpha_day3_repeat 3

value: 3 day IFN-α treatment 600U/ml


title: Subject E day 8 replicate 1 [E_d8_L1]


title: mock_day5/4h_repeat 2


title: alpha_day3_repeat 2


title: mock_day3_repeat 2

value: 3 day mock treatment


title: mock_day3_repeat 3


title: Subject D day 28 replicate 2 [D_d28_L2]

source_name: Subject D day 28_whole blood

value: healthy flavivirus-naive volunteers infected with the live attenuated dengue serotype 2 challenge virus (rDEN2delta30)

value: Subject D


title: Subject E day 0 replicate 2 [E_d0_L2]

source_name: Subject E day 0_whole blood

value: Whole Blood


title: Subject E day 0 replicate 1 [E_d0_L1]


title: Subject D day 28 replicate 3 [D_d28_L3]

value: day 28


title: mock_day3_repeat 1


title: Subject D day 28 replicate 1 [D_d28_L1]


title: beta_day3_repeat 2


title: lambda_day2_repeat 3

value: 2 day IFN-λ treatment 5ng/ml


title: Subject D day 8 replicate 2 [D_d8_L2]

source_name: Subject D day 8_whole blood

value: day 8


title: Subject D day 0 replicate 3 [D_d0_L3]

source_name: Subject D day 0_whole blood

value: day 0


title: lambda_day2_repeat 1

value: airway epithelia (AEC)

value: wt


title: Subject D day 0 replicate 2 [D_d0_L2]


title: beta_day2_repeat 3

value: primary

value: 2 day IFN-β treatment 1000U/ml


title: beta_day2_repeat 1


title: Subject D day 8 replicate 3 [D_d8_L3]


title: lambda_day2_repeat 2


title: Subject D day 0 replicate 1 [D_d0_L1]


title: beta_day2_repeat 2


title: Subject C day 28 replicate 3 [C_d28_L3]

source_name: Subject C day 28_whole blood

value: Subject C


title: alpha_day2_repeat 3

value: 2 day IFN-α treatment 600U/ml


title: Subject E day 0 replicate 3 [E_d0_L3]

value: Subject E


title: alpha_day2_repeat 2


title: alpha_day3_repeat 1


title: alpha_day2_repeat 1


title: Subject C day 28 replicate 1 [C_d28_L1]


title: Subject C day 28 replicate 2 [C_d28_L2]


title: mock_day2_repeat 3

value: 2 day mock treatment


title: mock_day2_repeat 2


title: Subject C day 8 replicate 2 [C_d8_L2]

source_name: Subject C day 8_whole blood


title: IFNL-R KO influenza_repeat 3

description:
IFN-λ-R KO influenza EpCam+ CD45- CD31- live single cells
MAJ537A12

source_name: lung epithelia

growth_protocol: Primary cells isolated from lungs by enzymatic treatment were stained and sorted as CD45+CD31-EpCam+

value: lung epithelia

value: IFNL-R KO

tag: passsage

value: EpCam+ CD45- CD31- live single cells

tag: infection

value: influenza


title: Subject D day 8 replicate 1 [D_d8_L1]

value: healthy flavivirus-naive volunteers infected with the live attenuated dengue serotype 2 challenge virus (rDEN2delta30)

value: Subject D

value: Whole Blood


title: Subject C day 8 replicate 1 [C_d8_L1]

value: day 8


title: mock_day2_repeat 1


title: Subject C day 8 replicate 3 [C_d8_L3]


title: Subject C day 0 replicate 3 [C_d0_L3]

source_name: Subject C day 0_whole blood

value: day 0


title: Subject C day 0 replicate 2 [C_d0_L2]


title: IFNL-R KO influenza_repeat 2

description:
IFN-λ-R KO influenza EpCam+ CD45- CD31- live single cells
MAJ537A11


title: WT influenza_repeat 3

description:
WT influenza EpCam+ CD45- CD31- live single cells
MAJ537A9


title: IFNL-R KO influenza_repeat 1

description:
IFN-λ-R KO influenza EpCam+ CD45- CD31- live single cells
MAJ537A10


title: Subject C day 0 replicate 1 [C_d0_L1]


title: Subject B day 28 replicate 2 [B_d28_L2]

source_name: Subject B day 28_whole blood

value: Subject B

value: day 28


title: IFNL-R KO naïve_repeat 4

description:
IFN-λ-R KO naïve EpCam+ CD45- CD31- live single cells
MAJ537A28

value: primary

value: naive


title: WT influenza_repeat 1

description:
WT influenza EpCam+ CD45- CD31- live single cells
MAJ537A7

value: wt


title: Subject B day 28 replicate 3 [B_d28_L3]


title: IFNL-R KO naïve_repeat 3

description:
IFN-λ-R KO naïve EpCam+ CD45- CD31- live single cells
MAJ537A27


title: IFNL-R KO naïve_repeat 2

description:
IFN-λ-R KO naïve EpCam+ CD45- CD31- live single cells
MAJ537A6


title: IFNL-R KO naïve_repeat 1

description:
IFN-λ-R KO naïve EpCam+ CD45- CD31- live single cells
MAJ537A5


title: WT naïve_repeat 5

description:
WT naïve EpCam+ CD45- CD31- live single cells
MAJ537A26


title: WT influenza_repeat 2

description:
WT influenza EpCam+ CD45- CD31- live single cells
MAJ537A8


title: WT naïve_repeat 4

description:
WT naïve EpCam+ CD45- CD31- live single cells
MAJ537A25


title: Subject B day 28 replicate 1 [B_d28_L1]


title: Subject B day 0 replicate 2 [B_d0_L2]

source_name: Subject B day 0_whole blood


title: Subject B day 8 replicate 2 [B_d8_L2]

source_name: Subject B day 8_whole blood


title: Subject B day 8 replicate 1 [B_d8_L1]


title: Subject B day 0 replicate 3 [B_d0_L3]


title: Subject B day 0 replicate 1 [B_d0_L1]


title: WT naïve_repeat 3

description:
WT naïve EpCam+ CD45- CD31- live single cells
MAJ537A3


title: Subject A day 28 replicate 3 [A_d28_L3]

source_name: Subject A day 28_whole blood

value: Subject A


title: WT naïve_repeat 2

description:
WT naïve EpCam+ CD45- CD31- live single cells
MAJ537A2


title: Subject A day 28 replicate 1 [A_d28_L1]


title: Subject A day 28 replicate 2 [A_d28_L2]


title: WT naïve_repeat 1

description:
WT naïve EpCam+ CD45- CD31- live single cells
MAJ537A1


title: Subject A day 8 replicate 3 [A_d8_L3]

source_name: Subject A day 8_whole blood


title: PBP-35

source_name: Hippocampus

extract_protocol:
RNA was extracted from snap frozen brain areas (both hemispheres for hippocampus) using the RNeasy Plus Universal Kit (QIAGEN), following manufacturer’s instructions.
TruSeq RNA stranded protocol

tag: age of inoculation

value: 6 weeks

tag: type of inoculation

value: intracerebral

value: PrP present

tag: date of sacrifice

value: terminal

value: RML6 prions + plasma

value: Hippocampus

tag: cohort

value: plasma cohort run #2


title: PBP-34

tag: genotype

tag: treatment


title: Subject A day 0 replicate 3 [A_d0_L3]

source_name: Subject A day 0_whole blood

value: healthy flavivirus-naive volunteers infected with the live attenuated dengue serotype 2 challenge virus (rDEN2delta30)


title: Subject A day 0 replicate 2 [A_d0_L2]

value: Whole Blood


title: PBP-32_Hp

value: plasma cohort run #1


title: PBP-33_Hp


title: PBP-37

value: non-infectious brain homogenate + plasma


title: PBP-38


title: Subject A day 0 replicate 1 [A_d0_L1]

value: day 0


title: oxRRBS WT IN

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

country: Canada

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

description:
processed data file: RRBSoxRRBS_WT.txt
YX_mix4_OXBS_index16_CCGTCC_L002

library_source: genomic

data_processing:
library strategy: (ox)RRBS
Illumina Casava1.8 software used for basecalling.
RRBS reads were mapped to human genome by bsmap software (v2.7) with “-s 12 -g 3 -w 3 -D C-CGG -r 0” options (Xi and Li, 2009)
Methylation ratio was calculated by methratio.py python script in bsmap package with “-q –z –u” options.
5hmC level were calculated by subtracting methylation ratio in oxRRBS from that in RRBS.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated file showing 5hmC and 5mC level

molecule: genomic DNA

source_name: in vitro differentiated INs

growth_protocol: hESCs were differentiated into cortical interneurons as described previously (Maroof et al., 2013)

extract_protocol:
RRBS was performed as described previously(Gu et al., 2011). For oxRRBS, we performed oxidation step with 15 mM potassium perruthenate solution (in 0.05M NaOH) for 1hr on ice before MspI digestion (Booth et al., 2013).
RRBS library was prepared as described previously (Gu et al., 2011)

tag: status

value: WT

tag: cell type

value: in vitro differentiated interneurons (INs)

tag: experiment

value: oxidative RRBS


title: oxRRBS R133C IN

description:
processed data file: RRBSoxRRBS_R133C.txt
YX_mix4_OXBS_index18_GTCCGC_L002

value: MeCP2 R133C mutant


title: PBP-39_Hp

tag: tissue


title: RRBS WT IN

description:
processed data file: RRBSoxRRBS_WT.txt
YX_mix4_BS_index16_CCGTCC_Lall

data_processing:
Illumina Casava1.8 software used for basecalling.
RRBS reads were mapped to human genome by bsmap software (v2.7) with “-s 12 -g 3 -w 3 -D C-CGG -r 0” options (Xi and Li, 2009)
Methylation ratio was calculated by methratio.py python script in bsmap package with “-q –z –u” options.
5hmC level were calculated by subtracting methylation ratio in oxRRBS from that in RRBS.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated file showing 5hmC and 5mC level

value: RRBS


title: PBP-24

value: 6 weeks

value: RML6 prions + saline


title: RRBS R133C IN

description:
processed data file: RRBSoxRRBS_R133C.txt
YX_mix4_BS_index18_GTCCGC_Lall


title: PBP-25

value: intracerebral

value: PrP present


title: RNA-seq R133C KCl+ JQ1+

description:
R133C KCl+JQ1+
YX8_1
processed data file: RPKM_table_JQ1KCl.xlsx

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by tophat2 (v2.3.0)
Gene expression was estimated by Cufflinks (v1.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-separated gene-sample matrix file

source_name: Gene expression of R133C INs

extract_protocol:
RNeasy Mini kit
Tru-Seq RNA library

treatment_protocol: Membrane was depolarized with 55mM KCl. 75nM JQ1 was added to the media starting from 2 weeks of neuronal maturation.

tag: genotype/variation

tag: stimulation

value: KCl

tag: time


title: RNA-seq R133C KCl- JQ1+

description:
R133C KCl-JQ1+
YX7_1
processed data file: RPKM_table_JQ1KCl.xlsx


title: RNA-seq R133C KCl+JQ1-

description:
R133C KCl+JQ1-
YX6_1
processed data file: RPKM_table_JQ1KCl.xlsx


title: PBP-22_Hp

value: terminal

value: Hippocampus


title: Subject A day 8 replicate 2 [A_d8_L2]

tag: subject status

value: healthy flavivirus-naive volunteers infected with the live attenuated dengue serotype 2 challenge virus (rDEN2delta30)

tag: subject id

value: Subject A

tag: time point

value: day 8


title: Subject A day 8 replicate 1 [A_d8_L1]

value: Whole Blood


title: PBP-21_Hp

value: plasma cohort run #1


title: RNA-seq WT KCl- JQ1+

description:
WT KCl-JQ1+
YX3_1
processed data file: RPKM_table_JQ1KCl.xlsx

source_name: Gene expression of WT INs

value: WT


title: RNA-seq WT KCl+ JQ1+

description:
WT KCl+JQ1+
YX4_1
processed data file: RPKM_table_JQ1KCl.xlsx

value: in vitro differentiated interneurons (INs)


title: PBP-23_Hp


title: PBP-29

value: non-infectious brain homogenate + saline

value: plasma cohort run #2


title: PBP-30


title: PBP-31_Hp

value: RML6 prions + plasma


title: RNA-seq R133C KCl-JQ1-

description:
R133C KCl-JQ1-
YX5_1
processed data file: RPKM_table_JQ1KCl.xlsx

value: MeCP2 R133C mutant


title: PBP-40_Hp

value: 6 weeks

value: non-infectious brain homogenate + plasma


title: PBP-28_Hp

value: intracerebral

value: PrP present


title: RNA-seq WT KCl+JQ1-

description:
WT KCl+JQ1-
YX2_1
processed data file: RPKM_table_JQ1KCl.xlsx

value: KCl


title: RNA-seq WT KCl-JQ1-

description:
WT KCl-JQ1-
YX1_1
processed data file: RPKM_table_JQ1KCl.xlsx


title: PBP-15

value: 8 wpi

value: Hippocampus


title: PBP-13


title: Subject B day 8 replicate 3 [B_d8_L3]

value: healthy flavivirus-naive volunteers infected with the live attenuated dengue serotype 2 challenge virus (rDEN2delta30)

value: Subject B


title: PBP-26_Hp

value: terminal


title: PBP-14_Hp

value: plasma cohort run #1


title: RNA-seq WT INs D32

description:
D32 WT
R6-4W_CAGATC_L004
processed data file: RPKM_table_IN.xlsx

source_name: Gene expression of WT INs with time scale

value: WT


title: RNA-seq WT INs D46

description:
D46 WT
R6-5W_CGATGT_L006
processed data file: RPKM_table_IN.xlsx

value: in vitro differentiated interneurons (INs)


title: RNA-seq R133C INs D74

description:
D74 R133C
R6-6M_CTTGTA_L006
processed data file: RPKM_table_IN.xlsx

source_name: Gene expression of MeCP2 mutant INs with time scale


title: PBP-11_Hp


title: PBP-12_Hp


title: PBP-20


title: RNA-seq R133C INs D46

description:
D46 R133C
R6-5M_CAGATC_L006
processed data file: RPKM_table_IN.xlsx


title: RNA-seq R133C INs D32

description:
D32 R133C
R6-4M_GCCAAT_L006
processed data file: RPKM_table_IN.xlsx


title: RNA-seq WT INs D18

description:
D18 WT
R6-3W_CGATGT_L004
processed data file: RPKM_table_IN.xlsx


title: PBP-18_Hp


title: PBP-19


title: RNA-seq R133C INs D18

description:
D18 R133C
R6-3M_ACAGTG_L006
processed data file: RPKM_table_IN.xlsx


title: RNA-seq WT INs D10

description:
D10 WT
R6-2W_CAGATC_L003
processed data file: RPKM_table_IN.xlsx


title: PBP-17_Hp


title: RNA-seq R133C INs D10

description:
D10 R133C
R6-2M_TGACCA_L006
processed data file: RPKM_table_IN.xlsx


title: PBP-5

value: RML6 prions + saline


title: RNA-seq WT INs D0

description:
D0 WT
R6-1W_CGATGT_L003
processed data file: RPKM_table_IN.xlsx


title: PBP-16_Hp


title: RNA-seq WT INs D74

description:
D74 WT
R6-6W_CAGATC_L005
processed data file: RPKM_table_IN.xlsx


title: PBP-3_Hp


title: PBP-4

value: plasma cohort run #2


title: PBP-2_Hp


title: Hi-C ChIP R133C KCl- JQ1+

description: 3D chromosomal interaction

data_processing:
library strategy: HiC-seq
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by HiC-Pro (v2.9.0)
Compartments were identified by HOMER (v4.10.1)
Genome_build: hg19
Supplementary_files_format_and_content: Bed format

source_name: Hi-C ChIP R133C

extract_protocol: Hi-C library was prepared as described previously (Belaghzal et al., 2017)


title: PBP-1_Hp


title: RNA-seq R133C INs D0

description:
D0 R133C
R6-1M_CGATGT_L005
processed data file: RPKM_table_IN.xlsx


title: Hi-C ChIP WT KCl- JQ1+

description: 3D chromosomal interaction

source_name: Hi-C ChIP WT


title: PBP-9

value: non-infectious brain homogenate + saline


title: Input

description:
Input for ChIP
YT_C14_GCCAAT_L003

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by Bowtie2 (v2.3.0)
Peaks were called by MACS2 (v2.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: Bed format

source_name: Input

extract_protocol:
iDeal ChIP-seq kit for transcription factors (C01010170, Diagenode)
ThruPLEX DNA-seq kit

tag: antibody


title: MeCP2 ChIP R133C

description:
Genomic binding of MeCP2
YT145_GCCAAT_L004

source_name: MeCP2 ChIP R133C

value: MeCP2 R133C mutant

value: MeCP2 (ab195393, Abcam)


title: PBP-7_Hp

tag: age of inoculation

value: 6 weeks


title: PBP-6_Hp

tag: type of inoculation

value: intracerebral


title: MeCP2 ChIP WT

description:
Genomic binding of MeCP2
YT141_ACAGTG_L004

source_name: MeCP2 ChIP WT


title: BRD4 ChIP R133C KCl+ JQ1+

description:
Genomic binding of BRD4
YTC113_GCCAAT_L007

source_name: BRD4 ChIP R133C

value: BRD4 (A301-985A50,Bethyl lab.)


title: BRD4 ChIP R133C KCl- JQ1+

description:
Genomic binding of BRD4
YTC112_ACAGTG_L007


title: BRD4 ChIP R133C KCl+JQ1-

description:
Genomic binding of BRD4
YTC111_TGACCA_L007

value: KCl


title: PBO-A3_Hp

value: 51 weeks

tag: date of sacrifice

value: RML6 prions

value: aging cohort


title: BRD4 ChIP R133C KCl-JQ1-

description:
Genomic binding of BRD4
YTC110_TTAGGC_L007


title: PBO-A2_Hp

value: Hippocampus

tag: cohort


title: PBO-A1_Hp

value: terminal


title: PBO-B2_Hp

value: non-infectious brain homogenate


title: Hi-C ChIP R133C KCl-JQ1-

description: 3D chromosomal interaction


title: BRD4 ChIP WT KCl+ JQ1+

description:
Genomic binding of BRD4
YTC109_CGATGT_L007

source_name: BRD4 ChIP WT

value: WT


title: PBP-10

tag: genotype

value: PrP present

value: 8 wpi


title: BRD4 ChIP WT KCl- JQ1+

description:
Genomic binding of BRD4
YTC108_ATCACG_L007

value: in vitro differentiated interneurons (INs)

tag: treatment


title: Hi-C ChIP WT KCl-JQ1-

description: 3D chromosomal interaction


title: BRD4 ChIP WT KCl-JQ1-

description:
Genomic binding of BRD4
YTC106_GGCTAC_L006


title: PBO-B3_Hp


title: CTCF ChIP R133C KCl- JQ1+

description:
Genomic binding of CTCF
YTC104_GATCAG_L006

source_name: CTCF ChIP R133C

value: CTCF (K09622002, Diagenode)


title: CTCF ChIP R133C KCl+ JQ1+

description:
Genomic binding of CTCF
YTC105_TAGCTT_L006

value: MeCP2 R133C mutant


title: BRD4 ChIP WT KCl+JQ1-

description:
Genomic binding of BRD4
YTC107_CTTGTA_L006


title: PBY-H2_Hp


title: PBY-H3_Hp


title: PBP-8_Hp

value: non-infectious brain homogenate + saline

value: plasma cohort run #1


title: PBY-H1_Hp

value: 6 weeks

value: intracerebral


title: PBY-I4_Hp


title: CTCF ChIP R133C KCl+JQ1-

description:
Genomic binding of CTCF
YTC103_ACTTGA_L006

value: KCl


title: PBY-I3_Hp


title: PBY-I1_Hp


title: PBO-C3_Hp

value: 51 weeks


title: CTCF ChIP WT KCl+ JQ1+

description:
Genomic binding of CTCF
YTC101_GCCAAT_L005

source_name: CTCF ChIP WT


title: CTCF ChIP WT KCl- JQ1+

description:
Genomic binding of CTCF
YTC100_ACAGTG_L005


title: PBO-B1_Hp


title: CTCF ChIP WT KCl+JQ1-

description:
Genomic binding of CTCF
YTC99_TGACCA_L005


title: PBO-C2_Hp

value: RML6 prions


title: PBO-D3_Hp

value: aging cohort


title: PBO-D2_Hp

value: Hippocampus


title: CTCF ChIP WT KCl-JQ1-

description:
Genomic binding of CTCF
YTC98_TTAGGC_L005


title: BRD4 ChIP KCl+

description:
Genomic binding of BRD4
YT_C13_ACAGTG_L003

source_name: BRD4 ChIP

value: BRD4 (A301-985A50,Bethyl lab.)


title: PB114

source_name: Hippocampus

value: terminal

value: validation cohort


title: PBO-D1_Hp

value: non-infectious brain homogenate


title: PB115

value: PrP present


title: PB119


title: PB113


title: PB19-Hp

value: 8 wpi


title: SP-A1(6A2)-F-6hr-4

city: hershey

first: Nithyananda

last: Thorenoor

address: 500 University Drive

department: Pediatrics

institute: Penn State University College of Medicine

description:
6hrs_MvsF_deseq2_SP-A1(6A2)
sample name:
G374-03_S3_R1_001
x3

data_processing:
Illumina CASAVA pipeline (released version 1.8, Illumina) was used to obtain de-multiplexed sequencing reads (fastq files) passed the default purify filter.  These were further subjected to QuantSeq data analysis pipeline on a Bluebee genomics analysis platform (Bluebee, Cambridge, MA).  The differentially expressed genes (DEG) between males and females were identified by using edgeR test method and TCC v1.14.0 R package.  The DEG are selected based on their fold change and their P-value (P < 0.05) for further analyses.  We chose genes for further analysis based on their P-value (P < 0.05) and their expression levels (≥ 2 fold change) in AM cells from K. pneumoniae infected mice.  The fold differences for the identified genes between males and females were determined by dividing a specific individual male gene value by the corresponding specific female gene value and vice versa for the same gene.
The DEG are selected based on their fold change and their P-value (P < 0.05) for further analyses.  We chose genes for further analysis based on their P-value (P < 0.05) and their expression levels (≥ 2 fold change) in AM cells from K. pneumoniae infected mice.  The fold differences for the identified genes between males and females were determined by dividing a specific individual male gene value by the corresponding specific female gene value and vice versa for the same gene.
Supplementary_files_format_and_content: Matrix- excel sheet

source_name: Female mouse exposed K.penumoniae-Alveolar Macrophage (AM) cells

extract_protocol:
AM cells were isoalated from Broncho alveolar lavage, QuantSeq 3' mRNA-Seq Library Prep Kit FWD from Illumina (Lexogen, Vienna, Austria) was used to generate mRNA-Seq libraries as per manufacturer’s recommendation, followed by deep sequencing on an Illumina HiSeq-2500 as per the manufacturer’s instructions.
The synthesis of the second cDNA strand is performed by random priming, in a manner that DNA polymerase is efficiently stopped when reaching the next hybridized random primer, so only the fragment closest to the 3′ end gets captured for later indexed adapter ligation and PCR amplification.  The processed libraries were assessed for fragment size distribution and quantity using a BioAnalyzer High Sensitivity DNA kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 (Illumina) and run for 50 cycles using a single-read recipe (TrueSeq SBS kit v3, Illumina) according to the manufacturer's instructions.  Illumina CASAVA pipeline (released version 1.8, Illumina) was used to obtain de-multiplexed sequencing reads (fastq files) passed the default purify filter.  These were further subjected to QuantSeq data analysis pipeline on a Bluebee genomics analysis platform (Bluebee, Cambridge, MA).  The differentially expressed genes (DEG) between males and females were identified by using edgeR test method and TCC v1.14.0 R package.  The DEG are selected based on their fold change and their P-value (P < 0.05) for further analyses.  We chose genes for further analysis based on their P-value (P < 0.05) and their expression levels (≥ 2 fold change) in AM cells from K. pneumoniae infected mice.  The fold differences for the identified genes between males and females were determined by dividing a specific individual male gene value by the corresponding specific female gene value and vice versa for the same gene.

treatment_protocol: Humanized transgenic (hTG) mice that carried SP-A1 (6A2, 6A4), SP-A2 (1A0, 1A3) variant,  as well as SP-A knockout (KO) mice were used in this study.  They were 12 weeks old.  hTG mice were generated on the C57BL/6J SP-A (KO) background. The animals were exposed  to K. peumoniae for 6hrs.  A group of 4 animals (males, females) were exposed and alveolar macrophages (AM) were isolated after 6 h of recovery.

tag: exposure time

value: 6 hours

tag: Sex

value: Female

tag: strain

value: Alveolar Macrophage (AM) cells


title: SP-A1(6A2)-M-6hr-4

description:
6hrs_MvsF_deseq2_SP-A1(6A2)
sample name:
G374-07_S7_R1_001
x7

source_name: Male mouse exposed K.penumoniae-Alveolar Macrophage (AM) cells

value: Male

tag: cell type


title: SP-A1(6A2)-M-6hr-2

description:
6hrs_MvsF_deseq2_SP-A1(6A2)
sample name:
G374-05_S5_R1_001
x5


title: CTCF ChIP R133C KCl-JQ1-

description:
Genomic binding of CTCF
YTC102_CAGATC_L006

value: in vitro differentiated interneurons (INs)

tag: genotype/variation

value: MeCP2 R133C mutant

value: CTCF (K09622002, Diagenode)


title: SP-A1(6A2)-M-6hr-5

description:
6hrs_MvsF_deseq2_SP-A1(6A2)
sample name:
G374-08_S8_R1_001
x8


title: BRD4 ChIP

description:
Genomic binding of BRD4
YT-C63_CAGATC_L006

value: WT

tag: stimulation


title: SP-A1(6A2)-M-6hr-3

description:
6hrs_MvsF_deseq2_SP-A1(6A2)
sample name:
G374-06_S6_R1_001
x6


title: PB120

value: 6 weeks

value: intracerebral

tag: tissue


title: SP-A1(6A2)-F-6hr-2

description:
6hrs_MvsF_deseq2_SP-A1(6A2)
sample name:
G374-01_S1_R1_001
x1


title: SP-A1(6A2)-F-6hr-3

description:
6hrs_MvsF_deseq2_SP-A1(6A2)
sample name:
G374-02_S2_R1_001
x2


title: SP-A1(6A2)-F-6hr-1

description:
6hrs_MvsF_deseq2_SP-A2(1A3)
sample name:
G305_JF24_S68_R1_001


title: PB24-Hp

value: Hippocampus


title: PB23-Hp


title: SP-A2(1A3)-M-6hr-4

description:
6hrs_MvsF_deseq2_SP-A2(1A3)
sample name:
G305_JF23_S67_R1_001


title: PB22-Hp


title: PB-122_Hp

value: RML6 prions

value: main cohort


title: SP-A2(1A3)-M-6hr-3

description:
6hrs_MvsF_deseq2_SP-A2(1A3)
sample name:
G305_JF22_S66_R1_001


title: PB-121_Hp

value: terminal


title: SP-A1(6A2)-M-6hr-1

description:
6hrs_MvsF_deseq2_SP-A1(6A2)
sample name:
G374-04_S4_R1_001
x4


title: SP-A2(1A3)-M-6hr-1

description:
6hrs_MvsF_deseq2_SP-A2(1A3)
sample name:
G305_JF20_S64_R1_001


title: PB-128_Hp

value: non-infectious brain homogenate


title: PB-127_Hp

value: PrP present


title: SP-A2(1A3)-F-6hr-2

description:
6hrs_MvsF_deseq2_SP-A2(1A3)
sample name:
G305_JF17_S61_R1_001


title: PB17-Hp

value: 8 wpi

value: validation cohort


title: PB18-Hp


title: PB-126_Hp


title: SP-A1(6A4)-M-6hr-2

description:
6hrs_MvsF_deseq2_SP-A1(6A4)
sample name:
G305_JF13_S57_R1_001

value: 6 hours


title: PB-107_Hp

value: 20 wpi


title: SP-A1(6A4)-M-6hr-3

description:
6hrs_MvsF_deseq2_SP-A1(6A4)
sample name:
G305_JF14_S58_R1_001

value: Male

value: Alveolar Macrophage (AM) cells


title: SP-A2(1A3)-F-6hr-1

description:
6hrs_MvsF_deseq2_SP-A1(6A4)
sample name:
G305_JF16_S60_R1_001

value: Female


title: PB-110_Hp


title: PB-106_Hp


title: SP-A1(6A4)-M-6hr-1

description:
6hrs_MvsF_deseq2_SP-A1(6A4)
sample name:
G305_JF12_S56_R1_001


title: SP-A1(6A4)-F-6hr-4

description:
6hrs_MvsF_deseq2_SP-A1(6A4)
sample name:
G305_JF11_S55_R1_001


title: PB-105_Hp


title: SP-A1(6A4)-F-6hr-3

description:
6hrs_MvsF_deseq2_SP-A1(6A4)
sample name:
G305_JF10_S54_R1_001


title: PB-90_Hp

value: 18 wpi


title: SP-A2(1A3)-M-6hr-2

description:
6hrs_MvsF_deseq2_SP-A2(1A3)
sample name:
G305_JF21_S65_R1_001


title: PB-123_Hp


title: SP-A2(1A3)-F-6hr-4

description:
6hrs_MvsF_deseq2_SP-A2(1A3)
sample name:
G305_JF19_S63_R1_001


title: SP-A1(6A4)-F-6hr-2

description:
6hrs_MvsF_deseq2_SP-A1(6A4)
sample name:
G305_JF9_S53_R1_001


title: PB-89_Hp


title: SP-A2(1A3)-F-6hr-3

description:
6hrs_MvsF_deseq2_SP-A2(1A3)
sample name:
G305_JF18_S62_R1_001


title: SP-A1(6A4)-F-6hr-1

description:
6hrs_MvsF_deseq2_KO
sample name:
G305_JF8_S52_R1_001


title: PB-96_Hp


title: KO-M-6hr-4

description:
6hrs_MvsF_deseq2_KO
sample name:
G305_JF7_S51_R1_001

value: SP-A-Knockout (KO)


title: PB-95_Hp

value: 6 weeks


title: Ddx5 PAR-CLIP-ES-rep2

city: Guangzhou

first: Yaoyi

last: Li

state: Guangdong province

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island

institute: Guangzhou National Laboratory

description: CLIP

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to the mm10 genome using bowtie2 version 2.3.2.
Read coverage normalized to 1 x sequencing depth (also known as Reads Per Genomic Content (RPGC))
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: bigwig, bed peaks

source_name: mES

growth_protocol: mES cells and iPS cells were cultured in DMEM/High Glucose medium (Hyclone) supplemented with β-mercaptoethanol (10 mM), sodium pyruvate (10 mM), non-essential amino acids (10 mM), GlutaMAX (10 mM), 15% FBS (Gibco), 1000 U/ml leukemia inhibitory factor (LIF), and 1 μM MEK inhibitor PD0325901 and 3 μM GSK3 inhibitor CHIR99021. MEF cells were cultured in 10% FBS medium supplemented with non-essential amino acids (10 mM) and GlutaMAX (10 mM).

extract_protocol:
For ssDRIP-seq, nucleic were isolated from cells, followed by SDS/proteinase K treatment at 37°C overnight. Genome DNA was extracted by the phenol-chloroform method and precipitated with isopropanol. DNA fragmentation was performed overnight using endonucleases (MboI, MseI, AluI, DdeI), and the negative control was treated with RNase H (New England Biolabs) overnight. Briefly, 3.5 ug of DNA was bound with 10 ug of S9.6 antibody in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4˚C. 50 μl Protein G sepharose beads were added for 4 hours. Bound beads were washed 4 times in binding buffer and elution was performed in elution buffer (50 mM Tris pH 8, 10 mM EDTA, Proteinase K) for 45 min at 55˚C. DNA was purified and sonicated to 150 bp fragments. For RNA-seq, Total RNAs were extracted with TRIzol. For quantitative PCR, cDNAs were synthesized with ReverTra Ace (Toyobo) and oligo dT (Takara), and then analyzed by qPCR with SYBR green mixture (Genstar) and performed on a CFX Real-Time System (Bio-Rad). For ATAC-seq, a total of 50,000 cells were washed once with cold PBS and resuspended in 50 μl lysis buffer. The suspension of nuclei was then centrifuged at 500 g at 4˚C for 10 min, followed by the addition of 50 μl transposition reaction mix (10 μl TD buffer, 5 μl Tn5 transposase and 35 μl nuclease-free H2O). DNA was purified using a MinElute Kit (QIAGEN). For CLIP-seq, mES cells were irradiated at 400 mJ/cm2 with 254 nm UV light. The crosslinked cells were lysed and 15 μg of anti-DDX5 antibody was applied to pull down protein-RNA complexes. After micrococcal nuclease treatment and 3’ DNA adaptor ligation, the immunoprecipitated complexes were fractionated on a 4-12% NuPAGE Bis-Tris gel and transferred onto a nitrocellulose membrane. The DDX5-specific smear bands were excised with scalpels and treated with proteinase K (Thermo Fisher Scientific) prior to the extraction of respective RNA by using phenol and chloroform.
For ssDRIP-seq, the first adapter was ligated to the 3’ end of the ssDNA using Adaptase (Swift Biosciences) via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified. For RNA-seq, RNA sequencing libraries were constructed using the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme). For ATAC-seq, ATAC-seq libraries were first subjected to 5 cycles of pre-amplification. To determine the suitable number of cycles required for the second round of PCR, the library was assessed by quantitative PCR as described, and the library was then PCR amplified for the appropriate number of cycles. Libraries were purified with AMPure XP beads. For CLIP-seq, A 5’ RNA linker was then added to the isolated RNA and reverse transcribed by superscript reverse transcriptase III (Life Technologies, 18080-051). The cDNA strands are PCR-amplified to produce libraries for deep sequencing. L3-IR800-biotin DNA adaptor: 5’OH -ATC TCG TAT GCC GTC TTC TGC TTG TAA AAA AAA AAA A/iAzideN/A AAA AAA AAA AA/3Bio/-3’, 5’ RNA linker: 5’-(OH) rArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU(rN)(rN) (rN)rU(OH) -3’.

treatment_protocol: 10,000 MEFs at passage 2 were plated in a 12-well plate and then infected twice with retroviral stocks generated with Plat-E cells. 3 volumes of OSK supernatants and 1/4 volume of M transcription factor were mixed with 1 volume of fresh MEF medium containing polybrene at a final concentration of 8 μg/ml. The infection efficiency was tested by MEFs transduced with virus of pMXs-EGFP. pMXs-RNaseH1 and RNaseH1(D209N) were also transfected into OG2-MEFs by retrovirus generated from PlatE cells. For infecting OG2-MEFs, the medium of OG2-MEFs was replaced with 2.125 mL of infection mixture per well in a 12-well plate. Infected cells were cultured with iCD1 medium or mESC medium containing Vitamin C (Sigma; 50 μg/ml) post infection and renewed daily.

value: mES


title: OSKM-FLAG-D7-ATACseq-rep2

description: ATAC

source_name: OSKM-reprogramming cells, overexpression of Flag

value: reprogramming cell

tag: the day of reprogramming


title: PB-102_Hp

value: intracerebral

value: Hippocampus


title: OSKM-FLAG-D7-ATACseq-rep1

description: ATAC


title: SP-A1(6A4)-M-6hr-4

description:
6hrs_MvsF_deseq2_SP-A1(6A4)
sample name:
G305_JF15_S59_R1_001


title: KO-M-6hr-3

description:
6hrs_MvsF_deseq2_KO
sample name:
G305_JF6_S50_R1_001


title: PB-94_Hp

value: main cohort


title: PB-91_Hp

value: RML6 prions


title: PB-75_Hp

value: PrP present

value: 16 wpi


title: KO-M-6hr-2

description:
6hrs_MvsF_deseq2_KO
sample name:
G305_JF5_S49_R1_001


title: OSKM-D209N-D7-ATACseq-rep2

description: ATAC

source_name: OSKM-reprogramming cells, overexpression of RNase H1(D209N)


title: KO-M-6hr-1

description:
6hrs_MvsF_deseq2_KO
sample name:
G305_JF4_S48_R1_001


title: OSKM-FLAG-D3-ATACseq-rep1

description: ATAC


title: OSKM-D209N-D7-ATACseq-rep1

description: ATAC


title: PB-74_Hp