title: RNA-seq-FL-WT-TEL-AML-2

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-WT-TEL-AML-2


title: RNA-seq-FL-WT-TEL-AML-1

status: Public on Jul 19 2019

type: SRA

city: Lund

first: Mikael

last: Sigvardsson

address: Sölvegatan 19

country: Sweden

institute: Lund University

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-WT-TEL-AML-1

library_source: transcriptomic

data_processing:
RNA-Sequencing and data analysis: Libraries  were single-end sequenced on a NexSeq500.  For analysis of RNA-Seq experiments the reads were aligned to mouse reference  genome (mm10 / GRCm38) using STAR (2.6.0b-1) (Dobin, A etal. 2012),) with single read, standard settings. If not indicated, further  analyses were performed using the HOMER platform (v4.8, v4.10) (Heinz et al. 2010). For analysis of statistically significance among  differently expressed genes, the data was analyzed using analyzeRepeats.pl with the –  noadj option, followed by the getDiffExpression.pl  command using edgeR(3.12.0).
ChIP-sequencing and data analysis: For ChIP-Seq samples, Libraries were single-end sequenced on a NexSeq500, reads were aligned to the mm10 genome using default single end parameters for Bowtie2 (2.3.4.2) (Langmead, B. etal. 209 and 2012).  Aligned read files from ChIP seq experiments were analyzed with HOMER (v4.8, v4.10) (Heinz et al. 2010) to find peaks,  perform motif-enrichment, and  other analyses in the study.
Genome_build: mm10
Supplementary_files_format_and_content: peak-files, annotated peak-files and expressionmatrices in txt format

molecule: total RNA

organism: Mus musculus

source_name: Wt FL

extract_protocol:
For RNA-seq: Total RNA was isolated by use of RNAeasy Micro Kit (Qiagen, Hilden, Germany) according to  manufacturer’s recommendations. For ChIP-seq: Cells for transcription factor ChIP were fixed at room temperature with DSG for 30 min followed by 1percent formaldehyde/PBS for 10 minutes. Reaction was then quenched by adding glycine to 0.125 M. Cells were washed  pelleted and snap-frozen and stored at -80°C until ready for ChIP or used immediately for ChIP.   Nuclei for ChIP were isolated  by 10 min incubation in Nuclei Isolation buffer (50 mM Tris-pH 8.0, 60 mM KCl, 0.5percent NP40) + protease inhibitor cocktail (PIC) (Roche) on ice. Pelleted nuclei were dissolved in Lysis buffer (0.5percent SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8))+ PIC and sonicated on a Bioruptor (Diagenode) max power for 30s followed by 30 s rest. Sonication was followed by pelleting of debris and the supernatant was transferred to new tube and chromatin was diluted 5X in Dilution Buffer (1percent Triton, 2mM EDTA, 150 mM NaCl, 20 mM Tris-HCl (pH 8) + PIC). Anti-bodies were hybridized to ProteinA or G Dynabeads®  (LifeTechnologies)  and added to the diluted chromatin. ChIP was performed over night at 4°C. and subsequently washed (1 time with 500 μl Low Salt Immune Complex Wash Buffer, 1 time with 200 μl High Salt Immune Complex Wash Buffer, 1 time with 200 μl LiCl Immune Complex Wash Buffer, 2 times with 200 μl TE buffer) and eluted for 4 h at 65°C ( 20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1percent SDS, 100 μg RNase A and 50 μg proteinase K) treated and finally cleaned up using Zymo ChIP DNA Clean & Concentrator before ChIP-seq libary preparation.
RNA-seq: Libraries were constructed using NuGEN’s Ovation Ultralow Library systems (NuGEN Technologies, San Calros, CA) and were subsequently subjected to 76 cycles of NextSeq500 sequencing (Illumina, San Diego,CA). ChIP-Seq: Libraries were constructed using Illumina Truseq Nano DNA library preparation kit or by addition of Bioo-scientiffic Nextflex barcodes following standard procedures. Libraries were run on the Illumina NexSeq500.

treatment_protocol:
Cell culture:  Fetal liver cells were purified from wild-type, Ebf1 deficient, or Pax5 deficient fetus, and expanded on OP9 stromal cells in Opti-MEM supplemented with 10percent heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, 50μM β-mercaptoethanol, 10ng/ml KIT ligand, 10ng/ml Fms-like tyrosine kinase 3 ligand, and 10ng/ml Interleukin-7. Murine pre-B cell line, 230-238 cells were maintained in RPMI1640 supplimented with 10percent heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, and 50μM β-mercaptoethanol.    Infection: Retronectin coated 24-well plates were pre-inkubated with 500ul viral supernatant. Cells were harvested,  resuspended 500ul media and added to 500μl of virus supernatant. Polybrene was added to supernatant at concentration of 0.5μg/ml. Spin-infection was performed at 1800xg, for 90min at 32°C.
230-238-cells were cultured in RPMI1640 with UltraGlutamine (Lonza, Basel, Swiss) supplemented with 10percent heat-inactivated FCS, 20mM HEPES, 50mg/ml Gentamicin and 50mM β-ME.

tag: strain background

tag: genotype/variation

value: Wild type

tag: cell type

value: ProB

tag: cuture protocol

value: Cultured in Optimem +10percent FBS, 25mM HEPES, 50microg/ml Gentamicin, 50microM beta-mercaptoethanol FL, KL, IL7 on OP9

tag: antibody


title: RNA-seq-FL-WT-MiGR1-3

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-WT-MiGR1-3


title: CPT.SPH_1

city: Jingzhou

first: Tinghua

last: Huang

address: Jingmi Road #266

country: China

institute: Yangtze University

description: Conceptus spherical

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-Seq reads were mapped to pig reference mRNA (Sscrofa 10.2) using the SAGE data processiong software
Using R version 3.4.2 software to find differential genes
Clustering analysis was performed by first using K-means clustering method to separate the transcripts to several big groups, and then using Hierarchical clustering to build the internal structure of the transcripts within the groups according to method reported by Gu et al. (Gu et al. 2016).
The CLOVER software (Frith et al. 2004) with JASPAR PWM database (Khan et al. 2018) were used to identify over-represented transcription factor binding motifs for each cluster of genes.
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: Reads count (tab deli text)

organism: Sus scrofa

source_name: Conceptus spherical

extract_protocol:
Total RNA were extrated by PAXgene RNA kit using the standard protocols.All samples were quantified using a NanoDrop 2000 (Thermo-Fisher Scientific, Waltham, MA, USA), and assessed with an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). The RNA integrity number (RIN) of each sample was >8.
RNA libraries were prepared for sequencing using Super deepSAGE protocols

tag: tissue

value: Conceptus spherical

tag: replicate


title: RNA-seq-FL-WT-MiGR1-2

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-WT-MiGR1-2


title: RNA-seq-FL-WT-MiGR1-1

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-WT-MiGR1-1


title: RNA-seq-FL-WT-dn-IKZF1-2

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-WT-dn-IKZF1-2


title: RNA-seq-FL-WT-dn-IKZF1-3

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-WT-dn-IKZF1-3


title: ChIP-seq-230-238-a-IKZF1-ChIP

description:
Peaks-230-238-a-IKZF1-vs-Input
Annotated-230-238-IKZF1-15-norm-tag-peaks

library_source: genomic

molecule: genomic DNA

source_name: 230-238 murine PreB celline

tag: cell line background

value: Abelson transformed PreB cell-line

value: PreB

value: Cultured in RPMI1640 + UltraGlutamine +10percent FBS, 20mM HEPES, 50ug/ml Gentamicin and 50uM beta-ME.

value: Rabbit anti-Ikzf1 polyclonal IgG [ab26083, Abcam]


title: AM_7

description: Adrenal medulla

source_name: Adrenal medulla

value: Adrenal medulla


title: ChIP-seq-230-238-ChIP-Input-2

description:
Peaks-230-238-a-RUNX1-vs-Input
Peaks-230-238-a-Pax5-vs-Input


title: CPT.SPH_6

description: Conceptus spherical


title: CPT.SPH_4

description: Conceptus spherical


title: NS3 colony p13_repl3

type: RNA

city: Columbus

first: Kay

last: Huebner

address: 460 W. 12th Ave

country: USA

institute: The Ohio State University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

label: biotin

source_name: NS3 colony p13

label_protocol: Total RNA (+/+kd2 p14, −/−kd3 p48, NS3 colony p13) was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). A 100‐ng aliquot of total RNA was linearly amplified. Then 5.5 μg cDNA was labeled and fragmented using the GeneChip WT PLUS reagent kit (Affymetrix, Santa Clara, CA, USA) following the manufacturer's instructions. Labeled cDNA targets were hybridized to the Affymetrix GeneChip Mouse Transcriptome Array 1.0 for 16 h at 45°C, with rotation at 60 rpm. Arrays were washed and stained using the Fluidics Station 450 (Ohio State University Medical Center Shared Facility, Columbus, OH, USA) and scanned using the GeneChip Scanner 3000 (Ohio State University Medical Center Shared Facility, Columbus, OH, USA). For gene expression analysis, arrays were normalized using the RMA algorithm in Expression Console and comparisons made in Transcriptome Analysis Console (Affymetrix).

growth_protocol: Mouse kidney cell lines were established by culturing minced mouse kidney tissue from three Fhit +/+ C57Bl6 (B6 +/+ kd cell lines 1, 2, 3) and three Fhit −/− (B6x129SvJ backcross, >99% B6 at genomic level)17 5‐week‐old mice (−/− kd cell lines 2, 3, 4). After emergence of epithelial cells from minced kidney fragments, cells could be subcultured; these epithelial kidney cell lines did not show an obvious crisis phase but rather grew steadily from first subculturing. Early passage +/+ and −/− kidney lines did not show obvious morphological or proliferation differences (Figs S1,S2). However, late passage −/− kidney lines grew more rapidly than +/+ (Fig. S2). RNA, DNA, and protein were isolated at alternate passages. To establish nutritionally stressed (NS) cell lines, early passage cells were maintained without replenishing medium for several months, followed by fresh medium and culture of surviving colonies; +/+ cell lines did not survive nutritional stress. The NS cell lines exhibited new morphological features as they transitioned from epithelial to mesenchymal phenotype (Fig. S1). Nutritionally stressed cells also grew to a higher density than +/+ cells (Fig. S2). Some DS and NS cell lines formed colonies in soft agar. Colonies were isolated and replated to establish colony‐forming cell lines (Table 1 summarizes cell line characteristics). The mouse cell lines were cultured in MEM with 5% FBS and 100 μg/mL gentamicin. H1299, a human non‐small‐cell lung carcinoma cell line, was cultured in MEM with 10% FBS and 100 μg/mL gentamicin.

extract_protocol: none provided by the submitter

treatment_protocol: nutritional stress cell lines were isolated from -/-kd3 line after maintenance without replenishing medium for 3 months, followed by fresh medium and continued subculture; Carcinogenic stress cell lines were established after treatment with 20 uM DMBA. Colony forming cell lines were established after excision of soft agar colonies and plated for subculture.

tag: cell line

value: derived from -/-kd3

tag: treatment

value: nutritional stress followed by soft agar colony assay

tag: stage of invasiveness

value: in-vitro invasive cell line (anchorage-independent colony formation occurs)


title: RNA-seq-FL-Pax-het-TEL-AML-3

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-Pax-het-TEL-AML-3

source_name: Pax5+/- FL

value: Pax5 heterozygout knock out


title: -/- kd3 p48_repl3

value: Parent cell line

value: none; solely subcultured

value: non-invasive


title: -/- kd3 p48_repl1


title: NS3 colony p13_repl1


title: CPT.SPH_2

description: Conceptus spherical


title: -/- kd3 p48_repl2


title: AZie-FK16_WT2: Female WT 2

city: Ann Arbor

first: Pierre

middle: A.

last: Coulombe Ph.D..

state: MI

address: 109 Zina Pitcher Place

department: Cell & Developmental Biology

institute: University of Michigan

hyb_protocol: 17 hours at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Affymetrix CEL files were extracted with the Partek GS 6.6 platform, excluding the Affymetrix JUC junction probes, and their data RMA and quantile-normalized to create log2 transcript signal values, which were used in subsequent ANOVA analysis. Transcript annotation was subsequently updated.

source_name: Paw skin

label_protocol: RNA was labeled with the Affymetrix GeneChip WT PLUS Reagent Kit using the manufacturer's protocol.

growth_protocol: Mice were housed in under specific pathogen free conditions, fed chow and water ad libitum. Mice were aged to 8 weeks old before harvest. Mice were genotyped at the  Krt16 locus at the time of weaning (~4 weeks of age). Krt16 null mice were generated by our laboratory (Lessard and Coulombe, JID, 2012) using embryonic stem cells obtained from KOMP where the Krt16 locus was disrupted by replacement of the Krt16 coding sequence with the bacterial LacZ gene.

extract_protocol: Paw skin was removed from whole paw at time of harvest, homogenized in Trizol, then RNA was extracted using Trizol protocol. Purification and Dnase digestion was done using Clontech NucleoSpin RNA Purification kit.

treatment_protocol: Not applicable.

tag: strain

tag: age

value: 8 weeks

tag: Sex

value: Female

tag: genotype

value: Krt16 WT

tag: lesion status

value: Normal

value: Paw skin


title: AZie-FK16Nul1: Female Krt16 Null 1

value: Krt16 Null

value: Lesion


title: AM_6

description: Adrenal medulla


title: AZie-FK16Nul2: Female Krt16 Null 2


title: AZie-FK16_WT1: Female WT 1


title: RNA-seq-FL-Pax-het-MiGR1-3

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-Pax-het-MiGR1-3

value: ProB

value: Cultured in Optimem +10percent FBS, 25mM HEPES, 50microg/ml Gentamicin, 50microM beta-mercaptoethanol FL, KL, IL7 on OP9


title: RNA-seq-FL-Pax-het-TEL-AML-1

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-Pax-het-TEL-AML-1


title: RNA-seq-FL-WT-dn-IKZF1-1

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-WT-dn-IKZF1-1

value: Wild type


title: RNA-seq-FL-Pax-het-MiGR1-2

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-Pax-het-MiGR1-2


title: AM_8

description: Adrenal medulla

value: Adrenal medulla


title: RNA-seq-FL-Pax-het-dn-IKZF1-3

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-Pax-het-dn-IKZF1-3


title: RNA-seq-FL-Pax-het-dn-IKZF1-2

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-Pax-het-dn-IKZF1-2


title: RNA-seq-FL-Pax-het-dn-IKZF1-1

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-Pax-het-dn-IKZF1-1


title: Postnatal BDE-47, C88

city: Amherst

first: Alexander

last: Suvorov

state: MA

address: 149A Goessman, 686 N.Pleasant Str

department: Environmental Health Sciences

institute: University of Massachusetts

description: Postnatal BDE-47 vs Control.xlsx

data_processing:
Read filtering, trimming and de-multiplexing were performed using the BaseSpace cloud computing service supported by Illumina (https://basespace.illumina.com/home/index).
Reads were mapped to the reference mouse genome (MM10) using TopHat 2 aligner with Bowtie 2.
Aligned reads were then used for assembly of novel transcripts with Cufflinks 2.1.1 and differential expression of novel and reference transcripts with Cuffdiff 2.1.1
Genome_build: MM10
Supplementary_files_format_and_content: Excel spreadshit containing read coordinates, gene name, Log2(FPKM), Log2(ratio), and q-values.

source_name: Liver

growth_protocol: Timed pregnant CD-1 mice were obtained from Charles River Laboratories (Kingston, NY, USA) at pregnancy day 6 and housed in a temperature (23±2°C)- and humidity (40±10%)-controlled environment, with a 12-h light/dark cycle, and food and water available ad libitum.

extract_protocol:
Total RNA was isolated from liver samples using TRIzol reagent (Invitrogen) and quantified using a NanoDrop 1000 instrument (Thermo Fisher Scientific, Wilmington, DE).
Samples of RNA isolated from liver tissue with integrity values > 9 were used for library preparation. RS-122-2101-TruSeq® Stranded mRNA LT – SetA kit (Illumina, San-Diego, CA) was used to isolate intact poly(A)+ RNA from 4 µg of total RNA and to construct strand-specific libraries with multiplexing indexes.
RNA-seq was performed using NextSeq500 sequencing system (Illumina, San-Diego, CA) in the Genomic Resource Laboratory of the University of Massachusetts – Amherst. cDNA libraries were single-end sequenced in 76 cycles using a NextSeq 500 Kit v2 (FC-404-2005, Illumina, San-Diego, CA) in one multiplex run (3-4 samples per exposure group).

treatment_protocol: The dams were assigned to one of three treatment groups (n=10 per group) based on weight match. The control group was exposed to vehicle – tocopherol-stripped corn oil (MP Biomedicals, Solon, OH) from pregnancy day 8 till postpartum day 21. The prenatal exposure group received 1 mg/ml solution of BDE-47 (AccuStandard, Inc., New Haven, CT; 100% purity) in tocopherol-stripped corn oil from pregnancy day 8 through delivery and then vehicle only from the day of delivery till postpartum day 21. Neonatal exposure group received only vehicle from gestational day 8 till delivery and was then exposed to 1 mg/ml solution of BDE-47 in tocopherol-stripped corn oil through postpartum day 21. Either vehicle or BDE-47 solution was orally administered daily via micropipette in a volume of 1 µl/gram body weight (BW) resulting in exposures to 1 mg/kg BW/day during pre- or neonatal periods.

value: Liver

value: exposed to corn oil from pregnancy day 8 till delivery and then to 1 mg/kg BDE-47 till postpartum day 21

value: male


title: AM_5

description: Adrenal medulla


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 48 [1156]

city: DAVIS

first: PEROT

last: SAELAO

state: CA

address: One Shields Ave, 3307 Meyer Hall

institute: UC DAVIS

data_processing:
Adapter contamination trimmed using trimmomatic
aligned to galgal 5 using tophat2
counts assembled using htseq
Genome_build: galgal5
Supplementary_files_format_and_content: read counts

organism: Gallus gallus

source_name: Fayoumi_NDV Infection and heat stress_Harderian gland

growth_protocol: Chickens were reared for 13 days under standard conditions then heat treated at 38C and 60% humidity on day 14. The heat treatment continued till the conclusion of the study. At 21 days of age the birds were innoculated with 10^7 EID50 of La Sota NDV.

extract_protocol:
Total RNA was extracted from the Harderian gland of four individuals per treatment and genetic line for each of the three time points. The Harderian gland was homogenized in ice cold TRIzol (ThermoFisher Cat#15596026) and processed using a standard phenol:chloroform method and precipitated in 100% ethanol. The RNA pellet was then dissolved into water and treated with DNase I (ThermoFisher Cat#EN0521).
Strand specific RNA library preparation was prepared exactly as stated in the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB Cat#E7420S). Library validation and quantification was done using the Agilent Bioanalyzer High Sensitivity Kit (Agilent Cat#5067-4626) and Qubit dsDNA HS Assay kit (ThermoFisher Cat#Q32854).

treatment_protocol: 38C and 60% humidity and  innoculated with 10^7 EID50 of La Sota NDV for treated birds.

tag: breed

value: Fayoumi

value: NDV Infected and heat treated

tag: time point

value: 10 days post-infection

value: Harderian gland


title: RNA-seq-FL-Pax-het-MiGR1-1

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-Pax-het-MiGR1-1

tag: strain background

tag: genotype/variation

value: Pax5 heterozygout knock out


title: AZie-MK16Nul2: Male Krt16 Null 2

value: 8 weeks

value: Male


title: NS3 colony p13_repl2

value: derived from -/-kd3

value: nutritional stress followed by soft agar colony assay

value: in-vitro invasive cell line (anchorage-independent colony formation occurs)


title: AZie-MK16Nul1: Male Krt16 Null 1

value: Krt16 Null

value: Lesion

value: Paw skin


title: Postnatal BDE-47, C39

description: Postnatal BDE-47 vs Control.xlsx


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 46 [1153]

value: 6 days post-infection


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 47 [1155]


title: AM_4

description: Adrenal medulla

value: Adrenal medulla


title: Prenatal BDE-47, B84

description: Prenatal BDE-47 vs Control.xlsx

value: Liver

value: exposed to BDE-47 in corn oil from pregnancy day 8 till delivery and then to oil only till postpartum day 21


title: AZie-MK16_WT1: Male WT 1

value: Krt16 WT

value: Normal


title: Postnatal BDE-47, C18

description: Postnatal BDE-47 vs Control.xlsx

value: exposed to corn oil from pregnancy day 8 till delivery and then to 1 mg/kg BDE-47 till postpartum day 21

value: male


title: RNA-seq-FL-Pax-het-TEL-AML-2

description:
Raw-RNA-seq-count data-from-HOMER-AnalyzeRepeats
RNA-seq-FL-Pax-het-TEL-AML-2

value: Pax5 heterozygout knock out

tag: cell type

value: ProB

tag: cuture protocol

value: Cultured in Optimem +10percent FBS, 25mM HEPES, 50microg/ml Gentamicin, 50microM beta-mercaptoethanol FL, KL, IL7 on OP9


title: Postnatal BDE-47, C28

description: Postnatal BDE-47 vs Control.xlsx

tag: tissue


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 45 [1152]

source_name: Fayoumi_Control_Harderian gland

value: Fayoumi

value: Control

value: 10 days post-infection

value: Harderian gland


title: Prenatal BDE-47, B82

description: Prenatal BDE-47 vs Control.xlsx


title: AM_1

description: Adrenal medulla

tag: replicate


title: AZie-MK16_WT2: Male WT 2

value: 8 weeks

value: Male


title: AM_3

description: Adrenal medulla


title: AM_2

description: Adrenal medulla


title: Prenatal BDE-47, B21

description: Prenatal BDE-47 vs Control.xlsx


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 44 [1147]

value: 2 days post-infection


title: AC_7

description: Adrenal cortex

source_name: Adrenal cortex

value: Adrenal cortex


title: AC_8

description: Adrenal cortex


title: Control, A33

description: Prenatal BDE-47 vs Control.xlsx, Postnatal BDE-47 vs Control.xlsx

value: Liver

value: exposed to tocopherol striped corn oil from pregnancy day 8 till postpartum day 21


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 43 [1145]

value: female

value: NDV Infected and heat treated

value: 6 days post-infection


title: Prenatal BDE-47, B12

description: Prenatal BDE-47 vs Control.xlsx

value: exposed to BDE-47 in corn oil from pregnancy day 8 till delivery and then to oil only till postpartum day 21

value: male


title: AC_6

description: Adrenal cortex


title: Control, A30


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 42 [1142]


title: AC_5

description: Adrenal cortex


title: Control, A9


title: Control, A2


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 41 [1138]


title: Ly5.1.d7_rep2

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
Sequence reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped read pairs (fragments) were retained.
Genewise counts were obtained using featureCounts. Fragments overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped fragments) value of 0.5 or greater in at least two libraries.
Counts were converted to log2 counts per million(CPM), quantile normalized and precision weighted with the ‘voom’ function of the limma package. After normalization, the expression levels were converted into log2 reads per kilobase per million(RPKM), and a linear model was fitted to each gene. Empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.15 or less.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-RPKM values for each library. The supplementary file 'Supp_Raw_Counts.txt' includes raw read counts for genes in each library.

source_name: Lung

extract_protocol:
RNA purification was performed following the manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the Smart Seq v4 Low RNA v3.0  Sample preparation kit (Clontech) following the manufacturer’s instructions.

treatment_protocol: Challenged with B16 melanoma cells and lung harvested on day 7 after inoculation. Cells were purified by high speed flow cytometric sorting.

value: Ly5.1 (WEHI)

value: Lung

value: NK1.1+ NK cells


title: Ly5.1.d7_rep1


title: AC_4

description: Adrenal cortex


title: B6.d7_rep2

value: wildtype


title: Ly5.1.naive_rep1


title: Ly5.1.naive_rep2


title: B6.d7_rep1


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 40 [1132]

value: Fayoumi


title: AC_3

description: Adrenal cortex


title: B6.naive_rep1


title: B6.naive_rep2


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 39 [1131]

value: Harderian gland


title: AC_2

description: Adrenal cortex


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 36 [1124]

value: 10 days post-infection


title: AC_1

description: Adrenal cortex


title: 8week_HBx,Src(p53-)_DIO_sample 2

city: Hsinchu

first: Yong Chun

last: Luo

address: Boai Street

country: Taiwan

institute: National Chiao Tung University

description:
8wTRIDIO11
Treatment of overfed in 8week HBx,Src(p53-) fish, sample 2.

data_processing:
Reads were trimmed and Read quality was checked using FastQC (v0.11.5).
Reads were aligned to the zebrafish genome (GRCz10/danRer10) using HISAT2 (v2.1.0) with parameters --mm --dta -x -1 -2 -S
SAMtools (v1.7) was then converted SAM files to BAM files and sorted.
BAM files were transmitted to StringTie (v1.3.4d) for transcript assembly.
The expression levels of all transcripts were estimated and calculated by StringTie and ballgown (v2.16.0) in R (v3.5.3).
Genome_build: GRCz10/danRer10
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values for each Sample using ballgown package.

organism: Danio rerio

growth_protocol: The AB zebrafish strain (Danio rerio), Tg(fabp10a:src,p53-), Tg(fabp10a:HBx,p53-), and Tg(fabp10a:HBx,src,p53-), were used and growth for 8 weeks.

extract_protocol:
Total RNA was isolated by NucleoSpin® RNA kit (MACHEREY-NAGEL, US) following the manufacturer manual, and RNA samples was eluted in 40 μl RNase-free water. RNA quantity and purity were assessed using NanoDrop ND-1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7.
Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly, fragmentation was performed at elevated temperature using divalent cations after mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-), and DNA Polymerase I and RNase H, respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next, the adaptor-ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then, the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The three months old of four types of fish were fed using three different feeding methods: normal diet, overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily, and high-fat diet fish food (one spoon, about 0.22g) three times daily. For 8 weeks, the zebrafishes were sacrificed and liver specimens were collected.

tag: strain/background

value: AB

tag: diet

value: Overfed


title: Cnr_42DPA_Input_ Rep3

city: Beijing

first: Leilei

last: Zhou

state: Beijing

address: No. 20 Nanxincun, Xiangshan, Haidian District

department: Institute of botany

institute: Chinese Academy of Sciences

description:
grown in a standard greenhouse
Cnr_42DPA_Peaks_Rep3.tsv

data_processing:
The quality of raw sequencing reads in m6A-seq was assessed using FastQC tool (Version 0.11.7). Adaptors and low-quality bases with a score < 20 located in the 3’-end were trimmed from all raw reads by Cutadapt software (version 1.16). After trimming, reads containing ambiguous nucleotides or with a length < 18 nt were filtered out by Trimmomatic (version 0.30). The remaining reads were analyzed by using FastQC tool once again to ensure sufficient quality assessment.
Reads alignment was performed with BWA (version 0.30) by using the tomato build_SL3.0 as a reference genome, and the ITAG3.2_release as a reference annotation (ftp://ftp.solgenomics.net/tomato_genome/).
Mapping Quality (MAPQ) of all aligned reads was concurrently calculated and only uniquely mapped reads with a MAPQ ≥ 13 were remained for the subsequent analysis for each sample (Dominissini et al., 2012).
MACS software (version 2.0.10) was used for the m6A peak identification in each anti-m6A immunoprecipitation sample with the corresponding input sample serving as a control. A stringent cutoff threshold for MACS-assigned false discovery rate (FDR) < 0.05 was used to obtain high-confidence peaks.
Genome_build: Tomato build_SL3.0
Supplementary_files_format_and_content: Tab-delimited tsv files include called peaks for each Sample

organism: Solanum lycopersicum

source_name: Total RNA from 42 DPA Cnr pericarps

extract_protocol:
Total RNA was extracted with hot-phenol reagent from 39 DPA and 42 DPA WT pericarps and 42 DPA Cnr mutant peicarps. mRNA was isolated from the total RNA and then fragmented, followed by immunoprecipitation with specific anti-m6A antibody.
For library construction, 50 ng of immunoprecipitated mRNAs or pre-immunoprecipitated mRNAs (input control) were used for library construction with NEBNext ultra RNA library prepare kit for illumina (NEB, E7530). High-throughput sequencing was performed on the illumina HiSeq X sequencer with a paired-end read length of 150 bp according to the standard protocols.

value: Colorless non-ripening

value: pericarps

tag: developmental stage

value: 42 DPA


title: Cnr_42DPA_Input_ Rep2

description:
grown in a standard greenhouse
Cnr_42DPA_Peaks_Rep2.tsv


title: Cnr_42DPA_Input_ Rep1

description:
grown in a standard greenhouse
Cnr_42DPA_Peaks_Rep1.tsv


title: 8week_HBx,Src(p53-)_NOR_sample 2

description:
8wTRINOR11
Treatment of normal diet in 8week HBx,Src(p53-) fish, sample 2.

source_name: 8week_HBx,Src(p53-)_Normal diet

value: Liver

value: Normal diet


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 35 [1122]

tag: treatment

value: Control

value: 2 days post-infection


title: Cnr_42DPA_IP_ Rep3

tag: strain


title: 8week_HBx,Src(p53-)_NOR_sample 1

description:
8wTRINOR3
Treatment of normal diet in 8week HBx,Src(p53-) fish, sample 1.


title: 8week_HBx,Src(p53-)_DIO_sample 1

description:
8wTRIDIO7
Treatment of overfed in 8week HBx,Src(p53-) fish, sample 1.


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 37 [1125]

value: male

value: NDV Infected and heat treated


title: Cnr_42DPA_IP_ Rep2


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 34 [1118]

value: female


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 33 [1117]


title: Cnr_42DPA_IP_ Rep1


title: WT_42DPA_Input_ Rep3

description:
grown in a standard greenhouse
WT_42DPA_Peaks_Rep3.tsv

source_name: Total RNA from 42 DPA WT pericarps

value: Ailsa Craig


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 32 [1116]


title: WT_42DPA_Input_ Rep2

description:
grown in a standard greenhouse
WT_42DPA_Peaks_Rep2.tsv


title: 8week_Src(p53-)_FAT

description:
8wSRCFAT4
Treatment of high fat diet in 8week Src(p53-) fish.

source_name: 8week_Src(p53-)_High fat diet

value: High fat diet


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 38 [1126]

value: Fayoumi

value: 6 days post-infection


title: WT_42DPA_Input_ Rep1

description:
grown in a standard greenhouse
WT_42DPA_Peaks_Rep1.tsv


title: 8week_Src(p53-)_DIO

description:
8wSRCDIO11
Treatment of overfed in 8week Src(p53-) fish.


title: 8week_Src(p53-)_NOR_sample 2

description:
8wSRCNOR9
Treatment of normal diet in 8week Src(p53-) fish, sample 2.

source_name: 8week_Src(p53-)_Normal diet


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 31 [1114]

value: Harderian gland


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 30 [1113]

value: 10 days post-infection


title: WT_42DPA_IP_ Rep2


title: WT_42DPA_IP_ Rep1


title: 8week_Src(p53-)_NOR_sample 1

description:
8wSRCNOR5
Treatment of normal diet in 8week Src(p53-) fish, sample 1.

value: AB


title: WT_39DPA_Input_ Rep1

description:
grown in a standard greenhouse
WT_39DPA_Peaks_Rep1.tsv

source_name: Total RNA from 39 DPA WT pericarps

value: 39 DPA


title: WT_42DPA_IP_ Rep3

value: pericarps


title: 8week_HBx(p53-)_FAT

description:
8wHBxFAT12
Treatment of high fat diet in 8week HBx(p53-) fish.

source_name: 8week_HBx(p53-)_High fat diet


title: WT_39DPA_Input_ Rep3

description:
grown in a standard greenhouse
WT_39DPA_Peaks_Rep3.tsv


title: WT_39DPA_IP_ Rep2

description:
grown in a standard greenhouse
WT_39DPA_Peaks_Rep2.tsv


title: 8week_HBx(p53-)_DIO

description:
8wHBxDIO13
Treatment of overfed in 8week HBx(p53-) fish.

value: Overfed


title: WT_39DPA_IP_ Rep1


title: WT_39DPA_IP_ Rep3


title: WT_39DPA_Input_ Rep2


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 28 [1110]


title: 8week_HBx(p53-)_NOR_sample 2

description:
8wHBxNOR15
Treatment of normal diet in 8week HBx(p53-) fish, sample 2.

source_name: 8week_HBx(p53-)_Normal diet

value: Liver


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 27 [1106]


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 25 [1103]


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 26 [1105]


title: 8week_HBx(p53-)_NOR_sample 1

description:
8wHBxNOR2
Treatment of normal diet in 8week HBx(p53-) fish, sample 1.

value: Normal diet


title: CP17_cy3

city: San Diego

first: Goran

last: Bozinovic

address: 3370 Dale Street

institute: Boz Institute

hyb_protocol: Labeled aRNA samples (2 pmol dye/µl) were hybridized to slides in 10 µl of hybridization buffer [50% formamide buffer, 5x SSPE, 1% sodium dodecyl sulfate, 0.2 mg/ml bovine serum albumin, 1 mg/ml denatured salmon sperm DNA (Sigma), and 1 mg/ml RNase free poly(A) RNA (Sigma)] for 44 hours at 42° C.  Slides were prepared for hybridization by blocking in 5% ethanolamine, 100 mM Tris pH 7.8, and 0.1% SDS added just before use for 30 minutes at room temperature, washed for one hour in 4x SSC, 0.1% SDS at 50° C, and then boiled for 2 minutes in distilled water to denature the cDNAs.

scan_protocol: Arrays were scanned using  a ScanArray Express 4000 (Perkin Elmer).  Resulting 16 bit Tiff Images were quantified using ImaGene® (Biodiscovery, Inc.) spotfinding software.

data_processing: A linear mixed model was used to test for the difference between “clean” and polluted” embryo populations. Log2 measures of gene expression were normalized using liner mixed model in SAS (JMP v6.0.0. with microarray platform beta-version in SAS v9.1.3) to remove the effect of a dye (fixed effects) and array (random effects), following a spatial Lowess transformation that accounts for signal intensity and spatial bias.  Normalized data were modeled by residual maximum likelihood on gene-by-gene basis using linear mixed model in SAS using PROC MIXED.  The normalized data was analyzed based on the model Yij = μ + Ai + Dj + (AXD)ij + Eij, where μ is the sample mean, Ai is the effect of ith array (i = 1-20), Dj is the effect of the jth dye (Cy3 or Cy5), (AXD)ij is the array-dye interaction (spot effect), and Eij is stochastic error. Residuals form this model, representing relative “normalized” expression levels, were used for the gene-by-gene analysis of treatment effect (treatment = CC, CP, PC, and PP). This normalized data was modeled using treatment, population nested in the treatment and dye as fixed effects, and array and spot nested in array as random effects, based on the model Rijkm = μ + Ai + Dj + Tk +S(A)mi + Eijkm, where Tk is the kth treatment (CC, CP, PC, or PP), and S(A)m in the mth spot nested in array.

organism: Fundulus heteroclitus

label_protocol: RNA for hybridization was prepared by one round of amplification (aRNA) using Ambion’s Amino Allyl MessageAmp aRNA Kit to form copy template RNA by T7 amplification.  Amino-allyl UTP was incorporated into targets during T7 transcription, and resulting amino-allyl aRNA was coupled to Cy3 and Cy5 dyes (GE Healthcare, Piscataway, NJ, USA).

growth_protocol: Adult Fundulus were captured from the Elizabeth River, VA (polluted Superfund site; N 36° 10.551’; W 75° 56.533”)  and Magotha, VA (clean, reference site; N 36° 48.473’; W 76° 17.654’) by minnow traps in March 2004 and transported under controlled temperature and aeration condition to the NCSU Aquatic Laboratory.  Fish were acclimated to common conditions of 20° C and 15 ppt salinity in 40-gal flow-through re-circulating aquatic system tanks for 4 months prior to laboratory spawning.  Effluent from the tanks was passed through an activated charcoal filter system and 20% water was changed weekly.  Tanks were maintained, and fish were fed (brine shrimp flake, blood meal flake, and Spirulina flake - FOD, Aquatic Biosystems) daily and monitored for heath.  Fish were maintained under a pseudo-summer cycle (8 h dark / 16 h light). Eggs and sperm were collected from adult fish maintained in the laboratory for nine months.  Eggs from females from Elizabeth River (ER) and Magotha Bay (MB) were fertilized by sperm collected from males from ER and MB,  resulting in “clean / clean” (CC),  hybrid “clean / polluted” (CP),  hybrid “polluted / clean” (PC), and polluted (PP) family sets with multiple embryo offspring.The first letter in each family sets denotes the female, the second is the make; for example, a CP hybrid embryo is generated by fetrilizing an egg from the adult female collected at the clean site by the sperm of the male collected at the polluted site (clean egg x polluted sperm = CP embryo; polluted eggs x clean sperm = PC embryo).  Developing “polluted” (PP), clean (CC), and hybrid (CP and PC) embryos were cultured in the environmental chamber (818 Low Temperature Illuminated Incubator, Precision Scientific, USA) at 25°C and 16 h light / 8 h dark cycle.  Embryo progress was monitored daily by examining representative stages using dissecting stereo microscope (Nikon SME1500, Japan), and the time to stage, normal vs. abnormal development, and mortality were noted.  Unfertilized eggs, malformed and/or   dead embryos were removed from the population, and times and stages of arrest and abnormal development were recorded accordingly. Once the normally-developing embryos reached late organogenesis stage (Stage 31, Armstrong and Childs 1965), images of embryos were recorded by Micropublisher 5.0 RTV Camera (QImaging) fitted on the stereo microscope, and the embryos were immediately placed in the pre-chilled 1.5 ml epindorf tubes and snap-frozen at -80°C prior to subsequent RNA extraction and analysis..  Embryos that successfully reached 2-cell stage within a predetermined time (25) were used in the sediment extract exposure experiment.  All experiments were performed according to approved protocols (Institutional Animal Care and Use Committees, North Carolina State University and Duke University).

extract_protocol: Individual embryo identified during late organodifferentation stage  (stage 31; Bozinovic  et al., 2011;  Armstrong and Childs, 1965) were utilized for RNA isolation, amplification, labeling, and microarray hybridization.  Embryo RNA was extracted using a Trizol buffer (Invitrogen, Carlsbad, CA, USA) followed by purification using the Qiagen RNeasy Mini Kit (Qiagen Inc., Valencia, CA, USA).

treatment_protocol: Developing sensitive , resistant, and hybrid embryos were maintained in an environmental chamber (818 Low Temperature Illuminated Incubator, Precision Scientific, USA) at 25°C and 16 h light / 8 h dark cycle.  Embryo condition and development were monitored daily by examining representative stages using a dissecting stereo microscope (Nikon SME1500, Japan), and time to stage, % normal versus abnormal development, and % mortality were noted.  Unfertilized eggs, malformed and/or dead embryos were removed from the population, and times and stages of arrest and abnormal development were recorded accordingly.  Criteria for time-to-stage was based on >80% success rate of reference embryos cultured in the vials with 15 ppt filtered seawater as well as established developmental timelines .  Once the normally developing embryos reachedlate organodifferentiation stage (stage 31; Bozinovic et al., 2011; Armstriong and Childs, 1965), images of embryos were recorded using a Micropublisher 5.0 RTV Camera (QImaging) fitted on the stereo microscope, and heart rates and time-to-stage measurement were recorded; embryos were then placed in pre-chilled 1.5 ml eppendorf tubes and snap-frozen at -80°C for chemical and microarray analyses (stages 31)  prior to subsequent RNA extraction and analysis.

tag: population

value: Magotha Bay, VA / Elizabeth River, VA

value: Whole embryo

value: CP

tag: Stage


title: PC25_cy3

value: Elizabeth River, VA / Magotha Bay, VA

value: PC


title: CC5_cy5

value: Magotha Bay, VA

value: CC


title: 8week_WT_DIO

description:
8wWTDIO16
Treatment of overfed in 8week WT fish.

value: WT


title: 8week_WT_NOR_sample 2

description:
8wWTNOR20
Treatment of normal diet in 8week WT fish, sample 2.

source_name: 8week_WT_Normal diet


title: CP17_cy5


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 23 [1055]

source_name: Leghorn_NDV Infection and heat stress_Harderian gland

value: Leghorn

tag: Sex

value: male

value: NDV Infected and heat treated

value: 2 days post-infection


title: RNA-Seq of Fayoumi Chicken Harderian gland Individual 29 [1111]

value: Fayoumi

value: female

value: Control

value: 6 days post-infection

value: Harderian gland


title: PP40_cy3

value: PP


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 22 [1052]

source_name: Leghorn_Control_Harderian gland


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 24 [1057]


title: CC7_cy3

value: Whole embryo


title: CC7_cy5


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 20 [1048]


title: PP40_cy5


title: 8week_WT_FAT

description:
8wWTFAT12
Treatment of high fat diet in 8week WT fish.

source_name: 8week_WT_High fat diet

value: AB

value: Liver

value: High fat diet


title: PC27_cy3

value: Elizabeth River, VA / Magotha Bay, VA

value: PC


title: PP33_cy3

value: Elizabeth River, VA


title: PC27_cy5


title: CP18_cy3

value: Magotha Bay, VA / Elizabeth River, VA

value: CP


title: CP18_cy5


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 19 [1047]

value: Leghorn


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 18 [1045]

value: male

value: NDV Infected and heat treated


title: PC25_cy5


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 17 [1039]


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 16 [1037]

value: 10 days post-infection


title: 8week_WT_NOR_sample 1

description:
8wWTNOR2
Treatment of normal diet in 8week WT fish, sample 1.

value: WT

value: Normal diet


title: PC28_cy3


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 15 [1035]

value: Harderian gland


title: PP33_cy5

value: PP


title: ACY142 (Dot6Δ/Tod6Δ) + Glucose + 1-NMPP1 + Rapamycin 20 min

city: Tucson

first: Andrew

last: Capaldi

state: AZ

address: 1007 E Lowell St

department: MCB

institute: Univ of Arizona

hyb_protocol: Hybridization was performed using Agilent Hyb buffers and cambers following the manufactures suggested protocols

scan_protocol: Arrays were scanned on a Genepix 300b scanner

data_processing: Arrays were analyzed using GenePix 3.0. The data from Genepix was filtered to eliminate spots where the Cy3 and Cy5 signals are both less than 1.5-fold above the average negative control signal, and then curvature in the Cy5/Cy3 scatter plot removed by LOWESS normalization.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: ACY142 (Dot6Δ/Tod6Δ) in glucose (20min)

label_protocol: mRNA was reverse transcribed incooperatigin aa-UTP and then labelled with Cy5 or Cy3

growth_protocol: Cells were grown to log phase in glycerol and harvested, or grown to log phase in glycerol and glucose added to the synthetic medium.

extract_protocol: Cells were lysed in hot phenol and the polyA RNA purdified using oligoDT cellulose

treatment_protocol: cells were treated with 1-NM-PP1 and/or rapamycin as described above

value: DMSO

source_name: ACY142 (Dot6Δ/Tod6Δ) in glucose (20min) + drug

value: 1-NM-PP1 + rapamycin


title: ACY142 (Dot6Δ/Tod6Δ) + Glucose + 1-NMPP1 + Rapamycin 150 min


title: ACY142 (Dot6Δ/Tod6Δ) + Glucose + 1-NMPP1 150 min


title: CC10_cy5

value: Magotha Bay, VA

value: Whole embryo

value: CC


title: ACY142 (Dot6Δ/Tod6Δ) + Glucose + Rapamycin 150 min

value: rapamycin


title: CP16_cy3


title: PC28_cy5

value: Elizabeth River, VA / Magotha Bay, VA

value: PC


title: CP16_cy5

value: Magotha Bay, VA / Elizabeth River, VA

value: CP


title: CC10_cy3


title: PP34_cy3

value: Elizabeth River, VA


title: CC6_cy3


title: PP34_cy5


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 13 [1027]

value: Leghorn

value: male

value: NDV Infected and heat treated

value: 2 days post-infection


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 14 [1029]

value: Control

value: 10 days post-infection

value: Harderian gland


title: ACY142 (Dot6Δ/Tod6Δ) + Glucose + Rapamycin 20 min

value: DMSO


title: ACY142 (Dot6Δ/Tod6Δ) + Glucose + 1-NMPP1 20 min


title: ACY142 + Glucose + Rapamycin 150 min

source_name: ACY142 in glucose (150min)

value: wild type

source_name: ACY142 in glucose (150min) + drug


title: ACY142 + Glucose + 1-NMPP1 + Rapamycin 150 min

value: 1-NM-PP1 + rapamycin


title: CC6_cy5

value: Magotha Bay, VA

value: Whole embryo

value: CC


title: PC24_cy3

value: Elizabeth River, VA / Magotha Bay, VA

value: PC


title: CP13_cy3

value: Magotha Bay, VA / Elizabeth River, VA

value: CP


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 12 [1026]

value: Leghorn


title: CP13_cy5


title: ACY142 + Glucose + 1-NMPP1 150 min

source_name: ACY142 in glucose (150min) +drug


title: PP32_cy3

value: Elizabeth River, VA

value: PP


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 9 [1020]

value: male

value: 6 days post-infection


title: PC24_cy5


title: CC9_cy3


title: PC26_cy3


title: PP32_cy5


title: PC26_cy5


title: ACY142 + Glucose + 1-NMPP1 + Rapamycin 90 min

source_name: ACY142 in glucose (90min)

source_name: ACY142 in glucose (90min) + drug


title: ACY142 + Glucose + Rapamycin 90 min

value: rapamycin


title: CP21_cy3


title: CP21_cy5


title: ACY142 + Glucose + 1-NMPP1 + Rapamycin 20 min

source_name: ACY142 in glucose (20min)

source_name: ACY142 in glucose (20min) +drug


title: ACY142 + Glucose + 1-NMPP1 90 min


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 7 [1012]

value: female

value: Control

value: 10 days post-infection

value: Harderian gland


title: PP41_cy3


title: PP41_cy5


title: CC5_cy3

value: Magotha Bay, VA


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 6 [1011]

value: NDV Infected and heat treated


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 10 [1021]


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 11 [1023]


title: ACY142 + Glucose + Rapamycin 20 min

value: wild type

value: DMSO

source_name: ACY142 in glucose (20min) + drug


title: ACY142 + Glucose + 1-NMPP1 20 min


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 3 [1006]


title: ACY142 Glycerol + 1-NMPP1 + Rapamycin 20 min

source_name: ACY142 in glycerol

source_name: ACY142 in glycerol +drug

value: 1-NM-PP1 + rapamycin


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 5 [1010]


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 8 [1015]

value: 2 days post-infection


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 1 [1002]


title: Glucose Introduction timecourse 150 min. ACY142


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 4 [1008]


title: Foxn#4-102518: Foxn1933/1089

city: Dallas

first: Igor

middle: M

last: Dozmorov

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

hyb_protocol: Samples were hybridized with GeneChip Mouse clariom S array

scan_protocol: Array scanning was per manufacturer (Affymetrix)

data_processing: Raw data was processed with normalization method  based on the use of “internal standards”, that characterize some aspects of the system’s behavior, such as technical variability. The two-step normalization procedure and the Associative analysis functions are presented in our publications (Dozmorov, I. and I. Lefkovits, Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res, 2009. 37(19): p. 6323-39). These algorithms are also obtainable from an R package diffGeneAnalysis, available as a part of Bioconductor packages (http://www.bioconductor.org/packages/2.5/bioc/html/diffGeneAnalysis.html).

source_name: e13.5 fetal thymii

label_protocol: Single-stranded cDNA was generated from amplified cRNA with the WT plus cDNA synthesis kit (Afffymetrix), fragments and labeled with the WT terminal labeling kit

extract_protocol: Embryonic thymic lobes were isolated and placed in miRVANA small RNA isolation buffers. The RNA was extracted according to the manufacturers protocol

value: Embryonic thymic lobes

tag: age


title: Foxn#5-091118: Foxn1933/1089


title: Tbx#1-102918: Tbx1neo2/neo2


title: Tbx#2-102918: Tbx1neo2/neo2


title: Foxn#5-102518: Foxn1933/1089


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 2 [1005]

tag: breed

value: Leghorn


title: Foxn#4-091118: wt

value: wt


title: Glucose Introduction timecourse 20 min. ACY142


title: Tbx#1-091118: Tbx1neo2/neo2


title: Glucose Introduction timecourse 90 min. ACY142


title: ACY142 Glycerol + 1-NMPP1 20 min

source_name: ACY142 in glycerol + drug


title: Foxn#2-102918: wt


title: HCT-15_M1 virus plus U0126_24h_rep1

city: Guang Zhou

first: Jing

last: Cai

address: Zhongshan School of Medicine, Sun Yat-sen University   74 Zhongshan 2nd Road

institute: Sun yat-sen university

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were analyzed with Affymetrix GeneChip Command Console Software

organism: Homo sapiens

source_name: HCT-15 colorectal carcinoma cell, 1MOI of M1 virus plus 16μM of U0126, 24hours

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

growth_protocol: HCT15 tumor cells are grown in DMEM supplied with 10%FBS and 1%Penicillin-Streptomycin

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

treatment_protocol: HCT15 tumor cells were treated with Control, 1MOI of  M1 virus, 16μM U0126, 1MOI of  M1 virus plus 16μM U0126 for 24 hours.

value: Colorectal carcinoma cell

value: 16μM of U0126 plus 1MOI of M1 virus for 24 hours

tag: cell line


title: HCT-15_U0126_24h_rep1

source_name: HCT-15 colorectal carcinoma cell, 16μM of U0126, 24hours

value: 16μM of U0126 for 24 hours


title: Foxn#3-102518: wt


title: HCT-15_Control_24h_rep1

source_name: HCT-15 colorectal carcinoma cell, no treatment, 24hours

value: no treatment


title: RNA-Seq of Leghorn Chicken Harderian gland Individual 21 [1050]

source_name: Leghorn_NDV Infection and heat stress_Harderian gland

value: male

tag: time point

value: 6 days post-infection


title: ACY142 Glycerol + Rapamycin 20 min

tag: strain background

tag: genotype/variation

value: rapamycin


title: CC9_cy5

value: Whole embryo

value: CC


title: HCT-15_M1 virus_24h_rep1

source_name: HCT-15 colorectal carcinoma cell, 1MOI of M1 virus, 24hours

tag: cell type

value: 1MOI of M1 virus for 24 hours


title: Tumor from BCM-9161 TNBC PDX model residual disease to docetaxel (BCM-9161RD2)

status: Public on Jul 18 2019

type: genomic

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

description: Matrix_processed_GPL21145.csv, Matrix_signal_intensities_GPL21145.csv

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Minfi R package standard protocol

label: Cy5 and Cy3

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: tissue


title: Tumor from VHIO-270 TNBC PDX model residual disease to docetaxel (VHIO-270RD1)


title: Tumor from BCM-9161 TNBC PDX model residual disease to docetaxel (BCM-9161RD1)


title: Tumor from BCM-9161 TNBC PDX model sensitive to docetaxel (BCM-9161S2)


title: Tumor from BCM-4664 TNBC PDX model sensitive to docetaxel (BCM-9161S1)


title: Tumor from VHIO-270 TNBC PDX model sensitive to docetaxel (VHIO-270S1)


title: Tumor from BCM-4664 TNBC PDX model sensitive to docetaxel (BCM-4664S1)


title: Tumor from VHIO-98 TNBC PDX model resistant to docetaxel (VHIO-98R1)


title: Tumor from VHIO-270 TNBC PDX model residual disease to docetaxel (VHIO-270RD2)


title: Tumor from IDB-09 TNBC PDX model sensitive to docetaxel (IDB-09S2)


title: Tumor from VHIO-98 TNBC PDX model sensitive to docetaxel (VHIO-98S1)


title: Tumor from BCM-4664 TNBC PDX model residual disease to docetaxel (BCM-4664RD2)


title: Tumor from HCI-001 TNBC PDX model residual disease to docetaxel (HCI-001RD1)


title: Tumor from IDB-09 TNBC PDX model sensitive to docetaxel (IDB-09S1)


title: Tumor from IDB-09 TNBC PDX model residual disease to docetaxel (IDB-09RD1)


title: Tumor from HCI-001 TNBC PDX model sensitive to docetaxel (HCI-001S2)


title: Tumor from IDB-09 TNBC PDX model residual disease to docetaxel (IDB-09RD2)


title: Tumor from IDB-09 TNBC PDX model resistant to docetaxel (IDB-09R1)


title: Tumor from IDB-09 TNBC PDX model resistant to docetaxel (IDB-09R2)


title: Tumor from VHIO-127 TNBC PDX model residual disease to docetaxel (VHIO-127RD2)


title: Tumor from VHIO-98 TNBC PDX model residual disease to docetaxel (VHIO-98RD1)


title: Tumor from VHIO-98 TNBC PDX model residual disease to docetaxel (VHIO-98RD2)


title: Tumor from VHIO-270 TNBC PDX model sensitive to docetaxel (VHIO-270S2)


title: Tumor from VHIO-98 TNBC PDX model sensitive to docetaxel (VHIO-98S2)


title: Tumor from HCI-001 TNBC PDX model residual disease to docetaxel (HCI-001RD2)


title: Tumor from VHIO-98 TNBC PDX model resistant to docetaxel (VHIO-98R2)


title: Tumor from BCM-4664 TNBC PDX model residual disease to docetaxel (BCM-4664RD1)


title: Tumor from HCI-001 TNBC PDX model sensitive to docetaxel (HCI-001S1)


title: Tumor from BCM-4664 TNBC PDX model senstive to docetaxel (BCM-4664S2)


title: eGFP-tagged FoxH1

city: Innsbruck

first: Dietmar

last: Rieder

address: Innrain 80

department: Biocenter

country: Austria

institute: Medical University of Innsbruck

data_processing:
Reads were processed and filtered to remove low quality reads and artifacts using flexbar (to remove LinDA adapters), fastx_trimmer (-f 5), fastq_quality_trimmer (-t 20 -l 20), fastq_quality_filter (-q 25 -p 50) and fastx_artifacts_filter
Reads were mapped to the zebrafish genome assembly Zv9/danRer7 using the BWA (v0.6.2)
Alignments were filtered using samtools to retain only uniquely mapping reads
Peaks were called using MACS 1.4.2 ( --bw=120 -m 8,50 --pvalue 1e-4 -g 1.357e9)
Peaks were filtered to remove peaks that overlap by more than 50% with nonUTR ensembl exons ore contained repeats of CTCTCTCTCTCTCTCTCTCTCTCTCTCTCT, AGAGAGAGA[GA]AGAGAGAGAGA or GAGAGAAA (using Bedtools, and fimo from Meme suite)
Genome_build: danRer7
Supplementary_files_format_and_content: peak

source_name: whole embryo

growth_protocol: Embryos were raised at 28.5 °C

extract_protocol:
Chromatin of 6000 embryos was extracted, sheared and immunoprecipitated with anti-GFP and Dynabeads.
Library construction followed the protocol of LinDA [Shankaranarayanan et al., Nat Methods 2011; 8(7):565–7; Shankaranarayanan et al., Nat Protoc 2012; 7(2):328–38]

value: 6hpf epiboly-stage

tag: chip antibody

value: Anti-eGFP (Torrey Pine Biolabs, 0715119, Protein A purified rabbit IgG)


title: Tri21#1 [GPL16699]

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: Trisomy 21 dermal fibroblasts

hyb_protocol: Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: For analysis with RNA spike-in controls, data were normalized using the median value for ERCC spike-in probes in each dataset.

source_name: Trisomy 21 dermal fibroblasts

label_protocol: 100 ng of total RNA containing RNA spike-in controls (ERCC ExFold RNA Spike-In Mixes, Thermo Fisher Scientific Inc.) was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 100 ng of total RNA with an oligo-dT-T7 promoter primer and AffinityScript MT -RT. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: On day 0, 1×105 cells were seeded into 10-cm dishes. Three days after seeding, without changing the medium, the number of cells was counted after detaching cells from the culture plate using trypsin–EDTA solution (0.25% (w/v) trypsin, 1 mmol/l EDTA-4Na solution, FUJIFILM Wako Pure Chemical Corporation).

extract_protocol: RNA was extracted from 1×105 cells using NucleoSpin RNA II (Macherey-Nagel, Oensingen, Switzerland)

value: fibroblast


title: Tumor from VHIO-127 TNBC PDX model residual disease to docetaxel (VHIO-127RD1)


title: Tri18#1 [GPL16699]

description: Trisomy 18 dermal fibroblasts

source_name: Trisomy 18 dermal fibroblasts


title: Tri21#2 [GPL16699]

description: Trisomy 21 dermal fibroblasts


title: Dip#3 [GPL16699]

description: normal dermal fibroblasts

source_name: normal dermal fibroblasts


title: Dip#1 [GPL16699]

description: normal dermal fibroblasts


title: TYE7

city: Saint Louis

first: Christian

last: Shively

state: MO

address: 4523 Clayton Avenue

department: Genetics

institute: Washington University in St Louis

description: "Calling Card" Assay for in vivo Transcription Factor Binding: a retrotransposon is directed into the genome at loci bound by a given transcription factor

data_processing:
Library strategy: Calling Card
Paired-End sequence reads were filtered for presence of Read1 initial 5bp barcode followed by unique 17-mer sequence (AATTCACTACGTCAACA) and Read2 initial 8bp barcode.
80bp of Read1 insert sequence was mapped to the 2008 S. cerevisiae reference genome (R-61-1-1) sequence using NovoAlign with default parameter settings. (Insertion position and number of reads mapping to each insertion is given in gnashy file.)
Number of insertions into each S. cerevisiae intergenic region was normalized to a total of 100,000 retrotransposon insertions per experiment and p-value was generated using poisson statistics.  (Significantly bound intergenic regions file)
Genome_build: 2008 S. cerevisiae reference genome (R-61-1-1)
Supplementary_files_format_and_content: .gnashy - a table indicating genomic position (chromosome, chromosome coordinate) of the retrotransposon insertion and number of reads aligning to that position
Supplementary_files_format_and_content: .gnashy.txt - Significantly bound intergenic regions file giving S. cerevisiae intergenic region, flanking ORFs (standard and systematic names), number of detected retrotransposon "calling card" insertions, normalized number of insertions (TPH), hyper-geometric p-value

growth_protocol: The indicated yeast strain was co-transformed with a plasmid carrying the indicated transcription factor fused at the C-terminus to Sir4p and a plasmid carrying a barcoded HIS3-carrying Ty5 retrotransposon under the control of the GAL1/10 promoter.  A single clone was then incubated for 3 days on selective media with galactose as the carbon source.  Plates were then sequentially replica-plated to YPD (2 days), followed by SC-HIS with 5'FOA agar plates (3 days).

extract_protocol:
Genomic DNA was extracted from all cells using standard glass bead-beating, phenol chloroform isoamyl alcohol purification, and NH4Ac ethanol protocol.
Genomc DNA was digested in three separate restriction enzyme digests (HinPI1, HpaII, and Taq-alphaI), self-ligated with T4 DNA ligase, and an inverse PCR reaction was performed to amplify genomic DNA downstream of each inserted Ty5 retrotransposon.
"Calling Card" Assay to identify in vivo genomic targets of DNA-binding factors
"Calling Card" Assay performed as previously described: 1. "Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins." Wang H, Mayhew D, Chen X, Johnston M, Mitra RD.  Genome Research, 2011, May 21(5):748-55. PMID 21471402. 2. "Calling Card Analysis in Budding Yeast." Mayhew D, Mitra RD.  Cold Spring Harbor Protocols, 2016, Feb 1, 2016(2). PMID 26832687.

tag: genotype

value: sir4D tye7D

tag: transcription factor


title: Dip#2 [GPL16699]

description: normal dermal fibroblasts


title: Tumor from IDB-02 TNBC PDX model residual disease to docetaxel (IDB-02RD1)


title: Sarcoma MEF input 12h

city: Tokyo

first: Yasuhiro

last: Yamada

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

department: Department of Molecular Pathology

institute: University of Tokyo

data_processing:
we checked the Sequenced data using FastQC.
Sequenced data was trimmed for adaptor sequence  by Cutadapt softweare to remove adapter sequences with parameter -q 20 -m 20 .
Chip-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.2.0 -p 4 -q .
We used the MACS  version 1.4.2 peak finding algorithm to identify regions of ChIP-seq enrichment over background with p value = 1×10-9
Genome_build: mm9

source_name: Sarcoma iPSCs #3-derived MEF

growth_protocol: G1297; DMEM+10%FBS, PS/MEF; DMEM+10%FBS, PS, NEAA, L-Glu, 2-ME/iPSCs;  Knockout DMEM+15%FBS, PS, NEAA, L-Glu, 2-ME, LIF

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. We used anti HA antibody(Monoclonal Mouse IgG 1-κ):nacalai cat# 06340-54 Lot#M4H0340 .
Libraries were prepared according to illumina'sTrueseq ChIP sample prep kit set A(Part#IP-202-1012)

treatment_protocol: Dox ON samples were treated with Dox (0.2µg/ml) containing medium for indicated hours.

value: sarcoma MEF


title: Sarcoma MEF Dox ON 12h


title: LEF1MO_DMZ_1

city: Karlsruhe

last: Gradl

address: Fritz Haber Weg 2

country: Germany

institute: Karlsruhe Institute of Technology

description: Stage 12 dorsal marginal zone explants, LEF1MO injected

hyb_protocol: at least 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes according to the Gene Expression Hybridization Kit (Agilent). The probes were hybridized to a Xenopus 4x44K gene expression chip (Agilent) for 17 h at 65°C.  After hybridization, the chips were washed.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software (Version 10.7.3.1, Agilent) using default parameters (protocol: GE1_107_Sep09 and Grid: 023448_D_F_20130122) to obtain background and spatially detrended processed signal intensities.

organism: Xenopus laevis

source_name: Dorsal marginal zone explants, LEF1MO injected

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the Low Input Quick Amp Labeling Kit, One Colour (Agilent) according to the manufacturer's instructions, purification by RNAeasy Mini Kit (Qiagen, Germany).  Dye incorporation and cRNA yield were checked with a Spectrophotometer.

growth_protocol: Xeopus laevis were injected in both dorsal blastomeres at 8-cell stage (COMO, LEF1MO) and cultivated until stage 10.25

extract_protocol: Total RNA was isolated from 30 DMZ explants via TRIzol Plus RNA Purification Kit (Life Technologies GmbH, Germany) according to manufactur's instructions. Total RNA was concentrated by Rneasy MinElute Cleanup Kit (Qiagen, Germany). Only probes with a RIN-value over 8 were used for the analysis (Agilent 2100 Bioanalyzer)

treatment_protocol: DMZ explants were dissected at stage 10.25 and cultivated until their siblings reach stage 12

value: Stage 12


title: LEF1MO_DMZ_2


title: CoMO injected_DMZ_1

description: Stage 12 dorsal marginal zone explants, CoMO injected

source_name: Dorsal marginal zone explants, CoMO injected


title: Tri18#2 [GPL16699]

description: Trisomy 18 dermal fibroblasts


title: Tumor from IDB-01 TNBC PDX model sensitive to docetaxel (IDB-01S1)


title: CoMO injected_DMZ_3


title: G1297 Dox ON 12h 2

source_name: murine EWS/ATF1-induced sarcoma cell line


title: CoMO injected_DMZ_2


title: G1297 input DNA 1


title: Tumor from IDB-02 TNBC PDX model residual disease to docetaxel (IDB-02RD2)


title: MP-CCS-SY siEWS/ATF1 96h

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99℃ for 5 minutes, then 45℃ for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 80μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 TG

data_processing: Data were processed using Genespring software.

label: Biotin

source_name: MP-CCS-SY siEWS/ATF1 96h

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

extract_protocol: RNeasy Plus Mini kit

value: clear cell sarcoma cell line MP-CCS-SY

value: EWS/ATF1 KD

tag: time


title: MPNST 1082

source_name: surgically resected human sarcoma sample

tag: sample type

value: NF1 patient


title: MPNST 1080

value: surgically resected human sarcoma sample


title: MP-CCS-SY siControl 48h

source_name: MP-CCS-SY siControl 48h

value: control


title: MP-CCS-SY siEWS/ATF1 48h

source_name: MP-CCS-SY siEWS/ATF1 48h


title: Tumor from IDB-02 TNBC PDX model sensitive to docetaxel (IDB-02S1)


title: MPNST 830


title: MPNST 937


title: MP-CCS-SY siControl 96h

source_name: MP-CCS-SY siControl 96h


title: LEF1MO_DMZ_3


title: Tri21#3 [GPL16699]

description: Trisomy 21 dermal fibroblasts


title: G1297 Dox ON 12h 1


title: CCS 1666


title: Tumor from VHIO-127 TNBC PDX model sensitive to docetaxel (VHIO-127S2)


title: G1297 input DNA 2


title: Tumor from IDB-01 TNBC PDX model resistant to docetaxel (IDB-01S2)


title: CCS 1657


title: Human origin tumor from IDB-02 (Pleural effusion) (13_5_PL)


title: CCS 935


title: Tumor from VHIO-127 TNBC PDX model resistant to docetaxel (VHIO-127R2)


title: Tumor from IDB-02 TNBC PDX model resistant to docetaxel (IDB-02R1)


title: CCS 1062


title: CCS 1139


title: Tumor from IDB-01 TNBC PDX model residual disease to docetaxel (IDB-01RD2)


title: CCS 636


title: CCS 956


title: Tumor from IDB-02 TNBC PDX model resistant to docetaxel (IDB-02R2)


title: Sarcoma MEF Dox ON 12h

value: Sarcoma iPSCs #3-derived MEF


title: Sarcoma MEF Dox ON 3h


title: Tumor from IDB-01 TNBC PDX model resistant to docetaxel (IDB-01R1)


title: Tumor from VHIO-127 TNBC PDX model sensitive to docetaxel (VHIO-127S1)


title: Human origin tumor from IDB-03 (primary tumor) (1070_PT)


title: Human origin tumor from IDB-01 (Pleural effusion) (24_11_PL)


title: Sarcoma iPSC #1

source_name: G1297-derived iPSCs

value: G1297-derived iPSCs


title: Sarcoma MEF Dox OFF


title: G1297 Dox ON 48h

value: murine EWS/ATF1-induced sarcoma cell line


title: CCS 424


title: G1297 Dox ON 12h


title: Sarcoma iPSC #3


title: G1297 Dox OFF


title: G1297 Dox ON 3h


title: Tumor from IDB-02 TNBC PDX model sensitive to docetaxel (IDB-02S2)


title: Tumor from IDB-01 TNBC PDX model residual disease to docetaxel (IDB-01RD1)


title: Tumor from IDB-01 TNBC PDX model resistant to docetaxel (IDB-01R2)


title: NPAS2_bHLH_CBF1Zip

tag: strain

value: sir4D cbf1D

value: NPAS2bHLH with Cbf1p ZIP


title: NPAS2_bHLH


title: GCR2


title: GCR1


title: 12A12LN29

city: La Jolla

first: Luc

last: Teyton

address: 10550 North Torrey Pines Road

institute: TSRI

description: 12-20A 12weeks UPDATED.csv

data_processing: Custom R analysis pipeline

label: EVAGREEN

source_name: LymphNode

label_protocol: IAg7 tetramers with PE fluorphores. Stain at 4C for 60 minutes

extract_protocol: Tetramer used to stain CD4+ T cells specific to either 12-20 or 13-21 of the insulin Beta chain from various NOD mice tissues.

value: CD4+ T cell

value: NOD/ShiLtJ

tag: iag7 tetramer

tag: age (in weeks)


title: 12A12LN30

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN27

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN26

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN25

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN24

description: 12-20A 12weeks UPDATED.csv


title: Cbf1bHLHZIP(Tye7 Basic)

value: Cbf1p bHLH-ZIP with Tye7p Basic Region


title: 12A12LN28

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN23

description: 12-20A 12weeks UPDATED.csv


title: Human origin tumor from IDB-04 (Pleural effusion) (25_5_PL)


title: HT22 CORT 4hrs rep2

city: Quezon City

first: Pia

middle: Dano

last: Bagamasbad

email: piab@umich.edu, pdbagamasbad@up.edu.ph

state: Metro Manila

address: National Science Complex

department: National Institute of Molecular Biology and Biotechnology

country: Philippines

institute: University of the Philippines Diliman

description: H2 replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using rank invariant with IlluminaGUI in R

source_name: HT22 CORT 4hrs

label_protocol: Biotyinylated RNA was prepared using the Illumina Totalprep RNA Amplification Kit (Ambion, Inc.)

growth_protocol: HT22 cells Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen) supplemented with sodium bicarbonate (2.2 g/L), penicillin G (100 units/mL), streptomycin sulfate (100 µg/mL) and 10% fetal bovine serum (FBS) that had been stripped of thyroid and steroid hormones.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNaseI treatment with Qiagen RNAeasy with the prescribed protocol provided with the kit. Quality control was performed with by measuring gene expression of previously validated, T3 and CORT-regulated genes.

treatment_protocol: HT22 cells were treated with either vehicle (DMSO 0.03%, ethanol 0.001%), T3 (30 nM), CORT (100 nM), or T3 (30 nM) + CORT (100 nM) in  serum free media for 4h before harvest for RNA extraction

value: Hippocampal neuron

tag: treatment

value: CORT 4hrs


title: 12A12LN22

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN18

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN20

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN17

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN16

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN21

description: 12-20A 12weeks UPDATED.csv


title: HT22 T3+CORT 4hrs rep1

description: H3 replicate 1

source_name: HT22 T3+CORT 4hrs

value: T3+CORT 4hrs


title: 12A12LN14

description: 12-20A 12weeks UPDATED.csv


title: HT22 T3 4hrs rep2

description: H1 replicate 2

source_name: HT22 T3 4hrs

value: T3 4hrs


title: 12A12LN15

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN12

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN10

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN13

description: 12-20A 12weeks UPDATED.csv


title: Sarcoma MEF Dox ON 48h


title: 12A12LN9

description: 12-20A 12weeks UPDATED.csv


title: HT22 T3+CORT 4hrs rep2

description: H3 replicate 2


title: 12A12LN8

description: 12-20A 12weeks UPDATED.csv


title: HT22 T3 4hrs rep1

description: H1 replicate 1


title: HT22 CORT 4hrs rep3

description: H2 replicate 3


title: HT22 CORT 4hrs rep1

description: H2 replicate 1


title: HT22 vehicle 4hrs rep3

description: Ctrl replicate 3

source_name: HT22 vehicle 4hrs

value: vehicle 4hrs


title: HT22 T3+CORT 4hrs rep3

description: H3 replicate 3


title: 12A12LN6

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN19

description: 12-20A 12weeks UPDATED.csv


title: HT22 vehicle 4hrs rep2

description: Ctrl replicate 2


title: HT22 vehicle 4hrs rep1

description: Ctrl replicate 1


title: HT22 T3 4hrs rep3

description: H1 replicate 3


title: 12A12LN5

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN4

description: 12-20A 12weeks UPDATED.csv


title: 12A12S40

description: 12-20A 12weeks UPDATED.csv

source_name: Spleen


title: 12A12S42

description: 12-20A 12weeks UPDATED.csv


title: 12A12S39

description: 12-20A 12weeks UPDATED.csv


title: 12A12S41

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN11

description: 12-20A 12weeks UPDATED.csv


title: 12A12S37

description: 12-20A 12weeks UPDATED.csv


title: 12A12S36

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN7

description: 12-20A 12weeks UPDATED.csv


title: 12A12S32

description: 12-20A 12weeks UPDATED.csv


title: 12A12S34

description: 12-20A 12weeks UPDATED.csv


title: 12A12S33

description: 12-20A 12weeks UPDATED.csv


title: 12A12S31

description: 12-20A 12weeks UPDATED.csv


title: 12A12S29

description: 12-20A 12weeks UPDATED.csv


title: 12A12S28

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN3

description: 12-20A 12weeks UPDATED.csv


title: 12A12LN1

description: 12-20A 12weeks UPDATED.csv


title: 12A12S21

description: 12-20A 12weeks UPDATED.csv


title: 12A12S22

description: 12-20A 12weeks UPDATED.csv


title: 12A12S27

description: 12-20A 12weeks UPDATED.csv


title: 12A12S20

description: 12-20A 12weeks UPDATED.csv


title: 12A12S23

description: 12-20A 12weeks UPDATED.csv


title: Tumor from VHIO-127 TNBC PDX model resistant to docetaxel (VHIO-127R1)


title: 12A12S26

description: 12-20A 12weeks UPDATED.csv


title: 12A12S38

description: 12-20A 12weeks UPDATED.csv


title: 12A12S17

description: 12-20A 12weeks UPDATED.csv


title: 12A12S19

description: 12-20A 12weeks UPDATED.csv


title: 12A12S13

description: 12-20A 12weeks UPDATED.csv


title: 12A12S14

description: 12-20A 12weeks UPDATED.csv


title: 12A12S15

description: 12-20A 12weeks UPDATED.csv


title: 12A12S16

description: 12-20A 12weeks UPDATED.csv


title: 12A12S12

description: 12-20A 12weeks UPDATED.csv


title: 12A12S30

description: 12-20A 12weeks UPDATED.csv


title: 12A12S18

description: 12-20A 12weeks UPDATED.csv


title: 12A12S11

description: 12-20A 12weeks UPDATED.csv


title: 12A12S9

description: 12-20A 12weeks UPDATED.csv


title: 12A12S25

description: 12-20A 12weeks UPDATED.csv


title: 12A12S8

description: 12-20A 12weeks UPDATED.csv


title: 12A12S7

description: 12-20A 12weeks UPDATED.csv


title: 12A12S6

description: 12-20A 12weeks UPDATED.csv


title: 12A12S10

description: 12-20A 12weeks UPDATED.csv


title: 12A12S5

description: 12-20A 12weeks UPDATED.csv


title: 12A12S4

description: 12-20A 12weeks UPDATED.csv


title: 12B6S44

description: 12-20B 6 weeks UPDATED.csv


title: 12A12S1

description: 12-20A 12weeks UPDATED.csv


title: 12A12S2

description: 12-20A 12weeks UPDATED.csv


title: 12A12S3

description: 12-20A 12weeks UPDATED.csv


title: 12B6S43

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN43

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN41

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN40

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN44

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN37

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN39

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN36

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN38

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN34

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN33

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN32

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN29

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN35

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN30

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN31

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN27

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN26

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN24

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN25

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN23

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN21

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN42

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN20

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN19

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN18

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN17

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN15

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN14

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN22

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN16

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN12

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN13

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN8

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN9

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN28

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN6

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN7

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN5

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S42

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN4

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S41

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S36

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S37

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S38

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S35

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S40

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S32

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S39

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S34

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S33

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN11

description: 12-20B 6 weeks UPDATED.csv


title: 12B6LN10

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S31

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S27

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S30

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S28

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S29

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S26

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S25

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S23

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S22

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S21

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S24

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S19

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S17

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S13

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S12

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S15

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S8

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S6

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S11

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S7

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S3

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S14

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S4

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S1

description: 12-20B 6 weeks UPDATED.csv


title: 12B6S9

description: 12-20B 6 weeks UPDATED.csv


title: 12A6LN43

description: 12-20A 6weeks UPDATED.csv


title: 12B6S2

description: 12-20B 6 weeks UPDATED.csv


title: 12A6LN44

description: 12-20A 6weeks UPDATED.csv


title: 12A12LN2

description: 12-20A 12weeks UPDATED.csv


title: 12B6S20

description: 12-20B 6 weeks UPDATED.csv


title: 12A6LN42

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN41

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN40

description: 12-20A 6weeks UPDATED.csv


title: 12B6S16

description: 12-20B 6 weeks UPDATED.csv


title: 12A6LN38

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN39

description: 12-20A 6weeks UPDATED.csv


title: 12A6S44

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN37

description: 12-20A 6weeks UPDATED.csv


title: 12B6S10

description: 12-20B 6 weeks UPDATED.csv


title: 12A12S24

description: 12-20A 12weeks UPDATED.csv


title: 12A6LN31

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN30

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN33

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN32

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN29

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN28

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN36

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN34

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN35

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN25

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN27

description: 12-20A 6weeks UPDATED.csv


title: 12A6S43

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN18

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN16

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN20

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN19

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN17

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN22

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN23

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN15

description: 12-20A 6weeks UPDATED.csv


title: 12A12S35

description: 12-20A 12weeks UPDATED.csv


title: 12A6LN13

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN11

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN10

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN14

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN8

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN5

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN4

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN9

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN26

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN24

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN6

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN12

description: 12-20A 6weeks UPDATED.csv


title: HBVP-mix1

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2 (Langmead and Salzberg, 2012). Bowtie2 indices were either generated from genome assembly sequence or the representative transcript sequences for aligning to the genome and transcriptome.
The alignment file was used for assembling transcripts, estimating their abundances and detecting differential expression of genes.
Differentially expressed gene were determined based on counts from unique and multiple alignments using coverage in Bedtools (Quinlan AR, 2010). The RT (Read Count) data were processed based on Quantile normalization method using EdgeR within R (R development Core Team, 2016) using Bioconductor (Gentleman et al.,2004).
Genome_build: mm10, hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: pericyte

growth_protocol: HT22 and BV-2 cells were maintained in Dulbecco's Modified Eagle's medium (Hyclone/Thermo, Rockford, IL), supplemented with 10% fetal bovine serum (FBS) (Hyclone/Thermo, Rockford, IL) and 1% penicillin/streptomycin in a 5% CO2 at 37℃. Human brain vascular pericyte (HBVP) was purchased from ScienCell Research Laboratories (Carlsbad, CA, USA) and maintained pericyte medium (PM) supplemented with 2% FBS, 1% pericyte growth supplement (PGS), and 1% penicillin/streptomycin in a 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed by Agilent 2100 bioanalyzer using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and RNA quantification was performed using ND-2000 Spectrophotometer (Thermo Inc., DE, USA).
For control and test RNAs, the construction of library was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions. In brief, each 500ng total RNA were prepared and an oligo-dT primer containing an Illumina-compatible sequence at its 5’ end was hybridized to the RNA and reverse transcription was performed. After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5’ end. The double-stranded library was purified by using magnetic beads to remove all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library is purified from PCR components. High-throughput sequencing was performed as single-end 75 sequencing using NextSeq 500 (Illumina, Inc., USA).

treatment_protocol: HT22 cells were plated on 96 well microplates at a density of 5 x 10^3/well and treated with hydrogen peroxide (H2O2) (250 μM) and each herbal extract for 6 h. BV-2 cells were pretreated with each herbal extract for 2 h and then stimulated with LPS (1 μ/mL) for an additional 22 h. HBVP were plated onto 6 well plates and maintained to 90% confluence in 2 ml of culture media. Cells were treated with TGF-ß (10 ng/mL) and each herbal extract for 24 h.   Seven crude herbal extracts forming UGS, including Uncariae Ramulus et Uncus (C1), Atractylodis Rhizoma Alba (C2), Poria Sclerotium (C3), Bupleuri Radix (C4), Angelicae Gigantis Radix (C5), Cnidii Rhizoma (C6), and Glycyrrhizae Radix et Rhizoma (C7) were purchased from Kwangmyungdang Pharmaceutical Co. LTD (Ulsan, Republic of Korea). In the preparation of mixture groups (Mix1 ~ Mix3), the ratios of the two herbal extracts reproduced those contained in UGS. To prepare Mix1, Uncariae Ramulus et Uncus (C1) and Atractylodis Rhizoma Alba (C2) were mixed in the ratio 3:4. For Mix 2, Poria Sclerotium (C3) and Bupleuri Radix (C4) were mixed in the ratio 2:1. For Mix 3, Angelicae Gigantis Radix (C5) and Cnidii Rhizoma (C6) and were mixed in the ratio 1:1.

value: HBVP

value: Human brain vascular pericyte


title: HBVP-mix2


title: HBVP-C7


title: HBVP-mix3


title: 12A6LN3

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN7

description: 12-20A 6weeks UPDATED.csv


title: HBVP-TGFB1


title: 12A6S41

description: 12-20A 6weeks UPDATED.csv


title: 12A6S42

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN1

description: 12-20A 6weeks UPDATED.csv


title: HBVP-UGS


title: 12A6S40

description: 12-20A 6weeks UPDATED.csv


title: 12A6LN2

description: 12-20A 6weeks UPDATED.csv


title: HBVP-Control


title: 12A6S39

description: 12-20A 6weeks UPDATED.csv


title: 12A6S38

description: 12-20A 6weeks UPDATED.csv


title: 12A6S37

description: 12-20A 6weeks UPDATED.csv


title: 12A6S36

description: 12-20A 6weeks UPDATED.csv


title: 12A6S35

description: 12-20A 6weeks UPDATED.csv


title: disease rep11 [W_040]

city: Columbia

first: Trupti

last: Joshi

state: Missouri

address: NW 502, One Hospital Drive

institute: University of Missouri

data_processing:
checked the quality of the data using FastQC
remove reads with low‐quality bases, adapter sequences, and other contaminating sequences using Cutadapt
Bowtie2 was used to build the index of reference genome
TopHat was used to map the short sequence reads to the reference genome
HTSeq was applied to generate the read count data
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes the raw read counts for all samples

source_name: disease_endometrial tissue

extract_protocol:
Total RNA was extracted with the Qiagen RNeasy kit following storage in RNAlater
Libraries were constructed following the manufacturer’s protocol with reagents supplied in Illumina’s TruSeq mRNA stranded library preparation kit.  The method involves mRNA enrichment from total RNA followed by RNA fragmentation and conversion to double-stranded cDNA using random hexamers.

tag: group

value: disease

value: endometrial tissue


title: disease rep12 [W_047]


title: disease rep13 [W_049]


title: control rep21 [W_054]

source_name: control_endometrial tissue

value: control


title: disease rep14 [W_052]


title: control rep22 [W_058]


title: disease rep16 [W_007]


title: disease rep15 [W_053]


title: control rep20 [W_039]


title: 12A6S33

description: 12-20A 6weeks UPDATED.csv


title: disease rep10 [W_037]


title: disease rep9 [W_035]


title: control rep18 [W_028]


title: disease rep8 [W_030]


title: 12A6S31

description: 12-20A 6weeks UPDATED.csv


title: control rep17 [W_023]


title: 12A6S34

description: 12-20A 6weeks UPDATED.csv


title: control rep19 [W_033]


title: control rep16 [W_018]


title: 12A6S30

description: 12-20A 6weeks UPDATED.csv


title: 12A6S27

description: 12-20A 6weeks UPDATED.csv


title: 12A6S29

description: 12-20A 6weeks UPDATED.csv


title: disease rep7 [W_017]


title: disease rep6 [W_015]


title: 12A6S28

description: 12-20A 6weeks UPDATED.csv


title: 12A6S26

description: 12-20A 6weeks UPDATED.csv


title: 12B6S18

description: 12-20B 6 weeks UPDATED.csv


title: 12A6S25

description: 12-20A 6weeks UPDATED.csv


title: disease rep5 [W_012]


title: 12A6S32

description: 12-20A 6weeks UPDATED.csv


title: 12A6S24

description: 12-20A 6weeks UPDATED.csv


title: 12A6S23

description: 12-20A 6weeks UPDATED.csv


title: disease rep4 [W_011]


title: control rep15 [W_010]


title: 12A6S20

description: 12-20A 6weeks UPDATED.csv


title: 12A6S19

description: 12-20A 6weeks UPDATED.csv


title: 12A6S18

description: 12-20A 6weeks UPDATED.csv


title: control rep14 [W_004]


title: 12A6S17

description: 12-20A 6weeks UPDATED.csv


title: disease rep1 [W_001]


title: control rep13 [W_002]


title: control rep12 [N_0060]


title: 12A6S16

description: 12-20A 6weeks UPDATED.csv


title: 12A6S15

description: 12-20A 6weeks UPDATED.csv


title: control rep11 [N_0058]


title: control rep10 [N_0057]


title: 12A6S14

description: 12-20A 6weeks UPDATED.csv


title: control rep9 [N_0055]


title: 12A6S13

description: 12-20A 6weeks UPDATED.csv


title: control rep8 [N_0054]


title: 12A6S21

description: 12-20A 6weeks UPDATED.csv


title: 12A6S12

description: 12-20A 6weeks UPDATED.csv


title: 12A6S22

description: 12-20A 6weeks UPDATED.csv


title: disease rep3 [W_008]


title: 12A6S9

description: 12-20A 6weeks UPDATED.csv


title: disease rep2 [W_006]


title: control rep6 [N_0045]


title: control rep5 [N_0042]


title: 12A6S8

description: 12-20A 6weeks UPDATED.csv


title: control rep7 [N_0046]


title: control rep4 [N_0039]


title: control rep3 [N_0036]


title: control rep2 [N_0035]


title: 12A6S4

description: 12-20A 6weeks UPDATED.csv


title: 12A6S7

description: 12-20A 6weeks UPDATED.csv


title: 12A6S6

description: 12-20A 6weeks UPDATED.csv


title: 12A6S5

description: 12-20A 6weeks UPDATED.csv


title: control rep1 [N_0026]


title: 12A6S2

description: 12-20A 6weeks UPDATED.csv


title: TTseq_TotalRNA_Jurkat_30min_unstimulated_Rep2

city: Solna

first: Gert-Jan

last: Hendriks

address: Solnavägen 9

department: Cell and Molecular Biology

institute: Karolinska Institutet

description: DESeq2_results_lfcThreshold1_TotalRNA_Jurkat_30min_stimulated_vs_unstimulated.csv

data_processing:
NASC-seq: Trimming of reads was performed with trimgalore
NASC-seq: Reads were aligned to Hg38 using STAR aligner
NASC-seq: Duplicates were removed with Picard
NASC-seq: Data was further processed using the NASC-seq analysis pipeline
NASC-seq: Cell filtering for processing was performed, cells with less than 100000 total reads, less than 50000 mapping reads or less than 10% of reads mapping were removed from the analysis.
TT-seq data processing. Paired-end 75 base reads with additional 6 base reads of barcodes were demultiplexed and mapped with STAR (Dobin and Gingeras 2015) to the Hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). Samtools (Li, Handsaker et al. 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f2) were selected. Read counts per gene were calculated using HTSeq (Anders, Pyl et al. 2015). The resulting count tables were used as input for differential expression analysis using the R/Bioconductor implementation of DESeq2.
Genome_build: Hg38
Supplementary_files_format_and_content: NASC-seq: The readcounts.csv file contains the readcounts for all features for all cells (even those filtered out during NASC-seq pipeline processing) for the corresponding experiment
Supplementary_files_format_and_content: NASC-seq: The newcounts.csv contains the 'counts' for reads that are considered newly produced for the corresponding experiment. Since we calculate fractions of total reads, this field may contain decimal values. Please note that we cannot caluclate the fraction of reads that is new/old for lowly expressed genes, (i.e. less than 16 reads), which results in the introduction of NA values.
Supplementary_files_format_and_content: NASC-seq: The oldcounts.csv contains the 'counts' for reads that are considered pre-existing for the corresponding experiment. Since we calculate fractions of total reads, this field may contain decimal values. Please note that we cannot caluclate the fraction of reads that is new/old for lowly expressed genes, (i.e. less than 16 reads), which results in the introduction of NA values.
Supplementary_files_format_and_content: TT-seq: DESeq2_results .csv files contain results from differential expression analysis using DESeq2 setting lfcThreshold = 1.

source_name: Jurkat

growth_protocol:
NASC-seq: Cells were grown in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (Sigma) and 1% Penicillin/Streptomycin (HyClone) at 37°C under 5% CO2.
TT-seq: Cells were grown in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (Sigma) and 1% Penicillin/Streptomycin (HyClone) at 37°C under 5% CO2.

extract_protocol:
NASC-seq: Cells were distributed to NASC-seq lysis buffer with FACS.
TT-seq: Total RNA was extracted using TRIzol (Life Technologies), 4sU-labeled RNA was extracted according to Dolken et al., RNA, 2008 and fragmented with a BioRuptor Next Gen (Diagenode) at high power for one cycle of 30’’/30’’ ON/OFF (see also Schwalb et al., 2016)
NASC-seq: Libraries were prepared using the NASC-seq protocol
TT-seq: Sequencing libraries were prepared with the Ovation Universal RNA-Seq System (NuGEN) following the manufacturer's’ instructions

treatment_protocol:
NASC-seq: On the day of the experiment, Jurkat cells were seeded to a density of 1*10^6 cells/ml and stimulated with 50ng/μl phorbol 12-myristate 13-acetate (PMA) and 1μM ionomycin (Sigma) or treated with solvent control (DMSO, Sigma) for the indicated time at 37°C under 5% CO2. NASC-seq (Jurkat cells): Cells were labelled grown with 4sU (50μM) during the entire stimulus.
NASC-seq: K562 cells were passaged the day before the experiment and labeled with 4sU (50μM) for 60 minutes.
TT-seq: On the day of the experiment, Jurkat cells were seeded to a density of 1*10^6 cells/ml and stimulated with 50ng/μl phorbol 12-myristate 13-acetate (PMA) and 1μM ionomycin (Sigma) or treated with solvent control (DMSO, Sigma) for the indicated time at 37°C under 5% CO2. During the last 5 minutes of each time point cells were labelled in media with 500μM 4sU (Sigma) at 37°C under 5% CO2. Cells were harvested by centrifugation at 1400xg for 2 min.

tag: 4su labelling

value: 5min 4sU

tag: pma + ionomycin stimulation

value: Unstimulated

tag: method

value: TT-seq

tag: molecule

value: total RNA


title: TTseq_TotalRNA_Jurkat_15min_unstimulated_Rep2

description: DESeq2_results_lfcThreshold1_TotalRNA_Jurkat_15min_stimulated_vs_unstimulated.csv


title: 12A6S3

description: 12-20A 6weeks UPDATED.csv

value: CD4+ T cell


title: TTseq_TotalRNA_Jurkat_30min_stimulated_Rep1

value: PMA + ionomycin stimulated, 30 minutes