title: H3K56 acetylation in meiosis mapped in a wild type strain

type: genomic

city: Debrecen

first: Lorant

last: Szekvolgyi

address: Egyetem ter 1.

department: Department of Pharmacy

country: Hungary

institute: University of Debrecen

hyb_protocol: The ChIP-on-Chip protocol of Agilent was followed.

scan_protocol: RPA ChIP: Axon 4000B scanner.  Spp1-HA ChIP: SureScan microarray scanner. Images were quantified, background subtracted and intra-array normalized using the GenePix5.1 software (RPA ChIP) and Agilent Feature Extraction Software v9.5.1.1 (Spp1-ChIP).

data_processing: RPA-ChIP data were normalized using the background-based normalization method described by Buhler et al. (2007). Rfa1 enrichment - marking DSB sites - was expressed as log2 Rfa1 ChIP/ WCE ratios. H3K56ac enrichment was normalized to input.

source_name: wild type strain

label_protocol: Two-thirds of the immunoprecipitated DNA was amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye (Cy5 or Cy3) coupling.

growth_protocol: Cells were grown in rich medium (YPD) for 24 hours, then transferred to pre-sporulation medium (SPS) and grown overnight to a density of ~4x10e7 cells/ml. SPS cultures were harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended in sporulation medium (SPM; 1% potassium acetate supplemented with amino acids and nucleotides according to auxotrophic requirements, and 0.0001 % of polypropylene glycol 2000 as an anti-clumping agent) at a density of 2x10e7 cells/ml.

extract_protocol: At 4 hrs and 5 hrs in SPM sample aliquots were collected and crosslinked with 1% formaldehyde for 20 min at room temperature. Reaction was stopped by the addition of 125 mM glycine for 5 minutes. Cells were washed three times with cold TBS, and then chromatin immunoprecipitation was performed using 2.5 µl of rabbit polyclonal anti-Rfa1 antibody (from S. Brill) (RPA-ChIP) or 3 µl of anti-H3K56ac antibody (K56Ac ChIP). Immunoprecipitates were captured by using pan Mouse IgG magnetic beads (Dynal) blocked with 5% BSA (Diagenode).

tag: strain id

tag: genomic background

value: LEU2/leu2 HIS4/his4

value: anti-H3K56ac antibody

tag: fraction

value: IP fraction

value: Whole-cell extract (input chromatin)


title: IMR90.iBMEC.Day 16 rep3

status: Public on Dec 25 2019

type: SRA

city: New York

first: Tyler

last: Lu

state: New York

address: 1300 York Avenue

country: USA

institute: Weill Cornell Medicine

library_source: transcriptomic

data_processing:
Analyses were performed using the Seurat package in R (version 3.0.3).
UMI counts files that had been knee-filtered were downloaded from the Illumina BaseSpace Sequence Hub.
Following best practices in the package suggestions UMI counts were log-normalized and after the most highly variable genes selected the data matrices were scaled using a linear model with variation arising from UMI counts mitigated for.
Principal component analysis was subsequently performed on this matrix and after reviewing principal component heatmaps and jackstraw plots Uniform Manifold Approximation and Projection (UMAP) visualization was performed using the top 30 components and clustering resolution was set at 0.8.

molecule: total RNA

organism: Homo sapiens

source_name: hPSC-Derived

growth_protocol: Cells were grown in 10cm coated tissue culture dishes using media specific for each cell type.

extract_protocol:
A single-cell suspension was loaded into the Bio-Rad ddSEQ Single-Cell Isolator on which cells were isolated, lysed and barcoded in droplets.
Libraries were generated with direct tagmentation followed by 3’ enrichment and sample indexing using Illumina Nextera library prep kit.
ddSeq

tag: cell type

value: hPSC-Derived cell

tag: differentiation condition

value: With Retinoic Acid


title: Meiotic DSBs mapped in a H3K56A mutant plasmid shuffle strain

description: Replicates:  H3K56A_DSBs_1, H3K56A_DSBs_2

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: histone H3K56A point-mutant plasmid shuffle strain

tag: genotype

value: hht1::HphMX  hht2::KanMX  dmc1::LEU2  pARS-CEN(hht2-k56A, HHF2-TRP1)

tag: chip antibody

value: anti-Rfa1 antibody


title: IMR90.iBMEC.Day 16 rep2


title: Meiotic DSBs mapped in a control (H3) plasmid shuffle strain

description:
Replicates:  H3_DSBs_1, H3_DSBs_2
H3_DSBs_2

source_name: control (H3) plasmid shuffle strain

value: H3 (ctrl)

value: hht1::HphMX  hht2::KanMX  dmc1::LEU2  pARS-CEN(HHT2, HHF2-TRP1)


title: BMSC from Patient 4

type: RNA

city: Ann Arbor

first: Ming-Sing

last: Si

state: MI

address: 11-735 C.S. Mott Children's Hospital, 1540 E. Hospital Drive

department: Cardiac Surgery

institute: University of Michigan

description: Gene expression data from Patient 4 BMSCs

hyb_protocol: Following labeling procedure, 5.2 ug of cDNA were hybridized at 48C on Human Gene ST 2.1 Strip.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
oligo and limma package of bioconductor implemented in the R statistical environment.
expression values for each gene using a robust multi-array average. Please note that these values are log2 transformed

label: biotin

source_name: Sternal MSCs from Patient 4

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: MSCs were grown under standard conditions and analyzed prior to passage 6.

extract_protocol: RNA extraction was performed with the Rneasy kit from Qiagen according to the manufacturer's instructions.

treatment_protocol: Cells were detached from the culture surface with trypsin, washed three times in PBS and subjected to RNA extraction.

tag: individual

value: Patient 4

tag: tissue

value: Sternum

value: MSCs

tag: developmental stage

value: neonatal


title: BMSC from Patient 5

description: Gene expression data from Patient 5 BMSCs

source_name: Sternal MSCs from Patient 5

value: Patient 5


title: TMSC from Patient 4

description: Gene expression data from Patient 4 TMSCs

source_name: Thymus MSCs from Patient 4

value: Thymus


title: TMSC from Patient 5

description: Gene expression data from Patient 5 TMSCs

source_name: Thymus MSCs from Patient 5


title: 5-8F

city: Guangzhou

first: HAIDE

last: QIN

state: Guangdong  Province

address: No. 135, Xingang Xi Road

department: Sun Yat-sen Memorial Hospital

country: China

institute: SUN YAT-SEN UNIVERSITY

description: Gene expression profiling

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 2 out of 4 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

source_name: NPC cell lines 5-8F

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: NPC cells were preserved in our cancer center and routinely maintained in RPMI-1640 containing 100 units/ml penicillin, 100 µg/ml streptomycin, and 10% FBS (Invitrogen, CA, USA) at 37°C in a 5% CO2 humidified atmosphere.

extract_protocol: Total RNA was extracted from cell lines and fresh tissues with TRIzol reagent (Invitrogen, CA, USA) or paraffin-embedded tissues with phenol chloroform according to the manufacturer’s instructions. cDNA was synthesized with the PrimeScript RT reagent Kit (Promega, Madison, WI, USA).

treatment_protocol: Transient transfection of miR-18a inhibitor was performed using Lipofectamine 2000 reagent (Invitrogen, CA, USA) in OPTI-MEM media. For miR-18a overexpression, NPC cells were infected with recombinant lentivirus transducing units plus 8 mg/ml Polybrene (Sigma, St Louis, Missouri, USA). Stable cell lines were selected using 4 μg/mL puromycin.

value: NPC

tag: group

value: high tumorigenic and metastatic, subclones of SUNE1

tag: treatment

value: untreated


title: BMSC from Patient 3

description: Gene expression data from Patient 3 BMSCs

source_name: Sternal MSCs from Patient 3

value: Patient 3


title: 6_10B_miR-18a overexpression

description: Gene expression profiling

source_name: NPC cell lines 6-10B, stable miR-18a overexpression

value: low tumorigenic and metastatic, subclones of SUNE1

value: stable miR-18a overexpression


title: TMSC from Patient 2

description: Gene expression data from Patient 2 TMSCs

source_name: Thymus MSCs from Patient 2

value: Patient 2


title: 6_10B

description: Gene expression profiling

source_name: NPC cell lines 6-10B


title: IMR90.iBMEC.Day 16 rep1

value: hPSC-Derived cell

value: Without Retinoic Acid


title: TMSC from Patient 3

description: Gene expression data from Patient 3 TMSCs

source_name: Thymus MSCs from Patient 3


title: 5-8F_miR-18a_knockdown

description: Gene expression profiling

source_name: NPC cell lines 5-8F,transient knockdown of miR-18a

value: transient knockdown of miR-18a


title: TMSC from Patient 1a

description: Gene expression data from Patient 1 TMSCs technical replicate

source_name: Thymus MSCs from Patient 1 technical replicate

value: Patient 1


title: BMSC from Patient 1a

description: Gene expression data from Patient 1 BMSCs technical replicate

source_name: Sternal MSCs from Patient 1 technical replicate


title: H6.iBMEC.Day 16

value: With Retinoic Acid


title: BMSC from Patient 2

description: Gene expression data from Patient 2 BMSCs

source_name: Sternal MSCs from Patient 2

value: Sternum


title: S8c

city: Yangzhou

first: Li

last: Wang

address: Wenhui east road no. 48

institute: Yangzhou University

data_processing:
Illumina HiSeq X-ten used for basecalling.
Clean reads were obtained by removing contaminating reads, adapter sequences, poly-A tails and other artifacts.
The clean reads were mapped to the reference Vitis vinifera genome  (http://www.genoscope.cns.fr/externe/Download/Projets/Projet_ML/data/)
The fragments per kilobase of exon per million reads (FPKM) values of gene expression were calculated using Cuffdiff program
Genome_build: Vitis vinifera 12X
Supplementary_files_format_and_content: The tab-delimited text files files include genes read count for each sample (.txt)

organism: Vitis vinifera

source_name: Sanbenti

growth_protocol: Three-year-old ‘Sanbenti’ and its bud sport ‘11-06-25’ grape berries growing in Longcong village of Huzhou city in the Zhejiang province, China

extract_protocol:
The berries of  ‘Sanbenti’ and its bud sport ‘11-06-25’ were used for RNA isolation. Total RNAs were extracted using TaKaRa MiniBEST plant RNA extraction kit (TaKaRa Bio Inc., Japan).
For RNA-Seq, the cDNA libraries were constructed using the TruSeqTM RNA Sample Preparation Kit (Illumina, Inc.) according to the manufacturer’s instructions, with three replicates for each sample.

treatment_protocol: Three-year-old ‘Sanbenti’ and its bud sport ‘11-06-25’ grape berries was sampled every 7 days from veraison (S5) to berry ripening (S10)

value: 21 days after veraison for 'Sanbenti'

tag: organ

value: berries


title: S8b


title: S9b

value: 28 days after veraison for 'Sanbenti'


title: S9a

value: 28 days after veraison for ''Sanbenti'


title: S9c


title: S8a


title: S7c

value: 14 days after veraison for 'Sanbenti'


title: S7b


title: S7a


title: S6c

value: 7 days after veraison for 'Sanbenti'


title: IMR90.iBMEC.Day 11 rep3

source_name: hPSC-Derived


title: IMR90.iBMEC.Day 11 rep2


title: S6b


title: TMSC from Patient 1

description: Gene expression data from Patient 1 TMSCs

source_name: Thymus MSCs from Patient 1

value: Thymus

value: MSCs

value: neonatal


title: S6a


title: S5c

value: veraison for 'Sanbenti'


title: H1.iBMEC.Day 16


title: S5b


title: S5a


title: H1.iBMEC.Day 11


title: S10c

value: maturity for 'Sanbenti'


title: S10b


title: IMR90.iBMEC.Day 6 rep3

value: hPSC-Derived cell


title: S10a


title: B9c

value: 28 days after veraison for '11-06-25'


title: IMR90.iBMEC.Day 11 rep1

value: Without Retinoic Acid


title: IMR90.iBMEC.Day 6 rep2


title: B9b


title: H6.iBMEC.Day 11


title: IMR90.iBMEC.Day 6 rep1


title: B9a


title: No. 4 cage number 3 rat [4-3]

city: Xiamen

first: Zhenghong

last: Zuo

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District, Xiamen, Fujian Province, China

department: School of Life Sciences, Xiamen University

institute: Xiamen University

description:
4-3
raw data file: 4-2--4-3.gpr
TBT+BPA, inject TBT 100ng/kg+ BPA 50ug/kg which were dissolved in ethanol and then sesame oil at a ratio of 10% ethanol and 90% oil.Eg:if the weight of rat is 5g, the TBT100+BPA50 is 25ul.

hyb_protocol: pre-hybridization:  1)Assembled  CustomArray™ microarray with Hybridization Cap and Clips；  2)Fill the hybridization chambers with nuclease-free water.Avoid introducing air bubbles into the chambers. Cover the solution portals with adhesive tape to evaporation.  3)Incubate at 65°C for 10min.  4)Remove the microarray from the incubator and bring to room temperature.Remove the adhesive tape and aspirate the water out of the hybridization chambers.  5)Fill the hybridization chambers with Pre-hybridization Solution.Mix gently by pipetting.A small air bubble can be introduced to improve the mixing process if the arrays are rotated.Wipe the surface clean with a lint-free tissue and cover the solution portals with adhesive tape.  6)Load the microarry onto the rotisserie in the hybridization oven and incubate at 37°C for 60 min with gentle rotation.    Hybridization:  1)Prepare the hybridization solution with labeled mRNA target .  2)Denature the hybridization solution at 95°C for 3 minutes,and then cool for 20 seconds on ice.Remove the hybridization solution from ice and keep it at room temperature.  3)Spin down the hybridization solution in a microcentrifuge for 5 seconds at maximum speed.  4)Remove the adhesive tape and pipet the pre-hybridization solution out of the hybridization chambers.  5)Fill the hybridization chambers with the hybridization solution and mix gently with repeated pipetting.A small air bubble wil form,and it will improve the mixing process if the arrays are rotated in the hybridization rotisserie oven.  6)Carefully wipe excess solution from the surface of the hybridization cap with a lint-free tissue,and cover the solution portals with adhesive tape.  7)Load the microarry onto the rotisserie in the hybridization oven and incubate at 37°C for 16 hours with gentle rotation.    Hybridization washing:  1)Remove the microarray from the hybridization oven.Remove the adhesive tape and pipet the hybridization solution out of the chambers.  2)Using the Wash solution 1,rinse the hybridization chambers,fill the chambers,and incubate the array for 3 minutes at room temperatrue.Remove the Wash solution 1 from the hybridization chambers.  3)Using the Wash solution 2,rinse the hybridization chambers,fill the chambers,and incubate the array for 3 minutes at room temperatrue.Remove the Wash solution 2 from the hybridization chambers.  4)Using the Wash solution 3,rinse the hybridization chambers,fill the chambers,and incubate the array for 3 minutes at room temperatrue.Remove the Wash solution 3 from the hybridization chambers.  5)Repeat step one more time for a total of two washings with the Wash solution 3.

scan_protocol: Imaging is done by laser scanner GenePix4000B(Molecular Device). At first, remove the microarray from the clamp and place it horizontally. Then cover the semiconductor microarray surface with the imaging solution. Using a fresh lifterslip cover it,taking care not to introduce air bubbles. At last, load the microarray into the scanner to scan.

data_processing: Raw signals were normalized with subtract background correction and quantile normalization method, Normalized intensities were transformed to gene expression log2 value. Ratio and log2 ratio of normalized spot intensites between test sample and control sample were calculated. The p-values are calculated with ANOVA Method(O'Mahony, Michael (1986). Sensory Evaluation of Food: Statistical Methods and Procedures. CRC Press. pp. 487. ISBN 0-8247-7337-3). It means the probability of control sample and test sample are no differential expression. So, if p-value (Differentially expressed) is greater than thethreshold it means no differential expression was observed.

organism: Rattus norvegicus

label_protocol: 1. Reverse Transcription to Synthesize First Strand cDNA is primed with the T7 Oligo(dT) Primer to synthesize cDNA containing a T7 promoter sequence.  2. Second Strand cDNA Synthesis converts the single-stranded cDNA into a double-stranded DNA (dsDNA) template for transcription. The reaction employs DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second-strand cDNA.  3. cDNA Purification removes RNA, primers, enzymes, and salts that would inhibit in vitro transcription.  4. In Vitro Transcription to Synthesize Amino Allyl-Modified aRNA with aaUTP generates multiple copies of amino allyl-modified aRNA from the double-stranded cDNA templates; this is the amplification step.  5. aRNA Purification removes unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the aRNA and to facilitate NHS ester coupling or subsequent enzymatic reactions.  6.aRNA:Dye Coupling Reaction takes place between the amino allyl-modified UTP residues on the aRNA and amine reactive Cy5 dyes.  7. Dye Labeled aRNA Purification removes free dye and exchanges the buffer with Nuclease-free Water.

growth_protocol: All the procedures involving animals were conducted in accordance with the ethical principles adopted by the Animal Experimental Center of Xiamen University and were approved by the Ethics Committee on Animal Experiments (CEEA) at Xiamen University. Sprague-Dawley rats (200-250 g body weight) from Shanghai SLAC Laboratory Animal Co. Ltd. were transferred to the Animal Experimental Center of Xiamen University, where they were kept in individual polypropylene cages with corn cob as bedding material and maintained under ambient temperature (25 ± 1℃) with a 12/12 h light /dark cycle and ad libitum access to water and food.

extract_protocol: 1. For proper amount of cells or homogenized tissue, add 1mL of TRIzol reagent and mix by briefly vortex. Stand for 5 mins at room temperature. If a lot of insoluble material exists after homogenization and room-temperature incubation, remove by centrifugation at 12,000Xg for 10 mins at 4ºC. Transfer the supernatant to a fresh tube.  2. Add 200ul chloroform for 1ml mixture and vortex for 15 sec. Then stand for 5 mins at room temperature.  3. Centrifuge the mixture for 15 min at ≥12000xg at 4ºC.  4. Transfer the aqueous phase (the upper layer containing RNA) to a fresh tube.  5. Add equal volume of 100% Isopropanol to the aqueous phase, mix by inverting the tube several times.  6. Incubate at ‐20ºC for ≥30 min.  7. Centrifuge at 13000 rpm for 15 min at 4ºC.  8. Wash the pellet with 80% EtOH, invert the tube several times. Centrifuge at 7500 rpm for 5 min at -4ºC.  9. Carefully discard the supernatant without touching the pellet, dry the pellet at room temperature.  10. Dissolve the pellet with 20‐30ul DEPC-treated H2O, based on the size of the pellet. RNA solution should be stored at -80ºC.

treatment_protocol: Pregnant females were housed singly, and on postnatal day 1 (PND1), pups in each litter were reduced to five females.  TBT 100 ng/kg (TBT100), BPA 50μg/kg (BPA50) and TBT100 combined with BPA50 (TBT+BPA) were administered by subcutaneous injection daily from PND1 to PND16, whereas the control rats received an equal volume of vehicle (5 μL/g). All compounds were dissolved in ethanol and then sesame oil at a ratio of 10% ethanol and 90% oil. The vehicle was also prepared with this ratio. Actual dosing volumes were adjusted based on the body weights recorded every day.

tag: strain

value: Sprague-Dawley

tag: gender

value: female

tag: injected with

value: TBT100 combined with BPA50 (TBT+BPA)

value: ovary

tag: tissue type

value: polycystic ovaries


title: BMSC from Patient 1

description: Gene expression data from Patient 1 BMSCs

source_name: Sternal MSCs from Patient 1

value: Patient 1

value: Sternum


title: No. 4 cage number 1 rat [4-1]

description:
4-1
raw data file: 3-3--4-1.gpr
TBT+BPA, inject TBT 100ng/kg+ BPA 50ug/kg which were dissolved in ethanol and then sesame oil at a ratio of 10% ethanol and 90% oil.Eg:if the weight of rat is 5g, the TBT100+BPA50 is 25ul.


title: No. 3 cage number 2 rat [3-2]

description:
3-2
raw data file: 2-3--3-2.gpr
BPA50, inject BPA 50ug/kg which were dissolved in ethanol and then sesame oil at a ratio of 10% ethanol and 90% oil.Eg:if the weight of rat is 5g, the BPA50 is 25ul.

value: BPA 50μg/kg (BPA50)


title: B8c

value: 21 days after veraison for '11-06-25'

value: berries


title: No. 4 cage number 2 rat [4-2]

description:
4-2
raw data file: 4-2--4-3.gpr
TBT+BPA, inject TBT 100ng/kg+ BPA 50ug/kg which were dissolved in ethanol and then sesame oil at a ratio of 10% ethanol and 90% oil.Eg:if the weight of rat is 5g, the TBT100+BPA50 is 25ul.


title: PGCs 8dpf rep3

city: Greensboro

first: Ramji

middle: Kumar

last: Bhandari

state: NC

address: 321 McIver St

department: Biology

institute: University of North Carolina Greensboro

library_source: genomic

data_processing:
Bismark (Version: v0.19.0) was used to map bisulfite sequencing reads onto medaka genome (Ensembl release-95) with default parameters (Krueger and Andrews, 2011). To guarantee getting the most accurate mapping result, we only retained the reads being mapped on unique position of genome. The utility “bismark_methylation_extractor” wrapped in Bismark was used to extract methylation levels on each site.
Genome_build: medaka genome (Ensembl release-95)
Supplementary_files_format_and_content: bedGraph

organism: Oryzias latipes

source_name: PGCs 8dpf

growth_protocol: The medaka strain Hd-rR was used and maintained under standard conditions

extract_protocol:
Genomic DNA and total RNA from each embryo samples were extracted using AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN, Cat No.: 80224) according to the manufacturer’s instruction.
Whole genome bisulfite sequencing (WGBS) libraries were prepared with NEBNext® Ultra™ II FS DNA Library Prep Kit (NEB, E7805S) according to the manufacturer’s user manual.

treatment_protocol: wildtype

value: Hd-rR

value: primordial germ cells


title: No. 3 cage number 1 rat [3-1]

description:
3-1
raw data file: 2-2--3-1.gpr
BPA50, inject BPA 50ug/kg which were dissolved in ethanol and then sesame oil at a ratio of 10% ethanol and 90% oil.Eg:if the weight of rat is 5g, the BPA50 is 25ul.


title: No. 3 cage number 3 rat [3-3]

description:
3-3
raw data file: 3-3--4-1.gpr
BPA50, inject BPA 50ug/kg which were dissolved in ethanol and then sesame oil at a ratio of 10% ethanol and 90% oil.Eg:if the weight of rat is 5g, the BPA50 is 25ul.


title: No. 2 cage number 3 rat [2-3]

description:
2-3
raw data file: 2-3--3-2.gpr
TBT100, inject TBT 100ng/kg which were dissolved in ethanol and then sesame oil at a ratio of 10% ethanol and 90% oil.Eg:if the weight of rat is 5g, the TBT100 is 25ul.

value: TBT 100 ng/kg (TBT100)


title: H6.IBMEC.Day 6


title: No. 2 cage number 2 rat [2-2]

description:
2-2
raw data file: 2-2--3-1.gpr
TBT100, inject TBT 100ng/kg which were dissolved in ethanol and then sesame oil at a ratio of 10% ethanol and 90% oil.Eg:if the weight of rat is 5g, the TBT100 is 25ul.


title: No. 2 cage number 1 rat [2-1]

description:
2-1
raw data file: 1-1--2-1.gpr
TBT100, inject TBT 100ng/kg which were dissolved in ethanol and then sesame oil at a ratio of 10% ethanol and 90% oil.Eg:if the weight of rat is 5g, the TBT100 is 25ul.


title: B8b


title: EZH2 KO-DDX18-KD2

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

description:
messenger RNA
EZH2KO-DDX18 KD-RNA-seq.xlsx

data_processing:
RNA-seq, ChIP/CLAP-seq reads were aligned to the mm9 or mm10 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
Basecalls performed using CASAVA version
FPKM was calculated by Cufflink 2.1.1
Genome_build: mm10

organism: Mus musculus

source_name: EZH2 KO mES cells

extract_protocol:
Cell culture: ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).
RNA-seq: Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
ChIP-seq: BirA- or FLAG-Biotin-ESCs were cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with glycine to a final concentration of 0.125 M for another 5min. Chromatin was sonicated, cleared by centrifugation, and incubated overnight at 4℃ with Dynabeads M280 streptavidin. followed by stringent washes and elution. Eluates were reverse cross-linked overnight at 65℃ and deproteinated with proteinase K at 56℃ for 30 min. DNA was purified using DNA purification kit (Qiagen).
CLIP and TAP-seq: The CLIP method was performed as described before with the specific modifications below. TAP method was developed by our lab sharing most of the same steps with CLIP, but including tandom purification and avoiding SDS-PAGE separation. About 107 cells of FbioDDX18 ESCs grown on one 15-cm plate were harvested and resuspended with 5 ml cold PBS. The cells were plated back to the plate and crosslinked with 600 mJ/cm2 of 254 nm UV light. The nucleuses were prepared by incubated the cells in hypotonic buffer (20 mM HEPES, pH 7.5, 10 mM KCl, 1.5 mM MgCl2, 1 mM EDTA, 0.2% NP-40, 10% glycerol, 1 mM DTT, 1 mM PMSF, 1/500 proteinase inhibitor cocktail, 400 U/ml RNase Inhibitor) for 4 minutes and the cells were lysed by a 26 5/8 Gauge needle and briefly sonicated. Incubate the cells for 30mins on a rotator at 4℃. Treat the lysate with 30 µl RQ1 DNase at 37℃ for 10mins. The insoluble pellet was spun down and the supernatant was harvested. About 40 µl pre-equilibrated FLAG M2 resins (Sigma) were used for each purification. The FLAG resins were incubated with lysate overnight at 4 °C and washed twice with cold CLIP lysis buffer and two more times with high salt wash buffer (5XPBS, 0.5% NP-40, 0.5% sodium deoxycholate, 0.1% SDS). For TAP experiments, the proteins were eluted with 200 ng/ml 3xFLAG peptide dissolved in CLIP lysis buffer (sigma) for three times. The eluents were pooled together and incubated with 60 µl pre-equilibrated streptavidin (M-280, Invitrogen) beads for three hours. The samples were washed twice with SDS-urea wash buffer (50 mM Tris pH 7.4, 2% SDS, 1 M urea) and twice with SDS-high salt wash buffer (5XPBS, 0.5% NP-40, 0.5% SDS) at room temperature. The protein-RNA complex bound beads were washed four times with PNK buffer (50 mM Tris pH 7.4, 10 mM MgCl2, 0.5% NP-40). Then the RNAs were partially digested with MNase (NEB, 1:105 diluted) at 37 °C for 10 min (mixed with an Eppendorf Thermomixer at 1,200 rpm for 5 second per 30 seconds). The reaction was stopped by PNK-EGTA buffer (PNK buffer with 2 mM EGTA). Then the beads were washed twice with SDS-urea wash buffer and twice with PNK buffer. To dephosphorylate the RNA, the beads were treated with CIP (NEB) for 10 min at 37 °C (mixed with an Eppendorf Thermomixer at 1,200 rpm for 5 seconds per 30 seconds). After two more washes with PNK buffer, the pre-adenylated 3’ linker (rAppAGATCGGAAGAGCACACGTCT-NH2, Takara) was ligated with truncated T4 RNA ligase 2 (NEB) at 16 °C overnight. The non-ligated 3’ linker was washed away with two washes of CLIP lysis buffer and two washes of PNK buffer. The RNAs were then phosphorylated by T4 PNK (NEB) for 10 min at 37 °C. Then for CLIP experiments, the RNA was subjected to SDS–PAGE separation and transfer, autoradiograph, ribonucleoprotein isolation, proteinase K treatment, and overnight RNA precipitation. For TAP experiments, the samples were treated with Proteinase K (50 mM Tris, pH 7.4, 150 mM NaCl, 0.5% SDS, and 20 µg Proteinase K) for 30 min at 37 °C to elute the protein-RNA complex. Then the RNAs were purified and ligated with 5’ RNA adaptor (GUUCAGAGUUCUACAGUCCGACGAUC, TAKARA) by T4 RNA ligase (Ambion). Then the RNAs were reverse transcribed by Superscript III with RT primer (AGACGTGTGCTCTTCCGATCT, Takara) and amplified for 20 cycles with Q5 DNA polymerase (NEB)
NEBNext Ultra RNA/DNA Library Prep Kit for Illumina

value: embryonic stem cells

value: serum+LIF


title: No. 1 cage number 2 rat [1-2]

description:
1-2
raw data file: 1-2--1-3.gpr
control, inject ethanol and sesame oil at a ratio of 10% ethanol and 90% oil. Eg:if the weight of rat is 5g, the vehicle is 25ul.

value: vehicle (5 μL/g)

value: normal


title: EZH2 KO-DDX18-KD1


title: H1.iBMEC.Day 6

value: hPSC-Derived cell


title: No. 1 cage number 3 rat [1-3]

description:
1-3
raw data file: 1-2--1-3.gpr
control, inject ethanol and sesame oil at a ratio of 10% ethanol and 90% oil. Eg:if the weight of rat is 5g, the vehicle is 25ul.

value: Sprague-Dawley

value: female


title: PGCs 8dpf rep1


title: No. 1 cage number 1 rat [1-1]

description:
1-1
raw data file: 1-1--2-1.gpr
control, inject ethanol and sesame oil at a ratio of 10% ethanol and 90% oil. Eg:if the weight of rat is 5g, the vehicle is 25ul.

value: ovary


title: PGCs 10dpf rep3

source_name: PGCs 10dpf


title: EZH2 KO-control-2


title: H6.iBMEC.Day 3


title: B7c

value: 14 days after veraison for '11-06-25'


title: IMR90.iBMEC.Day 3


title: EZH2 KO-control-1


title: PGCs 10dpf rep2


title: H1.iBMEC.Day 3


title: PGCs 10dpf rep1


title: PGCs 8dpf rep2


title: IMR90.hiPSC

source_name: hPSC

value: hPSC


title: p53 KO-DDX18-KD2

description:
messenger RNA
p53KO-DDX18 KD-RNA-seq.xlsx

source_name: p53 KO mES cells


title: B7b


title: p53 KO-DDX18-KD1


title: p53 KO-control-2


title: PGCs 12dpf rep3

source_name: PGCs 12dpf


title: B6c

value: 7 days after veraison for '11-06-25'


title: H6.hiPSC


title: B8a


title: PGCs 12dpf rep2


title: H1.hESC


title: p53 KO-control-1


title: PGCs 12dpf rep1


title: IMR90.EEF-iBMEC

value: hPSC-Derived endothelial cell

value: With Retinoic Acid


title: B6a

value: berries


title: B5c

value: veraison for '11-06-25'


title: PGCs 15dpf rep3

source_name: PGCs 15dpf

value: Hd-rR

value: primordial germ cells


title: mESC-CX-5461-1-2

description:
messenger RNA
ESC-CX-5461-RNA-seq.xlsx

source_name: CJ9 mES cells

value: embryonic stem cells

value: serum+LIF+1 µM CX-5461


title: B7a


title: H1.iEC

value: Without Retinoic Acid


title: B5b


title: H6.iEC


title: PGCs 15dpf rep2


title: mESC-CX-5461-control-3

description:
messenger RNA
ESC-CX-5461-RNA-seq.xlsx

value: serum+LIF+0 µM CX-5461


title: mESC-CX-5461-control-2

description:
messenger RNA
ESC-CX-5461-RNA-seq.xlsx


title: IMR90.iEC


title: PGCs 15dpf rep1


title: B10c

value: maturity for '11-06-25'


title: PGCs 25dpf female

source_name: PGCs 25dpf female


title: BMEC

source_name: Brain

value: Primary human endothelial cell


title: HUVEC

source_name: Human Umbilical Vein


title: B6b


title: mESC-CX-5461-control-1

description:
messenger RNA
ESC-CX-5461-RNA-seq.xlsx


title: mESC-CX-5461-1-3

description:
messenger RNA
ESC-CX-5461-RNA-seq.xlsx


title: B10b


title: PGCs 25dpf male rep2

source_name: PGCs 25dpf male

value: male


title: B10a


title: B5a


title: Isolated single cells from digested naïve heart of 10 weeks old C57/B6J wild type mice

status: Public on Dec 24 2019

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
10x genomics cell ranger v.2.2.0 pipeline
quality control, Cell Ranger Single Cell Software Suite (v2.2.0)
sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v2.2.0)
barcode processing, Cell Ranger Single Cell Software Suite (v2.2.0)
single-cell 5′ gene counting , Cell Ranger Single Cell Software Suite (v2.2.0)
alignment, Cell Ranger Single Cell Software Suite (v2.2.0)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

molecule: polyA RNA

source_name: Isolated single cells from spleens of wild type mice that were infected with chikungunya virus at day 0 and administered isotype monoclonal antibody

extract_protocol:
At 10 weeks of age female C57/B6J mice were bleed via cheek bleed. Blood was anticoagualted with heaprin. Mice were sacrificed in a CO2 chanber. Hearts were harvested, cleaned of extracrdiac tissues and perfused with PBS. HEarts were digested via incubation with collagenase, DNAse and RNAse at 37C for 30'.  Both digested hearts and peripheral blood were incubated with ACK lysis buffer. Celsl were staiend with Anti-CD45, Anti CD19 and Live/Dead aqua. Single CD45+, CD19+ Aqua - cells were facs sorted an processed to prepare single cell cDNA linraries using the Chromium 10X plarform.
Isolated single nuclei were subjected to droplet-based 5′ end massively parallel single-cell RNA sequencing, and libraries were prepared using Chromium Single Cell 5′ Reagent Kits in a BSL-3 level laboratory according to manufacturer’s protocol (10x Genomics).  The generated scRNAseq libraries were sequenced a NovaSeq S4 flow cell.

tag: age

value: 10 weeks old

value: wt

value: Heart

value: myocardial cells


title: Isolated single cells from peripheral blood of 10 weeks old C57/B6J wild type mice

source_name: Isolated single cells from spleens of wild type mice

value: Blood

value: peripheral blood cells


title: PGCs 25dpf male rep1


title: mESC-CX-5461-1-1

description:
messenger RNA
ESC-CX-5461-RNA-seq.xlsx


title: 3999875051_R02C02: Postoperative day1 following hip fracture surgery

city: Exeter

first: Jonathan

last: Mill

address: Barrack Road

country: United Kingdom

institute: Complex Disease Epigenetics Group, University of Exeter Medical School

description: genomic DNA from elderly patient undergoing major surgery

hyb_protocol: Bisulfite converted DNA was amplified with bisulfite specific primers to confirm conversion efficiency prior to array analysis. DNA methylation was then profiled using the Illumina Human Methylation 450 array.

scan_protocol: Genome-wide DNA methylation was profiled using the Illumina Infinium HumanMethylation450 BeadChip (Illumina Inc. San Diego, CA) (g450K arrayh) and scanned on an Illumina iScan.

data_processing: Following stringent quality control of the raw data, the data was normalized using the dasen function in the wateRmelon package for a combination of background adjustment and between-array quantile normalization.

label_protocol: Standard Illumina Protocol

extract_protocol: DNA samples was isolated from purified PBMCs collected at three time-points: i) immediately before surgery (timepointA), ii) in the morning of post-operative day 1 (timepointB) and iii) between post-operative day 4 and 7 (timepointC) prior to discharge from hospital.

value: Whole blood

tag: time point

value: B

tag: proportion of cd8t cell

tag: proportion of  cd4t cell

tag: proportion of nk cell

tag: proportion of bcell

tag: proportion of mono

tag: proportion of gran

tag: illuminabatch

value: Chip 7

value: F

tag: surgery

value: HipTrauma

tag: anesthesia

value: IA

tag: delirium

value: Control

tag: cancer

value: N


title: 3999875053_R03C02: Postoperative day4-7 following hip fracture surgery

tag: tissue

value: C

value: Chip 4


title: 3999875051_R03C02: Postoperative day4-7 following hip fracture surgery

tag: gender


title: 3999875025_R03C02: Postoperative day4-7 following hip fracture surgery

value: Chip 8


title: 3999875080_R03C02: Postoperative day4-7 following hip fracture surgery

value: Chip 5

value: M


title: 3999875080_R02C02: Postoperative day1 following hip fracture surgery


title: 3999875041_R01C02: Postoperative day4-7 following hip fracture surgery

value: Chip 3

value: TIVA

value: Delirium


title: 3999875025_R01C02: Baseline of hip fracture surgery

source_name: Baseline of hip fracture surgery

value: A


title: 3999875051_R01C02: Baseline of hip fracture surgery

value: Whole blood


title: 3999875025_R02C02: Postoperative day1 following hip fracture surgery

value: B


title: 3999875080_R01C02: Baseline of hip fracture surgery


title: 3999875041_R06C01: Postoperative day1 following hip fracture surgery


title: 3999875041_R05C01: Baseline of hip fracture surgery


title: 3999875053_R02C02: Postoperative day1 following hip fracture surgery


title: 3999875053_R01C02: Baseline of hip fracture surgery


title: 3999875053_R06C02: Postoperative day4-7 following hip fracture surgery


title: 3999875053_R05C02: Postoperative day1 following hip fracture surgery


title: 3999875053_R04C02: Baseline of hip fracture surgery


title: 3999875050_R06C02: Postoperative day4-7 following hip fracture surgery

value: Chip 6


title: 3999875080_R03C01: Postoperative day4-7 following hip fracture surgery

value: F


title: 3999875014_R03C02: Postoperative day4-7 following hip elective surgery

value: Chip 2

value: HipElective


title: 3999875050_R05C02: Postoperative day1 following hip fracture surgery

value: HipTrauma

value: IA

value: Control


title: 3999875013_R02C02: Postoperative day1 following hip fracture surgery

value: Chip 1

value: N


title: 3999875025_R05C02: Postoperative day1 following hip elective surgery

value: Chip 8


title: 3999875014_R01C02: Baseline of hip elective surgery

source_name: Baseline of hip elective surgery


title: 3999875025_R06C02: Postoperative day4-7 following hip elective surgery

value: C

value: M


title: 3999875014_R02C02: Postoperative day1 following hip elective surgery


title: 3999875080_R01C01: Baseline of hip fracture surgery

value: Chip 5

value: TIVA


title: NC4

city: Beijing

first: zhang

middle: zi

last: long

address: NO.1 Beichen West Road

institute: Beijing Institute of Genomics

hyb_protocol: Genome DNA was bisulfite converted using EZ DNA Methylation-Gold Kit, and then DNA was whole-genome amplified, enzymatically fragmented, purified, and applied to the Illumina Infinium Methylation 450k array according to the Illumina methylation protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: DNA methylation files were processed in R software packages using the Illumina Methylation Analyzer (IMA) package.

label: Cy5 and Cy3

source_name: Heel blood

extract_protocol: Genomic DNA was extracted using the QIAamp DNA Mini Kit according to the manufacturer`s instructions.

value: Male

value: blood

tag: protocol

value: Naturally Conceived Pregnancy


title: 3999875050_R05C01: Postoperative day1 following hip elective surgery

value: Whole blood

value: B

value: Chip 6


title: 3999875050_R04C01: Baseline of hip elective surgery

value: A

value: F

value: HipElective


title: 3999875080_R02C01: Postoperative day1 following hip fracture surgery

value: HipTrauma

value: Control


title: 3999875025_R05C01: Postoperative day1 following hip elective surgery

value: N


title: 3999875013_R04C01: Baseline of hip elective surgery

value: Chip 1

value: IA


title: 3999875013_R06C01: Postoperative day4-7 following hip elective surgery

value: C

value: M


title: 3999875050_R06C01: Postoperative day4-7 following hip elective surgery

value: TIVA


title: 3999875025_R06C01: Postoperative day4-7 following hip elective surgery

value: Chip 8


title: ART4

value: Female

value: blood

value: Assisted Reproductive Technology


title: 3999875051_R06C01: Postoperative day4-7 following hip elective surgery

value: Whole blood

value: Chip 7


title: 3999875013_R01C02: Baseline of hip fracture surgery

value: A


title: NC3

value: Male

value: Naturally Conceived Pregnancy


title: NC6


title: 3999875051_R05C01: Postoperative day1 following hip elective surgery

value: B

value: F

value: HipElective


title: 3999875025_R04C01: Baseline of hip elective surgery

value: Control

value: N


title: NC1


title: 3999875053_R06C01: Postoperative day4-7 following hip elective surgery

value: C

value: Chip 4


title: 3999875051_R04C01: Baseline of hip elective surgery

value: IA


title: NC2


title: ART5


title: NC5


title: ART2


title: ART6


title: ART3


title: 3999875025_R04C02: Baseline of hip elective surgery

value: Chip 8

value: M

value: TIVA


title: 3999875080_R06C01: Postoperative day4-7 following hip elective surgery

value: Chip 5


title: 3999875080_R05C01: Postoperative day1 following hip elective surgery

value: Whole blood


title: 3999875053_R04C01: Baseline of hip elective surgery


title: 3999875080_R04C01: Baseline of hip elective surgery


title: 3999875053_R05C01: Postoperative day1 following hip elective surgery


title: 786 AA2 MspI

city: Bronx

first: Amit

last: Verma

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

data_processing:
Library strategy: HELPGT
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (versions 1.3-1.4). Initial data processing was performed using the default read length of 36 bp, after which we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).
The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg19 freeze of the human genome at the UCSC genome browser. We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome. For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.
Genome_build: hg19
Supplementary_files_format_and_content: Hcount format; col1:  unique identifier for CCGG site;  col2: chromosome; col3: base position; col4: #reads mapped to this location on the forward strand; col5: #reads mapped to reverse strand; col6: #total reads mapped

source_name: ccRCC cell line

extract_protocol: Genomic DNA from cell lines were isolated by Puregene Core Kit A (Qiagen) Two custom adapters were created for HELP-tagging, referred to as AE and AS. As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence. Adapter AS contains an Illumina sequencing primer sequence. Five micrograms of genomic DNA were digested with HpaII and MspI in separate 200 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation. The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 3 μg of HpaII-digested DNA or 1 μg of MspI-digested DNA, 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl). After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB). The restriction fragments were end-repaired to inhibit to dimerization of adapters, and tailed with a single dA, at the 3’ end. After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl). After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion). Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen). The first strand cDNA produced was used as a template for PCR using the following conditions: 96°C for 2 minutes, then 18 cycles of 96°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension. After PCR, the library was purified using a QIAQuick PCR clean-up kit (Qiagen).

tag: cell line

value: ccRCC cell line

tag: enzyme

value: MspI

tag: agent

value: AA-treated


title: 786 AA2 HpaII

value: HpaII


title: 3999875041_R04C02: Postoperative day1 following hip elective surgery

tag: time point

value: B

tag: proportion of cd8t cell

value: Chip 3

tag: age

value: Delirium


title: 786 AA1 HpaII


title: 3999875041_R03C02: Baseline of hip elective surgery

value: A

tag: proportion of  cd4t cell

tag: proportion of nk cell

tag: proportion of bcell

value: F

value: HipElective


title: ART1

value: Female

value: blood

value: Assisted Reproductive Technology


title: 3999875014_R03C01: Postoperative day4-7 following hip elective surgery

value: C

tag: proportion of mono

tag: proportion of gran

tag: illuminabatch

value: Chip 2

value: M

value: Control

value: N


title: 3999875014_R01C01: Baseline of hip elective surgery

value: Whole blood

tag: surgery

tag: anesthesia

value: TIVA

tag: delirium


title: 3999875014_R02C01: Postoperative day1 following hip elective surgery

tag: tissue

tag: gender

tag: cancer


title: 3999875050_R03C02: Postoperative day4-7 following colorectal surgery

value: Chip 6

value: Colo

value: IA

value: Y


title: 786 Ctrl MspI

tag: cell line

value: ccRCC cell line

tag: enzyme

value: MspI

value: control


title: 769 AA2 HpaII

value: HpaII

tag: agent

value: AA-treated


title: 786 Ctrl HpaII


title: 3999875050_R02C02: Postoperative day1 following colorectal surgery

tag: time point

value: B

tag: proportion of cd8t cell

value: F


title: 769 AA1 HpaII


title: 769 AA2 MspI


title: 3999875013_R03C01: Postoperative day4-7 following colorectal surgery

value: C

tag: proportion of  cd4t cell

value: Chip 1

tag: age


title: 769 AA1 MspI


title: 769 Ctrl HpaII


title: 3999875050_R01C02: Baseline of colorectal surgery

source_name: Baseline of colorectal surgery

value: A

tag: proportion of nk cell

tag: proportion of bcell

value: Control


title: 3999875013_R06C02: Postoperative day4-7 following colorectal surgery

value: Whole blood

tag: proportion of mono

tag: proportion of gran

value: M

value: Delirium


title: 769 Ctrl MspI


title: 3999875013_R05C02: Postoperative day1 following colorectal surgery

tag: illuminabatch

tag: surgery

value: Colo


title: 3999875013_R02C01: Postoperative day1 following colorectal surgery

tag: anesthesia

value: IA

tag: delirium


title: 3999875053_R03C01: Postoperative day4-7 following colorectal surgery

tag: tissue

value: Chip 4

tag: gender

value: N


title: 3999875053_R02C01: Postoperative day1 following colorectal surgery

tag: cancer


title: SMS-CTR_DMSO_Input

city: bethesda

first: Jack

last: Shern

state: MD

address: 10 Center drive

institute: NCI

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome using bwa and then use the MACS2 for peak calling
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using deeptools. The coverage is calculated as the number of reads per bin.

growth_protocol: SMS-CTR cells are cultured in RPMI 1640 containing 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody following the Active Motif's instructions of the ChIP-IT High Sensitivity Kit.
Libraries were prepared according to Illumina's TruSeq ChIP Sample Preparation Guide.

treatment_protocol: ChIP experiment was performed after SMS-CTR cells were treated with or without 100 nM trametinib for 48 hr. CASZ1 expression is induced by trametinib treatment.

tag: cell type

value: Rhabdomyosarcoma

tag: chip antibody


title: SMS-CTR_Trametinib_CASZ1

value: CASZ1 (in collaboration with Rockland, ab8540)


title: CTRtetCASZ1b_Input_Dox

source_name: SMS-CTR cells

growth_protocol: The CASZ1b stably transfected SMS-CTR cells (CTRtetCASZ1b) are cultured in RPMI 1640 containing 10% FBS. CASZ1b expression is induced by Dox treatment.

treatment_protocol: ChIP experiment was performed after CTRtetCASZ1b cells being treated with or without Dox for 48 hr.

tag: genotype

value: stably transfected with CASZ1b, Dox inducible

tag: dox status

value: Dox


title: SMS-CTR_Trametinib_Input


title: 3999875013_R04C02: Baseline of colorectal surgery

tag: time point

tag: proportion of cd8t cell

tag: proportion of  cd4t cell

value: Y


title: SMS-CTR_DMSO_CASZ1


title: CTRtetCASZ1b_Input_Ctrl

value: No dox


title: 3999875050_R04C02: Baseline of hip fracture surgery

tag: proportion of nk cell

tag: proportion of bcell

value: Chip 6

tag: age

value: HipTrauma


title: 3999875041_R04C01: Postoperative day4-7 following colorectal surgery

value: C

tag: proportion of mono

tag: proportion of gran

tag: illuminabatch

value: Chip 3


title: 3999875053_R01C01: Baseline of colorectal surgery

value: Whole blood

value: A

tag: surgery

tag: anesthesia

tag: delirium

value: Control


title: CTRtetCASZ1b_RNA_PolII_Dox

value: RNA Pol II (Active Motif, 39097)


title: CTRtetCASZ1b_RNA_PolII_Ctrl


title: 3999875041_R03C01: Postoperative day1 following colorectal surgery

tag: tissue

value: B

tag: gender

value: M

value: Colo

value: IA

tag: cancer


title: CTRtetCASZ1b_H3K4me3_Dox

tag: cell type

value: Rhabdomyosarcoma

tag: genotype

tag: chip antibody


title: C2C12_shCtrl-Rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg19 whole genome using STAR 2.5.1
Counts per million (CPM) were quantified using the Partek E/M model
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each Sample.

source_name: C2C12 cells

growth_protocol: C2C12 cells are maintained in growth medium. To induce C2C12 cells differentiation, the cells are cultured in differentiation medium. Growth medium: DMEM, 10% fetal calf serum, 100µg/mL streptomycin, 100U/mL penicillin, and L-glutamine. Differentiation medium: DMEM, 2% horse serum, 100µg/mL streptomycin, 100U/mL penicillin, and L-glutamine.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CASZ1a, CASZ1b or EV was transiently transfected into C2C12 cells by nucleofector electroporation and cultured in GM for 48 hr before RNA extraction. To generate Casz1 stable knockdown, C2C12 cells were infected with control shRNA (shCtrl) or Casz1 shRNA (shCasz1) particles. The stable Casz1 knockdown cells were cultured in DM for 48 hr before RNA extraction.

value: Differentiated C2C12

tag: transfected with

value: shCtrl


title: 3999875041_R02C01: Baseline of colorectal surgery

tag: time point

tag: proportion of cd8t cell

tag: proportion of  cd4t cell

value: Y


title: CTRtetCASZ1b_H3K4me3_Ctrl

value: stably transfected with CASZ1b, Dox inducible

tag: dox status

value: No dox


title: CTRtetCASZ1b_H3K27me3_Dox

value: Dox

value: H3K27me3 (Millipore, 07-449)


title: C2C12_shCtrl-Rep1


title: 3999875051_R05C02: Postoperative day1 following colorectal surgery

tag: proportion of nk cell

tag: proportion of bcell

tag: proportion of mono

value: Chip 7

tag: age


title: 3999875051_R06C02: Postoperative day4-7 following colorectal surgery

value: Whole blood

value: C

tag: proportion of gran

tag: illuminabatch

tag: surgery

tag: anesthesia


title: C2C12_shCtrl-Rep2


title: C2C12_CASZ1a-Rep1

description: RNA-seq_C2C12_CASZ1_Overexpression_CPM.txt

value: Undifferentiated C2C12


title: CTRtetCASZ1b_H3K27Ac_Dox

value: H3K27ac (Abcam, ab4729)


title: CTRtetCASZ1b_H3K27Ac_Ctrl


title: CTRtetCASZ1b_CASZ1_Dox

value: CASZ1 (in collaboration with Rockland, ab8540)


title: CTRtetCASZ1b_CASZ1_Ctrl


title: CTRtetCASZ1b_Ty1_Dox

value: Ty1 (Diagenode, C15200054)


title: CTRtetCASZ1b_H3K27me3_Ctrl


title: C2C12_EV-Rep3

value: empty vector


title: CTRtetCASZ1b_Ty1_Ctrl


title: 3999875051_R03C01: Postoperative day4-7 following colorectal surgery

tag: tissue

tag: gender

value: M

value: Colo

value: IA

tag: delirium

value: Control

tag: cancer


title: C2C12_EV-Rep2

tag: cell type

tag: transfected with


title: ATAC-seq_CTRtetCASZ1b_Dox

data_processing:
Basecalls performed using CASAVA version 1.4
Data was analyzed by Encode ATAC-seq pipeline
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using deeptools. The coverage is calculated as the number of reads per bin.

growth_protocol: The CASZ1b stably transfected SMS-CTR cells (CTRtetCASZ1b) cells are cultured in RPMI 1640 containing 10% FBS.

extract_protocol:
Chromatin extraction and ATAC-seq was performed as previously described by William J Greenleaf and Howard Y Chang's group (Nature Methods. 960 | VOL.14 NO.10 | OCTOBER 2017, PMID 28846090).
Libraries were prepared according to the protocol from William J Greenleaf and Howard Y Chang's group using Illumina's Nextera DNA library prep kit.

treatment_protocol: ATACseq experiment was performed after CTRtetCASZ1b cells being treated with or without Dox for 48 hr.

value: Rhabdomyosarcoma


title: 3999875051_R02C01: Postoperative day1 following colorectal surgery

tag: time point

value: B

tag: proportion of cd8t cell

value: Y


title: ATAC-seq_CTRtetCASZ1b_Ctrl


title: C2C12_Input_shCas

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm10 genome using bwa and then use the MACS2 for peak calling
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using deeptools. The coverage is calculated as the number of reads per bin.

growth_protocol: C2C12 cells are cultured in RPMI 1640 containing 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody following the Active Motif's instructions of the ChIP-IT High Sensitivity Kit.
Libraries were prepared according to Illumina's TruSeq ChIP Sample Preparation Guide.

treatment_protocol: ChIP experiment was performed after shCtrl and shCasz1 C2C12 cells being cultured in differentiation medium (DMEM containing 2% horse serum) for 48 hr.

value: Differentiated C2C12

tag: chip antibody

tag: genotype

value: shCas


title: 786 AA1 MspI

tag: cell line

value: ccRCC cell line

tag: enzyme

value: MspI

tag: agent

value: AA-treated


title: C2C12_Input_shCtrl

value: shCtrl


title: C2C12_EV-Rep1

value: Undifferentiated C2C12


title: 3999875051_R01C01: Baseline of colorectal surgery

value: Whole blood

value: A

tag: proportion of  cd4t cell

tag: proportion of nk cell

tag: proportion of bcell

tag: proportion of mono

tag: proportion of gran

value: Chip 7

tag: age


title: MAZR-cKO 3

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgase 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

description: Sample 6 (LA124)

data_processing:
The quality of the sequenced reads was checked using FastQC tool.
STAR 2.5.2b was used to align the reads to the mouse reference genome mm10 (UCSC; downloaded from Illumina iGenomes website). The number of uniquely mapped reads associated with each gene according to Ensembl gene annotation was counted using subread v1.5.1 package.
The downstream data analysis was performed using R version 3.4 and its corresponding Bioconductor module. The count data were normalized for library size using the Trimmed Mean of M-values (TMM) method implemented in edgeR R package. Genes that did not have at least one count per million (CPM) in at least three samples among the compared sample groups were filtered out as lowly expressed.
Prior to statistical testing, an offset of 1 was added to the normalized expression values and the data were log2 transformed. R package ROTS was used for performing the statistical testing and p-value < 0.05 and absolute fold change > 1.5 were required for detecting the differentially expressed genes. The Gh gene was removed from the final DE gene list as the inspection of the aligned reads revealed that the alignments for Gh had almost identical positions on a narrow region and contained many mismatches
Genome_build: mm10
Supplementary_files_format_and_content: normalized expression value

source_name: Spleen

extract_protocol:
Total RNA was prepared from approximately 0.8 - 2 x 10^6 FACS-purified WT,DEREG and MAZR-cKO,DEREG CD4+eGFP+ Treg cells with the RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using a Sciclone NGS Workstation (PerkinElmer) and a Zepyhr NGS Workstation (PerkinElmer) with the TruSeq Stranded mRNA LT sample preparation kit (Illumina).

tag: strain

tag: tissue

value: Spleen

value: CD4+Foxp3+ Treg cell

value: MAZRf/f DEREG-eGFP+ CD4-cre+


title: C2C12_H3K4me3_DM_shCas

tag: cell type


title: 3999875051_R04C02: Baseline of colorectal surgery

tag: illuminabatch

tag: gender

value: M

tag: surgery

value: Colo

tag: anesthesia

value: IA

tag: delirium

value: Control

tag: cancer


title: MAZR-cKO 2

description: Sample 5 (LA121)

tag: genotype


title: C2C12_H3K27Ac_DM_shCas

value: Differentiated C2C12

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: 3999875014_R05C01: Postoperative day1 following colorectal surgery

tag: time point

value: B

tag: proportion of cd8t cell

tag: proportion of  cd4t cell

value: Chip 2

value: F

value: Y


title: 3999875014_R04C01: Baseline of colorectal surgery

tag: proportion of nk cell

tag: proportion of bcell

tag: proportion of mono


title: C2C12_H3K27Ac_DM_shCtrl

value: shCtrl


title: C2C12_H3K4me3_DM_shCtrl


title: WT 3

description: Sample 3 (LA124)

tag: strain

value: wild type DEREG-eGFP+


title: CD4_10000_L1 rep3

city: Tokyo

first: Kenji

last: Shimizu

address: 1-1-1 Yayoi, Bunkyo-ku

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

data_processing:
Basecalls performed using RTA version 2.4.11.
The sequenced CAGE tags were mapped to the mouse mm9 genomes using BWA software (v0.7.12) after discarding ribosomal RNAs. CAGE tags not mapped by BWA software were re-mapped by using HISAT2 (v2.0.5) software.
For tag-clustering, CAGE-tag 5' coordinates were subjected to Reclu clustering, with the maximum irreproducible discovery rate (IDR) of 0.1 and the minimum tag per million (TPM) value of 0.1 (Ohmiya, H. et al. RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE). BMC Genomics 15, 269. 2014). After merging overlapping bottom and top peaks, tag-clusters with the max TPM ≥ 3 were used for further analysis. Tag-clusters existed in the intron of known gene were omitted from the analysis as degraded mRNA. When tag-clusters existed within ±500 bp from 5’end of known transcripts, these were assigned to those genes. Within each tag-cluster, TSS was defined as the spacing between the positions of the 10% and 90% quantiles of tags in the cluster (Haberle, V., Forrest, A. R. R., Hayashizaki, Y., Carninci, P. & Lenhard, B. CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. Nucleic Acids Res. 43, e51. 2015).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample.

source_name: CD4+ T cell

extract_protocol:
Total RNA was extracted from purified T cells using TRIzol.
First strand cDNAs were transcribed to the 5’ end of capped RNAs and attached to CAGE "bar code" tags.

value: BALB/cCrSlc

value: CD4+ T cell

tag: treatment

value: 10000 ng/ml 2C11 with PD-1 engagemant


title: CD4_1000_L1 rep2

tag: cell type

value: 1000 ng/ml 2C11 with PD-1 engagemant


title: CD4_1000_L1 rep1


title: WT 2

description: Sample 2 (LA121)

tag: tissue

value: Spleen

value: CD4+Foxp3+ Treg cell


title: CD4_100_L1 rep1

value: 100 ng/ml 2C11 with PD-1 engagemant


title: 3999875025_R02C01: Postoperative day1 following colorectal surgery

value: Whole blood

tag: proportion of gran

tag: illuminabatch

value: Chip 8

tag: age

tag: gender

value: M

value: Colo

value: IA

value: N


title: CD4_100_L1 rep2


title: WT 1

description: Sample 1 (LA117)


title: 3999875025_R01C01: Baseline of colorectal surgery

value: A

tag: surgery

tag: anesthesia

tag: delirium

value: Control

tag: cancer


title: CD4_10_L1 rep2

value: 10 ng/ml 2C11 with PD-1 engagemant


title: CD4_10_L1 rep1


title: 3999875014_R06C01: Postoperative day4-7 following colorectal surgery

tag: time point

value: C

tag: proportion of cd8t cell

value: Chip 2

value: F

value: Y


title: CD4_10000 rep3

value: BALB/cCrSlc

value: CD4+ T cell

value: 10000 ng/ml 2C11 without PD-1 engagemant


title: 3999875050_R03C01: Postoperative day4-7 following colorectal surgery

tag: proportion of  cd4t cell

tag: proportion of nk cell

value: Chip 6


title: RNA_CCR6_Pos_2

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Basecalls performed using CASAVA 1.8.4
Sequence reads were mapped to the mouse (mm9) genomes with bowtie2 (2.2.2) with default settings. We kept one hit if multiple reads were mapped to the same position for each RNA-Seq libraries.
For each RNA-Seq sample, gene expression was quantified by RPKM with in-house script and RefSeq gene annotation.
Genome_build: mm9
Supplementary_files_format_and_content: rpkm: plan text file. Columns from left to right denote RefSeq ID, RPKM, gene transcript size, number of read mapped to exons, a combination of RefSeq ID, gene symbol, etc, and reserved column for future development.

source_name: CCR6+ LTi progenitor

extract_protocol: Single cell suspension were obtained from the bone marrow of C57BL/6 mice. For sorting CLP and rChILP, the lineage negative cells were enriched with the "Lineage Cell Depletion Kit, mouse" from Miltenyi Biotec according to the manual. Enriched Lineage negative bone marrow cells were stained with relative antibodies followed by sorting on a cell sorter FACS Aria III (BD Biosciences) for "live Lineage-CD127+Flt-3+Integrin α4β7-Sca1+c-Kit+" CLP and "live Lineage-CD127+Flt-3-Integrin α4β7+T1/ST2-c-Κit+" rChILP. For sorting PD-1+ non-LTi ILC progenitors and CCR6+ LTi progenitors, the Fc receptor-blocked bone marrow single-cell suspension was stained with PE-conjugated anti-integrin α4β7 antibody, followed by washing and incubation with anti-PE microbeads. The samples were then applied to the Miltenyi LS columns in magnetic field and washed three times by PBS with 3% FBS according to the manufacturer’s instruction. The integrin α4β7+ cells on the column were finally flushed into a collection tube for further surface molecule staining. Non-LTi ILC progenitors (live Lineage-CD127+Flt-3-Integrin α4β7+T1/ST2-c-Κit+PD-1+CCR6-) and LTi progenitors (live Lineage-CD127+Flt-3-Integrin α4β7+T1/ST2-c-Κit+PD-1-CCR6+) were then sorted via FACS Aria III (BD Biosciences). CLPs, total rChILPs, PD-1+ or CCR6+ progenitors described above were sorted directly into 700 μL of QIAzol Lysis Reagent in the miRNAeasy Micro Kit (QIAGEN, Cat#217084). Total RNA was extracted and RNA-Seq libraries were prepared through the Smart-seq2 method (PMID: 24385147) as previously described (PMID: 29466755). Multiplex sequencing reads of 50 bp were generated by the NHLBI DNA Sequencing and Computational Biology Core.

value: CCR6+ LTi progenitor

value: isolated from bone marrow


title: CD4_10000_L1 rep2

value: 10000 ng/ml 2C11 with PD-1 engagemant


title: CD4_10000 rep2


title: CD4_10000_L1 rep1


title: 3999875050_R02C01: Postoperative day1 following colorectal surgery

value: Whole blood

value: B

tag: proportion of bcell

tag: proportion of mono

value: Colo


title: 3999875013_R05C01: Postoperative day1 following hip elective surgery

value: Chip 1

value: M

value: HipElective

value: IA

value: N


title: 3999875025_R03C01: Postoperative day4-7 following colorectal surgery

value: C

value: Chip 8

value: Control


title: CD4_1000 rep2

tag: strain

value: BALB/cCrSlc

value: CD4+ T cell

tag: treatment

value: 1000 ng/ml 2C11 without PD-1 engagemant


title: CD4_10000 rep1

tag: cell type

value: 10000 ng/ml 2C11 without PD-1 engagemant


title: MAZR-cKO 1

description: Sample 4 (LA117)

tag: tissue

value: Spleen

value: CD4+Foxp3+ Treg cell

tag: genotype

value: MAZRf/f DEREG-eGFP+ CD4-cre+


title: RNA_PD1_Pos_2

source_name: PD-1+ non-LTi ILC progenitor

value: PD-1+ non-LTi ILC progenitor

value: isolated from bone marrow


title: CD4_100 rep2

value: 100 ng/ml 2C11 without PD-1 engagemant


title: CD4_1000 rep1


title: RNA_CCR6_Pos_1

value: CCR6+ LTi progenitor


title: RNA_PD1_Pos_1


title: CD4_100 rep1


title: RNA_CLP_2

source_name: common lymphoid progenitor (CLP)

value: common lymphoid progenitor (CLP)


title: CD4_10 rep2

value: 10 ng/ml 2C11 without PD-1 engagemant


title: 3999875080_R05C02: Postoperative day1 following colorectal surgery

value: Whole blood

value: B

tag: proportion of gran

tag: illuminabatch

value: Chip 5

tag: age

value: F

value: Colo

value: IA

value: N


title: CD4_0_L1 rep2

value: BALB/cCrSlc

value: CD4+ T cell

value: 0 ng/ml 2C11 with PD-1 engagemant


title: 3999875080_R04C02: Baseline of colorectal surgery

value: A

tag: gender

tag: surgery

tag: anesthesia

value: Control


title: CD4_0_L1 rep1


title: RNA_ChILP_2

source_name: common helper-like innate lymphoid progenitor (ChILP)

value: isolated from bone marrow


title: CD4_0 rep2

value: 0 ng/ml 2C11 without PD-1 engagemant


title: RNA_CLP_1


title: RNA_ChILP_1

value: common helper-like innate lymphoid progenitor (ChILP)


title: DO_10000_L1 rep3

description: DO.txt

source_name: DO11.10 T hybridoma

value: BALB/c x AKR/J

value: DO11.10 T hybridoma

value: 10000 nM pOVA with PD-1 engagemant


title: CD4_0 rep1


title: 3999875050_R01C01: Baseline of colorectal surgery

value: Whole blood

tag: time point

value: Chip 6

tag: delirium

tag: cancer

value: Y


title: dkfz-RIG-ref-PXA_19

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_19

hyb_protocol: Illumina

scan_protocol: Illumina

data_processing: Normalization was performed by applying the function preprocessIllumina available in Bioconductor package minfi, matrix processed value definition: Average Beta

label: Cy3, Cy5

source_name: Primary brain tumor tissue

label_protocol: Illumina

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

tag: methylation class

value: PXA

tag: location

tag: primary malignancy

tag: pdgfra amplified

tag: cdkn2a/b loss


title: DO_10000_L1 rep2

description: DO.txt

tag: strain

tag: cell type

tag: treatment


title: dkfz-RIG-ref-PXA_18

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_18


title: DO_10000_L1 rep1

description: DO.txt


title: 3999875080_R06C02: Postoperative day4-7 following colorectal surgery

tag: tissue

value: C

tag: proportion of cd8t cell

tag: proportion of  cd4t cell

tag: proportion of nk cell

tag: proportion of bcell

tag: proportion of mono

tag: proportion of gran

value: Chip 5

value: F

value: Colo

value: IA


title: dkfz-RIG-ref-PXA_17

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_17

tag: age

tag: gender


title: DO_1000_L1 rep2

description: DO.txt

value: 1000 nM pOVA with PD-1 engagemant


title: CD4_10 rep1

value: BALB/cCrSlc

value: CD4+ T cell

value: 10 ng/ml 2C11 without PD-1 engagemant


title: dkfz-RIG-ref-pedGBM-RTK2_04

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_04

tag: methylation class


title: DO_100_L1 rep2

description: DO.txt

value: 100 nM pOVA with PD-1 engagemant


title: dkfz-RIG-ref-PXA_16

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_16

tag: location


title: dkfz-RIG-ref-pedGBM-RTK1_11

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_11

tag: primary malignancy


title: DO_100_L1 rep1

description: DO.txt

value: BALB/c x AKR/J


title: dkfz-RIG-ref-PXA_15

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_15

tag: pdgfra amplified


title: DO_1_L1 rep2

description: DO.txt

value: DO11.10 T hybridoma

value: 1 nM pOVA with PD-1 engagemant


title: dkfz-RIG-ref-PXA_20

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_20

tag: cdkn2a/b loss


title: dkfz-RIG-ref-pedGBM-RTK2_05

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_05


title: DO_1_L1 rep1

description: DO.txt

tag: strain


title: dkfz-RIG-ref-PXA_14

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_14


title: DO_10000 rep3

description: DO.txt

tag: cell type

value: 10000 nM pOVA without PD-1 engagemant


title: RDtetCASZ1b_Tet-Rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg19 whole genome using STAR 2.5.1
Counts per million (CPM) were quantified using the Partek E/M model
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each Sample.

source_name: RD cells

growth_protocol: The CASZ1b stably transfected RD cells (RDtetCASZ1b) in which CASZ1b expression is tetracycline (Tet) inducible. The cells are cultured in RPMI 1640 containing 10% FBS.

treatment_protocol: RNA was isolated from RDtetCASZ1b cells that treated with or without Tet for 48 hr

value: Rhabdomyosarcoma

tag: genotype

tag: tetracycline status

value: tetracycline-treated


title: dkfz-RIG-ref-pedGBM-RTK1_09

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_09


title: dkfz-RIG-ref-PXA_13

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_13

value: PXA


title: DO_1000_L1 rep1

description: DO.txt

tag: treatment


title: RDtetCASZ1b_Tet-Rep1

value: CASZ1b stably transfected RD cells (RDtetCASZ1b)


title: dkfz-RIG-ref-pedGBM-RTK2_03

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_03


title: dkfz-RIG-ref-PXA_12

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_12


title: DO_10_L1 rep2

description: DO.txt

value: 10 nM pOVA with PD-1 engagemant


title: DO_10000 rep1

description: DO.txt


title: RDtetCASZ1b_Ctrl-Rep3

value: untreated


title: dkfz_RIG_31

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_31

value: f

value: cerebellum

value: MB Group4

value: yes

value: no


title: DO_10_L1 rep1

description: DO.txt


title: dkfz_RIG_30

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_30

value: MB SHH-AD


title: RDtetCASZ1b_Ctrl-Rep2


title: dkfz-RIG-ref-pedGBM-RTK1_10

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_10


title: dkfz-RIG-ref-PXA_10

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_10


title: dkfz_RIG_29

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_29

value: MB SHH-INF


title: DO_1000 rep1

description: DO.txt

value: BALB/c x AKR/J

value: 1000 nM pOVA without PD-1 engagemant


title: RDtetCASZ1b_Tet-Rep3


title: RDtetCASZ1b_Ctrl-Rep1


title: dkfz-RIG-ref-PXA_09

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_09


title: DO_10000 rep2

description: DO.txt

value: DO11.10 T hybridoma


title: dkfz_RIG_32

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_32

value: m

value: MB WNT


title: DO_100 rep2

description: DO.txt

value: 100 nM pOVA without PD-1 engagemant


title: dkfz-RIG-ref-PXA_08

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_08

value: PXA


title: dkfz_RIG_28

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_28


title: dkfz_RIG_26

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_26

value: MB


title: DO_100 rep1

description: DO.txt


title: 3999875013_R01C01: Baseline of colorectal surgery

description: genomic DNA from elderly patient undergoing major surgery

tag: tissue

value: Whole blood

tag: time point

value: A

tag: proportion of cd8t cell

tag: proportion of  cd4t cell

tag: illuminabatch

value: Chip 1

value: M

tag: surgery

value: Colo

tag: anesthesia

value: IA

tag: delirium

value: Control

tag: cancer

value: Y


title: dkfz-RIG-ref-PXA_11

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_11

tag: methylation class

tag: age

tag: gender

tag: location

tag: primary malignancy


title: dkfz-RIG-ref-PXA_07

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_07

tag: pdgfra amplified

tag: cdkn2a/b loss


title: 3999875013_R03C02: Postoperative day4-7 following hip fracture surgery

value: C

tag: proportion of nk cell

tag: proportion of bcell

tag: proportion of mono

tag: proportion of gran

value: F

value: HipTrauma

value: N


title: dkfz_RIG_25

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_25

value: f

value: cerebellum

value: no

value: yes


title: DO_10 rep2

description: DO.txt

tag: strain

value: BALB/c x AKR/J

tag: cell type

value: DO11.10 T hybridoma

tag: treatment

value: 10 nM pOVA without PD-1 engagemant


title: dkfz-RIG-ref-PXA_06

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_06

value: PXA


title: DO_1000 rep2

description: DO.txt

value: 1000 nM pOVA without PD-1 engagemant


title: dkfz-RIG-ref-PXA_05

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_05


title: dkfz_RIG_24

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_24

value: frontal lobe

value: MB


title: DO_10 rep1

description: DO.txt


title: DO_1 rep2

description: DO.txt

value: 1 nM pOVA without PD-1 engagemant


title: 3999875041_R05C02: Postoperative day4-7 following hip elective surgery

tag: tissue

value: Whole blood

tag: time point

tag: proportion of cd8t cell

tag: proportion of  cd4t cell

tag: illuminabatch

value: Chip 3

tag: surgery

value: HipElective

tag: anesthesia

value: TIVA

value: Delirium


title: dkfz_RIG_23

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_23

tag: methylation class

tag: age

tag: gender

value: m

tag: location

tag: primary malignancy


title: dkfz_RIG_08

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_08

value: f

value: parietal left

value: ALL

tag: pdgfra amplified

tag: cdkn2a/b loss


title: dkfz-RIG-ref-PXA_03

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_03


title: DO_0_L1 rep2

description: DO.txt

tag: strain

value: BALB/c x AKR/J

value: 0 nM pOVA with PD-1 engagemant


title: dkfz-RIG-ref-PXA_02

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_02


title: C2C12_shCasz1-Rep3

tag: cell type

value: Differentiated C2C12

tag: transfected with


title: DO_0_L1 rep1

description: DO.txt

value: DO11.10 T hybridoma

tag: treatment


title: DO_0 rep2

description: DO.txt

value: 0 nM pOVA without PD-1 engagemant


title: C2C12_shCasz1-Rep2


title: dkfz-RIG-ref-PXA_01

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_01

value: PXA


title: dkfz-RIG-ref-pedGBM-RTK2_20

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_20


title: C2C12_shCasz1-Rep1


title: DO_0 rep1

description: DO.txt


title: ASA01081 continuous 13 weeks

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Gene expression from nasal epithelium of ASA01081 (continuous dosing regimen) at 13 weeks.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.48.0), using R version 3.2.3 and the Brainarray hugene10sthsentrezgcdf R package (version 20.0.0).

source_name: brushing of nasal epithelium

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

extract_protocol: Total RNA was isolated using Qiagen miRNeasy Mini Kit following manufacturer’s instruction. Integrity of the RNA samples was assessed by Agilent BioAnalyzer, and purity of the RNA was confirmed using a NanoDrop spectrophotometer.

tag: batch

value: batch 3

tag: subject

tag: dosing regimen

value: continuous

tag: timepoint

value: 13 weeks

tag: Sex

value: female


title: C2C12_CASZ1b-Rep3

description: RNA-seq_C2C12_CASZ1_Overexpression_CPM.txt

value: Undifferentiated C2C12


title: dkfz-RIG-ref-pedGBM-RTK2_19

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_19


title: dkfz-RIG-ref-pedGBM-RTK2_18

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_18


title: C2C12_CASZ1b-Rep1


title: dkfz-RIG-ref-pedGBM-RTK2_17

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_17


title: dkfz-RIG-ref-PXA_04

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-PXA_04


title: DO_1 rep1

description: DO.txt

value: 1 nM pOVA without PD-1 engagemant


title: T11R1

city: Thuwal

first: Magdalena

last: Julkowska

state: Makkah

address: KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

description:
replicate 1
batch2

data_processing:
bcl2fastq v1.8.4 for raw data processing
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR genome by Tophat, and quantified in samtools htseq-count
Reads were mapped to TAIR10 genome by TopHat (v2.0.14), with Bowtie (2.1.0.0)
Transcripts were quantified using Samtools ht-seq-count
Counts per million (cpm) were calculated and normalized by the size of the library.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Expression values of cpm (log2 transformed) for each sample.

organism: Arabidopsis thaliana

source_name: seedling leaf tissue

growth_protocol: Plates each containing about 80 Arabidopsis Col-0 seedlings were grown inside growth chamber (Percival) with 22°C under 16h / 8h of light / dark cycle (~100 μmol m−2 s−1) with 60% relative humidity. The acclimation treatment was applied by subjecting plates with Arabidopsis seedlings into the growth chamber (Percival) with the temperature gradually rising from 22C to 45C over the course of 6 hours (starting at the beginning of the photoperiod) in the light and keep at 45C for 90 mins. Subsequently, the plates were transferred back to a growth chamber with standard (22C) temperature. For the heat shock application, the growth chamber (Percival) was pre-heated to 45C with lighting (~100 μmol m−2 s−1) and 60% relative humidity. Each plate containing 80 acclimated or non-acclimated seedlings was transferred from the control growth condition (22C) chamber to a heated growth chamber (45C) for 90 mins from 1:30 pm to 3:00 pm (7.5 - 9h after the beginning of the photoperiod).

extract_protocol:
RNA extraction was performed for each sample using RNeasy Plant Mini Kit (Qiagen)
2μg of RNA for each sample was used to construct mRNA library following the protocol of Illumina’s TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: We collected samples of 11 time-points. 11 plates each containing about 80 germinated Arabidopsis seedlings were divided into the acclimated and non-acclimated group. At each sampling time-point from the experimental design (Figure 2.2 A), all leaf tissue from the designated plate was harvested and divided into two separate Eppendorf tubes, snap-frozen in liquid nitrogen and stored at -80°C. At day 12 after seed germination, T1 samples were taken right after the start of the photoperiod and before acclimation treatment starts. Plates from acclimated group were exposed to the heat acclimation treatment and samples were taken after 3 h (T2), 6 h (T3) and 7.5 h (T4), while other plates were returned to normal growth conditions and samples were collected two days (T5) and four days (T6) after at 1:30 pm. At day 16, the remaining acclimated and all the non-acclimated plants were exposed to heat shock treatment (45°C for 90 min), and samples were taken before the heat treatment (T7 for acclimated seedlings, T9 for non-acclimated seedlings), at the end of the heat shock (T8 for acclimated seedlings, T10 for non-acclimated seedlings) and two days after the application of heat stress at 1:30pm (T9 for the acclimated seedlings, T11 for non-acclimated seedlings).

tag: time point

tag: cultivar

tag: tissue

value: leaf

tag: sampling temperature


title: C2C12_CASZ1a-Rep3


title: T10R2

description:
replicate 2
batch2


title: ASA01081 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01081 (continuous dosing regimen) at 12 weeks.

value: 12 weeks

tag: age


title: dkfz-RIG-ref-pedGBM-RTK2_16

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_16

tag: methylation class

tag: gender

tag: location

tag: primary malignancy


title: ASA01081 continuous baseline

description: Gene expression from nasal epithelium of ASA01081 (continuous dosing regimen) at baseline.

value: baseline


title: T11R2

description:
replicate 2
batch2


title: T10R1

description:
replicate 1
batch2


title: ASA01079 intermittent baseline

description: Gene expression from nasal epithelium of ASA01079 (intermittent dosing regimen) at baseline.

value: intermittent

value: male


title: dkfz-RIG-ref-pedGBM-RTK2_15

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_15

tag: pdgfra amplified

tag: cdkn2a/b loss


title: CTRtetCASZ1b_Dox-Rep3

description: RNA-seq_CTRtetCASZ1b-CTRtetEV_Dox_vs_Ctrl_CPM.txt

growth_protocol: The CASZ1b stably transfected SMS-CTR cells (CTRtetCASZ1b)  are cultured in RPMI 1640 containing 10% FBS. CASZ1b expression is induced by Dox treatment.

treatment_protocol: RNA was isolated from CTRtetCASZ1b cells that treated with or without Dox for 48 hr

tag: cell type

value: Rhabdomyosarcoma

tag: cell line

value: SMS-CTR

tag: genotype

tag: dox treatment status

value: Dox-treated


title: C2C12_CASZ1b-Rep2

tag: transfected with


title: dkfz-RIG-ref-pedGBM-RTK2_14

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_14


title: ASA01079 intermittent 12 weeks

description: Gene expression from nasal epithelium of ASA01079 (intermittent dosing regimen) at 12 weeks.

tag: batch

tag: subject

tag: dosing regimen

tag: timepoint

tag: Sex


title: T9R2

description:
replicate 2
batch2

tag: time point

tag: cultivar

tag: tissue

tag: sampling temperature


title: T9R1

description:
replicate 1
batch2


title: CTRtetCASZ1b_Dox-Rep2


title: dkfz-RIG-ref-pedGBM-RTK2_13

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_13

tag: methylation class

tag: age

tag: gender

tag: location

tag: primary malignancy


title: ASA01079 intermittent 13 weeks

description: Gene expression from nasal epithelium of ASA01079 (intermittent dosing regimen) at 13 weeks.


title: C2C12_CASZ1a-Rep2

tag: cell type


title: T8R2

description:
replicate 2
batch2


title: CTRtetCASZ1b_Dox-Rep1

tag: cell line

tag: genotype

tag: dox treatment status


title: dkfz-RIG-ref-pedGBM-RTK2_12

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_12

tag: pdgfra amplified

tag: cdkn2a/b loss


title: ASA01075 intermittent 13 weeks

description: Gene expression from nasal epithelium of ASA01075 (intermittent dosing regimen) at 13 weeks.

tag: batch

tag: subject

tag: dosing regimen

tag: timepoint


title: dkfz-RIG-ref-pedGBM-RTK2_11

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_11


title: T8R1

description:
replicate 1
batch2

tag: time point

tag: cultivar

tag: tissue


title: T7R2

description:
replicate 2
batch2

tag: sampling temperature


title: dkfz-RIG-ref-pedGBM-RTK2_10

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_10

tag: methylation class

tag: age

tag: gender


title: T7R1

description:
replicate 1
batch2


title: ASA01074 intermittent 13 weeks

description: Gene expression from nasal epithelium of ASA01074 (intermittent dosing regimen) at 13 weeks.

tag: Sex


title: dkfz-RIG-ref-pedGBM-RTK2_09

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_09

tag: location

tag: primary malignancy


title: CTRtetCASZ1b_Ctrl-Rep1

tag: cell type

tag: cell line

tag: genotype

tag: dox treatment status

value: untreated


title: ASA01074 intermittent 12 weeks

description: Gene expression from nasal epithelium of ASA01074 (intermittent dosing regimen) at 12 weeks.

tag: batch

tag: subject


title: T6R2

description:
replicate 2
batch2


title: ASA01074 intermittent baseline

description: Gene expression from nasal epithelium of ASA01074 (intermittent dosing regimen) at baseline.

tag: dosing regimen

tag: timepoint


title: ASA01077 intermittent 13 weeks

description: Gene expression from nasal epithelium of ASA01077 (intermittent dosing regimen) at 13 weeks.


title: dkfz-RIG-ref-pedGBM-RTK2_08

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_08

tag: pdgfra amplified

tag: cdkn2a/b loss


title: CTRtetEV_Dox-Rep2

value: CTRtetEV


title: T6R1

description:
replicate 1
batch2

tag: time point

tag: cultivar

tag: tissue

tag: sampling temperature


title: ASA01077 intermittent baseline

description: Gene expression from nasal epithelium of ASA01077 (intermittent dosing regimen) at baseline.

tag: Sex

tag: age


title: ASA01073 intermittent 12 weeks

description: Gene expression from nasal epithelium of ASA01073 (intermittent dosing regimen) at 12 weeks.


title: ASA01073 intermittent baseline

description: Gene expression from nasal epithelium of ASA01073 (intermittent dosing regimen) at baseline.


title: dkfz-RIG-ref-pedGBM-RTK2_07

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_07

tag: methylation class

tag: gender

tag: location

tag: primary malignancy


title: T5R2

description:
replicate 2
batch2


title: dkfz-RIG-ref-pedGBM-RTK2_06

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_06


title: CTRtetEV_Dox-Rep1

description: RNA-seq_CTRtetCASZ1b-CTRtetEV_Dox_vs_Ctrl_CPM.txt

tag: cell type

tag: cell line

tag: genotype

tag: dox treatment status


title: T5R1

description:
replicate 1
batch2


title: CTRtetEV_Ctrl-Rep2


title: ASA01067 intermittent 13 weeks

description: Gene expression from nasal epithelium of ASA01067 (intermittent dosing regimen) at 13 weeks.

tag: batch

tag: subject

tag: dosing regimen

tag: timepoint


title: CTRtetCASZ1b_Ctrl-Rep3


title: CTRtetCASZ1b_Ctrl-Rep2


title: T4R2

description:
replicate 2
batch2

tag: time point

tag: cultivar


title: dkfz-RIG-ref-pedGBM-RTK2_01

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_01

tag: pdgfra amplified

tag: cdkn2a/b loss


title: CTRtetEV_Ctrl-Rep1


title: dkfz-RIG-ref-pedGBM-RTK1_20

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_20

tag: age


title: dkfz-RIG-ref-pedGBM-RTK1_19

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_19

tag: methylation class


title: dkfz-RIG-ref-pedGBM-RTK1_18

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_18

tag: gender


title: ASA01065 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01065 (continuous dosing regimen) at 13 weeks.

tag: Sex


title: T3R2

description:
replicate 2
batch2

tag: tissue

tag: sampling temperature


title: T2R2

description:
replicate 2
batch2


title: T4R1

description:
replicate 1
batch2


title: T3R1

description:
replicate 1
batch2


title: T2R1

description:
replicate 1
batch2


title: dkfz-RIG-ref-pedGBM-RTK1_16

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_16

tag: location

tag: primary malignancy


title: ASA01067 intermittent 12 weeks

description: Gene expression from nasal epithelium of ASA01067 (intermittent dosing regimen) at 12 weeks.


title: T1R2

description:
replicate 2
batch2


title: ASA01063 intermittent 12 weeks

description: Gene expression from nasal epithelium of ASA01063 (intermittent dosing regimen) at 12 weeks.


title: ASA01063 intermittent baseline

description: Gene expression from nasal epithelium of ASA01063 (intermittent dosing regimen) at baseline.


title: ASA01065 continuous baseline

description: Gene expression from nasal epithelium of ASA01065 (continuous dosing regimen) at baseline.


title: SMC_5 Myc ChIP-seq (no SM) Repl.2

city: Bethesda

first: Alan

middle: G.

last: Hinnubusch

address: 6 Center Dr. Bldg 6, Rm 230

institute: NICHD

description:
Biological replicate 2
Myc ChIP-seq (no SM) Repl.2

data_processing:
Paired-end sequences of immunoprecipited DNA were aligned to the yeast genome (SacCer3) using Bowtie2 with parameters -X 1000 --very-sensitive, to map sequences up to 1 kb with maximum accuracy.
Histones H3 and H2B, Rpb3, TBP and Ino80-myc occupancies profiles were created using custom R programs.
The processed data were converted to the bigwig files supplied here: different DNA length exclusion limits were used in the processing (listed with Processed Data Files)
Genome_build: SacCer3

source_name: S. cerevisiae

growth_protocol: All strains were grown to mid-log phase (OD600 about 0.6 to 0.8) at 30 degC in synthetic complete medium lacking isoleucine and valine (SC-Ilv), sulfometuron (SM) was added at 1µg/ml for 25 min to induce Gcn4, or without adding SM (no SM).

extract_protocol:
The procedure of ChIP-seq has been described in Qiu et al., Genome Research 26:211-225, 2016.
Libraries were prepared using DNA Library Prep Kit for llumina (Cat# E7370) from New England Biolabs.

tag: strain

tag: genotype

value: MATa his3delta1 leu2delta met15delta ura3delta

tag: antibody

value: anti-myc epitope from Sigma, Cat# 11667203001

tag: treatment

value: Formaldehyde-fixed and sonicated


title: ASA01065 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01065 (continuous dosing regimen) at 12 weeks.

tag: batch

value: batch 3

tag: subject

tag: dosing regimen

value: continuous

tag: timepoint


title: SMC_1 Myc ChIP-seq (+SM) Repl.1

description:
Biological replicate 1
Myc ChIP-seq (+SM) Repl.1


title: SMC_4 Myc ChIP-seq (no SM) Repl.1

description:
Biological replicate 1
Myc ChIP-seq (no SM) Repl.1


title: SMC_2 Myc ChIP-seq (+SM) Repl.2

description:
Biological replicate 2
Myc ChIP-seq (+SM) Repl.2


title: SMC_6 Myc ChIP-seq (no SM) Repl.3

description:
Biological replicate 3
Myc ChIP-seq (no SM) Repl.3


title: dkfz-RIG-ref-pedGBM-RTK1_15

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_15

tag: pdgfra amplified

tag: cdkn2a/b loss


title: dkfz-RIG-ref-pedGBM-RTK2_02

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK2_02

tag: methylation class

tag: age


title: AGH121_12 TBP ChIP-seq (+SM) Repl.3

description:
Biological replicate 3
TBP ChIP-seq (+SM) Repl.3

value: MATa his3delta1 leu2delta met15delta ura3delta ino80delta::kanMX4

value: anti-TBP antibody is a generous gift from Joe Reese


title: ASA01067 intermittent baseline

description: Gene expression from nasal epithelium of ASA01067 (intermittent dosing regimen) at baseline.

tag: Sex

value: female


title: SMC_3 Myc ChIP-seq (+SM) Repl.3

description:
Biological replicate 3
Myc ChIP-seq (+SM) Repl.3


title: T1R1

description:
replicate 1
batch2

tag: time point

tag: cultivar

tag: tissue

value: leaf


title: ASA01063 intermittent 13 weeks

description: Gene expression from nasal epithelium of ASA01063 (intermittent dosing regimen) at 13 weeks.

value: 13 weeks


title: AGH121_11 TBP ChIP-seq (+SM) Repl.2

description:
Biological replicate 2
TBP ChIP-seq (+SM) Repl.2


title: dkfz-RIG-ref-pedGBM-RTK1_13

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_13

tag: gender

tag: location

tag: primary malignancy


title: p-T11R2

description:
replicate 2
batch1

tag: sampling temperature


title: dkfz-RIG-ref-pedGBM-RTK1_14

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_14


title: AGH121_10 TBP ChIP-seq (+SM) Repl.1

description:
Biological replicate 1
TBP ChIP-seq (+SM) Repl.1

tag: strain

tag: genotype

tag: antibody

tag: treatment


title: AGH121_9 TBP ChIP-seq (no SM) Repl.3

description:
Biological replicate 3
TBP ChIP-seq (no SM) Repl.3


title: dkfz-RIG-ref-pedGBM-RTK1_12

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_12


title: p-T10R2

description:
replicate 2
batch1


title: dkfz-RIG-ref-pedGBM-RTK1_08

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_08


title: p-T9R2

description:
replicate 2
batch1


title: dkfz-RIG-ref-pedGBM-RTK1_06

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_06


title: dkfz-RIG-ref-pedGBM-RTK1_07

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_07


title: ASA01060 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01060 (continuous dosing regimen) at 12 weeks.

tag: batch

tag: subject

tag: dosing regimen

tag: timepoint

value: 12 weeks


title: ASA01058 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01058 (continuous dosing regimen) at 12 weeks.

tag: age


title: p-T9R1

description:
replicate 1
batch1


title: p-T8R2

description:
replicate 2
batch1


title: AGH121_7 TBP ChIP-seq (no SM) Repl.1

description:
Biological replicate 1
TBP ChIP-seq (no SM) Repl.1


title: ASA01060 continuous baseline

description: Gene expression from nasal epithelium of ASA01060 (continuous dosing regimen) at baseline.

value: baseline

tag: Sex


title: ASA01058 continuous baseline

description: Gene expression from nasal epithelium of ASA01058 (continuous dosing regimen) at baseline.


title: AGH121_4 TBP ChIP-seq (+SM) Repl.1


title: dkfz-RIG-ref-pedGBM-RTK1_05

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_05

tag: methylation class

tag: pdgfra amplified

tag: cdkn2a/b loss


title: AGH121_5 TBP ChIP-seq (+SM) Repl.2


title: AGH121_3 TBP ChIP-seq (no SM) Repl.3


title: dkfz-RIG-ref-pedGBM-RTK1_04

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_04

tag: gender


title: p-T8R1

description:
replicate 1
batch1

tag: time point

tag: cultivar

tag: tissue


title: ASA01058 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01058 (continuous dosing regimen) at 13 weeks.


title: ASA01056 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01056 (continuous dosing regimen) at 13 weeks.

value: male


title: dkfz-RIG-ref-pedGBM-RTK1_03

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_03

tag: location

tag: primary malignancy