title: Donor_18_AMD

description:
all_metadata.csv
all_normalized_expression_data.csv
donor_18_nAMD

data_processing:
FASTQ files were generated from the raw BCL files using Illumina’s bcl2fastq conversion program.
Sequenced reads were mapped to the CellRanger human genome build GRCh38 with CellRanger (v6.0.0) using the CellRanger human GTF
Cells were filtered with the Seurat (v4.0.3) subset function. Cells with nUMIs less than 500 (to remove cells with poor read quality) or greater than 7000 (to remove cells likely to be doublets) were removed. Cells with greater than 15% of reads originating from mitochondrial genes  or 25% of reads originating from ribosomal reads were also removed.
For each of the eight libraries, reads were normalized with the Seurat (v4.0.3) NormalizeData function, and variable features were found with the following commands: my _object <- NormalizeData(my_object, normalization.method = "LogNormalize", scale.factor = 10000), my_object <- FindVariableFeatures(my_object, selection.method = “vst”, nfeatures = 2000)
Integration anchors from the first 24 dimensions of the canonical correlation analysis were used to integrate data with the following commands: choroid.anchors <- FindIntegrationAnchors(object.list = my_object_list, dims=1:25), choroid.combined <- IntegrateData(anchorset = choroid.anchors, dims = 1:25)
Data scaling, principal component analysis, and clustering were performed with the following commands: choroid.combined <- ScaleData(choroid.combined, verbose = FALSE), choroid.combined <- RunPCA(choroid.combined, npcs = 30, verbose = FALSE), choroid.combined <- RunUMAP(choroid.combined, reduction = "pca", dims = 1:23), choroid.combined <- FindNeighbors(choroid.combined, reduction = "pca", dims = 1:23), choroid.combined <- FindClusters(choroid.combined, resolution = 0.35)
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed expression data matrix files are provided in tab-delimited format for count(*_count.csv) and processed/normalized (*_normalized.csv) expression values. For processed/normalized files, log-normalized expression values (from GetAssayData(object = seurat_object)) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values. For count files, raw counts were obtained (from GetAssayData(object = seurat_object, slot = “counts”)) for each cell type in each cluster and appended to relevant metadata (barcode, cluster label, and donor number from the manuscript).


title: CX3CR1_pos dendritic cells (Sample_2046)

status: Public on Feb 21 2022

type: SRA

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

library_source: transcriptomic

data_processing:
Illumina Casava1.82 software used for basecalling and demultiplexing.
After demultiplexing, raw reads were pseudoaligned to the murine transcriptome (mm10, GENCODE general assembly release vM16) using Kallisto with default settings
Based on the pseudoalignment estimated by Kallisto, transcript levels were quantified and counts were imported into R using tximport. Transcript information was summarized on gene-level. We imported the resulting dataset and performed the downstream analysis using the DESeq2 pipeline.
Genome_build: mm10
Transcriptome_build: mm10, GENCODE general assembly release vM16
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference transcriptome

molecule: total RNA

organism: Mus musculus

source_name: muscularis externa of the small bowel wall

extract_protocol:
For RNA sequencing, 6-25x10e5 cells were harvested for each sample and lysed in TRIzol (Invitrogen). Total RNA was extracted according to the manufacturer’s protocol.
Library preparation for subsequent RNA-sequencing analysis was performed using the TruSeq. RNA Library Prep Kitv2 (Illumina) following manufacturer’s protocol instructions

treatment_protocol: mice/cells did not receive any treatment

tag: tissue

tag: cell type

value: dendritic cell

tag: genotype


title: DIO-NASH Vehicle 12w Rep 8

city: Hørsholm

first: Martin

middle: Rønn

last: Madsen

state: Please Select

address: Hørsholm Kongevej 11

department: Computation Biology

country: Denmark

institute: Gubra

data_processing:
Reads were mapped to the GRCm38.p96 Ensembl mouse genome using STAR v.2.5.2a with default parameters.
Counts in protein coding genes was quantified using STAR and can be found in supplementary.
Genome_build: GRCm38
Supplementary_files_format_and_content: .txt file of RPKM-normalized gene expression

source_name: Liver

extract_protocol: Illumina TruSeq Stranded mRNA Library Prep kit (#20020594, Illumina, San Diego, CA, USA)

tag: treatment

value: DIO-NASH Vehicle 12w

tag: weeks treatment


title: Donor_17_AMD

city: Iowa City

first: Andrew

middle: P

last: Voigt

state: IA

address: 375 Newton Road

country: USA

institute: University of Iowa

description:
all_metadata.csv
all_normalized_expression_data.csv

organism: Homo sapiens

extract_protocol:
An 8 or 12-mm macular centered punch of RPE/choroid was acquired from twenty human donors. After dissection away from the retina and sclera, the RPE/choroid was finely diced into small squares (approximately 1 mm x 1 mm) with a razor blade. The resulting suspension was dissociated in 450 units/mL of collagenase II (Gibco, Grand Island NY) reconstituted in Hank’s Balanced Salt Solution containing calcium chloride and magnesium chloride (Life technologies, Grand Island NY). Dissociated cells were resuspended in DMSO-based Recovery Cell Culture Freezing Media (Life Technologies Corporation, Grand Island NY). Suspensions were placed in a Cryo-Safe cooler (CryoSafe, Summerville SC) to cool at 1°C/minute in a -80°C freezer for 3-8 hours before storage in liquid nitrogen.
Cryopreserved cells from single-cell donors were rapidly thawed before pre-enrichment for endothelial cells. Cells were incubated for 15 minutes with anti-CD31 microbeads (Miltenyi Biotech, Bergisch Gladbach Germany) according to the manufacturer’s instructions before automated autoMACs magnetic separation (Miltenyi Biotech, Bergisch Gladbach Germany) into CD31+ fractions. Sequencing of CD31-positive fractions was performed on pooled libraries using the Illumina NovaSeq platform (San Diego, CA).
Single-cell RNA-Seq

tag: condition

value: AMD

tag: region

value: macula


title: CX3CR1_pos dendritic cells (Sample_2044)

value: muscularis externa of the small bowel wall


title: DIO-NASH Vehicle 12w Rep 7


title: aerial_D-3

city: Yinchuan

first: Xiang

last: Xiao

state: Ningxia

address: Shengli Street

country: China

institute: Ningxia Medical University

data_processing:
Transcriptome analysis using reference genome-based reads mapping：Low quality reads, such as only adaptor, unknown nucleotides>5%, or Q20 <20%(percentage of sequences with sequencing error rates <1%), were removed by perl script.  The clean reads that were filtered from the raw reads were mapped to honeybee (Apis mellifera) genome (OGSv3.2) using Tophat2 software. The aligned records from the aligners in BAM/SAM format were further examined to remove potential duplicate molecules. Gene expression levels were estimated using FPKM values(fragments per kilobase of exon per million fragments mapped) by the Cufflinks software.
Genome_build: Glycyrrhiza_uralensis.gdb.genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Glycyrrhiza uralensis

source_name: Glycyrrhiza uralensis Fisch.

growth_protocol: 75 water-absorbing, full-filled seeds were selected, blotted surface moisture, and sown evenly in each pot filled with 1900 g high-pressure sterilized and fully dried sand medium collected from native desert regions which do not contain any nutrients.

extract_protocol:
Glycyrrhiza uralensis Fisch. seedling in aerial and underground part were collected. Then RNA was extracted and its purity, concentration and integrity were tested. 1ug total RNA was prepared for cDNA libraries using protocol provided by Oxford Nanopore Technologies (ONT). Briefly, SuperScript IV First-Strand Synthesis System (Invitrogen) was used for full length mRNA reverse transcription and following cDNA PCR for 14 circles with LongAmp Tag (NEB). The PCR products were then subjected to FFPE DNA repair and end-repair (NEB) steps and following adaptor ligation using T4 DNA ligase (NEB). Agencourt XP beads was used for DNA purification according to ONT protocol. The final cDNA libraries were added to FLO-MIN109 flowcells and were run on PromethION platform at Biomarker Technology Company (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: (i) control with or without 2 mM Si, (ii) 35~45% of saturation moisture content (drought stress) with or without 2 mM Si, (iii) 75 mM NaCl (salt stress) with or without 2 mM Si, (iv) 35~45% of saturation moisture content + 75 mM NaCl (drought-salt stress) with or without 2 mM Si (Control treatment was added distilled water, Si was added as K2SiO3).

value: aerial part

value: drought treatment

tag: age

value: 45 days

tag: stress

value: drought stress


title: aerial_S-1

value: salt treatment

value: salt stress


title: aerial_D-2


title: CX3CR1_neg dendritic cells (Sample_2043)


title: Donor_16_AMD


title: Donor_21_AMD


title: aerial_D-1


title: Donor_15_AMD


title: DIO-NASH Vehicle 12w Rep 5


title: DIO-NASH Vehicle 12w Rep 6


title: Donor_14_AMD


title: CX3CR1_pos dendritic cells (Sample_2040)


title: CX3CR1_neg dendritic cells (Sample_2041)


title: aerial_CK+Si-3

value: Si treatment

value: no stress


title: aerial_CK+Si-2


title: DIO-NASH Vehicle 12w Rep 3


title: aerial_CK+Si-1


title: Donor_13_AMD


title: Donor_10_control

value: control


title: NICD-4 [C2831]

city: Madrid

first: Alberto

last: Bartolomé

state: Madrid

address: Arturo Duperier 4

country: Spain

institute: Instituto de Investigaciones Biomédicas Alberto Sols (CSIC/UAM)

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq. Adapters are not trimmed away from the reads.
Raw counts were pseudoaligned to the mouse transcriptome (GRCm38) by Kallisto and gene count tables generated
Differenrial gene expression analyses were performed with limma, implemented in the BioJupies application
Genome_build: mm10, GCRm38
Supplementary_files_format_and_content: gene count table csv
Supplementary_files_format_and_content: differential expression gene table csv

source_name: pancreatic islets

extract_protocol:
Islets were islated from mice after doxyciline supplementatuoon in drinking water for 8 weeks, and RNA was harvested using Trizol reagent. For
TruSeq Stranded mRNA LT Sample Prep Kit/TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E. Macrogen. For library construction, RNA is extracted from a sample. After performing quality control(QC), qualified samples proceed to library construction. The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed by 5’ and 3’ adapter ligation. Alternatively, “tagmentation” combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.

tag: strain background

value: Mixed; C57BL/6J, 129X1/SvJ, BALB/c

tag: sample group

value: NICD

tag: doxyciline supplementation

value: 8 weeks

value: RIP-Cre+, Rosa26-rtTA+, tetO_NICD+

tag: tissue/cell type

value: pancreatic islets


title: DIO-NASH Vehicle 12w Rep 2

value: DIO-NASH Vehicle 12w


title: aerial_CK-3

value: control treatment


title: NICD-3 [C2826]


title: Control-4 [C2824]

value: Control

value: RIP-Cre+, Rosa26-rtTA+, tetO_NICD-


title: DIO-NASH Vehicle 12w Rep 1


title: aerial_CK-2

value: aerial part


title: Control-3 [C2817]


title: aerial_CK-1

value: 45 days


title: Donor_7_control

value: macula


title: NICD-2 [C2816]


title: Donor_6_control


title: Donor_8_control


title: DIO-NASH Vehicle 12w Rep 4


title: SPL_BM.double_24

city: Boston

first: Tanya

last: Mayadas

state: MA

address: 77 Avenue Louis Pasteur, NRB  Rm. 752K

department: Department of Pathology

institute: Brigham and Women's Hospital, Harvard Medical School

data_processing:
Illumina Bcl2fastq v2.18
Sequencing reads were aligned to mm9 reference genome using STAR (v2.5)
Raw gene counts calculated by STAR
normalized FPKM counts were generated using cufflinks v2.2.1
Genome_build: mm9

source_name: Spleen, BM

extract_protocol:
Cell pellets were  re-suspended in RLT buffer and total RNA was purified using the TNeasy Mini kit according to manufacturers instructions and RNA concentration was estimated by an agilent bio analyzer.
cDNA was synthesized using Clontech Smart Seq v4 reagents from 2ng of RNA. Full length cDNA was fragmented to a mean size of 150bp with a Covaris M220 ultrasonicator and Illumina libraries were prepared from 2ng of sheared cDNA using Rubicon Genomics ThruPLEX DNAseq reagents

treatment_protocol: NTN induced ten, 8-10 week old micce were sacrificed on day 13 and kidneys, spleen and bone marrow were harvested. Renal monocytes were enriched using the EasySep mouse monocyte isolation kit and sorted.

tag: strain

value: Spleen, BM

value: 8-10 week


title: Kid.double_pos_22

source_name: Kidney

value: Kidney


title: SPL_BM.double_26


title: Control-1 [C2804]


title: Kid.double_pos_8


title: Donor_5_control

description:
GSM4490474
all_metadata.csv
all_normalized_expression_data.csv


title: Kid.double_pos_7


title: NICD-1 [C2803]


title: Donor_9_control


title: Donor_4_control


title: Donor_3_control

description:
GSM4490472
all_metadata.csv
all_normalized_expression_data.csv


title: SPL_BM.double_2


title: Control-2 [C2808]


title: aptamer m12-3773 replicate 1

type: protein

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Islet14 replicate A

hyb_protocol: HuProt 2.0 arrays (ArrayIt) were prepared for binding as recommended by the manufacturer. The protein surface of the array was deactivated with 3 ml of “Chem block “buffer (Arrayit) for one hour at room temperature. After deactivation, the array was blocked with blocking buffer (Blockit - Arrayit, supplemented to 450µg/ml yeast RNA - Ambion) for one hour and then hybridized for 30’ at 4ºC with the streptavidin aptamer-conjugate (20 picomoles) in 200µl of blocking buffer. Then, the arrays were washed (5 x 5’) in washing buffer  (0.01 % Tween 20 - Biorad in 0.5mM Mg2+ PBS), and dried using a Microarray centrifuge (ArrayIt).

scan_protocol: Array have been analyzed on a genepix 4000B microarray reader.

data_processing: Protein arrays have been analyzed using the PAA package (v. 1.0)(Turewicz et al, 2016) in R (v. 3.4.4); before preprocessing, each microarray has been visually inspected for any artifact using the plotArray function. Then, the raw intensity signals were extracted from the .gpr files and B11the median fluorescence intensities at 635nm wavelength was imputed as raw intensity foreground signals; specifically, intensity signals of replicated spots were mean centered and background corrected using the default parameters, e.g. the saddle variant of the normexpr method in the backgroundCorrect function, and were finally normalized using the quantile method of the normalizeArrays function.

molecule: protein

source_name: aptamer library selected on human islet

label_protocol: 5'Biotinylated aptamers were conjugated overnight at 4C with Alexafluor 647 labelled straptavidin (Biolegend) 4:1 molar ratio.  The conjugates were purified with an Amicon 50,000 MWCO - (Millipore) spin filter.

tag: target

value: unknonw protein expressed on human islets


title: aptamer m12-3773 replicate 2

description: Islet14 replicate B


title: aptamer 1-717 replicate 2

description: Islet9 replicate B


title: Affymetrix_PCM1

status: Public on Feb 20 2022

type: RNA

city: Louisville

first: Norman

middle: L

last: Lehman

state: Kentucky

address: CTRB Room 307, 505 South Hancock St.

institute: The University of Louisville

hyb_protocol: Hybridization cocktail was hybridized on the array rotating at 60 rpm for 16 hr at 45 degrees C.

scan_protocol: After overnight hybridization, the hybridization cocktail mix was extracted from the array. Each array was washed and stained using Affymetrix® GeneChip® Fluidics Station 450 according to the user manual (P/N 08-0295) and the arrays were scanned using GeneChip Scanner 7G. Each array image was collected using the GeneChip Command Console, QC and saved as .cel files.

data_processing: Probes were mapped to 33720 unique gene symbols using the pd.hta.2.0 package (ver: 3.12.2) with median summarization.

label: biotin

source_name: control

label_protocol: Affymetrix GeneChip Human Transcriptome Array 2.0 (HTA-2) microarray analysis was performed according to the manufacturer’s instructions using the GeneChip™ WT Pico sample preparation Kit (Thermo Fisher Scientific). Total RNA (50 ng) was converted to single-stranded cDNA with T7 promoter sequence at the 5' end. A 3' Adaptor, as a template for double-stranded cDNA synthesis, was added and the single-stranded cDNA was converted to double-stranded cDNA. Six amplification cycles were applied as recommended by the protocol to enrich the samples. The amplified product was converted to cRNA and purified using purification binding beads. Eluted cRNA yield was measured by NanoDrop. cRNA (20 μg)   were reverse transcribed to sense-strand cDNA containing dUTP at a fixed ratio relative to dTTP. The cRNA was removed using RNase H and the 2nd-cycle single-stranded cDNA was purified using purification binding beads.Eluted single straded cDNA was fragmented by uracil DNA glycosylase and apurinic/apyrimidinic nuclease 1, and labeled by terminal deoxynucleodide transferase with Affimetrix labeling agent linked to biotin.

extract_protocol: Total RNA was extracted from three 30μm scrolls cut from FFPE tissue blocks containing control tissue or minimally 90% tumor using the RecoverAll total nucleic acid isolation kit (Ambion/Thermo Fisher Scientific, Waltham, MA) per the manufacturer’s instructions. RNA was then passed through concentration and clean-up columns (Norgen Biotek, Thorold, ON) and quantified using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA).

value: brain

tag: histological type

value: pediatric cerebellum


title: aptamer 1-717 replicate 1

description: Islet9 replicate A


title: Affymetrix_ACP5

value: adult choroid plexus


title: Affymetrix_PHP3

value: pediatric hippocampus


title: Affymetrix_ACP2


title: Affymetrix_AA1

value: adult amygdala


title: Affymetrix_AFL11

value: adult frontal lobe


title: Affymetrix_PCM3


title: Affymetrix_AFL10


title: Affymetrix_AFL14


title: Affymetrix_AFL9


title: Affymetrix_FHP1

value: fetal hippocampus


title: Affymetrix_PXA9

source_name: tumor

value: tumor

value: PXA


title: Affymetrix_AA2


title: Affymetrix_FGM2

value: fetal germinal matrix


title: Affymetrix_PXA5


title: Affymetrix_ACP4


title: Affymetrix_AFL4


title: Affymetrix_ACP3


title: Affymetrix_ATH6

value: adult thalamus


title: Affymetrix_AFL13


title: Affymetrix_FCM2

value: fetal cerebellum


title: Affymetrix_PXA3


title: Affymetrix_FCE1

value: fetal cerebrum


title: Affymetrix_PXA2


title: Affymetrix_PXA1


title: Affymetrix_PXA11


title: Affymetrix_PTPR9

value: PTPR


title: Affymetrix_C35

value: astroblastoma


title: Affymetrix_PTPR7


title: Affymetrix_PTPR3


title: Affymetrix_C26


title: Affymetrix_C22


title: Affymetrix_PTH3

value: pediatric thalamus


title: Affymetrix_PTPR2


title: OrceSOro_2

city: Blacksburg

first: James

middle: H

last: Westwood

state: VA

address: 401 Latham Hall

department: School of Plant and Environmental Sciences

institute: Virginia Tech

data_processing:
Raw read quality was assessed using FastQC. Prior to assembly, raw reads were trimmed to remove poor quality reads and Illumina adaptor sequences using Trimmomatic. A minimum length of 50bp after trimming was required to retain the read. The reads that retained their PE mate were used for transcriptome sequence assembly.
The Trinity software package (version 2.4.0) was used for de novo transcriptome assembly of O. cernua and O. cumana transcriptomes using default parameters. Transcriptomes were assembled for each species using the processed PE reads from all sequenced stages of that species. Raw reads were mapped back to the de novo transcriptomes using Bowtie2 software and had a mapping efficiency of greater than ninety percent for both species
Genome_build: N/A These were de novo transcriptomes
Supplementary_files_format_and_content: Data were assembled into de novo transcriptomes (fasta format). For each species and stage, expression of genes/isoforms was estimated by read counts and RPKM

organism: Orobanche cernua

source_name: Seeds

growth_protocol: Seeds O. cernua and O. cumana were surface sterilized according to Plakhine et al. (Plakhine D, Tadmor Y, Ziadne H, Joel DM. 2012. Maternal tissue is involved in stimulant reception by seeds of the parasitic plant Orobanche. Annals of Botany 109: 979-986).

extract_protocol:
RNA was extracted with a Spectrum Plant Total RNA kit (Sigma-Aldrich)
Strand-specific RNA-seq libraries were constructed, barcoded and sequenced to obtain 100bp paired-end (PE) reads on two lanes of Illumina HiSeq 2000 sequencing system at the Technion Genome Center in Haifa, Israel.

treatment_protocol: For the “conditioning” treatment, seeds were placed on moist glass fiber paper in a Petri dish and stored in darkness at 23°C for 1, 3 or 5 days, and seeds from each time point were pooled. For “fully conditioned”, seeds were placed in a Petri dish, with sterilized water, in darkness for 7 days. For “stimulated”, seeds that had been conditioned for 7 days were exposed for 4 or 8 hrs to either dehydrocostos lactone (DCL) (10-7 µM), Orobanchol (10-8 µM), or rac-GR24 (10-6 µM).

value: Seeds

tag: Stage

value: Conditioned, stimulated with orobanchol

tag: timings

value: Pools of seeds collected 4 or 8 hours after addition of indicated germination stimulant

tag: replicates


title: OrceSOro_1

tag: tissue


title: OrceSGR24_2

value: Conditioned, stimulated with racemic GR24


title: OrceSGR24_1


title: Affymetrix_C20


title: OrceF_2

value: Fully conditioned

value: Seeds collected 7 days after addition of water


title: Affymetrix_C19


title: Affymetrix_C16


title: Affymetrix_C10


title: Affymetrix_C10r


title: OrcuF_2

organism: Orobanche cernua var. cumana


title: OrcuC_1

value: Conditioning

value: Pools of seeds collected 1, 3, or 5 days after addition of water


title: OrceC_1


title: OrcuC_2


title: OrcuSDCL_1

value: Conditioned, stimulated with dehydrocostus lactone


title: Affymetrix_C14

value: tumor


title: Affymetrix_C17


title: OrcuSGR24_2


title: Affymetrix_C6


title: Affymetrix_C11


title: Affymetrix_C4


title: OrcuF_1


title: OrcuSGR24_1


title: Affymetrix_C21


title: OrceF_1


title: Affymetrix_C9


title: OrcuSDCL_2


title: P0-NSC-2

city: changsha

first: dan

last: zhu

address: hunan

institute: Hunan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Brain

extract_protocol:
Total RNA was isolated from mouse astrocytes (negative control), mouse brain-derived NPCs (positive controls), and A-iSCs using Trizol. A total amount of 3 μg RNA per sample was collected for sequencing. Sequencing libraries were generated using NEBNext® UltraTM RNA library prep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: treatment

value: positive controls


title: P0-NSC-3


title: Affymetrix_C3


title: P0-NSC-1


title: R108 - nitrate, rep3 [WTwoNO3-10_Cy5]

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

hyb_protocol: The hybridization performed on a rotative Agilent Hybridization Oven, 17h at 65°C, 10g. Afterwards, the slide were washed, and scanned.

scan_protocol: Scanning was performed on 2µm NimbleGen MS 200 Scanner Scanning was performed on 3µm Innoscan 710 scanner (Innopsys)

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

organism: Medicago truncatula

label_protocol:
400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), After purification, labelled samples were combined as 30 pmol for each dye and co-hybridized to the arrays.
Labelling was performed with G4140-90050_GeneExpression_TwoColor_6.9 (Agilent) protocol

growth_protocol: Seeds scarified with an abrasive paper were surface-washed with sterilized water and then imbibed on a sterilized filter paper in a Petri dish (Φ= 90 mm) containing 3.5 mL of N-free Murashige and Skoog (MS) medium at 4°C in darkness for 4 d, as described by Pellizzaro et al. (2014). After this step of cold stratification to homogenize further seed germination, the Petri dish was incubated at 20°C for seed germination. Then, germinated seeds with a radicle of about 1 cm long were transferred for 2 or 10 d of growth on a sterilized filter paper in a square transparent plate (12.4 cm x 12.4 cm) containing 8 mL of either N-free MS solution or MS solution supplied with 5 mM NO3−. The plate was inclined at a 45° angle on a rack under a 16-h-light/8-h-dark photoperiod with a light intensity of 45 µmol.m-2.s-1 at 20°C in a growth chamber (the watering being regularly readjusted). Zang et al, 2020 Plant Physiol Biochem 146, 363-373

extract_protocol: Total RNAs were extrated using  Nucleospin® RNA Plus kit (Macherey-Nagel, Düren, Germany) according to manufacturer's instructions.

treatment_protocol: MS with or without 5mM nitrate

tag: tissus

value: primary root apex

tag: genetic background

value: WT

tag: genotype

tag: phenotype

value: nitrate sensitive

value: MS without nitrate

value: 10 days

tag: harvest date

value: begining of 2018


title: OrceC_2

value: Seeds


title: npf6.8 + nitrate,  rep3 [MuTwNO3-11_Cy3]

value: npf6.8-3 mutant line

value: nitrate insensitive

value: MS with 5 mM nitrate

tag: age


title: npf6.8 + nitrate,  rep1 [MuTwNO3-3_Cy5]

value: end of 2017


title: npf6.8 - nitrate,  rep3 [MuTwoNO3-12_Cy5]


title: npf6.8 - nitrate,  rep3 [MuTwoNO3-12_Cy3]


title: R108 - nitrate, rep3 [WTwoNO3-10_Cy3]


title: P56-NSC-2


title: P56-NSC-3


title: R108 - nitrate, rep1 [WTwoNO3-2_Cy3]


title: P56-NSC-1


title: A-iSCs-3

value: 5 day incubation


title: npf6.8 - nitrate,  rep1 [MuTwoNO3-4_Cy3]


title: A-iSCs-2


title: R108 + nitrate, rep3 [WTwNO3-9_Cy5]


title: R108 + nitrate, rep1 [WTwNO3-1_Cy3]


title: R108 + nitrate, rep3 [WTwNO3-9_Cy3]


title: npf6.8 - nitrate,  rep2 [MuTwoNO3-8_Cy5]


title: A-iSCs-1


title: AST-1

value: 0 day incubation, negative control


title: AST-3


title: npf6.8 - nitrate,  rep1 [MuTwoNO3-4_Cy5]


title: R108 + nitrate, rep2 [WTwNO3-5_Cy3]


title: R108 - nitrate, rep1 [WTwoNO3-2_Cy5]


title: NoE2-INPUT_in9

city: Riverside

first: Sihem

last: Cheloufi

state: California

address: 3401 Watkins Dr.

department: Biochemistry

institute: University fo California Riverside

description: input for "_in9" samples

library_source: genomic

data_processing:
Basecalling was performed with CASAVA version 1.4
Adapter sequences were removed with cutadapt (v2.1).
Paired-end reads were mapped to mm9 genome using Bowtie2  version 2.2.9 with parameters:  --end-to-end --very-sensitive -–no-mixed -–no-discordant --phred33 -I 10 -X 700.
PCR duplications were removed with bamUtil version 1.0.14
CPM normalized bigwig files were generated with bamCoverage tools from deeptools version 3.5.1
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig

molecule: genomic DNA

source_name: granulocyte-macrophage progenitors

growth_protocol: Granulocyte-macrophage progenitor cells containing Hoxa9::ER were cultured in RPMI-1640 supplemented with 10% FBS, 100U ml-1 penicillin, 100 µg ml−1 streptomycin, 2mM L-alanyl-L-glutamine dipeptide and stem cell factor (SCF). The source of SCF was conditioned media generated from a Chinese hamster ovary (CHO) cell line that stably secretes SCF. Conditioned medium was added at a final concentration of 1 - 2 % depending on the batch. β-Estradiol (abbreviated E2) was added to a final concentration of 150 ng/ml from a 3 mg/ml stock dissolved in 100% ethanol.

extract_protocol:
For ChIPseq data, 10 million cells were crosslinked, lysed, sonicated, and chromatin was immunoprecipitated with 10ug (ELF1, CEBPA) or  2ug (histone marks) antibody. Immunoprecipitations were reversecrosslinked and DNA purified with AmPure XP beads was used for library preparation. For CUT&RUN, 0.5 million cells were collected and incubated with a 1:100 dilution of antibody. pAG Mnase was used at 1:20 dilution and isolated DNA used for library generation.
NEBNext Ultra II DNA Library Prep Kit (E7645) with NEBNext Multiplex Oligos (E6440) with optimized PCR extension time and number of cycles.

treatment_protocol: For CAF-1 suppression, IPTG was added at a concentration of 500 µM to express IPTG-inducible Chaf1b shRNA. For Hoxa9 inactivation, cells were washed with PBS twice and then cultured in media without Estradiol.

tag: chip antibody

value: 48hrs estradiol withdrawal.

value: Lys::GFP / ER-HoxA9 / LacO-shChaf1b

tag: cell type

value: HoxA9 transformed bone marrow, granulocyte macorphage progenitors


title: NoE2-INPUT_in7

description: input for "_in7" samples


title: R108 - nitrate, rep2 [WTwoNO3-6_Cy3]


title: NoE2-INPUT_in8

description: input for "_in8" samples


title: IPTG-INPUT_in6

description: input for "_in6" samples

value: 48hrs IPTG-treated


title: npf6.8 + nitrate,  rep1 [MuTwNO3-3_Cy3]

value: primary root apex


title: npf6.8 - nitrate,  rep2 [MuTwoNO3-8_Cy3]


title: npf6.8 + nitrate,  rep3 [MuTwNO3-11_Cy5]


title: R108 + nitrate, rep2 [WTwNO3-5_Cy5]

value: WT


title: AST-2

value: brain


title: IPTG-INPUT_in5

description: input for "_in5" samples


title: IPTG-INPUT_in4

description: input for "_in4" samples


title: Untreated-INPUT_in3

description: input for "_in3" samples

value: untreated


title: Untreated-INPUT_in2

description: input for "_in2" samples


title: npf6.8 + nitrate,  rep2 [MuTwNO3-7_Cy3]

value: 10 days


title: R108 + nitrate, rep1 [WTwNO3-1_Cy5]

value: nitrate sensitive


title: R108 - nitrate, rep2 [WTwoNO3-6_Cy5]

value: MS without nitrate


title: Untreated-INPUT_in1

description: input for "_in1" samples


title: npf6.8 + nitrate,  rep2 [MuTwNO3-7_Cy5]

value: npf6.8-3 mutant line


title: Untreated-H3K4me3_Rep2_in3

description: H3K4me3 chromatin in untreated cells


title: NoE2-CEBPA_Rep1_in7

description: CEBPA binding in HOXA9-inactivated cells.

value: CEBPA (Cell Signaling, 8178BF, Lot2)


title: Untreated-H3K27ac_Rep1_in1

description: H3K27ac chromatin in untreated cells


title: NoE2-CEBPA_Rep2_in9


title: IPTG-CEBPA_Rep1_in4

description: CEBPA binding in Chaf1b-depleted cells.


title: Untreated-CEBPA_Rep2_in3

description: CEBPA binding in untreated cells


title: Untreated-CEBPA_Rep1_in1

description: CEBPA binding in untreated cells


title: IPTG-CEBPA_Rep2_in6

description: CEBPA binding in Chaf1b-depleted cells.


title: Untreated-H3K4me3_Rep1_in2

description: H3K4me3 chromatin in untreated cells


title: NoE2-ELF1_Rep1_in7

description: ELF1 binding in HOXA9-inactivated cells.

value: ELF1 (Bethyl, A301-443A, Lot1)


title: IPTG-ELF1_Rep2_in5

description: ELF1 binding in Chaf1b-depleted cells.


title: Untreated-ELF1_Rep2_in2

description: ELF1 binding in untreated cells


title: cellcycle_arrest:H6:rat1

city: Jerusalem

first: Alon

last: Chappleboim

address: Givat Ram

department: Biological chemistry

country: Israel

institute: Hebrew University of Jerusalem

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|H6

data_processing:
bcl2fastq (v2.20) for splitting libraries with "-l WARNING --minimum-trimmed-read-length 5 --no-lane-splitting --mask-short-adapter-reads 5 -p 8 -o <output_dir>"
Splitting internal barcodes with a python script (perfect matches only)
R1 were aligned using bowtie2 (2.3.4.3) to the S.cer genome (SacCer3-R64), K.lac genome (build 2515-2), and to K.lac genome were any 18-mer found in the S.cer genome was removed. This alignment was only used to count aligned reads.
R1 were ACG-converted with an awk script and aligned using bowtie2 (2.3.4.3) to a version of the S.cer genome (SacCer3-R64) and the K.lac genome (build 2515-2) that were also converted to an ACG-only alphabet. This alignment was only used to count aligned reads.
R1 were ACG-converted with an awk script and aligned using bowtie2 (2.3.4.3) to a version of the S.cer genome (SacCer3-R64) that was also converted to an ACG-only alphabet. Multiple alignments were allowed. Following alignment an awk script was used to count and mark all deviations of the original observed sequence from the reference genome.
Read filteration and dedupping; Reads in all sequencing runs had lengths between 44-46, and we discarded reads with more than 30 observed Ts (binomial probability < 4e-7, observed fraction ~ 4e-3). For typical analyses of mRNA, we only considered reads that were aligned less than five times with at most 3 errors excluding T→C conversions. Out of these alignments, only the best one was reported. Reads were de-duplicated by grouping according to  (chromosome, strand, position, and UMI), and in each such group, the read with least amount of deviations from the reference was selected.
Filtered and deduplicated alignments were assigned to transcripts by their intersection with a window of 300 bp upstream and 100 bp downstream of previously reported transcription termination site annotations. Read statistics were then collected on individual transcripts, groups of transcripts, or the whole transcriptome in the form of a table with the number of reads for each combination of observed Ts and observed T→C vonersions.
Binomial mixture model was applied to read statistics to estimate conversion/nascent parameters. K. lac proportion of each sample was used to estaimte the relative amount of mRNA between sampels in the same experiment.
Genome_build: SacCer3-R64 (GCA_000146045.2)
Supplementary_files_format_and_content: features.csv.gz - each row is a genomic feature used in analysis (corresponds to "acc" in processed tables)
Supplementary_files_format_and_content: genotypes.csv - each row is a strain and its genotype description
Supplementary_files_format_and_content: samples.csv - each row is a sample with its metadata  (corresponds to "sample" in processed tables)
Supplementary_files_format_and_content: tc_data.csv.gz - gzipped table in which each row is the number of reads with observed Ts and T-C conversions in a specific transcript and a specific sample.
Supplementary_files_format_and_content: reads.csv.gz - gzipped table containing the number of reads (and spike-in-scaled reads) observed in each transcript in each sample
Supplementary_files_format_and_content: pnew.csv.gz - gzipped table containing the estimated proportion of nascent molecules in each transcript in each sample

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: midlog yeast

growth_protocol: Cells were grown overnight in YPD 2% Glucose at 30C. 1-2 hours prior to experiments, cells are distributed to a deep well plate, grown at 25C, and (robotically) pipette-mixed every 10-15 minutes.

extract_protocol:
MetOH is washed twice with ddw. Cells are subjected to proteinaseK treatment, followed by potassium-acetate precipiation. Supernatanant is passed through nucleic-acid binding column, washed multuple time in 60% EtOH and eluted in 10 mM TRIS  pH 7.5. Up to this point DTT is added to maintain reducing conditions. Finally, RNA is roughly quantified and subjected to an alkylation reaction (4tU->C), followed by another binding-washing-elution step.
polyT primers with barcode and UMI are added to each sample and reverse transcription is performed. Samples are pooled, and subjected to a tn5 reaction. Finally an elongation step to extend transposase adapters and a PCR is performed to enrich tagged cDNA. In this protocol R2 starts with a 7bp sample barcode, followed by a 8 bp UMI followed by putative polyT. R1 immediately starts by reading the sense strand, enriched to the 3' of polyA mRNA. I2 is added in PCR and denotes a specific library/experiment. I1 is a constant sequence - ATCTCGTA.

treatment_protocol: At indiicated timepoints auxin (1-2.5 mM, per exp) was added to each sample. 6-10 minutes prior to harvesting 5 mM 4tU is added to samples. Finally cells are harvested by transferring 500 ul to 600 ul of pre-frozen MetOH (-80) that included a constant spike-in of K. lactis cells, and frozen (-80) until further processing.

tag: alphafactor

value: yes

tag: repeat


title: cellcycle_arrest:H9:rat1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|H9

value: no


title: cellcycle_arrest:H5:rat1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|H5


title: cellcycle_arrest:G12:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|G12


title: cellcycle_arrest:H3:rat1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|H3


title: cellcycle_arrest:H4:rat1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|H4


title: cellcycle_arrest:G8:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|G8


title: cellcycle_arrest:H2:rat1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|H2


title: cellcycle_arrest:G10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|G10


title: Affymetrix_ATH7

value: adult thalamus


title: cellcycle_arrest:H12:rat1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|H12


title: cellcycle_arrest:G6:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|G6


title: NoE2-ELF1_Rep2_in8

tag: strain

value: 48hrs estradiol withdrawal.


title: cellcycle_arrest:G9:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|G9


title: cellcycle_arrest:H8:rat1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|H8


title: cellcycle_arrest:G2:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|G2


title: cellcycle_arrest:G3:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|G3


title: cellcycle_arrest:G5:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|G5


title: Untreated-ELF1_Rep1_in1

description: ELF1 binding in untreated cells

value: Lys::GFP / ER-HoxA9 / LacO-shChaf1b


title: cellcycle_arrest:G4:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|G4


title: cellcycle_arrest:F12:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|F12


title: cellcycle_arrest:H11:rat1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|H11


title: cellcycle_arrest:F11:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|F11


title: IPTG-ELF1_Rep1_in4

description: ELF1 binding in Chaf1b-depleted cells.

value: HoxA9 transformed bone marrow, granulocyte macorphage progenitors


title: cellcycle_arrest:H10:rat1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|H10


title: cellcycle_arrest:F10:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|F10


title: cellcycle_arrest:F8:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|F8


title: cellcycle_arrest:G11:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|G11


title: cellcycle_arrest:F6:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|F6


title: cellcycle_arrest:F5:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|F5


title: cellcycle_arrest:F9:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|F9


title: cellcycle_arrest:E12:med14

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|E12


title: cellcycle_arrest:E11:med14

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|E11


title: cellcycle_arrest:E10:med14

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|E10


title: cellcycle_arrest:F2:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|F2


title: cellcycle_arrest:E9:med14

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|E9


title: cellcycle_arrest:D11:sth1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|D11


title: cellcycle_arrest:F4:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|F4


title: cellcycle_arrest:D6:sth1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|D6


title: cellcycle_arrest:D12:sth1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|D12


title: cellcycle_arrest:E8:med14

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|E8


title: cellcycle_arrest:E2:med14

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|E2


title: cellcycle_arrest:E6:med14

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|E6


title: cellcycle_arrest:E3:med14

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|E3


title: cellcycle_arrest:D10:sth1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|D10


title: cellcycle_arrest:D8:sth1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|D8


title: cellcycle_arrest:D4:sth1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|D4


title: cellcycle_arrest:D3:sth1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|D3


title: cellcycle_arrest:C12:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|C12


title: cellcycle_arrest:E5:med14

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|E5


title: cellcycle_arrest:D2:sth1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|D2


title: cellcycle_arrest:E4:med14

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|E4


title: cellcycle_arrest:C11:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|C11


title: cellcycle_arrest:D9:sth1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|D9


title: cellcycle_arrest:C9:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|C9


title: cellcycle_arrest:C10:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|C10


title: cellcycle_arrest:F3:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|F3


title: cellcycle_arrest:C8:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|C8


title: cellcycle_arrest:C6:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|C6


title: cellcycle_arrest:D5:sth1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|D5


title: cellcycle_arrest:C5:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|C5


title: cellcycle_arrest:C3:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|C3


title: cellcycle_arrest:C4:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|C4


title: cellcycle_arrest:C2:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|C2


title: cellcycle_arrest:B2:spt6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|B2


title: cellcycle_arrest:A8:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|A8


title: cellcycle_arrest:B5:spt6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|B5


title: cellcycle_arrest:A10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|A10


title: cellcycle_arrest:B10:spt6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|B10


title: cellcycle_arrest:A6:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|A6


title: cellcycle_arrest:B11:spt6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|B11


title: cellcycle_arrest:B9:spt6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|B9


title: cellcycle_arrest:A9:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|A9


title: cellcycle_arrest:B3:spt6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|B3


title: cellcycle_arrest:A5:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|A5


title: cellcycle_arrest:A3:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|A3


title: cellcycle_arrest:A12:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|A12


title: xrn1_dep_rep:H1:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|H1

value: A


title: xrn1_dep_rep:G1:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|G1


title: xrn1_dep_rep:F1:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|F1


title: xrn1_dep_rep:E1:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|E1


title: cellcycle_arrest:B12:spt6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|B12


title: cellcycle_arrest:A11:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|A11


title: xrn1_dep_rep:D1:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|D1


title: cellcycle_arrest:A4:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|A4


title: cellcycle_arrest:B8:spt6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|B8


title: cellcycle_arrest:B6:spt6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|B6


title: xrn1_dep_rep:B1:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|B1


title: xrn1_dep_rep:H3:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|H3

value: B


title: cellcycle_arrest:A2:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|A2


title: xrn1_dep_rep:A1:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|A1


title: xrn1_dep_rep:A2:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|A2


title: xrn1_dep_rep:F2:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|F2


title: xrn1_dep_rep:A3:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|A3


title: xrn1_dep_rep:G2:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|G2


title: xrn1_dep_rep:B3:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|B3


title: xrn1_dep_rep:F3:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|F3


title: xrn1_dep_rep:E3:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|E3


title: xrn1_dep_rep:C2:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|C2


title: xrn1_dep_rep:D3:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|D3


title: xrn1_dep_rep:C3:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|C3


title: cellcycle_arrest:B4:spt6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
aArrest|B4


title: xrn1_dep_rep:G3:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|G3


title: screen_2:H12:dcp2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|H12


title: xrn1_dep_rep:E2:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|E2


title: screen_2:H11:pab1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|H11


title: xrn1_dep_rep:D2:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|D2


title: xrn1_dep_rep:B2:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|B2


title: screen_2:H9:dis3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|H9


title: screen_2:H8:rat1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|H8


title: xrn1_dep_rep:H2:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|H2


title: screen_2:H6:rrp6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|H6


title: screen_2:H4:pan3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|H4


title: screen_2:H2:not1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|H2


title: screen_2:H3:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|H3


title: screen_2:G12:dcp2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|G12


title: screen_2:H1:pop2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|H1


title: screen_2:G8:rat1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|G8


title: screen_2:G7:pan3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|G7


title: screen_2:G11:pab1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|G11


title: screen_2:G2:not1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|G2


title: screen_2:G4:pan3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|G4


title: screen_2:F12:dcp2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|F12


title: screen_2:G9:dis3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|G9


title: screen_2:H10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|H10


title: screen_2:G10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|G10


title: screen_2:G3:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|G3


title: screen_2:F7:pan3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|F7


title: screen_2:G6:rrp6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|G6


title: screen_2:G5:ccr4

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|G5


title: screen_2:F10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|F10


title: screen_2:H7:pan3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|H7


title: screen_2:F9:dis3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|F9


title: screen_2:F6:rrp6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|F6


title: screen_2:G1:pop2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|G1


title: screen_2:F11:pab1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|F11


title: screen_2:F4:pan3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|F4


title: screen_2:F8:rat1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|F8


title: screen_2:H5:ccr4

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|H5


title: screen_2:F3:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|F3


title: screen_2:F2:not1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|F2


title: screen_2:F5:ccr4

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|F5


title: screen_2:E11:pab1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|E11


title: screen_2:F1:pop2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|F1


title: screen_2:E12:dcp2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|E12


title: screen_2:E10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|E10


title: Untreated-IgG

description: IgG control pull-down in untreated cells

data_processing:
Library strategy: CUT&RUN
Basecalling was performed with CASAVA version 1.4
Adapter sequences were removed with cutadapt (v2.1).
Paired-end reads were mapped to mm9 genome using Bowtie2  version 2.2.9 with parameters:  --end-to-end --very-sensitive -–no-mixed -–no-discordant --phred33 -I 10 -X 700.
PCR duplications were removed with bamUtil version 1.0.14
CPM normalized bigwig files were generated with bamCoverage tools from deeptools version 3.5.1
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig

value: IgG


title: screen_2:E9:dis3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|E9


title: screen_2:E7:pan3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|E7


title: Untreated-H3K27me3

description: H3K27me3 chromatin in untreated cells


title: Untreated-H3K9me3

description: H3K9me3 chromatin in untreated cells


title: screen_2:E6:rrp6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|E6


title: Untreated-H3K4me1

description: H3K4me1 chromatin in untreated cells


title: screen_2:E4:pan3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|E4


title: screen_2:E3:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|E3


title: NASH_3

city: Nanjing

first: MINYI

last: QIAN

address: Longmiandadao

institute: CPU

description: after HFD-feeding, obese mice were termed as NASH

data_processing:
Basecalling based on Illumina Casava1.7 software
After RNA sequencing reads quality checking, the reads were  mapped to the mouse genome (mm10) using tophat2 by requiring 3 edit distance (mismatch+indel) at maximum
The gene expression abundance was estimated by counting number of reads mapped to the cognate gene exons using HTSeq
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include gene ID and expression level in reads count for each sample

growth_protocol: 5-week age of C57BL/6J mice feed with high-fat diet (HFD, 12492, 60% kcal from fat; Research Diets, New Brunswick, NJ, USA) for 21 weeks

extract_protocol:
Total RNA was extracted with RNAiso Plus (TaKaRa) from mice livers.
A cDNA library was generated from polyA+ RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq4000 by a 2X150 bp run.

treatment_protocol: obese mice were classified into two groups termed as isolated steatosis and NASH based on H&E staining of liver biopsies, we aimed to identify key factors promoting this transition.

tag: group

value: nonalcoholic steatohepatitis


title: NASH_1


title: NASH_2


title: Steatosis_1

description: after HFD-feeding, obese mice were termed as isolated steatosis

value: steatosis


title: Steatosis_3


title: Steatosis_2


title: screen_2:E1:pop2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|E1


title: Heroin_WT___HW9

city: New York

first: Sasha

middle: Leilani

last: Fulton

state: NY

address: 3227 Broadway

institute: Columbia University

description: concatenated read data from 2 flow cells

data_processing:
fastq files were aligned to ensembl Rnor_6.0 (GCA_000001895.4) rat reference genome using HISAT2 (Version 2.1.0) and ensembl v90.
BAM files resulting from the alignments were summarized to genes using the featureCounts (Version 2.0.1) algorithm
Expression data was normalized using RUVr from RUVseq (Version 4.1.1)followed by DESEQ2 (Version 2.11.40.6)
Differentially expressed genes (5% false discovery rate) were identified using DESEQ2 based on a model using the negative binomial distribution
Genome_build: rnor6 rat genome
Supplementary_files_format_and_content: tab-delimited text files are VST normalized counts matrix for each sample from DESEQ2 output

organism: Rattus norvegicus

source_name: Virally-infected tissue from Ventral Tegmental Area brain reion

extract_protocol:
RNA was isolated using trizol-chloroform extraction followed by cleanup on the RNeasy Micro Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the Illumina Truseq RNA Library Prep Kit V2 , according to the manufacturer’s instructions.

treatment_protocol: Animals went through either Saline or Heroin SA for 10d, and virus was injected (GFP, H3.3WT, or H3.3 Q5A) intra-VTA at 11d, tissue was collected at abstinence d30

tag: background strain

value: Sprague-Dawley

tag: weight

value: wild-type

tag: Sex

value: male

value: 10d Heroin Self Administration + Virus treatment (@ d11) + 30d Abstinence

value: H3.3 WT Virus treatment


title: screen_2:E2:not1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|E2


title: screen_2:D12:dcp2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|D12


title: screen_2:D11:pab1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|D11


title: Heroin_WT___HW38


title: screen_2:D9:dis3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|D9


title: screen_2:D10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|D10


title: screen_2:D8:rat1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|D8


title: screen_2:E8:rat1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|E8


title: Heroin_WT___HW20


title: screen_2:D7:pan3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|D7


title: screen_2:E5:ccr4

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|E5


title: screen_2:D6:rrp6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|D6


title: Heroin_WT__HW1


title: Heroin_WT___HW11


title: screen_2:D5:ccr4

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|D5


title: Heroin_Q5A__HQ43

value: H3.3Q5A Virus treatment


title: screen_2:D3:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|D3


title: Heroin_WT___HW51


title: Heroin_Q5A__HQ39


title: Heroin_Q5A__HQ37


title: screen_2:C11:pab1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|C11


title: screen_2:C12:dcp2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|C12


title: Heroin_Q5A__HQ26


title: Heroin_Q5A__HQ24


title: screen_2:D2:not1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|D2


title: Heroin_Q5A__HQ25


title: Heroin_Q5A__HQ21


title: Heroin_WT___HW3


title: screen_2:C10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|C10


title: screen_2:C9:dis3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|C9


title: screen_2:C8:rat1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|C8


title: screen_2:C7:pan3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|C7


title: screen_2:C6:rrp6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|C6


title: Heroin_GFP__HG6

description: concatenated read data from 2 flow cells

value: GFP Virus treatment


title: Heroin_GFP__HG5


title: Heroin_GFP__HG21


title: screen_2:D4:pan3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|D4


title: Heroin_Q5A__HQ40


title: screen_2:C5:ccr4

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|C5


title: screen_2:D1:pop2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|D1


title: Heroin_GFP__HG2


title: screen_2:C4:pan3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|C4


title: Heroin_GFP__HG14


title: Heroin_GFP__HG16


title: Heroin_GFP__HG13


title: screen_2:C2:not1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|C2


title: screen_2:C1:pop2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|C1


title: screen_2:B12:dcp2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|B12


title: Saline_WT__SW49

value: 10d Saline Self Administration + Virus treatment (@ d11) + 30d Abstinence


title: Heroin_GFP__HG7


title: Saline_WT__SW44


title: screen_2:C3:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|C3


title: screen_2:B11:pab1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|B11


title: screen_2:B10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|B10


title: screen_2:B9:dis3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|B9


title: Saline_WT__SW4


title: screen_2:B8:rat1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|B8


title: Saline_WT__SW50


title: Saline_WT__SW27


title: Saline_WT__SW23


title: screen_2:B7:pan3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|B7


title: Saline_Q5A__SQ48


title: Saline_Q5A__SQ47


title: screen_2:B6:rrp6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|B6


title: screen_2:B5:ccr4

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|B5


title: screen_2:B4:pan3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|B4


title: Saline_Q5A__SQ46

description: concatenated read data from 2 flow cells


title: Saline_Q5A__SQ32


title: screen_2:B1:pop2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|B1


title: Saline_Q5A__SQ33


title: screen_2:B2:not1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|B2


title: Saline_Q5A__SQ31


title: screen_2:B3:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|B3


title: Saline_WT__SW8


title: Saline_Q5A__SQ30


title: screen_2:A12:dcp2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|A12


title: screen_2:A10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|A10


title: Saline_GFP__SG41


title: Saline_GFP__SG22


title: screen_2:A8:rat1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|A8


title: screen_2:A9:dis3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|A9


title: screen_2:A6:rrp6

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|A6


title: screen_2:A7:pan3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|A7


title: screen_2:A11:pab1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|A11


title: Saline_GFP__SG18


title: Saline_GFP__SG15


title: Saline_GFP_SG42


title: screen_2:A4:pan3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|A4


title: screen_2:A3:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|A3


title: screen_2:A5:ccr4

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|A5


title: Saline_GFP__SG10


title: Saline_GFP__SG13


title: PTPR9

data_processing:
Fusion detection was performed using JAFFA 17 after merging across replicate lanes. For gene expression, read alignment was performed with hisat2-2.0.5 18 to human genome GRCh38 and aligned files were converted to bam and sorted with samtools v1.3.1 19. Alignment QC was generated with RSeQC v2.6.4 20. Counts from the subread package v1.5.1 21 was used to count the number of reads aligning to Ensembl IDs according to GRCh38.86 annotation.
Variant calling was performed following GATK's best practices for variant calling in RNAseq using a 2-pass sTAR alignment. Alignments were made with STAR v2.5.2a 22 to human reference genome GRCh38. The junctions detected in all samples were merged and used to make a custom STAR genome index for a second pass alignment. Picard v2.4.1 was used to preprocess the alignment files, add read groups, mark duplicates, sort, and index. GATK v3.6 23 was used to split reads containing junctions, realign around indels, and recalibrate the base qualities. Samtools v1.3.1 was used to generate mpilup format. BRAF mutations were identified by a visual inspection of the alignment BAM in the Integrated Genomic Viewer 24 since they were not detected by VarScan analysis. VarScan v2.4.1 25 was used to call and filter variants from mpilup format from the whole genome. Called variants were annotated with Ensembl Variant Effect Predictor (VEP) 26. Variants were eliminated if listed in dbSNP alone. Variants with MEDIUM or HIGH impact as designated by VEP were retained. After filtering variants detected by the same set of reads were eliminated. The variant list was uploaded to VEP and several functional prediction algorithms were run, i.e., all of the ones provided by VEP. PolyPhen, SIFT and FathmmMKL predictions were determined using respective versions available July 2018.
Voom from the limma package in R was used to normalize the gene expression data.  By using voom we transformed the data to counts/million (cpm) and took the log of the value. Genes with a relatively small number of counts will have a cpm value between 0 and 1. The log of any number between 0 and 1 is a negative number.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: JAFFA fuson analysis table
Supplementary_files_format_and_content: VEP gene sequence variants and predictors
Supplementary_files_format_and_content: RNAseq gene expression matrix table

growth_protocol: not applicable

extract_protocol:
Total RNA was extracted from three 30μm scrolls cut from FFPE tissue blocks containing 90% tumor or more, using the RecoverAll total nucleic acid isolation kit (Ambion/Thermo Fisher Scientific, Waltham, MA) per the manufacturer’s instructions. RNA was then passed through concentration and clean-up columns (Norgen Biotek, Thorold, ON) and quantified using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA).
Capture-based RNAseq was performed using a modified SureSelect strand-specific RNA library prep and target enrichment protocol (Agilent Technologies, Santa Clara, CA). Briefly, 200ng of FFPE-derived total RNA was heated to 65 °C for 5 min and used for first-strand cDNA synthesis. Second-strand cDNA was synthesized, and the ends repaired. The 3ʹ ends of ds-cDNA were adenylated, ligated with adapters and fragments were PCR-amplified. PCR product (700ng) was hybridized overnight to SureSelect XT Human All Exon V5+lncRNA baits. The hybridized fragments were captured on magnetic beads and PCR-amplified using uniquely barcoded index primers.
RNAseq. Barcoded libraries were pooled and underwent paired-end 150bp sequencing on an Illumina HiSeq4000 instrument (Illumina, San Diego, CA).

treatment_protocol: not applicable

tag: patient gender

tag: disease

value: papillary tumor of thepineal reqion (PTTR)


title: xrn1_dep_rep:C1:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
HU|C1


title: PTPR7

value: female


title: PTPR3


title: screen_1:H12:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|H12


title: screen_1:H10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|H10


title: PTPR2


title: C40

value: atroblastomas


title: screen_2:A1:pop2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|A1


title: Saline_Q5A__SQ28

description: concatenated read data from 2 flow cells

tag: treatment


title: screen_1:H9:nab3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|H9


title: screen_1:H8:sen1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|H8


title: C39


title: screen_2:A2:not1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
tc|A2


title: C38


title: C36


title: screen_1:H7:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|H7


title: screen_1:H5:nrd1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|H5


title: C35


title: screen_1:H6:nrd1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|H6


title: C31


title: C29


title: screen_1:H2:not1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|H2


title: screen_1:H4:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|H4


title: screen_1:H1:pap2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|H1


title: screen_1:G12:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|G12


title: C26


title: C23


title: C24


title: C21


title: screen_1:H3:pop2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|H3


title: screen_1:G11:fcp1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|G11


title: screen_1:G10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|G10


title: C22


title: C20


title: screen_1:G9:nab3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|G9


title: screen_1:G8:sen1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|G8


title: screen_1:G7:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|G7


title: C17


title: screen_1:G6:nrd1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|G6


title: C19


title: C14


title: C13


title: screen_1:G5:nrd1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|G5


title: screen_1:G4:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|G4


title: C12


title: C10


title: screen_1:G3:pop2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|G3


title: screen_1:G2:not1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|G2


title: C6


title: C8


title: C11


title: C18


title: screen_1:G1:pap2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|G1


title: C16


title: MS-Blood Methylation

city: Thousand Oaks

first: Xianglong

last: Zhang

state: CA

address: One Amgen Center Dr.

department: Department of Cardiometabolic Disorders

institute: Amgen Inc.

data_processing:
RNA-Seq data: Cutadapt (Version 1.8.1) was used to trim Illumina TruSeq adapters and low-quality ends from the raw reads. Bowtie2 (Version 2.3.1) was used to align the trimmed reads to the RefSeq transcriptome (GRCh38.p10) and RSEM (Version 1.2.30) was used to quantify gene expression in a strand-specific manner by setting parameter “--forward-prob 0”. DESeq2 (Version 1.12.4) was used to perform differential expression analysis between cell types as well as between patients and controls within each cell type.
Methylation data: Cutadapt (Version 1.8.1) was used to trim Illumina adapters and low-quality ends from the raw reads. The trimmed reads were mapped to human RefSeq genome (GRCh38.p10) using Bismark (Version 0.16.3). Duplicates were removed by the deduplicate_bismark script in Bismark. Only one copy of the overlapping parts in the middle of paired-end reads was retained after clipping the read with the lower average quality in the overlap region by the “clipOverlap” tool in bamUtil (Version 1.0.14). Methylation ratio for each CpG was extracted by the bismark_methylation_extractor script in Bismark. Differentially methylated regions (DMRs) were identified between cell types as well as between patients and controls within each cell type by metilene (Version 0.2-6) with >= 3 CpGs and a mean methylation difference between the two compared groups of >= 0.2. DMRs with FDR corrected p-value < 0.05 were considered significant.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: RNA-Seq data — gene name, transcript id, length, effective_length, expected count, TPM, FPKM
Supplementary_files_format_and_content: Methylation data — chromosome, CpG position, CpG methylation ratio

source_name: blood

growth_protocol: In order to generate induced neurons (iNs), iPSCs cells were maintained under feeder-free conditions in mTeSR1 media ( STEMCELL Technologies). Media was changed daily.  Once cell density reached 75%-80% confluence, clones were dissociated and plated onto 6 well plates.  On day 1, cells were infected with lentivirus ( RTTa, GFP and Ngn2) in mTESR1 media.  Day 2, media was replace with N2 media and doxycycline.  From days 3-6, puromycin selection continued with N2 media changes every day.

extract_protocol:
Genomic DNA was extracted from fibroblast and iPSC’s using Blood & Cell Culture DNA mini kit (Qiagen) and iN’s using Quick –DNA Miniprep Plus Kit (Zymo Research).  Total RNA was extracted from fibroblast, iPSC’s and iN’s using the RNeasy mini kit and RNeasy micro kit (Qiagen).
Libraries were prepared according to KAPA biosystems instructions accompanying KAPA library Preparation Kit Illumina platforms. In brief, genomic DNA was sonicated (Covaris) to generate fragments 180-220 bp in size. Following fragmentation, DNA was used to construct library. After library construction, DNA libraries were bisulfite converted and purified using the EZ DNA Methylation Lightning Kit (Zymo Research). Bisulfite converted samples libraries were amplified using LM-PCR. Amplified bisulfite converted samples and SeqCap Epi probes were hybridized for 64-72 h. Captured DNA samples were washed and recovered, followed by amplification of the capture DNA samples using LM-PCR. Amplified samples were purified using Agencourt AMPure XP Beads (Beckman Coulter). Bisulfite converted libraries captured by SeqCap Epi CpGiant Probes kit sequenced on Illumina HiSeq 4000 platform by 2x150 paired-end.   For RNA-seq, library construction was performed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s instructions. Briefly, total RNA was converted to mRNA using polyA purification. The mRNA was then fragmented and primed for cDNA synthesis. The cDNA was adenylated and adapters were ligated onto the cDNA. Samples were amplified using PCR, amplified library was then purified using Agencount AMPure XP beads (Beckman Coulter). Final libraries were checked for quality on a Bioanalyzer DNA High Sensitivity chip (Agilent). Stand-specific RNA libraries of all the samples were sequenced on Illumina NextSeq 550 platform using 2x150 paired-end sequencing.

tag: individual

value: MS

value: wild type

value: blood


title: GR-Blood Methylation

value: GR


title: C9


title: screen_1:F10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|F10


title: screen_1:F11:fcp1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|F11


title: C4


title: C3


title: screen_1:F9:nab3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|F9


title: screen_1:F12:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|F12


title: MS-3iN Methylation

source_name: induced neuron

value: induced neuron


title: screen_1:F8:sen1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|F8


title: C1


title: F01-Blood Methylation

value: patient with ADCA-DN


title: MS-1iPSC Methylation

source_name: induced pluripotent stem cell

value: induced pluripotent stem cell


title: MS-FB Methylation

source_name: fibroblast

value: fibroblast


title: 81214-Blood Methylation


title: MS-3iPSC Methylation


title: MK-Blood Methylation

value: MK


title: F03-Blood Methylation


title: MS-1iN Methylation


title: screen_1:F7:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|F7


title: F03-FB Methylation


title: screen_1:F6:nrd1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|F6


title: F03-3iPSC Methylation


title: screen_1:F5:nrd1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|F5


title: F03-1iPSC Methylation


title: F03-3iN Methylation


title: screen_1:F4:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|F4


title: F01-FB Methylation


title: F03-1iN Methylation


title: F01-3iPSC Methylation


title: screen_1:F2:not1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|F2


title: screen_1:F3:pop2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|F3


title: F01-1iPSC Methylation


title: F01-3iN Methylation


title: F01-1iN Methylation


title: screen_1:F1:pap2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|F1


title: 81214-FB Methylation


title: 81214-3iPSC Methylation


title: 81214-3iN Methylation


title: screen_1:E12:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|E12


title: Methylation_C20

type: genomic

hyb_protocol: Bisulphite-converted FFPE DNA was processed with the Infinium FFPE DNA Restore kit (Illumina, UK) and assayed on the Infinium Methylation EPIC BeadChip (Illumina), according to the Infinium HD FFPE Methylation Assay automated protocol (Illumina). The tSNE plot was generated using the 32,000 most variably methylated probes of the study samples and 2,801 German Cancer Center (DKFZ) reference samples

scan_protocol: Arrays were imaged with BeadArray Reader.

data_processing: A tSNE plot was generated using the 32,000 most variably methylated probes of the study samples and 2,801 German Cancer Center (DKFZ) reference samples.

label: Cy3 and Cy5

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from 4 um sections of formalin-fixed paraffin-embedded (FFPE) tissues using the AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) and quantified using a Qubit High Sensitivity assay (Thermo Fisher Scientific, UK), before bisulphite conversion of up to 250 ng DNA, using the EZ DNA Methylation kit (Zymo Research, Irvine, CA).

tag: tissue

value: tumor

tag: histological type

value: astroblastoma


title: Methylation_C1


title: screen_1:E11:fcp1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|E11


title: Methylation_C12


title: Methylation_C5


title: 81214-1iN Methylation

tag: phenotype


title: 81214-1iPSC Methylation


title: screen_1:E10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|E10


title: Methylation_C14


title: Methylation_C29


title: screen_1:E6:nrd1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|E6


title: 0425-FB Methylation


title: Methylation_C11


title: 0425-3iPSC Methylation


title: 0425-3iN Methylation


title: Methylation_C22


title: Methylation_C9


title: screen_1:E4:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|E4


title: Methylation_C30


title: screen_1:E5:nrd1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|E5


title: 0425-1iPSC Methylation


title: screen_1:E3:pop2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|E3


title: 0425-1iN Methylation


title: Methylation_C24


title: AI007_P58_PRE

city: Chicago

first: Swati

last: Kulkarni

state: Illinois

address: 600 N. Lake Shore Drive, Apt 3602

department: Surgery

institute: Northwestern University

description: KAPA HyperPrep

data_processing:
RNA sequencing data analysis was performed using Artificial Intelligene’s (AI, www.artificialintelligene.com) RNAseq analysis platform. Briefly, short reads were aligned to the hg19 human genome using STAR. Subsequently cufflinks packages were used to perform transcript assemblies. Downstream differential gene expression calling on the reference and experimental groups of interest was performed using DESeq2. To perform clustering analyses on a group of samples, a union of all the genes and their expression RPKM values within that group was generated to build a read count matrix for the group of interest. Various unsupervised and other machine learning techniques were applied to this composite read count matrix of interest. The sample-sample correlation heatmaps represent the correlation observed between any two samples. The sample-feature heatmaps represent the signal intensity of a feature for any given sample. ggplot2, heatmap.2 and Pheatmap packages in R were used to build various heatmaps. Functional analysis was performed using gene set enrichment analyses.
Genome_build: HG19
Supplementary_files_format_and_content: counts

source_name: Breast tissue

extract_protocol:
Tissue frozen in RNAlater was homogenized and RNA isolated by Qiagen RNEasy Plus Kit. RNA sample was treated with DNASeq I.
Libraries were prepared using KAPA mRNA HyperPrep Kit (KK8580). 100ng RNA was used for each library

treatment_protocol: Bariatric surgery

value: pre

tag: patientid

tag: race

value: White

tag: age

tag: childhood obesity

value: No known history

tag: menopause

value: Premenopausal

tag: hypertension

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: depression

value: Yes

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: post waist to hip ratio

tag: percent ebw loss

tag: type of surgery

value: Sleeve Gastrectomy

tag: pre or post surgery

value: pre surgery


title: AI007_P5_PRE

description: KAPA HyperPrep

tag: treatment

tag: patientid

tag: race

tag: age

tag: childhood obesity

tag: menopause

value: Postmenopausal

tag: hypertension

value: Unknown

value: No

value: Roux-En-Y Gastric Bypass


title: screen_1:E2:not1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|E2


title: screen_1:D12:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|D12


title: screen_1:E1:pap2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|E1


title: screen_1:D11:fcp1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|D11


title: screen_1:D10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|D10


title: Methylation_C23

tag: tissue

tag: histological type


title: AI007_P55_PRE

description: KAPA HyperPrep

tag: diabetes

value: yes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: depression

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio


title: AI007_P53_PRE

description: KAPA HyperPrep

tag: treatment

tag: patientid

tag: post weight

tag: post height

tag: post bmi

tag: post waist to hip ratio

tag: percent ebw loss

tag: type of surgery

tag: pre or post surgery


title: AI007_P37_PRE

description: KAPA HyperPrep

tag: race

tag: age

tag: childhood obesity

tag: menopause

tag: hypertension

tag: diabetes

tag: metabolic syndrome


title: Methylation_C19

tag: tissue

tag: histological type


title: screen_1:D9:nab3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|D9


title: Methylation_C6


title: Methylation_C13


title: AI007_P1_PRE

description: KAPA HyperPrep

tag: treatment

tag: patientid

value: African American

value: Yes and currently active.

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: depression

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio


title: Methylation_C34


title: AI007_P17_PRE

description: KAPA HyperPrep

tag: race

tag: age

tag: post weight

tag: post height

tag: post bmi

tag: post waist to hip ratio

tag: percent ebw loss

tag: type of surgery

tag: pre or post surgery


title: Methylation_C3

tag: tissue

tag: histological type


title: AI007_P15_PRE

description: KAPA HyperPrep

tag: treatment

tag: patientid

tag: childhood obesity

tag: menopause

tag: hypertension

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche


title: Methylation_C10


title: MS-3iPSC RNA-Seq

tag: individual

value: MS

tag: phenotype

value: wild type

tag: cell type

value: induced pluripotent stem cell


title: MS-FB RNA-Seq

value: fibroblast


title: MS-1iPSC RNA-Seq


title: screen_1:D7:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|D7


title: screen_1:D8:sen1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|D8


title: screen_1:D6:nrd1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|D6


title: AI007_P19_PRE

description: KAPA HyperPrep

value: pre

tag: race

tag: age

tag: depression

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: post waist to hip ratio

tag: percent ebw loss


title: AI007_P8_PRE

description: KAPA HyperPrep

tag: treatment

tag: patientid

value: White

tag: childhood obesity

value: No known history

tag: menopause

tag: hypertension

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: type of surgery

value: Biliopancreatic Diversion with Duodenal Switch

tag: pre or post surgery


title: screen_1:D4:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|D4


title: Methylation_C33

tag: tissue

value: tumor

tag: histological type

value: astroblastoma


title: MS-1iN RNA-Seq

tag: individual

tag: phenotype

tag: cell type

value: induced neuron


title: F03-FB RNA-Seq

value: patient with ADCA-DN


title: Methylation_C7


title: Methylation_C32


title: screen_1:D3:pop2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|D3


title: Methylation_C44

tag: gender

value: female


title: screen_1:D5:nrd1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|D5


title: MS-3iN RNA-Seq


title: AI007_P69_PRE

description: KAPA HyperPrep

tag: race

tag: age

value: Postmenopausal

tag: age of menarche

tag: depression

value: No

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: post waist to hip ratio

tag: percent ebw loss

value: Roux-en-Y Gastric Bypass

value: pre surgery


title: F03-3iN RNA-Seq

tag: individual


title: Methylation_C40

tag: tissue

tag: histological type


title: Methylation_C38

tag: gender

value: male


title: Methylation_C36


title: screen_1:D2:not1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|D2


title: Methylation_C39


title: Methylation_C42


title: F03-3iPSC RNA-Seq

tag: phenotype

tag: cell type


title: screen_1:D1:pap2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|D1


title: AI007_P29_PRE

description: KAPA HyperPrep

tag: treatment

tag: patientid

tag: race

value: African American

tag: age

tag: childhood obesity

tag: menopause

tag: hypertension

value: yes

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: type of surgery

value: Sleeve Gastrectomy

tag: pre or post surgery


title: F03-1iN RNA-Seq

tag: individual


title: Methylation_C35

tag: tissue

tag: histological type

tag: gender


title: F03-1iPSC RNA-Seq

tag: phenotype

tag: cell type

value: induced pluripotent stem cell


title: RetinaMll5-KO rep2

city: Singapore

first: Xiaoming

address: 10 Medical Drive

country: Singapore

institute: National University of Singapore

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and discarded uncertain nucleotides constitute more than 10 percents of either read (N > 10%) and  low quality nucleotides (base quality less than 20) constitute more than 50 percents of the read, then mapped to mm10 whole genome using TopHat2 (v2.0.12) with mismatch parameter was set to two, and other parameters were set to default.
HTSeq software (v0.6.1) was used to analyze the gene expression levels in this experiment using the union mode. The result files present the number of genes with different expression  levels and the expression level of single genes. In general, an FPKM value of 0.1 or 1 is set as the threshold for determining whether the gene is expressed or not.
To compare gene expression levels under different conditions, an FPKM distribution diagram and violin Plot are used.
DEGseq (v1.12.0) was used for he differential gene expression analysis. Negdaitsivtreibbuitnioonmial was used for p-value estimation, and BH was used for FDR estimation.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include readcount and FPKM values for each Sample

source_name: Retina

extract_protocol:
For the preparation of total RNA for RNA-seq, 8 eyeballs of two pairs of female Mll5-WT and Mll5-KO mice at the age of P18 were dissected. Total RNA was extracted with RNeasy mini kit (Qiagen, 74104).  A minimum of 2 μg of total RNA obtained from mixture of 2 eyeballs were used for library construction
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: retina

value: postnatal day 18

tag: genotype


title: Retina Mll5-KO rep1

tag: age


title: screen_1:C12:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|C12


title: AI007_P26_PRE

description: KAPA HyperPrep

tag: treatment

value: pre

tag: patientid

tag: race

value: White

tag: childhood obesity

value: Yes and currently active.

tag: menopause

value: No known history

tag: depression

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: post waist to hip ratio

tag: percent ebw loss

value: Roux-En-Y Gastric Bypass


title: Methylation_C41

tag: tissue

value: tumor

tag: histological type

value: astroblastoma

tag: gender


title: Retina WT rep2

tag: strain

tag: age

tag: genotype

value: wild type


title: AI007_P25_PRE

description: KAPA HyperPrep

tag: treatment

tag: patientid

tag: race

tag: childhood obesity

tag: menopause

value: Postmenopausal

tag: hypertension

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

value: No

tag: type of surgery

tag: pre or post surgery


title: Methylation_C21

tag: tissue

tag: histological type

value: female


title: Methylation_C27

tag: gender

value: male


title: screen_1:C11:fcp1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|C11


title: Methylation_C43


title: F01-3iPSC RNA-Seq

tag: individual

tag: phenotype

value: patient with ADCA-DN

tag: cell type


title: Retina WT rep1

tag: strain

tag: age

tag: genotype


title: screen_1:C9:nab3

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|C9


title: screen_1:C10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|C10


title: F01-FB RNA-Seq

value: fibroblast


title: Methylation_C16


title: Methylation_C17


title: F01-3iN RNA-Seq

value: induced neuron


title: AI007_P33_PRE

description: KAPA HyperPrep

tag: treatment

tag: patientid

tag: race

tag: childhood obesity

value: Yes but currently inactive.

tag: menopause

value: Premenopausal

tag: depression

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height

tag: post bmi

tag: post waist to hip ratio

tag: percent ebw loss

value: Biliopancreatic Diversion with Duodenial Switch

value: pre surgery


title: F01-1iPSC RNA-Seq

tag: individual

tag: phenotype

tag: cell type

value: induced pluripotent stem cell


title: screen_1:C8:sen1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|C8


title: F01-1iN RNA-Seq


title: AI007_P30_PRE

description: KAPA HyperPrep

tag: treatment

value: pre

tag: patientid

value: African American

tag: age

value: Yes and currently active.

tag: hypertension

value: yes

tag: diabetes

tag: metabolic syndrome

value: No known history

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: type of surgery

value: Sleeve Gastrectomy

tag: pre or post surgery


title: AI007_P2_PRE

description: KAPA HyperPrep

tag: race

value: White

tag: childhood obesity

tag: menopause

value: Postmenopausal

tag: depression

value: Yes

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: post height


title: screen_1:C7:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|C7


title: 81214-FB RNA-Seq

tag: individual

tag: phenotype

value: patient with ADCA-DN

tag: cell type


title: screen_1:C6:nrd1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|C6


title: 81214-3iPSC RNA-Seq


title: C30

hyb_protocol: Per manufacturer's instructions.

scan_protocol: Per manufacturer's instructions.

data_processing: Nsolver 2.1

label_protocol: Per manufacturer's instructions.

extract_protocol: Total RNA was extracted from three 30μm scrolls cut from FFPE tissue blocks containing minimally 90% tumor using the RecoverAll total nucleic acid isolation kit (Ambion/Thermo Fisher Scientific, Waltham, MA) per the manufacturer’s instructions. RNA was then passed through concentration and clean-up columns (Norgen Biotek, Thorold, ON) and quantified using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA).

tag: histology

value: astroblastoma


title: AI007_P62_PRE

description: KAPA HyperPrep

tag: treatment

tag: patientid

tag: age

tag: hypertension

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

value: No

tag: post bmi

tag: post waist to hip ratio

tag: percent ebw loss


title: screen_1:C5:nrd1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|C5


title: AI007_P56_PRE

description: KAPA HyperPrep

tag: race

tag: childhood obesity

tag: menopause

tag: depression

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post weight

tag: type of surgery

tag: pre or post surgery


title: Methylation_C8

tag: tissue

value: tumor

tag: histological type

tag: gender

value: female


title: AI007_P59_PRE

description: KAPA HyperPrep

tag: treatment

tag: patientid

tag: age

tag: hypertension

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: post height

tag: post bmi


title: Methylation_C31


title: screen_1:C4:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|C4


title: Methylation_C15

value: male


title: AI007_P54_PRE

description: KAPA HyperPrep

tag: race

tag: childhood obesity

tag: menopause

tag: depression

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post waist to hip ratio

tag: percent ebw loss

value: pre surgery


title: C31

tag: histology


title: C29


title: C24


title: AI007_P64_PRE

description: KAPA HyperPrep

tag: treatment

tag: patientid

tag: age

value: Premenopausal

tag: hypertension

tag: diabetes

tag: post weight

tag: type of surgery

tag: pre or post surgery


title: AI007_P39_PRE

description: KAPA HyperPrep

value: pre

tag: race

tag: childhood obesity

tag: menopause

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: post height

tag: post bmi

value: Biliopancreatic Diversion with Duodenal Switch


title: screen_1:C3:pop2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|C3


title: 81214-1iPSC RNA-Seq

tag: individual

tag: phenotype

tag: cell type

value: induced pluripotent stem cell


title: screen_1:C2:not1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|C2


title: 81214-1iN RNA-Seq

value: induced neuron


title: C26

tag: histology


title: AI007_P43_PRE

description: KAPA HyperPrep

tag: treatment

tag: patientid

value: African American

tag: age

value: No known history

tag: hypertension

value: yes

tag: depression

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post waist to hip ratio

tag: percent ebw loss


title: 0425-FB RNA-Seq

value: wild type

value: fibroblast


title: screen_1:C1:pap2

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|C1


title: Methylation_C18

tag: tissue

tag: histological type

tag: gender


title: 0425-3iPSC RNA-Seq

tag: individual

tag: phenotype


title: screen_1:B11:fcp1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|B11


title: 81214-3iN RNA-Seq

value: patient with ADCA-DN

tag: cell type


title: screen_1:B12:wt

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|B12


title: screen_1:B10:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|B10


title: C21

tag: histology

value: astroblastoma


title: C22


title: 0425-3iN RNA-Seq


title: C20


title: AI007_P45_PRE

description: KAPA HyperPrep

tag: treatment

tag: patientid

tag: race

tag: childhood obesity

tag: menopause

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

value: No

tag: post weight

tag: post height

tag: post bmi

tag: type of surgery

value: Roux-En-Y Gastric Bypass

tag: pre or post surgery


title: AI007_P40_PRE

description: KAPA HyperPrep

tag: age

tag: hypertension

tag: depression

tag: pre weight

tag: pre height

tag: pre bmi

tag: pre waist to hip ratio

tag: post waist to hip ratio

tag: percent ebw loss

value: Sleeve Gastrectomy


title: C19

tag: histology


title: AI007_P41_PRE

description: KAPA HyperPrep

tag: treatment

tag: patientid

tag: race

tag: childhood obesity

tag: menopause

value: Postmenopausal

tag: diabetes

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia


title: C18


title: C23


title: 0425-1iPSC RNA-Seq

tag: individual

tag: phenotype

tag: cell type


title: screen_1:B8:sen1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|B8


title: AI007_P44_PRE

description: KAPA HyperPrep

value: White

tag: age

tag: hypertension

tag: age of menarche

tag: depression

value: Yes

tag: pre weight

tag: pre height

tag: post weight

tag: post height

tag: post bmi

tag: type of surgery

tag: pre or post surgery

value: pre surgery


title: AI007_P55_POST

description: KAPA HyperPrep

tag: treatment

value: post

tag: patientid

tag: race

tag: childhood obesity

tag: menopause

value: Premenopausal

tag: diabetes

tag: pre bmi

tag: pre waist to hip ratio

tag: post waist to hip ratio

tag: percent ebw loss

value: post 25% EBW loss


title: AI007_P20_PRE

description: KAPA HyperPrep

value: pre

value: African American

tag: age

value: Yes and currently active.

tag: hypertension

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: depression

tag: pre weight


title: C15

tag: histology


title: C17


title: AI007_P53_POST

description: KAPA HyperPrep

tag: treatment

tag: patientid

value: No known history

value: yes

tag: pre height

tag: post weight

tag: post height

tag: post bmi

tag: type of surgery

tag: pre or post surgery


title: AI007_P42_PRE

description: KAPA HyperPrep

tag: race

tag: childhood obesity

tag: menopause

tag: diabetes

tag: pre bmi

tag: pre waist to hip ratio

tag: post waist to hip ratio

tag: percent ebw loss


title: screen_1:B5:nrd1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|B5


title: AI007_P37_POST

description: KAPA HyperPrep

tag: age

tag: hypertension

tag: metabolic syndrome

tag: dislipidemia hypercholesterolemia

tag: age of menarche

tag: depression

tag: pre weight


title: screen_1:B7:xrn1

description:
tc_data.csv.gz
reads.csv.gz
pnew.csv.gz
TC-14Apr2019|B7