title: ES-6

status: Public on Dec 31 2020

type: protein

city: Houston

first: Joseph

middle: A.

last: Ludwig

state: Texas

department: Sarcoma Medical Oncology

country: USA

institute: UT-MD-Anderson Cancer Center

description:
RPPA
SAMPLE 30

scan_protocol: Slides were scanned on a flatbed scanner to produce 16-bit tiff images. Spots from tiff images were identified and their densities were quantified by MicroVigene. Relative protein levels for each sample were determined by interpolation of each dilution curve from the standard curve (supercurve) of the slide (antibody). Supercurve is constructed from a script in R written by the informatics department. These values are given as Normalized values.

data_processing: Expression data was normalized for possible unequal protein loading, taking into account the signal intensity for each sample for all antibodies tested. Log2 values were media-centered by protein to account for variability in signal intensity by time and were calculated using the formula log2 signal – log2 median. Principal component analysis was used to check for a batch effect and feature-by-feature two-sample t-tests were used to assess differences between treatment and control groups. We also used feature-by-feature one-way analysis of variance (ANOVA) followed by the Tukey test to perform pair comparisons for all groups. Beta-uniform mixture models were used to fit the resulting p value distributions to adjust for multiple comparisons. The cutoff p values and number of significant proteins were computed for several different false discovery rates (FDRs).  Biostatistical analyses comparing two groups were performed using an unpaired t-test with Gaussian distribution followed by the Welch correction. To distinguish between treatment groups, we used one-way ANOVA with the Geisser-Greenhouse correction. Differences with p values <0.05 were considered significant. Within clustered image maps (CIM), unsupervised double hierarchical clustering used the Pearson correlation distance and Ward’s linkage method as the clustering algorithm to link entities (proteins or genes) and samples.

label: 149 Primary Antibodies

molecule: protein

organism: Homo sapiens

label_protocol: Using a 2470 Arrayer (Aushon BioSystems, tumor or normal tissue lysates were serially diluted 2-fold for 5 dilutions (From undiluted to 1:16 dilutio) and arrayed on nitrocellulose-coated FAST slides in an 11X11 format. Samples were probed with antibodies using the Dako CSA tyramide-amplification approach and visualized by DAB colorimetric reaction.

growth_protocol: Proteomic analysis using a reverse-phase protein lysate array (RPPA) was used to elucidate biomarkers that distinguish DSRCT from adjacent normal tissue and Ewing sarcoma, a molecular cousin treated similarly

extract_protocol: Protein extraction from tumor was performed by homogenizing an approximate 10 mg of frozen tissue in 500 ul of the lysis buffer containing protease and phosphatase inhibitors using an electric tissue homogenizer (Pro Scientific). Total lysed proteins were quantified using BCA protein assay kit and stored for further analyses for RPPA.

treatment_protocol: Snap-frozen DSRCT (n=16) or ES (n=6) specimens, and normal-appearing mesenteric tissue (n=8), were collected from core needle biopsies or Complete cytoreductive surgery using clinical protocols approved by MDACC’s Institutional Review Board.

tag: tissue

value: ES Tumor

tag: status after 5 years

value: Dead

tag: age at resectiom

tag: Sex

value: Male


title: ES-4

description:
RPPA
SAMPLE 29

hyb_protocol: Samples were probed with antibodies using the Dako CSA tyramide-amplification approach and visualized by DAB colorimetric reaction.


title: ES-2

description:
RPPA
SAMPLE 26


title: ES-1

description:
RPPA
SAMPLE 25

value: Female


title: DSRCT-(15N)

description:
RPPA
SAMPLE 24

value: Normal Mesenteric Tissues

value: Alive


title: ES-5

description:
RPPA
SAMPLE 27


title: DSRCT-(12N)

description:
RPPA
SAMPLE 23


title: DSRCT-(7N)

description:
RPPA
SAMPLE 19


title: DSRCT-(3N)

description:
RPPA
SAMPLE 17


title: DSRCT-(6N)

description:
RPPA
SAMPLE 18


title: DSRCT-(9N)

description:
RPPA
SAMPLE 21


title: DSRCT-(8N)

description:
RPPA
SAMPLE 20


title: DSRCT-(10N)

description:
RPPA
SAMPLE 22


title: DSRCT-(13T)

description:
RPPA
SAMPLE 14

value: DSRCT tumor


title: DSRCT-(11T)

description:
RPPA
SAMPLE 12


title: DSRCT-(14T)

description:
RPPA
SAMPLE 15


title: ES-3

description:
RPPA
SAMPLE 28


title: DSRCT-15T)

description:
RPPA
SAMPLE 16


title: DSRCT-(12T)

description:
RPPA
SAMPLE 13


title: CS59_Ch_Combined stress (CS)

type: SRA

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description:
sample name in processed data file:
CS59_Ch

library_source: transcriptomic

data_processing:
Base calling was done with RTA3 implemeation software in the NovaSeq 6000 system
3' trimming for Illumina adapters was performed using cutadapt v1.18
Quality control of reads were performed using FastQC v0.11.7
RNA-seq reads were aligned to Arabidopsis thaliana genome obtained from TAIR using STAR aligner v2.4.0.1
Differential gene expression analysis was performed using DeSeq2 v1.20.0
Genome_build: Glycine_max_v2.1
Supplementary_files_format_and_content: tab-deliminated files included mean normalized counts for each sample

molecule: total RNA

organism: Glycine max

source_name: Glycine max leaves

growth_protocol: Soybean plants were grown under control conditions and watered 3 times a week in growth chambers

extract_protocol:
Total RNA was isolated using Plant RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Soybean plants were subjected to drought, heat or a combination of drought and heat stress

tag: treatment

value: Combined stress

tag: genotype

value: Wild type

value: Leaves

tag: cultivar

value: Magellan, PI595362


title: DSRCT-(9T)

description:
RPPA
SAMPLE 10


title: DSRCT-(8T)

description:
RPPA
SAMPLE 9


title: DSRCT-(6T)

description:
RPPA
SAMPLE 7


title: CS60_Ch_Combined stress (CS)

description:
sample name in processed data file:
CS60_Ch


title: DSRCT-(1T)

description:
RPPA
SAMPLE 1


title: DSRCT-(16T)

description:
RPPA
SAMPLE 2


title: DSRCT-(2T)

description:
RPPA
SAMPLE 3


title: DSRCT-(4T)

description:
RPPA
SAMPLE 4


title: DSRCT-(10T)

description:
RPPA
SAMPLE 11


title: DSRCT-(3T)

description:
RPPA
SAMPLE 5


title: DSRCT-(7T)

description:
RPPA
SAMPLE 8


title: HS55_Ch_Heat (HS)

description:
sample name in processed data file:
HS55_Ch

value: Heat stress


title: HS57_Ch_Heat (HS)

description:
sample name in processed data file:
HS57_Ch


title: CS58_Ch_Combined stress (CS)

description:
sample name in processed data file:
CS58_Ch


title: HS56_Ch_Heat (HS)

description:
sample name in processed data file:
HS56_Ch


title: CT50_Ch_control (CT)

description:
sample name in processed data file:
CT50_Ch

value: No treatment


title: CT49_Ch_control (CT)

description:
sample name in processed data file:
CT49_Ch


title: WD52_Ch_Water deficit (WD)

description:
sample name in processed data file:
WD52_Ch

value: Water deficit


title: DSRCT-(5T)

description:
RPPA
SAMPLE 6


title: PDAC_serum [S033]

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

description: SOMAscan human proteomic assay [SOMAscan Assay 1.3k]

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Sample data was first normalized to remove hybridization variation within a run followed by median normalization across all samples to remove all other assay biases within the run and finally calibrated to remove assay differences between runs. After all the preprocessing steps, quantile normalization was performed across all samples for proteins which will be used for downstream analyses.

source_name: Serum

label_protocol: not provided

growth_protocol: Serial blood samples were collected from the patients followed for advanced PDAC; and prior to surgery, and during postoperative standard follow up for patients with resectable PDAC. The collected blood was stored in -80⁰C until further use.

extract_protocol: Blood was collected in the clinic during pre-surgical or pre-chemotherapy visits. Blood was collected in EDTA tubes, centrifuged, aliquoted, and stored first at -20C then at -80C until assay.

tag: tumor type

value: Pancreatic ductal adenocarcinoma

tag: age (in years)


title: PDAC_serum [S032]


title: PDAC_serum [S024]


title: PDAC_serum [S021]


title: PDAC_serum [S028]


title: PDAC_serum [S027]


title: WD54_Ch_Water deficit (WD)

description:
sample name in processed data file:
WD54_Ch


title: PDAC_serum [S020]


title: CT51_Ch_control (CT)

description:
sample name in processed data file:
CT51_Ch


title: PDAC_serum [S018]


title: PDAC_serum [S004]


title: PDAC_serum [S015]


title: PDAC_serum [S011]


title: PDAC_serum [S029]


title: PDAC_serum [S007]


title: PDAC_serum [S002]


title: PDAC_serum [S005]


title: PDAC_serum [S017]


title: PDAC_serum [M027]


title: PDAC_serum [S012]


title: PDAC_serum [M028]


title: PDAC_serum [M038]


title: PDAC_serum [M032]


title: PDAC_serum [S023]


title: PDAC_serum [M021]


title: PDAC_serum [M019]


title: RNA-Seq of Corynebacterium glutamicum C1, untreated control, independet replicate 2

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

country: Germany

institute: Bielefeld University

data_processing:
Basecalls were performed using RTA v.1.18.66.3
Sequenced reads were mapped to the reference genome Corynebacterium glutamicum C1 (CP017995) using bowtie2 v2.4.1 with parameters -X 600
Raw read counts per CDS were calculated using ReadXplorer v.2.2.3
Read count normalization and data analysis were performed using DESeq2 within ReadXplorer v.2.2.3
Genome_build: CP017995.1
Supplementary_files_format_and_content: tab-delimited text files containing the raw read count data from readXporer

organism: Corynebacterium glutamicum

source_name: cell culture

growth_protocol: Cells were grown in CGXII minimal medium with 40g/L glucose +/- 3 mM indole-alanine dipeptide at 30 degree celsius in a rotary shaker to an o.D.600 of 4 in three independent cultivations per treatment.

extract_protocol:
RNA was extracted with the NucleoSpin RNA isolation kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions. Residual DNA was removed by digestion using the RNase-free DNase set (Qiagen, Hilden, Germany).  After DNA digestion, the RNA was again purified with the same kit. RNA quality was checked by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA 6000 Nano Kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany).
Ribosomal RNA molecules were removed from total RNA with the Ribo-Zero rRNA Removal Kit bateria (Illumina, San Diego, USA) and removal of rRNA was checked with the Agilent RNA 6000 Pico Kit on an Agilent 2100 Bioanalyzer. Libraries of cDNA were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, USA). The resulting cDNA was sequenced in a paired end run on an Illumina HiSeq 1500 system in a 2 x 70 nt run.

treatment_protocol: The controls were grown in pure CGXII minimal medium with 40g/L glucose. In case of the treated samples, 3 mM indole-alanine dipeptide was added prior to inocculation.

value: control

tag: strain

value: Corynebacterium glutamicum C1


title: RNA-Seq of Corynebacterium glutamicum C1, untreated control, independet replicate 1


title: RNA-Seq of Corynebacterium glutamicum C1, untreated control, independet replicate 3


title: RNA-Seq of Corynebacterium glutamicum C1, treated with 3 mM indole-alanine dipeptide,  independet replicate 3

value: 3 mM indole-alanine dipeptide


title: PDAC_serum [M011]


title: PDAC_serum [M009]


title: PDAC_serum [M003]


title: PDAC_serum [M002]


title: RNA-Seq of Corynebacterium glutamicum ATCC 13032, untreated control

data_processing:
Basecalls were performed using RTA v.1.18.66.3
Sequenced reads were mapped to the reference genome using bowtie2 v2.4.1 with parameters -X 600
Raw read counts per CDS were calculated using ReadXplorer v.2.2.3
Read count normalization and data analysis were performed using DESeq within ReadXplorer v.2.2.3
Genome_build: BA000036.1
Supplementary_files_format_and_content: tab-delimited text files containing the normalized count data from DESeq

source_name: Corynebacterium glutamicum ATCC 13032

growth_protocol: Cells were grown in CGXII minimal medium with 40g/L glucose +/- 2.5 mM indole at 30 degree celsius in a rotary shaker to an o.D.600 of 4 in three independent cultivations per treatment.

extract_protocol:
RNA was extracted with the NucleoSpin RNA isolation kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions. Residual DNA was removed by digestion using the RNase-free DNase set (Qiagen, Hilden, Germany). The extracted RNA samples of each treatment group were pooled. After DNA digestion, the RNA was again purified with the same kit. RNA quality was checked by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA 6000 Nano Kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany).
Ribosomal RNA molecules were removed from total RNA with the Ribo-Zero rRNA Removal Kit (Illumina, San Diego, USA) and removal of rRNA was checked with the Agilent RNA 6000 Pico Kit on an Agilent 2100 Bioanalyzer. Libraries of cDNA were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, USA). The resulting cDNA was sequenced in a paired end run on an Illumina HiSeq 1500 system in a 2x 70 nt run.

treatment_protocol: The controls were grown in pure CGXII minimal medium with 40g/L glucose. In case of the treated samples, 2.5 mM indole was added prior to inocculation.

value: 2.5 mM indole

value: Corynebacterium glutamicum ATCC 13032


title: RNA-Seq of Corynebacterium glutamicum ATCC 13032, treated with 2.5 mM indole


title: PDAC_serum [M013]

value: Male


title: RNA-Seq of Corynebacterium glutamicum C1, treated with 3 mM indole-alanine dipeptide,  independet replicate 1


title: PDAC_serum [M018]

value: Female


title: RNA-Seq of Corynebacterium glutamicum C1, treated with 3 mM indole-alanine dipeptide,  independet replicate 2


title: SC00193A

type: RNA

city: Oxford

first: Andrew

last: Blake

state: Oxfordshire, UK

address: Old Road Campus

country: United Kingdom

institute: Department of Oncology

description:
Almac Diagnostics XCEL array (Almac, Craigavon, UK)
Almac’s Diagnostic CLIA Laboratories

hyb_protocol: The amplified product was hybridised to the Almac Diagnostics XCEL array (Almac, Craigavon, UK), a cDNA microarray-based technology optimised for archival FFPE tissue, and analysed using the Affymetrix Genechip 3000 7G scanner (Affymetrix, Santa Clara, California, USA) as previously described (12).

scan_protocol: Affymetrix protocol

data_processing: Microarray data were quality checked (see Supplementary methods) then pre-processed where raw CEL files underwent the Robust Multiarray Average (RMA) normalisation for the Almac Diagnostic XCEL array with the affy package (v1.56.0) (17).

label: biotin

source_name: Primary Colorectal Cancer

label_protocol: Affymetrix protocol

extract_protocol: All the archival formalin-fixed paraffin-embedded (FFPE) tumour tissue samples were tested at Almac’s Diagnostic CLIA Laboratories. Samples were reviewed and tumour material identified on an adjacent H&E stained slide for microdissection. Total RNA was extracted from two sequential 5µm sections using the Roche High Pure FFPE Extraction Kit (Roche Life Sciences, Penzberg, Germany) and amplified using the NuGen Ovation FFPE Amplification System v3 (NuGen San Carlos, California, USA).

tag: dna damage  immune response call

value: DDIR POS

tag: dna damage repair deficient score

tag: consensus molecular subtype

tag: colorectal cancer intrinsic sub-type

value: CRIS-C

tag: msi

value: MSS

value: Formalin-Fixed Paraffin-Embedded tumour

tag: kras

value: Mut

tag: nras

value: Wt

tag: braf


title: SC00188A

value: DDIR NEG

value: CRIS-B

tag: tissue


title: SC00194A


title: SC00187A

value: CRIS-D


title: SC00191A

value: Unclassified

value: CRIS-A


title: SC00192A


title: SC00189A


title: SC00184A


title: SC00195A


title: SC00181A


title: SC00190A


title: SC00179A

value: CRIS-E


title: SC00182A


title: SC00176A


title: SC00174A


title: SC00178A


title: SC00173A


title: SC00177A


title: SC00172A

tag: msi:


title: SC00171A


title: SC00175A

value: MSI


title: SC00169A


title: SC00180A


title: SC00170A


title: SC00165A


title: SC00162A


title: WD53_Ch_Water deficit (WD)

description:
sample name in processed data file:
WD53_Ch

value: Water deficit

value: Wild type

value: Leaves

value: Magellan, PI595362


title: SC00160A

value: DDIR POS


title: SC00163A


title: SC00156A


title: SC00155A


title: SC00158A


title: SC00152A


title: SC00146A


title: SC00157A


title: SC00149A


title: SC00164A

value: CRIS-C


title: SC00142A

value: MSS


title: SC00161A

value: Formalin-Fixed Paraffin-Embedded tumour


title: SC00159A

value: Mut


title: SC00148A

value: Wt


title: SC00141A

value: DDIR NEG


title: SC00150A


title: SC00145A


title: SC00154A


title: SC00140A


title: SC00139A


title: SC00144A


title: SC00138A


title: SC00137A


title: SC00136A


title: SC00134A


title: SC00147A


title: SC00126A


title: SC00166A


title: SC00133A


title: SC00128A

value: CRIS-B


title: SC00132A

value: CRIS-D


title: SC00131A


title: SC00534A

value: Unclassified


title: SC00127A


title: SC00124A


title: SC00129A


title: SC00529A


title: SC00532A

value: CRIS-A


title: SC00520A


title: SC00521A

value: CRIS-E


title: SC00524A


title: SC00530A


title: SC00528A


title: SC00527A


title: SC00130A


title: SC00135A


title: SC00125A


title: SC00531A


title: SC00525A


title: SC00533A


title: SC00526A


title: SC00523A


title: SC00522A


title: SC00516A


title: SC00515A


title: SC00514A


title: SC00519A


title: SC00512A


title: SC00511A


title: SC00507A


title: SC00505A


title: SC00509A


title: SC00510A


title: SC00504A


title: SC00513A


title: SC00500A


title: SC00490A


title: SC00492A


title: SC00493A


title: SC00487A


title: SC00497A


title: SC00486A

value: MSI


title: SC00501A


title: SC00508A


title: SC00496A


title: SC00502A


title: SC00491A


title: SC00488A


title: SC00499A


title: SC00494A


title: SC00498A


title: SC00485A


title: SC00482A


title: SC00481A


title: SC00479A


title: SC00483A


title: SC00478A


title: SC00473A


title: SC00476A


title: SC00469A


title: SC00470A


title: SC00467A


title: SC00464A


title: SC00484A


title: SC00466A


title: SC00459A


title: SC00480A


title: SC00472A


title: SC00475A


title: SC00465A


title: SC00458A


title: SC00462A


title: SC00461A


title: SC00463A


title: SC00468A


title: SC00457A


title: SC00456A


title: SC00452A


title: SC00451A


title: SC00454A


title: SC00449A


title: SC00450A


title: SC00444A


title: SC00446A


title: SC00439A


title: SC00447A


title: SC00442A


title: SC00440A


title: SC00448A


title: SC00435A


title: SC00441A


title: SC00431A


title: SC00437A


title: SC00424A


title: SC00429A


title: SC00433A


title: SC00443A


title: SC00426A


title: SC00425A


title: SC00438A


title: SC00432A


title: SC00423A


title: SC00445A


title: SC00428A


title: SC00434A


title: SC00422A


title: SC00455A


title: SC00391A


title: SC00403A


title: SC00416A


title: SC00418A


title: SC00420A


title: SC00419A


title: SC00413A


title: SC00408A


title: SC00410A


title: SC00412A


title: SC00411A


title: SC00417A


title: SC00401A


title: SC00407A


title: SC00409A


title: SC00415A


title: SC00405A


title: SC00399A


title: SC00402A


title: SC00398A


title: SC00396A


title: SC00404A


title: SC00406A


title: SC00397A


title: SC00400A


title: SC00395A


title: SC00393A


title: SC00392A


title: SC00394A


title: SC00387A


title: SC00378A


title: SC00377A


title: SC00383A


title: SC00371A


title: SC00372A


title: SC00365A


title: SC00360A


title: SC00386A


title: SC00381A


title: SC00389A


title: SC00376A


title: SC00379A


title: SC00373A


title: SC00380A


title: SC00385A


title: SC00368A


title: SC00375A


title: SC00361A


title: SC00369A


title: SC00362A


title: SC00384A


title: SC00358A


title: SC00366A


title: SC00370A


title: SC00364A


title: SC00359A


title: SC00350A


title: SC00382A


title: SC00348A


title: SC00351A


title: SC00355A


title: SC00356A


title: SC00345A


title: SC00357A


title: SC00354A


title: SC00346A


title: SC00342A


title: SC00353A


title: SC00340A


title: SC00334A


title: SC00331A


title: SC00349A


title: SC00339A


title: SC00337A


title: SC00341A


title: SC00338A


title: SC00336A


title: SC00343A


title: SC00330A


title: SC00344A


title: SC00333A


title: SC00332A


title: SC00329A


title: SC00326A


title: SC00323A


title: SC00319A


title: SC00328A


title: SC00318A


title: SC00327A


title: SC00316A


title: SC00322A


title: SC00321A


title: SC00315A


title: SC00312A


title: SC00310A


title: SC00313A


title: SC00314A


title: SC00309A


title: SC00307A


title: SC00303A


title: SC00296A


title: SC00325A


title: SC00301A


title: SC00308A


title: SC00311A


title: SC00302A


title: SC00320A


title: SC00298A


title: SC00305A


title: SC00297A


title: SC00299A


title: SC00295A


title: SC00289A


title: SC00294A


title: SC00291A


title: SC00293A


title: SC00288A


title: SC00290A


title: SC00278A


title: SC00283A


title: SC00279A


title: SC00284A


title: SC00277A


title: SC00273A


title: SC00281A


title: SC00274A


title: SC00287A


title: SC00271A


title: SC00282A


title: SC00292A


title: SC00280A


title: SC00285A


title: SC00275A


title: SC00276A


title: SC00286A


title: SC00272A


title: SC00269A


title: SC00268A


title: SC00270A


title: SC00267A


title: SC00262A


title: SC00266A


title: SC00265A


title: SC00264A


title: SC00258A


title: SC00259A


title: SC00261A


title: SC00254A


title: SC00255A


title: SC00260A


title: SC00250A


title: SC00243A


title: SC00246A


title: SC00257A


title: SC00252A


title: SC00233A


title: SC00247A


title: SC00236A


title: SC00237A


title: SC00232A


title: SC00240A


title: SC00239A


title: SC00241A


title: SC00244A


title: SC00245A


title: SC00229A


title: SC00235A


title: SC00228A


title: SC00227A


title: SC00230A


title: SC00253A


title: SC00242A


title: SC00226A


title: SC00224A


title: SC00221A


title: SC00222A


title: SC00219A


title: SC00218A


title: SC00217A


title: SC00216A


title: SC00215A


title: SC00214A


title: SC00213A


title: SC00212A


title: Treatment OVKATE rep2

city: Bangkok

first: Nakarin

last: Kitkumthorn

address: Yothee road

department: Oral Biology

country: Thailand

institute: Mahidol University

data_processing:
The quality of the raw sequencing reads were assessed with the FastQC v.0.11.2 software. The raw sequencing reads were subjected to trimming process with Trimmomatic v.0.32 software. The surviving paired-end reads were aligned to the Homo sapiens reference genome (Ensembl GRCh38 genome) with HISAT2 v.2.1.0 software. The alignment files were analyzed individually with the StringTie version 1.3.3b software to detect and quantify previously known transcripts. Invidual annotation files generated from transcript assembly process were merged together parsimoniously using StringTie version 1.3.3b. With the merged annotation file.
The expression unit calculated is FPKM, Fragments Per Kilobase Million. Besides, differential expression (DE) analysis was performed according to the given comparison groups . The expression fold change between each comparison group were calculated and log-transformed. Multiple output files were generated by DESeq2 version 1.16.1 and the detail files information are described in the table of result files below. Significant DE genes or transcripts (p-value < 0.05) were extracted for each comparison groups and cancer type.
Genome_build: HG19
Supplementary_files_format_and_content: ID, Gene_id, FPKM of each sample,fold change and p-value of each gene.

source_name: RCF5 treated with OVKATE

growth_protocol: The ovarian cancer cells were obtained from Nation Institutes of Biomedical Innovation, Health and Nutrition JCRB Cell Bank (Osaka, Japan) including OVISE (JCRB1043) and OVKATE (JCRB1044). The Cells were grown with DMEM medium (Gibco BRL, USA) supplemented with 10% FBS at 37 ºc 5 % CO2 in culture flask. The cells were harvested at 80% confluence by using 0.05% Trypsin (with 0.5 mM EDTA) and washed by using phosphate buffer saline (PBS). All of this were used for maintaining cells.

extract_protocol:
PBMCs were collected from Transwell culture six well plates and RNA was harvested using Trizol reagent.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®). The poly(A) mRNA isolation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified (by AxyPrep Mag PCR Clean-up (Axygen)) double-stranded cDNA was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer ( Agilent Technologies, Palo Alto, CA, USA ) , and quantified by Qubit 2.0 Fluorometer ( Invitrogen, Carlsbad, CA, USA ).

treatment_protocol: Indirect or co-culture ovarian cancer cells with PBMCs from healthy were performed in Transwell culture six well plates (Costar, France). The ovarian cancer cells were seeded into plate (106 cells) with DMEM in experiment wells but not in control wells and then incubated overnight at 37 ºc 5 % CO2. The PBMCs from healthy were plated on permanent membrane culture of Transwell (2 × 106 cells) and incubated for 4 hours at 37 ºc 5 % CO2.

tag: cell type

value: PBMC

value: co-cultured with cell line OVKATE


title: Treatment OVISE rep3

source_name: RCF6 treated with OVISE

tag: treatment

value: co-cultured with cell line OVISE


title: Treatment OVKATE rep1

source_name: RCF4 treated with OVKATE


title: Treatment OVKATE rep3

source_name: RCF6 treated with OVKATE


title: Treatment OVISE rep2

source_name: RCF5 treated with OVISE


title: SC00202A


title: Treatment OVISE rep1

source_name: RCF4 treated with OVISE


title: SC00199A


title: SC00201A


title: SC00205A


title: Control Female rep3

source_name: Female PBMC


title: SC00197A


title: SC00196A


title: Control Female rep2


title: Control Female rep1


title: SC00208A


title: SC00210A


title: SC00207A


title: SC00200A


title: SC00198A


title: leaf2

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

country: China

institute: Yunnan Agricultural University

data_processing:
Hisat2 was used to aligned the obtained reads to the genome of Camellia sinensis.
Stringtie was used to merge the transcripts.
CuffCompare was used to compare the merged transcripts to the annotated transcripts in the Camellia sinensis database.
Cuffquant was used to quantify the expression levels (FPKM) values of  transcripts.
Cuffnorm was used to normalize the FPKM values of  transcripts.
Supplementary_files_format_and_content: FPKM values of genes

organism: Camellia sinensis

source_name: C sinensis_leaf

extract_protocol:
Total RNA was isolated from selected tissues using TRIzol reagent with the manufacture's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols with only ribosomal RNA removal.

treatment_protocol: no treatment

value: leaf


title: flower45 [miRNA-seq]

data_processing:
Remove low quality reads with nucleotides of scores lower than 30 in the first 25 nucleotides
Keep the sequences with lengths are greater than or equal to 18 bp (the 3'adapter sequence of reads had been removed by the sequenceing faclility)
Sort and remove repetitive sequences
Calculate the counts of unique sequences
The unique sequences were aligned to  assembled genome with BLAST
Supplementary_files_format_and_content: sequences and count values

source_name: C sinensis_flower

value: flower

tag: molecule subtype

value: miRNA


title: flower1 [miRNA-seq]


title: root23 [miRNA-seq]

source_name: C sinensis_root

value: root


title: leaf41


title: flower2 [miRNA-seq]


title: leaf23 [miRNA-seq]


title: leaf41 [miRNA-seq]


title: root13 [miRNA-seq]


title: root33 [miRNA-seq]


title: leaf1 [miRNA-seq]


title: flower45


title: flower2


title: leaf1


title: flower1


title: Zea mays L. hybrid Norma_3rd_leaf_14d 15°C_107_PPFD_rep1

city: Martonvásár

first: Imre

last: Majláth

state: Fejér

address: Brunszvik u. 2.

department: Plant Physiology

country: Hungary

institute: Centre for Agricultural Research, Hungarian Academy of Sciences

description:
Gene expression after 14d in at 15°C and PPFD=107 in maize 3rd leaf
LL4_1

hyb_protocol: 1650 ng cRNA was hybridized to the Agilent Whole Corn Gene Expression Microarray 4x44K chip according to the manufacturer’s instructions.

scan_protocol: The array was scanned using an Agilent Scanner, Extended Dynamic Range (100% and 10% laser intensities, 5 micron resolution).

data_processing: Signal intensities were detected and pre-normalized using the Agilent Feature Extraction (FE 9.5) and GeneSpring (Agilent) Softwares.

organism: Zea mays

source_name: 3rd_leaf_14d 15°C_107_PPFD

label_protocol: The samples were labelled with Cy3 (Low Input QuickAmp, Agilent) according to the manufacturer’s instructions.

growth_protocol: Maize plants were grown for 11 days at 22/20 °C at higher PPFD, (growth light 2, GL2 = 387 µmol m-2 s-1) with 16/8 h light/dark periodicity. Some of the plants were then cold acclimated at 15/13 °C for 3 days either at GL2 or at  moderately low light intensity 3 (LL3): 283 µmol m-2 s-1; or at moderately low light intensity 4 (LL4): 107 µmol m-2 s-1.

extract_protocol: 200 ng of the total RNA was extracted using an RNEasy Plant Mini Kit (Qiagen, Hilden, Germany) and pooled from the three technical replicates and used for cRNA amplification. The quality of the extracted RNA was examined using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA).

treatment_protocol: Three biological replicates each with three technical replicates (each consisting of seven plants) for the microarray analysis were harvested from the 3rd leaves of maize plants.

tag: hybrid

value: Norma

value: 3rd leaf

tag: time

tag: temperature

tag: light intensity


title: Zea mays L. hybrid Norma_3rd_leaf 14d 15°C_387_PPFD_rep4

description:
Gene expression after 14d in at 15°C and PPFD=387 in maize 3rd leaf
GL2_4

source_name: 3rd_leaf 14d 15°C_387_PPFD


title: Zea mays L. hybrid Norma_3rd_leaf 14d 15°C_283_PPFD_rep1

description:
Gene expression after 14d in at 15°C and PPFD=283 in maize 3rd leaf
LL3_1

source_name: 3rd_leaf 14d 15°C_283_PPFD


title: Zea mays L. hybrid Norma_3rd_leaf 14d 15°C_283_PPFD_rep4

description:
Gene expression after 14d in at 15°C and PPFD=283 in maize 3rd leaf
LL3_4


title: Zea mays L. hybrid Norma_3rd_leaf 14d 15°C_387_PPFD_rep3

description:
Gene expression after 14d in at 15°C and PPFD=387 in maize 3rd leaf
GL2_3


title: Zea mays L. hybrid Norma_3rd_leaf 11d 20°C_387_PPFD_rep4

description:
Gene expression after 11d in at 20°C and PPFD=387 in maize 3rd leaf
K_4

source_name: 3rd_leaf 11d 20°C_387_PPFD


title: Zea mays L. hybrid Norma_3rd_leaf 11d 20°C_387_PPFD_rep3

description:
Gene expression after 11d in at 20°C and PPFD=387 in maize 3rd leaf
K_3


title: Zea mays L. hybrid Norma_3rd_leaf_14d 15°C_107_PPFD_rep3

description:
Gene expression after 14d in at 15°C and PPFD=107 in maize 3rd leaf
LL4_3


title: Zea mays L. hybrid Norma_3rd_leaf 14d 15°C_387_PPFD_rep1

description:
Gene expression after 14d in at 15°C and PPFD=387 in maize 3rd leaf
GL2_1


title: Zea mays L. hybrid Norma_3rd_leaf 14d 15°C_283_PPFD_rep2

description:
Gene expression after 14d in at 15°C and PPFD=283 in maize 3rd leaf
LL3_2


title: Zea mays L. hybrid Norma_3rd_leaf 11d 20°C_387_PPFD_rep1

description:
Gene expression after 11d in at 20°C and PPFD=387 in maize 3rd leaf
K_1


title: Zea mays L. hybrid Norma_3rd_leaf_14d 15°C_107_PPFD_rep2

description:
Gene expression after 14d in at 15°C and PPFD=107 in maize 3rd leaf
LL4_2


title: root33


title: root13


title: root23


title: Ventral tegmental area [M64]

city: Pittsburgh

first: WEI

last: ZONG

state: PA

address: 130 De Soto St

institute: UNIVERSITY OF PITTSBURGH

data_processing:
Quality control using FastQC
Trim data using Trimmomatic
Alignment using HISAT2
Read counts using HTSeq
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Ventral tegmental area

extract_protocol:
RNeasy Plus Micro Kit (Qiagen, Hilden, Germany).
Libraries were prepared using TruSeq Stranded mRNA (PolyA+) kit (Illumina, San Diego, CA) and sequenced by Illumina NextSeq 500. The read length was 75bp with 30-40M reads per sample. FastQC (v0.11.3) was performed to assess data quality.
Libraries were prepared using TruSeq Stranded mRNA (PolyA+) kit (Illumina, San Diego, CA) and sequenced by Illumina NextSeq 500. The read length was 75bp with 30-40M reads per sample. FastQC (v0.11.3) was performed to assess data quality.

treatment_protocol: Mice treated for 14 days with valproate, ACY957 or vehicle control

tag: strain

tag: genotype

value: Clock delta 19 mutant


title: Ventral tegmental area [M59]


title: Ventral tegmental area [M63]


title: Ventral tegmental area [M56]


title: Ventral tegmental area [M60]


title: Ventral tegmental area [M53]


title: Ventral tegmental area [M58]

value: VPA


title: Ventral tegmental area [M54]


title: Ventral tegmental area [M62]


title: Ventral tegmental area [M55]


title: Ventral tegmental area [M61]


title: Ventral tegmental area [M52]


title: Ventral tegmental area [M51]


title: Ventral tegmental area [M43]

value: ACY


title: Ventral tegmental area [M57]


title: Ventral tegmental area [M47]


title: Ventral tegmental area [M46]


title: Ventral tegmental area [M50]


title: Ventral tegmental area [M49]


title: Ventral tegmental area [M45]


title: Ventral tegmental area [M44]


title: Ventral tegmental area [M48]


title: Ventral tegmental area [M41]


title: Ventral tegmental area [M42]


title: Ventral tegmental area [M40]


title: Ventral tegmental area [M39]


title: Ventral tegmental area [M38]


title: Ventral tegmental area [M36]


title: Ventral tegmental area [M34]


title: Ventral tegmental area [M31]


title: Ventral tegmental area [M33]


title: Ventral tegmental area [M32]


title: Ventral tegmental area [M28]


title: Ventral tegmental area [M27]


title: Ventral tegmental area [M35]


title: Ventral tegmental area [M37]


title: Ventral tegmental area [M26]


title: Ventral tegmental area [M23]

value: Wildtype


title: Ventral tegmental area [M21]


title: Ventral tegmental area [M25]


title: Ventral tegmental area [M24]


title: Ventral tegmental area [M22]


title: Ventral tegmental area [M19]


title: Ventral tegmental area [M20]


title: Ventral tegmental area [M29]


title: Ventral tegmental area [M18]


title: Ventral tegmental area [M30]


title: Ventral tegmental area [M15]


title: Ventral tegmental area [M17]


title: Ventral tegmental area [M14]


title: Ventral tegmental area [M16]


title: Ventral tegmental area [M13]


title: Ventral tegmental area [M12]


title: Ventral tegmental area [M11]


title: Ventral tegmental area [M10]


title: Ventral tegmental area [M9]


title: Ventral tegmental area [M7]


title: Ventral tegmental area [M5]


title: Ventral tegmental area [M4]


title: Ventral tegmental area [M6]


title: Ventral tegmental area [M8]


title: Ventral tegmental area [M3]


title: Colon_act_CD4_Tconv_CD355+#2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts (subread 2.0.0) with GENCODE annotation (vM25)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: CD4+TCRb+CRTAM+ Colonic LP 13 days post Salmonella infection

growth_protocol: Live CD4+ TCRb+ cells were sorted by flow cytometry from the colon LP

extract_protocol:
1,000 Cells were double-sorted by Moflo into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

treatment_protocol: Colons were enzymatically dissociated and digested with collagenase/dispase to single cell suspensions. Live cells were sorted using appropriate gates.

value: Colon LP

value: WT


title: Colon_act_CD4_Tconv_CD355+#1


title: Ventral tegmental area [M2]


title: Colon_act_CD4_Tconv_MHCII_hi#3

source_name: CD4+TCRb+MHCII hi Colonic LP 13 days post Salmonella infection


title: Ventral tegmental area [M1]


title: Colon_act_CD4_Tconv_MHCII_hi#2


title: Colon_act_CD4_Tconv_MHCII_lo#1

source_name: CD4+TCRb+MHCII lo Colonic LP 13 days post Salmonella infection


title: BMC.CD45.2+.Colon.act.CD4.T.cells#2

source_name: CD4+TCRb+CD45.2+ Colonic LP 13 days post Salmonella infection

value: CD45.1/CD45.2 H2-Ab KO BM chimera


title: Colon_act_CD4_Tconv_MHCII_lo#2


title: Colon_act_CD4_Tconv_MHCII_hi#1


title: BMC.CD45.2+.Colon.act.CD4.T.cells#3


title: BMC.CD45.1+.Colon.act.CD4.T.cells#3

source_name: CD4+TCRb+CD45.1+ Colonic LP 13 days post Salmonella infection


title: BMC.CD45.1+.Colon.act.CD4.T.cells#1


title: BMC.CD45.2+.Colon.act.CD4.T.cells#1


title: Colon.act.CD4.Tconv.Klrg1+CXCR6+#3

source_name: CD4+TCRb+CXCR6+KLRG1+ Colonic LP 13 days post Salmonella infection


title: BMC.CD45.1+.Colon.act.CD4.T.cells#2


title: Colon.act.CD4.Tconv.Klrg1+CXCR6+#1


title: Colon.act.CD4.Tconv.CXCR6loCD69loSCA1lo#2

source_name: CD4+TCRb+CXCR6lo CD69lo SCA-1lo Colonic LP 13 days post Salmonella infection


title: Colon.act.CD4.Tconv.CXCR6loCD69loSCA1lo#1


title: Colon.act.CD4.Tconv.CXCR6hiCD69hiSCA1hi#1

source_name: CD4+TCRb+CXCR6+CD69+SCA-1+ Colonic LP 13 days post Salmonella infection


title: SPF.IL17+#2

source_name: CD4+ TCRb+ IL17-GFP+ Colonic LP SPF


title: Citrobacter.IL17+#3

source_name: CD4+ TCRb+ IL17-GFP+ Colonic LP 13 days post Citrobacter infection


title: Citrobacter.IL17+#2


title: Salmonella.IL17+#2

source_name: CD4+ TCRb+ IL17-GFP+ Colonic LP 13 days post Salmonella infection


title: Citrobacter.IL17+#1


title: Salmonella.IL17+#1


title: Colon.act.CD4.Tconv.Klrg1+CXCR6+#2


title: Colon.act.CD4.Tconv.CXCR6hiCD69hiSCA1hi#3


title: p16-AS-200

city: Vancouver

first: Howard

last: Cen

state: BC

address: 2350 Health Sciences Mall

country: Canada

institute: University of British Columbia

data_processing:
Sequencing was performed on the Illumina NextSeq 500 with Paired End 42bp × 42bp reads.
Sequencing data was demultiplexed using Illumina's bcl2fastq2.
De-multiplexed read sequences were then aligned to the Mus Musculus mm10 reference sequence using STAR aligner (https://www.ncbi.nlm.nih.gov/ pubmed/23104886).
Assembly was estimated using Cufflinks (http://cole-trapnell-lab.github.io/cufflinks/) through bioinformatics apps available on Illumina Sequence Hub using default settings
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts for each sample

source_name: C2C12 myotube

growth_protocol: C2C12 myoblasts were differentiated in differentiation media (DMEM with 2% Horse serum and 1% Pen/Strep) for 10 days into myotubes.

extract_protocol:
Total RNA were extracted with Qiagen Rneasy Kit.
Sample quality control was performed using the Agilent 2100 Bioanalyzer. Qualifying samples were then prepped following the standard protocol for the NEBNext Ultra II Stranded mRNA (New England Biolabs).

treatment_protocol: C2C12 myotubes were incubated in the same differentiation media supplemented with 0 or 200 nM insulin for 16 hours followed by a 6-hour serum starvation.

tag: prolonged insulin

tag: serum starvation

value: After starvation

value: C2C12 myotube


title: SC00220A

source_name: Primary Colorectal Cancer

tag: dna damage  immune response call

value: DDIR NEG

tag: dna damage repair deficient score

tag: consensus molecular subtype

tag: colorectal cancer intrinsic sub-type

value: CRIS-C

tag: msi

value: MSS

value: Formalin-Fixed Paraffin-Embedded tumour

value: Mut

value: Wt


title: p18-AS-200


title: p17-AS-200


title: Mimics_3

city: Jerusalem

first: Katarzyna

last: Winek

state: Israel

address: The Edmond J. Safra Campus

department: ELSC

country: Israel

institute: Hebrew University of Jersusalem

data_processing:
Fastq files were generated within BaseSpace using FASTQ Generation, Version: 1.0.0
Quality control was performed using FastQC. Long RNA was aligned to the mouse reference transcriptome (mm10) using salmon with default parameters
Differential expression was determined using the R/DESeq2 package. Genes were considered differentially expressed at an adjusted p-value of < 0.05. The analysis was performed on the raw count tables.
Genome_build: mm10
Supplementary_files_format_and_content: csv file used as input to DESeq2 analysis

source_name: RAW 264.7 cells

growth_protocol: Murine RAW264.7 cells (ATCC TIB-71)were cultured according to standard protocols in Dulbecco’s Modified Eagle’s Medium supplemented with 10% Fetal Calf Serum, 1% Penicillin-Streptomycin-Amphotericin B and 1% L-Glutamine (all reagents from Biological Industries, Beit HaEmek, Israel)

extract_protocol:
Total RNA was isolated using miRNeasy kit (Qiagen, Hilden, Germany).
PolyA-selected long mRNA sequencing (180 ng total RNA per sample, using KAPA Stranded mRNA-Seq Kit (Roche, Basel, Switzerland) for library construction). Sequencing was performed on the Illumina NextSeq 500 platform at the Hebrew University’s Center for Genomic Technologies.

treatment_protocol: Transfections were performed using HiPerFect transfection agent (Qiagen, Hilden, Germany) following a standard protocol for transfecting RAW 264.7 macrophages. Briefly, 2x105 RAW 264.7 cells per well were seeded in 24-well plates and transfected using 6 ul HiPerFect reagent per well and 50nM final ssRNA tRF-mimics: /5PHOS/rArU rCrCrC rArCrC rGrCrU rGrCrC rAmCmC rA, using NC5 /5PHOS/rGrC rGrArC rUrArU rArCrG rCrGrC rArArU mAmUrG (both from IDT, Coralville IA, USA) as negative control. Cells were collected after 24h following the transfection in Tri-Reagent (Sigma Aldrich, St. Louis, USA).

value: mimcs


title: NegativeControl_3


title: NegativeControl_2


title: Mimics_2


title: NegativeControl_1


title: Mimics_1


title: Colon.act.CD4.Tconv.CXCR6loCD69loSCA1lo#3

tag: tissue


title: Colon_act_CD4_Tconv_MHCII_lo#3


title: Colon.act.CD4.Tconv.CXCR6hiCD69hiSCA1hi#2


title: SPF.IL17+#1


title: p16-AS-0

value: 0 nM

tag: cell type


title: SC00225A

tag: kras

tag: nras

tag: braf


title: p14-AS-200


title: p15-AS-200


title: p18-BS-0

value: Before starvation


title: p15-BS-0


title: p18-AS-0


title: p15-AS-0


title: p14-AS-0


title: p17-AS-0


title: p18-BS-200


title: p15-BS-200


title: P3_NBN_32

city: Basel

first: Verdon

last: Taylor

address: Mattenstrasse 28

department: Department of Biomedizin

country: Switzerland

institute: University of Basel

description:
mRNA
Forebrain NBN at stage P3, replicate 32
processed data file: gene_tpm_SC_P3_NBN.txt.gz

data_processing:
Reads mapped to the transcriptome (GENCODE Release M2 GRCm38.p2) with kallisto 0.43.0 with option --single -l 200.0 -s 100.0 –pseudobam. Last option is to obtain pseudoalignments to transcriptome in BAM files.
The reads mapping to multiple transcripts are uniformly distributed.
Expression per transcript normalized by first dividing the number of reads mapping to each transcript by the length of the transcript in nucleotides and then transform the length-normalized read counts in transcript per million (TPM).
Gene expression was obtained by summing for each gene the TPM of the transcripts corresponding to the gene.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *txt: Tab-delimited text files, TPM table, genes in rows and samples in columns.

source_name: dorsal cerebral cortex

extract_protocol:
GFP positive cells were FAC-sorted from Hes5::GFP and Tbr2::GFP transgenic lines. A time course was performed with NSCs, BPs and NBNs isolated at almost alternate time points during development E10.5 to postnatal day 3 (P3). Single cell capture, lysis and cDNA preparation were performed with the Fluidigm C1 system. Cells were loaded on a microfluidic C1 Single Cell Auto Prep Array for mRNA Seq (5-10µm), and capture efficiency evaluated using microscopy.
Lysis, reverse transcription and cDNA amplification were performed with the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech/Takara) according to Fluidigm’s guidelines for single-cell RNA-seq on the C1 system. cDNA was harvested, profiles checked on the Fragment Analyzer (AATI) and their concentration determined using Quant-iT PicoGreen dsDNA Assay Kit. For subsequent library preparation using Nextera XT DNA library preparation kit (Illumina) following the Fluidigm manual, cDNAs were normalized to 0.3 ng/µl. Libraries were pooled and sequenced SR75 on an Illumina NextSeq 500 system (75 cycles High Output v2 kit).

treatment_protocol: Dorsal cortices from embryonic day E10.5 to postnatal day 3 (P3) were micro-dissected and dissociated into single cell suspensions using Papain and Ovo-mucoid mix (Giachino et al, 2009). Cells were washed with L15 medium and FAC-sorted for GFP positive NSCs using FACSariaIII (BD Biosciences) derived from Hes5::GFP transgenic embryos for NSCs and Tbr2::GFP transgenic embryos for BPs and NBNs.

tag: strain/background

tag: isolate

value: Wild-type

value: Forebrain

value: Newborn neuron

tag: Sex

value: Female

tag: age


title: P3_NBN_34

description:
mRNA
Forebrain NBN at stage P3, replicate 34
processed data file: gene_tpm_SC_P3_NBN.txt.gz

tag: genotype


title: P3_NBN_33

description:
mRNA
Forebrain NBN at stage P3, replicate 33
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_30

description:
mRNA
Forebrain NBN at stage P3, replicate 30
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_35

description:
mRNA
Forebrain NBN at stage P3, replicate 35
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: p17-BS-200

tag: prolonged insulin


title: p14-BS-200

tag: serum starvation


title: p17-BS-0


title: P3_NBN_28

description:
mRNA
Forebrain NBN at stage P3, replicate 28
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_29

description:
mRNA
Forebrain NBN at stage P3, replicate 29
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: p14-BS-0


title: p16-BS-0


title: Genomic Input-ChipSeq BK3-4 input

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

library_source: genomic

data_processing:
read quality was accessed using FastQC 0.11.8
fastq files were trimmed of Illumina adapters with Trimgalore Version 0.6.4 using Illumina parameters
fastq files were aligned to mouse genome GRCm38 mm10 patch release 6 using STAR 2.7.0 using default parameters
fastq files were aligned to Drosophila BDGP R5/dm3 using STAR 2.7.0 using default parameters
bam files were sorted and selected for primary reads using Samtools view 1.9 with the following parameters: -F 256, -@ 5
PCR duplicates were removed from bam files using Picard Tools 2.20.2 using default parameters
read totals were determined and scaling factors were determined using Samtools Flagstat 1.9
coverage for each bam file was calculated using Deeptools bamCoverage 2.0 using the appropriate scaling factor and output as bigwig file
matrices were calculated using Deeptools computeMatrix 2.0 using the parameters ----referencePoint TSS, -S (appropriate .bw files), --sortUsing region_length, --sortUsingSamples 1, -b (appropriate upstream starting position), -a (appropriate downstream ending position), o- (appropriate .gz file)
heatmaps were plotted using Deeptools plotHeatmap 2.0
Tag counts between DMSO controls and EZH2i treated samples were then determined across the entire mouse genome using Bedtools multicov bedtools v2.26.0 and log2 fold change and percent change (i.e. decrease or increase) was calculated.
Genome_build: GRCm38 mm10 patch release 6

molecule: genomic DNA

source_name: Activated CD8+ T Cells

growth_protocol: unknown

extract_protocol:
For H3K27me3 and H3K36me3 ChIP-Seq, 40 million of cells were cross-linked with 1% formaldehyde for 10 minutes, followed by addition of glycine to stop crosslinking. After washing, cell lysis and sonication, the chromatin samples were incubated with antibody-conjugated Dynabeads (Invitrogen) at 4 degrees Celsius. Beads bound with chromatin were then subject to extensive washing and elution. Eluted chromatin was de-crosslinked overnight at 65 degrees, followed by protein digestion with proteinase K and DNA purification with Qiagen PCR purification kit.
The obtained ChIP DNA samples were submitted to the UNC-Chapel Hill High-Throughput Sequencing Facility (HTSF) for preparation of multiplexed libraries and deep sequencing with an Illumina High-Seq platform according to the manufacturer’s instructions.

treatment_protocol: We performed H3K27me3 and H3K36me3 ChIP-Seq on control and EZH2 inhibited T cells.

tag: chip antibody

value: Genomic Input


title: P3_NBN_38

description:
mRNA
Forebrain NBN at stage P3, replicate 38
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: p16-BS-200


title: P3_NBN_27

description:
mRNA
Forebrain NBN at stage P3, replicate 27
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_26

description:
mRNA
Forebrain NBN at stage P3, replicate 26
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: Genomic Input-ChipSeq BK1-2 input


title: P3_NBN_39

description:
mRNA
Forebrain NBN at stage P3, replicate 39
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_25

description:
mRNA
Forebrain NBN at stage P3, replicate 25
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_37

description:
mRNA
Forebrain NBN at stage P3, replicate 37
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_36

description:
mRNA
Forebrain NBN at stage P3, replicate 36
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_24

description:
mRNA
Forebrain NBN at stage P3, replicate 24
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_31

description:
mRNA
Forebrain NBN at stage P3, replicate 31
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_22

description:
mRNA
Forebrain NBN at stage P3, replicate 22
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_40

description:
mRNA
Forebrain NBN at stage P3, replicate 40
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_21

description:
mRNA
Forebrain NBN at stage P3, replicate 21
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_23

description:
mRNA
Forebrain NBN at stage P3, replicate 23
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_20

description:
mRNA
Forebrain NBN at stage P3, replicate 20
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_15

description:
mRNA
Forebrain NBN at stage P3, replicate 15
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_16

description:
mRNA
Forebrain NBN at stage P3, replicate 16
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_17

description:
mRNA
Forebrain NBN at stage P3, replicate 17
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_19

description:
mRNA
Forebrain NBN at stage P3, replicate 19
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_12

description:
mRNA
Forebrain NBN at stage P3, replicate 12
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_14

description:
mRNA
Forebrain NBN at stage P3, replicate 14
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_10

description:
mRNA
Forebrain NBN at stage P3, replicate 10
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_8

description:
mRNA
Forebrain NBN at stage P3, replicate 8
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_9

description:
mRNA
Forebrain NBN at stage P3, replicate 9
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_7

description:
mRNA
Forebrain NBN at stage P3, replicate 7
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_11

description:
mRNA
Forebrain NBN at stage P3, replicate 11
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_5

description:
mRNA
Forebrain NBN at stage P3, replicate 5
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_6

description:
mRNA
Forebrain NBN at stage P3, replicate 6
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_4

description:
mRNA
Forebrain NBN at stage P3, replicate 4
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_1

description:
mRNA
Forebrain NBN at stage P3, replicate 1
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_2

description:
mRNA
Forebrain NBN at stage P3, replicate 2
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P3_NBN_3

description:
mRNA
Forebrain NBN at stage P3, replicate 3
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P1_NBN_37

description:
mRNA
Forebrain NBN at stage P1, replicate 37
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_38

description:
mRNA
Forebrain NBN at stage P1, replicate 38
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_36

description:
mRNA
Forebrain NBN at stage P1, replicate 36
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_39

description:
mRNA
Forebrain NBN at stage P1, replicate 39
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_35

description:
mRNA
Forebrain NBN at stage P1, replicate 35
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P3_NBN_13

description:
mRNA
Forebrain NBN at stage P3, replicate 13
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P1_NBN_33

description:
mRNA
Forebrain NBN at stage P1, replicate 33
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_34

description:
mRNA
Forebrain NBN at stage P1, replicate 34
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_32

description:
mRNA
Forebrain NBN at stage P1, replicate 32
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_31

description:
mRNA
Forebrain NBN at stage P1, replicate 31
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P3_NBN_18

description:
mRNA
Forebrain NBN at stage P3, replicate 18
processed data file: gene_tpm_SC_P3_NBN.txt.gz


title: P1_NBN_30

description:
mRNA
Forebrain NBN at stage P1, replicate 30
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_28

description:
mRNA
Forebrain NBN at stage P1, replicate 28
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_29

description:
mRNA
Forebrain NBN at stage P1, replicate 29
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_27

description:
mRNA
Forebrain NBN at stage P1, replicate 27
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_22

description:
mRNA
Forebrain NBN at stage P1, replicate 22
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_26

description:
mRNA
Forebrain NBN at stage P1, replicate 26
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_23

description:
mRNA
Forebrain NBN at stage P1, replicate 23
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_24

description:
mRNA
Forebrain NBN at stage P1, replicate 24
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_25

description:
mRNA
Forebrain NBN at stage P1, replicate 25
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_21

description:
mRNA
Forebrain NBN at stage P1, replicate 21
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_17

description:
mRNA
Forebrain NBN at stage P1, replicate 17
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_19

description:
mRNA
Forebrain NBN at stage P1, replicate 19
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_20

description:
mRNA
Forebrain NBN at stage P1, replicate 20
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_14

description:
mRNA
Forebrain NBN at stage P1, replicate 14
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_18

description:
mRNA
Forebrain NBN at stage P1, replicate 18
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_15

description:
mRNA
Forebrain NBN at stage P1, replicate 15
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_16

description:
mRNA
Forebrain NBN at stage P1, replicate 16
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_13

description:
mRNA
Forebrain NBN at stage P1, replicate 13
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_11

description:
mRNA
Forebrain NBN at stage P1, replicate 11
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_12

description:
mRNA
Forebrain NBN at stage P1, replicate 12
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_10

description:
mRNA
Forebrain NBN at stage P1, replicate 10
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_7

description:
mRNA
Forebrain NBN at stage P1, replicate 7
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_5

description:
mRNA
Forebrain NBN at stage P1, replicate 5
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_6

description:
mRNA
Forebrain NBN at stage P1, replicate 6
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_9

description:
mRNA
Forebrain NBN at stage P1, replicate 9
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_4

description:
mRNA
Forebrain NBN at stage P1, replicate 4
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_8

description:
mRNA
Forebrain NBN at stage P1, replicate 8
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NBN_3

description:
mRNA
Forebrain NBN at stage P1, replicate 3
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NSC_44

description:
mRNA
Forebrain NSC at stage P1, replicate 44
processed data file: gene_tpm_SC_P1_NSC.txt.gz

value: Neural stem cell


title: P1_NSC_45

description:
mRNA
Forebrain NSC at stage P1, replicate 45
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_47

description:
mRNA
Forebrain NSC at stage P1, replicate 47
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NBN_2

description:
mRNA
Forebrain NBN at stage P1, replicate 2
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NSC_43

description:
mRNA
Forebrain NSC at stage P1, replicate 43
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NBN_1

description:
mRNA
Forebrain NBN at stage P1, replicate 1
processed data file: gene_tpm_SC_P1_NBN.txt.gz


title: P1_NSC_42

description:
mRNA
Forebrain NSC at stage P1, replicate 42
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_41

description:
mRNA
Forebrain NSC at stage P1, replicate 41
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_46

description:
mRNA
Forebrain NSC at stage P1, replicate 46
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_38

description:
mRNA
Forebrain NSC at stage P1, replicate 38
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_40

description:
mRNA
Forebrain NSC at stage P1, replicate 40
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_35

description:
mRNA
Forebrain NSC at stage P1, replicate 35
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_36

description:
mRNA
Forebrain NSC at stage P1, replicate 36
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_37

description:
mRNA
Forebrain NSC at stage P1, replicate 37
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_30

description:
mRNA
Forebrain NSC at stage P1, replicate 30
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_31

description:
mRNA
Forebrain NSC at stage P1, replicate 31
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_34

description:
mRNA
Forebrain NSC at stage P1, replicate 34
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_32

description:
mRNA
Forebrain NSC at stage P1, replicate 32
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_33

description:
mRNA
Forebrain NSC at stage P1, replicate 33
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_28

description:
mRNA
Forebrain NSC at stage P1, replicate 28
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_39

description:
mRNA
Forebrain NSC at stage P1, replicate 39
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_29

description:
mRNA
Forebrain NSC at stage P1, replicate 29
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_23

description:
mRNA
Forebrain NSC at stage P1, replicate 23
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_24

description:
mRNA
Forebrain NSC at stage P1, replicate 24
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_22

description:
mRNA
Forebrain NSC at stage P1, replicate 22
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_26

description:
mRNA
Forebrain NSC at stage P1, replicate 26
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_21

description:
mRNA
Forebrain NSC at stage P1, replicate 21
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_25

description:
mRNA
Forebrain NSC at stage P1, replicate 25
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_27

description:
mRNA
Forebrain NSC at stage P1, replicate 27
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_18

description:
mRNA
Forebrain NSC at stage P1, replicate 18
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_19

description:
mRNA
Forebrain NSC at stage P1, replicate 19
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_17

description:
mRNA
Forebrain NSC at stage P1, replicate 17
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_15

description:
mRNA
Forebrain NSC at stage P1, replicate 15
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_16

description:
mRNA
Forebrain NSC at stage P1, replicate 16
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_14

description:
mRNA
Forebrain NSC at stage P1, replicate 14
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_20

description:
mRNA
Forebrain NSC at stage P1, replicate 20
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_13

description:
mRNA
Forebrain NSC at stage P1, replicate 13
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_12

description:
mRNA
Forebrain NSC at stage P1, replicate 12
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_10

description:
mRNA
Forebrain NSC at stage P1, replicate 10
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: SC00388A

description:
Almac Diagnostics XCEL array (Almac, Craigavon, UK)
Almac’s Diagnostic CLIA Laboratories

tag: dna damage  immune response call

tag: dna damage repair deficient score

value: CRIS-D


title: P1_NSC_11

description:
mRNA
Forebrain NSC at stage P1, replicate 11
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_7

description:
mRNA
Forebrain NSC at stage P1, replicate 7
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_4

description:
mRNA
Forebrain NSC at stage P1, replicate 4
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_3

description:
mRNA
Forebrain NSC at stage P1, replicate 3
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_6

description:
mRNA
Forebrain NSC at stage P1, replicate 6
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_8

description:
mRNA
Forebrain NSC at stage P1, replicate 8
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_9

description:
mRNA
Forebrain NSC at stage P1, replicate 9
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_2

description:
mRNA
Forebrain NSC at stage P1, replicate 2
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P1_NSC_1

description:
mRNA
Forebrain NSC at stage P1, replicate 1
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P0_BP_74

description:
mRNA
Forebrain BP at stage P0, replicate 74
processed data file: gene_tpm_SC_P0_BP.txt.gz

value: Basal progenitor


title: P0_BP_71

description:
mRNA
Forebrain BP at stage P0, replicate 71
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_70

description:
mRNA
Forebrain BP at stage P0, replicate 70
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_69

description:
mRNA
Forebrain BP at stage P0, replicate 69
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_73

description:
mRNA
Forebrain BP at stage P0, replicate 73
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_72

description:
mRNA
Forebrain BP at stage P0, replicate 72
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_76

description:
mRNA
Forebrain BP at stage P0, replicate 76
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_68

description:
mRNA
Forebrain BP at stage P0, replicate 68
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_63

description:
mRNA
Forebrain BP at stage P0, replicate 63
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_66

description:
mRNA
Forebrain BP at stage P0, replicate 66
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_65

description:
mRNA
Forebrain BP at stage P0, replicate 65
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_75

description:
mRNA
Forebrain BP at stage P0, replicate 75
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_62

description:
mRNA
Forebrain BP at stage P0, replicate 62
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_64

description:
mRNA
Forebrain BP at stage P0, replicate 64
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_61

description:
mRNA
Forebrain BP at stage P0, replicate 61
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P1_NSC_5

description:
mRNA
Forebrain NSC at stage P1, replicate 5
processed data file: gene_tpm_SC_P1_NSC.txt.gz


title: P0_BP_57

description:
mRNA
Forebrain BP at stage P0, replicate 57
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_56

description:
mRNA
Forebrain BP at stage P0, replicate 56
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_58

description:
mRNA
Forebrain BP at stage P0, replicate 58
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_55

description:
mRNA
Forebrain BP at stage P0, replicate 55
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_60

description:
mRNA
Forebrain BP at stage P0, replicate 60
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_59

description:
mRNA
Forebrain BP at stage P0, replicate 59
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_54

description:
mRNA
Forebrain BP at stage P0, replicate 54
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_53

description:
mRNA
Forebrain BP at stage P0, replicate 53
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_52

description:
mRNA
Forebrain BP at stage P0, replicate 52
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_51

description:
mRNA
Forebrain BP at stage P0, replicate 51
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_50

description:
mRNA
Forebrain BP at stage P0, replicate 50
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_49

description:
mRNA
Forebrain BP at stage P0, replicate 49
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_48

description:
mRNA
Forebrain BP at stage P0, replicate 48
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_47

description:
mRNA
Forebrain BP at stage P0, replicate 47
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_43

description:
mRNA
Forebrain BP at stage P0, replicate 43
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_46

description:
mRNA
Forebrain BP at stage P0, replicate 46
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_45

description:
mRNA
Forebrain BP at stage P0, replicate 45
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_42

description:
mRNA
Forebrain BP at stage P0, replicate 42
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_44

description:
mRNA
Forebrain BP at stage P0, replicate 44
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_40

description:
mRNA
Forebrain BP at stage P0, replicate 40
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_41

description:
mRNA
Forebrain BP at stage P0, replicate 41
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_39

description:
mRNA
Forebrain BP at stage P0, replicate 39
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_38

description:
mRNA
Forebrain BP at stage P0, replicate 38
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_37

description:
mRNA
Forebrain BP at stage P0, replicate 37
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_67

description:
mRNA
Forebrain BP at stage P0, replicate 67
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_35

description:
mRNA
Forebrain BP at stage P0, replicate 35
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_32

description:
mRNA
Forebrain BP at stage P0, replicate 32
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_34

description:
mRNA
Forebrain BP at stage P0, replicate 34
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_33

description:
mRNA
Forebrain BP at stage P0, replicate 33
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_31

description:
mRNA
Forebrain BP at stage P0, replicate 31
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_28

description:
mRNA
Forebrain BP at stage P0, replicate 28
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_30

description:
mRNA
Forebrain BP at stage P0, replicate 30
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_27

description:
mRNA
Forebrain BP at stage P0, replicate 27
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_25

description:
mRNA
Forebrain BP at stage P0, replicate 25
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_23

description:
mRNA
Forebrain BP at stage P0, replicate 23
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_26

description:
mRNA
Forebrain BP at stage P0, replicate 26
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_24

description:
mRNA
Forebrain BP at stage P0, replicate 24
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_36

description:
mRNA
Forebrain BP at stage P0, replicate 36
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_21

description:
mRNA
Forebrain BP at stage P0, replicate 21
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_20

description:
mRNA
Forebrain BP at stage P0, replicate 20
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_22

description:
mRNA
Forebrain BP at stage P0, replicate 22
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_17

description:
mRNA
Forebrain BP at stage P0, replicate 17
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_14

description:
mRNA
Forebrain BP at stage P0, replicate 14
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_29

description:
mRNA
Forebrain BP at stage P0, replicate 29
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_19

description:
mRNA
Forebrain BP at stage P0, replicate 19
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_15

description:
mRNA
Forebrain BP at stage P0, replicate 15
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_16

description:
mRNA
Forebrain BP at stage P0, replicate 16
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_13

description:
mRNA
Forebrain BP at stage P0, replicate 13
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_18

description:
mRNA
Forebrain BP at stage P0, replicate 18
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_11

description:
mRNA
Forebrain BP at stage P0, replicate 11
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_12

description:
mRNA
Forebrain BP at stage P0, replicate 12
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_10

description:
mRNA
Forebrain BP at stage P0, replicate 10
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_9

description:
mRNA
Forebrain BP at stage P0, replicate 9
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_8

description:
mRNA
Forebrain BP at stage P0, replicate 8
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_7

description:
mRNA
Forebrain BP at stage P0, replicate 7
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_6

description:
mRNA
Forebrain BP at stage P0, replicate 6
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_5

description:
mRNA
Forebrain BP at stage P0, replicate 5
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_4

description:
mRNA
Forebrain BP at stage P0, replicate 4
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_2

description:
mRNA
Forebrain BP at stage P0, replicate 2
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_NSC_47

description:
mRNA
Forebrain NSC at stage P0, replicate 47
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_48

description:
mRNA
Forebrain NSC at stage P0, replicate 48
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_BP_3

description:
mRNA
Forebrain BP at stage P0, replicate 3
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_BP_1

description:
mRNA
Forebrain BP at stage P0, replicate 1
processed data file: gene_tpm_SC_P0_BP.txt.gz


title: P0_NSC_42

description:
mRNA
Forebrain NSC at stage P0, replicate 42
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_46

description:
mRNA
Forebrain NSC at stage P0, replicate 46
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_45

description:
mRNA
Forebrain NSC at stage P0, replicate 45
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_39

description:
mRNA
Forebrain NSC at stage P0, replicate 39
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_44

description:
mRNA
Forebrain NSC at stage P0, replicate 44
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_41

description:
mRNA
Forebrain NSC at stage P0, replicate 41
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_38

description:
mRNA
Forebrain NSC at stage P0, replicate 38
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_40

description:
mRNA
Forebrain NSC at stage P0, replicate 40
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_33

description:
mRNA
Forebrain NSC at stage P0, replicate 33
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_35

description:
mRNA
Forebrain NSC at stage P0, replicate 35
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_43

description:
mRNA
Forebrain NSC at stage P0, replicate 43
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_34

description:
mRNA
Forebrain NSC at stage P0, replicate 34
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_31

description:
mRNA
Forebrain NSC at stage P0, replicate 31
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_37

description:
mRNA
Forebrain NSC at stage P0, replicate 37
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_32

description:
mRNA
Forebrain NSC at stage P0, replicate 32
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_30

description:
mRNA
Forebrain NSC at stage P0, replicate 30
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_28

description:
mRNA
Forebrain NSC at stage P0, replicate 28
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_26

description:
mRNA
Forebrain NSC at stage P0, replicate 26
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_27

description:
mRNA
Forebrain NSC at stage P0, replicate 27
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_25

description:
mRNA
Forebrain NSC at stage P0, replicate 25
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_36

description:
mRNA
Forebrain NSC at stage P0, replicate 36
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_24

description:
mRNA
Forebrain NSC at stage P0, replicate 24
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_29

description:
mRNA
Forebrain NSC at stage P0, replicate 29
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_23

description:
mRNA
Forebrain NSC at stage P0, replicate 23
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_21

description:
mRNA
Forebrain NSC at stage P0, replicate 21
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_22

description:
mRNA
Forebrain NSC at stage P0, replicate 22
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_19

description:
mRNA
Forebrain NSC at stage P0, replicate 19
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_16

description:
mRNA
Forebrain NSC at stage P0, replicate 16
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_18

description:
mRNA
Forebrain NSC at stage P0, replicate 18
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_20

description:
mRNA
Forebrain NSC at stage P0, replicate 20
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_17

description:
mRNA
Forebrain NSC at stage P0, replicate 17
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_15

description:
mRNA
Forebrain NSC at stage P0, replicate 15
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_14

description:
mRNA
Forebrain NSC at stage P0, replicate 14
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_13

description:
mRNA
Forebrain NSC at stage P0, replicate 13
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_11

description:
mRNA
Forebrain NSC at stage P0, replicate 11
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_10

description:
mRNA
Forebrain NSC at stage P0, replicate 10
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_12

description:
mRNA
Forebrain NSC at stage P0, replicate 12
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_6

description:
mRNA
Forebrain NSC at stage P0, replicate 6
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_8

description:
mRNA
Forebrain NSC at stage P0, replicate 8
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_9

description:
mRNA
Forebrain NSC at stage P0, replicate 9
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_7

description:
mRNA
Forebrain NSC at stage P0, replicate 7
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_5

description:
mRNA
Forebrain NSC at stage P0, replicate 5
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_1

description:
mRNA
Forebrain NSC at stage P0, replicate 1
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_4

description:
mRNA
Forebrain NSC at stage P0, replicate 4
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: P0_NSC_3

description:
mRNA
Forebrain NSC at stage P0, replicate 3
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: E185_NSC_64

description:
mRNA
Forebrain NSC at stage E185, replicate 64
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_66

description:
mRNA
Forebrain NSC at stage E185, replicate 66
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: P0_NSC_2

description:
mRNA
Forebrain NSC at stage P0, replicate 2
processed data file: gene_tpm_SC_P0_NSC.txt.gz


title: E185_NSC_65

description:
mRNA
Forebrain NSC at stage E185, replicate 65
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_61

description:
mRNA
Forebrain NSC at stage E185, replicate 61
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_62

description:
mRNA
Forebrain NSC at stage E185, replicate 62
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_63

description:
mRNA
Forebrain NSC at stage E185, replicate 63
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_60

description:
mRNA
Forebrain NSC at stage E185, replicate 60
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_58

description:
mRNA
Forebrain NSC at stage E185, replicate 58
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_57

description:
mRNA
Forebrain NSC at stage E185, replicate 57
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_59

description:
mRNA
Forebrain NSC at stage E185, replicate 59
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_56

description:
mRNA
Forebrain NSC at stage E185, replicate 56
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_55

description:
mRNA
Forebrain NSC at stage E185, replicate 55
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_54

description:
mRNA
Forebrain NSC at stage E185, replicate 54
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_53

description:
mRNA
Forebrain NSC at stage E185, replicate 53
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_51

description:
mRNA
Forebrain NSC at stage E185, replicate 51
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_52

description:
mRNA
Forebrain NSC at stage E185, replicate 52
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_49

description:
mRNA
Forebrain NSC at stage E185, replicate 49
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_50

description:
mRNA
Forebrain NSC at stage E185, replicate 50
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_47

description:
mRNA
Forebrain NSC at stage E185, replicate 47
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_48

description:
mRNA
Forebrain NSC at stage E185, replicate 48
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_42

description:
mRNA
Forebrain NSC at stage E185, replicate 42
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_46

description:
mRNA
Forebrain NSC at stage E185, replicate 46
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_44

description:
mRNA
Forebrain NSC at stage E185, replicate 44
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_43

description:
mRNA
Forebrain NSC at stage E185, replicate 43
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_41

description:
mRNA
Forebrain NSC at stage E185, replicate 41
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_32

description:
mRNA
Forebrain NSC at stage E185, replicate 32
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_40

description:
mRNA
Forebrain NSC at stage E185, replicate 40
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_39

description:
mRNA
Forebrain NSC at stage E185, replicate 39
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_38

description:
mRNA
Forebrain NSC at stage E185, replicate 38
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_34

description:
mRNA
Forebrain NSC at stage E185, replicate 34
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_31

description:
mRNA
Forebrain NSC at stage E185, replicate 31
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_35

description:
mRNA
Forebrain NSC at stage E185, replicate 35
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_30

description:
mRNA
Forebrain NSC at stage E185, replicate 30
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_29

description:
mRNA
Forebrain NSC at stage E185, replicate 29
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_26

description:
mRNA
Forebrain NSC at stage E185, replicate 26
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_27

description:
mRNA
Forebrain NSC at stage E185, replicate 27
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_28

description:
mRNA
Forebrain NSC at stage E185, replicate 28
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_24

description:
mRNA
Forebrain NSC at stage E185, replicate 24
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_23

description:
mRNA
Forebrain NSC at stage E185, replicate 23
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_45

description:
mRNA
Forebrain NSC at stage E185, replicate 45
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_22

description:
mRNA
Forebrain NSC at stage E185, replicate 22
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_20

description:
mRNA
Forebrain NSC at stage E185, replicate 20
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_25

description:
mRNA
Forebrain NSC at stage E185, replicate 25
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_19

description:
mRNA
Forebrain NSC at stage E185, replicate 19
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_36

description:
mRNA
Forebrain NSC at stage E185, replicate 36
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_17

description:
mRNA
Forebrain NSC at stage E185, replicate 17
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_33

description:
mRNA
Forebrain NSC at stage E185, replicate 33
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_37

description:
mRNA
Forebrain NSC at stage E185, replicate 37
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_13

description:
mRNA
Forebrain NSC at stage E185, replicate 13
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_8

description:
mRNA
Forebrain NSC at stage E185, replicate 8
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_11

description:
mRNA
Forebrain NSC at stage E185, replicate 11
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_7

description:
mRNA
Forebrain NSC at stage E185, replicate 7
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_21

description:
mRNA
Forebrain NSC at stage E185, replicate 21
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_1

description:
mRNA
Forebrain NSC at stage E185, replicate 1
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_6

description:
mRNA
Forebrain NSC at stage E185, replicate 6
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_3

description:
mRNA
Forebrain NSC at stage E185, replicate 3
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_10

description:
mRNA
Forebrain NSC at stage E185, replicate 10
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_18

description:
mRNA
Forebrain NSC at stage E185, replicate 18
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_4

description:
mRNA
Forebrain NSC at stage E185, replicate 4
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_16

description:
mRNA
Forebrain NSC at stage E185, replicate 16
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_5

description:
mRNA
Forebrain NSC at stage E185, replicate 5
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NBN_64

description:
mRNA
Forebrain NBN at stage E185, replicate 64
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_62

description:
mRNA
Forebrain NBN at stage E185, replicate 62
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NSC_12

description:
mRNA
Forebrain NSC at stage E185, replicate 12
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_9

description:
mRNA
Forebrain NSC at stage E185, replicate 9
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NBN_67

description:
mRNA
Forebrain NBN at stage E185, replicate 67
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NSC_15

description:
mRNA
Forebrain NSC at stage E185, replicate 15
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NSC_14

description:
mRNA
Forebrain NSC at stage E185, replicate 14
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NBN_59

description:
mRNA
Forebrain NBN at stage E185, replicate 59
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_60

description:
mRNA
Forebrain NBN at stage E185, replicate 60
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NSC_2

description:
mRNA
Forebrain NSC at stage E185, replicate 2
processed data file: gene_tpm_SC_E185_NSC.txt.gz


title: E185_NBN_69

description:
mRNA
Forebrain NBN at stage E185, replicate 69
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_55

description:
mRNA
Forebrain NBN at stage E185, replicate 55
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_70

description:
mRNA
Forebrain NBN at stage E185, replicate 70
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_66

description:
mRNA
Forebrain NBN at stage E185, replicate 66
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_54

description:
mRNA
Forebrain NBN at stage E185, replicate 54
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_47

description:
mRNA
Forebrain NBN at stage E185, replicate 47
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_51

description:
mRNA
Forebrain NBN at stage E185, replicate 51
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_53

description:
mRNA
Forebrain NBN at stage E185, replicate 53
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_52

description:
mRNA
Forebrain NBN at stage E185, replicate 52
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_49

description:
mRNA
Forebrain NBN at stage E185, replicate 49
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_68

description:
mRNA
Forebrain NBN at stage E185, replicate 68
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_65

description:
mRNA
Forebrain NBN at stage E185, replicate 65
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_63

description:
mRNA
Forebrain NBN at stage E185, replicate 63
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_61

description:
mRNA
Forebrain NBN at stage E185, replicate 61
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_58

description:
mRNA
Forebrain NBN at stage E185, replicate 58
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_39

description:
mRNA
Forebrain NBN at stage E185, replicate 39
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_43

description:
mRNA
Forebrain NBN at stage E185, replicate 43
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_42

description:
mRNA
Forebrain NBN at stage E185, replicate 42
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_38

description:
mRNA
Forebrain NBN at stage E185, replicate 38
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_56

description:
mRNA
Forebrain NBN at stage E185, replicate 56
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_40

description:
mRNA
Forebrain NBN at stage E185, replicate 40
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_44

description:
mRNA
Forebrain NBN at stage E185, replicate 44
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_41

description:
mRNA
Forebrain NBN at stage E185, replicate 41
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_57

description:
mRNA
Forebrain NBN at stage E185, replicate 57
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_46

description:
mRNA
Forebrain NBN at stage E185, replicate 46
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_50

description:
mRNA
Forebrain NBN at stage E185, replicate 50
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_48

description:
mRNA
Forebrain NBN at stage E185, replicate 48
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_37

description:
mRNA
Forebrain NBN at stage E185, replicate 37
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_32

description:
mRNA
Forebrain NBN at stage E185, replicate 32
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_35

description:
mRNA
Forebrain NBN at stage E185, replicate 35
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_33

description:
mRNA
Forebrain NBN at stage E185, replicate 33
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_36

description:
mRNA
Forebrain NBN at stage E185, replicate 36
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_30

description:
mRNA
Forebrain NBN at stage E185, replicate 30
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_45

description:
mRNA
Forebrain NBN at stage E185, replicate 45
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_31

description:
mRNA
Forebrain NBN at stage E185, replicate 31
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_27

description:
mRNA
Forebrain NBN at stage E185, replicate 27
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_29

description:
mRNA
Forebrain NBN at stage E185, replicate 29
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_28

description:
mRNA
Forebrain NBN at stage E185, replicate 28
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_24

description:
mRNA
Forebrain NBN at stage E185, replicate 24
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_26

description:
mRNA
Forebrain NBN at stage E185, replicate 26
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_25

description:
mRNA
Forebrain NBN at stage E185, replicate 25
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_19

description:
mRNA
Forebrain NBN at stage E185, replicate 19
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_20

description:
mRNA
Forebrain NBN at stage E185, replicate 20
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_22

description:
mRNA
Forebrain NBN at stage E185, replicate 22
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_21

description:
mRNA
Forebrain NBN at stage E185, replicate 21
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_15

description:
mRNA
Forebrain NBN at stage E185, replicate 15
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_16

description:
mRNA
Forebrain NBN at stage E185, replicate 16
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_17

description:
mRNA
Forebrain NBN at stage E185, replicate 17
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_18

description:
mRNA
Forebrain NBN at stage E185, replicate 18
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_23

description:
mRNA
Forebrain NBN at stage E185, replicate 23
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_34

description:
mRNA
Forebrain NBN at stage E185, replicate 34
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_14

description:
mRNA
Forebrain NBN at stage E185, replicate 14
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_13

description:
mRNA
Forebrain NBN at stage E185, replicate 13
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_12

description:
mRNA
Forebrain NBN at stage E185, replicate 12
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_8

description:
mRNA
Forebrain NBN at stage E185, replicate 8
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_9

description:
mRNA
Forebrain NBN at stage E185, replicate 9
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_7

description:
mRNA
Forebrain NBN at stage E185, replicate 7
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_10

description:
mRNA
Forebrain NBN at stage E185, replicate 10
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_11

description:
mRNA
Forebrain NBN at stage E185, replicate 11
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_5

description:
mRNA
Forebrain NBN at stage E185, replicate 5
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_NBN_6

description:
mRNA
Forebrain NBN at stage E185, replicate 6
processed data file: gene_tpm_SC_E185_NBN.txt.gz


title: E185_BP_60

description:
mRNA
Forebrain BP at stage E185, replicate 60
processed data file: gene_tpm_SC_E185_BP.txt.gz


title: E185_BP_61

description:
mRNA
Forebrain BP at stage E185, replicate 61
processed data file: gene_tpm_SC_E185_BP.txt.gz