title: Human cortex

description: single-cell ATAC seq data

data_processing:
FastQ files were generated from BCL files using bcl2fastq (v 2.19.0, Illumina Inc.) with the following options with-failed-reads, no-lane-splitting, fastq-compression-level=9, create-fastq-for-index-reads
FastQ reads were assigned to their expected primer index sequence allowing for sequencing error (Hamming distance ≤2) and indexes were concatenated to form a “cellID”. cellIDs are stored in the FastQ header
Reads that could be assigned unambiguously to a cellID were then aligned to reference genomes. For GM12878, paired reads were aligned with bwa mem (v0.7.15-r1140) to hg38. For s3-ATAC libraries, reads were first aligned to a concatenated hybrid genome of hg38 and GRCm38 (“mm10”, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)).
Reads were then de-duplicated to remove PCR and optical duplicates by a perl (v5.16.3) script aware of cellID, chromosome and read start, read end and strand. From there putative single-cells were distinguished from debris and error-generated cellIDs by both unique reads and percentage of unique reads.
For s3-ATAC libraries, cellIDs with ≥90% of reads aligning to a single reference genome were considered bona fide single-cells and fastQ files were filtered prior to realigning to the correct genome.
Pseudo-bulked data (agnostic of cellID) was then used to call read pile-ups or “peaks” via macs2 (v.2.2.7.1) with option –keep-dup all
A scitools perl script was then used to generate a sparse matrix of peaks × cellID to count occurrence of reads within peak regions per cell.
The peaks x cellID counts matrix was then used to generate Seurat Objects for Signac processing (see Online Methods for more downstream analyses).
Genome_build: GRCm38 (“mm10”, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2) and GRCh38 (“hg38”,Genome Reference Consortium Human Reference 38 (GCA_000001405.2).
Supplementary_files_format_and_content: SeuratObject.Rds files are RDS files used in Signac processing of data (see https://satijalab.org/signac/ and our Online Methods for more detail). Metadata.csv files are csv files containing metadata information per cell (each row), with relevant cell information (each column). Counts.csv files contain the CSV formatted peaks (rows) by cellIDs (columns) matrix, where each value denotes read counts overlapping peaks per cell. Bam files are standard bams with cellIDs filtered to those used in downstream analyses.
Supplementary_files_format_and_content: s3atac.hg38.fragments.tsv: Tab-separated fragment files in bed format with fields <chr> <start> <end> <cell identifier> <count> for the s3ATAC human sample. Generated with custom scripts for input into Signac R library.

source_name: Cortical sample, middle frontal gyrus

tag: age

value: 50 yo

value: normal health status


title: ANI treated sample rep 2

status: Public on Aug 06 2021

type: SRA

city: Göttingen

first: Hsu-Min

last: Sung

state: Niedersachsen

address: Humboldtallee 23

country: Germany

institute: Heart Centre Göttingen

library_source: transcriptomic

data_processing:
Reads were aligned using STAR v.2.4.2a to the Human RefSeq genome GRCh38.p10 and the ERCC spike-in sequence.
Reads were counted using the DEXSeq read counting script.
Splicing analysis was performed with DEXSeq using the GENCODE 27 gene annotation.
Differential gene expression analysis was performed using DESeq2.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: HeLa TREx_YFP-TIARr

growth_protocol: HeLa TREx cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% tetracyclin-free FBS, 2 mM L-glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin , 2 mM L-glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin, 5 µg/ml blasticidin and 100 µg/ml zeocin. Cells were cultured at 37°C in 5% CO2.

extract_protocol:
Total RNA was purified with the GeneMATRIX universal RNA purification kit (EURx), including a DNase (Promega) on-column digestion step. 350 ng of total RNA as quantified by Qubit (Invitrogen) was used for subsequent RNA-Seq. Ribosomal RNA was depleted with the Ribo Zero Human Gold Kit (Illumina)
Libraries were prepared using the TruSeq Directional RNA LT Preparation Kit (Illumina) using standard Illumina protocols.  Before library preparation RNA was prepared without poly(A)-mRNA enrichment step for acquiring pre-mRNA

treatment_protocol: For pretreatment with the p38 inhibitor (SB202190), final concentration of 10 µM SB202190 was added to cell culture medium 1 hour prior to DMSO or Anisomycin treatment. For Anisomycin treatment, final concentration of 0.1 µg/ml anisomycin was added to cell culture medium and incubated for 90 minutes prior to RNA extraction,

tag: cell type

value: epithelial cell

tag: tissue

value: Cervical cancer

tag: cell line

value: HeLa TREx_YFP-TIARr

tag: stable expression

value: Tet repressor

tag: inducible expression

value: YFP-fused TIARb resistant to siRNA

tag: treatment

value: Anisomycin 0.1 ug/ml, 90 minutes


title: Control and CTE from Run4.1

status: Public on May 24 2021

city: Boston

first: Kevin

middle: Blake

last: Chancellor

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Harvard Medical School

data_processing:
Data processing, from binary base call files produced from next-generation sequencing to generation of counts matrices, was carried out using the inDrops processing pipeline (https://github.com/indrops/indrops). Project specific details can be found at https://github.com/blakechancellor/Altered-oligodendroglia-and-astroglia-in-chronic-traumatic-encephalopathy.
Step 1. Produciont of fastq files. Fastq files were produced using bcl2fastq with default settings.
Step 2. Filter. This step filters reads and only keeps reads that match the expected inDrops read structure. Default settings were used.
Step 3. Identify abundant barcodes. Reads are organized by abundant barcodes (nuclei) and separated by library (sample) of origin. Default settings were used.
Step 4. Sort reads. Reads within samples were sorted by nucleus of origin. Barcodes with fewer than 250 reads were ignored. Default setting were used.
Step 5. Quantify expression. Reads were mapped to the reference genome using bowtie1.1.1. Alignment created BAM files using samtools. Aligned counts were quantified to create unique molecular identifier filter mapped counts matrices.
Step 6 Aggregate. The pipeline can divide the data and run each step in parallel to expedite the process. This step combines data from several parallelized steps.
Genome_build: GRCh38.97
Supplementary_files_format_and_content: Processed files contain the gene expression counts for each sample. Each file is a counts matrix with cellular barcodes as columns and gene names as rows. Values indicate raw counts for each time a gene was detected in a specific cellular barcode.

molecule: polyA RNA

source_name: Dorsolateral frontal white matter

extract_protocol:
All tissue was macrodissected into 30mg sections from dorsolateral frontal white matter (Brodmann area 8/9) with a scalpel blade and stored at -80° Celsius. On the day of single-nucleus encapsulation, tissue was placed in a 7mL dounce with ice cold buffer (0.5M sucrose, 2M KCl, 1M MgCl2, 1M Tricine-KOH pH 7.8, spermine, spermidine, DTT, RNasin, H2O) and dounced with a tight pestle ten times to mechanically dissociate and homogenize the tissue. To further dissociate the tissue, 5% IGEPAL-CA630 was added to the homogenate and dounced 5 times. The homogenate was then strained through a 40μm cell strainer (VWR) on ice. 5mL of 50% iodixanol was added to the homogenate and mixed. In a 13mL ultraclear ultracentrifuge tube, 1mL of 40% iodixanol was added with 1mL of 30% iodixanol carefully layered on top, followed by 10mL of the tissue homogenate. The tissue was then ultracentrifuged in a swing-bucket rotor at 10,000xg for 18 minutes. Following ultracentrifugation, the 35% iodixanol layer was collected and the nuclei were counted. Nuclei were diluted with 30% iodixanol to 90,000 nuclei/mL for inDrops chip loading. Nuclei were isolated for inDrops using a previously described method.
Libraries were constructed following the inDrops single-nucleus RNA sequencing pipeline: https://singlecellcore.hms.harvard.edu/ and Klein, et al. Cell. 2015. Briefly, nuclei were encapsulated in a hydrogel via a microfluidic chip. Once encapsulated, nuclei were lysed and free-floating mRNA molecules were reverse transcribed to cDNA and ligated with cellular barcodes, library indices, unique molecular identifiers, and next-generation sequencing primers. Prepared cDNA molecules were pooled, sequenced on a NextSeq500 and de-multiplexed to cell and sample of origin bioinformatically.

tag: brodmann  area

tag: brain region

value: Dorsolateral frontal sulcus


title: DMSO treated control rep 1

value: DMSO 90 minutes


title: Control and CTE from Run4.2


title: Control and CTE from Run3.2


title: DFMC-33043

status: Public on Aug 12 2021

first: Yingtian

last: Xie

address: 450 BROOKLINE AVE

institute: DANA FARBER CANCER INSTITUTE INC

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using STAR.
Differential analysis was performed by DESeq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files include RPKM values for each Sample.

source_name: primary tissue

extract_protocol:
A fragment of frozen tissues (PDX models) or 50 um sections (liver metastases) were cut and homogenized in 1 ml of AllPrep DNA/RNA Mini Kit (Qiagen) using a plastic pestle (Cole-Palmer #44468-23). DNA and RNA were simultaneously isolated.
500 ng RNA was used to prepare libraries using the NEBNext Ultra™ RNA Library Prep Kit for Illumina. RNA quantity and quality were assessed on an Agilent 2100 Bioanalyzer. For all RNA-seq, reads were sequenced on a NextSeq 500 instrument (Illumina).

value: MCC


title: Control and CTE from Run3.1


title: Control and CTE from Run2


title: DMSO treated control rep 3


title: BPN-15477-treated WT fibroblasts 8402

status: Public on Mar 29 2021

first: Susan

last: Slaugenhaupt

address: 185 Cambridge St

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

data_processing:
RNASeq reads were mapped against Ensembl GRCh37 (version 75) by STAR (version 2.4.2) allowing 5% mismatch
Number of reads covering splice junction was measured by STAR during alignment
Exon triplet index was built on Ensembl GRCh37 (version 75) where each triplet is a three-consecutive exons, namely exon 1, 2 and 3, according to the annotation
For each triplet, two values are measured. The first value, representing exon inclusion, is the average of number of reads connecting exon 1 and 2 and number of reads connecting exon 2 and 3. This value is an integer
The second value, representing exon exclusion, is the number of reads connecting exon 1 and 3, which is an integer as well.
Genome_build: Ensembl GRCh37 version 75
Supplementary_files_format_and_content: Fastq format for RNASeq reads; Tab-delimited txt format for splice junction counts

source_name: Human fibroblast

growth_protocol: Six different human WT fibroblast cell lines were obtained from Coriell Institute and cultured in Dulbecco's modified Eagle's medium (D-MEM, Gibco) with 10% fetal bovine serum (FBS, Sigma). Cells were counted and plated in order to achieve semi-confluence after eight days.

extract_protocol:
After seven days of treatment, cells were collected, and RNA was extracted using the TRI reagent procedure provided by the manufacturer.
RNA-Seq libraries were prepared by the Genomic and Technology Core (GTC) of MGH using strand-specific dUTP method. In brief, RNA sample quality (based on RNA Integrity Number, or RIN) and quantity was determined using the Agilent 2200 TapeStation and between 100-1000 ng of total RNA was used for library preparation. Each RNA sample was spiked with 1 µl of diluted (1:100) External RNA Controls Consortium (ERCC) RNA Spike-In Mix (4456740, ThermoFisher) alternating between mix 1 and mix 2 for each well in the batch. Samples were then enriched for mRNA using polyA capture, followed by stranded reverse transcription and chemical shearing to make appropriate stranded cDNA inserts. Libraries were finished by adding Y-adapters, with sample specific barcodes, followed by between 10-15 rounds of PCR amplification. Libraries were evaluated for final concentration and size distribution by Agilent 2200 TapeStation and/or qPCR, using Library Quantification Kit (KK4854, Kapa Biosystems), and multiplexed by pooling equimolar amounts of each library prior to sequencing.

treatment_protocol: Twenty-four hours after plating, the medium was changed and cells were treated with BPN-15477 or DMSO to a final concentration of 30 µM and 0.5%, respectively. DMSO was used as vehicle and the concentration of BPN-15477 was chosen based on our previous studies, since at this concentration BPN-15477 induces robust splicing changes.

value: fibroblast

tag: genotype

value: WT

value: BPN-15477 treated

tag: coriell accession


title: BPN-15477-treated WT fibroblasts 2036


title: BPN-15477-treated WT fibroblasts 0041


title: BPN-15477-treated WT fibroblasts 1652


title: BPN-15477-treated WT fibroblasts 3348

description: Cell line has been discontinued at Coriell. Here is further information on this cell line: Cellosaurus: https://web.expasy.org/cellosaurus/CVCL_7382


title: BPN-15477-treated WT fibroblasts 16409


title: DFMC-96712


title: Untreated WT fibroblasts 2036

value: DMSO


title: Untreated WT fibroblasts 8402


title: Untreated WT fibroblasts 1652


title: Untreated WT fibroblasts 16409


title: Control and CTE from Run5.1


title: KYSE70_H3K27ac_ChIP

status: Public on Mar 23 2021

description: ESCC (esophageal squamous cell carcinoma) cell line KYSE70 H3K27ac ChIP-seq baseline

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to mm9 using BWA
For peak calling MACS2 was used.
Genome_build: mm9
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

molecule: genomic DNA

extract_protocol:
Cells was fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep kit (Rubicon Genomics). Libraries were sequenced using 75-bp reads on the Illumina platform at the Dana-Farber Cancer Institute.

value: esophagus

tag: chip antibody

value: H3K27ac(Abcam, ab 4729)


title: TE10_H3K27ac_ChIP

description: ESCC (esophageal squamous cell carcinoma) cell line TE10 H3K27ac ChIP-seq baseline


title: TE10_SOX2_ChIP

description: ESCC (esophageal squamous cell carcinoma) cell line TE10 SOX2 ChIP-seq baseline


title: TT_H3K27ac_ChIP

description: ESCC (esophageal squamous cell carcinoma) cell line TT H3K27ac ChIP-seq baseline


title: TT_SOX2_ChIP

description: ESCC (esophageal squamous cell carcinoma) cell line TT SOX2 ChIP-seq baseline


title: KYSE70_SOX2_ChIP

description: ESCC (esophageal squamous cell carcinoma) cell line KYSE70 SOX2 ChIP-seq baseline


title: SCPP_shKLF5_DOX(+)_replicate_1

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to mm9 using STAR
Differential analysis was performed by Deseq2
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Mus musculus

source_name: mouse organoids

growth_protocol: organoids grow in metri-gel and cells grow in 2d plates

extract_protocol:
RNA was harvested using QIAGEN Rneasy plus Micro and Mini Kits
500 ng RNA was used to prepare libraries using the NEBNext. Ultra™ RNA Library Prep Kit for Illumina. RNA quantity and quality were assessed on an Agilent 2100 Bioanalyzer. For all RNA-seq, reads were sequenced on a NextSeq 500 instrument (Illumina).

value: Mouse Esophagus

value: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids shRNA mediated knock-down Klf5 replicate1


title: SCPP_shKLF5_DOX(+)_replicate_2

value: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids shRNA mediated knock-down Klf5 replicate2


title: SCPP_shNT_DOX(+)_replicate_2

value: shNT

value: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids shRNA mediated knock-down non-target replicate2


title: SCPP_shNT_DOX(+)_replicate_1

value: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids shRNA mediated knock-down non-target replicate1


title: Control and CTE from Run1


title: Untreated WT fibroblasts 0041


title: KYSE70 shSOX2 DOX(+)  ATAC-seq replicate1

status: Public on Mar 17 2021

description:
KYSE70_shSOX2number4_dox_plus_1
cell line

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to mm9 using BWA
For peak calling MACS2 was used.
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

source_name: KYSE70 SOX2 knockdown  ATAC-seq replicate1

value: ESCC(Esopheageal squamous cell carcinoma)


title: Untreated WT fibroblasts 3348


title: KYSE70 shKLF5 DOX(+)  ATAC-seq replicate2

description:
KYSE70_shKLF5number7_dox_plus_2
cell line

source_name: KYSE70 KLF5 knockdown  ATAC-seq replicate2


title: KYSE70 shKLF5 DOX(+) replicate2

description:
KYSE70-12
Cell line

source_name: ESCC(Esopheageal squamous cell carcinoma)


title: KYSE70 shNT DOX(+)  ATAC-seq replicate2

description:
KYSE70_shNT_dox_plus_2
cell line

source_name: KYSE70 shNT DOX(+)  ATAC-seq  replicate2


title: KYSE70 shNT DOX(+)  ATAC-seq replicate1

description:
KYSE70_shNT_dox_plus_1
cell line

source_name: KYSE70 shNT DOX(+)  ATAC-seq replicate1


title: KYSE70 shSOX2 DOX(+)  ATAC-seq replicate2

description:
KYSE70_shSOX2number4_dox_plus_2
cell line

source_name: KYSE70 SOX2 knockdown  ATAC-seq replicate2


title: KYSE70 shKLF5 DOX(+)  ATAC-seq replicate1

description:
KYSE70_shKLF5number7_dox_plus_1
cell line

source_name: KYSE70 KLF5 knockdown  ATAC-seq replicate1


title: KYSE70 shSOX2 DOX(+) replicate1

description:
KYSE70-5
Cell line


title: KYSE70 shSOX2 DOX(+) replicate2

description:
KYSE70-6
Cell line


title: TT shKLF5 DOX(+) replicate2

description:
TT-12
Cell line


title: KYSE70 shNT DOX(+) replicate2

description:
KYSE70-4
Cell line


title: TT shSOX2 DOX(+) replicate2

description:
TT-8
Cell line


title: KYSE70 shKLF5 DOX(+) replicate1

description:
KYSE70-11
Cell line


title: KYSE70 shNT DOX(+) replicate1

description:
KYSE70-3
Cell line


title: TT shSOX2 DOX(+) replicate1

description:
TT-7
Cell line


title: TT shKLF5 DOX(+) replicate1

description:
TT-11
Cell line


title: TT shNT DOX(+) replicate1

description:
TT-3
Cell line


title: TT shNT DOX(+) replicate2

description:
TT-4
Cell line


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids shKlf5 dox(+) Sox2 ChIP-seq replicate1

description:
SCPP_shKLF5_1_rep1
cell line

source_name: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids shKlf5 dox(+)  replicate1


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids shScrambe dox(+) Sox2 ChIP-seq replicate2

description:
SCPP_shSRC_rep2
cell line

source_name: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids shScrambe dox(+)  replicate2


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids shKlf5 dox(+) Sox2 ChIP-seq replicate2

description:
SCPP_shKLF5_1_rep2
cell line

source_name: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids shKlf5 dox(+)  replicate2


title: Sox2 overexpression mouse esophageal organoids H3K4me1 ChIP-seq replicate2

description:
H4K4me_C-S_+2
cell line

source_name: Sox2 overexpression mouse esophageal organoids replicate2


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids H3K4me1 ChIP-seq replicate2

description:
H4K4me_C-S_+_P-P-2
cell line

source_name: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids replicate2


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids shScrambe dox(+) Sox2 ChIP-seq replicate1

description:
SCPP_shSRC_rep1
cell line

source_name: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids shScrambe dox(+)  replicate1


title: P53 knockout/p16 knockout mouse esophageal organoids H3K4me1 ChIP-seq replicate2

description:
H4K4me_C+_P-P-2
cell line

source_name: P53 knockout/p16 knockout mouse esophageal organoids replicate2


title: Sox2 overexpression mouse esophageal organoids H3K4me1 ChIP-seq replicate1

description:
H4K4me_C-S_+1
cell line

source_name: Sox2 overexpression mouse esophageal organoids replicate1


title: P53 knockout/p16 knockout mouse esophageal organoids H3K4me1 ChIP-seq replicate1

description:
H4K4me_C+_P-P-1
cell line

source_name: P53 knockout/p16 knockout mouse esophageal organoids replicate1


title: Normal mouse esophageal organoids H3K4me1 ChIP-seq replicate2

description:
H4K4me_C-S_Normal-2
cell line

source_name: Normal mouse esophageal organoids replicate2


title: Normal mouse esophageal organoids H3K4me1 ChIP-seq replicate1

description:
H4K4me_C-S_Normal-1
cell line

source_name: Normal mouse esophageal organoids replicate1


title: Normal mouse esophageal organoids Klf5 ChIP-seq replicate1

description:
402E_Klf5_A.rep1
cell line


title: Sox2 overexpression mouse esophageal organoids Klf5 ChIP-seq replicate1

description:
402ELAZ_Klf5_A.rep1
cell line


title: P53 knockout/p16 knockout mouse esophageal organoids Klf5 ChIP-seq replicate2

description:
CPP_Klf5_B.rep1
cell line


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids ATAC-seq replicate1

description:
ATAC_C-S_+_P-P-1
cell line

source_name: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids replicate1


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids Klf5 ChIP-seq replicate2

description:
SCPP_Klf5_B.rep1
cell line


title: P53 knockout/p16 knockout mouse esophageal organoids Klf5 ChIP-seq replicate1

description:
CPP_Klf5_A.rep1
cell line


title: P53 knockout/p16 knockout mouse esophageal organoids ATAC-seq replicate2

description:
ATAC_C+_P-P-2
cell line


title: P53 knockout/p16 knockout mouse esophageal organoids ATAC-seq replicate1

description:
ATAC_C+_P-P-1
cell line


title: Normal mouse esophageal organoids Klf5 ChIP-seq replicate2

description:
402E_Klf5_B.rep1
cell line


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids ATAC-seq replicate2

description:
ATAC_C-S_+_P-P-2
cell line


title: Normal mouse esophageal organoids ATAC-seq replicate2

description:
ATAC_C-S_Normal-2
cell line


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids Klf5 ChIP-seq replicate1

description:
SCPP_Klf5_A.rep1
cell line


title: Normal mouse esophageal organoids ATAC-seq replicate1

description:
ATAC_C-S_Normal-1
cell line


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids H3K27ac ChIP-seq replicate2

description:
JZ_SOX2_CHIPH3K_2_resubmission_12B
cell line


title: Sox2 overexpression mouse esophageal organoids Klf5 ChIP-seq replicate2

description:
402ELAZ_Klf5_B.rep1
cell line


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids H3K27ac ChIP-seq replicate1

description:
JZ_SOX2_CHIPH3K_2_resubmission_12A
cell line


title: Sox2 overexpression mouse esophageal organoids ATAC-seq replicate2

description:
ATAC_C-S_+2
cell line


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids H3K4me1 ChIP-seq replicate1

description:
H4K4me_C-S_+_P-P-1
cell line


title: Sox2 overexpression mouse esophageal organoids H3K27ac ChIP-seq replicate2

description:
JZ_SOX2_CHIPH3K_2_resubmission_2B
cell line


title: P53 knockout/p16 knockout mouse esophageal organoids H3K27ac ChIP-seq replicate2

description:
JZ_SOX2_CHIPS2H3K_3_2B
cell line


title: Normal mouse esophageal organoids H3K27ac ChIP-seq replicate2

description:
JZ_SOX2_CHIPH3K_2_resubmission_1B
cell line


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids Sox2 ChIP-seq replicate2

description:
JZ_SOX2_CHIP_1_12B
cell line


title: Normal mouse esophageal organoids H3K27ac ChIP-seq replicate1

description:
JZ_SOX2_CHIPH3K_2_resubmission_1A
cell line


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids Sox2 ChIP-seq replicate1

description:
JZ_SOX2_CHIP_1_12A
cell line


title: P53 knockout/p16 knockout mouse esophageal organoids H3K27ac ChIP-seq replicate1

description:
JZ_SOX2_CHIPS2H3K_3_2A
cell line


title: Sox2 overexpression mouse esophageal organoids Sox2 ChIP-seq replicate2

description:
JZ_SOX2_CHIP_1_2B
cell line


title: Sox2 overexpression mouse esophageal organoids ATAC-seq replicate1

description:
ATAC_C-S_+1
cell line


title: P53 knockout/p16 knockout mouse esophageal organoids Sox2 ChIP-seq replicate2

description:
JZ_SOX2_CHIPS2H3K_3_8B
cell line


title: Sox2 overexpression mouse esophageal organoids Sox2 ChIP-seq replicate1

description:
JZ_SOX2_CHIP_1_2A
cell line


title: P53 knockout/p16 knockout mouse esophageal organoids Sox2 ChIP-seq replicate1

description:
JZ_SOX2_CHIPS2H3K_3_8A
cell line


title: Normal mouse esophageal organoids Sox2 ChIP-seq replicate1

description:
JZ_SOX2_CHIP_1_1A
cell line


title: Normal mouse esophageal organoids Sox2 ChIP-seq replicate2

description:
JZ_SOX2_CHIP_1_1B
cell line


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids replicate2n

description:
SCPP_replicate2n
mouse organoids

source_name: Mouse Esophagus

value: baseline


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids replicate3n

description:
SCPP_replicate3n
mouse organoids


title: Sox2 overexpression mouse esophageal organoids H3K27ac ChIP-seq replicate1

description:
JZ_SOX2_CHIPH3K_2_resubmission_2A
cell line


title: P53 knockout/p16 knockout mouse esophageal organoids replicate2n

description:
CPP_replicate2n
mouse organoids


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids replicate2

description:
SCPP_replicate2
mouse organoids


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids replicate1

description:
SCPP_replicate1
mouse organoids


title: P53 knockout/p16 knockout mouse esophageal organoids replicate3n

description:
CPP_replicate3n
mouse organoids


title: Sox2 overexpression mouse esophageal organoids replicate2

description:
SC_replicate2
mouse organoids


title: Normal mouse esophageal organoids replicate2

description:
CS_Nprmal_replicate2
mouse organoids


title: Sox2 overexpression mouse esophageal organoids replicate1

description:
SC_replicate1
mouse organoids


title: Sox2 overexpression/P53 knockout/p16 knockout mouse esophageal organoids replicate1n

description:
SCPP_replicate1n
mouse organoids


title: Normal mouse esophageal organoids replicate1

description:
CS_Nprmal_replicate1
mouse organoids


title: P53 knockout/p16 knockout mouse esophageal organoids replicate1n

description:
CPP_replicate1n
mouse organoids


title: sorted germcell ChIPseq_16CFC_H3K27me3

status: Public on Aug 10 2020

city: Baltimore

first: Allan

middle: C

last: Spradling

state: MD

address: 3520 San Martin Dr.

department: Embryology

institute: Carnegie Institution/HHMI

description:
processed data file:
3state_enrichment_counts.txt

data_processing:
RNAseq: reads mapped with Hisat2.1.0, processed with Stringtie1.3.5
RNAseq: raw read counts per gene extracted with htseq0.10.0
ChIPseq: reads mapped with bowtie2.3.2
ChIPseq: MAPQ30 filtered with samtools1.6
ChIPseq: RPM normalized (additionally normalized to spike in if applicaple)
Genome_build: RNAseq: dmel6.02, Ensembl 81; ChIPseq: dmel6.02 (no spike in), dmel6.02/dpse3.0 (D. pseudoobscura spike-in), or dmel6.02/mm10 (mouse spike-in)
Supplementary_files_format_and_content: RNAseq: htseq are text files with raw readcounts, polyA_RNAseq_stringtieO.txt is txt file with TPMs for all genes/samples from stringtie

organism: Drosophila melanogaster

source_name: sorted germcell ChIPseq_FACS purified germ cell

growth_protocol: flies were grown on standard food plus wet yeast paste for 3-6 days

extract_protocol: FACS-purified Drosophila melanogaster germ cells were mixed with either FACS purified Drosophila pseudoobscura follicle cells, mouse embryonic fibroblasts, or in some cases, no spike-in. Sequences were mapped to the D.mel6.02 genome or a hybrid genome of D.mel6.02/D.pse3.0 or D.mel /M.m10 and MAPQ 30 filtered. The ratio of Spike-in to D.mel reads was used to normalize enrichment between IP samples and normalized genome wide read coverage was calculated with Bedtools and supplied as a bigWig file for each sample. Normalized read depth was also was also calculated for overlapping 5kb bins annotated with a 3 or 4 state chromatin model and supplied as a modified bed file.

tag: uas-rnai

value: white

value: otu-Gal4, mata-gal4, nos-gal4, UASz-tdTomato

tag: developmental stage

value: 3-6 day old adult

tag: tissue/cell type

value: FACS-purified 16C follicle cells

value: H3K27me3 (Cell Signaling C36B11 (#139619) Lot 14)

tag: spike-in normalization

tag: library construction

value: DNA libraries prepared with Takara Bio ThruPLEX DNA seq


title: sorted germcell ChIPseq_16CFC_In

value: Input


title: sortedGSC RNAseq_bam_vas-GFP_3

description:
processed data file:
polyA_RNAseq_stringtieO.txt
sortedGSC_3_TPM

source_name: sortedGSC RNAseq_FACS purified germ cell

extract_protocol: Total RNA prepared from whole ovaries expressing germline-specific RNAi, or from FACS-purified germline stem cells. Sequences were mapped to dmel 6.02 with Hisat2. Whole gene TPMs from Stringtie were aggregated into polyA_RNAseq_stringtieO.txt. For differential analysis, raw read counts from htseq-count were processed with DEseq2 and custom annotation, code at: github.com/ciwemb/polycomb-development

value: bam ovary

value: FACS-purified germ cells

value: polyA-enriched mRNA libraries prepared with Illumina TRUseq v2


title: sortedGSC RNAseq_bam_Vas-GFP_1

description:
processed data file:
polyA_RNAseq_stringtieO.txt
sortedGSC_1_TPM


title: sorted germcell ChIPseq_GSC_sortA_H3K27me3

description:
processed data file:
4state_enrichment_counts.txt
3state_enrichment_counts.txt

value: nos-Gal4, UASp-NLS-GFP

value: mouse embryonic fibroblast culture


title: sorted germcell ChIPseq_512CNC_wGLKD_In

value: FACS-purified 512C germ cells


title: sorted germcell ChIPseq_GSC_sortA_H3K27ac


title: sorted germcell ChIPseq_512CNC_wGLKD_H3K27me3


title: sorted germcell ChIPseq_GSC_sortA_In


title: sorted germcell ChIPseq_St5NC_wGLKD_H3K27me3

description:
processed data file:
4state_enrichment_counts.txt

value: FACS-purified 64C germ cells


title: P53 knockout/p16 knockout mouse esophageal organoids replicate1

description:
CPP_replicate1
mouse organoids

value: Mouse Esophagus


title: sorted germcell ChIPseq_St5NC_wGLKD_In


title: P53 knockout/p16 knockout mouse esophageal organoids replicate2

description:
CPP_replicate2
mouse organoids


title: sorted germcell ChIPseq_St5NC_wGLKD_Pse_In

value: Drosophila pseudoobscura follicle cells


title: sortedGSC RNAseq_bam_vas-GFP_2

description:
processed data file:
polyA_RNAseq_stringtieO.txt
sortedGSC_2_TPM


title: sorted germcell ChIPseq_St5NC_wGLKD_Pse_H3K27me3


title: PcGGLKD RNAseq_LucGLKD_3

description:
processed data file:
polyA_RNAseq_stringtieO.txt
lucGLKD_YoungOvary_3_TPM

source_name: PcGGLKD RNAseq_whole ovary

value: luciferase

value: otu-Gal4, mata-gal4, nos-gal4

value: 0-6 hour old adult, up to stage6

value: whole ovary


title: PcGGLKD RNAseq_LucGLKD_2

description:
processed data file:
polyA_RNAseq_stringtieO.txt
lucGLKD_YoungOvary_2_TPM


title: PcGGLKD RNAseq_wGLKD_3

description:
processed data file:
polyA_RNAseq_stringtieO.txt
wGLKD_Ovary_3_TPM

value: white

value: 3-6 day-old old adult, up to stage14


title: PcGGLKD RNAseq_LucGLKD_1

description:
processed data file:
polyA_RNAseq_stringtieO.txt
lucGLKD_YoungOvary_1_TPM


title: Tdp-43_sd__2

status: Public on Jul 27 2020

city: Würzburg

first: Silke

last: Appenzeller

address: Schweinfurter Str. 28

institute: University Wuerzburg

description: Gene expression data from somatodendritic compartment of cultured Tdp-43 knockdown motoneurons.

data_processing:
Quality Assessment (FASTQC version 0.10.1).
Adapter Clipping and Collapsing (inhouse script).
Alignment (Star version 2.4.0d).
Calculation of expression and differential expression (Cufflinks package version 2.2.1).
Genome_build: Mus_musculus.GRCm38.75
Supplementary_files_format_and_content: *_trimmed_Star_genes.fpkm_tracking_annotated.csv: Comma-separated text files

source_name: Primary mouse motoneuron culture

growth_protocol: Primary mouse motoneurons were cultured in microfluidic chambers as described in Saal et al. (RNA 20: 1789).

extract_protocol:
Total RNA was extracted from the somatodendritic and the axonal compartment using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems) with 10 μl elution volume.
For whole transcriptome profiling, see Briese et al. (Nucleic Acids Res, doi: 10.1093/nar/gkv1027).

tag: strain

tag: genotype/variation

value: Tdp-43 knockdown

value: Primary mouse motoneuron culture

tag: cell compartment

value: Somatodendritic


title: PcGGLKD RNAseq_wGLKD_2

description:
processed data file:
polyA_RNAseq_stringtieO.txt
wGLKD_Ovary_2_TPM


title: Tdp-43_sd__1

tag: cell type


title: Tdp-43_sd__6


title: Tdp-43_sd__3


title: Tdp-43_ax__5

description: Gene expression data from axonal compartment of cultured Tdp-43 knockdown motoneurons.

value: Axonal


title: PcGGLKD RNAseq_wGLKD_1

description:
processed data file:
polyA_RNAseq_stringtieO.txt
wGLKD_Ovary_1_TPM

value: polyA-enriched mRNA libraries prepared with Illumina TRUseq v2


title: Tdp-43_ax__6


title: Tdp-43_ax__2


title: Tdp-43_ax__1


title: GFP_sd__3

description: Gene expression data from somatodendritic compartment of cultured control motoneurons.

value: Control


title: GFP_sd__4


title: Tdp-43_ax__3


title: Tdp-43_sd__4


title: Tdp-43_sd__5


title: GFP_ax__2

description: Gene expression data from axonal compartment of cultured control motoneurons.


title: GFP_ax__1


title: GFP_sd__2


title: GFP_sd__1


title: GFP_ax__4


title: GFP_ax__3


title: 20180515_d5_WT3_20180502

status: Public on Apr 22 2020

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to mm9 using STAR
Differential analysis was performed by Deseq2
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: OT-I CD8 T cells

growth_protocol: CD8 T cells were magnetically isolated from OT-I transgenic mice and activated by co-culture with irradiated, OVA peptide-pulsed bone marrow-derived dendritic cells

extract_protocol:
RNA was harvested using Trizol reagent
A standard mRNA library preparation kit (RS-122-2101, Illumina) was used for library preparation. Single-end 75 bp sequencing was done on an Illumina NextSeq 500 at the Dana-Farber Cancer Institute

treatment_protocol: For 'RGFP966' and 'no drug' samples, OT-I T cells were treated with 10 μM of Hdac3 inhibitor RGFP966 or an equivalent volume of DMSO control, respectively. Fresh media containing 10 μM RGFP966 or DMSO control was added to the respective samples on day 3.

tag: strain background

value: OT-I transgenic

tag: hdac3 genotype

value: WT

value: CD8 T cells

tag: drug treatment

tag: day post-activation

value: Day 5


title: E10.5 CD44+ E+HE+IAC

status: Public on Apr 27 2020

city: San Francisco

first: Qin

last: Zhu

state: CA

address: 600 Minnesota Street

institute: UCSF

description: 10X scATAC-Seq with cells from dissociated mouse embryos

data_processing:
scATAC-Seq reads were aligned to the mouse mm10 reference genome using the “cellranger-atac mkfastq” command.
Peaks were called using MACS2 with the FDR cutoff of 0.10 using the following parameters:  -q 0.10 --broad --broad-cutoff 0.10).
We implemented a custom script (in perl) to quantify the reads overlapping with peaks individually for each cell. If at least half of a read overlaps with a peak, the read is considered to overlap with the peak.
We filtered the peak-barcode matrix , requiring a barcode to have at least 2000 fragments, 1000 detected peaks and at least 20 percent fragments in peak to be considered as a cell.
For each peak, we computed the fraction of cells with non-zero values, and removed peaks that were detected in fewer than 1% of all cells.
Genome_build: mm10
Supplementary_files_format_and_content: peak_by_cell_fragment_matrix.txt contains a sparse matrix where rows are peaks (with peak information in the peak_annotation.csv), columns are cells (with cell information in the cell_annotation.csv), and values are fragment counts for the given peak in the given cell. cell_annotation.csv contains a data frame with annotations (i.e. 10X barcode,  etc.) for each cell. peak_annotation.csv contains a data frame with peak name and genomic range. fragments.tsv.gz is a BED-like tabular file, where each line represents a unique ATAC-seq fragment captured by the assay.

source_name: dissociated mouse embryos

extract_protocol:
Cells were sorted into IMDM/10-20% FBS. Cells were lyzed and transposed. Using the Chromium controller (10x Genomics) and reagents from the Chromium Single Cell ATAC Reagent Kit (10x Genomics), the nuclei were partitioned into nanoliter-scale Gel Beads-in-emulsion (GEMs) where the transposed DNA of each individual nucleus was uniquely indexed with 10x barCode. DNA were purified for sequencing library preparation.
Transposed and indexed DNA were used for library preparation using the Chromium Single Cell ATAC Reagent Kit (10x Genomics) according to manufacturer’s protocol (CG000168, Rev B).

treatment_protocol: Females were superovulated by administering 5 IU of Pregnant Mare Serum Gonadotrophin and 5 IU human chorionic gonadotrophip at 48 and 0 hours prior to paring with males. Embryos were harvested at the appropriate embryonic day and cells were sorted on the same day as harvest.

value: Embryonic day 10.5

value: wild type

tag: marker

tag: tissue

value: dorsal aorta plus umbilical and vitelline arteries


title: 20180515_d5_KO2_20180502

description: 20180515_d5_KO2_20180502_IDX14_RV5607_S14

value: KO


title: 20180515_d5_WT2_20180502


title: 20180515_d0_WT2_20180502

value: Day 0 (naïve cells)


title: 20180515_d0_WT3_20180502


title: 20180515_d5_KO1_20180502

description: 20180515_d5_KO1_20180502_IDX13_RV5607_S13


title: 20180515_d5_WT1_20180502


title: 20180515_d0_WT1_20180502


title: Tdp-43_ax__4


title: 20180515_d0_KO3_20180502

description: 20180515_d0_KO3_20180502_IDX12_RV5607_S12


title: 20170928_d5-RGFP966-3_20170824

description: 20170928_d5-RGFP966-3_20170824_IDX1_RV4829_S9

value: 10 μM RGFP966


title: 20180515_d0_KO2_20180502

description: 20180515_d0_KO2_20180502_IDX11_RV5607_S11


title: 20170928_d5-RGFP966-2_20170824

description: 20170928_d5-RGFP966-2_20170824_IDX27_RV4829_S8


title: SNWT4

description: Gene expression data from sciatic nerves of wildtype mice

data_processing:
Quality Assessment (FASTQC version 0.10.1)
Adapter trimming (TrimGalore version 0.4.0)
Alignment (Star version 2.5.0a)
Calculation of expression and differential expression (Cufflinks package version 2.2.1)
Genome_build: Mus_musculus.GRCm38.75

source_name: Sciatic nerves

growth_protocol: Sciatic nerves were dissected from adult mice and directly used for RNA extraction

extract_protocol:
Total RNA was extracted using TRIReagent
mRNA-Seq Library Prep Kit V2 (Lexogen)

value: Sciatic nerves

value: wildtype


title: SNP5

description: Gene expression data from sciatic nerves of Plekhg5-/- mice


title: SNP3


title: SNWT5


title: 20170928_d5-RGFP966-1_20170824

description: 20170928_d5-RGFP966-1_20170824_IDX25_RV4829_S7


title: SNWT2


title: SNP2


title: 20180515_d5_KO3_20180502

description: 20180515_d5_KO3_20180502_IDX15_RV5607_S15


title: 20170928_d5-No_drug-3_20170824

description: 20170928_d5-No_drug-3_20170824_IDX23_RV4829_S6

value: DMSO Control


title: 20190319_OH3_Input_IDX792

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to mm9 using BWA
For peak calling MACS2 was used.
Genome_build: mm9, mm10
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

extract_protocol:
Cells were fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep kit (Rubicon Genomics). Libraries were sequenced using 75-bp reads on the Illumina platform at the Dana-Farber Cancer Institute.


title: 20190319_O8H3_Input_IDX793


title: 20170928_d5-No_drug-2_20170824

description: 20170928_d5-No_drug-2_20170824_IDX22_RV4829_S5


title: 20170928_d5-No_drug-1_20170824

description: 20170928_d5-No_drug-1_20170824_IDX21_RV4829_S4


title: 20180529_d0_WT_Input_IDX1

value: Day 0 (naïve)


title: 20180703_d5_KO_40ugRUNX3_IDX782

description: 20180703_d5_KO_40ugRUNX3_IDX782_RV5780_S14


title: 20180703_d5_WT_40ugRUNX3_IDX779

description: 20180703_d5_WT_40ugRUNX3_IDX779_RV5780_S11


title: 20171023_Day5-drug_Input_D11


title: 20180529_d0_KO_Input_IDX4


title: 20171023_Day5-drug_2_H3K27ac_C6


title: 20180529_d0_WT1_5ug_H3k27ac_IDX18

description: 20180529_d0_WT1_5ug_H3k27ac_IDX18_RV5650_S1


title: 20180529_d0_KO2_5ug_H3k27ac_IDX27

description: 20180529_d0_KO2_5ug_H3k27ac_IDX27_RV5650_S8


title: 20171023_Day5-drug_1_H3K27ac_C5


title: 20171023_Day5-no-drug_2_H3K27ac_C4


title: 20171023_Day5-no-drug_1_H3K27ac_C3


title: 20180529_d0_KO1_5ug_H3k27ac_IDX25

description: 20180529_d0_KO1_5ug_H3k27ac_IDX25_RV5650_S7


title: 20180515_d0_KO1_20180502

description: 20180515_d0_KO1_20180502_IDX10_RV5607_S10


title: 20171023_Day5-no-drug_Input_D3


title: 20190319_OH3_H3K27ac_kacyl_IDX789

description: 20190319_OH3_H3K27ac_kacyl_IDX789_RV6774_S9


title: 11A_14892_2W_PBMC

status: Public on Mar 09 2020

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq v2.20.0.422.
The quality of raw reads was assessed with FastQC v0.11.8.
Reads were mapped to the Rhesus macaque (MacaM v7) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the htseq-count algorithm.
Normalized expression (normalized read counts) was obtained with DESeq2 v1.22.1.
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: Peripheral blood mononuclear cells

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kits with DNase digest and QIAcube automation stations. RNA was quantified on NanoDrop 2000 spectrophotometer and the quality was assessed by Bioanalyzer analysis.
Set A samples: Libraries were prepared using the Illumina TruSeq mRNA stranded kit, as per manufacturer’s instructions, with 400 ng of total RNA as input. The amplified libraries were validated by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq 3000 system employing a single-end 101 cycles run at average read depths of 16 million reads/sample.
Set B samples: 10 ng of total RNA was used as input for cDNA amplification using 5’ template-switch PCR with the Clontech SMART-Seq v4 Ultra Low Input RNA kit. Amplified cDNA was fragmented and appended with dual indexed bar codes using Illumina NexteraXT DNA Library Prep kits. The amplified libraries were validated by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq 3000 system employing a single-end 101 cycles run at average read depths of 25 million reads/sample.

tag: set

value: A

tag: subject id

tag: siv genotype

value: wt

value: PBMC

tag: timepoint (weeks)

tag: infection status


title: 12A_14893_2W_PBMC


title: 13A_15226_2W_PBMC


title: 39B_15934_2W_PBMC

value: B


title: 37B_2729_2W_PBMC


title: 38B_15925_2W_PBMC


title: 20180529_d0_WT2_5ug_H3k27ac_IDX19

description: 20180529_d0_WT2_5ug_H3k27ac_IDX19_RV5650_S2

value: OT-I transgenic

value: WT

tag: chip antibody


title: 10B_2729_minus4W_PBMC

value: uninfected


title: 12B_15934_minus4W_PBMC


title: 11B_15925_minus4W_PBMC


title: 99A_7406_27W_PBMC

value: ctl


title: 98A_14954_27W_PBMC


title: 96A_2564_27W_PBMC


title: 97A_2612_27W_PBMC


title: 20190319_O8H3_H3K27ac_kacyl_IDX790

description: 20190319_O8H3_H3K27ac_kacyl_IDX790_RV6774_S10

value: CD8 T cells

value: Day 5


title: 55A_2447_27W_PBMC


title: 54A_2363_27W_PBMC


title: 95A_2522_27W_PBMC


title: Smn_m_m_plus_R2

status: Public on Jan 28 2020

description: Gene expression data from Smn-/-;SMN2 motoneurons treated with R-Roscovitine

data_processing:
Quality Assessment (FASTQC version 0.10.1)
Adapter trimming (TrimGalore version 0.4.0)
Alignment (Star version 2.5.0a)
Calculation of expression and differential expression (Cufflinks package version 2.2.1)
Genome_build: Mus_musculus.GRCm38.75
Supplementary_files_format_and_content: FPKM

growth_protocol: Motoneurons were obtained and cultured as described in Wiese et al. (Nat Protoc 5: 31-8)

extract_protocol:
Total RNA was extracted using the Nucleospin RNA kit (Macherey-Nagel)
mRNA-Seq Library Prep Kit V2 (Lexogen)

treatment_protocol: Untreated or treated with 0.5 µM R-Roscovitine

value: FVB


title: Smn_m_m_plus_R3


title: 51A_2136_27W_PBMC


title: Smn_m_m_plus_R1


title: 53A_2232_27W_PBMC


title: Smn_p_p_plus_R1

description: Gene expression data from Smn+/+;SMN2 motoneurons treated with R-Roscovitine


title: Smn_m_m_minus_R3

description: Gene expression data from untreated Smn-/-;SMN2 motoneurons


title: 52A_2146_27W_PBMC


title: Smn_p_p_plus_R3


title: Smn_m_m_minus_R2


title: Smn_p_p_plus_R2


title: Smn_p_p_minus_R3

description: Gene expression data from untreated Smn+/+;SMN2 motoneurons


title: Smn_p_p_minus_R1


title: Smn_p_p_minus_R2


title: Smn_m_m_minus_R1


title: Healthy_20

status: Public on Dec 06 2019

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: small RNAsequencing analysis

data_processing:
BCL basecall files were converted to FASTQ per sample using CASAVA v1.8.2 (Illumina) with default parameters to generate demultiplexed per sample fastq raw sequencing data files.
Per sample read quality was assessed using FastQC.
Trimming, quality filtering, mapping and raw read counting data processing steps were performed with mirPRo software (Shi J, et al, Sci Rep, 5:14617, 2015), which uses Novoalign (Li, H. & Homer, N. Brief. Bioinform. 11, 473–483, 2010) to map the reads.
Statistically significant differences in miRNA expression were determined both by DESeq2 (Love, 2014) with multiple testing adjustment. A dataset consistency step was perfomed by principal components analysis (PCA) to detect outliers. Data were renormalized after outlier removal prior to the final analysis.
Genome_build: Reads were mapped to GRCh38.87  and annotated with miRBase 21 mature database.
Supplementary_files_format_and_content: Processed miRNA expression profiling data table is provided as a supplementary file in excel workbook (.xlsx) format. It includes a single worksheet. This contains DESeq2 outputs. Column headers: FC or FoldChange (fold changes), pvalue (nominal p value), padj (adjusted pvalue by default Benjamini and Hochberg method) for all 7 comparisons presented in the publication, followed by baseMean (average normalized counts), and normalized counts for all samples.

source_name: plasma

extract_protocol:
Blood samples were collected in EDTA tubes, then, plasma samples were obtained by a single centrifugation (1000g, 15min. at room temperature). For RNA extraction from 200ul of plasma, miRCURY RNA insolation kit-Biofluids (#300112) was used following manufacturer indications with modifications that included using glycogen as carrier and a 1:50 dilution of spike in RNA.
Barcoded sequencing libraries were prepared using the TruSeq SmallRNA library kit (Illumina) with slight modifications from the default recommendations (Part # 15004197 Rev. F, February 2014). Modifications included using all RNA extracted from 200 ul of plasma, in the subnanogram range, and increasing the number of cycles in the final PCR reaction (from 12 to 15).
Libraries were quality assessed with Bioanalyzer DNA 1000 assays (Agilent). Bioanalyzer concentration estimates were used to generate an equimolar library mix. The library pool was automatically size selected (135-160bp) using 3% agarose dye free cassettes with 3% DF marker F on a Pippin Prep system with software v.6.0 (Sage Science). QIAquick (Qiagen) column purifications were performed prior and after to size selection. The library pool was quantifiedby PCR with theKAPA Library Quantification Kit following manufacturer’s instructions (Roche). The library pool was run on 4 lanes of 1x50 bp sequencing was performed on HiSeq2500 platform (Illumina) using adapted protocols for TruSeq SR cluster kit v3 (Part#15023335) following cBot™ (Part#15006165) and HiSeq2500 System (Part#15035786) user guidelines. Raw data were analysed by Real Time Analysis software v. 1.17.21.3 and Sequence Analysis Viewer software v. 1.8.20 (Illumina.).

tag: individual unique id

tag: clinical grouping

value: Healthy

tag: hcv infection status

value: HCV negative

tag: virus

value: HIV negative

tag: gender

value: female

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)

tag: library batch

tag: size selection and sequencing pool

tag: inclusion in final analysis

value: included


title: Healthy_16

description: small RNAsequencing analysis


title: Healthy_21

description: small RNAsequencing analysis

value: male


title: Healthy_6

description: small RNAsequencing analysis


title: Healthy_15

description: small RNAsequencing analysis


title: Healthy_13

description: small RNAsequencing analysis


title: Healthy_12

description: small RNAsequencing analysis


title: Healthy_1

description: small RNAsequencing analysis


title: Healthy_17

description: small RNAsequencing analysis


title: Healthy_2

description: small RNAsequencing analysis


title: Healthy_8

description: small RNAsequencing analysis


title: Healthy_10

description: small RNAsequencing analysis


title: Healthy_9

description: small RNAsequencing analysis


title: Kinetin-treated FD fibroblasts 3

status: Public on Mar 21 2019

description:
SEMatrix_kin_on_fd.txt
2343_KIN-A-FD

data_processing:
RNASeq reads were mapped against Ensembl GRCh37 (version 75) by STAR (version 2.4.2) allowing 5% mismatch
Number of reads covering splice junction was measured by STAR during alignment
Exon triplet index was built on Ensembl GRCh37 (version 75) where each triplet is a three-consecutive exons, namely exon 1, 2 and 3, according to the annotation
For each triplet, two values are measured. The first value is the average of number of reads connecting exon 1 and 2 and number of reads connecting exon 2 and 3. This value is an integer
The second value is the number of reads connecting exon 1 and 3, which is an integer as well.
Genome_build: Ensembl GRCh37 version 75
Supplementary_files_format_and_content: Fastq format for RNASeq reads; Tab-delimited txt format for splice junction counts

source_name: Human fibroblast

growth_protocol: Six different human FD fibroblast cell lines were obtained from Coriell Institute and cultured in Dulbecco's modified Eagle's medium (D-MEM, Gibco) with 10% fetal bovine serum (FBS, Sigma). Cells were counted and plated in order to achieve semi-confluence after eight days.

treatment_protocol: Twenty-four hours after plating, the medium was changed and cells were treated with kinetin or DMSO to a final concentration of 200 µM and 0.5%, respectively. DMSO was used as vehicle and the concentration of kinetin was chosen based on our previous studies, since at this concentration kinetin induces robust splicing changes.

tag: tissue

value: fibroblast

tag: genotype/variation

value: ELP1 mutation

tag: treatment

value: Kinetin treated


title: Kinetin-treated FD fibroblasts 4

description:
SEMatrix_kin_on_fd.txt
4589_KIN-A-FD


title: Kinetin-treated FD fibroblasts 6

description:
SEMatrix_kin_on_fd.txt
4899_KIN-A-FD


title: Healthy_11

description: small RNAsequencing analysis


title: Healthy_19

description: small RNAsequencing analysis


title: Healthy_4

description: small RNAsequencing analysis


title: Healthy_18

description: small RNAsequencing analysis


title: Healthy_14

description: small RNAsequencing analysis


title: Kinetin-treated FD fibroblasts 5

description:
SEMatrix_kin_on_fd.txt
4663_KIN-A-FD


title: Healthy_3

description: small RNAsequencing analysis


title: Healthy_7

description: small RNAsequencing analysis


title: Healthy_5

description: small RNAsequencing analysis


title: Kinetin-treated FD fibroblasts 2

description:
SEMatrix_kin_on_fd.txt
2341_KIN-A-FD


title: Kinetin-treated FD fibroblasts 1

description:
SEMatrix_kin_on_fd.txt
0850_KIN-A-FD


title: Untreated FD fibroblasts 6

description:
SEMatrix_kin_on_fd.txt
4899_CTRL-A-FD

value: untreated


title: Untreated FD fibroblasts 5

description:
SEMatrix_kin_on_fd.txt
4663_CTRL-A-FD


title: Untreated FD fibroblasts 4

description:
SEMatrix_kin_on_fd.txt
4589_CTRL-A-FD


title: Untreated FD fibroblasts 2

description:
SEMatrix_kin_on_fd.txt
2341_CTRL-A-FD


title: Untreated FD fibroblasts 1

description:
SEMatrix_kin_on_fd.txt
0850_CTRL-A-FD


title: Nmd_-_-_2

status: Public on Aug 21 2018

description: Gene expression data from Nmd-/- motoneurons

data_processing:
Quality Assessment (FASTQC version 0.10.1)
Adapter trimming inlcuding removal of 9 bp from the 5' end of read 1 (TrimGalore version 0.4.0 with Cutadapt version 1.8)
Alignment (Star version 2.5.0a)
Sam-file conversion (Samtools version 1.3)
Calculation of expression and differential expression (Cufflinks package version 2.2.1)
Genome_build: Mus_musculus.GRCm38.75
Supplementary_files_format_and_content: csv-files with FPKM-values

tag: strain

value: Primary mouse motoneuron culture

tag: genotype

value: Nmd-/-


title: Nmd_+_+_3

description: Gene expression data from Nmd+/+ motoneurons

value: Nmd+/+


title: Nmd_+_+_2


title: Nmd_-_-_1


title: Nmd_+_+_1


title: Nmd_-_-_3


title: 7SK_ax_4

status: Public on Mar 06 2018

description:
Sample 18
Gene expression data from axonal compartment of cultured 7SK knockdown motoneurons
GFP_ax_vs_7SK_ax_gene_exp.diff.txt

data_processing:
Quality Assessment (FASTQC version 0.10.1) for samples 1-22
Adapter Clipping and Collapsing (inhouse script) for samples 1-22
Alignment (Star version 2.4.0d) for samples 1-22
Calculation of expression and differential expression (Cufflinks package version 2.2.1) for samples 1-22
For iCLIP (samples 23-33), see König et al. (Nat Struct Mol Biol 17: 909)
Genome_build: Mus_musculus.GRCm38.75 for RNA-seq and mm9 for iCLIP

extract_protocol: For whole transcriptome profiling see Briese et al. (Nucleic Acids Res, doi: 10.1093/nar/gkv1027); for iCLIP see König et al. (Nat Struct Mol Biol 17: 909)

tag: growth protocol

value: Primary mouse motoneurons were cultured in microfluidic chambers as described in Saal et al. (RNA 20:1789).

tag: extract protocol

value: Total RNA was extracted from the somatodendritic and the axonal compartment using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems) with 10 μl elution volume.


title: 7SK_ax_3

description:
Sample 17
Gene expression data from axonal compartment of cultured 7SK knockdown motoneurons
GFP_ax_vs_7SK_ax_gene_exp.diff.txt


title: hnRNPR_ax_1

description:
Sample 9
Gene expression data from axonal compartment of cultured hnRNP R knockdown motoneurons
GFP_ax_vs_hnRNPR_ax_gene_exp.diff.txt


title: 7SK_sd_4

description:
Sample 22
Gene expression data from somatodendritic compartment of cultured 7SK knockdown motoneurons
GFP_sd_vs_7SK_sd_gene_exp.diff.txt


title: 7SK_ax_1

description:
Sample 15
Gene expression data from axonal compartment of cultured 7SK knockdown motoneurons
GFP_ax_vs_7SK_ax_gene_exp.diff.txt, GFP_sd_vs_hnRNPR_sd_gene_exp.diff.txt


title: hnRNPR_sd_3

description:
Sample 14
Gene expression data from somatodendritic compartment of cultured hnRNP R knockdown motoneurons
GFP_sd_vs_7SK_sd_gene_exp.diff.txt, GFP_sd_vs_hnRNPR_sd_gene_exp.diff.txt


title: hnRNPR_sd_1

description:
Sample 12
Gene expression data from somatodendritic compartment of cultured hnRNP R knockdown motoneurons
GFP_sd_vs_7SK_sd_gene_exp.diff.txt, GFP_sd_vs_hnRNPR_sd_gene_exp.diff.txt


title: 7SK_sd_2

description:
Sample 20
Gene expression data from somatodendritic compartment of cultured 7SK knockdown motoneurons
GFP_sd_vs_7SK_sd_gene_exp.diff.txt


title: 7SK_ax_2

description:
Sample 16
Gene expression data from axonal compartment of cultured 7SK knockdown motoneurons
GFP_ax_vs_7SK_ax_gene_exp.diff.txt


title: hnRNPR_ax_2

description:
Sample 10
Gene expression data from axonal compartment of cultured hnRNP R knockdown motoneurons
GFP_ax_vs_hnRNPR_ax_gene_exp.diff.txt


title: 7SK_sd_1

description:
Sample 19
Gene expression data from somatodendritic compartment of cultured 7SK knockdown motoneurons
GFP_sd_vs_7SK_sd_gene_exp.diff.txt


title: 7SK_sd_3

description:
Sample 21
Gene expression data from somatodendritic compartment of cultured 7SK knockdown motoneurons
GFP_sd_vs_7SK_sd_gene_exp.diff.txt


title: hnRNPR_sd_2

description:
Sample 13
Gene expression data from somatodendritic compartment of cultured hnRNP R knockdown motoneurons
GFP_sd_vs_7SK_sd_gene_exp.diff.txt, GFP_sd_vs_hnRNPR_sd_gene_exp.diff.txt


title: GFP_sd_4

description:
Sample 8
Gene expression data from somatodendritic compartment of cultured control motoneurons
GFP_sd_vs_hnRNPR_sd_gene_exp.diff.txt


title: GFP_sd_3

description:
Sample 7
Gene expression data from somatodendritic compartment of cultured control motoneurons
GFP_sd_vs_hnRNPR_sd_gene_exp.diff.txt


title: GFP_ax_4

description:
Sample 4
Gene expression data from axonal compartment of cultured control motoneurons
GFP_ax_vs_7SK_ax_gene_exp.diff.txt, GFP_ax_vs_hnRNPR_ax_gene_exp.diff.txt


title: GFP_sd_2

description:
Sample 6
Gene expression data from somatodendritic compartment of cultured control motoneurons
GFP_sd_vs_hnRNPR_sd_gene_exp.diff.txt


title: Untreated FD fibroblasts 3

description:
SEMatrix_kin_on_fd.txt
2343_CTRL-A-FD


title: GFP_ax_3

description:
Sample 3
Gene expression data from axonal compartment of cultured control motoneurons
GFP_ax_vs_7SK_ax_gene_exp.diff.txt, GFP_ax_vs_hnRNPR_ax_gene_exp.diff.txt


title: GFP_ax_2

description:
Sample 2
Gene expression data from axonal compartment of cultured control motoneurons
GFP_ax_vs_7SK_ax_gene_exp.diff.txt, GFP_ax_vs_hnRNPR_ax_gene_exp.diff.txt


title: GFP_sd_1

description:
Sample 5
Gene expression data from somatodendritic compartment of cultured control motoneurons
GFP_sd_vs_hnRNPR_sd_gene_exp.diff.txt


title: hnRNPR_ax_3

description:
Sample 11
Gene expression data from axonal compartment of cultured hnRNP R knockdown motoneurons
GFP_ax_vs_hnRNPR_ax_gene_exp.diff.txt


title: GFP_ax_1

description:
Sample 1
Gene expression data from axonal compartment of cultured control motoneurons
GFP_ax_vs_7SK_ax_gene_exp.diff.txt, GFP_ax_vs_hnRNPR_ax_gene_exp.diff.txt


title: iCLIP_IgG_NSC34

description:
Sample 33
IgG control iCLIP dataset from NSC34 cells
iCLIP_IgG_NSC34_cDNAcounts.txt

source_name: NSC34 cells

value: NSC34 cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal calf serum and 1% penicillin/streptavidin.

value: iCLIP


title: iCLIP_hnRNPR_Ab2_NSC34_nuclear

description:
Sample 32
hnRNP R iCLIP dataset from nuclear fraction of cultured NSC34 cells
iCLIP_hnRNPR_Ab2_NSC34_nuclear_cDNAcounts.txt


title: iCLIP_hnRNPR_Ab2_NSC34_cytoplasmic

description:
Sample 31
hnRNP R iCLIP dataset from cytoplasmic fraction of cultured NSC34 cells
iCLIP_hnRNPR_Ab2_NSC34_cytoplasmic_cDNAcounts.txt


title: iCLIP_hnRNPR_Ab1_NSC34_rep2

description:
Sample 30
hnRNP R iCLIP dataset from NSC34 cells
iCLIP_hnRNPR_Ab1_NSC34_rep2_cDNAcounts.txt


title: iCLIP_hnRNPR_Ab1_NSC34_nuclear

description:
Sample 28
hnRNP R iCLIP dataset from nuclear fraction of cultured NSC34 cells
iCLIP_hnRNPR_Ab1_NSC34_nuclear_cDNAcounts.txt


title: iCLIP_hnRNPR_Ab1_NSC34_rep1

description:
Sample 29
hnRNP R iCLIP dataset from NSC34 cells
iCLIP_hnRNPR_Ab1_NSC34_rep1_cDNAcounts.txt


title: iCLIP_hnRNPR_Ab1_NSC34_cytoplasmic

description:
Sample 27
hnRNP R iCLIP dataset from cytoplasmic fraction of cultured NSC34 cells
iCLIP_hnRNPR_Ab1_NSC34_cytoplasmic_cDNAcounts.txt


title: iCLIP_hnRNPR_Ab1_motoneuron_rep2

description:
Sample 26
hnRNP R iCLIP dataset from wildtype motoneurons
iCLIP_hnRNPR_Ab1_motoneuron_rep2_cDNAcounts.txt

value: Motoneurons were cultured in neurobasal medium supplemented with B27 (1:50, Gibco), 2% heat-inactivated horse serum (Linaris), 500 μM Glutamax (Invitrogen) and 5 ng/ml BDNF. Medium was replaced 24 h after plating and then every second day.


title: iCLIP_hnRNPR_Ab1_motoneuron_nuclear

description:
Sample 24
hnRNP R iCLIP dataset from nuclear fraction of cultured wildtype motoneurons
iCLIP_hnRNPR_Ab1_motoneuron_nuclear_cDNAcounts.txt


title: HiC_ncx_CN_2

status: Public on Oct 18 2017

city: Montpellier

first: Boyan

last: Bonev

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics - CNRS

data_processing:
Library strategy: HiC
Hi-C data was processed using the Cwalks pipeline (http://compgenomics.weizmann.ac.il/tanay/?page_id=690). In brief, raw sequencing reads were mapped independently to the mm10 reference genome using Bowtie2 in local alignment mode. The uniquely mapped (MAPQ > 36) reads were translated into a pair of fragment-ends (fends) by associating each read with its downstream fend. PCR duplicates and reads mapping to the same restriction fragment were excluded.
supplementary_files_format_and_content:Each processed file represent pairwise information of the observed genome contacts and can be further analyzed using the "Shaman" pipeline (https://bitbucket.org/tanaylab/shaman).
assembly: mm10

source_name: CN purified in-vivo from E14.5 neocortex

growth_protocol: To purify in-vivo cortical progenitors and differentiating neurons, heterozygous parents (Hes5-GFP+/- and Dcx-mRFP+/-) were bred, at E14.5 embryos were examined using whole mount fluorescence and the brains of double-postive (GFP+/RFP+) littermates were dissected. The somatosensory neocortex was placed in DMEM/F-12 media, mechanically dissociated using P1000 tip and further incubated for 2 min with StemPro Accutase at 37C. 3x volume of DMEM/F12 was then added, cells were transferred to cold 1xPBS + 2% FBS, and immediately processed for FACS. Each biological replicate represents a separate mating with 1-3 pooled littermates.

extract_protocol:
HiC and library preparation was carried out using the in-situ method as described previously (Rao et. al., 2014) with minor modifications. In order to maximize library complexity, FACS-purified samples were split into batches of 1x10^6 cells and processed separately. In brief, cells were digested overnight at 37C using 500U of DpnII. After biotin filling, proximity ligation was carried out for 4 hours at 18C with 2000U T4 DNA Ligase. After reverse-crosslinking, DNA was purified using ethanol precipitation and sheared to 300-400bp fragments using Covaris S220 sonicator.
Ligation fragments containing biotin were immobilized on MyOne Streptavidin T1 beads (ThermoFished Cat.N: 65602), end-repaired and a-tailed as described. NEXTflex adaptors (Bioo Scientific, Cat.N: 514101) were then ligated and fragments were PCR amplified using KAPA HiFi Library Ampification Kit (Kapa Biosystems, Cat.N: KK2620) for 6-8 cycles. DNA was then double-size selected using AMPure XP beads (Agencourt, Cat.N: A63881) in order to isolate fragments between 300 and 800bp.

value: cortical neurons purified in-vivo from E14.5 neocortex

tag: strain/genotype

value: C57BL/6J Hes5-GFP+/- dcx-mRFP+/-

tag: sorting

value: GFP-/mRFP+


title: HiC_ncx_CN_3


title: HiC_ES_2

source_name: embryonic stem cells (ES)

growth_protocol: E14Tg2a, Oct4-GFP and Sox1-GFP feeder-free or Tau-GFP (grown on irradiated CF-1 MEF feeders (Tebu-Bio, Cat.N: GSC-6001G)) cell lines were maintained as described in (Gaspard et. al., 2009). In brief, cells were cultured in DMEM (ThermoFished, Cat.N:21969-035), suppelemented with 15% FBS (ES-qualified, ThermoFished, Cat.N:16141-079) 1,000 U ml of LIF (Millipore, Cat.N: ESG1106), 0.1 mM of non-essential amino acids (ThermoFished, Cat.N: 11140-035), 1 mM of glutamax (ThermoFisher, Cat.N: 35050-038), 50U of penicillin and streptomycin (ThermoFirsher, Cat.N: 15070-063) and 0.1 mM of 2-mercaptoethanol (ThermoFisher, Cat.N: 31350-010). Media was changed every day and cells were passaged every two days using StemPro Accutase (ThermoFisher, Cat.N: A11105-01).

value: embryonic stem cells (ES)


title: HiC_ncx_CN_4


title: HiC_ncx_NPC_3

source_name: NPC purified in-vivo from E14.5 neocortex

value: neural progenitor cells purified in-vivo from E14.5 neocortex

value: GFP+/mRFP-


title: HiC_ES_4


title: HiC_ncx_NPC_2


title: HiC_ES_3


title: HiC_ncx_CN_1


title: iCLIP_hnRNPR_Ab1_motoneuron_rep1

description:
Sample 25
hnRNP R iCLIP dataset from wildtype motoneurons
iCLIP_hnRNPR_Ab1_motoneuron_rep1_cDNAcounts.txt


title: HiC_ncx_NPC_4


title: iCLIP_hnRNPR_Ab1_motoneuron_cytoplasmic

description:
Sample 23
hnRNP R iCLIP dataset from cytoplasmic fraction of cultured wildtype motoneurons
iCLIP_hnRNPR_Ab1_motoneuron_cytoplasmic_cDNAcounts.txt


title: HiC_ncx_NPC_1


title: HiC_ES_1

extract_protocol:
HiC and library preparation was carried out using the in-situ method as described previously (Rao et. al., 2014) with minor modifications. In order to maximize library complexity, FACS-purified samples were split into batches of 1x10^6 cells and processed separately. In brief, cells were digested overnight at 37C using 500U of DpnII. After biotin filling, proximity ligation was carried out for 4 hours at 18C with 2000U T4 DNA Ligase. After reverse-crosslinking, DNA was purified using ethanol precipitation and sheared to 300-400bp fragments using Covaris S220 sonicator.
Ligation fragments containing biotin were immobilized on MyOne Streptavidin T1 beads (ThermoFished Cat.N: 65602), end-repaired and a-tailed as described (Rao et al., 2014). NEXTflex adaptors (Bioo Scientific, Cat.N: 514101) were then ligated and fragments were PCR amplified using KAPA HiFi Library Ampification Kit (Kapa Biosystems, Cat.N: KK2620) for 6-8 cycles. DNA was then double-size selected using AMPure XP beads (Agencourt, Cat.N: A63881) in order to isolate fragments between 300 and 800bp.


title: 35S-STKR1-2 dark Rep2

status: Public on Oct 06 2017

type: RNA

city: Erlangen

first: Weber

last: Simone

state: Bavaria

address: Ulmenweg 18

department: Medicine

description: Gene expression after 6h of extended night

scan_protocol: conducted by OakLab Gmbh, Hennigsdorf, Germany, Agilent Scanner G2505C

data_processing: txt. Files derived from feature extraction were imported into Genespring GX 12.5 (Silicon Genetics). Data were log2 transformed followed by normalization to the 75th percentile and adjusted to the median of all samples. Subsequently entities present in all replicates in at least one conditions were selected by filtering and subjected to an One-Way-ANOVA test (p-value </= 0.05) corrected by Bejamini-Hochberg-FDR) against all conditions. Differentially expressed entities were determined by selecting entities that were changed at least 2-fold change in their expression level (p-Value </= 0.05) by means of Volcano Plots.

organism: Arabidopsis thaliana

source_name: 35S-STKR1 line 2, 6h dark, Rep2

label_protocol: conducted by OakLab Gmbh, Hennigsdorf, Germany, Cy3-labelled cRNA was synthezied with Agilent Quick Amp labelling kit according manufacture's instruction

growth_protocol: Arabidopsis plants were grown in a phytochamber under short day conditions  with 8h light and ca. 100µE m-2 s-1  at 22°C and 16h darkness at 18-19°C. Relative humidty was adjusted to 60%.

extract_protocol: Qiagen RNAeasy Kit according to the manufacturer's protocol

treatment_protocol: Samples were either taken after 6 h of illumination (light) or after an extended dark period for 6 h (dark)

value: transgenic line STKR2

value: leaf

tag: line

value: 6h dark


title: 35S-STKR1-2 light Rep3

description: Gene expression 6h after begin of illumination

hyb_protocol: conducted by OakLab Gmbh, Hennigsdorf, Germany,

source_name: 35S-STKR1 line 2, 6h light, Rep3

value: 6h light


title: 35S-STKR1-5 dark Rep1

source_name: 35S-STKR1 line 5, 6h dark,  Rep1

value: transgenic line STKR5


title: 35S-STKR1-5 dark Rep2

source_name: 35S-STKR1 line 5, 6h dark,  Rep2


title: 35S-STKR1-2 dark Rep1

source_name: 35S-STKR1 line 2, 6h dark, Rep1


title: 35S-STKR1-1 light Rep3

source_name: 35S-STKR1 line 1, 6h light, Rep3

value: transgenic line STKR1


title: 35S-STKR1-2 dark Rep3

source_name: 35S-STKR1 line 2, 6h dark, Rep3


title: 35S-STKR1-2 light Rep1

source_name: 35S-STKR1 line 2, 6h light, Rep1


title: 35S-STKR1-1 dark Rep3

source_name: 35S-STKR1 line 1, 6h dark ,Rep3


title: 35S-STKR1-5 light Rep2

source_name: 35S-STKR1 line 5, 6h light, Rep2


title: 35S-STKR1-5 light Rep3

source_name: 35S-STKR1 line 5, 6h light, Rep3


title: 35S-STKR1-2 light Rep2

source_name: 35S-STKR1 line 2, 6h light, Rep2


title: 35S-STKR1-5 dark Rep3

source_name: 35S-STKR1 line 5, 6h dark,  Rep3


title: 35S-STKR1-5 light Rep1

source_name: 35S-STKR1 line 5, 6h light, Rep1


title: 35S-STKR1-1 light Rep2

source_name: 35S-STKR1 line 1, 6h light, Rep2


title: 35S-STKR1-1 dark Rep2

source_name: 35S-STKR1 line 1, 6h dark ,Rep2


title: Col-0 dark Rep3

source_name: Col-0, 6h dark, Rep3

value: wild-type


title: Col-0 dark Rep2

source_name: Col-0, 6h dark, Rep2


title: Col-0 light Rep3

source_name: Col-0, 6h light, Rep3


title: 35S-STKR1-1 light Rep1

source_name: 35S-STKR1 line 1, 6h light, Rep1


title: 35S-STKR1-1 dark Rep1

source_name: 35S-STKR1 line 1, 6h dark ,Rep1


title: ID-003046_bystanders

status: Public on Sep 14 2016

data_processing:
Illumina adapters and SMARTSeq2 PCR primer (5'-AAGCAGTGGTATCAACGCAGAGT-3') were removed using cutadapt (v1.3) (Martin et al. 2011).
Reads below a phred score of 20 were trimmed using the program fastq_quality_trimmer from the FASTX toolkit (v 0.0.13).
After quality trimming and adapter clipping unmatched paired end reads were removed using inhouse scripts.
Trimmed reads were mapped to the mouse genome reference sequence (GRCm38.p3) and 92 ERCC spike-ins sequences.
Alignment was performed using Bowtie2 (v 2.2.4) (Langmead and Salzberg, 2012) and Tophat (v 2.0.13) (Trapnell et al., 2009) with default settings. The incorrectly annotated transcript ENSMUSG0000092329 was removed from the mouse annotation file.
Read counts of each gene were determined using the HTSeq program (Anders et al., 2015).
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: text file containing raw read counts

source_name: Bone-marrow derived macrophages

growth_protocol: Bone marrow derived MΦs were obtained by isolation and differentiation of the marrow of the hind-leg bones of 8-12 week old C57/BL6 wild-type mice (Janvier labs). Briefly, a bone marrow suspension in X-Vivo 15 medium (Lonza), supplemented with 10 % fetal bovine serum (FBS superior, Biochrom) and 10 % L929 conditioned DMEM medium (herein called ‘differentiation medium’) was seeded into 6-well plates at a density of 106 leukocyte cells in 2 ml per well. Cells were incubated at 37 °C in a CO2-incubator with humidified atmosphere up to 7 days. At day 3 the cultures were supplemented with 0.3 volumes of fresh differentiation medium. At day 7, cells were harvested and seeded into 6 well tissue culture plates at a density of 106 cells per well in a fresh 2 mL differentiation medium.

extract_protocol:
Single-cell libraries were prepared as reported in Smartseq2 protocol (Picelli et al., 2013; Picelli et al., 2014) with some technical adaptation: 1µL of ERCC spike-Mix 1 (Life Technologies) diluted at 1:106 in RNAse-free water was added after cell sorting to the lysis buffer; template-switching oligo (TSO) was modified to add isomeric nucleotide at the 5’end to minimize background cDNA synthesis as previously described (Kapteyn et al., 2010) (5’-(iso-dC)(iso-dG)(iso-dC)AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’, Eurogentec); after first strand synthesis primer-dimers were removed using 11 µL of Ampure XP beads (Beckman Coulter). After the cDNA amplification, libraries were quantified using Qubit Hs Assay (Life Technologies) and quality of libraries were checked using Bioanalyser (Agilent)
Using the modified protocol described in (Patel et al., 2014), 1 ng of cDNA was subjected to tagmentation-based protocol (Nextera XT, Illumina) using ¼ of the recommended volumes, 10 min for tagmentation at 55°C and 1 min extension time during PCR. After PCR and cDNA purification, cDNA was purified and resuspended in 15 µL of elution buffer (EB) (Qiagen). Finally, libraries were pooled (16 libraries for Miseq sequencing and sequencing was performed in paired-end mode for 2 x 75 cycles using Illumina's MiSeq.

treatment_protocol: S. Typhimurium SL1344 strain harboring the pFCcGi plasmid (Figueira et al., 2013) was used for Fluorescence Dilution (FD) (Helaine et al., 2014). The strain was cultured for 16 h at 37°C in a minimum medium MgMES supplemented with 0.2% arabinose and 50 µg/mL ampicillin. Before infection, 180 µL of bacteria culture were opsonized 20 min at RT by supplementing 20 µL of mouse serum and 80 µL of differentiation medium.

tag: group

value: Bystanders

tag: age

value: 8-12 week old


title: H01N1_shCCAR2

status: Public on Feb 01 2017

first: Matthew

last: Ramsey

address: 77 Ave Louis Pasteur, HIM 668

department: Dermatology

institute: Brigham and Women's Hospital

hyb_protocol: Total RNA was hybridized to Illumina Human HT-12 BeadChip arrays using standard protocols

scan_protocol: Chips were scanned with Illumina BeadArray Reader

data_processing: The data were normalised using quantile normalization with lumi in R

label: biotin

source_name: tumor-derived cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit

growth_protocol: SCC-13 and SCC-15 cells were grown in GIBCO Keratinocyte serum free media with 12.5 μg Bovine Pituitary Extract, 0.2 ng/ml Epidermal Growth Factor, and 0,4mM Ca2+.  H01N1 cells were grown in RPMI, 10% Fetal Calf Serum

extract_protocol: RNA was extracted from cells using Qiagen RNeasy Kit according to manufacturer’s instructions.  Quality control was performed with Agilent Bioanalyser.

treatment_protocol: cells were incubated for 6 hours with media containing lentiviral shRNA.  Cells were then re-fed with appropriate culture media and harvested 48 hours after start of infection

tag: tumor type

value: Oral Squamous Cell Carcinoma


title: SCC-13_pLKO

value: Epidermal Squamous Cell Carcinoma


title: SCC-15_pLKO


title: SCC-13_shCCAR2


title: H01N1_pLKO


title: ID-003045_bystanders


title: ID-003039_bystanders


title: SCC-15_shCCAR2


title: Col-0 light Rep2

source_name: Col-0, 6h light, Rep2


title: ID-003044_bystanders


title: ID-003037_bystanders


title: Col-0 dark Rep1

source_name: Col-0, 6h dark, Rep1


title: ID-003036_bystanders


title: ID-003047_bystanders


title: ID-003042_bystanders


title: ID-003049_bystanders


title: ID-003050_bystanders


title: ID-003043_bystanders


title: ID-003048_bystanders


title: Col-0 light Rep1

source_name: Col-0, 6h light, Rep1


title: ID-003041_bystanders


title: ID-003038_bystanders


title: ID-002949_NNI

value: Naive Macrophage


title: ID-003035_bystanders


title: ID-002945_NNI


title: ID-002948_NNI


title: ID-002946_NNI


title: ID-002950_NNI


title: ID-002947_NNI


title: ID-002944_NNI


title: ID-002943_NNI


title: ID-002932_MGB

value: Macrophage with growing bacteria


title: ID-002927_MGB


title: ID-002937_NNI


title: ID-002941_NNI


title: ID-002934_MGB


title: ID-002924_MGB


title: ID-002929_MGB


title: ID-002935_MGB


title: ID-002940_NNI


title: ID-002931_MGB


title: ID-002926_MGB


title: ID-002925_MGB


title: ID-002928_MGB


title: ID-002939_NNI


title: ID-002923_MGB


title: ID-002920_MNGB

value: Macrophage with non growing bacteria


title: ID-002921_MGB


title: ID-002922_MGB


title: ID-002919_MNGB


title: ID-002915_MNGB


title: ID-002918_MNGB


title: ID-002917_MNGB


title: ID-002916_MNGB


title: ID-002936_NNI


title: ID-002914_MNGB


title: ID-002938_NNI


title: ID-002913_MNGB


title: ID-002912_MNGB


title: ID-002911_MNGB


title: ID-002910_MNGB


title: ID-002908_MNGB


title: ID-002906_MNGB


title: ID-002905_MNGB


title: ID-002942_NNI


title: ID-002909_MNGB


title: ID-002907_MNGB


title: 10pg_3

status: Public on Oct 13 2015

description:
Gene expression data from 10 pg total RNA
Sample 22

data_processing:
Quality Assessment (FASTQC version 0.10.1)
Adapter Clipping and Collapsing (inhouse script)
Alignment (Star version 2.4.0d)
Calculation of expression and differential expression (Cufflinks package version 2.2.1)
Genome_build: Mus_musculus.GRCm38.75
Supplementary_files_format_and_content: tab-delimited csv files include FPKM values for each Sample

source_name: Mouse embryonic day 14 spinal cords

extract_protocol:
Total RNA was extracted from mouse embryonic day 14 spinal cords using the RNeasy Mini Kit (Qiagen). DNA was removed with the TURBO DNA-free kit (Ambion)
cDNAs were first amplified using a double-random priming strategy followed by library construction with the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB). Briefly, total RNAs was reverse-transcribed with an oligonucleotide used previously for whole genome amplification [multiple annealing and looping-based amplification cycles (MALBAC)] containing a 3' random octamer and a 5' adapter sequence. The same oligonucleotide was used for one round of second strand synthesis generating cDNA fragments that harbor the adapter sequence in a reverse-complementary manner at both ends. These fragments are then amplified by PCR using adapter oligonucleotides to produce sufficient cDNA amounts for generating high-throughput sequencing libraries.

tag: cell type

value: embryonic day 14 spinal cords


title: ID-002930_MGB


title: 10pg_2

description:
Gene expression data from 10 pg total RNA
Sample 21


title: 10pg_1

description:
Gene expression data from 10 pg total RNA
Sample 20


title: sd_3

description:
Sample 40
Gene expression data from somatodendritic compartment of cultured wild-type motoneurons

data_processing:
Quality Assessment (FASTQC version 0.10.1)
Adapter Clipping and Collapsing (inhouse script) for samples 1-34
Alignment (Star version 2.4.0d)
Calculation of expression and differential expression (Cufflinks package version 2.2.1)
Genome_build: Mus_musculus.GRCm38.75
Supplementary_files_format_and_content: tab-delimited csv files include FPKM values for each Sample

source_name: Primary mouse motoneuron culture

growth_protocol: Spinal cords were isolated from E12.5 CD-1 mouse embryos and motoneurons derived from them were cultured as previously described (Wiese et al. 2010). Briefly, lumbar spinal cord tissues were dissected and motoneurons enriched using p75NTR antibody panning. Microfluidic chambers (Xona Microfluidics, SND 150) were precoated with polyornithine and laminin-111 (Life Technologies) and 1,000,000 motoneurons were directly plated in the somatodendritic main channel of a microfluidic chamber. Motoneurons were grown in neurobasal medium (Invitrogen) containing 500 µM GlutaMAX (Invitrogen), 2% horse serum (Linaris), 2% B27 supplement (Invitrogen) for 7 days at 37°C and 5% CO2. CNTF (5 ng/ml) was applied to both the somatodendritic and the axonal compartment. To induce axon growth through the microchannels of the chamber BDNF (20 ng/ml) was added to the axonal compartment. Culture medium was exchanged on day 1 and then every second day.

extract_protocol:
Total RNA was extracted from the somatodendritic and the axonal compartment using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems) with 10 μl elution volume.
For samples 1-34 and 38-43 cDNAs were first amplified using a double-random priming strategy followed by library construction with the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB). Briefly, total RNAs was reverse-transcribed with an oligonucleotide used previously for whole genome amplification [multiple annealing and looping-based amplification cycles (MALBAC)] containing a 3' random octamer and a 5' adapter sequence. The same oligonucleotide was used for one round of second strand synthesis generating cDNA fragments that harbor the adapter sequence in a reverse-complementary manner at both ends. These fragments were then amplified by PCR using adapter oligonucleotides to produce sufficient cDNA amounts for generating high-throughput sequencing libraries. For samples 35-37 RNAseq libraries were generated with the NEBNext Ultra RNA Library Kit for Illumina (NEB) with omission of the mRNA isolation step.

value: spinal cord

value: somatodendritic compartment of cultured wild-type motor neurons

tag: developmental stage


title: sd_2

description:
Sample 39
Gene expression data from somatodendritic compartment of cultured wild-type motoneurons


title: sd_dil_1

description:
Sample 41
Gene expression data from somatodendritic compartment of cultured wild-type motoneurons; total RNA was diluted 1:2000


title: 50pg_3

description:
Gene expression data from 50 pg total RNA
Sample 19


title: sd_dil_2

description:
Sample 42
Gene expression data from somatodendritic compartment of cultured wild-type motoneurons; total RNA was diluted 1:2000


title: sd_dil_3

description:
Sample 43
Gene expression data from somatodendritic compartment of cultured wild-type motoneurons; total RNA was diluted 1:2000


title: 50pg_2

description:
Gene expression data from 50 pg total RNA
Sample 18


title: 500pg_3

description:
Gene expression data from 500 pg total RNA
Sample 16


title: 500pg_2

description:
Gene expression data from 500 pg total RNA
Sample 15


title: 50pg_1

description:
Gene expression data from 50 pg total RNA
Sample 17


title: NEB_5ng_HBRR_3

description:
Gene expression data from 5 ng total RNA
Sample 37

data_processing:
Quality Assessment (FASTQC version 0.10.1)
Adapter Clipping and Collapsing (inhouse script) for samples 1-34
Alignment (Star version 2.4.0d)
Calculation of expression and differential expression (Cufflinks package version 2.2.1)
Genome_build: Mus_musculus.GRCm38.75, or Homo_sapiens.GRCh37.75
Supplementary_files_format_and_content: tab-delimited csv files include FPKM values for each Sample

source_name: human brain reference RNA (HBRR) with ERCC control RNAs

extract_protocol: For samples 1-34 cDNAs were first amplified using a double-random priming strategy followed by library construction with the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB). Briefly, total RNAs was reverse-transcribed with an oligonucleotide used previously for whole genome amplification [multiple annealing and looping-based amplification cycles (MALBAC)] containing a 3' random octamer and a 5' adapter sequence. The same oligonucleotide was used for one round of second strand synthesis generating cDNA fragments that harbor the adapter sequence in a reverse-complementary manner at both ends. These fragments were then amplified by PCR using adapter oligonucleotides to produce sufficient cDNA amounts for generating high-throughput sequencing libraries. For samples 35-37 RNAseq libraries were generated with the NEBNext Ultra RNA Library Kit for Illumina (NEB) with omission of the mRNA isolation step.

tag: tissue type

value: brain


title: NEB_5ng_HBRR_2

description:
Gene expression data from 5 ng total RNA
Sample 36


title: NEB_5ng_HBRR_1

description:
Gene expression data from 5 ng total RNA
Sample 35


title: 10pg_HBRR_3

description:
Gene expression data from 10 pg total RNA
Sample 34


title: 500pg_1

description:
Gene expression data from 500 pg total RNA
Sample 14


title: 5ng_3

description:
Gene expression data from 5 ng total RNA
Sample 13


title: sd_1

description:
Sample 38
Gene expression data from somatodendritic compartment of cultured wild-type motoneurons


title: 10pg_HBRR_2

description:
Gene expression data from 10 pg total RNA
Sample 33


title: 10pg_HBRR_1

description:
Gene expression data from 10 pg total RNA
Sample 32


title: 5ng_1

description:
Gene expression data from 5 ng total RNA
Sample 11


title: wt_zk_5

description:
Gene expression data from somatodendritic compartment of cultured wild-type motoneurons
Sample 10

extract_protocol:
Total RNA was extracted from the somatodendritic and the axonal compartment using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems) with 10 μl elution volume.
cDNAs were first amplified using a double-random priming strategy followed by library construction with the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB). Briefly, total RNAs was reverse-transcribed with an oligonucleotide used previously for whole genome amplification [multiple annealing and looping-based amplification cycles (MALBAC)] containing a 3' random octamer and a 5' adapter sequence. The same oligonucleotide was used for one round of second strand synthesis generating cDNA fragments that harbor the adapter sequence in a reverse-complementary manner at both ends. These fragments are then amplified by PCR using adapter oligonucleotides to produce sufficient cDNA amounts for generating high-throughput sequencing libraries.


title: 5ng_2

description:
Gene expression data from 5 ng total RNA
Sample 12


title: 50pg_HBRR_2

description:
Gene expression data from 50 pg total RNA
Sample 30


title: 50pg_HBRR_3

description:
Gene expression data from 50 pg total RNA
Sample 31


title: wt_zk_2

description:
Gene expression data from somatodendritic compartment of cultured wild-type motoneurons
Sample 7


title: wt_zk_3

description:
Gene expression data from somatodendritic compartment of cultured wild-type motoneurons
Sample 8


title: wt_zk_4

description:
Gene expression data from somatodendritic compartment of cultured wild-type motoneurons
Sample 9


title: wt_zk_1

description:
Gene expression data from somatodendritic compartment of cultured wild-type motoneurons
Sample 6


title: 50pg_HBRR_1

description:
Gene expression data from 50 pg total RNA
Sample 29


title: 500pg_HBRR_3

description:
Gene expression data from 500 pg total RNA
Sample 28


title: 500pg_HBRR_1

description:
Gene expression data from 500 pg total RNA
Sample 26


title: 5ng_HBRR_2

description:
Gene expression data from 5 ng total RNA
Sample 24


title: 5ng_HBRR_3

description:
Gene expression data from 5 ng total RNA
Sample 25


title: wt_ax_4

description:
Gene expression data from axonal compartment of cultured wild-type motoneurons
Sample 4


title: 500pg_HBRR_2

description:
Gene expression data from 500 pg total RNA
Sample 27


title: wt_ax_2

description:
Gene expression data from axonal compartment of cultured wild-type motoneurons
Sample 2


title: wt_ax_1

description:
Gene expression data from axonal compartment of cultured wild-type motoneurons
Sample 1


title: 5ng_HBRR_1

description:
Gene expression data from 5 ng total RNA
Sample 23


title: wt_ax_3

description:
Gene expression data from axonal compartment of cultured wild-type motoneurons
Sample 3


title: wt_ax_5

description:
Gene expression data from axonal compartment of cultured wild-type motoneurons
Sample 5


title: Col-0_4h_rep.1

status: Public on Oct 01 2015

description: Gene expression 4h after watering with ethanol (sampling time 12.30)

hyb_protocol: following fragmentation, 1.65 µg of Cy3-labeled cRNA were hybridisied for 17h at 65°C on 4x44K Agilent Arabidopsis_v4 arrays. Arrays were washed according to the protocol (One-Color Microarray-based gene expression analysis v.5.5)

scan_protocol: Microarrays were scanned using Agilent G2565B Microarray Scanner. Data were extracted using Feature Extraction Version: FE Version 9.5.3.1 (Agilent Technologies Germany). Data extraction using protocol GE1_v5_95_Feb07

data_processing: txt. Files derived from feature extraction were imported into Genespring GX 12.5 (Silicon Genetics). Data were log2 transformed followed by normalization to the 75th percentile and adjusted to the median of all samples. Subsequently entities present in all replicates in at least one conditions were selected by filtering and subjected to an One-Way-ANOVA test (p-value </= 0.05) corrected by Bejamini-Hochberg-FDR). Entities differentially expressed mean an at least 2-fold change in expression level in all transgenic lines compared to wild-type Col-0 plants were further analysed.

source_name: wild-type Col-0, 4h after ethanol watering, replicate 1

label_protocol: Cy3-labeled cRNA were prepared according to the agilent protocol from 500ng total RNA (One-Color Microarray-based gene expression analysis v.5.5)

extract_protocol: RNA Extraktion nach Logemann et al (1987)

treatment_protocol: each plant was watered with 10ml 1% ethanol to induce expression of the transgene (xopB)

value: leaf


title: #12_4h_rep.2

source_name: EtOH::xopB #12, 4h after ethanol watering, replicate 2

value: transgenic line


title: #12_4h_rep.1

source_name: EtOH::xopB #12, 4h after ethanol watering, replicate 1


title: #10_4h_rep.1

source_name: EtOH::xopB #10, 4h after ethanol watering, replicate 1


title: Col-0_4h_rep.2

source_name: wild-type Col-0, 4h after ethanol watering, replicate 2


title: Col-0_4h_rep.3

source_name: wild-type Col-0, 4h after ethanol watering, replicate 3


title: Non-malignant_8

status: Public on Apr 02 2015

city: Kalyani

first: Sharmila

last: Sengupta

state: West Bengal

address: P.O.: N.S.S., Kalyani 741251 West Bengal, INDIA

country: India

institute: National Institute of Biomedical Genomics

description:
Replicate1
SAMPLE 33

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using limma package in Bioconductor

source_name: Histologically normal cervical tissues

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit for Illumina arrays

extract_protocol: RNA was extracted with  QIAGEN RNeasy mini kit followed by DNase I treatment and clean-up using QIAGEN Rneasy mini kit according to the manufacturer's protocol provided for frozen tissues stored in RNA Later . RNA quality was assesed using Agilent Bioanalyser and quantified using Nanodrop 8000.

tag: hpv status

value: HPV16 Positive

tag: age (years)

value: Cervix


title: #12_4h_rep.3

source_name: EtOH::xopB #12, 4h after ethanol watering, replicate 3

tag: tissue


title: #27_4h_rep.1

source_name: EtOH::xopB #27, 4h after ethanol watering, replicate 1


title: #10_4h_rep.2

source_name: EtOH::xopB #10, 4h after ethanol watering, replicate 2


title: #27_4h_rep.2

source_name: EtOH::xopB #27, 4h after ethanol watering, replicate 2


title: Low HOTAIR CaCx_17

description:
Replicate1
SAMPLE 41

source_name: Cervical cancer Tissue (SCC)


title: HPV Negative Control_8

description:
Replicate1
SAMPLE 29

value: HPV Negative


title: Low HOTAIR CaCx_18

description:
Replicate1
SAMPLE 42


title: Non-malignant_10

description:
Replicate1
SAMPLE 38

value: HPV Positive


title: HPV Negative Control_10

description:
Replicate1
SAMPLE 35


title: Low HOTAIR CaCx_14

description:
Replicate1
SAMPLE 26


title: HPV Negative Control_9

description:
Replicate1
SAMPLE 34


title: HPV Negative Control_11

description:
Replicate1
SAMPLE 37


title: Low HOTAIR CaCx_15

description:
Replicate1
SAMPLE 27


title: Non-malignant_11

description:
Replicate1
SAMPLE 39


title: Non-malignant_9

description:
Replicate1
SAMPLE 36


title: Low HOTAIR CaCx_16

description:
Replicate1
SAMPLE 40


title: Non-malignant_7

description:
Replicate1
SAMPLE 32


title: Low HOTAIR CaCx_13

description:
Replicate1
SAMPLE 25


title: Low HOTAIR CaCx_12

description:
Replicate1
SAMPLE 24


title: HPV Negative Control_7

description:
Replicate1
SAMPLE 28


title: Non-malignant_5

description:
Replicate1
SAMPLE 30


title: Non-malignant_6

description:
Replicate1
SAMPLE 31


title: Low HOTAIR CaCx_11

description:
Replicate1
SAMPLE 23


title: Non-malignant_4

description:
Replicate1
SAMPLE 15


title: Low HOTAIR CaCx_10

description:
Replicate1
SAMPLE 22


title: HPV Negative Control_5

description:
Replicate1
SAMPLE 16


title: HPV Negative Control_6

description:
Replicate1
SAMPLE 17


title: HPV Negative Control_3

description:
Replicate1
SAMPLE 7


title: Low HOTAIR CaCx_6

description:
Replicate1
SAMPLE 18


title: Low HOTAIR CaCx_4

description:
Replicate1
SAMPLE 11


title: High HOTAIR CaCx_2

description:
Replicate1
SAMPLE 9


title: Low HOTAIR CaCx_9

description:
Replicate1
SAMPLE 21


title: Low HOTAIR CaCx_8

description:
Replicate1
SAMPLE 20


title: Low HOTAIR CaCx_3

description:
Replicate1
SAMPLE 10


title: Non-malignant_1

description:
Replicate1
SAMPLE 5


title: Non-malignant_3

description:
Replicate1
SAMPLE 14


title: HPV Negative Control_2

description:
Replicate1
SAMPLE 3


title: Non-malignant_2

description:
Replicate1
SAMPLE 13


title: Low HOTAIR CaCx_1

description:
Replicate1
SAMPLE 4


title: HPV Negative Control_4

description:
Replicate1
SAMPLE 8


title: Low HOTAIR CaCx_2

description:
Replicate1
SAMPLE 6


title: Low HOTAIR CaCx_5

description:
Replicate1
SAMPLE 12


title: Low HOTAIR CaCx_7

description:
Replicate1
SAMPLE 19


title: High HOTAIR CaCx_1

description:
Replicate1
SAMPLE 2


title: HPV Negative Control_1

description:
Replicate1
SAMPLE 1


title: CAST/EiJ E18.5 5-3-07

status: Public on Mar 15 2012

first: Neena

middle: B

last: Haider

state: Massachusetts

address: 20 Staniford Steret

department: Ophthalmology

institute: Schepens Eye Research Institute/MEE/Harvard Medical School

hyb_protocol: Samples were labeled using the Affymetrix Eukaryotic Target Labeling Assays to generate biotin-labeled samples for hybridization to Affymetrix GeneChips.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: MAS5 data in the Sample data tables. Data were further processed using the following steps. Data quality was assessed using the affyPLM package for R. Differential expression analysis was performed using the Linear Models for Microarray Analysis portion of Bioconductor. Genes found to be differentially expressed for each pair wise comparison using a FDR-adjusted p-value of 0.001 and at least a 2 fold change were combined and used to perform clustering analysis. A self-organizing map  (SOM) clustering algorithm was applied to genes showing significant expression differences as judged by mean log2 intensity per strain. The gap statistic was used to estimate the optimal number of clusters. Additional analysis was performed using BRB Array Tools for Excel 2007, as well as the Stanford Statistical Analysis of Microarrays  (SAM) plug-in for Excel 2007. Subsequent pathway analysis based on genes found to be statistically significant by these methods was performed using Ingenuity Pathway Analysis software. Gene ontology and further annotation of genes was performed using the Affymetrix NetAffx database, BRB Array Tools, the Database for Annotation, Visualization, and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov), and the UCSC Genome Browser.

source_name: CAST/EiJ E18.5 pool

label_protocol: Labeling was performed by the UNMC Microarray Core facility

extract_protocol: RNA was isolated at E18.5 and P30.5 as previously described  (Haider et al. 2009). Briefly, eyes were enucleated and placed in PBS on ice. Retinas were dissected using a stereo microscope (Zeiss Stemi SV 11) and RNA was isolated by TRIzol extraction. A total of 30 retinas were collected from 15 mice of each strain at similar time points during the day. Equimolar amounts of RNA isolated from ten retinas were pooled into three separate pools from each strain and time point.

value: retina

value: CAST/EiJ

tag: development age


title: CAST/EiJ E18.5 4-19-07

tag: strain


title: NOD.NON-H2-NB1 E18.5 4-19-07

source_name: NOD.NON-H2-nb1 E18.5 pool


title: CAST/EiJ P30.5 4-12-07

source_name: CAST/EiJ P30.5 pool


title: CAST/EiJ P30.5 5-3-07


title: CAST/EiJ E18.5 4-12-07


title: NOD.NON-H2-NB1 E18.5 4-12-07


title: CAST/EiJ P30.5 4-19-07


title: AKR/J P30.5 15  4-19-07

source_name: AKR/J P30.5 pool

value: AKR/J


title: NOD.NON-H2-NB1 P30.5 5-3-07

source_name: NOD.NON-H2-nb1 P30.5 pool


title: AKR/J E18.5 5-3-07

source_name: AKR/J E18.5 pool


title: AKR/J P30.5 5-3-07


title: AKR/J P30.5 14  4-19-07


title: NOD.NON-H2-NB1 P30.5 4-12-07


title: NOD.NON-H2-NB1 E18.5 5-3-07


title: AKR/J E18.5 4-19-07