title: Chromium10X_Idh2R140Q_2_4wk

data_processing:
For Chromium 10X, data was processed using the Cell Ranger 2.1.0. with default parameters.
Data were filtered by minimum number of UMIs (<1,000 for Chromium) per cell and a maximum of 20% UMIs mapping to mitochondrial genes
The fastq R1 contains the cell barcode (positions 1-16)  and UMI (position 17-26). The R2 contains the insert.
Genome_build: mm10
Supplementary_files_format_and_content: csv; Single-cell expression matrices were generated using cellular barcodes and unique molecular identifiers (UMIs). UMItabs contain the UMI count for each specified gene (rows) for each cell (columns). Cell barcodes are provided in the ".CellBarcodes" file for each sample.

extract_protocol:
Bone marrow (BM) cells were isolated into cold phosphate-buffered saline (PBS), without Ca2+ and Mg2+, and supplemented with 2% bovine serum albumin (BSA) to generate single cell suspensions. Red blood cells (RBCs) were removed using ammonium chloride-potassium bicarbonate (ACK) lysis buffer, resuspended in PBS/2% BSA, and filtered through a 40μm cell strainer. Cells were sorted and inmediately underwent Chromium 10X protocol.
For Chromium samples, libraries were prepared according to the Chromium Single Cell 3' Reagent Kits v2 User Guide.

value: Mx1-Cre Idh2 R140Q/WT


title: Krt13 KO tongue at P0, biological rep 2

status: Public on Feb 13 2020

type: SRA

city: Madison

first: Hao

last: Chang

state: WI

address: 1300 University Ave

department: Dermatology

country: USA

institute: University of Wisconsin-Madison

description: Sample KO-A2

library_source: transcriptomic

data_processing:
Illumina bcl2fastq v2.20
Read trimming with Skewer v0.2.2b -m pe -q 20 -k 15 -l 25
Read alignment with STAR v2.5.3a --runThreadN 10 --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD XS --outSAMunmapped Within --outFilterMultimapNmax 50
Expression estimation with RSEM rsem-calculare-expression v1.2.31 --alignments --paired-end --no-bam-output
Differential expression estimation with edgeR v3.28.0
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: MS Excel differential expression results

molecule: total RNA

organism: Mus musculus

source_name: Krt13 KO tongue at P0

growth_protocol: P0 or P20 mice were euthanized and tongues were dissected in cold PBS

extract_protocol:
Trizol and Rneasy according to the manufacturer's instructions
Illumina TruSeq stranded
mRNA library for sequencing

treatment_protocol: P0 whole tongues and P20 ventral tongues were dissected and kept in Trizol

tag: genotype

value: Krt13 KO

tag: age

tag: tissue

value: tongue


title: Krt13 KO tongue at P0, biological rep 1

description: Sample KO-A1


title: Sample_AML-4_10day14_n2

city: New York

first: Franco

last: Izzo

state: NY

address: 1470 Madison Avenue

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Data was processed using the Cell Ranger 2.1.0. with default parameters.
The fastq R1 contains the cell barcode (1-16) and the UMI (17-26).  R2 contains the insert.
Genome_build: hg19
Supplementary_files_format_and_content: csv; Single-cell expression matrix was generated using cellular barcodes and unique molecular identifiers (UMIs), columns represent cells and rows represent genes.

molecule: polyA RNA

organism: Homo sapiens

source_name: DAPI negative, CD45 positive

growth_protocol: Spin embryoid bodies (spin-EBs) were prepared and cultured in APEL2 medium. Briefly, cells were dissociated into single cells with accutase and plated at 3,500 cells per well in round-bottom low-attachment 96-well plates in APEL2 medium containing 5% protein-free hybridoma medium (PFHM-II), 30 ng/ml bone morphogenetic protein 4 (BMP4) and 10 µM Y-27632. The plates were centrifuged at 800 rpm for 5 min to induce EB aggregation. After 24 hours, the medium was replaced by APEL2 medium containing 5% PFHM-II, 30 ng/mL BMP4 and 50 ng/mL FGF2. After 2 days, the cytokine cocktail was changed to 5% PFHM-II, 20 ng/ml vascular endothelial growth factor (VEGF), 10 ng/ml FGF2, 100 ng/ml stem cell factor (SCF), 20 ng/ml Flt3 ligand (FL), 20 ng/ml thrombopoietin (TPO), 40 ng/ml IL-3. On day 8, EBs were collected and resuspended in Stem Pro34 SFM medium with 1% nonessential amino acids (NEAA), 1 mM L-glutamine and 0.1 mM β-mercaptoethanol (2ME), supplemented with 100 ng/ml SCF, 20 ng/ml Flt3L, 20 ng/ml TPO, 40 ng/ml IL-3. The medium was thereafter replaced every two days. For manual separation of adherent and suspension cells, single cells from bulk liquid hematopoietic culture in low adherence plates were plated on tissue culture-treated plates on day 14-16 of hematopoietic differentiation. After two and four days the supernatant containing the S cells was collected and transferred into new tissue culture-treated plates. S cells from both collection days were pooled together. The adherent cells remaining in the initial tissue culture-treated plates were maintained as adherent cells.

extract_protocol: Libraries were prepared according to the Chromium Single Cell 3' Reagent Kits v2 User Guide.

treatment_protocol: Recombination was induced by 3 doses of polyinosinic:polycytidylic acid (pIpC; 12mg/kg/day; GE Healthcare) every other day via intra-peritoneal injection.

tag: cell line

value: AML-4.10 iPSC line

tag: days after plating

tag: sorting strategy

value: DAPI-, CD45+


title: control tongue at P0, biological rep 5

description: Sample WT-A5

source_name: control tongue at P0

value: control


title: Sample_AML-4_10day7_n2


title: Sample_AML-4_10day7_n1


title: Chromium10X_Dnmt3aKO_4_4wk

description: Single cell RNA sequencing

data_processing:
Single cell RNA sequencing data generated with Chromium 10x v2 was processed using Cell Ranger (v2.1.0) with default parameters, and data generated with Chromium v3 was processed using the updated version of Cell Ranger (v3.1). For both chemistry versions, samples were sequenced at an average of 50,000 reads per cell. Raw sequencing data was de-multiplexed and post-processed following the custom pipelines provided by 10x Genomics. Briefly, raw base calls were de-multiplexed into fastq files using the cellranger mkfastq command, followed by alignment to the selected reference mm10 genome for mouse samples or hg19 genome for the human subject data, respectively. Barcode and UMI counting was performed using the cellranger count command with default parameters. Cell barcodes with UMI < 1,000 or mitochondrial gene percentage > 20% were filtered out.
For Drop-seq data, samples were prepared for sequencing using the Illumina Nextera XT kit, and sequenced on a NextSeq 500 (Illumina, San Diego, CA) at an average of 70,000 reads per cell. Libraries with large numbers of cells were divided into technical replicates, which were processed independently. Raw reads were processed and aligned (STAR aligner106) using the standard Drop-seq pipeline, and according to the ‘Drop-seq Alignment Cookbook’, both found at http://mccarrolllab.com/dropseq/.Reads were aligned to the mm10 transcriptome. For each read, a single optimal mapping position was retained. Unique transcripts mapping to alternative splice variants were combined for subsequent analysis. Single-cell expression matrices were generated using cellular barcodes and unique molecular identifiers (UMIs). Cells with UMI < 200 or mitochondrial gene percentage > 20% were filtered out.
For the dual protocol experiments, each pool of 96 cells was first demultiplexed by Illumina i7 barcodes, resulting in four pools of 24 cells. Each pool of 24 cells was further demultiplexed by unique cell barcodes. Reads were assigned to a given cell if they matched 80% of the template adapters. Adapters and adapter reverse complements (6 bp) were trimmed from the raw sequence reads. After adapter removal, reads were trimmed from their 3’ end for read quality by applying a 4 bp sliding window and removing bases until the mean base quality of the window had a Phred quality score greater than 15. We aligned trimmed reads in single-end mode to the mm10 mouse genome assembly using Bismark (v.0.14.5; parameters: -multicore 4 -X 1000 --un –ambiguous) running on bowtie2-2.2.8 aligner. Bismark methylation extractor (--bedgraph --comprehensive) was used to determine the methylation state of each individual CpG. For the single cell RNA, the sequenced paired-end read fragments were mapped against the mm10 mouse genome assembly using the 2pass default mode of STAR (version 2.5.2a) with the annotation of GENCODE (version 19). The number of read counts overlapping with annotated genes was quantified applying the ‘GeneCounts’ option in the STAR alignment.
ATAC-Bseq data was aligned to mm10 genome and methylation calling was performed through Bismark (version 0.14.4; parameters: --q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --maxins 500 Option '--directional' specified) running on bowtie2-2.2.8 aligner112. Accessibility peaks for each individual replicate were defined using MACS2 (v2.1.1.2); parameters: -f BAMPE --broad --broad-cutoff 0.1 -m 2 100).
Genome_build: mm10 for Mus musculus samples,  hg19 for Homo sapiens sample.
Supplementary_files_format_and_content: csv; Single-cell expression matrices were generated using cellular barcodes and unique molecular identifiers (UMIs). UMItabs contain the UMI count for each specified gene (rows) for each cell (columns). Cell barcodes are provided in the ".CellBarcodes" file for each sample.

source_name: Lineage negative hematopoietic bone marrow progenitors

extract_protocol: Bone marrow (BM) cells were isolated into cold phosphate-buffered saline (PBS), without Ca2+ and Mg2+, and supplemented with 2% bovine serum albumin (BSA) to generate single cell suspensions. Red blood cells (RBCs) were removed using ammonium chloride-potassium bicarbonate (ACK) lysis buffer, resuspended in PBS/2% BSA, and filtered through a 40μm cell strainer. Cells were sorted and inmediately underwent the indicated protocol.

tag: weeks after recombination

value: Lin-

tag: genotype/variation

value: Mx1-Cre Dnmt3a fl/fl


title: FTO-sh2-1

city: DUARTE

first: Lei

last: Dong

state: CA

address: 1500 DUARTE RD

institute: City of Hope

description: shFTO rep1

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
the TPM were calculated using RSEM 1.2.31 with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: RSEM output file containing the expression of genes

source_name: cervix squamous cell carcinoma SiHa cell line

growth_protocol: Human SiHa cell line was grown in MEM media supplemented with 10% FBS and 1% 100 Pen Strep .

extract_protocol:
Total mRNA was extracted using TRIZOL reagent
FastTrack MAG Maxi mRNA isolation kit

treatment_protocol: SiHa cells were havested at 48 h after virius infection.

tag: celll line

value: SiHa

tag: lentivirus

value: FTO shRNA


title: 12_C564_osa-IR_Mlut24h_C

city: TAMPERE

first: Mika

last: Ramet

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: sequencing was done in 1 lane

data_processing:
The base calling was done using bcl2fastq (v. 1.8.4)
Read alignment was done using TopHat (2.0.10) to BDGP6 assembly of Drosophila melanogaster genome reference
Genewise read counts were calculated using subread (v1.5.0)
Genome_build: Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047)
Supplementary_files_format_and_content: RNA-seq

organism: Drosophila melanogaster

source_name: whole organism

extract_protocol:
total RNAs were extracted with TRI reagent according to the manufacturers protocol (ThermoFisher Scientific) and the resulting RNAs treated with the RapidOut DNA Removal Kit (ThermoFisher Scientific).
Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047)

tag: infect

value: Micrococcus luteus

tag: infection time

value: 24 hours


title: Hs PNC p53WT_1

city: Houston

first: Moran

last: Amit

state: TX

address: 1515 Holcombe Blvd

department: Head & Neck Surgery - Research

institute: The University of Texas MD Anderson Cancer Center

data_processing:
mRNA: Paired-end sequenced reads were checked by FastQC and aligned to the reference genome, UCSC mouse mm10 or GENCODE human GRCh38, using TopHat2. HTSeq was then used to estimate the number of reads that are mapped to each gene. The R Bioconductor package edgeR was applied to normalize the data using the trimmed mean of M (TMM) method and to determine significant differentially expressed genes between groups.
miRNA: Single-end sequenced reads were checked by FastQC. The QIAseq miRNA Library specific 3′ adapter sequence was trimmed from the 3’ ends of sequenced reads using cutadapt. The trimmed reads were then aligned to the reference genome, human GRCh38, using BWA. FeatureCounts was used to estimate the number of reads that are mapped to each mature miRNA. The R Bioconductor package edgeR was applied to normalize the data using the trimmed mean of M (TMM) method and to determine significant differentially expressed miRNAs between groups.
Genome_build: UCSC mouse mm10 or GENCODE human GRCh38
Supplementary_files_format_and_content: tab-delimited files include raw read count values for each sample (output of HTSeq-count or FeatureCounts)

source_name: Primary neuron culture

growth_protocol: Primary culture ; in vivo innoculation

extract_protocol:
RNa and miRNA were extracted in vitro or ex vivo using qiagen kits per manufacturer's instruction
mRNA: Illumina Compatible low input RNA libraries were prepared using the Smart-Seq V4 Ultra Low Input RNA (Clontech) and KAPA HyperPlus Library Preparation kits. The libraries were then sequenced on the Illumina HiSeq4000 sequencer using the 76bp paired end format.
miRNA: Illumina compatible miRNA libraries were prepared using the QIAseq miRNA Library Kit (Qiagen). The libraries were then sequenced on the Illumina NextSeq500 Sequencer using the 76nt SR High-Output flow cell.

treatment_protocol: HNSCC cells derived exosome (in vitro)

value: Human DRG neurons

tag: cell type


title: control tongue at P0, biological rep 4

description: Sample WT-A4


title: Sample_AML-4_10day1_n2


title: 11_C564_osa-IR_Mlut24h_B

description: sequencing was done in 1 lane


title: Hs PNC p53WT_2


title: Chromium10X_Idh2R140Q_1_4wk


title: Chromium10X_Dnmt3aKO_2_4wk


title: Chromium10X_Dnmt3aKO_1_4wk


title: control tongue at P0, biological rep 3

description: Sample WT-A3


title: Sample_AML_4_10day1_n1


title: Chromium10x_Tet2KO_2_4wk

value: Mx1-Cre Tet2 fl/fl


title: Hs PNC p53WT_3


title: Sample_AML-4_10day14_n1


title: 10_C564_osa-IR_Mlut24h_A

description: sequencing was done in 1 lane


title: control tongue at P0, biological rep 2

description: Sample WT-A2


title: Chromium10X_Tet2KO_1_4wk


title: 9_C564_osa-IR_C

description: sequencing was done in 1 lane

value: 0 hours


title: control tongue at P0, biological rep 1

description: Sample WT-A1


title: 8_C564_osa-IR_B

description: sequencing was done in 1 lane


title: Chromium10X_WT3_4wk


title: Mex3a KO replicate #3

city: Porto

first: Bruno

last: Pereira

address: Rua Alfredo Allen, 208

country: Portugal

data_processing:
Trimming_The analysis of the generated sequence raw data was carried out using CLC Genomics Workbench 12.0.3 (Qiagen). Bioinformatic analysis started with trimming of raw sequences to generate high quality data. For each original read, the regions of the sequence to be removed were determined independently for each type of trimming operation based on the following parameters: a) Ambiguous limit – 2 nucleotides; b) Quality limit – 0.01 (error probability); c) Minimum number of nucleotides in reads – 15 nucleotides; d) Discard short reads.
Mapping_The high-quality sequencing reads were mapped against the reference genome, Mus musculus, using length and similarity fractions of 0.8.
Gene expression_The result of mapping served to determine the gene expression levels based on the TPM (Trancripts per Million), which is a variation of the RPKM method. RPKM is defined as the Reads per Kilobase of exon model per Million mapped reads. In other words, and in this case, it is given by dividing the total number of reads from a particular gene by the number of total mapped reads of the transcriptome (in Millions), times the length (kb) of that gene (Mortazavi et al., 2008, Nat. Methods).
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: Tab-delimited excel files include annotated transcripts, transcript lenght, number of exons, total transcript reads and associated TPM and RPKM values for each sample.

source_name: Small intestine

growth_protocol: Mice at P16

extract_protocol:
Small intestine tissue fragments were incubated with crypt chelating buffer (2 mM EDTA pH 8.0 in PBS) for 1 hour at 4°C with gentle rotation. After incubation, the fragments were allowed to settle, the supernatant discarded, and 8 mL of ice-cold PBS added. Fragments were shaken by hand at 3 cycles/second for 1 minute to dissociate the epithelial crypts from the basement membrane. Cell suspensions were observed under a microscope to check for crypt enrichment and filtered through a 40 μm mesh into a 50 mL falcon tube on ice to collect the first crypt fraction. Previous steps were repeated to release remaining crypts still attached to the tissue, combining both fractions in the same tube. The crypt suspension was centrifuged for 10 minutes at 300 × g at 4°C. Tri reagent (1 mL) was added to freshly isolated crypts and total RNA extracted according to the manufacturer`s guidelines (Sigma).
The library construction of cDNA molecules was carried out using a Stranded mRNA Library Preparation Kit. ). The generated DNA fragments were sequenced in the illumina Novaseq platform (illumina), using 150bp paired-end sequencing reads.

value: Small intestine crypts

tag: strain

value: Small intestine

value: Postnatal day 16 (P16)


title: Chromium10X_WT1_4wk


title: WT replicate #3

value: Wild-type


title: miR-21 [9_21-3]

type: RNA

first: MORAN

last: AMIT

state: Texas

address: 1881 East Road

institute: UT MD Anderson CC

hyb_protocol: Following fragmentation, 5 micrograms of biotin-labeled sense-strand cDNA fragments in 200 µL of hybridization mix was loaded onto a mouse Clariom S array and hybridized to probes on the array in a GeneChip Hybridization Oven 645 (Affymetrix) for 16 h at 45°C with 60 rpm rotation.

scan_protocol: GeneChips were scanned using GeneArray G7 scanner (Affymetrix) and quantified into .CEL files with image and signal intensities.

data_processing: Transcriptome Analysis Console software v4.0 (Affymetrix) was used for probe set summarization and robust multiarray average (RMA) normalization procedures.

label: biotin

source_name: TG neuron

label_protocol: The fragmented cDNA was labeled by terminal deoxynucleotidyl transferase using the Affymetrix proprietary DNA labeling reagent, which is covalently linked to biotin.

growth_protocol: TG neurons were isolated and plated on laminin-coated coverslips.

extract_protocol: Total RNA was isolated from neurons using RNeasy Micro Kit (QIAGEN) according to the manufacturer’s protocol.

treatment_protocol: TG neurons were transfected with miR-21, miR-34a, miR-324, or scramble

value: primary culture


title: WT replicate #2


title: Mex3a KO replicate #2


title: Chromium10X_WT2_4wk


title: 7_C564_osa-IR_A

description: sequencing was done in 1 lane


title: Tumor, patient 3

city: Shenyang

first: Peng

last: Shen

state: Liaoning

address: 36 Sanhao street

country: China

institute: Shengjing Hospital of China Medical University

description:
Test
Qiagen Custom RT² PCR Arrays
SAMPLE 6

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/au/analyze/
For the normalization it uses the average of five housekeeping genes: SNORD61, SNORD68, SNORD72, SNORD95, SNORD96A, RNU6-2.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (tumor/adjacent) ratios.

label: SYBR Green

source_name: melanoma

label_protocol: PCR assays were performed using the Custom RT2 PCR Arrays (QIAGEN, Hilden, Germany) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (QIAGEN, Hilden, Germany). Quantitative real-time PCR were performed (Light Cycler 480, Roche) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

growth_protocol: Adjacent tissues and tumor tissues were collected simultaneously. All the resected or biopsy specimens were placed immediately into liquid nitrogen and stored at - 80°C.

extract_protocol: Total RNA was extracted by 1 mL TRIzol (Thermo Fisher Scientific, Waltham, MA, USA) followed by Ribonuclease R treatment (RNase R; Epicenter, Madison, USA).

tag: Sex

value: female

value: skin


title: Tumor, patient 2

description:
Test
Qiagen Custom RT² PCR Arrays
SAMPLE 5

value: male


title: Liver-FVB-B6_rep4

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

hyb_protocol: 1.5 µg labelled cRNA were hybridized onto the GeneChip Mouse Gene1.0 ST Arrays (Affymetrix, CA, USA) for 16h at 45°C using Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 using the GeneChip Operating Software (Affymetrix).

data_processing: R/Bioconductor using Single-Channel Array Normalization (SCAN), (Picolo et al., Genomics 2012). Custom probe grouping (CDF): Brainarray Version 22.0, Entrezg  [CDF: mogene10st_Mm_ENTREZG.cdf]

label: Biotin

source_name: Liver-mtFVB

label_protocol: Biotinylated cRNA was generated from 1.5 µg total RNA using the One-Cycle Target Labeling Assay (Affymetrix).

growth_protocol: Total RNA was isolated from liver samples of 4 male mice per strain (12 weeks old, CD feeding) and used for genome wide expression analysis.

extract_protocol: RNA was purified using standard procedures using the RNeasy Mini Plus Kit (Qiagen, Hilden, Germany).

treatment_protocol: Liver tissue (100 mg) was homogenized, lysed using lysis buffer (50 mM Tris; 2 mM CaCl2; 80 mM NaCl; 1% Triton X-100; pH 8.0) and centrifuged to remove remaining cell debris.

value: Liver

tag: gender

value: 12 weeks


title: miR-34a [5-miR34a-2_4-10]


title: Liver-FVB-B6_rep3


title: P53 NULL CELL [P53-/-_CELL_2]

hyb_protocol: Hybridization done according to Agilent Gene expression hybridization kit

scan_protocol: Scanned on Agilent SureScan Microarray Scanner (Agilent Technologies G2600D SG12434244)

data_processing: Data pre-processing steps of background-correction, normalization and summarization were performed in R using functions in Limma library.  The raw intensity for each probe is the median feature pixel intensity with the median background subtracted.  Data was quantile normalized followed by log2 transform.  Signals from probes measuring same ncRNA were averaged.

source_name: OCSCC CELL LINE

label_protocol: Labbeling was done according to Nimblegen one color DNA Labeling kit.

value: CELL CULTURE


title: Liver-FVB-B6_rep1


title: miR-21 [7_21-1]


title: scramble miRNAs [3-mimic-Scr-1_3-11]


title: P53 NULL CELL DERIVED EVS [P53-/-_EXOS_2]


title: P53 WT CELL DERIVED EVS [P53+/+_EXOS_2]


title: scramble miRNAs [2-SCR-2_4-10]


title: Liver-FVB-B6_rep2


title: Tumor, patient 1

description:
Test
Qiagen Custom RT² PCR Arrays
SAMPLE 4


title: P53 NULL CELL [P53-/-_CELL_1]


title: P53 NULL CELL DERIVED EVS [P53-/-_EXOS_1]


title: Adjacent, patient 1

description:
Control
Qiagen Custom RT² PCR Arrays
SAMPLE 1

source_name: Adjacent tissue


title: miR-324 [11-324-4]


title: miR-34a [6-34a-3]


title: Liver-WT-B6_rep3


title: Liver-WT-B6_rep2


title: miR-324 [12-mimic-324-2_3-11]


title: Liver-WT-B6_rep4


title: miR-21 [8_21-2]


title: Liver-WT-B6_rep1


title: WT_2

status: Public on Feb 12 2020

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
For each genotype the RNA-seq data from two biological replicate samples from the L1 stage were mapped to the C. elegans genome (ce10) using the R package QuasR v1.22.0 (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html). QuasR includes the short read aligner bowtie using the parameters "-m 1 --best --strata --phred33-quals" to consider only uniquely mapping reads (command: "proj <-qAlign("samples.txt","BSgenome. Celegans.UCSC.ce10")") and subsequently extract count tables of reads mapping within exon gene annotation from WormBase (WS220).
To normalize for sequencing depth, each sample was divided by the total number of reads and multiplied by the average library size. Transformation into log2 space was performed after the addition of a pseudocount of 8 in order to minimize large changes in expression caused by low count numbers. The various count tables used throughout this study were normalized separately.
The EdgeR package v 3.24.0 was used to determine fold changes (Fc) and false discovery rates (FDR) of differential transcript abundances. (in contrast to L3 samples no blocking factor in linear models applied).
Genome_build: ce10

organism: Caenorhabditis elegans

source_name: L1 larval stage sorted for non green (no balancer)

growth_protocol: For L1 RNA-seq experiment, worms were synchronized prior to the sorting process. Synchronized L1 larvae were obtained by bleaching gravid adults grown on  petone rich plates (15 cm) seeded with OP50 bacteria and the eggs recovered were left to hatch 16h at RT in M9. For all RNA based experiments, before RNA extraction, worms were washed 3x in M9 and re-suspended in 100μl of M9, 400μl of Trizol® (Ambion) and snap-frozen in liquid nitrogen.

extract_protocol:
For L1 RNA-seq samples, the extraction was done using the Zymo DirectZol microRNA kit (R2060).
Library preparation for the L1 samples was performed with the TrueSeq Total RNA preparation kit, stranded (Illumina).  The quality of the resulting libraries was assessed with an Agilent Bioanalyzer and concentrations were measured with a Qubit fluorometer prior to pooling. 50 bp single-end sequencing was done on an Illumina HiSeq 2500.

treatment_protocol: The isolation of WT and lsm-8-/- L1 larvae was made similarly with the fluorescent criteria (non-green pharynx worms) and the size criteria of L1 stage larvae.  The larvae were refeed for 2.5h after the sorting process.

value: GW1 / N2 (WT)

value: wild-type, Bristol


title: Adjacent, patient 2

description:
Control
Qiagen Custom RT² PCR Arrays
SAMPLE 2


title: scramble miRNAs [1-SCR-1_4-10]


title: miR-34a [4-miR34a-1_4-10]


title: lsm-8_2

value: lsm-8  (xe17 [myo2p::mcherry::unc54 3'UTR])IV/nT1[qIs51](IV;V)


title: lsm-8_1


title: WT_1


title: met-2 set-25 (638_4,rep2)

data_processing:
The RNA-seq samples were mapped to the c.elegans genome (ce6) with the R package QuasR (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html) using the included aligner bowtie considering only uniquely mapping reads for mRNA as well as for repeat element quantification. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce6")" which instructs bowtie to align using the parameters "-m 1 --best --strata --phred33-quals". For splice junction quantification we used the spliced alignment algorithm SpliceMap. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce6",splicedAlignment=TRUE)". The command used to create the various count tables was qCount(proj,exons,orientation="same"). For gene quantification (ce_mRNA_lsm8_*.txt), gene annotation from WormBase was used (WS190). The repeat element quantification was based on UCSC (genome.uscsc.edu) repeat annotation (ce_repeats_*.txt). To normalize for sequencing depth, each sample was divided by the total number of reads and multiplied by the average library size. Transformation into log2 space was performed after the addition of a pseudocount of 8 in order to minimize large changes in expression caused by low count numbers. To quantify potential changes in splicing in lsm8 as apposed to N2, we quantified the expression of all the exon-exon junctions from the spliced alignments using no annotation (ce_junctions_*.txt). The command used to create the exon-exon junction count table was qCount(proj2,NULL,reportLevel="junction"). These junction counts were then normalized for library size (as described above) and overlapped with gene annotation to assign them to their host gene.
Genome_build: ce6
Supplementary_files_format_and_content: text files with raw or normalized counts.

source_name: L3 larval stage sorted for non green (no balancer)

growth_protocol: Worms from each genotype were  grown on 2-6  petone rich plates (15 cm) seeded with OP50 bacteria.

extract_protocol:
For the RNA-seq experiment L3-L4 worms from the four following genotypes: WT, met-2 set-25, lsm-8-/- and met-2 set-25; lsm-8-/- worms were isolated using the COPAS BIOSORT instrument in four independent biological replicates. The sorted worms were harvested, washed three times in M9 and finally re-suspended in 100μl of M9, 400μl of Trizol® (Ambion) was added and the samples were snap-freezed in liquid nitrogen. Total RNA was treated additionally with the Turbo DNA free kit (Ambion, AM1907), depleted for rRNA using Ribo-Zero Gold kit from Epicentre and depletion validated through Agilent Bioanalyzer analysis.
Library preparation was performed with a ScriptSeq v2 RNA-Seq library preparation kit (Epicentre). The quality of the resulting libraries was assessed with an Agilent Bioanalyzer and concentrations were measured with a Qubit fluorometer prior to pooling.

treatment_protocol: The worms have been sorted for L3-L4 stage and non-green pahrynx (balancer) in all strains in order to get only the L3-L4 homozygous for the deletion allele(s). The N2 and GW638 have been sorted in the same conditions to get similar treated worms, even though they do not have a green/GFP balancer to sort out. During the validation for the genotype done with the wiggle files, we found that the marked samples (*) had relatively a high number of reads on the deletion of interest compared to all other related samples indicating that the sorting process  was probably not very efficient with some heterozygous worms or other worms that might have contaminated partially the sample.

tag: developmental stage


title: lsm-8 met-2 set-25 (1148_3,rep1)

tag: genotype


title: lsm-8 (1125_3,unused)


title: miR-324 [10-324-1]


title: P53 WT CELL DERIVED EVS [P53+/+_EXOS_1]


title: P53 WT CELL [P53+/+_CELL_2]


title: lsm-8 met-2 set-25 (1148_4,unused)


title: WT (N2_2,unused)


title: P53 WT CELL [P53+/+_CELL_3]


title: met-2 set-25 (638_2,unused*)

tag: sorting efficiency and genotype validation with wiggle files

value: * poor


title: WT (N2_3,rep1)


title: met-2 set-25 (638_3,rep1)


title: lsm-8 met-2 set-25 (1148_2,unused*)


title: lsm-8 (1125_2,unused*)


title: lsm-8 (1125_4,rep2)


title: WT (N2_4,unused)


title: lsm-8 (1125_1,rep1)


title: WT (N2_1,rep2)


title: N20

city: Montpellier

first: Jacques

last: Colinge

address: 208, avenue des Apothicaires

country: France

institute: Inserm

description: original data

data_processing:
Adaptor trimming using trimmomatic
reads alignment with STAR (default parameters and 2 passes)
reads counts with HTSeq 0-7-2
reads count normalization using edgeR
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized reads count per sample

source_name: SDC

extract_protocol:
RNA was extracted using DNeasy Blood and Tissue Kit (Qiagen) and quantified by spectrophotometry using the Nanodrop 2000 (ThermoFisher Scientific) and 2100 Bioanalyzer (Agilent). Quality was checked by Fragment analyzer (RIN > 7). 400 ng was used for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions. DNA library was prepared with the NEBNext Ultra II mRNA-Seq, implicating a capture of mRNA with a poly T oligonucleotide.

tag: tissue

value: salivary gland

value: normal


title: SDC23

description: original data

value: tumor


title: siNC-rep-2

first: Iman

last: Osman

address: 522 1st Avenue, Smilow 403

institute: NYU School of Medicine

data_processing:
Raw fastq reads were aligned to hg19 human reference genome using STAR aligner (Dobin, A, 2012).
Fastq Screen was used to check for sample contaminations.
Picard RnaSeqMetrics was used to obtain metrics of all aligned RNA-Seq reads.
FeatureCounts (Liao, Y, 2013) was used to quantify gene expression levels.
DESeq2 R package (Love, M, 2014) was used to identify  differentially expressed genes (DEGs); those with genes with FDR < 0.05 were considered significant.
Pheatmap R package was used to generate heatmaps.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each sample.

source_name: WM3248 primary melanoma cell line transfected with siNC

growth_protocol: WM3248 primary melanoma cells were cultured in MCDB153/L15 medium (4:1 v/v) supplemented with 2% fetal bovine serum, 5 mg/mL insulin, 15 mg/mL bovine pituitary extract, 1.68 mmol/L calcium chloride, 5 ng/mL epidermal growth factor, and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was isolated from WM3248 cells (48 hr post-transfection) with the Rneasy Plus Mini Kit (QIAGEN, Germantown, MD), according to the manufacturer's instructions.
RNA-Seq library preps were made using the Illumina TruSeq® Stranded mRNA LT kit (Cat #RS- RS-122-2101 or RS-122-2102), on a Beckman Biomek FX instrument, using 100 ng of total RNA as input, amplified by 12 cycles of PCR, and run on an Illumina 4000 as single read 50.

treatment_protocol: Cells were transfected with siNC (AllStarts Negative Control siRNA) or siPGC1-alpha (PPARGC1A siRNA) at a final concentration of 30 nM, using Lipofectamine 2000 reagent (Life Technologies, Grand Island, NY), according to the manufacturer's instructions.

value: VGP primary melanoma cell

tag: cell line

tag: sirna

value: negative control siRNA (QIAGEN cat#102780


title: SDC25

description: original data


title: siPGC1a-rep-3

source_name: WM3248 primary melanoma cell line transfected with siPGC1-alpha

value: PGC1-alpha siRNA (QIGEN cat#SI02639833)


title: siNC-rep-3


title: SDC24

description: original data


title: siPGC1a-rep-1


title: SDC22

description: original data


title: siNC-rep-1


title: N22

description: original data


title: lsm-8 met-2 set-25 (1148_1,rep2)


title: SDC21

description: original data


title: SDC19

description: original data


title: SDC17

description: original data


title: met-2 set-25 (638_1,unused)


title: SDC20

description: original data


title: Control3 [OPK363NC]

city: Boston

first: Michael

last: Wheeler

state: MA

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline (version 1.3).
Cellranger mkfastq demultiplexed libraries based on sample indices and generated FASTQ files
Cellranger count performed alignment against hg38 human genome using STAR , filtering, and feature counting for unique molecular identifier (UMI)
Genome_build: hg38
Supplementary_files_format_and_content: csv format with rows as genes and columns as cells

source_name: CNS Percoll pellet

extract_protocol:
Tissue was mechanically dissociated, treated with 0.25% trypsin and 25ug/mL Dnase for 30 min at 37C, and then passed through a 140um nylon mesh. The resulting cells were then separated on 30% percoll gradient to remove myelin and erythrocytes.
Libraries were created according to the 10X Genomics protocol (Zheng et al. Nature Communications 2017).

tag: disease

value: glioblastoma patient

value: Healthy control tissue


title: siPGC1a-rep-2


title: Control1 [HAM737]

value: hippocampal sclerosis patient


title: MS patient 2-8

description:
Sample 19
7_HMVNKBBXX.7.CAGAGAGG

data_processing:
Reads were processed using the DropSeq analysis pipeline developed by the McCarroll lab (http://mccarrolllab.com/dropseq/)
Individual cells were tagged with barcodes, and transcripts within each cell were tagged with distinct UMIs (Unique Molecular Identifiers).
Reads were trimmed at 3' end to remove poly(A) tails with length greater than 5 and trimmed at the 5' end for adapters
Reads with barcode base quality less than 10 were filtered out
Raw reads were aligned to human (GRCh38) genome by STAR (v2.4.0) with default settings
UMI counts expression matrix were generated using Dropseq Tools software (v1.13.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file consisting of UMI gene counts for cells with minimum 200 genes.

extract_protocol:
A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and cell density was quantified. Cells were suspended in PBS and 16% Opti-prep.
Libraries were created according to the Drop-seq protocol in Macosko et al. Cell 2015. Following reverse transcription, exonuclease I treatment, and PCR, cDNA libraries were quantified and 600 pg of cDNA was tagmented using Nextera XT library prep kit.

treatment_protocol: Following rapid autopsy, samples were immediately incubated in Hibernate (Life Technologies, #A1247601) for 8-18 hours prior to processing.

tag: subject status

value: Multiple sclerosis (MS) patient

tag: subject group

value: relapsing-remitting MS (RRMS)


title: MS patient 2-5

description:
Sample 18
5_HMVNKBBXX.5.GGACTCCT


title: MS patient 2-4

description:
Sample 14
6_HMVNKBBXX.6.TCCTGAGC


title: Control2 [HAM738]


title: MS patient 2-3

description:
Sample 13
5_HMVNKBBXX.5.AGGCAGAA


title: MS patient 2-6

description:
Sample 16
6_HMVNKBBXX.6.TAGGCATG


title: MS patient 2-2

description:
Sample 17
6_HMVNKBBXX.6.CGTACTAG


title: MS patient 2-1

description:
Sample 15
5_HMVNKBBXX.5.TAAGGCGA


title: MS patient 1-5

description:
Sample 6
1_HMVNKBBXX.1.GGACTCCT

value: secondary progressive MS (SPMS)


title: MS patient 1-7

description:
Sample 7
3_HMVNKBBXX.3.CTCTCTAC


title: MS patient 1-2

description:
Sample 5
2_HMVNKBBXX.2.CGTACTAG


title: WT_replicate2 [ATAC-seq]

description:
10_R*_001
processed data: WT_merged_FE.bdg

library_source: genomic

data_processing:
Reads were trimmed using Cutadapt (v1.14) to remove adapters and low quality reads.
ATAC-seq paired-end reads were aligned using Bowtie2 (v2.3.0) with maximum fragment size 2000 (-X2000).
Duplicated reads were marked with Picard (v2.5.0).
Alignments were filtered with SAMtools (v1.3) to exclude reads with mapping quality <30, not properly paired, duplicated, aligned to mitochondrial genome, and/or aligned to ENCODE blacklist regions.
ATAC-Seq peaks were called for each replicate using MACS2, using --format BAMPE and --keep-dup all, and were selected with p<0.01
IDR (v2.0.2) was used to determine consistency of peak detection between individual replicates and peaks with FDR<0.10 were merged between replicates for downstream analysis.
Fold enrichment tracks were generated in MACS using bdgcmp and were visualized using IGV (v 2.3.59).
Genome_build: GRCm38
Supplementary_files_format_and_content: bedgraph file containing fold enrichment peaks provided by MACS2 bdgcmp

molecule: genomic DNA

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and stained with primary antibodies for flow cytometry. Once cells were sorted, cells were pelleted, washed, and tagmented according to the ATAC-seq protocol (Buenrostro et al., Nature Methods 2013).
Nextera DNA Library Prep Kit

treatment_protocol: Induction of EAE in mice intracranially transduced with pLenti-U6-sgMafg-Gfap-Cas9-2A-EGFP-WPRE or pLenti-U6-sgScrmbl-Gfap-Cas9-2A-EGFP-WPRE. EAE was induced by injecting 25 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

tag: genotype/variation

value: wild type

value: Male

tag: age

tag: sample group

value: undergoing EAE transduced with non-targeting lentiviruses

value: Flow cytometry sorted astrocytes


title: MS patient 1-3

description:
Sample 1
1_HMVNKBBXX.1.AGGCAGAA


title: WT_replicate3 [ATAC-seq]

description:
11_R*_001
processed data: WT_merged_FE.bdg


title: MS patient 1-6

description:
Sample 4
2_HMVNKBBXX.2.TAGGCATG


title: MS patient 1-4

description:
Sample 2
2_HMVNKBBXX.2.TCCTGAGC


title: MafgKO_replicate1 [ATAC-seq]

description:
6_R*_001
processed data: Mafg_merged_FE.bdg

value: undergoing EAE transduced with Mafg-targeting lentiviruses


title: MS patient 1-1

description:
Sample 3
1_HMVNKBBXX.1.TAAGGCGA


title: WT_replicate1 [ATAC-seq]

description:
9_R*_001
processed data: WT_merged_FE.bdg


title: EAE_MAFG_Input_Replicate1

description:
processed data file:
EAE_merged_p0.01_peaks.narrowPeak

data_processing:
ChIP-seq Reads were aligned using BWA mem (v0.7.8) against the GRCm38 genome with default settings.
Duplicated reads were removed using Picard (v2.5.0).
Alignments were filtered with SAMtools (v1.3) to exclude reads with mapping quality <30, not properly aligned, and aligned to the mitochondrial genome.
For peak calling, MACS2 callpeaks (V2.1.1) were called using IP as treatment and Input as control sample, with pval 0.01 as threshold.
Fold enrichment tracks were generated in MACS using bdgcmp to compare treatment against control and were visualized using IGV (v 2.3.59).
Genome_build: GRCm38
Supplementary_files_format_and_content: narrowPeaks output from MACS2

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by trypsinization, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and stained with primary antibodies for flow cytometry. Once cells were sorted, chromatin was isolated using the Active Motif ChIP-IT Express Enzymatic shearing kit. Chromatin complexes were IPed with MAFG antibody (Genetex, GTX114541), cross-links were reversed, and DNA was cleaned up for library prep using QIAquick PCR purification kit.
NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: Induction of EAE or Naïve. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

value: female

value: experimental autoimmune encephalomyelitis (EAE)

tag: chip antibody

value: none (input)


title: Naive_MAFG_Input_Replicate3

description:
processed data file:
Naive_merged_p0.01_peaks.narrowPeak

value: naïve

tag: cell type


title: MS patient 2-7

description:
Sample 20
7_HMVNKBBXX.7.CTCTCTAC


title: EAE_MAFG_Input_Replicate2

tag: strain


title: EAE_MAFG_IP_Replicate3

tag: Sex

value: MAFG antibody (Genetex, GTX114541)


title: Naive_MAFG_Input_Replicate1


title: Naive_MAFG_IP_Replicate2


title: MafgKO_replicate2 [ATAC-seq]

description:
7_R*_001
processed data: Mafg_merged_FE.bdg


title: Naive_MAFG_Input_Replicate2


title: EAE_MAFG_IP_Replicate1


title: KO-3 [Sample12]

data_processing:
Reads were trimmed using Cutadapt (v1.14) to remove adapters and low quality reads.
Trimmed reads were then aligned to GRCm38 genome using Bismark (v0.20.1) and Bowtie2 (v0.20.1) with default settings.
Duplicated reads were removed using paired end mode
Methylation counts and percentages were extracted using bismark_methylation_extractor
Percentage methylation were visualized using IGV (v2.3.59)
Genome_build: GRCm38
Supplementary_files_format_and_content: bedgraph file with percent methylation at each CpG position

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and stained with primary antibodies for flow cytometry. Once cells were sorted, cells were pelleted, washed, and genomic DNA was isolated using the Qiagen DNeasy Blood & Tissue Kit kit (Qiagen, #69504).
Bisulfite converted DNA libraries were generated by using the Zymo Pico-Methyl DNA kit (Zymo Research, #D5455) according to the manufacturer's protocol.

treatment_protocol: Induction of EAE in mice intracranially transduced with pLenti-U6-sgMafg-Gfap-Cas9-2A-EGFP-WPRE or pLenti-U6-sgScrmbl-Gfap-Cas9-2A-EGFP-WPRE or non-transduced naive mice. EAE was induced by injecting 25 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

value: male


title: Naive_MAFG_IP_Replicate3


title: KO-2 [Sample11]


title: EAE_MAFG_IP_Replicate2


title: EAE-1 [Sample13]


title: Adjacent , patient 3

description:
Control
Qiagen Custom RT² PCR Arrays
SAMPLE 3

value: skin


title: MafgKO_replicate3 [ATAC-seq]

description:
8_R*_001
processed data: Mafg_merged_FE.bdg


title: WT-2 [Sample8]


title: Naive_MAFG_IP_Replicate1


title: P2F2_Bisulfite-seq_discovery

city: Grand Rapids

first: Peipei

last: Li

state: MI

address: 333 Bostwick Ave N.E.

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

data_processing:
The libraries were sequenced on the HiSeq 2500 platform (Illumina) using custom sequencing primers.
The FASTQ reads were quality trimmed using trimgalore.
The trimmed reads were then aligned using Bismark.
Bismark was used to align reads to the target reference genome and perform methylation calls.
Genome_build: hg19
Supplementary_files_format_and_content: Each txt file contain the following information in order: chromosome #, genomic coordinate, strand, unmethylation count, methylation count, CHH/CHG/CG context of cytosine, exact sequence of the previous context

source_name: Brain prefrontal cortex neurons (NeuN+)

growth_protocol: Human prefrontal cortex neurons.

extract_protocol:
Neuronal nuclei from prefrontal cotex were isoated by an antibody (NeuN) and flow cytometry approach; DNA were extracted by standard phenol chloroform extraction; Bisulfite padlock probes were designed to humans brain enhancers and promoters (NIH Roadmap Chromm)
We scanned brain-relevant enhancers and promoters genome-wide using the bisulfite padlock probe approach. Padlock probes (n=59,009) were designed using the PP Designer software and synthesized using a programmable microfluidic microarray platform (CustomArray, Inc.). Isolated genomic DNA for each sample was bisulfite-converted and purified using the EZ DNA Methylation-Lightning Kit (Zymo Research). The bisulfite-converted DNA (200 ng) was hybridized to the padlock probes (1.5 ng). Targeted regions were extended using PfuTurbo Cx (Agilent Technologies) and circularization was completed using Ampligase (Epicentre). Non-circularized DNA was digested using an exonuclease cocktail and the remaining circularized DNA was amplified using a common linker sequence in the padlock probe. Libraries were PCR amplified, pooled in equimolar amounts, purified by QIAquick Gel Extraction kit (Qiagen) and quantified by qPCR (Kapa Biosystems) on a ViiA 7 Real-time PCR system (Applied Biosystems).

tag: brain bank

value: Michigan

tag: tissue id

tag: replicate

value: No

value: Brain prefrontal cortex neurons (NeuN+)

value: M

tag: pmi

tag: diagnosis

value: Control

tag: asymmetry group

tag: brain hemisphere

value: R

tag: duration


title: P2F6_Bisulfite-seq_discovery

value: Maryland

value: Yes

value: L


title: P2E11_Bisulfite-seq_discovery


title: P2G4_Bisulfite-seq_discovery


title: P2G2_Bisulfite-seq_discovery

value: Parkinson’s UK Brain Bank Centre for Neuroscience Imperial College London

value: F


title: P2E10_Bisulfite-seq_discovery


title: P2F8_Bisulfite-seq_discovery


title: P2F4_Bisulfite-seq_discovery


title: P2E12_Bisulfite-seq_discovery


title: KO-1 [Sample10]

value: wild type

value: undergoing EAE transduced with Mafg-targeting lentiviruses

value: Flow cytometry sorted astrocytes


title: P2F5_Bisulfite-seq_discovery


title: P2F3_Bisulfite-seq_discovery


title: P2F9_Bisulfite-seq_discovery


title: P2G3_Bisulfite-seq_discovery

value: Harvard

value: PD


title: P2D10_Bisulfite-seq_discovery

value: Miami


title: P2G1_Bisulfite-seq_discovery


title: P2E9_Bisulfite-seq_discovery


title: P2F7_Bisulfite-seq_discovery


title: P2D11_Bisulfite-seq_discovery


title: P2D12_Bisulfite-seq_discovery


title: P2E8_Bisulfite-seq_discovery


title: P2E1_Bisulfite-seq_discovery


title: P2D8_Bisulfite-seq_discovery


title: P2F10_Bisulfite-seq_discovery

value: Michigan


title: P2D7_Bisulfite-seq_discovery


title: P2D5_Bisulfite-seq_discovery

value: No


title: P2E5_Bisulfite-seq_discovery

value: Brain prefrontal cortex neurons (NeuN+)


title: P2E7_Bisulfite-seq_discovery


title: P2D4_Bisulfite-seq_discovery

value: M


title: P2D1_Bisulfite-seq_discovery

value: Control


title: P2C2_Bisulfite-seq_discovery

value: R


title: P2C6_Bisulfite-seq_discovery


title: P2D3_Bisulfite-seq_discovery


title: P2B9_Bisulfite-seq_discovery

value: The UK Multiple Sclerosis Tissue Bank


title: P2C9_Bisulfite-seq_discovery

value: UK PD Society Tissue Bank at Imperial College

value: Unmatched


title: P2A10_Bisulfite-seq_discovery


title: P2A7_Bisulfite-seq_discovery


title: P2B6_Bisulfite-seq_discovery

value: Yes


title: P2C1_Bisulfite-seq_discovery

value: F


title: P2B5_Bisulfite-seq_discovery

value: Parkinson’s UK Brain Bank Centre for Neuroscience Imperial College London


title: P2A11_Bisulfite-seq_discovery

value: matched

value: L


title: P2C8_Bisulfite-seq_discovery


title: P2C5_Bisulfite-seq_discovery

value: Sepulveda


title: P2D9_Bisulfite-seq_discovery


title: P2B8_Bisulfite-seq_discovery

value: PD


title: P2A8_Bisulfite-seq_discovery


title: P2B11_Bisulfite-seq_discovery


title: P2A3_Bisulfite-seq_discovery


title: P2A5_Bisulfite-seq_discovery


title: G12_Bisulfite-seq_discovery


title: P2A6_Bisulfite-seq_discovery


title: P2C10_Bisulfite-seq_discovery


title: P2A1_Bisulfite-seq_discovery


title: G11_Bisulfite-seq_discovery

value: Harvard


title: P2C12_Bisulfite-seq_discovery


title: P2D2_Bisulfite-seq_discovery


title: G10_Bisulfite-seq_discovery


title: P2B10_Bisulfite-seq_discovery


title: G8_Bisulfite-seq_discovery


title: G7_Bisulfite-seq_discovery


title: G6_Bisulfite-seq_discovery


title: G3_Bisulfite-seq_discovery


title: G5_Bisulfite-seq_discovery


title: G4_Bisulfite-seq_discovery


title: ChIA-PET from HepG2 (ENCLB951KEQ)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR146FPM/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIA-PET in human HepG2 cells
experiment encode accession: ENCSR146FPM
assay title: ChIA-PET
encode release date: 2018-04-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB951KEQ
size range: 450-650

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens HepG2 cell line

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

value: male

tag: health state

value: hepatocellular carcinoma

tag: dev stage

value: child

value: 15 year

tag: lab

value: Michael Snyder, Stanford

tag: link

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCBS224IXA at ENCODE; https://www.encodeproject.org/ENCBS224IXA/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; https://web.expasy.org/cellosaurus/CVCL_0027


title: G2_Bisulfite-seq_discovery

value: No

tag: cell type

value: Brain prefrontal cortex neurons (NeuN+)

value: M

tag: age

value: Control


title: F11_Bisulfite-seq_discovery

tag: brain bank

value: Parkinson’s UK Brain Bank Centre for Neuroscience Imperial College London

tag: Sex

value: R


title: F10_Bisulfite-seq_discovery

tag: tissue id

tag: replicate

value: PD

value: Unmatched

value: L


title: F9_Bisulfite-seq_discovery

value: UK PD Society Tissue Bank at Imperial College

tag: pmi

tag: diagnosis

value: matched


title: F12_Bisulfite-seq_discovery

value: Yes

value: F

tag: asymmetry group

tag: brain hemisphere


title: F1_Bisulfite-seq_discovery

tag: duration


title: E10_Bisulfite-seq_discovery


title: TF ChIP-seq from HEK293 (ENCLB731NAM)

description:
https://www.encodeproject.org/experiments/ENCSR146NLL/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-REPIN1 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR146NLL
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR598OXI, ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2017-03-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB731NAM
size range: 450-650

source_name: Homo sapiens HEK293 cell line genetically modified (insertion) using site-specific recombination targeting eGFP-REPIN1 originated from HEK293

tag: antibody

tag: line

value: cell line

tag: description

value: HEK293 cell line stably expressing N-terminal tagged eGFP-REPIN1 under the control of a CMV promoter.

value: female

value: unknown

value: embryonic

value: Michael Snyder, Stanford

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/

value: ENCBS313ZXJ at ENCODE; https://www.encodeproject.org/ENCBS313ZXJ/

value: ENCODE dbxrefs Cellosaurus CVCL_0045; https://web.expasy.org/cellosaurus/CVCL_0045


title: E11_Bisulfite-seq_discovery

value: No

value: Brain prefrontal cortex neurons (NeuN+)

value: M

value: R


title: ChIA-PET from HepG2 (ENCLB607ZTO)

description:
https://www.encodeproject.org/experiments/ENCSR146FPM/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIA-PET in human HepG2 cells
experiment encode accession: ENCSR146FPM
assay title: ChIA-PET
encode release date: 2018-04-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB607ZTO
size range: 450-650

tag: biosample encode accession

value: male

tag: health state

value: hepatocellular carcinoma

tag: dev stage

value: child

value: 15 year

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCBS742SWZ at ENCODE; https://www.encodeproject.org/ENCBS742SWZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; https://web.expasy.org/cellosaurus/CVCL_0027


title: E12_Bisulfite-seq_discovery

value: UK PD Society Tissue Bank at Imperial College

tag: cell type

value: PD

value: Unmatched

value: L


title: G1_Bisulfite-seq_discovery

value: Parkinson’s UK Brain Bank Centre for Neuroscience Imperial College London

tag: age

value: Control


title: E9_Bisulfite-seq_discovery

tag: brain bank

value: No


title: E5_Bisulfite-seq_discovery

value: Harvard

value: Brain prefrontal cortex neurons (NeuN+)

tag: Sex

value: F


title: F2_Bisulfite-seq_discovery

tag: tissue id

value: M


title: E4_Bisulfite-seq_discovery

tag: replicate

value: matched


title: TF ChIP-seq from HEK293 (ENCLB077RTM)

description:
https://www.encodeproject.org/experiments/ENCSR443MVV/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-PRDM4 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR443MVV
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR598OXI, ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2017-02-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB077RTM
size range: 450-650

source_name: Homo sapiens HEK293 cell line genetically modified (insertion) using site-specific recombination targeting eGFP-PRDM4 originated from HEK293

value: cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-PRDM4 under the control of a CMV promoter.

value: female

value: unknown

value: embryonic

tag: lab

value: Michael Snyder, Stanford

tag: link

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/

value: ENCBS564GDD at ENCODE; https://www.encodeproject.org/ENCBS564GDD/

value: ENCODE dbxrefs Cellosaurus CVCL_0045; https://web.expasy.org/cellosaurus/CVCL_0045


title: E3_Bisulfite-seq_discovery

value: Parkinson’s UK Brain Bank Centre for Neuroscience Imperial College London

tag: pmi

tag: diagnosis

value: PD

tag: asymmetry group

value: Unmatched

value: L


title: E1_Bisulfite-seq_discovery

value: UK PD Society Tissue Bank at Imperial College

value: No

value: Brain prefrontal cortex neurons (NeuN+)

tag: brain hemisphere

value: R

tag: duration


title: PC DNA

city: beijing

first: guo

last: runzhi

address: 205 chengfu road, haidian district, Beijing

institute: Peking university

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: periodontal ligament cells

growth_protocol: When the cell confluence reached 80%, the plasmids H19 and PCDNA3.1 were transfected into PDLCs for 48 h.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cells

value: periodontal ligament cells

tag: overexpression

value: control


title: H19


title: D12_Bisulfite-seq_discovery

value: M


title: D11_Bisulfite-seq_discovery

value: Harvard

value: F


title: Sample_sh_3

city: ShenYang

first: Ke

last: Ning

state: LiaoNing

address: PuHe street No.77

institute: China Medial University

data_processing:
Raw data (raw reads) were processed using NGS QC Toolkit. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks , and the read counts of each gene were obtained by htseq-count . DEGs were identified using the DESeq (2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
If it was transcript-level quantification, FPKM and read counts value of each transcript (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using the DESeq (2012) functions estimateSizeFactors and nbinomTest. P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore transcripts expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
The reads were reassembled using cufflinks. Then gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using cuffcompare software.
The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was performed using ASprofile.SNP and INDEL were called using samtools and bcftools, and the details were shown on samtools webpage (http://samtools.sourceforge.net/mpileup.shtml). Then snpeff annotates and predicts the effects of variants on genes (such as amino acid changes).
Genome_build: Human Ch38
Supplementary_files_format_and_content: FPKM

source_name: Stomach adenocarcinoma

growth_protocol: Cells were cucltured in DMEM medium with 10% FBS

extract_protocol:
Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Negative control shcontrol (NC) and shJMJD1A (sh) were transfected into cells. The transfected cells were screened with purinomycin. After screening for three times, Cell were harvested and performed to analyze JMJD1A downstream genes.

tag: cell line

value: SGC-7901 cell

tag: knockdown

value: JMJD1A knockdown


title: D10_Bisulfite-seq_discovery

tag: cell type

value: matched


title: D7_Bisulfite-seq_discovery

tag: age

value: Control


title: Sample_sh_1


title: Sample_NC_3

value: wild type


title: Sample_sh_2


title: D6_Bisulfite-seq_discovery

tag: brain bank


title: TC568c.A1533

first: Yuanxin

last: Xi

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

description: SC49 and "TC568" are from the same patient.

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
RNA-seq reads were aligned to hg19 genome using tophat v2.0.13
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq/miRNAseq reads count were calculated using HTSeq 0.6.1p1

growth_protocol: Tumors were grown in mice to between 500-800 mm3

extract_protocol:
Tumors were collected and RNA extracted using Trizol reagent and purified with a Qiagen RNeasy kit
Libraries were prepared using the Illumina TruSeq RNA Library Prep kit following the manufactory manual.

treatment_protocol: Mice were untreated

tag: disease state

value: Small cell lung cancer (SCLC)

tag: tissue

value: flank

tag: sample type

value: PDX

tag: treatment

value: untreated

tag: platinum response

value: resistant


title: Sample_NC_1


title: Sample_NC_2


title: D3_Bisulfite-seq_discovery

tag: tissue id

tag: replicate

value: No

value: Brain prefrontal cortex neurons (NeuN+)

tag: Sex

tag: pmi


title: D5_Bisulfite-seq_discovery

tag: diagnosis

tag: asymmetry group

tag: brain hemisphere

value: L

tag: duration


title: TC568c.A1532


title: D2_Bisulfite-seq_discovery

value: R


title: D4_Bisulfite-seq_discovery

value: PD


title: TC568c.A1531


title: SC49.A1430

value: CDX


title: D1_Bisulfite-seq_discovery

value: Harvard

value: F


title: SC49.A1428


title: C12_Bisulfite-seq_discovery

value: Parkinson’s UK Brain Bank Centre for Neuroscience Imperial College London

value: M


title: C11_Bisulfite-seq_discovery

value: Sepulveda

value: Control


title: C10_Bisulfite-seq_discovery

value: Yes


title: SC4.920_flank

value: Small cell lung cancer (SCLC)

value: flank

value: sensitive


title: C9_Bisulfite-seq_discovery


title: SC4.918_flank

value: untreated


title: C8_Bisulfite-seq_discovery

value: No


title: SC4.616_flank


title: SC4.917_flank


title: C7_Bisulfite-seq_discovery

value: Brain prefrontal cortex neurons (NeuN+)

value: matched


title: SC4.613_flank


title: C6_Bisulfite-seq_discovery

value: R


title: C4_Bisulfite-seq_discovery

value: UK PD Society Tissue Bank at Imperial College

value: PD


title: SC49.A1431

value: CDX

value: resistant


title: SC39.963_flank


title: SC39.739_flank


title: SC16.A1466


title: B8_Bisulfite-seq_discovery

value: Parkinson’s UK Brain Bank Centre for Neuroscience Imperial College London

value: Unmatched


title: SC39.964_flank


title: SC16.A1467


title: B5_Bisulfite-seq_discovery

value: F

value: L


title: B6_Bisulfite-seq_discovery

value: M


title: C1_Bisulfite-seq_discovery

value: Yes

value: Control


title: B7_Bisulfite-seq_discovery


title: B4_Bisulfite-seq_discovery


title: B12_Bisulfite-seq_discovery


title: B10_Bisulfite-seq_discovery


title: B11_Bisulfite-seq_discovery


title: SC16.A1465

value: Small cell lung cancer (SCLC)

value: flank


title: B1_Bisulfite-seq_discovery

value: No


title: B3_Bisulfite-seq_discovery

value: Brain prefrontal cortex neurons (NeuN+)


title: B9_Bisulfite-seq_discovery

value: matched


title: B2_Bisulfite-seq_discovery


title: A11_Bisulfite-seq_discovery

value: R


title: SC4.435_flank

value: untreated

value: sensitive


title: A12_Bisulfite-seq_discovery

value: PD


title: C5_Bisulfite-seq_discovery

value: UK PD Society Tissue Bank at Imperial College


title: A10_Bisulfite-seq_discovery


title: A7_Bisulfite-seq_discovery

value: Parkinson’s UK Brain Bank Centre for Neuroscience Imperial College London


title: C3_Bisulfite-seq_discovery

value: The UK Multiple Sclerosis Tissue Bank


title: A9_Bisulfite-seq_discovery


title: A6_Bisulfite-seq_discovery


title: A8_Bisulfite-seq_discovery


title: A4_Bisulfite-seq_discovery

value: Unmatched


title: larp1dko_torin_RPF_rep2_reseq

city: New Haven

first: Carson

middle: C

last: Thoreen

state: CT

address: 333 Cedar St. SHM B 145

department: Cellular and Molecular Physiology

institute: Yale School of Medicine

description:
LP_CTGACG_CTAGA_larp1dko_torin_RPF_rep2
processed data file: DKO_torinb_RPF_unique.htseqcounts.txt

data_processing:
Library strategy: Ribosome profiling
Basecalls performed using CASAVA 1.8.
Sequenced reads were trimmed for adaptor sequence using fastx toolkit with command line fastx_clipper -Q33 -c -a [adapter sequence]. For WT and sgLARP1 samples adapter sequence was CTGTAGGCACCATCAAT, and for sgLARP1/1B samples adapter sequence was AGATCGGAAGAGCAC. For the double knock out ribo-seq samples, all samples were originally in a single fastq file and reads contained unique molecular identifiers (UMI). Reads from this file were adapter trimmed and then split according to sample-specific barcodes in the reads, generating the fastq files here deposited and incorporating the 5 nt UMIs at the end of the read name. For the double knock out RNA-seq samples, the first nt of each read was removed with fastx_trimmer -f 2.
Reads were then filtered for human rRNA sequences using bowtie2 (version 2.2.9.0) with default parameters.
Unmapped reads were aligned to the hg19 human genome using tophat2 (v2.1.1) using default parameters and ucsc hg19 GTF file. For the double knock out ribo-seq data, all UMI-duplicate alignments were removed
Aligned footprint and RNA reads mapping to CDS regions were quantified using HTSeq-count (htseq-count -f bam -t CDS, htseq-count -f bam -t CDS -s reverse for sgLARP1+sgLARP1B RNA sample), using a ucsc hg19 GTF file containing gene ids. The resulting counts were compared per genotype separately, using DESeq (design = ~ sampletype + condition + sampletype:condition).
Genome_build: hg19
Supplementary_files_format_and_content: htseq-count, txt

source_name: RPF from sgLARP1+sgLARP1B HEK-293T cells treated with 250 nM Torin 1 for 2h

growth_protocol: Cells were grown in DMEM + 10%FBS.

extract_protocol:
Cells were lysed on plate in 15 mM Hepes pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1% Triton-X100. Clarified lysates were split in two to make libraries for ribosome profiling and RNA-seq.
For ribosome profiling lysates were RNase I treated and centrifuged through a sucrose cushion. RNA was extracted from the resulting ribosome pellet by proteinase K treatment and acid phenol extraction. rRNA was removed with the Ribo-Zero Gold kit. 28-34 nt footprints were then isolated on polyacrylamide gel, dephosphorylated followed by 5' adapter ligation (in case of the double knock out samples, this adapter contained a unique molecular identifier and an additional barcode) and reverse transcription. The resulting cDNA was circularized and PCR amplified, incorporating Illumina sequences. For RNA-seq on WT cells RNA was extracted from the lysate by proteinase K digestion followed by phenol acid extraction and fragmented by alkaline hydrolysis. 40-80 nt fragments were purified and libraries were further prepared similar to the RPF libraries. For sgLARP1 and sgLARP1/1B cells, RNA-seq libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep kit along with the NEBNext rRNA Depletion kit. RPF libraries for LARP1/1B DKO cells were sequenced twice to improve coverage. These samples are identified with "reseq" in the sample name.

treatment_protocol: Cells were treatred with 250 nM Torin 1 or an equivalent volume of vehicle (DMSO) for 2 h.

tag: cell line

tag: genotype/variation

value: 250 nM Torin 1 for 2h

tag: molecule subtype

value: RNA  (RPFs)


title: larp1dko_torin_RPF_rep1_reseq

description:
LP_CTGACG_AGCTA_larp1dko_torin_RPF_rep1
processed data file: DKO_torina_RPF_unique.htseqcounts.txt


title: P2C3

source_name: Control_Brain prefrontal cortex neurons (NeuN+)

value: F

tag: age

tag: asymmetrygroup

tag: brainhemisphere

tag: tissue/cell type

value: Brain prefrontal cortex neurons(NeuN+)

tag: brain bank

value: U. of Miami Brain Endowment Bank

tag: tissueid


title: P2C1

source_name: PD_Brain prefrontal cortex neurons (NeuN+)

value: Parkinson's disease (PD)

value: Yes


title: P2C2

value: Control

value: L

value: No


title: P2C4


title: P2C6

value: R


title: P2C7


title: ARCaPM replicate 1

city: Oxford

first: Srinivasa

middle: R

last: Rao

address: Botnar Research Centre, Institute of Musculoskeletal Sciences, Windmill Road, Headington

department: Nuffield Dept. of Surgical Sciences

country: United Kingdom

institute: University of Oxford

data_processing:
compressed sequencing files in fastq format were uploaded to the Chimira (v 1.0) website - http://wwwdev.ebi.ac.uk/enright-dev/chimira/index.php to generate known and novel miRNA counts
The counts matrix was analysed for differential expression using DESeq2 (v 3.5)
Genome_build: hg37
Supplementary_files_format_and_content: Each processed file contains the full microRNA name and the corresponding counts normalized to total reads for that sample

source_name: ARCaPM cell line

growth_protocol: Both ARCaPE and ARCaPM cells were cultured in T medium as described in Zhau et al. (PMID: 8986779)

extract_protocol:
Total RNA was extracted using Trizol/phenol/chloroform method and Dnase-treated
50 bp paired end small RNA libraries (<200 nt) were prepared at the Wellcome Trust Centre for Human Genetics

value: ARCaPM

tag: cell type

value: prostate cancer cell

tag: phenotype

value: Mesenchymal


title: ARCaPM replicate 2


title: ARCaPE replicate 3

source_name: ARCaPE cell line

value: ARCaPE

value: Epithelial


title: P2C5

tag: Sex

tag: replicate


title: ARCaPE replicate 2


title: ARCaPE replicate 1


title: P2B11

tag: diagnosis

tag: pmi

value: UCLA Human Brain and Spinal Fluid Resource Center


title: P2B10


title: P2B8

value: M


title: larp1dko_dmso_RPF_rep1_reseq

description:
LP_CTGACG_ATCGT_larp1dko_dmso_RPF_rep1
processed data file: DKO_DMSOa_RPF_unique.htseqcounts.txt

source_name: RPF from sgLARP1+sgLARP1B HEK-293T cells treated with DMSO for 2h

tag: treatment

value: DMSO for 2h

value: RNA  (RPFs)


title: P2B7

value: Matched

tag: duration

value: Brain prefrontal cortex neurons(NeuN+)


title: P2B6

value: Parkinson's disease (PD)

value: Unmatched

value: U. of Miami Brain Endowment Bank


title: P2B9

value: Control

value: Yes


title: larp1dko_dmso_RPF_rep2_reseq

description:
LP_CTGACG_CGTAA_larp1dko_dmso_RPF_rep2
processed data file: DKO_DMSOb_RPF_unique.htseqcounts.txt

tag: cell line


title: P2B5

value: R

value: No


title: P2B12

value: F

value: L


title: ARCaPM replicate 3

value: ARCaPM

value: prostate cancer cell

value: Mesenchymal


title: Low-grade serous ovarian carcinoma sample 5

city: Jinan

first: Xiaoxue

last: Tian

state: Shandong Province

address: 44 Wenhua Xi Road

department: Department of Cell Biology

institute: Shandong University

description: The Low-grade serous ovarian carcinoma specimens were from primary ovarian cancer patients with no surgery or chemotherapy previously

hyb_protocol: Cy3-Labeled cRNA was hybridized to Custom Arraystar Human LncRNA Array v2.0 (8x 60K, Arraystar) using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX software package (Agilent Technologies). After quantile normalization of the raw data, lncRNAs and mRNAs that at least 7 out of 14 samples have flags in Present or Marginal (All Targets Value) were chosen for further data analysis.

source_name: The Low-grade serous ovarian carcinoma

label_protocol: One ug of total RNA was labelled with Cy3 and specific activity of the labeled cRNAs were measured by NanoDrop ND-1000

growth_protocol: Serous ovarian carcinoma and normal fallopian tube were collected within 2 hours of surgery. Then we using the Biopulverizer to the cryopulverization of tissue and using the Mini-Bead-Beater-16 to the Homogenization. Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. The amount of TRIzol Reagent added is based on the area of the culture dish (1 ml per 10 cm2) and not on the number of cells present.

extract_protocol: The mRNA of each samples was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

treatment_protocol: not applicable

tag: disease state

value: Low-grade serous ovarian cancer

tag: tissue

value: Low-grade serous ovarian carcinoma


title: Low-grade serous ovarian carcinoma sample 3


title: Low-grade serous ovarian carcinoma sample 6


title: Low-grade serous ovarian carcinoma sample 4


title: Low-grade serous ovarian carcinoma sample 2


title: Low-grade serous ovarian carcinoma sample 1


title: P2B2

tag: age


title: P2B4

value: M

tag: asymmetrygroup


title: P2A11

value: Matched

tag: brainhemisphere


title: P2B1

tag: tissue/cell type

value: Brain prefrontal cortex neurons(NeuN+)


title: P2B3

tag: brain bank


title: P2A12

value: Parkinson's disease (PD)

tag: tissueid


title: P2A9

value: UCLA Human Brain and Spinal Fluid Resource Center


title: P2A7

value: U. of Miami Brain Endowment Bank


title: P2A8

value: Unmatched


title: P2A10

value: Control


title: P2A6

value: R


title: P2A5

value: No


title: P2A4

value: F

value: Yes


title: P2A3


title: P2A2

value: L


title: Fallopian tube sample 2

description: Normal fallopian tube from patients who received a total hysterectomy and bilateral salpingo-oophorectomy for uterine diseases or benign neoplastic adnexal pathologic changes.

source_name: Normal fallopian tube

value: control

value: Normal fallopian tube


title: High-grade serous ovarian carcinoma sample 4

description: The High-grade serous ovarian carcinoma specimens were from primary ovarian cancer patients with no surgery or chemotherapy previously

source_name: The High-grade serous ovarian carcinoma

value: High-grade serous ovarian cancer

value: High-grade serous ovarian carcinoma


title: H11


title: H12


title: Fallopian tube sample 1


title: Fallopian tube sample 5


title: Cyp1b1-/-RAC rep3

city: Madison

first: Nader

last: Sheibani

address: 1111 Highland Ave, 9453 WIMR

department: Ophthalmology and Visual Sciences

institute: University of Wisconsin_Madison

data_processing:
Illumina bcl2fastq v2.20
Read trimming with Skewer v0.2.2b -m pe -q 20 -k 15 -l 25
Read alignment with STAR v2.5.3a --runThreadN 10 --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD XS --outSAMunmapped Within --outFilterMultimapNmax 50
Expression estimation with RSEM rsem-calculare-expression v1.2.31 --alignments --paired-end --no-bam-output
Differential expression estimation with edgeR v3.28.0
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: The data file format is xlsx and shows the differential expression list

source_name: retina astrocytes cells

growth_protocol: Retinal AC were isolated from mouse retina, minced and digested for 45 min with collagenase Type I, Cells were washed twice with DMEM containing 10% FBS, resuspended in 1 ml of DMEM containing 10% FBS in and incubated with rat-anti-mouse CD31 coated with sheep anti-rat magnetic beads

extract_protocol:
Total RNA from retinal AC cells was extracted using mirVana PARIS kit (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: cell type

value: Retina astrocytes

tag: genotype


title: Cyp1b1-/-RAC rep1


title: Cyp1b1-/-RAC rep4


title: Cyp1b1-/-RAC rep2


title: High-grade serous ovarian carcinoma sample 5


title: Wt RAC rep4

value: Wild-type


title: Fallopian tube sample 6


title: Fallopian tube sample 4


title: High-grade serous ovarian carcinoma sample 1


title: High-grade serous ovarian carcinoma sample 3


title: High-grade serous ovarian carcinoma sample 2


title: Wt RAC rep3


title: Wt RAC rep2


title: H10

tag: Sex

value: M

value: Brain prefrontal cortex neurons(NeuN+)

tag: replicate


title: Wt RAC rep1


title: High-grade serous ovarian carcinoma sample 6


title: Fallopian tube sample 3


title: H9

tag: diagnosis

tag: pmi


title: H8

tag: duration


title: H7


title: P2A1

value: Parkinson's disease (PD)


title: H6

value: U. of Miami Brain Endowment Bank


title: TFP

city: Galveston

first: Sara

last: Dann

address: 301 University Blvd

institute: University of Texas Medical Branch

data_processing:
Fastq files were uploaded to the Park Flow server and sequences aligned to the mm10 assemply of the mouse genome using STAR 2.5.3a.
Resulting summary of reads were quantified at the gene level to Ensemble transcripts 83 using Partek's expectation maximization (E/M) annotation model.
Gene counts were normalized to total read counts per sample and then log transformed with an offset of 0.0001.
To identify differentially expressed genes, statistical analysis was performed using Partek's Gene Specific Analysis (GSA) multi-model estimation algorithm. Hierarchical clustering was performed on normalized and log transformed counts with Partek Genomics Suite 6.6 using average linkage and Euclidian distance.
Supplementary_files_format_and_content: Tab-delimited text file includes normalized gene counts for all samples.

source_name: Total RNA was isolated from 5 individual animals and then pooled for RNAseq analysis.

extract_protocol:
Whole mouse cecal tissues were removed, treated with RNAlater at 4oC for 24 hours, snap-frozen, and stored at -80oC until use. Total RNA was isolated using a Directzol kit
Poly(A) enrichment was used to perform ribosomal reduction on 2µg total RNA. Following purification, the mRNA was reverse transcribed into cDNA
RNA-seq by single-end sequencing was performed on an Illumina Hiseq 2500.

tag: background strain

value: whole cecal tissue

tag: treatment

value: Mice were treated with antibiotics, infected with C. difficile spores, and treated with trifluoperazine (TFP). Cecal tissue was harvested 30 hours post-infection.


title: AXPN

tag: tissue

value: treated with antibiotics, infected with C. difficile spores, and treated with amoxapine (AXPN)


title: PBS

value: Mice were treated with antibiotics, infected with C. difficile spores, and treated with phosphate buffered saline (PBS). Cecal tissue was harvested 30 hours post-infection.


title: DXP

value: Mice were treated with antibiotics, infected with C. difficile spores, and treated with doxapram (DXP). Cecal tissue was harvested 30 hours post-infection.


title: Naïve

value: Mice were untreated.


title: H5

value: F

tag: age

value: Matched

value: L

value: No


title: ABX

value: Mice were treated with antibiotics only.


title: Naïve_replicate4

data_processing:
Reads were processed using the DropSeq analysis pipeline developed by the McCarroll lab (http://mccarrolllab.com/dropseq/)
Individual cells were tagged with barcodes, and transcripts within each cell were tagged with distinct UMIs (Unique Molecular Identifiers).
Reads were trimmed at 3' end to remove poly(A) tails with length greater than 5 and at the 5' end for adapters
Reads with barcode base quality less than 10 were filtered out..
Raw reads were aligned to mouse  (GRCm38) genome by STAR (v2.4.0) with default settings
UMI counts expression matrix were generated using Dropseq Tools software (v1.13.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file consisting of UMI gene counts for cells with minimum 100 genes.

source_name: Flow cytometry sorted astrocytes based on TdTomato fluorscence

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on TdTomato fluorescence. Post-sort, cells were suspended in PBS and 16% Opti-prep.
Libraries were created according to the Drop-seq protocol in Macosko et al. Cell 2015. Following reverse transcription, exonuclease I treatment, and PCR, cDNA libraries were quantified and 600 pg of cDNA was tagmented using Nextera XT library prep kit.

treatment_protocol: Induction of EAE in mice. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

tag: genotype/variation

value: wild type

value: Female

tag: mouse status

value: Naive mice


title: H3

value: Control

tag: asymmetrygroup

tag: brainhemisphere

tag: tissue/cell type

value: Brain prefrontal cortex neurons(NeuN+)


title: H4

value: R

tag: brain bank

value: U. of Miami Brain Endowment Bank

tag: tissueid


title: H1


title: Acute_replicate4

tag: strain

value: EAE peak phase

tag: cell type

value: Flow cytometry sorted astrocytes based on TdTomato fluorscence


title: G12

value: Parkinson's disease (PD)

tag: Sex

value: M

value: Unmatched

tag: replicate


title: Acute_replicate3


title: G5

tag: diagnosis

value: F

tag: pmi


title: G10

tag: duration


title: Remitting_replicate3

value: EAE remission phase


title: G9

value: L


title: G8

value: Yes


title: G11

value: Matched

value: No


title: G4


title: G7


title: G6


title: Naive_replicate6 [scRNA-seq]

data_processing:
Reads were processed using the DropSeq analysis pipeline developed by the McCarroll lab (http://mccarrolllab.com/dropseq/)
Individual cells were tagged with barcodes, and transcripts within each cell were tagged with distinct UMIs (Unique Molecular Identifiers).
Reads were trimmed at 3' end to remove poly(A) tails with length greater than 5 and at the 5' end for adapters
Reads with barcode base quality less than 10 were filtered out..
Raw reads were aligned to mouse  (GRCm38) genome by STAR (v2.4.0) with default settings
UMI counts expression matrix were generated using Dropseq Tools software (v1.13.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file consisting of UMI gene counts for cells with minimum 500 genes.

source_name: CNS pellet following Percoll gradient

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and cell density was quantified. Cells were suspended in PBS and 16% Opti-prep.
Libraries were created according to the Drop-seq protocol in Macosko et al. Cell 2015. Following reverse transcription, exonuclease I treatment, and PCR, cDNA libraries were quantified and 600 pg of cDNA was tagmented using Nextera XT library prep kit.

tag: genotype

value: WT

value: Male

value: between 74-96 days of age

tag: diease

value: naive


title: Priming_replicate6 [scRNA-seq]

tag: age

value: EAE


title: G3

value: R

value: Brain prefrontal cortex neurons(NeuN+)

value: U. of Miami Brain Endowment Bank


title: Priming_replicate5 [scRNA-seq]


title: H2

value: Control


title: Priming_replicate4 [scRNA-seq]


title: Remitting_replicate4

tag: genotype/variation

value: wild type

value: Flow cytometry sorted astrocytes based on TdTomato fluorscence


title: Remitting_replicate4 [scRNA-seq]


title: Naive_replicate5 [scRNA-seq]


title: F12

value: M


title: Acute_replicate6 [scRNA-seq]


title: Remitting_replicate5 [scRNA-seq]


title: F11


title: G1

value: Parkinson's disease (PD)

value: F

value: Unmatched


title: Acute_replicate5 [scRNA-seq]


title: F9

value: L


title: Naive_replicate4 [scRNA-seq]


title: F8

value: No


title: H3K9me2.mP.rep2

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

data_processing:
Base-calling was performed using CASAVA.
Firstly, All of the Histone modification ChIP-seq data were send to trim-galore to remove adapter contamination and low quality sequences, Phred score of any bases in a reads under 20 and adapter sequence were removed, reads after trimming shorter than 30 were discarded.
Trimmed sequences were then mapped with Bowtie (v2.2.6) using default parameters. Duplicate reads were removed by samtools rmdup -s. Unique and monoclonal mapped reads were extended to 150-bp based on the average sonicated chromatin DNA length.
Spike-in reads were mapped to drosophila genome (dm6) using same parameters.
GenomeCoverageBed (bedtools) was used to transfer bed files to bedGraph files, then spikein reads was used as a normalization factor that equalizes the signal across samples. Normalized bedGraph files were subsequently transferred to bigwig files.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig&bed

growth_protocol: Spermatogenesis was synchronized and validated as previously described.

extract_protocol:
ChIP assay was carried out as previously described. The sorted homogenous synchronous spermatogenic cells were crosslinked with 1% formaldehyde for 10 mins and then stopped by adding 125 mM Glycine. Chromatin samples were lysed with lysis buffer (20 mM Tris-HCl pH8.0, 500 mM NaCl, 1 mM EDTA, 1% TritonX-100 and 0.1% SDS) and sonicated with Qsonica. Histone modification specific antibody was incubated with chromatin samples overnight at 4 ℃.0.5 ug spike-in antibody (Active motif #61686) and 25 ng spike-in chromatin (Active motif #53083) were used in this ChIP assay according to the manufacture’s guidelines.
DNA samples were analyzed using real time PCR and prepared for deep sequencing according to the manufacture’s guidelines (KAPA Biosystems KK8503 and VAHTS Universal DNA Library Prep Kit for Illumina V3 ND607). Finally, libraries were pooled and sequenced on the Illumina HiSeq 2500 sequencer for 150-bp paired-end sequencing.

treatment_protocol: Briefly, 2-dpp mice were pipette fed 100 μg/g body weight WIN 18,446 (MP), suspended in 1% gum tragacanth, for 7 consecutive days. At Day 8 of WIN 18,446 treatments, these animals were received an i.p. injection of RA (Sigma; 30 μg/g body weight) in dimethyl sulfoxide (DMSO), and were then left to recover for sample collections. The undifferentiated spermatogonia was isolated from Lin28-YFP knockin mice. Testes from 3-week-old Lin28-YFP knockin mice were collected and digested by type I collagenase and 0.25% Trypsin as described previously1. After centrifugation, the pellet was resuspended in DMEM containing 2% BSA at a concentration of 1×106 cells/40 μL, followed by incubating with PE-conjugated anti-CD117 antibody (0.1 μg/106 cells; Molecular probes) for 30 min on ice. The undifferentiated spermatogonia (YFP-positive, PE-negative population) was collected using FACS (BD). The type A1 spermatogonia was isolated from synchronous Stra8-GFPCre mice. Testes were collected and digested. The type A1 spermatogonia (GFP-positive population) was collected using FACS. The type B spermatogonia and different stages of spermatocytes were isolated from synchronous Lin28-YFP and Vasa-tdTomato double positive mice. To isolate the type B spermatogonia, testes were digested and the synchronous advanced spermatogenic cells (tdTomato positive population) were collected using FACS. To isolate different stages of spermatocytes, testes were digested and the cell suspensions were stained with Hoechst 33342. The tdTomato positive 4N population were collected using FACS. The identity of sorted spermatocytes were validated using surface spreading and immunofluorescence.

tag: stage during meiotic process

value: mP

tag: chip antibody


title: H3K9me2.Late-Z.rep1

value: homogenous synchronous spermatogenic cells

value: Late-Z


title: H3K9me2.TypeB.rep2

value: TypeB


title: Acute_replicate4 [scRNA-seq]

value: WT

value: Male

value: between 74-96 days of age

value: EAE


title: H3K9me2.Undiff.rep2

value: Undiff


title: H3K9me3.D.rep2

value: wild type

value: D


title: F6

value: M

tag: asymmetrygroup

tag: brainhemisphere

value: R

value: Brain prefrontal cortex neurons(NeuN+)

value: U. of Miami Brain Endowment Bank


title: H3K9me2.L.rep2

value: L


title: F10

value: Parkinson's disease (PD)

value: Matched

tag: tissue/cell type

tag: brain bank

value: No


title: H3K9me2.D.rep2

tag: strain

value: homogenous synchronous spermatogenic cells


title: H3K9me2.mPL.rep2

tag: cell type

value: mPL


title: H3K9me3.mP.rep2

value: mP


title: H3K9me2.A1.rep2


title: G2

tag: Sex

value: F

tag: tissueid


title: F5

tag: diagnosis

tag: replicate


title: H3K9me3.Late-Z.rep1

value: Late-Z


title: Remitting_replicate6 [scRNA-seq]

value: WT

value: Male

value: between 74-96 days of age

value: EAE


title: F4

value: M

tag: pmi

tag: duration


title: F7

value: Control

value: Yes


title: H3K9me3.L.rep2

value: wild type


title: H3K9me3.mPL.rep2


title: H3K9me3.TypeB.rep2

value: TypeB


title: H3K9me3.Undiff.rep2

value: Undiff


title: H3K9me3.A1.rep2


title: H3K27me3.mP.rep2


title: H3K27me3.Late-Z.rep1


title: F3

value: Parkinson's disease (PD)

value: Unmatched

value: L

value: Brain prefrontal cortex neurons(NeuN+)

value: U. of Miami Brain Endowment Bank


title: F2

value: R

value: No


title: H3K27me3.D.rep2

value: homogenous synchronous spermatogenic cells

value: D


title: P4

city: Ceske Budejovice

first: Lenka

last: Gahurova

address: Branisovska 1760

department: Department of molecular biology and genetics

country: Czech Republic

institute: University of South Bohemia

description: total+polyA RNA

data_processing:
Library strategy: ribosome profiling
Read trimming (adapters and low quality bases) - Trim Galore! v0.4.1
Quality control - FastQC v0.11.5
Mapping - Hisat2 v2.0.5
Genome_build: GRCm38
Supplementary_files_format_and_content: all_genes_fpkm.txt - a text file with information about gene coordinates and fpkm values in individual replicates and averaged value per sample type in all genes
Supplementary_files_format_and_content: Expressed_genes.txt - a text file with information about fpkm and tpm levels of expressed genes (mean fpkm>0.1 in 4 replicates of at least one sample type )
Supplementary_files_format_and_content: DESeq2_P_vs_NP.txt - a text file with information about fpkm and tpm expression values  and fold change values of genes identified as differentially enriched between NP and P datasets

source_name: polysomal fractions

growth_protocol: GV oocytes were obtained from 8 weeks old CD1 mice 46 h after injection by 5 IU pregnant mare serum gonadotropin. Oocytes were isolated in germinal vesicle stage by puncturing ovarian follicles in M2 medium supplemented with 100 µM 3-isobutyl-1-methylxanthine (IBMX) to prevent nuclear envelope breakdown. Selected fully grown oocytes were denuded and cultured in M16 (IBMX free) medium at 37 ᵒC, 5% CO2 for next 180 minutes.

extract_protocol:
Supernatants were loaded onto 10–50% linear sucrose gradients prepared in SW55 Ti tubes and centrifugated at 35,000× g for 65 min at 4 °C. Polysome profiles were recorded using ISCO UA-5 UV absorbance reader. Ten equal fractions were recovered from each sample and subjected to RNA isolation by Trizol reagent. Fractions corresponding to polysomal and non-polysomal part, respectively, were pulled together. These sub-samples were concentrated to 16 µL of Clean & Concentrator-5 (R1014, Zymo Research).
Ribosomal RNA was removed by Ribozero-Gold (MRZG12324, Illumina). Afterwards, RNA was reverse transcribed with a mixture of random and oligodT primers and amplified using the REPLI-g WTA Single Cell Kit (150063, Qiagen), followed by library preparation using the Nextera DNA Library Prep Kit (FC-121-1030, Illumina)

treatment_protocol: Cycloheximide at final concentration 0.1 mg/ml was added to medium and oocytes were cultured for next 10 minutes. 200 NEBD-stage oocytes  were washed three times in PBS/PVA supplemented with cycloheximide and frozen at –80 °C in low-binding tube. To disrupt the zona pellucida and lysate the oocytes, 250 µL of zirconia-silica beads were added to the tube with frozen oocytes together with 350 µL of lysis buffer and Ribolock. Oocytes were disrupted in the mixer mill apparatus MM301. Lysates were clarified by centrifugation at 8000× g for 5 min at 4 °C.

tag: tissue

value: oocytes

tag: developmental stage

value: NEBD


title: H3K27me3.L.rep2

tag: genotype/variation


title: E12

value: M

tag: age


title: H3K27me3.mPL.rep2

tag: stage during meiotic process

value: mPL

tag: chip antibody


title: H3K27me3.TypeB.rep2


title: H3K27me3.A1.rep2


title: H3K27me3.Undiff.rep2


title: E11

value: Control

tag: asymmetrygroup

tag: brainhemisphere


title: H3K36me3.D.rep2

value: wild type


title: P1

description: total+polyA RNA


title: H3K36me3.mP.rep2

value: mP


title: E9

tag: tissue/cell type

tag: brain bank


title: NP4

description: total+polyA RNA

data_processing:
Read trimming (adapters and low quality bases) - Trim Galore! v0.4.1
Quality control - FastQC v0.11.5
Mapping - Hisat2 v2.0.5
Genome_build: GRCm38
Supplementary_files_format_and_content: all_genes_fpkm.txt - a text file with information about gene coordinates and fpkm values in individual replicates and averaged value per sample type in all genes
Supplementary_files_format_and_content: Expressed_genes.txt - a text file with information about fpkm and tpm levels of expressed genes (mean fpkm>0.1 in 4 replicates of at least one sample type )
Supplementary_files_format_and_content: DESeq2_P_vs_NP.txt - a text file with information about fpkm and tpm expression values  and fold change values of genes identified as differentially enriched between NP and P datasets

source_name: non-polysomal fractions

tag: strain


title: H3K36me3.Late-Z.rep1

tag: cell type

value: Late-Z


title: F1

tag: Sex

tag: tissueid


title: E8

tag: diagnosis

value: F

tag: replicate


title: NP3

description: total+polyA RNA


title: H3K36me3.mPL.rep2


title: H3K36me3.TypeB.rep2

value: TypeB


title: H3K36me3.A1.rep2


title: NP2

description: total+polyA RNA


title: E7

tag: pmi

value: L

tag: duration


title: P2

description: total+polyA RNA

tag: tissue

tag: developmental stage


title: P3

description: total+polyA RNA


title: E5

value: Parkinson's disease (PD)

tag: age

value: Unmatched

value: Brain prefrontal cortex neurons(NeuN+)


title: NP1

description: total+polyA RNA


title: E10

value: Matched

value: R

value: U. of Miami Brain Endowment Bank

value: No


title: H3K36me3.Undiff.rep2

tag: genotype/variation

value: homogenous synchronous spermatogenic cells

tag: stage during meiotic process

value: Undiff


title: E4

tag: asymmetrygroup

value: Yes


title: H3K27ac.D.rep2

value: D

tag: chip antibody


title: H3K27ac.mP.rep2

value: wild type


title: H3K27ac.L.rep2


title: H3K27ac.TypeB.rep2


title: H3K27ac.A1.rep2


title: H3K27ac.Undiff.rep2


title: E3

tag: brainhemisphere

tag: tissue/cell type


title: H3K36me3.L.rep2

tag: strain


title: E2

tag: brain bank


title: E1

value: Control

tag: Sex


title: H3K4me3.D.rep2

tag: cell type


title: E6

tag: diagnosis

tag: tissueid


title: H3K27ac.Late-Z.rep1

value: Late-Z


title: Relapse replicate 8

city: Essen

first: Sied

last: Kebir

address: Hufelandstr. 55

institute: DKFZ-Division Translational Neurooncology at the West German Cancer Center (WTZ)

description:
DE77SHFUKBR100140
Gene expression data

hyb_protocol: Standard Affymetric hybridization protocol

scan_protocol: Standard Affymetric scanning protocol

data_processing:
Probe level summarization was performed via a median polish and data quality checked via the ArrayQualityMetrics package (Kauffmann, Gentleman et al. 2009). Background correction carried out via RMA (Bolstad et al., 2003). The RMA algorithm only uses the sequence information of the PM (positive matches) probes in order to calculate probe affinity values. After background correction data quantile normalization was performed, ensuring that signal distributions across chips were identical. The R-package ‘affy’ (Gautier, Cope et al. 2004) was used to perform all the steps previously described.
Mapping of probesets to genes was based on the Affymetrix “HTA-2_0.na34.hg19.transcript” annotation file, which can be downloaded from the Affymetrix web page.

source_name: Glioblastoma

label_protocol: Biotinylated cRNA were prepared with the standard labelling kit for Affymetrix arrays (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Conditions for cell expansion where applicable

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit

treatment_protocol: Radiotherapy and Temozolomide

tag: sample type

value: Tissue glioblastoma sample


title: D12

value: F

tag: pmi

tag: duration

tag: replicate


title: H3K4me3.mP.rep2

value: mP


title: H3K4me3.mPL.rep2

value: mPL


title: H3K4me3.L.rep2

value: L


title: H3K27ac.mPL.rep2


title: Relapse replicate 7

description:
DE74SHFUKBR100097
Gene expression data