title: MUTZ3 - CTBP2 Input - PLASS ctrl Rep2

status: Public on Jul 12 2023

first: Ruud

last: Delwel

address: Dr. Molewaterplein 40

institute: Erasmus MC

data_processing:
Base calling was conducted with bcl2fastq v1.8.4 for runs sequenced on the Hiseq 2500 and v2.20.422 for runs sequenced on the Novaseq 6000
ChIP-seq reads were aligned to the human reference genome build hg19 with either BBMap (v34.92) or bowtie (v1.1.1)
Peak calling was performed with MACS2 (v 2.1.2) using the default settings, using input sequencing data as controls.
Bigwig files were generated for visualization with deepTools bamCoverage (v3.5.1) and the options  --normalizeUsing RPKM --smoothLength 100 --binSize 20
Assembly: hg19
Supplementary files format and content: narrowPeak (except for Input samples)
Supplementary files format and content: bigwig

source_name: Bone marrow

growth_protocol: The MOLM-1 cell line was cultured in RPMI with 10% FCS. The MUTZ3 cell lines were cultured in αMEM with 20% FCS and 20% conditioned 5637 medium

extract_protocol:
Nuclear lysates were sonicated and pulled down with antibody according to one of three different protocols: the Upstate histone protocol, with a single formaldehyde crosslink, or with a double DSG crosslink (see methods)
ChIP samples were processed according to the Illumina TruSeq ChIP Sample Preparation Protocol (Illumina) or Diagenode Library V3 preparation protocol (Diagenode) and either sequenced single-end (1 × 50 bp) on the HiSeq 2500 platform (Illumina) or paired-end (2 × 100 bp) on the Novaseq 6000 platform (Illumina)

value: Bone marrow

tag: cell line

value: acute myelomonocytic leukemia

value: PLASS

tag: antibody

tag: protocol

value: Single crosslink


title: MUTZ3 - CTBP2 ChIP-seq - PLDLS treated Rep1

type: SRA

city: Rotterdam

country: Netherlands

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: cell type

tag: genotype

tag: treatment

value: PLDLS

value: Double-crosslink DSG


title: MUTZ3 - Input (single crosslink)  - Untreated

value: WT

value: Untreated


title: MOLM1 - CTBP2 Input  - Untreated

value: chronic myeloid leukemia in blast crisis


title: MUTZ3 - CTBP2 ChIP-seq - PLASS ctrl Rep1


title: MUTZ3 - Input (DSG double crosslink) - Untreated


title: MUTZ3 - CTBP2 ChIP-seq - PLASS ctrl Rep2


title: MUTZ3 - CTBP2 ChIP-seq - PLDLS treated Rep2


title: APP;ST2WT_Microglia, PBS, 3hours, rep2 [BulkRNA_ST2WT_Con_2]

status: Public on Jul 18 2023

city: Hong Kong

first: Nancy

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

country: China

description:
BulkRNA_ST2WT_Con_2
BulkRNA_ST2WT_Con_2
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_ST2KO_DESeq2_normalized_count.csv

library_source: transcriptomic

data_processing:
We aligned the sequencing data to the mm10 mouse reference genome using STAR and quantified the data using the Rsubread package in R. We also performed differential expression analysis using the DESeq2 package in R. Genes were considered differentially regulated if the adjusted p value was < 0.1. We visualized the gene expression of differentially expressed genes (DEGs) under different conditions using Morpheus online software. We functionally annotated the DEGs by GO enrichment analysis and the STRING database.
assembly: mm10
csv file include DESeq2 normalized count for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: brain

extract_protocol:
In brief, we deeply anesthetized adult mice using isoflurane and then perfused them with ice-cold PBS. We isolated the forebrain, minced them into small pieces, then mechanically dissociated them with a Dounce homogenizer on ice. We used a Percoll gradient (30%; Sigma-Aldrich) to remove myelin. We blocked the resultant mononuclear cell suspensions with an FcR blocker for 10 min on ice, then incubated them with antibody in the dark for 30 min on ice. Next, we performed flow cytometry analysis and cell sorting with a BD Influx Cell Sorter. We used unstained controls to identify cell populations and visualized clear subpopulations of living microglia on scatter plots; the purity of microglial isolation was routinely >90% according to a reanalysis of the sorted cells.
We sorted approximately 10,000 living microglia directly into RA1 Lysis Buffer and stored them at −80 °C until RNA extraction. We then extracted RNA from the microglia using a NucleoSpin RNA XS Kit (Macherey-Nagel) according to the manufacturer’s instructions. We immediately converted the extracted RNA into full-length complementary DNA (cDNA) using a SMART-Seq v4 kit (Takara Bio). Next, we quantified the concentrations of the cDNA libraries with Qubit (Thermo Fisher Scientific) and fragment lengths with Fragment Analyzer (Advanced Analytical). For library construction, we tagmented 1 ng cDNA by incubation with Tn5 transposase (Illumina) for 30 min at 55 °C and then amplified the tagmented cDNA by PCR for 12 cycles. We size-selected the libraries (100–600 bp) with AMPure XP beads (Beckman Coulter). We quantified the concentrations of the final libraries with Qubit (Thermo Fisher Scientific) and fragment lengths with Fragment Analyzer (Advanced Analytical). We performed paired-end sequencing using a NextSeq 500 or NovaSeq 6000 instrument (Novogene) according to the manufacturer’s instructions.

value: brain

value: Microglia

value: PBS, 3hours


title: MOLM1 - CTBP2 ChIP-seq - Dox

value: Doxycycline


title: APP;ST2WT_Microglia, PBS, 3hours, rep1 [BulkRNA_ST2WT_Con_1]

institute: Hong Kong University of Science and Technology

description:
BulkRNA_ST2WT_Con_1
BulkRNA_ST2WT_Con_1
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_ST2KO_DESeq2_normalized_count.csv


title: MOLM1 - EVI1 ChIP-seq  - Untreated

value: Cell Signaling, cat 2593


title: MOLM1 - CTBP2 ChIP-seq  - Untreated


title: MUTZ3 - RUNX1 ChIP-seq  - Untreated

value: Abcam cat AB23980, lot GR3364239-1


title: MUTZ3 - ERG ChIP-seq  - Untreated

value: Santa-cruz Erg-1/2/3 Antibody (D-3):sc-271048


title: MUTZ3 - CTBP2 ChIP-seq  - Untreated


title: MUTZ3 - EVI1 ChIP-seq - Untreated


title: MUTZ3 - P300 ChIP-seq  - Untreated

value: Diagenode, #C15200211


title: MUTZ3 - MYB ChIP-seq  - Untreated

value: Bone marrow

value: Millipore, catalog no. 05-175


title: MUTZ3 - H3K9Me3 ChIP-seq  - Untreated

value: acute myelomonocytic leukemia

value: H3K9ME3, Diagenode, cat no C15410193, lot A2217P


title: MUTZ3 - H3K27Me3 ChIP-seq  - Untreated

value: H3K27ME3 Diagenode cat no C15410195, lot A0824D


title: MUTZ3 - H3K27Ac ChIP-seq  - Untreated

value: Abcam, catalog no. ab4729

value: Histone


title: LNCaP_clone1, H3K27ac

status: Public on Jul 11 2023

city: Budapest

first: Andras

last: Furedi

state: HU

address: Magyar tudosok krt 2

department: Molecular Life Sciences

country: Hungary

institute: HUN-REN RCNS

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
Reads were aligned to hg19 using BWA.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: LNCaP

growth_protocol: LNCaP metastatic prostate cancer cells were maintained in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the ThruPLEX DNA-seq Kit (Takara). 10 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 10 cycles on the thermocycler. Post amplification libraries were size selected at 200-500bp in length using Agencourt AMPure XP beads (Beckman Coulter). Library fragment size distributions were analyzed using 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent).
Diagenode Cat# C15410196 H3K27ac antibody was used.

treatment_protocol: H3K27ac signal intensities were interrogated at the IRX4 genomic region in single copy IRX4 enhancer (47bp long allele) knock in isogenic cell lines (clone 1 (C1) and clone 2(C2)) compared to the wild type (carrying 4 21 bp short allele) parental LNCaP cell line.

value: LNCaP

value: human metastatic prostate cancer

tag: chip antibody

value: H3K27ac Diagenode (Cat# C15410196)


title: LNCaP_clone2, H3K27ac


title: MUTZ3 - CTBP2 Input - PLASS ctrl Rep1

value: PLASS

value: Single crosslink


title: 7A_M_271

status: Public on Jul 08 2023

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: biopsy, sample34

status: Public on Jul 05 2023

city: DIJON

first: François

last: Ghiringhelli

address: 1 rue du Professeur Marion

country: France

institute: UMR INSERM 1231

data_processing:
Pseudo alignment and quantification were performed using kallisto 0.45
Assembly: GRCh37
Supplementary files format and content: Processed data file is a csv file containing TPM expression values

molecule: total RNA

source_name: CRC Tumor

extract_protocol:
RNA was extracted using the Maxwell RSC RNA FFPE kit (Promega)
RNA depleted of ribosomal RNA was used for the library preparation with a NEBNext Ultra II RNA Directional library Prep kit

value: CRC Tumor

tag: recist criterion

value: Partial response


title: anti-H3K9ac, APOE4-KI

status: Public on Jul 31 2023

city: Bonn

first: Rayk

last: Behrendt

address: Venusberg-Campus 1

department: Institute for Clinical Chemistry and Clinical Pharmacology

country: Germany

institute: University Bonn

data_processing:
Raw fastq files were first checked for quality using Multiqc sequence analysis
Cutadapt (v.4.0) was used to cut adaptors (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT)
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were normalized (to size of mouse genome, 2652783500, RPGC) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.001
BigWig files were created using deeptools and counts were extracted using bedtools multicov command from Bam files. Extracted counts were summarized as matrix file and imported in DESeq2 for normalization and differential analysis.
Motifs were determined using HOMER findMotifsGenome.pl
Assembly: mm10
Supplementary files format and content: BigWig

source_name: Microglia

extract_protocol:
The sonication program was 20 cycles (30 seconds “ON”, 30 seconds “OFF”) each at High power setting. Two ul of anti-H3K9ac antibody (Millipore, 07-352) was added per IP reaction.
The DNA libraries were prepared using NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (NEB, E7103S) following the manufacturer’s instruction. The DNA libraries were analyzed using Qubit 4 Fluorometer (Invitrogen, Q33238) and 2100 Bioanalyzer DNA system (Agilent). The pooled libraries were sent to Genewiz, lnc and sequenced 2x150 bp in Illumina HiSeq platform.

value: Microglia


title: biopsy, sample32


title: biopsy, sample30

value: Stable disease


title: biopsy, sample31


title: biopsy, sample28


title: biopsy, sample27

value: Complete response


title: AD:APOEε3/ε4, female, rep 4

data_processing:
Samples were processed according to Smart-Seq2 protocol and sequenced on Illumina sequencers.
Reads in FASTQ were quantified at the transcript level using Salmon (v1.4) against the Homo_sapiens Ensembl gene catalog (May 2020).
Differential expression analysis was conducted using R (v4.1.1) and DESeq2 (v1.34.0). Hypothesis testing was performed by using either DESeq2’s Wald test on appropriate variable contrasts or with a Likelihood Ratio Test (LRT) for models with greater than two variable conditions being tested.
Assembly: hg38
Supplementary files format and content: tar file of salmon outputs including plaint text  quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters

extract_protocol:
mRNA were isolated using mirVana miRNA isolation kit and 10ng total RNA in 5ul Rnase-free water
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

value: whole tissue

tag: Sex

value: Female


title: biopsy, sample24


title: biopsy, sample23


title: biopsy, sample25


title: biopsy, sample20


title: APP_Microglia, PBS, 24hours, rep3 [BulkRNA_Con_3]

description:
BulkRNA_Con_3
BulkRNA_Con_3
NextSeq 500/NovaSeq 6000
bulkRNA_IL33_timecourse_DESeq2_normalized_count.csv

value: PBS, 24hours


title: biopsy, sample19


title: biopsy, sample14


title: biopsy, sample18


title: biopsy, sample17


title: biopsy, sample15


title: biopsy, sample33


title: biopsy, sample10


title: biopsy, sample13


title: biopsy, sample9


title: biopsy, sample11


title: biopsy, sample16


title: biopsy, sample8


title: biopsy, sample7


title: biopsy, sample12


title: biopsy, sample26


title: biopsy, sample5


title: biopsy, sample4


title: biopsy, sample2


title: biopsy, sample3


title: biopsy, sample6


title: biopsy, sample1


title: biopsy, sample21


title: biopsy, sample22


title: biopsy, sample29


title: T2384_PS49: Bronchoalveolar Lavage - Smoker (96) [re-analysis]

city: Columbus

first: Peter

last: Shields

state: OH

address: 420 West 12th Ave

institute: The Ohio State University

description:
reanalysis of GSM5470860
This is duplicated sample record of GSM5470860 for the convenient retrieval of the complete raw data from SRA.

data_processing:
FASTQC was applied to FASTQ files to assess quality of reads. Reads with average PHRED quality scores >=30 were retained. Cutadapt version v. 1.14 was applied to trim adapter sequences.
Samples with more than 2 sequencing reads were concatanated into one r1 and r2 fastq files for each subject before aligning to human genome
The remaining reads were then aligned to the human genome (hg19) by TopHat v.2.1.0, using the following parameters: -p 8 --no-coverage-search --library-type fr-firststrand hg19.genome Read1.fastq.gz Read2.fastq.gz. To calculate human gene counts, reads that mapped to the human genome (hg19) were contained in a BAM file. The BAM file was provided to subread v.1.6.2 with the following parameters: subread-1.6.2-source/bin/featureCounts -p -a gencode.v19.annotation.gtf -o Featurecount.txt Sample_File.bam
Assembly: hg19
Supplementary files format and content: Raw gene counts for each sample listed in csv file

organism: human lung metagenome

source_name: Bronchoalveolar Lavage

extract_protocol:
Total RNA was extracted from the BAL cell pellets using miRNeasy kit
Total RNA was then treated with TruSeq Stranded Total RNA Gold (Illumina) to remove rRNA; cDNA was then synthesized from the remaining total RNA and the library was generated with the Illumina TruSeq kit.

value: Bronchoalveolar Lavage

tag: smoking status

value: Smoker


title: T2390_PS55: Bronchoalveolar Lavage - Never-Smoker (53) [re-analysis]

description:
reanalysis of GSM5470865
This is duplicated sample record of GSM5470865 for the convenient retrieval of the complete raw data from SRA.

value: Never-Smoker


title: T2386_PS51: Bronchoalveolar Lavage - E-cig User (66) [re-analysis]

description:
reanalysis of GSM5470862
This is duplicated sample record of GSM5470862 for the convenient retrieval of the complete raw data from SRA.

value: E-cig User


title: T2383_PS48: Bronchoalveolar Lavage - E-cig User (101) [re-analysis]

description:
reanalysis of GSM5470859
This is duplicated sample record of GSM5470859 for the convenient retrieval of the complete raw data from SRA.


title: T2380_PS45: Bronchoalveolar Lavage - E-cig User (77) [re-analysis]

description:
reanalysis of GSM5470856
This is duplicated sample record of GSM5470856 for the convenient retrieval of the complete raw data from SRA.


title: T2374_PS39: Bronchoalveolar Lavage - Never-Smoker (64) [re-analysis]

description:
reanalysis of GSM5470851
This is duplicated sample record of GSM5470851 for the convenient retrieval of the complete raw data from SRA.


title: T2379_PS44: Bronchoalveolar Lavage - Smoker (99) [re-analysis]

description:
reanalysis of GSM5470855
This is duplicated sample record of GSM5470855 for the convenient retrieval of the complete raw data from SRA.


title: T2373_PS38: Bronchoalveolar Lavage - E-cig User (88) [re-analysis]

description:
reanalysis of GSM5470850
This is duplicated sample record of GSM5470850 for the convenient retrieval of the complete raw data from SRA.


title: T2376_PS41: Bronchoalveolar Lavage - Smoker (97) [re-analysis]

description:
reanalysis of GSM5470853
This is duplicated sample record of GSM5470853 for the convenient retrieval of the complete raw data from SRA.


title: T2371_PS36: Bronchoalveolar Lavage - Smoker (62) [re-analysis]

description:
reanalysis of GSM5470848
This is duplicated sample record of GSM5470848 for the convenient retrieval of the complete raw data from SRA.


title: T2368_PS33: Bronchoalveolar Lavage - Never-Smoker (73) [re-analysis]

description:
reanalysis of GSM5470845
This is duplicated sample record of GSM5470845 for the convenient retrieval of the complete raw data from SRA.


title: T2364_PS29: Bronchoalveolar Lavage - Never-Smoker (59) [re-analysis]

description:
reanalysis of GSM5470841
This is duplicated sample record of GSM5470841 for the convenient retrieval of the complete raw data from SRA.


title: T2366_PS31: Bronchoalveolar Lavage - E-cig User (79) [re-analysis]

description:
reanalysis of GSM5470843
This is duplicated sample record of GSM5470843 for the convenient retrieval of the complete raw data from SRA.


title: T2360_PS25: Bronchoalveolar Lavage - Smoker (67) [re-analysis]

description:
reanalysis of GSM5470837
This is duplicated sample record of GSM5470837 for the convenient retrieval of the complete raw data from SRA.


title: T2362_PS27: Bronchoalveolar Lavage - Smoker (100) [re-analysis]

description:
reanalysis of GSM5470839
This is duplicated sample record of GSM5470839 for the convenient retrieval of the complete raw data from SRA.


title: T2359_PS24: Bronchoalveolar Lavage - Never-Smoker (60) [re-analysis]

description:
reanalysis of GSM5470836
This is duplicated sample record of GSM5470836 for the convenient retrieval of the complete raw data from SRA.


title: T2354_PS19: Bronchoalveolar Lavage - E-cig User (87) [re-analysis]

description:
reanalysis of GSM5470831
This is duplicated sample record of GSM5470831 for the convenient retrieval of the complete raw data from SRA.


title: T2356_PS21: Bronchoalveolar Lavage - E-cig User (98) [re-analysis]

description:
reanalysis of GSM5470833
This is duplicated sample record of GSM5470833 for the convenient retrieval of the complete raw data from SRA.


title: T2351_PS16: Bronchoalveolar Lavage - Smoker (102) [re-analysis]

description:
reanalysis of GSM5470828
This is duplicated sample record of GSM5470828 for the convenient retrieval of the complete raw data from SRA.


title: T2344_PS9: Bronchoalveolar Lavage - E-cig User (58) [re-analysis]

description:
reanalysis of GSM5470821
This is duplicated sample record of GSM5470821 for the convenient retrieval of the complete raw data from SRA.


title: T2389_PS54: Bronchoalveolar Lavage - Never-Smoker (89) [re-analysis]

description:
reanalysis of GSM5470864
This is duplicated sample record of GSM5470864 for the convenient retrieval of the complete raw data from SRA.


title: T2341_PS6: Bronchoalveolar Lavage - E-cig User (81) [re-analysis]

description:
reanalysis of GSM5470818
This is duplicated sample record of GSM5470818 for the convenient retrieval of the complete raw data from SRA.


title: T2336_PS1: Bronchoalveolar Lavage - Smoker (84) [re-analysis]

description:
reanalysis of GSM5470813
This is duplicated sample record of GSM5470813 for the convenient retrieval of the complete raw data from SRA.


title: T2339_PS4: Bronchoalveolar Lavage - Never-Smoker (78) [re-analysis]

description:
reanalysis of GSM5470816
This is duplicated sample record of GSM5470816 for the convenient retrieval of the complete raw data from SRA.


title: 2uMa-AMA1-1uMEZ2

status: Public on Jun 30 2023

city: Kunming

first: Jinfang

last: Xue

address: No 157 Jinbi Road, Xishan District, Kunming

institute: Kunming University of Science and Technology

description: 2uM α-AMA1-1uM EZ2

data_processing:
Use fastp v 0.19.3 to filter the original data, mainly to remove reads with adapters; when the N content in any sequencing reads exceeds 10% of the base number of the reads, remove the paired reads; when any sequencing reads When the number of low-quality (Q<=20) bases contained in reads exceeds 50% of the bases of the reads, this paired reads will be removed. All subsequent analyses are based on clean reads.
Download the reference genome and its annotation files from the designated website, use HISAT v2.1.0 to construct the index, and compare clean reads to the reference genome.
Use StringTie v1.3.4d for new gene prediction. StringTie applies network streaming algorithms and optional de novo to splice transcripts. Compared with Cufflinks and other software, StringTie can splice a more complete and accurate transcript, and the splicing speed is faster.
Use featureCounts v1.6.2 /StringTie v1.3.4d to calculate the gene alignment and FPKM . FPKM is currently the most commonly used method to estimate gene expression levels.
DESeq2 v1.22.1 /edgeR v3.24.3 was used to analyze the differential expression between the two groups, and the P value was corrected using the Benjamini & Hochberg method. The corrected P value and |log2foldchange| are used as the threshold for significant difference expression.
Assembly: hg38
Supplementary files format and content: XLS files include RPKM values for each Sample

source_name: liver

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels.
RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)

treatment_protocol: L-02 cells were cultured in 10% serum (CHI Scientific, China), 1% penicillin/streptomycin (Gibco, USA), and PRMI1640 (Gibco, USA). When the cell density was greater than 80% of the area of the culture bottle, the cells were passed 5 to 10 times, and then modeling was performed.Normal liver cells L-02 to the third generation were cultured and divided into a control group, a 2μM α-amanitin poisoning group, and a 2μM α-amanitin+1μM Ezetimibe treatment group. Three biological replicates were set up in each group, and the cells were modeled and incubated for 24h after administration and collected for high-throughput sequencing

value: liver

value: WT

value: 2μM α-amanitin poisonning 24h+1μM Ezetimibe


title: 2uMa-AMA1-1uMEZ3

description: 2uM α-AMA1-1uM EZ3


title: 2uMa-AMA1-2uMEZ2

description: 2uM α-AMA1-2uM EZ2

value: 2μM α-amanitin poisonning 24h+3μM Ezetimibe


title: 2uMa-AMA1-2uMEZ3

description: 2uM α-AMA1-2uM EZ3

value: 2μM α-amanitin poisonning 24h+4μM Ezetimibe


title: 2uMa-AMA1-2uMEZ1

description: 2uM α-AMA1-2uM EZ1

value: 2μM α-amanitin poisonning 24h+2μM Ezetimibe


title: 2uMa-AMA2

description: 2uM α-AMA2

value: 2μM α-amanitin poisonning 24h


title: 2uMa-AMA1-1uMEZ1

description: 2uM α-AMA1-1uM EZ1


title: 2uMa-AMA3

description: 2uM α-AMA3


title: T2352_PS17: Bronchoalveolar Lavage - Never-Smoker (63) [re-analysis]

description:
reanalysis of GSM5470829
This is duplicated sample record of GSM5470829 for the convenient retrieval of the complete raw data from SRA.


title: CON3

value: control


title: Day5_PostInjury

status: Public on Jun 16 2023

city: Tarrytown

first: Michael

last: Stec

state: NY

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

data_processing:
Spaceranger 1.3.0
Assembly: mm10

source_name: Gastrocnemius

extract_protocol: 10x Genomics Visium Spatial Gene Expression for Fresh Frozen Tissue v1.0

value: Gastrocnemius

value: cardiotoxin


title: CON1


title: Day3_PostInjury


title: MDX5

value: MDX


title: T2348_PS13: Bronchoalveolar Lavage - Never-Smoker (70) [re-analysis]

description:
reanalysis of GSM5470825
This is duplicated sample record of GSM5470825 for the convenient retrieval of the complete raw data from SRA.


title: CON2


title: T2346_PS11: Bronchoalveolar Lavage - E-cig User (55) [re-analysis]

description:
reanalysis of GSM5470823
This is duplicated sample record of GSM5470823 for the convenient retrieval of the complete raw data from SRA.


title: WT3


title: T2342_PS7: Bronchoalveolar Lavage - Never-Smoker (44) [re-analysis]

description:
reanalysis of GSM5470819
This is duplicated sample record of GSM5470819 for the convenient retrieval of the complete raw data from SRA.


title: hBJ,MNaseSeq,rep2

status: Public on Jun 06 2023

city: Philadelphia

first: Kenneth

middle: S.

last: Zaret

state: PA

address: 9-132, SCTR, 3400 Civic Center Boulevard

department: Cell and Developmental Biology

institute: University of Pennsylvania School of Medicine

data_processing:
Basecalling and Fastq generation was automated through BaseSpace.
Paired-end MNase-seq reads were trimmed with trim_galore version 0.4.3 with parameters --paired -q 20 --minimum-length 20
Reads were aligned to the human genome build hg19 using STAR aligner version 2.5.2a, with run parameters --alignSJDBoverhangMin 999 --alignIntronMax 1 --alignMatesGapMax 1000 --outFilterMultimapNmax 1
A quality-filtered BAM file was generated with the command samtools view -q 5 -f 2 -bS.
Bigwig files were generated using DANPOS3 command dpos.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: BJ fibroblasts

growth_protocol: DMEM, 4.5g/L D-Glucose, L-Glutamine, 110 mg/L Sodium Pyruvate, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were washed, permeabilized, and digested with 80U/mL MNase for 2 minutes at 37C. DNA from chromatin was purified, at which point, mononucleosome-sized DNA fragments were isolated using an AMPure XP bead selection.
MNase-seq libraries were prepared using the NEBNect Ultra II for DNA Library Prep, following manufacturers protocols, with an input of 5-10 ng of purified DNA. The  size distribution of amplified fragments was assessed by TapeStation, and the concentration of libraries was determined by Qubit.

value: BJ fibroblasts

value: Human foreskin fibroblasts


title: MDX4


title: WT1


title: 2uMa-AMA1

description: 2uM α-AMA1


title: SOX2dbd,V5,hBJ,rep2

data_processing:
library strategy: CUT&RUN
Basecalling and Fastq generation was automated through BaseSpace.
Paired-end reads were mapped to the human genome build hg19 using bowtie2 (v2.3.4.1) with run parameters --local --very-sensitive --no-unal --no-mixed --no-discordant -I 10 -X 700.
A quality-filtered BAM file was generated with the command samtools view -q 5 -f 2 -bS.
BED files were generated from BAMs using the bedtools command bamToBed (bedtools v2.27.1).
BED files were converted to bedgraph format using the bedtools command genomecov.
Peaks were called on the bedgraph files with SEACR v1.3, using the stringent setting and selecting the top 0.01% of regions by AUC, with the final peak sets  selected by taking the union of biological replicates.
Bigwig files for visualization of signal over specific genomic regions was generated with deeptools (version 3.5.0).
Assembly: hg19
Supplementary files format and content: bigWig, bed

extract_protocol:
CUT&RUN targeting the V5 tag on SOX2 and SOX2-DBD was performed folloiwng the protocol from Skene et al., 2018 and Janssens et al., 2018.
CUT&RUN libraries were prepared using the NEBNect Ultra II for DNA Library Prep, following the protocol described in Liu et al., 2019.

tag: cut&run antibody

value: V5(Thermo R90-25)

tag: time

value: CUT&RUN after 48 hours ectopic expression


title: MDX1


title: WT2


title: MDX2


title: hBJ,MNaseSeq,rep1


title: MDX3


title: Day1_PostInjury


title: H2Bhalo,t6,rep2

data_processing:
Basecalling and Fastq generation was automated through BaseSpace.
Single-end reads were aligned to the human genome build hg19 using bowtie2 v2.3.4.1 with run parameters --local -X 1000.
Optical and PCR duplicate reads were marked and removed using PICARD MarkDuplicates REMOVE_DUPLICATES=TRUE ASSUME_SORT_ORDER=queryname (GATK 4.2.6.0).
BED files were generated from BAMs using the bedtools command bamToBed (bedtools v2.27.1).
Peaks were called from BED files using MACS2 callpeak against a matched input control with a FDR of 0.1% (MACS2 v2.2.7.1), with final peak sets selected by taking the union of biological replicates.
Bigwig files for visualization of signal over specific genomic regions was generated with deeptools (version 3.5.0).
Assembly: hg19
Supplementary files format and content: bigWig, bed (except for input samples)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a COVARIS.
ChIP-seq libraries were prepared using the NEBNect Ultra II for DNA Library Prep, following manufacturers protocols, with an input of 5-10 ng of immunoprecipitated DNA. The  size distribution of amplified fragments was assessed by TapeStation, and the concentration of libraries was determined by Qubit.

value: HALO(Promega G9281)

value: ChIP-seq at 6 hours dox induction


title: SOX2,V5,hBJ,rep2


title: SOX2dbd,V5,hBJ,rep1


title: HNF4A,HALO,hBJ,rep2,input

value: ChIP-seq after 48 hours ectopic expression


title: SOX2,V5,hBJ,rep1


title: H2Bhalo,t6,input


title: H2Bhalo,t6,rep1


title: FOXA1rraa,HALO,hBJ,rep2,input


title: H2Bhalo,t0,input

value: ChIP-seq at 0 hours dox induction


title: H2Bhalo,t0,rep1


title: HNF4A,HALO,hBJ,rep2


title: H2Bhalo,t0,rep2


title: HNF4A,HALO,hBJ,rep1,input


title: HNF4A,HALO,hBJ,rep1


title: FOXA1rraa,HALO,hBJ,rep2


title: FOXA1rraa,HALO,hBJ,rep1


title: FOXA1rraa,HALO,hBJ,rep1,input


title: FOXA1nhaa,HALO,hBJ,rep2,input


title: FOXA1nhaa,HALO,hBJ,rep2


title: FOXA1dbd,HALO,hBJ,rep2,input


title: FOXA1nhaa,HALO,hBJ,rep1


title: FOXA1nhaa,HALO,hBJ,rep1,input


title: FOXA1,HALO,hBJ,rep1,input


title: FOXA1dbd,HALO,hBJ,rep1


title: FOXA1dbd,HALO,hBJ,rep2


title: FOXA1,HALO,hBJ,rep2


title: FOXA1,HALO,hBJ,rep2,input


title: FOXA1,HALO,hBJ,rep1


title: K8Y CR LY6D+ cells_D7

status: Public on May 12 2023

city: Manchester

first: Esther

last: Baena

address: The University of Manchester, Wilmslow Road

department: Prostate Oncobiology

country: United Kingdom

institute: Cancer Research UK Manchester Institute

data_processing:
Genome generation with STAR (version 2.5.1b); Mus_musculus.GRCm38.dna.primary_assembly.fa (ensembl release 81) and Mus_musculus.GRCm38.81.gtf with --sjdbOverhang set to 74
For samples generated from "Run_1_EB3" or "Run_2_EB3"; fastq files were trimmed with trim_galore (version 0.6.5) with --nextera. Trimmed values were concatenated together and subjected to STAR alignment
For samples generated from "Run_3_EB5"; fastq files were concatenated together (no trimming with trim_galore) and subjected to STAR alignment
Reads were aligned with STAR (version 2.5.1b); --outSAMstrandField intronMotif  --quantMode GeneCounts --outSAMattributes All and --outSAMtype BAM SortedByCoordinate as parameters
Count matrix generated by collapsing together reads-per-gene STAR output files (second column - unstranded RNA-seq)
Genome_build: GRCm38 (ensembl release 81)
Supplementary_files_format_and_content: R object (class DGEList for edgeR)

source_name: PTEN-WT CR_YFP+LY6D+ population rep2

extract_protocol:
Prostate was removed and dissected, cells were FACS-isolated based on YFP expression and cell surface markers, and RNA was harvested using RNA/DNA purification micro kit (Norgen, #50300). RNA Sequence library prep was performed according to a modified Smartseq2 protocol (Picelli, 2014) using Superscript II (Thermo Fisher #18064022) for reverse transcription of polyA-RNA and Kapa Hifi Hotstart Readymix PCR kit (#KR0370) for second strand synthesis and amplification. Tagmentation reactions were carried out using a Nextera XT DNA Library Preparation Kit (Illumina, #FC-131-1024). Libraries were quantified using Kapa Library Quantification Kit for Illumina Sequencing Platforms (Roche, #07960336001). Single read 75bp sequencing was carried out by clustering 2pM of pooled libraries on a Nextseq500 sequencer (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 4-months post-Tamoxifen

tag: condition

value: Castrated

value: PTEN-WT

tag: subpopulation

value: P7_YFP+ LY6D+

value: Luminal prostate cells


title: K8Y CR LY6D+ cells_A7

source_name: PTEN-WT CR_YFP+LY6D+ population rep1


title: K8Y CR LY6D- cells_E8

source_name: PTEN-WT CR_YFP+LY6D- population rep3

value: P8_YFP+ LY6D-


title: K8Y CR LY6D+ cells_E7

source_name: PTEN-WT CR_YFP+LY6D+ population rep3


title: K8Y CR LY6D- cells_D8

source_name: PTEN-WT CR_YFP+LY6D- population rep2


title: K8Y CR LY6D- cells_A8

source_name: PTEN-WT CR_YFP+LY6D- population rep1


title: K8Y HS LY6D- cells_E4

source_name: PTEN-WT HS_YFP+LY6D- population rep5

value: Hormone Sensitive

value: P4_YFP+ LY6D-


title: K8Y HS LY6D- cells_B4

source_name: PTEN-WT HS_YFP+LY6D- population rep2


title: K8Y HS LY6D- cells_A4

source_name: PTEN-WT HS_YFP+LY6D- population rep1


title: K8Y HS LY6D+ cells_D3

source_name: PTEN-WT HS_YFP+LY6D+ population rep4

value: P3_YFP+ LY6D+


title: K8Y HS LY6D+ cells_E3

source_name: PTEN-WT HS_YFP+LY6D+ population rep5


title: K8Y HS LY6D+ cells_C3

source_name: PTEN-WT HS_YFP+LY6D+ population rep3


title: FOXA1dbd,HALO,hBJ,rep1,input

tag: cell line

value: BJ fibroblasts


title: K8Y HS LY6D+ cells_A3

source_name: PTEN-WT HS_YFP+LY6D+ population rep1


title: K8PY CR LY6D+ cells_C5

source_name: PTEN-KO CR_YFP+LY6D+ population rep3

value: PTEN-KO

value: P5_YFP+ LY6D+


title: K8PY CR LY6D- cells_C6

source_name: PTEN-KO CR_YFP+LY6D- population rep3

value: P6_YFP+ LY6D-


title: K8PY CR LY6D+ cells_B5

source_name: PTEN-KO CR_YFP+LY6D+ population rep2


title: K8PY CR LY6D- cells_A6

source_name: PTEN-KO CR_YFP+LY6D- population rep1


title: K8PY HS LY6D- cells_A2

source_name: PTEN-KO HS_YFP+LY6D- population rep1

value: P2_YFP+ LY6D-


title: K8PY CR LY6D- cells_B6

source_name: PTEN-KO CR_YFP+LY6D- population rep2


title: K8PY HS LY6D- cells_C2

source_name: PTEN-KO HS_YFP+LY6D- population rep3


title: K8PY HS LY6D- cells_B2

source_name: PTEN-KO HS_YFP+LY6D- population rep2


title: K8Y HS LY6D+ cells_B3

source_name: PTEN-WT HS_YFP+LY6D+ population rep2


title: K8PY CR LY6D+ cells_A5

source_name: PTEN-KO CR_YFP+LY6D+ population rep1


title: K8PY HS LY6D+ cells_A1

source_name: PTEN-KO HS_YFP+LY6D+ population rep1

value: P1_YFP+ LY6D+


title: K8PY HS LY6D+ cells_B1

source_name: PTEN-KO HS_YFP+LY6D+ population rep2


title: K8Y HS LY6D- cells_D4

source_name: PTEN-WT HS_YFP+LY6D- population rep4


title: K8PY HS LY6D+ cells_C1

source_name: PTEN-KO HS_YFP+LY6D+ population rep3


title: Mafa Fl/Fl cont ,   Ins2.Apple+,  females, # 1

status: Public on May 01 2023

city: Nashville

first: Jeeyeon

last: Cha

state: Tennessee

address: 300A 54th Avenue North

institute: Vanderbilt University Medical Center

data_processing:
Paired end raw fastq files were assessed for quality by FASTQC and trimmed for adaptor sequence/low-quality sequence by TrimGalore
Trimmed sequence reads were mapped to the reference mouse genome mm10 (GRCm38) using The Spliced Transcripts Alignment to a Reference (STAR) version 2.6. Reference genome annotation used were gencode.vM17.annotation.gtf
Raw read counts were obtained performed using HTSeq v0.9.1.
Assembly: mm10/GRCm38
Supplementary files format and content: tab-delimited text files include HTseq generated raw counts per sample.

source_name: pancreas

extract_protocol:
RNA was harvested using Maxwell simplyRNA kit (Promega). ~12 ng of total RNA was used for amplification and construction of sequencing libraries.
RNA per sample were amplified using  SMART-Seq v4 (Takara)  Library Prep Kit following manufacturer's protocols.

value: pancreas

value: females

value: pancreatic islets

value: Mafa Fl/Fl cont ,   Ins2.Apple+


title: Mafa Fl/Fl cont ,   Ins2.Apple+,  females, # 4


title: Mafa Fl/Fl cont ,   Ins2.Apple+,  males, # 2

value: males


title: Mafa Fl/Fl cont ,   Ins2.Apple+,  females, # 3


title: K8Y HS LY6D- cells_C4

source_name: PTEN-WT HS_YFP+LY6D- population rep3

value: 4-months post-Tamoxifen

value: PTEN-WT


title: Mafa Fl/Fl cont ,   Ins2.Apple+,  males, # 3


title: Mafa Fl/Fl cont ,   Ins2.Apple+,  males, # 1


title: Mafa Fl/Fl cont ,   Ins2.Apple+,  males, # 4


title: Mafa Fl/Fl cont ,   Ins2.Apple+,  females, # 2


title: Mafa -/-, Ins2.Apple+,   Ins1.Cre+,  females, # 2

value: Mafa -/-, Ins2.Apple+,   Ins1.Cre+


title: Mafa -/-, Ins2.Apple+,   Ins1.Cre+,  females, # 4


title: Mafa -/-, Ins2.Apple+,   Ins1.Cre+,  females, # 1


title: Mafa -/-, Ins2.Apple+,   Ins1.Cre+,  males, # 2


title: Mafa -/-, Ins2.Apple+,   Ins1.Cre+,  females, # 3


title: Mafa -/-, Ins2.Apple+,   Ins1.Cre+,  males, # 1


title: Mafa -/-, Ins2.Apple+,   Ins1.Cre+,  males, # 3


title: Mafa -/-, Ins2.Apple+,   Ins1.Cre+,  males, # 4


title: LMP1 KO_biol rep 3

status: Public on Apr 25 2023

city: Boston

first: Bidisha

last: Mitra

state: MA

address: 181 Longwood Avenue, 8th floor

department: Medicine

institute: Brigham and Women's Hospital

description: Sample 3

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental (induced) group and the control (uninduced) group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Assembly: GRCh37.83
Supplementary files format and content: Raw files in fastq.gz format
Supplementary files format and content: Tab-delimited text files with normalized counts of genes also provided.

growth_protocol: Cells cultured in GIBCO RPMI 1640 medium (Life Technologies) with 10% fetal bovine serum (FBS) and penicillin-streptomycin in a humidified chamber at 37 degrees Celcius with 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (#74106, Qiagen) as per manufacturer's protocol. An in-column DNA digestion step was included to remove any residual genomic DNA contamination.
To construct RNA-seq libraries, 1ug total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc.  Ipswich, MA), followed by library construction via NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (#E7765, New England Biolabs, Inc., Ipswich, MA).

treatment_protocol: GM12878 LCL were transduced with lentiviruses expressing control or LMP1 sgRNA. Transduced cells were subjected to 3ug/ml puromycin(#A1113803, Thermo Fisher) selection for 2 days post transduction and collected for RNA extraction.

value: Lymphoblastoid

value: LMP1 Knockout


title: LMP1 KO_biol rep 1

description: Sample 1


title: Control_biol rep 2

description: Sample 5

value: Wildtype


title: LMP1 KO_biol rep 2

description: Sample 2


title: Control_biol rep 3

description: Sample 6


title: Control_biol rep 1

description: Sample 4


title: pulldown_exp2_VHY68_2

status: Public on Apr 12 2023

city: Lund

first: Vasili

last: Hauryliuk

address: BMC, Sölvegatan 17

department: Experimental Medical Science

country: Sweden

institute: Lund University

data_processing:
The quality of Illumina reads was controlled using FastQC (Andrews, 2010). The adaptor sequence (5'-NNNNCTGTAGGCACCATCAAT-3') was removed using Cutadapt (Martin, 2011).
After removing reads mapping to non-coding RNA, reads were mapped to the S. cerevisiae reference genome R64-1-1.85 using HISAT2 (Pertea et al., 2016).
BedGraph profiles were produced from SAM data with samtools (Li H et al., 2009) and plastid (Dunn et al., 2016).
Assembly: R64-1-1
Supplementary files format and content: BedGraph profiles for forward (fw) and reverse (rc) strands.
Library strategy: 5P-Seq

organism: Saccharomyces cerevisiae

growth_protocol: For 5PSeq analysis (with the exception of New1 associated ribosome pulldown samples) 50 ml cultures were grown in SC media, at 180 rpm until OD600 ≈ 0.8 with shaking at 160 rpm. Yeast media was prepared as described (Amberg et al., 2005), with the difference that the composition of the drop-out mix was as per Johansson (Johansson, 2017). Difco Yeast Nitrogen Base w/o Amino Acids was purchased from Becton Dickinson (291940), amino acids and other supplements from Sigma-Aldrich.  For 5Pseq analysis on New1 associated ribosomes. 1L cultures were grown in SC-Ura at 180 rpm in a baffled flask until OD600 ≈ 0.6 with shaking at 160 rpm before induction of New1-HTF for 6 hours with 2µM β-estriadiol.

extract_protocol:
RNA was extracted from all samples via hot-phenolic extraction directly from frozen cell pellets or, where appropriate, from 200 µl of eluate/lysate whereas previously described (Johansson, 2017).    For preparation of New1 associated ribosomal complexes, cryomilled samples were resuspended in 10 ml of 1 x Polymix buffer; (95 mM KCl, 5 mM NH4Cl, 20 mM HEPES pH 7.5, 1 mM DTT, 5 mM Mg(OAc)2, 0.5 mM CaCl2, 8 mM putrescine, 1 mM spermidine supplemented with 0.5 mM ATP  and 0.5 mM EDTA). The lysate was cleared by centrifugation – 2000g, 10 minutes. The lysate was incubated with 100 µl of equilibrated anti-FLAG M2 Affinity Gel for 2 hours with end over end mixing at 4 °C for binding before loading to a gravity flow column. The column was then washed 10 times with 1x polymix buffer before elution in 200 µl of 1x polymix supplemented with 0.1 mg/mL FLAG3 peptide (Sigma). 200 µl of the input lysate was reserved and incubated at 4 °C to use as a control for 5PSeqencing.  5PSeq libraries were prepared as previously described (Zhang and Pelechano,  2021).
5PSeq libraries were prepared as previously described (Zhang and Pelechano,  2021).

treatment_protocol: For 5Pseq analysis (with the exception of New1 associated ribosome pulldown samples) cells were harvested by centrifugation for two minutes at 2000 rpm. Cell pellets were frozen on liquid nitrogen and stored at -80 C until further use.  For 5Pseq analysis of New1 associated ribosomes. Cells were harvested via vacuum filtration, frozen in liquid nitrogen and stored at -80 C until further use.

value: MAT[alpha] ura3[delta]0  leu2[delta]0 his3[delta]1::FRP880 (PACT1(1-520)-LexA-ER-haB112-TCYC1, HIS3) new1::kanMX6

tag: batch


title: pulldown_exp2_VHY68_3


title: pulldown_exp2_VHY68_1


title: pulldown_exp2_VHY68_4


title: lysate_exp2_VHY68_2


title: wt_exp1_MYJ1171_5

tag: temparature

value: MAT[alpha] ura3[delta]0


title: lysate_exp2_VHY68_1


title: lysate_exp2_VHY68_4


title: wt_exp1_MYJ1171_4


title: wt_exp1_MYJ1171_6


title: lysate_exp2_VHY68_3


title: wt_exp1_MYJ1171_3


title: wt_exp1_MYJ1171_1


title: wt_exp1_MYJ1171_2


title: ko_exp1_MYJ1173_4


title: ko_exp1_MYJ1173_5


title: ko_exp1_MYJ1173_3


title: ko_exp1_MYJ1173_2


title: ko_exp1_MYJ1173_6


title: ko_exp1_MYJ1173_1


title: Memory_WT_ATAC_rep3

status: Public on Apr 10 2023

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

country: Australia

institute: Monash Bioinformatics Platform

data_processing:
The nf-core ATACseq (v1.1.0) pipeline was run to process the ATACseq fastq files. In summary, the pipeline trims adapters from the raw fastq files, aligns the reads to a reference genome and then marks duplicates. It then performs filtering to remove various quality thresholds including low quality reads, duplicate reads, blacklisted reads, etc. Peaks are called with MACS2, annotated with HOMER and a consensus peak set is created which is then used to count reads to peaks with featureCounts. Differential accessiblity is performed using DeSeq2.
Assembly: mm10
Supplementary files format and content: ATAC: ATAC: narrowPeak files called by MACS2
Supplementary files format and content: bigWig files are generated from the merged replicates for each condition. These bigWig files have been normalised to 1 million mapped reads.

source_name: Spleen

extract_protocol: ATAC-Seq was performed as per the Omni-ATAC protocol (Corces et al., 2017), using the Illumina Nextera kit (FC-131-1024) for tagmentation, and NEBNext Multiplex Oligos for Illumina (cat # E7335S) for library amplification.

tag: tissue

value: Spleen

value: WT

tag: cell type

value: CD8+ T cells


title: Effector_WT_ATAC_rep3

tag: genotype


title: Memory_WT_ATAC_rep2


title: Memory_WT_ATAC_rep1


title: Effector_WT_ATAC_rep2


title: Naïve_WT_ATAC_rep2


title: Naïve_WT_ATAC_rep3


title: Naïve_WT_ATAC_rep1


title: Sample_1

status: Public on Mar 31 2023

type: genomic

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

hyb_protocol: Sodium bisulfite treated gDNA was amplified and enzymatically fragmented before hybridization to the microarray. After washing and staining, the microarray was scanned using the iScan device (Illumina).

scan_protocol: Infinium MethylationEPIC microarray platform

data_processing:
Raw red/green channel *.idat files were imported into R using the RnBeads packages for initial quality  control, data normalization (SWAN) and extraction of β-values representing the percentage of  methylation for each CpG site on the microarray. SNP-enriched, cross-reactive, non-CpG  and sex chromosome specific probes were removed from further analyses. Unreliable  measurements were determined using the Greedycut algorithm implemented in RnBeads and  probes of highest impurity were iteratively removed from the dataset. Differential methylation  was calculated using limma and RnBead´s rank cutoff. The top 1000 differentially methylated  CpG sites were used for further analyses.
Matrix_processed*csv contains normalized Average Beta
Matrix_signal_intensities*csv contains unmethylated and methylated signal intensities

label: cy3, cy5

source_name: Breast cancer BM

label_protocol: 500ng of gDNA was sodium bisulfite converted using the EpiTect Fast DNA Bisulfite Kit (Qiagen, Germantown, MD, USA), processed using the Infinium HD FFPE DNA Restore Kit (Illumina, San Diego, CA, USA) and processed for microarray hybridization using Infinium MethylationEPIC Kit.

extract_protocol: Genomic DNA (gDNA) was extracted using the Maxwell FFPE Plus Kit (Promega, Madison, Wisconsin, USA).

tag: tissue type

value: TNBC


title: Sample_17


title: Sample_15


title: Sample_13


title: Sample_12


title: Sample_16


title: Sample_14


title: Sample_19


title: Sample_2


title: Sample_20


title: Sample_11


title: Sample_10


title: Sample_22


title: Sample_21


title: Sample_23


title: Sample_24


title: Sample_26


title: Sample_28


title: Sample_31

value: Luminal


title: Sample_30


title: Sample_29


title: Sample_27


title: Effector_WT_ATAC_rep1


title: Sample_3


title: Sample_35


title: Sample_33


title: Sample_18


title: Sample_36


title: Sample_32


title: Sample_43

source_name: Lung cancer BM

value: NSCLC


title: Sample_4


title: Sample_41


title: Sample_40


title: Sample_44


title: Sample_25


title: Sample_39


title: Sample_37


title: Sample_38


title: Sample_42


title: Sample_46


title: Sample_48


title: Sample_47


title: Sample_49


title: Sample_34


title: Sample_50


title: Sample_5


title: Sample_51


title: Sample_52


title: Sample_53


title: Sample_54


title: Sample_56


title: Sample_45


title: Sample_55


title: Sample_58


title: Sample_59


title: Sample_6


title: Sample_61


title: Sample_67


title: Sample_66


title: Sample_62


title: Sample_64


title: Sample_8


title: Sample_68


title: Sample_7


title: Sample_65


title: Sample_70


title: Sample_71


title: Sample_69


title: Sample_9


title: Brain-cortex, WT, 18 weeks old rep2

status: Public on Mar 06 2023

city: Pittsburgh

first: Dwi

last: Kemaladewi

address: 4200 Fifth Avenue

department: Pediatrics

institute: University of Pittsburgh

data_processing:
Sequence reads were trimmed for adaptor sequence during demultiplexing
Sequencce reads quality was checked using CLC Genomics Workbench v 22.0.1
Sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchwork
Principal component analysis of the samples was person for each of the conditions (WT and G56S mutant (HM))
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Brain cortex

growth_protocol: Colony of healthy (C57BL/6J) and hemizygotes mutant (SMS mutation) mice were maintined at the animal facility, Rangos Research building, University of Pittsburgh.

extract_protocol:
Total RNA was isolated from the brain cortex harvested using Nucleospin RNA Plus kit (Macherey-Nagel, cat# 740984.50). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using the Illumina Stranded mRNA library preparation kit (Illumina). Sequencing was performed using NextSeq 2000 platform with pair-end 58 bp reads

treatment_protocol: At age 18 weeks old, mice were sacrificed and brain isolated. The brain cortex was carefuly dissected in each mouse from the other parts of the brain.

value: Brain cortex

value: Male

tag: disease state

value: Healthy Control Mouse

value: 18 weeks


title: Brain-cortex, HM(G56S), 18 weeks old rep1

value: SMS Mutant

value: SRS diseased Mouse

tag: age


title: Brain-cortex, WT, 18 weeks old rep3

tag: strain


title: Brain-cortex, HM(G56S), 18 weeks old rep2


title: Sample_60


title: Brain-cortex, WT, 18 weeks old rep1


title: Sample_57


title: colorectal cancer, liver metastatic tumor, sample 2

status: Public on Feb 22 2023

city: Guangzhou

first: Jie

last: Long

address: No.106 Zhongshan 2nd Road

institute: Guangdong Provincial People's Hospital

data_processing:
For scRNA-seq, the BD Genomics Rhapsody Targeted Analysis pipeline was used to demultiplex cellular barcodes, map reads to the reference genome.
For ST-seq, raw sequencing reads were processed with CellRanger V3 and aligned to human genome
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw UMI counts and metadata for every cells
Supplementary files format and content: H&E staining images for ST-seq tissues
Library strategy: Spatial Transcriptomics

source_name: liver tissue

extract_protocol:
For scRNA-seq, freshly resected tumors were rinsed with 1×PBS for three times, cut into small pieces and transferred to 15 mL digestion medium containing collagenase IV (1 mg/mL, C5138, Sigma-Aldrich) in DME/F-12 1:1 (70100300, Biosharp). Tissues were digested for 45 minutes at 37 ℃ under agitation at 120 rpm, afterwards, the samples were filtered using a 150 μm nylon mesh. Following the centrifugation at 450 g for 5 minutes, the supernatants were discarded and the cell pellets were resuspended in 3 mL red blood cell lysis buffer (C3702, Beyotime) at 4 ℃ for 10 minutes. After washing with 1×PBS, the cell pellets were suspended in 1×PBS containing 0.2% bovine serum albumin (4240GR500, BioFroxx) and filtered using a 74 μm nylon mesh. Single cell suspensions were stained with APC/Cy7-CD45 (HI30, BioLegend) and 7-aminoactinomycin D (7-AAD, B226396, BioLegend) for fluorescence-activated cell sorting using BD Aria ⅡI (BD Biosciences). Non-immune cells were sorted as 7-AAD-CD45-, and immune cells as 7-AAD-CD45+. For spatial transcriptome sequencing (ST-seq), The tissues were obtained from patients after resection, fixed by formalin and embedded in the paraffin. 10x FFPE gene expression slide (PN-1000185, 10x Genomics) was used for ST. Slide with 5μm FFPE section was dewaxed with xylene (214736, Sigma-Aldrich) and stained with hematoxylin (51275, Sigma-Aldrich) and eosin (HT110116, Sigma-Aldrich). After visualizing and scanning the whole slide, decrosslinking was performed using the TE buffer (10-0046, GeneMed) to release the RNA. Forward and reverse human transcriptome probes (PN-1000364, 10x Genomics) were used for probe hybridization overnight.
Single-cell library preparation was carried out according to the BD Rhapsody™ Single-Cell Whole transcriptome analysis alpha protocol (https://www.bdbiosciences.com/) and ST library were constructed according to the 10x protocol (CG000407_VisiumSpatialGeneExpressionforFFPE_UserGuide_RevA)

value: liver tissue


title: colorectal cancer, primary tumor, sample 4

source_name: colorectal tissue

value: colorectal tissue


title: Sample_63


title: colorectal cancer, primary tumor, sample 3


title: colorectal cancer, primary tumor, sample 1


title: colorectal cancer, primary tumor, sample 2


title: colorectal cancer, liver metastatic tumor, sample 1


title: Brain-cortex, HM(G56S), 18 weeks old rep3


title: 203189480065_R06C01

status: Public on Feb 21 2023

city: Berlin

first: David

last: Kaul

address: Augustenburger Platz 1

department: Department of Radiation Oncology

institute: Charité - Universitätsmedizin Berlin

hyb_protocol: After bisulfite conversion using the Zymo EZ Methylation Kit (Zymo Research Irvine, USA), the Infinium HD FFPE DNA Restore Kit was used for DNA restoration. DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation450k BeadChip and Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing:
The calculations were carried out in R, version 4.2.0 "Virgorous Calesthenics"
Average beta-Values after normalization using detection p values

source_name: Tumor

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted form FFPE tumor samples using the Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA) , according to the manufacturer’s instructions

value: Female

tag: incoming diagnosis

value: Ependymoma (WHO grade II)

tag: tumor location

value: infratentorial

tag: material type

value: FFPE


title: 205537620136_R07C01

tag: Sex

value: supratentorial

tag: progression-free survival (months)

tag: progression (0=no, 1=yes)

tag: overall survival (months)

tag: death (0=no, 1=yes)


title: 204958100087_R03C01


title: 204958100087_R05C01

value: Anaplastic ependymoma (WHO grade III)


title: 205567980145_R07C01


title: 204958100087_R06C01


title: 205537620156_R07C01


title: 204958100087_R01C01


title: 205049770023_R08C01


title: 204958100087_R08C01


title: 205049770023_R06C01


title: 205023300092_R01C01


title: 204776820130_R01C01

tag: chromosome 6 status

value: retained


title: 205134950122_R01C01


title: 205049770023_R07C01


title: 205049770023_R02C01


title: 204294120088_R07C01


title: 203821710016_R05C01


title: 203072530029_R06C01


title: 205051010098_R07C01


title: 204316900163_R04C01

tag: tert mutation status

value: Wildtype

value: loss


title: 204229190080_R03C01


title: 204229180151_R05C01


title: 204316900163_R08C01


title: 204294120088_R08C01


title: 204425710142_R05C01


title: 204425710142_R04C01


title: 205049770023_R04C01

value: infratentoriell


title: 204339300091_R06C01


title: 204294120088_R06C01


title: 205049770023_R05C01

value: Male


title: 204339300091_R05C01


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title: 203866300058_R01C01


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title: 203927450065_R07C01


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title: 9701417056_R03C02


title: 9701417056_R02C02


title: 203740910036_R06C01


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title: 203755070086_R06C01


title: 9611518029_R01C02


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title: 9406922007_R01C02


title: 9611518029_R04C02


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title: 9406922007_R03C01


title: P70_deafened_scMultiome_ATAC

status: Public on Feb 07 2023

city: Los Angeles

first: John

middle: Duc

last: Nguyen

address: 3711 Baldwin Street, Unit 602

department: Stem Cell

institute: USC

description:
P70_integrate_wildtype_deaf_10x_scRNA_scATAC.h5seurat
P70_cochlea_deafened_10x_scRNA_scATAC_raw_feature_bc_matrix_barcodes.tsv.gz
P70_cochlea_deafened_10x_scRNA_scATAC_raw_feature_bc_matrix_features.tsv.gz
P70_cochlea_deafened_10x_scRNA_scATAC_raw_feature_bc_matrix_matrix.tsv.gz

data_processing:
WGBS: libraries were sequenced at 150 base pairs paired-end. Reads were trimmed with a hard clip of 20bp at both the 5’ and 3’ ends using Trim Galore (20) and aligned as paired end reads to a bisulfite-converted GRCm38/mm10 genome assembly using Bismark with the options --bowtie2 -N 1 -L 20 --non_directional --unmapped -X 800 --dovetail. Spiked-in lambda DNA was aligned to a bisulfite-converted J02459.1 lambda genome to assess bisulfite conversion percentage. Only libraries with >98% bisulfite conversion rate were kept. Unmapped paired end reads were mapped separately as single end read1 and read2 using Bismark with the options --bowtie2 --non_directional. Paired end and single end mapped reads were individually deduplicated using deduplicate_bismark, and then merged using samtools (htslib v1.7). The methylation status of individual cytosine in the genome was called using Bismark Methylation Extractor (21). The cytosine methylation and coverage data was used to call differentially methylated regions (DMR) between samples using methylKit (22) with the following parameters: only cytosine sites with at least a coverage of 2 were kept, tiling window of 1000 bp, step size of 1000 bp, percent methylation difference of at least 10 (sensitivity), and a false discovery rate (FDR) of < 0.05. Differential analysis was iteratively called between two samples from all possible combinations C(4,2) of the following cell types and stages: E13.5 PG, P1 HC, P1 SC, P21 SC. Bedtools intersect was used to identify the 4 sets of mutually exclusive DMRs capturing distinct DNA methylation signatures. DMRs were centered on Atoh1 peaks to be used in downstream analyses.
CUT&Tag: libraries were sequenced at 37 base pairs paired-end. We processed CUT&Tag data using the CUT&Tag Data Processing and Analysis pipeline from the Henikoff lab (15). Briefly, reads were hard-trimmed to 25bp and aligned to the GRCm38/mm10 genome assembly using bowtie2 (16) using parameters --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Duplicates were removed using Picard (17). Next, we applied a normalization factor to each sample based on the signal over the common peak regions. Briefly, for histones with narrow peak distributions such as H3K4me1 and CUTAC (H3K4me2), SEACR (18) was used to call peaks with non-normalized IgG control track and stringent threshold, and taking only the top 1% of regions by AUC. For histones with broad peak distributions such as H3K27me3, MACS2 (11, 19) was used to call peaks with the --broad and --q 0.1 options set against an IgG control. Bedtools intersect was used to filter for only common overlapping peaks between all samples and replicates. 4,718 shared peaks were called for H3K27me3; 4,869 shared peaks were called for CUTAC; 4,620 shared peaks were called for H3K4me1. Alignment count data was quantified over shared peaks using summarizedOverlaps (GenomicAlignments_1.30.0). calcNormFactors (edgeR v3.36.0) was used to calculate normalization factors for each sample and scaled to total library size. Samples were scaled to the normalization factor for visualization in IGV or heatmaps.
scMultiome: Raw sequencing data from multiple flow cells for both RNA and ATAC libraries in fastq format were used as input into cellranger-arc count (10x Genomics, v2.0.0) for simultaneous alignment against the mouse mm10 genome.
The cellranger- arc output files ‘filtered_feature_bc_matrix.h5’ and ‘atac_fragments.tsv.gz’ were used as input into Seurat v4.1.0 for standard quality control pre-processing, resulting in 4,882 nuclei post-filtering for the P1 dataset, and 7,049 nuclei post-filtering for the P8 dataset. ATAC peaks were called using macs2 v2.1.2. Multiome datasets were clustered based on RNA, ATAC, and weighted-nearest neighbor (Hao et al, 2021) to generate UMAPs. This resulted in 20 clusters for the P1 dataset, and 19 clusters for the P8 dataset. Clusters were assigned cell types based on known cell markers.
Representative signal tracks were visualized in IGV v2.4.14. ATAC peaks were filtered by hair cell enhancers previously identified (Tao et al., 2021), and intersected to find common, P1-specific, and P8-specific regions. Heatmaps were generated using deepTools v3.2.0 computeMatrix and plotHeatmap.
Cell barcodes from clusters of interest (P1 GER, P8 GER, P1 IPh/BC, P8 IPh, and P8 BC) were used to extract ATAC reads belonging to each respective cell type and generate a pseudobulk ATAC dataset.
Peaks were called on the pseudobulk ATAC datasets and common peaks were used as input into DESeq2 v1.34.0 to scale the signal between P1 and P8 datasets.
Assembly: mm10
Supplementary files format and content: DMR.bed regions were generated as follows: The cytosine methylation and coverage data was used to call differentially methylated regions (DMR) between samples using methylKit (22) with the following parameters: only cytosine sites with at least a coverage of 2 were kept, tiling window of 1000 bp, step size of 1000 bp, percent methylation difference of at least 10 (sensitivity), and a false discovery rate (FDR) of < 0.05. Differential analysis was iteratively called between two samples from all possible combinations C(4,2) of the following cell types and stages: E13.5 PG, P1 HC, P1 SC, P21 SC. Bedtools intersect was used to identify the 4 sets of mutually exclusive DMRs capturing distinct DNA methylation signatures. DMRs were centered on Atoh1 peaks to be used in downstream analyses.
Supplementary files format and content: WGBS.cov replicates were generated as follows: libraries were sequenced at 150 base pairs paired-end. Reads were trimmed with a hard clip of 20bp at both the 5’ and 3’ ends using Trim Galore (20) and aligned as paired end reads to a bisulfite-converted GRCm38/mm10 genome assembly using Bismark (21) with the options --bowtie2 -N 1 -L 20 --non_directional --unmapped -X 800 --dovetail. Spiked-in lambda DNA was aligned to a bisulfite-converted J02459.1 lambda genome to assess bisulfite conversion percentage. Only libraries with >98% bisulfite conversion rate were kept. Unmapped paired end reads were mapped separately as single end read1 and read2 using Bismark with the options --bowtie2 --non_directional. Paired end and single end mapped reads were individually deduplicated using deduplicate_bismark, and then merged using samtools (htslib v1.7). The methylation status of individual cytosine in the genome was called using Bismark Methylation Extractor (21).
Supplementary files format and content: WGBS.bw are converted from WGBS.cov files.
Supplementary files format and content: 10x.h5seurat files were generated as follows: The cellranger-arc output files ‘filtered_feature_bc_matrix.h5’ and ‘atac_fragments.tsv.gz’ were used as input into Seurat v4.1.0 for standard quality control pre-processing and filtering out poor-quality nuclei.scMultiome datasets were clustered using ‘uniform manifold approximation and projection’ (UMAP) and ‘weighted-nearest neighbor’ (WNN) from Seurat, which integrates both the gene expression and the accessibility information to define a “joint” cellular state. Datasets were also clustered based on RNA and ATAC for comparison. Clusters were assigned cell type identities based on known cell markers. For the P8 dataset, clusters identified as spiral ganglia neurons, roof cells, and spiral prominence cells were removed because they were driving the majority of the differences between the clusters. Afterwards, P8 cells were re-clustered and re-assigned cell type identity. The P70_integrate_wildtype_deaf_10x_scRNA_scATAC.h5seurat file is an integration of the P70_wildtype and P70_deafened cochlea datasets.

source_name: Inner ear cochlea

growth_protocol: Wildtype mice in a mixed background of CD1 and FVB/NJ, and C57BL/6 were bred

extract_protocol:
Isolate cochlear sensory epithelium: For E13.5, the inner ear was dissected from the mouse head, followed by incubation in PBS containing 0.5 U/ml of Dispase II (Sigma D4693) and 275 U/ml of Collagenase Type 1 (Worthington LS004196) at room temperature for 10 minutes. The Dispase II and Collagenase were removed and quenched with PBS + 5% Fetal Bovine Serum (FBS) (Genclone 25-514).  The cochlear epithelium was separated from the mesenchyme and dissociated into single cells. For P1, P6, P8, and P21 cochleas, the inner ear was extracted and placed in a dish containing ice-cold modified artificial cerebrospinal fluid solution (ACSF) [119 mM NaCl, 2.5 mM KCl, 2.5 mM CaCl2, 1.3 mM MgCl2, 1 mM NaH2PO4, 26.2 mM NaHCO3, 10mM HEPES, 11mM D-Glucose] on top of an ice block. Cartilage and bone were removed to expose the cochlear epithelium. Finally, the cochlear epithelium was separated from the spiral ganglion and modiolus, and then placed into a separate dish containing ACSF on ice until all ears were processed.    Obtain single cell/nuclei: For E13.5 and P1, cochleas were enzymatically dissociated with a cocktail of 400µl of 0.25% Trypsin, 50µl of 1 mg/ml Dispase, and 50µl of 1 mg/ml collagenase for 20 minutes at 37°C. After incubation, the digested tissue was titurated 100 times using a small-bore 200µl pipette and centrifuged at 500x g for 5 minutes at 4°C. For P6, P8, and P21, the sensory epithelium and stria were placed into a 1ml Dounce tissue grinder (Wheaton 357538) on ice with 1 ml of chilled homogenization buffer (250mM sucrose, 25mM KCl, 5mM MgCl2, 20 mM HEPES-KOH pH 7.9, 20% glycerol). Before use, the following components were added at their respective concentrations: 1mM DTT (Thermo Scientific R0861), 0.5mM Spermidine (Sigma S0266), 1% BSA (Sigma A4503), and 1x cOmplete EDTA-free protease inhibitor cocktail (Roche 11836170001). NP-40 (Calbiochem 492015) was spiked into the Dounce tissue grinder at a final concentration of 0.3%. The tissue was homogenized with a chilled loose pestle by first pressing the pestle down and turning to grind the tissue, followed by quick upstrokes 10 to 15 times to create cavitation. It was critical to not lift the Dounce pestle above the liquid layer to reduce bubbles. This process was repeated with a chilled tight pestle. Although some epithelial tissue was sometimes still visible, no further homogenization was performed as this may jeopardize the integrity of the already-released nuclei. The homogenate was filtered using a Falcon 5ml round bottom polystyrene test tube with a 40 µm cell strainer snap cap and spun down at 1000 x g and 4°C for 10 minutes. The supernatant was decanted, and the pellet was resuspended in 1ml of nuclei wash buffer (NWB) (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.1% NP-40). Before use, the following components were added at the respective concentrations: 1mM DTT, 0.5mM Spermidine, 2% BSA, and 1x cOmplete EDTA-free protease inhibitor cocktail.     Purifying celltypes: Fluorescence-activated cell sorting (FACS) of cells or nuclei was performed on either an Aria I, Aria II, or FACSymphony (BD Biosciences). For CUT&RUN and CUT&Tag, cells or nuclei were sorted into NWB. For WGBS, cells or nuclei were sorted into lysis buffer (10 mM Tris pH 7.5, 100 mM NaCl, 1 mM EDTA, and 0.01% Triton X-100). For Single Cell Multiome ATAC + Gene expression (10x Genomics), cells or nuclei were sorted into PBS and 0.1% BSA. Cells/nuclei were used for downstream NGS experiments (WGBS, CUT&Tag, 10x Genomics scMultiome).
WGBS: Cells/nuclei were lysed in lysis buffer (10mM Tris pH 7.5, 100mM NaCl, 1mM EDTA, and 0.01% Triton X-100) and digested with Proteinase K at 3mAU/ml at 65C for at least 1 hour. gDNA was purified using Genomic DNA Clean & Concentrator-10 (Zymo Research). Unmethylated Lambda DNA was spiked in at 0.5% of input gDNA. Libraries were prepared using the Pico Methyl-Seq Library Prep Kit (Zymo Research)  CUT&Tag: The following antibodies were used: Rabbit anti-H3K4me1 antibody (Active Motif 61633), rabbit anti-H3K4me2 antibody (Epicypher 13-0027), rabbit anti-H3K4me3 antibody (Active Motif 39159), rabbit anti-H3K27me3 antibody (Active Motif 39155). The guinea pig anti-Rabbit IgG antibody (Antibodies-online.com ABIN101961) was used as the secondary antibody. Tn5-tagmented DNA fragments were amplified using NEBNext HiFi 2x PCR Master Mix, a universal i5 primer and a uniquely barcoded i7 primer for 14 cycles. Library concentration and fragment distribution were measured on the Agilent Tapestation using a High Sensitivity D5000 ScreenTape (Agilent 5067-5592). Libraries were size-selected for DNA fragments greater than 150 bp using SPRISelect beads (Beckman Coulter B23318).    scMultiome  ATAC + Gene Expression protocol (10x Genomics)

treatment_protocol: For transdifferentiation experiments, the cochlear sensory epithelium cultured on SPI black filter membranes. To initiate Lfng-CreER-mediated lineage tracing of supporting cells, (Z)-4-Hydroxytamoxifen (Sigma H7904) was added to the culture media. For transdifferentiation experiments, DAPT was added to the culture media.    To generate P70 long-term deafened mice, we used a Lfng-CreERT2; NuTRAP; Pou4f3DTR mouse to lineage trace SCs and specifically kill hair cells after diphtheria toxin treatment. Lfng-CreERT2;NuTRAP mice were used as wildtype controls. Mice received tamoxifen at P21, diphtheria toxin (Sigma-Aldrich D0564) at P28, and allowed to mature to P70, at which point cochlear tissues were harvested for input into a scMultiome reaction.

tag: tissue

value: Inner ear cochlea

tag: developmental stage

value: mixed (CD1,FVB/NJ, C57BL/6)

value: Lfng-creERT2, NuTRAP, Pou4f3-DTR

tag: treatment

value: 100 mg/kg tamoxifen, 0.01 mg/kg diphtheria toxin


title: 9701417056_R04C02


title: 9611518029_R04C01


title: P70_wildtype_scMultiome_RNA

description:
P70_integrate_wildtype_deaf_10x_scRNA_scATAC.h5seurat
P70_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_barcodes.tsv.gz
P70_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_features.tsv.gz
P70_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_matrix.tsv.gz

molecule: nuclear RNA

tag: genotype

value: Lfng-creERT2, NuTRAP


title: P70_wildtype_scMultiome_ATAC


title: P8_cochlea_scMultiome_RNA

description:
P8_wildtype_10x_scRNA_scATAC.h5seurat
P8_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_barcodes.tsv.gz
P8_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_features.tsv.gz
P8_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_matrix.mtx.gz

value: no treatment


title: 9611518029_R06C01

value: Female


title: P1_cochlea_scMultiome_RNA

description:
P1_wildtype_10x_scRNA_scATAC.h5seurat
P1_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_barcodes.tsv.gz
P1_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_features.tsv.gz
P1_cochlea_wildtype_10x_scRNA_scATAC_raw_feature_bc_matrix_matrix.mtx.gz


title: 9701417098_R01C02


title: 9611519086_R01C02

value: Ependymoma (WHO grade II)

value: infratentorial


title: 203755070086_R04C01

value: supratentorial

value: FFPE


title: 9406922009_R02C01

value: Anaplastic ependymoma (WHO grade III)


title: 100973330057_R03C01


title: P70_deafened_scMultiome_RNA


title: P8_cochlea_scMultiome_ATAC

value: Wildtype


title: Anti PDL1+CTLA4 3

status: Public on Feb 01 2023

type: RNA

city: Stanford

first: Renumathy

last: Dhanasekaran

address: 300 Pasteur Drive, Alway M211

institute: Stanford University

description: Total RNA was extracted from FFPE tissue and targeted RNA sequencing was performed using mouse IO360 panel.

hyb_protocol: According to nanostring protocol

scan_protocol: According to nanostring protocol

data_processing: Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library. Abundance of various cell populations is calculated on ROSALIND using the Nanostring Cell Type Profiling Module. ROSALIND performs a filtering of Cell Type Profiling results to include results that have scores with a p-Value greater than or equal to 0.05. Fold changes and pValues are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR). Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library that takes into consideration the direction and type of all signals on a pathway, the position, role and type of every gene, etc. Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library, was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro, NCBI, MSigDB, REACTOME, WikiPathways. Enrichment was calculated relative to a set of background genes relevant for the experiment.

organism: Mus

source_name: MYC-HCC

label_protocol: According to nanostring protocol

extract_protocol: Total RNA was extracted from FFPE tissue.

treatment_protocol: Murine MYC-HCC were treated with control IgG or anti PDL1 or anti CTLA4, or their combination. Tumors were sequenced using Nanostring IO360.

value: Liver tumor

value: Anti PDL1+CTLA4


title: Anti CTLA4 1

value: Anti CTLA4


title: P1_cochlea_scMultiome_ATAC


title: MYC-HCC, MYC- Off Day 4 3

description: F_170914_I89_CL100030177_L2_HK500MUSkkrRAAFRAAPEI-22_1.fq.gz

data_processing:
Trim adapters and low quality bases (Trimmomatic).
Align to the reference genome (STAR).
Determine the distribution of the bases within the transcripts and 5'/3' biases (Picard).
FPKM value was quantified by FeatureCounts tool
DESeq2 was used for differential expression analysis
Assembly: mm10
Supplementary files format and content: FPKM value was quantified by FeatureCounts tool

source_name: Liver

extract_protocol:
Liver tumors were removed, flash frozen on dry ice, and RNA was harvested using Qiagen Rneasy kit.
RNA libraries were prepared for sequencing using standard BGI protocols

value: Liver

tag: cell type

value: tumor

value: MYC-LAP-tTA

value: MYC inactivation


title: Anti PDL1 3

value: Anti PDL1


title: Ctrl IgG 3

value: Ctrl IgG


title: MYC-HCC, MYC- Off Day 4 1

description: D_170914_I89_CL100030177_L2_HK500MUSkkrRAADRBAPEI-43_1.fq.gz


title: MYC-HCC, MYC-On 3

description: C_170914_I89_CL100030177_L2_HK500MUSkkrRAACRBAPEI-42_1.fq.gz

value: MYC activation


title: MYC-HCC, MYC-On 2

description: B_170914_I89_CL100030177_L2_HK500MUSkkrRAABRBAPEI-41_1.fq.gz


title: MYC-HCC, MYC-On 1

description: A_170914_I89_CL100030177_L2_HK500MUSkkrRAAARBAPEI-40_1.fq.gz


title: MYC-HCC, MYC- Off Day 4 2

description: E_170914_I89_CL100030177_L2_HK500MUSkkrRAAERBAPEI-44_1.fq.gz


title: mnp-20-0885

status: Public on Jan 30 2023

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

source_name: CNS tumor tissue

label_protocol: Illumina

extract_protocol: DNA from FFPE tissue was extracted using a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: "material"

value: FFPE tissue

tag: "tumor type"

value: Ependymoma, WHO grade III

tag: "patient age (years)"

tag: "patient gender"

value: male

tag: "tumor location"

value: cerebellum, fourth ventricle


title: Anti PDL1+CTLA4 2


title: Anti CTLA4 3


title: Anti PDL1+CTLA4 1


title: mnp-20-0563


title: Anti PDL1 2


title: Anti PDL1 1


title: Ctrl IgG 2


title: mnp-20-0181

value: female


title: Anti CTLA4 2


title: mnp-20-0560

value: Ependymoma, WHO grade II

value: fourth ventricle


title: mnp-20-0619


title: mnp-20-1423

value: pons


title: Ctrl IgG 1

value: Liver tumor


title: mnp-20-0392


title: mnp-20-0647


title: mnp-20-1259

value: Ependymoma, ZFTA fusion-positive

value: third ventricle


title: mnp-20-0846

value: cerebellum, fourth ventricle, pons


title: mnp-20-0427


title: mnp-20-1351

value: brain stem


title: mnp-20-1539

value: Pilocytic Astrocytoma


title: mnp-20-0097


title: mnp-20-0702

value: cerebellum


title: mnp-20-1239


title: mnp-20-0813


title: mnp-20-0457


title: mnp-20-0433


title: mnp-20-0263


title: mnp-20-0854

value: Ependymoma, YAP1 fusion-positive

value: temporal lobe, thalamus


title: mnp-20-0021

value: FFPE tissue

value: primary somatosensory cortex, primary motor cortex


title: mnp-20-0727

value: Ependymoma, WHO grade III


title: mnp-20-0301

value: male


title: mnp-20-0451

value: cerebellum, fourth ventricle


title: mnp-20-0500


title: mnp-20-0571


title: mnp-20-0736


title: mnp-20-0167

value: Glioblastoma (GBM)


title: mnp-20-1145


title: mnp-20-0024

value: Anaplastic pilocytic astrocytoma


title: mnp-20-0718


title: mnp-20-0696

value: parietal lobe


title: mnp-20-0161

value: Myxopapillary ependymoma (MPE)

value: female

value: spinal cord


title: mnp-20-0503

value: Ependymoma, ZFTA fusion-positive

value: frontal lobe


title: mnp-20-1080


title: mnp-20-0972

value: fourth ventricle, brain stem


title: mnp-20-0079

value: cerebellum


title: mnp-20-0467

value: brain stem, cerebellum


title: mnp-20-1193


title: mnp-20-1238

value: Non-neoplastic tissue

value: pineal region


title: mnp-20-0112

value: FFPE tissue


title: mnp-20-1022

value: Ependymoma, WHO grade III


title: mnp-20-0850

value: male

value: third ventricle


title: mnp-20-1545


title: mnp-20-0014

value: fourth ventricle


title: mnp-20-1447


title: mnp-20-1524

value: cerebellum, fourth ventricle, pons


title: mnp-20-0774


title: mnp-20-0875


title: mnp-20-0214

value: Descriptive diagnosis

value: temporal lobe


title: mnp-20-0012

value: Myxopapillary ependymoma (MPE)


title: mnp-20-0337

value: female

value: cerebellum, fourth ventricle, medulla oblongata


title: mnp-20-0343


title: mnp-20-1015

value: Ependymoma, WHO grade II

value: spinal cord


title: mnp-20-0738

value: cerebellum, brain stem


title: mnp-20-1155


title: mnp-20-1056


title: mnp-20-1079


title: mnp-20-1359

value: cerebellum, fourth ventricle


title: mnp-20-0275


title: mnp-20-0530


title: mnp-20-1237

value: Ependymoma, ZFTA fusion-positive


title: mnp-20-1338


title: mnp-20-0320


title: mnp-20-0212


title: mnp-20-0459

value: fourth ventricle, brain stem


title: mnp-20-1095

value: FFPE tissue


title: mnp-20-1437


title: mnp-20-0936

value: Ependymoma, WHO grade III


title: mnp-20-1386

value: brain stem


title: mnp-20-0967

value: male

value: cerebellum


title: mnp-20-1184


title: mnp-20-0082

value: cerebellum, fourth ventricle, pons


title: mnp-20-0597

value: fourth ventricle


title: mnp-20-1175

value: parietal lobe


title: mnp-20-0888

value: fourth ventricle, spinal cord


title: mnp-20-0740

value: female


title: mnp-20-0812


title: mnp-20-0201

value: cerebellum, fourth ventricle, medulla oblongata


title: mnp-20-0004


title: mnp-20-0247

value: brain stem, fourth ventricle


title: mnp-20-0616


title: mnp-20-1565

value: Descriptive diagnosis


title: mnp-20-0712


title: mnp-20-0260

value: Myxopapillary ependymoma (MPE)

value: spinal cord


title: mnp-20-0998


title: mnp-20-0810


title: mnp-20-0882


title: mnp-20-0424

value: cerebellum, fourth ventricle


title: mnp-20-0357

value: Ependymoma, ZFTA fusion-positive

value: angular gyrus, posterior (caudal) superior temporal cortex, primary auditory cortex, inferior parietal cortex


title: mnp-20-1073

value: FFPE tissue

value: Ependymoma, WHO grade III


title: mnp-20-0733

value: male

value: cerebellum, pons, fourth ventricle


title: mnp-20-0002

value: Astroblastoma


title: mnp-20-1482


title: mnp-20-0043


title: mnp-20-1012

value: cerebellum, fourth ventricle, pons


title: mnp-20-0785


title: mnp-20-0234

value: frontal lobe


title: mnp-20-0991

value: parietal lobe


title: mnp-20-0853


title: mnp-20-1532

value: female

value: fourth ventricle


title: mnp-20-0006


title: mnp-20-0013


title: mnp-20-0904


title: mnp-20-0107


title: mnp-20-0894


title: mnp-20-0358


title: mnp-20-1465


title: mnp-20-0471


title: mnp-20-0924


title: mnp-20-0544


title: mnp-20-1400

value: Ependymoma, WHO grade II


title: Library 16 - Peritoneal macs Old: 3hrs

status: Public on Dec 19 2022

first: Katherine

middle: M

last: Sheu

address: 611 Charles E Young Dr E

institute: UCLA

description: BD Rhapsody

library_source: transcriptomic single cell

data_processing:
Raw fastq files were processed using the BD Rhapsody™ Targeted Analysis Pipeline (version v1.0) 23 hosted on Seven Bridges Genomics. Distribution-Based Error Correction (DBEC)-adjusted UMI counts (molecules per cell) were used in the downstream analysis. Multiplets, cells with undetermined barcodes, and cells with less than 80 features were removed from the analysis. (Due to the highly multiplexed nature of the experiments, fastq files also include data not described in the paper. Users should refer to supplementary file 'samptag.all_cellannotations_metadata.txt' to extract the relevant cells after processing. Processed and subsetted data is available on the manuscript's associated Zenodo repository.)
Assembly: mm10
Supplementary files format and content: Comma-separated values files for mRNA counts
Supplementary files format and content: Comma-separated values Sample Tag files for cell identities

source_name: inlcudes either Unstim or 3hr cells, mixed M0, M1, M2, scRNAseq

growth_protocol: Macrophages were obtained either via injection and extraction of 10mL PBS +1% FBS into the mouse peritoneum, followed by plating and washing off non-attached cells, or by differentiating immortalized myeloid progenitors (HoxB4 iMPs). For iMP-derived macrophages, differentiation was performed in DMEM/10% FBS + 30% L929 supernatant for a total of 10 days: iMPs were initially thawed into 10cm non-adherent petri dishes for 3 days. On day 0 of differentiation, cells were then washed once and transferred into differentiation media (DMEM/10% FBS, 30% L929 supernatant, 1% PS, 1% L-Glut, b-Me (1:1000)). Cells were replated into 6cm plates with new media on day 7, at a density of ~20k cells/cm2.

extract_protocol:
Cells were washed once with cold PBS after 3hrs of stimulation and lifted into suspension by incubating at 37C for 5 minutes with Accutase, which resulted in cell viability typically >85%. Cells were centrifuged at 4C, 400g for 5 minutes, and resuspended in PBS + 2% FBS for the Rhapsody scRNAseq assay. Cells were hash-tagged with anti-CD45-hashtags (BD Rhapsody # 633793) and loaded onto the cartridge following manufacturer’s instructions (BD Rhapsody # 633771), with the following modifications, which helped ensure sufficient cell viability for the subsequent steps: Incubation with hashtags was performed for 30mins on ice, instead of 20mins at room temperature; only two washes were performed after hashtag incubation to minimize cell loss. Each cartridge was then loaded with a total of ~36k cells across 12 hash-tagged samples (~3k cells/sample).
Libraries were prepared according to manufacturer’s instructions (BD Rhapsody # 633771) and sequenced 2x100 on Novaseq 6000.

treatment_protocol: On day 10, the iMP-derived macrophages (iMPDMs) were stimulated with 100ng/mL lipopolysaccharide (LPS, Sigma Aldrich), 10ng/mL murine TNF, and 50μg/mL low molecular weight polyinosine-polycytidylic acid (Poly(I:C)), 100nM synthetic CpG ODN 1668 (CpG), 500U/ml IFNβ, or media only Untreated control. For polarized macrophages, cells were incubated in 50ng/ml IFNγ or 50ng/ml IL4 for 24 hours prior to stimulation on day 10.

value: Peritoneal macropahges

tag: cell line

value: primary cells

value: macrophages

value: multiplexed sample:various immune ligands


title: Library 15 - Peritoneal macs High-fat/low-fat diet: 3hrs

description: BD Rhapsody


title: Library 12 - M0: 5hrs, 3hrs

description: BD Rhapsody

value: iMPDMs


title: Library 8 - M0: 3hrs, 1hr

description: BD Rhapsody


title: mnp-20-0498


title: Library 5 - M1(IFNg): 5hrs, 3hrs

description: BD Rhapsody


title: Library 3 - M2(IL4): 1hr; M0 Unstim, M1 Unstim, M2 Unstim

description: BD Rhapsody


title: SKOV3_48h_SSO_200_M_rep3_S114848

status: Public on Dec 05 2022

data_processing:
HiSeq Control Software (HCS, HD 3.4.0.38) and Real-Time Analysis Software (RTA, 2.7.7) were used for raw data acquisition and base calling, respectively.
STAR was used for read mapping to hg38.
DESeq2 was used to test for differential gene expression.
Assembly: hg38
Supplementary files format and content: Read count table

extract_protocol:
Total RNA was extracted using Qiagen´s Rneasy kit
QuantSeq 3’ mRNA-Seq FWD library preparation protocol (Lexogen GmbH, Vienna, Austria)

value: Tumor cell line

value: wt


title: Library 1 - M2(IL4): 5hrs, 3hrs

description: BD Rhapsody


title: SKOV3_48h_SSO_200_M_rep2_S114849


title: SKOV3_48h_SSO_200_M_rep1_S114846


title: SKOV3_48h_SBFI26_80_M_rep2_S114843


title: SKOV3_48h_SBFI26_80_M_rep1_S114840


title: SKOV3_48h_SBFI26_80_M_rep3_S114842


title: SKOV3_48h_NAV2729_10_M_rep2_S114832


title: mnp-20-0198

value: FFPE tissue

value: Ependymoma, WHO grade III

value: cerebellum, fourth ventricle


title: mnp-20-1013

value: male


title: SKOV3_48h_DMSO_0_16_rep1_S114828


title: SKOV3_48h_NAV2729_10_M_rep3_S114835


title: SKOV3_48h_HTS01037_80_M_rep3_S114841


title: SKOV3_48h_DMSO_0_4_rep2_S114844


title: SKOV3_48h_DMSO_0_16_rep3_S114830


title: SKOV3_48h_DMSO_0_4_rep3_S114847


title: SKOV3_48h_DMSO_0_16_rep2_S114831


title: SKOV3_48h_HTS01037_80_M_rep2_S114838


title: Library 13 - M0: 3hrs, Unstim

description: BD Rhapsody


title: SKOV3_48h_DMSO_0_4_rep1_S114845


title: SKOV3_48h_BMS309403_80_M_rep3_S114836


title: SKOV3_4hDMSO_0_4_rep2_S114825


title: SKOV3_48h_NAV2729_10_M_rep1_S114833


title: SKOV3_4hDMSO_0_4_rep1_S114822


title: SKOV3_4h_SBFI26_80_M_rep3_S114823


title: SKOV3_4h_SSO_200_M_rep2_S114826


title: SKOV3_4h_SBFI26_80_M_rep2_S114820


title: SKOV3_4h_SSO_200_M_rep3_S114829


title: SKOV3_4h_NAV2729_10_M_rep2_S114813


title: SKOV3_48h_HTS01037_80_M_rep1_S114839


title: SKOV3_4h_SBFI26_80_M_rep1_S114821


title: SKOV3_4h_HTS01037_80_M_rep1_S114816


title: SKOV3_4h_SSO_200_M_rep1_S114827


title: SKOV3_4h_DMSO_0_16_rep2_S114808


title: SKOV3_4h_DMSO_0_16_rep3_S114811


title: SKOV3_4h_DMSO_0_16_rep1_S114809


title: SKOV3_4h_HTS01037_80_M_rep2_S114819


title: SKOV3_4h_NAV2729_10_M_rep1_S114810


title: SKOV3_4h_BMS309403_80_M_rep3_S114817


title: SKOV3_4h_BMS309403_80_M_rep1_S114815


title: A2780_48h_SSO_100_M_rep3_S114806


title: SKOV3_48h_BMS309403_80_M_rep2_S114837


title: A2780_48h_SSO_100_M_rep2_S114807


title: A2780_48h_SBFI26_30_M_rep3_S114800


title: SKOV3_4h_HTS01037_80_M_rep3_S114818


title: SKOV3_4h_BMS309403_80_M_rep2_S114814


title: A2780_48h_SBFI26_30_M_rep2_S114801


title: SKOV3_4h_NAV2729_10_M_rep3_S114812


title: SKOV3_48h_BMS309403_80_M_rep1_S114834


title: SKOV3_4hDMSO_0_4_rep3_S114824


title: A2780_48h_SSO_100_M_rep1_S114804


title: A2780_48h_SBFI26_30_M_rep1_S114798


title: A2780_48h_NAV2729_6_M_rep3_S114793


title: A2780_48h_NAV2729_6_M_rep2_S114790


title: A2780_48h_NAV2729_6_M_rep1_S114791


title: A2780_48h_HTS01037_20_M_rep3_S114799


title: A2780_48h_HTS01037_20_M_rep1_S114797


title: A2780_48h_DMSO_0_06_rep3_S114788


title: A2780_48h_DMSO_0_06_rep1_S114786


title: A2780_48h_DMSO_0_06_rep2_S114789


title: A2780_48h_DMSO_0_2_rep3_S114805


title: A2780_48h_DMSO_0_2_rep2_S114802


title: A2780_48h_BMS309403_30_M_rep2_S114795


title: A2780_4h_SBFI26_30_M_rep3_S114781


title: A2780_4h_SBFI26_30_M_rep2_S114778


title: A2780_48h_BMS309403_30_M_rep3_S114794


title: A2780_4h_SSO_100_M_rep1_S114785


title: A2780_4h_SSO_100_M_rep3_S114787


title: A2780_4h_SSO_100_M_rep2_S114784


title: A2780_48h_DMSO_0_2_rep1_S114803


title: A2780_48h_BMS309403_30_M_rep1_S114792


title: A2780_4h_NAV2729_6_M_rep1_S114768


title: A2780_4h_HTS01037_20_M_rep3_S114776


title: A2780_4h_DMSO_0_06_rep2_S114766


title: A2780_4h_SBFI26_30_M_rep1_S114779


title: A2780_4h_NAV2729_6_M_rep2_S114771


title: A2780_4h_DMSO_0_06_rep3_S114769


title: A2780_4h_NAV2729_6_M_rep3_S114770


title: A2780_4h_DMSO_0_2_rep2_S114783


title: A2780_4h_HTS01037_20_M_rep2_S114777


title: A2780_4h_DMSO_0_2_rep3_S114782


title: A2780_4h_BMS309403_30_M_rep3_S114775


title: A2780_48h_HTS01037_20_M_rep2_S114796


title: A2780_4h_DMSO_0_2_rep1_S114780


title: A2780_4h_HTS01037_20_M_rep1_S114774


title: A2780_4h_BMS309403_30_M_rep2_S114772


title: A2780_4h_BMS309403_30_M_rep1_S114773


title: s, ESC, WT+MosIR, RS7.3

status: Public on Nov 03 2022

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

description: Wrong sample was originally uploaded as GSM5870284 (s, ESC, WT+MosIR, RS7.3). Mistake was noticed on 2023-09-07 and files were replaced with correct samples.

data_processing:
Small RNA-seq reads were trimmed using fastx 0.0.14 and cutadapt 1.8.3:  zcat ${FILE}.fastq.gz | fastx_trimmer -f 5 -i - -o ${FILE}.tmp.fastq  cutadapt --format="fastq" --front=GTTCAGAGTTCTACAGTCCGACGATCNNNN --adapter=NNNNTGGAATTCTCGGGTGCCAAGG --error-rate=0.075 --times=2 --overlap=14 --minimum-length=12 --max-n=0.1 --output="${FILE}.fastq" --trim-n --match-read-wildcards ${FILE}.tmp.fastq
Trimmed reads were mapped to mouse (mm10) genome using STAR 2.7.3a with following parameters:  STAR --readFilesIn ${FILE}.fastq.gz --genomeDir ${GENOME_INDEX} --runThreadN 12 --genomeLoad NoSharedMemory --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix ${FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMultimapNmax 99999  --outFilterMismatchNoverLmax 0.1 --outFilterMatchNminOverLread 0.66 --alignSJoverhangMin 999 --alignSJDBoverhangMin 999
Genome browser coverage tracks in bigWig format were produced using bedtools v2.29.2 and wigToBigWig v 4 from UCSC:  genomeCoverageBed -ibam ${FILE} -bg -split > ${FILE}.bedGraph  wigToBigWig ${FILE}.bedGraph chrNameLength.txt ${FILE}.bw
Genome_build: mm10
Supplementary_files_format_and_content: coverage genome browser tracks files:  - .bigWig format  - generated in a non-stranded mode.   - not normalized for library size

source_name: mouse ESC

growth_protocol: Mouse ESCs were cultured in 2i-LIF media: KnockOut-DMEM (ThermoFisher) supplemented with 15% fetal calf serum (Sigma), 1x L-Glutamine (Sigma), 1x non-essential amino acids (ThermoFisher), 50 µM β-Mercaptoethanol (ThermoFisher), 1000 U/mL LIF (Isokine), 1 µM PD0325901, 3 µM CHIR99021 (Selleck Chemicals), penicillin (100 U/mL), and streptomycin (100 µg/mL). All plastic was coated with 1% gelatin (Sigma) in PBS.

extract_protocol:
Cells were washed with PBS, homogenized in Qiazol lysis reagent (Qiagen) and total RNA was isolated by Qiazol-chloroform extraction and ethanol precipitation method. RNA quality was verified by Agilent 2100 Bioanalyzer.
Small RNA libraries were constructed using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturer’s protocol. Small RNA libraries were size selected on 6% PAAGE gel, a band of 140 - 150 bp was cut from the gel and RNA was extracted using Monarch® Genomic DNA Purification Kit. Quality of the libraries was assessed by Agilent 2100 bioanalyzer.

treatment_protocol: Cells were transfected with 2 μg/well of pCAG-EGFP-MosIR plasmid and cultured for 48 hours.

value: Dicer wt/wt

tag: transfection

value: MosIR

value: ESC

tag: fraction

value: small RNA

tag: replicate


title: s-E15.5-XHOM-7B

source_name: mouse E15.5 embryos

extract_protocol:
Embryos were homogenized in Qiazol lysis reagent (Qiagen) and total RNA was isolated by Qiazol-chloroform extraction and ethanol precipitation method.
Small RNA libraries were constructed using Nextflex Small RNA-seq kit v3 for Illumina (Perkin Elmer) according to the manufacturer’s protocol; 3′ adapter ligation was performed overnight at 20 °C, 15 cycles were used for PCR amplification and NextFlex beads were used for size selection.

treatment_protocol: E15.5 embryos were removed from the uterus and washed in PBS. The yolk sac was taken for genotyping and embryos were transferred into RNAlater (Thermo Fisher Scientific)

value: Dicer X/X

tag: age

value: embryo


title: s-E15.5-XHOM-3B


title: s-E15.5-XHOM-2


title: A2780_4h_DMSO_0_06_rep1_S114767