title: H9CerebralOrganoid, automated, techRep1 (201026-C2-auto)

description:
Sample 6
auto_d18_C2_rsem_genes.results

value: H9 cerebral cortex organoid (Experimental-group)

value: Automated


title: H9CerebralOrganoid, control, techRep2, bioRep1 (201026-A1a-susp)

status: Public on Jul 14 2022

type: SRA

city: Santa Cruz

first: Spencer

last: Seiler

state: CA

address: 1156 High Street

department: Biomolecular Engineering

country: USA

institute: UC Santa Cruz

description:
Sample 8
susp_d18_A1a_rsem_genes.results

library_source: transcriptomic

data_processing:
toil-rnaseq pipeline v 4.0.3 (https://github.com/BD2KGenomics/toil-rnaseq).
Samples were demultiplexed using Illumina i5 and i7 barcodes
Multiple fastqs were merged on a per sample basis using toil-rnaseq
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CutAdapt v 1.9 through toil-rnaseq
Trimmed sequence reads were mapped to hg38 UCSC assembly using GENCODE v 37 annotations with STAR v 2.7.9a alignment using parameters from ENCODE's DCC pipeline (parameters- outFilterMultimapNmax: 20, outFilterMismatchNmax: 999, outFilterMismatchNoverReadLmax: 0.04, alignSJoverhangMin: 8, alignSJDBoverhangMin: 1, sjdbScore: 1)
Gene and isoform counts were extracted using RSEM v 1.2.25
Assembly: hg38 UCSC assembly with GENCODE v 37 annotations
Supplementary files format and content: tab-delimited text files include gene IDs, expected counts, TPM, and FPKM values for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: 3D organoid culture

growth_protocol: To generate cerebral organoids, adherent cultures were dissociated into single cells using Accutase Cell Dissociation Reagent (Gibco) and then aggregated in AggreWell 800 24-well plates (STEMCELL Technologies) at a density of 3,000,000 cells per well with 2mL of AggreWell Medium (STEMCELL Technologies) supplemented with Rho Kinase Inhibitor (Y-27632, 10 μM, Tocris, 1254) (day 0). The following day (day 1), 1mL of the AggreWell medium was manually replaced with supplemented medium containing WNT inhibitor (IWR1-ε, 3 μM, Cayman Chemical, 13659, days 1-10) and Nodal/Activin inhibitor (SB431542, Tocris, 1614, 5 μM, days 1-10). On day 2, aggregates were transferred onto a 37 μm filter (STEMCELL Technologies) by carefully aspirating with a  p1000 wide-bore pipette out of the AggreWell plate. The organoids were transferred into ultra-low adhesion 6-well plates (Corning) by inversion and rinsing of the filters with fresh AggreWell medium. Media was changed on days 3, 4, 5, 6, 8, and 10 by manually replacing 2 mL of conditioned media with fresh media. On day 11 and onward, the medium was changed to Neuronal Differentiation Medium containing Eagle Medium: Nutrient Mixture F-12 with GlutaMAX supplement (DMEM/F12, Thermo Fisher Scientific, 10565018), 1X N-2 Supplement (Thermo Fisher Scientific, 17502048), 1X Chemically Defined Lipid Concentrate (Thermo Fisher Scientific, 11905031) and 100 U/mL Penicillin/Streptomycin supplemented with 0.1\% recombinant human Fibroblast Growth Factor b (Alamone F-170) and 0.1\% recombinant human Epidermal Growth Factor (R&D systems 236-EG).

extract_protocol:
Zymo Research RNA Lysis Buffer was used to render cell lysate from whole organoid tissue.
RNA libraries were prepared using Smart-seq2 protocol for RNA-seq directly from the whole organoid lysate

treatment_protocol: Control-group “Suspension” organoids remained suspended in 6-well plates and were maintained with 2 mL media changes every other day for the remainder of the culture. Experimental-group “Automated” organoids were loaded onto the microfluidic chip and experienced media changes of 70 μL once every hour for the remainder of the culture.

tag: tissue

value: H9 cerebral cortex organoid (Control-group)

tag: cell line

tag: cell type

value: Neural precursor cells

tag: genotype

value: WT

tag: treatment

value: Suspension

tag: time

value: Day 18


title: H9CerebralOrganoid, automated, techRep1 (201026-C3-auto)

description:
Sample 7
auto_d18_C3_rsem_genes.results


title: T1D patients with Fibrous Carotid Plaque A4

city: Padova

first: Giulio

last: Ceolotto

address: Via Orus 2B

department: Medicine

country: Italy

institute: University of Padova

data_processing:
Data analysis was performed using CLC Genomics Workbench software 21.0.3 (Quiagen)
Reads from FASTq files was filtered for quality and aligned to the Ensembl-v99-hg38 version of the reference human genome and miRbase v.22.1  as annotation model
Normalization of the data was performed using TMM method (trimmed Mean of M-values)
Differential Expression analysis was performed using Generalized Linear Model (GLM) and Trimmed mean of M-values (TMM) normalized counts (CPM) were used as input data, considering significant Benjamini-Hochberg adjusted p-values ≤ 0.05
Assembly: Ensembl-v99-hg38
Supplementary files format and content: tab-delimited text files include raw data and cpm values (TMM-adjusted) for each Sample

molecule: total RNA

source_name: blood

growth_protocol: This study was performed with the collaboration of the Unit of Metabolic Diseases, Department of Medicine, University of Padova, Italy, and the Center of Biomedical Research on Diabetes and Associated Metabolic Diseases, Department of Endocrinology, and Nutrition, University Hospital de la Santa Creu i Sant Pau, Barcelona, Spain. One hundred four subjects with T1D were recruited from the diabetic outpatient clinics at University Hospital Germans Trias i Pujol, Hospital Clinic of Barcelona, and University Hospital Arnau de Vilanova of Lleida in the North Western region of Spain (Catalonia). Inclusion criteria were as follows: age >18 years; type 1 diabetes for at least 1 year; estimated glomerular filtration rate (eGFR) >60 mL/1.73mq.min. Exclusion criteria were: previous cardiovascular diseases, defined as clinical coronary heart disease, stroke, or peripheral vascular disease (including any form of diabetic foot disease); and a urine albumin/creatinine excretion ratio >300 mg/g. Patients were enrolled in the study if they showed a uniformly CFP or CCP; the two groups were matched by sex and age. This study was carried out following the International Ethical Guidelines and the principles of the Declaration of Helsinki; the Local Ethics Committee of the participating centers approved the protocol (PI11/11, C0000046, and PI-13-095); all participants signed informed consent forms. Patients filled out a complete lifestyle questionnaire regarding medical history, current therapy, smoking habits, and physical activity. Plasma glucose, total serum cholesterol, HDL cholesterol, and triglyceride were measured using routine enzymatic methods. For NGS analysis, fasting blood samples were collected into EDTA-containing tubes, centrifuged at 3000g for 10 min and plasma aliquots were stored at -80°C until use.

extract_protocol:
Total RNA was isolated from plasma by miRNeasy Serum/plasma kit (Qiagen, Germany).
Small RNA libraries from plasma samples were obtained using QIAseq® miRNA Library kit (Qiagen, Hilden, Germany), according to the manufacturer protocol. NGS Library Quality Control (QC) analysis and quantification were performed before sequencing. Replicates were included.

tag: disease state

value: type 1 diabetes

value: blood

value: plasma


title: T1D patients with Fibrous Carotid Plaque A3


title: WBJPE166284.53

city: Hangzhou

first: Yuzi

last: Xu

state: Zhejiang

address: Yuhangtang Road

country: China

institute: Zhejiang University

data_processing:
Raw read counts for all genes were annotated based on GENCODE Release 35 (GRCh38.p13) (https://www.gencodegenes.org/human/)
The RNA-seq data were normalized by calculating CPM (counts per million) for genes.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: cartilage

extract_protocol:
Total RNA was isolated from homogenized cartilage using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Duesseldorf, Germany) following the manufacturer's instructions.
RNA-seq library preparation of the cartilage samples was performed using the BRB-seq protocol following manufacturer's protocols.

value: cartilage

tag: disease

value: osteoarthritic human cartilage


title: WBJPE166284.50


title: H9CerebralOrganoid, automated, techRep1 (201026-B3-auto)

description:
Sample 4
auto_d18_B3_rsem_genes.results


title: H9CerebralOrganoid, automated, techRep1 (201026-B2-auto)

description:
Sample 3
auto_d18_B2_rsem_genes.results


title: T1D patients with Fibrous Carotid Plaque A2


title: H9CerebralOrganoid, automated, techRep1 (201026-A3-auto)

description:
Sample 2
auto_d18_A3_rsem_genes.results


title: WBJPE166284.49


title: H9CerebralOrganoid, control, techRep1, bioRep2 (201026-A1b-susp)

description:
Sample 8
susp_d18_A1b_rsem_genes.results


title: T1D patients with Fibrous Carotid Plaque A1


title: H9CerebralOrganoid, automated, techRep1 (201026-A2-auto)

description:
Sample 1
auto_d18_A2_rsem_genes.results


title: WBJPE166284.46


title: LSRA rep3

city: shanghai

first: zhibin

last: zhou

address: 415 Fengyang Road

department: orthopedics

institute: changzheng hospital

description:
CircRNA.txt
LncRNA.txt
mRNA.txt

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain high-quality clean reads.
Then the clean reads were mapped to reference genome using hisat2.
The result of alignment with the reference genome was stored in a binary file, called a bam file. Using the Stringtie software to assemble the reads, the new transcript was spliced. Then the candidate lncRNA transcripts were selected by comparing the gene annotation information of the reference sequence produced by Cuffcompare software. Finally, transcripts with coding potential were screened out by CPC, CNCI, Pfam and PLEK to obtain lncRNA predicted sequences.
Aligning the sequencing reads of each sample with the sequence of mRNA transcript sequences, known lncRNA sequences and lncRNA prediction sequences by bowtie2, and using eXpress to make gene quantitative analysis, the FPKM value and counts value (the number of reads for each gene in each sample) were obtained.
In order to generate SAM file, we used BWA software to align the sequencing reads of each sample with reference genome. Then CIRI software was used to scan for PCC signals (paired chiastic clipping signals), and circRNA sequences were predicted based on junction reads and GT-AG cleavage signals.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text files include normalized FPKM values

organism: Rattus

source_name: spinal cord

extract_protocol:
Total RNA was isolated using mirVana™ miRNA ISOlation Kit (Ambion-1561). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA)
The paired-end libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina, RS-122-2301) according to the manufacturer’s instructions.

tag: strain

value: Sprague-Dawley

value: spinal cord

tag: weight

value: LSRA


title: LSRA rep1

description:
CircRNA.txt
LncRNA.txt
mRNA.txt


title: LSRA rep2

description:
CircRNA.txt
LncRNA.txt
mRNA.txt


title: WBJPE166284.45


title: U251 cells, TWIST1 WT rep2

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

data_processing:
Adaptor removal and bad quality filtering were performed using Trimmomatic-0.32 (samples 1-9) or Cutadapt (samples 10-13)
Resulting reads shorter than 30bp were discarded
Reads were mapped to the Homo Sapiens GRCh38 reference genome using STAR supplied with gene annotations downloaded from Ensembl (and with EndToEnd option and outFilterMismatchNoverLmax was set to 0.04
Expression levels for each gene were quantified using htseq‐count (Anders, Pyl, & Huber, 2014, (“HTSeq,” n.d.)). TPM values were estimated independently using Kallisto (Bray, Pimentel, Melsted, & Pachter,2016)
Genome_build: hg38
Supplementary_files_format_and_content: raw_counts

growth_protocol: U251 were maintained in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum (FBS), penicillin-streptomycin , 2 mg/ml L-glutamine and non-essential amino acids.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA Kit (Macherey-Nagel)
mRNA was purified from 500 ng of total input RNA followed by fragmentation and the generation of double-stranded cDNA. After Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent)

value: Glioblastoma cells

value: TWIST1 WT


title: WBJPE166284.43


title: H9CerebralOrganoid, automated, techRep1 (201026-B5-auto)

description:
Sample 5
auto_d18_B5_rsem_genes.results

value: H9 cerebral cortex organoid (Experimental-group)


title: Sham control rep3

description:
CircRNA.txt
LncRNA.txt
mRNA.txt

value: control


title: MYCS62A_Splenomegaly_I123

city: Portland

first: Rosalie

last: Sears

state: OR

address: 2730 SW Moody Ave, CL4RS

department: Molecular and Medical Genetics

institute: Oregon Health & Science University

data_processing:
Base calling using Illumina RTA version 2.4.11.
Conversion to FASTQ using bcl2fastq2 version 2.20.0.422
All reads were trimmed to 44 bases and aligned to mm9 with Bowtie version 1.0.0 (allowing up to 3 mismatches, but requiring unique best matches.)
Used R scripts to count tags that aligned to the exons of UCSC RefSeq gene models and calculate FPKM values.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary files  are tab delimited text files with un-normalized tag counts for each RefSeq gene model (suitable for count based tools such as DESeq2) and FPKM normalized values.

organism: Mus musculus

source_name: Thymic tissue

growth_protocol: Spontaneous thymic lymphoma or splenomegaly

extract_protocol:
Trizol extraction per manufacturer's protocol
Sequencing libraries were constructed using a NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) per manufactuer instructions. Briefly, poly(A)+ RNA was isolated from 500ng of total RNA (per sample) using oligo-dT-coated magnetic beads. The recovered RNA was then chemically fragmented. First strand cDNA was generated using random hexamers as primers for reverse transcriptase. Strand-specific second strand cDNA synthesis was performed and a single ‘A’ nucleotide was then added to each end. Illumina adaptors were ligated to the cDNAs. Limited-round (15-cycle) PCR was used to amplify the material to yield the final libraries.  Library concentration was determined using real-time PCR with primers complementary to the Illumina adaptors.  All libraries were prepared with indexing barcodes to permit multiplexing in a single lane. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: Lymphocytes (T and B-cells)

tag: expressing

value: ect. MYCS62A and endo. MYC


title: MYCS62A_Splenomegaly_I86


title: WBJPE166284.168


title: Sham control rep2

description:
CircRNA.txt
LncRNA.txt
mRNA.txt


title: MYCS62A_Splenomegaly_I170


title: WBJPE166284.165


title: U251 cells, Empty rep2

value: Empty


title: WBJPE166284.166

value: healthy human cartilage


title: U251 cells, Empty rep1


title: U251 cells, TWIST1 WT rep1


title: WBJPE166284.162


title: Airway 2D culture, rep 4

city: Winston-Salem

first: Sean

middle: V

last: Murphy

state: NC

address: 391 Technology Way

institute: Wake Forest Institue for Regenerative Medicine

data_processing:
Raw sequence reads were imported into Partek Flow (Version: 10.0.21.0509) for analysis.
CUTADAPT was used to trim sequence reads based on quality and to remove sequencing adapters; rDNA and mtrDNA contaminants were filtered out using Bowtie 2.
High-quality reads were mapped to the human GENCODE reference database (release 36) using STAR (Spliced Transcripts Alignment to a Reference).
Aligned reads were quantified using the Partek E/M algorithm and then normalized using DESeq2.
Assembly: hg38 GENCODE Genes, release 36
Supplementary files format and content: The 'Normalized_RNA_Counts_All_Samples.txt' processed data file contains normalized read counts for each of the 14 samples. The first column contains the Ensembl Transcript ID, the second column includes the Gene ID, and the subsequent columns contain the normalized counts for each designated transcript.

source_name: Airway 2D ALI culture

extract_protocol:
RNA was extracted using a Zymo Direct-zol RNA MiniPrep Plus Kit. The quantity of the RNA extracts was determined using a DeNovix RNA Fluorescence Assay Kit and DeNovix DS-11 FX+ Spectrophotometer/Fluorometer, and the integrity of each extract was determined using an Agilent 4200 TapeStation and reagents.
cDNA libraries were prepared using a Perkin Elmer NEXTFLEX Combo-Seq mRNA/miRNA Kit. Proper sizing of cDNA libraries were validated using an Agilent 4200 TapeStation, and library quantities were determined by qPCR using a KAPA Library Quantification Kit (Roche). The cDNA libraries were then normalized prior to pooling to ensure equal library representation. Pooled cDNA libraries were sequenced using an Illumina NovaSeq 6000 System, generating ~25 million 1 x 100 nt reads.

value: Airway 2D ALI culture

value: Primary human bronchial epithelial cells


title: Airway 2D culture, rep 5


title: MYCS62A_Thymic_Lymphoma_I42

value: Lymphocytes (T-cells)

value: ectopic MYCS62A only


title: WBJPE166284.164

value: cartilage


title: MYCT58A_Thymic_Lymphoma_H128

value: ectopic MYCT58A only


title: Airway 2D culture, rep 3


title: U251 cells, SETD6 KO2 rep3

value: SETD6 KO2


title: U251 cells, SETD6 KO2 rep2


title: WBJPE166284.163

value: osteoarthritic human cartilage


title: WBJPE166284.161


title: Airway 2D culture, rep 2


title: U251 cells, SETD6 KO2 rep1


title: Sham control rep1

description:
CircRNA.txt
LncRNA.txt
mRNA.txt

value: Sprague-Dawley

value: spinal cord


title: U251 cells, SETD6 KO1 rep3

value: Glioblastoma cells

value: SETD6 KO1


title: MYCT58A_Thymic_Lymphoma_H119


title: U251 cells, SETD6 KO1 rep2


title: U251 cells, SETD6 KO1 rep1


title: Control_H176

value: endo. MYC only


title: MYCT58A_Thymic_Lymphoma_H101


title: Airway 2D culture, rep 1


title: WBJPE166284.159


title: Airway OTE, Stiff Hydrogel, rep 3

source_name: Airway OTE

value: Airway OTE

value: Primary human bronchial epithelial cells and human lung fibroblasts

tag: hydrogel

value: Stiff Hydrogel

value: FB+/ECM+


title: MYCS62A_Thymic_Lymphoma_I109


title: MYCS62A_Thymic_Lymphoma_I116


title: Airway OTE, Stiff Hydrogel, rep 2


title: Control_G182


title: WBJPE166284.154


title: Control_G184


title: U251 cells, Control rep3

value: Control


title: Airway OTE, Medium Hydrogel, rep 3

value: Medium Hydrogel


title: Airway OTE, Stiff Hydrogel, rep 1


title: WBJPE166284.151

value: healthy human cartilage


title: T1D patients with Fibrous Carotid Plaque AC14

value: type 1 diabetes

value: blood

value: plasma


title: WBJPE166284.156

value: cartilage


title: WBJPE166284.158

value: osteoarthritic human cartilage


title: HepaRG d30DMSO H3K4me3 Rep2

city: Saarbrücken

first: Kathrin

last: Kattler-Lackes

state: non-US Resident

address: Campus A2.4 Raum 0.13

department: Epigenetics

country: Germany

institute: Saarland University

library_source: genomic

data_processing:
Low quality ends (phred score=20) of FastQ format reads were trimmed in addition to adapter removal using Trim Galore (version 0.3.3) [http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/]. Trimmed reads were aligned to the human reference genome (hs37d5) using GEM mapper (version 1.376 beta) (Marco-Sola et al., 2012). Samtools (version 1.3) was used to convert SAM to BAM format (H. Li et al., 2009). MarkDuplicate (version 1.115) from Picard tools [http://broadinstitute.github.io/picard/] was used to mark PCR duplications. Differential analysis and annotation of differential sites (DERs) to associated genes and promoter regions were performed using diffReps (version 1.55.5) with padj<0.001 and |FC|>2 (Shen et al., 2013). A circle plot of differential sites was generated using Circlize (version 0.3.10) (Gu et al., 2014). GREAT (version 3.0.0) was used for prediction of associated GO terms with default extension settings (binominal p-value<0.05) (McLean et al., 2010). ChIP-seq coverage tracks normalized to 1 X sequencing depth and mean coverage plots around TSS (bin size = 50 bp) were generated with deepTools (Ramírez et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files containing ChIP-seq signals normalized to sequencing depth

molecule: genomic DNA

source_name: HepaRG cell line

extract_protocol:
Detached HepaRG cells were fixed with 1% formaldehyde in William’s E medium for 10 min. Crosslinking was stopped by adding glycine to a final concentration of 125 mM for 5 min at room temperature. If not mentioned otherwise samples were thereafter kept on ice or at 4 °C and centrifugations were performed at 800 x g for 5 min. After washing twice with 125 mM glycine in PBS and once in PBS, cells were resuspended consecutively in 5 ml buffer A (10 mM HEPES-NaOH, 10 mM EDTA, 0.5 mM EGTA, 0.25 % Triton X-100, 1 x PIC (Complete Protease Inhibitor Cocktail Tablets)), respectively buffer B (10 mM HEPES-NaOH, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.01 % Triton X-100, 1 x PIC) and rotated for 10 min followed by centrifugation each. Cells were resuspended in 600 μl buffer C (25 mM Tris-HCl, 150 mM NaCl, 2 mM EDTA, 1 % Triton X-100, 0.25 % SDS, 1 x PIC). Sonication of chromatin into fragments between 100 and 800 bp was performed using the Bioruptor NGS (Diagenode, Liège, Belgium) on high power setting in 200 μl volumes, either in 0.5 ml shearing tubes with 30 cycles or in 1.5 ml microtubes (Diagenode, Liège, Belgium) with 10 cycles and each cycle consisting of 30 seconds sonication and 30 seconds recovery time. Samples were diluted with double volume dilution buffer (25 mM Tris-HCl (pH 8.0), 150 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.75 % Glycerol).
For each immunoprecipitation 10 µl protein G beads (Invitrogen, Carlsbad, USA) were combined either with 2 μg H3K4me3 (Diagenode, Liège, Belgium, pAb-003-050), H3K27ac (pAb-196-050) or H3K4me1 (pAb-194-050) antibody, 5 μl BSA (NEB, Frankfurt am Main, Germany, 10 mg/ml) and rotated for 2 h. Then, 300 μl sonicated chromatin (equivalent to 1 million cells) were added. Immunoprecipitations of H3K27ac were supplemented with Na-Butyrate to a final concentration of 10 mM. After rotation overnight beads were consecutively washed with 1 ml of WB1 (20 mM Tris-HCl, (pH 8.0), 150 mM NaCl, 2 mM EDTA, 1 % Triton X-100, 0.25 % SDS), twice WB2 (20 mM Tris-HCl (pH 8.0), 500 mM NaCl, 2 mM EDTA, 1 % Triton X-100, 0.25 % SDS), WB3 (10 mM Tris-HCl, (pH 8.0), 250 mM LiCl, 1 mM EDTA, 0.5 % Nonident P-40, 0.5 % Sodiumdesoxycholate) and twice TE / NaCl (10 mM Tris-HCl (pH 8.0), 50 mM NaCl, 1 mM EDTA) under rotation for 10 min. Elution was performed using 200 µl EB (100 mM NaHCO3, 1 % SDS) for 30 min in a shaking device at room temperature. Eluates were supplemented with crosslink reversal solution (4 μl 5 M NaCl, 2 μl 0.5 M EDTA and 2.5 μl Proteinase K (20 mg/ml)) and incubated overnight at 55 °C. ChIP DNA was purified by phenol chloroform extraction followed by ethanol precipitation. Library preparation was performed using the Truseq ChIP Sample Preparation Kit (Illumina, San Diego, USA) following the manual except for omitting size selection. All ChIP-seq libraries were sequenced 2 x 100 bp paired-end on a HiSeq2500 (Illumina, San Diego, USA).

value: differentiated HepaRG cells day 30

tag: antibody

tag: agent

value: DMSO


title: WBJPE166284.149


title: U251 cells, Control rep1

value: Glioblastoma cells


title: Airway OTE, Medium Hydrogel, rep 2


title: WBJPE166284.145


title: WBJPE166284.148


title: HepaRG d30DMSO H3K4me3 Rep1


title: U251 cells, Control rep2


title: HepaRG d30DMSO H3K4me1 Rep2


title: S_13_Rep2_CT26_Day_17_Isotype

city: Princeton

first: Namit

last: Kumar

state: NJ

address: 3551 lawrenceville

department: Informatics & Predictive Sciences

institute: Bristol-Myers Squibb

description: CD45+ tumor infiltrating lymphocytes were FACS sorted from mice (strain) bearing tumors (cell line), and indicated treatment (treatment)

data_processing:
single-cell RNA sequencing reads were mapped to mm10 reference genome.
Transcripts were quantified using 10X Genomic's Cell Ranger pipeline (version 3.1.0)
Genome_build: mm10
Supplementary_files_format_and_content: raw count table
Supplementary_files_format_and_content: SCTransform normalized count table

source_name: in vivo murine colorectal carcinoma

growth_protocol: Cells were cultured at 37C in RPMI 1640, supplemented with 10% FBS.  For MC38, cells were resuspended in PBS at 2x107 cells/mL and 2x106 cells were subcutaneously injected into the right flank of C57BL/6 mice on Day 0.  For CT26, cells were resuspended in PBS at 1x107 cells/mL and 1x106 cells were subcutaneously injected into the right flank of BALB/c mice on Day 0

extract_protocol:
Tumors were harvested at the indicated time points post-implantation.  Single-cell suspensions were created using a gentleMACS dissociator and associated digestion kit (Miltenyl).  Post-digestion ACK Lysis Buffer (Life Technologies) was used to eliminate red blood cells.  For cell sorting, after surface staining cells were resuspended in PBS supplemented with 2% FBS (Gibco) and sorted on a SH300S (Sony).
RNA libraries were prepared for sequencing using standard Chromium platfrom from 10x Genomics 5' v2 kit.

treatment_protocol: Anti-PD1 and isotype control were diluted with PBS and administered at a dose of 10 mg/kg.  Antibodies were dosed via intraperitoneal injection every 4 days for a total of two doses in sequencing studies.

value: in vivo murine colorectal carcinoma

value: CD45+ tumor infiltrating lymphocytes

value: BALB/c

value: Isotype


title: WBJPE166284.155


title: S_14_Rep2_MC38_Day_6_Untx

source_name: in vivo murine colon adenocarcinoma

value: in vivo murine colon adenocarcinoma

value: Untx


title: Airway OTE, Soft Hydrogel, rep 3

value: Airway OTE

value: Primary human bronchial epithelial cells and human lung fibroblasts

value: Soft Hydrogel

value: FB+/ECM+


title: hp1b_rep1

city: Jerusalem, Kiryat Shemona

first: Neta

last: Herman

address: Kiryat Shemona

department: Gentics, Nutrition

institute: Hebrew University Of Jerusalem, Migal

data_processing:
ChIP-seq reads were aligned by bowtie2 software to the full genome sequence of Drosophila melanogaster (UCSC version dm3)
Duplicate reads were removed using the samtools rmdup function and uniquely mapped reads were kept (samtools view -q 10).
Peak calling was performed with the callpeak function of the MACS2 tool with a q-value<0.05
For visualization, bigwig files were created by deepTools (a python tool) with bamCoverage function and normalization parameter set to RPKM
Genome_build: dm3
Supplementary_files_format_and_content: bigwig file for each replica and bed peaks file per protein (antibody), MACS2 narrowPeak peaks file

organism: Drosophila melanogaster

source_name: fly heads

growth_protocol: All flies were raised at 25°C in 12-hour light: 12-hour dark cycles on standard diets

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
Chromatin immobilization and barcoding performed as previously described (Gutin, J. et al. Fine-Resolution Mapping of TF Binding and Chromatin Interactions. Cell Rep. 22, 2797–2807 (2018).)

value: fly heads

value: Actin-gal4/+ (W1118) control

tag: chip antibody


title: WBJPE166284.144

value: cartilage


title: S_15_Rep2_CT26_Day_17_PD1


title: Airway OTE, Medium Hydrogel, rep 1

value: Medium Hydrogel


title: Airway OTE, Soft Hydrogel, rep 2


title: S_16_Rep2_MC38_Day_13_Isotype


title: Airway OTE, Soft Hydrogel, rep 1


title: S_12_Rep2_MC38_Day_13_PD1


title: S_9_Rep2_MC38_Day_13_Untx


title: HepaRG d30DMSO H3K4me1 Rep1

value: differentiated HepaRG cells day 30


title: HepaRG d30DMSO H3K27ac Rep2

value: DMSO


title: H9CerebralOrganoid, control, techRep3, bioRep3 (201026-B2c-susp)

description:
Sample 11
susp_d18_B2c_rsem_genes.results

value: H9 cerebral cortex organoid (Control-group)

value: Neural precursor cells

value: WT

value: Suspension

value: Day 18


title: S_11_Rep2_CT26_Day_10_Untx

value: in vivo murine colorectal carcinoma

value: CD45+ tumor infiltrating lymphocytes

value: BALB/c


title: WBJPE166284.142

value: osteoarthritic human cartilage


title: HepaRG d30DMSO H3K27ac Rep1


title: S_10_Rep2_CT26_Day_17_Untx

value: Untx


title: H9CerebralOrganoid, control, techRep3, bioRep2 (201026-B2b-susp)

description:
Sample 11
susp_d18_B2b_rsem_genes.results


title: WBJPE166284.141


title: H9CerebralOrganoid, control, techRep2, bioRep1 (201026-B2a-susp)

description:
Sample 11
susp_d18_B2a_rsem_genes.results


title: WBJPE166284.140


title: S_24_Rep2_CT26_Day_10_Untx


title: HepaRG d30 control H3K4me3 Rep2


title: WBJPE166284.143


title: S_22_Rep2_CT26_Day_17_Isotype

value: Isotype


title: S_23_Rep2_MC38_Day_13_PD1

value: in vivo murine colon adenocarcinoma


title: WBJPE166284.139


title: HepaRG d30 control H3K4me1 Rep2


title: S_21_Rep2_MC38_Day_6_Untx


title: H9CerebralOrganoid, control, techRep3, bioRep2 (201026-A2b-susp)

description:
Sample 9
susp_d18_A2b_rsem_genes.results


title: H9CerebralOrganoid, control, techRep3, bioRep2 (201026-B1b-susp)

description:
Sample 10
susp_d18_B1b_rsem_genes.results


title: H9CerebralOrganoid, control, techRep3, bioRep1 (201026-B1a-susp)

description:
Sample 10
susp_d18_B1a_rsem_genes.results


title: HepaRG d30 control H3K4me3 Rep1


title: HepaRG d30 control H3K27ac Rep2


title: WBJPE166284.137


title: H9CerebralOrganoid, control, techRep3, bioRep1 (201026-A2a-susp)

description:
Sample 9
susp_d18_A2a_rsem_genes.results


title: H9CerebralOrganoid, control, techRep2, bioRep3 (201026-A1c-susp)

description:
Sample 8
susp_d18_A1c_rsem_genes.results


title: HepaRG d30 control H3K27ac Rep1


title: S_19_Rep2_CT26_Day_17_Untx


title: S_20_Rep2_MC38_Day_13_Isotype


title: H9CerebralOrganoid, control, techRep2, bioRep2 (201026-A1b-susp)


title: WBJPE166284.132


title: WBJPE166284.129


title: WBJPE166284.128


title: WBJPE166284.138


title: S_17_Rep2_MC38_Day_13_Untx


title: S_18_Rep2_CT26_Day_17_PD1


title: HepaRG d30 control H3K4me1 Rep1


title: H9CerebralOrganoid, control, techRep3, bioRep1 (201026-A1a-susp)


title: sac3 24h DNA

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

data_processing:
After adapter and quality trimming using Trim Galore (v0.6.6), RNA-seq data was mapped to yeast genome R64-1-1 using HISAT2 v2.1.0 (Kim et al., 2019) by the Babraham Institute Bioinformatics Facility. Mapped data was imported into SeqMonk v1.47.0
Assembly: R64-1-1
Reads were quantified in 25kb windows spaced every 5kb. Windows overlapping Ty elements and LTRs, mitochondrial DNA, ENA locus and CUP1 locus were excluded then Size Factor normalisation applied

organism: Saccharomyces cerevisiae

source_name: MEP diploid sac3 mutant

extract_protocol:
All cells were grown in YPD media (2% peptone, 1% yeast extract, 2% glucose) at 30°C with shaking at 200 rpm. Media components were purchased from Formedium and media was sterilised by filtration. MEP experiments were performed as described with modifications (Cruz et al., 2018): cells were inoculated in 4 ml YPx (where x is the sugar) and grown for 6-8 hours then diluted in 25 ml YPD and grown for 16-18 hours to 0.2-0.6x107 cells/ml in 50 ml Erlenmeyer flasks. 0.125x107 cells per aged culture were harvested by centrifugation (15 s at 13,000 g), washed twice with 125 µl PBS and re-suspended in 125 µl of PBS containing ~3 mg/ml Biotin-NHS (Pierce 10538723). Cells were incubated for 30 min on a wheel at room temperature, washed once with 125 µl PBS and re-suspended in 125 µl YPD then inoculated in 125 ml YPD at 1x104 cells/ml in a 250 ml Erlenmeyer flask (FisherBrand FB33132) sealed with Parafilm. 1 µM β-estradiol (from stock of 1 mM Sigma E2758 in ethanol) was added after 2 hours. An additional 0.125x107 cells were harvested from the log phase culture while biotin labelling reactions were incubating at room temperature. Cells were harvested by centrifugation for 1 min, 4600 rpm, immediately fixed by resuspension in 70% ethanol and stored at -80°C.
Percoll gradients (1-2 per sample depending on harvest density) were formed by vortexing 1 ml Percoll (Sigma P1644) with 110 µl 10x PBS in 2 ml tubes and centrifuging 15 min at 15,000 g, 4 °C. Ethanol fixed cells were defrosted and washed once with 1 volume of cold PBSE (PBS + 2 mM EDTA) before resuspension in ~100 µl cold PBSE per gradient and layering on top of the pre-formed gradients. Gradients were centrifuged for 4 min at 2,000 g, 4 °C, then the upper phase and brown layer of cell debris removed and discarded. 1 ml PBSE was added, mixed by inversion and centrifuged 1 min at 2,000 g, 4 °C to pellet the cells, which were then re-suspended in 1 ml PBSE per time point (re-uniting samples where split across two gradients). 25 µl Streptavidin microbeads (Miltenyi Biotech 1010007) were added and cells incubated for 5 min on a wheel at room temperature. Meanwhile, 1 LS column per sample (Miltenyi Biotech 1050236) was loaded on a QuadroMACS magnet and equilibrated with cold PBSE in 4 °C room. Cells were loaded on columns and allowed to flow through under gravity, washed with 1 ml cold PBSE and eluted with 1 ml PBSE using plunger. Cells were re-loaded on the same columns after re-equilibration with ~500 µl PBSE, washed and re-eluted, and this process repeated for a total of three successive purifications. After addition of Triton X-100 to 0.01% to aid pelleting, cells were split into 2 fractions in 1.5 ml tubes, pelleted 30 s at 20,000 g, 4 °C, frozen on N2 and stored at -70 °C.
Cells were resuspended in 60 µl PFGE wash buffer (10 mM Tris HCl pH 7.5, 50 mM EDTA) with 1 µl lyticase (17 U/ µl in 10 mM KPO4 pH 7, 50% glycerol, Merck >2000 U/mg L2524), heated to 50°C for 2 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl PFGE wash buffer with 10 µl 17 U/µl lyticase and incubated 3 hours at 37°C. Solution was replaced with 500 µl PK buffer (100 mM EDTA pH 8, 0.2% sodium deoxycholate, 1% sodium N-lauroyl sarcosine, 1 mg/ml Proteinase K) and incubated overnight at 50°C. Plugs were washed four times with 1 ml TE for 1-2 hours at room temperature with rocking, 10 mM PMSF was added to the second and third washes from 100 mM stock (Merck 93482). ½ plugs were equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol and resuspended in 130 µl 0.1x TE. DNA was fragmented in an AFA microTUBE (Covaris 520045) in a Covaris E220 duty factor 10, PIP 175, Cycles 200, Temp 11°C, then ethanol precipitated. 10 ng DNA was used to prepare libraries using the NEBNext Ultra II DNA kit (NEB E7645S) as described with modifications: Reagent volumes for tailing and adaptor ligation were reduced by 75%; libraries were amplified for 9 cycles using 2 µl each primer per 50 µl reaction before two rounds of AMPure bead purification at 0.9x and elution in 11 µl 0.1x TE prior to quality control using a Bioanalyzer HS DNA ChIP (Agilent) and quantification using a KAPA Library Quantification Kit (Roche).

value: MEP diploid sac3 mutant

tag: media

value: YPD


title: sac3 log DNA

value: log


title: rad52 48h DNA

source_name: MEP diploid rad52 mutant

value: MEP diploid rad52 mutant


title: H9CerebralOrganoid, automated, techRep2 (201026-C3-auto)

description:
Sample 7
auto_d18_C3_rsem_genes.results

value: H9 cerebral cortex organoid (Experimental-group)

value: Automated


title: WBJPE166284.133

value: cartilage


title: H9CerebralOrganoid, automated, techRep2 (201026-B5-auto)

description:
Sample 5
auto_d18_B5_rsem_genes.results

value: Neural precursor cells

value: WT


title: S_7_Rep2_CT26_Day_17_Isotype


title: rad52 24h DNA


title: H9CerebralOrganoid, automated, techRep2 (201026-C2-auto)

description:
Sample 6
auto_d18_C2_rsem_genes.results

value: Day 18


title: sac3 48h DNA


title: WBJPE166284.126


title: WBJPE166284.125


title: S_6_Rep2_CT26_Day_17_Untx

value: in vivo murine colorectal carcinoma


title: rad52 log DNA


title: WBJPE166284.124


title: H9CerebralOrganoid, automated, techRep2 (201026-B3-auto)

description:
Sample 4
auto_d18_B3_rsem_genes.results


title: S_8_Rep2_CT26_Day_17_PD1

value: CD45+ tumor infiltrating lymphocytes


title: S_4_Rep2_MC38_Day_13_PD1


title: spt3 24h DNA

source_name: MEP diploid spt3 mutant

value: MEP diploid spt3 mutant


title: S_3_Rep2_MC38_Day_13_Isotype


title: H9CerebralOrganoid, automated, techRep2 (201026-A3-auto)

description:
Sample 2
auto_d18_A3_rsem_genes.results


title: WBJPE166284.122

value: osteoarthritic human cartilage


title: S_5_Rep2_CT26_Day_10_Untx

value: BALB/c

value: Untx


title: WBJPE166284.127


title: H9CerebralOrganoid, automated, techRep2 (201026-B2-auto)

description:
Sample 3
auto_d18_B2_rsem_genes.results


title: H9CerebralOrganoid, automated, techRep2 (201026-A2-auto)

description:
Sample 1
auto_d18_A2_rsem_genes.results


title: WBJPE166284.123


title: S_1_Rep2_MC38_Day_6_Untx

value: in vivo murine colon adenocarcinoma


title: spt3 log DNA


title: WBJPE166284.121


title: WBJPE166284.114


title: wt 24h DNA

source_name: MEP diploid

value: MEP diploid


title: spt3 48h DNA

value: YPD


title: WBJPE166284.115


title: wt log DNA

value: log


title: S_9_Rep1_MC38_Day_13_Untx


title: siRPS15A-1

city: La Jolla

first: Georg

last: Vogler

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

description: hPSC-derived CMs treated with siRPS15A

data_processing:
nextflow run nf-core/rnaseq -r 3.0 -profile docker -params-file nf-params.json -resume
see execution_report.html and pipeline_report.txt
Assembly: GRCh37
Supplementary files format and content: ENSG gene names and raw read counts per gene for each condition and replicate.

source_name: cardiomyocyte

extract_protocol:
Cells were pelleted and resuspended in 500µl TRIzol reagent followed by total RNA extraction using Qiagen RNAeasy Mini Kit.
Illumina stranded mRNA; 100ng RNA input - 13 cycles in amp step

treatment_protocol: hPSCs and hPSC-derived CMs were transfected with 25nM final concentrations of siRNA against RPS15A, RPL39 and with scrambled control siRNAs.

value: cardiomyocyte

value: RPS15A knockdown


title: siRPS15A-3

description: hPSCs treated with siRPS15A

source_name: hPSC

value: hPSC


title: S_15_Rep1_CT26_Day_17_PD1


title: siRPS15A-4

description: hPSCs treated with siRPS15A


title: wt 48h DNA


title: XIIr<>V 48h

description: All_probe_quantification_for_GEO_submission_translocation_libraries.txt

data_processing:
After adapter and quality trimming using Trim Galore (v0.6.6), RNA-seq data was mapped to yeast genome R64-1-1 using HISAT2 v2.1.0 (Kim et al., 2019) by the Babraham Institute Bioinformatics Facility. Mapped data was imported into SeqMonk v1.47.0
Assembly: R64-1-1
Quantified for log2 total reads mapping to the antisense strand of annotated open reading frames (opposite strand specific libraries) including probes to the rDNA intergrenic regions. Read counts were adjusted by Size Factor normalisation for the full set of quantified probes.

source_name: MEP haploid Chr XIIr <> V translocation

extract_protocol:
All cells were grown in YPD media (2% peptone, 1% yeast extract, 2% glucose) at 30°C with shaking at 200 rpm. Media components were purchased from Formedium and media was sterilised by filtration. MEP experiments were performed as described with modifications (Cruz et al., 2018): cells were inoculated in 4 ml YPx (where x is the sugar) and grown for 6-8 hours then diluted in 25 ml YPD and grown for 16-18 hours to 0.2-0.6x107 cells/ml in 50 ml Erlenmeyer flasks. 0.125x107 cells per aged culture were harvested by centrifugation (15 s at 13,000 g), washed twice with 125 µl PBS and re-suspended in 125 µl of PBS containing ~3 mg/ml Biotin-NHS (Pierce 10538723). Cells were incubated for 30 min on a wheel at room temperature, washed once with 125 µl PBS and re-suspended in 125 µl YPD then inoculated in 125 ml YPD at 1x104 cells/ml in a 250 ml Erlenmeyer flask (FisherBrand FB33132) sealed with Parafilm. 1 µM β-estradiol (from stock of 1 mM Sigma E2758 in ethanol) was added after 2 hours. An additional 0.125x107 cells were harvested from the log phase culture while biotin labelling reactions were incubating at room temperature. Cells were harvested by centrifugation for 1 min, 4600 rpm, immediately fixed by resuspension in 70% ethanol and stored at -80°C.
Percoll gradients (1-2 per sample depending on harvest density) were formed by vortexing 1 ml Percoll (Sigma P1644) with 110 µl 10x PBS in 2 ml tubes and centrifuging 15 min at 15,000 g, 4 °C. Ethanol fixed cells were defrosted and washed once with 1 volume of cold PBSE (PBS + 2 mM EDTA) before resuspension in ~100 µl cold PBSE per gradient and layering on top of the pre-formed gradients. Gradients were centrifuged for 4 min at 2,000 g, 4 °C, then the upper phase and brown layer of cell debris removed and discarded. 1 ml PBSE was added, mixed by inversion and centrifuged 1 min at 2,000 g, 4 °C to pellet the cells, which were then re-suspended in 1 ml PBSE per time point (re-uniting samples where split across two gradients). 25 µl Streptavidin microbeads (Miltenyi Biotech 1010007) were added and cells incubated for 5 min on a wheel at room temperature. Meanwhile, 1 LS column per sample (Miltenyi Biotech 1050236) was loaded on a QuadroMACS magnet and equilibrated with cold PBSE in 4 °C room. Cells were loaded on columns and allowed to flow through under gravity, washed with 1 ml cold PBSE and eluted with 1 ml PBSE using plunger. Cells were re-loaded on the same columns after re-equilibration with ~500 µl PBSE, washed and re-eluted, and this process repeated for a total of three successive purifications. After addition of Triton X-100 to 0.01% to aid pelleting, cells were split into 2 fractions in 1.5 ml tubes, pelleted 30 s at 20,000 g, 4 °C, frozen on N2 and stored at -70 °C.
Cells were re-suspended in 50 µl Lysis/Binding Buffer (from mirVANA kit, Life Technologies AM1560), and 50 µl 0.5 µm zirconium beads (Thistle Scientific 11079105Z) added. Cells were lysed with 5 cycles of 30 s 6500 ms-1 / 30 s ice in an MP Fastprep bead beater or for 3 min at power 12 in a Bullet Blender (ThermoFisher) in cold room, then 250 µl Lysis/Binding buffer added followed by 15 µl miRNA Homogenate Additive and cells were briefly vortexed before incubating for 10 minutes on ice. 300 µl acid phenol : chloroform was added, vortexed and centrifuged 5 min at 13,000 g, room temperature before extraction of the upper phase. 400 µl room temperature ethanol and 2 µl glycogen (Sigma G1767) were added and mixture incubated for 1 hour at -30 °C before centrifugation for 15 minutes at 20,000 g, 4 °C. The pellet was washed with cold 70% ethanol and re-suspended in 10 µl water. 1 µl RNA was glyoxylated and analysed on a BPTE mini-gel, and RNA was quantified using a PicoGreen RNA kit (Life Technologies R11490) or Qubit® RNA HS Assay Kit. 150 ng RNA was used to prepare libraries using the NEBNext Ultra II Directional mRNAseq kit with poly(A)+ purification module (NEB E7760, E7490) as described with modifications: Reagent volumes for elution from poly(T) beads, reverse transcription, second strand synthesis, tailing and adaptor ligation were reduced by 50%; libraries were amplified for 13 cycles using 2 µl each primer per 50 µl reaction before two rounds of AMPure bead purification at 0.9x and elution in 11 µl 0.1x TE prior to quality control using a Bioanalyzer HS DNA ChIP (Agilent) and quantification using a KAPA Library Quantification Kit (Roche).

value: MEP haploid Chr XIIr <> V translocation


title: WBJPE166284.107

value: cartilage

value: healthy human cartilage


title: WBJPE166284.106


title: XIIr<>V 24h


title: WBJPE166284.105


title: S_14_Rep1_MC38_Day_6_Untx


title: siRPL39-4

description: hPSCs treated with siRPL39

value: RPL39 knockdown


title: S_2_Rep2_MC38_Day_13_Untx


title: XIIr<>V log


title: S_13_Rep1_CT26_Day_17_Isotype

value: in vivo murine colorectal carcinoma

value: Isotype


title: siRPS15A-2

description: hPSC-derived CMs treated with siRPS15A


title: S_16_Rep1_MC38_Day_13_Isotype

value: CD45+ tumor infiltrating lymphocytes


title: WBJPE166284.104

value: osteoarthritic human cartilage


title: wt GST-V-U 48h

source_name: MEP haploid wild type with GST-V-U insert


title: siRPL39-3

description: hPSCs treated with siRPL39


title: WBJPE166284.103

source_name: cartilage


title: wt GST-V-U 24h

value: MEP haploid wild type with GST-V-U insert


title: siRPL39-2

description: hPSC-derived CMs treated with siRPL39


title: siRPL39-1

description: hPSC-derived CMs treated with siRPL39


title: S_11_Rep1_CT26_Day_10_Untx

value: BALB/c

value: Untx


title: wt GST-V-U log


title: siCtrl-3

description: hPSCs treated with siCTRL

value: WT

value: siCTRL


title: WBJPE166284.101


title: S_10_Rep1_CT26_Day_17_Untx


title: wt_log_3

description:
featureCounts_RNAseq_read_count_quantification.txt
DESeq2_normalised_RNAseq_read_counts.csv

source_name: MEP diploid wild type

value: MEP diploid wild type

value: YPD

value: log


title: WBJPE166284.100


title: siCtrl-4

description: hPSCs treated with siCTRL

value: hPSC


title: wt_log_2


title: ipsilateral, scRNAseq

city: Aurora

first: ANDRA

last: DINGMAN

state: CO

department: Pediatrics

institute: University of Colorado Anschutz Medical Campus

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10

source_name: brain

extract_protocol:
mice were anesthetized with 2-3% inhaled isoflurane and transcardially perfused with ice cold artificial cerebral spinal fluid (aCSF).  The aCSF was composed of the following (in mmol/L): 126 NaCl, 2.5 KCl, 25 NaHCO3, 1.3 NaH2PO4, 2.5 CaCl2, 1.2 MgCl2 and 12 glucose. Coronal slices from each hemisphere (300μm thick) were cut with a Vibratome 1200 (Leica).  Lateral striatum was dissected from each hemi-section and placed in HABG media (Hibernate A Media, BrainBits, Springfield, IL, HA500; 2% B27 Supplement, ThermoFisher, Cat #17504044; 0.26% Glutamax, ThermoFisher, Cat# 35050061). For each sample (ipsilateral and contralateral), striata from 3 animals was pooled in the same sample for biologic variability.  Tissue was washed by centrifugation and  the tissue was resuspended in 3 mL of 3.5% Collagenase/Dispase (Sigma, USA, 11097113001, 100mg/mL stock) in Hibernate A minus Calcium Media (BrainBits, HACA100) with 0.125% Glutamax.  Samples were then dissociated using the GentleMacs Octo Dissociator (Miltenyi Biotech, Githersburg, MD, 130-195-937) on program 37_NDK_01. After dissociation enzymes were quenched with HABG up to 15 mL. Tubes were spun and the tissue was resuspended in 2 mL HABG media, and 50 uL of Deoxyribonuclease I from bovine pancrease (DNASE) was added. Each sample was triturated about 10 times with a flame polished glass pipette.  Dissociated tissue was then passed through a 100 micron cell strainer (Falcon, 352360), followed by a 40micron cell strainer (Falcon, 352340).  Each strainer was washed with 20mL of HABG media.  Samples were then spun  and resuspended in 4mL of 30% Percol (Sigma, P1644) in Calcium and Magnesium free Hank’s Balanced Salt Solution (HBSS, ThermoFisher, 14170112).  One milliliter of HBSS free of calcium and magnesium was then carefully layered on top of the Percol, and layers were allowed to separate for 5 minutes on ice.  Samples were then centrifuged for 15 minutes at 700xg with the brake turned off.  The top layer of myelin and cellular debris was discarded, and the remaining layer was washed with 15mL of HABG media.  Following centrifugation at 400xg for five minutes, the cell pellet was used for fluorescent activated cell sorting (FACS). Cells were inculbated with flourescent antibodies for A2B5, O4 and CD45 and stained with Dapi.  FACS was performed and CD45+ Dapi+ cells were excluded.  Cells positive for A2B5 and/or O4 were collected for scRNAseq.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics)

value: brain

value: oligodendrocyte

value: MCAO, ipsialteral striatum


title: S_24_Rep1_CT26_Day_10_Untx


title: S_12_Rep1_MC38_Day_13_PD1

value: in vivo murine colon adenocarcinoma


title: WBJPE166284.102

value: cartilage


title: contralateral, scRNAseq

description: 10x Genomics

value: MCAO, contralateral striatum


title: S_22_Rep1_CT26_Day_17_Isotype

value: in vivo murine colorectal carcinoma

value: CD45+ tumor infiltrating lymphocytes

value: Isotype


title: S_21_Rep1_MC38_Day_6_Untx


title: S_23_Rep1_MC38_Day_13_PD1


title: siCtrl-1

description: hPSC-derived CMs treated with siCTRL

value: cardiomyocyte


title: wt_48h_3


title: S_20_Rep1_MC38_Day_13_Isotype


title: dox_blebb_rep3

city: Iowa City

first: Dakota

middle: L

last: Jones

state: IA

address: 51 Newton Road

department: Department of Anatomy and Cell Biology

institute: University of Iowa

description: dox_noblebb_vs_dox_blebb_diffbind_FCcutFDRcut_anno.txt

data_processing:
RNA quality was evaluated using a BioAnalyzer. RNA libraries were prepared using Illumina truSeq polyA high-throughput kit and single-end reads were sequenced to 100 base pairs using an Illumina NovaSeq. Reads were aligned to the mm10 genome using Hisat2. Picard was used to generate bam files and sorted by chromosomal coordinates. FeatureCounts was used to generate count files. Deseq2 was used for differential expression analysis between groups (n=3 biological replicates/group). Pathway analysis was completed using Panther.
DNA fragment size was analyzed using a Fragment Analyzer. Libraries were sequenced to 50 base pairs from both ends using an Illumina NovaSeq. Raw reads were aligned to the mm10 genome using Bowtie2. Picard and Samtools were used to generate bam files and to filter out duplicates and mitochondrial reads. Peaks were called using MACS2 using the following options: ““--keep-dup all -q 0.01 -no model”. Diffbind was used to identify differentially accessibility chromatin loci between groups (n=3 biological replicates/group). Motif analysis was completed using the findMotifsGenome.pl command within Homer.
Assembly: mm10
Supplementary files format and content: RNAseq differential expression files (.txt) and ATAC differential chromatin accessibility changes (.txt)

source_name: tail tendon

growth_protocol: Fibroblasts were grown and maintained in DMEM supplemented with 10% FBS with antibiotics/antimycotics

extract_protocol:
mRNA isolation was carried out using the Qiagen mRNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared using Illumina truSeq polyA high-throughput kit. ATAC libraries were generated according to a previously published protocol (Corces MR, et al, 2017)

treatment_protocol: Fibroblasts were treated in DMEM media supplemented with 0.1% FBS with antibiotics/antimycotics. Blebbistatin was used at a concentration of 10uM. Y27632 was used at a concentration of 30uM. Doxycycline was used at a concentration of 10ng/mL.

value: tail tendon

value: primary

value: fibroblast

value: wildtype

value: doxycycline + blebbistatin


title: wt_48h_1

value: MEP diploid wild type

value: YPD


title: wt_log_1

value: log


title: S_19_Rep1_CT26_Day_17_Untx

value: BALB/c

value: Untx


title: Thymus_ISP_3scRNAseq

city: Ghent

first: Tom

last: Taghon

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

data_processing:
Fastq files were mapped using CellRanger version 6.0.1
Assembly: GRCh38
Supplementary files format and content: h5 files obtained from CellRanger

source_name: thymus

extract_protocol:
Pediatric thymus from a 4 month old child undergoing cardiac surgery was obtained and used according to and with the approval of the Medical Ethical Commission of Ghent University Hospital (Belgium). Thymus tissue was cut into small pieces and digested with 1.6mg/ml collagenase (Gibco, 17104-019) in IMDM medium for 30min at 37°C to generate a single cell suspension. The reaction was quenched with 10% FBS and the thymocyte suspension was passed through a 70μm filter to remove undigested tissue. Cells were frozen in FBS containing 10% DMSO and stored in liquid nitrogen until needed. Upon thawing thymocytes were enriched for cell types of interest (CD34+ cells, ISPs, DPs, TCRγδ+ thymocytes) using bead-based enrichment/depletion and FACS. To obtain DP thymocytes, cells were labelled with antibodies and FACS sorting was used to obtain equal proportions of CD8α+CD4+CD3+ and CD45+CD8α+CD4+CD3- thymocytes. CD34+ cells were obtained through enrichment with CD34 magnetic-activated cell-sorting (MACS) microbeads (Miltenyi, 130-046-703), labelled with anti-CD1a and subsequently FACS sorted to include equal proportions of CD1a+ and CD1a- cells. To enrich ISPs thymocytes were labelled with anti-CD3 (clone OKT3, produced in house) and anti-glycophorin A (clone 10F7MN, produced in-house) and CD3+ and Glycophorin+ cells were subsequently depleted using sheep anti-mouse IgG magnetic Dynabeads (Invitrogen). This was followed by FACS sorting for CD3-CD8α-CD4+ thymocytes. To obtain TCRγδ+ thymocytes, cells were enriched using anti-γδ TCR hapten antibodies and anti-hapten MACS microbeads (Miltenyi, 130-050-701) according to the manufacturer’s instructions and subsequently FACS sorted for TCRγδ+CD3+.
library construction according to protocol for 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1

value: thymus

value: ISP thymocytes


title: siCtrl-2

description: hPSC-derived CMs treated with siCTRL

value: WT

value: siCTRL


title: Thymus_gd_3scRNAseq

value: gdTCR+ thymocytes


title: S_18_Rep1_CT26_Day_17_PD1

value: in vivo murine colorectal carcinoma

value: CD45+ tumor infiltrating lymphocytes


title: RNA.hESCs

city: GuangZhou

first: Hanwen

last: Yu

state: GuangDong

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-*Sen Road, Yuexiu District, Guangzhou City, Guangdong Province, 510080, PRC

institute: SUN YAT-SEN UNIVERSITY

description:
RNA.hESCs
Pathul-seq_hESCs_gene_count.txt

data_processing:
The bulk RNA-seq and scRNA-seq (SMART-seq2) data were analyzed with following steps. First, the sequencing quality of raw data were examined by package FastQC (release 0.11.9) and MultiQC (release 1.9) (Ewels et al., 2016). Then, the sequencing adapters were trimmed and read pairs with low quality or complexity were filtered from raw data through TrimGalore (release 0.6.5). The clean read pairs were mapping to reference genome (hg38 for human; mm10 for mouse) with STAR (release 2.7.4a) (Dobin et al., 2013) with the following arguments: --outSAMmapqUnique 255. Lastly, the uniquely mapped reads unambiguously attributed to each gene and repeat locus were counted using featureCounts (release 2.0.0) (Liao et al., 2014).
Assembly: hg38
Supplementary files format and content: txt files are count matries of gene expression

source_name: hESCs

growth_protocol: Human embryonic stem cells (hESCs) were cultured in matrigel-coated plates in the Essential 8 hESC medium (Thermo, catalog. no. A1517001). The medium was changed daily. hESCs were treated with 0.48 mM EDTA for dissociation and then passaged onto new Matrigel -coated plates every 4–5 days.

extract_protocol:
To obtain MII oocytes, the immature oocytes were collected and matured in vitro in medium (Cooper Surgical/SAGE, Trumbull, CT) supplemented with 75 mIU/ml FSH and LH for 24-28h. After the in vitro maturation, the MII oocytes were fertilized by intracytoplasmic sperm injection (ICSI), and then cultured in IVF medium (Vitrolife, catalog. no. 10136). 16-18h later, the fertilization were observed, 2PN zygotes were cultured in G1 medium (Vitrolife) at 37°C in 6% CO2, 5% O2 and 89% N2 for 3 days to 8-cell embryo stage, and then switched to G2 medium (Vitrolife) until the blastocyst stage. The 4-cell, 8-cell and morula embryos (zona pellucida and Polar body removed) were collected into the nuclear isolation buffer for AULIChIP-seq. The inner cell mass (ICM) and mural trophectoderm were separated by gently pipetting in a pipette with a diameter of 40-60 μm and collected into the nuclear isolation buffer.  Human ESCs were dissociated with Accutase (Thermo Fisher Scientific, catalog. no. A1110501) into single cells and washed with PBS solution twice. Then, 50 or 500 hESCs were collected into the nuclear isolation buffer.   Lysates were clarified from micrococcal nuclease-treated nuclei and histone-DNA complexes were isolated with anti-H3K9me3 antibody.
Sequencing libraries were generated and indexed from 1ng of cDNA per sample using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat#TD503) according to the manufacturer’s instructions.

treatment_protocol: Without any chemical or genetic treatment on human embryos and embryonic stem cells prior to AULIChIP-seq.

value: hESCs

value: untreated


title: Thymus_DP_3scRNAseq

value: DP thymocytes


title: TRP1_log_3

source_name: MEP diploid wild type TRP1 restored

value: MEP diploid wild type TRP1 restored


title: S_7_Rep1_CT26_Day_17_Isotype

source_name: in vivo murine colorectal carcinoma

value: Isotype


title: nodox_blebb_rep3

description: nodox_noblebb_vs_nodox_blebb_diffbind_FCcutFDRcut_anno.txt

value: tail tendon

value: primary

value: fibroblast

value: wildtype

value: blebbistatin


title: dox_noblebb_rep2

description:
dox_noblebb_vs_dox_blebb_diffbind_FCcutFDRcut_anno.txt
nodox_noblebb_vs_dox_noblebb_diffbind_FCcutFDRcut_anno.txt

value: doxycycline


title: wt_24h_2

value: MEP diploid wild type

value: YPD


title: S_8_Rep1_CT26_Day_17_PD1

value: BALB/c


title: dox_noblebb_rep3


title: wt_24h_3


title: TRP1_log_2

value: log


title: S_17_Rep1_MC38_Day_13_Untx

source_name: in vivo murine colon adenocarcinoma

value: in vivo murine colon adenocarcinoma

value: Untx


title: wt_24h_1


title: wt_48h_2


title: RNA.Blast.gRNA2.rep1

description:
RNA.Blast.gRNA2.rep1
SVA_dCas9_KRAB_editing_Blast_gene_count.txt

source_name: Blastocyst

value: Blastocyst


title: dox_blebb_rep1

value: doxycycline + blebbistatin


title: Thymus_CD34_3scRNAseq

value: thymus

value: CD34+ thymocytes


title: RNA.Blast.gRNA1.rep1

description:
RNA.Blast.gRNA1.rep1
SVA_dCas9_KRAB_editing_Blast_gene_count.txt


title: dox_blebb_rep2


title: S_3_Rep1_MC38_Day_13_Isotype

description: CD45+ tumor infiltrating lymphocytes were FACS sorted from mice (strain) bearing tumors (cell line), and indicated treatment (treatment)

value: CD45+ tumor infiltrating lymphocytes

value: Isotype


title: S_4_Rep1_MC38_Day_13_PD1


title: nodox_blebb_rep2

value: tail tendon

value: primary


title: nodox_blebb_rep1

value: fibroblast

value: wildtype


title: TRP1_log_1

value: MEP diploid wild type TRP1 restored


title: dox_noblebb_rep1

value: doxycycline


title: nodox_noblebb_rep3

description:
nodox_noblebb_vs_dox_noblebb_diffbind_FCcutFDRcut_anno.txt
nodox_noblebb_vs_nodox_blebb_diffbind_FCcutFDRcut_anno.txt

value: DMSO


title: RNA.Blast.gRNA2.rep2

description:
RNA.Blast.gRNA2.rep2
SVA_dCas9_KRAB_editing_Blast_gene_count.txt


title: TRP1_48h_3

value: YPD


title: RNA.Blast.gRNA1.rep2

description:
RNA.Blast.gRNA1.rep2
SVA_dCas9_KRAB_editing_Blast_gene_count.txt


title: RNA.Blast.Ctrl.rep2

description:
RNA.Blast.Ctrl.rep2
SVA_dCas9_KRAB_editing_Blast_gene_count.txt

value: untreated


title: S_5_Rep1_CT26_Day_10_Untx

value: in vivo murine colorectal carcinoma

value: BALB/c


title: S_2_Rep1_MC38_Day_13_Untx

value: in vivo murine colon adenocarcinoma

value: Untx


title: RNA.8Cell.NoDox

description:
RNA.8Cell.NoDox
SVA_dCas9_KRAB_editing_8Cell_gene_count.txt

source_name: 8Cell embryo

value: without Dox


title: RNA.Blast.Ctrl.rep1

description:
RNA.Blast.Ctrl.rep1
SVA_dCas9_KRAB_editing_Blast_gene_count.txt

value: Blastocyst


title: nodox_noblebb_rep2


title: TRP1_24h_3


title: S_1_Rep1_MC38_Day_6_Untx

value: CD45+ tumor infiltrating lymphocytes


title: RNA.8Cell.Ctrl

description:
RNA.8Cell.Ctrl
SVA_dCas9_KRAB_editing_8Cell_gene_count.txt


title: LSK_Taz_S89A rep3 [RNA-seq]

city: Jena

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

institute: Leibniz Institute on Aging

description:
LSK from old mouse
KSL_Taz_S89A_3_CGGCTATG_L008_R1_001
KSL_taz_s89a_oe_rpkm_table.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by cutadapt (v2.10), then mapped to mm10 whole genome using bowtie2-2.2.9 with default parameters.
Differential gene expression was performed by edgeR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_rpkm_table.txt: RPKM tables as tab-delimited text files.

growth_protocol: Freshly sorted LSK cells (1-2 × 10^4 cells/replicate) were seeded into 200 μL of HSPC culture medium composed of StemSpanTM Serum-free expansion medium (SFEM, #09650, STEMCELL Technologies) supplemented with 1% Penicillin-Streptomycin (Thermo Fisher Scientific) and 50 ng/mL recombinant mouse SCF and TPO (STEMCELL Technologies) per well of a 48-well-plate and incubated at 37 °C, with 5% CO2 and 95% relative humidity. After 8-24 hours of incubation, cells were transduced by concentrated lentivirus in SFEM medium supplemented with 10 ng/mL SCF, TPO and IL-3 (STEMCELL Technologies). 48 h post transduction, cells were washed extensively in 0.1% BSA/PBS and single cells were plated in 96-well plates containing HSPC culture medium. For RNA-Sequencing from Taz S89A overexpressing LSK cells, RNA was isolated three days after lentiviral transduction.

extract_protocol:
RNA was isolated by the RNeasy Micro kit (Qiagen).
Libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit (kit) using the RNA purified by the NEBNext® Poly(A) mRNA Magnetic Isolation Module. 10 ng of total RNA were used as input.

tag: age

value: 22-28 months

value: LSK

tag: construct

value: Taz S89A (Lego-iG2-Puro-Taz-S89A)


title: Y27_ATACseq_rep3

tag: tissue

value: tail tendon

tag: cell line

value: primary

value: fibroblast


title: RNA.8Cell.Dox

description:
RNA.8Cell.Dox
SVA_dCas9_KRAB_editing_8Cell_gene_count.txt

tag: cell type

value: with Dox


title: TRP1_48h_1

description:
featureCounts_RNAseq_read_count_quantification.txt
DESeq2_normalised_RNAseq_read_counts.csv

value: MEP diploid wild type TRP1 restored


title: TRP1_24h_2

value: YPD


title: Y27_ATACseq_rep2

tag: genotype

value: wildtype

tag: treatment


title: LSK_Taz_S89A rep1 [RNA-seq]

description:
LSK from old mouse
KSL_Taz_S89A_1_CTGAAGCT_L008_R1_001
KSL_taz_s89a_oe_rpkm_table.txt


title: S_6_Rep1_CT26_Day_17_Untx

value: in vivo murine colorectal carcinoma


title: TRP1_24h_1

tag: time


title: Y27_ATACseq_rep1


title: H3K9me3.hESCs

data_processing:
Bioinformatic analyses ChIP-seq data generated in this study were performed by custom shell scripts in which raw data were first trimmed and filtered by TrimGalore with default parameter; then qualified read pairs were aligned to reference genome by Bowtie2 (release 2.4.1); after that biological and optical duplicates were removed with Sambamba (release 0.7.1); last we used MACS2 (release 2.2.7.1; parameters for broad peaks H3K9me3: --broad --broad-cutoff 0.05 -g hs -f BAMPE) to call peaks. All peaks were filtered with blacklisted regions. The highly reproducible peaks were identified by package IDR, which is a uniﬁed approach to measure the reproducibility of ﬁndings identiﬁed from replicate experiments and provides highly stable thresholds based on reproducibility. For downstream analysis, package deepTools (release 3.5.0) was used to generate genome coverage track files for UCSC visualization and heatmap based on scores of specific genomic regions, such as RPKM value.
Assembly: hg38
Supplementary files format and content: wig files were generated using deeptools; Scores represent RPKM values.
Library strategy: CUT&TAG

extract_protocol:
To obtain MII oocytes, the immature oocytes were collected and matured in vitro in medium (Cooper Surgical/SAGE, Trumbull, CT) supplemented with 75 mIU/ml FSH and LH for 24-28h. After the in vitro maturation, the MII oocytes were fertilized by intracytoplasmic sperm injection (ICSI), and then cultured in IVF medium (Vitrolife, catalog. no. 10136). 16-18h later, the fertilization were observed, 2PN zygotes were cultured in G1 medium (Vitrolife) at 37°C in 6% CO2, 5% O2 and 89% N2 for 3 days to 8-cell embryo stage, and then switched to G2 medium (Vitrolife) until the blastocyst stage. The 4-cell, 8-cell and morula embryos (zona pellucida and Polar body removed) were collected into the nuclear isolation buffer for AULIChIP-seq. The inner cell mass (ICM) and mural trophectoderm were separated by gently pipetting in a pipette with a diameter of 40-60 μm and collected into the nuclear isolation buffer.  Human ESCs were dissociated with Accutase (Thermo Fisher Scientific, catalog. no. A1110501) into single cells and washed with PBS solution twice. Then, 50 or 500 hESCs were collected into the nuclear isolation buffer.   Lysates were clarified from micrococcal nuclease-treated nuclei and histone-DNA complexes were isolated with anti-H3K9me3 antibody.
Libraries were prepared according to the Accel-NGS  2S Plus DNA Liibrary Kit from Swift Biosciences.

treatment_protocol: Without any chemical or genetic treatment on human embryos and embryonic stem cells prior to Pathul-seq.

value: hESCs

value: untreated


title: LSK_Taz_S89A rep2 [RNA-seq]

description:
LSK from old mouse
KSL_Taz_S89A_2_TCTCGCGC_L008_R1_001
KSL_taz_s89a_oe_rpkm_table.txt


title: TRP1_48h_2


title: H3K9me3.Blast.gRNA2.rep2


title: spt3_log_3

source_name: MEP diploid spt3 mutant

value: MEP diploid spt3 mutant

value: log


title: nodox_noblebb_rep1

value: DMSO


title: spt3_log_1


title: Blebb_ATACseq_rep3

value: Blebbistatin


title: H3K9me3.Blast.gRNA2.rep1

value: Blastocyst


title: Blebb_ATACseq_rep2


title: spt3_log_2


title: LSK_empty_vector rep2 [RNA-seq]

description:
LSK from old mouse
KSL_pLEGO_2_TCCGGAGA_L008_R1_001
KSL_taz_s89a_oe_rpkm_table.txt

value: 22-28 months

value: LSK

value: empty vector (Lego-iG2-Puro)


title: spt3_48h_3


title: DMSO_ATACseq_rep3

description:
DMSOvsBleb_anno.txt
DMSOvsY27_anno.txt

value: tail tendon

value: primary


title: Blebb_ATACseq_rep1

value: fibroblast


title: H3K9me3.Blast.gRNA1.rep1


title: LSK_empty_vector rep1 [RNA-seq]

description:
LSK from old mouse
KSL_pLEGO_1_ATTACTCG_L008_R1_001
KSL_taz_s89a_oe_rpkm_table.txt


title: H3K9me3.Blast.gRNA1.rep2


title: H3K9me3.Blast.Ctrl.rep2


title: spt3_48h_1


title: hAR ChIPseq hARtg-Osr1Cre

city: Duarte

first: Zijie

last: Sun

address: 1500 E. Duarte Rd.

department: Cancer Biology

institute: City of Hope

description: Chromatin IP against hAR

data_processing:
The libraries were quantified by Qubit dsDNA HS Assay Kit and validated with Agilent Bioanlyzer DNA high Sensitivity Kit.
DNA was purified twice with Agencourt AMPure XP beads (A63880, Beckman Coulter, Pasadena, CA, USA) and sequenced on Illumina Hiseq 2500 Sequencer.
Reads were mapped to mouse genome assembly mm9 using Novoalign v3.02.07.
MACS v2.0 was used to call Peaks and to generate bed graph files for visualization of peaks.
Genome_build: mm19 reference genome
Supplementary_files_format_and_content: bedGraph files containing permissive peaks of samples

source_name: Prostatic intraepithelial neoplasia

extract_protocol:
Mouse prostate tissues were minced, cross-linked with 1% formaldehyde for 25 min at RT. The chromatin was resuspended in lysis buffer and fragmented to size of 200-500 bp with with a Sonic Dismembrator Model 100 (Fisher Scientific) at 4°C.  The cell lysates was subjected to immunoprecipitation with Dynabead Protein G conjugated with AR antibody (sc-7305X, Santa Cruz Biotechnology, Dallas, TX, USA). After RNase A and Proteinase K treatment, ChIP DNA was purified with phenol/chloroform/isoamylalcohol (Invitrogen).
ChIP DNA samples were subjected to amplification using MicroPlex Library Preparation kit (AB-004-0012, Diagenode, Denville, NJ, USA) on a StepOnePlus Real-Time PCR System (Applied Biosystems). The libraries were quantified by Qubit dsDNA HS Assay Kit and validated with Agilent Bioanlyzer DNA high Sensitivity Kit.

value: Prostate

tag: disease state

value: Prostatic intraepithelial neoplasia

value: anti-hAR (sc-7305X)


title: H3K9me3.Blast.Ctrl.rep1


title: DMSO_ATACseq_rep2

description:
DMSOvsBleb_anno.txt
DMSOvsY27_anno.txt

value: wildtype


title: spt3_48h_2

value: YPD


title: hARtg-Osr1Cre-PCa-replicate2

data_processing:
Adapter sequences and other redundant sequences were removed from raw paired-end reads using cutadapt (v1.9.1)
Reads were aligned against the mouse genome (mm9) using HISAT2 (2.1.0) .
Read counts were tabulated using  HTSeq (v0.6.1)
Genome_build: UCSC. The mouse genome (mm9).
Supplementary_files_format_and_content: Txt file with raw reads for each sample corresponding to each gene

source_name: Prostatic adenocarcinoma

extract_protocol:
RNA samples were extracted from fresh normal, PIN, or PCa mouse prostate using RNeasy Mini Kit (#74104, Qiagen, Hilden, Germany)
cDNA libraries were prepared using Kapa RNA HyperPrep Kit with RiboErase (KR1351, Kapa Biosystems, Wilmington, MA, USA)

value: Prostatic adenocarcinoma


title: H3K9me3.8Cell.NoDox

value: without Dox


title: spt3_24h_3

value: MEP diploid spt3 mutant


title: LSK_empty_vector rep3 [RNA-seq]

description:
LSK from old mouse
KSL_pLEGO_3_CGCTCATT_L008_R1_001
KSL_taz_s89a_oe_rpkm_table.txt

tag: strain


title: DMSO_ATACseq_rep1

description:
DMSOvsBleb_anno.txt
DMSOvsY27_anno.txt

value: DMSO


title: Y27_RNAseq_rep3


title: H3K9me3.8Cell.Dox

value: with Dox


title: spt3_24h_2


title: hAR ChIPseq Input

description: input DNA


title: hARtg-Osr1Cre-PCa-replicate1


title: hARtg-Osr1Cre-PIN-replicate3


title: H3K9me3.8Cell.Ctrl

value: untreated


title: spt3_24h_1


title: abnormal_human_embryo_8-2 [8-2_L3_807D73]

data_processing:
Sequencing quality of all high-throughput sequencing data were first comprehensively examined by FastQC (release 0.11.9) whose results were parsed with MultiQC (release 1.9). Next, adapter sequences and bases with sequencing quality < 20 were trimmed from raw data by TrimGalore (release 0.6.5; default parameter). Trimmed read pairs were aligned to genome with STAR (release 2.7.4a) according to different aims. For quantification of gene and repeat locus expression, the following command-line arguments were used: --outSAMmapqUnique 255; for repeat element expression analysis in sub-family level, the arguments included: --winAnchorMultimapNmax 200 --outFilterMultimapNmax 100. We computed the number of mapping reads unambiguously attributed to each gene and repeat locus using the featureCounts package (release 2.0.0; default parameter). TEtranscripts (version 2.2.1; default parameter) was used to quantify expression of repeat in sub-family level.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: human abnormal embryo

growth_protocol: The immature oocytes were collected and matured in vitro in medium (Cooper Surgical/SAGE, Trumbull, CT) supplemented with 75 mIU/ml FSH and LH for 24-28h. After the in vitro maturation, the MII oocytes were fertilized by intracytoplasmic sperm injection (ICSI), and then cultured in IVF medium (Vitrolife). 16-18h later, the fertilization were observed, 2PN zygotes were cultured in G1 medium (Vitrolife) at 37°C in 6% CO2, 5% O2 and 89% N2 for 3 days to 8-cell embryo stage, and then switched to G2 medium (Vitrolife) until the blastocyst stage. The developmental arrested blastomeres were isolated from Day 6 blastocyst for single-cell RNA-seq experiments.

extract_protocol:
Human embryo single cell RNA-seq libraries were performed as previously described with minor modifications (Picelli et al., 2014, Macaulay et al., 2016). Briefly, human blastomeres were picked individually into 2.5 μl RLT plus buffer (Qiagen, catalog. no. 1053393). RNA was captured on streptomycin C1 beads conjugated with Biotinylated Oligo-dT30VN primer and the remaining DNA supernatant was collected for HAT-seq. The volume of reverse transcription was adjusted to 10 μl. cDNA was generated according to the smart-seq2 protocol(Picelli et al., 2014).
Sequencing libraries were generated and indexed from 1ng of cDNA per sample using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, catalog. no. TD503) according to manufacturer’s instructions. Samples were pooled and sequenced using paired-end sequencing on the Illumina Novaseq platform.

treatment_protocol: Without any chemical or genetic treatment on human embryos.

tag: tissue/ell type

value: human abnormal embryo

tag: developmental stage

value: Day 6 blastocyst

tag: tissue/cell subtype

value: developmentally arrested blastomeres


title: Y27_RNAseq_rep1

value: tail tendon


title: Y27_RNAseq_rep2

value: primary


title: sac3_log_3

source_name: MEP diploid sac3 mutant

value: MEP diploid sac3 mutant

value: log


title: hARtg-Osr1Cre-PIN-replicate2

value: Prostate

value: Prostatic intraepithelial neoplasia


title: Blebb_RNAseq_rep3

value: fibroblast

value: wildtype

value: Blebbistatin


title: abnormal_human_embryo_8-1 [8-1_L3_806D73]


title: sac3_log_2

value: YPD


title: abnormal_human_embryo_6-2 [6-2_L3_805D73]


title: Blebb_RNAseq_rep1


title: WT-control-replicate 3

source_name: Prostate tissue

value: Normal


title: Blebb_RNAseq_rep2


title: sac3_log_1


title: abnormal_human_embryo_6-1 [6-1_L3_804D73]


title: WT-control-replicate 2


title: sac3_48h_3


title: WT-control-replicate 1


title: abnormal_human_embryo_4-3 [4-3_L3_803D73]


title: DMSO_RNAseq_rep1

description:
diffexpr-results_DMSOvsBlebb.txt
diffexpr-results_DMSOvsY27.txt

value: DMSO


title: DMSO_RNAseq_rep2


title: sac3_48h_2


title: abnormal_human_embryo_4-2 [4-2_L3_802D73]


title: abnormal_human_embryo_4-1 [4-1_L3_801D73]


title: LT-HSC low old rep3 [RNA-seq]

description:
No3_Clca3a1_neg
Clca3a1High_vs_Clca3a1Low_HSCs_rpkm_table.txt

extract_protocol:
HSPCs from young and old C57BL/6 mice were sorted into RLT buffer (Qiagen) and purified by the RNeasy Micro kit (Qiagen).
Libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit (kit) using the RNA purified by the NEBNext® Poly(A) mRNA Magnetic Isolation Module. 10 ng of total RNA were used as input.

value: 22-28 months

value: LT-HSC Clca3a1_low

tag: antibody

value: Clca3a1 antibody (DHSB; clone 10.1.1)


title: abnormal_human_embryo_1-6 [1-6_L3_806F10]

value: human abnormal embryo

value: Day 6 blastocyst


title: Hpb-CM

city: Montreal

first: Irah

last: King

address: 1001 Decarie Blv

country: Canada

institute: McGill University

data_processing:
Single-cell matrices were generated using Cellranger (v.4.0.0)
Assembly: mm10
Supplementary files format and content: tsv and mtx, scRNAseq matrices

source_name: Small intestinal organoids

growth_protocol: The small intestine (SI) was harvested, flushed with PBS, cut into approximately three-10cm pieces, and opened longitudinally. Intestine pieces were rinsed with PBS, and then incubated in 2mM EDTA at 4°C for 30 min with gentle agitation. Crypts were further released from the SI by vigorous shaking in 10mL PBS, three times, and passed through a 70μm cell strainer. Isolated crypts were resuspended in 10mL basal organoid medium (Advanced DMEM/F12 (Gibco), 10 mM HEPES (Gibco), 1× GlutaMAX (Gibco), 1% penicillin/streptomycin (Gibco). Crypts were plated in 30μL Matrigel (Corning) domes in 24-well plates and 500μL of culture medium was added to each well. Organoids culture medium (ENR): basal organoid medium with the addition of N2 Supplement (1:100, Gibco), B27 Supplement (1:50, Gibco), 1mM N-Acetylcysteine, 50ng/mL recombinant Epithelial Growth Factor (EGF), in-house made R-spondin 1 and Noggin conditioned mediums (1:50).

extract_protocol:
Single cell suspensions were prepared by manual disturbance of Matrigel domes followed by incubation in TrypLE (Gibco) for 40 minutes at 370C, were loaded on a Next GEM Chip G (PN-1000120) together with Next GEM Single Cell 3ʹ GEM Kit v3.1 (PN-1000121) and single cells were captured on a 10X Genomics Chromium controller with a recovery target of 5000 cells per sample.
cDNAs were generated following the 10X Genomics protocol. cDNAs were size selected using SPRIselect beads from Beckman Coulter (B23318), and their quality was checked with a Bioanalyzer High Sensitivity DNA Kit from Agilent (5067-4626). One quarter of the total cDNA was used to generate libraries using Next GEM Single Cell Library Kit (PN-1000121) and barcoded using the Single Index Kit Set A (PN-111213) following the 10X protocol. Libraries were size selected using SPRIselect beads and their quality was checked with the Bioanalyzer High Sensitivity DNA Kit. Libraries size were centered at 440 bp

treatment_protocol: Organoids were treated with Hpb-CM for 24h at day 0 of culture or left in ENR control medium

value: Hpb-CM for 24h at day 0


title: hARtg-Osr1Cre-PIN-replicate1


title: sac3_24h_2


title: LT-HSC high old rep3 [RNA-seq]

description:
No3_Clca3a1_pos
Clca3a1High_vs_Clca3a1Low_HSCs_rpkm_table.txt

value: LT-HSC Clca3a1_high


title: sac3_24h_3

value: MEP diploid sac3 mutant


title: sac3_48h_1


title: LT-HSC high old rep2 [RNA-seq]

description:
No2_Clca3a1_pos
Clca3a1High_vs_Clca3a1Low_HSCs_rpkm_table.txt


title: sac3_24h_1

value: log


title: abnormal_human_embryo_1-4 [1-4_L3_804F10]

value: developmentally arrested blastomeres


title: ENR

value: left in ENR control medium


title: abnormal_human_embryo_1-5 [1-5_L3_805F10]


title: DMSO_RNAseq_rep3

value: tail tendon

value: primary

value: fibroblast


title: E2 Hpb-CM

data_processing:
Star aligner
Homer make tag directories
Home analyzeRepeats
Assembly: mm10
Supplementary files format and content: csv tag counts

extract_protocol: Trizol-based RNA extraction according to manufacturer guidelines


title: rad52_log_2

source_name: MEP diploid rad52 mutant

value: MEP diploid rad52 mutant

value: YPD


title: D2 Hpb-CM


title: abnormal_human_embryo_1-3 [1-3_L3_803F10]


title: LT-HSC low old rep1 [RNA-seq]

description:
No1_Clca3a1_neg
Clca3a1High_vs_Clca3a1Low_HSCs_rpkm_table.txt


title: LT-HSC high old rep1 [RNA-seq]

description:
No1_Clca3a1_pos
Clca3a1High_vs_Clca3a1Low_HSCs_rpkm_table.txt


title: rad52_log_1


title: abnormal_human_embryo_1-2 [1-2_L3_802F10]


title: LT-HSC low old rep2 [RNA-seq]

description:
No2_Clca3a1_neg
Clca3a1High_vs_Clca3a1Low_HSCs_rpkm_table.txt


title: rad52_48h_2


title: C2 ENR


title: rad52_48h_1


title: Kos3_V2_orc1P179AM_LRY3216

city: Buffalo

middle: N

last: Rusche

state: NY

address: 109 Cooke Hall, UB North/Amherst Campus

department: Biological Sciences

institute: State University of New York at Buffalo

data_processing:
T. delbrueckii genome index was built using Bowtie2/2.3.4.1.
ChIP- seq reads for single-end sequencing were aligned to the T. delbrueckii genome index using Bowtie2/2.3.4.1.
ChIP peaks were called using MACS2/2.2.7.1 with the parameters: --nomodel, --extsize 200, --keep-dup 3
Genome_build: CBS1146 (GCA_000243375.1)
Supplementary_files_format_and_content: bigWig

organism: Torulaspora delbrueckii

source_name: Yeast

growth_protocol: Yeast cells were grown at 30˚C in YPD medium containing 1% yeast extract, 2% peptone, and 2% glucose.

extract_protocol:
Cells were grown in YPD overnight. Following day, cells were diluted at OD600 0.3, grown at 30˚C, and harvested at an OD600 of ∼1.
Libraries were prepared using Takara Bio SMARTer ThruPlex DNA seq kit

treatment_protocol: Cells were cross-linked for 1 hour in 1% formaldehyde. After cell lysis, chromatin was sonicated. Immunoprecipitation was conducted with 10μL Protein A agarose beads and 4 µl of anti MYC (Millipore 06-549) or anti V5 antibody (Millipore AB3792) antibody.

tag: epitope tag

value: V5 (Millipore AB3792)


title: ST-HSC young rep3 [RNA-seq]

description:
ST_HSC_young_3
young_old_HSPC_populations_rpkm_table.txt

value: 3-5 months

value: ST-HSC


title: rad52_24h_2


title: ST-HSC young rep1 [RNA-seq]

description:
ST_HSC_young_1
young_old_HSPC_populations_rpkm_table.txt


title: 50 DPH female RA 7

first: Claudio

last: Mello

address: 3181 SW Sam Jackson Park Rd, L470

department: Behavioral Neuroscience

data_processing:
Base calls were made by Illumina's RTA v3.4.4
Quality control and trimming were performed prior to genome alignment using trimmomatic (v0.36, parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36), and no issues were detected from FastQC (v0.11.9) reports.
Splice-aware STAR (v2.6.1, parameters --sjdbOverhang 99 --quantMode GeneCounts) was used to align reads and generate read counts per gene based on the bTaeGut1_v1.p zebra finch assembly (GCF_003957565.1) and associated genome features from the NCBI Taeniopygia guttata Annotation Release 104.
Genome_build: GCF_003957565.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Taeniopygia guttata

source_name: brain

growth_protocol: Birds were sacrificed within 20 min of lights-on and no singing was observed in any individual.

extract_protocol:
Brains were removed, flash frozen in a slurry of dry ice and isopropanol, cryosectioned onto PEN membrane glass slides (Leica, No. 11505158), fixed in 100% cold ethanol, and stained using cresyl violet. Brain nucleus RA was extracted from PEN slides into RLT buffer (Qiagen) using laser capture microdissection (Leica LMD 6500). RNA was isolated using the RNeasy Micro Kit (Qiagen) with on-column DNase digestion.
Using the SmartSeq v4 PLUS Kit (Takara Bio USA), cDNAs were generated from 1 ng total RNA , then the resulting cDNA was bioanalyzed on a High Sensitivity DNA chip, and 5 ng was used as input for the libraries.

tag: Sex

value: Female

value: 50 days posthatch

tag: brain id


title: rad52_24h_1

tag: media


title: abnormal_human_embryo_1-1 [1-1_L3_801F10]

value: human abnormal embryo

value: Day 6 blastocyst


title: ST-HSC young rep2 [RNA-seq]

description:
ST_HSC_young_2
young_old_HSPC_populations_rpkm_table.txt

tag: age


title: ST-HSC old rep3 [RNA-seq]

description:
ST_HSC_old_3
young_old_HSPC_populations_rpkm_table.txt

value: 22-28 months


title: GATA2cKO_Mouse7_snATAC

city: Los Angeles

first: Michel

middle: A

last: Zamojski

state: California

address: 8700 Beverly Boulevard

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

description: Male

data_processing:
Single Nuclei ATAC-seq data were processed using Cell Ranger-ATAC pipeline version 1.2.0 with mm10 as the reference genome.
Genome_build: mm10
Supplementary_files_format_and_content: Peak accessibility count matrices in Hierarchical Data Format HDF5 for cell barcodes.
Supplementary_files_format_and_content: Metadata files that include per barcode QC, ATAC signal and cell calling metrics in comma-separated values (CSV) format.
Supplementary_files_format_and_content: BED-like tabular files listing all unique fragments captured by the assay in tab-separated values (TSV) format.

source_name: Pituitary gland

growth_protocol: Animals were on a 12-hour on, 12-hour off light cycle, with lights on at 7 AM and off at 7 PM. Pituitaries were collected from male and randomly-cycling C57BL/6 female mice aged 10-12 weeks.

extract_protocol:
Snap-frozen pituitaries were thawed on ice. For nuclei isolation, a modified protocol from Mathys et al Nat 2019 was followed, all on ice. RNAse inhibitor (NEB MO314L) was added to the homogenization buffer (0.32 M sucrose, 1 mM EDTA, 10 mM Tris-HCl, pH 7.4, 5mM CaCL2, 3mM Mg(Ac)2, 0.1% IGEPAL CA-630), 50% OptiPrep (Stock is 60% Media from Sigma; cat# D1556), 35% OptiPrep and 30% OptiPrep right before isolation. Each pituitary was homogenized with 10 strokes (loose pestle) in an individual autoclaved dounce glass homogenizer (1ml, VWR cat# 71000-514). The homogenate was filtered through a 40-micrometer cell strainer. The volume was measured and an equal volume of 50% OptiPrep was added. The gradient was centrifuged using an SW41 rotor at 9200 rpm and at 4C for 25 min. Nuclei were collected from the interphase between 30% and 35% OptiPrep. The nuclei were washed, resuspended either in 1x nuclei dilution buffer for snATACseq (10X Genomics) or in 1X PBS/0.04% BSA for snRNAseq, and counted on an Invitrogen Countess II cell counter. ii) Dissociated pituitary cells were cryopreserved in 90% FBS/10% DMSO and shipped to New York on dry-ice. Upon arrival, cells were stored in liquid nitrogen. On the day of an experiment, the vial was removed from liquid nitrogen on dry-ice, thawed quickly in a 37C waterbath, and cells were serially diluted with 10% FBS /DMEM until a minimum volume of 8ml was reached. Cells were centrifuged at 300xg for 5min, resuspended in 1ml of medium and counted. Nuclei were isolated from all cells remaining after the scGEM Drop-seq RNA-seq assay was done. Cells were centrifuged at 500g for 5min at 4C. The supernatant was carefully removed and 0.1X lysis buffer (1x: 10mM Tris-HCL pH 7.5, 10mM NaCl, 3mM MgCl2, nuclease-free H2O, 0.1% v/v NP-40, 0.1% v/v Tween-20, 0.01% v/v digitonin) was added. After 5min incubation on ice, 1ml of wash buffer was added. The nuclei were pelleted at 500xg for 5min at RT, resuspended either in 1X PBS/0.04% BSA for scGEM Drop-seq RNA-seq or in diluted nuclei buffer for snATAC-seq. Nuclei were counted and the concentration adjusted to run the given assay.
snATACseq was performed as described (10x Genomics, Pleasanton, CA), following the Chromium Single Cell ATAC Reagent Kits V1 User Guide. Nuclei were counted on a Nexclome instrument, and the final concentration was used to calculate the volume of nuclei stock to use. Transposition was performed in 10 microliter at 37C for 60min. Then the Chromium Chip E (PN-2000121) was loaded to target up to 10,000 nuclei. Barcoding was performed in the emulsion for 12 cycles following the Chromium protocol. Each library was tagged with a different index for multiplexing (Chromium i7 Sample Index N, Set A kit PN-3000262). Quality control and quantification of the libraries were assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit). Sequencing was carried out at the NYGC on Illumina Novaseq using 98+26 paired-end reads.

value: GATA2 cKO

value: Mixed

value: 8-10 weeks

tag: source type

value: snap-frozen pituitaries


title: ST-HSC old rep2 [RNA-seq]

description:
ST_HSC_old_2
young_old_HSPC_populations_rpkm_table.txt


title: Kos3_V1_orc1bahM_LRY3212

tag: chip antibody


title: GATA2cKO_Mouse3_snATAC

description: Male


title: Control_Mouse9_snATAC

description: Male

value: control


title: Kos3_V1_orc1P179AM_LRY3215


title: 50 DPH female RA 5


title: B2 ENR

value: left in ENR control medium


title: 50 DPH male RA 5

value: Male


title: ST-HSC old rep1 [RNA-seq]

description:
ST_HSC_old_1
young_old_HSPC_populations_rpkm_table.txt

tag: cell type


title: MPP young rep2 [RNA-seq]

description:
MPP_young_2
young_old_HSPC_populations_rpkm_table.txt

value: MPP


title: Control_Mouse8_snATAC

description: Male

tag: genotype


title: Kos3_V2_orc1bahM_LRY3212


title: GATA2cKO_Mouse17_snRNA

data_processing:
single-nuclei RNA-seq data were processed using the Cell Ranger pipeline v5.0.0, and aligned to the mm10 transcriptome, including introns.
Genome_build: mm10
Supplementary_files_format_and_content: UMI count matrices in Hierarchical Data Format HDF5 for cell barcodes

growth_protocol: Animals were on a 12-hour on, 12-hour off light cycle, with lights on at 7 AM and off at 7 PM.

extract_protocol:
Snap-frozen pituitaries were thawed on ice. For nuclei isolation, a modified protocol from Mathys et al Nat 2019 was followed, all on ice. RNAse inhibitor (NEB MO314L) was added to the homogenization buffer (0.32 M sucrose, 1 mM EDTA, 10 mM Tris-HCl, pH 7.4, 5mM CaCL2, 3mM Mg(Ac)2, 0.1% IGEPAL CA-630), 50% OptiPrep (Stock is 60% Media from Sigma; cat# D1556), 35% OptiPrep and 30% OptiPrep right before isolation. Each pituitary was homogenized with 10 strokes (loose pestle) in an individual autoclaved dounce glass homogenizer (1ml, VWR cat# 71000-514). The homogenate was filtered through a 40-micrometer cell strainer. The volume was measured and an equal volume of 50% OptiPrep was added. The gradient was centrifuged using an SW41 rotor at 9200 rpm and at 4C for 25 min. Nuclei were collected from the interphase between 30% and 35% OptiPrep. The nuclei were washed, resuspended either in 1x nuclei dilution buffer for snATACseq (10X Genomics) or in 1X PBS/0.04% BSA for snRNAseq, and counted on an Invitrogen Countess II cell counter. ii) Dissociated pituitary cells were cryopreserved in 90% FBS/10% DMSO and shipped to New York on dry-ice. Upon arrival, cells were stored in liquid nitrogen. On the day of an experiment, the vial was removed from liquid nitrogen on dry-ice, thawed quickly in a 37C waterbath, and cells were serially diluted with 10% FBS /DMEM until a minimum volume of 8ml was reached. Cells were centrifuged at 300xg for 5min, resuspended in 1ml of medium and counted. Nuclei were isolated from all cells remaining after the scGEM Drop-seq RNA-seq assay was done. Cells were centrifuged at 500g for 5min at 4C. The supernatant was carefully removed and 0.1X lysis buffer (1x: 10mM Tris-HCL pH 7.5, 10mM NaCl, 3mM MgCl2, nuclease-free H2O, 0.1% v/v NP-40, 0.1% v/v Tween-20, 0.01% v/v digitonin) was added. After 5min incubation on ice, 1ml of wash buffer was added. The nuclei were pelleted at 500xg for 5min at RT, resuspended either in 1X PBS/0.04% BSA for scGEM Drop-seq RNA-seq or in diluted nuclei buffer for snATAC-seq. Nuclei were counted and the concentration adjusted to run the given assay.
GEM RNAseq was performed as described (10x Genomics, Pleasanton, CA), following the Single Cell 3’ Reagents Kits V3 User Guides. Nuclei were filtered, counted on a Nxcelome instrument, and the final concentration was set at 1,000 cells/μl for nuclei. The amount of nuclei loaded on the chip was determined based on the 10X Genomics protocol. The 10X chip (Chromium Single Cell 3’ Chip kit A v2 PN-12036 or v3 chip kit B PN-2000060) was loaded to target up to 10,000 cells final. Reverse-transcription was performed in the emulsion and cDNA was amplified before library construction following the Chromium protocols v3. Each library was tagged with a different index for multiplexing (Chromium i7 Multiplex kit PN-12062). Quality control and quantification of the amplified cDNA were assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit). Sequencing was carried out at the NYGC on Illumina Novaseq using  98+26 paired-end reads.

tag: gender


title: Control_Mouse2_snATAC

description: Male


title: 50 DPH female RA 6


title: orc1P179A_M1_KOS3V_LRY3215

value: MYC

value: MYC (Millipore 06-549)


title: MPP young rep1 [RNA-seq]

description:
MPP_young_1
young_old_HSPC_populations_rpkm_table.txt

value: 3-5 months


title: orc1bah_M2_KOS3V_LRY3212


title: MPP young rep3 [RNA-seq]

description:
MPP_young_3
young_old_HSPC_populations_rpkm_table.txt


title: 50 DPH female RA 3


title: 50 DPH female RA 4


title: orc1P179A_M2_KOS3V_LRY3216


title: GATA2cKO_Mouse3_snRNA


title: MPP old rep2 [RNA-seq]

description:
MPP_old_2
young_old_HSPC_populations_rpkm_table.txt


title: Kos3_V2_ORC1M_LRY3211

value: V5 (Millipore AB3792)


title: Kos3_V1_ORC1M_LRY3211


title: orc1bah_M1_KOS3V_LRY3212


title: Control_Mouse9_snRNA


title: MPP old rep1 [RNA-seq]

description:
MPP_old_1
young_old_HSPC_populations_rpkm_table.txt


title: Orc1_M1_kos3_LRY3205


title: 20 DPH female RA 5

value: Female

value: 20 days posthatch


title: 50 DPH male RA 3

value: 50 days posthatch


title: Orc1_M1_sir2_LRY3206


title: 50 DPH female RA 2


title: Control_Mouse8_snRNA


title: Control_Mouse2_snRNA


title: Orc1_M2_KOS3V_LRY3211


title: GATA2cKO_Mouse7_snRNA


title: 20 DPH male RA 5


title: 50 DPH male RA 4


title: LT-HSC young rep2 [RNA-seq]

description:
LT_HSC_young_2
young_old_HSPC_populations_rpkm_table.txt

value: LT-HSC


title: MPP old rep3 [RNA-seq]

description:
MPP_old_3
young_old_HSPC_populations_rpkm_table.txt

value: 22-28 months


title: GATA2cKO_Mouse17_snATAC

description: Male

value: GATA2 cKO


title: GATA2_CON2

city: New York

first: Yongchao

last: Ge

address: One Gustave L Levy Place #1137

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The RNA-seq fastq files were aligned with STAR v2.5.1b with the mouse GENCODE annotation.
featureCounts v1.5.0-p1 is used to summarize the reads for all genes and samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file including the counts of reads for all genes and for all samples

extract_protocol:
RNA extraction was performed according to manufacturers’ instructions using the NucleoSpin RNA XS kit (cat # 740902, Macherey-Nagel). Briefly, FACS isolated gonadotrope cells were lysed in 100ul of lysis buffer (RA1 reagent + TCEP), DNA was digested with rDNAse for 15min at RT, and the final RNA eluted in 10ul of RNAse-free water. RNA concentration was measured by Nanodrop-One (Thermo Scientific), and the RNA quality was assessed on a Bioanalyzer (cat# 5067-1513, Eukaryote Total RNA Pico Bioanalyzer kit, Agilent).
RNAseq libraries were prepared with the extracted RNA using the Universal plus mRNA-seq library preparation kit (NuGEN). Library quality control and quantification were assessed by fluorometry (cat # Q32854, Qubit dsDNA High sensitivity Assay Kit), and on a Bioanalyzer (cat # 5067-4626, High-Sensitivity DNA Bioanalyzer kit, Agilent). The 4 libraries were pooled together at equal concentration, the pooled sample was first assessed by mi-seq (Illumina), and then sequenced at the New York Genome Center on Novaseq 6000 (Illumina) with a depth of ~30 million paired-end reads per sample.

treatment_protocol: Pituitaries were extracted from control or cKO mice and gonadotropes were sorted. Sorted gonadotropes were lysed in lysis buffer (RA1 reagent + TCEP) from the NucleoSpin RNA XS kit (cat # 740902, Macherey-Nagel) and frozen prior to following the kit's protocol

value: Mixed

value: 10-12 weeks

value: Lysed purified gonadotropes


title: LT-HSC young rep3 [RNA-seq]

description:
LT_HSC_young_3
young_old_HSPC_populations_rpkm_table.txt


title: LT-HSC old rep1 [RNA-seq]

description:
LT_HSC_old_1
young_old_HSPC_populations_rpkm_table.txt


title: Untreated-control 4

city: Daejeon

first: Woosuk

last: Chung

address: 282, Munhwa-ro

department: Department of Medical Science

country: South Korea

institute: Chungnam National University School of Medicine

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.5.3) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.30.1).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Brain

growth_protocol: Mice were housed at a relative temperature of 22°C and humidity 40%, with a 12-h reverse light/dark cycle and allowed free access to food and water. Mice were weaned at postnatal (PND) 21 days and housed in groups of three to five per cage

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were randomly divided into two groups (saline and ketamine group) at PND 16. Ketamine group mice received a daily intraperitoneal injection of ketamine (i.p., 35 mg/kg) for five consecutive days.  After injection, mice were placed in an empty cage containing fresh bedding (36°C) for at least 30 minutes before returning to its original cage. Mice in the saline group received identical treatment with normal saline.

tag: tissue

value: hippocampus

value: male


title: GATA2_KO1

value: GATA2  cKO

value: Male


title: 20 DPH female RA 4

city: Portland

institute: Oregon Health & Science University


title: LT-HSC old rep3 [RNA-seq]

description:
LT_HSC_old_3
young_old_HSPC_populations_rpkm_table.txt


title: GATA2_KO2


title: Orc1_M2_sir2_LRY3206

value: MYC


title: 20 DPH male RA 2


title: LT-HSC old rep2 [RNA-seq]

description:
LT_HSC_old_2
young_old_HSPC_populations_rpkm_table.txt


title: Orc1_M1_SIR_LRY3204

value: MYC (Millipore 06-549)


title: GATA2_CON1

value: control


title: LT-HSC young rep1 [RNA-seq]

description:
LT_HSC_young_1
young_old_HSPC_populations_rpkm_table.txt

value: 3-5 months


title: 20 DPH male RA 4


title: Untreated-control 1


title: 20 DPH female RA 2

value: Female


title: Input2_Td_JRY10156