title: E5.25, replica 2, plate b, VASAseq

city: Utrecht

first: Peter

last: Zeller

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: VASAseq

data_processing:
library strategy: vast transcriptome analysis of single cells by dA-tailing (VASA-seq)
Raw fastq files were processed according to the VASA-seq Snakemake workflow of the SingleCellMultiOmics (SCMO) package (version 0.1.30). In brief, reads were demultiplexed for VASA barcodes with a hamming distance of 0, trimmed for default adapters with CutAdapt (version 4.1), and the remaining polyA stretches were trimmed off with the SCMO script trim_vasa.py. Read 2 was mapped to the mouse GRCm38 genome (Ensembl 97) using STAR (version 2.5.3a). Mapped reads were tagged, filtered for a mapping quality > 50, and deduplicated using samtools (version 1.15.1). Transcript counts of deduplicated files were generated using velocyto (version 0.17.17).  Downstream analysis was performed with Scanpy (version 1.9.1). Cells with less than 1500 reads and 50 genes detected as well as genes detected in less than 2 cells were removed. Cells with more than 40% mitochondrial reads were also excluded. Protein coding genes were used for further analysis (excluding mitochondrial genes, Malat1, rpls). Counts were normalized to 10.000 transcripts per cell (scanpy.pp.normalize_per_cell) and logarithmized (scanpy.pp.log1p). The number of total counts and percentage of mitochondrial reads were regressed out (scanpy.pp.regress_out) and each gene was scaled to unit variance with a maximum of 10 (scanpy.pp.scale). Principal component analysis was performed and the 30 highest principal components were used to generate the UMAP. The data was clustered using the Leiden algorithm (scanpy.tl.leiden, resolution set to 0.3).
Assembly: GRCm38 genome (Ensembl 97)
Supplementary files format and content: loom files

source_name: embryo

extract_protocol:
E4.5 and E5.25 embryos, dissected from the uterus, and day two and day three embryos, grown in 3E-uterus, were dissociated in the TrypLE solution for up to 12 minutes. Half-way through the incubation in TrypLE, embryos were gently pipetted up and down with a glass pipette to facilitate dissociation. Glass pipette diameter was chosen to first mechanically decouple trophectoderm and the Reichert’s membrane, followed by a narrower pipette to dissociate the remaining tissues. At room temperature, single-cell suspension was transferred into M2 media drops under the oil to prevent media evaporation. Also, using a glass pipette and an aspirator, the single cells were then manually distributed into 384-well plates with a primer mix under oil.
Plate-based VASA-seq was performed according to Salmen et al., 2022 with double volumes. Briefly, cells were mouth pipetted into 384-well plates containing barcoded polyT primers. Cells were lysed and RNA was heat fragmented. Fragmented RNA was end-repaired using T4-PNK and A-tailed by E. coli Poly(A) Polymerase. Repaired RNA was reverse transcribed with SuperScriptIII (SSIII) and Second Strand was carried out in the plate. After pooling, cDNA was amplified by in vitro transcription (IVT). Amplified RNA was depleted for ribosomal RNA using mouse-specific DNA probes in combination with RNAseH. RA3 was ligated onto the 3’ end of the depleted aRNA, reverse transcription was performed using SSIII and the final PCR amplification was performed to introduce small RNA PCR primer indexes. Plates were sequenced paired-end on the Illumina NextSeq2000 2x50bp, with 25bp for read1 and 75bp for read 2.

value: in utero

value: embryo


title: D3, replica 2, plate a, VASAseq

status: Public on Jul 31 2023

type: SRA

description: VASAseq

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: treatment

tag: tissue

tag: strain

tag: age

value: day 3


title: E5.25, replica 2, plate a, VASAseq

description: VASAseq


title: E5.25, replica 1, plate a, VASAseq

description: VASAseq


title: 123992

city: Ann Arbor

first: Joanna

last: Spencer-Segal

address: 205 Zina Pitcher PI

department: Michigan Neuroscience Institute

country: USA

institute: University of Michgan

library_source: transcriptomic

data_processing:
Alignment & Generation of Count Summaries: the RNA-Seq reads were aligned to the mouse genome (GRCm38) using the Subread aligner (Liao et al. 2014, Bioinformatics. 30: 923–930) with multi-mapping enabled. The featureCounts program (Liao et al. 2014, Bioinformatics. 30: 923–930) then generated the gene-level RNA-Seq count summaries for each sample based on ENSEMBL annotation (Ensembl release 95). The counts were then filtered. Genes with counts per million of less than 0.5 in ten or fewer samples were filtered out.
Quality Control: Quality control was performed in R (v.3.6.1) and included visualization of the overall log CPM gene expression across all subjects via boxplots and MDS plots. Outlier samples were detected and removed at this stage. We also noted that all samples from batch 3 were contaminated and were removed in the subsequent analysis. A list of which samples were removed is below in the RAW FILES section.
Differential Expression Analysis was performed using the limma-voom workflow provided by the limma package (v 3.42.0). Contrasts were developed for each comparison and interaction term of interest.
Assembly: GRCm38
Supplementary files format and content: Gene level unfiltered raw counts using ENSEMBL annotation

molecule: polyA RNA

source_name: Brain

extract_protocol:
mRNA was isolated from dorsal and ventral hippocampi using the Qiagen RNAeasy kit in five batches, with groups counterbalanced across batches. RNA was assessed for quality using the TapeStation (Agilent, Santa Clara, CA).
Samples with RINs (RNA Integrity Numbers) of 8 or greater were prepared using theKAPA mRNA Hyper prep (KAPA/Roche #KK8581) according to the protocol using 400ng input and 11 cycles PCR. Final libraries were checked for quality and quantity by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (catalog # KK4835) (Kapa Biosystems,Wilmington MA).
The samples were pooled and sequenced on 50% of an Illumina NovaSeq S4 Paired-end 50bp, according to the manufacturer's recommended protocols.

tag: animal id

value: Brain

tag: brain region

value: DHC

value: CORT

tag: surgery

value: SHAM

tag: Sex

value: Female

value: Adult

tag: batch

tag: passed qc

value: Yes

tag: adrenal weight

tag: max weight loss

tag: cort baseline

tag: acth baseline


title: D3, replica 1, plate a, VASAseq

description: VASAseq


title: Pt-13_GEX

city: Woodbury

first: Jonathan

last: Preall

state: NEW YORK

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

description:
single-cell 5' Gene Expression
10x Genomics

data_processing:
Sequencing data was demultiplexed, mapped, and processed into gene/cell expression matrices using 10X Genomics' Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Gene expression reads were aligned to the human reference genome version gex-GRCh38-2020-A, while V(D)J reads were mapped to vdj-GRCh38-alts-ensembl-7.0.0, both available from the 10X Genomics website. Matrices from each separate sample were aggregated without read-depth normalization using the Cell Ranger aggr (v6.0.0) pipeline using the “normalize=None”.
Secondary analysis was carried out primarily using Loupe Browser (10X Genomics). Dead cells (% mitochondrial reads > 10%) and cells with the number of genes expressed less than 200 were also filtered out. Doublets were removed using a R package ‘Scrublet’. ScRNA-Seq Data was normalized, logarithm transformed and scaled. Principle component analysis (PCA) was run with 50 components using the top 4000 genes of each sample. The nearest neighbor algorithm was run with 50 PCAs and clustered in UMAP projections using Leiden clustering. All additional analyses were performed using Loupe Browser (10X Genomics) and the Python toolkit Scanpy. Immune cells clusters were defined using the set of markers and UMAP clusters: T cells (CD3+, TCR+, NCAM-), NK cells (CD3-, NCAM+), B cells (CD20+, CD79A+, IgKC low), PCs (JChainhi, IgKChi), myeloid cells (CD14+, CSF1R+), mast cells (CPA3+, GATA2+), fibroblasts (FAP+, ACTA2+, PDGFRA1+), epithelial cells (CK19+, CK18+, CK5+, CK14+).
Assembly: GRCh38
Supplementary files format and content: Gene expression: Single cell 5' cell/gene matrices in .mtx format generated by Cell Ranger for individual samples and for all samples aggregated.  V(D)J analysis: annotated contig files in .csv format and assembled contig sequences in FASTA format for all detected BCR sequences output by cellranger vdj.

organism: Homo sapiens

source_name: FNA

extract_protocol:
Live immune cells were sorted by EpCAM- /CD45+ (Biolegend, # clone 2D1 and 9C4) on a Sony SH800 cell sorter, stained with AO/PI (acridine orange / propidium iodide, Nexcelom ViaStain), and checked for viability > 80% using a Countess FL II Automated Cell Counter.
Gene expression (GEX) and V(D)J BCR libraries were constructed according to the manufacturer’s instructions (Single Cell 5’ Gene Expression V1 protocol, 10x Genomics). Libraries were sequenced on a combination of Illumina NextSeq500 (for GEX and V(D)J) and MiSeq (for V(D)J) flow cells.

tag: patient diagnosis

value: PDAC

value: FNA


title: E4.5, replica 1, plate a, VASAseq

description: VASAseq


title: D2, replica 2, plate a, VASAseq

description: VASAseq

value: day 2


title: Pt-13_BCR

description:
single-cell BCR
10x Genomics

data_processing:
Sequencing data was demultiplexed, mapped, and processed into gene/cell expression matrices using 10X Genomics' Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Gene expression reads were aligned to the human reference genome version gex-GRCh38-2020-A, while V(D)J reads were mapped to vdj-GRCh38-alts-ensembl-7.0.0, both available from the 10X Genomics website. Matrices from each separate sample were aggregated without read-depth normalization using the Cell Ranger aggr (v6.0.0) pipeline using the “normalize=None”.
Secondary analysis was carried out primarily using Loupe Browser (10X Genomics). Dead cells (% mitochondrial reads > 10%) and cells with the number of genes expressed less than 200 were also filtered out. Doublets were removed using a R package ‘Scrublet’. ScRNA-Seq Data was normalized, logarithm transformed and scaled. Principle component analysis (PCA) was run with 50 components using the top 4000 genes of each sample. The nearest neighbor algorithm was run with 50 PCAs and clustered in UMAP projections using Leiden clustering. All additional analyses were performed using Loupe Browser (10X Genomics) and the Python toolkit Scanpy. Immune cells clusters were defined using the set of markers and UMAP clusters: T cells (CD3+, TCR+, NCAM-), NK cells (CD3-, NCAM+), B cells (CD20+, CD79A+, IgKC low), PCs (JChainhi, IgKChi), myeloid cells (CD14+, CSF1R+), mast cells (CPA3+, GATA2+), fibroblasts (FAP+, ACTA2+, PDGFRA1+), epithelial cells (CK19+, CK18+, CK5+, CK14+).
Assembly: GRCh38
Supplementary files format and content: Gene expression: Single cell 5' cell/gene matrices in .mtx format generated by Cell Ranger for individual samples and for all samples aggregated.  V(D)J analysis: annotated contig files in .csv format and assembled contig sequences in FASTA format for all detected BCR sequences output by cellranger vdj.
Library strategy: scBCR-seq


title: D2, replica 1, plate a, VASAseq

description: VASAseq


title: 123991

value: VHC

value: No


title: RP-7 Peptide-treated MDA-MB-231 Rep3

city: West haven

first: Antariksh

last: Tyagi

state: CT

address: 830 West Campus Dr

institute: Yale University

data_processing:
raw sequencing reads were trimmed and filtered using fastp
processed reads were mapped to hg38 reference genome using hisat2
ballgown and stringtie were used to produce raw read count matrix
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw read counts for each sample

source_name: MDA-MB-231 Cell Line

growth_protocol: MDA-MB-231 cells  were routinely cultured in 10% FBS containing  DMEM  media supplemented with antibiotics . The cells are grown to a subconfluent number of 1X 106  cells  per well in 6 well petridish(Falcon ;353046)Prior to peptide treatment, established cells were cultured in serum-free DMEM for 6h.

extract_protocol:
Total RNA was isolated from all the three replicates of  Untreated and peptide-treated MDA-MB-231 the cells after 48h  using the MiniRNeasy Kit (QiagenCat No;74104). DNAase treatemnt was also performed during the RNA isolation to get purer form of total RNA from all samples
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The peptides LA3IK and RP-7  were suspended in the media containing 0.1% serum and supplemented to the cells at a concentration of 90 micromolar  for 48 h in 5% Co2 incubator/ The treatment was performed in three replicates of each sample type.

tag: cell line

value: MDA-MB-231 Cell Line

tag: cell type

value: Breast Cancer

value: RP-7 Peptide-treated for 48h


title: MBH, Control, Rep1

city: Barcelona

first: Arnaud

last: Obri

address: C/ del Rosselló, 149

country: Spain

institute: IDIBAPS

data_processing:
Quality control of samples was performed using FastQC v0.11.9
Transcript quantification was done using Kallisto v0.46.1 with default parameters
normalized log2 CPM TMM gene values for all samples were obtained using edgeR v3.40.1
Assembly: mm10
Supplementary files format and content: Sample abundance tab-delimited text files include TPM values for the corresponding Sample
Supplementary files format and content: CPM_allsamples tab-delimited text file includes log2 CPM TMM gene values for all samples

source_name: Mediobasal hypothalamus

growth_protocol: Offspring mice were kept with their dams until weaning at P21.

extract_protocol:
mRNA strand-specific RNA libraries were generated using 200 ng of total RNA using the Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer’s instructions
Libraries were sequenced on an Illumina NextSeq2000 (Illumina) in paired-end mode with a read length of 2×50 bp. Around 40 million of paired-end reads were generated for each sample/condition.

treatment_protocol: After weaning, the offspring were subdivided into control (drinking water without supplementation) and emulsifier group (CMC+P80; 1% in drinking water), ending up with four different conditions:  maternal control - offspring control (CTRL – CTRL); maternal control - offspring emulsifiers (CTRL – Emul); maternal emulsifiers - offspring control (Emul – CTRL) and maternal emulsifiers - offspring emulsifiers (Emul – Emul).

value: Mediobasal hypothalamus

tag: genotype

value: wild-type C57Bl/6

tag: treatment

value: Control

value: P21, after weaning


title: Induced+5-AZA-CdR, rep3

city: Dublin

first: Michaela

last: Kearney

address: 2 Lincoln Place

country: Ireland

institute: Dublin Dental University Hospital

data_processing:
Strand NGS ver4.3 used for quality assessment, trimming and alignment against rat reference genome Rnor_6.0
Data were normalised using DEseq prior to bioinformatic analysis
Assembly: Rnor_6.0
Supplementary files format and content: Matrix table with raw and normalised gene counts for all genes

organism: Rattus norvegicus

source_name: Dental pulp

growth_protocol: Rodent DPCs were maintained in αMEM supplemented with 10% FCS until cell numbers were sufficient for experimentation.

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit (Qiagen)
Libraries were prepared using the TruSeq Small RNA Library Prep Kit (Illumina)

treatment_protocol: DPCs were induced to mineralise by culture in DMEM supplemented with 50mg/l ascorbic acid, 10nM dexamethasone and 10mM β-glycerophosphate. For treatment with epigenetic inhibitors, SAHA and 5-AZA-CdR were added to the relevant media at a final concentration of 1μM.

tag: tissue

value: Dental pulp

value: Dental pulp cell

value: Mineralisation-inducing + 5-AZA-CdR


title: 123990

value: Brain

value: DHC

value: CORT

value: SHAM

value: Female

tag: age

value: Adult


title: RP-7 Peptide-treated MDA-MB-231 Rep1


title: Induced+SAHA, rep3

value: Mineralisation-inducing + SAHA


title: Pt-15_BCR

description:
single-cell BCR
10x Genomics

value: PDAC

value: FNA


title: LA3IK Peptide-treated MDA-MB-231 Rep3

value: MDA-MB-231 Cell Line

value: Breast Cancer

value: LA3IK Peptide-treated for 48h


title: 123989

tag: animal id

value: VHC

value: Yes


title: LA3IK Peptide-treated MDA-MB-231 Rep1


title: LA3IK Peptide-treated MDA-MB-231 Rep2


title: Induced, rep3

value: Dental pulp

value: Mineralisation-inducing


title: Induced+5-AZA-CdR, rep2

value: Dental pulp cell

value: Mineralisation-inducing + 5-AZA-CdR


title: Induced+SAHA, rep2


title: 5plex-scRNAseq-mixed-species, guide-derived cDNA

city: Houston

first: Pawel

last: Mazur

state: Texas

address: 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

description:
small RNA
Sample 1-2
Exp1_barcodes.tsv.gz
Exp1_features.tsv.gz
Exp1_matrix.mtx.gz

data_processing:
Gene expressing reads were aligned to the GRCh38 genome (human) and/or mm10 genome (mouse) using the 10x Genomics Cell Ranger, with the pipeline cellranger count. Small RNA counts were retrieved through cellranger count using the pattern containing group barcodes and sequences derived from constant regions of corresponding small RNAs.
Assembly: GRCh38, mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: SSN-Seq

organism:
Homo sapiens
Mus musculus

source_name: T cells and tumor cells

extract_protocol:
Lentiviral barcoded multi-type cell lines and/or primary T cells were pooled and loaded into a Chromium Controller (10X Genomics).
10x Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (with Feature Barcoding technology for CRISPR Screening) was used to construct the mRNA and small RNA libraries, according to the manufacturer’s protocol (CG000205 Rev D).

value: T cells and tumor cells


title: Non-Induced, rep3


title: 20plex-SSNseq-mixed-species, SSN-derived cDNA

description:
small RNA
Sample 2-2
Exp2_barcodes.tsv.gz
Exp2_features.tsv.gz
Exp2_matrix.mtx.gz


title: 123988

value: Brain

tag: brain region

value: DHC

value: CORT


title: 123987

tag: surgery

value: SHAM

value: Female

value: Adult


title: Untreated MDA-MB-231 Rep2

value: Untreated


title: Untreated MDA-MB-231 Rep1

value: MDA-MB-231 Cell Line


title: 123985

value: CLP

tag: Sex


title: RP-7 Peptide-treated MDA-MB-231 Rep2

value: Breast Cancer

value: RP-7 Peptide-treated for 48h


title: Induced, rep2


title: 123984

tag: batch

value: Yes


title: 5plex-scRNAseq-mixed-species, mRNA-derived cDNA

description:
mRNA
Sample 1-1
Exp1_barcodes.tsv.gz
Exp1_features.tsv.gz
Exp1_matrix.mtx.gz


title: Non-Induced, rep2

value: Dental pulp


title: 123983

value: VHC

tag: passed qc

value: No


title: Induced+5-AZA-CdR, rep1

value: Dental pulp cell

value: Mineralisation-inducing + 5-AZA-CdR


type: RNA

city: Foshan

first: He

middle: Yan

last: Bin

state: GUANGDONG

address: Sino-European Center A, 2 Lingnan Avenue South, Shunde, Foshan, Guangdong, China

country: China

institute: BCBIO

description:
miRNA expression in pulmonary_with_pleural_tuberculosis patient_3
PPLTB_3

hyb_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Agilent technologies, Santa Clara, CA, USA) followed the manufacturer's instructions. Each slide (8*60 K Agilent Human miRNA Microarray, version 21.0) was hybridized with 100 ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Agilent technologies, Santa Clara, CA, USA) in hybridization Oven (Agilent technologies, Santa Clara, CA, USA) at 55°C, 20 rpm for 20 h according to the manufacturer's instructions, hybridization section. After hybridization, slides were washed in staining dishes (Thermo Shandon, Waltham, MA, USA) with Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, USA). Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, USA), and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, USA) with default settings.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: PPLTB patient 3, PBMC

extract_protocol: Total RNA was extracted from PBMCs using the miRNeasy® Mini kit (QIAGEN, Germany) according to the protocols recommended by the manufacturer. Total RNA was extracted from PBMC (200 μL) using the miRNeasy Serum/Plasma kit (QIAGEN, Germany) according to the protocols recommended by the manufacturer, and the exogenous non-human spike-in cel-miR-39-3p (5.6×108 copies) was added simultaneously (QIAGEN, Germany). RNase-free DNase I (QIAGEN, Germany) was added to remove the genomic or cell-free DNA contamination. The integrity and quality of RNA from PBMCs was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technology). RNA with a 2100 RIN (RNA integrity number) ≥ 7.0 and 28S/18S > 0.7 was used for the microarray study. The quality of RNA from PBMC was evaluated by spectrophotometry according to the absorbance (A) at 260 and 280 nm, respectively. Only PBMC miRNA samples with A260/A280 ratios between 1.80 and 2.10 were used for miRNA microarray test.

tag: disease state

value: pulmonary with pleural tuberculosis

value: PBMC

tag: gender

value: female


title: 123982

value: Brain

value: DHC

value: CORT

tag: adrenal weight

tag: max weight loss

tag: cort baseline


description:
miRNA expression in pulmonary_with_pleural_tuberculosis patient_4
PPLTB_4

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, USA), and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, USA) with default settings.

source_name: PPLTB patient 4, PBMC

label_protocol: Each slide (8*60 K Agilent Human miRNA Microarray, version 21.0) was hybridized with 100 ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Agilent technologies, Santa Clara, CA, USA) in hybridization Oven (Agilent technologies, Santa Clara, CA, USA) at 55°C, 20 rpm for 20 h according to the manufacturer's instructions, hybridization section.


title: Untreated MDA-MB-231 Rep3

tag: cell line

value: Untreated


title: 20plex-SSNseq-mixed-species, mRNA-derived cDNA

description:
mRNA
Sample 2-1
Exp2_barcodes.tsv.gz
Exp2_features.tsv.gz
Exp2_matrix.mtx.gz

tag: cell type

value: T cells and tumor cells


title: 123986

value: SHAM

value: Female

value: Adult

tag: acth baseline


description:
miRNA expression in pulmonary_with_pleural_tuberculosis patient_2
PPLTB_2

source_name: PPLTB patient 2, PBMC

value: male


description:
miRNA expression in pulmonary_with_pleural_tuberculosis patient_1
PPLTB_1

source_name: PPLTB patient 1, PBMC


title: Induced+SAHA, rep1

value: Dental pulp

tag: treatment

value: Mineralisation-inducing + SAHA


title: pulmonary_tuberculosis_4

description:
miRNA expression in pulmonary_tuberculosis_4
PTB_4

source_name: PTB patient 4, PBMC

value: pulmonary tuberculosis

tag: tissue


title: Induced, rep1

value: Dental pulp cell

value: Mineralisation-inducing


title: 123980

value: CLP

tag: age

value: Yes


title: Non-Induced, rep1


title: 123979

tag: animal id

value: VHC


title: Pro-E_HiC_KOGATA1_72h_rep2

city: Bei Jing

first: Hsiang-Ying

last: Lee

state: Bei Jing

address: Yiheyuan Road

institute: Peking University

description: pooled different cord blood samples

library_source: genomic

data_processing:
The paired-end raw reads of Hi-C libraries were generated, and HiC-Pro (version 2.10.0) was used to map, filter invalid reads and process ICE normalization with default parameters59. Human genome hg19 was used as reference. Then valid read pairs were binned at a series of different resolutions. The “sample.hic” file was created by using the HiC-Pro additional scripts and visualized through the Juicebox (version 1.9.0) software60
The DLR (distal to local) and ICF (inter-chromosome frequency) were calculated using Homer (v4.11.1) 61.
Genome_build: hg19
Supplementary_files_format_and_content: hic files

molecule: genomic DNA

source_name: cord blood

growth_protocol: CD34+ cells were purified by using MACS MicroBead kit (Miltenyi, Cat. # 130-100-453) and cultured by a two-phase erythroid differentiation method modified from a previously published method57. The base medium contains IMDM, 10% FBS (Gibco, Cat. #10099141), 300 μg/ml holo-transferrin (Sigma, Cat. #T0665), 5% human AB serum (Wokavi Biotech, Beijing), 10 ng/ml heparin (Sigma, Cat. #H3149), 10 μg/ml insulin (Sigma, Cat. #I9278), 2 mM L-Glutamine (Gibco, Cat. #25030081) and 3 IU/ml erythropoietin (Amgen, Cat. #55513-144-10). Phase-I medium was supplemented with 50 ng/ml hSCF (StemCell, Cat. #78062) and 10 ng/ml hIL-3 (StemCell, Cat. #78042). Phase-II medium was supplemented with 50 ng/ml hSCF only. Cells were maintained in Phase-I until day 8 and then transferred to Phase-II medium for the rest of the culture period.

extract_protocol:
Cell populations of distinct differentiation stages were isolated by the following cell surface markers: Pro-E cells are CD235a+CD71+CD45lowCD36+CD117highCD105high; Baso-E cells are CD235a+CD71+CD45lowCD36+CD117dimCD105dim; Poly-E cells are CD235a+CD71+CD45lowCD36+CD117-CD105-FSChigh; Ortho-E cells are CD235a+CD71+CD45lowCD36+CD117-CD105-FSClow.
Hi-C assay was carried out using the in-situ method as described before with minor modifications17. Half a million FACS-purified primary erythroblasts were used for each reaction. In brief, after fixation with 1% formaldehyde, cells were digested overnight at 37°C using 50U of MboI (NEB, Cat. #R0147). After biotin filling, proximity ligation was carried out overnight at 25 °C with 1600U T4 DNA Ligase (Vazyme, Cat. # N103-01). After reverse-crosslinking, DNA was purified and sheared to 300-500bp fragments using Covaris M220 sonicator. Ligation fragments containing biotin were immobilized on MyOne Streptavidin C1 beads (ThermoFisher Cat. #: 65602), and then library preparation was performed using the DNA library preparation kit (Vazyme, Cat.# ND607) as per the manufacturer’s protocol. DNA was then subjected to double-size selection using DNA Clean Beads (Vazyme, Cat. # N411) in order to isolate fragments between 300 and 600bp.

treatment_protocol: For each knockout experiment, 300 pmol of Cas9 protein (IDT) and 500 pmol of modified sgRNA (Genescript) were mixed and incubated for 20 min at room temperature. One million sorted Pro-E cells were resuspended with 100 μl solution P3 for primary cells (Lonza); preassembled RNP were then added to the cell suspension for nucleofection. Nucleofection was performed in a 4D-Nucleofector X unit (Lonza) using program EO-100. Cells were centrifuged and transferred to 2 ml Phase-II medium for continuing culture under erythroid differentiation conditions. Then the cells were lysed for genomic DNA extraction. Primers spanning the edited sites were used to amplify the genomic region. A pair of gRNAs or three gRNAs were introduced to perform knocking-out of KLF1 and GATA1, respectively. The sequences of gRNAs and genotyping primers are listed in the Supplementary Table 7.

value: proerythroblast

value: cord blood

tag: genotype

value: KO GATA1

value: culture 72h after KO GATA1 in proerythroblast


title: Pro-E_HiC_KOEKLF_72h_rep1

description: pooled different cord blood samples

value: KO EKLF

value: culture 72h after KO EKLF in proerythroblast


title: Pro-E_HiC_KOGATA1_72h_rep1

description: pooled different cord blood samples


title: BMO 2% B.breve midlog growth 2

city: Davis

first: David

middle: A

last: Mills

state: CA

address: One Shields ave

department: Dept. of Food Science and Technology

institute: University of California Davis

data_processing:
Raw sequence files were uploaded in to CLC genomic work bench 12.0 (https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-clc-genomics-workbench/). Data quality was checked and then the RNAseq analysis was conducted by aligining the sequence read in to to the genome of B. breve 1107E in CLC genomic work bench.
Assembly: B. breve SW 1107E genome is deposited in the JGI/IMG database and will be released upon manuscript submission.
Supplementary files format and content: Processed files are obtained from CLC genomic work bench and each file was exported as tab limited txt file. Processed files cotain the gene ID and the expression in RPKM

organism: Bifidobacterium breve

source_name: bacterial cells

growth_protocol: Grown in the anaerobic hood at 37 degrees celcius. Growth media is basal MRS and 2% Lactose or 3SL or BMO as the energy source

extract_protocol:
RNA was collected to RNA protect and Qiagen RNA easy kit was used. Before Qiagen protocol Mutanolysin and Protnase K was used.to open the cells
Ribodepletion was conducted using RiboZero plus kit and illumina prokaryotic RNA seq library was constructed

treatment_protocol: Three different carbon sources as energy - Lactose, 3SL or BMO

value: bacterial cells

value: BMO


title: Pro-E_HiC_KOCON_72h_rep2

description: pooled different cord blood samples

value: KO control

value: culture 72h after KO control in proerythroblast


title: 123977

value: Brain

tag: brain region

value: Saline

tag: surgery

value: SHAM

value: Female

value: Adult


title: 123978

value: DHC

value: CORT

value: CLP

tag: Sex

tag: batch

value: Yes


title: 123976

tag: passed qc


title: 123981

value: VHC


title: Pro-E_HiC_KOCON_72h_rep1

description: pooled different cord blood samples

value: proerythroblast

value: cord blood


title: Anti-GD2- transduced T-cells (Donor 19) co-cultured with SK-Mel-37

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

country: Russia

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

description: We performed mRNA profiling for 579 target genes, for 14 housekeeping genes, for 8 negative and 6 positive spike-in controls

hyb_protocol: 100ng of total RNA was hybridized with NanoString Immunology V2 panel according to the manufacturer's protocols.

scan_protocol: not provided

data_processing: We performed QC on the raw data, normalized gene expression using 15 housekeeping genes, performed background thresholding using the sum(mean of negative controls + 2 SD + mean of POS_E controls).

label: not provided

source_name: Anti-GD2- transduced T-cells co-cultured with SK-Mel-37

label_protocol: not provided

extract_protocol: We obtained peripheral blood mononucler cells using Ficoll-paque density gradient, co-cultured them with anti-CD3 beads, transduced the resulting T-cells with the MMLV-based retrovirus containing the anti-GD2 construct.

tag: subject id

value: Donor 19

value: 23 years

tag: gender

value: female

value: Peripheral blood

value: Anti-GD2- transduced T-cells

value: co-cultured with SK-Mel-37


title: 123975

value: Brain

value: Saline

tag: adrenal weight

tag: max weight loss


title: Ortho-E_HiC_rep1

description: pooled different cord blood samples

value: orthochromatic erythroblast

value: no


title: Pro-E_HiC_rep2

description: pooled different cord blood samples


title: Ortho-E_HiC_rep2

description: pooled different cord blood samples


title: Anti-GD2- transduced T-cells (Donor 20) co-cultured with SK-Mel-37

value: Donor 20


title: pulmonary_tuberculosis_1

description:
miRNA expression in pulmonary_tuberculosis_1
PTB_1

source_name: PTB patient 1, PBMC

tag: disease state

value: pulmonary tuberculosis

value: PBMC

value: male


title: pulmonary_tuberculosis_2

description:
miRNA expression in pulmonary_tuberculosis_2
PTB_2

source_name: PTB patient 2, PBMC


title: Pro-E_HiC_rep1

description: pooled different cord blood samples

tag: cell type


title: pulmonary_tuberculosis_3

description:
miRNA expression in pulmonary_tuberculosis_3
PTB_3

source_name: PTB patient 3, PBMC


title: Anti-GD2- transduced T-cells (Donor 17) co-cultured with SK-Mel-37

value: Donor 17

value: 24 years


title: Anti-GD2- transduced T-cells (Donor 18) co-cultured with SK-Mel-37

value: Donor 18


title: Anti-GD2- transduced T-cells (Donor 16) co-cultured with SK-Mel-37

value: Donor 16

value: 26 years


title: 123974

source_name: Brain

value: DHC

value: SHAM

value: Female

value: Adult

value: Yes

tag: cort baseline

tag: acth baseline


title: non-tuberculous_pleurisy_patients_3

description:
miRNA expression in non-tuberculous_pleurisy_patients_3
NTP_3

source_name: NTP patient 3, PBMC

value: non-tuberculous pleurisy

tag: tissue

value: female


title: non-tuberculous_pleurisy_patients_1

description:
miRNA expression in non-tuberculous_pleurisy_patients_1
NTP_1

source_name: NTP patient 1, PBMC

tag: age


title: non-tuberculous_pleurisy_patients_2

description:
miRNA expression in non-tuberculous_pleurisy_patients_2
NTP_2

source_name: NTP patient 2, PBMC


title: non-tuberculous_pleurisy_patients_4

description:
miRNA expression in non-tuberculous_pleurisy_patients_4
NTP_4

source_name: NTP patient 4, PBMC


title: Anti-GD2- transduced T-cells (Donor 15) co-cultured with SK-Mel-37

value: Donor 15

value: 25 years

value: Peripheral blood

value: Anti-GD2- transduced T-cells

tag: treatment

value: co-cultured with SK-Mel-37


title: 123973

tag: animal id

value: Brain

value: VHC

value: Saline

value: No


title: Ortho-E_RNAseq_rep1

description: pooled different cord blood samples

data_processing:
The qualitu of sequencing data were performed with fastQC (version 0.11.7).
RNA-seq reads were aligned to the human hg19 reference assembly by using HISAT2 (version 2.1.0) with parameters "hisat2 -x hg19 -t -p 8 -1 fq1 -2 fq2 --rna-strandness RF -S sample.sam".
HTSeq (v0.9.1) was used to estimate the reads counts and then using counts to calculate the TPM.
DESeq2 was used to calculate the differential expression genes.
Genome_build: hg19
Supplementary_files_format_and_content: txt file

extract_protocol:
Cell populations of distinct differentiation stages were isolated by the following cell surface markers: Pro-E cells are CD235a+CD71+CD45lowCD36+CD117highCD105high; Baso-E cells are CD235a+CD71+CD45lowCD36+CD117dimCD105dim; Poly-E cells are CD235a+CD71+CD45lowCD36+CD117-CD105-FSChigh; Ortho-E cells are CD235a+CD71+CD45lowCD36+CD117-CD105-FSClow.
RNA was extracted with TRIzol and cleaned with RNeasy MinElute Cleanup Kit (Qiagen, Cat.# 74204). For RNA-seq, RNA samples were quantified and the quality was evaluated by Agilent 2100 Bioanalyzer. 1 μg of total RNA was used to prepare RNA-seq libraries with ribosomal RNA depletion using TruSeq Stranded Total RNA Library Prep Kit (Illumina, RS-122-2201).

value: cord blood

value: orthochromatic erythroblast


title: Pro-E_RNAseq_rep2

description: pooled different cord blood samples

value: proerythroblast


title: Pro-E_RNAseq_rep1

description: pooled different cord blood samples


title: 123972

tag: brain region

value: DHC

value: SHAM

value: Female


title: Ortho-E_MNaseseq_rep1

description: pooled different cord blood samples

data_processing:
Trim_galore (0.4.4_dev) was used to trim adaptors.
The raw reads were aligned to the hg19 genome using Bowrie2 (version 2.3.4.1) with default parameters.
Only the reads with MAPQ > 30 and a unique match to the genome were maintained, ChrM reads were removing.
The nucleosome repeat length was calculated using Nuctools (v3).
The CAM software (v1.0.0) was applied to determine the nucleosome position.
Genome_build: hg19
Supplementary_files_format_and_content: txt files generated by CAM software(v1.0.0)

extract_protocol:
Cell populations of distinct differentiation stages were isolated by the following cell surface markers: Pro-E cells are CD235a+CD71+CD45lowCD36+CD117highCD105high; Baso-E cells are CD235a+CD71+CD45lowCD36+CD117dimCD105dim; Poly-E cells are CD235a+CD71+CD45lowCD36+CD117-CD105-FSChigh; Ortho-E cells are CD235a+CD71+CD45lowCD36+CD117-CD105-FSClow.
MNase-seq was performed as described before with minor changes40. Half a million FACS-purified primary erythroblasts were used for each reaction. Briefly, cells were lysed in MD buffer (50 mM Tris‐HCl, 2 mM CaCl2, 0.2 % Triton X‐100) supplied with 40U MNase for 5 min at 37°C to digest the chromatin, then 10µl STOP buffer (110 mM Tris‐HCl, 55 mM EDTA) was added. After digestion with RNase A and Proteinase K, DNA fragments of 50bp-450bp was extracted for sequential library construction using the DNA library preparation kit (Vazyme, Cat. # ND607) following the manufacturer’s protocol.


title: Ortho-E_MNaseseq_rep2

description: pooled different cord blood samples


title: D12_HiChIP_KLF1_rep2

description: pooled different cord blood samples

data_processing:
library strategy: HiChIP
The reads were aligned to hg19 reference genome using the HiC-Pro (v2.10.0) pipeline with default settings.
Total valid pairs were normalized to same among samples.
These hic files were created using hicpro2juicebox.sh script.
Loops were called through hichipper (v0.7.7) with “EACH, ALL” parameter.
The loops were visualized in WashU browser.
Genome_build: hg19
Supplementary_files_format_and_content: hic files

extract_protocol:
Cell populations of distinct differentiation stages were isolated by the following cell surface markers: Pro-E cells are CD235a+CD71+CD45lowCD36+CD117highCD105high; Baso-E cells are CD235a+CD71+CD45lowCD36+CD117dimCD105dim; Poly-E cells are CD235a+CD71+CD45lowCD36+CD117-CD105-FSChigh; Ortho-E cells are CD235a+CD71+CD45lowCD36+CD117-CD105-FSClow. Day-12 erythroblasts generated from ex vivo CD34+ erythroid differentiation culture were used.
The library was prepared using the Tn5 transposome DNA library preparation kit (Vazyme, Cat.# TD502) as per the manufacturer’s protocol. DNA was then subjected to double-size selection using DNA Clean Beads (Vazyme, Cat. # N411) in order to isolate fragments between 300 and 600bp.

value: Day12 CD34+ cells

tag: antibody


title: Pro-E_MNaseseq_rep1

description: pooled different cord blood samples


title: 123971

tag: surgery

tag: Sex

value: Adult

value: Yes


title: Ortho-E_RNAseq_rep2

description: pooled different cord blood samples


title: D12_HiChIP_KLF1_rep1

description: pooled different cord blood samples


title: 123970

tag: batch

tag: passed qc


title: D12_HiChIP_GATA1_rep2

description: pooled different cord blood samples


title: 123969


title: Pro-E_MNaseseq_rep2

description: pooled different cord blood samples


title: 123968


title: Anti-GD2- transduced T-cells (Donor 19)

source_name: Anti-GD2- transduced T-cells

tag: subject id

value: Donor 19

value: 23 years

tag: gender

value: female


title: Ortho-E_HiChIP_K9me3_rep2

description: pooled different cord blood samples


title: D12_HiChIP_GATA1_rep1

description: pooled different cord blood samples


title: 123967

value: CLP

tag: adrenal weight

tag: max weight loss


title: Pro-E_HiChIP_K9me3_rep2

description: pooled different cord blood samples

tag: cell type


title: Ortho-E_HiChIP_K9me3_rep1

description: pooled different cord blood samples


title: 123966

value: Brain

tag: cort baseline


title: Anti-GD2- transduced T-cells (Donor 17)

value: Donor 17

value: 24 years

value: male

value: Peripheral blood

value: Anti-GD2- transduced T-cells


title: Anti-GD2- transduced T-cells (Donor 18)

value: Donor 18


title: Pro-E_HiChIP_K9me3_rep1

description: pooled different cord blood samples

value: cord blood

value: proerythroblast


title: Ortho-E_CUTRUN_SMC3_rep2

description: pooled different cord blood samples

data_processing:
library strategy: CUT&RUN
Raw reads were trimmed using trim_galore (version 0.4.4_dev).
Then reads were mapped to hg19 using bowtie2 (v 2.3.4.1).
Duplicate reads, chrM reads and low quality reads were removing using picard tools (v v2.20.2), samtools and bedtools (v2.28.0).
Insert size < 120bp for TF-samples and H3K27ac samples, 150bp-500bp for histone modifications.
The bigwig files were generated through bamCoverage (v3.2.0).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cell populations of distinct differentiation stages were isolated by the following cell surface markers: Pro-E cells are CD235a+CD71+CD45lowCD36+CD117highCD105high; Baso-E cells are CD235a+CD71+CD45lowCD36+CD117dimCD105dim; Poly-E cells are CD235a+CD71+CD45lowCD36+CD117-CD105-FSChigh; Ortho-E cells are CD235a+CD71+CD45lowCD36+CD117-CD105-FSClow.
The CUT&RUN library was prepared using the DNA library preparation kit (Vazyme, Cat. # ND607) following the manufacturer’s protocol with minor modifications71. Briefly, the temperature of dA-tailing was decreased to 50°C to avoid DNA melting, and the reaction time was increased to 1 hour. After adaptor ligation, 2X volume of DNA Clean beads (Vazyme, Cat. # N411) was added to the reaction to ensure high recovery efficiency of short fragments. After 14 or 15 cycles of PCR amplification, the reaction was cleaned up with 1.2X volume of DNA Clean beads. The adaptor/PCR dimers were removed by E-Gel NGS Size Select II gel (Thermo Cat.# G661012). Two biological replicates per condition were sequenced in a HiSeq X-Ten (PE150, Illumina) by Novogene (Beijing).

value: orthochromatic erythroblast


title: Anti-GD2- transduced T-cells (Donor 20)

value: Donor 20


title: Anti-NY-ESO1- transduced T-cells (Donor 18) co-cultured with SK-Mel-37

source_name: Anti-NY-ESO1- transduced T-cells co-cultured with SK-Mel-37

extract_protocol: We obtained peripheral blood mononucler cells using Ficoll-paque density gradient, co-cultured them with anti-CD3 beads, transduced the resulting T-cells with the MMLV-based retrovirus containing the anti-NY-ESO1 construct.

value: co-cultured with SK-Mel-37


title: Anti-GD2- transduced T-cells (Donor 16)

value: Donor 16

value: 26 years


title: Anti-GD2- transduced T-cells (Donor 15)

value: Donor 15

value: 25 years


title: Ortho-E_CUTRUN_SMC3_rep1

description: pooled different cord blood samples


title: 123965

value: DHC

value: Saline

value: CLP

value: Female

value: Adult

value: No

tag: acth baseline


title: Pro-E_CUTRUN_SMC3_rep2

description: pooled different cord blood samples

tag: tissue


title: Pro-E_CUTRUN_SMC3_rep1

description: pooled different cord blood samples


title: Ortho-E_CUTRUN_CTCF_rep2

description: pooled different cord blood samples

value: CTCF


title: Anti-NY-ESO1- transduced T-cells (Donor 17) co-cultured with SK-Mel-37

value: Donor 17

tag: age

value: 24 years

value: male

value: Peripheral blood

value: Anti-NY-ESO1- transduced T-cells co-cultured with SK-Mel-37


title: 123963

value: Brain

tag: treatment

value: Yes


title: Ortho-E_CUTRUN_CTCF_rep1

description: pooled different cord blood samples

value: cord blood

value: orthochromatic erythroblast


title: Pro-E_CUTRUN_CTCF_rep1

description: pooled different cord blood samples

value: proerythroblast


title: Anti-NY-ESO1- transduced T-cells (Donor 16) co-cultured with SK-Mel-37

value: Donor 16

value: 26 years

value: female

value: co-cultured with SK-Mel-37


title: 123964

tag: animal id

value: VHC

value: Saline

value: CLP

value: Female

value: Adult


title: 123962

tag: brain region


title: Ortho-E_CUTRUN_PolII_rep2

description: pooled different cord blood samples

tag: antibody

value: PolII


title: Anti-NY-ESO1- transduced T-cells (Donor 18)

source_name: Anti-NY-ESO1- transduced T-cells

value: Donor 18

value: 23 years

value: Peripheral blood

value: Anti-NY-ESO1- transduced T-cells


title: Pro-E_CUTRUN_CTCF_rep2

description: pooled different cord blood samples

value: cord blood

value: CTCF


title: 123961

value: Brain

value: DHC

tag: surgery

value: Yes


title: Anti-NY-ESO1- transduced T-cells (Donor 17)

value: Donor 17

value: 24 years

value: male


title: Ortho-E_CUTRUN_PolII_rep1

description: pooled different cord blood samples

value: orthochromatic erythroblast


title: Anti-NY-ESO1- transduced T-cells (Donor 16)

value: Donor 16

value: 26 years

value: female


title: Pro-E_CUTRUN_PolII_rep2

description: pooled different cord blood samples

value: proerythroblast

value: PolII


title: 123960

value: VHC

value: CORT

value: SHAM

tag: Sex

value: Male

value: Adult

value: No


title: Pro-E_CUTRUN_PolII_rep1

description: pooled different cord blood samples

value: cord blood


title: Anti-NY-ESO1- transduced T-cells (Donor 15)

value: Donor 15

value: 25 years

value: Peripheral blood

value: Anti-NY-ESO1- transduced T-cells


title: Ortho-E_CUTRUN_KLF1_rep2

description: pooled different cord blood samples

value: orthochromatic erythroblast


title: Ortho-E_CUTRUN_KLF1_rep1

description: pooled different cord blood samples


title: 123959

value: Brain

value: DHC

tag: batch

value: Yes


title: 123958

tag: passed qc


title: Anti-MAGE-A4- transduced T-cells (Donor 18) co-cultured with SK-Mel-37

source_name: Anti-MAGE-A4- transduced T-cells co-cultured with SK-Mel-37

extract_protocol: We obtained peripheral blood mononucler cells using Ficoll-paque density gradient, co-cultured them with anti-CD3 beads, transduced the resulting T-cells with the MMLV-based retrovirus containing the anti-MAGE-A4 construct.

tag: subject id

value: Donor 18

value: 23 years

value: female

value: Anti-MAGE-A4- transduced T-cells

value: co-cultured with SK-Mel-37


title: Pro-E_CUTRUN_KLF1_rep1

description: pooled different cord blood samples

value: proerythroblast


title: Ortho-E_CUTRUN_GATA1_rep2

description: pooled different cord blood samples


title: Anti-MAGE-A4- transduced T-cells (Donor 17) co-cultured with SK-Mel-37

value: Donor 17

value: 24 years

tag: gender

value: male


title: 123957

value: CORT

value: SHAM

value: Male

value: Adult

tag: adrenal weight


title: Ortho-E_CUTRUN_GATA1_rep1

description: pooled different cord blood samples

value: cord blood

value: orthochromatic erythroblast


title: 123956

value: Brain

value: VHC

value: No

tag: max weight loss


title: 123955

value: DHC


title: Pro-E_CUTRUN_GATA1_rep1

description: pooled different cord blood samples

tag: cell type


title: Anti-MAGE-A4- transduced T-cells (Donor 16) co-cultured with SK-Mel-37

value: Donor 16

value: 26 years

value: female

value: Peripheral blood


title: Anti-MAGE-A4- transduced T-cells (Donor 17)

source_name: Anti-MAGE-A4- transduced T-cells

value: Donor 17

value: Anti-MAGE-A4- transduced T-cells


title: Anti-MAGE-A4- transduced T-cells (Donor 18)

value: Donor 18

value: 23 years


title: Pro-E_CUTRUN_K27ac_rep1

description: pooled different cord blood samples

value: proerythroblast


title: 123954

value: CORT

value: SHAM

value: Male

value: Yes

tag: cort baseline


title: Ortho-E_CUTRUN_K9me3_rep1

description: pooled different cord blood samples

value: cord blood

value: orthochromatic erythroblast


title: Ortho-E_CUTRUN_K9me3_rep2

description: pooled different cord blood samples


title: Pro-E_CUTRUN_GATA1_rep2

description: pooled different cord blood samples


title: Pro-E_CUTRUN_KLF1_rep2

description: pooled different cord blood samples


title: 123953

value: Brain

value: Adult

tag: acth baseline


title: Pro-E_CUTRUN_K27ac_rep2

description: pooled different cord blood samples

tag: tissue


title: Pro-E_CUTRUN_K9me3_rep2

description: pooled different cord blood samples


title: Pro-E_CUTRUN_K9me3_rep1

description: pooled different cord blood samples


title: Ortho-E_ATACseq_rep1

description: pooled different cord blood samples

data_processing:
Trim_galore (0.4.4_dev) was used to trim adaptors.
Alignment was performed with Bowtie2 (version 2.3.4.1).
Filtering deduplication, removing ChrM reads and processed peaks files were performed with picard tools (v2.20.2), samtools and bedtools(v2.28.0).
Peak calling was performed with MACS2(v2.1.2) with parameters -q 0.05 --nomodel --shift -100 --extsize 200.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

source_name: orthochromatic erythroblast

growth_protocol: Cord blood cells were obtained from the Cord Blood Bank of Beijing. CD34+ cells were purified by using MACS MicroBead kit (Miltenyi, Cat. # 130-100-453) and cultured by a two-phase erythroid differentiation method modified from a previously published method57. The base medium contains IMDM, 10% FBS (Gibco, Cat. #10099141), 300 μg/ml holo-transferrin (Sigma, Cat. #T0665), 5% human AB serum (Wokavi Biotech, Beijing), 10 ng/ml heparin (Sigma, Cat. #H3149), 10 μg/ml insulin (Sigma, Cat. #I9278), 2 mM L-Glutamine (Gibco, Cat. #25030081) and 3 IU/ml erythropoietin (Amgen, Cat. #55513-144-10). Phase-I medium was supplemented with 50 ng/ml hSCF (StemCell, Cat. #78062) and 10 ng/ml hIL-3 (StemCell, Cat. #78042). Phase-II medium was supplemented with 50 ng/ml hSCF only. Cells were maintained in Phase-I until day 8 and then transferred to Phase-II medium for the rest of the culture period.

extract_protocol:
Cell populations of distinct differentiation stages were isolated by the following cell surface markers: Pro-E cells are CD235a+CD71+CD45lowCD36+CD117highCD105high; Baso-E cells are CD235a+CD71+CD45lowCD36+CD117dimCD105dim; Poly-E cells are CD235a+CD71+CD45lowCD36+CD117-CD105-FSChigh; Ortho-E cells are CD235a+CD71+CD45lowCD36+CD117-CD105-FSClow.
ATAC-seq was performed as described before with minor changes80. In brief, ~10,000 cells were lysed in the lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and NP-40) for 5 min on ice to extract the nuclei. After lysis, nuclei were spun at 500g for 5 min to remove the supernatant. Nuclei were then incubated with the Tn5 transposome and tagmentation buffer at 37 °C for 30 min (Vazyme, Cat. #  TD502). After tagmentation, the stop buffer was added directly into the reaction to quench the tagmentation. DNA were cleaned by DNA Clean Beads, followed by a subsequent PCR step with 13 amplification cycles for adding additional index sequence to the fragments. The library were quantified by qPCR and the quality was assessed by Polyacrylamide Gel Electrophoresis (PAGE).


title: 123952

extract_protocol:
mRNA was isolated from dorsal and ventral hippocampi using the Qiagen RNAeasy kit in five batches, with groups counterbalanced across batches. RNA was assessed for quality using the TapeStation (Agilent, Santa Clara, CA).
Samples with RINs (RNA Integrity Numbers) of 8 or greater were prepared using theKAPA mRNA Hyper prep (KAPA/Roche #KK8581) according to the protocol using 400ng input and 11 cycles PCR. Final libraries were checked for quality and quantity by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (catalog # KK4835) (Kapa Biosystems,Wilmington MA).
The samples were pooled and sequenced on 50% of an Illumina NovaSeq S4 Paired-end 50bp, according to the manufacturer's recommended protocols.

value: VHC

tag: age


title: Anti-MAGE-A4- transduced T-cells (Donor 16)

value: Donor 16

value: 26 years


title: 123951

value: DHC

tag: treatment


title: Ortho-E_ATACseq_rep2

description: pooled different cord blood samples


title: Anti-MAGE-A4- transduced T-cells (Donor 15)

value: Donor 15

value: 25 years

value: male

value: Peripheral blood


title: Ortho-E_CUTRUN_K27ac_rep1

description: pooled different cord blood samples


title: Ortho-E_CUTRUN_K27ac_rep2

description: pooled different cord blood samples


title: Pro-E_ATACseq_rep1

description: pooled different cord blood samples

source_name: proerythroblast

value: proerythroblast


title: 123950

tag: animal id

value: CORT

value: CLP


title: H3122-CAR3_1

city: Aurora

first: Robert

last: Doebele

state: CO

address: 12801 E. 17th Ave, Building RC1-S, Rm L18-8401A

department: Devision of Medical Oncology

institute: University of Colorado Anschutz Medical Campus

description:
H3122-CARvsH3122_DEG.xls
H3122-CRvsH3122-CAR_DEG.xls

data_processing:
Low quality reads were trimmed following three steps: 1) remove reads with adaptor contamination; 2) remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%); 3) remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Trimmed reads were mapped to the reference genome hg19 using STAR (v2.6.1d) and quantified by FeatureCounts (v1.5.0-p3).
Raw counts were further normalized and differential expression analyses were performed by DESeq2 (v1.26.0).
Assembly: hg19
Supplementary files format and content: Each processed file (xls) contains (from left to right column header): gene id, DESeq2 median of ratio-normalized counts, differential expression analysis performed by DESeq2 (log2foldchange, pvalue and padjust), gene name, chromosome location, start and end positions of the gene at the chromosome, strand orientation, gene length, gene type, gene description, TF family annotation, raw read counts, FPKM counts.

source_name: Lung adenocarcinoma

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with fetal bovine serum at 37 °C in a humidified 5% CO2 incubator. H3122-CR and H3122-CAR cells were generated by chronically treating with a fixed dose of 500 nM crizotinib for approximately 3 months, and a fixed dose combination of 500 nM crizotinib plus 25 nM afatinib for approximately 6 months, respectively.

extract_protocol:
RNA was extracted using RNeasy Plus Kit (Qiagen).
The Ultra II RNA Library Prep Kit for Illumina was used for library construction.

treatment_protocol: To minimize the direct impact of acute drug treatment, resistant cells were seeded and cultured without inhibitors for 24 hours before the harvest. Each cell line was seeded in biological triplicates at different dishes and different times.

value: Lung adenocarcinoma

tag: genotype

value: 500 nM crizotinib + 25 nM afatinib


title: H3122-CAR3_2


title: H3122-CAR1_3


title: 123949

data_processing:
Alignment & Generation of Count Summaries: the RNA-Seq reads were aligned to the mouse genome (GRCm38) using the Subread aligner (Liao et al. 2014, Bioinformatics. 30: 923–930) with multi-mapping enabled. The featureCounts program (Liao et al. 2014, Bioinformatics. 30: 923–930) then generated the gene-level RNA-Seq count summaries for each sample based on ENSEMBL annotation (Ensembl release 95). The counts were then filtered. Genes with counts per million of less than 0.5 in ten or fewer samples were filtered out.
Quality Control: Quality control was performed in R (v.3.6.1) and included visualization of the overall log CPM gene expression across all subjects via boxplots and MDS plots. Outlier samples were detected and removed at this stage. We also noted that all samples from batch 3 were contaminated and were removed in the subsequent analysis. A list of which samples were removed is below in the RAW FILES section.
Differential Expression Analysis was performed using the limma-voom workflow provided by the limma package (v 3.42.0). Contrasts were developed for each comparison and interaction term of interest.
Assembly: GRCm38
Supplementary files format and content: Gene level unfiltered raw counts using ENSEMBL annotation

tag: brain region

value: Male

value: Yes


title: H3122-CAR1_1


title: 123948

value: Brain

tag: surgery


title: H3122-CAR3_3


title: 123947

tag: Sex

value: Adult


title: 123946

value: VHC

tag: batch

value: No


title: 123945

tag: passed qc


title: H3122-CR3_2

description:
H3122-CRvsH3122_DEG.xls
H3122-CRvsH3122-CAR_DEG.xls

value: 500 nM crizotinib


title: H3122-CR3_3


title: 123944


title: H3122-CR3_1


title: H3122-CR2_2


title: H3122-CR2_1


title: 123943

value: DHC


title: H3122-CR1_3


title: 123942


title: WT

city: Beijing

first: Yue

last: Yin

address: No. 38 Xueyuan Road, Haidian District

data_processing:
The Cell ranger software pipeline (version 5.0.0) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.0.2) was used for generation of Seurat object.
Low-quality cells with UMI numbers greater than 6000 or less than 500, or having over 20% mitochondrial-derived UMI counts were removed.
The count matrix was normalized with SCTransform function.
RunHarmony function was used to integrate data.
PCA was performed by R package Seurat (version 4.0.2). Top 30 PCs were used for tSNE and UMAP.
tSNE and UMAP were performed by R package Seurat (version 4.0.2).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.
10x scRNA-Seq

value: brain


title: 123940

value: Saline

value: SHAM


title: 123939


title: H3122-CR1_1


title: 123938


title: H3122-CR1_2


title: KO


title: H3122_3

description:
H3122-CRvsH3122_DEG.xls
H3122-CARvsH3122_DEG.xls

value: DMSO


title: H3122-CAR1_2


title: H3122_2


title: 123937


title: Pro-E_ATACseq_rep2

description: pooled different cord blood samples

value: cord blood

value: proerythroblast


title: H3122-CR2_3


title: 123936


title: 123935


title: 123932


title: 123933


title: 123941

value: CORT

value: CLP


title: 123931


title: H3122_1

value: Lung adenocarcinoma


title: 123929

value: Male


title: 123928

value: Yes


title: Control2

city: Hefei

first: mingming

last: wu

address: University of Science and Technology of China, No.96, JinZhai Road Baohe District

description: Bulk RNA-seq for NK cells

data_processing:
Adaptors were trimmed using Cutadapt
Quality control of the sequenced raw FASTQ-files was performed with Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N:0.1) and mapped to Ensembl human genome reference version GRCh38.104  using Hisat2 (v2.0.1).
Gene abundance was also determined by HTSeq (v0.6.1) software using respective Ensembl GTF annotations.
Assembly: GRCh38.104
Supplementary files format and content: tab- -delimited text files include FPKM values for each Sample

source_name: NK cells

extract_protocol:
Total RNA was extracted using Maxwell RSC simply RNA kit and 1 μg total RNA was used for following library preparation.
The library generated with the VAHTS® Universal V8 RNA-seq Library Prep Kit according to manufacturer’s instructions.

treatment_protocol: Purified NK cells derived from umbilical cord blood were treated with 400nM venetoclax for 18 hours in vitro

value: NK cells


title: Ven2

institute: University of Science and Technology of China

description: Bulk RNA-seq for NK cells

value: Venetoclax treat


title: Control3

description: Bulk RNA-seq for NK cells


title: NK-ctrl

description: scRNA for NK cells

data_processing:
The Raw data (FASTQ files) for each sample were matched to the hg19 reference genome. The quantification of UMI counts was performed using the 10×Genomics Cell Ranger pipeline (V3.1.0) with default setting
Quality control and dimensionality reduction analyses were conducted using R version 4.1.2 and the Seurat package version.We created Seurat objects for the venetoclax-treated and control groups and samples were filtered using the following criteria: unique RNA features between 500 and 3000 and less than 10% of mitochondrial genes. Moreover, genes with expression observed in less than 5 cells were excluded from the analysis. Then, we used the "IntegrateData" function to integrate the two datasets together.
Assembly: hg19
Supplementary files format and content: UMI count for each cell in mtx format and cell barcodes/genes in tsv format

extract_protocol:
For the scRNA-seq analysis of human cord blood NK cells, NK cells from cord blood were sorted using the NK Cell Isolation Kit human (Miltenyi Biotec); the purity reached more than 95%. Pool 4 cells from the control group in one tube and 4 cells from the Venetoclax-treated group in another tube.We then counted and resuspended the pooled cells at a concentration of 1000 cells/µL, targeting an estimated 6000 cells per library, following the instructions of the Single Cell 3ʹ Solution v3 Kit (10X Genomics).
Single-cell libraries were constructed strictly according to the manufacturer's standard protocol. Each sequencing library is generated using a unique sample index. Libraries were sequenced on the Illumina NovaSeq 6000 System.

treatment_protocol: Purified NK cells derived from  cord blood were treated with venetoclax for 18 hours in vitro


title: 123927

value: Brain

value: Adult


title: Control4

description: Bulk RNA-seq for NK cells


title: Ven4

description: Bulk RNA-seq for NK cells


title: NK-ven

description: scRNA for NK cells

value: venetoclax


title: 123926

value: VHC

value: No


title: Ven1

description: Bulk RNA-seq for NK cells


title: 123925

value: DHC

value: Saline


title: Ven3

description: Bulk RNA-seq for NK cells


title: Control1

description: Bulk RNA-seq for NK cells


title: 123924


title: 123923


title: 123934

value: SHAM


title: 123921


title: iCtrl, 30d, scRNA-seq

city: Belvaux

first: Claudia

last: Saraiva

state: Luxembourg

address: 6, avenue du Swing

department: Luxembourg Centre for Systems Biomedicine

country: Luxembourg

institute: University of Luxembourg

data_processing:
The reads were demultiplexed according to the multiplexing index sequencing on Illumina’s BaseCloud platform
Pre-processing of Fastq data were conducted using CeleScope® (v.1.3.0;www.github.com/singleron-RD/CeleScope; Singleron Biotechnologies GmbH) to generate raw data, using default parameters. Low-quality reads were removed.
Sequences were mapped usingSTAR(https://github.com/alexdobin/STAR), and the human reference GRCh38 and genes were annotated using Ensembl 92.
The reads were assigned to genes usingfeatureCount(https://subread.sourceforge.net/) and the cell calling was performed by fitting a negative bimodal distribution and determining the threshold between empty wells and cell-associated wells to generate a count matrix file containing the number of Unique Molecular Identifier (UMI) for each gene within each cell.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values file and count matrix

source_name: midbrain organoid

growth_protocol: Organoids were generated and culturedas described in Monzel et al. 2017.

extract_protocol:
Midbrain organoids were collected from their culture medium and washed with 1x PBS (phosphate-buffered saline, Gibco, cat. nr. 10010-23). Organoids were digested in 1 ml sCelLive™ Tissue Dissociation Solution (Singleron Biotechnologies, cat. nr. 1190062) in a 15 ml conical tube (Sarstedt, cat. nr. 62.5544.003) and placed in a thermal shaker at 50 rpm at 37°C for 30 minutes. The state of dissociation was checked at regular intervals under a light microscope. Following digestion, the suspension was filtered using a 40-µm sterile strainer (Greiner, cat nr. 542040). The cells were centrifuged at 350xg for 5 minutes at 4°C, and the cell pellets were resuspended in 500µl PBS. Cells were stained with Acridine Orange/Propidium Iodide Stain (Logos Biosystems, cat. nr. F23001), and the cell number and viability were calculated using LUNA-FX7™ Automated Cell Counter (Logos Biosystems, Villeneuve d’Ascq, France).
The single-cell RNA-seq libraries were constructed using GEXSCOPE™ Single Cell RNAseq Library Kit (Singleron Biotechnologies, cat nr. 4161031) according to the manufacturer´s instructions. Briefly, for each library, the concentration of the single-cell suspension was adjusted to 3x105 cells/ml with PBS, and the suspension was loaded onto an SD microfluidic chip to capture 6000 cells. Paramagnetic beads conjugated to oligodT probes that carry a unique molecular identifier (UMI) and a barcode unique to each bead (from the same kit) were loaded, after which the cells were lysed. The beads bound to polyadenylated mRNA were extracted from the chip and reverse transcribed into cDNA at 42°C for 1.5 hours, and the cDNA was amplified by PCR. The cDNA was then fragmented and ligated to indexed Illumina adapters. The fragment size distribution of the final amplified library was obtained on an Agilent Fragment Analyzer.

value: midbrain organoid

value: GC Miro1 R272Q

value: 30 days culture


title: PD, 30d, scRNA-seq

value: PD Miro1 R272Q


title: 123930

value: CLP


title: Ctrl, 30d, scRNA-seq

value: Ctrl


title: MEFs_KANSL3_iKO_Rep2

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: K3_iWTvsiKO_MEFs_DESeq2.counts_normalized.tsv

data_processing:
The data processing, quality control, trimming and mapping were performed using snakePipes mRNA-seq pipeline (Bhardwaj et al., 2019)
Differential expression analysis was performed using DESeq2 with a FDR cut-off of 0.05
Assembly: mm10
Supplementary files format and content: Tab deliminated file of DESEQ2 normalized counts

source_name: Mouse Embryonic Fibroblasts

extract_protocol:
RNA extractions were performed simultaneously for all samples using Quick-RNA Miniprep Kit (Zymo, R1055)
Libraries were prepared using a TruSeq® Stranded Total RNA Library Prep Gold (Illumina, 20020599)

value: Mouse Embryonic Fibroblasts

value: KANSL3 inducible Knockout

value: 4 Hydroxyltamoxifen for 4 days in culture


title: MEFs_KANSL3_iKO_Rep3


title: 123922

source_name: Brain

value: Brain

value: Male


title: OlredBRCA1-deficient, passage56, rep2

city: Dresden

first: Jan

middle: Dominik

last: Kuhlmann

state: Saxony

address: Fetscherstraße 74

department: Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe

institute: Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden

description:
AN14028318
CountReads.csv
DeSeq2_Deficient.xlsx

data_processing:
Trimming: Trimmomatic v0.39;ILLUMINACLIP:data.fa:2:30:10:2:true;LEADING:15;TRAILING:15;SLIDINGWINDOW:4:15;MINLEN:36;CROP:75'
Mapping: star v2.5.2b;--alignIntronMax 500000;--alignMatesGapMax 500000;--outBAMcompression 0;--outSAMtype BAM SortedByCoordinate;--outSAMprimaryFlag OneBestScore;--outFilterMultimapNmax 100;--outFilterMismatchNoverLmax 0.05;--chimSegmentMin 15;--chimOutType WithinBAM;--chimScoreMin 1;--chimScoreJunctionNonGTAG 0;--chimJunctionOverhangMin 15;--chimSegmentReadGapMax 3;--alignSJstitchMismatchNmax 5 -1 5 5;--twopassMode Basic
FeatureCounts (subread v2.0.1);--ignoreDup
DeSeq2 (bioconductor-deseq2 v1.24.0);padj<0.05
Assembly: GRCh37
Supplementary files format and content: CountReads.csv : FeatureCounts results, semicolon separated
Supplementary files format and content: Deseq2_Proficient: DeSeq2 results of all proficient cell lines, excluded padj > 0.05, Excel format
Supplementary files format and content: Deseq2_Deficient: DeSeq2 results of all deficient cell lines, excluded padj > 0.05, Excel format

source_name: ovarian cancer

growth_protocol: standard drug-free medium

extract_protocol: RNeasy Kit (Qiagen)

value: ovarian cancer

tag: cell line

value: ovarian cancer cell


title: OlresBRCA1-proficient, passage45, rep2

description:
AN14028326
CountReads.csv
DeSeq2_Proficient.xlsx


title: OlresBRCA1-deficient, passage56, rep1

description:
AN14028316
CountReads.csv
DeSeq2_Deficient.xlsx


title: MEFs_KANSL3_iKO_Rep1


title: BRCA1-proficient, passage10, rep2

description:
AN14028330
CountReads.csv
DeSeq2_Proficient.xlsx


title: BRCA1-deficient, passage29, rep2

description:
AN14028322
CountReads.csv
DeSeq2_Deficient.xlsx


title: MEFs_KANSL2_iKO_Rep2

description: K2_iWTvsiKO_MEFs_DESeq2.counts_normalized.tsv

value: KANSL2 inducible Knockout


title: MEFs_KANSL2_iKO_Rep3


title: K_2

city: New York

first: Jin-Gyu

last: Cheong

address: 1300 York Avenue

institute: Weill Cornell Medicine

data_processing:
Reads were aligned and quantified by STAR
Assembly: hg38
Supplementary files format and content: normalized count matrix
Supplementary files format and content: fastq file

source_name: PBMC

extract_protocol: Material extraction and library construction followed protocols for NEBNext low input RNA library prep kit for Illumina (NEB E6420S)

value: PBMC

value: Stimulated CD14 Monocytes

tag: disease

value: Healthy


title: Z_2


title: MEFs_KANSL2_iKO_Rep1


title: K_1


title: MEFs_KANSL2_iWT_Rep2

value: WT (Kansl2 floxed)


title: MEFs_KANSL2_iWT_Rep3


title: Z_1


title: MEFs_KANSL3_iWT_Rep1

value: WT (Kansl3 floxed)


title: OlresBRCA1-proficient, passage45, rep1

description:
AN14028324
CountReads.csv
DeSeq2_Proficient.xlsx


title: G_2


title: Podocytes_KANSL3-pKO_Rep3

description: nCre_vs_K3pKO_podo_DESeq2.counts_normalized.tsv

source_name: Podocytes isolated ex-vivo

extract_protocol:
RNA extractions were performed simultaneously for all samples using Quick-RNA Microprep Kit (Zymo, R1051)
Libraries were prepared using a NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB, E6420)

value: Podocytes isolated ex-vivo

value: KANSL3 Knockout


title: Podocytes_KANSL3-pKO_Rep4


title: C_2


title: C_1


title: B_2


title: G_1


title: Podocytes_KANSL3-pKO_Rep2


title: Podocytes_KANSL3-pKO_Rep1


title: B_1


title: BRCA1-deficient, passage29, rep1

description:
AN14028320
CountReads.csv
DeSeq2_Deficient.xlsx


title: BRCA1-proficient, passage10, rep1

description:
AN14028328
CountReads.csv
DeSeq2_Proficient.xlsx


title: MEFs_KANSL3_iWT_Rep2


title: MEFs_KANSL3_iWT_Rep3


title: AC_2


title: Podocytes_KANSL2-pKO_Rep4

description: nCre_vs_K2pKO_podo_DESeq2.counts_normalized.tsv

value: KANSL2 Knockout


title: Podocytes_KANSL2-pKO_Rep3


title: Podocytes_KANSL2-pKO_Rep2


title: Podocytes_nCre_Rep4

description:
nCre_vs_K2pKO_podo_DESeq2.counts_normalized.tsv
nCre_vs_K3pKO_podo_DESeq2.counts_normalized.tsv

value: WT (Cre positive)


title: Podocytes_KANSL2-pKO_Rep1


title: A_1


title: AC_1


title: 75_1

value: severe convalescent COVID-19


title: Podocytes_nCre_Rep3


title: 75_2


title: 66_2


title: MEFs_KANSL2_iWT_Rep1

value: Mouse Embryonic Fibroblasts


title: 66_1


title: Podocytes_nCre_Rep1


title: 64_2


title: 64_1


title: RELACS_TFs_nCre_H3_Pellet4

data_processing:
The data processing, quality control, trimming, mapping and H3-Normalized coverage file were performed using snakePipes DNA-mapping and ChIP-seq pipeline (Bhardwaj et al., 2019).
Assembly: mm10
Supplementary files format and content: BigWig file , H3 normalized

extract_protocol:
Cells were fixed with 1% PFA for 10 minutes at RT , Nuclei extraction, quantification and ChIP was performed using the published RELACS (Arrigoni et al, 2018)
Libraries were prepared using a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645)

tag: chip antibody


title: RELACS_TFs_nCre_KANSL3_Pellet4

value: KANSL3 (Sigma HPA035018)


title: RELACS_TFs_nCre_H3_Pellet3


title: RELACS_TFs_nCre_KANSL3_Pellet3


title: 60_2


title: RELACS_TFs_nCre_MOF_Pellet2

value: MOF (Abcam, ab200660)


title: RELACS_TFs_nCre_H3_Pellet2


title: 59_2


title: A_2


title: Podocytes_nCre_Rep2


title: 58_2


title: 60_1


title: RELACS_TFs_nCre_MOF_Pellet1


title: 56_2


title: rice leaf sheaths, osh1, rep3

city: Hangzhou

first: Yang

last: lijia

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
Raw sequencing reads were filtered by Trimmomatic (version 0.39) and aligned to the rice genome (MSU RGAP, release 7) using Hisat2 (version 2.0.5) with default parameters.
Abundances of annotated reference genes were quantified using StringTie (version 2.0).
Genes with a multiple-test corrected padj less than 0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: msu7.0
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

organism: Oryza sativa

source_name: leaf

extract_protocol:
Total RNAs were extracted using TRIzol reagent (Invitrogen) according to the manufacturer's instructions.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and then used for constructing sequencing libraries with the TruSeq PE Cluster Kit v3-cBot-HS (Illumina).

value: leaf


title: RELACS_Histone_K2-pKO_H4K16ac_Rep2

value: H4K16ac (Millipore, 07329)


title: 56_1


title: 59_1


title: rice leaf sheaths, osh1, rep2


title: rice leaf sheaths, Osbhlh002, rep3


title: RELACS_Histone_K2-pKO_H4K12ac_Rep2

value: H4K12ac (Millipore, 07595)


title: RELACS_Histone_K2-pKO_H4K5ac_Rep2

value: H4K5ac (Activ Motif, 39169


title: RELACS_Histone_K2-pKO_H3K27ac_Rep2

value: H3K27ac (Diagenode, C15410196)


title: 42_1

value: PBMC

value: Stimulated CD14 Monocytes


title: 34_2


title: rice leaf sheaths, Osbhlh002, rep1


title: RELACS_Histone_K2-pKO_H3K9ac_Rep2


title: rice leaf sheaths, WT, rep3

value: WT


title: rice leaf sheaths, Osbhlh002, rep2


title: 34_1


title: RELACS_Histone_K2-pKO_H3K4Me3_Rep2

value: H3K4Me3 (Diagenode, C15410003)


title: RELACS_Histone_K2-pKO_H3_Rep2

value: Podocytes isolated ex-vivo


title: 27_2


title: RELACS_TFs_nCre_H3_Pellet1


title: RELACS_Histone_K2-pKO_H4K16ac_Rep1


title: rice leaf sheaths, WT, rep1


title: rice leaf sheaths, WT, rep2


title: rice leaf sheaths, osh1, rep1


title: 58_1


title: 27_1


title: RELACS_Histone_K2-pKO_H4K12ac_Rep1


title: 23_2


title: RELACS_Histone_K2-pKO_H3K27ac_Rep1


title: 138_2


title: 23_1


title: 138_1


title: RELACS_Histone_K2-pKO_H3K9ac_Rep1


title: 42_2


title: RELACS_Histone_K2-pKO_H3K4Me3_Rep1


title: 135_2


title: PC3 MTID V7 Y22S 1

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

description: PC3 expressing MiniTurboID-AR V7-22YtoS

data_processing: Raw counts - RSEM

growth_protocol: PC3 cells transduced with lentiviruses expressing the AR V7, empty vector or AR V7 mutants, were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using the SV Total RNA Isolation System (Promega) according to the manufacturer’s protocol.
Total RNA-seq libraries were then prepared using 800ng of resulting RNA from each sample and NEBNext Ultra II RNA Library Prep Kit for Illumina with Poly(A) mRNA Magnetic Isolation Module (NEB #E7760, E7490 and E6440) according to the manufacturer’s protocol with 11 amplification cycles. Libraries were sequenced on a NextSeq550 with paired-end reads of 75 base pairs, with a read depth of 60 million fragments / library. Two libraries from two corresponding biological replicates were prepared for each sample.

value: Prostate adenocarcinoma bone metastasis, epithelial

value: AR V7 22YtoS

tag: time

value: 48 hrs post plating


title: PC3 MTID V7 Y22S 2

description: PC3 expressing MiniTurboID-AR V7-22YtoS

tag: cell type


title: PC3 MTID V7 Y22F 1

description: PC3 expressing MiniTurboID-AR V7-22YtoF

value: AR V7 22YtoF


title: PC3 MTID V7 Y22F 2

description: PC3 expressing MiniTurboID-AR V7-22YtoF


title: 134_2

value: severe convalescent COVID-19


title: RELACS_Histone_nCre_H4K16ac_Rep2

value: WT (Cre positive)


title: 135_1


title: RELACS_Histone_nCre_H4K12ac_Rep2


title: PC3 MTID EV 2

description: PC3 expressing MiniTurboID


title: 134_1


title: PC3 MTID EV 1

description: PC3 expressing MiniTurboID


title: RELACS_Histone_K2-pKO_H4K5ac_Rep1

value: KANSL2 Knockout


title: RELACS_Histone_nCre_H4K5ac_Rep2


title: 128_2


title: RELACS_Histone_nCre_H3K27ac_Rep2


title: 128_1


title: RELACS_Histone_nCre_H3K9ac_Rep2


title: K562_H3K27ac_ChIP-seq

city: Shanghai

first: Ya

last: Guo

address: 800 Dongchuan Road

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

data_processing:
Basecalls were performed using Illumina bcl2fastq 2.20.
CUT&Tag or ChIP-seq reads were aligned to the GRCh38 genome using Bowtie2 version 2.3.5.1. Duplicates were removed by the picard version 2.26.6.
Peaks were called using MACS v2.1.0 with the significance cut-off q-value <=0.05
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: K562 was cultured in Iscove’s Modified Dulbecco’s Medium (Gibco) supplemented with 10% (vol/vol) feta bovine serum (Gibco) and 1% penicillin-streptomycin. The HeLa cells were cultured in Dulbecco's Modified Eagle Medium (Gibco) supplemented with 10% (vol/vol) feta bovine serum (Gibco) and 1% penicillin-streptomycin. Cell were maintained in an incubator with 5% (vol/vol) CO2 at 37℃.

extract_protocol:
[ChIP-seq] Cells were crosslinked with 1% formaldehyde (vol/vol, Thermo) for 10 min at room temperature, followed by quenching with 125 mM glycine for 5 min. Crosslinked chromatin was then fragmented using a sonicator (Scientz) for 28 cycles (30 seconds on, 30 seconds off).
[CUT&Tag] Cleavage under targets and tagmentation (CUT&Tag) libraries were prepared using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (TD901, Vazyme Biotech). 100,000 cells were used for each assay. These cells were bound to conA beads and incubated with anti-H3K27ac (ab4729, Abcam) or anti-NIPBL antibody (A301-779A, Bethyl) for 2h at room temperature. After washing, a secondary antibody (Goat Anti-Rabbit IgG, Sangon) was diluted (1:100) in DIG Wash buffer and incubated with cells at room temperature for 1h on a shaker with slow rotation. The nuclei were then incubated with the Hyperactive pG-Tn5 Transposon for 1h at room temperature with slow rotation. After washing three times with Dig-300 buffer, these cells were then resuspended in tagmentation buffer and incubated for 1h at 37 °C. Chromatin was purified using standard phenol/chloroform/alcohol extraction method. Fragmented DNA were then amplificated by PCR and then purified by magnetic beads. The final libraries were sequenced on an Illumina HiSeq 2500 System. [ChIP-seq] The sonicated lysate was incubated with a H3K27ac antibody (ab4729, Abcam). Dynabeads Protein G beads (Invitrogen) were added to the extract–antibody complex. After DNA purification, ChIP-Seq library was prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645, NEB) following the manufacturer’s protocol and sequenced on an Illumina HiSeq 2500 System.

value: Human leukemia

value: anti-H3K27ac (Abcam, #ab4729)


title: K562_Input_ChIP-seq


title: RELACS_Histone_nCre_H3K4Me3_Rep2


title: 111_2


title: K562_H3K27ac_CUT&Tag

data_processing:
Basecalls were performed using Illumina bcl2fastq 2.20.
CUT&Tag or ChIP-seq reads were aligned to the GRCh38 genome using Bowtie2 version 2.3.5.1. Duplicates were removed by the picard version 2.26.6.
Peaks were called using MACS v2.1.0 with the significance cut-off q-value <=0.05
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&TAG


title: 111_1


title: RELACS_Histone_nCre_H3_Rep2


title: RELACS_Histone_K2-pKO_H3_Rep1


title: 110_2


title: PC3 MTID V7 2

description: PC3 expressing MiniTurboID-AR V7

value: AR V7


title: PC3 MTID V7 1

description: PC3 expressing MiniTurboID-AR V7


title: K562, Nipbl, CUT&Tag

value: anti-NIPBL (Bethyl, #A301-779A)


title: 110_1


title: RELACS_Histone_nCre_H4K16ac_Rep1

value: H4K16ac (Millipore, 07329)


title: LE90N_YELLOW

first: Hong-wei

last: Sun

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

data_processing:
Raw sequencing data were processed with bcl2fastq 1.8.4 to generate FastQ files. Reads were mapped to hg19 using Bowtie0.12.8
Genome_build: hg19
Supplementary_files_format_and_content: Excel file containing rpkm data generated using Partek6.6 and annotation data generated using HOMER4.9.1

source_name: NET

extract_protocol:
Normal density neutrophils were isolated by dextran sedimentation from control and SLE patients. LDG was isolated by negative selection from the PBMC fraction. Cells were allowed to spontaneusly NET. RNA was isolated from NETs using the ExoMir Kit from BIOO Scientific (catalog #5145).
cDNA libraries were prepared using the protocol described by Hafner et al. 2012 Methods 58(2): 164-170.
Sequencing data were generated on Illumina HiSeq2500 instrument according to the manufacturer's instructions

tag: condition

value: SLE

tag: description for exp id


title: RELACS_Histone_nCre_H4K5ac_Rep1

value: H4K5ac (Activ Motif, 39169


title: LELDG50


title: RELACS_Histone_nCre_H4K12ac_Rep1

value: H4K12ac (Millipore, 07595)


title: 108_1

tag: tissue

value: PBMC

value: Stimulated CD14 Monocytes


title: 108_2


title: LE85N_BLUE


title: RELACS_Histone_nCre_H3K27ac_Rep1

value: Podocytes isolated ex-vivo

value: H3K27ac (Diagenode, C15410196)


title: LE83N_BLUE


title: EndoC-βH1, HBSS, Input 2

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

data_processing:
Basecalls performed using bcl2fastq v2.20.0.422
Paired sequencing reads were aligned on human hg38 reference genome using BWA and filtered with samtools to remove unmapped read pairs, not primary alignments, reads failing platform quality, with mapping quality score below 30 and duplicate reads were then removed using picard MarkDuplicates
Each sample was equally split in two pseudo-replicates, peaks were called with MACS2 with p < 0.1 on each sample and pseudoreplicates and filtered after Irreproducible Discovery Rate analysis with a threshold of 0.01
The two replicates were merged and the pooled sample reads were as well split in two pseudo-replicates, peaks were called with MACS2 with p < 0.1 on pool and pseudo-replicates and Irreproducible Discovery Rate analysis was performed with a threshold of 0.01 on pool vs its pseudo-replicates and vs the two biological replicates
The coordinates peaks called by the two replicates individually and the pool were merged and as final selection only the peaks supported by at least two out of the three analyses were kept
Assembly: hg38
Supplementary files format and content: bigWig containing IP vs input fc

extract_protocol:
After the immunoprecipitation step, DNA was purified using AMPure XP beads. Briefly, beads were incubated with the reaction mix and washed several times using 70% Ethanol. Then, immunoprecipitated DNA was recovered by incubating  with 10 mM Tris, pH 8.5, 0.1 mM EDTA buffer and used for DNA library preparation
Libraries were prepared from 10 ng of DNA using the NEBNext UltraTM II DNA Library Prep Kit for Illumina (New England Biolabs)

value: Human pancreatic beta

value: HBSS supplemented with HEPES


title: HeLa_Nipbl_CUT&Tag

source_name: HeLa

value: HeLa

value: Human cervical carcinoma


title: RELACS_Histone_nCre_H3K4Me3_Rep1

value: WT (Cre positive)

value: H3K4Me3 (Diagenode, C15410003)


title: RELACS_Histone_nCre_H3K9ac_Rep1


title: CTR67_YELLOW

value: Control healthy


title: EndoC-βH1, HBSS, Input 1


title: RELACS_Histone_nCre_H3_Rep1


title: LE72N_BLUE


title: EndoC-βH1, HBSS, TFEB 2

value: TFEB


title: CTR67_BLUE


title: EndoC-βH1, HBSS, TFEB 1


title: Alb-Cre; Pak4 flox/flox, fasted, rep 1

city: Jeonju-si

first: Byung-Hyun

last: Park

address: 567 Baekje-daero, Deokjin-gu

country: South Korea

institute: Jeonbuk National University Medical School

data_processing:
bcl2fastq2-v2.20.0 package was used for basecalling.
Quality check of basecalling was done using FastQC v0.11.7 by calculating phred quality score.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic0.38, then mapped to mm10 whole genome using HISAT2 v2.1.0 and Bowtie2 v2.3.4.1
Transcript assembly and calculation of normalized Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were done using StringTie v2.1.3b.
Assembly: mm10
Supplementary files format and content: Expression_Profile.mm10.gene.txt includes FPKM, TPM, count values for each Sample

source_name: Liver

extract_protocol:
Liver tissues were excised from mice and stored in RNAlater solution. Total RNA was extracted using Trizol.
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA LT Sample Prep Kit (#RS-122-2001)

tag: strain

value: Liver

tag: age

value: 8 weeks

value: Hepatocyte-specific Pak4 KO

value: fasted


title: CTR61_YELLOW


title: Alb-Cre; Pak4 flox/flox, fasted, rep 2

tag: treatment


title: CTR61_BLUE


title: MCFDCIS_shANCO1_#3_3D_3

city: Washington

first: Meng

last: Yuan

state: DC

address: 3970 Reservoir Road NW

department: Lombardi Comprehensive Cancer Center

institute: Georgetown University

data_processing:
Quality check: fastqc
Alignment to GRCh38: hisat2
Sorting: samtools
Expression count calculation: featureCounts
Expression data statistical analysis: edgeR
Plotting: Heatplus, dplyr, ggplot2, ggrepel
Signaling enrichment analysis: GSEA, IPA
Visualization: UCSC genome browser
Assembly: GRCh38
Supplementary files format and content: Processed files are raw read counts for each condition (2D/3D, shGFP and shANCO1). ShGFP is shCTRL. Sh14 is shANCO1_#1. Sh209 is shANCO1_#2. Sh474 is shANCO1_#3. Sh34 is shANCO1_#4. Bigwig files for display in genome browser.

source_name: MCFDCIS

growth_protocol: MCF10A and MCFDCIS cells were maintained in DMEM/F12 (1:1) medium (Gibco, 11039-021) with 5% horse serum, 20 µg/ml epidermal growth factor (EGF), 100 µg/ml hydrocortisone, 10 µg/ml insulin, and 100 ng/ml cholera toxin.

extract_protocol: RNA was extracted from 2D-cultured cells or 3D-cultured spheres with DNase digestion using the RNeasy Mini Kit (Qiagen, 74106) following manufacturer’s instructions.

treatment_protocol: ANCO1 knockdown lines were generated by lentiviral infection.

value: MCFDCIS

value: Ductal carcinoma in situ cells derived from mammary epthelial cells

tag: genotype

value: ANCO1 knockdown


title: Alb-Cre; Pak4 flox/flox, fasted, rep 3


title: MCFDCIS_shANCO1_#3_3D_2


title: Pak4 flox/flox, fasted, rep 3

value: WT


title: MCFDCIS_shANCO1_#3_3D_1


title: MCFDCIS_shANCO1_#2_3D_2


title: MCFDCIS_shANCO1_#2_3D_3


title: LE85N_YELLOW

value: SLE


title: CTR0185_BLUE


title: Pak4 flox/flox, fasted, rep 1


title: MCFDCIS_shANCO1_#2_3D_1


title: Pak4 flox/flox, fasted, rep 2


title: CTR60_YELLOW


title: MCFDCIS_shCTRL_3D_6

value: shGFP control


title: Choroid plexus ZT20 6

city: Copenhagen

first: Søren

middle: Norge

last: Andreassen

state: Region Hovedstaden

address: Blegdamsvej 3

department: Department of Neuroscience

country: Denmark

institute: University of Copenhagen

data_processing:
QC quality control and adapter removal was done by Novogene (UK) Company Limited.
Mapping to reference genome (rattus norvegicus Rnor_6.0.104) using STAR (v. 2.7.9a) (--sjdbOverhang 100 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --quantMode TranscriptomeSAM)
Abundance quantified by RSEM (v. 1.3.3) (--bam --paired-end --forward-prob 0)
Differentially expressed genes are produced with standard procedure of DEseq2 (v. 3.16) using GeneCount output from STAR (--quantMode)
Assembly: Rnor_6.0 (rn6) v.104
Supplementary files format and content: tab-delimited text files for gene abundance for each samples in TPM and FPKM

source_name: Choroid plexus

extract_protocol:
Extraction was performed by Novogene (UK) Company Limited.
Done by Novogene (UK) Company using NEB Next® Ultra™ RNA Library Prep Kit, and sequenced on Illumina NovaSeq 6000, paired-end 150 bp, 12Gb output.

value: Choroid plexus

value: 9 weeks

tag: tissue type

value: Whole tissue

value: Sprague-Dawley


title: ATDC5_Day10_RUNX2_2

city: Toronto

first: Zoe

last: Gillespie

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

description:
75 bp
ATDC5_Day10_RUNX2_CombinedReps.bedGraph.gz

data_processing:
Raw reads were quality checked with FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and adaptors/poor quality sequences trimmed using Trim Galore!
Sequence quality was then re-examined by FastQC. Trimmed reads were mapped to Mus musculus reference genome GRCm39 using HISAT2 (v. 2.2.0).
Peaks were called with macs2 against input files, and narrowPeak and bedGraph.gz files generated
Assembly: GRCm39

growth_protocol: ATDC5 cells were initially grown in DME/F12 media containing 5% FBS and incubated at 37oC, 5% CO2, until 70% confluent. For undifferentiated cells, cultures where maintained by serial passaging.

extract_protocol:
Day 0, 3 and 10 ATDC5 cells were fixed with 1% formaldehyde (Electron Microscopy Sciences, Cat #: 15714) in 37 oC DEM/F12 media without FBS for 10min. Media/formaldehyde was removed and formaldehyde quenched with 155mM glycine in PBS for 10min at RT. Cells were washed 3 X 5 min 4 oC PBS. Cells were scrapped and collected in 1.5mL centrifuge tubes (300 X g, 4oC 5min) and resuspended in 750 uL ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris HCl pH8.0, protease inhibitors (Sigma-Aldrich, Cat #: P5726), Phosphatase Inhibitor Cocktail 2 (Sigma-Aldrich, Cat #: P5726)). Cells were sonicated (Branson Sonifier) for 2.5 min with a 30% duty cycle and 7% power output setting. 50uL of the suspension was taken and evaluated for chromatin shearing and the concentration of chromatin/DNA per uL evaluated (Qubit 4, Life Technologies). For each ChIP assay, a volume of sample containing 50ug of chromatin was mixed with ChIP dilution buffer (0.01% SDS, 1.1% Triton X 100, 1.2mM EDTA, 16.7 mM Tris HCl pH8.0, 167mM NaCl, protease inhibitors (Sigma-Aldrich, Cat #: P5726), Phosphatase Inhibitor Cocktail 2 (Sigma-Aldrich, Cat #: P5726)) to a final volume of 500uL.  A total of 5 µg of each antibody was used for each assay (mouse anti RUNX2, Santa Cruz Biotechnology, cat#: sc-390351; rabbit anti-SOX9, EMD Millipore, cat#: 05-636; rabbit anti-H3K4me3, Abcam, cat#:ab8580). A total of 2.5 µg donkey anti-mouse antibody (Jackson Scientific, UK, Cat #: 715-035-150) was used as non-specific antibody control. The mixture was incubated at 4 °C overnight with rotation, followed by binding to 50 µL Dynabead Protein A (Invitrogen, Cat #: 10006D) at 4 °C for 1 h. Samples were then treated with ChIP washing buffer I (0.1% SDS, 1% Triton X 100, 2 mM EDTA, 20 mM Tris pH 8.0 and 150 mM NaCl), ChIP washing buffer II (0.1% SDS, 1% Triton X 100, 2 mM EDTA, 20 mM Tris pH 8.0 and 500 mM NaCl) and ChIP washing buffer III (1 mM EDTA and 10 mM Tris-HCl pH 8.0). Samples were eluted with 500 µL of freshly made elution buffer (1% SDS and 0.1 M NaHCO3) for 1 h at RT. Crosslinks were reversed by adding 200 mM NaCl, 12.5 mM EDTA and 2 µL proteinase K (Invitrogen, Cat #: 25530049), followed by incubating at 65 °C for 5 h agitating at 900 rpm. DNA from each sample was extracted by phenol-chloroform and resuspended in nuclease free water.
Sequencing was performed using the Illumina Novoseq protocol and generated 75bp single end reads.

treatment_protocol: To differentiate the ATDC5 cells from day 0 to day 3 and day 10 time points, 10ul droplets of cells at a density of 3000 cell/ul were spotted into 10cm culture dishes and allowed to attach for 24h. Cells were differentiated by the addition of DEM/F12 media containing 10mM bGP and 50mg/ml L-acorbate-2-phosphate. Media was changed every 2-3 days to maintain nutrient levels.

value: mouse anti RUNX2, Santa Cruz Biotechnology, cat#:sc-390351

value: teratocarcinoma AT818

value: Day 10


title: Choroid plexus ZT20 5


title: MCFDCIS_shCTRL_3D_4


title: Choroid plexus ZT20 4


title: ATDC5_Day3_RUNX2_2

description:
75 bp
ATDC5_Day3_RUNX2_CombinedReps.bedGraph.gz

value: teratocarcinoma AT816

value: Day 3


title: ATDC5_Day10_RUNX2_1

value: teratocarcinoma AT817


title: Choroid plexus ZT20 3


title: Choroid plexus ZT20 2


title: ATDC5_Day3_RUNX2_1

value: teratocarcinoma AT815


title: ATDC5_Day0_RUNX2_2

description:
75 bp
ATDC5_Day0_RUNX2_CombinedReps.bedGraph.gz

value: teratocarcinoma AT814

value: Day 0


title: MCFDCIS_shCTRL_3D_3

value: MCFDCIS

value: Ductal carcinoma in situ cells derived from mammary epthelial cells


title: MCFDCIS_shCTRL_3D_2


title: Choroid plexus ZT8 6


title: MCFDCIS_shCTRL_3D_1


title: MCF10A_shANCO1_#4_3D_3

value: Mammary epthelial cells

value: ANCO1 knockdown


title: Choroid plexus ZT20 1

value: Choroid plexus


title: Choroid plexus ZT8 5

value: 9 weeks


title: ATDC5_Day0_RUNX2_1

value: teratocarcinoma AT813


title: ATDC5_Day10_H3K4me3_2

description:
75 bp
ATDC5_Day10_H3K4me3_CombinedReps.bedGraph.gz

value: rabbit anti-H3K4me3, Abcam, cat#:ab8580

value: teratocarcinoma AT812


title: MCF10A_shANCO1_#4_3D_1


title: Choroid plexus ZT8 4

value: Whole tissue

value: Sprague-Dawley


title: MCF10A_shANCO1_#4_3D_2


title: Choroid plexus ZT8 3


title: ATDC5_Day3_H3K4me3_2

description:
75 bp
ATDC5_Day3_H3K4me3_CombinedReps.bedGraph.gz

value: teratocarcinoma AT810


title: MCFDCIS_shCTRL_3D_5

value: shGFP control


title: Choroid plexus ZT8 2


title: ATDC5_Day3_H3K4me3_1

value: teratocarcinoma AT809

value: Day 3


title: ATDC5_Day0_H3K4me3_2

description:
75 bp
ATDC5_Day0_H3K4me3_CombinedReps.bedGraph.gz

value: teratocarcinoma AT808


title: ATDC5_Day0_H3K4me3_1

value: teratocarcinoma AT807

value: Day 0


title: ATDC5_Input_2

description: 75 bp

value: teratocarcinoma AT806


title: MCF10A_shANCO1_#1_3D_1

value: Mammary epthelial cells


title: Choroid plexus ZT8 1


title: MCF10A_shANCO1_#1_3D_2

value: ANCO1 knockdown


title: ATDC5_Input_1

description: 75 bp

value: teratocarcinoma AT805


title: MCF10A_shCTRL_3D_3


title: ATDC5_Day10_H3K4me3_1

value: teratocarcinoma AT811

value: Day 10


title: MCF10A_shCTRL_3D_1


title: CD4+ T cells, U5-52K KO_11.12.

city: Berlin

first: Miriam

last: Bertazzon

address: Thielallee 63

institute: Freie Universität Berlin

data_processing:
Sequence was trimmed to remove Illumina adaptor sequences, the value lower 20 and reads length lower than 25,using cutadapt program
Trimmed sequenced were aligned with the mouse genome GRCm38/mm10 (GENCODE database) using STAR alignment software
Read count extraction and normalization were performed using Deseq2 package in R.
Differentially sliced variant were analyzed with rMATS.
Assembly: GRCm38/mm10 (GENCODE database)
Supplementary files format and content: Differential Expressed Genes and Differntially Spliced Variant

source_name: CD4+ T cells from spleen and lymph nodes

extract_protocol:
RNA was isolated from sorted T cells using RNeasy Plus Mini Kit (QIAGEN, #74136)
RNA libraries for RNA-seq were prepared using NovaSeq 6000 S1 Reagent Kit following manufacturer's protocols.

value: U5-52Kf/f CD4-Cretg


title: MCF10A_shCTRL_3D_2


title: CD4+ T cells, CTRL_5.6.

value: CD4+ T cells from spleen and lymph nodes

value: U5-52Kf/f CD4-Cre-


title: CD4+ T cells, U5-52K KO_9.10.


title: CD4+ T cells, U5-52K KO_7.8.


title: MCFDCIS_shANCO1_#3_2D_3

value: MCFDCIS

value: Ductal carcinoma in situ cells derived from mammary epthelial cells


title: CD4+ T cells, CTRL_3.4.

value: U5-52Kwt/f CD4-Cretg


title: MCFDCIS_shANCO1_#3_2D_1


title: MCFDCIS_shANCO1_#3_2D_2


title: MCFDCIS_shANCO1_#2_2D_3


title: MCFDCIS_shANCO1_#2_2D_1


title: MCFDCIS_shANCO1_#1_2D_3


title: F_CMS_ARS

city: Rehovot

first: Alon

last: Chen

address: Arison Neurobiology Building

department: Brain Sciences

country: Israel

institute: Weizmann Institute of Science

data_processing:
10x Genomics CellRanger v. 3.0.2 (baseline batch)
10x Genomics CellRanger v. 3.1.0 (CMS batch)
Filtered count matrices obtained from CellRanger were imported in Seurat v 3.1.3 for quality control and clustering.
Cells with less than 350 genes, and mitochondrial gene content higher than 30%, and putative droplets identified with the package scran v.1.14.6 were removed before clustering.
Clustering was performed on lognormalized and scaled expression data using the top 4000 variable genes. 22 PCs and a resolution of 1.2 were used for the final clustering.
Assembly: mm10
Supplementary files format and content: filtered count matrices generated by CellRanger
Supplementary files format and content: CSV table containing metadata for each cell

source_name: Paraventricular nucleus of the hypothalamus (PVN)

extract_protocol:
Five hours after the acute stress, animals were sacrificed and perfused in cold PBS. The PVN was dissected from the fresh brain, and digested in Papain supplemented with DNAse I. After dissociation and filtering, cells were concentrated to 700,000-900,000 cells/ml and loaded on a v2 chip in the 10x Genomics Chromium Controller.
Libraries were prepared using the the 10x Genomics Single Cell 3’ Reagent Kits v2 according to the manufacturer’s protocol.

treatment_protocol: Chronic mild stress was applied for 21 days. Acute restraint stress was applied for 15 minutes.

value: 11 weeks old

value: chronic mild stress (CMS) + acute restraint stress (ARS)

tag: gender

value: female


title: M_CMS_ARS

value: male


title: M_CMS_ctrl

value: control (unstressed)


title: MCFDCIS_shANCO1_#1_2D_2


title: CD4+ T cells, CTRL_1.2.


title: F_CMS_ctrl


title: MCFDCIS_shCTRL_2D_2

value: shGFP control


title: MCFDCIS_shCTRL_2D_3


title: F_baseline_ARS

value: 10 weeks old

value: acute restraint stress (ARS)


title: F_baseline_ctrl


title: MCFDCIS_shANCO1_#1_2D_1

value: ANCO1 knockdown


title: MCFDCIS_shCTRL_2D_1


title: M_baseline_ARS


title: M_baseline_ctrl


title: MCF10A_shANCO1_#3_2D_3

value: Mammary epthelial cells