title: NSC-B15 pE

description: single-cell RNA-seq

data_processing:
mapping with STAR via zUMIs
transcript quantification with featureCounts via zUMIs
Assembly: GRCm38 (mm10)
Supplementary files format and content: Single-cell RNA-seq count matrix in gzip-compressed csv (comma-separated values) format. Values are not normalized, decimals are due to distribution of multimapping reads.

extract_protocol:
For the ischemia experiment, the vSVZ and striatum were isolated. For the naïve experiments, vSVZ, striatum, and olfactory bulb were isolated. Depending on the plate, individual or pooled mice were used to sort cells on plate. Tissues were processed and sorted in a BD FACSAria II at the DKFZ Flow Cytometry Facility. Cells were stained with the following antibodies (all conditions and tissues together): O4-APC and O4-APC-Vio770 (Miltenyi; diluted 1:50), Ter119-APC-Cy7 (Biolegend; 1:100), CD45-APC-Cy7 (BD; 1:200), GLAST (ACSA-1)-PE (Miltenyi: 1:20), PSA-NCAM-PE-Vio770 (Miltenyi; 1:75), Prominin1-A488 (eBioscience; 1:75), and Sytox Blue (Life Technologies, 1:1000), CD9-eFluo450 (eBioscience, 1:300).
For profiling the transcriptome and epigenome of single cells we developed and implemented a miniaturized and higher throughput version of the scNMT-seq protocol (Clark et al., 2018). On this new version, the Smart-seq3 (Hagemann-Jensen et al., 2020) method and specific normalization steps were implemented. A detailed version of the protocol is described in Cerrizuela et al., (2022). The samples listed here represent the transcriptomic portion of this multi-omic data set.
Single-cell RNA-seq (Smart-seq3)


title: F16-CLow-S4_710

status: Public on Sep 16 2022

type: SRA

city: Lawrence

first: Jennifer

middle: L

last: Robinson

state: Kansas

department: Department of Chemical and Petroleum Engineering

country: USA

institute: University of Kansas

library_source: transcriptomic

data_processing:
Base calling was carried out by the Illumina NextSeq 550 Real Time Analysis (RTA) software.
Raw reads were filtered using fastp (Experiment 1) or trimmomatic 0.39 (Experiment 2) and aligned to the reference transcriptome using Kallisto 0.46.1-1.
Kallisto 0.46.1-1 was used for transcript abundance estimates
tximport was used to import Kallisto transcript abundance estimates into DeSeq2 1.3 for differential expression analysis
Assembly: ENSEMBL Homo sapiens reference transcriptome build GRCh38 release 101
Supplementary files format and content: .tsv files containing raw quantified counts and TPM counts

molecule: total RNA

organism: Homo sapiens

source_name: Meniscal Fibrochondrocytes

growth_protocol: Cells were cultured in tissue culture flasks in DMEM supplemented with 10% Premium FBS (Atlanta Biologicals, 511150) and 1% penicillin/streptomycin and passaged at 70-80% confluency using trypsin (Sigma, T4174, diluted to 1x before use). When passage 1 cells reached 70-80% confluency, cells were washed with PBS (Gibco, 20012-207) and cultured in phenol red-free DMEM (pfDMEM, Gibco, 31053-028) with 15% charcoal/dextran treated FBS (Atlanta Biologicals, S11650) for 3 days to starve them of endogenous hormones. Cells were then passaged and seeded in 24 well plates in pfDMEM and allowed to adhere overnight.

extract_protocol:
For Experiment 1 cells were collected in TRIzol, and total RNA was purified using a PureLink RNA Mini Kit (Life Technologies, 12183025) according to the manual. DNA was removed using a DNA-free DNA Removal Kit (Life Technologies, AM1906) according to the manual. For Experiment 2 cells were collected and total RNA was purified using a QIAGEN RNeasy Mini Kit (QIAGEN, 74104) with no DNase treatment.
Sequencing libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760). The sequencing library construction process included mRNA purification with polyA selection beads, fragmentation to inserts of ~200 bp, strand specific cDNA synthesis, end repair, 3’ end adenylation, adapter ligation, and PCR amplification. Samples were run across 3 flow cells (Experiment 1: A, B, and C; Experiment 2: 708, 709, and 710).

treatment_protocol: Cells were treated in triplicate with 17β-estradiol (E2, Sigma, E2758) in pfDMEM supplemented with 15% charcoal/dextran treated FBS and 1% penicillin/streptomycin under pulsed or continuous dosing. For pulsed dosing, cells were exposed to E2 for 1 h, after which the E2 media was replaced with E2-free media for 23 h. This pattern was repeated for the length of the experiment. For continuous dosing, cells were exposed to E2 for the entire treatment period.

tag: tissue

value: Meniscus

tag: cell type

value: Meniscal Fibrochondrocytes

tag: experiment

value: Experiment 2

tag: age

tag: gender

value: Female

tag: treatment

value: 0.1 nM E2, Continuous

tag: treatment duration

tag: flow cell


title: NSC-B13 pE

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

country: Germany

institute: German Cancer Research Center

description: single-cell RNA-seq

library_source: transcriptomic single cell

organism: Mus musculus

source_name: striatum & ventricular-subventricular zone

treatment_protocol: Two months old TiCY mice were intraperitoneally injected with tamoxifen. In these mice, tamoxifen-induced Cre recombination takes place in neural stem cells in the vSVZ, which express Tlx (Nr2e1) and will stably activate the production of enhanced YFP, labeling NSCs and their progeny. Two weeks after injection, an injury by bilateral carotid artery occlusion (BCCAO) was performed as described (Llorens-Bobadilla et al., 2015). The animals were sacrificed for single cell sorting either 48 h or 3 weeks after ischemia. WT mice were not subjected to tamoxifen or ischemia.

tag: genotype

value: WT

value: naive


title: NoBleo

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: 10x 3' v2 scRNA-seq

data_processing:
Read alignment and gene-expression quantification of mouse single-cell RNA-seq (scRNA-seq) were performed using Cell Ranger version 2.0.0 pipeline (10x Genomics).
For scRNA-seq alignment and quantification, Cell Ranger pre-built mouse (mm10) reference package was used.
Assembly: mm10
Supplementary files format and content: Raw Feature Barcode Matrix and 10x Cell Ranger filtered Feature Barcode Matirx in HDF5 format

source_name: Normal mouse lung

growth_protocol: Mice were housed in barrier and all experiments were performed in accordance with approved IACUC protocols

extract_protocol:
Single-cell suspensions were processed through the 10X Chromium to generate single-cell cDNA libraries attached to microbeads.
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA was prepared for sequencing using a modified Nextera XT protocol.

treatment_protocol: For single cell RNAseq, adult mice were treated or untreated with  bleomycin every week for total 4 weeks. Mice lung were collected. Fresh lung tissue was minced and incubated in an enzymatic cocktail containing 60 ml dispase (5U/ml, Stemcell Technologies), 900 µl liberase (1g/l, Sigma Aldrich), 0.03 g DNase (Sigma Aldrich) at 37 ℃ for 45 minutes.  Suspensions were washed with media, cell counts were performed and cells were resuspended in RPMI at a final concentration of 100 cells/ml.

tag: number

value: lung

value: Normal untreated


title: F16-CLow-S4_709


title: Ascl1-mutAscl1-Myod1, 72h scRNA-seq

city: Planegg-Martinsried

first: Bob

last: Hersbach

address: Großhaderner Str. 9

department: Institute of Stem Cell Research

institute: Helmholtz Zentrum Munich

description: 10x Genomics scMultiome

data_processing:
scRNA-seq & scATAC-seq data was processed using the cellranger-arc software (v2.0.0)
CellRanger arc was run with the cellranger-arc count command using standard parameters and the mouse GRCm38 genome.
To build the reference genome index for mouse, GRCm38 was used and the sequences and custom annotations of the syunthetic transcription factors were appended to the genome fasta and annotation files
The samples processed with cellranger-arc were aggregated using the cellranger-arc aggr command with the –normalize = none parameter
Assembly: GRCm38
Supplementary files format and content: ATAC Peaks in .bed format
Supplementary files format and content: Annotated ATAC peaks in .tsv format
Supplementary files format and content: Raw and filtered CellRanger output in .h5 format. Note: this data contains both the ATAC and scRNAseq data
Supplementary files format and content: Processed RNA and ATAC-seq data in .h5ad format

molecule: polyA RNA

source_name: Skin

growth_protocol: DMEM (High Glucose), 10% fetal bovine serum,1x Sodium Pyruvate, 1 mM HEPES, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol: Library preparation was performed according to the manufacter’s instructions (Single Cell Multiome ATAC + Gene Expression, 10x Genomics). Briefly, nuclei were isolated from MEFs, resuspended in a transposition master mix and incubated at 60°C for 60 min. Transposed nuclei were added to the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The transposed genomic DNA was barcoded during transposition and contains Illumina R1, R2 and P5 primer sequences as well as  a 10x Barcode. Both transposed DNA and retrotranscribed cDNA were pre-amplified via PCR. ATAC-seq libraries were generated by a final PCR during which a P7 primer sequence and an i7 sample index are added. Gene expression libraries were generated through further amplification of the cDNA by PCR followed by enzymatic fragmentation and final PCR amplification adding both P5 and P7 Illumina primer sequences as well as i5 and i7 indexes. Library quality was validated using the Agilent High Sensitivity DNA Kit.

value: Skin

value: Mouse Embryonic fibroblasts

tag: strain

value: Doxycyline


title: AQ9690

city: Madrid

first: Jose Maria

middle: Moreno

last: Navarrete

state: (None)

address: Calle de Monforte de Lemos nº 5

country: Spain

institute: CIBER

data_processing:
RNA-seq reads mapped with STAR software v2.5.3a with ENCODE parameters.
Annotated genes quantified with RSEM v1.3.0
Assembly: GRCh38
Supplementary files format and content: Matrix with samples as columns and raw gene counts as rows

source_name: Subcutaneous adipose tissue

extract_protocol:
RNA purification was performed using RNeasy Lipid Tissue Mini Kit (QIAgen, Izasa SA, Barcelona, Spain)
RNA libraries were prepared using TruSeq Stranded total RNA kit (Ribozero)

value: Subcutaneous adipose tissue

tag: condition

value: morbidly obese


title: AQ9700


title: NSC-B11 pE

description: single-cell RNA-seq

value: striatum & ventricular-subventricular zone

value: aNSC


title: AQ9686


title: AQ9682


title: intestine, Control

city: Shanghai

first: Ting

last: Guo

state: Shanghai

address: Shanghai Putuo District,Luding road No.355

department: Department of General surgery

country: China

institute: Shanghai Children's Hospital

data_processing:
mRNA sequencing libraries were generated using an NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations
Clustering of the index-coded samples was performed on a cBot Cluster Generation System using a TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes count values for each Sample

source_name: intestine

growth_protocol: Con group mice were fed with dam. NEC group and PCI34051+NEC group were fed with  40 μl of 33% Esbilac formula (Pet-Ag, Abbott Laboratories) every 4 h for 96 h.PCI34051+NEC group mice were also fed with PCI34051  (10 mg/kg/d,once a day for 5 days).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) and chloroform, and RNA integrity was assessed using an RNA Nano 6000 Assay Kit for the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The library preparations were sequenced on the Illumina NovaSeq platform, and 150 bp paired-end reads were generated.

treatment_protocol:
NEC group mice was induced using formula gavage every 4 h for 96 h using 40 μl of 33% Esbilac formula (Pet-Ag, Abbott Laboratories). Meanwhile, pups were exposed to hypoxia treatments (99.9% N2 for 100 s), followed by cold stress (4 °C for 10 min) every 12 h. The control group were dam-fed without hypoxia and cold stress. In the PCI34051-treated NEC group, the PCI34051  (10 mg/kg/d) was fed once  from the day before the modle made  to the end. At the same time, the mice in the other two groups were fed with the equal volume of PBS.
All animals were euthanized after 96 h of modling.

tag: cell line

value: intestine

value: PBS

tag: time


title: Ascl1-Foxa2-Myod1-Oct4-Sox2 72h tech rep 2

description: 10x Genomics v3.1

data_processing:
For the alignment of reads we used the sequences and annotation files for the Mouse genome (GRCm38) from Ensembl (release 97).
The synthetic transcription factors and reporter sequences and a custom generated annotation were appended to the genome sequence and annotation. The Cell Ranger software (version 3.1.0) run with the command ‘cellranger mkref’ created an index of the genome.
The Cell Ranger pipeline run with the command ‘cellranger count’ aligned the reads, generated QC metrics, estimated the number of valid barcodes and created the count matrices.
The command was executed with standard parameters, except that we adjusted the number of expected cells and the chemistry parameter accordingly
AnnData objects of the raw and filtered count matrices were created using the Python package Scanpy (Wolf, Angerer and Theis, 2018), version 1.4.4).
The alignment files (bam) were sorted by barcode using samtools (Li et al., 2009), version 1.10) and Velocyto ((la Manno et al., 2018), version 0.17.17) was run using the ‘velocyto run’ command with the filtered barcodes list from the Cell Ranger run.
Assembly: GRCm38
Supplementary files format and content: Raw and filtered CellRanger output in .h5 file format
Supplementary files format and content: Velocyto ouput containing spliced and unspliced read information in .loom format
Supplementary files format and content: Processed scRNA-seq data in .h5ad format

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2/3.1 protocol, 10x Genomics). Briefly, MEFs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Libraries were validated using the Agilent High Sensitivity DNA Kit.


title: Ascl1-mutAscl1-Myod1, 72h ATAC

description: 10x Genomics scMultiome

library_source: genomic single cell

molecule: genomic DNA


title: F16-CLow-S3_709

value: Meniscus

value: Meniscal Fibrochondrocytes


title: Ascl1-Foxa2-Myod1-Oct4-Sox2 72h tech rep 1

description: 10x Genomics v3.1


title: F16-CLow-S3_708

value: Experiment 2

value: Female


title: OLIGO8 pB

description: single-cell RNA-seq

source_name: ventricular-subventricular zone

value: ventricular-subventricular zone

value: oligodendrocyte

value: WT


title: STRASTRO9 pE [scNOMe-seq]

description: single-cell NOMe-seq

library_source: genomic

data_processing:
read trimming and adapter removal
Bisulfite-aware read mapping
quantification of CpG and GpC methylation
Assembly: GRCm38 (mm10)
Supplementary files format and content: .csv.gz files: cell x region methylation matrices in gzip-compressed csv (comma-separated values) format. acc: chromatin accessibility (=GpC methylation). meth: DNA (=CpG) methylation. VMR: variably methylated regions identified with the ‘scbs’ software. mfrac: fraction of methylated sites. shrunkResid: shrunken mean of residuals quantified with ‘scbs’.
Supplementary files format and content: .cov.gz files: gzip-compressed tab-separated files produced by Bismark with the following columns: chromosome, start position, end position, methylation percentage, number of methylated cytosines, number of unmethylated cytosines.
Library strategy: Single-cell NOMe-seq

extract_protocol:
For the ischemia experiment, the vSVZ and striatum were isolated. For the naïve experiments, vSVZ, striatum, and olfactory bulb were isolated. Depending on the plate, individual or pooled mice were used to sort cells on plate. Tissues were processed and sorted in a BD FACSAria II at the DKFZ Flow Cytometry Facility. Cells were stained with the following antibodies (all conditions and tissues together): O4-APC and O4-APC-Vio770 (Miltenyi; diluted 1:50), Ter119-APC-Cy7 (Biolegend; 1:100), CD45-APC-Cy7 (BD; 1:200), GLAST (ACSA-1)-PE (Miltenyi: 1:20), PSA-NCAM-PE-Vio770 (Miltenyi; 1:75), Prominin1-A488 (eBioscience; 1:75), and Sytox Blue (Life Technologies, 1:1000), CD9-eFluo450 (eBioscience, 1:300).
For profiling the transcriptome and epigenome of single cells we developed and implemented a miniaturized and higher throughput version of the scNMT-seq protocol (Clark et al., 2018). On this new version, the Smart-seq3 (Hagemann-Jensen et al., 2020) method and specific normalization steps were implemented. A detailed version of the protocol is described in Cerrizuela et al., (2022). The samples listed here represent the epigenomic portion of this multi-omic data set, i.e. DNA methylation and chromatin accessibility assessed with single-cell NOMe-seq.

value: astrocyte (striatum)

value: naive


title: NSC-B10 pE

description: single-cell RNA-seq


title: AQ9680


title: F16-CLow-S4_708

value: 0.1 nM E2, Continuous


title: NSC-B1 pE

description: single-cell RNA-seq


title: AQ9674


title: F16-CLow-S2_710


title: OLIGO6 pB

description: single-cell RNA-seq


title: AQ9672


title: AQ9670


title: F16-CLow-S2_708


title: OLIGO4 pB

description: single-cell RNA-seq


title: STRASTRO21 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: AQ9668


title: STRASTRO23 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO3 pB

description: single-cell RNA-seq


title: F16-CLow-S3_710


title: OLIGO9 pB

description: single-cell RNA-seq


title: F16-PHigh-S4_710

value: 24 nM E2, Pulsed


title: AQ9678

value: Subcutaneous adipose tissue


title: STRASTRO15 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: AQ9666

value: morbidly obese


title: F16-CLow-S2_709


title: STRASTRO13 pE [scNOMe-seq]

description: single-cell NOMe-seq

value: striatum & ventricular-subventricular zone


title: STRASTRO12 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: F16-PHigh-S4_709


title: OLIGO23 pB

description: single-cell RNA-seq


title: AQ9664


title: STRASTRO6 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO2 pB

description: single-cell RNA-seq


title: OLIGO18 pB

description: single-cell RNA-seq


title: STRASTRO10 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO20 pB

description: single-cell RNA-seq


title: AQ9660


title: AQ9658


title: F16-PHigh-S3_709


title: AQ9656


title: F16-PHigh-S4_708


title: STRASTRO-B7 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: F16-PHigh-S1_710


title: F16-PHigh-S3_708


title: STRASTRO-B6 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: F16-PHigh-S1_709


title: STRASTRO11 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: AQ9662


title: OLIGO19 pB

description: single-cell RNA-seq


title: F16-PHigh-S3_710


title: OLIGO16 pB

description: single-cell RNA-seq


title: OLIGO17 pB

description: single-cell RNA-seq


title: F16-PHigh-S1_708


title: AQ9652


title: STRASTRO-B2 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO14 pB

description: single-cell RNA-seq


title: OLIGO13 pB

description: single-cell RNA-seq


title: F16-PLow-S4_710

value: 2.4 nM E2, Pulsed


title: F16-PLow-S4_709


title: AQ9650


title: AQ9654


title: AF8387


title: AQ9648


title: OLIGO12 pB

description: single-cell RNA-seq


title: STRASTRO-B22 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC9 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: F16-PLow-S3_710


title: F16-PLow-S4_708


title: OLIGO1 pB

description: single-cell RNA-seq


title: NSC8 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO10 pB

description: single-cell RNA-seq


title: NSC9 pB

description: single-cell RNA-seq


title: AF8383


title: NSC6 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC7 pB

description: single-cell RNA-seq


title: AF8381


title: F16-PLow-S3_709


title: F16-PLow-S3_708


title: NSC5 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC3 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC6 pB

description: single-cell RNA-seq


title: NSC7 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: AF8379


title: NSC4 pB

description: single-cell RNA-seq


title: F16-PLow-S2_710


title: AF8377


title: NSC3 pB

description: single-cell RNA-seq


title: F16-NoE2-S4_710

value: Control (No E2)


title: NSC23 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC23 pB

description: single-cell RNA-seq


title: AF8373


title: AF8371


title: NSC4 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC2 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC22 pE [scNOMe-seq]

description: single-cell NOMe-seq

value: TAP


title: AF8375


title: NSC2 pB

description: single-cell RNA-seq


title: F16-NoE2-S4_708

value: Meniscus


title: NSC18 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: IPF2

description: 10x 3' v2 scRNA-seq

data_processing:
Read alignment and gene-expression quantification of mouse single-cell RNA-seq (scRNA-seq) were performed using Cell Ranger version 2.1.1 pipeline (10x Genomics).
For scRNA-seq alignment and quantification, Cell Ranger pre-built mouse (hg19) reference package was used.
Assembly: hg19
Supplementary files format and content: Raw Feature Barcode Matrix and 10x Cell Ranger filtered Feature Barcode Matirx in HDF5 format

source_name: Human IPF lung with CD45 beads negative selection

extract_protocol:
Single-cell suspensions were processed through the 10X Chromium to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA was prepared for sequencing using a modified Nextera XT protocol

value: lung

tag: sample type

value: IPF


title: NSC19 pB

description: single-cell RNA-seq


title: F16-NoE2-S3_710

value: Meniscal Fibrochondrocytes

value: Experiment 2

value: Female


title: F16-PLow-S2_709


title: NSC18 pB

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: WT


title: IPF1

description: 10x 3' v2 scRNA-seq

source_name: Human IPF lung with total cell selection


title: NSC17 pE [scNOMe-seq]

description: single-cell NOMe-seq

value: naive


title: F16-NoE2-S3_709


title: NSC21 pB

description: single-cell RNA-seq


title: F16-NoE2-S4_709


title: NSC17 pB

description: single-cell RNA-seq

value: oligodendrocyte


title: NSC16 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: HCT116-NUP93-mAC,HiChIP,H3K4me1,MboI,UT,biological replicate 1

city: HOUSTON

first: chuangye

last: Qi

state: Texas

address: One plaza

department: Huffington Center

institute: Baylor College of Medicine

data_processing:
library strategy: in situ HiC and HiChIP
FASTQ data were trimmed by Cutadapt and Trimmomatic.
RNASeq Reads were aligned using STAR with the hg19 build of the human genome. Read counts for Refseq mRNAs were determined using HTSeq-count.
HiC-Pro was used to process Hi-C and HiChIP data.
Identification of significant chromatin contacts(loops interaction) from HiChIP data by using FitHiChIP.
Assembly: hg19
Supplementary files format and content: pairs, bigwig

source_name: colorectal cancer cells

extract_protocol:
RNA-seq:
Total cellular RNA was extracted with TRIzol (Invitrogen, 15596-018) following the manufacturer’s instructions.   Ploy A RNA was selected by using NEBNext® Poly(A) mRNA Magnetic Isolation Module.
RNAseq  library construction using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645L).
in situ HiC and HiChIP:
5-10 million cells were cross-linked using 1% formaldehyde for 10mins at room temperature, quenched with 0.125M glycine for 10mins at room temperature, and were washed with cold PBS. Cross-linked cell pellets were resuspended in 1ml iced-cold Hi-C lysis buffer (10 mM Tris-HCl, pH 8.0; 10mM NaCl, 0.2% NP-40 and protease inhibitor cocktail), and rotated at 4°C for 30 mins. After pelleting down the nuclei, 100 ul of 0.5% SDS was used to resuspend and permeabilize the nuclei at 62 °C for 10 mins.  Then 260 ul H20 and 50 ul 10% Triton-X100 were added to quench the SDS at 37 °C for 15 mins. Subsequently, enzyme digestion of chromatin was performed at 37 °C overnight by adding an additional 50 ul of 10X NEB buffer 2 and 400U MboI (NEB, R0147M). After overnight incubation, the MboI in solution was inactivated at 62 °C for 20 mins. To fill-in the DNA overhangs and mark the ends with biotin, 35U DNA polymerase I (Klenow, NEB, M0210) together with 10 ul of 1mM biotin-dATP (Jeana Bioscience), 1ul 10mM dCTP/dGTP/dTTP were added and incubated at 37°C for 1 hour with rotation. Blunt end Hi-C DNA ligation was performed using 5000 U NEB T4 DNA ligase with 10X NEB T4 Ligase buffer with 10mM ATP, 90 ul 10% Triton X-100, 2.2 ul 50mg/ml BSA at room temperature for four hours with rotation. After ligation, nuclei were pelleted down and resuspended with 440 ul Hi-C nuclear lysis buffer (50mM Tris-HCl pH7.5; 10mM EDTA, 1% SDS and protease inhibitor cocktail), and further sheared using the parameter of 10/20 secs ON/OFF cycle, 25% Amp, 5mins by a QSonica 800R sonicator. Hi-C will use 5-10% of the sonicated chromatin in the next section. For HiChIP, the sonicated chromatin was incubated with appropriate antibody (here by 4ug H3K27ac polyclonal antibody) overnight, and the immunocomplex was captured by dynabeads protein G in the next day. The immunocomplex was washed 2 times by low salt wash buffer (20 mM Tris-HCl pH 7.5, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl), 2 times by high salt wash buffer (20 mM Tris-HCl pH 7.5, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl), 1 time with Tris-EDTA buffer + 0.1% triton-100, and one more time with TE only. The immunocomplex was subjected to overnight decrosslinking at 65°C, protein K treatment, and DNA extraction
For both Hi-C and HiChIP library making , after DNA extraction, they were used for biotin DNA enrichment by 20 ul Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher 65002). The biotin bound DNA on beads was used to perform on-beads library making with KAPA Hyper DNA library kit, or using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645L).

tag: antibody

value: H3K4me1(Abcam,Cat# ab8895)

value: untreated


title: NSC13 pB

description: single-cell RNA-seq


title: F16-NoE2-S2_710


title: F16-NoE2-S2_709


title: NSC15 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC16 pB

description: single-cell RNA-seq


title: NSC14 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC13 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: F16-NoE2-S2_708


title: NSC12 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC1 pB

description: single-cell RNA-seq


title: NB9 pB

description: single-cell RNA-seq

value: neuroblast


title: NSC11 pE [scNOMe-seq]

description: single-cell NOMe-seq

value: striatum & ventricular-subventricular zone


title: M47-CHigh-S4_C

value: Experiment 1

value: Male

value: 10 microM E2, Continuous

value: C


title: single-cell RNA seq data of organoids cocultured with microglia

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

institute: University Hospital Muenster

data_processing:
The bcl files were demultiplexed with cellranger mkfastq v3.1.
Subsequent reads alignments and transcript counting was done individually for each sample using the cellranger count pipeline with default parameters.
Assembly: GRCh38
Supplementary files format and content: Standard cellranger/spaceranger output format

source_name: coculture

extract_protocol:
We developed a 3D coculture of microglia in organoids. For this, we added microglia to the culture medium of preformed cerebral organoids that had been differentiated for 30 days according to the original Lancaster protocol. Following another 30 days of coculture, organoids were harvested. Immunohistochemistry demonstrated the presence of ramified IBA1+ cells in both superficial and deeper layers of the organoid, demonstrating survival and migration of microglia within the preformed organoid . We next performed single cell RNA sequencing by pooling and dissociating organoids to single cells and FACS-sorting for 3’ microfluidics-based scRNA-seq (Chromium 10x). Three groups were compared: (i) microglia-like cells in vitro (2436 cells, 4204 median genes per cell) (ii) cerebral organoids (6642 cells, 3720 median genes per cell), and (iii) cerebral organoids with microglia (5873 cells, 4204 median genes per cell).
The samples were loaded onto the 10x Genomics Chromium Single Cell Controller with the Chromium Single Cell 3’ Library and Gel Beads Kit v3. Library preparation was carried out according to the manufacturer’s instruction using AMPure beads (Beckman Coulter). Sequencing was performed on an Illumina Nextseq 6000 with a 150-8-0-150 read setup.

value: organoids cocultured with microglia


title: M47-CHigh-S4_B

value: Meniscus

value: B


title: single-cell RNA seq data of organoids without microglia

source_name: organoid

value: organoids without microglia


title: NB8 pB

description: single-cell RNA-seq


title: NSC10 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: M47-CHigh-S4_A

value: Meniscal Fibrochondrocytes

value: A


title: NB7 pB

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: WT


title: single-cell RNA seq data of 2D microglia monoculture

source_name: microglia

value: 2D microglia monoculture


title: NSC1 pE [scNOMe-seq]

description: single-cell NOMe-seq

value: naive


title: NSC-B9 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC12 pB

description: single-cell RNA-seq


title: NB6 pB

description: single-cell RNA-seq


title: M47-CHigh-S2_C


title: M47-CHigh-S2_B


title: NB5 pB

description: single-cell RNA-seq


title: NSC-B4 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: 3s170_High

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

data_processing:
De-multiplexed raw sequencing data (FASTQ format) was evaluated using FastQC (Babraham Bioinformatics) and passed standard quality metrics, such as per base quality scores with ≥ 85% of bases >Q30. Additional NGS data quality control, pre-processing, alignment, quantification, differential expression, and statistical analysis were performed with Partek Flow Genomic Analysis software (Partek Inc., Chesterfield, MO). Sequence reads were pre-processed to trim 3’ adapter sequences and SMART-Seq Stranded library-specific sequence (i.e., first 3 bases of read 2). Reads were then mapped to the GRCh38/hg38 human reference genome assembly using the STAR (Spliced Transcripts Alignment to a Reference; version 2.7.8a) aligner. Transcript expression quantification as gene- and transcript-level read counts was performed using the quantify to annotation model (Partek E/M) with GENCODE Release 36 (GRCh38.p13) annotation.
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data is provided as a text file (Satake_LIC_RNAseq_Gene_counts.txt) consisting of a gene count matrix. Each column contains feature information (Gene Symbol, first column) and then gene count data for each sample. Each row contains the gene count data for each feature across the sample panel.

source_name: B-cell acute lymphoblastic leukemia

extract_protocol:
RNA was not isolated from cells. Instead, sequencing libraries were prepared directly from cell lysates.
Indexed, directional sequencing libraries were prepared directly from intact cells using the SMART-Seq Stranded Kit (Takara Bio, Inc.) according to the manufacturer’s standard protocol. Briefly, 300 cells were lysed and followed by random-primed first-strand cDNA synthesis, tailing, and template switching with reverse transcriptase (SMARTScribe RT). Illumina barcoded adapters were incorporated by PCR with SeqAmp DNA Polymerase and rRNA-derived cDNA was selectively depleted. The remaining mRNA-derived cDNA fragments were PCR-enriched and the resulting libraries purified with AMPure XP beads (Beckman Coulter, Indianapolis, IN).

value: B-cell acute lymphoblastic leukemia

tag: phenotype 1

value: NBDG-high

tag: phenotype 2

value: high glucose uptake

value: NBDG


title: M47-CHigh-S2_A

tag: tissue

tag: cell type

value: Experiment 1

value: Male


title: NB4 pB

description: single-cell RNA-seq

value: neuroblast


title: NSC-B23 pE [scNOMe-seq]

description: single-cell NOMe-seq

value: striatum & ventricular-subventricular zone

value: TAP


title: M47-CHigh-S1_C

value: Meniscus

tag: experiment

tag: age

value: 10 microM E2, Continuous

value: C


title: 3s170_Low

value: NBDG-low

value: low glucose uptake

tag: treatment


title: NSC-B22 pE [scNOMe-seq]

description: single-cell NOMe-seq

value: aNSC

value: WT


title: NB3 pB

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: naive


title: M47-CHigh-S1_B

value: Meniscal Fibrochondrocytes

tag: gender

tag: treatment duration

value: B


title: NB23 pB

description: single-cell RNA-seq

tag: genotype


title: F16-PLow-S2_708

value: Experiment 2

value: Female

value: 2.4 nM E2, Pulsed

tag: flow cell


title: NSC19 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: M47-CHigh-S1_A

value: Experiment 1

value: Male

value: A


title: NSC-B21 pE [scNOMe-seq]

description: single-cell NOMe-seq

value: striatum & ventricular-subventricular zone


title: 170_Low

value: B-cell acute lymphoblastic leukemia

value: NBDG


title: NB22 pB

description: single-cell RNA-seq

value: neuroblast


title: 170_Med

value: NBDG-medium

value: medium glucose uptake


title: 3s170_Med


title: F16-NoE2-S3_708

value: Meniscus

value: Control (No E2)


title: NSC-B19 pE [scNOMe-seq]

description: single-cell NOMe-seq

value: TAP

value: WT

value: naive


title: 105_Low

value: NBDG-low

value: low glucose uptake


title: M47-CLow-S4_B

value: Meniscal Fibrochondrocytes

value: 1.0 microM E2, Continuous

value: B


title: NB21 pB

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: 105_Med


title: M47-CLow-S4_C

value: Experiment 1

value: Male

value: C


title: NSC-B17 pE [scNOMe-seq]

description: single-cell NOMe-seq

value: striatum & ventricular-subventricular zone


title: 4s96_High

value: B-cell acute lymphoblastic leukemia

value: NBDG-high

value: high glucose uptake

value: NBDG


title: NB20 pB

description: single-cell RNA-seq

value: neuroblast


title: M47-CLow-S4_A

value: Meniscus

value: A


title: NB2 pB

description: single-cell RNA-seq

value: WT

value: naive


title: NSC-B16 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: M47-CLow-S3_C

value: Meniscal Fibrochondrocytes


title: 4s96_Med

value: NBDG-medium

value: medium glucose uptake


title: NSC-B15 pE [scNOMe-seq]

description: single-cell NOMe-seq

value: aNSC


title: NB19 pB

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: M47-CLow-S3_B

value: Experiment 1

value: Male

value: 1.0 microM E2, Continuous

value: B


title: NSC-B20 pE [scNOMe-seq]

description: single-cell NOMe-seq

value: striatum & ventricular-subventricular zone


title: 4s96_Low

value: B-cell acute lymphoblastic leukemia

value: NBDG-low

value: low glucose uptake


title: NB18 pB

description: single-cell RNA-seq

value: neuroblast


title: NSC-B13 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: 96_Med

value: NBDG


title: M47-CLow-S1_C

value: Meniscus

value: C


title: M47-CLow-S3_A

value: Meniscal Fibrochondrocytes

value: A


title: M47-CLow-S1_B


title: NB16 pB

description: single-cell RNA-seq

value: WT

value: naive


title: NB17 pB

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: M47-CLow-S1_A

value: Experiment 1


title: NSC-B1 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC-B10 pE [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO9 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: oligodendrocyte


title: NB14 pB

description: single-cell RNA-seq


title: NB15 pB

description: single-cell RNA-seq


title: 90_Low


title: 90_Med

value: NBDG-medium

value: medium glucose uptake


title: 86_Med


title: M47-PHigh-S3_C

value: Male

value: 240 microM E2, Pulsed


title: 96_Low

value: B-cell acute lymphoblastic leukemia

value: NBDG-low


title: NSC-B11 pE [scNOMe-seq]

description: single-cell NOMe-seq

value: striatum & ventricular-subventricular zone

value: aNSC


title: NB13 pB

description: single-cell RNA-seq

value: neuroblast


title: OLIGO8 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: 86_Low

value: low glucose uptake

value: NBDG


title: M47-PHigh-S3_B

value: Meniscus

value: Meniscal Fibrochondrocytes

value: B


title: NB12 pB

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: WT

value: naive


title: 83_Med

value: NBDG-medium


title: OLIGO4 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: oligodendrocyte


title: 83_Low


title: ASTRO9 pB

description: single-cell RNA-seq


title: OLIGO3 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: M47-PHigh-S2_C

value: Experiment 1

value: Male

value: C


title: M47-PHigh-S2_B

value: 240 microM E2, Pulsed


title: ZMYND8-DOX_RA, rep 2 [SKRAOE2]

city: kolkata

first: Chandrima

last: Das

state: West Bengal

address: 1/AF Bidhan nagar, Sector-III, Salt Lake

department: Biophysics & Structural Genomics

country: India

institute: Saha Institute of Nuclear Physics

data_processing:
RNA-seq reads were aligned to the human genome (hg38) reference genome using hisat2 pipeline with an index built in-house using hisat2-build
Gene counts were called using feature counts (gencode V36). Treated sample was compared with that of Control sample using DeSeq2. Transcripts with log2 Fold change cutoff of 1 and p value <=0.05 were considered as significantly differential expressed.
Gene ontologies and pathways that harbor significantly expressed transcripts were identified using DAVID Functional Annotation Tool.
Genome_build: hg38
Supplementary_files_format_and_content: raw count matrix

source_name: SK-N-SH

growth_protocol: SK-N-SH cells were procurred from ATCC, and grown in DMEM (Dulbecco’s Modified Eagle’s Medium; Gibco). The media was supplemented with 10% FBS (fetal bovine serum; Gibco) and 1% antibiotic-antimycotic (Gibco) and cells were maintained at humified37°C and 5% CO2

extract_protocol:
RNA-seq libraries were generated from two biological replicates for each condition.  The total RNA was extracted using the RNAeasy kit.  The extracted RNA with an RNA integrity number (RIN) of >7.0 was used for rRNA depletion. The purified rRNA depleted total RNA was fragmented at 90°C in the presence of divalent cations. The fragments were reverse transcribed using random hexamers and Superscript II Reverse Transcriptase (Life Technologies).
The sequencing library was prepared by 5' and 3' adapter ligation, after end-repair and the addition of an ‘A’ base and SPRI cleanup. The prepared cDNA library was amplified using PCR for the enrichment of the adapter-ligated fragments. The individual libraries were quantified using a Qubit fluorometer and validated for quality with a Bioanalyzer (Agilent Technologies). SPRI-based (Beckman Coulter Agencourt Ampure XP)-based purification was used to clean after each enzymatic reaction.

treatment_protocol: SK-N-SH cells were differentiated to neurons by shifting the cells in a differentiation medium (DMEM/F12 with 5% FBS and 1% Antibiotic-antimycotic) and supplemented with 10uM ATRA for 24hrs.

value: SK-N-SH

value: Neuroblastoma epithelial cells

value: FLAG ZMYND8+RA+Dox treated


title: ASTRO8 pB

description: single-cell RNA-seq

value: aNSC


title: M47-PHigh-S2_A

value: A


title: OLIGO2 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: M47-PHigh-S1_B

value: Meniscus


title: Parental_DOX_RA, rep 2 [SKRAC2]

value: parental cells+RA+Dox treated


title: OLIGO20 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO23 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO5 pB

description: single-cell RNA-seq


title: OLIGO19 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: Parental_DOX_RA, rep 1 [SKRAC1]


title: M47-PHigh-S1_C

value: Meniscal Fibrochondrocytes


title: ASTRO6 pB

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: OLIGO6 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: WT


title: M47-PHigh-S3_A


title: M47-PHigh-S1_A


title: NB10 pB

description: single-cell RNA-seq

value: neuroblast

value: naive


title: ZMYND8_KD_RA, rep 2 [ZM8_S4R2]

value: ZMYND8 KD+RA


title: ASTRO20 pB

description: single-cell RNA-seq


title: ASTRO21 pB

description: single-cell RNA-seq


title: OLIGO18 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: oligodendrocyte


title: ZMYND8_KD_RA, rep 1 [ZM8_S4R1]


title: ASTRO19 pB

description: single-cell RNA-seq


title: ZMYND8-DOX_RA, rep 1 [SKRAOE1]


title: CONTROLII_RA, rep 2 [ZM8_CR2]

value: Control KD+RA


title: M47-PLow-S4_C

value: Experiment 1

value: Male

value: 24 microM E2, Pulsed

value: C


title: ASTRO18 pB

description: single-cell RNA-seq


title: OLIGO16 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO17 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: CONTROLI_RA, rep 1 [ZM8_CR1]

value: SK-N-SH

value: Neuroblastoma epithelial cells


title: OLIGO14 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: M47-PLow-S4_A

value: A


title: M47-PLow-S3_C

value: Meniscus


title: ASTRO16 pB

description: single-cell RNA-seq

value: TAP


title: Kasumi-1 treated with I3_2

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM value

source_name: Kasumi-1 cell line treated with I3 2

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

tag: protocol

value: incubating with I3 for 48 h

tag: agent


title: ASTRO15 pB

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: Kasumi-1 treated with I3_3

source_name: Kasumi-1 cell line treated with I3 3

tag: cell line


title: OLIGO12 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: WT


title: ASTRO14 pB

description: single-cell RNA-seq


title: OLIGO13 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: Kasumi-1 treated with I3_1

source_name: Kasumi-1 cell line treated with I3 1


title: M47-PLow-S3_B

source_name: Meniscal Fibrochondrocytes

value: Meniscal Fibrochondrocytes

value: B


title: M47-PLow-S3_A


title: OLIGO10 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: naive


title: D071 (IPF control)

description: 10x 3' v2 scRNA-seq

source_name: Normal Donor lung 24 years old

tag: number

value: lung

value: Control


title: ASTRO12 pB

description: single-cell RNA-seq

value: neuroblast


title: HCT116-NUP93-mAC,HiChIP,H3K4me1,MboI,IAA,biological replicate 1

description: HCT116-NUP93-mAC_IAA_H3K4me1_HiChIP_Rep1

value: H3K4me1(Abcam,Cat# ab8895)

value: treated with IAA for 8hr (500uM indole-3-acetic acid (IAA, Sigma Aldrich, catalog#:87514))


title: M47-PLow-S1_C

value: Experiment 1

value: Male

value: 24 microM E2, Pulsed

value: C


title: Kasumi-1 treated with control_sample 3

source_name: Kasumi-1 cell line treated with control 3

value: incubating with control for 48 h


title: OLIGO1 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: oligodendrocyte


title: ASTRO10 pB

description: single-cell RNA-seq


title: Kasumi-1 treated with control_sample 2

source_name: Kasumi-1 cell line treated with control 2


title: M47-PLow-S1_B

value: Meniscus


title: ASTRO1 pB

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: M47-PLow-S1_A

value: A


title: Kasumi-1 treated with control_sample 1

source_name: Kasumi-1 cell line treated with control 1


title: M47-PLow-S4_B

value: Meniscal Fibrochondrocytes


title: NSC7 pB [scNOMe-seq]

description: single-cell NOMe-seq

source_name: ventricular-subventricular zone

value: WT


title: HiC sample replicate 2

city: Miami

first: Qin

last: Yang

state: FL

address: 1501 NW 10th Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

data_processing:
Juicer (Version: 1.5.6) was used to call chromatin interactions.
Two replicates were analyzed separately, then two .hic files were combined
Arrowhead function from Juicer was used for calling TAD regions with 40K resolution.
Genome_build: hg19
Supplementary_files_format_and_content: BED file

source_name: Peripheral blood CD34+ cells

growth_protocol: Mobilized peripheral blood CD34+ cells were purchased from Fred Hutchinson Hematopoietic Cell Procurement Services. One million freshly thawed cells were used for the Hi-C experiment

extract_protocol:
The Arima-HiC Kit (Arima Genomics, A510008) was used following manufacturer’s protocol for low input crosslinking
Libraries were prepared with Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences, 21024). ). Libraries were sequenced on a NovaSeq 6000 (Illumina) in paired-end mode by the Sylvester Comprehensive Cancer Center Onco-Genomics Shared Resource.

value: peripheral blood

tag: marker

value: CD34 positive


title: M47-NoE2-S3_C

value: Control (No E2)


title: HiC sample replicate 1


title: NSC6 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: naive


title: NSC4 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO6 pA

description: single-cell RNA-seq


title: M47-NoE2-S3_B

value: B


title: OLIGO4 pA

description: single-cell RNA-seq


title: OLIGO23 pA

description: single-cell RNA-seq


title: M47-NoE2-S3_A


title: HDF_post_3

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

data_processing:
Sequenced reads from fasq files were mapped to GRCh38.101 whole genome using STAR 2.7.6a aligner.
Transcripts Per Kilobase Million (TPM) value of each gene was calculated using RSEM 1.3.3.
Genome_build: GRCh38.101
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: HDF

growth_protocol: HFLF in pre-3D culture condition was maintained in DMEM supplemented with 10%FBS. HDF(TIG120) in pre-3D culture condition was maintained in MEM medium supplemented with 10%FBS. Cells in post-3D culture condition were isolated from alveolar organoids using FACS.

extract_protocol:
Total RNA was extracted using the RNeasy micro kit (Qiagen) according to manufacturer's protocol.
Library preparation was performed with the TrueSeq stranded mRNA sample preparation kit (Illumina) according to the manufacturer's instructions.

tag: culture condition

value: After 3D culture condition


title: OLIGO22 pA

description: single-cell RNA-seq


title: iMES_AO_P2

data_processing:
Reads were mapped to GRCh38 and count matrices were generated using Cell Ranger.
Genome_build: GRCh38
Supplementary_files_format_and_content: Format: H5. Content: filtered_feature_bc_matrix

source_name: iPSC derived alveolar organoids

extract_protocol:
iPSC-derived alveolar organoids were trypsinized, washed twice, filtered through 40 μm strainer and suspended in the alveolarization medium containing 10 μM Y-27632 . Then the single cell suspension of iPSC-derived alveolar organoids was loaded onto a Chromium device (10x Genomics) for generating single cell libraries.
Single cell libraries were generated using Chromium Next GEM Chip G single Cell Kit (PN-1000127), Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead kit v3.1 (PN-1000128) and Single Index Kit T Set A (PN-1000213) according to the manufacturer’s instructions.

value: SFTPC-GFP reporter iPSC (B2-3) and its parental iPSC (201B7)

value: 3D culture


title: HDF_post_2


title: M47-NoE2-S2_B

value: Experiment 1

value: Male


title: M47-NoE2-S2_C

value: C


title: NSC3 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: oligodendrocyte


title: NSC23 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO20 pA

description: single-cell RNA-seq

data_processing:
mapping with STAR via zUMIs
transcript quantification with featureCounts via zUMIs
Assembly: GRCm38 (mm10)
Supplementary files format and content: Single-cell RNA-seq count matrix in gzip-compressed csv (comma-separated values) format. Values are not normalized, decimals are due to distribution of multimapping reads.

extract_protocol:
For the ischemia experiment, the vSVZ and striatum were isolated. For the naïve experiments, vSVZ, striatum, and olfactory bulb were isolated. Depending on the plate, individual or pooled mice were used to sort cells on plate. Tissues were processed and sorted in a BD FACSAria II at the DKFZ Flow Cytometry Facility. Cells were stained with the following antibodies (all conditions and tissues together): O4-APC and O4-APC-Vio770 (Miltenyi; diluted 1:50), Ter119-APC-Cy7 (Biolegend; 1:100), CD45-APC-Cy7 (BD; 1:200), GLAST (ACSA-1)-PE (Miltenyi: 1:20), PSA-NCAM-PE-Vio770 (Miltenyi; 1:75), Prominin1-A488 (eBioscience; 1:75), and Sytox Blue (Life Technologies, 1:1000), CD9-eFluo450 (eBioscience, 1:300).
For profiling the transcriptome and epigenome of single cells we developed and implemented a miniaturized and higher throughput version of the scNMT-seq protocol (Clark et al., 2018). On this new version, the Smart-seq3 (Hagemann-Jensen et al., 2020) method and specific normalization steps were implemented. A detailed version of the protocol is described in Cerrizuela et al., (2022). The samples listed here represent the transcriptomic portion of this multi-omic data set.
Single-cell RNA-seq (Smart-seq3)


title: NSC21 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: HDF_post_1


title: OLIGO7 pA

description: single-cell RNA-seq


title: HDF_pre_3

value: Before 3D culture condition


title: OLIGO19 pA

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: M47-NoE2-S1_C

data_processing:
Base calling was carried out by the Illumina NextSeq 550 Real Time Analysis (RTA) software.
Raw reads were filtered using fastp (Experiment 1) or trimmomatic 0.39 (Experiment 2) and aligned to the reference transcriptome using Kallisto 0.46.1-1.
Kallisto 0.46.1-1 was used for transcript abundance estimates
tximport was used to import Kallisto transcript abundance estimates into DeSeq2 1.3 for differential expression analysis
Assembly: ENSEMBL Homo sapiens reference transcriptome build GRCh38 release 101
Supplementary files format and content: .tsv files containing raw quantified counts and TPM counts

extract_protocol:
For Experiment 1 cells were collected in TRIzol, and total RNA was purified using a PureLink RNA Mini Kit (Life Technologies, 12183025) according to the manual. DNA was removed using a DNA-free DNA Removal Kit (Life Technologies, AM1906) according to the manual. For Experiment 2 cells were collected and total RNA was purified using a QIAGEN RNeasy Mini Kit (QIAGEN, 74104) with no DNase treatment.
Sequencing libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760). The sequencing library construction process included mRNA purification with polyA selection beads, fragmentation to inserts of ~200 bp, strand specific cDNA synthesis, end repair, 3’ end adenylation, adapter ligation, and PCR amplification. Samples were run across 3 flow cells (Experiment 1: A, B, and C; Experiment 2: 708, 709, and 710).

value: Meniscus


title: OLIGO10 pA

description: single-cell RNA-seq


title: NSC2 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: HDF_pre_2


title: NSC19 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: M47-NoE2-S1_B

value: Meniscal Fibrochondrocytes


title: NSC18 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: WT


title: NSC9 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC5 pA

description: single-cell RNA-seq


title: HDF_pre_1


title: NSC17 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: M47-NoE2-S1_A

value: A


title: HDF_iMES_post_3

source_name: iMES derived from HDF-iPSC

value: HDF-iPSC (GC23)


title: F47-CHigh-S4_B

value: Female

value: 10 microM E2, Continuous


title: NSC4 pA

description: single-cell RNA-seq

value: naive


title: AF8385

source_name: Subcutaneous adipose tissue

value: Subcutaneous adipose tissue

tag: condition

value: morbidly obese


title: M47-NoE2-S2_A

value: Control (No E2)


title: HDF_iMES_post_2

value: After 3D culture condition


title: HDF_iMES_post_1


title: NSC13 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC12 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC22 pA

description: single-cell RNA-seq


title: HDF_iMES_pre_3


title: F47-CHigh-S4_A

value: Experiment 1


title: NSC21 pA

description: single-cell RNA-seq


title: NSC1 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: TAP


title: NB9 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: neuroblast


title: F47-CHigh-S3_A


title: NSC16 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: HDF_iMES_pre_1

value: Before 3D culture condition


title: NSC3 pA

description: single-cell RNA-seq

value: ventricular-subventricular zone


title: NSC19 pA

description: single-cell RNA-seq


title: F47-CHigh-S4_C

value: Meniscus

value: C


title: F47-CHigh-S2_C

value: Meniscal Fibrochondrocytes


title: NB7 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: WT


title: NB8 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: HFLF_post_2

source_name: HFLF

value: HFLF


title: NB8 pA

description: single-cell RNA-seq


title: NSC1 pA

description: single-cell RNA-seq


title: F47-CHigh-S2_B

value: Female

value: B


title: NB6 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: naive


title: NSC23 pA

description: single-cell RNA-seq


title: HFLF_post_1


title: NB5 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: F47-CHigh-S2_A

value: 10 microM E2, Continuous

value: A


title: NB7 pA

description: single-cell RNA-seq


title: F47-CLow-S4_C

value: 1.0 microM E2, Continuous


title: HDF_iMES_pre_2

value: HDF-iPSC (GC23)


title: F47-CHigh-S3_B

value: Experiment 1


title: F47-CHigh-S3_C


title: NB4 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: HFLF_pre_3


title: NB6 pA

description: single-cell RNA-seq


title: NSC2 pA

description: single-cell RNA-seq

value: oligodendrocyte


title: F47-CLow-S4_B


title: HFLF_post_3

value: After 3D culture condition


title: HFLF_pre_1

value: Before 3D culture condition


title: NB4 pA

description: single-cell RNA-seq

value: ventricular-subventricular zone

value: neuroblast


title: NB5 pA

description: single-cell RNA-seq


title: NB23 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: F47-CLow-S4_A

value: Meniscus


title: NB3 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: NB22 pA

description: single-cell RNA-seq


title: HFLF_iMES_post_3

source_name: iMES derived from HFLF-iPSC

value: HFLF-iPSC (HFA)


title: NB22 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: WT


title: HFLF_iMES_post_1


title: NB21 pA

description: single-cell RNA-seq


title: HFLF_iMES_post_2


title: NB21 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: F47-CLow-S3_B

value: Meniscal Fibrochondrocytes


title: HFLF_pre_2

value: HFLF


title: HFLF_iMES_pre_3


title: NB2 pA

description: single-cell RNA-seq


title: HFLF_iMES_pre_2


title: F47-CLow-S2_B

value: Female

value: B


title: F47-CLow-S2_C

value: C


title: NB19 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: naive


title: NB2 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: HFLF_iMES_pre_1


title: NB19 pA

description: single-cell RNA-seq


title: F47-CLow-S2_A

value: 1.0 microM E2, Continuous

value: A


title: NB18 pA

description: single-cell RNA-seq


title: F47-CLow-S3_C

value: Experiment 1


title: NB17 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: F47-PHigh-S3_C

value: 240 microM E2, Pulsed


title: NB18 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: RIF6

city: shanghai

first: li

last: mingqing

address: NO.419 fangxie Road, Shanghai

institute: Affiliated obstetrics and Gynecology Hospital of Fudan University

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 40%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: endometrium

extract_protocol:
Sample washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

value: endometrium

tag: Stage

value: 5 days after ovulation

tag: group

value: RIF


title: NB17 pA

description: single-cell RNA-seq

tag: tissue

value: ventricular-subventricular zone

tag: cell type

value: neuroblast


title: NB20 pA

description: single-cell RNA-seq


title: F47-CLow-S3_A

value: Meniscus

tag: experiment

tag: age


title: NB20 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: WT

tag: treatment


title: NB16 pA

description: single-cell RNA-seq


title: NB16 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: RIF5


title: RIF4


title: F47-PHigh-S3_A

value: Meniscal Fibrochondrocytes

tag: gender

tag: treatment duration


title: NB15 pB [scNOMe-seq]

description: single-cell NOMe-seq

tag: genotype


title: NB15 pA

description: single-cell RNA-seq


title: RIF3


title: F47-PHigh-S2_C

tag: flow cell


title: NB14 pA

description: single-cell RNA-seq


title: RIF2


title: NB13 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: RIF1


title: NB12 pA

description: single-cell RNA-seq


title: F47-PHigh-S2_A


title: NB12 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: F47-PHigh-S1_C


title: NB11 pA

description: single-cell RNA-seq


title: F47-PHigh-S3_B


title: NB10 pA

description: single-cell RNA-seq


title: NB10 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: Ctrl2

value: control


title: F47-PHigh-S1_B

value: Female


title: ASTRO9 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: NB1 pA

description: single-cell RNA-seq


title: ASTRO8 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: aNSC


title: F47-PHigh-S1_A


title: ASTRO9 pA

description: single-cell RNA-seq


title: ASTRO6 pA

description: single-cell RNA-seq


title: F47-PHigh-S2_B

value: B


title: Adipo+EX527,Day16, R3

city: MEXICO CITY

first: LORENA

last: AGUILAR ARNAL

address: TERCER CIRCUITO EXTERIOR, CU

department: BIOLOGIA CELULAR Y FISIOLOGIA

country: Mexico

institute: INSTITUTO DE INVESTIGACIONES BIOMEDICAS- UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO

data_processing:
Human Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the Homo sapiens assembly GRCh38/hg38, with the STAR aligner v2.5
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. Afterwards, FPKM of each gene was calculated based on the length of the gene and reads count mapped to it
Differential expression analysis between conditions (three biological replicates per condition) was performed with the DESeq2 R package (2_1.6.3). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P-value <0.05 were assigned as differentially expressed.
Genome_build: Homo sapiens assembly GRCh38/hg38,
Supplementary_files_format_and_content: Matrix table with FPKM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human mesenchymal cell

growth_protocol: hMSCs were maintained in LG-DMEM (Gibco, cat. no. 31600-034) supplemented with 10% FBS, 4mM L-glutamine, 100 mg/ml of penicillin and streptomycin (Gibco), and incubated at 37°C and 5% of CO2. Adipogenic differentiation was induced in MSCs in growing phase (70%-80% confluency),using the StemPro™ Adipogenic differentiation kit (Gibco A1007001). The medium and drugs were replaced every four days during the differentiation process.

extract_protocol:
Total RNA from MSCs was extracted using Quick RNA MiniPrep Kit (Zymo Research, USA) following the manufacturer´s instructions
RNA samples with RNA integrity number (RINs) > 7.0 were sent for library preparation and sequencing to Novogene Corporation Inc., California, USA. Briefly, mRNA was isolated using oligo(dT) beads and randomly fragmented by adding fragmentation buffer, followed by cDNA synthesis primed with random hexamers. Next, a second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added for second-strand synthesis. After end repair, barcode ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed with size selection to 250-300 bp, and PCR enrichment

treatment_protocol: Indicated drugs were present in the medium as follows: NAD+ (5 mM), FK866 (1 nM) or EX527 (50 μM).

value: Mesenchymal cell

tag: differentiation stage

value: Adipogenic induction

tag: days on adipogenic induction


title: Ctrl1


title: ASTRO6 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: naive


title: F47-PLow-S4_B

value: Experiment 1

value: 24 microM E2, Pulsed


title: Adipo+EX527,Day16, R2

tag: cell line


title: ASTRO4 pA

description: single-cell RNA-seq


title: ASTRO5 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: F47-PLow-S4_C

value: C


title: ASTRO22 pA

description: single-cell RNA-seq


title: ASTRO21 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: Adipo+EX527,Day16, R1


title: Adipo+FK866,Day16, R3


title: Ctrl3

value: endometrium

value: 5 days after ovulation


title: F47-PLow-S4_A

value: A


title: F47-PLow-S2_C


title: ASTRO20 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: ventricular-subventricular zone


title: ASTRO20 pA

description: single-cell RNA-seq


title: ASTRO17 pA

description: single-cell RNA-seq


title: Adipo+FK866,Day16, R1


title: Adipo+FK866,Day16, R2


title: ASTRO19 pA

description: single-cell RNA-seq


title: F47-PLow-S2_B

value: Meniscus


title: F47-PLow-S2_A


title: ASTRO19 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: WT


title: ASTRO18 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO16 pA

description: single-cell RNA-seq


title: ASTRO16 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: TAP


title: NB14 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: neuroblast


title: F47-PLow-S1_B

value: Meniscal Fibrochondrocytes

value: Female


title: Adipo+NAD+,Day16, R1

value: NAD+


title: Adipo+NAD+,Day16, R3

value: Mesenchymal cell


title: F47-PLow-S1_C


title: F47-PLow-S1_A


title: ASTRO15 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO11 pA

description: single-cell RNA-seq


title: ASTRO14 pA

description: single-cell RNA-seq

value: aNSC


title: ASTRO14 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: naive


title: F47-NoE2-S4_C

value: Experiment 1

value: Control (No E2)


title: ASTRO1 pA

description: single-cell RNA-seq


title: ASTRO12 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: F47-NoE2-S4_B

value: B


title: Adipo, Day16, R2

value: Adipogenic induction

value: untreated


title: Adipo, Day16, R3


title: ASTRO10 pB [scNOMe-seq]

description: single-cell NOMe-seq


title: Adipo+NAD+,Day16, R2


title: Adipo+EX527,Day8, R3


title: CTO24 [0612_2022]

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

data_processing:
Reads were aligned to the musmusculus reference genome version mm10 using STAR (v2.5.2) with default parameters. SAM files were converted to BAM and sorted using Sambamba (v0.7.1)
Count matrices were generated using The Rsubread R package with the ENSEMBL Mus_musculus.GRCm38.97 custom annotation
Assembly: mm10
Supplementary files format and content: Raw count matrix in xls comma separated format

source_name: CTO

growth_protocol: Organoids were grown in full stem cell medium.

extract_protocol:
BME drops were disrupted with Cell Lysis buffer and RNA was purified with RNAeasy kit.
RNA libraries were prepared for sequencing using the kits NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# E7490) and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (Cat#E7770), following manufacturer´s instructions and 9 cycles of amplification

treatment_protocol: No treatment applies

value: AKPS

value: Organoids


title: F47-NoE2-S3_B

value: Meniscus


title: CTO24 [0611_2022]


title: CTO23 [0610_2022]

value: AKS


title: F47-NoE2-S3_C

value: C


title: F47-NoE2-S4_A

value: A


title: ASTRO1 pB [scNOMe-seq]

description: single-cell NOMe-seq

value: ventricular-subventricular zone

value: neuroblast

value: WT


title: Adipo+EX527,Day8, R2

value: Mesenchymal cell


title: F47-NoE2-S3_A

value: Meniscal Fibrochondrocytes

value: Female


title: Adipo+EX527,Day8, R1


title: CTO22 [0608_2022]

value: AKPT


title: CTO22 [0607_2022]


title: Adipo+FK866,Day8, R2


title: CTO20 [0606_2022]

value: APK


title: F47-NoE2-S1_A

value: Experiment 1

tag: gender:

value: Control (No E2)


title: CTO20 [0605_2022]


title: CTO23 [0609_2022]


title: F47-NoE2-S1_B

value: B


title: Adipo+FK866,Day8, R3

value: Adipogenic induction


title: Adipo+NAD+,Day8, R3

value: NAD+


title: CTO19 [0604_2022]

value: APS

value: Organoids


title: CTO19 [0603_2022]


title: HCT116-NUP93-mAC,Hi-C,MboI,IAA,biological replicate 3

data_processing:
FASTQ data were trimmed by Cutadapt and Trimmomatic.
PRO-Seq Reads were aligned using STAR with the hg19 build of the human genome. Read counts for Refseq mRNAs were determined using HTSeq-count.
Peaks for ChIP-Seq and Cut&Run  were called by using MACS2.
HiC-Pro was used to process Hi-C and HiChIP data. The HiC contact matrix normalized by ICE method was converted into mcool by cooler.
Identification of significant chromatin contacts(loops interaction) from HiChIP data by using FitHiChIP.
Assembly: hg19

source_name: colorectal cancer cells

extract_protocol:
5-10 million cells were cross-linked using 1% formaldehyde for 10mins at room temperature, quenched with 0.125M glycine for 10mins at room temperature, and were washed with cold PBS. Cross-linked cell pellets were resuspended in 1ml iced-cold Hi-C lysis buffer (10 mM Tris-HCl, pH 8.0; 10mM NaCl, 0.2% NP-40 and protease inhibitor cocktail), and rotated at 4°C for 30 mins. After pelleting down the nuclei, 100 ul of 0.5% SDS was used to resuspend and permeabilize the nuclei at 62 °C for 10 mins.  Then 260 ul H20 and 50 ul 10% Triton-X100 were added to quench the SDS at 37 °C for 15 mins. Subsequently, enzyme digestion of chromatin was performed at 37 °C overnight by adding an additional 50 ul of 10X NEB buffer 2 and 400U MboI (NEB, R0147M). After overnight incubation, the MboI in solution was inactivated at 62 °C for 20 mins. To fill-in the DNA overhangs and mark the ends with biotin, 35U DNA polymerase I (Klenow, NEB, M0210) together with 10 ul of 1mM biotin-dATP (Jeana Bioscience), 1ul 10mM dCTP/dGTP/dTTP were added and incubated at 37°C for 1 hour with rotation. Blunt end Hi-C DNA ligation was performed using 5000 U NEB T4 DNA ligase with 10X NEB T4 Ligase buffer with 10mM ATP, 90 ul 10% Triton X-100, 2.2 ul 50mg/ml BSA at room temperature for four hours with rotation. After ligation, nuclei were pelleted down and resuspended with 440 ul Hi-C nuclear lysis buffer (50mM Tris-HCl pH7.5; 10mM EDTA, 1% SDS and protease inhibitor cocktail), and further sheared using the parameter of 10/20 secs ON/OFF cycle, 25% Amp, 5mins by a QSonica 800R sonicator. Hi-C will use 5-10% of the sonicated chromatin in the next section. For HiChIP, the sonicated chromatin was incubated with appropriate antibody (here by 4ug H3K27ac polyclonal antibody) overnight, and the immunocomplex was captured by dynabeads protein G in the next day. The immunocomplex was washed 2 times by low salt wash buffer (20 mM Tris-HCl pH 7.5, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl), 2 times by high salt wash buffer (20 mM Tris-HCl pH 7.5, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl), 1 time with Tris-EDTA buffer + 0.1% triton-100, and one more time with TE only. The immunocomplex was subjected to overnight decrosslinking at 65°C, protein K treatment, and DNA extraction
For both Hi-C and HiChIP library making , after DNA extraction, they were used for biotin DNA enrichment by 20 ul Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher 65002). The biotin bound DNA on beads was used to perform on-beads library making with KAPA Hyper DNA library kit, or using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645L).

tag: antibody

value: treated with IAA for 8hr (500uM indole-3-acetic acid (IAA, Sigma Aldrich, catalog#:87514))


title: Adipo, Day16, R1

value: untreated


title: HCT116-NUP93-mAC,Hi-C,MboI,UT,biological replicate 3


title: Adipo+NAD+,Day8, R2


title: Adipo+NAD+,Day8, R1


title: HCT116-NUP93-mAC,Hi-C,MboI,IAA,biological replicate 2


title: CTO18 [0602_2022]

value: APT


title: CTO18 [0601_2022]


title: Adipo, Day8, R3


title: HCT116-NUP93-mAC,Hi-C,MboI,UT,biological replicate 2


title: Adipo, Day8, R2


title: IM_Control

city: Belfast

first: Jose

last: Bengoechea

state: Northern Ireland

address: 97 Lisburn Road

department: WWIEM

country: United Kingdom

institute: Queen's University Belfast

data_processing:
bcl2fastq (2.20) was used to demultiplex the samples and convert to FASTQ files
FASTQ files processed in Cell Ranger (3.0.2) Count aligned against mm10 reference package with default parameters
10X-filtered count matrices subject to additional gene- and cell-QC filtering in seurat (3.2.3) excluding genes found in <3 cells, and cells with <200 genes
Seurat LogNormalize used to generate normalised expression matrix
Normalised data subject to automated celltype annotation in SingleR (1.0.6) using ImmGen reference dataset.
In silico cell selection using predicted annotation: cells matching non-macrophage expression profile were removed. Purified datasets downsampled to same cell total (422 cells)
Genome_build: mm10
Supplementary_files_format_and_content: count matrix: unpurified count data for each sample with default cellranger cell detection
Supplementary_files_format_and_content: purified downsampled count matrix: count data after in silico purification of macrophages, each downsampled to 422 cells total

source_name: Lung

extract_protocol:
10X Chromium v3.1 GEX 3' recovery
Chromium Single Cell 3ʹ v3

tag: strain

value: Lung

value: Interstitial Macrophage


title: AM_Control

value: Alveolar Macrophage


title: Adipo, Day8, R1

value: Mesenchymal cell


title: CTO17 [0600_2022]

value: AK


title: HCT116-NUP93-mAC,ChIP-Seq for BRD4,IAA, biological replicate 1

extract_protocol:
HCT116 cells were crosslinked in 2 mM discuccinimidyl glutarate (DSG, CovaChem, 13301-100) for 30 min first, then in 1% formaldehyde for 15 min at room temperature. Except for NUP93, all other ChIP-Seq experiments used cells that were crosslinked by 1% formaldehyde for 10 min at room temperature. After quenching with 0.125M glycine, we collected cell pellets, and extracted the nuclei by using buffer LB1 [50 mM HEPES-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA (pH 8.0), 10% (v/v) glycerol, 0.5% NP-40, 0.25% Triton X-100 and 1×cocktail protease inhibitor], and then LB2 [10 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 1×cocktail protease inhibitor]. After centrifuge, cell nuclei were suspended in buffer LB3 [10 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0), 0.1% Na-deoxycholate, 0.5% N-lauroyl sarcosine and 1×cocktail protease inhibitor], and fragmented using Q800R3 sonicator (QSONICA).Sheared chromatins were collected by centrifugation, and were incubated with appropriate antibodies at 4°C overnight. The next morning, the antibody-protein-chromatin complex was retrieved by adding 40ul Protein G Dynabeads (Thermo Fisher Scientific, 10004D). Immunoprecipitated DNA was de-crosslinked by 65ºC heating overnight, treated by proteinase-K, and were harvested by phenol chloroform or by Qiagen Quick DNA extraction kit.
ChIP-Seq  library construction using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645L).


title: Adipo+FK866,Day8, R1


title: IM_KP+

value: Associated with Klebsiella pneumoniae


title: CTO17 [0599_2022]


title: HCT116-NUP93-mAC,ChIP-Seq for BRD4,UT, biological replicate 1


title: HCT116-NUP93-mAC,ChIP-Seq,RPB2,IAA

data_processing:
FASTQ data were trimmed by Cutadapt and Trimmomatic.
PRO-Seq Reads were aligned using STAR with the hg19 build of the human genome. Read counts for Refseq mRNAs were determined using HTSeq-count.
Peaks for ChIP-Seq and Cut&Run  were called by using MACS2.
HiC-Pro was used to process Hi-C and HiChIP data. The HiC contact matrix normalized by ICE method was converted into mcool by cooler.
Identification of significant chromatin contacts(loops interaction) from HiChIP data by using FitHiChIP.
Genome_build: hg19

value: treated with IAA for 8hr(500uM indole-3-acetic acid (IAA, Sigma Aldrich, catalog#:87514))


title: CTO16 [0598_2022]

value: AS


title: HCT116-NUP93-mAC,ChIP-Seq,RPB2,UT


title: AM_KP+


title: IM_KP-

value: Bystander cells


title: hMSC, R3

value: Undifferentiatiated


title: hMSC, R2


title: CTO16 [0597_2022]


title: hMSC, R1


title: HCT116-NUP93-mAC,ChIP-Seq,RPB1,IAA

value: Rabbit Monoclonal RPB1(CST:#14958S)


title: AM_KP-


title: HCT116-NUP93-mAC,ChIP-Seq,H3K27me3,IAA


title: CTO14 [0596_2022]

value: AT


title: CTO14 [0595_2022]


title: HCT116,HiChIP, MboI, H3K27ac


title: HCT116-NUP93-mAC,Hi-C,MboI,IAA,biological replicate 1


title: HCT116-NUP93-mAC,Cut&Run for BRD4,IAA, biological replicate 2

data_processing:
Library strategy: Cut&Run
FASTQ data were trimmed by Cutadapt and Trimmomatic.
PRO-Seq Reads were aligned using STAR with the hg19 build of the human genome. Read counts for Refseq mRNAs were determined using HTSeq-count.
Peaks for ChIP-Seq and Cut&Run  were called by using MACS2.
HiC-Pro was used to process Hi-C and HiChIP data. The HiC contact matrix normalized by ICE method was converted into mcool by cooler.
Identification of significant chromatin contacts(loops interaction) from HiChIP data by using FitHiChIP.
Genome_build: hg19

extract_protocol:
0.5 million live HCT116 or HeLa cells were harvested and resuspended in 100ul wash buffer [20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, supplemented with Protease Inhibitor EDTA-Free tablet (Roche 11836170001)]. Activated Concanavalin A (EpiCypher 21-1401) was incubated with cells at room temperature for 10min to let the cells bind to the beads. For each target protein factor, 0.5ug antibody was added to each sample and incubated in the antibody buffer (wash buffer + 0.01% Digitonin and 2 mM EDTA) at 4ºC for 4-6hr. The beads were then washed twice with digitonin buffer [wash buffer + 0.01% Digitonin], and 2.5 µL pAG-MNase (EpiCypher, 15-1116) was added to each sample. After ten minutes of incubation at room temperature, excessive pAG-MNase was washed out by a two-time digitonin buffer wash. Then targeted chromatin was digested and released from cells by 2 hours of incubation with the presence of 2 mM CaCl2 at 4ºC, which were collected from the supernatant, were subjected to phenol/chloroform DNA extraction,
sequencing library construction using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645L).


title: Glioma stem cell hG021 rep2

city: Stanford

first: Kent

last: Imaizumi

address: 318 Campus Drive

institute: Stanford University

data_processing:
Sequences were produced using a NovaSeq6000 (Illumina)
Raw FASTQ files were trimmed for adapters by Cutadapt
We used Salmon to generate the TPM counts by using the transcript index from GRCh38 (Gencode v33)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: GSC

extract_protocol:
Total RNA was isolated by RNeasy mini kit (QIAGEN)
The indexed cDNA libraries were prepared using the TruSeq stranded mRNA Library Preparation kit (Illumina)

value: Glioma stem cell hG021


title: HCT116-NUP93-mAC,Hi-C,MboI,UT,biological replicate 1


title: CTO13 [0593_2022]

value: AP

value: Organoids


title: Glioma stem cell hG008 rep2

value: Glioma stem cell hG008


title: Glioma stem cell hG021 rep1


title: CTO12 [0591_2022]

value: A


title: minu, rep1

city: Valencia

first: Jaime

last: Pérez

address: Calle del Ingeniero Fausto Elio, s/n

institute: IBMCP

data_processing:
Read quality control was performed using FastQC v0.11.9. Reads were aligned to TAIR10 using bowtie2 v2.4.4 using default parameters. Alignments were sorted by coordinate and indexed using samtools v1.14. Duplicate alignments were labeled with picard MarkDuplicates v2.26. Uniquely mapping reads were obtained using samtools view with parameters "-f 2 -F 1024 -F 4 -q 5". Regions with anomalous signal were detected using chipseq-greylist v1.0.2. These regions were excluded from a TAIR10 chromosome bedfile with the complementBed command from bedtools v2.30.9 to generate a bedfile of included regions, and then converted to wig using a python script. Normalized coverage wigs and nucleosome dynamics analysis files were obtained with DANPOS2 v2.2.2. The dpos.py command was run with parameters "--save 1 --paired 1 --span 1 --clonalcut 1e-10 --nor_regions_file <included_regions.wig>". The normalization method was set as default (F). Finally, coverage wig files were converted to bedgraph format using the write_bg command from wiggletools v1.2.11, and these were converted to bigwig with the bedGraphToBigWig command from UCSC tools.
Assembly: TAIR10
Supplementary files format and content: Normalized coverage tracks in bigwig format
Supplementary files format and content: Nucleosome dynamics analysis in tab-separated text file

organism: Arabidopsis thaliana

source_name: inflorescences

growth_protocol: Inflorescences of plants grown on soil in long days condition

extract_protocol:
0.35gr of inflorescences from Col-0, minu1-2 minu2-1, and tpf1-1 tpf2-1 were ground and resuspended in 20ml of Isolation Buffer 1 (20mM Tris pH8, 0.3 M sucrose, 5mM MgCl2, 0.2% Triton X100- 5mM BME 14.3M, 35% glycerol, 5ul 0.2M PMSF in 10ml, Complete mini –EDTA). After filtering through 1 layer of miracloth samples were spun at 3200rpm 4C for 20 min. The pellet was resuspended in 1ml of HBB buffer (25 mm Tris–HCl, pH 7.6, 0.44 M sucrose, 10 Mm MgCl2, 0.1% Triton-X and 10 mm β-mercaptoethanol, 5ul 0.2M PMSF in 10ml. Complete mini –EDTA) and spun at 3200rpm 4C for 10 min. The pellet was resuspended in 1ml of MNB buffer (10% sucrose, 50 mM Tris-HCl, pH 7.5, 4 mM MgCl2, and 1 mM CaCl2) and spun at 3200 rpm 4C for 10 min. The pellet was resuspended in 900 ul of MNB buffer and 180 ul aliquots were digested with different amounts of Micrococcal Nuclease (N3755, Sigma) (0, 1, 3, 5 and 8U) followed 10 min incubation at 37C, quickly mixing samples every 3 min. Reactions were stopped by addition of 20 μL of 0.5 mM EDTA, and 4ul of DNAse-Free RNAse (10mg/ml) were added followed by incubation at 37C for 1h. 1ul proteinase K (20mg/ml) was added followed by incubation at 45C for 1h. DNA was extracted with Phenol:Chloroform:isoamyl followed by chloroform extraction and precipitation with NaOAc/glycogen/ethanol at −20 °C overnight. Samples were centrifuged at 13,000 × g for 15 min at 4 °C, washed with 70% ethanol and resuspended in 30ul elution buffer. Samples were run in a 2% agarose gel to recover mononucleosomal DNA (aprox. 150bp) from digestions that presented 20% di-nucleosome and 80% of mono-nucleosome. Gel bands were cut and purified with Zymo gel extraction kit. Libraries for sequencing were prepared at BGI following the BGISEQ-500 ChIP-Seq library preparation protocol.
Libraries for sequencing were prepared at BGI following the BGISEQ-500 ChIP-Seq library preparation protocol.

value: inflorescences

value: minu1-2 minu2-1


title: HCT116-NUP93-mAC,Cut&Run for BRD4,UT, biological replicate 2

value: untreated


title: Glioma cell line SF126

source_name: GC

value: Glioma cell line SF126


title: Glioma stem cell hG008 rep1


title: F47-NoE2-S1_C

city: Lawrence

first: Jennifer

last: Robinson

institute: University of Kansas

source_name: Meniscal Fibrochondrocytes

value: Meniscus

value: Meniscal Fibrochondrocytes

value: Experiment 1

value: Female

value: Control (No E2)

value: C


title: HCT116-NUP93-mAC,Cut&Run for BRD4,IAA, biological replicate 1

value: treated with IAA for 8hr (500uM indole-3-acetic acid (IAA, Sigma Aldrich, catalog#:87514))


title: Glioma cell line U251 rep2

value: Glioma cell line U251


title: HCT116-NUP93-mAC,ChIP-Seq,RPB1,UT

value: Rabbit Monoclonal RPB1(CST:#14958S)


title: tpf, rep2

value: tpf1-1 tpf1-2


title: CTO13 [0594_2022]

value: AP

value: Organoids


title: HCT116-NUP93-mAC,ChIP-Seq,H3K27me3,UT


title: tpf, rep1


title: Glioma cell line U251 rep1


title: minu, rep2


title: HeLa,Cut&Run,NUP93

source_name: cervical adenocarcinoma

value: HeLa


title: HCT116,Cut&Run,IgG


title: Glioma cell line U87 rep2

value: Glioma cell line U87


title: col0, rep2

value: inflorescences


title: HCT116,Cut&Run,NUP35

value: untreated


title: col0, rep1


title: H2AZ

data_processing:
Read quality control was performed using FastQC v0.11.9. Reads were aligned to TAIR10 using bowtie2 v2.4.4 using default parameters. Alignments were sorted by coordinate, compressed, and indexed using samtools v1.14. Duplicate alignments were labeled with picard MarkDuplicates v2.26. Uniquely mapping reads were obtained using samtools view with parameters "-F 1024 -F 4 -q 5". Fragment sizes were estimated with phantompeakqualtools v1.2.2. Regions with anomalous signal in controls were detected using chipseq-greylist v1.0.2. These regions were excluded from a TAIR10 chromosome bedfile with the complementBed command from bedtools v2.30.9 to generate a bedfile of included regions. Library sizes were estimated as the number of uniquely mapping reads overlapping these regions. Coverage bedgraphs were generated with bedtools genomecov with parameters “-scale <10E6 / library_size > -fs <fragment_size> -bga”. These files were converted to bigwig using bedGraphToBigWig from UCSC tools. Finally, peaks were called using MACS2 with parameters “--keep-dup all --nomodel --shitsize <fragment_size>”.
Assembly: TAIR10
Supplementary files format and content: Normalized coverage (Counts Per Million)  tracks in bigwig format
Supplementary files format and content: MACS2 peaks in narrowPeak format

extract_protocol:
The chromatin immunoprecipitation protocol was done as previously described with minor changes (28). Briefly, 1 gram of inflorescences were ground in liquid nitrogen and fixed in Nuclei Isolation buffer containing 1% formaldehyde for 10 min at RT. In the case of CHR23-FLAG ChIPs, samples were first fixed with in Nuclei Isolation buffer containing 1.5mM EGS for 10 minutes at RT followed by addition of 1% formaldehyde and incubation for 10 additional minutes. Reactions were stopped with glycine followed by nuclei isolated and chromatin shearing using a Bioruptoptor pico (Diagenode). Chromatin was immunoprecipitated overnight at 4 °C with the following antibodies: Anti-FLAG M2 (5 ul/ChIP used, F1804, Sigma), Pol II Ser5 (5 ul/ChIP used, Ab5131), H3K4me3 (5 ul/ChIP used, 04-745, Millipore), H3K36me3 (10 ul/ChIP used, Ab9050, Abcam), H3K27me3 (10 ul/ChIP used, 07-449, Millipore), H3 (5 ul/ChIP used, Ab1791, Abcam), H2A (10 ul/ChIP used, Ab13923, Abcam), H2A.Z (3 ul/ChIP used), and PanH3Ac (5 ul/ChIP used, 39140, Active motif). Complexes were captured with a 1:1 mixture of magnetic Protein A and Protein G Dynabeads (Invitrogen) for 3 h at 4 °C, washed with low salt, high salt, LiCl, and TE buffers for 10 min each at 4 °C and eluted for 2 × 20 min at 65 °C with elution buffer. Reverse crosslink was done overnight at 65 °C, followed by proteinase K treatment at 45 °C for 5 h. DNA was purified using Phenol:Chloroform:Isoamyl Alcohol 25:24:1 (Fisher Scientific) and precipitated with GlycoBlue (Invitrogen) and NaAc/EtOH overnight at −20 °C. DNA was resuspended in 75ul of elution buffer. Libraries for TPF2-FLAG and CHR23-FLAG experiments were prepared using the Ovation Ultra Low System V2 1-16 kit (NuGEN) following the manufacturer’s instructions.
The Nugen Ultralow V2 kit (TECAN) was used to make the libraries


title: Glioma cell line U87 rep1


title: BM-derived MSC line B rep2

source_name: MSC

value: BM-derived MSC line B


title: sural nerve_biopsy_diagnostic_inflammatory neuropathy 1

type: RNA

city: Milan

first: Nilo

last: Riva

address: via Olgettina 60

department: Neuroscience

country: Italy

institute: IRCCS San Raffaele

hyb_protocol: Standard Illumina hybridization protocol: Whole Genome Gene Expression DASL HT Assay

scan_protocol: Standard Illumina scanning protocol using the Illumina BeadArray Reader

data_processing: The data were normalized using quantile normalization as implemented within lumi R Bioconductor package

label: biotin

label_protocol: Total RNA underwent a reverse transcription reaction to generate double-stranded cDNA using biotinylated oligo (dT) and random nonamer primers with  the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA extracted with DASL from human nerve biopsy embedded in OCT

treatment_protocol: human nerve biopsy embedded in OCT

value: F

value: Sural Nerve

tag: developmental stage

value: Adult

tag: pathological diagnosis

value: inflammatory neuropathy


title: sural nerve_biopsy_diagnostic_inflammatory neuropathy 2

value: M

tag: tissue


title: sural nerve_biopsy_diagnostic_inflammatory neuropathy 3


title: sural nerve_biopsy_diagnostic_inflammatory neuropathy 4


title: sural nerve_biopsy_diagnostic_Lymphomatous neuropathy 3

value: Lymphomatous neuropathy


title: sural nerve_biopsy_diagnostic_vasculitic neuropathy 9

value: vasculitic neuropathy


title: sural nerve_biopsy_diagnostic_Lymphomatous neuropathy 2


title: sural nerve_biopsy_diagnostic_Lymphomatous neuropathy 1


title: sural nerve_biopsy_diagnostic_vasculitic neuropathy 8


title: H3K27me3


title: sural nerve_biopsy_diagnostic_vasculitic neuropathy 6


title: BM-derived MSC line B rep1

tag: cell type


title: HCT116-NUP93-mAC,Cut&Run for BRD4,UT, biological replicate 1


title: BM-derived MSC line A rep2

value: BM-derived MSC line A


title: HCT116,Cut&Run,NUP205


title: sural nerve_biopsy_diagnostic_vasculitic neuropathy 7


title: H3K4me3


title: BM-derived MSC line A rep1


title: H3K36me3


title: HCT116,Cut&Run,SEC13


title: Adipose-derived MSC line B rep2

value: Adipose-derived MSC line B


title: H3panAc


title: HCT116,Cut&Run,NUP93, biological replicate 2


title: sural nerve_biopsy_diagnostic_vasculitic neuropathy 4


title: Adipose-derived MSC line B rep1


title: HCT116-NUP93-mAC,ChIP-Seq,Ser2p,IAA,biological replicate 2

value: treated with IAA for 8hr(500uM indole-3-acetic acid (IAA, Sigma Aldrich, catalog#:87514))


title: Adipose-derived MSC line A rep2

value: Adipose-derived MSC line A


title: HCT116-NUP93-mAC,ChIP-Seq,Ser2p,UT,biological replicate 2


title: H3


title: MINU2, line2

value: 3xFLAG-MINU2 line10


title: sural nerve_biopsy_diagnostic_vasculitic neuropathy 5


title: HCT116-NUP93-mAC,ChIP-Seq,Ser2p,IAA,biological replicate 1


title: sural nerve_biopsy_diagnostic_vasculitic neuropathy 2


title: c-kit+ leukemic cells from bone marrow, MA9-IL-34 2

city: Tianjin

first: Dongyue

last: Zhang

address: 288 nanjing Road

institute: institute of blood

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse genes.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary files format and content: RPKMs

source_name: leukemia cells

extract_protocol:
c-kit+ cells were isolated from MA9 and MA9-IL-34 mice. c-kit- cells were isolated from MA9 mice. Total RNA was isolated from these enriched c-Kit+ cells following standard protocol with TRIzol reagent (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GFP+BFP+ leukemia cells were transplanted into 6-8 weeks old C57BL/6J mice (1×105 cells/mouse) without irradiation. The mice were sacrified at day 18 and the leukemia cells were sorted from BM. RNA-seq libraries were generated using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer's protocol.

value: BM

value: c-kit+ leukemic cells

value: IL-34-GFPBFP overexpression


title: c-kit+ leukemic cells from bone marrow, MA9-IL-34 3


title: HCT116,Cut&Run,NUP93, biological replicate 1

value: untreated


title: MINU2, line1

value: inflorescences

value: 3xFLAG-MINU2 line7


title: Adipose-derived MSC line A rep1


title: c-kit+ leukemic cells from bone marrow, MA9-IL-34 1


title: MINU2, control


title: sural nerve_biopsy_diagnostic_vasculitic neuropathy 3

value: F

value: Sural Nerve


title: c-kit+ leukemic cells from bone marrow, MA9 c-kit+3

value: control-GFPBFP overexpression


title: sural nerve_biopsy_diagnostic_vasculitic neuropathy 1

value: M

value: Adult


title: Fetal NSC derived from hippocampus rep2

source_name: FNSC

value: Fetal NSC derived from hippocampus


title: Fetal NSC derived from cortex

value: Fetal NSC derived from cortex


title: TPF2, line2

value: TPF2-3xFLAG line15


title: HCT116-NUP93-mAC,ChIP-Seq,H3K27ac,UT


title: HCT116-NUP93-mAC,ChIP-Seq,H3K27ac,IAA

value: treated with IAA for 8hr (500uM indole-3-acetic acid (IAA, Sigma Aldrich, catalog#:87514))


title: c-kit+ leukemic cells from bone marrow, MA9 c-kit+2


title: TPF2, line1

value: TPF2-3xFLAG line9


title: HCT116-NUP93-mAC, PRO-Seq, IAA, biological replicate 2

data_processing:
Library strategy: PRO-seq
FASTQ data were trimmed by Cutadapt and Trimmomatic.
PRO-Seq Reads were aligned using STAR with the hg19 build of the human genome. Read counts for Refseq mRNAs were determined using HTSeq-count.
Peaks for ChIP-Seq and Cut&Run  were called by using MACS2.
HiC-Pro was used to process Hi-C and HiChIP data. The HiC contact matrix normalized by ICE method was converted into mcool by cooler.
Identification of significant chromatin contacts(loops interaction) from HiChIP data by using FitHiChIP.
Genome_build: hg19

extract_protocol:
about 10 million cell nuclei were extracted on ice. They were incubated in the nuclear run-on buffer at 37°C for 5minutes in the presence of 500μM of ATP and GTP together with 50μM of biotin-11-CTP and biotin-11-UTP. Total RNAs were extracted using TRIzol and were fragmented using NaOH hydrolysis on ice for 10 minutes. The fragmented biotin labeled nuclear Run-on RNAs (NRO RNAs) were purified using the Dynabeads® MyOne™ Streptavidin C1 (Thermo Fisher 65002). The NRO RNAs were further purified twice using TRIzol beads.
For library making, the NRO RNAs were end-repaired by a fast Alkaline Phosphatase (Thermo Fisher) and by T4 PNK (NEB), cleaned up using Dynabeads MyOne Silane (37002D), and were then ligated to a HPLC purified 3’end RNA linker: RiL19 /5phos/rArGrArUrCrGrGrArArGrArGrCrGrUrCrGrUrG/3SpC3/. The ligated RNA was reverse transcribed using AffinityScript first strand cDNA synthesis kit (Agilent) by using AR17 primer (5’- ACACGACGCTCTTCCGA - 3’).  The cDNA was then cleaned up and ligated with a DNA linker carrying 10 nucleotides unique molecular index (UMI), rand10-3Tr3 (/5Phos/NNNNNNNNNNAGATCGGAAGAGCACACGTCTG/3SpC3/). This cDNA with both ends carrying ligated adaptors was cleaned up by Dynabeads MyOne Silane (37002D), and PCR was conducted to test the library abundance. Final PCR primers for library amplification were based on PCR_F_D501: 5’- AATGATACGGCGACCACCGAGATCTACACTATAGCCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -3’ and one of the indexed 3’end primers PCR_Rev_p7x: 5'- CAAGCAGAAGACGGCATACGAGAT XXXXXX GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC  -3' (where XXXXXX indicates 6-nucleotide index sequence), and the library was made using NEB Q5 2x PCR master mix by around 9-13 cycles. Final library was sized-selected using TBE 10% PAGE gels with a range of ~170-400nt, or by dual size selection using KAPApure beads (0.55X and 0.9X).


title: c-kit+ leukemic cells from bone marrow, MA9 c-kit+1


title: TPF2, control


title: Fetal NSC derived from hippocampus rep1


title: HCT116-NUP93-mAC, PRO-Seq,UT, biological replicate 2


title: HCT116-NUP93-mAC,ChIP-Seq,Ser2p,UT,biological replicate 1


title: c-kit- leukemic cells from bone marrow, MA9 c-kit-3

value: c-kit- leukemic cells


title: c-kit- leukemic cells from bone marrow, MA9 c-kit-2

value: BM


title: HCT116-NUP93-mAC, PRO-Seq, IAA, biological replicate 1


title: TPF1, line2

value: TPF1-3xFLAG line11


title: iPSC-NSC derived from yCD KI iPSC rep1

source_name: iPSC-NSC

value: iPSC-NSC derived from yCD KI iPSC


title: iPSC-NSC derived from control iPSC 1210 B2 rep2


title: TPF1, line1

value: TPF1-3xFLAG line4


title: HCT116-NUP93-mAC, PRO-Seq,UT, biological replicate 1

value: untreated


title: c-kit- leukemic cells from bone marrow, MA9 c-kit-1


title: TPF1, control

value: inflorescences


title: CD138+ D19 bio rep 2 [CD138.D17.2]

status: Public on Sep 15 2022

city: Seattle

first: Rene

last: Cheng

state: WA

address: 1900 9th AVE

institute: Seattle children research institute

data_processing:
FASTQ files were filtered and adaptors were trimmed using Trimmomatic .
We then use STAR to map high-quality reads to the human genome reference sequence (version hg38) and associate read counts with each gene.
Assembly: hg38
Supplementary files format and content: gene count matrix in csv.

source_name: Primary cells

extract_protocol:
CD138 positive beads isolation and flow through of CD138 negative contonue isolated by CD38 positive enrichment.
Clontech’s SMARTseq and Illumina’s NexteraXT kits

tag: time

value: Primary cells

value: B cells

value: CD38 isolation


title: CD138+ D19 bio rep 4 [CD138.D17.4]


title: iPSC-NSC derived from control iPSC 1210 B2 rep1


title: CD138+ D19 bio rep 3 [CD138.D17.3]


title: CD38+ D19 bio rep 4 [CD38.D17.4]


title: CD138+ D19 bio rep 1 [CD138.D17.1]


title: CD38+ D19 bio rep 3 [CD38.D17.3]


title: CD38+ D19 bio rep 2 [CD38.D17.2]


title: iPSC-NSC derived from yCD KI iPSC rep2


title: CD38+ D19 bio rep 1 [CD38.D17.1]


title: CD38+ D13 bio rep 2 [CD38.D11.2]


title: CD38+ D13 bio rep 3 [CD38.D11.3]


title: CD138+ D13 bio rep 2 [CD138.D11.2]

value: CD138 isolation


title: CD138+ D13 bio rep 4 [CD138.D11.4]


title: CD38+ D13 bio rep 4 [CD38.D11.4]


title: CD138+ D13 bio rep 3 [CD138.D11.3]


title: CD138+ D13 bio rep 1 [CD138.D11.1]


title: CD38+ D13 bio rep 1 [CD38.D11.1]